Dipeptide frequency/bias analysis identifies conserved sites of nonrandomness shared by cysteine-rich motifs.

PubMed

Campion, S R; Ameen, A S; Lai, L; King, J M; Munzenmaier, T N

2001-08-15

This report describes the application of a simple computational tool, AAPAIR.TAB, for the systematic analysis of the cysteine-rich EGF, Sushi, and Laminin motif/sequence families at the two-amino acid level. Automated dipeptide frequency/bias analysis detects preferences in the distribution of amino acids in established protein families, by determining which "ordered dipeptides" occur most frequently in comprehensive motif-specific sequence data sets. Graphic display of the dipeptide frequency/bias data revealed family-specific preferences for certain dipeptides, but more importantly detected a shared preference for employment of the ordered dipeptides Gly-Tyr (GY) and Gly-Phe (GF) in all three protein families. The dipeptide Asn-Gly (NG) also exhibited high-frequency and bias in the EGF and Sushi motif families, whereas Asn-Thr (NT) was distinguished in the Laminin family. Evaluation of the distribution of dipeptides identified by frequency/bias analysis subsequently revealed the highly restricted localization of the G(F/Y) and N(G/T) sequence elements at two separate sites of extreme conservation in the consensus sequence of all three sequence families. The similar employment of the high-frequency/bias dipeptides in three distinct protein sequence families was further correlated with the concurrence of these shared molecular determinants at similar positions within the distinctive scaffolds of three structurally divergent, but similarly employed, motif modules.

DLocalMotif: a discriminative approach for discovering local motifs in protein sequences.

PubMed

Mehdi, Ahmed M; Sehgal, Muhammad Shoaib B; Kobe, Bostjan; Bailey, Timothy L; Bodén, Mikael

2013-01-01

Local motifs are patterns of DNA or protein sequences that occur within a sequence interval relative to a biologically defined anchor or landmark. Current protein motif discovery methods do not adequately consider such constraints to identify biologically significant motifs that are only weakly over-represented but spatially confined. Using negatives, i.e. sequences known to not contain a local motif, can further increase the specificity of their discovery. This article introduces the method DLocalMotif that makes use of positional information and negative data for local motif discovery in protein sequences. DLocalMotif combines three scoring functions, measuring degrees of motif over-representation, entropy and spatial confinement, specifically designed to discriminatively exploit the availability of negative data. The method is shown to outperform current methods that use only a subset of these motif characteristics. We apply the method to several biological datasets. The analysis of peroxisomal targeting signals uncovers several novel motifs that occur immediately upstream of the dominant peroxisomal targeting signal-1 signal. The analysis of proline-tyrosine nuclear localization signals uncovers multiple novel motifs that overlap with C2H2 zinc finger domains. We also evaluate the method on classical nuclear localization signals and endoplasmic reticulum retention signals and find that DLocalMotif successfully recovers biologically relevant sequence properties. http://bioinf.scmb.uq.edu.au/dlocalmotif/

Comparative Analysis of P450 Signature Motifs EXXR and CXG in the Large and Diverse Kingdom of Fungi: Identification of Evolutionarily Conserved Amino Acid Patterns Characteristic of P450 Family

PubMed Central

Syed, Khajamohiddin; Mashele, Samson Sitheni

2014-01-01

Cytochrome P450 monooxygenases (P450s) are heme-thiolate proteins distributed across the biological kingdoms. P450s are catalytically versatile and play key roles in organisms primary and secondary metabolism. Identification of P450s across the biological kingdoms depends largely on the identification of two P450 signature motifs, EXXR and CXG, in the protein sequence. Once a putative protein has been identified as P450, it will be assigned to a family and subfamily based on the criteria that P450s within a family share more than 40% homology and members of subfamilies share more than 55% homology. However, to date, no evidence has been presented that can distinguish members of a P450 family. Here, for the first time we report the identification of EXXR- and CXG-motifs-based amino acid patterns that are characteristic of the P450 family. Analysis of P450 signature motifs in the under-explored fungal P450s from four different phyla, ascomycota, basidiomycota, zygomycota and chytridiomycota, indicated that the EXXR motif is highly variable and the CXG motif is somewhat variable. The amino acids threonine and leucine are preferred as second and third amino acids in the EXXR motif and proline and glycine are preferred as second and third amino acids in the CXG motif in fungal P450s. Analysis of 67 P450 families from biological kingdoms such as plants, animals, bacteria and fungi showed conservation of a set of amino acid patterns characteristic of a particular P450 family in EXXR and CXG motifs. This suggests that during the divergence of P450 families from a common ancestor these amino acids patterns evolve and are retained in each P450 family as a signature of that family. The role of amino acid patterns characteristic of a P450 family in the structural and/or functional aspects of members of the P450 family is a topic for future research. PMID:24743800

Identification of E-cadherin signature motifs functioning as cleavage sites for Helicobacter pylori HtrA

NASA Astrophysics Data System (ADS)

Schmidt, Thomas P.; Perna, Anna M.; Fugmann, Tim; Böhm, Manja; Jan Hiss; Haller, Sarah; Götz, Camilla; Tegtmeyer, Nicole; Hoy, Benjamin; Rau, Tilman T.; Neri, Dario; Backert, Steffen; Schneider, Gisbert; Wessler, Silja

2016-03-01

The cell adhesion protein and tumour suppressor E-cadherin exhibits important functions in the prevention of gastric cancer. As a class-I carcinogen, Helicobacter pylori (H. pylori) has developed a unique strategy to interfere with E-cadherin functions. In previous studies, we have demonstrated that H. pylori secretes the protease high temperature requirement A (HtrA) which cleaves off the E-cadherin ectodomain (NTF) on epithelial cells. This opens cell-to-cell junctions, allowing bacterial transmigration across the polarised epithelium. Here, we investigated the molecular mechanism of the HtrA-E-cadherin interaction and identified E-cadherin cleavage sites for HtrA. Mass-spectrometry-based proteomics and Edman degradation revealed three signature motifs containing the [VITA]-[VITA]-x-x-D-[DN] sequence pattern, which were preferentially cleaved by HtrA. Based on these sites, we developed a substrate-derived peptide inhibitor that selectively bound and inhibited HtrA, thereby blocking transmigration of H. pylori. The discovery of HtrA-targeted signature sites might further explain why we detected a stable 90 kDa NTF fragment during H. pylori infection, but also additional E-cadherin fragments ranging from 105 kDa to 48 kDa in in vitro cleavage experiments. In conclusion, HtrA targets E-cadherin signature sites that are accessible in in vitro reactions, but might be partially masked on epithelial cells through functional homophilic E-cadherin interactions.

Nucleophosmin integrates within the nucleolus via multi-modal interactions with proteins displaying R-rich linear motifs and rRNA.

PubMed

Mitrea, Diana M; Cika, Jaclyn A; Guy, Clifford S; Ban, David; Banerjee, Priya R; Stanley, Christopher B; Nourse, Amanda; Deniz, Ashok A; Kriwacki, Richard W

2016-02-02

The nucleolus is a membrane-less organelle formed through liquid-liquid phase separation of its components from the surrounding nucleoplasm. Here, we show that nucleophosmin (NPM1) integrates within the nucleolus via a multi-modal mechanism involving multivalent interactions with proteins containing arginine-rich linear motifs (R-motifs) and ribosomal RNA (rRNA). Importantly, these R-motifs are found in canonical nucleolar localization signals. Based on a novel combination of biophysical approaches, we propose a model for the molecular organization within liquid-like droplets formed by the N-terminal domain of NPM1 and R-motif peptides, thus providing insights into the structural organization of the nucleolus. We identify multivalency of acidic tracts and folded nucleic acid binding domains, mediated by N-terminal domain oligomerization, as structural features required for phase separation of NPM1 with other nucleolar components in vitro and for localization within mammalian nucleoli. We propose that one mechanism of nucleolar localization involves phase separation of proteins within the nucleolus.

Evolution of the Ferric Reductase Domain (FRD) Superfamily: Modularity, Functional Diversification, and Signature Motifs

PubMed Central

Zhang, Xuezhi; Krause, Karl-Heinz; Xenarios, Ioannis; Soldati, Thierry; Boeckmann, Brigitte

2013-01-01

A heme-containing transmembrane ferric reductase domain (FRD) is found in bacterial and eukaryotic protein families, including ferric reductases (FRE), and NADPH oxidases (NOX). The aim of this study was to understand the phylogeny of the FRD superfamily. Bacteria contain FRD proteins consisting only of the ferric reductase domain, such as YedZ and short bFRE proteins. Full length FRE and NOX enzymes are mostly found in eukaryotic cells and all possess a dehydrogenase domain, allowing them to catalyze electron transfer from cytosolic NADPH to extracellular metal ions (FRE) or oxygen (NOX). Metazoa possess YedZ-related STEAP proteins, possibly derived from bacteria through horizontal gene transfer. Phylogenetic analyses suggests that FRE enzymes appeared early in evolution, followed by a transition towards EF-hand containing NOX enzymes (NOX5- and DUOX-like). An ancestral gene of the NOX(1-4) family probably lost the EF-hands and new regulatory mechanisms of increasing complexity evolved in this clade. Two signature motifs were identified: NOX enzymes are distinguished from FRE enzymes through a four amino acid motif spanning from transmembrane domain 3 (TM3) to TM4, and YedZ/STEAP proteins are identified by the replacement of the first canonical heme-spanning histidine by a highly conserved arginine. The FRD superfamily most likely originated in bacteria. PMID:23505460

Evolution of the ferric reductase domain (FRD) superfamily: modularity, functional diversification, and signature motifs.

PubMed

Zhang, Xuezhi; Krause, Karl-Heinz; Xenarios, Ioannis; Soldati, Thierry; Boeckmann, Brigitte

2013-01-01

A heme-containing transmembrane ferric reductase domain (FRD) is found in bacterial and eukaryotic protein families, including ferric reductases (FRE), and NADPH oxidases (NOX). The aim of this study was to understand the phylogeny of the FRD superfamily. Bacteria contain FRD proteins consisting only of the ferric reductase domain, such as YedZ and short bFRE proteins. Full length FRE and NOX enzymes are mostly found in eukaryotic cells and all possess a dehydrogenase domain, allowing them to catalyze electron transfer from cytosolic NADPH to extracellular metal ions (FRE) or oxygen (NOX). Metazoa possess YedZ-related STEAP proteins, possibly derived from bacteria through horizontal gene transfer. Phylogenetic analyses suggests that FRE enzymes appeared early in evolution, followed by a transition towards EF-hand containing NOX enzymes (NOX5- and DUOX-like). An ancestral gene of the NOX(1-4) family probably lost the EF-hands and new regulatory mechanisms of increasing complexity evolved in this clade. Two signature motifs were identified: NOX enzymes are distinguished from FRE enzymes through a four amino acid motif spanning from transmembrane domain 3 (TM3) to TM4, and YedZ/STEAP proteins are identified by the replacement of the first canonical heme-spanning histidine by a highly conserved arginine. The FRD superfamily most likely originated in bacteria.

Tests for coronal electron temperature signatures in suprathermal electron populations at 1 AU

NASA Astrophysics Data System (ADS)

Macneil, Allan R.; Owen, Christopher J.; Wicks, Robert T.

2017-12-01

The development of knowledge of how the coronal origin of the solar wind affects its in situ properties is one of the keys to understanding the relationship between the Sun and the heliosphere. In this paper, we analyse ACE/SWICS and WIND/3DP data spanning > 12 years, and test properties of solar wind suprathermal electron distributions for the presence of signatures of the coronal temperature at their origin which may remain at 1 AU. In particular we re-examine a previous suggestion that these properties correlate with the oxygen charge state ratio O7+ / O6+, an established proxy for coronal electron temperature. We find only a very weak but variable correlation between measures of suprathermal electron energy content and O7+ / O6+. The weak nature of the correlation leads us to conclude, in contrast to earlier results, that an initial relationship with core electron temperature has the possibility to exist in the corona, but that in most cases no strong signatures remain in the suprathermal electron distributions at 1 AU. It cannot yet be confirmed whether this is due to the effects of coronal conditions on the establishment of this relationship or due to the altering of the electron distributions by processing during transport in the solar wind en route to 1 AU. Contrasting results for the halo and strahl population favours the latter interpretation. Confirmation of this will be possible using Solar Orbiter data (cruise and nominal mission phase) to test whether the weakness of the relationship persists over a range of heliocentric distances. If the correlation is found to strengthen when closer to the Sun, then this would indicate an initial relationship which is being degraded, perhaps by wave-particle interactions, en route to the observer.

Structural polymorphism of a cytosine-rich DNA sequence forming i-motif structure: Exploring pH based biosensors.

PubMed

Ahmed, Saami; Kaushik, Mahima; Chaudhary, Swati; Kukreti, Shrikant

2018-05-01

Sequence recognition and conformational polymorphism enable DNA to emerge out as a substantial tool in fabricating the devices within nano-dimensions. These DNA associated nano devices work on the principle of conformational switches, which can be facilitated by many factors like sequence of DNA/RNA strand, change in pH or temperature, enzyme or ligand interactions etc. Thus, controlling these DNA conformational changes to acquire the desired function is significant for evolving DNA hybridization biosensor, used in genetic screening and molecular diagnosis. For exploring this conformational switching ability of cytosine-rich DNA oligonucleotides as a function of pH for their potential usage as biosensors, this study has been designed. A C-rich stretch of DNA sequence (5'-TCCCCCAATTAATTCCCCCA-3'; SG20c) has been investigated using UV-Thermal denaturation, poly-acrylamide gel electrophoresis and CD spectroscopy. The SG20c sequence is shown to adopt various topologies of i-motif structure at low pH. This pH dependent transition of SG20c from unstructured single strand to unimolecular and bimolecular i-motif structures can further be exploited for its utilization as switching on/off pH-based biosensors. Copyright © 2018. Published by Elsevier B.V.

Nucleophosmin integrates within the nucleolus via multi-modal interactions with proteins displaying R-rich linear motifs and rRNA

PubMed Central

Mitrea, Diana M; Cika, Jaclyn A; Guy, Clifford S; Ban, David; Banerjee, Priya R; Stanley, Christopher B; Nourse, Amanda; Deniz, Ashok A; Kriwacki, Richard W

2016-01-01

The nucleolus is a membrane-less organelle formed through liquid-liquid phase separation of its components from the surrounding nucleoplasm. Here, we show that nucleophosmin (NPM1) integrates within the nucleolus via a multi-modal mechanism involving multivalent interactions with proteins containing arginine-rich linear motifs (R-motifs) and ribosomal RNA (rRNA). Importantly, these R-motifs are found in canonical nucleolar localization signals. Based on a novel combination of biophysical approaches, we propose a model for the molecular organization within liquid-like droplets formed by the N-terminal domain of NPM1 and R-motif peptides, thus providing insights into the structural organization of the nucleolus. We identify multivalency of acidic tracts and folded nucleic acid binding domains, mediated by N-terminal domain oligomerization, as structural features required for phase separation of NPM1 with other nucleolar components in vitro and for localization within mammalian nucleoli. We propose that one mechanism of nucleolar localization involves phase separation of proteins within the nucleolus. DOI: http://dx.doi.org/10.7554/eLife.13571.001 PMID:26836305

Nucleophosmin integrates within the nucleolus via multi-modal interactions with proteins displaying R-rich linear motifs and rRNA

DOE PAGES

Mitrea, Diana M.; Cika, Jaclyn A.; Guy, Clifford S.; ...

2016-02-02

In this study, the nucleolus is a membrane-less organelle formed through liquid-liquid phase separation of its components from the surrounding nucleoplasm. Here, we show that nucleophosmin (NPM1) integrates within the nucleolus via a multi-modal mechanism involving multivalent interactions with proteins containing arginine-rich linear motifs (R-motifs) and ribosomal RNA (rRNA). Importantly, these R-motifs are found in canonical nucleolar localization signals. Based on a novel combination of biophysical approaches, we propose a model for the molecular organization within liquid-like droplets formed by the N-terminal domain of NPM1 and R-motif peptides, thus providing insights into the structural organization of the nucleolus. We identifymore » multivalency of acidic tracts and folded nucleic acid binding domains, mediated by N-terminal domain oligomerization, as structural features required for phase separation of NPM1 with other nucleolar components in vitro and for localization within mammalian nucleoli. We propose that one mechanism of nucleolar localization involves phase separation of proteins within the nucleolus.« less

Hybrid DNA i-motif: Aminoethylprolyl-PNA (pC5) enhance the stability of DNA (dC5) i-motif structure.

PubMed

Gade, Chandrasekhar Reddy; Sharma, Nagendra K

2017-12-15

This report describes the synthesis of C-rich sequence, cytosine pentamer, of aep-PNA and its biophysical studies for the formation of hybrid DNA:aep-PNAi-motif structure with DNA cytosine pentamer (dC 5 ) under acidic pH conditions. Herein, the CD/UV/NMR/ESI-Mass studies strongly support the formation of stable hybrid DNA i-motif structure with aep-PNA even near acidic conditions. Hence aep-PNA C-rich sequence cytosine could be considered as potential DNA i-motif stabilizing agents in vivo conditions. Copyright © 2017 Elsevier Ltd. All rights reserved.

MDD-carb: a combinatorial model for the identification of protein carbonylation sites with substrate motifs.

PubMed

Kao, Hui-Ju; Weng, Shun-Long; Huang, Kai-Yao; Kaunang, Fergie Joanda; Hsu, Justin Bo-Kai; Huang, Chien-Hsun; Lee, Tzong-Yi

2017-12-21

Carbonylation, which takes place through oxidation of reactive oxygen species (ROS) on specific residues, is an irreversibly oxidative modification of proteins. It has been reported that the carbonylation is related to a number of metabolic or aging diseases including diabetes, chronic lung disease, Parkinson's disease, and Alzheimer's disease. Due to the lack of computational methods dedicated to exploring motif signatures of protein carbonylation sites, we were motivated to exploit an iterative statistical method to characterize and identify carbonylated sites with motif signatures. By manually curating experimental data from research articles, we obtained 332, 144, 135, and 140 verified substrate sites for K (lysine), R (arginine), T (threonine), and P (proline) residues, respectively, from 241 carbonylated proteins. In order to examine the informative attributes for classifying between carbonylated and non-carbonylated sites, multifarious features including composition of twenty amino acids (AAC), composition of amino acid pairs (AAPC), position-specific scoring matrix (PSSM), and positional weighted matrix (PWM) were investigated in this study. Additionally, in an attempt to explore the motif signatures of carbonylation sites, an iterative statistical method was adopted to detect statistically significant dependencies of amino acid compositions between specific positions around substrate sites. Profile hidden Markov model (HMM) was then utilized to train a predictive model from each motif signature. Moreover, based on the method of support vector machine (SVM), we adopted it to construct an integrative model by combining the values of bit scores obtained from profile HMMs. The combinatorial model could provide an enhanced performance with evenly predictive sensitivity and specificity in the evaluation of cross-validation and independent testing. This study provides a new scheme for exploring potential motif signatures at substrate sites of protein

A R/K-rich motif in the C-terminal of the homeodomain is required for complete translocating of NKX2.5 protein into nucleus.

PubMed

Ouyang, Ping; Zhang, He; Fan, Zhaolan; Wei, Pei; Huang, Zhigang; Wang, Sen; Li, Tao

2016-11-05

NKX2.5 plays important roles in heart development. Being a transcription factor, NKX2.5 exerts its biological functions in nucleus. However, the sequence motif that localize NKX2.5 into nucleus is still not clear. Here, we found a R/K-rich sequence motif from Q187 to R197 (QNRRYKCKRQR) was required for exclusive nuclear localization of NKX2.5. Eight truncated plasmids (E109X, Q149X, Q170X, Q187X, Q198X, Y256X, Y259X, and C264X) which were associated with congenital heart disease (CHD) were constructed. Compared with the wild type NKX2.5, the proteins E109X, Q149X, Q170X, Q187X without intact homeodomain (HD) showed no transcriptional activity while Q198X, Y256X, Y259X and C264X with intact HD showed 50 to 66% transcriptional activity. E109X, Q149X, Q170X, Q187X without intact HD localized in the cytoplasm and nucleus simultaneously and Q198X, Y256X, Y259X and C264X with intact HD localized completely in nucleus. These results inferred the indispensability of 187QNRRYKCKRQR197 in exclusive nucleus localization. Additionally, this sequence motif was very conservative among human, mouse and rat, indicating this motif was important for NKX2.5 function. Thus, we concluded that R/K-rich sequence motif 187QNRRYKCKRQR197 played a central role for NKX2.5 nuclear localization. Our findings provided a clue to understand the mechanisms between the truncated NKX2.5 mutants and CHD. Copyright © 2016 Elsevier B.V. All rights reserved.

RNA Helicase Associated with AU-rich Element (RHAU/DHX36) Interacts with the 3′-Tail of the Long Non-coding RNA BC200 (BCYRN1)*

PubMed Central

Booy, Evan P.; McRae, Ewan K. S.; Howard, Ryan; Deo, Soumya R.; Ariyo, Emmanuel O.; Dzananovic, Edis; Meier, Markus; Stetefeld, Jörg; McKenna, Sean A.

2016-01-01

RNA helicase associated with AU-rich element (RHAU) is an ATP-dependent RNA helicase that demonstrates high affinity for quadruplex structures in DNA and RNA. To elucidate the significance of these quadruplex-RHAU interactions, we have performed RNA co-immunoprecipitation screens to identify novel RNAs bound to RHAU and characterize their function. In the course of this study, we have identified the non-coding RNA BC200 (BCYRN1) as specifically enriched upon RHAU immunoprecipitation. Although BC200 does not adopt a quadruplex structure and does not bind the quadruplex-interacting motif of RHAU, it has direct affinity for RHAU in vitro. Specifically designed BC200 truncations and RNase footprinting assays demonstrate that RHAU binds to an adenosine-rich region near the 3′-end of the RNA. RHAU truncations support binding that is dependent upon a region within the C terminus and is specific to RHAU isoform 1. Tests performed to assess whether BC200 interferes with RHAU helicase activity have demonstrated the ability of BC200 to act as an acceptor of unwound quadruplexes via a cytosine-rich region near the 3′-end of the RNA. Furthermore, an interaction between BC200 and the quadruplex-containing telomerase RNA was confirmed by pull-down assays of the endogenous RNAs. This leads to the possibility that RHAU may direct BC200 to bind and exert regulatory functions at quadruplex-containing RNA or DNA sequences. PMID:26740632

Discovering Sequence Motifs with Arbitrary Insertions and Deletions

PubMed Central

Frith, Martin C.; Saunders, Neil F. W.; Kobe, Bostjan; Bailey, Timothy L.

2008-01-01

Biology is encoded in molecular sequences: deciphering this encoding remains a grand scientific challenge. Functional regions of DNA, RNA, and protein sequences often exhibit characteristic but subtle motifs; thus, computational discovery of motifs in sequences is a fundamental and much-studied problem. However, most current algorithms do not allow for insertions or deletions (indels) within motifs, and the few that do have other limitations. We present a method, GLAM2 (Gapped Local Alignment of Motifs), for discovering motifs allowing indels in a fully general manner, and a companion method GLAM2SCAN for searching sequence databases using such motifs. glam2 is a generalization of the gapless Gibbs sampling algorithm. It re-discovers variable-width protein motifs from the PROSITE database significantly more accurately than the alternative methods PRATT and SAM-T2K. Furthermore, it usefully refines protein motifs from the ELM database: in some cases, the refined motifs make orders of magnitude fewer overpredictions than the original ELM regular expressions. GLAM2 performs respectably on the BAliBASE multiple alignment benchmark, and may be superior to leading multiple alignment methods for “motif-like” alignments with N- and C-terminal extensions. Finally, we demonstrate the use of GLAM2 to discover protein kinase substrate motifs and a gapped DNA motif for the LIM-only transcriptional regulatory complex: using GLAM2SCAN, we identify promising targets for the latter. GLAM2 is especially promising for short protein motifs, and it should improve our ability to identify the protein cleavage sites, interaction sites, post-translational modification attachment sites, etc., that underlie much of biology. It may be equally useful for arbitrarily gapped motifs in DNA and RNA, although fewer examples of such motifs are known at present. GLAM2 is public domain software, available for download at http://bioinformatics.org.au/glam2. PMID:18437229

HK022 Nun Requires Arginine-Rich Motif Residues Distinct from λ N

PubMed Central

Tawk, Caroline S.; Ghattas, Ingrid R.

2015-01-01

ABSTRACT Bacteriophage λ N protein binds boxB RNA hairpins in the nut (N utilization) sites of immediate early λ transcripts and interacts with host factors to suppress transcriptional termination at downstream terminators. In opposition to λ N, the Nun protein of HK022 binds the boxBs of coinfecting λ transcripts, interacts with a similar or identical set of host factors, and terminates transcription to suppress λ replication. Comparison of N-boxB and Nun-boxB nuclear magnetic resonance (NMR) structural models suggests similar interactions, though limited mutagenesis of Nun is available. Here, libraries of Nun's arginine-rich motif (ARM) were screened for the ability to exclude λ coinfection, and mutants were assayed for Nun termination with a boxB plasmid reporter system. Several Nun ARM residues appear to be immutable: Asp26, Arg28, Arg29, Arg32, Trp33, and Arg36. Asp26 and Trp33 appear to be unable to contact boxB and are not found at equivalent positions in λ N ARM. To understand if the requirement of Asp26, Trp33, and Arg36 indicated differences between HK022 Nun termination and λ N antitermination complexes, the same Nun libraries were fused to the activation domain of λ N and screened for clones able to complement N-deficient λ. Mutants were assayed for N antitermination. Surprisingly, Asp26 and Trp33 were still essential when Nun ARM was fused to N. Docking suggests that Nun ARM contacts a hydrophobic surface of the NusG carboxy-terminal domain containing residues necessary for Nun function. These findings indicate that Nun ARM relies on distinct contacts in its ternary complex and illustrate how protein-RNA recognition can evolve new regulatory functions. IMPORTANCE λ N protein interacts with host factors to allow λ nut-containing transcripts to elongate past termination signals. A competing bacteriophage, HK022, expresses Nun protein, which causes termination of λ nut transcripts. λ N and HK022 Nun use similar arginine-rich motifs (ARMs) to

HK022 Nun Requires Arginine-Rich Motif Residues Distinct from λ N.

PubMed

Tawk, Caroline S; Ghattas, Ingrid R; Smith, Colin A

2015-11-01

Bacteriophage λ N protein binds boxB RNA hairpins in the nut (N utilization) sites of immediate early λ transcripts and interacts with host factors to suppress transcriptional termination at downstream terminators. In opposition to λ N, the Nun protein of HK022 binds the boxBs of coinfecting λ transcripts, interacts with a similar or identical set of host factors, and terminates transcription to suppress λ replication. Comparison of N-boxB and Nun-boxB nuclear magnetic resonance (NMR) structural models suggests similar interactions, though limited mutagenesis of Nun is available. Here, libraries of Nun's arginine-rich motif (ARM) were screened for the ability to exclude λ coinfection, and mutants were assayed for Nun termination with a boxB plasmid reporter system. Several Nun ARM residues appear to be immutable: Asp26, Arg28, Arg29, Arg32, Trp33, and Arg36. Asp26 and Trp33 appear to be unable to contact boxB and are not found at equivalent positions in λ N ARM. To understand if the requirement of Asp26, Trp33, and Arg36 indicated differences between HK022 Nun termination and λ N antitermination complexes, the same Nun libraries were fused to the activation domain of λ N and screened for clones able to complement N-deficient λ. Mutants were assayed for N antitermination. Surprisingly, Asp26 and Trp33 were still essential when Nun ARM was fused to N. Docking suggests that Nun ARM contacts a hydrophobic surface of the NusG carboxy-terminal domain containing residues necessary for Nun function. These findings indicate that Nun ARM relies on distinct contacts in its ternary complex and illustrate how protein-RNA recognition can evolve new regulatory functions. λ N protein interacts with host factors to allow λ nut-containing transcripts to elongate past termination signals. A competing bacteriophage, HK022, expresses Nun protein, which causes termination of λ nut transcripts. λ N and HK022 Nun use similar arginine-rich motifs (ARMs) to bind the same box

Gold enrichment and the Bi-Au association in pyrrhotite-rich massive sulfide deposits, Escanaba trough, Southern Gorda Ridge

USGS Publications Warehouse

Tormanen, T.O.; Koski, R.A.

2005-01-01

High gold contents (to 10.1 ppm, avg 1.4 ppm, n = 34) occur in pyrrhotite-rich massive sulfide samples from the sediment-covered floor of the Escanaba trough, the slow-spreading, southernmost segment of Gorda Ridge. These concentrations reflect the presence of primary gold, formed during high-temperature hydrothermal activity in mounds and chimneys, and secondary gold deposited during sea-floor weathering of massive sulfide. Primary gold occurs as fine-grained (2 ??m) secondary gold grains have a porous, flaky morphology and occur in samples in which pyrrhotite is oxidized and replaced by Fe oxyhydroxides, Fe sulfate, and sulfur. Mounds and chimneys dominated by pyrrhotite and containing lesser amounts of isocubanite, chalcopyrite, and Fe-rich sphalerite were formed by high-temperature (estimated range 325??-275??C), reduced, low-sulfur vent fluids. The mineral and fluid compositions during this main stage of hydrothermal venting reflect subsurface interaction between circulating hydrothermal fluids and turbiditic sediment containing as much as 1.1 percent organic carbon. As the deposition of pyrrhotite, Cu-Fe sulfides, and sphalerite waned, a volumetrically minor suite of sulfarsenide, arsenide, Bi, and Au minerals was deposited from highly reduced, late main-stage fluids diffusing through mounds and chimneys. The low solubility of Au as a bisulfide complex and the absence of fluid mixing during this stage of hydrothermal activity apparently inhibited the precipitation of gold directly from solution. Instead, gold precipitation is thought to be linked to elevated concentrations of Bi in the late main-stage fluids. The textural relationships of Au and Bi minerals in pyrrhotite-rich samples, low melting point of native bismuth (271.4??C), and recent experimental results on Au and Bi in hydrothermal fluids contribute to the hypothesis that gold was effectively scavenged from the Escanaba trough vent fluids by coexisting droplets of liquid bismuth. Additional phase

Stable and Efficient CuO Based Photocathode through Oxygen-Rich Composition and Au-Pd Nanostructure Incorporation for Solar-Hydrogen Production.

PubMed

Masudy-Panah, Saeid; Siavash Moakhar, Roozbeh; Chua, Chin Sheng; Kushwaha, Ajay; Dalapati, Goutam Kumar

2017-08-23

Enhancing stability against photocorrosion and improving photocurrent response are the main challenges toward the development of cupric oxide (CuO) based photocathodes for solar-driven hydrogen production. In this paper, stable and efficient CuO-photocathodes have been developed using in situ materials engineering and through gold-palladium (Au-Pd) nanoparticles deposition on the CuO surface. The CuO photocathode exhibits a photocurrent generation of ∼3 mA/cm 2 at 0 V v/s RHE. Time-of-flight secondary ion mass spectrometry (TOF-SIMS) analysis and X-ray spectroscopy (XPS) confirm the formation of oxygen-rich (O-rich) CuO film which demonstrates a highly stable photocathode with retained photocurrent of ∼90% for 20 min. The influence of chemical composition on the photocathode performance and stability has been discussed in detail. In addition, O-rich CuO photocathodes deposited with Au-Pd nanostructures have shown enhanced photoelectrochemical performance. Linear scan voltammetry characteristic shows ∼25% enhancement in photocurrent after Au-Pd deposition and reaches ∼4 mA/cm 2 at "0" V v/s RHE. Hydrogen evolution rate significantly depends on the elemental composition of CuO and metal nanostructure. The present work has demonstrated a stable photocathode with high photocurrent for visible-light-driven water splitting and hydrogen production.

Thermodynamic contribution of backbone conformational entropy in the binding between SH3 domain and proline-rich motif.

PubMed

Zeng, Danyun; Shen, Qingliang; Cho, Jae-Hyun

2017-02-26

Biological functions of intrinsically disordered proteins (IDPs), and proteins containing intrinsically disordered regions (IDRs) are often mediated by short linear motifs, like proline-rich motifs (PRMs). Upon binding to their target proteins, IDPs undergo a disorder-to-order transition which is accompanied by a large conformational entropy penalty. Hence, the molecular mechanisms underlying control of conformational entropy are critical for understanding the binding affinity and selectivity of IDPs-mediated protein-protein interactions (PPIs). Here, we investigated the backbone conformational entropy change accompanied by binding of the N-terminal SH3 domain (nSH3) of CrkII and PRM derived from guanine nucleotide exchange factor 1 (C3G). In particular, we focused on the estimation of conformational entropy change of disordered PRM upon binding to the nSH3 domain. Quantitative characterization of conformational dynamics of disordered peptides like PRMs is limited. Hence, we combined various methods, including NMR model-free analysis, δ2D, DynaMine, and structure-based calculation of entropy loss. This study demonstrates that the contribution of backbone conformational entropy change is significant in the PPIs mediated by IDPs/IDRs. Copyright © 2017 Elsevier Inc. All rights reserved.

Automated Recognition of RNA Structure Motifs by Their SHAPE Data Signatures.

PubMed

Radecki, Pierce; Ledda, Mirko; Aviran, Sharon

2018-06-14

High-throughput structure profiling (SP) experiments that provide information at nucleotide resolution are revolutionizing our ability to study RNA structures. Of particular interest are RNA elements whose underlying structures are necessary for their biological functions. We previously introduced patteRNA , an algorithm for rapidly mining SP data for patterns characteristic of such motifs. This work provided a proof-of-concept for the detection of motifs and the capability of distinguishing structures displaying pronounced conformational changes. Here, we describe several improvements and automation routines to patteRNA . We then consider more elaborate biological situations starting with the comparison or integration of results from searches for distinct motifs and across datasets. To facilitate such analyses, we characterize patteRNA ’s outputs and describe a normalization framework that regularizes results. We then demonstrate that our algorithm successfully discerns between highly similar structural variants of the human immunodeficiency virus type 1 (HIV-1) Rev response element (RRE) and readily identifies its exact location in whole-genome structure profiles of HIV-1. This work highlights the breadth of information that can be gleaned from SP data and broadens the utility of data-driven methods as tools for the detection of novel RNA elements.

Controlling the stereochemistry and regularity of butanethiol self-assembled monolayers on au(111).

PubMed

Yan, Jiawei; Ouyang, Runhai; Jensen, Palle S; Ascic, Erhad; Tanner, David; Mao, Bingwei; Zhang, Jingdong; Tang, Chunguang; Hush, Noel S; Ulstrup, Jens; Reimers, Jeffrey R

2014-12-10

The rich stereochemistry of the self-assembled monolayers (SAMs) of four butanethiols on Au(111) is described, the SAMs containing up to 12 individual C, S, or Au chiral centers per surface unit cell. This is facilitated by synthesis of enantiomerically pure 2-butanethiol (the smallest unsubstituted chiral alkanethiol), followed by in situ scanning tunneling microscopy (STM) imaging combined with density functional theory molecular dynamics STM image simulations. Even though butanethiol SAMs manifest strong headgroup interactions, steric interactions are shown to dominate SAM structure and chirality. Indeed, steric interactions are shown to dictate the nature of the headgroup itself, whether it takes on the adatom-bound motif RS(•)Au(0)S(•)R or involves direct binding of RS(•) to face-centered-cubic or hexagonal-close-packed sites. Binding as RS(•) produces large, organizationally chiral domains even when R is achiral, while adatom binding leads to rectangular plane groups that suppress long-range expression of chirality. Binding as RS(•) also inhibits the pitting intrinsically associated with adatom binding, desirably producing more regularly structured SAMs.

Perspectives on the energy landscape of Au-Cl binary systems from the structural phase diagram of AuxCly (x + y = 20).

PubMed

Tian, Zhimei; Cheng, Longjiu

2015-05-28

Ligand-protected gold (Au-L) nanoclusters have attracted much attention, where the reported electronic and geometric structures show great diversity. To give a direct and overall view of the energy landscape of Au-L binary systems, the AuxCly (x + y = 20) system is taken as a test case. By intensive global search of the potential energy surface at the level of density functional theory, a diverse set of global minima and low-lying isomers are found at each composition, and the structural phase diagram is obtained. The unbiased global search is carried out using the method combining the genetic algorithm with the TPSS functional. At x = 10 with the stoichiometric ratio of Au and Cl (1 : 1), the cluster presents a catenane structure. When x is in the range of 11-20, the clusters are Au-rich, and the Au-Cl system can be viewed as Cl-protected gold nanoclusters, where the gold cores consist of superatoms, superatom networks, or superatomic molecules in electronic structures. At x = 11-15, the gold cores consist of Au3, Au4 and Au5 2e-superatoms protected by staple motifs. At x = 16-20, the clusters are pyramidal superatomic molecules with one Au16 superatom core bonding with the four vertical atoms (Au or Cl). When x is in the scope of 9-5, the clusters are Cl-rich, and the 5d electrons of Au participate in bonding, resulting in high multiplicities. The Au-Cl binary system shows great diversity and flexibility in electronic and geometric structures, and there are corresponding structures to most of the experimentally produced Au-L nanoclusters in our structural phase diagram. We believe that the structural phase diagram gives an overall perspective on the universe of Au-L nanoclusters.

The combinatorial PP1-binding consensus Motif (R/K)x( (0,1))V/IxFxx(R/K)x(R/K) is a new apoptotic signature.

PubMed

Godet, Angélique N; Guergnon, Julien; Maire, Virginie; Croset, Amélie; Garcia, Alphonse

2010-04-01

Previous studies established that PP1 is a target for Bcl-2 proteins and an important regulator of apoptosis. The two distinct functional PP1 consensus docking motifs, R/Kx((0,1))V/IxF and FxxR/KxR/K, involved in PP1 binding and cell death were previously characterized in the BH1 and BH3 domains of some Bcl-2 proteins. In this study, we demonstrate that DPT-AIF(1), a peptide containing the AIF(562-571) sequence located in a c-terminal domain of AIF, is a new PP1 interacting and cell penetrating molecule. We also showed that DPT-AIF(1) provoked apoptosis in several human cell lines. Furthermore, DPT-APAF(1) a bi-partite cell penetrating peptide containing APAF-1(122-131), a non penetrating sequence from APAF-1 protein, linked to our previously described DPT-sh1 peptide shuttle, is also a PP1-interacting death molecule. Both AIF(562-571) and APAF-1(122-131) sequences contain a common R/Kx((0,1))V/IxFxxR/KxR/K motif, shared by several proteins involved in control of cell survival pathways. This motif combines the two distinct PP1c consensus docking motifs initially identified in some Bcl-2 proteins. Interestingly DPT-AIF(2) and DPT-APAF(2) that carry a F to A mutation within this combinatorial motif, no longer exhibited any PP1c binding or apoptotic effects. Moreover the F to A mutation in DPT-AIF(2) also suppressed cell penetration. These results indicate that the combinatorial PP1c docking motif R/Kx((0,1))V/IxFxxR/KxR/K, deduced from AIF(562-571) and APAF-1(122-131) sequences, is a new PP1c-dependent Apoptotic Signature. This motif is also a new tool for drug design that could be used to characterize potential anti-tumour molecules.

Ratiometric fluorescent sensing of pH values in living cells by dual-fluorophore-labeled i-motif nanoprobes.

PubMed

Huang, Jin; Ying, Le; Yang, Xiaohai; Yang, Yanjing; Quan, Ke; Wang, He; Xie, Nuli; Ou, Min; Zhou, Qifeng; Wang, Kemin

2015-09-01

We designed a new ratiometric fluorescent nanoprobe for sensing pH values in living cells. Briefly, the nanoprobe consists of a gold nanoparticle (AuNP), short single-stranded oligonucleotides, and dual-fluorophore-labeled i-motif sequences. The short oligonucleotides are designed to bind with the i-motif sequences and immobilized on the AuNP surface via Au-S bond. At neutral pH, the dual fluorophores are separated, resulting in very low fluorescence resonance energy transfer (FRET) efficiency. At acidic pH, the i-motif strands fold into a quadruplex structure and leave the AuNP, bringing the dual fluorophores into close proximity, resulting in high FRET efficiency, which could be used as a signal for pH sensing. The nanoprobe possesses abilities of cellular transfection, enzymatic protection, fast response and quantitative pH detection. The in vitro and intracellular applications of the nanoprobe were demonstrated, which showed excellent response in the physiological pH range. Furthermore, our experimental results suggested that the nanoprobe showed excellent spatial and temporal resolution in living cells. We think that the ratiometric sensing strategy could potentially be applied to create a variety of new multicolor sensors for intracellular detection.

Origin of Zn-Pb-Sb-Au mineralization adjacent to the Paleoproterozoic Boliden Au-rich VMS deposit, Sweden: evidence from petrographic and oxygen isotope characteristics

NASA Astrophysics Data System (ADS)

Adomako-Ansah, Kofi; Ishiyama, Daizo; Allen, Rodney

2018-06-01

Adjacent to the world-class Boliden deposit, fine- to coarse-grained Zn-Pb-Sb-Au-rich sulfide-sulfosalt-bearing horizons occur within the base of a metasedimentary succession that has previously been regarded to stratigraphically overlie the Skellefte Volcanics and Boliden deposit. The metasedimentary succession comprises interbedded mudstone and normal-graded crystal-rich volcanic sandstone-siltstone units, interpreted to be low-density turbidity currents in a subaqueous environment below wave base. The sharp contact between the mineralized intervals and volcanic sandstone is concordant to the bedding planes and compaction foliation. Above and below the mineralization, the wall rocks contain well-preserved plagioclase crystals, partly enclosed by a weak alteration composed of bedding-parallel metamorphic biotite±sericite minerals. These observations are consistent with burial (or tectonic) compaction and diagenetic alteration that was overprinted by metamorphic biotite. The occurrence of biotite in the wall rocks and homogenization recrystallization of the sulfide-sulfosalt assemblage in the mineralized intervals are consistent with peak metamorphic conditions ( 350-450 °C, < 4 kbars) in the Boliden area. However, preservation of plagioclase and water-rock interaction under rock-dominant conditions suggest that high δ18O values (+ 10.7 to + 13.5‰) acquired during diagenesis were unchanged by the metamorphic overprint. The δ18O values yield low temperatures (< 150 °C), which indicate pre-metamorphic conditions. These data suggest that the Zn-Pb-Sb-Au-rich intervals formed as pre-metamorphic distal syn-volcanic exhalative mineralization during sedimentation of the Vargfors group metasedimentary rocks. This implies that massive sulfide formation continued even during Vargfors group time and, therefore, there is still potential for discovery of gold-rich base-metal ores in this part of the Skellefte field stratigraphy.

Crystal Structure of Faradaurate-279: Au279(SPh-tBu)84 Plasmonic Nanocrystal Molecules.

PubMed

Sakthivel, Naga Arjun; Theivendran, Shevanuja; Ganeshraj, Vigneshraja; Oliver, Allen G; Dass, Amala

2017-11-01

We report the discovery of an unprecedentedly large, 2.2 nm diameter, thiolate protected gold nanocrystal characterized by single crystal X-ray crystallography (sc-XRD), Au 279 (SPh-tBu) 84 named Faradaurate-279 (F-279) in honor of Michael Faraday's (1857) pioneering work on nanoparticles. F-279 nanocrystal has a core-shell structure containing a truncated octahedral core with bulk face-centered cubic-like arrangement, yet a nanomolecule with a precise number of metal atoms and thiolate ligands. The Au 279 S 84 geometry was established from a low-temperature 120 K sc-XRD study at 0.90 Å resolution. The atom counts in core-shell structure of Au 279 follows the mathematical formula for magic number shells: Au@Au 12 @Au 42 @Au 92 @Au 54 , which is further protected by a final shell of Au 48 . Au 249 core is protected by three types of staple motifs, namely: 30 bridging, 18 monomeric, and 6 dimeric staple motifs. Despite the presence of such diverse staple motifs, Au 279 S 84 structure has a chiral pseudo-D 3 symmetry. The core-shell structure can be viewed as nested, concentric polyhedra, containing a total of five forms of Archimedean solids. A comparison between the Au 279 and Au 309 cuboctahedral superatom model in shell-wise growth is illustrated. F-279 can be synthesized and isolated in high purity in milligram quantities using size exclusion chromatography, as evidenced by mass spectrometry. Electrospray ionization-mass spectrometry independently verifies the X-ray diffraction study based heavy atoms formula, Au 279 S 84 , and establishes the molecular formula with the complete ligands, namely, Au 279 (SPh-tBu) 84 . It is also the smallest gold nanocrystal to exhibit metallic behavior, with a surface plasmon resonance band around 510 nm.

Magnetic susceptibilities of liquid Cr-Au, Mn-Au and Fe-Au alloys

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

Ohno, S.; Shimakura, H.; Tahara, S.

The magnetic susceptibility of liquid Cr-Au, Mn-Au, Fe-Au and Cu-Au alloys was investigated as a function of temperature and composition. Liquid Cr{sub 1-c}Au{sub c} with 0.5 ≤ c and Mn{sub 1-c}Au{sub c} with 0.3≤c obeyed the Curie-Weiss law with regard to their dependence of χ on temperature. The magnetic susceptibilities of liquid Fe-Au alloys also exhibited Curie-Weiss behavior with a reasonable value for the effective number of Bohr magneton. On the Au-rich side, the composition dependence of χ for liquid TM-Au (TM=Cr, Mn, Fe) alloys increased rapidly with increasing TM content, respectively. Additionally, the composition dependences of χ for liquidmore » Cr-Au, Mn-Au, and Fe-Au alloys had maxima at compositions of 50 at% Cr, 70 at% Mn, and 85 at% Fe, respectively. We compared the composition dependences of χ{sub 3d} due to 3d electrons for liquid binary TM-M (M=Au, Al, Si, Sb), and investigated the relationship between χ{sub 3d} and E{sub F} in liquid binary TM-M alloys at a composition of 50 at% TM.« less

Gene Isolation Using Degenerate Primers Targeting Protein Motif: A Laboratory Exercise

ERIC Educational Resources Information Center

Yeo, Brandon Pei Hui; Foong, Lian Chee; Tam, Sheh May; Lee, Vivian; Hwang, Siaw San

2018-01-01

Structures and functions of protein motifs are widely included in many biology-based course syllabi. However, little emphasis is placed to link this knowledge to applications in biotechnology to enhance the learning experience. Here, the conserved motifs of nucleotide binding site-leucine rich repeats (NBS-LRR) proteins, successfully used for the…

cWINNOWER Algorithm for Finding Fuzzy DNA Motifs

NASA Technical Reports Server (NTRS)

Liang, Shoudan

2003-01-01

The cWINNOWER algorithm detects fuzzy motifs in DNA sequences rich in protein-binding signals. A signal is defined as any short nucleotide pattern having up to d mutations differing from a motif of length l. The algorithm finds such motifs if multiple mutated copies of the motif (i.e., the signals) are present in the DNA sequence in sufficient abundance. The cWINNOWER algorithm substantially improves the sensitivity of the winnower method of Pevzner and Sze by imposing a consensus constraint, enabling it to detect much weaker signals. We studied the minimum number of detectable motifs qc as a function of sequence length N for random sequences. We found that qc increases linearly with N for a fast version of the algorithm based on counting three-member sub-cliques. Imposing consensus constraints reduces qc, by a factor of three in this case, which makes the algorithm dramatically more sensitive. Our most sensitive algorithm, which counts four-member sub-cliques, needs a minimum of only 13 signals to detect motifs in a sequence of length N = 12000 for (l,d) = (15,4).

Genesis of Middle Miocene Yellowstone hotspot-related bonanza epithermal Au-Ag deposits, Northern Great Basin, USA

NASA Astrophysics Data System (ADS)

Saunders, J. A.; Unger, D. L.; Kamenov, G. D.; Fayek, M.; Hames, W. E.; Utterback, W. C.

2008-09-01

Epithermal deposits with bonanza Au-Ag veins in the northern Great Basin (NGB) are spatially and temporally associated with Middle Miocene bimodal volcanism that was related to a mantle plume that has now migrated to the Yellowstone National Park area. The Au-Ag deposits formed between 16.5 and 14 Ma, but exhibit different mineralogical compositions, the latter due to the nature of the country rocks hosting the deposits. Where host rocks were primarily of meta-sedimentary or granitic origin, adularia-rich gold mineralization formed. Where glassy rhyolitic country rocks host veins, colloidal silica textures and precious metal-colloid aggregation textures resulted. Where basalts are the country rocks, clay-rich mineralization (with silica minerals, adularia, and carbonate) developed. Oxygen isotope data from quartz (originally amorphous silica and gels) from super-high-grade banded ores from the Sleeper deposit show that ore-forming solutions had δ 18O values up to 10‰ heavier than mid-Miocene meteoric water. The geochemical signature of the ores (including their Se-rich nature) is interpreted here to reflect a mantle source for the “epithermal suite” elements (Au, Ag, Se, Te, As, Sb, Hg) and that signature is preserved to shallow crustal levels because of the similar volatility and aqueous geochemical behavior of the “epithermal suite” elements. A mantle source for the gold in the deposits is further supported by the Pb isotopic signature of the gold ores. Apparently the host rocks control the mineralization style and gangue mineralogy of ores. However, all deposits are considered to have derived precious metals and metalloids from mafic magmas related to the initial emergence of the Yellowstone hotspot. Basalt-derived volatiles and metal(loid)s are inferred to have been absorbed by meteoric-water-dominated geothermal systems heated by shallow rhyolitic magma chambers. Episodic discharge of volatiles and metal(loid)s from deep basaltic magmas mixed with

Atomic and electronic structures of Si(1 1 1)-(√3 x √3)R30°-Au and (6 × 6)-Au surfaces.

PubMed

Patterson, C H

2015-12-02

Si(1 1 1)-Au surfaces with around one monolayer of Au exhibit many ordered structures and structures containing disordered domain walls. Hybrid density functional theory (DFT) calculations presented here reveal the origin of these complex structures and tendency to form domain walls. The conjugate honeycomb chain trimer (CHCT) structure of the [Formula: see text]-Au phase contains Si atoms with non-bonding surface states which can bind Au atoms in pairs in interstices of the CHCT structure and make this surface metallic. Si adatoms adsorbed on the [Formula: see text]-Au surface induce a gapped surface through interaction with the non-bonding states. Adsorption of extra Au atoms in interstitial sites of the [Formula: see text]-Au surface is stabilized by interaction with the non-bonding orbitals and leads to higher coverage ordered structures including the [Formula: see text]-Au phase. Extra Au atoms bound in interstitial sites of the [Formula: see text]-Au surface result in top layer Si atoms with an SiAu4 butterfly wing configuration. The structure of a [Formula: see text]-Au phase, whose in-plane top atomic layer positions were previously determined by an electron holography technique (Grozea et al 1998 Surf. Sci. 418 32), is calculated using total energy minimization. The Patterson function for this structure is calculated and is in good agreement with data from an in-plane x-ray diffraction study (Dornisch et al 1991 Phys. Rev. B 44 11221). Filled and empty state scanning tunneling microscopy (STM) images are calculated for domain walls and the [Formula: see text]-Au structure. The [Formula: see text]-Au phase is 2D chiral and this is evident in computed and actual STM images. [Formula: see text]-Au and domain wall structures contain the SiAu4 motif with a butterfly wing shape. Chemical bonding within the Si-Au top layers of the [Formula: see text]-Au and [Formula: see text]-Au surfaces is analyzed and an explanation for the SiAu4 motif structure is given.

Large scale structural optimization of trimetallic Cu-Au-Pt clusters up to 147 atoms

NASA Astrophysics Data System (ADS)

Wu, Genhua; Sun, Yan; Wu, Xia; Chen, Run; Wang, Yan

2017-10-01

The stable structures of Cu-Au-Pt clusters up to 147 atoms are optimized by using an improved adaptive immune optimization algorithm (AIOA-IC method), in which several motifs, such as decahedron, icosahedron, face centered cubic, sixfold pancake, and Leary tetrahedron, are randomly selected as the inner cores of the starting structures. The structures of Cu8AunPt30-n (n = 1-29), Cu8AunPt47-n (n = 1-46), and partial 75-, 79-, 100-, and 147-atom clusters are analyzed. Cu12Au93Pt42 cluster has onion-like Mackay icosahedral motif. The segregation phenomena of Cu, Au and Pt in clusters are explained by the atomic radius, surface energy, and cohesive energy.

An Atomically Precise Au10 Ag2 Nanocluster with Red-Near-IR Dual Emission.

PubMed

Lei, Zhen; Guan, Zong-Jie; Pei, Xiao-Li; Yuan, Shang-Fu; Wan, Xian-Kai; Zhang, Jin-Yuan; Wang, Quan-Ming

2016-08-01

A red-near-IR dual-emissive nanocluster with the composition [Au10 Ag2 (2-py-C≡C)3 (dppy)6 ](BF4 )5 (1; 2-py-C≡C is 2-pyridylethynyl, dppy=2-pyridyldiphenylphosphine) has been synthesized. Single-crystal X-ray structural analysis reveals that 1 has a trigonal bipyramidal Au10 Ag2 core that contains a planar Au4 (2-py-C≡C)3 unit sandwiched by two Au3 Ag(dppy)3 motifs. Cluster 1 shows intense red-NIR dual emission in solution. The visible emission originates from metal-to-ligand charge transfer (MLCT) from silver atoms to phosphine ligands in the Au3 Ag(dppy)3 motifs, and the intense NIR emission is associated with the participation of 2-pyridylethynyl in the frontier orbitals of the cluster, which is confirmed by a time-dependent density functional theory (TD-DFT) calculation. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Crystal structure and electronic properties of a thiolate-protected Au24 nanocluster

NASA Astrophysics Data System (ADS)

Das, Anindita; Li, Tao; Li, Gao; Nobusada, Katsuyuki; Zeng, Chenjie; Rosi, Nathaniel L.; Jin, Rongchao

2014-05-01

Solving the total structures of gold nanoclusters is of critical importance for understanding their electronic, optical and catalytic properties. Herein, we report the X-ray structure of a charge-neutral Au24(SCH2Ph-tBu)20 nanocluster. This structure features a bi-tetrahedral Au8 kernel protected by four tetrameric staple-like motifs. Electronic structure analysis is further carried out and the optical absorption spectrum is interpreted. The Au24(SCH2Ph-tBu)20, Au23(S-c-C6H11)16 and Au25(SCH2CH2Ph)18 nanoclusters constitute the first crystallographically characterized ``trio''.Solving the total structures of gold nanoclusters is of critical importance for understanding their electronic, optical and catalytic properties. Herein, we report the X-ray structure of a charge-neutral Au24(SCH2Ph-tBu)20 nanocluster. This structure features a bi-tetrahedral Au8 kernel protected by four tetrameric staple-like motifs. Electronic structure analysis is further carried out and the optical absorption spectrum is interpreted. The Au24(SCH2Ph-tBu)20, Au23(S-c-C6H11)16 and Au25(SCH2CH2Ph)18 nanoclusters constitute the first crystallographically characterized ``trio''. Electronic supplementary information (ESI) available: Experimental and supporting Fig. S1-S3. CCDC NUMBER(1000102). For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c4nr01350f

Microstructure and opto-electronic properties of Sn-rich Au-Sn diffusive solders

NASA Astrophysics Data System (ADS)

Rerek, T.; Skowronski, L.; Kobierski, M.; Naparty, M. K.; Derkowska-Zielinska, B.

2018-09-01

Microstructural and opto-electronic properties of Au ⧹ Sn and Sn ⧹ Au bilayers, obtained by sequential evaporating of metals on the Si substrate, were investigated by means of atomic force microscopy, X-ray diffraction and spectroscopic ellipsometry. Thicknesses of individual films were established to obtain the atomic ratio of Au:Sn atoms 1:1, 1:2 and 1:4, which were favor the formation of AuSn, AuSn2 and AuSn4, respectively. However, the produced intermatallic compounds were detected as AuSn and AuSn2. Additionally, the unbounded Sn was found. The sequence of deposition of Au and Sn films as well as their thickness strongly affect on the composition, microstructure, optical and electrical properties of the produced layers. The Au ⧹ Sn (Sn on the top) layers were more smooth than Sn ⧹ Au (Au on the top) films. Generally, the Au ⧹ Sn layers exhibit a better electrical and optical properties than Sn ⧹ Au films. The optical parameters: plasma energy, free-carrier damping, mean relaxation time of conduction electrons and optical resistivity were determined from the effective complex dielectric function of the formed Au, Sn and Au-Sn films. The optical resistivity values are in the range from 17.8 μΩ cm to 85.1 μΩ cm and from 29.6 μΩ cm to 113.3 μΩ cm for Au ⧹ Sn and Sn ⧹ Au layers, respectively.

CompariMotif: quick and easy comparisons of sequence motifs.

PubMed

Edwards, Richard J; Davey, Norman E; Shields, Denis C

2008-05-15

CompariMotif is a novel tool for making motif-motif comparisons, identifying and describing similarities between regular expression motifs. CompariMotif can identify a number of different relationships between motifs, including exact matches, variants of degenerate motifs and complex overlapping motifs. Motif relationships are scored using shared information content, allowing the best matches to be easily identified in large comparisons. Many input and search options are available, enabling a list of motifs to be compared to itself (to identify recurring motifs) or to datasets of known motifs. CompariMotif can be run online at http://bioware.ucd.ie/ and is freely available for academic use as a set of open source Python modules under a GNU General Public License from http://bioinformatics.ucd.ie/shields/software/comparimotif/

cWINNOWER algorithm for finding fuzzy dna motifs

NASA Technical Reports Server (NTRS)

Liang, S.; Samanta, M. P.; Biegel, B. A.

2004-01-01

The cWINNOWER algorithm detects fuzzy motifs in DNA sequences rich in protein-binding signals. A signal is defined as any short nucleotide pattern having up to d mutations differing from a motif of length l. The algorithm finds such motifs if a clique consisting of a sufficiently large number of mutated copies of the motif (i.e., the signals) is present in the DNA sequence. The cWINNOWER algorithm substantially improves the sensitivity of the winnower method of Pevzner and Sze by imposing a consensus constraint, enabling it to detect much weaker signals. We studied the minimum detectable clique size qc as a function of sequence length N for random sequences. We found that qc increases linearly with N for a fast version of the algorithm based on counting three-member sub-cliques. Imposing consensus constraints reduces qc by a factor of three in this case, which makes the algorithm dramatically more sensitive. Our most sensitive algorithm, which counts four-member sub-cliques, needs a minimum of only 13 signals to detect motifs in a sequence of length N = 12,000 for (l, d) = (15, 4). Copyright Imperial College Press.

Functional identification of a Lippia dulcis bornyl diphosphate synthase that contains a duplicated, inhibitory arginine-rich motif.

PubMed

Hurd, Matthew C; Kwon, Moonhyuk; Ro, Dae-Kyun

2017-08-26

Lippia dulcis (Aztec sweet herb) contains the potent natural sweetener hernandulcin, a sesquiterpene ketone found in the leaves and flowers. Utilizing the leaves for agricultural application is challenging due to the presence of the bitter-tasting and toxic monoterpene, camphor. To unlock the commercial potential of L. dulcis leaves, the first step of camphor biosynthesis by a bornyl diphosphate synthase needs to be elucidated. Two putative monoterpene synthases (LdTPS3 and LdTPS9) were isolated from L. dulcis leaf cDNA. To elucidate their catalytic functions, E. coli-produced recombinant enzymes with truncations of their chloroplast transit peptides were assayed with geranyl diphosphate (GPP). In vitro enzyme assays showed that LdTPS3 encodes bornyl diphosphate synthase (thus named LdBPPS) while LdTPS9 encodes linalool synthase. Interestingly, the N-terminus of LdBPPS possesses two arginine-rich (RRX 8 W) motifs, and enzyme assays showed that the presence of both RRX 8 W motifs completely inhibits the catalytic activity of LdBPPS. Only after the removal of the putative chloroplast transit peptide and the first RRX 8 W, LdBPPS could react with GPP to produce bornyl diphosphate. LdBPPS is distantly related to the known bornyl diphosphate synthase from sage in a phylogenetic analysis, indicating a converged evolution of camphor biosynthesis in sage and L. dulcis. The discovery of LdBPPS opens up the possibility of engineering L. dulcis to remove the undesirable product, camphor. Copyright © 2017 Elsevier Inc. All rights reserved.

Human telomeric DNA: G-quadruplex, i-motif and Watson–Crick double helix

PubMed Central

Phan, Anh Tuân; Mergny, Jean-Louis

2002-01-01

Human telomeric DNA composed of (TTAGGG/CCCTAA)n repeats may form a classical Watson–Crick double helix. Each individual strand is also prone to quadruplex formation: the G-rich strand may adopt a G-quadruplex conformation involving G-quartets whereas the C-rich strand may fold into an i-motif based on intercalated C·C+ base pairs. Using an equimolar mixture of the telomeric oligonucleotides d[AGGG(TTAGGG)3] and d[(CCCTAA)3CCCT], we defined which structures existed and which would be the predominant species under a variety of experimental conditions. Under near-physiological conditions of pH, temperature and salt concentration, telomeric DNA was predominantly in a double-helix form. However, at lower pH values or higher temperatures, the G-quadruplex and/or the i-motif efficiently competed with the duplex. We also present kinetic and thermodynamic data for duplex association and for G-quadruplex/i-motif unfolding. PMID:12409451

A novel homodimeric geranyl diphosphate synthase from the orchid Phalaenopsis bellina lacking a DD(X)2-4D motif.

PubMed

Hsiao, Yu-Yun; Jeng, Mei-Fen; Tsai, Wen-Chieh; Chuang, Yu-Chen; Li, Chia-Ying; Wu, Tian-Shung; Kuoh, Chang-Sheng; Chen, Wen-Huei; Chen, Hong-Hwa

2008-09-01

Geranyl diphosphate (GDP) is the precursor of monoterpenes, which are the major floral scent compounds in Phalaenopsis bellina. The cDNA of P. bellina GDP synthase (PbGDPS) was cloned, and its sequence corresponds to the second Asp-rich motif (SARM), but not to any aspartate-rich (Asp-rich) motif. The recombinant PbGDPS enzyme exhibits dual prenyltransferase activity, producing both GDP and farnesyl diphosphate (FDP), and a yeast two-hybrid assay and gel filtration revealed that PbGDPS was able to form a homodimer. Spatial and temporal expression analyses showed that the expression of PbGDPS was flower specific, and that maximal PbGDPS expression was concomitant with maximal emission of monoterpenes on day 5 post-anthesis. Homology modelling of PbGDPS indicated that the Glu-rich motif might provide a binding site for Mg(2+) and catalyze the formation of prenyl products in a similar way to SARM. Replacement of the key Glu residues with alanine totally abolished enzyme activity, whereas their mutation to Asp resulted in a mutant with two-thirds of the activity of the wild-type protein. Phylogenetic analysis indicated that plant GDPS proteins formed four clades: members of both GDPS-a and GDPS-b clades contain Asp-rich motifs, and function as homodimers. In contrast, proteins in the GDPS-c and GDPS-d clades do not contain Asp-rich motifs, but although members of the GDPS-c clade function as heterodimers, PbGDPS, which is more closely related to the GDPS-c clade proteins than to GDPS-a and GDPS-b proteins, and is currently the sole member of the GDPS-d clade, functions as a homodimer.

Defect-rich Ni-Ti layered double hydroxide as a highly efficient support for Au nanoparticles in base-free and solvent-free selective oxidation of benzyl alcohol.

PubMed

Liu, Mengran; Fan, Guoli; Yu, Jiaying; Yang, Lan; Li, Feng

2018-04-17

Tuning the surface properties of supported metal catalysts is of vital importance for governing their catalytic performances in nanocatalysis. Here, we report highly dispersed nanometric gold nanoparticles (NPs) supported on Ni-Ti layered double hydroxides (NiTi-LDHs), which were employed in solvent-free and base-free selective oxidation of benzyl alcohol. A series of characterization techniques demonstrated that defect-rich NiTi-LDHs could efficiently stabilize Au NPs and decrease surface electron density of Au NPs. The as-formed Au/NiTi-LDH catalyst with a Ni/Ti molar ratio of 3 : 1 and an Au loading of 0.71 wt% yielded the highest turnover frequency value of ∼4981 h-1 at 120 °C among tested Au/NiTi-LDH catalysts with different Ni/Ti molar ratios, along with a high benzaldehyde selectivity of 98%. High catalytic efficiency of the catalyst was mainly correlated with surface cooperation between unique defects (i.e. defective Ti3+ species and oxygen vacancies) and abundant hydroxyl groups on the brucite-like layers of the NiTi-LDH support, which could lead to the preferential adsorption and activation of an alcohol hydroxyl moiety in benzyl alcohol and oxygen molecule, as well as the formation of more electron-deficient Ni3+ and Au0 species on the catalyst surface. Furthermore, the present Au/NiTi-LDH catalyst tolerated the oxidation of a wide variety of substrate structures into the corresponding aldehydes, acids or ketones. Our primary results illustrate that defect-rich NiTi-LDHs are promising supports which can efficiently modify surface structure and electronic properties of supported metal catalysts and consequently improve their catalytic performances.

A new record of silica-rich coating on carbonate substrates in southeast-central Iran: Constraints on geochemical signatures

NASA Astrophysics Data System (ADS)

Aftabi, Alijan; Atapour, Habibeh

2018-10-01

There exist few data on the geochemical signatures and occurrence of silica-rich coatings developed on siliceous carbonate substrates. The rock coatings in the Maran-e-Galu area in southeast-central Iran are composed of four layers; a lower thick layer (1 mm) of silica, a lower thin film of Fe-Mn oxide, an upper thick (1 mm) silica-rich layer, and an upper thin film of Fe-Mn oxide. Energy dispersive X-ray spectrometer (EDS), X-ray diffraction and bulk coating geochemistry data obtained by XRF and ICP-MS highlight that the 1-3 mm thick silica-rich coatings occur as a silica glaze of opal composition on the siliceous carbonate substrate. The coatings were probably formed by the interaction of rainfall, water vapor or dew with silicate and carbonate-rich detrital atmospheric dust, releasing H4SiO4with a pH of 5-10 in this semiarid-arid desert environment. This led to the formation of silica gels as well as minor Fe-Mn oxide gels by evaporation and supersaturation, and finally changed to the black brown silica glaze probably at ambient temperatures of >40 °C Major and minor element signatures are consistent with the known silica glazes, displaying enrichment in Ba, Sr, P, and LREEs with little to no Eu and Ce anomalies and a weak Tm anomaly. However, the very low content of aluminum oxide is well correlated with the known classified silica glaze of genetic type 1, reflecting the absence of detrital clay minerals. The low Fe and Mn contents in bulk coatings (3.6 and 10 magnitudes lower than crustal abundance, respectively) and lack of biochemical processes in the atmospheric dust highlight the semiarid-arid climate setting. We thereby conclude that a new variant of silica glaze of 1-3 mm thickness could form on siliceous carbonate substrates under an alkaline pH in semiarid-arid regions.

Structural basis for genome wide recognition of 5-bp GC motifs by SMAD transcription factors.

PubMed

Martin-Malpartida, Pau; Batet, Marta; Kaczmarska, Zuzanna; Freier, Regina; Gomes, Tiago; Aragón, Eric; Zou, Yilong; Wang, Qiong; Xi, Qiaoran; Ruiz, Lidia; Vea, Angela; Márquez, José A; Massagué, Joan; Macias, Maria J

2017-12-12

Smad transcription factors activated by TGF-β or by BMP receptors form trimeric complexes with Smad4 to target specific genes for cell fate regulation. The CAGAC motif has been considered as the main binding element for Smad2/3/4, whereas Smad1/5/8 have been thought to preferentially bind GC-rich elements. However, chromatin immunoprecipitation analysis in embryonic stem cells showed extensive binding of Smad2/3/4 to GC-rich cis-regulatory elements. Here, we present the structural basis for specific binding of Smad3 and Smad4 to GC-rich motifs in the goosecoid promoter, a nodal-regulated differentiation gene. The structures revealed a 5-bp consensus sequence GGC(GC)|(CG) as the binding site for both TGF-β and BMP-activated Smads and for Smad4. These 5GC motifs are highly represented as clusters in Smad-bound regions genome-wide. Our results provide a basis for understanding the functional adaptability of Smads in different cellular contexts, and their dependence on lineage-determining transcription factors to target specific genes in TGF-β and BMP pathways.

I-motif DNA structures are formed in the nuclei of human cells

NASA Astrophysics Data System (ADS)

Zeraati, Mahdi; Langley, David B.; Schofield, Peter; Moye, Aaron L.; Rouet, Romain; Hughes, William E.; Bryan, Tracy M.; Dinger, Marcel E.; Christ, Daniel

2018-06-01

Human genome function is underpinned by the primary storage of genetic information in canonical B-form DNA, with a second layer of DNA structure providing regulatory control. I-motif structures are thought to form in cytosine-rich regions of the genome and to have regulatory functions; however, in vivo evidence for the existence of such structures has so far remained elusive. Here we report the generation and characterization of an antibody fragment (iMab) that recognizes i-motif structures with high selectivity and affinity, enabling the detection of i-motifs in the nuclei of human cells. We demonstrate that the in vivo formation of such structures is cell-cycle and pH dependent. Furthermore, we provide evidence that i-motif structures are formed in regulatory regions of the human genome, including promoters and telomeric regions. Our results support the notion that i-motif structures provide key regulatory roles in the genome.

Electronic structure and optical properties of the thiolate-protected Au28(SMe)20 cluster.

PubMed

Knoppe, Stefan; Malola, Sami; Lehtovaara, Lauri; Bürgi, Thomas; Häkkinen, Hannu

2013-10-10

The recently reported crystal structure of the Au28(TBBT)20 cluster (TBBT: p-tert-butylbenzenethiolate) is analyzed with (time-dependent) density functional theory (TD-DFT). Bader charge analysis reveals a novel trimeric Au3(SR)4 binding motif. The cluster can be formulated as Au14(Au2(SR)3)4(Au3(SR)4)2. The electronic structure of the Au14(6+) core and the ligand-protected cluster were analyzed, and their stability can be explained by formation of distorted eight-electron superatoms. Optical absorption and circular dichroism (CD) spectra were calculated and compared to the experiment. Assignment of handedness of the intrinsically chiral cluster is possible.

Mass spectrometric identification of Au68(SR)34 molecular gold nanoclusters with 34-electron shell closing.

PubMed

Dass, Amala

2009-08-26

The molecular formula Au(68)(SCH(2)CH(2)Ph)(34) has been assigned to the 14 kDa nanocluster using MALDI-TOF mass spectrometry. The 34-electron shell closing in a macroscopically obtained thiolated gold nanocluster is demonstrated. The Au(68) nanocluster is predicted to have a 49 atom Marks decahedral core with 19 inner core atoms and 30 outer atoms chelating with the staple motifs. The nanoclusters' predicted formulation is [Au](19+30) [Au(SR)(2)](11) [Au(2)(SR)(3)](4).

MotifNet: a web-server for network motif analysis.

PubMed

Smoly, Ilan Y; Lerman, Eugene; Ziv-Ukelson, Michal; Yeger-Lotem, Esti

2017-06-15

Network motifs are small topological patterns that recur in a network significantly more often than expected by chance. Their identification emerged as a powerful approach for uncovering the design principles underlying complex networks. However, available tools for network motif analysis typically require download and execution of computationally intensive software on a local computer. We present MotifNet, the first open-access web-server for network motif analysis. MotifNet allows researchers to analyze integrated networks, where nodes and edges may be labeled, and to search for motifs of up to eight nodes. The output motifs are presented graphically and the user can interactively filter them by their significance, number of instances, node and edge labels, and node identities, and view their instances. MotifNet also allows the user to distinguish between motifs that are centered on specific nodes and motifs that recur in distinct parts of the network. MotifNet is freely available at http://netbio.bgu.ac.il/motifnet . The website was implemented using ReactJs and supports all major browsers. The server interface was implemented in Python with data stored on a MySQL database. estiyl@bgu.ac.il or michaluz@cs.bgu.ac.il. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

BayesMotif: de novo protein sorting motif discovery from impure datasets.

PubMed

Hu, Jianjun; Zhang, Fan

2010-01-18

Protein sorting is the process that newly synthesized proteins are transported to their target locations within or outside of the cell. This process is precisely regulated by protein sorting signals in different forms. A major category of sorting signals are amino acid sub-sequences usually located at the N-terminals or C-terminals of protein sequences. Genome-wide experimental identification of protein sorting signals is extremely time-consuming and costly. Effective computational algorithms for de novo discovery of protein sorting signals is needed to improve the understanding of protein sorting mechanisms. We formulated the protein sorting motif discovery problem as a classification problem and proposed a Bayesian classifier based algorithm (BayesMotif) for de novo identification of a common type of protein sorting motifs in which a highly conserved anchor is present along with a less conserved motif regions. A false positive removal procedure is developed to iteratively remove sequences that are unlikely to contain true motifs so that the algorithm can identify motifs from impure input sequences. Experiments on both implanted motif datasets and real-world datasets showed that the enhanced BayesMotif algorithm can identify anchored sorting motifs from pure or impure protein sequence dataset. It also shows that the false positive removal procedure can help to identify true motifs even when there is only 20% of the input sequences containing true motif instances. We proposed BayesMotif, a novel Bayesian classification based algorithm for de novo discovery of a special category of anchored protein sorting motifs from impure datasets. Compared to conventional motif discovery algorithms such as MEME, our algorithm can find less-conserved motifs with short highly conserved anchors. Our algorithm also has the advantage of easy incorporation of additional meta-sequence features such as hydrophobicity or charge of the motifs which may help to overcome the limitations of

Atomic and electronic structures of Si(1 1 1)-\\left(\\sqrt{\\mathbf{3}}\\times\\sqrt{\\mathbf{3}}\\right)\\text{R}\\mathbf{3}{{\\mathbf{0}}^{\\circ}} -Au and (6 × 6)-Au surfaces

NASA Astrophysics Data System (ADS)

Patterson, C. H.

2015-12-01

Si(1 1 1)-Au surfaces with around one monolayer of Au exhibit many ordered structures and structures containing disordered domain walls. Hybrid density functional theory (DFT) calculations presented here reveal the origin of these complex structures and tendency to form domain walls. The conjugate honeycomb chain trimer (CHCT) structure of the \\sqrt{3} -Au phase contains Si atoms with non-bonding surface states which can bind Au atoms in pairs in interstices of the CHCT structure and make this surface metallic. Si adatoms adsorbed on the \\sqrt{3} -Au surface induce a gapped surface through interaction with the non-bonding states. Adsorption of extra Au atoms in interstitial sites of the \\sqrt{3} -Au surface is stabilized by interaction with the non-bonding orbitals and leads to higher coverage ordered structures including the ≤ft(6× 6\\right) -Au phase. Extra Au atoms bound in interstitial sites of the \\sqrt{3} -Au surface result in top layer Si atoms with an SiAu4 butterfly wing configuration. The structure of a ≤ft(6× 6\\right) -Au phase, whose in-plane top atomic layer positions were previously determined by an electron holography technique (Grozea et al 1998 Surf. Sci. 418 32), is calculated using total energy minimization. The Patterson function for this structure is calculated and is in good agreement with data from an in-plane x-ray diffraction study (Dornisch et al 1991 Phys. Rev. B 44 11221). Filled and empty state scanning tunneling microscopy (STM) images are calculated for domain walls and the ≤ft(6× 6\\right) -Au structure. The ≤ft(6× 6\\right) -Au phase is 2D chiral and this is evident in computed and actual STM images. ≤ft(6× 6\\right) -Au and domain wall structures contain the SiAu4 motif with a butterfly wing shape. Chemical bonding within the Si-Au top layers of the \\sqrt{3} -Au and ≤ft(6× 6\\right) -Au surfaces is analyzed and an explanation for the SiAu4 motif structure is given.

Biophysical characterization of the basic cluster in the transcription repression domain of human MeCP2 with AT-rich DNA.

PubMed

Mushtaq, Ameeq Ul; Lee, Yejin; Hwang, Eunha; Bang, Jeong Kyu; Hong, Eunmi; Byun, Youngjoo; Song, Ji-Joon; Jeon, Young Ho

2018-01-01

MeCP2 is a chromatin associated protein which is highly expressed in brain and relevant with Rett syndrome (RTT). There are AT-hook motifs in MeCP2 which can bind with AT-rich DNA, suggesting a role in chromatin binding. Here, we report the identification and characterization of another AT-rich DNA binding motif (residues 295 to 313) from the C-terminal transcription repression domain of MeCP2 by nuclear magnetic resonance (NMR) and isothermal calorimetry (ITC). This motif shows a micromolar affinity to AT-rich DNA, and it binds to the minor groove of DNA like AT-hook motifs. Together with the previous studies, our results provide an insight into a critical role of this motif in chromatin structure and function. Copyright © 2017 Elsevier Inc. All rights reserved.

Structural modelling and phylogenetic analyses of PgeIF4A2 (Eukaryotic translation initiation factor) from Pennisetum glaucum reveal signature motifs with a role in stress tolerance and development

PubMed Central

Agarwal, Aakrati; Mudgil, Yashwanti; Pandey, Saurabh; Fartyal, Dhirendra; Reddy, Malireddy K

2016-01-01

Eukaryotic translation initiation factor 4A (eIF4A) is an indispensable component of the translation machinery and also play a role in developmental processes and stress alleviation in plants and animals. Different eIF4A isoforms are present in the cytosol of the cell, namely, eIF4A1, eIF4A2, and eIF4A3 and their expression is tightly regulated in cap-dependent translation. We revealed the structural model of PgeIF4A2 protein using the crystal structure of Homo sapiens eIF4A3 (PDB ID: 2J0S) as template by Modeller 9.12. The resultant PgeIF4A2 model structure was refined by PROCHECK, ProSA, Verify3D and RMSD that showed the model structure is reliable with 77 % amino acid sequence identity with template. Investigation revealed two conserved signatures for ATP-dependent RNA Helicase DEAD-box conserved site (VLDEADEML) and RNA helicase DEAD-box type, Q-motif in sheet-turn-helix and α-helical region respectively. All these conserved motifs are responsible for response during developmental stages and stress tolerance in plants. PMID:28358146

Structural modelling and phylogenetic analyses of PgeIF4A2 (Eukaryotic translation initiation factor) from Pennisetum glaucum reveal signature motifs with a role in stress tolerance and development.

PubMed

Agarwal, Aakrati; Mudgil, Yashwanti; Pandey, Saurabh; Fartyal, Dhirendra; Reddy, Malireddy K

2016-01-01

Eukaryotic translation initiation factor 4A (eIF4A) is an indispensable component of the translation machinery and also play a role in developmental processes and stress alleviation in plants and animals. Different eIF4A isoforms are present in the cytosol of the cell, namely, eIF4A1, eIF4A2, and eIF4A3 and their expression is tightly regulated in cap-dependent translation. We revealed the structural model of PgeIF4A2 protein using the crystal structure of Homo sapiens eIF4A3 (PDB ID: 2J0S) as template by Modeller 9.12. The resultant PgeIF4A2 model structure was refined by PROCHECK, ProSA, Verify3D and RMSD that showed the model structure is reliable with 77 % amino acid sequence identity with template. Investigation revealed two conserved signatures for ATP-dependent RNA Helicase DEAD-box conserved site (VLDEADEML) and RNA helicase DEAD-box type, Q-motif in sheet-turn-helix and α-helical region respectively. All these conserved motifs are responsible for response during developmental stages and stress tolerance in plants.

Magmatic controls on the genesis of porphyry Cu-Mo-Au deposits: The Bingham Canyon example

NASA Astrophysics Data System (ADS)

Grondahl, Carter; Zajacz, Zoltán

2017-12-01

Bingham Canyon is one of the world's largest porphyry Cu-Mo-Au deposits and was previously used as an example to emphasize the role of magma mixing and magmatic sulphide saturation in the enhancement of ore fertility of magmatic systems. We analyzed whole rocks, minerals, and silicate melt inclusions (SMI) from the co-genetic, ore-contemporaneous volcanic package (∼38 Ma). As opposed to previous propositions, whole-rock trace element signatures preclude shoshonite-latite genesis via mixing of melanephelinite and trachyte or rhyolite, whereas core to rim compositional profiles of large clinopyroxene phenocrysts suggests the amalgamation of the ore-related magma reservoir by episodic recharge of shoshonitic to latitic magmas with various degrees of differentiation. Major and trace element and Sr and Nd isotopic signatures indicate that the ore-related shoshonite-latite series were generated by low-degree partial melting of an ancient metasomatized mantle source yielding volatile and ore metal rich magmas. Latite and SMI compositions can be reproduced by MELTS modeling assuming 2-step lower and upper crustal fractionation of a primary shoshonite with minimal country rock assimilation. High oxygen fugacities (≈ NNO + 1) are prevalent as evidenced by olivine-spinel oxybarometry, high SO3 in apatite, and anhydrite saturation. The magma could therefore carry significantly more S than would have been possible at more reducing conditions, and the extent of ore metal sequestration by magmatic sulphide saturation was minimal. The SMI data show that the latites were Cu rich, with Cu concentrations in the silicate melt reaching up to 300-400 ppm at about 60 wt% SiO2. The Au and Ag concentrations are also high (1.5-4 and 50-200 ppb, respectively), but show less variation with SiO2. A sudden drop in Cu and S concentrations in the silicate melt at around 65 wt% SiO2 in the presence of high Cl, Mo, Ag, and Au shows that the onset of effective metal extraction by fluid

Aptamer/Au nanoparticles/cobalt sulfide nanosheets biosensor for 17β-estradiol detection using a guanine-rich complementary DNA sequence for signal amplification.

PubMed

Huang, Ke-Jing; Liu, Yu-Jie; Zhang, Ji-Zong; Cao, Jun-Tao; Liu, Yan-Ming

2015-05-15

We have developed a sensitive sensing platform for 17β-estradiol by combining the aptamer probe and hybridization reaction. In this assay, 2-dimensional cobalt sulfide nanosheet (CoS) was synthesized by a simple hydrothermal method with L-cysteine as sulfur donor. An electrochemical aptamer biosensor was constructed by assembling a thiol group tagged 17β-estradiol aptamer on CoS and gold nanoparticles (AuNPs) modified electrode. Methylene blue was applied as a tracer and a guanine-rich complementary DNA sequence was designed to bind with the unbound 17β-estradiol aptamer for signal amplification. The binding of guanine-rich DNA to the aptamer was inhibited when the aptamer captured 17β-estradiol. Using guanine-rich DNA in the assay greatly amplified the redox signal of methylene blue bound to the detection probe. The CoS/AuNPs film formed on the biosensor surface appeared to be a good conductor for accelerating the electron transfer. The method demonstrated a high sensitivity of detection with the dynamic concentration range spanning from 1.0×10(-9) to 1.0×10(-12) M and a detection limit of 7.0×10(-13) M. Besides, the fabricated biosensor exhibited good selectivity toward 17β-estradiol even when interferents were presented at 100-fold concentrations. Our attempt will extend the application of the CoS nanosheet and this signal amplification assay to biosensing areas. Copyright © 2014 Elsevier B.V. All rights reserved.

Bio-mimicking of Proline-Rich Motif Applied to Carbon Nanotube Reveals Unexpected Subtleties Underlying Nanoparticle Functionalization

NASA Astrophysics Data System (ADS)

Zhang, Yuanzhao; Jimenez-Cruz, Camilo A.; Wang, Jian; Zhou, Bo; Yang, Zaixing; Zhou, Ruhong

2014-11-01

Here, we report computational studies of the SH3 protein domain interacting with various single-walled carbon nanotubes (SWCNT) either bare or functionalized by mimicking the proline-rich motif (PRM) ligand (PPPVPPRR) and compare it to the SH3-PRM complex binding. With prolines or a single arginine attached, the SWCNT gained slightly on specificity when compared with the bare control, whereas with multi-arginine systems the specificity dropped dramatically to our surprise. Although the electrostatic interaction provided by arginines is crucial in the recognition between PRM and SH3 domain, our results suggest that attaching multiple arginines to the SWCNT has a detrimental effect on the binding affinity. Detailed analysis of the MD trajectories found two main factors that modulate the specificity of the binding: the existence of competing acidic patches at the surface of SH3 that leads to ``trapping and clamping'' by the arginines, and the rigidity of the SWCNT introducing entropic penalties in the proper binding. Further investigation revealed that the same ``clamping'' phenomenon exits in the PRM-SH3 system, which has not been reported in previous literature. The competing effects between nanoparticle and its functionalization components revealed by our model system should be of value to current and future nanomedicine designs.

Bio-mimicking of Proline-Rich Motif Applied to Carbon Nanotube Reveals Unexpected Subtleties Underlying Nanoparticle Functionalization

PubMed Central

Zhang, Yuanzhao; Jimenez-Cruz, Camilo A.; Wang, Jian; Zhou, Bo; Yang, Zaixing; Zhou, Ruhong

2014-01-01

Here, we report computational studies of the SH3 protein domain interacting with various single-walled carbon nanotubes (SWCNT) either bare or functionalized by mimicking the proline-rich motif (PRM) ligand (PPPVPPRR) and compare it to the SH3-PRM complex binding. With prolines or a single arginine attached, the SWCNT gained slightly on specificity when compared with the bare control, whereas with multi-arginine systems the specificity dropped dramatically to our surprise. Although the electrostatic interaction provided by arginines is crucial in the recognition between PRM and SH3 domain, our results suggest that attaching multiple arginines to the SWCNT has a detrimental effect on the binding affinity. Detailed analysis of the MD trajectories found two main factors that modulate the specificity of the binding: the existence of competing acidic patches at the surface of SH3 that leads to “trapping and clamping” by the arginines, and the rigidity of the SWCNT introducing entropic penalties in the proper binding. Further investigation revealed that the same “clamping” phenomenon exits in the PRM-SH3 system, which has not been reported in previous literature. The competing effects between nanoparticle and its functionalization components revealed by our model system should be of value to current and future nanomedicine designs. PMID:25427563

Analyses of the Large Subunit Histidine-Rich Motif Expose an Alternative Proton Transfer Pathway in [NiFe] Hydrogenases

PubMed Central

Szőri-Dorogházi, Emma; Maróti, Gergely; Szőri, Milán; Nyilasi, Andrea; Rákhely, Gábor; Kovács, Kornél L.

2012-01-01

A highly conserved histidine-rich region with unknown function was recognized in the large subunit of [NiFe] hydrogenases. The HxHxxHxxHxH sequence occurs in most membrane-bound hydrogenases, but only two of these histidines are present in the cytoplasmic ones. Site-directed mutagenesis of the His-rich region of the T. roseopersicina membrane-attached Hyn hydrogenase disclosed that the enzyme activity was significantly affected only by the replacement of the His104 residue. Computational analysis of the hydrogen bond network in the large subunits indicated that the second histidine of this motif might be a component of a proton transfer pathway including Arg487, Asp103, His104 and Glu436. Substitutions of the conserved amino acids of the presumed transfer route impaired the activity of the Hyn hydrogenase. Western hybridization was applied to demonstrate that the cellular level of the mutant hydrogenases was similar to that of the wild type. Mostly based on theoretical modeling, few proton transfer pathways have already been suggested for [NiFe] hydrogenases. Our results propose an alternative route for proton transfer between the [NiFe] active center and the surface of the protein. A novel feature of this model is that this proton pathway is located on the opposite side of the large subunit relative to the position of the small subunit. This is the first study presenting a systematic analysis of an in silico predicted proton translocation pathway in [NiFe] hydrogenases by site-directed mutagenesis. PMID:22511957

Crystal structure of Au25(SePh)18 nanoclusters and insights into their electronic, optical and catalytic properties

NASA Astrophysics Data System (ADS)

Song, Yongbo; Zhong, Juan; Yang, Sha; Wang, Shuxin; Cao, Tiantian; Zhang, Jun; Li, Peng; Hu, Daqiao; Pei, Yong; Zhu, Manzhou

2014-10-01

The crystal structure of selenolate-capped Au25(SePh)18- nanoclusters has been unambiguously determined for the first time, and provides a solid basis for a deeper understanding of the structure-property relationships. The selenolate-capped Au25 cluster shows noticeable differences from the previously reported Au25(SCH2CH2Ph)18- counterpart, albeit both share the icosahedral Au13 core and semi-ring Au2(SeR)3 or Au2(SR)3 motifs. Distinct differences in the electronic structure and optical, catalytic and electrochemical properties are revealed by the coupling experiments with density functional theory (TD-DFT) calculations. Overall, the successful determination of the Au25(SePh)18- structure removes any ambiguity about its structure, and comparison with the thiolated Au25 counterpart helps us to further understand how the ligands affect the properties of the nanocluster.The crystal structure of selenolate-capped Au25(SePh)18- nanoclusters has been unambiguously determined for the first time, and provides a solid basis for a deeper understanding of the structure-property relationships. The selenolate-capped Au25 cluster shows noticeable differences from the previously reported Au25(SCH2CH2Ph)18- counterpart, albeit both share the icosahedral Au13 core and semi-ring Au2(SeR)3 or Au2(SR)3 motifs. Distinct differences in the electronic structure and optical, catalytic and electrochemical properties are revealed by the coupling experiments with density functional theory (TD-DFT) calculations. Overall, the successful determination of the Au25(SePh)18- structure removes any ambiguity about its structure, and comparison with the thiolated Au25 counterpart helps us to further understand how the ligands affect the properties of the nanocluster. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr04631e

Reversible conformational switching of i-motif DNA studied by fluorescence spectroscopy.

PubMed

Choi, Jungkweon; Majima, Tetsuro

2013-01-01

Non-B DNAs, which can form unique structures other than double helix of B-DNA, have attracted considerable attention from scientists in various fields including biology, chemistry and physics etc. Among them, i-motif DNA, which is formed from cytosine (C)-rich sequences found in telomeric DNA and the promoter region of oncogenes, has been extensively investigated as a signpost and controller for the oncogene expression at the transcription level and as a promising material in nanotechnology. Fluorescence techniques such as fluorescence resonance energy transfer (FRET) and the fluorescence quenching are important for studying DNA and in particular for the visualization of reversible conformational switching of i-motif DNA that is triggered by the protonation. Here, we review the latest studies on the conformational dynamics of i-motif DNA as well as the application of FRET and fluorescence quenching techniques to the visualization of reversible conformational switching of i-motif DNA in nano-biotechnology. © 2013 Wiley Periodicals, Inc. Photochemistry and Photobiology © 2013 The American Society of Photobiology.

MotifMark: Finding regulatory motifs in DNA sequences.

PubMed

Hassanzadeh, Hamid Reza; Kolhe, Pushkar; Isbell, Charles L; Wang, May D

2017-07-01

The interaction between proteins and DNA is a key driving force in a significant number of biological processes such as transcriptional regulation, repair, recombination, splicing, and DNA modification. The identification of DNA-binding sites and the specificity of target proteins in binding to these regions are two important steps in understanding the mechanisms of these biological activities. A number of high-throughput technologies have recently emerged that try to quantify the affinity between proteins and DNA motifs. Despite their success, these technologies have their own limitations and fall short in precise characterization of motifs, and as a result, require further downstream analysis to extract useful and interpretable information from a haystack of noisy and inaccurate data. Here we propose MotifMark, a new algorithm based on graph theory and machine learning, that can find binding sites on candidate probes and rank their specificity in regard to the underlying transcription factor. We developed a pipeline to analyze experimental data derived from compact universal protein binding microarrays and benchmarked it against two of the most accurate motif search methods. Our results indicate that MotifMark can be a viable alternative technique for prediction of motif from protein binding microarrays and possibly other related high-throughput techniques.

Sephardic signature in haplogroup T mitochondrial DNA

PubMed Central

Bedford, Felice L

2012-01-01

A rare combination of mutations within mitochondrial DNA subhaplogroup T2e is identified as affiliated with Sephardic Jews, a group that has received relatively little attention. Four investigations were pursued: Search of the motif in 250 000 control region records across 8 databases, comparison of frequencies of T subhaplogroups (T1, T2b, T2c, T2e, T4, T*) across 11 diverse populations, creation of a phylogenic median-joining network from public T2e control region entries, and analysis of one Sephardic mitochondrial full genomic sequence with the motif. It was found that the rare motif belonged only to Sephardic descendents (Turkey, Bulgaria), to inhabitants of North American regions known for secret Spanish–Jewish colonization, or were consistent with Sephardic ancestry. The incidence of subhaplogroup T2e decreased from the Western Arabian Peninsula to Italy to Spain and into Western Europe. The ratio of sister subhaplogroups T2e to T2b was found to vary 40-fold across populations from a low in the British Isles to a high in Saudi Arabia with the ratio in Sephardim more similar to Saudi Arabia, Egypt, and Italy than to hosts Spain and Portugal. Coding region mutations of 2308G and 14499T may locate the Sephardic signature within T2e, but additional samples and reworking of current T2e phylogenetic branch structure is needed. The Sephardic Turkish community has a less pronounced founder effect than some Ashkenazi groups considered singly (eg, Polish), but other comparisons of interest await comparable averaging. Registries of signatures will benefit the study of populations with a large number of smaller-size founders. PMID:22108605

A Conserved GPG-Motif in the HIV-1 Nef Core Is Required for Principal Nef-Activities

PubMed Central

Martínez-Bonet, Marta; Palladino, Claudia; Briz, Veronica; Rudolph, Jochen M.; Fackler, Oliver T.; Relloso, Miguel; Muñoz-Fernandez, Maria Angeles; Madrid, Ricardo

2015-01-01

To find out new determinants required for Nef activity we performed a functional alanine scanning analysis along a discrete but highly conserved region at the core of HIV-1 Nef. We identified the GPG-motif, located at the 121–137 region of HIV-1 NL4.3 Nef, as a novel protein signature strictly required for the p56Lck dependent Nef-induced CD4-downregulation in T-cells. Since the Nef-GPG motif was dispensable for CD4-downregulation in HeLa-CD4 cells, Nef/AP-1 interaction and Nef-dependent effects on Tf-R trafficking, the observed effects on CD4 downregulation cannot be attributed to structure constraints or to alterations on general protein trafficking. Besides, we found that the GPG-motif was also required for Nef-dependent inhibition of ring actin re-organization upon TCR triggering and MHCI downregulation, suggesting that the GPG-motif could actively cooperate with the Nef PxxP motif for these HIV-1 Nef-related effects. Finally, we observed that the Nef-GPG motif was required for optimal infectivity of those viruses produced in T-cells. According to these findings, we propose the conserved GPG-motif in HIV-1 Nef as functional region required for HIV-1 infectivity and therefore with a potential interest for the interference of Nef activity during HIV-1 infection. PMID:26700863

Characteristics of Au Migration and Concentration Distributions in Au-Doped HgCdTe LPE Materials

NASA Astrophysics Data System (ADS)

Sun, Quanzhi; Yang, Jianrong; Wei, Yanfeng; Zhang, Juan; Sun, Ruiyun

2015-08-01

Annealing techniques and secondary ion mass spectrometry have been used to study the characteristics of Au migration and concentration distributions in HgCdTe materials grown by liquid phase epitaxy. Secondary ion mass spectrometry measurements showed that Au concentrations had obvious positive correlations with Hg-vacancy concentration and dislocation density of the materials. Au atoms migrate toward regions of high Hg-vacancy concentration or move away from these regions when the Hg-vacancy concentration decreases during annealing. The phenomenon can be explained by defect chemical equilibrium theory if Au atoms have a very large migration velocity compared with Hg vacancies. Au atoms will also migrate toward regions of high dislocation density, leading to a peak concentration in the inter-diffusion region of HgCdTe materials near the substrate. By use of an Hg and Te-rich annealing technique, different concentration distributions of both Au atoms and Hg vacancies in HgCdTe materials were obtained, indicating that Au-doped HgCdTe materials can be designed and prepared to satisfy the requirements of HgCdTe devices.

Osmium, tungsten, and chromium isotopes in sediments and in Ni-rich spinel at the K-T boundary: Signature of a chondritic impactor

NASA Astrophysics Data System (ADS)

Quitté, Ghylaine; Robin, Eric; Levasseur, Sylvain; Capmas, Françoise; Rocchia, Robert; Birck, Jean-Louis; Allègre, Claude Jean

It is now established that a large extraterrestrial object hit the Earth at the end of the Cretaceous period, about 65 Ma ago. We have investigated Re-Os, Hf-W, and Mn-Cr isotope systems in sediments from the Cretaceous and the Paleogene in order to characterize the type of impactor. Within the Cretaceous-Tertiary (K-T) boundary layer, extraterrestrial material is mixed with terrestrial material, causing a dilution of the extraterrestrial isotope signature that is difficult to quantify. A phase essentially composed of Ni-rich spinel, formed in the atmosphere mainly from melted projectile material, is likely to contain the extraterrestrial isotopic signature of the impactor. We show that the analysis of spinel is indeed the best approach to determine the initial isotope composition of the impactor, and that W and Cr isotopes confirm that the projectile was a carbonaceous chondrite.

STAR Au + Au Fixed Target Results

NASA Astrophysics Data System (ADS)

Meehan, Kathryn; STAR Collaboration

2015-10-01

The RHIC Beam Energy Scan (BES) program was proposed to look for the turn-off of signatures of the quark gluon plasma (QGP), search for a possible QCD critical point, and study the nature of the phase transition between hadronic and partonic matter. The results from the NA49 experiment at CERN have been used to claim that the onset of deconfinement occurs at a collision energy around a center-of-mass energy of 7 GeV, the low end of the BES range. Data from lower energies are needed to test if this onset occurs. The goal of the STAR Fixed-Target Program is to extend the collision energy range in BES II with the same detector to energies that are likely below the onset of deconfinement. Currently, STAR has inserted a gold target into the beam pipe and conducted test runs at center-of-mass energies 3.9 and 4.5 GeV. Tests have been done with both Au and Al beams. First physics results from a Coulomb analysis of Au + Au fixed-target collisions, which are found to be consistent with previous experiments, will be presented. These results demonstrate that STAR has good particle identification capabilities in this novel detector setup. Furthermore, the Coulomb potential, which is sensitive to the Z of the projectile and degree of baryonic stopping, will be compared with published results from the AGS. This material is based upon work supported by the National Science Foundation under Grant No. 1068833.

The signature-based radiation-scanning approach to standoff detection of improvised explosive devices.

PubMed

Brewer, R L; Dunn, W L; Heider, S; Matthew, C; Yang, X

2012-07-01

The signature-based radiation-scanning technique for detection of improvised explosive devices is described. The technique seeks to detect nitrogen-rich chemical explosives present in a target. The technology compares a set of "signatures" obtained from a test target to a collection of "templates", sets of signatures for a target that contain an explosive in a specific configuration. Interrogation of nitrogen-rich fertilizer samples, which serve as surrogates for explosives, is shown experimentally to be able to discriminate samples of 3.8L and larger. Copyright © 2011 Elsevier Ltd. All rights reserved.

Motif discovery and motif finding from genome-mapped DNase footprint data.

PubMed

Kulakovskiy, Ivan V; Favorov, Alexander V; Makeev, Vsevolod J

2009-09-15

Footprint data is an important source of information on transcription factor recognition motifs. However, a footprinting fragment can contain no sequences similar to known protein recognition sites. Inspection of genome fragments nearby can help to identify missing site positions. Genome fragments containing footprints were supplied to a pipeline that constructed a position weight matrix (PWM) for different motif lengths and selected the optimal PWM. Fragments were aligned with the SeSiMCMC sampler and a new heuristic algorithm, Bigfoot. Footprints with missing hits were found for approximately 50% of factors. Adding only 2 bp on both sides of a footprinting fragment recovered most hits. We automatically constructed motifs for 41 Drosophila factors. New motifs can recognize footprints with a greater sensitivity at the same false positive rate than existing models. Also we discuss possible overfitting of constructed motifs. Software and the collection of regulatory motifs are freely available at http://line.imb.ac.ru/DMMPMM.

Local structure and X-ray magnetic circular dichroism of Au in Au-Co nanoalloys

NASA Astrophysics Data System (ADS)

Maurizio, C.; Michieli, N.; Kalinic, B.; Mattarello, V.; Bello, V.; Wilhelm, F.; Ollefs, K.; Mattei, G.

2018-03-01

Coupling a plasmonic metal with a magnetic one in thin films and nanostructures is very interesting for the emerging field of magnetoplasmonics. In particular, coupling through alloying is a promising strategy to induce a magnetic moment on the plasmonic metal atoms, in a way that is intimately related to the local structure of the (metastable) alloy material. In this framework, Au:Co bimetallic films have been produced via magnetron co-sputtering deposition. X-ray absorption spectroscopy (XAS) at both Au- and Co-edges clearly indicates the formation of a full-metallic layer composed for the major part of a binary AuxCo1-x alloy, with x = 0.7-0.8. XAS and transmission electron microscopy analyses suggest the presence of a minor fraction of segregated metals. X-ray magnetic circular dichroism (XMCD) analysis at Au L2,3 edges detected a net magnetic moment of Au atoms (μ = 0.06 μB), significantly larger (≈3.5 times) that the one for Au-capped Co nanoclusters and comparable to the one for a Co-rich Au/Co multilayer, despite the 4 times larger concentration of Co with respect to the present case. This Au-Co magnetic coupling is favored by a high degree of mixing of the two metals in the alloy.

Signature properties of water: Their molecular electronic origins

PubMed Central

Jones, Andrew P.; Cipcigan, Flaviu S.; Crain, Jason; Martyna, Glenn J.

2015-01-01

Water challenges our fundamental understanding of emergent materials properties from a molecular perspective. It exhibits a uniquely rich phenomenology including dramatic variations in behavior over the wide temperature range of the liquid into water’s crystalline phases and amorphous states. We show that many-body responses arising from water’s electronic structure are essential mechanisms harnessed by the molecule to encode for the distinguishing features of its condensed states. We treat the complete set of these many-body responses nonperturbatively within a coarse-grained electronic structure derived exclusively from single-molecule properties. Such a “strong coupling” approach generates interaction terms of all symmetries to all orders, thereby enabling unique transferability to diverse local environments such as those encountered along the coexistence curve. The symmetries of local motifs that can potentially emerge are not known a priori. Consequently, electronic responses unfiltered by artificial truncation are then required to embody the terms that tip the balance to the correct set of structures. Therefore, our fully responsive molecular model produces, a simple, accurate, and intuitive picture of water’s complexity and its molecular origin, predicting water’s signature physical properties from ice, through liquid–vapor coexistence, to the critical point. PMID:25941394

Genome-wide colonization of gene regulatory elements by G4 DNA motifs

PubMed Central

Du, Zhuo; Zhao, Yiqiang; Li, Ning

2009-01-01

G-quadruplex (or G4 DNA), a stable four-stranded structure found in guanine-rich regions, is implicated in the transcriptional regulation of genes involved in growth and development. Previous studies on the role of G4 DNA in gene regulation mostly focused on genomic regions proximal to transcription start sites (TSSs). To gain a more comprehensive understanding of the regulatory role of G4 DNA, we examined the landscape of potential G4 DNA (PG4Ms) motifs in the human genome and found that G4 motifs, not restricted to those found in the TSS-proximal regions, are bias toward gene-associated regions. Significantly, analyses of G4 motifs in seven types of well-known gene regulatory elements revealed a constitutive enrichment pattern and the clusters of G4 motifs tend to be colocalized with regulatory elements. Considering our analysis from a genome evolutionary perspective, we found evidence that the occurrence and accumulation of certain progenitors and canonical G4 DNA motifs within regulatory regions were progressively favored by natural selection. Our results suggest that G4 DNA motifs are ‘colonized’ in regulatory regions, supporting a likely genome-wide role of G4 DNA in gene regulation. We hypothesize that G4 DNA is a regulatory apparatus situated in regulatory elements, acting as a molecular switch that can modulate the role of the host functional regions, by transition in DNA structure. PMID:19759215

R 3Au 9 Pn ( R = Y, Gd–Tm; Pn = Sb, Bi): A link between Cu 10Sn 3 and Gd 14Ag 51

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

Celania, Chris; Smetana, Volodymyr; Provino, Alessia

A new series of intermetallic compounds R 3Au 9 Pn ( R = Y, Gd–Tm; Pn = Sb, Bi) has been discovered during the explorations of the Au-rich parts of rare-earth-containing ternary systems with p-block elements. The existence of the series is strongly restricted by both geometric and electronic factors. R 3Au 9 Pn compounds crystallize in the hexagonal crystal system with space group P6 3/m (a = 8.08–8.24 Å, c = 8.98–9.08 Å). All compounds feature Au- Pn, formally anionic, networks built up by layers of alternating edge-sharing Au@Au 6 and Sb@Au 6 trigonal antiprisms of overall composition Aumore » 6/2 Pn connected through additional Au atoms and separated by a triangular cationic substructure formed by R atoms. From a first look, the series appears to be isostructural with recently reported R 3Au 7Sn 3 (a ternary ordered derivative of the Cu 10Sn 3-structure type), but no example of R 3Au 9M is known when M is a triel or tetrel element. R 3Au 9 Pn also contains Au@Au 6Au 2 R 3 fully capped trigonal prisms, which are found to be isostructural with those found in the well-researched R 14Au 51 series. This structural motif, not present in R 3Au 7Sn 3, represents a previously unrecognized link between Cu 10Sn 3 and Gd 14Ag 51 parent structure types. Magnetic property measurements carried out for Ho 3Au 9Sb reveal a complex magnetic structure characterized by antiferromagnetic interactions at low temperature ( T N = 10 K). Two metamagnetic transitions occur at high field with a change from antiferromagnetic toward ferromagnetic ordering. Density functional theory based computations were performed to understand the materials’ properties and to shed some light on the stability ranges. As a result, this allowed a better understanding of the bonding pattern, especially of the Au-containing substructure, and elucidation of the role of the third element in the stability of the structure type.« less

R 3Au 9 Pn ( R = Y, Gd–Tm; Pn = Sb, Bi): A link between Cu 10Sn 3 and Gd 14Ag 51

DOE PAGES

Celania, Chris; Smetana, Volodymyr; Provino, Alessia; ...

2017-06-05

A new series of intermetallic compounds R 3Au 9 Pn ( R = Y, Gd–Tm; Pn = Sb, Bi) has been discovered during the explorations of the Au-rich parts of rare-earth-containing ternary systems with p-block elements. The existence of the series is strongly restricted by both geometric and electronic factors. R 3Au 9 Pn compounds crystallize in the hexagonal crystal system with space group P6 3/m (a = 8.08–8.24 Å, c = 8.98–9.08 Å). All compounds feature Au- Pn, formally anionic, networks built up by layers of alternating edge-sharing Au@Au 6 and Sb@Au 6 trigonal antiprisms of overall composition Aumore » 6/2 Pn connected through additional Au atoms and separated by a triangular cationic substructure formed by R atoms. From a first look, the series appears to be isostructural with recently reported R 3Au 7Sn 3 (a ternary ordered derivative of the Cu 10Sn 3-structure type), but no example of R 3Au 9M is known when M is a triel or tetrel element. R 3Au 9 Pn also contains Au@Au 6Au 2 R 3 fully capped trigonal prisms, which are found to be isostructural with those found in the well-researched R 14Au 51 series. This structural motif, not present in R 3Au 7Sn 3, represents a previously unrecognized link between Cu 10Sn 3 and Gd 14Ag 51 parent structure types. Magnetic property measurements carried out for Ho 3Au 9Sb reveal a complex magnetic structure characterized by antiferromagnetic interactions at low temperature ( T N = 10 K). Two metamagnetic transitions occur at high field with a change from antiferromagnetic toward ferromagnetic ordering. Density functional theory based computations were performed to understand the materials’ properties and to shed some light on the stability ranges. As a result, this allowed a better understanding of the bonding pattern, especially of the Au-containing substructure, and elucidation of the role of the third element in the stability of the structure type.« less

Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas

PubMed Central

Petrov, Anton I.; Zirbel, Craig L.; Leontis, Neocles B.

2013-01-01

The analysis of atomic-resolution RNA three-dimensional (3D) structures reveals that many internal and hairpin loops are modular, recurrent, and structured by conserved non-Watson–Crick base pairs. Structurally similar loops define RNA 3D motifs that are conserved in homologous RNA molecules, but can also occur at nonhomologous sites in diverse RNAs, and which often vary in sequence. To further our understanding of RNA motif structure and sequence variability and to provide a useful resource for structure modeling and prediction, we present a new method for automated classification of internal and hairpin loop RNA 3D motifs and a new online database called the RNA 3D Motif Atlas. To classify the motif instances, a representative set of internal and hairpin loops is automatically extracted from a nonredundant list of RNA-containing PDB files. Their structures are compared geometrically, all-against-all, using the FR3D program suite. The loops are clustered into motif groups, taking into account geometric similarity and structural annotations and making allowance for a variable number of bulged bases. The automated procedure that we have implemented identifies all hairpin and internal loop motifs previously described in the literature. All motif instances and motif groups are assigned unique and stable identifiers and are made available in the RNA 3D Motif Atlas (http://rna.bgsu.edu/motifs), which is automatically updated every four weeks. The RNA 3D Motif Atlas provides an interactive user interface for exploring motif diversity and tools for programmatic data access. PMID:23970545

Signature CERN-URSS

ScienceCinema

None

2017-12-09

Le DG W.Jentschke souhaite la bienvenue à l'assemblée et aux invités pour la signature du protocole entre le Cern et l'URSS qui est un événement important. C'est en 1955 que 55 visiteurs soviétiques ont visité le Cern pour la première fois. Le premier DG au Cern, F.Bloch, et Mons.Amaldi sont aussi présents. Tandis que le discours anglais de W.Jentschke est traduit en russe, le discours russe de Mons.Morozov est traduit en anglais.

Measurements of Strangeness Production on Au+Au collisions at 62 GeV

NASA Astrophysics Data System (ADS)

Guimaraes, K. S. F. F.; Munhoz, M. G.; Takahashi, J.; Moura, M. M.; Suaide, A. A. P.; Cosentino, M.

2005-10-01

The STAR (Solenoidal Tracker at RHIC) experiment is a large acceptance collider detector that measures primarily hadronic observables to search for signatures of the quark-gluon plasma phase transition and study strongly interacting matter at high energy density. Operational since June 2000, the new heavy ion collider RHIC has already provided Au+Au collisions at σNN = 62, 130 and 200 GeV as well as p+p and d+Au collisions at 200 GeV. The various collision energies and systems allow the systematic study of particle production in heavy ion collisions. In particular, the production of strange (anti-)particles is one of the major topics of STAR. This detector allows the measurement of a variety of particle species at mid-rapidity, like neutral kaons; Λ, Ξ, and Ω. hyperons; and their anti-particles that are reconstructed via their decay topology. The strangeness measurements should provide important information on various phenomenological aspects of ultra-relativistic heavy ion collisions. The goal of this work is to perform the measurement of neutral kaons on Au+Au collisions at 62 GeV. This measurement will bring important information about strangeness production in the energy range between the top RHIC energy and the top SPS energy, where important questions regarding particle production are still open. In this poster, preliminary results of the analysis will be presented, mainly the evaluation of the topological cuts necessary for the neutral kaon reconstruction and the corrections that are necessary to obtain the transverse momentum spectra.

G4 motifs affect origin positioning and efficiency in two vertebrate replicators

PubMed Central

Valton, Anne-Laure; Hassan-Zadeh, Vahideh; Lema, Ingrid; Boggetto, Nicole; Alberti, Patrizia; Saintomé, Carole; Riou, Jean-François; Prioleau, Marie-Noëlle

2014-01-01

DNA replication ensures the accurate duplication of the genome at each cell cycle. It begins at specific sites called replication origins. Genome-wide studies in vertebrates have recently identified a consensus G-rich motif potentially able to form G-quadruplexes (G4) in most replication origins. However, there is no experimental evidence to demonstrate that G4 are actually required for replication initiation. We show here, with two model origins, that G4 motifs are required for replication initiation. Two G4 motifs cooperate in one of our model origins. The other contains only one critical G4, and its orientation determines the precise position of the replication start site. Point mutations affecting the stability of this G4 in vitro also impair origin function. Finally, this G4 is not sufficient for origin activity and must cooperate with a 200-bp cis-regulatory element. In conclusion, our study strongly supports the predicted essential role of G4 in replication initiation. PMID:24521668

Synthesis and energetics of gold nanoclusters tailored by interfacial bonding structure

NASA Astrophysics Data System (ADS)

Tang, Zhenghua

In addition to the well known quantum confinement effects resulted from size and shape, interfacial bond structure is another factor, affecting the properties of the nanomaterial that is rarely studied. Inspired by the "Au-S-Au" staple motif discovered from the crystal structure of monothiol protected Au102 nanocluster (Science, 2007, 318, 430), dithiol molecules (e.g. 1, 2-dithiol, 1, 4-dithiol, etc.) with molecular structural constraint have been employed to create dithiolate protected clusters or mixed monothiolate and dithiolate protected clusters. The structure and properties of the Au clusters are expected to change due to two effects: The entropy gain of dithiol over monothiol protection and the constraint to the formation of the thiol bridging motif. DMPS (1, 2-dithiol molecule) stabilized clusters with characteristic absorption bands have been obtained, and characterized by multiple techniques. Monolayer reaction on gold core surface between the monothiol tiopronin and dithiol DMPS has been performed, and the mechanism has been probed. Mixed phenylethanethiolate and durene-dithiolate (1, 4-dithiol molecule) protected Au130 clusters with rich electrochemical features have been created, and the optical and electrochemical energetics have been successfully correlated based on core and core-ligand energy states. Furthermore, the impact of 1, 4-dithiolate-Au bonding on the near infrared luminescence has been studied. INDEX WORDS: Au MPCs, Staple motif, DMPS, Au DTCs, Au4, Tiopronin, Monolayer reaction, Durene-DT, Au MTCs, Au130, Optical energetic, Electrochemistry, Near infrared luminescence, 1, 4-Dithiolate-Au bonding.

Regulation of p21/CIP1/WAF-1 mediated cell-cycle arrest by RNase L and tristetraprolin, and involvement of AU-rich elements

PubMed Central

Al-Haj, Latifa; Blackshear, Perry J.; Khabar, Khalid S.A.

2012-01-01

The p21Cip1/WAF1 plays an important role in cell-cycle arrest. Here, we find that RNase L regulates p21-mediated G1 growth arrest in AU-rich elements-dependent manner. We found a significant loss of p21 mRNA expression in RNASEL−/− MEFs and that the overexpression of RNase L in HeLa cells induces p21 mRNA expression. The p21 mRNA half-life significantly changes as a result of RNase L modulation, indicating a post-transcriptional effect. Indeed, we found that RNase L promotes tristetraprolin (TTP/ZFP36) mRNA decay. This activity was not seen with dimerization- and nuclease-deficient RNase L mutants. Deficiency in TTP led to increases in p21 mRNA and protein. With induced ablation of RNase L, TTP mRNA and protein expressions were higher, while p21 expression became reduced. We further establish that TTP, but not C124R TTP mutant, binds to, and accelerates the decay of p21 mRNA. The p21 mRNA half-life was prolonged in TTP−/− MEFs. The TTP regulation of p21 mRNA decay required functional AU-rich elements. Thus, we demonstrate a novel mechanism of regulating G1 growth arrest by an RNase L-TTP-p21 axis. PMID:22718976

A survey of motif finding Web tools for detecting binding site motifs in ChIP-Seq data

PubMed Central

2014-01-01

Abstract ChIP-Seq (chromatin immunoprecipitation sequencing) has provided the advantage for finding motifs as ChIP-Seq experiments narrow down the motif finding to binding site locations. Recent motif finding tools facilitate the motif detection by providing user-friendly Web interface. In this work, we reviewed nine motif finding Web tools that are capable for detecting binding site motifs in ChIP-Seq data. We showed each motif finding Web tool has its own advantages for detecting motifs that other tools may not discover. We recommended the users to use multiple motif finding Web tools that implement different algorithms for obtaining significant motifs, overlapping resemble motifs, and non-overlapping motifs. Finally, we provided our suggestions for future development of motif finding Web tool that better assists researchers for finding motifs in ChIP-Seq data. Reviewers This article was reviewed by Prof. Sandor Pongor, Dr. Yuriy Gusev, and Dr. Shyam Prabhakar (nominated by Prof. Limsoon Wong). PMID:24555784

Electrochemical sensor based on electrodeposited graphene-Au modified electrode and nanoAu carrier amplified signal strategy for attomolar mercury detection.

PubMed

Zhang, Yi; Zeng, Guang Ming; Tang, Lin; Chen, Jun; Zhu, Yuan; He, Xiao Xiao; He, Yan

2015-01-20

An electrochemical sensor was developed for attomolar Hg(2+) detection. Three single-stranded DNA probes were rationally designed for selective and sensitive detection of the target, which combined T-Hg(2+)-T coordination chemistry and the characteristic of convenient modification of electrochemical signal indicator. Graphene and nanoAu were successively electrodeposited on a glass carbon electrode surface to improve the electrode conductivity and functionalize with the 10-mer thymine-rich DNA probe (P1). NanoAu carriers functionalized with 29-mer guanine-rich DNA probe (P3) labeled methyl blue (MB-nanoAu-P 3s) were used to further strengthen signal response. In the presence of Hg(2+), a T-T mismatched dsDNA would occur between P1 and a 22-mer thymine-rich DNA probe (P2) on the electrode surface due to T-Hg(2+)-T coordination chemistry. Followed by adding the MB-nanoAu-P 3s for hybridization with P2, square wave voltammetry was executed. Under optimal conditions, Hg(2+) could be detected in the range from 1.0 aM to 100 nM with a detection limit of 0.001 aM. Selectivity measurements reveal that the sensor is specific for Hg(2+) even with interference by high concentrations of other metal ions. Three different environmental samples were analyzed by the sensor and the results were compared with that from an atomic fluorescence spectrometry. The developed sensor was demonstrated to achieve excellent detectability. It may be applied to development of ultrasensitive detection strategies.

Novel condensation of Au-centered trigonal prisms in rare-earth-metal-rich tellurides: Er7Au2Te2 and Lu7Au2Te2.

PubMed

Gupta, Shalabh; Corbett, John D

2010-07-14

A new monoclinic structure occurs for Er(7)Au(2)Te(2) according to X-ray diffraction analysis of single crystals grown at 1200 degrees C: C2/m, Z = 4, a = 17.8310(9) A, b = 3.9819(5) A, c = 16.9089(9) A, beta = 104.361(4) degrees. The isostructural Lu(7)Au(2)Te(2) also exists according to X-ray powder pattern means, a = 17.536(4) A, b = 3.9719(4) A, c = 16.695(2) A, beta = 104.33(1) degrees. The structure contains zigzag chains of condensed, Au-centered tricapped trigonal prisms (TCTP) of Er along c that also share basal faces along b to generate puckered sheets. Further bi-face-capping Er atoms between these generate the three dimensional network along a, with tellurium in cavities outlined by augmented trigonal prismatic Er polyhedra. Bonding analysis via LMTO-DFT methods reveal very significant Er-Au bonding interactions, as quantified by their energy-weighted Hamilton overlap populations (-ICOHP), approximately 49% of the total for all interactions. These and similar Er-Te contributions sharply contrast with the small Er-Er population, only approximately 14% of the total in spite of the high proportion of Er-Er contacts. The strong polar bonding of Er to the electronegative Au and Te leaves Er relatively oxidized, with many of its 5d states falling above the Fermi level and empty. The contradiction with customary representations of structures that highlight rare-earth metal clusters is manifest. The large Er-Au Hamilton overlap population is in accord with the strong bonding between early and late transition metals first noted by Brewer in 1973. The relationship of this structure to the more distorted orthorhombic (Imm2) structure type of neighboring Dy(7)Ir(2)Te(2) is considered.

Bleogens: Cactus-Derived Anti-Candida Cysteine-Rich Peptides with Three Different Precursor Arrangements

PubMed Central

Loo, Shining; Kam, Antony; Xiao, Tianshu; Tam, James P.

2017-01-01

Cysteine-rich peptides (CRPs) play important host-defense roles in plants. However, information concerning CRPs in the Cactaceae (cactus) family is limited, with only a single cactus-derived CRP described to date. Here, we report the identification of 15 novel CRPs with three different precursor architectures, bleogens pB1-15 from Pereskia bleo of the Cactaceae family. By combining proteomic and transcriptomic methods, we showed that the prototype, bleogen pB1, contained 36 amino acid residues, a six-cysteine motif typical of the six-cysteine-hevein-like peptide (6C-HLP) family, and a type I two-domain precursor consisting of an endoplasmic reticulum (ER) and a mature domain. In contrast, the precursors of the other 14 bleogens contained a type II three-domain architecture with a propeptide domain inserted between the ER and the mature bleogen domain. Four of these 14 bleogens display a third type of architecture with a tandemly repeating bleogen domain. A search of the Onekp database revealed that <1% plant species possess three different precursor architectures for the biosynthesis of 6C-HLPs, including Lophophora williamsii, Pereskia aculeate, Portulaca cryptopetala, Portulaca oleracea, Portulaca suffruticosa, and Talinum sp. NMR analysis confirmed that bleogen pB1 has cystine-knot disulfide connectivity as well as a two-beta-sheet and a four-loop structural fold that is similar to other 6C-HLPs. Sequence analysis, structural studies, and in silico modeling revealed that bleogen pB1 has a cation-polar-cation motif, a signature heparin-binding motif that was confirmed by heparin affinity chromatography. Cell-based assays showed that bleogen pB1 is non-toxic to mammalian cells but functions as an anti-Candida peptide. Taken together, our findings provide insight into the occurrence, functions and precursor architectures of CRPs in the cactus family. PMID:29312404

The Rich Club of the C. elegans Neuronal Connectome

PubMed Central

Vértes, Petra E.; Ahnert, Sebastian E.; Schafer, William R.; Bullmore, Edward T.

2013-01-01

There is increasing interest in topological analysis of brain networks as complex systems, with researchers often using neuroimaging to represent the large-scale organization of nervous systems without precise cellular resolution. Here we used graph theory to investigate the neuronal connectome of the nematode worm Caenorhabditis elegans, which is defined anatomically at a cellular scale as 2287 synaptic connections between 279 neurons. We identified a small number of highly connected neurons as a rich club (N = 11) interconnected with high efficiency and high connection distance. Rich club neurons comprise almost exclusively the interneurons of the locomotor circuits, with known functional importance for coordinated movement. The rich club neurons are connector hubs, with high betweenness centrality, and many intermodular connections to nodes in different modules. On identifying the shortest topological paths (motifs) between pairs of peripheral neurons, the motifs that are found most frequently traverse the rich club. The rich club neurons are born early in development, before visible movement of the animal and before the main phase of developmental elongation of its body. We conclude that the high wiring cost of the globally integrative rich club of neurons in the C. elegans connectome is justified by the adaptive value of coordinated movement of the animal. The economical trade-off between physical cost and behavioral value of rich club organization in a cellular connectome confirms theoretical expectations and recapitulates comparable results from human neuroimaging on much larger scale networks, suggesting that this may be a general and scale-invariant principle of brain network organization. PMID:23575836

DNA polymerase η mutational signatures are found in a variety of different types of cancer.

PubMed

Rogozin, Igor B; Goncearenco, Alexander; Lada, Artem G; De, Subhajyoti; Yurchenko, Vyacheslav; Nudelman, German; Panchenko, Anna R; Cooper, David N; Pavlov, Youri I

2018-01-01

DNA polymerase (pol) η is a specialized error-prone polymerase with at least two quite different and contrasting cellular roles: to mitigate the genetic consequences of solar UV irradiation, and promote somatic hypermutation in the variable regions of immunoglobulin genes. Misregulation and mistargeting of pol η can compromise genome integrity. We explored whether the mutational signature of pol η could be found in datasets of human somatic mutations derived from normal and cancer cells. A substantial excess of single and tandem somatic mutations within known pol η mutable motifs was noted in skin cancer as well as in many other types of human cancer, suggesting that somatic mutations in A:T bases generated by DNA polymerase η are a common feature of tumorigenesis. Another peculiarity of pol ηmutational signatures, mutations in YCG motifs, led us to speculate that error-prone DNA synthesis opposite methylated CpG dinucleotides by misregulated pol η in tumors might constitute an additional mechanism of cytosine demethylation in this hypermutable dinucleotide.

Constitutional Dynamics of Metal-Organic Motifs on a Au(111) Surface.

PubMed

Kong, Huihui; Zhang, Chi; Xie, Lei; Wang, Likun; Xu, Wei

2016-06-13

Constitutional dynamic chemistry (CDC), including both dynamic covalent chemistry and dynamic noncovalent chemistry, relies on reversible formation and breakage of bonds to achieve continuous changes in constitution by reorganization of components. In this regard, CDC is considered to be an efficient and appealing strategy for selective fabrication of surface nanostructures by virtue of dynamic diversity. Although constitutional dynamics of monolayered structures has been recently demonstrated at liquid/solid interfaces, most of molecular reorganization/reaction processes were thought to be irreversible under ultrahigh vacuum (UHV) conditions where CDC is therefore a challenge to be achieved. Here, we have successfully constructed a system that presents constitutional dynamics on a solid surface based on dynamic coordination chemistry, in which selective formation of metal-organic motifs is achieved under UHV conditions. The key to making this reversible switching successful is the molecule-substrate interaction as revealed by DFT calculations. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Efficient red luminescence from organic-soluble Au25 clusters by ligand structure modification

NASA Astrophysics Data System (ADS)

Mathew, Ammu; Varghese, Elizabeth; Choudhury, Susobhan; Pal, Samir Kumar; Pradeep, T.

2015-08-01

An efficient method to enhance visible luminescence in a visibly non-luminescent organic-soluble 4-(tert butyl)benzyl mercaptan (SBB)-stabilized Au25 cluster has been developed. This method relies mainly on enhancing the surface charge density on the cluster by creating an additional shell of thiolate on the cluster surface, which enhances visible luminescence. The viability of this method has been demonstrated by imparting red luminescence to various ligand-protected quantum clusters (QCs), observable to the naked eye. The bright red luminescent material derived from Au25SBB18 clusters was characterized using UV-vis and luminescence spectroscopy, TEM, SEM/EDS, XPS, TG, ESI and MALDI mass spectrometry, which collectively proposed an uncommon molecular formula of Au29SBB24S, suggested to be due to different stapler motifs protecting the Au25 core. The critical role of temperature on the emergence of luminescence in QCs has been studied. The restoration of the surface ligand shell on the Au25 cluster and subsequent physicochemical modification to the cluster were probed by various mass spectral and spectroscopic techniques. Our results provide fundamental insights into the ligand characteristics determining luminescence in QCs.An efficient method to enhance visible luminescence in a visibly non-luminescent organic-soluble 4-(tert butyl)benzyl mercaptan (SBB)-stabilized Au25 cluster has been developed. This method relies mainly on enhancing the surface charge density on the cluster by creating an additional shell of thiolate on the cluster surface, which enhances visible luminescence. The viability of this method has been demonstrated by imparting red luminescence to various ligand-protected quantum clusters (QCs), observable to the naked eye. The bright red luminescent material derived from Au25SBB18 clusters was characterized using UV-vis and luminescence spectroscopy, TEM, SEM/EDS, XPS, TG, ESI and MALDI mass spectrometry, which collectively proposed an uncommon

Evidence of significant covalent bonding in Au(CN)(2)(-).

PubMed

Wang, Xue-Bin; Wang, Yi-Lei; Yang, Jie; Xing, Xiao-Peng; Li, Jun; Wang, Lai-Sheng

2009-11-18

The Au(CN)(2)(-) ion is the most stable Au compound known for centuries, yet a detailed understanding of its chemical bonding is still lacking. Here we report direct experimental evidence of significant covalent bonding character in the Au-C bonds in Au(CN)(2)(-) using photoelectron spectroscopy and comparisons with its lighter congeners, Ag(CN)(2)(-) and Cu(CN)(2)(-). Vibrational progressions in the Au-C stretching mode were observed for all detachment transitions for Au(CN)(2)(-), in contrast to the atomic-like transitions for Cu(CN)(2)(-), revealing the Au-C covalent bonding character. In addition, rich electronic structural information was obtained for Au(CN)(2)(-) by employing 118 nm detachment photons. Density functional theory and high-level ab initio calculations were carried out to understand the photoelectron spectra and obtain insight into the nature of the chemical bonding in the M(CN)(2)(-) complexes. Significant covalent character in the Au-C bonding due to the strong relativistic effects was revealed in Au(CN)(2)(-), consistent with its high stability.

Magnetism and 155Gd Mössbauer spectroscopy of GdAuMg

NASA Astrophysics Data System (ADS)

Łątka, Kazimierz; Kmieć, Roman; Pacyna, Andrzej W.; Fickenscher, Thomas; Hoffmann, Rolf-Dieter; Pöttgen, Rainer

2004-03-01

GdAuMg was synthesized by reaction of the elements in a sealed tantalum ampule in a high-frequency furnace. The structure was investigated by X-ray diffraction on both powders and single crystals: ZrNiAl type, P 6¯2m , a=756.3(1), c=412.71(7) pm, wR2=0.0285 for 308 F2 values, 14 variables. Geometrical motifs of the GdAuMg structure are gold centered tricapped trigonal prisms [Au1Mg 3Gd 6] and [Au2Mg 6Gd 3]. Together the gold and magnesium atoms form a three-dimensional [AuMg] network in which the gadolinium atoms fill distorted hexagonal channels. Bulk magnetic properties have been investigated by means of AC and DC magnetic susceptibility measurements and 155Gd Mössbauer spectroscopy was used to monitor the local electronic and magnetic structure. Two magnetic phase transitions were found. One transition, at T1= TN=81.1(1) K, is from a paramagnetic to an antiferromagnetic state of collinear character and the other at T2=19.0(1) from the antiferromagnetic to a kind of canted magnetic ordering characterized by a very narrow hysteresis loop.

Space-related pharma-motifs for fast search of protein binding motifs and polypharmacological targets

PubMed Central

2012-01-01

Background To discover a compound inhibiting multiple proteins (i.e. polypharmacological targets) is a new paradigm for the complex diseases (e.g. cancers and diabetes). In general, the polypharmacological proteins often share similar local binding environments and motifs. As the exponential growth of the number of protein structures, to find the similar structural binding motifs (pharma-motifs) is an emergency task for drug discovery (e.g. side effects and new uses for old drugs) and protein functions. Results We have developed a Space-Related Pharmamotifs (called SRPmotif) method to recognize the binding motifs by searching against protein structure database. SRPmotif is able to recognize conserved binding environments containing spatially discontinuous pharma-motifs which are often short conserved peptides with specific physico-chemical properties for protein functions. Among 356 pharma-motifs, 56.5% interacting residues are highly conserved. Experimental results indicate that 81.1% and 92.7% polypharmacological targets of each protein-ligand complex are annotated with same biological process (BP) and molecular function (MF) terms, respectively, based on Gene Ontology (GO). Our experimental results show that the identified pharma-motifs often consist of key residues in functional (active) sites and play the key roles for protein functions. The SRPmotif is available at http://gemdock.life.nctu.edu.tw/SRP/. Conclusions SRPmotif is able to identify similar pharma-interfaces and pharma-motifs sharing similar binding environments for polypharmacological targets by rapidly searching against the protein structure database. Pharma-motifs describe the conservations of binding environments for drug discovery and protein functions. Additionally, these pharma-motifs provide the clues for discovering new sequence-based motifs to predict protein functions from protein sequence databases. We believe that SRPmotif is useful for elucidating protein functions and drug discovery

Space-related pharma-motifs for fast search of protein binding motifs and polypharmacological targets.

PubMed

Chiu, Yi-Yuan; Lin, Chun-Yu; Lin, Chih-Ta; Hsu, Kai-Cheng; Chang, Li-Zen; Yang, Jinn-Moon

2012-01-01

To discover a compound inhibiting multiple proteins (i.e. polypharmacological targets) is a new paradigm for the complex diseases (e.g. cancers and diabetes). In general, the polypharmacological proteins often share similar local binding environments and motifs. As the exponential growth of the number of protein structures, to find the similar structural binding motifs (pharma-motifs) is an emergency task for drug discovery (e.g. side effects and new uses for old drugs) and protein functions. We have developed a Space-Related Pharmamotifs (called SRPmotif) method to recognize the binding motifs by searching against protein structure database. SRPmotif is able to recognize conserved binding environments containing spatially discontinuous pharma-motifs which are often short conserved peptides with specific physico-chemical properties for protein functions. Among 356 pharma-motifs, 56.5% interacting residues are highly conserved. Experimental results indicate that 81.1% and 92.7% polypharmacological targets of each protein-ligand complex are annotated with same biological process (BP) and molecular function (MF) terms, respectively, based on Gene Ontology (GO). Our experimental results show that the identified pharma-motifs often consist of key residues in functional (active) sites and play the key roles for protein functions. The SRPmotif is available at http://gemdock.life.nctu.edu.tw/SRP/. SRPmotif is able to identify similar pharma-interfaces and pharma-motifs sharing similar binding environments for polypharmacological targets by rapidly searching against the protein structure database. Pharma-motifs describe the conservations of binding environments for drug discovery and protein functions. Additionally, these pharma-motifs provide the clues for discovering new sequence-based motifs to predict protein functions from protein sequence databases. We believe that SRPmotif is useful for elucidating protein functions and drug discovery.

WebMOTIFS: automated discovery, filtering and scoring of DNA sequence motifs using multiple programs and Bayesian approaches

PubMed Central

Romer, Katherine A.; Kayombya, Guy-Richard; Fraenkel, Ernest

2007-01-01

WebMOTIFS provides a web interface that facilitates the discovery and analysis of DNA-sequence motifs. Several studies have shown that the accuracy of motif discovery can be significantly improved by using multiple de novo motif discovery programs and using randomized control calculations to identify the most significant motifs or by using Bayesian approaches. WebMOTIFS makes it easy to apply these strategies. Using a single submission form, users can run several motif discovery programs and score, cluster and visualize the results. In addition, the Bayesian motif discovery program THEME can be used to determine the class of transcription factors that is most likely to regulate a set of sequences. Input can be provided as a list of gene or probe identifiers. Used with the default settings, WebMOTIFS accurately identifies biologically relevant motifs from diverse data in several species. WebMOTIFS is freely available at http://fraenkel.mit.edu/webmotifs. PMID:17584794

A polymorphism in a conserved posttranscriptional regulatory motif alters bone morphogenetic protein 2 (BMP2) RNA:protein interactions.

PubMed

Fritz, David T; Jiang, Shan; Xu, Junwang; Rogers, Melissa B

2006-07-01

The bone morphogenetic protein (BMP)2 gene has been genetically linked to osteoporosis and osteoarthritis. We have shown that the 3'-untranslated regions (UTR) of BMP2 genes from mammals to fishes are extraordinarily conserved. This indicates that the BMP2 3'-UTR is under stringent selective pressure. We present evidence that the conserved region is a strong posttranscriptional regulator of BMP2 expression. Polymorphisms in cis-regulatory elements have been proven to influence susceptibility to a growing number of diseases. A common single nucleotide polymorphism (SNP) disrupts a putative posttranscriptional regulatory motif, an AU-rich element, within the BMP2 3'-UTR. The affinity of specific proteins for the rs15705 SNP sequence differs from their affinity for the normal human sequence. More importantly, the in vitro decay rate of RNAs with the SNP is higher than that of RNAs with the normal sequence. Such changes in mRNA:protein interactions may influence the posttranscriptional mechanisms that control BMP2 gene expression. The consequent alterations in BMP2 protein levels may influence the development or physiology of bone or other BMP2-influenced tissues.

Phospholipid composition and a polybasic motif determine D6 PROTEIN KINASE polar association with the plasma membrane and tropic responses.

PubMed

Barbosa, Inês C R; Shikata, Hiromasa; Zourelidou, Melina; Heilmann, Mareike; Heilmann, Ingo; Schwechheimer, Claus

2016-12-15

Polar transport of the phytohormone auxin through PIN-FORMED (PIN) auxin efflux carriers is essential for the spatiotemporal control of plant development. The Arabidopsis thaliana serine/threonine kinase D6 PROTEIN KINASE (D6PK) is polarly localized at the plasma membrane of many cells where it colocalizes with PINs and activates PIN-mediated auxin efflux. Here, we show that the association of D6PK with the basal plasma membrane and PINs is dependent on the phospholipid composition of the plasma membrane as well as on the phosphatidylinositol phosphate 5-kinases PIP5K1 and PIP5K2 in epidermis cells of the primary root. We further show that D6PK directly binds polyacidic phospholipids through a polybasic lysine-rich motif in the middle domain of the kinase. The lysine-rich motif is required for proper PIN3 phosphorylation and for auxin transport-dependent tropic growth. Polybasic motifs are also present at a conserved position in other D6PK-related kinases and required for membrane and phospholipid binding. Thus, phospholipid-dependent recruitment to membranes through polybasic motifs might not only be required for D6PK-mediated auxin transport but also other processes regulated by these, as yet, functionally uncharacterized kinases. © 2016. Published by The Company of Biologists Ltd.

Biological network motif detection and evaluation

PubMed Central

2011-01-01

Background Molecular level of biological data can be constructed into system level of data as biological networks. Network motifs are defined as over-represented small connected subgraphs in networks and they have been used for many biological applications. Since network motif discovery involves computationally challenging processes, previous algorithms have focused on computational efficiency. However, we believe that the biological quality of network motifs is also very important. Results We define biological network motifs as biologically significant subgraphs and traditional network motifs are differentiated as structural network motifs in this paper. We develop five algorithms, namely, EDGEGO-BNM, EDGEBETWEENNESS-BNM, NMF-BNM, NMFGO-BNM and VOLTAGE-BNM, for efficient detection of biological network motifs, and introduce several evaluation measures including motifs included in complex, motifs included in functional module and GO term clustering score in this paper. Experimental results show that EDGEGO-BNM and EDGEBETWEENNESS-BNM perform better than existing algorithms and all of our algorithms are applicable to find structural network motifs as well. Conclusion We provide new approaches to finding network motifs in biological networks. Our algorithms efficiently detect biological network motifs and further improve existing algorithms to find high quality structural network motifs, which would be impossible using existing algorithms. The performances of the algorithms are compared based on our new evaluation measures in biological contexts. We believe that our work gives some guidelines of network motifs research for the biological networks. PMID:22784624

Nucleic Acid i-Motif Structures in Analytical Chemistry.

PubMed

Alba, Joan Josep; Sadurní, Anna; Gargallo, Raimundo

2016-09-02

Under the appropriate experimental conditions of pH and temperature, cytosine-rich segments in DNA or RNA sequences may produce a characteristic folded structure known as an i-motif. Besides its potential role in vivo, which is still under investigation, this structure has attracted increasing interest in other fields due to its sharp, fast and reversible pH-driven conformational changes. This "on/off" switch at molecular level is being used in nanotechnology and analytical chemistry to develop nanomachines and sensors, respectively. This paper presents a review of the latest applications of this structure in the field of chemical analysis.

Gold-rich R 3Au 7Sn 3: Establishing the interdependence between electronic features and physical properties

DOE PAGES

Provino, Alessia; Steinberg, Simon; Smetana, Volodymyr; ...

2015-05-18

Two new polar intermetallic compounds Y 3Au 7Sn 3 (I) and Gd 3Au 7Sn 3 (II) have been synthesized and their structures have been determined by single crystal X-ray diffraction (P6 3/m; Z = 2, a = 8.148(1)/8.185(3), and c = 9.394(2)/9.415(3) for I/II, respectively). They can formally be assigned to the Cu 10Sn 3 type and consist of parallel slabs of Sn centered, edge-sharing trigonal Au 6 antiprisms connected through R 3 (R = Y, Gd) triangles. Additional Au atoms reside in the centres of trigonal Au 6 prisms forming Au@Au 6 clusters with Au–Au distances of 2.906–2.960 Å,more » while the R–R contacts in the R 3 groups are considerably larger than the sums of their metallic radii. These exclusive structural arrangements provide alluring systems to study the synergism between strongly correlated systems, particularly, those in the structure of (II), and extensive polar intermetallic contacts, which has been inspected by measurements of the magnetic properties, heat capacities and electrical conductivities of both compounds. Gd 3Au 7Sn 3 shows an antiferromagnetic ordering at 13 K, while Y 3Au 7Sn 3 is a Pauli paramagnet and a downward curvature in its electrical resistivity at about 1.9 K points to a superconducting transition. DFT-based band structure calculations on R 3Au 7Sn 3 (R = Y, Gd) account for the results of the conductivity measurements and different spin ordering models of (II) provide conclusive hints about its magnetic structure. As a result, chemical bonding analyses of both compounds indicate that the vast majority of bonding originates from the heteroatomic Au–Gd and Au–Sn interactions, while homoatomic Au–Au bonding is evident within the Au@Au 6 clusters.« less

E-motif formed by extrahelical cytosine bases in DNA homoduplexes of trinucleotide and hexanucleotide repeats

PubMed Central

Pan, Feng; Zhang, Yuan; Man, Viet Hoang; Roland, Christopher

2018-01-01

Abstract Atypical DNA secondary structures play an important role in expandable trinucleotide repeat (TR) and hexanucleotide repeat (HR) diseases. The cytosine mismatches in C-rich homoduplexes and hairpin stems are weakly bonded; experiments show that for certain sequences these may flip out of the helix core, forming an unusual structure termed an ‘e-motif’. We have performed molecular dynamics simulations of C-rich TR and HR DNA homoduplexes in order to characterize the conformations, stability and dynamics of formation of the e-motif, where the mismatched cytosines symmetrically flip out in the minor groove, pointing their base moieties towards the 5′-direction in each strand. TRs have two non-equivalent reading frames, (GCC)n and (CCG)n; while HRs have three: (CCCGGC)n, (CGGCCC)n, (CCCCGG)n. We define three types of pseudo basepair steps related to the mismatches and show that the e-motif is only stable in (GCC)n and (CCCGGC)n homoduplexes due to the favorable stacking of pseudo GpC steps (whose nature depends on whether TRs or HRs are involved) and the formation of hydrogen bonds between the mismatched cytosine at position i and the cytosine (TRs) or guanine (HRs) at position i − 2 along the same strand. We also characterize the extended e-motif, where all mismatched cytosines are extruded, their extra-helical stacking additionally stabilizing the homoduplexes. PMID:29190385

Composition of Meridiani Hematite-rich Spherules: A Mass-Balance Mixing-Model Approach

NASA Technical Reports Server (NTRS)

jOLLIFF, b. l.

2005-01-01

One of the great surprises of the Mars Exploration Rovers (MER) mission is the discovery at Meridiani Planum that the surface hematite signature observed from orbit is attributable largely to a surface enrichment of hematite-rich spherules, thought to be concretions, that have weathered out of rocks similar to the underlying sulfate-rich rock formation [1]. A strong hematite signature has been observed by the Mini-TES [2] and by in-situ measurements of spherule-rich targets by the Mossbauer spectrometer (MB) [3] and the alpha-particle X-ray spectrometer (APXS) [4]. The Mini-TES derived spectrum of spherule-rich targets on the plains is consistent with nearly pure coarse-grained hematite, with perhaps as little as 5-10 areal % of other components [2]. The occurrence and abundance of the spherules as the bearer of the widespread hematite signature observed by MGS TES over much of Meridiani Planum is significant for global remote sensing, and their occurrence as concretions in the outcrop lithology is significant for the diagenetic history and role of water in the formation of the sedimentary rock formation [5].

(R-X-R)4 -Motif Peptides Containing Conformationally Constrained Cyclohexane-Derived Spacers: Effect on Cellular Uptake.

PubMed

Bhosle, Govind S; Fernandes, Moneesha

2017-11-08

Arginine-rich peptides having the (R-X-R) n motif are among the most effective cell-penetrating peptides (CPPs). Herein we report a several-fold increase in the efficacy of such CPPs if the linear flexible spacer (-X-) in the (R-X-R) motif is replaced by constrained cyclic 1,4-substituted-cyclohexane-derived spacers. Internalization of these oligomers in mammalian cell lines was found to be an energy-dependent process. Incorporation of these constrained, non-proteinogenic amino acid spacers in the CPPs is shown to enhance their proteolytic stability. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effects Of Hydrothermal Alteration On Magnetic Properties And Magnetic Signatures - Implications For Predictive Magnetic Exploration Models

NASA Astrophysics Data System (ADS)

Clark, D.

2012-12-01

Magnetics is the most widely used geophysical method in hard rock exploration and magnetic surveys are an integral part of exploration programs for many types of mineral deposit, including porphyry Cu, intrusive-related gold, volcanic-hosted epithermal Au, IOCG, VMS, and Ni sulfide deposits. However, the magnetic signatures of ore deposits and their associated mineralized systems are extremely variable and exploration that is based simply on searching for signatures that resemble those of known deposits and systems is rarely successful. Predictive magnetic exploration models are based upon well-established geological models, combined with magnetic property measurements and geological information from well-studied deposits, and guided by magnetic petrological understanding of the processes that create, destroy and modify magnetic minerals in rocks. These models are designed to guide exploration by predicting magnetic signatures that are appropriate to specific geological settings, taking into account factors such as tectonic province; protolith composition; post-formation tilting/faulting/ burial/ exhumation and partial erosion; and metamorphism. Patterns of zoned hydrothermal alteration are important indicators of potentially mineralized systems and, if properly interpreted, can provided vectors to ore. Magnetic signatures associated with these patterns at a range of scales can provide valuable information on prospectivity and can guide drilling, provided they are correctly interpreted in geological terms. This presentation reviews effects of the important types of hydrothermal alteration on magnetic properties within mineralized systems, with particular reference to porphyry copper and IOCG deposits. For example, an unmodified gold-rich porphyry copper system, emplaced into mafic-intermediate volcanic host rocks (such as Bajo de la Alumbrera, Argentina) exhibits an inner potassic zone that is strongly mineralized and magnetite-rich, which is surrounded by an outer

Atomic structure of water/Au, Ag, Cu and Pt atomic junctions.

PubMed

Li, Yu; Kaneko, Satoshi; Fujii, Shintaro; Nishino, Tomoaki; Kiguchi, Manabu

2017-02-08

Much progress has been made in understanding the transport properties of atomic-scale conductors. We prepared atomic-scale metal contacts of Cu, Ag, Au and Pt using a mechanically controllable break junction method at 10 K in a cryogenic vacuum. Water molecules were exposed to the metal atomic contacts and the effect of molecular adsorption was investigated by electronic conductance measurements. Statistical analysis of the electronic conductance showed that the water molecule(s) interacted with the surface of the inert Au contact and the reactive Cu ant Pt contacts, where molecular adsorption decreased the electronic conductance. A clear conductance signature of water adsorption was not apparent at the Ag contact. Detailed analysis of the conductance behaviour during a contact-stretching process indicated that metal atomic wires were formed for the Au and Pt contacts. The formation of an Au atomic wire consisting of low coordination number atoms leads to increased reactivity of the inert Au surface towards the adsorption of water.

Isosteric And Non-Isosteric Base Pairs In RNA Motifs: Molecular Dynamics And Bioinformatics Study Of The Sarcin-Ricin Internal Loop

PubMed Central

Havrila, Marek; Réblová, Kamila; Zirbel, Craig L.; Leontis, Neocles B.; Šponer, Jiří

2013-01-01

The Sarcin-Ricin RNA motif (SR motif) is one of the most prominent recurrent RNA building blocks that occurs in many different RNA contexts and folds autonomously, i.e., in a context-independent manner. In this study, we combined bioinformatics analysis with explicit-solvent molecular dynamics (MD) simulations to better understand the relation between the RNA sequence and the evolutionary patterns of SR motif. SHAPE probing experiment was also performed to confirm fidelity of MD simulations. We identified 57 instances of the SR motif in a non-redundant subset of the RNA X-ray structure database and analyzed their basepairing, base-phosphate, and backbone-backbone interactions. We extracted sequences aligned to these instances from large ribosomal RNA alignments to determine frequency of occurrence for different sequence variants. We then used a simple scoring scheme based on isostericity to suggest 10 sequence variants with highly variable expected degree of compatibility with the SR motif 3D structure. We carried out MD simulations of SR motifs with these base substitutions. Non isosteric base substitutions led to unstable structures, but so did isosteric substitutions which were unable to make key base-phosphate interactions. MD technique explains why some potentially isosteric SR motifs are not realized during evolution. We also found that inability to form stable cWW geometry is an important factor in case of the first base pair of the flexible region of the SR motif. Comparison of structural, bioinformatics, SHAPE probing and MD simulation data reveals that explicit solvent MD simulations neatly reflect viability of different sequence variants of the SR motif. Thus, MD simulations can efficiently complement bioinformatics tools in studies of conservation patterns of RNA motifs and provide atomistic insight into the role of their different signature interactions. PMID:24144333

Geochemical and Sulfur-Isotopic Signatures of Volcanogenic Massive Sulfide Deposits on Prince of Wales Island and Vicinity, Southeastern Alaska

USGS Publications Warehouse

Slack, John F.; Shanks, Wayne C.; Karl, Susan M.; Gemery, Pamela A.; Bittenbender, Peter E.; Ridley, W. Ian

2007-01-01

Stratabound volcanogenic massive sulfide (VMS) deposits on Prince of Wales Island and vicinity, southeastern Alaska, occur in two volcanosedimentary sequences of Late Proterozoic through Cambrian and of Ordovician through Early Silurian age. This study presents geochemical data on sulfide-rich samples, in situ laser-ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) of sulfide minerals, and sulfur-isotopic analyses of sulfides and sulfates (barite) for identifying and distinguishing between primary sea-floor signatures and later regional metamorphic overprints. These datasets are also used here in an attempt to discriminate the VMS deposits in the older Wales Group from those in the younger Moira Sound unit (new informal name). The Wales Group and its contained VMS deposits have been multiply deformed and metamorphosed from greenschist to amphibolite grade, whereas the Moira Sound unit and related VMS deposits are less deformed and generally less metamorphosed (lower to middle greenschist grade). Variations in the sulfide mineral assemblages and textures of the VMS deposits in both sequences reflect a combination of processes, including primary sea-floor mineralization and sub-sea-floor zone refining, followed by metamorphic recrystallization. Very coarse grained (>1 cm diam) sulfide minerals and abundant pyrrhotite are restricted to VMS deposits in a small area of the Wales Group, at Khayyam and Stumble-On, which record high-grade metamorphism of the sulfides. Geochemical and sulfur-isotopic data distinguish the VMS deposits in the Wales Group from those in the Moira Sound unit. Although base- and precious-metal contents vary widely in sulfide-rich samples from both sequences, samples from the Moira Sound generally have proportionately higher Ag contents relative to base metals and Au. In situ LA-ICP-MS analysis of trace elements in the sulfide minerals suggests that primary sea-floor hydrothermal signatures are preserved in some samples (for

Efficient exact motif discovery.

PubMed

Marschall, Tobias; Rahmann, Sven

2009-06-15

The motif discovery problem consists of finding over-represented patterns in a collection of biosequences. It is one of the classical sequence analysis problems, but still has not been satisfactorily solved in an exact and efficient manner. This is partly due to the large number of possibilities of defining the motif search space and the notion of over-representation. Even for well-defined formalizations, the problem is frequently solved in an ad hoc manner with heuristics that do not guarantee to find the best motif. We show how to solve the motif discovery problem (almost) exactly on a practically relevant space of IUPAC generalized string patterns, using the p-value with respect to an i.i.d. model or a Markov model as the measure of over-representation. In particular, (i) we use a highly accurate compound Poisson approximation for the null distribution of the number of motif occurrences. We show how to compute the exact clump size distribution using a recently introduced device called probabilistic arithmetic automaton (PAA). (ii) We define two p-value scores for over-representation, the first one based on the total number of motif occurrences, the second one based on the number of sequences in a collection with at least one occurrence. (iii) We describe an algorithm to discover the optimal pattern with respect to either of the scores. The method exploits monotonicity properties of the compound Poisson approximation and is by orders of magnitude faster than exhaustive enumeration of IUPAC strings (11.8 h compared with an extrapolated runtime of 4.8 years). (iv) We justify the use of the proposed scores for motif discovery by showing our method to outperform other motif discovery algorithms (e.g. MEME, Weeder) on benchmark datasets. We also propose new motifs on Mycobacterium tuberculosis. The method has been implemented in Java. It can be obtained from http://ls11-www.cs.tu-dortmund.de/people/marschal/paa_md/.

Ultra-relativistic Au+Au and d+Au collisions:

NASA Astrophysics Data System (ADS)

Back, B. B.; Baker, M. D.; Ballintijn, M.; Barton, D. S.; Betts, R. R.; Bickley, A. A.; Bindel, R.; Budzanowski, A.; Busza, W.; Carroll, A.; Chai, Z.; Decowski, M. P.; García, E.; Gburek, T.; George, N.; Gulbrandsen, K.; Gushue, S.; Halliwell, C.; Hamblen, J.; Hauer, M.; Heintzelman, G. A.; Henderson, C.; Hofman, D. J.; Hollis, R. S.; Hołyński, R.; Holzman, B.; Iordanova, A.; Johnson, E.; Kane, J. L.; Katzy, J.; Khan, N.; Kucewicz, W.; Kulinich, P.; Kuo, C. M.; Lin, W. T.; Manly, S.; McLeod, D.; Mignerey, A. C.; Nouicer, R.; Olszewski, A.; Pak, R.; Park, I. C.; Pernegger, H.; Reed, C.; Remsberg, L. P.; Reuter, M.; Roland, C.; Roland, G.; Rosenberg, L.; Sagerer, J.; Sarin, P.; Sawicki, P.; Seals, H.; Sedykh, I.; Skulski, W.; Smith, C. E.; Stankiewicz, M. A.; Steinberg, P.; Stephans, G. S. F.; Sukhanov, A.; Tang, J.-L.; Tonjes, M. B.; Trzupek, A.; Vale, C.; van Nieuwenhuizen, G. J.; Vaurynovich, S. S.; Verdier, R.; Veres, G. I.; Wenger, E.; Wolfs, F. L. H.; Wosiek, B.; Woźniak, K.; Wuosmaa, A. H.; Wysłouch, B.

In this talk I will review PHOBOS data on charged particle multiplicities, obtained in Au+Au and d+Au collisions at RHIC. The general features of the Au+Au pseudorapidity distributions results will be discussed and compared to those of /line{p}p collisions. The total charged particle multiplicity, scaled by the number of participant pairs, is observed to be about 40% higher in Au+Au collisions than in /line{p}p and d+Au systems, but, surprisingly at the same level of e+e- collisions. Limiting fragmentation scaling is seen to be obeyed in Au+Au collisions.

Counting motifs in dynamic networks.

PubMed

Mukherjee, Kingshuk; Hasan, Md Mahmudul; Boucher, Christina; Kahveci, Tamer

2018-04-11

A network motif is a sub-network that occurs frequently in a given network. Detection of such motifs is important since they uncover functions and local properties of the given biological network. Finding motifs is however a computationally challenging task as it requires solving the costly subgraph isomorphism problem. Moreover, the topology of biological networks change over time. These changing networks are called dynamic biological networks. As the network evolves, frequency of each motif in the network also changes. Computing the frequency of a given motif from scratch in a dynamic network as the network topology evolves is infeasible, particularly for large and fast evolving networks. In this article, we design and develop a scalable method for counting the number of motifs in a dynamic biological network. Our method incrementally updates the frequency of each motif as the underlying network's topology evolves. Our experiments demonstrate that our method can update the frequency of each motif in orders of magnitude faster than counting the motif embeddings every time the network changes. If the network evolves more frequently, the margin with which our method outperforms the existing static methods, increases. We evaluated our method extensively using synthetic and real datasets, and show that our method is highly accurate(≥ 96%) and that it can be scaled to large dense networks. The results on real data demonstrate the utility of our method in revealing interesting insights on the evolution of biological processes.

Exploring Short Linear Motifs Using the ELM Database and Tools.

PubMed

Gouw, Marc; Sámano-Sánchez, Hugo; Van Roey, Kim; Diella, Francesca; Gibson, Toby J; Dinkel, Holger

2017-06-27

The Eukaryotic Linear Motif (ELM) resource is dedicated to the characterization and prediction of short linear motifs (SLiMs). SLiMs are compact, degenerate peptide segments found in many proteins and essential to almost all cellular processes. However, despite their abundance, SLiMs remain largely uncharacterized. The ELM database is a collection of manually annotated SLiM instances curated from experimental literature. In this article we illustrate how to browse and search the database for curated SLiM data, and cover the different types of data integrated in the resource. We also cover how to use this resource in order to predict SLiMs in known as well as novel proteins, and how to interpret the results generated by the ELM prediction pipeline. The ELM database is a very rich resource, and in the following protocols we give helpful examples to demonstrate how this knowledge can be used to improve your own research. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

Solution structure and base pair opening kinetics of the i-motif dimer of d(5mCCTTTACC): a noncanonical structure with possible roles in chromosome stability.

PubMed

Nonin, S; Phan, A T; Leroy, J L

1997-09-15

Repetitive cytosine-rich DNA sequences have been identified in telomeres and centromeres of eukaryotic chromosomes. These sequences play a role in maintaining chromosome stability during replication and may be involved in chromosome pairing during meiosis. The C-rich repeats can fold into an 'i-motif' structure, in which two parallel-stranded duplexes with hemiprotonated C.C+ pairs are intercalated. Previous NMR studies of naturally occurring repeats have produced poor NMR spectra. This led us to investigate oligonucleotides, based on natural sequences, to produce higher quality spectra and thus provide further information as to the structure and possible biological function of the i-motif. NMR spectroscopy has shown that d(5mCCTTTACC) forms an i-motif dimer of symmetry-related and intercalated folded strands. The high-definition structure is computed on the basis of the build-up rates of 29 intraresidue and 35 interresidue nuclear Overhauser effect (NOE) connectivities. The i-motif core includes intercalated interstrand C.C+ pairs stacked in the order 2*.8/1.7*/1*.7/2.8* (where one strand is distinguished by an asterisk and the numbers relate to the base positions within the repeat). The TTTA sequences form two loops which span the two wide grooves on opposite sides of the i-motif core; the i-motif core is extended at both ends by the stacking of A6 onto C2.C8+. The lifetimes of pairs C2.C8+ and 5mC1.C7+ are 1 ms and 1 s, respectively, at 15 degrees C. Anomalous exchange properties of the T3 imino proton indicate hydrogen bonding to A6 N7 via a water bridge. The d(5mCCTTTTCC) deoxyoligonucleotide, in which position 6 is occupied by a thymidine instead of an adenine, also forms a symmetric i-motif dimer. However, in this structure the two TTTT loops are located on the same side of the i-motif core and the C.C+ pairs are formed by equivalent cytidines stacked in the order 8*.8/1.1*/7*.7/2.2*. Oligodeoxynucleotides containing two C-rich repeats can fold and dimerize

Measured and Modeled Long-Wave Infrared Signature of Quest in Q280

DTIC Science & Technology

2008-03-01

l’eau chaude par rapport à l’air froid , a constitué un autre cas permet- tant de mieux comprendre les signatures infrarouge et de mettre au point des...d’intensité énergétique infrarouge à l’horizon et dans la valeur absolue de l’in- tensité énergétique de la mer : le modèle laisse prévoir...ports de l’Arctique favorise fortement d’autres recherches sur les signatures infrarouge des navires en eaux froides et dans des conditions hivernales

A periodic mixed gaussians-plane waves DFT study on simple thiols on Au(111): adsorbate species, surface reconstruction, and thiols functionalization.

PubMed

Rajaraman, Gopalan; Caneschi, Andrea; Gatteschi, Dante; Totti, Federico

2011-03-07

Here we present DFT calculations based on a periodic mixed gaussians/plane waves approach to study the energetics, structure, bonding of SAMs of simple thiols on Au(111). Several open issues such as structure, bonding and the nature of adsorbate are taken into account. We started with methyl thiols (MeSH) on Au(111) to establish the nature of the adsorbate. We have considered several structural models embracing the reconstructed surface scenario along with the MeS˙-Au(ad)-MeS˙ type motif put forward in recent years. Our calculations suggest a clear preference for the homolytic cleavage of the S-H bond leading to a stable MeS˙ on a gold surface. In agreement with the recent literature studies, the reconstructed models of the MeS˙ species are found to be energetically preferred over unreconstructed models. Besides, our calculations reveal that the model with 1:2 Au(ad)/thiols ratio, i.e. MeS˙-Au(ad)-MeS˙, is energetically preferred compared to the clean and 1:1 ratio models, in agreement with the experimental and theoretical evidences. We have also performed Molecular Orbital/Natural Bond Orbital, MO/NBO, analysis to understand the electronic structure and bonding in different structural motifs and many useful insights have been gained. Finally, the studies have then been extended to alkyl thiols of the RSR' (R, R' = Me, Et and Ph) type and here our calculations again reveal a preference for the RS˙ type species adsorption for clean as well as for reconstructed 1:2 Au(ad)/thiols ratio models.

Metastable phase formation in the Au-Si system via ultrafast nanocalorimetry

NASA Astrophysics Data System (ADS)

Zhang, M.; Wen, J. G.; Efremov, M. Y.; Olson, E. A.; Zhang, Z. S.; Hu, L.; de la Rama, L. P.; Kummamuru, R.; Kavanagh, K. L.; Ma, Z.; Allen, L. H.

2012-05-01

We have investigated the stability and solidification of nanometer size Au-Si droplets using an ultrafast heating/cooling nanocalorimetry and in situ growth techniques. The liquid can be supercooled to very low temperatures for both Au-rich (ΔT ˜ 95 K) and Si-rich (ΔT ˜ 220 K) samples. Solidification of a unique metastable phase δ1 is observed with a composition of 74 ± 4 at. % Au and a b-centered orthorhombic structure (a = 0.92, b = 0.72, and c = 1.35 nm; body-center in the a-c plane), which grows heteroepitaxially to Aus. Its melting temperature Tm is 305 ± 5 °C. There is competition during formation between the eutectic and δ1 phases but δ1 is the only metastable alloy observed. For small size droplets, both the δ1 and eutectic phases show considerable depression of the melting point (size-dependent melting).

De Novo Regulatory Motif Discovery Identifies Significant Motifs in Promoters of Five Classes of Plant Dehydrin Genes.

PubMed

Zolotarov, Yevgen; Strömvik, Martina

2015-01-01

Plants accumulate dehydrins in response to osmotic stresses. Dehydrins are divided into five different classes, which are thought to be regulated in different manners. To better understand differences in transcriptional regulation of the five dehydrin classes, de novo motif discovery was performed on 350 dehydrin promoter sequences from a total of 51 plant genomes. Overrepresented motifs were identified in the promoters of five dehydrin classes. The Kn dehydrin promoters contain motifs linked with meristem specific expression, as well as motifs linked with cold/dehydration and abscisic acid response. KS dehydrin promoters contain a motif with a GATA core. SKn and YnSKn dehydrin promoters contain motifs that match elements connected with cold/dehydration, abscisic acid and light response. YnKn dehydrin promoters contain motifs that match abscisic acid and light response elements, but not cold/dehydration response elements. Conserved promoter motifs are present in the dehydrin classes and across different plant lineages, indicating that dehydrin gene regulation is likely also conserved.

Vasa promotes Drosophila germline stem cell differentiation by activating mei-P26 translation by directly interacting with a (U)-rich motif in its 3' UTR.

PubMed

Liu, Niankun; Han, Hong; Lasko, Paul

2009-12-01

Vasa (Vas) is a DEAD-box RNA-binding protein required in Drosophila at several steps of oogenesis and for primordial germ cell (PGC) specification. Vas associates with eukaryotic initiation factor 5B (eIF5B), and this interaction has been implicated in translational activation of gurken mRNA in the oocyte. Vas is expressed in all ovarian germline cells, and aspects of the vas-null phenotype suggest a function in regulating the balance between germline stem cells (GSCs) and their fate-restricted descendants. We used a biochemical approach to recover Vas-associated mRNAs and obtained mei-P26, whose product represses microRNA activity and promotes GSC differentiation. We found that vas and mei-P26 mutants interact, and that mei-P26 translation is substantially reduced in vas mutant cells. In vitro, Vas protein bound specifically to a (U)-rich motif in the mei-P26 3' untranslated region (UTR), and Vas-dependent regulation of GFP-mei-P26 transgenes in vivo was dependent on the same (U)-rich 3' UTR domain. The ability of Vas to activate mei-P26 expression in vivo was abrogated by a mutation that greatly reduces its interaction with eIF5B. Taken together, our data support the conclusion that Vas promotes germ cell differentiation by directly activating mei-P26 translation in early-stage committed cells.

Measurements of Multiparticle Correlations in d +Au Collisions at 200, 62.4, 39, and 19.6 GeV and p +Au Collisions at 200 GeV and Implications for Collective Behavior

NASA Astrophysics Data System (ADS)

Aidala, C.; Akiba, Y.; Alfred, M.; Andrieux, V.; Aoki, K.; Apadula, N.; Asano, H.; Ayuso, C.; Azmoun, B.; Babintsev, V.; Bagoly, A.; Bandara, N. S.; Barish, K. N.; Bathe, S.; Bazilevsky, A.; Beaumier, M.; Belmont, R.; Berdnikov, A.; Berdnikov, Y.; Blau, D. S.; Boer, M.; Bok, J. S.; Brooks, M. L.; Bryslawskyj, J.; Bumazhnov, V.; Butler, C.; Campbell, S.; Canoa Roman, V.; Cervantes, R.; Chi, C. Y.; Chiu, M.; Choi, I. J.; Choi, J. B.; Citron, Z.; Connors, M.; Cronin, N.; Csanád, M.; Csörgő, T.; Danley, T. W.; Daugherity, M. S.; David, G.; Deblasio, K.; Dehmelt, K.; Denisov, A.; Deshpande, A.; Desmond, E. J.; Dion, A.; Dixit, D.; Do, J. H.; Drees, A.; Drees, K. A.; Dumancic, M.; Durham, J. M.; Durum, A.; Elder, T.; Enokizono, A.; En'yo, H.; Esumi, S.; Fadem, B.; Fan, W.; Feege, N.; Fields, D. E.; Finger, M.; Finger, M.; Fokin, S. L.; Frantz, J. E.; Franz, A.; Frawley, A. D.; Fukuda, Y.; Gal, C.; Gallus, P.; Garg, P.; Ge, H.; Giordano, F.; Goto, Y.; Grau, N.; Greene, S. V.; Grosse Perdekamp, M.; Gunji, T.; Guragain, H.; Hachiya, T.; Haggerty, J. S.; Hahn, K. I.; Hamagaki, H.; Hamilton, H. F.; Han, S. Y.; Hanks, J.; Hasegawa, S.; Haseler, T. O. S.; He, X.; Hemmick, T. K.; Hill, J. C.; Hill, K.; Hodges, A.; Hollis, R. S.; Homma, K.; Hong, B.; Hoshino, T.; Hotvedt, N.; Huang, J.; Huang, S.; Imai, K.; Imrek, J.; Inaba, M.; Iordanova, A.; Isenhower, D.; Ito, Y.; Ivanishchev, D.; Jacak, B. V.; Jezghani, M.; Ji, Z.; Jiang, X.; Johnson, B. M.; Jorjadze, V.; Jouan, D.; Jumper, D. S.; Kang, J. H.; Kapukchyan, D.; Karthas, S.; Kawall, D.; Kazantsev, A. V.; Khachatryan, V.; Khanzadeev, A.; Kim, C.; Kim, D. J.; Kim, E.-J.; Kim, M.; Kim, M. H.; Kincses, D.; Kistenev, E.; Klatsky, J.; Kline, P.; Koblesky, T.; Kotov, D.; Kudo, S.; Kurita, K.; Kwon, Y.; Lajoie, J. G.; Lallow, E. O.; Lebedev, A.; Lee, S.; Lee, S. H.; Leitch, M. J.; Leung, Y. H.; Lewis, N. A.; Li, X.; Lim, S. H.; Liu, L. D.; Liu, M. X.; Loggins, V.-R.; Lökös, S.; Lovasz, K.; Lynch, D.; Majoros, T.; Makdisi, Y. I.; Makek, M.; Malaev, M.; Manko, V. I.; Mannel, E.; Masuda, H.; McCumber, M.; McGaughey, P. L.; McGlinchey, D.; McKinney, C.; Mendoza, M.; Metzger, W. J.; Mignerey, A. C.; Mihalik, D. E.; Milov, A.; Mishra, D. K.; Mitchell, J. T.; Mitsuka, G.; Miyasaka, S.; Mizuno, S.; Montuenga, P.; Moon, T.; Morrison, D. P.; Morrow, S. I. M.; Murakami, T.; Murata, J.; Nagai, K.; Nagashima, K.; Nagashima, T.; Nagle, J. L.; Nagy, M. I.; Nakagawa, I.; Nakagomi, H.; Nakano, K.; Nattrass, C.; Niida, T.; Nouicer, R.; Novák, T.; Novitzky, N.; Novotny, R.; Nyanin, A. S.; O'Brien, E.; Ogilvie, C. A.; Orjuela Koop, J. D.; Osborn, J. D.; Oskarsson, A.; Ottino, G. J.; Ozawa, K.; Pantuev, V.; Papavassiliou, V.; Park, J. S.; Park, S.; Pate, S. F.; Patel, M.; Peng, W.; Perepelitsa, D. V.; Perera, G. D. N.; Peressounko, D. Yu.; Perezlara, C. E.; Perry, J.; Petti, R.; Phipps, M.; Pinkenburg, C.; Pisani, R. P.; Pun, A.; Purschke, M. L.; Radzevich, P. V.; Read, K. F.; Reynolds, D.; Riabov, V.; Riabov, Y.; Richford, D.; Rinn, T.; Rolnick, S. D.; Rosati, M.; Rowan, Z.; Runchey, J.; Safonov, A. S.; Sakaguchi, T.; Sako, H.; Samsonov, V.; Sarsour, M.; Sato, K.; Sato, S.; Schaefer, B.; Schmoll, B. K.; Sedgwick, K.; Seidl, R.; Sen, A.; Seto, R.; Sexton, A.; Sharma, D.; Shein, I.; Shibata, T.-A.; Shigaki, K.; Shimomura, M.; Shioya, T.; Shukla, P.; Sickles, A.; Silva, C. L.; Silvermyr, D.; Singh, B. K.; Singh, C. P.; Singh, V.; Skoby, M. J.; Slunečka, M.; Smith, K. L.; Snowball, M.; Soltz, R. A.; Sondheim, W. E.; Sorensen, S. P.; Sourikova, I. V.; Stankus, P. W.; Stoll, S. P.; Sugitate, T.; Sukhanov, A.; Sumita, T.; Sun, J.; Syed, S.; Sziklai, J.; Takeda, A.; Tanida, K.; Tannenbaum, M. J.; Tarafdar, S.; Taranenko, A.; Tarnai, G.; Tieulent, R.; Timilsina, A.; Todoroki, T.; Tomášek, M.; Towell, C. L.; Towell, R. S.; Tserruya, I.; Ueda, Y.; Ujvari, B.; van Hecke, H. W.; Vazquez-Carson, S.; Velkovska, J.; Virius, M.; Vrba, V.; Vukman, N.; Wang, X. R.; Wang, Z.; Watanabe, Y.; Watanabe, Y. S.; Wong, C. P.; Woody, C. L.; Xu, C.; Xu, Q.; Xue, L.; Yalcin, S.; Yamaguchi, Y. L.; Yamamoto, H.; Yanovich, A.; Yin, P.; Yoo, J. H.; Yoon, I.; Yu, H.; Yushmanov, I. E.; Zajc, W. A.; Zelenski, A.; Zharko, S.; Zou, L.; Phenix Collaboration

2018-02-01

Recently, multiparticle-correlation measurements of relativistic p /d /He 3 +Au , p +Pb , and even p +p collisions show surprising collective signatures. Here, we present beam-energy-scan measurements of two-, four-, and six-particle angular correlations in d +Au collisions at √{sN N}=200 , 62.4, 39, and 19.6 GeV. We also present measurements of two- and four-particle angular correlations in p +Au collisions at √{sN N}=200 GeV . We find the four-particle cumulant to be real valued for d +Au collisions at all four energies. We also find that the four-particle cumulant in p +Au has the opposite sign as that in d +Au . Further, we find that the six-particle cumulant agrees with the four-particle cumulant in d +Au collisions at 200 GeV, indicating that nonflow effects are subdominant. These observations provide strong evidence that the correlations originate from the initial geometric configuration, which is then translated into the momentum distribution for all particles, commonly referred to as collectivity.

A tryptophan-rich motif in the human parainfluenza virus type 2 V protein is critical for the blockade of toll-like receptor 7 (TLR7)- and TLR9-dependent signaling.

PubMed

Kitagawa, Yoshinori; Yamaguchi, Mayu; Zhou, Min; Komatsu, Takayuki; Nishio, Machiko; Sugiyama, Tsuyoshi; Takeuchi, Kenji; Itoh, Masae; Gotoh, Bin

2011-05-01

Plasmacytoid dendritic cells (pDCs) do not produce alpha interferon (IFN-α) unless viruses cause a systemic infection or overcome the first-line defense provided by conventional DCs and macrophages. We show here that even paramyxoviruses, whose infections are restricted to the respiratory tract, have a V protein able to prevent Toll-like receptor 7 (TLR7)- and TLR9-dependent IFN-α induction specific to pDCs. Mutational analysis of human parainfluenza virus type 2 demonstrates that the second Trp residue of the Trp-rich motif (Trp-X(3)-Trp-X(9)-Trp) in the C-terminal domain unique to V, a determinant for IRF7 binding, is critical for the blockade of TLR7/9-dependent signaling.

Layered Structures and Disordered Polyanionic Nets in the Cation-Poor Polar Intermetallics CsAu 1.4 Ga 2.8 and CsAu 2 Ga 2.6

DOE PAGES

Smetana, Volodymyr; Steinberg, Simon; Mudring, Anja-Verena

2016-12-27

Gold intermetallics are known for their unusual structures and bonding patterns. Two new compounds have been discovered in the cation-poor part of the Cs–Au–Ga system. We obtained both compounds directly by heating the elements at elevated temperatures. Structure determinations based on single-crystal X-ray diffraction analyses revealed two structurally and compositionally related formations: CsAu 1.4Ga 2.8 (I) and CsAu 2Ga 2.6 (II) crystallize in their own structure types (I: Rmore » $$\\bar{3}$$, a = 11.160(2) Å, c = 21.706(4) Å, Z = 18; II: R$$\\bar{3}$$, a = 11.106(1) Å, Å, c = 77.243(9) Å, Z = 54) and contain hexagonal cationic layers of cesium. Furthermore, this is a unique structural motif, which has never been observed for the other (lighter) alkali metals in combination with Au and post transition elements. The polyanionic part is characterized in contrast by Au/Ga tetrahedral stars, a structural feature that is characteristic for light alkali metal representatives, and disordered sites with mixed Au/Ga occupancies that occur in both structures with a more significant disorder in the polyanionic component of CsAu 2Ga 2.6. Examinations of the electronic band structure for a model approximating the composition of CsAu 1.4Ga 2.8 have been completed using density-functional-theory-based methods and reveal a deep pseudogap at E F. Bonding analysis by evaluating the crystal orbital Hamilton populations show dominant heteroatomic Au–Ga bonds and only a negligible contribution from Cs pairs.« less

Signature Motifs Identify an Acinetobacter Cif Virulence Factor with Epoxide Hydrolase Activity*

PubMed Central

Bahl, Christopher D.; Hvorecny, Kelli L.; Bridges, Andrew A.; Ballok, Alicia E.; Bomberger, Jennifer M.; Cady, Kyle C.; O'Toole, George A.; Madden, Dean R.

2014-01-01

Endocytic recycling of the cystic fibrosis transmembrane conductance regulator (CFTR) is blocked by the CFTR inhibitory factor (Cif). Originally discovered in Pseudomonas aeruginosa, Cif is a secreted epoxide hydrolase that is transcriptionally regulated by CifR, an epoxide-sensitive repressor. In this report, we investigate a homologous protein found in strains of the emerging nosocomial pathogens Acinetobacter nosocomialis and Acinetobacter baumannii (“aCif”). Like Cif, aCif is an epoxide hydrolase that carries an N-terminal secretion signal and can be purified from culture supernatants. When applied directly to polarized airway epithelial cells, mature aCif triggers a reduction in CFTR abundance at the apical membrane. Biochemical and crystallographic studies reveal a dimeric assembly with a stereochemically conserved active site, confirming our motif-based identification of candidate Cif-like pathogenic EH sequences. Furthermore, cif expression is transcriptionally repressed by a CifR homolog (“aCifR”) and is induced in the presence of epoxides. Overall, this Acinetobacter protein recapitulates the essential attributes of the Pseudomonas Cif system and thus may facilitate airway colonization in nosocomial lung infections. PMID:24474692

Overexpression of AtGRDP2, a novel glycine-rich domain protein, accelerates plant growth and improves stress tolerance

PubMed Central

Ortega-Amaro, María A.; Rodríguez-Hernández, Aída A.; Rodríguez-Kessler, Margarita; Hernández-Lucero, Eloísa; Rosales-Mendoza, Sergio; Ibáñez-Salazar, Alejandro; Delgado-Sánchez, Pablo; Jiménez-Bremont, Juan F.

2015-01-01

Proteins with glycine-rich signatures have been reported in a wide variety of organisms including plants, mammalians, fungi, and bacteria. Plant glycine-rich protein genes exhibit developmental and tissue-specific expression patterns. Herein, we present the characterization of the AtGRDP2 gene using Arabidopsis null and knockdown mutants and, Arabidopsis and lettuce over-expression lines. AtGRDP2 encodes a short glycine-rich domain protein, containing a DUF1399 domain and a putative RNA recognition motif (RRM). AtGRDP2 transcript is mainly expressed in Arabidopsis floral organs, and its deregulation in Arabidopsis Atgrdp2 mutants and 35S::AtGRDP2 over-expression lines produces alterations in development. The 35S::AtGRDP2 over-expression lines grow faster than the WT, while the Atgrdp2 mutants have a delay in growth and development. The over-expression lines accumulate higher levels of indole-3-acetic acid and, have alterations in the expression pattern of ARF6, ARF8, and miR167 regulators of floral development and auxin signaling. Under salt stress conditions, 35S::AtGRDP2 over-expression lines displayed higher tolerance and increased expression of stress marker genes. Likewise, transgenic lettuce plants over-expressing the AtGRDP2 gene manifest increased growth rate and early flowering time. Our data reveal an important role for AtGRDP2 in Arabidopsis development and stress response, and suggest a connection between AtGRDP2 and auxin signaling. PMID:25653657

Structural and functional studies of a phosphatidic acid-binding antifungal plant defensin MtDef4: Identification of an RGFRRR motif governing fungal cell entry

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

Sagaram, Uma S.; El-Mounadi, Kaoutar; Buchko, Garry W.

A highly conserved plant defensin MtDef4 potently inhibits the growth of a filamentous fungus Fusarium graminearum. MtDef4 is internalized by cells of F. graminearum. To determine its mechanism of fungal cell entry and antifungal action, NMR solution structure of MtDef4 has been determined. The analysis of its structure has revealed a positively charged patch on the surface of the protein consisting of arginine residues in its γ-core signature, a major determinant of the antifungal activity of MtDef4. Here, we report functional analysis of the RGFRRR motif of the γ-core signature of MtDef4. The replacement of RGFRRR to AAAARR or tomore » RGFRAA not only abolishes fungal cell entry but also results in loss of the antifungal activity of MtDef4. MtDef4 binds strongly to phosphatidic acid (PA), a precursor for the biosynthesis of membrane phospholipids and a signaling lipid known to recruit cytosolic proteins to membranes. Mutations of RGFRRR which abolish fungal cell entry of MtDef4 also impair its binding to PA. Our results suggest that RGFRRR motif is a translocation signal for entry of MtDef4 into fungal cells and that this positively charged motif likely mediates interaction of this defensin with PA as part of its antifungal action.« less

The cytidine deaminase signature HxE(x)n CxxC of DYW1 binds zinc and is necessary for RNA editing of ndhD-1.

PubMed

Boussardon, Clément; Avon, Alexandra; Kindgren, Peter; Bond, Charles S; Challenor, Michael; Lurin, Claire; Small, Ian

2014-09-01

In flowering plants, RNA editing involves deamination of specific cytidines to uridines in both mitochondrial and chloroplast transcripts. Pentatricopeptide repeat (PPR) proteins and multiple organellar RNA editing factor (MORF) proteins have been shown to be involved in RNA editing but none have been shown to possess cytidine deaminase activity. The DYW domain of some PPR proteins contains a highly conserved signature resembling the zinc-binding active site motif of known nucleotide deaminases. We modified these highly conserved amino acids in the DYW motif of DYW1, an editing factor required for editing of the ndhD-1 site in Arabidopsis chloroplasts. We demonstrate that several amino acids of this signature motif are required for RNA editing in vivo and for zinc binding in vitro. We conclude that the DYW domain of DYW1 has features in common with cytidine deaminases, reinforcing the hypothesis that this domain forms part of the active enzyme that carries out RNA editing in plants. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

CombiMotif: A new algorithm for network motifs discovery in protein-protein interaction networks

NASA Astrophysics Data System (ADS)

Luo, Jiawei; Li, Guanghui; Song, Dan; Liang, Cheng

2014-12-01

Discovering motifs in protein-protein interaction networks is becoming a current major challenge in computational biology, since the distribution of the number of network motifs can reveal significant systemic differences among species. However, this task can be computationally expensive because of the involvement of graph isomorphic detection. In this paper, we present a new algorithm (CombiMotif) that incorporates combinatorial techniques to count non-induced occurrences of subgraph topologies in the form of trees. The efficiency of our algorithm is demonstrated by comparing the obtained results with the current state-of-the art subgraph counting algorithms. We also show major differences between unicellular and multicellular organisms. The datasets and source code of CombiMotif are freely available upon request.

Assessment of composite motif discovery methods.

PubMed

Klepper, Kjetil; Sandve, Geir K; Abul, Osman; Johansen, Jostein; Drablos, Finn

2008-02-26

Computational discovery of regulatory elements is an important area of bioinformatics research and more than a hundred motif discovery methods have been published. Traditionally, most of these methods have addressed the problem of single motif discovery - discovering binding motifs for individual transcription factors. In higher organisms, however, transcription factors usually act in combination with nearby bound factors to induce specific regulatory behaviours. Hence, recent focus has shifted from single motifs to the discovery of sets of motifs bound by multiple cooperating transcription factors, so called composite motifs or cis-regulatory modules. Given the large number and diversity of methods available, independent assessment of methods becomes important. Although there have been several benchmark studies of single motif discovery, no similar studies have previously been conducted concerning composite motif discovery. We have developed a benchmarking framework for composite motif discovery and used it to evaluate the performance of eight published module discovery tools. Benchmark datasets were constructed based on real genomic sequences containing experimentally verified regulatory modules, and the module discovery programs were asked to predict both the locations of these modules and to specify the single motifs involved. To aid the programs in their search, we provided position weight matrices corresponding to the binding motifs of the transcription factors involved. In addition, selections of decoy matrices were mixed with the genuine matrices on one dataset to test the response of programs to varying levels of noise. Although some of the methods tested tended to score somewhat better than others overall, there were still large variations between individual datasets and no single method performed consistently better than the rest in all situations. The variation in performance on individual datasets also shows that the new benchmark datasets represents a

Rapid motif compliance scoring with match weight sets.

PubMed

Venezia, D; O'Hara, P J

1993-02-01

Most current implementations of motif matching in biological sequences have sacrificed the generality of weight matrix scoring for shorter runtimes. The program MOTIF incorporates a weight matrix and a rapid, backtracking tree-search algorithm to score motif compliance with greatly enhanced performance while placing no constraints on the motif. In addition, any positions within a motif can be marked as 'inviolate', thereby requiring an exact match. MOTIF allows a choice of regular expression formats and can use both motif and sequence libraries as either targets or queries. Nucleic acid sequences can optionally be translated by MOTIF in any frame(s) and used against peptide motifs.

Measurements of Multiparticle Correlations in d + Au Collisions at 200, 62.4, 39, and 19.6 GeV and p + Au Collisions at 200 GeV and Implications for Collective Behavior

DOE PAGES

Aidala, C.; Akiba, Y.; Alfred, M.; ...

2018-02-06

Recently, multiparticle-correlation measurements of relativistic p/d/ 3He + Au, p + Pb, and even p + p collisions show surprising collective signatures. In this paper, we present beam-energy-scan measurements of two-, four-, and six-particle angular correlations in d + Au collisions at √ sNN = 200, 62.4, 39, and 19.6 GeV. We also present measurements of two- and four-particle angular correlations in p + Au collisions at √ sNN = 200 GeV. We find the four-particle cumulant to be real valued for d + Au collisions at all four energies. We also find that the four-particle cumulant in p +more » Au has the opposite sign as that in d + Au. Further, we find that the six-particle cumulant agrees with the four-particle cumulant in d + Au collisions at 200 GeV, indicating that nonflow effects are subdominant. Finally, these observations provide strong evidence that the correlations originate from the initial geometric configuration, which is then translated into the momentum distribution for all particles, commonly referred to as collectivity.« less

Measurements of Multiparticle Correlations in d+Au Collisions at 200, 62.4, 39, and 19.6 GeV and p+Au Collisions at 200 GeV and Implications for Collective Behavior.

PubMed

Aidala, C; Akiba, Y; Alfred, M; Andrieux, V; Aoki, K; Apadula, N; Asano, H; Ayuso, C; Azmoun, B; Babintsev, V; Bagoly, A; Bandara, N S; Barish, K N; Bathe, S; Bazilevsky, A; Beaumier, M; Belmont, R; Berdnikov, A; Berdnikov, Y; Blau, D S; Boer, M; Bok, J S; Brooks, M L; Bryslawskyj, J; Bumazhnov, V; Butler, C; Campbell, S; Canoa Roman, V; Cervantes, R; Chi, C Y; Chiu, M; Choi, I J; Choi, J B; Citron, Z; Connors, M; Cronin, N; Csanád, M; Csörgő, T; Danley, T W; Daugherity, M S; David, G; DeBlasio, K; Dehmelt, K; Denisov, A; Deshpande, A; Desmond, E J; Dion, A; Dixit, D; Do, J H; Drees, A; Drees, K A; Dumancic, M; Durham, J M; Durum, A; Elder, T; Enokizono, A; En'yo, H; Esumi, S; Fadem, B; Fan, W; Feege, N; Fields, D E; Finger, M; Finger, M; Fokin, S L; Frantz, J E; Franz, A; Frawley, A D; Fukuda, Y; Gal, C; Gallus, P; Garg, P; Ge, H; Giordano, F; Goto, Y; Grau, N; Greene, S V; Grosse Perdekamp, M; Gunji, T; Guragain, H; Hachiya, T; Haggerty, J S; Hahn, K I; Hamagaki, H; Hamilton, H F; Han, S Y; Hanks, J; Hasegawa, S; Haseler, T O S; He, X; Hemmick, T K; Hill, J C; Hill, K; Hodges, A; Hollis, R S; Homma, K; Hong, B; Hoshino, T; Hotvedt, N; Huang, J; Huang, S; Imai, K; Imrek, J; Inaba, M; Iordanova, A; Isenhower, D; Ito, Y; Ivanishchev, D; Jacak, B V; Jezghani, M; Ji, Z; Jiang, X; Johnson, B M; Jorjadze, V; Jouan, D; Jumper, D S; Kang, J H; Kapukchyan, D; Karthas, S; Kawall, D; Kazantsev, A V; Khachatryan, V; Khanzadeev, A; Kim, C; Kim, D J; Kim, E-J; Kim, M; Kim, M H; Kincses, D; Kistenev, E; Klatsky, J; Kline, P; Koblesky, T; Kotov, D; Kudo, S; Kurita, K; Kwon, Y; Lajoie, J G; Lallow, E O; Lebedev, A; Lee, S; Lee, S H; Leitch, M J; Leung, Y H; Lewis, N A; Li, X; Lim, S H; Liu, L D; Liu, M X; Loggins, V-R; Lökös, S; Lovasz, K; Lynch, D; Majoros, T; Makdisi, Y I; Makek, M; Malaev, M; Manko, V I; Mannel, E; Masuda, H; McCumber, M; McGaughey, P L; McGlinchey, D; McKinney, C; Mendoza, M; Metzger, W J; Mignerey, A C; Mihalik, D E; Milov, A; Mishra, D K; Mitchell, J T; Mitsuka, G; Miyasaka, S; Mizuno, S; Montuenga, P; Moon, T; Morrison, D P; Morrow, S I M; Murakami, T; Murata, J; Nagai, K; Nagashima, K; Nagashima, T; Nagle, J L; Nagy, M I; Nakagawa, I; Nakagomi, H; Nakano, K; Nattrass, C; Niida, T; Nouicer, R; Novák, T; Novitzky, N; Novotny, R; Nyanin, A S; O'Brien, E; Ogilvie, C A; Orjuela Koop, J D; Osborn, J D; Oskarsson, A; Ottino, G J; Ozawa, K; Pantuev, V; Papavassiliou, V; Park, J S; Park, S; Pate, S F; Patel, M; Peng, W; Perepelitsa, D V; Perera, G D N; Peressounko, D Yu; PerezLara, C E; Perry, J; Petti, R; Phipps, M; Pinkenburg, C; Pisani, R P; Pun, A; Purschke, M L; Radzevich, P V; Read, K F; Reynolds, D; Riabov, V; Riabov, Y; Richford, D; Rinn, T; Rolnick, S D; Rosati, M; Rowan, Z; Runchey, J; Safonov, A S; Sakaguchi, T; Sako, H; Samsonov, V; Sarsour, M; Sato, K; Sato, S; Schaefer, B; Schmoll, B K; Sedgwick, K; Seidl, R; Sen, A; Seto, R; Sexton, A; Sharma, D; Shein, I; Shibata, T-A; Shigaki, K; Shimomura, M; Shioya, T; Shukla, P; Sickles, A; Silva, C L; Silvermyr, D; Singh, B K; Singh, C P; Singh, V; Skoby, M J; Slunečka, M; Smith, K L; Snowball, M; Soltz, R A; Sondheim, W E; Sorensen, S P; Sourikova, I V; Stankus, P W; Stoll, S P; Sugitate, T; Sukhanov, A; Sumita, T; Sun, J; Syed, S; Sziklai, J; Takeda, A; Tanida, K; Tannenbaum, M J; Tarafdar, S; Taranenko, A; Tarnai, G; Tieulent, R; Timilsina, A; Todoroki, T; Tomášek, M; Towell, C L; Towell, R S; Tserruya, I; Ueda, Y; Ujvari, B; van Hecke, H W; Vazquez-Carson, S; Velkovska, J; Virius, M; Vrba, V; Vukman, N; Wang, X R; Wang, Z; Watanabe, Y; Watanabe, Y S; Wong, C P; Woody, C L; Xu, C; Xu, Q; Xue, L; Yalcin, S; Yamaguchi, Y L; Yamamoto, H; Yanovich, A; Yin, P; Yoo, J H; Yoon, I; Yu, H; Yushmanov, I E; Zajc, W A; Zelenski, A; Zharko, S; Zou, L

2018-02-09

Recently, multiparticle-correlation measurements of relativistic p/d/^{3}He+Au, p+Pb, and even p+p collisions show surprising collective signatures. Here, we present beam-energy-scan measurements of two-, four-, and six-particle angular correlations in d+Au collisions at sqrt[s_{NN}]=200, 62.4, 39, and 19.6 GeV. We also present measurements of two- and four-particle angular correlations in p+Au collisions at sqrt[s_{NN}]=200  GeV. We find the four-particle cumulant to be real valued for d+Au collisions at all four energies. We also find that the four-particle cumulant in p+Au has the opposite sign as that in d+Au. Further, we find that the six-particle cumulant agrees with the four-particle cumulant in d+Au collisions at 200 GeV, indicating that nonflow effects are subdominant. These observations provide strong evidence that the correlations originate from the initial geometric configuration, which is then translated into the momentum distribution for all particles, commonly referred to as collectivity.

Measurements of Multiparticle Correlations in d + Au Collisions at 200, 62.4, 39, and 19.6 GeV and p + Au Collisions at 200 GeV and Implications for Collective Behavior

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

Aidala, C.; Akiba, Y.; Alfred, M.

Recently, multiparticle-correlation measurements of relativistic p/d/ 3He + Au, p + Pb, and even p + p collisions show surprising collective signatures. In this paper, we present beam-energy-scan measurements of two-, four-, and six-particle angular correlations in d + Au collisions at √ sNN = 200, 62.4, 39, and 19.6 GeV. We also present measurements of two- and four-particle angular correlations in p + Au collisions at √ sNN = 200 GeV. We find the four-particle cumulant to be real valued for d + Au collisions at all four energies. We also find that the four-particle cumulant in p +more » Au has the opposite sign as that in d + Au. Further, we find that the six-particle cumulant agrees with the four-particle cumulant in d + Au collisions at 200 GeV, indicating that nonflow effects are subdominant. Finally, these observations provide strong evidence that the correlations originate from the initial geometric configuration, which is then translated into the momentum distribution for all particles, commonly referred to as collectivity.« less

OSR1 regulates a subset of inward rectifier potassium channels via a binding motif variant.

PubMed

Taylor, Clinton A; An, Sung-Wan; Kankanamalage, Sachith Gallolu; Stippec, Steve; Earnest, Svetlana; Trivedi, Ashesh T; Yang, Jonathan Zijiang; Mirzaei, Hamid; Huang, Chou-Long; Cobb, Melanie H

2018-04-10

The with-no-lysine (K) (WNK) signaling pathway to STE20/SPS1-related proline- and alanine-rich kinase (SPAK) and oxidative stress-responsive 1 (OSR1) kinase is an important mediator of cell volume and ion transport. SPAK and OSR1 associate with upstream kinases WNK 1-4, substrates, and other proteins through their C-terminal domains which interact with linear R-F-x-V/I sequence motifs. In this study we find that SPAK and OSR1 also interact with similar affinity with a motif variant, R-x-F-x-V/I. Eight of 16 human inward rectifier K + channels have an R-x-F-x-V motif. We demonstrate that two of these channels, Kir2.1 and Kir2.3, are activated by OSR1, while Kir4.1, which does not contain the motif, is not sensitive to changes in OSR1 or WNK activity. Mutation of the motif prevents activation of Kir2.3 by OSR1. Both siRNA knockdown of OSR1 and chemical inhibition of WNK activity disrupt NaCl-induced plasma membrane localization of Kir2.3. Our results suggest a mechanism by which WNK-OSR1 enhance Kir2.1 and Kir2.3 channel activity by increasing their plasma membrane localization. Regulation of members of the inward rectifier K + channel family adds functional and mechanistic insight into the physiological impact of the WNK pathway.

Statistical tests to compare motif count exceptionalities

PubMed Central

Robin, Stéphane; Schbath, Sophie; Vandewalle, Vincent

2007-01-01

Background Finding over- or under-represented motifs in biological sequences is now a common task in genomics. Thanks to p-value calculation for motif counts, exceptional motifs are identified and represent candidate functional motifs. The present work addresses the related question of comparing the exceptionality of one motif in two different sequences. Just comparing the motif count p-values in each sequence is indeed not sufficient to decide if this motif is significantly more exceptional in one sequence compared to the other one. A statistical test is required. Results We develop and analyze two statistical tests, an exact binomial one and an asymptotic likelihood ratio test, to decide whether the exceptionality of a given motif is equivalent or significantly different in two sequences of interest. For that purpose, motif occurrences are modeled by Poisson processes, with a special care for overlapping motifs. Both tests can take the sequence compositions into account. As an illustration, we compare the octamer exceptionalities in the Escherichia coli K-12 backbone versus variable strain-specific loops. Conclusion The exact binomial test is particularly adapted for small counts. For large counts, we advise to use the likelihood ratio test which is asymptotic but strongly correlated with the exact binomial test and very simple to use. PMID:17346349

Roles of conserved proline and glycosyltransferase motifs of EmbC in biosynthesis of lipoarabinomannan.

PubMed

Berg, Stefan; Starbuck, James; Torrelles, Jordi B; Vissa, Varalakshmi D; Crick, Dean C; Chatterjee, Delphi; Brennan, Patrick J

2005-02-18

D-Arabinans, composed of D-arabinofuranose (D-Araf), dominate the structure of mycobacterial cell walls in two settings, as part of lipoarabinomannan (LAM) and arabinogalactan, each with markedly different structures and functions. Little is known of the complexity of their biosynthesis. beta-D-Arabinofuranosyl-1-monophosphoryldecaprenol is the only known sugar donor. EmbA, EmbB, and EmbC, products of the paralogous genes embA, embB, and embC, the sites of resistance to the anti-tuberculosis drug ethambutol (EMB), are the only known implicated enzymes. EmbA and -B apparently contribute to the synthesis of arabinogalactan, whereas EmbC is reserved for the synthesis of LAM. The Emb proteins show no overall similarity to any known proteins beyond Mycobacterium and related genera. However, functional motifs, equivalent to a proline-rich motif of several bacterial polysaccharide co-polymerases and a superfamily of glycosyltransferases, were found. Site-directed mutagenesis in glycosyltransferase superfamily C resulted in complete ablation of LAM synthesis. Point mutations in three amino acids of the proline motif of EmbC resulted in marked reduction of LAM-arabinan synthesis and accumulation of an unknown intermediate and of the known precursor lipomannan. Yet the pattern of the differently linked d-Araf units observed in wild type LAM-arabinan was largely retained in the proline motif mutants. The results allow for the presentation of a unique model of arabinan synthesis.

Discriminative motif optimization based on perceptron training

PubMed Central

Patel, Ronak Y.; Stormo, Gary D.

2014-01-01

Motivation: Generating accurate transcription factor (TF) binding site motifs from data generated using the next-generation sequencing, especially ChIP-seq, is challenging. The challenge arises because a typical experiment reports a large number of sequences bound by a TF, and the length of each sequence is relatively long. Most traditional motif finders are slow in handling such enormous amount of data. To overcome this limitation, tools have been developed that compromise accuracy with speed by using heuristic discrete search strategies or limited optimization of identified seed motifs. However, such strategies may not fully use the information in input sequences to generate motifs. Such motifs often form good seeds and can be further improved with appropriate scoring functions and rapid optimization. Results: We report a tool named discriminative motif optimizer (DiMO). DiMO takes a seed motif along with a positive and a negative database and improves the motif based on a discriminative strategy. We use area under receiver-operating characteristic curve (AUC) as a measure of discriminating power of motifs and a strategy based on perceptron training that maximizes AUC rapidly in a discriminative manner. Using DiMO, on a large test set of 87 TFs from human, drosophila and yeast, we show that it is possible to significantly improve motifs identified by nine motif finders. The motifs are generated/optimized using training sets and evaluated on test sets. The AUC is improved for almost 90% of the TFs on test sets and the magnitude of increase is up to 39%. Availability and implementation: DiMO is available at http://stormo.wustl.edu/DiMO Contact: rpatel@genetics.wustl.edu, ronakypatel@gmail.com PMID:24369152

Metallofullerenol Gd@C82(OH)22 distracts the proline-rich-motif from putative binding on the SH3 domain

NASA Astrophysics Data System (ADS)

Kang, Seung-Gu; Huynh, Tien; Zhou, Ruhong

2013-03-01

Biocompatibility is often regarded as one important aspect of de novo designed nanomaterials for biosafety. However, the toxicological effect, appearing along with its latency, is much more difficult to address by linearly mapping physicochemical properties of related nanomaterials with biological effects such as immune or cellular regulatory responses due to the complicated protein-protein interactions. Here, we investigate a potential interference of a metallofullerenol, Gd@C82(OH)22, on the function of SH3 domain, a highly promiscuous protein-protein interaction mediator involved in signaling and regulatory pathways through its binding with the proline-rich motif (PRM) peptides, using the atomistic molecular dynamics simulation. Our study shows that when only Gd@C82(OH)22 and the SH3 domain are present (without the PRM ligand), Gd@C82(OH)22 can interact with the SH3 domain by either directly blocking the hydrophobic active site or binding with a hydrophilic off-site with almost equal probability, which can be understood from its intrinsic amphiphilic nature. In a binding competition with the PRM onto the SH3 domain, however, the on-site binding mode is depleted while Gd@C82(OH)22 effectively intercepts the PRM from the putative binding site of the SH3 domain, implying that Gd@C82(OH)22 can disturb protein-protein interactions mediated by the SH3 domain. Despite a successful surface modification in an aqueous biological medium and a more recent demonstration as potential de novo cancer therapeutics, our study indicates that greater attention is needed in assessing the potential cytotoxicity of these nanomaterials.Biocompatibility is often regarded as one important aspect of de novo designed nanomaterials for biosafety. However, the toxicological effect, appearing along with its latency, is much more difficult to address by linearly mapping physicochemical properties of related nanomaterials with biological effects such as immune or cellular regulatory responses

Genome signature analysis of thermal virus metagenomes reveals Archaea and thermophilic signatures.

PubMed

Pride, David T; Schoenfeld, Thomas

2008-09-17

Metagenomic analysis provides a rich source of biological information for otherwise intractable viral communities. However, study of viral metagenomes has been hampered by its nearly complete reliance on BLAST algorithms for identification of DNA sequences. We sought to develop algorithms for examination of viral metagenomes to identify the origin of sequences independent of BLAST algorithms. We chose viral metagenomes obtained from two hot springs, Bear Paw and Octopus, in Yellowstone National Park, as they represent simple microbial populations where comparatively large contigs were obtained. Thermal spring metagenomes have high proportions of sequences without significant Genbank homology, which has hampered identification of viruses and their linkage with hosts. To analyze each metagenome, we developed a method to classify DNA fragments using genome signature-based phylogenetic classification (GSPC), where metagenomic fragments are compared to a database of oligonucleotide signatures for all previously sequenced Bacteria, Archaea, and viruses. From both Bear Paw and Octopus hot springs, each assembled contig had more similarity to other metagenome contigs than to any sequenced microbial genome based on GSPC analysis, suggesting a genome signature common to each of these extreme environments. While viral metagenomes from Bear Paw and Octopus share some similarity, the genome signatures from each locale are largely unique. GSPC using a microbial database predicts most of the Octopus metagenome has archaeal signatures, while bacterial signatures predominate in Bear Paw; a finding consistent with those of Genbank BLAST. When using a viral database, the majority of the Octopus metagenome is predicted to belong to archaeal virus Families Globuloviridae and Fuselloviridae, while none of the Bear Paw metagenome is predicted to belong to archaeal viruses. As expected, when microbial and viral databases are combined, each of the Octopus and Bear Paw metagenomic contigs

Uncertainty in hydrological signatures

NASA Astrophysics Data System (ADS)

McMillan, Hilary; Westerberg, Ida

2015-04-01

Information that summarises the hydrological behaviour or flow regime of a catchment is essential for comparing responses of different catchments to understand catchment organisation and similarity, and for many other modelling and water-management applications. Such information types derived as an index value from observed data are known as hydrological signatures, and can include descriptors of high flows (e.g. mean annual flood), low flows (e.g. mean annual low flow, recession shape), the flow variability, flow duration curve, and runoff ratio. Because the hydrological signatures are calculated from observed data such as rainfall and flow records, they are affected by uncertainty in those data. Subjective choices in the method used to calculate the signatures create a further source of uncertainty. Uncertainties in the signatures may affect our ability to compare different locations, to detect changes, or to compare future water resource management scenarios. The aim of this study was to contribute to the hydrological community's awareness and knowledge of data uncertainty in hydrological signatures, including typical sources, magnitude and methods for its assessment. We proposed a generally applicable method to calculate these uncertainties based on Monte Carlo sampling and demonstrated it for a variety of commonly used signatures. The study was made for two data rich catchments, the 50 km2 Mahurangi catchment in New Zealand and the 135 km2 Brue catchment in the UK. For rainfall data the uncertainty sources included point measurement uncertainty, the number of gauges used in calculation of the catchment spatial average, and uncertainties relating to lack of quality control. For flow data the uncertainty sources included uncertainties in stage/discharge measurement and in the approximation of the true stage-discharge relation by a rating curve. The resulting uncertainties were compared across the different signatures and catchments, to quantify uncertainty

Identity and functions of CxxC-derived motifs.

PubMed

Fomenko, Dmitri E; Gladyshev, Vadim N

2003-09-30

Two cysteines separated by two other residues (the CxxC motif) are employed by many redox proteins for formation, isomerization, and reduction of disulfide bonds and for other redox functions. The place of the C-terminal cysteine in this motif may be occupied by serine (the CxxS motif), modifying the functional repertoire of redox proteins. Here we found that the CxxC motif may also give rise to a motif, in which the C-terminal cysteine is replaced with threonine (the CxxT motif). Moreover, in contrast to a view that the N-terminal cysteine in the CxxC motif always serves as a nucleophilic attacking group, this residue could also be replaced with threonine (the TxxC motif), serine (the SxxC motif), or other residues. In each of these CxxC-derived motifs, the presence of a downstream alpha-helix was strongly favored. A search for conserved CxxC-derived motif/helix patterns in four complete genomes representing bacteria, archaea, and eukaryotes identified known redox proteins and suggested possible redox functions for several additional proteins. Catalytic sites in peroxiredoxins were major representatives of the TxxC motif, whereas those in glutathione peroxidases represented the CxxT motif. Structural assessments indicated that threonines in these enzymes could stabilize catalytic thiolates, suggesting revisions to previously proposed catalytic triads. Each of the CxxC-derived motifs was also observed in natural selenium-containing proteins, in which selenocysteine was present in place of a catalytic cysteine.

Unitary circular code motifs in genomes of eukaryotes.

PubMed

El Soufi, Karim; Michel, Christian J

A set X of 20 trinucleotides was identified in genes of bacteria, eukaryotes, plasmids and viruses, which has in average the highest occurrence in reading frame compared to its two shifted frames (Michel, 2015; Arquès and Michel, 1996). This set X has an interesting mathematical property as X is a circular code (Arquès and Michel, 1996). Thus, the motifs from this circular code X, called X motifs, have the property to always retrieve, synchronize and maintain the reading frame in genes. The origin of this circular code X in genes is an open problem since its discovery in 1996. Here, we first show that the unitary circular codes (UCC), i.e. sets of one word, allow to generate unitary circular code motifs (UCC motifs), i.e. a concatenation of the same motif (simple repeats) leading to low complexity DNA. Three classes of UCC motifs are studied here: repeated dinucleotides (D + motifs), repeated trinucleotides (T + motifs) and repeated tetranucleotides (T + motifs). Thus, the D + , T + and T + motifs allow to retrieve, synchronize and maintain a frame modulo 2, modulo 3 and modulo 4, respectively, and their shifted frames (1 modulo 2; 1 and 2 modulo 3; 1, 2 and 3 modulo 4 according to the C 2 , C 3 and C 4 properties, respectively) in the DNA sequences. The statistical distribution of the D + , T + and T + motifs is analyzed in the genomes of eukaryotes. A UCC motif and its comp lementary UCC motif have the same distribution in the eukaryotic genomes. Furthermore, a UCC motif and its complementary UCC motif have increasing occurrences contrary to their number of hydrogen bonds, very significant with the T + motifs. The longest D + , T + and T + motifs in the studied eukaryotic genomes are also given. Surprisingly, a scarcity of repeated trinucleotides (T + motifs) in the large eukaryotic genomes is observed compared to the D + and T + motifs. This result has been investigated and may be explained by two outcomes. Repeated trinucleotides (T + motifs) are identified

TrawlerWeb: an online de novo motif discovery tool for next-generation sequencing datasets.

PubMed

Dang, Louis T; Tondl, Markus; Chiu, Man Ho H; Revote, Jerico; Paten, Benedict; Tano, Vincent; Tokolyi, Alex; Besse, Florence; Quaife-Ryan, Greg; Cumming, Helen; Drvodelic, Mark J; Eichenlaub, Michael P; Hallab, Jeannette C; Stolper, Julian S; Rossello, Fernando J; Bogoyevitch, Marie A; Jans, David A; Nim, Hieu T; Porrello, Enzo R; Hudson, James E; Ramialison, Mirana

2018-04-05

interface for de novo motif discovery. This will assist in rapidly analysing NGS datasets that are now being routinely generated. TrawlerWeb is freely available and accessible at: http://trawler.erc.monash.edu.au .

Tailoring characteristic thermal stability of Ni-Au binary nanocrystals via structure and composition engineering: theoretical insights into structural evolution and atomic inter-diffusion

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

Li, Bangquan; Wang, Hailong; Xing, Guozhong

We report on the structural evolution and atomic inter-diffusion characteristics of the bimetallic Ni-Au nanocrystals (NCs) by molecular dynamics simulations studies. Our results reveal that the thermal stability dynamics of Ni-Au NCs strongly depends on the atomic configurations. By engineering the structural construction with Ni:Au = 1:1 atomic composition, compared with core-shell Au@Ni and alloy NCs, the melting point of core-shell Ni@Au NCs is significantly enhanced up to 1215 K. Unexpectedly, with atomic ratio of Au:Ni= 1:9, the melting process initiates from the atoms in the shell of Ni@Au and alloy NCs, while starts from the core of Au@Ni NCs.more » The corresponding features and evolution process of structural motifs, mixing and segregation are illustrated via a series of dynamic simulations videos. Moreover, our results revealed that the face centered cubic phase Au{sub 0.75}Ni{sub 0.25} favorably stabilizes in NCs form but does not exist in the bulk counterpart, which elucidates the anomalies of previously reported experimental results on such bimetallic NCs.« less

[Personal motif in art].

PubMed

Gerevich, József

2015-01-01

One of the basic questions of the art psychology is whether a personal motif is to be found behind works of art and if so, how openly or indirectly it appears in the work itself. Analysis of examples and documents from the fine arts and literature allow us to conclude that the personal motif that can be identified by the viewer through symbols, at times easily at others with more difficulty, gives an emotional plus to the artistic product. The personal motif may be found in traumatic experiences, in communication to the model or with other emotionally important persons (mourning, disappointment, revenge, hatred, rivalry, revolt etc.), in self-searching, or self-analysis. The emotions are expressed in artistic activity either directly or indirectly. The intention nourished by the artist's identity (Kunstwollen) may stand in the way of spontaneous self-expression, channelling it into hidden paths. Under the influence of certain circumstances, the artist may arouse in the viewer, consciously or unconsciously, an illusionary, misleading image of himself. An examination of the personal motif is one of the important research areas of art therapy.

Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures

PubMed Central

Stark, Alexander; Lin, Michael F.; Kheradpour, Pouya; Pedersen, Jakob S.; Parts, Leopold; Carlson, Joseph W.; Crosby, Madeline A.; Rasmussen, Matthew D.; Roy, Sushmita; Deoras, Ameya N.; Ruby, J. Graham; Brennecke, Julius; Hodges, Emily; Hinrichs, Angie S.; Caspi, Anat; Paten, Benedict; Park, Seung-Won; Han, Mira V.; Maeder, Morgan L.; Polansky, Benjamin J.; Robson, Bryanne E.; Aerts, Stein; van Helden, Jacques; Hassan, Bassem; Gilbert, Donald G.; Eastman, Deborah A.; Rice, Michael; Weir, Michael; Hahn, Matthew W.; Park, Yongkyu; Dewey, Colin N.; Pachter, Lior; Kent, W. James; Haussler, David; Lai, Eric C.; Bartel, David P.; Hannon, Gregory J.; Kaufman, Thomas C.; Eisen, Michael B.; Clark, Andrew G.; Smith, Douglas; Celniker, Susan E.; Gelbart, William M.; Kellis, Manolis

2008-01-01

Sequencing of multiple related species followed by comparative genomics analysis constitutes a powerful approach for the systematic understanding of any genome. Here, we use the genomes of 12 Drosophila species for the de novo discovery of functional elements in the fly. Each type of functional element shows characteristic patterns of change, or ‘evolutionary signatures’, dictated by its precise selective constraints. Such signatures enable recognition of new protein-coding genes and exons, spurious and incorrect gene annotations, and numerous unusual gene structures, including abundant stop-codon readthrough. Similarly, we predict non-protein-coding RNA genes and structures, and new microRNA (miRNA) genes. We provide evidence of miRNA processing and functionality from both hairpin arms and both DNA strands. We identify several classes of pre- and post-transcriptional regulatory motifs, and predict individual motif instances with high confidence. We also study how discovery power scales with the divergence and number of species compared, and we provide general guidelines for comparative studies. PMID:17994088

Sedimentary rock-hosted Au deposits of the Dian-Qian-Gui area, Guizhou, and Yunnan Provinces, and Guangxi District, China

USGS Publications Warehouse

Peters, S.G.; Jiazhan, H.; Zhiping, L.; Chenggui, J.

2007-01-01

Sedimentary rock-hosted Au deposits in the Dian-Qian-Gui area in southwest China are hosted in Paleozoic and early Mesozoic sedimentary rocks along the southwest margin of the Yangtze (South China) Precambrian craton. Most deposits have characteristics similar to Carlin-type Au deposits and are spatially associated, on a regional scale, with deposits of coal, Sb, barite, As, Tl, and Hg. Sedimentary rock-hosted Au deposits are disseminated stratabound and(or) structurally controlled. The deposits have many similar characteristics, particularly mineralogy, geochemistry, host rock, and structural control. Most deposits are associated with structural domes, stratabound breccia bodies, unconformity surfaces or intense brittle-ductile deformation zones, such as the Youjiang fault system. Typical characteristics include impure carbonate rock or calcareous and carbonaceous host rock that contains disseminated pyrite, marcasite, and arsenopyrite-usually with ??m-sized Au, commonly in As-rich rims of pyrite and in disseminations. Late realgar, orpiment, stibnite, and Hg minerals are spatially associated with earlier forming sulfide minerals. Minor base-metal sulfides, such as galena, sphalerite, chalcopyrite, and Pb-Sb-As-sulphosalts also are present. The rocks locally are silicified and altered to sericite-clay (illite). Rocks and(or) stream-sediment geochemical signatures typically include elevated concentrations of As, Sb, Hg, Tl, and Ba. A general lack of igneous rocks in the Dian-Qian-Gui area implies non-pluton-related, ore forming processes. Some deposits contain evidence that sources of the metal may have originated in carbonaceous parts of the sedimentary pile or other sedimentary or volcanic horizons. This genetic process may be associated with formation and mobilization of petroleum and Hg in the region and may also be related to As-, Au-, and Tl-bearing coal horizons. Many deposits also contain textures and features indicative of strong structural control by

Decoding a Signature-Based Model of Transcription Cofactor Recruitment Dictated by Cardinal Cis-Regulatory Elements in Proximal Promoter Regions

PubMed Central

Benner, Christopher; Hutt, Kasey R.; Stunnenberg, Rieka; Garcia-Bassets, Ivan

2013-01-01

Genome-wide maps of DNase I hypersensitive sites (DHSs) reveal that most human promoters contain perpetually active cis-regulatory elements between −150 bp and +50 bp (−150/+50 bp) relative to the transcription start site (TSS). Transcription factors (TFs) recruit cofactors (chromatin remodelers, histone/protein-modifying enzymes, and scaffold proteins) to these elements in order to organize the local chromatin structure and coordinate the balance of post-translational modifications nearby, contributing to the overall regulation of transcription. However, the rules of TF-mediated cofactor recruitment to the −150/+50 bp promoter regions remain poorly understood. Here, we provide evidence for a general model in which a series of cis-regulatory elements (here termed ‘cardinal’ motifs) prefer acting individually, rather than in fixed combinations, within the −150/+50 bp regions to recruit TFs that dictate cofactor signatures distinctive of specific promoter subsets. Subsequently, human promoters can be subclassified based on the presence of cardinal elements and their associated cofactor signatures. In this study, furthermore, we have focused on promoters containing the nuclear respiratory factor 1 (NRF1) motif as the cardinal cis-regulatory element and have identified the pervasive association of NRF1 with the cofactor lysine-specific demethylase 1 (LSD1/KDM1A). This signature might be distinctive of promoters regulating nuclear-encoded mitochondrial and other particular genes in at least some cells. Together, we propose that decoding a signature-based, expanded model of control at proximal promoter regions should lead to a better understanding of coordinated regulation of gene transcription. PMID:24244184

Motif enrichment tool.

PubMed

Blatti, Charles; Sinha, Saurabh

2014-07-01

The Motif Enrichment Tool (MET) provides an online interface that enables users to find major transcriptional regulators of their gene sets of interest. MET searches the appropriate regulatory region around each gene and identifies which transcription factor DNA-binding specificities (motifs) are statistically overrepresented. Motif enrichment analysis is currently available for many metazoan species including human, mouse, fruit fly, planaria and flowering plants. MET also leverages high-throughput experimental data such as ChIP-seq and DNase-seq from ENCODE and ModENCODE to identify the regulatory targets of a transcription factor with greater precision. The results from MET are produced in real time and are linked to a genome browser for easy follow-up analysis. Use of the web tool is free and open to all, and there is no login requirement. ADDRESS: http://veda.cs.uiuc.edu/MET/. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Na8Au9.8(4)Ga7.2 and Na17Au5.87(2)Ga46.63: The diversity of pseudo 5-fold symmetries in the Na-Au-Ga system

NASA Astrophysics Data System (ADS)

Smetana, Volodymyr; Corbett, John D.; Miller, Gordon J.

2013-11-01

The Na-rich part (~30% Na) of the Na-Au-Ga system between NaAu2, NaGa4, and Na22Ga39 has been found to contain the ternary phases Na8Au9.8(4)Ga7.2 (I) and Na17Au5.87(2)Ga46.63 (II), according to the results of single crystal X-ray diffraction measurements. I is orthorhombic, Cmcm, a=5.3040(1), b=24.519(5), c=14.573(3) Å, and contains a network of clusters with local 5-fold symmetry along the a-axis. Such clusters are frequent building units in decagonal quasicrystals and their approximants. II is rhombohedral, R3¯m, a=16.325(2), c=35.242(7) Å, and contains building blocks that are structurally identical to the Bergman-type clusters as well as fused icosahedral units known with active metals, triels and late transition elements. II also contains a polycationic network with elements of the clathrate V type structure. Tight-binding electronic structure calculations using linear muffin-tin-orbital (LMTO) methods on idealized models of I and II indicate that both compounds are metallic with evident pseudogaps at the corresponding Fermi levels. The overall Hamilton bond populations are generally dominated by Au-Ga and Au-Au bonds in I and by Ga-Ga bonds in II; moreover, the Na-Au and Na-Ga contributions in I are unexpectedly large, ~20% of the total. A similar involvement of sodium in covalent bonding has also been found in the electron-richer i-Na13Au12Ga15 quasicrystal approximant.

A Rich Man, Poor Man Story of S-Adenosylmethionine and Cobalamin Revisited.

PubMed

Bridwell-Rabb, Jennifer; Grell, Tsehai A J; Drennan, Catherine L

2018-06-20

S-adenosylmethionine (AdoMet) has been referred to as both "a poor man's adenosylcobalamin (AdoCbl)" and "a rich man's AdoCbl," but today, with the ever-increasing number of functions attributed to each cofactor, both appear equally rich and surprising. The recent characterization of an organometallic species in an AdoMet radical enzyme suggests that the line that differentiates them in nature will be constantly challenged. Here, we compare and contrast AdoMet and cobalamin (Cbl) and consider why Cbl-dependent AdoMet radical enzymes require two cofactors that are so similar in their reactivity. We further carry out structural comparisons employing the recently determined crystal structure of oxetanocin-A biosynthetic enzyme OxsB, the first three-dimensional structural data on a Cbl-dependent AdoMet radical enzyme. We find that the structural motifs responsible for housing the AdoMet radical machinery are largely conserved, whereas the motifs responsible for binding additional cofactors are much more varied.

Distinguishing between biochemical and cellular function: Are there peptide signatures for cellular function of proteins?

PubMed

Jain, Shruti; Bhattacharyya, Kausik; Bakshi, Rachit; Narang, Ankita; Brahmachari, Vani

2017-04-01

The genome annotation and identification of gene function depends on conserved biochemical activity. However, in the cell, proteins with the same biochemical function can participate in different cellular pathways and cannot complement one another. Similarly, two proteins of very different biochemical functions are put in the same class of cellular function; for example, the classification of a gene as an oncogene or a tumour suppressor gene is not related to its biochemical function, but is related to its cellular function. We have taken an approach to identify peptide signatures for cellular function in proteins with known biochemical function. ATPases as a test case, we classified ATPases (2360 proteins) and kinases (517 proteins) from the human genome into different cellular function categories such as transcriptional, replicative, and chromatin remodelling proteins. Using publicly available tool, MEME, we identify peptide signatures shared among the members of a given category but not between cellular functional categories; for example, no motif sharing is seen between chromatin remodelling and transporter ATPases, similarly between receptor Serine/Threonine Kinase and Receptor Tyrosine Kinase. There are motifs shared within each category with significant E value and high occurrence. This concept of signature for cellular function was applied to developmental regulators, the polycomb and trithorax proteins which led to the prediction of the role of INO80, a chromatin remodelling protein, in development. This has been experimentally validated earlier for its role in homeotic gene regulation and its interaction with regulatory complexes like the Polycomb and Trithorax complex. Proteins 2017; 85:682-693. © 2016 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Genome-wide identification of novel expression signatures reveal distinct patterns and prevalence of binding motifs for p53, nuclear factor-κB and other signal transcription factors in head and neck squamous cell carcinoma

PubMed Central

Yan, Bin; Yang, Xinping; Lee, Tin-Lap; Friedman, Jay; Tang, Jun; Van Waes, Carter; Chen, Zhong

2007-01-01

Background Differentially expressed gene profiles have previously been observed among pathologically defined cancers by microarray technologies, including head and neck squamous cell carcinomas (HNSCCs). However, the molecular expression signatures and transcriptional regulatory controls that underlie the heterogeneity in HNSCCs are not well defined. Results Genome-wide cDNA microarray profiling of ten HNSCC cell lines revealed novel gene expression signatures that distinguished cancer cell subsets associated with p53 status. Three major clusters of over-expressed genes (A to C) were defined through hierarchical clustering, Gene Ontology, and statistical modeling. The promoters of genes in these clusters exhibited different patterns and prevalence of transcription factor binding sites for p53, nuclear factor-κB (NF-κB), activator protein (AP)-1, signal transducer and activator of transcription (STAT)3 and early growth response (EGR)1, as compared with the frequency in vertebrate promoters. Cluster A genes involved in chromatin structure and function exhibited enrichment for p53 and decreased AP-1 binding sites, whereas clusters B and C, containing cytokine and antiapoptotic genes, exhibited a significant increase in prevalence of NF-κB binding sites. An increase in STAT3 and EGR1 binding sites was distributed among the over-expressed clusters. Novel regulatory modules containing p53 or NF-κB concomitant with other transcription factor binding motifs were identified, and experimental data supported the predicted transcriptional regulation and binding activity. Conclusion The transcription factors p53, NF-κB, and AP-1 may be important determinants of the heterogeneous pattern of gene expression, whereas STAT3 and EGR1 may broadly enhance gene expression in HNSCCs. Defining these novel gene signatures and regulatory mechanisms will be important for establishing new molecular classifications and subtyping, which in turn will promote development of targeted

Identification of vibrational signatures from short chains of interlinked molecule-nanoparticle junctions obtained by inelastic electron tunnelling spectroscopy

NASA Astrophysics Data System (ADS)

Jafri, S. H. M.; Löfås, H.; Fransson, J.; Blom, T.; Grigoriev, A.; Wallner, A.; Ahuja, R.; Ottosson, H.; Leifer, K.

2013-05-01

Short chains containing a series of metal-molecule-nanoparticle nanojunctions are a nano-material system with the potential to give electrical signatures close to those from single molecule experiments while enabling us to build portable devices on a chip. Inelastic electron tunnelling spectroscopy (IETS) measurements provide one of the most characteristic electrical signals of single and few molecules. In interlinked molecule-nanoparticle (NP) chains containing typically 5-7 molecules in a chain, the spectrum is expected to be a superposition of the vibrational signatures of individual molecules. We have established a stable and reproducible molecule-AuNP multi-junction by placing a few 1,8-octanedithiol (ODT) molecules onto a versatile and portable nanoparticle-nanoelectrode platform and measured for the first time vibrational molecular signatures at complex and coupled few-molecule-NP junctions. From quantum transport calculations, we model the IETS spectra and identify vibrational modes as well as the number of molecules contributing to the electron transport in the measured spectra.Short chains containing a series of metal-molecule-nanoparticle nanojunctions are a nano-material system with the potential to give electrical signatures close to those from single molecule experiments while enabling us to build portable devices on a chip. Inelastic electron tunnelling spectroscopy (IETS) measurements provide one of the most characteristic electrical signals of single and few molecules. In interlinked molecule-nanoparticle (NP) chains containing typically 5-7 molecules in a chain, the spectrum is expected to be a superposition of the vibrational signatures of individual molecules. We have established a stable and reproducible molecule-AuNP multi-junction by placing a few 1,8-octanedithiol (ODT) molecules onto a versatile and portable nanoparticle-nanoelectrode platform and measured for the first time vibrational molecular signatures at complex and coupled few

A New Family of Giardial Cysteine-Rich Non-VSP Protein Genes and a Novel Cyst Protein

PubMed Central

Birkeland, Shanda R.; Preheim, Sarah P.; Cipriano, Michael J.; McArthur, Andrew G.; Gillin, Frances D.

2006-01-01

Since the Giardia lamblia cyst wall is necessary for survival in the environment and host infection, we tested the hypothesis that it contains proteins other than the three known cyst wall proteins. Serial analysis of gene expression during growth and encystation revealed a gene, “HCNCp” (High Cysteine Non-variant Cyst protein), that was upregulated late in encystation, and that resembled the classic Giardia variable surface proteins (VSPs) that cover the trophozoite plasmalemma. HCNCp is 13.9% cysteine, with many “CxxC” tetrapeptide motifs and a transmembrane sequence near the C-terminus. However, HCNCp has multiple “CxC” motifs rarely found in VSPs, and does not localize to the trophozoite plasmalemma. Moreover, the HCNCp C-terminus differed from the canonical VSP signature. Full-length epitope-tagged HCNCp expressed under its own promoter was upregulated during encystation with highest expression in cysts, including 42 and 21 kDa C-terminal fragments. Tagged HCNCp targeted to the nuclear envelope in trophozoites, and co-localized with cyst proteins to encystation-specific secretory vesicles during encystation. HCNCp defined a novel trafficking pathway as it localized to the wall and body of cysts, while the cyst proteins were exclusively in the wall. Unlike VSPs, HCNCp is expressed in at least five giardial strains and four WB subclones expressing different VSPs. Bioinformatics identified 60 additional large high cysteine membrane proteins (HCMp) containing ≥20 CxxC/CxC's lacking the VSP-specific C-terminal CRGKA. HCMp were absent or rare in other model or parasite genomes, except for Tetrahymena thermophila with 30. MEME analysis classified the 61 gHCMp genes into nine groups with similar internal motifs. Our data suggest that HCNCp is a novel invariant cyst protein belonging to a new HCMp family that is abundant in the Giardia genome. HCNCp and the other HCMp provide a rich source for developing parasite-specific diagnostic reagents, vaccine

Gold as hydrogen: Structural and electronic properties and chemical bonding in Si3Au3+/0/- and comparisons to Si3H3+/0/-

NASA Astrophysics Data System (ADS)

Kiran, Boggavarapu; Li, Xi; Zhai, Hua-Jin; Wang, Lai-Sheng

2006-10-01

A single Au atom has been shown to behave like H in its bonding to Si in several mono- and disilicon gold clusters. In the current work, we investigate the Au /H analogy in trisilicon gold clusters, Si3Au3+/0/-. Photoelectron spectroscopy and density functional calculations are combined to examine the geometric and electronic structure of Si3Au3-. We find that there are three isomers competing for the ground state of Si3Au3- as is the case for Si3H3-. Extensive structural searches show that the potential energy surfaces of the trisilicon gold clusters (Si3Au3-, Si3Au3, and Si3Au3+) are similar to those of the corresponding silicon hydrides. The lowest energy isomers for Si3Au3- and Si3Au3 are structurally similar to a Si3Au four-membered ring serving as a common structural motif. For Si3Au3+, the 2π aromatic cyclotrisilenylium auride ion, analogous to the aromatic cyclotrisilenylium ion (Si3H3+), is the most stable species. Comparison of the structures and chemical bonding between Si3Au3+/0/- and the corresponding silicon hydrides further extends the isolobal analogy between Au and H.

Computational study of the fibril organization of polyglutamine repeats reveals a common motif identified in beta-helices.

PubMed

Zanuy, David; Gunasekaran, Kannan; Lesk, Arthur M; Nussinov, Ruth

2006-04-21

The formation of fibril aggregates by long polyglutamine sequences is assumed to play a major role in neurodegenerative diseases such as Huntington. Here, we model peptides rich in glutamine, through a series of molecular dynamics simulations. Starting from a rigid nanotube-like conformation, we have obtained a new conformational template that shares structural features of a tubular helix and of a beta-helix conformational organization. Our new model can be described as a super-helical arrangement of flat beta-sheet segments linked by planar turns or bends. Interestingly, our comprehensive analysis of the Protein Data Bank reveals that this is a common motif in beta-helices (termed beta-bend), although it has not been identified so far. The motif is based on the alternation of beta-sheet and helical conformation as the protein sequence is followed from the N to the C termini (beta-alpha(R)-beta-polyPro-beta). We further identify this motif in the ssNMR structure of the protofibril of the amyloidogenic peptide Abeta(1-40). The recurrence of the beta-bend suggests a general mode of connecting long parallel beta-sheet segments that would allow the growth of partially ordered fibril structures. The design allows the peptide backbone to change direction with a minimal loss of main chain hydrogen bonds. The identification of a coherent organization beyond that of the beta-sheet segments in different folds rich in parallel beta-sheets suggests a higher degree of ordered structure in protein fibrils, in agreement with their low solubility and dense molecular packing.

Genome signature analysis of thermal virus metagenomes reveals Archaea and thermophilic signatures

PubMed Central

Pride, David T; Schoenfeld, Thomas

2008-01-01

Background Metagenomic analysis provides a rich source of biological information for otherwise intractable viral communities. However, study of viral metagenomes has been hampered by its nearly complete reliance on BLAST algorithms for identification of DNA sequences. We sought to develop algorithms for examination of viral metagenomes to identify the origin of sequences independent of BLAST algorithms. We chose viral metagenomes obtained from two hot springs, Bear Paw and Octopus, in Yellowstone National Park, as they represent simple microbial populations where comparatively large contigs were obtained. Thermal spring metagenomes have high proportions of sequences without significant Genbank homology, which has hampered identification of viruses and their linkage with hosts. To analyze each metagenome, we developed a method to classify DNA fragments using genome signature-based phylogenetic classification (GSPC), where metagenomic fragments are compared to a database of oligonucleotide signatures for all previously sequenced Bacteria, Archaea, and viruses. Results From both Bear Paw and Octopus hot springs, each assembled contig had more similarity to other metagenome contigs than to any sequenced microbial genome based on GSPC analysis, suggesting a genome signature common to each of these extreme environments. While viral metagenomes from Bear Paw and Octopus share some similarity, the genome signatures from each locale are largely unique. GSPC using a microbial database predicts most of the Octopus metagenome has archaeal signatures, while bacterial signatures predominate in Bear Paw; a finding consistent with those of Genbank BLAST. When using a viral database, the majority of the Octopus metagenome is predicted to belong to archaeal virus Families Globuloviridae and Fuselloviridae, while none of the Bear Paw metagenome is predicted to belong to archaeal viruses. As expected, when microbial and viral databases are combined, each of the Octopus and Bear Paw

Junctions between i-motif tetramers in supramolecular structures

PubMed Central

Guittet, Eric; Renciuk, Daniel; Leroy, Jean-Louis

2012-01-01

The symmetry of i-motif tetramers gives to cytidine-rich oligonucleotides the capacity to associate into supramolecular structures (sms). In order to determine how the tetramers are linked together in such structures, we have measured by gel filtration chromatography and NMR the formation and dissociation kinetics of sms built by oligonucleotides containing two short C stretches separated by a non-cytidine-base. We show that a stretch of only two cytidines either at the 3′- or 5′-end is long enough to link the tetramers into sms. The analysis of the properties of sms formed by oligonucleotides differing by the length of the oligo-C stretches, the sequence orientation and the nature of the non-C base provides a model of the junction connecting the tetramers in sms. PMID:22362739

Discovery of phosphorylation motif mixtures in phosphoproteomics data

PubMed Central

Ritz, Anna; Shakhnarovich, Gregory; Salomon, Arthur R.; Raphael, Benjamin J.

2009-01-01

Motivation: Modification of proteins via phosphorylation is a primary mechanism for signal transduction in cells. Phosphorylation sites on proteins are determined in part through particular patterns, or motifs, present in the amino acid sequence. Results: We describe an algorithm that simultaneously discovers multiple motifs in a set of peptides that were phosphorylated by several different kinases. Such sets of peptides are routinely produced in proteomics experiments.Our motif-finding algorithm uses the principle of minimum description length to determine a mixture of sequence motifs that distinguish a foreground set of phosphopeptides from a background set of unphosphorylated peptides. We show that our algorithm outperforms existing motif-finding algorithms on synthetic datasets consisting of mixtures of known phosphorylation sites. We also derive a motif specificity score that quantifies whether or not the phosphoproteins containing an instance of a motif have a significant number of known interactions. Application of our motif-finding algorithm to recently published human and mouse proteomic studies recovers several known phosphorylation motifs and reveals a number of novel motifs that are enriched for interactions with a particular kinase or phosphatase. Our tools provide a new approach for uncovering the sequence specificities of uncharacterized kinases or phosphatases. Availability: Software is available at http:/cs.brown.edu/people/braphael/software.html. Contact: aritz@cs.brown.edu; braphael@cs.brown.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:18996944

Three RNA recognition motifs participate in RNA recognition and structural organization by the pro-apoptotic factor TIA-1

PubMed Central

Bauer, William J.; Heath, Jason; Jenkins, Jermaine L.; Kielkopf, Clara L.

2012-01-01

T-cell intracellular antigen-1 (TIA-1) regulates developmental and stress-responsive pathways through distinct activities at the levels of alternative pre-mRNA splicing and mRNA translation. The TIA-1 polypeptide contains three RNA recognition motifs (RRMs). The central RRM2 and C-terminal RRM3 associate with cellular mRNAs. The N-terminal RRM1 enhances interactions of a C-terminal Q-rich domain of TIA-1 with the U1-C splicing factor, despite linear separation of the domains in the TIA-1 sequence. Given the expanded functional repertoire of the RRM family, it was unknown whether TIA-1 RRM1 contributes to RNA binding as well as documented protein interactions. To address this question, we used isothermal titration calorimetry and small-angle X-ray scattering (SAXS) to dissect the roles of the TIA-1 RRMs in RNA recognition. Notably, the fas RNA exhibited two binding sites with indistinguishable affinities for TIA-1. Analyses of TIA-1 variants established that RRM1 was dispensable for binding AU-rich fas sites, yet all three RRMs were required to bind a polyU RNA with high affinity. SAXS analyses demonstrated a `V' shape for a TIA-1 construct comprising the three RRMs, and revealed that its dimensions became more compact in the RNA-bound state. The sequence-selective involvement of TIA-1 RRM1 in RNA recognition suggests a possible role for RNA sequences in regulating the distinct functions of TIA-1. Further implications for U1-C recruitment by the adjacent TIA-1 binding sites of the fas pre-mRNA and the bent TIA-1 shape, which organizes the N- and C-termini on the same side of the protein, are discussed. PMID:22154808

Helix-packing motifs in membrane proteins.

PubMed

Walters, R F S; DeGrado, W F

2006-09-12

The fold of a helical membrane protein is largely determined by interactions between membrane-imbedded helices. To elucidate recurring helix-helix interaction motifs, we dissected the crystallographic structures of membrane proteins into a library of interacting helical pairs. The pairs were clustered according to their three-dimensional similarity (rmsd motifs whose structural features can be understood in terms of simple principles of helix-helix packing. Thus, the universe of common transmembrane helix-pairing motifs is relatively simple. The largest cluster, which comprises 29% of the library members, consists of an antiparallel motif with left-handed packing angles, and it is frequently stabilized by packing of small side chains occurring every seven residues in the sequence. Right-handed parallel and antiparallel structures show a similar tendency to segregate small residues to the helix-helix interface but spaced at four-residue intervals. Position-specific sequence propensities were derived for the most populated motifs. These structural and sequential motifs should be quite useful for the design and structural prediction of membrane proteins.

Folding and Hydrodynamics of a DNA i-Motif from the c-MYC Promoter Determined by Fluorescent Cytidine Analogs

PubMed Central

Reilly, Samantha M.; Lyons, Daniel F.; Wingate, Sara E.; Wright, Robert T.; Correia, John J.; Jameson, David M.; Wadkins, Randy M.

2014-01-01

The four-stranded i-motif (iM) conformation of cytosine-rich DNA has importance to a wide variety of biochemical systems that range from their use in nanomaterials to potential roles in oncogene regulation. The iM structure is formed at slightly acidic pH, where hemiprotonation of cytosine results in a stable C-C+ basepair. Here, we performed fundamental studies to examine iM formation from a C-rich strand from the promoter of the human c-MYC gene. We used a number of biophysical techniques to characterize both the hydrodynamic properties and folding kinetics of a folded iM. Our hydrodynamic studies using fluorescence anisotropy decay and analytical ultracentrifugation show that the iM structure has a compact size in solution and displays the rigidity of a double strand. By studying the rates of circular dichroism spectral changes and quenching of fluorescent cytidine analogs, we also established a mechanism for the folding of a random coil oligo into the iM. In the course of determining this folding pathway, we established that the fluorescent dC analogs tC° and PdC can be used to monitor individual residues of an iM structure and to determine the pKa of an iM. We established that the C-C+ hydrogen bonding of certain bases initiates the folding of the iM structure. We also showed that substitutions in the loop regions of iMs give a distinctly different kinetic signature during folding compared with bases that are intercalated. Our data reveal that the iM passes through a distinct intermediate form between the unfolded and folded forms. Taken together, our results lay the foundation for using fluorescent dC analogs to follow structural changes during iM formation. Our technique may also be useful for examining folding and structural changes in more complex iMs. PMID:25296324

Leucine zipper motif in RRS1 is crucial for the regulation of Arabidopsis dual resistance protein complex RPS4/RRS1

PubMed Central

Narusaka, Mari; Toyoda, Kazuhiro; Shiraishi, Tomonori; Iuchi, Satoshi; Takano, Yoshitaka; Shirasu, Ken; Narusaka, Yoshihiro

2016-01-01

Arabidopsis thaliana leucine-rich repeat-containing (NLR) proteins RPS4 and RRS1, known as dual resistance proteins, confer resistance to multiple pathogen isolates, such as the bacterial pathogens Pseudomonas syringae and Ralstonia solanacearum and the fungal pathogen Colletotrichum higginsianum. RPS4 is a typical Toll/interleukin 1 Receptor (TIR)-type NLR, whereas RRS1 is an atypical TIR-NLR that contains a leucine zipper (LZ) motif and a C-terminal WRKY domain. RPS4 and RRS1 are localised near each other in a head-to-head orientation. In this study, direct mutagenesis of the C-terminal LZ motif in RRS1 caused an autoimmune response and stunting in the mutant. Co-immunoprecipitation analysis indicated that full-length RPS4 and RRS1 are physically associated with one another. Furthermore, virus-induced gene silencing experiments showed that hypersensitive-like cell death triggered by RPS4/LZ motif-mutated RRS1 depends on EDS1. In conclusion, we suggest that the RRS1-LZ motif is crucial for the regulation of the RPS4/RRS1 complex. PMID:26750751

A generic motif discovery algorithm for sequential data.

PubMed

Jensen, Kyle L; Styczynski, Mark P; Rigoutsos, Isidore; Stephanopoulos, Gregory N

2006-01-01

Motif discovery in sequential data is a problem of great interest and with many applications. However, previous methods have been unable to combine exhaustive search with complex motif representations and are each typically only applicable to a certain class of problems. Here we present a generic motif discovery algorithm (Gemoda) for sequential data. Gemoda can be applied to any dataset with a sequential character, including both categorical and real-valued data. As we show, Gemoda deterministically discovers motifs that are maximal in composition and length. As well, the algorithm allows any choice of similarity metric for finding motifs. Finally, Gemoda's output motifs are representation-agnostic: they can be represented using regular expressions, position weight matrices or any number of other models for any type of sequential data. We demonstrate a number of applications of the algorithm, including the discovery of motifs in amino acids sequences, a new solution to the (l,d)-motif problem in DNA sequences and the discovery of conserved protein substructures. Gemoda is freely available at http://web.mit.edu/bamel/gemoda

Chaperone Hsp27 Modulates AUF1 Proteolysis and AU-Rich Element-Mediated mRNA Degradation▿

PubMed Central

Knapinska, Anna M.; Gratacós, Frances M.; Krause, Christopher D.; Hernandez, Kristina; Jensen, Amber G.; Bradley, Jacquelyn J.; Wu, Xiangyue; Pestka, Sidney; Brewer, Gary

2011-01-01

AUF1 is an AU-rich element (ARE)-binding protein that recruits translation initiation factors, molecular chaperones, and mRNA degradation enzymes to the ARE for mRNA destruction. We recently found chaperone Hsp27 to be an AUF1-associated ARE-binding protein required for tumor necrosis factor alpha (TNF-α) mRNA degradation in monocytes. Hsp27 is a multifunctional protein that participates in ubiquitination of proteins for their degradation by proteasomes. A variety of extracellular stimuli promote Hsp27 phosphorylation on three serine residues—Ser15, Ser78, and Ser82—by a number of kinases, including the mitogen-activated protein (MAP) pathway kinases p38 and MK2. Activating either kinase stabilizes ARE mRNAs. Likewise, ectopic expression of phosphomimetic mutant forms of Hsp27 stabilizes reporter ARE mRNAs. Here, we continued to examine the contributions of Hsp27 to mRNA degradation. As AUF1 is ubiquitinated and degraded by proteasomes, we addressed the hypothesis that Hsp27 phosphorylation controls AUF1 levels to modulate ARE mRNA degradation. Indeed, selected phosphomimetic mutants of Hsp27 promote proteolysis of AUF1 in a proteasome-dependent fashion and render ARE mRNAs more stable. Our results suggest that the p38 MAP kinase (MAPK)-MK2–Hsp27 signaling axis may target AUF1 destruction by proteasomes, thereby promoting ARE mRNA stabilization. PMID:21245386

Anomalous creep in Sn-rich solder joints

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

Song, Ho Geon; Morris Jr., John W.; Hua, Fay

2002-03-15

This paper discusses the creep behavior of example Sn-rich solders that have become candidates for use in Pb-free solder joints. The specific solders discussed are Sn-3.5Ag, Sn-3Ag-0.5Cu, Sn-0.7Cu and Sn-10In-3.1Ag, used in thin joints between Cu and Ni-Au metallized pads.

Platelet-rich plasma affects bacterial growth in vitro.

PubMed

Mariani, Erminia; Filardo, Giuseppe; Canella, Valentina; Berlingeri, Andrea; Bielli, Alessandra; Cattini, Luca; Landini, Maria Paola; Kon, Elizaveta; Marcacci, Maurilio; Facchini, Andrea

2014-09-01

Platelet-rich plasma (PRP), a blood derivative rich in platelets, is a relatively new technique used in tissue regeneration and engineering. The increased quantity of platelets makes this formulation of considerable value for their role in tissue healing and microbicidal activity. This activity was investigated against five of the most important strains involved in nosocomial infections (Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, Klebsiella pneumoniae and Streptococcus faecalis) to understand the prophylactic role of pure (P)-PRP. Microbicidal proteins released from activated P-PRP platelets were also determined. The microbicidal activity of P-PRP and platelet-poor plasma (PPP) was evaluated on different concentrations of the five bacterial strains incubated for 1, 2, 4 and 18 h and plated on agar for 18-24 h. P-PRP and PPP-released microbicidal proteins were evaluated by means of multiplex bead-based immunoassays. P-PRP and PPP inhibited bacterial growth for up to 2 h of incubation. The effect of P-PRP was significantly higher than that of PPP, mainly at the low seeding concentrations and/or shorter incubation times, depending on the bacterial strain. Chemokine (C-C motif) ligand-3, chemokine (C-C motif) ligand-5 and chemokine (C-X-C motif) ligand-1 were the molecules mostly related to Pseudomonas aeruginosa, Staphylococcus aureus and Streptococcus faecalis inhibition. Escherichia coli and Klebsiella pneumoniae were less influenced. The present results show that P-PRP might supply an early protection against bacterial contaminations during surgical interventions because the inhibitory activity is already evident from the first hour of treatment, which suggests that physiological molecules supplied in loco might be important in the time frame needed for the activation of the innate immune response. Copyright © 2014 International Society for Cellular Therapy. Published by Elsevier Inc. All rights reserved.

Deciphering functional glycosaminoglycan motifs in development.

PubMed

Townley, Robert A; Bülow, Hannes E

2018-03-23

Glycosaminoglycans (GAGs) such as heparan sulfate, chondroitin/dermatan sulfate, and keratan sulfate are linear glycans, which when attached to protein backbones form proteoglycans. GAGs are essential components of the extracellular space in metazoans. Extensive modifications of the glycans such as sulfation, deacetylation and epimerization create structural GAG motifs. These motifs regulate protein-protein interactions and are thereby repsonsible for many of the essential functions of GAGs. This review focusses on recent genetic approaches to characterize GAG motifs and their function in defined signaling pathways during development. We discuss a coding approach for GAGs that would enable computational analyses of GAG sequences such as alignments and the computation of position weight matrices to describe GAG motifs. Copyright © 2018 Elsevier Ltd. All rights reserved.

Metal-phthalocyanine ordered layers on Au(110): Metal-dependent adsorption energy

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

Massimi, Lorenzo, E-mail: lorenzo.massimi@uniroma1.it; Angelucci, Marco; Gargiani, Pierluigi

2014-06-28

Iron-phthalocyanine and cobalt-phthalocyanine chains, assembled along the Au(110)-(1×2) reconstructed channels, present a strong interaction with the Au metallic states, via the central metal ion. X-ray photoemission spectroscopy from the metal-2p core-levels and valence band high-resolution ultraviolet photoelectron spectroscopy bring to light signatures of the interaction of the metal-phthalocyanine single-layer with gold. The charge transfer from Au to the molecule causes the emerging of a metal-2p core level component at lower binding energy with respect to that measured in the molecular thin films, while the core-levels associated to the organic macrocycle (C and N 1s) are less influenced by the adsorption,more » and the macrocycles stabilize the interaction, inducing a strong interface dipole. Temperature Programmed Desorption experiments and photoemission as a function of temperature allow to estimate the adsorption energy for the thin-films, mainly due to the molecule-molecule van der Waals interaction, while the FePc and CoPc single-layers remain adsorbed on the Au surface up to at least 820 K.« less

Binding preference of carbon nanotube over proline-rich motif ligand on SH3-domain: a comparison with different force fields.

PubMed

Shi, Biyun; Zuo, Guanghong; Xiu, Peng; Zhou, Ruhong

2013-04-04

With the widespread applications of nanomaterials such as carbon nanotubes, there is a growing concern on the biosafety of these engineered nanoparticles, in particular their interactions with proteins. In molecular simulations of nanoparticle-protein interactions, the choice of empirical parameters (force fields) plays a decisive role, and thus is of great importance and should be examined carefully before wider applications. Here we compare three commonly used force fields, CHARMM, OPLSAA, and AMBER in study of the competitive binding of a single wall carbon nanotube (SWCNT) with a native proline-rich motif (PRM) ligand on its target protein SH3 domain, a ubiquitous protein-protein interaction mediator involved in signaling and regulatory pathways. We find that the SWCNT displays a general preference over the PRM in binding with SH3 domain in all the three force fields examined, although the degree of preference can be somewhat different, with the AMBER force field showing the highest preference. The SWCNT prevents the ligand from reaching its native binding pocket by (i) occupying the binding pocket directly, and (ii) binding with the ligand itself and then being trapped together onto some off-sites. The π-π stacking interactions between the SWCNT and aromatic residues are found to play a significant role in its binding to the SH3 domain in all the three force fields. Further analyses show that even the SWCNT-ligand binding can also be relatively more stable than the native ligand-protein binding, indicating a serious potential disruption to the protein SH3 function.

A private DNA motif finding algorithm.

PubMed

Chen, Rui; Peng, Yun; Choi, Byron; Xu, Jianliang; Hu, Haibo

2014-08-01

With the increasing availability of genomic sequence data, numerous methods have been proposed for finding DNA motifs. The discovery of DNA motifs serves a critical step in many biological applications. However, the privacy implication of DNA analysis is normally neglected in the existing methods. In this work, we propose a private DNA motif finding algorithm in which a DNA owner's privacy is protected by a rigorous privacy model, known as ∊-differential privacy. It provides provable privacy guarantees that are independent of adversaries' background knowledge. Our algorithm makes use of the n-gram model and is optimized for processing large-scale DNA sequences. We evaluate the performance of our algorithm over real-life genomic data and demonstrate the promise of integrating privacy into DNA motif finding. Copyright © 2014 Elsevier Inc. All rights reserved.

Corticosteroid receptors adopt distinct cyclical transcriptional signatures.

PubMed

Le Billan, Florian; Amazit, Larbi; Bleakley, Kevin; Xue, Qiong-Yao; Pussard, Eric; Lhadj, Christophe; Kolkhof, Peter; Viengchareun, Say; Fagart, Jérôme; Lombès, Marc

2018-05-07

Mineralocorticoid receptors (MRs) and glucocorticoid receptors (GRs) are two closely related hormone-activated transcription factors that regulate major pathophysiologic functions. High homology between these receptors accounts for the crossbinding of their corresponding ligands, MR being activated by both aldosterone and cortisol and GR essentially activated by cortisol. Their coexpression and ability to bind similar DNA motifs highlight the need to investigate their respective contributions to overall corticosteroid signaling. Here, we decipher the transcriptional regulatory mechanisms that underlie selective effects of MRs and GRs on shared genomic targets in a human renal cellular model. Kinetic, serial, and sequential chromatin immunoprecipitation approaches were performed on the period circadian protein 1 ( PER1) target gene, providing evidence that both receptors dynamically and cyclically interact at the same target promoter in a specific and distinct transcriptional signature. During this process, both receptors regulate PER1 gene by binding as homo- or heterodimers to the same promoter region. Our results suggest a novel level of MR-GR target gene regulation, which should be considered for a better and integrated understanding of corticosteroid-related pathophysiology.-Le Billan, F., Amazit, L., Bleakley, K., Xue, Q.-Y., Pussard, E., Lhadj, C., Kolkhof, P., Viengchareun, S., Fagart, J., Lombès, M. Corticosteroid receptors adopt distinct cyclical transcriptional signatures.

Molecular mechanisms involved in gamete interaction: evidence for the participation of cysteine-rich secretory proteins (CRISP) in sperm-egg fusion.

PubMed

Da Ros, V; Busso, D; Cohen, D J; Maldera, J; Goldweic, N; Cuasnicu, P S

2007-01-01

Epididymal protein DE and testicular protein Tpx-1 are two cysteine-rich secretory proteins also known as CRISP-1 and CRISP-2, respectively. DE/ CRISP-1 is localised on the equatorial segment of acrosome-reacted sperm and participates in rat gamete fusion through its binding to egg-complementary sites. Recent results using bacterially-expressed recombinant fragments of DE as well as synthetic peptides revealed that the ability of DE to bind to the egg surface and inhibit gamete fusion resides in a region of 12 amino acids corresponding to an evolutionary conserved motif of the CRISP family (Signature 2). Given the high degree of homology between DE/CRISP-1 and Tpx-1/CRISP-2, we also explored the potential participation of the testicular intra-acrosomal protein in gamete fusion. Results showing the ability of recombinant Tpx-1 to bind to the surface of rat eggs (evaluated by indirect immunofluorescence) and to significantly inhibit zona-free egg penetration, support the participation of this protein in gamete fusion through its interaction with egg-binding sites. Interestingly, rat Tpx-1 exhibits only two substitutions in Signature 2 when compared to this region in DE. Together, these results provide evidence for the involvement of both epididymal DE/CRISP-1 and testicular Tpx-1/CRISP-2 in gamete fusion suggesting the existence of a functional cooperation between homologue molecules as a mechanism to ensure the success of fertilisation.

New Structural and Functional Contexts of the Dx[DN]xDG Linear Motif: Insights into Evolution of Calcium-Binding Proteins

PubMed Central

Rigden, Daniel J.; Woodhead, Duncan D.; Wong, Prudence W. H.; Galperin, Michael Y.

2011-01-01

Binding of calcium ions (Ca2+) to proteins can have profound effects on their structure and function. Common roles of calcium binding include structure stabilization and regulation of activity. It is known that diverse families – EF-hands being one of at least twelve – use a Dx[DN]xDG linear motif to bind calcium in near-identical fashion. Here, four novel structural contexts for the motif are described. Existing experimental data for one of them, a thermophilic archaeal subtilisin, demonstrate for the first time a role for Dx[DN]xDG-bound calcium in protein folding. An integrin-like embedding of the motif in the blade of a β-propeller fold – here named the calcium blade – is discovered in structures of bacterial and fungal proteins. Furthermore, sensitive database searches suggest a common origin for the calcium blade in β-propeller structures of different sizes and a pan-kingdom distribution of these proteins. Factors favouring the multiple convergent evolution of the motif appear to include its general Asp-richness, the regular spacing of the Asp residues and the fact that change of Asp into Gly and vice versa can occur though a single nucleotide change. Among the known structural contexts for the Dx[DN]xDG motif, only the calcium blade and the EF-hand are currently found intracellularly in large numbers, perhaps because the higher extracellular concentration of Ca2+ allows for easier fixing of newly evolved motifs that have acquired useful functions. The analysis presented here will inform ongoing efforts toward prediction of similar calcium-binding motifs from sequence information alone. PMID:21720552

Wetting Behavior of Ternary Au-Ge-X (X = Sb, Sn) Alloys on Cu and Ni

NASA Astrophysics Data System (ADS)

Jin, S.; Valenza, F.; Novakovic, R.; Leinenbach, C.

2013-06-01

Au-Ge-based alloys are potential substitutes for Pb-rich solders currently used for high-temperature applications. In the present work, the wetting behavior of two Au-Ge-X (X = Sb, Sn) ternary alloys, i.e., Au-15Ge-17Sb and Au-13.7 Ge-15.3Sn (at.%), in contact with Cu and Ni substrates has been investigated. Au-13.7Ge-15.3Sn alloy showed complete wetting on both Cu and Ni substrates. Total spreading of Au-15Ge-17Sb alloy on Cu was also observed, while the final contact angle of this alloy on Ni was about 29°. Pronounced dissolution of Cu substrates into the solder alloys investigated was detected, while the formation of Ni-Ge intermetallic compounds at the interface of both solder/Ni systems suppressed the dissolution of Ni into the solder.

Chaotic Motifs in Gene Regulatory Networks

PubMed Central

Zhang, Zhaoyang; Ye, Weiming; Qian, Yu; Zheng, Zhigang; Huang, Xuhui; Hu, Gang

2012-01-01

Chaos should occur often in gene regulatory networks (GRNs) which have been widely described by nonlinear coupled ordinary differential equations, if their dimensions are no less than 3. It is therefore puzzling that chaos has never been reported in GRNs in nature and is also extremely rare in models of GRNs. On the other hand, the topic of motifs has attracted great attention in studying biological networks, and network motifs are suggested to be elementary building blocks that carry out some key functions in the network. In this paper, chaotic motifs (subnetworks with chaos) in GRNs are systematically investigated. The conclusion is that: (i) chaos can only appear through competitions between different oscillatory modes with rivaling intensities. Conditions required for chaotic GRNs are found to be very strict, which make chaotic GRNs extremely rare. (ii) Chaotic motifs are explored as the simplest few-node structures capable of producing chaos, and serve as the intrinsic source of chaos of random few-node GRNs. Several optimal motifs causing chaos with atypically high probability are figured out. (iii) Moreover, we discovered that a number of special oscillators can never produce chaos. These structures bring some advantages on rhythmic functions and may help us understand the robustness of diverse biological rhythms. (iv) The methods of dominant phase-advanced driving (DPAD) and DPAD time fraction are proposed to quantitatively identify chaotic motifs and to explain the origin of chaotic behaviors in GRNs. PMID:22792171

Investigating the role of GXXXG motifs in helical folding and self-association of plasticins, Gly/Leu-rich antimicrobial peptides.

PubMed

Carlier, Ludovic; Joanne, Pierre; Khemtémourian, Lucie; Lacombe, Claire; Nicolas, Pierre; El Amri, Chahrazade; Lequin, Olivier

2015-01-01

Plasticins (PTC) are dermaseptin-related antimicrobial peptides characterized by a large number of leucine and glycine residues arranged in GXXXG motifs that are often described to promote helix association within biological membranes. We report the structure and interaction properties of two plasticins, PTC-B1 from Phyllomedusa bicolor and a cationic analog of PTC-DA1 from Pachymedusa dacnicolor, which exhibit membrane-lytic activities on a broad range of microorganisms. Despite a high number of glycine, CD and NMR spectroscopy show that the two plasticins adopt mainly alpha-helical conformations in a wide variety of environments such as trifluoroethanol, detergent micelles and lipid vesicles. In DPC and SDS, plasticins adopt well-defined helices that lie parallel to the micelle surface, all glycine residues being located on the solvent-exposed face. Spectroscopic data and cross-linking experiments indicate that the GXXXG repeats in these amphipathic helices do not provide a strong oligomerization interface, suggesting a different role from GXXXG motifs found in transmembrane helices. Copyright © 2014 Elsevier B.V. All rights reserved.

Sequential visibility-graph motifs

NASA Astrophysics Data System (ADS)

Iacovacci, Jacopo; Lacasa, Lucas

2016-04-01

Visibility algorithms transform time series into graphs and encode dynamical information in their topology, paving the way for graph-theoretical time series analysis as well as building a bridge between nonlinear dynamics and network science. In this work we introduce and study the concept of sequential visibility-graph motifs, smaller substructures of n consecutive nodes that appear with characteristic frequencies. We develop a theory to compute in an exact way the motif profiles associated with general classes of deterministic and stochastic dynamics. We find that this simple property is indeed a highly informative and computationally efficient feature capable of distinguishing among different dynamics and robust against noise contamination. We finally confirm that it can be used in practice to perform unsupervised learning, by extracting motif profiles from experimental heart-rate series and being able, accordingly, to disentangle meditative from other relaxation states. Applications of this general theory include the automatic classification and description of physical, biological, and financial time series.

The Thiamin Pyrophosphate-Motif

NASA Technical Reports Server (NTRS)

Dominiak, P.; Ciszak, E.

2003-01-01

Using databases the authors have identified a common thiamin pyrophosphate (TPP)-motif in the family of functionally diverse TPP-dependent enzymes. This common motif consists of multimeric organization of subunits and two catalytic centers. Each catalytic center (PP:PYR) is formed at the interface of the PP-domain binding the magnesium ion, pyrophosphate and amhopyrimidine ring of TPP, and the PYR-domain binding the aminopyrimidine ring of that cofactor. A pair of these catalytic centers constitutes the catalytic core (PP:PYR)(sub 2) within these enzymes. Analysis of the structural elements of this catalytic core reveals novel definition of the common amino acid sequences, which are GXPhiX(sub 4)(G)PhiXXGQ and GDGX(sub 25-30)NN in the PP-domain, and the EX(sub 4)(G)PhiXXGPhi in the PYR-domain, where Phi corresponds to a hydrophobic amino acid. This TPP-motif provides a novel tool for annotation of TPP-dependent enzymes useful in advancing functional proteomics.

The Thiamin Pyrophosphate-Motif

NASA Technical Reports Server (NTRS)

Dominiak, Paulina M.; Ciszak, Ewa M.

2003-01-01

Using databases the authors have identified a common thiamin pyrophosphate (TPP)-motif in the family of functionally diverse TPP-dependent enzymes. This common motif consists of multimeric organization of subunits, two catalytic centers, common amino acid sequence, and specific contacts to provide a flip-flop, or alternate site, mechanism of action. Each catalytic center [PP:PYR] is formed at the interface of the PP-domain binding the magnesium ion, pyrophosphate and aminopyrimidine ring of TPP, and the PYR-domain binding the aminopyrimidine ring of that cofactor. A pair of these catalytic centers constitutes the catalytic core [PP:PYR]* within these enzymes. Analysis of the structural elements of this catalytic core reveals novel definition of the common amino acid sequences, which are GX@&(G)@XXGQ, and GDGX25-30 within the PP- domain, and the E&(G)@XXG@ within the PYR-domain, where Q, corresponds to a hydrophobic amino acid. This TPP-motif provides a novel tool for annotation of TPP-dependent enzymes useful in advancing functional proteomics.

Occurrence probability of structured motifs in random sequences.

PubMed

Robin, S; Daudin, J-J; Richard, H; Sagot, M-F; Schbath, S

2002-01-01

The problem of extracting from a set of nucleic acid sequences motifs which may have biological function is more and more important. In this paper, we are interested in particular motifs that may be implicated in the transcription process. These motifs, called structured motifs, are composed of two ordered parts separated by a variable distance and allowing for substitutions. In order to assess their statistical significance, we propose approximations of the probability of occurrences of such a structured motif in a given sequence. An application of our method to evaluate candidate promoters in E. coli and B. subtilis is presented. Simulations show the goodness of the approximations.

Hsp70 Is a Novel Posttranscriptional Regulator of Gene Expression That Binds and Stabilizes Selected mRNAs Containing AU-Rich Elements

PubMed Central

Kishor, Aparna; Tandukar, Bishal; Ly, Yann V.; Toth, Eric A.; Suarez, Yvelisse; Brewer, Gary

2013-01-01

The AU-rich elements (AREs) encoded within many mRNA 3′ untranslated regions (3′UTRs) are targets for factors that control transcript longevity and translational efficiency. Hsp70, best known as a protein chaperone with well-defined peptide-refolding properties, is known to interact with ARE-like RNA substrates in vitro. Here, we show that cofactor-free preparations of Hsp70 form direct, high-affinity complexes with ARE substrates based on specific recognition of U-rich sequences by both the ATP- and peptide-binding domains. Suppressing Hsp70 in HeLa cells destabilized an ARE reporter mRNA, indicating a novel ARE-directed mRNA-stabilizing role for this protein. Hsp70 also bound and stabilized endogenous ARE-containing mRNAs encoding vascular endothelial growth factor (VEGF) and Cox-2, which involved a mechanism that was unaffected by an inhibitor of its protein chaperone function. Hsp70 recognition and stabilization of VEGF mRNA was mediated by an ARE-like sequence in the proximal 3′UTR. Finally, stabilization of VEGF mRNA coincided with the accumulation of Hsp70 protein in HL60 promyelocytic leukemia cells recovering from acute thermal stress. We propose that the binding and stabilization of selected ARE-containing mRNAs may contribute to the cytoprotective effects of Hsp70 following cellular stress but may also provide a novel mechanism linking constitutively elevated Hsp70 expression to the development of aggressive neoplastic phenotypes. PMID:23109422

Iron and chlorine as guides to stratiform Cu-Co-Au deposits, Idaho Cobalt Belt, USA

USGS Publications Warehouse

Nash, J.T.; Connor, J.J.

1993-01-01

The Cu-Co-Au deposits of the Idaho Cobalt Belt are in lithostratigraphic zones of the Middle Proterozoic Yellowjacket Formation characterized by distinctive chemical and mineralogical compositions including high concentrations of Fe (15- > 30 wt. percent Fe2O3), Cl (0.1-1.10 wt. percent), and magnetite or biotite (> 50 vol. percent). The Cu-Co-Au deposits of the Blackbird mine are stratabound in Fe-silicate facies rocks that are rich in biotite, Fe, and Cl, but stratigraphically equivalent rocks farther than 10 km from ore deposits have similar compositions. A lower lithostratigraphic zone containing magnetite and small Cu-Co-Au deposits extends for more than 40 km. The Fe-rich strata are probably exhalative units related to mafic volcanism and submarine hot springs, but the origin of the high Cl concentrations is less clear. Former chlorine-rich pore fluids are suggested by the presence of supersaline fluid inclusions, by Cl-rich biotite and scapolite (as much as 1.87 percent Cl in Fe-rich biotite), and by high Cl concentrations in rock samples. Chlorine is enriched in specific strata and in zones characterized by soft-sediment deformation, thus probably was introduced during sedimentation or diagenesis. Unlike some metasedimentary rocks containing scapolite and high Cl, the Yellowjacket Formation lacks evidence for evaporitic strata that could have been a source of Cl. More likely, the Cl reflects a submarine brine that carried Fe, K, and base metals. Strata containing anomalous Fe-K-Cl are considered to be a guide to sub-basins favorable for the occurrence of stratiform base-metal deposits. ?? 1993 Springer-Verlag.

Using SCOPE to identify potential regulatory motifs in coregulated genes.

PubMed

Martyanov, Viktor; Gross, Robert H

2011-05-31

SCOPE is an ensemble motif finder that uses three component algorithms in parallel to identify potential regulatory motifs by over-representation and motif position preference. Each component algorithm is optimized to find a different kind of motif. By taking the best of these three approaches, SCOPE performs better than any single algorithm, even in the presence of noisy data. In this article, we utilize a web version of SCOPE to examine genes that are involved in telomere maintenance. SCOPE has been incorporated into at least two other motif finding programs and has been used in other studies. The three algorithms that comprise SCOPE are BEAM, which finds non-degenerate motifs (ACCGGT), PRISM, which finds degenerate motifs (ASCGWT), and SPACER, which finds longer bipartite motifs (ACCnnnnnnnnGGT). These three algorithms have been optimized to find their corresponding type of motif. Together, they allow SCOPE to perform extremely well. Once a gene set has been analyzed and candidate motifs identified, SCOPE can look for other genes that contain the motif which, when added to the original set, will improve the motif score. This can occur through over-representation or motif position preference. Working with partial gene sets that have biologically verified transcription factor binding sites, SCOPE was able to identify most of the rest of the genes also regulated by the given transcription factor. Output from SCOPE shows candidate motifs, their significance, and other information both as a table and as a graphical motif map. FAQs and video tutorials are available at the SCOPE web site which also includes a "Sample Search" button that allows the user to perform a trial run. Scope has a very friendly user interface that enables novice users to access the algorithm's full power without having to become an expert in the bioinformatics of motif finding. As input, SCOPE can take a list of genes, or FASTA sequences. These can be entered in browser text fields, or read from

Multiple Dileucine-like Motifs Direct VGLUT1 Trafficking

PubMed Central

Foss, Sarah M.; Li, Haiyan; Santos, Magda S.; Edwards, Robert H.

2013-01-01

The vesicular glutamate transporters (VGLUTs) package glutamate into synaptic vesicles, and the two principal isoforms VGLUT1 and VGLUT2 have been suggested to influence the properties of release. To understand how a VGLUT isoform might influence transmitter release, we have studied their trafficking and previously identified a dileucine-like endocytic motif in the C terminus of VGLUT1. Disruption of this motif impairs the activity-dependent recycling of VGLUT1, but does not eliminate its endocytosis. We now report the identification of two additional dileucine-like motifs in the N terminus of VGLUT1 that are not well conserved in the other isoforms. In the absence of all three motifs, rat VGLUT1 shows limited accumulation at synaptic sites and no longer responds to stimulation. In addition, shRNA-mediated knockdown of clathrin adaptor proteins AP-1 and AP-2 shows that the C-terminal motif acts largely via AP-2, whereas the N-terminal motifs use AP-1. Without the C-terminal motif, knockdown of AP-1 reduces the proportion of VGLUT1 that responds to stimulation. VGLUT1 thus contains multiple sorting signals that engage distinct trafficking mechanisms. In contrast to VGLUT1, the trafficking of VGLUT2 depends almost entirely on the conserved C-terminal dileucine-like motif: without this motif, a substantial fraction of VGLUT2 redistributes to the plasma membrane and the transporter's synaptic localization is disrupted. Consistent with these differences in trafficking signals, wild-type VGLUT1 and VGLUT2 differ in their response to stimulation. PMID:23804088

Multiple dileucine-like motifs direct VGLUT1 trafficking.

PubMed

Foss, Sarah M; Li, Haiyan; Santos, Magda S; Edwards, Robert H; Voglmaier, Susan M

2013-06-26

The vesicular glutamate transporters (VGLUTs) package glutamate into synaptic vesicles, and the two principal isoforms VGLUT1 and VGLUT2 have been suggested to influence the properties of release. To understand how a VGLUT isoform might influence transmitter release, we have studied their trafficking and previously identified a dileucine-like endocytic motif in the C terminus of VGLUT1. Disruption of this motif impairs the activity-dependent recycling of VGLUT1, but does not eliminate its endocytosis. We now report the identification of two additional dileucine-like motifs in the N terminus of VGLUT1 that are not well conserved in the other isoforms. In the absence of all three motifs, rat VGLUT1 shows limited accumulation at synaptic sites and no longer responds to stimulation. In addition, shRNA-mediated knockdown of clathrin adaptor proteins AP-1 and AP-2 shows that the C-terminal motif acts largely via AP-2, whereas the N-terminal motifs use AP-1. Without the C-terminal motif, knockdown of AP-1 reduces the proportion of VGLUT1 that responds to stimulation. VGLUT1 thus contains multiple sorting signals that engage distinct trafficking mechanisms. In contrast to VGLUT1, the trafficking of VGLUT2 depends almost entirely on the conserved C-terminal dileucine-like motif: without this motif, a substantial fraction of VGLUT2 redistributes to the plasma membrane and the transporter's synaptic localization is disrupted. Consistent with these differences in trafficking signals, wild-type VGLUT1 and VGLUT2 differ in their response to stimulation.

The coupled geochemistry of Au and As in pyrite from hydrothermal ore deposits

NASA Astrophysics Data System (ADS)

Deditius, Artur P.; Reich, Martin; Kesler, Stephen E.; Utsunomiya, Satoshi; Chryssoulis, Stephen L.; Walshe, John; Ewing, Rodney C.

2014-09-01

alteration by hydrothermal fluids. The second trend consists of pyrites from porphyry Cu and epithermal Au deposits, which are characterised by compositions that preserve the Au/As signature of mineralizing magmatic-hydrothermal fluids, confirming the role of this sulfide in controlling metal ratios in ore systems.

RNA motif search with data-driven element ordering.

PubMed

Rampášek, Ladislav; Jimenez, Randi M; Lupták, Andrej; Vinař, Tomáš; Brejová, Broňa

2016-05-18

In this paper, we study the problem of RNA motif search in long genomic sequences. This approach uses a combination of sequence and structure constraints to uncover new distant homologs of known functional RNAs. The problem is NP-hard and is traditionally solved by backtracking algorithms. We have designed a new algorithm for RNA motif search and implemented a new motif search tool RNArobo. The tool enhances the RNAbob descriptor language, allowing insertions in helices, which enables better characterization of ribozymes and aptamers. A typical RNA motif consists of multiple elements and the running time of the algorithm is highly dependent on their ordering. By approaching the element ordering problem in a principled way, we demonstrate more than 100-fold speedup of the search for complex motifs compared to previously published tools. We have developed a new method for RNA motif search that allows for a significant speedup of the search of complex motifs that include pseudoknots. Such speed improvements are crucial at a time when the rate of DNA sequencing outpaces growth in computing. RNArobo is available at http://compbio.fmph.uniba.sk/rnarobo .

40Ar-39Ar dating of Archean iron oxide Cu-Au and Paleoproterozoic granite-related Cu-Au deposits in the Carajás Mineral Province, Brazil: implications for genetic models

NASA Astrophysics Data System (ADS)

Pollard, Peter J.; Taylor, Roger G.; Peters, Lisa; Matos, Fernando; Freitas, Cantidiano; Saboia, Lineu; Huhn, Sergio

2018-05-01

40Ar-39Ar dating of biotite from IOCG and granite-related Cu-Au deposits in the Carajás Mineral Province provides evidence for the timing of mineralization and constraints on genetic models of ore formation. Ages of biotite from greisen and quartz-rich vein and breccia deposits, Alvo 118—1885 ± 4 Ma, Breves—1886 ± 5 Ma, Estrela—1896 ± 7 Ma, and Gameleira—1908 ± 7 Ma, demonstrate the close temporal relationship between Cu-Au mineralization and subjacent A-type granites. Mineralization is hosted within granite cupolas (Breves) or in vein/breccia systems emanating from the cupolas (Estrela and Gameleira), consistent with a genetic relationship of mineralization to the B-Li-F-rich granites. Plateau and minimum ages of biotite from IOCG deposits, including Igarapé Bahia, Cristalino, Corta Goela, and GT34, range from 2537 ± 6 Ma to 2193 ± 4 Ma. The 40Ar-39Ar age of biotite from Igarapé Bahia (2537 ± 6 Ma) is similar to a previous SHRIMP 207Pb-206Pb age for monazite of 2575 ± 12 Ma when the uncertainties in the respective analyses and standards are taken into account. The age spectrum for biotite from Cristalino shows increasing ages for successive steps, consistent with post-crystallization Ar loss, and the age of 2388 ± 5 Ma for the last three steps is considered a minimum age for Cu-Au mineralization. The age of biotite from the GT34 prospect (2512 ± 7 Ma) coincides with a previously identified period of basement reactivation and may indicate the formation of Cu-Au mineralization at this time or resetting of biotite from an older mineralization event at this time. At Corta Goela, within the Canaã Shear Zone, the biotite age of 2193 ± 4 Ma lies between the ages of IOCG (2.57-2.76 Ga) and granite-related Cu-Au ( 1.88 Ga) deposits elsewhere in the Carajás district but is similar to previously reported 40Ar-39Ar ages for amphibole from Sossego, possibly indicating that mineralization at both Sossego and Corta Goela was affected by a thermal event at

Identification of sequence motifs significantly associated with antisense activity.

PubMed

McQuisten, Kyle A; Peek, Andrew S

2007-06-07

Predicting the suppression activity of antisense oligonucleotide sequences is the main goal of the rational design of nucleic acids. To create an effective predictive model, it is important to know what properties of an oligonucleotide sequence associate significantly with antisense activity. Also, for the model to be efficient we must know what properties do not associate significantly and can be omitted from the model. This paper will discuss the results of a randomization procedure to find motifs that associate significantly with either high or low antisense suppression activity, analysis of their properties, as well as the results of support vector machine modelling using these significant motifs as features. We discovered 155 motifs that associate significantly with high antisense suppression activity and 202 motifs that associate significantly with low suppression activity. The motifs range in length from 2 to 5 bases, contain several motifs that have been previously discovered as associating highly with antisense activity, and have thermodynamic properties consistent with previous work associating thermodynamic properties of sequences with their antisense activity. Statistical analysis revealed no correlation between a motif's position within an antisense sequence and that sequences antisense activity. Also, many significant motifs existed as subwords of other significant motifs. Support vector regression experiments indicated that the feature set of significant motifs increased correlation compared to all possible motifs as well as several subsets of the significant motifs. The thermodynamic properties of the significantly associated motifs support existing data correlating the thermodynamic properties of the antisense oligonucleotide with antisense efficiency, reinforcing our hypothesis that antisense suppression is strongly associated with probe/target thermodynamics, as there are no enzymatic mediators to speed the process along like the RNA Induced

Characteristic motifs for families of allergenic proteins

PubMed Central

Ivanciuc, Ovidiu; Garcia, Tzintzuni; Torres, Miguel; Schein, Catherine H.; Braun, Werner

2008-01-01

The identification of potential allergenic proteins is usually done by scanning a database of allergenic proteins and locating known allergens with a high sequence similarity. However, there is no universally accepted cut-off value for sequence similarity to indicate potential IgE cross-reactivity. Further, overall sequence similarity may be less important than discrete areas of similarity in proteins with homologous structure. To identify such areas, we first classified all allergens and their subdomains in the Structural Database of Allergenic Proteins (SDAP, http://fermi.utmb.edu/SDAP/) to their closest protein families as defined in Pfam, and identified conserved physicochemical property motifs characteristic of each group of sequences. Allergens populate only a small subset of all known Pfam families, as all allergenic proteins in SDAP could be grouped to only 130 (of 9318 total) Pfams, and 31 families contain more than four allergens. Conserved physicochemical property motifs for the aligned sequences of the most populated Pfam families were identified with the PCPMer program suite and catalogued in the webserver Motif-Mate (http://born.utmb.edu/motifmate/summary.php). We also determined specific motifs for allergenic members of a family that could distinguish them from non-allergenic ones. These allergen specific motifs should be most useful in database searches for potential allergens. We found that sequence motifs unique to the allergens in three families (seed storage proteins, Bet v 1, and tropomyosin) overlap with known IgE epitopes, thus providing evidence that our motif based approach can be used to assess the potential allergenicity of novel proteins. PMID:18951633

Structural evolution of atomically precise thiolated bimetallic [Au(12+n)Cu₃₂(SR)(30+n)]⁴⁻ (n = 0, 2, 4, 6) nanoclusters.

PubMed

Yang, Huayan; Wang, Yu; Yan, Juanzhu; Chen, Xi; Zhang, Xin; Häkkinen, Hannu; Zheng, Nanfeng

2014-05-21

A series of all-thiol stabilized bimetallic Au-Cu nanoclusters, [Au(12+n)Cu32(SR)(30+n)](4-) (n = 0, 2, 4, 6 and SR = SPhCF3), are successfully synthesized and characterized by X-ray single-crystal analysis and density functional theory (DFT) calculations. Each cluster consists of a Keplerate two-shell Au12@Cu20 core protected by (6 - n) units of Cu2(SR)5 and n units of Cu2Au(SR)6 (n = 0, 2, 4, 6) motifs on its surface. The size and structural evolution of the clusters is atomically controlled by the Au precursors and countercations used in the syntheses. The clusters exhibit similar optical absorption properties that are not dependent on the number of surface Cu2Au(SR)6 units. Although DFT suggests an electronic structure with an 18-electron superatom shell closure, the clusters display different thermal stabilities. [Au(12+n)Cu32(SR)(30+n)](4-) clusters with n = 0 and 2 are more stable than those with n = 4 and 6. Moreover, an oxidation product of the clusters, [Au13Cu12(SR)20](4-), is structurally identified to gain insight into how the clusters are oxidized.

Abundant Cool Magnesium-Rich Pyroxene Crystals in Comet Hale-Bopp

NASA Technical Reports Server (NTRS)

Wooden, D. H.

1999-01-01

Modeling of the observed dust emission from Comet Hale-Bopp over a large range of heliocentric distances (2.8 AU - 0.93 AU -1.7 AU) led to the discovery of Mg-rich pyroxene crystals in the coma These pyroxene crystals are apparent in the 10 micron spectrum only when the comet is close to perihelion (r(sub h) = 1.2 AU) because they are cooler than the other silicate minerals. The pyroxene crystals are cooler than the other species because of their high Mg-content. They do not absorb as efficiently as the other silicate minerals. Given the same high Mg content of Mg/(Mg + Fe) = 0.9, radiative equilibrium computations show that pyroxene crystals are expected to be 150 K cooler than olivine crystals. The pyroxene crystals are also about 10x more abundant than the other silicate mineral species. Their high Mg content and relatively large abundance are in agreement with the preponderance of pyroxene interplanetary dust particles (IDPs) and the recent reanalysis of the PUMA-I flyby of Comet Halley. Before Hale-Bopp, only olivine crystals were detected spectroscopically in comets, probably because the pyroxene crystals are less optically active, hence significantly cooler and harder to detect in contrast to the warmer silicate species. Determining the relative abundances of silicate minerals depends on their Mg contents. If the pyroxene crystals in Comet Hale-Bopp are solar nebula condensates, then they probably had to form during the early FU Orionis epoch when the inner disk was hot enough and be transported out to the region of formation of icy planetesimals without being reheated. Reheating events appear to reincorporate Fe back into the crystals or form Fe-rich rims, which are not consistent with the high-Mg-content crystals. The condensation of Mg-rich pyroxene crystals is expected from solar nebula thermal equilibrium computations. However, their subsequent transport to the outer solar nebula unaltered has yet to be theoretically demonstrated. The discovery of Mg-rich

Astronomy in Denver: The polarization evolution of the luminous Type Ib SN 2012au

NASA Astrophysics Data System (ADS)

Hoffman, Jennifer L.; DeKlotz, Sophia; Cooper, Kevin; Slay, Hannah; Williams, George Grant; Supernova Spectropolarimetry Project (SNSPOL)

2018-06-01

We present an analysis of the spectropolarimetric behavior of the Type Ib SN 2012au over the first 315 days of its evolution. Our data were obtained by the Supernova Spectropolarimetry Project using the CCD Imaging/Spectropolarimeter (SPOL) at the 61" Kuiper, the 90" Bok, and the 6.5-m MMT telescopes. SN 2012au was a very energetic, luminous, and slowly evolving event that may represent an intermediate case between normal core-collapse supernovae and the enigmatic superluminous supernovae. Strong, time-variable line polarization signatures, particularly in the He Il λ5876 line, support previous hypotheses of an asymmetric explosion and allow us to trace detailed structures within the supernova ejecta as they change over time. We compare the polarimetric evolution of the continuum and emission lines in SN 2012au and compare its behavior with that of other bright and polarimetrically variable supernovae.

Regional setting and characteristics of the Neoproterozoic Wadi Hamama Zn-Cu-Ag-Au prospect: evidence for an intra-oceanic island arc-hosted volcanogenic hydrothermal system

NASA Astrophysics Data System (ADS)

Abd El-Rahman, Yasser; Surour, Adel A.; El-Manawi, Abdel Hamid W.; El-Dougdoug, Abdel-Monem A.; Omar, Sayed

2015-04-01

The Wadi Hamama area is a volcanogenic Zn-Cu-Au-Ag prospect. It is hosted by a Neoproterozoic bimodal-mafic sequence, which comprises basalt, dacite and rhyolite along with volcaniclastic rocks. The rocks have a low-K tholeiitic affinity and are enriched in large ion lithophile elements over high field strength elements, which indicated their formation in an intra-oceanic island arc tectonic setting. The area was intruded by a tonalite-trondhjemite body, which has an intra-oceanic island arc affinity and later by diorite, which has a cordilleran-margin geochemical affinity. These rock units were intruded by post-tectonic granite dykes, which have a within-plate geochemical signature. There is a quartz-carbonate horizon extending along the contact between the basalt and the volcaniclastic rocks, mainly banded and lapilli tuffs. This horizon is of exhalative origin and is underlain by a mushroom-shaped alteration zone extending from the horizon down to the massive basalt. The footwall alteration is characterized by a silica-rich core surrounded by a thick chlorite sheath. Both the quartz-carbonate horizon and the footwall-altered rocks enclose historical trenches and pits. Sulfide-rich core samples are enriched in Zn, relative to Cu, and in Ag, which indicates the low-temperature nature of the hydrothermal system. The prospect was affected by supergene processes, which led to the widespread occurrence of secondary copper minerals and gold enrichment relative to the leached base metals, especially Zn. The prospect formed through a limited rifting of an intra-oceanic island arc which resulted in the formation of a small-scale volcanogenic Zn-Cu-Ag-Au prospect.

Classification and assessment tools for structural motif discovery algorithms.

PubMed

Badr, Ghada; Al-Turaiki, Isra; Mathkour, Hassan

2013-01-01

Motif discovery is the problem of finding recurring patterns in biological data. Patterns can be sequential, mainly when discovered in DNA sequences. They can also be structural (e.g. when discovering RNA motifs). Finding common structural patterns helps to gain a better understanding of the mechanism of action (e.g. post-transcriptional regulation). Unlike DNA motifs, which are sequentially conserved, RNA motifs exhibit conservation in structure, which may be common even if the sequences are different. Over the past few years, hundreds of algorithms have been developed to solve the sequential motif discovery problem, while less work has been done for the structural case. In this paper, we survey, classify, and compare different algorithms that solve the structural motif discovery problem, where the underlying sequences may be different. We highlight their strengths and weaknesses. We start by proposing a benchmark dataset and a measurement tool that can be used to evaluate different motif discovery approaches. Then, we proceed by proposing our experimental setup. Finally, results are obtained using the proposed benchmark to compare available tools. To the best of our knowledge, this is the first attempt to compare tools solely designed for structural motif discovery. Results show that the accuracy of discovered motifs is relatively low. The results also suggest a complementary behavior among tools where some tools perform well on simple structures, while other tools are better for complex structures. We have classified and evaluated the performance of available structural motif discovery tools. In addition, we have proposed a benchmark dataset with tools that can be used to evaluate newly developed tools.

DynaMIT: the dynamic motif integration toolkit

PubMed Central

Dassi, Erik; Quattrone, Alessandro

2016-01-01

De-novo motif search is a frequently applied bioinformatics procedure to identify and prioritize recurrent elements in sequences sets for biological investigation, such as the ones derived from high-throughput differential expression experiments. Several algorithms have been developed to perform motif search, employing widely different approaches and often giving divergent results. In order to maximize the power of these investigations and ultimately be able to draft solid biological hypotheses, there is the need for applying multiple tools on the same sequences and merge the obtained results. However, motif reporting formats and statistical evaluation methods currently make such an integration task difficult to perform and mostly restricted to specific scenarios. We thus introduce here the Dynamic Motif Integration Toolkit (DynaMIT), an extremely flexible platform allowing to identify motifs employing multiple algorithms, integrate them by means of a user-selected strategy and visualize results in several ways; furthermore, the platform is user-extendible in all its aspects. DynaMIT is freely available at http://cibioltg.bitbucket.org. PMID:26253738

Acoustic emission and acousto-ultrasonic signature analysis of failure mechanisms in carbon fiber reinforced polymer materials

NASA Astrophysics Data System (ADS)

Carey, Shawn Allen

Fiber reinforced polymer composite materials, particularly carbon (CFRPs), are being used for primary structural applications, particularly in the aerospace and naval industries. Advantages of CFRP materials, compared to traditional materials such as steel and aluminum, include: light weight, high strength to weight ratio, corrosion resistance, and long life expectancy. A concern with CFRPs is that despite quality control during fabrication, the material can contain many hidden internal flaws. These flaws in combination with unseen damage due to fatigue and low velocity impact have led to catastrophic failure of structures and components. Therefore a large amount of research has been conducted regarding nondestructive testing (NDT) and structural health monitoring (SHM) of CFRP materials. The principal objective of this research program was to develop methods to characterize failure mechanisms in CFRP materials used by the U.S. Army using acoustic emission (AE) and/or acousto-ultrasonic (AU) data. Failure mechanisms addressed include fiber breakage, matrix cracking, and delamination due to shear between layers. CFRP specimens were fabricated and tested in uniaxial tension to obtain AE and AU data. The specimens were designed with carbon fibers in different orientations to produce the different failure mechanisms. Some specimens were impacted with a blunt indenter prior to testing to simulate low-velocity impact. A signature analysis program was developed to characterize the AE data based on data examination using visual pattern recognition techniques. It was determined that it was important to characterize the AE event , using the location of the event as a parameter, rather than just the AE hit (signal recorded by an AE sensor). A back propagation neural network was also trained based on the results of the signature analysis program. Damage observed on the specimens visually with the aid of a scanning electron microscope agreed with the damage type assigned by the

The origin of Ag-Au-S-Se minerals in adularia-sericite epithermal deposits: constraints from the Broken Hills deposit, Hauraki Goldfield, New Zealand

NASA Astrophysics Data System (ADS)

Cocker, Helen A.; Mauk, Jeffrey L.; Rabone, Stuart D. C.

2013-02-01

The 7.1 Ma Broken Hills adularia-sericite Au-Ag deposit is currently the only producing rhyolite-hosted epithermal deposit in the Hauraki Goldfield of New Zealand. The opaque minerals include pyrite, electrum, acanthite (Ag2S), sphalerite, and galena, which are common in other adularia-sericite epithermal deposits in the Hauraki Goldfield and elsewhere worldwide. Broken Hills ores also contain the less common minerals aguilarite (Ag4SeS), naumannite (Ag2Se), petrovskaite (AuAgS), uytenbogaardtite (Ag3AuS2), fischesserite (Ag3AuSe2), an unnamed silver chloride (Ag2Cl), and unnamed Ag ± Au minerals. Uytenbogaardtite and petrovskaite occur with high-fineness electrum. Broken Hills is the only deposit in the Hauraki Goldfield where uytenbogaardtite and petrovskaite have been identified, and these phases appear to have formed predominantly from unmixing of a precursor high-temperature phase under hypogene conditions. Supergene minerals include covellite, chalcocite, Au-rich electrum, barite, and a variety of iron oxyhydroxide minerals. Uytenbogaardtite can form under supergene and hypogene conditions, and textural relationships between uytenbogaardtite and associated high-fineness electrum may be similar in both conditions. Distinguishing the likely environment of formation rests principally on identification of other supergene minerals and documenting their relationships with uytenbogaardtite. The presence of aguilarite, naumannite, petrovskaite, and fischesserite at Broken Hills reflects a Se-rich mineral assemblage. In the Hauraki Goldfield and the western Great Basin, USA, Se-rich minerals are more abundant in provinces that are characterized by bimodal rhyolite-andesite volcanism, but in other epithermal provinces worldwide, the controls on the occurrences of Se-bearing minerals remain poorly constrained, in spite of the unusually high grades associated with many Se-rich epithermal deposits.

Modeling gene regulatory network motifs using statecharts

PubMed Central

2012-01-01

Background Gene regulatory networks are widely used by biologists to describe the interactions among genes, proteins and other components at the intra-cellular level. Recently, a great effort has been devoted to give gene regulatory networks a formal semantics based on existing computational frameworks. For this purpose, we consider Statecharts, which are a modular, hierarchical and executable formal model widely used to represent software systems. We use Statecharts for modeling small and recurring patterns of interactions in gene regulatory networks, called motifs. Results We present an improved method for modeling gene regulatory network motifs using Statecharts and we describe the successful modeling of several motifs, including those which could not be modeled or whose models could not be distinguished using the method of a previous proposal. We model motifs in an easy and intuitive way by taking advantage of the visual features of Statecharts. Our modeling approach is able to simulate some interesting temporal properties of gene regulatory network motifs: the delay in the activation and the deactivation of the "output" gene in the coherent type-1 feedforward loop, the pulse in the incoherent type-1 feedforward loop, the bistability nature of double positive and double negative feedback loops, the oscillatory behavior of the negative feedback loop, and the "lock-in" effect of positive autoregulation. Conclusions We present a Statecharts-based approach for the modeling of gene regulatory network motifs in biological systems. The basic motifs used to build more complex networks (that is, simple regulation, reciprocal regulation, feedback loop, feedforward loop, and autoregulation) can be faithfully described and their temporal dynamics can be analyzed. PMID:22536967

FPGA implementation of motifs-based neuronal network and synchronization analysis

NASA Astrophysics Data System (ADS)

Deng, Bin; Zhu, Zechen; Yang, Shuangming; Wei, Xile; Wang, Jiang; Yu, Haitao

2016-06-01

Motifs in complex networks play a crucial role in determining the brain functions. In this paper, 13 kinds of motifs are implemented with Field Programmable Gate Array (FPGA) to investigate the relationships between the networks properties and motifs properties. We use discretization method and pipelined architecture to construct various motifs with Hindmarsh-Rose (HR) neuron as the node model. We also build a small-world network based on these motifs and conduct the synchronization analysis of motifs as well as the constructed network. We find that the synchronization properties of motif determine that of motif-based small-world network, which demonstrates effectiveness of our proposed hardware simulation platform. By imitation of some vital nuclei in the brain to generate normal discharges, our proposed FPGA-based artificial neuronal networks have the potential to replace the injured nuclei to complete the brain function in the treatment of Parkinson's disease and epilepsy.

An arginine-rich motif of ring finger protein 4 (RNF4) oversees the recruitment and degradation of the phosphorylated and SUMOylated Krüppel-associated box domain-associated protein 1 (KAP1)/TRIM28 protein during genotoxic stress.

PubMed

Kuo, Ching-Ying; Li, Xu; Kong, Xiang-Qian; Luo, Cheng; Chang, Che-Chang; Chung, Yiyin; Shih, Hsiu-Ming; Li, Keqin Kathy; Ann, David K

2014-07-25

Krüppel-associated box domain-associated protein 1 (KAP1) is a universal transcriptional corepressor that undergoes multiple posttranslational modifications (PTMs), including SUMOylation and Ser-824 phosphorylation. However, the functional interplay of KAP1 PTMs in regulating KAP1 turnover during DNA damage response remains unclear. To decipher the role and cross-talk of multiple KAP1 PTMs, we show here that DNA double strand break-induced KAP1 Ser-824 phosphorylation promoted the recruitment of small ubiquitin-like modifier (SUMO)-targeted ubiquitin E3 ligase, ring finger protein 4 (RNF4), and subsequent RNF4-mediated, SUMO-dependent degradation. Besides the SUMO interacting motif (SIM), a previously unrecognized, but evolutionarily conserved, arginine-rich motif (ARM) in RNF4 acts as a novel recognition motif for selective target recruitment. Results from combined mutagenesis and computational modeling studies suggest that RNF4 utilizes concerted bimodular recognition, namely SIM for Lys-676 SUMOylation and ARM for Ser(P)-824 of simultaneously phosphorylated and SUMOylated KAP1 (Ser(P)-824-SUMO-KAP1). Furthermore, we proved that arginines 73 and 74 within the ARM of RNF4 are required for efficient recruitment to KAP1 or accelerated degradation of promyelocytic leukemia protein (PML) under stress. In parallel, results of bimolecular fluorescence complementation assays validated the role of the ARM in recognizing Ser(P)-824 in living cells. Taken together, we establish that the ARM is required for RNF4 to efficiently target Ser(P)-824-SUMO-KAP1, conferring ubiquitin Lys-48-mediated proteasomal degradation in the context of double strand breaks. The conservation of such a motif may possibly explain the requirement for timely substrate selectivity determination among a myriad of SUMOylated proteins under stress conditions. Thus, the ARM dynamically regulates the SIM-dependent recruitment of targets to RNF4, which could be critical to dynamically fine-tune the

An Arginine-rich Motif of Ring Finger Protein 4 (RNF4) Oversees the Recruitment and Degradation of the Phosphorylated and SUMOylated Krüppel-associated Box Domain-associated Protein 1 (KAP1)/TRIM28 Protein during Genotoxic Stress*

PubMed Central

Kuo, Ching-Ying; Li, Xu; Kong, Xiang-Qian; Luo, Cheng; Chang, Che-Chang; Chung, Yiyin; Shih, Hsiu-Ming; Li, Keqin Kathy; Ann, David K.

2014-01-01

Krüppel-associated box domain-associated protein 1 (KAP1) is a universal transcriptional corepressor that undergoes multiple posttranslational modifications (PTMs), including SUMOylation and Ser-824 phosphorylation. However, the functional interplay of KAP1 PTMs in regulating KAP1 turnover during DNA damage response remains unclear. To decipher the role and cross-talk of multiple KAP1 PTMs, we show here that DNA double strand break-induced KAP1 Ser-824 phosphorylation promoted the recruitment of small ubiquitin-like modifier (SUMO)-targeted ubiquitin E3 ligase, ring finger protein 4 (RNF4), and subsequent RNF4-mediated, SUMO-dependent degradation. Besides the SUMO interacting motif (SIM), a previously unrecognized, but evolutionarily conserved, arginine-rich motif (ARM) in RNF4 acts as a novel recognition motif for selective target recruitment. Results from combined mutagenesis and computational modeling studies suggest that RNF4 utilizes concerted bimodular recognition, namely SIM for Lys-676 SUMOylation and ARM for Ser(P)-824 of simultaneously phosphorylated and SUMOylated KAP1 (Ser(P)-824-SUMO-KAP1). Furthermore, we proved that arginines 73 and 74 within the ARM of RNF4 are required for efficient recruitment to KAP1 or accelerated degradation of promyelocytic leukemia protein (PML) under stress. In parallel, results of bimolecular fluorescence complementation assays validated the role of the ARM in recognizing Ser(P)-824 in living cells. Taken together, we establish that the ARM is required for RNF4 to efficiently target Ser(P)-824-SUMO-KAP1, conferring ubiquitin Lys-48-mediated proteasomal degradation in the context of double strand breaks. The conservation of such a motif may possibly explain the requirement for timely substrate selectivity determination among a myriad of SUMOylated proteins under stress conditions. Thus, the ARM dynamically regulates the SIM-dependent recruitment of targets to RNF4, which could be critical to dynamically fine-tune the

Origin of the world-class PGE-Au mineralisation in the Skaergaard intrusion by bulk S-saturation, accumulation, partial dissolution, and secondary reef formation.

NASA Astrophysics Data System (ADS)

Daugaard Nielsen, Troels Frederik

2013-04-01

The Skaergaard intrusion is the type locality for stratiform "Skaergaard-type" PGE-Au mineralisations with layers rich in PGE, followed by Au and Cu. Models for stratiform PGE mineralisations divide into uppers and downers models. Downers models assume bulk liquid S-saturation followed by a variety of accumulation processes and the second model the scavenging of metals by fluids deep in intrusions and deposition in chemical traps above. This investigation is based on continuous profiling in roof, walls and floor. Cu anomalies in roof, walls and floor are contemporaneous and systematics in Pd/Pt and Pd/Au ratios document bulk liquid S-saturation, no loss of precious metal below the mineralisation and no obvious chemical traps. A classic downers process is documented. The timing of the mineralisation is controlled by composition of liquidus plagioclase and fraction of residual magma (F). PGE concentrations are an order of magnitude higher in the floor mineralisation due to accumulation. Systematics across the mineralisation shows in the centre of the intrusion 5 main levels of Pd-concentration followed by an Au and a Cu-level. All levels PGE and Au levels have c. 100 ppm Cu and show no correlation to PGE and Au. 90% of all PGE is contained in one phase, skaergaardite (PdCu).The lower and main PGE concentration has moderate Pd/Pt ratios. Overlying secondary reefs have high, basal Pd/Pt and show local S-saturation reflecting d-values of PGE between sulphide and silicate liquid. No basal high Pd/Pt anomaly occurs at Au and Cu levels and the floor shows four types of mineralisation. The main PGE reef (Pd5) has gradual increase and decrease in PGE and Pd/Pt, dissolution of sulphide, increasing PGE+Au/Cu due to reaction between interstial and documented reactive Fe-rich silicate melt and the bulk magma sulfides. Dissolution of Cu-sulfide increases PGE/Cu, reduces the size of droplets to 30µ (av.) and provides metals for secondary reefs above - formed by migration of

DMINDA: an integrated web server for DNA motif identification and analyses

PubMed Central

Ma, Qin; Zhang, Hanyuan; Mao, Xizeng; Zhou, Chuan; Liu, Bingqiang; Chen, Xin; Xu, Ying

2014-01-01

DMINDA (DNA motif identification and analyses) is an integrated web server for DNA motif identification and analyses, which is accessible at http://csbl.bmb.uga.edu/DMINDA/. This web site is freely available to all users and there is no login requirement. This server provides a suite of cis-regulatory motif analysis functions on DNA sequences, which are important to elucidation of the mechanisms of transcriptional regulation: (i) de novo motif finding for a given set of promoter sequences along with statistical scores for the predicted motifs derived based on information extracted from a control set, (ii) scanning motif instances of a query motif in provided genomic sequences, (iii) motif comparison and clustering of identified motifs, and (iv) co-occurrence analyses of query motifs in given promoter sequences. The server is powered by a backend computer cluster with over 150 computing nodes, and is particularly useful for motif prediction and analyses in prokaryotic genomes. We believe that DMINDA, as a new and comprehensive web server for cis-regulatory motif finding and analyses, will benefit the genomic research community in general and prokaryotic genome researchers in particular. PMID:24753419

Cysteine-rich secretory proteins (CRISP) and their role in mammalian fertilization.

PubMed

Cohen, Débora J; Maldera, Julieta A; Weigel Muñoz, Mariana; Ernesto, Juan I; Vasen, Gustavo; Cuasnicu, Patricia S

2011-01-01

Epididymal protein CRISPI is a member of the CRISP (Cysteine-RIch Secretory proteins) family and is involved in sperm-egg fusion through its interaction with complementary sites on the egg surface. Results from our laboratory have shown that this binding ability resides in a 12-amino-acid region corresponding to a highly conserved motif of the CRISP family, named Signature 2 (S2). In addition to this, our results revealed that CRISP1 could also be involved in the previous step of sperm binding to the zona pellucida, identifying a novel role for this protein in fertilization. As another approach to elucidate the participation of CRISP1 in fertilization, a mouse line containing a targeted disruption of CRISP1 was generated. Although CRISP1-deficient mice exhibited normal fertility, CRISP1-defficient sperm presented a decreased level of protein tyrosine phosphorylation during capacitation, and an impaired ability to fertilize both zona-intact and zona-free eggs in vitro, confirming the proposed roles for the protein in fertilization. Evidence obtained in our laboratory indicated that testicular CRISP2 would also be involved in sperm-egg fusion. Competition assays between CRISP1 and CRISP2, as well as the comparison of their corresponding S2 regions, suggest that both proteins bind to common complementary sites in the egg. Together, these results suggest a functional cooperation between CRISP1 and CRISP2 to ensure the success of fertilization.

SCOPE: a web server for practical de novo motif discovery.

PubMed

Carlson, Jonathan M; Chakravarty, Arijit; DeZiel, Charles E; Gross, Robert H

2007-07-01

SCOPE is a novel parameter-free method for the de novo identification of potential regulatory motifs in sets of coordinately regulated genes. The SCOPE algorithm combines the output of three component algorithms, each designed to identify a particular class of motifs. Using an ensemble learning approach, SCOPE identifies the best candidate motifs from its component algorithms. In tests on experimentally determined datasets, SCOPE identified motifs with a significantly higher level of accuracy than a number of other web-based motif finders run with their default parameters. Because SCOPE has no adjustable parameters, the web server has an intuitive interface, requiring only a set of gene names or FASTA sequences and a choice of species. The most significant motifs found by SCOPE are displayed graphically on the main results page with a table containing summary statistics for each motif. Detailed motif information, including the sequence logo, PWM, consensus sequence and specific matching sites can be viewed through a single click on a motif. SCOPE's efficient, parameter-free search strategy has enabled the development of a web server that is readily accessible to the practising biologist while providing results that compare favorably with those of other motif finders. The SCOPE web server is at .

Identifying novel sequence variants of RNA 3D motifs

PubMed Central

Zirbel, Craig L.; Roll, James; Sweeney, Blake A.; Petrov, Anton I.; Pirrung, Meg; Leontis, Neocles B.

2015-01-01

Predicting RNA 3D structure from sequence is a major challenge in biophysics. An important sub-goal is accurately identifying recurrent 3D motifs from RNA internal and hairpin loop sequences extracted from secondary structure (2D) diagrams. We have developed and validated new probabilistic models for 3D motif sequences based on hybrid Stochastic Context-Free Grammars and Markov Random Fields (SCFG/MRF). The SCFG/MRF models are constructed using atomic-resolution RNA 3D structures. To parameterize each model, we use all instances of each motif found in the RNA 3D Motif Atlas and annotations of pairwise nucleotide interactions generated by the FR3D software. Isostericity relations between non-Watson–Crick basepairs are used in scoring sequence variants. SCFG techniques model nested pairs and insertions, while MRF ideas handle crossing interactions and base triples. We use test sets of randomly-generated sequences to set acceptance and rejection thresholds for each motif group and thus control the false positive rate. Validation was carried out by comparing results for four motif groups to RMDetect. The software developed for sequence scoring (JAR3D) is structured to automatically incorporate new motifs as they accumulate in the RNA 3D Motif Atlas when new structures are solved and is available free for download. PMID:26130723

A flexible motif search technique based on generalized profiles.

PubMed

Bucher, P; Karplus, K; Moeri, N; Hofmann, K

1996-03-01

A flexible motif search technique is presented which has two major components: (1) a generalized profile syntax serving as a motif definition language; and (2) a motif search method specifically adapted to the problem of finding multiple instances of a motif in the same sequence. The new profile structure, which is the core of the generalized profile syntax, combines the functions of a variety of motif descriptors implemented in other methods, including regular expression-like patterns, weight matrices, previously used profiles, and certain types of hidden Markov models (HMMs). The relationship between generalized profiles and other biomolecular motif descriptors is analyzed in detail, with special attention to HMMs. Generalized profiles are shown to be equivalent to a particular class of HMMs, and conversion procedures in both directions are given. The conversion procedures provide an interpretation for local alignment in the framework of stochastic models, allowing for clear, simple significance tests. A mathematical statement of the motif search problem defines the new method exactly without linking it to a specific algorithmic solution. Part of the definition includes a new definition of disjointness of alignments.

Triadic motifs in the dependence networks of virtual societies.

PubMed

Xie, Wen-Jie; Li, Ming-Xia; Jiang, Zhi-Qiang; Zhou, Wei-Xing

2014-06-10

In friendship networks, individuals have different numbers of friends, and the closeness or intimacy between an individual and her friends is heterogeneous. Using a statistical filtering method to identify relationships about who depends on whom, we construct dependence networks (which are directed) from weighted friendship networks of avatars in more than two hundred virtual societies of a massively multiplayer online role-playing game (MMORPG). We investigate the evolution of triadic motifs in dependence networks. Several metrics show that the virtual societies evolved through a transient stage in the first two to three weeks and reached a relatively stable stage. We find that the unidirectional loop motif (M9) is underrepresented and does not appear, open motifs are also underrepresented, while other close motifs are overrepresented. We also find that, for most motifs, the overall level difference of the three avatars in the same motif is significantly lower than average, whereas the sum of ranks is only slightly larger than average. Our findings show that avatars' social status plays an important role in the formation of triadic motifs.

Triadic motifs in the dependence networks of virtual societies

NASA Astrophysics Data System (ADS)

Xie, Wen-Jie; Li, Ming-Xia; Jiang, Zhi-Qiang; Zhou, Wei-Xing

2014-06-01

In friendship networks, individuals have different numbers of friends, and the closeness or intimacy between an individual and her friends is heterogeneous. Using a statistical filtering method to identify relationships about who depends on whom, we construct dependence networks (which are directed) from weighted friendship networks of avatars in more than two hundred virtual societies of a massively multiplayer online role-playing game (MMORPG). We investigate the evolution of triadic motifs in dependence networks. Several metrics show that the virtual societies evolved through a transient stage in the first two to three weeks and reached a relatively stable stage. We find that the unidirectional loop motif (M9) is underrepresented and does not appear, open motifs are also underrepresented, while other close motifs are overrepresented. We also find that, for most motifs, the overall level difference of the three avatars in the same motif is significantly lower than average, whereas the sum of ranks is only slightly larger than average. Our findings show that avatars' social status plays an important role in the formation of triadic motifs.

Triadic motifs in the dependence networks of virtual societies

PubMed Central

Xie, Wen-Jie; Li, Ming-Xia; Jiang, Zhi-Qiang; Zhou, Wei-Xing

2014-01-01

In friendship networks, individuals have different numbers of friends, and the closeness or intimacy between an individual and her friends is heterogeneous. Using a statistical filtering method to identify relationships about who depends on whom, we construct dependence networks (which are directed) from weighted friendship networks of avatars in more than two hundred virtual societies of a massively multiplayer online role-playing game (MMORPG). We investigate the evolution of triadic motifs in dependence networks. Several metrics show that the virtual societies evolved through a transient stage in the first two to three weeks and reached a relatively stable stage. We find that the unidirectional loop motif (M9) is underrepresented and does not appear, open motifs are also underrepresented, while other close motifs are overrepresented. We also find that, for most motifs, the overall level difference of the three avatars in the same motif is significantly lower than average, whereas the sum of ranks is only slightly larger than average. Our findings show that avatars' social status plays an important role in the formation of triadic motifs. PMID:24912755

Direct AUC optimization of regulatory motifs.

PubMed

Zhu, Lin; Zhang, Hong-Bo; Huang, De-Shuang

2017-07-15

The discovery of transcription factor binding site (TFBS) motifs is essential for untangling the complex mechanism of genetic variation under different developmental and environmental conditions. Among the huge amount of computational approaches for de novo identification of TFBS motifs, discriminative motif learning (DML) methods have been proven to be promising for harnessing the discovery power of accumulated huge amount of high-throughput binding data. However, they have to sacrifice accuracy for speed and could fail to fully utilize the information of the input sequences. We propose a novel algorithm called CDAUC for optimizing DML-learned motifs based on the area under the receiver-operating characteristic curve (AUC) criterion, which has been widely used in the literature to evaluate the significance of extracted motifs. We show that when the considered AUC loss function is optimized in a coordinate-wise manner, the cost function of each resultant sub-problem is a piece-wise constant function, whose optimal value can be found exactly and efficiently. Further, a key step of each iteration of CDAUC can be efficiently solved as a computational geometry problem. Experimental results on real world high-throughput datasets illustrate that CDAUC outperforms competing methods for refining DML motifs, while being one order of magnitude faster. Meanwhile, preliminary results also show that CDAUC may also be useful for improving the interpretability of convolutional kernels generated by the emerging deep learning approaches for predicting TF sequences specificities. CDAUC is available at: https://drive.google.com/drive/folders/0BxOW5MtIZbJjNFpCeHlBVWJHeW8 . dshuang@tongji.edu.cn. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Signatures of Pleiotropy, Economy and Convergent Evolution in a Domain-Resolved Map of Human–Virus Protein–Protein Interaction Networks

PubMed Central

Garamszegi, Sara; Franzosa, Eric A.; Xia, Yu

2013-01-01

A central challenge in host-pathogen systems biology is the elucidation of general, systems-level principles that distinguish host-pathogen interactions from within-host interactions. Current analyses of host-pathogen and within-host protein-protein interaction networks are largely limited by their resolution, treating proteins as nodes and interactions as edges. Here, we construct a domain-resolved map of human-virus and within-human protein-protein interaction networks by annotating protein interactions with high-coverage, high-accuracy, domain-centric interaction mechanisms: (1) domain-domain interactions, in which a domain in one protein binds to a domain in a second protein, and (2) domain-motif interactions, in which a domain in one protein binds to a short, linear peptide motif in a second protein. Analysis of these domain-resolved networks reveals, for the first time, significant mechanistic differences between virus-human and within-human interactions at the resolution of single domains. While human proteins tend to compete with each other for domain binding sites by means of sequence similarity, viral proteins tend to compete with human proteins for domain binding sites in the absence of sequence similarity. Independent of their previously established preference for targeting human protein hubs, viral proteins also preferentially target human proteins containing linear motif-binding domains. Compared to human proteins, viral proteins participate in more domain-motif interactions, target more unique linear motif-binding domains per residue, and contain more unique linear motifs per residue. Together, these results suggest that viruses surmount genome size constraints by convergently evolving multiple short linear motifs in order to effectively mimic, hijack, and manipulate complex host processes for their survival. Our domain-resolved analyses reveal unique signatures of pleiotropy, economy, and convergent evolution in viral-host interactions that are

Signatures of pleiotropy, economy and convergent evolution in a domain-resolved map of human-virus protein-protein interaction networks.

PubMed

Garamszegi, Sara; Franzosa, Eric A; Xia, Yu

2013-01-01

A central challenge in host-pathogen systems biology is the elucidation of general, systems-level principles that distinguish host-pathogen interactions from within-host interactions. Current analyses of host-pathogen and within-host protein-protein interaction networks are largely limited by their resolution, treating proteins as nodes and interactions as edges. Here, we construct a domain-resolved map of human-virus and within-human protein-protein interaction networks by annotating protein interactions with high-coverage, high-accuracy, domain-centric interaction mechanisms: (1) domain-domain interactions, in which a domain in one protein binds to a domain in a second protein, and (2) domain-motif interactions, in which a domain in one protein binds to a short, linear peptide motif in a second protein. Analysis of these domain-resolved networks reveals, for the first time, significant mechanistic differences between virus-human and within-human interactions at the resolution of single domains. While human proteins tend to compete with each other for domain binding sites by means of sequence similarity, viral proteins tend to compete with human proteins for domain binding sites in the absence of sequence similarity. Independent of their previously established preference for targeting human protein hubs, viral proteins also preferentially target human proteins containing linear motif-binding domains. Compared to human proteins, viral proteins participate in more domain-motif interactions, target more unique linear motif-binding domains per residue, and contain more unique linear motifs per residue. Together, these results suggest that viruses surmount genome size constraints by convergently evolving multiple short linear motifs in order to effectively mimic, hijack, and manipulate complex host processes for their survival. Our domain-resolved analyses reveal unique signatures of pleiotropy, economy, and convergent evolution in viral-host interactions that are

Unravelling daily human mobility motifs

PubMed Central

Schneider, Christian M.; Belik, Vitaly; Couronné, Thomas; Smoreda, Zbigniew; González, Marta C.

2013-01-01

Human mobility is differentiated by time scales. While the mechanism for long time scales has been studied, the underlying mechanism on the daily scale is still unrevealed. Here, we uncover the mechanism responsible for the daily mobility patterns by analysing the temporal and spatial trajectories of thousands of persons as individual networks. Using the concept of motifs from network theory, we find only 17 unique networks are present in daily mobility and they follow simple rules. These networks, called here motifs, are sufficient to capture up to 90 per cent of the population in surveys and mobile phone datasets for different countries. Each individual exhibits a characteristic motif, which seems to be stable over several months. Consequently, daily human mobility can be reproduced by an analytically tractable framework for Markov chains by modelling periods of high-frequency trips followed by periods of lower activity as the key ingredient. PMID:23658117

DMINDA: an integrated web server for DNA motif identification and analyses.

PubMed

Ma, Qin; Zhang, Hanyuan; Mao, Xizeng; Zhou, Chuan; Liu, Bingqiang; Chen, Xin; Xu, Ying

2014-07-01

DMINDA (DNA motif identification and analyses) is an integrated web server for DNA motif identification and analyses, which is accessible at http://csbl.bmb.uga.edu/DMINDA/. This web site is freely available to all users and there is no login requirement. This server provides a suite of cis-regulatory motif analysis functions on DNA sequences, which are important to elucidation of the mechanisms of transcriptional regulation: (i) de novo motif finding for a given set of promoter sequences along with statistical scores for the predicted motifs derived based on information extracted from a control set, (ii) scanning motif instances of a query motif in provided genomic sequences, (iii) motif comparison and clustering of identified motifs, and (iv) co-occurrence analyses of query motifs in given promoter sequences. The server is powered by a backend computer cluster with over 150 computing nodes, and is particularly useful for motif prediction and analyses in prokaryotic genomes. We believe that DMINDA, as a new and comprehensive web server for cis-regulatory motif finding and analyses, will benefit the genomic research community in general and prokaryotic genome researchers in particular. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Characterization of stress-responsive lncRNAs in Arabidopsis thaliana by integrating expression, epigenetic and structural features.

PubMed

Di, Chao; Yuan, Jiapei; Wu, Yue; Li, Jingrui; Lin, Huixin; Hu, Long; Zhang, Ting; Qi, Yijun; Gerstein, Mark B; Guo, Yan; Lu, Zhi John

2014-12-01

Recently, in addition to poly(A)+ long non-coding RNAs (lncRNAs), many lncRNAs without poly(A) tails, have been characterized in mammals. However, the non-polyA lncRNAs and their conserved motifs, especially those associated with environmental stresses, have not been fully investigated in plant genomes. We performed poly(A)- RNA-seq for seedlings of Arabidopsis thaliana under four stress conditions, and predicted lncRNA transcripts. We classified the lncRNAs into three confidence levels according to their expression patterns, epigenetic signatures and RNA secondary structures. Then, we further classified the lncRNAs to poly(A)+ and poly(A)- transcripts. Compared with poly(A)+ lncRNAs and coding genes, we found that poly(A)- lncRNAs tend to have shorter transcripts and lower expression levels, and they show significant expression specificity in response to stresses. In addition, their differential expression is significantly enriched in drought condition and depleted in heat condition. Overall, we identified 245 poly(A)+ and 58 poly(A)- lncRNAs that are differentially expressed under various stress stimuli. The differential expression was validated by qRT-PCR, and the signaling pathways involved were supported by specific binding of transcription factors (TFs), phytochrome-interacting factor 4 (PIF4) and PIF5. Moreover, we found many conserved sequence and structural motifs of lncRNAs from different functional groups (e.g. a UUC motif responding to salt and a AU-rich stem-loop responding to cold), indicated that the conserved elements might be responsible for the stress-responsive functions of lncRNAs. © 2014 The Authors The Plant Journal © 2014 John Wiley & Sons Ltd.

A dinucleotide motif in oligonucleotides shows potent immunomodulatory activity and overrides species-specific recognition observed with CpG motif.

PubMed

Kandimalla, Ekambar R; Bhagat, Lakshmi; Zhu, Fu-Gang; Yu, Dong; Cong, Yan-Ping; Wang, Daqing; Tang, Jimmy X; Tang, Jin-Yan; Knetter, Cathrine F; Lien, Egil; Agrawal, Sudhir

2003-11-25

Bacterial and synthetic DNAs containing CpG dinucleotides in specific sequence contexts activate the vertebrate immune system through Toll-like receptor 9 (TLR9). In the present study, we used a synthetic nucleoside with a bicyclic heterobase [1-(2'-deoxy-beta-d-ribofuranosyl)-2-oxo-7-deaza-8-methyl-purine; R] to replace the C in CpG, resulting in an RpG dinucleotide. The RpG dinucleotide was incorporated in mouse- and human-specific motifs in oligodeoxynucleotides (oligos) and 3'-3-linked oligos, referred to as immunomers. Oligos containing the RpG motif induced cytokine secretion in mouse spleen-cell cultures. Immunomers containing RpG dinucleotides showed activity in transfected-HEK293 cells stably expressing mouse TLR9, suggesting direct involvement of TLR9 in the recognition of RpG motif. In J774 macrophages, RpG motifs activated NF-kappa B and mitogen-activated protein kinase pathways. Immunomers containing the RpG dinucleotide induced high levels of IL-12 and IFN-gamma, but lower IL-6 in time- and concentration-dependent fashion in mouse spleen-cell cultures costimulated with IL-2. Importantly, immunomers containing GTRGTT and GARGTT motifs were recognized to a similar extent by both mouse and human immune systems. Additionally, both mouse- and human-specific RpG immunomers potently stimulated proliferation of peripheral blood mononuclear cells obtained from diverse vertebrate species, including monkey, pig, horse, sheep, goat, rat, and chicken. An immunomer containing GTRGTT motif prevented conalbumin-induced and ragweed allergen-induced allergic inflammation in mice. We show that a synthetic bicyclic nucleotide is recognized in the C position of a CpG dinucleotide by immune cells from diverse vertebrate species without bias for flanking sequences, suggesting a divergent nucleotide motif recognition pattern of TLR9.

The human RNA-binding protein and E3 ligase MEX-3C binds the MEX-3-recognition element (MRE) motif with high affinity.

PubMed

Yang, Lingna; Wang, Chongyuan; Li, Fudong; Zhang, Jiahai; Nayab, Anam; Wu, Jihui; Shi, Yunyu; Gong, Qingguo

2017-09-29

MEX-3 is a K-homology (KH) domain-containing RNA-binding protein first identified as a translational repressor in Caenorhabditis elegans , and its four orthologs (MEX-3A-D) in human and mouse were subsequently found to have E3 ubiquitin ligase activity mediated by a RING domain and critical for RNA degradation. Current evidence implicates human MEX-3C in many essential biological processes and suggests a strong connection with immune diseases and carcinogenesis. The highly conserved dual KH domains in MEX-3 proteins enable RNA binding and are essential for the recognition of the 3'-UTR and post-transcriptional regulation of MEX-3 target transcripts. However, the molecular mechanisms of translational repression and the consensus RNA sequence recognized by the MEX-3C KH domain are unknown. Here, using X-ray crystallography and isothermal titration calorimetry, we investigated the RNA-binding activity and selectivity of human MEX-3C dual KH domains. Our high-resolution crystal structures of individual KH domains complexed with a noncanonical U-rich and a GA-rich RNA sequence revealed that the KH1/2 domains of human MEX-3C bound MRE10, a 10-mer RNA (5'-CAGAGUUUAG-3') consisting of an eight-nucleotide MEX-3-recognition element (MRE) motif, with high affinity. Of note, we also identified a consensus RNA motif recognized by human MEX-3C. The potential RNA-binding sites in the 3'-UTR of the human leukocyte antigen serotype ( HLA-A2 ) mRNA were mapped with this RNA-binding motif and further confirmed by fluorescence polarization. The binding motif identified here will provide valuable information for future investigations of the functional pathways controlled by human MEX-3C and for predicting potential mRNAs regulated by this enzyme. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Discovery of candidate KEN-box motifs using cell cycle keyword enrichment combined with native disorder prediction and motif conservation.

PubMed

Michael, Sushama; Travé, Gilles; Ramu, Chenna; Chica, Claudia; Gibson, Toby J

2008-02-15

KEN-box-mediated target selection is one of the mechanisms used in the proteasomal destruction of mitotic cell cycle proteins via the APC/C complex. While annotating the Eukaryotic Linear Motif resource (ELM, http://elm.eu.org/), we found that KEN motifs were significantly enriched in human protein entries with cell cycle keywords in the UniProt/Swiss-Prot database-implying that KEN-boxes might be more common than reported. Matches to short linear motifs in protein database searches are not, per se, significant. KEN-box enrichment with cell cycle Gene Ontology terms suggests that collectively these motifs are functional but does not prove that any given instance is so. Candidates were surveyed for native disorder prediction using GlobPlot and IUPred and for motif conservation in homologues. Among >25 strong new candidates, the most notable are human HIPK2, CHFR, CDC27, Dab2, Upf2, kinesin Eg5, DNA Topoisomerase 1 and yeast Cdc5 and Swi5. A similar number of weaker candidates were present. These proteins have yet to be tested for APC/C targeted destruction, providing potential new avenues of research.

Sequence Analysis and Domain Motifs in the Porcine Skin Decorin Glycosaminoglycan Chain*

PubMed Central

Zhao, Xue; Yang, Bo; Solakylidirim, Kemal; Joo, Eun Ji; Toida, Toshihiko; Higashi, Kyohei; Linhardt, Robert J.; Li, Lingyun

2013-01-01

Decorin proteoglycan is comprised of a core protein containing a single O-linked dermatan sulfate/chondroitin sulfate glycosaminoglycan (GAG) chain. Although the sequence of the decorin core protein is determined by the gene encoding its structure, the structure of its GAG chain is determined in the Golgi. The recent application of modern MS to bikunin, a far simpler chondroitin sulfate proteoglycans, suggests that it has a single or small number of defined sequences. On this basis, a similar approach to sequence the decorin of porcine skin much larger and more structurally complex dermatan sulfate/chondroitin sulfate GAG chain was undertaken. This approach resulted in information on the consistency/variability of its linkage region at the reducing end of the GAG chain, its iduronic acid-rich domain, glucuronic acid-rich domain, and non-reducing end. A general motif for the porcine skin decorin GAG chain was established. A single small decorin GAG chain was sequenced using MS/MS analysis. The data obtained in the study suggest that the decorin GAG chain has a small or a limited number of sequences. PMID:23423381

Cluster-to-cluster transformation among Au6, Au8 and Au11 nanoclusters.

PubMed

Ren, Xiuqing; Fu, Junhong; Lin, Xinzhang; Fu, Xuemei; Yan, Jinghui; Wu, Ren'an; Liu, Chao; Huang, Jiahui

2018-05-22

We present the cluster-to-cluster transformations among three gold nanoclusters, [Au6(dppp)4]2+ (Au6), [Au8(dppp)4Cl2]2+ (Au8) and [Au11(dppp)5]3+ (Au11). The conversion process follows a rule that states that the transformation of a small cluster to a large cluster is achieved through an oxidation process with an oxidizing agent (H2O2) or with heating, while the conversion of a large cluster to a small one occurs through a reduction process with a reducing agent (NaBH4). All the reactions were monitored using UV-Vis spectroscopy and ESI-MS. This work may provide an alternative approach to the synthesis of novel gold nanoclusters and a further understanding of the structural transformation relationship of gold nanoclusters.

Interfacial nanodroplets guided construction of hierarchical Au, Au-Pt, and Au-Pd particles as excellent catalysts

NASA Astrophysics Data System (ADS)

Ma, Aijing; Xu, Jie; Zhang, Xuehua; Zhang, Bin; Wang, Dayang; Xu, Haolan

2014-05-01

Interfacial nanodroplets were grafted to the surfaces of self-sacrificed template particles in a galvanic reaction system to assist the construction of 3D Au porous structures. The interfacial nanodroplets were formed via direct adsorption of surfactant-free emulsions onto the particle surfaces. The interfacial nanodroplets discretely distributed at the template particle surfaces and served as soft templates to guide the formation of porous Au structures. The self-variation of footprint sizes of interfacial nanodroplets during Au growth gave rise to a hierarchical pore size distribution of the obtained Au porous particles. This strategy could be easily extended to synthesize bimetal porous particles such as Au-Pt and Au-Pd. The obtained porous Au, Au-Pt, and Au-Pd particles showed excellent catalytic activity in catalytic reduction of 4-nitrophenol.

STEME: A Robust, Accurate Motif Finder for Large Data Sets

PubMed Central

Reid, John E.; Wernisch, Lorenz

2014-01-01

Motif finding is a difficult problem that has been studied for over 20 years. Some older popular motif finders are not suitable for analysis of the large data sets generated by next-generation sequencing. We recently published an efficient approximation (STEME) to the EM algorithm that is at the core of many motif finders such as MEME. This approximation allows the EM algorithm to be applied to large data sets. In this work we describe several efficient extensions to STEME that are based on the MEME algorithm. Together with the original STEME EM approximation, these extensions make STEME a fully-fledged motif finder with similar properties to MEME. We discuss the difficulty of objectively comparing motif finders. We show that STEME performs comparably to existing prominent discriminative motif finders, DREME and Trawler, on 13 sets of transcription factor binding data in mouse ES cells. We demonstrate the ability of STEME to find long degenerate motifs which these discriminative motif finders do not find. As part of our method, we extend an earlier method due to Nagarajan et al. for the efficient calculation of motif E-values. STEME's source code is available under an open source license and STEME is available via a web interface. PMID:24625410

Structural motif screening reveals a novel, conserved carbohydrate-binding surface in the pathogenesis-related protein PR-5d.

PubMed

Doxey, Andrew C; Cheng, Zhenyu; Moffatt, Barbara A; McConkey, Brendan J

2010-08-03

Aromatic amino acids play a critical role in protein-glycan interactions. Clusters of surface aromatic residues and their features may therefore be useful in distinguishing glycan-binding sites as well as predicting novel glycan-binding proteins. In this work, a structural bioinformatics approach was used to screen the Protein Data Bank (PDB) for coplanar aromatic motifs similar to those found in known glycan-binding proteins. The proteins identified in the screen were significantly associated with carbohydrate-related functions according to gene ontology (GO) enrichment analysis, and predicted motifs were found frequently within novel folds and glycan-binding sites not included in the training set. In addition to numerous binding sites predicted in structural genomics proteins of unknown function, one novel prediction was a surface motif (W34/W36/W192) in the tobacco pathogenesis-related protein, PR-5d. Phylogenetic analysis revealed that the surface motif is exclusive to a subfamily of PR-5 proteins from the Solanaceae family of plants, and is absent completely in more distant homologs. To confirm PR-5d's insoluble-polysaccharide binding activity, a cellulose-pulldown assay of tobacco proteins was performed and PR-5d was identified in the cellulose-binding fraction by mass spectrometry. Based on the combined results, we propose that the putative binding site in PR-5d may be an evolutionary adaptation of Solanaceae plants including potato, tomato, and tobacco, towards defense against cellulose-containing pathogens such as species of the deadly oomycete genus, Phytophthora. More generally, the results demonstrate that coplanar aromatic clusters on protein surfaces are a structural signature of glycan-binding proteins, and can be used to computationally predict novel glycan-binding proteins from 3 D structure.

Di-isodityrosine is the intermolecular cross-link of isodityrosine-rich extensin analogs cross-linked in vitro.

PubMed

Held, Michael A; Tan, Li; Kamyab, Abdolreza; Hare, Michael; Shpak, Elena; Kieliszewski, Marcia J

2004-12-31

Extensins are cell wall hydroxyproline-rich glycoproteins that form covalent networks putatively involving tyrosyl and lysyl residues in cross-links catalyzed by one or more extensin peroxidases. The precise cross-links remain to be chemically identified both as network components in muro and as enzymic products generated in vitro with native extensin monomers as substrates. However, some extensin monomers contain variations within their putative cross-linking motifs that complicate cross-link identification. Other simpler extensins are recalcitrant to isolation including the ubiquitous P3-type extensin whose major repetitive motif, Hyp)(4)-Ser-Hyp-Ser-(Hyp)(4)-Tyr-Tyr-Tyr-Lys, is of particular interest, not least because its Tyr-Tyr-Tyr intramolecular isodityrosine cross-link motifs are also putative candidates for further intermolecular cross-linking to form di-isodityrosine. Therefore, we designed a set of extensin analogs encoding tandem repeats of the P3 motif, including Tyr --> Phe and Lys --> Leu variations. Expression of these P3 analogs in Nicotiana tabacum cells yielded glycoproteins with virtually all Pro residues hydroxylated and subsequently arabinosylated and with likely galactosylated Ser residues. This was consistent with earlier analyses of P3 glycopeptides isolated from cell wall digests and the predictions of the Hyp contiguity hypothesis. The tyrosine-rich P3 analogs also contained isodityrosine, formed in vivo. Significantly, these isodityrosine-containing analogs were further cross-linked in vitro by an extensin peroxidase to form the tetra-tyrosine intermolecular cross-link amino acid di-isodityrosine. This is the first identification of an inter-molecular cross-link amino acid in an extensin module and corroborates earlier suggestions that di-isodityrosine represents one mechanism for cross-linking extensins in muro.

Porphyry Cu-Au and associated polymetallic Fe-Cu-Au deposits in the Beiya Area, western Yunnan Province, south China

USGS Publications Warehouse

Xu, X.-W.; Cai, X.-P.; Xiao, Q.-B.; Peters, S.G.

2007-01-01

The Alkaline porphyries in the Beiya area are located east of the Jinshajiang suture, as part of a Cenozoic alkali-rich porphyry belt in western Yunnan. The main rock types include quartz-albite porphyry, quartz-K-feldspar porphyry and biotite-K-feldspar porphyry. These porphyries are characterised by high alkalinity [(K2O + Na2O)% > 10%], high silica (SiO2% > 65%), high Sr (> 400??ppm) and 87Sr/86Sr (> 0.706)] ratio and were intruded at 65.5??Ma, between 25.5 to 32.5??Ma, and about 3.8??Ma, respectively. There are five main types of mineral deposits in the Beiya area: (1) porphyry Cu-Au deposits, (2) magmatic Fe-Au deposits, (3) sedimentary polymetallic deposits, (4) polymetallic skarn deposits, and (5) palaeoplacers associated with karsts. The porphyry Cu-Au and polymetallic skarn deposits are associated with quartz-albite porphyry bodies. The Fe-Au and polymetallic sedimentary deposits are part of an ore-forming system that produced considerable Au in the Beiya area, and are characterised by low concentrations of La, Ti, and Co, and high concentrations of Y, Yb, and Sc. The Cenozoic porphyries in western Yunnan display increased alkalinity away from the Triassic Jinshajiang suture. Distribution of both the porphyries and sedimentary deposits in the Beiya area are interpreted to be related to partial melting in a disjointed region between upper mantle lithosphere of the Yangtze Plate and Gondwana continent, and lie within a shear zone between buried Palaeo-Tethyan oceanic lithosphere and upper mantle lithosphere, caused by the subduction and collision of India and Asia. ?? 2006 Elsevier B.V. All rights reserved.

Bipyrimidine Signatures as a Photoprotective Genome Strategy in G + C-rich Halophilic Archaea.

PubMed

Jones, Daniel L; Baxter, Bonnie K

2016-09-02

Halophilic archaea experience high levels of ultraviolet (UV) light in their environments and demonstrate resistance to UV irradiation. DNA repair systems and carotenoids provide UV protection but do not account for the high resistance observed. Herein, we consider genomic signatures as an additional photoprotective strategy. The predominant forms of UV-induced DNA damage are cyclobutane pyrimidine dimers, most notoriously thymine dimers (T^Ts), which form at adjacent Ts. We tested whether the high G + C content seen in halophilic archaea serves a photoprotective function through limiting T nucleotides, and thus T^T lesions. However, this speculation overlooks the other bipyrimidine sequences, all of which capable of forming photolesions to varying degrees. Therefore, we designed a program to determine the frequencies of the four bipyrimidine pairs (5' to 3': TT, TC, CT, and CC) within genomes of halophilic archaea and four other randomized sample groups for comparison. The outputs for each sampled genome were weighted by the intrinsic photoreactivities of each dinucleotide pair. Statistical methods were employed to investigate intergroup differences. Our findings indicate that the UV-resistance seen in halophilic archaea can be attributed in part to a genomic strategy: high G + C content and the resulting bipyrimidine signature reduces the genomic photoreactivity.

Bipyrimidine Signatures as a Photoprotective Genome Strategy in G + C-rich Halophilic Archaea

PubMed Central

Jones, Daniel L.; Baxter, Bonnie K.

2016-01-01

Halophilic archaea experience high levels of ultraviolet (UV) light in their environments and demonstrate resistance to UV irradiation. DNA repair systems and carotenoids provide UV protection but do not account for the high resistance observed. Herein, we consider genomic signatures as an additional photoprotective strategy. The predominant forms of UV-induced DNA damage are cyclobutane pyrimidine dimers, most notoriously thymine dimers (T^Ts), which form at adjacent Ts. We tested whether the high G + C content seen in halophilic archaea serves a photoprotective function through limiting T nucleotides, and thus T^T lesions. However, this speculation overlooks the other bipyrimidine sequences, all of which capable of forming photolesions to varying degrees. Therefore, we designed a program to determine the frequencies of the four bipyrimidine pairs (5’ to 3’: TT, TC, CT, and CC) within genomes of halophilic archaea and four other randomized sample groups for comparison. The outputs for each sampled genome were weighted by the intrinsic photoreactivities of each dinucleotide pair. Statistical methods were employed to investigate intergroup differences. Our findings indicate that the UV-resistance seen in halophilic archaea can be attributed in part to a genomic strategy: high G + C content and the resulting bipyrimidine signature reduces the genomic photoreactivity. PMID:27598206

DNA motif alignment by evolving a population of Markov chains.

PubMed

Bi, Chengpeng

2009-01-30

Deciphering cis-regulatory elements or de novo motif-finding in genomes still remains elusive although much algorithmic effort has been expended. The Markov chain Monte Carlo (MCMC) method such as Gibbs motif samplers has been widely employed to solve the de novo motif-finding problem through sequence local alignment. Nonetheless, the MCMC-based motif samplers still suffer from local maxima like EM. Therefore, as a prerequisite for finding good local alignments, these motif algorithms are often independently run a multitude of times, but without information exchange between different chains. Hence it would be worth a new algorithm design enabling such information exchange. This paper presents a novel motif-finding algorithm by evolving a population of Markov chains with information exchange (PMC), each of which is initialized as a random alignment and run by the Metropolis-Hastings sampler (MHS). It is progressively updated through a series of local alignments stochastically sampled. Explicitly, the PMC motif algorithm performs stochastic sampling as specified by a population-based proposal distribution rather than individual ones, and adaptively evolves the population as a whole towards a global maximum. The alignment information exchange is accomplished by taking advantage of the pooled motif site distributions. A distinct method for running multiple independent Markov chains (IMC) without information exchange, or dubbed as the IMC motif algorithm, is also devised to compare with its PMC counterpart. Experimental studies demonstrate that the performance could be improved if pooled information were used to run a population of motif samplers. The new PMC algorithm was able to improve the convergence and outperformed other popular algorithms tested using simulated and biological motif sequences.

Automatic annotation of protein motif function with Gene Ontology terms.

PubMed

Lu, Xinghua; Zhai, Chengxiang; Gopalakrishnan, Vanathi; Buchanan, Bruce G

2004-09-02

Conserved protein sequence motifs are short stretches of amino acid sequence patterns that potentially encode the function of proteins. Several sequence pattern searching algorithms and programs exist foridentifying candidate protein motifs at the whole genome level. However, a much needed and important task is to determine the functions of the newly identified protein motifs. The Gene Ontology (GO) project is an endeavor to annotate the function of genes or protein sequences with terms from a dynamic, controlled vocabulary and these annotations serve well as a knowledge base. This paper presents methods to mine the GO knowledge base and use the association between the GO terms assigned to a sequence and the motifs matched by the same sequence as evidence for predicting the functions of novel protein motifs automatically. The task of assigning GO terms to protein motifs is viewed as both a binary classification and information retrieval problem, where PROSITE motifs are used as samples for mode training and functional prediction. The mutual information of a motif and aGO term association is found to be a very useful feature. We take advantage of the known motifs to train a logistic regression classifier, which allows us to combine mutual information with other frequency-based features and obtain a probability of correct association. The trained logistic regression model has intuitively meaningful and logically plausible parameter values, and performs very well empirically according to our evaluation criteria. In this research, different methods for automatic annotation of protein motifs have been investigated. Empirical result demonstrated that the methods have a great potential for detecting and augmenting information about the functions of newly discovered candidate protein motifs.

Permuting the PGF Signature Motif Blocks both Archaeosortase-Dependent C-Terminal Cleavage and Prenyl Lipid Attachment for the Haloferax volcanii S-Layer Glycoprotein.

PubMed

Abdul Halim, Mohd Farid; Karch, Kelly R; Zhou, Yitian; Haft, Daniel H; Garcia, Benjamin A; Pohlschroder, Mechthild

2015-12-28

For years, the S-layer glycoprotein (SLG), the sole component of many archaeal cell walls, was thought to be anchored to the cell surface by a C-terminal transmembrane segment. Recently, however, we demonstrated that the Haloferax volcanii SLG C terminus is removed by an archaeosortase (ArtA), a novel peptidase. SLG, which was previously shown to be lipid modified, contains a C-terminal tripartite structure, including a highly conserved proline-glycine-phenylalanine (PGF) motif. Here, we demonstrate that ArtA does not process an SLG variant where the PGF motif is replaced with a PFG motif (slg(G796F,F797G)). Furthermore, using radiolabeling, we show that SLG lipid modification requires the PGF motif and is ArtA dependent, lending confirmation to the use of a novel C-terminal lipid-mediated protein-anchoring mechanism by prokaryotes. Similar to the case for the ΔartA strain, the growth, cellular morphology, and cell wall of the slg(G796F,F797G) strain, in which modifications of additional H. volcanii ArtA substrates should not be altered, are adversely affected, demonstrating the importance of these posttranslational SLG modifications. Our data suggest that ArtA is either directly or indirectly involved in a novel proteolysis-coupled, covalent lipid-mediated anchoring mechanism. Given that archaeosortase homologs are encoded by a broad range of prokaryotes, it is likely that this anchoring mechanism is widely conserved. Prokaryotic proteins bound to cell surfaces through intercalation, covalent attachment, or protein-protein interactions play critical roles in essential cellular processes. Unfortunately, the molecular mechanisms that anchor proteins to archaeal cell surfaces remain poorly characterized. Here, using the archaeon H. volcanii as a model system, we report the first in vivo studies of a novel protein-anchoring pathway involving lipid modification of a peptidase-processed C terminus. Our findings not only yield important insights into poorly understood

The heavy-ion compositional signature in He-3-rich solar particle events

NASA Technical Reports Server (NTRS)

Mason, G. M.; Reames, D. V.; Von Rosenvinge, T. T.; Klecker, B.; Hovestadt, D.

1986-01-01

A survey of the approx. 1 MeV/nucleon heavy ion abundances in 66 He-3-rich solar particle events was performed using the Max-Planck-Institut/University of Maryland and Goddard Space Flight Center instruments on the ISEE-3 spacecraft. The observations were carried out in interplanetary space over the period 1978 October through 1982 June. Earlier observations were confirmed which show an enrichment of heavy ions in He-3-rich events, relative to the average solar energetic particle composition in large particle events. For the survey near 1.5 MeV/nucleon the enrichments compared to large solar particle events are approximately He4:C:O:Ne:Mg:Si:Fe = 0.44:0.66:1.:3.4:3.5:4.1:9.6. Surprising new results emerging from the present broad survey are that the heavy ion enrichment pattern is the same within a factor of approx. 2 for almost all cases, and the degree of heavy ion enrichment is uncorrelated with the He-3 enrichment. Overall, the features established appear to be best explained by an acceleration mechanism in which the He-3 enrichment process is not responsible for the heavy ion enrichment, but rather the heavy ion enrichment is a measure of the ambient coronal composition at the sites where the He-3-rich events occur.

The heavy ion compositional signature in 3He-rich solar particle events

NASA Technical Reports Server (NTRS)

Mason, G. M.; Reames, D. V.; Klecker, B.; Hovestadt, D.; Vonrosenvinge, T. T.

1985-01-01

A survey of the approx. 1 MeV/nucleon heavy ion abundances in 66 He3-rich solar particle events was performed using the Max-Planck-Institut/University of Maryland and Goddard Space Flight Center instruments on the ISEE-3 spacecraft. The observations were carried out in interplanetary space over the period 1978 October through 1982 June. Earlier observations were confirmed which show an enrichment of heavy ions in HE3-rich events, relative to the average solar energetic particle composition in large particle events. For the survey near 1.5 MeV/nucleon the enrichments compared to large solar particle events are approximately He4:C:O:Ne:Mg:Si:Fe = 0.44:0.66:1.:3.4:3.5:4.1:9.6. Surprising new results emerging from the present broad survey are that the heavy ion enrichment pattern is the same within a factor of approx. 2 for almost all cases, and the degree of heavy ion enrichment is uncorrelated with the He3 enrichment. Overall, the features established appear to be best explained by an acceleration mechanism in which the He3 enrichment process is not responsible for the heavy ion enrichment, but rather the heavy ion enrichment is a measure of the ambient coronal composition at the sites where the He3-rich events occur.

Participation of cysteine-rich secretory proteins (CRISP) in mammalian sperm-egg interaction.

PubMed

Cohen, Débora J; Busso, Dolores; Da Ros, Vanina; Ellerman, Diego A; Maldera, Julieta A; Goldweic, Nadia; Cuasnicu, Patricia S

2008-01-01

Mammalian fertilization is a complex multi-step process mediated by different molecules present on both gametes. CRISP1 (cysteine-rich secretory protein 1) is an epididymal protein thought to participate in gamete fusion through its binding to egg-complementary sites. Structure-function studies using recombinant fragments of CRISP1 as well as synthetic peptides reveal that its egg-binding ability resides in a 12 amino acid region corresponding to an evolutionary conserved motif of the CRISP family, named Signature 2 (S2). Further experiments analyzing both the ability of other CRISP proteins to bind to the rat egg and the amino acid sequence of their S2 regions show that the amino acid sequence of the S2 is needed for CRISP1 to interact with the egg. CRISP1 appears to be involved in the first step of sperm binding to the zona pellucida, identifying a novel role for this protein in fertilization. The observation that sperm testicular CRISP2 is also able to bind to the egg surface suggests a role for this protein in gamete fusion. Subsequent experiments confirmed the participation of CRISP2 in this step of fertilization and revealed that CRISP1 and CRISP2 interact with common egg surface binding sites. Together, these results suggest a functional cooperation between CRISP1 and CRISP2 to ensure the success of fertilization. These observations contribute to a better understanding of the molecular mechanisms underlying mammalian fertilization.

A Bioinformatics Approach for Detecting Repetitive Nested Motifs using Pattern Matching.

PubMed

Romero, José R; Carballido, Jessica A; Garbus, Ingrid; Echenique, Viviana C; Ponzoni, Ignacio

2016-01-01

The identification of nested motifs in genomic sequences is a complex computational problem. The detection of these patterns is important to allow the discovery of transposable element (TE) insertions, incomplete reverse transcripts, deletions, and/or mutations. In this study, a de novo strategy for detecting patterns that represent nested motifs was designed based on exhaustive searches for pairs of motifs and combinatorial pattern analysis. These patterns can be grouped into three categories, motifs within other motifs, motifs flanked by other motifs, and motifs of large size. The methodology used in this study, applied to genomic sequences from the plant species Aegilops tauschii and Oryza sativa , revealed that it is possible to identify putative nested TEs by detecting these three types of patterns. The results were validated through BLAST alignments, which revealed the efficacy and usefulness of the new method, which is called Mamushka.

A fluorescence glucose sensor based on pH induced conformational switch of i-motif DNA.

PubMed

Ke, Qingqing; Zheng, Yu; Yang, Fan; Zhang, Hanchang; Yang, Xiurong

2014-11-01

A facile fluorescence biosensor for the detection of glucose is proposed based on the pH-induced conformational switch of i-motif DNA in this paper. Glucose can be oxidized by oxygen (O2) in the presence of glucose oxidase (GOD), and the generated gluconic acid can decrease the pH value of the solution and then induce the fluorophore- and quencher-labeled cytosine-rich single-stranded DNA to fold into a close-packed i-motif structure. As a result, the fluorescence quenching occurs because of the resonance energy transfer between fluorophore and quencher. Based on this working principle, the concentration of glucose can be detected by the decrease of fluorescence density. Under the optimal experimental conditions, the assay shows a linear response range of 5-100 µM for the glucose concentration with a detection limit of 4 µM. This glucose biosensor was applied to determine glucose in real samples successfully, suggesting its potential in the practical applicability. Copyright © 2014 Elsevier B.V. All rights reserved.

Motif discovery with data mining in 3D protein structure databases: discovery, validation and prediction of the U-shape zinc binding ("Huf-Zinc") motif.

PubMed

Maurer-Stroh, Sebastian; Gao, He; Han, Hao; Baeten, Lies; Schymkowitz, Joost; Rousseau, Frederic; Zhang, Louxin; Eisenhaber, Frank

2013-02-01

Data mining in protein databases, derivatives from more fundamental protein 3D structure and sequence databases, has considerable unearthed potential for the discovery of sequence motif--structural motif--function relationships as the finding of the U-shape (Huf-Zinc) motif, originally a small student's project, exemplifies. The metal ion zinc is critically involved in universal biological processes, ranging from protein-DNA complexes and transcription regulation to enzymatic catalysis and metabolic pathways. Proteins have evolved a series of motifs to specifically recognize and bind zinc ions. Many of these, so called zinc fingers, are structurally independent globular domains with discontinuous binding motifs made up of residues mostly far apart in sequence. Through a systematic approach starting from the BRIX structure fragment database, we discovered that there exists another predictable subset of zinc-binding motifs that not only have a conserved continuous sequence pattern but also share a characteristic local conformation, despite being included in totally different overall folds. While this does not allow general prediction of all Zn binding motifs, a HMM-based web server, Huf-Zinc, is available for prediction of these novel, as well as conventional, zinc finger motifs in protein sequences. The Huf-Zinc webserver can be freely accessed through this URL (http://mendel.bii.a-star.edu.sg/METHODS/hufzinc/).

DNA motif elucidation using belief propagation.

PubMed

Wong, Ka-Chun; Chan, Tak-Ming; Peng, Chengbin; Li, Yue; Zhang, Zhaolei

2013-09-01

Protein-binding microarray (PBM) is a high-throughout platform that can measure the DNA-binding preference of a protein in a comprehensive and unbiased manner. A typical PBM experiment can measure binding signal intensities of a protein to all the possible DNA k-mers (k=8∼10); such comprehensive binding affinity data usually need to be reduced and represented as motif models before they can be further analyzed and applied. Since proteins can often bind to DNA in multiple modes, one of the major challenges is to decompose the comprehensive affinity data into multimodal motif representations. Here, we describe a new algorithm that uses Hidden Markov Models (HMMs) and can derive precise and multimodal motifs using belief propagations. We describe an HMM-based approach using belief propagations (kmerHMM), which accepts and preprocesses PBM probe raw data into median-binding intensities of individual k-mers. The k-mers are ranked and aligned for training an HMM as the underlying motif representation. Multiple motifs are then extracted from the HMM using belief propagations. Comparisons of kmerHMM with other leading methods on several data sets demonstrated its effectiveness and uniqueness. Especially, it achieved the best performance on more than half of the data sets. In addition, the multiple binding modes derived by kmerHMM are biologically meaningful and will be useful in interpreting other genome-wide data such as those generated from ChIP-seq. The executables and source codes are available at the authors' websites: e.g. http://www.cs.toronto.edu/∼wkc/kmerHMM.

Facet-controlled phase separation in supersaturated Au-Ni nanoparticles upon shape equilibration

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

Herz, A., E-mail: andreas.herz@tu-ilmenau.de, E-mail: dong.wang@tu-ilmenau.de; Rossberg, D.; Hentschel, M.

2015-08-17

Solid-state dewetting is used to fabricate supersaturated, submicron-sized Au-Ni solid solution particles out of thin Au/Ni bilayers by means of a rapid thermal annealing technique. Phase separation in such particles is studied with respect to their equilibrium crystal (or Wulff) shape by subsequent annealing at elevated temperature. It is found that (100) faceting planes of the equilibrated particles are enriched with Ni and (111) faces with Au. Both phases are considered by quantum-mechanical calculations in combination with an error-reduction scheme that was developed to compensate for a missing exchange-correlation potential that would reliably describe both Au and Ni. The observedmore » phase configuration is then related to the minimization of strongly anisotropic elastic energies of Au- and Ni-rich phases and results in a rather unique nanoparticle composite state that is characterized by nearly uniform value of elastic response to epitaxial strains all over the faceted surface. The same conclusion is yielded also by evaluating bi-axial elastic moduli when employing interpolated experimental elastic constants. This work demonstrates a useful route for studying features of physical metallurgy at the mesoscale.« less

MicroRNA-15b regulates reversion-inducing cysteine-rich protein with Kazal motifs (RECK) expression in human uterine leiomyoma.

PubMed

Guan, Yichun; Guo, Lankai; Zukerberg, Lawrence; Rueda, Bo R; Styer, Aaron K

2016-08-17

Human uterine leiomyoma (fibroids; LYO) are the most common benign neoplasms in reproductive-aged women. Dysregulated extracellular matrix and irregular LYO reversion-inducing cysteine-rich protein with Kazal motifs (RECK) expression are thought to be mediated by aberrant microRNA (miR) expression. The relationship of miR-15b and RECK expression in LYO has not been studied. The expression levels of miR-15b and RECK were determined by quantitative RT-PCR, Western blot, and immunohistochemistry in cultures derived from commercial primary leiomyoma (cpLYO) and myometrial (cpMYO) cell lines and leiomyoma (pLYO) and myometrium (pMYO) tissue from surgical samples respectively. The relationship between miR-15b and RECK expression in cpLYO and pLYO (compared to their respective myometrial controls) was evaluated following transfection of cell cultures with either miR-15b mimic or inhibitor. Elevated levels of miR-15b were observed in cpLYO (2.82-fold; p = 0.04) and pLYO cell (1.30-fold; p = 0.0001) cultures respectively compared to corresponding MYO cell controls. Following transfection with miR-15b mimic, cpLYO cells (0.62-fold; p < 0.0001) and pLYO cells (0.68-fold; p < 0.0001) demonstrated reduced RECK protein expression. Following transfection with miR-15b inhibitor, cpLYO cells (1.20-fold; p < 0.0001) and pLYO cells (1.31-fold; p = 0.0007) demonstrated elevated RECK protein expression. RECK protein expression was reduced in pLYO tissues (0.73-fold; p < 0.0001) and pLYO (0.47-fold; p = 0.047) cells when compared to the corresponding MYO tissue controls. Our findings suggest that miR-15b negatively regulates RECK expression in LYO, and increased miR-15b and decreased RECK expression may contribute to the pathobiology of LYO. The functional significance of miR-15b and RECK expression warrants further investigation as potential therapeutic targets for the treatment of human LYO.

Stress-caused Anergy of Leukocytes towards Staphylococcal enterotoxin B and Exposure Transcriptome Signatures

DTIC Science & Technology

2015-05-28

Chemokine (C-X-C motif ) ligand 10 − 77.7 − 53.6 − 14.4 AU138239 INDO Indoleamine- pyrrole 2,3 dioxygenase − 29.3 − 31.5 − 14.0 AV734258 CCL8 Chemokine...immunomodulatory enzyme indoleamine- pyrrole 2,3 dioxygenase (INDO), the growth factors CSF1 and CSF2 and other T-cell response genes. Using NSC...2.8 − 2.2 AK026053 BCL2 B-cell CLL/lymphoma 2 − 2.2 − 2.0 − 2.3 − 2.2 AB015331 INDO Indoleamine- pyrrole 2,3 dioxygenase − 2.1 − 29.3 − 2.2 − 31.5

BlockLogo: visualization of peptide and sequence motif conservation

PubMed Central

Olsen, Lars Rønn; Kudahl, Ulrich Johan; Simon, Christian; Sun, Jing; Schönbach, Christian; Reinherz, Ellis L.; Zhang, Guang Lan; Brusic, Vladimir

2013-01-01

BlockLogo is a web-server application for visualization of protein and nucleotide fragments, continuous protein sequence motifs, and discontinuous sequence motifs using calculation of block entropy from multiple sequence alignments. The user input consists of a multiple sequence alignment, selection of motif positions, type of sequence, and output format definition. The output has BlockLogo along with the sequence logo, and a table of motif frequencies. We deployed BlockLogo as an online application and have demonstrated its utility through examples that show visualization of T-cell epitopes and B-cell epitopes (both continuous and discontinuous). Our additional example shows a visualization and analysis of structural motifs that determine specificity of peptide binding to HLA-DR molecules. The BlockLogo server also employs selected experimentally validated prediction algorithms to enable on-the-fly prediction of MHC binding affinity to 15 common HLA class I and class II alleles as well as visual analysis of discontinuous epitopes from multiple sequence alignments. It enables the visualization and analysis of structural and functional motifs that are usually described as regular expressions. It provides a compact view of discontinuous motifs composed of distant positions within biological sequences. BlockLogo is available at: http://research4.dfci.harvard.edu/cvc/blocklogo/ and http://methilab.bu.edu/blocklogo/ PMID:24001880

Motivated Proteins: A web application for studying small three-dimensional protein motifs

PubMed Central

Leader, David P; Milner-White, E James

2009-01-01

Background Small loop-shaped motifs are common constituents of the three-dimensional structure of proteins. Typically they comprise between three and seven amino acid residues, and are defined by a combination of dihedral angles and hydrogen bonding partners. The most abundant of these are αβ-motifs, asx-motifs, asx-turns, β-bulges, β-bulge loops, β-turns, nests, niches, Schellmann loops, ST-motifs, ST-staples and ST-turns. We have constructed a database of such motifs from a range of high-quality protein structures and built a web application as a visual interface to this. Description The web application, Motivated Proteins, provides access to these 12 motifs (with 48 sub-categories) in a database of over 400 representative proteins. Queries can be made for specific categories or sub-categories of motif, motifs in the vicinity of ligands, motifs which include part of an enzyme active site, overlapping motifs, or motifs which include a particular amino acid sequence. Individual proteins can be specified, or, where appropriate, motifs for all proteins listed. The results of queries are presented in textual form as an (X)HTML table, and may be saved as parsable plain text or XML. Motifs can be viewed and manipulated either individually or in the context of the protein in the Jmol applet structural viewer. Cartoons of the motifs imposed on a linear representation of protein secondary structure are also provided. Summary information for the motifs is available, as are histograms of amino acid distribution, and graphs of dihedral angles at individual positions in the motifs. Conclusion Motivated Proteins is a publicly and freely accessible web application that enables protein scientists to study small three-dimensional motifs without requiring knowledge of either Structured Query Language or the underlying database schema. PMID:19210785

Presence of a consensus DNA motif at nearby DNA sequence of the mutation susceptible CG nucleotides.

PubMed

Chowdhury, Kaushik; Kumar, Suresh; Sharma, Tanu; Sharma, Ankit; Bhagat, Meenakshi; Kamai, Asangla; Ford, Bridget M; Asthana, Shailendra; Mandal, Chandi C

2018-01-10

Complexity in tissues affected by cancer arises from somatic mutations and epigenetic modifications in the genome. The mutation susceptible hotspots present within the genome indicate a non-random nature and/or a position specific selection of mutation. An association exists between the occurrence of mutations and epigenetic DNA methylation. This study is primarily aimed at determining mutation status, and identifying a signature for predicting mutation prone zones of tumor suppressor (TS) genes. Nearby sequences from the top five positions having a higher mutation frequency in each gene of 42 TS genes were selected from a cosmic database and were considered as mutation prone zones. The conserved motifs present in the mutation prone DNA fragments were identified. Molecular docking studies were done to determine putative interactions between the identified conserved motifs and enzyme methyltransferase DNMT1. Collective analysis of 42 TS genes found GC as the most commonly replaced and AT as the most commonly formed residues after mutation. Analysis of the top 5 mutated positions of each gene (210 DNA segments for 42 TS genes) identified that CG nucleotides of the amino acid codons (e.g., Arginine) are most susceptible to mutation, and found a consensus DNA "T/AGC/GAGGA/TG" sequence present in these mutation prone DNA segments. Similar to TS genes, analysis of 54 oncogenes not only found CG nucleotides of the amino acid Arg as the most susceptible to mutation, but also identified the presence of similar consensus DNA motifs in the mutation prone DNA fragments (270 DNA segments for 54 oncogenes) of oncogenes. Docking studies depicted that, upon binding of DNMT1 methylates to this consensus DNA motif (C residues of CpG islands), mutation was likely to occur. Thus, this study proposes that DNMT1 mediated methylation in chromosomal DNA may decrease if a foreign DNA segment containing this consensus sequence along with CG nucleotides is exogenously introduced to dividing

The Transcriptional Complex Between the BCL2 i-Motif and hnRNP LL Is a Molecular Switch for Control of Gene Expression That Can Be Modulated by Small Molecules

PubMed Central

2015-01-01

In a companion paper (DOI: 10.021/ja410934b) we demonstrate that the C-rich strand of the cis-regulatory element in the BCL2 promoter element is highly dynamic in nature and can form either an i-motif or a flexible hairpin. Under physiological conditions these two secondary DNA structures are found in an equilibrium mixture, which can be shifted by the addition of small molecules that trap out either the i-motif (IMC-48) or the flexible hairpin (IMC-76). In cellular experiments we demonstrate that the addition of these molecules has opposite effects on BCL2 gene expression and furthermore that these effects are antagonistic. In this contribution we have identified a transcriptional factor that recognizes and binds to the BCL2 i-motif to activate transcription. The molecular basis for the recognition of the i-motif by hnRNP LL is determined, and we demonstrate that the protein unfolds the i-motif structure to form a stable single-stranded complex. In subsequent experiments we show that IMC-48 and IMC-76 have opposite, antagonistic effects on the formation of the hnRNP LL–i-motif complex as well as on the transcription factor occupancy at the BCL2 promoter. For the first time we propose that the i-motif acts as a molecular switch that controls gene expression and that small molecules that target the dynamic equilibrium of the i-motif and the flexible hairpin can differentially modulate gene expression. PMID:24559432

Coupling between magnetic and optical properties of stable Au-Fe solid solution nanoparticles

NASA Astrophysics Data System (ADS)

de Julián Fernández, C.; Mattei, G.; Paz, E.; Novak, R. L.; Cavigli, L.; Bogani, L.; Palomares, F. J.; Mazzoldi, P.; Caneschi, A.

2010-04-01

Au-Fe nanoparticles constitute one of the simplest prototypes of a multifunctional nanomaterial that can exhibit both magnetic and optical (plasmonic) properties. This solid solution, not feasible in the bulk phase diagram in thermal equilibrium, can be formed as a nanostructure by out-of-equilibrium processes. Here, the novel magnetic, optical and magneto-optical properties of ion-implanted Au-Fe solid solution nanoparticles dispersed in a SiO2 matrix are investigated and correlated. The surface plasmon resonance of the Au-Fe nanoparticles with almost equicomposition is strongly damped when compared to pure Au and to Au-rich Au-Fe nanoparticles. In all cases, the Au atoms are magnetically polarized, as measured by x-ray magnetic circular dichroism, and ferromagnetically coupled with Fe atoms. Although the chemical stability of Au-Fe nanoparticles is larger than that of Fe nanoparticles, both the magnetic moment per Fe atom and the order temperature are smaller. These results suggest that electronic and magnetic properties are more influenced by the hybridization of the electronic bands in the Au-Fe solid solution than by size effects. On the other hand, the magneto-optical transitions allowed in the vis-nIR spectral regions are very similar. In addition, we also observe, after studying the properties of thermally treated samples, that the Au-Fe alloy is stabilized, not by surface effects, but by the combination of the out-of-equilibrium nature of the ion implantation technique and by changes in the properties due to size effects.

Coupling between magnetic and optical properties of stable Au-Fe solid solution nanoparticles.

PubMed

de Julián Fernández, C; Mattei, G; Paz, E; Novak, R L; Cavigli, L; Bogani, L; Palomares, F J; Mazzoldi, P; Caneschi, A

2010-04-23

Au-Fe nanoparticles constitute one of the simplest prototypes of a multifunctional nanomaterial that can exhibit both magnetic and optical (plasmonic) properties. This solid solution, not feasible in the bulk phase diagram in thermal equilibrium, can be formed as a nanostructure by out-of-equilibrium processes. Here, the novel magnetic, optical and magneto-optical properties of ion-implanted Au-Fe solid solution nanoparticles dispersed in a SiO(2) matrix are investigated and correlated. The surface plasmon resonance of the Au-Fe nanoparticles with almost equicomposition is strongly damped when compared to pure Au and to Au-rich Au-Fe nanoparticles. In all cases, the Au atoms are magnetically polarized, as measured by x-ray magnetic circular dichroism, and ferromagnetically coupled with Fe atoms. Although the chemical stability of Au-Fe nanoparticles is larger than that of Fe nanoparticles, both the magnetic moment per Fe atom and the order temperature are smaller. These results suggest that electronic and magnetic properties are more influenced by the hybridization of the electronic bands in the Au-Fe solid solution than by size effects. On the other hand, the magneto-optical transitions allowed in the vis-nIR spectral regions are very similar. In addition, we also observe, after studying the properties of thermally treated samples, that the Au-Fe alloy is stabilized, not by surface effects, but by the combination of the out-of-equilibrium nature of the ion implantation technique and by changes in the properties due to size effects.

DNA containing CpG motifs induces angiogenesis

NASA Astrophysics Data System (ADS)

Zheng, Mei; Klinman, Dennis M.; Gierynska, Malgorzata; Rouse, Barry T.

2002-06-01

New blood vessel formation in the cornea is an essential step in the pathogenesis of a blinding immunoinflammatory reaction caused by ocular infection with herpes simplex virus (HSV). By using a murine corneal micropocket assay, we found that HSV DNA (which contains a significant excess of potentially bioactive "CpG" motifs when compared with mammalian DNA) induces angiogenesis. Moreover, synthetic oligodeoxynucleotides containing CpG motifs attract inflammatory cells and stimulate the release of vascular endothelial growth factor (VEGF), which in turn triggers new blood vessel formation. In vitro, CpG DNA induces the J774A.1 murine macrophage cell line to produce VEGF. In vivo CpG-induced angiogenesis was blocked by the administration of anti-mVEGF Ab or the inclusion of "neutralizing" oligodeoxynucleotides that specifically oppose the stimulatory activity of CpG DNA. These findings establish that DNA containing bioactive CpG motifs induces angiogenesis, and suggest that CpG motifs in HSV DNA may contribute to the blinding lesions of stromal keratitis.

Ca2+-binding Motif of βγ-Crystallins*

PubMed Central

Srivastava, Shanti Swaroop; Mishra, Amita; Krishnan, Bal; Sharma, Yogendra

2014-01-01

βγ-Crystallin-type double clamp (N/D)(N/D)XX(S/T)S motif is an established but sparsely investigated motif for Ca2+ binding. A βγ-crystallin domain is formed of two Greek key motifs, accommodating two Ca2+-binding sites. βγ-Crystallins make a separate class of Ca2+-binding proteins (CaBP), apparently a major group of CaBP in bacteria. Paralleling the diversity in βγ-crystallin domains, these motifs also show great diversity, both in structure and in function. Although the expression of some of them has been associated with stress, virulence, and adhesion, the functional implications of Ca2+ binding to βγ-crystallins in mediating biological processes are yet to be elucidated. PMID:24567326

Thermal signature characteristics of vehicle/terrain interaction disturbances: implications for battlefield vehicle classification.

PubMed

Eastes, John W; Mason, George L; Kusinger, Alan E

2004-05-01

Thermal emissivity spectra (8-14 microm) of track impressions/background were determined in conjunction with operation of six military vehicle types, T-72 and M1 Tanks, an M2 Bradley Fighting Vehicle, a 5-ton truck, a D7 tractor, and a High Mobility Multipurpose Wheeled Vehicle (HMMWV), over diverse soil surfaces to determine if vehicle type could be related to track thermal signatures. Results suggest soil compaction and fragmentation/pulverization are primary parameters affecting track signatures and that soil and vehicle/terrain-contact type determine which parameter dominates. Steel-tracked vehicles exert relatively low ground-contact pressure but tend to fragment/pulverize soil more so than do rubber-tired vehicles, which tend mainly to compact. In quartz-rich, lean clay soil tracked vehicles produced impressions with spectral contrast of the quartz reststrahlen features decreased from that of the background. At the same time, 5-ton truck tracks exhibited increased contrast on the same surface, suggesting that steel tracks fragmented soil while rubber tires mainly produced compaction. The structure of materials such as sand and moist clay-rich river sediment makes them less subject to further fragmentation/pulverization; thus, compaction was the main factor affecting signatures in these media, and both tracked and wheeled vehicles created impressions with increased spectral contrast on these surfaces. These results suggest that remotely sensed thermal signatures could differentiate tracked and wheeled vehicles on terrain in many areas of the world of strategic interest. Significant applications include distinguishing visually/spectrally identical lightweight decoys from actual threat vehicles.

Motif-based analysis of large nucleotide data sets using MEME-ChIP

PubMed Central

Ma, Wenxiu; Noble, William S; Bailey, Timothy L

2014-01-01

MEME-ChIP is a web-based tool for analyzing motifs in large DNA or RNA data sets. It can analyze peak regions identified by ChIP-seq, cross-linking sites identified by cLIP-seq and related assays, as well as sets of genomic regions selected using other criteria. MEME-ChIP performs de novo motif discovery, motif enrichment analysis, motif location analysis and motif clustering, providing a comprehensive picture of the DNA or RNA motifs that are enriched in the input sequences. MEME-ChIP performs two complementary types of de novo motif discovery: weight matrix–based discovery for high accuracy; and word-based discovery for high sensitivity. Motif enrichment analysis using DNA or RNA motifs from human, mouse, worm, fly and other model organisms provides even greater sensitivity. MEME-ChIP’s interactive HTML output groups and aligns significant motifs to ease interpretation. this protocol takes less than 3 h, and it provides motif discovery approaches that are distinct and complementary to other online methods. PMID:24853928

Spectroscopic Signatures and Structural Motifs of Dopamine: a Computational Study

NASA Astrophysics Data System (ADS)

Srivastava, Santosh Kumar; Singh, Vipin Bahadur

2016-06-01

Dopamine (DA) is an essential neurotransmitter in the central nervous system and it plays integral role in numerous brain functions including behaviour, cognition, emotion, working memory and associated learning. In the present work the conformational landscapes of neutral and protonated dopamine have been investigated in the gas phase and in aqueous solution by MP2 and DFT (M06-2X, ωB97X-D, B3LYP and B3LYP-D3) methods. Twenty lowest energy structures of neutral DA were subjected to geometry optimization and the gauche conformer, GIa, was found to be the lowest gas phase structure at the each level of theory in agreement with the experimental rotational spectroscopy. All folded gauche conformers (GI) where lone electron pair of the NH2 group is directed towards the π system of the aromatic ring ( 'non up' ) are found more stable in the gas phase. While in aqueous solution, all those gauche conformers (GII) where lone electron pair of the NH2 group is directed opposite from the π system of the aromatic ring ('up' structures) are stabilized significantly.Nine lowest energy structures, protonated at the amino group, are optimized at the same MP2/aug-cc-pVDZ level of theory. In the most stable gauche structures, g-1 and g+1, mainly electrostatic cation - π interaction is further stabilized by significant dispersion forces as predicted by the substantial differences between the DFT and dispersion corrected DFT-D3 calculations. In aqueous environment the intra-molecular cation- π distance in g-1 and g+1 isomers, slightly increases compared to the gas phase and the magnitude of the cation- π interaction is reduced relative to the gas phase, because solvation of the cation decreases its interaction energy with the π face of aromatic system. The IR intensity of the bound N-H+ stretching mode provides characteristic 'IR spectroscopic signatures' which can reflect the strength of cation- π interaction energy. The CC2 lowest lying S1 ( 1ππ* ) excited state of neutral

Gibbs motif sampling: detection of bacterial outer membrane protein repeats.

PubMed Central

Neuwald, A. F.; Liu, J. S.; Lawrence, C. E.

1995-01-01

The detection and alignment of locally conserved regions (motifs) in multiple sequences can provide insight into protein structure, function, and evolution. A new Gibbs sampling algorithm is described that detects motif-encoding regions in sequences and optimally partitions them into distinct motif models; this is illustrated using a set of immunoglobulin fold proteins. When applied to sequences sharing a single motif, the sampler can be used to classify motif regions into related submodels, as is illustrated using helix-turn-helix DNA-binding proteins. Other statistically based procedures are described for searching a database for sequences matching motifs found by the sampler. When applied to a set of 32 very distantly related bacterial integral outer membrane proteins, the sampler revealed that they share a subtle, repetitive motif. Although BLAST (Altschul SF et al., 1990, J Mol Biol 215:403-410) fails to detect significant pairwise similarity between any of the sequences, the repeats present in these outer membrane proteins, taken as a whole, are highly significant (based on a generally applicable statistical test for motifs described here). Analysis of bacterial porins with known trimeric beta-barrel structure and related proteins reveals a similar repetitive motif corresponding to alternating membrane-spanning beta-strands. These beta-strands occur on the membrane interface (as opposed to the trimeric interface) of the beta-barrel. The broad conservation and structural location of these repeats suggests that they play important functional roles. PMID:8520488

ELM: the status of the 2010 eukaryotic linear motif resource

PubMed Central

Gould, Cathryn M.; Diella, Francesca; Via, Allegra; Puntervoll, Pål; Gemünd, Christine; Chabanis-Davidson, Sophie; Michael, Sushama; Sayadi, Ahmed; Bryne, Jan Christian; Chica, Claudia; Seiler, Markus; Davey, Norman E.; Haslam, Niall; Weatheritt, Robert J.; Budd, Aidan; Hughes, Tim; Paś, Jakub; Rychlewski, Leszek; Travé, Gilles; Aasland, Rein; Helmer-Citterich, Manuela; Linding, Rune; Gibson, Toby J.

2010-01-01

Linear motifs are short segments of multidomain proteins that provide regulatory functions independently of protein tertiary structure. Much of intracellular signalling passes through protein modifications at linear motifs. Many thousands of linear motif instances, most notably phosphorylation sites, have now been reported. Although clearly very abundant, linear motifs are difficult to predict de novo in protein sequences due to the difficulty of obtaining robust statistical assessments. The ELM resource at http://elm.eu.org/ provides an expanding knowledge base, currently covering 146 known motifs, with annotation that includes >1300 experimentally reported instances. ELM is also an exploratory tool for suggesting new candidates of known linear motifs in proteins of interest. Information about protein domains, protein structure and native disorder, cellular and taxonomic contexts is used to reduce or deprecate false positive matches. Results are graphically displayed in a ‘Bar Code’ format, which also displays known instances from homologous proteins through a novel ‘Instance Mapper’ protocol based on PHI-BLAST. ELM server output provides links to the ELM annotation as well as to a number of remote resources. Using the links, researchers can explore the motifs, proteins, complex structures and associated literature to evaluate whether candidate motifs might be worth experimental investigation. PMID:19920119

Application of a case-control study design to investigate genotypic signatures of HIV-1 transmission.

PubMed

Mota, Talia M; Murray, John M; Center, Rob J; Purcell, Damian F J; McCaw, James M

2012-06-25

The characterization of HIV-1 transmission strains may inform the design of an effective vaccine. Shorter variable loops with fewer predicted glycosites have been suggested as signatures enriched in envelope sequences derived during acute HIV-1 infection. Specifically, a transmission-linked lack of glycosites within the V1 and V2 loops of gp120 provides greater access to an α4β7 binding motif, which promotes the establishment of infection. Also, a histidine at position 12 in the leader sequence of Env has been described as a transmission signature that is selected against during chronic infection. The purpose of this study is to measure the association of the presence of an α4β7 binding motif, the number of N-linked glycosites, the length of the variable loops, and the prevalence of histidine at position 12 with HIV-1 transmission. A case-control study design was used to measure the prevalence of these variables between subtype B and C transmission sequences and frequency-matched randomly-selected sequences derived from chronically infected controls. Subtype B transmission strains had shorter V3 regions than chronic strains (p = 0.031); subtype C transmission strains had shorter V1 loops than chronic strains (p = 0.047); subtype B transmission strains had more V3 loop glycosites (p = 0.024) than chronic strains. Further investigation showed that these statistically significant results were unlikely to be biologically meaningful. Also, there was no difference observed in the prevalence of a histidine at position 12 among transmission strains and controls of either subtype. Although a genetic bottleneck is observed after HIV-1 transmission, our results indicate that summary characteristics of Env hypothesised to be important in transmission are not divergent between transmission and chronic strains of either subtype. The success of a transmission strain to initiate infection may be a random event from the divergent pool of donor viral sequences. The

Suppression of Υ production in d + Au + and Au + Au collisions at √ sNN =200 GeV

DOE PAGES

None

2014-07-01

We report measurements of Upsilon meson production in p + p, d +Au, and Au+Au collisions using the STAR detector at RHIC. We compare the Upsilon yield to the measured cross section in p + p collisions in order to quantify any modifications of the yield in cold nuclear matter using d +Au data and in hot nuclear matter using Au+Au data separated into three centrality classes. Our p +p measurement is based on three times the statistics of our previous result. We obtain a nuclear modification factor for Upsilon (1S + 2S + 3S) in the rapidity range |y|more » < 1 in d + Au collisions of R dAu = 0.79 ± 0.24(stat.) ± 0.03(syst.) ± 0.10(p + p syst.). A comparison with models including shadowing and initial state part on energy loss indicates the presence of additional cold-nuclear matter suppression. Similarly, in the top 10% most-central Au + Au collisions, we measure a nuclear modification factor of R AA = 0.49 ±0.1(stat.) ±0.02(syst.) ±0.06(p + p syst.), which is a larger suppression factor than that seen in cold nuclear matter. Our results are consistent with complete suppression of excited-state Upsilon mesons in Au + Au collisions. The additional suppression in Au + Au is consistent with the level expected in model calculations that include the presence of a hot, deconfined Quark–Gluon Plasma. However, understanding the suppression seen in d + Au is still needed before any definitive statements about the nature of the suppression in Au + Au can be made.« less

Recurring sequence-structure motifs in (βα)8-barrel proteins and experimental optimization of a chimeric protein designed based on such motifs.

PubMed

Wang, Jichao; Zhang, Tongchuan; Liu, Ruicun; Song, Meilin; Wang, Juncheng; Hong, Jiong; Chen, Quan; Liu, Haiyan

2017-02-01

An interesting way of generating novel artificial proteins is to combine sequence motifs from natural proteins, mimicking the evolutionary path suggested by natural proteins comprising recurring motifs. We analyzed the βα and αβ modules of TIM barrel proteins by structure alignment-based sequence clustering. A number of preferred motifs were identified. A chimeric TIM was designed by using recurring elements as mutually compatible interfaces. The foldability of the designed TIM protein was then significantly improved by six rounds of directed evolution. The melting temperature has been improved by more than 20°C. A variety of characteristics suggested that the resulting protein is well-folded. Our analysis provided a library of peptide motifs that is potentially useful for different protein engineering studies. The protein engineering strategy of using recurring motifs as interfaces to connect partial natural proteins may be applied to other protein folds. Copyright © 2016 Elsevier B.V. All rights reserved.

An experimental test of a fundamental food web motif.

PubMed

Rip, Jason M K; McCann, Kevin S; Lynn, Denis H; Fawcett, Sonia

2010-06-07

Large-scale changes to the world's ecosystem are resulting in the deterioration of biostructure-the complex web of species interactions that make up ecological communities. A difficult, yet crucial task is to identify food web structures, or food web motifs, that are the building blocks of this baroque network of interactions. Once identified, these food web motifs can then be examined through experiments and theory to provide mechanistic explanations for how structure governs ecosystem stability. Here, we synthesize recent ecological research to show that generalist consumers coupling resources with different interaction strengths, is one such motif. This motif amazingly occurs across an enormous range of spatial scales, and so acts to distribute coupled weak and strong interactions throughout food webs. We then perform an experiment that illustrates the importance of this motif to ecological stability. We find that weak interactions coupled to strong interactions by generalist consumers dampen strong interaction strengths and increase community stability. This study takes a critical step by isolating a common food web motif and through clear, experimental manipulation, identifies the fundamental stabilizing consequences of this structure for ecological communities.

Chiral magnetic effect search in p+Au, d+Au and Au+Au collisions at RHIC

NASA Astrophysics Data System (ADS)

Zhao, Jie

2018-01-01

Metastable domains of fluctuating topological charges can change the chirality of quarks and induce local parity violation in quantum chromodynamics. This can lead to observable charge separation along the direction of the strong magnetic field produced by spectator protons in relativistic heavy-ion collisions, a phenomenon called the chiral magnetic effect (CME). A major background source for CME measurements using the charge-dependent azimuthal correlator (Δϒ) is the intrinsic particle correlations (such as resonance decays) coupled with the azimuthal elliptical anisotropy (v2). In heavy-ion collisions, the magnetic field direction and event plane angle are correlated, thus the CME and the v2-induced background are entangled. In this report, we present two studies from STAR to shed further lights on the background issue. (1) The Δϒ should be all background in small system p+Au and d+Au collisions, because the event plane angles are dominated by geometry fluctuations uncorrelated to the magnetic field direction. However, significant Δϒ is observed, comparable to the peripheral Au+Au data, suggesting a background dominance in the latter, and likely also in the mid-central Au+Au collisions where the multiplicity and v2 scaled correlator is similar. (2) A new approach is devised to study Δϒ as a function of the particle pair invariant mass (minv) to identify the resonance backgrounds and hence to extract the possible CME signal. Signal is consistent with zero within uncertainties at high minv. Signal at low minv, extracted from a two-component model assuming smooth mass dependence, is consistent with zero within uncertainties.

Mechanisms of Zero-Lag Synchronization in Cortical Motifs

PubMed Central

Gollo, Leonardo L.; Mirasso, Claudio; Sporns, Olaf; Breakspear, Michael

2014-01-01

Zero-lag synchronization between distant cortical areas has been observed in a diversity of experimental data sets and between many different regions of the brain. Several computational mechanisms have been proposed to account for such isochronous synchronization in the presence of long conduction delays: Of these, the phenomenon of “dynamical relaying” – a mechanism that relies on a specific network motif – has proven to be the most robust with respect to parameter mismatch and system noise. Surprisingly, despite a contrary belief in the community, the common driving motif is an unreliable means of establishing zero-lag synchrony. Although dynamical relaying has been validated in empirical and computational studies, the deeper dynamical mechanisms and comparison to dynamics on other motifs is lacking. By systematically comparing synchronization on a variety of small motifs, we establish that the presence of a single reciprocally connected pair – a “resonance pair” – plays a crucial role in disambiguating those motifs that foster zero-lag synchrony in the presence of conduction delays (such as dynamical relaying) from those that do not (such as the common driving triad). Remarkably, minor structural changes to the common driving motif that incorporate a reciprocal pair recover robust zero-lag synchrony. The findings are observed in computational models of spiking neurons, populations of spiking neurons and neural mass models, and arise whether the oscillatory systems are periodic, chaotic, noise-free or driven by stochastic inputs. The influence of the resonance pair is also robust to parameter mismatch and asymmetrical time delays amongst the elements of the motif. We call this manner of facilitating zero-lag synchrony resonance-induced synchronization, outline the conditions for its occurrence, and propose that it may be a general mechanism to promote zero-lag synchrony in the brain. PMID:24763382

The effect of orthology and coregulation on detecting regulatory motifs.

PubMed

Storms, Valerie; Claeys, Marleen; Sanchez, Aminael; De Moor, Bart; Verstuyf, Annemieke; Marchal, Kathleen

2010-02-03

Computational de novo discovery of transcription factor binding sites is still a challenging problem. The growing number of sequenced genomes allows integrating orthology evidence with coregulation information when searching for motifs. Moreover, the more advanced motif detection algorithms explicitly model the phylogenetic relatedness between the orthologous input sequences and thus should be well adapted towards using orthologous information. In this study, we evaluated the conditions under which complementing coregulation with orthologous information improves motif detection for the class of probabilistic motif detection algorithms with an explicit evolutionary model. We designed datasets (real and synthetic) covering different degrees of coregulation and orthologous information to test how well Phylogibbs and Phylogenetic sampler, as representatives of the motif detection algorithms with evolutionary model performed as compared to MEME, a more classical motif detection algorithm that treats orthologs independently. Under certain conditions detecting motifs in the combined coregulation-orthology space is indeed more efficient than using each space separately, but this is not always the case. Moreover, the difference in success rate between the advanced algorithms and MEME is still marginal. The success rate of motif detection depends on the complex interplay between the added information and the specificities of the applied algorithms. Insights in this relation provide information useful to both developers and users. All benchmark datasets are available at http://homes.esat.kuleuven.be/~kmarchal/Supplementary_Storms_Valerie_PlosONE.

Porphyry Cu-Au mineralization in the Mirkuh Ali Mirza magmatic complex, NW Iran

NASA Astrophysics Data System (ADS)

Maghsoudi, A.; Yazdi, M.; Mehrpartou, M.; Vosoughi, M.; Younesi, S.

2014-01-01

The Mirkuh Ali Mirza Cu-Au porphyry system in East Azerbaijan Province is located on the western part of the Cenozoic Alborz-Azerbaijan volcanic belt. The belt is also an important Cu-Mo-Au metallogenic province in northwestern Iran. The exposed rocks in the study area consist of a volcaniclastic sequence, subvolcanic rocks and intermediate to mafic lava flows of Neogene age. The volcanic rocks show a typical subduction-related magmatic arc geological and geochemical signature, with low concentration of Nb, Ta, and Ti. Mineralization is hosted by Neogene dacitic tuff and porphyritic dacite situated at the intersections of northeast and northwest faults. Field observations, alteration zonation, geochemical haloes and isotopic data of the Mirkuh Ali Mirza magmatic complex show similarities with typical convergent margin Cu-Au porphyry type deposits. The following features confirm the classic model for Cu-Au porphyry systems: (a) close spatial association with high-K calcalkaline to shoshonitic rock related to post-collision extensional setting (b) low grade Cu (0.57%) (c) stockworks as well as disseminated sulfides (c) zonality of the alteration patterns from intense phyllic at the center to outward weak-phyllic, argillic, and propylitic (d) the presence of a pyritic halo (e) accompanied by sheeted veins and low-sulfidation epithermal gold (f) mineralization spatially associated with intersection of structures, (g) genetically related to diorite porphyry stocks at depth (h) geochemical zonation of (Cu ± Au ± Ag ± Bi) → (Cu + Mo ± Bi ± Au ± Pb ± Zn ± As) → (Au + Mo ± Pb ± Zn) → (As + Ag + Sb + Mn + Ba + Pb + Zn + Hg) → Hg from center to outwards (i) The range of sulfur isotopic values is approximately zero (interpreted to have magmatic source) and similar to other subduction-related porphyry Cu deposits.

DNA motifs associated with aberrant CpG island methylation.

PubMed

Feltus, F Alex; Lee, Eva K; Costello, Joseph F; Plass, Christoph; Vertino, Paula M

2006-05-01

Epigenetic silencing involving the aberrant methylation of promoter region CpG islands is widely recognized as a tumor suppressor silencing mechanism in cancer. However, the molecular pathways underlying aberrant DNA methylation remain elusive. Recently we showed that, on a genome-wide level, CpG island loci differ in their intrinsic susceptibility to aberrant methylation and that this susceptibility can be predicted based on underlying sequence context. These data suggest that there are sequence/structural features that contribute to the protection from or susceptibility to aberrant methylation. Here we use motif elicitation coupled with classification techniques to identify DNA sequence motifs that selectively define methylation-prone or methylation-resistant CpG islands. Motifs common to 28 methylation-prone or 47 methylation-resistant CpG island-containing genomic fragments were determined using the MEME and MAST algorithms (). The five most discriminatory motifs derived from methylation-prone sequences were found to be associated with CpG islands in general and were nonrandomly distributed throughout the genome. In contrast, the eight most discriminatory motifs derived from the methylation-resistant CpG islands were randomly distributed throughout the genome. Interestingly, this latter group tended to associate with Alu and other repetitive sequences. Used together, the frequency of occurrence of these motifs successfully discriminated methylation-prone and methylation-resistant CpG island groups with an accuracy of 87% after 10-fold cross-validation. The motifs identified here are candidate methylation-targeting or methylation-protection DNA sequences.

Discriminative motif discovery via simulated evolution and random under-sampling.

PubMed

Song, Tao; Gu, Hong

2014-01-01

Conserved motifs in biological sequences are closely related to their structure and functions. Recently, discriminative motif discovery methods have attracted more and more attention. However, little attention has been devoted to the data imbalance problem, which is one of the main reasons affecting the performance of the discriminative models. In this article, a simulated evolution method is applied to solve the multi-class imbalance problem at the stage of data preprocessing, and at the stage of Hidden Markov Models (HMMs) training, a random under-sampling method is introduced for the imbalance between the positive and negative datasets. It is shown that, in the task of discovering targeting motifs of nine subcellular compartments, the motifs found by our method are more conserved than the methods without considering data imbalance problem and recover the most known targeting motifs from Minimotif Miner and InterPro. Meanwhile, we use the found motifs to predict protein subcellular localization and achieve higher prediction precision and recall for the minority classes.

A Gibbs sampler for motif detection in phylogenetically close sequences

NASA Astrophysics Data System (ADS)

Siddharthan, Rahul; van Nimwegen, Erik; Siggia, Eric

2004-03-01

Genes are regulated by transcription factors that bind to DNA upstream of genes and recognize short conserved ``motifs'' in a random intergenic ``background''. Motif-finders such as the Gibbs sampler compare the probability of these short sequences being represented by ``weight matrices'' to the probability of their arising from the background ``null model'', and explore this space (analogous to a free-energy landscape). But closely related species may show conservation not because of functional sites but simply because they have not had sufficient time to diverge, so conventional methods will fail. We introduce a new Gibbs sampler algorithm that accounts for common ancestry when searching for motifs, while requiring minimal ``prior'' assumptions on the number and types of motifs, assessing the significance of detected motifs by ``tracking'' clusters that stay together. We apply this scheme to motif detection in sporulation-cycle genes in the yeast S. cerevisiae, using recent sequences of other closely-related Saccharomyces species.

Rb-Sr Isotopic Systematics of Alkali-Rich Fragments in the Yamato-74442 LL-Chondritic Breccia

NASA Technical Reports Server (NTRS)

Yokoyama, T.; Misawa, K.; Okano, O.; Shih, C.-Y.; Nyquist, L. E.; Simo, J. I.; Tappa, M. J.; Yoneda, S.

2012-01-01

Alkali-rich igneous fragments were identified in the brecciated LL-chondrites, Kr henberg (LL5)], Bhola (LL3-6) and Yamato (Y)-74442 (LL4), and show characteristic fractionation patterns of alkaline elements. The K-Rb-Cs-rich fragments in Kr henberg, Bhola, and Y-74442 are very similar in mineralogy and petrography (olivine + pyroxene + glass), suggesting that they could have come from related precursor materials. We have undertaken Rb-Sr isotopic studies on alkali-rich fragments in Y-74442 to precisely determine their crystallization ages and the isotopic signatures of their precursor material(s).

Sequence information gain based motif analysis.

PubMed

Maynou, Joan; Pairó, Erola; Marco, Santiago; Perera, Alexandre

2015-11-09

The detection of regulatory regions in candidate sequences is essential for the understanding of the regulation of a particular gene and the mechanisms involved. This paper proposes a novel methodology based on information theoretic metrics for finding regulatory sequences in promoter regions. This methodology (SIGMA) has been tested on genomic sequence data for Homo sapiens and Mus musculus. SIGMA has been compared with different publicly available alternatives for motif detection, such as MEME/MAST, Biostrings (Bioconductor package), MotifRegressor, and previous work such Qresiduals projections or information theoretic based detectors. Comparative results, in the form of Receiver Operating Characteristic curves, show how, in 70% of the studied Transcription Factor Binding Sites, the SIGMA detector has a better performance and behaves more robustly than the methods compared, while having a similar computational time. The performance of SIGMA can be explained by its parametric simplicity in the modelling of the non-linear co-variability in the binding motif positions. Sequence Information Gain based Motif Analysis is a generalisation of a non-linear model of the cis-regulatory sequences detection based on Information Theory. This generalisation allows us to detect transcription factor binding sites with maximum performance disregarding the covariability observed in the positions of the training set of sequences. SIGMA is freely available to the public at http://b2slab.upc.edu.

RNA 3D Structural Motifs: Definition, Identification, Annotation, and Database Searching

NASA Astrophysics Data System (ADS)

Nasalean, Lorena; Stombaugh, Jesse; Zirbel, Craig L.; Leontis, Neocles B.

Structured RNA molecules resemble proteins in the hierarchical organization of their global structures, folding and broad range of functions. Structured RNAs are composed of recurrent modular motifs that play specific functional roles. Some motifs direct the folding of the RNA or stabilize the folded structure through tertiary interactions. Others bind ligands or proteins or catalyze chemical reactions. Therefore, it is desirable, starting from the RNA sequence, to be able to predict the locations of recurrent motifs in RNA molecules. Conversely, the potential occurrence of one or more known 3D RNA motifs may indicate that a genomic sequence codes for a structured RNA molecule. To identify known RNA structural motifs in new RNA sequences, precise structure-based definitions are needed that specify the core nucleotides of each motif and their conserved interactions. By comparing instances of each recurrent motif and applying base pair isosteriCity relations, one can identify neutral mutations that preserve its structure and function in the contexts in which it occurs.

Electron-Poor Polar Intermetallics: Complex Structures, Novel Clusters, and Intriguing Bonding with Pronounced Electron Delocalization.

PubMed

Lin, Qisheng; Miller, Gordon J

2018-01-16

Intermetallic compounds represent an extensive pool of candidates for energy related applications stemming from magnetic, electric, optic, caloric, and catalytic properties. The discovery of novel intermetallic compounds can enhance understanding of the chemical principles that govern structural stability and chemical bonding as well as finding new applications. Valence electron-poor polar intermetallics with valence electron concentrations (VECs) between 2.0 and 3.0 e - /atom show a plethora of unprecedented and fascinating structural motifs and bonding features. Therefore, establishing simple structure-bonding-property relationships is especially challenging for this compound class because commonly accepted valence electron counting rules are inappropriate. During our efforts to find quasicrystals and crystalline approximants by valence electron tuning near 2.0 e - /atom, we observed that compositions close to those of quasicrystals are exceptional sources for unprecedented valence electron-poor polar intermetallics, e.g., Ca 4 Au 10 In 3 containing (Au 10 In 3 ) wavy layers, Li 14.7 Mg 36.8 Cu 21.5 Ga 66 adopting a type IV clathrate framework, and Sc 4 Mg x Cu 15-x Ga 7.5 that is incommensurately modulated. In particular, exploratory syntheses of AAu 3 T (A = Ca, Sr, Ba and T = Ge, Sn) phases led to interesting bonding features for Au, such as columns, layers, and lonsdaleite-type tetrahedral frameworks. Overall, the breadth of Au-rich polar intermetallics originates, in part, from significant relativistics effect on the valence electrons of Au, effects which result in greater 6s/5d orbital mixing, a small effective metallic radius, and an enhanced Mulliken electronegativity, all leading to ultimate enhanced binding with nearly all metals including itself. Two other successful strategies to mine electron-poor polar intermetallics include lithiation and "cation-rich" phases. Along these lines, we have studied lithiated Zn-rich compounds in which structural

The Effect of Orthology and Coregulation on Detecting Regulatory Motifs

PubMed Central

Storms, Valerie; Claeys, Marleen; Sanchez, Aminael; De Moor, Bart; Verstuyf, Annemieke; Marchal, Kathleen

2010-01-01

Background Computational de novo discovery of transcription factor binding sites is still a challenging problem. The growing number of sequenced genomes allows integrating orthology evidence with coregulation information when searching for motifs. Moreover, the more advanced motif detection algorithms explicitly model the phylogenetic relatedness between the orthologous input sequences and thus should be well adapted towards using orthologous information. In this study, we evaluated the conditions under which complementing coregulation with orthologous information improves motif detection for the class of probabilistic motif detection algorithms with an explicit evolutionary model. Methodology We designed datasets (real and synthetic) covering different degrees of coregulation and orthologous information to test how well Phylogibbs and Phylogenetic sampler, as representatives of the motif detection algorithms with evolutionary model performed as compared to MEME, a more classical motif detection algorithm that treats orthologs independently. Results and Conclusions Under certain conditions detecting motifs in the combined coregulation-orthology space is indeed more efficient than using each space separately, but this is not always the case. Moreover, the difference in success rate between the advanced algorithms and MEME is still marginal. The success rate of motif detection depends on the complex interplay between the added information and the specificities of the applied algorithms. Insights in this relation provide information useful to both developers and users. All benchmark datasets are available at http://homes.esat.kuleuven.be/~kmarchal/Supplementary_Storms_Valerie_PlosONE. PMID:20140085

Molecular evolution and expression of oxygen transport genes in livebearing fishes (Poeciliidae) from hydrogen sulfide rich springs.

PubMed

Barts, Nicholas; Greenway, Ryan; Passow, Courtney N; Arias-Rodriguez, Lenin; Kelley, Joanna L; Tobler, Michael

2018-04-01

Hydrogen sulfide (H 2 S) is a natural toxicant in some aquatic environments that has diverse molecular targets. It binds to oxygen transport proteins, rendering them non-functional by reducing oxygen-binding affinity. Hence, organisms permanently inhabiting H 2 S-rich environments are predicted to exhibit adaptive modifications to compensate for the reduced capacity to transport oxygen. We investigated 10 lineages of fish of the family Poeciliidae that have colonized freshwater springs rich in H 2 S-along with related lineages from non-sulfidic environments-to test hypotheses about the expression and evolution of oxygen transport genes in a phylogenetic context. We predicted shifts in the expression of and signatures of positive selection on oxygen transport genes upon colonization of H 2 S-rich habitats. Our analyses indicated significant shifts in gene expression for multiple hemoglobin genes in lineages that have colonized H 2 S-rich environments, and three hemoglobin genes exhibited relaxed selection in sulfidic compared to non-sulfidic lineages. However, neither changes in gene expression nor signatures of selection were consistent among all lineages in H 2 S-rich environments. Oxygen transport genes may consequently be predictable targets of selection during adaptation to sulfidic environments, but changes in gene expression and molecular evolution of oxygen transport genes in H 2 S-rich environments are not necessarily repeatable across replicated lineages.

Comparative analyses of the thermodynamic RNA binding signatures of different types of RNA recognition motifs

PubMed Central

Cléry, Antoine; Allain, Frédéric H-T

2017-01-01

Abstract RNA recognition motifs (RRMs) are structurally versatile domains important in regulation of alternative splicing. Structural mechanisms of sequence-specific recognition of single-stranded RNAs (ssRNAs) by RRMs are well understood. The thermodynamic strategies are however unclear. Therefore, we utilized microcalorimetry and semi-empirical analyses to comparatively analyze the cognate ssRNA binding thermodynamics of four different RRM domains, each with a different RNA binding mode. The different binding modes are: canonical binding to the β-sheet surface; canonical binding with involvement of N- and C-termini; binding to conserved loops; and binding to an α-helix. Our results identify enthalpy as the sole and general force driving association at physiological temperatures. Also, networks of weak interactions are a general feature regulating stability of the different RRM–ssRNA complexes. In agreement, non-polyelectrolyte effects contributed between ∼75 and 90% of the overall free energy of binding in the considered complexes. The various RNA binding modes also displayed enormous heat capacity differences, that upon dissection revealed large differential changes in hydration, conformations and dynamics upon binding RNA. Altogether, different modes employed by RRMs to bind cognate ssRNAs utilize various thermodynamics strategies during the association process. PMID:28334819

Successful synthesis and thermal stability of immiscible metal Au-Rh, Au-Ir andAu-Ir-Rh nanoalloys

NASA Astrophysics Data System (ADS)

Shubin, Yury; Plyusnin, Pavel; Sharafutdinov, Marat; Makotchenko, Evgenia; Korenev, Sergey

2017-05-01

We successfully prepared face-centred cubic nanoalloys in systems of Au-Ir, Au-Rh and Au-Ir-Rh, with large bulk miscibility gaps, in one-run reactions under thermal decomposition of specially synthesised single-source precursors, namely, [AuEn2][Ir(NO2)6], [AuEn2][Ir(NO2)6] х [Rh(NO2)6]1-х and [AuEn2][Rh(NO2)6]. The precursors employed contain all desired metals ‘mixed’ at the atomic level, thus providing significant advantages for obtaining alloys. The observations using high-resolution transmission electron microscopy show that the nanoalloy structures are composed of well-dispersed aggregates of crystalline domains with a mean size of 5 ± 3 nm. Еnergy dispersive x-ray spectroscopy and x-ray powder diffraction (XRD) measurements confirm the formation of AuIr, AuRh, AuIr0.75Rh0.25, AuIr0.50Rh0.50 and AuIr0.25Rh0.75 metastable solid solutions. In situ high-temperature synchrotron XRD (HTXRD) was used to study the formation mechanism of nanoalloys. The observed transformations are described by the ‘conversion chemistry’ mechanism characterised by the primary development of particles comprising atoms of only one type, followed by a chemical reaction resulting in the final formation of a nanoalloy. The obtained metastable nanoalloys exhibit essential thermal stability. Exposure to 180 °C for 30 h does not cause any dealloying process.

Successful synthesis and thermal stability of immiscible metal Au-Rh, Au-Ir andAu-Ir-Rh nanoalloys.

PubMed

Shubin, Yury; Plyusnin, Pavel; Sharafutdinov, Marat; Makotchenko, Evgenia; Korenev, Sergey

2017-05-19

We successfully prepared face-centred cubic nanoalloys in systems of Au-Ir, Au-Rh and Au-Ir-Rh, with large bulk miscibility gaps, in one-run reactions under thermal decomposition of specially synthesised single-source precursors, namely, [AuEn 2 ][Ir(NO 2 ) 6 ], [AuEn 2 ][Ir(NO 2 ) 6 ] х [Rh(NO 2 ) 6 ] 1-х and [AuEn 2 ][Rh(NO 2 ) 6 ]. The precursors employed contain all desired metals 'mixed' at the atomic level, thus providing significant advantages for obtaining alloys. The observations using high-resolution transmission electron microscopy show that the nanoalloy structures are composed of well-dispersed aggregates of crystalline domains with a mean size of 5 ± 3 nm. Еnergy dispersive x-ray spectroscopy and x-ray powder diffraction (XRD) measurements confirm the formation of AuIr, AuRh, AuIr 0.75 Rh 0.25 , AuIr 0.50 Rh 0.50 and AuIr 0.25 Rh 0.75 metastable solid solutions. In situ high-temperature synchrotron XRD (HTXRD) was used to study the formation mechanism of nanoalloys. The observed transformations are described by the 'conversion chemistry' mechanism characterised by the primary development of particles comprising atoms of only one type, followed by a chemical reaction resulting in the final formation of a nanoalloy. The obtained metastable nanoalloys exhibit essential thermal stability. Exposure to 180 °C for 30 h does not cause any dealloying process.

Rice MEL2, the RNA recognition motif (RRM) protein, binds in vitro to meiosis-expressed genes containing U-rich RNA consensus sequences in the 3'-UTR.

PubMed

Miyazaki, Saori; Sato, Yutaka; Asano, Tomoya; Nagamura, Yoshiaki; Nonomura, Ken-Ichi

2015-10-01

Post-transcriptional gene regulation by RNA recognition motif (RRM) proteins through binding to cis-elements in the 3'-untranslated region (3'-UTR) is widely used in eukaryotes to complete various biological processes. Rice MEIOSIS ARRESTED AT LEPTOTENE2 (MEL2) is the RRM protein that functions in the transition to meiosis in proper timing. The MEL2 RRM preferentially associated with the U-rich RNA consensus, UUAGUU[U/A][U/G][A/U/G]U, dependently on sequences and proportionally to MEL2 protein amounts in vitro. The consensus sequences were located in the putative looped structures of the RNA ligand. A genome-wide survey revealed a tendency of MEL2-binding consensus appearing in 3'-UTR of rice genes. Of 249 genes that conserved the consensus in their 3'-UTR, 13 genes spatiotemporally co-expressed with MEL2 in meiotic flowers, and included several genes whose function was supposed in meiosis; such as Replication protein A and OsMADS3. The proteome analysis revealed that the amounts of small ubiquitin-related modifier-like protein and eukaryotic translation initiation factor3-like protein were dramatically altered in mel2 mutant anthers. Taken together with transcriptome and gene ontology results, we propose that the rice MEL2 is involved in the translational regulation of key meiotic genes on 3'-UTRs to achieve the faithful transition of germ cells to meiosis.

Computational Analyses of Synergism in Small Molecular Network Motifs

PubMed Central

Zhang, Yili; Smolen, Paul; Baxter, Douglas A.; Byrne, John H.

2014-01-01

Cellular functions and responses to stimuli are controlled by complex regulatory networks that comprise a large diversity of molecular components and their interactions. However, achieving an intuitive understanding of the dynamical properties and responses to stimuli of these networks is hampered by their large scale and complexity. To address this issue, analyses of regulatory networks often focus on reduced models that depict distinct, reoccurring connectivity patterns referred to as motifs. Previous modeling studies have begun to characterize the dynamics of small motifs, and to describe ways in which variations in parameters affect their responses to stimuli. The present study investigates how variations in pairs of parameters affect responses in a series of ten common network motifs, identifying concurrent variations that act synergistically (or antagonistically) to alter the responses of the motifs to stimuli. Synergism (or antagonism) was quantified using degrees of nonlinear blending and additive synergism. Simulations identified concurrent variations that maximized synergism, and examined the ways in which it was affected by stimulus protocols and the architecture of a motif. Only a subset of architectures exhibited synergism following paired changes in parameters. The approach was then applied to a model describing interlocked feedback loops governing the synthesis of the CREB1 and CREB2 transcription factors. The effects of motifs on synergism for this biologically realistic model were consistent with those for the abstract models of single motifs. These results have implications for the rational design of combination drug therapies with the potential for synergistic interactions. PMID:24651495

Identifying the scale-dependent motifs in atmospheric surface layer by ordinal pattern analysis

NASA Astrophysics Data System (ADS)

Li, Qinglei; Fu, Zuntao

2018-07-01

Ramp-like structures in various atmospheric surface layer time series have been long studied, but the presence of motifs with the finer scale embedded within larger scale ramp-like structures has largely been overlooked in the reported literature. Here a novel, objective and well-adapted methodology, the ordinal pattern analysis, is adopted to study the finer-scaled motifs in atmospheric boundary-layer (ABL) time series. The studies show that the motifs represented by different ordinal patterns take clustering properties and 6 dominated motifs out of the whole 24 motifs account for about 45% of the time series under particular scales, which indicates the higher contribution of motifs with the finer scale to the series. Further studies indicate that motif statistics are similar for both stable conditions and unstable conditions at larger scales, but large discrepancies are found at smaller scales, and the frequencies of motifs "1234" and/or "4321" are a bit higher under stable conditions than unstable conditions. Under stable conditions, there are great changes for the occurrence frequencies of motifs "1234" and "4321", where the occurrence frequencies of motif "1234" decrease from nearly 24% to 4.5% with the scale factor increasing, and the occurrence frequencies of motif "4321" change nonlinearly with the scale increasing. These great differences of dominated motifs change with scale can be taken as an indicator to quantify the flow structure changes under different stability conditions, and motif entropy can be defined just by only 6 dominated motifs to quantify this time-scale independent property of the motifs. All these results suggest that the defined scale of motifs with the finer scale should be carefully taken into consideration in the interpretation of turbulence coherent structures.

Limitations and potentials of current motif discovery algorithms

PubMed Central

Hu, Jianjun; Li, Bin; Kihara, Daisuke

2005-01-01

Computational methods for de novo identification of gene regulation elements, such as transcription factor binding sites, have proved to be useful for deciphering genetic regulatory networks. However, despite the availability of a large number of algorithms, their strengths and weaknesses are not sufficiently understood. Here, we designed a comprehensive set of performance measures and benchmarked five modern sequence-based motif discovery algorithms using large datasets generated from Escherichia coli RegulonDB. Factors that affect the prediction accuracy, scalability and reliability are characterized. It is revealed that the nucleotide and the binding site level accuracy are very low, while the motif level accuracy is relatively high, which indicates that the algorithms can usually capture at least one correct motif in an input sequence. To exploit diverse predictions from multiple runs of one or more algorithms, a consensus ensemble algorithm has been developed, which achieved 6–45% improvement over the base algorithms by increasing both the sensitivity and specificity. Our study illustrates limitations and potentials of existing sequence-based motif discovery algorithms. Taking advantage of the revealed potentials, several promising directions for further improvements are discussed. Since the sequence-based algorithms are the baseline of most of the modern motif discovery algorithms, this paper suggests substantial improvements would be possible for them. PMID:16284194

Observational Signatures Of Agn Feedback Across Cosmic Time

NASA Astrophysics Data System (ADS)

Wylezalek, Dominika

2017-06-01

While many compelling models of AGN feedback exist, there is no clear data-driven picture of how winds are launched, how they propagate through the galaxy and what impact they have on the galactic gas. Recent work suggests that AGN luminosity plays an important role. The following described projects focus on understanding the power, reach and impact of feedback processes exerted by AGN of different power. I first describe recent efforts in our group of relating feedback signatures in powerful quasars to the specific star formation rate in their host galaxies, where our results are consistent with the AGN having a `negative' impact through feedback on the galaxies' star formation history. Feedback signatures seem to be best observable in gas-rich galaxies where the coupling of the AGN-driven wind to the gas is strongest, in agreement with recent simulations. But how and where does this quenching happen? Is it accomplished through the mechanical action of jets or through nuclear winds driven by radiation pressure? Finally, I show that AGN signatures and AGN-driven winds can be easily hidden and not be apparent in the integrated spectrum of a galaxy hosting a low/intermediate-luminosity AGN. Using data from the new SDSS-IV MaNGA survey, we have developed a new AGN selection algorithm tailored to IFU data and we are uncovering a much more nuanced picture of AGN activity allowing us to discover AGN signatures at large distances from the galaxy center. This implies that large IFU surveys, such as the SDSS-IV MaNGA survey, might uncover many previously unknown AGN and feedback signatures related to them. Outflows and feedback from low- and intermediate-luminosity AGN might have been underestimated in the past but can potentially significantly contribute to the AGN/host-galaxy self-regulation.

Convergent evolution and mimicry of protein linear motifs in host-pathogen interactions.

PubMed

Chemes, Lucía Beatriz; de Prat-Gay, Gonzalo; Sánchez, Ignacio Enrique

2015-06-01

Pathogen linear motif mimics are highly evolvable elements that facilitate rewiring of host protein interaction networks. Host linear motifs and pathogen mimics differ in sequence, leading to thermodynamic and structural differences in the resulting protein-protein interactions. Moreover, the functional output of a mimic depends on the motif and domain repertoire of the pathogen protein. Regulatory evolution mediated by linear motifs can be understood by measuring evolutionary rates, quantifying positive and negative selection and performing phylogenetic reconstructions of linear motif natural history. Convergent evolution of linear motif mimics is widespread among unrelated proteins from viral, prokaryotic and eukaryotic pathogens and can also take place within individual protein phylogenies. Statistics, biochemistry and laboratory models of infection link pathogen linear motifs to phenotypic traits such as tropism, virulence and oncogenicity. In vitro evolution experiments and analysis of natural sequences suggest that changes in linear motif composition underlie pathogen adaptation to a changing environment. Copyright © 2015 Elsevier Ltd. All rights reserved.

PISMA: A Visual Representation of Motif Distribution in DNA Sequences.

PubMed

Alcántara-Silva, Rogelio; Alvarado-Hermida, Moisés; Díaz-Contreras, Gibrán; Sánchez-Barrios, Martha; Carrera, Samantha; Galván, Silvia Carolina

2017-01-01

Because the graphical presentation and analysis of motif distribution can provide insights for experimental hypothesis, PISMA aims at identifying motifs on DNA sequences, counting and showing them graphically. The motif length ranges from 2 to 10 bases, and the DNA sequences range up to 10 kb. The motif distribution is shown as a bar-code-like, as a gene-map-like, and as a transcript scheme. We obtained graphical schemes of the CpG site distribution from 91 human papillomavirus genomes. Also, we present 2 analyses: one of DNA motifs associated with either methylation-resistant or methylation-sensitive CpG islands and another analysis of motifs associated with exosome RNA secretion. PISMA is developed in Java; it is executable in any type of hardware and in diverse operating systems. PISMA is freely available to noncommercial users. The English version and the User Manual are provided in Supplementary Files 1 and 2, and a Spanish version is available at www.biomedicas.unam.mx/wp-content/software/pisma.zip and www.biomedicas.unam.mx/wp-content/pdf/manual/pisma.pdf.

Kaposi's Sarcoma-Associated Herpesvirus G-Protein-Coupled Receptor Prevents AU-Rich-Element-Mediated mRNA Decay

PubMed Central

Corcoran, Jennifer A.; Khaperskyy, Denys A.; Johnston, Benjamin P.; King, Christine A.; Cyr, David P.; Olsthoorn, Alisha V.

2012-01-01

During lytic Kaposi's sarcoma-associated herpesvirus (KSHV) infection, host gene expression is severely restricted by a process of global mRNA degradation known as host shutoff, which rededicates translational machinery to the expression of viral proteins. A subset of host mRNAs is spared from shutoff, and a number of these contain cis-acting AU-rich elements (AREs) in their 3′ untranslated regions. AREs are found in labile mRNAs encoding cytokines, growth factors, and proto-oncogenes. Activation of the p38/MK2 signal transduction pathway reverses constitutive decay of ARE-mRNAs, resulting in increased protein production. The viral G-protein-coupled receptor (vGPCR) is thought to play an important role in promoting the secretion of angiogenic molecules from KSHV-infected cells during lytic replication, but to date it has not been clear how vGPCR circumvents host shutoff. Here, we demonstrate that vGPCR activates the p38/MK2 pathway and stabilizes ARE-mRNAs, augmenting the levels of their protein products. Using MK2-deficient cells, we demonstrate that MK2 is essential for maximal vGPCR-mediated ARE-mRNA stabilization. ARE-mRNAs are normally delivered to cytoplasmic ribonucleoprotein granules known as processing bodies (PBs) for translational silencing and decay. We demonstrate that PB formation is prevented during KSHV lytic replication or in response to vGPCR-mediated activation of RhoA subfamily GTPases. Together, these data show for the first time that vGPCR impacts gene expression at the posttranscriptional level, coordinating an attack on the host mRNA degradation machinery. By suppressing ARE-mRNA turnover, vGPCR may facilitate escape of certain target mRNAs from host shutoff and allow secretion of angiogenic factors from lytically infected cells. PMID:22696654

Highly accessible AU-rich regions in 3' untranslated regions are hotspots for binding of regulatory factors.

PubMed

Plass, Mireya; Rasmussen, Simon H; Krogh, Anders

2017-04-01

Post-transcriptional regulation is regarded as one of the major processes involved in the regulation of gene expression. It is mainly performed by RNA binding proteins and microRNAs, which target RNAs and typically affect their stability. Recent efforts from the scientific community have aimed at understanding post-transcriptional regulation at a global scale by using high-throughput sequencing techniques such as cross-linking and immunoprecipitation (CLIP), which facilitates identification of binding sites of these regulatory factors. However, the diversity in the experimental procedures and bioinformatics analyses has hindered the integration of multiple datasets and thus limited the development of an integrated view of post-transcriptional regulation. In this work, we have performed a comprehensive analysis of 107 CLIP datasets from 49 different RBPs in HEK293 cells to shed light on the complex interactions that govern post-transcriptional regulation. By developing a more stringent CLIP analysis pipeline we have discovered the existence of conserved regulatory AU-rich regions in the 3'UTRs where miRNAs and RBPs that regulate several processes such as polyadenylation or mRNA stability bind. Analogous to promoters, many factors have binding sites overlapping or in close proximity in these hotspots and hence the regulation of the mRNA may depend on their relative concentrations. This hypothesis is supported by RBP knockdown experiments that alter the relative concentration of RBPs in the cell. Upon AGO2 knockdown (KD), transcripts containing "free" target sites show increased expression levels compared to those containing target sites in hotspots, which suggests that target sites within hotspots are less available for miRNAs to bind. Interestingly, these hotspots appear enriched in genes with regulatory functions such as DNA binding and RNA binding. Taken together, our results suggest that hotspots are functional regulatory elements that define an extra layer of

Insights into the Evolution of Hydroxyproline-Rich Glycoproteins from 1000 Plant Transcriptomes.

PubMed

Johnson, Kim L; Cassin, Andrew M; Lonsdale, Andrew; Wong, Gane Ka-Shu; Soltis, Douglas E; Miles, Nicholas W; Melkonian, Michael; Melkonian, Barbara; Deyholos, Michael K; Leebens-Mack, James; Rothfels, Carl J; Stevenson, Dennis W; Graham, Sean W; Wang, Xumin; Wu, Shuangxiu; Pires, J Chris; Edger, Patrick P; Carpenter, Eric J; Bacic, Antony; Doblin, Monika S; Schultz, Carolyn J

2017-06-01

The carbohydrate-rich cell walls of land plants and algae have been the focus of much interest given the value of cell wall-based products to our current and future economies. Hydroxyproline-rich glycoproteins (HRGPs), a major group of wall glycoproteins, play important roles in plant growth and development, yet little is known about how they have evolved in parallel with the polysaccharide components of walls. We investigate the origins and evolution of the HRGP superfamily, which is commonly divided into three major multigene families: the arabinogalactan proteins (AGPs), extensins (EXTs), and proline-rich proteins. Using motif and amino acid bias, a newly developed bioinformatics pipeline, we identified HRGPs in sequences from the 1000 Plants transcriptome project (www.onekp.com). Our analyses provide new insights into the evolution of HRGPs across major evolutionary milestones, including the transition to land and the early radiation of angiosperms. Significantly, data mining reveals the origin of glycosylphosphatidylinositol (GPI)-anchored AGPs in green algae and a 3- to 4-fold increase in GPI-AGPs in liverworts and mosses. The first detection of cross-linking (CL)-EXTs is observed in bryophytes, which suggests that CL-EXTs arose though the juxtaposition of preexisting SP n EXT glycomotifs with refined Y-based motifs. We also detected the loss of CL-EXT in a few lineages, including the grass family (Poaceae), that have a cell wall composition distinct from other monocots and eudicots. A key challenge in HRGP research is tracking individual HRGPs throughout evolution. Using the 1000 Plants output, we were able to find putative orthologs of Arabidopsis pollen-specific GPI-AGPs in basal eudicots. © 2017 American Society of Plant Biologists. All Rights Reserved.

Methods and statistics for combining motif match scores.

PubMed

Bailey, T L; Gribskov, M

1998-01-01

Position-specific scoring matrices are useful for representing and searching for protein sequence motifs. A sequence family can often be described by a group of one or more motifs, and an effective search must combine the scores for matching a sequence to each of the motifs in the group. We describe three methods for combining match scores and estimating the statistical significance of the combined scores and evaluate the search quality (classification accuracy) and the accuracy of the estimate of statistical significance of each. The three methods are: 1) sum of scores, 2) sum of reduced variates, 3) product of score p-values. We show that method 3) is superior to the other two methods in both regards, and that combining motif scores indeed gives better search accuracy. The MAST sequence homology search algorithm utilizing the product of p-values scoring method is available for interactive use and downloading at URL http:/(/)www.sdsc.edu/MEME.

A Monte Carlo-based framework enhances the discovery and interpretation of regulatory sequence motifs

PubMed Central

2012-01-01

Background Discovery of functionally significant short, statistically overrepresented subsequence patterns (motifs) in a set of sequences is a challenging problem in bioinformatics. Oftentimes, not all sequences in the set contain a motif. These non-motif-containing sequences complicate the algorithmic discovery of motifs. Filtering the non-motif-containing sequences from the larger set of sequences while simultaneously determining the identity of the motif is, therefore, desirable and a non-trivial problem in motif discovery research. Results We describe MotifCatcher, a framework that extends the sensitivity of existing motif-finding tools by employing random sampling to effectively remove non-motif-containing sequences from the motif search. We developed two implementations of our algorithm; each built around a commonly used motif-finding tool, and applied our algorithm to three diverse chromatin immunoprecipitation (ChIP) data sets. In each case, the motif finder with the MotifCatcher extension demonstrated improved sensitivity over the motif finder alone. Our approach organizes candidate functionally significant discovered motifs into a tree, which allowed us to make additional insights. In all cases, we were able to support our findings with experimental work from the literature. Conclusions Our framework demonstrates that additional processing at the sequence entry level can significantly improve the performance of existing motif-finding tools. For each biological data set tested, we were able to propose novel biological hypotheses supported by experimental work from the literature. Specifically, in Escherichia coli, we suggested binding site motifs for 6 non-traditional LexA protein binding sites; in Saccharomyces cerevisiae, we hypothesize 2 disparate mechanisms for novel binding sites of the Cse4p protein; and in Halobacterium sp. NRC-1, we discoverd subtle differences in a general transcription factor (GTF) binding site motif across several data sets. We

MOCCS: Clarifying DNA-binding motif ambiguity using ChIP-Seq data.

PubMed

Ozaki, Haruka; Iwasaki, Wataru

2016-08-01

As a key mechanism of gene regulation, transcription factors (TFs) bind to DNA by recognizing specific short sequence patterns that are called DNA-binding motifs. A single TF can accept ambiguity within its DNA-binding motifs, which comprise both canonical (typical) and non-canonical motifs. Clarification of such DNA-binding motif ambiguity is crucial for revealing gene regulatory networks and evaluating mutations in cis-regulatory elements. Although chromatin immunoprecipitation sequencing (ChIP-seq) now provides abundant data on the genomic sequences to which a given TF binds, existing motif discovery methods are unable to directly answer whether a given TF can bind to a specific DNA-binding motif. Here, we report a method for clarifying the DNA-binding motif ambiguity, MOCCS. Given ChIP-Seq data of any TF, MOCCS comprehensively analyzes and describes every k-mer to which that TF binds. Analysis of simulated datasets revealed that MOCCS is applicable to various ChIP-Seq datasets, requiring only a few minutes per dataset. Application to the ENCODE ChIP-Seq datasets proved that MOCCS directly evaluates whether a given TF binds to each DNA-binding motif, even if known position weight matrix models do not provide sufficient information on DNA-binding motif ambiguity. Furthermore, users are not required to provide numerous parameters or background genomic sequence models that are typically unavailable. MOCCS is implemented in Perl and R and is freely available via https://github.com/yuifu/moccs. By complementing existing motif-discovery software, MOCCS will contribute to the basic understanding of how the genome controls diverse cellular processes via DNA-protein interactions. Copyright © 2016 Elsevier Ltd. All rights reserved.

A structural-alphabet-based strategy for finding structural motifs across protein families

PubMed Central

Wu, Chih Yuan; Chen, Yao Chi; Lim, Carmay

2010-01-01

Proteins with insignificant sequence and overall structure similarity may still share locally conserved contiguous structural segments; i.e. structural/3D motifs. Most methods for finding 3D motifs require a known motif to search for other similar structures or functionally/structurally crucial residues. Here, without requiring a query motif or essential residues, a fully automated method for discovering 3D motifs of various sizes across protein families with different folds based on a 16-letter structural alphabet is presented. It was applied to structurally non-redundant proteins bound to DNA, RNA, obligate/non-obligate proteins as well as free DNA-binding proteins (DBPs) and proteins with known structures but unknown function. Its usefulness was illustrated by analyzing the 3D motifs found in DBPs. A non-specific motif was found with a ‘corner’ architecture that confers a stable scaffold and enables diverse interactions, making it suitable for binding not only DNA but also RNA and proteins. Furthermore, DNA-specific motifs present ‘only’ in DBPs were discovered. The motifs found can provide useful guidelines in detecting binding sites and computational protein redesign. PMID:20525797

CircularLogo: A lightweight web application to visualize intra-motif dependencies.

PubMed

Ye, Zhenqing; Ma, Tao; Kalmbach, Michael T; Dasari, Surendra; Kocher, Jean-Pierre A; Wang, Liguo

2017-05-22

The sequence logo has been widely used to represent DNA or RNA motifs for more than three decades. Despite its intelligibility and intuitiveness, the traditional sequence logo is unable to display the intra-motif dependencies and therefore is insufficient to fully characterize nucleotide motifs. Many methods have been developed to quantify the intra-motif dependencies, but fewer tools are available for visualization. We developed CircularLogo, a web-based interactive application, which is able to not only visualize the position-specific nucleotide consensus and diversity but also display the intra-motif dependencies. Applying CircularLogo to HNF6 binding sites and tRNA sequences demonstrated its ability to show intra-motif dependencies and intuitively reveal biomolecular structure. CircularLogo is implemented in JavaScript and Python based on the Django web framework. The program's source code and user's manual are freely available at http://circularlogo.sourceforge.net . CircularLogo web server can be accessed from http://bioinformaticstools.mayo.edu/circularlogo/index.html . CircularLogo is an innovative web application that is specifically designed to visualize and interactively explore intra-motif dependencies.

Descriptive and geoenvironmental model for Co-Cu-Au deposits in metasedimentary rocks: Chapter G in Mineral deposit models for resource assessment

USGS Publications Warehouse

Slack, John F.; Johnson, Craig A.; Causey, J. Douglas; Lund, Karen; Schulz, Klaus J.; Gray, John E.; Eppinger, Robert G.; Slack, John F.

2013-01-01

Additional geologically and compositionally similar deposits are known, but have average Co grades less than 0.1 percent. Most of these deposits contain cobalt-rich pyrite and lack appreciable amounts of distinct Co sulfide and (or) sulfarsenide minerals. Such deposits are not discussed in detail in the following sections, but these deposits may be revelant to the descriptive and genetic models presented below. Examples include the Scadding Au-Co-Cu deposit in Ontario, Canada; the Vähäjoki Co-Cu-Au deposit in Finland; the Tuolugou Co-Au deposit in Qinghai Province, China; the Lala Co-Cu-UREE deposit in Sichuan Province, China; the Guelb Moghrein Cu-Au-Co deposit in Mauritania; and the Great Australia Co-Cu, Greenmount Cu-Au-Co, and Monakoff Cu-Au-Co-UAg deposits in Queensland, Australia. Detailed information on these deposits is presented in appendix 2.

Au38(SPh)24: Au38 Protected with Aromatic Thiolate Ligands.

PubMed

Rambukwella, Milan; Burrage, Shayna; Neubrander, Marie; Baseggio, Oscar; Aprà, Edoardo; Stener, Mauro; Fortunelli, Alessandro; Dass, Amala

2017-04-06

Au 38 (SR) 24 is one of the most extensively investigated gold nanomolecules along with Au 25 (SR) 18 and Au 144 (SR) 60 . However, so far it has only been prepared using aliphatic-like ligands, where R = -SC 6 H 13 , -SC 12 H 25 and -SCH 2 CH 2 Ph. Au 38 (SCH 2 CH 2 Ph) 24 when reacted with HSPh undergoes core-size conversion to Au 36 (SPh) 24 , and existing literature suggests that Au 38 (SPh) 24 cannot be synthesized. Here, contrary to prevailing knowledge, we demonstrate that Au 38 (SPh) 24 can be prepared if the ligand exchanged conditions are optimized, under delicate conditions, without any formation of Au 36 (SPh) 24 . Conclusive evidence is presented in the form of matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), electrospray ionization mass spectra (ESI-MS) characterization, and optical spectra of Au 38 (SPh) 24 in a solid glass form showing distinct differences from that of Au 38 (S-aliphatic) 24 . Theoretical analysis confirms experimental assignment of the optical spectrum and shows that the stability of Au 38 (SPh) 24 is not negligible with respect to that of its aliphatic analogous, and contains a significant component of ligand-ligand attractive interactions. Thus, while Au 38 (SPh) 24 is stable at RT, it converts to Au 36 (SPh) 24 either on prolonged etching (longer than 2 hours) at RT or when etched at 80 °C.

Evidence of final-state suppression of high-p{_ T} hadrons in Au + Au collisions using d + Au measurements at RHIC

NASA Astrophysics Data System (ADS)

Back, B. B.; Baker, M. D.; Ballintijn, M.; Barton, D. S.; Becker, B.; Betts, R. R.; Bickley, A. A.; Bindel, R.; Busza, W.; Carroll, A.; Decowski, M. P.; García, E.; Gburek, T.; George, N.; Gulbrandsen, K.; Gushue, S.; Halliwell, C.; Hamblen, J.; Harrington, A. S.; Henderson, C.; Hofman, D. J.; Hollis, R. S.; Hołyński, R.; Holzman, B.; Iordanova, A.; Johnson, E.; Kane, J. L.; Khan, N.; Kulinich, P.; Kuo, C. M.; Lee, J. W.; Lin, W. T.; Manly, S.; Mignerey, A. C.; Nouicer, R.; Olszewski, A.; Pak, R.; Park, I. C.; Pernegger, H.; Reed, C.; Roland, C.; Roland, G.; Sagerer, J.; Sarin, P.; Sedykh, I.; Skulski, W.; Smith, C. E.; Steinberg, P.; Stephans, G. S. F.; Sukhanov, A.; Tonjes, M. B.; Trzupek, A.; Vale, C.; van Nieuwenhuizen, G. J.; Verdier, R.; Veres, G. I.; Wolfs, F. L. H.; Wosiek, B.; Woźniak, K.; Wysłouch, B.; Zhang, J.

Transverse momentum spectra of charged hadrons with pT < 6 GeV/c have been measured near mid-rapidity (0.2 < ɛ < 1.4) by the PHOBOS experiment at RHIC in Au + Au and d + Au collisions at {√ {s{NN}} = {200 GeV}}. The spectra for different collision centralities are compared to {p + ¯ {p}} collisions at the same energy. The resulting nuclear modification factor for central Au + Au collisions shows evidence of strong suppression of charged hadrons in the high-pT region (>2 GeV/c). In contrast, the d + Au nuclear modification factor exhibits no suppression of the high-pT yields. These measurements suggest a large energy loss of the high-pT particles in the highly interacting medium created in the central Au + Au collisions. The lack of suppression in d + Au collisions suggests that it is unlikely that initial state effects can explain the suppression in the central Au + Au collisions. PACS: 25.75.-q

Proteomics assisted profiling of antimicrobial peptide signatures from black pepper (Piper nigrum L.).

PubMed

Umadevi, P; Soumya, M; George, Johnson K; Anandaraj, M

2018-05-01

Plant antimicrobial peptides are the interesting source of studies in defense response as they are essential components of innate immunity which exert rapid defense response. In spite of abundant reports on the isolation of antimicrobial peptides (AMPs) from many sources, the profile of AMPs expressed/identified from single crop species under certain stress/physiological condition is still unknown. This work describes the AMP signature profile of black pepper and their expression upon Phytophthora infection using label-free quantitative proteomics strategy. The differential expression of 24 AMPs suggests that a combinatorial strategy is working in the defense network. The 24 AMP signatures belonged to the cationic, anionic, cysteine-rich and cysteine-free group. As the first report on the possible involvement of AMP signature in Phytophthora infection, our results offer a platform for further study on regulation, evolutionary importance and exploitation of theses AMPs as next generation molecules against pathogens.

Signatures support program

NASA Astrophysics Data System (ADS)

Hawley, Chadwick T.

2009-05-01

The Signatures Support Program (SSP) leverages the full spectrum of signature-related activities (collections, processing, development, storage, maintenance, and dissemination) within the Department of Defense (DOD), the intelligence community (IC), other Federal agencies, and civil institutions. The Enterprise encompasses acoustic, seismic, radio frequency, infrared, radar, nuclear radiation, and electro-optical signatures. The SSP serves the war fighter, the IC, and civil institutions by supporting military operations, intelligence operations, homeland defense, disaster relief, acquisitions, and research and development. Data centers host and maintain signature holdings, collectively forming the national signatures pool. The geographically distributed organizations are the authoritative sources and repositories for signature data; the centers are responsible for data content and quality. The SSP proactively engages DOD, IC, other Federal entities, academia, and industry to locate signatures for inclusion in the distributed national signatures pool and provides world-wide 24/7 access via the SSP application.

Design of character-based DNA barcode motif for species identification: A computational approach and its validation in fishes.

PubMed

Chakraborty, Mohua; Dhar, Bishal; Ghosh, Sankar Kumar

2017-11-01

The DNA barcodes are generally interpreted using distance-based and character-based methods. The former uses clustering of comparable groups, based on the relative genetic distance, while the latter is based on the presence or absence of discrete nucleotide substitutions. The distance-based approach has a limitation in defining a universal species boundary across the taxa as the rate of mtDNA evolution is not constant throughout the taxa. However, character-based approach more accurately defines this using a unique set of nucleotide characters. The character-based analysis of full-length barcode has some inherent limitations, like sequencing of the full-length barcode, use of a sparse-data matrix and lack of a uniform diagnostic position for each group. A short continuous stretch of a fragment can be used to resolve the limitations. Here, we observe that a 154-bp fragment, from the transversion-rich domain of 1367 COI barcode sequences can successfully delimit species in the three most diverse orders of freshwater fishes. This fragment is used to design species-specific barcode motifs for 109 species by the character-based method, which successfully identifies the correct species using a pattern-matching program. The motifs also correctly identify geographically isolated population of the Cypriniformes species. Further, this region is validated as a species-specific mini-barcode for freshwater fishes by successful PCR amplification and sequencing of the motif (154 bp) using the designed primers. We anticipate that use of such motifs will enhance the diagnostic power of DNA barcode, and the mini-barcode approach will greatly benefit the field-based system of rapid species identification. © 2017 John Wiley & Sons Ltd.

3D morphology of Au and Au@Ag nanobipyramids

NASA Astrophysics Data System (ADS)

Burgin, Julien; Florea, Ileana; Majimel, Jérôme; Dobri, Adam; Ersen, Ovidiu; Tréguer-Delapierre, Mona

2012-02-01

The morphologies of Au and Au@Ag nanobipyramids were investigated using electron tomography. The 3D reconstruction reveals that the Au bipyramids have an irregular six-fold twinning structure with highly stepped dominant {151} facets. These short steps/edges stabilized via surface adsorbed CTAB favor the growth of silver on the lateral facets leading to strong blue shifts in longitudinal plasmon surface resonance.The morphologies of Au and Au@Ag nanobipyramids were investigated using electron tomography. The 3D reconstruction reveals that the Au bipyramids have an irregular six-fold twinning structure with highly stepped dominant {151} facets. These short steps/edges stabilized via surface adsorbed CTAB favor the growth of silver on the lateral facets leading to strong blue shifts in longitudinal plasmon surface resonance. Electronic supplementary information (ESI) available. See DOI: 10.1039/c2nr11454b

Real Traceable Signatures

NASA Astrophysics Data System (ADS)

Chow, Sherman S. M.

Traceable signature scheme extends a group signature scheme with an enhanced anonymity management mechanism. The group manager can compute a tracing trapdoor which enables anyone to test if a signature is signed by a given misbehaving user, while the only way to do so for group signatures requires revealing the signer of all signatures. Nevertheless, it is not tracing in a strict sense. For all existing schemes, T tracing agents need to recollect all N' signatures ever produced and perform RN' “checks” for R revoked users. This involves a high volume of transfer and computations. Increasing T increases the degree of parallelism for tracing but also the probability of “missing” some signatures in case some of the agents are dishonest.

Atomistic Description of Thiostannate-Capped CdSe Nanocrystals: Retention of Four-Coordinate SnS4 Motif and Preservation of Cd-Rich Stoichiometry

PubMed Central

2016-01-01

Colloidal semiconductor nanocrystals (NCs) are widely studied as building blocks for novel solid-state materials. Inorganic surface functionalization, used to displace native organic capping ligands from NC surfaces, has been a major enabler of electronic solid-state devices based on colloidal NCs. At the same time, very little is known about the atomistic details of the organic-to-inorganic ligand exchange and binding motifs at the NC surface, severely limiting further progress in designing all-inorganic NCs and NC solids. Taking thiostannates (K4SnS4, K4Sn2S6, K6Sn2S7) as typical examples of chalcogenidometallate ligands and oleate-capped CdSe NCs as a model NC system, in this study we address these questions through the combined application of solution 1H NMR spectroscopy, solution and solid-state 119Sn NMR spectroscopy, far-infrared and X-ray absorption spectroscopies, elemental analysis, and by DFT modeling. We show that through the X-type oleate-to-thiostannate ligand exchange, CdSe NCs retain their Cd-rich stoichiometry, with a stoichiometric CdSe core and surface Cd adatoms serving as binding sites for terminal S atoms of the thiostannates ligands, leading to all-inorganic (CdSe)core[Cdm(Sn2S7)yK(6y-2m)]shell (taking Sn2S76– ligand as an example). Thiostannates SnS44– and Sn2S76– retain (distorted) tetrahedral SnS4 geometry upon binding to NC surface. At the same time, experiments and simulations point to lower stability of Sn2S64– (and SnS32–) in most solvents and its lower adaptability to the NC surface caused by rigid Sn2S2 rings. PMID:25597625

Noble Gas Isotopic Signatures and X-Ray and Electron Diffraction Characteristics of Tagish Lake Carbonaceous Chondrite

NASA Technical Reports Server (NTRS)

Nakamura, T.; Noguchi, T.; Zolensky, M. E.; Takaoka, N.

2001-01-01

Noble gas isotopic signatures and X-ray and electron diffraction characteristics of Tagish Lake indicate that it is a unique carbonaceous chondrite rich in saponite, Fe-Mg-Ca carbonate, primordial noble gases, and presolar grains. Additional information is contained in the original extended abstract.

SARNAclust: Semi-automatic detection of RNA protein binding motifs from immunoprecipitation data

PubMed Central

Dotu, Ivan; Adamson, Scott I.; Coleman, Benjamin; Fournier, Cyril; Ricart-Altimiras, Emma; Eyras, Eduardo

2018-01-01

RNA-protein binding is critical to gene regulation, controlling fundamental processes including splicing, translation, localization and stability, and aberrant RNA-protein interactions are known to play a role in a wide variety of diseases. However, molecular understanding of RNA-protein interactions remains limited; in particular, identification of RNA motifs that bind proteins has long been challenging, especially when such motifs depend on both sequence and structure. Moreover, although RNA binding proteins (RBPs) often contain more than one binding domain, algorithms capable of identifying more than one binding motif simultaneously have not been developed. In this paper we present a novel pipeline to determine binding peaks in crosslinking immunoprecipitation (CLIP) data, to discover multiple possible RNA sequence/structure motifs among them, and to experimentally validate such motifs. At the core is a new semi-automatic algorithm SARNAclust, the first unsupervised method to identify and deconvolve multiple sequence/structure motifs simultaneously. SARNAclust computes similarity between sequence/structure objects using a graph kernel, providing the ability to isolate the impact of specific features through the bulge graph formalism. Application of SARNAclust to synthetic data shows its capability of clustering 5 motifs at once with a V-measure value of over 0.95, while GraphClust achieves only a V-measure of 0.083 and RNAcontext cannot detect any of the motifs. When applied to existing eCLIP sets, SARNAclust finds known motifs for SLBP and HNRNPC and novel motifs for several other RBPs such as AGGF1, AKAP8L and ILF3. We demonstrate an experimental validation protocol, a targeted Bind-n-Seq-like high-throughput sequencing approach that relies on RNA inverse folding for oligo pool design, that can validate the components within the SLBP motif. Finally, we use this protocol to experimentally interrogate the SARNAclust motif predictions for protein ILF3. Our

Memetic algorithms for de novo motif-finding in biomedical sequences.

PubMed

Bi, Chengpeng

2012-09-01

The objectives of this study are to design and implement a new memetic algorithm for de novo motif discovery, which is then applied to detect important signals hidden in various biomedical molecular sequences. In this paper, memetic algorithms are developed and tested in de novo motif-finding problems. Several strategies in the algorithm design are employed that are to not only efficiently explore the multiple sequence local alignment space, but also effectively uncover the molecular signals. As a result, there are a number of key features in the implementation of the memetic motif-finding algorithm (MaMotif), including a chromosome replacement operator, a chromosome alteration-aware local search operator, a truncated local search strategy, and a stochastic operation of local search imposed on individual learning. To test the new algorithm, we compare MaMotif with a few of other similar algorithms using simulated and experimental data including genomic DNA, primary microRNA sequences (let-7 family), and transmembrane protein sequences. The new memetic motif-finding algorithm is successfully implemented in C++, and exhaustively tested with various simulated and real biological sequences. In the simulation, it shows that MaMotif is the most time-efficient algorithm compared with others, that is, it runs 2 times faster than the expectation maximization (EM) method and 16 times faster than the genetic algorithm-based EM hybrid. In both simulated and experimental testing, results show that the new algorithm is compared favorably or superior to other algorithms. Notably, MaMotif is able to successfully discover the transcription factors' binding sites in the chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-Seq) data, correctly uncover the RNA splicing signals in gene expression, and precisely find the highly conserved helix motif in the transmembrane protein sequences, as well as rightly detect the palindromic segments in the primary micro

Discovering Motifs in Biological Sequences Using the Micron Automata Processor.

PubMed

Roy, Indranil; Aluru, Srinivas

2016-01-01

Finding approximately conserved sequences, called motifs, across multiple DNA or protein sequences is an important problem in computational biology. In this paper, we consider the (l, d) motif search problem of identifying one or more motifs of length l present in at least q of the n given sequences, with each occurrence differing from the motif in at most d substitutions. The problem is known to be NP-complete, and the largest solved instance reported to date is (26,11). We propose a novel algorithm for the (l,d) motif search problem using streaming execution over a large set of non-deterministic finite automata (NFA). This solution is designed to take advantage of the micron automata processor, a new technology close to deployment that can simultaneously execute multiple NFA in parallel. We demonstrate the capability for solving much larger instances of the (l, d) motif search problem using the resources available within a single automata processor board, by estimating run-times for problem instances (39,18) and (40,17). The paper serves as a useful guide to solving problems using this new accelerator technology.

PISMA: A Visual Representation of Motif Distribution in DNA Sequences

PubMed Central

Alcántara-Silva, Rogelio; Alvarado-Hermida, Moisés; Díaz-Contreras, Gibrán; Sánchez-Barrios, Martha; Carrera, Samantha; Galván, Silvia Carolina

2017-01-01

Background: Because the graphical presentation and analysis of motif distribution can provide insights for experimental hypothesis, PISMA aims at identifying motifs on DNA sequences, counting and showing them graphically. The motif length ranges from 2 to 10 bases, and the DNA sequences range up to 10 kb. The motif distribution is shown as a bar-code–like, as a gene-map–like, and as a transcript scheme. Results: We obtained graphical schemes of the CpG site distribution from 91 human papillomavirus genomes. Also, we present 2 analyses: one of DNA motifs associated with either methylation-resistant or methylation-sensitive CpG islands and another analysis of motifs associated with exosome RNA secretion. Availability and Implementation: PISMA is developed in Java; it is executable in any type of hardware and in diverse operating systems. PISMA is freely available to noncommercial users. The English version and the User Manual are provided in Supplementary Files 1 and 2, and a Spanish version is available at www.biomedicas.unam.mx/wp-content/software/pisma.zip and www.biomedicas.unam.mx/wp-content/pdf/manual/pisma.pdf. PMID:28469418

Observational signature of high spin at the Event Horizon Telescope

NASA Astrophysics Data System (ADS)

Gralla, Samuel E.; Lupsasca, Alexandru; Strominger, Andrew

2018-04-01

We analytically compute the observational appearance of an isotropically emitting point source on a circular, equatorial orbit near the horizon of a rapidly spinning black hole. The primary image moves on a vertical line segment, in contrast to the primarily horizontal motion of the spinless case. Secondary images, also on the vertical line, display a rich caustic structure. If detected, this unique signature could serve as a `smoking gun' for a high spin black hole in nature.

Symmetry compression method for discovering network motifs.

PubMed

Wang, Jianxin; Huang, Yuannan; Wu, Fang-Xiang; Pan, Yi

2012-01-01

Discovering network motifs could provide a significant insight into systems biology. Interestingly, many biological networks have been found to have a high degree of symmetry (automorphism), which is inherent in biological network topologies. The symmetry due to the large number of basic symmetric subgraphs (BSSs) causes a certain redundant calculation in discovering network motifs. Therefore, we compress all basic symmetric subgraphs before extracting compressed subgraphs and propose an efficient decompression algorithm to decompress all compressed subgraphs without loss of any information. In contrast to previous approaches, the novel Symmetry Compression method for Motif Detection, named as SCMD, eliminates most redundant calculations caused by widespread symmetry of biological networks. We use SCMD to improve three notable exact algorithms and two efficient sampling algorithms. Results of all exact algorithms with SCMD are the same as those of the original algorithms, since SCMD is a lossless method. The sampling results show that the use of SCMD almost does not affect the quality of sampling results. For highly symmetric networks, we find that SCMD used in both exact and sampling algorithms can help get a remarkable speedup. Furthermore, SCMD enables us to find larger motifs in biological networks with notable symmetry than previously possible.

Identification of vibrational signatures from short chains of interlinked molecule-nanoparticle junctions obtained by inelastic electron tunnelling spectroscopy.

PubMed

Jafri, S H M; Löfås, H; Fransson, J; Blom, T; Grigoriev, A; Wallner, A; Ahuja, R; Ottosson, H; Leifer, K

2013-06-07

Short chains containing a series of metal-molecule-nanoparticle nanojunctions are a nano-material system with the potential to give electrical signatures close to those from single molecule experiments while enabling us to build portable devices on a chip. Inelastic electron tunnelling spectroscopy (IETS) measurements provide one of the most characteristic electrical signals of single and few molecules. In interlinked molecule-nanoparticle (NP) chains containing typically 5-7 molecules in a chain, the spectrum is expected to be a superposition of the vibrational signatures of individual molecules. We have established a stable and reproducible molecule-AuNP multi-junction by placing a few 1,8-octanedithiol (ODT) molecules onto a versatile and portable nanoparticle-nanoelectrode platform and measured for the first time vibrational molecular signatures at complex and coupled few-molecule-NP junctions. From quantum transport calculations, we model the IETS spectra and identify vibrational modes as well as the number of molecules contributing to the electron transport in the measured spectra.

Different modes of interaction by TIAR and HuR with target RNA and DNA

PubMed Central

Kim, Henry S.; Wilce, Matthew C. J.; Yoga, Yano M. K.; Pendini, Nicole R.; Gunzburg, Menachem J.; Cowieson, Nathan P.; Wilson, Gerald M.; Williams, Bryan R. G.; Gorospe, Myriam; Wilce, Jacqueline A.

2011-01-01

TIAR and HuR are mRNA-binding proteins that play important roles in the regulation of translation. They both possess three RNA recognition motifs (RRMs) and bind to AU-rich elements (AREs), with seemingly overlapping specificity. Here we show using SPR that TIAR and HuR bind to both U-rich and AU-rich RNA in the nanomolar range, with higher overall affinity for U-rich RNA. However, the higher affinity for U–rich sequences is mainly due to faster association with U-rich RNA, which we propose is a reflection of the higher probability of association. Differences between TIAR and HuR are observed in their modes of binding to RNA. TIAR is able to bind deoxy-oligonucleotides with nanomolar affinity, whereas HuR affinity is reduced to a micromolar level. Studies with U-rich DNA reveal that TIAR binding depends less on the 2′-hydroxyl group of RNA than HuR binding. Finally we show that SAXS data, recorded for the first two domains of TIAR in complex with RNA, are more consistent with a flexible, elongated shape and not the compact shape that the first two domains of Hu proteins adopt upon binding to RNA. We thus propose that these triple-RRM proteins, which compete for the same binding sites in cells, interact with their targets in fundamentally different ways. PMID:21233170

Different modes of interaction by TIAR and HuR with target RNA and DNA.

PubMed

Kim, Henry S; Wilce, Matthew C J; Yoga, Yano M K; Pendini, Nicole R; Gunzburg, Menachem J; Cowieson, Nathan P; Wilson, Gerald M; Williams, Bryan R G; Gorospe, Myriam; Wilce, Jacqueline A

2011-02-01

TIAR and HuR are mRNA-binding proteins that play important roles in the regulation of translation. They both possess three RNA recognition motifs (RRMs) and bind to AU-rich elements (AREs), with seemingly overlapping specificity. Here we show using SPR that TIAR and HuR bind to both U-rich and AU-rich RNA in the nanomolar range, with higher overall affinity for U-rich RNA. However, the higher affinity for U-rich sequences is mainly due to faster association with U-rich RNA, which we propose is a reflection of the higher probability of association. Differences between TIAR and HuR are observed in their modes of binding to RNA. TIAR is able to bind deoxy-oligonucleotides with nanomolar affinity, whereas HuR affinity is reduced to a micromolar level. Studies with U-rich DNA reveal that TIAR binding depends less on the 2'-hydroxyl group of RNA than HuR binding. Finally we show that SAXS data, recorded for the first two domains of TIAR in complex with RNA, are more consistent with a flexible, elongated shape and not the compact shape that the first two domains of Hu proteins adopt upon binding to RNA. We thus propose that these triple-RRM proteins, which compete for the same binding sites in cells, interact with their targets in fundamentally different ways.

Dynamic motifs in socio-economic networks

NASA Astrophysics Data System (ADS)

Zhang, Xin; Shao, Shuai; Stanley, H. Eugene; Havlin, Shlomo

2014-12-01

Socio-economic networks are of central importance in economic life. We develop a method of identifying and studying motifs in socio-economic networks by focusing on “dynamic motifs,” i.e., evolutionary connection patterns that, because of “node acquaintances” in the network, occur much more frequently than random patterns. We examine two evolving bi-partite networks: i) the world-wide commercial ship chartering market and ii) the ship build-to-order market. We find similar dynamic motifs in both bipartite networks, even though they describe different economic activities. We also find that “influence” and “persistence” are strong factors in the interaction behavior of organizations. When two companies are doing business with the same customer, it is highly probable that another customer who currently only has business relationship with one of these two companies, will become customer of the second in the future. This is the effect of influence. Persistence means that companies with close business ties to customers tend to maintain their relationships over a long period of time.

Distinguishing Signatures of Multipathway Conformational Transitions

NASA Astrophysics Data System (ADS)

Pierse, Christopher A.; Dudko, Olga K.

2017-02-01

The folding and binding of biomolecules into functional conformations are thought to be commonly mediated by multiple pathways rather than a unique route. Yet even in experiments where one can "see" individual conformational transitions, their stochastic nature generally precludes one from determining whether the transitions occurred through one or multiple pathways. We establish model-free, observable signatures in the response of macromolecules to force that unambiguously identify multiple pathways—even when the pathways themselves cannot be resolved. The unified analytical description reveals that, through multiple pathways, the response of molecules to external forces can be shaped in diverse ways, resulting in a rich design space for a tailored biological function already at the single-molecule level.

MicroED Structure of Au146(p-MBA)57 at Subatomic Resolution Reveals a Twinned FCC Cluster.

PubMed

Vergara, Sandra; Lukes, Dylan A; Martynowycz, Michael W; Santiago, Ulises; Plascencia-Villa, Germán; Weiss, Simon C; de la Cruz, M Jason; Black, David M; Alvarez, Marcos M; López-Lozano, Xochitl; Barnes, Christopher O; Lin, Guowu; Weissker, Hans-Christian; Whetten, Robert L; Gonen, Tamir; Yacaman, Miguel Jose; Calero, Guillermo

2017-11-16

Solving the atomic structure of metallic clusters is fundamental to understanding their optical, electronic, and chemical properties. Herein we present the structure of the largest aqueous gold cluster, Au 146 (p-MBA) 57 (p-MBA: para-mercaptobenzoic acid), solved by electron micro-diffraction (MicroED) to subatomic resolution (0.85 Å) and by X-ray diffraction at atomic resolution (1.3 Å). The 146 gold atoms may be decomposed into two constituent sets consisting of 119 core and 27 peripheral atoms. The core atoms are organized in a twinned FCC structure, whereas the surface gold atoms follow a C 2 rotational symmetry about an axis bisecting the twinning plane. The protective layer of 57 p-MBAs fully encloses the cluster and comprises bridging, monomeric, and dimeric staple motifs. Au 146 (p-MBA) 57 is the largest cluster observed exhibiting a bulk-like FCC structure as well as the smallest gold particle exhibiting a stacking fault.

MicroED structure of Au146(p-MBA)57 at subatomic resolution reveals a twinned FCC cluster

PubMed Central

Vergara, Sandra; Lukes, Dylan A.; Martynowycz, Michael W.; Santiago, Ulises; Plascencia-Villa, German; Weiss, Simon C.; de la Cruz, M. Jason; Black, David M.; Alvarez, Marcos M.; Lopez-Lozano, Xochitl; Barnes, Christopher O.; Lin, Guowu; Weissker, Hans-Christian; Whetten, Robert L.; Gonen, Tamir; Jose-Yacaman, Miguel; Calero, Guillermo

2018-01-01

Solving the atomic structure of metallic clusters is fundamental to understanding their optical, electronic, and chemical properties. Herein we present the structure of the largest aqueous gold cluster, Au146(p-MBA)57 (p-MBA: para-mercaptobenzoic acid), solved by electron diffraction (MicroED) to subatomic resolution (0.85 Å) and by X-ray diffraction at atomic resolution (1.3 Å). The 146 gold atoms may be decomposed into two constituent sets consisting of 119 core and 27 peripheral atoms. The core atoms are organized in a twinned FCC structure whereas the surface gold atoms follow a C2 rotational symmetry about an axis bisecting the twinning plane. The protective layer of 57 p-MBAs fully encloses the cluster and comprises bridging, monomeric, and dimeric staple motifs. Au146(p-MBA)57 is the largest cluster observed exhibiting a bulk-like FCC structure as well as the smallest gold particle exhibiting a stacking fault. PMID:29072840

Correlation functions of net-proton multiplicity distributions in Au + Au collisions at energies available at the BNL Relativistic Heavy Ion Collider from a multiphase transport model

NASA Astrophysics Data System (ADS)

Lin, Yufu; Chen, Lizhu; Li, Zhiming

2017-10-01

Fluctuations of conserved quantities are believed to be sensitive observables to probe the signature of the QCD phase transition and critical point. It was argued recently that measuring the genuine correlation functions (CFs) could provide cleaner information on possible nontrivial dynamics in heavy-ion collisions. With the AMPT (a multiphase transport) model, the centrality and energy dependence of various orders of CFs of net protons in Au + Au collisions at √{sN N}=7.7 , 11.5, 19.6, 27, 39, 62.4, and 200 GeV are investigated. The model results show that the number of antiprotons is important and should be taken into account in the calculation of CFs at high energy and/or in peripheral collisions. It is also found that the contribution of antiprotons is more important for higher order correlations than for lower ones. The CFs of antiprotons and mixed correlations play roles comparable to those of protons at high energies. Finally, we make comparisons between the model calculation and experimental data measured in the STAR experiment at the BNL Relativistic Heavy Ion Collider.

Identifying DNA-binding proteins using structural motifs and the electrostatic potential

PubMed Central

Shanahan, Hugh P.; Garcia, Mario A.; Jones, Susan; Thornton, Janet M.

2004-01-01

Robust methods to detect DNA-binding proteins from structures of unknown function are important for structural biology. This paper describes a method for identifying such proteins that (i) have a solvent accessible structural motif necessary for DNA-binding and (ii) a positive electrostatic potential in the region of the binding region. We focus on three structural motifs: helix–turn-helix (HTH), helix–hairpin–helix (HhH) and helix–loop–helix (HLH). We find that the combination of these variables detect 78% of proteins with an HTH motif, which is a substantial improvement over previous work based purely on structural templates and is comparable to more complex methods of identifying DNA-binding proteins. Similar true positive fractions are achieved for the HhH and HLH motifs. We see evidence of wide evolutionary diversity for DNA-binding proteins with an HTH motif, and much smaller diversity for those with an HhH or HLH motif. PMID:15356290

Finding specific RNA motifs: Function in a zeptomole world?

PubMed Central

KNIGHT, ROB; YARUS, MICHAEL

2003-01-01

We have developed a new method for estimating the abundance of any modular (piecewise) RNA motif within a longer random region. We have used this method to estimate the size of the active motifs available to modern SELEX experiments (picomoles of unique sequences) and to a plausible RNA World (zeptomoles of unique sequences: 1 zmole = 602 sequences). Unexpectedly, activities such as specific isoleucine binding are almost certainly present in zeptomoles of molecules, and even ribozymes such as self-cleavage motifs may appear (depending on assumptions about the minimal structures). The number of specified nucleotides is not the only important determinant of a motif’s rarity: The number of modules into which it is divided, and the details of this division, are also crucial. We propose three maxims for easily isolated motifs: the Maxim of Minimization, the Maxim of Multiplicity, and the Maxim of the Median. These maxims together state that selected motifs should be small and composed of as many separate, equally sized modules as possible. For evenly divided motifs with four modules, the largest accessible activity in picomole scale (1–1000 pmole) pools of length 100 is about 34 nucleotides; while for zeptomole scale (1–1000 zmole) pools it is about 20 specific nucleotides (50% probability of occurrence). This latter figure includes some ribozymes and aptamers. Consequently, an RNA metabolism apparently could have begun with only zeptomoles of RNA molecules. PMID:12554865

IndeCut evaluates performance of network motif discovery algorithms.

PubMed

Ansariola, Mitra; Megraw, Molly; Koslicki, David

2018-05-01

Genomic networks represent a complex map of molecular interactions which are descriptive of the biological processes occurring in living cells. Identifying the small over-represented circuitry patterns in these networks helps generate hypotheses about the functional basis of such complex processes. Network motif discovery is a systematic way of achieving this goal. However, a reliable network motif discovery outcome requires generating random background networks which are the result of a uniform and independent graph sampling method. To date, there has been no method to numerically evaluate whether any network motif discovery algorithm performs as intended on realistically sized datasets-thus it was not possible to assess the validity of resulting network motifs. In this work, we present IndeCut, the first method to date that characterizes network motif finding algorithm performance in terms of uniform sampling on realistically sized networks. We demonstrate that it is critical to use IndeCut prior to running any network motif finder for two reasons. First, IndeCut indicates the number of samples needed for a tool to produce an outcome that is both reproducible and accurate. Second, IndeCut allows users to choose the tool that generates samples in the most independent fashion for their network of interest among many available options. The open source software package is available at https://github.com/megrawlab/IndeCut. megrawm@science.oregonstate.edu or david.koslicki@math.oregonstate.edu. Supplementary data are available at Bioinformatics online.

SSMART: Sequence-structure motif identification for RNA-binding proteins.

PubMed

Munteanu, Alina; Mukherjee, Neelanjan; Ohler, Uwe

2018-06-11

RNA-binding proteins (RBPs) regulate every aspect of RNA metabolism and function. There are hundreds of RBPs encoded in the eukaryotic genomes, and each recognize its RNA targets through a specific mixture of RNA sequence and structure properties. For most RBPs, however, only a primary sequence motif has been determined, while the structure of the binding sites is uncharacterized. We developed SSMART, an RNA motif finder that simultaneously models the primary sequence and the structural properties of the RNA targets sites. The sequence-structure motifs are represented as consensus strings over a degenerate alphabet, extending the IUPAC codes for nucleotides to account for secondary structure preferences. Evaluation on synthetic data showed that SSMART is able to recover both sequence and structure motifs implanted into 3'UTR-like sequences, for various degrees of structured/unstructured binding sites. In addition, we successfully used SSMART on high-throughput in vivo and in vitro data, showing that we not only recover the known sequence motif, but also gain insight into the structural preferences of the RBP. Availability: SSMART is freely available at https://ohlerlab.mdc-berlin.de/software/SSMART_137/. Supplementary data are available at Bioinformatics online.

Assessing local structure motifs using order parameters for motif recognition, interstitial identification, and diffusion path characterization

NASA Astrophysics Data System (ADS)

Zimmermann, Nils E. R.; Horton, Matthew K.; Jain, Anubhav; Haranczyk, Maciej

2017-11-01

Structure-property relationships form the basis of many design rules in materials science, including synthesizability and long-term stability of catalysts, control of electrical and optoelectronic behavior in semiconductors as well as the capacity of and transport properties in cathode materials for rechargeable batteries. The immediate atomic environments (i.e., the first coordination shells) of a few atomic sites are often a key factor in achieving a desired property. Some of the most frequently encountered coordination patterns are tetrahedra, octahedra, body and face-centered cubic as well as hexagonal closed packed-like environments. Here, we showcase the usefulness of local order parameters to identify these basic structural motifs in inorganic solid materials by developing classification criteria. We introduce a systematic testing framework, the Einstein crystal test rig, that probes the response of order parameters to distortions in perfect motifs to validate our approach. Subsequently, we highlight three important application cases. First, we map basic crystal structure information of a large materials database in an intuitive manner by screening the Materials Project (MP) database (61,422 compounds) for element-specific motif distributions. Second, we use the structure-motif recognition capabilities to automatically find interstitials in metals, semiconductor, and insulator materials. Our Interstitialcy Finding Tool (InFiT) facilitates high-throughput screenings of defect properties. Third, the order parameters are reliable and compact quantitative structure descriptors for characterizing diffusion hops of intercalants as our example of magnesium in MnO2-spinel indicates. Finally, the tools developed in our work are readily and freely available as software implementations in the pymatgen library, and we expect them to be further applied to machine-learning approaches for emerging applications in materials science.

[Conserved motifs in voltage sensing proteins].

PubMed

Wang, Chang-He; Xie, Zhen-Li; Lv, Jian-Wei; Yu, Zhi-Dan; Shao, Shu-Li

2012-08-25

This paper was aimed to study conserved motifs of voltage sensing proteins (VSPs) and establish a voltage sensing model. All VSPs were collected from the Uniprot database using a comprehensive keyword search followed by manual curation, and the results indicated that there are only two types of known VSPs, voltage gated ion channels and voltage dependent phosphatases. All the VSPs have a common domain of four helical transmembrane segments (TMS, S1-S4), which constitute the voltage sensing module of the VSPs. The S1 segment was shown to be responsible for membrane targeting and insertion of these proteins, while S2-S4 segments, which can sense membrane potential, for protein properties. Conserved motifs/residues and their functional significance of each TMS were identified using profile-to-profile sequence alignments. Conserved motifs in these four segments are strikingly similar for all VSPs, especially, the conserved motif [RK]-X(2)-R-X(2)-R-X(2)-[RK] was presented in all the S4 segments, with positively charged arginine (R) alternating with two hydrophobic or uncharged residues. Movement of these arginines across the membrane electric field is the core mechanism by which the VSPs detect changes in membrane potential. The negatively charged aspartate (D) in the S3 segment is universally conserved in all the VSPs, suggesting that the aspartate residue may be involved in voltage sensing properties of VSPs as well as the electrostatic interactions with the positively charged residues in the S4 segment, which may enhance the thermodynamic stability of the S4 segments in plasma membrane.

Identification of the sequence motif of glycoside hydrolase 13 family members

PubMed Central

Kumar, Vikash

2011-01-01

A bioinformatics analysis of sequences of enzymes of the glycoside hydrolase (GH) 13 family members such as α-amylase, cyclodextrin glycosyltransferase (CGTase), branching enzyme and cyclomaltodextrinase has been carried out in order to find out the sequence motifs that govern the reactions specificities of these enzymes by using hidden Markov model (HMM) profile. This analysis suggests the existence of such sequence motifs and residues of these motifs constituting the −1 to +3 catalytic subsites of the enzyme. Hence, by introducing mutations in the residues of these four subsites, one can change the reaction specificities of the enzymes. In general it has been observed that α -amylase sequence motif have low sequence conservation than rest of the motifs of the GH13 family members. PMID:21544166

Composite Structural Motifs of Binding Sites for Delineating Biological Functions of Proteins

PubMed Central

Kinjo, Akira R.; Nakamura, Haruki

2012-01-01

Most biological processes are described as a series of interactions between proteins and other molecules, and interactions are in turn described in terms of atomic structures. To annotate protein functions as sets of interaction states at atomic resolution, and thereby to better understand the relation between protein interactions and biological functions, we conducted exhaustive all-against-all atomic structure comparisons of all known binding sites for ligands including small molecules, proteins and nucleic acids, and identified recurring elementary motifs. By integrating the elementary motifs associated with each subunit, we defined composite motifs that represent context-dependent combinations of elementary motifs. It is demonstrated that function similarity can be better inferred from composite motif similarity compared to the similarity of protein sequences or of individual binding sites. By integrating the composite motifs associated with each protein function, we define meta-composite motifs each of which is regarded as a time-independent diagrammatic representation of a biological process. It is shown that meta-composite motifs provide richer annotations of biological processes than sequence clusters. The present results serve as a basis for bridging atomic structures to higher-order biological phenomena by classification and integration of binding site structures. PMID:22347478

Genome-Wide Prediction of the Polymorphic Ser Gene Family in Tetrahymena thermophila Based on Motif Analysis

PubMed Central

Ponsuwanna, Patrath; Kümpornsin, Krittikorn; Chookajorn, Thanat

2014-01-01

Even though antigenic variation is employed among parasitic protozoa for host immune evasion, Tetrahymena thermophila, a free-living ciliate, can also change its surface protein antigens. These cysteine-rich glycosylphosphatidylinositol (GPI)-linked surface proteins are encoded by a family of polymorphic Ser genes. Despite the availability of T. thermophila genome, a comprehensive analysis of the Ser family is limited by its high degree of polymorphism. In order to overcome this problem, a new approach was adopted by searching for Ser candidates with common motif sequences, namely length-specific repetitive cysteine pattern and GPI anchor site. The candidate genes were phylogenetically compared with the previously identified Ser genes and classified into subtypes. Ser candidates were often found to be located as tandem arrays of the same subtypes on several chromosomal scaffolds. Certain Ser candidates located in the same chromosomal arrays were transcriptionally expressed at specific T. thermophila developmental stages. These Ser candidates selected by the motif analysis approach can form the foundation for a systematic identification of the entire Ser gene family, which will contribute to the understanding of their function and the basis of T. thermophila antigenic variation. PMID:25133747

A motif detection and classification method for peptide sequences using genetic programming.

PubMed

Tomita, Yasuyuki; Kato, Ryuji; Okochi, Mina; Honda, Hiroyuki

2008-08-01

An exploration of common rules (property motifs) in amino acid sequences has been required for the design of novel sequences and elucidation of the interactions between molecules controlled by the structural or physical environment. In the present study, we developed a new method to search property motifs that are common in peptide sequence data. Our method comprises the following two characteristics: (i) the automatic determination of the position and length of common property motifs by calculating the physicochemical similarity of amino acids, and (ii) the quick and effective exploration of motif candidates that discriminates the positives and negatives by the introduction of genetic programming (GP). Our method was evaluated by two types of model data sets. First, the intentionally buried property motifs were searched in the artificially derived peptide data containing intentionally buried property motifs. As a result, the expected property motifs were correctly extracted by our algorithm. Second, the peptide data that interact with MHC class II molecules were analyzed as one of the models of biologically active peptides with buried motifs in various lengths. Twofold MHC class II binding peptides were identified with the rule using our method, compared to the existing scoring matrix method. In conclusion, our GP based motif searching approach enabled to obtain knowledge of functional aspects of the peptides without any prior knowledge.

[Au]/[Ag]-catalysed expedient synthesis of branched heneicosafuranosyl arabinogalactan motif of Mycobacterium tuberculosis cell wall

NASA Astrophysics Data System (ADS)

Thadke, Shivaji A.; Mishra, Bijoyananda; Islam, Maidul; Pasari, Sandip; Manmode, Sujit; Rao, Boddu Venkateswara; Neralkar, Mahesh; Shinde, Ganesh P.; Walke, Gulab; Hotha, Srinivas

2017-01-01

Emergence of multidrug-resistant and extreme-drug-resistant strains of Mycobacterium tuberculosis (MTb) can cause serious socioeconomic burdens. Arabinogalactan present on the cellular envelope of MTb is unique and is required for its survival; access to arabinogalactan is essential for understanding the biosynthetic machinery that assembles it. Isolation from Nature is a herculean task and, as a result, chemical synthesis is the most sought after technique. Here we report a convergent synthesis of branched heneicosafuranosyl arabinogalactan (HAG) of MTb. Key furanosylations are performed using [Au]/[Ag] catalysts. The synthesis of HAG is achieved by the repetitive use of three reactions namely 1,2-trans furanoside synthesis by propargyl 1,2-orthoester donors, unmasking of silyl ether, and conversion of n-pentenyl furanosides into 1,2-orthoesters. Synthesis of HAG is achieved in 47 steps (with an overall yield of 0.09%) of which 21 are installation of furanosidic linkages in a stereoselective manner.

Mining for class-specific motifs in protein sequence classification

PubMed Central

2013-01-01

Background In protein sequence classification, identification of the sequence motifs or n-grams that can precisely discriminate between classes is a more interesting scientific question than the classification itself. A number of classification methods aim at accurate classification but fail to explain which sequence features indeed contribute to the accuracy. We hypothesize that sequences in lower denominations (n-grams) can be used to explore the sequence landscape and to identify class-specific motifs that discriminate between classes during classification. Discriminative n-grams are short peptide sequences that are highly frequent in one class but are either minimally present or absent in other classes. In this study, we present a new substitution-based scoring function for identifying discriminative n-grams that are highly specific to a class. Results We present a scoring function based on discriminative n-grams that can effectively discriminate between classes. The scoring function, initially, harvests the entire set of 4- to 8-grams from the protein sequences of different classes in the dataset. Similar n-grams of the same size are combined to form new n-grams, where the similarity is defined by positive amino acid substitution scores in the BLOSUM62 matrix. Substitution has resulted in a large increase in the number of discriminatory n-grams harvested. Due to the unbalanced nature of the dataset, the frequencies of the n-grams are normalized using a dampening factor, which gives more weightage to the n-grams that appear in fewer classes and vice-versa. After the n-grams are normalized, the scoring function identifies discriminative 4- to 8-grams for each class that are frequent enough to be above a selection threshold. By mapping these discriminative n-grams back to the protein sequences, we obtained contiguous n-grams that represent short class-specific motifs in protein sequences. Our method fared well compared to an existing motif finding method known as

Messenger Observations Inside 1 AU of Low-Frequency Magnetic Waves due to Inner Source Pickup Protons

NASA Astrophysics Data System (ADS)

Smith, C. W.; Argall, M. R.; Schwadron, N.; Joyce, C.; Isenberg, P. A.; Vasquez, B. J.; Korth, H.; Anderson, B. J.

2017-12-01

Wave excitation by pickup protons inside 1 AU have not been previously reported. Waves excited by pickup protons have a characteristic signature, a spectral peak at and above the proton gyrofrequency, that demonstrates a significant lack of particle energization beyond the initial pickup proton energy combined with pitch-angle scattering. Interstellar Hydrogen atoms cannot penetrate significantly inside about 3.5 AU due to loss of these atoms through ionization. Since the waves reported here, which are observed by the Messenger spacecraft during the cruise phase to Mercury, are not seen near the Mercury and Venus planetary encounters and there is no evidence of low-frequency waves that would indicate proximity to comets, we conclude that these waves originate from pickup protons created by the interaction of solar wind with dust relatively close to the Sun, inside 0.4 AU (Schwadron et al. 2000; Schwadron & Geiss 2000). This is the so-called inner source of pickup protons. We will present our analyses of these wave observations.Schwadron et al., J. Geophys. Res., 105, 7465, 2000.Schwadron & Geiss, J. Geophys. Res., 10, 7473, 2000.

Rich variety of substrates for surface enhanced Raman spectroscopy

NASA Astrophysics Data System (ADS)

Nguyen, Bich Ha; Hieu Nguyen, Van; Nhung Tran, Hong

2016-09-01

The efficiency of the application of surface enhanced Raman spectroscopy (SERS) technique to each specified purpose significantly depends on the choice of the SERS substrate with an appropriate structure as well as on its performance. Until the present time a rich variety of SERS substrates was fabricated. They can be classified according to their structures. The present work is a review of main types of SERS substrates for using in the trace analysis application. They can be classified into 4 groups: (1) Substrates using gold nanoparticles (AuNPs) with spherical shape such as colloidal AuNPs, AuNPs fabricated by pulsed laser deposition, by sputtering or by capillary force assembly (CFA), substrates fabricated by electrospinning technique, substrates using metallic nanoparticle arrays fabricated by electron beam lithography combined with CFA method, substrates using silver nanoparticle (AgNP) arrays grain by chemical seeded method, substrates with tunable surface plasmon resonance, substrates based on precies subnanometer plasmonic junctions within AuNP assemblies, substrates fabricated by simultaneously immobilizing both AuNPs and AgNPs on the same glass sides etc. (2) Substrates using nanostructures with non-spherical shapes such as gold nanowire (NW), or highly anisotropic nickel NW together with large area, free-standing carpets, substrates with obviously angular, quasi-vertically aligned cuboid-shaped TiO2 NW arrays decorated with AgNPs, substrates using gold nanoprism monolayer films, substrates using silver nanocube dimmers or monodisperse close-packed gold nanotriangle monolayers. (3) Substrates using multiparticle complex nanostructure such as nanoparticle cluster arrays, gold nanoflowers and nanodendrites. (4) Flexible substrate such as paper-based swab with gold nanorods, adhesive polymer tapes fabricated by inkjet printing method and flexible and adhesive SERS tapes fabricated by decorating AuNPs via the conventional drop-dry method.

New ligand platforms featuring boron-rich clusters as organomimetic substituents*,**

PubMed Central

Spokoyny, Alexander M.

2013-01-01

200 years of research with carbon-rich molecules have shaped the development of modern chemistry. Research pertaining to the chemistry of boron-rich species has historically trailed behind its more distinguished neighbor (carbon) in the periodic table. Notably, a potentially rich and, in many cases, unmatched field of coordination chemistry using boronrich clusters remains fundamentally underdeveloped. Our work has been devoted to examining several basic concepts related to the functionalization of icosahedral boron-rich clusters and their use as ligands, aimed at designing fundamentally new hybrid molecular motifs and materials. Particularly interesting are icosahedral carboranes, which can be regarded as 3D analogs of benzene. These species comprise a class of boron-rich clusters that were discovered in the 1950s during the “space race” while researchers were developing energetic materials for rocket fuels. Ultimately, the unique chemical and physical properties of carborane species, such as rigidity, indefinite stability to air and moisture, and 3D aromaticity, may allow one to access a set of properties not normally available in carbon-based chemistry. While technically these species are considered as inorganic clusters, the chemical properties they possess make these boron-rich species suitable for replacing and/or altering structural and functional features of the organic and organometallic molecules—a phenomenon best described as “organomimetic”. Aside from purely fundamental features associated with the organomimetic chemistry of icosahedral carboranes, their use can also provide new avenues in the development of systems relevant to solving current problems associated with energy production, storage, and conversion. PMID:24311823

A computational approach to candidate gene prioritization for X-linked mental retardation using annotation-based binary filtering and motif-based linear discriminatory analysis

PubMed Central

2011-01-01

Background Several computational candidate gene selection and prioritization methods have recently been developed. These in silico selection and prioritization techniques are usually based on two central approaches - the examination of similarities to known disease genes and/or the evaluation of functional annotation of genes. Each of these approaches has its own caveats. Here we employ a previously described method of candidate gene prioritization based mainly on gene annotation, in accompaniment with a technique based on the evaluation of pertinent sequence motifs or signatures, in an attempt to refine the gene prioritization approach. We apply this approach to X-linked mental retardation (XLMR), a group of heterogeneous disorders for which some of the underlying genetics is known. Results The gene annotation-based binary filtering method yielded a ranked list of putative XLMR candidate genes with good plausibility of being associated with the development of mental retardation. In parallel, a motif finding approach based on linear discriminatory analysis (LDA) was employed to identify short sequence patterns that may discriminate XLMR from non-XLMR genes. High rates (>80%) of correct classification was achieved, suggesting that the identification of these motifs effectively captures genomic signals associated with XLMR vs. non-XLMR genes. The computational tools developed for the motif-based LDA is integrated into the freely available genomic analysis portal Galaxy (http://main.g2.bx.psu.edu/). Nine genes (APLN, ZC4H2, MAGED4, MAGED4B, RAP2C, FAM156A, FAM156B, TBL1X, and UXT) were highlighted as highly-ranked XLMR methods. Conclusions The combination of gene annotation information and sequence motif-orientated computational candidate gene prediction methods highlight an added benefit in generating a list of plausible candidate genes, as has been demonstrated for XLMR. Reviewers: This article was reviewed by Dr Barbara Bardoni (nominated by Prof Juergen Brosius

Secretome weaponries of Cochliobolus lunatus interacting with potato leaf at different temperature regimes reveal a CL[xxxx]LHM - motif

PubMed Central

2014-01-01

Background Plant and animal pathogenic fungus Cochliobolus lunatus cause great economic damages worldwide every year. C. lunatus displays an increased temperature dependent-virulence to a wide range of hosts. Nonetheless, this phenomenon is poorly understood due to lack of insights on the coordinated secretome weaponries produced by C. lunatus under heat-stress conditions on putative hosts. To understand the mechanism better, we dissected the secretome of C. lunatus interacting with potato (Solanum tuberosum L.) leaf at different temperature regimes. Results C. lunatus produced melanized colonizing hyphae in and on potato leaf, finely modulated the ambient pH as a function of temperature and secreted diverse set of proteins. Using two dimensional gel electrophoresis (2-D) and mass spectrometry (MS) technology, we observed discrete secretomes at 20°C, 28°C and 38°C. A total of 21 differentially expressed peptide spots and 10 unique peptide spots (that did not align on the gels) matched with 28 unique protein models predicted from C. lunatus m118 v.2 genome peptides. Furthermore, C. lunatus secreted peptides via classical and non-classical pathways related to virulence, proteolysis, nucleic acid metabolism, carbohydrate metabolism, heat stress, signal trafficking and some with unidentified catalytic domains. Conclusions We have identified a set of 5 soluble candidate effectors of unknown function from C. lunatus secretome weaponries against potato crop at different temperature regimes. Our findings demonstrate that C. lunatus has a repertoire of signature secretome which mediates thermo-pathogenicity and share a leucine rich “CL[xxxx]LHM”-motif. Considering the rapidly evolving temperature dependent-virulence and host diversity of C. lunatus, this data will be useful for designing new protection strategies. PMID:24650331

Secretome weaponries of Cochliobolus lunatus interacting with potato leaf at different temperature regimes reveal a CL[xxxx]LHM - motif.

PubMed

Louis, Bengyella; Waikhom, Sayanika Devi; Roy, Pranab; Bhardwaj, Pardeep Kumar; Singh, Mohendro Wakambam; Goyari, Sailendra; Sharma, Chandradev K; Talukdar, Narayan Chandra

2014-03-20

Plant and animal pathogenic fungus Cochliobolus lunatus cause great economic damages worldwide every year. C. lunatus displays an increased temperature dependent-virulence to a wide range of hosts. Nonetheless, this phenomenon is poorly understood due to lack of insights on the coordinated secretome weaponries produced by C. lunatus under heat-stress conditions on putative hosts. To understand the mechanism better, we dissected the secretome of C. lunatus interacting with potato (Solanum tuberosum L.) leaf at different temperature regimes. C. lunatus produced melanized colonizing hyphae in and on potato leaf, finely modulated the ambient pH as a function of temperature and secreted diverse set of proteins. Using two dimensional gel electrophoresis (2-D) and mass spectrometry (MS) technology, we observed discrete secretomes at 20°C, 28°C and 38°C. A total of 21 differentially expressed peptide spots and 10 unique peptide spots (that did not align on the gels) matched with 28 unique protein models predicted from C. lunatus m118 v.2 genome peptides. Furthermore, C. lunatus secreted peptides via classical and non-classical pathways related to virulence, proteolysis, nucleic acid metabolism, carbohydrate metabolism, heat stress, signal trafficking and some with unidentified catalytic domains. We have identified a set of 5 soluble candidate effectors of unknown function from C. lunatus secretome weaponries against potato crop at different temperature regimes. Our findings demonstrate that C. lunatus has a repertoire of signature secretome which mediates thermo-pathogenicity and share a leucine rich "CL[xxxx]LHM"-motif. Considering the rapidly evolving temperature dependent-virulence and host diversity of C. lunatus, this data will be useful for designing new protection strategies.

Modeling protein homopolymeric repeats: possible polyglutamine structural motifs for Huntington's disease.

PubMed

Lathrop, R H; Casale, M; Tobias, D J; Marsh, J L; Thompson, L M

1998-01-01

We describe a prototype system (Poly-X) for assisting an expert user in modeling protein repeats. Poly-X reduces the large number of degrees of freedom required to specify a protein motif in complete atomic detail. The result is a small number of parameters that are easily understood by, and under the direct control of, a domain expert. The system was applied to the polyglutamine (poly-Q) repeat in the first exon of huntingtin, the gene implicated in Huntington's disease. We present four poly-Q structural motifs: two poly-Q beta-sheet motifs (parallel and antiparallel) that constitute plausible alternatives to a similar previously published poly-Q beta-sheet motif, and two novel poly-Q helix motifs (alpha-helix and pi-helix). To our knowledge, helical forms of polyglutamine have not been proposed before. The motifs suggest that there may be several plausible aggregation structures for the intranuclear inclusion bodies which have been found in diseased neurons, and may help in the effort to understand the structural basis for Huntington's disease.

Interstaple Dithiol Cross-Linking in Au(25)(SR)(18) Nanomolecules: A Combined Mass Spectrometric and Computational Study

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

Jiang, Deen; Dass, Amala; Tschumper, Gregory

2011-01-01

A systematic study of cross-linking chemistry of the Au{sub 25}(SR){sub 18} nanomolecule by dithiols of varying chain length, HS-(CH2)n-SH where n = 2, 3, 4, 5, and 6, is presented here. Monothiolated Au{sub 25} has six [RSAuSRAuSR] staple motifs on its surface, and MALDI mass spectrometry data of the ligand exchanged clusters show that propane (C3) and butane (C4) dithiols have ideal chain lengths for interstaple cross-linking and that up to six C3 or C4 dithiols can be facilely exchanged onto the cluster surface. Propanedithiol predominately exchanges with two monothiols at a time, making cross-linking bridges, while butanedithiol can exchangemore » with either one or two monothiols at a time. The extent of cross-linking can be controlled by the Au{sub 25}(SR){sub 18} to dithiol ratio, the reaction time of ligand exchange, or the addition of a hydrophobic tail to the dithiol. MALDI MS suggests that during ethane (C2) dithiol exchange, two ethanedithiols become connected by a disulfide bond; this result is supported by density functional theory (DFT) prediction of the optimal chain length for the intrastaple coupling. Both optical absorption spectroscopy and DFT computations show that the electronic structure of the Au{sub 25} nanomolecule retains its main features after exchange of up to eight monothiol ligands.« less

Enrichment of Circular Code Motifs in the Genes of the Yeast Saccharomyces cerevisiae.

PubMed

Michel, Christian J; Ngoune, Viviane Nguefack; Poch, Olivier; Ripp, Raymond; Thompson, Julie D

2017-12-03

A set X of 20 trinucleotides has been found to have the highest average occurrence in the reading frame, compared to the two shifted frames, of genes of bacteria, archaea, eukaryotes, plasmids and viruses. This set X has an interesting mathematical property, since X is a maximal C3 self-complementary trinucleotide circular code. Furthermore, any motif obtained from this circular code X has the capacity to retrieve, maintain and synchronize the original (reading) frame. Since 1996, the theory of circular codes in genes has mainly been developed by analysing the properties of the 20 trinucleotides of X, using combinatorics and statistical approaches. For the first time, we test this theory by analysing the X motifs, i.e., motifs from the circular code X, in the complete genome of the yeast Saccharomyces cerevisiae . Several properties of X motifs are identified by basic statistics (at the frequency level), and evaluated by comparison to R motifs, i.e., random motifs generated from 30 different random codes R. We first show that the frequency of X motifs is significantly greater than that of R motifs in the genome of S. cerevisiae . We then verify that no significant difference is observed between the frequencies of X and R motifs in the non-coding regions of S. cerevisiae , but that the occurrence number of X motifs is significantly higher than R motifs in the genes (protein-coding regions). This property is true for all cardinalities of X motifs (from 4 to 20) and for all 16 chromosomes. We further investigate the distribution of X motifs in the three frames of S. cerevisiae genes and show that they occur more frequently in the reading frame, regardless of their cardinality or their length. Finally, the ratio of X genes, i.e., genes with at least one X motif, to non-X genes, in the set of verified genes is significantly different to that observed in the set of putative or dubious genes with no experimental evidence. These results, taken together, represent the first

SLiMSearch 2.0: biological context for short linear motifs in proteins

PubMed Central

Davey, Norman E.; Haslam, Niall J.; Shields, Denis C.

2011-01-01

Short, linear motifs (SLiMs) play a critical role in many biological processes. The SLiMSearch 2.0 (Short, Linear Motif Search) web server allows researchers to identify occurrences of a user-defined SLiM in a proteome, using conservation and protein disorder context statistics to rank occurrences. User-friendly output and visualizations of motif context allow the user to quickly gain insight into the validity of a putatively functional motif occurrence. For each motif occurrence, overlapping UniProt features and annotated SLiMs are displayed. Visualization also includes annotated multiple sequence alignments surrounding each occurrence, showing conservation and protein disorder statistics in addition to known and predicted SLiMs, protein domains and known post-translational modifications. In addition, enrichment of Gene Ontology terms and protein interaction partners are provided as indicators of possible motif function. All web server results are available for download. Users can search motifs against the human proteome or a subset thereof defined by Uniprot accession numbers or GO term. The SLiMSearch server is available at: http://bioware.ucd.ie/slimsearch2.html. PMID:21622654

Assessing Local Structure Motifs Using Order Parameters for Motif Recognition, Interstitial Identification, and Diffusion Path Characterization

DOE PAGES

Zimmermann, Nils E. R.; Horton, Matthew K.; Jain, Anubhav; ...

2017-11-13

Structure–property relationships form the basis of many design rules in materials science, including synthesizability and long-term stability of catalysts, control of electrical and optoelectronic behavior in semiconductors, as well as the capacity of and transport properties in cathode materials for rechargeable batteries. The immediate atomic environments (i.e., the first coordination shells) of a few atomic sites are often a key factor in achieving a desired property. Some of the most frequently encountered coordination patterns are tetrahedra, octahedra, body and face-centered cubic as well as hexagonal close packed-like environments. Here, we showcase the usefulness of local order parameters to identify thesemore » basic structural motifs in inorganic solid materials by developing classification criteria. We introduce a systematic testing framework, the Einstein crystal test rig, that probes the response of order parameters to distortions in perfect motifs to validate our approach. Subsequently, we highlight three important application cases. First, we map basic crystal structure information of a large materials database in an intuitive manner by screening the Materials Project (MP) database (61,422 compounds) for element-specific motif distributions. Second, we use the structure-motif recognition capabilities to automatically find interstitials in metals, semiconductor, and insulator materials. Our Interstitialcy Finding Tool (InFiT) facilitates high-throughput screenings of defect properties. Third, the order parameters are reliable and compact quantitative structure descriptors for characterizing diffusion hops of intercalants as our example of magnesium in MnO 2-spinel indicates. Finally, the tools developed in our work are readily and freely available as software implementations in the pymatgen library, and we expect them to be further applied to machine-learning approaches for emerging applications in materials science.« less

Assessing Local Structure Motifs Using Order Parameters for Motif Recognition, Interstitial Identification, and Diffusion Path Characterization

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

Zimmermann, Nils E. R.; Horton, Matthew K.; Jain, Anubhav

Structure–property relationships form the basis of many design rules in materials science, including synthesizability and long-term stability of catalysts, control of electrical and optoelectronic behavior in semiconductors, as well as the capacity of and transport properties in cathode materials for rechargeable batteries. The immediate atomic environments (i.e., the first coordination shells) of a few atomic sites are often a key factor in achieving a desired property. Some of the most frequently encountered coordination patterns are tetrahedra, octahedra, body and face-centered cubic as well as hexagonal close packed-like environments. Here, we showcase the usefulness of local order parameters to identify thesemore » basic structural motifs in inorganic solid materials by developing classification criteria. We introduce a systematic testing framework, the Einstein crystal test rig, that probes the response of order parameters to distortions in perfect motifs to validate our approach. Subsequently, we highlight three important application cases. First, we map basic crystal structure information of a large materials database in an intuitive manner by screening the Materials Project (MP) database (61,422 compounds) for element-specific motif distributions. Second, we use the structure-motif recognition capabilities to automatically find interstitials in metals, semiconductor, and insulator materials. Our Interstitialcy Finding Tool (InFiT) facilitates high-throughput screenings of defect properties. Third, the order parameters are reliable and compact quantitative structure descriptors for characterizing diffusion hops of intercalants as our example of magnesium in MnO 2-spinel indicates. Finally, the tools developed in our work are readily and freely available as software implementations in the pymatgen library, and we expect them to be further applied to machine-learning approaches for emerging applications in materials science.« less

Detecting DNA regulatory motifs by incorporating positional trendsin information content

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

Kechris, Katherina J.; van Zwet, Erik; Bickel, Peter J.

2004-05-04

On the basis of the observation that conserved positions in transcription factor binding sites are often clustered together, we propose a simple extension to the model-based motif discovery methods. We assign position-specific prior distributions to the frequency parameters of the model, penalizing deviations from a specified conservation profile. Examples with both simulated and real data show that this extension helps discover motifs as the data become noisier or when there is a competing false motif.

Unfolding Kinetics of the Human Telomere i-Motif Under a 10 pN Force Imposed by the α-Hemolysin Nanopore Identify Transient Folded-State Lifetimes at Physiological pH.

PubMed

Ding, Yun; Fleming, Aaron M; He, Lidong; Burrows, Cynthia J

2015-07-22

Cytosine (C)-rich DNA can adopt i-motif folds under acidic conditions, with the human telomere i-motif providing a well-studied example. The dimensions of this i-motif are appropriate for capture in the nanocavity of the α-hemolysin (α-HL) protein pore under an electrophoretic force. Interrogation of the current vs time (i-t) traces when the i-motif interacts with α-HL identified characteristic signals that were pH dependent. These features were evaluated from pH 5.0 to 7.2, a region surrounding the transition pH of the i-motif (6.1). When the i-motif without polynucleotide tails was studied at pH 5.0, the folded structure entered the nanocavity of α-HL from either the top or bottom face to yield characteristic current patterns. Addition of a 5' 25-mer poly-2'-deoxyadensosine tail allowed capture of the i-motif from the unfolded terminus, and this was used to analyze the pH dependency of unfolding. At pH values below the transition point, only folded strands were observed, and when the pH was increased above the transition pH, the number of folded events decreased, while the unfolded events increased. At pH 6.8 and 7.2 4% and 2% of the strands were still folded, respectively. The lifetimes for the folded states at pH 6.8 and 7.2 were 21 and 9 ms, respectively, at 160 mV electrophoretic force. These lifetimes are sufficiently long to affect enzymes operating on DNA. Furthermore, these transient lifetimes are readily obtained using the α-HL nanopore, a feature that is not easily achievable by other methods.

Highly accessible AU-rich regions in 3’ untranslated regions are hotspots for binding of regulatory factors

PubMed Central

2017-01-01

Post-transcriptional regulation is regarded as one of the major processes involved in the regulation of gene expression. It is mainly performed by RNA binding proteins and microRNAs, which target RNAs and typically affect their stability. Recent efforts from the scientific community have aimed at understanding post-transcriptional regulation at a global scale by using high-throughput sequencing techniques such as cross-linking and immunoprecipitation (CLIP), which facilitates identification of binding sites of these regulatory factors. However, the diversity in the experimental procedures and bioinformatics analyses has hindered the integration of multiple datasets and thus limited the development of an integrated view of post-transcriptional regulation. In this work, we have performed a comprehensive analysis of 107 CLIP datasets from 49 different RBPs in HEK293 cells to shed light on the complex interactions that govern post-transcriptional regulation. By developing a more stringent CLIP analysis pipeline we have discovered the existence of conserved regulatory AU-rich regions in the 3’UTRs where miRNAs and RBPs that regulate several processes such as polyadenylation or mRNA stability bind. Analogous to promoters, many factors have binding sites overlapping or in close proximity in these hotspots and hence the regulation of the mRNA may depend on their relative concentrations. This hypothesis is supported by RBP knockdown experiments that alter the relative concentration of RBPs in the cell. Upon AGO2 knockdown (KD), transcripts containing “free” target sites show increased expression levels compared to those containing target sites in hotspots, which suggests that target sites within hotspots are less available for miRNAs to bind. Interestingly, these hotspots appear enriched in genes with regulatory functions such as DNA binding and RNA binding. Taken together, our results suggest that hotspots are functional regulatory elements that define an extra layer

The BaMM web server for de-novo motif discovery and regulatory sequence analysis.

PubMed

Kiesel, Anja; Roth, Christian; Ge, Wanwan; Wess, Maximilian; Meier, Markus; Söding, Johannes

2018-05-28

The BaMM web server offers four tools: (i) de-novo discovery of enriched motifs in a set of nucleotide sequences, (ii) scanning a set of nucleotide sequences with motifs to find motif occurrences, (iii) searching with an input motif for similar motifs in our BaMM database with motifs for >1000 transcription factors, trained from the GTRD ChIP-seq database and (iv) browsing and keyword searching the motif database. In contrast to most other servers, we represent sequence motifs not by position weight matrices (PWMs) but by Bayesian Markov Models (BaMMs) of order 4, which we showed previously to perform substantially better in ROC analyses than PWMs or first order models. To address the inadequacy of P- and E-values as measures of motif quality, we introduce the AvRec score, the average recall over the TP-to-FP ratio between 1 and 100. The BaMM server is freely accessible without registration at https://bammmotif.mpibpc.mpg.de.

Rules for the recognition of dilysine retrieval motifs by coatomer

PubMed Central

Ma, Wenfu; Goldberg, Jonathan

2013-01-01

Cytoplasmic dilysine motifs on transmembrane proteins are captured by coatomer α-COP and β′-COP subunits and packaged into COPI-coated vesicles for Golgi-to-ER retrieval. Numerous ER/Golgi proteins contain K(x)Kxx motifs, but the rules for their recognition are unclear. We present crystal structures of α-COP and β′-COP bound to a series of naturally occurring retrieval motifs—encompassing KKxx, KxKxx and non-canonical RKxx and viral KxHxx sequences. Binding experiments show that α-COP and β′-COP have generally the same specificity for KKxx and KxKxx, but only β′-COP recognizes the RKxx signal. Dilysine motif recognition involves lysine side-chain interactions with two acidic patches. Surprisingly, however, KKxx and KxKxx motifs bind differently, with their lysine residues transposed at the binding patches. We derive rules for retrieval motif recognition from key structural features: the reversed binding modes, the recognition of the C-terminal carboxylate group which enforces lysine positional context, and the tolerance of the acidic patches for non-lysine residues. PMID:23481256

Do In Situ Observations Contain Signatures of Intermittent Fast Solar Wind Acceleration?

NASA Astrophysics Data System (ADS)

Matteini, L.; Horbury, T. S.; Stansby, D.

2017-12-01

Disentangling local plasma properties and Solar origin structures in in situ data is a crucial aspect for the understanding of solar wind acceleration and evolution. This is particularly challenging at 1 AU and beyond, where structures of various origin have had time to interact and merge, smoothing out their main characteristics. Observations of more pristine plasma closer to the Sun are therefore needed. In preparation of the forthcoming Solar Orbiter and Parker Solar Probe missions, Helios observations as close as to 0.3 AU - although old, not yet fully exploited - can be used to test our expectations and make new predictions. Recent observations (Matteini et al. 2014, 2015) have outlined the presence of intense (up to 1000km/s) and short-living velocity peaks that ubiquitously characterize the typical profile of the fast solar wind at 0.3 AU, suggesting that these features could be remnants of processes occurring in the Solar atmosphere and a signature of intermittent solar wind acceleration from coronal holes. We discuss results about statistics of these events, characterizing their physical properties and trying to link them with typical Solar temporal and spatial scales. Finally we also discuss how these velocity peaks will likely affect the future in situ exploration of the inner heliosphere by Solar Orbiter and the Parker Solar Probe.

RNA Binding of T-cell Intracellular Antigen-1 (TIA-1) C-terminal RNA Recognition Motif Is Modified by pH Conditions*

PubMed Central

Cruz-Gallardo, Isabel; Aroca, Ángeles; Persson, Cecilia; Karlsson, B. Göran; Díaz-Moreno, Irene

2013-01-01

T-cell intracellular antigen-1 (TIA-1) is a DNA/RNA-binding protein that regulates critical events in cell physiology by the regulation of pre-mRNA splicing and mRNA translation. TIA-1 is composed of three RNA recognition motifs (RRMs) and a glutamine-rich domain and binds to uridine-rich RNA sequences through its C-terminal RRM2 and RRM3 domains. Here, we show that RNA binding mediated by either isolated RRM3 or the RRM23 construct is controlled by slight environmental pH changes due to the protonation/deprotonation of TIA-1 RRM3 histidine residues. The auxiliary role of the C-terminal RRM3 domain in TIA-1 RNA recognition is poorly understood, and this work provides insight into its binding mechanisms. PMID:23902765

One motif to bind them: A small-XXX-small motif affects transmembrane domain 1 oligomerization, function, localization, and cross-talk between two yeast GPCRs.

PubMed

Lock, Antonia; Forfar, Rachel; Weston, Cathryn; Bowsher, Leo; Upton, Graham J G; Reynolds, Christopher A; Ladds, Graham; Dixon, Ann M

2014-12-01

G protein-coupled receptors (GPCRs) are the largest family of cell-surface receptors in mammals and facilitate a range of physiological responses triggered by a variety of ligands. GPCRs were thought to function as monomers, however it is now accepted that GPCR homo- and hetero-oligomers also exist and influence receptor properties. The Schizosaccharomyces pombe GPCR Mam2 is a pheromone-sensing receptor involved in mating and has previously been shown to form oligomers in vivo. The first transmembrane domain (TMD) of Mam2 contains a small-XXX-small motif, overrepresented in membrane proteins and well-known for promoting helix-helix interactions. An ortholog of Mam2 in Saccharomyces cerevisiae, Ste2, contains an analogous small-XXX-small motif which has been shown to contribute to receptor homo-oligomerization, localization and function. Here we have used experimental and computational techniques to characterize the role of the small-XXX-small motif in function and assembly of Mam2 for the first time. We find that disruption of the motif via mutagenesis leads to reduction of Mam2 TMD1 homo-oligomerization and pheromone-responsive cellular signaling of the full-length protein. It also impairs correct targeting to the plasma membrane. Mutation of the analogous motif in Ste2 yielded similar results, suggesting a conserved mechanism for assembly. Using co-expression of the two fungal receptors in conjunction with computational models, we demonstrate a functional change in G protein specificity and propose that this is brought about through hetero-dimeric interactions of Mam2 with Ste2 via the complementary small-XXX-small motifs. This highlights the potential of these motifs to affect a range of properties that can be investigated in other GPCRs. Copyright © 2014. Published by Elsevier B.V.

Prediction of virus-host protein-protein interactions mediated by short linear motifs.

PubMed

Becerra, Andrés; Bucheli, Victor A; Moreno, Pedro A

2017-03-09

Short linear motifs in host organisms proteins can be mimicked by viruses to create protein-protein interactions that disable or control metabolic pathways. Given that viral linear motif instances of host motif regular expressions can be found by chance, it is necessary to develop filtering methods of functional linear motifs. We conduct a systematic comparison of linear motifs filtering methods to develop a computational approach for predicting motif-mediated protein-protein interactions between human and the human immunodeficiency virus 1 (HIV-1). We implemented three filtering methods to obtain linear motif sets: 1) conserved in viral proteins (C), 2) located in disordered regions (D) and 3) rare or scarce in a set of randomized viral sequences (R). The sets C,D,R are united and intersected. The resulting sets are compared by the number of protein-protein interactions correctly inferred with them - with experimental validation. The comparison is done with HIV-1 sequences and interactions from the National Institute of Allergy and Infectious Diseases (NIAID). The number of correctly inferred interactions allows to rank the interactions by the sets used to deduce them: D∪R and C. The ordering of the sets is descending on the probability of capturing functional interactions. With respect to HIV-1, the sets C∪R, D∪R, C∪D∪R infer all known interactions between HIV1 and human proteins mediated by linear motifs. We found that the majority of conserved linear motifs in the virus are located in disordered regions. We have developed a method for predicting protein-protein interactions mediated by linear motifs between HIV-1 and human proteins. The method only use protein sequences as inputs. We can extend the software developed to any other eukaryotic virus and host in order to find and rank candidate interactions. In future works we will use it to explore possible viral attack mechanisms based on linear motif mimicry.

D-MATRIX: A web tool for constructing weight matrix of conserved DNA motifs

PubMed Central

Sen, Naresh; Mishra, Manoj; Khan, Feroz; Meena, Abha; Sharma, Ashok

2009-01-01

Despite considerable efforts to date, DNA motif prediction in whole genome remains a challenge for researchers. Currently the genome wide motif prediction tools required either direct pattern sequence (for single motif) or weight matrix (for multiple motifs). Although there are known motif pattern databases and tools for genome level prediction but no tool for weight matrix construction. Considering this, we developed a D-MATRIX tool which predicts the different types of weight matrix based on user defined aligned motif sequence set and motif width. For retrieval of known motif sequences user can access the commonly used databases such as TFD, RegulonDB, DBTBS, Transfac. D­MATRIX program uses a simple statistical approach for weight matrix construction, which can be converted into different file formats according to user requirement. It provides the possibility to identify the conserved motifs in the co­regulated genes or whole genome. As example, we successfully constructed the weight matrix of LexA transcription factor binding site with the help of known sos­box cis­regulatory elements in Deinococcus radiodurans genome. The algorithm is implemented in C-Sharp and wrapped in ASP.Net to maintain a user friendly web interface. D­MATRIX tool is accessible through the CIMAP domain network. Availability http://203.190.147.116/dmatrix/ PMID:19759861

D-MATRIX: a web tool for constructing weight matrix of conserved DNA motifs.

PubMed

Sen, Naresh; Mishra, Manoj; Khan, Feroz; Meena, Abha; Sharma, Ashok

2009-07-27

Despite considerable efforts to date, DNA motif prediction in whole genome remains a challenge for researchers. Currently the genome wide motif prediction tools required either direct pattern sequence (for single motif) or weight matrix (for multiple motifs). Although there are known motif pattern databases and tools for genome level prediction but no tool for weight matrix construction. Considering this, we developed a D-MATRIX tool which predicts the different types of weight matrix based on user defined aligned motif sequence set and motif width. For retrieval of known motif sequences user can access the commonly used databases such as TFD, RegulonDB, DBTBS, Transfac. D-MATRIX program uses a simple statistical approach for weight matrix construction, which can be converted into different file formats according to user requirement. It provides the possibility to identify the conserved motifs in the co-regulated genes or whole genome. As example, we successfully constructed the weight matrix of LexA transcription factor binding site with the help of known sos-box cis-regulatory elements in Deinococcus radiodurans genome. The algorithm is implemented in C-Sharp and wrapped in ASP.Net to maintain a user friendly web interface. D-MATRIX tool is accessible through the CIMAP domain network. http://203.190.147.116/dmatrix/

ORF73 LANA homologs of RRV and MneRV2 contain an extended RGG/RG-rich nuclear and nucleolar localization signal that interacts directly with importin β1 for non-classical nuclear import.

PubMed

Howard, Kellie; Cherezova, Lidia; DeMaster, Laura K; Rose, Timothy M

2017-11-01

The latency-associated nuclear antigens (LANA) of KSHV and macaque RFHVMn, members of the RV1 rhadinovirus lineage, are closely related with conservation of complex nuclear localization signals (NLS) containing bipartite KR-rich motifs and RG-rich domains, which interact distinctly with importins α and ß1 for nuclear import via classical and non-classical pathways, respectively. RV1 LANAs are expressed in the nucleus of latently-infected cells where they inhibit replication and establish a dominant RV1 latency. Here we show that LANA homologs of macaque RRV and MneRV2 from the more distantly-related RV2 lineage, lack the KR-rich NLS, and instead have a large RG-rich NLS with multiple RG dipeptides and a conserved RGG motif. The RG-NLS interacts uniquely with importin β1, which mediates nuclear import and accumulation of RV2 LANA in the nucleolus. The alternative nuclear import and localization of RV2 LANA homologs may contribute to the dominant RV2 lytic replication phenotype. Copyright © 2017. Published by Elsevier Inc.

Beet juice utilization: Expeditious green synthesis of nobel metal nanoparticles (Ag, Au, Pt, and Pd) using microwaves

EPA Science Inventory

Metal nanoparticles of Ag, Au, Pt, and Pd were prepared in aqueous solutions via a rapid microwave-assisted green method using beet juice, an abundant sugar-rich agricultural produce, served as both a reducing and a capping reagent. The Ag nanoparticles with capping prepared by b...

Insights into the Evolution of Hydroxyproline-Rich Glycoproteins from 1000 Plant Transcriptomes1[OPEN

PubMed Central

Cassin, Andrew M.; Soltis, Douglas E.; Miles, Nicholas W.; Melkonian, Michael; Melkonian, Barbara; Wu, Shuangxiu; Edger, Patrick P.; Carpenter, Eric J.

2017-01-01

The carbohydrate-rich cell walls of land plants and algae have been the focus of much interest given the value of cell wall-based products to our current and future economies. Hydroxyproline-rich glycoproteins (HRGPs), a major group of wall glycoproteins, play important roles in plant growth and development, yet little is known about how they have evolved in parallel with the polysaccharide components of walls. We investigate the origins and evolution of the HRGP superfamily, which is commonly divided into three major multigene families: the arabinogalactan proteins (AGPs), extensins (EXTs), and proline-rich proteins. Using motif and amino acid bias, a newly developed bioinformatics pipeline, we identified HRGPs in sequences from the 1000 Plants transcriptome project (www.onekp.com). Our analyses provide new insights into the evolution of HRGPs across major evolutionary milestones, including the transition to land and the early radiation of angiosperms. Significantly, data mining reveals the origin of glycosylphosphatidylinositol (GPI)-anchored AGPs in green algae and a 3- to 4-fold increase in GPI-AGPs in liverworts and mosses. The first detection of cross-linking (CL)-EXTs is observed in bryophytes, which suggests that CL-EXTs arose though the juxtaposition of preexisting SPn EXT glycomotifs with refined Y-based motifs. We also detected the loss of CL-EXT in a few lineages, including the grass family (Poaceae), that have a cell wall composition distinct from other monocots and eudicots. A key challenge in HRGP research is tracking individual HRGPs throughout evolution. Using the 1000 Plants output, we were able to find putative orthologs of Arabidopsis pollen-specific GPI-AGPs in basal eudicots. PMID:28446636

Superstructures and Electronic Properties of Manganese-Phthalocyanine Molecules on Au(110) from Submonolayer Coverage to Ultrathin Molecular Films.

PubMed

Topyła, M; Néel, N; Kröger, J

2016-07-12

The adsorption of manganese-phthalocyanine molecules on Au(110) was investigated using a low-temperature scanning tunneling microscope. A rich variety of commensurate superstructures was observed upon increasing the molecule coverage from submonolayers to ultrathin films. All structures were associated with reconstructions of the Au(110) substrate. Molecules adsorbed in the second molecular layer exhibited negative differential conductance occurring symmetrically around zero bias voltage. A double-barrier tunneling model rationalized this observation in terms of a peaked molecular resonance at the Fermi energy together with a voltage drop across the molecular film.

Anion induced conformational preference of Cα NN motif residues in functional proteins.

PubMed

Patra, Piya; Ghosh, Mahua; Banerjee, Raja; Chakrabarti, Jaydeb

2017-12-01

Among different ligand binding motifs, anion binding C α NN motif consisting of peptide backbone atoms of three consecutive residues are observed to be important for recognition of free anions, like sulphate or biphosphate and participate in different key functions. Here we study the interaction of sulphate and biphosphate with C α NN motif present in different proteins. Instead of total protein, a peptide fragment has been studied keeping C α NN motif flanked in between other residues. We use classical force field based molecular dynamics simulations to understand the stability of this motif. Our data indicate fluctuations in conformational preferences of the motif residues in absence of the anion. The anion gives stability to one of these conformations. However, the anion induced conformational preferences are highly sequence dependent and specific to the type of anion. In particular, the polar residues are more favourable compared to the other residues for recognising the anion. © 2017 Wiley Periodicals, Inc.

Evolution of Excited-State Dynamics in Periodic Au 28, Au 36, Au 44, and Au 52 Nanoclusters

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

Zhou, Meng; Zeng, Chenjie; Sfeir, Matthew Y.

An understanding of the correlation between the atomic structure and optical properties of gold nanoclusters is essential for exploration of their functionalities and applications involving light harvesting and electron transfer. We report the femto-nanosecond excited state dynamics of a periodic series of face-centered cubic (FCC) gold nanoclusters (including Au 28, Au 36, Au 44, and Au 52), which exhibit a set of unique features compared with other similar sized clusters. Molecular-like ultrafast S n → S 1 internal conversions (i.e., radiationless electronic transitions) are observed in the relaxation dynamics of FCC periodic series. Excited-state dynamics with near-HOMO–LUMO gap excitation lacksmore » ultrafast decay component, and only the structural relaxation dominates in the dynamical process, which proves the absence of core–shell relaxation. Interestingly, both the relaxation of the hot carriers and the band-edge carrier recombination become slower as the size increases. The evolution in excited-state properties of this FCC series offers new insight into the structure-dependent properties of metal nanoclusters, which will benefit their optical energy harvesting and photocatalytic applications.« less

Evolution of Excited-State Dynamics in Periodic Au 28, Au 36, Au 44, and Au 52 Nanoclusters

DOE PAGES

Zhou, Meng; Zeng, Chenjie; Sfeir, Matthew Y.; ...

2017-08-10

An understanding of the correlation between the atomic structure and optical properties of gold nanoclusters is essential for exploration of their functionalities and applications involving light harvesting and electron transfer. We report the femto-nanosecond excited state dynamics of a periodic series of face-centered cubic (FCC) gold nanoclusters (including Au 28, Au 36, Au 44, and Au 52), which exhibit a set of unique features compared with other similar sized clusters. Molecular-like ultrafast S n → S 1 internal conversions (i.e., radiationless electronic transitions) are observed in the relaxation dynamics of FCC periodic series. Excited-state dynamics with near-HOMO–LUMO gap excitation lacksmore » ultrafast decay component, and only the structural relaxation dominates in the dynamical process, which proves the absence of core–shell relaxation. Interestingly, both the relaxation of the hot carriers and the band-edge carrier recombination become slower as the size increases. The evolution in excited-state properties of this FCC series offers new insight into the structure-dependent properties of metal nanoclusters, which will benefit their optical energy harvesting and photocatalytic applications.« less

Gene regulatory and signaling networks exhibit distinct topological distributions of motifs

NASA Astrophysics Data System (ADS)

Ferreira, Gustavo Rodrigues; Nakaya, Helder Imoto; Costa, Luciano da Fontoura

2018-04-01

The biological processes of cellular decision making and differentiation involve a plethora of signaling pathways and gene regulatory circuits. These networks in turn exhibit a multitude of motifs playing crucial parts in regulating network activity. Here we compare the topological placement of motifs in gene regulatory and signaling networks and observe that it suggests different evolutionary strategies in motif distribution for distinct cellular subnetworks.

Interconnected network motifs control podocyte morphology and kidney function.

PubMed

Azeloglu, Evren U; Hardy, Simon V; Eungdamrong, Narat John; Chen, Yibang; Jayaraman, Gomathi; Chuang, Peter Y; Fang, Wei; Xiong, Huabao; Neves, Susana R; Jain, Mohit R; Li, Hong; Ma'ayan, Avi; Gordon, Ronald E; He, John Cijiang; Iyengar, Ravi

2014-02-04

Podocytes are kidney cells with specialized morphology that is required for glomerular filtration. Diseases, such as diabetes, or drug exposure that causes disruption of the podocyte foot process morphology results in kidney pathophysiology. Proteomic analysis of glomeruli isolated from rats with puromycin-induced kidney disease and control rats indicated that protein kinase A (PKA), which is activated by adenosine 3',5'-monophosphate (cAMP), is a key regulator of podocyte morphology and function. In podocytes, cAMP signaling activates cAMP response element-binding protein (CREB) to enhance expression of the gene encoding a differentiation marker, synaptopodin, a protein that associates with actin and promotes its bundling. We constructed and experimentally verified a β-adrenergic receptor-driven network with multiple feedback and feedforward motifs that controls CREB activity. To determine how the motifs interacted to regulate gene expression, we mapped multicompartment dynamical models, including information about protein subcellular localization, onto the network topology using Petri net formalisms. These computational analyses indicated that the juxtaposition of multiple feedback and feedforward motifs enabled the prolonged CREB activation necessary for synaptopodin expression and actin bundling. Drug-induced modulation of these motifs in diseased rats led to recovery of normal morphology and physiological function in vivo. Thus, analysis of regulatory motifs using network dynamics can provide insights into pathophysiology that enable predictions for drug intervention strategies to treat kidney disease.

Interconnected Network Motifs Control Podocyte Morphology and Kidney Function

PubMed Central

Azeloglu, Evren U.; Hardy, Simon V.; Eungdamrong, Narat John; Chen, Yibang; Jayaraman, Gomathi; Chuang, Peter Y.; Fang, Wei; Xiong, Huabao; Neves, Susana R.; Jain, Mohit R.; Li, Hong; Ma’ayan, Avi; Gordon, Ronald E.; He, John Cijiang; Iyengar, Ravi

2014-01-01

Podocytes are kidney cells with specialized morphology that is required for glomerular filtration. Diseases, such as diabetes, or drug exposure that causes disruption of the podocyte foot process morphology results in kidney pathophysiology. Proteomic analysis of glomeruli isolated from rats with puromycin-induced kidney disease and control rats indicated that protein kinase A (PKA), which is activated by adenosine 3′,5′-monophosphate (cAMP), is a key regulator of podocyte morphology and function. In podocytes, cAMP signaling activates cAMP response element–binding protein (CREB) to enhance expression of the gene encoding a differentiation marker, synaptopodin, a protein that associates with actin and promotes its bundling. We constructed and experimentally verified a β-adrenergic receptor–driven network with multiple feedback and feedforward motifs that controls CREB activity. To determine how the motifs interacted to regulate gene expression, we mapped multicompartment dynamical models, including information about protein subcellular localization, onto the network topology using Petri net formalisms. These computational analyses indicated that the juxtaposition of multiple feedback and feedforward motifs enabled the prolonged CREB activation necessary for synaptopodin expression and actin bundling. Drug-induced modulation of these motifs in diseased rats led to recovery of normal morphology and physiological function in vivo. Thus, analysis of regulatory motifs using network dynamics can provide insights into pathophysiology that enable predictions for drug intervention strategies to treat kidney disease. PMID:24497609

Statistical Methods for Identifying Sequence Motifs Affecting Point Mutations

PubMed Central

Zhu, Yicheng; Neeman, Teresa; Yap, Von Bing; Huttley, Gavin A.

2017-01-01

Mutation processes differ between types of point mutation, genomic locations, cells, and biological species. For some point mutations, specific neighboring bases are known to be mechanistically influential. Beyond these cases, numerous questions remain unresolved, including: what are the sequence motifs that affect point mutations? How large are the motifs? Are they strand symmetric? And, do they vary between samples? We present new log-linear models that allow explicit examination of these questions, along with sequence logo style visualization to enable identifying specific motifs. We demonstrate the performance of these methods by analyzing mutation processes in human germline and malignant melanoma. We recapitulate the known CpG effect, and identify novel motifs, including a highly significant motif associated with A→G mutations. We show that major effects of neighbors on germline mutation lie within ±2 of the mutating base. Models are also presented for contrasting the entire mutation spectra (the distribution of the different point mutations). We show the spectra vary significantly between autosomes and X-chromosome, with a difference in T→C transition dominating. Analyses of malignant melanoma confirmed reported characteristic features of this cancer, including statistically significant strand asymmetry, and markedly different neighboring influences. The methods we present are made freely available as a Python library https://bitbucket.org/pycogent3/mutationmotif. PMID:27974498

Spectral Evidence for an Inner Carbon-rich Circumstellar Belt in the Young HD 36546 A-star System

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

Lisse, C. M.; Sitko, M. L.; Russell, R. W.

Using the NASA/IRTF SpeX and BASS spectrometers we have obtained 0.7–13 μ m observations of the newly imaged 3–10 Myr old HD 36546 disk system. The SpeX spectrum is most consistent with the photospheric emission expected from an L {sub *} ∼ 20 L {sub ⊙}, solar abundance A1.5V star with little to no extinction, and excess emission from circumstellar dust detectable beyond 4.5 μ m. Non-detections of CO emission lines and accretion signatures point to the gas-poor circumstellar environment of a very old transition disk. Combining the SpeX + BASS spectra with archival WISE / AKARI / IRAS /more » Herschel photometry, we find an outer cold dust belt at ∼135 K and 20–40 au from the primary, likely coincident with the disk imaged by Subaru, and a new second inner belt with a temperature ∼570 K and an unusual, broad SED maximum in the 6–9 μ m region, tracing dust at 1.1–2.2 au. An SED maximum at 6–9 μ m has been reported in just two other A-star systems, HD 131488 and HD 121191, both of ∼10 Myr age. From Spitzer , we have also identified the ∼12 Myr old A7V HD 148657 system as having similar 5–35 μ m excess spectral features. The Spitzer data allows us to rule out water emission and rule in carbonaceous materials—organics, carbonates, SiC—as the source of the 6–9 μ m excess. Assuming a common origin for the four young A-star systems’ disks, we suggest they are experiencing an early era of carbon-rich planetesimal processing.« less

Di-hadron correlations with identified leading hadrons in 200 GeV Au + Au and d + Au collisions at STAR

NASA Astrophysics Data System (ADS)

Adamczyk, L.; Adkins, J. K.; Agakishiev, G.; Aggarwal, M. M.; Ahammed, Z.; Alekseev, I.; Aparin, A.; Arkhipkin, D.; Aschenauer, E. C.; Averichev, G. S.; Bai, X.; Bairathi, V.; Banerjee, A.; Bellwied, R.; Bhasin, A.; Bhati, A. K.; Bhattarai, P.; Bielcik, J.; Bielcikova, J.; Bland, L. C.; Bordyuzhin, I. G.; Bouchet, J.; Brandenburg, D.; Brandin, A. V.; Bunzarov, I.; Butterworth, J.; Caines, H.; Calderón de la Barca Sánchez, M.; Campbell, J. M.; Cebra, D.; Cervantes, M. C.; Chakaberia, I.; Chaloupka, P.; Chang, Z.; Chattopadhyay, S.; Chen, X.; Chen, J. H.; Cheng, J.; Cherney, M.; Christie, W.; Contin, G.; Crawford, H. J.; Das, S.; De Silva, L. C.; Debbe, R. R.; Dedovich, T. G.; Deng, J.; Derevschikov, A. A.; di Ruzza, B.; Didenko, L.; Dilks, C.; Dong, X.; Drachenberg, J. L.; Draper, J. E.; Du, C. M.; Dunkelberger, L. E.; Dunlop, J. C.; Efimov, L. G.; Engelage, J.; Eppley, G.; Esha, R.; Evdokimov, O.; Eyser, O.; Fatemi, R.; Fazio, S.; Federic, P.; Fedorisin, J.; Feng, Z.; Filip, P.; Fisyak, Y.; Flores, C. E.; Fulek, L.; Gagliardi, C. A.; Garand, D.; Geurts, F.; Gibson, A.; Girard, M.; Greiner, L.; Grosnick, D.; Gunarathne, D. S.; Guo, Y.; Gupta, S.; Gupta, A.; Guryn, W.; Hamad, A.; Hamed, A.; Haque, R.; Harris, J. W.; He, L.; Heppelmann, S.; Heppelmann, S.; Hirsch, A.; Hoffmann, G. W.; Hofman, D. J.; Horvat, S.; Huang, T.; Huang, B.; Huang, H. Z.; Huang, X.; Huck, P.; Humanic, T. J.; Igo, G.; Jacobs, W. W.; Jang, H.; Jia, J.; Jiang, K.; Judd, E. G.; Kabana, S.; Kalinkin, D.; Kang, K.; Kauder, K.; Ke, H. W.; Keane, D.; Kechechyan, A.; Khan, Z. H.; Kikoła, D. P.; Kisiel, A.; Kochenda, L.; Koetke, D. D.; Kosarzewski, L. K.; Kraishan, A. F.; Kravtsov, P.; Krueger, K.; Kumar, L.; Lamont, M. A. C.; Landgraf, J. M.; Landry, K. D.; Lauret, J.; Lebedev, A.; Lednicky, R.; Lee, J. H.; Li, X.; Li, W.; Li, Z. M.; Li, Y.; Li, C.; Li, X.; Lisa, M. A.; Liu, F.; Ljubicic, T.; Llope, W. J.; Lomnitz, M.; Longacre, R. S.; Luo, X.; Ma, G. L.; Ma, Y. G.; Ma, R.; Ma, L.; Magdy, N.; Majka, R.; Manion, A.; Margetis, S.; Markert, C.; Masui, H.; Matis, H. S.; McDonald, D.; Meehan, K.; Mei, J. C.; Minaev, N. G.; Mioduszewski, S.; Mishra, D.; Mohanty, B.; Mondal, M. M.; Morozov, D. A.; Mustafa, M. K.; Nandi, B. K.; Nasim, Md.; Nayak, T. K.; Nigmatkulov, G.; Niida, T.; Nogach, L. V.; Noh, S. Y.; Novak, J.; Nurushev, S. B.; Odyniec, G.; Ogawa, A.; Oh, K.; Okorokov, V.; Olvitt, D.; Page, B. S.; Pak, R.; Pan, Y. X.; Pandit, Y.; Panebratsev, Y.; Pawlik, B.; Pei, H.; Perkins, C.; Peterson, A.; Pile, P.; Pluta, J.; Poniatowska, K.; Porter, J.; Posik, M.; Poskanzer, A. M.; Pruthi, N. K.; Putschke, J.; Qiu, H.; Quintero, A.; Ramachandran, S.; Raniwala, R.; Raniwala, S.; Ray, R. L.; Ritter, H. G.; Roberts, J. B.; Rogachevskiy, O. V.; Romero, J. L.; Roy, A.; Ruan, L.; Rusnak, J.; Rusnakova, O.; Sahoo, N. R.; Sahu, P. K.; Sakrejda, I.; Salur, S.; Sandweiss, J.; Sarkar, A.; Schambach, J.; Scharenberg, R. P.; Schmah, A. M.; Schmidke, W. B.; Schmitz, N.; Seger, J.; Seyboth, P.; Shah, N.; Shahaliev, E.; Shanmuganathan, P. V.; Shao, M.; Sharma, B.; Sharma, M. K.; Shen, W. Q.; Shi, S. S.; Shou, Q. Y.; Sichtermann, E. P.; Sikora, R.; Simko, M.; Singha, S.; Skoby, M. J.; Smirnov, N.; Smirnov, D.; Song, L.; Sorensen, P.; Spinka, H. M.; Srivastava, B.; Stanislaus, T. D. S.; Stepanov, M.; Strikhanov, M.; Stringfellow, B.; Sumbera, M.; Summa, B.; Sun, Y.; Sun, Z.; Sun, X. M.; Sun, X.; Surrow, B.; Svirida, D. N.; Szelezniak, M. A.; Tang, A. H.; Tang, Z.; Tarnowsky, T.; Tawfik, A.; Thomas, J. H.; Timmins, A. R.; Tlusty, D.; Todoroki, T.; Tokarev, M.; Trentalange, S.; Tribble, R. E.; Tribedy, P.; Tripathy, S. K.; Tsai, O. D.; Ullrich, T.; Underwood, D. G.; Upsal, I.; Van Buren, G.; van Nieuwenhuizen, G.; Vandenbroucke, M.; Varma, R.; Vasiliev, A. N.; Vertesi, R.; Videbæk, F.; Viyogi, Y. P.; Vokal, S.; Voloshin, S. A.; Vossen, A.; Wang, J. S.; Wang, F.; Wang, H.; Wang, G.; Wang, Y.; Wang, Y.; Webb, G.; Webb, J. C.; Wen, L.; Westfall, G. D.; Wieman, H.; Wissink, S. W.; Witt, R.; Wu, Y. F.; Wu; Xiao, Z. G.; Xie, W.; Xin, K.; Xu, H.; Xu, Z.; Xu, Q. H.; Xu, Y. F.; Xu, N.; Yang, S.; Yang, Y.; Yang, Q.; Yang, Y.; Yang, C.; Yang, Y.; Ye, Z.; Ye, Z.; Yepes, P.; Yi, L.; Yip, K.; Yoo, I.-K.; Yu, N.; Zbroszczyk, H.; Zha, W.; Zhang, Y.; Zhang, Z.; Zhang, J. B.; Zhang, J.; Zhang, X. P.; Zhang, S.; Zhang, J.; Zhao, J.; Zhong, C.; Zhou, L.; Zhu, X.; Zoulkarneeva, Y.

2015-12-01

The STAR Collaboration presents for the first time two-dimensional di-hadron correlations with identified leading hadrons in 200 GeV central Au + Au and minimum-bias d + Au collisions to explore hadronization mechanisms in the quark gluon plasma. The enhancement of the jet-like yield for leading pions in Au + Au data with respect to the d + Au reference and the absence of such an enhancement for leading non-pions (protons and kaons) are discussed within the context of a quark recombination scenario. The correlated yield at large angles, specifically in the ridge region, is found to be significantly higher for leading non-pions than pions. The consistencies of the constituent quark scaling, azimuthal harmonic model and a mini-jet modification model description of the data are tested, providing further constraints on hadronization.

BEAM web server: a tool for structural RNA motif discovery.

PubMed

Pietrosanto, Marco; Adinolfi, Marta; Casula, Riccardo; Ausiello, Gabriele; Ferrè, Fabrizio; Helmer-Citterich, Manuela

2018-03-15

RNA structural motif finding is a relevant problem that becomes computationally hard when working on high-throughput data (e.g. eCLIP, PAR-CLIP), often represented by thousands of RNA molecules. Currently, the BEAM server is the only web tool capable to handle tens of thousands of RNA in input with a motif discovery procedure that is only limited by the current secondary structure prediction accuracies. The recently developed method BEAM (BEAr Motifs finder) can analyze tens of thousands of RNA molecules and identify RNA secondary structure motifs associated to a measure of their statistical significance. BEAM is extremely fast thanks to the BEAR encoding that transforms each RNA secondary structure in a string of characters. BEAM also exploits the evolutionary knowledge contained in a substitution matrix of secondary structure elements, extracted from the RFAM database of families of homologous RNAs. The BEAM web server has been designed to streamline data pre-processing by automatically handling folding and encoding of RNA sequences, giving users a choice for the preferred folding program. The server provides an intuitive and informative results page with the list of secondary structure motifs identified, the logo of each motif, its significance, graphic representation and information about its position in the RNA molecules sharing it. The web server is freely available at http://beam.uniroma2.it/ and it is implemented in NodeJS and Python with all major browsers supported. marco.pietrosanto@uniroma2.it. Supplementary data are available at Bioinformatics online.

Connected Au network in annealed Ni/Au thin films on p-GaN

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

Lee, S. P.; Jang, H. W.; Noh, D. Y.

2007-11-12

We report the formation of a connected Au network in annealed Ni/Au thin films on p-GaN, which was studied by scanning electron microscopy, transmission electron microscopy, and synchrotron x-ray diffraction. As the Ni was oxidized into NiO upon annealing at 530 deg. C in air, the Au layer was transformed to an interconnected network with an increased thickness. During annealing, Ni atoms diffuse out onto the Au through defects to form NiO, while Au atoms replace the Ni positions. The Au network grows downward until it reaches the p-GaN substrate, and NiO columns fill the space between the Au network.

Combinatorial Histone Acetylation Patterns Are Generated by Motif-Specific Reactions.

PubMed

Blasi, Thomas; Feller, Christian; Feigelman, Justin; Hasenauer, Jan; Imhof, Axel; Theis, Fabian J; Becker, Peter B; Marr, Carsten

2016-01-27

Post-translational modifications (PTMs) are pivotal to cellular information processing, but how combinatorial PTM patterns ("motifs") are set remains elusive. We develop a computational framework, which we provide as open source code, to investigate the design principles generating the combinatorial acetylation patterns on histone H4 in Drosophila melanogaster. We find that models assuming purely unspecific or lysine site-specific acetylation rates were insufficient to explain the experimentally determined motif abundances. Rather, these abundances were best described by an ensemble of models with acetylation rates that were specific to motifs. The model ensemble converged upon four acetylation pathways; we validated three of these using independent data from a systematic enzyme depletion study. Our findings suggest that histone acetylation patterns originate through specific pathways involving motif-specific acetylation activity. Copyright © 2016 Elsevier Inc. All rights reserved.

Seed storage protein gene promoters contain conserved DNA motifs in Brassicaceae, Fabaceae and Poaceae

PubMed Central

Fauteux, François; Strömvik, Martina V

2009-01-01

Background Accurate computational identification of cis-regulatory motifs is difficult, particularly in eukaryotic promoters, which typically contain multiple short and degenerate DNA sequences bound by several interacting factors. Enrichment in combinations of rare motifs in the promoter sequence of functionally or evolutionarily related genes among several species is an indicator of conserved transcriptional regulatory mechanisms. This provides a basis for the computational identification of cis-regulatory motifs. Results We have used a discriminative seeding DNA motif discovery algorithm for an in-depth analysis of 54 seed storage protein (SSP) gene promoters from three plant families, namely Brassicaceae (mustards), Fabaceae (legumes) and Poaceae (grasses) using backgrounds based on complete sets of promoters from a representative species in each family, namely Arabidopsis (Arabidopsis thaliana (L.) Heynh.), soybean (Glycine max (L.) Merr.) and rice (Oryza sativa L.) respectively. We have identified three conserved motifs (two RY-like and one ACGT-like) in Brassicaceae and Fabaceae SSP gene promoters that are similar to experimentally characterized seed-specific cis-regulatory elements. Fabaceae SSP gene promoter sequences are also enriched in a novel, seed-specific E2Fb-like motif. Conserved motifs identified in Poaceae SSP gene promoters include a GCN4-like motif, two prolamin-box-like motifs and an Skn-1-like motif. Evidence of the presence of a variant of the TATA-box is found in the SSP gene promoters from the three plant families. Motifs discovered in SSP gene promoters were used to score whole-genome sets of promoters from Arabidopsis, soybean and rice. The highest-scoring promoters are associated with genes coding for different subunits or precursors of seed storage proteins. Conclusion Seed storage protein gene promoter motifs are conserved in diverse species, and different plant families are characterized by a distinct combination of conserved motifs

Dimerization model of the C-terminal RNA Recognition Motif of HuR.

PubMed

Díaz-Quintana, Antonio; García-Mauriño, Sofía M; Díaz-Moreno, Irene

2015-04-28

Human antigen R (HuR) is a ubiquitous 32 kDa protein comprising three RNA Recognition Motifs (RRMs), whose main function is to bind Adenylate and uridylate Rich Elements (AREs) in 3' UnTranslated Regions (UTRs) of mRNAs. In addition to binding RNA molecules, the third domain (RRM3) is involved in HuR oligomerization and apoptotic signaling. The RRM3 monomer is able to dimerize, with its self-binding affinity being dependent on ionic strength. Here we provide a deeper structural insight into the nature of the encounter complexes leading to the formation of RRM3 dimers by using Brownian Dynamics and Molecular Dynamics. Our computational data show that the initial unspecific encounter follows a downhill pathway until reaching an optimum conformation stabilized by hydrophobic interactions. Copyright © 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Plasmon-enhanced versatile optical nonlinearities in a Au-Ag-Au multi-segmental hybrid structure.

PubMed

Yao, Lin-Hua; Zhang, Jun-Pei; Dai, Hong-Wei; Wang, Ming-Shan; Zhang, Lu-Man; Wang, Xia; Han, Jun-Bo

2018-06-27

A Au-Ag-Au multi-segmental hybrid structure has been synthesized by using an electrodeposition method based on an anodic aluminum oxide (AAO) membrane. The third-order optical nonlinearities, second harmonic generation (SHG) and photoluminescence (PL) properties containing ultrafast supercontinuum generation and plasmon mediated thermal emission have been investigated. Significant optical enhancements have been obtained near surface plasmon resonance wavelength in all the abovementioned nonlinear processes. Comparative studies between the Au-Ag-Au multi-segmental hybrid structure and the corresponding single-component Au and Ag hybrid structures demonstrate that the Au-Ag-Au multi-segmental hybrid structure has much larger optical nonlinearities than its counterparts. These results demonstrate that the Au-Ag-Au hybrid structure is a promising candidate for applications in plasmonic devices and enhancement substrates.

Di-hadron correlations with identified leading hadrons in 200 GeV Au + Au and d + Au collisions at STAR

DOE PAGES

Adamczyk, L.

2015-10-23

The STAR Collaboration presents for the first time two-dimensional di-hadron correlations with identified leading hadrons in 200 GeV central Au + Au and minimum-bias d + Au collisions to explore hadronization mechanisms in the quark gluon plasma. The enhancement of the jet-like yield for leading pions in Au + Au data with respect to the d + Au reference and the absence of such an enhancement for leading non-pions (protons and kaons) are discussed within the context of a quark recombination scenario. The correlated yield at large angles, specifically in the ridge region, is found to be significantly higher formore » leading non-pions than pions. As a result, the consistencies of the constituent quark scaling, azimuthal harmonic model and a mini-jet modification model description of the data are tested, providing further constraints on hadronization.« less

High-Pressure NMR and SAXS Reveals How Capping Modulates Folding Cooperativity of the pp32 Leucine-rich Repeat Protein.

PubMed

Zhang, Yi; Berghaus, Melanie; Klein, Sean; Jenkins, Kelly; Zhang, Siwen; McCallum, Scott A; Morgan, Joel E; Winter, Roland; Barrick, Doug; Royer, Catherine A

2018-04-27

Many repeat proteins contain capping motifs, which serve to shield the hydrophobic core from solvent and maintain structural integrity. While the role of capping motifs in enhancing the stability and structural integrity of repeat proteins is well documented, their contribution to folding cooperativity is not. Here we examined the role of capping motifs in defining the folding cooperativity of the leucine-rich repeat protein, pp32, by monitoring the pressure- and urea-induced unfolding of an N-terminal capping motif (N-cap) deletion mutant, pp32-∆N-cap, and a C-terminal capping motif destabilization mutant pp32-Y131F/D146L, using residue-specific NMR and small-angle X-ray scattering. Destabilization of the C-terminal capping motif resulted in higher cooperativity for the unfolding transition compared to wild-type pp32, as these mutations render the stability of the C-terminus similar to that of the rest of the protein. In contrast, deletion of the N-cap led to strong deviation from two-state unfolding. In both urea- and pressure-induced unfolding, residues in repeats 1-3 of pp32-ΔN-cap lost their native structure first, while the C-terminal half was more stable. The residue-specific free energy changes in all regions of pp32-ΔN-cap were larger in urea compared to high pressure, indicating a less cooperative destabilization by pressure. Moreover, in contrast to complete structural disruption of pp32-ΔN-cap at high urea concentration, its pressure unfolded state remained compact. The contrasting effects of the capping motifs on folding cooperativity arise from the differential local stabilities of pp32, whereas the contrasting effects of pressure and urea on the pp32-ΔN-cap variant arise from their distinct mechanisms of action. Copyright © 2018 Elsevier Ltd. All rights reserved.

Distance-dependent duplex DNA destabilization proximal to G-quadruplex/i-motif sequences

PubMed Central

König, Sebastian L. B.; Huppert, Julian L.; Sigel, Roland K. O.; Evans, Amanda C.

2013-01-01

G-quadruplexes and i-motifs are complementary examples of non-canonical nucleic acid substructure conformations. G-quadruplex thermodynamic stability has been extensively studied for a variety of base sequences, but the degree of duplex destabilization that adjacent quadruplex structure formation can cause has yet to be fully addressed. Stable in vivo formation of these alternative nucleic acid structures is likely to be highly dependent on whether sufficient spacing exists between neighbouring duplex- and quadruplex-/i-motif-forming regions to accommodate quadruplexes or i-motifs without disrupting duplex stability. Prediction of putative G-quadruplex-forming regions is likely to be assisted by further understanding of what distance (number of base pairs) is required for duplexes to remain stable as quadruplexes or i-motifs form. Using oligonucleotide constructs derived from precedented G-quadruplexes and i-motif-forming bcl-2 P1 promoter region, initial biophysical stability studies indicate that the formation of G-quadruplex and i-motif conformations do destabilize proximal duplex regions. The undermining effect that quadruplex formation can have on duplex stability is mitigated with increased distance from the duplex region: a spacing of five base pairs or more is sufficient to maintain duplex stability proximal to predicted quadruplex/i-motif-forming regions. PMID:23771141

The Methionine-aromatic Motif Plays a Unique Role in Stabilizing Protein Structure*

PubMed Central

Valley, Christopher C.; Cembran, Alessandro; Perlmutter, Jason D.; Lewis, Andrew K.; Labello, Nicholas P.; Gao, Jiali; Sachs, Jonathan N.

2012-01-01

Of the 20 amino acids, the precise function of methionine (Met) remains among the least well understood. To establish a determining characteristic of methionine that fundamentally differentiates it from purely hydrophobic residues, we have used in vitro cellular experiments, molecular simulations, quantum calculations, and a bioinformatics screen of the Protein Data Bank. We show that approximately one-third of all known protein structures contain an energetically stabilizing Met-aromatic motif and, remarkably, that greater than 10,000 structures contain this motif more than 10 times. Critically, we show that as compared with a purely hydrophobic interaction, the Met-aromatic motif yields an additional stabilization of 1–1.5 kcal/mol. To highlight its importance and to dissect the energetic underpinnings of this motif, we have studied two clinically relevant TNF ligand-receptor complexes, namely TRAIL-DR5 and LTα-TNFR1. In both cases, we show that the motif is necessary for high affinity ligand binding as well as function. Additionally, we highlight previously overlooked instances of the motif in several disease-related Met mutations. Our results strongly suggest that the Met-aromatic motif should be exploited in the rational design of therapeutics targeting a range of proteins. PMID:22859300

Systematic comparison of the response properties of protein and RNA mediated gene regulatory motifs.

PubMed

Iyengar, Bharat Ravi; Pillai, Beena; Venkatesh, K V; Gadgil, Chetan J

2017-05-30

We present a framework enabling the dissection of the effects of motif structure (feedback or feedforward), the nature of the controller (RNA or protein), and the regulation mode (transcriptional, post-transcriptional or translational) on the response to a step change in the input. We have used a common model framework for gene expression where both motif structures have an activating input and repressing regulator, with the same set of parameters, to enable a comparison of the responses. We studied the global sensitivity of the system properties, such as steady-state gain, overshoot, peak time, and peak duration, to parameters. We find that, in all motifs, overshoot correlated negatively whereas peak duration varied concavely with peak time. Differences in the other system properties were found to be mainly dependent on the nature of the controller rather than the motif structure. Protein mediated motifs showed a higher degree of adaptation i.e. a tendency to return to baseline levels; in particular, feedforward motifs exhibited perfect adaptation. RNA mediated motifs had a mild regulatory effect; they also exhibited a lower peaking tendency and mean overshoot. Protein mediated feedforward motifs showed higher overshoot and lower peak time compared to the corresponding feedback motifs.

Spontaneous formation of Au-Pt alloyed nanoparticles using pure nano-counterparts as starters: a ligand and size dependent process.

PubMed

Usón, Laura; Sebastian, Victor; Mayoral, Alvaro; Hueso, Jose L; Eguizabal, Adela; Arruebo, Manuel; Santamaria, Jesus

2015-06-14

In this work we investigate the formation of PtAu monodisperse alloyed nanoparticles by ageing pure metallic Au and Pt small nanoparticles (sNPs), nanoparticle size <5 nm, under certain conditions. We demonstrate that those bimetallic entities can be obtained by controlling the size of the initial metallic sNPs separately prepared and by selecting their appropriate capping agents. The formation of this spontaneous phenomenon was studied using HR-STEM, EDS, ionic conductivity, UV-Vis spectroscopy and cyclic voltammetry. Depending on the type of capping agent used and the size of the initial Au sNPs, three different materials were obtained: (i) AuPt bimetallic sNPs showing a surface rich in Au atoms, (ii) segregated Au and Pt sNPs and (iii) a mixture of bimetallic nanoparticles as well as Pt sNPs and Au NPs. Surface segregation energies and the nature of the reaction environment are the driving forces to direct the distribution of atoms in the bimetallic sNPs. PtAu alloyed nanoparticles were obtained after 150 h of reaction at room temperature if a weak capping agent was used for the stabilization of the nanoparticles. It was also found that Au atoms diffuse towards Pt sNPs, producing a surface enriched in Au atoms. This study shows that even pure nanoparticles are prone to be modified by the surrounding nanoparticles to give rise to new nanomaterials if atomic diffusion is feasible.

Automatic Network Fingerprinting through Single-Node Motifs

PubMed Central

Echtermeyer, Christoph; da Fontoura Costa, Luciano; Rodrigues, Francisco A.; Kaiser, Marcus

2011-01-01

Complex networks have been characterised by their specific connectivity patterns (network motifs), but their building blocks can also be identified and described by node-motifs—a combination of local network features. One technique to identify single node-motifs has been presented by Costa et al. (L. D. F. Costa, F. A. Rodrigues, C. C. Hilgetag, and M. Kaiser, Europhys. Lett., 87, 1, 2009). Here, we first suggest improvements to the method including how its parameters can be determined automatically. Such automatic routines make high-throughput studies of many networks feasible. Second, the new routines are validated in different network-series. Third, we provide an example of how the method can be used to analyse network time-series. In conclusion, we provide a robust method for systematically discovering and classifying characteristic nodes of a network. In contrast to classical motif analysis, our approach can identify individual components (here: nodes) that are specific to a network. Such special nodes, as hubs before, might be found to play critical roles in real-world networks. PMID:21297963

Fast social-like learning of complex behaviors based on motor motifs.

PubMed

Calvo Tapia, Carlos; Tyukin, Ivan Y; Makarov, Valeri A

2018-05-01

Social learning is widely observed in many species. Less experienced agents copy successful behaviors exhibited by more experienced individuals. Nevertheless, the dynamical mechanisms behind this process remain largely unknown. Here we assume that a complex behavior can be decomposed into a sequence of n motor motifs. Then a neural network capable of activating motor motifs in a given sequence can drive an agent. To account for (n-1)! possible sequences of motifs in a neural network, we employ the winnerless competition approach. We then consider a teacher-learner situation: one agent exhibits a complex movement, while another one aims at mimicking the teacher's behavior. Despite the huge variety of possible motif sequences we show that the learner, equipped with the provided learning model, can rewire "on the fly" its synaptic couplings in no more than (n-1) learning cycles and converge exponentially to the durations of the teacher's motifs. We validate the learning model on mobile robots. Experimental results show that the learner is indeed capable of copying the teacher's behavior composed of six motor motifs in a few learning cycles. The reported mechanism of learning is general and can be used for replicating different functions, including, for example, sound patterns or speech.

Fast social-like learning of complex behaviors based on motor motifs

NASA Astrophysics Data System (ADS)

Calvo Tapia, Carlos; Tyukin, Ivan Y.; Makarov, Valeri A.

2018-05-01

Social learning is widely observed in many species. Less experienced agents copy successful behaviors exhibited by more experienced individuals. Nevertheless, the dynamical mechanisms behind this process remain largely unknown. Here we assume that a complex behavior can be decomposed into a sequence of n motor motifs. Then a neural network capable of activating motor motifs in a given sequence can drive an agent. To account for (n -1 )! possible sequences of motifs in a neural network, we employ the winnerless competition approach. We then consider a teacher-learner situation: one agent exhibits a complex movement, while another one aims at mimicking the teacher's behavior. Despite the huge variety of possible motif sequences we show that the learner, equipped with the provided learning model, can rewire "on the fly" its synaptic couplings in no more than (n -1 ) learning cycles and converge exponentially to the durations of the teacher's motifs. We validate the learning model on mobile robots. Experimental results show that the learner is indeed capable of copying the teacher's behavior composed of six motor motifs in a few learning cycles. The reported mechanism of learning is general and can be used for replicating different functions, including, for example, sound patterns or speech.

In search of the noble gas 3.52 Ga atmospheric signatures

NASA Astrophysics Data System (ADS)

Pujol, M.; Marty, B.; Philippot, P.

2008-12-01

The isotopic signatures of noble gases in the Present-day mantle and in the atmosphere permit exceptional insight into the evolution of these reservoirs through time ([1]). However, related exchange models are under- constrained and would require direct measurements of the atmospheric composition long ago, e.g., in the Archaean. Drilling in the the 3.52 Ga chert-barite ([2]) of the Dresser formation(Pilbara Drilling Project) , North Pole, Pilbara craton (Western Australia), led to recovery of exceptionally fresh samples preserving primary fluid inclusions unaffected by surface weathering. The whole formation is considered to be an already established basin when hydrothermal processes started. The chemical composition of primary fluid inclusions trapped in hydrothermal quartz from vacuolar komatiitic basalt from 110 m depth were determined by synchrotron X-ray microfluorescence (ESRF, Grenoble,France). Data show that fluids are relatively homogenous, consisting of a Ba-rich fluid and a Fe (+Ba)-rich fluid of hydrothermal origin as concluded by Foriel et al.([3]). The isotopic compositions of xenon and argon trapped in these fluids were measured by mass spectrometry following vacuum crushing. The three argon isotopes show a homogeneous signature quite different from present-day Earth atmosphere but we cannot exclude the possibility that secondary nuclear reactions produced these anomalies. Despite this, the Xe isotopic trends indicate a less radiogenic signature than the Present-day atmosphere, and probably represent a remnant of the Archaean atmosphere. If this xenon composition is primitive then it implies that there is no cosmogenic production through time. However, argon ratios could be explained by cosmogenic production which implies significant surface exposure times. Cosmogenic production will produce correlated argon and xenon isotope signatures. Therefore it is necessary to differentiate primary from secondary composition. To investigate the effects of these

Projected shell model study of odd-odd f-p-g shell proton-rich nuclei

NASA Astrophysics Data System (ADS)

Palit, R.; Sheikh, J. A.; Sun, Y.; Jain, H. C.

2003-01-01

A systematic study of two-quasiparticle bands of the proton-rich odd-odd nuclei in the mass A˜70 80 region is performed using the projected shell model approach. The study includes Br, Rb, and Y isotopes with N=Z+2 and Z+4. We describe the energy spectra and electromagnetic transition strengths in terms of the configuration mixing of the angular-momentum projected multi-quasiparticle states. Signature splitting and signature inversion in the rotational bands are discussed and are shown to be well described. A preliminary study of the odd-odd N=Z nucleus 74Rb, using the concept of spontaneous symmetry breaking is also presented.

Intragenic motifs regulate the transcriptional complexity of Pkhd1/PKHD1

PubMed Central

Boddu, Ravindra; Yang, Chaozhe; O’Connor, Amber K.; Hendrickson, Robert Curtis; Boone, Braden; Cui, Xiangqin; Garcia-Gonzalez, Miguel; Igarashi, Peter; Onuchic, Luiz F.; Germino, Gregory G.

2014-01-01

Autosomal recessive polycystic kidney disease (ARPKD) results from mutations in the human PKHD1 gene. Both this gene, and its mouse ortholog, Pkhd1, are primarily expressed in renal and biliary ductal structures. The mouse protein product, fibrocystin/polyductin complex (FPC), is a 445-kDa protein encoded by a 67-exon transcript that spans >500 kb of genomic DNA. In the current study, we observed multiple alternatively spliced Pkhd1 transcripts that varied in size and exon composition in embryonic mouse kidney, liver, and placenta samples, as well as among adult mouse pancreas, brain, heart, lung, testes, liver, and kidney. Using reverse transcription PCR and RNASeq, we identified 22 novel Pkhd1 kidney transcripts with unique exon junctions. Various mechanisms of alternative splicing were observed, including exon skipping, use of alternate acceptor/donor splice sites, and inclusion of novel exons. Bioinformatic analyses identified, and exon-trapping minigene experiments validated, consensus binding sites for serine/arginine-rich proteins that modulate alternative splicing. Using site-directed mutagenesis, we examined the functional importance of selected splice enhancers. In addition, we demonstrated that many of the novel transcripts were polysome bound, thus likely translated. Finally, we determined that the human PKHD1 R760H missense variant alters a splice enhancer motif that disrupts exon splicing in vitro and is predicted to truncate the protein. Taken together, these data provide evidence of the complex transcriptional regulation of Pkhd1/PKHD1 and identified motifs that regulate its splicing. Our studies indicate that Pkhd1/PKHD1 transcription is modulated, in part by intragenic factors, suggesting that aberrant PKHD1 splicing represents an unappreciated pathogenic mechanism in ARPKD. PMID:24984783

RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections

PubMed Central

Jaeger, Sébastien; Thieffry, Denis

2017-01-01

Abstract Transcription factor (TF) databases contain multitudes of binding motifs (TFBMs) from various sources, from which non-redundant collections are derived by manual curation. The advent of high-throughput methods stimulated the production of novel collections with increasing numbers of motifs. Meta-databases, built by merging these collections, contain redundant versions, because available tools are not suited to automatically identify and explore biologically relevant clusters among thousands of motifs. Motif discovery from genome-scale data sets (e.g. ChIP-seq) also produces redundant motifs, hampering the interpretation of results. We present matrix-clustering, a versatile tool that clusters similar TFBMs into multiple trees, and automatically creates non-redundant TFBM collections. A feature unique to matrix-clustering is its dynamic visualisation of aligned TFBMs, and its capability to simultaneously treat multiple collections from various sources. We demonstrate that matrix-clustering considerably simplifies the interpretation of combined results from multiple motif discovery tools, and highlights biologically relevant variations of similar motifs. We also ran a large-scale application to cluster ∼11 000 motifs from 24 entire databases, showing that matrix-clustering correctly groups motifs belonging to the same TF families, and drastically reduced motif redundancy. matrix-clustering is integrated within the RSAT suite (http://rsat.eu/), accessible through a user-friendly web interface or command-line for its integration in pipelines. PMID:28591841

World Color Survey color naming reveals universal motifs and their within-language diversity

PubMed Central

Lindsey, Delwin T.; Brown, Angela M.

2009-01-01

We analyzed the color terms in the World Color Survey (WCS) (www.icsi.berkeley.edu/wcs/), a large color-naming database obtained from informants of mostly unwritten languages spoken in preindustrialized cultures that have had limited contact with modern, industrialized society. The color naming idiolects of 2,367 WCS informants fall into three to six “motifs,” where each motif is a different color-naming system based on a subset of a universal glossary of 11 color terms. These motifs are universal in that they occur worldwide, with some individual variation, in completely unrelated languages. Strikingly, these few motifs are distributed across the WCS informants in such a way that multiple motifs occur in most languages. Thus, the culture a speaker comes from does not completely determine how he or she will use color terms. An analysis of the modern patterns of motif usage in the WCS languages, based on the assumption that they reflect historical patterns of color term evolution, suggests that color lexicons have changed over time in a complex but orderly way. The worldwide distribution of the motifs and the cooccurrence of multiple motifs within languages suggest that universal processes control the naming of colors. PMID:19901327

Physics with Heavy Neutron Rich Ribs at the Hribf

NASA Astrophysics Data System (ADS)

Radford, David

2002-10-01

The Holifield Radioactive Ion Beam Facility at the Oak Ridge National Laboratory has recently produced the world's first post-accelerated beams of heavy neutron-rich nuclei. B(E2;0^+ arrow 2^+) values for neutron-rich ^126,128Sn and ^132,134,136Te isotopes have been measured by Coulomb excitation of radioactive ion beams in inverse kinematics. The results for ^132Te and ^134Te (N=80,82) show excellent agreement with systematics of lighter Te isotopes, but the B(E2) value for ^136Te (N=84) is unexpectedly small. Single-neutron transfer reactions leading to ^135Te were identified using a ^134Te beam on ^natBe and ^13C targets at energies just above the Coulomb barrier. The use of the Be target provided an unambiguous signature for neutron transfer through the detection of two correlated α particles, arising from the breakup of unstable ^8Be. The results of these experiments will be discussed, togther with plans for future experiments with these heavy n-rich RIBs.

Etude descriptive et analytique du cancer de l’œsophage au Togo

PubMed Central

Oumboma, Bouglouga; Mawuli, Lawson-Ananissoh Laté; Aklesso, Bagny; Laconi, Kaaga; Datouda, Redah

2014-01-01

Introduction Décrire les aspects épidémiologiques, cliniques, endoscopiques et histologiques du cancer de l’œsophage (CO) au Togo. Méthodes Il s'agit d'une étude rétrospective descriptive et analytique menée sur 8 ans (Janvier 2005-Décembre 2012) dans le service d'hépato-gastroentérologie (HGE) du CHU Campus de Lomé. Etaient inclus les dossiers des patients hospitalisés pour CO confirmé histologiquement. Résultats Sur 8 ans, 24 patients remplissant nos critères d'inclusion ont été retenus soit 3cas de CO par an et 0,55% des hospitalisations. L’âge moyen des patients était de 57,08 ans (extrêmes: 32 et 82 ans). La dysphagie et l’épigastralgie étaient les motifs d'hospitalisation les plus rencontrés. L'alcool (n=15), le tabac (n=13) étaient les facteurs de risque les plus présents. A la fibroscopie, les lésions étaient ulcéro-bourgeonnantes et hémorragiques (n=12), ulcéro-bourgeonnantes (n=5); ces lésions siégeaient au niveau du 1/3 inférieur (n= 11), à l'union 1/3 supérieur 1/3moyen de l’œsophage (n= 13) et aucun au niveau du 1/3 supérieur. Seize lésions étaient des carcinomes épidermoïdes et 3 des adénocarcinomes. L’évolution dans le service a été fatale dans 2cas; 16 patients avaient été transférés en chirurgie pour des soins palliatifs et 5 patients (20,8%) étaient perdus de vue. Conclusion Le CO semble en augmentation au Togo. L'alcool et le tabac sont les facteurs de risque et le pronostic sévère dans notre série est lié au retard diagnostic. Son dépistage précoce passe par une consultation rapide devant toute dysphagie chez un sujet de 50 ans et plus. PMID:25883742

Motif formation and industry specific topologies in the Japanese business firm network

NASA Astrophysics Data System (ADS)

Maluck, Julian; Donner, Reik V.; Takayasu, Hideki; Takayasu, Misako

2017-05-01

Motifs and roles are basic quantities for the characterization of interactions among 3-node subsets in complex networks. In this work, we investigate how the distribution of 3-node motifs can be influenced by modifying the rules of an evolving network model while keeping the statistics of simpler network characteristics, such as the link density and the degree distribution, invariant. We exemplify this problem for the special case of the Japanese Business Firm Network, where a well-studied and relatively simple yet realistic evolving network model is available, and compare the resulting motif distribution in the real-world and simulated networks. To better approximate the motif distribution of the real-world network in the model, we introduce both subgraph dependent and global additional rules. We find that a specific rule that allows only for the merging process between nodes with similar link directionality patterns reduces the observed excess of densely connected motifs with bidirectional links. Our study improves the mechanistic understanding of motif formation in evolving network models to better describe the characteristic features of real-world networks with a scale-free topology.

VAR2CSA signatures of high Plasmodium falciparum parasitemia in the placenta.

PubMed

Rovira-Vallbona, Eduard; Monteiro, Isadora; Bardají, Azucena; Serra-Casas, Elisa; Neafsey, Daniel E; Quelhas, Diana; Valim, Clarissa; Alonso, Pedro; Dobaño, Carlota; Ordi, Jaume; Menéndez, Clara; Mayor, Alfredo

2013-01-01

Plasmodium falciparum infected erythrocytes (IE) accumulate in the placenta through the interaction between Duffy-binding like (DBL) domains of parasite-encoded ligand VAR2CSA and chondroitin sulphate-A (CSA) receptor. Polymorphisms in these domains, including DBL2X and DBL3X, may affect their antigenicity or CSA-binding affinity, eventually increasing parasitemia and its adverse effects on pregnancy outcomes. A total of 373 DBL2X and 328 DBL3X sequences were obtained from transcripts of 20 placental isolates infecting Mozambican women, resulting in 176 DBL2X and 191 DBL3X unique sequences at the protein level. Sequence alignments were divided in segments containing combinations of correlated polymorphisms and the association of segment sequences with placental parasite density was tested using Bonferroni corrected regression models, taking into consideration the weight of each sequence in the infection. Three DBL2X and three DBL3X segments contained signatures of high parasite density (P<0.003) that were highly prevalent in the parasite population (49-91%). Identified regions included a flexible loop that contributes to DBL3X-CSA interaction and two DBL3X motifs with evidence of positive natural selection. Limited antibody responses against signatures of high parasite density among malaria-exposed pregnant women could not explain the increased placental parasitemia. These results suggest that a higher binding efficiency to CSA rather than reduced antigenicity might provide a biological advantage to parasites with high parasite density signatures in VAR2CSA. Sequences contributing to high parasitemia may be critical for the functional characterization of VAR2CSA and the development of tools against placental malaria.

Identification of sequence motifs in oligonucleotides whose presence is correlated with antisense activity

PubMed Central

Matveeva, O. V.; Tsodikov, A. D.; Giddings, M.; Freier, S. M.; Wyatt, J. R.; Spiridonov, A. N.; Shabalina, S. A.; Gesteland, R. F.; Atkins, J. F.

2000-01-01

Design of antisense oligonucleotides targeting any mRNA can be much more efficient when several activity-enhancing motifs are included and activity-decreasing motifs are avoided. This conclusion was made after statistical analysis of data collected from >1000 experiments with phosphorothioate-modified oligonucleotides. Highly significant positive correlation between the presence of motifs CCAC, TCCC, ACTC, GCCA and CTCT in the oligonucleotide and its antisense efficiency was demonstrated. In addition, negative correlation was revealed for the motifs GGGG, ACTG, AAA and TAA. It was found that the likelihood of activity of an oligonucleotide against a desired mRNA target is sequence motif content dependent. PMID:10908347

Mapping Hfq-RNA interaction surfaces using tryptophan fluorescence quenching

PubMed Central

Robinson, Kirsten E.; Orans, Jillian; Kovach, Alexander R.; Link, Todd M.; Brennan, Richard G.

2014-01-01

Hfq is a posttranscriptional riboregulator and RNA chaperone that binds small RNAs and target mRNAs to effect their annealing and message-specific regulation in response to environmental stressors. Structures of Hfq-RNA complexes indicate that U-rich sequences prefer the proximal face and A-rich sequences the distal face; however, the Hfq-binding sites of most RNAs are unknown. Here, we present an Hfq-RNA mapping approach that uses single tryptophan-substituted Hfq proteins, all of which retain the wild-type Hfq structure, and tryptophan fluorescence quenching (TFQ) by proximal RNA binding. TFQ properly identified the respective distal and proximal binding of A15 and U6 RNA to Gram-negative Escherichia coli (Ec) Hfq and the distal face binding of (AA)3A, (AU)3A and (AC)3A to Gram-positive Staphylococcus aureus (Sa) Hfq. The inability of (GU)3G to bind the distal face of Sa Hfq reveals the (R-L)n binding motif is a more restrictive (A-L)n binding motif. Remarkably Hfq from Gram-positive Listeria monocytogenes (Lm) binds (GU)3G on its proximal face. TFQ experiments also revealed the Ec Hfq (A-R-N)n distal face-binding motif should be redefined as an (A-A-N)n binding motif. TFQ data also demonstrated that the 5′-untranslated region of hfq mRNA binds both the proximal and distal faces of Ec Hfq and the unstructured C-terminus. PMID:24288369

Biosynthesis and stabilization of Au and Au Ag alloy nanoparticles by fungus, Fusarium semitectum

NASA Astrophysics Data System (ADS)

Dasaratrao Sawle, Balaji; Salimath, Basavaraja; Deshpande, Raghunandan; Dhondojirao Bedre, Mahesh; Krishnamurthy Prabhakar, Belawadi; Venkataraman, Abbaraju

2008-09-01

Crystallized and spherical-shaped Au and Au-Ag alloy nanoparticles have been synthesized and stabilized using a fungus, F . semitectum in an aqueous system. Aqueous solutions of chloroaurate ions for Au and chloroaurate and Ag+ ions (1 : 1 ratio) for Au-Ag alloy were treated with an extracellular filtrate of F . semitectum biomass for the formation of Au nanoparticles (AuNP) and Au-Ag alloy nanoparticles (Au-AgNP). Analysis of the feasibility of the biosynthesized nanoparticles and core-shell alloy nanoparticles from fungal strains is particularly significant. The resultant colloidal suspensions are highly stable for many weeks. The obtained Au and Au-Ag alloy nanoparticles were characterized by the surface plasmon resonance (SPR) peaks using a UV-vis spectrophotometer, and the structure, morphology and size were determined by Fourier transform infrared spectroscopy (FTIR), x-ray diffraction (XRD), and transmission electron microscopy (TEM). Possible optoelectronics and medical applications of these nanoparticles are envisaged.

Binding properties of SUMO-interacting motifs (SIMs) in yeast.

PubMed

Jardin, Christophe; Horn, Anselm H C; Sticht, Heinrich

2015-03-01

Small ubiquitin-like modifier (SUMO) conjugation and interaction play an essential role in many cellular processes. A large number of yeast proteins is known to interact non-covalently with SUMO via short SUMO-interacting motifs (SIMs), but the structural details of this interaction are yet poorly characterized. In the present work, sequence analysis of a large dataset of 148 yeast SIMs revealed the existence of a hydrophobic core binding motif and a preference for acidic residues either within or adjacent to the core motif. Thus the sequence properties of yeast SIMs are highly similar to those described for human. Molecular dynamics simulations were performed to investigate the binding preferences for four representative SIM peptides differing in the number and distribution of acidic residues. Furthermore, the relative stability of two previously observed alternative binding orientations (parallel, antiparallel) was assessed. For all SIMs investigated, the antiparallel binding mode remained stable in the simulations and the SIMs were tightly bound via their hydrophobic core residues supplemented by polar interactions of the acidic residues. In contrary, the stability of the parallel binding mode is more dependent on the sequence features of the SIM motif like the number and position of acidic residues or the presence of additional adjacent interaction motifs. This information should be helpful to enhance the prediction of SIMs and their binding properties in different organisms to facilitate the reconstruction of the SUMO interactome.

Surface-enhanced Raman spectroscopic studies of the Au-pentacene interface: a combined experimental and theoretical investigation.

PubMed

Adil, D; Guha, S

2013-07-28

It has recently been shown [D. Adil and S. Guha, J. Phys. Chem. C 116, 12779 (2012)] that a large enhancement in the Raman intensity due to surface-enhanced Raman scattering (SERS) is observed from pentacene when probed through the Au contact in organic field-effect transistors (OFET) structures. Here, the SERS spectrum is shown to exhibit a high sensitivity to disorder introduced in the pentacene film by Au atoms. The Raman signature of the metal-semiconductor interface in pentacene OFETs is calculated with density-functional theory by explicitly considering the Au-pentacene interaction. The observed enhancement in the 1380 cm(-1) and the 1560 cm(-1) regions of the experimental Raman spectrum of pentacene is successfully modeled by Au-pentacene complexes, giving insights into the nature of disorder in the pentacene sp(2) network. Finally, we extend our previous work on high-operating voltage pentacene OFETs to low-operating voltage pentacene OFETs. No changes in the SERS spectra before and after subjecting the OFETs to a bias stress are observed, concurrent with no degradation in the threshold voltage. This shows that bias stress induced performance degradation is, in part, caused by field-induced structural changes in the pentacene molecule. Thus, we confirm that the SERS spectrum can be used as a visualization tool for correlating transport properties to structural changes, if any, in organic semiconductor based devices.

Lead isotope compositions as guides to early gold mineralization: The North Amethyst vein system, Creede district, Colorado

USGS Publications Warehouse

Foley, Nora K.; Ayuso, Robert A.

1994-01-01

Pb isotope compositions from the late stage of the North Amethyst vein system and from the Bondholder and central and southern Creede mining districts are more radiogenic than the host volcanic rocks of the central cluster of the San Juan volcanic field. Our Pb isotope results indicate that early Au mineralization of the North Amethyst area may represent the product of an older and relatively local hydrothermal system distinct from that of the younger base metal and Ag mineralization found throughout the region. Fluids that deposited Au minerals may have derived their Pb isotope composition by a greater degree of interaction with shallow, relatively less radiogenic volcanic wall rocks. The younger, base metal and Ag-rich mineralization that overprints the Au mineralization in the North Amethyst area clearly has a more radiogenic isotopic signature, which implies that the later mineralization derived a greater component of its Pb from Proterozoic source rocks, or sediments derived from them.Paragenetically early sulfide-rich vein assemblages have the least radiogenic galenas and generally also have the highest Au contents. Thus, identification of paragenetically early vein assemblages with relatively unradiogenic Pb isotope compositions similar to those of the North Amethyst area provides an additional exploration tool for Au in the central San Juan Mountains area.

Multi-scale modularity and motif distributional effect in metabolic networks.

PubMed

Gao, Shang; Chen, Alan; Rahmani, Ali; Zeng, Jia; Tan, Mehmet; Alhajj, Reda; Rokne, Jon; Demetrick, Douglas; Wei, Xiaohui

2016-01-01

Metabolism is a set of fundamental processes that play important roles in a plethora of biological and medical contexts. It is understood that the topological information of reconstructed metabolic networks, such as modular organization, has crucial implications on biological functions. Recent interpretations of modularity in network settings provide a view of multiple network partitions induced by different resolution parameters. Here we ask the question: How do multiple network partitions affect the organization of metabolic networks? Since network motifs are often interpreted as the super families of evolved units, we further investigate their impact under multiple network partitions and investigate how the distribution of network motifs influences the organization of metabolic networks. We studied Homo sapiens, Saccharomyces cerevisiae and Escherichia coli metabolic networks; we analyzed the relationship between different community structures and motif distribution patterns. Further, we quantified the degree to which motifs participate in the modular organization of metabolic networks.

Periodicity, Electronic Structures, and Bonding of Gold Tetrahalides [AuX4](-) (X = F, CI, Br, I, At, Uus)

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

Li, Wan-Lu; Li, Yong; Xu, Congqiao

2015-12-07

Systematic theoretical and experimental investigations have been performed to understand the periodicity and electronic structures of trivalent-gold halides using gold tetrahalides [AuX4]⁻ anions (X = F, Cl, Br, I, At, Uus). The [AuX4]⁻ (X = Cl, Br, I) anions were produced in gas phase and their negative-ion photoelectron spectra were obtained, which exhibited rich and well-resolved spectral peaks. We calculated the adiabatic as well as vertical electron detachment energies using density functional methods with scalar and spin-orbit coupling relativistic effects. The simulated photoelectron spectra based on these calculations are in good agreement with the experimental spectra. Our results show thatmore » the trivalent Au(III) oxidation state becomes progressively less stable while Au(I) is preferred when the halides become heavier along the Period Table. This trend reveals that the oxidation state of metals in complexes can be manipulated through ligand design« less

pH-Modulated Watson-Crick duplex-quadruplex equilibria of guanine-rich and cytosine-rich DNA sequences 140 base pairs upstream of the c-kit transcription initiation site.

PubMed

Bucek, Pavel; Jaumot, Joaquim; Aviñó, Anna; Eritja, Ramon; Gargallo, Raimundo

2009-11-23

Guanine-rich regions of DNA are sequences capable of forming G-quadruplex structures. The formation of a G-quadruplex structure in a region 140 base pairs (bp) upstream of the c-kit transcription initiation site was recently proposed (Fernando et al., Biochemistry, 2006, 45, 7854). In the present study, the acid-base equilibria and the thermally induced unfolding of the structures formed by a guanine-rich region and by its complementary cytosine-rich strand in c-kit were studied by means of circular dichroism and molecular absorption spectroscopies. In addition, competition between the Watson-Crick duplex and the isolated structures was studied as a function of pH value and temperature. Multivariate data analysis methods based on both hard and soft modeling were used to allow accurate quantification of the various acid-base species present in the mixtures. Results showed that the G-quadruplex and i-motif coexist with the Watson-Crick duplex over the pH range from 3.0 to 6.5, approximately, under the experimental conditions tested in this study. At pH 7.0, the duplex is practically the only species present.

Solid-state dewetting of Au-Ni bi-layer films mediated through individual layer thickness and stacking sequence

NASA Astrophysics Data System (ADS)

Herz, Andreas; Theska, Felix; Rossberg, Diana; Kups, Thomas; Wang, Dong; Schaaf, Peter

2018-06-01

In the present work, the solid-state dewetting of Au-Ni bi-layer thin films deposited on SiO2/Si is systematically studied with respect to individual layer thickness and stacking sequence. For this purpose, a rapid heat treatment at medium temperatures is applied in order to examine void formation at the early stages of the dewetting. Compositional variations are realized by changing the thickness ratio of the bi-layer films, while the total thickness is maintained at 20 nm throughout the study. In the event of Au/Ni films annealed at 500 °C, crystal voids exposing the substrate are missing regardless of chemical composition. In reverse order, the number of voids per unit area in two-phase Au-Ni thin films is found to be governed by the amount of Au-rich material. At higher temperatures up to 650 °C, a decreased probability of nucleation comes at the expense of a major portion of cavities, resulting in the formation of bubbles in 15 nm Ni/5 nm Au bi-layers. Film buckling predominantly occurred at phase boundaries crossing the bubbles.

Feedback Inhibition Shapes Emergent Computational Properties of Cortical Microcircuit Motifs.

PubMed

Jonke, Zeno; Legenstein, Robert; Habenschuss, Stefan; Maass, Wolfgang

2017-08-30

Cortical microcircuits are very complex networks, but they are composed of a relatively small number of stereotypical motifs. Hence, one strategy for throwing light on the computational function of cortical microcircuits is to analyze emergent computational properties of these stereotypical microcircuit motifs. We are addressing here the question how spike timing-dependent plasticity shapes the computational properties of one motif that has frequently been studied experimentally: interconnected populations of pyramidal cells and parvalbumin-positive inhibitory cells in layer 2/3. Experimental studies suggest that these inhibitory neurons exert some form of divisive inhibition on the pyramidal cells. We show that this data-based form of feedback inhibition, which is softer than that of winner-take-all models that are commonly considered in theoretical analyses, contributes to the emergence of an important computational function through spike timing-dependent plasticity: The capability to disentangle superimposed firing patterns in upstream networks, and to represent their information content through a sparse assembly code. SIGNIFICANCE STATEMENT We analyze emergent computational properties of a ubiquitous cortical microcircuit motif: populations of pyramidal cells that are densely interconnected with inhibitory neurons. Simulations of this model predict that sparse assembly codes emerge in this microcircuit motif under spike timing-dependent plasticity. Furthermore, we show that different assemblies will represent different hidden sources of upstream firing activity. Hence, we propose that spike timing-dependent plasticity enables this microcircuit motif to perform a fundamental computational operation on neural activity patterns. Copyright © 2017 the authors 0270-6474/17/378511-13$15.00/0.

Molecular dynamics simulations of the formation of 1D spin-valves from stretched Au-Co and Pt-Co nanowires

NASA Astrophysics Data System (ADS)

Cortes-Huerto, R.; Sondon, T.; Saúl, A.

2014-11-01

We have performed molecular dynamics (MD) simulations of stretched Aux-Co1 - x and Ptx-Co1 - x nanowires to investigate the formation of bimetallic monoatomic wires between two electrodes. We have considered nanowires with two concentrations x = 0.2 and 0.8, aspect ratio of 13, a cross section of 1 nm2 and a wide range of temperatures (from 10 to 400 K). For the MD simulations we have used a semi-empirical interatomic potential based on the second moment approximation (SMA) of the density of states to the tight-binding Hamiltonian. For Au-Co alloys, Au atoms tends to migrate towards the narrowed region to form almost pure Au wires. In the PtCo case the formed chains usually consist of Pt enriched alternating structures. The most striking result is probably the Au0.2-Co0.8 alloy where pure monoatomic Au chains form between two Co electrodes constituting a potential 1D spin valve. Despite the known ease with which the 5d metals (Pt, Ir, and Au) form monoatomic chains (MACS), our results show that in the presence of Co (x = 0.2), the percentage of chain formation is higher than in the Pt and Au rich cases (x = 0.8).

Keratinization-associated miR-7 and miR-21 Regulate Tumor Suppressor Reversion-inducing Cysteine-rich Protein with Kazal Motifs (RECK) in Oral Cancer*

PubMed Central

Jung, Hyun Min; Phillips, Brittany L.; Patel, Rushi S.; Cohen, Donald M.; Jakymiw, Andrew; Kong, William W.; Cheng, Jin Q.; Chan, Edward K. L.

2012-01-01

MicroRNAs (miRNAs) are small non-coding RNAs that posttranscriptionally regulate gene expression during many biological processes. Recently, the aberrant expressions of miRNAs have become a major focus in cancer research. The purpose of this study was to identify deregulated miRNAs in oral cancer and further focus on specific miRNAs that were related to patient survival. Here, we report that miRNA expression profiling provided more precise information when oral squamous cell carcinomas were subcategorized on the basis of clinicopathological parameters (tumor primary site, histological subtype, tumor stage, and HPV16 status). An innovative radar chart analysis method was developed to depict subcategories of cancers taking into consideration the expression patterns of multiple miRNAs combined with the clinicopathological parameters. Keratinization of tumors and the high expression of miR-21 were the major factors related to the poor prognosis of patients. Interestingly, a majority of the keratinized tumors expressed high levels of miR-21. Further investigations demonstrated the regulation of the tumor suppressor gene reversion-inducing cysteine-rich protein with kazal motifs (RECK) by two keratinization-associated miRNAs, miR-7 and miR-21. Transfection of miR-7 and miR-21-mimics reduced the expression of RECK through direct miRNA-mediated regulation, and these miRNAs were inversely correlated with RECK in CAL 27 orthotopic xenograft tumors. Furthermore, a similar inverse correlation was demonstrated in CAL 27 cells treated in vitro by different external stimuli such as trypsinization, cell density, and serum concentration. Taken together, our data show that keratinization is associated with poor prognosis of oral cancer patients and keratinization-associated miRNAs mediate deregulation of RECK which may contribute to the aggressiveness of tumors. PMID:22761427

Efficient sequential and parallel algorithms for finding edit distance based motifs.

PubMed

Pal, Soumitra; Xiao, Peng; Rajasekaran, Sanguthevar

2016-08-18

Motif search is an important step in extracting meaningful patterns from biological data. The general problem of motif search is intractable and there is a pressing need to develop efficient, exact and approximation algorithms to solve this problem. In this paper, we present several novel, exact, sequential and parallel algorithms for solving the (l,d) Edit-distance-based Motif Search (EMS) problem: given two integers l,d and n biological strings, find all strings of length l that appear in each input string with atmost d errors of types substitution, insertion and deletion. One popular technique to solve the problem is to explore for each input string the set of all possible l-mers that belong to the d-neighborhood of any substring of the input string and output those which are common for all input strings. We introduce a novel and provably efficient neighborhood exploration technique. We show that it is enough to consider the candidates in neighborhood which are at a distance exactly d. We compactly represent these candidate motifs using wildcard characters and efficiently explore them with very few repetitions. Our sequential algorithm uses a trie based data structure to efficiently store and sort the candidate motifs. Our parallel algorithm in a multi-core shared memory setting uses arrays for storing and a novel modification of radix-sort for sorting the candidate motifs. The algorithms for EMS are customarily evaluated on several challenging instances such as (8,1), (12,2), (16,3), (20,4), and so on. The best previously known algorithm, EMS1, is sequential and in estimated 3 days solves up to instance (16,3). Our sequential algorithms are more than 20 times faster on (16,3). On other hard instances such as (9,2), (11,3), (13,4), our algorithms are much faster. Our parallel algorithm has more than 600 % scaling performance while using 16 threads. Our algorithms have pushed up the state-of-the-art of EMS solvers and we believe that the techniques introduced in

Physical-chemical property based sequence motifs and methods regarding same

DOEpatents

Braun, Werner [Friendswood, TX; Mathura, Venkatarajan S [Sarasota, FL; Schein, Catherine H [Friendswood, TX

2008-09-09

A data analysis system, program, and/or method, e.g., a data mining/data exploration method, using physical-chemical property motifs. For example, a sequence database may be searched for identifying segments thereof having physical-chemical properties similar to the physical-chemical property motifs.

DETAIL VIEW, MAIN ENTRANCE GATES, SHOWING A WINGED HOURGLASS MOTIF, ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

DETAIL VIEW, MAIN ENTRANCE GATES, SHOWING A WINGED HOURGLASS MOTIF, WHICH REFERS TO THE QUICK PASSAGE OF TIME AND THE SHORTNESS OF HUMAN LIFE. USE OF THIS MOTIF WAS A CARRYOVER FROM THE MCARTHUR GATES. - Woodlands Cemetery, 4000 Woodlands Avenue, Philadelphia, Philadelphia County, PA

Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs.

PubMed

Regad, Leslie; Martin, Juliette; Camproux, Anne-Claude

2011-06-20

One of the strategies for protein function annotation is to search particular structural motifs that are known to be shared by proteins with a given function. Here, we present a systematic extraction of structural motifs of seven residues from protein loops and we explore their correspondence with functional sites. Our approach is based on the structural alphabet HMM-SA (Hidden Markov Model - Structural Alphabet), which allows simplification of protein structures into uni-dimensional sequences, and advanced pattern statistics adapted to short sequences. Structural motifs of interest are selected by looking for structural motifs significantly over-represented in SCOP superfamilies in protein loops. We discovered two types of structural motifs significantly over-represented in SCOP superfamilies: (i) ubiquitous motifs, shared by several superfamilies and (ii) superfamily-specific motifs, over-represented in few superfamilies. A comparison of ubiquitous words with known small structural motifs shows that they contain well-described motifs as turn, niche or nest motifs. A comparison between superfamily-specific motifs and biological annotations of Swiss-Prot reveals that some of them actually correspond to functional sites involved in the binding sites of small ligands, such as ATP/GTP, NAD(P) and SAH/SAM. Our findings show that statistical over-representation in SCOP superfamilies is linked to functional features. The detection of over-represented motifs within structures simplified by HMM-SA is therefore a promising approach for prediction of functional sites and annotation of uncharacterized proteins.