Adequate representations of protein evolution should consider how the acceptance of mutations depends on the sequence context in which they arise. However, epistatic interactions among sites in a protein result in hererogeneities in the substitution rate, both temporal and spatial, that are beyond the capabilities of current models. Here we use parallels between amino acid substitutions and chemical reaction kinetics to develop an improved theory of protein evolution. We constructed a mechanistic framework for modelling amino acid substitution rates that uses the formalisms of statistical mechanics, with principles of population genetics underlying the analysis. Theoretical analyses and computer simulations of proteins under purifying selection for thermodynamic stability show that substitution rates and the stabilization of resident amino acids (the evolutionary Stokes shift) can be predicted from biophysics and the effect of sequence entropy alone. Furthermore, we demonstrate that ...
A key element in evaluating the quality of a pairwise sequence alignment is the "substitution matrix", which assigns a score for aligning any possible pair of residues. The theory of amino acid substitution matrices is described in [1], and applied to DNA sequence comparison in [2]. In general, different substitution matrices are tailored to detecting similarities among sequences that are diverged by differing degrees [1-3]. A single matrix may nevertheless be reasonably efficient over a relatively broad range of evolutionary change [1-3]. Experimentation has shown that the BLOSUM-62 matrix [4] is among the best for detecting most weak protein similarities. For particularly long and weak alignments, the BLOSUM-45 matrix may prove superior. A detailed statistical theory for gapped alignments has not been developed, and the best gap costs to use with a given substitution matrix are determined empirically. Short alignments need to be relatively strong (i.e. have a higher percentage of matching ...
Identification of specificity determining residues in enzymes using environment specific substitution tables - Quantitative Biology > Quantitative Methods. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
In this project, we develop a general framework that applies 3D convolutional neural network (3DCNN) technology to structure-based protein analysis. The framework automatically extracts task-specific features from the raw atom distribution, driven by supervised labels. As a pilot study, we use our network to analyze local protein microenvironments surrounding the 20 amino acids, and predict the amino acids most compatible with environments within a protein structure. To further validate the power of our method, we construct two amino acid substitution matrices from the prediction statistics and use them to predict effects of mutations in T4 lysozyme structures. ...
1C5I: Hydrogen bonding and catalysis: a novel explanation for how a single amino acid substitution can change the pH optimum of a glycosidase.
Single Amino Acid Mutation related change of Binding Energy (SAAMBE) method addresses the demand for computational tools of predicting the effect of single amino acid substitution on the binding free energy of protein complexes. It is based on the fast (,, 1 minute) modified MM-PBSA protocol that is successfully tested and optimized for more than thousand experimental data points. If the usage of the server results in scientific publication, please, cite the following papers: References SAAMBE is running on Clemson Universitys Palmetto Supercomputer Cluster. If you experience problems, they may be due to Palmetto Cluster being not functional or under maintenance. Contact us at [email protected] ...
Substitution Mutations: In substitution mutations, a nitrogenous base of a triplet codon of DNA is replaced by another nitrogen base or some derivative of the nitrogen base, changing the codon. The altered codon codes for a different amino acid substitution.The substitution mutations are of two types: 1.Transitions: It is the replacement of one purine in a polynucleotide chain by another purine(A by G or G by A) or one pyrimidine by another pyrimidine(T by C or C by T) 2.Transversions:A base pair substitution involving the substitution of a purine by pyrimidine or pyrimidine by a purine is called transversion. ...
Structure-function studies of potassium channels have shown that many pore loop substitutions result in a loss of functional channel expression. Some point mutations in the pore loop disrupt subunit tetramerization (Heginbotham et al., 1997), whereas in other cases channels are delivered to the cell surface, as determined by voltage-dependent gating charge movement, but potassium ion conduction through the pore is eliminated (Perozo et al., 1993). Glutamate receptor channels appear to tolerate a larger repertoire of substitutions, possibly owing to their larger pore dimensions. Estimates of pore size at the selectivity filter based on permeation of organic cations suggest a diameter of ∼5.5 Å for NMDA receptors (Villarroel et al., 1995), 7.5-7.6 Å for both Q and R forms of kainate receptors and ∼7.8 Å for AMPA receptors (Burnashev et al., 1996). In contrast, potassium channels exhibit a narrower pore diameter of ∼3 Å (Hille, 2001). With some notable exceptions, single amino acid ...
These are internal identifiers that are unique to a mutation on a particular transcript and are displayed in the URL of the mutation pages. Therefore, several of these internal ids could be associated with a single genomic COSV id where the mutation has been mapped to all overlapping genes and transcripts. Similarly, since every COSM id is mapped to one COSV id (where genomic coordinates are known), each COSM id can also be associated with several alternative (internal) identifiers. These ids are expected to change between assemblies (GRCh37 and GRCh38) and between the releases ...
The sessile nature of plants forces them to cope directly with environmental stresses, which include insect herbivory, pathogen attack, UV light radiation, and drought. Secondary metabolites are believed to be an important mechanism that allows plants to respond to these environmental challenges. There are more than 100,000 known plant secondary metabolites, which probably represent less than 10% of the actual total in nature (Wink, 1988). A large fraction of this diversity is derived from differential modification of common backbone structures, which requires the evolution of numerous enzymes with different product specificities. There are several mechanisms by which this can occur. First, as is the case with terpene synthases, a single protein can produce numerous products from a single substrate (Steele et al., 1998). A few amino acid substitutions can alter the ratio of products generated by a terpene synthase (Back and Chappell, 1996). The second mechanism is the use of gene duplication. In ...
These findings suggest that a specific substitution in a 3S-based immunogen might allow the generation of specific antibodies, providing a foundation for a rational vaccine that combine a capacity to neutralize HIV-1 and to protect CD4(+) T cells.
ants in an amino-acid sequence can bedetermined if the In addition to identifying important genetic variants substitution is in an annotated active or binding site, for research prioritization, genotyping efforts could be affects interaction with ligands present in the crystallo- reduced by eliminating amino-acid substitutions that graphic structure, leadsto hydrophobicity or electrostatic have been deemed neutral by algorithms such as charge change in a buriedsite, destroys a disulfide bond, PolyPhen. In some cases, some genes could be removed affects the proteins solubility, inserts proline in an from further consideration if all of the variant alleles α-helix,or is incompatiblewith the profile of amino-acid were deemed to be non-functional. Because prediction substitutions observed at this site in the set of homolo- algorithms provide numerical data, it is feasible to fur- gous proteins. Mapping the amino-acid substitution tothe ther subdivide the variant alleles of a gene into those ...
1LYF: Dissection of helix capping in T4 lysozyme by structural and thermodynamic analysis of six amino acid substitutions at Thr 59.
Dalla Chiesa, Marta, Martensen, Pia, Simmons, Cameron, Porakishvili, Nino, Justesen, Just, Dougan, Gordon, Roitt, Ivan M., Delves, Peter J. and Lund, Torben (2001) Refocusing of B-cell responses following a single amino acid substitution in an antigen. Immunology, 103 (2). pp. 172-178. ISSN 0019-2805 ...
Lindner, B. D., Engelhart, J. U., Tverskoy, O., Appleton, A. L., Rominger, F., Peters, A., Himmel, H.-J. and Bunz, U. H. F. (2011), Stable Hexacenes through Nitrogen Substitution. Angew. Chem. Int. Ed., 50: 8588-8591. doi: 10.1002/anie.201103676 ...
Computational prediction of protein stability change due to single-site amino acid substitutions is of interest in protein design and analysis. We consider the following four ways to improve the performance of the currently available predictors: (1) We include additional sequence- and structure-based features, namely, the amino acid substitution likelihoods, the equilibrium fluctuations of the alpha- and beta-carbon atoms, and the packing density. (2) By implementing different machine learning integration approaches, we combine information from different features or representations. (3) We compare classification vs. regression methods to predict the sign vs. the output of stability change. (4) We allow a reject option for doubtful cases where the risk of misclassification is high. We investigate three different approaches: early, intermediate and late integration, which respectively combine features, kernels over feature subsets, and decisions. We perform simulations on two data sets: (1) S1615 is used
Classifying and predicting amino acid substitutions are important in pharmaceutical and pathological research. We proposed a novel feature set from amino acids physicochemical properties, evolutionary profile of proteins, and protein sequence information. Large scale size of human disease-associated data were collected and processed, together with the unbiased experimental amino acid substitutions. Machine learning methods of decision tree, support vector machine, Gaussian mixture model, and random forests were used to classify neutral and deleterious substitutions, and the comparison of classification accuracy with published results showed that our feature set is superior to the existing ones.; We designed a simulated annealing bump hunting method to automatically extract interpretable rules for amino acid substitutions. Rules are consistent with current biological knowledge or provide new insights for understanding substitutions.; We also designed a Multiple Selection and Rule Voting (MS-RV) ...
BioAssay record AID 198913 submitted by ChEMBL: Inhibition of HIV-1 Mutant HIV-1 RT enzymes containing the single amino acid substitution V106A.
Accumulation of somatic mutations is critical for the transition of a normal cell to become cancerous. Mutations cause amino acid substitutions that change properties of proteins. However, it has not been studied as to what extent the composition and accordingly chemical properties of the cell proteome is altered as a result of the increased mutation load in cancer. Here, we analyzed data on amino acid substitutions caused by mutations in about 2000 protein coding genes from the Cancer Cell Line Encyclopedia that contains information on nucleotide and amino acid alterations in 782 cancer cell lines, and validated the analysis with information on amino acid substitutions for the same set of proteins in the Catalogue of Somatic Mutations in Cancer (COSMIC; v78) in circa 18,000 tumor samples. We found that nonsynonymous single nucleotide substitutions in the analyzed proteome subset ultimately result in a net gain of cysteine, histidine, and tryptophan at the expense of a net loss of arginine. The
Methods: In this study, E6 and E7 gene sequences were obtained from 12 samples of Indonesian isolates, which were compared with HPV16R (prototype) and 6 standard isolates in the category of European (E), Asian (As), Asian-American (AA), African-1 (Af-1), African-2 (Af-2), and North American (NA) branch from Genbank. Bioedit v.7.0.0 was used to analyze the composition and substitution of single amino acids. Phylogenetic analysis of E6 and E7 genes and proteins was performed using Clustal X (1.81) and NJPLOT softwares. Effects of single amino acid substitutions on protein function of E6 and E7 were analysed by SNAP. ...
We have previously demonstrated that substitution of Asn for Ser at position 17 of RasH yields a dominant inhibitory protein whose expression in cells interferes with endogenous Ras function (L. A. Feig, and G. M. Cooper, Mol. Cell. Biol. 8:3235-3243, 1988). Subsequent structural studies have shown that the hydroxyl group of Ser-17 contributes to the binding of Mg2+ associated with bound nucleotide. In this report, we show that more subtle amino acid substitutions at this site that would be expected to interfere with complexing Mg2+, such as Cys or Ala, also generated dominant inhibitory mutants. In contrast, a Thr substitution that conserves a reactive hydroxyl group maintained normal Ras function. These results argue that the defect responsible for the inhibitory activity is improper coordination of Mg2+. Preferential affinity for GDP, observed in the original Asn-17 mutant, was found exclusively in inhibitory mutants. However, this binding specificity did not completely block the mutant ...
Study shows that seasonal flu escapes immunity with single amino acid substitutions. Scientists have identified a potential way to improve future flu vaccines after discovering that seasonal flu typically escapes immunity from vaccines with as little as a single amino acid substitution. Additionally, they found these single amino acid changes occur at only seven places on its surface - not the 130 places previously believed. The research was published today, 21 November, in the journal Science.. "This work is a major step forward in our understanding of the evolution of flu viruses, and could possibly enable us to predict that evolution. If we can do that, then we can make flu vaccines that would be even more effective than the current vaccine," said Professor Derek Smith from the University of Cambridge, one of the two leaders of the research, together with Professor Ron Fouchier from Erasmus Medical Center in The Netherlands.. The flu vaccine works by exposing the body to parts of inactivated ...
Dear Colleagues, I am seeking pdb files to use as paired examples of the effects of a single amino acid substitution on protein structure/function. Ideally I would like to have some examples of substitutions that alter function, and some that have little or no evident functional effect. If both types of substitutions are available for the same protein, so much the better. A good example is normal and sickle cell hemoglobin, but I would like to have somewhere between four and ten different protein examples. I need some that affect binding or enzymatic activity and are located in the binding or active site. Thanks in advance for suggestions on this topic. Frieda Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures www.moleculesinmotion.com MyDNA Project www.bio.umass.edu/biochem/mydna ...
Ns done by the Polyphen-2 software used by the Exome Variant Server (EVS) database to predict the effect of amino acid substitution on 115103-85-0 manufacturer
http://​genetics.bwh.harvard.edu/​pph2,PolyPhen-2]] is a tool for predicting the effect of an amino acid substitution on protein structure and function, based on comparative genomics and experimentally determined protein structures. It is available as a web service, and can also be downloaded as a standalone application ...
UCL Discovery is UCLs open access repository, showcasing and providing access to UCL research outputs from all UCL disciplines.
The PPARγ2 Pro12Ala variant is protective against progression of nephropathy in people with type 2 diabetes. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
The R779C variant in the IFIH1 gene has been reported previously in two unrelated individuals with Aicardi-Goutières syndrome, one which the R779C variant was shown to occur de novo (Rice et al., 2014; Marguet et al., 2016). The R779C variant is not observed in large population cohorts (Lek et al., 2016). The R779C variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. Functional studies show the R779C variant demonstrates a gain of function mechanism, enhancing the interferon signaling pathway activation, stability of filament formation, and dsRNA binding activity (Rice et al., 2014). We interpret R779C as a pathogenic variant. (less) ...
It contains the values of a, b, c and E damping parameters for amino acid substitution scores. Generally, if a residue is completely buried ( Area=0), its substitution scores will be used without changes. If it is completely exposed, its substitution scores will be multiplied by the minimal possible value of a. Between these cases the substitution scores are modulated by a smooth ("arctangent") function with a saddle point at Area=c, where the slope will be -b. The fourth parameter is reserved for development ...
TY - JOUR. T1 - Enhancement of thermoelectric properties by Se substitution in layered bismuth-chalcogenide LaOBiS2-xSex. AU - Mizuguchi, Yoshikazu. AU - Omachi, Atsushi. AU - Goto, Yosuke. AU - Kamihara, Yoichi. AU - Matoba, Masanori. AU - Hiroi, Takafumi. AU - Kajitani, Joe. AU - Miura, Osuke. PY - 2014/1/1. Y1 - 2014/1/1. N2 - We have investigated the thermoelectric properties of the novel layered bismuth chalcogenides LaOBiS2-xSex. The partial substitution of S by Se produced the enhancement of electrical conductivity (metallic characteristics) in LaOBiS2-xSex. The power factor largely increased with increasing Se concentration. The highest power factor was 4.5 μW/cmK2 at around 470 °C for LaOBiS1.2Se0.8. The obtained dimensionless figure-of-merit (ZT) was 0.17 at around 470 °C in LaOBiS1.2Se0.8.. AB - We have investigated the thermoelectric properties of the novel layered bismuth chalcogenides LaOBiS2-xSex. The partial substitution of S by Se produced the enhancement of electrical ...
[104 Pages Report] Check for Discount on United States Dura Substitution Market Report 2017 report by QYResearch Group. In this report, the United States Dura Substitution market is...
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2 Substitutions 2 Recoveries / 5 Chills Items = Training All Abilities 2 Day DQ Ransei... the wartorn region of seventeen. Seventeen daimyos...
A crucial prerequisite for plant growth and survival is the maintenance of potassium uptake, especially when high sodium surrounds the root zone. The Arabidopsis HIGH-AFFINITY K+ TRANSPORTER1 (HKT1), and its homologs in other salt-sensitive dicots, contributes to salinity tolerance by removing Na+ from the transpiration stream. However, TsHKT1;2, one of three HKT1 copies in Thellungiella salsuginea, a halophytic Arabidopsis relative, acts as a K+ transporter in the presence of Na+ in yeast (Saccharomyces cerevisiae). Amino-acid sequence comparisons indicated differences between TsHKT1;2 and most other published HKT1 sequences with respect to an Asp residue (D207) in the second pore-loop domain. Two additional T. salsuginea and most other HKT1 sequences contain Asn (n) in this position. Wild-type TsHKT1;2 and altered AtHKT1 (AtHKT1N-D) complemented K+-uptake deficiency of yeast cells. Mutant hkt1-1 plants complemented with both AtHKT1N-D and TsHKT1;2 showed higher tolerance to salt stress than ...
Where did the nylon-eating ability come from? Carboxylesterases are enzymes with broad substrate specificities; they can carry out a variety of reactions. Their binding pocket is large and can accommodate a lot of different substrates. They are "promiscuous" enzymes, in other words. Furthermore, the carboxylesterase reaction hydrolyzes a chemical bond similar to the one hydrolyzed by nylonase.. […]. From Kato et al. (1991):. "Our studies demonstrated that among the 47 amino acids altered between the EII and EII proteins, a single amino acid substitution at position 181 was essential for the activity of 6-aminohexanoate-dimer hydrolase [nylonase] and substitution at position 266 enhanced the effect.". So. This is not the story of a highly improbable frame-shift producing a new functional enzyme. This is the story of a pre-existing enzyme with a low level of promiscuous nylonase activity, which improved its activity toward nylon by first one, then another selectable mutation. In other words ...
English) A Simple Mechanism Based on Amino Acid Substitutions is not a Critical Determinant of High Mortality of Japanese Encephalitis Virus Infection in Mice ...
The Y155H amino acid substitution in the neuraminidase gene (NA) has previously been associated with highly reduced inhibition by neuraminidase inhibitors in the seasonal H1N1 influenza A virus which circulated in humans before the 2009 pandemic. During the 2012/13 epidemic season in Spain, two A(H1N1)pdm09 viruses bearing the specific Y155H substitution in the NA were detected and isolated from two patients diagnosed with severe respiratory syndrome and pneumonia requiring admission to the intensive care unit. Contrary to what was observed in the seasonal A(H1N1) viruses, neither of the Y155H A(H1N1)pdm09 viruses described here showed a phenotype of reduced inhibition by NAIs as determined by the neuraminidase enzyme inhibition assay (MUNANA). High-throughput sequencing of the NA of both Y155H viruses showed that they were composed to >99% of H155 variants. We believe that this report can contribute to a better understanding of the biological significance of amino acid substitutions in the
Five point mutations within the amyloid beta-protein (Abeta) sequence of the APP gene are associated with hereditary diseases which are similar or identical to Alzheimers disease and encode: the A21G (Flemish), E22G (Arctic), E22K (Italian), E22Q (Dutch) and the D23N (Iowa) amino acid substitutions. Although a substantial body of data exists on the effects of these mutations on Abeta production, whether or not intra-Abeta mutations alter degradation and how this relates to their aggregation state remain unclear. Here we report that the E22G, E22Q and the D23N substitutions significantly increase fibril nucleation and extension, whereas the E22K substitution exhibits only an increased rate of extension and the A21G substitution actually causes a decrease in the extension rate. These substantial differences in aggregation together with our observation that aggregated wild type Abeta(1-40) was much less well degraded than monomeric wild type Abeta(1-40), prompted us to assess whether or not ...
Abstract: Proteomic studies of some human tissues and organs (skeletal muscles, myometrium, motor zone of the brain, prostate), and also cultivated myoblasts revealed 41 of 300 identified proteins, in which the present of certain variants of amino acids (conflicts) was recognized at several positions. Among the 93 registered amino acids conflicts, seven cases represented the results of the protein polymorphisms caused by corresponding substitution of individual amino acid. Moreover, among prostate proteins the proteomic analysis revealed two isoforms of prostate-specific antigen, formed due to alternative splicing. Thus, our results have shown, that proteomic technologies allow to specify effectively the features of primary structures and to characterize various kinds of polymorphism in many human proteins ...
Mutations leading to hemophilia A by substitution of amino acids in coagulation factor VIII may provide important clues to the structure and function of this large and enigmatic protein. To efficiently find missense mutations, hemophiliacs with mild
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Lower your blood pressure with one single amino acid If you have stubborn hypertension, you might be interested in a simple and inexpensive treatment. Its a single amino acid. As you may know, amino acids are the building blocks of proteins. But many amino acids serve as raw materials for key molecules. For example, tryptophan and phenylalanine serve as raw materials for neurotransmitters. A deficiency in either of these can lead to mood disorders.
Just a few viruses fell into subgroup 3B and group 6 (Fig. 4, Fig. S4). Some isolates from North America, Europe and Asia belonged to groups 5 and 6, which have signature AA substitutions D53N, Y94H, I230V and E280A in HA1, with group 6 isolates carrying an additional AA substitution S199A. Viruses with low HI titres to post-infection ferret antisera raised against cell-propagated A/Victoria/361/2011 viruses were scattered throughout the HA tree and did not form monophyletic groups or share common AA substitutions. Genetic analysis OSI 906 of the HA sequences of several egg-propagated A/Victoria/361/2011-like. viruses were compared in order to see if low HI titres might be associated with amino acid substitutions linked to adaptation to growth in eggs. A number of such substitutions were noted in the HA of the initial egg-propagated A/Victoria/361/2011 wild-type virus, including a H156R substitution. A. subsequent R156Q change was acquired in the high growth reassortants IVR-165 and X221, ...
The S14L variant has been reported in individuals with autism and seizures, although the phenotype was variable with reduced penetrance and did not uniformly include seizures (Feng et al., 2006; Gauthier et al., 2011; Yangngam et al., 2014). This variant is in the shorter transcript of NRXN1 (NM_138735.2), and alters a residue that is predicted to be in the signal peptide of the beta-neurexin protein (Zweier et al., 2009; Gauthier et al., 2011). Although the S14L was not observed in 1,201 controls studied separately (Feng et al., 2006; Gauthier et al., 2011; Kim et al., 2008), it was observed in 1/200 controls in an additional publication (Camacho-Garcia et al., 2012). This variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size, and/or other properties. However, this substitution occurs at a position that is not conserved, and functional studies have shown no abnormalities in beta-neurexin ...
In article ,90luod$kkb$1 at mercury.hgmp.mrc.ac.uk,, James McInerney ,james.o.mcinerney at may.ie, wrote: ,I have a question about selection on genes in HIV (but probably anywhere). ,In some HIV genes there is often a great excess of replacement substitutions ,over silent substitutions. In the past we would say that this meant that ,there was a positive selection event involved. However, if there is no ,selective difference between substitutions that occur in synonymous and ,non-synonymous sites then we would see about three times as many ,substitutions that are replacement than silent. I believe such studies generally take this into account. They reckon up how many sites *could* have a synonymous or nonsynonymous (S and N from here on) substitution, and weight by how many such substitutions could occur (a fourfold degenerate site contributes more possible S substitutions than a twofold ones). So the actual statistic is the ratio of S mutations per S site and N mutations per N site. This is ...
The R633S variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The R633S variant is observed in 49/7604 (0.6%) alleles from individuals of East Asian background (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). This substitution occurs at a position where amino acids with similar properties to Arginine are tolerated across species. However, this variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. (less) ...
Downloadable! The relationship between the goods-time elasticity of substitution with consumption time as an input and the goods-time elasticity of substitution without consumption time as an input is derived analytically. Under some reasonable assumptions, the goods-time elasticity of substitution is shown to be greater if consumption time is not included as an input. An empirical example of food production for single headed households is consistent with this result and indicates the goods-time elasticity of substitution is about 60% greater when consumption time is not included as an input than when it is included.
We discovered that replacing residue D23 with a non-negatively charged amino acid leads to dramatically enhanced affinity of leptin for its receptor, D23L substitution being the most effective. The resulting D23L/L39A/D40A/F41A mutant acted as super leptin antagonist. ...
Effect of B-Cation Substitution on the Activity of LaCrO3 and LaNiO3 Perovskites for Autothermal Reforming of Methane Conference Abstracts ...