WorldWideScience

Sample records for randomly selected proteins

  1. The Jackprot Simulation Couples Mutation Rate with Natural Selection to Illustrate How Protein Evolution Is Not Random

    Science.gov (United States)

    Espinosa, Avelina; Bai, Chunyan Y.

    2016-01-01

    Protein evolution is not a random process. Views which attribute randomness to molecular change, deleterious nature to single-gene mutations, insufficient geological time, or population size for molecular improvements to occur, or invoke “design creationism” to account for complexity in molecular structures and biological processes, are unfounded. Scientific evidence suggests that natural selection tinkers with molecular improvements by retaining adaptive peptide sequence. We used slot-machine probabilities and ion channels to show biological directionality on molecular change. Because ion channels reside in the lipid bilayer of cell membranes, their residue location must be in balance with the membrane's hydrophobic/philic nature; a selective “pore” for ion passage is located within the hydrophobic region. We contrasted the random generation of DNA sequence for KcsA, a bacterial two-transmembrane-domain (2TM) potassium channel, from Streptomyces lividans, with an under-selection scenario, the “jackprot,” which predicted much faster evolution than by chance. We wrote a computer program in JAVA APPLET version 1.0 and designed an online interface, The Jackprot Simulation http://faculty.rwu.edu/cbai/JackprotSimulation.htm, to model a numerical interaction between mutation rate and natural selection during a scenario of polypeptide evolution. Winning the “jackprot,” or highest-fitness complete-peptide sequence, required cumulative smaller “wins” (rewarded by selection) at the first, second, and third positions in each of the 161 KcsA codons (“jackdons” that led to “jackacids” that led to the “jackprot”). The “jackprot” is a didactic tool to demonstrate how mutation rate coupled with natural selection suffices to explain the evolution of specialized proteins, such as the complex six-transmembrane (6TM) domain potassium, sodium, or calcium channels. Ancestral DNA sequences coding for 2TM-like proteins underwent nucleotide

  2. The Jackprot Simulation Couples Mutation Rate with Natural Selection to Illustrate How Protein Evolution Is Not Random.

    Science.gov (United States)

    Paz-Y-Miño C, Guillermo; Espinosa, Avelina; Bai, Chunyan Y

    2011-09-01

    Protein evolution is not a random process. Views which attribute randomness to molecular change, deleterious nature to single-gene mutations, insufficient geological time, or population size for molecular improvements to occur, or invoke "design creationism" to account for complexity in molecular structures and biological processes, are unfounded. Scientific evidence suggests that natural selection tinkers with molecular improvements by retaining adaptive peptide sequence. We used slot-machine probabilities and ion channels to show biological directionality on molecular change. Because ion channels reside in the lipid bilayer of cell membranes, their residue location must be in balance with the membrane's hydrophobic/philic nature; a selective "pore" for ion passage is located within the hydrophobic region. We contrasted the random generation of DNA sequence for KcsA, a bacterial two-transmembrane-domain (2TM) potassium channel, from Streptomyces lividans, with an under-selection scenario, the "jackprot," which predicted much faster evolution than by chance. We wrote a computer program in JAVA APPLET version 1.0 and designed an online interface, The Jackprot Simulation http://faculty.rwu.edu/cbai/JackprotSimulation.htm, to model a numerical interaction between mutation rate and natural selection during a scenario of polypeptide evolution. Winning the "jackprot," or highest-fitness complete-peptide sequence, required cumulative smaller "wins" (rewarded by selection) at the first, second, and third positions in each of the 161 KcsA codons ("jackdons" that led to "jackacids" that led to the "jackprot"). The "jackprot" is a didactic tool to demonstrate how mutation rate coupled with natural selection suffices to explain the evolution of specialized proteins, such as the complex six-transmembrane (6TM) domain potassium, sodium, or calcium channels. Ancestral DNA sequences coding for 2TM-like proteins underwent nucleotide "edition" and gene duplications to generate the 6

  3. Sequence-Based Prediction of RNA-Binding Proteins Using Random Forest with Minimum Redundancy Maximum Relevance Feature Selection

    Directory of Open Access Journals (Sweden)

    Xin Ma

    2015-01-01

    Full Text Available The prediction of RNA-binding proteins is one of the most challenging problems in computation biology. Although some studies have investigated this problem, the accuracy of prediction is still not sufficient. In this study, a highly accurate method was developed to predict RNA-binding proteins from amino acid sequences using random forests with the minimum redundancy maximum relevance (mRMR method, followed by incremental feature selection (IFS. We incorporated features of conjoint triad features and three novel features: binding propensity (BP, nonbinding propensity (NBP, and evolutionary information combined with physicochemical properties (EIPP. The results showed that these novel features have important roles in improving the performance of the predictor. Using the mRMR-IFS method, our predictor achieved the best performance (86.62% accuracy and 0.737 Matthews correlation coefficient. High prediction accuracy and successful prediction performance suggested that our method can be a useful approach to identify RNA-binding proteins from sequence information.

  4. EcmPred: Prediction of extracellular matrix proteins based on random forest with maximum relevance minimum redundancy feature selection

    KAUST Repository

    Kandaswamy, Krishna Kumar Umar

    2013-01-01

    The extracellular matrix (ECM) is a major component of tissues of multicellular organisms. It consists of secreted macromolecules, mainly polysaccharides and glycoproteins. Malfunctions of ECM proteins lead to severe disorders such as marfan syndrome, osteogenesis imperfecta, numerous chondrodysplasias, and skin diseases. In this work, we report a random forest approach, EcmPred, for the prediction of ECM proteins from protein sequences. EcmPred was trained on a dataset containing 300 ECM and 300 non-ECM and tested on a dataset containing 145 ECM and 4187 non-ECM proteins. EcmPred achieved 83% accuracy on the training and 77% on the test dataset. EcmPred predicted 15 out of 20 experimentally verified ECM proteins. By scanning the entire human proteome, we predicted novel ECM proteins validated with gene ontology and InterPro. The dataset and standalone version of the EcmPred software is available at http://www.inb.uni-luebeck.de/tools-demos/Extracellular_matrix_proteins/EcmPred. © 2012 Elsevier Ltd.

  5. Blocked Randomization with Randomly Selected Block Sizes

    Directory of Open Access Journals (Sweden)

    Jimmy Efird

    2010-12-01

    Full Text Available When planning a randomized clinical trial, careful consideration must be given to how participants are selected for various arms of a study. Selection and accidental bias may occur when participants are not assigned to study groups with equal probability. A simple random allocation scheme is a process by which each participant has equal likelihood of being assigned to treatment versus referent groups. However, by chance an unequal number of individuals may be assigned to each arm of the study and thus decrease the power to detect statistically significant differences between groups. Block randomization is a commonly used technique in clinical trial design to reduce bias and achieve balance in the allocation of participants to treatment arms, especially when the sample size is small. This method increases the probability that each arm will contain an equal number of individuals by sequencing participant assignments by block. Yet still, the allocation process may be predictable, for example, when the investigator is not blind and the block size is fixed. This paper provides an overview of blocked randomization and illustrates how to avoid selection bias by using random block sizes.

  6. Blocked randomization with randomly selected block sizes.

    Science.gov (United States)

    Efird, Jimmy

    2011-01-01

    When planning a randomized clinical trial, careful consideration must be given to how participants are selected for various arms of a study. Selection and accidental bias may occur when participants are not assigned to study groups with equal probability. A simple random allocation scheme is a process by which each participant has equal likelihood of being assigned to treatment versus referent groups. However, by chance an unequal number of individuals may be assigned to each arm of the study and thus decrease the power to detect statistically significant differences between groups. Block randomization is a commonly used technique in clinical trial design to reduce bias and achieve balance in the allocation of participants to treatment arms, especially when the sample size is small. This method increases the probability that each arm will contain an equal number of individuals by sequencing participant assignments by block. Yet still, the allocation process may be predictable, for example, when the investigator is not blind and the block size is fixed. This paper provides an overview of blocked randomization and illustrates how to avoid selection bias by using random block sizes.

  7. Randomized selection on the GPU

    Energy Technology Data Exchange (ETDEWEB)

    Monroe, Laura Marie [Los Alamos National Laboratory; Wendelberger, Joanne R [Los Alamos National Laboratory; Michalak, Sarah E [Los Alamos National Laboratory

    2011-01-13

    We implement here a fast and memory-sparing probabilistic top N selection algorithm on the GPU. To our knowledge, this is the first direct selection in the literature for the GPU. The algorithm proceeds via a probabilistic-guess-and-chcck process searching for the Nth element. It always gives a correct result and always terminates. The use of randomization reduces the amount of data that needs heavy processing, and so reduces the average time required for the algorithm. Probabilistic Las Vegas algorithms of this kind are a form of stochastic optimization and can be well suited to more general parallel processors with limited amounts of fast memory.

  8. Sequence based prediction of DNA-binding proteins based on hybrid feature selection using random forest and Gaussian naïve Bayes.

    Directory of Open Access Journals (Sweden)

    Wangchao Lou

    Full Text Available Developing an efficient method for determination of the DNA-binding proteins, due to their vital roles in gene regulation, is becoming highly desired since it would be invaluable to advance our understanding of protein functions. In this study, we proposed a new method for the prediction of the DNA-binding proteins, by performing the feature rank using random forest and the wrapper-based feature selection using forward best-first search strategy. The features comprise information from primary sequence, predicted secondary structure, predicted relative solvent accessibility, and position specific scoring matrix. The proposed method, called DBPPred, used Gaussian naïve Bayes as the underlying classifier since it outperformed five other classifiers, including decision tree, logistic regression, k-nearest neighbor, support vector machine with polynomial kernel, and support vector machine with radial basis function. As a result, the proposed DBPPred yields the highest average accuracy of 0.791 and average MCC of 0.583 according to the five-fold cross validation with ten runs on the training benchmark dataset PDB594. Subsequently, blind tests on the independent dataset PDB186 by the proposed model trained on the entire PDB594 dataset and by other five existing methods (including iDNA-Prot, DNA-Prot, DNAbinder, DNABIND and DBD-Threader were performed, resulting in that the proposed DBPPred yielded the highest accuracy of 0.769, MCC of 0.538, and AUC of 0.790. The independent tests performed by the proposed DBPPred on completely a large non-DNA binding protein dataset and two RNA binding protein datasets also showed improved or comparable quality when compared with the relevant prediction methods. Moreover, we observed that majority of the selected features by the proposed method are statistically significantly different between the mean feature values of the DNA-binding and the non DNA-binding proteins. All of the experimental results indicate that

  9. Random selection of Borel sets

    Directory of Open Access Journals (Sweden)

    Bernd Günther

    2010-10-01

    Full Text Available A theory of random Borel sets is presented, based on dyadic resolutions of compact metric spaces. The conditional expectation of the intersection of two independent random Borel sets is investigated. An example based on an embedding of Sierpinski’s universal curve into the space of Borel sets is given.

  10. Directional Darwinian Selection in proteins.

    Science.gov (United States)

    McClellan, David A

    2013-01-01

    Molecular evolution is a very active field of research, with several complementary approaches, including dN/dS, HON90, MM01, and others. Each has documented strengths and weaknesses, and no one approach provides a clear picture of how natural selection works at the molecular level. The purpose of this work is to present a simple new method that uses quantitative amino acid properties to identify and characterize directional selection in proteins. Inferred amino acid replacements are viewed through the prism of a single physicochemical property to determine the amount and direction of change caused by each replacement. This allows the calculation of the probability that the mean change in the single property associated with the amino acid replacements is equal to zero (H0: μ = 0; i.e., no net change) using a simple two-tailed t-test. Example data from calanoid and cyclopoid copepod cytochrome oxidase subunit I sequence pairs are presented to demonstrate how directional selection may be linked to major shifts in adaptive zones, and that convergent evolution at the whole organism level may be the result of convergent protein adaptations. Rather than replace previous methods, this new method further complements existing methods to provide a holistic glimpse of how natural selection shapes protein structure and function over evolutionary time.

  11. Do natural proteins differ from random sequences polypeptides? Natural vs. random proteins classification using an evolutionary neural network.

    Directory of Open Access Journals (Sweden)

    Davide De Lucrezia

    Full Text Available Are extant proteins the exquisite result of natural selection or are they random sequences slightly edited by evolution? This question has puzzled biochemists for long time and several groups have addressed this issue comparing natural protein sequences to completely random ones coming to contradicting conclusions. Previous works in literature focused on the analysis of primary structure in an attempt to identify possible signature of evolutionary editing. Conversely, in this work we compare a set of 762 natural proteins with an average length of 70 amino acids and an equal number of completely random ones of comparable length on the basis of their structural features. We use an ad hoc Evolutionary Neural Network Algorithm (ENNA in order to assess whether and to what extent natural proteins are edited from random polypeptides employing 11 different structure-related variables (i.e. net charge, volume, surface area, coil, alpha helix, beta sheet, percentage of coil, percentage of alpha helix, percentage of beta sheet, percentage of secondary structure and surface hydrophobicity. The ENNA algorithm is capable to correctly distinguish natural proteins from random ones with an accuracy of 94.36%. Furthermore, we study the structural features of 32 random polypeptides misclassified as natural ones to unveil any structural similarity to natural proteins. Results show that random proteins misclassified by the ENNA algorithm exhibit a significant fold similarity to portions or subdomains of extant proteins at atomic resolution. Altogether, our results suggest that natural proteins are significantly edited from random polypeptides and evolutionary editing can be readily detected analyzing structural features. Furthermore, we also show that the ENNA, employing simple structural descriptors, can predict whether a protein chain is natural or random.

  12. Species selection and random drift in macroevolution.

    Science.gov (United States)

    Chevin, Luis-Miguel

    2016-03-01

    Species selection resulting from trait-dependent speciation and extinction is increasingly recognized as an important mechanism of phenotypic macroevolution. However, the recent bloom in statistical methods quantifying this process faces a scarcity of dynamical theory for their interpretation, notably regarding the relative contributions of deterministic versus stochastic evolutionary forces. I use simple diffusion approximations of birth-death processes to investigate how the expected and random components of macroevolutionary change depend on phenotype-dependent speciation and extinction rates, as can be estimated empirically. I show that the species selection coefficient for a binary trait, and selection differential for a quantitative trait, depend not only on differences in net diversification rates (speciation minus extinction), but also on differences in species turnover rates (speciation plus extinction), especially in small clades. The randomness in speciation and extinction events also produces a species-level equivalent to random genetic drift, which is stronger for higher turnover rates. I then show how microevolutionary processes including mutation, organismic selection, and random genetic drift cause state transitions at the species level, allowing comparison of evolutionary forces across levels. A key parameter that would be needed to apply this theory is the distribution and rate of origination of new optimum phenotypes along a phylogeny. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

  13. Improving randomness characterization through Bayesian model selection.

    Science.gov (United States)

    Díaz Hernández Rojas, Rafael; Solís, Aldo; Angulo Martínez, Alí M; U'Ren, Alfred B; Hirsch, Jorge G; Marsili, Matteo; Pérez Castillo, Isaac

    2017-06-08

    Random number generation plays an essential role in technology with important applications in areas ranging from cryptography to Monte Carlo methods, and other probabilistic algorithms. All such applications require high-quality sources of random numbers, yet effective methods for assessing whether a source produce truly random sequences are still missing. Current methods either do not rely on a formal description of randomness (NIST test suite) on the one hand, or are inapplicable in principle (the characterization derived from the Algorithmic Theory of Information), on the other, for they require testing all the possible computer programs that could produce the sequence to be analysed. Here we present a rigorous method that overcomes these problems based on Bayesian model selection. We derive analytic expressions for a model's likelihood which is then used to compute its posterior distribution. Our method proves to be more rigorous than NIST's suite and Borel-Normality criterion and its implementation is straightforward. We applied our method to an experimental device based on the process of spontaneous parametric downconversion to confirm it behaves as a genuine quantum random number generator. As our approach relies on Bayesian inference our scheme transcends individual sequence analysis, leading to a characterization of the source itself.

  14. 32 CFR 1624.1 - Random selection procedures for induction.

    Science.gov (United States)

    2010-07-01

    ... 32 National Defense 6 2010-07-01 2010-07-01 false Random selection procedures for induction. 1624... SYSTEM INDUCTIONS § 1624.1 Random selection procedures for induction. (a) The Director of Selective Service shall from time to time establish a random selection sequence for induction by a drawing to be...

  15. Peptide Selection for Targeted Protein Quantitation.

    Science.gov (United States)

    Chiva, Cristina; Sabidó, Eduard

    2017-03-03

    Targeted proteomics methods in their different flavors rely on the use of a few peptides as proxies for protein quantitation, which need to be specified either prior to or after data acquisition. However, in contrast with discovery methods that use all identified peptides for a given protein to estimate its abundance, targeted proteomics methods are limited in the number of peptides that are used for protein quantitation. Because only a few peptides per protein are acquired or extracted in targeted experiments, the selection of peptides that are used for targeted protein quantitation becomes crucial. Several rules have been proposed to guide peptide selection for targeted proteomics studies, which have generally been based on the amino acidic composition of the peptide sequences. However, the compliance of these rules does not imply that not-conformed peptides are not reproducibly generated nor do they guarantee that the selected peptides correctly represent the behavior of the protein abundance under different conditions.

  16. Maintaining life and health by natural selection of protein molecules.

    Science.gov (United States)

    Pirlet, K; Arthur-Goettig, A

    1999-11-07

    A concept for a life and health-preserving principle is presented, with reference to evolutionary, medical, and biochemical observations. Life comprises two basic phenomena: it unfolds over longer periods at the population level, and is sustained for the duration of individual life spans. The evolution of life within populations by means of natural selection of individuals is central to Darwin's theory of evolution. An important component of maintaining individual life is proposed here to be the natural selection of molecular components-the proteins, a process of preferred removal of denatured and old, synonymous with the selection of younger, functional molecules. The proteins of the cell are committed to fulfilling all the tasks programmed by the genome while continuously maintaining all appropriate cellular functions, including protecting the DNA. Physiological and environmental influences accelerate the breakdown of aged protein molecules, driving this renewal process so that the cell can maintain its protein stock at high-performance levels. The principle of selection makes the incredible dynamics of continual protein turnover, and hence not only the preservation of life, but the maintenance of health in individual beings, comprehensible. Arguments are presented to counter the hypothesis that protein breakdown is a stochastic, random process governed by first-order kinetics. Copyright 1999 Academic Press.

  17. Nonlinear deterministic structures and the randomness of protein sequences

    CERN Document Server

    Huang Yan Zhao

    2003-01-01

    To clarify the randomness of protein sequences, we make a detailed analysis of a set of typical protein sequences representing each structural classes by using nonlinear prediction method. No deterministic structures are found in these protein sequences and this implies that they behave as random sequences. We also give an explanation to the controversial results obtained in previous investigations.

  18. In-Place Randomized Slope Selection

    DEFF Research Database (Denmark)

    Blunck, Henrik; Vahrenhold, Jan

    2006-01-01

    Slope selection is a well-known algorithmic tool used in the context of computing robust estimators for fitting a line to a collection P of n points in the plane. We demonstrate that it is possible to perform slope selection in expected O(nlogn) time using only constant extra space in addition to...

  19. Random effect selection in generalised linear models

    DEFF Research Database (Denmark)

    Denwood, Matt; Houe, Hans; Forkman, Björn

    We analysed abattoir recordings of meat inspection codes with possible relevance to onfarm animal welfare in cattle. Random effects logistic regression models were used to describe individual-level data obtained from 461,406 cattle slaughtered in Denmark. Our results demonstrate that the largest ...

  20. Understanding Protein Evolution: From Protein Physics to Darwinian Selection

    Science.gov (United States)

    Zeldovich, Konstantin B.; Shakhnovich, Eugene I.

    2008-05-01

    Efforts in whole-genome sequencing and structural proteomics start to provide a global view of the protein universe, the set of existing protein structures and sequences. However, approaches based on the selection of individual sequences have not been entirely successful at the quantitative description of the distribution of structures and sequences in the protein universe because evolutionary pressure acts on the entire organism, rather than on a particular molecule. In parallel to this line of study, studies in population genetics and phenomenological molecular evolution established a mathematical framework to describe the changes in genome sequences in populations of organisms over time. Here, we review both microscopic (physics-based) and macroscopic (organism-level) models of protein-sequence evolution and demonstrate that bridging the two scales provides the most complete description of the protein universe starting from clearly defined, testable, and physiologically relevant assumptions.

  1. Sequential selection of random vectors under a sum constraint

    OpenAIRE

    Stanke, Mario

    2004-01-01

    We observe a sequence X1,X2,...,Xn of independent and identically distributed coordinatewise nonnegative d-dimensional random vectors. When a vector is observed it can either be selected or rejected but once made this decision is final. In each coordinate the sum of the selected vectors must not exceed a given constant. The problem is to find a selection policy that maximizes the expected number of selected vectors. For a general absolutely continuous distribution of t...

  2. Selectivity and sparseness in randomly connected balanced networks.

    Directory of Open Access Journals (Sweden)

    Cengiz Pehlevan

    Full Text Available Neurons in sensory cortex show stimulus selectivity and sparse population response, even in cases where no strong functionally specific structure in connectivity can be detected. This raises the question whether selectivity and sparseness can be generated and maintained in randomly connected networks. We consider a recurrent network of excitatory and inhibitory spiking neurons with random connectivity, driven by random projections from an input layer of stimulus selective neurons. In this architecture, the stimulus-to-stimulus and neuron-to-neuron modulation of total synaptic input is weak compared to the mean input. Surprisingly, we show that in the balanced state the network can still support high stimulus selectivity and sparse population response. In the balanced state, strong synapses amplify the variation in synaptic input and recurrent inhibition cancels the mean. Functional specificity in connectivity emerges due to the inhomogeneity caused by the generative statistical rule used to build the network. We further elucidate the mechanism behind and evaluate the effects of model parameters on population sparseness and stimulus selectivity. Network response to mixtures of stimuli is investigated. It is shown that a balanced state with unselective inhibition can be achieved with densely connected input to inhibitory population. Balanced networks exhibit the "paradoxical" effect: an increase in excitatory drive to inhibition leads to decreased inhibitory population firing rate. We compare and contrast selectivity and sparseness generated by the balanced network to randomly connected unbalanced networks. Finally, we discuss our results in light of experiments.

  3. Natural vs. random protein sequences: Discovering combinatorics properties on amino acid words.

    Science.gov (United States)

    Santoni, Daniele; Felici, Giovanni; Vergni, Davide

    2016-02-21

    Casual mutations and natural selection have driven the evolution of protein amino acid sequences that we observe at present in nature. The question about which is the dominant force of proteins evolution is still lacking of an unambiguous answer. Casual mutations tend to randomize protein sequences while, in order to have the correct functionality, one expects that selection mechanisms impose rigid constraints on amino acid sequences. Moreover, one also has to consider that the space of all possible amino acid sequences is so astonishingly large that it could be reasonable to have a well tuned amino acid sequence indistinguishable from a random one. In order to study the possibility to discriminate between random and natural amino acid sequences, we introduce different measures of association between pairs of amino acids in a sequence, and apply them to a dataset of 1047 natural protein sequences and 10,470 random sequences, carefully generated in order to preserve the relative length and amino acid distribution of the natural proteins. We analyze the multidimensional measures with machine learning techniques and show that, to a reasonable extent, natural protein sequences can be differentiated from random ones. Copyright © 2015 Elsevier Ltd. All rights reserved.

  4. Fast, Randomized Join-Order Selection - Why Use Transformations?

    NARCIS (Netherlands)

    C.A. Galindo-Legaria; A.J. Pellenkoft (Jan); M.L. Kersten (Martin)

    1994-01-01

    textabstractWe study the effectiveness of probabilistic selection of join-query evaluation plans, without reliance on tree transformation rules. Instead, each candidate plan is chosen uniformly at random from the space of valid evaluation orders. This leads to a transformation-free strategy where a

  5. The reliability of randomly selected final year pharmacy students in ...

    African Journals Online (AJOL)

    Employing ANOVA, factorial experimental analysis, and the theory of error, reliability studies were conducted on the assessment of the drug product chloroquine phosphate tablets. The G–Study employed equal numbers of the factors for uniform control, and involved three analysts (randomly selected final year Pharmacy ...

  6. Random coil chemical shift for intrinsically disordered proteins

    DEFF Research Database (Denmark)

    Kjærgaard, Magnus; Brander, Søren; Poulsen, Flemming Martin

    2011-01-01

    Secondary chemical shift analysis is the main NMR method for detection of transiently formed secondary structure in intrinsically disordered proteins. The quality of the secondary chemical shifts is dependent on an appropriate choice of random coil chemical shifts. We report random coil chemical....... Temperature has a non-negligible effect on the (13)C random coil chemical shifts, so temperature coefficients are reported for the random coil chemical shifts to allow extrapolation to other temperatures. The pH dependence of the histidine random coil chemical shifts is investigated in a titration series...... shifts and sequence correction factors determined for a GGXGG peptide series following the approach of Schwarzinger et al. (J Am Chem Soc 123(13):2970-2978, 2001). The chemical shifts are determined at neutral pH in order to match the conditions of most studies of intrinsically disordered proteins...

  7. Local randomization in neighbor selection improves PRM roadmap quality

    KAUST Repository

    McMahon, Troy

    2012-10-01

    Probabilistic Roadmap Methods (PRMs) are one of the most used classes of motion planning methods. These sampling-based methods generate robot configurations (nodes) and then connect them to form a graph (roadmap) containing representative feasible pathways. A key step in PRM roadmap construction involves identifying a set of candidate neighbors for each node. Traditionally, these candidates are chosen to be the k-closest nodes based on a given distance metric. In this paper, we propose a new neighbor selection policy called LocalRand(k,K\\'), that first computes the K\\' closest nodes to a specified node and then selects k of those nodes at random. Intuitively, LocalRand attempts to benefit from random sampling while maintaining the higher levels of local planner success inherent to selecting more local neighbors. We provide a methodology for selecting the parameters k and K\\'. We perform an experimental comparison which shows that for both rigid and articulated robots, LocalRand results in roadmaps that are better connected than the traditional k-closest policy or a purely random neighbor selection policy. The cost required to achieve these results is shown to be comparable to k-closest. © 2012 IEEE.

  8. Selecting a phoneme-to-grapheme mapping: Random or weighted selection?

    Directory of Open Access Journals (Sweden)

    Binna Lee

    2015-05-01

    Our findings demonstrate that random selection underestimates MOA’s PG correspondences whereas weighted selection predicts higher PG correspondences than he produces. To explain his intermediate spelling performance on PPEs, we will test additional approaches to weighing the relative probability of PG mappings, including using log frequencies, separating consonant and vowel status, and considering the number of grapheme options in each phoneme.

  9. Selection for altruism through random drift in variable size populations.

    Science.gov (United States)

    Houchmandzadeh, Bahram; Vallade, Marcel

    2012-05-10

    Altruistic behavior is defined as helping others at a cost to oneself and a lowered fitness. The lower fitness implies that altruists should be selected against, which is in contradiction with their widespread presence is nature. Present models of selection for altruism (kin or multilevel) show that altruistic behaviors can have 'hidden' advantages if the 'common good' produced by altruists is restricted to some related or unrelated groups. These models are mostly deterministic, or assume a frequency dependent fitness. Evolutionary dynamics is a competition between deterministic selection pressure and stochastic events due to random sampling from one generation to the next. We show here that an altruistic allele extending the carrying capacity of the habitat can win by increasing the random drift of "selfish" alleles. In other terms, the fixation probability of altruistic genes can be higher than those of a selfish ones, even though altruists have a smaller fitness. Moreover when populations are geographically structured, the altruists advantage can be highly amplified and the fixation probability of selfish genes can tend toward zero. The above results are obtained both by numerical and analytical calculations. Analytical results are obtained in the limit of large populations. The theory we present does not involve kin or multilevel selection, but is based on the existence of random drift in variable size populations. The model is a generalization of the original Fisher-Wright and Moran models where the carrying capacity depends on the number of altruists.

  10. Selection for altruism through random drift in variable size populations

    Directory of Open Access Journals (Sweden)

    Houchmandzadeh Bahram

    2012-05-01

    Full Text Available Abstract Background Altruistic behavior is defined as helping others at a cost to oneself and a lowered fitness. The lower fitness implies that altruists should be selected against, which is in contradiction with their widespread presence is nature. Present models of selection for altruism (kin or multilevel show that altruistic behaviors can have ‘hidden’ advantages if the ‘common good’ produced by altruists is restricted to some related or unrelated groups. These models are mostly deterministic, or assume a frequency dependent fitness. Results Evolutionary dynamics is a competition between deterministic selection pressure and stochastic events due to random sampling from one generation to the next. We show here that an altruistic allele extending the carrying capacity of the habitat can win by increasing the random drift of “selfish” alleles. In other terms, the fixation probability of altruistic genes can be higher than those of a selfish ones, even though altruists have a smaller fitness. Moreover when populations are geographically structured, the altruists advantage can be highly amplified and the fixation probability of selfish genes can tend toward zero. The above results are obtained both by numerical and analytical calculations. Analytical results are obtained in the limit of large populations. Conclusions The theory we present does not involve kin or multilevel selection, but is based on the existence of random drift in variable size populations. The model is a generalization of the original Fisher-Wright and Moran models where the carrying capacity depends on the number of altruists.

  11. DENDRIMER CONJUGATES FOR SELECTIVE OF PROTEIN AGGREGATES

    DEFF Research Database (Denmark)

    2004-01-01

    Dendrimer conjugates are presented, which are formed between a dendrimer and a protein solubilising substance. Such dendrimer conjugates are effective in the treatment of protein aggregate-related diseases (e.g. prion-related diseases). The protein solubilising substance and the dendrimer together...

  12. Selectivity determinants of GPCR-G-protein binding

    DEFF Research Database (Denmark)

    Flock, Tilman; Hauser, Alexander S; Lund, Nadia

    2017-01-01

    The selective coupling of G-protein-coupled receptors (GPCRs) to specific G proteins is critical to trigger the appropriate physiological response. However, the determinants of selective binding have remained elusive. Here we reveal the existence of a selectivity barcode (that is, patterns of amino...... of the G-protein barcode through distinct residues, like multiple keys (receptors) opening the same lock (G protein) using non-identical cuts. Considering the evolutionary history of GPCRs allows the identification of these selectivity-determining residues. These findings lay the foundation...

  13. Interference-aware random beam selection for spectrum sharing systems

    KAUST Repository

    Abdallah, Mohamed M.

    2012-09-01

    Spectrum sharing systems have been introduced to alleviate the problem of spectrum scarcity by allowing secondary unlicensed networks to share the spectrum with primary licensed networks under acceptable interference levels to the primary users. In this paper, we develop interference-aware random beam selection schemes that provide enhanced throughput for the secondary link under the condition that the interference observed at the primary link is within a predetermined acceptable value. For a secondary transmitter equipped with multiple antennas, our schemes select a random beam, among a set of power- optimized orthogonal random beams, that maximizes the capacity of the secondary link while satisfying the interference constraint at the primary receiver for different levels of feedback information describing the interference level at the primary receiver. For the proposed schemes, we develop a statistical analysis for the signal-to-noise and interference ratio (SINR) statistics as well as the capacity of the secondary link. Finally, we present numerical results that study the effect of system parameters including number of beams and the maximum transmission power on the capacity of the secondary link attained using the proposed schemes. © 2012 IEEE.

  14. Statistical theory of neutral protein evolution by random site mutations

    Indian Academy of Sciences (India)

    Alternatively, a self-consistent mean-field based theory is developed to evaluate the protein neutrality through random single-point and multiple-point mutations by calculating the pair-wise probability profile of the amino acid residues in a library of sequences, consistent with a particular foldability criterion. The theory ...

  15. Prediction of Protein Hotspots from Whole Protein Sequences by a Random Projection Ensemble System

    Directory of Open Access Journals (Sweden)

    Jinjian Jiang

    2017-07-01

    Full Text Available Hotspot residues are important in the determination of protein-protein interactions, and they always perform specific functions in biological processes. The determination of hotspot residues is by the commonly-used method of alanine scanning mutagenesis experiments, which is always costly and time consuming. To address this issue, computational methods have been developed. Most of them are structure based, i.e., using the information of solved protein structures. However, the number of solved protein structures is extremely less than that of sequences. Moreover, almost all of the predictors identified hotspots from the interfaces of protein complexes, seldom from the whole protein sequences. Therefore, determining hotspots from whole protein sequences by sequence information alone is urgent. To address the issue of hotspot predictions from the whole sequences of proteins, we proposed an ensemble system with random projections using statistical physicochemical properties of amino acids. First, an encoding scheme involving sequence profiles of residues and physicochemical properties from the AAindex1 dataset is developed. Then, the random projection technique was adopted to project the encoding instances into a reduced space. Then, several better random projections were obtained by training an IBk classifier based on the training dataset, which were thus applied to the test dataset. The ensemble of random projection classifiers is therefore obtained. Experimental results showed that although the performance of our method is not good enough for real applications of hotspots, it is very promising in the determination of hotspot residues from whole sequences.

  16. Prediction of Protein Hotspots from Whole Protein Sequences by a Random Projection Ensemble System

    Science.gov (United States)

    Jiang, Jinjian; Wang, Nian; Chen, Peng; Zheng, Chunhou; Wang, Bing

    2017-01-01

    Hotspot residues are important in the determination of protein-protein interactions, and they always perform specific functions in biological processes. The determination of hotspot residues is by the commonly-used method of alanine scanning mutagenesis experiments, which is always costly and time consuming. To address this issue, computational methods have been developed. Most of them are structure based, i.e., using the information of solved protein structures. However, the number of solved protein structures is extremely less than that of sequences. Moreover, almost all of the predictors identified hotspots from the interfaces of protein complexes, seldom from the whole protein sequences. Therefore, determining hotspots from whole protein sequences by sequence information alone is urgent. To address the issue of hotspot predictions from the whole sequences of proteins, we proposed an ensemble system with random projections using statistical physicochemical properties of amino acids. First, an encoding scheme involving sequence profiles of residues and physicochemical properties from the AAindex1 dataset is developed. Then, the random projection technique was adopted to project the encoding instances into a reduced space. Then, several better random projections were obtained by training an IBk classifier based on the training dataset, which were thus applied to the test dataset. The ensemble of random projection classifiers is therefore obtained. Experimental results showed that although the performance of our method is not good enough for real applications of hotspots, it is very promising in the determination of hotspot residues from whole sequences. PMID:28718782

  17. Unbiased split variable selection for random survival forests using maximally selected rank statistics.

    Science.gov (United States)

    Wright, Marvin N; Dankowski, Theresa; Ziegler, Andreas

    2017-04-15

    The most popular approach for analyzing survival data is the Cox regression model. The Cox model may, however, be misspecified, and its proportionality assumption may not always be fulfilled. An alternative approach for survival prediction is random forests for survival outcomes. The standard split criterion for random survival forests is the log-rank test statistic, which favors splitting variables with many possible split points. Conditional inference forests avoid this split variable selection bias. However, linear rank statistics are utilized by default in conditional inference forests to select the optimal splitting variable, which cannot detect non-linear effects in the independent variables. An alternative is to use maximally selected rank statistics for the split point selection. As in conditional inference forests, splitting variables are compared on the p-value scale. However, instead of the conditional Monte-Carlo approach used in conditional inference forests, p-value approximations are employed. We describe several p-value approximations and the implementation of the proposed random forest approach. A simulation study demonstrates that unbiased split variable selection is possible. However, there is a trade-off between unbiased split variable selection and runtime. In benchmark studies of prediction performance on simulated and real datasets, the new method performs better than random survival forests if informative dichotomous variables are combined with uninformative variables with more categories and better than conditional inference forests if non-linear covariate effects are included. In a runtime comparison, the method proves to be computationally faster than both alternatives, if a simple p-value approximation is used. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

  18. Effects of Selected Protein Diets on Biochemical profiles and ...

    African Journals Online (AJOL)

    The aim of this study was to compare, using randomized controlled design, the metabolic effects of four low-protein diets, A, B, C and D obtained from different protein sources, in out-patients with moderate Chronic Renal Failure (CRF). Thirty two adult outpatients (20 males and 12 females) aged 43.9+17.3 years were ...

  19. The signature of positive selection at randomly chosen loci.

    Science.gov (United States)

    Przeworski, Molly

    2002-03-01

    In Drosophila and humans, there are accumulating examples of loci with a significant excess of high-frequency-derived alleles or high levels of linkage disequilibrium, relative to a neutral model of a random-mating population of constant size. These are features expected after a recent selective sweep. Their prevalence suggests that positive directional selection may be widespread in both species. However, as I show here, these features do not persist long after the sweep ends: The high-frequency alleles drift to fixation and no longer contribute to polymorphism, while linkage disequilibrium is broken down by recombination. As a result, loci chosen without independent evidence of recent selection are not expected to exhibit either of these features, even if they have been affected by numerous sweeps in their genealogical history. How then can we explain the patterns in the data? One possibility is population structure, with unequal sampling from different subpopulations. Alternatively, positive selection may not operate as is commonly modeled. In particular, the rate of fixation of advantageous mutations may have increased in the recent past.

  20. Quantification of protein-lipid selectivity using FRET: Application of the M13 major coat protein

    NARCIS (Netherlands)

    Fernandes, F.; Loura, L.M.S.; Koehorst, R.B.M.; Spruijt, R.B.; Hemminga, M.A.; Federov, A.; Prieto, M.

    2004-01-01

    Quantification of lipid selectivity by membrane proteins has been previously addressed mainly from electron spin resonance studies. We present here a new methodology for quanti. cation of protein-lipid selectivity based on fluorescence resonance energy transfer. A mutant of M13 major coat protein

  1. Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches

    Energy Technology Data Exchange (ETDEWEB)

    Chandonia, John-Marc; Brenner, Steven E.

    2004-07-14

    The structural genomics project is an international effort to determine the three-dimensional shapes of all important biological macromolecules, with a primary focus on proteins. Target proteins should be selected according to a strategy which is medically and biologically relevant, of good value, and tractable. As an option to consider, we present the Pfam5000 strategy, which involves selecting the 5000 most important families from the Pfam database as sources for targets. We compare the Pfam5000 strategy to several other proposed strategies that would require similar numbers of targets. These include including complete solution of several small to moderately sized bacterial proteomes, partial coverage of the human proteome, and random selection of approximately 5000 targets from sequenced genomes. We measure the impact that successful implementation of these strategies would have upon structural interpretation of the proteins in Swiss-Prot, TrEMBL, and 131 complete proteomes (including 10 of eukaryotes) from the Proteome Analysis database at EBI. Solving the structures of proteins from the 5000 largest Pfam families would allow accurate fold assignment for approximately 68 percent of all prokaryotic proteins (covering 59 percent of residues) and 61 percent of eukaryotic proteins (40 percent of residues). More fine-grained coverage which would allow accurate modeling of these proteins would require an order of magnitude more targets. The Pfam5000 strategy may be modified in several ways, for example to focus on larger families, bacterial sequences, or eukaryotic sequences; as long as secondary consideration is given to large families within Pfam, coverage results vary only slightly. In contrast, focusing structural genomics on a single tractable genome would have only a limited impact in structural knowledge of other proteomes: a significant fraction (about 30-40 percent of the proteins, and 40-60 percent of the residues) of each proteome is classified in small

  2. Blind Measurement Selection: A Random Matrix Theory Approach

    KAUST Repository

    Elkhalil, Khalil

    2016-12-14

    This paper considers the problem of selecting a set of $k$ measurements from $n$ available sensor observations. The selected measurements should minimize a certain error function assessing the error in estimating a certain $m$ dimensional parameter vector. The exhaustive search inspecting each of the $n\\\\choose k$ possible choices would require a very high computational complexity and as such is not practical for large $n$ and $k$. Alternative methods with low complexity have recently been investigated but their main drawbacks are that 1) they require perfect knowledge of the measurement matrix and 2) they need to be applied at the pace of change of the measurement matrix. To overcome these issues, we consider the asymptotic regime in which $k$, $n$ and $m$ grow large at the same pace. Tools from random matrix theory are then used to approximate in closed-form the most important error measures that are commonly used. The asymptotic approximations are then leveraged to select properly $k$ measurements exhibiting low values for the asymptotic error measures. Two heuristic algorithms are proposed: the first one merely consists in applying the convex optimization artifice to the asymptotic error measure. The second algorithm is a low-complexity greedy algorithm that attempts to look for a sufficiently good solution for the original minimization problem. The greedy algorithm can be applied to both the exact and the asymptotic error measures and can be thus implemented in blind and channel-aware fashions. We present two potential applications where the proposed algorithms can be used, namely antenna selection for uplink transmissions in large scale multi-user systems and sensor selection for wireless sensor networks. Numerical results are also presented and sustain the efficiency of the proposed blind methods in reaching the performances of channel-aware algorithms.

  3. Pediatric selective mutism therapy: a randomized controlled trial.

    Science.gov (United States)

    Esposito, Maria; Gimigliano, Francesca; Barillari, Maria R; Precenzano, Francesco; Ruberto, Maria; Sepe, Joseph; Barillari, Umberto; Gimigliano, Raffaele; Militerni, Roberto; Messina, Giovanni; Carotenuto, Marco

    2017-10-01

    Selective mutism (SM) is a rare disease in children coded by DSM-5 as an anxiety disorder. Despite the disabling nature of the disease, there is still no specific treatment. The aims of this study were to verify the efficacy of six-month standard psychomotor treatment and the positive changes in lifestyle, in a population of children affected by SM. Randomized controlled trial registered in the European Clinical Trials Registry (EuDract 2015-001161-36). University third level Centre (Child and Adolescent Neuropsychiatry Clinic). Study population was composed by 67 children in group A (psychomotricity treatment) (35 M, mean age 7.84±1.15) and 71 children in group B (behavioral and educational counseling) (37 M, mean age 7.75±1.36). Psychomotor treatment was administered by trained child therapists in residential settings three times per week. Each child was treated for the whole period by the same therapist and all the therapists shared the same protocol. The standard psychomotor session length is of 45 minutes. At T0 and after 6 months (T1) of treatments, patients underwent a behavioral and SM severity assessment. To verify the effects of the psychomotor management, the Child Behavior Checklist questionnaire (CBCL) and Selective Mutism Questionnaire (SMQ) were administered to the parents. After 6 months of psychomotor treatment SM children showed a significant reduction among CBCL scores such as in social relations, anxious/depressed, social problems and total problems (Ppsychomotricity a safe and efficacy therapy for pediatric selective mutism.

  4. Optimizing Event Selection with the Random Grid Search

    Energy Technology Data Exchange (ETDEWEB)

    Bhat, Pushpalatha C. [Fermilab; Prosper, Harrison B. [Florida State U.; Sekmen, Sezen [Kyungpook Natl. U.; Stewart, Chip [Broad Inst., Cambridge

    2017-06-29

    The random grid search (RGS) is a simple, but efficient, stochastic algorithm to find optimal cuts that was developed in the context of the search for the top quark at Fermilab in the mid-1990s. The algorithm, and associated code, have been enhanced recently with the introduction of two new cut types, one of which has been successfully used in searches for supersymmetry at the Large Hadron Collider. The RGS optimization algorithm is described along with the recent developments, which are illustrated with two examples from particle physics. One explores the optimization of the selection of vector boson fusion events in the four-lepton decay mode of the Higgs boson and the other optimizes SUSY searches using boosted objects and the razor variables.

  5. Novel Zn2+-chelating peptides selected from a fimbria-displayed random peptide library

    DEFF Research Database (Denmark)

    Kjærgaard, Kristian; Schembri, Mark; Klemm, Per

    2001-01-01

    H adhesin. FimH is a component of the fimbrial organelle that can accommodate and display a diverse range of peptide sequences on the E. coli cell surface. In this study we have constructed a random peptide library in FimH. The library, consisting of similar to 40 million individual clones, was screened...... for peptide sequences that conferred on recombinant cells the ability to bind Zn2+. By serial selection, sequences that exhibited various degrees of binding affinity and specificity toward Zn2+ were enriched. None of the isolated sequences showed similarity to known Zn2+-binding proteins, indicating...

  6. Recombinant protein expression by targeting pre-selected chromosomal loci

    Directory of Open Access Journals (Sweden)

    Krömer Wolfgang

    2009-12-01

    Full Text Available Abstract Background Recombinant protein expression in mammalian cells is mostly achieved by stable integration of transgenes into the chromosomal DNA of established cell lines. The chromosomal surroundings have strong influences on the expression of transgenes. The exploitation of defined loci by targeting expression constructs with different regulatory elements is an approach to design high level expression systems. Further, this allows to evaluate the impact of chromosomal surroundings on distinct vector constructs. Results We explored antibody expression upon targeting diverse expression constructs into previously tagged loci in CHO-K1 and HEK293 cells that exhibit high reporter gene expression. These loci were selected by random transfer of reporter cassettes and subsequent screening. Both, retroviral infection and plasmid transfection with eGFP or antibody expression cassettes were employed for tagging. The tagged cell clones were screened for expression and single copy integration. Cell clones producing > 20 pg/cell in 24 hours could be identified. Selected integration sites that had been flanked with heterologous recombinase target sites (FRTs were targeted by Flp recombinase mediated cassette exchange (RMCE. The results give proof of principle for consistent protein expression upon RMCE. Upon targeting antibody expression cassettes 90-100% of all resulting cell clones showed correct integration. Antibody production was found to be highly consistent within the individual cell clones as expected from their isogenic nature. However, the nature and orientation of expression control elements revealed to be critical. The impact of different promoters was examined with the tag-and-targeting approach. For each of the chosen promoters high expression sites were identified. However, each site supported the chosen promoters to a different extent, indicating that the strength of a particular promoter is dominantly defined by its chromosomal context

  7. Site-Selective Conjugation of Native Proteins with DNA

    DEFF Research Database (Denmark)

    Trads, Julie Brender; Tørring, Thomas; Gothelf, Kurt Vesterager

    2017-01-01

    because approximately one-third of all wild-type proteins contain metal-binding sites, including many IgG antibodies, and it is also applicable to His-tagged proteins. This emerging field provides direct access to site-selective conjugates of DNA to commercially available proteins. In this Account, we......Conjugation of DNA to proteins is increasingly used in academia and industry to provide proteins with tags for identification or handles for hybridization to other DNA strands. Assay technologies such as immuno-PCR and proximity ligation and the imaging technology DNA-PAINT require DNA...

  8. TSTMP: target selection for structural genomics of human transmembrane proteins.

    Science.gov (United States)

    Varga, Julia; Dobson, László; Reményi, István; Tusnády, Gábor E

    2017-01-04

    The TSTMP database is designed to help the target selection of human transmembrane proteins for structural genomics projects and structure modeling studies. Currently, there are only 60 known 3D structures among the polytopic human transmembrane proteins and about a further 600 could be modeled using existing structures. Although there are a great number of human transmembrane protein structures left to be determined, surprisingly only a small fraction of these proteins have 'selected' (or above) status according to the current version the TargetDB/TargetTrack database. This figure is even worse regarding those transmembrane proteins that would contribute the most to the structural coverage of the human transmembrane proteome. The database was built by sorting out proteins from the human transmembrane proteome with known structure and searching for suitable model structures for the remaining proteins by combining the results of a state-of-the-art transmembrane specific fold recognition algorithm and a sequence similarity search algorithm. Proteins were searched for homologues among the human transmembrane proteins in order to select targets whose successful structure determination would lead to the best structural coverage of the human transmembrane proteome. The pipeline constructed for creating the TSTMP database guarantees to keep the database up-to-date. The database is available at http://tstmp.enzim.ttk.mta.hu. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  9. Positively selected sites in cetacean myoglobins contribute to protein stability

    DEFF Research Database (Denmark)

    Dasmeh, Pouria; Serohijos, Adrian W R; Kepp, Kasper P

    2013-01-01

    between Mb folding stability and protein abundance, suggesting that a selection pressure for stability acts proportionally to higher expression. We also identify a major divergence event leading to the common ancestor of whales, during which major stabilization occurred. Most of the positively selected...

  10. Probing the Extent of Randomness in Protein Interaction Networks

    Science.gov (United States)

    2008-07-11

    scale-free networks are born equal: the role of the seed graph in PPI network evolution. PLoS Comput Biol 3: e118. doi:10.1371/journal.pcbi.0030118. 57...from seeds [56]. In the degree-conserving degree-weighted (DCDW) model, each node is considered once, in a random order, and a set number of edges are...gene duplication in fungi . Nature 449: 54–61. 63. Fraser HB, Hirsh AE, Steinmetz LM, Scharfe C, Feldman MW (2002) Evolutionary rate in the protein

  11. Deep recurrent conditional random field network for protein secondary prediction

    DEFF Research Database (Denmark)

    Johansen, Alexander Rosenberg; Sønderby, Søren Kaae; Sønderby, Casper Kaae

    2017-01-01

    Deep learning has become the state-of-the-art method for predicting protein secondary structure from only its amino acid residues and sequence profile. Building upon these results, we propose to combine a bi-directional recurrent neural network (biRNN) with a conditional random field (CRF), which...... of the labels for all time-steps. We condition the CRF on the output of biRNN, which learns a distributed representation based on the entire sequence. The biRNN-CRF is therefore close to ideally suited for the secondary structure task because a high degree of cross-talk between neighboring elements can...

  12. Site-Selective Conjugation of Native Proteins with DNA.

    Science.gov (United States)

    Trads, Julie B; Tørring, Thomas; Gothelf, Kurt V

    2017-06-20

    Conjugation of DNA to proteins is increasingly used in academia and industry to provide proteins with tags for identification or handles for hybridization to other DNA strands. Assay technologies such as immuno-PCR and proximity ligation and the imaging technology DNA-PAINT require DNA-protein conjugates. In DNA nanotechnology, the DNA handle is exploited to precisely position proteins by self-assembly. For these applications, site-selective conjugation is almost always desired because fully functional proteins are required to maintain the specificity of antibodies and the activity of enzymes. The introduction of a bioorthogonal handle at a specific position of a protein by recombinant techniques provides an excellent approach to site-specific conjugation, but for many laboratories and for applications where several proteins are to be labeled, the expression of recombinant proteins may be cumbersome. In recent years, a number of chemical methods that target conjugation to specific sites at native proteins have become available, and an overview of these methods is provided in this Account. Our laboratory has investigated DNA-templated protein conjugation (DTPC), which offers an alternative approach to site-selective conjugation of DNA to proteins. The method is inspired by the concept of DNA-templated synthesis where functional groups conjugated to DNA strands are preorganized by DNA hybridization to dramatically increase the reaction rate. In DPTC, we target metal binding sites in proteins to template selective covalent conjugation reactions. By chelation of a DNA-metal complex with a metal binding site of the protein, an electrophile on a second DNA strand is aligned for reaction with a lysine side chain on the protein in the proximity of the metal binding site. The method is quite general because approximately one-third of all wild-type proteins contain metal-binding sites, including many IgG antibodies, and it is also applicable to His-tagged proteins. This

  13. Positive Selection and Centrality in the Yeast and Fly Protein-Protein Interaction Networks

    Directory of Open Access Journals (Sweden)

    Sandip Chakraborty

    2016-01-01

    Full Text Available Proteins within a molecular network are expected to be subject to different selective pressures depending on their relative hierarchical positions. However, it is not obvious what genes within a network should be more likely to evolve under positive selection. On one hand, only mutations at genes with a relatively high degree of control over adaptive phenotypes (such as those encoding highly connected proteins are expected to be “seen” by natural selection. On the other hand, a high degree of pleiotropy at these genes is expected to hinder adaptation. Previous analyses of the human protein-protein interaction network have shown that genes under long-term, recurrent positive selection (as inferred from interspecific comparisons tend to act at the periphery of the network. It is unknown, however, whether these trends apply to other organisms. Here, we show that long-term positive selection has preferentially targeted the periphery of the yeast interactome. Conversely, in flies, genes under positive selection encode significantly more connected and central proteins. These observations are not due to covariation of genes’ adaptability and centrality with confounding factors. Therefore, the distribution of proteins encoded by genes under recurrent positive selection across protein-protein interaction networks varies from one species to another.

  14. Zeolite Nanoparticles for Selective Sorption of Plasma Proteins.

    Science.gov (United States)

    Rahimi, M; Ng, E-P; Bakhtiari, K; Vinciguerra, M; Ali Ahmad, H; Awala, H; Mintova, S; Daghighi, M; Bakhshandeh Rostami, F; de Vries, M; Motazacker, M M; Peppelenbosch, M P; Mahmoudi, M; Rezaee, F

    2015-11-30

    The affinity of zeolite nanoparticles (diameter of 8-12 nm) possessing high surface area and high pore volume towards human plasma proteins has been investigated. The protein composition (corona) of zeolite nanoparticles has been shown to be more dependent on the plasma protein concentrations and the type of zeolites than zeolite nanoparticles concentration. The number of proteins present in the corona of zeolite nanoparticles at 100% plasma (in vivo state) is less than with 10% plasma exposure. This could be due to a competition between the proteins to occupy the corona of the zeolite nanoparticles. Moreover, a high selective adsorption for apolipoprotein C-III (APOC-III) and fibrinogen on the zeolite nanoparticles at high plasma concentration (100%) was observed. While the zeolite nanoparticles exposed to low plasma concentration (10%) exhibited a high selective adsorption for immunoglobulin gamma (i.e. IGHG1, IGHG2 and IGHG4) proteins. The zeolite nanoparticles can potentially be used for selectively capture of APOC-III in order to reduce the activation of lipoprotein lipase inhibition during hypertriglyceridemia treatment. The zeolite nanoparticles can be adapted to hemophilic patients (hemophilia A (F-VIII deficient) and hemophilia B (F-IX deficient)) with a risk of bleeding, and thus might be potentially used in combination with the existing therapy.

  15. Zeolite Nanoparticles for Selective Sorption of Plasma Proteins

    Science.gov (United States)

    Rahimi, M.; Ng, E.-P.; Bakhtiari, K.; Vinciguerra, M.; Ahmad, H. Ali; Awala, H.; Mintova, S.; Daghighi, M.; Bakhshandeh Rostami, F.; de Vries, M.; Motazacker, M. M.; Peppelenbosch, M. P.; Mahmoudi, M.; Rezaee, F.

    2015-01-01

    The affinity of zeolite nanoparticles (diameter of 8–12 nm) possessing high surface area and high pore volume towards human plasma proteins has been investigated. The protein composition (corona) of zeolite nanoparticles has been shown to be more dependent on the plasma protein concentrations and the type of zeolites than zeolite nanoparticles concentration. The number of proteins present in the corona of zeolite nanoparticles at 100% plasma (in vivo state) is less than with 10% plasma exposure. This could be due to a competition between the proteins to occupy the corona of the zeolite nanoparticles. Moreover, a high selective adsorption for apolipoprotein C-III (APOC-III) and fibrinogen on the zeolite nanoparticles at high plasma concentration (100%) was observed. While the zeolite nanoparticles exposed to low plasma concentration (10%) exhibited a high selective adsorption for immunoglobulin gamma (i.e. IGHG1, IGHG2 and IGHG4) proteins. The zeolite nanoparticles can potentially be used for selectively capture of APOC-III in order to reduce the activation of lipoprotein lipase inhibition during hypertriglyceridemia treatment. The zeolite nanoparticles can be adapted to hemophilic patients (hemophilia A (F-VIII deficient) and hemophilia B (F-IX deficient)) with a risk of bleeding, and thus might be potentially used in combination with the existing therapy. PMID:26616161

  16. An Antibiotic Selection System For Protein Overproducing Bacteria

    DEFF Research Database (Denmark)

    Rennig, Maja; Nørholm, Morten

    2015-01-01

    membrane proteins of Escherichia coli can be used as a fast and simple selection system for protein overproduction.Methods: We designed an expression plasmid encoding the gene of interest and an additional, inducible antibiotic resistance marker. Both genes were linked by a hairpin structure...... that translationally couples the genes. Consequently, high expressing gene variants also allow for higher production of the coupled antibiotic resistance marker. Therefore, high expressing gene variants in a library can be determined either by plating the expression library on selection plates or by growing...... sequence and the start codon, an integral part of the translation initiation region. We successfully tested the expression of these libraries with the antibiotic selection system on plates and in liquid cultures.Conclusions: We successfully implemented the antibiotic selection system and confirmed enhanced...

  17. Event selection with a Random Forest in IceCube

    Energy Technology Data Exchange (ETDEWEB)

    Ruhe, Tim [TU, Dortmund (Germany); Collaboration: IceCube-Collaboration

    2011-07-01

    The Random Forest method is a multivariate algorithm that can be used for classification and regression respectively. The Random Forest implemented in the RapidMiner learning environment has been used for training and validation on data and Monte Carlo simulations of the IceCube neutrino telescope. Latest results are presented.

  18. Olefin metathesis for site-selective protein modification.

    Science.gov (United States)

    Lin, Yuya A; Chalker, Justin M; Davis, Benjamin G

    2009-04-17

    For a reaction to be generally useful for protein modification, it must be site-selective and efficient under conditions compatible with proteins: aqueous media, low to ambient temperature, and at or near neutral pH. To engineer a reaction that satisfies these conditions is not a simple task. Olefin metathesis is one of most useful reactions for carbon-carbon bond formation, but does it fit these requirements? This minireview is an account of the development of olefin metathesis for protein modification. Highlighted below are examples of olefin metathesis in peptidic systems and in aqueous media that laid the groundwork for successful metathesis on protein substrates. Also discussed are the opportunities in protein engineering for the genetic introduction of amino acids suitable for metathesis and the related challenges in chemistry and biology.

  19. Protein pharmacophore selection using hydration-site analysis

    Science.gov (United States)

    Hu, Bingjie; Lill, Markus A.

    2012-01-01

    Virtual screening using pharmacophore models is an efficient method to identify potential lead compounds for target proteins. Pharmacophore models based on protein structures are advantageous because a priori knowledge of active ligands is not required and the models are not biased by the chemical space of previously identified actives. However, in order to capture most potential interactions between all potentially binding ligands and the protein, the size of the pharmacophore model, i.e. number of pharmacophore elements, is typically quite large and therefore reduces the efficiency of pharmacophore based screening. We have developed a new method to select important pharmacophore elements using hydration-site information. The basic premise is that ligand functional groups that replace water molecules in the apo protein contribute strongly to the overall binding affinity of the ligand, due to the additional free energy gained from releasing the water molecule into the bulk solvent. We computed the free energy of water released from the binding site for each hydration site using thermodynamic analysis of molecular dynamics (MD) simulations. Pharmacophores which are co-localized with hydration sites with estimated favorable contributions to the free energy of binding are selected to generate a reduced pharmacophore model. We constructed reduced pharmacophore models for three protein systems and demonstrated good enrichment quality combined with high efficiency. The reduction in pharmacophore model size reduces the required screening time by a factor of 200–500 compared to using all protein pharmacophore elements. We also describe a training process using a small set of known actives to reliably select the optimal set of criteria for pharmacophore selection for each protein system. PMID:22397751

  20. Cotranslational protein folding reveals the selective use of ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 93; Issue 3. Cotranslational protein folding reveals the selective use of synonymous codons along the coding sequence of a low expression gene. Suvendra Kumar Ray Vishwa Jyoti Baruah Siddhartha Sankar Satapathy Rajat Banerjee. Research Commentary Volume 93 Issue ...

  1. Study on MAX-MIN Ant System with Random Selection in Quadratic Assignment Problem

    Science.gov (United States)

    Iimura, Ichiro; Yoshida, Kenji; Ishibashi, Ken; Nakayama, Shigeru

    Ant Colony Optimization (ACO), which is a type of swarm intelligence inspired by ants' foraging behavior, has been studied extensively and its effectiveness has been shown by many researchers. The previous studies have reported that MAX-MIN Ant System (MMAS) is one of effective ACO algorithms. The MMAS maintains the balance of intensification and diversification concerning pheromone by limiting the quantity of pheromone to the range of minimum and maximum values. In this paper, we propose MAX-MIN Ant System with Random Selection (MMASRS) for improving the search performance even further. The MMASRS is a new ACO algorithm that is MMAS into which random selection was newly introduced. The random selection is one of the edgechoosing methods by agents (ants). In our experimental evaluation using ten quadratic assignment problems, we have proved that the proposed MMASRS with the random selection is superior to the conventional MMAS without the random selection in the viewpoint of the search performance.

  2. Non-random retention of protein-coding overlapping genes in Metazoa

    Directory of Open Access Journals (Sweden)

    Bork Peer

    2008-04-01

    Full Text Available Abstract Background Although the overlap of transcriptional units occurs frequently in eukaryotic genomes, its evolutionary and biological significance remains largely unclear. Here we report a comparative analysis of overlaps between genes coding for well-annotated proteins in five metazoan genomes (human, mouse, zebrafish, fruit fly and worm. Results For all analyzed species the observed number of overlapping genes is always lower than expected assuming functional neutrality, suggesting that gene overlap is negatively selected. The comparison to the random distribution also shows that retained overlaps do not exhibit random features: antiparallel overlaps are significantly enriched, while overlaps lying on the same strand and those involving coding sequences are highly underrepresented. We confirm that overlap is mostly species-specific and provide evidence that it frequently originates through the acquisition of terminal, non-coding exons. Finally, we show that overlapping genes tend to be significantly co-expressed in a breast cancer cDNA library obtained by 454 deep sequencing, and that different overlap types display different patterns of reciprocal expression. Conclusion Our data suggest that overlap between protein-coding genes is selected against in Metazoa. However, when retained it may be used as a species-specific mechanism for the reciprocal regulation of neighboring genes. The tendency of overlaps to involve non-coding regions of the genes leads to the speculation that the advantages achieved by an overlapping arrangement may be optimized by evolving regulatory non-coding transcripts.

  3. Selectivity by small-molecule inhibitors of protein interactions can be driven by protein surface fluctuations.

    Directory of Open Access Journals (Sweden)

    David K Johnson

    2015-02-01

    Full Text Available Small-molecules that inhibit interactions between specific pairs of proteins have long represented a promising avenue for therapeutic intervention in a variety of settings. Structural studies have shown that in many cases, the inhibitor-bound protein adopts a conformation that is distinct from its unbound and its protein-bound conformations. This plasticity of the protein surface presents a major challenge in predicting which members of a protein family will be inhibited by a given ligand. Here, we use biased simulations of Bcl-2-family proteins to generate ensembles of low-energy conformations that contain surface pockets suitable for small molecule binding. We find that the resulting conformational ensembles include surface pockets that mimic those observed in inhibitor-bound crystal structures. Next, we find that the ensembles generated using different members of this protein family are overlapping but distinct, and that the activity of a given compound against a particular family member (ligand selectivity can be predicted from whether the corresponding ensemble samples a complementary surface pocket. Finally, we find that each ensemble includes certain surface pockets that are not shared by any other family member: while no inhibitors have yet been identified to take advantage of these pockets, we expect that chemical scaffolds complementing these "distinct" pockets will prove highly selective for their targets. The opportunity to achieve target selectivity within a protein family by exploiting differences in surface fluctuations represents a new paradigm that may facilitate design of family-selective small-molecule inhibitors of protein-protein interactions.

  4. Detergent selection for enhanced extraction of membrane proteins.

    Science.gov (United States)

    Arachea, Buenafe T; Sun, Zhen; Potente, Nina; Malik, Radhika; Isailovic, Dragan; Viola, Ronald E

    2012-11-01

    Generating stable conditions for membrane proteins after extraction from their lipid bilayer environment is essential for subsequent characterization. Detergents are the most widely used means to obtain this stable environment; however, different types of membrane proteins have been found to require detergents with varying properties for optimal extraction efficiency and stability after extraction. The extraction profiles of several detergent types have been examined for membranes isolated from bacteria and yeast, and for a set of recombinant target proteins. The extraction efficiencies of these detergents increase at higher concentrations, and were shown to correlate with their respective CMC values. Two alkyl sugar detergents, octyl-β-d-glucoside (OG) and 5-cyclohexyl-1-pentyl-β-d-maltoside (Cymal-5), and a zwitterionic surfactant, N-decylphosphocholine (Fos-choline-10), were generally effective in the extraction of a broad range of membrane proteins. However, certain detergents were more effective than others in the extraction of specific classes of integral membrane proteins, offering guidelines for initial detergent selection. The differences in extraction efficiencies among this small set of detergents supports the value of detergent screening and optimization to increase the yields of targeted membrane proteins. Copyright © 2012 Elsevier Inc. All rights reserved.

  5. Automatic selection of representative proteins for bacterial phylogeny

    Directory of Open Access Journals (Sweden)

    Goldberg David

    2005-05-01

    Full Text Available Abstract Background Although there are now about 200 complete bacterial genomes in GenBank, deep bacterial phylogeny remains a difficult problem, due to confounding horizontal gene transfers and other phylogenetic "noise". Previous methods have relied primarily upon biological intuition or manual curation for choosing genomic sequences unlikely to be horizontally transferred, and have given inconsistent phylogenies with poor bootstrap confidence. Results We describe an algorithm that automatically picks "representative" protein families from entire genomes for use as phylogenetic characters. A representative protein family is one that, taken alone, gives an organismal distance matrix in good agreement with a distance matrix computed from all sufficiently conserved proteins. We then use maximum-likelihood methods to compute phylogenetic trees from a concatenation of representative sequences. We validate the use of representative proteins on a number of small phylogenetic questions with accepted answers. We then use our methodology to compute a robust and well-resolved phylogenetic tree for a diverse set of sequenced bacteria. The tree agrees closely with a recently published tree computed using manually curated proteins, and supports two proposed high-level clades: one containing Actinobacteria, Deinococcus, and Cyanobacteria ("Terrabacteria", and another containing Planctomycetes and Chlamydiales. Conclusion Representative proteins provide an effective solution to the problem of selecting phylogenetic characters.

  6. Prediction of Protein-Protein Interactions with Physicochemical Descriptors and Wavelet Transform via Random Forests.

    Science.gov (United States)

    Jia, Jianhua; Xiao, Xuan; Liu, Bingxiang

    2016-06-01

    Protein-protein interactions (PPIs) provide valuable insight into the inner workings of cells, and it is significant to study the network of PPIs. It is vitally important to develop an automated method as a high-throughput tool to timely predict PPIs. Based on the physicochemical descriptors, a protein was converted into several digital signals, and then wavelet transform was used to analyze them. With such a formulation frame to represent the samples of protein sequences, the random forests algorithm was adopted to conduct prediction. The results on a large-scale independent-test data set show that the proposed model can achieve a good performance with an accuracy value of about 0.86 and a geometric mean value of about 0.85. Therefore, it can be a usefully supplementary tool for PPI prediction. The predictor used in this article is freely available at http://www.jci-bioinfo.cn/PPI_RF. © 2015 Society for Laboratory Automation and Screening.

  7. Selective Reaction Monitoring for Quantitation of Cellular Proteins.

    Science.gov (United States)

    Faça, Vitor M

    2017-01-01

    Proteins and proteomes are dynamic and complex. The accurate identification and measurement of their properties such as abundance, location, and turnover are challenging tasks. Even though high-throughput proteomics has significantly evolved, the technique still lacks fully quantitative and reproducible qualities. A mass spectrometry-based targeted proteomic strategy called selective reaction monitoring (SRM) has emerged in recent years as an important multiplex platform to precisely quantify sets of proteins in multiple samples. This has several advantages in terms of sensitivity, reproducibility, and sample consumption compared to classical methods including those based on antibodies. Here, we present a detailed protocol for quantitation of panels of proteins from cell line extracts using the SRM targeted proteomics approach.

  8. Protein and energy metabolism in two lines of chickens selected for growth on high or low protein diets

    DEFF Research Database (Denmark)

    Chwalibog, André; Eggum, B O; Sørensen, Peter

    1983-01-01

    Genetic adaptation was investigated in broilers selected for seven generations on a normal (A) or a low (B) protein diet. Protein and energy metabolism were studied in males from these selected lines fed on a diet of intermediate protein content. All selected birds retained more nitrogen than those...

  9. Assessment of proteinuria by using protein: creatinine index in random urine sample.

    Science.gov (United States)

    Khan, Dilshad Ahmed; Ahmad, Tariq Mahmood; Qureshil, Ayaz Hussain; Halim, Abdul; Ahmad, Mumtaz; Afzal, Saeed

    2005-10-01

    To assess the quantitative measurement of proteinuria by using random urine protein:creatinine index/ratio in comparison with 24 hours urinary protein excretion in patients of renal diseases having normal glomerular filtration rate. One hundred and thirty patients, 94 males and 36 females, with an age range of 5 to 60 years; having proteinuria of more than 150 mg/day were included in this study. Qualitative urinary protein estimation was done on random urine specimen by dipstick. Quantitative measurement of protein in the random and 24 hours urine specimens were carried out by a method based on the formation of a red complex of protein with pyrogallal red in acid medium on Micro lab 200 (Merck). Estimation of creatinine was done on Selectra -2 (Merck) by Jaffe's reaction. The urine protein:creatinine index and ratio were calculated by dividing the urine protein concentration (mg/L) by urine creatinine concentration (mmol/L) multilplied by 10 and mg/mg respectively. The protein:creatinine index and ratio of more than 140 and 0.18 respectively in a random urine sample indicated pathological proteinuria. An excellent correlation (r=0.96) was found between random urine protein:creatinine index/ratio and standard 24 hours urinary protein excretion in these patients (pprotein:creatinine index in random urine is a convenient, quick and reliable method of estimation of proteinuria as compared to 24 hours of urinary protein excretion for diagnosis and monitoring of renal diseases in our medical setup.

  10. Statistical theory of neutral protein evolution by random site mutations

    Indian Academy of Sciences (India)

    Administrator

    theory may provide a new perspective in de novo protein design, in-vivo/in-vitro protein evolution and site-directed mutagenesis experiments. Keywords. Neutral evolution; protein design; mutations; foldability criteria. 1. Introduction. Understanding the relationship between protein sequences and structures can be partially ...

  11. In vivo selection of randomly mutated retroviral genomes

    NARCIS (Netherlands)

    Berkhout, B.; Klaver, B.

    1993-01-01

    Darwinian evolution, that is the outgrowth of the fittest variants in a population, usually applies to living organisms over long periods of time. Recently, in vitro selection/amplification techniques have been developed that allow for the rapid evolution of functionally active nucleic acids from a

  12. The evolution of proteins from random amino acid sequences: II. Evidence from the statistical distributions of the lengths of modern protein sequences.

    Science.gov (United States)

    White, S H

    1994-04-01

    This paper continues an examination of the hypothesis that modern proteins evolved from random heteropeptide sequences. In support of the hypothesis, White and Jacobs (1993, J Mol Evol 36:79-95) have shown that any sequence chosen randomly from a large collection of nonhomologous proteins has a 90% or better chance of having a lengthwise distribution of amino acids that is indistinguishable from the random expectation regardless of amino acid type. The goal of the present study was to investigate the possibility that the random-origin hypothesis could explain the lengths of modern protein sequences without invoking specific mechanisms such as gene duplication or exon splicing. The sets of sequences examined were taken from the 1989 PIR database and consisted of 1,792 "super-family" proteins selected to have little sequence identity, 623 E. coli sequences, and 398 human sequences. The length distributions of the proteins could be described with high significance by either of two closely related probability density functions: The gamma distribution with parameter 2 or the distribution for the sum of two exponential random independent variables. A simple theory for the distributions was developed which assumes that (1) protoprotein sequences had exponentially distributed random independent lengths, (2) the length dependence of protein stability determined which of these protoproteins could fold into compact primitive proteins and thereby attain the potential for biochemical activity, (3) the useful protein sequences were preserved by the primitive genome, and (4) the resulting distribution of sequence lengths is reflected by modern proteins. The theory successfully predicts the two observed distributions which can be distinguished by the functional form of the dependence of protein stability on length. The theory leads to three interesting conclusions. First, it predicts that a tetra-nucleotide was the signal for primitive translation termination. This prediction is

  13. The adverse effect of selective cyclooxygenase-2 inhibitor on random skin flap survival in rats.

    Directory of Open Access Journals (Sweden)

    Haiyong Ren

    Full Text Available BACKGROUND: Cyclooxygenase-2(COX-2 inhibitors provide desired analgesic effects after injury or surgery, but evidences suggested they also attenuate wound healing. The study is to investigate the effect of COX-2 inhibitor on random skin flap survival. METHODS: The McFarlane flap model was established in 40 rats and evaluated within two groups, each group gave the same volume of Parecoxib and saline injection for 7 days. The necrotic area of the flap was measured, the specimens of the flap were stained with haematoxylin-eosin(HE for histologic analysis. Immunohistochemical staining was performed to analyse the level of VEGF and COX-2 . RESULTS: 7 days after operation, the flap necrotic area ratio in study group (66.65 ± 2.81% was significantly enlarged than that of the control group(48.81 ± 2.33%(P <0.01. Histological analysis demonstrated angiogenesis with mean vessel density per mm(2 being lower in study group (15.4 ± 4.4 than in control group (27.2 ± 4.1 (P <0.05. To evaluate the expression of COX-2 and VEGF protein in the intermediate area II in the two groups by immunohistochemistry test .The expression of COX-2 in study group was (1022.45 ± 153.1, and in control group was (2638.05 ± 132.2 (P <0.01. The expression of VEGF in the study and control groups were (2779.45 ± 472.0 vs (4938.05 ± 123.6(P <0.01.In the COX-2 inhibitor group, the expressions of COX-2 and VEGF protein were remarkably down-regulated as compared with the control group. CONCLUSION: Selective COX-2 inhibitor had adverse effect on random skin flap survival. Suppression of neovascularization induced by low level of VEGF was supposed to be the biological mechanism.

  14. Assessing the accuracy and stability of variable selection methods for random forest modeling in ecology

    Science.gov (United States)

    Random forest (RF) modeling has emerged as an important statistical learning method in ecology due to its exceptional predictive performance. However, for large and complex ecological datasets there is limited guidance on variable selection methods for RF modeling. Typically, e...

  15. Generation of Aptamers from A Primer-Free Randomized ssDNA Library Using Magnetic-Assisted Rapid Aptamer Selection

    Science.gov (United States)

    Tsao, Shih-Ming; Lai, Ji-Ching; Horng, Horng-Er; Liu, Tu-Chen; Hong, Chin-Yih

    2017-04-01

    Aptamers are oligonucleotides that can bind to specific target molecules. Most aptamers are generated using random libraries in the standard systematic evolution of ligands by exponential enrichment (SELEX). Each random library contains oligonucleotides with a randomized central region and two fixed primer regions at both ends. The fixed primer regions are necessary for amplifying target-bound sequences by PCR. However, these extra-sequences may cause non-specific bindings, which potentially interfere with good binding for random sequences. The Magnetic-Assisted Rapid Aptamer Selection (MARAS) is a newly developed protocol for generating single-strand DNA aptamers. No repeat selection cycle is required in the protocol. This study proposes and demonstrates a method to isolate aptamers for C-reactive proteins (CRP) from a randomized ssDNA library containing no fixed sequences at 5‧ and 3‧ termini using the MARAS platform. Furthermore, the isolated primer-free aptamer was sequenced and binding affinity for CRP was analyzed. The specificity of the obtained aptamer was validated using blind serum samples. The result was consistent with monoclonal antibody-based nephelometry analysis, which indicated that a primer-free aptamer has high specificity toward targets. MARAS is a feasible platform for efficiently generating primer-free aptamers for clinical diagnoses.

  16. The frequency of drugs in randomly selected drivers in Denmark

    DEFF Research Database (Denmark)

    Simonsen, Kirsten Wiese; Steentoft, Anni; Hels, Tove

    Introduction Driving under the influence of alcohol and drugs is a global problem. In Denmark as well as in other countries there is an increasing focus on impaired driving. Little is known about the occurrence of psychoactive drugs in the general traffic. Therefore the European commission...... initiated the DRUID project. This roadside study is the Danish part of the EU-project DRUID (Driving under the Influence of Drugs, Alcohol, and Medicines) and included three representative regions in Denmark. Methods Oral fluid samples (n = 3002) were collected randomly from drivers using a sampling scheme...... stratified by time, season, and road type. The oral fluid samples were screened for 29 illegal and legal psychoactive substances and metabolites as well as ethanol. Results Fourteen (0.5%) drivers were positive for ethanol (alone or in combination with drugs) at concentrations above 0.53 g/l, which...

  17. Sample Selection in Randomized Experiments: A New Method Using Propensity Score Stratified Sampling

    Science.gov (United States)

    Tipton, Elizabeth; Hedges, Larry; Vaden-Kiernan, Michael; Borman, Geoffrey; Sullivan, Kate; Caverly, Sarah

    2014-01-01

    Randomized experiments are often seen as the "gold standard" for causal research. Despite the fact that experiments use random assignment to treatment conditions, units are seldom selected into the experiment using probability sampling. Very little research on experimental design has focused on how to make generalizations to well-defined…

  18. Pseudo cluster randomization dealt with selection bias and contamination in clinical trials

    NARCIS (Netherlands)

    Teerenstra, S.; Melis, R.J.F.; Peer, P.G.M.; Borm, G.F.

    2006-01-01

    BACKGROUND AND OBJECTIVES: When contamination is present, randomization on a patient level leads to dilution of the treatment effect. The usual solution is to randomize on a cluster level, but at the cost of efficiency and more importantly, this may introduce selection bias. Furthermore, it may slow

  19. Acceptance sampling using judgmental and randomly selected samples

    Energy Technology Data Exchange (ETDEWEB)

    Sego, Landon H.; Shulman, Stanley A.; Anderson, Kevin K.; Wilson, John E.; Pulsipher, Brent A.; Sieber, W. Karl

    2010-09-01

    We present a Bayesian model for acceptance sampling where the population consists of two groups, each with different levels of risk of containing unacceptable items. Expert opinion, or judgment, may be required to distinguish between the high and low-risk groups. Hence, high-risk items are likely to be identifed (and sampled) using expert judgment, while the remaining low-risk items are sampled randomly. We focus on the situation where all observed samples must be acceptable. Consequently, the objective of the statistical inference is to quantify the probability that a large percentage of the unsampled items in the population are also acceptable. We demonstrate that traditional (frequentist) acceptance sampling and simpler Bayesian formulations of the problem are essentially special cases of the proposed model. We explore the properties of the model in detail, and discuss the conditions necessary to ensure that required samples sizes are non-decreasing function of the population size. The method is applicable to a variety of acceptance sampling problems, and, in particular, to environmental sampling where the objective is to demonstrate the safety of reoccupying a remediated facility that has been contaminated with a lethal agent.

  20. Conformational Selection in a Protein-Protein Interaction Revealed by Dynamic Pathway Analysis

    Directory of Open Access Journals (Sweden)

    Kalyan S. Chakrabarti

    2016-01-01

    Full Text Available Molecular recognition plays a central role in biology, and protein dynamics has been acknowledged to be important in this process. However, it is highly debated whether conformational changes happen before ligand binding to produce a binding-competent state (conformational selection or are caused in response to ligand binding (induced fit. Proposals for both mechanisms in protein/protein recognition have been primarily based on structural arguments. However, the distinction between them is a question of the probabilities of going via these two opposing pathways. Here, we present a direct demonstration of exclusive conformational selection in protein/protein recognition by measuring the flux for rhodopsin kinase binding to its regulator recoverin, an important molecular recognition in the vision system. Using nuclear magnetic resonance (NMR spectroscopy, stopped-flow kinetics, and isothermal titration calorimetry, we show that recoverin populates a minor conformation in solution that exposes a hydrophobic binding pocket responsible for binding rhodopsin kinase. Protein dynamics in free recoverin limits the overall rate of binding.

  1. Probing protein flexibility reveals a mechanism for selective promiscuity.

    Science.gov (United States)

    Pabon, Nicolas A; Camacho, Carlos J

    2017-04-22

    Many eukaryotic regulatory proteins adopt distinct bound and unbound conformations, and use this structural flexibility to bind specifically to multiple partners. However, we lack an understanding of how an interface can select some ligands, but not others. Here, we present a molecular dynamics approach to identify and quantitatively evaluate the interactions responsible for this selective promiscuity. We apply this approach to the anticancer target PD-1 and its ligands PD-L1 and PD-L2. We discover that while unbound PD-1 exhibits a hard-to-drug hydrophilic interface, conserved specific triggers encoded in the cognate ligands activate a promiscuous binding pathway that reveals a flexible hydrophobic binding cavity. Specificity is then established by additional contacts that stabilize the PD-1 cavity into distinct bound-like modes. Collectively, our studies provide insight into the structural basis and evolution of multiple binding partners, and also suggest a biophysical approach to exploit innate binding pathways to drug seemingly undruggable targets.

  2. Improved protein structure selection using decoy-dependent discriminatory functions

    Directory of Open Access Journals (Sweden)

    Levitt Michael

    2004-06-01

    Full Text Available Abstract Background A key component in protein structure prediction is a scoring or discriminatory function that can distinguish near-native conformations from misfolded ones. Various types of scoring functions have been developed to accomplish this goal, but their performance is not adequate to solve the structure selection problem. In addition, there is poor correlation between the scores and the accuracy of the generated conformations. Results We present a simple and nonparametric formula to estimate the accuracy of predicted conformations (or decoys. This scoring function, called the density score function, evaluates decoy conformations by performing an all-against-all Cα RMSD (Root Mean Square Deviation calculation in a given decoy set. We tested the density score function on 83 decoy sets grouped by their generation methods (4state_reduced, fisa, fisa_casp3, lmds, lattice_ssfit, semfold and Rosetta. The density scores have correlations as high as 0.9 with the Cα RMSDs of the decoy conformations, measured relative to the experimental conformation for each decoy. We previously developed a residue-specific all-atom probability discriminatory function (RAPDF, which compiles statistics from a database of experimentally determined conformations, to aid in structure selection. Here, we present a decoy-dependent discriminatory function called self-RAPDF, where we compiled the atom-atom contact probabilities from all the conformations in a decoy set instead of using an ensemble of native conformations, with a weighting scheme based on the density scores. The self-RAPDF has a higher correlation with Cα RMSD than RAPDF for 76/83 decoy sets, and selects better near-native conformations for 62/83 decoy sets. Self-RAPDF may be useful not only for selecting near-native conformations from decoy sets, but also for fold simulations and protein structure refinement. Conclusions Both the density score and the self-RAPDF functions are decoy

  3. RANDOM FORESTS-BASED FEATURE SELECTION FOR LAND-USE CLASSIFICATION USING LIDAR DATA AND ORTHOIMAGERY

    Directory of Open Access Journals (Sweden)

    H. Guan

    2012-07-01

    Full Text Available The development of lidar system, especially incorporated with high-resolution camera components, has shown great potential for urban classification. However, how to automatically select the best features for land-use classification is challenging. Random Forests, a newly developed machine learning algorithm, is receiving considerable attention in the field of image classification and pattern recognition. Especially, it can provide the measure of variable importance. Thus, in this study the performance of the Random Forests-based feature selection for urban areas was explored. First, we extract features from lidar data, including height-based, intensity-based GLCM measures; other spectral features can be obtained from imagery, such as Red, Blue and Green three bands, and GLCM-based measures. Finally, Random Forests is used to automatically select the optimal and uncorrelated features for landuse classification. 0.5-meter resolution lidar data and aerial imagery are used to assess the feature selection performance of Random Forests in the study area located in Mannheim, Germany. The results clearly demonstrate that the use of Random Forests-based feature selection can improve the classification performance by the selected features.

  4. Uncovering Molecular Bases Underlying Bone Morphogenetic Protein Receptor Inhibitor Selectivity.

    Directory of Open Access Journals (Sweden)

    Abdelaziz Alsamarah

    Full Text Available Abnormal alteration of bone morphogenetic protein (BMP signaling is implicated in many types of diseases including cancer and heterotopic ossifications. Hence, small molecules targeting BMP type I receptors (BMPRI to interrupt BMP signaling are believed to be an effective approach to treat these diseases. However, lack of understanding of the molecular determinants responsible for the binding selectivity of current BMP inhibitors has been a big hindrance to the development of BMP inhibitors for clinical use. To address this issue, we carried out in silico experiments to test whether computational methods can reproduce and explain the high selectivity of a small molecule BMP inhibitor DMH1 on BMPRI kinase ALK2 vs. the closely related TGF-β type I receptor kinase ALK5 and vascular endothelial growth factor receptor type 2 (VEGFR2 tyrosine kinase. We found that, while the rigid docking method used here gave nearly identical binding affinity scores among the three kinases; free energy perturbation coupled with Hamiltonian replica-exchange molecular dynamics (FEP/H-REMD simulations reproduced the absolute binding free energies in excellent agreement with experimental data. Furthermore, the binding poses identified by FEP/H-REMD led to a quantitative analysis of physical/chemical determinants governing DMH1 selectivity. The current work illustrates that small changes in the binding site residue type (e.g. pre-hinge region in ALK2 vs. ALK5 or side chain orientation (e.g. Tyr219 in caALK2 vs. wtALK2, as well as a subtle structural modification on the ligand (e.g. DMH1 vs. LDN193189 will cause distinct binding profiles and selectivity among BMP inhibitors. Therefore, the current computational approach represents a new way of investigating BMP inhibitors. Our results provide critical information for designing exclusively selective BMP inhibitors for the development of effective pharmacotherapy for diseases caused by aberrant BMP signaling.

  5. Select host cell proteins coelute with monoclonal antibodies in protein A chromatography.

    Science.gov (United States)

    Nogal, Bartek; Chhiba, Krishan; Emery, Jefferson C

    2012-01-01

    The most significant factor contributing to the presence of host cell protein (HCP) impurities in Protein A chromatography eluates is their association with the product monoclonal antibodies (mAbs) has been reported previously, and it has been suggested that more efficacious column washes may be developed by targeting the disruption of the mAbs-HCP interaction. However, characterization of this interaction is not straight forward as it is likely to involve multiple proteins and/or types of interaction. This work is an attempt to begin to understand the contribution of HCP subpopulations and/or mAb interaction propensity to the variability in HCP levels in the Protein A eluate. We performed a flowthrough (FT) recycling study with product respiking using two antibody molecules of apparently different HCP interaction propensities. In each case, the ELISA assay showed depletion of select subpopulations of HCP in Protein A eluates in subsequent column runs, while the feedstock HCP in the FTs remained unchanged from its native harvested cell culture fluid (HCCF) levels. In a separate study, the final FT from each molecule's recycling study was cross-spiked with various mAbs. In this case, Protein A eluate levels remained low for all but two molecules which were known as having high apparent HCP interaction propensity. The results of these studies suggest that mAbs may preferentially bind to select subsets of HCPs, and the degree of interaction and/or identity of the associated HCPs may vary depending on the mAb. Copyright © 2012 American Institute of Chemical Engineers (AIChE).

  6. SNP selection and classification of genome-wide SNP data using stratified sampling random forests.

    Science.gov (United States)

    Wu, Qingyao; Ye, Yunming; Liu, Yang; Ng, Michael K

    2012-09-01

    For high dimensional genome-wide association (GWA) case-control data of complex disease, there are usually a large portion of single-nucleotide polymorphisms (SNPs) that are irrelevant with the disease. A simple random sampling method in random forest using default mtry parameter to choose feature subspace, will select too many subspaces without informative SNPs. Exhaustive searching an optimal mtry is often required in order to include useful and relevant SNPs and get rid of vast of non-informative SNPs. However, it is too time-consuming and not favorable in GWA for high-dimensional data. The main aim of this paper is to propose a stratified sampling method for feature subspace selection to generate decision trees in a random forest for GWA high-dimensional data. Our idea is to design an equal-width discretization scheme for informativeness to divide SNPs into multiple groups. In feature subspace selection, we randomly select the same number of SNPs from each group and combine them to form a subspace to generate a decision tree. The advantage of this stratified sampling procedure can make sure each subspace contains enough useful SNPs, but can avoid a very high computational cost of exhaustive search of an optimal mtry, and maintain the randomness of a random forest. We employ two genome-wide SNP data sets (Parkinson case-control data comprised of 408 803 SNPs and Alzheimer case-control data comprised of 380 157 SNPs) to demonstrate that the proposed stratified sampling method is effective, and it can generate better random forest with higher accuracy and lower error bound than those by Breiman's random forest generation method. For Parkinson data, we also show some interesting genes identified by the method, which may be associated with neurological disorders for further biological investigations.

  7. An efficient method of wavelength interval selection based on random frog for multivariate spectral calibration

    Science.gov (United States)

    Yun, Yong-Huan; Li, Hong-Dong; Wood, Leslie R. E.; Fan, Wei; Wang, Jia-Jun; Cao, Dong-Sheng; Xu, Qing-Song; Liang, Yi-Zeng

    2013-07-01

    Wavelength selection is a critical step for producing better prediction performance when applied to spectral data. Considering the fact that the vibrational and rotational spectra have continuous features of spectral bands, we propose a novel method of wavelength interval selection based on random frog, called interval random frog (iRF). To obtain all the possible continuous intervals, spectra are first divided into intervals by moving window of a fix width over the whole spectra. These overlapping intervals are ranked applying random frog coupled with PLS and the optimal ones are chosen. This method has been applied to two near-infrared spectral datasets displaying higher efficiency in wavelength interval selection than others. The source code of iRF can be freely downloaded for academy research at the website: http://code.google.com/p/multivariate-calibration/downloads/list.

  8. Delay line length selection in generating fast random numbers with a chaotic laser.

    Science.gov (United States)

    Zhang, Jianzhong; Wang, Yuncai; Xue, Lugang; Hou, Jiayin; Zhang, Beibei; Wang, Anbang; Zhang, Mingjiang

    2012-04-10

    The chaotic light signals generated by an external cavity semiconductor laser have been experimentally demonstrated to extract fast random numbers. However, the photon round-trip time in the external cavity can cause the occurrence of the periodicity in random sequences. To overcome it, the exclusive-or operation on corresponding random bits in samples of the chaotic signal and its time-delay signal from a chaotic laser is required. In this scheme, the proper selection of delay length is a key issue. By doing a large number of experiments and theoretically analyzing the interplay between the Runs test and the threshold value of the autocorrelation function, we find when the corresponding delay time of autocorrelation trace with the correlation coefficient of less than 0.007 is considered as the delay time between the chaotic signal and its time-delay signal, streams of random numbers can be generated with verified randomness.

  9. Sequence Based Prediction of Antioxidant Proteins Using a Classifier Selection Strategy.

    Science.gov (United States)

    Zhang, Lina; Zhang, Chengjin; Gao, Rui; Yang, Runtao; Song, Qing

    Antioxidant proteins perform significant functions in maintaining oxidation/antioxidation balance and have potential therapies for some diseases. Accurate identification of antioxidant proteins could contribute to revealing physiological processes of oxidation/antioxidation balance and developing novel antioxidation-based drugs. In this study, an ensemble method is presented to predict antioxidant proteins with hybrid features, incorporating SSI (Secondary Structure Information), PSSM (Position Specific Scoring Matrix), RSA (Relative Solvent Accessibility), and CTD (Composition, Transition, Distribution). The prediction results of the ensemble predictor are determined by an average of prediction results of multiple base classifiers. Based on a classifier selection strategy, we obtain an optimal ensemble classifier composed of RF (Random Forest), SMO (Sequential Minimal Optimization), NNA (Nearest Neighbor Algorithm), and J48 with an accuracy of 0.925. A Relief combined with IFS (Incremental Feature Selection) method is adopted to obtain optimal features from hybrid features. With the optimal features, the ensemble method achieves improved performance with a sensitivity of 0.95, a specificity of 0.93, an accuracy of 0.94, and an MCC (Matthew's Correlation Coefficient) of 0.880, far better than the existing method. To evaluate the prediction performance objectively, the proposed method is compared with existing methods on the same independent testing dataset. Encouragingly, our method performs better than previous studies. In addition, our method achieves more balanced performance with a sensitivity of 0.878 and a specificity of 0.860. These results suggest that the proposed ensemble method can be a potential candidate for antioxidant protein prediction. For public access, we develop a user-friendly web server for antioxidant protein identification that is freely accessible at http://antioxidant.weka.cc.

  10. Two-year Randomized Clinical Trial Of Self-etching Adhesives And Selective Enamel Etching

    OpenAIRE

    Pena, MR; Rodrigues CE; JA; Ely; Giannini, C.; Reis, M; AF

    2016-01-01

    Objective: The aim of this randomized, controlled prospective clinical trial was to evaluate the clinical effectiveness of restoring noncarious cervical lesions with two self-etching adhesive systems applied with or without selective enamel etching. Methods: A one-step self-etching adhesive (Xeno V+) and a two-step self-etching system (Clearfil SE Bond) were used. The effectiveness of phosphoric acid selective etching of enamel margins was also evaluated. Fifty-six cavities were restored with...

  11. Use of protein: creatinine ratio in a random spot urine sample for predicting significant proteinuria in diabetes mellitus.

    Science.gov (United States)

    Yadav, B K; Adhikari, S; Gyawali, P; Shrestha, R; Poudel, B; Khanal, M

    2010-06-01

    Present study was undertaken during a period of 6 months (September 2008-February 2009) to see an correlation of 24 hours urine protein estimation with random spot protein-creatinine (P:C) ratio among a diabetic patients. The study comprised of 144 patients aged 30-70 years, recruited from Kantipur hospital, Kathmandu. The 24-hr urine sample was collected, followed by spot random urine sample. Both samples were analyzed for protein and creatinine excretion. An informed consent was taken from all participants. Sixteen inadequately collected urine samples as defined by (predicted creatinine--measured creatinine)/predicted creatinine > 0.2 were excluded from analysis. The Spearman's rank correlation between the spot urine P:C ratio and 24-hr total protein were performed by the Statistical Package for Social Service. At the P:C ratio cutoff of 0.15 and reference method (24-hr urine protein) cutoff of 150 mg/day, the correlation coefficient was found to be 0.892 (p urine collection but the cutoff should be carefully selected for different patients group under different laboratory procedures and settings.

  12. Hebbian Learning in a Random Network Captures Selectivity Properties of the Prefrontal Cortex.

    Science.gov (United States)

    Lindsay, Grace W; Rigotti, Mattia; Warden, Melissa R; Miller, Earl K; Fusi, Stefano

    2017-11-08

    Complex cognitive behaviors, such as context-switching and rule-following, are thought to be supported by the prefrontal cortex (PFC). Neural activity in the PFC must thus be specialized to specific tasks while retaining flexibility. Nonlinear "mixed" selectivity is an important neurophysiological trait for enabling complex and context-dependent behaviors. Here we investigate (1) the extent to which the PFC exhibits computationally relevant properties, such as mixed selectivity, and (2) how such properties could arise via circuit mechanisms. We show that PFC cells recorded from male and female rhesus macaques during a complex task show a moderate level of specialization and structure that is not replicated by a model wherein cells receive random feedforward inputs. While random connectivity can be effective at generating mixed selectivity, the data show significantly more mixed selectivity than predicted by a model with otherwise matched parameters. A simple Hebbian learning rule applied to the random connectivity, however, increases mixed selectivity and enables the model to match the data more accurately. To explain how learning achieves this, we provide analysis along with a clear geometric interpretation of the impact of learning on selectivity. After learning, the model also matches the data on measures of noise, response density, clustering, and the distribution of selectivities. Of two styles of Hebbian learning tested, the simpler and more biologically plausible option better matches the data. These modeling results provide clues about how neural properties important for cognition can arise in a circuit and make clear experimental predictions regarding how various measures of selectivity would evolve during animal training. SIGNIFICANCE STATEMENT The prefrontal cortex is a brain region believed to support the ability of animals to engage in complex behavior. How neurons in this area respond to stimuli-and in particular, to combinations of stimuli ("mixed

  13. Selecting Optimal Parameters of Random Linear Network Coding for Wireless Sensor Networks

    DEFF Research Database (Denmark)

    Heide, Janus; Zhang, Qi; Fitzek, Frank

    2013-01-01

    This work studies how to select optimal code parameters of Random Linear Network Coding (RLNC) in Wireless Sensor Networks (WSNs). With Rateless Deluge [1] the authors proposed to apply Network Coding (NC) for Over-the-Air Programming (OAP) in WSNs, and demonstrated that with NC a significant...

  14. Folded Proteins Occur Frequently in Libraries of Random Amino Acid Sequences

    Science.gov (United States)

    Davidson, Alan R.; Sauer, Robert T.

    1994-03-01

    A library of synthetic genes encoding 80- to 100-residue proteins composed mainly of random combinations of glutamine (Q), leucine (L), and arginine (R) has been expressed in Escherichia coli. These genes also encode an epitope tag and six carboxyl-terminal histidines. Screening of this library by immunoblotting showed that 5% of these QLR proteins are expressed at readily detectable levels. Three well-expressed QLR proteins were purified and characterized. Each of these proteins has significant α-helical content, is largely resistant to degradation by Pronase, and has a distinct oligomeric structure. In addition, one protein unfolds in a highly cooperative manner. These properties of the QLR proteins demonstrate that they possess folded structures with some native-like properties. The QLR proteins differ from most natural proteins, however, in being remarkably resistant to denaturant-induced and thermal-induced unfolding and in being relatively insoluble in the absence of denaturants.

  15. Selective prediction of interaction sites in protein structures with THEMATICS

    Directory of Open Access Journals (Sweden)

    Murga Leonel F

    2007-04-01

    Full Text Available Abstract Background Methods are now available for the prediction of interaction sites in protein 3D structures. While many of these methods report high success rates for site prediction, often these predictions are not very selective and have low precision. Precision in site prediction is addressed using Theoretical Microscopic Titration Curves (THEMATICS, a simple computational method for the identification of active sites in enzymes. Recall and precision are measured and compared with other methods for the prediction of catalytic sites. Results Using a test set of 169 enzymes from the original Catalytic Residue Dataset (CatRes it is shown that THEMATICS can deliver precise, localised site predictions. Furthermore, adjustment of the cut-off criteria can improve the recall rates for catalytic residues with only a small sacrifice in precision. Recall rates for CatRes/CSA annotated catalytic residues are 41.1%, 50.4%, and 54.2% for Z score cut-off values of 1.00, 0.99, and 0.98, respectively. The corresponding precision rates are 19.4%, 17.9%, and 16.4%. The success rate for catalytic sites is higher, with correct or partially correct predictions for 77.5%, 85.8%, and 88.2% of the enzymes in the test set, corresponding to the same respective Z score cut-offs, if only the CatRes annotations are used as the reference set. Incorporation of additional literature annotations into the reference set gives total success rates of 89.9%, 92.9%, and 94.1%, again for corresponding cut-off values of 1.00, 0.99, and 0.98. False positive rates for a 75-protein test set are 1.95%, 2.60%, and 3.12% for Z score cut-offs of 1.00, 0.99, and 0.98, respectively. Conclusion With a preferred cut-off value of 0.99, THEMATICS achieves a high success rate of interaction site prediction, about 86% correct or partially correct using CatRes/CSA annotations only and about 93% with an expanded reference set. Success rates for catalytic residue prediction are similar to those of

  16. Combining rational and random strategies in β-glucosidase Zm-p60.1 protein library construction.

    Directory of Open Access Journals (Sweden)

    Dušan Turek

    Full Text Available Saturation mutagenesis is a cornerstone technique in protein engineering because of its utility (in conjunction with appropriate analytical techniques for assessing effects of varying residues at selected positions on proteins' structures and functions. Site-directed mutagenesis with degenerate primers is the simplest and most rapid saturation mutagenesis technique. Thus, it is highly appropriate for assessing whether or not variation at certain sites is permissible, but not necessarily the most time- and cost-effective technique for detailed assessment of variations' effects. Thus, in the presented study we applied the technique to randomize position W373 in β-glucosidase Zm-p60.1, which is highly conserved among β-glucosidases. Unexpectedly, β-glucosidase activity screening of the generated variants showed that most variants were active, although they generally had significantly lower activity than the wild type enzyme. Further characterization of the library led us to conclude that a carefully selected combination of randomized codon-based saturation mutagenesis and site-directed mutagenesis may be most efficient, particularly when constructing and investigating randomized libraries with high fractions of positive hits.

  17. Functional divergence of the NIP III subgroup proteins involved altered selective constraints and positive selection

    Directory of Open Access Journals (Sweden)

    Zhu Zhujun

    2010-11-01

    Full Text Available Abstract Background Nod26-like intrinsic proteins (NIPs that belong to the aquaporin superfamily are unique to plants. According to homology modeling and phylogenetic analysis, the NIP subfamily can be further divided into three subgroups with distinct biological functions (NIP I, NIP II, and NIP III. In some grasses, the NIP III subgroup proteins (NIP2s were demonstrated to be permeable to solutes with larger diameter, such as silicic acid and arsenous acids. However, to date there is no data-mining or direct experimental evidences for the permeability of such larger solutes for dicot NIP2s, although they exhibit similar three-dimensional structures as those in grasses. It is therefore intriguing to investigate the molecular mechanisms that drive the evolution of plant NIP2s. Results The NIP III subgroup is more ancient with a divergence time that predates the monocot-dicot split. The proliferation of NIP2 genes in modern grass species is primarily attributed to whole genome and segmental chromosomal duplication events. The structure of NIP2 genes is relatively conserved, possessing five exons and four introns. All NIP2s possess an ar/R filter consisting of G, S, G, and R, except for the cucumber CsNIP2;2, where a small G in the H2 is substituted with the bulkier C residue. Our maximum likelihood analysis revealed that NIP2s, especially the loop A (LA region, have undergone strong selective pressure for adaptive evolution. The analysis at the amino acid level provided strong statistical evidences for the functional divergence between monocot and dicot NIP III subgroup proteins. In addition, several SDPs (Specificity Determining Positions responsible for functional specificity were predicted. Conclusions The present study provides the first evidences of functional divergence between dicot and monocot NIP2s, and suggests that positive selection, as well as a radical shift of evolutionary rate at some critical amino acid sites is the primary

  18. Tehran Air Pollutants Prediction Based on Random Forest Feature Selection Method

    Science.gov (United States)

    Shamsoddini, A.; Aboodi, M. R.; Karami, J.

    2017-09-01

    Air pollution as one of the most serious forms of environmental pollutions poses huge threat to human life. Air pollution leads to environmental instability, and has harmful and undesirable effects on the environment. Modern prediction methods of the pollutant concentration are able to improve decision making and provide appropriate solutions. This study examines the performance of the Random Forest feature selection in combination with multiple-linear regression and Multilayer Perceptron Artificial Neural Networks methods, in order to achieve an efficient model to estimate carbon monoxide and nitrogen dioxide, sulfur dioxide and PM2.5 contents in the air. The results indicated that Artificial Neural Networks fed by the attributes selected by Random Forest feature selection method performed more accurate than other models for the modeling of all pollutants. The estimation accuracy of sulfur dioxide emissions was lower than the other air contaminants whereas the nitrogen dioxide was predicted more accurate than the other pollutants.

  19. TEHRAN AIR POLLUTANTS PREDICTION BASED ON RANDOM FOREST FEATURE SELECTION METHOD

    Directory of Open Access Journals (Sweden)

    A. Shamsoddini

    2017-09-01

    Full Text Available Air pollution as one of the most serious forms of environmental pollutions poses huge threat to human life. Air pollution leads to environmental instability, and has harmful and undesirable effects on the environment. Modern prediction methods of the pollutant concentration are able to improve decision making and provide appropriate solutions. This study examines the performance of the Random Forest feature selection in combination with multiple-linear regression and Multilayer Perceptron Artificial Neural Networks methods, in order to achieve an efficient model to estimate carbon monoxide and nitrogen dioxide, sulfur dioxide and PM2.5 contents in the air. The results indicated that Artificial Neural Networks fed by the attributes selected by Random Forest feature selection method performed more accurate than other models for the modeling of all pollutants. The estimation accuracy of sulfur dioxide emissions was lower than the other air contaminants whereas the nitrogen dioxide was predicted more accurate than the other pollutants.

  20. Effect of dietary protein supplementation on blood pressure: a randomized, controlled trial.

    Science.gov (United States)

    He, Jiang; Wofford, Marion R; Reynolds, Kristi; Chen, Jing; Chen, Chung-Shiuan; Myers, Leann; Minor, Deborah L; Elmer, Patricia J; Jones, Daniel W; Whelton, Paul K

    2011-08-02

    Observational studies have reported an inverse association between dietary protein intake and blood pressure (BP). We compared the effect of soy protein, milk protein, and carbohydrate supplementation on BP among healthy adults. We conducted a randomized, double-blind crossover trial with 3 intervention phases among 352 adults with prehypertension or stage 1 hypertension in New Orleans, LA, and Jackson, MS, from September 2003 to April 2008. The trial participants were assigned to take 40 g/d soy protein, milk protein, or carbohydrate supplementation each for 8 weeks in a random order. A 3-week washout period was implemented between the interventions. Three BPs were measured at 2 baseline and 2 termination visits during each of 3 intervention phases with a random-zero sphygmomanometer. Compared with carbohydrate controls, soy protein and milk protein supplementations were significantly associated with -2.0 mm Hg (95% confidence interval -3.2 to -0.7 mm Hg, P=0.002) and -2.3 mm Hg (-3.7 to -1.0 mm Hg, P=0.0007) net changes in systolic BP, respectively. Diastolic BP was also reduced, but this change did not reach statistical significance. There was no significant difference in the BP reductions achieved between soy or milk protein supplementation. The results from this randomized, controlled trial indicate that both soy and milk protein intake reduce systolic BP compared with a high-glycemic-index refined carbohydrate among patients with prehypertension and stage 1 hypertension. Furthermore, these findings suggest that partially replacing carbohydrate with soy or milk protein might be an important component of nutrition intervention strategies for the prevention and treatment of hypertension. URL: http://www.clinicaltrials.gov. Unique identifier: NCT00107744.

  1. Bayesian Markov Random Field analysis for protein function prediction based on network data.

    Science.gov (United States)

    Kourmpetis, Yiannis A I; van Dijk, Aalt D J; Bink, Marco C A M; van Ham, Roeland C H J; ter Braak, Cajo J F

    2010-02-24

    Inference of protein functions is one of the most important aims of modern biology. To fully exploit the large volumes of genomic data typically produced in modern-day genomic experiments, automated computational methods for protein function prediction are urgently needed. Established methods use sequence or structure similarity to infer functions but those types of data do not suffice to determine the biological context in which proteins act. Current high-throughput biological experiments produce large amounts of data on the interactions between proteins. Such data can be used to infer interaction networks and to predict the biological process that the protein is involved in. Here, we develop a probabilistic approach for protein function prediction using network data, such as protein-protein interaction measurements. We take a Bayesian approach to an existing Markov Random Field method by performing simultaneous estimation of the model parameters and prediction of protein functions. We use an adaptive Markov Chain Monte Carlo algorithm that leads to more accurate parameter estimates and consequently to improved prediction performance compared to the standard Markov Random Fields method. We tested our method using a high quality S. cereviciae validation network with 1622 proteins against 90 Gene Ontology terms of different levels of abstraction. Compared to three other protein function prediction methods, our approach shows very good prediction performance. Our method can be directly applied to protein-protein interaction or coexpression networks, but also can be extended to use multiple data sources. We apply our method to physical protein interaction data from S. cerevisiae and provide novel predictions, using 340 Gene Ontology terms, for 1170 unannotated proteins and we evaluate the predictions using the available literature.

  2. Classification of epileptic EEG signals based on simple random sampling and sequential feature selection.

    Science.gov (United States)

    Ghayab, Hadi Ratham Al; Li, Yan; Abdulla, Shahab; Diykh, Mohammed; Wan, Xiangkui

    2016-06-01

    Electroencephalogram (EEG) signals are used broadly in the medical fields. The main applications of EEG signals are the diagnosis and treatment of diseases such as epilepsy, Alzheimer, sleep problems and so on. This paper presents a new method which extracts and selects features from multi-channel EEG signals. This research focuses on three main points. Firstly, simple random sampling (SRS) technique is used to extract features from the time domain of EEG signals. Secondly, the sequential feature selection (SFS) algorithm is applied to select the key features and to reduce the dimensionality of the data. Finally, the selected features are forwarded to a least square support vector machine (LS_SVM) classifier to classify the EEG signals. The LS_SVM classifier classified the features which are extracted and selected from the SRS and the SFS. The experimental results show that the method achieves 99.90, 99.80 and 100 % for classification accuracy, sensitivity and specificity, respectively.

  3. Zeolite Nanoparticles for Selective Sorption of Plasma Proteins

    NARCIS (Netherlands)

    Rahimi, M.; Ng, E.-P.; Bakhtiari, K.; Vinciguerra, M.; Ali Ahmad, H.; Awala, H.; Mintova, S.; Daghighi, M.; Bakhshandeh Rostami, F.; de Vries, M.; Motazacker, M. M.; Peppelenbosch, M. P.; Mahmoudi, M.; Rezaee, F.

    2015-01-01

    The affinity of zeolite nanoparticles (diameter of 8-12 nm) possessing high surface area and high pore volume towards human plasma proteins has been investigated. The protein composition (corona) of zeolite nanoparticles has been shown to be more dependent on the plasma protein concentrations and

  4. Zeolite Nanoparticles for Selective Sorption of Plasma Proteins

    NARCIS (Netherlands)

    Rahimi, Mehran; Ng, E. -P.; Bakhtiari, K.; Vinciguerra, M.; Ahmad, H. Ali; Awala, H.; Mintova, S.; Daghighi, M.; Rostami, F. Bakhshandeh; de Vries, Marcel; Motazacker, M. M.; Peppelenbosch, M. P.; Mahmoudi, M.; Rezaee, F.

    2015-01-01

    The affinity of zeolite nanoparticles (diameter of 8-12 nm) possessing high surface area and high pore volume towards human plasma proteins has been investigated. The protein composition (corona) of zeolite nanoparticles has been shown to be more dependent on the plasma protein concentrations and

  5. Zeolite Nanoparticles for Selective Sorption of Plasma Proteins

    NARCIS (Netherlands)

    M. Rahimi (Mehran); E.-P. Ng; K. Bakhtiari (Kamran); M. Vinciguerra (Manlio); H.A. Ahmad (H. Ali); H. Awala; S. Mintova; M. Daghighi (Mojtaba); F. Bakhshandeh Rostami; M. de Vries (Marieke); M.M. Motazacker (Mohammad); M.P. Peppelenbosch (Maikel); M. Mahmoudi; F. Rezaee (Farhad)

    2015-01-01

    textabstractThe affinity of zeolite nanoparticles (diameter of 8-12 nm) possessing high surface area and high pore volume towards human plasma proteins has been investigated. The protein composition (corona) of zeolite nanoparticles has been shown to be more dependent on the plasma protein

  6. Personal name in Igbo Culture: A dataset on randomly selected personal names and their statistical analysis.

    Science.gov (United States)

    Okagbue, Hilary I; Opanuga, Abiodun A; Adamu, Muminu O; Ugwoke, Paulinus O; Obasi, Emmanuela C M; Eze, Grace A

    2017-12-01

    This data article contains the statistical analysis of Igbo personal names and a sample of randomly selected of such names. This was presented as the following: 1). A simple random sampling of some Igbo personal names and their respective gender associated with each name. 2). The distribution of the vowels, consonants and letters of alphabets of the personal names. 3). The distribution of name length. 4). The distribution of initial and terminal letters of Igbo personal names. The significance of the data was discussed.

  7. Protein-enriched familiar foods and drinks improve protein intake of hospitalized older patients: A randomized controlled trial.

    Science.gov (United States)

    Beelen, Janne; Vasse, Emmelyne; Janssen, Nancy; Janse, André; de Roos, Nicole M; de Groot, Lisette C P G M

    2017-05-18

    Adequate protein intake is important in preventing and treating undernutrition. Hospitalized older patients are recommended to consume 1.2-1.5 g of protein per kg body weight per day (g/kg/d) but most of them fail to do so. Therefore, we investigated whether a range of newly developed protein-enriched familiar foods and drinks were effective in increasing protein intake of hospitalized older patients. This randomized controlled trial involved 147 patients of ≥65 years (mean age: 78.5 ± 7.4 years). The control group (n = 80) received the standard energy and protein rich hospital menu. The intervention group (n = 67) received the same menu with various protein-enriched intervention products replacing regular products or added to the menu. Macronutrient intake on the fourth day of hospitalization, based on food ordering data, was compared between the two groups by using Independent T-tests and Mann Whitney U-tests. In the intervention group 30% of total protein was provided by the intervention products. The intervention group consumed 105.7 ± 34.2 g protein compared to 88.2 ± 24.4 g in the control group (p protein intake of 1.2 g/kg/d (79.1% vs 47.5%). Protein intake was significantly higher in the intervention group at breakfast, during the morning between breakfast and lunch, and at dinner. This study shows that providing protein-enriched familiar foods and drinks, as replacement of regular products or as additions to the hospital menu, better enables hospitalized older patients to reach protein intake recommendations. This trial is registered on ClinicalTrials.gov, Identifier: NCT02213393. Copyright © 2017 Elsevier Ltd and European Society for Clinical Nutrition and Metabolism. All rights reserved.

  8. Isolation of novel single-chain Cro proteins targeted for binding to the bcl-2 transcription initiation site by repertoire selection and subunit combinatorics.

    Science.gov (United States)

    Jonas, Kristina; Van Der Vries, Erhard; Nilsson, Mikael T I; Widersten, Mikael

    2005-11-01

    New designed DNA-binding proteins may be recruited to act as transcriptional regulators and could provide new therapeutic agents in the treatment of genetic disorders such as cancer. We have isolated tailored DNA-binding proteins selected for affinity to a region spanning the transcription initiation site of the human bcl-2 gene. The proteins were derived from a single-chain derivative of the lambda Cro protein (scCro), randomly mutated in its recognition helices to construct libraries of protein variants of distinct DNA-binding properties. By phage display-afforded affinity selections combined with recombination of shuffled subunits, protein variants were isolated, which displayed high affinity for the target bcl-2 sequence, as determined by electrophoretic mobility shift and biosensor assays. The proteins analyzed were moderately sequence-specific but provide a starting point for further maturation of desired function.

  9. Protein/creatinine ratio on random urine samples for prediction of proteinuria in preeclampsia.

    Science.gov (United States)

    Roudsari, F Vahid; Ayati, S; Ayatollahi, H; Shakeri, M T

    2012-01-01

    To evaluate Protein/Creatinine ratio on random urine samples for prediction of proteinuria in preeclampsia. This study was performed on 150 pregnant women who were hospitalized as preeclampsia in Ghaem Hospital during 2006. At first, a 24-hours urine sample was collected for each patient to determine protein/creatinine ratio. Then, 24-hours urine collection was analyzed for the evaluation of proteinuria. Statistical analysis was performed with SPSS software. A total of 150 patients entered the study. There was a significant relation between the 24-hours urine protein and protein/creatinine ratio (r = 0.659, P < 0.001). Since the measurement of protein/creatinine ratio is more accurate, reliable, and cost-effective, it can be replaced by the method of measurement the 24-hours urine protein.

  10. Simulated Performance Evaluation of a Selective Tracker Through Random Scenario Generation

    DEFF Research Database (Denmark)

    Hussain, Dil Muhammad Akbar

    2006-01-01

      The paper presents a simulation study on the performance of a target tracker using selective track splitting filter algorithm through a random scenario implemented on a digital signal processor.  In a typical track splitting filter all the observation which fall inside a likelihood ellipse...... are used for update, however, in our proposed selective track splitting filter less number of observations are used for track update.  Much of the previous performance work [1] has been done on specific (deterministic) scenarios. One of the reasons for considering the specific scenarios, which were...

  11. A multi-directional rapidly exploring random graph (mRRG) for protein folding

    KAUST Repository

    Nath, Shuvra Kanti

    2012-01-01

    Modeling large-scale protein motions, such as those involved in folding and binding interactions, is crucial to better understanding not only how proteins move and interact with other molecules but also how proteins misfold, thus causing many devastating diseases. Robotic motion planning algorithms, such as Rapidly Exploring Random Trees (RRTs), have been successful in simulating protein folding pathways. Here, we propose a new multi-directional Rapidly Exploring Random Graph (mRRG) specifically tailored for proteins. Unlike traditional RRGs which only expand a parent conformation in a single direction, our strategy expands the parent conformation in multiple directions to generate new samples. Resulting samples are connected to the parent conformation and its nearest neighbors. By leveraging multiple directions, mRRG can model the protein motion landscape with reduced computational time compared to several other robotics-based methods for small to moderate-sized proteins. Our results on several proteins agree with experimental hydrogen out-exchange, pulse-labeling, and F-value analysis. We also show that mRRG covers the conformation space better as compared to the other computation methods. Copyright © 2012 ACM.

  12. Classification of epileptic EEG signals based on simple random sampling and sequential feature selection

    OpenAIRE

    Ghayab, Hadi Ratham Al; Li, Yan; Abdulla, Shahab; Diykh, Mohammed; Wan, Xiangkui

    2016-01-01

    Electroencephalogram (EEG) signals are used broadly in the medical fields. The main applications of EEG signals are the diagnosis and treatment of diseases such as epilepsy, Alzheimer, sleep problems and so on. This paper presents a new method which extracts and selects features from multi-channel EEG signals. This research focuses on three main points. Firstly, simple random sampling (SRS) technique is used to extract features from the time domain of EEG signals. Secondly, the sequential fea...

  13. Selective Knockdowns in Maize by Sequence-Specific Protein Aggregation.

    Science.gov (United States)

    Betti, Camilla; Schymkowitz, Joost; Rousseau, Frederic; Russinova, Eugenia

    2018-01-01

    Protein aggregation is determined by 5-15 amino acids peptides of the target protein sequence, so-called aggregation-prone regions (APRs) that specifically self-associate to form β-structured inclusions. The presence of APRs in a target protein can be predicted by a dedicated algorithm, such as TANGO. Synthetic aggregation-prone proteins are designed by expressing specific APRs fused to a fluorescent carrier for stability and visualization. Previously, the stable expression of these proteins in Zea mays (maize) has been demonstrated to induce aggregation of target proteins with specific localization, such as the starch-degrading enzyme α-glucan water dikinase, giving rise to plants displaying knockdown phenotypes. Here, we describe how to design synthetic aggregation-prone proteins to harness the sequence specificity of APRs to generate aggregation-associated phenotypes in a targeted manner and in different subcellular compartments. This method points toward the application of induced targeted aggregation as a useful tool to knock down protein functions in maize and to generate crops with improved traits.

  14. Semiotic Selection of Mutated or Misfolded Receptor Proteins

    DEFF Research Database (Denmark)

    Giorgi, Franco; Bruni, Luis Emilio; Maggio, Roberto

    2013-01-01

    Receptor oligomerization plays a key role in maintaining genome stability and restricting protein mutagenesis. When properly folded, protein monomers assemble as oligomeric receptors and interact with environmental ligands. In a gene-centered view, the ligand specificity expressed by these recept......Receptor oligomerization plays a key role in maintaining genome stability and restricting protein mutagenesis. When properly folded, protein monomers assemble as oligomeric receptors and interact with environmental ligands. In a gene-centered view, the ligand specificity expressed...... for receptor monomers to assemble along the membrane and to sustain meaningful relationships with environmental ligands. How could a cell lineage deal with these loss-of-function mutations during evolution and restrain gene redundancy accordingly? In this paper, we will be arguing that the easiest way...... focused on the significance and semiotic nature of the interplay between membrane receptors and the epigenetic control of gene expression, as mediated by the control of mismatched repairing and protein folding mechanisms....

  15. Statistical inference of selection and divergence from a time-dependent Poisson random field model.

    Directory of Open Access Journals (Sweden)

    Amei Amei

    Full Text Available We apply a recently developed time-dependent Poisson random field model to aligned DNA sequences from two related biological species to estimate selection coefficients and divergence time. We use Markov chain Monte Carlo methods to estimate species divergence time and selection coefficients for each locus. The model assumes that the selective effects of non-synonymous mutations are normally distributed across genetic loci but constant within loci, and synonymous mutations are selectively neutral. In contrast with previous models, we do not assume that the individual species are at population equilibrium after divergence. Using a data set of 91 genes in two Drosophila species, D. melanogaster and D. simulans, we estimate the species divergence time t(div = 2.16 N(e (or 1.68 million years, assuming the haploid effective population size N(e = 6.45 x 10(5 years and a mean selection coefficient per generation μ(γ = 1.98/N(e. Although the average selection coefficient is positive, the magnitude of the selection is quite small. Results from numerical simulations are also presented as an accuracy check for the time-dependent model.

  16. Selection bias and subject refusal in a cluster-randomized controlled trial

    Directory of Open Access Journals (Sweden)

    Rochelle Yang

    2017-07-01

    Full Text Available Abstract Background Selection bias and non-participation bias are major methodological concerns which impact external validity. Cluster-randomized controlled trials are especially prone to selection bias as it is impractical to blind clusters to their allocation into intervention or control. This study assessed the impact of selection bias in a large cluster-randomized controlled trial. Methods The Improved Cardiovascular Risk Reduction to Enhance Rural Primary Care (ICARE study examined the impact of a remote pharmacist-led intervention in twelve medical offices. To assess eligibility, a standardized form containing patient demographics and medical information was completed for each screened patient. Eligible patients were approached by the study coordinator for recruitment. Both the study coordinator and the patient were aware of the site’s allocation prior to consent. Patients who consented or declined to participate were compared across control and intervention arms for differing characteristics. Statistical significance was determined using a two-tailed, equal variance t-test and a chi-square test with adjusted Bonferroni p-values. Results were adjusted for random cluster variation. Results There were 2749 completed screening forms returned to research staff with 461 subjects who had either consented or declined participation. Patients with poorly controlled diabetes were found to be significantly more likely to decline participation in intervention sites compared to those in control sites. A higher mean diastolic blood pressure was seen in patients with uncontrolled hypertension who declined in the control sites compared to those who declined in the intervention sites. However, these findings were no longer significant after adjustment for random variation among the sites. After this adjustment, females were now found to be significantly more likely to consent than males (odds ratio = 1.41; 95% confidence interval = 1.03, 1

  17. Type and amount of dietary protein in the treatment of metabolic syndrome: a randomized controlled trial.

    Science.gov (United States)

    Hill, Alison M; Harris Jackson, Kristina A; Roussell, Michael A; West, Sheila G; Kris-Etherton, Penny M

    2015-10-01

    Food-based dietary patterns emphasizing plant protein that were evaluated in the Dietary Approaches to Stop Hypertension (DASH) and OmniHeart trials are recommended for the treatment of metabolic syndrome (MetS). However, the contribution of plant protein to total protein in these diets is proportionally less than that of animal protein. This study compared 3 diets varying in type (animal compared with plant) and amount of protein on MetS criteria. Sixty-two overweight adults with MetS consumed a healthy American diet for 2 wk before being randomly allocated to either a modified DASH diet rich in plant protein (18% protein, two-thirds plant sources, n = 9 males, 12 females), a modified DASH diet rich in animal protein (Beef in an Optimal Lean Diet: 18.4% protein, two-thirds animal sources, n = 9 males, 11 females), or a moderate-protein diet (Beef in an Optimal Lean Diet Plus Protein: 27% protein, two-thirds animal sources, n = 10 males, 11 females). Diets were compared across 3 phases of energy balance: 5 wk of controlled (all foods provided) weight maintenance (WM), 6 wk of controlled weight loss (minimum 500-kcal/d deficit) including exercise (WL), and 12 wk of prescribed, free-living weight loss (FL). The primary endpoint was change in MetS criteria. All groups achieved ∼5% weight loss at the end of the WL phase and maintained it through FL, with no between-diet differences (WM compared with WL, FL, P protein source or amount. Our findings demonstrate that heart-healthy weight-loss dietary patterns that emphasize either animal or plant protein improve MetS criteria similarly. This study was registered at clinicaltrials.gov as NCT00937638. © 2015 American Society for Nutrition.

  18. Cotranslational protein folding reveals the selective use of ...

    Indian Academy of Sciences (India)

    mining factor for CUB in HEGs. In contrast, translational selection pressure is believed to ... genes. Therefore, CUB in LEGs are predominantly deter- mined by mutation pressures such as genome G+C composi- ... date whether nonoptimal codon in the low expression FRQ is under any selection, the frq gene was expressed ...

  19. Randomized controlled trial of a protein substitute with prolonged release on the protein status of children with phenylketonuria.

    Science.gov (United States)

    Giovannini, Marcello; Riva, Enrica; Salvatici, Elisabetta; Cefalo, Graziella; Radaelli, Giovanni

    2014-01-01

    To examine whether a phenylalanine-free protein substitute with prolonged release may be beneficial to the protein status of children with phenylketonuria (PKU) compared to conventional substitutes. Sixty children with PKU, 7 to 16 years of age, were randomly allocated to receive either a prolonged-release (test) or the current conventional protein substitute for 30 days. Subjects were additionally sex and age matched with 60 subjects with mild hyperphenylalaninemia and 60 unaffected subjects. The protein status in children with PKU was assessed by albumin, transthyretin, and retinol-binding protein (RBP), and changes throughout the trial period were the primary outcome measures. Children with PKU did not differ in anthropometry from children with mild hyperphenylalaninemia or unaffected children but they ingested lower amounts of proteins (p substitute for macronutrient intake. Albumin and RBP concentrations were within the age-specific reference range for all children. The rate of protein insufficiency (transthyretin concentration less than 20 mg/dL) did not differ statistically between children receiving test or conventional substitute (recruitment 51.8% vs 53.6%; end of the trial 44.4% vs 50.0%) but mean transthyretin recovered over 20 mg/dL in children who received the test substitute, increasing from 19.1 to 20.7 mg/dL (mean change, 1.6 mg/dL; 95% confidence interval 0.4 to 2.8 mg/dL). In children receiving conventional substitute mean transthyretin changed from 19.0 to 19.2 mg/dL (0.2; -0.2 to 0.6) mg/dL. Protein substitutes with prolonged release might be beneficial to protein status in children with phenylketonuria.

  20. Role of Water in the Selection of Stable Proteins at Ambient and Extreme Thermodynamic Conditions

    Science.gov (United States)

    Bianco, Valentino; Franzese, Giancarlo; Dellago, Christoph; Coluzza, Ivan

    2017-04-01

    Proteins that are functional at ambient conditions do not necessarily work at extreme conditions of temperature T and pressure P . Furthermore, there are limits of T and P above which no protein has a stable functional state. Here, we show that these limits and the selection mechanisms for working proteins depend on how the properties of the surrounding water change with T and P . We find that proteins selected at high T are superstable and are characterized by a nonextreme segregation of a hydrophilic surface and a hydrophobic core. Surprisingly, a larger segregation reduces the stability range in T and P . Our computer simulations, based on a new protein design protocol, explain the hydropathy profile of proteins as a consequence of a selection process influenced by water. Our results, potentially useful for engineering proteins and drugs working far from ambient conditions, offer an alternative rationale to the evolutionary action exerted by the environment in extreme conditions.

  1. Effect of non-random mating on genomic and BLUP selection schemes

    Directory of Open Access Journals (Sweden)

    Nirea Kahsay G

    2012-04-01

    Full Text Available Abstract Background The risk of long-term unequal contribution of mating pairs to the gene pool is that deleterious recessive genes can be expressed. Such consequences could be alleviated by appropriately designing and optimizing breeding schemes i.e. by improving selection and mating procedures. Methods We studied the effect of mating designs, random, minimum coancestry and minimum covariance of ancestral contributions on rate of inbreeding and genetic gain for schemes with different information sources, i.e. sib test or own performance records, different genetic evaluation methods, i.e. BLUP or genomic selection, and different family structures, i.e. factorial or pair-wise. Results Results showed that substantial differences in rates of inbreeding due to mating design were present under schemes with a pair-wise family structure, for which minimum coancestry turned out to be more effective to generate lower rates of inbreeding. Specifically, substantial reductions in rates of inbreeding were observed in schemes using sib test records and BLUP evaluation. However, with a factorial family structure, differences in rates of inbreeding due mating designs were minor. Moreover, non-random mating had only a small effect in breeding schemes that used genomic evaluation, regardless of the information source. Conclusions It was concluded that minimum coancestry remains an efficient mating design when BLUP is used for genetic evaluation or when the size of the population is small, whereas the effect of non-random mating is smaller in schemes using genomic evaluation.

  2. A random protein-creatinine ratio accurately predicts baseline proteinuria in early pregnancy.

    Science.gov (United States)

    Hirshberg, Adi; Draper, Jennifer; Curley, Cara; Sammel, Mary D; Schwartz, Nadav

    2014-12-01

    Data surrounding the use of a random urine protein:creatinine ratio (PCR) in the diagnosis of preeclampsia is conflicting. We sought to determine whether PCR in early pregnancy can replace the 24-hour urine collection as the primary screening test in patients at risk for baseline proteinuria. Women requiring a baseline evaluation for proteinuria supplied a urine sample the morning after their 24-hour collection. The PCR was analyzed as a predictor of significant proteinuria (≥150 mg). A regression equation to estimate the 24-hour protein value from the PCR was then developed. Sixty of 135 subjects enrolled completed the study. The median 24-hour urine protein and PCR were 90 mg (IQR: 50-145) and 0.063 (IQR: 0.039-0.083), respectively. Fifteen patients (25%) had significant proteinuria. PCR was strongly correlated with the 24-hour protein value (r = 0.99, p protein = 46.5 + 904.2*PCR] accurately estimates the actual 24-hour protein (95% CI: ±88 mg). A random urine PCR accurately estimates the 24-hour protein excretion in the first half of pregnancy and can be used as the primary screening test for baseline proteinuria in at-risk patients.

  3. Library of binding protein scaffolds (LibBP): a computational platform for selection of binding protein scaffolds.

    Science.gov (United States)

    Hong, Seungpyo; Kim, Dongsup

    2016-06-01

    Developments in biotechnology have enabled the in vitro evolution of binding proteins. The emerging limitations of antibodies in binding protein engineering have led to suggestions for other proteins as alternative binding protein scaffolds. Most of these proteins were selected based on human intuition rather than systematic analysis of the available data. To improve this strategy, we developed a computational framework for finding desirable binding protein scaffolds by utilizing protein structure and sequence information. For each protein, its structure and the sequences of evolutionarily-related proteins were analyzed, and spatially contiguous regions composed of highly variable residues were identified. A large number of proteins have these regions, but leucine rich repeats (LRRs), histidine kinase domains and immunoglobulin domains are predominant among them. The candidates suggested as new binding protein scaffolds include histidine kinase, LRR, titin and pentapeptide repeat protein. The database and web-service are accessible via http://bcbl.kaist.ac.kr/LibBP CONTACT: kds@kaist.ac.krSupplementary data: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  4. Emulsion PCR: a high efficient way of PCR amplification of random DNA libraries in aptamer selection.

    Directory of Open Access Journals (Sweden)

    Keke Shao

    Full Text Available Aptamers are short RNA or DNA oligonucleotides which can bind with different targets. Typically, they are selected from a large number of random DNA sequence libraries. The main strategy to obtain aptamers is systematic evolution of ligands by exponential enrichment (SELEX. Low efficiency is one of the limitations for conventional PCR amplification of random DNA sequence library in aptamer selection because of relative low products and high by-products formation efficiency. Here, we developed emulsion PCR for aptamer selection. With this method, the by-products formation decreased tremendously to an undetectable level, while the products formation increased significantly. Our results indicated that by-products in conventional PCR amplification were from primer-product and product-product hybridization. In emulsion PCR, we can completely avoid the product-product hybridization and avoid the most of primer-product hybridization if the conditions were optimized. In addition, it also showed that the molecule ratio of template to compartment was crucial to by-product formation efficiency in emulsion PCR amplification. Furthermore, the concentration of the Taq DNA polymerase in the emulsion PCR mixture had a significant impact on product formation efficiency. So, the results of our study indicated that emulsion PCR could improve the efficiency of SELEX.

  5. Controlling the rejection of protein during membrane filtration by adding selected polyelectrolytes

    DEFF Research Database (Denmark)

    Pinelo, Manuel; Ferrer Roca, Carme; Meyer, Anne S.

    2012-01-01

    Electrostatic interactions among the charged groups on proteins and/or between proteins and other solutes significantly affect the aggregation/deposition phenomena that induce fouling and decrease permeate flux during membrane purification of proteins. Such interactions can be turned into an adva...... help enhance the performance of membrane filtration for fractionation/purification of a target protein by significantly reducing fouling and modifying rejection/selectivity....

  6. Influence of biofortification with provitamin A on protein, selected ...

    African Journals Online (AJOL)

    oyaide

    2013-08-21

    Aug 21, 2013 ... Provitamin A-biofortified maize is currently being evaluated for use in the alleviation of vitamin A deficiency. Apart from the differences in provitamin A content, the nutritional composition of provitamin. A-biofortified maize compared to white maize is hardly known. This study aimed to evaluate the protein.

  7. Plasma C-Reactive Protein and Selected Nutritional Indices in ...

    African Journals Online (AJOL)

    Context: Caesarean Section (CS) is a major surgical procedure, often performed when a vaginal delivery is considered unsafe. Objective: This study was carried out to understand the interaction between acute phase proteins and nutritional factors consequent to caesarean section. The knowledge of this interaction is ...

  8. The effects of controlled intake of selected protein foods on ...

    African Journals Online (AJOL)

    ... catfish had more beneficial effects on food intake, anthropometric parameters, blood urea and creatinine levels in NR. It is recommended that low-protein diets containing egg white and fish be offered to patients suffering from early to moderately severe CRF as conservative therapy to ameliorate its symptoms in patients.

  9. Affinity-Guided Oxime Chemistry for Selective Protein Acylation in Live Tissue Systems.

    Science.gov (United States)

    Tamura, Tomonori; Song, Zhining; Amaike, Kazuma; Lee, Shin; Yin, Sifei; Kiyonaka, Shigeki; Hamachi, Itaru

    2017-10-11

    Catalyst-mediated protein modification is a powerful approach for the imaging and engineering of natural proteins. We have previously developed affinity-guided 4-dimethylaminopyridine (AGD) chemistry as an efficient protein modification method using a catalytic acyl transfer reaction. However, because of the high electrophilicity of the thioester acyl donor molecule, AGD chemistry suffers from nonspecific reactions to proteins other than the target protein in crude biological environments, such as cell lysates, live cells, and tissue samples. To overcome this shortcoming, we here report a new acyl donor/organocatalyst system that allows more specific and efficient protein modification. In this method, a highly nucleophilic pyridinium oxime (PyOx) catalyst is conjugated to a ligand specific to the target protein. The ligand-tethered PyOx selectively binds to the target protein and facilitates the acyl transfer reaction of a mild electrophilic N-acyl-N-alkylsulfonamide acyl donor on the protein surface. We demonstrated that the new catalytic system, called AGOX (affinity-guided oxime) chemistry, can modify target proteins, both in test tubes and cell lysates, more selectively and efficiently than AGD chemistry. Low-background fluorescence labeling of the endogenous cell-membrane proteins, carbonic anhydrase XII and the folate receptor, in live cells allowed for the precise quantification of diffusion coefficients in the protein's native environment. Furthermore, the excellent biocompatibility and bioorthogonality of AGOX chemistry were demonstrated by the selective labeling of an endogenous neurotransmitter receptor in mouse brain slices, which are highly complicated tissue samples.

  10. Structural genomics target selection for the New York consortium on membrane protein structure.

    Science.gov (United States)

    Punta, Marco; Love, James; Handelman, Samuel; Hunt, John F; Shapiro, Lawrence; Hendrickson, Wayne A; Rost, Burkhard

    2009-12-01

    The New York Consortium on Membrane Protein Structure (NYCOMPS), a part of the Protein Structure Initiative (PSI) in the USA, has as its mission to establish a high-throughput pipeline for determination of novel integral membrane protein structures. Here we describe our current target selection protocol, which applies structural genomics approaches informed by the collective experience of our team of investigators. We first extract all annotated proteins from our reagent genomes, i.e. the 96 fully sequenced prokaryotic genomes from which we clone DNA. We filter this initial pool of sequences and obtain a list of valid targets. NYCOMPS defines valid targets as those that, among other features, have at least two predicted transmembrane helices, no predicted long disordered regions and, except for community nominated targets, no significant sequence similarity in the predicted transmembrane region to any known protein structure. Proteins that feed our experimental pipeline are selected by defining a protein seed and searching the set of all valid targets for proteins that are likely to have a transmembrane region structurally similar to that of the seed. We require sequence similarity aligning at least half of the predicted transmembrane region of seed and target. Seeds are selected according to their feasibility and/or biological interest, and they include both centrally selected targets and community nominated targets. As of December 2008, over 6,000 targets have been selected and are currently being processed by the experimental pipeline. We discuss how our target list may impact structural coverage of the membrane protein space.

  11. Superoxide dismutase 1 is positively selected to minimize protein aggregation in great apes

    DEFF Research Database (Denmark)

    Dasmeh, Pouria; Kepp, Kasper Planeta

    2017-01-01

    Positive (adaptive) selection has recently been implied in human superoxide dismutase 1 (SOD1), a highly abundant antioxidant protein with energy signaling and antiaging functions, one of very few examples of direct selection on a human protein product (exon); the molecular drivers of this select...... and SOD1 aggregates and triggered by aging. Our study thus marks an example of direct selection for a particular chemical phenotype (high net charge and stability) in a single human protein with possible implications for the evolution of aging.......Positive (adaptive) selection has recently been implied in human superoxide dismutase 1 (SOD1), a highly abundant antioxidant protein with energy signaling and antiaging functions, one of very few examples of direct selection on a human protein product (exon); the molecular drivers...... of this selection are unknown. We mapped 30 extant SOD1 sequences to the recently established mammalian species tree and inferred ancestors, key substitutions, and signatures of selection during the protein's evolution. We detected elevated substitution rates leading to great apes (Hominidae) at ~1 per 2 million...

  12. Positive selection neighboring functionally essential sites and disease-implicated regions of mammalian reproductive proteins.

    LENUS (Irish Health Repository)

    Morgan, Claire C

    2010-01-01

    ABSTRACT: BACKGROUND: Reproductive proteins are central to the continuation of all mammalian species. The evolution of these proteins has been greatly influenced by environmental pressures induced by pathogens, rival sperm, sexual selection and sexual conflict. Positive selection has been demonstrated in many of these proteins with particular focus on primate lineages. However, the mammalia are a diverse group in terms of mating habits, population sizes and germ line generation times. We have examined the selective pressures at work on a number of novel reproductive proteins across a wide variety of mammalia. RESULTS: We show that selective pressures on reproductive proteins are highly varied. Of the 10 genes analyzed in detail, all contain signatures of positive selection either across specific sites or in specific lineages or a combination of both. Our analysis of SP56 and Col1a1 are entirely novel and the results show positively selected sites present in each gene. Our findings for the Col1a1 gene are suggestive of a link between positive selection and severe disease type. We find evidence in our dataset to suggest that interacting proteins are evolving in symphony: most likely to maintain interacting functionality. CONCLUSION: Our in silico analyses show positively selected sites are occurring near catalytically important regions suggesting selective pressure to maximize efficient fertilization. In those cases where a mechanism of protein function is not fully understood, the sites presented here represent ideal candidates for mutational study. This work has highlighted the widespread rate heterogeneity in mutational rates across the mammalia and specifically has shown that the evolution of reproductive proteins is highly varied depending on the species and interacting partners. We have shown that positive selection and disease are closely linked in the Col1a1 gene.

  13. Assessing the accuracy and stability of variable selection methods for random forest modeling in ecology.

    Science.gov (United States)

    Fox, Eric W; Hill, Ryan A; Leibowitz, Scott G; Olsen, Anthony R; Thornbrugh, Darren J; Weber, Marc H

    2017-07-01

    Random forest (RF) modeling has emerged as an important statistical learning method in ecology due to its exceptional predictive performance. However, for large and complex ecological data sets, there is limited guidance on variable selection methods for RF modeling. Typically, either a preselected set of predictor variables are used or stepwise procedures are employed which iteratively remove variables according to their importance measures. This paper investigates the application of variable selection methods to RF models for predicting probable biological stream condition. Our motivating data set consists of the good/poor condition of n = 1365 stream survey sites from the 2008/2009 National Rivers and Stream Assessment, and a large set (p = 212) of landscape features from the StreamCat data set as potential predictors. We compare two types of RF models: a full variable set model with all 212 predictors and a reduced variable set model selected using a backward elimination approach. We assess model accuracy using RF's internal out-of-bag estimate, and a cross-validation procedure with validation folds external to the variable selection process. We also assess the stability of the spatial predictions generated by the RF models to changes in the number of predictors and argue that model selection needs to consider both accuracy and stability. The results suggest that RF modeling is robust to the inclusion of many variables of moderate to low importance. We found no substantial improvement in cross-validated accuracy as a result of variable reduction. Moreover, the backward elimination procedure tended to select too few variables and exhibited numerous issues such as upwardly biased out-of-bag accuracy estimates and instabilities in the spatial predictions. We use simulations to further support and generalize results from the analysis of real data. A main purpose of this work is to elucidate issues of model selection bias and instability to ecologists interested in

  14. Selective acylation of primary amines in peptides and proteins

    NARCIS (Netherlands)

    Abello, N.; Kerstjens, H.A.M.; Postma, D.S; Bischoff, Rainer

    2007-01-01

    N-hydroxysuccinimide (NHS) esters are derivatizing agents that target primary amine groups. However, even a small molar excess of NHS may lead to acylation of hydroxyl-containing amino acids as a side reaction. We report a straightforward method for the selective removal of ester-linked acyl groups

  15. Influence of biofortification with provitamin A on protein, selected ...

    African Journals Online (AJOL)

    oyaide

    2013-08-21

    Aug 21, 2013 ... Eurotium and Penicillum spp.; and pentachlorobenzene agar. (PCNB) for the selective growth of Fusarium spp. (Rabie and. Lübben, 1984). Kernels of each grain type were surface-disinfected by shaking them in a flask of 76% (v/v) ethanol and then rinsing them three times with sterile distilled water.

  16. Random amino acid mutations and protein misfolding lead to Shannon limit in sequence-structure communication.

    Directory of Open Access Journals (Sweden)

    Andreas Martin Lisewski

    2008-09-01

    Full Text Available The transmission of genomic information from coding sequence to protein structure during protein synthesis is subject to stochastic errors. To analyze transmission limits in the presence of spurious errors, Shannon's noisy channel theorem is applied to a communication channel between amino acid sequences and their structures established from a large-scale statistical analysis of protein atomic coordinates. While Shannon's theorem confirms that in close to native conformations information is transmitted with limited error probability, additional random errors in sequence (amino acid substitutions and in structure (structural defects trigger a decrease in communication capacity toward a Shannon limit at 0.010 bits per amino acid symbol at which communication breaks down. In several controls, simulated error rates above a critical threshold and models of unfolded structures always produce capacities below this limiting value. Thus an essential biological system can be realistically modeled as a digital communication channel that is (a sensitive to random errors and (b restricted by a Shannon error limit. This forms a novel basis for predictions consistent with observed rates of defective ribosomal products during protein synthesis, and with the estimated excess of mutual information in protein contact potentials.

  17. Random amino acid mutations and protein misfolding lead to Shannon limit in sequence-structure communication.

    Science.gov (United States)

    Lisewski, Andreas Martin

    2008-09-01

    The transmission of genomic information from coding sequence to protein structure during protein synthesis is subject to stochastic errors. To analyze transmission limits in the presence of spurious errors, Shannon's noisy channel theorem is applied to a communication channel between amino acid sequences and their structures established from a large-scale statistical analysis of protein atomic coordinates. While Shannon's theorem confirms that in close to native conformations information is transmitted with limited error probability, additional random errors in sequence (amino acid substitutions) and in structure (structural defects) trigger a decrease in communication capacity toward a Shannon limit at 0.010 bits per amino acid symbol at which communication breaks down. In several controls, simulated error rates above a critical threshold and models of unfolded structures always produce capacities below this limiting value. Thus an essential biological system can be realistically modeled as a digital communication channel that is (a) sensitive to random errors and (b) restricted by a Shannon error limit. This forms a novel basis for predictions consistent with observed rates of defective ribosomal products during protein synthesis, and with the estimated excess of mutual information in protein contact potentials.

  18. PReFerSim: fast simulation of demography and selection under the Poisson Random Field model.

    Science.gov (United States)

    Ortega-Del Vecchyo, Diego; Marsden, Clare D; Lohmueller, Kirk E

    2016-11-15

    The Poisson Random Field (PRF) model has become an important tool in population genetics to study weakly deleterious genetic variation under complicated demographic scenarios. Currently, there are no freely available software applications that allow simulation of genetic variation data under this model. Here we present PReFerSim, an ANSI C program that performs forward simulations under the PRF model. PReFerSim models changes in population size, arbitrary amounts of inbreeding, dominance and distributions of selective effects. Users can track summaries of genetic variation over time and output trajectories of selected alleles. PReFerSim is freely available at: https://github.com/LohmuellerLab/PReFerSim CONTACT: klohmueller@ucla.eduSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  19. A versatile selection system for folding competent proteins using genetic complementation in a eukaryotic host

    DEFF Research Database (Denmark)

    Lyngsø, C.; Kjaerulff, S.; Muller, S.

    2010-01-01

    -control systems to retain misfolded proteins in the ER and redirect them for cytosolic degradation, thereby only allowing folded proteins to reach the cell surface. Accordingly, the folding potential of the tested protein determines the ability of autotrophic colony growth. This system was successfully......Recombinant expression of native or modified eukaryotic proteins is pivotal for structural and functional studies and for industrial and pharmaceutical production of proteins. However, it is often impeded by the lack of proper folding. Here, we present a stringent and broadly applicable eukaryotic...... in vivo selection system for folded proteins. It is based on genetic complementation of the Schizosaccharomyces pombe growth marker gene invertase fused C-terminally to a protein library. The fusion proteins are directed to the secretion system, utilizing the ability of the eukaryotic protein quality...

  20. Selective oropharyngeal decontamination versus selective digestive decontamination in critically ill patients: a meta-analysis of randomized controlled trials

    Directory of Open Access Journals (Sweden)

    Zhao D

    2015-07-01

    Full Text Available Di Zhao,1,* Jian Song,2,* Xuan Gao,3 Fei Gao,4 Yupeng Wu,2 Yingying Lu,5 Kai Hou1 1Department of Neurosurgery, The First Hospital of Hebei Medical University, 2Department of Neurosurgery, 3Department of Neurology, The Second Hospital of Hebei Medical University, 4Hebei Provincial Procurement Centers for Medical Drugs and Devices, 5Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang People’s Republic of China *These authors contributed equally to this work Background: Selective digestive decontamination (SDD and selective oropharyngeal decontamination (SOD are associated with reduced mortality and infection rates among patients in intensive care units (ICUs; however, whether SOD has a superior effect than SDD remains uncertain. Hence, we conducted a meta-analysis of randomized controlled trials (RCTs to compare SOD with SDD in terms of clinical outcomes and antimicrobial resistance rates in patients who were critically ill. Methods: RCTs published in PubMed, Embase, and Web of Science were systematically reviewed to compare the effects of SOD and SDD in patients who were critically ill. Outcomes included day-28 mortality, length of ICU stay, length of hospital stay, duration of mechanical ventilation, ICU-acquired bacteremia, and prevalence of antibiotic-resistant Gram-negative bacteria. Results were expressed as risk ratio (RR with 95% confidence intervals (CIs, and weighted mean differences (WMDs with 95% CIs. Pooled estimates were performed using a fixed-effects model or random-effects model, depending on the heterogeneity among studies. Results: A total of four RCTs involving 23,822 patients met the inclusion criteria and were included in this meta-analysis. Among patients whose admitting specialty was surgery, cardiothoracic surgery (57.3% and neurosurgery (29.7% were the two main types of surgery being performed. Pooled results showed that SOD had similar effects as SDD in day-28 mortality (RR =1

  1. WSPMaker: a web tool for calculating selection pressure in proteins and domains using window-sliding.

    Science.gov (United States)

    Lee, Yong Seok; Kim, Tae-Hyung; Kang, Tae-Wook; Chung, Won-Hyong; Shin, Gwang-Sik

    2008-12-12

    In the study of adaptive evolution, it is important to detect the protein coding sites where natural selection is acting. In general, the ratio of the rate of non-synonymous substitutions (Ka) to the rate of synonymous substitutions (Ks) is used to estimate either negative or positive selection for an entire gene region of interest. However, since each amino acid in a region has a different function and structure, the type and strength of natural selection may be different for each amino acid. Specifically, domain sites on the protein are indicative of structurally and functionally important sites. Therefore, Window-sliding tools can be used to detect evolutionary forces acting on mutation sites. This paper reports the development of a web-based tool, WSPMaker (Window-sliding Selection pressure Plot Maker), for calculating selection pressures (estimated by Ka/Ks) in the sub-regions of two protein-coding DNA sequences (CDSs). The program uses a sliding window on DNA with a user-defined window length. This enables the investigation of adaptive protein evolution and shows selective constraints of the overall/specific region(s) of two orthologous gene-coding DNA sequences. The method accommodates various evolutionary models and options such as the sliding window size. WSPmaker uses domain information from Pfam HMM models to detect highly conserved residues within orthologous proteins. WSPMaker is a web tool for scanning and calculating selection pressures (estimated by Ka/Ks) in sub-regions of two protein-coding DNA sequences (CDSs).

  2. RSARF: Prediction of residue solvent accessibility from protein sequence using random forest method

    KAUST Repository

    Ganesan, Pugalenthi

    2012-01-01

    Prediction of protein structure from its amino acid sequence is still a challenging problem. The complete physicochemical understanding of protein folding is essential for the accurate structure prediction. Knowledge of residue solvent accessibility gives useful insights into protein structure prediction and function prediction. In this work, we propose a random forest method, RSARF, to predict residue accessible surface area from protein sequence information. The training and testing was performed using 120 proteins containing 22006 residues. For each residue, buried and exposed state was computed using five thresholds (0%, 5%, 10%, 25%, and 50%). The prediction accuracy for 0%, 5%, 10%, 25%, and 50% thresholds are 72.9%, 78.25%, 78.12%, 77.57% and 72.07% respectively. Further, comparison of RSARF with other methods using a benchmark dataset containing 20 proteins shows that our approach is useful for prediction of residue solvent accessibility from protein sequence without using structural information. The RSARF program, datasets and supplementary data are available at http://caps.ncbs.res.in/download/pugal/RSARF/. - See more at: http://www.eurekaselect.com/89216/article#sthash.pwVGFUjq.dpuf

  3. Ethnopharmacological versus random plant selection methods for the evaluation of the antimycobacterial activity

    Directory of Open Access Journals (Sweden)

    Danilo R. Oliveira

    2011-05-01

    Full Text Available The municipality of Oriximiná, Brazil, has 33 quilombola communities in remote areas, endowed with wide experience in the use of medicinal plants. An ethnobotanical survey was carried out in five of these communities. A free-listing method directed for the survey of species locally indicated against Tuberculosis and lung problems was also applied. Data were analyzed by quantitative techniques: saliency index and major use agreement. Thirty four informants related 254 ethnospecies. Among these, 43 were surveyed for possible antimycobacterial activity. As a result of those informations, ten species obtained from the ethnodirected approach (ETHNO and eighteen species obtained from the random approach (RANDOM were assayed against Mycobacterium tuberculosis by the microdilution method, using resazurin as an indicator of cell viability. The best results for antimycobacterial activity were obtained of some plants selected by the ethnopharmacological approach (50% ETHNO x 16,7% RANDOM. These results can be even more significant if we consider that the therapeutic success obtained among the quilombola practice is complex, being the use of some plants acting as fortifying agents, depurative, vomitory, purgative and bitter remedy, especially to infectious diseases, of great importance to the communities in the curing or recovering of health as a whole.

  4. Random forest variable selection in spatial malaria transmission modelling in Mpumalanga Province, South Africa.

    Science.gov (United States)

    Kapwata, Thandi; Gebreslasie, Michael T

    2016-11-16

    Malaria is an environmentally driven disease. In order to quantify the spatial variability of malaria transmission, it is imperative to understand the interactions between environmental variables and malaria epidemiology at a micro-geographic level using a novel statistical approach. The random forest (RF) statistical learning method, a relatively new variable-importance ranking method, measures the variable importance of potentially influential parameters through the percent increase of the mean squared error. As this value increases, so does the relative importance of the associated variable. The principal aim of this study was to create predictive malaria maps generated using the selected variables based on the RF algorithm in the Ehlanzeni District of Mpumalanga Province, South Africa. From the seven environmental variables used [temperature, lag temperature, rainfall, lag rainfall, humidity, altitude, and the normalized difference vegetation index (NDVI)], altitude was identified as the most influential predictor variable due its high selection frequency. It was selected as the top predictor for 4 out of 12 months of the year, followed by NDVI, temperature and lag rainfall, which were each selected twice. The combination of climatic variables that produced the highest prediction accuracy was altitude, NDVI, and temperature. This suggests that these three variables have high predictive capabilities in relation to malaria transmission. Furthermore, it is anticipated that the predictive maps generated from predictions made by the RF algorithm could be used to monitor the progression of malaria and assist in intervention and prevention efforts with respect to malaria.

  5. Random forest variable selection in spatial malaria transmission modelling in Mpumalanga Province, South Africa

    Directory of Open Access Journals (Sweden)

    Thandi Kapwata

    2016-11-01

    Full Text Available Malaria is an environmentally driven disease. In order to quantify the spatial variability of malaria transmission, it is imperative to understand the interactions between environmental variables and malaria epidemiology at a micro-geographic level using a novel statistical approach. The random forest (RF statistical learning method, a relatively new variable-importance ranking method, measures the variable importance of potentially influential parameters through the percent increase of the mean squared error. As this value increases, so does the relative importance of the associated variable. The principal aim of this study was to create predictive malaria maps generated using the selected variables based on the RF algorithm in the Ehlanzeni District of Mpumalanga Province, South Africa. From the seven environmental variables used [temperature, lag temperature, rainfall, lag rainfall, humidity, altitude, and the normalized difference vegetation index (NDVI], altitude was identified as the most influential predictor variable due its high selection frequency. It was selected as the top predictor for 4 out of 12 months of the year, followed by NDVI, temperature and lag rainfall, which were each selected twice. The combination of climatic variables that produced the highest prediction accuracy was altitude, NDVI, and temperature. This suggests that these three variables have high predictive capabilities in relation to malaria transmission. Furthermore, it is anticipated that the predictive maps generated from predictions made by the RF algorithm could be used to monitor the progression of malaria and assist in intervention and prevention efforts with respect to malaria.

  6. Selecting the appropriate pacing mode for patients with sick sinus syndrome: evidence from randomized clinical trials.

    Science.gov (United States)

    Albertsen, A E; Nielsen, J C

    2003-12-01

    Several observational studies have indicated that selection of pacing mode may be important for the clinical outcome in patients with symptomatic bradycardia, affecting the development of atrial fibrillation (AF), thromboembolism, congestive heart failure, mortality and quality of life. In this paper we present and discuss the most recent data from six randomized trials on mode selection in patients with sick sinus syndrome (SSS). In pacing mode selection, VVI(R) pacing is the least attractive solution, increasing the incidence of AF and-as compared with AAI(R) pacing, also the incidence of heart failure, thromboembolism and death. VVI(R) pacing should not be used as the primary pacing mode in patients with SSS, who haven't chronic AF. AAIR pacing is superior to DDDR pacing, reducing AF and preserving left ventricular function. Single site right ventricular pacing-VVI(R) or DDD(R) mode-causes an abnormal ventricular activation and contraction (called ventricular desynchronization), which results in a reduced left ventricular function. Despite the risk of AV block, we consider AAIR pacing to be the optimal pacing mode for isolated SSS today and an algorithm to select patients for AAIR pacing is suggested. Trials on new pacemaker algorithms minimizing right ventricular pacing as well as trials testing alternative pacing sites and multisite pacing to reduce ventricular desynchronization can be expected within the next years.

  7. Geography and genography: prediction of continental origin using randomly selected single nucleotide polymorphisms

    Directory of Open Access Journals (Sweden)

    Ramoni Marco F

    2007-03-01

    Full Text Available Abstract Background Recent studies have shown that when individuals are grouped on the basis of genetic similarity, group membership corresponds closely to continental origin. There has been considerable debate about the implications of these findings in the context of larger debates about race and the extent of genetic variation between groups. Some have argued that clustering according to continental origin demonstrates the existence of significant genetic differences between groups and that these differences may have important implications for differences in health and disease. Others argue that clustering according to continental origin requires the use of large amounts of genetic data or specifically chosen markers and is indicative only of very subtle genetic differences that are unlikely to have biomedical significance. Results We used small numbers of randomly selected single nucleotide polymorphisms (SNPs from the International HapMap Project to train naïve Bayes classifiers for prediction of ancestral continent of origin. Predictive accuracy was tested on two independent data sets. Genetically similar groups should be difficult to distinguish, especially if only a small number of genetic markers are used. The genetic differences between continentally defined groups are sufficiently large that one can accurately predict ancestral continent of origin using only a minute, randomly selected fraction of the genetic variation present in the human genome. Genotype data from only 50 random SNPs was sufficient to predict ancestral continent of origin in our primary test data set with an average accuracy of 95%. Genetic variations informative about ancestry were common and widely distributed throughout the genome. Conclusion Accurate characterization of ancestry is possible using small numbers of randomly selected SNPs. The results presented here show how investigators conducting genetic association studies can use small numbers of arbitrarily

  8. Joint random beam and spectrum selection for spectrum sharing systems with partial channel state information

    KAUST Repository

    Abdallah, Mohamed M.

    2013-11-01

    In this work, we develop joint interference-aware random beam and spectrum selection scheme that provide enhanced performance for the secondary network under the condition that the interference observed at the primary receiver is below a predetermined acceptable value. We consider a secondary link composed of a transmitter equipped with multiple antennas and a single-antenna receiver sharing the same spectrum with a set of primary links composed of a single-antenna transmitter and a single-antenna receiver. The proposed schemes jointly select a beam, among a set of power-optimized random beams, as well as the primary spectrum that maximizes the signal-to-interference-plus-noise ratio (SINR) of the secondary link while satisfying the primary interference constraint. In particular, we consider the case where the interference level is described by a q-bit description of its magnitude, whereby we propose a technique to find the optimal quantizer thresholds in a mean square error (MSE) sense. © 2013 IEEE.

  9. Interference-aware random beam selection schemes for spectrum sharing systems

    KAUST Repository

    Abdallah, Mohamed

    2012-10-19

    Spectrum sharing systems have been recently introduced to alleviate the problem of spectrum scarcity by allowing secondary unlicensed networks to share the spectrum with primary licensed networks under acceptable interference levels to the primary users. In this work, we develop interference-aware random beam selection schemes that provide enhanced performance for the secondary network under the condition that the interference observed by the receivers of the primary network is below a predetermined/acceptable value. We consider a secondary link composed of a transmitter equipped with multiple antennas and a single-antenna receiver sharing the same spectrum with a primary link composed of a single-antenna transmitter and a single-antenna receiver. The proposed schemes select a beam, among a set of power-optimized random beams, that maximizes the signal-to-interference-plus-noise ratio (SINR) of the secondary link while satisfying the primary interference constraint for different levels of feedback information describing the interference level at the primary receiver. For the proposed schemes, we develop a statistical analysis for the SINR statistics as well as the capacity and bit error rate (BER) of the secondary link.

  10. Feature selection for outcome prediction in oesophageal cancer using genetic algorithm and random forest classifier.

    Science.gov (United States)

    Paul, Desbordes; Su, Ruan; Romain, Modzelewski; Sébastien, Vauclin; Pierre, Vera; Isabelle, Gardin

    2017-09-01

    The outcome prediction of patients can greatly help to personalize cancer treatment. A large amount of quantitative features (clinical exams, imaging, …) are potentially useful to assess the patient outcome. The challenge is to choose the most predictive subset of features. In this paper, we propose a new feature selection strategy called GARF (genetic algorithm based on random forest) extracted from positron emission tomography (PET) images and clinical data. The most relevant features, predictive of the therapeutic response or which are prognoses of the patient survival 3 years after the end of treatment, were selected using GARF on a cohort of 65 patients with a local advanced oesophageal cancer eligible for chemo-radiation therapy. The most relevant predictive results were obtained with a subset of 9 features leading to a random forest misclassification rate of 18±4% and an areas under the of receiver operating characteristic (ROC) curves (AUC) of 0.823±0.032. The most relevant prognostic results were obtained with 8 features leading to an error rate of 20±7% and an AUC of 0.750±0.108. Both predictive and prognostic results show better performances using GARF than using 4 other studied methods. Copyright © 2016 Elsevier Ltd. All rights reserved.

  11. Protease-resistant prions selectively decrease Shadoo protein.

    Directory of Open Access Journals (Sweden)

    Joel C Watts

    2011-11-01

    Full Text Available The central event in prion diseases is the conformational conversion of the cellular prion protein (PrP(C into PrP(Sc, a partially protease-resistant and infectious conformer. However, the mechanism by which PrP(Sc causes neuronal dysfunction remains poorly understood. Levels of Shadoo (Sho, a protein that resembles the flexibly disordered N-terminal domain of PrP(C, were found to be reduced in the brains of mice infected with the RML strain of prions [1], implying that Sho levels may reflect the presence of PrP(Sc in the brain. To test this hypothesis, we examined levels of Sho during prion infection using a variety of experimental systems. Sho protein levels were decreased in the brains of mice, hamsters, voles, and sheep infected with different natural and experimental prion strains. Furthermore, Sho levels were decreased in the brains of prion-infected, transgenic mice overexpressing Sho and in infected neuroblastoma cells. Time-course experiments revealed that Sho levels were inversely proportional to levels of protease-resistant PrP(Sc. Membrane anchoring and the N-terminal domain of PrP both influenced the inverse relationship between Sho and PrP(Sc. Although increased Sho levels had no discernible effect on prion replication in mice, we conclude that Sho is the first non-PrP marker specific for prion disease. Additional studies using this paradigm may provide insight into the cellular pathways and systems subverted by PrP(Sc during prion disease.

  12. Artificial membranes with selective nanochannels for protein transport

    KAUST Repository

    Sutisna, B.

    2016-09-05

    A poly(styrene-b-tert-butoxystyrene-b-styrene) copolymer was synthesized by anionic polymerization and hydrolyzed to poly(styrene-b-4-hydroxystyrene-b-styrene). Lamellar morphology was confirmed in the bulk after annealing. Membranes were fabricated by self-assembly of the hydrolyzed copolymer in solution, followed by water induced phase separation. A high density of pores of 4 to 5 nm diameter led to a water permeance of 40 L m−2 h−1 bar−1 and molecular weight cut-off around 8 kg mol−1. The morphology was controlled by tuning the polymer concentration, evaporation time, and the addition of imidazole and pyridine to stabilize the terpolymer micelles in the casting solution via hydrogen bond complexes. Transmission electron microscopy of the membrane cross-sections confirmed the formation of channels with hydroxyl groups beneficial for hydrogen-bond forming sites. The morphology evolution was investigated by time-resolved grazing incidence small angle X-ray scattering experiments. The membrane channels reject polyethylene glycol with a molecular size of 10 kg mol−1, but are permeable to proteins, such as lysozyme (14.3 kg mol−1) and cytochrome c (12.4 kg mol−1), due to the right balance of hydrogen bond interactions along the channels, electrostatic attraction, as well as the right pore sizes. Our results demonstrate that artificial channels can be designed for protein transport via block copolymer self-assembly using classical methods of membrane preparation.

  13. NMR resonance assignment of selectively labeled proteins by the use of paramagnetic ligands

    Energy Technology Data Exchange (ETDEWEB)

    Cutting, Brian; Strauss, Andre; Fendrich, Gabriele; Manley, Paul W.; Jahnke, Wolfgang [Novartis Institutes of Biomedical Research (Switzerland)], E-mail: wolfgang.jahnke@pharma.novartis.com

    2004-10-15

    Selective isotopic labeling of larger proteins greatly simplifies protein NMR spectra and reduces signal overlap, but selectively labeled proteins cannot be easily assigned since the sequential assignment method is not applicable. Here we describe a strategy for resonance assignment in selectively labeled proteins. Our approach involves a spin-labeled analog of a ligand of which the three-dimensional structure in complex with the target protein is known. Other methods for introduction of the spin label are possible. The paramagnetic center causes faster relaxation of all neighboring nuclei in a distance-dependent manner. Measurement of this effect allows to deduce distances between isotopically labeled residues and the paramagnetic center which can be used for resonance assignment. The method is demonstrated for the catalytic domain of Abl kinase in complex with the inhibitor, STI571.

  14. Multimodal chromatography: Characterization of protein binding and selectivity enhancement through mobile phase modulators.

    Science.gov (United States)

    Wolfe, Leslie S; Barringer, Cartney P; Mostafa, Sigma S; Shukla, Abhinav A

    2014-05-02

    The unique selectivity of mixed mode chromatography resins is driving increasing utilization of these novel selectivities into bioprocess applications. There is a need for improved fundamental understanding of protein binding to these stationary phases to enable the development of efficient and robust purification processes. A panel of four monoclonal antibodies and two model proteins were employed to characterize protein interaction with a mixed-mode chromatographic resin comprising a hydrophobic ligand with cation-exchange functionality. Binding of these proteins was studied as a function of salt concentration and pH in the presence of various mobile phase modulators. This knowledge was applied towards screening mobile phase modulators that could selectively decrease host cell protein levels during monoclonal antibody purification. Copyright © 2014 Elsevier B.V. All rights reserved.

  15. The REH theory of protein and nucleic acid divergence - A retrospective update. [Random Evolutionary Hits

    Science.gov (United States)

    Holmquist, R.

    1978-01-01

    The random evolutionary hits (REH) theory of evolutionary divergence, originally proposed in 1972, is restated with attention to certain aspects of the theory that have caused confusion. The theory assumes that natural selection and stochastic processes interact and that natural selection restricts those codon sites which may fix mutations. The predicted total number of fixed nucleotide replacements agrees with data for cytochrome c, a-hemoglobin, beta-hemoglobin, and myoglobin. The restatement analyzes the magnitude of possible sources of errors and simplifies calculational methodology by supplying polynomial expressions to replace tables and graphs.

  16. Protein complexes are under evolutionary selection to assemble via ordered pathways.

    Science.gov (United States)

    Marsh, Joseph A; Hernández, Helena; Hall, Zoe; Ahnert, Sebastian E; Perica, Tina; Robinson, Carol V; Teichmann, Sarah A

    2013-04-11

    Is the order in which proteins assemble into complexes important for biological function? Here, we seek to address this by searching for evidence of evolutionary selection for ordered protein complex assembly. First, we experimentally characterize the assembly pathways of several heteromeric complexes and show that they can be simply predicted from their three-dimensional structures. Then, by mapping gene fusion events identified from fully sequenced genomes onto protein complex assembly pathways, we demonstrate evolutionary selection for conservation of assembly order. Furthermore, using structural and high-throughput interaction data, we show that fusion tends to optimize assembly by simplifying protein complex topologies. Finally, we observe protein structural constraints on the gene order of fusion that impact the potential for fusion to affect assembly. Together, these results reveal the intimate relationships among protein assembly, quaternary structure, and evolution and demonstrate on a genome-wide scale the biological importance of ordered assembly pathways. Copyright © 2013 Elsevier Inc. All rights reserved.

  17. Discovery and Optimization of Sulfonyl Acrylonitriles as Selective, Covalent Inhibitors of Protein Phosphatase Methylesterase-1

    OpenAIRE

    Bachovchin, Daniel A.; Zuhl, Andrea M.; Speers, Anna E.; Wolfe, Monique R.; Weerapana, Eranthie; Brown, Steven J.; Rosen, Hugh; Cravatt, Benjamin F

    2011-01-01

    The serine hydrolase protein phosphatase methylesterase-1 (PME-1) regulates the methylesterification state of protein phosphatase 2A (PP2A) and has been implicated in cancer and Alzheimer's disease. We recently reported a fluorescence polarization-activity-based protein profiling (fluopol-ABPP) high-throughput screen for PME-1 that uncovered a remarkably potent and selective class of aza-β-lactam (ABL) PME-1 inhibitors. Here, we describe a distinct set of sulfonyl acrylonitrile inhibitors tha...

  18. Green fluorescent protein as a visual selection marker for papaya (Carica papaya L.) transformation.

    Science.gov (United States)

    Zhu, Y J; Agbayani, R; Moore, P H

    2004-04-01

    Chemical-based selection for plant transformation is associated with a number of real and perceived problems that might be avoided through visual selection. We have used green fluorescent protein (GFP), as a visual selectable marker to produce transformed papaya ( Carica papaya) plants following microprojectile bombardment of embryogenic callus. GFP selection reduced the selection time from 3 months on a geneticin (G418) antibiotic-containing medium to 3-4 weeks. Moreover, GFP selection increased the number of transformed papaya plants by five-to eightfold compared to selection in the presence of antibiotics. Overall, the use of GFP for selecting transgenic papaya lines improved our throughput for transformation by 15- to 24-fold while avoiding the drawbacks associated with the use of antibiotic resistance-based selection markers.

  19. Versatile selection technology for intracellular protein–protein interactions mediated by a unique bacterial hitchhiker transport mechanism

    Science.gov (United States)

    Waraho, Dujduan; DeLisa, Matthew P.

    2009-01-01

    We have developed a reliable genetic selection strategy for isolating interacting proteins based on the “hitchhiker” mechanism of the Escherichia coli twin-arginine translocation (Tat) pathway. This method, designated FLI-TRAP (functional ligand-binding identification by Tat-based recognition of associating proteins), is based on the unique ability of the Tat system to efficiently cotranslocate noncovalent complexes of 2 folded polypeptides. In the FLI-TRAP assay, the protein to be screened for interactions is engineered with an N-terminal Tat signal peptide, whereas the known or putative partner protein is fused to mature TEM-1 β-lactamase (Bla). Using a series of c-Jun and c-Fos leucine zipper (JunLZ and FosLZ) variants of known affinities, we observed that only those chimeras that expressed well and interacted strongly in the cytoplasm were able to colocalize Bla into the periplasm and confer β-lactam antibiotic resistance to cells. Likewise, the assay was able to efficiently detect interactions between intracellular single-chain Fv (scFv) antibodies and their cognate antigens. The utility of FLI-TRAP was then demonstrated through random library selections of amino acid substitutions that restored (i) heterodimerization to a noninteracting FosLZ variant, and (ii) antigen binding to a low-affinity scFv antibody. Because Tat substrates must be correctly folded before transport, FLI-TRAP favors the identification of soluble, nonaggregating, protease-resistant protein pairs and, thus, provides a powerful tool for routine selection of interacting partners (e.g., antibody-antigen), without the need for purification or immobilization of the binding target. PMID:19234130

  20. Efficient one-cycle affinity selection of binding proteins or peptides specific for a small-molecule using a T7 phage display pool.

    Science.gov (United States)

    Takakusagi, Yoichi; Kuramochi, Kouji; Takagi, Manami; Kusayanagi, Tomoe; Manita, Daisuke; Ozawa, Hiroko; Iwakiri, Kanako; Takakusagi, Kaori; Miyano, Yuka; Nakazaki, Atsuo; Kobayashi, Susumu; Sugawara, Fumio; Sakaguchi, Kengo

    2008-11-15

    Here, we report an efficient one-cycle affinity selection using a natural-protein or random-peptide T7 phage pool for identification of binding proteins or peptides specific for small-molecules. The screening procedure involved a cuvette type 27-MHz quartz-crystal microbalance (QCM) apparatus with introduction of self-assembled monolayer (SAM) for a specific small-molecule immobilization on the gold electrode surface of a sensor chip. Using this apparatus, we attempted an affinity selection of proteins or peptides against synthetic ligand for FK506-binding protein (SLF) or irinotecan (Iri, CPT-11). An affinity selection using SLF-SAM and a natural-protein T7 phage pool successfully detected FK506-binding protein 12 (FKBP12)-displaying T7 phage after an interaction time of only 10 min. Extensive exploration of time-consuming wash and/or elution conditions together with several rounds of selection was not required. Furthermore, in the selection using a 15-mer random-peptide T7 phage pool and subsequent analysis utilizing receptor ligand contact (RELIC) software, a subset of SLF-selected peptides clearly pinpointed several amino-acid residues within the binding site of FKBP12. Likewise, a subset of Iri-selected peptides pinpointed part of the positive amino-acid region of residues from the Iri-binding site of the well-known direct targets, acetylcholinesterase (AChE) and carboxylesterase (CE). Our findings demonstrate the effectiveness of this method and general applicability for a wide range of small-molecules.

  1. Selected reaction monitoring as an effective method for reliable quantification of disease-associated proteins in maple syrup urine disease

    DEFF Research Database (Denmark)

    Fernández-Guerra, Paula; Birkler, Rune I D; Merinero, Begoña

    2014-01-01

    Selected reaction monitoring (SRM) mass spectrometry can quantitatively measure proteins by specific targeting of peptide sequences, and allows the determination of multiple proteins in one single analysis. Here, we show the feasibility of simultaneous measurements of multiple proteins in mitocho...

  2. Selection of locations of knots for linear splines in random regression test-day models.

    Science.gov (United States)

    Jamrozik, J; Bohmanova, J; Schaeffer, L R

    2010-04-01

    Using spline functions (segmented polynomials) in regression models requires the knowledge of the location of the knots. Knots are the points at which independent linear segments are connected. Optimal positions of knots for linear splines of different orders were determined in this study for different scenarios, using existing estimates of covariance functions and an optimization algorithm. The traits considered were test-day milk, fat and protein yields, and somatic cell score (SCS) in the first three lactations of Canadian Holsteins. Two ranges of days in milk (from 5 to 305 and from 5 to 365) were taken into account. In addition, four different populations of Holstein cows, from Australia, Canada, Italy and New Zealand, were examined with respect to first lactation (305 days) milk only. The estimates of genetic and permanent environmental covariance functions were based on single- and multiple-trait test-day models, with Legendre polynomials of order 4 as random regressions. A differential evolution algorithm was applied to find the best location of knots for splines of orders 4 to 7 and the criterion for optimization was the goodness-of-fit of the spline covariance function. Results indicated that the optimal position of knots for linear splines differed between genetic and permanent environmental effects, as well as between traits and lactations. Different populations also exhibited different patterns of optimal knot locations. With linear splines, different positions of knots should therefore be used for different effects and traits in random regression test-day models when analysing milk production traits.

  3. From Extraction of Local Structures of Protein Energy Landscapes to Improved Decoy Selection in Template-Free Protein Structure Prediction

    Directory of Open Access Journals (Sweden)

    Nasrin Akhter

    2018-01-01

    Full Text Available Due to the essential role that the three-dimensional conformation of a protein plays in regulating interactions with molecular partners, wet and dry laboratories seek biologically-active conformations of a protein to decode its function. Computational approaches are gaining prominence due to the labor and cost demands of wet laboratory investigations. Template-free methods can now compute thousands of conformations known as decoys, but selecting native conformations from the generated decoys remains challenging. Repeatedly, research has shown that the protein energy functions whose minima are sought in the generation of decoys are unreliable indicators of nativeness. The prevalent approach ignores energy altogether and clusters decoys by conformational similarity. Complementary recent efforts design protein-specific scoring functions or train machine learning models on labeled decoys. In this paper, we show that an informative consideration of energy can be carried out under the energy landscape view. Specifically, we leverage local structures known as basins in the energy landscape probed by a template-free method. We propose and compare various strategies of basin-based decoy selection that we demonstrate are superior to clustering-based strategies. The presented results point to further directions of research for improving decoy selection, including the ability to properly consider the multiplicity of native conformations of proteins.

  4. VSV-tumor selective replication and protein translation.

    Science.gov (United States)

    Barber, Glen N

    2005-11-21

    The emergence of vesicular stomatatis virus (VSV) as a potent antitumor agent has made a dissection of the molecular determinants of host-cell permissiveness to this virus an important objective. Such insight would not only enable the intelligent design of future generations of recombinant VSV vectors to combat disease, but may also resolve general features of cellular transformation that may be exploited by this virus, and perhaps other oncolytic viruses. The defective pathways underlining the oncolytic activity of VSV remain to be fully determined but recent data indicates that flaws in innate immune responses, involving the interferon (IFN) system, may commonly occur in tumor cells and thus play a large role in facilitating oncolysis. Aside from the IFN system, however, it is almost certain that other key cellular pathways may be similarly defective and therefore cooperatively contribute towards mediating rapid oncolytic virus activity. Recent data have indicated that defects in cancer cell translational regulation could be one area that may be exploited by VSV. Certainly, all viruses require cellular protein synthesis pathways to facilitate their replication and many have devised numerous mechanisms to ensure that viral mRNAs become translated at the expense of the host. Using VSV as a model, this review will discuss some of the recent developments in the fields of innate immunity and translational regulation that may help explain mechanisms of viral oncolysis.

  5. Does the Use of a Decision Aid Improve Decision Making in Prosthetic Heart Valve Selection? A Multicenter Randomized Trial

    NARCIS (Netherlands)

    Korteland, Nelleke M.; Ahmed, Yunus; Koolbergen, David R.; Brouwer, Marjan; de Heer, Frederiek; Kluin, Jolanda; Bruggemans, Eline F.; Klautz, Robert J. M.; Stiggelbout, Anne M.; Bucx, Jeroen J. J.; Roos-Hesselink, Jolien W.; Polak, Peter; Markou, Thanasie; van den Broek, Inge; Ligthart, Rene; Bogers, Ad J. J. C.; Takkenberg, Johanna J. M.

    2017-01-01

    A Dutch online patient decision aid to support prosthetic heart valve selection was recently developed. A multicenter randomized controlled trial was conducted to assess whether use of the patient decision aid results in optimization of shared decision making in prosthetic heart valve selection. In

  6. Protein Ordered Sequences are Formed by Random Joining of Amino Acids in Protein 0th-Order Structure, Followed by Evolutionary Process

    Science.gov (United States)

    Ikehara, Kenji

    2014-12-01

    Only random processes should occur on the primitive Earth. In contrast, many ordered sequences are synthesized according to genetic information on the present Earth. In this communication, I have proposed an idea that protein 0th-order structures or specific amino acid compositions would mediate the transfer from random process to formation of ordered sequences, after formation of double-stranded genes.

  7. Selective outcome reporting and sponsorship in randomized controlled trials in IVF and ICSI.

    Science.gov (United States)

    Braakhekke, M; Scholten, I; Mol, F; Limpens, J; Mol, B W; van der Veen, F

    2017-10-01

    Are randomized controlled trials (RCTs) on IVF and ICSI subject to selective outcome reporting and is this related to sponsorship? There are inconsistencies, independent from sponsorship, in the reporting of primary outcome measures in the majority of IVF and ICSI trials, indicating selective outcome reporting. RCTs are subject to bias at various levels. Of these biases, selective outcome reporting is particularly relevant to IVF and ICSI trials since there is a wide variety of outcome measures to choose from. An established cause of reporting bias is sponsorship. It is, at present, unknown whether RCTs in IVF/ICSI are subject to selective outcome reporting and whether this is related with sponsorship. We systematically searched RCTs on IVF and ICSI published between January 2009 and March 2016 in MEDLINE, EMBASE, the Cochrane Central Register of Controlled Trials and the publisher subset of PubMed. We analysed 415 RCTs. Per included RCT, we extracted data on impact factor of the journal, sample size, power calculation, and trial registry and thereafter data on primary outcome measure, the direction of trial results and sponsorship. Of the 415 identified RCTs, 235 were excluded for our primary analysis, because the sponsorship was not reported. Of the 180 RCTs included in our analysis, 7 trials did not report on any primary outcome measure and 107 of the remaining 173 trials (62%) reported on surrogate primary outcome measures. Of the 114 registered trials, 21 trials (18%) provided primary outcomes in their manuscript that were different from those in the trial registry. This indicates selective outcome reporting. We found no association between selective outcome reporting and sponsorship. We ran additional analyses to include the trials that had not reported sponsorship and found no outcomes that differed from our primary analysis. Since the majority of the trials did not report on sponsorship, there is a risk on sampling bias. IVF and ICSI trials are subject, to

  8. Pneumococcal Predictive Proteins Selected by Microbial Genomic Approach Are Serotype Cross-Reactive and Bind to Host Extracellular Matrix Proteins.

    Science.gov (United States)

    Argondizzo, Ana Paula Corrêa; Rocha-de-Souza, Cláudio Marcos; de Almeida Santiago, Marta; Galler, Ricardo; Reis, Joice Neves; Medeiros, Marco Alberto

    2017-08-01

    Streptococcus pneumoniae is a colonizer of the human nasopharynx, which accounts for most of the community-acquired pneumonia cases and can cause non-invasive and invasive diseases. Current available vaccines are serotype-specific and the use of recombinant proteins associated with virulence is an alternative to compose vaccines and to overcome these problems. In a previous work, we describe the identification of proteins in S. pneumoniae by reverse vaccinology and the genetic diversity of these proteins in clinical isolates. It was possible to purify a half of 20 selected proteins in soluble form. The expression of these proteins on the pneumococcal cells surface was confirmed by flow cytometry. We demonstrated that some of these proteins were able to bind to extracellular matrix proteins and were recognized by sera from patients with pneumococcal meningitis infection caused by several pneumococcal serotypes. In this context, our results suggest that these proteins may play a role in pneumococcal pathogenesis and might be considered as potential vaccine candidates.

  9. Coarsening of protein clusters on subcellular drops exhibits strong and sudden size selectivity

    Science.gov (United States)

    Brown, Aidan; Rutenberg, Andrew

    2015-03-01

    Autophagy is an important process for the degradation of cellular components, with receptor proteins targeting substrates to downstream autophagy machinery. An important question is how receptor protein interactions lead to their selective accumulation on autophagy substrates. Receptor proteins have recently been observed in clusters, raising the possibility that clustering could affect autophagy selectivity. We investigate the clustering dynamics of the autophagy receptor protein NBR1. In addition to standard receptor protein domains, NBR1 has a ``J'' domain that anchors it to membranes, and a coiled-coil domain that enhances self-interaction. We model coarsening clusters of NBR1 on the surfaces of a polydisperse collection of drops, representing organelles. Despite the disconnected nature of the drop surfaces, we recover dynamical scaling of cluster sizes. Significantly, we find that at a well-defined time after coarsening begins, clusters evaporate from smaller drops and grow on larger drops. Thus, coarsening-driven size selection will localize protein clusters to larger substrates, leaving smaller substrates without clusters. This provides a possible physical mechanism for autophagy selectivity, and can explain reports of size selection during peroxisome degradation.

  10. Active classifier selection for RGB-D object categorization using a Markov random field ensemble method

    Science.gov (United States)

    Durner, Maximilian; Márton, Zoltán.; Hillenbrand, Ulrich; Ali, Haider; Kleinsteuber, Martin

    2017-03-01

    In this work, a new ensemble method for the task of category recognition in different environments is presented. The focus is on service robotic perception in an open environment, where the robot's task is to recognize previously unseen objects of predefined categories, based on training on a public dataset. We propose an ensemble learning approach to be able to flexibly combine complementary sources of information (different state-of-the-art descriptors computed on color and depth images), based on a Markov Random Field (MRF). By exploiting its specific characteristics, the MRF ensemble method can also be executed as a Dynamic Classifier Selection (DCS) system. In the experiments, the committee- and topology-dependent performance boost of our ensemble is shown. Despite reduced computational costs and using less information, our strategy performs on the same level as common ensemble approaches. Finally, the impact of large differences between datasets is analyzed.

  11. Clinical outcome of intracytoplasmic injection of spermatozoa morphologically selected under high magnification: a prospective randomized study.

    Science.gov (United States)

    Balaban, Basak; Yakin, Kayhan; Alatas, Cengiz; Oktem, Ozgur; Isiklar, Aycan; Urman, Bulent

    2011-05-01

    Recent evidence shows that the selection of spermatozoa based on the analysis of morphology under high magnification (×6000) may have a positive impact on embryo development in cases with severe male factor infertility and/or previous implantation failures. The objective of this prospective randomized study was to compare the clinical outcome of 87 intracytoplasmic morphologically selected sperm injection (IMSI) cycles with 81 conventional intracytoplasmic sperm injection (ICSI) cycles in an unselected infertile population. IMSI did not provide a significant improvement in the clinical outcome compared with ICSI although there were trends for higher implantation (28.9% versus 19.5%), clinical pregnancy (54.0% versus 44.4%) and live birth rates (43.7% versus 38.3%) in the IMSI group. However, severe male factor patients benefited from the IMSI procedure as shown by significantly higher implantation rates compared with their counterparts in the ICSI group (29.6% versus 15.2%, P=0.01). These results suggest that IMSI may improve IVF success rates in a selected group of patients with male factor infertility. New technological developments enable the real time examination of motile spermatozoa with an inverted light microscope equipped with high-power differential interference contrast optics, enhanced by digital imaging. High magnification (over ×6000) provides the identification of spermatozoa with a normal nucleus and nuclear content. Intracytoplasmic injection of spermatozoa selected according to fine nuclear morphology under high magnification may improve the clinical outcome in cases with severe male factor infertility. Copyright © 2010 Reproductive Healthcare Ltd. Published by Elsevier Ltd. All rights reserved.

  12. A Comparison of Dietary Habits between Recreational Runners and a Randomly Selected Adult Population in Slovenia.

    Science.gov (United States)

    Škof, Branko; Rotovnik Kozjek, Nada

    2015-09-01

    The aim of the study was to compare the dietary habits of recreational runners with those of a random sample of the general population. We also wanted to determine the influence of gender, age and sports performance of recreational runners on their basic diet and compliance with recommendations in sports nutrition. The study population consisted of 1,212 adult Slovenian recreational runners and 774 randomly selected residents of Slovenia between the ages of 18 and 65 years. The data on the dietary habits of our subjects was gathered by means of two questionnaires. The following parameters were evaluated: the type of diet, a food pattern, and the frequency of consumption of individual food groups, the use of dietary supplements, fluid intake, and alcohol consumption. Recreational runners had better compliance with recommendations for healthy nutrition than the general population. This pattern increased with the runner's age and performance level. Compared to male runners, female runners ate more regularly and had a more frequent consumption of food groups associated with a healthy diet (fruit, vegetables, whole grain foods, and low-fat dairy products). The consumption of simple sugars and use of nutritional supplements by well-trained runners was inadequate with values recommended for physically active individuals. Recreational runners are an exemplary population group that actively seeks to adopt a healthier lifestyle.

  13. Specific and selective probes for Staphylococcus aureus from phage-displayed random peptide libraries.

    Science.gov (United States)

    De Plano, Laura M; Carnazza, Santina; Messina, Grazia M L; Rizzo, Maria Giovanna; Marletta, Giovanni; Guglielmino, Salvatore P P

    2017-09-01

    Staphylococcus aureus is a major human pathogen causing health care-associated and community-associated infections. Early diagnosis is essential to prevent disease progression and to reduce complications that can be serious. In this study, we selected, from a 9-mer phage peptide library, a phage clone displaying peptide capable of specific binding to S. aureus cell surface, namely St.au9IVS5 (sequence peptide RVRSAPSSS).The ability of the isolated phage clone to interact specifically with S. aureus and the efficacy of its bacteria-binding properties were established by using enzyme linked immune-sorbent assay (ELISA). We also demonstrated by Western blot analysis that the most reactive and selective phage peptide binds a 78KDa protein on the bacterial cell surface. Furthermore, we observed selectivity of phage-bacteria-binding allowing to identify clinical isolates of S. aureus in comparison with a panel of other bacterial species. In order to explore the possibility of realizing a selective bacteria biosensor device, based on immobilization of affinity-selected phage, we have studied the physisorbed phage deposition onto a mica surface. Atomic Force Microscopy (AFM) was used to determine the organization of phage on mica surface and then the binding performance of mica-physisorbed phage to bacterial target was evaluated during the time by fluorescent microscopy. The system is able to bind specifically about 50% of S. aureus cells after 15' and 90% after one hour. Due to specificity and rapidness, this biosensing strategy paves the way to the further development of new cheap biosensors to be used in developing countries, as lab-on-chip (LOC) to detect bacterial agents in clinical diagnostics applications. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. Radiographic methods used before removal of mandibular third molars among randomly selected general dental clinics.

    Science.gov (United States)

    Matzen, Louise H; Petersen, Lars B; Wenzel, Ann

    2016-01-01

    To assess radiographic methods and diagnostically sufficient images used before removal of mandibular third molars among randomly selected general dental clinics. Furthermore, to assess factors predisposing for an additional radiographic examination. 2 observers visited 18 randomly selected clinics in Denmark and studied patient files, including radiographs of patients who had their mandibular third molar(s) removed. The radiographic unit and type of receptor were registered. A diagnostically sufficient image was defined as the whole tooth and mandibular canal were displayed in the radiograph (yes/no). Overprojection between the tooth and mandibular canal (yes/no) and patient-reported inferior alveolar nerve sensory disturbances (yes/no) were recorded. Regression analyses tested if overprojection between the third molar and the mandibular canal and an insufficient intraoral image predisposed for additional radiographic examination(s). 1500 mandibular third molars had been removed; 1090 had intraoral, 468 had panoramic and 67 had CBCT examination. 1000 teeth were removed after an intraoral examination alone, 433 after panoramic examination and 67 after CBCT examination. 90 teeth had an additional examination after intraoral. Overprojection between the tooth and mandibular canal was a significant factor (p < 0.001, odds ratio = 3.56) for an additional examination. 63.7% of the intraoral images were sufficient and 36.3% were insufficient, with no significant difference between images performed with phosphor plates and solid-state sensors (p = 0.6). An insufficient image predisposed for an additional examination (p = 0.008, odds ratio = 1.8) but was only performed in 11% of the cases. Most mandibular third molars were removed based on an intraoral examination although 36.3% were insufficient.

  15. In vivo protein quality of selected cereal-based staple foods enriched with soybean proteins

    Directory of Open Access Journals (Sweden)

    Laura Acevedo-Pacheco

    2016-10-01

    Full Text Available Background: One way to diminish protein malnutrition in children is by enriching cereal-based flours for the manufacturing of maize tortillas, wheat flour tortillas, and yeast-leavened breads, which are widely consumed among low socio-economic groups. Objective: The aim was to determine and compare the essential amino acid (EAA scores, protein digestibility corrected amino acid scores (PDCAAS, and in vivo protein quality (protein digestibility, protein efficiency ratio (PER, biological values (BV, and net protein utilization (NPU values of regular versus soybean-fortified maize tortillas, yeast-leavened bread, and wheat flour tortillas. Design: To comparatively assess differences in protein quality among maize tortillas, wheat flour tortillas, and yeast-leavened breads, EAA compositions and in vivo studies with weanling rats were performed. The experimental diets based on regular or soybean-fortified food products were compared with a casein-based diet. Food intake, weight gains, PER, dry matter and protein digestibility, BV, NPU, and PDCAAS were assessed. The soybean-fortified tortillas contained 6% of defatted soybean flour, whereas the yeast-leavened bread flour contained 4.5% of soybean concentrate. Results: The soybean-fortified tortillas and bread contained higher amounts of lysine and tryptophan, which improved their EAA scores and PDCAAS. Rats fed diets based on soybean-fortified maize or wheat tortillas gained considerably more weight and had better BV and NPU values compared with counterparts fed with respective regular products. As a result, fortified maize tortillas and wheat flour tortillas improved PER from 0.73 to 1.64 and 0.69 to 1.77, respectively. The PER improvement was not as evident in rats fed the enriched yeast-leavened bread because the formulation contained sugar that decreased lysine availability possibly to Maillard reactions. Conclusions: The proposed enrichment of cereal-based foods with soybean proteins greatly

  16. Coupled selection of protein solubility in E. coli using uroporphyrinogen III methyltransferase as red fluorescent reporter.

    Science.gov (United States)

    Wang, Zhenzhen; Yan, Hanwei; Li, Si; Zhang, Kuanliang; Cheng, Beijiu; Fan, Jun

    2014-09-30

    Uroporphyrinogen III methyltransferase (UMT) is a novel reporter owing to the catalytic products accumulated in cells emitting red florescence. Overexpression of UMT confers resistance of the Escherichia coli cells to potassium tellurite that inhibits cell growth. In this study, we applied UMT reporter for monitoring protein solubility of MBP or TEV protease variants under different expression conditions, as well as 12 maize proteins with either the designed linker or N-terminal SUMO tag. Effects of five enzymes involved in heme and siroheme biosynthesis on the reporter were also investigated. With increasing concentrations of potassium tellurite, colony numbers of the mixed cells expressing the selected five proteins with different solubility were decreased, but colonies displaying red fluorescence was identified to be produced the protein with relatively high solubility. The developed UMT reporter system is sensitive for monitoring protein solubility based on coupled fluorescence and chemical selection. Copyright © 2014 Elsevier B.V. All rights reserved.

  17. Alzheimer Disease Susceptibility Loci: Evidence for a Protein Network under Natural Selection

    Science.gov (United States)

    Raj, Towfique; Shulman, Joshua M.; Keenan, Brendan T.; Chibnik, Lori B.; Evans, Denis A.; Bennett, David A.; Stranger, Barbara E.; De Jager, Philip L.

    2012-01-01

    Recent genome-wide association studies have identified a number of susceptibility loci for Alzheimer disease (AD). To understand the functional consequences and potential interactions of the associated loci, we explored large-scale data sets interrogating the human genome for evidence of positive natural selection. Our findings provide significant evidence for signatures of recent positive selection acting on several haplotypes carrying AD susceptibility alleles; interestingly, the genes found in these selected haplotypes can be assembled, independently, into a molecular complex via a protein-protein interaction (PPI) network approach. These results suggest a possible coevolution of genes encoding physically-interacting proteins that underlie AD susceptibility and are coexpressed in different tissues. In particular, PICALM, BIN1, CD2AP, and EPHA1 are interconnected through multiple interacting proteins and appear to have coordinated evidence of selection in the same human population, suggesting that they may be involved in the execution of a shared molecular function. This observation may be AD-specific, as the 12 loci associated with Parkinson disease do not demonstrate excess evidence of natural selection. The context for selection is probably unrelated to AD itself; it is likely that these genes interact in another context, such as in immune cells, where we observe cis-regulatory effects at several of the selected AD loci. PMID:22482808

  18. Screening and expression of selected taxonomically conserved and unique hypothetical proteins in Burkholderia pseudomallei K96243

    Science.gov (United States)

    Akhir, Nor Azurah Mat; Nadzirin, Nurul; Mohamed, Rahmah; Firdaus-Raih, Mohd

    2015-09-01

    Hypothetical proteins of bacterial pathogens represent a large numbers of novel biological mechanisms which could belong to essential pathways in the bacteria. They lack functional characterizations mainly due to the inability of sequence homology based methods to detect functional relationships in the absence of detectable sequence similarity. The dataset derived from this study showed 550 candidates conserved in genomes that has pathogenicity information and only present in the Burkholderiales order. The dataset has been narrowed down to taxonomic clusters. Ten proteins were selected for ORF amplification, seven of them were successfully amplified, and only four proteins were successfully expressed. These proteins will be great candidates in determining the true function via structural biology.

  19. In vitro Selection and Interaction Studies of a DNA Aptamer Targeting Protein A

    Science.gov (United States)

    Stoltenburg, Regina; Schubert, Thomas; Strehlitz, Beate

    2015-01-01

    A new DNA aptamer targeting Protein A is presented. The aptamer was selected by use of the FluMag-SELEX procedure. The SELEX technology (Systematic Evolution of Ligands by EXponential enrichment) is widely applied as an in vitro selection and amplification method to generate target-specific aptamers and exists in various modified variants. FluMag-SELEX is one of them and is characterized by the use of magnetic beads for target immobilization and fluorescently labeled oligonucleotides for monitoring the aptamer selection progress. Structural investigations and sequence truncation experiments of the selected aptamer for Protein A led to the conclusion, that a stem-loop structure at its 5’-end including the 5’-primer binding site is essential for aptamer-target binding. Extensive interaction analyses between aptamer and Protein A were performed by methods like surface plasmon resonance, MicroScale Thermophoresis and bead-based binding assays using fluorescence measurements. The binding of the aptamer to its target was thus investigated in assays with immobilization of one of the binding partners each, and with both binding partners in solution. Affinity constants were determined in the low micromolar to submicromolar range, increasing to the nanomolar range under the assumption of avidity. Protein A provides more than one binding site for the aptamer, which may overlap with the known binding sites for immunoglobulins. The aptamer binds specifically to both native and recombinant Protein A, but not to other immunoglobulin-binding proteins like Protein G and L. Cross specificity to other proteins was not found. The application of the aptamer is directed to Protein A detection or affinity purification. Moreover, whole cells of Staphylococcus aureus, presenting Protein A on the cell surface, could also be bound by the aptamer. PMID:26221730

  20. The nucleoid protein Dps binds genomic DNA of Escherichia coli in a non-random manner

    Science.gov (United States)

    Kondrashov, F. A.; Toshchakov, S. V.; Dominova, I.; Shvyreva, U. S.; Vrublevskaya, V. V.; Morenkov, O. S.; Panyukov, V. V.

    2017-01-01

    Dps is a multifunctional homododecameric protein that oxidizes Fe2+ ions accumulating them in the form of Fe2O3 within its protein cavity, interacts with DNA tightly condensing bacterial nucleoid upon starvation and performs some other functions. During the last two decades from discovery of this protein, its ferroxidase activity became rather well studied, but the mechanism of Dps interaction with DNA still remains enigmatic. The crucial role of lysine residues in the unstructured N-terminal tails led to the conventional point of view that Dps binds DNA without sequence or structural specificity. However, deletion of dps changed the profile of proteins in starved cells, SELEX screen revealed genomic regions preferentially bound in vitro and certain affinity of Dps for artificial branched molecules was detected by atomic force microscopy. Here we report a non-random distribution of Dps binding sites across the bacterial chromosome in exponentially growing cells and show their enrichment with inverted repeats prone to form secondary structures. We found that the Dps-bound regions overlap with sites occupied by other nucleoid proteins, and contain overrepresented motifs typical for their consensus sequences. Of the two types of genomic domains with extensive protein occupancy, which can be highly expressed or transcriptionally silent only those that are enriched with RNA polymerase molecules were preferentially occupied by Dps. In the dps-null mutant we, therefore, observed a differentially altered expression of several targeted genes and found suppressed transcription from the dps promoter. In most cases this can be explained by the relieved interference with Dps for nucleoid proteins exploiting sequence-specific modes of DNA binding. Thus, protecting bacterial cells from different stresses during exponential growth, Dps can modulate transcriptional integrity of the bacterial chromosome hampering RNA biosynthesis from some genes via competition with RNA polymerase

  1. Nano Random Forests to mine protein complexes and their relationships in quantitative proteomics data.

    Science.gov (United States)

    Montaño-Gutierrez, Luis F; Ohta, Shinya; Kustatscher, Georg; Earnshaw, William C; Rappsilber, Juri

    2017-03-01

    Ever-increasing numbers of quantitative proteomics data sets constitute an underexploited resource for investigating protein function. Multiprotein complexes often follow consistent trends in these experiments, which could provide insights about their biology. Yet, as more experiments are considered, a complex's signature may become conditional and less identifiable. Previously we successfully distinguished the general proteomic signature of genuine chromosomal proteins from hitchhikers using the Random Forests (RF) machine learning algorithm. Here we test whether small protein complexes can define distinguishable signatures of their own, despite the assumption that machine learning needs large training sets. We show, with simulated and real proteomics data, that RF can detect small protein complexes and relationships between them. We identify several complexes in quantitative proteomics results of wild-type and knockout mitotic chromosomes. Other proteins covary strongly with these complexes, suggesting novel functional links for later study. Integrating the RF analysis for several complexes reveals known interdependences among kinetochore subunits and a novel dependence between the inner kinetochore and condensin. Ribosomal proteins, although identified, remained independent of kinetochore subcomplexes. Together these results show that this complex-oriented RF (NanoRF) approach can integrate proteomics data to uncover subtle protein relationships. Our NanoRF pipeline is available online. © 2017 Montaño-Gutierrez et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  2. rMotifGen: random motif generator for DNA and protein sequences

    Directory of Open Access Journals (Sweden)

    Hardin C Timothy

    2007-08-01

    Full Text Available Abstract Background Detection of short, subtle conserved motif regions within a set of related DNA or amino acid sequences can lead to discoveries about important regulatory domains such as transcription factor and DNA binding sites as well as conserved protein domains. In order to help assess motif detection algorithms on motifs with varying properties and levels of conservation, we have developed a computational tool, rMotifGen, with the sole purpose of generating a number of random DNA or protein sequences containing short sequence motifs. Each motif consensus can be user-defined, randomly generated, or created from a position-specific scoring matrix (PSSM. Insertions and mutations within these motifs are created according to user-defined parameters and substitution matrices. The resulting sequences can be helpful in mutational simulations and in testing the limits of motif detection algorithms. Results Two implementations of rMotifGen have been created, one providing a graphical user interface (GUI for random motif construction, and the other serving as a command line interface. The second implementation has the added advantages of platform independence and being able to be called in a batch mode. rMotifGen was used to construct sample sets of sequences containing DNA motifs and amino acid motifs that were then tested against the Gibbs sampler and MEME packages. Conclusion rMotifGen provides an efficient and convenient method for creating random DNA or amino acid sequences with a variable number of motifs, where the instance of each motif can be incorporated using a position-specific scoring matrix (PSSM or by creating an instance mutated from its corresponding consensus using an evolutionary model based on substitution matrices. rMotifGen is freely available at: http://bioinformatics.louisville.edu/brg/rMotifGen/.

  3. Biophysical mimicry of lung surfactant protein B by random nylon-3 copolymers.

    Science.gov (United States)

    Dohm, Michelle T; Mowery, Brendan P; Czyzewski, Ann M; Stahl, Shannon S; Gellman, Samuel H; Barron, Annelise E

    2010-06-16

    Non-natural oligomers have recently shown promise as functional analogues of lung surfactant proteins B and C (SP-B and SP-C), two helical and amphiphilic proteins that are critical for normal respiration. The generation of non-natural mimics of SP-B and SP-C has previously been restricted to step-by-step, sequence-specific synthesis, which results in discrete oligomers that are intended to manifest specific structural attributes. Here we present an alternative approach to SP-B mimicry that is based on sequence-random copolymers containing cationic and lipophilic subunits. These materials, members of the nylon-3 family, are prepared by ring-opening polymerization of beta-lactams. The best of the nylon-3 polymers display promising in vitro surfactant activities in a mixed lipid film. Pulsating bubble surfactometry data indicate that films containing the most surface-active polymers attain adsorptive and dynamic-cycling properties that surpass those of discrete peptides intended to mimic SP-B. Attachment of an N-terminal octadecanoyl unit to the nylon-3 copolymers, inspired by the post-translational modifications found in SP-C, affords further improvements by reducing the percent surface area compression to reach low minimum surface tension. Cytotoxic effects of the copolymers are diminished relative to that of an SP-B-derived peptide and a peptoid-based mimic. The current study provides evidence that sequence-random copolymers can mimic the in vitro surface-active behavior of lung surfactant proteins in a mixed lipid film. These findings raise the possibility that random copolymers might be useful for developing a lung surfactant replacement, which is an attractive prospect given that such polymers are easier to prepare than are sequence-specific oligomers.

  4. Selective blockade of trypanosomatid protein synthesis by a recombinant antibody anti-Trypanosoma cruzi P2β protein.

    Science.gov (United States)

    Ayub, Maximiliano Juri; Nyambega, Benson; Simonetti, Leandro; Duffy, Tomas; Longhi, Silvia A; Gómez, Karina A; Hoebeke, Johan; Levin, Mariano J; Smulski, Cristian R

    2012-01-01

    The ribosomal P proteins are located on the stalk of the ribosomal large subunit and play a critical role during the elongation step of protein synthesis. The single chain recombinant antibody C5 (scFv C5) directed against the C-terminal region of the Trypanosoma cruzi P2β protein (TcP2β) recognizes the conserved C-terminal end of all T. cruzi ribosomal P proteins. Although this region is highly conserved among different species, surface plasmon resonance analysis showed that the scFv C5 possesses very low affinity for the corresponding mammalian epitope, despite having only one single amino-acid change. Crystallographic analysis, in silico modelization and NMR assays support the analysis, increasing our understanding on the structural basis of epitope specificity. In vitro protein synthesis experiments showed that scFv C5 was able to specifically block translation by T. cruzi and Crithidia fasciculata ribosomes, but virtually had no effect on Rattus norvegicus ribosomes. Therefore, we used the scFv C5 coding sequence to make inducible intrabodies in Trypanosoma brucei. Transgenic parasites showed a strong decrease in their growth rate after induction. These results strengthen the importance of the P protein C terminal regions for ribosomal translation activity and suggest that trypanosomatid ribosomal P proteins could be a possible target for selective therapeutic agents that could be derived from structural analysis of the scFv C5 antibody paratope.

  5. Selective blockade of trypanosomatid protein synthesis by a recombinant antibody anti-Trypanosoma cruzi P2β protein.

    Directory of Open Access Journals (Sweden)

    Maximiliano Juri Ayub

    Full Text Available The ribosomal P proteins are located on the stalk of the ribosomal large subunit and play a critical role during the elongation step of protein synthesis. The single chain recombinant antibody C5 (scFv C5 directed against the C-terminal region of the Trypanosoma cruzi P2β protein (TcP2β recognizes the conserved C-terminal end of all T. cruzi ribosomal P proteins. Although this region is highly conserved among different species, surface plasmon resonance analysis showed that the scFv C5 possesses very low affinity for the corresponding mammalian epitope, despite having only one single amino-acid change. Crystallographic analysis, in silico modelization and NMR assays support the analysis, increasing our understanding on the structural basis of epitope specificity. In vitro protein synthesis experiments showed that scFv C5 was able to specifically block translation by T. cruzi and Crithidia fasciculata ribosomes, but virtually had no effect on Rattus norvegicus ribosomes. Therefore, we used the scFv C5 coding sequence to make inducible intrabodies in Trypanosoma brucei. Transgenic parasites showed a strong decrease in their growth rate after induction. These results strengthen the importance of the P protein C terminal regions for ribosomal translation activity and suggest that trypanosomatid ribosomal P proteins could be a possible target for selective therapeutic agents that could be derived from structural analysis of the scFv C5 antibody paratope.

  6. Changing folding and binding stability in a viral coat protein: a comparison between substitutions accessible through mutation and those fixed by natural selection.

    Directory of Open Access Journals (Sweden)

    Craig R Miller

    Full Text Available Previous studies have shown that most random amino acid substitutions destabilize protein folding (i.e. increase the folding free energy. No analogous studies have been carried out for protein-protein binding. Here we use a structure-based model of the major coat protein in a simple virus, bacteriophage φX174, to estimate the free energy of folding of a single coat protein and binding of five coat proteins within a pentameric unit. We confirm and extend previous work in finding that most accessible substitutions destabilize both protein folding and protein-protein binding. We compare the pool of accessible substitutions with those observed among the φX174-like wild phage and in experimental evolution with φX174. We find that observed substitutions have smaller effects on stability than expected by chance. An analysis of adaptations at high temperatures suggests that selection favors either substitutions with no effect on stability or those that simultaneously stabilize protein folding and slightly destabilize protein binding. We speculate that these mutations might involve adjusting the rate of capsid assembly. At normal laboratory temperature there is little evidence of directional selection. Finally, we show that cumulative changes in stability are highly variable; sometimes they are well beyond the bounds of single substitution changes and sometimes they are not. The variation leads us to conclude that phenotype selection acts on more than just stability. Instances of larger cumulative stability change (never via a single substitution despite their availability lead us to conclude that selection views stability at a local, not a global, level.

  7. Changing folding and binding stability in a viral coat protein: a comparison between substitutions accessible through mutation and those fixed by natural selection.

    Science.gov (United States)

    Miller, Craig R; Lee, Kuo Hao; Wichman, Holly A; Ytreberg, F Marty

    2014-01-01

    Previous studies have shown that most random amino acid substitutions destabilize protein folding (i.e. increase the folding free energy). No analogous studies have been carried out for protein-protein binding. Here we use a structure-based model of the major coat protein in a simple virus, bacteriophage φX174, to estimate the free energy of folding of a single coat protein and binding of five coat proteins within a pentameric unit. We confirm and extend previous work in finding that most accessible substitutions destabilize both protein folding and protein-protein binding. We compare the pool of accessible substitutions with those observed among the φX174-like wild phage and in experimental evolution with φX174. We find that observed substitutions have smaller effects on stability than expected by chance. An analysis of adaptations at high temperatures suggests that selection favors either substitutions with no effect on stability or those that simultaneously stabilize protein folding and slightly destabilize protein binding. We speculate that these mutations might involve adjusting the rate of capsid assembly. At normal laboratory temperature there is little evidence of directional selection. Finally, we show that cumulative changes in stability are highly variable; sometimes they are well beyond the bounds of single substitution changes and sometimes they are not. The variation leads us to conclude that phenotype selection acts on more than just stability. Instances of larger cumulative stability change (never via a single substitution despite their availability) lead us to conclude that selection views stability at a local, not a global, level.

  8. BLProt: Prediction of bioluminescent proteins based on support vector machine and relieff feature selection

    KAUST Repository

    Kandaswamy, Krishna Kumar

    2011-08-17

    Background: Bioluminescence is a process in which light is emitted by a living organism. Most creatures that emit light are sea creatures, but some insects, plants, fungi etc, also emit light. The biotechnological application of bioluminescence has become routine and is considered essential for many medical and general technological advances. Identification of bioluminescent proteins is more challenging due to their poor similarity in sequence. So far, no specific method has been reported to identify bioluminescent proteins from primary sequence.Results: In this paper, we propose a novel predictive method that uses a Support Vector Machine (SVM) and physicochemical properties to predict bioluminescent proteins. BLProt was trained using a dataset consisting of 300 bioluminescent proteins and 300 non-bioluminescent proteins, and evaluated by an independent set of 141 bioluminescent proteins and 18202 non-bioluminescent proteins. To identify the most prominent features, we carried out feature selection with three different filter approaches, ReliefF, infogain, and mRMR. We selected five different feature subsets by decreasing the number of features, and the performance of each feature subset was evaluated.Conclusion: BLProt achieves 80% accuracy from training (5 fold cross-validations) and 80.06% accuracy from testing. The performance of BLProt was compared with BLAST and HMM. High prediction accuracy and successful prediction of hypothetical proteins suggests that BLProt can be a useful approach to identify bioluminescent proteins from sequence information, irrespective of their sequence similarity. 2011 Kandaswamy et al; licensee BioMed Central Ltd.

  9. Phenotypic recurrent selection to improve protein quality in non-opaque maize populations

    Directory of Open Access Journals (Sweden)

    Garcia Antonio Augusto Franco

    2002-01-01

    Full Text Available Maize (Zea mays L. protein is considered to be of low quality due to low levels of the essential lysine and tryptophan amino acids. An alternative to solve this problem is to use the opaque-2 gene, which improves the level of these amino acids, but has negative pleiotropic effects on agronomic characters. A phenotypic recurrent selection scheme was carried out in two non-opaque maize populations to verify the possibility of improving their protein quality without using this gene. Four cycles were completed and a 20% selection intensity for tryptophan content in the kernels was used in two populations, IG-1 and IG-2. The original and the four-cycle populations were evaluated in three locations for agronomic traits. For protein and tryptophan content, a separated trial was carried out because plants of the plots were hand-pollinated. No increase in tryptophan content was observed in the IG-2 population, whereas IG-1 presented a small increase (0.70% per cycle. The ratio tryptophan/protein increased 1.26% per cycle in IG-1 and the protein content did not increase in both populations. The ESALQ-VD2-opaque check was superior in relation to both populations for protein quality, as expected, even after completion of four selection cycles. The kernel yield (2.5% per cycle prolificacy, plant and ear heights, decreased with selection cycles, as a correlated response to selection. Phenotypic recurrent selection in non-opaque maize was not able to increase, at reasonable rates, the protein quality of maize kernels.

  10. Effect of Replacing Animal Protein with Plant Protein on Glycemic Control in Diabetes: A Systematic Review and Meta-Analysis of Randomized Controlled Trials

    OpenAIRE

    Effie Viguiliouk; Stewart, Sarah E.; Viranda H Jayalath; Alena Praneet Ng; Arash Mirrahimi; de Souza, Russell J.; Hanley, Anthony J.; Bazinet, Richard P.; Sonia Blanco Mejia; Leiter, Lawrence A; Josse, Robert G.; Kendall, Cyril W. C.; Jenkins, David J.A.; John L Sievenpiper

    2015-01-01

    Previous research on the effect of replacing sources of animal protein with plant protein on glycemic control has been inconsistent. We therefore conducted a systematic review and meta-analysis of randomized controlled trials (RCTs) to assess the effect of this replacement on glycemic control in individuals with diabetes. We searched MEDLINE, EMBASE, and Cochrane databases through 26 August 2015. We included RCTs ? 3-weeks comparing the effect of replacing animal with plant protein on HbA1c, ...

  11. Control group selection in critical care randomized controlled trials evaluating interventional strategies: An ethical assessment.

    Science.gov (United States)

    Silverman, Henry J; Miller, Franklin G

    2004-03-01

    Ethical concern has been raised with critical care randomized controlled trials in which the standard of care reflects a broad range of clinical practices. Commentators have argued that trials without an unrestricted control group, in which standard practices are implemented at the discretion of the attending physician, lack the ability to redefine the standard of care and might expose subjects to excessive harms due to an inability to stop early. To develop a framework for analyzing control group selection for critical care trials. Ethical analysis. A key ethical variable in trial design is the extent with which the control group adequately reflects standard care practices. Such a control group might incorporate either the "unrestricted" practices of physicians or a protocol that specifies and restricts the parameters of standard practices. Control group selection should be determined with respect to the following ethical objectives of trial design: 1) clinical value, 2) scientific validity, 3) efficiency and feasibility, and 4) protection of human subjects. Because these objectives may conflict, control group selection will involve trade-offs and compromises. Trials using a protocolized rather than an unrestricted standard care control group will likely have enhanced validity. However, if the protocolized control group lacks representativeness to standard care practices, then trials that use such groups will offer less clinical value and could provide less assurance of protecting subjects compared with trials that use unrestricted control groups. For trials evaluating contrasting strategies that do not adequately represent standard practices, use of a third group that is more representative of standard practices will enhance clinical value and increase the ability to stop early if needed to protect subjects. These advantages might come at the expense of efficiency and feasibility. Weighing and balancing the competing ethical objectives of trial design should be

  12. Determination of Cell Wall Protein from Selected Feedstuffs and its Relationship with Ruminal Protein Digestibility in Vitro

    Directory of Open Access Journals (Sweden)

    Anuraga Jayanegara

    2016-08-01

    Full Text Available This study was aimed to analyze neutral detergent insoluble crude protein (NDICP and acid detergent insoluble crude protein (ADICP contents of various commonly used forage and concentrate feedstuffs in Indonesia. A number of forages and concentrates, i.e. gliricidia, trichantera, indigofera, calliandra, papaya leaves, cassava leaves, leucaena, rapeseed meal, corn gluten feed, soybean meal, copra meal, palm kernel meal, fish and bone meal and wheat bran were subjected to proximate analysis, cell wall nitrogen determination and in vitro rumen fermentation evaluation. Chemical composition analysis was done in duplicate. The in vitro incubation was conducted in 14 treatments and 3 replicates by following a randomized complete block design. Variables measured after the incubation were total volatile fatty acid (VFA, ammonia, dry matter digestibility (DMD, organic matter digestibility (OMD and crude protein digestibility (CPD. Results revealed that among the forages, cassava leaf had the highest proportion of NDICP while corn gluten feed was the highest among the concentrates. Different from that of NDICP, the highest proportion of ADICP was obtained in papaya leaf and copra meal for the forages and concentrates, respectively. Higher proportion of NDICP tended to decrease CPD (P<0.1. Although higher ADICP apparently tended to decrease CPD as well, the relationship was insignificant due to the higher variation of the dependent variable. It was concluded that cell wall protein proportion in feed may be used as an indicator to determine the quality of protein and its utilization in the rumen.

  13. Extension of the selection of protein chromatography and the rate model to affinity chromatography.

    Science.gov (United States)

    Sandoval, G; Shene, C; Andrews, B A; Asenjo, J A

    2010-01-01

    The rational selection of optimal protein purification sequences, as well as mathematical models that simulate and allow optimization of chromatographic protein purification processes have been developed for purification procedures such as ion-exchange, hydrophobic interaction and gel filtration chromatography. This paper investigates the extension of such analysis to affinity chromatography both in the selection of chromatographic processes and in the use of the rate model for mathematical modelling and simulation. Two affinity systems were used: Blue Sepharose and Protein A. The extension of the theory developed previously for ion-exchange and HIC chromatography to affinity separations is analyzed in this paper. For the selection of operations two algorithms are used. In the first, the value of η, which corresponds to the efficiency (resolution) of the actual chromatography and, Σ, which determines the amount of a particular contaminant eliminated after each separation step, which determines the purity, have to be determined. It was found that the value of both these parameters is not generic for affinity separations but will depend on the type of affinity system used and will have to be determined on a case by case basis. With Blue Sepharose a salt gradient was used and with Protein A, a pH gradient. Parameters were determined with individual proteins and simulations of the protein mixtures were done. This approach allows investigation of chromatographic protein purification in a holistic manner that includes ion-exchange, HIC, gel filtration and affinity separations for the first time. Copyright © 2010 John Wiley & Sons, Ltd.

  14. Widespread Positive Selection Drives Differentiation of Centromeric Proteins in the Drosophila melanogaster subgroup.

    Science.gov (United States)

    Beck, Emily A; Llopart, Ana

    2015-11-25

    Rapid evolution of centromeric satellite repeats is thought to cause compensatory amino acid evolution in interacting centromere-associated kinetochore proteins. Cid, a protein that mediates kinetochore/centromere interactions, displays particularly high amino acid turnover. Rapid evolution of both Cid and centromeric satellite repeats led us to hypothesize that the apparent compensatory evolution may extend to interacting partners in the Condensin I complex (i.e., SMC2, SMC4, Cap-H, Cap-D2, and Cap-G) and HP1s. Missense mutations in these proteins often result in improper centromere formation and aberrant chromosome segregation, thus selection for maintained function and coevolution among proteins of the complex is likely strong. Here, we report evidence of rapid evolution and recurrent positive selection in seven centromere-associated proteins in species of the Drosophila melanogaster subgroup, and further postulate that positive selection on these proteins could be a result of centromere drive and compensatory changes, with kinetochore proteins competing for optimal spindle attachment.

  15. The Epc-N domain: a predicted protein-protein interaction domain found in select chromatin associated proteins

    Directory of Open Access Journals (Sweden)

    Perry Jason

    2006-01-01

    Full Text Available Abstract Background An underlying tenet of the epigenetic code hypothesis is the existence of protein domains that can recognize various chromatin structures. To date, two major candidates have emerged: (i the bromodomain, which can recognize certain acetylation marks and (ii the chromodomain, which can recognize certain methylation marks. Results The Epc-N (Enhancer of Polycomb-N-terminus domain is formally defined herein. This domain is conserved across eukaryotes and is predicted to form a right-handed orthogonal four-helix bundle with extended strands at both termini. The types of amino acid residues that define the Epc-N domain suggest a role in mediating protein-protein interactions, possibly specifically in the context of chromatin binding, and the types of proteins in which it is found (known components of histone acetyltransferase complexes strongly suggest a role in epigenetic structure formation and/or recognition. There appear to be two major Epc-N protein families that can be divided into four unique protein subfamilies. Two of these subfamilies (I and II may be related to one another in that subfamily I can be viewed as a plant-specific expansion of subfamily II. The other two subfamilies (III and IV appear to be related to one another by duplication events in a primordial fungal-metazoan-mycetozoan ancestor. Subfamilies III and IV are further defined by the presence of an evolutionarily conserved five-center-zinc-binding motif in the loop connecting the second and third helices of the four-helix bundle. This motif appears to consist of a PHD followed by a mononuclear Zn knuckle, followed by a PHD-like derivative, and will thus be referred to as the PZPM. All non-Epc-N proteins studied thus far that contain the PZPM have been implicated in histone methylation and/or gene silencing. In addition, an unusual phyletic distribution of Epc-N-containing proteins is observed. Conclusion The data suggest that the Epc-N domain is a protein-protein

  16. A Feature and Algorithm Selection Method for Improving the Prediction of Protein Structural Class.

    Science.gov (United States)

    Ni, Qianwu; Chen, Lei

    2017-01-01

    Correct prediction of protein structural class is beneficial to investigation on protein functions, regulations and interactions. In recent years, several computational methods have been proposed in this regard. However, based on various features, it is still a great challenge to select proper classification algorithm and extract essential features to participate in classification. In this study, a feature and algorithm selection method was presented for improving the accuracy of protein structural class prediction. The amino acid compositions and physiochemical features were adopted to represent features and thirty-eight machine learning algorithms collected in Weka were employed. All features were first analyzed by a feature selection method, minimum redundancy maximum relevance (mRMR), producing a feature list. Then, several feature sets were constructed by adding features in the list one by one. For each feature set, thirtyeight algorithms were executed on a dataset, in which proteins were represented by features in the set. The predicted classes yielded by these algorithms and true class of each protein were collected to construct a dataset, which were analyzed by mRMR method, yielding an algorithm list. From the algorithm list, the algorithm was taken one by one to build an ensemble prediction model. Finally, we selected the ensemble prediction model with the best performance as the optimal ensemble prediction model. Experimental results indicate that the constructed model is much superior to models using single algorithm and other models that only adopt feature selection procedure or algorithm selection procedure. The feature selection procedure or algorithm selection procedure are really helpful for building an ensemble prediction model that can yield a better performance. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  17. Prediction of hot spots in protein interfaces using a random forest model with hybrid features.

    Science.gov (United States)

    Wang, Lin; Liu, Zhi-Ping; Zhang, Xiang-Sun; Chen, Luonan

    2012-03-01

    Prediction of hot spots in protein interfaces provides crucial information for the research on protein-protein interaction and drug design. Existing machine learning methods generally judge whether a given residue is likely to be a hot spot by extracting features only from the target residue. However, hot spots usually form a small cluster of residues which are tightly packed together at the center of protein interface. With this in mind, we present a novel method to extract hybrid features which incorporate a wide range of information of the target residue and its spatially neighboring residues, i.e. the nearest contact residue in the other face (mirror-contact residue) and the nearest contact residue in the same face (intra-contact residue). We provide a novel random forest (RF) model to effectively integrate these hybrid features for predicting hot spots in protein interfaces. Our method can achieve accuracy (ACC) of 82.4% and Matthew's correlation coefficient (MCC) of 0.482 in Alanine Scanning Energetics Database, and ACC of 77.6% and MCC of 0.429 in Binding Interface Database. In a comparison study, performance of our RF model exceeds other existing methods, such as Robetta, FOLDEF, KFC, KFC2, MINERVA and HotPoint. Of our hybrid features, three physicochemical features of target residues (mass, polarizability and isoelectric point), the relative side-chain accessible surface area and the average depth index of mirror-contact residues are found to be the main discriminative features in hot spots prediction. We also confirm that hot spots tend to form large contact surface areas between two interacting proteins. Source data and code are available at: http://www.aporc.org/doc/wiki/HotSpot.

  18. Prediction of subcellular location apoptosis proteins with ensemble classifier and feature selection.

    Science.gov (United States)

    Gu, Quan; Ding, Yong-Sheng; Jiang, Xiao-Ying; Zhang, Tong-Liang

    2010-04-01

    Apoptosis proteins have a central role in the development and the homeostasis of an organism. These proteins are very important for understanding the mechanism of programmed cell death. The function of an apoptosis protein is closely related to its subcellular location. It is crucial to develop powerful tools to predict apoptosis protein locations for rapidly increasing gap between the number of known structural proteins and the number of known sequences in protein databank. In this study, amino acids pair compositions with different spaces are used to construct feature sets for representing sample of protein feature selection approach based on binary particle swarm optimization, which is applied to extract effective feature. Ensemble classifier is used as prediction engine, of which the basic classifier is the fuzzy K-nearest neighbor. Each basic classifier is trained with different feature sets. Two datasets often used in prior works are selected to validate the performance of proposed approach. The results obtained by jackknife test are quite encouraging, indicating that the proposed method might become a potentially useful tool for subcellular location of apoptosis protein, or at least can play a complimentary role to the existing methods in the relevant areas. The supplement information and software written in Matlab are available by contacting the corresponding author.

  19. Superoxide dismutase 1 is positively selected to minimize protein aggregation in great apes.

    Science.gov (United States)

    Dasmeh, Pouria; Kepp, Kasper P

    2017-08-01

    Positive (adaptive) selection has recently been implied in human superoxide dismutase 1 (SOD1), a highly abundant antioxidant protein with energy signaling and antiaging functions, one of very few examples of direct selection on a human protein product (exon); the molecular drivers of this selection are unknown. We mapped 30 extant SOD1 sequences to the recently established mammalian species tree and inferred ancestors, key substitutions, and signatures of selection during the protein's evolution. We detected elevated substitution rates leading to great apes (Hominidae) at ~1 per 2 million years, significantly higher than in other primates and rodents, although these paradoxically generally evolve much faster. The high evolutionary rate was partly due to relaxation of some selection pressures and partly to distinct positive selection of SOD1 in great apes. We then show that higher stability and net charge and changes at the dimer interface were selectively introduced upon separation from old world monkeys and lesser apes (gibbons). Consequently, human, chimpanzee and gorilla SOD1s have a net charge of -6 at physiological pH, whereas the closely related gibbons and macaques have -3. These features consistently point towards selection against the malicious aggregation effects of elevated SOD1 levels in long-living great apes. The findings mirror the impact of human SOD1 mutations that reduce net charge and/or stability and cause ALS, a motor neuron disease characterized by oxidative stress and SOD1 aggregates and triggered by aging. Our study thus marks an example of direct selection for a particular chemical phenotype (high net charge and stability) in a single human protein with possible implications for the evolution of aging.

  20. Moderate alcohol consumption reduces plasma C-reactive protein and fibrinogen levels : a randomized, diet-controlled intervention study

    NARCIS (Netherlands)

    Sierksma, A.; Gaag, M.S. van der; Kluft, C.; Hendriks, H.F.J.

    2002-01-01

    Objective: To evaluate the effect of moderate alcohol consumption on the acute phase proteins C-reactive protein and fibrinogen. Design: Randomized, diet-controlled, cross-over study. Setting: The study was performed at TNO Nutrition and Food Research, Zeist, The Netherlands. Subjects: Ten

  1. A strategy of plasma protein quantitation by selective reaction monitoring of an intact protein.

    Science.gov (United States)

    Ji, Qin C; Rodila, Ramona; Gage, Eric M; El-Shourbagy, Tawakol A

    2003-12-15

    Immunoassays are used extensively in the quantitative analysis of proteins in plasma, urine, and other biological matrixes to support preclinical and clinical studies. Although immunoassays are both sensitive and rapid, difficulties during development of these assays are compounded by the need to have a specific antibody or antigen to the protein of interest. Furthermore, calibration curves of immunoassays are inherently nonlinear, and the technique often detects many structurally related components in addition to the analyte of interest. We have developed a novel strategy of analyzing protein concentrations in plasma by utilizing 96-well solid-phase extraction and LC-MS/MS detection of the intact protein. This strategy has been successfully applied in method development and assay validation of quantitatively analyzing protein rK5 concentrations in monkey plasma samples. Additional techniques such as precolumn regeneration and column heating were also incorporated into the assay. Total run time for each sample was approximately 15 min. An LLOQ of 99.2 ng/mL from a sample volume of 50 microL, corresponding to only 380 fmol (3.97 ng) of the rK5 analyte being injected onto the analytical column (assuming 100% extraction recovery), was obtained. The validated linear dynamic range was between 99.2 and 52 920.0 ng/mL, with a correlation coefficient (r(2)) ranging from 0.9972 and 0.9994. The intraassay CV for this assay was between 0.6 and 3.8%, and the interassay CV was between 1.7 and 3.2%. Interassay mean accuracies were between 101.5 and 104.7%. The assay has proven rugged and specific and has been employed to generate data in support of preclinical studies. This strategy for rK5 assay could be used for the development of bioanalytical assays to provide preclinical and clinical support for other protein drug candidates and, furthermore, for the validation of biomarkers discovered from proteomic research.

  2. Rapid selection of accessible and cleavable sites in RNA by Escherichia coli RNase P and random external guide sequences

    OpenAIRE

    Lundblad, Eirik W.; Xiao, Gaoping; Ko, Jae-hyeong; Altman, Sidney

    2008-01-01

    A method of inhibiting the expression of particular genes by using external guide sequences (EGSs) has been improved in its rapidity and specificity. Random EGSs that have 14-nt random sequences are used in the selection procedure for an EGS that attacks the mRNA for a gene in a particular location. A mixture of the random EGSs, the particular target RNA, and RNase P is used in the diagnostic procedure, which, after completion, is analyzed in a gel with suitable control lanes. Within a few ho...

  3. Affinity chromatographic selection of carbonylated proteins followed by identification of oxidation sites using tandem mass spectrometry.

    Science.gov (United States)

    Mirzaei, Hamid; Regnier, Fred

    2005-04-15

    It has been shown that oxidatively modified forms of proteins accumulate during oxidative stress, aging, and in some age-related diseases. One of the unique features of a wide variety of routes by which proteins are oxidized is the generation of carbonyl groups. This paper reports a method for the isolation of oxidized proteins, which involves (1) biotinylation of oxidized proteins with biotin hydrazide and (2) affinity enrichment using monomeric avidin affinity chromatography columns. The selectivity of the method was validated by adding in vitro oxidized biotinylated BSA to a yeast lysate and showing that the predominant protein recovered was BSA. This method was applied to the question of whether large doses of 2-nitropropane produce oxidized proteins. A study of rat liver homogenates showed that animals dosed with 2-nitropropane produced 17 times more oxidized protein than controls in 6 h. Tryptic digestion of these oxidized proteins followed by reversed-phase chromatography and tandem mass spectrometry led to the identification of 14 peptides and their parent proteins. Nine of the 14 identified peptides were found to carry 1 or 2 oxidation sites and 5 of the 9 peptides were biotinylated. The significance of this affinity method is that it allows the isolation of oxidized proteins from the rest of the proteome and facilitates their identification. In some cases, it is even possible to identify the site of oxidation.

  4. Random regression models for milk, fat and protein in Colombian Buffaloes

    Directory of Open Access Journals (Sweden)

    Naudin Hurtado-Lugo

    2015-01-01

    Full Text Available Objective. Covariance functions for additive genetic and permanent environmental effects and, subsequently, genetic parameters for test-day milk (MY, fat (FY protein (PY yields and mozzarella cheese (MP in buffaloes from Colombia were estimate by using Random regression models (RRM with Legendre polynomials (LP. Materials and Methods. Test-day records of MY, FY, PY and MP from 1884 first lactations of buffalo cows from 228 sires were analyzed. The animals belonged to 14 herds in Colombia between 1995 and 2011. Ten monthly classes of days in milk were considered for test-day yields. The contemporary groups were defined as herd-year-month of milk test-day. Random additive genetic, permanent environmental and residual effects were included in the model. Fixed effects included the contemporary group, linear and quadratic effects of age at calving, and the average lactation curve of the population, which was modeled by third-order LP. Random additive genetic and permanent environmental effects were estimated by RRM using third- to- sixth-order LP. Residual variances were modeled using homogeneous and heterogeneous structures. Results. The heritabilities for MY, FY, PY and MP ranged from 0.38 to 0.05, 0.67 to 0.11, 0.50 to 0.07 and 0.50 to 0.11, respectively. Conclusions. In general, the RRM are adequate to describe the genetic variation in test-day of MY, FY, PY and MP in Colombian buffaloes.

  5. Site‐Selective Disulfide Modification of Proteins: Expanding Diversity beyond the Proteome

    OpenAIRE

    Kuan, Seah Ling; Wang, Tao; Weil, Tanja

    2016-01-01

    Abstract The synthetic transformation of polypeptides with molecular accuracy holds great promise for providing functional and structural diversity beyond the proteome. Consequently, the last decade has seen an exponential growth of site‐directed chemistry to install additional features into peptides and proteins even inside living cells. The disulfide rebridging strategy has emerged as a powerful tool for site‐selective modifications since most proteins contain disulfide bonds. In this Revie...

  6. Enroute to investigating protein dynamics under selective vibrational excitation at the THz FEL FELBE

    Science.gov (United States)

    Bauer, C.; Gensch, M.; Heberle, J.

    2012-05-01

    We aim at investigating proteins under irradiation with intense THz radiation tuned into resonance to specific vibrational modes. This approach is much in analogy to recent experiments that showed selective vibrational control in Complex materials [1, 2, 3]. To achieve the necessary sensitivity for protein dynamics we combine a novel time-resolved IR difference spectroscopic setup with uniquely intense, tuneable narrow bandwidth THz radiation (1.2 - 75 THz) of the free electron laser FELBE.

  7. Strong Selection Significantly Increases Epistatic Interactions in the Long-Term Evolution of a Protein.

    Directory of Open Access Journals (Sweden)

    Aditi Gupta

    2016-03-01

    Full Text Available Epistatic interactions between residues determine a protein's adaptability and shape its evolutionary trajectory. When a protein experiences a changed environment, it is under strong selection to find a peak in the new fitness landscape. It has been shown that strong selection increases epistatic interactions as well as the ruggedness of the fitness landscape, but little is known about how the epistatic interactions change under selection in the long-term evolution of a protein. Here we analyze the evolution of epistasis in the protease of the human immunodeficiency virus type 1 (HIV-1 using protease sequences collected for almost a decade from both treated and untreated patients, to understand how epistasis changes and how those changes impact the long-term evolvability of a protein. We use an information-theoretic proxy for epistasis that quantifies the co-variation between sites, and show that positive information is a necessary (but not sufficient condition that detects epistasis in most cases. We analyze the "fossils" of the evolutionary trajectories of the protein contained in the sequence data, and show that epistasis continues to enrich under strong selection, but not for proteins whose environment is unchanged. The increase in epistasis compensates for the information loss due to sequence variability brought about by treatment, and facilitates adaptation in the increasingly rugged fitness landscape of treatment. While epistasis is thought to enhance evolvability via valley-crossing early-on in adaptation, it can hinder adaptation later when the landscape has turned rugged. However, we find no evidence that the HIV-1 protease has reached its potential for evolution after 9 years of adapting to a drug environment that itself is constantly changing. We suggest that the mechanism of encoding new information into pairwise interactions is central to protein evolution not just in HIV-1 protease, but for any protein adapting to a changing

  8. Selective precipitation of DNA by spermine during the chemical extraction of insoluble cytoplasmic protein.

    Science.gov (United States)

    Choe, W S; Middelberg, A P

    2001-01-01

    The direct chemical extraction of recombinant L1 protein (the major capsid protein of human papillomavirus type 16) from the cytoplasm of E. coli HMS174(DE3) has recently been demonstrated at high cell density (to OD(600) = 160) without the use of reducing agent (1). Coextraction of DNA at high concentration prevents direct coupling to postextraction recovery operations including expanded bed adsorption. In this study, spermine is used to selectively precipitate DNA during chemical extraction. Highly efficient and selective DNA precipitation was achieved. An approximate 10-fold increase in the specific spermine concentration (mg of spermine/mg of DNA) was required to precipitate DNA when 8 M urea was added to the extraction buffer. EDTA (3 mM), required for effective chemical extraction, does not significantly inhibit DNA precipitation. Precipitation selectivity was demonstrated in a bovine serum albumin spiking test, with almost complete recovery of the spiked protein. During studies on the direct extraction of L1 protein from cells at OD(600) = 80, high DNA removal efficiency (>85%) and negligible L1 protein coprecipitation were achieved. This selective precipitation technique simply requires the addition of spermine to the chemical extraction buffer and therefore does not increase technique complexity. This modification enhances the method's general applicability and enables direct coupling to downstream recovery units following chemical extraction at high cell and product concentrations.

  9. An experimental framework for improved selection of binding proteins using SNAP display.

    Science.gov (United States)

    Houlihan, Gillian; Gatti-Lafranconi, Pietro; Kaltenbach, Miriam; Lowe, David; Hollfelder, Florian

    2014-03-01

    Display technologies (e.g. phage and ribosome display) are powerful tools for selecting and evolving protein binders against various target molecules. SNAP display is a DNA display technology that is conducted entirely in vitro: DNA encoding a library of variants is encapsulated in water-in-oil droplets wherein in vitro protein expression and covalent coupling to the encoding DNA occurs. Here, we explore critical factors for the successful performance of SNAP display based on a set of experiments designed to measure and quantify to what extent they affect selection efficiency. We find that, in SNAP display, the reconstituted cell free expression system PURExpress led to 1.5-fold more active protein and achieved 3.5-fold greater DNA recovery in model selections compared to the RTS 100 Escherichia coli lysate based expression system. We report on the influence parameters including droplet occupancy, valency and selection stringency have on recovery and enrichment. An improved procedure involving bivalent display and stringent selection against a model target, Her2, led to a 10(7)-fold enrichment of a DARPin (H10-2-G3, known to bind Her2 with picomolar affinity) over a non-binding DARPin after three rounds of selection. Furthermore, when spiked into a mixture of DARPins with different affinities, DARPin H10-2-G3 outcompeted all other variants demonstrating SNAP display's ability to efficiently resolve clones with affinities in the nano- to picomolar range. These data establish SNAP display as an in vitro protein engineering tool for isolating protein binders and provide a framework for troubleshooting affinity selections. Copyright © 2014 The Authors. Published by Elsevier B.V. All rights reserved.

  10. Validity of protein-osmolality versus protein-creatinine ratios in the estimation of quantitative proteinuria from random samples of urine in children.

    Science.gov (United States)

    Morgenstern, Bruce Z; Butani, Lavjay; Wollan, Peter; Wilson, David M; Larson, Timothy S

    2003-04-01

    Proteinuria is an important marker of kidney disease. Simple methods to determine the presence of proteinuria in a semiquantitative fashion require measurement of either a protein-creatinine or protein-osmolality ratio. Urine samples from 134 healthy infants and children and 150 children from the pediatric nephrology practice were analyzed to develop normative data for protein-osmolality ratios on random urine samples and compare protein-osmolality with protein-creatinine ratio as a predictor of 24-hour urine protein excretion. Children were grouped according to age. Three groups were established: infants (protein excretion was determined to be a protein-osmolality ratio of 0.15 mg x kg H2O/mOsm. L; for children between 2 and 8 years old, 0.14; and for children older than 8 years, 0.17 (P = not significant between age groups). The corresponding optimal cutoff value for protein-creatinine ratio for the entire group of children older than 2 years is 0.20. Area under the curve analysis of receiver operator characteristic curves showed protein-creatinine ratio was superior to protein-osmolality ratio for predicting abnormal amounts of proteinuria in children and adolescents (P protein-creatinine ratio in children, it would be appropriate to screen urine samples for proteinuria using protein-creatinine ratio rather than protein-osmolality ratio.

  11. Magnetic Materials for the Selective Analysis of Peptide and Protein Biomarkers.

    Science.gov (United States)

    Piovesana, Susy; Capriotti, Anna Laura

    2017-01-01

    This mini-review article provides an overview on the use of magnetic materials for the analysis of protein biomarkers. In particular, the advantage provided by magnetic solid phase extraction will be discussed with selected examples, considering untargeted analysis for screening new biomarker proteins and targeted investigation on known and suggested new biomarkers. Aspects, such as enrichment efficiency over conventional techniques, ease of use, functionalization versatility and automation will be considered, together with quantification and deeper structure elucidation provided by coupling selective or specific enrichment to powerful characterization techniques, such as mass spectrometry. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  12. Random genetic drift, natural selection, and noise in human cranial evolution.

    Science.gov (United States)

    Roseman, Charles C

    2016-08-01

    This study assesses the extent to which relationships among groups complicate comparative studies of adaptation in recent human cranial variation and the extent to which departures from neutral additive models of evolution hinder the reconstruction of population relationships among groups using cranial morphology. Using a maximum likelihood evolutionary model fitting approach and a mixed population genomic and cranial data set, I evaluate the relative fits of several widely used models of human cranial evolution. Moreover, I compare the goodness of fit of models of cranial evolution constrained by genomic variation to test hypotheses about population specific departures from neutrality. Models from population genomics are much better fits to cranial variation than are traditional models from comparative human biology. There is not enough evolutionary information in the cranium to reconstruct much of recent human evolution but the influence of population history on cranial variation is strong enough to cause comparative studies of adaptation serious difficulties. Deviations from a model of random genetic drift along a tree-like population history show the importance of environmental effects, gene flow, and/or natural selection on human cranial variation. Moreover, there is a strong signal of the effect of natural selection or an environmental factor on a group of humans from Siberia. The evolution of the human cranium is complex and no one evolutionary process has prevailed at the expense of all others. A holistic unification of phenome, genome, and environmental context, gives us a strong point of purchase on these problems, which is unavailable to any one traditional approach alone. Am J Phys Anthropol 160:582-592, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  13. Luminescent trimethoprim-polyaminocarboxylate lanthanide complex conjugates for selective protein labeling and time-resolved bioassays

    Science.gov (United States)

    Reddy, D. Rajasekhar; Pedró Rosa, Laura E.; Miller, Lawrence W.

    2011-01-01

    Labeling proteins with long-lifetime emitting lanthanide (III) chelate reporters enables sensitive, time-resolved luminescence bioaffinity assays. Heterodimers of trimethoprim (TMP) covalently linked to various cs124-sensitized, polyaminocarboxylate chelates stably retain lanthanide ions and exhibit quantum yields of europium emission up to 20% in water. A time-resolved, luminescence resonance energy transfer (LRET) assay showed that TMP-polyaminocarboxylates bind to Escherichia coli dihydrofolate reductase (eDHFR) fusion proteins with nanomolar affinity in purified solutions and in bacterial lysates. The ability to selectively impart terbium or europium luminescence to fusion proteins in complex physiological mixtures bypasses the need for specific antibodies and simplifies sample preparation. PMID:21619068

  14. CURE-SMOTE algorithm and hybrid algorithm for feature selection and parameter optimization based on random forests.

    Science.gov (United States)

    Ma, Li; Fan, Suohai

    2017-03-14

    The random forests algorithm is a type of classifier with prominent universality, a wide application range, and robustness for avoiding overfitting. But there are still some drawbacks to random forests. Therefore, to improve the performance of random forests, this paper seeks to improve imbalanced data processing, feature selection and parameter optimization. We propose the CURE-SMOTE algorithm for the imbalanced data classification problem. Experiments on imbalanced UCI data reveal that the combination of Clustering Using Representatives (CURE) enhances the original synthetic minority oversampling technique (SMOTE) algorithms effectively compared with the classification results on the original data using random sampling, Borderline-SMOTE1, safe-level SMOTE, C-SMOTE, and k-means-SMOTE. Additionally, the hybrid RF (random forests) algorithm has been proposed for feature selection and parameter optimization, which uses the minimum out of bag (OOB) data error as its objective function. Simulation results on binary and higher-dimensional data indicate that the proposed hybrid RF algorithms, hybrid genetic-random forests algorithm, hybrid particle swarm-random forests algorithm and hybrid fish swarm-random forests algorithm can achieve the minimum OOB error and show the best generalization ability. The training set produced from the proposed CURE-SMOTE algorithm is closer to the original data distribution because it contains minimal noise. Thus, better classification results are produced from this feasible and effective algorithm. Moreover, the hybrid algorithm's F-value, G-mean, AUC and OOB scores demonstrate that they surpass the performance of the original RF algorithm. Hence, this hybrid algorithm provides a new way to perform feature selection and parameter optimization.

  15. The description of protein internal motions aids selection of ligand binding poses by the INPHARMA method

    Energy Technology Data Exchange (ETDEWEB)

    Stauch, Benjamin [European Bioinformatics Institute (EBI) (United Kingdom); Orts, Julien [Eidgenoessische Technische Hochschule (ETH) (Switzerland); Carlomagno, Teresa, E-mail: carlomagno@embl.de [European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit (Germany)

    2012-11-15

    Protein internal motions influence observables of NMR experiments. The effect of internal motions occurring at the sub-nanosecond timescale can be described by NMR order parameters. Here, we report that the use of order parameters derived from Molecular Dynamics (MD) simulations of two holo-structures of Protein Kinase A increase the discrimination power of INPHARMA, an NMR based methodology that selects docked ligand orientations by maximizing the correlation of back-calculated to experimental data. By including internal motion in the back-calculation of the INPHARMA transfer, we obtain a more realistic description of the system, which better represents the experimental data. Furthermore, we propose a set of generic order parameters, derived from MD simulations of globular proteins, which can be used in the back-calculation of INPHARMA NOEs for any protein-ligand complex, thus by-passing the need of obtaining system-specific order parameters for new protein-ligand complexes.

  16. The description of protein internal motions aids selection of ligand binding poses by the INPHARMA method.

    Science.gov (United States)

    Stauch, Benjamin; Orts, Julien; Carlomagno, Teresa

    2012-11-01

    Protein internal motions influence observables of NMR experiments. The effect of internal motions occurring at the sub-nanosecond timescale can be described by NMR order parameters. Here, we report that the use of order parameters derived from Molecular Dynamics (MD) simulations of two holo-structures of Protein Kinase A increase the discrimination power of INPHARMA, an NMR based methodology that selects docked ligand orientations by maximizing the correlation of back-calculated to experimental data. By including internal motion in the back-calculation of the INPHARMA transfer, we obtain a more realistic description of the system, which better represents the experimental data. Furthermore, we propose a set of generic order parameters, derived from MD simulations of globular proteins, which can be used in the back-calculation of INPHARMA NOEs for any protein-ligand complex, thus by-passing the need of obtaining system-specific order parameters for new protein-ligand complexes.

  17. Noise-induced hearing loss in randomly selected New York dairy farmers.

    Science.gov (United States)

    May, J J; Marvel, M; Regan, M; Marvel, L H; Pratt, D S

    1990-01-01

    To understand better the effects of noise levels associated with dairy farming, we randomly selected 49 full-time dairy farmers from an established cohort. Medical and occupational histories were taken and standard audiometric testing was done. Forty-six males (94%) and three females (6%) with a mean age of 43.5 (+/- 13) years and an average of 29.4 (+/- 14) years in farming were tested. Pure Tone Average thresholds (PTA4) at 0.5, 1.0, 2.0, and 3.0 kHz plus High Frequency Average thresholds (HFA3) at 3.0, 4.0, and 6.0 kHz were calculated. Subjects with a loss of greater than or equal to 20 db in either ear were considered abnormal. Eighteen subjects (37%) had abnormal PTA4S and 32 (65%) abnormal HFA3S. The left ear was more severely affected in both groups (p less than or equal to .05, t-test). Significant associations were found between hearing loss and years worked (odds ratio 4.1, r = .53) and age (odds ratio 4.1, r = .59). No association could be found between hearing loss and measles; mumps; previous ear infections; or use of power tools, guns, motorcycles, snowmobiles, or stereo headphones. Our data suggest that among farmers, substantial hearing loss occurs especially in the high-frequency ranges. Presbycusis is an important confounding variable.

  18. Modeling Slotted Aloha as a Stochastic Game with Random Discrete Power Selection Algorithms

    Directory of Open Access Journals (Sweden)

    Rachid El-Azouzi

    2009-01-01

    Full Text Available We consider the uplink case of a cellular system where bufferless mobiles transmit over a common channel to a base station, using the slotted aloha medium access protocol. We study the performance of this system under several power differentiation schemes. Indeed, we consider a random set of selectable transmission powers and further study the impact of priorities given either to new arrival packets or to the backlogged ones. Later, we address a general capture model where a mobile transmits successfully a packet if its instantaneous SINR (signal to interferences plus noise ratio is lager than some fixed threshold. Under this capture model, we analyze both the cooperative team in which a common goal is jointly optimized as well as the noncooperative game problem where mobiles reach to optimize their own objectives. Furthermore, we derive the throughput and the expected delay and use them as the objectives to optimize and provide a stability analysis as alternative study. Exhaustive performance evaluations were carried out, we show that schemes with power differentiation improve significantly the individual as well as global performances, and could eliminate in some cases the bi-stable nature of slotted aloha.

  19. Engineering and rapid selection of a low-affinity glucose/galactose-binding protein for a glucose biosensor.

    Science.gov (United States)

    Amiss, Terry J; Sherman, Douglas B; Nycz, Colleen M; Andaluz, Sandra A; Pitner, J Bruce

    2007-11-01

    Periplasmic expression screening is a selection technique used to enrich high-affinity proteins in Escherichia coli. We report using this screening method to rapidly select a mutated D-glucose/D-galactose-binding protein (GGBP) having low affinity to glucose. Wild-type GGBP has an equilibrium dissociation constant of 0.2 microM and mediates the transport of glucose within the periplasm of E. coli. The protein undergoes a large conformational change on binding glucose and, when labeled with an environmentally sensitive fluorophore, GGBP can relay glucose concentrations, making it of potential interest as a biosensor for diabetics. This use necessitates altering the glucose affinity of GGBP, bringing it into the physiologically relevant range for monitoring glucose in humans (1.7-33 mM). To accomplish this a focused library was constructed using structure-based site-saturation mutagenesis to randomize amino acids in the binding pocket of GGBP at or near direct H-bonding sites and screening the library within the bacterial periplasm. After selection, equilibrium dissociation constants were confirmed by glucose titration and fluorescence monitoring of purified mutants labeled site-specifically at E149C with the fluorophore IANBD (N,N'-dimethyl-N-(iodoacetyl)-N'-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)ethylene-diamine). The screening identified a single mutation A213R that lowers GGBP glucose affinity 5000-fold to 1 mM. Computational modeling suggested the large decrease in affinity was accomplished by the arginine side chain perturbing H-bonding and increasing the entropic barrier to the closed conformation. Overall, these experiments demonstrate the ability of structure-based site-saturation mutagenesis and periplasmic expression screening to discover low-affinity GGBP mutants having potential utility for measuring glucose in humans.

  20. Robust and selective nano cavities for protein separation: an interpenetrating polymer network modified hierarchically protein imprinted hydrogel.

    Science.gov (United States)

    Nematollahzadeh, Ali; Lindemann, Patrick; Sun, Wei; Stute, Jörg; Lütkemeyer, Dirk; Sellergren, Börje

    2014-06-06

    In the present work, we report a novel method for the reinforcement of hierarchically structured molecularly imprinted polymer (MIP) for the separation of human serum albumin (HSA) and immunoglobulin G (IgG) proteins under pressure driven flow conditions. The template proteins (HSA or IgG) were first physically adsorbed at their isoelectric point on the surface of wide pore silica particles. Thereafter, the pore system was filled with a monomer solution and polymerized to form a lightly crosslinked polyacrylamide network covering the protein template. In order to enhance the rigidity of the hydrogels, different type of crosslinkers such as ethylene glycol dimethacrylate (EGDMA), 3,4-dihydroxyphenethylamine (DA) and methylene-bis-acrylamide (MBA), at least partially interpenetrated into the initially made acrylamide base hydrogel leading to formation of an interpenetrating polymer network (IPN). Then the silica matrix was removed to leave highly porous and reinforced MIP. TGA together with FT-IR and TEM analysis supported the interpenetration of the secondary crosslinkers in the initially formed polymer matrix. The compression property of the modified hydrogels as a function of degree of swelling was in the following order: DA>EGDMA>MBA-IPN-modified hydrogel. Batch binding assay verified the capability of the IPN modified MIPs to capture the target proteins. Moreover, solid phase extraction, HPLC and SDS-PAGE revealed that the EGDMA modified MIP could selectively capture and separate the proteins from human serum or fermentation broth. Copyright © 2014 Elsevier B.V. All rights reserved.

  1. ProtASR: An Evolutionary Framework for Ancestral Protein Reconstruction with Selection on Folding Stability.

    Science.gov (United States)

    Arenas, Miguel; Weber, Claudia C; Liberles, David A; Bastolla, Ugo

    2017-11-01

    The computational reconstruction of ancestral proteins provides information on past biological events and has practical implications for biomedicine and biotechnology. Currently available tools for ancestral sequence reconstruction (ASR) are often based on empirical amino acid substitution models that assume that all sites evolve at the same rate and under the same process. However, this assumption is frequently violated because protein evolution is highly heterogeneous due to different selective constraints among sites. Here, we present ProtASR, a new evolutionary framework to infer ancestral protein sequences accounting for selection on protein stability. First, ProtASR generates site-specific substitution matrices through the structurally constrained mean-field (MF) substitution model, which considers both unfolding and misfolding stability. We previously showed that MF models outperform empirical amino acid substitution models, as well as other structurally constrained substitution models, both in terms of likelihood and correctly inferring amino acid distributions across sites. In the second step, ProtASR adapts a well-established maximum-likelihood (ML) ASR procedure to infer ancestral proteins under MF models. A known bias of ML ASR methods is that they tend to overestimate the stability of ancestral proteins by underestimating the frequency of deleterious mutations. We compared ProtASR under MF to two empirical substitution models (JTT and CAT), reconstructing the ancestral sequences of simulated proteins. ProtASR yields reconstructed proteins with less biased stabilities, which are significantly closer to those of the simulated proteins. Analysis of extant protein families suggests that folding stability evolves through time across protein families, potentially reflecting neutral fluctuation. Some families exhibit a more constant protein folding stability, while others are more variable. ProtASR is freely available from https

  2. The prevalence of symptoms associated with pulmonary tuberculosis in randomly selected children from a high burden community

    OpenAIRE

    Marais, B.; Obihara, C; Gie, R.; Schaaf, H; Hesseling, A.; Lombard, C.; Enarson, D; Bateman, E; Beyers, N

    2005-01-01

    Background: Diagnosis of childhood tuberculosis is problematic and symptom based diagnostic approaches are often promoted in high burden settings. This study aimed (i) to document the prevalence of symptoms associated with tuberculosis among randomly selected children living in a high burden community, and (ii) to compare the prevalence of these symptoms in children without tuberculosis to those in children with newly diagnosed tuberculosis.

  3. Automation of specimen selection and data acquisition for protein electron crystallography

    NARCIS (Netherlands)

    Oostergetel, G.T.; Keegstra, W.; Brisson, A.D R

    A system is presented for semi-automatic specimen selection and data acquisition for protein electron crystallography, based on a slow-scan CCD camera connected to a transmission electron microscope and control from an external computer. Areas of interest on the specimen are localised at low

  4. Automatic selection of reference taxa for protein–protein interaction prediction with phylogenetic profiling

    DEFF Research Database (Denmark)

    Simonsen, Martin; Maetschke, Stefan R.; Ragan, Mark A

    2012-01-01

    : We present three novel methods for automating the selection of RT, using machine learning based on known protein–protein interaction networks. One of these methods in particular, Tree-Based Search, yields greatly improved prediction accuracies. We further show that different methods for constituting...

  5. Detection of G protein-selective G protein-coupled receptor (GPCR) conformations in live cells.

    Science.gov (United States)

    Malik, Rabia U; Ritt, Michael; DeVree, Brian T; Neubig, Richard R; Sunahara, Roger K; Sivaramakrishnan, Sivaraj

    2013-06-14

    Although several recent studies have reported that GPCRs adopt multiple conformations, it remains unclear how subtle conformational changes are translated into divergent downstream responses. In this study, we report on a novel class of FRET-based sensors that can detect the ligand/mutagenic stabilization of GPCR conformations that promote interactions with G proteins in live cells. These sensors rely on the well characterized interaction between a GPCR and the C terminus of a Gα subunit. We use these sensors to elucidate the influence of the highly conserved (E/D)RY motif on GPCR conformation. Specifically, Glu/Asp but not Arg mutants of the (E/D)RY motif are known to enhance basal GPCR signaling. Hence, it is unclear whether ionic interactions formed by the (E/D)RY motif (ionic lock) are necessary to stabilize basal GPCR states. We find that mutagenesis of the β2-AR (E/D)RY ionic lock enhances interaction with Gs. However, only Glu/Asp but not Arg mutants increase G protein activation. In contrast, mutagenesis of the opsin (E/D)RY ionic lock does not alter its interaction with transducin. Instead, opsin-specific ionic interactions centered on residue Lys-296 are both necessary and sufficient to promote interactions with transducin. Effective suppression of β2-AR basal activity by inverse agonist ICI 118,551 requires ionic interactions formed by the (E/D)RY motif. In contrast, the inverse agonist metoprolol suppresses interactions with Gs and promotes Gi binding, with concomitant pertussis toxin-sensitive inhibition of adenylyl cyclase activity. Taken together, these studies validate the use of the new FRET sensors while revealing distinct structural mechanisms for ligand-dependent GPCR function.

  6. Selective ligand recognition by a diversity-generating retroelement variable protein.

    Directory of Open Access Journals (Sweden)

    Jason L Miller

    2008-06-01

    Full Text Available Diversity-generating retroelements (DGRs recognize novel ligands through massive protein sequence variation, a property shared uniquely with the adaptive immune response. Little is known about how recognition is achieved by DGR variable proteins. Here, we present the structure of the Bordetella bacteriophage DGR variable protein major tropism determinant (Mtd bound to the receptor pertactin, revealing remarkable adaptability in the static binding sites of Mtd. Despite large dissimilarities in ligand binding mode, principles underlying selective recognition were strikingly conserved between Mtd and immunoreceptors. Central to this was the differential amplification of binding strengths by avidity (i.e., multivalency, which not only relaxed the demand for optimal complementarity between Mtd and pertactin but also enhanced distinctions among binding events to provide selectivity. A quantitatively similar balance between complementarity and avidity was observed for Bordetella bacteriophage DGR as occurs in the immune system, suggesting that variable repertoires operate under a narrow set of conditions to recognize novel ligands.

  7. Stoichiometric and irreversible cysteine-selective protein modification using carbonylacrylic reagents

    Science.gov (United States)

    Bernardim, Barbara; Cal, Pedro M. S. D.; Matos, Maria J.; Oliveira, Bruno L.; Martínez-Sáez, Nuria; Albuquerque, Inês S.; Perkins, Elizabeth; Corzana, Francisco; Burtoloso, Antonio C. B.; Jiménez-Osés, Gonzalo; Bernardes, Gonçalo J. L.

    2016-10-01

    Maleimides remain the reagents of choice for the preparation of therapeutic and imaging protein conjugates despite the known instability of the resulting products that undergo thiol-exchange reactions in vivo. Here we present the rational design of carbonylacrylic reagents for chemoselective cysteine bioconjugation. These reagents undergo rapid thiol Michael-addition under biocompatible conditions in stoichiometric amounts. When using carbonylacrylic reagents equipped with PEG or fluorophore moieties, this method enables access to protein and antibody conjugates precisely modified at pre-determined sites. Importantly, the conjugates formed are resistant to degradation in plasma and are biologically functional, as demonstrated by the selective imaging and detection of apoptotic and HER2+ cells, respectively. The straightforward preparation, stoichiometric use and exquisite cysteine selectivity of the carbonylacrylic reagents combined with the stability of the products and the availability of biologically relevant cysteine-tagged proteins make this method suitable for the routine preparation of chemically defined conjugates for in vivo applications.

  8. Structural Basis for Receptor Activity-Modifying Protein-Dependent Selective Peptide Recognition by a G Protein-Coupled Receptor.

    Science.gov (United States)

    Booe, Jason M; Walker, Christopher S; Barwell, James; Kuteyi, Gabriel; Simms, John; Jamaluddin, Muhammad A; Warner, Margaret L; Bill, Roslyn M; Harris, Paul W; Brimble, Margaret A; Poyner, David R; Hay, Debbie L; Pioszak, Augen A

    2015-06-18

    Association of receptor activity-modifying proteins (RAMP1-3) with the G protein-coupled receptor (GPCR) calcitonin receptor-like receptor (CLR) enables selective recognition of the peptides calcitonin gene-related peptide (CGRP) and adrenomedullin (AM) that have diverse functions in the cardiovascular and lymphatic systems. How peptides selectively bind GPCR:RAMP complexes is unknown. We report crystal structures of CGRP analog-bound CLR:RAMP1 and AM-bound CLR:RAMP2 extracellular domain heterodimers at 2.5 and 1.8 Å resolutions, respectively. The peptides similarly occupy a shared binding site on CLR with conformations characterized by a β-turn structure near their C termini rather than the α-helical structure common to peptides that bind related GPCRs. The RAMPs augment the binding site with distinct contacts to the variable C-terminal peptide residues and elicit subtly different CLR conformations. The structures and accompanying pharmacology data reveal how a class of accessory membrane proteins modulate ligand binding of a GPCR and may inform drug development targeting CLR:RAMP complexes. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  9. Rapid selection of accessible and cleavable sites in RNA by Escherichia coli RNase P and random external guide sequences.

    Science.gov (United States)

    Lundblad, Eirik W; Xiao, Gaoping; Ko, Jae-Hyeong; Altman, Sidney

    2008-02-19

    A method of inhibiting the expression of particular genes by using external guide sequences (EGSs) has been improved in its rapidity and specificity. Random EGSs that have 14-nt random sequences are used in the selection procedure for an EGS that attacks the mRNA for a gene in a particular location. A mixture of the random EGSs, the particular target RNA, and RNase P is used in the diagnostic procedure, which, after completion, is analyzed in a gel with suitable control lanes. Within a few hours, the procedure is complete. The action of EGSs designed by an older method is compared with EGSs designed by the random EGS method on mRNAs from two bacterial pathogens.

  10. Digestibility of protein and amino acids in selected foods as determined by a rat balance method.

    Science.gov (United States)

    Sarwar, G; Peace, R W; Botting, H G; Brulé, D

    1989-01-01

    Values (%) for true digestibility of crude protein and individual amino acids in 20 selected foods were determined by the rat balance (fecal) method. The products were fed as the sole source of protein in diets containing 8% crude protein (N x 6.25). Lowest true protein digestibility values (79-84) were obtained for pinto beans, kidney beans and lentils; intermediate values (89-92) were obtained for chick peas, beef stew, skim milk (over heated), rolled oats, whole wheat cereal, and pea protein concentrate; and highest values (94-100) were obtained for sausage, macaroni-cheese, rice-wheat gluten cereal, skim milk, tuna, soy isolate, peanut butter, chicken frankfurters, beef salami, casein and casein + methionine. In animal foods, peanut butter and soy isolate, the differences between true digestibility of crude protein and most individual amino acids were less than 5%. However, the values for true digestibility of methionine and cystine were up to 44% lower than those of crude protein in pinto beans, kidney beans, lentils, chick peas and pea concentrate. In these legumes, digestibility of crude protein was not a good predictor of digestibility of the limiting amino acids.

  11. Identification of bacteriophage virion proteins by the ANOVA feature selection and analysis.

    Science.gov (United States)

    Ding, Hui; Feng, Peng-Mian; Chen, Wei; Lin, Hao

    2014-08-01

    The bacteriophage virion proteins play extremely important roles in the fate of host bacterial cells. Accurate identification of bacteriophage virion proteins is very important for understanding their functions and clarifying the lysis mechanism of bacterial cells. In this study, a new sequence-based method was developed to identify phage virion proteins. In the new method, the protein sequences were initially formulated by the g-gap dipeptide compositions. Subsequently, the analysis of variance (ANOVA) with incremental feature selection (IFS) was used to search for the optimal feature set. It was observed that, in jackknife cross-validation, the optimal feature set including 160 optimized features can produce the maximum accuracy of 85.02%. By performing feature analysis, we found that the correlation between two amino acids with one gap was more important than other correlations for phage virion protein prediction and that some of the 1-gap dipeptides were important and mainly contributed to the virion protein prediction. This analysis will provide novel insights into the function of phage virion proteins. On the basis of the proposed method, an online web-server, PVPred, was established and can be freely accessed from the website (http://lin.uestc.edu.cn/server/PVPred). We believe that the PVPred will become a powerful tool to study phage virion proteins and to guide the related experimental validations.

  12. Improving Antigenicity of the Recombinant Hepatitis C Virus Core Protein via Random Mutagenesis

    Directory of Open Access Journals (Sweden)

    Chen-Ji Huang

    2011-01-01

    Full Text Available In order to enhance the sensitivity of diagnosis, a recombinant clone containing domain I of HCV core (amino acid residues 1 to 123 was subjected to random mutagenesis. Five mutants with higher sensitivity were obtained by colony screening of 616 mutants using reverse ELISA. Sequence analysis of these mutants revealed alterations focusing on W84, P95, P110, or V129. The inclusion bodies of these recombinant proteins overexpressed in E. coli BL21(DE3 were subsequently dissolved using 6 M urea and then refolded by stepwise dialysis. Compared to the unfolded wild-type antigen, the refolded M3b antigen (W84S, P110S and V129L exhibited an increase of 66% antigenicity with binding capacity of 0.96 and affinity of 113 μM−1. Moreover, the 33% decrease of the production demand suggests that M3b is a potential substitute for anti-HCV antibody detection.

  13. Highly Selective Fluorescent Sensing of Proteins Based on a Fluorescent Molecularly Imprinted Nanosensor

    Directory of Open Access Journals (Sweden)

    Shuo Wang

    2013-09-01

    Full Text Available A fluorescent molecularly imprinted nanosensor was obtained by grafting imprinted polymer onto the surface of multi-wall carbon nanotubes and post-imprinting treatment with fluorescein isothiocyanate (FITC. The fluorescence of lysozyme-imprinted polymer (Lys-MIP was quenched more strongly by Lys than that of nonimprinted polymer (NIP, which indicated that the Lys-MIP could recognize Lys. The resulted imprinted material has the ability to selectively sense a target protein, and an imprinting factor of 3.34 was achieved. The Lys-MIP also showed selective detection for Lys among other proteins such as cytochrome C (Cyt C, hemoglobin (HB and bovine serum albumin (BSA due to the imprinted sites in the Lys-MIP. This approach combines the high selectivity of surface molecular imprinting technology and fluorescence, and converts binding events into detectable signals by monitoring fluorescence spectra. Therefore, it will have further applications for Lys sensing.

  14. Structural Basis for Binding and Selectivity of Antimalarial and Anticancer Ethylenediamine Inhibitors to Protein Farnesyltransferase

    Energy Technology Data Exchange (ETDEWEB)

    Hast, Michael A.; Fletcher, Steven; Cummings, Christopher G.; Pusateri, Erin E.; Blaskovich, Michelle A.; Rivas, Kasey; Gelb, Michael H.; Voorhis, Wesley C.Van; Sebti, Said M.; Hamilton, Andrew D.; Beese, Lorena S. ((Yale)); ((USF)); ((UWASH)); ((Duke))

    2009-03-20

    Protein farnesyltransferase (FTase) catalyzes an essential posttranslational lipid modification of more than 60 proteins involved in intracellular signal transduction networks. FTase inhibitors have emerged as a significant target for development of anticancer therapeutics and, more recently, for the treatment of parasitic diseases caused by protozoan pathogens, including malaria (Plasmodium falciparum). We present the X-ray crystallographic structures of complexes of mammalian FTase with five inhibitors based on an ethylenediamine scaffold, two of which exhibit over 1000-fold selective inhibition of P. falciparum FTase. These structures reveal the dominant determinants in both the inhibitor and enzyme that control binding and selectivity. Comparison to a homology model constructed for the P. falciparum FTase suggests opportunities for further improving selectivity of a new generation of antimalarial inhibitors.

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

    Science.gov (United States)

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

    2018-02-01

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

  16. Structural Basis for Binding and Selectivity of Antimalarial and Anticancer Ethylenediamine Inhibitors to Protein Farnesyltransferase

    Science.gov (United States)

    Hast, Michael A.; Fletcher, Steven; Cummings, Christopher G.; Pusateri, Erin E.; Blaskovich, Michelle A.; Rivas, Kasey; Gelb, Michael H.; Van Voorhis, Wesley C.; Sebti, Said M.; Hamilton, Andrew D.; Beese, Lorena S.

    2009-01-01

    SUMMARY Protein farnesyltransferase (FTase) catalyzes an essential posttranslational lipid modification of more than 60 proteins involved in intracellular signal transduction networks. FTase inhibitors have emerged as a significant target for development of anticancer therapeutics and, more recently, for the treatment of parasitic diseases caused by protozoan pathogens, including malaria (Plasmodium falciparum). We present the X-ray crystallographic structures of complexes of mammalian FTase with five inhibitors based on an ethylenediamine scaffold, two of which exhibit over 1000-fold selective inhibition of P. falciparum FTase. These structures reveal the dominant determinants in both the inhibitor and enzyme that control binding and selectivity. Comparison to a homology model constructed for the P. falciparum FTase suggests opportunities for further improving selectivity of a new generation of antimalarial inhibitors. PMID:19246009

  17. Differential privacy-based evaporative cooling feature selection and classification with relief-F and random forests.

    Science.gov (United States)

    Le, Trang T; Simmons, W Kyle; Misaki, Masaya; Bodurka, Jerzy; White, Bill C; Savitz, Jonathan; McKinney, Brett A

    2017-09-15

    Classification of individuals into disease or clinical categories from high-dimensional biological data with low prediction error is an important challenge of statistical learning in bioinformatics. Feature selection can improve classification accuracy but must be incorporated carefully into cross-validation to avoid overfitting. Recently, feature selection methods based on differential privacy, such as differentially private random forests and reusable holdout sets, have been proposed. However, for domains such as bioinformatics, where the number of features is much larger than the number of observations p≫n , these differential privacy methods are susceptible to overfitting. We introduce private Evaporative Cooling, a stochastic privacy-preserving machine learning algorithm that uses Relief-F for feature selection and random forest for privacy preserving classification that also prevents overfitting. We relate the privacy-preserving threshold mechanism to a thermodynamic Maxwell-Boltzmann distribution, where the temperature represents the privacy threshold. We use the thermal statistical physics concept of Evaporative Cooling of atomic gases to perform backward stepwise privacy-preserving feature selection. On simulated data with main effects and statistical interactions, we compare accuracies on holdout and validation sets for three privacy-preserving methods: the reusable holdout, reusable holdout with random forest, and private Evaporative Cooling, which uses Relief-F feature selection and random forest classification. In simulations where interactions exist between attributes, private Evaporative Cooling provides higher classification accuracy without overfitting based on an independent validation set. In simulations without interactions, thresholdout with random forest and private Evaporative Cooling give comparable accuracies. We also apply these privacy methods to human brain resting-state fMRI data from a study of major depressive disorder. Code

  18. Different alternative splicing patterns are subject to opposite selection pressure for protein reading frame preservation

    Directory of Open Access Journals (Sweden)

    Chuang Trees-Juen

    2007-09-01

    Full Text Available Abstract Background Alternative splicing (AS has been regarded capable of altering selection pressure on protein subsequences. Particularly, the frequency of reading frame preservation (FRFP, as a measure of selection pressure, has been reported to be higher in alternatively spliced exons (ASEs than in constitutively spliced exons (CSEs. However, recently it has been reported that different ASE types – simple and complex ASEs – may be subject to opposite selection forces. Therefore, it is necessary to re-evaluate the evolutionary effects of such splicing patterns on frame preservation. Results Here we show that simple and complex ASEs, respectively, have higher and lower FRFPs than CSEs. Since complex ASEs may alter the ends of their flanking exons, the selection pressure on frame preservation is likely relaxed in this ASE type. Furthermore, conservation of the ASE/CSE splicing pattern increases the FRFPs of simple ASEs but decreases those of complex ASEs. Contrary to the well-recognized concept of strong selection pressure on conserved ASEs for protein reading frame preservation, our results show that conserved complex ASEs are relaxed from such pressure and the frame-disrupting effect caused by the insertion of complex ASEs can be offset by compensatory changes in their flanking exons. Conclusion In this study, we find that simple and complex ASEs undergo opposite selection pressure for protein reading frame preservation, with CSEs in-between. Simple ASEs have much higher FRFPs than complex ones. We further find that the FRFPs of complex ASEs coupled with flanking exons are close to those of simple ASEs, indicating that neighboring exons of an ASE may evolve in a coordinated way to avoid protein dysfunction. Therefore, we suggest that evolutionary analyses of AS should take into consideration the effects of different splicing patterns and the joint effects of multiple AS events.

  19. Sexual selection and the adaptive evolution of PKDREJ protein in primates and rodents.

    Science.gov (United States)

    Vicens, Alberto; Gómez Montoto, Laura; Couso-Ferrer, Francisco; Sutton, Keith A; Roldan, Eduardo R S

    2015-02-01

    PKDREJ is a testis-specific protein thought to be located on the sperm surface. Functional studies in the mouse revealed that loss of PKDREJ has effects on sperm transport and the ability to undergo an induced acrosome reaction. Thus, PKDREJ has been considered a potential target of post-copulatory sexual selection in the form of sperm competition. Proteins involved in reproductive processes often show accelerated evolution. In many cases, this rapid divergence is promoted by positive selection which may be driven, at least in part, by post-copulatory sexual selection. We analysed the evolution of the PKDREJ protein in primates and rodents and assessed whether PKDREJ divergence is associated with testes mass relative to body mass, which is a reliable proxy of sperm competition levels. Evidence of an association between the evolutionary rate of the PKDREJ gene and testes mass relative to body mass was not found in primates. Among rodents, evidence of positive selection was detected in the Pkdrej gene in the family Cricetidae but not in Muridae. We then assessed whether Pkdrej divergence is associated with episodes of sperm competition in these families. We detected a positive significant correlation between the evolutionary rates of Pkdrej and testes mass relative to body mass in cricetids. These findings constitute the first evidence of post-copulatory sexual selection influencing the evolution of a protein that participates in the mechanisms regulating sperm transport and the acrosome reaction, strongly suggesting that positive selection may act on these fertilization steps, leading to advantages in situations of sperm competition. © The Author 2014. Published by Oxford University Press on behalf of the European Society of Human Reproduction and Embryology. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  20. Bayesian dose selection design for a binary outcome using restricted response adaptive randomization.

    Science.gov (United States)

    Meinzer, Caitlyn; Martin, Renee; Suarez, Jose I

    2017-09-08

    In phase II trials, the most efficacious dose is usually not known. Moreover, given limited resources, it is difficult to robustly identify a dose while also testing for a signal of efficacy that would support a phase III trial. Recent designs have sought to be more efficient by exploring multiple doses through the use of adaptive strategies. However, the added flexibility may potentially increase the risk of making incorrect assumptions and reduce the total amount of information available across the dose range as a function of imbalanced sample size. To balance these challenges, a novel placebo-controlled design is presented in which a restricted Bayesian response adaptive randomization (RAR) is used to allocate a majority of subjects to the optimal dose of active drug, defined as the dose with the lowest probability of poor outcome. However, the allocation between subjects who receive active drug or placebo is held constant to retain the maximum possible power for a hypothesis test of overall efficacy comparing the optimal dose to placebo. The design properties and optimization of the design are presented in the context of a phase II trial for subarachnoid hemorrhage. For a fixed total sample size, a trade-off exists between the ability to select the optimal dose and the probability of rejecting the null hypothesis. This relationship is modified by the allocation ratio between active and control subjects, the choice of RAR algorithm, and the number of subjects allocated to an initial fixed allocation period. While a responsive RAR algorithm improves the ability to select the correct dose, there is an increased risk of assigning more subjects to a worse arm as a function of ephemeral trends in the data. A subarachnoid treatment trial is used to illustrate how this design can be customized for specific objectives and available data. Bayesian adaptive designs are a flexible approach to addressing multiple questions surrounding the optimal dose for treatment efficacy

  1. Using ArcMap, Google Earth, and Global Positioning Systems to select and locate random households in rural Haiti

    Directory of Open Access Journals (Sweden)

    Wampler Peter J

    2013-01-01

    Full Text Available Abstract Background A remote sensing technique was developed which combines a Geographic Information System (GIS; Google Earth, and Microsoft Excel to identify home locations for a random sample of households in rural Haiti. The method was used to select homes for ethnographic and water quality research in a region of rural Haiti located within 9 km of a local hospital and source of health education in Deschapelles, Haiti. The technique does not require access to governmental records or ground based surveys to collect household location data and can be performed in a rapid, cost-effective manner. Methods The random selection of households and the location of these households during field surveys were accomplished using GIS, Google Earth, Microsoft Excel, and handheld Garmin GPSmap 76CSx GPS units. Homes were identified and mapped in Google Earth, exported to ArcMap 10.0, and a random list of homes was generated using Microsoft Excel which was then loaded onto handheld GPS units for field location. The development and use of a remote sensing method was essential to the selection and location of random households. Results A total of 537 homes initially were mapped and a randomized subset of 96 was identified as potential survey locations. Over 96% of the homes mapped using Google Earth imagery were correctly identified as occupied dwellings. Only 3.6% of the occupants of mapped homes visited declined to be interviewed. 16.4% of the homes visited were not occupied at the time of the visit due to work away from the home or market days. A total of 55 households were located using this method during the 10 days of fieldwork in May and June of 2012. Conclusions The method used to generate and field locate random homes for surveys and water sampling was an effective means of selecting random households in a rural environment lacking geolocation infrastructure. The success rate for locating households using a handheld GPS was excellent and only

  2. Using ArcMap, Google Earth, and Global Positioning Systems to select and locate random households in rural Haiti.

    Science.gov (United States)

    Wampler, Peter J; Rediske, Richard R; Molla, Azizur R

    2013-01-18

    A remote sensing technique was developed which combines a Geographic Information System (GIS); Google Earth, and Microsoft Excel to identify home locations for a random sample of households in rural Haiti. The method was used to select homes for ethnographic and water quality research in a region of rural Haiti located within 9 km of a local hospital and source of health education in Deschapelles, Haiti. The technique does not require access to governmental records or ground based surveys to collect household location data and can be performed in a rapid, cost-effective manner. The random selection of households and the location of these households during field surveys were accomplished using GIS, Google Earth, Microsoft Excel, and handheld Garmin GPSmap 76CSx GPS units. Homes were identified and mapped in Google Earth, exported to ArcMap 10.0, and a random list of homes was generated using Microsoft Excel which was then loaded onto handheld GPS units for field location. The development and use of a remote sensing method was essential to the selection and location of random households. A total of 537 homes initially were mapped and a randomized subset of 96 was identified as potential survey locations. Over 96% of the homes mapped using Google Earth imagery were correctly identified as occupied dwellings. Only 3.6% of the occupants of mapped homes visited declined to be interviewed. 16.4% of the homes visited were not occupied at the time of the visit due to work away from the home or market days. A total of 55 households were located using this method during the 10 days of fieldwork in May and June of 2012. The method used to generate and field locate random homes for surveys and water sampling was an effective means of selecting random households in a rural environment lacking geolocation infrastructure. The success rate for locating households using a handheld GPS was excellent and only rarely was local knowledge required to identify and locate households. This

  3. Membrane proteins bind lipids selectively to modulate their structure and function.

    Science.gov (United States)

    Laganowsky, Arthur; Reading, Eamonn; Allison, Timothy M; Ulmschneider, Martin B; Degiacomi, Matteo T; Baldwin, Andrew J; Robinson, Carol V

    2014-06-05

    Previous studies have established that the folding, structure and function of membrane proteins are influenced by their lipid environments and that lipids can bind to specific sites, for example, in potassium channels. Fundamental questions remain however regarding the extent of membrane protein selectivity towards lipids. Here we report a mass spectrometry approach designed to determine the selectivity of lipid binding to membrane protein complexes. We investigate the mechanosensitive channel of large conductance (MscL) from Mycobacterium tuberculosis and aquaporin Z (AqpZ) and the ammonia channel (AmtB) from Escherichia coli, using ion mobility mass spectrometry (IM-MS), which reports gas-phase collision cross-sections. We demonstrate that folded conformations of membrane protein complexes can exist in the gas phase. By resolving lipid-bound states, we then rank bound lipids on the basis of their ability to resist gas phase unfolding and thereby stabilize membrane protein structure. Lipids bind non-selectively and with high avidity to MscL, all imparting comparable stability; however, the highest-ranking lipid is phosphatidylinositol phosphate, in line with its proposed functional role in mechanosensation. AqpZ is also stabilized by many lipids, with cardiolipin imparting the most significant resistance to unfolding. Subsequently, through functional assays we show that cardiolipin modulates AqpZ function. Similar experiments identify AmtB as being highly selective for phosphatidylglycerol, prompting us to obtain an X-ray structure in this lipid membrane-like environment. The 2.3 Å resolution structure, when compared with others obtained without lipid bound, reveals distinct conformational changes that re-position AmtB residues to interact with the lipid bilayer. Our results demonstrate that resistance to unfolding correlates with specific lipid-binding events, enabling a distinction to be made between lipids that merely bind from those that modulate membrane

  4. Habituation to low or high protein intake does not modulate basal or postprandial muscle protein synthesis rates: a randomized trial

    NARCIS (Netherlands)

    Gorissen, S.H.; Horstman, Astrid; Franssen, Rinske; Kouw, I.W.; Wall, B.T.; Burd, N.A.; Groot, de C.P.G.M.; Loon, van L.J.C.

    2017-01-01

    Background: Muscle mass maintenance is largely regulated by basal muscle protein synthesis rates and the ability to increase muscle protein synthesis after protein ingestion. To our knowledge, no previous studies have evaluated the impact of habituation to either low protein intake (LOW PRO) or high

  5. Effects of protein intake and gender on body composition changes: a randomized clinical weight loss trial

    Directory of Open Access Journals (Sweden)

    Evans Ellen M

    2012-06-01

    Full Text Available Abstract Limited data on sex differences in body composition changes in response to higher protein diets (PRO compared to higher carbohydrate diets (CARB suggest that a PRO diet helps preserve lean mass (LM in women more so than in men. Objective To compare male and female body composition responses to weight loss diets differing in macronutrient content. Design Twelve month randomized clinical trial with 4mo of weight loss and 8mo weight maintenance. Subjects Overweight (N = 130; 58 male (M, 72 female (F; BMI = 32.5 ± 0.5 kg/m2 middle-aged subjects were randomized to energy-restricted (deficit ~500 kcal/d diets providing protein at 1.6 g.kg-1.d-1 (PRO or 0.8 g.kg-1.d-1 (CARB. LM and fat mass (FM were measured using dual X-ray absorptiometry. Body composition outcomes were tested in a repeated measures ANOVA controlling for sex, diet, time and their two- and three-way interactions at 0, 4, 8 and 12mo. Results When expressed as percent change from baseline, males and females lost similar amounts of weight at 12mo (M:-11.2 ± 7.1 %, F:-9.9 ± 6.0 %, as did diet groups (PRO:-10.7 ± 6.8 %, CARB:-10.1 ± 6.2 %, with no interaction of gender and diet. A similar pattern emerged for fat mass and lean mass, however percent body fat was significantly influenced by both gender (M:-18.0 ± 12.8 %, F:-7.3 ± 8.1 %, p  Conclusion PRO was more effective in reducing percent body fat vs. CARB over 12mo weight loss and maintenance. Men lost percent total body fat and trunk fat more effectively than women. No interactive effects of protein intake and gender are evident.

  6. Monoclonal antibody recognizes a conformational epitope in a random coil protein.

    Science.gov (United States)

    Saad, B; Corradin, G; Bosshard, H R

    1988-12-01

    The antigenic determinants for two monoclonal antibodies directed against horse apo-cytochrome c, a protein of disordered structure, as judged by spectroscopic and hydrodynamic criteria, have been studied by a combination of methods: antigen competition in solution by radio immunoassay and enzyme-linked immunoassay, and differential acetylation of free and antibody-bound antigen. In the latter method the accessibility of lysine residues of the antigen in the antigen-antibody complex is compared to the accessibility in the free antigen. The two antibodies against the heme-free protein do not recognize intact native cytochrome c, but they crossreact with the heme-containing peptides 1-38 and 1-65 of cytochrome c. The antigenic determinant recognized by monoclonal antibody SJL 2-4 is conformational and discontiguous, it is composed of residues close to the N-terminus and around position 25. The other monoclonal antibody, Cyt-1-59, seems to recognize a contiguous epitope close to the N-terminus. The present results show that even a seemingly disordered protein which is conventionally classified as a random coil may feature subtle spatial regularities. The presence of ordered conformational elements in apocytochrome c may be important for the enzyme-catalyzed covalent attachment of the heme and the import of cytochrome c into mitochondria. A discontiguous determinant for SJL 2-4 is particularly interesting because this antibody inhibits the proliferation of a T-cell clone specific for apo-cytochrome c [Corradin & Engers (1984) Nature (Lond.) 308, 547-548].

  7. The impact of an exercise intervention on C - reactive protein during pregnancy: a randomized controlled trial.

    Science.gov (United States)

    Hawkins, Marquis; Braun, Barry; Marcus, Bess H; Stanek, Edward; Markenson, Glenn; Chasan-Taber, Lisa

    2015-06-24

    C-reactive protein (CRP) during pregnancy has been associated with adverse maternal outcomes such as preeclampsia and gestational diabetes mellitus. Randomized trials suggest that exercise programs may be associated with reductions in CRP in non-pregnant populations; however, such studies have not been conducted among pregnant women. The purpose of this study was to evaluate the impact of an individually-tailored motivationally-matched exercise intervention on CRP in pregnant women. The Behaviors Affecting Baby and You study was a randomized controlled trial of prenatal physical activity to prevent the development of gestational diabetes mellitus in women at increased risk. Women were randomized to either a 12-week exercise intervention (n = 84) or a comparison health and wellness intervention (n = 87). High sensitivity CRP (mg/dL) was measured using a commercial immunoassay kit. Physical activity was measured using the Pregnancy Physical Activity Questionnaire. Mixed model analyses were used to evaluate the impact of the intervention on change in CRP using an intent-to-treat approach. CRP decreased (-0.09 mg/dL, 95 % CI: -0.25, 0.07) from pre- to post-intervention in the exercise arm (p = 0.14) and increased (0.08 mg/dL, 95 % CI: -0.07, 0.24) (p = 0.64) in the health and wellness arm; however the between group difference was not statistically significant (p = 0.14). Findings did not differ according to ethnic group or pre-pregnancy body mass index. In a secondary analysis based on self-reported physical activity, women who decreased their time spent in sports/exercise experienced a mean increase in CRP (0.09 mg/dL, 95 % CI: -0.14, 0.33), whereas women who maintained or increased their sports/ exercise experienced a mean decrease in CRP (-0.08 mg/dL, 95 % CI: -0.23, 0.08) (p = 0.046). Findings from this randomized trial in an ethnically and socio-economically diverse population of pregnant women were consistent with a positive impact

  8. Automated Hydrophobic Interaction Chromatography Column Selection for Use in Protein Purification

    Science.gov (United States)

    Murphy, Patrick J. M.; Stone, Orrin J.; Anderson, Michelle E.

    2011-01-01

    In contrast to other chromatographic methods for purifying proteins (e.g. gel filtration, affinity, and ion exchange), hydrophobic interaction chromatography (HIC) commonly requires experimental determination (referred to as screening or "scouting") in order to select the most suitable chromatographic medium for purifying a given protein 1. The method presented here describes an automated approach to scouting for an optimal HIC media to be used in protein purification. HIC separates proteins and other biomolecules from a crude lysate based on differences in hydrophobicity. Similar to affinity chromatography (AC) and ion exchange chromatography (IEX), HIC is capable of concentrating the protein of interest as it progresses through the chromatographic process. Proteins best suited for purification by HIC include those with hydrophobic surface regions and able to withstand exposure to salt concentrations in excess of 2 M ammonium sulfate ((NH4)2SO4). HIC is often chosen as a purification method for proteins lacking an affinity tag, and thus unsuitable for AC, and when IEX fails to provide adequate purification. Hydrophobic moieties on the protein surface temporarily bind to a nonpolar ligand coupled to an inert, immobile matrix. The interaction between protein and ligand are highly dependent on the salt concentration of the buffer flowing through the chromatography column, with high ionic concentrations strengthening the protein-ligand interaction and making the protein immobile (i.e. bound inside the column) 2. As salt concentrations decrease, the protein-ligand interaction dissipates, the protein again becomes mobile and elutes from the column. Several HIC media are commercially available in pre-packed columns, each containing one of several hydrophobic ligands (e.g. S-butyl, butyl, octyl, and phenyl) cross-linked at varying densities to agarose beads of a specific diameter 3. Automated column scouting allows for an efficient approach for determining which HIC media

  9. Effects of high-protein diets on fat-free mass and muscle protein synthesis following weight loss: a randomized controlled trial.

    Science.gov (United States)

    Pasiakos, Stefan M; Cao, Jay J; Margolis, Lee M; Sauter, Edward R; Whigham, Leah D; McClung, James P; Rood, Jennifer C; Carbone, John W; Combs, Gerald F; Young, Andrew J

    2013-09-01

    The purpose of this work was to determine the effects of varying levels of dietary protein on body composition and muscle protein synthesis during energy deficit (ED). A randomized controlled trial of 39 adults assigned the subjects diets providing protein at 0.8 (recommended dietary allowance; RDA), 1.6 (2×-RDA), and 2.4 (3×-RDA) g kg(-1) d(-1) for 31 d. A 10-d weight-maintenance (WM) period was followed by a 21 d, 40% ED. Body composition and postabsorptive and postprandial muscle protein synthesis were assessed during WM (d 9-10) and ED (d 30-31). Volunteers lost (Pregardless of dietary protein. The proportion of weight loss due to reductions in fat-free mass was lower (P0.05) from WM for 2×-RDA and 3×-RDA, but was lower during ED than WM for those consuming RDA levels of protein (energy × protein interaction, P<0.05). To assess muscle protein metabolic responses to varied protein intakes during ED, RDA served as the study control. In summary, we determined that consuming dietary protein at levels exceeding the RDA may protect fat-free mass during short-term weight loss.

  10. Identification and Structure-Function Analysis of Subfamily Selective G Protein-Coupled Receptor Kinase Inhibitors

    Energy Technology Data Exchange (ETDEWEB)

    Homan, Kristoff T.; Larimore, Kelly M.; Elkins, Jonathan M.; Szklarz, Marta; Knapp, Stefan; Tesmer, John J.G. [Michigan; (Oxford)

    2015-02-13

    Selective inhibitors of individual subfamilies of G protein-coupled receptor kinases (GRKs) would serve as useful chemical probes as well as leads for therapeutic applications ranging from heart failure to Parkinson’s disease. To identify such inhibitors, differential scanning fluorimetry was used to screen a collection of known protein kinase inhibitors that could increase the melting points of the two most ubiquitously expressed GRKs: GRK2 and GRK5. Enzymatic assays on 14 of the most stabilizing hits revealed that three exhibit nanomolar potency of inhibition for individual GRKs, some of which exhibiting orders of magnitude selectivity. Most of the identified compounds can be clustered into two chemical classes: indazole/dihydropyrimidine-containing compounds that are selective for GRK2 and pyrrolopyrimidine-containing compounds that potently inhibit GRK1 and GRK5 but with more modest selectivity. The two most potent inhibitors representing each class, GSK180736A and GSK2163632A, were cocrystallized with GRK2 and GRK1, and their atomic structures were determined to 2.6 and 1.85 Å spacings, respectively. GSK180736A, developed as a Rho-associated, coiled-coil-containing protein kinase inhibitor, binds to GRK2 in a manner analogous to that of paroxetine, whereas GSK2163632A, developed as an insulin-like growth factor 1 receptor inhibitor, occupies a novel region of the GRK active site cleft that could likely be exploited to achieve more selectivity. However, neither compound inhibits GRKs more potently than their initial targets. This data provides the foundation for future efforts to rationally design even more potent and selective GRK inhibitors.

  11. Characterization of quinone derived protein adducts and their selective identification using redox cycling based chemiluminescence assay.

    Science.gov (United States)

    Elgawish, Mohamed Saleh; Kishikawa, Naoya; Ohyama, Kaname; Kuroda, Naotaka

    2015-07-17

    The cytotoxic mechanism of many quinones has been correlated to covalent modification of cellular proteins. However, the identification of relevant proteins targets is essential but challenging goals. To better understand the quinones cytotoxic mechanism, human serum albumin (HSA) was incubated in vitro with different concentration of menadione (MQ). In this respect, the initial nucleophilic addition of proteins to quinone converts the conjugates to redox-cycling quinoproteins with altered conformation and secondary structure and extended life span than the short lived, free quinones. The conjugation of MQ with nucleophilic sites likewise, free cysteine as well as ɛ-amino group of lysine residue of HSA has been found to be in concentration dependent manner. The conventional methods for modified proteins identification in complex mixtures are complicated and time consuming. Herein, we describe a highly selective, sensitive, simple, and fast strategy for quinoproteins identification. The suggested strategy exploited the unique redox-cycling capability of quinoproteins in presence of a reductant, dithiothreitol (DTT), to generate reactive oxygen species (ROS) that gave sufficient chemiluminescence (CL) when mixed with luminol. The CL approach is highly selective and sensitive to detect the quinoproteins in ten-fold molar excess of native proteins without adduct enrichment. The approach was also coupled with gel filtration chromatography (GFC) and used to identify adducts in complex mixture of proteins in vitro as well as in rat plasma after MQ administration. Albumin was identified as the main protein in human and rat plasma forming adduct with MQ. Overall, the identification of quinoproteins will encourage further studies of toxicological impact of quinones on human health. Copyright © 2015 Elsevier B.V. All rights reserved.

  12. Discovery of Potent and Selective Inhibitors for G9a-Like Protein (GLP) Lysine Methyltransferase

    Energy Technology Data Exchange (ETDEWEB)

    Xiong, Yan; Li, Fengling; Babault, Nicolas; Dong, Aiping; Zeng, Hong; Wu, Hong; Chen, Xin; Arrowsmith, Cheryl H.; Brown, Peter J.; Liu, Jing; Vedadi, Masoud; Jin, Jian

    2017-02-14

    G9a-like protein (GLP) and G9a are highly homologous protein lysine methyltransferases (PKMTs) sharing approximately 80% sequence identity in their catalytic domains. GLP and G9a form a heterodimer complex and catalyze mono- and dimethylation of histone H3 lysine 9 and nonhistone substrates. Although they are closely related, GLP and G9a possess distinct physiological and pathophysiological functions. Thus, GLP or G9a selective small-molecule inhibitors are useful tools to dissect their distinct biological functions. We previously reported potent and selective G9a/GLP dual inhibitors including UNC0638 and UNC0642. Here we report the discovery of potent and selective GLP inhibitors including 4 (MS0124) and 18 (MS012), which are >30-fold and 140-fold selective for GLP over G9a and other methyltransferases, respectively. The cocrystal structures of GLP and G9a in the complex with either 4 or 18 displayed virtually identical binding modes and interactions, highlighting the challenges in structure-based design of selective inhibitors for either enzyme.

  13. Soy-protein consumption and kidney-related biomarkers among type 2 diabetics: a crossover, randomized clinical trial.

    Science.gov (United States)

    Azadbakht, Leila; Esmaillzadeh, Ahmad

    2009-11-01

    Renal disease is a major problem among diabetic patients. The type of protein consumed may affect alterations in kidney-related biomarkers in these patients. This study sought to assess the effects of soy-protein consumption on renal-related markers among type 2 diabetic patients with nephropathy. A crossover, randomized clinical trial was conducted among 14 patients (10 men and 4 women). One diet contained 0.8 g/kg protein (70% animal and 30% vegetable proteins), and a similar diet contained the same amount of protein with 35% animal protein, 35% soy protein, and 30% other vegetable proteins. These two diets were prescribed in each phase of the trial for 7 weeks. There was a 4-week washout between the two phases of the study. Consumption of soy protein reduced urinary urea nitrogen (-0.9 +/- 0.8 vs. 0.2 +/- 0.6 mg/dL, respectively, SD; P anima-protein consumption. Soy-protein consumption reduces proteinuria in type 2 diabetes with nephropathy.

  14. Expanding the Circuitry of Pluripotency by Selective Isolation of Chromatin-Associated Proteins.

    Science.gov (United States)

    Rafiee, Mahmoud-Reza; Girardot, Charles; Sigismondo, Gianluca; Krijgsveld, Jeroen

    2016-11-03

    Maintenance of pluripotency is regulated by a network of transcription factors coordinated by Oct4, Sox2, and Nanog (OSN), yet a systematic investigation of the composition and dynamics of the OSN protein network specifically on chromatin is still missing. Here we have developed a method combining ChIP with selective isolation of chromatin-associated proteins (SICAP) followed by mass spectrometry to identify chromatin-bound partners of a protein of interest. ChIP-SICAP in mouse embryonic stem cells (ESCs) identified over 400 proteins associating with OSN, including several whose interaction depends on the pluripotent state. Trim24, a previously unrecognized protein in the network, converges with OSN on multiple enhancers and suppresses the expression of developmental genes while activating cell cycle genes. Consistently, Trim24 significantly improved efficiency of cellular reprogramming, demonstrating its direct functionality in establishing pluripotency. Collectively, ChIP-SICAP provides a powerful tool to decode chromatin protein composition, further enhanced by its integrative capacity to perform ChIP-seq. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  15. Magnetic deep eutectic solvents molecularly imprinted polymers for the selective recognition and separation of protein

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Yanjin [State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 (China); Wang, Yuzhi, E-mail: wyzss@hnu.edu.cn [State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 (China); Dai, Qingzhou [State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 (China); Zhou, Yigang [Department of Microbiology, College of Basic Medicine, Central South University, Changsha, 410083 (China)

    2016-09-14

    A novel and facile magnetic deep eutectic solvents (DES) molecularly imprinted polymers (MIPs) for the selective recognition and separation of Bovine hemoglobin (BHb) was prepared. The new-type DES was adopted as the functional monomer which would bring molecular imprinted technology to a new direction. The amounts of DES were optimized. The obtained magnetic DES-MIPs were characterized with fourier transform infrared spectrometry (FT-IR), thermogravimetric analysis (TGA), field emission scanning electron microscope (FESEM), dynamic light scattering (DLS), elemental analysis and vibrating sample magnetometer (VSM). The results suggested that the imprinted polymers were successfully formed and possessed a charming magnetism. The maximum adsorption capability (Q{sub max}) and dissociation constant (K{sub L}) were analyzed by Langmuir isotherms (R{sup 2} = 0.9983) and the value were estimated to be 175.44 mg/g and 0.035 mg/mL for the imprinted particles. And the imprinted particles showed a high imprinting factor of 4.77. In addition, the magnetic DES-MIPs presented outstanding recognition specificity and selectivity so that it can be utilized to separate template protein from the mixture of proteins and real samples. Last but not least, the combination of deep eutectic solvents and molecular imprinted technology in this paper provides a new perspective for the recognition and separation of proteins. - Highlights: • Combined green deep eutectic solvents (DES) and molecular imprinted technology in recognition and separation of proteins. • DES was adopted as a new-type functional monomer. • The obtained magnetic DES-MIPs can separate proteins rapidly by an external magnetic field. • Adsorption and selectivity properties were discussed.

  16. The basic science and mathematics of random mutation and natural selection.

    Science.gov (United States)

    Kleinman, Alan

    2014-12-20

    The mutation and natural selection phenomenon can and often does cause the failure of antimicrobial, herbicidal, pesticide and cancer treatments selection pressures. This phenomenon operates in a mathematically predictable behavior, which when understood leads to approaches to reduce and prevent the failure of the use of these selection pressures. The mathematical behavior of mutation and selection is derived using the principles given by probability theory. The derivation of the equations describing the mutation and selection phenomenon is carried out in the context of an empirical example. Copyright © 2014 John Wiley & Sons, Ltd.

  17. Selective detection of airborne asbestos fibers using protein-based fluorescent probes.

    Science.gov (United States)

    Ishida, Takenori; Alexandrov, Maxym; Nishimura, Tomoki; Minakawa, Kenji; Hirota, Ryuichi; Sekiguchi, Kiyoshi; Kohyama, Norihiko; Kuroda, Akio

    2010-01-15

    Fluorescence microscopy (FM) is one of the most important analytical tools in modern life sciences, sufficiently sensitive to allow observation of single molecules. Here we describe the first application of the FM technique for the detection of inorganic environmental pollutants-airborne asbestos fibers that can cause asbestosis, mesothelioma, and lung cancer. In order to assess FM capabilities for detecting and counting asbestos fibers, we screened E. coli lysate for proteins that bind to amphibole asbestos. In combination with the previously discovered E. coli protein DksA (Kuroda et al., Biotechnol. Bioeng. 2008, 99, 285-289) that can specifically bind to chrysotile, the newly identified GatZ protein was used for selective and highly sensitive detection of two different asbestos types. Our novel FM-based method overcomes a number of limitations of the commonly used phase-contrast microscopy (PCM) method, offering a convenient alternative to PCM for airborne asbestos monitoring.

  18. A Novel Inducible Protein Production System and Neomycin Resistance as Selection Marker for Methanosarcina mazei

    Directory of Open Access Journals (Sweden)

    Sebastian Mondorf

    2012-01-01

    Full Text Available Methanosarcina mazei is one of the model organisms for the methanogenic order Methanosarcinales whose metabolism has been studied in detail. However, the genetic toolbox is still limited. This study was aimed at widening the scope of utilizable methods in this group of organisms. (i Proteins specific to methanogens are oftentimes difficult to produce in E. coli. However, a protein production system is not available for methanogens. Here we present an inducible system to produce Strep-tagged proteins in Ms. mazei. The promoter p1687, which directs the transcription of methyl transferases that demethylate methylamines, was cloned into plasmid pWM321 and its activity was determined by monitoring β-glucuronidase production. The promoter was inactive during growth on methanol but was rapidly activated when trimethylamine was added to the medium. The gene encoding the β-glucuronidase from E. coli was fused to a Strep-tag and was cloned downstream of the p1687 promoter. The protein was overproduced in Ms. mazei and was purified in an active form by affinity chromatography. (ii Puromycin is currently the only antibiotic used as a selectable marker in Ms. mazei and its relatives. We established neomycin resistance as a second selectable marker by designing a plasmid that confers neomycin resistance in Ms. mazei.

  19. Aromatic Functionality of Target Proteins Influences Monomer Selection for Creating Artificial Antibodies on Plasmonic Biosensors.

    Science.gov (United States)

    Hu, Rong; Luan, Jingyi; Kharasch, Evan D; Singamaneni, Srikanth; Morrissey, Jeremiah J

    2017-01-11

    Natural antibodies used as biorecognition elements suffer from numerous shortcomings, such as limited chemical and environmental stability and cost. Artificial antibodies based on molecular imprinting are an attractive alternative to natural antibodies. We investigated the role of aromatic interactions in target recognition capabilities of artificial antibodies. Three proteins with different aromatic amino acid content were employed as model targets. Artificial antibodies were formed on nanostructures using combinations of silane monomers of varying aromatic functionality. We employed refractive index sensitivity of plasmonic nanostructures as a transduction platform for monitoring various steps in the imprinting process and to quantify the target recognition capabilities of the artificial antibodies. The sensitivity of the artificial antibodies with aromatic interactions exhibited a protein-dependent enhancement. Selectivity and sensitivity enhancement due to the presence of aromatic groups in imprinted polymer matrix was found to be higher for target proteins with higher aromatic amino acid content. Our results indicate that tailoring the monomer composition based on the amino acid content of the target protein can improve the sensitivity of plasmonic biosensors based on artificial antibodies without affecting the selectivity.

  20. Ubiquitin, a central component of selective cytoplasmic proteolysis, is linked to proteins residing at the locus of non-selective proteolysis, the vacuole

    NARCIS (Netherlands)

    Simeon, Angela; Klei, Ida J. van der; Veenhuis, Marten; Wolf, Dieter H.

    1992-01-01

    Ubiquitin, an evolutionary highly conserved protein, is known to be involved in selective proteolysis in the cytoplasm. Here we show that ubiquitin-protein conjugates are also found in the yeast vacuole. Mutants defective in the major vacuolar endopeptidases, proteinase yscA and yscB, lead to

  1. A new way to rapidly create functional, fluorescent fusion proteins: random insertion of GFP with an in vitro transposition reaction

    Directory of Open Access Journals (Sweden)

    Jakobsdottir Klara B

    2002-06-01

    Full Text Available Abstract Background The jellyfish green fluorescent protein (GFP can be inserted into the middle of another protein to produce a functional, fluorescent fusion protein. Finding permissive sites for insertion, however, can be difficult. Here we describe a transposon-based approach for rapidly creating libraries of GFP fusion proteins. Results We tested our approach on the glutamate receptor subunit, GluR1, and the G protein subunit, αs. All of the in-frame GFP insertions produced a fluorescent protein, consistent with the idea that GFP will fold and form a fluorophore when inserted into virtually any domain of another protein. Some of the proteins retained their signaling function, and the random nature of the transposition process revealed permissive sites for insertion that would not have been predicted on the basis of structural or functional models of how that protein works. Conclusion This technique should greatly speed the discovery of functional fusion proteins, genetically encodable sensors, and optimized fluorescence resonance energy transfer pairs.

  2. Physicochemical evolution and positive selection of the gymnosperm matK proteins.

    Science.gov (United States)

    Hao, Da Cheng; Mu, Jun; Chen, Shi Lin; Xiao, Pei Gen

    2010-04-01

    It is not clear whether matK evolves under Darwinian selection. In this study, the gymnosperm Taxaceae, Cephalotaxaceae and Pinaceae were used to illustrate the physicochemical evolution, molecular adaptation and evolutionary dynamics of gene divergence in matKs. matK sequences were amplified from 27 Taxaceae and 12 Cephalotaxaceae species. matK sequences of 19 Pinaceae species were retrieved from GenBank. The phylogenetic tree was generated using conceptual-translated amino acid sequences. Selective influences were investigated using standard dN/dS ratio methods and more sensitive techniques investigating the amino acid property changes resulting from nonsynonymous replacements in a phylogenetic context. Analyses revealed the presence of positive selection in matKs (N-terminal region, RT domain and domain X) of Taxaceae and Pinaceae,and found positive destabilizing selection in N-terminal region and RT domain of Cephalotaxaceae matK. Moreover, various amino acid properties were found to be influenced by destabilizing positive selection. Amino acid sites relating to these properties and to different secondary structures were found and have the potential to affect group II intron maturase function. Despite the evolutionary constraint on the rapidly evolving matK, this protein evolves under positive selection in gymnosperm. Several regions of matK have experienced molecular adaptation which fine-tunes maturase performance.

  3. Effect of Increased Enteral Protein Intake on Growth in Human Milk-Fed Preterm Infants: A Randomized Clinical Trial.

    Science.gov (United States)

    Maas, Christoph; Mathes, Michaela; Bleeker, Christine; Vek, Julia; Bernhard, Wolfgang; Wiechers, Cornelia; Peter, Andreas; Poets, Christian F; Franz, Axel R

    2017-01-01

    Protein, supplied in currently available commercial fortifiers, may be inadequate to meet the requirements of very preterm infants; in addition, intraindividual and interindividual variability of human milk protein and energy content potentially contribute to unsatisfactory early postnatal growth. To determine effects on growth of different levels of enteral protein supplementation in predominantly human milk-fed preterm infants. This randomized clinical and partially blinded single-center trial was conducted in a neonatal tertiary referral center in Germany. Sixty preterm infants (gestation protein (adding 1 g of bovine protein/100 mL of breast milk through a commercial human milk fortifier; n = 30) or a higher-protein group at a median (IQR) postnatal age of 7 (6-8) days. The higher-protein group (n = 30) received either standardized higher-protein supplementation (study fortifier adding 1.8 g of bovine protein/100 mL of breast milk [n = 15]) or individualized high-protein supplementation based on protein and fat content of administered breast milk (n = 15). Study interventions were continued for a median (IQR) of 41 (30-57) days and until definite discharge planning. Primary outcome was weight gain (g/kg/d) from birth to the end of intervention. Sixty preterm infants (gestation protein group and 490 to 1470 g in the higher-protein group. Weight gain was similar in the lower- and higher-protein groups: mean (95% CI), 16.3 g/kg/d (15.4-17.1 g/kg/d) in the lower-protein group vs 16.0 g/kg/d (15.1-16.9 g/kg/d) in the higher-protein group) (P = .70), despite an increase in actual protein intake by 0.6 g/kg/d (0.4-0.7 g/kg/d) (P total enteral feeding volume provided as breast milk: median (IQR) proportion of breast milk, 92% (79%-98%) in the lower-protein group vs 94% (62%-99%) in the higher-protein group (P = .89). An increase in protein intake by 0.6 g/kg/d to a mean intake of 4.3 g/kg/d did not further enhance growth of very preterm

  4. Type and amount of dietary protein in the treatment of metabolic syndrome: a randomized controlled trial12

    Science.gov (United States)

    Hill, Alison M; Harris Jackson, Kristina A; Roussell, Michael A; West, Sheila G; Kris-Etherton, Penny M

    2015-01-01

    Background: Food-based dietary patterns emphasizing plant protein that were evaluated in the Dietary Approaches to Stop Hypertension (DASH) and OmniHeart trials are recommended for the treatment of metabolic syndrome (MetS). However, the contribution of plant protein to total protein in these diets is proportionally less than that of animal protein. Objective: This study compared 3 diets varying in type (animal compared with plant) and amount of protein on MetS criteria. Design: Sixty-two overweight adults with MetS consumed a healthy American diet for 2 wk before being randomly allocated to either a modified DASH diet rich in plant protein (18% protein, two-thirds plant sources, n = 9 males, 12 females), a modified DASH diet rich in animal protein (Beef in an Optimal Lean Diet: 18.4% protein, two-thirds animal sources, n = 9 males, 11 females), or a moderate-protein diet (Beef in an Optimal Lean Diet Plus Protein: 27% protein, two-thirds animal sources, n = 10 males, 11 females). Diets were compared across 3 phases of energy balance: 5 wk of controlled (all foods provided) weight maintenance (WM), 6 wk of controlled weight loss (minimum 500-kcal/d deficit) including exercise (WL), and 12 wk of prescribed, free-living weight loss (FL). The primary endpoint was change in MetS criteria. Results: All groups achieved ∼5% weight loss at the end of the WL phase and maintained it through FL, with no between-diet differences (WM compared with WL, FL, P protein source or amount. Our findings demonstrate that heart-healthy weight-loss dietary patterns that emphasize either animal or plant protein improve MetS criteria similarly. This study was registered at clinicaltrials.gov as NCT00937638. PMID:26354540

  5. P-glycoprotein-like protein, a possible genetic marker for ivermectin resistance selection in Onchocerca volvulus.

    Science.gov (United States)

    Bourguinat, Catherine; Ardelli, Bernadette F; Pion, Sébastien D S; Kamgno, Joseph; Gardon, Jacques; Duke, Brian O L; Boussinesq, Michel; Prichard, Roger K

    2008-04-01

    Ivermectin (IVM) is the only safe drug for mass-treatment of onchocerciasis. IVM resistance has been reported in gastrointestinal nematode parasites of animals. A reduction in response to IVM in Onchocerca volvulus could have significant consequences for the onchocerciasis control programs. We have found evidence that, in O. volvulus, repeated IVM treatment selects for specific alleles, of P-glycoprotein-like protein (PLP), a half-sized ABC transporter. In this study, O. volvulus samples were derived from a clinical trial in Cameroon, in which patients were sampled before, and following 3 years (1994-1997) of IVM treatments. There were four treatment groups: 150 microg/kg (1 x p.a. or 4 x p.a.) and 800 microg/kg (1 x p.a. or 4 x p.a.). DNA of O. volvulus macrofilariae was genotyped over a 476bp region of the PLP gene and at two control genes. Of the six polymorphic positions found in the PLP amplicon, three of them showed significant selection after 4 x p.a. treatment with IVM (total of 13 IVM treatments) in female worms, and one of the same single nucleotide polymorphisms (SNPs) showed significant selection in the male worms. One of the selected SNPs in the female worms caused an amino acid coding change in the putative protein sequence. We found a clear selection of some genotypes, a high SNPs association and a loss of polymorphism following 4 x p.a. treatment with IVM. These PLP SNPs and genotypes could be useful markers to follow selection for IVM resistance in the field.

  6. Site-selective {sup 13}C labeling of proteins using erythrose

    Energy Technology Data Exchange (ETDEWEB)

    Weininger, Ulrich, E-mail: ulrich.weininger@physik.uni-halle.de [Lund University, Department of Biophysical Chemistry, Center for Molecular Protein Science (Sweden)

    2017-03-15

    NMR-spectroscopy enables unique experimental studies on protein dynamics at atomic resolution. In order to obtain a full atom view on protein dynamics, and to study specific local processes like ring-flips, proton-transfer, or tautomerization, one has to perform studies on amino-acid side chains. A key requirement for these studies is site-selective labeling with {sup 13}C and/or {sup 1}H, which is achieved in the most general way by using site-selectively {sup 13}C-enriched glucose (1- and 2-{sup 13}C) as the carbon source in bacterial expression systems. Using this strategy, multiple sites in side chains, including aromatics, become site-selectively labeled and suitable for relaxation studies. Here we systematically investigate the use of site-selectively {sup 13}C-enriched erythrose (1-, 2-, 3- and 4-{sup 13}C) as a suitable precursor for {sup 13}C labeled aromatic side chains. We quantify {sup 13}C incorporation in nearly all sites in all 20 amino acids and compare the results to glucose based labeling. In general the erythrose approach results in more selective labeling. While there is only a minor gain for phenylalanine and tyrosine side-chains, the {sup 13}C incorporation level for tryptophan is at least doubled. Additionally, the Phe ζ and Trp η2 positions become labeled. In the aliphatic side chains, labeling using erythrose yields isolated {sup 13}C labels for certain positions, like Ile β and His β, making these sites suitable for dynamics studies. Using erythrose instead of glucose as a source for site-selective {sup 13}C labeling enables unique or superior labeling for certain positions and is thereby expanding the toolbox for customized isotope labeling of amino-acid side-chains.

  7. Selective actions of Lynx proteins on different nicotinic acetylcholine receptors in the locust, Locusta migratoria manilensis.

    Science.gov (United States)

    Wang, Xin; Bao, Haibo; Sun, Huahua; Zhang, Yixi; Fang, Jichao; Liu, Qinghong; Liu, Zewen

    2015-08-01

    Nicotinic acetylcholine receptors (nAChRs) are major neurotransmitter receptors and targets of neonicotinoid insecticides in the insect nervous system. The full function of nAChRs is often dependent on associated proteins, such as chaperones, regulators and modulators. Here, three Lynx (Ly-6/neurotoxin) proteins, Loc-lynx1, Loc-lynx2 and Loc-lynx3, were identified in the locust, Locusta migratoria manilensis. Co-expression with Lynx resulted in a dramatic increase in agonist-evoked macroscopic currents on nAChRs Locα1/β2 and Locα2/β2 in Xenopus oocytes, but no changes in agonist sensitivity. Loc-lynx1 and Loc-lynx3 only modulated nAChRs Locα1/β2 while Loc-lynx2 modulated Locα2/β2 specifically. Meanwhile, Loc-lynx1 induced a more significant increase in currents evoked by imidacloprid and epibatidine than Loc-lynx3, and the effects of Loc-lynx1 on imidacloprid and epibatidine were significantly higher than those on acetylcholine. Among three lynx proteins, only Loc-lynx1 significantly increased [(3) H]epibatidine binding on Locα1/β2. The results indicated that Loc-lynx1 had different modulation patterns in nAChRs compared to Loc-lynx2 and Loc-lynx3. Taken together, these findings indicated that three Lynx proteins were nAChR modulators and had selective activities in different nAChRs. Lynx proteins might display their selectivities from three aspects: nAChR subtypes, various agonists and different modulation patterns. Insect Lynx (Ly-6/neurotoxin) proteins act as the allosteric modulators on insect nicotinic acetylcholine receptors (nAChRs), the important targets of insecticides. We found that insect lynx proteins showed their selectivities from at least three aspects: nAChR subtypes, various agonists and different modulation patterns. © 2015 International Society for Neurochemistry.

  8. Novel random peptide libraries displayed on AAV serotype 9 for selection of endothelial cell-directed gene transfer vectors.

    Science.gov (United States)

    Varadi, K; Michelfelder, S; Korff, T; Hecker, M; Trepel, M; Katus, H A; Kleinschmidt, J A; Müller, O J

    2012-08-01

    We have demonstrated the potential of random peptide libraries displayed on adeno-associated virus (AAV)2 to select for AAV2 vectors with improved efficiency for cell type-directed gene transfer. AAV9, however, may have advantages over AAV2 because of a lower prevalence of neutralizing antibodies in humans and more efficient gene transfer in vivo. Here we provide evidence that random peptide libraries can be displayed on AAV9 and can be utilized to select for AAV9 capsids redirected to the cell type of interest. We generated an AAV9 peptide display library, which ensures that the displayed peptides correspond to the packaged genomes and performed four consecutive selection rounds on human coronary artery endothelial cells in vitro. This screening yielded AAV9 library capsids with distinct peptide motifs enabling up to 40-fold improved transduction efficiencies compared with wild-type (wt) AAV9 vectors. Incorporating sequences selected from AAV9 libraries into AAV2 capsids could not increase transduction as efficiently as in the AAV9 context. To analyze the potential on endothelial cells in the intact natural vascular context, human umbilical veins were incubated with the selected AAV in situ and endothelial cells were isolated. Fluorescence-activated cell sorting analysis revealed a 200-fold improved transduction efficiency compared with wt AAV9 vectors. Furthermore, AAV9 vectors with targeting sequences selected from AAV9 libraries revealed an increased transduction efficiency in the presence of human intravenous immunoglobulins, suggesting a reduced immunogenicity. We conclude that our novel AAV9 peptide library is functional and can be used to select for vectors for future preclinical and clinical gene transfer applications.

  9. Antisense oligonucleotides targeting translation inhibitory elements in 5' UTRs can selectively increase protein levels.

    Science.gov (United States)

    Liang, Xue-Hai; Sun, Hong; Shen, Wen; Wang, Shiyu; Yao, Joyee; Migawa, Michael T; Bui, Huynh-Hoa; Damle, Sagar S; Riney, Stan; Graham, Mark J; Crooke, Rosanne M; Crooke, Stanley T

    2017-09-19

    A variety of diseases are caused by deficiencies in amounts or activity of key proteins. An approach that increases the amount of a specific protein might be of therapeutic benefit. We reasoned that translation could be specifically enhanced using trans-acting agents that counter the function of negative regulatory elements present in the 5' UTRs of some mRNAs. We recently showed that translation can be enhanced by antisense oligonucleotides (ASOs) that target upstream open reading frames. Here we report the amount of a protein can also be selectively increased using ASOs designed to hybridize to other translation inhibitory elements in 5' UTRs. Levels of human RNASEH1, LDLR, and ACP1 and of mouse ACP1 and ARF1 were increased up to 2.7-fold in different cell types and species upon treatment with chemically modified ASOs targeting 5' UTR inhibitory regions in the mRNAs encoding these proteins. The activities of ASOs in enhancing translation were sequence and position dependent and required helicase activity. The ASOs appear to improve the recruitment of translation initiation factors to the target mRNA. Importantly, ASOs targeting ACP1 mRNA significantly increased the level of ACP1 protein in mice, suggesting that this approach has therapeutic and research potentials. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  10. Toward improving selectivity in affinity chromatography with PEGylated affinity ligands: the performance of PEGylated protein A.

    Science.gov (United States)

    González-Valdez, José; Yoshikawa, Alex; Weinberg, Justin; Benavides, Jorge; Rito-Palomares, Marco; Przybycien, Todd M

    2014-01-01

    Chemical modification of macromolecular affinity chromatography ligands with polyethylene glycol chains or "PEGylation" can potentially improve selectivity by sterically suppressing non-specific binding interactions without sacrificing binding capacity. For a commercial protein A affinity media and with yeast extract (YE) and fetal bovine serum (FBS) serving as mock contaminants, we found that the ligand accounted for more than 90% of the media-associated non-specific binding, demonstrating an opportunity for improvement. The IgG static binding affinity of protein A mono-PEGylated with 5.0 and 20.7 kDa poly(ethylene glycol) chains was found to be preserved using a biomolecular interaction screening platform. Similar in situ PEGylations of the commercial protein A media were conducted and the modified media was functionally characterized with IgG solutions spiked with YE and FBS. Ligand PEGylation reduced the mass of media-associated contaminants by a factor of two to three or more. Curiously, we also found an increase of up to 15% in the average recovery of IgG on elution after PEGylation. Combined, these effects produced an order of magnitude increase in the IgG selectivity on average when spiked with YE and a two- to three-fold increase when spiked with FBS relative to the commercial media. Dynamic binding capacity and mass-transfer resistance measurements revealed a reduction in dynamic capacity attributed to a decrease in IgG effective pore diffusivity and possibly slower IgG association kinetics for the PEGylated protein A ligands. Ligand PEGylation is a viable approach to improving selectivity in affinity chromatography with macromolecular ligands. © 2014 American Institute of Chemical Engineers.

  11. Nerve growth factor selectively regulates expression of transcripts encoding ribosomal proteins

    Directory of Open Access Journals (Sweden)

    Töröcsik Béata

    2002-02-01

    Full Text Available Abstract Background NGF exerts a variety of actions including promotion of neuronal differentiation and survival. The PC12 rat pheochromocytoma cell line has proved valuable for studying how NGF works and has revealed that the NGF mechanism includes regulation of gene expression. Accordingly, we used SAGE (Serial Analysis of Gene Expression to compare levels of specific transcripts in PC12 cells before and after long-term NGF exposure. Of the approximately 22,000 transcripts detected and quantified, 4% are NGF-regulated by 6-fold or more. Here, we used database information to identify transcripts in our SAGE libraries that encode ribosomal proteins and have compared the effect of NGF on their relative levels of expression. Results Among the transcripts detected in our SAGE analysis, 74 were identified as encoding ribosomal proteins. Ribosomal protein transcripts were among the most abundantly expressed and, for naive and NGF-treated PC12 cells, represented 5.2% and 3.5%, respectively, of total transcripts analyzed. Surprisingly, nearly half of ribosomal protein transcripts underwent statistically significant NGF-promoted alterations in relative abundance, with changes of up to 5-fold. Of the changes, approximately 2/3 represented decreases. A time course revealed that the relative abundance of transcripts encoding RPL9 increases within 1 hr of NGF treatment and is maximally elevated by 8 hr. Conclusions These data establish that NGF selectively changes expression of ribosomal protein transcripts. These findings raise potential roles for regulation of ribosomal protein transcripts in NGF-promoted withdrawal from the cell cycle and neuronal differentiation and indicate that regulation of individual ribosomal protein transcripts is cell- and stimulus-specific.

  12. Pseudo cluster randomization: a treatment allocation method to minimize contamination and selection bias.

    NARCIS (Netherlands)

    Borm, G.F.; Melis, R.J.F.; Teerenstra, S.; Peer, P.G.M.

    2005-01-01

    In some clinical trials, treatment allocation on a patient level is not feasible, and whole groups or clusters of patients are allocated to the same treatment. If, for example, a clinical trial is investigating the efficacy of various patient coaching methods and randomization is done on a patient

  13. Prediction of Protein Structural Class Based on Gapped-Dipeptides and a Recursive Feature Selection Approach

    Directory of Open Access Journals (Sweden)

    Taigang Liu

    2015-12-01

    Full Text Available The prior knowledge of protein structural class may offer useful clues on understanding its functionality as well as its tertiary structure. Though various significant efforts have been made to find a fast and effective computational approach to address this problem, it is still a challenging topic in the field of bioinformatics. The position-specific score matrix (PSSM profile has been shown to provide a useful source of information for improving the prediction performance of protein structural class. However, this information has not been adequately explored. To this end, in this study, we present a feature extraction technique which is based on gapped-dipeptides composition computed directly from PSSM. Then, a careful feature selection technique is performed based on support vector machine-recursive feature elimination (SVM-RFE. These optimal features are selected to construct a final predictor. The results of jackknife tests on four working datasets show that our method obtains satisfactory prediction accuracies by extracting features solely based on PSSM and could serve as a very promising tool to predict protein structural class.

  14. Discovery and optimization of sulfonyl acrylonitriles as selective, covalent inhibitors of protein phosphatase methylesterase-1.

    Science.gov (United States)

    Bachovchin, Daniel A; Zuhl, Andrea M; Speers, Anna E; Wolfe, Monique R; Weerapana, Eranthie; Brown, Steven J; Rosen, Hugh; Cravatt, Benjamin F

    2011-07-28

    The serine hydrolase protein phosphatase methylesterase-1 (PME-1) regulates the methylesterification state of protein phosphatase 2A (PP2A) and has been implicated in cancer and Alzheimer's disease. We recently reported a fluorescence polarization-activity-based protein profiling (fluopol-ABPP) high-throughput screen for PME-1 that uncovered a remarkably potent and selective class of aza-β-lactam (ABL) PME-1 inhibitors. Here, we describe a distinct set of sulfonyl acrylonitrile inhibitors that also emerged from this screen. The optimized compound, 28 (AMZ30), selectively inactivates PME-1 and reduces the demethylated form of PP2A in living cells. Considering that 28 is structurally unrelated to ABL inhibitors of PME-1, these agents, together, provide a valuable set of pharmacological probes to study the role of methylation in regulating PP2A function. We furthermore observed that several serine hydrolases were sensitive to analogues of 28, suggesting that more extensive structural exploration of the sulfonyl acrylonitrile chemotype may result in useful inhibitors for other members of this large enzyme class.

  15. Magnetic deep eutectic solvents molecularly imprinted polymers for the selective recognition and separation of protein.

    Science.gov (United States)

    Liu, Yanjin; Wang, Yuzhi; Dai, Qingzhou; Zhou, Yigang

    2016-09-14

    A novel and facile magnetic deep eutectic solvents (DES) molecularly imprinted polymers (MIPs) for the selective recognition and separation of Bovine hemoglobin (BHb) was prepared. The new-type DES was adopted as the functional monomer which would bring molecular imprinted technology to a new direction. The amounts of DES were optimized. The obtained magnetic DES-MIPs were characterized with fourier transform infrared spectrometry (FT-IR), thermogravimetric analysis (TGA), field emission scanning electron microscope (FESEM), dynamic light scattering (DLS), elemental analysis and vibrating sample magnetometer (VSM). The results suggested that the imprinted polymers were successfully formed and possessed a charming magnetism. The maximum adsorption capability (Qmax) and dissociation constant (KL) were analyzed by Langmuir isotherms (R(2) = 0.9983) and the value were estimated to be 175.44 mg/g and 0.035 mg/mL for the imprinted particles. And the imprinted particles showed a high imprinting factor of 4.77. In addition, the magnetic DES-MIPs presented outstanding recognition specificity and selectivity so that it can be utilized to separate template protein from the mixture of proteins and real samples. Last but not least, the combination of deep eutectic solvents and molecular imprinted technology in this paper provides a new perspective for the recognition and separation of proteins. Copyright © 2016 Elsevier B.V. All rights reserved.

  16. Molecular Mechanism of Selectivity among G Protein-Coupled Receptor Kinase 2 Inhibitors

    Energy Technology Data Exchange (ETDEWEB)

    Thal, David M.; Yeow, Raymond Y.; Schoenau, Christian; Huber, Jochen; Tesmer, John J.G. (Sanofi); (Michigan)

    2012-07-11

    G protein-coupled receptors (GPCRs) are key regulators of cell physiology and control processes ranging from glucose homeostasis to contractility of the heart. A major mechanism for the desensitization of activated GPCRs is their phosphorylation by GPCR kinases (GRKs). Overexpression of GRK2 is strongly linked to heart failure, and GRK2 has long been considered a pharmaceutical target for the treatment of cardiovascular disease. Several lead compounds developed by Takeda Pharmaceuticals show high selectivity for GRK2 and therapeutic potential for the treatment of heart failure. To understand how these drugs achieve their selectivity, we determined crystal structures of the bovine GRK2-G{beta}{gamma} complex in the presence of two of these inhibitors. Comparison with the apoGRK2-G{beta}{gamma} structure demonstrates that the compounds bind in the kinase active site in a manner similar to that of the AGC kinase inhibitor balanol. Both balanol and the Takeda compounds induce a slight closure of the kinase domain, the degree of which correlates with the potencies of the inhibitors. Based on our crystal structures and homology modeling, we identified five amino acids surrounding the inhibitor binding site that we hypothesized could contribute to inhibitor selectivity. However, our results indicate that these residues are not major determinants of selectivity among GRK subfamilies. Rather, selectivity is achieved by the stabilization of a unique inactive conformation of the GRK2 kinase domain.

  17. Protein-enriched familiar foods and drinks improve protein intake of hospitalized older patients: A randomized controlled trial

    NARCIS (Netherlands)

    Beelen, J.; Vasse, Emmelyne; Janssen, N.; Janse, A.; Roos, de N.M.; Groot, de C.P.G.M.

    2017-01-01

    Background & aims Adequate protein intake is important in preventing and treating undernutrition. Hospitalized older patients are recommended to consume 1.2–1.5 g of protein per kg body weight per day (g/kg/d) but most of them fail to do so. Therefore, we investigated whether a range of newly

  18. Protein supplementation lowers blood pressure in overweight adults : effect of dietary proteins on blood pressure (PROPRES), a randomized trial

    NARCIS (Netherlands)

    Teunissen-Beekman, Karianna F. M.; Dopheide, Janneke; Geleijnse, Johanna M.; Bakker, Stephan J. L.; Brink, Elizabeth J.; de Leeuw, Peter W.; van Baak, Marleen A.

    Background: Dietary protein intake may help to manage blood pressure (BP) and prevent complications associated with elevated BR Objective: The objective of this study was to determine whether 4 wk of increased protein intake (similar to 25% compared with similar to 15% of energy intake that

  19. Protein supplementation lowers blood pressure in overweight adults: Effect of dietary proteins on blood pressure (PROPRES), a randomized trial

    NARCIS (Netherlands)

    Teunissen-Beekman, K.F.M.; Dopheide, J.; Geleijnse, J.M.; Bakker, S.J.L.; Brink, E.J.; Leeuw, P.W. de; Baak, M.A. van

    2012-01-01

    Background: Dietary protein intake may help to manage blood pressure (BP) and prevent complications associated with elevated BP. Objective: The objective of this study was to determine whether 4 wk of increased protein intake (∼25% compared with ;15% of energy intake that isoenergetically replaces

  20. Protein Requirements in the Critically Ill: A Randomized Controlled Trial Using Parenteral Nutrition.

    Science.gov (United States)

    Ferrie, Suzie; Allman-Farinelli, Margaret; Daley, Mark; Smith, Kristine

    2016-08-01

    Current recommendations for higher protein/amino acid provision in the critically ill are based on weak evidence. This double-blinded randomized controlled trial aimed to compare standard amino acid intake with the higher level recommended as the minimum for critically ill patients. In total, 119 patients requiring parenteral nutrition (PN) in an intensive care unit (ICU) were randomized to receive blinded PN solutions containing amino acids at either 0.8 g/kg or 1.2 g/kg. Primary outcome was handgrip strength at ICU discharge. Secondary outcomes measured at study day 7 included handgrip strength, fatigue score (using the Chalder scale), and ultrasound measurements of muscle thickness at defined body sites. Analysis of covariance was used to control for age, sex, nutrition status (Subjective Global Assessment), Acute Physiology and Chronic Health Evaluation II (APACHE II) score, and baseline measurement. Actual amino acid delivery to the 2 groups was 0.9 and 1.1 g/kg respectively, averaged over the first 7 days. Grip strength at ICU discharge was not significantly different between groups (P =054) despite being improved at study day 7 in the group receiving the higher level of amino acids (mean [SD], 22.1 [10.1] vs 18.5 [11.8] kg, P =025). These patients also had less fatigue (Chalder score, mean [SD], 5.4 [2.2] vs 6.2 [2.2], P = .045) and greater forearm muscle thickness on ultrasound (mean [SD], 3.2 [0.4] vs 2.8 [0.4] cm, P < .0001). Nitrogen balance was significantly better at study day 3 but not at day 7. There was no difference between groups in mortality or length-of-stay measures. The higher level of amino acids was associated with small improvements in a number of different measures, supporting guideline recommendations for ICU patients. This trial was registered at Australian New Zealand Clinical Trials Registry (www.anzctr.org.au) as ACTRN12609000366257. © 2015 American Society for Parenteral and Enteral Nutrition.

  1. Effect of Plant Protein on Blood Lipids: A Systematic Review and Meta-Analysis of Randomized Controlled Trials.

    Science.gov (United States)

    Li, Siying S; Blanco Mejia, Sonia; Lytvyn, Lyubov; Stewart, Sarah E; Viguiliouk, Effie; Ha, Vanessa; de Souza, Russell J; Leiter, Lawrence A; Kendall, Cyril W C; Jenkins, David J A; Sievenpiper, John L

    2017-12-20

    There is a heightened interest in plant-based diets for cardiovascular disease prevention. Although plant protein is thought to mediate such prevention through modifying blood lipids, the effect of plant protein in specific substitution for animal protein on blood lipids remains unclear. To assess the effect of this substitution on established lipid targets for cardiovascular risk reduction, we conducted a systematic review and meta-analysis of randomized controlled trials using the Grading of Recommendations Assessment, Development, and Evaluation system. MEDLINE, EMBASE, and the Cochrane Registry were searched through September 9, 2017. We included randomized controlled trials of ≥3 weeks comparing the effect of plant protein in substitution for animal protein on low-density lipoprotein cholesterol, non-high-density lipoprotein cholesterol, and apolipoprotein B. Two independent reviewers extracted relevant data and assessed risk of bias. Data were pooled by the generic inverse variance method and expressed as mean differences with 95% confidence intervals. Heterogeneity was assessed (Cochran Q statistic) and quantified (I2 statistic). The overall quality (certainty) of the evidence was assessed using the Grading of Recommendations Assessment, Development, and Evaluation system. One-hundred twelve randomized controlled trials met the eligibility criteria. Plant protein in substitution for animal protein decreased low-density lipoprotein cholesterol by 0.16 mmol/L (95% confidence interval, -0.20 to -0.12 mmol/L; PURL: http://www.clinicaltrials.gov. Unique identifier: NCT02037321. © 2017 The Authors. Published on behalf of the American Heart Association, Inc., by Wiley.

  2. [Rapid selection of recombinant orf virus expression vectors using green fluorescent protein].

    Science.gov (United States)

    Zhang, Jiachun; Guo, Xianfeng; Zhang, Min; Wu, Feifan; Peng, Yongzheng

    2016-01-01

    To construct a universal, highly attenuated orf virus expression vector for exogenous genes using green fluorescent protein (GFP) as the reporter gene. The flanking regions of the ORFV132 of orf virus DNA were amplified by PCR to construct the shuttle plasmid pSPV-132LF-EGFP-132RF. The shuttle plasmid was transfected into OFTu cells and GFP was incorporated into orf virus IA82Delta 121 by homologous recombination. The recombinant IA82Delta121-V was selected by green fluorescent signal. The deletion gene was identified by PCR and sequencing. The effects of ORFV132 knockout were evaluated by virus titration and by observing the proliferation of the infected vascular endothelial cells in vitro. The recombinant orf virus IA82Delta121-V was obtained successfully and quickly, and the deletion of ORFV132 did not affect the replication of the virus in vitro but reduced its virulence. Green fluorescent protein is a selectable marker for rapid, convenient and stable selection of the recombinant viruses. Highly attenuated recombinant orf virus IA82Delta121-V can serve as a new expression vector for exogenous genes.

  3. Functional selectivity of G-protein-coupled receptors: from recombinant systems to native human cells.

    Science.gov (United States)

    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.

  4. C-reactive protein levels and body mass index: elucidating direction of causation through reciprocal Mendelian randomization

    DEFF Research Database (Denmark)

    Timpson, N J; Nordestgaard, B G; Harbord, R M

    2011-01-01

    Context:The assignment of direction and causality within networks of observational associations is problematic outside randomized control trials, and the presence of a causal relationship between body mass index (BMI) and C-reactive protein (CRP) is disputed.Objective:Using reciprocal Mendelian...... randomization, we aim to assess the direction of causality in relationships between BMI and CRP and to demonstrate this as a promising analytical technique.Participants and methods:The study was based on a large, cross-sectional European study from Copenhagen, Denmark. Genetic associates of BMI (FTO(rs9939609...

  5. Acetylation of pregnane X receptor protein determines selective function independent of ligand activation

    Energy Technology Data Exchange (ETDEWEB)

    Biswas, Arunima; Pasquel, Danielle [Albert Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY 10461 (United States); Tyagi, Rakesh Kumar [Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067 (India); Mani, Sridhar, E-mail: sridhar.mani@einstein.yu.edu [Albert Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY 10461 (United States)

    2011-03-18

    Research highlights: {yields} Pregnane X receptor (PXR), a major regulatory protein, is modified by acetylation. {yields} PXR undergoes dynamic deacetylation upon ligand-mediated activation. {yields} SIRT1 partially mediates PXR deacetylation. {yields} PXR deacetylation per se induces lipogenesis mimicking ligand-mediated activation. -- Abstract: Pregnane X receptor (PXR), like other members of its class of nuclear receptors, undergoes post-translational modification [PTM] (e.g., phosphorylation). However, it is unknown if acetylation (a major and common form of protein PTM) is observed on PXR and, if it is, whether it is of functional consequence. PXR has recently emerged as an important regulatory protein with multiple ligand-dependent functions. In the present work we show that PXR is indeed acetylated in vivo. SIRT1 (Sirtuin 1), a NAD-dependent class III histone deacetylase and a member of the sirtuin family of proteins, partially mediates deacetylation of PXR. Most importantly, the acetylation status of PXR regulates its selective function independent of ligand activation.

  6. Discovering short linear protein motif based on selective training of profile hidden Markov models.

    Science.gov (United States)

    Song, Tao; Gu, Hong

    2015-07-21

    Short linear motifs (SLiMs) in proteins are relatively conservative sequence patterns within disordered regions of proteins, typically 3-10 amino acids in length. They play an important role in mediating protein-protein interactions. Discovering SLiMs by computational methods has attracted more and more attention, most of which were based on regular expressions and profiles. In this paper, a de novo motif discovery method was proposed based on profile hidden Markov models (HMMs), which can not only provide the emission probabilities of amino acids in the defined positions of SLiMs, but also model the undefined positions. We adopted the ordered region masking and the relative local conservation (RLC) masking to improve the signal to noise ratio of the query sequences while applying evolutionary weighting to make the important sequences in evolutionary process get more attention by the selective training of profile HMMs. The experimental results show that our method and the profile-based method returned different subsets within a SLiMs dataset, and the performance of the two approaches are equivalent on a more realistic discovery dataset. Profile HMM-based motif discovery methods complement the existing methods and provide another way for SLiMs analysis. Copyright © 2015 Elsevier Ltd. All rights reserved.

  7. Crude protein, fibre and phytic acid in vitro digestibility of selected legume and buckwheat samples

    Directory of Open Access Journals (Sweden)

    Petra Vojtíšková

    2013-01-01

    Full Text Available The aim of this study was to determine crude protein, fibre and phytic acid in vitro digestibility of selected legumes and buckwheat products. All analyses except the phytic acid contents were performed in the line with the Commission Regulation (EC No. 152/2009. A modified version of Holt’s Method was used for phytic acid (phytate determination. None of all samples contained more than 11% of moisture. Soybeans are rich in crude protein; they contain nearly 40% of this compound. The content of crude protein in buckwheat flours was about 14%. The highest amount of phytate was found in common beans and soybeans-about 2 g/100 g of dry matter. On the other hand, the lowest phytate content was observed in buckwheat pasta (F. esculentum groats was 1.9 g per 100 g of dry matter. In vitro digestibility was determined using an incubator Daisy and pepsin enzymes and the combination of pepsin and pancreatin. The highest coefficient of crude protein digestibility was discovered to be in peels and wholemeal flour. The greatest fibre digestibility coefficients were obtained for peels, which contain about 65% of fibre in their dry matter. When pepsin was used, a higher phytic acid digestibility coefficient for G. max, Ph. vulgaris, peels, flour, groats and broken groats was observed; while when the combination of pepsin and pancreatin was used, higher phytic acid digestibility coefficients for peas, lentil and wholemeal flour were observed.

  8. Improved production of membrane proteins in Escherichia coli by selective codon substitutions

    DEFF Research Database (Denmark)

    Nørholm, Morten H.H.; Toddo, Stephen; Virkki, Minttu T.I.

    2013-01-01

    K) for membrane transporters. For both coding sequences, synonymous codon substitutions in the region adjacent to the AUG start led to significant improvements in expression, whereas multi-parameter sequence optimization of codons throughout the coding sequence failed. We conclude that coding sequences can be re......Membrane proteins are extremely challenging to produce in sufficient quantities for biochemical and structural analysis and there is a growing demand for solutions to this problem. In this study we attempted to improve expression of two difficult-to-express coding sequences (araH and nar......-wired for high-level protein expression by selective engineering of the 5′ coding sequence with synonymous codons, thus circumventing the need to consider whole sequence optimization....

  9. Presence of psychoactive substances in oral fluid from randomly selected drivers in Denmark

    DEFF Research Database (Denmark)

    Simonsen, K. Wiese; Steentoft, A.; Hels, Tove

    2012-01-01

    This roadside study is the Danish part of the EU-project DRUID (Driving under the Influence of Drugs, Alcohol, and Medicines) and included three representative regions in Denmark. Oral fluid samples (n = 3002) were collected randomly from drivers using a sampling scheme stratified by time, season...... of narcotic drugs. It can be concluded that driving under the influence of drugs is as serious a road safety problem as drunk driving.......This roadside study is the Danish part of the EU-project DRUID (Driving under the Influence of Drugs, Alcohol, and Medicines) and included three representative regions in Denmark. Oral fluid samples (n = 3002) were collected randomly from drivers using a sampling scheme stratified by time, season...

  10. Presence of psychoactive substances in oral fluid from randomly selected drivers in Denmark

    DEFF Research Database (Denmark)

    Simonsen, Kirsten Wiese; Steentoft, Anni; Hels, Tove

    2012-01-01

    This roadside study is the Danish part of the EU-project DRUID (Driving under the Influence of Drugs, Alcohol, and Medicines) and included three representative regions in Denmark. Oral fluid samples (n = 3002) were collected randomly from drivers using a sampling scheme stratified by time, season....... It can be concluded that driving under the influence of drugs is as serious a road safety problem as drunk driving.......This roadside study is the Danish part of the EU-project DRUID (Driving under the Influence of Drugs, Alcohol, and Medicines) and included three representative regions in Denmark. Oral fluid samples (n = 3002) were collected randomly from drivers using a sampling scheme stratified by time, season...

  11. Feature selection and classification of mechanical fault of an induction motor using random forest classifier

    Directory of Open Access Journals (Sweden)

    Raj Kumar Patel

    2016-09-01

    Full Text Available Fault detection and diagnosis is the most important technology in condition-based maintenance (CBM system for rotating machinery. This paper experimentally explores the development of a random forest (RF classifier, a recently emerged machine learning technique, for multi-class mechanical fault diagnosis in bearing of an induction motor. Firstly, the vibration signals are collected from the bearing using accelerometer sensor. Parameters from the vibration signal are extracted in the form of statistical features and used as input feature for the classification problem. These features are classified through RF classifiers for four class problems. The prime objective of this paper is to evaluate effectiveness of random forest classifier on bearing fault diagnosis. The obtained results compared with the existing artificial intelligence techniques, neural network. The analysis of results shows the better performance and higher accuracy than the well existing techniques.

  12. Timing and pattern of postexercise protein ingestion affects whole-body protein balance in healthy children: a randomized trial.

    Science.gov (United States)

    Volterman, Kimberly A; Moore, Daniel R; Breithaupt, Peter; Grathwohl, Dominik; Offord, Elizabeth A; Karagounis, Leonidas G; Timmons, Brian W

    2017-11-01

    The dose and timing of postexercise protein ingestion can influence whole-body protein balance (WBPB) in adults, although comparable data from children are scarce. This study investigated how protein intake (both amount and distribution) postexercise can affect WBPB in physically active children. Thirty-five children (26 males; 9-13 years old) underwent a 5-day adaptation diet, maintaining a protein intake of 0.95 g·kg-1·day-1. Participants consumed [15N]glycine (2 mg·kg-1) before performing 3 × 20 min of variable-intensity cycling, and whole-body protein kinetics were assessed over 6 and 24 h of recovery. Fifteen grams of protein was distributed across 2 isoenergetic carbohydrate-containing beverages (15 and 240 min postexercise) containing reciprocal amounts of protein (i.e., 0 + 15 g, 5 + 10 g, 10 + 5 g, and 15 + 0 g for Groups A-D, respectively). Over the 6 h that included the exercise bout and consumption of the first beverage at 15 min postexercise, WBPB (i.e., synthesis - breakdown) demonstrated a linear increase of 0.647 g·kg-1·day-1 per 1 g protein intake (P < 0.001). Over 24 h, robust regression revealed that WBPB was best modeled by a parabola (P < 0.05), suggesting that a maximum in WBPB was achieved between groups B and C. In conclusion, despite a dose response early in recovery, a periodized protein intake with multiple smaller doses after physical activity may be more beneficial than a single bolus dose in promoting daily WBPB in healthy active children.

  13. Differential Evolutionary Selection and Natural Evolvability Observed in ALT Proteins of Human Filarial Parasites.

    Directory of Open Access Journals (Sweden)

    Neil C Devoe

    Full Text Available The abundant larval transcript (ALT-2 protein is present in all members of the Filarioidea, and has been reported as a potential candidate antigen for a subunit vaccine against lymphatic filariasis. To assess the potential for vaccine escape or heterologous protection, we examined the evolutionary selection acting on ALT-2. The ratios of nonsynonymous (K(a to synonymous (K(s mutation frequencies (ω were calculated for the alt-2 genes of the lymphatic filariasis agents Brugia malayi and Wuchereria bancrofti and the agents of river blindness and African eyeworm disease Onchocerca volvulus and Loa loa. Two distinct Bayesian models of sequence evolution showed that ALT-2 of W. bancrofti and L. loa were under significant (P<0.05; P < 0.001 diversifying selection, while ALT-2 of B. malayi and O. volvulus were under neutral to stabilizing selection. Diversifying selection as measured by ω values was notably strongest on the region of ALT-2 encoding the signal peptide of L. loa and was elevated in the variable acidic domain of L. loa and W. bancrofti. Phylogenetic analysis indicated that the ALT-2 consensus sequences formed three clades: the first consisting of B. malayi, the second consisting of W. bancrofti, and the third containing both O. volvulus and L. loa. ALT-2 selection was therefore not predictable by phylogeny or pathology, as the two species parasitizing the eye were selected differently, as were the two species parasitizing the lymphatic system. The most immunogenic regions of L. loa and W. bancrofti ALT-2 sequence as modeled by antigenicity prediction analysis did not correspond with elevated levels of diversifying selection, and were not selected differently than predicted antigenic epitopes in B. malayi and O. volvulus. Measurements of ALT-2 evolvability made by χ2 analysis between alleles that were stable (O. volvulus and B. malayi and those that were under diversifying selection (W. bancrofti and L. loa indicated significant (P<0

  14. PClass: Protein Quaternary Structure Classification by Using Bootstrapping Strategy as Model Selection

    Directory of Open Access Journals (Sweden)

    Chi-Chou Huang

    2018-02-01

    Full Text Available Protein quaternary structure complex is also known as a multimer, which plays an important role in a cell. The dimer structure of transcription factors is involved in gene regulation, but the trimer structure of virus-infection-associated glycoproteins is related to the human immunodeficiency virus. The classification of the protein quaternary structure complex for the post-genome era of proteomics research will be of great help. Classification systems among protein quaternary structures have not been widely developed. Therefore, we designed the architecture of a two-layer machine learning technique in this study, and developed the classification system PClass. The protein quaternary structure of the complex is divided into five categories, namely, monomer, dimer, trimer, tetramer, and other subunit classes. In the framework of the bootstrap method with a support vector machine, we propose a new model selection method. Each type of complex is classified based on sequences, entropy, and accessible surface area, thereby generating a plurality of feature modules. Subsequently, the optimal model of effectiveness is selected as each kind of complex feature module. In this stage, the optimal performance can reach as high as 70% of Matthews correlation coefficient (MCC. The second layer of construction combines the first-layer module to integrate mechanisms and the use of six machine learning methods to improve the prediction performance. This system can be improved over 10% in MCC. Finally, we analyzed the performance of our classification system using transcription factors in dimer structure and virus-infection-associated glycoprotein in trimer structure. PClass is available via a web interface at http://predictor.nchu.edu.tw/PClass/.

  15. Fundamental role of the fostriecin unsaturated lactone and implications for selective protein phosphatase inhibition.

    Science.gov (United States)

    Buck, Suzanne B; Hardouin, Christophe; Ichikawa, Satoshi; Soenen, Danielle R; Gauss, C-M; Hwang, Inkyu; Swingle, Mark R; Bonness, Kathy M; Honkanen, Richard E; Boger, Dale L

    2003-12-24

    Key derivatives and analogues of fostriecin were prepared and examined that revealed a fundamental role for the unsaturated lactone and confirmed the essential nature of the phosphate monoester. Thus, an identical 200-fold reduction in protein phosphatase 2A (PP2A) inhibition is observed with either the saturated lactone (7) or with an analogue that lacks the entire lactone (15). This 200-fold increase in PP2A inhibition attributable to the unsaturated lactone potentially may be due to reversible C269 alkylation within the PP beta12-beta13 active site loop accounting for PP2A/4 potency and selectivity.

  16. Selective nerve root blocks vs. caudal epidural injection for single level prolapsed lumbar intervertebral disc - A prospective randomized study.

    Science.gov (United States)

    Singh, Sudhir; Kumar, Sanjiv; Chahal, Gaurav; Verma, Reetu

    2017-01-01

    Chronic lumbar radiculopathy has a lifetime prevalence of 5.3% in men and 3.7% in women. It usually resolves spontaneously, but up to 30% cases will have pronounced symptoms even after one year. A prospective randomized single-blind study was conducted to compare the efficacy of caudal epidural steroid injection and selective nerve root block in management of pain and disability in cases of lumbar disc herniation. Eighty patients with confirmed single-level lumbar disc herniation were equally divided in two groups: (a) caudal epidural and (b) selective nerve root block group, by a computer-generated random allocation method. The caudal group received three injections of steroid mixed with local anesthetics while selective nerve root block group received single injection of steroid mixed with local anesthetic agent. Patients were assessed for pain relief and reduction in disability. In SNRB group, pain reduced by more than 50% up till 6 months, while in caudal group more than 50% reduction of pain was maintained till 1 year. The reduction in ODI in SNRB group was 52.8% till 3 months, 48.6% till 6 months, and 46.7% at 1 year, while in caudal group the improvement was 59.6%, 64.6%, 65.1%, and 65.4% at corresponding follow-up periods, respectively. Caudal epidural block is an easy and safe method with better pain relief and improvement in functional disability than selective nerve root block. Selective nerve root block injection is technically more demanding and has to be given by a skilled anesthetist.

  17. Consuming a mixed diet enriched with lupin protein beneficially affects plasma lipids in hypercholesterolemic subjects: a randomized controlled trial.

    Science.gov (United States)

    Bähr, Melanie; Fechner, Anita; Kiehntopf, Michael; Jahreis, Gerhard

    2015-02-01

    The objectives of this study were to assess whether 25 g/d lupin protein, integrated into a mixed diet, might affect cardiovascular risk factors and whether l-arginine was responsible for these effects. Seventy-two hypercholesterolemic subjects participated in the randomized, controlled, double-blind three-phase crossover study. They were assigned to three diets with 25 g/d lupin protein (LP), milk protein (MP) or milk protein plus 1.6 g/d arginine (MPA) each for 28 d in a random order interrupted by 6-week washout periods. Lupin protein and the comparator milk protein were incorporated into complex food products (bread, roll, sausage, and vegetarian spread). Arginine was administered via capsules. Sixty-eight subjects were included in final analyses. Compared with MP, LDL cholesterol was significantly lower after LP. Compared with MP and MPA, homocysteine was significantly lower after LP. Compared with baseline, concentrations of total, LDL, and HDL cholesterol significantly decreased after LP and MPA. Triacylglycerols and uric acid significantly decreased after LP. The relative changes in total and LDL cholesterol were significantly greater for subjects with severe hypercholesterolemia (>6.6 mmol/L) than those with moderate hypercholesterolemia (5.2-6.6 mmol/L). The present study showed for the first time that incorporation of 25 g/d of lupin protein into a variety of complex food products lowers total and LDL cholesterol, triacylglycerols, homocysteine, and uric acid in hypercholesterolemic subjects. The hypocholesterolemic effect is stronger in subjects with severe hypercholesterolemia. Arginine might be responsible for some, but not all of the beneficial effects of lupin protein. This trial was registered at http://clinicaltrials.gov (study ID number NCT01598649). Copyright © 2014 Elsevier Ltd and European Society for Clinical Nutrition and Metabolism. All rights reserved.

  18. An intein with genetically selectable markers provides a new approach to internally label proteins with GFP

    Directory of Open Access Journals (Sweden)

    Davis Trisha N

    2011-06-01

    Full Text Available Abstract Background Inteins are proteins that catalyze their own removal from within larger precursor proteins. In the process they splice the flanking protein sequences, termed the N-and C-terminal exteins. Large inteins frequently have a homing endonuclease that is involved in maintaining the intein in the host. Splicing and nuclease activity are independent and distinct domains in the folded structure. We show here that other biochemical activities can be incorporated into an intein in place of the endonuclease without affecting splicing and that these activities can provide genetic selection for the intein. We have coupled such a genetically marked intein with GFP as the N-terminal extein to create a cassette to introduce GFP within the interior of a targeted protein. Results The Pch PRP8 mini-intein of Penicillium chrysogenum was modified to include: 1 aminoglycoside phosphotransferase; 2 imidazoleglycerol-phosphate dehydratase, His5 from S. pombe ; 3 hygromycin B phosphotransferase; and 4 the transcriptional activator LexA-VP16. The proteins were inserted at the site of the lost endonuclease. When expressed in E. coli, all of the modified inteins spliced at high efficiency. Splicing efficiency was also greater than 96% when expressed from a plasmid in S. cerevisiae. In addition the inteins conferred either G418 or hygromycin resistance, or histidine or leucine prototropy, depending on the inserted marker and the yeast genetic background. DNA encoding the marked inteins coupled to GFP as the N-terminal extein was PCR amplified with ends homologous to an internal site in the yeast calmodulin gene CMD1. The DNA was transformed into yeast and integrants obtained by direct selection for the intein's marker. The His5-marked intein yielded a fully functional calmodulin that was tagged with GFP within its central linker. Conclusions Inteins continue to show their flexibility as tools in molecular biology. The Pch PRP8 intein can successfully

  19. A theory for the origin of a self-replicating chemical system. I - Natural selection of the autogen from short, random oligomers

    Science.gov (United States)

    White, D. H.

    1980-01-01

    A general theory is presented for the origin of a self-replicating chemical system, termed an autogen, which is capable of both crude replication and translation (protein synthesis). The theory requires the availability of free energy and monomers to the system, a significant background low-yield synthesis of kinetically stable oligopeptides and oligonucleotides, the localization of the oligomers, crude oligonucleotide selectivity of amino acids during oligopeptide synthesis, crude oligonucleotide replication, and two short peptide families which catalyze replication and translation, to produce a localized group of at least one copy each of two protogenes and two protoenzymes. The model posits a process of random oligomerization, followed by the random nucleation of functional components and the rapid autocatalytic growth of the functioning autogen to macroscopic amounts, to account for the origin of the first self-replicating system. Such a process contains steps of such high probability and short time periods that it is suggested that the emergence of an autogen in a laboratory experiment of reasonable time scale may be possible.

  20. KinMutRF: a random forest classifier of sequence variants in the human protein kinase superfamily

    DEFF Research Database (Denmark)

    Pons, Tirso; Vazquez, Miguel; Matey-Hernandez, María Luisa

    2016-01-01

    remains challenging: cells tolerate most genomic alterations and only a minor fraction disrupt molecular function sufficiently and drive disease. Results: KinMutRF is a novel random-forest method to automatically identify pathogenic variants in human kinases. Twenty six decision trees implemented......Background: The association between aberrant signal processing by protein kinases and human diseases such as cancer was established long time ago. However, understanding the link between sequence variants in the protein kinase superfamily and the mechanistic complex traits at the molecular level...... as a random forest ponder a battery of features that characterize the variants: a) at the gene level, including membership to a Kinbase group and Gene Ontology terms; b) at the PFAM domain level; and c) at the residue level, the types of amino acids involved, changes in biochemical properties, functional...

  1. DNA display selection of peptide ligands for a full-length human G protein-coupled receptor on CHO-K1 cells.

    Directory of Open Access Journals (Sweden)

    Nobuhide Doi

    Full Text Available The G protein-coupled receptors (GPCRs, which form the largest group of transmembrane proteins involved in signal transduction, are major targets of currently available drugs. Thus, the search for cognate and surrogate peptide ligands for GPCRs is of both basic and therapeutic interest. Here we describe the application of an in vitro DNA display technology to screening libraries of peptide ligands for full-length GPCRs expressed on whole cells. We used human angiotensin II (Ang II type-1 receptor (hAT1R as a model GPCR. Under improved selection conditions using hAT1R-expressing Chinese hamster ovary (CHO-K1 cells as bait, we confirmed that Ang II gene could be enriched more than 10,000-fold after four rounds of selection. Further, we successfully selected diverse Ang II-like peptides from randomized peptide libraries. The results provide more precise information on the sequence-function relationships of hAT1R ligands than can be obtained by conventional alanine-scanning mutagenesis. Completely in vitro DNA display can overcome the limitations of current display technologies and is expected to prove widely useful for screening diverse libraries of mutant peptide and protein ligands for receptors that can be expressed functionally on the surface of CHO-K1 cells.

  2. Chemical biology based on target-selective degradation of proteins and carbohydrates using light-activatable organic molecules.

    Science.gov (United States)

    Toshima, Kazunobu

    2013-05-01

    Proteins and carbohydrates play crucial roles in a wide range of biological processes, including serious diseases. The development of novel and innovative methods for selective control of specific proteins and carbohydrates functions has attracted much attention in the field of chemical biology. In this account article, the development of novel chemical tools, which can degrade target proteins and carbohydrates by irradiation with a specific wavelength of light under mild conditions without any additives, is introduced. This novel class of photochemical agents promise bright prospects for finding not only molecular-targeted bioprobes for understanding of the structure-activity relationships of proteins and carbohydrates but also novel therapeutic drugs targeting proteins and carbohydrates.

  3. Selective binding modes and allosteric inhibitory effects of lupane triterpenes on protein tyrosine phosphatase 1B.

    Science.gov (United States)

    Jin, Tiantian; Yu, Haibo; Huang, Xu-Feng

    2016-02-11

    Protein Tyrosine Phosphatase 1B (PTP1B) has been recognized as a promising therapeutic target for treating obesity, diabetes, and certain cancers for over a decade. Previous drug design has focused on inhibitors targeting the active site of PTP1B. However, this has not been successful because the active site is positively charged and conserved among the protein tyrosine phosphatases. Therefore, it is important to develop PTP1B inhibitors with alternative inhibitory strategies. Using computational studies including molecular docking, molecular dynamics simulations, and binding free energy calculations, we found that lupane triterpenes selectively inhibited PTP1B by targeting its more hydrophobic and less conserved allosteric site. These findings were verified using two enzymatic assays. Furthermore, the cell culture studies showed that lupeol and betulinic acid inhibited the PTP1B activity stimulated by TNFα in neurons. Our study indicates that lupane triterpenes are selective PTP1B allosteric inhibitors with significant potential for treating those diseases with elevated PTP1B activity.

  4. Bayesian Markov random field analysis for integrated network-based protein function prediction

    NARCIS (Netherlands)

    Kourmpetis, Y.I.A.

    2011-01-01

    Unravelling the functions of proteins is one of the most important aims of modern biology. Experimental inference of protein function is expensive and not scalable to large datasets. In this thesis a probabilistic method for protein function prediction is presented that integrates different types of

  5. Novel approach for selecting the best predictor for identifying the binding sites in DNA binding proteins.

    Science.gov (United States)

    Nagarajan, R; Ahmad, Shandar; Gromiha, M Michael

    2013-09-01

    Protein-DNA complexes play vital roles in many cellular processes by the interactions of amino acids with DNA. Several computational methods have been developed for predicting the interacting residues in DNA-binding proteins using sequence and/or structural information. These methods showed different levels of accuracies, which may depend on the choice of data sets used in training, the feature sets selected for developing a predictive model, the ability of the models to capture information useful for prediction or a combination of these factors. In many cases, different methods are likely to produce similar results, whereas in others, the predictors may return contradictory predictions. In this situation, a priori estimates of prediction performance applicable to the system being investigated would be helpful for biologists to choose the best method for designing their experiments. In this work, we have constructed unbiased, stringent and diverse data sets for DNA-binding proteins based on various biologically relevant considerations: (i) seven structural classes, (ii) 86 folds, (iii) 106 superfamilies, (iv) 194 families, (v) 15 binding motifs, (vi) single/double-stranded DNA, (vii) DNA conformation (A, B, Z, etc.), (viii) three functions and (ix) disordered regions. These data sets were culled as non-redundant with sequence identities of 25 and 40% and used to evaluate the performance of 11 different methods in which online services or standalone programs are available. We observed that the best performing methods for each of the data sets showed significant biases toward the data sets selected for their benchmark. Our analysis revealed important data set features, which could be used to estimate these context-specific biases and hence suggest the best method to be used for a given problem. We have developed a web server, which considers these features on demand and displays the best method that the investigator should use. The web server is freely available at

  6. Towards understanding the crosstalk between protein post-translational modifications: Homo- and heterotypic PTM pair distances on protein surfaces are not random.

    Science.gov (United States)

    Korkuć, Paula; Walther, Dirk

    2017-01-01

    Post-translational modifications (PTMs) represent an important regulatory layer influencing the structure and function of proteins. With broader availability of experimental information on the occurrences of different PTM types, the investigation of a potential "crosstalk" between different PTM types and combinatorial effects have moved into the research focus. Hypothesizing that relevant interferences between different PTM types and sites may become apparent when investigating their mutual physical distances, we performed a systematic survey of pairwise homo- and heterotypic distances of seven frequent PTM types considering their sequence and spatial distances in resolved protein structures. We found that actual PTM site distance distributions differ from random distributions with most PTM type pairs exhibiting larger than expected distances with the exception of homotypic phosphorylation site distances and distances between phosphorylation and ubiquitination sites that were found to be closer than expected by chance. Random reference distributions considering canonical acceptor amino acid residues only were found to be shifted to larger distances compared to distances between any amino acid residue type indicating an underlying tendency of PTM-amenable residue types to be further apart than randomly expected. Distance distributions based on sequence separations were found largely consistent with their spatial counterparts suggesting a primary role of sequence-based pairwise PTM-location encoding rather than folding-mediated effects. Our analysis provides a systematic and comprehensive overview of the characteristics of pairwise PTM site distances on proteins and reveals that, predominantly, PTM sites tend to avoid close proximity with the potential implication that an independent attachment or removal of PTMs remains possible. Proteins 2016; 85:78-92. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  7. Amyloid precursor protein selective gamma-secretase inhibitors for treatment of Alzheimer's disease.

    Science.gov (United States)

    Basi, Guriqbal S; Hemphill, Susanna; Brigham, Elizabeth F; Liao, Anna; Aubele, Danielle L; Baker, Jeanne; Barbour, Robin; Bova, Michael; Chen, Xiao-Hua; Dappen, Michael S; Eichenbaum, Tovah; Goldbach, Erich; Hawkinson, Jon; Lawler-Herbold, Rose; Hu, Kang; Hui, Terence; Jagodzinski, Jacek J; Keim, Pamela S; Kholodenko, Dora; Latimer, Lee H; Lee, Mike; Marugg, Jennifer; Mattson, Matthew N; McCauley, Scott; Miller, James L; Motter, Ruth; Mutter, Linda; Neitzel, Martin L; Ni, Huifang; Nguyen, Lan; Quinn, Kevin; Ruslim, Lany; Semko, Christopher M; Shapiro, Paul; Smith, Jenifer; Soriano, Ferdie; Szoke, Balazs; Tanaka, Kevin; Tang, Pearl; Tucker, John A; Ye, Xiacong Michael; Yu, Mei; Wu, Jing; Xu, Ying-Zi; Garofalo, Albert W; Sauer, John Michael; Konradi, Andrei W; Ness, Daniel; Shopp, George; Pleiss, Michael A; Freedman, Stephen B; Schenk, Dale

    2010-12-29

    Inhibition of gamma-secretase presents a direct target for lowering Aβ production in the brain as a therapy for Alzheimer's disease (AD). However, gamma-secretase is known to process multiple substrates in addition to amyloid precursor protein (APP), most notably Notch, which has limited clinical development of inhibitors targeting this enzyme. It has been postulated that APP substrate selective inhibitors of gamma-secretase would be preferable to non-selective inhibitors from a safety perspective for AD therapy. In vitro assays monitoring inhibitor potencies at APP γ-site cleavage (equivalent to Aβ40), and Notch ε-site cleavage, in conjunction with a single cell assay to simultaneously monitor selectivity for inhibition of Aβ production vs. Notch signaling were developed to discover APP selective gamma-secretase inhibitors. In vivo efficacy for acute reduction of brain Aβ was determined in the PDAPP transgene model of AD, as well as in wild-type FVB strain mice. In vivo selectivity was determined following seven days x twice per day (b.i.d.) treatment with 15 mg/kg/dose to 1,000 mg/kg/dose ELN475516, and monitoring brain Aβ reduction vs. Notch signaling endpoints in periphery. The APP selective gamma-secretase inhibitors ELN318463 and ELN475516 reported here behave as classic gamma-secretase inhibitors, demonstrate 75- to 120-fold selectivity for inhibiting Aβ production compared with Notch signaling in cells, and displace an active site directed inhibitor at very high concentrations only in the presence of substrate. ELN318463 demonstrated discordant efficacy for reduction of brain Aβ in the PDAPP compared with wild-type FVB, not observed with ELN475516. Improved in vivo safety of ELN475516 was demonstrated in the 7d repeat dose study in wild-type mice, where a 33% reduction of brain Aβ was observed in mice terminated three hours post last dose at the lowest dose of inhibitor tested. No overt in-life or post-mortem indications of systemic toxicity, nor

  8. Protein corona and phospholipase activity drive selective accumulation of nanomicelles in atherosclerotic plaques.

    Science.gov (United States)

    Lechuga-Vieco, Ana V; Groult, Hugo; Pellico, Juan; Mateo, Jesús; Enríquez, Jose A; Ruiz-Cabello, Jesús; Herranz, Fernando

    2018-01-06

    ApoB-100 and Phosphatidylcholine-specific phospholipase C (PC-PLC) are important contributors to atherosclerosis development. ApoB-100 is the main structural protein of LDL, being directly associated with atherosclerosis plaque generation. PC-PLC is highly expressed in atherosclerosis lesions and contributes to their progression. We show how phosphatidylcholine-coated nanomicelles can be used for specific characterisation of atherosclerosis plaque. Results show that ApoB-100 in the protein corona of the nanomicelle targets the particles to atherosclerotic areas in apolipoprotein E -/- mice. Furthermore, PC-PLC selectively removes the polar heads from the phospholipid coating of the nanomicelles leading to their accumulation. To fully characterise the behaviour of the nanomicelles, we developed multimodal probes using a nanoemulsion step. Hybrid imaging revealed plaque accumulation of the nanomicelles and colocalisation with PC-PLC expression and ApoB-100 in the plaque. This study shows how protein corona composition and enzyme-driven nanomaterial accumulation can be used for detection of atherosclerosis. Copyright © 2018. Published by Elsevier Inc.

  9. Handheld highly selective plasmonic chem/biosensor using engineered binding proteins for extreme conformational changes

    Science.gov (United States)

    Kosciolek, Derek J.; Sonar, Ajay; Lepak, Lori A.; Schnatz, Peter; Bendoym, Igor; Brown, Mia C.; Koder, Ronald L.; Crouse, David T.

    2017-08-01

    In this project we develop a handheld, portable, highly selective and sensitive chem/biosensor that has potential applications in both airborne and water-based environmental sensing. The device relies on a plasmonic chip of subwavelength-scale periodic gold rods engineered to resonate in the near infrared. The chip is functionalized with a novel class of proteins that exhibit large conformational changes upon binding to a specific target analyte. The subsequent change in local refractive index near the surface of the gold is one to two orders of magnitude greater than current conventional methods, which produces a readily measurable 5 to 10 percent difference in light transmission. This allows us to forgo traditional, bulky tabletop setups in favor of a compact form factor. Using commercially available optics to construct a transmission-based optical train, measured changes in bulk refractive index are presented here. While synthesis of binding protein efforts are focused on heme as analyte for proof of concept validation, the functionalized protein can be engineered to pair with a wide variety of analytes with minimal alterations to the plasmonic chip or device design. Such flexibility allows for this device to potentially meet the needs of first responders and health care professionals in a multitude of scenarios.

  10. Biotransformation and in vivo stability of protein biotherapeutics: impact on candidate selection and pharmacokinetic profiling.

    Science.gov (United States)

    Hall, Michael P

    2014-11-01

    Historically, since the metabolism of administered peptide/protein drugs ("biotherapeutics") has been expected to undergo predictable pathways similar to endogenous proteins, comprehensive biotherapeutic metabolism studies have not been widely reported in the literature. However, since biotherapeutics have rapidly evolved into an impressive array of eclectic modalities, there has been a shift toward understanding the impact of metabolism on biotherapeutic development. For biotherapeutics containing non-native chemical linkers and other moieties besides natural amino acids, metabolism studies are critical as these moieties may impart undesired toxicology. For biotherapeutics that are composed solely of natural amino acids, where end-stage peptide and amino acid catabolites do not generally pose toxicity concerns, the understanding of biotherapeutic biotransformation, defined as in vivo modifications such as peripherally generated intermediate circulating catabolites prior to end-stage degradation or elimination, may impact in vivo stability and potency/clearance. As of yet, there are no harmonized methodologies for understanding biotherapeutic biotransformation and its impact on drug development, nor is there clear guidance from regulatory agencies on how and when these studies should be conducted. This review provides an update on biotherapeutic biotransformation studies and an overview of lessons learned, tools that have been developed, and suggestions of approaches to address issues. Biotherapeutic biotransformation studies, especially for certain modalities, should be implemented at an early stage of development to 1) understand the impact on potency/clearance, 2) select the most stable candidates or direct protein re-engineering efforts, and 3) select the best bioanalytical technique(s) for proper drug quantification and subsequent pharmacokinetic profiling and exposure/response assessment. Copyright © 2014 by The American Society for Pharmacology and

  11. Positive evolutionary selection of an HD motif on Alzheimer precursor protein orthologues suggests a functional role.

    Directory of Open Access Journals (Sweden)

    István Miklós

    2012-02-01

    Full Text Available HD amino acid duplex has been found in the active center of many different enzymes. The dyad plays remarkably different roles in their catalytic processes that usually involve metal coordination. An HD motif is positioned directly on the amyloid beta fragment (Aβ and on the carboxy-terminal region of the extracellular domain (CAED of the human amyloid precursor protein (APP and a taxonomically well defined group of APP orthologues (APPOs. In human Aβ HD is part of a presumed, RGD-like integrin-binding motif RHD; however, neither RHD nor RXD demonstrates reasonable conservation in APPOs. The sequences of CAEDs and the position of the HD are not particularly conserved either, yet we show with a novel statistical method using evolutionary modeling that the presence of HD on CAEDs cannot be the result of neutral evolutionary forces (p<0.0001. The motif is positively selected along the evolutionary process in the majority of APPOs, despite the fact that HD motif is underrepresented in the proteomes of all species of the animal kingdom. Position migration can be explained by high probability occurrence of multiple copies of HD on intermediate sequences, from which only one is kept by selective evolutionary forces, in a similar way as in the case of the "transcription binding site turnover." CAED of all APP orthologues and homologues are predicted to bind metal ions including Amyloid-like protein 1 (APLP1 and Amyloid-like protein 2 (APLP2. Our results suggest that HDs on the CAEDs are most probably key components of metal-binding domains, which facilitate and/or regulate inter- or intra-molecular interactions in a metal ion-dependent or metal ion concentration-dependent manner. The involvement of naturally occurring mutations of HD (Tottori (D7N and English (H6R mutations in early onset Alzheimer's disease gives additional support to our finding that HD has an evolutionary preserved function on APPOs.

  12. Genetic polymorphism and natural selection of Duffy binding protein of Plasmodium vivax Myanmar isolates

    Science.gov (United States)

    2012-01-01

    Background Plasmodium vivax Duffy binding protein (PvDBP) plays an essential role in erythrocyte invasion and a potential asexual blood stage vaccine candidate antigen against P. vivax. The polymorphic nature of PvDBP, particularly amino terminal cysteine-rich region (PvDBPII), represents a major impediment to the successful design of a protective vaccine against vivax malaria. In this study, the genetic polymorphism and natural selection at PvDBPII among Myanmar P. vivax isolates were analysed. Methods Fifty-four P. vivax infected blood samples collected from patients in Myanmar were used. The region flanking PvDBPII was amplified by PCR, cloned into Escherichia coli, and sequenced. The polymorphic characters and natural selection of the region were analysed using the DnaSP and MEGA4 programs. Results Thirty-two point mutations (28 non-synonymous and four synonymous mutations) were identified in PvDBPII among the Myanmar P. vivax isolates. Sequence analyses revealed that 12 different PvDBPII haplotypes were identified in Myanmar P. vivax isolates and that the region has evolved under positive natural selection. High selective pressure preferentially acted on regions identified as B- and T-cell epitopes of PvDBPII. Recombination may also be played a role in the resulting genetic diversity of PvDBPII. Conclusions PvDBPII of Myanmar P. vivax isolates displays a high level of genetic polymorphism and is under selective pressure. Myanmar P. vivax isolates share distinct types of PvDBPII alleles that are different from those of other geographical areas. These results will be useful for understanding the nature of the P. vivax population in Myanmar and for development of PvDBPII-based vaccine. PMID:22380592

  13. Design and synthesis of triarylacrylonitrile analogues of tamoxifen with improved binding selectivity to protein kinase C.

    Science.gov (United States)

    Carpenter, Colleen; Sorenson, Roderick J; Jin, Yafei; Klossowski, Szymon; Cierpicki, Tomasz; Gnegy, Margaret; Showalter, Hollis D

    2016-11-01

    The clinical selective estrogen receptor modulator tamoxifen is also a modest inhibitor of protein kinase C, a target implicated in several untreatable brain diseases such as amphetamine abuse. This inhibition and tamoxifen's ability to cross the blood brain barrier make it an attractive scaffold to conduct further SAR studies toward uncovering effective therapies for such diseases. Utilizing the known compound 6a as a starting template and guided by computational tools to derive physicochemical properties known to be important for CNS permeable drugs, the design and synthesis of a small series of novel triarylacrylonitrile analogues have been carried out providing compounds with enhanced potency and selectivity for PKC over the estrogen receptor relative to tamoxifen. Shortened synthetic routes compared to classical procedures have been developed for analogues incorporating a β-phenyl ring, which involve installing dialkylaminoalkoxy side chains first off the α and/or α' rings of a precursor benzophenone and then condensing the resultant ketones with phenylacetonitrile anion. A second novel, efficient and versatile route utilizing Suzuki chemistry has also been developed, which will allow for the introduction of a wide range of β-aryl or β-heteroaryl moieties and side-chain substituents onto the acrylonitrile core. For analogues possessing a single side chain off the α- or α'-ring, novel 2D NMR experiments have been carried out that allow for unambiguous assignment of E- and Z-stereochemistry. From the SAR analysis, one compound, 6c, shows markedly increased potency and selectivity for inhibiting PKC with an IC50 of 80nM for inhibition of PKC protein substrate and >10μM for binding to the estrogen receptor α (tamoxifen IC50=20μM and 222nM, respectively). The data on 6c provide support for further exploration of PKC as a druggable target for the treatment of amphetamine abuse. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. Selective processing and metabolism of disease-causing mutant prion proteins.

    Directory of Open Access Journals (Sweden)

    Aarthi Ashok

    2009-06-01

    Full Text Available Prion diseases are fatal neurodegenerative disorders caused by aberrant metabolism of the cellular prion protein (PrP(C. In genetic forms of these diseases, mutations in the globular C-terminal domain are hypothesized to favor the spontaneous generation of misfolded PrP conformers (including the transmissible PrP(Sc form that trigger downstream pathways leading to neuronal death. A mechanistic understanding of these diseases therefore requires knowledge of the quality control pathways that recognize and degrade aberrant PrPs. Here, we present comparative analyses of the biosynthesis, trafficking, and metabolism of a panel of genetic disease-causing prion protein mutants in the C-terminal domain. Using quantitative imaging and biochemistry, we identify a misfolded subpopulation of each mutant PrP characterized by relative detergent insolubility, inaccessibility to the cell surface, and incomplete glycan modifications. The misfolded populations of mutant PrPs were neither recognized by ER quality control pathways nor routed to ER-associated degradation despite demonstrable misfolding in the ER. Instead, mutant PrPs trafficked to the Golgi, from where the misfolded subpopulation was selectively trafficked for degradation in acidic compartments. Surprisingly, selective re-routing was dependent not only on a mutant globular domain, but on an additional lysine-based motif in the highly conserved unstructured N-terminus. These results define a specific trafficking and degradation pathway shared by many disease-causing PrP mutants. As the acidic lysosomal environment has been implicated in facilitating the conversion of PrP(C to PrP(Sc, our identification of a mutant-selective trafficking pathway to this compartment may provide a cell biological basis for spontaneous generation of PrP(Sc in familial prion disease.

  15. A Randomized Controlled Trial of Cognitive Debiasing Improves Assessment and Treatment Selection for Pediatric Bipolar Disorder

    Science.gov (United States)

    Jenkins, Melissa M.; Youngstrom, Eric A.

    2015-01-01

    Objective This study examined the efficacy of a new cognitive debiasing intervention in reducing decision-making errors in the assessment of pediatric bipolar disorder (PBD). Method The study was a randomized controlled trial using case vignette methodology. Participants were 137 mental health professionals working in different regions of the US (M=8.6±7.5 years of experience). Participants were randomly assigned to a (1) brief overview of PBD (control condition), or (2) the same brief overview plus a cognitive debiasing intervention (treatment condition) that educated participants about common cognitive pitfalls (e.g., base-rate neglect; search satisficing) and taught corrective strategies (e.g., mnemonics, Bayesian tools). Both groups evaluated four identical case vignettes. Primary outcome measures were clinicians’ diagnoses and treatment decisions. The vignette characters’ race/ethnicity was experimentally manipulated. Results Participants in the treatment group showed better overall judgment accuracy, p < .001, and committed significantly fewer decision-making errors, p < .001. Inaccurate and somewhat accurate diagnostic decisions were significantly associated with different treatment and clinical recommendations, particularly in cases where participants missed comorbid conditions, failed to detect the possibility of hypomania or mania in depressed youths, and misdiagnosed classic manic symptoms. In contrast, effects of patient race were negligible. Conclusions The cognitive debiasing intervention outperformed the control condition. Examining specific heuristics in cases of PBD may identify especially problematic mismatches between typical habits of thought and characteristics of the disorder. The debiasing intervention was brief and delivered via the Web; it has the potential to generalize and extend to other diagnoses as well as to various practice and training settings. PMID:26727411

  16. Mining flexible-receptor docking experiments to select promising protein receptor snapshots.

    Science.gov (United States)

    Machado, Karina S; Winck, Ana T; Ruiz, Duncan D A; de Souza, Osmar Norberto

    2010-12-22

    Molecular docking simulation is the Rational Drug Design (RDD) step that investigates the affinity between protein receptors and ligands. Typically, molecular docking algorithms consider receptors as rigid bodies. Receptors are, however, intrinsically flexible in the cellular environment. The use of a time series of receptor conformations is an approach to explore its flexibility in molecular docking computer simulations, but it is extensively time-consuming. Hence, selection of the most promising conformations can accelerate docking experiments and, consequently, the RDD efforts. We previously docked four ligands (NADH, TCL, PIF and ETH) to 3,100 conformations of the InhA receptor from M. tuberculosis. Based on the receptor residues-ligand distances we preprocessed all docking results to generate appropriate input to mine data. Data preprocessing was done by calculating the shortest interatomic distances between the ligand and the receptor's residues for each docking result. They were the predictive attributes. The target attribute was the estimated free-energy of binding (FEB) value calculated by the AutodDock3.0.5 software. The mining inputs were submitted to the M5P model tree algorithm. It resulted in short and understandable trees. On the basis of the correlation values, for NADH, TCL and PIF we obtained more than 95% correlation while for ETH, only about 60%. Post processing the generated model trees for each of its linear models (LMs), we calculated the average FEB for their associated instances. From these values we considered a LM as representative if its average FEB was smaller than or equal the average FEB of the test set. The instances in the selected LMs were considered the most promising snapshots. It totalized 1,521, 1,780, 2,085 and 902 snapshots, for NADH, TCL, PIF and ETH respectively. By post processing the generated model trees we were able to propose a criterion of selection of linear models which, in turn, is capable of selecting a set of

  17. Selective transport and packaging of the major yolk protein in the sea urchin.

    Science.gov (United States)

    Brooks, Jacqueline M; Wessel, Gary M

    2003-09-15

    The major yolk protein of sea urchins is an iron-binding, transferrin-like molecule that is made in the adult gut. Its final destination though is the developing oocytes that are embedded in somatic accessory cells and encompassed by two epithelial layers of the ovary. In this study, we address the dynamics of yolk transport, endocytosis, and packaging during the vitellogenic phase of oogenesis in the sea urchin by use of fluorescently labeled major yolk protein (MYP). Incorporation of MYP into the accessory cells of the ovary and its packaging into yolk platelets of developing oocytes is visualized in isolated oocytes, ovary explants, and in whole animals. When MYP is introduced into the coelom of adult females, it is first accumulated by the somatic cells of the ovarian capsule and is then transported to the oocytes and packaged into yolk platelets. This phenomenon is specific for MYP and accurately reflects the endogenous MYP packaging. We find that oocytes cultured in isolation are endocytically active and capable of selectively packaging MYP into yolk platelets. Furthermore, oocytes that packaged exogenous MYP are capable of in vitro maturation, fertilization, and early development, enabling an in vivo documentation of MYP utilization and yolk platelet dynamics. These results demonstrate that the endocytic uptake of yolk proteins in sea urchins does not require a signal from their surrounding epithelial cells and can occur autonomous of the ovary. In addition, these results demonstrate that the entire population of yolk platelets is competent to receive new yolk protein input, suggesting that they are all made simultaneously during oogenesis.

  18. The expanded octarepeat domain selectively binds prions and disrupts homomeric prion protein interactions.

    Science.gov (United States)

    Leliveld, Sirik Rutger; Dame, Remus Thei; Wuite, Gijs J L; Stitz, Lothar; Korth, Carsten

    2006-02-10

    Insertion of additional octarepeats into the prion protein gene has been genetically linked to familial Creutzfeldt Jakob disease and hence to de novo generation of infectious prions. The pivotal event during prion formation is the conversion of the normal prion protein (PrPC) into the pathogenic conformer PrPSc, which subsequently induces further conversion in an autocatalytic manner. Apparently, an expanded octarepeat domain directs folding of PrP toward the PrPSc conformation and initiates a self-replicating conversion process. Here, based on three main observations, we have provided a model on how altered molecular interactions between wild-type and mutant PrP set the stage for familial Creutzfeldt Jakob disease with octarepeat insertions. First, we showed that wild-type octarepeat domains interact in a copper-dependent and reversible manner, a "copper switch." This interaction becomes irreversible upon domain expansion, possibly reflecting a loss of function. Second, expanded octarepeat domains of increasing length gradually form homogenous globular multimers of 11-21 nm in the absence of copper ions when expressed as soluble glutathione S-transferase fusion proteins. Third, octarepeat domain expansion causes a gain of function with at least 10 repeats selectively binding PrPSc in a denaturant-resistant complex in the absence of copper ions. Thus, the combination of both a loss and gain of function profoundly influences homomeric interaction behavior of PrP with an expanded octarepeat domain. A multimeric cluster of prion proteins carrying expanded octarepeat domains may therefore capture and incorporate spontaneously arising short-lived PrPSc-like conformers, thereby providing a matrix for their conversion.

  19. A reusable electrochemical proximity assay for highly selective, real-time protein quantitation in biological matrices.

    Science.gov (United States)

    Hu, Jiaming; Yu, Yajiao; Brooks, Jessica C; Godwin, Leah A; Somasundaram, Subramaniam; Torabinejad, Ferdous; Kim, Joonyul; Shannon, Curtis; Easley, Christopher J

    2014-06-11

    Rapid and specific quantitation of a variety of proteins over a wide concentration range is highly desirable for biosensing at the point-of-care, in clinical laboratories, and in research settings. Our recently developed electrochemical proximity assay (ECPA) is a target-flexible, DNA-directed, direct-readout protein quantitation method with detection limits in the low femtomolar range, making it particularly amenable to point-of-care detection. However, consistent quantitation in more complex matrices is required at the point-of-care, and improvements in measurement speed are needed for clinical and research settings. Here, we address these concerns with a reusable ECPA, where a gentle regeneration of the surface DNA monolayer (used to capture the proximity complex) is achieved enzymatically through a novel combination of molecular biology and electrochemistry. Strategically placed uracils in the DNA sequence trigger selective cleavage of the backbone, releasing the assembled proximity complex. This allows repeated protein quantitation by square-wave voltammetry (SWV)-as quickly as 3 min between runs. The process can be repeated up to 19 times on a single electrode without loss of assay sensitivity, and currents are shown to be highly repeatable with similar calibrations using seven different electrodes. The utility of reusable ECPA is demonstrated through two important applications in complex matrices: (1) direct, quantitative monitoring of hormone secretion in real time from as few as five murine pancreatic islets and (2) standard addition experiments in unspiked serum for direct quantitation of insulin at clinically relevant levels. Results from both applications distinguish ECPA as an exceptional tool in protein quantitation.

  20. Determination of the Influence of Substrate Concentration on Enzyme Selectivity Using Whey Protein Isolate and Bacillus licheniformis Protease

    NARCIS (Netherlands)

    Butré, C.I.; Sforza, S.; Gruppen, H.; Wierenga, P.A.

    2014-01-01

    Increasing substrate concentration during enzymatic protein hydrolysis results in a decrease in hydrolysis rate. To test if changes in the mechanism of hydrolysis also occur, the enzyme selectivity was determined. The selectivity is defined quantitatively as the relative rate of hydrolysis of each

  1. ORGANIC INFLAMMATORY RESPONSE TO REDUCED PREOPERATIVE FASTING TIME, WITH A CARBOHYDRATE AND PROTEIN ENRICHED SOLUTION; A RANDOMIZED TRIAL.

    Science.gov (United States)

    de Andrade Gagheggi Ravanini, Guilherme; Portari Filho, Pedro Eder; Abrantes Luna, Renato; Almeida de Oliveira, Vinicius

    2015-08-01

    this study aims to assess the organic inflammatory response of the video laparoscopic cholecystectomy, with abbreviation of the preoperative fasting to 2h using a carbohydrate and protein enriched solution. this is a randomized, prospective study with patients divided into the following 2 groups: group A, conventional fasting and group B, 2h abbreviated fasting with oral ingestion of a carbohydrate and protein solution. Serum glucose, insulin, interleukin 1, and TNF-α were mesasured before ingestion of the solution, during induction of anesthesia, and 4 h after the end of surgery. thirty-eight patients completed the study without presenting pulmonary complications associated with bronchoaspiration. The postoperative HOMA-IR variance was greater in group A (p = 0.001). the abbreviation of preoperative fasting for 2 h, using carbohydrate and protein enriched solutions, is safe, reduces insulin resistance, and does not increase the risk of bronchoaspiration. Copyright AULA MEDICA EDICIONES 2014. Published by AULA MEDICA. All rights reserved.

  2. Selectively Labeling the Heterologous Protein in Escherichia coli for NMR Studies: A Strategy to Speed Up NMR Spectroscopy

    Science.gov (United States)

    Almeida, F. C. L.; Amorim, G. C.; Moreau, V. H.; Sousa, V. O.; Creazola, A. T.; Américo, T. A.; Pais, A. P. N.; Leite, A.; Netto, L. E. S.; Giordano, R. J.; Valente, A. P.

    2001-01-01

    Nuclear magnetic resonance is an important tool for high-resolution structural studies of proteins. It demands high protein concentration and high purity; however, the expression of proteins at high levels often leads to protein aggregation and the protein purification step can correspond to a high percentage of the overall time in the structural determination process. In the present article we show that the step of sample optimization can be simplified by selective labeling the heterologous protein expressed in Escherichia coli by the use of rifampicin. Yeast thioredoxin and a coix transcription factor Opaque 2 leucine zipper (LZ) were used to show the effectiveness of the protocol. The 1H/15N heteronuclear correlation two-dimensional NMR spectrum (HMQC) of the selective 15N-labeled thioredoxin without any purification is remarkably similar to the spectrum of the purified protein. The method has high yields and a good 1H/15N HMQC spectrum can be obtained with 50 ml of M9 growth medium. Opaque 2 LZ, a difficult protein due to the lower expression level and high hydrophobicity, was also probed. The 15N-edited spectrum of Opaque 2 LZ showed only the resonances of the protein of heterologous expression (Opaque 2 LZ) while the 1H spectrum shows several other resonances from other proteins of the cell lysate. The demand for a fast methodology for structural determination is increasing with the advent of genome/proteome projects. Selective labeling the heterologous protein can speed up NMR structural studies as well as NMR-based drug screening. This methodology is especially effective for difficult proteins such as hydrophobic transcription factors, membrane proteins, and others.

  3. Selective Permeation and Organic Extraction of Recombinant Green Fluorescent Protein (gfpuv from Escherichia coli

    Directory of Open Access Journals (Sweden)

    Ishii Marina

    2002-04-01

    Full Text Available Abstract Background Transformed cells of Escherichia coli DH5-α with pGFPuv, induced by IPTG (isopropyl-β-d-thiogalactopyranoside, express the green fluorescent protein (gfpuv during growth phases. E. coli subjected to the combination of selective permeation by freezing/thawing/sonication cycles followed by the three-phase partitioning extraction (TPP method were compared to the direct application of TPP to the same culture of E. coli on releasing gfpuv from the over-expressing cells. Material and Methods Cultures (37°C/100 rpm/ 24 h; μ = 0.99 h-1 - 1.10 h-1 of transformed (pGFP Escherichia coli DH5-α, expressing the green fluorescent protein (gfpuv, absorbance at 394 nm and emission at 509 nm were sonicated in successive intervals of sonication (25 vibrations/pulse to determine the maximum amount of gfpuv released from the cells. For selective permeation, the transformed previously frozen (-75°C cells were subjected to three freeze/thaw (-20°C/ 0.83°C/min cycles interlaid by sonication (3 pulses/ 6 seconds/ 25 vibrations. The intracellular permeate with gfpuv in extraction buffer (TE solution (25 mM Tris-HCl, pH 8.0, 1 mM β-mercaptoethanol β-ME, 0.1 mM PMSF was subjected to the three-phase partitioning (TPP method with t-butanol and 1.6 M ammonium sulfate. Sonication efficiency was verified on the application to the cells previously treated by the TPP method. The intra-cell releases were mixed and eluted through methyl HIC column with a buffer solution (10 mM Tris-HCl, 10 mM EDTA, pH 8.0. Results The sonication maximum released amount obtained from the cells was 327.67 μg gfpuv/mL (20.73 μg gfpuv/mg total proteins – BSA, after 9 min of treatment. Through the selective permeation by three repeated freezing/thawing/sonication cycles applied to the cells, a close content of 241.19 μg gfpuv/mL (29.74 μg gfpuv/mg BSA was obtained. The specific mass range of gfpuv released from the same cultures, by the three-phase partitioning (TPP

  4. Genome-wide association data classification and SNPs selection using two-stage quality-based Random Forests.

    Science.gov (United States)

    Nguyen, Thanh-Tung; Huang, Joshua; Wu, Qingyao; Nguyen, Thuy; Li, Mark

    2015-01-01

    Single-nucleotide polymorphisms (SNPs) selection and identification are the most important tasks in Genome-wide association data analysis. The problem is difficult because genome-wide association data is very high dimensional and a large portion of SNPs in the data is irrelevant to the disease. Advanced machine learning methods have been successfully used in Genome-wide association studies (GWAS) for identification of genetic variants that have relatively big effects in some common, complex diseases. Among them, the most successful one is Random Forests (RF). Despite of performing well in terms of prediction accuracy in some data sets with moderate size, RF still suffers from working in GWAS for selecting informative SNPs and building accurate prediction models. In this paper, we propose to use a new two-stage quality-based sampling method in random forests, named ts-RF, for SNP subspace selection for GWAS. The method first applies p-value assessment to find a cut-off point that separates informative and irrelevant SNPs in two groups. The informative SNPs group is further divided into two sub-groups: highly informative and weak informative SNPs. When sampling the SNP subspace for building trees for the forest, only those SNPs from the two sub-groups are taken into account. The feature subspaces always contain highly informative SNPs when used to split a node at a tree. This approach enables one to generate more accurate trees with a lower prediction error, meanwhile possibly avoiding overfitting. It allows one to detect interactions of multiple SNPs with the diseases, and to reduce the dimensionality and the amount of Genome-wide association data needed for learning the RF model. Extensive experiments on two genome-wide SNP data sets (Parkinson case-control data comprised of 408,803 SNPs and Alzheimer case-control data comprised of 380,157 SNPs) and 10 gene data sets have demonstrated that the proposed model significantly reduced prediction errors and outperformed

  5. Role of selective V2-receptor-antagonism in septic shock: a randomized, controlled, experimental study

    OpenAIRE

    Rehberg, Sebastian; Ertmer, Christian; Lange, Matthias; Morelli, Andrea; Whorton, Elbert; Strohhäcker, Anne-Katrin; Dünser, Martin Wolfgang; Lipke, Erik; Kampmeier, Tim G; Aken, Hugo; Traber, Daniel L; Westphal, Martin

    2010-01-01

    ABSTRACT : INTRODUCTION : V2-receptor (V2R) stimulation potentially aggravates sepsis-induced vasodilation, fluid accumulation and microvascular thrombosis. Therefore, the present study was performed to determine the effects of a first-line therapy with the selective V2R-antagonist (Propionyl1-D-Tyr(Et)2-Val4-Abu6-Arg8,9)-Vasopressin on cardiopulmonary hemodynamics and organ function vs. the mixed V1aR/V2R-agonist arginine vasopressin (AVP) or placebo in an established ovine model of septic s...

  6. ZP domain proteins in the abalone egg coat include a paralog of VERL under positive selection that binds lysin and 18-kDa sperm proteins.

    Science.gov (United States)

    Aagaard, Jan E; Vacquier, Victor D; MacCoss, Michael J; Swanson, Willie J

    2010-01-01

    Identifying fertilization molecules is key to our understanding of reproductive biology, yet only a few examples of interacting sperm and egg proteins are known. One of the best characterized comes from the invertebrate archeogastropod abalone (Haliotis spp.), where sperm lysin mediates passage through the protective egg vitelline envelope (VE) by binding to the VE protein vitelline envelope receptor for lysin (VERL). Rapid adaptive divergence of abalone lysin and VERL are an example of positive selection on interacting fertilization proteins contributing to reproductive isolation. Previously, we characterized a subset of the abalone VE proteins that share a structural feature, the zona pellucida (ZP) domain, which is common to VERL and the egg envelopes of vertebrates. Here, we use additional expressed sequence tag sequencing and shotgun proteomics to characterize this family of proteins in the abalone egg VE. We expand 3-fold the number of known ZP domain proteins present within the VE (now 30 in total) and identify a paralog of VERL (vitelline envelope zona pellucida domain protein [VEZP] 14) that contains a putative lysin-binding motif. We find that, like VERL, the divergence of VEZP14 among abalone species is driven by positive selection on the lysin-binding motif alone and that these paralogous egg VE proteins bind a similar set of sperm proteins including a rapidly evolving 18-kDa paralog of lysin, which may mediate sperm-egg fusion. This work identifies an egg coat paralog of VERL under positive selection and the candidate sperm proteins with which it may interact during abalone fertilization.

  7. Tolerability, pharmacokinetics and pharmacodynamics of TA-8995, a selective cholesteryl ester transfer protein (CETP) inhibitor, in healthy subjects

    NARCIS (Netherlands)

    Ford, John; Lawson, Matt; Fowler, David; Maruyama, Nobuko; Mito, Seiji; Tomiyasu, Koichi; Kinoshita, Shuji; Suzuki, Chisa; Kawaguchi, Atsuhiro; Round, Patrick; Boyce, Malcolm; Warrington, Steve; Weber, Werner; van Deventer, Sander; Kastelein, John J. P.

    2014-01-01

    Two double-blind, randomized studies were conducted to assess the tolerability, pharmacokinetics and pharmacodynamics of oral TA-8995, a new cholesteryl ester transfer protein (CETP) inhibitor, in healthy subjects. Study 1: Subjects received single doses of TA-8995 or placebo (fasted). Doses were 5,

  8. Conflicts of Interest, Selective Inertia, and Research Malpractice in Randomized Clinical Trials: An Unholy Trinity.

    Science.gov (United States)

    Berger, Vance W

    2015-08-01

    Recently a great deal of attention has been paid to conflicts of interest in medical research, and the Institute of Medicine has called for more research into this important area. One research question that has not received sufficient attention concerns the mechanisms of action by which conflicts of interest can result in biased and/or flawed research. What discretion do conflicted researchers have to sway the results one way or the other? We address this issue from the perspective of selective inertia, or an unnatural selection of research methods based on which are most likely to establish the preferred conclusions, rather than on which are most valid. In many cases it is abundantly clear that a method that is not being used in practice is superior to the one that is being used in practice, at least from the perspective of validity, and that it is only inertia, as opposed to any serious suggestion that the incumbent method is superior (or even comparable), that keeps the inferior procedure in use, to the exclusion of the superior one. By focusing on these flawed research methods we can go beyond statements of potential harm from real conflicts of interest, and can more directly assess actual (not potential) harm.

  9. Participant-selected music and physical activity in older adults following cardiac rehabilitation: a randomized controlled trial.

    Science.gov (United States)

    Clark, Imogen N; Baker, Felicity A; Peiris, Casey L; Shoebridge, Georgie; Taylor, Nicholas F

    2017-03-01

    To evaluate effects of participant-selected music on older adults' achievement of activity levels recommended in the physical activity guidelines following cardiac rehabilitation. A parallel group randomized controlled trial with measurements at Weeks 0, 6 and 26. A multisite outpatient rehabilitation programme of a publicly funded metropolitan health service. Adults aged 60 years and older who had completed a cardiac rehabilitation programme. Experimental participants selected music to support walking with guidance from a music therapist. Control participants received usual care only. The primary outcome was the proportion of participants achieving activity levels recommended in physical activity guidelines. Secondary outcomes compared amounts of physical activity, exercise capacity, cardiac risk factors, and exercise self-efficacy. A total of 56 participants, mean age 68.2 years (SD = 6.5), were randomized to the experimental ( n = 28) and control groups ( n = 28). There were no differences between groups in proportions of participants achieving activity recommended in physical activity guidelines at Week 6 or 26. Secondary outcomes demonstrated between-group differences in male waist circumference at both measurements (Week 6 difference -2.0 cm, 95% CI -4.0 to 0; Week 26 difference -2.8 cm, 95% CI -5.4 to -0.1), and observed effect sizes favoured the experimental group for amounts of physical activity (d = 0.30), exercise capacity (d = 0.48), and blood pressure (d = -0.32). Participant-selected music did not increase the proportion of participants achieving recommended amounts of physical activity, but may have contributed to exercise-related benefits.

  10. Ligand-inducible dimeric antibody for selecting antibodies against a membrane protein based on mammalian cell proliferation.

    Science.gov (United States)

    Miura, Tomohiro; Nagamune, Teruyuki; Kawahara, Masahiro

    2016-05-01

    A method for selecting antibodies against a membrane protein is important for attaining a variety of antibody-based diagnostics and therapies. In this study, we propose a novel system to select specific antibodies against a membrane protein based on mammalian cell proliferation as a readout. The system employs a chimeric membrane protein in which a target membrane protein of interest is fused to the intracellular signaling domain of a cytokine receptor. The chimeric membrane protein transduces a cell proliferation signal through dimerization when co-expressed with a specific single-chain Fv fused with a mutant of FK-binding protein 12 (scFv-Fk) that can be conditionally dimerized by a synthetic ligand AP20187. To demonstrate this system, ErbB2 and gp130 were chosen as the target membrane protein and cytokine receptor, respectively. Consequently, co-expression of the ErbB2/gp130 chimera and ErbB2-specific scFv-Fk rendered the cells proliferative in response to AP20187. The system also allowed selection of high-affinity binders from a mixture composed of dominant low-affinity binders. This system may be extended to affinity maturation of scFvs by modulating AP20187 concentration in the selection process. © 2015 Wiley Periodicals, Inc.

  11. Content analysis of a stratified random selection of JVME articles: 1974-2004.

    Science.gov (United States)

    Olson, Lynne E

    2011-01-01

    A content analysis was performed on a random sample (N = 168) of 25% of the articles published in the Journal of Veterinary Medical Education (JVME) per year from 1974 through 2004. Over time, there were increased numbers of authors per paper, more cross-institutional collaborations, greater prevalence of references or endnotes, and lengthier articles, which could indicate a trend toward publications describing more complex or complete work. The number of first authors that could be identified as female was greatest for the most recent time period studied (2000-2004). Two different categorization schemes were created to assess the content of the publications. The first categorization scheme identified the most frequently published topics as admissions, descriptions of courses, the effect of changing teaching methods, issues facing the profession, and examples of uses of technology. The second categorization scheme identified the subset of articles that described medical education research on the basis of the purpose of the research, which represented only 14% of the sample articles (24 of 168). Of that group, only three of 24, or 12%, represented studies based on a firm conceptual framework that could be confirmed or refuted by the study's results. The results indicate that JVME is meeting its broadly based mission and that publications in the veterinary medical education literature have features common to publications in medicine and medical education.

  12. Capturing the Flatness of a peer-to-peer lending network through random and selected perturbations

    Science.gov (United States)

    Karampourniotis, Panagiotis D.; Singh, Pramesh; Uparna, Jayaram; Horvat, Emoke-Agnes; Szymanski, Boleslaw K.; Korniss, Gyorgy; Bakdash, Jonathan Z.; Uzzi, Brian

    Null models are established tools that have been used in network analysis to uncover various structural patterns. They quantify the deviance of an observed network measure to that given by the null model. We construct a null model for weighted, directed networks to identify biased links (carrying significantly different weights than expected according to the null model) and thus quantify the flatness of the system. Using this model, we study the flatness of Kiva, a large international crownfinancing network of borrowers and lenders, aggregated to the country level. The dataset spans the years from 2006 to 2013. Our longitudinal analysis shows that flatness of the system is reducing over time, meaning the proportion of biased inter-country links is growing. We extend our analysis by testing the robustness of the flatness of the network in perturbations on the links' weights or the nodes themselves. Examples of such perturbations are event shocks (e.g. erecting walls) or regulatory shocks (e.g. Brexit). We find that flatness is unaffected by random shocks, but changes after shocks target links with a large weight or bias. The methods we use to capture the flatness are based on analytics, simulations, and numerical computations using Shannon's maximum entropy. Supported by ARL NS-CTA.

  13. Benefits of Selected Physical Exercise Programs in Detention: A Randomized Controlled Study

    Directory of Open Access Journals (Sweden)

    Claudia Battaglia

    2013-10-01

    Full Text Available The aim of the study was to determine which kind of physical activity could be useful to inmate populations to improve their health status and fitness levels. A repeated measure design was used to evaluate the effects of two different training protocols on subjects in a state of detention, tested pre- and post-experimental protocol.Seventy-five male subjects were enrolled in the studyand randomly allocated to three groups: the cardiovascular plus resistance training protocol group (CRT (n = 25; mean age 30.9 ± 8.9 years,the high-intensity strength training protocol group (HIST (n = 25; mean age 33.9 ± 6.8 years, and a control group (C (n = 25; mean age 32.9 ± 8.9 years receiving no treatment. All subjects underwent a clinical assessmentandfitness tests. MANOVA revealed significant multivariate effects on group (p < 0.01 and group-training interaction (p < 0.05. CRT protocol resulted the most effective protocol to reach the best outcome in fitness tests. Both CRT and HIST protocols produced significant gains in the functional capacity (cardio-respiratory capacity and cardiovascular disease risk decrease of incarcerated males. The significant gains obtained in functional capacity reflect the great potential of supervised exercise interventions for improving the health status of incarcerated people.

  14. Beneficial effects of a high-protein, low-glycemic-load hypocaloric diet in overweight and obese women with polycystic ovary syndrome: a randomized controlled intervention study.

    Science.gov (United States)

    Mehrabani, Homeira Hamayeli; Salehpour, Saghar; Amiri, Zohreh; Farahani, Sara Jalali; Meyer, Barbara J; Tahbaz, Farideh

    2012-04-01

    The recommended composition of a hypocaloric diet for obese women with polycystic ovary syndrome (PCOS) is unclear. The aim of this study was to investigate the effects of a high-protein, low-glycemic-load diet compared with a conventional hypocaloric diet on reproductive hormones, inflammatory markers, lipids, glucose, and insulin levels in obese women with PCOS. A total of 60 overweight and obese women with PCOS who did not use insulin-sensitizing agents were recruited and randomly assigned to 1 of the 2 hypocaloric diet groups for a single-blind clinical trial. The groups included a conventional hypocaloric diet (CHCD) (15% of daily energy from protein) and a modified hypocaloric diet (MHCD) with a high-protein, low-glycemic load (30% of daily energy from protein plus low-glycemic-load foods selected from a list) that was prescribed via counseling visits weekly during 12 weeks of study. Anthropometric assessments and biochemical measurements including reproductive hormones, inflammatory factors, lipids, glucose, and insulin were performed on fasting blood samples at baseline and after 12 weeks of dietary intervention. Weight loss was significant and similar in the 2 groups. Mean of testosterone in the MHCD and CHCD groups decreased from 1.78 ± 0.32 to 1.31 ± 0.26 ng/ml and from 1.51 ± 0.12 to 1.15 ± 0.11 ng/ml, respectively (p diets significantly led to reduced body weight and androgen levels in these two groups of women with PCOS. The combination of high-protein and low-glycemic-load foods in a modified diet caused a significant increase in insulin sensitivity and a decrease in hsCRP level when compared with a conventional diet.

  15. Determination of the influence of substrate concentration on enzyme selectivity using whey protein Isolate and Bacillus licheniformis protease.

    Science.gov (United States)

    Butré, Claire I; Sforza, Stefano; Gruppen, Harry; Wierenga, Peter A

    2014-10-22

    Increasing substrate concentration during enzymatic protein hydrolysis results in a decrease in hydrolysis rate. To test if changes in the mechanism of hydrolysis also occur, the enzyme selectivity was determined. The selectivity is defined quantitatively as the relative rate of hydrolysis of each cleavage site in the protein. It was determined from the identification and quantification of the peptides present in the hydrolysates. Solutions of 0.1-10% (w/v) whey protein isolate (WPI) were hydrolyzed by Bacillus licheniformis protease at constant enzyme-to-substrate ratio. The cleavage sites were divided into five groups, from very high (>10%) to very low selectivity (concentrations. This finding shows that both the rate of hydrolysis and the enzyme selectivity were influenced by the substrate concentration.

  16. Border control: selectivity of chloroplast protein import and regulation at the TOC-complex.

    Science.gov (United States)

    Demarsy, Emilie; Lakshmanan, Ashok M; Kessler, Felix

    2014-01-01

    Plants have evolved complex and sophisticated molecular mechanisms to regulate their development and adapt to their surrounding environment. Particularly the development of their specific organelles, chloroplasts and other plastid-types, is finely tuned in accordance with the metabolic needs of the cell. The normal development and functioning of plastids require import of particular subsets of nuclear encoded proteins. Most preproteins contain a cleavable sequence at their N terminal (transit peptide) serving as a signal for targeting to the organelle and recognition by the translocation machinery TOC-TIC (translocon of outer membrane complex-translocon of inner membrane complex) spanning the dual membrane envelope. The plastid proteome needs constant remodeling in response to developmental and environmental factors. Therefore selective regulation of preprotein import plays a crucial role in plant development. In this review we describe the diversity of transit peptides and TOC receptor complexes, and summarize the current knowledge and potential directions for future research concerning regulation of the different Toc isoforms.

  17. Quantifying the Tendency of Therapeutic Target Proteins to Bind Promiscuous or Selective Compounds

    Science.gov (United States)

    Hu, Ye; Bajorath, Jürgen

    2015-01-01

    The ability of target proteins to bind structurally diverse compounds and compounds with different degrees of promiscuity (multi-target activity) was systematically assessed on the basis of currently available activity data and target annotations. Intuitive first- and second-order target promiscuity indices were introduced to quantify these binding characteristics and relate them to each other. For compounds and targets, opposite promiscuity trends were observed. Furthermore, the analysis detected many targets that interacted with compounds representing a similar degree of structural diversity but displayed strong tendencies to recognize either promiscuous or selective compounds. Moreover, target families were identified that preferentially interacted with promiscuous compounds. Taken together, these findings further extend our understanding of the molecular basis of polypharmacology. PMID:26000736

  18. High protein intake from meat as complementary food increases growth but not adiposity in breastfed infants: a randomized trial.

    Science.gov (United States)

    Tang, Minghua; Krebs, Nancy F

    2014-11-01

    High intake of cow-milk protein in formula-fed infants is associated with higher weight gain and increased adiposity, which have led to recommendations to limit protein intake in later infancy. The impact of protein from meats for breastfed infants during complementary feeding may be different. We examined the effect of protein from meat as complementary foods on growth and metabolic profiles of breastfed infants. This was a secondary analysis from a trial in which exclusively breastfed infants (5-6 mo old from the Denver, CO, metro area) were randomly assigned to receive commercially available pureed meats (Meat group; n = 14) or infant cereal (Cereal group; n = 28) as their primary complementary feedings for ∼ 5 mo. Anthropometric measures and diet records were collected monthly from 5 to 9 mo of age; intakes from complementary feeding and breast milk were assessed at 9 mo of age. The Meat group had significantly higher protein intake, whereas energy, carbohydrate, and fat intakes from complementary feeding did not differ by group over time. At 9 mo of age, mean (± SEM) intakes of total (complementary feeding plus breast milk) protein were 2.9 ± 0.6 and 1.4 ± 0.4 g · kg(-1) · d(-1), ∼ 17% and ∼ 9% of daily energy intake, for Meat and Cereal groups, respectively (P Meat group (ΔWAZ: 0.24 ± 0.19; ΔLAZ: 0.14 ± 0.12) and decreased in the Cereal group (ΔWAZ: -0.07 ± 0.17; ΔLAZ: -0.27 ± 0.24) (P-group by time meats was associated with greater linear growth and weight gain but without excessive gain in adiposity, suggesting that potential risks of high protein intake may differ between breastfed and formula-fed infants and by the source of protein. © 2014 American Society for Nutrition.

  19. Bayesian Markov Random Rield Analysis for Protein Function Prediction Based on Network Data

    NARCIS (Netherlands)

    Kourmpetis, Y.I.A.; Dijk, van A.D.J.; Bink, M.C.A.M.; Ham, van R.C.H.J.; Braak, ter C.J.F.

    2010-01-01

    Inference of protein functions is one of the most important aims of modern biology. To fully exploit the large volumes of genomic data typically produced in modern-day genomic experiments, automated computational methods for protein function prediction are urgently needed. Established methods use

  20. Dietary protein intake, energy deficit, and nitrogen balance in normal-weight adults: a randomized controlled

    Science.gov (United States)

    Consuming protein at levels higher than the recommended dietary allowance (RDA) may be metabolically advantageous for overweight and obese individuals attempting weight loss. However, the dose-response characteristics that define the optimal level of dietary protein necessary to sustain measures of...

  1. Reduced plasma aldosterone concentrations in randomly selected patients with insulin-dependent diabetes mellitus.

    LENUS (Irish Health Repository)

    Cronin, C C

    2012-02-03

    Abnormalities of the renin-angiotensin system have been reported in patients with diabetes mellitus and with diabetic complications. In this study, plasma concentrations of prorenin, renin, and aldosterone were measured in a stratified random sample of 110 insulin-dependent (Type 1) diabetic patients attending our outpatient clinic. Fifty-four age- and sex-matched control subjects were also examined. Plasma prorenin concentration was higher in patients without complications than in control subjects when upright (geometric mean (95% confidence intervals (CI): 75.9 (55.0-105.6) vs 45.1 (31.6-64.3) mU I-1, p < 0.05). There was no difference in plasma prorenin concentration between patients without and with microalbuminuria and between patients without and with background retinopathy. Plasma renin concentration, both when supine and upright, was similar in control subjects, in patients without complications, and in patients with varying degrees of diabetic microangiopathy. Plasma aldosterone was suppressed in patients without complications in comparison to control subjects (74 (58-95) vs 167 (140-199) ng I-1, p < 0.001) and was also suppressed in patients with microvascular disease. Plasma potassium was significantly higher in patients than in control subjects (mean +\\/- standard deviation: 4.10 +\\/- 0.36 vs 3.89 +\\/- 0.26 mmol I-1; p < 0.001) and plasma sodium was significantly lower (138 +\\/- 4 vs 140 +\\/- 2 mmol I-1; p < 0.001). We conclude that plasma prorenin is not a useful early marker for diabetic microvascular disease. Despite apparently normal plasma renin concentrations, plasma aldosterone is suppressed in insulin-dependent diabetic patients.

  2. A Permutation Importance-Based Feature Selection Method for Short-Term Electricity Load Forecasting Using Random Forest

    Directory of Open Access Journals (Sweden)

    Nantian Huang

    2016-09-01

    Full Text Available The prediction accuracy of short-term load forecast (STLF depends on prediction model choice and feature selection result. In this paper, a novel random forest (RF-based feature selection method for STLF is proposed. First, 243 related features were extracted from historical load data and the time information of prediction points to form the original feature set. Subsequently, the original feature set was used to train an RF as the original model. After the training process, the prediction error of the original model on the test set was recorded and the permutation importance (PI value of each feature was obtained. Then, an improved sequential backward search method was used to select the optimal forecasting feature subset based on the PI value of each feature. Finally, the optimal forecasting feature subset was used to train a new RF model as the final prediction model. Experiments showed that the prediction accuracy of RF trained by the optimal forecasting feature subset was higher than that of the original model and comparative models based on support vector regression and artificial neural network.

  3. Effect of soy protein isolate supplementation on biochemical recurrence of prostate cancer after radical prostatectomy: a randomized trial.

    Science.gov (United States)

    Bosland, Maarten C; Kato, Ikuko; Zeleniuch-Jacquotte, Anne; Schmoll, Joanne; Enk Rueter, Erika; Melamed, Jonathan; Kong, Max Xiangtian; Macias, Virgilia; Kajdacsy-Balla, Andre; Lumey, L H; Xie, Hui; Gao, Weihua; Walden, Paul; Lepor, Herbert; Taneja, Samir S; Randolph, Carla; Schlicht, Michael J; Meserve-Watanabe, Hiroko; Deaton, Ryan J; Davies, Joanne A

    2013-07-10

    Soy consumption has been suggested to reduce risk or recurrence of prostate cancer, but this has not been tested in a randomized trial with prostate cancer as the end point. To determine whether daily consumption of a soy protein isolate supplement for 2 years reduces the rate of biochemical recurrence of prostate cancer after radical prostatectomy or delays such recurrence. Randomized, double-blind trial conducted from July 1997 to May 2010 at 7 US centers comparing daily consumption of a soy protein supplement vs placebo in 177 men at high risk of recurrence after radical prostatectomy for prostate cancer. Supplement intervention was started within 4 months after surgery and continued for up to 2 years, with prostate-specific antigen (PSA) measurements made at 2-month intervals in the first year and every 3 months thereafter. Participants were randomized to receive a daily serving of a beverage powder containing 20 g of protein in the form of either soy protein isolate (n=87) or, as placebo, calcium caseinate (n=90). Biochemical recurrence rate of prostate cancer (defined as development of a PSA level of ≥0.07 ng/mL) over the first 2 years following randomization and time to recurrence. The trial was stopped early for lack of treatment effects at a planned interim analysis with 81 evaluable participants in the intervention group and 78 in the placebo group. Overall, 28.3% of participants developed biochemical recurrence within 2 years of entering the trial (close to the a priori predicted recurrence rate of 30%). Among these, 22 (27.2%) occurred in the intervention group and 23 (29.5%) in the placebo group. The resulting hazard ratio for active treatment was 0.96 (95% CI, 0.53-1.72; log-rank P = .89). Adherence was greater than 90% and there were no apparent adverse events related to supplementation. Daily consumption of a beverage powder supplement containing soy protein isolate for 2 years following radical prostatectomy did not reduce biochemical

  4. Ptc7p Dephosphorylates Select Mitochondrial Proteins to Enhance Metabolic Function

    Directory of Open Access Journals (Sweden)

    Xiao Guo

    2017-01-01

    Full Text Available Proper maintenance of mitochondrial activity is essential for metabolic homeostasis. Widespread phosphorylation of mitochondrial proteins may be an important element of this process; yet, little is known about which enzymes control mitochondrial phosphorylation or which phosphosites have functional impact. We investigate these issues by disrupting Ptc7p, a conserved but largely uncharacterized mitochondrial matrix PP2C-type phosphatase. Loss of Ptc7p causes respiratory growth defects concomitant with elevated phosphorylation of select matrix proteins. Among these, Δptc7 yeast exhibit an increase in phosphorylation of Cit1p, the canonical citrate synthase of the tricarboxylic acid (TCA cycle, that diminishes its activity. We find that phosphorylation of S462 can eliminate Cit1p enzymatic activity likely by disrupting its proper dimerization, and that Ptc7p-driven dephosphorylation rescues Cit1p activity. Collectively, our work connects Ptc7p to an essential TCA cycle function and to additional phosphorylation events that may affect mitochondrial activity inadvertently or in a regulatory manner.

  5. sDFIRE: Sequence-specific statistical energy function for protein structure prediction by decoy selections.

    Science.gov (United States)

    Hoque, Md Tamjidul; Yang, Yuedong; Mishra, Avdesh; Zhou, Yaoqi

    2016-05-05

    An important unsolved problem in molecular and structural biology is the protein folding and structure prediction problem. One major bottleneck for solving this is the lack of an accurate energy to discriminate near-native conformations against other possible conformations. Here we have developed sDFIRE energy function, which is an optimized linear combination of DFIRE (the Distance-scaled Finite Ideal gas Reference state based Energy), the orientation dependent (polar-polar and polar-nonpolar) statistical potentials, and the matching scores between predicted and model structural properties including predicted main-chain torsion angles and solvent accessible surface area. The weights for these scoring terms are optimized by three widely used decoy sets consisting of a total of 134 proteins. Independent tests on CASP8 and CASP9 decoy sets indicate that sDFIRE outperforms other state-of-the-art energy functions in selecting near native structures and in the Pearson's correlation coefficient between the energy score and structural accuracy of the model (measured by TM-score). © 2016 Wiley Periodicals, Inc.

  6. Chronic administration of OB protein decreases food intake by selectively reducing meal size in female rats.

    Science.gov (United States)

    Eckel, L A; Langhans, W; Kahler, A; Campfield, L A; Smith, F J; Geary, N

    1998-07-01

    The mechanisms by which OB protein controls food intake and energy balance are unknown. Therefore, we investigated the effects of a novel modified human recombinant OB protein (Mod-OB) on spontaneous feeding patterns, body weight, running wheel activity, and ovarian cycling in female rats. Mod-OB or vehicle was injected (4 mg . kg-1 . day-1 sc) for 2 ovarian cycles (8 days) using a within-subjects design. Observations were continued for five ovarian cycles after injections; treatments were then reversed. Mod-OB reduced food intake approximately 20% from injection day 1 to postinjection day 2. Body weight was reduced from injection day 3 to postinjection day 15 (maximum decrease, 25 +/- 4 g, postinjection days 3 and 4). Food intake was reduced due to decreases in nocturnal meal size, which appeared to be superimposed on the normal pattern of spontaneous feeding (i.e., reductions in meal size at estrus). Mod-OB did not significantly affect diurnal food intake or meal patterns, failed to alter wheel running, and did not disrupt the rats' ovarian cycles. We conclude that chronically administered Mod-OB reduces food intake in female rats by selectively affecting the mechanisms controlling meal size.

  7. Effectiveness of a selective, personality-targeted prevention program for adolescent alcohol use and misuse: a cluster randomized controlled trial.

    Science.gov (United States)

    Conrod, Patricia J; O'Leary-Barrett, Maeve; Newton, Nicola; Topper, Lauren; Castellanos-Ryan, Natalie; Mackie, Clare; Girard, Alain

    2013-03-01

    Selective school-based alcohol prevention programs targeting youth with personality risk factors for addiction and mental health problems have been found to reduce substance use and misuse in those with elevated personality profiles. To report 24-month outcomes of the Teacher-Delivered Personality-Targeted Interventions for Substance Misuse Trial (Adventure trial) in which school staff were trained to provide interventions to students with 1 of 4 high-risk (HR) profiles: anxiety sensitivity, hopelessness, impulsivity, and sensation seeking and to examine the indirect herd effects of this program on the broader low-risk (LR) population of students who were not selected for intervention. Cluster randomized controlled trial. Secondary schools in London, United Kingdom. A total of 1210 HR and 1433 LR students in the ninth grade (mean [SD] age, 13.7 [0.33] years). Schools were randomized to provide brief personality-targeted interventions to HR youth or treatment as usual (statutory drug education in class). Participants were assessed for drinking, binge drinking, and problem drinking before randomization and at 6-monthly intervals for 2 years. Two-part latent growth models indicated long-term effects of the intervention on drinking rates (β = -0.320, SE = 0.145, P = .03) and binge drinking rates (β = -0.400, SE = 0.179, P = .03) and growth in binge drinking (β = -0.716, SE = 0.274, P = .009) and problem drinking (β = -0.452, SE = 0.193, P = .02) for HR youth. The HR youth were also found to benefit from the interventions during the 24-month follow-up on drinking quantity (β = -0.098, SE = 0.047, P = .04), growth in drinking quantity (β = -0.176, SE = 0.073, P = .02), and growth in binge drinking frequency (β = -0.183, SE = 0.092, P = .047). Some herd effects in LR youth were observed, specifically on drinking rates (β = -0.259, SE = 0.132, P = .049) and growth of binge drinking (β = -0.244, SE = 0.073, P = .001), during the 24-month follow-up. Findings further

  8. Blocking peptides against HBV: PreS1 protein selected from a phage display library

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Wei; Liu, Yang; Zu, Xiangyang; Jin, Rui [State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071 (China); Xiao, Gengfu, E-mail: xiaogf@wh.iov.cn [State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071 (China)

    2011-09-09

    Highlights: {yields} Successfully selected specific PreS1-interacting peptides by using phage displayed library. {yields} Alignment of the positive phage clones revealed a consensus PreS1 binding motif. {yields} A highly enriched peptide named P7 had a strong binding ability for PreS1. {yields} P7 could block PreS1 attachment. -- Abstract: The PreS1 protein is present on the outermost part of the hepatitis B virus (HBV) surface and has been shown to have a pivotal function in viral infectivity and assembly. The development of reagents with high affinity and specificity for PreS1 is of great significance for early diagnosis and treatment of HBV infection. A phage display library of dodecapeptide was screened for interactions with purified PreS1 protein. Alignment of the positive phage clones revealed a putative consensus PreS1 binding motif of HX{sub n}HX{sub m}HP/R. Moreover, a peptide named P7 (KHMHWHPPALNT) was highly enriched and occurred with a surprisingly high frequency of 72%. A thermodynamic study revealed that P7 has a higher binding affinity to PreS1 than the other peptides. Furthermore, P7 was able to abrogate the binding of HBV virions to the PreS1 antibody, suggesting that P7 covers key functional sites on the native PreS1 protein. This newly isolated peptide may, therefore, be a new therapeutic candidate for the treatment of HBV. The consensus motif could be modified to deliver imaging, diagnostic, and therapeutic agents to tissues affected by HBV.

  9. Selective electrodiffusion of zinc ions in a Zrt-, Irt-like protein, ZIPB

    Energy Technology Data Exchange (ETDEWEB)

    Lin, W.; Fu, D.; Chai, J.; Love, J.

    2010-12-10

    All living cells need zinc ions to support cell growth. Zrt-, Irt-like proteins (ZIPs) represent a major route for entry of zinc ions into cells, but how ZIPs promote zinc uptake has been unclear. Here we report the molecular characterization of ZIPB from Bordetella bronchiseptica, the first ZIP homolog to be purified and functionally reconstituted into proteoliposomes. Zinc flux through ZIPB was found to be nonsaturable and electrogenic, yielding membrane potentials as predicted by the Nernst equation. Conversely, membrane potentials drove zinc fluxes with a linear voltage-flux relationship. Direct measurements of metal uptake by inductively coupled plasma mass spectroscopy demonstrated that ZIPB is selective for two group 12 transition metal ions, Zn{sup 2+} and Cd{sup 2+}, whereas rejecting transition metal ions in groups 7 through 11. Our results provide the molecular basis for cellular zinc acquisition by a zinc-selective channel that exploits in vivo zinc concentration gradients to move zinc ions into the cytoplasm.

  10. A Chemical-Genetic Approach to Generate Selective Covalent Inhibitors of Protein Kinases.

    Science.gov (United States)

    Kung, Alvin; Schimpl, Marianne; Ekanayake, Arunika; Chen, Ying-Chu; Overman, Ross; Zhang, Chao

    2017-06-16

    Although a previously developed bump-hole approach has proven powerful in generating specific inhibitors for mapping functions of protein kinases, its application is limited by the intolerance of the large-to-small mutation by certain kinases and the inability to control two kinases separately in the same cells. Herein, we describe the development of an alternative chemical-genetic approach to overcome these limitations. Our approach features the use of an engineered cysteine residue at a particular position as a reactive feature to sensitize a kinase of interest to selective covalent blockade by electrophilic inhibitors and is thus termed the Ele-Cys approach. We successfully applied the Ele-Cys approach to identify selective covalent inhibitors of a receptor tyrosine kinase EphB1 and solved cocrystal structures to determine the mode of covalent binding. Importantly, the Ele-Cys and bump-hole approaches afforded orthogonal inhibition of two distinct kinases in the cell, opening the door to their combined use in the study of multikinase signaling pathways.

  11. Hepatic mitogen-activated protein kinase phosphatase 1 selectively regulates glucose metabolism and energy homeostasis.

    Science.gov (United States)

    Lawan, Ahmed; Zhang, Lei; Gatzke, Florian; Min, Kisuk; Jurczak, Michael J; Al-Mutairi, Mashael; Richter, Patric; Camporez, Joao Paulo G; Couvillon, Anthony; Pesta, Dominik; Roth Flach, Rachel J; Shulman, Gerald I; Bennett, Anton M

    2015-01-01

    The liver plays a critical role in glucose metabolism and communicates with peripheral tissues to maintain energy homeostasis. Obesity and insulin resistance are highly associated with nonalcoholic fatty liver disease (NAFLD). However, the precise molecular details of NAFLD remain incomplete. The p38 mitogen-activated protein kinase (MAPK) and c-Jun NH2-terminal kinase (JNK) regulate liver metabolism. However, the physiological contribution of MAPK phosphatase 1 (MKP-1) as a nuclear antagonist of both p38 MAPK and JNK in the liver is unknown. Here we show that hepatic MKP-1 becomes overexpressed following high-fat feeding. Liver-specific deletion of MKP-1 enhances gluconeogenesis and causes hepatic insulin resistance in chow-fed mice while selectively conferring protection from hepatosteatosis upon high-fat feeding. Further, hepatic MKP-1 regulates both interleukin-6 (IL-6) and fibroblast growth factor 21 (FGF21). Mice lacking hepatic MKP-1 exhibit reduced circulating IL-6 and FGF21 levels that were associated with impaired skeletal muscle mitochondrial oxidation and susceptibility to diet-induced obesity. Hence, hepatic MKP-1 serves as a selective regulator of MAPK-dependent signals that contributes to the maintenance of glucose homeostasis and peripheral tissue energy balance. These results also demonstrate that hepatic MKP-1 overexpression in obesity is causally linked to the promotion of hepatosteatosis. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  12. Automated selected reaction monitoring software for accurate label-free protein quantification.

    Science.gov (United States)

    Teleman, Johan; Karlsson, Christofer; Waldemarson, Sofia; Hansson, Karin; James, Peter; Malmström, Johan; Levander, Fredrik

    2012-07-06

    Selected reaction monitoring (SRM) is a mass spectrometry method with documented ability to quantify proteins accurately and reproducibly using labeled reference peptides. However, the use of labeled reference peptides becomes impractical if large numbers of peptides are targeted and when high flexibility is desired when selecting peptides. We have developed a label-free quantitative SRM workflow that relies on a new automated algorithm, Anubis, for accurate peak detection. Anubis efficiently removes interfering signals from contaminating peptides to estimate the true signal of the targeted peptides. We evaluated the algorithm on a published multisite data set and achieved results in line with manual data analysis. In complex peptide mixtures from whole proteome digests of Streptococcus pyogenes we achieved a technical variability across the entire proteome abundance range of 6.5-19.2%, which was considerably below the total variation across biological samples. Our results show that the label-free SRM workflow with automated data analysis is feasible for large-scale biological studies, opening up new possibilities for quantitative proteomics and systems biology.

  13. Selective adsorption of protein by a high-efficiency Cu(2+) -cooperated magnetic imprinted nanomaterial.

    Science.gov (United States)

    Shi, Lu; Tang, Yuhai; Hao, Yi; He, Gaiyan; Gao, Ruixia; Tang, Xiaoshuang

    2016-07-01

    We report a core-shell magnetic molecularly imprinted polymer with high affinity through a facile sol-gel method for the selective adsorption of bovine hemoglobin from real bovine blood. Copper ions grafted on the surface of the matrix could immobilize template protein through chelation, which greatly enhances the orderliness of imprinted cavities and affinity of polymers. The obtained products exhibit a desired level of magnetic susceptibility, resulting in the highly efficient adsorption process. The results of adsorption experiments show that the saturation adsorption capacity of imprinted products could reach 116.3 mg/g within 30 min. Meanwhile, the specific binding experiment demonstrates the high selectivity of polymers for bovine hemoglobin. Furthermore, satisfactory reusability is demonstrated by ten adsorption-desorption cycles with no obvious deterioration in binding capacity. Electrophoretic analysis suggests the polymer could be used successfully in separation and enrichment of bovine hemoglobin from the bovine blood sample, which exhibits potential application in pretreatment of proteomics. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. G Protein-Coupled Estrogen Receptor-Selective Ligands Modulate Endometrial Tumor Growth

    Directory of Open Access Journals (Sweden)

    Whitney K. Petrie

    2013-01-01

    Full Text Available Endometrial carcinoma is the most common cancer of the female reproductive tract. GPER/GPR30 is a 7-transmembrane spanning G protein-coupled receptor that has been identified as the third estrogen receptor, in addition to ERα and ERβ. High GPER expression is predictive of poor survival in endometrial and ovarian cancer, but despite this, the estrogen-mediated signaling pathways and specific estrogen receptors involved in endometrial cancer remain unclear. Here, employing ERα-negative Hec50 endometrial cancer cells, we demonstrate that GPER mediates estrogen-stimulated activation of ERK and PI3K via matrix metalloproteinase activation and subsequent transactivation of the EGFR and that ER-targeted therapeutic agents (4-hydroxytamoxifen, ICI182,780/fulvestrant, and Raloxifene, the phytoestrogen genistein, and the “ERα-selective” agonist propylpyrazole triol also function as GPER agonists. Furthermore, xenograft tumors of Hec50 cells yield enhanced growth with G-1 and estrogen, the latter being inhibited by GPER-selective pharmacologic antagonism with G36. These results have important implications with respect to the use of putatively ER-selective ligands and particularly for the widespread long-term use of “ER-targeted” therapeutics. Moreover, our findings shed light on the potential mechanisms of SERM/SERD side effects reported in many clinical studies. Finally, our results provide the first demonstration that pharmacological inhibition of GPER activity in vivo prevents estrogen-mediated tumor growth.

  15. Effect of Replacing Animal Protein with Plant Protein on Glycemic Control in Diabetes: A Systematic Review and Meta-Analysis of Randomized Controlled Trials.

    Science.gov (United States)

    Viguiliouk, Effie; Stewart, Sarah E; Jayalath, Viranda H; Ng, Alena Praneet; Mirrahimi, Arash; de Souza, Russell J; Hanley, Anthony J; Bazinet, Richard P; Blanco Mejia, Sonia; Leiter, Lawrence A; Josse, Robert G; Kendall, Cyril W C; Jenkins, David J A; Sievenpiper, John L

    2015-12-01

    Previous research on the effect of replacing sources of animal protein with plant protein on glycemic control has been inconsistent. We therefore conducted a systematic review and meta-analysis of randomized controlled trials (RCTs) to assess the effect of this replacement on glycemic control in individuals with diabetes. We searched MEDLINE, EMBASE, and Cochrane databases through 26 August 2015. We included RCTs ≥ 3-weeks comparing the effect of replacing animal with plant protein on HbA1c, fasting glucose (FG), and fasting insulin (FI). Two independent reviewers extracted relevant data, assessed study quality and risk of bias. Data were pooled by the generic inverse variance method and expressed as mean differences (MD) with 95% confidence intervals (CIs). Heterogeneity was assessed (Cochran Q-statistic) and quantified (I²-statistic). Thirteen RCTs (n = 280) met the eligibility criteria. Diets emphasizing a replacement of animal with plant protein at a median level of ~35% of total protein per day significantly lowered HbA1c (MD = -0.15%; 95%-CI: -0.26, -0.05%), FG (MD = -0.53 mmol/L; 95%-CI: -0.92, -0.13 mmol/L) and FI (MD = -10.09 pmol/L; 95%-CI: -17.31, -2.86 pmol/L) compared with control arms. Overall, the results indicate that replacing sources of animal with plant protein leads to modest improvements in glycemic control in individuals with diabetes. Owing to uncertainties in our analyses there is a need for larger, longer, higher quality trials. ClinicalTrials.gov registration number: NCT02037321.

  16. Effect of Replacing Animal Protein with Plant Protein on Glycemic Control in Diabetes: A Systematic Review and Meta-Analysis of Randomized Controlled Trials

    Directory of Open Access Journals (Sweden)

    Effie Viguiliouk

    2015-12-01

    Full Text Available Previous research on the effect of replacing sources of animal protein with plant protein on glycemic control has been inconsistent. We therefore conducted a systematic review and meta-analysis of randomized controlled trials (RCTs to assess the effect of this replacement on glycemic control in individuals with diabetes. We searched MEDLINE, EMBASE, and Cochrane databases through 26 August 2015. We included RCTs ≥ 3-weeks comparing the effect of replacing animal with plant protein on HbA1c, fasting glucose (FG, and fasting insulin (FI. Two independent reviewers extracted relevant data, assessed study quality and risk of bias. Data were pooled by the generic inverse variance method and expressed as mean differences (MD with 95% confidence intervals (CIs. Heterogeneity was assessed (Cochran Q-statistic and quantified (I2-statistic. Thirteen RCTs (n = 280 met the eligibility criteria. Diets emphasizing a replacement of animal with plant protein at a median level of ~35% of total protein per day significantly lowered HbA1c (MD = −0.15%; 95%-CI: −0.26, −0.05%, FG (MD = −0.53 mmol/L; 95%-CI: −0.92, −0.13 mmol/L and FI (MD = −10.09 pmol/L; 95%-CI: −17.31, −2.86 pmol/L compared with control arms. Overall, the results indicate that replacing sources of animal with plant protein leads to modest improvements in glycemic control in individuals with diabetes. Owing to uncertainties in our analyses there is a need for larger, longer, higher quality trials. Trial Registration: ClinicalTrials.gov registration number: NCT02037321.

  17. Preference option randomized design (PORD) for comparative effectiveness research: Statistical power for testing comparative effect, preference effect, selection effect, intent-to-treat effect, and overall effect.

    Science.gov (United States)

    Heo, Moonseong; Meissner, Paul; Litwin, Alain H; Arnsten, Julia H; McKee, M Diane; Karasz, Alison; McKinley, Paula; Rehm, Colin D; Chambers, Earle C; Yeh, Ming-Chin; Wylie-Rosett, Judith

    2017-01-01

    Comparative effectiveness research trials in real-world settings may require participants to choose between preferred intervention options. A randomized clinical trial with parallel experimental and control arms is straightforward and regarded as a gold standard design, but by design it forces and anticipates the participants to comply with a randomly assigned intervention regardless of their preference. Therefore, the randomized clinical trial may impose impractical limitations when planning comparative effectiveness research trials. To accommodate participants' preference if they are expressed, and to maintain randomization, we propose an alternative design that allows participants' preference after randomization, which we call a "preference option randomized design (PORD)". In contrast to other preference designs, which ask whether or not participants consent to the assigned intervention after randomization, the crucial feature of preference option randomized design is its unique informed consent process before randomization. Specifically, the preference option randomized design consent process informs participants that they can opt out and switch to the other intervention only if after randomization they actively express the desire to do so. Participants who do not independently express explicit alternate preference or assent to the randomly assigned intervention are considered to not have an alternate preference. In sum, preference option randomized design intends to maximize retention, minimize possibility of forced assignment for any participants, and to maintain randomization by allowing participants with no or equal preference to represent random assignments. This design scheme enables to define five effects that are interconnected with each other through common design parameters-comparative, preference, selection, intent-to-treat, and overall/as-treated-to collectively guide decision making between interventions. Statistical power functions for testing

  18. Single-chain lipopeptide vaccines for the induction of virus-specific cytotoxic T cell responses in randomly selected populations.

    Science.gov (United States)

    Gras-Masse, H

    2001-12-01

    Effective vaccine development is now taking advantage of the rapidly accumulating information concerning the molecular basis of a protective immune response. Analysts and medicinal chemists have joined forces with immunologists and taken up the clear challenge of identifying immunologically active structural elements and synthesizing them in pure, reproducible forms. Current literature reveals the growing interest for extremely reductionist approaches aiming at producing totally synthetic vaccines that would be fully defined at the molecular level and particularly safe. The sequential information contained in these formulations tends to be minimized to those epitopes which elicit neutralizing antibodies, or cell-mediated responses. In the following review, we describe some of our results in developing fully synthetic, clinically acceptable lipopeptide vaccines for inducing cytotoxic T lymphocytes (CTL) responses in randomly selected populations.

  19. Treatment of metabolic syndrome by combination of physical activity and diet needs an optimal protein intake: a randomized controlled trial.

    Science.gov (United States)

    Dutheil, Frédéric; Lac, Gérard; Courteix, Daniel; Doré, Eric; Chapier, Robert; Roszyk, Laurence; Sapin, Vincent; Lesourd, Bruno

    2012-09-17

    The recommended dietary allowance (RDA) for protein intake has been set at 1.0-1.3 g/kg/day for senior. To date, no consensus exists on the lower threshold intake (LTI = RDA/1.3) for the protein intake (PI) needed in senior patients ongoing both combined caloric restriction and physical activity treatment for metabolic syndrome. Considering that age, caloric restriction and exercise are three increasing factors of protein need, this study was dedicated to determine the minimal PI in this situation, through the determination of albuminemia that is the blood marker of protein homeostasis. Twenty eight subjects (19 M, 9 F, 61.8 ± 6.5 years, BMI 33.4 ± 4.1 kg/m²) with metabolic syndrome completed a three-week residential programme (Day 0 to Day 21) controlled for nutrition (energy balance of -500 kcal/day) and physical activity (3.5 hours/day). Patients were randomly assigned in two groups: Normal-PI (NPI: 1.0 g/kg/day) and High-PI (HPI: 1.2 g/kg/day). Then, patients returned home and were followed for six months. Albuminemia was measured at D0, D21, D90 and D180. At baseline, PI was spontaneously 1.0 g/kg/day for both groups. Albuminemia was 40.6 g/l for NPI and 40.8 g/l for HPI. A marginal protein under-nutrition appeared in NPI with a decreased albuminemia at D90 below 35 g/l (34.3 versus 41.5 g/l for HPI, p metabolic syndrome, the lower threshold intake for protein must be set at 1.2 g/kg/day to maintain blood protein homeostasis.

  20. Selecting Optimal Random Forest Predictive Models: A Case Study on Predicting the Spatial Distribution of Seabed Hardness

    Science.gov (United States)

    Li, Jin; Tran, Maggie; Siwabessy, Justy

    2016-01-01

    Spatially continuous predictions of seabed hardness are important baseline environmental information for sustainable management of Australia’s marine jurisdiction. Seabed hardness is often inferred from multibeam backscatter data with unknown accuracy and can be inferred from underwater video footage at limited locations. In this study, we classified the seabed into four classes based on two new seabed hardness classification schemes (i.e., hard90 and hard70). We developed optimal predictive models to predict seabed hardness using random forest (RF) based on the point data of hardness classes and spatially continuous multibeam data. Five feature selection (FS) methods that are variable importance (VI), averaged variable importance (AVI), knowledge informed AVI (KIAVI), Boruta and regularized RF (RRF) were tested based on predictive accuracy. Effects of highly correlated, important and unimportant predictors on the accuracy of RF predictive models were examined. Finally, spatial predictions generated using the most accurate models were visually examined and analysed. This study confirmed that: 1) hard90 and hard70 are effective seabed hardness classification schemes; 2) seabed hardness of four classes can be predicted with a high degree of accuracy; 3) the typical approach used to pre-select predictive variables by excluding highly correlated variables needs to be re-examined; 4) the identification of the important and unimportant predictors provides useful guidelines for further improving predictive models; 5) FS methods select the most accurate predictive model(s) instead of the most parsimonious ones, and AVI and Boruta are recommended for future studies; and 6) RF is an effective modelling method with high predictive accuracy for multi-level categorical data and can be applied to ‘small p and large n’ problems in environmental sciences. Additionally, automated computational programs for AVI need to be developed to increase its computational efficiency and

  1. Selecting Optimal Random Forest Predictive Models: A Case Study on Predicting the Spatial Distribution of Seabed Hardness.

    Directory of Open Access Journals (Sweden)

    Jin Li

    Full Text Available Spatially continuous predictions of seabed hardness are important baseline environmental information for sustainable management of Australia's marine jurisdiction. Seabed hardness is often inferred from multibeam backscatter data with unknown accuracy and can be inferred from underwater video footage at limited locations. In this study, we classified the seabed into four classes based on two new seabed hardness classification schemes (i.e., hard90 and hard70. We developed optimal predictive models to predict seabed hardness using random forest (RF based on the point data of hardness classes and spatially continuous multibeam data. Five feature selection (FS methods that are variable importance (VI, averaged variable importance (AVI, knowledge informed AVI (KIAVI, Boruta and regularized RF (RRF were tested based on predictive accuracy. Effects of highly correlated, important and unimportant predictors on the accuracy of RF predictive models were examined. Finally, spatial predictions generated using the most accurate models were visually examined and analysed. This study confirmed that: 1 hard90 and hard70 are effective seabed hardness classification schemes; 2 seabed hardness of four classes can be predicted with a high degree of accuracy; 3 the typical approach used to pre-select predictive variables by excluding highly correlated variables needs to be re-examined; 4 the identification of the important and unimportant predictors provides useful guidelines for further improving predictive models; 5 FS methods select the most accurate predictive model(s instead of the most parsimonious ones, and AVI and Boruta are recommended for future studies; and 6 RF is an effective modelling method with high predictive accuracy for multi-level categorical data and can be applied to 'small p and large n' problems in environmental sciences. Additionally, automated computational programs for AVI need to be developed to increase its computational efficiency and

  2. Effect of a High-Protein Diet versus Standard-Protein Diet on Weight Loss and Biomarkers of Metabolic Syndrome: A Randomized Clinical Trial

    Directory of Open Access Journals (Sweden)

    Ismael Campos-Nonato

    2017-06-01

    Full Text Available Background: Some studies have shown that protein-enriched diets can lead to greater weight loss and improvements in biomarkers of metabolic syndrome (MeS than standard protein diets. Therefore, the aim of this study was to determine the effect of increased protein intake on weight loss in Mexican adults with MeS. Methods: Randomized controlled trial in 118 adults aged 47.4 ± 11.5 years and meeting the established criteria for MeS were randomized to prescribed hypocaloric diets (500 kcal less than resting metabolic rate providing either 0.8 g/kg body weight (standard protein diet (SPD or 1.34 g/kg body weight (higher protein diet (HPD for 6 months. Body weight, waist circumference, percent body fat by bioimpedance analysis, fasting blood glucose, fasting insulin, hemoglobin A1c, total cholesterol, high-density lipoprotein (HDL cholesterol, very-low-density lipoprotein (VLDL cholesterol, triglycerides, C-reactive protein, creatinine, blood urea nitrogen, alanine aminotransferase, aspartate aminotransferase, and gamma-glutamyl transferase were measured at baseline, 3 months and at 6 months. Results: There were 105 subjects (51 for SPD and 54 for HPD who completed the trial. Overall weight loss was 5.1 ± 3.6 kg in the SPD group compared to 7.0 ± 3.7 kg in the in HPD group. Both groups lost a significant percent of centimeters of waist circumference (SPD -6.5 ± 2.6 cm and HPD -8.8 ± 2.6 cm. There was no statistical difference Except for the varying weight losses the two groups did not show any further differences overall. However in the subgroup judged to be adherent more than 75% of the time with the prescribed diets, there was a significant difference in mean weight loss (SPD -5.8% vs. HPD -9.5% after adjusting for baseline BMI. Both groups demonstrated significant decreases in waist circumference, glucose, insulin, triglycerides, and VLDL cholesterol, but there were no differences between the groups. There were no changes in blood tests for

  3. Generation of a selectively cytotoxic fusion protein against p53 mutated cancers

    Directory of Open Access Journals (Sweden)

    Kousparou Christina A

    2012-08-01

    Full Text Available Abstract Background A significant number of cancers are caused by defects in p21 causing functional defects in p21 or p53 tumour-suppressor proteins. This has led to many therapeutic approaches including restoration by gene therapy with wild-type p53 or p21 using viral or liposomal vectors, which have toxicity or side-effect limitations. We set out to develop a safer, novel fusion protein which has the ability to reconstitute cancer cell lines with active p21 by protein transduction. Methods The fusion protein was produced from the cell-translocating peptide Antennapedia (Antp and wild-type, full-length p21 (Antp-p21. This was expressed and refolded from E. coli and tested on a variety of cell lines and tumours (in a BALB/c nude xenograft model with differing p21 or p53 status. Results Antp-p21 penetrated and killed cancer cells that do not express wild type p53 or p21. This included cells that were matched to cogenic parental cell lines. Antp-p21 killed cancer cells selectively that were malignant as a result of mutations or nuclear exclusion of the p53 and p21 genes and over-expression of MDM2. Non-specific toxicity was excluded by showing that Antp-p21 penetrated but did not kill p53- or p21- wild-type cells. Antp-p21 was not immunogenic in normal New Zealand White rabbits. Recombinant Antp peptide alone was not cytotoxic, showing that killing was due to the transduction of the p21 component of Antp-p21. Antp-p21 was shown to penetrate cancer cells engrafted in vivo and resulted in tumour eradication when administered with conventionally-used chemotherapeutic agents, which alone were unable to produce such an effect. Conclusions Antp-p21 may represent a new and promising targeted therapy for patients with p53-associated cancers supporting the concept that rational design of therapies directed against specific cancer mutations will play a part in the future of medical oncology.

  4. Selective quantitative bioanalysis of proteins in biological fluids by on-line immunoaffinity chromatography-protein digestion-liquid chromatography-mass spectrometry

    NARCIS (Netherlands)

    Hoos, J.S.; Sudergat, H.; Hoelck, J.P.; Stahl, M.; de Vlieger, J.S.B.; Niessen, W.M.A.; Lingeman, H.; Irth, H.

    2006-01-01

    A quantitative method for the determination of proteins in complex biological matrices has been developed based on the selectivity of antibodies for sample purification followed by proteolytic digestion and quantitative mass spectrometry. An immunosorbent of polyclonal anti-bovine serum albumin

  5. A Method for Large-Scale Screening of Random Sequence Libraries to Determine the Function of Unstructured Regions from Essential Proteins.

    Science.gov (United States)

    Millau, Jean-François; Guillemette, Benoit; Gaudreau, Luc

    2017-01-01

    In this chapter we present a method allowing the screening of random sequences to discover essential aspects of unstructured protein regions in yeast. The approach can be applied to any protein with unstructured peptide sequences for which functions are difficult to decipher, for example the N-terminal tails of histones. The protocol first describes the building and preparation of a large library of random peptides in fusion with a protein of interest. Recent technical advances in oligonucleotide synthesis allow the construction of long random sequences up to 35 residues long. The protocol details the screening of the library in yeast for sequences that can functionally replace an unstructured domain in an essential protein in vivo. Our method typically identifies sequences that, while being totally different from the wild type, retain essential features allowing yeast to live. This collection of proteins with functional synthetic sequences can subsequently be used in phenotypic tests or genetic screens in order to discover genetic interaction.

  6. Cophenetic correlation analysis as a strategy to select phylogenetically informative proteins: an example from the fungal kingdom

    Directory of Open Access Journals (Sweden)

    Echavarri-Erasun Carlos

    2007-08-01

    Full Text Available Abstract Background The construction of robust and well resolved phylogenetic trees is important for our understanding of many, if not all biological processes, including speciation and origin of higher taxa, genome evolution, metabolic diversification, multicellularity, origin of life styles, pathogenicity and so on. Many older phylogenies were not well supported due to insufficient phylogenetic signal present in the single or few genes used in phylogenetic reconstructions. Importantly, single gene phylogenies were not always found to be congruent. The phylogenetic signal may, therefore, be increased by enlarging the number of genes included in phylogenetic studies. Unfortunately, concatenation of many genes does not take into consideration the evolutionary history of each individual gene. Here, we describe an approach to select informative phylogenetic proteins to be used in the Tree of Life (TOL and barcoding projects by comparing the cophenetic correlation coefficients (CCC among individual protein distance matrices of proteins, using the fungi as an example. The method demonstrated that the quality and number of concatenated proteins is important for a reliable estimation of TOL. Approximately 40–45 concatenated proteins seem needed to resolve fungal TOL. Results In total 4852 orthologous proteins (KOGs were assigned among 33 fungal genomes from the Asco- and Basidiomycota and 70 of these represented single copy proteins. The individual protein distance matrices based on 531 concatenated proteins that has been used for phylogeny reconstruction before 14 were compared one with another in order to select those with the highest CCC, which then was used as a reference. This reference distance matrix was compared with those of the 70 single copy proteins selected and their CCC values were calculated. Sixty four KOGs showed a CCC above 0.50 and these were further considered for their phylogenetic potential. Proteins belonging to the cellular

  7. Can C-reactive protein inform antidepressant medication selection in depressed outpatients? Findings from the CO-MED trial.

    Science.gov (United States)

    Jha, Manish K; Minhajuddin, Abu; Gadad, Bharathi S; Greer, Tracy; Grannemann, Bruce; Soyombo, Abigail; Mayes, Taryn L; Rush, A John; Trivedi, Madhukar H

    2017-04-01

    Currently, no valid measures inform treatment selection for depressed patients. Whether C-reactive protein (CRP) in particular and two other acute phase reactants (inflammatory markers) could differentiate between patients responding to either of two treatments with different mechanisms of action was assessed. Subjects included Combining Medications to Enhance Depression Outcomes (CO-MED) trial participants randomly assigned to either escitalopram plus placebo (SSRI monotherapy, n=51) or bupropion plus escitalopram combination (bupropion-SSRI combination, n=55) with baseline plasma samples. CRP, serum amyloid P component, and alpha-2-macroglobulin were measured using the Bioplex Pro™ human acute-phase 4-plex panel. We conducted mixed model analyses of depressive symptom (Quick Inventory of Depressive Symptomatology Self-Report) and side-effect burden (Frequency, Intensity, and Burden of Side-Effects Rating Scale) obtained weekly or every other week over the 12-week acute-phase of CO-MED trial to evaluate the relationship between these outcomes and baseline CRP and other acute-phase reactants. The treatment arms did not differ in depressive symptom or side effect outcomes. Most participants (69.8%, 74/106) had baseline CRP levels greater than 1mg/L (indicative of systemic inflammatory activity). Higher baseline CRP levels were associated lower depression severity (correlation coefficient=-0.63) with bupropion-SSRI combination but not with SSRI monotherapy (correlation coefficient=0.40). The overall remission rate was 41.5%. The estimated remission rate with CRP threshold based assignment (SSRI monotherapy for <1mg/L and Bupropion-SSRI for ≥1mg/L) was 53.1%, with a number needed to treat of 8.6. Side effect burden was unrelated to any baseline inflammatory marker. Baseline CRP levels relate differentially to antidepressant treatment outcomes in persons with major depressive disorder. Clinicaltrials.gov identifier: NCT00590863. Copyright © 2017 Elsevier Ltd. All

  8. Whey Protein Supplementation Enhances Body Fat and Weight Loss in Women Long After Bariatric Surgery: a Randomized Controlled Trial.

    Science.gov (United States)

    Lopes Gomes, Daniela; Moehlecke, Milene; Lopes da Silva, Fernanda Bassan; Dutra, Eliane Said; D'Agord Schaan, Beatriz; Baiocchi de Carvalho, Kenia Mara

    2017-02-01

    The ideal nutritional approach for weight regain after bariatric surgery remains unclear. The objective of this study is to assess the effect of whey protein supplementation on weight loss and body composition of women who regained weight 24 or more months after bariatric surgery. This is a 16-week open-label, parallel-group, randomized controlled trial of women who regained at least 5 % of their lowest postoperative weight after a Roux-en-Y gastric bypass (RYGB). A total of 34 participants were treated with hypocaloric diet and randomized (1:1) to receive or not supplementation with whey protein, 0.5 g/kg of the ideal body weight. The primary outcomes were changes in body weight, fat free mass (FFM), and fat mass (FM), evaluated by tetrapolar bioelectrical impedance analysis (BIA). Secondary outcomes included resting energy expenditure, blood glucose, lipids, adiponectin, interleukin 6 (IL-6), and cholecystokinin levels. Statistical analyses included generalized estimating equations adjusted for age and physical activity. Fifteen patients in each group were evaluated: mean age was 45 ± 11 years, body mass index (BMI) was 35.7 ± 5.2 kg/m2, and time since surgery was 69 ± 23 months. Protein intake during follow-up increased by approximately 75 % in the intervention group (p = 0.01). The intervention group presented more body weight loss (1.86 kg, p = 0.017), accounted for FM loss (2.78, p = 0.021) and no change in FFM, as compared to controls (gain of 0.42 kg of body weight and 0.6 kg of FM). No differences in secondary outcomes were observed between groups. Whey protein supplementation promoted body weight and FM loss in women with long-term weight regain following RYGB.

  9. Stapled Voltage-Gated Calcium Channel (CaV) α-Interaction Domain (AID) Peptides Act As Selective Protein-Protein Interaction Inhibitors of CaV Function.

    Science.gov (United States)

    Findeisen, Felix; Campiglio, Marta; Jo, Hyunil; Abderemane-Ali, Fayal; Rumpf, Christine H; Pope, Lianne; Rossen, Nathan D; Flucher, Bernhard E; DeGrado, William F; Minor, Daniel L

    2017-06-21

    For many voltage-gated ion channels (VGICs), creation of a properly functioning ion channel requires the formation of specific protein-protein interactions between the transmembrane pore-forming subunits and cystoplasmic accessory subunits. Despite the importance of such protein-protein interactions in VGIC function and assembly, their potential as sites for VGIC modulator development has been largely overlooked. Here, we develop meta-xylyl (m-xylyl) stapled peptides that target a prototypic VGIC high affinity protein-protein interaction, the interaction between the voltage-gated calcium channel (CaV) pore-forming subunit α-interaction domain (AID) and cytoplasmic β-subunit (CaVβ). We show using circular dichroism spectroscopy, X-ray crystallography, and isothermal titration calorimetry that the m-xylyl staples enhance AID helix formation are structurally compatible with native-like AID:CaVβ interactions and reduce the entropic penalty associated with AID binding to CaVβ. Importantly, electrophysiological studies reveal that stapled AID peptides act as effective inhibitors of the CaVα1:CaVβ interaction that modulate CaV function in an CaVβ isoform-selective manner. Together, our studies provide a proof-of-concept demonstration of the use of protein-protein interaction inhibitors to control VGIC function and point to strategies for improved AID-based CaV modulator design.

  10. A potential new selection criterion for breeding winter barley optimal protein and amino acid profiles for liquid pig feed

    DEFF Research Database (Denmark)

    Christensen, Jesper Bjerg; Blaabjerg, Karoline; Poulsen, Hanne Damgaard

    of glutamic acid revealed differences between the cultivars and the solubilised protein at all three times. These preliminary results may indicate that improvements of the nitrogen utilization in pigs fed soaked winter barley depends on the choice of cultivar and soaking time, and may serve as a new selection...... was to evaluate the effect of soaking on the amount of water soluble protein and AAs from different winter barley (Hordeum vulgare) cultivars. In this experiment, grains from 9 different barley cultivars were soaked and samples were collected at 15 minutes, 2, 4, 6, 8, 24, 48 and 72 hours. The protein...... concentration was analysed in the supernatant after centrifugation. After 15 min., app. 16% of the total protein was soluble and until 8 hours an increase of 5% units was observed. However, from 8 to 48 hours it increased with 10% units for some cultivars. Based on these analyses, cultivars were selected...

  11. Comprehensive comparative analysis and identification of RNA-binding protein domains: multi-class classification and feature selection.

    Science.gov (United States)

    Jahandideh, Samad; Srinivasasainagendra, Vinodh; Zhi, Degui

    2012-11-07

    RNA-protein interaction plays an important role in various cellular processes, such as protein synthesis, gene regulation, post-transcriptional gene regulation, alternative splicing, and infections by RNA viruses. In this study, using Gene Ontology Annotated (GOA) and Structural Classification of Proteins (SCOP) databases an automatic procedure was designed to capture structurally solved RNA-binding protein domains in different subclasses. Subsequently, we applied tuned multi-class SVM (TMCSVM), Random Forest (RF), and multi-class ℓ1/ℓq-regularized logistic regression (MCRLR) for analysis and classifying RNA-binding protein domains based on a comprehensive set of sequence and structural features. In this study, we compared prediction accuracy of three different state-of-the-art predictor methods. From our results, TMCSVM outperforms the other methods and suggests the potential of TMCSVM as a useful tool for facilitating the multi-class prediction of RNA-binding protein domains. On the other hand, MCRLR by elucidating importance of features for their contribution in predictive accuracy of RNA-binding protein domains subclasses, helps us to provide some biological insights into the roles of sequences and structures in protein-RNA interactions.

  12. Randomized trial of switching from prescribed non-selective non-steroidal anti-inflammatory drugs to prescribed celecoxib

    DEFF Research Database (Denmark)

    Macdonald, Thomas M; Hawkey, Chris J; Ford, Ian

    2017-01-01

    BACKGROUND: Selective cyclooxygenase-2 inhibitors and conventional non-selective non-steroidal anti-inflammatory drugs (nsNSAIDs) have been associated with adverse cardiovascular (CV) effects. We compared the CV safety of switching to celecoxib vs. continuing nsNSAID therapy in a European setting....... METHOD: Patients aged 60 years and over with osteoarthritis or rheumatoid arthritis, free from established CV disease and taking chronic prescribed nsNSAIDs, were randomized to switch to celecoxib or to continue their previous nsNSAID. The primary endpoint was hospitalization for non-fatal myocardial...... expected developed an on-treatment (OT) primary CV event and the rate was similar for celecoxib, 0.95 per 100 patient-years, and nsNSAIDs, 0.86 per 100 patient-years (HR = 1.12, 95% confidence interval, 0.81-1.55; P = 0.50). Comparable intention-to-treat (ITT) rates were 1.14 per 100 patient...

  13. Randomized trial of enteral protein and energy supplementation in infants less than or equal to 1250 g at birth.

    Science.gov (United States)

    Brumberg, H L; Kowalski, L; Troxell-Dorgan, A; Gettner, P; Konstantino, M; Poulsen, J F; Ehrenkranz, R A

    2010-08-01

    To determine if enteral protein and energy supplementation would significantly improve weight gain as compared with energy supplementation alone in or=14 days, diet of >or=75% enteral nutrition (fortified human milk or formula) and either failure to regain BW or weight gain<15 g kg(-1) per days. Infants were randomized to a multinutrient supplement that provided increased protein and energy (P/E) intake or energy alone (medium chain triglyceride oil, MCT). Growth rates were compared at the end of the 4-week study period. Of 30 eligible infants, 23 were enrolled, 12 received MCT (BW=862+/-252 g, mean+/-s.d.) and 11 received P/E (BW=879+/-241 g). Significantly higher protein intake (P/E=3.5+/-0.3 g kg(-1) per day, MCT=3.0+/-0.5 g kg(-1) per day) and better growth (P/E=17.0+/-2.4 g kg(-1) per day, MCT=11.5+/-4.8 g kg(-1) per day) were observed in the P/E group. These data are consistent with the importance of providing additional daily protein intake to achieve increased postnatal growth in very low birth weight infants experiencing slow growth.

  14. Protein-enriched meal replacements do not adversely affect liver, kidney or bone density: an outpatient randomized controlled trial

    Directory of Open Access Journals (Sweden)

    Yan Eric

    2010-12-01

    Full Text Available Abstract Background There is concern that recommending protein-enriched meal replacements as part of a weight management program could lead to changes in biomarkers of liver or renal function and reductions in bone density. This study was designed as a placebo-controlled clinical trial utilizing two isocaloric meal plans utilizing either a high protein-enriched (HP or a standard protein (SP meal replacement in an outpatient weight loss program. Subjects/methods 100 obese men and women over 30 years of age with a body mass index (BMI between 27 to 40 kg/m2 were randomized to one of two isocaloric weight loss meal plans 1. HP group: providing 2.2 g protein/kg of lean body mass (LBM/day or 2. SP group: providing 1.1 g protein/kg LBM/day. Meal replacement (MR was used twice daily (one meal, one snack for 3 months and then once a day for 9 months. Body weight, lipid profiles, liver function, renal function and bone density were measured at baseline and 12 months. Results Seventy subjects completed the study. Both groups lost weight (HP -4.29 ± 5.90 kg vs. SP -4.66 ± 6.91 kg, p 2, p = 0.210; SP -0.03 ± 0.17 g/cm2, p = 0.320 in either group over one year. Conclusions These studies demonstrate that protein-enriched meals replacements as compared to standard meal replacements recommended for weight management do not have adverse effects on routine measures of liver function, renal function or bone density at one year. Clinicaltrial.gov: NCT01030354.

  15. Spatially transformed fluorescence image data for ERK-MAPK and selected proteins within human epidermis.

    Science.gov (United States)

    Cursons, Joseph; Angel, Catherine E; Hurley, Daniel G; Print, Cristin G; Dunbar, P Rod; Jacobs, Marc D; Crampin, Edmund J

    2015-01-01

    Phosphoprotein signalling pathways have been intensively studied in vitro, yet their role in regulating tissue homeostasis is not fully understood. In the skin, interfollicular keratinocytes differentiate over approximately 2 weeks as they traverse the epidermis. The extracellular signal-regulated kinase (ERK) branch of the mitogen-activated protein kinase (MAPK) pathway has been implicated in this process. Therefore, we examined ERK-MAPK activity within human epidermal keratinocytes in situ. We used confocal microscopy and immunofluorescence labelling to measure the relative abundances of Raf-1, MEK1/2 and ERK1/2, and their phosphorylated (active) forms within three human skin samples. Additionally, we measured the abundance of selected proteins thought to modulate ERK-MAPK activity, including calmodulin, β1 integrin and stratifin (14-3-3σ); and of transcription factors known to act as effectors of ERK1/2, including the AP-1 components Jun-B, Fra2 and c-Fos. Imaging was performed with sufficient resolution to identify the plasma membrane, cytoplasm and nucleus as distinct domains within cells across the epidermis. The image field of view was also sufficiently large to capture the entire epidermis in cross-section, and thus the full range of keratinocyte differentiation in a single observation. Image processing methods were developed to quantify image data for mathematical and statistical analysis. Here, we provide raw image data and processed outputs. These data indicate coordinated changes in ERK-MAPK signalling activity throughout the depth of the epidermis, with changes in relative phosphorylation-mediated signalling activity occurring along the gradient of cellular differentiation. We believe these data provide unique information about intracellular signalling as they are obtained from a homeostatic human tissue, and they might be useful for investigating intercellular heterogeneity.

  16. Secondary structure prediction of protein constructs using random incremental truncation and vacuum-ultraviolet CD spectroscopy

    CERN Document Server

    Pukáncsik, M; Matsuo, K; Gekko, K; Hart, D; Kézsmárki, I; Vértessy, B G

    2014-01-01

    A novel uracil-DNA degrading protein factor (termed UDE) was identified in Drosophila melanogaster with no significant structural and functional homology to other uracil-DNA binding or processing factors. Determination of the 3D structure of UDE will be a true breakthrough in description of the molecular mechanism of action of UDE catalysis, as well as in general uracil-recognition and nuclease action. The revolutionary ESPRIT technology was applied to the novel protein UDE to overcome problems in identifying soluble expressing constructs given the absence of precise information on domain content and arrangement. Nine specimen from the created numerous truncated constructs of UDE were choosen to dechiper structural and functional relationships. VUVCD with neural network was performed to define the secondary structure content and location of UDE and its truncated variants. The quantitative analysis demonstrated exclusive {\\alpha}-helical content for the full-length protein, which is preserved in the truncated ...

  17. Selective labeling of polypeptides using protein farnesyltransferase via rapid oxime ligation.

    Science.gov (United States)

    Rashidian, Mohammad; Dozier, Jonathan K; Lenevich, Stepan; Distefano, Mark D

    2010-12-21

    An aldehyde-containing alternative substrate for protein farnesyltransferase was prepared and shown to be enzymatically incorporated into a peptide and a protein. The protein was subsequently immobilized onto aminooxy-functionalized agarose beads or labeled with a fluorophore. This method for protein modification provides an alternative to the commonly employed Cu(I)-catalyzed click reaction.

  18. Site selective fragmentation of peptides and proteins at quinone modified cysteine residues investigated by ESI-MS

    Science.gov (United States)

    Diedrich, Jolene K.; Julian, Ryan R.

    2010-01-01

    Described herein are several unique analytical applications utilizing mass spectrometry and the selective modification of the free thiol form of cysteine in both peptides and proteins by various quinones. This simple modification can be used to quantify the number of free or disulfide bound cysteines in a protein. In addition, quinone modification can also be used to easily probe the solvent accessibility of cysteine residues, which provides information about protein structure or folding state. Furthermore, the chromophoric properties of the quinone moiety can be leveraged for site specific photodissociation of the backbone. The photodissociation reveals both the presence and location of modified cysteine residues. For example, cleavage of the protein backbone of alpha Hemoglobin is observed selectively at a single cysteine out of 140 residues in the whole protein. This selective backbone fragmentation is accompanied by a parent ion mass loss which is unique to the modifying quinone. When combined, this information can be used to determine both the presence and site of modification generated by naturally occurring molecules, such as dopamine, which can harness quinone chemistry to modify proteins. PMID:20405909

  19. K-Ras(G12D)-selective inhibitory peptides generated by random peptide T7 phage display technology.

    Science.gov (United States)

    Sakamoto, Kotaro; Kamada, Yusuke; Sameshima, Tomoya; Yaguchi, Masahiro; Niida, Ayumu; Sasaki, Shigekazu; Miwa, Masanori; Ohkubo, Shoichi; Sakamoto, Jun-Ichi; Kamaura, Masahiro; Cho, Nobuo; Tani, Akiyoshi

    2017-03-11

    Amino-acid mutations of Gly 12 (e.g. G12D, G12V, G12C) of V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (K-Ras), the most promising drug target in cancer therapy, are major growth drivers in various cancers. Although over 30 years have passed since the discovery of these mutations in most cancer patients, effective mutated K-Ras inhibitors have not been marketed. Here, we report novel and selective inhibitory peptides to K-Ras(G12D). We screened random peptide libraries displayed on T7 phage against purified recombinant K-Ras(G12D), with thorough subtraction of phages bound to wild-type K-Ras, and obtained KRpep-2 (Ac-RRCPLYISYDPVCRR-NH 2 ) as a consensus sequence. KRpep-2 showed more than 10-fold binding- and inhibition-selectivity to K-Ras(G12D), both in SPR analysis and GDP/GTP exchange enzyme assay. K D and IC 50 values were 51 and 8.9 nM, respectively. After subsequent sequence optimization, we successfully generated KRpep-2d (Ac-RRRRCPLYISYDPVCRRRR-NH 2 ) that inhibited enzyme activity of K-Ras(G12D) with IC 50  = 1.6 nM and significantly suppressed ERK-phosphorylation, downstream of K-Ras(G12D), along with A427 cancer cell proliferation at 30 μM peptide concentration. To our knowledge, this is the first report of a K-Ras(G12D)-selective inhibitor, contributing to the development and study of K-Ras(G12D)-targeting drugs. Copyright © 2017 Elsevier Inc. All rights reserved.

  20. Escherichia coli MazF leads to the simultaneous selective synthesis of both "death proteins" and "survival proteins".

    Directory of Open Access Journals (Sweden)

    Shahar Amitai

    2009-03-01

    Full Text Available The Escherichia coli mazEF module is one of the most thoroughly studied toxin-antitoxin systems. mazF encodes a stable toxin, MazF, and mazE encodes a labile antitoxin, MazE, which prevents the lethal effect of MazF. MazF is an endoribonuclease that leads to the inhibition of protein synthesis by cleaving mRNAs at ACA sequences. Here, using 2D-gels, we show that in E. coli, although MazF induction leads to the inhibition of the synthesis of most proteins, the synthesis of an exclusive group of proteins, mostly smaller than about 20 kDa, is still permitted. We identified some of those small proteins by mass spectrometry. By deleting the genes encoding those proteins from the E. coli chromosome, we showed that they were required for the death of most of the cellular population. Under the same experimental conditions, which induce mazEF-mediated cell death, other such proteins were found to be required for the survival of a small sub-population of cells. Thus, MazF appears to be a regulator that induces downstream pathways leading to death of most of the population and the continued survival of a small sub-population, which will likely become the nucleus of a new population when growth conditions become less stressful.

  1. Cholesterol selectively regulates IL-5 induced mitogen activated protein kinase signaling in human eosinophils.

    Directory of Open Access Journals (Sweden)

    Mandy E Burnham

    Full Text Available Eosinophils function contributes to human allergic and autoimmune diseases, many of which currently lack curative treatment. Development of more effective treatments for eosinophil-related diseases requires expanded understanding of eosinophil signaling and biology. Cell signaling requires integration of extracellular signals with intracellular responses, and is organized in part by cholesterol rich membrane microdomains (CRMMs, commonly referred to as lipid rafts. Formation of these organizational membrane domains is in turn dependent upon the amount of available cholesterol, which can fluctuate widely with a variety of disease states. We tested the hypothesis that manipulating membrane cholesterol content in primary human peripheral blood eosinophils (PBEos would selectively alter signaling pathways that depend upon membrane-anchored signaling proteins localized within CRMMs (e.g., mitogen activated protein kinase [MAPK] pathway, while not affecting pathways that signal through soluble proteins, like the Janus Kinase/Signal Transducer and Activator of Transcription [JAK/STAT] pathway. Cholesterol levels were increased or decreased utilizing cholesterol-chelating methyl-β-cyclodextrin (MβCD, which can either extract membrane cholesterol or add exogenous membrane cholesterol depending on whether MβCD is preloaded with cholesterol. Human PBEos were pretreated with MβCD (cholesterol removal or MβCD+Cholesterol (MβCD+Chol; cholesterol delivery; subsequent IL-5-stimulated signaling and physiological endpoints were assessed. MβCD reduced membrane cholesterol in PBEos, and attenuated an IL-5-stimulated p38 and extracellular-regulated kinase 1/2 phosphorylation (p-p38, p-ERK1/2, and an IL-5-dependent increase in interleukin-1β (IL-1β mRNA levels. In contrast, MβCD+Chol treatment elevated PBEos membrane cholesterol levels and basal p-p38, but did not alter IL-5-stimulated phosphorylation of ERK1/2, STAT5, or STAT3. Furthermore, M

  2. Use of FabV-Triclosan Plasmid Selection System for Efficient Expression and Production of Recombinant Proteins in Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Syed A Ali

    Full Text Available Maintenance of recombinant plasmid vectors in host bacteria relies on the presence of selection antibiotics in the growth media to suppress plasmid -free segregants. However, presence of antibiotic resistance genes and antibiotics themselves is not acceptable in several applications of biotechnology. Previously, we have shown that FabV-Triclosan selection system can be used to select high and medium copy number plasmid vectors in E. coli. Here, we have extended our previous work and demonstrated that expression vectors containing FabV can be used efficiently to express heterologous recombinant proteins in similar or better amounts in E. coli host when compared with expression vectors containing β-lactamase. Use of small amount of non-antibiotic Triclosan as selection agent in growth medium, enhanced plasmid stability, applicability in various culture media, and compatibility with other selection systems for multiple plasmid maintenance are noteworthy features of FabV-Triclosan selection system.

  3. Effect of Production Phase on Growth, Enzyme Activities and Feed Selection of Broilers Raised on Vegetable Protein Diet

    Directory of Open Access Journals (Sweden)

    M. A. Hossain

    2014-11-01

    Full Text Available This study consisted of two experiments, conducted to assess the impact of phase at which vegetable protein (VP diets are introduced to broiler chicks, and preference of birds for diets based on soybean or canola meal (CM. Two hundred and ten day-old Cobb 500 chicks were randomly distributed into five dietary groups in the main experiment. One group was fed on animal protein (AP diet all through to 21 days of age; two other groups were started on AP diet for 7 days and then switched to diets containing soybean meal (AP-SBM or AP-CM, while two other diets (SBM-AP and CM-AP were started on one of the VP diets for 7 days and then switched to AP diet. A sub-experiment on thirty birds raised on a commercial diet to 7 days was used in a feed selection test to quantify the preference of birds for the diets containing mainly CM or SBM. Chicks were reared under similar care and management conditions and the diets were iso-caloric and iso-nitrogenous. Results of the main experiment showed that chicks on CM-AP diet ate more (p<0.05 than those on the other diets up to day 7. Body weight gain was highest (p<0.001 on the AP-SBM diet while birds on the CM-AP diet weighed the least at 7 d. Feed intake, body weight gain, feed conversion ratio, mortality, bone growth, visceral organ development, and activities of digestive enzymes were similar between the groups from hatch to 21 days of age. Results of the second sub-experiment showed that chicks preferred the CM-based diets to the SBM-based diets at 8 to 14 d (p<0.001 and 15 to 21 d (p<0.01 when given a choice. Overall, the birds were not affected by the nature of the starter diet although they tended to prefer the canola to soybean diets.

  4. Effect of a high-protein diet on maintenance of blood pressure levels achieved after initial weight loss: the DiOGenes randomized study

    NARCIS (Netherlands)

    Engberink, M.F.; Geleijnse, J.M.; Bakker, S.J.L.; Larsen, T.

    2015-01-01

    Randomized trials have shown significant blood pressure (BP) reductions after increased protein compared with carbohydrate intake, but the effect on BP maintenance after initial weight loss is unclear. We examined the effect of a high-protein diet on the maintenance of reduced BP after weight loss

  5. Post-Exercise Protein Trial: Interactions between Diet and Exercise (PEPTIDE): study protocol for randomized controlled trial.

    Science.gov (United States)

    Alghannam, Abdullah F; Tsintzas, Kostas; Thompson, Dylan; Bilzon, James; Betts, James A

    2014-11-24

    Performing regular exercise is known to manifest a number of health benefits that mainly relate to cardiovascular and muscular adaptations to allow for greater oxygen extraction and utilization. There is increasing evidence that nutrient intake can affect the adaptive response to a single exercise bout, and that protein feeding is important to facilitate this process. Thus, the exercise-nutrient interaction may potentially lead to a greater response to training. The role of post-exercise protein ingestion in enhancing the effects of running-based endurance exercise training relative to energy-matched carbohydrate intervention remains to be established. Additionally, the influence of immediate versus overnight protein ingestion in mediating these training effects is currently unknown. The current protocol aims to establish whether post-exercise nutrient intake and timing would influence the magnitude of improvements during a prescribed endurance training program. The project involves two phases with each involving two treatment arms applied in a randomized investigator-participant double-blind parallel group design. For each treatment, participants will be required to undergo six weeks of running-based endurance training. Immediately post-exercise, participants will be prescribed solutions providing 0.4 grams per kilogram of body mass (g · kg(-1)) of whey protein hydrolysate plus 0.4 g · kg(-1) sucrose, relative to an isocaloric sucrose control (0.8 g · kg(-1); Phase I). In Phase II, identical protein supplements will be provided (0.4 + 0.4 g · kg(-1) · h(-1) of whey protein hydrolysate and sucrose, respectively), with the timing of ingestion manipulated to compare immediate versus overnight recovery feedings. Anthropometric, expired gas, venous blood and muscle biopsy samples will be obtained at baseline and following the six-week training period. By investigating the role of nutrition in enhancing the effects of endurance exercise training, we will provide

  6. Selectivity analysis of protein kinase CK2 inhibitors DMAT, TBB and resorufin in cisplatin-induced stress responses

    DEFF Research Database (Denmark)

    Fritz, Gerhard; Issinger, Olaf-Georg; Olsen, Birgitte Brinkmann

    2009-01-01

    by phosphorylation of JNK and H2AX). In the case of resorufin no interference with the stress-signaling pathway is observed, supporting the notion that TBB and DMAT interfere with upstream molecules involved in genotoxic stress signaling. We have also tested the protein kinase CK2 inhibitors with respect to cell......Targeting protein kinases as a therapeutic approach to treat various diseases, especially cancer is currently a fast growing business. Although many inhibitors are available, exhibiting remarkable potency, the major challenge is their selectivity. Here we show that the protein kinase CK2 inhibitors...

  7. Polyanion cluster patterning on polymer surface through microemulsion approach for selective adsorption of proteins.

    Science.gov (United States)

    Liang, Jing; Ma, Yingyi; Sun, Hang; Li, Wen; Wu, Lixin

    2013-11-01

    A facile method to fabricate honeycomb-patterned polymer films bearing cavities that are locally decorated with inorganic component is developed in this study. By mixing poly(methyl methacrylate) dichloromethane solution containing P123 with polyoxometalate (POM) aqueous solution through shaking, a reversed hybrid microemulsion is obtained. The evaporation of solvent in the microemulsion on solid surface yields an ordered porous film accompanied by the accumulation of P123 and POMs on the inner surface of the cavities. The formation of patterned structure is proved to be independent from the type of POMs, but the size of the cavities can be adjusted to some extent by changing the concentration of surfactant and polymer, and the volume ratio of water and dichloromethane in the solution used for casting. The locally anchored POMs can be readily applied for the selective recognition of proteins. BSA and hemoglobin patterns are then fabricated through their electrostatic interactions with POMs. At lower pH, POM pattern could prior recognize hemoglobin from its mixed solution of BSA, generating a characteristic pattern. The reported work creates an efficient way of patterning organically incompatible components, such as water-soluble molecules and nanoparticles, on porous polymer films for the fabrication of multi-functional hybrid surface structures. Copyright © 2013 Elsevier Inc. All rights reserved.

  8. Chronic administration of OB protein decreases food intake by selectively reducing meal size in male rats.

    Science.gov (United States)

    Kahler, A; Geary, N; Eckel, L A; Campfield, L A; Smith, F J; Langhans, W

    1998-07-01

    The potent hypophagic effect of OB protein (OB) is well established, but the mechanism of this effect is largely unknown. We investigated the effects of chronic administration of a novel modified recombinant human OB (Mod-OB) with a prolonged half-life (>48 h) on ad libitum food intake, spontaneous meal patterns, and body weight in 24 adult, male Sprague-Dawley rats (body weight at study onset: 292 g). Single daily subcutaneous injections of Mod-OB (4 mg/kg daily) for 8 consecutive days significantly reduced ad libitum food intake compared with vehicle injections from injection day 3 through postinjection day 3. Mod-OB-injected rats ate between 4.5 and 7.1 g (or 13-20%) per day less than controls, with the reduction primarily occurring during the dark period. Body weight gain was significantly decreased in response to Mod-OB from injection day 8 until postinjection day 4, with a maximum difference of 24 g on postinjection day 3. The reduction of food intake by Mod-OB was mainly due to a 21-34% decrease in nocturnal spontaneous meal size. There was no significant effect of Mod-OB on nocturnal meal frequency or duration. Mod-OB also did not reliably affect the size, duration, or frequency of diurnal meals. Mod-OB-injected rats displayed no compensatory hyperphagia after the injection period. These results indicate that chronically administered OB selectively affects the mechanisms controlling meal size in male rats.

  9. Moderate carbohydrate, moderate protein weight loss diet reduces cardiovascular disease risk compared to high carbohydrate, low protein diet in obese adults: A randomized clinical trial

    Directory of Open Access Journals (Sweden)

    Evans Ellen M

    2008-11-01

    Full Text Available Abstract Background To evaluate the metabolic effects of two weight loss diets differing in macronutrient composition on features of dyslipidemia and post-prandial insulin (INS response to a meal challenge in overweight/obese individuals. Methods This study was a parallel-arm randomized 4 mo weight loss trial. Adults (n = 50, 47 ± 7 y matched on BMI (33.6 ± 0.6 kg/m2, P = 0.79 consumed energy restricted diets (deficit ~500 kcal/d: PRO (1.6 g.kg-1.d-1 protein and -1.d-1 protein and > 220 g/d carbohydrate for 4 mos. Meal challenges of respective diets were utilized for determination of blood lipids and post-prandial INS and glucose response at the beginning and end of the study. Results There was a trend for PRO to lose more weight (-9.1% vs. -7.3%, P = 0.07 with a significant reduction in percent fat mass compared to CHO (-8.7% vs. -5.7%; P = 0.03. PRO also favored reductions in triacylglycerol (-34% vs. -14%; P P = 0.05; however, CHO favored reduction in LDL-C (-7% vs. +2.5%; P P P Conclusion A weight loss diet with moderate carbohydrate, moderate protein results in more favorable changes in body composition, dyslipidemia, and post-prandial INS response compared to a high carbohydrate, low protein diet suggesting an additional benefit beyond weight management to include augmented risk reduction for metabolic disease.

  10. Inactive matrix Gla protein is causally related to adverse health outcomes: a Mendelian randomization study in a Flemish population.

    Science.gov (United States)

    Liu, Yan-Ping; Gu, Yu-Mei; Thijs, Lutgarde; Knapen, Marjo H J; Salvi, Erika; Citterio, Lorena; Petit, Thibault; Carpini, Simona Delli; Zhang, Zhenyu; Jacobs, Lotte; Jin, Yu; Barlassina, Cristina; Manunta, Paolo; Kuznetsova, Tatiana; Verhamme, Peter; Struijker-Boudier, Harry A; Cusi, Daniele; Vermeer, Cees; Staessen, Jan A

    2015-02-01

    Matrix Gla-protein is a vitamin K-dependent protein that strongly inhibits arterial calcification. Vitamin K deficiency leads to production of inactive nonphosphorylated and uncarboxylated matrix Gla protein (dp-ucMGP). The risk associated with dp-ucMGP in the population is unknown. In a Flemish population study, we measured circulating dp-ucMGP at baseline (1996-2011), genotyped MGP, recorded adverse health outcomes until December 31, 2012, and assessed the multivariable-adjusted associations of adverse health outcomes with dp-ucMGP. We applied a Mendelian randomization analysis using MGP genotypes as instrumental variables. Among 2318 participants, baseline dp-ucMGP averaged 3.61 μg/L. Over 14.1 years (median), 197 deaths occurred, 58 from cancer and 70 from cardiovascular disease; 85 participants experienced a coronary event. The risk of death and non-cancer mortality curvilinearly increased (P≤0.008) by 15.0% (95% confidence interval, 6.9-25.3) and by 21.5% (11.1-32.9) for a doubling of the nadir (1.43 and 0.97 μg/L, respectively). With higher dp-ucMGP, cardiovascular mortality log-linearly increased (hazard ratio for dp-ucMGP doubling, 1.14 [1.01-1.28]; P=0.027), but coronary events log-linearly decreased (0.93 [0.88-0.99]; P=0.021). dp-ucMGP levels were associated (P≤0.001) with MGP variants rs2098435, rs4236, and rs2430692. For non-cancer mortality and coronary events (P≤0.022), but not for total and cardiovascular mortality (P≥0.13), the Mendelian randomization analysis suggested causality. Higher dp-ucMGP predicts total, non-cancer and cardiovascular mortality, but lower coronary risk. For non-cancer mortality and coronary events, these associations are likely causal. © 2014 American Heart Association, Inc.

  11. Predicting Zoonotic Risk of Influenza A Viruses from Host Tropism Protein Signature Using Random Forest

    Directory of Open Access Journals (Sweden)

    Christine L. P. Eng

    2017-05-01

    Full Text Available Influenza A viruses remain a significant health problem, especially when a novel subtype emerges from the avian population to cause severe outbreaks in humans. Zoonotic viruses arise from the animal population as a result of mutations and reassortments, giving rise to novel strains with the capability to evade the host species barrier and cause human infections. Despite progress in understanding interspecies transmission of influenza viruses, we are no closer to predicting zoonotic strains that can lead to an outbreak. We have previously discovered distinct host tropism protein signatures of avian, human and zoonotic influenza strains obtained from host tropism predictions on individual protein sequences. Here, we apply machine learning approaches on the signatures to build a computational model capable of predicting zoonotic strains. The zoonotic strain prediction model can classify avian, human or zoonotic strains with high accuracy, as well as providing an estimated zoonotic risk. This would therefore allow us to quickly determine if an influenza virus strain has the potential to be zoonotic using only protein sequences. The swift identification of potential zoonotic strains in the animal population using the zoonotic strain prediction model could provide us with an early indication of an imminent influenza outbreak.

  12. Evolution of species-specific major seminal fluid proteins in placental mammals by gene death and positive selection

    NARCIS (Netherlands)

    Meslin, C.; Laurin, M.; Callebaut, I.; Druart, X.; Monget, P.

    2015-01-01

    The seminal fluid is a complex substance composed of a variety of secreted proteins and has been shown to play an important role in the fertilisation process in mammals and also in Drosophila. Several genes under positive selection have been documented in some rodents and primates. Our study

  13. A randomized trial to manipulate the quality instead of quantity of dietary proteins to influence the markers of satiety.

    Science.gov (United States)

    Bayham, Brooke E; Greenway, Frank L; Johnson, William D; Dhurandhar, Nikhil V

    2014-01-01

    To test whether a breakfast including eggs (EB) containing high-quality protein decreases subsequent food intake and increases satiety-related hormones in overweight or obese adults more than a breakfast including cereal (CB) of lower protein quality, but matched for energy density and macronutrient composition. Twenty healthy overweight or obese subjects were randomized to eat an EB or a CB daily under supervision for one week, followed by a crossover to the opposite breakfast week after a two-week washout period. On days 1 and 7 of each test week, a structured lunch was provided ad libitum. Food intake, hunger and satiety scores, and blood parameters were measured before and after breakfast. Outcomes were analyzed using mixed effects statistical models for repeated measures analysis of variance. Compared to the CB week, during the EB week, a) feeling of fullness was greater (Pbenefits are pronounced and lasting, if protein quality of all meals is increased. Copyright © 2014 Elsevier Inc. All rights reserved.

  14. Protein Tyrosine Nitration: Selectivity, physicochemical and biological consequences, denitration and proteomics methods for the identification of tyrosine-nitrated proteins

    NARCIS (Netherlands)

    Abello, N.; Kerstjens, H.A.M.; Postma, D.S; Bischoff, Rainer

    2009-01-01

    Protein tyrosine nitration (PTN) is a post-translational modification occurring under the action of a nitrating agent. Tyrosine is modified in the 3-position of the phenolic ring through the addition of a nitro group (NO2). In the present article, we review the main nitration reactions and elucidate

  15. PLASMA PROTEIN ELECTROPHORESIS AND SELECT ACUTE PHASE PROTEINS IN HEALTHY BONNETHEAD SHARKS (SPHYRNA TIBURO) UNDER MANAGED CARE.

    Science.gov (United States)

    Hyatt, Michael W; Field, Cara L; Clauss, Tonya M; Arheart, Kristopher L; Cray, Carolyn

    2016-12-01

    Preventative health care of elasmobranchs is an important but understudied field of aquatic veterinary medicine. Evaluation of inflammation through the acute phase response is a valuable tool in health assessments. To better assess the health of bonnethead sharks ( Sphyrna tiburo ) under managed care, normal reference intervals of protein electrophoresis (EPH) and the acute phase proteins, C-reactive protein (CRP) and haptoglobin (HP), were established. Blood was collected from wild caught, captive raised bonnethead sharks housed at public aquaria. Lithium heparinized plasma was either submitted fresh or stored at -80°C prior to submission. Electrophoresis identified protein fractions with migration characteristics similar to other animals with albumin, α-1 globulin, α-2 globulin, β globulin, and γ globulin. These fractions were classified as fractions 1-5 as fractional contents are unknown in this species. Commercial reagents for CRP and HP were validated for use in bonnethead sharks. Reference intervals were established using the robust method recommended by the American Society for Veterinary Clinical Pathology for the calculation of 90% reference intervals. Once established, the diagnostic and clinical applicability of these reference intervals was used to assess blood from individuals with known infectious diseases that resulted in systemic inflammation and eventual death. Unhealthy bonnethead sharks had significantly decreased fraction 2, fraction 3, and fraction 3:4 ratio and significantly increased fraction 5, CRP, and HP. These findings advance our understanding of elasmobranch acute phase inflammatory response and health and aid clinicians in the diagnosis of inflammatory disease in bonnethead sharks.

  16. Total synthesis and structure–activity relationship studies of a series of selective G protein inhibitors

    DEFF Research Database (Denmark)

    Xiong, Xiaofeng; Zhang, Hang; Underwood, Christina R.

    2016-01-01

    G proteins are key mediators of G protein-coupled receptor signalling, which facilitates a plethora of important physiological processes. The cyclic depsipeptides YM-254890 and FR900359 are the only known specific inhibitors of the Gq subfamily of G proteins; however, no synthetic route has been ...

  17. Design and synthesis of artificial phospholipid for selective cleavage of integral membrane protein.

    Science.gov (United States)

    Furuta, Takumi; Sakai, Minatsu; Hayashi, Hiroyasu; Asakawa, Tomohiro; Kataoka, Fumi; Fujii, Satoshi; Suzuki, Takashi; Suzuki, Yasuo; Tanaka, Kiyoshi; Fishkin, Nathan; Nakanishi, Koji

    2005-09-28

    An artificial phospholipid, possessing saturated alkyl chains as a membrane anchor and protein recognition site as well as an Fe(III)-EDTA moiety as a protein cleavable polar head group, was designed and synthesized based on the amidite method for the purpose of examination of cleavage of integral membrane proteins.

  18. MscL of Bacillus subtilis prevents selective release of cytoplasmic proteins in a hypotonic environment

    NARCIS (Netherlands)

    Kouwen, Thijs R. H. M.; Antelmann, Haike; van der Ploeg, Rene; Denham, Emma L.; Hecker, Michael; van Dijl, Jan Maarten

    Bacillus subtilis serves as an excellent model to study protein secretion at a proteomic scale. Most of the extracellular proteins are exported from the cytoplasm via the secretory (Sec) pathway. Despite extensive studies, the secretion mechanisms of about 25% of the extracellular proteins are

  19. Selectivity of Chemoresistive Sensors Made of Chemically Functionalized Carbon Nanotube Random Networks for Volatile Organic Compounds (VOC

    Directory of Open Access Journals (Sweden)

    Jean-François Feller

    2014-01-01

    Full Text Available Different grades of chemically functionalized carbon nanotubes (CNT have been processed by spraying layer-by-layer (sLbL to obtain an array of chemoresistive transducers for volatile organic compound (VOC detection. The sLbL process led to random networks of CNT less conductive, but more sensitive to vapors than filtration under vacuum (bucky papers. Shorter CNT were also found to be more sensitive due to the less entangled and more easily disconnectable conducting networks they are making. Chemical functionalization of the CNT’ surface is changing their selectivity towards VOC, which makes it possible to easily discriminate methanol, chloroform and tetrahydrofuran (THF from toluene vapors after the assembly of CNT transducers into an array to make an e-nose. Interestingly, the amplitude of the CNT transducers’ responses can be enhanced by a factor of five (methanol to 100 (chloroform by dispersing them into a polymer matrix, such as poly(styrene (PS, poly(carbonate (PC or poly(methyl methacrylate (PMMA. COOH functionalization of CNT was found to penalize their dispersion in polymers and to decrease the sensors’ sensitivity. The resulting conductive polymer nanocomposites (CPCs not only allow for a more easy tuning of the sensors’ selectivity by changing the chemical nature of the matrix, but they also allow them to adjust their sensitivity by changing the average gap between CNT (acting on quantum tunneling in the CNT network. Quantum resistive sensors (QRSs appear promising for environmental monitoring and anticipated disease diagnostics that are both based on VOC analysis.

  20. Selective protein patterning based on the micro-structured organosilane self-assembled monolayer by vacuum ultraviolet light lithography.

    Science.gov (United States)

    Lim, Sung-Hyuk; Yamaguchi, Munehiro; Nishimura, Okio; Mie, Yasuhiro; Tamura, Tomohiro; Kim, Byung-Woo; Suzuki, Masaaki

    2009-12-01

    We have succeeded to immobilize fluorescent proteins selectively using a micro-structured organosilane self-assembled monolayer as a template. An organosilane layer with amino terminal group was formed on a thermally oxidized Si wafer by liquid-phase method and then was pattern-etched by vacuum ultraviolet light (VUV). The second organosilane layer with thiol terminal group was deposited on the etched area by chemical vapor surface modification method (CVSM). These micro-structured organosilane layer containing two reactive terminal groups were chemically modified using bi-functional linkers. Two kinds of fluorescent protein, Enhanced Cyan Fluorescent Protein (ECFP) and R-phycoerythrin were selectively immobilized on the chemically modified surface.

  1. Peptidomics of Peptic Digest of Selected Potato Tuber Proteins: Post-Translational Modifications and Limited Cleavage Specificity.

    Science.gov (United States)

    C K Rajendran, Subin R; Mason, Beth; Udenigwe, Chibuike C

    2016-03-23

    Bioinformatic tools are useful in predicting bioactive peptides from food proteins. This study was focused on using bioinformatics and peptidomics to evaluate the specificity of peptide release and post-translational modifications (PTMs) in a peptic digest of potato protein isolate. Peptides in the protein hydrolysate were identified by LC-MS/MS and subsequently aligned to their parent potato tuber proteins. Five major proteins were selected for further analysis, namely, lipoxygenase, α-1,4-glucan phosphorylase, annexin, patatin, and polyubiquitin, based on protein coverage, abundance, confidence levels, and function. Comparison of the in silico peptide profile generated with ExPASy PeptideCutter and experimental peptidomics data revealed several differences. The experimental peptic cleavage sites were found to vary in number and specificity from PeptideCutter predictions. Average peptide chain length was also found to be higher than predicted with hexapeptides as the smallest detected peptides. Moreover, PTMs, particularly Met oxidation and Glu/Asp deamidation, were observed in some peptides, and these were unaccounted for during in silico analysis. PTMs can be formed during aging of potato tubers, or as a result of processing conditions during protein isolation and hydrolysis. The findings provide insights on the limitations of current bioinformatics tools for predicting bioactive peptide release from proteins, and on the existence of structural modifications that can alter the peptide bioactivity and functionality.

  2. A Venom Gland Extracellular Chitin-Binding-Like Protein from Pupal Endoparasitoid Wasps, Pteromalus Puparum, Selectively Binds Chitin

    Directory of Open Access Journals (Sweden)

    Yu Zhu

    2015-11-01

    Full Text Available Chitin-binding proteins (CBPs are present in many species and they act in a variety of biological processes. We analyzed a Pteromalus puparum venom apparatus proteome and transcriptome and identified a partial gene encoding a possible CBP. Here, we report cloning a full-length cDNA of a sequence encoding a chitin-binding-like protein (PpCBP from P. puparum, a pupal endoparasitoid of Pieris rapae. The cDNA encoded a 96-amino-acid protein, including a secretory signal peptide and a chitin-binding peritrophin-A domain. Phylogenetic analysis of chitin binding domains (CBDs of cuticle proteins and peritrophic matrix proteins in selected insects revealed that the CBD of PpCBP clustered with the CBD of Nasonia vitripennis. The PpCBP is specifically expressed in the venom apparatus of P. puparum, mostly in the venom gland. PpCBP expression was highest at day one after adult eclosion and much lower for the following five days. We produced a recombinant PpCBP and binding assays showed the recombinant protein selectively binds chitin but not cellulose in vitro. We infer that PpCBP serves a structural role in the venom reservoir, or may be injected into the host to help wound healing of the host exoskeleton.

  3. Selection of an Appropriate Protein Extraction Method to Study the Phosphoproteome of Maize Photosynthetic Tissue.

    Directory of Open Access Journals (Sweden)

    Inês M Luís

    Full Text Available Often plant tissues are recalcitrant and, due to that, methods relying on protein precipitation, such as TCA/acetone precipitation and phenol extraction, are usually the methods of choice for protein extraction in plant proteomic studies. However, the addition of precipitation steps to protein extraction methods may negatively impact protein recovery, due to problems associated with protein re-solubilization. Moreover, we show that when working with non-recalcitrant plant tissues, such as young maize leaves, protein extraction methods with precipitation steps compromise the maintenance of some labile post-translational modifications (PTMs, such as phosphorylation. Therefore, a critical issue when studying PTMs in plant proteins is to ensure that the protein extraction method is the most appropriate, both at qualitative and quantitative levels. In this work, we compared five methods for protein extraction of the C4-photosynthesis related proteins, in the tip of fully expanded third-leaves. These included: TCA/Acetone Precipitation; Phenol Extraction; TCA/Acetone Precipitation followed by Phenol Extraction; direct extraction in Lysis Buffer (a urea-based buffer; and direct extraction in Lysis Buffer followed by Cleanup with a commercial kit. Protein extraction in Lysis Buffer performed better in comparison to the other methods. It gave one of the highest protein yields, good coverage of the extracted proteome and phosphoproteome, high reproducibility, and little protein degradation. This was also the easiest and fastest method, warranting minimal sample handling. We also show that this method is adequate for the successful extraction of key enzymes of the C4-photosynthetic metabolism, such as PEPC, PPDK, PEPCK, and NADP-ME. This was confirmed by MALDI-TOF/TOF MS analysis of excised spots of 2DE analyses of the extracted protein pools. Staining for phosphorylated proteins in 2DE revealed the presence of several phosphorylated isoforms of PEPC, PPDK

  4. Two Plasmodium falciparum genes express merozoite proteins that are related to Plasmodium vivax and Plasmodium yoelii adhesive proteins involved in host cell selection and invasion

    Science.gov (United States)

    Rayner, Julian C.; Galinski, Mary R.; Ingravallo, Paul; Barnwell, John W.

    2000-01-01

    Two related Plasmodium falciparum genes and their encoded proteins have been identified by comparative analyses with Plasmodium vivax reticulocyte binding protein 2 (PvRBP-2). The P. falciparum genes have a structure which suggests that they may be the result of an evolutionary duplication event, as they share more than 8 kb of closely related nucleotide sequence but then have quite divergent unique 3′ ends. Between these shared and unique regions is a complex set of repeats, the nature and number of which differs between the two genes, as well as between different P. falciparum strains. Both genes encode large hydrophilic proteins, which are concentrated at the invasive apical end of the merozoite and are predicted to be more than 350 kDa, with an N-terminal signal sequence and a single transmembrane domain near their C termini. Importantly, they also share gene structure and amino acid homology with the Plasmodium yoelii 235-kDa rhoptry protein family, which is also related to PvRBP-2. Together these Plasmodium proteins define an extended family of proteins that appear to function in erythrocyte selection and invasion. As such, they may prove to be essential components of malaria vaccine preparations. PMID:10920203

  5. Optimal Subset Selection of Time-Series MODIS Images and Sample Data Transfer with Random Forests for Supervised Classification Modelling

    Directory of Open Access Journals (Sweden)

    Fuqun Zhou

    2016-10-01

    Full Text Available Nowadays, various time-series Earth Observation data with multiple bands are freely available, such as Moderate Resolution Imaging Spectroradiometer (MODIS datasets including 8-day composites from NASA, and 10-day composites from the Canada Centre for Remote Sensing (CCRS. It is challenging to efficiently use these time-series MODIS datasets for long-term environmental monitoring due to their vast volume and information redundancy. This challenge will be greater when Sentinel 2–3 data become available. Another challenge that researchers face is the lack of in-situ data for supervised modelling, especially for time-series data analysis. In this study, we attempt to tackle the two important issues with a case study of land cover mapping using CCRS 10-day MODIS composites with the help of Random Forests’ features: variable importance, outlier identification. The variable importance feature is used to analyze and select optimal subsets of time-series MODIS imagery for efficient land cover mapping, and the outlier identification feature is utilized for transferring sample data available from one year to an adjacent year for supervised classification modelling. The results of the case study of agricultural land cover classification at a regional scale show that using only about a half of the variables we can achieve land cover classification accuracy close to that generated using the full dataset. The proposed simple but effective solution of sample transferring could make supervised modelling possible for applications lacking sample data.

  6. Biased random key genetic algorithm with insertion and gender selection for capacitated vehicle routing problem with time windows

    Science.gov (United States)

    Rochman, Auliya Noor; Prasetyo, Hari; Nugroho, Munajat Tri

    2017-06-01

    Vehicle Routing Problem (VRP) often occurs when the manufacturers need to distribute their product to some customers/outlets. The distribution process is typically restricted by the capacity of the vehicle and the working hours at the distributor. This type of VRP is also known as Capacitated Vehicle Routing Problem with Time Windows (CVRPTW). A Biased Random Key Genetic Algorithm (BRKGA) was designed and coded in MATLAB to solve the CVRPTW case of soft drink distribution. The standard BRKGA was then modified by applying chromosome insertion into the initial population and defining chromosome gender for parent undergoing crossover operation. The performance of the established algorithms was then compared to a heuristic procedure for solving a soft drink distribution. Some findings are revealed (1) the total distribution cost of BRKGA with insertion (BRKGA-I) results in a cost saving of 39% compared to the total cost of heuristic method, (2) BRKGA with the gender selection (BRKGA-GS) could further improve the performance of the heuristic method. However, the BRKGA-GS tends to yield worse results compared to that obtained from the standard BRKGA.

  7. A preliminary investigation of the jack-bean urease inhibition by randomly selected traditionally used herbal medicine.

    Science.gov (United States)

    Biglar, Mahmood; Soltani, Khadijeh; Nabati, Farzaneh; Bazl, Roya; Mojab, Faraz; Amanlou, Massoud

    2012-01-01

    Helicobacter pylori (H. pylori) infection leads to different clinical and pathological outcomes in humans, including chronic gastritis, peptic ulcer disease and gastric neoplasia and even gastric cancer and its eradiation dependst upon multi-drug therapy. The most effective therapy is still unknown and prompts people to make great efforts to find better and more modern natural or synthetic anti-H. pylori agents. In this report 21 randomly selected herbal methanolic extracts were evaluated for their effect on inhibition of Jack-bean urease using the indophenol method as described by Weatherburn. The inhibition potency was measured by UV spectroscopy technique at 630 nm which attributes to released ammonium. Among these extracts, five showed potent inhibitory activities with IC50 ranges of 18-35 μg/mL. These plants are Matricaria disciforme (IC50:35 μg/mL), Nasturtium officinale (IC50:18 μg/mL), Punica granatum (IC50:30 μg/mL), Camelia sinensis (IC50:35 μg/mL), Citrus aurantifolia (IC50:28 μg/mL).

  8. A brief, web-based personalized feedback selective intervention for college student marijuana use: a randomized clinical trial.

    Science.gov (United States)

    Lee, Christine M; Neighbors, Clayton; Kilmer, Jason R; Larimer, Mary E

    2010-06-01

    Despite clear need, brief web-based interventions for marijuana-using college students have not been evaluated in the literature. The current study was designed to evaluate a brief, web-based personalized feedback intervention for at-risk marijuana users transitioning to college. All entering first-year students were invited to complete a brief questionnaire. Participants meeting criteria completed a baseline assessment (N = 341) and were randomly assigned to web-based personalized feedback or assessment-only control conditions. Participants completed 3-month (95.0%) and 6-month (94.4%) follow-up assessments. Results indicated that although there was no overall intervention effect, moderator analyses found promising effects for those with a family history of drug problems and, to a smaller extent, students who were higher in contemplation of changing marijuana use at baseline. Implications of these findings for selective intervention of college marijuana use and web-based interventions in general are discussed. (PsycINFO Database Record (c) 2010 APA, all rights reserved).

  9. Optimal Subset Selection of Time-Series MODIS Images and Sample Data Transfer with Random Forests for Supervised Classification Modelling.

    Science.gov (United States)

    Zhou, Fuqun; Zhang, Aining

    2016-10-25

    Nowadays, various time-series Earth Observation data with multiple bands are freely available, such as Moderate Resolution Imaging Spectroradiometer (MODIS) datasets including 8-day composites from NASA, and 10-day composites from the Canada Centre for Remote Sensing (CCRS). It is challenging to efficiently use these time-series MODIS datasets for long-term environmental monitoring due to their vast volume and information redundancy. This challenge will be greater when Sentinel 2-3 data become available. Another challenge that researchers face is the lack of in-situ data for supervised modelling, especially for time-series data analysis. In this study, we attempt to tackle the two important issues with a case study of land cover mapping using CCRS 10-day MODIS composites with the help of Random Forests' features: variable importance, outlier identification. The variable importance feature is used to analyze and select optimal subsets of time-series MODIS imagery for efficient land cover mapping, and the outlier identification feature is utilized for transferring sample data available from one year to an adjacent year for supervised classification modelling. The results of the case study of agricultural land cover classification at a regional scale show that using only about a half of the variables we can achieve land cover classification accuracy close to that generated using the full dataset. The proposed simple but effective solution of sample transferring could make supervised modelling possible for applications lacking sample data.

  10. Mapping Protein Surface Accessibility via an Electron Transfer Dissociation Selectively Cleavable Hydrazone Probe*

    Science.gov (United States)

    Vasicek, Lisa; O'Brien, John P.; Browning, Karen S.; Tao, Zhihua; Liu, Hung-Wen; Brodbelt, Jennifer S.

    2012-01-01

    A protein's surface influences its role in protein-protein interactions and protein-ligand binding. Mass spectrometry can be used to give low resolution structural information about protein surfaces and conformations when used in combination with derivatization methods that target surface accessible amino acid residues. However, pinpointing the resulting modified peptides upon enzymatic digestion of the surface-modified protein is challenging because of the complexity of the peptide mixture and low abundance of modified peptides. Here a novel hydrazone reagent (NN) is presented that allows facile identification of all modified surface residues through a preferential cleavage upon activation by electron transfer dissociation coupled with a collision activation scan to pinpoint the modified residue in the peptide sequence. Using this approach, the correlation between percent reactivity and surface accessibility is demonstrated for two biologically active proteins, wheat eIF4E and PARP-1 Domain C. PMID:22393264

  11. Selection on Network Dynamics Drives Differential Rates of Protein Domain Evolution.

    Directory of Open Access Journals (Sweden)

    Brian K Mannakee

    2016-07-01

    Full Text Available The long-held principle that functionally important proteins evolve slowly has recently been challenged by studies in mice and yeast showing that the severity of a protein knockout only weakly predicts that protein's rate of evolution. However, the relevance of these studies to evolutionary changes within proteins is unknown, because amino acid substitutions, unlike knockouts, often only slightly perturb protein activity. To quantify the phenotypic effect of small biochemical perturbations, we developed an approach to use computational systems biology models to measure the influence of individual reaction rate constants on network dynamics. We show that this dynamical influence is predictive of protein domain evolutionary rate within networks in vertebrates and yeast, even after controlling for expression level and breadth, network topology, and knockout effect. Thus, our results not only demonstrate the importance of protein domain function in determining evolutionary rate, but also the power of systems biology modeling to uncover unanticipated evolutionary forces.

  12. C-reactive protein and the risk of cancer: a mendelian randomization study

    DEFF Research Database (Denmark)

    Allin, Kristine H; Nordestgaard, Børge G; Zacho, Jeppe

    2010-01-01

    Elevated plasma levels of C-reactive protein (CRP), a marker of inflammation, are associated with an increased risk of cancer, but it is unclear whether this association is causal. We examined whether four common single-nucleotide polymorphisms (SNPs) in the CRP gene that are associated with alte......Elevated plasma levels of C-reactive protein (CRP), a marker of inflammation, are associated with an increased risk of cancer, but it is unclear whether this association is causal. We examined whether four common single-nucleotide polymorphisms (SNPs) in the CRP gene that are associated...... with altered plasma CRP levels are causally associated with an increased risk of cancer. The study population included participants in a prospective study (n = 10 215) and a cross-sectional study (n = 36 403) of the adult general population in Denmark, all of whom were genotyped for the CRP SNPs....... The association between plasma CRP levels measured by a high-sensitivity turbidimetry assay and the risk of cancer was examined for 8224 participants in the prospective study. The hazard ratio of cancer for a doubling of the plasma CRP level was 1.09 (95% confidence interval [CI] = 1.03 to 1.14). The nine most...

  13. The prediction of organelle-targeting peptides in eukaryotic proteins with Grammatical-Restrained Hidden Conditional Random Fields.

    Science.gov (United States)

    Indio, Valentina; Martelli, Pier Luigi; Savojardo, Castrense; Fariselli, Piero; Casadio, Rita

    2013-04-15

    Targeting peptides are the most important signal controlling the import of nuclear encoded proteins into mitochondria and plastids. In the lack of experimental information, their prediction is an essential step when proteomes are annotated for inferring both the localization and the sequence of mature proteins. We developed TPpred a new predictor of organelle-targeting peptides based on Grammatical-Restrained Hidden Conditional Random Fields. TPpred is trained on a non-redundant dataset of proteins where the presence of a target peptide was experimentally validated, comprising 297 sequences. When tested on the 297 positive and some other 8010 negative examples, TPpred outperformed available methods in both accuracy and Matthews correlation index (96% and 0.58, respectively). Given its very low-false-positive rate (3.0%), TPpred is, therefore, well suited for large-scale analyses at the proteome level. We predicted that from ∼4 to 9% of the sequences of human, Arabidopsis thaliana and yeast proteomes contain targeting peptides and are, therefore, likely to be localized in mitochondria and plastids. TPpred predictions correlate to a good extent with the experimental annotation of the subcellular localization, when available. TPpred was also trained and tested to predict the cleavage site of the organelle-targeting peptide: on this task, the average error of TPpred on mitochondrial and plastidic proteins is 7 and 15 residues, respectively. This value is lower than the error reported by other methods currently available. The TPpred datasets are available at http://biocomp.unibo.it/valentina/TPpred/. TPpred is available on request from the authors. Supplementary data are available at Bioinformatics online.

  14. Chapter 1. Target selection in structural genomics projects to increase knowledge of protein structure and function space.

    Science.gov (United States)

    Carter, Phil; Lee, David; Orengo, Christine

    2008-01-01

    Structural genomics aims to solve the three-dimensional structures of proteins at a rapid rate and in a cost-effective manner, with the hope of significantly impacting on the life sciences, biotechnology, and drug discovery in the long-term. Structural genomics initiatives started in Japan in 1997 with the advent of the Protein Folds Project. Since then many new initiatives have begun worldwide, with diverse aims motivating the selection of proteins for structure determination. In this chapter, we consider the biological goals of high-throughput structural biology, while focusing on the Protein Structure Initiative in the United States. This is the most productive of the structural genomics initiatives, having solved 3,363 new structures between September 2000 and October 2008.

  15. KinMutRF: a random forest classifier of sequence variants in the human protein kinase superfamily.

    Science.gov (United States)

    Pons, Tirso; Vazquez, Miguel; Matey-Hernandez, María Luisa; Brunak, Søren; Valencia, Alfonso; Izarzugaza, Jose Mg

    2016-06-23

    The association between aberrant signal processing by protein kinases and human diseases such as cancer was established long time ago. However, understanding the link between sequence variants in the protein kinase superfamily and the mechanistic complex traits at the molecular level remains challenging: cells tolerate most genomic alterations and only a minor fraction disrupt molecular function sufficiently and drive disease. KinMutRF is a novel random-forest method to automatically identify pathogenic variants in human kinases. Twenty six decision trees implemented as a random forest ponder a battery of features that characterize the variants: a) at the gene level, including membership to a Kinbase group and Gene Ontology terms; b) at the PFAM domain level; and c) at the residue level, the types of amino acids involved, changes in biochemical properties, functional annotations from UniProt, Phospho.ELM and FireDB. KinMutRF identifies disease-associated variants satisfactorily (Acc: 0.88, Prec:0.82, Rec:0.75, F-score:0.78, MCC:0.68) when trained and cross-validated with the 3689 human kinase variants from UniProt that have been annotated as neutral or pathogenic. All unclassified variants were excluded from the training set. Furthermore, KinMutRF is discussed with respect to two independent kinase-specific sets of mutations no included in the training and testing, Kin-Driver (643 variants) and Pon-BTK (1495 variants). Moreover, we provide predictions for the 848 protein kinase variants in UniProt that remained unclassified. A public implementation of KinMutRF, including documentation and examples, is available online ( http://kinmut2.bioinfo.cnio.es ). The source code for local installation is released under a GPL version 3 license, and can be downloaded from https://github.com/Rbbt-Workflows/KinMut2 . KinMutRF is capable of classifying kinase variation with good performance. Predictions by KinMutRF compare favorably in a benchmark with other state

  16. Effect of antifreeze protein on heterogeneous ice nucleation based on a two-dimensional random-field Ising model.

    Science.gov (United States)

    Dong, Zhen; Wang, Jianjun; Zhou, Xin

    2017-05-01

    Antifreeze proteins (AFPs) are the key biomolecules that protect many species from suffering the extreme conditions. Their unique properties of antifreezing provide the potential of a wide range of applications. Inspired by the present experimental approaches of creating an antifreeze surface by coating AFPs, here we present a two-dimensional random-field lattice Ising model to study the effect of AFPs on heterogeneous ice nucleation. The model shows that both the size and the free-energy effect of individual AFPs and their surface coverage dominate the antifreeze capacity of an AFP-coated surface. The simulation results are consistent with the recent experiments qualitatively, revealing the origin of the surprisingly low antifreeze capacity of an AFP-coated surface when the coverage is not particularly high as shown in experiment. These results will hopefully deepen our understanding of the antifreeze effects and thus be potentially useful for designing novel antifreeze coating materials based on biomolecules.

  17. Effect of antifreeze protein on heterogeneous ice nucleation based on a two-dimensional random-field Ising model

    Science.gov (United States)

    Dong, Zhen; Wang, Jianjun; Zhou, Xin

    2017-05-01

    Antifreeze proteins (AFPs) are the key biomolecules that protect many species from suffering the extreme conditions. Their unique properties of antifreezing provide the potential of a wide range of applications. Inspired by the present experimental approaches of creating an antifreeze surface by coating AFPs, here we present a two-dimensional random-field lattice Ising model to study the effect of AFPs on heterogeneous ice nucleation. The model shows that both the size and the free-energy effect of individual AFPs and their surface coverage dominate the antifreeze capacity of an AFP-coated surface. The simulation results are consistent with the recent experiments qualitatively, revealing the origin of the surprisingly low antifreeze capacity of an AFP-coated surface when the coverage is not particularly high as shown in experiment. These results will hopefully deepen our understanding of the antifreeze effects and thus be potentially useful for designing novel antifreeze coating materials based on biomolecules.

  18. The SARS coronavirus spike glycoprotein is selectively recognized by lung surfactant protein D and activates macrophages

    DEFF Research Database (Denmark)

    Leth-Larsen, Rikke; Zhong, Fei; Chow, Vincent T K

    2007-01-01

    Da glycosylated protein. It was not secreted in the presence of tunicamycin and was detected as a 130 kDa protein in the cell lysate. The purified S-protein bound to Vero but not 293T cells and was itself recognized by lung surfactant protein D (SP-D), a collectin found in the lung alveoli. The binding required......The severe acute respiratory syndrome coronavirus (SARS-CoV) infects host cells with its surface glycosylated spike-protein (S-protein). Here we expressed the SARS-CoV S-protein to investigate its interactions with innate immune mechanisms in the lung. The purified S-protein was detected as a 210 k...... Ca(2+) and was inhibited by maltose. The serum collectin, mannan-binding lectin (MBL), exhibited no detectable binding to the purified S-protein. S-protein binds and activates macrophages but not dendritic cells (DCs). It suggests that SARS-CoV interacts with innate immune mechanisms in the lung...

  19. Selective labelling of cell-surface proteins using CyDye DIGE Fluor minimal dyes.

    Science.gov (United States)

    Hagner-McWhirter, Asa; Winkvist, Maria; Bourin, Stephanie; Marouga, Rita

    2008-11-26

    Surface proteins are central to the cell's ability to react to its environment and to interact with neighboring cells. They are known to be inducers of almost all intracellular signaling. Moreover, they play an important role in environmental adaptation and drug treatment, and are often involved in disease pathogenesis and pathology (1). Protein-protein interactions are intrinsic to signaling pathways, and to gain more insight in these complex biological processes, sensitive and reliable methods are needed for studying cell surface proteins. Two-dimensional (2-D) electrophoresis is used extensively for detection of biomarkers and other targets in complex protein samples to study differential changes. Cell surface proteins, partly due to their low abundance (1 2% of cellular proteins), are difficult to detect in a 2-D gel without fractionation or some other type of enrichment. They are also often poorly represented in 2-D gels due to their hydrophobic nature and high molecular weight (2). In this study, we present a new protocol for intact cells using CyDye DIGE Fluor minimal dyes for specific labeling and detection of this important group of proteins. The results showed specific labeling of a large number of cell surface proteins with minimal labeling of intracellular proteins. This protocol is rapid, simple to use, and all three CyDye DIGE Fluor minimal dyes (Cy 2, Cy 3 and Cy 5) can be used to label cell-surface proteins. These features allow for multiplexing using the 2-D Fluorescence Difference Gel Electrophoresis (2-D DIGE) with Ettan DIGE technology and analysis of protein expression changes using DeCyder 2-D Differential Analysis Software. The level of cell-surface proteins was followed during serum starvation of CHO cells for various lengths of time (see Table 1). Small changes in abundance were detected with high accuracy, and results are supported by defined statistical methods.

  20. A randomized trial of protein supplementation compared with extra fast food on the effects of resistance training to increase metabolism.

    Science.gov (United States)

    Hambre, David; Vergara, Marta; Lood, Yvonne; Bachrach-Lindström, Margareta; Lindström, Torbjörn; Nystrom, Fredrik H

    2012-10-01

    To prospectively evaluate the effects of resistance training combined with increased energy intake or protein-supplementation on lean body-mass, resting metabolic-rate (RMR) and cardiovascular risk factors. Twenty-four healthy males (aged 19-32 years) performed resistance exercise for 12 weeks aiming for at least 1 hour training-sessions 3 times a week. The participants were randomized to consume extra protein (33 g whey protein/day) or a meal of fast-food/day (1350 kcal, 41 g protein). Body-composition was measured with Dual-Energy X-ray Absorptiometry (DEXA) and RMR by indirect calorimetry. Fasting blood samples were drawn before and after the 3-month training period and after 12 months. The body weight increased from 75.1 ± 6.9 kg to 78.7 ± 7.2 kg (p < 0.0001), without differences between the groups. RMR increased from 1787 ± 143 kcal/24 h to 1954 ± 187 kcal/24 h (p < 0.0001, N = 24), which was more than expected from the increase in lean body-mass (increase from 59.7 ± 4.3 kg to 61.8 ± 4.1 kg p = 0.004). Fasting serum-insulin levels increased in the fast-food group compared with the extra-protein group (p = 0.03). ApoB increased from 0.691 ± 0.14 g/L to 0.768 ± 0.17 g/L, p = 0.004, in the fast-food group only. Long-term follow up after 12 months showed that RMR, body weight, total fat and lean body-masses did not differ from baseline (n = 19). Resistance training for 12 weeks increased RMR and lean body-mass similarly when based on either an increased energy-intake or protein supplement. However, the increase in RMR was higher than expected from the increase in lean body-mass. Thus resistance training could potentially decrease the risk of obesity by induction of increased RMR.

  1. Enumeration of Escherichia coli cells on chicken carcasses as a potential measure of microbial process control in a random selection of slaughter establishments in the United States

    Science.gov (United States)

    The purpose of this study was to evaluate whether the measurement of Escherichia coli levels at two points during the chicken slaughter process has utility as a measure of quality control. A one year long survey was conducted during 2004 and 2005 in 20 randomly selected United States chicken slaught...

  2. Impact of amoxicillin therapy on resistance selection in patients with community-acquired lower respiratory tract infections : A randomized, placebo-controlled study

    NARCIS (Netherlands)

    Malhotra-Kumar, Surbhi; Van Heirstraeten, Liesbet; Coenen, Samuel; Lammens, Christine; Adriaenssens, Niels; Kowalczyk, Anna; Godycki-Cwirko, Maciek; Bielicka, Zuzana; Hupkova, Helena; Lannering, Christina; Mölstad, Sigvard; Fernandez-Vandellos, Patricia; Torres, Antoni; Parizel, Maxim; Ieven, Margareta; Butler, Chris C.; Verheij, Theo; Little, Paul; Goossens, Hermanon; Frimodt-Møller, Niels; Bruno, Pascale; Hering, Iris; Lemiengre, Marieke; Loens, Katherine; Malmvall, Bo Eric; Muras, Magdalena; Romano, Nuria Sanchez; Prat, Matteu Serra; Svab, Igor; Swain, Jackie; Tarsia, Paolo; Leus, Frank; Veen, Robert; Worby, Tricia

    2016-01-01

    Objectives: To determine the effect of amoxicillin treatment on resistance selection in patients with community-acquired lower respiratory tract infections in a randomized, placebo-controlled trial. Methods: Patients were prescribed amoxicillin 1 g, three times daily (n = 52) or placebo (n = 50) for

  3. The Long-Term Effectiveness of a Selective, Personality-Targeted Prevention Program in Reducing Alcohol Use and Related Harms: A Cluster Randomized Controlled Trial

    Science.gov (United States)

    Newton, Nicola C.; Conrod, Patricia J.; Slade, Tim; Carragher, Natacha; Champion, Katrina E.; Barrett, Emma L.; Kelly, Erin V.; Nair, Natasha K.; Stapinski, Lexine; Teesson, Maree

    2016-01-01

    Background: This study investigated the long-term effectiveness of Preventure, a selective personality-targeted prevention program, in reducing the uptake of alcohol, harmful use of alcohol, and alcohol-related harms over a 3-year period. Methods: A cluster randomized controlled trial was conducted to assess the effectiveness of Preventure.…

  4. Selection of dietary protein and carbohydrate by rats: Changes with maturation

    Science.gov (United States)

    Yokogoshi, Hidehiko; Theall, Cynthia L.; Wurtman, Richard J.

    1985-01-01

    Weaning (21-day-old; 40-50 g) male rats given simultaneous access to foods, containing 18 percent casein and 15 or 70 percent carbohydrate (dextrin), tended to consume only 29-35 percent as much protein as carbohydrate (i.e., protein/carbohydrate ratios were 0.29-0.35). With maturation, when animals weighed 100 g or more, about half continued this pattern of nutrient choice, but the others abruptly began to consume considerably larger proportions of protein, exhibiting protein/carbohydrate ratios as high as 0.80-1.00. Each adult animal's protein/carbohydrate ratio tended to vary only slightly (s.e. = 3 percent of means). Adult protein/carbohydrate ratios were not correlated with fasting brain 5-HT or 5-HIAA levels. These marked differences among rats in eating behavior would not be observed when--as is usually the case--animals are given access to only one diet.

  5. The Role of Negative Selection in Protein Evolution Revealed through the Energetics of the Native State Ensemble

    Science.gov (United States)

    Hoffmann, Jordan; Wrabl, James O.; Hilser, Vincent J.

    2016-01-01

    Knowing the determinants of conformational specificity is essential for understanding protein structure, stability, and fold evolution. To address this issue, a novel statistical measure of energetic compatibility between sequence and structure was developed, using an experimentally validated model of the energetics of the native state ensemble. This approach successfully matched sequences from a diverse subset of the human proteome to their respective folds. Unexpectedly, significant energetic compatibility between ostensibly unrelated sequences and structures was also observed. Interrogation of these matches revealed a general framework for understanding the origins of conformational specificity within a proteome: specificity is a complex function of both the ability of a sequence to adopt folds other than the native, and ability of a fold to accommodate sequences other than the native. The regional variation in energetic compatibility indicates that the compatibility is dominated by incompatibility of sequence for alternative fold segments, suggesting that evolution of protein sequences has involved substantial negative selection, with certain segments serving as “gatekeepers” that presumably prevent alternative structures. Beyond these global trends, a size dependence exists in the degree to which the energetic compatibility is determined from negative selection, with smaller proteins displaying more negative selection. This partially explains how short sequences can adopt unique folds, despite the higher probability in shorter proteins for small numbers of mutations to increase compatibility with other folds. In providing evolutionary ground rules for the thermodynamic relationship between sequence and fold, this framework imparts valuable insight for rational design of unique folds or fold switches. PMID:26800099

  6. Selection for Protein Kinetic Stability Connects Denaturation Temperatures to Organismal Temperatures and Provides Clues to Archaean Life.

    Science.gov (United States)

    Romero-Romero, M Luisa; Risso, Valeria A; Martinez-Rodriguez, Sergio; Gaucher, Eric A; Ibarra-Molero, Beatriz; Sanchez-Ruiz, Jose M

    2016-01-01

    The relationship between the denaturation temperatures of proteins (Tm values) and the living temperatures of their host organisms (environmental temperatures: TENV values) is poorly understood. Since different proteins in the same organism may show widely different Tm's, no simple universal relationship between Tm and TENV should hold, other than Tm≥TENV. Yet, when analyzing a set of homologous proteins from different hosts, Tm's are oftentimes found to correlate with TENV's but this correlation is shifted upward on the Tm axis. Supporting this trend, we recently reported Tm's for resurrected Precambrian thioredoxins that mirror a proposed environmental cooling over long geological time, while remaining a shocking ~50°C above the proposed ancestral ocean temperatures. Here, we show that natural selection for protein kinetic stability (denaturation rate) can produce a Tm↔TENV correlation with a large upward shift in Tm. A model for protein stability evolution suggests a link between the Tm shift and the in vivo lifetime of a protein and, more specifically, allows us to estimate ancestral environmental temperatures from experimental denaturation rates for resurrected Precambrian thioredoxins. The TENV values thus obtained match the proposed ancestral ocean cooling, support comparatively high Archaean temperatures, and are consistent with a recent proposal for the environmental temperature (above 75°C) that hosted the last universal common ancestor. More generally, this work provides a framework for understanding how features of protein stability reflect the environmental temperatures of the host organisms.

  7. Seven Transmembrane Receptors as Shapeshifting Proteins: The Impact of Allosteric Modulation and Functional Selectivity on New Drug Discovery

    Science.gov (United States)

    Miller, Laurence J.

    2010-01-01

    It is useful to consider seven transmembrane receptors (7TMRs) as disordered proteins able to allosterically respond to a number of binding partners. Considering 7TMRs as allosteric systems, affinity and efficacy can be thought of in terms of energy flow between a modulator, conduit (the receptor protein), and a number of guests. These guests can be other molecules, receptors, membrane-bound proteins, or signaling proteins in the cytosol. These vectorial flows of energy can yield standard canonical guest allostery (allosteric modification of drug effect), effects along the plane of the cell membrane (receptor oligomerization), or effects directed into the cytosol (differential signaling as functional selectivity). This review discusses these apparently diverse pharmacological effects in terms of molecular dynamics and protein ensemble theory, which tends to unify 7TMR behavior toward cells. Special consideration will be given to functional selectivity (biased agonism and biased antagonism) in terms of mechanism of action and potential therapeutic application. The explosion of technology that has enabled observation of diverse 7TMR behavior has also shown how drugs can have multiple (pluridimensional) efficacies and how this can cause paradoxical drug classification and nomenclatures. PMID:20392808

  8. Single-particle electron microscopy structure of UDP-glucose:glycoprotein glucosyltransferase suggests a selectivity mechanism for misfolded proteins.

    Science.gov (United States)

    Calles-Garcia, Daniel; Yang, Meng; Soya, Naoto; Melero, Roberto; Ménade, Marie; Ito, Yukishige; Vargas, Javier; Lukacs, Gergely L; Kollman, Justin M; Kozlov, Guennadi; Gehring, Kalle

    2017-07-07

    The enzyme UDP-glucose:glycoprotein glucosyltransferase (UGGT) mediates quality control of glycoproteins in the endoplasmic reticulum by attaching glucose to N-linked glycan of misfolded proteins. As a sensor, UGGT ensures that misfolded proteins are recognized by the lectin chaperones and do not leave the secretory pathway. The structure of UGGT and the mechanism of its selectivity for misfolded proteins have been unknown for 25 years. Here, we used negative-stain electron microscopy and small-angle X-ray scattering to determine the structure of UGGT from Drosophila melanogaster at 18-Å resolution. Three-dimensional reconstructions revealed a cage-like structure with a large central cavity. Particle classification revealed flexibility that precluded determination of a high-resolution structure. Introduction of biotinylation sites into a fungal UGGT expressed in Escherichia coli allowed identification of the catalytic and first thioredoxin-like domains. We also used hydrogen-deuterium exchange mass spectrometry to map the binding site of an accessory protein, Sep15, to the first thioredoxin-like domain. The UGGT structural features identified suggest that the central cavity contains the catalytic site and is lined with hydrophobic surfaces. This enhances the binding of misfolded substrates with exposed hydrophobic residues and excludes folded proteins with hydrophilic surfaces. In conclusion, we have determined the UGGT structure, which enabled us to develop a plausible functional model of the mechanism for UGGT's selectivity for misfolded glycoproteins. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  9. Emergence, Retention and Selection: A Trilogy of Origination for Functional De Novo Proteins from Ancestral LncRNAs in Primates.

    Directory of Open Access Journals (Sweden)

    Jia-Yu Chen

    2015-07-01

    Full Text Available While some human-specific protein-coding genes have been proposed to originate from ancestral lncRNAs, the transition process remains poorly understood. Here we identified 64 hominoid-specific de novo genes and report a mechanism for the origination of functional de novo proteins from ancestral lncRNAs with precise splicing structures and specific tissue expression profiles. Whole-genome sequencing of dozens of rhesus macaque animals revealed that these lncRNAs are generally not more selectively constrained than other lncRNA loci. The existence of these newly-originated de novo proteins is also not beyond anticipation under neutral expectation, as they generally have longer theoretical lifespan than their current age, due to their GC-rich sequence property enabling stable ORFs with lower chance of non-sense mutations. Interestingly, although the emergence and retention of these de novo genes are likely driven by neutral forces, population genetics study in 67 human individuals and 82 macaque animals revealed signatures of purifying selection on these genes specifically in human population, indicating a proportion of these newly-originated proteins are already functional in human. We thus propose a mechanism for creation of functional de novo proteins from ancestral lncRNAs during the primate evolution, which may contribute to human-specific genetic novelties by taking advantage of existed genomic contexts.

  10. Prediction of protein modification sites of pyrrolidone carboxylic acid using mRMR feature selection and analysis.

    Directory of Open Access Journals (Sweden)

    Lu-Lu Zheng

    Full Text Available Pyrrolidone carboxylic acid (PCA is formed during a common post-translational modification (PTM of extracellular and multi-pass membrane proteins. In this study, we developed a new predictor to predict the modification sites of PCA based on maximum relevance minimum redundancy (mRMR and incremental feature selection (IFS. We incorporated 727 features that belonged to 7 kinds of protein properties to predict the modification sites, including sequence conservation, residual disorder, amino acid factor, secondary structure and solvent accessibility, gain/loss of amino acid during evolution, propensity of amino acid to be conserved at protein-protein interface and protein surface, and deviation of side chain carbon atom number. Among these 727 features, 244 features were selected by mRMR and IFS as the optimized features for the prediction, with which the prediction model achieved a maximum of MCC of 0.7812. Feature analysis showed that all feature types contributed to the modification process. Further site-specific feature analysis showed that the features derived from PCA's surrounding sites contributed more to the determination of PCA sites than other sites. The detailed feature analysis in this paper might provide important clues for understanding the mechanism of the PCA formation and guide relevant experimental validations.

  11. Genetic algorithm with alternating selection pressure for protein side-chain packing and pK(a) prediction.

    Science.gov (United States)

    Comte, Pascal; Vassiliev, Sergei; Houghten, Sheridan; Bruce, Doug

    2011-09-01

    The prediction of protein side-chain conformation is central for understanding protein functions. Side-chain packing is a sub-problem of protein folding and its computational complexity has been shown to be NP-hard. We investigated the capabilities of a hybrid (genetic algorithm/simulated annealing) technique for side-chain packing and for the generation of an ensemble of low energy side-chain conformations. Our method first relies on obtaining a near-optimal low energy protein conformation by optimizing its amino-acid side-chains. Upon convergence, the genetic algorithm is allowed to undergo forward and "backward" evolution by alternating selection pressures between minimal and higher energy setpoints. We show that this technique is very efficient for obtaining distributions of solutions centered at any desired energy from the minimum. We outline the general concepts of our evolutionary sampling methodology using three different alternating selective pressure schemes. Quality of the method was assessed by using it for protein pK(a) prediction. Crown Copyright © 2011. Published by Elsevier Ireland Ltd. All rights reserved.

  12. Discovery and evaluation of the hybrid of bromophenol and saccharide as potent and selective protein tyrosine phosphatase 1B inhibitors.

    Science.gov (United States)

    Zhang, Renshuai; Yu, Rilei; Xu, Qi; Li, Xiangqian; Luo, Jiao; Jiang, Bo; Wang, Lijun; Guo, Shuju; Wu, Ning; Shi, Dayong

    2017-07-07

    Protein tyrosine phosphatase 1B (PTP1B) is a key negative regulator of insulin signaling pathway. Inhibition of PTP1B is expected to improve insulin action. Appropriate selectivity and permeability are the gold standard for excellent PTP1B inhibitors. In this work, molecular hybridization-based screening identified a selective competitive PTP1B inhibitor. Compound 10a has IC50 values of 199 nM against PTP1B, and shows 32-fold selectivity for PTP1B over the closely related phosphatase TCPTP. Molecule docking and molecular dynamics studies reveal the reason of selectivity for PTP1B over TCPTP. Moreover, the cell permeability and cellular activity of compound 10a are demonstrated respectively. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  13. Anticariogenic and Hemolytic Activity of Selected Seed Protein Extracts In vitro conditions.

    Directory of Open Access Journals (Sweden)

    Kalpesh B Ishnava

    2014-10-01

    Full Text Available This study aimed to assess the anticariogenic and hemolytic activity of crude plant seed protein extracts against tooth decaying bacteria.The proteins from seeds of 12 different plants were extracted and used for antimicrobial assay against six different organisms. The extraction was carried out in 10mM of sodium phosphate buffer (pH 7.0. Protein concentrations were determined as described by Bradford method. Anticariogenic activity was studied by agar well diffusion method and Minimum Inhibitory Concentration (MIC was evaluated by the two-fold serial broth dilution method. Hemolytic activity, treatment of proteinase K and Kinetic study in Mimusops elengi crude seed protein extract.The anticariogenic assay demonstrated the activity of Mimusops elengi against Staphylococcus aureus and Streptococcus pyogenes. A minor activity of Glycine wightii against Streptococcus mutans was also found. The protein content of Mimusops elengi seed protein extract was 5.84mg/ml. The MIC values for Staphylococcus aureus and Streptococcus pyogenes against Mimusops elengi seed protein extract were 364.36μg/ml and 182.19μg/ml, respectively. Kinetic study further elucidated the mode of inhibition in the presence of the Mimusops elengi plant seed protein with respect to time. The concentration of crude extract which gave 50% hemolysis compared to Triton X-100 treatment (HC50 value was 1.58 mg/ml; which is more than five times larger than that of the MIC. Treatment with proteinase K of the Mimusops elengi seed protein resulted in absence of the inhibition zone; which clearly indicates that the activity was only due to protein.Our results showed the prominence of Mimusops elengi plant seed protein extract as an effective herbal medication against tooth decaying bacteria.

  14. Characterization and reactivity of broiler chicken sera to selected recombinant Campylobacter jejuni chemotactic proteins.

    Science.gov (United States)

    Yeh, Hung-Yueh; Hiett, Kelli L; Line, John E; Seal, Bruce S

    2014-05-01

    Campylobacter jejuni, a Gram-negative rod bacterium, is the leading causative agent of human acute bacterial gastroenteritis worldwide. Consumption and handling of raw or undercooked poultry are regarded as a major source for human infection. Because bacterial chemotaxis guides microorganisms to colonization and invasion in the host cells, proteins involved in chemotactic processes can be novel targets for vaccine development. In this communication, we report amplification, cloning and expression of the C. jejuni chemotactic proteins in an Escherichia coli expression system. A total of 15 chemotactic protein genes were successfully expressed. These recombinant proteins were confirmed by nucleotide sequencing, SDS-PAGE analysis and immunoblot analysis of six-His and hemagglutinin tags. Twelve recombinant chemotactic proteins were further tested whether they were antigenic using sera from broiler chickens older than 4 weeks. The immunoblot results show that each chicken serum reacted to a variety of the recombinant proteins, but all sera reacted to the Cjj0473 gene product (annotated as a methyl-accepting chemotaxis protein), suggesting that anti-Campylobacter antibodies may be prevalent in the poultry population. These antibody screening results provide a rationale for further evaluation of the Cjj0473 protein as a potential vaccine for broilers to improve human food safety.

  15. Selective contribution of the twin-arginine translocation pathway to protein secretion in Bacillus subtilis

    NARCIS (Netherlands)

    Jongbloed, JDH; Antelmann, H; Hecker, M; Bron, S; Airaksinen, U; Pries, F; Quax, WJ; van Dijl, JM; Braun, PG

    2002-01-01

    The availability of the complete genome sequence of Bacillus subtilis has allowed the prediction of all exported proteins of this Gram-positive eubacterium. Recently, similar to180 secretory and 114 lipoprotein signal peptides were predicted to direct protein export from the cytoplasm. Whereas most

  16. Feature Selection and the Class Imbalance Problem in Predicting Protein Function from Sequence

    NARCIS (Netherlands)

    Al-Shahib, A.; Breitling, R.; Gilbert, D.

    2005-01-01

    Abstract: When the standard approach to predict protein function by sequence homology fails, other alternative methods can be used that require only the amino acid sequence for predicting function. One such approach uses machine learning to predict protein function directly from amino acid sequence

  17. Selective labeling of pulmonary surfactant protein SP-C in organic solution

    DEFF Research Database (Denmark)

    Plasencia, I; Cruz, A; López-Lacomba, J L

    2001-01-01

    Pulmonary surfactant protein SP-C has been isolated from porcine lungs and treated with dansyl isothiocyanate in chloroform:methanol 2:1 (v/v) solutions,under conditions optimized to introduce a single dansyl group covalently attached to the N-terminalamine group of the protein without loss of its...

  18. Exploring variation in pea protein composition by natural selection and genetic transformation

    NARCIS (Netherlands)

    Tzitzikas, E.

    2005-01-01

    Pea (Pisumsativum L.) seeds are a rich and valuable source of proteins, which can have potential for food industrial applications. Pea storage proteins are classified into two major classes: the salt-soluble globulins, and the water-soluble

  19. The expanded octarepeat domain selectively binds prions and disrupts homomeric prion protein interactions

    NARCIS (Netherlands)

    Leliveld, S. R.; Dame, R.T.; Wuite, G.J.L.; Stitz, L.; Korth, C.

    2006-01-01

    Insertion of additional octarepeats into the prion protein gene has been genetically linked to familial Creutzfeldt Jakob disease and hence to de novo generation of infectious prions. The pivotal event during prion formation is the conversion of the normal prion protein (PrP

  20. Impact of amoxicillin therapy on resistance selection in patients with community-acquired lower respiratory tract infections: a randomized, placebo-controlled study.

    Science.gov (United States)

    Malhotra-Kumar, Surbhi; Van Heirstraeten, Liesbet; Coenen, Samuel; Lammens, Christine; Adriaenssens, Niels; Kowalczyk, Anna; Godycki-Cwirko, Maciek; Bielicka, Zuzana; Hupkova, Helena; Lannering, Christina; Mölstad, Sigvard; Fernandez-Vandellos, Patricia; Torres, Antoni; Parizel, Maxim; Ieven, Margareta; Butler, Chris C; Verheij, Theo; Little, Paul; Goossens, Herman

    2016-11-01

    To determine the effect of amoxicillin treatment on resistance selection in patients with community-acquired lower respiratory tract infections in a randomized, placebo-controlled trial. Patients were prescribed amoxicillin 1 g, three times daily (n = 52) or placebo (n = 50) for 7 days. Oropharyngeal swabs obtained before, within 48 h post-treatment and at 28-35 days were assessed for proportions of amoxicillin-resistant (ARS; amoxicillin MIC ≥2 mg/L) and -non-susceptible (ANS; MIC ≥0.5 mg/L) streptococci. Alterations in amoxicillin MICs and in penicillin-binding-proteins were also investigated. ITT and PP analyses were conducted. ARS and ANS proportions increased 11- and 2.5-fold, respectively, within 48 h post-amoxicillin treatment compared with placebo [ARS mean increase (MI) 9.46, 95% CI 5.57-13.35; ANS MI 39.87, 95% CI 30.96-48.78; P  0.1588). ARS/ANS were grouped by pbp mutations. Group 1 strains exhibited significantly lower amoxicillin resistance (mean MIC 2.8 mg/L, 95% CI 2.6-3.1) than group 2 (mean MIC 9.3 mg/L, 95% CI 8.1-10.5; P amoxicillin is modest and short-lived, probably due to 'fitness costs' engendered by high-level resistance-conferring mutations. This evidence further supports European guidelines that recommend amoxicillin when an antibiotic is indicated for community-acquired lower respiratory tract infections. © The Author 2016. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy.

  1. Palatability of water-soluble extracts of protein sources and replacement of fishmeal by a selected mixture of protein sources for juvenile turbot ( Scophthalmus maximus)

    Science.gov (United States)

    Dong, Chun; He, Gen; Mai, Kangsen; Zhou, Huihui; Xu, Wei

    2016-06-01

    Poor palatability is a limiting factor for replacing fishmeal with other protein sources in aquaculture. The water-soluble molecules with low molecular weights are the major determinants of the palatability of diets. The present study was conducted to investigate the palatability of water-soluble extracts from single protein source (single extract pellets) and the mixture of these extracts with different proportions (blended extract pellets) in juvenile turbot ( Scophthalmus maximus). Then according to the palatability of blended extract pellets, an optimal mixture proportion was selected, and a new protein source made from raw protein materials with the selected proportion was formulated to replace fishmeal. Summarily, the palatability of single extract pellets for turbot was descendent from fishmeal to pet-food grade poultry by-product meal, wheat gluten meal, soybean meal, peanut meal, meat and bone meal, and corn gluten meal. Subsequently, according to the palatability of single extract pellets, 52 kinds of blended extract pellets were designed to test their palatability. The results showed that the pellets presented remarkably different palatability, and the optimal one was diet 52 (wheat gluten meal: pet-food grade poultry by-product meal: meat and bone meal: corn gluten meal = 1:6:1:2). The highest ingestion ratio (the number of pellets ingested/the number of pellets fed) was 0.73 ± 0.03, which was observed in Diet 52. Then five isonitrogenous (52% crude protein) and isocaloric (20 kJ g-1 gross energy) diets were formulated by replacing 0 (control), 35%, 50%, 65% and 80% of fishmeal with No.52 blending proportion. After a 10-weeks feeding trial, a consistent feed intake was found among all replacement treatments. Replacement level of fishmeal up to 35% did not significantly influence final body weight, specific growth rate, feed efficiency ratio, and protein efficiency ratio of turbot. Therefore, the water-soluble extracts of protein sources play an

  2. Surveillance for cancer recurrence in long-term young breast cancer survivors randomly selected from a statewide cancer registry.

    Science.gov (United States)

    Jones, Tarsha; Duquette, Debra; Underhill, Meghan; Ming, Chang; Mendelsohn-Victor, Kari E; Anderson, Beth; Milliron, Kara J; Copeland, Glenn; Janz, Nancy K; Northouse, Laurel L; Duffy, Sonia M; Merajver, Sofia D; Katapodi, Maria C

    2018-01-20

    This study examined clinical breast exam (CBE) and mammography surveillance in long-term young breast cancer survivors (YBCS) and identified barriers and facilitators to cancer surveillance practices. Data collected with a self-administered survey from a statewide, randomly selected sample of YBCS diagnosed with invasive breast cancer or ductal carcinoma in situ younger than 45 years old, stratified by race (Black vs. White/Other). Multivariate logistic regression models identified predictors of annual CBEs and mammograms. Among 859 YBCS (n = 340 Black; n = 519 White/Other; mean age = 51.0 ± 5.9; diagnosed 11.0 ± 4.0 years ago), the majority (> 85%) reported an annual CBE and a mammogram. Black YBCS in the study were more likely to report lower rates of annual mammography and more barriers accessing care compared to White/Other YBCS. Having a routine source of care, confidence to use healthcare services, perceived expectations from family members and healthcare providers to engage in cancer surveillance, and motivation to comply with these expectations were significant predictors of having annual CBEs and annual mammograms. Cost-related lack of access to care was a significant barrier to annual mammograms. Routine source of post-treatment care facilitated breast cancer surveillance above national average rates. Persistent disparities regarding access to mammography surveillance were identified for Black YBCS, primarily due to lack of access to routine source of care and high out-of-pocket costs. Public health action targeting cancer surveillance in YBCS should ensure routine source of post-treatment care and address cost-related barriers. Clinical Trials Registration Number: NCT01612338.

  3. Evaluation of Randomly Selected Completed Medical Records Sheets in Teaching Hospitals of Jahrom University of Medical Sciences, 2009

    Directory of Open Access Journals (Sweden)

    Mohammad Parsa Mahjob

    2011-06-01

    Full Text Available Background and objective: Medical record documentation, often use to protect the patients legal rights, also providing information for medical researchers, general studies, education of health care staff and qualitative surveys is used. There is a need to control the amount of data entered in the medical record sheets of patients, considering the completion of these sheets is often carried out after completion of service delivery to the patients. Therefore, in this study the prevalence of completeness of medical history, operation reports, and physician order sheets by different documentaries in Jahrom teaching hospitals during year 2009 was analyzed. Methods and Materials: In this descriptive / retrospective study, the 400 medical record sheets of the patients from two teaching hospitals affiliated to Jahrom medical university was randomly selected. The tool of data collection was a checklist based on the content of medical history sheet, operation report and physician order sheets. The data were analyzed by SPSS (Version10 software and Microsoft Office Excel 2003. Results: Average of personal (Demography data entered in medical history, physician order and operation report sheets which is done by department's secretaries were 32.9, 35.8 and 40.18 percent. Average of clinical data entered by physician in medical history sheet is 38 percent. Surgical data entered by the surgeon in operation report sheet was 94.77 percent. Average of data entered by operation room's nurse in operation report sheet was 36.78 percent; Average of physician order data in physician order sheet entered by physician was 99.3 percent. Conclusion: According to this study, the rate of completed record papers reviewed by documentary in Jahrom teaching hospitals were not desirable and in some cases were very weak and incomplete. This deficiency was due to different reason such as medical record documentaries negligence, lack of adequate education for documentaries, High work

  4. Sexual selection has minimal impact on effective population sizes in species with high rates of random offspring mortality: An empirical demonstration using fitness distributions.

    Science.gov (United States)

    Pischedda, Alison; Friberg, Urban; Stewart, Andrew D; Miller, Paige M; Rice, William R

    2015-10-01

    The effective population size (N(e)) is a fundamental parameter in population genetics that influences the rate of loss of genetic diversity. Sexual selection has the potential to reduce N(e) by causing the sex-specific distributions of individuals that successfully reproduce to diverge. To empirically estimate the effect of sexual selection on N(e), we obtained fitness distributions for males and females from an outbred, laboratory-adapted population of Drosophila melanogaster. We observed strong sexual selection in this population (the variance in male reproductive success was ∼14 times higher than that for females), but found that sexual selection had only a modest effect on N(e), which was 75% of the census size. This occurs because the substantial random offspring mortality in this population diminishes the effects of sexual selection on N(e), a result that necessarily applies to other high fecundity species. The inclusion of this random offspring mortality creates a scaling effect that reduces the variance/mean ratios for male and female reproductive success and causes them to converge. Our results demonstrate that measuring reproductive success without considering offspring mortality can underestimate Ne and overestimate the genetic consequences of sexual selection. Similarly, comparing genetic diversity among different genomic components may fail to detect strong sexual selection. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

  5. Proteus: a random forest classifier to predict disorder-to-order transitioning binding regions in intrinsically disordered proteins

    Science.gov (United States)

    Basu, Sankar; Söderquist, Fredrik; Wallner, Björn

    2017-05-01

    The focus of the computational structural biology community has taken a dramatic shift over the past one-and-a-half decades from the classical protein structure prediction problem to the possible understanding of intrinsically disordered proteins (IDP) or proteins containing regions of disorder (IDPR). The current interest lies in the unraveling of a disorder-to-order transitioning code embedded in the amino acid sequences of IDPs/IDPRs. Disordered proteins are characterized by an enormous amount of structural plasticity which makes them promiscuous in binding to different partners, multi-functional in cellular activity and atypical in folding energy landscapes resembling partially folded molten globules. Also, their involvement in several deadly human diseases (e.g. cancer, cardiovascular and neurodegenerative diseases) makes them attractive drug targets, and important for a biochemical understanding of the disease(s). The study of the structural ensemble of IDPs is rather difficult, in particular for transient interactions. When bound to a structured partner, an IDPR adapts an ordered conformation in the complex. The residues that undergo this disorder-to-order transition are called protean residues, generally found in short contiguous stretches and the first step in understanding the modus operandi of an IDP/IDPR would be to predict these residues. There are a few available methods which predict these protean segments from their amino acid sequences; however, their performance reported in the literature leaves clear room for improvement. With this background, the current study presents `Proteus', a random forest classifier that predicts the likelihood of a residue undergoing a disorder-to-order transition upon binding to a potential partner protein. The prediction is based on features that can be calculated using the amino acid sequence alone. Proteus compares favorably with existing methods predicting twice as many true positives as the second best method (55

  6. An efficient method for native protein purification in the selected range from prostate cancer tissue digests

    Energy Technology Data Exchange (ETDEWEB)

    Ahmad, Rumana; Nicora, Carrie D.; Shukla, Anil K.; Smith, Richard D.; Qian, Wei-Jun; Liu, Alvin Y.

    2016-12-01

    Prostate cancer (CP) cells differ from their normal counterpart in gene expression. Genes encoding secreted or extracellular proteins with increased expression in CP may serve as potential biomarkers. For their detection and quantification, assays based on monoclonal antibodies are best suited for development in a clinical setting. One approach to obtain antibodies is to use recombinant proteins as immunogen. However, the synthesis of recombinant protein for each identified candidate is time-consuming and expensive. It is also not practical to generate high quality antibodies to all identified candidates individually. Furthermore, non-native forms (e.g., recombinant) of proteins may not always lead to useful antibodies. Our approach was to purify a subset of proteins from CP tissue specimens for use as immunogen.

  7. Meals based on vegetable protein sources (beans and peas) are more satiating than meals based on animal protein sources (veal and pork) - a randomized cross-over meal test study

    DEFF Research Database (Denmark)

    Kristensen, Marlene Dahlwad; Bendsen, Nathalie Tommerup; Christensen, Sheena M

    2016-01-01

    BACKGROUND: Recent nutrition recommendations advocate a reduction in protein from animal sources (pork, beef) because of environmental concerns. Instead, protein from vegetable sources (beans, peas) should be increased. However, little is known about the effect of these vegetable protein sources...... on appetite regulation. OBJECTIVE: To examine whether meals based on vegetable protein sources (beans/peas) are comparable to meals based on animal protein sources (veal/pork) regarding meal-induced appetite sensations. DESIGN: In total, 43 healthy, normal-weight, young men completed this randomized, double......-Legume compared to HP-Meat or LP-Legume (pVegetable-based meals (beans/peas) influenced appetite sensations favorably compared to animal-based meals (pork/veal) with similar energy and protein content, but lower fiber content. Interestingly, a vegetable-based meal with low protein content...

  8. Effects of supplementation with green tea catechins on plasma C-reactive protein concentrations: A systematic review and meta-analysis of randomized controlled trials.

    Science.gov (United States)

    Serban, Corina; Sahebkar, Amirhossein; Antal, Diana; Ursoniu, Sorin; Banach, Maciej

    2015-09-01

    Promising experimental and clinical trials suggest that green tea decreases the inflammatory process in cardiometabolic diseases, but evidence from epidemiologic studies about the effects on plasma C-reactive protein (CRP) seems inconsistent and ambiguous. Therefore, the aim of this meta-analysis was to evaluate the effects of green tea supplementation on plasma CRP concentrations. We searched selected database up to October 26, 2014 to identify randomized controlled trials (RCTs) investigating the effects of green tea supplementation on plasma CRP concentrations. Two independent reviewers extracted data on study characteristics, methods, and outcomes. Meta-analysis of data from 11 RCTs arms did not indicate a significant effect of supplementation with green tea catechins on plasma CRP concentrations (weighted mean difference [WMD], 0.085 mg/L; 95% confidence interval [CI], -0.225 to 0.395; P = 0.592). This effect size was robust in sensitivity analysis and omission of each individual study did not have a significant effect. The nonsignificant effects of green tea catechins on plasma CRP concentrations were also observed in subgroups of studies with green tea supplementation with a duration of catechins doses catechins on plasma CRP concentrations. Furthermore, well-designed trials are necessary to validate these results. Copyright © 2015 Elsevier Inc. All rights reserved.

  9. Effects of supplementation with pomegranate juice on plasma C-reactive protein concentrations: A systematic review and meta-analysis of randomized controlled trials.

    Science.gov (United States)

    Sahebkar, Amirhossein; Gurban, Camelia; Serban, Alexandru; Andrica, Florina; Serban, Maria-Corina

    2016-10-15

    Pomegranate juice (PJ) has a high content of antioxidants and bioactive polyphenols, being widely used for its antioxidant, anti-inflammatory and chemopreventive effects. The objective of this meta-analysis consisted in investigating the impact of PJ on plasma C-reactive protein (CRP) concentrations. The search included SCOPUS, Medline and two Iranian bibliographic databases namely MagIran and Scientific Information Database (from inception to December 09, 2014) to identify prospective trials for investigating the impact of pomegranate preparations on serum concentrations of CRP. Two independent reviewers extracted data on study characteristics, methods and outcomes. Among 427 participants in the selected studies, 216 were allocated to PJ groups, and 211 to control group. Meta-analysis of data from 5 eligible randomized controlled trials (RCTs) arms did not provide compelling evidence as to a significant CRP-lowering effect of supplementation with pomegranate juice (WMD: -0.22 mg/l, 95% CI: -0.45, 0.01, p = 0.061). The impact of pomegranate juice on plasma CRP levels was found to be independent of duration of supplementation (slope: 0.003; 95% CI: -0.005, 0.011; p = 0.444). In conclusion, this meta-analysis of data from 5 prospective trials did not indicate a significant effect of PJ on plasma CRP levels, and this effect was independent of duration of supplementation. Copyright © 2016. Published by Elsevier GmbH.

  10. Selection shaped the evolution of mouse androgen-binding protein (ABP) function and promoted the duplication of Abp genes.

    Science.gov (United States)

    Karn, Robert C; Laukaitis, Christina M

    2014-08-01

    In the present article, we summarize two aspects of our work on mouse ABP (androgen-binding protein): (i) the sexual selection function producing incipient reinforcement on the European house mouse hybrid zone, and (ii) the mechanism behind the dramatic expansion of the Abp gene region in the mouse genome. Selection unifies these two components, although the ways in which selection has acted differ. At the functional level, strong positive selection has acted on key sites on the surface of one face of the ABP dimer, possibly to influence binding to a receptor. A different kind of selection has apparently driven the recent and rapid expansion of the gene region, probably by increasing the amount of Abp transcript, in one or both of two ways. We have shown previously that groups of Abp genes behave as LCRs (low-copy repeats), duplicating as relatively large blocks of genes by NAHR (non-allelic homologous recombination). The second type of selection involves the close link between the accumulation of L1 elements and the expansion of the Abp gene family by NAHR. It is probably predicated on an initial selection for increased transcription of existing Abp genes and/or an increase in Abp gene number providing more transcriptional sites. Either or both could increase initial transcript production, a quantitative change similar to increasing the volume of a radio transmission. In closing, we also provide a note on Abp gene nomenclature.

  11. Identification and validation of selected universal stress protein domain containing drought-responsive genes in pigeonpea (Cajanus cajan L.

    Directory of Open Access Journals (Sweden)

    Pallavi eSinha

    2016-01-01

    Full Text Available Pigeonpea is a resilient crop, which is relatively more drought tolerant than many other legume crops. To understand the molecular mechanisms of this unique feature of pigeonpea, 51 genes were selected using the Hidden Markov Models those codes for proteins having close similarity to universal stress protein domain. Validation of these genes was conducted on three pigeonpea genotypes (ICPL 151, ICPL 8755 and ICPL 227 having different levels of drought tolerance. Gene expression analysis using qRT-PCR revealed 6, 8 and 18 genes to be ≥2 fold differentially expressed in ICPL 151, ICPL 8755 and ICPL 227, respectively. A total of 10 differentially expressed genes showed ≥2 fold up-regulation in the more drought tolerant genotype. Of these, four genes each encoded proteins for plant U-box and universal stress protein A- (uspA like, while one gene encoded for cation/H(+ antiporter protein and one uncharacterized protein. Genes C.cajan_29830 and C.cajan_33874 belonging to uspA, were found significantly expressed in all the three genotypes with ≥2 fold expression variations. Expression profiling of these two genes on the four other legume crops revealed their specific role in pigeonpea. Therefore, these genes seem to be promising candidates for conferring drought tolerance specifically to pigeonpea.

  12. Molecular Mechanism for Inhibition of G Protein-Coupled Receptor Kinase 2 by a Selective RNA Aptamer

    Energy Technology Data Exchange (ETDEWEB)

    Tesmer, Valerie M.; Lennarz, Sabine; Mayer, Günter; Tesmer, John J.G. (Bonn); (Michigan)

    2012-08-31

    Cardiovascular homeostasis is maintained in part by the rapid desensitization of activated heptahelical receptors that have been phosphorylated by G protein-coupled receptor kinase 2 (GRK2). However, during chronic heart failure GRK2 is upregulated and believed to contribute to disease progression. We have determined crystallographic structures of GRK2 bound to an RNA aptamer that potently and selectively inhibits kinase activity. Key to the mechanism of inhibition is the positioning of an adenine nucleotide into the ATP-binding pocket and interactions with the basic {alpha}F-{alpha}G loop region of the GRK2 kinase domain. Constraints imposed on the RNA by the terminal stem of the aptamer also play a role. These results highlight how a high-affinity aptamer can be used to selectively trap a novel conformational state of a protein kinase.

  13. Quantification of gene effects on single milk proteins in selected groups of dairy cows.

    Science.gov (United States)

    Ehrmann, S; Bartenschlager, H; Geldermann, H

    1997-01-12

    Different alleles and genotypes per polymorphic milk protein were compared, within the concentration and quantity of the protein which is coded from the corresponding locus. Cows were chosen according to their diversity in milk-protein content, as well as in the polymorphic milk proteins. Polymorphic milk proteins were analysed by isoelectric focusing. The contents and quantities of total milk protein and whey protein were measured photometrically. Single milk proteins were quantified after poly-acrylamide gel electrophoresis, using computer-assisted densitometer. The contents of single milk proteins could be measured with repeatabilities between 0.58 (α-lactalbumin) and 0.97 (β-lactoglobulin). Close associations were observed between alleles/genotypes of milk-protein-coding gene loci, and the contents, as well as the yields, of the corresponding milk proteins, Superior alleles concerned with the content yield of corresponding proteins have been β-lactoglobulin A, α(s1) -casein C, and β-casein B. Simultaneous comparison of genotypes of the casein gene cluster with the milk-protein values revealed significant effects through distinct allele combinations. Breed influences on the associations between genes and milk proteins were considerably smaller than the influences from single milk-protein-coding loci. Intragenic haplotypes may explain the associations between variants in coding DNA sequences and gene expression, estimated for single milk proteins. An analysis of balancing forces on allele frequencies and haplotype combinations per population will be necessary, before genotype screening can be applied usefully for breeding. ZUSAMMENFASSUNG: Quantifizierung von Geneffekten auf einzelne Milchproteine in selektierten Milchkuh-Gruppen Verschiedene Allele und Genotypen pro polymorphes Milchprotein wurden mit der Konzentration und Menge des Proteins verglichen, das vom betreffenden Locus kodiert wird. Zu diesem Zweck wurden Kühe aufgrund des Proteingehaltes in der

  14. Mature Epitope Density - A strategy for target selection based on immunoinformatics and exported prokaryotic proteins

    DEFF Research Database (Denmark)

    Santos, Anderson R; Pereira, Vanessa Bastos; Barbosa, Eudes

    2013-01-01

    organisms. We evaluated our computational approach by using the Mycobacterium tuberculosis (Mtb) H37Rv exoproteome as a gold standard model. A literature search was carried out on 60 out of 553 Mtb's predicted exoproteins, looking for previous experimental evidence concerning their possible antigenicity...... proteins were confirmed as related. There was no experimental evidence of antigenic or pathogenic contributions for three of the highest MED-scored Mtb proteins. Hence, these three proteins could represent novel putative vaccine and drug targets for Mtb. A web version of MED is publicly available online...

  15. Selection of symptomatic patients with Crohn's disease for abdominopelvic computed tomography: role of serum C-reactive protein.

    LENUS (Irish Health Repository)

    Desmond, Alan N

    2012-11-01

    Results of previous studies have shown that repeated abdominopelvic computed tomography (CT) examinations can lead to substantial cumulative diagnostic radiation exposure in patients with Crohn\\'s disease (CD). Improved selection of patients referred for CT will reduce unnecessary radiation exposure. This study examines if serum C-reactive protein (CRP) concentration predicts which symptomatic patients with CD are likely to have significant disease activity or disease complications (such as abscess) detected on abdominopelvic CT.

  16. Substituted imidazopyridazines are potent and selective inhibitors of Plasmodium falciparum calcium-dependent protein kinase 1 (PfCDPK1)

    OpenAIRE

    Chapman, Timothy M.; Osborne, Simon A.; Bouloc, Nathalie; Large, Jonathan M.; Wallace, Claire; Birchall, Kristian; Ansell, Keith H.; Jones, Hayley M.; Taylor, Debra; Clough, Barbara; Green, Judith L.; Holder, Anthony A.

    2013-01-01

    A series of imidazopyridazines which are potent inhibitors of Plasmodium falciparum calcium-dependent protein kinase 1 (PfCDPK1) was identified from a high-throughput screen against the isolated enzyme. Subsequent exploration of the SAR and optimisation has yielded leading members which show promising in vitro anti-parasite activity along with good in vitro ADME and selectivity against human kinases. Initial in vivo testing has revealed good oral bioavailability in a mouse PK study and modest...

  17. Chemical treatment of Escherichia coli: 3. Selective extraction of a recombinant protein from cytoplasmic inclusion bodies in intact cells.

    Science.gov (United States)

    Falconer, R J; O'Neill, B K; Middelberg, A P

    1999-02-20

    In previous parts of this study we developed procedures for the high-efficiency chemical extraction of soluble and insoluble protein from intact Escherichia coli cells. Although high yields were obtained, extraction of recombinant protein directly from cytoplasmic inclusion bodies led to low product purity due to coextraction of soluble contaminants. In this work, a two-stage procedure for the selective extraction of recombinant protein at high efficiency and high purity is reported. In the first stage, inclusion-body stability is promoted by the addition of 15 mM 2-hydroxyethyldisulfide (2-HEDS), also known as oxidized beta-mercaptoethanol, to the permeabilization buffer (6 M urea + 3 mM ethylenediaminetetraacetate [EDTA]). 2-HEDS is an oxidizing agent believed to promote disulfide bond formation, rendering the inclusion body resistant to solubilization in 6 M urea. Contaminating proteins are separated from the inclusion-body fraction by centrifugation. In the second stage, disulfide bonds are readily eliminated by including reducing agent (20 mM dithiothreitol [DTT]) into the permeabilization buffer. Extraction using this selective two-stage process yielded an 81% (w/w) recovery of the recombinant protein Long-R3-IGF-I from inclusion bodies located in the cytoplasm of intact E. coli, at a purity of 46% (w/w). This was comparable to that achieved by conventional extraction (mechanical disruption followed by centrifugation and solubilization). A pilot-scale procedure was also demonstrated using a stirred reactor and diafiltration. This is the first reported study that achieves both high extraction efficiency and selectivity by the chemical treatment of cytoplasmic inclusion bodies in intact bacterial cells.

  18. A high level of estrogen-stimulated proteins selects breast cancer patients treated with adjuvant endocrine therapy with good prognosis

    DEFF Research Database (Denmark)

    L H Weischenfeldt, Katrine; Kirkegaard, Tove; Rasmussen, Birgitte B

    2017-01-01

    BACKGROUND: Adjuvant endocrine therapy has significantly improved survival of estrogen receptor α (ER)-positive breast cancer patients, but around 20% relapse within 10 years. High expression of ER-stimulated proteins like progesterone receptor (PR), Bcl-2 and insulin-like growth factor receptor I...... (IGF-IR) is a marker for estrogen-driven cell growth. Therefore, patients with high tumor levels of these proteins may have particularly good prognosis following adjuvant endocrine therapy. PATIENTS AND METHODS: Archival tumor tissue was available from 1323 of 1396 Danish breast cancer patients...... enrolled in BIG 1-98, a randomized phase-III clinical trial comparing adjuvant letrozole, tamoxifen or a sequence of the two drugs. Immunohistochemical staining for ER, HER-2, PR, Bcl-2 and IGF-IR was performed and determined by Allred scoring (ER, PR and Bcl-2) or HercepTest (HER-2 and IGF-IR). RESULTS...

  19. Olefin cross-metathesis on proteins: investigation of allylic chalcogen effects and guiding principles in metathesis partner selection.

    Science.gov (United States)

    Lin, Yuya A; Chalker, Justin M; Davis, Benjamin G

    2010-12-01

    Olefin metathesis has recently emerged as a viable reaction for chemical protein modification. The scope and limitations of olefin metathesis in bioconjugation, however, remain unclear. Herein we report an assessment of various factors that contribute to productive cross-metathesis on protein substrates. Sterics, substrate scope, and linker selection are all considered. It was discovered during this investigation that allyl chalcogenides generally enhance the rate of alkene metathesis reactions. Allyl selenides were found to be exceptionally reactive olefin metathesis substrates, enabling a broad range of protein modifications not previously possible. The principles considered in this report are important not only for expanding the repertoire of bioconjugation but also for the application of olefin metathesis in general synthetic endeavors.

  20. Facile fabrication of hydrophilic nanofibrous membranes with an immobilized metal-chelate affinity complex for selective protein separation.

    Science.gov (United States)

    Zhu, Jing; Sun, Gang

    2014-01-22

    In this study, we report a facile approach to fabricate functionalized poly(vinyl alcohol-co-ethylene) (PVA-co-PE) nanofibrous membranes as immobilized metal affinity membranes for selective protein separation. Hydrophilic PVA-co-PE nanofibrous membranes with controlled fiber sizes were prepared via a melt extrusion process. A chelating group, iminodiacetic acid (IDA), was covalently attached to cyanuric acid activated membrane surfaces to form coordinative complexes with metal ions. The prepared membranes were applied to recover a model protein, lysozyme, under various conditions, and a high lysozyme adsorption capacity of 199 mg/g membrane was found under the defined optimum conditions. Smaller fiber size with a higher immobilized metal ion density on membrane surfaces showed greater lysozyme adsorption capacity. The lysozyme adsorption capacity remained consistent during five repeated cycles of adsorption-elution operations, and up to 95% of adsorbed lysozyme was efficiently eluted by using a phosphate buffer containing 0.5 M NaCl and 0.5 M imidazole as an elution media. The successful separation of lysozyme with high purity from fresh chicken egg white was achieved by using the present affinity membrane. These remarkable features, such as high capacity and selectivity, easy regeneration, as well as reliable reusability, demonstrated the great potential of the metal-chelate affinity complex immobilized nanofibrous membranes for selective protein separation.

  1. A Protocol for Phage Display and Affinity Selection Using Recombinant Protein Baits

    National Research Council Canada - National Science Library

    Kushwaha, Rekha; Schäfermeyer, Kim R; Downie, A. Bruce

    2014-01-01

    Using recombinant phage as a scaffold to present various protein portions encoded by a directionally cloned cDNA library to immobilized bait molecules is an efficient means to discover interactions...

  2. BET Bromodomain Proteins Brd2, Brd3 and Brd4 Selectively Regulate Metabolic Pathways in the Pancreatic β-Cell.

    Directory of Open Access Journals (Sweden)

    Jude T Deeney

    Full Text Available Displacement of Bromodomain and Extra-Terminal (BET proteins from chromatin has promise for cancer and inflammatory disease treatments, but roles of BET proteins in metabolic disease remain unexplored. Small molecule BET inhibitors, such as JQ1, block BET protein binding to acetylated lysines, but lack selectivity within the BET family (Brd2, Brd3, Brd4, Brdt, making it difficult to disentangle contributions of each family member to transcriptional and cellular outcomes. Here, we demonstrate multiple improvements in pancreatic β-cells upon BET inhibition with JQ1 or BET-specific siRNAs. JQ1 (50-400 nM increases insulin secretion from INS-1 cells in a concentration dependent manner. JQ1 increases insulin content in INS-1 cells, accounting for increased secretion, in both rat and human islets. Higher concentrations of JQ1 decrease intracellular triglyceride stores in INS-1 cells, a result of increased fatty acid oxidation. Specific inhibition of both Brd2 and Brd4 enhances insulin transcription, leading to increased insulin content. Inhibition of Brd2 alone increases fatty acid oxidation. Overlapping yet discrete roles for individual BET proteins in metabolic regulation suggest new isoform-selective BET inhibitors may be useful to treat insulin resistant/diabetic patients. Results imply that cancer and diseases of chronic inflammation or disordered metabolism are related through shared chromatin regulatory mechanisms.

  3. Developing a NIR multispectral imaging for prediction and visualization of peanut protein content using variable selection algorithms

    Science.gov (United States)

    Cheng, Jun-Hu; Jin, Huali; Liu, Zhiwei

    2018-01-01

    The feasibility of developing a multispectral imaging method using important wavelengths from hyperspectral images selected by genetic algorithm (GA), successive projection algorithm (SPA) and regression coefficient (RC) methods for modeling and predicting protein content in peanut kernel was investigated for the first time. Partial least squares regression (PLSR) calibration model was established between the spectral data from the selected optimal wavelengths and the reference measured protein content ranged from 23.46% to 28.43%. The RC-PLSR model established using eight key wavelengths (1153, 1567, 1972, 2143, 2288, 2339, 2389 and 2446 nm) showed the best predictive results with the coefficient of determination of prediction (R2P) of 0.901, and root mean square error of prediction (RMSEP) of 0.108 and residual predictive deviation (RPD) of 2.32. Based on the obtained best model and image processing algorithms, the distribution maps of protein content were generated. The overall results of this study indicated that developing a rapid and online multispectral imaging system using the feature wavelengths and PLSR analysis is potential and feasible for determination of the protein content in peanut kernels.

  4. Heterologous production, characterization and isolation of selected G protein-coupled receptors for structural studies

    OpenAIRE

    Shukla, Arun Kumar

    2006-01-01

    G protein-coupled receptors (GPCRs) play regulatory roles in many different physiological processes and they represent one of the most important class of drug targets. However, due to the lack of three-dimensional structures, structure based drug design has not been possible. The major bottleneck in getting three-dimensional crystal structure of GPCRs is to obtain milligram quantities of pure, homogenous and stable protein. Therefore, during my Ph.D. thesis, I focused on expression, character...

  5. Multi-Population Selective Genotyping to Identify Soybean [Glycine max (L. Merr.] Seed Protein and Oil QTLs

    Directory of Open Access Journals (Sweden)

    Piyaporn Phansak

    2016-06-01

    Full Text Available Plant breeders continually generate ever-higher yielding cultivars, but also want to improve seed constituent value, which is mainly protein and oil, in soybean [Glycine max (L. Merr.]. Identification of genetic loci governing those two traits would facilitate that effort. Though genome-wide association offers one such approach, selective genotyping of multiple biparental populations offers a complementary alternative, and was evaluated here, using 48 F2:3 populations (n = ∼224 plants created by mating 48 high protein germplasm accessions to cultivars of similar maturity, but with normal seed protein content. All F2:3 progeny were phenotyped for seed protein and oil, but only 22 high and 22 low extreme progeny in each F2:3 phenotypic distribution were genotyped with a 1536-SNP chip (ca. 450 bimorphic SNPs detected per mating. A significant quantitative trait locus (QTL on one or more chromosomes was detected for protein in 35 (73%, and for oil in 25 (52%, of the 48 matings, and these QTL exhibited additive effects of ≥ 4 g kg–1 and R2 values of 0.07 or more. These results demonstrated that a multiple-population selective genotyping strategy, when focused on matings between parental phenotype extremes, can be used successfully to identify germplasm accessions possessing large-effect QTL alleles. Such accessions would be of interest to breeders to serve as parental donors of those alleles in cultivar development programs, though 17 of the 48 accessions were not unique in terms of SNP genotype, indicating that diversity among high protein accessions in the germplasm collection is less than what might ordinarily be assumed.

  6. Selection on Coding and Regulatory Variation Maintains Individuality in Major Urinary Protein Scent Marks in Wild Mice.

    Directory of Open Access Journals (Sweden)

    Michael J Sheehan

    2016-03-01

    Full Text Available Recognition of individuals by scent is widespread across animal taxa. Though animals can often discriminate chemical blends based on many compounds, recent work shows that specific protein pheromones are necessary and sufficient for individual recognition via scent marks in mice. The genetic nature of individuality in scent marks (e.g. coding versus regulatory variation and the evolutionary processes that maintain diversity are poorly understood. The individual signatures in scent marks of house mice are the protein products of a group of highly similar paralogs in the major urinary protein (Mup gene family. Using the offspring of wild-caught mice, we examine individuality in the major urinary protein (MUP scent marks at the DNA, RNA and protein levels. We show that individuality arises through a combination of variation at amino acid coding sites and differential transcription of central Mup genes across individuals, and we identify eSNPs in promoters. There is no evidence of post-transcriptional processes influencing phenotypic diversity as transcripts accurately predict the relative abundance of proteins in urine samples. The match between transcripts and urine samples taken six months earlier also emphasizes that the proportional relationships across central MUP isoforms in urine is stable. Balancing selection maintains coding variants at moderate frequencies, though pheromone diversity appears limited by interactions with vomeronasal receptors. We find that differential transcription of the central Mup paralogs within and between individuals significantly increases the individuality of pheromone blends. Balancing selection on gene regulation allows for increased individuality via combinatorial diversity in a limited number of pheromones.

  7. Downmodulation of El A Protein Expression as a Novel Strategy to Design Cancer-Selective Adenoviruses

    Directory of Open Access Journals (Sweden)

    Hong Jiang

    2005-08-01

    Full Text Available Oncolytic adenoviruses are being tested as potential therapies for human malignant tumors, including gliomas. Here we report for the first time that a mutation in the E1A gene results in low levels of ElA protein, conditioning the replication of mutant adenoviruses specifically to cancer cells. In this study, we compared the oncolytic potencies of three mutant adenoviruses encompassing deletions within the CRi (Delta-39, CR2 (Delta-24 regions, or both regions (Delta-24/39 of the ElA protein. Delta-39, Delta-24 induced a cytopathic effect with similar efficiency in glioma cells, a comparable capacity for replication. Importantly, the activity of Delta-39 was significantly attenuated compared to Delta-24 in proliferating normal human astrocytes. Direct analyses of the activation of E2F-1 promoter demonstrated the inability of Delta-39 to induce S-phase-related transcriptional activity in normal cells. Interestingly, ElA protein levels in cells infected with Delta-39 were remarkably downmodulated. Furthermore, protein stability studies revealed enhanced degradation of CRi mutant ElA proteins, inhibition of the proteasome activity resulted in the striking rescue of ElA levels. We conclude that the level of ElA protein is a critical determinant of oncolytic phenotype, we propose a completely novel strategy for the design, construction of conditionally replicative adenoviruses.

  8. Selective translational repression of truncated proteins from frameshift mutation-derived mRNAs in tumors.

    Directory of Open Access Journals (Sweden)

    Kwon Tae You

    2007-05-01

    Full Text Available Frameshift and nonsense mutations are common in tumors with microsatellite instability, and mRNAs from these mutated genes have premature termination codons (PTCs. Abnormal mRNAs containing PTCs are normally degraded by the nonsense-mediated mRNA decay (NMD system. However, PTCs located within 50-55 nucleotides of the last exon-exon junction are not recognized by NMD (NMD-irrelevant, and some PTC-containing mRNAs can escape from the NMD system (NMD-escape. We investigated protein expression from NMD-irrelevant and NMD-escape PTC-containing mRNAs by Western blotting and transfection assays. We demonstrated that transfection of NMD-irrelevant PTC-containing genomic DNA of MARCKS generates truncated protein. In contrast, NMD-escape PTC-containing versions of hMSH3 and TGFBR2 generate normal levels of mRNA, but do not generate detectable levels of protein. Transfection of NMD-escape mutant TGFBR2 genomic DNA failed to generate expression of truncated proteins, whereas transfection of wild-type TGFBR2 genomic DNA or mutant PTC-containing TGFBR2 cDNA generated expression of wild-type protein and truncated protein