Rich Amino Research Articles

Contrasted evolutionary constraints on carbohydrate active enzymes (CAZymes) in selected Frankia strains.

Carbohydrate active enzymes (CAZymes) are capable of breaking complex polysaccharides into simpler form. In plant-host-associated microorganisms CAZymes are known to be involved in plant cell wall degradation. However, the biology and evolution of Frankia CAZymes are largely unknown. In the present study, we took a genomic approach to evaluate the presence and putative roles of CAZymes in Frankia. The CAZymes were found to be potentially highly expressed (PHX) proteins and contained more aromatic amino acids, which increased their biosynthetic energy cost. These energy rich amino acids were present in the active sites of CAZymes aiding in their carbohydrate binding capacity. Phylogenetic and evolutionary analyses showed that, in Frankia strains with the capacity to nodulate host plants, CAZymes were evolving slower than the other PHX genes, whereas similar genes from non-nodulating (or ineffectively nodulating) Frankia strains showed little variation in their evolutionary constraints compared to other PHX genes. Thus, the present study revealed the persistence of a strong purifying selection on CAZymes of Frankia indicating their crucial role.

Voltammetric immunoassay for α-fetoprotein by using a gold nanoparticle/dendrimer conjugate and a ferrocene derived ionic liquid.

An immunosensor is described for the voltammetric determination of α-fetoprotein. It is making use of an AuNP-dendrimer conjugate and an ionic liquid. A gold electrode was first modified with chitosan. Then, the AuNP-dendrimer conjugate was covalently immobilized on the electrode. Following this, an ionic liquid was placed on the electrode via formation of a covalent bond between the amino groups of PAMAM and the aldehyde groups of an ionic liquid containing ferrocene. Thus, the redox probe ferrocene becomes immobilized on the electrode surface. PAMAM increases the amount of ferrocene immobilized on the electrode due to its globular shape and rich amino groups. The use of AuNPs improves the conductivity of the electrode. The modified electrode was applied to the determination of α-fetoprotein in human serum and has a linear response that covers the 0.05 to 30ngmL-1 α-fetoprotein concentration range, with a detection limit of 0.02ngmL-1. This assay is stable, selective and reproducible. It is perceived to provide a powerful tool for the early detection of cancer markers. Graphical abstract Schematic of a voltammetric immunoassay for α-fetoprotein based on a gold nanoparticle/dendrimer conjugate and ionic liquids anchored with both aldehyde and ferrocene. Chit: chitosan; GA: glutaraldehyde ; PAMAM: G4 polyamidoaminic dendrimers; AuNP: Au nanoparticle; Fc: ferrocene; IL: ionic liquid. PB: phosphate buffer solution.

Self-sensibilized polymeric prodrug co-delivering MMP-9 shRNA plasmid for combined treatment of tumors

Polymeric prodrugs are of immense interest as anticancer drug-delivery system owing to their superior drug stability during circulation and satisfactory drug loading capacity. However, they are usually less effective than free drugs due to imperfect degradable characteristics or active sites blockage. A polymeric prodrug (HPAA-MTX) with chemotherapeutic self-sensibilization effect consisting of glutathione (GSH)-triggered hyperbranched poly(amido amine) (HPAA) and methotrexate (MTX) was designed and synthesized in this work. This prodrug not only showed better inhibition effect on the tumor cells proliferation compared with free MTX, but also displayed selective sensibilization to tumor cells rather than normal cells. Meanwhile, HPAA-MTX was also explored as a MMP-9 shRNA plasmid delivery vector due to their rich amino group of HPAA, accompanying with MTX for simultaneous inhibiting tumor cells proliferation and migration. As expected, HPAA-MTX possessed excellent gene delivery capacity with significant down-regulation expression of MMP-9 protein and further inhibition of MCF-7 cells migration. Benefiting from the self-sensibilization effect and MTX/MMP-9 co-delivery strategy, this HPAA-MTX/MMP-9 co-delivery system exhibited significantly improved therapeutic efficacy to breast cancer in a combined manner which was confirmed through in vitro and in vivo assays. The strategy established in this study provided a facile “all-in-one” platform to integrate the drug/gene co-delivery strategy and self-sensibilization effect into one single nanocomposite for potential cancer treatment. Statement of significanceA cationic polymeric prodrug with chemotherapeutic self-sensibilization effect was designed and showed better inhibition effect on tumor cells proliferation compared with its free drug, as well displayed the selective sensibilization effect to tumor cells rather than normal cells. Moreover, the prodrug could also deliver MMP-9 shRNA plasmid for a combined therapy. As expected, the prodrug possessed excellent gene delivery capacity with significant down-regulation expression of MMP-9 protein and further inhibition of MCF-7 cells migration. Benefiting from the self-sensibilization effect and the drug/gene co-delivery strategy, this prodrug exhibited significantly improved therapeutic efficacy to breast cancer in a combined manner.

Separation and Characterization of Antioxidative and Angiotensin Converting Enzyme Inhibitory Peptide from Jellyfish Gonad Hydrolysate.

The gonad of jellyfish (Rhopilema esculentum Kishinouye), containing high protein content with a rich amino acid composition, is suitable for the preparation of bioactive peptides. Jellyfish gonad was hydrolysed with neutral protease to obtain jellyfish gonad protein hydrolysate (JGPH), which was then purified sequentially by ultrafiltration, gel filtration chromatography, and RP-HPLC. The peptides were characterized with HPLC-MS/MS. One peptide with amino acid sequence Ser-Tyr (SY) was identified and synthesized, which showed good ACE inhibitory and antioxidant activity. The IC50 of this peptide on DPPH, ·OH, super oxygen anion scavenging activities, and ACE inhibitory activity are 84.623 μM, 1177.632 μM, 456.663 μM, and 1164.179 μM, respectively. The anchor in the binding site of SY and ACE C-domain (ACE-C) was obtained by molecular simulations. The results showed that the dipeptide purified from jellyfish gonad protein hydrolysates can be used as functional food material and is helpful in the study of antioxidant and inhibition of ACE.

Removal of various pollutants from water and wastewater by modified chitosan adsorbents

ABSTRACTChitosan-based adsorbents have attracted increasing attention in water and wastewater treatment in recent years due to its abundance and low price, as well as rich amino and hydroxyl groups. However, there are some drawbacks hindering its practical use, such as low mechanical strength, low solubility in acidic mediums, low adsorption capacity, and lack of selectivity. Therefore, a variety of modification methods, including physical and chemical modifications, have been investigated to improve the physicochemical properties of chitosan. This review provides a summary of (a) the intrinsic nature of chitosan associated with its structure and physicochemical properties; (b) the preparation strategies for modified chitosan together with its characterization; (c) the application of chitosan-based adsorbents for the removal of both organic pollutants (e.g., dyes, PPCPs, PFOS, and humus) and inorganic pollutants (e.g., heavy metal ions, nitrate, phosphate, borate, and fluoride). Recent advances in the fabrication and application of chitosan-based adsorbents involving the intrinsic nature of pollutants are highlighted in this review, as well as the effects of process variables (e.g., pH, contact time, ionic strength, competitive ions, temperature), modeling (kinetics and isotherm), adsorption mechanisms, and regeneration.

Melamine-containing polyphosphazene wrapped ammonium polyphosphate: A novel multifunctional organic-inorganic hybrid flame retardant

To achieve superior fire safety epoxy resins (EP), a novel multifunctional organic-inorganic hybrid, melamine-containing polyphosphazene wrapped ammonium polyphosphate (PZMA@APP) with rich amino groups was prepared and used as an efficient flame retardant. Thanks to the cross-linked polyphosphazene part, PZMA@APP exhibited high flame retardant efficiency and smoke suppression to the EP composites. Thermogravimetric analysis indicated that PZMA@APP significantly enhanced the thermal stability of EP composites. The obtained sample passed UL-94 V-0 rating with 10.0wt% addition of PZMA@APP. Notably, inclusion of incorporating PZMA@APP leads to significantly decrease on fire hazards of EP, for instance, bring about a 75.6% maximum decrease in peak heat release rate and 65.9% maximum reduction in total heat release, accompanied with lower smoke production rate and higher graphitized char layer. With regards to mechanical property, the glass transition temperature of EP/PZMA@APP10.0 was as high as 184.5°C. In particular, the addition of PZMA@APP did not worsen the mechanical properties, compared to pure APP. It was confirmed that the participation of melamine-containing polyphosphazene could significantly enhance the quality of char layer and thereby resulting the higher flame retardant efficiency of PZMA@APP.

Highly efficient visible-light driven photocatalytic reduction of CO2 over g-C3N4 nanosheets/tetra(4-carboxyphenyl)porphyrin iron(III) chloride heterogeneous catalysts

Photocatalytic reduction of CO2 into value-added chemicals is particularly attractive as it could produce renewable energy and capture greenhouse gas. Photoreduction of CO2 can be realized over molecular and inorganic catalysts. The former usually exhibit high activity, but low stability and often inactive under visible-light irradiation; the latter has low activity, but good stability. Here we use g-C3N4 nanosheets as the photosensitizer to integrate with Fe tetra(4-carboxylphenyl)porphyrin chloride (FeTCPP) molecular catalyst. Besides π-π stacking between tri-s-triazine unit and porphyrin, the carboxyl group modified Fe porphyrin is used for the first time in CO2 photoreduction so as to form hydrogen bonding with the rich amino groups in g-C3N4 nanosheets. g-C3N4/FeTCPP heterogeneous catalysts are prepared via a facile self-assembly approach, in which light harvest is separated from catalysis spatially and temporally. The obtained g-C3N4/FeTCPP heterogeneous catalysts exhibit high activity for CO2 reduction under visible-light irradiation, with CO yield of 6.52mmolg−1 in 6h and selectivity up to 98%. Fluorescence data indicate that the electrons can efficiently transfer from the g-C3N4 nanosheets to FeTCPP. The mechanism for CO2 reduction over the g-C3N4/FeTCPP heterogeneous catalysts is proposed based on the results of quasi in-situ ESR and UV–vis measurements. This work may pave a facile approach for fabricating the high-efficient photocatalysts for CO2 reduction, as well as better understanding the related mechanism.

Cellulose nanocrystal supported superparamagnetic nanorods with aminated silica shell: synthesis and properties

Superparamagnetic nanorods consisting of cellulose nanocrystals (CNCs), ferrosoferric oxide (Fe3O4), and surface-aminated silica (SiO2–NH2) were synthesized for the first time for targeted biomedical applications (i.e., cell imaging). CNCs and Fe3O4 were used as the template and magnetic property provider, respectively. The silica was functionized as magnetite core protector and rich amino group supplier. The synthesized nanorods exhibited a core–shell architecture (i.e., CNCs/Fe3O4 core and aminated silica shell). Due to the coated silica shell, thermal stability of the nanorods was improved with the onset decomposition temperature increased by 135 °C compared with that of the uncoated CNCs. Because of the existence of the positively charged amino groups, the nanorods were easily linked with fluorescent dyes for cell imaging in biomedical applications.

Efficient electrochemical detection of cancer cells on in situ surface-functionalized MoS2nanosheets

In situsurface functionalization by reactant molecules (thiourea) is feasible to engineer MoS2surfaces with rich amino groups, leading to facile antigen immobilization and thus selective recognition of cancer cells.

A study on optimal concentrations of isodiospyrin putative inhibitory actions against exonic splicing enhancers of Dystrophin gene exon 53 skipping in Duchenne Muscular Dystrophy

Event Abstract Back to Event A study on optimal concentrations of isodiospyrin putative inhibitory actions against exonic splicing enhancers of Dystrophin gene exon 53 skipping in Duchenne Muscular Dystrophy Hussain S. Alzahrani1*, Roslina Rashid2, Muzaimi Mustapha1 and Teguh H. Sasongko2 1 Universiti Sains Malaysia, Department of Neuroscience, School of Medical Sciences, Health Campus, Malaysia 2 Universiti Sains Malaysia, Human Genome Center, School of Medical Sciences, Health Campus, Malaysia Duchene muscular dystrophy (DMD) is an X-linked recessive disorder. It is characterized by rapid loss of muscular tissues due lacking gene of muscle replacement. The DMD gene is responsible for Dystrophin protein expression, which exists within a complex called Dystrophin glycol-protein complex (DGC). Exon mutations within DMD gene cause defective expression of Dystrophin. This study aimed to determine the inhibitory actions of Isodiospyrin targeting splicing factors and SR protein (Serine-arginine rich amino acids) a known topoisomerase inhibitor, which plays a critical role in splice site selection. previous studies demonstrated that Isodiospyrin has antitumor activity and inhibits topoisomerase enzyme from phosphorylating SF2/ASF splicing factor. In the current study we used plasmid of non-mutated exon 53 minigenes, transfected into non-mutated HEK-293 cell lines. Then, observed its actions on cells viability and exon splicing modification. The later was confirmed using RT-PCR, followed by exon 53 sequence software analysis. In consistence with previous studies, concentration of half maximal inhibitory effect (IC50) was 3.58µM, and the optimal inhibitory concentrations were: 1.79, 0.90, and 0.60µM. However, there was no detection of exon 53 skipping when exposing non-mutated HEK-293 cells to the optimal concentrations of Isodiospyrin compound. The results suggest that exon 53 splicing may occur without phosphorylation of SR proteins targeted by Isodiospyrin, which indicated that the splicing of exon 53 occurred independently of SR proteins targeted by the splicing inhibitor Isodiospyrin ,in non-mutated HEK-293 cells. Keywords: Gene Expression, inhibition, in vitro, Exon splicing, Duchenne muscular dystrophy Conference: 14th Meeting of the Asian-Pacific Society for Neurochemistry, Kuala Lumpur, Malaysia, 27 Aug - 30 Aug, 2016. Presentation Type: Poster Presentation Session Topic: 14th Meeting of the Asian-Pacific Society for Neurochemistry Citation: Alzahrani HS, Rashid R, Mustapha M and Sasongko TH (2016). A study on optimal concentrations of isodiospyrin putative inhibitory actions against exonic splicing enhancers of Dystrophin gene exon 53 skipping in Duchenne Muscular Dystrophy. Conference Abstract: 14th Meeting of the Asian-Pacific Society for Neurochemistry. doi: 10.3389/conf.fncel.2016.36.00120 Copyright: The abstracts in this collection have not been subject to any Frontiers peer review or checks, and are not endorsed by Frontiers. They are made available through the Frontiers publishing platform as a service to conference organizers and presenters. The copyright in the individual abstracts is owned by the author of each abstract or his/her employer unless otherwise stated. Each abstract, as well as the collection of abstracts, are published under a Creative Commons CC-BY 4.0 (attribution) licence (https://creativecommons.org/licenses/by/4.0/) and may thus be reproduced, translated, adapted and be the subject of derivative works provided the authors and Frontiers are attributed. For Frontiers’ terms and conditions please see https://www.frontiersin.org/legal/terms-and-conditions. Received: 04 Aug 2016; Published Online: 11 Aug 2016. * Correspondence: Mr. Hussain S Alzahrani, Universiti Sains Malaysia, Department of Neuroscience, School of Medical Sciences, Health Campus, Kota Bharu, Kelantan, 16150, Malaysia, hssz_23@hotmail.com Login Required This action requires you to be registered with Frontiers and logged in. To register or login click here. Abstract Info Abstract The Authors in Frontiers Hussain S Alzahrani Roslina Rashid Muzaimi Mustapha Teguh H Sasongko Google Hussain S Alzahrani Roslina Rashid Muzaimi Mustapha Teguh H Sasongko Google Scholar Hussain S Alzahrani Roslina Rashid Muzaimi Mustapha Teguh H Sasongko PubMed Hussain S Alzahrani Roslina Rashid Muzaimi Mustapha Teguh H Sasongko Related Article in Frontiers Google Scholar PubMed Abstract Close Back to top Javascript is disabled. Please enable Javascript in your browser settings in order to see all the content on this page.

Aggregate formation prevents dTDP-43 neurotoxicity in the Drosophila melanogaster eye

TDP-43 inclusions are an important histopathological feature in various neurodegenerative disorders, including Amyotrophic Lateral Sclerosis and Fronto-Temporal Lobar Degeneration. However, the relation of these inclusions with the pathogenesis of the disease is still unclear. In fact, the inclusions could be toxic themselves, induce loss of function by sequestering TDP-43 or a combination of both. Previously, we have developed a cellular model of aggregation using the TDP-43 Q/N rich amino acid sequence 331–369 repeated 12 times (12xQ/N) and have shown that these cellular inclusions are capable of sequestering the endogenous TDP-43 both in non-neuronal and neuronal cells. We have tested this model in vivo in the Drosophila melanogaster eye. The eye structure develops normally in the absence of dTDP-43, a fact previously seen in knock out fly strains. We show here that expression of EGFP 12xQ/N does not alter the structure of the eye. In contrast, TBPH overexpression is neurotoxic and causes necrosis and loss of function of the eye. More important, the neurotoxicity of TBPH can be abolished by its incorporation to the insoluble aggregates induced by EGFP 12xQ/N. This data indicates that aggregation is not toxic per se and instead has a protective role, modulating the functional TBPH available in the tissue. This is an important indication for the possible pathological mechanism in action on ALS patients.

Pollen feeding, resource allocation and the evolution of chemical defence in passion vine butterflies

Evolution of pollen feeding in Heliconius has allowed exploitation of rich amino acid sources and dramatically reorganized life-history traits. In Heliconius, eggs are produced mainly from adult-acquired resources, leaving somatic development and maintenance to larva effort. This innovation may also have spurred evolution of chemical defence via amino acid-derived cyanogenic glycosides. In contrast, nonpollen-feeding heliconiines must rely almost exclusively on larval-acquired resources for both reproduction and defence. We tested whether adult amino acid intake has an immediate influence on cyanogenesis in Heliconius. Because Heliconius are more distasteful to bird predators than close relatives that do not utilize pollen, we also compared cyanogenesis due to larval input across Heliconius species and nonpollen-feeding relatives. Except for one species, we found that varying the amino acid diet of an adult Heliconius has negligible effect on its cyanide concentration. Adults denied amino acids showed no decrease in cyanide and no adults showed cyanide increase when fed amino acids. Yet, pollen-feeding butterflies were capable of producing more defence than nonpollen-feeding relatives and differences were detectable in freshly emerged adults, before input of adult resources. Our data points to a larger role of larval input in adult chemical defence. This coupled with the compartmentalization of adult nutrition to reproduction and longevity suggests that one evolutionary consequence of pollen feeding, shifting the burden of reproduction to adults, is to allow the evolution of greater allocation of host plant amino acids to defensive compounds by larvae.

One-step syntheses and properties of carbon microspheres with amino groups

This paper proposes a method that can be used to synthesize carbon microspheres with controllable sizes, rich amino groups and oxygen-containing groups. The synthesized materials are portrayed by various methods including SEM, FT-IR, XRD, and EDX. The resulting carbon spheres presented an amorphous characteristic, which displayed a broad range in diameter, high degree of sphericity, and smoothness with amino groups and oxygen-containing groups. Pyknotic and smooth silver shells were deposited on carbon spheres by electroless silver plating. Moreover, it could directly reduce Ag+ to Ag in aqueous silver nitrate. These materials can potentially be used as adsorbents for heavy-metal removal from aqueous solutions.

Enhancing CO2adsorption enthalpy and selectivity viaamino functionalization of a tetrahedral framework material

The cooperative assembly of mixed 2-aminoisonicotinate and adeninate ligands with Zn2+ centers generates a porous tetrahedral framework material with rich amino groups in the pores, which shows high CO2 uptake at 0.1 bar, high enthalpy of CO2 adsorption (40 kJ mol−1) and excellent adsorption selectivity of CO2 over N2 under ambient conditions.

Molecular and biological role of the FOXP3 N-terminal domain in immune regulation by T regulatory/suppressor cells

Regulatory T (Treg) cells are essential in preventing the host from developing certain autoimmune diseases and limiting excessive immune responses against pathogens. The normal function of most Treg cells requires sustained expression of functional FOXP3, a member of the FOXP family transcription factors. FOXP3 is distinct from other subfamily members because of its unique proline rich amino (N)-terminal domain. Mutations in this region are occasionally identified in certain patients with X-linked autoimmunity-allergic dysregulation syndrome (XLAAD) and similar mutations also increase susceptibility of autoimmune diseases in rodent models. Previous analyses of the FOXP3 N-terminal domain revealed a role in nuclear import, interaction with other transcription factors, and as sites of specific post-translational modifications of FOXP3 that contribute to FOXP3 stability.

Metabolite profiling of wheat flag leaf and grains during grain filling phase as affected by sulfur fertilisation.

Increasing prices for wheat products and fertilisers call for an adjusted agricultural management to maintain yield and to improve product quality. With the increased use of sulfur-free fertilisers in modern cropping systems and the decrease of atmospheric sulfur emissions by industry, sulfur has become a major limiting factor for crop production. The presented data showed that by using GC-MS it was possible to quantitatively detect a set of 72 different metabolites including amino acids, organic acids, sugars, sugar phosphates, and sugar alcohols, phenolic compounds and nucleotides from wheat grains and flag leaves of a pot experiment. A principal component analysis (PCA) revealed a clear separation of flag leaves and grains and a clear separation of non-fertilised and fertilised flag leaves. It could further be shown by PCA, that the low level sulfur fertilisation is also separated from the higher fertilised grains. A considerable influence of the sulfur fertilisation not only on sulfur rich amino acids but also on the sugar metabolism was detected. With increasing sulfur fertilisation six sugars and sugar derivates in the grain such as glucose-6P, galactose, trehalose, cellobiose, melibiose, fumarate, glycerate and the nucleotide uracil were enhanced. Therefore, it was concluded that photosynthesis was limited in developing plants suffering from sulfur deficiency. Late sulfur fertilisation is a procedure that can help to prevent sulfur deficiency. A latent sulfur deficiency at ear emergence can be compensated by late sulfur fertilisation, as wheat plants can replenish sulfate deficits within a short time.

Characterization and in vitro antioxidation of papain hydrolysate from black-bone silky fowl (Gallus gallus domesticus Brisson) muscle and its fractions

Black-bone silky fowl (Gallus gallus domesticus Brisson) (BSF) muscle was hydrolyzed by papain, and the hydrolysate was separated by preparative high performance liquid chromatography (HPLC). The amino acid composition of the BSF hydrolysate (BSFH) and its fractions was determined by HPLC precolumn derivation with 2,4-dinitrofluorobenzene. The molecular weight (MW) distribution of the BSFH and its fractions was measured by a peptide column on an HPLC system. Antioxidant activities of the BSFH and its fractions were studied by testing the reducing power and four radical scavenging systems: superoxide anion (O2−), hydroxyl (·OH), 1,1-diphenyl-2-picrylhydrazyl (DPPH) and 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS+) radicals. The results demonstrated that the BSFH had strong antioxidant capacity to scavenge O2−, DPPH and ABTS+, and displayed strong reducing power, but revealed less powerful ability to scavenge ·OH. Fraction II of the BSFH exhibited the highest activity in scavenging O2− and DPPH, and reducing power, whereas fraction I displayed the strongest ·OH scavenging ability. Besides Glu, Asp and Gly, the rich amino acids of Ala and Leu played an important role in antioxidant activity. The small-size peptides with MW ranging from approximately 200–6000Da probably contributed to higher antioxidant activity. Results from this study indicated that BSFH and its fractions could be used as food additives and diet nutrients.

Amino acid classification based spectrum kernel fusion for protein subnuclear localization.

BackgroundPrediction of protein localization in subnuclear organelles is more challenging than general protein subcelluar localization. There are only three computational models for protein subnuclear localization thus far, to the best of our knowledge. Two models were based on protein primary sequence only. The first model assumed homogeneous amino acid substitution pattern across all protein sequence residue sites and used BLOSUM62 to encode k-mer of protein sequence. Ensemble of SVM based on different k-mers drew the final conclusion, achieving 50% overall accuracy. The simplified assumption did not exploit protein sequence profile and ignored the fact of heterogeneous amino acid substitution patterns across sites. The second model derived the PsePSSM feature representation from protein sequence by simply averaging the profile PSSM and combined the PseAA feature representation to construct a kNN ensemble classifier Nuc-PLoc, achieving 67.4% overall accuracy. The two models based on protein primary sequence only both achieved relatively poor predictive performance. The third model required that GO annotations be available, thus restricting the model's applicability.MethodsIn this paper, we only use the amino acid information of protein sequence without any other information to design a widely-applicable model for protein subnuclear localization. We use K-spectrum kernel to exploit the contextual information around an amino acid and the conserved motif information. Besides expanding window size, we adopt various amino acid classification approaches to capture diverse aspects of amino acid physiochemical properties. Each amino acid classification generates a series of spectrum kernels based on different window size. Thus, (I) window expansion can capture more contextual information and cover size-varying motifs; (II) various amino acid classifications can exploit multi-aspect biological information from the protein sequence. Finally, we combine all the spectrum kernels by simple addition into one single kernel called SpectrumKernel+ for protein subnuclear localization.ResultsWe conduct the performance evaluation experiments on two benchmark datasets: Lei and Nuc-PLoc. Experimental results show that SpectrumKernel+ achieves substantial performance improvement against the previous model Nuc-PLoc, with overall accuracy 83.47% against 67.4%; and 71.23% against 50% of Lei SVM Ensemble, against 66.50% of Lei GO SVM Ensemble.ConclusionThe method SpectrumKernel+ can exploit rich amino acid information of protein sequence by embedding into implicit size-varying motifs the multi-aspect amino acid physiochemical properties captured by amino acid classification approaches. The kernels derived from diverse amino acid classification approaches and different sizes of k-mer are summed together for data integration. Experiments show that the method SpectrumKernel+ significantly outperforms the existing models for protein subnuclear localization.

Evolutionary advantages of secreted peptide signalling molecules in plants

Peptide signalling molecules create diverse modular signals in animal systems, but it is only relatively recently that an expanding array of peptide signalling groups has been identified in plants. Representatives occur in moss although most are in angiosperms (both monocot and dicot) including many agronomically important crops. Some groups show high diversity within a species, whereas other peptide signalling groups are small or represented by a single peptide or only found in a single family of plants. Plant peptide signals regulate meristem organogenesis and growth, modulate plant homeostasis and growth, and recognise damage or imminent danger from pathogen attack. The peptide signalling molecules are secreted into the apoplast where they are often further proteolytically processed before acting on receptors in nearby or adjacent cells with all the hallmarks of paracrine molecules. Where the receptors have been identified, they are receptor-like kinases that form oligomers upon peptide binding and relay messages via phosphorylation cascades. The use of nitrogen rich amino acids in the signalling peptides was analysed and nitrogen scores were obtained that are higher than the mean nitrogen score for the overall average of the Arabidopsis proteome. These findings are discussed in terms of nutritional availability and energy use.

Probing Enantioselectivity with X-Ray Photoelectron Spectroscopy and Density Functional Theory

The enantioselectivity of gold is investigated by x-ray photoelectron spectroscopy (XPS) and density functional theory (DFT). Cysteine molecules on a chiral Au(17 11 9);{S} surface show enantiospecific core level binding energies in the amino and in the thiol group. The sign and order of magnitude of the XPS core level shifts is reproduced by DFT. Identical preparations of D- and L-cysteine layers lead to D-cysteine molecules in the pure NH2 form, while a small portion of L-cysteine molecules maintains a hydrogen rich amino group (NH3). This implies enantiospecific adsorption reaction pathways and is consistent with DFT that indicates an activated hydrogen abstraction reaction from the amino group, which is downhill for D-cysteine.