Distribution and Evolution of Yersinia Leucine-Rich Repeat Proteins

PubMed Central

Hu, Yueming; Huang, He; Hui, Xinjie; Cheng, Xi; White, Aaron P.

2016-01-01

Leucine-rich repeat (LRR) proteins are widely distributed in bacteria, playing important roles in various protein-protein interaction processes. In Yersinia, the well-characterized type III secreted effector YopM also belongs to the LRR protein family and is encoded by virulence plasmids. However, little has been known about other LRR members encoded by Yersinia genomes or their evolution. In this study, the Yersinia LRR proteins were comprehensively screened, categorized, and compared. The LRR proteins encoded by chromosomes (LRR1 proteins) appeared to be more similar to each other and different from those encoded by plasmids (LRR2 proteins) with regard to repeat-unit length, amino acid composition profile, and gene expression regulation circuits. LRR1 proteins were also different from LRR2 proteins in that the LRR1 proteins contained an E3 ligase domain (NEL domain) in the C-terminal region or an NEL domain-encoding nucleotide relic in flanking genomic sequences. The LRR1 protein-encoding genes (LRR1 genes) varied dramatically and were categorized into 4 subgroups (a to d), with the LRR1a to -c genes evolving from the same ancestor and LRR1d genes evolving from another ancestor. The consensus and ancestor repeat-unit sequences were inferred for different LRR1 protein subgroups by use of a maximum parsimony modeling strategy. Structural modeling disclosed very similar repeat-unit structures between LRR1 and LRR2 proteins despite the different unit lengths and amino acid compositions. Structural constraints may serve as the driving force to explain the observed mutations in the LRR regions. This study suggests that there may be functional variation and lays the foundation for future experiments investigating the functions of the chromosomally encoded LRR proteins of Yersinia. PMID:27217422

Exploring the repeat protein universe through computational protein design

DOE PAGES

Brunette, TJ; Parmeggiani, Fabio; Huang, Po-Ssu; ...

2015-12-16

A central question in protein evolution is the extent to which naturally occurring proteins sample the space of folded structures accessible to the polypeptide chain. Repeat proteins composed of multiple tandem copies of a modular structure unit are widespread in nature and have critical roles in molecular recognition, signalling, and other essential biological processes. Naturally occurring repeat proteins have been re-engineered for molecular recognition and modular scaffolding applications. In this paper, we use computational protein design to investigate the space of folded structures that can be generated by tandem repeating a simple helix–loop–helix–loop structural motif. Eighty-three designs with sequences unrelatedmore » to known repeat proteins were experimentally characterized. Of these, 53 are monomeric and stable at 95 °C, and 43 have solution X-ray scattering spectra consistent with the design models. Crystal structures of 15 designs spanning a broad range of curvatures are in close agreement with the design models with root mean square deviations ranging from 0.7 to 2.5 Å. Finally, our results show that existing repeat proteins occupy only a small fraction of the possible repeat protein sequence and structure space and that it is possible to design novel repeat proteins with precisely specified geometries, opening up a wide array of new possibilities for biomolecular engineering.« less

Novel structure of cockroach allergen Bla g 1 has implications for allergenicity and exposure assessment

PubMed Central

Mueller, Geoffrey A.; Pedersen, Lars C.; Lih, Fred B.; Glesner, Jill; Moon, Andrea F.; Chapman, Martin D.; Tomer, Kenneth B.; London, Robert E.; Pomés, Anna

2013-01-01

Background Sensitization to cockroach allergens is a major risk factor for asthma. The cockroach allergen Bla g 1 has multiple repeats of ~100 amino acids, but the fold of the protein and the biological function are unknown. Objective To determine the structure of Bla g 1, investigate the implications for allergic disease, and standardize cockroach exposure assays. Methods Natural Bla g 1 and recombinant constructs were compared by ELISA using specific murine IgG and human IgE. The structure of Bla g 1 was determined by X-ray crystallography. Mass spectrometry and NMR were utilized to examine ligand-binding properties of the allergen. Results The structure of a recombinant Bla g 1 construct with comparable IgE and IgG reactivity to the natural allergen was solved by X-ray crystallography. The Bla g 1 repeat forms a novel fold with 6 helices. Two repeats encapsulate a large and nearly spherical hydrophobic cavity, defining the basic structural unit. Lipids in the cavity varied depending on the allergen origin. Palmitic, oleic and stearic acids were associated with nBla g 1 from cockroach frass. One Unit of Bla g 1 was equivalent to 104 ng of allergen. Conclusions Bla g 1 has a novel fold with a capacity to bind various lipids, which suggests a digestive function associated with non-specific transport of lipid molecules in cockroaches. Defining the basic structural unit of Bla g 1 facilitates the standardization of assays in absolute units for the assessment of environmental allergen exposure. PMID:23915714

Investigation of a Quadruplex-Forming Repeat Sequence Highly Enriched in Xanthomonas and Nostoc sp.

PubMed

Rehm, Charlotte; Wurmthaler, Lena A; Li, Yuanhao; Frickey, Tancred; Hartig, Jörg S

2015-01-01

In prokaryotes simple sequence repeats (SSRs) with unit sizes of 1-5 nucleotides (nt) are causative for phase and antigenic variation. Although an increased abundance of heptameric repeats was noticed in bacteria, reports about SSRs of 6-9 nt are rare. In particular G-rich repeat sequences with the propensity to fold into G-quadruplex (G4) structures have received little attention. In silico analysis of prokaryotic genomes show putative G4 forming sequences to be abundant. This report focuses on a surprisingly enriched G-rich repeat of the type GGGNATC in Xanthomonas and cyanobacteria such as Nostoc. We studied in detail the genomes of Xanthomonas campestris pv. campestris ATCC 33913 (Xcc), Xanthomonas axonopodis pv. citri str. 306 (Xac), and Nostoc sp. strain PCC7120 (Ana). In all three organisms repeats are spread all over the genome with an over-representation in non-coding regions. Extensive variation of the number of repetitive units was observed with repeat numbers ranging from two up to 26 units. However a clear preference for four units was detected. The strong bias for four units coincides with the requirement of four consecutive G-tracts for G4 formation. Evidence for G4 formation of the consensus repeat sequences was found in biophysical studies utilizing CD spectroscopy. The G-rich repeats are preferably located between aligned open reading frames (ORFs) and are under-represented in coding regions or between divergent ORFs. The G-rich repeats are preferentially located within a distance of 50 bp upstream of an ORF on the anti-sense strand or within 50 bp from the stop codon on the sense strand. Analysis of whole transcriptome sequence data showed that the majority of repeat sequences are transcribed. The genetic loci in the vicinity of repeat regions show increased genomic stability. In conclusion, we introduce and characterize a special class of highly abundant and wide-spread quadruplex-forming repeat sequences in bacteria.

Investigation of a Quadruplex-Forming Repeat Sequence Highly Enriched in Xanthomonas and Nostoc sp.

PubMed Central

Rehm, Charlotte; Wurmthaler, Lena A.; Li, Yuanhao; Frickey, Tancred; Hartig, Jörg S.

2015-01-01

In prokaryotes simple sequence repeats (SSRs) with unit sizes of 1–5 nucleotides (nt) are causative for phase and antigenic variation. Although an increased abundance of heptameric repeats was noticed in bacteria, reports about SSRs of 6–9 nt are rare. In particular G-rich repeat sequences with the propensity to fold into G-quadruplex (G4) structures have received little attention. In silico analysis of prokaryotic genomes show putative G4 forming sequences to be abundant. This report focuses on a surprisingly enriched G-rich repeat of the type GGGNATC in Xanthomonas and cyanobacteria such as Nostoc. We studied in detail the genomes of Xanthomonas campestris pv. campestris ATCC 33913 (Xcc), Xanthomonas axonopodis pv. citri str. 306 (Xac), and Nostoc sp. strain PCC7120 (Ana). In all three organisms repeats are spread all over the genome with an over-representation in non-coding regions. Extensive variation of the number of repetitive units was observed with repeat numbers ranging from two up to 26 units. However a clear preference for four units was detected. The strong bias for four units coincides with the requirement of four consecutive G-tracts for G4 formation. Evidence for G4 formation of the consensus repeat sequences was found in biophysical studies utilizing CD spectroscopy. The G-rich repeats are preferably located between aligned open reading frames (ORFs) and are under-represented in coding regions or between divergent ORFs. The G-rich repeats are preferentially located within a distance of 50 bp upstream of an ORF on the anti-sense strand or within 50 bp from the stop codon on the sense strand. Analysis of whole transcriptome sequence data showed that the majority of repeat sequences are transcribed. The genetic loci in the vicinity of repeat regions show increased genomic stability. In conclusion, we introduce and characterize a special class of highly abundant and wide-spread quadruplex-forming repeat sequences in bacteria. PMID:26695179

Distinct C9orf72-Associated Dipeptide Repeat Structures Correlate with Neuronal Toxicity

PubMed Central

Krans, Amy; Sawaya, Michael R.; Paulson, Henry L.; Todd, Peter K.; Barmada, Sami J.; Ivanova, Magdalena I.

2016-01-01

Hexanucleotide repeat expansions in C9orf72 are the most common inherited cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The expansions elicit toxicity in part through repeat-associated non-AUG (RAN) translation of the intronic (GGGGCC)n sequence into dipeptide repeat-containing proteins (DPRs). Little is known, however, about the structural characteristics and aggregation propensities of the dipeptide units comprising DPRs. To address this question, we synthesized dipeptide units corresponding to the three sense-strand RAN translation products, analyzed their structures by circular dichroism, electron microscopy and dye binding assays, and assessed their relative toxicity when applied to primary cortical neurons. Short, glycine-arginine (GR)3 dipeptides formed spherical aggregates and selectively reduced neuronal survival compared to glycine-alanine (GA)3 and glycine-proline (GP)3 dipeptides. Doubling peptide length had little effect on the structure of GR or GP peptides, but (GA)6 peptides formed β-sheet rich aggregates that bound thioflavin T and Congo red yet lacked the typical fibrillar morphology of amyloids. Aging of (GA)6 dipeptides increased their β-sheet content and enhanced their toxicity when applied to neurons. We also observed that the relative toxicity of each tested dipeptide was proportional to peptide internalization. Our results demonstrate that different C9orf72-related dipeptides exhibit distinct structural properties that correlate with their relative toxicity. PMID:27776165

Using a Virtual Manipulative Environment to Support Students' Organizational Structuring of Volume Units

ERIC Educational Resources Information Center

O'Dell, Jenna R.; Barrett, Jeffrey E.; Cullen, Craig J.; Rupnow, Theodore J.; Clements, Douglas H.; Sarama, Julie; Rutherford, George; Beck, Pamela S.

2017-01-01

In this study, we investigated how Grade 3 and 4 students' organizational structure for volume units develops through repeated experiences with a virtual manipulative for building prisms. Our data consist of taped clinical interviews within a micro-genetic experiment. We report on student strategy development using a virtual manipulative for…

Subnanometre-resolution structure of the doublet microtubule reveals new classes of microtubule-associated proteins

PubMed Central

Ichikawa, Muneyoshi; Liu, Dinan; Kastritis, Panagiotis L.; Basu, Kaustuv; Hsu, Tzu Chin; Yang, Shunkai; Bui, Khanh Huy

2017-01-01

Cilia are ubiquitous, hair-like appendages found in eukaryotic cells that carry out functions of cell motility and sensory reception. Cilia contain an intriguing cytoskeletal structure, termed the axoneme that consists of nine doublet microtubules radially interlinked and longitudinally organized in multiple specific repeat units. Little is known, however, about how the axoneme allows cilia to be both actively bendable and sturdy or how it is assembled. To answer these questions, we used cryo-electron microscopy to structurally analyse several of the repeating units of the doublet at sub-nanometre resolution. This structural detail enables us to unambiguously assign α- and β-tubulins in the doublet microtubule lattice. Our study demonstrates the existence of an inner sheath composed of different kinds of microtubule inner proteins inside the doublet that likely stabilizes the structure and facilitates the specific building of the B-tubule. PMID:28462916

Poly(phenylene)-based anion exchange membrane

DOEpatents

Hibbs, Michael [Albuquerque, NM; Cornelius, Christopher J [Albuquerque, NM; Fujimoto, Cy H [Albuquerque, NM

2011-02-15

A poly(phenylene) compound of copolymers that can be prepared with either random or multiblock structures where a first polymer has a repeat unit with a structure of four sequentially connected phenyl rings with a total of 2 pendant phenyl groups and 4 pendant tolyl groups and the second polymer has a repeat unit with a structure of four sequentially connected phenyl rings with a total of 6 pendant phenyl groups. The second polymer has chemical groups attached to some of the pendant phenyl groups selected from CH.sub.3, CH.sub.2Br, and CH.sub.2N(CH.sub.3).sub.3Br groups. When at least one group is CH.sub.2N(CH.sub.3).sub.3Br, the material functions as an anion exchange membrane.

Identification of a highly sulfated fucoidan from sea cucumber Pearsonothuria graeffei with well-repeated tetrasaccharides units.

PubMed

Hu, Yaqin; Li, Shan; Li, Junhui; Ye, Xingqian; Ding, Tian; Liu, Donghong; Chen, Jianchu; Ge, Zhiwei; Chen, Shiguo

2015-12-10

Sea cucumber fucoidan is a major bioactive component of sea cucumber. The structures of fucoidans have significant influences on their biological activities. The present study clarified the delicate structure of a fucoidan from Pearsonothuria graeffei. Fucoidan was obtained after papain digestion and purified by ion chromatography. The carbohydrate sequence of fucoidan was firstly determined by negative-ion electrospray tandem mass spectrometry (ES-MS) with collision-induced dissociation of the oligosaccharide fragments, which were obtained by mild acid hydrolysis, and completed by NMR for assignment of the anomeric conformation. It was unambiguously identified as a tetrasaccharide repeating unit with a backbone of [ → 3Fuc (2S, 4S) α1 → 3Fucα1→ 3Fuc (4S) α1 → 3Fuc#7 × 10#]n. The glycosidic bonds between the non-sulfated and 2,4-O-disulfated fucose residues were selectively cleaved, and highly ordered oligosaccharide fragments with a tetrasaccharide repeating unit were obtained. The highly 4-O- and 2, 4-di-O-sulfated polysaccharide deserves further developments for Pharmacia use. Copyright © 2015 Elsevier Ltd. All rights reserved.

Solid polymeric electrolytes for lithium batteries

DOEpatents

Angell, Charles A.; Xu, Wu; Sun, Xiaoguang

2006-03-14

Novel conductive polyanionic polymers and methods for their preparion are provided. The polyanionic polymers comprise repeating units of weakly-coordinating anionic groups chemically linked to polymer chains. The polymer chains in turn comprise repeating spacer groups. Spacer groups can be chosen to be of length and structure to impart desired electrochemical and physical properties to the polymers. Preferred embodiments are prepared from precursor polymers comprising the Lewis acid borate tri-coordinated to a selected ligand and repeating spacer groups to form repeating polymer chain units. These precursor polymers are reacted with a chosen Lewis base to form a polyanionic polymer comprising weakly coordinating anionic groups spaced at chosen intervals along the polymer chain. The polyanionic polymers exhibit high conductivity and physical properties which make them suitable as solid polymeric electrolytes in lithium batteries, especially secondary lithium batteries.

Structural elucidation of the Brucella melitensis M antigen by high-resolution NMR at 500 MHz

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

Bundle, D.R.; Cherwonogrodzky, J.W.; Perry, M.B.

The Brucella M antigen from the species type strain Brucella melitensis 16M has been identified as a component of the cell wall lipopolysaccharide (LPS). O polysaccharide liberated from this LPS by mild acid hydrolysis exhibited M activity in serological tests and was shown to be a homopolymer of 4-formamido-4,6-dideoxy-..cap alpha..-D-mannopyranosyl residues arranged in an oligosaccharide repeating unit as judged by sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the native lipopolysaccharide. Structural analysis of the O polysaccharide by NMR methods was difficult due to apparent microheterogeneity of the repeating unit, which was in fact caused by the presence of rotational isomers ofmore » the N-formyl moiety. This problem was resolved by chemical modification of the polysaccharide to its amino and N-acetyl derivatives, the 500-MHz /sup 1/H and 125-MHz /sup 13/C NMR spectra of which could be analyzed in terms of a unique structure through application of pH-dependent ..beta..-shifts and two-dimensional techniques that included COSY, relayed COSY, and NOESY experiments together with heteronuclear C/H shift correlation spectroscopy. On the basis of these experiments and supported by methylation and periodate oxidation data, the structure of the M polysaccharide was determined as a linear polymer of unbranched pentasaccharide repeating units consisting of four 1,2-linked and one 1,3-lined 4,6-dideoxy-4-formamido-..cap alpha..-D-mannopyranosyl residues. The marked structural similarity of the M antigen and the A antigen, which is known to be a 1,2-linked homopolysaccharide of 4,6-dideoxy-4-formamido-..cap alpha..-D-mannopyranosyl units, accounts for cross-serological reactions of the two and the long-standing confusion surrounding the nature of their antigenic determinants.« less

Structure, organization, and sequence of alpha satellite DNA from human chromosome 17: evidence for evolution by unequal crossing-over and an ancestral pentamer repeat shared with the human X chromosome.

PubMed

Waye, J S; Willard, H F

1986-09-01

The centromeric regions of all human chromosomes are characterized by distinct subsets of a diverse tandemly repeated DNA family, alpha satellite. On human chromosome 17, the predominant form of alpha satellite is a 2.7-kilobase-pair higher-order repeat unit consisting of 16 alphoid monomers. We present the complete nucleotide sequence of the 16-monomer repeat, which is present in 500 to 1,000 copies per chromosome 17, as well as that of a less abundant 15-monomer repeat, also from chromosome 17. These repeat units were approximately 98% identical in sequence, differing by the exclusion of precisely 1 monomer from the 15-monomer repeat. Homologous unequal crossing-over is suggested as a probable mechanism by which the different repeat lengths on chromosome 17 were generated, and the putative site of such a recombination event is identified. The monomer organization of the chromosome 17 higher-order repeat unit is based, in part, on tandemly repeated pentamers. A similar pentameric suborganization has been previously demonstrated for alpha satellite of the human X chromosome. Despite the organizational similarities, substantial sequence divergence distinguishes these subsets. Hybridization experiments indicate that the chromosome 17 and X subsets are more similar to each other than to the subsets found on several other human chromosomes. We suggest that the chromosome 17 and X alpha satellite subsets may be related components of a larger alphoid subfamily which have evolved from a common ancestral repeat into the contemporary chromosome-specific subsets.

Molecular tandem repeat strategy for elucidating mechanical properties of high-strength proteins

PubMed Central

Jung, Huihun; Pena-Francesch, Abdon; Saadat, Alham; Sebastian, Aswathy; Kim, Dong Hwan; Hamilton, Reginald F.; Albert, Istvan; Allen, Benjamin D.; Demirel, Melik C.

2016-01-01

Many globular and structural proteins have repetitions in their sequences or structures. However, a clear relationship between these repeats and their contribution to the mechanical properties remains elusive. We propose a new approach for the design and production of synthetic polypeptides that comprise one or more tandem copies of a single unit with distinct amorphous and ordered regions. Our designed sequences are based on a structural protein produced in squid suction cups that has a segmented copolymer structure with amorphous and crystalline domains. We produced segmented polypeptides with varying repeat number, while keeping the lengths and compositions of the amorphous and crystalline regions fixed. We showed that mechanical properties of these synthetic proteins could be tuned by modulating their molecular weights. Specifically, the toughness and extensibility of synthetic polypeptides increase as a function of the number of tandem repeats. This result suggests that the repetitions in native squid proteins could have a genetic advantage for increased toughness and flexibility. PMID:27222581

Complete structure of the cell surface polysaccharide of Streptococcus oralis C104: A 600-MHz NMR study

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

Abeygunawardana, C.; Bush, C.A.; Cisar, J.O.

1991-09-03

Specific lectin-carbohydrate interactions between certain oral streptococci and actinomyces contribute to the microbial colonization of teeth. The receptor molecules of Streptococcus oralis, 34, ATCC 10557, and Streptococcus mitis J22 for the galactose and N-acetylgalactosamine reactive fimbrial lectins of Actinomyces viscosus and Actinomyces naeslundii are antigenically distinct polysaccharides, each formed by a different phosphodiester-linked oligosaccharide repeating unit. Receptor polysaccharide was isolated form S. oralis C104 cells and was shown to contain galactose, N-acetylgalactosamine, ribitol, and phosphate with molar ratios of 4:1:1:1. The {sup 1}H NMR spectrum of the polysaccharide shows that it contains a repeating structure. The individual sugars in themore » repeating unit were identified by {sup 1}H coupling constants observed in E-COSY and DQF-COSY spectra. NMR methods included complete resonance assignments ({sup 1}H and {sup 13}C) by various homonuclear and heteronuclear correlation experiments that utilize scalar couplings. Sequence and linkage assignments were obtained from the heteronuclear multiple-bond correlation (HMBC) spectrum. This analysis shows that the receptor polysaccharide of S. oralis C104 is a ribitol teichoic acid polymer composed of a linear hexasaccharide repeating unit containing two residues each of galactopyranose and galactofuranose and a residue each of GalNAc and ribitol joined end to end by phosphodiester linkages.« less

Comparative Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) of Streptococcus thermophilus St-I and its Bacteriophage-Insensitive Mutants (BIM) Derivatives.

PubMed

Li, Wan; Bian, Xin; Evivie, Smith Etareri; Huo, Gui-Cheng

2016-09-01

The CRISPR-Cas (CRISPR together with CRISPR-associated proteins) modules are the adaptive immune system, acting as an adaptive and heritable immune system in bacteria and archaea. CRISPR-based immunity acts by integrating short virus sequences in the cell's CRISPR locus, allowing the cell to remember, recognize, and clear infections. In this study, the homology of CRISPRs sequence in BIMs (bacteriophage-insensitive mutants) of Streptococcus thermophilus St-I were analyzed. Secondary structures of the repeats and the PAMs (protospacer-associated motif) of each CRISPR locus were also predicted. Results showed that CRISPR1 has 27 repeat-spacer units, 5 of them had duplicates; CRISPR2 has one repeat-spacer unit; CRISPR3 has 28 repeat-spacer units. Only BIM1 had a new spacer acquisition in CRISPR3, while BIM2 and BIM3 had no new spacers' insertion, thus indicating that while most CRISPR1 were more active than CRISPR3, new spacer acquisition occurred just in CRSPR3 in some situations. These findings will help establish the foundation for the study of CRSPR-Cas systems in lactic acid bacteria.

The Disruptive Effect of Lysozyme on the Bacterial Cell Wall Explored by an "In-Silico" Structural Outlook

ERIC Educational Resources Information Center

Primo, Emiliano D.; Otero, Lisandro H.; Ruiz, Francisco; Klinke, Sebastián; Giordano, Walter

2018-01-01

The bacterial cell wall, a structural unit of peptidoglycan polymer comprised of glycan strands consisting of a repeating disaccharide motif [N-acetylglucosamine (NAG) and N-acetylmuramylpentapeptide (NAM pentapeptide)], encases bacteria and provides structural integrity and protection. Lysozymes are enzymes that break down the bacterial cell wall…

A tensegrity model for hydrogen bond networks in proteins.

PubMed

Bywater, Robert P

2017-05-01

Hydrogen-bonding networks in proteins considered as structural tensile elements are in balance separately from any other stabilising interactions that may be in operation. The hydrogen bond arrangement in the network is reminiscent of tensegrity structures in architecture and sculpture. Tensegrity has been discussed before in cells and tissues and in proteins. In contrast to previous work only hydrogen bonds are studied here. The other interactions within proteins are either much stronger - covalent bonds connecting the atoms in the molecular skeleton or weaker forces like the so-called hydrophobic interactions. It has been demonstrated that the latter operate independently from hydrogen bonds. Each category of interaction must, if the protein is to have a stable structure, balance out. The hypothesis here is that the entire hydrogen bond network is in balance without any compensating contributions from other types of interaction. For sidechain-sidechain, sidechain-backbone and backbone-backbone hydrogen bonds in proteins, tensegrity balance ("closure") is required over the entire length of the polypeptide chain that defines individually folding units in globular proteins ("domains") as well as within the repeating elements in fibrous proteins that consist of extended chain structures. There is no closure to be found in extended structures that do not have repeating elements. This suggests an explanation as to why globular domains, as well as the repeat units in fibrous proteins, have to have a defined number of residues. Apart from networks of sidechain-sidechain hydrogen bonds there are certain key points at which this closure is achieved in the sidechain-backbone hydrogen bonds and these are associated with demarcation points at the start or end of stretches of secondary structure. Together, these three categories of hydrogen bond achieve the closure that is necessary for the stability of globular protein domains as well as repeating elements in fibrous proteins.

Studies on the primary structure of short polysaccharides using SEC MALDI mass spectroscopy.

PubMed

Garozzo, D; Spina, E; Cozzolino, R; Cescutti, P; Fett, W F

2000-01-12

The introduction of size-exclusion chromatography (SEC) analysis of polysaccharides prior to MALDI mass spectroscopy accounts for the determination of the molecular mass of the repeating unit when neutral homopolymers are investigated. In the case of natural polysaccharides characterised by more complicated structural features (presence of non-carbohydrate substituents, charged groups, etc.), this mass value usually is in agreement with more than one sugar composition. Therefore, it is not sufficient to give the correct monosaccharidic composition of the polysaccharide investigated. To solve this problem, MALDI spectra were recorded on the permethylated sample and post-source decay experiments were performed on precursor ions. In this way, the composition (in terms of Hex, HexNAc, etc.), size and sequence of the repeating unit were determined.

Ionic strength and temperature induced conformational changes in mononucleosomes and oligonucleosomes. [Chromatin

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

Schmitz, K.S.; Kent, J.C.; Parthasarathy, N.

1980-10-01

Chromatin is a nucleohistone complex which exhibits a repeat unit structure as inferred from nuclease digestion studies. The repeat unit, or nucleosome, is defined as approx. 200 base pairs of DNA wrapped about the surface of an octameric histone complex (two copies each of the histones H2A, H2B, H3, and H4). We report in this communication preliminary studies on the conformation of chromatin mononucleosomes and oligonucleosomes as a function of temperature and ionic strength. The methods used were conductivity, fluorescence of bound proflavine, and quasielastic light scattering.

An examination of the origin and evolution of additional tandem repeats in the mitochondrial DNA control region of Japanese sika deer (Cervus Nippon).

PubMed

Ba, Hengxing; Wu, Lang; Liu, Zongyue; Li, Chunyi

2016-01-01

Tandem repeat units are only detected in the left domain of the mitochondrial DNA control region in sika deer. Previous studies showed that Japanese sika deer have more tandem repeat units than its cousins from the Asian continent and Taiwan, which often have only three repeat units. To determine the origin and evolution of these additional repeat units in Japanese sika deer, we obtained the sequence of repeat units from an expanded dataset of the control region from all sika deer lineages. The functional constraint is inferred to act on the first repeat unit because this repeat has the least sequence divergence in comparison to the other units. Based on slipped-strand mispairing mechanisms, the illegitimate elongation model could account for the addition or deletion of these additional repeat units in the Japanese sika deer population. We also report that these additional repeat units could be occurring in the internal positions of tandem repeat regions, possibly via coupling with a homogenization mechanism within and among these lineages. Moreover, the increased number of repeat units in the Japanese sika deer population could reflect a balance between mutation and selection, as well as genetic drift.

Genetic Transfer of Salmonella typhimurium and Escherichia coli Lipopolysaccharide Antigens to Escherichia coli K-12

PubMed Central

Jones, Randall T.; Koeltzow, Donald E.; Stocker, B. A. D.

1972-01-01

Escherichia coli K-12 ϰ971 was crossed with a smooth Salmonella typhimurium donor, HfrK6, which transfers early the ilv-linked rfa region determining lipopolysaccharide (LPS) core structure. Two ilv+ hybrids differing in their response to the LPS-specific phages FO and C21 were then crossed with S. typhimurium HfrK9, which transfers early the rfb gene cluster determining O repeat unit structure. Most recombinants selected for his+ (near rfb) were agglutinated by Salmonella factor 4 antiserum. Transfer of an F′ factor (FS400) carrying the rfb–his region of S. typhimurium to the same two ilv+ hybrids gave similar results. LPS extracted from two ilv+,his+, factor 4-positive hybrids contained abequose, the immunodominant sugar for factor 4 specificity. By contrast, his+ hybrids obtained from ϰ971 itself by similar HfrK9 and F′FS400 crosses were not agglutinated by factor 4 antiserum, indicating that the parental E. coli ϰ971 does not have the capacity to attach Salmonella O repeat units to its LPS core. It is concluded that the Salmonella rfb genes are expressed only in E. coli ϰ971 hybrids which have also acquired ilv-linked genes (presumably rfa genes affecting core structure or O-translocase ability, or both) from a S. typhimurium donor. When E. coli ϰ971 was crossed with a smooth E. coli donor, Hfr59, of serotype O8, which transfers his early, most his+ recombinants were agglutinated by E. coli O8 antiserum and lysed by the O8-specific phage, Ω8. This suggests that, although the parental E. coli K-12 strain ϰ971 cannot attach Salmonella-specific repeat units to its LPS core, it does have the capacity to attach E. coli O8-specific repeat units. PMID:4559827

Identification and characterization of tandem repeats in exon III of dopamine receptor D4 (DRD4) genes from different mammalian species.

PubMed

Larsen, Svend Arild; Mogensen, Line; Dietz, Rune; Baagøe, Hans Jørgen; Andersen, Mogens; Werge, Thomas; Rasmussen, Henrik Berg

2005-12-01

In this study we have identified and characterized dopamine receptor D4 (DRD4) exon III tandem repeats in 33 public available nucleotide sequences from different mammalian species. We found that the tandem repeat in canids could be described in a novel and simple way, namely, as a structure composed of 15- and 12- bp modules. Tandem repeats composed of 18-bp modules were found in sequences from the horse, zebra, onager, and donkey, Asiatic bear, polar bear, common raccoon, dolphin, harbor porpoise, and domestic cat. Several of these sequences have been analyzed previously without a tandem repeat being found. In the domestic cow and gray seal we identified tandem repeats composed of 36-bp modules, each consisting of two closely related 18-bp basic units. A tandem repeat consisting of 9-bp modules was identified in sequences from mink and ferret. In the European otter we detected an 18-bp tandem repeat, while a tandem repeat consisting of 27-bp modules was identified in a sequence from European badger. Both these tandem repeats were composed of 9-bp basic units, which were closely related with the 9-bp repeat modules identified in the mink and ferret. Tandem repeats could not be identified in sequences from rodents. All tandem repeats possessed a high GC content with a strong bias for C. On phylogenetic analysis of the tandem repeats evolutionary related species were clustered into the same groups. The degree of conservation of the tandem repeats varied significantly between species. The deduced amino acid sequences of most of the tandem repeats exhibited a high propensity for disorder. This was also the case with an amino acid sequence of the human DRD4 exon III tandem repeat, which was included in the study for comparative purposes. We identified proline-containing motifs for SH3 and WW domain binding proteins, potential phosphorylation sites, PDZ domain binding motifs, and FHA domain binding motifs in the amino acid sequences of the tandem repeats. The numbers of potential functional sites varied pronouncedly between species. Our observations provide a platform for future studies of the architecture and evolution of the DRD4 exon III tandem repeat, and they suggest that differences in the structure of this tandem repeat contribute to specialization and generation of diversity in receptor function.

PolySac3DB: an annotated data base of 3 dimensional structures of polysaccharides.

PubMed

Sarkar, Anita; Pérez, Serge

2012-11-14

Polysaccharides are ubiquitously present in the living world. Their structural versatility makes them important and interesting components in numerous biological and technological processes ranging from structural stabilization to a variety of immunologically important molecular recognition events. The knowledge of polysaccharide three-dimensional (3D) structure is important in studying carbohydrate-mediated host-pathogen interactions, interactions with other bio-macromolecules, drug design and vaccine development as well as material science applications or production of bio-ethanol. PolySac3DB is an annotated database that contains the 3D structural information of 157 polysaccharide entries that have been collected from an extensive screening of scientific literature. They have been systematically organized using standard names in the field of carbohydrate research into 18 categories representing polysaccharide families. Structure-related information includes the saccharides making up the repeat unit(s) and their glycosidic linkages, the expanded 3D representation of the repeat unit, unit cell dimensions and space group, helix type, diffraction diagram(s) (when applicable), experimental and/or simulation methods used for structure description, link to the abstract of the publication, reference and the atomic coordinate files for visualization and download. The database is accompanied by a user-friendly graphical user interface (GUI). It features interactive displays of polysaccharide structures and customized search options for beginners and experts, respectively. The site also serves as an information portal for polysaccharide structure determination techniques. The web-interface also references external links where other carbohydrate-related resources are available. PolySac3DB is established to maintain information on the detailed 3D structures of polysaccharides. All the data and features are available via the web-interface utilizing the search engine and can be accessed at http://polysac3db.cermav.cnrs.fr.

De novo identification of highly diverged protein repeats by probabilistic consistency.

PubMed

Biegert, A; Söding, J

2008-03-15

An estimated 25% of all eukaryotic proteins contain repeats, which underlines the importance of duplication for evolving new protein functions. Internal repeats often correspond to structural or functional units in proteins. Methods capable of identifying diverged repeated segments or domains at the sequence level can therefore assist in predicting domain structures, inferring hypotheses about function and mechanism, and investigating the evolution of proteins from smaller fragments. We present HHrepID, a method for the de novo identification of repeats in protein sequences. It is able to detect the sequence signature of structural repeats in many proteins that have not yet been known to possess internal sequence symmetry, such as outer membrane beta-barrels. HHrepID uses HMM-HMM comparison to exploit evolutionary information in the form of multiple sequence alignments of homologs. In contrast to a previous method, the new method (1) generates a multiple alignment of repeats; (2) utilizes the transitive nature of homology through a novel merging procedure with fully probabilistic treatment of alignments; (3) improves alignment quality through an algorithm that maximizes the expected accuracy; (4) is able to identify different kinds of repeats within complex architectures by a probabilistic domain boundary detection method and (5) improves sensitivity through a new approach to assess statistical significance. Server: http://toolkit.tuebingen.mpg.de/hhrepid; Executables: ftp://ftp.tuebingen.mpg.de/pub/protevo/HHrepID

Fragmentary and incidental behaviour of columns, slabs and crystals

PubMed Central

Whiteley, Walter

2014-01-01

Between the study of small finite frameworks and infinite incidentally periodic frameworks, we find the real materials which are large, but finite, fragments that fit into the infinite periodic frameworks. To understand these materials, we seek insights from both (i) their analysis as large frameworks with associated geometric and combinatorial properties (including the geometric repetitions) and (ii) embedding them into appropriate infinite periodic structures with motions that may break the periodic structure. A review of real materials identifies a number of examples with a local appearance of ‘unit cells’ which repeat under isometries but perhaps in unusual forms. These examples also refocus attention on several new classes of infinite ‘periodic’ frameworks: (i) columns—three-dimensional structures generated with one repeating isometry and (ii) slabs—three-dimensional structures with two independent repeating translations. With this larger vision of structures to be studied, we find some patterns and partial results that suggest new conjectures as well as many additional open questions. These invite a search for new examples and additional theorems. PMID:24379423

Structure and method for controlling band offset and alignment at a crystalline oxide-on-semiconductor interface

DOEpatents

McKee, Rodney A.; Walker, Frederick J.

2003-11-25

A crystalline oxide-on-semiconductor structure and a process for constructing the structure involves a substrate of silicon, germanium or a silicon-germanium alloy and an epitaxial thin film overlying the surface of the substrate wherein the thin film consists of a first epitaxial stratum of single atomic plane layers of an alkaline earth oxide designated generally as (AO).sub.n and a second stratum of single unit cell layers of an oxide material designated as (A'BO.sub.3).sub.m so that the multilayer film arranged upon the substrate surface is designated (AO).sub.n (A'BO.sub.3).sub.m wherein n is an integer repeat of single atomic plane layers of the alkaline earth oxide AO and m is an integer repeat of single unit cell layers of the A'BO.sub.3 oxide material. Within the multilayer film, the values of n and m have been selected to provide the structure with a desired electrical structure at the substrate/thin film interface that can be optimized to control band offset and alignment.

Single-Chain Folding of Synthetic Polymers: A Critical Update.

PubMed

Altintas, Ozcan; Barner-Kowollik, Christopher

2015-11-23

The current contribution serves as a critical update to a previous feature article from us (Macromol. Rapid Commun. 2012, 33, 958-971), and highlights the latest advances in the preparation of single chain polymeric nanoparticles and initial-yet promising-attempts towards mimicking the structure of natural biomacromolecules via single-chain folding of well-defined linear polymers via so-called single chain selective point folding and repeat unit folding. The contribution covers selected examples from the literature published up to ca. September 2015. Our aim is not to provide an exhaustive review but rather highlight a selection of new and exciting examples for single-chain folding based on advanced macromolecular precision chemistry. Initially, the discussion focuses on the synthesis and characterization of single-chain folded structures via selective point folding. The second part of the feature article addresses the folding of well-defined single-chain polymers by means of repeat unit folding. The current state of the art in the field of single-chain folding indicates that repeat unit folding-driven nanoparticle preparation is well-advanced, while initial encouraging steps towards building selective point folding systems have been taken. In addition, a summary of the-in our view-open key questions is provided that may guide future biomimetic design efforts. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

O-Acetyl location on cepacian, the principal exopolysaccharide of Burkholderia cepacia complex bacteria.

PubMed

Cescutti, Paola; Impallomeni, Giuseppe; Garozzo, Domenico; Rizzo, Roberto

2011-12-27

Cepacian is an exopolysaccharide produced by the majority of the isolates belonging to the Burkholderia cepacia complex bacteria, a group of 17 species, some of which infect cystic fibrosis patients, sometime with fatal outcome. The repeating unit of cepacian consists of a backbone having a trisaccharidic repeating unit with three side chains, as reported in the formula below. The exopolysaccharide is also acetylated, carrying from one to three acetyl esters per repeating unit, depending on the strain examined. The consequences of O-acetyl substitution in a polysaccharide are important both for its biological functions and for industrial applications, including the preparation of conjugated vaccines, since O-acetyl groups are important immunogenic determinants. The location of acetyl groups was achieved by NMR spectroscopy and ESI mass spectrometry and revealed that these substituents are scattered in non-stoichiometric ratio on many sugar residues in different positions, a feature which adds to the already unique carbohydrate structure of the polysaccharide. Copyright © 2011 Elsevier Ltd. All rights reserved.

Fluorinated monomers useful for preparing fluorinated polyquinoline polymers

NASA Technical Reports Server (NTRS)

Hendricks, Neil H. (Inventor)

1994-01-01

A new class of polymers is provided, as well as the monomers used for their preparation. The polymers provided in accordance with practice of the present invention include repeating units comprising one or more quinoline groups, wherein at least a portion of the repeating units includes a hexafluoroisopropylidene (6F) group or a 1-aryl-2,2,2-trifluoroethylidene (3F) group, or both. The hexafluoroisopropylidene group is referred to herein as a 6F group and has the following structure: ##STR1## The 6F group includes a tetravalent carbon atom bound to two trifluoromethyl moieties, with its other two bonds forming linkages in the polymer chain. The 1-aryl-2,2,2-trifluoroethylidene group is referred to herein as a 3F group and has the following structure: ##STR2## wherein Ar' is an aryl group.

Gross rearrangements within the 5'-untranslated region of the picornaviral genomes.

PubMed

Pilipenko, E V; Blinov, V M; Agol, V I

1990-06-11

An analysis of reported nucleotide sequences revealed several cases of gross rearrangements in the 5'-untranslated region (5-UTR) of picornaviral genomes. A large (greater than 100 nt) duplication was discovered in a downstream region of poliovirus 5-UTR involved in the translational control. Properties of the poliovirus mutants with large deletions [Kuge and Nomoto (1987) J. Virol. 61, 1478-1487] show that a single copy of the appropriate repeating unit is compatible with a wild type phenotype of the virus. In contrast to poliovirus and another enterovirus genomes, human rhinovirus RNAs contain only a single copy of this repeating unit. Another similarly large repeat was found in an upstream segment of the bovine enterovirus 5-UTR. A comparison of the primary and secondary structures of cardio- and aphthovirus 5-UTRs demonstrated the existence of a large (ca. 250 nucleotides) insertion/deletion in a region preceding the poly(C) tract. The two latter rearrangements appear to involve elements of the viral genome replication machinery. Possible origin as well as evolutionary and functional implications of these structural peculiarities are discussed.

Effects of repeated prescribed fires on the structure, composition, and regeneration of mixed-oak forests in Ohio

Treesearch

Todd F. Hutchinson; Elaine Kennedy Sutherland; Daniel A. Yaussy

2005-01-01

This study quantifies prescribed fire effects at four sites in southern Ohio, from 1995 to 2002. Each site had three treatment units: an unburned control, a unit burned 2x (1996 and 1999), and a unit burned 4 x (1996-1999). Vegetation plots were stratified by an integrated moisture index (IMI) into xeric, intermediate, and mesic classes. Prior to treatments, oak (...

Ligand-Binding Properties and Conformational Dynamics of Autolysin Repeat Domains in Staphylococcal Cell Wall Recognition

PubMed Central

Zoll, Sebastian; Schlag, Martin; Shkumatov, Alexander V.; Rautenberg, Maren; Svergun, Dmitri I.; Götz, Friedrich

2012-01-01

The bifunctional major autolysin Atl plays a key role in staphylococcal cell separation. Processing of Atl yields catalytically active amidase (AM) and glucosaminidase (GL) domains that are each fused to repeating units. The two repeats of AM (R1 and R2) target the enzyme to the septum, where it cleaves murein between dividing cells. We have determined the crystal structure of R2, which reveals that each repeat folds into two half-open β-barrel subunits. We further demonstrate that lipoteichoic acid serves as a receptor for the repeats and that this interaction depends on conserved surfaces in each subunit. Small-angle X-ray scattering of the mature amidase reveals the presence of flexible linkers separating the AM, R1, and R2 units. Different levels of flexibility for each linker provide mechanistic insights into the conformational dynamics of the full-length protein and the roles of its components in cell wall association and catalysis. Our analysis supports a model in which the repeats direct the catalytic AM domain to the septum, where it can optimally perform the final step of cell division. PMID:22609916

Molecular structure and chromosome distribution of three repetitive DNA families in Anemone hortensis L. (Ranunculaceae).

PubMed

Mlinarec, Jelena; Chester, Mike; Siljak-Yakovlev, Sonja; Papes, Drazena; Leitch, Andrew R; Besendorfer, Visnja

2009-01-01

The structure, abundance and location of repetitive DNA sequences on chromosomes can characterize the nature of higher plant genomes. Here we report on three new repeat DNA families isolated from Anemone hortensis L.; (i) AhTR1, a family of satellite DNA (stDNA) composed of a 554-561 bp long EcoRV monomer; (ii) AhTR2, a stDNA family composed of a 743 bp long HindIII monomer and; (iii) AhDR, a repeat family composed of a 945 bp long HindIII fragment that exhibits some sequence similarity to Ty3/gypsy-like retroelements. Fluorescence in-situ hybridization (FISH) to metaphase chromosomes of A. hortensis (2n = 16) revealed that both AhTR1 and AhTR2 sequences co-localized with DAPI-positive AT-rich heterochromatic regions. AhTR1 sequences occur at intercalary DAPI bands while AhTR2 sequences occur at 8-10 terminally located heterochromatic blocks. In contrast AhDR sequences are dispersed over all chromosomes as expected of a Ty3/gypsy-like element. AhTR2 and AhTR1 repeat families include polyA- and polyT-tracks, AT/TA-motifs and a pentanucleotide sequence (CAAAA) that may have consequences for chromatin packing and sequence homogeneity. AhTR2 repeats also contain TTTAGGG motifs and degenerate variants. We suggest that they arose by interspersion of telomeric repeats with subtelomeric repeats, before hybrid unit(s) amplified through the heterochromatic domain. The three repetitive DNA families together occupy approximately 10% of the A. hortensis genome. Comparative analyses of eight Anemone species revealed that the divergence of the A. hortensis genome was accompanied by considerable modification and/or amplification of repeats.

Synthetic beta-solenoid proteins with the fragment-free computational design of a beta-hairpin extension

PubMed Central

MacDonald, James T.; Kabasakal, Burak V.; Godding, David; Kraatz, Sebastian; Henderson, Louie; Barber, James; Freemont, Paul S.; Murray, James W.

2016-01-01

The ability to design and construct structures with atomic level precision is one of the key goals of nanotechnology. Proteins offer an attractive target for atomic design because they can be synthesized chemically or biologically and can self-assemble. However, the generalized protein folding and design problem is unsolved. One approach to simplifying the problem is to use a repetitive protein as a scaffold. Repeat proteins are intrinsically modular, and their folding and structures are better understood than large globular domains. Here, we have developed a class of synthetic repeat proteins based on the pentapeptide repeat family of beta-solenoid proteins. We have constructed length variants of the basic scaffold and computationally designed de novo loops projecting from the scaffold core. The experimentally solved 3.56-Å resolution crystal structure of one designed loop matches closely the designed hairpin structure, showing the computational design of a backbone extension onto a synthetic protein core without the use of backbone fragments from known structures. Two other loop designs were not clearly resolved in the crystal structures, and one loop appeared to be in an incorrect conformation. We have also shown that the repeat unit can accommodate whole-domain insertions by inserting a domain into one of the designed loops. PMID:27573845

Distribution and sequence homogeneity of an abundant satellite DNA in the beetle, Tenebrio molitor.

PubMed Central

Davis, C A; Wyatt, G R

1989-01-01

The mealworm beetle, Tenebrio molitor, contains an unusually abundant and homogeneous satellite DNA which constitutes up to 60% of its genome. The satellite DNA is shown to be present in all of the chromosomes by in situ hybridization. 18 dimers of the repeat unit were cloned and sequenced. The consensus sequence is 142 nt long and lacks any internal repeat structure. Monomers of the sequence are very similar, showing on average a 2% divergence from the calculated consensus. Variant nucleotides are scattered randomly throughout the sequence although some variants are more common than others. Neighboring repeat units are no more alike than randomly chosen ones. The results suggest that some mechanism, perhaps gene conversion, is acting to maintain the homogeneity of the satellite DNA despite its abundance and distribution on all of the chromosomes. Images PMID:2762148

Crystal structure of alpha poly-p-xylylene.

NASA Technical Reports Server (NTRS)

Kubo, S.; Wunderlich, B.

1971-01-01

A crystal structure of alpha poly-p-xylylene is proposed with the help of data of oriented crystals grown during polymerization. The unit cell is monoclinic with the parameters a = 8.57 A, b = 10.62 A, c = 6.54 A (chain axis), and beta = 101.3 deg. Four repeating units per cell lead to a calculated density of 1.185 g/cu cm and a packing density of 0.71. The probable space group is P2 sub 1/m.

Leishmania infantum: Lipophosphoglycan intraspecific variation and interaction with vertebrate and invertebrate hosts.

PubMed

Coelho-Finamore, J M; Freitas, V C; Assis, R R; Melo, M N; Novozhilova, N; Secundino, N F; Pimenta, P F; Turco, S J; Soares, R P

2011-03-01

Interspecies variations in lipophosphoglycan (LPG) have been the focus of intense study over the years due its role in specificity during sand fly-Leishmania interaction. This cell surface glycoconjugate is highly polymorphic among species with variations in sugars that branch off the conserved Gal(β1,4)Man(α1)-PO(4) backbone of repeat units. However, the degree of intraspecies polymorphism in LPG of Leishmania infantum (syn. Leishmania chagasi) is not known. In this study, intraspecific variation in the repeat units of LPG was evaluated in 16 strains of L. infantum from Brazil, France, Algeria and Tunisia. The structural polymorphism in the L. infantum LPG repeat units was relatively slight and consisted of three types: type I does not have side chains; type II has one β-glucose residue that branches off the disaccharide-phosphate repeat units and type III has up to three glucose residues (oligo-glucosylated). The significance of these modifications was investigated during in vivo interaction of L. infantum with Lutzomyia longipalpis, and in vitro interaction of the parasites and respective LPGs with murine macrophages. There were no consequential differences in the parasite densities in sand fly midguts infected with Leishmania strains exhibiting type I, II and III LPGs. However, higher nitric oxide production was observed in macrophages exposed to glucosylated type II LPG. Copyright © 2010 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

Synthesis and study of the vibrational spectra of a first generation phosphorus-containing dendrimer with pyridyl functional groups

NASA Astrophysics Data System (ADS)

Furer, V. L.; Vandyukov, A. E.; Tripathi, V.; Majoral, J. P.; Caminade, A. M.; Kovalenko, V. I.

2018-06-01

A new phosphorus-containing dendrimer of the first-generation with potential pharmacological activity was synthesized and studied by spectral methods. The FTIR, FT Raman, 1H and 31P NMR spectra of the first generation dendrimer G1 with a cyclotriphosphazene core, six branches sbnd Osbnd C6H4sbnd CHdbnd Nsbnd N(CH3)sbnd P(S) < and twelve 4-oxyphenethylamidopyridyl end groups sbnd Osbnd C6H4sbnd (CH2)2sbnd NHsbnd COsbnd C5NH4 were recorded. Amide groups of the dendrimer participate in the formation of an intermolecular hydrogen bond. Structure, geometric parameters, the frequency and intensity of the bands in the vibrational spectra were calculated using DFT with PBE functional and TZ2P basis set. Spectral characteristics, charge distribution and reactivity of the core, repeating units and terminal groups of the dendrimer were determined. The first-generation dendrimer molecule has the shape of a concave lens with a slightly non-planar cyclotriphosphazene core and flat repeating units. Repeating units are arranged symmetrically on three on each side of the core, there are no steric hindrances in it and the end groups are able to enter into subsequent reactions and dendrimer has a sufficiently large cavity for accommodating guest molecules. The HOMO covers the repeating units with a noticeable conjugation and the LUMO belongs to the terminal groups.

Dithiopheneindenofluorene (TIF) Semiconducting Polymers with Very High Mobility in Field-Effect Transistors.

PubMed

Chen, Hu; Hurhangee, Michael; Nikolka, Mark; Zhang, Weimin; Kirkus, Mindaugas; Neophytou, Marios; Cryer, Samuel J; Harkin, David; Hayoz, Pascal; Abdi-Jalebi, Mojtaba; McNeill, Christopher R; Sirringhaus, Henning; McCulloch, Iain

2017-09-01

The charge-carrier mobility of organic semiconducting polymers is known to be enhanced when the energetic disorder of the polymer is minimized. Fused, planar aromatic ring structures contribute to reducing the polymer conformational disorder, as demonstrated by polymers containing the indacenodithiophene (IDT) repeat unit, which have both a low Urbach energy and a high mobility in thin-film-transistor (TFT) devices. Expanding on this design motif, copolymers containing the dithiopheneindenofluorene repeat unit are synthesized, which extends the fused aromatic structure with two additional phenyl rings, further rigidifying the polymer backbone. A range of copolymers are prepared and their electrical properties and thin-film morphology evaluated, with the co-benzothiadiazole polymer having a twofold increase in hole mobility when compared to the IDT analog, reaching values of almost 3 cm 2 V -1 s -1 in bottom-gate top-contact organic field-effect transistors. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The structure of cell adhesion molecule uvomorulin. Insights into the molecular mechanism of Ca2+-dependent cell adhesion.

PubMed Central

Ringwald, M; Schuh, R; Vestweber, D; Eistetter, H; Lottspeich, F; Engel, J; Dölz, R; Jähnig, F; Epplen, J; Mayer, S

1987-01-01

We have determined the amino acid sequence of the Ca2+-dependent cell adhesion molecule uvomorulin as it appears on the cell surface. The extracellular part of the molecule exhibits three internally repeated domains of 112 residues which are most likely generated by gene duplication. Each of the repeated domains contains two highly conserved units which could represent putative Ca2+-binding sites. Secondary structure predictions suggest that the putative Ca2+-binding units are located in external loops at the surface of the protein. The protein sequence exhibits a single membrane-spanning region and a cytoplasmic domain. Sequence comparison reveals extensive homology to the chicken L-CAM. Both uvomorulin and L-CAM are identical in 65% of their entire amino acid sequence suggesting a common origin for both CAMs. Images Fig. 1. Fig. 4. Fig. 7. PMID:3501370

Different mechanisms are involved in the transcriptional activation by yeast heat shock transcription factor through two different types of heat shock elements.

PubMed

Hashikawa, Naoya; Yamamoto, Noritaka; Sakurai, Hiroshi

2007-04-06

The hydrophobic repeat is a conserved structural motif of eukaryotic heat shock transcription factor (HSF) that enables HSF to form a homotrimer. Homotrimeric HSF binds to heat shock elements (HSEs) consisting of three inverted repeats of the sequence nGAAn. Sequences consisting of four or more nGAAn units are bound cooperatively by two HSF trimers. We show that in Saccharomyces cerevisiae cells oligomerization-defective Hsf1 is not able to bind HSEs with three units and is not extensively phosphorylated in response to stress; it is therefore unable to activate genes containing this type of HSE. Several lines of evidence indicate that oligomerization is a prerequisite for stress-induced hyperphosphorylation of Hsf1. In contrast, oligomerization and hyperphosphorylation are not necessary for gene activation via HSEs with four units. Intragenic suppressor screening of oligomerization-defective hsf1 showed that an interface between adjacent DNA-binding domains is important for the binding of Hsf1 to the HSE. We suggest that Saccharomyces cerevisiae HSEs with different structures are regulated differently; HSEs with three units require Hsf1 to be both oligomerized and hyperphosphorylated, whereas HSEs with four or more units do not require either.

Structural characterization of an all-aminosugar-containing capsular polysaccharide from Colwellia psychrerythraea 34H

PubMed Central

Casillo, Angela; Ståhle, Jonas; Parrilli, Ermenegilda; Sannino, Filomena; Mitchell, Daniel E.; Pieretti, Giuseppina; Gibson, Matthew I.; Marino, Gennaro; Lanzetta, Rosa; Parrilli, Michelangelo; Widmalm, Göran; Tutino, Maria L.; Corsaro, Maria M.

2017-01-01

Colwellia psychrerythraea strain 34H, a Gram-negative bacterium isolated from Arctic marine sediments, is considered a model to study the adaptation to cold environments. Recently, we demonstrated that C. psychrerythraea 34H produces two different extracellular polysaccharides, a capsular polysaccharide and a medium released polysaccharide, which confer cryoprotection to the bacterium. In this study, we report the structure of an additional capsular polysaccharide produced by Colwellia grown at a different temperature. The structure was determined using chemical methods, and one- and two-dimensional NMR spectroscopy. The results showed a trisaccharide repeating unit made up of only amino-sugar residues: N-acetyl-galactosamine, 2,4-diacetamido-2,4,6-trideoxy-glucose (bacillosamine), and 2-acetamido-2-deoxyglucuronic acid with the following structure: →4)-β-d-GlcpNAcA-(1→3)-β-d-QuipNAc4NAc-(1→3)-β-d-GalpNAc-(1→. The 3D model, generated in accordance with 1H,1H-NOE NMR correlations and consisting of ten repeating units, shows a helical structure. In contrast with the other extracellular polysaccharides produced from Colwellia at 4 °C, this molecule displays only a low ice recrystallization inhibition activity. PMID:28161737

Solution structure of a repeated unit of the ABA-1 nematode polyprotein allergen of Ascaris reveals a novel fold and two discrete lipid-binding sites.

PubMed

Meenan, Nicola A G; Ball, Graeme; Bromek, Krystyna; Uhrín, Dušan; Cooper, Alan; Kennedy, Malcolm W; Smith, Brian O

2011-04-19

Nematode polyprotein allergens (NPAs) are an unusual class of lipid-binding proteins found only in nematodes. They are synthesized as large, tandemly repetitive polyproteins that are post-translationally cleaved into multiple copies of small lipid binding proteins with virtually identical fatty acid and retinol (Vitamin A)-binding characteristics. They are probably central to transport and distribution of small hydrophobic compounds between the tissues of nematodes, and may play key roles in nutrient scavenging, immunomodulation, and IgE antibody-based responses in infection. In some species the repeating units are diverse in amino acid sequence, but, in ascarid and filarial nematodes, many of the units are identical or near-identical. ABA-1A is the most common repeating unit of the NPA of Ascaris suum, and is closely similar to that of Ascaris lumbricoides, the large intestinal roundworm of humans. Immune responses to NPAs have been associated with naturally-acquired resistance to infection in humans, and the immune repertoire to them is under strict genetic control. The solution structure of ABA-1A was determined by protein nuclear magnetic resonance spectroscopy. The protein adopts a novel seven-helical fold comprising a long central helix that participates in two hollow four-helical bundles on either side. Discrete hydrophobic ligand-binding pockets are found in the N-terminal and C-terminal bundles, and the amino acid sidechains affected by ligand (fatty acid) binding were identified. Recombinant ABA-1A contains tightly-bound ligand(s) of bacterial culture origin in one of its binding sites. This is the first mature, post-translationally processed, unit of a naturally-occurring tandemly-repetitive polyprotein to be structurally characterized from any source, and it belongs to a new structural class. NPAs have no counterparts in vertebrates, so represent potential targets for drug or immunological intervention. The nature of the (as yet) unidentified bacterial ligand(s) may be pertinent to this, as will our characterization of the unusual binding sites.

Placement of molecules in (not out of) the cell

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

Dauter, Zbigniew, E-mail: dauter@anl.gov

2013-01-01

The importance of presenting macromolecular structures in unified, standard ways is discussed. To uniquely describe a crystal structure, it is sufficient to specify the crystal unit cell and symmetry, and describe the unique structural motif which is repeated by the space-group symmetry throughout the whole crystal. It is somewhat arbitrary how such a unique motif can be defined and positioned with respect to the unit-cell origin. As a result of such freedom, some isomorphous structures are presented in the Protein Data Bank in different locations and appear as if they have different atomic coordinates, despite being completely equivalent structurally. Thismore » may easily confuse those users of the PDB who are less familiar with crystallographic symmetry transformations. It would therefore be beneficial for the community of PDB users to introduce standard rules for locating crystal structures of macromolecules in the unit cells of various space groups.« less

Improving Photovoltaic Performance of a Fused-Ring Azepinedione Copolymer via a D-A-A Design.

PubMed

Zhang, Honghong; Li, Ting; Xiao, Zuo; Lei, Zhongli; Ding, Liming

2018-04-01

Two conjugated copolymer donors, PTTABDT and PBTTABDT, based on a fused-ring azepinedione acceptor unit, 5-(2-octyldodecyl)-4H-thieno[2',3':4,5]thieno[3,2-c]thieno[2',3':4,5]thieno[2,3-e]azepine-4,6(5H)-dione (TTA), are prepared. PTTABDT possesses a conventional donor-acceptor (D-A) structure with one TTA in the repeat unit, while PBTTABDT has a D-A-A structure with two TTAs in the repeat unit. Compared with PTTABDT, PBTTABDT shows a deeper highest occupied molecular orbital (HOMO) level, a narrower bandgap, and a higher hole mobility, and exhibits better performance in bulk heterojunction solar cells. Power conversion efficiencies of 6.18% and 7.81% are achieved from PTTABDT:PC 71 BM and PBTTABDT:PC 71 BM solar cells, respectively. The higher performance of PBTTABDT:PC 71 BM solar cells results from the enhanced open-circuit voltage (V oc ) and short-circuit current density (  J sc ). © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Human minisatellite alleles detectable only after PCR amplification.

PubMed

Armour, J A; Crosier, M; Jeffreys, A J

1992-01-01

We present evidence that a proportion of alleles at two human minisatellite loci is undetected by standard Southern blot hybridization. In each case the missing allele(s) can be identified after PCR amplification and correspond to tandem arrays too short to detect by hybridization. At one locus, there is only one undetected allele (population frequency 0.3), which contains just three repeat units. At the second locus, there are at least five undetected alleles (total population frequency 0.9) containing 60-120 repeats; they are not detected because these tandem repeats give very poor signals when used as a probe in standard Southern blot hybridization, and also cross-hybridize with other sequences in the genome. Under these circumstances only signals from the longest tandemly repeated alleles are detectable above the nonspecific background. The structures of these loci have been compared in human and primate DNA, and at one locus the short human allele containing three repeat units is shown to be an intermediate state in the expansion of a monomeric precursor allele in primates to high copy number in the longer human arrays. We discuss the implications of such loci for studies of human populations, minisatellite isolation by cloning, and the evolution of highly variable tandem arrays.

Divergence in centromere structure distinguishes related genomes in Coix lacryma-jobi and its wild relative.

PubMed

Han, Yonghua; Wang, Guixiang; Liu, Zhao; Liu, Jinhua; Yue, Wei; Song, Rentao; Zhang, Xueyong; Jin, Weiwei

2010-02-01

Knowledge about the composition and structure of centromeres is critical for understanding how centromeres perform their functional roles. Here, we report the sequences of one centromere-associated bacterial artificial chromosome clone from a Coix lacryma-jobi library. Two Ty3/gypsy-class retrotransposons, centromeric retrotransposon of C. lacryma-jobi (CRC) and peri-centromeric retrotransposon of C. lacryma-jobi, and a (peri)centromere-specific tandem repeat with a unit length of 153 bp were identified. The CRC is highly homologous to centromere-specific retrotransposons reported in grass species. An 80-bp DNA region in the 153-bp satellite repeat was found to be conserved to centromeric satellite repeats from maize, rice, and pearl millet. Fluorescence in situ hybridization showed that the three repetitive sequences were located in (peri-)centromeric regions of both C. lacryma-jobi and Coix aquatica. However, the 153-bp satellite repeat was only detected on 20 out of the 30 chromosomes in C. aquatica. Immunostaining with an antibody against rice CENH3 indicates that the 153-bp satellite repeat and CRC might be both the major components for functional centromeres, but not all the 153-bp satellite repeats or CRC sequences are associated with CENH3. The evolution of centromeric repeats of C. lacryma-jobi during the polyploidization was discussed.

Structural study and conformational behavior of the two different lipopolysaccharide O-antigens produced by the cystic fibrosis pathogen Burkholderia multivorans.

PubMed

Ieranò, Teresa; Silipo, Alba; Cescutti, Paola; Leone, Maria Rosaria; Rizzo, Roberto; Lanzetta, Rosa; Parrilli, Michelangelo; Molinaro, Antonio

2009-07-20

Lipopolysaccharides (LPSs) are virulence factors expressed by gram-negative bacteria; they are among those mainly responsible for bacterial virulence. In this work we define the primary structure and the conformational features of the O-chain from the LPS produced by the highly virulent clinical isolate Burkholderia multivorans strain C1576, an opportunistic human pathogen isolated in a cystic fibrosis center and causative of an outbreak with lethal outcome. We demonstrate that the LPS from this clinical isolate consists of two O-polysaccharide chains present in different amounts and made up of repeating units, both containing deoxy sugar. Additionally, conformational studies have been performed to establish and compare the spatial arrangements of the two polysaccharides and differences in their shape have been highlighted. The comprehension of the structural and conformational features of the two repeating units may help to explain their biological significance, the molecular shape of the bacterial external surface, and the comprehension at the molecular level of the recognition mechanisms of the antibodies.

Complete mitochondrial genome of the Asian pencil halfbeak Hyporhamphus intermedius (Beloniformes, Hemirhamphidae).

PubMed

Song, Chao; Hu, Gengdong; Qiu, Liping; Fan, Limin; Meng, Shunlong; Chen, Jiazhang

2016-11-01

The complete mitochondrial genome of Hyporhamphus intermedius was determined to be 16,720 bp in length with (A + T) content of 56.3%, and it consists of 13 protein-coding genes, 22 tRNAs, two ribosomal RNAs, and a control region. The gene composition and the structural arrangement of the H. intermedius complete mtDNA were identical to most of the other vertebrates. Interestingly, two tandem repeat units were identified across tRNA-Pro and control region (2*41 bp), while in most of the fishes the tandem repeat units are located in the control region. The molecular data we presented here could play a useful role to study the evolutionary relationships and population genetics of Hemirhamphidae fish.

Electronic Band Structure of Helical Polyisocyanides.

PubMed

Champagne, Benoît; Liégeois, Vincent; Fripiat, Joseph G; Harris, Frank E

2017-10-19

Restricted Hartree-Fock computations are reported for a methyl isocyanide polymer (repeating unit -C═N-CH 3 ), whose most stable conformation is expected to be a helical chain. The computations used a standard contracted Gaussian orbital set at the computational levels STO-3G, 3-21G, 6-31G, and 6-31G**, and studies were made for two line-group configurations motivated by earlier work and by studies of space-filling molecular models: (1) A structure of line-group symmetry L9 5 , containing a 9-fold screw axis with atoms displaced in the axial direction by 5/9 times the lattice constant, and (2) a structure of symmetry L4 1 that had been proposed, containing a 4-fold screw axis with translation by 1/4 of the lattice constant. Full use of the line-group symmetry was employed to cause most of the computational complexity to depend only on the size of the asymmetric repeating unit. Data reported include computed bond properties, atomic charge distribution, longitudinal polarizability, band structure, and the convoluted density of states. Most features of the description were found to be insensitive to the level of computational approximation. The work also illustrates the importance of exploiting line-group symmetry to extend the range of polymer structural problems that can be treated computationally.

In situ optical sequencing and structure analysis of a trinucleotide repeat genome region by localization microscopy after specific COMBO-FISH nano-probing

NASA Astrophysics Data System (ADS)

Stuhlmüller, M.; Schwarz-Finsterle, J.; Fey, E.; Lux, J.; Bach, M.; Cremer, C.; Hinderhofer, K.; Hausmann, M.; Hildenbrand, G.

2015-10-01

Trinucleotide repeat expansions (like (CGG)n) of chromatin in the genome of cell nuclei can cause neurological disorders such as for example the Fragile-X syndrome. Until now the mechanisms are not clearly understood as to how these expansions develop during cell proliferation. Therefore in situ investigations of chromatin structures on the nanoscale are required to better understand supra-molecular mechanisms on the single cell level. By super-resolution localization microscopy (Spectral Position Determination Microscopy; SPDM) in combination with nano-probing using COMBO-FISH (COMBinatorial Oligonucleotide FISH), novel insights into the nano-architecture of the genome will become possible. The native spatial structure of trinucleotide repeat expansion genome regions was analysed and optical sequencing of repetitive units was performed within 3D-conserved nuclei using SPDM after COMBO-FISH. We analysed a (CGG)n-expansion region inside the 5' untranslated region of the FMR1 gene. The number of CGG repeats for a full mutation causing the Fragile-X syndrome was found and also verified by Southern blot. The FMR1 promotor region was similarly condensed like a centromeric region whereas the arrangement of the probes labelling the expansion region seemed to indicate a loop-like nano-structure. These results for the first time demonstrate that in situ chromatin structure measurements on the nanoscale are feasible. Due to further methodological progress it will become possible to estimate the state of trinucleotide repeat mutations in detail and to determine the associated chromatin strand structural changes on the single cell level. In general, the application of the described approach to any genome region will lead to new insights into genome nano-architecture and open new avenues for understanding mechanisms and their relevance in the development of heredity diseases.

DNA CTG triplet repeats involved in dynamic mutations of neurologically related gene sequences form stable duplexes

NASA Technical Reports Server (NTRS)

Smith, G. K.; Jie, J.; Fox, G. E.; Gao, X.

1995-01-01

DNA triplet repeats, 5'-d(CTG)n and 5'-d(CAG)n, are present in genes which have been implicated in several neurodegenerative disorders. To investigate possible stable structures formed by these repeating sequences, we have examined d(CTG)n, d(CAG)n and d(CTG).d(CAG)n (n = 2 and 3) using NMR and UV optical spectroscopy. These studies reveal that single stranded (CTG)n (n > 2) forms stable, antiparallel helical duplexes, while the single stranded (CAG)n requires at least three repeating units to form a duplex. NMR and UV melting experiments show that the Tm increases in the order of [(CAG)3]2 < [(CTG)3]2 << (CAG)3.(CTG)3. The (CTG)3 duplex is stable and exhibits similar NMR spectra in solutions containing 0.1-4 M NaCl and at a pH range from 4.6 to 8.8. The (CTG)3 duplex, which contains multiple-T.T mismatches, displays many NMR spectral characteristics similar to those of B-form DNA. However, unique NOE and 1H-31P coupling patterns associated with the repetitive T.T mismatches in the CTG repeats are discerned. These results, in conjunction with recent in vitro studies suggest that longer CTG repeats may form hairpin structures, which can potentially cause interruption in replication, leading to dynamic expansion or deletion of triplet repeats.

Analysis of tandem repeat units of the promoter of capsanthin/capsorubin synthase (Ccs) gene in pepper fruit.

PubMed

Tian, Shi-Lin; Li, Zheng; Li, Li; Shah, S N M; Gong, Zhen-Hui

2017-07-01

Capsanthin/capsorubin synthase ( Ccs ) gene is a key gene that regulates the synthesis of capsanthin and the development of red coloration in pepper fruits. There are three tandem repeat units in the promoter region of Ccs , but the potential effects of the number of repetitive units on the transcriptional regulation of Ccs has been unclear. In the present study, expression vectors carrying different numbers of repeat units of the Ccs promoter were constructed, and the transient expression of the β-glucuronidase ( GUS ) gene was used to detect differences in expression levels associated with the promoter fragments. These repeat fragments and the plant expression vector PBI121 containing the 35s CaMV promoter were ligated to form recombinant vectors that were transfected into Agrobacterium tumefaciens GV3101. A fluorescence spectrophotometer was used to analyze the expression associated with the various repeat units. It was concluded that the constructs containing at least one repeat were associated with GUS expression, though they did not differ from one another. This repeating unit likely plays a role in transcription and regulation of Ccs expression.

ST proteins, a new family of plant tandem repeat proteins with a DUF2775 domain mainly found in Fabaceae and Asteraceae.

PubMed

Albornos, Lucía; Martín, Ignacio; Iglesias, Rebeca; Jiménez, Teresa; Labrador, Emilia; Dopico, Berta

2012-11-07

Many proteins with tandem repeats in their sequence have been described and classified according to the length of the repeats: I) Repeats of short oligopeptides (from 2 to 20 amino acids), including structural cell wall proteins and arabinogalactan proteins. II) Repeats that range in length from 20 to 40 residues, including proteins with a well-established three-dimensional structure often involved in mediating protein-protein interactions. (III) Longer repeats in the order of 100 amino acids that constitute structurally and functionally independent units. Here we analyse ShooT specific (ST) proteins, a family of proteins with tandem repeats of unknown function that were first found in Leguminosae, and their possible similarities to other proteins with tandem repeats. ST protein sequences were only found in dicotyledonous plants, limited to several plant families, mainly the Fabaceae and the Asteraceae. ST mRNAs accumulate mainly in the roots and under biotic interactions. Most ST proteins have one or several Domain(s) of Unknown Function 2775 (DUF2775). All deduced ST proteins have a signal peptide, indicating that these proteins enter the secretory pathway, and the mature proteins have tandem repeat oligopeptides that share a hexapeptide (E/D)FEPRP followed by 4 partially conserved amino acids, which could determine a putative N-glycosylation signal, and a fully conserved tyrosine. In a phylogenetic tree, the sequences clade according to taxonomic group. A possible involvement in symbiosis and abiotic stress as well as in plant cell elongation is suggested, although different STs could play different roles in plant development. We describe a new family of proteins called ST whose presence is limited to the plant kingdom, specifically to a few families of dicotyledonous plants. They present 20 to 40 amino acid tandem repeat sequences with different characteristics (signal peptide, DUF2775 domain, conservative repeat regions) from the described group of 20 to 40 amino acid tandem repeat proteins and also from known cell wall proteins with repeat sequences. Several putative roles in plant physiology can be inferred from the characteristics found.

ST proteins, a new family of plant tandem repeat proteins with a DUF2775 domain mainly found in Fabaceae and Asteraceae

PubMed Central

2012-01-01

Background Many proteins with tandem repeats in their sequence have been described and classified according to the length of the repeats: I) Repeats of short oligopeptides (from 2 to 20 amino acids), including structural cell wall proteins and arabinogalactan proteins. II) Repeats that range in length from 20 to 40 residues, including proteins with a well-established three-dimensional structure often involved in mediating protein-protein interactions. (III) Longer repeats in the order of 100 amino acids that constitute structurally and functionally independent units. Here we analyse ShooT specific (ST) proteins, a family of proteins with tandem repeats of unknown function that were first found in Leguminosae, and their possible similarities to other proteins with tandem repeats. Results ST protein sequences were only found in dicotyledonous plants, limited to several plant families, mainly the Fabaceae and the Asteraceae. ST mRNAs accumulate mainly in the roots and under biotic interactions. Most ST proteins have one or several Domain(s) of Unknown Function 2775 (DUF2775). All deduced ST proteins have a signal peptide, indicating that these proteins enter the secretory pathway, and the mature proteins have tandem repeat oligopeptides that share a hexapeptide (E/D)FEPRP followed by 4 partially conserved amino acids, which could determine a putative N-glycosylation signal, and a fully conserved tyrosine. In a phylogenetic tree, the sequences clade according to taxonomic group. A possible involvement in symbiosis and abiotic stress as well as in plant cell elongation is suggested, although different STs could play different roles in plant development. Conclusions We describe a new family of proteins called ST whose presence is limited to the plant kingdom, specifically to a few families of dicotyledonous plants. They present 20 to 40 amino acid tandem repeat sequences with different characteristics (signal peptide, DUF2775 domain, conservative repeat regions) from the described group of 20 to 40 amino acid tandem repeat proteins and also from known cell wall proteins with repeat sequences. Several putative roles in plant physiology can be inferred from the characteristics found. PMID:23134664

Explicit parametric solutions of lattice structures with proper generalized decomposition (PGD) - Applications to the design of 3D-printed architectured materials

NASA Astrophysics Data System (ADS)

Sibileau, Alberto; Auricchio, Ferdinando; Morganti, Simone; Díez, Pedro

2018-01-01

Architectured materials (or metamaterials) are constituted by a unit-cell with a complex structural design repeated periodically forming a bulk material with emergent mechanical properties. One may obtain specific macro-scale (or bulk) properties in the resulting architectured material by properly designing the unit-cell. Typically, this is stated as an optimal design problem in which the parameters describing the shape and mechanical properties of the unit-cell are selected in order to produce the desired bulk characteristics. This is especially pertinent due to the ease manufacturing of these complex structures with 3D printers. The proper generalized decomposition provides explicit parametic solutions of parametric PDEs. Here, the same ideas are used to obtain parametric solutions of the algebraic equations arising from lattice structural models. Once the explicit parametric solution is available, the optimal design problem is a simple post-process. The same strategy is applied in the numerical illustrations, first to a unit-cell (and then homogenized with periodicity conditions), and in a second phase to the complete structure of a lattice material specimen.

Structural investigation of cell wall polysaccharides of Lactobacillus delbrueckii subsp. bulgaricus 17.

PubMed

Vinogradov, E; Sadovskaya, I; Cornelissen, A; van Sinderen, D

2015-09-02

Lactobacilli are valuable strains for commercial (functional) food fermentations. Their cell surface-associated polysaccharides (sPSs) possess important functional properties, such as acting as receptors for bacteriophages (bacterial viruses), influencing autolytic characteristics and providing protection against antimicrobial peptides. The current report provides an elaborate molecular description of several surface carbohydrates of Lactobacillus delbrueckii subsp. bulgaricus strain 17. The cell surface of this strain was shown to contain short chain poly(glycerophosphate) teichoic acids and at least two different sPSs, designated here as sPS1 and sPS2, whose chemical structures were examined by 2D nuclear magnetic resonance spectroscopy and methylation analysis. Neutral branched sPS1, extracted with n-butanol, was shown to be composed of hexasaccharide repeating units (-[α-d-Glcp-(1-3)-]-4-β-l-Rhap2OAc-4-β-d-Glcp-[α-d-Galp-(1-3)]-4-α-Rhap-3-α-d-Galp-), while the major component of the TCA-extracted sPS2 was demonstrated to be a linear d-galactan with the repeating unit structure being (-[Gro-3P-(1-6)-]-3-β-Galf-3-α-Galp-2-β-Galf-6-β-Galf-3-β-Galp-). Copyright © 2015 Elsevier Ltd. All rights reserved.

Complex structure of knob DNA on maize chromosome 9. Retrotransposon invasion into heterochromatin.

PubMed Central

Ananiev, E V; Phillips, R L; Rines, H W

1998-01-01

The recovery of maize (Zea mays L.) chromosome addition lines of oat (Avena sativa L.) from oat x maize crosses enables us to analyze the structure and composition of specific regions, such as knobs, of individual maize chromosomes. A DNA hybridization blot panel of eight individual maize chromosome addition lines revealed that 180-bp repeats found in knobs are present in each of these maize chromosomes, but the copy number varies from approximately 100 to 25, 000. Cosmid clones with knob DNA segments were isolated from a genomic library of an oat-maize chromosome 9 addition line with the help of the 180-bp knob-associated repeated DNA sequence used as a probe. Cloned knob DNA segments revealed a complex organization in which blocks of tandemly arranged 180-bp repeating units are interrupted by insertions of other repeated DNA sequences, mostly represented by individual full size copies of retrotransposable elements. There is an obvious preference for the integration of retrotransposable elements into certain sites (hot spots) of the 180-bp repeat. Sequence microheterogeneity including point mutations and duplications was found in copies of 180-bp repeats. The 180-bp repeats within an array all had the same polarity. Restriction maps constructed for 23 cloned knob DNA fragments revealed the positions of polymorphic sites and sites of integration of insertion elements. Discovery of the interspersion of retrotransposable elements among blocks of tandem repeats in maize and some other organisms suggests that this pattern may be basic to heterochromatin organization for eukaryotes. PMID:9691055

Adhesive compositions and methods

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

Allen, Scott D.; Sendijarevic, Vahid; O'Connor, James

The present invention encompasses polyurethane adhesive compositions comprising aliphatic polycarbonate chains. In one aspect, the present invention encompasses polyurethane adhesives derived from aliphatic polycarbonate polyols and polyisocyanates wherein the polyol chains contain a primary repeating unit having a structure:. In another aspect, the invention provides articles comprising the inventive polyurethane compositions as well as methods of making such compositions.

Utilization of Exocellular Mannan from Rhodotorula glutinis as an Immunoreactive Antigen in Diagnosis of Leptospirosis

PubMed Central

Matsuo, Kouki; Isogai, Emiko; Araki, Yoshio

2000-01-01

Previously, Rhodotorula glutinis was reported to produce a large amount of exocellular mannan, having a repeating unit of →3)-d-Manp-(1→4)-d-Manp-(1→. Recently, we found that antigenic polysaccharides of Leptospira biflexa serovar patoc strain Patoc I have the same repeating unit and cross-react with antisera raised against extended strains of other leptospires (K. Matsuo, E. Isogai, and Y. Araki, Carbohydr. Res., in press). This structural identity and the difficulty of producing and isolating antigens led us to confirm the usefulness of Rhodotorula mannan as an immunoreactive antigen in a serological diagnosis of leptospirosis. In the present investigation, we confirmed the structural identity of an exocellular mannan isolated from R. glutinis AHU 3479 and tried to use it as an immunoreactive antigen in a serological diagnosis of leptospirosis. From its chemical analysis and 1H- and 13C-labeled nuclear magnetic resonance spectrometry, the Rhodotorula mannan was confirmed to consist of the same disaccharide units. Furthermore, such a preparation was shown to immunoreact to various sera from patients suffering with leptospirosis as well as to most rabbit antiserum preparations obtained from immunization with various strains of pathogenic leptospires. Therefore, the Rhodotorula mannan preparation is useful as an immunoreactive antigen in the serological diagnosis for leptospirosis. PMID:11015396

[Structural organization of 5S ribosomal DNA of Rosa rugosa].

PubMed

Tynkevych, Iu O; Volkov, R A

2014-01-01

In order to clarify molecular organization of the genomic region encoding 5S rRNA in diploid species Rosa rugosa several 5S rDNA repeated units were cloned and sequenced. Analysis of the obtained sequences revealed that only one length variant of 5S rDNA repeated units, which contains intact promoter elements in the intergenic spacer region (IGS) and appears to be transcriptionally active is present in the genome. Additionally, a limited number of 5S rDNA pseudogenes lacking a portion of coding sequence and the complete IGS was detected. A high level of sequence similarity (from 93.7 to 97.5%) between the IGS of major 5S rDNA variants of East Asian R. rugosa and North American R. nitida was found indicating comparatively recent divergence of these species.

Comparison of the carboxy-terminal DP-repeat region in the co-chaperones Hop and Hip

PubMed Central

Nelson, Gregory M.; Huffman, Holly; Smith, David F.

2003-01-01

Functional steroid receptor complexes are assembled and maintained by an ordered pathway of interactions involving multiple components of the cellular chaperone machinery. Two of these components, Hop and Hip, serve as co-chaperones to the major heat shock proteins (Hsps), Hsp70 and Hsp90, and participate in intermediate stages of receptor assembly. In an effort to better understand the functions of Hop and Hip in the assembly process, we focused on a region of similarity located near the C-terminus of each co-chaperone. Contained within this region is a repeated sequence motif we have termed the DP repeat. Earlier mutagenesis studies implicated the DP repeat of either Hop or Hip in Hsp70 binding and in normal assembly of the co-chaperones with progesterone receptor (PR) complexes. We report here that the DP repeat lies within a protease-resistant domain that extends to or is near the C-terminus of both co-chaperones. Point mutations in the DP repeats render the C-terminal regions hypersensitive to proteolysis. In addition, a Hop DP mutant displays altered proteolytic digestion patterns, which suggest that the DP-repeat region influences the folding of other Hop domains. Although the respective DP regions of Hop and Hip share sequence and structural similarities, they are not functionally interchangeable. Moreover, a double-point mutation within the second DP-repeat unit of Hop that converts this to the sequence found in Hip disrupts Hop function; however, the corresponding mutation in Hip does not alter its function. We conclude that the DP repeats are important structural elements within a C-terminal domain, which is important for Hop and Hip function. PMID:14627198

Comparison of the carboxy-terminal DP-repeat region in the co-chaperones Hop and Hip.

PubMed

Nelson, Gregory M; Huffman, Holly; Smith, David F

2003-01-01

Functional steroid receptor complexes are assembled and maintained by an ordered pathway of interactions involving multiple components of the cellular chaperone machinery. Two of these components, Hop and Hip, serve as co-chaperones to the major heat shock proteins (Hsps), Hsp70 and Hsp90, and participate in intermediate stages of receptor assembly. In an effort to better understand the functions of Hop and Hip in the assembly process, we focused on a region of similarity located near the C-terminus of each co-chaperone. Contained within this region is a repeated sequence motif we have termed the DP repeat. Earlier mutagenesis studies implicated the DP repeat of either Hop or Hip in Hsp70 binding and in normal assembly of the co-chaperones with progesterone receptor (PR) complexes. We report here that the DP repeat lies within a protease-resistant domain that extends to or is near the C-terminus of both co-chaperones. Point mutations in the DP repeats render the C-terminal regions hypersensitive to proteolysis. In addition, a Hop DP mutant displays altered proteolytic digestion patterns, which suggest that the DP-repeat region influences the folding of other Hop domains. Although the respective DP regions of Hop and Hip share sequence and structural similarities, they are not functionally interchangeable. Moreover, a double-point mutation within the second DP-repeat unit of Hop that converts this to the sequence found in Hip disrupts Hop function; however, the corresponding mutation in Hip does not alter its function. We conclude that the DP repeats are important structural elements within a C-terminal domain, which is important for Hop and Hip function.

Acoustic Signaling by Singing Humpback Whales (Megaptera novaeangliae): What Role Does Reverberation Play?

PubMed

Mercado, Eduardo

2016-01-01

When humpback whales (Megaptera novaeangliae) sing in coastal waters, the units they produce can generate reverberation. Traditionally, such reverberant acoustic energy has been viewed as an incidental side-effect of high-amplitude, long-distance, sound transmission in the ocean. An alternative possibility, however, is that reverberation actually contributes to the structure and function of songs. In the current study, this possibility was assessed by analyzing reverberation generated by humpback whale song units, as well as the spectral structure of unit sequences, produced by singers from different regions. Acoustical analyses revealed that: (1) a subset of units within songs generated narrowband reverberant energy that in some cases persisted for periods longer than the interval between units; (2) these highly reverberant units were regularly repeated throughout the production of songs; and (3) units occurring before and after these units often contained spectral energy peaks at non-overlapping, adjacent frequencies that were systematically related to the bands of reverberant energy generated by the units. These findings strongly suggest that some singing humpback whales not only produce sounds conducive to long-duration reverberation, but also may sequentially structure songs to avoid spectral overlap between units and ongoing reverberation. Singer-generated reverberant energy that is received simultaneously with directly transmitted song units can potentially provide listening whales with spatial cues that may enable them to more accurately determine a singer's position.

Acoustic Signaling by Singing Humpback Whales (Megaptera novaeangliae): What Role Does Reverberation Play?

PubMed Central

Mercado, Eduardo

2016-01-01

When humpback whales (Megaptera novaeangliae) sing in coastal waters, the units they produce can generate reverberation. Traditionally, such reverberant acoustic energy has been viewed as an incidental side-effect of high-amplitude, long-distance, sound transmission in the ocean. An alternative possibility, however, is that reverberation actually contributes to the structure and function of songs. In the current study, this possibility was assessed by analyzing reverberation generated by humpback whale song units, as well as the spectral structure of unit sequences, produced by singers from different regions. Acoustical analyses revealed that: (1) a subset of units within songs generated narrowband reverberant energy that in some cases persisted for periods longer than the interval between units; (2) these highly reverberant units were regularly repeated throughout the production of songs; and (3) units occurring before and after these units often contained spectral energy peaks at non-overlapping, adjacent frequencies that were systematically related to the bands of reverberant energy generated by the units. These findings strongly suggest that some singing humpback whales not only produce sounds conducive to long-duration reverberation, but also may sequentially structure songs to avoid spectral overlap between units and ongoing reverberation. Singer-generated reverberant energy that is received simultaneously with directly transmitted song units can potentially provide listening whales with spatial cues that may enable them to more accurately determine a singer’s position. PMID:27907182

Structural analysis of two length variants of the rDNA intergenic spacer from Eruca sativa.

PubMed

Lakshmikumaran, M; Negi, M S

1994-03-01

Restriction enzyme analysis of the rRNA genes of Eruca sativa indicated the presence of many length variants within a single plant and also between different cultivars which is unusual for most crucifers studied so far. Two length variants of the rDNA intergenic spacer (IGS) from a single individual E. sativa (cv. Itsa) plant were cloned and characterized. The complete nucleotide sequences of both the variants (3 kb and 4 kb) were determined. The intergenic spacer contains three families of tandemly repeated DNA sequences denoted as A, B and C. However, the long (4 kb) variant shows the presence of an additional repeat, denoted as D, which is a duplication of a 224 bp sequence just upstream of the putative transcription initiation site. Repeat units belonging to the three different families (A, B and C) were in the size range of 22 to 30 bp. Such short repeat elements are present in the IGS of most of the crucifers analysed so far. Sequence analysis of the variants (3 kb and 4 kb) revealed that the length heterogeneity of the spacer is located at three different regions and is due to the varying copy numbers of repeat units belonging to families A and B. Length variation of the spacer is also due to the presence of a large duplication (D repeats) in the 4 kb variant which is absent in the 3 kb variant. The putative transcription initiation site was identified by comparisons with the rDNA sequences from other plant species.

Determination of the chemical structure of the capsular polysaccharide of strain B33, a fast-growing soya bean-nodulating bacterium isolated from an arid region of China.

PubMed Central

Rodríguez-Carvajal, M A; Tejero-Mateo, P; Espartero, J L; Ruiz-Sainz, J E; Buendía-Clavería, A M; Ollero, F J; Yang, S S; Gil-Serrano, A M

2001-01-01

We have determined the structure of a polysaccharide from strain B33, a fast-growing bacterium that forms nitrogen-fixing nodules with Asiatic and American soya bean cultivars. On the basis of monosaccharide analysis, methylation analysis, one-dimensional 1H- and 13C-NMR and two-dimensional NMR experiments, the structure was shown to consist of a polymer having the repeating unit -->6)-4-O-methyl-alpha-D-Glcp-(1-->4)-3-O-methyl-beta-D-GlcpA-(1--> (where GlcpA is glucopyranuronic acid and Glcp is glucopyranose). Strain B33 produces a K-antigen polysaccharide repeating unit that does not have the structural motif sugar-Kdx [where Kdx is 3-deoxy-D-manno-2-octulosonic acid (Kdo) or a Kdo-related acid] proposed for different Sinorhizobium fredii strains, all of them being effective with Asiatic soya bean cultivars but unable to form nitrogen-fixing nodules with American soya bean cultivars. Instead, it resembles the K-antigen of S. fredii strain HH303 (rhamnose, galacturonic acid)n, which is also effective with both groups of soya bean cultivars. Only the capsular polysaccharide from strains B33 and HH303 have monosaccharide components that are also present in the surface polysaccharide of Bradyrhizobium elkanii strains, which consists of a 4-O-methyl-D-glucurono-L-rhamnan. PMID:11439101

Distribution of dopant ions around poly(3,4-ethylenedioxythiophene) chains: a theoretical study.

PubMed

Casanovas, Jordi; Zanuy, David; Alemán, Carlos

2017-04-12

The effect of counterions and multiple polymer chains on the properties and structure of poly(3,4-ethylenedioxythiophene) (PEDOT) doped with ClO 4 - has been examined using density functional theory (DFT) calculations with periodic boundary conditions (PBCs). Calculations on a one-dimensional periodic model with four explicit polymer repeat units and two ClO 4 - molecules indicate that the latter are separated as much as possible, with the salt structure and band gap obtained from such ClO 4 - distribution being in excellent agreement with those determined experimentally. On the other hand, DFT calculations on periodic models that include two chains indicate that neighboring PEDOT chains are shifted along the molecular axis by a half of the repeat unit length, with dopant ions intercalated between the polymer molecules acting as cement. In order to support these structural features, classical molecular dynamics (MD) simulations have been performed on a multiphasic system consisting of 69 explicit PEDOT chains anchored onto a steel surface, explicit ClO 4 - anions embedded in the polymer matrix, and an acetonitrile phase layer onto the polymer matrix. Analyses of the radial distribution functions indicate that the all-anti conformation, the relative disposition of adjacent PEDOT chains and the distribution of ClO 4 - dopant ions are fully consistent with periodic DFT predictions. The agreement between two such different methodologies allows reinforcing the microscopic understanding of the PEDOT film structure.

Clay Mineral Crystal Structure Tied to Composition

NASA Image and Video Library

2016-12-13

This diagram illustrates how the dimensions of clay minerals' crystal structure are affected by which ions are present in the composition of the mineral. Different clay minerals were identified this way at two sites in Mars' Gale Crater: "Murray Buttes" and "Yellowknife Bay." In otherwise identical clay minerals, a composition that includes aluminum and ferric iron ions (red dots) results in slightly smaller crystalline unit cells than one that instead includes magnesium and ferrous iron ions (green dots). Ferric iron is more highly oxidized than ferrous iron. Crystalline cell units are the basic repeating building blocks that define minerals. X-ray diffraction analysis, a capability of the Chemistry and Mineralogy (CheMin) instrument on NASA's Curiosity Mars rover, identifies minerals from their crystalline structure. http://photojournal.jpl.nasa.gov/catalog/PIA21148

Chemical analysis of a polysaccharide of unripe (green) tomato (Lycopersicon esculentum).

PubMed

Chandra, Krishnendu; Ghosh, Kaushik; Ojha, Arnab K; Islam, Syed S

2009-11-02

A polysaccharide (PS-I) isolated from the aqueous extract of the unripe (green) tomatoes (Lycopersicon esculentum) consists of D-galactose, D-methyl galacturonate, D-arabinose, L-arabinose, and L-rhamnose. Structural investigation of the polysaccharide was carried out using total acid hydrolysis, methylation analysis, periodate oxidation study, and NMR studies ((1)H, (13)C, DQF-COSY, TOCSY, NOESY, ROESY, HMQC, and HMBC). On the basis of above-mentioned experiments the structure of the repeating unit of the polysaccharide (PS-I) was established as: [structure: see text].

Microphase separation of comb copolymers with two different lengths of side chains

NASA Astrophysics Data System (ADS)

Aliev, M. A.; Kuzminyh, N. Yu.

2009-10-01

The phase behavior of the monodisperse AB comb copolymer melt contained the macromolecules of special architecture is discussed. Each macromolecule is assumed to be composed of two comb blocks which differ in numbers of side chains and numbers of monomer units in these chains. It is shown (by analysis of the structure factor of the melt) that microphase separation at two different length scales in the melt is possible. The large and small length scales correspond to separation between comb blocks and separation between monomer units in repeating fragments of blocks, respectively. The classification diagrams indicated which length scale is favored for a given parameters of chemical structure of macromolecules are constructed.

Restoring fire suppressed Texas pak woodlands to historic conditions using prescribed fire

Treesearch

Jeff C. Sparks; Michael C. Stambaugh; Eric L. Keith

2012-01-01

Comparable to many oak ecosystems across the eastern United States, oak woodlands in Texas display characteristics of changing composition and structure due to altered fire regimes. Information describing historic fire regimes suggests woodlands underwent relatively frequent and repeated burning prior to major Euro-American influence in the early 19th century. Oak...

Repeats of base oligomers as the primordial coding sequences of the primeval earth and their vestiges in modern genes.

PubMed

Ohno, S

1984-01-01

Three outstanding properties uniquely qualify repeats of base oligomers as the primordial coding sequences of all polypeptide chains. First, when compared with randomly generated base sequences in general, they are more likely to have long open reading frames. Second, periodical polypeptide chains specified by such repeats are more likely to assume either alpha-helical or beta-sheet secondary structures than are polypeptide chains of random sequence. Third, provided that the number of bases in the oligomeric unit is not a multiple of 3, these internally repetitious coding sequences are impervious to randomly sustained base substitutions, deletions, and insertions. This is because the recurring periodicity of their polypeptide chains is given by three consecutive copies of the oligomeric unit translated in three different reading frames. Accordingly, when one reading frame is open, the other two are automatically open as well, all three being capable of coding for polypeptide chains of identical periodicity. Under this circumstance, a frame shift due to the deletion or insertion of a number of bases that is not a multiple of 3 fails to alter the down-stream amino acid sequence, and even a base change causing premature chain-termination can silence only one of the three potential coding units. Newly arisen coding sequences in modern organisms are oligomeric repeats, and most of the older genes retain various vestiges of their original internal repetitions. Some of the genes (e.g., oncogenes) have even inherited the property of being impervious to randomly sustained base changes.

Biophysical characterization of soluble Pseudomonas syringae ice nucleation protein InaZ fragments.

PubMed

Han, Yu Jin; Song, HyoJin; Lee, Chang Woo; Ly, Nguyễn Hoàng; Joo, Sang-Woo; Lee, Jun Hyuck; Kim, Soon-Jong; Park, SangYoun

2017-01-01

Ice nucleation protein (INP) with its functional domain consisting of multiple 48-residue repeat units effectively induces super-cooled water into ice. Circular dichroism and infrared deconvolution analyses on a soluble 240-residue fragment of Pseudomonas syringae InaZ (InaZ240) containing five 48-residue repeat units indicated that it is mostly composed of β-sheet and random coil. Analytical ultracentrifugation suggested that InaZ240 behaves as a monomer of an elongated ellipsoid. However, InaZ240 showed only minimum ice binding compared to anti-freeze proteins. Other P. syringae InaZ proteins with more 48-residue repeat units were made, in which the largest soluble fragment obtainable was an InaZ with twelve 48-residue repeat units. Size-exclusion chromatography analyses further suggested that the overall shape of the expressed InaZ fragments is pH-dependent, which becomes compact as the numbers of 48-residue repeat unit increase. Copyright © 2016 Elsevier B.V. All rights reserved.

Analytical relationships for prediction of the mechanical properties of additively manufactured porous biomaterials

PubMed Central

Hedayati, Reza

2016-01-01

Abstract Recent developments in additive manufacturing techniques have motivated an increasing number of researchers to study regular porous biomaterials that are based on repeating unit cells. The physical and mechanical properties of such porous biomaterials have therefore received increasing attention during recent years. One of the areas that have revived is analytical study of the mechanical behavior of regular porous biomaterials with the aim of deriving analytical relationships that could predict the relative density and mechanical properties of porous biomaterials, given the design and dimensions of their repeating unit cells. In this article, we review the analytical relationships that have been presented in the literature for predicting the relative density, elastic modulus, Poisson's ratio, yield stress, and buckling limit of regular porous structures based on various types of unit cells. The reviewed analytical relationships are used to compare the mechanical properties of porous biomaterials based on different types of unit cells. The major areas where the analytical relationships have improved during the recent years are discussed and suggestions are made for future research directions. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 3164–3174, 2016. PMID:27502358

Revisiting the structure of the anti-neoplastic glucans of Mycobacterium bovis Bacille Calmette-Guerin. Structural analysis of the extracellular and boiling water extract-derived glucans of the vaccine substrains.

PubMed

Dinadayala, Premkumar; Lemassu, Anne; Granovski, Pierre; Cérantola, Stéphane; Winter, Nathalie; Daffé, Mamadou

2004-03-26

The attenuated strain of Mycobacterium bovis Bacille Calmette-Guérin (BCG), used worldwide to prevent tuberculosis and leprosy, is also clinically used as an immunotherapeutic agent against superficial bladder cancer. An anti-tumor polysaccharide has been isolated from the boiling water extract of the Tice substrain of BCG and tentatively characterized as consisting primarily of repeating units of 6-linked-glucosyl residues. Mycobacterium tuberculosis and other mycobacterial species produce a glycogen-like alpha-glucan composed of repeating units of 4-linked glucosyl residues substituted at some 6 positions by short oligoglucosyl units that also exhibits an anti-tumor activity. Therefore, the impression prevails that mycobacteria synthesize different types of anti-neoplastic glucans or, alternatively, the BCG substrains are singular in producing a unique type of glucan that may confer to them their immunotherapeutic property. The present study addresses this question through the comparative analysis of alpha-glucans purified from the extracellular materials and boiling water extracts of three vaccine substrains. The polysaccharides were purified, and their structural features were established by mono- and two-dimensional NMR spectroscopy and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry of the enzymatic and chemical degradation products of the purified compounds. The glucans isolated by the two methods from the three substrains of BCG were shown to exhibit identical structural features shared with the glycogen-like alpha-glucan of M. tuberculosis and other mycobacteria. Incidentally, we observed an occasional release of dextrans from Sephadex columns that may explain the reported occurrence of 6-substituted alpha-glucans in mycobacteria.

Repeater F-waves are signs of motor unit pathology in polio survivors.

PubMed

Hachisuka, Akiko; Komori, Tetsuo; Abe, Tatsuya; Hachisuka, Kenji

2015-05-01

The purpose of this study was to determine whether F-waves reveal electrophysiological features of anterior horn cells in polio survivors. Forty-three polio survivors and 20 healthy controls underwent motor nerve conduction studies of the median and tibial nerves bilaterally, including sampling of F-waves elicited by 100 stimuli and the determination of motor unit number estimation (MUNE). A significant increase in abnormally stereotyped ("repeater") F-waves and a reduction of F-wave persistence were observed in both nerves in the polio group as compared with the control group. Repeater F-waves had a negative correlation with MUNE. These trends in F-wave persistence and repeater F-waves after motor unit loss are characteristic findings in polio survivors. Repeater F-waves are a sign of motor unit pathology. © 2014 The Authors. Muscle & Nerve Published by Wiley Periodicals, Inc.

Binding of New Methylene Blue to Endotoxins and Its Effects on the Endotoxin Activity Studied By Double Diffusion and Limulus Amebocyte Lysate Assays

DTIC Science & Technology

1989-05-30

bacteria. Its structure (Figure 1-I) contains O-antigen polysaccharide , core polysaccharide and lipid A (Rietschel et al., 1984; Luderitz et al., 1982...The O-antigen polysaccharide is composed of repeating oligosaccharide, specific to the species and the strain of the bacteria; the core polysaccharide ...consists of 11 or less monosaccharide units including three 2-keto-3-deoxyoctonate (KDO), and is more conserved structurally than the O-antigen

Structure of a polysaccharide from Urtica fissa determined by NMR spectra.

PubMed

Wang, Yan-Liang; Li, Li; Cheng, Xiao-Chen; Lu, Yu-Xin; Zhang, Qing-Lin

2012-01-01

A polysaccharide, isolated and purified from the aqueous extract of nettle plant Urtica fissa, was found to consist of D-glucose and D-arabinose. Molecular weight was determined to be Mn 4140. The NMR experiments (¹H, ¹³C, ¹H--¹H COSY, TOCSY, HSQC, NOESY, and HMBC) revealed the structure as the following repeating unit: -->6)-α-D-Glcp-(1-->6)-α-D-Glcp-(1-->6)-β-D-Glcp--(1-->5)-β-D-Araf-(1-->3)-β-D-Glcp-(1-->

[The structure of the glycerophosphate-containing O-specific polysaccharide from Escherichia coli 0130].

PubMed

Perepelov, A V; Lu, B; Sebchenkova, S N; Shevelev, S D; Wang, V; Shashkov, A S; Feng, L; Wang, L; Knirel', Iu A

2007-01-01

A phosphorylated O-specific polysaccharide was obtained by mild acidic degradation of the lipopolysaccharide from the intestinal bacterium Escherichia coli 0130 and characterized by the methods of chemical analysis, including dephosphorylation, and 1H and 13C NMR spectroscopy. The polysaccharide was shown to be composed of branched tetrasaccharide repeating units containing two N-acetyl-D-galactosamine residues, D-galactose, D-glucose, and glycerophosphate residues (one of each). The polysaccharide has the following structure, which is unique among the known bacterial polysaccharides.

Characterization of natural photonic crystals in iridescent wings of damselfly Chalcopteryx rutilans by FIB/SEM, TEM, and TOF-SIMS.

PubMed

Carr, David M; Ellsworth, Ashley A; Fisher, Gregory L; Valeriano, Wescley W; Vasco, Juan P; Guimarães, Paulo S S; de Andrade, Rodrigo R; da Silva, Elizabeth R; Rodrigues, Wagner N

2018-02-05

The iridescent wings of the Chalcopterix rutilans damselfly (Rambur) (Odonata, Polythoridae) are investigated with focused ion beam/scanning electron microscopy, transmission electron microscopy, and time-of-flight secondary ion mass spectrometry. The electron microscopy images reveal a natural photonic crystal as the source of the varying colors. The photonic crystal has a consistent number and thickness (∼195 nm) of the repeat units on the ventral side of the wing, which is consistent with the red color visible from the bottom side of the wing in all regions. The dorsal side of the wing shows strong color variations ranging from red to blue depending on the region. In the electron microscopy images, the dorsal side of the wing exhibits varied number and thicknesses of the repeat units. The repeat unit spacings for the red, yellow/green, and blue regions are approximately 195, 180, and 145 nm, respectively. Three-dimensional analysis of the natural photonic crystals by time-of-flight secondary ion mass spectrometry reveals that changes in the relative levels of Na, K, and eumelanin are responsible for the varying dielectric constant needed to generate the photonic crystal. The photonic crystal also appears to be assembled with a chemical tricomponent layer structure due to the enhancement of the CH 6 N 3 + species at every other interface between the high/low dielectric constant layers.

Comparative Mitogenomics of the Assassin Bug Genus Peirates (Hemiptera: Reduviidae: Peiratinae) Reveal Conserved Mitochondrial Genome Organization of P. atromaculatus, P. fulvescens and P. turpis

PubMed Central

Zhao, Guangyu; Li, Hu; Zhao, Ping; Cai, Wanzhi

2015-01-01

In this study, we sequenced four new mitochondrial genomes and presented comparative mitogenomic analyses of five species in the genus Peirates (Hemiptera: Reduviidae). Mitochondrial genomes of these five assassin bugs had a typical set of 37 genes and retained the ancestral gene arrangement of insects. The A+T content, AT- and GC-skews were similar to the common base composition biases of insect mtDNA. Genomic size ranges from 15,702 bp to 16,314 bp and most of the size variation was due to length and copy number of the repeat unit in the putative control region. All of the control region sequences included large tandem repeats present in two or more copies. Our result revealed similarity in mitochondrial genomes of P. atromaculatus, P. fulvescens and P. turpis, as well as the highly conserved genomic-level characteristics of these three species, e.g., the same start and stop codons of protein-coding genes, conserved secondary structure of tRNAs, identical location and length of non-coding and overlapping regions, and conservation of structural elements and tandem repeat unit in control region. Phylogenetic analyses also supported a close relationship between P. atromaculatus, P. fulvescens and P. turpis, which might be recently diverged species. The present study indicates that mitochondrial genome has important implications on phylogenetics, population genetics and speciation in the genus Peirates. PMID:25689825

Structure-guided investigation of lipopolysaccharide O-antigen chain length regulators reveals regions critical for modal length control.

PubMed

Kalynych, Sergei; Ruan, Xiang; Valvano, Miguel A; Cygler, Miroslaw

2011-08-01

The O-antigen component of the lipopolysaccharide (LPS) represents a population of polysaccharide molecules with nonrandom (modal) chain length distribution. The number of the repeat O units in each individual O-antigen polymer depends on the Wzz chain length regulator, an inner membrane protein belonging to the polysaccharide copolymerase (PCP) family. Different Wzz proteins confer vastly different ranges of modal lengths (4 to >100 repeat units), despite having remarkably conserved structural folds. The molecular mechanism responsible for the selective preference for a certain number of O units is unknown. Guided by the three-dimensional structures of PCPs, we constructed a panel of chimeric molecules containing parts of two closely related Wzz proteins from Salmonella enterica and Shigella flexneri which confer different O-antigen chain length distributions. Analysis of the O-antigen length distribution imparted by each chimera revealed the region spanning amino acids 67 to 95 (region 67 to 95), region 200 to 255, and region 269 to 274 as primarily affecting the length distribution. We also showed that there is no synergy between these regions. In particular, region 269 to 274 also influenced chain length distribution mediated by two distantly related PCPs, WzzB and FepE. Furthermore, from the 3 regions uncovered in this study, region 269 to 274 appeared to be critical for the stability of the oligomeric form of Wzz, as determined by cross-linking experiments. Together, our data suggest that chain length determination depends on regions that likely contribute to stabilize a supramolecular complex.

Polymer compositions and methods

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

Allen, Scott D.; Willkomm, Wayne R.

The present invention encompasses polyurethane compositions comprising aliphatic polycarbonate chains. In one aspect, the present invention encompasses polyurethane foams, thermoplastics and elastomers derived from aliphatic polycarbonate polyols and polyisocyanates wherein the polyol chains contain a primary repeating unit having a structure: ##STR00001## In another aspect, the invention provides articles comprising the inventive foam and elastomer compositions as well as methods of making such compositions.

Eighty-eight years of change in a managed ponderosa pine forest

Treesearch

Helen Y. Smith; Stephen F. Arno

1999-01-01

This publication gives an overview of structural and other ecological changes associated with forest management and fire suppression since the early 1900's in a ponderosa pine forest, the most widespread forest type in the Western United States. Three sources of information are presented: (1) changes seen in a series of repeat photographs taken between 1909 and...

Crystallization of Stretched Polyimides: A Structure-Property Study

NASA Technical Reports Server (NTRS)

Hinkley, Jeffrey A.; Dezern, James F.

2002-01-01

A simple rotational isomeric state model was used to detect the degree to which polyimide repeat units might align to give an extended crystal. It was found experimentally that the hallmarks of stretch-crystallization were more likely to occur in materials whose molecules could readily give extended, aligned conformations. A proposed screening criterion was 84% accurate in selecting crystallizing molecules.

Cofacial porphyrin-ferrocene dyads and a new class of conjugated porphyrin.

PubMed

Cammidge, Andrew N; Scaife, Peter J; Berber, Gûlen; Hughes, David L

2005-08-04

A porphyrin-ferrocene dyad has been synthesized in which there is close face-to-face contact between the two aromatic systems, providing a model for heterobimetallic polymers based on the same repeating unit. Attempts to synthesize the 2:1 adduct instead led to a remarkable intramolecular Heck-type cyclization which planarizes the system and extends the conjugation. [structure: see text

Polymer compositions and methods

DOEpatents

Allen, Scott D.; Willkomm, Wayne R.

2016-09-27

The present invention encompasses polyurethane compositions comprising aliphatic polycarbonate chains. In one aspect, the present invention encompasses polyurethane foams, thermoplastics and elastomers derived from aliphatic polycarbonate polyols and polyisocyanates wherein the polyol chains contain a primary repeating unit having a structure: ##STR00001## In another aspect, the invention provides articles comprising the inventive foam and elastomer compositions as well as methods of making such compositions.

Cas5d Protein Processes Pre-crRNA and Assembles into a Cascade-like Interference Complex in Subtype I-C/Dvulg CRISPR-Cas System

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

Nam, Ki Hyun; Haitjema, Charles; Liu, Xueqi

Clustered regularly interspaced short palindromic repeats (CRISPRs), together with an operon of CRISPR-associated (Cas) proteins, form an RNA-based prokaryotic immune system against exogenous genetic elements. Cas5 family proteins are found in several type I CRISPR-Cas systems. Here, we report the molecular function of subtype I-C/Dvulg Cas5d from Bacillus halodurans. We show that Cas5d cleaves pre-crRNA into unit length by recognizing both the hairpin structure and the 3 single stranded sequence in the CRISPR repeat region. Cas5d structure reveals a ferredoxin domain-based architecture and a catalytic triad formed by Y46, K116, and H117 residues. We further show that after pre-crRNA processing,more » Cas5d assembles with crRNA, Csd1, and Csd2 proteins to form a multi-sub-unit interference complex similar to Escherichia coli Cascade (CRISPR-associated complex for antiviral defense) in architecture. Our results suggest that formation of a crRNA-presenting Cascade-like complex is likely a common theme among type I CRISPR subtypes.« less

Conformational features of cepacian: the exopolysaccharide produced by clinical strains of Burkholderia cepacia.

PubMed

Nogueira, Carlos E Sampaio; Ruggiero, Jose R; Sist, Paola; Cescutti, Paola; Urbani, Ranieri; Rizzo, Roberto

2005-04-11

Conformational energy calculations and molecular dynamics investigations, both in water and in dimethyl sulfoxide, were carried out on the exopolysaccharide cepacian produced by the majority of the clinical strains of Burkholderia cepacia, an opportunistic pathogen causing serious lung infection in patients affected by cystic fibrosis, The investigation was aimed at defining the structural and conformational features, which might be relevant for clarification of the structure-function relationships of the polymer. The molecular dynamics calculations were carried out by Ramachandran-type energy plots of the disaccharides that constitute the polymer repeating unit. The dynamics of an oligomer composed of three repeating units were investigated in water and in Me2SO, a non-aggregating solvent. Analysis of the time persistence of hydrogen bonds showed the presence of a large number of favourable interactions in water, which were less evident in Me2SO. The calculations on the cepacian chain indicated that polymer conformational features in water were affected by the lateral chains, but were also largely dictated by the presence of solvent. Moreover, the large number of intra-chain hydrogen bonds in water disappeared in Me2SO solution, increasing the average dimension of the polymer chains.

Regions flanking ori sequences affect the replication efficiency of the mitochondrial genome of ori+ petite mutants from yeast.

PubMed

Rayko, E; Goursot, R; Cherif-Zahar, B; Melis, R; Bernardi, G

1988-03-31

The mitochondrial genomes of progenies from 26 crosses between 17 cytoplasmic, spontaneous, suppressive, ori+ petite mutants of Saccharomyces cerevisiae have been studied by electrophoresis of restriction fragments. Only parental genomes (or occasionally, genomes derived from them by secondary excisions) were found in the progenies of the almost 500 diploids investigated; no evidence for illegitimate, site-specific mitochondrial recombination was detected. One of the parental genomes was always found to be predominate over the other one, although to different extents in different crosses. This predominance appears to be due to a higher replication efficiency, which is correlated with a greater density of ori sequences on the mitochondrial genome (and with a shorter repeat unit size of the latter). Exceptions to the 'repeat-unit-size rule' were found, however, even when the parental mitochondrial genomes carried the same ori sequence. This indicates that noncoding, intergenic sequences outside ori sequences also play a role in modulating replication efficiency. Since in different petites such sequences differ in primary structure, size, and position relative to ori sequences, this modulation is likely to take place through an indirect effect on DNA and nucleoid structure.

Analysis of humpback whale sounds in shallow waters of the Southeastern Arabian Sea: An indication of breeding habitat.

PubMed

Mahanty, Madan M; Latha, G; Thirunavukkarasu, A

2015-06-01

The primary objective of this work was to present the acoustical identification of humpback whales, detected by using an autonomous ambient noise measurement system, deployed in the shallow waters of the Southeastern Arabian Sea (SEAS) during the period January to May 2011. Seven types of sounds were detected. These were characteristically upsweeps and downsweeps along with harmonics. Sounds produced repeatedly in a specific pattern were referred to as phrases (PQRS and ABC). Repeated phrases in a particular pattern were referred to as themes, and from the spectrographic analysis, two themes (I and II) were identified. The variation in the acoustic characteristics such as fundamental frequency, range, duration of the sound unit, and the structure of the phrases and themes are discussed. Sound units were recorded from mid-January to mid-March, with a peak in February, when the mean SST is approx. 28 degree C, and no presence was recorded after mid-March. The temporal and thematic structures strongly determine the functions of the humpback whale song form. Given the use of song in the SEAS, this area is possibly used as an active breeding habitat by humpback whales during the winter season.

Electromyographic analysis of repeated bouts of eccentric exercise.

PubMed

McHugh, M P; Connolly, D A; Eston, R G; Gartman, E J; Gleim, G W

2001-03-01

The repeated bout effect refers to the protective effect provided by a single bout of eccentric exercise against muscle damage from a similar subsequent bout. The aim of this study was to determine if the repeated bout was associated with an increase in motor unit activation relative to force production, an increased recruitment of slow-twitch motor units or increased motor unit synchronization. Surface electromyographic (EMG) signals were recorded from the hamstring muscles during two bouts of submaximal isokinetic (2.6 rad x s(-1)) eccentric (11 men, 9 women) or concentric (6 men, 4 women) contractions separated by 2 weeks. The EMG per unit torque and median frequency were analysed. The initial bout of eccentric exercise resulted in strength loss, pain and muscle tenderness, while the repeated eccentric bout resulted in a slight increase in strength, no pain and no muscle tenderness (bout x time effects, P < 0.05). Strength, pain and tenderness were unaffected by either bout of concentric exercise. The EMG per unit torque and median frequency were not different between the initial and repeated bouts of eccentric exercise. The EMG per unit torque and median frequency increased during both bouts of eccentric exercise (P < 0.01) but did not change during either concentric bout. In conclusion, there was no evidence that the repeated bout effect was due to a neural adaptation.

Modulation of the multistate folding of designed TPR proteins through intrinsic and extrinsic factors

PubMed Central

Phillips, J J; Javadi, Y; Millership, C; Main, E R G

2012-01-01

Tetratricopeptide repeats (TPRs) are a class of all alpha-helical repeat proteins that are comprised of 34-aa helix-turn-helix motifs. These stack together to form nonglobular structures that are stabilized by short-range interactions from residues close in primary sequence. Unlike globular proteins, they have few, if any, long-range nonlocal stabilizing interactions. Several studies on designed TPR proteins have shown that this modular structure is reflected in their folding, that is, modular multistate folding is observed as opposed to two-state folding. Here we show that TPR multistate folding can be suppressed to approximate two-state folding through modulation of intrinsic stability or extrinsic environmental variables. This modulation was investigated by comparing the thermodynamic unfolding under differing buffer regimes of two distinct series of consensus-designed TPR proteins, which possess different intrinsic stabilities. A total of nine proteins of differing sizes and differing consensus TPR motifs were each thermally and chemically denatured and their unfolding monitored using differential scanning calorimetry (DSC) and CD/fluorescence, respectively. Analyses of both the DSC and chemical denaturation data show that reducing the total stability of each protein and repeat units leads to observable two-state unfolding. These data highlight the intimate link between global and intrinsic repeat stability that governs whether folding proceeds by an observably two-state mechanism, or whether partial unfolding yields stable intermediate structures which retain sufficient stability to be populated at equilibrium. PMID:22170589

Tandem Repeat Proteins Inspired By Squid Ring Teeth

NASA Astrophysics Data System (ADS)

Pena-Francesch, Abdon

Proteins are large biomolecules consisting of long chains of amino acids that hierarchically assemble into complex structures, and provide a variety of building blocks for biological materials. The repetition of structural building blocks is a natural evolutionary strategy for increasing the complexity and stability of protein structures. However, the relationship between amino acid sequence, structure, and material properties of protein systems remains unclear due to the lack of control over the protein sequence and the intricacies of the assembly process. In order to investigate the repetition of protein building blocks, a recently discovered protein from squids is examined as an ideal protein system. Squid ring teeth are predatory appendages located inside the suction cups that provide a strong grasp of prey, and are solely composed of a group of proteins with tandem repetition of building blocks. The objective of this thesis is the understanding of sequence, structure and property relationship in repetitive protein materials inspired in squid ring teeth for the first time. Specifically, this work focuses on squid-inspired structural proteins with tandem repeat units in their sequence (i.e., repetition of alternating building blocks) that are physically cross-linked via beta-sheet structures. The research work presented here tests the hypothesis that, in these systems, increasing the number of building blocks in the polypeptide chain decreases the protein network defects and improves the material properties. Hence, the sequence, nanostructure, and properties (thermal, mechanical, and conducting) of tandem repeat squid-inspired protein materials are examined. Spectroscopic structural analysis, advanced materials characterization, and entropic elasticity theory are combined to elucidate the structure and material properties of these repetitive proteins. This approach is applied not only to native squid proteins but also to squid-inspired synthetic polypeptides that allow for a fine control of the sequence and network morphology. The results provided in this work establish a clear dependence between the repetitive building blocks, the network morphology, and the properties of squid-inspired repetitive protein materials. Increasing the number of tandem repeat units in SRT-inspired proteins led to more effective protein networks with superior properties. Through increasing tandem repetition and optimization of network morphology, highly efficient protein materials capable of withstanding deformations up to 400% of their original length, with MPa-GPa modulus, high energy absorption (50 MJ m-3), peak proton conductivity of 3.7 mS cm-1 (at pH 7, highest reported to date for biological materials), and peak thermal conductivity of 1.4 W m-1 K -1 (which exceeds that of most polymer materials) were developed. These findings introduce new design rules in the engineering of proteins based on tandem repetition and morphology control, and provide a novel framework for tailoring and optimizing the properties of protein-based materials.

Structural building principles of complex face-centered cubic intermetallics.

PubMed

Dshemuchadse, Julia; Jung, Daniel Y; Steurer, Walter

2011-08-01

Fundamental structural building principles are discussed for all 56 known intermetallic phases with approximately 400 or more atoms per unit cell and space-group symmetry F43m, Fd3m, Fd3, Fm3m or Fm3c. Despite fundamental differences in chemical composition, bonding and electronic band structure, their complex crystal structures show striking similarities indicating common building principles. We demonstrate that the structure-determining elements are flat and puckered atomic {110} layers stacked with periodicities 2p. The atoms on this set of layers, which intersect each other, form pentagon face-sharing endohedral fullerene-like clusters arranged in a face-centered cubic packing (f.c.c.). Due to their topological layer structure, all these crystal structures can be described as (p × p × p) = p(3)-fold superstructures of a common basic structure of the double-diamond type. The parameter p, with p = 3, 4, 7 or 11, is determined by the number of layers per repeat unit and the type of cluster packing, which in turn are controlled by chemical composition.

Concerted evolution of the tandem array encoding primate U2 snRNA occurs in situ, without changing the cytological context of the RNU2 locus.

PubMed Central

Pavelitz, T; Rusché, L; Matera, A G; Scharf, J M; Weiner, A M

1995-01-01

In primates, the tandemly repeated genes encoding U2 small nuclear RNA evolve concertedly, i.e. the sequence of the U2 repeat unit is essentially homogeneous within each species but differs somewhat between species. Using chromosome painting and the NGFR gene as an outside marker, we show that the U2 tandem array (RNU2) has remained at the same chromosomal locus (equivalent to human 17q21) through multiple speciation events over > 35 million years leading to the Old World monkey and hominoid lineages. The data suggest that the U2 tandem repeat, once established in the primate lineage, contained sequence elements favoring perpetuation and concerted evolution of the array in situ, despite a pericentric inversion in chimpanzee, a reciprocal translocation in gorilla and a paracentric inversion in orang utan. Comparison of the 11 kb U2 repeat unit found in baboon and other Old World monkeys with the 6 kb U2 repeat unit in humans and other hominids revealed that an ancestral U2 repeat unit was expanded by insertion of a 5 kb retrovirus bearing 1 kb long terminal repeats (LTRs). Subsequent excision of the provirus by homologous recombination between the LTRs generated a 6 kb U2 repeat unit containing a solo LTR. Remarkably, both junctions between the human U2 tandem array and flanking chromosomal DNA at 17q21 fall within the solo LTR sequence, suggesting a role for the LTR in the origin or maintenance of the primate U2 array. Images PMID:7828589

Thermally crosslinked polymeric compositions and methods of making the same

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

Koros, William John; Kratochvil, Adam Michal

2014-03-04

The various embodiments of the present disclosure relate generally to thermally crosslinked polymeric compositions and methods of making thermally crosslinked polymeric compositions. An embodiment of the present invention comprises a composition comprising: a first polymer comprising a first repeat unit, the first repeat unit comprising a carboxyl group, wherein the first polymer crosslinks to a second polymer formed from a second repeat unit, and wherein the first polymer crosslinks to the second polymer without formation of an ester group.

Structural-electrochemical relations in the aqueous copper hexacyanoferrate-zinc system examined by synchrotron X-ray diffraction

NASA Astrophysics Data System (ADS)

Renman, Viktor; Ojwang, Dickson O.; Valvo, Mario; Gómez, Cesar Pay; Gustafsson, Torbjörn; Svensson, Gunnar

2017-11-01

The storage process of Zn2+ in the Prussian blue analogue (PBA) copper hexacyanoferrate (Cu[Fe(CN)6]2/3·nH2O - CuHCF) framework structure in a context of rechargeable aqueous batteries is examined by means of in operando synchrotron X-ray diffraction. Via sequential unit-cell parameter refinements of time-resolved diffraction data, it is revealed that the step-profile of the cell output voltage curves during repeated electrochemical insertion and removal of Zn2+ in the CuHCF host structure is associated with a non-linear contraction and expansion of the unit-cell in the range 0.36 < x < 1.32 for Znx/3Cu[Fe(CN)6]2/3·nH2O. For a high insertion cation content there is no apparent change in the unit-cell contraction. Furthermore, a structural analysis with respect to the occupancies of possible Zn2+ sites suggests that the Fe(CN)6 vacancies within the CuHCF framework play an important role in the structural-electrochemical behavior of this particular system. More specifically, it is observed that Zn2+ swaps position during electrochemical cycling, hopping between cavity sites to vacant ferricyanide sites.

A Helical Structural Nucleus Is the Primary Elongating Unit of Insulin Amyloid Fibrils

PubMed Central

Roessle, Manfred; Kastrup, Jette S; van de Weert, Marco; Flink, James M; Frokjaer, Sven; Gajhede, Michael; Svergun, Dmitri I

2007-01-01

Although amyloid fibrillation is generally believed to be a nucleation-dependent process, the nuclei are largely structurally uncharacterized. This is in part due to the inherent experimental challenge associated with structural descriptions of individual components in a dynamic multi-component equilibrium. There are indications that oligomeric aggregated precursors of fibrillation, and not mature fibrils, are the main cause of cytotoxicity in amyloid disease. This further emphasizes the importance of characterizing early fibrillation events. Here we present a kinetic x-ray solution scattering study of insulin fibrillation, revealing three major components: insulin monomers, mature fibrils, and an oligomeric species. Low-resolution three-dimensional structures are determined for the fibril repeating unit and for the oligomer, the latter being a helical unit composed of five to six insulin monomers. This helical oligomer is likely to be a structural nucleus, which accumulates above the supercritical concentration used in our experiments. The growth rate of the fibrils is proportional to the amount of the helical oligomer present in solution, suggesting that these oligomers elongate the fibrils. Hence, the structural nucleus and elongating unit in insulin amyloid fibrillation may be the same structural component above supercritical concentrations. A novel elongation pathway of insulin amyloid fibrils is proposed, based on the shape and size of the fibrillation precursor. The distinct helical oligomer described in this study defines a conceptually new basis of structure-based drug design against amyloid diseases. PMID:17472440

Unexpected fold in the circumsporozoite protein target of malaria vaccines

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

Doud, Michael B.; Koksal, Adem C.; Mi, Li-Zhi

Circumsporozoite (CS) protein is the major surface component of Plasmodium falciparum sporozoites and is essential for host cell invasion. A vaccine containing tandem repeats, region III, and thrombospondin type-I repeat (TSR) of CS is efficacious in phase III trials but gives only a 35% reduction in severe malaria in the first year postimmunization. We solved crystal structures showing that region III and TSR fold into a single unit, an '{alpha}TSR' domain. The {alpha}TSR domain possesses a hydrophobic pocket and core, missing in TSR domains. CS binds heparin, but {alpha}TSR does not. Interestingly, polymorphic T-cell epitopes map to specialized {alpha}TSR regions.more » The N and C termini are unexpectedly close, providing clues for sporozoite sheath organization. Elucidation of a unique structure of a domain within CS enables rational design of next-generation subunit vaccines and functional and medicinal chemical investigation of the conserved hydrophobic pocket.« less

Efficient production of artificially designed gelatins with a Bacillus brevis system.

PubMed

Kajino, T; Takahashi, H; Hirai, M; Yamada, Y

2000-01-01

Artificially designed gelatins comprising tandemly repeated 30-amino-acid peptide units derived from human alphaI collagen were successfully produced with a Bacillus brevis system. The DNA encoding the peptide unit was synthesized by taking into consideration the codon usage of the host cells, but no clones having a tandemly repeated gene were obtained through the above-mentioned strategy. Minirepeat genes could be selected in vivo from a mixture of every possible sequence encoding an artificial gelatin by randomly ligating the mixed sequence unit and transforming it into Escherichia coli. Larger repeat genes constructed by connecting minirepeat genes obtained by in vivo selection were also stable in the expression host cells. Gelatins derived from the eight-unit and six-unit repeat genes were extracellularly produced at the level of 0.5 g/liter and easily purified by ammonium sulfate fractionation and anion-exchange chromatography. The purified artificial gelatins had the predicted N-terminal sequences and amino acid compositions and a solgel property similar to that of the native gelatin. These results suggest that the selection of a repeat unit sequence stable in an expression host is a shortcut for the efficient production of repetitive proteins and that it can conveniently be achieved by the in vivo selection method. This study revealed the possible industrial application of artificially designed repetitive proteins.

Giant Reverse Transcriptase-Encoding Transposable Elements at Telomeres.

PubMed

Arkhipova, Irina R; Yushenova, Irina A; Rodriguez, Fernando

2017-09-01

Transposable elements are omnipresent in eukaryotic genomes and have a profound impact on chromosome structure, function and evolution. Their structural and functional diversity is thought to be reasonably well-understood, especially in retroelements, which transpose via an RNA intermediate copied into cDNA by the element-encoded reverse transcriptase, and are characterized by a compact structure. Here, we report a novel type of expandable eukaryotic retroelements, which we call Terminons. These elements can attach to G-rich telomeric repeat overhangs at the chromosome ends, in a process apparently facilitated by complementary C-rich repeats at the 3'-end of the RNA template immediately adjacent to a hammerhead ribozyme motif. Terminon units, which can exceed 40 kb in length, display an unusually complex and diverse structure, and can form very long chains, with host genes often captured between units. As the principal polymerizing component, Terminons contain Athena reverse transcriptases previously described in bdelloid rotifers and belonging to the enigmatic group of Penelope-like elements, but can additionally accumulate multiple cooriented ORFs, including DEDDy 3'-exonucleases, GDSL esterases/lipases, GIY-YIG-like endonucleases, rolling-circle replication initiator (Rep) proteins, and putatively structural ORFs with coiled-coil motifs and transmembrane domains. The extraordinary length and complexity of Terminons and the high degree of interfamily variability in their ORF content challenge the current views on the structural organization of eukaryotic retroelements, and highlight their possible connections with the viral world and the implications for the elevated frequency of gene transfer. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Novel surface attachment mechanism of the Streptococcus pneumoniae protein PspA.

PubMed Central

Yother, J; White, J M

1994-01-01

Pneumococcal surface protein A (PspA) of Streptococcus pneumoniae has been found to utilize a novel mechanism for anchoring to the bacterial cell surface. In contrast to that of surface proteins from other gram-positive bacteria, PspA anchoring required choline-mediated interactions between the membrane-associated lipoteichoic acid and the C-terminal repeat region of PspA. Release of PspA from the cell surface could be effected by deletion of 5 of the 10 C-terminal repeat units, by high concentrations of choline, or by growth in choline-deficient medium. Other pneumococcal proteins, including autolysin, which has a similar C-terminal repeat region, were not released by these treatments. The attachment mechanism utilized by PspA thus appears to be uniquely adapted to exploit the unusual structure of the pneumococcal cell surface. Further, it has provided the means for rapid and simple isolation of immunogenic PspA from S. pneumoniae. Images PMID:7910604

Analytical relationships for prediction of the mechanical properties of additively manufactured porous biomaterials.

PubMed

Zadpoor, Amir Abbas; Hedayati, Reza

2016-12-01

Recent developments in additive manufacturing techniques have motivated an increasing number of researchers to study regular porous biomaterials that are based on repeating unit cells. The physical and mechanical properties of such porous biomaterials have therefore received increasing attention during recent years. One of the areas that have revived is analytical study of the mechanical behavior of regular porous biomaterials with the aim of deriving analytical relationships that could predict the relative density and mechanical properties of porous biomaterials, given the design and dimensions of their repeating unit cells. In this article, we review the analytical relationships that have been presented in the literature for predicting the relative density, elastic modulus, Poisson's ratio, yield stress, and buckling limit of regular porous structures based on various types of unit cells. The reviewed analytical relationships are used to compare the mechanical properties of porous biomaterials based on different types of unit cells. The major areas where the analytical relationships have improved during the recent years are discussed and suggestions are made for future research directions. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 3164-3174, 2016. © 2016 The Authors Journal of Biomedical Materials Research Part A Published by Wiley Periodicals, Inc.

Molecular Structure Controlled Transitions between Free-Charge Generation and Trap Formation in a Conjugated Copolymer Series

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

Pandit, Bill; Jackson, Nicholas E.; Zheng, Tianyue

2016-03-03

Charge transfer copolymers, where each repeating unit has at least one “donor” and one “acceptor” block, have played important roles in recent advances in organic photovoltaic (OPV) devices, however design criteria for these materials are still not completely clear. Here we show that the well-recognized LUMO-LUMO energy off-set design criterion for OPV materials using a fullerene acceptor is challenged in a series of copolymers, PTRn (n = 3, 5, 7 and 9), where n is the number of fused aromatic rings in the “donor” block and thienothiophene is the “acceptor” block in each repeating unit. Photoexcitation dynamics of PTRn copolymersmore » in solution and BHJ (bulk heterojunction) films demonstrated that local push-pull interactions between the “donor” block and the “acceptor” block weakens with increasing n, whereas the LUMO-LUMO off-set between the polymer and PC71BM (Phenyl-C71-butyric acid methyl ester) increases. Such a counter intuitive trend can be explained by local energetics of each repeating unit as a function of n. The energetic changes transform the copolymer with strong local charge transfer character for efficient hole-electron separation to localized hole-electron pairs with low mobility, despite the apparent increase of the polymer/PC71BM LUMO-LUMO off-set. This suggests the importance of local charge transfer character in these copolymers in the initial exciton splitting dynamics, which could ultimately be reflected in the device performance.« less

Vibrational spectroscopic study of cationic phosphorus dendrimers with aminoethylpiperidine terminal groups

NASA Astrophysics Data System (ADS)

Furer, V. L.; Vandyukov, A. E.; Tripathi, V.; Majoral, J. P.; Caminade, A. M.; Kovalenko, V. I.

2018-04-01

Two generations of phosphoric dendrimers with piperidine functional groups were synthesized for use in biology and medicine. Neutral samples are soluble in organic solvents but after protonation these dendrimers become water soluble and can be used for biological experiments. The FTIR and FT Raman spectra of two generations of dendrimers Gi constructed from the cyclotriphosphazene core, repeating units sbnd Osbnd C6H4sbnd CHdbnd Nsbnd N(CH3)sbnd P(S)< and aminoethylpiperidine end groups sbnd NHsbnd (CH2)2sbnd C5NH11 were recorded. The study of the IR spectra shows that the NH groups form hydrogen bonds. The calculation of the molecular structure and vibrational spectra of the first generation dendrimer was performed by the method of DFT. This molecule has flat, repeating units and a plane of symmetry passing through the core. The calculation of the distribution of potential energy made it possible to classify the bands in the experimental spectra of dendrimers. Amine groups are manifested in the form of a band of NH stretching vibrations at 3389 cm-1 in the IR spectrum of G1. NH+ stretching bands located at 2646 and 2540 cm-1 in the IR spectrum of G2. The stretching vibrations of NH+ groups are noticeably shifted to low frequencies due to the formation of a hydrogen bond with the chlorine atom. The line at 1575 cm-1 in the Raman spectrum of G1 is characteristic for repeating units.

Multiple independent insertions of 5S rRNA genes in the spliced-leader gene family of trypanosome species.

PubMed

Beauparlant, Marc A; Drouin, Guy

2014-02-01

Analyses of the 5S rRNA genes found in the spliced-leader (SL) gene repeat units of numerous trypanosome species suggest that such linkages were not inherited from a common ancestor, but were the result of independent 5S rRNA gene insertions. In trypanosomes, 5S rRNA genes are found either in the tandemly repeated units coding for SL genes or in independent tandemly repeated units. Given that trypanosome species where 5S rRNA genes are within the tandemly repeated units coding for SL genes are phylogenetically related, one might hypothesize that this arrangement is the result of an ancestral insertion of 5S rRNA genes into the tandemly repeated SL gene family of trypanosomes. Here, we use the types of 5S rRNA genes found associated with SL genes, the flanking regions of the inserted 5S rRNA genes and the position of these insertions to show that most of the 5S rRNA genes found within SL gene repeat units of trypanosome species were not acquired from a common ancestor but are the results of independent insertions. These multiple 5S rRNA genes insertion events in trypanosomes are likely the result of frequent founder events in different hosts and/or geographical locations in species having short generation times.

Concerted evolution of the tandemly repeated genes encoding primate U2 small nuclear RNA (the RNU2 locus) does not prevent rapid diversification of the (CT){sub n} {center_dot} (GA){sub n} microsatellite embedded within the U2 repeat unit

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

Liao, D.; Weiner, A.M.

1995-12-10

The RNU2 locus encoding human U2 small nuclear RNA (snRNA) is organized as a nearly perfect tandem array containing 5 to 22 copies of a 5.8-kb repeat unit. Just downstream of the U2 snRNA gene in each 5.8-kb repeat unit lies a large (CT){sub n}{center_dot}(GA){sub n} dinucleotide repeat (n {approx} 70). This form of genomic organization, in which one repeat is embedded within another, provides an unusual opportunity to study the balance of forces maintaining the homogeneity of both kinds of repeats. Using a combination of field inversion gel electrophoresis and polymerase chain reaction, we have been able to studymore » the CT microsatellites within individual U2 tandem arrays. We find that the CT microsatellites within an RNU2 allele exhibit significant length polymorphism, despite the remarkable homogeneity of the surrounding U2 repeat units. Length polymorphism is due primarily to loss or gain of CT dinucleotide repeats, but other types of deletions, insertions, and substitutions are also frequent. Polymorphism is greatly reduced in regions where pure (CT){sub n} tracts are interrupted by occasional G residues, suggesting that irregularities stabilize both the length and the sequence of the dinucleotide repeat. We further show that the RNU2 loci of other catarrhine primates (gorilla, chimpanzee, ogangutan, and baboon) contain orthologous CT microsatellites; these also exhibit length polymorphism, but are highly divergent from each other. Thus, although the CT microsatellite is evolving far more rapidly than the rest of the U2 repeat unit, it has persisted through multiple speciation events spanning >35 Myr. The persistence of the CT microsatellite, despite polymorphism and rapid evolution, suggests that it might play a functional role in concerted evolution of the RNU2 loci, perhaps as an initiation site for recombination and/or gene conversion. 70 refs., 5 figs.« less

Ultrasound effects on the degradation kinetics, structure, and antioxidant activity of sea cucumber fucoidan.

PubMed

Guo, Xin; Ye, Xingqian; Sun, Yujing; Wu, Dan; Wu, Nian; Hu, Yaqin; Chen, Shiguo

2014-02-05

The effects of ultrasound on the molecular weight, structure, and antioxidant potential of a fucoidan found in Isostichopus badionotus were investigated. The results showed the molecular weight (Mw) of fucoidan decreased obviously after ultrasound treatment. Higher ultrasonic intensity, lower temperature, and lower fucoidan concentrations led to a more effective sonochemical effect. The kinetic model for fucoidan degradation fitted to 1/M(wt)-1/M(w0) = kt at the tested temperature. The optimized degradation conditions by response surface methodology (RSM) were temperature, 12 °C, and intensity, 508 W/cm². Structural analysis by FTIR and NMR indicated the fucoidan kept the linear tetrasaccharide repeating units as the original polysaccharides after the ultrasound treatment, with only slight destruction of the middle nonsulfated fucose units. Antioxidant activity assay showed the antioxidant activity was slightly improved by the ultrasound treatment. The results suggested that ultrasound treatment is an effective approach to decrease the M(w) of fucoidan with only minor structural destruction.

Additively Manufactured Open-Cell Porous Biomaterials Made from Six Different Space-Filling Unit Cells: The Mechanical and Morphological Properties

PubMed Central

Ahmadi, Seyed Mohammad; Amin Yavari, Saber; Wauthle, Ruebn; Pouran, Behdad; Schrooten, Jan; Weinans, Harrie; Zadpoor, Amir A.

2015-01-01

It is known that the mechanical properties of bone-mimicking porous biomaterials are a function of the morphological properties of the porous structure, including the configuration and size of the repeating unit cell from which they are made. However, the literature on this topic is limited, primarily because of the challenge in fabricating porous biomaterials with arbitrarily complex morphological designs. In the present work, we studied the relationship between relative density (RD) of porous Ti6Al4V EFI alloy and five compressive properties of the material, namely elastic gradient or modulus (Es20–70), first maximum stress, plateau stress, yield stress, and energy absorption. Porous structures with different RD and six different unit cell configurations (cubic (C), diamond (D), truncated cube (TC), truncated cuboctahedron (TCO), rhombic dodecahedron (RD), and rhombicuboctahedron (RCO)) were fabricated using selective laser melting. Each of the compressive properties increased with increase in RD, the relationship being of a power law type. Clear trends were seen in the influence of unit cell configuration and porosity on each of the compressive properties. For example, in terms of Es20–70, the structures may be divided into two groups: those that are stiff (comprising those made using C, TC, TCO, and RCO unit cell) and those that are compliant (comprising those made using D and RD unit cell). PMID:28788037

Additively Manufactured Open-Cell Porous Biomaterials Made from Six Different Space-Filling Unit Cells: The Mechanical and Morphological Properties.

PubMed

Ahmadi, Seyed Mohammad; Yavari, Saber Amin; Wauthle, Ruebn; Pouran, Behdad; Schrooten, Jan; Weinans, Harrie; Zadpoor, Amir A

2015-04-21

It is known that the mechanical properties of bone-mimicking porous biomaterials are a function of the morphological properties of the porous structure, including the configuration and size of the repeating unit cell from which they are made. However, the literature on this topic is limited, primarily because of the challenge in fabricating porous biomaterials with arbitrarily complex morphological designs. In the present work, we studied the relationship between relative density (RD) of porous Ti6Al4V EFI alloy and five compressive properties of the material, namely elastic gradient or modulus (E s20 -70 ), first maximum stress, plateau stress, yield stress, and energy absorption. Porous structures with different RD and six different unit cell configurations (cubic (C), diamond (D), truncated cube (TC), truncated cuboctahedron (TCO), rhombic dodecahedron (RD), and rhombicuboctahedron (RCO)) were fabricated using selective laser melting. Each of the compressive properties increased with increase in RD, the relationship being of a power law type. Clear trends were seen in the influence of unit cell configuration and porosity on each of the compressive properties. For example, in terms of E s20 -70 , the structures may be divided into two groups: those that are stiff (comprising those made using C, TC, TCO, and RCO unit cell) and those that are compliant (comprising those made using D and RD unit cell).

Sequence diagrams and the presentation of structural and evolutionary relationships among proteins.

PubMed

Thomas, B R

1975-01-01

Protein sequences mapped on two-dimensional diagrams show characteristic patterns that should be of value in visualising sequence information and in distinguishing simpler structures. A convenient map form for comparative purposes is the alpha-helix diagram with aminoacid distribution analogous to the surface of an alpha-helix oriented so that an alpha-helix structure corresponds on the diagram to a vertical band 3.6 residues wide. The sequence diagram for an alpha-keratin, high-sulphur protein suggests a new form of polypeptide helix based on a repeating unit of five which may be an important component of alpha-keratin fibres.

Dislocation structures of Σ3 {112} twin boundaries in face centered cubic metals

NASA Astrophysics Data System (ADS)

Wang, J.; Anderoglu, O.; Hirth, J. P.; Misra, A.; Zhang, X.

2009-07-01

High resolution transmission electron microscopy of nanotwinned Cu films revealed Σ3 {112} incoherent twin boundaries (ITBs), with a repeatable pattern involving units of three {111} atomic planes. Topological analysis shows that Σ3 {112} ITBs adopt two types of atomic structure with differing arrangements of Shockley partial dislocations. Atomistic simulations were performed for Cu and Al. These studies revealed the structure of the two types of ITBs, the formation mechanism and stability of the associated 9R phase, and the influence of stacking fault energies on them. The results suggest that Σ3 {112} ITBs may migrate through the collective glide of partial dislocations.

Structural studies of O-polysaccharide isolated from Cronobacter sakazakii Sequence Type 12 from a case of neonatal necrotizing enterocolitis.

PubMed

Marszewska, Kinga; Czerwicka, Małgorzata; Forsythe, Stephen J; Ossowska, Karolina; Dziadziuszko, Halina; Kaczyński, Zbigniew

2015-04-30

The O-polysaccharide (OPS) of Cronobacter sakazakii NTU 696 (Sequence Type 12) from a case of neonatal necrotizing enterocolitis was isolated from the polysaccharide fraction obtained after lipopolysaccharide (LPS) hydrolysis. Purified OPS was analyzed by NMR spectroscopy ((1)H, COSY, TOCSY, NOESY, HSQC, HSQC-TOCSY and HMBC experiments) and chemical methods. Obtained monosaccharide derivatives analyzed by gas chromatography and gas chromatography-mass spectrometry allowed the identification of six sugar components. Performed experiments enabled to establish a structure of the OPS repeating unit of C. sakazakii NTU 696, as: [structure: see text]. Copyright © 2015 Elsevier Ltd. All rights reserved.

Quantifying the atomic-level mechanics of single long physisorbed molecular chains.

PubMed

Kawai, Shigeki; Koch, Matthias; Gnecco, Enrico; Sadeghi, Ali; Pawlak, Rémy; Glatzel, Thilo; Schwarz, Jutta; Goedecker, Stefan; Hecht, Stefan; Baratoff, Alexis; Grill, Leonhard; Meyer, Ernst

2014-03-18

Individual in situ polymerized fluorene chains 10-100 nm long linked by C-C bonds are pulled vertically from an Au(111) substrate by the tip of a low-temperature atomic force microscope. The conformation of the selected chains is imaged before and after manipulation using scanning tunneling microscopy. The measured force gradient shows strong and periodic variations that correspond to the step-by-step detachment of individual fluorene repeat units. These variations persist at constant intensity until the entire polymer is completely removed from the surface. Calculations based on an extended Frenkel-Kontorova model reproduce the periodicity and magnitude of these features and allow us to relate them to the detachment force and desorption energy of the repeat units. The adsorbed part of the polymer slides easily along the surface during the pulling process, leading to only small oscillations as a result of the high stiffness of the fluorenes and of their length mismatch with respect to the substrate surface structure. A significant lateral force also is caused by the sequential detachment of individual units. The gained insight into the molecule-surface interactions during sliding and pulling should aid the design of mechanoresponsive nanosystems and devices.

Relationship between unit cell type and porosity and the fatigue behavior of selective laser melted meta-biomaterials.

PubMed

Amin Yavari, S; Ahmadi, S M; Wauthle, R; Pouran, B; Schrooten, J; Weinans, H; Zadpoor, A A

2015-03-01

Meta-materials are structures when their small-scale properties are considered, but behave as materials when their homogenized macroscopic properties are studied. There is an intimate relationship between the design of the small-scale structure and the homogenized properties of such materials. In this article, we studied that relationship for meta-biomaterials that are aimed for biomedical applications, otherwise known as meta-biomaterials. Selective laser melted porous titanium (Ti6Al4V ELI) structures were manufactured based on three different types of repeating unit cells, namely cube, diamond, and truncated cuboctahedron, and with different porosities. The morphological features, static mechanical properties, and fatigue behavior of the porous biomaterials were studied with a focus on their fatigue behavior. It was observed that, in addition to static mechanical properties, the fatigue properties of the porous biomaterials are highly dependent on the type of unit cell as well as on porosity. None of the porous structures based on the cube unit cell failed after 10(6) loading cycles even when the applied stress reached 80% of their yield strengths. For both other unit cells, higher porosities resulted in shorter fatigue lives for the same level of applied stress. When normalized with respect to their yield stresses, the S-N data points of structures with different porosities very well (R(2)>0.8) conformed to one single power law specific to the type of the unit cell. For the same level of normalized applied stress, the truncated cuboctahedron unit cell resulted in a longer fatigue life as compared to the diamond unit cell. In a similar comparison, the fatigue lives of the porous structures based on both truncated cuboctahedron and diamond unit cells were longer than that of the porous structures based on the rhombic dodecahedron unit cell (determined in a previous study). The data presented in this study could serve as a basis for design of porous biomaterials as well as for corroboration of relevant analytical and computational models. Copyright © 2014 Elsevier Ltd. All rights reserved.

Bioinspired Organic PV Cells Using Photosynthetic Pigment Complex for Energy Harvesting Materials

DTIC Science & Technology

2010-05-10

ultrafast laser spectroscopy. More recently the structures of the LH2 complexes has revealed the nonameric or octameric arrangement of repeating units...Scheme 1. Compartimentalization of light harvesting and charge separation. The antenna complexes( LH2 ,LH1-RC) efficiently realize various...photosynthetic functions using cofactors (BChl a and carotenoid) assembled into the apoproteins (LH1 and LH2 ). The light-harvesting mechanisms in these

Biology and applications of human minisatellite loci.

PubMed

Armour, J A; Jeffreys, A J

1992-12-01

Highly repetitive minisatellites' include the most variable human loci described to date. They have proved invaluable in a wide variety of genetic analyses, and despite some controversies surrounding their practical implementation, have been extensively adopted in civil and forensic casework. Molecular analysis of internal allelic structure has provided detailed insights into the repeat-unit turnover mechanisms operating in germline mutations, which are ultimately responsible for the extreme variability seen at these loci.

A versatile platform for precise synthesis of asymmetric molecular brush in one shot.

PubMed

Xu, Binbin; Feng, Chun; Huang, Xiaoyu

2017-08-24

Asymmetric molecular brushes emerge as a unique class of nanostructured polymers, while their versatile synthesis keeps a challenge for chemists. Here we show the synthesis of well-defined asymmetric molecular double-brushes comprising two different side chains linked to the same repeat unit along the backbone by one-pot concurrent atom transfer radical polymerization (ATRP) and Cu-catalyzed azide/alkyne cycloaddition (CuAAC) reaction. The double-brushes are based on a poly(Br-acrylate-alkyne) homopolymer possessing an alkynyl for CuAAC reaction and a 2-bromopropionate initiating group for ATRP in each repeat unit. The versatility of this one-shot approach is demonstrated by CuAAC reaction of alkynyl/poly(ethylene oxide)-N 3 and ATRP of various monomers. We also show the quantitative conversion of pentafluorophenyl ester groups to amide groups in side chains, allowing for the further fabrication of diverse building blocks. This work provides a versatile platform for facile synthesis of Janus-type double-brushes with structural and functional control, in a minimum number of reactions.Producing well-defined polymer compositions and structures facilitates their use in many different applications. Here the authors show the synthesis of well-defined asymmetric double-brushes by a one-pot concurrent atom transfer radical polymerization and Cu-catalyzed Click reaction.

Effect of donor to acceptor ratio on electrochemical and spectroscopic properties of oligoalkylthiophene 1,3,4-oxadiazole derivatives.

PubMed

Kurowska, Aleksandra; Zassowski, Pawel; Kostyuchenko, Anastasia S; Zheleznova, Tatyana Yu; Andryukhova, Kseniya V; Fisyuk, Alexander S; Pron, Adam; Domagala, Wojciech

2017-11-15

A structure-property study across a series of donor-acceptor-donor structures composed of mono- and bi-(1,3,4-oxadiazole) units symmetrically substituted with alkyl functionalized bi-, ter- and quaterthiophene segments is presented. Synthetically tailoring the ratio of electron-withdrawing 1,3,4-oxadiazole to electron-releasing thiophene units and their alkyl grafting pattern permitted us to scrutinize the impact of these structural factors on the redox, absorptive and emissive properties of these push-pull molecules. Contrasting trends of redox potentials were observed, with the oxidation potential closely following the donor-to-acceptor ratio, whereas the reduction potential being tuned independently by either the number of acceptor units or the conjugation length of the donor-acceptor system. Increasing the thiophene unit contribution delivered a shift from blue to green luminescence, while the structural rigidity afforded by intramolecular non-covalent interactions between 1,3,4-oxadiazole and the thiophene moieties has been identified as the prime factor determining the emission efficiency of these molecules. All six structures investigated electro-polymerize easily, yielding electroactive and electrochromic polymers. The polymer doping process is largely influenced by the length of the oligothiophene repeating unit and the alkyl chain grafting density. Polymers with relatively short oligothiophene segments are able to support polarons and polaron-pairs, whereas those with segments longer than six thiophene units could also stabilize diamagnetic charge carries - bipolarons. Increasing the alkyl chain grafting density improved the reversibility and broadened the working potential window of the p-doping process. Stable radical anions have also been investigated, bringing detailed information about the conjugation pattern of these electron-surplus species. This study delivers interesting clues towards the conscious structural design of bespoke frontier energy level oligothiophene functional materials and their polymers by incorporating a structurally matching 1,3,4-oxadiazole unit.

Early-onset facioscapulohumeral muscular dystrophy type 1 with some atypical features.

PubMed

Dorobek, Małgorzata; van der Maarel, Silvère M; Lemmers, Richard J L F; Ryniewicz, Barbara; Kabzińska, Dagmara; Frants, Rune R; Gawel, Malgorzata; Walecki, Jerzy; Hausmanowa-Petrusewicz, Irena

2015-04-01

Facioscapulohumeral muscular dystrophy cases with facial weakness before the age of 5 and signs of shoulder weakness by the age of 10 are defined as early onset. Contraction of the D4Z4 repeat on chromosome 4q35 is causally related to facioscapulohumeral muscular dystrophy type 1, and the residual size of the D4Z4 repeat shows a roughly inverse correlation with the severity of the disease. Contraction of the D4Z4 repeat on chromosome 4q35 is believed to induce a local change in chromatin structure and consequent transcriptional deregulation of 4qter genes. We present early-onset cases in the Polish population that amounted to 21% of our total population with facioscapulohumeral muscular dystrophy. More than 27% of them presented with severe phenotypes (wheelchair dependency). The residual D4Z4 repeat sizes ranged from 1 to 4 units. In addition, even within early-onset facioscapulohumeral muscular dystrophy type 1 phenotypes, some cases had uncommon features (head drop, early disabling contractures, progressive ptosis, and respiratory insufficiency and cardiomyopathy). © The Author(s) 2014.

CT visible internal stone structure, but not Hounsfield unit value, of calcium oxalate monohydrate (COM) calculi predicts lithotripsy fragility in vitro.

PubMed

Zarse, Chad A; Hameed, Tariq A; Jackson, Molly E; Pishchalnikov, Yuri A; Lingeman, James E; McAteer, James A; Williams, James C

2007-08-01

Calcium oxalate monohydrate (COM) stones are often resistant to breakage using shock wave (SW) lithotripsy. It would be useful to identify by computed tomography (CT) those COM stones that are susceptible to SW's. For this study, 47 COM stones (4-10 mm in diameter) were scanned with micro CT to verify composition and also for assessment of heterogeneity (presence of pronounced lobulation, voids, or apatite inclusions) by blinded observers. Stones were then placed in water and scanned using 64-channel helical CT. As with micro CT, heterogeneity was assessed by blinded observers, using high-bone viewing windows. Then stones were broken in a lithotripter (Dornier Doli-50) over 2 mm mesh, and SW's counted. Results showed that classification of stones using micro CT was highly repeatable among observers (kappa = 0.81), and also predictive of stone fragility. Stones graded as homogeneous required 1,874 +/- 821 SW/g for comminution, while stones with visible structure required half as many SW/g, 912 +/- 678. Similarly, when stones were graded by appearance on helical CT, classification was repeatable (kappa = 0.40), and homogeneous stones required more SW's for comminution than did heterogeneous stones (1,702 +/- 993 SW/g, compared to 907 +/- 773). Stone fragility normalized to stone size did not correlate with Hounsfield units (P = 0.85). In conclusion, COM stones of homogeneous structure require almost twice as many SW's to comminute than stones of similar mineral composition that exhibit internal structural features that are visible by CT. This suggests that stone fragility in patients could be predicted using pre-treatment CT imaging. The findings also show that Hounsfield unit values of COM stones did not correlate with stone fragility. Thus, it is stone morphology, rather than X-ray attenuation, which correlates with fragility to SW's in this common stone type.

The nucleotide sequence of the entire ribosomal DNA operon and the structure of the large subunit rRNA of Giardia muris.

PubMed

van Keulen, H; Gutell, R R; Campbell, S R; Erlandsen, S L; Jarroll, E L

1992-10-01

The total nucleotide sequence of the rDNA of Giardia muris, an intestinal protozoan parasite of rodents, has been determined. The repeat unit is 7668 basepairs (bp) in size and consists of a spacer of 3314 bp, a small-subunit rRNA (SSU-rRNA) gene of 1429, and a large-subunit rRNA (LSU-rRNA) gene of 2698 bp. The spacer contains long direct repeats and is heterogeneous in size. The LSU-rRNA of G. muris was compared to that of the human intestinal parasite Giardia duodenalis, to the bird parasite Giardia ardeae, and to that of Escherichia coli. The LSU-rRNA has a size comparable to the 23S rRNA of E. coli but shows structural features typical for eukaryotes. Some variable regions are typically small and account for the overall smaller size of this rRNA. The structure of the G. muris LSU-rRNA is similar to that of the other Giardia rRNA, but each rRNA has characteristic features residing in a number of variable regions.

Myotonic Dystrophy Type 1 RNA Crystal Structures Reveal Heterogeneous 1×1 Nucleotide UU Internal Loop Conformations⊥

PubMed Central

Kumar, Amit; Park, HaJeung; Fang, Pengfei; Parkesh, Raman; Guo, Min; Nettles, Kendall W.; Disney, Matthew D.

2011-01-01

RNA internal loops often display a variety of conformations in solution. Herein, we visualize conformational heterogeneity in the context of the 5′CUG/3′GUC repeat motif present in the RNA that causes myotonic dystrophy type 1 (DM1). Specifically, two crystal structures are disclosed of a model DM1 triplet repeating construct, 5′r(UUGGGC(CUG)3GUCC)2, refined to 2.20 Å and 1.52 Å resolution. Here, differences in orientation of the 5′ dangling UU end between the two structures induce changes in the backbone groove width, which reveals that non-canonical 1×1 nucleotide UU internal loops can display an ensemble of pairing conformations. In the 2.20 Å structure, CUGa, the 5′UU forms one hydrogen-bonded pairs with a 5′UU of a neighboring helix in the unit cell to form a pseudo-infinite helix. The central 1×1 nucleotide UU internal loop has no hydrogen bonds, while the terminal 1×1 nucleotide UU internal loops each form a one hydrogen-bonded pair. In the 1.52 Å structure, CUGb, the 5′ UU dangling end is tucked into the major groove of the duplex. While the canonical paired bases show no change in base pairing, in CUGb the terminal 1×1 nucleotide UU internal loops form now two hydrogen-bonded pairs. Thus, the shift in major groove induced by the 5′UU dangling end alters non-canonical base patterns. Collectively, these structures indicate that 1×1 nucleotide UU internal loops in DM1 may sample multiple conformations in vivo. This observation has implications for the recognition of this RNA, and other repeating transcripts, by protein and small molecule ligands. PMID:21988728

Myotonic dystrophy type 1 RNA crystal structures reveal heterogeneous 1 × 1 nucleotide UU internal loop conformations.

PubMed

Kumar, Amit; Park, HaJeung; Fang, Pengfei; Parkesh, Raman; Guo, Min; Nettles, Kendall W; Disney, Matthew D

2011-11-15

RNA internal loops often display a variety of conformations in solution. Herein, we visualize conformational heterogeneity in the context of the 5'CUG/3'GUC repeat motif present in the RNA that causes myotonic dystrophy type 1 (DM1). Specifically, two crystal structures of a model DM1 triplet repeating construct, 5'r[UUGGGC(CUG)(3)GUCC](2), refined to 2.20 and 1.52 Å resolution are disclosed. Here, differences in the orientation of the 5' dangling UU end between the two structures induce changes in the backbone groove width, which reveals that noncanonical 1 × 1 nucleotide UU internal loops can display an ensemble of pairing conformations. In the 2.20 Å structure, CUGa, the 5' UU forms a one hydrogen-bonded pair with a 5' UU of a neighboring helix in the unit cell to form a pseudoinfinite helix. The central 1 × 1 nucleotide UU internal loop has no hydrogen bonds, while the terminal 1 × 1 nucleotide UU internal loops each form a one-hydrogen bond pair. In the 1.52 Å structure, CUGb, the 5' UU dangling end is tucked into the major groove of the duplex. While the canonically paired bases show no change in base pairing, in CUGb the terminal 1 × 1 nucleotide UU internal loops now form two hydrogen-bonded pairs. Thus, the shift in the major groove induced by the 5' UU dangling end alters noncanonical base patterns. Collectively, these structures indicate that 1 × 1 nucleotide UU internal loops in DM1 may sample multiple conformations in vivo. This observation has implications for the recognition of this RNA, and other repeating transcripts, by protein and small molecule ligands.

Myotonic Dystrophy Type 1 RNA Crystal Structures Reveal Heterogeneous 1 × 1 Nucleotide UU Internal Loop Conformations

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

Kumar, Amit; Park, HaJeung; Fang, Pengfei

2012-03-27

RNA internal loops often display a variety of conformations in solution. Herein, we visualize conformational heterogeneity in the context of the 5'CUG/3'GUC repeat motif present in the RNA that causes myotonic dystrophy type 1 (DM1). Specifically, two crystal structures of a model DM1 triplet repeating construct, 5'r[{und UU}GGGC(C{und U}G){sub 3}GUCC]{sub 2}, refined to 2.20 and 1.52 {angstrom} resolution are disclosed. Here, differences in the orientation of the 5' dangling UU end between the two structures induce changes in the backbone groove width, which reveals that noncanonical 1 x 1 nucleotide UU internal loops can display an ensemble of pairing conformations.more » In the 2.20 {angstrom} structure, CUGa, the 5' UU forms a one hydrogen-bonded pair with a 5' UU of a neighboring helix in the unit cell to form a pseudoinfinite helix. The central 1 x 1 nucleotide UU internal loop has no hydrogen bonds, while the terminal 1 x 1 nucleotide UU internal loops each form a one-hydrogen bond pair. In the 1.52 {angstrom} structure, CUGb, the 5' UU dangling end is tucked into the major groove of the duplex. While the canonically paired bases show no change in base pairing, in CUGb the terminal 1 x 1 nucleotide UU internal loops now form two hydrogen-bonded pairs. Thus, the shift in the major groove induced by the 5' UU dangling end alters noncanonical base patterns. Collectively, these structures indicate that 1 x 1 nucleotide UU internal loops in DM1 may sample multiple conformations in vivo. This observation has implications for the recognition of this RNA, and other repeating transcripts, by protein and small molecule ligands.« less

Genetic instability associated with loop or stem–loop structures within transcription units can be independent of nucleotide excision repair

PubMed Central

Burns, John A; Chowdhury, Moinuddin A; Cartularo, Laura; Berens, Christian; Scicchitano, David A

2018-01-01

Abstract Simple sequence repeats (SSRs) are found throughout the genome, and under some conditions can change in length over time. Germline and somatic expansions of trinucleotide repeats are associated with a series of severely disabling illnesses, including Huntington's disease. The underlying mechanisms that effect SSR expansions and contractions have been experimentally elusive, but models suggesting a role for DNA repair have been proposed, in particular the involvement of transcription-coupled nucleotide excision repair (TCNER) that removes transcription-blocking DNA damage from the transcribed strand of actively expressed genes. If the formation of secondary DNA structures that are associated with SSRs were to block RNA polymerase progression, TCNER could be activated, resulting in the removal of the aberrant structure and a concomitant change in the region's length. To test this, TCNER activity in primary human fibroblasts was assessed on defined DNA substrates containing extrahelical DNA loops that lack discernible internal base pairs or DNA stem–loops that contain base pairs within the stem. The results show that both structures impede transcription elongation, but there is no corresponding evidence that nucleotide excision repair (NER) or TCNER operates to remove them. PMID:29474673

Characterization of a tandemly repeated DNA sequence family originally derived by retroposition of tRNA(Glu) in the newt.

PubMed

Nagahashi, S; Endoh, H; Suzuki, Y; Okada, N

1991-11-20

A previous report from this laboratory showed that in vitro transcription of total genomic DNA of the newt Cynopus pyrrhogaster resulted in a discrete sized 8 S RNA, which represented highly repetitive and transcribable sequences with a glutamic acid tRNA-like structure in the newt genome. We isolated four independent clones from a newt genomic library and determined the complete sequences of three 2000 to 2400 base-pair PstI fragments spanning the 8 S RNA gene. The glutamic acid tRNA-related segment in the 8 S RNA gene contains the CCA sequence expected as the 3' terminus of a tRNA molecule. Further, the 11 nucleotides located 13 nucleotides upstream from one of the two transcription initiation sites of the 8 S RNA were found to be repeated in the region upstream from the termination site, suggesting that the original unit, which is shorter than the 8 S RNA, was retrotransposed via cDNA intermediates from the PolIII transcript. In the upstream region of the 8 S RNA gene, a 360 nucleotide unit containing the glutamic acid tRNA-related segment was found to be duplicated (clones NE1 and NE10) or triplicated (clone NE3). Except for the difference in the number of the 360 nucleotide unit, the three sequences of the 2000 to 2400 base-pair PstI fragment were essentially the same with only a few mutations and minor deletions. Inverse polymerase chain reaction and sequence determination of the products, together with a Southern hybridization experiment, demonstrated that the family consists of a tandemly repeated unit of 3300, 3700 or 4100 base-pairs. Thus during evolution, this family in the newt was created by retroposition via cDNA intermediates, followed by duplication or triplication of the 360 nucleotide unit and multiplication of the 3300 to 4100 base-pair region at the DNA level.

Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus

PubMed Central

Lee, Tong Geon; Kumar, Indrajit; Diers, Brian W; Hudson, Matthew E

2015-01-01

The soybean cyst nematode (SCN) resistance locus Rhg1 is a tandem repeat of a 31.2 kb unit of the soybean genome. Each 31.2-kb unit contains four genes. One allele of Rhg1, Rhg1-b, is responsible for protecting most US soybean production from SCN. Whole-genome sequencing was performed, and PCR assays were developed to investigate allelic variation in sequence and copy number of the Rhg1 locus across a population of soybean germplasm accessions. Four distinct sequences of the 31.2-kb repeat unit were identified, and some Rhg1 alleles carry up to three different types of repeat unit. The total number of copies of the repeat varies from 1 to 10 per haploid genome. Both copy number and sequence of the repeat correlate with the resistance phenotype, and the Rhg1 locus shows strong signatures of selection. Significant linkage disequilibrium in the genome outside the boundaries of the repeat allowed the Rhg1 genotype to be inferred using high-density single nucleotide polymorphism genotyping of 15 996 accessions. Over 860 germplasm accessions were found likely to possess Rhg1 alleles. The regions surrounding the repeat show indications of non-neutral evolution and high genetic variability in populations from different geographic locations, but without evidence of fixation of the resistant genotype. A compelling explanation of these results is that balancing selection is in operation at Rhg1. PMID:25735447

Molecular characterization of organic electronic films.

PubMed

DeLongchamp, Dean M; Kline, R Joseph; Fischer, Daniel A; Richter, Lee J; Toney, Michael F

2011-01-18

Organic electronics have emerged as a viable competitor to amorphous silicon for the active layer in low-cost electronics. The critical performance of organic electronic materials is closely related to their morphology and molecular packing. Unlike their inorganic counterparts, polymers combine complex repeat unit structure and crystalline disorder. This combination prevents any single technique from being able to uniquely solve the packing arrangement of the molecules. Here, a general methodology for combining multiple, complementary techniques that provide accurate unit cell dimensions and molecular orientation is described. The combination of measurements results in a nearly complete picture of the organic film morphology. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Identification of an O-linked repetitive glycan chain of the polar flagellum flagellin of Azospirillum brasilense Sp7.

PubMed

Belyakov, Alexei Ye; Burygin, Gennady L; Arbatsky, Nikolai P; Shashkov, Alexander S; Selivanov, Nikolai Yu; Matora, Larisa Yu; Knirel, Yuriy A; Shchyogolev, Sergei Yu

2012-11-01

This is the first report to have identified an O-linked repetitive glycan in bacterial flagellin, a structural protein of the flagellum. Studies by sugar analysis, Smith degradation, (1)H and (13)C NMR spectroscopy, and mass spectrometry showed that the glycan chains of the polar flagellum flagellin of the plant-growth-promoting rhizobacterium Azospirillum brasilense Sp7 are represented by a polysaccharide with a molecular mass of 7.7 kDa, which has a branched tetrasaccharide repeating unit of the following structure: Copyright © 2012. Published by Elsevier Ltd.

Pectic polysaccharide from the green fruits of Momordica charantia (Karela): structural characterization and study of immunoenhancing and antioxidant properties.

PubMed

Panda, Bibhash C; Mondal, Soumitra; Devi, K Sanjana P; Maiti, Tapas K; Khatua, Somanjana; Acharya, Krishnendu; Islam, Syed S

2015-01-12

A water soluble pectic polysaccharide (PS) isolated from the aqueous extract of the green fruits of Momordica charantia contains D-galactose and D-methyl galacturonate in a molar ratio of nearly 1:4. It showed splenocyte, thymocyte as well as macrophage activations. Moreover, it exhibited potent antioxidant activities. On the basis of total acid hydrolysis, methylation analysis, periodate oxidation, and 1D and 2D NMR studies, the structure of the repeating unit of the pectic polysaccharide was established as: [Formula: see text]. Copyright © 2014 Elsevier Ltd. All rights reserved.

Assembly of Photosynthetic Antenna Protein Complexes from Algae for Development of Nano-biodevice and Its Fuelization

DTIC Science & Technology

2013-05-20

More recently the structures of the LH2 complexes has revealed the nonameric and octameric arrangement of repeating units consisting of two...Compartimentalization of light -harvesting and charge separation. The antenna complexes( LH2 ,LH1-RC) efficiently realize various photosynthetic functions...using cofactors (BChl a and carotenoid) assembled into the apoproteins (LH1 and LH2 ). The light-harvesting mechanisms in these light-harvesting

Assembly of Photosynthetic Antenna Protein / Pigments Complexes from Algae and Plants for Development of Nanobiodevices

DTIC Science & Technology

2012-07-10

recently the structures of the LH2 complexes has revealed the nonameric and octameric arrangement of repeating units consisting of two apoproteins and...Compartimentalization of light -harvesting and charge separation. The antenna complexes( LH2 ,LH1-RC) efficiently realize various photosynthetic functions using...cofactors (BChl a and carotenoid) assembled into the apoproteins (LH1 and LH2 ). The light-harvesting mechanisms in these light-harvesting complexes have

The Effect of Weld Penetration on Blast Performance of Welded Panels

DTIC Science & Technology

2014-08-01

requirements of blast and ballistic protection, structural strength, fatigue resistance, unit mass and production cost. The testing described in this report...UNCLASSIFIED 7 TETRA S 20 9 3-G is an austenitic filler material often selected for welding high strength armour steels to control hydrogen induced...repeatability, lower cost, faster test turnaround and a reduced number of variables to control . Figure 30 is an illustration of the simplifications made

The origin of the split B800 absorption peak in the LH2 complexes from Allochromatium vinosum.

PubMed

Löhner, Alexander; Carey, Anne-Marie; Hacking, Kirsty; Picken, Nichola; Kelly, Sharon; Cogdell, Richard; Köhler, Jürgen

2015-01-01

The absorption spectrum of the high-light peripheral light-harvesting (LH) complex from the photosynthetic purple bacterium Allochromatium vinosum features two strong absorptions around 800 and 850 nm. For the LH2 complexes from the species Rhodopseudomonas acidophila and Rhodospirillum molischianum, where high-resolution X-ray structures are available, similar bands have been observed and were assigned to two pigment pools of BChl a molecules that are arranged in two concentric rings (B800 and B850) with nine (acidophila) or eight (molischianum) repeat units, respectively. However, for the high-light peripheral LH complex from Alc. vinosum, the intruiging feature is that the B800 band is split into two components. We have studied this pigment-protein complex by ensemble CD spectroscopy and polarisation-resolved single-molecule spectroscopy. Assuming that the high-light peripheral LH complex in Alc. vinosum is constructed on the same modular principle as described for LH2 from Rps. acidophila and Rsp. molischianum, we used those repeat units as a starting point for simulating the spectra. We find the best agreement between simulation and experiment for a ring-like oligomer of 12 repeat units, where the mutual arrangement of the B800 and B850 rings resembles those from Rsp. molischianum. The splitting of the B800 band can be reproduced if both an excitonic coupling between dimers of B800 molecules and their interaction with the B850 manifold are taken into account. Such dimers predict an interesting apoprotein organisation as discussed below.

Analysis of the mechanical behavior of a titanium scaffold with a repeating unit-cell substructure.

PubMed

Ryan, Garrett; McGarry, Patrick; Pandit, Abhay; Apatsidis, Dimitrios

2009-08-01

Titanium scaffolds with controlled microarchitecture have been developed for load bearing orthopedic applications. The controlled microarchitecture refers to a repeating array of unit-cells, composed of sintered titanium powder, which make up the scaffold structure. The objective of this current research was to characterize the mechanical performance of three scaffolds with increasing porosity, using finite element analysis (FEA) and to compare the results with experimental data. Scaffolds were scanned using microcomputed tomography and FEA models were generated from the resulting computer models. Macroscale and unit-cell models of the scaffolds were created. The material properties of the sintered titanium powders were first evaluated in mechanical tests and the data used in the FEA. The macroscale and unit-cell FEA models proved to be a good predictor of Young's modulus and yield strength. Although macroscale models showed similar failure patterns and an expected trend in UCS, strain at UCS did not compare well with experimental data. Since a rapid prototyping method was used to create the scaffolds, the original CAD geometries of the scaffold were also evaluated using FEA but they did not reflect the mechanical properties of the physical scaffolds. This indicates that at present, determining the actual geometry of the scaffold through computed tomography imaging is important. Finally, a fatigue analysis was performed on the scaffold to simulate the loading conditions it would experience as a spinal interbody fusion device.

Exploration of polyamide structure-property relationships by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

PubMed

Barrère, Caroline; Rejaibi, Majed; Curat, Aurélien; Hubert-Roux, Marie; Lavanant, Hélène; Afonso, Carlos; Kebir, Nasreddine; Desilles, Nicolas; Lecamp, Laurence; Burel, Fabrice; Loutelier-Bourhis, Corinne

2014-08-15

Polyamides (PA) are among the most used classes of polymers because of their attractive properties. Depending on the nature and proportion of the co-monomers used for their synthesis, they can exhibit a very large range of melting temperatures (Tm ). This study aims at the correlation of data from mass spectrometry (MS) with differential scanning calorimetry (DSC) and X-ray diffraction analyses to relate molecular structure to physical properties such as melting temperature, enthalpy change and crystallinity rate. Six different PA copolymers with molecular weights around 3500 g mol(-1) were synthesized with varying proportions of different co-monomers (amino-acid AB/di-amine AA/di-acid BB). Their melting temperature, enthalpy change and crystallinity rate were measured by DSC and X-ray diffraction. Their structural characterization was carried out by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). Because of the poor solubility of PA, a solvent-free sample preparation strategy was used with 2,5-dihydroxybenzoic acid (2,5-DHB) as the matrix and sodium iodide as the cationizing agent. The different proportions of the repeating unit types led to the formation of PA with melting temperatures ranging from 115°C to 185°C. The structural characterization of these samples by MALDI-TOF-MS revealed a collection of different ion distributions with different sequences of repeating units (AA, BB; AB/AA, BB and AB) in different proportions according to the mixture of monomers used in the synthesis. The relative intensities of these ion distributions were related to sample complexity and structure. They were correlated to DSC and X-ray results, to explain the observed physical properties. The structural information obtained by MALDI-TOF-MS provided a better understanding of the variation of the PA melting temperature and established a structure-properties relationship. This work will allow future PA designs to be monitored. Copyright © 2014 John Wiley & Sons, Ltd.

Evolutionary mechanisms shaping the genetic population structure of coastal fish: insight from populations of Coilia nasus in Northwestern Pacific.

PubMed

Gao, Tianxiang; Wan, Zhenzhen; Song, Na; Zhang, Xiumei; Han, Zhiqiang

2014-12-01

A number of evolutionary mechanisms have been suggested for generating significant genetic structuring among marine fish populations in Northwestern Pacific. We used mtDNA control region to assess the factors in shaping the genetic structure of Japanese grenadier anchovy, Coilia nasus, an anadromous and estuarine coastal species, in Northwestern Pacific. Sixty seven individuals from four locations in Northwestern Pacific were sequenced for mitochondrial control region, detecting 61 haplotypes. The length of amplified control region varied from 677 to 754 bp. This length variability was due to the presence of varying numbers of a 38-bp tandemly repeated sequence. Two distinct lineages were detected, which might have diverged during Pleistocene low sea levels. There were strong differences in the geographical distribution of the two lineages. Analyses of molecular variance and the population statistic ΦST revealed significant genetic structure between China and Ariake Bay populations. Based on the frequency distribution of tandem repeat units, significant genetic differentiation was also detected between China and Ariake Bay populations. Isolation by distance seems to be the main factor driving present genetic structuring of C. nasus populations, indicating coastal dispersal pattern in this coastal species. Such an evolutionary process agrees well with some of the biological features characterizing this species.

α/β coiled coils

PubMed Central

Hartmann, Marcus D; Mendler, Claudia T; Bassler, Jens; Karamichali, Ioanna; Ridderbusch, Oswin; Lupas, Andrei N; Hernandez Alvarez, Birte

2016-01-01

Coiled coils are the best-understood protein fold, as their backbone structure can uniquely be described by parametric equations. This level of understanding has allowed their manipulation in unprecedented detail. They do not seem a likely source of surprises, yet we describe here the unexpected formation of a new type of fiber by the simple insertion of two or six residues into the underlying heptad repeat of a parallel, trimeric coiled coil. These insertions strain the supercoil to the breaking point, causing the local formation of short β-strands, which move the path of the chain by 120° around the trimer axis. The result is an α/β coiled coil, which retains only one backbone hydrogen bond per repeat unit from the parent coiled coil. Our results show that a substantially novel backbone structure is possible within the allowed regions of the Ramachandran space with only minor mutations to a known fold. DOI: http://dx.doi.org/10.7554/eLife.11861.001 PMID:26771248

Length and sequence heterogeneity in 5S rDNA of Populus deltoides.

PubMed

Negi, Madan S; Rajagopal, Jyothi; Chauhan, Neeti; Cronn, Richard; Lakshmikumaran, Malathi

2002-12-01

The 5S rRNA genes and their associated non-transcribed spacer (NTS) regions are present as repeat units arranged in tandem arrays in plant genomes. Length heterogeneity in 5S rDNA repeats was previously identified in Populus deltoides and was also observed in the present study. Primers were designed to amplify the 5S rDNA NTS variants from the P. deltoides genome. The PCR-amplified products from the two accessions of P. deltoides (G3 and G48) suggested the presence of length heterogeneity of 5S rDNA units within and among accessions, and the size of the spacers ranged from 385 to 434 bp. Sequence analysis of the non-transcribed spacer (NTS) revealed two distinct classes of 5S rDNA within both accessions: class 1, which contained GAA trinucleotide microsatellite repeats, and class 2, which lacked the repeats. The class 1 spacer shows length variation owing to the microsatellite, with two clones exhibiting 10 GAA repeat units and one clone exhibiting 16 such repeat units. However, distance analysis shows that class 1 spacer sequences are highly similar inter se, yielding nucleotide diversity (pi) estimates that are less than 0.15% of those obtained for class 2 spacers (pi = 0.0183 vs. 0.1433, respectively). The presence of microsatellite in the NTS region leading to variation in spacer length is reported and discussed for the first time in P. deltoides.

An exploration of risk for recurrent falls in two geriatric care settings

PubMed Central

2013-01-01

Background Fall events were examined in two distinct geriatric populations to identify factors associated with repeat fallers, and to examine whether patients who use gait aids, specifically a walker, were more likely to experience repeat falls. Each unit already had a generic program for falls prevention in place. Methods Secondary data analysis was conducted on information collected during the pilot testing of a new quality assurance Incident Reporting Tool between October 2006 and September 2008. The study settings included an in-patient geriatric rehabilitation unit (GRU) and a long stay veterans’ unit (LSVU) in a rehabilitation and long-stay hospital in Ontario. Participants were two hundred and twenty three individuals, aged 65 years or older on these two units, who experienced one or more fall incidents during the study period. Results Logistic regression analyses showed that on the GRU age was significantly associated with repeat falls. On the LSVU first falls in the morning or late evening were associated with repeat falling. Walker as a gait aid listed at time of first fall was not associated with repeat falls. Conclusions This study suggests that different intervention may be necessary in different geriatric settings to identify, for secondary prevention, certain individuals for which the generic programs prove inadequate. Information collection with a specific focus on the issue of repeat falls may be necessary for greater insight. PMID:24106879

Structures composing protein domains.

PubMed

Kubrycht, Jaroslav; Sigler, Karel; Souček, Pavel; Hudeček, Jiří

2013-08-01

This review summarizes available data concerning intradomain structures (IS) such as functionally important amino acid residues, short linear motifs, conserved or disordered regions, peptide repeats, broadly occurring secondary structures or folds, etc. IS form structural features (units or elements) necessary for interactions with proteins or non-peptidic ligands, enzyme reactions and some structural properties of proteins. These features have often been related to a single structural level (e.g. primary structure) mostly requiring certain structural context of other levels (e.g. secondary structures or supersecondary folds) as follows also from some examples reported or demonstrated here. In addition, we deal with some functionally important dynamic properties of IS (e.g. flexibility and different forms of accessibility), and more special dynamic changes of IS during enzyme reactions and allosteric regulation. Selected notes concern also some experimental methods, still more necessary tools of bioinformatic processing and clinically interesting relationships. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

[Cross sectional study of structural quality of German intensive care units. A reevaluation of the DIVI register].

PubMed

Fölsch, C; Kofahl, N; Waydhas, C; Stiletto, R

2013-09-01

Effectiveness of intensive care treatment is essential to cope with increasing costs. The German national register of intensive care established by the German Interdisciplinary Association for Intensive Care Medicine (DIVI) contains basic data on the structure of intensive care units in Germany. A repeat analysis of data of the DIVI register within 8 years provides information for the development of intensive care units under different economic circumstances. The recent data on the structure of intensive care units were obtained in 2008 and compared with the primary multicenter study from 2000. The hospitals selected were a representative sample for the whole of Germany. Data on the status of the hospital, staff and technical facilities, foundation of the hospital and the statistics of mechanically ventilated patients were analyzed. The technical facilities and the number of staff have improved from 2000 to 2008. A smaller availability of diagnostic procedures and staff remain in hospitals for basic treatment outside normal working hours. The average utilization of intensive care unit beds was not altered. The existence of intermediate care units did not significantly change the proportion of patients with artificial ventilation or ventilation times. The number of beds in intensive care units was unchanged as was the average number of beds in units and the number of patients treated. A relevant number of beds of intensive care units shifted towards hospitals with private foundation without changes in the overall numbers. The structure of the hospitals was comparable at both time points. The introduction of intermediate care units did not alter ventilation parameters of patients in 2008 compared with 2000. There is no obvious medical reason for the shift of intensive care beds towards private hospitals. The number of staff and patients varied considerably between the intensive care units. The average number of patients treated per bed was not different between the periods or between hospitals with different structures. Overall availability of medical staff and diagnostic procedures increased during the study period. An increase of availability of fully trained medical staff in intensive care medicine is desirable to increase the quality of treatment.

Brittle deformation during Alpine basal accretion and the origin of seismicity nests above the subduction interface

NASA Astrophysics Data System (ADS)

Menant, Armel; Angiboust, Samuel; Monié, Patrick; Oncken, Onno; Guigner, Jean-Michel

2018-04-01

Geophysical observations on active subduction zones have evidenced high seismicity clusters at 20-40 km depth in the fore-arc region whose origin remains controversial. We report here field observations of pervasive pseudotachylyte networks (interpreted as evidence for paleo-seismicity) in the now-exhumed Valpelline continental unit (Dent Blanche complex, NW. Alps, Italy), a tectonic sliver accreted to the upper plate at c. 30 km depth during the Paleocene Alpine subduction. Pre-alpine granulite-facies paragneiss from the core of the Valpelline unit are crosscut by widespread, mm to cm-thick pseudotachylyte veins. Co-seismic heating and subsequent cooling led to the formation of Ti-rich garnet rims, ilmenite needles, Ca-rich plagioclase, biotite microliths and hercynite micro-crystals. 39Ar-40Ar dating yields a 51-54 Ma age range for these veins, thus suggesting that frictional melting events occurred near peak burial conditions while the Valpelline unit was already inserted inside the duplex structure. In contrast, the base of the Valpelline unit underwent synchronous ductile and brittle, seismic deformation under water-bearing conditions followed by a re-equilibration at c. 40 Ma (39Ar-40Ar on retrograded pseudotachylyte veins) during exhumation-related deformation. Calculated rheological profiles suggest that pseudotachylyte veins from the dry core of the granulite unit record upper plate micro-seismicity (Mw 2-3) formed under very high differential stresses (>500 MPa) while the sheared base of the unit underwent repeated brittle-ductile deformation at much lower differential stresses (<40 MPa) in a fluid-saturated environment. These results demonstrate that some of the seismicity clusters nested along and above the plate interface may reflect the presence of stiff tectonic slivers rheologically analogous to the Valpelline unit acting as repeatedly breaking asperities in the basal accretion region of active subduction zones.

The structure of TON1937 from archaeon Thermococcus onnurineus NA1 reveals a eukaryotic HEAT-like architecture.

PubMed

Jeong, Jae-Hee; Kim, Yi-Seul; Rojviriya, Catleya; Cha, Hyung Jin; Ha, Sung-Chul; Kim, Yeon-Gil

2013-10-01

The members of the ARM/HEAT repeat-containing protein superfamily in eukaryotes have been known to mediate protein-protein interactions by using their concave surface. However, little is known about the ARM/HEAT repeat proteins in prokaryotes. Here we report the crystal structure of TON1937, a hypothetical protein from the hyperthermophilic archaeon Thermococcus onnurineus NA1. The structure reveals a crescent-shaped molecule composed of a double layer of α-helices with seven anti-parallel α-helical repeats. A structure-based sequence alignment of the α-helical repeats identified a conserved pattern of hydrophobic or aliphatic residues reminiscent of the consensus sequence of eukaryotic HEAT repeats. The individual repeats of TON1937 also share high structural similarity with the canonical eukaryotic HEAT repeats. In addition, the concave surface of TON1937 is proposed to be its potential binding interface based on this structural comparison and its surface properties. These observations lead us to speculate that the archaeal HEAT-like repeats of TON1937 have evolved to engage in protein-protein interactions in the same manner as eukaryotic HEAT repeats. Copyright © 2013 Elsevier B.V. All rights reserved.

Organometallic macromolecules with piano stool coordination repeating units: chain configuration and stimulated solution behaviour.

PubMed

Cao, Kai; Ward, Jonathan; Amos, Ryan C; Jeong, Moon Gon; Kim, Kyoung Taek; Gauthier, Mario; Foucher, Daniel; Wang, Xiaosong

2014-09-11

Theoretical calculations illustrate that organometallic macromolecules with piano stool coordination repeating units (Fe-acyl complex) adopt linear chain configuration with a P-Fe-C backbone surrounded by aromatic groups. The macromolecules show molecular weight-dependent and temperature stimulated solution behaviour in DMSO.

Modifications to toxic CUG RNAs induce structural stability, rescue mis-splicing in a myotonic dystrophy cell model and reduce toxicity in a myotonic dystrophy zebrafish model

DOE PAGES

deLorimier, Elaine; Coonrod, Leslie A.; Copperman, Jeremy; ...

2014-10-10

In this study, CUG repeat expansions in the 3' UTR of dystrophia myotonica protein kinase ( DMPK) cause myotonic dystrophy type 1 (DM1). As RNA, these repeats elicit toxicity by sequestering splicing proteins, such as MBNL1, into protein–RNA aggregates. Structural studies demonstrate that CUG repeats can form A-form helices, suggesting that repeat secondary structure could be important in pathogenicity. To evaluate this hypothesis, we utilized structure-stabilizing RNA modifications pseudouridine (Ψ) and 2'-O-methylation to determine if stabilization of CUG helical conformations affected toxicity. CUG repeats modified with Ψ or 2'-O-methyl groups exhibited enhanced structural stability and reduced affinity for MBNL1. Molecularmore » dynamics and X-ray crystallography suggest a potential water-bridging mechanism for Ψ-mediated CUG repeat stabilization. Ψ modification of CUG repeats rescued mis-splicing in a DM1 cell model and prevented CUG repeat toxicity in zebrafish embryos. This study indicates that the structure of toxic RNAs has a significant role in controlling the onset of neuromuscular diseases.« less

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

deLorimier, Elaine; Coonrod, Leslie A.; Copperman, Jeremy

In this study, CUG repeat expansions in the 3' UTR of dystrophia myotonica protein kinase ( DMPK) cause myotonic dystrophy type 1 (DM1). As RNA, these repeats elicit toxicity by sequestering splicing proteins, such as MBNL1, into protein–RNA aggregates. Structural studies demonstrate that CUG repeats can form A-form helices, suggesting that repeat secondary structure could be important in pathogenicity. To evaluate this hypothesis, we utilized structure-stabilizing RNA modifications pseudouridine (Ψ) and 2'-O-methylation to determine if stabilization of CUG helical conformations affected toxicity. CUG repeats modified with Ψ or 2'-O-methyl groups exhibited enhanced structural stability and reduced affinity for MBNL1. Molecularmore » dynamics and X-ray crystallography suggest a potential water-bridging mechanism for Ψ-mediated CUG repeat stabilization. Ψ modification of CUG repeats rescued mis-splicing in a DM1 cell model and prevented CUG repeat toxicity in zebrafish embryos. This study indicates that the structure of toxic RNAs has a significant role in controlling the onset of neuromuscular diseases.« less

Designing occupancy studies: general advice and allocating survey effort

USGS Publications Warehouse

MacKenzie, D.I.; Royle, J. Andrew

2005-01-01

1. The fraction of sampling units in a landscape where a target species is present (occupancy) is an extensively used concept in ecology. Yet in many applications the species will not always be detected in a sampling unit even when present, resulting in biased estimates of occupancy. Given that sampling units are surveyed repeatedly within a relatively short timeframe, a number of similar methods have now been developed to provide unbiased occupancy estimates. However, practical guidance on the efficient design of occupancy studies has been lacking. 2. In this paper we comment on a number of general issues related to designing occupancy studies, including the need for clear objectives that are explicitly linked to science or management, selection of sampling units, timing of repeat surveys and allocation of survey effort. Advice on the number of repeat surveys per sampling unit is considered in terms of the variance of the occupancy estimator, for three possible study designs. 3. We recommend that sampling units should be surveyed a minimum of three times when detection probability is high (> 0.5 survey-1), unless a removal design is used. 4. We found that an optimal removal design will generally be the most efficient, but we suggest it may be less robust to assumption violations than a standard design. 5. Our results suggest that for a rare species it is more efficient to survey more sampling units less intensively, while for a common species fewer sampling units should be surveyed more intensively. 6. Synthesis and applications. Reliable inferences can only result from quality data. To make the best use of logistical resources, study objectives must be clearly defined; sampling units must be selected, and repeated surveys timed appropriately; and a sufficient number of repeated surveys must be conducted. Failure to do so may compromise the integrity of the study. The guidance given here on study design issues is particularly applicable to studies of species occurrence and distribution, habitat selection and modelling, metapopulation studies and monitoring programmes.

Molecular architecture of silk fibroin of Indian golden silkmoth, Antheraea assama.

PubMed

Gupta, Adarsh K; Mita, Kazuei; Arunkumar, Kallare P; Nagaraju, Javaregowda

2015-08-03

The golden silk spun by Indian golden silkmoth Antheraea assama, is regarded for its shimmering golden luster, tenacity and value as biomaterial. This report describes the gene coding for golden silk H-fibroin (AaFhc), its expression, full-length sequence and structurally important motifs discerning the underlying genetic and biochemical factors responsible for its much sought-after properties. The coding region, with biased isocodons, encodes highly repetitious crystalline core, flanked by a pair of 5' and 3' non-repetitious ends. AaFhc mRNA expression is strictly territorial, confined to the posterior silk gland, encoding a protein of size 230 kDa, which makes homodimers making the elementary structural units of the fibrous core of the golden silk. Characteristic polyalanine repeats that make tight β-sheet crystals alternate with non-polyalanine repeats that make less orderly antiparallel β-sheets, β-turns and partial α-helices. Phylogenetic analysis of the conserved N-terminal amorphous motif and the comparative analysis of the crystalline region with other saturniid H-fibroins reveal that AaFhc has longer, numerous and relatively uniform repeat motifs with lower serine content that assume tighter β-crystals and denser packing, which are speculated to be responsible for its acclaimed properties of higher tensile strength and higher refractive index responsible for golden luster.

Characterization of the COL2A1 VNTR polymorphism

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

Berg, E.S.; Olaisen, B.

1993-05-01

The variable number of tandem repeat (VNTR) region 3{prime} to the collagen type II gene (COL2A1) was amplified in vitro by the polymerase chain reaction. Subsequent high-resolution gel electrophoresis showed that the five earlier reported alleles could be further subtyped. A total of 17 allelic variants with a heterozygosity of 73.0% were found in 202 unrelated Norwegians. DNA sequencing of 19 COL2A1 alleles has been performed. The internal organization of the VNTR was common for all alleles, as previously shown for a few alleles. Moreover, the polymorphism in the COL2A1 locus is mainly due to variation in the numbers ofmore » copies of two repeat units, containing 34 and 31 bp, respectively, and/or to small deletions in either of the two units. DNA sequencing of alleles with the same electrophoretic size revealed no heterogeneity such as an alternating order of the different units, a feature that might have been expected to be the result of unequal crossing-over events. The observed ordered structure of the VNTR and the possibility of single-stranded DNA from the cores in the VNTR forming hairpins and loops suggest that the COL2A1 polymorphism may have evolved mainly by replication slippage mechanisms. 23 refs., 2 figs., 3 tabs.« less

[Continuity and discontinuity of the geomerida: the bionomic and biotic aspects].

PubMed

Kafanov, A I

2005-01-01

The view of the spatial structure of the geomerida (Earth's life cover) as a continuum that prevails in modern phytocoenology is mostly determined by a physiognomic (landscape-bionomic) discrimination of vegetation components. In this connection, geography of life forms appears as subject of the landscapebionomic biogeography. In zoocoenology there is a tendency of synthesis of alternative concepts based on the assumption that there are no absolute continuum and absolute discontinuum in the organic nature. The problem of continuum and discontinuum of living cover being problem of scale aries from fractal structure of geomerida. This problem arises from fractal nature of the spatial structure of geomerida. The continuum mainly belongs to regularities of topological order. At regional and subregional scale the continuum of biochores is rather rare. The objective evidences of relative discontinuity of the living cover are determined by significant alterations of species diversity at the regional, subregional and even topological scale Alternatively to conventionally discriminated units in physionomically continuous vegetation, the same biotic complexes, represented as operational units of biogeographical and biocenological zoning, are distinguished repeatedly and independently by different researchers. An area occupied by certain flora (fauna, biota) could be considered as elementary unit of biotic diversity (elementary biotic complex).

Chain length effect on the structure and stability of antimicrobial peptides of the (RW)n series.

PubMed

Phambu, Nsoki; Almarwani, Bashiyar; Garcia, Arlette M; Hamza, Nafisa S; Muhsen, Amira; Baidoo, Jacqueline E; Sunda-Meya, Anderson

2017-08-01

Three peptides containing (RW) n -NH 2 units (where n=4, 6, and 8) have been chosen to study the effect of the chain length on the structure and stability of the peptide using Fourier transform infrared (FTIR), scanning electron microscopy (SEM), thermogravimetric analysis (TGA), and differential scanning calorimetry (DSC) techniques. Their interactions with Escherichia coli (E. coli) membrane mimetic vesicles are discussed. Infrared results indicate that addition of (RW) n -NH 2 units increases intermolecular H bonds with antiparallel orientation. TGA and DSC results reveal that (RW) 6 -NH 2 shows the optimal chain length in terms of stability and all three peptides show a preferential interaction with one of the anionic lipids in E. coli membranes. SEM images of (RW) 4 -NH 2 present large aggregates while those of (RW) 6 -NH 2 and (RW) 8 -NH 2 present layers of sheet-like structure. In the presence of model membranes, (RW) n -NH 2 show fibrillar peptide superstructures. This study suggests that repeating structures of (RW) n -NH 2 promotes lateral assembly. Copyright © 2017 Elsevier B.V. All rights reserved.

Nanofluidic Pre-Concentration Devices for Enhancing the Detection Sensitivity and Selectivity of Biomarkers for Human Performance Monitoring

DTIC Science & Technology

2012-12-01

fabricated with a depth of 50 nm, followed by immobilizing the patches of chemical ligands (biotin) using typical photolithography procedure. The nanoslit was...been used to functionalize bonds zero, one, or two carbons away from this type of activating group. Chemical compounds that could be useful in synthetic...repeat unit structure, molecular weight distribution, and Published: June 12, 2012 Spotlights pubs.acs.org/JACS © 2012 American Chemical Society 10307

Proposed Continental Operations Range. United States Air Force.

DTIC Science & Technology

1974-06-01

when de -ailed plans are formulated to link H/W/D with COR/Nellis with a microwave system. Location of microwave repeaters in US Forest lands will be...be of significance. Supersonic activity is planned to avoid population areas, known structures, and random activities like known archaeological...to Land Use Plans and Policies 1-11 1.4’ Probable Impacts of the Proposed Action 1-13 1.5 Alternatives to the Proposed Action 1-19 1.6 Offsetting

Mapping Optimal Charge Density and Length of ROMP-Based PTDMs for siRNA Internalization.

PubMed

Caffrey, Leah M; deRonde, Brittany M; Minter, Lisa M; Tew, Gregory N

2016-10-10

A fundamental understanding of how polymer structure impacts internalization and delivery of biologically relevant cargoes, particularly small interfering ribonucleic acid (siRNA), is of critical importance to the successful design of improved delivery reagents. Herein we report the use of ring-opening metathesis polymerization (ROMP) methods to synthesize two series of guanidinium-rich protein transduction domain mimics (PTDMs): one based on an imide scaffold that contains one guanidinium moiety per repeat unit, and another based on a diester scaffold that contains two guanidinium moieties per repeat unit. By varying both the degree of polymerization and, in effect, the relative number of cationic charges in each PTDM, the performances of the two ROMP backbones for siRNA internalization were evaluated and compared. Internalization of fluorescently labeled siRNA into Jurkat T cells demonstrated that fluorescein isothiocyanate (FITC)-siRNA internalization had a charge content dependence, with PTDMs containing approximately 40 to 60 cationic charges facilitating the most internalization. Despite this charge content dependence, the imide scaffold yielded much lower viabilities in Jurkat T cells than the corresponding diester PTDMs with similar numbers of cationic charges, suggesting that the diester scaffold is preferred for siRNA internalization and delivery applications. These developments will not only improve our understanding of the structural factors necessary for optimal siRNA internalization, but will also guide the future development of optimized PTDMs for siRNA internalization and delivery.

Independent movement, dimerization and stability of tandem repeats of chicken brain alpha-spectrin

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

Kusunoki, H.; Minasov, G.; Macdonald, R.I.

Previous X-ray crystal structures have shown that linkers of five amino acid residues connecting pairs of chicken brain {alpha}-spectrin and human erythroid {beta}-spectrin repeats can undergo bending without losing their {alpha}-helical structure. To test whether bending at one linker can influence bending at an adjacent linker, the structures of two and three repeat fragments of chicken brain {alpha}-spectrin have been determined by X-ray crystallography. The structure of the three-repeat fragment clearly shows that bending at one linker can occur independently of bending at an adjacent linker. This observation increases the possible trajectories of modeled chains of spectrin repeats. Furthermore, themore » three-repeat molecule crystallized as an antiparallel dimer with a significantly smaller buried interfacial area than that of {alpha}-actinin, a spectrin-related molecule, but large enough and of a type indicating biological specificity. Comparison of the structures of the spectrin and {alpha}-actinin dimers supports weak association of the former, which could not be detected by analytical ultracentrifugation, versus strong association of the latter, which has been observed by others. To correlate features of the structure with solution properties and to test a previous model of stable spectrin and dystrophin repeats, the number of inter-helical interactions in each repeat of several spectrin structures were counted and compared to their thermal stabilities. Inter-helical interactions, but not all interactions, increased in parallel with measured thermal stabilities of each repeat and in agreement with the thermal stabilities of two and three repeats and also partial repeats of spectrin.« less

Effects of electronics, aromaticity, and solvent polarity on the rate of azaquinone-methide-mediated depolymerization of aromatic carbamate oligomers.

PubMed

Robbins, Jessica S; Schmid, Kyle M; Phillips, Scott T

2013-04-05

This paper uses physical-organic studies on well-defined oligomers to establish design principles for creating aromatic poly(carbamates) that depolymerize from head-to-tail in low dielectric constant environments when exposed to specific applied signals. We show that either increasing electron density or decreasing the aromaticity of aromatic repeating units in poly(carbamates) increase the overall depolymerization rate. For example, a methoxybenzene-based repeating unit provides depolymerization rates that are 143× faster than oligomers that contain a benzene-based repeating unit. Furthermore, the rate of depolymerization in the methoxybenzene-based system is tolerant to low dielectric environments, whereas the benzene-based oligomers are not.

[Customer satisfaction with a quality management system according to DIN EN ISO 9001:2000: Increase in the satisfaction of cooperating clinics].

PubMed

Beholz, Sven; Konertz, Wolfgang

2006-01-01

The evaluation of customers' satisfaction is elementary for any quality management system. In our university cardiac surgery unit that has been certified according to DIN EN ISO 9001:2000 the influence of repeated evaluation of the referring physicians' satisfaction conducted in the course of three consecutive years on structures and processes in the scope of the quality management system was examined. Customers' satisfaction with the possibility of access to the department could be increased by targeted interventions. Further interventions in the field of documentation led to a measurable increase in satisfaction with postoperative communication. Repeated annual evaluation of the satisfaction of referring physicians has proved to be a valuable tool in the process of continuous quality improvement.

Tectono-stratigraphy and low-grade metamorphism of Late Permian and Early Jurassic accretionary complexes within the Kurosegawa belt, Southwest Japan: Implications for mechanisms of crustal displacement within active continental margin

NASA Astrophysics Data System (ADS)

Hara, Hidetoshi; Kurihara, Toshiyuki; Mori, Hiroshi

2013-04-01

We characterize the tectono-stratigraphic architecture and low-grade metamorphism of the accretionary complex preserved in the Kurosegawa belt of the Kitagawa district in eastern Shikoku, Southwest Japan, in order to understand its internal structure, tectono-metamorphic evolution, and assessments of displacement of continental fragments within the complex. We report the first ever documented occurrence of an Early Jurassic radiolarian assemblage within the accretionary complex of the Kurosegawa belt that has been previously classified as the Late Permian accretionary complex, thus providing a revised age interpretation for these rocks. The accretionary complex is subdivided into four distinct tectono-stratigraphic units: Late Permian mélange and phyllite units, and Early Jurassic mélange and sandstone units. The stratigraphy of these four units is structurally repeated due to an E-W striking, steeply dipping regional fault. We characterized low-grade metamorphism of the accretionary complex via illite crystallinity and Raman spectroscopy of carbonaceous material. The estimated pattern of low-grade metamorphism showed pronounced variability within the complex and revealed no discernible spatial trends. The primary thermal structure in these rocks was overprinted by later tectonic events. Based on geological and thermal structure, we conclude that continental fragments within the Kurosegawa belt were structurally translated into both the Late Permian and Early Jurassic accretionary complexes, which comprise a highly deformed zone affected by strike-slip tectonics during the Early Cretaceous. Different models have been proposed to explain the initial structural evolution of the Kurosegawa belt (i.e., micro-continent collision and klippe tectonic models). Even if we presuppose either model, the available geological evidence requires a new interpretation, whereby primary geological structures are overprinted and reconfigured by later tectonic events.

Repeated reunions and splits feature the highly dynamic evolution of 5S and 35S ribosomal RNA genes (rDNA) in the Asteraceae family.

PubMed

Garcia, Sònia; Panero, José L; Siroky, Jiri; Kovarik, Ales

2010-08-16

In flowering plants and animals the most common ribosomal RNA genes (rDNA) organisation is that in which 35S (encoding 18S-5.8S-26S rRNA) and 5S genes are physically separated occupying different chromosomal loci. However, recent observations established that both genes have been unified to a single 35S-5S unit in the genus Artemisia (Asteraceae), a genomic arrangement typical of primitive eukaryotes such as yeast, among others. Here we aim to reveal the origin, distribution and mechanisms leading to the linked organisation of rDNA in the Asteraceae by analysing unit structure (PCR, Southern blot, sequencing), gene copy number (quantitative PCR) and chromosomal position (FISH) of 5S and 35S rRNA genes in approximately 200 species representing the family diversity and other closely related groups. Dominant linked rDNA genotype was found within three large groups in subfamily Asteroideae: tribe Anthemideae (93% of the studied cases), tribe Gnaphalieae (100%) and in the "Heliantheae alliance" (23%). The remaining five tribes of the Asteroideae displayed canonical non linked arrangement of rDNA, as did the other groups in the Asteraceae. Nevertheless, low copy linked genes were identified among several species that amplified unlinked units. The conserved position of functional 5S insertions downstream from the 26S gene suggests a unique, perhaps retrotransposon-mediated integration event at the base of subfamily Asteroideae. Further evolution likely involved divergence of 26S-5S intergenic spacers, amplification and homogenisation of units across the chromosomes and concomitant elimination of unlinked arrays. However, the opposite trend, from linked towards unlinked arrangement was also surmised in few species indicating possible reversibility of these processes. Our results indicate that nearly 25% of Asteraceae species may have evolved unusual linked arrangement of rRNA genes. Thus, in plants, fundamental changes in intrinsic structure of rDNA units, their copy number and chromosomal organisation may occur within relatively short evolutionary time. We hypothesize that the 5S gene integration within the 35S unit might have repeatedly occurred during plant evolution, and probably once in Asteraceae.

Repeated reunions and splits feature the highly dynamic evolution of 5S and 35S ribosomal RNA genes (rDNA) in the Asteraceae family

PubMed Central

2010-01-01

Background In flowering plants and animals the most common ribosomal RNA genes (rDNA) organisation is that in which 35S (encoding 18S-5.8S-26S rRNA) and 5S genes are physically separated occupying different chromosomal loci. However, recent observations established that both genes have been unified to a single 35S-5S unit in the genus Artemisia (Asteraceae), a genomic arrangement typical of primitive eukaryotes such as yeast, among others. Here we aim to reveal the origin, distribution and mechanisms leading to the linked organisation of rDNA in the Asteraceae by analysing unit structure (PCR, Southern blot, sequencing), gene copy number (quantitative PCR) and chromosomal position (FISH) of 5S and 35S rRNA genes in ~200 species representing the family diversity and other closely related groups. Results Dominant linked rDNA genotype was found within three large groups in subfamily Asteroideae: tribe Anthemideae (93% of the studied cases), tribe Gnaphalieae (100%) and in the "Heliantheae alliance" (23%). The remaining five tribes of the Asteroideae displayed canonical non linked arrangement of rDNA, as did the other groups in the Asteraceae. Nevertheless, low copy linked genes were identified among several species that amplified unlinked units. The conserved position of functional 5S insertions downstream from the 26S gene suggests a unique, perhaps retrotransposon-mediated integration event at the base of subfamily Asteroideae. Further evolution likely involved divergence of 26S-5S intergenic spacers, amplification and homogenisation of units across the chromosomes and concomitant elimination of unlinked arrays. However, the opposite trend, from linked towards unlinked arrangement was also surmised in few species indicating possible reversibility of these processes. Conclusions Our results indicate that nearly 25% of Asteraceae species may have evolved unusual linked arrangement of rRNA genes. Thus, in plants, fundamental changes in intrinsic structure of rDNA units, their copy number and chromosomal organisation may occur within relatively short evolutionary time. We hypothesize that the 5S gene integration within the 35S unit might have repeatedly occurred during plant evolution, and probably once in Asteraceae. PMID:20712858

Revisiting the TALE repeat.

PubMed

Deng, Dong; Yan, Chuangye; Wu, Jianping; Pan, Xiaojing; Yan, Nieng

2014-04-01

Transcription activator-like (TAL) effectors specifically bind to double stranded (ds) DNA through a central domain of tandem repeats. Each TAL effector (TALE) repeat comprises 33-35 amino acids and recognizes one specific DNA base through a highly variable residue at a fixed position in the repeat. Structural studies have revealed the molecular basis of DNA recognition by TALE repeats. Examination of the overall structure reveals that the basic building block of TALE protein, namely a helical hairpin, is one-helix shifted from the previously defined TALE motif. Here we wish to suggest a structure-based re-demarcation of the TALE repeat which starts with the residues that bind to the DNA backbone phosphate and concludes with the base-recognition hyper-variable residue. This new numbering system is consistent with the α-solenoid superfamily to which TALE belongs, and reflects the structural integrity of TAL effectors. In addition, it confers integral number of TALE repeats that matches the number of bound DNA bases. We then present fifteen crystal structures of engineered dHax3 variants in complex with target DNA molecules, which elucidate the structural basis for the recognition of bases adenine (A) and guanine (G) by reported or uncharacterized TALE codes. Finally, we analyzed the sequence-structure correlation of the amino acid residues within a TALE repeat. The structural analyses reported here may advance the mechanistic understanding of TALE proteins and facilitate the design of TALEN with improved affinity and specificity.

Optimal Hydrophobicity in Ring-Opening Metathesis Polymerization-Based Protein Mimics Required for siRNA Internalization.

PubMed

deRonde, Brittany M; Posey, Nicholas D; Otter, Ronja; Caffrey, Leah M; Minter, Lisa M; Tew, Gregory N

2016-06-13

Exploring the role of polymer structure for the internalization of biologically relevant cargo, specifically siRNA, is of critical importance to the development of improved delivery reagents. Herein, we report guanidinium-rich protein transduction domain mimics (PTDMs) based on a ring-opening metathesis polymerization scaffold containing tunable hydrophobic moieties that promote siRNA internalization. Structure-activity relationships using Jurkat T cells and HeLa cells were explored to determine how the length of the hydrophobic block and the hydrophobic side chain compositions of these PTDMs impacted siRNA internalization. To explore the hydrophobic block length, two different series of diblock copolymers were synthesized: one series with symmetric block lengths and one with asymmetric block lengths. At similar cationic block lengths, asymmetric and symmetric PTDMs promoted siRNA internalization in the same percentages of the cell population regardless of the hydrophobic block length; however, with 20 repeat units of cationic charge, the asymmetric block length had greater siRNA internalization, highlighting the nontrivial relationships between hydrophobicity and overall cationic charge. To further probe how the hydrophobic side chains impacted siRNA internalization, an additional series of asymmetric PTDMs was synthesized that featured a fixed hydrophobic block length of five repeat units that contained either dimethyl (dMe), methyl phenyl (MePh), or diphenyl (dPh) side chains and varied cationic block lengths. This series was further expanded to incorporate hydrophobic blocks consisting of diethyl (dEt), diisobutyl (diBu), and dicyclohexyl (dCy) based repeat units to better define the hydrophobic window for which our PTDMs had optimal activity. High-performance liquid chromatography retention times quantified the relative hydrophobicities of the noncationic building blocks. PTDMs containing the MePh, diBu, and dPh hydrophobic blocks were shown to have superior siRNA internalization capabilities compared to their more and less hydrophobic counterparts, demonstrating a critical window of relative hydrophobicity for optimal internalization. This better understanding of how hydrophobicity impacts PTDM-induced internalization efficiencies will help guide the development of future delivery reagents.

Apo and InsP[subscript 3]-bound crystal structures of the ligand-binding domain of an InsP[subscript 3] receptor

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

Lin, Chun-Chi; Baek, Kyuwon; Lu, Zhe

2012-05-08

We report the crystal structures of the ligand-binding domain (LBD) of a rat inositol 1,4,5-trisphosphate receptor (InsP{sub 3}R) in its apo and InsP{sub 3}-bound conformations. Comparison of these two conformations reveals that LBD's first {beta}-trefoil fold ({beta}-TF1) and armadillo repeat fold (ARF) move together as a unit relative to its second {beta}-trefoil fold ({beta}-TF2). Whereas apo LBD may spontaneously transition between gating conformations, InsP{sub 3} binding shifts this equilibrium toward the active state.

Antigenic determinants of Staphylococcus aureus type 5 and type 8 capsular polysaccharide vaccines.

PubMed

Fattom, A I; Sarwar, J; Basham, L; Ennifar, S; Naso, R

1998-10-01

Bacterial capsular polysaccharides (CP) are carbohydrate polymers comprised of repeating saccharide units. Several of these CP have side chains attached to their backbone structures. The side chains may include O-acetyl, phosphate, sialic acid, and other moieties. Those moieties represent the immunodominant epitopes and the most functional ones. The clinically significant Staphylococcus aureus type 5 CP (CP 5) and type 8 CP (CP 8) are comprised of a trisaccharide repeat unit with one O-acetyl group attached to each repeat unit. The immunogenicity of these CP and the functionality of antibodies to the backbone and the O-acetyl moieties were investigated. Immunization with the native CP conjugates (CP with 75% O-acetylation) elicited a high proportion of antibodies directed against the O-acetyl moiety. Nonetheless, all of the vaccinees produced antibodies to the backbone moieties as well. Conjugate vaccines made of de-O-acetylated CP elicited backbone antibodies only. Antibodies to both backbone and O-acetyl groups were found to be opsonic against S. aureus strains which varied in their O-acetyl content. Absorption studies with O-acetylated and de-O-acetylated CP showed that (i) native CP conjugates generated antibodies to both backbone and O-acetyl groups and (ii) O-acetylated isolates were opsonized by both populations of antibodies while the non-O-acetylated strains were predominantly opsonized by the backbone antibodies. These results suggest that S. aureus CP conjugate vaccines elicit multiple populations of antibodies with diverse specificities. Moreover, the antibodies of different specificities (backbone or O-acetyl) are all functional and efficient against the variations in bacterial CP that may occur among clinically significant S. aureus pathogenic isolates.

Size and sequence polymorphisms in the glutamate-rich protein gene of the human malaria parasite Plasmodium falciparum in Thailand.

PubMed

Pattaradilokrat, Sittiporn; Trakoolsoontorn, Chawinya; Simpalipan, Phumin; Warrit, Natapot; Kaewthamasorn, Morakot; Harnyuttanakorn, Pongchai

2018-01-22

The glutamate-rich protein (GLURP) of the malaria parasite Plasmodium falciparum is a key surface antigen that serves as a component of a clinical vaccine. Moreover, the GLURP gene is also employed routinely as a genetic marker for malarial genotyping in epidemiological studies. While extensive size polymorphisms in GLURP are well recorded, the extent of the sequence diversity of this gene is rarely investigated. The present study aimed to explore the genetic diversity of GLURP in natural populations of P. falciparum. The polymorphic C-terminal repetitive R2 region of GLURP sequences from 65 P. falciparum isolates in Thailand were generated and combined with the data from 103 worldwide isolates to generate a GLURP database. The collection was comprised of 168 alleles, encoding 105 unique GLURP subtypes, characterized by 18 types of amino acid repeat units (AAU). Of these, 28 GLURP subtypes, formed by 10 AAU types, were detected in P. falciparum in Thailand. Among them, 19 GLURP subtypes and 2 AAU types are described for the first time in the Thai parasite population. The AAU sequences were highly conserved, which is likely due to negative selection. Standard Fst analysis revealed the shared distributions of GLURP types among the P. falciparum populations, providing evidence of gene flow among the different demographic populations. Sequence diversity causing size variations in GLURP in Thai P. falciparum populations were detected, and caused by non-synonymous substitutions in repeat units and some insertion/deletion of aspartic acid or glutamic acid codons between repeat units. The P. falciparum population structure based on GLURP showed promising implications for the development of GLURP-based vaccines and for monitoring vaccine efficacy.

Medium-sized tandem repeats represent an abundant component of the Drosophila virilis genome.

PubMed

Abdurashitov, Murat A; Gonchar, Danila A; Chernukhin, Valery A; Tomilov, Victor N; Tomilova, Julia E; Schostak, Natalia G; Zatsepina, Olga G; Zelentsova, Elena S; Evgen'ev, Michael B; Degtyarev, Sergey K H

2013-11-09

Previously, we developed a simple method for carrying out a restriction enzyme analysis of eukaryotic DNA in silico, based on the known DNA sequences of the genomes. This method allows the user to calculate lengths of all DNA fragments that are formed after a whole genome is digested at the theoretical recognition sites of a given restriction enzyme. A comparison of the observed peaks in distribution diagrams with the results from DNA cleavage using several restriction enzymes performed in vitro have shown good correspondence between the theoretical and experimental data in several cases. Here, we applied this approach to the annotated genome of Drosophila virilis which is extremely rich in various repeats. Here we explored the combined approach to perform the restriction analysis of D. virilis DNA. This approach enabled to reveal three abundant medium-sized tandem repeats within the D. virilis genome. While the 225 bp repeats were revealed previously in intergenic non-transcribed spacers between ribosomal genes of D. virilis, two other families comprised of 154 bp and 172 bp repeats were not described. Tandem Repeats Finder search demonstrated that 154 bp and 172 bp units are organized in multiple clusters in the genome of D. virilis. Characteristically, only 154 bp repeats derived from Helitron transposon are transcribed. Using in silico digestion in combination with conventional restriction analysis and sequencing of repeated DNA fragments enabled us to isolate and characterize three highly abundant families of medium-sized repeats present in the D. virilis genome. These repeats comprise a significant portion of the genome and may have important roles in genome function and structural integrity. Therefore, we demonstrated an approach which makes possible to investigate in detail the gross arrangement and expression of medium-sized repeats basing on sequencing data even in the case of incompletely assembled and/or annotated genomes.

Design and Theoretical Analysis of a Resonant Sensor for Liquid Density Measurement

PubMed Central

Zheng, Dezhi; Shi, Jiying; Fan, Shangchun

2012-01-01

In order to increase the accuracy of on-line liquid density measurements, a sensor equipped with a tuning fork as the resonant sensitive component is designed in this paper. It is a quasi-digital sensor with simple structure and high precision. The sensor is based on resonance theory and composed of a sensitive unit and a closed-loop control unit, where the sensitive unit consists of the actuator, the resonant tuning fork and the detector and the closed-loop control unit comprises precondition circuit, digital signal processing and control unit, analog-to-digital converter and digital-to-analog converter. An approximate parameters model of the tuning fork is established and the impact of liquid density, position of the tuning fork, temperature and structural parameters on the natural frequency of the tuning fork are also analyzed. On this basis, a tuning fork liquid density measurement sensor is developed. In addition, experimental testing on the sensor has been carried out on standard calibration facilities under constant 20 °C, and the sensor coefficients are calibrated. The experimental results show that the repeatability error is about 0.03% and the accuracy is about 0.4 kg/m3. The results also confirm that the method to increase the accuracy of liquid density measurement is feasible. PMID:22969378

Design and theoretical analysis of a resonant sensor for liquid density measurement.

PubMed

Zheng, Dezhi; Shi, Jiying; Fan, Shangchun

2012-01-01

In order to increase the accuracy of on-line liquid density measurements, a sensor equipped with a tuning fork as the resonant sensitive component is designed in this paper. It is a quasi-digital sensor with simple structure and high precision. The sensor is based on resonance theory and composed of a sensitive unit and a closed-loop control unit, where the sensitive unit consists of the actuator, the resonant tuning fork and the detector and the closed-loop control unit comprises precondition circuit, digital signal processing and control unit, analog-to-digital converter and digital-to-analog converter. An approximate parameters model of the tuning fork is established and the impact of liquid density, position of the tuning fork, temperature and structural parameters on the natural frequency of the tuning fork are also analyzed. On this basis, a tuning fork liquid density measurement sensor is developed. In addition, experimental testing on the sensor has been carried out on standard calibration facilities under constant 20 °C, and the sensor coefficients are calibrated. The experimental results show that the repeatability error is about 0.03% and the accuracy is about 0.4 kg/m(3). The results also confirm that the method to increase the accuracy of liquid density measurement is feasible.

Unique molecular architecture of silk fibroin in the waxmoth, Galleria mellonella.

PubMed

Zurovec, Michal; Sehnal, Frantisek

2002-06-21

Proteins of silk fibers are characterized by reiterations of amino acid repeats. Physical properties of the fiber are determined by the amino acid composition, the complexity of repetitive units, and arrangement of these units into higher order arrays. Except for very short motifs of 6-10 residues, the length of repetitive units and the number of these units concatenated in higher order assemblies vary in all spider and lepidopteran silks analyzed so far. This paper describes an exceptional silk protein represented by the 500-kDa heavy chain fibroin (H-fibroin) of the waxmoth, Galleria mellonella. Its non-repetitive N-terminal (175 residues) and C-terminal (60 residues) parts, the overall gene organization, and the nucleotide sequence around the TATA box show that it is homologous to the H-fibroins of other Lepidoptera. However, over 95% of the protein consists of highly ordered repetitive structures that are unmatched in other species. The repetitive region includes 11 assemblies AB(1)AB(1)AB(1)AB(2)(AB(2))AB(2) of remarkably conserved polypeptide repeats A (63 amino acid residues), B(1) (43 residues), and B(2) (18 residues). The repeats contain a high proportion of Gly (31.6%), Ala (23.8%), Ser (18.1%), and of residues with long hydrophobic side chains (16% for Leu, Ile, and Val combined). The presence of the GLGGLG and SSAASAA(AA) motifs suggests formation of pleated beta-sheets and their stacking into crystallites. Conspicuous conservation of the apolar sequence VIVI followed by DD or ED is interpreted as indicating the importance of hydrophobicity and electrostatic charge in H-fibroin cross-linking. The environment of G. mellonella larvae within bee cultures requires continuous production of silk that must be both strong and elastic. The spectacular arrangement of the repetitive H-fibroin region apparently evolved to meet these requirements.

Apo And Calcium-Bound Crystal Structures of Alpha-11 Giardin, An Unusual Annexin From 'Giardia Lamblia'

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

Pathuri, P.; Nguyen, E.T.; Svard, S.G.

2007-07-12

Alpha-11 giardin is a member of the multi-gene alpha-giardin family in the intestinal protozoan, Giardia lamblia. This gene family shares an ancestry with the annexin super family, whose common characteristic is calcium-dependent binding to membranes that contain acidic phospholipids. Several alpha giardins are highly expressed during parasite-induced diarrhea in humans. Despite being a member of a large family of proteins, little is known about the function and cellular localization of alpha-11 giardin, although giardins are often associated with the cytoskeleton. It has been shown that Giardia exhibits high levels of alpha-11 giardin mRNA transcript throughout its life cycle; however, constitutivemore » over-expression of this protein is lethal to the parasite. Determining the three-dimensional structure of an alpha-giardin is essential to identifying functional domains shared in the alpha-giardin family. Here we report the crystal structures of the apo and Ca{sup 2+}-bound forms of alpha-11 giardin, the first alpha giardin to be characterized structurally. Crystals of apo and Ca{sup 2+}-bound alpha-11 giardin diffracted to 1.1 angstroms and 2.93 angstroms, respectively. The crystal structure of selenium-substituted apo alpha-11 giardin reveals a planar array of four tandem repeats of predominantly {alpha}-helical domains, reminiscent of previously determined annexin structures, making this the highest-resolution structure of an annexin to date. The apo alpha-11 giardin structure also reveals a hydrophobic core formed between repeats I/IV and II/III, a region typically hydrophilic in other annexins. Surprisingly, the Ca{sup 2+}-bound structure contains only a single calcium ion, located in the DE loop of repeat I and coordinated differently from the two types of calcium sites observed in previous annexin structures. The apo and Ca{sup 2+}-bound alpha-11 giardin structures assume overall similar conformations; however, Ca2+-bound alpha-11 giardin crystallized in a lower-symmetry space group with four molecules in the asymmetric unit. Vesicle-binding studies suggest that alpha-11 giardin, unlike most other annexins, does not bind to vesicles composed of acidic phospholipids in a calcium-dependent manner.« less

[Comparative analysis of clustered regularly interspaced short palindromic repeats (CRISPRs) loci in the genomes of halophilic archaea].

PubMed

Zhang, Fan; Zhang, Bing; Xiang, Hua; Hu, Songnian

2009-11-01

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) is a widespread system that provides acquired resistance against phages in bacteria and archaea. Here we aim to genome-widely analyze the CRISPR in extreme halophilic archaea, of which the whole genome sequences are available at present time. We used bioinformatics methods including alignment, conservation analysis, GC content and RNA structure prediction to analyze the CRISPR structures of 7 haloarchaeal genomes. We identified the CRISPR structures in 5 halophilic archaea and revealed a conserved palindromic motif in the flanking regions of these CRISPR structures. In addition, we found that the repeat sequences of large CRISPR structures in halophilic archaea were greatly conserved, and two types of predicted RNA secondary structures derived from the repeat sequences were likely determined by the fourth base of the repeat sequence. Our results support the proposal that the leader sequence may function as recognition site by having palindromic structures in flanking regions, and the stem-loop secondary structure formed by repeat sequences may function in mediating the interaction between foreign genetic elements and CAS-encoded proteins.

The structure of the acidic exopolysaccharide produced by Pseudomonas "gingeri" strain Pf9.

PubMed

Cescutti, P; Osman, S F; Fett, W F; Weisleder, D

1995-10-02

The structure of the acidic exopolysaccharide produced by the mushroom pathogen Pseudomonas "gingeri" strain Pf9, a bacterium which causes ginger blotch, was investigated by chemical analysis, mass spectrometry and 1D and 2D NMR spectroscopy. The polysaccharide consists of the linear trisaccharide repeating unit [formula: see text] where the cyclic pyruvic acetal groups at O-4 and O-6 of the mannopyranosyl residues have the S-configuration. Methylation analysis under neutral conditions and NMR data showed that the mannose residues are acetylated at O-2. This exopolysaccharide has the same structure as the E. coli K55 capsular polysaccharide and differs from the Klebsiella K5 capsular polysaccharide only in the position of acetylation (C-2 of the glucopyranose residue).

Highly structured genetic diversity of the Mycobacterium tuberculosis population in Djibouti.

PubMed

Godreuil, S; Renaud, F; Choisy, M; Depina, J J; Garnotel, E; Morillon, M; Van de Perre, P; Bañuls, A L

2010-07-01

Djibouti is an East African country with a high tuberculosis incidence. This study was conducted over a 2-month period in Djibouti, during which 62 consecutive patients with pulmonary tuberculosis (TB) were included. Genetic characterization of Mycobacterium tuberculosis, using mycobacterial interspersed repetitive-unit variable-number tandem-repeat typing and spoligotyping, was performed. The genetic and phylogenetic analysis revealed only three major families (Central Asian, East African Indian and T). The high diversity and linkage disequilibrium within each family suggest a long period of clonal evolution. A Bayesian approach shows that the phylogenetic structure observed in our sample of 62 isolates is very likely to be representative of the phylogenetic structure of the M. tuberculosis population in the total number of TB cases.

Electron tomography and computer visualisation of a three-dimensional 'photonic' crystal in a butterfly wing-scale.

PubMed

Argyros, A; Manos, S; Large, M C J; McKenzie, D R; Cox, G C; Dwarte, D M

2002-01-01

A combination of transmission electron tomography and computer modelling has been used to determine the three-dimensional structure of the photonic crystals found in the wing-scales of the Kaiser-I-Hind butterfly (Teinopalpus imperialis). These scales presented challenges for electron microscopy because the periodicity of the structure was comparable to the thickness of a section and because of the complex connectivity of the object. The structure obtained has been confirmed by taking slices of the three-dimensional computer model constructed from the tomography and comparing these with transmission electron microscope (TEM) images of microtomed sections of the actual scale. The crystal was found to have chiral tetrahedral repeating units packed in a triclinic lattice.

Analysis of sequence repeats of proteins in the PDB.

PubMed

Mary Rajathei, David; Selvaraj, Samuel

2013-12-01

Internal repeats in protein sequences play a significant role in the evolution of protein structure and function. Applications of different bioinformatics tools help in the identification and characterization of these repeats. In the present study, we analyzed sequence repeats in a non-redundant set of proteins available in the Protein Data Bank (PDB). We used RADAR for detecting internal repeats in a protein, PDBeFOLD for assessing structural similarity, PDBsum for finding functional involvement and Pfam for domain assignment of the repeats in a protein. Through the analysis of sequence repeats, we found that identity of the sequence repeats falls in the range of 20-40% and, the superimposed structures of the most of the sequence repeats maintain similar overall folding. Analysis sequence repeats at the functional level reveals that most of the sequence repeats are involved in the function of the protein through functionally involved residues in the repeat regions. We also found that sequence repeats in single and two domain proteins often contained conserved sequence motifs for the function of the domain. Copyright © 2013 Elsevier Ltd. All rights reserved.

Population-scale whole genome sequencing identifies 271 highly polymorphic short tandem repeats from Japanese population.

PubMed

Hirata, Satoshi; Kojima, Kaname; Misawa, Kazuharu; Gervais, Olivier; Kawai, Yosuke; Nagasaki, Masao

2018-05-01

Forensic DNA typing is widely used to identify missing persons and plays a central role in forensic profiling. DNA typing usually uses capillary electrophoresis fragment analysis of PCR amplification products to detect the length of short tandem repeat (STR) markers. Here, we analyzed whole genome data from 1,070 Japanese individuals generated using massively parallel short-read sequencing of 162 paired-end bases. We have analyzed 843,473 STR loci with two to six basepair repeat units and cataloged highly polymorphic STR loci in the Japanese population. To evaluate the performance of the cataloged STR loci, we compared 23 STR loci, widely used in forensic DNA typing, with capillary electrophoresis based STR genotyping results in the Japanese population. Seventeen loci had high correlations and high call rates. The other six loci had low call rates or low correlations due to either the limitations of short-read sequencing technology, the bioinformatics tool used, or the complexity of repeat patterns. With these analyses, we have also purified the suitable 218 STR loci with four basepair repeat units and 53 loci with five basepair repeat units both for short read sequencing and PCR based technologies, which would be candidates to the actual forensic DNA typing in Japanese population.

Methods and compositions for removing carbon dioxide from a gaseous mixture

DOEpatents

Li, Jing; Wu, Haohan

2014-06-24

Provided is a method for adsorbing or separating carbon dioxide from a mixture of gases by passing the gas mixture through a porous three-dimensional polymeric coordination compound having a plurality of layers of two-dimensional arrays of repeating structural units, which results in a lower carbon dioxide content in the gas mixture. Thus, this invention provides useful compositions and methods for removal of greenhouse gases, in particular CO.sub.2, from industrial flue gases or from the atmosphere.

Do rational numbers play a role in selection for stochasticity?

PubMed

Sinclair, Robert

2014-01-01

When a given tissue must, to be able to perform its various functions, consist of different cell types, each fairly evenly distributed and with specific probabilities, then there are at least two quite different developmental mechanisms which might achieve the desired result. Let us begin with the case of two cell types, and first imagine that the proportion of numbers of cells of these types should be 1:3. Clearly, a regular structure composed of repeating units of four cells, three of which are of the dominant type, will easily satisfy the requirements, and a deterministic mechanism may lend itself to the task. What if, however, the proportion should be 10:33? The same simple, deterministic approach would now require a structure of repeating units of 43 cells, and this certainly seems to require a far more complex and potentially prohibitive deterministic developmental program. Stochastic development, replacing regular units with random distributions of given densities, might not be evolutionarily competitive in comparison with the deterministic program when the proportions should be 1:3, but it has the property that, whatever developmental mechanism underlies it, its complexity does not need to depend very much upon target cell densities at all. We are immediately led to speculate that proportions which correspond to fractions with large denominators (such as the 33 of 10/33) may be more easily achieved by stochastic developmental programs than by deterministic ones, and this is the core of our thesis: that stochastic development may tend to occur more often in cases involving rational numbers with large denominators. To be imprecise: that simple rationality and determinism belong together, as do irrationality and randomness.

A characteristic chondroitin sulfate trisaccharide unit with a sulfated fucose branch exhibits neurite outgrowth-promoting activity: Novel biological roles of fucosylated chondroitin sulfates isolated from the sea cucumber Apostichopus japonicus.

PubMed

Shida, Miharu; Mikami, Tadahisa; Tamura, Jun-Ichi; Kitagawa, Hiroshi

2017-06-03

Chondroitin sulfate (CS) is a class of sulfated glycosaminoglycan (GAG) chains that consist of repeating disaccharide unit composed of glucuronic acid (GlcA) and N-acetylgalactosamine (GalNAc). CS chains are found throughout the pericellular and extracellular spaces and contribute to the formation of functional microenvironments for numerous biological events. However, their structure-function relations remain to be fully characterized. Here, a fucosylated CS (FCS) was isolated from the body wall of the sea cucumber Apostichopus japonicus. Its promotional effects on neurite outgrowth were assessed by using isolated polysaccharides and the chemically synthesized FCS trisaccharide β-D-GalNAc(4,6-O-disulfate) (1-4)[α-l-fucose (2,4-O-disulfate) (1-3)]-β-D-GlcA. FCS polysaccharides contained the E-type disaccharide unit GlcA-GalNAc(4,6-O-disulfate) as a CS major backbone structure and carried distinct sulfated fucose branches. Despite their relatively lower abundance of E unit, FCS polysaccharides exhibited neurite outgrowth-promoting activity comparable to squid cartilage-derived CS-E polysaccharides, which are characterized by their predominant E units, suggesting potential roles of the fucose branch in neurite outgrowth. Indeed, the chemically synthesized FCS trisaccharide was as effective as CS-E tetrasaccharide in stimulating neurite elongation in vitro. In conclusion, FCS trisaccharide units with 2,4-O-disulfated fucose branches may provide new insights into understanding the structure-function relations of CS chains. Copyright © 2017 Elsevier Inc. All rights reserved.

Functional role of oligomerization for bacterial and plant SWEET sugar transporter family.

PubMed

Xuan, Yuan Hu; Hu, Yi Bing; Chen, Li-Qing; Sosso, Davide; Ducat, Daniel C; Hou, Bi-Huei; Frommer, Wolf B

2013-09-24

Eukaryotic sugar transporters of the MFS and SWEET superfamilies consist of 12 and 7 α-helical transmembrane domains (TMs), respectively. Structural analyses indicate that MFS transporters evolved from a series of tandem duplications of an ancestral 3-TM unit. SWEETs are heptahelical proteins carrying a tandem repeat of 3-TM separated by a single TM. Here, we show that prokaryotes have ancestral SWEET homologs with only 3-TM and that the Bradyrhizobium japonicum SemiSWEET1, like Arabidopsis SWEET11, mediates sucrose transport. Eukaryotic SWEETs most likely evolved by internal duplication of the 3-TM, suggesting that SemiSWEETs form oligomers to create a functional pore. However, it remains elusive whether the 7-TM SWEETs are the functional unit or require oligomerization to form a pore sufficiently large to allow for sucrose passage. Split ubiquitin yeast two-hybrid and split GFP assays indicate that Arabidopsis SWEETs homo- and heterooligomerize. We examined mutant SWEET variants for negative dominance to test if oligomerization is necessary for function. Mutation of the conserved Y57 or G58 in SWEET1 led to loss of activity. Coexpression of the defective mutants with functional A. thaliana SWEET1 inhibited glucose transport, indicating that homooligomerization is necessary for function. Collectively, these data imply that the basic unit of SWEETs, similar to MFS sugar transporters, is a 3-TM unit and that a functional transporter contains at least four such domains. We hypothesize that the functional unit of the SWEET family of transporters possesses a structure resembling the 12-TM MFS structure, however, with a parallel orientation of the 3-TM unit.

Functional role of oligomerization for bacterial and plant SWEET sugar transporter family

PubMed Central

Xuan, Yuan Hu; Hu, Yi Bing; Chen, Li-Qing; Sosso, Davide; Ducat, Daniel C.; Hou, Bi-Huei; Frommer, Wolf B.

2013-01-01

Eukaryotic sugar transporters of the MFS and SWEET superfamilies consist of 12 and 7 α-helical transmembrane domains (TMs), respectively. Structural analyses indicate that MFS transporters evolved from a series of tandem duplications of an ancestral 3-TM unit. SWEETs are heptahelical proteins carrying a tandem repeat of 3-TM separated by a single TM. Here, we show that prokaryotes have ancestral SWEET homologs with only 3-TM and that the Bradyrhizobium japonicum SemiSWEET1, like Arabidopsis SWEET11, mediates sucrose transport. Eukaryotic SWEETs most likely evolved by internal duplication of the 3-TM, suggesting that SemiSWEETs form oligomers to create a functional pore. However, it remains elusive whether the 7-TM SWEETs are the functional unit or require oligomerization to form a pore sufficiently large to allow for sucrose passage. Split ubiquitin yeast two-hybrid and split GFP assays indicate that Arabidopsis SWEETs homo- and heterooligomerize. We examined mutant SWEET variants for negative dominance to test if oligomerization is necessary for function. Mutation of the conserved Y57 or G58 in SWEET1 led to loss of activity. Coexpression of the defective mutants with functional A. thaliana SWEET1 inhibited glucose transport, indicating that homooligomerization is necessary for function. Collectively, these data imply that the basic unit of SWEETs, similar to MFS sugar transporters, is a 3-TM unit and that a functional transporter contains at least four such domains. We hypothesize that the functional unit of the SWEET family of transporters possesses a structure resembling the 12-TM MFS structure, however, with a parallel orientation of the 3-TM unit. PMID:24027245

Analysis of simple sequence repeat (SSR) structure and sequence within Epichloë endophyte genomes reveals impacts on gene structure and insights into ancestral hybridization events.

PubMed

Clayton, William; Eaton, Carla Jane; Dupont, Pierre-Yves; Gillanders, Tim; Cameron, Nick; Saikia, Sanjay; Scott, Barry

2017-01-01

Epichloë grass endophytes comprise a group of filamentous fungi of both sexual and asexual species. Known for the beneficial characteristics they endow upon their grass hosts, the identification of these endophyte species has been of great interest agronomically and scientifically. The use of simple sequence repeat loci and the variation in repeat elements has been used to rapidly identify endophyte species and strains, however, little is known of how the structure of repeat elements changes between species and strains, and where these repeat elements are located in the fungal genome. We report on an in-depth analysis of the structure and genomic location of the simple sequence repeat locus B10, commonly used for Epichloë endophyte species identification. The B10 repeat was found to be located within an exon of a putative bZIP transcription factor, suggesting possible impacts on polypeptide sequence and thus protein function. Analysis of this repeat in the asexual endophyte hybrid Epichloë uncinata revealed that the structure of B10 alleles reflects the ancestral species that hybridized to give rise to this species. Understanding the structure and sequence of these simple sequence repeats provides a useful set of tools for readily distinguishing strains and for gaining insights into the ancestral species that have undergone hybridization events.

Antifreeze (glyco)protein mimetic behavior of poly(vinyl alcohol): detailed structure ice recrystallization inhibition activity study.

PubMed

Congdon, Thomas; Notman, Rebecca; Gibson, Matthew I

2013-05-13

This manuscript reports a detailed study on the ability of poly(vinyl alcohol) to act as a biomimetic surrogate for antifreeze(glyco)proteins, with a focus on the specific property of ice-recrystallization inhibition (IRI). Despite over 40 years of study, the underlying mechanisms that govern the action of biological antifreezes are still poorly understood, which is in part due to their limited availability and challenging synthesis. Poly(vinyl alcohol) (PVA) has been shown to display remarkable ice recrystallization inhibition activity despite its major structural differences to native antifreeze proteins. Here, controlled radical polymerization is used to synthesize well-defined PVA, which has enabled us to obtain the first quantitative structure-activity relationships, to probe the role of molecular weight and comonomers on IRI activity. Crucially, it was found that IRI activity is "switched on" when the polymer chain length increases from 10 and 20 repeat units. Substitution of the polymer side chains with hydrophilic or hydrophobic units was found to diminish activity. Hydrophobic modifications to the backbone were slightly more tolerated than side chain modifications, which implies an unbroken sequence of hydroxyl units is necessary for activity. These results highlight that, although hydrophobic domains are key components of IRI activity, the random inclusion of addition hydrophobic units does not guarantee an increase in activity and that the actual polymer conformation is important.

Structure of the large FK506-binding protein FKBP51, an Hsp90-binding protein and a component of steroid receptor complexes

PubMed Central

Sinars, Cindy R.; Cheung-Flynn, Joyce; Rimerman, Ronald A.; Scammell, Jonathan G.; Smith, David F.; Clardy, Jon

2003-01-01

The ability to bind immunosuppressive drugs such as cyclosporin and FK506 defines the immunophilin family of proteins, and the FK506-binding proteins form the FKBP subfamily of immunophilins. Some FKBPs, notably FKBP12 (the 12-kDa FK506-binding protein), have defined roles in regulating ion channels or cell signaling, and well established structures. Other FKBPs, especially the larger ones, participate in important biological processes, but their exact roles and the structural bases for these roles are poorly defined. FKBP51 (the 51-kDa FKBP) associates with heat shock protein 90 (Hsp90) and appears in functionally mature steroid receptor complexes. In New World monkeys, FKBP51 has been implicated in cortisol resistance. We report here the x-ray structures of human FKBP51, to 2.7 Å, and squirrel monkey FKBP51, to 2.8 Å, by using multiwavelength anomalous dispersion phasing. FKBP51 is composed of three domains: two consecutive FKBP domains and a three-unit repeat of the TPR (tetratricopeptide repeat) domain. This structure of a multi-FKBP domain protein clarifies the arrangement of these domains and their possible interactions with other proteins. The two FKBP domains differ by an insertion in the second that affects the formation of the progesterone receptor complex. PMID:12538866

A Method for WD40 Repeat Detection and Secondary Structure Prediction

PubMed Central

Wang, Yang; Jiang, Fan; Zhuo, Zhu; Wu, Xian-Hui; Wu, Yun-Dong

2013-01-01

WD40-repeat proteins (WD40s), as one of the largest protein families in eukaryotes, play vital roles in assembling protein-protein/DNA/RNA complexes. WD40s fold into similar β-propeller structures despite diversified sequences. A program WDSP (WD40 repeat protein Structure Predictor) has been developed to accurately identify WD40 repeats and predict their secondary structures. The method is designed specifically for WD40 proteins by incorporating both local residue information and non-local family-specific structural features. It overcomes the problem of highly diversified protein sequences and variable loops. In addition, WDSP achieves a better prediction in identifying multiple WD40-domain proteins by taking the global combination of repeats into consideration. In secondary structure prediction, the average Q3 accuracy of WDSP in jack-knife test reaches 93.7%. A disease related protein LRRK2 was used as a representive example to demonstrate the structure prediction. PMID:23776530

Concise chemical synthesis of a tetrasaccharide repeating unit of the O-antigen of Hafnia alvei 10457.

PubMed

Kumar, Rishi; Maulik, Prakas R; Misra, Anup Kumar

2008-08-01

Concise chemical synthesis of a tetrasaccharide repeating unit of the O-antigen of Hafnia alvei 10457 is reported. Construction of the tetrasaccharide as its 4-methoxyphenyl glycoside was achieved by condensation of less abundant monosaccharide units such as, D-galactofuranose, N-acetyl-D-galactosamine and N-acetylneuraminic acid. The synthetic strategy consists of the preparation of suitably protected required monosaccharide intermediates from the commercially available reducing sugars and high yielding glycosylation reactions.

Genetic Studies of the Prp17 Gene of Saccharomyces Cerevisiae: A Domain Essential for Function Maps to a Nonconserved Region of the Protein

PubMed Central

Seshadri, V.; Vaidya, V. C.; Vijayraghavan, U.

1996-01-01

The PRP17 gene product is required for the second step of pre-mRNA splicing reactions. The C-terminal half of this protein bears four repeat units with homology to the β transducin repeat. Missense mutations in three temperature-sensitive prp17 mutants map to a region in the N-terminal half of the protein. We have generated, in vitro, 11 missense alleles at the β transducin repeat units and find that only one affects function in vivo. A phenotypically silent missense allele at the fourth repeat unit enhances the slow-growing phenotype conferred by an allele at the third repeat, suggesting an interaction between these domains. Although many missense mutations in highly conserved amino acids lack phenotypic effects, deletion analysis suggests an essential role for these units. Only mutations in the N-terminal nonconserved domain of PRP17 are synthetically lethal in combination with mutations in PRP16 and PRP18, two other gene products required for the second splicing reaction. A mutually allele-specific interaction between prp17 and snr7, with mutations in U5 snRNA, was observed. We therefore suggest that the functional region of Prp17p that interacts with Prp18p, Prp16p, and U5 snRNA is in the N terminal region of the protein. PMID:8722761

Triplet repeat RNA structure and its role as pathogenic agent and therapeutic target

PubMed Central

Krzyzosiak, Wlodzimierz J.; Sobczak, Krzysztof; Wojciechowska, Marzena; Fiszer, Agnieszka; Mykowska, Agnieszka; Kozlowski, Piotr

2012-01-01

This review presents detailed information about the structure of triplet repeat RNA and addresses the simple sequence repeats of normal and expanded lengths in the context of the physiological and pathogenic roles played in human cells. First, we discuss the occurrence and frequency of various trinucleotide repeats in transcripts and classify them according to the propensity to form RNA structures of different architectures and stabilities. We show that repeats capable of forming hairpin structures are overrepresented in exons, which implies that they may have important functions. We further describe long triplet repeat RNA as a pathogenic agent by presenting human neurological diseases caused by triplet repeat expansions in which mutant RNA gains a toxic function. Prominent examples of these diseases include myotonic dystrophy type 1 and fragile X-associated tremor ataxia syndrome, which are triggered by mutant CUG and CGG repeats, respectively. In addition, we discuss RNA-mediated pathogenesis in polyglutamine disorders such as Huntington's disease and spinocerebellar ataxia type 3, in which expanded CAG repeats may act as an auxiliary toxic agent. Finally, triplet repeat RNA is presented as a therapeutic target. We describe various concepts and approaches aimed at the selective inhibition of mutant transcript activity in experimental therapies developed for repeat-associated diseases. PMID:21908410

Plant chromosomes from end to end: telomeres, heterochromatin and centromeres.

PubMed

Lamb, Jonathan C; Yu, Weichang; Han, Fangpu; Birchler, James A

2007-04-01

Recent evidence indicates that heterochromatin in plants is composed of heterogeneous sequences, which are usually composed of transposable elements or tandem repeat arrays. These arrays are associated with chromatin modifications that produce a closed configuration that limits transcription. Centromere sequences in plants are usually composed of tandem repeat arrays that are homogenized across the genome. Analysis of such arrays in closely related taxa suggests a rapid turnover of the repeat unit that is typical of a particular species. In addition, two lines of evidence for an epigenetic component of centromere specification have been reported, namely an example of a neocentromere formed over sequences without the typical repeat array and examples of centromere inactivation. Although the telomere repeat unit is quite prevalent in the plant kingdom, unusual repeats have been found in some families. Recently, it was demonstrated that the introduction of telomere sequences into plants cells causes truncation of the chromosomes, and that this technique can be used to produce artificial chromosome platforms.

A Simple Method to Decode the Complete 18-5.8-28S rRNA Repeated Units of Green Algae by Genome Skimming.

PubMed

Lin, Geng-Ming; Lai, Yu-Heng; Audira, Gilbert; Hsiao, Chung-Der

2017-11-06

Green algae, Chlorella ellipsoidea , Haematococcus pluvialis and Aegagropila linnaei (Phylum Chlorophyta) were simultaneously decoded by a genomic skimming approach within 18-5.8-28S rRNA region. Whole genomic DNAs were isolated from green algae and directly subjected to low coverage genome skimming sequencing. After de novo assembly and mapping, the size of complete 18-5.8-28S rRNA repeated units for three green algae were ranged from 5785 to 6028 bp, which showed high nucleotide diversity (π is around 0.5-0.6) within ITS1 and ITS2 (Internal Transcribed Spacer) regions. Previously, the evolutional diversity of algae has been difficult to decode due to the inability design universal primers that amplify specific marker genes across diverse algal species. In this study, our method provided a rapid and universal approach to decode the 18-5.8-28S rRNA repeat unit in three green algal species. In addition, the completely sequenced 18-5.8-28S rRNA repeated units provided a solid nuclear marker for phylogenetic and evolutionary analysis for green algae for the first time.

The Effects of Repeated Writing and Repeated Revision Strategies on Composing Fluency of Learning Disabled Adolescents. Final Report.

ERIC Educational Resources Information Center

Harriman, Nancy E.; Gajar, Anna H.

The study investigated the use of repeated writings as a means of increasing written language fluency with 48 learning disabled students in senior high school resource room English classes. Subjects received one of four treatments for 4 days: repeated writing with structural cues, repeated revision with structural cues, writing on a new topic with…

5′CAG and 5′CTG Repeats Create Differential Impediment to the Progression of a Minimal Reconstituted T4 Replisome Depending on the Concentration of dNTPs

PubMed Central

Delagoutte, Emmanuelle; Baldacci, Giuseppe

2011-01-01

Instability of repetitive sequences originates from strand misalignment during repair or replicative DNA synthesis. To investigate the activity of reconstituted T4 replisomes across trinucleotide repeats (TNRs) during leading strand DNA synthesis, we developed a method to build replication miniforks containing a TNR unit of defined sequence and length. Each minifork consists of three strands, primer, leading strand template, and lagging strand template with a 5′ single-stranded (ss) tail. Each strand is prepared independently, and the minifork is assembled by hybridization of the three strands. Using these miniforks and a minimal reconstituted T4 replisome, we show that during leading strand DNA synthesis, the dNTP concentration dictates which strand of the structure-forming 5′CAG/5′CTG repeat creates the strongest impediment to the minimal replication complex. We discuss this result in the light of the known fluctuation of dNTP concentration during the cell cycle and cell growth and the known concentration balance among individual dNTPs. PMID:22096622

Histone and ribosomal RNA repetitive gene clusters of the boll weevil are linked in a tandem array.

PubMed

Roehrdanz, R; Heilmann, L; Senechal, P; Sears, S; Evenson, P

2010-08-01

Histones are the major protein component of chromatin structure. The histone family is made up of a quintet of proteins, four core histones (H2A, H2B, H3 & H4) and the linker histones (H1). Spacers are found between the coding regions. Among insects this quintet of genes is usually clustered and the clusters are tandemly repeated. Ribosomal DNA contains a cluster of the rRNA sequences 18S, 5.8S and 28S. The rRNA genes are separated by the spacers ITS1, ITS2 and IGS. This cluster is also tandemly repeated. We found that the ribosomal RNA repeat unit of at least two species of Anthonomine weevils, Anthonomus grandis and Anthonomus texanus (Coleoptera: Curculionidae), is interspersed with a block containing the histone gene quintet. The histone genes are situated between the rRNA 18S and 28S genes in what is known as the intergenic spacer region (IGS). The complete reiterated Anthonomus grandis histone-ribosomal sequence is 16,248 bp.

Full structure and insight into the gene cluster of the O-specific polysaccharide of Yersinia intermedia H9-36/83 (O:17).

PubMed

Sizova, Olga V; Shashkov, Alexander S; Kondakova, Anna N; Knirel, Yuriy A; Shaikhutdinova, Rima Z; Ivanov, Sergei A; Kislichkina, Angelina A; Kadnikova, Lidia A; Bogun, Aleksandr G; Dentovskaya, Svetlana V

2018-05-02

Lipopolysaccharide was isolated from bacteria Yersinia intermedia H9-36/83 (O:17) and degraded with mild acid to give an O-specific polysaccharide, which was isolated by GPC on Sephadex G-50 and studied by sugar analysis and 1D and 2D NMR spectroscopy. The polysaccharide was found to contain 3-deoxy-3-[(R)-3-hydroxybutanoylamino]-d-fucose (d-Fuc3NR3Hb) and the following structure of the heptasaccharide repeating unit was established: The structure established is consistent with the gene content of the O-antigen gene cluster. The O-polysaccharide structure and gene cluster of Y. intermedia are related to those of Hafnia alvei 1211 and Escherichia coli O:103. Copyright © 2018 Elsevier Ltd. All rights reserved.

Structure and genetics of the O-specific polysaccharide of Escherichia coli O27.

PubMed

Perepelov, Andrei V; Chen, Tingting; Senchenkova, Sofya N; Filatov, Andrei V; Song, Jingjie; Shashkov, Alexander S; Liu, Bin; Knirel, Yuriy A

2018-02-01

The O-specific polysaccharide (O-antigen) is a part of the lipopolysaccharide on the cell surface of Gram-negative bacteria. The O-polysaccharide was obtained by mild acid hydrolysis of the lipopolysaccharide of Escherichia coli O27 and studied by sugar analysis and Smith degradation along with 1 H and 13 C NMR spectroscopy. The following structure of the branched hexasaccharide repeating unit was established, which is unique among known structures of bacterial polysaccharides:where GlcA is non-stoichiometrically O-acetylated at position 3 (∼22%) or 4 (∼37%). Functions of genes in the O-antigen gene cluster of E. coli O27 were tentatively assigned by comparison with sequences in the available databases and found to be consistent with the O-polysaccharide structure. Copyright © 2017 Elsevier Ltd. All rights reserved.

Exploring the atomic structure and conformational flexibility of a 320 Å long engineered viral fiber using X-ray crystallography

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

Bhardwaj, Anshul; Casjens, Sherwood R.; Cingolani, Gino, E-mail: gino.cingolani@jefferson.edu

2014-02-01

This study presents the crystal structure of a ∼320 Å long protein fiber generated by in-frame extension of its repeated helical coiled-coil core. Protein fibers are widespread in nature, but only a limited number of high-resolution structures have been determined experimentally. Unlike globular proteins, fibers are usually recalcitrant to form three-dimensional crystals, preventing single-crystal X-ray diffraction analysis. In the absence of three-dimensional crystals, X-ray fiber diffraction is a powerful tool to determine the internal symmetry of a fiber, but it rarely yields atomic resolution structural information on complex protein fibers. An 85-residue-long minimal coiled-coil repeat unit (MiCRU) was previously identifiedmore » in the trimeric helical core of tail needle gp26, a fibrous protein emanating from the tail apparatus of the bacteriophage P22 virion. Here, evidence is provided that an MiCRU can be inserted in frame inside the gp26 helical core to generate a rationally extended fiber (gp26-2M) which, like gp26, retains a trimeric quaternary structure in solution. The 2.7 Å resolution crystal structure of this engineered fiber, which measures ∼320 Å in length and is only 20–35 Å wide, was determined. This structure, the longest for a trimeric protein fiber to be determined to such a high resolution, reveals the architecture of 22 consecutive trimerization heptads and provides a framework to decipher the structural determinants for protein fiber assembly, stability and flexibility.« less

A novel highly charged exopolysaccharide produced by two strains of Stenotrophomonas maltophilia recovered from patients with cystic fibrosis.

PubMed

Cescutti, Paola; Cuzzi, Bruno; Liut, Gianfranco; Segonds, Christine; Di Bonaventura, Giovanni; Rizzo, Roberto

2011-09-27

Stenotrophomonas maltophilia is a non-fermenting Gram-negative microorganism capable of causing chronic pulmonary infection in cystic fibrosis patients and its ability to form biofilms on polystyrene and glass surfaces, as well as on cystic fibrosis-derived bronchial epithelial IB3-I cells was recently demonstrated. The latter evidence might explain the power of S. maltophilia to produce persistent lung infections, despite intensive antibiotic treatment. In addition to being important components of the extracellular biofilm matrix, polysaccharides are involved in virulence, as they contribute to bacterial survival in a hostile environment. With the aim of contributing to the elucidation of S. maltophilia virulence factors, the exopolysaccharides produced by two mucoid clinical isolates of S. maltophilia obtained from two cystic fibrosis patients were completely characterised, mainly by means of ESI-MS and NMR spectroscopy. The results showed that, although the two isolates were recovered from two different patients living in different countries (Italy and France), the exopolysaccharides produced have an identical primary structure, with the following repeating unit: The exopolysaccharide is highly negatively charged for the presence of three uronic acids on four residues in the repeating unit. Moreover, an ether-linked d-lactate substituent is located on C-3 and one O-acetyl group on C-4 of the galacturonic acid side chain. Another O-acetyl group substitutes C-2 of the galacturonic acid in the backbone, making this primary structure unique. Copyright © 2011 Elsevier Ltd. All rights reserved.

Structures of the SER/THR linked variant oligosaccharides present in equine chorionic gonadotropin (eCG). beta. -subunit

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

Bahl, O.P.; Anumula, K.R.

1986-05-01

eCG ..beta..-subunit contains more than 50% carbohydrate and constitutes about 72% of the hormone. O-linked carbohydrate (85%) was separated from the N-linked (15%) by gel filtration of the endoproteinase Lys-C digest. Six O-linked carbohydrate units were released by NaOH/NaB/sup 3/H/sub 4/ treatment. Oligosaccharides were fractionated by gel filtration and paper chromatography. Several oligosaccharides were obtained ranging in size from a sialyl di-saccharide to megalosaccharide with about 50 sugar residues. Methylation analyses and tlc examination of the oligosaccharides after endo- and exoglycosidase digestions and nitrous acid deamination and Smith degradation revealed a core structure of Gal..beta..1-4 GlcNAc..beta..1-6 (Gal ..beta..1-3) GalNAcH/sub 2/more » with poly-N-acetyllactosamine peripheral extensions. Nearly 50% of the oligosaccharides were large and were preferentially extended on 1,6 arm of the GalNAcH/sub 2/ by repeating N-acetyllactosamine units. Furthermore, these oligosaccharides contained branching 1,3,6-linked galactoses giving rise to tri, penta and multiantennary structures.« less

New paradigm in ankyrin repeats: Beyond protein-protein interaction module.

PubMed

Islam, Zeyaul; Nagampalli, Raghavendra Sashi Krishna; Fatima, Munazza Tamkeen; Ashraf, Ghulam Md

2018-04-01

Classically, ankyrin repeat (ANK) proteins are built from tandems of two or more repeats and form curved solenoid structures that are associated with protein-protein interactions. These are short, widespread structural motif of around 33 amino acids repeats in tandem, having a canonical helix-loop-helix fold, found individually or in combination with other domains. The multiplicity of structural pattern enables it to form assemblies of diverse sizes, required for their abilities to confer multiple binding and structural roles of proteins. Three-dimensional structures of these repeats determined to date reveal a degree of structural variability that translates into the considerable functional versatility of this protein superfamily. Recent work on the ANK has proposed novel structural information, especially protein-lipid, protein-sugar and protein-protein interaction. Self-assembly of these repeats was also shown to prevent the associated protein in forming filaments. In this review, we summarize the latest findings and how the new structural information has increased our understanding of the structural determinants of ANK proteins. We discussed latest findings on how these proteins participate in various interactions to diversify the ANK roles in numerous biological processes, and explored the emerging and evolving field of designer ankyrins and its framework for protein engineering emphasizing on biotechnological applications. Copyright © 2017 Elsevier B.V. All rights reserved.

Deciphering structural and temporal interplays during the architectural development of mango trees.

PubMed

Dambreville, Anaëlle; Lauri, Pierre-Éric; Trottier, Catherine; Guédon, Yann; Normand, Frédéric

2013-05-01

Plant architecture is commonly defined by the adjacency of organs within the structure and their properties. Few studies consider the effect of endogenous temporal factors, namely phenological factors, on the establishment of plant architecture. This study hypothesized that, in addition to the effect of environmental factors, the observed plant architecture results from both endogenous structural and temporal components, and their interplays. Mango tree, which is characterized by strong phenological asynchronisms within and between trees and by repeated vegetative and reproductive flushes during a growing cycle, was chosen as a plant model. During two consecutive growing cycles, this study described vegetative and reproductive development of 20 trees submitted to the same environmental conditions. Four mango cultivars were considered to assess possible cultivar-specific patterns. Integrative vegetative and reproductive development models incorporating generalized linear models as components were built. These models described the occurrence, intensity, and timing of vegetative and reproductive development at the growth unit scale. This study showed significant interplays between structural and temporal components of plant architectural development at two temporal scales. Within a growing cycle, earliness of bud burst was highly and positively related to earliness of vegetative development and flowering. Between growing cycles, flowering growth units delayed vegetative development compared to growth units that did not flower. These interplays explained how vegetative and reproductive phenological asynchronisms within and between trees were generated and maintained. It is suggested that causation networks involving structural and temporal components may give rise to contrasted tree architectures.

Integrative structure and functional anatomy of a nuclear pore complex

NASA Astrophysics Data System (ADS)

Kim, Seung Joong; Fernandez-Martinez, Javier; Nudelman, Ilona; Shi, Yi; Zhang, Wenzhu; Raveh, Barak; Herricks, Thurston; Slaughter, Brian D.; Hogan, Joanna A.; Upla, Paula; Chemmama, Ilan E.; Pellarin, Riccardo; Echeverria, Ignacia; Shivaraju, Manjunatha; Chaudhury, Azraa S.; Wang, Junjie; Williams, Rosemary; Unruh, Jay R.; Greenberg, Charles H.; Jacobs, Erica Y.; Yu, Zhiheng; de La Cruz, M. Jason; Mironska, Roxana; Stokes, David L.; Aitchison, John D.; Jarrold, Martin F.; Gerton, Jennifer L.; Ludtke, Steven J.; Akey, Christopher W.; Chait, Brian T.; Sali, Andrej; Rout, Michael P.

2018-03-01

Nuclear pore complexes play central roles as gatekeepers of RNA and protein transport between the cytoplasm and nucleoplasm. However, their large size and dynamic nature have impeded a full structural and functional elucidation. Here we determined the structure of the entire 552-protein nuclear pore complex of the yeast Saccharomyces cerevisiae at sub-nanometre precision by satisfying a wide range of data relating to the molecular arrangement of its constituents. The nuclear pore complex incorporates sturdy diagonal columns and connector cables attached to these columns, imbuing the structure with strength and flexibility. These cables also tie together all other elements of the nuclear pore complex, including membrane-interacting regions, outer rings and RNA-processing platforms. Inwardly directed anchors create a high density of transport factor-docking Phe-Gly repeats in the central channel, organized into distinct functional units. This integrative structure enables us to rationalize the architecture, transport mechanism and evolutionary origins of the nuclear pore complex.

Integrative structure and functional anatomy of a nuclear pore complex.

PubMed

Kim, Seung Joong; Fernandez-Martinez, Javier; Nudelman, Ilona; Shi, Yi; Zhang, Wenzhu; Raveh, Barak; Herricks, Thurston; Slaughter, Brian D; Hogan, Joanna A; Upla, Paula; Chemmama, Ilan E; Pellarin, Riccardo; Echeverria, Ignacia; Shivaraju, Manjunatha; Chaudhury, Azraa S; Wang, Junjie; Williams, Rosemary; Unruh, Jay R; Greenberg, Charles H; Jacobs, Erica Y; Yu, Zhiheng; de la Cruz, M Jason; Mironska, Roxana; Stokes, David L; Aitchison, John D; Jarrold, Martin F; Gerton, Jennifer L; Ludtke, Steven J; Akey, Christopher W; Chait, Brian T; Sali, Andrej; Rout, Michael P

2018-03-22

Nuclear pore complexes play central roles as gatekeepers of RNA and protein transport between the cytoplasm and nucleoplasm. However, their large size and dynamic nature have impeded a full structural and functional elucidation. Here we determined the structure of the entire 552-protein nuclear pore complex of the yeast Saccharomyces cerevisiae at sub-nanometre precision by satisfying a wide range of data relating to the molecular arrangement of its constituents. The nuclear pore complex incorporates sturdy diagonal columns and connector cables attached to these columns, imbuing the structure with strength and flexibility. These cables also tie together all other elements of the nuclear pore complex, including membrane-interacting regions, outer rings and RNA-processing platforms. Inwardly directed anchors create a high density of transport factor-docking Phe-Gly repeats in the central channel, organized into distinct functional units. This integrative structure enables us to rationalize the architecture, transport mechanism and evolutionary origins of the nuclear pore complex.

Design and fabrication of the Mini-Brayton Recuperator (MBR)

NASA Technical Reports Server (NTRS)

Killackey, J. J.; Graves, R.; Mosinskis, G.

1978-01-01

Development of a recuperator for a 2.0 kW closed Brayton space power system is described. The plate-fin heat exchanger is fabricated entirely from Hastelloy X and is designed for 10 years continuous operation at 1000 K (1300 F) with a Xenon-helium working fluid. Special design provisions assure uniform flow distribution, crucial for meeting 0.975 temperature effectiveness. Low-cycle fatigue, resulting from repeated startup and shutdown cycles, was identified as the most critical structural design problem. It is predicted that the unit has a minimum fatigue life of 220 cycles. This is in excess of the BIPS requirement of 100 cycles. Heat transfer performance and thermal cycle testing with air, using a prototype unit, verified that all design objectives can be met.

Exopolysaccharides produced by Burkholderia cenocepacia recA lineages IIIA and IIIB.

PubMed

Chiarini, Luigi; Cescutti, Paola; Drigo, Laura; Impallomeni, Giuseppe; Herasimenka, Yury; Bevivino, Annamaria; Dalmastri, Claudia; Tabacchioni, Silvia; Manno, Graziana; Zanetti, Flavio; Rizzo, Roberto

2004-08-01

Clinical and environmental strains of Burkholderia cenocepacia belonging to the recA lineages IIIA and IIIB were examined for exopolysaccharide (EPS) production. The exopolysaccharides structure was determined using mainly gas chromatography coupled to mass spectrometry and NMR spectroscopy. All the strains produced Cepacian, a highly branched polysaccharide constituted of a heptasaccharide repeating unit, composed of one rhamnose, one glucose, one glucuronic acid, one mannose and three galactose residues. This polymer is the most common exopolysaccharide produced by strains of the Burkholderia cepacia (Bcc) complex. One clinical strain produced also another polysaccharide constituted of three galactose units and one 3-deoxy-D-manno-2-octulosonic acid residues, a polymer that was previously isolated from two strains of B. cepacia genomovar I and B. cenocepacia IIIA.

Combining living anionic polymerization with branching reactions in an iterative fashion to design branched polymers.

PubMed

Higashihara, Tomoya; Sugiyama, Kenji; Yoo, Hee-Soo; Hayashi, Mayumi; Hirao, Akira

2010-06-16

This paper reviews the precise synthesis of many-armed and multi-compositional star-branched polymers, exact graft (co)polymers, and structurally well-defined dendrimer-like star-branched polymers, which are synthetically difficult, by a commonly-featured iterative methodology combining living anionic polymerization with branched reactions to design branched polymers. The methodology basically involves only two synthetic steps; (a) preparation of a polymeric building block corresponding to each branched polymer and (b) connection of the resulting building unit to another unit. The synthetic steps were repeated in a stepwise fashion several times to successively synthesize a series of well-defined target branched polymers. Copyright © 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

47 CFR 90.247 - Mobile repeater stations.

Code of Federal Regulations, 2010 CFR

2010-10-01

... of the mobile unit and an automatic time-delay device that de-activates the transmitter after any... 47 Telecommunication 5 2010-10-01 2010-10-01 false Mobile repeater stations. 90.247 Section 90.247... MOBILE RADIO SERVICES Non-Voice and Other Specialized Operations § 90.247 Mobile repeater stations. A...

Confinement and the Glass Transition Temperature in Supported Polymer Films: Molecular Weight, Repeat Unit Modification, and Cooperativity Length Scale Investigations

NASA Astrophysics Data System (ADS)

Mundra, Manish K.

2005-03-01

It is well known that the glass transition temperatures, Tgs, of supported polystyrene (PS) films decrease dramatically with decreasing film thickness below 60-80 nm. However, a detailed understanding of the cause of this effect is lacking. We have investigated the impact of several parameters, including polymer molecular weight (MW), repeat unit structure, and the length scale of cooperatively rearranging regions in bulk. There is no significant effect of PS MW on the Tg-confinement effect over a range of 5,000 to 3,000,000 g/mol. In contrast, the strength of the Tg reduction and the onset of the confinement effect increase dramatically upon changing the polymer from PS to poly(4-tert-butylstyrene) (PTBS), with PTBS exhibiting a Tg reduction relative to bulk at a thickness of 300-400 nm. PTBS also shows a Tg reduction relative to bulk of 47 K in a 21-nm-thick film, more than twice that observed in a PS film of identical thickness. Characterization of the length scale of cooperatively rearranging regions has been done by differential scanning calorimetry but reveals at best a limited correlation with the confinement effect.

Functional Genomics of the Aeromonas salmonicida Lipopolysaccharide O-Antigen and A-Layer from Typical and Atypical Strains

PubMed Central

Merino, Susana; de Mendoza, Elena; Canals, Rocío; Tomás, Juan M.

2015-01-01

The A. salmonicida A450 LPS O-antigen, encoded by the wbsalmo gene cluster, is exported through an ABC-2 transporter-dependent pathway. It represents the first example of an O-antigen LPS polysaccharide with three different monosaccharides in their repeating unit assembled by this pathway. Until now, only repeating units with one or two different monosaccharides have been described. Functional genomic analysis of this wbsalmo region is mostly in agreement with the LPS O-antigen structure of acetylated l-rhamnose (Rha), d-glucose (Glc), and 2-amino-2-deoxy-d-mannose (ManN). Between genes of the wbsalmo we found the genes responsible for the biosynthesis and assembly of the S-layer (named A-layer in these strains). Through comparative genomic analysis and in-frame deletions of some of the genes, we concluded that all the A. salmonicida typical and atypical strains, other than A. salmonicida subsp. pectinolytica strains, shared the same wbsalmo and presence of A-layer. A. salmonicida subsp. pectinolytica strains lack wbsalmo and A-layer, two major virulence factors, and this could be the reason they are the only ones not found as fish pathogens. PMID:26082990

Mollecarbamates, Molleureas, and Molledihydroisoquinolone, o-Carboxyphenethylamide Metabolites of the Ascidian Didemnum molle Collected in Madagascar.

PubMed

Issac, Michal; Aknin, Maurice; Gauvin-Bialecki, Anne; Pond, Christopher D; Barrows, Louis R; Kashman, Yoel; Carmeli, Shmuel

2017-06-23

The extract of a sample of the tunicate Didemnum molle (MAY13-117) collected in Mayotte afforded eight new metabolites, mollecarbamates A-D (1-4) and molleureas B-E (5-8), along with the two known natural products, N,N'-diphenylethyl urea (10) and molleurea A (11). Another sample of D. molle (MAD11-BA065) collected in Baie des Assassins, Madagascar, afforded molledihydroisoquinolone (9). Mollecarbamates 1-4 are a family of compounds that possess repeating o-carboxyphenethylamide units and a carbamate moiety, while the molleureas 5-8 contain tetra- and penta-repeating carboxyphenethylamide units and a urea bridge in different positions. Molledihydroisoquinolone (9) is a cyclic form of o-carboxyphenethylamide. We propose that these unique natural products are most probably produced by an unprecedented biosynthetic pathway that contains a yet unknown chorismate mutase variant. The structures of the compounds were elucidated by interpretation of the data from 1D and 2D NMR, HRESIMS, and MS/MS analyses of the positive ESIMS experiments. Compounds 1-8 were tested against pathogenic bacteria and in a cytoprotective HIV cell based assay but did not show any significant effects in these assays.

Lipophosphoglycan polymorphisms do not affect Leishmania amazonensis development in the permissive vectors Lutzomyia migonei and Lutzomyia longipalpis.

PubMed

Nogueira, Paula M; Guimarães, Agna C; Assis, Rafael R; Sadlova, Jovana; Myskova, Jitka; Pruzinova, Katerina; Hlavackova, Jana; Turco, Salvatore J; Torrecilhas, Ana C; Volf, Petr; Soares, Rodrigo P

2017-12-16

Lipophosphoglycan (LPG) is a dominant surface molecule of Leishmania promastigotes. Its species-specific polymorphisms are found mainly in the sugars that branch off the conserved Gal(β1,4)Man(α1)-PO 4 backbone of repeat units. Leishmania amazonensis is one of the most important species causing human cutaneous leishmaniasis in the New World. Here, we describe LPG intraspecific polymorphisms in two Le. amazonensis reference strains and their role during the development in three sand fly species. Strains isolated from Lutzomyia flaviscutellata (PH8) and from a human patient (Josefa) displayed structural polymorphism in the LPG repeat units, possessing side chains with 1 and 2 β-glucose or 1 to 3 β-galactose, respectively. Both strains successfully infected permissive vectors Lutzomyia longipalpis and Lutzomyia migonei and could colonize their stomodeal valve and differentiate into metacyclic forms. Despite bearing terminal galactose residues on LPG, Josefa could not sustain infection in the restrictive vector Phlebotomus papatasi. LPG polymorphisms did not affect the ability of Le. amazonensis to develop late-stage infections in permissive vectors. However, the non-establishment of infection in Ph. papatasi by Josefa strain suggested other LPG-independent factors in this restrictive vector.

A description of the ABCD organizational structure and communication framework.

PubMed

Auchter, Allison M; Hernandez Mejia, Margie; Heyser, Charles J; Shilling, Paul D; Jernigan, Terry L; Brown, Sandra A; Tapert, Susan F; Dowling, Gayathri J

2018-04-16

The Adolescent Brain Cognitive Development (ABCD) study is designed to be the largest study of brain development and child health in the United States, performing comprehensive assessments of 11,500 children repeatedly for 10 years. An endeavor of this magnitude requires an organized framework of governance and communication that promotes collaborative decision-making and dissemination of information. The ABCD consortium structure, built upon the Matrix Management approach of organizational theory, facilitates the integration of input from all institutions, numerous internal workgroups and committees, federal partners, and external advisory groups to make use of a broad range of expertise to ensure the study's success. Copyright © 2018 Elsevier Ltd. All rights reserved.

Protein folding and misfolding: mechanism and principles

PubMed Central

Englander, S. Walter; Mayne, Leland; Krishna, Mallela M. G.

2012-01-01

Two fundamentally different views of how proteins fold are now being debated. Do proteins fold through multiple unpredictable routes directed only by the energetically downhill nature of the folding landscape or do they fold through specific intermediates in a defined pathway that systematically puts predetermined pieces of the target native protein into place? It has now become possible to determine the structure of protein folding intermediates, evaluate their equilibrium and kinetic parameters, and establish their pathway relationships. Results obtained for many proteins have serendipitously revealed a new dimension of protein structure. Cooperative structural units of the native protein, called foldons, unfold and refold repeatedly even under native conditions. Much evidence obtained by hydrogen exchange and other methods now indicates that cooperative foldon units and not individual amino acids account for the unit steps in protein folding pathways. The formation of foldons and their ordered pathway assembly systematically puts native-like foldon building blocks into place, guided by a sequential stabilization mechanism in which prior native-like structure templates the formation of incoming foldons with complementary structure. Thus the same propensities and interactions that specify the final native state, encoded in the amino-acid sequence of every protein, determine the pathway for getting there. Experimental observations that have been interpreted differently, in terms of multiple independent pathways, appear to be due to chance misfolding errors that cause different population fractions to block at different pathway points, populate different pathway intermediates, and fold at different rates. This paper summarizes the experimental basis for these three determining principles and their consequences. Cooperative native-like foldon units and the sequential stabilization process together generate predetermined stepwise pathways. Optional misfolding errors are responsible for 3-state and heterogeneous kinetic folding. PMID:18405419

Failure mechanisms of additively manufactured porous biomaterials: Effects of porosity and type of unit cell.

PubMed

Kadkhodapour, J; Montazerian, H; Darabi, A Ch; Anaraki, A P; Ahmadi, S M; Zadpoor, A A; Schmauder, S

2015-10-01

Since the advent of additive manufacturing techniques, regular porous biomaterials have emerged as promising candidates for tissue engineering scaffolds owing to their controllable pore architecture and feasibility in producing scaffolds from a variety of biomaterials. The architecture of scaffolds could be designed to achieve similar mechanical properties as in the host bone tissue, thereby avoiding issues such as stress shielding in bone replacement procedure. In this paper, the deformation and failure mechanisms of porous titanium (Ti6Al4V) biomaterials manufactured by selective laser melting from two different types of repeating unit cells, namely cubic and diamond lattice structures, with four different porosities are studied. The mechanical behavior of the above-mentioned porous biomaterials was studied using finite element models. The computational results were compared with the experimental findings from a previous study of ours. The Johnson-Cook plasticity and damage model was implemented in the finite element models to simulate the failure of the additively manufactured scaffolds under compression. The computationally predicted stress-strain curves were compared with the experimental ones. The computational models incorporating the Johnson-Cook damage model could predict the plateau stress and maximum stress at the first peak with less than 18% error. Moreover, the computationally predicted deformation modes were in good agreement with the results of scaling law analysis. A layer-by-layer failure mechanism was found for the stretch-dominated structures, i.e. structures made from the cubic unit cell, while the failure of the bending-dominated structures, i.e. structures made from the diamond unit cells, was accompanied by the shearing bands of 45°. Copyright © 2015 Elsevier Ltd. All rights reserved.

Discordant expression and variable numbers of neighboring GGA- and GAA-rich triplet repeats in the 3' untranslated regions of two groups of messenger RNAs encoded by the rat polymeric immunoglobulin receptor gene.

PubMed Central

Koch, K S; Gleiberman, A S; Aoki, T; Leffert, H L; Feren, A; Jones, A L; Fodor, E J

1995-01-01

An unusual S1-nuclease sensitive microsatellite (STMS) has been found in the single copy, rat polymeric immunoglobulin receptor gene (PIGR) terminal exon. In Fisher rats, elements within or beyond the STMS are expressed variably in the 3' untranslated regions (3'UTRs) of two 'Groups' of PIGR-encoded hepatic mRNAs (pIg-R) during liver regeneration. STMS elements include neighboring constant regions (a 60-bp d[GA]-rich tract with a chi-like octamer, followed by 15 tandem d[GGA] repeats) that merge directly with 36 or 39 tandem d[GAA] repeats (Fisher or Wistar strains, respectively) interrupted by d[AA] between their 5th-6th repeat units. The Wistar STMS is flanked upstream by two regions of nearly contiguous d[CA] or d[CT] repeats in the 3' end of intron 8; and downstream, by a 283 bp 'unit' containing several inversions at its 5' end, and two polyadenylation signals at its 3' end. The 283 nt unit is expressed in Group 1 pIg-R mRNAs; but it is absent in the Group 2 family so that their GAA repeats merge with their poly A tails. In contrast to genomic sequence, GGA triplet repeats are amplified (n > or = 24-26), whereas GAA triplet repeats are truncated variably (n < or = 9-37) and expressed uninterruptedly in both mRNA Groups. These results suggest that 3' end processing of the rat PIGR gene may involve misalignment, slippage and premature termination of RNA polymerase II. The function of this unusual processing and possible roles of chi-like octamers in quiescent or extrahepatic tissues are discussed. Images PMID:7739889

High Regional Variation in Urethroplasty in the United States

PubMed Central

Figler, Bradley D.; Gore, John L.; Holt, Sarah K.; Voelzke, Bryan B.; Wessells, Hunter

2015-01-01

Purpose We identified clinical and regional factors associated with the use of urethroplasty vs repeat endoscopic management for urethral stricture disease. Materials and Methods We analyzed claims for patients 18 to 65 years old in the 2007 to 2011 MarketScan ® Commercial Claims and Encounters Database with a diagnosis of urethral stricture. The primary outcome was treatment with urethroplasty vs repeat endoscopic management, defined as more than 2 dilations or direct vision internal urethrotomies. The likelihood of urethroplasty vs repeat endoscopic management was determined for each major metropolitan area in the United States. Multivariate logistic regression was done to identify factors associated with urethroplasty. Results We identified 41,056 patients with urethral stricture, yielding a diagnosis rate of 296/100,000 men in MarketScan. Repeat endoscopic management and urethroplasty were performed in 2,700 and 1,444 patients, respectively. Compared to patients treated with repeat endoscopic management those with urethroplasty were younger (median age 44 vs 54 years) and more likely to have a Charlson comorbidity score of 0 (84% vs 77%), have traveled out of a metropolitan area for care (34% vs 17%) and have a reconstructive urologist in the treatment metropolitan area (76% and 62%, each p < 0.001). When controlling for age and Charlson comorbidity score, travel out of a metropolitan area (OR 2.7, 95% CI 2.2–3.3) and a reconstructive urologist in the treatment metropolitan area (OR 2.0, 95% CI 1.7–2.5) were associated with a greater likelihood of urethroplasty vs repeat endoscopic management. Conclusions Despite the well established benefits of urethroplasty compared to repeat endoscopic management a strong bias for repeat endoscopic management exists in many regions in the United States. PMID:25072180

Disruption of Higher Order DNA Structures in Friedreich’s Ataxia (GAA)n Repeats by PNA or LNA Targeting

PubMed Central

Bergquist, Helen; Rocha, Cristina S. J.; Álvarez-Asencio, Rubén; Nguyen, Chi-Hung; Rutland, Mark. W.; Smith, C. I. Edvard; Good, Liam; Nielsen, Peter E.; Zain, Rula

2016-01-01

Expansion of (GAA)n repeats in the first intron of the Frataxin gene is associated with reduced mRNA and protein levels and the development of Friedreich’s ataxia. (GAA)n expansions form non-canonical structures, including intramolecular triplex (H-DNA), and R-loops and are associated with epigenetic modifications. With the aim of interfering with higher order H-DNA (like) DNA structures within pathological (GAA)n expansions, we examined sequence-specific interaction of peptide nucleic acid (PNA) with (GAA)n repeats of different lengths (short: n=9, medium: n=75 or long: n=115) by chemical probing of triple helical and single stranded regions. We found that a triplex structure (H-DNA) forms at GAA repeats of different lengths; however, single stranded regions were not detected within the medium size pathological repeat, suggesting the presence of a more complex structure. Furthermore, (GAA)4-PNA binding of the repeat abolished all detectable triplex DNA structures, whereas (CTT)5-PNA did not. We present evidence that (GAA)4-PNA can invade the DNA at the repeat region by binding the DNA CTT strand, thereby preventing non-canonical-DNA formation, and that triplex invasion complexes by (CTT)5-PNA form at the GAA repeats. Locked nucleic acid (LNA) oligonucleotides also inhibited triplex formation at GAA repeat expansions, and atomic force microscopy analysis showed significant relaxation of plasmid morphology in the presence of GAA-LNA. Thus, by inhibiting disease related higher order DNA structures in the Frataxin gene, such PNA and LNA oligomers may have potential for discovery of drugs aiming at recovering Frataxin expression. PMID:27846236

New Radar Altimeter Missions are Providing a Dramatically Sharper Image of Global Marine Tectonics

NASA Astrophysics Data System (ADS)

Sandwell, D. T.; Müller, D.; Garcia, E.; Matthews, K. J.; Smith, W. H. F.; Zaron, E.; Zhang, S.; Bassett, D.; Francis, R.

2015-12-01

Marine gravity, derived from satellite radar altimetry, is a powerful tool for mapping tectonic structures, especially in the deep ocean basins where the topography remains unmapped by ships or is buried by thick sediment. The ability to infer seafloor tectonics from space was first demonstrated in 1978 using Seasat altimeter data but the spatial coverage was incomplete because of the short three-month lifetime of the satellite. Most ocean altimeters have repeat ground tracks with spacings of hundreds of kilometers so they do not resolve tectonic structures. Adequate altimeter coverage became available in 1995 when the United States Navy declassified the Geosat radar altimeter data and the ERS-1 altimeter completed a 1-year mapping phase. These mid-1990's altimeter-derived images of the ocean basins remained static for 15 years because there were no new non-repeat altimeter missions. This situation changed dramatically in 2010 when CryoSat-2, with its advanced radar altimeter, was launched into a non-repeat orbit and continues to collect data until perhaps 2020. In addition the Jason-1 altimeter was placed into a 14-month geodetic phase at the end of its lifetime. More recently the 1.5 times higher precision measurements from the AltiKa altimeter aboard the SARAL spacecraft began to drift away from its 35-day repeat trackline. The Chinese HY-2 altimeter is scheduled to begin a dense mapping phase in early 2016. Moreover in 2020 we may enjoy significantly higher resolution maps of the ocean basins from the planned SWOT altimeter mission with its advanced swath mapping ability. All of this new data will provide a much sharper image of the tectonics of the deep ocean basins and continental margins. During this talk we will tour of the new tectonic structures revealed by CryoSat-2 and Jason-1 and speculate on the tectonic views of the ocean basins in 2020 and beyond.

Bioinformatic analyses implicate the collaborating meiotic crossover/chiasma proteins Zip2, Zip3, and Spo22/Zip4 in ubiquitin labeling

PubMed Central

Perry, Jason; Kleckner, Nancy; Börner, G. Valentin

2005-01-01

Zip2 and Zip3 are meiosis-specific proteins that, in collaboration with several partners, act at the sites of crossover-designated, axis-associated recombinational interactions to mediate crossover/chiasma formation. Here, Spo22 (also called Zip4) is identified as a probable functional collaborator of Zip2/3. The molecular roles of Zip2, Zip3, and Spo22/Zip4 are unknown. All three proteins are part of a small evolutionary cohort comprising similar homologs in four related yeasts. Zip3 is shown to contain a RING finger whose structural features most closely match those of known ubiquitin E3s. Further, Zip3 exhibits major domainal homologies to Rad18, a known DNA-binding ubiquitin E3. Also described is an approach to the identification and mapping of repeated protein sequence motifs, Alignment Based Repeat Annotation (ABRA), that we have developed. When ABRA is applied to Zip2 and Spo22/Zip4, they emerge as a 14-blade WD40-like repeat protein and a 22-unit tetratricopeptide repeat protein, respectively. WD40 repeats of Cdc20, Cdh1, and Cdc16 and tetratricopeptide repeats of Cdc16, Cdc23, and Cdc27, all components of the anaphase-promoting complex, are also analyzed. These and other findings suggest that Zip2, Zip3, and Zip4 act together to mediate a process that involves Zip3-mediated ubiquitin labeling, potentially as a unique type of ubiquitin-conjugating complex. PMID:16314568

Ultrastructural morphogenesis of a virus associated with lymphocystis-like lesions in parore Girella tricuspidata (Kyphosidae: Perciformes).

PubMed

Hine, P M; Wakefield, St J; Mackereth, G; Morrison, R

2016-09-26

The morphogenesis of large icosahedral viruses associated with lymphocystis-like lesions in the skin of parore Girella tricuspidata is described. The electron-lucent perinuclear viromatrix comprised putative DNA with open capsids at the periphery, very large arrays of smooth endoplasmic reticulum (sER), much of it with a reticulated appearance (rsER) or occurring as rows of vesicles. Lysosomes, degenerating mitochondria and virions in various stages of assembly, and paracrystalline arrays were also present. Long electron-dense inclusions (EDIs) with 15 nm repeating units split terminally and curled to form tubular structures internalising the 15 nm repeating structures. These tubular structures appeared to form the virion capsids. Large parallel arrays of sER sometimes alternated with aligned arrays of crinkled cisternae along which passed a uniformly wide (20 nm) thread-like structure. Strings of small vesicles near open capsids may also have been involved in formation of an inner lipid layer. Granules with a fine fibrillar appearance also occurred in the viromatrix, and from the presence of a halo around mature virions it appeared that the fibrils may form a layer around the capsid. The general features of virogenesis of large icosahedral dsDNA viruses, the large amount of ER, particularly rsER and the EDIs, are features of nucleo-cytoplasmic large DNA viruses, rather than features of 1 genus or family.

C9orf72 nucleotide repeat structures initiate molecular cascades of disease.

PubMed

Haeusler, Aaron R; Donnelly, Christopher J; Periz, Goran; Simko, Eric A J; Shaw, Patrick G; Kim, Min-Sik; Maragakis, Nicholas J; Troncoso, Juan C; Pandey, Akhilesh; Sattler, Rita; Rothstein, Jeffrey D; Wang, Jiou

2014-03-13

A hexanucleotide repeat expansion (HRE), (GGGGCC)n, in C9orf72 is the most common genetic cause of the neurodegenerative diseases amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Here we identify a molecular mechanism by which structural polymorphism of the HRE leads to ALS/FTD pathology and defects. The HRE forms DNA and RNA G-quadruplexes with distinct structures and promotes RNA•DNA hybrids (R-loops). The structural polymorphism causes a repeat-length-dependent accumulation of transcripts aborted in the HRE region. These transcribed repeats bind to ribonucleoproteins in a conformation-dependent manner. Specifically, nucleolin, an essential nucleolar protein, preferentially binds the HRE G-quadruplex, and patient cells show evidence of nucleolar stress. Our results demonstrate that distinct C9orf72 HRE structural polymorphism at both DNA and RNA levels initiates molecular cascades leading to ALS/FTD pathologies, and provide the basis for a mechanistic model for repeat-associated neurodegenerative diseases.

Novel variants of the 5S rRNA genes in Eruca sativa.

PubMed

Singh, K; Bhatia, S; Lakshmikumaran, M

1994-02-01

The 5S ribosomal RNA (rRNA) genes of Eruca sativa were cloned and characterized. They are organized into clusters of tandemly repeated units. Each repeat unit consists of a 119-bp coding region followed by a noncoding spacer region that separates it from the coding region of the next repeat unit. Our study reports novel gene variants of the 5S rRNA genes in plants. Two families of the 5S rDNA, the 0.5-kb size family and the 1-kb size family, coexist in the E. sativa genome. The 0.5-kb size family consists of the 5S rRNA genes (S4) that have coding regions similar to those of other reported plant 5S rDNA sequences, whereas the 1-kb size family consists of the 5S rRNA gene variants (S1) that exist as 1-kb BamHI tandem repeats. S1 is made up of two variant units (V1 and V2) of 5S rDNA where the BamHI site between the two units is mutated. Sequence heterogeneity among S4, V1, and V2 units exists throughout the sequence and is not limited to the noncoding spacer region only. The coding regions of V1 and V2 show approximately 20% dissimilarity to the coding regions of S4 and other reported plant 5S rDNA sequences. Such a large variation in the coding regions of the 5S rDNA units within the same plant species has been observed for the first time. Restriction site variation is observed between the two size classes of 5S rDNA in E. sativa.(ABSTRACT TRUNCATED AT 250 WORDS)

Repeating Patterns in Kindergarten: Findings from Children's Enactments of Two Activities

ERIC Educational Resources Information Center

Tsamir, Pessia; Tirosh, Dina; Levenson, Esther S.; Barkai, Ruthi; Tabach, Michal

2017-01-01

This paper describes kindergarten children's engagement with two patterning activities. The first activity includes two tasks in which children are asked to choose possible ways for extending two different repeating patterns and the second activity calls for comparing different pairs of repeating patterns. Children's recognition of the unit of…

Spectroscopic insights into quadruplexes of five-repeat telomere DNA sequences upon G-block damage.

PubMed

Dvořáková, Zuzana; Vorlíčková, Michaela; Renčiuk, Daniel

2017-11-01

The DNA lesions, resulting from oxidative damage, were shown to destabilize human telomere four-repeat quadruplex and to alter its structure. Long telomere DNA, as a repetitive sequence, offers, however, other mechanisms of dealing with the lesion: extrusion of the damaged repeat into loop or shifting the quadruplex position by one repeat. Using circular dichroism and UV absorption spectroscopy and polyacrylamide electrophoresis, we studied consequences of lesions at different positions of the model five-repeat human telomere DNA sequences on the structure and stability of their quadruplexes in sodium and in potassium. The repeats affected by lesion are preferentially positioned as terminal overhangs of the core quadruplex structurally similar to the four-repeat one. Forced affecting of the inner repeats leads to presence of variety of more parallel folds in potassium. In sodium the designed models form mixture of two dominant antiparallel quadruplexes whose population varies with the position of the affected repeat. The shapes of quadruplex CD spectra, namely the height of dominant peaks, significantly correlate with melting temperatures. Lesion in one guanine tract of a more than four repeats long human telomere DNA sequence may cause re-positioning of its quadruplex arrangement associated with a shift of the structure to less common quadruplex conformations. The type of the quadruplex depends on the loop position and external conditions. The telomere DNA quadruplexes are quite resistant to the effect of point mutations due to the telomere DNA repetitive nature, although their structure and, consequently, function might be altered. Copyright © 2017. Published by Elsevier B.V.

Purification and partial elucidation of the structure of an antioxidant carbohydrate biopolymer from the probiotic bacterium Bacillus coagulans RK-02.

PubMed

Kodali, Vidya P; Perali, Ramu S; Sen, R

2011-08-26

An exopolysaccharide (EPS) was isolated from Bacillus coagulans RK-02 and purified by size exclusion chromatography. The purified, homogeneous EPS had an average molecular weight of ∼3 × 10⁴ Da by comparison with FITC-labeled dextran standards. In vivo evaluations showed that, like other reported polysaccharides, this EPS displayed significant antioxidant activity. FTIR spectroscopy analysis showed the presence of hydroxy, carboxy, and α-glycosidic linkages and a mannose residue. GC analysis indicated that the EPS was a heteropolymer composed of glucose, mannose, galactose, glucosamine, and fucose as monomeric constituent units. Partial elucidation of the structure of the carbohydrate biopolymer based on GC-MS and NMR analysis showed the presence of two unique sets of tetrasaccharide repeating units that have 1→3 and 1→6 glycosidic linkages. This is also the first report of a Gram-positive bacterial polysaccharide with both fucose as a sugar monomer and 1→3 and 1→6 glycosidic linkages in the molecular backbone.

Approximate analysis for repeated eigenvalue problems with applications to controls-structure integrated design

NASA Technical Reports Server (NTRS)

Kenny, Sean P.; Hou, Gene J. W.

1994-01-01

A method for eigenvalue and eigenvector approximate analysis for the case of repeated eigenvalues with distinct first derivatives is presented. The approximate analysis method developed involves a reparameterization of the multivariable structural eigenvalue problem in terms of a single positive-valued parameter. The resulting equations yield first-order approximations to changes in the eigenvalues and the eigenvectors associated with the repeated eigenvalue problem. This work also presents a numerical technique that facilitates the definition of an eigenvector derivative for the case of repeated eigenvalues with repeated eigenvalue derivatives (of all orders). Examples are given which demonstrate the application of such equations for sensitivity and approximate analysis. Emphasis is placed on the application of sensitivity analysis to large-scale structural and controls-structures optimization problems.

Design, production and molecular structure of a new family of artificial alpha-helicoidal repeat proteins (αRep) based on thermostable HEAT-like repeats.

PubMed

Urvoas, Agathe; Guellouz, Asma; Valerio-Lepiniec, Marie; Graille, Marc; Durand, Dominique; Desravines, Danielle C; van Tilbeurgh, Herman; Desmadril, Michel; Minard, Philippe

2010-11-26

Repeat proteins have a modular organization and a regular architecture that make them attractive models for design and directed evolution experiments. HEAT repeat proteins, although very common, have not been used as a scaffold for artificial proteins, probably because they are made of long and irregular repeats. Here, we present and validate a consensus sequence for artificial HEAT repeat proteins. The sequence was defined from the structure-based sequence analysis of a thermostable HEAT-like repeat protein. Appropriate sequences were identified for the N- and C-caps. A library of genes coding for artificial proteins based on this sequence design, named αRep, was assembled using new and versatile methodology based on circular amplification. Proteins picked randomly from this library are expressed as soluble proteins. The biophysical properties of proteins with different numbers of repeats and different combinations of side chains in hypervariable positions were characterized. Circular dichroism and differential scanning calorimetry experiments showed that all these proteins are folded cooperatively and are very stable (T(m) >70 °C). Stability of these proteins increases with the number of repeats. Detailed gel filtration and small-angle X-ray scattering studies showed that the purified proteins form either monomers or dimers. The X-ray structure of a stable dimeric variant structure was solved. The protein is folded with a highly regular topology and the repeat structure is organized, as expected, as pairs of alpha helices. In this protein variant, the dimerization interface results directly from the variable surface enriched in aromatic residues located in the randomized positions of the repeats. The dimer was crystallized both in an apo and in a PEG-bound form, revealing a very well defined binding crevice and some structure flexibility at the interface. This fortuitous binding site could later prove to be a useful binding site for other low molecular mass partners. Copyright © 2010 Elsevier Ltd. All rights reserved.

Lessons that Bear Repeating and Repeating that Bears Lessons: An Interdisciplinary Unit on Principles of Minimalism in Modern Music, Art, and Poetry (Grades 4-8)

ERIC Educational Resources Information Center

Smigel, Eric; McDonald, Nan L.

2012-01-01

This theory-to-practice article focuses on interdisciplinary classroom activities based on principles of minimalism in modern music, art, and poetry. A lesson sequence was designed for an inner-city Grades 4 and 5 general classroom of English language learners, where the unit was taught, assessed, and documented by the authors. Included in the…

Tempered mlo broad-spectrum resistance to barley powdery mildew in an Ethiopian landrace

PubMed Central

Ge, Xintian; Deng, Weiwei; Lee, Zheng Zhou; Lopez-Ruiz, Francisco J.; Schweizer, Patrick; Ellwood, Simon R.

2016-01-01

Recessive mutations in the Mlo gene confer broad spectrum resistance in barley (Hordeum vulgare) to powdery mildew (Blumeria graminis f. sp. hordei), a widespread and damaging disease. However, all alleles discovered to date also display deleterious pleiotropic effects, including the naturally occurring mlo-11 mutant which is widely deployed in Europe. Recessive resistance was discovered in Eth295, an Ethiopian landrace, which was developmentally controlled and quantitative without spontaneous cell wall appositions or extensive necrosis and loss of photosynthetic tissue. This resistance is determined by two copies of the mlo-11 repeat units, that occur upstream to the wild-type Mlo gene, compared to 11–12 in commonly grown cultivars and was designated mlo-11 (cnv2). mlo-11 repeat unit copy number-dependent DNA methylation corresponded with cytological and macroscopic phenotypic differences between copy number variants. Sequence data indicated mlo-11 (cnv2) formed via recombination between progenitor mlo-11 repeat units and the 3′ end of an adjacent stowaway MITE containing region. mlo-11 (cnv2) is the only example of a moderated mlo variant discovered to date and may have arisen by natural selection against the deleterious effects of the progenitor mlo-11 repeat unit configuration. PMID:27404990

Testing the Predictive Capability of the High-Fidelity Generalized Method of Cells Using an Efficient Reformulation

NASA Technical Reports Server (NTRS)

Arnold, Steven M. (Technical Monitor); Bansal, Yogesh; Pindera, Marek-Jerzy

2004-01-01

The High-Fidelity Generalized Method of Cells is a new micromechanics model for unidirectionally reinforced periodic multiphase materials that was developed to overcome the original model's shortcomings. The high-fidelity version predicts the local stress and strain fields with dramatically greater accuracy relative to the original model through the use of a better displacement field representation. Herein, we test the high-fidelity model's predictive capability in estimating the elastic moduli of periodic composites characterized by repeating unit cells obtained by rotation of an infinite square fiber array through an angle about the fiber axis. Such repeating unit cells may contain a few or many fibers, depending on the rotation angle. In order to analyze such multi-inclusion repeating unit cells efficiently, the high-fidelity micromechanics model's framework is reformulated using the local/global stiffness matrix approach. The excellent agreement with the corresponding results obtained from the standard transformation equations confirms the new model's predictive capability for periodic composites characterized by multi-inclusion repeating unit cells lacking planes of material symmetry. Comparison of the effective moduli and local stress fields with the corresponding results obtained from the original Generalized Method of Cells dramatically highlights the original model's shortcomings for certain classes of unidirectional composites.

The suitability of lightfield camera depth maps for coordinate measurement applications

NASA Astrophysics Data System (ADS)

Rangappa, Shreedhar; Tailor, Mitul; Petzing, Jon; Kinnell, Peter; Jackson, Michael

2015-12-01

Plenoptic cameras can capture 3D information in one exposure without the need for structured illumination, allowing grey scale depth maps of the captured image to be created. The Lytro, a consumer grade plenoptic camera, provides a cost effective method of measuring depth of multiple objects under controlled lightning conditions. In this research, camera control variables, environmental sensitivity, image distortion characteristics, and the effective working range of two Lytro first generation cameras were evaluated. In addition, a calibration process has been created, for the Lytro cameras, to deliver three dimensional output depth maps represented in SI units (metre). The novel results show depth accuracy and repeatability of +10.0 mm to -20.0 mm, and 0.5 mm respectively. For the lateral X and Y coordinates, the accuracy was +1.56 μm to -2.59 μm and the repeatability was 0.25 μm.

Characterization of polymorphic microsatellites for the invasive grass Microstegium vimineum (Poaceae).

PubMed

Novy, Ari; Flory, S Luke; Honig, Joshua A; Bonos, Stacy; Hartman, Jean Marie

2012-02-01

Microsatellite markers were developed for the invasive plant Microstegium vimineum (Poaceae) to assess its population structure and to facilitate tracking of invasion expansion. Using 454 sequencing, 11 polymorphic and six monomorphic microsatellite primer sets were developed for M. vimineum. The primer sets were tested on individuals sampled from six populations in the United States and China. The polymorphic primers amplified di-, tri-, and tetranucleotide repeats with three to 10 alleles per locus. These markers will be useful for a variety of applications including tracking of invasion dynamics and population genetics studies.

Conjugated polymer zwitterions and solar cells comprising conjugated polymer zwitterions

DOEpatents

Emrick, Todd; Russell, Thomas; Page, Zachariah; Liu, Yao

2018-06-05

A conjugated polymer zwitterion includes repeating units having structure (I), (II), or a combination thereof ##STR00001## wherein Ar is independently at each occurrence a divalent substituted or unsubstituted C_3-30 arylene or heteroarylene group; L is independently at each occurrence a divalent C_1-16 alkylene group, C_6-30arylene or heteroarylene group, or alkylene oxide group; and R¹ is independently at each occurrence a zwitterion. A polymer solar cell including the conjugated polymer zwitterion is also disclosed.

Bottomland Hardwood Forests along the Upper Mississippi River

USGS Publications Warehouse

Yin, Y.; Nelson, J.C.; Lubinski, S.J.

1997-01-01

Bottomland hardwood forests along the United States' Upper Mississippi River have been drastically reduced in acreage and repeatedly logged during the nineteenth and twentieth centuries. Conversion to agricultural land, timber harvesting, and river modifications for flood prevention and for navigation were the primary factors that caused the changes. Navigation structures and flood-prevention levees have altered the fluvial geomorphic dynamics of the river and floodplain system. Restoration and maintenance of the diversity, productivity, and natural regeneration dynamics of the bottomland hardwood forests under the modified river environment represent a major management challenge.

Structure of a Multilayer Nanofilm To Increase the Encapsulation Efficiency of Basic Fibroblast Growth Factor.

PubMed

Han, Uiyoung; Hong, Jinkee

2018-03-05

In this study, we established the structure of a multilayer nanofilm that more efficiently encapsulates basic fibroblast growth factor (bFGF). First, a positively charged layer material was selected from biocompatible polymers such as collagen (Col), poly(beta-amino ester) (Poly2), and chitosan (Chi), while considering the film thickness. We then investigated the change in bFGF encapsulation efficiency when the multilayer structure was changed from a tetralayer to a trilayer. As a result, we obtained a highly improved bFGF encapsulation efficiency in the nanofilm using a positively charged layer formed by a blend of Col and Poly2 and a negatively charged poly(acrylic acid) (PAA) layer within a trilayered structure. In particular, we found that a significant amount of adsorbed bFGF was desorbed again during the film fabrication process of a tetralayered nanofilm. In the conventional nanofilm, bFGF was regarded as a polycation and formed a multilayer nanofilm that was composed of a tetralayered structure and was represented as (polycation/polyanion/bFGF/polyanion) n where n = number of repeated tetralayers. Here, we suggested that bFGF should not be considered a polycation, rather it should be considered as a small quantity of molecule that exists between the polyanion and polycation layers. In this case, the nanofilm is composed of repeating units of (polycation/polyanion/bFGF/polycation/polyanion), because the amount of adsorbed bFGF is considerably lower than that of other building blocks.

Interrogating Key Positions of Size-Reduced TALE Repeats Reveals a Programmable Sensor of 5-Carboxylcytosine.

PubMed

Maurer, Sara; Giess, Mario; Koch, Oliver; Summerer, Daniel

2016-12-16

Transcription-activator-like effector (TALE) proteins consist of concatenated repeats that recognize consecutive canonical nucleobases of DNA via the major groove in a programmable fashion. Since this groove displays unique chemical information for the four human epigenetic cytosine nucleobases, TALE repeats with epigenetic selectivity can be engineered, with potential to establish receptors for the programmable decoding of all human nucleobases. TALE repeats recognize nucleobases via key amino acids in a structurally conserved loop whose backbone is positioned very close to the cytosine 5-carbon. This complicates the engineering of selectivities for large 5-substituents. To interrogate a more promising structural space, we engineered size-reduced repeat loops, performed saturation mutagenesis of key positions, and screened a total of 200 repeat-nucleobase interactions for new selectivities. This provided insight into the structural requirements of TALE repeats for affinity and selectivity, revealed repeats with improved or relaxed selectivity, and resulted in the first selective sensor of 5-carboxylcytosine.

A novel species-specific tandem repeat DNA family from Sinapis arvensis: detection of telomere-like sequences.

PubMed

Kapila, R; Das, S; Srivastava, P S; Lakshmikumaran, M

1996-08-01

DNA sequences representing a tandemly repeated DNA family of the Sinapis arvensis genome were cloned and characterized. The 700-bp tandem repeat family is represented by two clones, pSA35 and pSA52, which are 697 and 709 bp in length, respectively. Dot matrix analysis of the sequences indicates the presence of repeated elements within each monomeric unit. Sequence analysis of the repetitive region of clones pSA35 and pSA52 shows that there are several copies of a 7-bp repeat element organized in tandem. The consensus sequence of this repeat element is 5'-TTTAGGG-3'. These elements are highly mutated and the difference in length between the two clones is due to different copy numbers of these elements. The repetitive region of clone pSA35 has 26 copies of the element TTTAGGG, whereas clone pSA52 has 28 copies. The repetitive region in both clones is flanked on either side by inverted repeats that may be footprints of a transposition event. Sequence comparison indicates that the element TTTAGGG is identical to telomeric repeats present in Arabidopsis, maize, tomato, and other plants. However, Bal31 digestion kinetics indicates non-telomeric localization of the 700-bp tandem repeats. The clones represent a novel repeat family as (i) they contain telomere-like motifs as subrepeats within each unit; and (ii) they do not hybridize to related crucifers and are species-specific in nature.

Thermodynamic stability of RNA structures formed by CNG trinucleotide repeats. Implication for prediction of RNA structure.

PubMed

Broda, Magdalena; Kierzek, Elzbieta; Gdaniec, Zofia; Kulinski, Tadeusz; Kierzek, Ryszard

2005-08-16

Trinucleotide repeat expansion diseases (TREDs) are correlated with elongation of CNG DNA and RNA repeats to pathological level. This paper shows, for the first time, complete data concerning thermodynamic stabilities of RNA with CNG trinucleotide repeats. Our studies include the stability of oligoribonucleotides composed of two to seven of CAG, CCG, CGG, and CUG repeats. The thermodynamic parameters of helix propagation correlated with the presence of multiple N-N mismatches within CNG RNA duplexes were also determined. Moreover, the total stability of CNG RNA hairpins, as well as the contribution of trinucleotide repeats placed only in the stem or loop regions, was evaluated. The improved thermodynamic parameters allow to predict much more accurately the thermodynamic stabilities and structures of CNG RNAs.

REPETITA: detection and discrimination of the periodicity of protein solenoid repeats by discrete Fourier transform

PubMed Central

Marsella, Luca; Sirocco, Francesco; Trovato, Antonio; Seno, Flavio; Tosatto, Silvio C.E.

2009-01-01

Motivation: Proteins with solenoid repeats evolve more quickly than non-repetitive ones and their periodicity may be rapidly hidden at sequence level, while still evident in structure. In order to identify these repeats, we propose here a novel method based on a metric characterizing amino-acid properties (polarity, secondary structure, molecular volume, codon diversity, electric charge) using five previously derived numerical functions. Results: The five spectra of the candidate sequences coding for structural repeats, obtained by Discrete Fourier Transform (DFT), show common features allowing determination of repeat periodicity with excellent results. Moreover it is possible to introduce a phase space parameterized by two quantities related to the Fourier spectra which allow for a clear distinction between a non-homologous set of globular proteins and proteins with solenoid repeats. The DFT method is shown to be competitive with other state of the art methods in the detection of solenoid structures, while improving its performance especially in the identification of periodicities, since it is able to recognize the actual repeat length in most cases. Moreover it highlights the relevance of local structural propensities in determining solenoid repeats. Availability: A web tool implementing the algorithm presented in the article (REPETITA) is available with additional details on the data sets at the URL: http://protein.bio.unipd.it/repetita/. Contact: silvio.tosatto@unipd.it PMID:19478001

Prevalence of Huntington's disease gene CAG trinucleotide repeat alleles in patients with bipolar disorder.

PubMed

Ramos, Eliana Marisa; Gillis, Tammy; Mysore, Jayalakshmi S; Lee, Jong-Min; Alonso, Isabel; Gusella, James F; Smoller, Jordan W; Sklar, Pamela; MacDonald, Marcy E; Perlis, Roy H

2015-06-01

Huntington's disease is a neurodegenerative disorder characterized by motor, cognitive, and psychiatric symptoms that are caused by huntingtin gene (HTT) CAG trinucleotide repeat alleles of 36 or more units. A greater than expected prevalence of incompletely penetrant HTT CAG repeat alleles observed among individuals diagnosed with major depressive disorder raises the possibility that another mood disorder, bipolar disorder, could likewise be associated with Huntington's disease. We assessed the distribution of HTT CAG repeat alleles in a cohort of individuals with bipolar disorder. HTT CAG allele sizes from 2,229 Caucasian individuals diagnosed with DSM-IV bipolar disorder were compared to allele sizes in 1,828 control individuals from multiple cohorts. We found that HTT CAG repeat alleles > 35 units were observed in only one of 4,458 chromosomes from individuals with bipolar disorder, compared to three of 3,656 chromosomes from control subjects. These findings do not support an association between bipolar disorder and Huntington's disease. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

The organization of repeating units in mitochondrial DNA from yeast petite mutants.

PubMed

Bos, J L; Heyting, C; Van der Horst, G; Borst, P

1980-04-01

We have reinvestigated the linkage orientation of repeating units in mtDNAs of yeast ρ(-) petite mutants containing an inverted duplication. All five petite mtDNAs studied contain a continuous segment of wild-type mtDNA, part of which is duplicated and present in inverted form in the repeat. We show by restriction enzyme analysis that the non-duplicated segments between the inverted duplications are present in random orientation in all five petite mtDNAs. There is no segregation of sub-types with unique orientation. We attribute this to the high rate of intramolecular recombination between the inverted duplications. The results provide additional evidence for the high rate of recombination of yeast mtDNA even in haploid ρ(-) petite cells.We conclude that only two types of stable sequence organization exist in petite mtDNA: petites without an inverted duplication have repeats linked in straight head-to-tail arrangement (abcabc); petites with an inverted duplication have repeats in which the non-duplicated segments are present in random orientation.

White OLED devices and processes for lighting applications

NASA Astrophysics Data System (ADS)

Ide, Nobuhiro; Tsuji, Hiroya; Ito, Norihiro; Matsuhisa, Yuko; Houzumi, Shingo; Nishimori, Taisuke

2010-05-01

In these days, the basic performances of white OLEDs are dramatically improved and application of OLEDs to "Lighting" is expected to be true in the near future. We have developed various technologies for OLED lighting with the aid of the Japanese governmental project, "High-efficiency lighting based on the organic light-emitting mechanism." In this project, a white OLED with high efficiency (37 lm/W) and high quality emission characteristics (CRI of 95 with a small variation of chromaticity in different directions and chromaticity just on the black-body radiation curve) applicable to "Lighting" was realized by a two-unit structure with a fluorescent deep blue emissive unit and a phosphorescent green and red emissive unit. Half-decay lifetime of this white OLED at 1,000 cd/m2 was over 40,000 h. A heat radiative, thin encapsulation structure (less than 1 mm) realized a very stable emission at high luminance of over 3,000 cd/m2. A new deposition source with a hot-wall and a rate controllable valve was developed. Thickness uniformity within +/- 3% at high deposition rate of over 8 nm/s, high material utilization of over 70 %, and repeatable deposition rate controllability were confirmed.

Functional group selective STM Imaging in self-assembled monolayers: Benzeneselenol on Au(111)

NASA Astrophysics Data System (ADS)

Azzam, Waleed; Zharnikov, Michael; Rohwerde, Michael; Bashir, Asif

2018-01-01

Benzeneselenol (PSe) self-assembled monolayers (SAMs) formed on Au(111) substrate by the immersion procedure with an immersion time of 24 h and 4 weeks were studied by high-resolution scanning tunneling microscopy (STM). The short molecular rows, which have been previously attributed to irregular translational domains, were found to be regularly repeated within a single domain in the SAMs fabricated upon the immersion for 4 weeks, forming adlayer structure with a very large unit cell. This structure could be assigned as a (27 × 5) superlattice (α phase) containing 36 molecules in the oblique unit cell. This phase coexisted with a different phase having a commensurate (8√{ 3 } × 4) superstructure (β phase) containing 28 protrusions per rectangular unit cell. Analysis of the STM images suggested that each PSe molecule in the β phase was imaged not as one but as a pair of protrusions, which were attributed to the benzene ring and the selenium headgroup of the PSe molecule. At the given molecular length, the spacing between the protrusions defined the molecular tilt, allowing us to derive the orientation of the SAM constituents directly from the STM image.

Intratypic variability of a tandem repeat locus within the DNA polymerase gene of human herpes simplex virus type 2.

PubMed

Sun, Yongjiang; Chan, Roy Kum Wah; Tan, Suat Hoon

2004-01-01

In this study, the irntratypic variability of a tandem repeat locus within the DNA polymerase (pol) gene of human herpes simplex virus type 2 (HSV2) was uncovered. The locus contained variable numbers of tandem dodecanucleotide (5'-GAC GAG GAC GGG-3') repetitive units. Our result showed that approximately 95% of analyzed HSV2 clinical isolates and the current GenBank HSV2 strains contained two copies of the repetitive units. From genital herpes specimens, three new HSV2 strains, which respectively contained 1, 3, and 4 copies of the repetitive units, were identified. This variable number of tandem repeat (VNTR) locus is absent in HSV1, and thus it also contributes to the intertypic variability of HSV1 and HSV2. The intratypic variability of the locus may be useful for HSV2 strain genotyping and this application is discussed.

Structural and functional diversity in Listeria cell wall teichoic acids.

PubMed

Shen, Yang; Boulos, Samy; Sumrall, Eric; Gerber, Benjamin; Julian-Rodero, Alicia; Eugster, Marcel R; Fieseler, Lars; Nyström, Laura; Ebert, Marc-Olivier; Loessner, Martin J

2017-10-27

Wall teichoic acids (WTAs) are the most abundant glycopolymers found on the cell wall of many Gram-positive bacteria, whose diverse surface structures play key roles in multiple biological processes. Despite recent technological advances in glycan analysis, structural elucidation of WTAs remains challenging due to their complex nature. Here, we employed a combination of ultra-performance liquid chromatography-coupled electrospray ionization tandem-MS/MS and NMR to determine the structural complexity of WTAs from Listeria species. We unveiled more than 10 different types of WTA polymers that vary in their linkage and repeating units. Disparity in GlcNAc to ribitol connectivity, as well as variable O -acetylation and glycosylation of GlcNAc contribute to the structural diversity of WTAs. Notably, SPR analysis indicated that constitution of WTA determines the recognition by bacteriophage endolysins. Collectively, these findings provide detailed insight into Listeria cell wall-associated carbohydrates, and will guide further studies on the structure-function relationship of WTAs. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Non-linearity of the collagen triple helix in solution and implications for collagen function.

PubMed

Walker, Kenneth T; Nan, Ruodan; Wright, David W; Gor, Jayesh; Bishop, Anthony C; Makhatadze, George I; Brodsky, Barbara; Perkins, Stephen J

2017-06-16

Collagen adopts a characteristic supercoiled triple helical conformation which requires a repeating (Xaa-Yaa-Gly) n sequence. Despite the abundance of collagen, a combined experimental and atomistic modelling approach has not so far quantitated the degree of flexibility seen experimentally in the solution structures of collagen triple helices. To address this question, we report an experimental study on the flexibility of varying lengths of collagen triple helical peptides, composed of six, eight, ten and twelve repeats of the most stable Pro-Hyp-Gly (POG) units. In addition, one unblocked peptide, (POG) 10unblocked , was compared with the blocked (POG) 10 as a control for the significance of end effects. Complementary analytical ultracentrifugation and synchrotron small angle X-ray scattering data showed that the conformations of the longer triple helical peptides were not well explained by a linear structure derived from crystallography. To interpret these data, molecular dynamics simulations were used to generate 50 000 physically realistic collagen structures for each of the helices. These structures were fitted against their respective scattering data to reveal the best fitting structures from this large ensemble of possible helix structures. This curve fitting confirmed a small degree of non-linearity to exist in these best fit triple helices, with the degree of bending approximated as 4-17° from linearity. Our results open the way for further studies of other collagen triple helices with different sequences and stabilities in order to clarify the role of molecular rigidity and flexibility in collagen extracellular and immune function and disease. © 2017 The Author(s).

The evolution and function of protein tandem repeats in plants.

PubMed

Schaper, Elke; Anisimova, Maria

2015-04-01

Sequence tandem repeats (TRs) are abundant in proteomes across all domains of life. For plants, little is known about their distribution or contribution to protein function. We exhaustively annotated TRs and studied the evolution of TR unit variations for all Ensembl plants. Using phylogenetic patterns of TR units, we detected conserved TRs with unit number and order preserved during evolution, and those TRs that have diverged via recent TR unit gains/losses. We correlated the mode of evolution of TRs to protein function. TR number was strongly correlated with proteome size, with about one-half of all TRs recognized as common protein domains. The majority of TRs have been highly conserved over long evolutionary distances, some since the separation of red algae and green plants c. 1.6 billion yr ago. Conversely, recurrent recent TR unit mutations were rare. Our results suggest that the first TRs by far predate the first plants, and that TR appearance is an ongoing process with similar rates across the plant kingdom. Interestingly, the few detected highly mutable TRs might provide a source of variation for rapid adaptation. In particular, such TRs are enriched in leucine-rich repeats (LRRs) commonly found in R genes, where TR unit gain/loss may facilitate resistance to emerging pathogens. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

TMPyP4 porphyrin distorts RNA G-quadruplex structures of the disease-associated r(GGGGCC)n repeat of the C9orf72 gene and blocks interaction of RNA-binding proteins.

PubMed

Zamiri, Bita; Reddy, Kaalak; Macgregor, Robert B; Pearson, Christopher E

2014-02-21

Certain DNA and RNA sequences can form G-quadruplexes, which can affect genetic instability, promoter activity, RNA splicing, RNA stability, and neurite mRNA localization. Amyotrophic lateral sclerosis and frontotemporal dementia can be caused by expansion of a (GGGGCC)n repeat in the C9orf72 gene. Mutant r(GGGGCC)n- and r(GGCCCC)n-containing transcripts aggregate in nuclear foci, possibly sequestering repeat-binding proteins such as ASF/SF2 and hnRNPA1, suggesting a toxic RNA pathogenesis, as occurs in myotonic dystrophy. Furthermore, the C9orf72 repeat RNA was recently demonstrated to undergo the noncanonical repeat-associated non-AUG translation (RAN translation) into pathologic dipeptide repeats in patient brains, a process that is thought to depend upon RNA structure. We previously demonstrated that the r(GGGGCC)n RNA forms repeat tract length-dependent G-quadruplex structures that bind the ASF/SF2 protein. Here we show that the cationic porphyrin (5,10,15,20-tetra(N-methyl-4-pyridyl) porphyrin (TMPyP4)), which can bind some G-quadruplex-forming sequences, can bind and distort the G-quadruplex formed by r(GGGGCC)8, and this ablates the interaction of either hnRNPA1 or ASF/SF2 with the repeat. These findings provide proof of concept that nucleic acid binding small molecules, such as TMPyP4, can distort the secondary structure of the C9orf72 repeat, which may beneficially disrupt protein interactions, which may ablate either protein sequestration and/or RAN translation into potentially toxic dipeptides. Disruption of secondary structure formation of the C9orf72 RNA repeats may be a viable therapeutic avenue, as well as a means to test the role of RNA structure upon RAN translation.

Insight into Amyloid Structure Using Chemical Probes

PubMed Central

Reinke, Ashley A.; Gestwicki, Jason E.

2011-01-01

Alzheimer’s disease (AD) is a common neurodegenerative disorder characterized by the deposition of amyloids in the brain. One prominent form of amyloid is composed of repeating units of the amyloid-β (Aβ) peptide. Over the past decade, it has become clear that these Aβ amyloids are not homogeneous; rather, they are composed of a series of structures varying in their overall size and shape and the number of Aβ peptides they contain. Recent theories suggest that these different amyloid conformations may play distinct roles in disease, although their relative contributions are still being discovered. Here, we review how chemical probes, such as congo red, thioflavin T and their derivatives, have been powerful tools for better understanding amyloid structure and function. Moreover, we discuss how design and deployment of conformationally selective probes might be used to test emerging models of AD. PMID:21457473

Ligand binding by repeat proteins: natural and designed

PubMed Central

Grove, Tijana Z; Cortajarena, Aitziber L; Regan, Lynne

2012-01-01

Repeat proteins contain tandem arrays of small structural motifs. As a consequence of this architecture, they adopt non-globular, extended structures that present large, highly specific surfaces for ligand binding. Here we discuss recent advances toward understanding the functional role of this unique modular architecture. We showcase specific examples of natural repeat proteins interacting with diverse ligands and also present examples of designed repeat protein–ligand interactions. PMID:18602006

Low-workfunction photocathodes based on acetylide compounds

DOEpatents

Terdik, Joseph Z; Spentzouris, Linda; Terry, Jr., Jeffrey H; Harkay, Katherine C; Nemeth, Karoly; Srajer, George

2014-05-20

A low-workfunction photocathode includes a photoemissive material employed as a coating on the photocathode. The photoemissive material includes A.sub.nMC.sub.2, where A is a first metal element, the first element is an alkali metal, an alkali-earth element or the element Al; n is an integer that is 0, 1, 2, 3 or 4; M is a second metal element, the second metal element is a transition metal or a metal stand-in; and C.sub.2 is the acetylide ion C.sub.2.sup.2-. The photoemissive material includes a crystalline structure or non-crystalline structure of rod-like or curvy 1-dimensional polymeric substructures with MC.sub.2 repeating units embedded in a matrix of A.

C9orf72 Nucleotide Repeat Structures Initiate Molecular Cascades of Disease

PubMed Central

Haeusler, Aaron R.; Donnelly, Christopher J.; Periz, Goran; Simko, Eric A.J.; Shaw, Patrick G.; Kim, Min-Sik; Maragakis, Nicholas J.; Troncoso, Juan C.; Pandey, Akhilesh; Sattler, Rita; Rothstein, Jeffrey D.; Wang, Jiou

2014-01-01

Summary A hexanucleotide repeat expansion (HRE), (GGGGCC)n, in C9orf72 is the most common genetic cause of the neurodegenerative diseases amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Here we identify a molecular mechanism by which structural polymorphism of the HRE leads to ALS/FTD pathology and defects. The HRE forms DNA and RNA G-quadruplexes with distinct structures and promotes RNA•DNA hybrids (R-loops). The structural polymorphism causes a repeat length-dependent accumulation of transcripts aborted in the HRE region. These transcribed repeats bind to ribonucleoproteins in a conformationdependent manner. Specifically, nucleolin (NCL), an essential nucleolar protein, preferentially binds the HRE G-quadruplex, and patient cells show evidence of nucleolar stress. Our results demonstrate that distinct C9orf72 HRE structural polymorphism at both DNA and RNA levels initiates molecular cascades leading to ALS/FTD pathologies, and provide the basis for a mechanistic model for repeat-associated neurodegenerative diseases. PMID:24598541

Structural studies of CNG repeats

PubMed Central

Kiliszek, Agnieszka; Rypniewski, Wojciech

2014-01-01

CNG repeats (where N denotes one of the four natural nucleotides) are abundant in the human genome. Their tendency to undergo expansion can lead to hereditary diseases known as TREDs (trinucleotide repeat expansion disorders). The toxic factor can be protein, if the abnormal gene is expressed, or the gene transcript, or both. The gene transcripts have attracted much attention in the biomedical community, but their molecular structures have only recently been investigated. Model RNA molecules comprising CNG repeats fold into long hairpins whose stems generally conform to an A-type helix, in which the non-canonical N-N pairs are flanked by C-G and G-C pairs. Each homobasic pair is accommodated in the helical context in a unique manner, with consequences for the local helical parameters, solvent structure, electrostatic potential and potential to interact with ligands. The detailed three-dimensional profiles of RNA CNG repeats can be used in screening of compound libraries for potential therapeutics and in structure-based drug design. Here is a brief survey of the CNG structures published to date. PMID:24939898

Two tandemly repeated telomere-associated sequences in Nicotiana plumbaginifolia.

PubMed

Chen, C M; Wang, C T; Wang, C J; Ho, C H; Kao, Y Y; Chen, C C

1997-12-01

Two tandemly repeated telomere-associated sequences, NP3R and NP4R, have been isolated from Nicotiana plumbaginifolia. The length of a repeating unit for NP3R and NP4R is 165 and 180 nucleotides respectively. The abundance of NP3R, NP4R and telomeric repeats is, respectively, 8.4 x 10(4), 6 x 10(3) and 1.5 x 10(6) copies per haploid genome of N. plumbaginifolia. Fluorescence in situ hybridization revealed that NP3R is located at the ends and/or in interstitial regions of all 10 chromosomes and NP4R on the terminal regions of three chromosomes in the haploid genome of N. plumbaginifolia. Sequence homology search revealed that not only are NP3R and NP4R homologous to HRS60 and GRS, respectively, two tandem repeats isolated from N. tabacum, but that NP3R and NP4R are also related to each other, suggesting that they originated from a common ancestral sequence. The role of these repeated sequences in chromosome healing is discussed based on the observation that two to three copies of a telomere-similar sequence were present in each repeating unit of NP3R and NP4R.

The Crystal Structure of TAL Effector PthXo1 Bound to Its DNA Target

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

Mak, Amanda Nga-Sze; Bradley, Philip; Cernadas, Raul A.

2012-02-10

DNA recognition by TAL effectors is mediated by tandem repeats, each 33 to 35 residues in length, that specify nucleotides via unique repeat-variable diresidues (RVDs). The crystal structure of PthXo1 bound to its DNA target was determined by high-throughput computational structure prediction and validated by heavy-atom derivatization. Each repeat forms a left-handed, two-helix bundle that presents an RVD-containing loop to the DNA. The repeats self-associate to form a right-handed superhelix wrapped around the DNA major groove. The first RVD residue forms a stabilizing contact with the protein backbone, while the second makes a base-specific contact to the DNA sense strand.more » Two degenerate amino-terminal repeats also interact with the DNA. Containing several RVDs and noncanonical associations, the structure illustrates the basis of TAL effector-DNA recognition.« less

Segmented and "equivalent" representation of the cable equation.

PubMed

Andrietti, F; Bernardini, G

1984-11-01

The linear cable theory has been applied to a modular structure consisting of n repeating units each composed of two subunits with different values of resistance and capacitance. For n going to infinity, i.e., for infinite cables, we have derived analytically the Laplace transform of the solution by making use of a difference method and we have inverted it by means of a numerical procedure. The results have been compared with those obtained by the direct application of the cable equation to a simplified nonmodular model with "equivalent" electrical parameters. The implication of our work in the analysis of the time and space course of the potential of real fibers has been discussed. In particular, we have shown that the simplified ("equivalent") model is a very good representation of the segmented model for the nodal regions of myelinated fibers in a steady situation and in every condition for muscle fibers. An approximate solution for the steady potential of myelinated fibers has been derived for both nodal and internodal regions. The applications of our work to other cases dealing with repeating structures, such as earthworm giant fibers, have been discussed and our results have been compared with other attempts to solve similar problems.

Structure and anticoagulant activity of a sulfated galactan from the red alga, Gelidium crinale. Is there a specific structural requirement for the anticoagulant action?

PubMed

Pereira, Maria G; Benevides, Norma M B; Melo, Marcia R S; Valente, Ana Paula; Melo, Fábio R; Mourão, Paulo A S

2005-09-05

Marine red algae are an abundant source of sulfated galactans with potent anticoagulant activity. However, the specific structural motifs that confer biological activity remain to be elucidated. We have now isolated and purified a sulfated galactan from the marine red alga, Gellidium crinale. The structure of this polysaccharide was determined using NMR spectroscopy. It is composed of the repeating structure -4-alpha-Galp-(1-->3)-beta-Galp1--> but with a variable sulfation pattern. Clearly 15% of the total alpha-units are 2,3-di-sulfated and another 55% are 2-sulfated. No evidence for the occurrence of 3,6-anhydro alpha-galactose units was observed in the NMR spectra. We also compared the anticoagulant activity of this sulfated galactan with a polysaccharide from the species, Botryocladia occidentalis, with a similar saccharide chain but with higher amounts of 2,3-di-sulfated alpha-units. The sulfated galactan from G. crinale has a lower anticoagulant activity on a clotting assay when compared with the polysaccharide from B. occidentalis. When tested in assays using specific proteases and coagulation inhibitors, these two galactans showed significant differences in their activity. They do not differ in thrombin inhibition mediated by antithrombin, but in assays where heparin cofactor II replaces antithrombin, the sulfated galactan from G. crinale requires a significantly higher concentration to achieve the same inhibitory effect as the polysaccharide from B. occidentalis. In contrast, when factor Xa instead of thrombin is used as the target protease, the sulfated galactan from G. crinale is a more potent anticoagulant. These observations suggest that the proportion and/or the distribution of 2,3-di-sulfated alpha-units along the galactan chain may be a critical structural motif to promote the interaction of the protease with specific protease and coagulation inhibitors.

Natively Unfolded FG Repeats Stabilize the Structure of the Nuclear Pore Complex.

PubMed

Onischenko, Evgeny; Tang, Jeffrey H; Andersen, Kasper R; Knockenhauer, Kevin E; Vallotton, Pascal; Derrer, Carina P; Kralt, Annemarie; Mugler, Christopher F; Chan, Leon Y; Schwartz, Thomas U; Weis, Karsten

2017-11-02

Nuclear pore complexes (NPCs) are ∼100 MDa transport channels assembled from multiple copies of ∼30 nucleoporins (Nups). One-third of these Nups contain phenylalanine-glycine (FG)-rich repeats, forming a diffusion barrier, which is selectively permeable for nuclear transport receptors that interact with these repeats. Here, we identify an additional function of FG repeats in the structure and biogenesis of the yeast NPC. We demonstrate that GLFG-containing FG repeats directly bind to multiple scaffold Nups in vitro and act as NPC-targeting determinants in vivo. Furthermore, we show that the GLFG repeats of Nup116 function in a redundant manner with Nup188, a nonessential scaffold Nup, to stabilize critical interactions within the NPC scaffold needed for late steps of NPC assembly. Our results reveal a previously unanticipated structural role for natively unfolded GLFG repeats as Velcro to link NPC subcomplexes and thus add a new layer of connections to current models of the NPC architecture. Copyright © 2017 Elsevier Inc. All rights reserved.

The Structure of Neurexin 1[alpha] Reveals Features Promoting a Role as Synaptic Organizer

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

Chen, Fang; Venugopal, Vandavasi; Murray, Beverly

{alpha}-Neurexins are essential synaptic adhesion molecules implicated in autism spectrum disorder and schizophrenia. The {alpha}-neurexin extracellular domain consists of six LNS domains interspersed by three EGF-like repeats and interacts with many different proteins in the synaptic cleft. To understand how {alpha}-neurexins might function as synaptic organizers, we solved the structure of the neurexin 1{alpha} extracellular domain (n1{alpha}) to 2.65 {angstrom}. The L-shaped molecule can be divided into a flexible repeat I (LNS1-EGF-A-LNS2), a rigid horseshoe-shaped repeat II (LNS3-EGF-B-LNS4) with structural similarity to so-called reelin repeats, and an extended repeat III (LNS5-EGF-B-LNS6) with controlled flexibility. A 2.95 {angstrom} structure of n1{alpha}more » carrying splice insert SS3 in LNS4 reveals that SS3 protrudes as a loop and does not alter the rigid arrangement of repeat II. The global architecture imposed by conserved structural features enables {alpha}-neurexins to recruit and organize proteins in distinct and variable ways, influenced by splicing, thereby promoting synaptic function.« less

Not all predicted CRISPR-Cas systems are equal: isolated cas genes and classes of CRISPR like elements.

PubMed

Zhang, Quan; Ye, Yuzhen

2017-02-06

The CRISPR-Cas systems in prokaryotes are RNA-guided immune systems that target and deactivate foreign nucleic acids. A typical CRISPR-Cas system consists of a CRISPR array of repeat and spacer units, and a locus of cas genes. The CRISPR and the cas locus are often located next to each other in the genomes. However, there is no quantitative estimate of the co-location. In addition, ad-hoc studies have shown that some non-CRISPR genomic elements contain repeat-spacer-like structures and are mistaken as CRISPRs. Using available genome sequences, we observed that a significant number of genomes have isolated cas loci and/or CRISPRs. We found that 11%, 22% and 28% of the type I, II and III cas loci are isolated (without CRISPRs in the same genomes at all or with CRISPRs distant in the genomes), respectively. We identified a large number of genomic elements that superficially reassemble CRISPRs but don't contain diverse spacers and have no companion cas genes. We called these elements false-CRISPRs and further classified them into groups, including tandem repeats and Staphylococcus aureus repeat (STAR)-like elements. This is the first systematic study to collect and characterize false-CRISPR elements. We demonstrated that false-CRISPRs could be used to reduce the false annotation of CRISPRs, therefore showing them to be useful for improving the annotation of CRISPR-Cas systems.

Expression, crystallization and preliminary crystallographic analysis of RNA-binding protein Hfq (YmaH) from Bacillus subtilis in complex with an RNA aptamer.

PubMed

Baba, Seiki; Someya, Tatsuhiko; Kawai, Gota; Nakamura, Kouji; Kumasaka, Takashi

2010-05-01

The Hfq protein is a hexameric RNA-binding protein which regulates gene expression by binding to RNA under the influence of diverse environmental stresses. Its ring structure binds various types of RNA, including mRNA and sRNA. RNA-bound structures of Hfq from Escherichia coli and Staphylococcus aureus have been revealed to have poly(A) RNA at the distal site and U-rich RNA at the proximal site, respectively. Here, crystals of a complex of the Bacillus subtilis Hfq protein with an A/G-repeat 7-mer RNA (Hfq-RNA) that were prepared using the hanging-drop vapour-diffusion technique are reported. The type 1 Hfq-RNA crystals belonged to space group I422, with unit-cell parameters a = b = 123.70, c = 119.13 A, while the type 2 Hfq-RNA crystals belonged to space group F222, with unit-cell parameters a = 91.92, b = 92.50, c = 114.92 A. Diffraction data were collected to a resolution of 2.20 A from both crystal forms. The hexameric structure of the Hfq protein was clearly shown by self-rotation analysis.

3-D phononic crystals with ultra-wide band gaps

PubMed Central

Lu, Yan; Yang, Yang; Guest, James K.; Srivastava, Ankit

2017-01-01

In this paper gradient based topology optimization (TO) is used to discover 3-D phononic structures that exhibit ultra-wide normalized all-angle all-mode band gaps. The challenging computational task of repeated 3-D phononic band-structure evaluations is accomplished by a combination of a fast mixed variational eigenvalue solver and distributed Graphic Processing Unit (GPU) parallel computations. The TO algorithm utilizes the material distribution-based approach and a gradient-based optimizer. The design sensitivity for the mixed variational eigenvalue problem is derived using the adjoint method and is implemented through highly efficient vectorization techniques. We present optimized results for two-material simple cubic (SC), body centered cubic (BCC), and face centered cubic (FCC) crystal structures and show that in each of these cases different initial designs converge to single inclusion network topologies within their corresponding primitive cells. The optimized results show that large phononic stop bands for bulk wave propagation can be achieved at lower than close packed spherical configurations leading to lighter unit cells. For tungsten carbide - epoxy crystals we identify all angle all mode normalized stop bands exceeding 100%, which is larger than what is possible with only spherical inclusions. PMID:28233812

3-D phononic crystals with ultra-wide band gaps.

PubMed

Lu, Yan; Yang, Yang; Guest, James K; Srivastava, Ankit

2017-02-24

In this paper gradient based topology optimization (TO) is used to discover 3-D phononic structures that exhibit ultra-wide normalized all-angle all-mode band gaps. The challenging computational task of repeated 3-D phononic band-structure evaluations is accomplished by a combination of a fast mixed variational eigenvalue solver and distributed Graphic Processing Unit (GPU) parallel computations. The TO algorithm utilizes the material distribution-based approach and a gradient-based optimizer. The design sensitivity for the mixed variational eigenvalue problem is derived using the adjoint method and is implemented through highly efficient vectorization techniques. We present optimized results for two-material simple cubic (SC), body centered cubic (BCC), and face centered cubic (FCC) crystal structures and show that in each of these cases different initial designs converge to single inclusion network topologies within their corresponding primitive cells. The optimized results show that large phononic stop bands for bulk wave propagation can be achieved at lower than close packed spherical configurations leading to lighter unit cells. For tungsten carbide - epoxy crystals we identify all angle all mode normalized stop bands exceeding 100%, which is larger than what is possible with only spherical inclusions.

The Nature of Hololignin

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

Meng, Xianzhi; Pu, Yunqiao; Sannigrahi, Poulomi

Acid chlorite delignification is frequently used to obtain a mixture of cellulose and hemicellulose known as holocellulose from biomass. While a majority of lignin is removed after holocellulose pulping, there appears to be a minor fraction of lignin that is more resistant to acid chlorite treatment and remains in the holocellulose even after repeated delignification treatment. This type of lignin, defined as hololignin, has not been characterized, is likely to contribute to biomass recalcitrance and is clearly of fundamental interest to understand its structural characteristics. In this study, hololignin isolated from poplar holocellulose was characterized with a wide array ofmore » techniques including GPC, quantitative 13C, DEPT-135, HSQC, and 31P NMR. The results were then compared to those from milled wood lignin (MWL), the representative native lignin isolated from poplar. NMR analysis demonstrated a depletion of cinnamyl aldehyde, acetyl group, and decrease of p-hydroxybenzoate structural units in hololignin. An enrichment of condensed structures in hololignin was observed. Hololignin also had a significantly lower molecular weight than MWL. Finally, hololignin is relatively enriched in guaiacyl units and has a lower S/G ratio, lower β-O-4 ether linkages, fewer aliphatic and phenolic hydroxyl groups, and more carboxylic acid groups than MWL.« less

The Nature of Hololignin

DOE PAGES

Meng, Xianzhi; Pu, Yunqiao; Sannigrahi, Poulomi; ...

2017-11-07

Acid chlorite delignification is frequently used to obtain a mixture of cellulose and hemicellulose known as holocellulose from biomass. While a majority of lignin is removed after holocellulose pulping, there appears to be a minor fraction of lignin that is more resistant to acid chlorite treatment and remains in the holocellulose even after repeated delignification treatment. This type of lignin, defined as hololignin, has not been characterized, is likely to contribute to biomass recalcitrance and is clearly of fundamental interest to understand its structural characteristics. In this study, hololignin isolated from poplar holocellulose was characterized with a wide array ofmore » techniques including GPC, quantitative 13C, DEPT-135, HSQC, and 31P NMR. The results were then compared to those from milled wood lignin (MWL), the representative native lignin isolated from poplar. NMR analysis demonstrated a depletion of cinnamyl aldehyde, acetyl group, and decrease of p-hydroxybenzoate structural units in hololignin. An enrichment of condensed structures in hololignin was observed. Hololignin also had a significantly lower molecular weight than MWL. Finally, hololignin is relatively enriched in guaiacyl units and has a lower S/G ratio, lower β-O-4 ether linkages, fewer aliphatic and phenolic hydroxyl groups, and more carboxylic acid groups than MWL.« less

The minisatellite of the GPI/AMF/NLK/MF gene: interspecies conservation and transcriptional activity.

PubMed

Williams, R R; Hassan-Walker, A F; Lavender, F L; Morgan, M; Faik, P; Ragoussis, J

2001-05-16

Minisatellites are tandemly repeated DNA sequences found throughout the genomes of all eukaryotes. They are regions often prone to instability and hence hypervariability; thus repeat unit sequence is generally not conserved beyond closely related species. We have studied the minisatellite located in intron 9 of the human glucose phosphate isomerase (GPI) gene (also known as neuroleukin, autocrine motility factor, maturation and differentiation factor) and have found, by Zoo blotting coupled with PCR amplification and DNA sequencing, that similar repeat units are present in seven other species of mammal. There is also evidence for the presence of the minisatellite in chicken. The repeat unit does not appear to be present at any other locus in these genomes. Minisatellite DNA has been reported to be involved in recombination activity, control of gene expression of nearby gene(s) (both transcriptional and translational), whilst others form protein coding regions. The high level of conservation exhibited by the GPI minisatellite, coupled with the unique location, strongly suggests a functional role. Our results from transient and stable transfections using luciferase reporter constructs have shown that the GPI minisatellite region can act to increase transcription from the SV40 promoter, CMV promoter and the human GPI promoter.

2-D Structure of the A Region of Xist RNA and Its Implication for PRC2 Association

PubMed Central

Maenner, Sylvain; Blaud, Magali; Fouillen, Laetitia; Savoye, Anne; Marchand, Virginie; Dubois, Agnès; Sanglier-Cianférani, Sarah; Van Dorsselaer, Alain; Clerc, Philippe; Avner, Philip; Visvikis, Athanase; Branlant, Christiane

2010-01-01

In placental mammals, inactivation of one of the X chromosomes in female cells ensures sex chromosome dosage compensation. The 17 kb non-coding Xist RNA is crucial to this process and accumulates on the future inactive X chromosome. The most conserved Xist RNA region, the A region, contains eight or nine repeats separated by U-rich spacers. It is implicated in the recruitment of late inactivated X genes to the silencing compartment and likely in the recruitment of complex PRC2. Little is known about the structure of the A region and more generally about Xist RNA structure. Knowledge of its structure is restricted to an NMR study of a single A repeat element. Our study is the first experimental analysis of the structure of the entire A region in solution. By the use of chemical and enzymatic probes and FRET experiments, using oligonucleotides carrying fluorescent dyes, we resolved problems linked to sequence redundancies and established a 2-D structure for the A region that contains two long stem-loop structures each including four repeats. Interactions formed between repeats and between repeats and spacers stabilize these structures. Conservation of the spacer terminal sequences allows formation of such structures in all sequenced Xist RNAs. By combination of RNP affinity chromatography, immunoprecipitation assays, mass spectrometry, and Western blot analysis, we demonstrate that the A region can associate with components of the PRC2 complex in mouse ES cell nuclear extracts. Whilst a single four-repeat motif is able to associate with components of this complex, recruitment of Suz12 is clearly more efficient when the entire A region is present. Our data with their emphasis on the importance of inter-repeat pairing change fundamentally our conception of the 2-D structure of the A region of Xist RNA and support its possible implication in recruitment of the PRC2 complex. PMID:20052282

DNA Replication Dynamics of the GGGGCC Repeat of the C9orf72 Gene.

PubMed

Thys, Ryan Griffin; Wang, Yuh-Hwa

2015-11-27

DNA has the ability to form a variety of secondary structures in addition to the normal B-form DNA, including hairpins and quadruplexes. These structures are implicated in a number of neurological diseases and cancer. Expansion of a GGGGCC repeat located at C9orf72 is associated with familial amyotrophic lateral sclerosis and frontotemporal dementia. This repeat expands from two to 24 copies in normal individuals to several hundreds or thousands of repeats in individuals with the disease. Biochemical studies have demonstrated that as little as four repeats have the ability to form a stable DNA secondary structure known as a G-quadruplex. Quadruplex structures have the ability to disrupt normal DNA processes such as DNA replication and transcription. Here we examine the role of GGGGCC repeat length and orientation on DNA replication using an SV40 replication system in human cells. Replication through GGGGCC repeats leads to a decrease in overall replication efficiency and an increase in instability in a length-dependent manner. Both repeat expansions and contractions are observed, and replication orientation is found to influence the propensity for expansions or contractions. The presence of replication stress, such as low-dose aphidicolin, diminishes replication efficiency but has no effect on instability. Two-dimensional gel electrophoresis analysis demonstrates a replication stall with as few as 20 GGGGCC repeats. These results suggest that replication of the GGGGCC repeat at C9orf72 is perturbed by the presence of expanded repeats, which has the potential to result in further expansion, leading to disease. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Clamping characteristics study on different types of clamping unit

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

Jiao, Zhiwei; Liu, Haichao; Xie, Pengcheng

2015-05-22

Plastic products are becoming more and more widely used in aerospace, IT, digital electronics and many other fields. With the development of technology, the requirement of product precision is getting higher and higher. However, type and working performance of clamping unit play a decisive role in product precision. Clamping characteristics of different types of clamping unit are discussed in this article, which use finite element numerical analysis method through the software ABAQUS to study the clamping uniformity, and detect the clamping force repeatability precision. The result shows that compared with toggled three-platen clamping unit, clamping characteristics of internal circulation two-platenmore » clamping unit are better, for instance, its mold cavity deformation and force that bars and mold parting surface suffered are more uniform, and its clamping uniformity and repeatability precision is also better.« less

An Evolutionarily Conserved Family of Virion Tail Needles Related to Bacteriophage P22 gp26: Correlation between Structural Stability and Length of the -Helical Trimeric Coiled Coil

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

Bhardwaj, A.; Walker-Kopp, N; Casjens, S

2009-01-01

Bacteriophages of the Podoviridae family use short noncontractile tails to inject their genetic material into Gram-negative bacteria. In phage P22, the tail contains a thin needle, encoded by the phage gene 26, which is essential both for stabilization and for ejection of the packaged viral genome. Bioinformatic analysis of the N-terminal domain of gp26 (residues 1-60) led us to identify a family of genes encoding putative homologues of the tail needle gp26. To validate this idea experimentally and to explore their diversity, we cloned the gp26-like gene from phages HK620, Sf6 and HS1, and characterized these gene products in solution.more » All gp26-like factors contain an elongated {alpha}-helical coiled-coil core consisting of repeating, adjacent trimerization heptads and form trimeric fibers with length ranging between about 240 to 300 {angstrom}. gp26 tail needles display a high level of structural stability in solution, with Tm (temperature of melting) between 85 and 95 C. To determine how the structural stability of these phage fibers correlates with the length of the {alpha}-helical core, we investigated the effect of insertions and deletions in the helical core. In the P22 tail needle, we identified an 85-residue-long helical domain, termed MiCRU (minimal coiled-coil repeat unit), that can be inserted in-frame inside the gp26 helical core, preserving the straight morphology of the fiber. Likewise, we were able to remove three quarters of the helical core of the HS1 tail needle, minimally decreasing the stability of the fiber. We conclude that in the gp26 family of tail needles, structural stability increases nonlinearly with the length of the {alpha}-helical core. Thus, the overall stability of these bacteriophage fibers is not solely dependent on the number of trimerization repeats in the {alpha}-helical core.« less

Top surface blade residues and the central channel water molecules are conserved in every repeat of the integrin-like β-propeller structures.

PubMed

Denesyuk, Alexander; Denessiouk, Konstantin; Johnson, Mark S

2018-02-01

An integrin-like β-propeller domain contains seven repeats of a four-stranded antiparallel β-sheet motif (blades). Previously we described a 3D structural motif within each blade of the integrin-type β-propeller. Here, we show unique structural links that join different blades of the β-propeller structure, which together with the structural motif for a single blade are repeated in a β-propeller to provide the functional top face of the barrel, found to be involved in protein-protein interactions and substrate recognition. We compare functional top face diagrams of the integrin-type β-propeller domain and two non-integrin type β-propeller domains of virginiamycin B lyase and WD Repeat-Containing Protein 5. Copyright © 2017 Elsevier Inc. All rights reserved.

Structural analysis and anticoagulant activities of two sulfated polysaccharides from the sea cucumber Holothuria coluber.

PubMed

Yang, Wenjiao; Cai, Ying; Yin, Ronghua; Lin, Lisha; Li, Zhongkun; Wu, Mingyi; Zhao, Jinhua

2018-05-01

Sulfated polysaccharides such as fucosylated glycosaminoglycan and fucan sulfate from echinoderm possess complex chemical structure and various biological activities. The two sulfated polysaccharides were purified from the low-value sea cucumber Holothuria coluber. Their physicochemical properties and chemical structures were analyzed and characterized by chemical and instrumental methods. Structural analysis clarified that the sea cucumber fucosylated glycosaminoglycan contains a chondroitin sulfate-like backbone and fucosyl branches with four various sulfation patterns. The fucan sulfate with molecular weight of 64.6 kDa comprises a central core of regular α(1 → 4)-linked tetrasaccharide repeating units, each of which is linked by a 4-O-sulfated fucose residue. Anticoagulant assays indicated that these sulfated polysaccharides possessed strong APTT prolonging activities and intrinsic factor Xase inhibitory activities, both of which decreased with the reduction of their molecular weights. Our results expand knowledge on the structural types of sulfated polysaccharides from sea cucumbers and further illustrate their functionality. Copyright © 2018. Published by Elsevier B.V.

Low resolution crystal structure of Arenicola erythrocruorin: influence of coiled coils on the architecture of a megadalton respiratory protein.

PubMed

Royer, William E; Omartian, Michael N; Knapp, James E

2007-01-05

Annelid erythrocruorins are extracellular respiratory complexes assembled from 180 subunits into hexagonal bilayers. Cryo-electron microscopic experiments have identified two different architectural classes. In one, designated type I, the vertices of the two hexagonal layers are partially staggered, with one hexagonal layer rotated by about 16 degrees relative to the other layer, whereas in the other class, termed type II, the vertices are essentially eclipsed. We report here the first crystal structure of a type II erythrocruorin, that from Arenicola marina, at 6.2 A resolution. The structure reveals the presence of long continuous triple-stranded coiled-coil "spokes" projecting towards the molecular center from each one-twelfth unit; interdigitation of these spokes provides the only contacts between the two hexagonal layers of the complex. This arrangement contrasts with that of a type I erythrocruorin from Lumbricus terrestris in which the spokes are broken into two triple-stranded coiled coils with a disjointed connection. The disjointed connection allows formation of a more compact structure in the type I architecture, with the two hexagonal layers closer together and additional extensive contacts between the layers. Comparison of sequences of the coiled-coil regions of various linker subunits shows that the linker subunits from type II erythrocruorins possess continuous heptad repeats, whereas a sequence gap places these repeats out of register in the type I linker subunits, consistent with a disjointed coiled-coil arrangement.

The Structure of Plant Cell Walls

PubMed Central

Wilder, Barry M.; Albersheim, Peter

1973-01-01

The molecular structure and chemical properties of the hemicellulose present in the isolated cell walls of suspension cultures of sycamore (Acer pseudoplatanus) cells has recently been described by Bauer et al. (Plant Physiol. 51: 174-187). The hemicellulose of the sycamore primary cell wall is a xyloglucan. This polymer functions as an important cross-link in the structure of the cell wall; the xyloglucan is hydrogen-bonded to cellulose and covalently attached to the pectic polymers. The present paper describes the structure of a xyloglucan present in the walls and in the extracellular medium of suspension-cultured Red Kidney bean (Phaseolus vulgaris) cells and compares the structure of the bean xyloglucan with the structure of the sycamore xyloglucan. Although some minor differences were found, the basic structure of the xyloglucans in the cell walls of these distantly related species is the same. The structure is based on a repeating heptasaccharide unit which consists of four residues of β-1, 4-linked glucose and three residues of terminal xylose linked to the 6 position of three of the glucosyl residues. PMID:16658434

Single Amino Acid Repeats in the Proteome World: Structural, Functional, and Evolutionary Insights

PubMed Central

Kumar, Amitha Sampath; Sowpati, Divya Tej; Mishra, Rakesh K.

2016-01-01

Microsatellites or simple sequence repeats (SSR) are abundant, highly diverse stretches of short DNA repeats present in all genomes. Tandem mono/tri/hexanucleotide repeats in the coding regions contribute to single amino acids repeats (SAARs) in the proteome. While SSRs in the coding region always result in amino acid repeats, a majority of SAARs arise due to a combination of various codons representing the same amino acid and not as a consequence of SSR events. Certain amino acids are abundant in repeat regions indicating a positive selection pressure behind the accumulation of SAARs. By analysing 22 proteomes including the human proteome, we explored the functional and structural relationship of amino acid repeats in an evolutionary context. Only ~15% of repeats are present in any known functional domain, while ~74% of repeats are present in the disordered regions, suggesting that SAARs add to the functionality of proteins by providing flexibility, stability and act as linker elements between domains. Comparison of SAAR containing proteins across species reveals that while shorter repeats are conserved among orthologs, proteins with longer repeats, >15 amino acids, are unique to the respective organism. Lysine repeats are well conserved among orthologs with respect to their length and number of occurrences in a protein. Other amino acids such as glutamic acid, proline, serine and alanine repeats are generally conserved among the orthologs with varying repeat lengths. These findings suggest that SAARs have accumulated in the proteome under positive selection pressure and that they provide flexibility for optimal folding of functional/structural domains of proteins. The insights gained from our observations can help in effective designing and engineering of proteins with novel features. PMID:27893794

A Legionella pneumophila collagen-like protein encoded by a gene with a variable number of tandem repeats is involved in the adherence and invasion of host cells.

PubMed

Vandersmissen, Liesbeth; De Buck, Emmy; Saels, Veerle; Coil, David A; Anné, Jozef

2010-05-01

Legionella pneumophila is a Gram-negative, facultative intracellular pathogen and the causative agent of Legionnaires' disease, a severe pneumonia in humans. Analysis of the Legionella sequenced genomes revealed a gene with a variable number of tandem repeats (VNTRs), whose number varies between strains. We examined the strain distribution of this gene among a collection of 108 clinical, environmental and hot spring serotype I strains. Twelve variants were identified, but no correlation was observed between the number of repeat units and clinical and environmental strains. The encoded protein contains the C-terminal consensus motif of outer membrane proteins and has a large region of collagen-like repeats that is encoded by the VNTR region. We have therefore annotated this protein Lcl for Legionella collagen-like protein. Lcl was shown to contribute to the adherence and invasion of host cells and it was demonstrated that the number of repeat units present in lcl had an influence on these adhesion characteristics.

Solution properties of the archaeal CRISPR DNA repeat-binding homeodomain protein Cbp2

PubMed Central

Kenchappa, Chandra S.; Heidarsson, Pétur O.; Kragelund, Birthe B.; Garrett, Roger A.; Poulsen, Flemming M.

2013-01-01

Clustered regularly interspaced short palindromic repeats (CRISPR) form the basis of diverse adaptive immune systems directed primarily against invading genetic elements of archaea and bacteria. Cbp1 of the crenarchaeal thermoacidophilic order Sulfolobales, carrying three imperfect repeats, binds specifically to CRISPR DNA repeats and has been implicated in facilitating production of long transcripts from CRISPR loci. Here, a second related class of CRISPR DNA repeat-binding protein, denoted Cbp2, is characterized that contains two imperfect repeats and is found amongst members of the crenarchaeal thermoneutrophilic order Desulfurococcales. DNA repeat-binding properties of the Hyperthermus butylicus protein Cbp2Hb were characterized and its three-dimensional structure was determined by NMR spectroscopy. The two repeats generate helix-turn-helix structures separated by a basic linker that is implicated in facilitating high affinity DNA binding of Cbp2 by tethering the two domains. Structural studies on mutant proteins provide support for Cys7 and Cys28 enhancing high thermal stability of Cbp2Hb through disulphide bridge formation. Consistent with their proposed CRISPR transcriptional regulatory role, Cbp2Hb and, by inference, other Cbp1 and Cbp2 proteins are closely related in structure to homeodomain proteins with linked helix-turn-helix (HTH) domains, in particular the paired domain Pax and Myb family proteins that are involved in eukaryal transcriptional regulation. PMID:23325851

Continuous Removal of Coal-Gasification Residue

NASA Technical Reports Server (NTRS)

Collins, Earl R., Jr.; Suitor, J.; Dubis, D.

1986-01-01

Continuous-flow hopper processes solid residue from coal gasification, converting it from ashes, cinders, and clinkers to particles size of sand granules. Unit does not require repeated depressurization of lockhopper to admit and release materials. Therefore consumes less energy. Because unit has no airlock valves opened and closed repeatedly on hot, abrasive particles, subjected to lesser wear. Coal-gasification residue flows slowly through pressure-letdown device. Material enters and leaves continuously. Cleanout door on each pressure-letdown chamber allows access for maintenance and emergencies.

Highly sensitive detection of individual HEAT and ARM repeats with HHpred and COACH.

PubMed

Kippert, Fred; Gerloff, Dietlind L

2009-09-24

HEAT and ARM repeats occur in a large number of eukaryotic proteins. As these repeats are often highly diverged, the prediction of HEAT or ARM domains can be challenging. Except for the most clear-cut cases, identification at the individual repeat level is indispensable, in particular for determining domain boundaries. However, methods using single sequence queries do not have the sensitivity required to deal with more divergent repeats and, when applied to proteins with known structures, in some cases failed to detect a single repeat. Testing algorithms which use multiple sequence alignments as queries, we found two of them, HHpred and COACH, to detect HEAT and ARM repeats with greatly enhanced sensitivity. Calibration against experimentally determined structures suggests the use of three score classes with increasing confidence in the prediction, and prediction thresholds for each method. When we applied a new protocol using both HHpred and COACH to these structures, it detected 82% of HEAT repeats and 90% of ARM repeats, with the minimum for a given protein of 57% for HEAT repeats and 60% for ARM repeats. Application to bona fide HEAT and ARM proteins or domains indicated that similar numbers can be expected for the full complement of HEAT/ARM proteins. A systematic screen of the Protein Data Bank for false positive hits revealed their number to be low, in particular for ARM repeats. Double false positive hits for a given protein were rare for HEAT and not at all observed for ARM repeats. In combination with fold prediction and consistency checking (multiple sequence alignments, secondary structure prediction, and position analysis), repeat prediction with the new HHpred/COACH protocol dramatically improves prediction in the twilight zone of fold prediction methods, as well as the delineation of HEAT/ARM domain boundaries. A protocol is presented for the identification of individual HEAT or ARM repeats which is straightforward to implement. It provides high sensitivity at a low false positive rate and will therefore greatly enhance the accuracy of predictions of HEAT and ARM domains.

Highly Sensitive Detection of Individual HEAT and ARM Repeats with HHpred and COACH

PubMed Central

Kippert, Fred; Gerloff, Dietlind L.

2009-01-01

Background HEAT and ARM repeats occur in a large number of eukaryotic proteins. As these repeats are often highly diverged, the prediction of HEAT or ARM domains can be challenging. Except for the most clear-cut cases, identification at the individual repeat level is indispensable, in particular for determining domain boundaries. However, methods using single sequence queries do not have the sensitivity required to deal with more divergent repeats and, when applied to proteins with known structures, in some cases failed to detect a single repeat. Methodology and Principal Findings Testing algorithms which use multiple sequence alignments as queries, we found two of them, HHpred and COACH, to detect HEAT and ARM repeats with greatly enhanced sensitivity. Calibration against experimentally determined structures suggests the use of three score classes with increasing confidence in the prediction, and prediction thresholds for each method. When we applied a new protocol using both HHpred and COACH to these structures, it detected 82% of HEAT repeats and 90% of ARM repeats, with the minimum for a given protein of 57% for HEAT repeats and 60% for ARM repeats. Application to bona fide HEAT and ARM proteins or domains indicated that similar numbers can be expected for the full complement of HEAT/ARM proteins. A systematic screen of the Protein Data Bank for false positive hits revealed their number to be low, in particular for ARM repeats. Double false positive hits for a given protein were rare for HEAT and not at all observed for ARM repeats. In combination with fold prediction and consistency checking (multiple sequence alignments, secondary structure prediction, and position analysis), repeat prediction with the new HHpred/COACH protocol dramatically improves prediction in the twilight zone of fold prediction methods, as well as the delineation of HEAT/ARM domain boundaries. Significance A protocol is presented for the identification of individual HEAT or ARM repeats which is straightforward to implement. It provides high sensitivity at a low false positive rate and will therefore greatly enhance the accuracy of predictions of HEAT and ARM domains. PMID:19777061

Telomere Organization in the Ligninolytic Basidiomycete Pleurotus ostreatus▿ †

PubMed Central

Pérez, Gúmer; Pangilinan, Jasmyn; Pisabarro, Antonio G.; Ramírez, Lucía

2009-01-01

Telomeres are structural and functional chromosome regions that are essential for the cell cycle to proceed normally. They are, however, difficult to map genetically and to identify in genome-wide sequence programs because of their structure and repetitive nature. We studied the telomeric and subtelomeric organization in the basidiomycete Pleurotus ostreatus using a combination of molecular and bioinformatics tools that permitted us to determine 19 out of the 22 telomeres expected in this fungus. The telomeric repeating unit in P. ostreatus is TTAGGG, and the numbers of repetitions of this unit range between 25 and 150. The mapping of the telomere restriction fragments to linkage groups 6 and 7 revealed polymorphisms compatible with those observed by pulsed field gel electrophoresis separation of the corresponding chromosomes. The subtelomeric regions in Pleurotus contain genes similar to those described in other eukaryotic systems. The presence of a cluster of laccase genes in chromosome 6 and a bipartite structure containing a Het-related protein and an alcohol dehydrogenase are especially relevant; this bipartite structure is characteristic of the Pezizomycotina fungi Neurospora crassa and Aspergillus terreus. As far as we know, this is the first report describing the presence of such structures in basidiomycetes and the location of a laccase gene cluster in the subtelomeric region, where, among others, species-specific genes allowing the organism to adapt rapidly to the environment usually map. PMID:19114509

Nano-optical conveyor belt, part I: Theory.

PubMed

Hansen, Paul; Zheng, Yuxin; Ryan, Jason; Hesselink, Lambertus

2014-06-11

We propose a method for peristaltic transport of nanoparticles using the optical force field over a nanostructured surface. Nanostructures may be designed to produce strong near-field hot spots when illuminated. The hot spots function as optical traps, separately addressable by their resonant wavelengths and polarizations. By activating closely packed traps sequentially, nanoparticles may be handed off between adjacent traps in a peristaltic fashion. A linear repeating structure of three separately addressable traps forms a "nano-optical conveyor belt"; a unit cell with four separately addressable traps permits controlled peristaltic transport in the plane. Using specifically designed activation sequences allows particle sorting.

Algorithm to find distant repeats in a single protein sequence

PubMed Central

Banerjee, Nirjhar; Sarani, Rangarajan; Ranjani, Chellamuthu Vasuki; Sowmiya, Govindaraj; Michael, Daliah; Balakrishnan, Narayanasamy; Sekar, Kanagaraj

2008-01-01

Distant repeats in protein sequence play an important role in various aspects of protein analysis. A keen analysis of the distant repeats would enable to establish a firm relation of the repeats with respect to their function and three-dimensional structure during the evolutionary process. Further, it enlightens the diversity of duplication during the evolution. To this end, an algorithm has been developed to find all distant repeats in a protein sequence. The scores from Point Accepted Mutation (PAM) matrix has been deployed for the identification of amino acid substitutions while detecting the distant repeats. Due to the biological importance of distant repeats, the proposed algorithm will be of importance to structural biologists, molecular biologists, biochemists and researchers involved in phylogenetic and evolutionary studies. PMID:19052663

Structural studies of CNG repeats.

PubMed

Kiliszek, Agnieszka; Rypniewski, Wojciech

2014-07-01

CNG repeats (where N denotes one of the four natural nucleotides) are abundant in the human genome. Their tendency to undergo expansion can lead to hereditary diseases known as TREDs (trinucleotide repeat expansion disorders). The toxic factor can be protein, if the abnormal gene is expressed, or the gene transcript, or both. The gene transcripts have attracted much attention in the biomedical community, but their molecular structures have only recently been investigated. Model RNA molecules comprising CNG repeats fold into long hairpins whose stems generally conform to an A-type helix, in which the non-canonical N-N pairs are flanked by C-G and G-C pairs. Each homobasic pair is accommodated in the helical context in a unique manner, with consequences for the local helical parameters, solvent structure, electrostatic potential and potential to interact with ligands. The detailed three-dimensional profiles of RNA CNG repeats can be used in screening of compound libraries for potential therapeutics and in structure-based drug design. Here is a brief survey of the CNG structures published to date. © Published by Oxford University Press on behalf of Nucleic Acids Research.

Hollow cathode heater development for the Space Station plasma contactor

NASA Technical Reports Server (NTRS)

Soulas, George C.

1993-01-01

A hollow cathode-based plasma contactor has been selected for use on the Space Station. During the operation of the plasma contactor, the hollow cathode heater will endure approximately 12000 thermal cycles. Since a hollow cathode heater failure would result in a plasma contactor failure, a hollow cathode heater development program was established to produce a reliable heater design. The development program includes the heater design, process documents for both heater fabrication and assembly, and heater testing. The heater design was a modification of a sheathed ion thruster cathode heater. Three heaters have been tested to date using direct current power supplies. Performance testing was conducted to determine input current and power requirements for achieving activation and ignition temperatures, single unit operational repeatability, and unit-to-unit operational repeatability. Comparisons of performance testing data at the ignition input current level for the three heaters show the unit-to-unit repeatability of input power and tube temperature near the cathode tip to be within 3.5 W and 44 degrees C, respectively. Cyclic testing was then conducted to evaluate reliability under thermal cycling. The first heater, although damaged during assembly, completed 5985 ignition cycles before failing. Two additional heaters were subsequently fabricated and have completed 3178 cycles to date in an on-going test.

Modeling cortical circuits.

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

Rohrer, Brandon Robinson; Rothganger, Fredrick H.; Verzi, Stephen J.

2010-09-01

The neocortex is perhaps the highest region of the human brain, where audio and visual perception takes place along with many important cognitive functions. An important research goal is to describe the mechanisms implemented by the neocortex. There is an apparent regularity in the structure of the neocortex [Brodmann 1909, Mountcastle 1957] which may help simplify this task. The work reported here addresses the problem of how to describe the putative repeated units ('cortical circuits') in a manner that is easily understood and manipulated, with the long-term goal of developing a mathematical and algorithmic description of their function. The approachmore » is to reduce each algorithm to an enhanced perceptron-like structure and describe its computation using difference equations. We organize this algorithmic processing into larger structures based on physiological observations, and implement key modeling concepts in software which runs on parallel computing hardware.« less

A tale of two centromeres--diversity of structure but conservation of function in plants and animals.

PubMed

Birchler, James A; Gao, Zhi; Han, Fangpu

2009-02-01

The structural and functional aspects of two specific centromeres, one drawn from the animal kingdom (Drosophila) and the other from the plant kingdom (maize), are compared. Both cases illustrate an epigenetic component to centromere specification. The observations of neocentromeres in Drosophila and inactive centromeres in maize constitute one line of evidence for this hypothesis. Another common feature is the divisibility of centromere function with reduced stability as the size decreases. The systems differ in that Drosophila has no common sequence repeat at all centromeres, whereas maize has a 150-bp unit present in tandem arrays together with a centromere-specific transposon, centromere retrotransposon maize, present at all primary constrictions. Aspects of centromere structure known only from one or the other system might be common to both, namely, the presence of centromere RNAs in the kinetochore as found in maize and the organization of the centromeric histone 3 in tetrameric nucleosomes.

Structure and anticancer activity of sulfated O-polysaccharide from marine bacterium Cobetia litoralis KMM 3880(T).

PubMed

Kokoulin, Maxim S; Kuzmich, Alexandra S; Kalinovsky, Anatoly I; Tomshich, Svetlana V; Romanenko, Lyudmila A; Mikhailov, Valery V; Komandrova, Nadezhda A

2016-12-10

We presented the structure of the polysaccharide moiety and anticancer activity in vitro of the sulfated lipopolysaccharide isolated from the marine bacterium Cobetia litoralis KMM 3880(T). The structure of O-polysaccharide was investigated by chemical methods along with (1)H and (13)C NMR spectroscopy. The O-polysaccharide was built up of branched trisaccharide repeating units consist of D-glucose (D-Glcр), D-mannose (D-Manр) and sulfated 3-deoxy-d-manno-oct-2-ulosonic acid (Kdo5S): →7-β-Kdoр4Ac5S-(2→4)-[β-d-Glcp-(1→2)-]-β-d-Manр6Ac-1→. We demonstrated that the lipopolysaccharide and О-deacetylated O-polysaccharide from Cobetia litoralis KMM 3880(T) inhibited a colony formation of human melanoma SK-MEL-28 and colorectal carcinoma HTC-116 cells. Copyright © 2016 Elsevier Ltd. All rights reserved.

Multiple energetic injections in a strong spike-like solar burst

NASA Technical Reports Server (NTRS)

Kaufmann, P.; Correia, E.; Costa, J. E. R.; Dennis, B. R.; Hurford, G. H.; Brown, J. C.

1983-01-01

An intense and fast spike-like solar burst was built up of short time scale structures superimposed on an underlying gradual emission, the time evolution of which shows remarkable proportionality between hard X-ray and microwave fluxes. The finer time structure were best defined at mm-microwaves. At the peak of the event, the finer structures repeat every 30x60ms. The more slowly varying component with a time scale of about 1 second was identified in microwave hard X-rays throughout the burst duration. It is suggested that X-ray fluxes might also be proportional to the repetition rate of basic units of energy injection (quasi-quantized). The relevant parameters of one primary energy release site are estimated both in the case where hard X-rays are produced primarily by thick-target bremsstrahlung, and when they are purely thermal. The relation of this figure to global energy considerations is discussed.

Structural Characteristics of the Novel Polysaccharide FVPA1 from Winter Culinary-Medicinal Mushroom, Flammulina velutipes (Agaricomycetes), Capable of Enhancing Natural Killer Cell Activity against K562 Tumor Cells.

PubMed

Jia, Wei; Feng, Jie; Zhang, Jing-Song; Lin, Chi-Chung; Wang, Wen-Han; Chen, Hong-Ge

2017-01-01

FVPA1, a novel polysaccharide, has been isolated from fruiting bodies of the culinary-medicinal mushroom Flammulina velutipes, a historically popular, widely cultivated and consumed functional food with an attractive taste, beneficial nutraceutical properties such as antitumor and immunomodulatory effects, and a number of essential biological activities. The average molecular weight was estimated to be ~1.8 × 104 Da based on high-performance size exclusion chromatography. Sugar analyses, methylation analyses, and 1H, 13C, and 2-dimensional nuclear magnetic resonance spectroscopy revealed the following structure of the repeating units of the FVPA1 polysaccharide Identification of this structure would conceivably lead to better understanding of the nutraceutical functions of this very important edible fungus. Bioactivity tests in vitro indicated that FVPA1 could significantly enhance natural killer cell activity against K562 tumor cells.

Structure-based membrane dome mechanism for Piezo mechanosensitivity

PubMed Central

Guo, Yusong R

2017-01-01

Mechanosensitive ion channels convert external mechanical stimuli into electrochemical signals for critical processes including touch sensation, balance, and cardiovascular regulation. The best understood mechanosensitive channel, MscL, opens a wide pore, which accounts for mechanosensitive gating due to in-plane area expansion. Eukaryotic Piezo channels have a narrow pore and therefore must capture mechanical forces to control gating in another way. We present a cryo-EM structure of mouse Piezo1 in a closed conformation at 3.7Å-resolution. The channel is a triskelion with arms consisting of repeated arrays of 4-TM structural units surrounding a pore. Its shape deforms the membrane locally into a dome. We present a hypothesis in which the membrane deformation changes upon channel opening. Quantitatively, membrane tension will alter gating energetics in proportion to the change in projected area under the dome. This mechanism can account for highly sensitive mechanical gating in the setting of a narrow, cation-selective pore. PMID:29231809

The Influence of Primary and Secondary DNA Structure in Deletion and Duplication between Direct Repeats in Escherichia Coli

PubMed Central

Trinh, T. Q.; Sinden, R. R.

1993-01-01

We describe a system to measure the frequency of both deletions and duplications between direct repeats. Short 17- and 18-bp palindromic and nonpalindromic DNA sequences were cloned into the EcoRI site within the chloramphenicol acetyltransferase gene of plasmids pBR325 and pJT7. This creates an insert between direct repeated EcoRI sites and results in a chloramphenicol-sensitive phenotype. Selection for chloramphenicol resistance was utilized to select chloramphenicol resistant revertants that included those with precise deletion of the insert from plasmid pBR325 and duplication of the insert in plasmid pJT7. The frequency of deletion or duplication varied more than 500-fold depending on the sequence of the short sequence inserted into the EcoRI site. For the nonpalindromic inserts, multiple internal direct repeats and the length of the direct repeats appear to influence the frequency of deletion. Certain palindromic DNA sequences with the potential to form DNA hairpin structures that might stabilize the misalignment of direct repeats had a high frequency of deletion. Other DNA sequences with the potential to form structures that might destabilize misalignment of direct repeats had a very low frequency of deletion. Duplication mutations occurred at the highest frequency when the DNA between the direct repeats contained no direct or inverted repeats. The presence of inverted repeats dramatically reduced the frequency of duplications. The results support the slippage-misalignment model, suggesting that misalignment occurring during DNA replication leads to deletion and duplication mutations. The results also support the idea that the formation of DNA secondary structures during DNA replication can facilitate and direct specific mutagenic events. PMID:8325478

[Bioinformatics Analysis of Clustered Regularly Interspaced Short Palindromic Repeats in the Genomes of Shigella].

PubMed

Wang, Pengfei; Wang, Yingfang; Duan, Guangcai; Xue, Zerun; Wang, Linlin; Guo, Xiangjiao; Yang, Haiyan; Xi, Yuanlin

2015-04-01

This study was aimed to explore the features of clustered regularly interspaced short palindromic repeats (CRISPR) structures in Shigella by using bioinformatics. We used bioinformatics methods, including BLAST, alignment and RNA structure prediction, to analyze the CRISPR structures of Shigella genomes. The results showed that the CRISPRs existed in the four groups of Shigella, and the flanking sequences of upstream CRISPRs could be classified into the same group with those of the downstream. We also found some relatively conserved palindromic motifs in the leader sequences. Repeat sequences had the same group with corresponding flanking sequences, and could be classified into two different types by their RNA secondary structures, which contain "stem" and "ring". Some spacers were found to homologize with part sequences of plasmids or phages. The study indicated that there were correlations between repeat sequences and flanking sequences, and the repeats might act as a kind of recognition mechanism to mediate the interaction between foreign genetic elements and Cas proteins.

The crystal structure of a partial mouse Notch-1 ankyrin domain: Repeats 4 through 7 preserve an ankyrin fold

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

Lubman, Olga Y.; Kopan, Raphael; Waksman, Gabriel

Folding and stability of proteins containing ankyrin repeats (ARs) is of great interest because they mediate numerous protein-protein interactions involved in a wide range of regulatory cellular processes. Notch, an ankyrin domain containing protein, signals by converting a transcriptional repression complex into an activation complex. The Notch ANK domain is essential for Notch function and contains seven ARs. Here, we present the 2.2 {angstrom} crystal structure of ARs 4-7 from mouse Notch 1 (m1ANK). These C-terminal repeats were resistant to degradation during crystallization, and their secondary and tertiary structures are maintained in the absence of repeats 1-3. The crystallized fragmentmore » adopts a typical ankyrin fold including the poorly conserved seventh AR, as seen in the Drosophila Notch ANK domain (dANK). The structural preservation and stability of the C-terminal repeats shed a new light onto the mechanism of hetero-oligomeric assembly during Notch-mediated transcriptional activation.« less

Mass distribution and spatial organization of the linear bacterial motor of Spiroplasma citri R8A2.

PubMed

Trachtenberg, Shlomo; Andrews, S Brian; Leapman, Richard D

2003-03-01

In the simple, helical, wall-less bacterial genus Spiroplasma, chemotaxis and motility are effected by a linear, contractile motor arranged as a flat cytoskeletal ribbon attached to the inner side of the membrane along the shortest helical line. With scanning transmission electron microscopy and diffraction analysis, we determined the hierarchical and spatial organization of the cytoskeleton of Spiroplasma citri R8A2. The structural unit appears to be a fibril, approximately 5 nm wide, composed of dimers of a 59-kDa protein; each ribbon is assembled from seven fibril pairs. The functional unit of the intact ribbon is a pair of aligned fibrils, along which pairs of dimers form tetrameric ring-like repeats. On average, isolated and purified ribbons contain 14 fibrils or seven well-aligned fibril pairs, which are the same structures observed in the intact cell. Scanning transmission electron microscopy mass analysis and sodium dodecyl sulfate-polyacrylamide gel electrophoresis of purified cytoskeletons indicate that the 59-kDa protein is the only constituent of the ribbons.

Structural modifications of polymethacrylates: impact on thermal behavior and release characteristics of glassy solid solutions.

PubMed

Claeys, Bart; De Coen, Ruben; De Geest, Bruno G; de la Rosa, Victor R; Hoogenboom, Richard; Carleer, Robert; Adriaensens, Peter; Remon, Jean Paul; Vervaet, Chris

2013-11-01

Polymethacrylates such as Eudragit® polymers are well established as drug delivery matrix. Here, we synthesize several Eudragit E PO (n-butyl-, dimethylaminoethyl-, methyl-methacrylate-terpolymer) analogues via free radical polymerization. These polymers are processed via hot melt extrusion, followed by injection molding and evaluated as carriers to produce immediate release solid solution tablets. Three chemical modifications increased the glass transition temperature of the polymer: (a) substitution of n-butyl by t-butyl groups, (b) reduction of the dimethylaminoethyl methacrylate (DMAEMA) content, and (c) incorporation of a bulky isobornyl repeating unit. These structural modifications revealed the possibility to increase the mechanical stability of the tablets via altering the polymer Tg without influencing the drug release characteristics and glassy solid solution forming properties. The presence of DMAEMA units proved to be crucial with respect to API/polymer interaction (essential in creating glassy solid solutions) and drug release characteristics. Moreover, these chemical modifications accentuate the need for a more rational design of (methacrylate) polymer matrix excipients for drug formulation via hot melt extrusion and injection molding. Copyright © 2013 Elsevier B.V. All rights reserved.

Duration of the speech disfluencies of beginning stutterers.

PubMed

Zebrowski, P M

1991-06-01

This study compared the duration of within-word disfluencies and the number of repeated units per instance of sound/syllable and whole-word repetitions of beginning stutterers to those produced by age- and sex-matched nonstuttering children. Subjects were 10 stuttering children [9 males and 1 female; mean age 4:1 (years:months); age range 3:2-5:1), and 10 nonstuttering children (9 males and 1 female; mean age 4:0; age range: 2:10-5:1). Mothers of the stuttering children reported that their children had been stuttering for 1 year or less. One 300-word conversational speech sample from each of the stuttering and nonstuttering children was analyzed for (a) mean duration of sound/syllable repetition and sound prolongation, (b) mean number of repeated units per instance of sound/syllable and whole-word repetition, and (c) various related measures of the frequency of all between- and within-word speech disfluencies. There were no significant between-group differences for either the duration of acoustically measured sound/syllable repetitions and sound prolongations or the number of repeated units per instance of sound/syllable and whole-word repetition. Unlike frequency and type of speech disfluency produced, average duration of within-word disfluencies and number of repeated units per repetition do not differentiate the disfluent speech of beginning stutterers and their nonstuttering peers. Additional analyses support findings from previous perceptual work that type and frequency of speech disfluency, not duration, are the principal characteristics listeners use in distinguishing these two talker groups.

Structure of the Type IX Group B Streptococcus Capsular Polysaccharide and Its Evolutionary Relationship with Types V and VII

PubMed Central

Berti, Francesco; Campisi, Edmondo; Toniolo, Chiara; Morelli, Laura; Crotti, Stefano; Rosini, Roberto; Romano, Maria Rosaria; Pinto, Vittoria; Brogioni, Barbara; Torricelli, Giulia; Janulczyk, Robert; Grandi, Guido; Margarit, Immaculada

2014-01-01

The Group B Streptococcus capsular polysaccharide type IX was isolated and purified, and the structure of its repeating unit was determined. Type IX capsule →4)[NeupNAc-α-(2→3)-Galp-β-(1→4)-GlcpNAc-β-(1→6)]-β-GlcpNAc-(1→4)-β-Galp-(1→4)-β-Glcp-(1→ appears most similar to types VII and V, although it contains two GlcpNAc residues. Genetic analysis identified differences in cpsM, cpsO, and cpsI gene sequences as responsible for the differentiation between the three capsular polysaccharide types, leading us to hypothesize that type V emerged from a recombination event in a type IX background. PMID:24990951

The O-antigen structure of bacterium Comamonas aquatica CJG.

PubMed

Wang, Xiqian; Kondakova, Anna N; Zhu, Yutong; Knirel, Yuriy A; Han, Aidong

2017-11-01

Genus Comamonas is a group of bacteria that are able to degrade a variety of environmental waste. Comamonas aquatica CJG (C. aquatica) in this genus is able to absorb low-density lipoprotein but not high-density lipoprotein of human serum. Using 1 H and 13 C NMR spectroscopy, we found that the O-polysaccharide (O-antigen) of this bacterium is comprised of a disaccharide repeat (O-unit) of d-glucose and 2-O-acetyl-l-rhamnose, which is shared by Serratia marcescens O6. The O-antigen gene cluster of C. aquatica, which is located between coaX and tnp4 genes, contains rhamnose synthesis genes, glycosyl and acetyl transferase genes, and ATP-binding cassette transporter genes, and therefore is consistent with the O-antigen structure determined here.

Two fucosylated chondroitin sulfates from the sea cucumber Eupentacta fraudatrix.

PubMed

Ustyuzhanina, Nadezhda E; Bilan, Maria I; Dmitrenok, Andrey S; Nifantiev, Nikolay E; Usov, Anatolii I

2017-05-15

Two fucosylated chondroitin sulfates EF1 and EF2 were isolated from the sea cucumber Eupentacta fraudatrix. Separation of the polysaccharides was performed using anion-exchange chromatography on DEAE-Sephacel by elution of 0.75M and 1.0M NaCl solutions. The structures of biopolymers were determined by chemical and NMR spectroscopic methods. The backbone of EF1 was found to be composed of chondroitin sulfate A and E units in a ratio of about 1:1. The core of EF2 along with chondroitin sulfate A and E fragments contained unusual disaccharide repeating units →4)-β-d-GlcpA2S3S-(1→3)-β-d-GalpNAc6S-(1→. The main type of branches in both polysaccharides was α-l-Fucp3S4S unit attached to O-3 of GlcA residues. Another type of branches was found to be the disaccharide fragment α-l-Fucp-(1→2)-α-l-Fucp3S4S-(1→ linked to O-3 of GlcA. The presence of structurally different fucosylated chondroitin sulfates in one species of sea cucumber is rather unusual and has not been described previously. Copyright © 2017 Elsevier Ltd. All rights reserved.

Optimization of sequence alignment for simple sequence repeat regions.

PubMed

Jighly, Abdulqader; Hamwieh, Aladdin; Ogbonnaya, Francis C

2011-07-20

Microsatellites, or simple sequence repeats (SSRs), are tandemly repeated DNA sequences, including tandem copies of specific sequences no longer than six bases, that are distributed in the genome. SSR has been used as a molecular marker because it is easy to detect and is used in a range of applications, including genetic diversity, genome mapping, and marker assisted selection. It is also very mutable because of slipping in the DNA polymerase during DNA replication. This unique mutation increases the insertion/deletion (INDELs) mutation frequency to a high ratio - more than other types of molecular markers such as single nucleotide polymorphism (SNPs).SNPs are more frequent than INDELs. Therefore, all designed algorithms for sequence alignment fit the vast majority of the genomic sequence without considering microsatellite regions, as unique sequences that require special consideration. The old algorithm is limited in its application because there are many overlaps between different repeat units which result in false evolutionary relationships. To overcome the limitation of the aligning algorithm when dealing with SSR loci, a new algorithm was developed using PERL script with a Tk graphical interface. This program is based on aligning sequences after determining the repeated units first, and the last SSR nucleotides positions. This results in a shifting process according to the inserted repeated unit type.When studying the phylogenic relations before and after applying the new algorithm, many differences in the trees were obtained by increasing the SSR length and complexity. However, less distance between different linage had been observed after applying the new algorithm. The new algorithm produces better estimates for aligning SSR loci because it reflects more reliable evolutionary relations between different linages. It reduces overlapping during SSR alignment, which results in a more realistic phylogenic relationship.

A novel tandem repeat sequence located on human chromosome 4p: isolation and characterization.

PubMed

Kogi, M; Fukushige, S; Lefevre, C; Hadano, S; Ikeda, J E

1997-06-01

In an effort to analyze the genomic region of the distal half of human chromosome 4p, to where Huntington disease and other diseases have been mapped, we have isolated the cosmid clone (CRS447) that was likely to contain a region with specific repeat sequences. Clone CRS447 was subjected to detailed analysis, including chromosome mapping, restriction mapping, and DNA sequencing. Chromosome mapping by both a human-CHO hybrid cell panel and FISH revealed that CRS447 was predominantly located in the 4p15.1-15.3 region. CRS447 was shown to consist of tandem repeats of 4.7-kb units present on chromosome 4p. A single EcoRI unit was subcloned (pRS447), and the complete sequence was determined as 4752 nucleotides. When pRS447 was used as a probe, the number of copies of this repeat per haploid genome was estimated to be 50-70. Sequence analysis revealed that it contained two internal CA repeats and one putative ORF. Database search established that this sequence was unreported. However, two homologous STS markers were found in the database. We concluded that CRS447/pRS447 is a novel tandem repeat sequence that is mainly specific to human chromosome 4p.

In Vitro Expansion of CAG, CAA, and Mixed CAG/CAA Repeats.

PubMed

Figura, Grzegorz; Koscianska, Edyta; Krzyzosiak, Wlodzimierz J

2015-08-11

Polyglutamine diseases, including Huntington's disease and a number of spinocerebellar ataxias, are caused by expanded CAG repeats that are located in translated sequences of individual, functionally-unrelated genes. Only mutant proteins containing polyglutamine expansions have long been thought to be pathogenic, but recent evidence has implicated mutant transcripts containing long CAG repeats in pathogenic processes. The presence of two pathogenic factors prompted us to attempt to distinguish the effects triggered by mutant protein from those caused by mutant RNA in cellular models of polyglutamine diseases. We used the SLIP (Synthesis of Long Iterative Polynucleotide) method to generate plasmids expressing long CAG repeats (forming a hairpin structure), CAA-interrupted CAG repeats (forming multiple unstable hairpins) or pure CAA repeats (not forming any secondary structure). We successfully modified the original SLIP protocol to generate repeats of desired length starting from constructs containing short repeat tracts. We demonstrated that the SLIP method is a time- and cost-effective approach to manipulate the lengths of expanded repeat sequences.

Unit Mastery Learning in an Introductory Geography Course

ERIC Educational Resources Information Center

Healy, John R.; Stephenson, Larry K.

1975-01-01

The unit mastery learning system is a method of individualized, self-paced learning which, through repeatable testing, enables students to attain a mastery of the content of one unit before proceeding to the next in the program. This article describes the unit mastery learning system and its application in an introductory geography course at Hilo…

Sequence repeats and protein structure

NASA Astrophysics Data System (ADS)

Hoang, Trinh X.; Trovato, Antonio; Seno, Flavio; Banavar, Jayanth R.; Maritan, Amos

2012-11-01

Repeats are frequently found in known protein sequences. The level of sequence conservation in tandem repeats correlates with their propensities to be intrinsically disordered. We employ a coarse-grained model of a protein with a two-letter amino acid alphabet, hydrophobic (H) and polar (P), to examine the sequence-structure relationship in the realm of repeated sequences. A fraction of repeated sequences comprises a distinct class of bad folders, whose folding temperatures are much lower than those of random sequences. Imperfection in sequence repetition improves the folding properties of the bad folders while deteriorating those of the good folders. Our results may explain why nature has utilized repeated sequences for their versatility and especially to design functional proteins that are intrinsically unstructured at physiological temperatures.

Highly sensitive MicroRNA 146a detection using a gold nanoparticle-based CTG repeat probing system and isothermal amplification.

PubMed

Le, Binh Huy; Seo, Young Jun

2018-01-25

We have developed a gold nanoparticle (AuNP)-based CTG repeat probing system displaying high quenching capability and combined it with isothermal amplification for the detection of miRNA 146a. This method of using a AuNP-based CTG repeat probing system with isothermal amplification allowed the highly sensitive (14 aM) and selective detection of miRNA 146a. A AuNP-based CTG repeat probing system having a hairpin structure and a dT F fluorophore exhibited highly efficient quenching because the CTG repeat-based stable hairpin structure imposed a close distance between the AuNP and the dT F residue. A small amount of miRNA 146a induced multiple copies of the CAG repeat sequence during rolling circle amplification; the AuNP-based CTG repeat probing system then bound to the complementary multiple-copy CAG repeat sequence, thereby inducing a structural change from a hairpin to a linear structure with amplified fluorescence. This AuNP-based CTG probing system combined with isothermal amplification could also discriminate target miRNA 146a from one- and two-base-mismatched miRNAs (ORN 1 and ORN 2, respectively). This simple AuNP-based CTG probing system, combined with isothermal amplification to induce a highly sensitive change in fluorescence, allows the detection of miRNA 146a with high sensitivity (14 aM) and selectivity. Copyright © 2017 Elsevier B.V. All rights reserved.

Evolution of Alternative Adaptive Immune Systems in Vertebrates.

PubMed

Boehm, Thomas; Hirano, Masayuki; Holland, Stephen J; Das, Sabyasachi; Schorpp, Michael; Cooper, Max D

2018-04-26

Adaptive immunity in jawless fishes is based on antigen recognition by three types of variable lymphocyte receptors (VLRs) composed of variable leucine-rich repeats, which are differentially expressed by two T-like lymphocyte lineages and one B-like lymphocyte lineage. The T-like cells express either VLRAs or VLRCs of yet undefined antigen specificity, whereas the VLRB antibodies secreted by B-like cells bind proteinaceous and carbohydrate antigens. The incomplete VLR germline genes are assembled into functional units by a gene conversion-like mechanism that employs flanking variable leucine-rich repeat sequences as templates in association with lineage-specific expression of cytidine deaminases. B-like cells develop in the hematopoietic typhlosole and kidneys, whereas T-like cells develop in the thymoid, a thymus-equivalent region at the gill fold tips. Thus, the dichotomy between T-like and B-like cells and the presence of dedicated lymphopoietic tissues emerge as ancestral vertebrate features, whereas the somatic diversification of structurally distinct antigen receptor genes evolved independently in jawless and jawed vertebrates.

42 CFR 84.307 - Environmental treatments.

Code of Federal Regulations, 2013 CFR

2013-10-01

... environmental treatments simulating extreme storage temperatures, shock, and vibration. (b) The units will be...) The units will be subjected to vibration according to the following procedure: (1) The unit will be...; and (3) The vibration frequency regimen applied to each axis will be cyclical, repeating the sequence...

42 CFR 84.307 - Environmental treatments.

Code of Federal Regulations, 2012 CFR

2012-10-01

... environmental treatments simulating extreme storage temperatures, shock, and vibration. (b) The units will be...) The units will be subjected to vibration according to the following procedure: (1) The unit will be...; and (3) The vibration frequency regimen applied to each axis will be cyclical, repeating the sequence...

42 CFR 84.307 - Environmental treatments.

Code of Federal Regulations, 2014 CFR

2014-10-01

... environmental treatments simulating extreme storage temperatures, shock, and vibration. (b) The units will be...) The units will be subjected to vibration according to the following procedure: (1) The unit will be...; and (3) The vibration frequency regimen applied to each axis will be cyclical, repeating the sequence...

Genome sequencing defines phylogeny and spread of methicillin-resistant Staphylococcus aureus in a high transmission setting

PubMed Central

Tong, Steven Y.C.; Holden, Matthew T.G.; Nickerson, Emma K.; Cooper, Ben S.; Köser, Claudio U.; Cori, Anne; Jombart, Thibaut; Cauchemez, Simon; Fraser, Christophe; Wuthiekanun, Vanaporn; Thaipadungpanit, Janjira; Hongsuwan, Maliwan; Day, Nicholas P.; Limmathurotsakul, Direk; Parkhill, Julian; Peacock, Sharon J.

2015-01-01

Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of nosocomial infection. Whole-genome sequencing of MRSA has been used to define phylogeny and transmission in well-resourced healthcare settings, yet the greatest burden of nosocomial infection occurs in resource-restricted settings where barriers to transmission are lower. Here, we study the flux and genetic diversity of MRSA on ward and individual patient levels in a hospital where transmission was common. We repeatedly screened all patients on two intensive care units for MRSA carriage over a 3-mo period. All MRSA belonged to multilocus sequence type 239 (ST 239). We defined the population structure and charted the spread of MRSA by sequencing 79 isolates from 46 patients and five members of staff, including the first MRSA-positive screen isolates and up to two repeat isolates where available. Phylogenetic analysis identified a flux of distinct ST 239 clades over time in each intensive care unit. In total, five main clades were identified, which varied in the carriage of plasmids encoding antiseptic and antimicrobial resistance determinants. Sequence data confirmed intra- and interwards transmission events and identified individual patients who were colonized by more than one clade. One patient on each unit was the source of numerous transmission events, and deep sampling of one of these cases demonstrated colonization with a “cloud” of related MRSA variants. The application of whole-genome sequencing and analysis provides novel insights into the transmission of MRSA in under-resourced healthcare settings and has relevance to wider global health. PMID:25491771

Transcription arrest by a G quadruplex forming-trinucleotide repeat sequence from the human c-myb gene.

PubMed

Broxson, Christopher; Beckett, Joshua; Tornaletti, Silvia

2011-05-17

Non canonical DNA structures correspond to genomic regions particularly susceptible to genetic instability. The transcription process facilitates formation of these structures and plays a major role in generating the instability associated with these genomic sites. However, little is known about how non canonical structures are processed when encountered by an elongating RNA polymerase. Here we have studied the behavior of T7 RNA polymerase (T7RNAP) when encountering a G quadruplex forming-(GGA)(4) repeat located in the human c-myb proto-oncogene. To make direct correlations between formation of the structure and effects on transcription, we have taken advantage of the ability of the T7 polymerase to transcribe single-stranded substrates and of G4 DNA to form in single-stranded G-rich sequences in the presence of potassium ions. Under physiological KCl concentrations, we found that T7 RNAP transcription was arrested at two sites that mapped to the c-myb (GGA)(4) repeat sequence. The extent of arrest did not change with time, indicating that the c-myb repeat represented an absolute block and not a transient pause to T7 RNAP. Consistent with G4 DNA formation, arrest was not observed in the absence of KCl or in the presence of LiCl. Furthermore, mutations in the c-myb (GGA)(4) repeat, expected to prevent transition to G4, also eliminated the transcription block. We show T7 RNAP arrest at the c-myb repeat in double-stranded DNA under conditions mimicking the cellular concentration of biomolecules and potassium ions, suggesting that the G4 structure formed in the c-myb repeat may represent a transcription roadblock in vivo. Our results support a mechanism of transcription-coupled DNA repair initiated by arrest of transcription at G4 structures.

Distinct Immunomodulation of Bone Marrow-Derived Dendritic Cell Responses to Lactobacillus plantarum WCFS1 by Two Different Polysaccharides Isolated from Lactobacillus rhamnosus LOCK 0900

PubMed Central

Jachymek, Wojciech; Srutkova, Dagmar; Brzozowska, Ewa; Kozakova, Hana; Gamian, Andrzej

2014-01-01

The structures of polysaccharides (PS) isolated from Lactobacillus rhamnosus LOCK 0900 and results from stimulation of mouse bone marrow-derived dendritic cells (BM-DC) and human embryonal kidney (HEK293) cells stably transfected with Toll-like receptors (TLR) upon exposure to these antigens were studied. L. rhamnosus LOCK 0900 produces PS that differ greatly in their structure. The polymer L900/2, with a high average molecular mass of 830 kDa, is a branched heteropolysaccharide with a unique repeating unit consisting of seven sugar residues and pyruvic acid, whereas L900/3 has a low average molecular mass of 18 kDa and contains a pentasaccharide repeating unit and phosphorus. Furthermore, we found that both described PS neither induce cytokine production and maturation of mouse BM-DC nor induce signaling through TLR2/TLR4 receptors. However, they differ profoundly in their abilities to modulate the BM-DC immune response to the well-characterized human isolate Lactobacillus plantarum WCFS1. Exposure to L900/2 enhanced interleukin-10 (IL-10) production induced by L. plantarum WCFS1, while in contrast, L900/3 enhanced the production of IL-12p70. We conclude that PS, probably due to their chemical features, are able to modulate the immune responses to third-party antigens. The ability to induce regulatory IL-10 by L900/2 opens up the possibility to use this PS in therapy of inflammatory conditions, such as inflammatory bowel disease, whereas L900/3 might be useful in reverting the antigen-dependent Th2-skewed immune responses in allergies. PMID:25107979

The dynamics of solvation dictates the conformation of polyethylene oxide in aqueous, isobutyric acid and binary solutions.

PubMed

Dahal, Udaya R; Dormidontova, Elena E

2017-04-12

Polymers hydrogen-bonding with solvent represent an important broad class of polymers, properties of which depend on solvation. Using atomistic molecular dynamics simulations with the OPLS/AA force field we investigate the effect of hydrogen bonding on PEO conformation and chain mobility by comparing its behavior in isobutyric acid and aqueous solutions. In agreement with experimental data, we found that in isobutyric acid PEO forms a rather rigid extended helical structure, while in water it assumes a highly flexible coil conformation. We show that the difference in PEO conformation and flexibility is the result of the hydrogen bond stability and overall solvent dynamics near PEO. Isobutyric acid forms up to one hydrogen bond per repeat unit of PEO and interacts with PEO for a prolonged period of time, thereby stabilizing the helical structure of the polymer and reducing its segmental mobility. In contrast, water forms on average 1.2 hydrogen bonds per repeat unit of PEO (with 60% of water forming a single hydrogen bond and 40% of water forming two hydrogen bonds) and resides near PEO for a noticeably shorter time than isobutyric acid, leading to the well-documented high segmental mobility of PEO in water. We also analyze PEO conformation, hydrogen bonding and segmental mobility in binary water/isobutyric acid solutions and find that in the phase separated region PEO resides in the isobutyric-rich phase forming about 25% of its hydrogen bonds with isobutyric acid and 75% with water. We show that the dynamics of solvation affects the equilibrium properties of macromolecules, such as conformation, and by mixing of hydrogen bond-donating solvents one can significantly alter both polymer conformation and its local dynamics.

Slipped-strand mispairing at noncontiguous repeats in Poecilia reticulata: a model for minisatellite birth.

PubMed Central

Taylor, J S; Breden, F

2000-01-01

The standard slipped-strand mispairing (SSM) model for the formation of variable number tandem repeats (VNTRs) proposes that a few tandem repeats, produced by chance mutations, provide the "raw material" for VNTR expansion. However, this model is unlikely to explain the formation of VNTRs with long motifs (e.g., minisatellites), because the likelihood of a tandem repeat forming by chance decreases rapidly as the length of the repeat motif increases. Phylogenetic reconstruction of the birth of a mitochondrial (mt) DNA minisatellite in guppies suggests that VNTRs with long motifs can form as a consequence of SSM at noncontiguous repeats. VNTRs formed in this manner have motifs longer than the noncontiguous repeat originally formed by chance and are flanked by one unit of the original, noncontiguous repeat. SSM at noncontiguous repeats can therefore explain the birth of VNTRs with long motifs and the "imperfect" or "short direct" repeats frequently observed adjacent to both mtDNA and nuclear VNTRs. PMID:10880490

Fluid-Structure Interaction in a Fluid-Filled Composite Structure Subjected to Low Velocity Impact

DTIC Science & Technology

2016-06-01

for creating an E-glass composite cubic structure and a pendulum was designed and built to provide a repeatable low velocity impact. The behavior of...structure and a pendulum was designed and built to provide a repeatable low velocity impact. The behavior of the composite structure was studied at various...SET-UP .......................................................31  1.  Impact Pendulum

GFP-based fluorescence assay for CAG repeat instability in cultured human cells.

PubMed

Santillan, Beatriz A; Moye, Christopher; Mittelman, David; Wilson, John H

2014-01-01

Trinucleotide repeats can be highly unstable, mutating far more frequently than point mutations. Repeats typically mutate by addition or loss of units of the repeat. CAG repeat expansions in humans trigger neurological diseases that include myotonic dystrophy, Huntington disease, and several spinocerebellar ataxias. In human cells, diverse mechanisms promote CAG repeat instability, and in mice, the mechanisms of instability are varied and tissue-dependent. Dissection of mechanistic complexity and discovery of potential therapeutics necessitates quantitative and scalable screens for repeat mutation. We describe a GFP-based assay for screening modifiers of CAG repeat instability in human cells. The assay exploits an engineered intronic CAG repeat tract that interferes with expression of an inducible GFP minigene. Like the phenotypes of many trinucleotide repeat disorders, we find that GFP function is impaired by repeat expansion, in a length-dependent manner. The intensity of fluorescence varies inversely with repeat length, allowing estimates of repeat tract changes in live cells. We validate the assay using transcription through the repeat and engineered CAG-specific nucleases, which have previously been reported to induce CAG repeat instability. The assay is relatively fast and should be adaptable to large-scale screens of chemical and shRNA libraries.

GFP-Based Fluorescence Assay for CAG Repeat Instability in Cultured Human Cells

PubMed Central

Santillan, Beatriz A.; Moye, Christopher; Mittelman, David; Wilson, John H.

2014-01-01

Trinucleotide repeats can be highly unstable, mutating far more frequently than point mutations. Repeats typically mutate by addition or loss of units of the repeat. CAG repeat expansions in humans trigger neurological diseases that include myotonic dystrophy, Huntington disease, and several spinocerebellar ataxias. In human cells, diverse mechanisms promote CAG repeat instability, and in mice, the mechanisms of instability are varied and tissue-dependent. Dissection of mechanistic complexity and discovery of potential therapeutics necessitates quantitative and scalable screens for repeat mutation. We describe a GFP-based assay for screening modifiers of CAG repeat instability in human cells. The assay exploits an engineered intronic CAG repeat tract that interferes with expression of an inducible GFP minigene. Like the phenotypes of many trinucleotide repeat disorders, we find that GFP function is impaired by repeat expansion, in a length-dependent manner. The intensity of fluorescence varies inversely with repeat length, allowing estimates of repeat tract changes in live cells. We validate the assay using transcription through the repeat and engineered CAG-specific nucleases, which have previously been reported to induce CAG repeat instability. The assay is relatively fast and should be adaptable to large-scale screens of chemical and shRNA libraries. PMID:25423602

Repeat-swap homology modeling of secondary active transporters: updated protocol and prediction of elevator-type mechanisms

PubMed Central

Vergara-Jaque, Ariela; Fenollar-Ferrer, Cristina; Kaufmann, Desirée; Forrest, Lucy R.

2015-01-01

Secondary active transporters are critical for neurotransmitter clearance and recycling during synaptic transmission and uptake of nutrients. These proteins mediate the movement of solutes against their concentration gradients, by using the energy released in the movement of ions down pre-existing concentration gradients. To achieve this, transporters conform to the so-called alternating-access hypothesis, whereby the protein adopts at least two conformations in which the substrate binding sites are exposed to one or other side of the membrane, but not both simultaneously. Structures of a bacterial homolog of neuronal glutamate transporters, GltPh, in several different conformational states have revealed that the protein structure is asymmetric in the outward- and inward-open states, and that the conformational change connecting them involves a elevator-like movement of a substrate binding domain across the membrane. The structural asymmetry is created by inverted-topology repeats, i.e., structural repeats with similar overall folds whose transmembrane topologies are related to each other by two-fold pseudo-symmetry around an axis parallel to the membrane plane. Inverted repeats have been found in around three-quarters of secondary transporter folds. Moreover, the (a)symmetry of these systems has been successfully used as a bioinformatic tool, called “repeat-swap modeling” to predict structural models of a transporter in one conformation using the known structure of the transporter in the complementary conformation as a template. Here, we describe an updated repeat-swap homology modeling protocol, and calibrate the accuracy of the method using GltPh, for which both inward- and outward-facing conformations are known. We then apply this repeat-swap homology modeling procedure to a concentrative nucleoside transporter, VcCNT, which has a three-dimensional arrangement related to that of GltPh. The repeat-swapped model of VcCNT predicts that nucleoside transport also occurs via an elevator-like mechanism. PMID:26388773

Probing disorder in isometric pyrochlore and related complex oxides

NASA Astrophysics Data System (ADS)

Shamblin, Jacob; Feygenson, Mikhail; Neuefeind, Joerg; Tracy, Cameron L.; Zhang, Fuxiang; Finkeldei, Sarah; Bosbach, Dirk; Zhou, Haidong; Ewing, Rodney C.; Lang, Maik

2016-05-01

There has been an increased focus on understanding the energetics of structures with unconventional ordering (for example, correlated disorder that is heterogeneous across different length scales). In particular, compounds with the isometric pyrochlore structure, A2B2O7, can adopt a disordered, isometric fluorite-type structure, (A, B)4O7, under extreme conditions. Despite the importance of the disordering process there exists only a limited understanding of the role of local ordering on the energy landscape. We have used neutron total scattering to show that disordered fluorite (induced intrinsically by composition/stoichiometry or at far-from-equilibrium conditions produced by high-energy radiation) consists of a local orthorhombic structural unit that is repeated by a pseudo-translational symmetry, such that orthorhombic and isometric arrays coexist at different length scales. We also show that inversion in isometric spinel occurs by a similar process. This insight provides a new basis for understanding order-to-disorder transformations important for applications such as plutonium immobilization, fast ion conduction, and thermal barrier coatings.

The Barley Phytomer

PubMed Central

Forster, Brian P.; Franckowiak, Jerome D.; Lundqvist, Udda; Lyon, Jackie; Pitkethly, Ian; Thomas, William T. B.

2007-01-01

Background and Aims Morphological mutants have been useful in elucidating the phytomeric structure of plants. Recently described mutants have shed new light on the ontogeny (development of plant structures) and the phytomeric system of barley (Hordeum vulgare). Since the current model for barley phytomers was not adequate to explain the nature of some mutants, a new model is proposed. Methods New phytomer mutants were detected by visual assessment of mutant families in the Optic barley mutation grid population. This was done at various growth stages using laboratory, glasshouse and field screens. Simple explanations were adopted to account for aberrant phytomer phenotypes and a thesis for a new phytomer model was developed. Key Results and Conclusions A barley phytomer model is presented, in which the origins of vegetative and generative structures can be explained by a single repeating phytomer unit. Organs on the barley plant are divided into two classes, single or paired, depending on their origin. Paired structures are often fused together to create specific organs. The model can be applied to wheat (Triticum aestivum) and related grasses. PMID:17901062

Exploration of ground instability factor causing slumping and related dewatering in high methane-flux and gentle continental slope off Shimokita Peninsula, NE Japan

NASA Astrophysics Data System (ADS)

Morita, S.; Nakajima, T.; Goto, S.; Yamada, Y.; Kawamura, K.

2012-12-01

A great number of slump (submarine landslide) units have been identified by reflection seismic surveys performed off Shimokita Peninsula, NE Japan (Morita, et al., 2011). A 3-D seismic data revealed typical deformations caused by slumping and related dewatering in the Pliocene and upper formations. The slumping was generated primarily by layer-parallel slip in a very gentle (<1 degree) and flat continental slope. The size of slump units extends over 30 km in both width and slip direction in maximum. The slump units often exhibit an imbrication structure formed by repeated thrusting in the bottom layers, being mostly composed of the thrust blocks and little matrix. The dewatering structure is observed as widespread parallel dikes of which distribution is strongly dependent on the imbrication of the slump units. Slip planes of the slumps are traceable in seismic data because of the layer-parallel slip. The layers which correspond to the slip planes proved to be generally characterized as low-amplitude layers having some thickness, and some of the slip planes exhibit flattened features under the slump units of the imbrication structure accompanied by parallel dikes. This implies that excess fluid in the slip plane caused the lubrication to enhance the slumping and was drained through the parallel dikes during slumping. Some typical structures related to natural gas, e.g. enhanced reflection, gas chimney, have been identified in the seismic data. The shakedown cruise of D/V Chikyu in 2006 reported a recovery of gas hydrate in nearby area (Higuchi et al., 2009). A shallow sulfate-methane interface (SMI) of 3.5-12 mbsf has been reported in the survey area (Kotani et al., 2007). These features indicate that a high methane flux in the area is likely an important ground instability factor to cause the slumping and the dewatering phenomena. We recognize that the set of the slump units in the survey area is one of the most suitable targets to approach mechanism of submarine landslides so that we started exploring the feasibility of a scientific drilling in this survey area.

Structural analysis and biological activity of a highly regular glycosaminoglycan from Achatina fulica.

PubMed

Liu, Jie; Zhou, Lutan; He, Zhicheng; Gao, Na; Shang, Feineng; Xu, Jianping; Li, Zi; Yang, Zengming; Wu, Mingyi; Zhao, Jinhua

2018-02-01

Edible snails have been widely used as a health food and medicine in many countries. A unique glycosaminoglycan (AF-GAG) was purified from Achatina fulica. Its structure was analyzed and characterized by chemical and instrumental methods, such as Fourier transform infrared spectroscopy, analysis of monosaccharide composition, and 1D/2D nuclear magnetic resonance spectroscopy. Chemical composition analysis indicated that AF-GAG is composed of iduronic acid (IdoA) and N-acetyl-glucosamine (GlcNAc) and its average molecular weight is 118kDa. Structural analysis clarified that the uronic acid unit in glycosaminoglycan (GAG) is the fully epimerized and the sequence of AF-GAG is →4)-α-GlcNAc (1→4)-α-IdoA2S (1→. Although its structure with a uniform repeating disaccharide is similar to those of heparin and heparan sulfate, this GAG is structurally highly regular and homogeneous. Anticoagulant activity assays indicated that AF-GAG exhibits no anticoagulant activities, but considering its structural characteristic, other bioactivities such as heparanase inhibition may be worthy of further study. Copyright © 2017 Elsevier Ltd. All rights reserved.

A prospective evaluation of the repeatability of left ventricular ejection fraction measurement by gated SPECT.

PubMed

Kliner, Dustin; Wang, Li; Winger, Daniel; Follansbee, William P; Soman, Prem

2015-12-01

Gated single-photon emission computed tomography (SPECT) is widely used for myocardial perfusion imaging and provides an automated assessment of left ventricular ejection fraction (LVEF). We prospectively tested the repeatability of serial SPECT-derived LVEF. This information is essential in order to inform the interpretation of a change in LV function on serial testing. Consenting patients (n = 50) from among those referred for clinically indicated gated myocardial perfusion SPECT (MPs) were recruited. Following the clinical rest-stress study, patients were repositioned on the camera table for a second acquisition using identical parameters. Patient positioning, image acquisition and processing for the second scan were independently performed by a technologist blinded to the clinical scan. Quantitative LVEF was generated by Quantitative Gated SPECT and recorded as EF1 and EF2, respectively. Repeatability of serial results was assessed using the Bland-Altman method. The limits of repeatability and repeatability coefficients were generated to determine the maximum variation in LVEF that can be expected to result from test variability. Repeatability was tested across a broad range of LV systolic function and myocardial perfusion. The mean difference between EF1 and EF2 was 1.6% (EF units), with 95% limits of repeatability of +9.1% to -6.0% (repeatability coefficient 7.5%). Correlation between serial EF measurements was excellent (r = 0.9809). Similar results were obtained in subgroups based on normal or abnormal EF and myocardial perfusion. The largest repeatability coefficient of 8.1% was seen in patients with abnormal LV systolic function. When test protocol and acquisition parameters are kept constant, a difference of >8% EF units on serial MPs is indicative of a true change 95% of the time.

Structural and biophysical properties of h-FANCI ARM repeat protein.

PubMed

Siddiqui, Mohd Quadir; Choudhary, Rajan Kumar; Thapa, Pankaj; Kulkarni, Neha; Rajpurohit, Yogendra S; Misra, Hari S; Gadewal, Nikhil; Kumar, Satish; Hasan, Syed K; Varma, Ashok K

2017-11-01

Fanconi anemia complementation groups - I (FANCI) protein facilitates DNA ICL (Inter-Cross-link) repair and plays a crucial role in genomic integrity. FANCI is a 1328 amino acids protein which contains armadillo (ARM) repeats and EDGE motif at the C-terminus. ARM repeats are functionally diverse and evolutionarily conserved domain that plays a pivotal role in protein-protein and protein-DNA interactions. Considering the importance of ARM repeats, we have explored comprehensive in silico and in vitro approach to examine folding pattern. Size exclusion chromatography, dynamic light scattering (DLS) and glutaraldehyde crosslinking studies suggest that FANCI ARM repeat exist as monomer as well as in oligomeric forms. Circular dichroism (CD) and fluorescence spectroscopy results demonstrate that protein has predominantly α- helices and well-folded tertiary structure. DNA binding was analysed using electrophoretic mobility shift assay by autoradiography. Temperature-dependent CD, Fluorescence spectroscopy and DLS studies concluded that protein unfolds and start forming oligomer from 30°C. The existence of stable portion within FANCI ARM repeat was examined using limited proteolysis and mass spectrometry. The normal mode analysis, molecular dynamics and principal component analysis demonstrated that helix-turn-helix (HTH) motif present in ARM repeat is highly dynamic and has anti-correlated motion. Furthermore, FANCI ARM repeat has HTH structural motif which binds to double-stranded DNA.

A Feature-adaptive Subdivision Method for Real-time 3D Reconstruction of Repeated Topology Surfaces

NASA Astrophysics Data System (ADS)

Lin, Jinhua; Wang, Yanjie; Sun, Honghai

2017-03-01

It's well known that rendering for a large number of triangles with GPU hardware tessellation has made great progress. However, due to the fixed nature of GPU pipeline, many off-line methods that perform well can not meet the on-line requirements. In this paper, an optimized Feature-adaptive subdivision method is proposed, which is more suitable for reconstructing surfaces with repeated cusps or creases. An Octree primitive is established in irregular regions where there are the same sharp vertices or creases, this method can find the neighbor geometry information quickly. Because of having the same topology structure between Octree primitive and feature region, the Octree feature points can match the arbitrary vertices in feature region more precisely. In the meanwhile, the patches is re-encoded in the Octree primitive by using the breadth-first strategy, resulting in a meta-table which allows for real-time reconstruction by GPU hardware tessellation unit. There is only one feature region needed to be calculated under Octree primitive, other regions with the same repeated feature generate their own meta-table directly, the reconstruction time is saved greatly for this step. With regard to the meshes having a large number of repeated topology feature, our algorithm improves the subdivision time by 17.575% and increases the average frame drawing time by 0.2373 ms compared to the traditional FAS (Feature-adaptive Subdivision), at the same time the model can be reconstructed in a watertight manner.

Repeated mild traumatic brain injury can cause acute neurologic impairment without overt structural damage in juvenile rats.

PubMed

Meconi, Alicia; Wortman, Ryan C; Wright, David K; Neale, Katie J; Clarkson, Melissa; Shultz, Sandy R; Christie, Brian R

2018-01-01

Repeated concussion is becoming increasingly recognized as a serious public health concern around the world. Moreover, there is a greater awareness amongst health professionals of the potential for repeated pediatric concussions to detrimentally alter the structure and function of the developing brain. To better study this issue, we developed an awake closed head injury (ACHI) model that enabled repeated concussions to be performed reliably and reproducibly in juvenile rats. A neurological assessment protocol (NAP) score was generated immediately after each ACHI to help quantify the cumulative effects of repeated injury on level of consciousness, and basic motor and reflexive capacity. Here we show that we can produce a repeated ACHI (4 impacts in two days) in both male and female juvenile rats without significant mortality or pain. We show that both single and repeated injuries produce acute neurological deficits resembling clinical concussion symptoms that can be quantified using the NAP score. Behavioural analyses indicate repeated ACHI acutely impaired spatial memory in the Barnes maze, and an interesting sex effect was revealed as memory impairment correlated moderately with poorer NAP score performance in a subset of females. These cognitive impairments occurred in the absence of motor impairments on the Rotarod, or emotional changes in the open field and elevated plus mazes. Cresyl violet histology and structural magnetic resonance imaging (MRI) indicated that repeated ACHI did not produce significant structural damage. MRI also confirmed there was no volumetric loss in the cortex, hippocampus, or corpus callosum of animals at 1 or 7 days post-ACHI. Together these data indicate that the ACHI model can provide a reliable, high throughput means to study the effects of concussions in juvenile rats.

Structure and stability of the ankyrin domain of the Drosophila Notch receptor.

PubMed

Zweifel, Mark E; Leahy, Daniel J; Hughson, Frederick M; Barrick, Doug

2003-11-01

The Notch receptor contains a conserved ankyrin repeat domain that is required for Notch-mediated signal transduction. The ankyrin domain of Drosophila Notch contains six ankyrin sequence repeats previously identified as closely matching the ankyrin repeat consensus sequence, and a putative seventh C-terminal sequence repeat that exhibits lower similarity to the consensus sequence. To better understand the role of the Notch ankyrin domain in Notch-mediated signaling and to examine how structure is distributed among the seven ankyrin sequence repeats, we have determined the crystal structure of this domain to 2.0 angstroms resolution. The seventh, C-terminal, ankyrin sequence repeat adopts a regular ankyrin fold, but the first, N-terminal ankyrin repeat, which contains a 15-residue insertion, appears to be largely disordered. The structure reveals a substantial interface between ankyrin polypeptides, showing a high degree of shape and charge complementarity, which may be related to homotypic interactions suggested from indirect studies. However, the Notch ankyrin domain remains largely monomeric in solution, demonstrating that this interface alone is not sufficient to promote tight association. Using the structure, we have classified reported mutations within the Notch ankyrin domain that are known to disrupt signaling into those that affect buried residues and those restricted to surface residues. We show that the buried substitutions greatly decrease protein stability, whereas the surface substitutions have only a marginal affect on stability. The surface substitutions are thus likely to interfere with Notch signaling by disrupting specific Notch-effector interactions and map the sites of these interactions.

Validity and repeatability of inertial measurement units for measuring gait parameters.

PubMed

Washabaugh, Edward P; Kalyanaraman, Tarun; Adamczyk, Peter G; Claflin, Edward S; Krishnan, Chandramouli

2017-06-01

Inertial measurement units (IMUs) are small wearable sensors that have tremendous potential to be applied to clinical gait analysis. They allow objective evaluation of gait and movement disorders outside the clinic and research laboratory, and permit evaluation on large numbers of steps. However, repeatability and validity data of these systems are sparse for gait metrics. The purpose of this study was to determine the validity and between-day repeatability of spatiotemporal metrics (gait speed, stance percent, swing percent, gait cycle time, stride length, cadence, and step duration) as measured with the APDM Opal IMUs and Mobility Lab system. We collected data on 39 healthy subjects. Subjects were tested over two days while walking on a standard treadmill, split-belt treadmill, or overground, with IMUs placed in two locations: both feet and both ankles. The spatiotemporal measurements taken with the IMU system were validated against data from an instrumented treadmill, or using standard clinical procedures. Repeatability and minimally detectable change (MDC) of the system was calculated between days. IMUs displayed high to moderate validity when measuring most of the gait metrics tested. Additionally, these measurements appear to be repeatable when used on the treadmill and overground. The foot configuration of the IMUs appeared to better measure gait parameters; however, both the foot and ankle configurations demonstrated good repeatability. In conclusion, the IMU system in this study appears to be both accurate and repeatable for measuring spatiotemporal gait parameters in healthy young adults. Copyright © 2017 Elsevier B.V. All rights reserved.

Online neural monitoring of statistical learning

PubMed Central

Batterink, Laura J.; Paller, Ken A.

2017-01-01

The extraction of patterns in the environment plays a critical role in many types of human learning, from motor skills to language acquisition. This process is known as statistical learning. Here we propose that statistical learning has two dissociable components: (1) perceptual binding of individual stimulus units into integrated composites and (2) storing those integrated representations for later use. Statistical learning is typically assessed using post-learning tasks, such that the two components are conflated. Our goal was to characterize the online perceptual component of statistical learning. Participants were exposed to a structured stream of repeating trisyllabic nonsense words and a random syllable stream. Online learning was indexed by an EEG-based measure that quantified neural entrainment at the frequency of the repeating words relative to that of individual syllables. Statistical learning was subsequently assessed using conventional measures in an explicit rating task and a reaction-time task. In the structured stream, neural entrainment to trisyllabic words was higher than in the random stream, increased as a function of exposure to track the progression of learning, and predicted performance on the RT task. These results demonstrate that monitoring this critical component of learning via rhythmic EEG entrainment reveals a gradual acquisition of knowledge whereby novel stimulus sequences are transformed into familiar composites. This online perceptual transformation is a critical component of learning. PMID:28324696

Structure revision of hupehensis saponin F and G and characterization of new trace triterpenoid saponins from Anemone hupehensis by tandem electrospray ionization mass spectrometry.

PubMed

Li, Fu; Liu, Xin; Tang, Minghai; Chen, Bin; Ding, Lisheng; Chen, Lijuan; Wang, Mingkui

2012-05-15

Electrospray ionization ion-trap tandem mass spectrometry (ESI-MS(n)) was first employed for reinvestigating the structures of hupehensis saponin F and G previously isolated from Anemone hupehensis in our lab. Hupehensis saponin G was determined to contain one more trisaccharide unit (Rha-(1→4)-Glc-(1→6)-Glc-), not a glucose residue, than saponin F based on their molecular weights deduced from their [M+Na](+) ions in ESI-MS spectra. The (2,4)A(4α)-ion at m/z 551.3 formed by retro-Diels-Alder (RDA) rearrangement in positive mode illustrated that the C-28 sugar chains of the two saponins were composed of trisaccharide repeating moieties with (1→4) linkages rather than (1→3) linkages. The interpretation of 2D-NMR spectra of the two compounds also confirmed the results obtained by ESI-MS(n). Moreover, from the water soluble part of A. hupehensis, two novel triterpene saponins were tentatively characterized to contain 4 and 5 (1→4)-linked above trisaccharide repeating moieties at C-28 position according to their ESI-MS(n) behaviors, respectively. Copyright © 2012 Elsevier Ltd. All rights reserved.

Uncertainty, variability, and earthquake physics in ground‐motion prediction equations

USGS Publications Warehouse

Baltay, Annemarie S.; Hanks, Thomas C.; Abrahamson, Norm A.

2017-01-01

Residuals between ground‐motion data and ground‐motion prediction equations (GMPEs) can be decomposed into terms representing earthquake source, path, and site effects. These terms can be cast in terms of repeatable (epistemic) residuals and the random (aleatory) components. Identifying the repeatable residuals leads to a GMPE with reduced uncertainty for a specific source, site, or path location, which in turn can yield a lower hazard level at small probabilities of exceedance. We illustrate a schematic framework for this residual partitioning with a dataset from the ANZA network, which straddles the central San Jacinto fault in southern California. The dataset consists of more than 3200 1.15≤M≤3 earthquakes and their peak ground accelerations (PGAs), recorded at close distances (R≤20  km). We construct a small‐magnitude GMPE for these PGA data, incorporating VS30 site conditions and geometrical spreading. Identification and removal of the repeatable source, path, and site terms yield an overall reduction in the standard deviation from 0.97 (in ln units) to 0.44, for a nonergodic assumption, that is, for a single‐source location, single site, and single path. We give examples of relationships between independent seismological observables and the repeatable terms. We find a correlation between location‐based source terms and stress drops in the San Jacinto fault zone region; an explanation of the site term as a function of kappa, the near‐site attenuation parameter; and a suggestion that the path component can be related directly to elastic structure. These correlations allow the repeatable source location, site, and path terms to be determined a priori using independent geophysical relationships. Those terms could be incorporated into location‐specific GMPEs for more accurate and precise ground‐motion prediction.

Structure of thrombospondin type 3 repeats in bacterial outer membrane protein A reveals its intra-repeat disulfide bond-dependent calcium-binding capability

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

Dai, Shuyan; Sun, Cancan; Tan, Kemin

Eukaryotic thrombospondin type 3 repeat (TT3R) is an efficient calcium ion (Ca2+) binding motif only found in mammalian thrombospondin family. TT3R has also been found in prokaryotic cellulase Cel5G, which was thought to forfeit the Ca2+-binding capability due to the formation of intra-repeat disulfide bonds, instead of the inter-repeat ones possessed by eukaryotic TT3Rs. In this study, we have identified an enormous number of prokaryotic TT3R-containing proteins belonging to several different protein families, including outer membrane protein A (OmpA), an important structural protein connecting the outer membrane and the periplasmic peptidoglycan layer in gram-negative bacteria. Here, we report the crystalmore » structure of the periplasmic region of OmpA from Capnocytophaga gingivalis, which contains a linker region comprising five consecutive TT3Rs. The structure of OmpA-TT3R exhibits a well-ordered architecture organized around two tightly-coordinated Ca2+ and confirms the presence of abnormal intra-repeat disulfide bonds. Further mutagenesis studies showed that the Ca2+-binding capability of OmpA-TT3R is indeed dependent on the proper formation of intra-repeat disulfide bonds, which help to fix a conserved glycine residue at its proper position for Ca2+ coordination. Additionally, despite lacking inter repeat disulfide bonds, the interfaces between adjacent OmpA-TT3Rs are enhanced by both hydrophobic and conserved aromatic-proline interactions.« less

Direct Observation of Parallel Folding Pathways Revealed Using a Symmetric Repeat Protein System

PubMed Central

Aksel, Tural; Barrick, Doug

2014-01-01

Although progress has been made to determine the native fold of a polypeptide from its primary structure, the diversity of pathways that connect the unfolded and folded states has not been adequately explored. Theoretical and computational studies predict that proteins fold through parallel pathways on funneled energy landscapes, although experimental detection of pathway diversity has been challenging. Here, we exploit the high translational symmetry and the direct length variation afforded by linear repeat proteins to directly detect folding through parallel pathways. By comparing folding rates of consensus ankyrin repeat proteins (CARPs), we find a clear increase in folding rates with increasing size and repeat number, although the size of the transition states (estimated from denaturant sensitivity) remains unchanged. The increase in folding rate with chain length, as opposed to a decrease expected from typical models for globular proteins, is a clear demonstration of parallel pathways. This conclusion is not dependent on extensive curve-fitting or structural perturbation of protein structure. By globally fitting a simple parallel-Ising pathway model, we have directly measured nucleation and propagation rates in protein folding, and have quantified the fluxes along each path, providing a detailed energy landscape for folding. This finding of parallel pathways differs from results from kinetic studies of repeat-proteins composed of sequence-variable repeats, where modest repeat-to-repeat energy variation coalesces folding into a single, dominant channel. Thus, for globular proteins, which have much higher variation in local structure and topology, parallel pathways are expected to be the exception rather than the rule. PMID:24988356

Impact of repeated uniaxial mechanical strain on flexible a-IGZO thin film transistors with symmetric and asymmetric structures

NASA Astrophysics Data System (ADS)

Liao, Po-Yung; Chang, Ting-Chang; Su, Wan-Ching; Chen, Bo-Wei; Chen, Li-Hui; Hsieh, Tien-Yu; Yang, Chung-Yi; Chang, Kuan-Chang; Zhang, Sheng-Dong; Huang, Yen-Yu; Chang, Hsi-Ming; Chiang, Shin-Chuan

2017-06-01

This letter investigates repeated uniaxial mechanical stress-induced degradation behavior in flexible amorphous In-Ga-Zn-O thin-film transistors (TFTs) of different geometric structures. Two types of via-contact structure TFTs are investigated: symmetrical and UI structure (TFTs with I- and U-shaped asymmetric electrodes). After repeated mechanical stress, I-V curves for the symmetrical structure show a significant negative threshold voltage (VT) shift, due to mechanical stress-induced oxygen vacancy generation. However, degradation in the UI structure TFTs after stress is a negative VT shift along with the parasitic transistor characteristic in the forward-operation mode, with this hump not evident in the reverse-operation mode. This asymmetrical degradation is clarified by the mechanical strain simulation of the UI TFTs.

Expression, crystallization and preliminary crystallographic analysis of RNA-binding protein Hfq (YmaH) from Bacillus subtilis in complex with an RNA aptamer

PubMed Central

Baba, Seiki; Someya, Tatsuhiko; Kawai, Gota; Nakamura, Kouji; Kumasaka, Takashi

2010-01-01

The Hfq protein is a hexameric RNA-binding protein which regulates gene expression by binding to RNA under the influence of diverse environmental stresses. Its ring structure binds various types of RNA, including mRNA and sRNA. RNA-bound structures of Hfq from Escherichia coli and Staphylococcus aureus have been revealed to have poly(A) RNA at the distal site and U-rich RNA at the proximal site, respectively. Here, crystals of a complex of the Bacillus subtilis Hfq protein with an A/G-repeat 7-mer RNA (Hfq–RNA) that were prepared using the hanging-drop vapour-diffusion technique are reported. The type 1 Hfq–RNA crystals belonged to space group I422, with unit-cell parameters a = b = 123.70, c = 119.13 Å, while the type 2 Hfq–RNA crystals belonged to space group F222, with unit-cell parameters a = 91.92, b = 92.50, c = 114.92 Å. Diffraction data were collected to a resolution of 2.20 Å from both crystal forms. The hexameric structure of the Hfq protein was clearly shown by self-rotation analysis. PMID:20445260

Periodic cation segregation in Cs0.44[Nb2.54W2.46O14] quantified by high-resolution scanning transmission electron microscopy.

PubMed

Heidelmann, Markus; Barthel, Juri; Cox, Gerhard; Weirich, Thomas E

2014-10-01

The atomic structure of Cs0.44[Nb2.54W2.46O14] closely resembles the structure of the most active catalyst for the synthesis of acrylic acid, the M1 phase of Mo10V2(4+)Nb2TeO42-x. Consistently with observations made for the latter compound, the high-angle electron scattering signal recorded by scanning transmission electron microscopy shows a significant intensity variation, which repeats periodically with the projected crystallographic unit cell. The occupation factors for the individual mixed Nb/W atomic columns are extracted from the observed intensity variations. For this purpose, experimental images and simulated images are compared on an identical intensity scale, which enables a quantification of the cation distribution. According to our analysis specific sites possess low tungsten concentrations of 25%, whereas other sites have tungsten concentrations above 70%. These findings allow us to refine the existing structure model of the target compound, which has until now described a uniform distribution of the niobium and tungsten atoms in the unit cell, showing that the similarity between Cs0.44[Nb2.54W2.46O14] and the related catalytic compounds also extends to the level of the cation segregation.

Role of Precambrian compositions and fabrics in the development of foreland structures, southern Front Range, Colorado

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

Chase, R.B.

1985-01-01

The Front Range terminates to the south as three basement-cored uplifts located north and west of the Canon City embayment. Precambrian units consist of foliated and non-foliated granitic rocks, augen gneiss, interlayered schist and gneiss, amphibolite, quartzite, and pegmatite. Precambrian deformations include at least three phases of folding, two phases of crenulation cleavage development, and local mylonitization. Metamorphic conditions reached those of cordierite-sillimanite grade. Paleozoic and Mesozoic sediments surround and overlap the exposed uplifts to form south-plunging arches. Excellent three-dimensional exposure of structural relationships between Precambrian rocks and overlying Phanerozoic sediments is present. Deformation styles in the sedimentary cover aremore » strongly influenced by underlying Precambrian lithologies and structural orientations. Where the crystalline units are granitic, with steeply-dipping foliation or no directional fabric, uplifts are bounded by high angle faults. Some such faults show evidence of repeated movements and reversals dating back to Precambrian time. The boundary between mechanical basement and suprastructure is clearly not defined as the base of the sedimentary section. Balanced cross-sections constructed through the southern Front Range must include contemporaneous flexural folds and thrusts in Precambrian schistose and gneissic rocks as well as in Phanerozoic sedimentary layers.« less

Rational Design of High-Performance Wide-Bandgap (≈2 eV) Polymer Semiconductors as Electron Donors in Organic Photovoltaics Exhibiting High Open Circuit Voltages (≈1 V).

PubMed

Chochos, Christos L; Katsouras, Athanasios; Gasparini, Nicola; Koulogiannis, Chrysanthos; Ameri, Tayebeh; Brabec, Christoph J; Avgeropoulos, Apostolos

2017-01-01

Systematic optimization of the chemical structure of wide-bandgap (≈2.0 eV) "donor-acceptor" copolymers consisting of indacenodithiophene or indacenodithieno[3,2-b]thiophene as the electron-rich unit and thieno[3,4-c]pyrrole-4,6-dione as the electron-deficient moiety in terms of alkyl side chain engineering and distance of the electron-rich and electron-deficient monomers within the repeat unit of the polymer chain results in high-performance electron donor materials for organic photovoltaics. Specifically, preliminary results demonstrate extremely high open circuit voltages (V oc s) of ≈1.0 V, reasonable short circuit current density (J sc ) of around 11 mA cm -2 , and moderate fill factors resulting in efficiencies close to 6%. All the devices are fabricated in an inverted architecture with the photoactive layer processed by doctor blade equipment, showing the compatibility with roll-to-roll large-scale manufacturing processes. From the correlation of the chemical structure-optoelectronic properties-photovoltaic performance, a rational guide toward further optimization of the chemical structure in this family of copolymers, has been achieved. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The impact of lignin source on its self-assembly in solution

DOE PAGES

Ratnaweera, Dilru R.; Saha, Dipendu; Pingali, Sai Venkatesh; ...

2015-07-30

Recently, there has been a growing interest in developing value added uses for lignin, including the utilization of lignins as a precursor for carbon materials. Proper understanding of the association behavior of lignins during solution processing provides important structural information that is needed to rationally optimize the use of lignins in industry in a range of value added applications. In this paper, we follow the assembly of lignin molecules from a variety of sources in dimethyl sulfoxide, a good solvent for lignins, using small angle neutron scattering. In order to mimic industrial processing conditions, concentrations of lignins were kept abovemore » the overlap concentration. At small length scales, short lignin segments with ~4–10 monolignol units associate to form rigid rod-like/cylindrical building blocks, where the number of repeat units in a cylindrical segment decreases with increasing lignin concentration. These cylindrical building blocks associate to form aggregates with low cross-linking densities and a random coil or network like structures from highly branched lignin structures. The degree of branching of the base lignin molecule, which varies with source, plays a crucial role in determining their association behavior. Finally, the overall sizes of the aggregates decrease with increasing concentration at low cross-linking densities, whereas the opposite trend is observed for highly branched lignins.« less

Rapid development of microsatellite markers with 454 pyrosequencing in a vulnerable fish, the mottled skate, Raja pulchra.

PubMed

Kang, Jung-Ha; Park, Jung-Youn; Jo, Hyun-Su

2012-01-01

The mottled skate, Raja pulchra, is an economically valuable fish. However, due to a severe population decline, it is listed as a vulnerable species by the International Union for Conservation of Nature. To analyze its genetic structure and diversity, microsatellite markers were developed using 454 pyrosequencing. A total of 17,033 reads containing dinucleotide microsatellite repeat units (mean, 487 base pairs) were identified from 453,549 reads. Among 32 loci containing more than nine repeat units, 20 primer sets (62%) produced strong PCR products, of which 14 were polymorphic. In an analysis of 60 individuals from two R. pulchra populations, the number of alleles per locus ranged from 1-10, and the mean allelic richness was 4.7. No linkage disequilibrium was found between any pair of loci, indicating that the markers were independent. The Hardy-Weinberg equilibrium test showed significant deviation in two of the 28 single-loci after sequential Bonferroni's correction. Using 11 primer sets, cross-species amplification was demonstrated in nine related species from four families within two classes. Among the 11 loci amplified from three other Rajidae family species; three loci were polymorphic. A monomorphic locus was amplified in all three Rajidae family species and the Dasyatidae family. Two Rajidae polymorphic loci amplified monomorphic target DNAs in four species belonging to the Carcharhiniformes class, and another was polymorphic in two Carcharhiniformes species.

Rapid Development of Microsatellite Markers with 454 Pyrosequencing in a Vulnerable Fish, the Mottled Skate, Raja pulchra

PubMed Central

Kang, Jung-Ha; Park, Jung-Youn; Jo, Hyun-Su

2012-01-01

The mottled skate, Raja pulchra, is an economically valuable fish. However, due to a severe population decline, it is listed as a vulnerable species by the International Union for Conservation of Nature. To analyze its genetic structure and diversity, microsatellite markers were developed using 454 pyrosequencing. A total of 17,033 reads containing dinucleotide microsatellite repeat units (mean, 487 base pairs) were identified from 453,549 reads. Among 32 loci containing more than nine repeat units, 20 primer sets (62%) produced strong PCR products, of which 14 were polymorphic. In an analysis of 60 individuals from two R. pulchra populations, the number of alleles per locus ranged from 1–10, and the mean allelic richness was 4.7. No linkage disequilibrium was found between any pair of loci, indicating that the markers were independent. The Hardy–Weinberg equilibrium test showed significant deviation in two of the 28 single-loci after sequential Bonferroni’s correction. Using 11 primer sets, cross-species amplification was demonstrated in nine related species from four families within two classes. Among the 11 loci amplified from three other Rajidae family species; three loci were polymorphic. A monomorphic locus was amplified in all three Rajidae family species and the Dasyatidae family. Two Rajidae polymorphic loci amplified monomorphic target DNAs in four species belonging to the Carcharhiniformes class, and another was polymorphic in two Carcharhiniformes species. PMID:22837688

19 CFR 10.619 - Repeated false or unsupported preference claims.

Code of Federal Regulations, 2010 CFR

2010-04-01

... Republic-Central America-United States Free Trade Agreement Origin Verifications and Determinations § 10... 19 Customs Duties 1 2010-04-01 2010-04-01 false Repeated false or unsupported preference claims. 10.619 Section 10.619 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT OF HOMELAND...

40 CFR 1066.20 - Units of measure and overview of calculations.

Code of Federal Regulations, 2014 CFR

2014-07-01

... POLLUTION CONTROLS VEHICLE-TESTING PROCEDURES Applicability and General Provisions § 1066.20 Units of..., repeatability, linearity, or noise specification. See 40 CFR 1065.1001 for the definition of tolerance. In this...

Hydration of sulfonated polyimide membranes. I. Na + and NH +(C 2H 5) 3 homopolymers

NASA Astrophysics Data System (ADS)

Jamróz, Dorota; Maréchal, Yves

2004-05-01

Hydration of Na + and HN +(C 2H 5) 3 sulfonated polyimide membranes is probed by infrared spectrometry using a recently described method. These membranes consist of identical sulfonated repeat unit (homopolymers) and form a good starting point to study more elaborated membranes, composed of these units plus similar ones with no sulfonic groups (block copolymers). These latter membranes may be used in fuel cells and will be described in a forthcoming article. We first identify the bands of hydrophilic groups, which will be anchor points for hydration. We then define three 'elementary hydration spectra' onto which all hydration spectra can be decomposed. Their analysis allows us to measure the water uptake of these membranes as a function of the hygrometry of the ambient atmosphere and to determine the structures of the dried membranes and their hydration mechanisms in terms of chemical reactions.

Twisting Right to Left: A…A Mismatch in a CAG Trinucleotide Repeat Overexpansion Provokes Left-Handed Z-DNA Conformation

PubMed Central

2015-01-01

Conformational polymorphism of DNA is a major causative factor behind several incurable trinucleotide repeat expansion disorders that arise from overexpansion of trinucleotide repeats located in coding/non-coding regions of specific genes. Hairpin DNA structures that are formed due to overexpansion of CAG repeat lead to Huntington’s disorder and spinocerebellar ataxias. Nonetheless, DNA hairpin stem structure that generally embraces B-form with canonical base pairs is poorly understood in the context of periodic noncanonical A…A mismatch as found in CAG repeat overexpansion. Molecular dynamics simulations on DNA hairpin stems containing A…A mismatches in a CAG repeat overexpansion show that A…A dictates local Z-form irrespective of starting glycosyl conformation, in sharp contrast to canonical DNA duplex. Transition from B-to-Z is due to the mechanistic effect that originates from its pronounced nonisostericity with flanking canonical base pairs facilitated by base extrusion, backbone and/or base flipping. Based on these structural insights we envisage that such an unusual DNA structure of the CAG hairpin stem may have a role in disease pathogenesis. As this is the first study that delineates the influence of a single A…A mismatch in reversing DNA helicity, it would further have an impact on understanding DNA mismatch repair. PMID:25876062

Variable Number Of Tandem Repeats (VNTR) and its application in bacterial epidemiology.

PubMed

Ramazanzadeh, Rashid; McNerney, Ruth

2007-08-15

Molecular epidemiology is the using of molecular techniques to study bacterial distribution in human populations. Recently molecular epidemiologist benefit from several techniques such as Variable Number Tandem Repeat (VNTR) typing method to typing bacterial strains. Variable Number Tandem Repeat (VNTR) typing is a tool for genotyping and provides data in a simple and numeric format based on the number of repetitive sequences. VNTR for first time identified in M. tuberculosis as Mycobacterial Interspersed Repeat Units (MIRUs). General terms of VNTR have now been reported in Bacillus anthracis, Legionella pneumophila, Pseudomonas aeruginosa, Salmonella enterica and Escherichia coli O157.

Thymidylate synthase repeat polymorphisms and risk of neural tube defects in a population from the northern United Kingdom.

PubMed

Wilding, Craig S; Relton, Caroline L; Sutton, Matthew J; Jonas, Pat A; Lynch, Sally-Ann; Tawn, E Janet; Burn, John

2004-07-01

A 28-bp repeat polymorphism in the 5'UTR of the thymidylate synthase (TYMS) gene represents a candidate risk factor for neural tube defects (NTDs) due to involvement in folate-dependent homocysteine metabolism. Non-Hispanic, white, U.S. citizens carrying at least one 2x 28-bp repeat allele have recently been shown to be at a four-fold increased risk of spina bifida (SB). We investigated the association between this polymorphism and risk of NTD in families affected by NTDs and controls from the northern United Kingdom (UK). PCR was performed on genomic DNA extracted from blood or mouth swabs of family members affected by NTDs (mothers, fathers, and cases), and unaffected controls (mothers and infants) to determine the number of 28-bp repeat units within the promoter region of TYMS. Case-control and TDT analyses of the influence of TYMS genotype on risk of NTD, or NTD pregnancy, were conducted. Odds ratio (OR) analysis indicated that individuals carrying the 2x 28-bp repeat allele either in homozygous or heterozygous form, are not at increased risk of NTDs, or of having an NTD affected pregnancy. Control population allele frequencies are seen to be markedly different between the U.S. controls and those in this study. TYMS polymorphism appears to be not universally associated with NTD risk across Caucasian samples. The elevated risk of spina bifida in U.S. samples appears to be driven by an unusually low risk allele (2x 28 bp) frequency in control samples. Family based (TDT) testing of U.S. samples is therefore advocated.

Novel fiber optic immunosensor instrument

NASA Astrophysics Data System (ADS)

Wang, Zhiyu; Huang, Wenling; Tang, Lei; Zhou, Bo; Li, Yugi; He, Jun

1996-09-01

It has developed and performed a novel fiberoptic immunosensor instrument with operating wavelength 400 - 760 nm and repeatability cv equals 0.27%. The instrument has many excellent features such as simplified operation, faster testing time, higher sensitivity and economic cost. It has completely eliminated recovery period which traditional immunosensor owned due to use separative sensor structure. It can widely apply to test for bacteria, virus, hormone, parasite and cancer protein in clinical examination. The instrument has operated in laboratory and relevant medicine units and successfully tested monoclonal rat-anti-human of 413 cases in clinic and prepared with existing ELISA method, the coincidence probability reached 94 to 100%.

Care of adolescent parents and their children.

PubMed

Pinzon, Jorge L; Jones, Veronnie F

2012-12-01

Teen pregnancy and parenting remain an important public health issue in the United States and the world, and many children live with their adolescent parents alone or as part of an extended family. A significant proportion of teen parents reside with their family of origin, significantly affecting the multigenerational family structure. Repeated births to teen parents are also common. This clinical report updates a previous policy statement on care of the adolescent parent and their children and addresses medical and psychosocial risks specific to this population. Challenges unique to teen parents and their children are reviewed, along with suggestions for the pediatrician on models for intervention and care.

Assessing the 5S ribosomal RNA heterogeneity in Arabidopsis thaliana using short RNA next generation sequencing data.

PubMed

Szymanski, Maciej; Karlowski, Wojciech M

2016-01-01

In eukaryotes, ribosomal 5S rRNAs are products of multigene families organized within clusters of tandemly repeated units. Accumulation of genomic data obtained from a variety of organisms demonstrated that the potential 5S rRNA coding sequences show a large number of variants, often incompatible with folding into a correct secondary structure. Here, we present results of an analysis of a large set of short RNA sequences generated by the next generation sequencing techniques, to address the problem of heterogeneity of the 5S rRNA transcripts in Arabidopsis and identification of potentially functional rRNA-derived fragments.

Super Secondary Structure Consisting of a Polyproline II Helix and a β-Turn in Leucine Rich Repeats in Bacterial Type III Secretion System Effectors.

PubMed

Batkhishig, Dashdavaa; Bilguun, Khurelbaatar; Enkhbayar, Purevjav; Miyashita, Hiroki; Kretsinger, Robert H; Matsushima, Norio

2018-06-01

Leucine rich repeats (LRRs) are present in over 100,000 proteins from viruses to eukaryotes. The LRRs are 20-30 residues long and occur in tandem. LRRs form parallel stacks of short β-strands and then assume a super helical arrangement called a solenoid structure. Individual LRRs are separated into highly conserved segment (HCS) with the consensus of LxxLxLxxNxL and variable segment (VS). Eight classes have been recognized. Bacterial LRRs are short and characterized by two prolines in the VS; the consensus is xxLPxLPxx with Nine residues (N-subtype) and xxLPxxLPxx with Ten residues (T-subtype). Bacterial LRRs are contained in type III secretion system effectors such as YopM, IpaH3/9.8, SspH1/2, and SlrP from bacteria. Some LRRs in decorin, fribromodulin, TLR8/9, and FLRT2/3 from vertebrate also contain the motifs. In order to understand structural features of bacterial LRRs, we performed both secondary structures assignments using four programs-DSSP-PPII, PROSS, SEGNO, and XTLSSTR-and HELFIT analyses (calculating helix axis, pitch, radius, residues per turn, and handedness), based on the atomic coordinates of their crystal structures. The N-subtype VS adopts a left handed polyproline II helix (PPII) with four, five or six residues and a type I β-turn at the C-terminal side. Thus, the N-subtype is characterized by a super secondary structure consisting of a PPII and a β-turn. In contrast, the T-subtype VS prefers two separate PPIIs with two or three and two residues. The HELFIT analysis indicates that the type I β-turn is a right handed helix. The HELFIT analysis determines three unit vectors of the helix axes of PPII (P), β-turn (B), and LRR domain (A). Three structural parameters using these three helix axes are suggested to characterize the super secondary structure and the LRR domain.

Implementation of a Smeared Crack Band Model in a Micromechanics Framework

NASA Technical Reports Server (NTRS)

Pineda, Evan J.; Bednarcyk, Brett A.; Waas, Anthony M.; Arnold, Steven M.

2012-01-01

The smeared crack band theory is implemented within the generalized method of cells and high-fidelity generalized method of cells micromechanics models to capture progressive failure within the constituents of a composite material while retaining objectivity with respect to the size of the discretization elements used in the model. An repeating unit cell containing 13 randomly arranged fibers is modeled and subjected to a combination of transverse tension/compression and transverse shear loading. The implementation is verified against experimental data (where available), and an equivalent finite element model utilizing the same implementation of the crack band theory. To evaluate the performance of the crack band theory within a repeating unit cell that is more amenable to a multiscale implementation, a single fiber is modeled with generalized method of cells and high-fidelity generalized method of cells using a relatively coarse subcell mesh which is subjected to the same loading scenarios as the multiple fiber repeating unit cell. The generalized method of cells and high-fidelity generalized method of cells models are validated against a very refined finite element model.

Progressive Failure of a Unidirectional Fiber-Reinforced Composite Using the Method of Cells: Discretization Objective Computational Results

NASA Technical Reports Server (NTRS)

Pineda, Evan J.; Bednarcyk, Brett A.; Waas, Anthony M.; Arnold, Steven M.

2012-01-01

The smeared crack band theory is implemented within the generalized method of cells and high-fidelity generalized method of cells micromechanics models to capture progressive failure within the constituents of a composite material while retaining objectivity with respect to the size of the discretization elements used in the model. An repeating unit cell containing 13 randomly arranged fibers is modeled and subjected to a combination of transverse tension/compression and transverse shear loading. The implementation is verified against experimental data (where available), and an equivalent finite element model utilizing the same implementation of the crack band theory. To evaluate the performance of the crack band theory within a repeating unit cell that is more amenable to a multiscale implementation, a single fiber is modeled with generalized method of cells and high-fidelity generalized method of cells using a relatively coarse subcell mesh which is subjected to the same loading scenarios as the multiple fiber repeating unit cell. The generalized method of cells and high-fidelity generalized method of cells models are validated against a very refined finite element model.

The Chromatin Remodeler Isw1 Prevents CAG Repeat Expansions During Transcription in Saccharomyces cerevisiae

PubMed Central

Koch, Melissa R.; House, Nealia C. M.; Cosetta, Casey M.; Jong, Robyn M.; Salomon, Christelle G.; Joyce, Cailin E.; Philips, Elliot A.; Su, Xiaofeng A.; Freudenreich, Catherine H.

2018-01-01

CAG/CTG trinucleotide repeats are unstable sequences that are difficult to replicate, repair, and transcribe due to their structure-forming nature. CAG repeats strongly position nucleosomes; however, little is known about the chromatin remodeling needed to prevent repeat instability. In a Saccharomyces cerevisiae model system with CAG repeats carried on a YAC, we discovered that the chromatin remodeler Isw1 is required to prevent CAG repeat expansions during transcription. CAG repeat expansions in the absence of Isw1 were dependent on both transcription-coupled repair (TCR) and base-excision repair (BER). Furthermore, isw1∆ mutants are sensitive to methyl methanesulfonate (MMS) and exhibit synergistic MMS sensitivity when combined with BER or TCR pathway mutants. We conclude that CAG expansions in the isw1∆ mutant occur during a transcription-coupled excision repair process that involves both TCR and BER pathways. We observed increased RNA polymerase II (RNAPII) occupancy at the CAG repeat when transcription of the repeat was induced, but RNAPII binding did not change in isw1∆ mutants, ruling out a role for Isw1 remodeling in RNAPII progression. However, nucleosome occupancy over a transcribed CAG tract was altered in isw1∆ mutants. Based on the known role of Isw1 in the reestablishment of nucleosomal spacing after transcription, we suggest that a defect in this function allows DNA structures to form within repetitive DNA tracts, resulting in inappropriate excision repair and repeat-length changes. These results establish a new function for Isw1 in directly maintaining the chromatin structure at the CAG repeat, thereby limiting expansions that can occur during transcription-coupled excision repair. PMID:29305386

The temporal characteristics of humpback whale songs

NASA Astrophysics Data System (ADS)

Au, Whitlow W. L.; Lammers, Marc O.; Stimpert, Alison; Schotten, Michiel

2005-09-01

Songs sung by male humpback whales consist of distinct, pulsed sounds that are designated as units. Units are produced in some sequence to form a phrase, a repeated set of phrases forms a theme, and repeated themes form a song. A song can last from minutes to hours. The songs of eight humpback whales were recorded with a vertical array of five hydrophones spaced 7 m apart with the array located within 100 m of the whales. At least seven distinct units were identified aurally from this data set obtained during the 2002 winter humpback whale session in Hawaii. Four distinct recurring themes were found in the songs, and for each whale at least two themes were recorded. The average duration of each unit sampled and the silent interval following the unit were determined in order to describe the temporal characteristics of the songs. From the data the temporal consistency and cadence control of unit production by each humpback whale and between whales were determined. Understanding the temporal and spectral characteristics of units within songs and how these units vary between whales could ultimately help in the design of computer algorithms to automatically identify individual whales.

Y-chromosomal testing of brown bears (Ursus arctos): Validation of a multiplex PCR-approach for nine STRs suitable for fecal and hair samples.

PubMed

Aarnes, Siv Grethe; Hagen, Snorre B; Andreassen, Rune; Schregel, Julia; Knappskog, Per M; Hailer, Frank; Stenhouse, Gordon; Janke, Axel; Eiken, Hans Geir

2015-11-01

High-resolution Y-chromosomal markers have been applied to humans and other primates to study population genetics, migration, social structures and reproduction. Y-linked markers allow the direct assessment of the genetic structure and gene flow of uniquely male inherited lineages and may also be useful for wildlife conservation and forensics, but have so far been available only for few wild species. Thus, we have developed two multiplex PCR reactions encompassing nine Y-STR markers identified from the brown bear (Ursus arctos) and tested them on hair, fecal and tissue samples. The multiplex PCR approach was optimized and analyzed for species specificity, sensitivity and stutter-peak ratios. The nine Y-STRs also showed specific STR-fragments for male black bears and male polar bears, while none of the nine markers produced any PCR products when using DNA from female bears or males from 12 other mammals. The multiplex PCR approach in two PCR reactions could be amplified with as low as 0.2 ng template input. Precision was high in DNA templates from hairs, fecal scats and tissues, with standard deviations less than 0.14 and median stutter ratios from 0.04 to 0.63. Among the eight di- and one tetra-nucleotide repeat markers, we detected simple repeat structures in seven of the nine markers with 9-25 repeat units. Allelic variation was found for eight of the nine Y-STRs, with 2-9 alleles for each marker and a total of 36 alleles among 453 male brown bears sampled mainly from Northern Europe. We conclude that the multiplex PCR approach with these nine Y-STRs would provide male bear Y-chromosomal specificity and evidence suited for samples from conservation and wildlife forensics. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Divergent Synthesis of Chondroitin Sulfate Disaccharides and Identification of Sulfate Motifs that Inhibit Triple Negative Breast Cancer

NASA Astrophysics Data System (ADS)

Wei Poh, Zhong; Heng Gan, Chin; Lee, Eric J.; Guo, Suxian; Yip, George W.; Lam, Yulin

2015-09-01

Glycosaminoglycans (GAGs) regulate many important physiological processes. A pertinent issue to address is whether GAGs encode important functional information via introduction of position specific sulfate groups in the GAG structure. However, procurement of pure, homogenous GAG motifs to probe the “sulfation code” is a challenging task due to isolation difficulty and structural complexity. To this end, we devised a versatile synthetic strategy to obtain all the 16 theoretically possible sulfation patterns in the chondroitin sulfate (CS) repeating unit; these include rare but potentially important sulfated motifs which have not been isolated earlier. Biological evaluation indicated that CS sulfation patterns had differing effects for different breast cancer cell types, and the greatest inhibitory effect was observed for the most aggressive, triple negative breast cancer cell line MDA-MB-231.

Redetermination of AgPO(3).

PubMed

Terebilenko, Katherina V; Zatovsky, Igor V; Ogorodnyk, Ivan V; Baumer, Vyacheslav N; Slobodyanik, Nikolay S

2011-02-09

Single crystals of silver(I) polyphosphate(V), AgPO(3), were prepared via a phospho-ric acid melt method using a solution of Ag(3)PO(4) in H(3)PO(4). In comparison with the previous study based on single-crystal Weissenberg photographs [Jost (1961 ▶). Acta Cryst. 14, 779-784], the results were mainly confirmed, but with much higher precision and with all displacement parameters refined anisotropically. The structure is built up from two types of distorted edge- and corner-sharing [AgO(5)] polyhedra, giving rise to multidirectional ribbons, and from two types of PO(4) tetra-hedra linked into meandering chains (PO(3))(n) spreading parallel to the b axis with a repeat unit of four tetra-hedra. The calculated bond-valence sum value of one of the two Ag(I) ions indicates a significant strain of the structure.

Structure determination of the neutral exopolysaccharide produced by Lactobacillus delbrueckii subsp. bulgaricus OLL1073R-1.

PubMed

Van Calsteren, Marie-Rose; Gagnon, Fleur; Nishimura, Junko; Makino, Seiya

2015-09-02

The neutral exopolysaccharide (NPS) of Lactobacillus delbrueckii subsp. bulgaricus strain OLL1073R-1 was purified and characterized. The molecular mass was 5.0×10(6) g/mol. Sugar and absolute configuration analyses gave the following composition: d-Glc, 1; d-Gal, 1.5. The NPS was also submitted to periodate oxidation followed by borohydride reduction and Smith degradation. Sugar and methylation analyses, (1)H and (13)C nuclear magnetic resonance, and mass spectrometry of the NPS or of its specifically modified products allowed determining the repeating unit sequence: {2)Glc(α1-3)Glc(β1-3)[Gal(β1-4)]Gal(β1-4)Gal(α1-}n. The structure is compared to that of exopolysaccharides produced by other Lactobacillus bulgaricus strains. Copyright © 2015. Published by Elsevier Ltd.

Structure of fructo-oligosaccharides from leaves and stem of Agave tequilana Weber, var. azul.

PubMed

Praznik, Werner; Löppert, Renate; Cruz Rubio, Josè M; Zangger, Klaus; Huber, Anton

2013-11-15

Fructo-oligosaccharides (FOSs) of a six year old agave plant variety, Agave tequilana, were isolated and fractionated by 2D preparative chromatography (SEC and rpHPLC). Structural analyses of different FOS-fractions were performed by reductive methylation analysis connected to GC/FID identification and NMR-analysis. FOSs from leaves (d.p. 3-8) contain single α-d-Glcp residues as well in terminal as internal position, however (2→1)-linked β-d-Fruf residues only. FOSs from stem, however, contain as well (2→1)- and (2→6)-linked β-d-Fruf residues with branched oligomeric repeating units. These characteristics indicate an enzymatically catalyzed metabolic regulation for the biosynthesis and transformation of fructans in A. tequilana which strongly depends on location and transport activities. Copyright © 2013 Elsevier Ltd. All rights reserved.

Differences among the cell wall galactomannans from Aspergillus wentii and Chaetosartorya chrysella and that of Aspergillus fumigatus.

PubMed

Gómez-Miranda, Begoña; Prieto, Alicia; Leal, Juan Antonio; Ahrazem, Oussama; Jiménez-Barbero, Jesús; Bernabé, Manuel

2004-01-01

The alkali extractable and water-soluble cell wall polysaccharides F1SS from Aspergillus wentii and Chaetosartorya chrysella have been studied by methylation analysis, 1D- and 2D-NMR, and MALDI-TOF analysis. Their structures are almost identical, corresponding to the following repeating unit: [--> 3)-beta-D-Gal f -(1 --> 5)-beta-D-Gal f-(1 -->]n --> mannan core. The structure of this galactofuranose side chain differs from that found in the pathogenic fungus Aspergillus fumigatus, in other Aspergillii and members of Trichocomaceae: [--> 5)-beta-D-Gal f-(1 -->]n --> mannan core. The mannan cores have also been investigated, and are constituted by a (1 --> 6)-alpha-mannan backbone, substituted at positions 2 by chains from 1 to 7 residues of (1 --> 2) linked alpha-mannopyranoses. Copyright 2004 Kluwer Academic Publishers

Crystallographic and Computational Analyses of AUUCU Repeating RNA That Causes Spinocerebellar Ataxia Type 10 (SCA10).

PubMed

Park, HaJeung; González, Àlex L; Yildirim, Ilyas; Tran, Tuan; Lohman, Jeremy R; Fang, Pengfei; Guo, Min; Disney, Matthew D

2015-06-23

Spinocerebellar ataxia type 10 (SCA10) is caused by a pentanucleotide repeat expansion of r(AUUCU) within intron 9 of the ATXN10 pre-mRNA. The RNA causes disease by a gain-of-function mechanism in which it inactivates proteins involved in RNA biogenesis. Spectroscopic studies showed that r(AUUCU) repeats form a hairpin structure; however, there were no high-resolution structural models prior to this work. Herein, we report the first crystal structure of model r(AUUCU) repeats refined to 2.8 Å and analysis of the structure via molecular dynamics simulations. The r(AUUCU) tracts adopt an overall A-form geometry in which 3 × 3 nucleotide (5')UCU(3')/(3')UCU(5') internal loops are closed by AU pairs. Helical parameters of the refined structure as well as the corresponding electron density map on the crystallographic model reflect dynamic features of the internal loop. The computational analyses captured dynamic motion of the loop closing pairs, which can form single-stranded conformations with relatively low energies. Overall, the results presented here suggest the possibility for r(AUUCU) repeats to form metastable A-from structures, which can rearrange into single-stranded conformations and attract proteins such as heterogeneous nuclear ribonucleoprotein K (hnRNP K). The information presented here may aid in the rational design of therapeutics targeting this RNA.

Crystallographic and Computational Analyses of AUUCU Repeating RNA That Causes Spinocerebellar Ataxia Type 10 (SCA10)

PubMed Central

Park, HaJeung; González, Àlex L.; Yildirim, Ilyas; Tran, Tuan; Lohman, Jeremy R.; Fang, Pengfei; Guo, Min; Disney, Matthew D.

2016-01-01

Spinocerebellar ataxia type 10 (SCA10) is caused by a pentanucleotide repeat expansion of r(AUUCU) within intron 9 of the ATXN10 pre-mRNA. The RNA causes disease by a gain-of-function mechanism in which it inactivates proteins involved in RNA biogenesis. Spectroscopic studies showed that r(AUUCU) repeats form a hairpin structure; however, there were no high-resolution structural models prior to this work. Herein, we report the first crystal structure of model r(AUUCU) repeats refined to 2.8 Å and analysis of the structure via molecular dynamics simulations. The r(AUUCU) tracts adopt an overall A-form geometry in which 3 × 3 nucleotide 5′UCU3′/3′UCU5′ internal loops are closed by AU pairs. Helical parameters of the refined structure as well as the corresponding electron density map on the crystallographic model reflect dynamic features of the internal loop. The computational analyses captured dynamic motion of the loop closing pairs, which can form single-stranded conformations with relatively low energies. Overall, the results presented here suggest the possibility for r(AUUCU) repeats to form metastable A-from structures, which can rearrange into single-stranded conformations and attract proteins such as heterogeneous nuclear ribonucleoprotein K (hnRNP K). The information presented here may aid in the rational design of therapeutics targeting this RNA. PMID:26039897

Automated quality checks on repeat prescribing.

PubMed Central

Rogers, Jeremy E; Wroe, Christopher J; Roberts, Angus; Swallow, Angela; Stables, David; Cantrill, Judith A; Rector, Alan L

2003-01-01

BACKGROUND: Good clinical practice in primary care includes periodic review of repeat prescriptions. Markers of prescriptions that may need review have been described, but manually checking all repeat prescriptions against the markers would be impractical. AIM: To investigate the feasibility of computerising the application of repeat prescribing quality checks to electronic patient records in United Kingdom (UK) primary care. DESIGN OF STUDY: Software performance test against benchmark manual analysis of cross-sectional convenience sample of prescribing documentation. SETTING: Three general practices in Greater Manchester, in the north west of England, during a 4-month period in 2001. METHOD: A machine-readable drug information resource, based on the British National Formulary (BNF) as the 'gold standard' for valid drug indications, was installed in three practices. Software raised alerts for each repeat prescribed item where the electronic patient record contained no valid indication for the medication. Alerts raised by the software in two practices were analysed manually. Clinical reaction to the software was assessed by semi-structured interviews in three practices. RESULTS: There was no valid indication in the electronic medical records for 14.8% of repeat prescribed items. Sixty-two per cent of all alerts generated were incorrect. Forty-three per cent of all incorrect alerts were as a result of errors in the drug information resource, 44% to locally idiosyncratic clinical coding, 8% to the use of the BNF without adaptation as a gold standard, and 5% to the inability of the system to infer diagnoses that, although unrecorded, would be 'obvious' to a clinical reading the record. The interviewed clinicians supported the goals of the software. CONCLUSION: Using electronic records for secondary decision support purposes will benefit from (and may require) both more consistent electronic clinical data collection across multiple sites, and reconciling clinicians' willingness to infer unstated but 'obvious' diagnoses with the machine's inability to do the same. PMID:14702902

Ca2+-stabilized adhesin helps an Antarctic bacterium reach out and bind ice.

PubMed

Vance, Tyler D R; Olijve, Luuk L C; Campbell, Robert L; Voets, Ilja K; Davies, Peter L; Guo, Shuaiqi

2014-07-04

The large size of a 1.5-MDa ice-binding adhesin [MpAFP (Marinomonas primoryensis antifreeze protein)] from an Antarctic Gram-negative bacterium, M. primoryensis, is mainly due to its highly repetitive RII (Region II). MpAFP_RII contains roughly 120 tandem copies of an identical 104-residue repeat. We have previously determined that a single RII repeat folds as a Ca2+-dependent immunoglobulin-like domain. Here, we solved the crystal structure of RII tetra-tandemer (four tandem RII repeats) to a resolution of 1.8 Å. The RII tetra-tandemer reveals an extended (~190-Å × ~25-Å), rod-like structure with four RII-repeats aligned in series with each other. The inter-repeat regions of the RII tetra-tandemer are strengthened by Ca2+ bound to acidic residues. SAXS (small-angle X-ray scattering) profiles indicate the RII tetra-tandemer is significantly rigidified upon Ca2+ binding, and that the protein's solution structure is in excellent agreement with its crystal structure. We hypothesize that >600 Ca2+ help rigidify the chain of ~120 104-residue repeats to form a ~0.6 μm rod-like structure in order to project the ice-binding domain of MpAFP away from the bacterial cell surface. The proposed extender role of RII can help the strictly aerobic, motile bacterium bind ice in the upper reaches of the Antarctic lake where oxygen and nutrients are most abundant. Ca2+-induced rigidity of tandem Ig-like repeats in large adhesins might be a general mechanism used by bacteria to bind to their substrates and help colonize specific niches.

Influence of a heptad repeat stutter on the pH-dependent conformational behavior of the central coiled-coil from influenza hemagglutinin HA2.

PubMed

Higgins, Chelsea D; Malashkevich, Vladimir N; Almo, Steven C; Lai, Jonathan R

2014-09-01

The coiled-coil is one of the most common protein structural motifs. Amino acid sequences of regions that participate in coiled-coils contain a heptad repeat in which every third then forth residue is occupied by a hydrophobic residue. Here we examine the consequences of a "stutter," a deviation of the idealized heptad repeat that is found in the central coiled-coil of influenza hemagluttinin HA2. Characterization of a peptide containing the native stutter-containing HA2 sequence, as well as several variants in which the stutter was engineered out to restore an idealized heptad repeat pattern, revealed that the stutter is important for allowing coiled-coil formation in the WT HA2 at both neutral and low pH (7.1 and 4.5). By contrast, all variants that contained idealized heptad repeats exhibited marked pH-dependent coiled-coil formation with structures forming much more stably at low pH. A crystal structure of one variant containing an idealized heptad repeat, and comparison to the WT HA2 structure, suggest that the stutter distorts the optimal interhelical core packing arrangement, resulting in unwinding of the coiled-coil superhelix. Interactions between acidic side chains, in particular E69 and E74 (present in all peptides studied), are suggested to play a role in mediating these pH-dependent conformational effects. This conclusion is partially supported by studies on HA2 variant peptides in which these positions were altered to aspartic acid. These results provide new insight into the structural role of the heptad repeat stutter in HA2. © 2014 Wiley Periodicals, Inc.

A Dynamic Tandem Repeat in Monocotyledons Inferred from a Comparative Analysis of Chloroplast Genomes in Melanthiaceae.

PubMed

Do, Hoang Dang Khoa; Kim, Joo-Hwan

2017-01-01

Chloroplast genomes (cpDNA) are highly valuable resources for evolutionary studies of angiosperms, since they are highly conserved, are small in size, and play critical roles in plants. Slipped-strand mispairing (SSM) was assumed to be a mechanism for generating repeat units in cpDNA. However, research on the employment of different small repeated sequences through SSM events, which may induce the accumulation of distinct types of repeats within the same region in cpDNA, has not been documented. Here, we sequenced two chloroplast genomes from the endemic species Heloniopsis tubiflora (Korea) and Xerophyllum tenax (USA) to cover the gap between molecular data and explore "hot spots" for genomic events in Melanthiaceae. Comparative analysis of 23 complete cpDNA sequences revealed that there were different stages of deletion in the rps16 region across the Melanthiaceae. Based on the partial or complete loss of rps16 gene in cpDNA, we have firstly reported potential molecular markers for recognizing two sections ( Veratrum and Fuscoveratrum ) of Veratrum . Melathiaceae exhibits a significant change in the junction between large single copy and inverted repeat regions, ranging from trnH_GUG to a part of rps3 . Our results show an accumulation of tandem repeats in the rpl23-ycf2 regions of cpDNAs. Small conserved sequences exist and flank tandem repeats in further observation of this region across most of the examined taxa of Liliales. Therefore, we propose three scenarios in which different small repeated sequences were used during SSM events to generate newly distinct types of repeats. Occasionally, prior to the SSM process, point mutation event and double strand break repair occurred and induced the formation of initial repeat units which are indispensable in the SSM process. SSM may have likely occurred more frequently for short repeats than for long repeat sequences in tribe Parideae (Melanthiaceae, Liliales). Collectively, these findings add new evidence of dynamic results from SSM in chloroplast genomes which can be useful for further evolutionary studies in angiosperms. Additionally, genomics events in cpDNA are potential resources for mining molecular markers in Liliales.

Structural studies on molecular interactions between camel peptidoglycan recognition protein, CPGRP-S, and peptidoglycan moieties N-acetylglucosamine and N-acetylmuramic acid.

PubMed

Sharma, Pradeep; Yamini, Shavait; Dube, Divya; Singh, Amar; Sinha, Mau; Dey, Sharmistha; Mitra, Dipendra K; Kaur, Punit; Sharma, Sujata; Singh, Tej P

2012-06-22

Peptidoglycan (PGN) consists of repeating units of N-acetylglucosamine (GlcNAc) and N-acetylmuramic acid (MurNAc), which are cross-linked by short peptides. It is well known that PGN forms a major cell wall component of bacteria making it an important ligand for the recognition by peptidoglycan recognition proteins (PGRPs) of the host. The binding studies showed that PGN, GlcNAc, and MurNAc bind to camel PGRP-S (CPGRP-S) with affinities corresponding to dissociation constants of 1.3 × 10(-9), 2.6 × 10(-7), and 1.8 × 10(-7) M, respectively. The crystal structure determinations of the complexes of CPGRP-S with GlcNAc and MurNAc showed that the structures consist of four crystallographically independent molecules, A, B, C, and D, in the asymmetric unit that exists as A-B and C-D units of two neighboring linear polymers. The structure determinations showed that compounds GlcNAc and MurNAc bound to CPGRP-S at the same subsite in molecule C. Both GlcNAc and MurNAc form several hydrogen bonds and extensive hydrophobic interactions with protein atoms, indicating the specific nature of their bindings. Flow cytometric studies showed that PGN enhanced the secretions of TNF-α and IL-6 from human peripheral blood mononuclear cells. The introduction of CPGRP-S to the PGN-challenged cultured peripheral blood mononuclear cells reduced the expressions of proinflammatory cytokines, TNF-α and IL-6. This showed that CPGRP-S inhibited PGN-induced production of proinflammatory cytokines and down-regulated macrophage-mediated inflammation, indicating its potential applications as an antibacterial agent.

DNA-binding proteins from marine bacteria expand the known sequence diversity of TALE-like repeats

PubMed Central

de Lange, Orlando; Wolf, Christina; Thiel, Philipp; Krüger, Jens; Kleusch, Christian; Kohlbacher, Oliver; Lahaye, Thomas

2015-01-01

Transcription Activator-Like Effectors (TALEs) of Xanthomonas bacteria are programmable DNA binding proteins with unprecedented target specificity. Comparative studies into TALE repeat structure and function are hindered by the limited sequence variation among TALE repeats. More sequence-diverse TALE-like proteins are known from Ralstonia solanacearum (RipTALs) and Burkholderia rhizoxinica (Bats), but RipTAL and Bat repeats are conserved with those of TALEs around the DNA-binding residue. We study two novel marine-organism TALE-like proteins (MOrTL1 and MOrTL2), the first to date of non-terrestrial origin. We have assessed their DNA-binding properties and modelled repeat structures. We found that repeats from these proteins mediate sequence specific DNA binding conforming to the TALE code, despite low sequence similarity to TALE repeats, and with novel residues around the BSR. However, MOrTL1 repeats show greater sequence discriminating power than MOrTL2 repeats. Sequence alignments show that there are only three residues conserved between repeats of all TALE-like proteins including the two new additions. This conserved motif could prove useful as an identifier for future TALE-likes. Additionally, comparing MOrTL repeats with those of other TALE-likes suggests a common evolutionary origin for the TALEs, RipTALs and Bats. PMID:26481363

The complete chloroplast DNA sequence of Eleutherococcus senticosus (Araliaceae); comparative evolutionary analyses with other three asterids.

PubMed

Yi, Dong-Keun; Lee, Hae-Lim; Sun, Byung-Yun; Chung, Mi Yoon; Kim, Ki-Joong

2012-05-01

This study reports the complete chloroplast (cp) DNA sequence of Eleutherococcus senticosus (GenBank: JN 637765), an endangered endemic species. The genome is 156,768 bp in length, and contains a pair of inverted repeat (IR) regions of 25,930 bp each, a large single copy (LSC) region of 86,755 bp and a small single copy (SSC) region of 18,153 bp. The structural organization, gene and intron contents, gene order, AT content, codon usage, and transcription units of the E. senticosus chloroplast genome are similar to that of typical land plant cp DNA. We aligned and analyzed the sequences of 86 coding genes, 19 introns and 113 intergenic spacers (IGS) in three different taxonomic hierarchies; Eleutherococcus vs. Panax, Eleutherococcus vs. Daucus, and Eleutherococcus vs. Nicotiana. The distribution of indels, the number of polymorphic sites and nucleotide diversity indicate that positional constraint is more important than functional constraint for the evolution of cp genome sequences in Asterids. For example, the intron sequences in the LSC region exhibited base substitution rates 5-11-times higher than that of the IR regions, while the intron sequences in the SSC region evolved 7-14-times faster than those in the IR region. Furthermore, the Ka/Ks ratio of the gene coding sequences supports a stronger evolutionary constraint in the IR region than in the LSC or SSC regions. Therefore, our data suggest that selective sweeps by base collection mechanisms more frequently eliminate polymorphisms in the IR region than in other regions. Chloroplast genome regions that have high levels of base substitutions also show higher incidences of indels. Thirty-five simple sequence repeat (SSR) loci were identified in the Eleutherococcus chloroplast genome. Of these, 27 are homopolymers, while six are di-polymers and two are tri-polymers. In addition to the SSR loci, we also identified 18 medium size repeat units ranging from 22 to 79 bp, 11 of which are distributed in the IGS or intron regions. These medium size repeats may contribute to developing a cp genome-specific gene introduction vector because the region may use for specific recombination sites.

Deletion of internal structured repeats increases the stability of a leucine-rich repeat protein, YopM

PubMed Central

Barrick, Doug

2011-01-01

Mapping the stability distributions of proteins in their native folded states provides a critical link between structure, thermodynamics, and function. Linear repeat proteins have proven more amenable to this kind of mapping than globular proteins. C-terminal deletion studies of YopM, a large, linear leucine-rich repeat (LRR) protein, show that stability is distributed quite heterogeneously, yet a high level of cooperativity is maintained [1]. Key components of this distribution are three interfaces that strongly stabilize adjacent sequences, thereby maintaining structural integrity and promoting cooperativity. To better understand the distribution of interaction energy around these critical interfaces, we studied internal (rather than terminal) deletions of three LRRs in this region, including one of these stabilizing interfaces. Contrary to our expectation that deletion of structured repeats should be destabilizing, we find that internal deletion of folded repeats can actually stabilize the native state, suggesting that these repeats are destabilizing, although paradoxically, they are folded in the native state. We identified two residues within this destabilizing segment that deviate from the consensus sequence at a position that normally forms a stacked leucine ladder in the hydrophobic core. Replacement of these nonconsensus residues with leucine is stabilizing. This stability enhancement can be reproduced in the context of nonnative interfaces, but it requires an extended hydrophobic core. Our results demonstrate that different LRRs vary widely in their contribution to stability, and that this variation is context-dependent. These two factors are likely to determine the types of rearrangements that lead to folded, functional proteins, and in turn, are likely to restrict the pathways available for the evolution of linear repeat proteins. PMID:21764506

Crystal structure of the Xpo1p nuclear export complex bound to the SxFG/PxFG repeats of the nucleoporin Nup42p.

PubMed

Koyama, Masako; Hirano, Hidemi; Shirai, Natsuki; Matsuura, Yoshiyuki

2017-10-01

Xpo1p (yeast CRM1) is the major nuclear export receptor that carries a plethora of proteins and ribonucleoproteins from the nucleus to cytoplasm. The passage of the Xpo1p nuclear export complex through nuclear pore complexes (NPCs) is facilitated by interactions with nucleoporins (Nups) containing extensive repeats of phenylalanine-glycine (so-called FG repeats), although the precise role of each Nup in the nuclear export reaction remains incompletely understood. Here we report structural and biochemical characterization of the interactions between the Xpo1p nuclear export complex and the FG repeats of Nup42p, a nucleoporin localized at the cytoplasmic face of yeast NPCs and has characteristic SxFG/PxFG sequence repeat motif. The crystal structure of Xpo1p-PKI-Nup42p-Gsp1p-GTP complex identified three binding sites for the SxFG/PxFG repeats on HEAT repeats 14-20 of Xpo1p. Mutational analyses of Nup42p showed that the conserved serines and prolines in the SxFG/PxFG repeats contribute to Xpo1p-Nup42p binding. Our structural and biochemical data suggest that SxFG/PxFG-Nups such as Nup42p and Nup159p at the cytoplasmic face of NPCs provide high-affinity docking sites for the Xpo1p nuclear export complex in the terminal stage of NPC passage and that subsequent disassembly of the nuclear export complex facilitates recycling of free Xpo1p back to the nucleus. © 2017 Molecular Biology Society of Japan and John Wiley & Sons Australia, Ltd.

An approach for evaluating the repeatability of rapid wetland assessment methods: The effects of training and experience

EPA Science Inventory

We sampled 92 wetlands from four different basins in the United States to quantify observer repeatability in rapid wetland condition assessment using the Delaware Rapid Assessment Protocol (DERAP). In the Inland Bays basin of Delaware, 58 wetland sites were sampled by multiple ob...

Repeatability estimates for oleoresin yield measurements in three species of the southern pines

Treesearch

James H. Roberds; Brain L. Strom

2006-01-01

Repeatability was estimated for constitutive oleoresin yield measurements in 10 stands of three species of pines native to southeastern United States. Trees of these species that discharge large quantities of oleoresin upon wounding are considered to be most resistant to attack by southern pine beetle (Dendroctonus frontalis Zimmermann). Oleoresin...

Structure prediction of polyglutamine disease proteins: comparison of methods

PubMed Central

2014-01-01

Background The expansion of polyglutamine (poly-Q) repeats in several unrelated proteins is associated with at least ten neurodegenerative diseases. The length of the poly-Q regions plays an important role in the progression of the diseases. The number of glutamines (Q) is inversely related to the onset age of these polyglutamine diseases, and the expansion of poly-Q repeats has been associated with protein misfolding. However, very little is known about the structural changes induced by the expansion of the repeats. Computational methods can provide an alternative to determine the structure of these poly-Q proteins, but it is important to evaluate their performance before large scale prediction work is done. Results In this paper, two popular protein structure prediction programs, I-TASSER and Rosetta, have been used to predict the structure of the N-terminal fragment of a protein associated with Huntington's disease with 17 glutamines. Results show that both programs have the ability to find the native structures, but I-TASSER performs better for the overall task. Conclusions Both I-TASSER and Rosetta can be used for structure prediction of proteins with poly-Q repeats. Knowledge of poly-Q structure may significantly contribute to development of therapeutic strategies for poly-Q diseases. PMID:25080018

Complete Chloroplast Genome Sequences of Important Oilseed Crop Sesamum indicum L

PubMed Central

Yi, Dong-Keun; Kim, Ki-Joong

2012-01-01

Sesamum indicum is an important crop plant species for yielding oil. The complete chloroplast (cp) genome of S. indicum (GenBank acc no. JN637766) is 153,324 bp in length, and has a pair of inverted repeat (IR) regions consisting of 25,141 bp each. The lengths of the large single copy (LSC) and the small single copy (SSC) regions are 85,170 bp and 17,872 bp, respectively. Comparative cp DNA sequence analyses of S. indicum with other cp genomes reveal that the genome structure, gene order, gene and intron contents, AT contents, codon usage, and transcription units are similar to the typical angiosperm cp genomes. Nucleotide diversity of the IR region between Sesamum and three other cp genomes is much lower than that of the LSC and SSC regions in both the coding region and noncoding region. As a summary, the regional constraints strongly affect the sequence evolution of the cp genomes, while the functional constraints weakly affect the sequence evolution of cp genomes. Five short inversions associated with short palindromic sequences that form step-loop structures were observed in the chloroplast genome of S. indicum. Twenty-eight different simple sequence repeat loci have been detected in the chloroplast genome of S. indicum. Almost all of the SSR loci were composed of A or T, so this may also contribute to the A-T richness of the cp genome of S. indicum. Seven large repeated loci in the chloroplast genome of S. indicum were also identified and these loci are useful to developing S. indicum-specific cp genome vectors. The complete cp DNA sequences of S. indicum reported in this paper are prerequisite to modifying this important oilseed crop by cp genetic engineering techniques. PMID:22606240

The impact of CRISPR repeat sequence on structures of a Cas6 protein-RNA complex

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

Wang, Ruiying; Zheng, Han; Preamplume, Gan

The repeat-associated mysterious proteins (RAMPs) comprise the most abundant family of proteins involved in prokaryotic immunity against invading genetic elements conferred by the clustered regularly interspaced short palindromic repeat (CRISPR) system. Cas6 is one of the first characterized RAMP proteins and is a key enzyme required for CRISPR RNA maturation. Despite a strong structural homology with other RAMP proteins that bind hairpin RNA, Cas6 distinctly recognizes single-stranded RNA. Previous structural and biochemical studies show that Cas6 captures the 5' end while cleaving the 3' end of the CRISPR RNA. Here, we describe three structures and complementary biochemical analysis of amore » noncatalytic Cas6 homolog from Pyrococcus horikoshii bound to CRISPR repeat RNA of different sequences. Our study confirms the specificity of the Cas6 protein for single-stranded RNA and further reveals the importance of the bases at Positions 5-7 in Cas6-RNA interactions. Substitutions of these bases result in structural changes in the protein-RNA complex including its oligomerization state.« less

Evolutionary conservation of sequence and secondary structures inCRISPR repeats

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

Kunin, Victor; Sorek, Rotem; Hugenholtz, Philip

Clustered Regularly Interspaced Palindromic Repeats (CRISPRs) are a novel class of direct repeats, separated by unique spacer sequences of similar length, that are present in {approx}40% of bacterial and all archaeal genomes analyzed to date. More than 40 gene families, called CRISPR-associated sequences (CAS), appear in conjunction with these repeats and are thought to be involved in the propagation and functioning of CRISPRs. It has been proposed that the CRISPR/CAS system samples, maintains a record of, and inactivates invasive DNA that the cell has encountered, and therefore constitutes a prokaryotic analog of an immune system. Here we analyze CRISPR repeatsmore » identified in 195 microbial genomes and show that they can be organized into multiple clusters based on sequence similarity. All individual repeats in any given cluster were inferred to form characteristic RNA secondary structure, ranging from non-existent to pronounced. Stable secondary structures included G:U base pairs and exhibited multiple compensatory base changes in the stem region, indicating evolutionary conservation and functional importance. We also show that the repeat-based classification corresponds to, and expands upon, a previously reported CAS gene-based classification including specific relationships between CRISPR and CAS subtypes.« less

Free-Space Measurements of Dielectrics and Three-Dimensional Periodic Metamaterials

NASA Astrophysics Data System (ADS)

Kintner, Clifford E.

This thesis presents the free-space measurements of a periodic metamaterial structure. The metamaterial unit cell consists of two dielectric sheets intersecting at 90 degrees. The dielectric is a polyetherimide-based material 0.001" thick. Each sheet has a copper capacitively-loaded loop (CLL) structure on the front and a cut-wire structure on the back. Foam material is used to support the unit cells. The unit cell repeats 40 times in the x-direction, 58 times in the y-direction and 5 times in the z-direction. The sample measures 12" x 12" x 1" in total. We use a free-space broadband system comprised of a pair of dielectric-lens horn antennas with bandwidth from 5.8 GHz to 110 GHz, which are connected to a HP PNA series network analyzer. The dielectric lenses focus the incident beam to a footprint measuring 1 wavelength by 1 wavelength. The sample holder is positioned at the focal point between the two antennas. In this work, the coefficients of transmission and reflection (the S-parameters S21 and S11) are measured at frequencies from 12.4 GHz up to 30 GHz. Simulations are used to validate the measurements, using the Ansys HFSS commercial software package on the Arkansas High Performance Computing Center cluster. The simulation results successfully validate the S-parameters measurements, in particular the amplitudes. An algorithm based on the Nicolson-Ross-Weir (NRW) method is implemented to extract the permittivity and permeability values of the metamaterial under test. The results show epsilon-negative, mu-negative and double-negative parameters within the measured frequency range.

Modeling Fungal Melanin Buildup: Biomimetic Polymerization of 1,8-Dihydroxynaphthalene Mapped by Mass Spectrometry.

PubMed

Cecchini, Martina Maya; Reale, Samantha; Manini, Paola; d'Ischia, Marco; De Angelis, Francesco

2017-06-12

Due to the emerging biomedical relevance and technological potential of fungal melanins, and prompted by the virtual lack of information about their structural arrangement, an optimized synthetic protocol has been devised for a potential structural model of Ascomyces allomelanin through enzyme-catalyzed oxidative polymerization of 1,8-dihydroxynaphthalene (1,8-DHN). Electrospray ionization mass spectrometry (ESI-MS) measurements of freshly synthesized DHN-polymer recorded in the negative ion mode allowed detection of oligomers up to m/z 4000, separated by 158 Da, corresponding to the in-chain DHN-unit. The dominant peaks were assigned to singly-charged distribution, up to 23 repeating units, whereas a doubly charged polymer distribution was also detectable. Chemical derivatization, ultra-performance liquid chromatography (UPLC)-ESI MS, and MS/MS data confirmed that oxidative polymerization of 1,8-DHN proceeds through C-C coupling of the naphthalene rings. The new insights reported here into synthetic 1,8-DHN oligomers/polymers as a mimic of fungal melanins may guide novel interesting advances and applications in the field of biomimetic functional materials. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Amyloid fibril formation from sequences of a natural beta-structured fibrous protein, the adenovirus fiber.

PubMed

Papanikolopoulou, Katerina; Schoehn, Guy; Forge, Vincent; Forsyth, V Trevor; Riekel, Christian; Hernandez, Jean-François; Ruigrok, Rob W H; Mitraki, Anna

2005-01-28

Amyloid fibrils are fibrous beta-structures that derive from abnormal folding and assembly of peptides and proteins. Despite a wealth of structural studies on amyloids, the nature of the amyloid structure remains elusive; possible connections to natural, beta-structured fibrous motifs have been suggested. In this work we focus on understanding amyloid structure and formation from sequences of a natural, beta-structured fibrous protein. We show that short peptides (25 to 6 amino acids) corresponding to repetitive sequences from the adenovirus fiber shaft have an intrinsic capacity to form amyloid fibrils as judged by electron microscopy, Congo Red binding, infrared spectroscopy, and x-ray fiber diffraction. In the presence of the globular C-terminal domain of the protein that acts as a trimerization motif, the shaft sequences adopt a triple-stranded, beta-fibrous motif. We discuss the possible structure and arrangement of these sequences within the amyloid fibril, as compared with the one adopted within the native structure. A 6-amino acid peptide, corresponding to the last beta-strand of the shaft, was found to be sufficient to form amyloid fibrils. Structural analysis of these amyloid fibrils suggests that perpendicular stacking of beta-strand repeat units is an underlying common feature of amyloid formation.

Independence of motor unit recruitment and rate modulation during precision force control.

PubMed

Kamen, G; Du, D C

1999-01-01

The vertebrate motor system chiefly employs motor unit recruitment and rate coding to modulate muscle force output. In this paper, we studied how the recruitment of new motor units altered the firing rate of already-active motor units during precision force production in the first dorsal interosseous muscle. Six healthy adults performed linearly increasing isometric voluntary contractions while motor unit activity and force output were recorded. After motor unit discharges were identified, motor unit firing rates were calculated before and after the instances of new motor unit recruitment. Three procedures were applied to compute motor unit firing rate, including the mean of a fixed number of inter-spike intervals and the constant width weighted Hanning window filter method, as well as a modified boxcar technique. In contrast to previous reports, the analysis of the firing rates of over 200 motor units revealed that reduction of the active firing rates was not a common mechanism used to accommodate the twitch force produced by the recruitment of a new motor unit. Similarly, during de-recruitment there was no tendency for motor unit firing rates to increase immediately following the cessation of activity in other motor units. Considerable consistency in recruitment behavior was observed during repeated contractions. However, firing rates during repeated contractions demonstrated considerably more fluctuation. It is concluded that the neuromuscular system does not use short-term preferential motor unit disfacilitation to effect precise regulation of muscular force output.

Identification of Simple Sequence Repeats in Chloroplast Genomes of Magnoliids Through Bioinformatics Approach.

PubMed

Srivastava, Deepika; Shanker, Asheesh

2016-12-01

Basal angiosperms or Magnoliids is an important clade of commercially important plants which mainly include spices and edible fruits. In this study, 17 chloroplast genome sequences belonging to clade Magnoliids were screened for the identification of chloroplast simple sequence repeats (cpSSRs). Simple sequence repeats or microsatellites are short stretches of DNA up to 1-6 base pair in length. These repeats are ubiquitous and play important role in the development of molecular markers and to study the mapping of traits of economic, medical or ecological interest. A total of 479 SSRs were detected, showing average density of 1 SSR/6.91 kb. Depending on the repeat units, the length of SSRs ranged from 12 to 24 bp for mono-, 12 to 18 bp for di-, 12 to 26 bp for tri-, 12 to 24 bp for tetra-, 15 bp for penta- and 18 bp for hexanucleotide repeats. Mononucleotide repeats were the most frequent (207, 43.21 %) followed by tetranucleotide repeats (130, 27.13 %). Penta- and hexanucleotide repeats were least frequent or absent in these chloroplast genomes.

Repeat-Associated Fission Yeast-Like Regional Centromeres in the Ascomycetous Budding Yeast Candida tropicalis

PubMed Central

Chatterjee, Gautam; Sankaranarayanan, Sundar Ram; Guin, Krishnendu; Thattikota, Yogitha; Padmanabhan, Sreedevi; Siddharthan, Rahul; Sanyal, Kaustuv

2016-01-01

The centromere, on which kinetochore proteins assemble, ensures precise chromosome segregation. Centromeres are largely specified by the histone H3 variant CENP-A (also known as Cse4 in yeasts). Structurally, centromere DNA sequences are highly diverse in nature. However, the evolutionary consequence of these structural diversities on de novo CENP-A chromatin formation remains elusive. Here, we report the identification of centromeres, as the binding sites of four evolutionarily conserved kinetochore proteins, in the human pathogenic budding yeast Candida tropicalis. Each of the seven centromeres comprises a 2 to 5 kb non-repetitive mid core flanked by 2 to 5 kb inverted repeats. The repeat-associated centromeres of C. tropicalis all share a high degree of sequence conservation with each other and are strikingly diverged from the unique and mostly non-repetitive centromeres of related Candida species—Candida albicans, Candida dubliniensis, and Candida lusitaniae. Using a plasmid-based assay, we further demonstrate that pericentric inverted repeats and the underlying DNA sequence provide a structural determinant in CENP-A recruitment in C. tropicalis, as opposed to epigenetically regulated CENP-A loading at centromeres in C. albicans. Thus, the centromere structure and its influence on de novo CENP-A recruitment has been significantly rewired in closely related Candida species. Strikingly, the centromere structural properties along with role of pericentric repeats in de novo CENP-A loading in C. tropicalis are more reminiscent to those of the distantly related fission yeast Schizosaccharomyces pombe. Taken together, we demonstrate, for the first time, fission yeast-like repeat-associated centromeres in an ascomycetous budding yeast. PMID:26845548

Multiple energetic injections in a strong spike-like solar burst

NASA Technical Reports Server (NTRS)

Kaufmann, P.; Correia, E.; Costa, J. E. R.; Dennis, B. R.; Hurford, G. J.; Brown, J. C.

1984-01-01

An intense and fast spike-like solar burst was built up of short time scale structures superimposed on an underlying gradual emission, the time evolution of which shows remarkable proportionality between hard X-ray and microwave fluxes. The finer time structures were best defined at mm-microwaves. At the peak of the event, the finer structures repeat every 30 x 60 ms. The more slowly varying component with a time scale of about 1 second was identified in microwave hard X-rays throughout the burst duration. It is suggested that X-ray fluxes might also be proportional to the repetition rate of basic units of energy injection (quasi-quantized). The relevant parameters of one primary energy release site are estimated both in the case where hard X-rays are produced primarily by thick-target bremsstrahlung, and when they are purely thermal. The relation of this figure to global energy considerations is discussed. Previously announced in STAR as N83-35983

Structure and in vitro anticancer activity of sulfated O-polysaccharide from marine bacterium Poseidonocella pacifica KMM 9010T.

PubMed

Kokoulin, Maxim S; Kuzmich, Alexandra S; Kalinovsky, Anatoly I; Rubtsov, Eugene S; Romanenko, Lyudmila A; Mikhailov, Valery V; Komandrova, Nadezhda A

2017-12-15

We presented the structure of the sulfated polysaccharide moiety and anticancer activity in vitro of the О-deacylated lipopolysaccharide (DPS) isolated from the marine bacterium Poseidonocella pacifica KMM 9010 T . The structure of O-polysaccharide was investigated by chemical methods along with 1 H and 13 C NMR spectroscopy. The O-polysaccharide was built up of sulfated disaccharide repeating units consisted of d-rhamnose (d-Rhaр) and 3-deoxy-d-manno-oct-2-ulosonic acid (Kdop): →7)-β-Kdoр4Ac5S-(2→3)-β-d-Rhaр2S-(1→. We demonstrated that the DPS from P. pacifica KMM 9010 T non-toxic for normal mouse epidermal cells (JB6 Cl41 cell line) and inhibited colony formation of human colorectal carcinoma HT-29, breast adenocarcinoma MCF-7 and melanoma SK-MEL-5 cells in a dose-dependent manner. Copyright © 2017 Elsevier Ltd. All rights reserved.

Simple extrapolation method to predict the electronic structure of conjugated polymers from calculations on oligomers

DOE PAGES

Larsen, Ross E.

2016-04-12

In this study, we introduce two simple tight-binding models, which we call fragment frontier orbital extrapolations (FFOE), to extrapolate important electronic properties to the polymer limit using electronic structure calculations on only a few small oligomers. In particular, we demonstrate by comparison to explicit density functional theory calculations that for long oligomers the energies of the highest occupied molecular orbital (HOMO), the lowest unoccupied molecular orbital (LUMO), and of the first electronic excited state are accurately described as a function of number of repeat units by a simple effective Hamiltonian parameterized from electronic structure calculations on monomers, dimers and, optionally,more » tetramers. For the alternating copolymer materials that currently comprise some of the most efficient polymer organic photovoltaic devices one can use these simple but rigorous models to extrapolate computed properties to the polymer limit based on calculations on a small number of low-molecular-weight oligomers.« less

Effects of star-shape poly(alkyl methacrylate) arm uniformity on lubricant properties

DOE PAGES

Robinson, Joshua W.; Qu, Jun; Erck, Robert; ...

2016-03-29

Star-shaped poly(alkyl methacrylate)s (PAMAs) were prepared and blended into an additive-free engine oil to assess the structure property relationship between macromolecular structure and lubricant performance. These additives were designed with a comparable number of repeating units per arm and the number of arms was varied between 3 and 6. Well-defined star-shaped PAMAs were synthesized by atom transfer radical polymerization (ATRP) via a core-first strategy from multi-functional headgroups. Observations of the polymer-oil blends suggest that stars with less than four arms are favorable as a viscosity index improver (VII), and molecular weight dominates viscosity-related effects over other structural features. Star-shaped PAMAs,more » as oil additives, effectively reduce the friction coefficient in both mixed and boundary lubrication regime. Several analogs outperformed commercial VIIs in both viscosity and friction performance. Furthermore, increased wear rates were observed for these star-shaped PAMAs in the boundary lubrication regime suggesting pressure-sensitive conformations may exist.« less

Structure-based membrane dome mechanism for Piezo mechanosensitivity.

PubMed

Guo, Yusong R; MacKinnon, Roderick

2017-12-12

Mechanosensitive ion channels convert external mechanical stimuli into electrochemical signals for critical processes including touch sensation, balance, and cardiovascular regulation. The best understood mechanosensitive channel, MscL, opens a wide pore, which accounts for mechanosensitive gating due to in-plane area expansion. Eukaryotic Piezo channels have a narrow pore and therefore must capture mechanical forces to control gating in another way. We present a cryo-EM structure of mouse Piezo1 in a closed conformation at 3.7Å-resolution. The channel is a triskelion with arms consisting of repeated arrays of 4-TM structural units surrounding a pore. Its shape deforms the membrane locally into a dome. We present a hypothesis in which the membrane deformation changes upon channel opening. Quantitatively, membrane tension will alter gating energetics in proportion to the change in projected area under the dome. This mechanism can account for highly sensitive mechanical gating in the setting of a narrow, cation-selective pore. © 2017, Guo et al.

Structural studies of the cell wall polysaccharide from Lactococcus lactis UC509.9.

PubMed

Vinogradov, Evgeny; Sadovskaya, Irina; Grard, Thierry; Murphy, James; Mahony, Jennifer; Chapot-Chartier, Marie-Pierre; van Sinderen, Douwe

2018-05-22

Lactococcus lactis is the most widely utilised starter bacterial species in dairy fermentations. The L. lactis cell envelope contains polysaccharides, which, among other known functions, serve as bacteriophage receptors. Our previous studies have highlighted the structural diversity of these so-called cell wall polysaccharides (CWPSs) among L. lactis strains that could account for the narrow host range of most lactococcal bacteriophages. In the present work, we studied the CWPS of L. lactis strain UC509.9, an Irish dairy starter strain that is host to the temperate and well-characterized P335-type phage Tuc2009. The UC509.9 CWPS structure was analyzed by methylation, deacetylation/deamination, Smith degradation and 2D NMR spectroscopy. The CWPS consists of a linear backbone composed of a tetrasaccharide repeat unit, partially substituted with a branched phosphorylated oligosaccharide having a common trisaccharide and three non-stoichiometric substitutions. Copyright © 2018 Elsevier Ltd. All rights reserved.

Engineering customized TALE nucleases (TALENs) and TALE transcription factors by fast ligation-based automatable solid-phase high-throughput (FLASH) assembly.

PubMed

Reyon, Deepak; Maeder, Morgan L; Khayter, Cyd; Tsai, Shengdar Q; Foley, Jonathan E; Sander, Jeffry D; Joung, J Keith

2013-07-01

Customized DNA-binding domains made using transcription activator-like effector (TALE) repeats are rapidly growing in importance as widely applicable research tools. TALE nucleases (TALENs), composed of an engineered array of TALE repeats fused to the FokI nuclease domain, have been used successfully for directed genome editing in various organisms and cell types. TALE transcription factors (TALE-TFs), consisting of engineered TALE repeat arrays linked to a transcriptional regulatory domain, have been used to up- or downregulate expression of endogenous genes in human cells and plants. This unit describes a detailed protocol for the recently described fast ligation-based automatable solid-phase high-throughput (FLASH) assembly method. FLASH enables automated high-throughput construction of engineered TALE repeats using an automated liquid handling robot or manually using a multichannel pipet. Using the automated approach, a single researcher can construct up to 96 DNA fragments encoding TALE repeat arrays of various lengths in a single day, and then clone these to construct sequence-verified TALEN or TALE-TF expression plasmids in a week or less. Plasmids required for FLASH are available by request from the Joung lab (http://eGenome.org). This unit also describes improvements to the Zinc Finger and TALE Targeter (ZiFiT Targeter) web server (http://ZiFiT.partners.org) that facilitate the design and construction of FLASH TALE repeat arrays in high throughput. © 2013 by John Wiley & Sons, Inc.

DNA-binding proteins from marine bacteria expand the known sequence diversity of TALE-like repeats.

PubMed

de Lange, Orlando; Wolf, Christina; Thiel, Philipp; Krüger, Jens; Kleusch, Christian; Kohlbacher, Oliver; Lahaye, Thomas

2015-11-16

Transcription Activator-Like Effectors (TALEs) of Xanthomonas bacteria are programmable DNA binding proteins with unprecedented target specificity. Comparative studies into TALE repeat structure and function are hindered by the limited sequence variation among TALE repeats. More sequence-diverse TALE-like proteins are known from Ralstonia solanacearum (RipTALs) and Burkholderia rhizoxinica (Bats), but RipTAL and Bat repeats are conserved with those of TALEs around the DNA-binding residue. We study two novel marine-organism TALE-like proteins (MOrTL1 and MOrTL2), the first to date of non-terrestrial origin. We have assessed their DNA-binding properties and modelled repeat structures. We found that repeats from these proteins mediate sequence specific DNA binding conforming to the TALE code, despite low sequence similarity to TALE repeats, and with novel residues around the BSR. However, MOrTL1 repeats show greater sequence discriminating power than MOrTL2 repeats. Sequence alignments show that there are only three residues conserved between repeats of all TALE-like proteins including the two new additions. This conserved motif could prove useful as an identifier for future TALE-likes. Additionally, comparing MOrTL repeats with those of other TALE-likes suggests a common evolutionary origin for the TALEs, RipTALs and Bats. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

3 CFR 8589 - Proclamation 8589 of October 22, 2010. United Nations Day, 2010

Code of Federal Regulations, 2011 CFR

2011-01-01

... devastating wars to rededicate themselves to peace, justice, and progress. The founders of the United Nations vowed to work together to ensure that the horrors seen in World War II would never be repeated. On... 3 The President 1 2011-01-01 2011-01-01 false Proclamation 8589 of October 22, 2010. United...

Longleaf pine site response to repeated fertilization and forest floor removal by raking and prescribed burning

Treesearch

Kim Ludovici; Robert Eaton; Stanley Zarnoch

2018-01-01

Removal of forest floor litter by pine needle raking and prescribed burning is a common practice in longleaf pine (Pinus palustris Mill.) stands on Coastal Plain sites in the Southeastern United States. Repeated removal of litter by raking and the loss of surface organic matter from controlled burns can affect the...

Effects of repeated burning on snag abundance in shortleaf pine woodlands

Treesearch

Roger W. Perry; Phillip N. Jordan; Virginia L. McDaniel

2017-01-01

Forest managers are restoring and maintaining forest woodlands across substantial areas of the United States, and these efforts typically require the use of frequent prescribed fire. The effects of frequent prescribed fire on important habitat components such as snags remain unknown. We conducted a study to determine how snag densities are affected by repeated...

Crystal structure of reovirus attachment protein σ1 in complex with sialylated oligosaccharides.

PubMed

Reiter, Dirk M; Frierson, Johnna M; Halvorson, Elizabeth E; Kobayashi, Takeshi; Dermody, Terence S; Stehle, Thilo

2011-08-01

Many viruses attach to target cells by binding to cell-surface glycans. To gain a better understanding of strategies used by viruses to engage carbohydrate receptors, we determined the crystal structures of reovirus attachment protein σ1 in complex with α-2,3-sialyllactose, α-2,6-sialyllactose, and α-2,8-di-siallylactose. All three oligosaccharides terminate in sialic acid, which serves as a receptor for the reovirus serotype studied here. The overall structure of σ1 resembles an elongated, filamentous trimer. It contains a globular head featuring a compact β-barrel, and a fibrous extension formed by seven repeating units of a triple β-spiral that is interrupted near its midpoint by a short α-helical coiled coil. The carbohydrate-binding site is located between β-spiral repeats two and three, distal from the head. In all three complexes, the terminal sialic acid forms almost all of the contacts with σ1 in an identical manner, while the remaining components of the oligosaccharides make little or no contacts. We used this structural information to guide mutagenesis studies to identify residues in σ1 that functionally engage sialic acid by assessing hemagglutination capacity and growth in murine erythroleukemia cells, which require sialic acid binding for productive infection. Our studies using σ1 mutant viruses reveal that residues 198, 202, 203, 204, and 205 are required for functional binding to sialic acid by reovirus. These findings provide insight into mechanisms of reovirus attachment to cell-surface glycans and contribute to an understanding of carbohydrate binding by viruses. They also establish a filamentous, trimeric carbohydrate-binding module that could potentially be used to endow other trimeric proteins with carbohydrate-binding properties.

Structural analysis of the rDNA intergenic spacer of Brassica nigra: evolutionary divergence of the spacers of the three diploid Brassica species.

PubMed

Bhatia, S; Singh Negi, M; Lakshmikumaran, M

1996-11-01

EcoRI restriction of the B. nigra rDNA recombinants, isolated from a lambda genomic library, showed that the 3.9-kb fragment corresponded to the Intergenic Spacer (IGS), which was sequenced and found to be 3,928 bp in size. Sequence and dot-matrix analyses showed that the organization of the B. nigra rDNA IGS was typical of most rDNA spacers, consisting of a central repetitive region and flanking unique sequences on either side. The repetitive region was composed of two repeat families-RF 'A' and RF 'B.' The B. nigra RF 'A' consisted of a tandem array of three full-length copies of a 106-bp sequence element. RF 'B' was composed of 66 tandemly repeated elements. Each 'B' element was only 21-bp in size and this is the smallest repeat unit identified in plant rDNA to date. The putative transcription initiation site (TIS) was identified as nucleotide position 3,110. Based on the sequence analysis it was suggested that the present organization of the repeat families was generated by successive cycles of deletions and amplifications and was being maintained by homogenization processes such as gene conversion and crossing-over.A detailed comparison of the rDNA IGS sequences of the three diploid Brassica species-namely, B. nigra, B. campestris, and B. oleracea-was carried out. First, comparisons revealed that B. campestris and B. oleracea were close to each other as the repeat families in both showed high sequence homology between each other. Second, the repeat elements in both the species were organized in an interspersed manner. Third, a 52-bp sequence, present just downstream of the repeats in B. campestris, was found to be identical to the B. oleracea repeats, thereby suggesting a common progenitor. On the other hand, in B. nigra no interspersion pattern of organization of repeats was observed. Further, the B. nigra RF 'A' was identified as distinct from the repeat families of B. campestris and B. oleracea. Based on this analysis, it was suggested that during speciation B. campestris and B. oleracea evolved in one lineage whereas B. nigra diverged into a separate lineage. The comparative analysis of the IGS helped in identifying not only conserved ancestral sequence motifs of possible functional significance such as promoters and enhancers, but also sequences which showed variation between the three diploid species and were therefore identified as species-specific sequences.

Genetic variability in maned wolf based on heterologous short-tandem repeat markers from domestic dog.

PubMed

Salim, D C; Akimoto, A A; Carvalho, C B; Oliveira, S F; Grisolia, C K; Moreira, J R; Klautau-Guimarães, M N

2007-06-20

The maned wolf (Chrysocyon brachyurus) is the largest South American canid. Habitat loss and fragmentation, due to agricultural expansion and predatory hunting, are the main threats to this species. It is included in the official list of threatened wildlife species in Brazil, and is also protected by IUCN and CITES. Highly variable genetic markers such as microsatellites have the potential to resolve genetic relationships at all levels of the population structure (among individuals, demes or metapopulations) and also to identify the evolutionary unit for strategies for the conservation of the species. Tests were carried out to verify whether a class of highly polymorphic tetranucleotide repeats described for the domestic dog effectively amplifies DNA in the maned wolf. All five loci studied were amplified; however, one of these, was shown to be monomorphic in 69 maned wolf samples. The average allele number and estimated heterozygosity per polymorphic locus were 4.3 and 67%, respectively. The genetic variability found for this species, which is considered threatened with extinction, showed similar results when compared to studies of other canids.

Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genome

PubMed Central

Shedlock, Andrew M.; Botka, Christopher W.; Zhao, Shaying; Shetty, Jyoti; Zhang, Tingting; Liu, Jun S.; Deschavanne, Patrick J.; Edwards, Scott V.

2007-01-01

We report results of a megabase-scale phylogenomic analysis of the Reptilia, the sister group of mammals. Large-scale end-sequence scanning of genomic clones of a turtle, alligator, and lizard reveals diverse, mammal-like landscapes of retroelements and simple sequence repeats (SSRs) not found in the chicken. Several global genomic traits, including distinctive phylogenetic lineages of CR1-like long interspersed elements (LINEs) and a paucity of A-T rich SSRs, characterize turtles and archosaur genomes, whereas higher frequencies of tandem repeats and a lower global GC content reveal mammal-like features in Anolis. Nonavian reptile genomes also possess a high frequency of diverse and novel 50-bp unit tandem duplications not found in chicken or mammals. The frequency distributions of ≈65,000 8-mer oligonucleotides suggest that rates of DNA-word frequency change are an order of magnitude slower in reptiles than in mammals. These results suggest a diverse array of interspersed and SSRs in the common ancestor of amniotes and a genomic conservatism and gradual loss of retroelements in reptiles that culminated in the minimalist chicken genome. PMID:17307883

Direct mapping of symbolic DNA sequence into frequency domain in global repeat map algorithm

PubMed Central

Glunčić, Matko; Paar, Vladimir

2013-01-01

The main feature of global repeat map (GRM) algorithm (www.hazu.hr/grm/software/win/grm2012.exe) is its ability to identify a broad variety of repeats of unbounded length that can be arbitrarily distant in sequences as large as human chromosomes. The efficacy is due to the use of complete set of a K-string ensemble which enables a new method of direct mapping of symbolic DNA sequence into frequency domain, with straightforward identification of repeats as peaks in GRM diagram. In this way, we obtain very fast, efficient and highly automatized repeat finding tool. The method is robust to substitutions and insertions/deletions, as well as to various complexities of the sequence pattern. We present several case studies of GRM use, in order to illustrate its capabilities: identification of α-satellite tandem repeats and higher order repeats (HORs), identification of Alu dispersed repeats and of Alu tandems, identification of Period 3 pattern in exons, implementation of ‘magnifying glass’ effect, identification of complex HOR pattern, identification of inter-tandem transitional dispersed repeat sequences and identification of long segmental duplications. GRM algorithm is convenient for use, in particular, in cases of large repeat units, of highly mutated and/or complex repeats, and of global repeat maps for large genomic sequences (chromosomes and genomes). PMID:22977183

Rapid and accurate synthesis of TALE genes from synthetic oligonucleotides.

PubMed

Wang, Fenghua; Zhang, Hefei; Gao, Jingxia; Chen, Fengjiao; Chen, Sijie; Zhang, Cuizhen; Peng, Gang

2016-01-01

Custom synthesis of transcription activator-like effector (TALE) genes has relied upon plasmid libraries of pre-fabricated TALE-repeat monomers or oligomers. Here we describe a novel synthesis method that directly incorporates annealed synthetic oligonucleotides into the TALE-repeat units. Our approach utilizes iterative sets of oligonucleotides and a translational frame check strategy to ensure the high efficiency and accuracy of TALE-gene synthesis. TALE arrays of more than 20 repeats can be constructed, and the majority of the synthesized constructs have perfect sequences. In addition, this novel oligonucleotide-based method can readily accommodate design changes to the TALE repeats. We demonstrated an increased gene targeting efficiency against a genomic site containing a potentially methylated cytosine by incorporating non-conventional repeat variable di-residue (RVD) sequences.

Depressive Symptoms and Violence Exposure: Contributors to Repeat Pregnancies Among Adolescents

PubMed Central

Anderson, Cheryl A.; Pierce, Lisa

2015-01-01

ABSTRACT Depressive symptoms and violence exposure (VE) often cooccur and have been recognized to influence childbearing; contribution to repeat pregnancy is unclear and examined in this article. This cross-sectional, descriptive, study screened for depressive symptoms and VE among 193 adolescent mothers at a large county hospital in Southwestern United States. Repeat pregnancy and depressive symptoms characterized one-third and one-quarter of adolescents, respectively. Despite minimal disclosure of VE, repeat pregnancy was significantly influenced by child abuse and past traumatic life experiences. Assessments and interventions with adolescents should focus on frequency of repeat pregnancies and symptoms of depression and VE. Nurses and childbirth educators are poised to offer birth control information and education, support, and resources highlighting depression and VE to adolescents. PMID:26834444

Chemical synthesis of the tetrasaccharide repeating unit of the O-polysaccharide isolated from Azospirillum brasilense SR80.

PubMed

Sarkar, Vikramjit; Mukhopadhyay, Balaram

2015-04-10

A linear strategy has been developed for the synthesis of the tetrasaccharide repeating unit of the O-polysaccharide from Azospirillum brasilense SR80. Stepwise glycosylation of the rationally protected thioglycoside donors activated by NIS in the presence of La(OTf)3 furnished the target tetrasaccharide. The glycosylation reactions resulted in the formation of the desired linkage with absolute stereoselectivity and afforded the required derivatives in good to excellent yields. The phthalimido group has been used as the precursor of the desired acetamido group to meet the requirement of 1,2-trans glycosidic linkage. Copyright © 2015 Elsevier Ltd. All rights reserved.

Iron balance in the red blood cell donor.

PubMed

Brittenham, G M

2005-01-01

Phlebotomy of a unit of blood produces a loss of 200 to 250 mg of iron in haemoglobin. Because of physiological differences in iron balance between women of childbearing age and men, the loss of similar amounts of iron at donation has divergent consequences for committed donors. Women of childbearing age have an increased risk of iron deficiency if they donate more than one unit per year while men are usually able to maintain iron balance while donating four or more units of blood per year. Lack of iron is the most important medical reason for deferral from repeat donation and primarily affects women of childbearing age. Deferral of these women discourages them from further donation and may lead to their loss as donors. Provisions for blood donation should protect those who give blood from adverse consequences of their altruism. Safe and effective approaches to iron replacement after donation have been developed that can prevent iron deficiency in women who give blood repeatedly. Blood centres should consider incorporating programmes of iron replacement for women of childbearing age who give blood repeatedly to protect these donors against iron deficiency and to enhance their retention and commitment as dedicated donors.

A model of high-affinity antibody binding to type III group B Streptococcus capsular polysaccharide.

PubMed

Wessels, M R; Muñoz, A; Kasper, D L

1987-12-01

We recently reported that the single repeating-unit pentasaccharide of type III group B Streptococcus (GBS) capsular polysaccharide is only weakly reactive with type III GBS antiserum. To further elucidate the relationship between antigen-chain length and antigenicity, tritiated oligosaccharides derived from type III capsular polysaccharide were used to generate detailed saturation binding curves with a fixed concentration of rabbit antiserum in a radioactive antigen-binding assay. A graded increase in affinity of antigen-antibody binding was seen as oligosaccharide size increased from 2.6 repeating units to 92 repeating units. These differences in affinity of antibody binding to oligosaccharides of different molecular size were confirmed by immunoprecipitation and competitive ELISA, two independent assays of antigen-antibody binding. Analysis of the saturation binding experiment indicated a difference of 300-fold in antibody-binding affinity for the largest versus the smallest tested oligosaccharides. Unexpectedly, the saturation binding values approached by the individual curves were inversely related to oligosaccharide chain length on a molar basis but equivalent on a weight basis. This observation is compatible with a model in which binding of an immunoglobulin molecule to an antigenic site on the polysaccharide facilitates subsequent binding of antibody to that antigen.

Structural investigation of the capsular polysaccharide produced by a novel Klebsiella serotype (SK1). Location of O-acetyl substituents using NMR and MS techniques.

PubMed

Cescutti, P; Ravenscroft, N; Ng, S; Lam, Z; Dutton, G G

1993-06-21

The capsular polysaccharide of Klebsiella SK1 was investigated by methylation analysis, Smith degradation, and 1H NMR spectroscopy. The oligosaccharides (P1 and P2) obtained by bacteriophage phi SK1 degradation of the polymer were studied by methylation analysis, and 1D- and 2D-NMR spectroscopy. The resulting data showed that the parent repeating unit is a branched pentasaccharide having a structure identical to the revised structure recently proposed for Klebsiella serotype K8 capsular polysaccharide. [Formula: see text] The 2D-NMR data showed that one third of the glucuronic acid residues in the SK1 polymer are acetylated at O-2, O-3, or O-4. FABMS studies confirmed the presence of monoacetylated glucuronic acid residues. Thus, the relationship between the Klebsiella K8 and SK1 polymers is akin to that found for Klebsiella polysaccharides K30 and K33, which have been typed as serologically distinct yet their structures differ only in the degree of acetylation.

Improving the Quality of Radiographs in Neonatal Intensive Care Unit Utilizing Educational Interventions.

PubMed

Gupta, Ashish O; Rorke, Jeanne; Abubakar, Kabir

2015-08-01

We aimed to develop an educational tool to improve the radiograph quality, sustain this improvement overtime, and reduce the number of repeat radiographs. A three phase quality control study was conducted at a tertiary care NICU. A retrospective data collection (phase1) revealed suboptimal radiograph quality and led to an educational intervention and development of X-ray preparation checklist (primary intervention), followed by a prospective data collection for 4 months (phase 2). At the end of phase 2, interim analysis revealed a gradual decline in radiograph quality, which prompted a more comprehensive educational session with constructive feedback to the NICU staff (secondary intervention), followed by another data collection for 6 months (phase 3). There was a significant improvement in the quality of radiographs obtained after primary educational intervention (phase 2) compared with phase 1 (p < 0.001). During interim analysis after phase 2, radiograph quality declined but still remained significantly better than phase 1. Secondary intervention resulted in significant improvement in radiograph quality to > 95% in all domains of image quality. No radiographs were repeated in phase 3, compared with 5.8% (16/277) in phase 1. A structured, collaborated educational intervention successfully improves the radiograph quality and decreases the need for repeat radiographs and radiation exposure in the neonates. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

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

Zweifel,M.; Leahy, D.; Barrick, D.

Deltex is a cytosolic effector of Notch signaling thought to bind through its N-terminal domain to the Notch receptor. Here we report the structure of the Drosophila Deltex N-terminal domain, which contains two tandem WWE sequence repeats. The WWE repeats, which adopt a novel fold, are related by an approximate two-fold axis of rotation. Although the WWE repeats are structurally distinct, they interact extensively and form a deep cleft at their junction that appears well suited for ligand binding. The two repeats are thermodynamically coupled; this coupling is mediated in part by a conserved segment that is immediately C-terminal tomore » the second WWE domain. We demonstrate that although the Deltex WWE tandem is monomeric in solution, it forms a heterodimer with the ankyrin domain of the Notch receptor. These results provide structural and functional insight into how Deltex modulates Notch signaling, and how WWE modules recognize targets for ubiquitination.« less

Complete sequence and analysis of the mitochondrial genome of Hemiselmis andersenii CCMP644 (Cryptophyceae).

PubMed

Kim, Eunsoo; Lane, Christopher E; Curtis, Bruce A; Kozera, Catherine; Bowman, Sharen; Archibald, John M

2008-05-12

Cryptophytes are an enigmatic group of unicellular eukaryotes with plastids derived by secondary (i.e., eukaryote-eukaryote) endosymbiosis. Cryptophytes are unusual in that they possess four genomes-a host cell-derived nuclear and mitochondrial genome and an endosymbiont-derived plastid and 'nucleomorph' genome. The evolutionary origins of the host and endosymbiont components of cryptophyte algae are at present poorly understood. Thus far, a single complete mitochondrial genome sequence has been determined for the cryptophyte Rhodomonas salina. Here, the second complete mitochondrial genome of the cryptophyte alga Hemiselmis andersenii CCMP644 is presented. The H. andersenii mtDNA is 60,553 bp in size and encodes 30 structural RNAs and 36 protein-coding genes, all located on the same strand. A prominent feature of the genome is the presence of a approximately 20 Kbp long intergenic region comprised of numerous tandem and dispersed repeat units of between 22-336 bp. Adjacent to these repeats are 27 copies of palindromic sequences predicted to form stable DNA stem-loop structures. One such stem-loop is located near a GC-rich and GC-poor region and may have a regulatory function in replication or transcription. The H. andersenii mtDNA shares a number of features in common with the genome of the cryptophyte Rhodomonas salina, including general architecture, gene content, and the presence of a large repeat region. However, the H. andersenii mtDNA is devoid of inverted repeats and introns, which are present in R. salina. Comparative analyses of the suite of tRNAs encoded in the two genomes reveal that the H. andersenii mtDNA has lost or converted its original trnK(uuu) gene and possesses a trnS-derived 'trnK(uuu)', which appears unable to produce a functional tRNA. Mitochondrial protein coding gene phylogenies strongly support a variety of previously established eukaryotic groups, but fail to resolve the relationships among higher-order eukaryotic lineages. Comparison of the H. andersenii and R. salina mitochondrial genomes reveals a number of cryptophyte-specific genomic features, most notably the presence of a large repeat-rich intergenic region. However, unlike R. salina, the H. andersenii mtDNA does not possess introns and lacks a Lys-tRNA, which is presumably imported from the cytosol.

Complete Sequence and Analysis of the Mitochondrial Genome of Hemiselmis andersenii CCMP644 (Cryptophyceae)

PubMed Central

Kim, Eunsoo; Lane, Christopher E; Curtis, Bruce A; Kozera, Catherine; Bowman, Sharen; Archibald, John M

2008-01-01

Background Cryptophytes are an enigmatic group of unicellular eukaryotes with plastids derived by secondary (i.e., eukaryote-eukaryote) endosymbiosis. Cryptophytes are unusual in that they possess four genomes–a host cell-derived nuclear and mitochondrial genome and an endosymbiont-derived plastid and 'nucleomorph' genome. The evolutionary origins of the host and endosymbiont components of cryptophyte algae are at present poorly understood. Thus far, a single complete mitochondrial genome sequence has been determined for the cryptophyte Rhodomonas salina. Here, the second complete mitochondrial genome of the cryptophyte alga Hemiselmis andersenii CCMP644 is presented. Results The H. andersenii mtDNA is 60,553 bp in size and encodes 30 structural RNAs and 36 protein-coding genes, all located on the same strand. A prominent feature of the genome is the presence of a ~20 Kbp long intergenic region comprised of numerous tandem and dispersed repeat units of between 22–336 bp. Adjacent to these repeats are 27 copies of palindromic sequences predicted to form stable DNA stem-loop structures. One such stem-loop is located near a GC-rich and GC-poor region and may have a regulatory function in replication or transcription. The H. andersenii mtDNA shares a number of features in common with the genome of the cryptophyte Rhodomonas salina, including general architecture, gene content, and the presence of a large repeat region. However, the H. andersenii mtDNA is devoid of inverted repeats and introns, which are present in R. salina. Comparative analyses of the suite of tRNAs encoded in the two genomes reveal that the H. andersenii mtDNA has lost or converted its original trnK(uuu) gene and possesses a trnS-derived 'trnK(uuu)', which appears unable to produce a functional tRNA. Mitochondrial protein coding gene phylogenies strongly support a variety of previously established eukaryotic groups, but fail to resolve the relationships among higher-order eukaryotic lineages. Conclusion Comparison of the H. andersenii and R. salina mitochondrial genomes reveals a number of cryptophyte-specific genomic features, most notably the presence of a large repeat-rich intergenic region. However, unlike R. salina, the H. andersenii mtDNA does not possess introns and lacks a Lys-tRNA, which is presumably imported from the cytosol. PMID:18474103

Structural and functional peculiarities of the lipopolysaccharide of Azospirillum brasilense SR55, isolated from the roots of Triticum durum.

PubMed

Boyko, Alevtina S; Konnova, Svetlana A; Fedonenko, Yulia P; Zdorovenko, Evelina L; Smol'kina, Olga N; Kachala, Vadim V; Ignatov, Vladimir V

2011-10-20

Azospirillum brasilense SR55, isolated from the rhizosphere of Triticum durum, was classified as serogroup II on the basis of serological tests. Such serogroup affiliation is uncharacteristic of wheat-associated Azospirillum species. The lipid A of A. brasilense SR55 lipopolysaccharide contained 3-hydroxytetradecanoic, 3-hydroxyhexadecanoic, hexadecanoic and octadecenoic fatty acids. The structure of the lipopolysaccharide's O polysaccharide was established, with the branched octasaccharide repeating unit being represented by l-rhamnose, l-3-O-Me-rhamnose, d-galactose and d-glucuronic acid. The SR55 lipopolysaccharide induced deformations of wheat root hairs. The lipopolysaccharide was not involved in bacterial cell aggregation, but its use to pretreat wheat roots was conducive to cell adsorption. This study shows that Azospirillum bacteria can utilise their own lipopolysaccharide as a carbon source, which may give them an advantage in competitive natural environments. Copyright © 2011 Elsevier GmbH. All rights reserved.

Folding control in cyclic peptides through N-methylation pattern selection: formation of antiparallel beta-sheet dimers, double reverse turns and supramolecular helices by 3alpha,gamma cyclic peptides.

PubMed

Amorín, Manuel; Castedo, Luis; Granja, Juan R

2008-01-01

Peptide foldamers constitute a growing class of nanomaterials with potential applications in a wide variety of chemical, medical and technological fields. Here we describe the preparation and structural characteristics of a new class of cyclic peptide foldamers (3alpha,gamma-CPs) that, depending on their backbone N-methylation patterns and the medium, can either remain as flat rings that dimerize through arrays of hydrogen bonds of antiparallel beta-sheet type, or can fold into twisted double reverse turns that, in the case of double gamma-turns, associate in nonpolar solvents to form helical supramolecular structures. A 3alpha,gamma-CP consists of a number of multiples of a repeat unit made up of four amino acid residues of alternating chirality: three corresponding to alpha-amino acids and one to a gamma-amino acid (a cis-3-aminocycloalkanecarboxylic acid).

Using the self-select paradigm to delineate the nature of speech motor programming.

PubMed

Wright, David L; Robin, Don A; Rhee, Jooyhun; Vaculin, Amber; Jacks, Adam; Guenther, Frank H; Fox, Peter T

2009-06-01

The authors examined the involvement of 2 speech motor programming processes identified by S. T. Klapp (1995, 2003) during the articulation of utterances differing in syllable and sequence complexity. According to S. T. Klapp, 1 process, INT, resolves the demands of the programmed unit, whereas a second process, SEQ, oversees the serial order demands of longer sequences. A modified reaction time paradigm was used to assess INT and SEQ demands. Specifically, syllable complexity was dependent on syllable structure, whereas sequence complexity involved either repeated or unique syllabi within an utterance. INT execution was slowed when articulating single syllables in the form CCCV compared to simpler CV syllables. Planning unique syllables within a multisyllabic utterance rather than repetitions of the same syllable slowed INT but not SEQ. The INT speech motor programming process, important for mental syllabary access, is sensitive to changes in both syllable structure and the number of unique syllables in an utterance.

Redetermination of AgPO3

PubMed Central

Terebilenko, Katherina V.; Zatovsky, Igor V.; Ogorodnyk, Ivan V.; Baumer, Vyacheslav N.; Slobodyanik, Nikolay S.

2011-01-01

Single crystals of silver(I) polyphosphate(V), AgPO3, were prepared via a phospho­ric acid melt method using a solution of Ag3PO4 in H3PO4. In comparison with the previous study based on single-crystal Weissenberg photographs [Jost (1961 ▶). Acta Cryst. 14, 779–784], the results were mainly confirmed, but with much higher precision and with all displacement parameters refined anisotropically. The structure is built up from two types of distorted edge- and corner-sharing [AgO5] polyhedra, giving rise to multidirectional ribbons, and from two types of PO4 tetra­hedra linked into meandering chains (PO3)n spreading parallel to the b axis with a repeat unit of four tetra­hedra. The calculated bond-valence sum value of one of the two AgI ions indicates a significant strain of the structure. PMID:21522230

The ability of the Coincidence Doppler Broadening Spectroscopy to characterize polymers containing different chemical elements

NASA Astrophysics Data System (ADS)

Yang, J.; Zhang, T.; Han, L. A.; Cao, X. Z.; Yu, R. S.; Wang, B. Y.

2017-04-01

Hydrocarbon polymers, O-containing, F-containing and Cl-containing polymers are comprehensively studied by Coincidence Doppler Broadening Spectroscopy (CDBS). It is shown that for polymers with different chemical structure, CDBS results can effectively distinguish polar groups C dbnd O, Csbnd Cl, and Csbnd F. For polymers with similar chemical structure, the intensity of the element-specific peak in the CDBS ratio curve is dependent not only on the fraction of free positrons, but also on the content of characteristic atom in polymer repeated unit, and the polarity of the polymer molecule. For polymers containing several different polar groups, such as PCTFE (Csbnd F & Csbnd Cl) and PFA (Csbnd F & C dbnd O), whether the element-specific peak appears or not depends on the amount of the polar groups and its positron capture ability. This work may provide insights into potential applications of CDBS for studying complex polymer systems.

Nanoparticle self-assembly by a highly stable recombinant spider wrapping silk protein subunit.

PubMed

Xu, Lingling; Tremblay, Marie-Laurence; Orrell, Kathleen E; Leclerc, Jérémie; Meng, Qing; Liu, Xiang-Qin; Rainey, Jan K

2013-10-01

Artificial spider silk proteins may form fibers with exceptional strength and elasticity. Wrapping silk, or aciniform silk, is the toughest of the spider silks, and has a very different protein composition than other spider silks. Here, we present the characterization of an aciniform protein (AcSp1) subunit named W1, consisting of one AcSp1 199 residue repeat unit from Argiope trifasciata. The structural integrity of recombinant W1 is demonstrated in a variety of buffer conditions and time points. Furthermore, we show that W1 has a high thermal stability with reversible denaturation at ∼71°C and forms self-assembled nanoparticle in near-physiological conditions. W1 therefore represents a highly stable and structurally robust module for protein-based nanoparticle formation. Copyright © 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Gating Topology of the Proton-Coupled Oligopeptide Symporters

PubMed Central

Fowler, Philip W.; Orwick-Rydmark, Marcella; Radestock, Sebastian; Solcan, Nicolae; Dijkman, Patricia M.; Lyons, Joseph A.; Kwok, Jane; Caffrey, Martin; Watts, Anthony; Forrest, Lucy R.; Newstead, Simon

2015-01-01

Summary Proton-coupled oligopeptide transporters belong to the major facilitator superfamily (MFS) of membrane transporters. Recent crystal structures suggest the MFS fold facilitates transport through rearrangement of their two six-helix bundles around a central ligand binding site; how this is achieved, however, is poorly understood. Using modeling, molecular dynamics, crystallography, functional assays, and site-directed spin labeling combined with double electron-electron resonance (DEER) spectroscopy, we present a detailed study of the transport dynamics of two bacterial oligopeptide transporters, PepTSo and PepTSt. Our results identify several salt bridges that stabilize outward-facing conformations and we show that, for all the current structures of MFS transporters, the first two helices of each of the four inverted-topology repeat units form half of either the periplasmic or cytoplasmic gate and that these function cooperatively in a scissor-like motion to control access to the peptide binding site during transport. PMID:25651061

Structural and immunochemical studies of neutral exopolysaccharide produced by Lactobacillus johnsonii 142.

PubMed

Górska, Sabina; Jachymek, Wojciech; Rybka, Jacek; Strus, Magdalena; Heczko, Piotr B; Gamian, Andrzej

2010-01-11

This paper describes the structure of neutral exopolysaccharide (EPS) produced by Lactobacillus johnsonii 142, strain of the lactic acid bacteria isolated from the intestine of mice with experimentally induced inflammatory bowel disease (IBD). Sugar and methylation analyses along with (1)H and (13)C NMR spectroscopy, including two-dimensional (1)H,(1)H COSY, TOCSY, NOESY, and (1)H,(13)C HSQC experiments revealed that the repeating unit of the EPS is a pentasaccharide: -->3)-alpha-D-Galp-(1-->3)-beta-d-Glcp-(1-->5)-beta-D-Galf-(1-->3)-alpha-D-Galp-(1-->3)-alpha-D-Galp-(1--> The rabbit antiserum raised against whole cells of L. johnsonii 142 reacted with homologous EPS, and cross-reacted with exopolysaccharide from Lactobacillus animalis/murinus 148 isolated also from mice with IBD, but not reacted with EPS of L. johnsonii 151 from healthy mice. Copyright 2009 Elsevier Ltd. All rights reserved.

A remote sensing based vegetation classification logic for global land cover analysis

USGS Publications Warehouse

Running, Steven W.; Loveland, Thomas R.; Pierce, Lars L.; Nemani, R.R.; Hunt, E. Raymond

1995-01-01

This article proposes a simple new logic for classifying global vegetation. The critical features of this classification are that 1) it is based on simple, observable, unambiguous characteristics of vegetation structure that are important to ecosystem biogeochemistry and can be measured in the field for validation, 2) the structural characteristics are remotely sensible so that repeatable and efficient global reclassifications of existing vegetation will be possible, and 3) the defined vegetation classes directly translate into the biophysical parameters of interest by global climate and biogeochemical models. A first test of this logic for the continental United States is presented based on an existing 1 km AVHRR normalized difference vegetation index database. Procedures for solving critical remote sensing problems needed to implement the classification are discussed. Also, some inferences from this classification to advanced vegetation biophysical variables such as specific leaf area and photosynthetic capacity useful to global biogeochemical modeling are suggested.

Highly sulfated hexasaccharide sequences isolated from chondroitin sulfate of shark fin cartilage: insights into the sugar sequences with bioactivities.

PubMed

Mizumoto, Shuji; Murakoshi, Saori; Kalayanamitra, Kittiwan; Deepa, Sarama Sathyaseelan; Fukui, Shigeyuki; Kongtawelert, Prachya; Yamada, Shuhei; Sugahara, Kazuyuki

2013-02-01

Chondroitin sulfate (CS) chains regulate the development of the central nervous system in vertebrates and are linear polysaccharides consisting of variously sulfated repeating disaccharides, [-4GlcUAβ1-3GalNAcβ1-](n), where GlcUA and GalNAc represent D-glucuronic acid and N-acetyl-D-galactosamine, respectively. CS chains containing D-disaccharide units [GlcUA(2-O-sulfate)-GalNAc(6-O-sulfate)] are involved in the development of cerebellar Purkinje cells and neurite outgrowth-promoting activity through interaction with a neurotrophic factor, pleiotrophin, resulting in the regulation of signaling. In this study, to obtain further structural information on the CS chains containing d-disaccharide units involved in brain development, oligosaccharides containing D-units were isolated from a shark fin cartilage. Seven novel hexasaccharide sequences, ΔO-D-D, ΔA-D-D, ΔC-D-D, ΔE-A-D, ΔD-D-C, ΔE-D-D and ΔA-B-D, in addition to three previously reported sequences, ΔC-A-D, ΔC-D-C and ΔA-D-A, were isolated from a CS preparation of shark fin cartilage after exhaustive digestion with chondroitinase AC-I, which cannot act on the galactosaminidic linkages bound to D-units. The symbol Δ stands for a 4,5-unsaturated bond of uronic acids, whereas A, B, C, D, E and O represent [GlcUA-GalNAc(4-O-sulfate)], [GlcUA(2-O-sulfate)-GalNAc(4-O-sulfate)], [GlcUA-GalNAc(6-O-sulfate)], [GlcUA(2-O-sulfate)-GalNAc(6-O-sulfate)], [GlcUA-GalNAc(4-O-, 6-O-sulfate)] and [GlcUA-GalNAc], respectively. In binding studies using an anti-CS monoclonal antibody, MO-225, the epitopes of which are involved in cerebellar development in mammals, novel epitope structures, ΔA-D-A, ΔA-D-D and ΔA-B-D, were revealed. Hexasaccharides containing two consecutive D-units or a B-unit will be useful for the structural and functional analyses of CS chains particularly in the neuroglycobiological fields.

Spatial transcriptomics: paving the way for tissue-level systems biology.

PubMed

Moor, Andreas E; Itzkovitz, Shalev

2017-08-01

The tissues in our bodies are complex systems composed of diverse cell types that often interact in highly structured repeating anatomical units. External gradients of morphogens, directional blood flow, as well as the secretion and absorption of materials by cells generate distinct microenvironments at different tissue coordinates. Such spatial heterogeneity enables optimized function through division of labor among cells. Unraveling the design principles that govern this spatial division of labor requires techniques to quantify the entire transcriptomes of cells while accounting for their spatial coordinates. In this review we describe how recent advances in spatial transcriptomics open the way for tissue-level systems biology. Copyright © 2017 Elsevier Ltd. All rights reserved.

Transient formation of nano-crystalline structures during fibrillation of an Aβ-like peptide

PubMed Central

Otzen, Daniel E.; Oliveberg, Mikael

2004-01-01

During the first few minutes of fibrillation of a 14-residue peptide homologous to the hydrophobic C-terminal part of the Aβ-peptide, EM micrographs reveal small crystalline areas (100 to 150 nm, repeating unit 47 Å) scattered in more amorphous material. On a longer time scale, these crystalline areas disappear and are replaced by tangled clusters resembling protofilaments (hours), and eventually by more regular amyloid fibrils of 60 Å to 120 Å diameter (days). The transient population of the crystalline areas indicates the presence of ordered substructures in the early fibrillation process, the diameter of which matches the length of the 14-mer peptide in an extended β-strand conformation. PMID:15096642

Simplified Estimation and Testing in Unbalanced Repeated Measures Designs.

PubMed

Spiess, Martin; Jordan, Pascal; Wendt, Mike

2018-05-07

In this paper we propose a simple estimator for unbalanced repeated measures design models where each unit is observed at least once in each cell of the experimental design. The estimator does not require a model of the error covariance structure. Thus, circularity of the error covariance matrix and estimation of correlation parameters and variances are not necessary. Together with a weak assumption about the reason for the varying number of observations, the proposed estimator and its variance estimator are unbiased. As an alternative to confidence intervals based on the normality assumption, a bias-corrected and accelerated bootstrap technique is considered. We also propose the naive percentile bootstrap for Wald-type tests where the standard Wald test may break down when the number of observations is small relative to the number of parameters to be estimated. In a simulation study we illustrate the properties of the estimator and the bootstrap techniques to calculate confidence intervals and conduct hypothesis tests in small and large samples under normality and non-normality of the errors. The results imply that the simple estimator is only slightly less efficient than an estimator that correctly assumes a block structure of the error correlation matrix, a special case of which is an equi-correlation matrix. Application of the estimator and the bootstrap technique is illustrated using data from a task switch experiment based on an experimental within design with 32 cells and 33 participants.

Online neural monitoring of statistical learning.

PubMed

Batterink, Laura J; Paller, Ken A

2017-05-01

The extraction of patterns in the environment plays a critical role in many types of human learning, from motor skills to language acquisition. This process is known as statistical learning. Here we propose that statistical learning has two dissociable components: (1) perceptual binding of individual stimulus units into integrated composites and (2) storing those integrated representations for later use. Statistical learning is typically assessed using post-learning tasks, such that the two components are conflated. Our goal was to characterize the online perceptual component of statistical learning. Participants were exposed to a structured stream of repeating trisyllabic nonsense words and a random syllable stream. Online learning was indexed by an EEG-based measure that quantified neural entrainment at the frequency of the repeating words relative to that of individual syllables. Statistical learning was subsequently assessed using conventional measures in an explicit rating task and a reaction-time task. In the structured stream, neural entrainment to trisyllabic words was higher than in the random stream, increased as a function of exposure to track the progression of learning, and predicted performance on the reaction time (RT) task. These results demonstrate that monitoring this critical component of learning via rhythmic EEG entrainment reveals a gradual acquisition of knowledge whereby novel stimulus sequences are transformed into familiar composites. This online perceptual transformation is a critical component of learning. Copyright © 2017 Elsevier Ltd. All rights reserved.

Diverticular disease of the colon does not increase risk of repeat C. difficile infection.

PubMed

Feuerstadt, Paul; Das, Rohit; Brandt, Lawrence J

2013-01-01

Studies have suggested that colonic diverticulosis might increase the likelihood of repeat Clostridium difficile infection (CDI). Our study was designed to compare rates of repeat infection in patients with and without colon diverticula. Patients who had a positive C. difficile toxin assay and colonoscopic evidence of diverticulosis were classified as CDI and diverticulosis (CDI-D), whereas those with a positive toxin assay but no such colonoscopic evidence were classified as CDI and no diverticulosis (CDI-ND). Various clinical and epidemiologic factors were recorded for each patient. Primary outcomes were "relapse" (repeat CDI within 3 mo of initial infection) and "recurrent" infection (repeat CDI≥3 mo after initial infection). Secondary outcomes 30 days after diagnosis were mortality, intensive care unit transfer, and continuous hospitalization. A total of 128 patients were classified as CDI-D, whereas 137 had CDI-ND. There were no significant differences between CDI-D and CDI-ND when comparing frequencies of repeat infection and its subclassifications, relapse or recurrence. There were, however, statistical associations seen between diverticulosis of the ascending colon and increased recurrence rates [hazard ratio (HR): 1.4±0.38, P<0.05] and decreased rates of relapse in diverticular disease of the descending (HR: 0.40±0.46, P<0.05), and sigmoid colon (HR: 0.39±0.49, P<0.05). The ascending colon association is limited by a small patient population. There were no significant differences in any of the 30-day outcomes including intensive care unit requirement, hospitalization stay, or mortality. Patients with diverticular disease of the colon are not at increased risk of repeat CDI.

Microevolution of Pandemic Vibrio parahaemolyticus Assessed by the Number of Repeat Units in Short Sequence Tandem Repeat Regions

PubMed Central

García, Katherine; Gavilán, Ronnie G.; Höfle, Manfred G.; Martínez-Urtaza, Jaime; Espejo, Romilio T.

2012-01-01

The emergence of the pandemic strain Vibrio parahaemolyticus O3:K6 in 1996 caused a large increase of diarrhea outbreaks related to seafood consumption in Southeast Asia, and later worldwide. Isolates of this strain constitutes a clonal complex, and their effectual differentiation is possible by comparison of their variable number tandem repeats (VNTRs). The differentiation of the isolates by the differences in VNTRs will allow inferring the population dynamics and microevolution of this strain but this requires knowing the rate and mechanism of VNTRs' variation. Our study of mutants obtained after serial cultivation of clones showed that mutation rates of the six VNTRs examined are on the order of 10−4 mutant per generation and that difference increases by stepwise addition of single mutations. The single stepwise mutation (SSM) was deduced because mutants with 1, 2, 3, or more repeat unit deletions or insertions follow a geometric distribution. Plausible phylogenetic trees are obtained when, according to SSM, the genetic distance between clusters with different number of repeats is assessed by the absolute differences in repeats. Using this approach, mutants originated from different isolates of pandemic V. parahaemolyticus after serial cultivation are clustered with their parental isolates. Additionally, isolates of pandemic V. parahaemolyticus from Southeast Asia, Tokyo, and northern and southern Chile are clustered according their geographical origin. The deepest split in these four populations is observed between the Tokyo and southern Chile populations. We conclude that proper phylogenetic relations and successful tracing of pandemic V. parahaemolyticus requires measuring the differences between isolates by the absolute number of repeats in the VNTRs considered. PMID:22292049

Tandemly repeated sequences in mtDNA control region of whitefish, Coregonus lavaretus.

PubMed

Brzuzan, P

2000-06-01

Length variation of the mitochondrial DNA control region was observed with PCR amplification of a sample of 138 whitefish (Coregonus lavaretus). Nucleotide sequences of representative PCR products showed that the variation was due to the presence of an approximately 100-bp motif tandemly repeated two, three, or five times in the region between the conserved sequence block-3 (CSB-3) and the gene for phenylalanine tRNA. This is the first report on the tandem array composed of long repeat units in mitochondrial DNA of salmonids.

Molecular dynamics simulation of thermomechanical properties of montmorillonite crystal. 3. montmorillonite crystals with PEO oligomer intercalates.

PubMed

Mazo, Mikhail A; Manevitch, Leonid I; Gusarova, Elena B; Shamaev, Mikhail Yu; Berlin, Alexander A; Balabaev, Nikolay K; Rutledge, Gregory C

2008-03-27

We present the results of molecular dynamics (MD) simulation of the structure and thermomechanical behavior of Wyoming-type Na+-montmorillonite (MMT) with poly(ethylene oxide) (PEO) oligomer intercalates. Periodic boundary conditions in all three directions and simulation cells containing two MMT lamellae [Si248Al8][Al112Mg16]O640[OH]128 oriented parallel to the XY-plane were used. The interlamellar space, or gallery, between neighboring MMT lamellae was populated by 24 Na+ counterions and PEO macromolecules of different lengths, ranging from 2 up to 240 repeat units. We considered three different loadings of PEO within the gallery: 80, 160, and 240 repeat units, corresponding to 13, 23, and 31 wt % PEO based on total mass of the nanocomposite, respectively. In the cases of 13 and 23 wt %, the polymer chains formed one or two well-defined amorphous layers with interlayer distances of 1.35 and 1.8 nm, respectively. We have observed also formation of a wider monolayer gallery with interlayer distances of 1.6 nm. Three-layer PEO films formed in the case of 31 wt % loading. The thermal properties were analyzed over the range 300-400 K, and the isothermal linear compressibility, transversal moduli, and shear moduli were calculated at 300 K. These properties are compared with the results of our simulation of thermal and mechanical properties of MMT crystal with galleries filled by one or two water layers as well as with those of an isolated clay nanoplate.

Structural characterization of fucosylated chondroitin sulfates from sea cucumbers Apostichopus japonicus and Actinopyga mauritiana.

PubMed

Ustyuzhanina, Nadezhda E; Bilan, Maria I; Dmitrenok, Andrey S; Tsvetkova, Eugenia A; Shashkov, Alexander S; Stonik, Valentin A; Nifantiev, Nikolay E; Usov, Anatolii I

2016-11-20

Two samples of fucosylated chondroitin sulfate (FCS), AJ and AM, were isolated from holothurian species Apostichopus japonicus and Actinopyga mauritiana, respectively. Purification of FCS was performed by ion exchange chromatography followed by gel filtration. Structure of the biopolymers was elucidated using chemical and NMR spectroscopic methods. Both polysaccharides were shown to contain a typical chondroitin core built up of repeating disaccharide units →3)-β-d-GalNAc-(1→4)-β-d-GlcA-(1→ and decorated by sulfate groups and α-l-Fuc branches. Two polysaccharides were different in pattern of sulfation of GalNAc and fucosyl branches connected to O-3 of GlcA. The ratio of GalNAc4S6S:GalNAc4S for AJ was about 2:1, whereas for AM this value was approximately 1:1. AJ contained Fucp2S4S and Fucp3S4S residues linked to O-3 of GlcA in a ratio of 3:1, while for AM this ratio was 1:4. Small portions of Fucp4S units attached to O-3 of GlcA were also found in both polysaccharides. Moreover, in a structure of AM the presence of Fucp3S residues linked to O-6 of GalNAc were determined using the data of NMR spectra. Copyright © 2016 Elsevier Ltd. All rights reserved.

The heptad repeats region is essential for AcMNPV P10 filament formation and not the proline-rich or the C-terminus basic regions.

PubMed

Dong, Chunsheng; Deng, Fei; Li, Dan; Wang, Hualin; Hu, Zhihong

2007-09-01

Baculovirus P10 protein is a small conserved protein and is expressed as bundles of filaments in the host cell during the late phase of virus infection. So far the published results on the domain responsible for filament structural formation have been contradictory. Electron microscopy revealed that the C-terminus basic region was involved in filament structural formation in the Autographa californica multiple nucleocapsid nucleopolyhedrovirus (AcMNPV) [van Oers, M.M., Flipsen, J.T., Reusken, C.B., Sliwinsky, E.L., Vlak, J.M., 1993. Functional domains of the p10 protein of Autographa californica nuclear polyhedorsis virus. J. Gen. Virol. 74, 563-574.]. While in the Helicoverpa armigera nucleopolyhedrovirus (HearNPV), the heptad repeats region but not the C-terminus domain was proven to be responsible for filament formation [Dong, C., Li, D., Long, G., Deng, F., Wang, H., Hu, Z., 2005. Identification of functional domains required for HearNPV P10 filament formation. Virology 338, 112-120.]. In this manuscript, fluorescence confocal microscopy was applied to study AcMNPV P10 filament formation. A set of plasmids containing different P10 structural domains fused with a fluorescent protein were constructed and transfected into Sf-9 cells. The data indicated that the heptad repeats region, but not the proline-rich region or the C-terminus basic region, is essential for AcMNPV P10 filament formation. Co-transfection of P10s tagged with different fluorescent revealed that P10s with defective heptad repeats region could not interact with intact heptad repeats region or even full-length P10s to form filament structure. Within the heptad repeats region, deletion of the three amino acids spacing of AcMNPV P10 appeared to have no significant impact on the formation of filament structures, but the content of the heptad repeats region appeared to play a role in the morphology of the filaments.

R-loops: targets for nuclease cleavage and repeat instability.

PubMed

Freudenreich, Catherine H

2018-01-11

R-loops form when transcribed RNA remains bound to its DNA template to form a stable RNA:DNA hybrid. Stable R-loops form when the RNA is purine-rich, and are further stabilized by DNA secondary structures on the non-template strand. Interestingly, many expandable and disease-causing repeat sequences form stable R-loops, and R-loops can contribute to repeat instability. Repeat expansions are responsible for multiple neurodegenerative diseases, including Huntington's disease, myotonic dystrophy, and several types of ataxias. Recently, it was found that R-loops at an expanded CAG/CTG repeat tract cause DNA breaks as well as repeat instability (Su and Freudenreich, Proc Natl Acad Sci USA 114, E8392-E8401, 2017). Two factors were identified as causing R-loop-dependent breaks at CAG/CTG tracts: deamination of cytosines and the MutLγ (Mlh1-Mlh3) endonuclease, defining two new mechanisms for how R-loops can generate DNA breaks (Su and Freudenreich, Proc Natl Acad Sci USA 114, E8392-E8401, 2017). Following R-loop-dependent nicking, base excision repair resulted in repeat instability. These results have implications for human repeat expansion diseases and provide a paradigm for how RNA:DNA hybrids can cause genome instability at structure-forming DNA sequences. This perspective summarizes mechanisms of R-loop-induced fragility at G-rich repeats and new links between DNA breaks and repeat instability.

History Repeats Itself at Yorktown Middle.

ERIC Educational Resources Information Center

Haskin, Teresa T.

1999-01-01

Describes two interdisciplinary units that can be used in most middle school classrooms, one on the sinking of the "Titanic" and one on Pickett's charge at Gettysburg during the Civil War. Describes how each unit involves English, math, social studies, and science classes and activities. (SR)

Generation, Analysis and Characterization of Anisotropic Engineered Meta Materials

NASA Astrophysics Data System (ADS)

Trifale, Ninad T.

A methodology for a systematic generation of highly anisotropic micro-lattice structures was investigated. Multiple algorithms for generation and validation of engineered structures are developed and evaluated. Set of all possible permutations of structures for an 8-node cubic unit cell were considered and the degree of anisotropy of meta-properties in heat transport and mechanical elasticity were evaluated. Feasibility checks were performed to ensure that the generated unit cell network was repeatable and a continuous lattice structure. Four different strategies for generating permutations of the structures are discussed. Analytical models were developed to predict effective thermal, mechanical and permeability characteristics of these cellular structures.Experimentation and numerical modeling techniques were used to validate the models that are developed. A self-consistent mechanical elasticity model was developed which connects the meso-scale properties to stiffness of individual struts. A three dimensional thermal resistance network analogy was used to evaluate the effective thermal conductivity of the structures. The struts were modeled as a network of one dimensional thermal resistive elements and effective conductivity evaluated. Models were validated against numerical simulations and experimental measurements on 3D printed samples. Model was developed to predict effective permeability of these engineered structures based on Darcy's law. Drag coefficients were evaluated for individual connections in transverse and longitudinal directions and an interaction term was calibrated from the experimental data in literature in order to predict permeability. Generic optimization framework coupled to finite element solver is developed for analyzing any application involving use of porous structures. An objective functions were generated structure to address frequently observed trade-off between the stiffness, thermal conductivity, permeability and porosity. Three application were analyzed for potential use of engineered materials. Heat spreader application involving thermal and mechanical constraints, artificial bone grafts application involving mechanical and permeability constraints and structural materials applications involving mechanical, thermal and porosity constraints is analyzed. Recommendations for optimum topologies for specific operating conditions are provided.

Structure and magnetism in Co/X, Fe/Si, and Fe/(FeSi) multilayers

NASA Astrophysics Data System (ADS)

Franklin, Michael Ray

Previous studies have shown that magnetic behavior in multilayers formed by repeating a bilayer unit comprised of a ferromagnetic layer and a non-magnetic spacer layer can be affected by small structural differences. For example, a macroscopic property such as giant magnetoresistance (GMR) is believed to depend significantly upon interfacial roughness. In this study, several complimentary structural probes were used to carefully characterize the structure of several sputtered multilayer systems-Co/Ag, Co/Cu, Co/Mo, Fe/Si, and Fe//[FeSi/]. X-ray diffraction (XRD) studies were used to examine the long-range structural order of the multilayers perpendicular to the plane of the layers. Transmission electron diffraction (TED) studies were used to probe the long-range order parallel to the layer plane. X-ray Absorption Fine Structure (XAFS) studies were used to determine the average local structural environment of the ferromagnetic atoms. For the Co/X systems, a simple correlation between crystal structure and saturation magnetization is discovered for the Co/Mo system. For the Fe/X systems, direct evidence of an Fe-silicide is found for the /[FeSi/] spacer layer but not for the Si spacer layer. Additionally, differences were observed in the magnetic behavior between the Fe in the nominally pure Fe layer and the Fe contained in the /[FeSi/] spacer layers.

Structural Basis of Egg Coat-Sperm Recognition at Fertilization.

PubMed

Raj, Isha; Sadat Al Hosseini, Hamed; Dioguardi, Elisa; Nishimura, Kaoru; Han, Ling; Villa, Alessandra; de Sanctis, Daniele; Jovine, Luca

2017-06-15

Recognition between sperm and the egg surface marks the beginning of life in all sexually reproducing organisms. This fundamental biological event depends on the species-specific interaction between rapidly evolving counterpart molecules on the gametes. We report biochemical, crystallographic, and mutational studies of domain repeats 1-3 of invertebrate egg coat protein VERL and their interaction with cognate sperm protein lysin. VERL repeats fold like the functionally essential N-terminal repeat of mammalian sperm receptor ZP2, whose structure is also described here. Whereas sequence-divergent repeat 1 does not bind lysin, repeat 3 binds it non-species specifically via a high-affinity, largely hydrophobic interface. Due to its intermediate binding affinity, repeat 2 selectively interacts with lysin from the same species. Exposure of a highly positively charged surface of VERL-bound lysin suggests that complex formation both disrupts the organization of egg coat filaments and triggers their electrostatic repulsion, thereby opening a hole for sperm penetration and fusion. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Translocation and gross deletion breakpoints in human inherited disease and cancer II: Potential involvement of repetitive sequence elements in secondary structure formation between DNA ends.

PubMed

Chuzhanova, Nadia; Abeysinghe, Shaun S; Krawczak, Michael; Cooper, David N

2003-09-01

Translocations and gross deletions are responsible for a significant proportion of both cancer and inherited disease. Although such gene rearrangements are nonuniformly distributed in the human genome, the underlying mutational mechanisms remain unclear. We have studied the potential involvement of various types of repetitive sequence elements in the formation of secondary structure intermediates between the single-stranded DNA ends that recombine during rearrangements. Complexity analysis was used to assess the potential of these ends to form secondary structures, the maximum decrease in complexity consequent to a gross rearrangement being used as an indicator of the type of repeat and the specific DNA ends involved. A total of 175 pairs of deletion/translocation breakpoint junction sequences available from the Gross Rearrangement Breakpoint Database [GRaBD; www.uwcm.ac.uk/uwcm/mg/grabd/grabd.html] were analyzed. Potential secondary structure was noted between the 5' flanking sequence of the first breakpoint and the 3' flanking sequence of the second breakpoint in 49% of rearrangements and between the 5' flanking sequence of the second breakpoint and the 3' flanking sequence of the first breakpoint in 36% of rearrangements. Inverted repeats, inversions of inverted repeats, and symmetric elements were found in association with gross rearrangements at approximately the same frequency. However, inverted repeats and inversions of inverted repeats accounted for the vast majority (83%) of deletions plus small insertions, symmetric elements for one-half of all antigen receptor-mediated translocations, while direct repeats appear only to be involved in mediating simple deletions. These findings extend our understanding of illegitimate recombination by highlighting the importance of secondary structure formation between single-stranded DNA ends at breakpoint junctions. Copyright 2003 Wiley-Liss, Inc.

The principles of collective animal behaviour

PubMed Central

Sumpter, D.J.T

2005-01-01

In recent years, the concept of self-organization has been used to understand collective behaviour of animals. The central tenet of self-organization is that simple repeated interactions between individuals can produce complex adaptive patterns at the level of the group. Inspiration comes from patterns seen in physical systems, such as spiralling chemical waves, which arise without complexity at the level of the individual units of which the system is composed. The suggestion is that biological structures such as termite mounds, ant trail networks and even human crowds can be explained in terms of repeated interactions between the animals and their environment, without invoking individual complexity. Here, I review cases in which the self-organization approach has been successful in explaining collective behaviour of animal groups and societies. Ant pheromone trail networks, aggregation of cockroaches, the applause of opera audiences and the migration of fish schools have all been accurately described in terms of individuals following simple sets of rules. Unlike the simple units composing physical systems, however, animals are themselves complex entities, and other examples of collective behaviour, such as honey bee foraging with its myriad of dance signals and behavioural cues, cannot be fully understood in terms of simple individuals alone. I argue that the key to understanding collective behaviour lies in identifying the principles of the behavioural algorithms followed by individual animals and of how information flows between the animals. These principles, such as positive feedback, response thresholds and individual integrity, are repeatedly observed in very different animal societies. The future of collective behaviour research lies in classifying these principles, establishing the properties they produce at a group level and asking why they have evolved in so many different and distinct natural systems. Ultimately, this research could inform not only our understanding of animal societies, but also the principles by which we organize our own society. PMID:16553306

The principles of collective animal behaviour.

PubMed

Sumpter, D J T

2006-01-29

In recent years, the concept of self-organization has been used to understand collective behaviour of animals. The central tenet of self-organization is that simple repeated interactions between individuals can produce complex adaptive patterns at the level of the group. Inspiration comes from patterns seen in physical systems, such as spiralling chemical waves, which arise without complexity at the level of the individual units of which the system is composed. The suggestion is that biological structures such as termite mounds, ant trail networks and even human crowds can be explained in terms of repeated interactions between the animals and their environment, without invoking individual complexity. Here, I review cases in which the self-organization approach has been successful in explaining collective behaviour of animal groups and societies. Ant pheromone trail networks, aggregation of cockroaches, the applause of opera audiences and the migration of fish schools have all been accurately described in terms of individuals following simple sets of rules. Unlike the simple units composing physical systems, however, animals are themselves complex entities, and other examples of collective behaviour, such as honey bee foraging with its myriad of dance signals and behavioural cues, cannot be fully understood in terms of simple individuals alone. I argue that the key to understanding collective behaviour lies in identifying the principles of the behavioural algorithms followed by individual animals and of how information flows between the animals. These principles, such as positive feedback, response thresholds and individual integrity, are repeatedly observed in very different animal societies. The future of collective behaviour research lies in classifying these principles, establishing the properties they produce at a group level and asking why they have evolved in so many different and distinct natural systems. Ultimately, this research could inform not only our understanding of animal societies, but also the principles by which we organize our own society.

Comprehensive analysis of all triple helical repeats in beta-spectrins reveals patterns of selective evolutionary conservation.

PubMed

Baines, Anthony J

2003-01-01

The spectrin superfamily (spectrin, alpha-actinin, utrophin and dystrophin) has in common a triple helical repeating unit of ~106 amino acid residues. In spectrin, alpha and beta chains contain multiple copies of this repeat. beta-spectrin chains contain the majority of binding activities in spectrin and are essential for animal life. Canonical beta-spectrins have 17 repeats; beta-heavy spectrins have 30. Here, the repeats of five human beta-spectrins, plus beta-spectrins from several other vertebrates and invertebrates, have been analysed. Repeats 1, 2, 14 and 17 in canonical beta are highly conserved between invertebrates and vertebrates, and repeat 8 in some isoforms. This is consistent with conservation of critical functions, since repeats 1, 2 and 17 bind alpha-spectrin. Repeats 1 of beta-spectrins are not always detected by SMART or Pfam tools. A profile hidden Markov model of beta-spectrin repeat 1 detects alpha-actinins, but not utrophin or dystrophin. Novel examples of repeat 1 were detected in the spectraplakins MACF1, BPAG1 and plectin close to the actin-binding domain. Ankyrin binds to the C-terminal portion of repeat 14; the high conservation of this entire repeat may point to additional, undiscovered ligand-binding activities. This analysis indicates that the basic triple helical repeat pattern was adapted early in the evolution of the spectrin superfamily to encompass essential binding activities, which characterise individual repeats in proteins extant today.

Adaptive cellular structures and devices with internal features for enhanced structural performance

NASA Astrophysics Data System (ADS)

Pontecorvo, Michael Eugene

This dissertation aims to develop a family of cellular and repeatable devices that exhibit a variety of force-displacement behaviors. It is envisioned that these cellular structures might be used either as stand-alone elements, or combined and repeated to create multiple types of structures (i.e. buildings, ship hulls, vehicle subfloors, etc.) with the ability to passively or actively perform multiple functions (harmonic energy dissipation, impact mitigation, modulus change) over a range of loading types, amplitudes, and frequencies. To accomplish this goal, this work combines repeatable structural frameworks, such as that provided by a hexagonal cellular structure, with internal structural elements such as springs, viscous dampers, buckling plates, bi-stable von Mises trusses (VMTs), and pneumatic artificial muscles (PAMs). The repeatable framework serves to position damping and load carrying elements throughout the structure, and the configuration of the internal elements allow each cell to be tuned to exhibit a desired force-displacement response. Therefore, gradient structures or structures with variable load paths can be created for an optimal global response to a range of loads. This dissertation focuses on the development of cellular structures for three functions: combined load-carrying capability with harmonic energy dissipation, impact mitigation, and cell modulus variation. One or more conceptual designs are presented for devices that can perform each of these functions, and both experimental measurements and simulations are used to gain a fundamental understanding of each device. Chapter 2 begins with a presentation of a VMT model that is the basis for many of the elements. The equations of motion for the VMT are derived and the static and dynamic behavior of the VMT are discussed in detail. Next, two metrics for the energy dissipation of the VMT - hysteresis loop area and loss factor - are presented. The responses of the VMT to harmonic displacement and force inputs are contrasted in relation to these metrics. The key innovation to the early structural elements presented here is the combination of the VMT with the pin-jointed hexagonal cell. Chapter 3 explores several prototypes of repeatable structural elements for simultaneous load-carrying capability and energy dissipation that are based on this innovation. The final demonstration prototype presented in this chapter is a column-like element that is based on a hexagonal cell containing two horizontal springs and one vertical damper. The unit is enclosed by a pair of buckling plates that serve to give the prototype a high initial stiffness and load carrying capability. The prototype is tested in both displacement and force input and its behavior is compared to simulation. Chapter 4 builds on the conceptual designs of Chapter 3 with the introduction of a plate-like element, that contains two compact VMTs connected by a horizontally oriented damper. Pre-loaded springs are used in the prototype to perform the same load carrying function as the buckling plates in the column-like prototype with increased predictability. The plate-like prototype is studied under impact to demonstrate its effectiveness as a protective layer. It is shown to reduce peak impact loads transmitted to the base of the device by over 60%. In most cases, the prototype compares well with a conventional protective rubber layer, and in cases of extreme impact loads, it exceeds the performance of the rubber layer. In addition to impact testing, the prototype is also experimentally tested under harmonic displacement input, and is simulated under both harmonic displacement and force input. The experiments illustrate that while the VMT parameters of a single layer can be optimized to a particular harmonic load amplitude, having two layers with softer and stiffer VMTs allows the system to show good energy dissipation characteristics at different harmonic load amplitude levels. Chapter 5 examines using PAM inclusions within planar hexagonal cells as variable stiffness springs to create a variable modulus cellular structure. The proposed concept is envisioned as a first step toward a structural unit cell whose in-plane modulus in a given direction can be tuned based on the orientation of PAMs within the cell and the pressure supplied to the individual muscles. To begin, a pin-jointed cell is considered, loaded in the horizontal direction, with three PAMs (one vertical PAM and two horizontal PAMs) oriented in an "H" configuration between the vertices of the cell. A method for calculation of the hexagonal cell modulus is introduced, as is an expression for the balance of tensile forces between the horizontal and vertical PAMs. An aluminum hexagonal unit cell is fabricated and simulation of the hexagonal cell with PAM inclusions is then compared to experimental measurement of the unit cell modulus in the horizontal direction over a pressure range up to 682 kPa. An increase in cell modulus of 200% and a corresponding change in cell angle of 1.53 degrees are demonstrated experimentally. A design study via simulation predicts that differential pressurization of the PAMs up to 1992 kPa can increase the cell modulus in the horizontal direction by a factor of 6.66 with a change in cell angle of only 2.75 degrees. Additionally, simulation predicts that variation of unpressurized cell equilibrium angle and vertical wall length coefficient can result in changes in cell modulus greater than 1000%. A drawback of the pin-jointed cell with PAM inclusions is that it is inherently underconstrained. To solve this problem, the pin-jointed cell walls are replaced with a continuous Delrin hexagon which gives the cell kinematic stability and allows for experimental measurement of modulus in both the horizontal and vertical directions. The Delrin cell is designed to have a modulus on the same order as that of the pin-jointed cell at zero pressure and is experimentally measured without the PAM inclusions. These measurements validate the use of a combined flexural/hinging analytical model that accurately simulates the cell modulus. This analysis is then combined with the PAM force equations to model the complete hexagonal cell with PAM inclusions. Simulation and experimental measurement of the cell modulus with the PAM inclusions are compared in both the horizontal and vertical directions over an expanded pressure range up to 1302 kPa. The interplay between the contraction ratio and pressure in orthogonal sets of PAMs is highlighted as the primary driver of overall cell modulus.

Structure-Based Rational Design of a Toll-like Receptor 4 (TLR4) Decoy Receptor with High Binding Affinity for a Target Protein

PubMed Central

Lee, Sang-Chul; Hong, Seungpyo; Park, Keunwan; Jeon, Young Ho; Kim, Dongsup; Cheong, Hae-Kap; Kim, Hak-Sung

2012-01-01

Repeat proteins are increasingly attracting much attention as alternative scaffolds to immunoglobulin antibodies due to their unique structural features. Nonetheless, engineering interaction interface and understanding molecular basis for affinity maturation of repeat proteins still remain a challenge. Here, we present a structure-based rational design of a repeat protein with high binding affinity for a target protein. As a model repeat protein, a Toll-like receptor4 (TLR4) decoy receptor composed of leucine-rich repeat (LRR) modules was used, and its interaction interface was rationally engineered to increase the binding affinity for myeloid differentiation protein 2 (MD2). Based on the complex crystal structure of the decoy receptor with MD2, we first designed single amino acid substitutions in the decoy receptor, and obtained three variants showing a binding affinity (KD) one-order of magnitude higher than the wild-type decoy receptor. The interacting modes and contributions of individual residues were elucidated by analyzing the crystal structures of the single variants. To further increase the binding affinity, single positive mutations were combined, and two double mutants were shown to have about 3000- and 565-fold higher binding affinities than the wild-type decoy receptor. Molecular dynamics simulations and energetic analysis indicate that an additive effect by two mutations occurring at nearby modules was the major contributor to the remarkable increase in the binding affinities. PMID:22363519

Modelling conflicts with cluster dynamics in networks

NASA Astrophysics Data System (ADS)

Tadić, Bosiljka; Rodgers, G. J.

2010-12-01

We introduce cluster dynamical models of conflicts in which only the largest cluster can be involved in an action. This mimics the situations in which an attack is planned by a central body, and the largest attack force is used. We study the model in its annealed random graph version, on a fixed network, and on a network evolving through the actions. The sizes of actions are distributed with a power-law tail, however, the exponent is non-universal and depends on the frequency of actions and sparseness of the available connections between units. Allowing the network reconstruction over time in a self-organized manner, e.g., by adding the links based on previous liaisons between units, we find that the power-law exponent depends on the evolution time of the network. Its lower limit is given by the universal value 5/2, derived analytically for the case of random fragmentation processes. In the temporal patterns behind the size of actions we find long-range correlations in the time series of the number of clusters and the non-trivial distribution of time that a unit waits between two actions. In the case of an evolving network the distribution develops a power-law tail, indicating that through repeated actions, the system develops an internal structure with a hierarchy of units.

Supramolecular structure formation of Langmuir-Blodgett films of comblike precursor and polyimide

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

Goloudina, S. I., E-mail: goloudina@mail.ru; Luchinin, V. V.; Rozanov, V. V.

2013-03-15

The surface structure of Langmuir-Blodgett films of a comblike polyimide precursor-a rigid-chain polyamic acid alkylamine salt bearing multichains of tertiary amine-and films of the corresponding polyimide were studied by atomic force microscopy (AFM). An analysis of the images of the surface of three-layer films revealed a domain structure. It was found that the Langmuir-Blodgett film formation of the precursor occurs as a result of the layer-by-layer deposition of two-dimensional domains (composed of polyamic acid salt molecules on the water surface) onto a substrate. The formation of domains in a monolayer is associated with the chemical structure of the precursor, tomore » be more precise, with the rigidity of the main chain and the presence of closely spaced aliphatic side chains in the polymer chain, whose total cross-section area is close to the surface area of the projection onto the plane of the repeating unit of the main chain. Polyimide films inherit the domain structure of the precursor films; the inhomogeneity of the film thickness substantially decreases, whereas the domain size and character of their distribution in the film remain unchanged.« less

Structure and Dynamics of RNA Repeat Expansions That Cause Huntington's Disease and Myotonic Dystrophy Type 1.

PubMed

Chen, Jonathan L; VanEtten, Damian M; Fountain, Matthew A; Yildirim, Ilyas; Disney, Matthew D

2017-07-11

RNA repeat expansions cause a host of incurable, genetically defined diseases. The most common class of RNA repeats consists of trinucleotide repeats. These long, repeating transcripts fold into hairpins containing 1 × 1 internal loops that can mediate disease via a variety of mechanism(s) in which RNA is the central player. Two of these disorders are Huntington's disease and myotonic dystrophy type 1, which are caused by r(CAG) and r(CUG) repeats, respectively. We report the structures of two RNA constructs containing three copies of a r(CAG) [r(3×CAG)] or r(CUG) [r(3×CUG)] motif that were modeled with nuclear magnetic resonance spectroscopy and simulated annealing with restrained molecular dynamics. The 1 × 1 internal loops of r(3×CAG) are stabilized by one-hydrogen bond (cis Watson-Crick/Watson-Crick) AA pairs, while those of r(3×CUG) prefer one- or two-hydrogen bond (cis Watson-Crick/Watson-Crick) UU pairs. Assigned chemical shifts for the residues depended on the identity of neighbors or next nearest neighbors. Additional insights into the dynamics of these RNA constructs were gained by molecular dynamics simulations and a discrete path sampling method. Results indicate that the global structures of the RNA are A-form and that the loop regions are dynamic. The results will be useful for understanding the dynamic trajectory of these RNA repeats but also may aid in the development of therapeutics.

Context-Dependent Sensitivity to Mutations Disrupting the Structural Integrity of Individual EGF Repeats in the Mouse Notch Ligand DLL1

PubMed Central

Schuster-Gossler, Karin; Cordes, Ralf; Müller, Julia; Geffers, Insa; Delany-Heiken, Patricia; Taft, Manuel; Preller, Matthias; Gossler, Achim

2016-01-01

The highly conserved Notch-signaling pathway mediates cell-to-cell communication and is pivotal for multiple developmental processes and tissue homeostasis in adult organisms. Notch receptors and their ligands are transmembrane proteins with multiple epidermal-growth-factor-like (EGF) repeats in their extracellular domains. In vitro the EGF repeats of mammalian ligands that are essential for Notch activation have been defined. However, in vivo the significance of the structural integrity of each EGF repeat in the ligand ectodomain for ligand function is still unclear. Here, we analyzed the mouse Notch ligand DLL1. We expressed DLL1 proteins with mutations disrupting disulfide bridges in each individual EGF repeat from single-copy transgenes in the HPRT locus of embryonic stem cells. In Notch transactivation assays all mutations impinged on DLL1 function and affected both NOTCH1 and NOTCH2 receptors similarly. An allelic series in mice that carried the same point mutations in endogenous Dll1, generated using a mini-gene strategy, showed that early developmental processes depending on DLL1-mediated NOTCH activation were differently sensitive to mutation of individual EGF repeats in DLL1. Notably, some mutations affected only somite patterning and resulted in vertebral column defects resembling spondylocostal dysostosis. In conclusion, the structural integrity of each individual EGF repeat in the extracellular domain of DLL1 is necessary for full DLL1 activity, and certain mutations in Dll1 might contribute to spondylocostal dysostosis in humans. PMID:26801181

A TALE-inspired computational screen for proteins that contain approximate tandem repeats.

PubMed

Perycz, Malgorzata; Krwawicz, Joanna; Bochtler, Matthias

2017-01-01

TAL (transcription activator-like) effectors (TALEs) are bacterial proteins that are secreted from bacteria to plant cells to act as transcriptional activators. TALEs and related proteins (RipTALs, BurrH, MOrTL1 and MOrTL2) contain approximate tandem repeats that differ in conserved positions that define specificity. Using PERL, we screened ~47 million protein sequences for TALE-like architecture characterized by approximate tandem repeats (between 30 and 43 amino acids in length) and sequence variability in conserved positions, without requiring sequence similarity to TALEs. Candidate proteins were scored according to their propensity for nuclear localization, secondary structure, repeat sequence complexity, as well as covariation and predicted structural proximity of variable residues. Biological context was tentatively inferred from co-occurrence of other domains and interactome predictions. Approximate repeats with TALE-like features that merit experimental characterization were found in a protein of chestnut blight fungus, a eukaryotic plant pathogen.

A TALE-inspired computational screen for proteins that contain approximate tandem repeats

PubMed Central

Krwawicz, Joanna

2017-01-01

TAL (transcription activator-like) effectors (TALEs) are bacterial proteins that are secreted from bacteria to plant cells to act as transcriptional activators. TALEs and related proteins (RipTALs, BurrH, MOrTL1 and MOrTL2) contain approximate tandem repeats that differ in conserved positions that define specificity. Using PERL, we screened ~47 million protein sequences for TALE-like architecture characterized by approximate tandem repeats (between 30 and 43 amino acids in length) and sequence variability in conserved positions, without requiring sequence similarity to TALEs. Candidate proteins were scored according to their propensity for nuclear localization, secondary structure, repeat sequence complexity, as well as covariation and predicted structural proximity of variable residues. Biological context was tentatively inferred from co-occurrence of other domains and interactome predictions. Approximate repeats with TALE-like features that merit experimental characterization were found in a protein of chestnut blight fungus, a eukaryotic plant pathogen. PMID:28617832

Strain-specific Fibril Propagation by an Aβ Dodecamer

NASA Astrophysics Data System (ADS)

Dean, Dexter N.; Das, Pradipta K.; Rana, Pratip; Burg, Franklin; Levites, Yona; Morgan, Sarah E.; Ghosh, Preetam; Rangachari, Vijayaraghavan

2017-01-01

Low molecular weight oligomers of amyloid-β (Aβ) have emerged as the primary toxic agents in the etiology of Alzheimer disease (AD). Polymorphism observed within the aggregation end products of fibrils are known to arise due to microstructural differences among the oligomers. Diversity in aggregate morphology correlates with the differences in AD, cementing the idea that conformational strains of oligomers could be significant in phenotypic outcomes. Therefore, it is imperative to determine the ability of strains to faithfully propagate their structure. Here we report fibril propagation of an Aβ42 dodecamer called large fatty acid-derived oligomers (LFAOs). The LFAO oligomeric strain selectively induces acute cerebral amyloid angiopathy (CAA) in neonatally-injected transgenic CRND8 mice. Propagation in-vitro occurs as a three-step process involving the association of LFAO units. LFAO-seeded fibrils possess distinct morphology made of repeating LFAO units that could be regenerated upon sonication. Overall, these data bring forth an important mechanistic perspective into strain-specific propagation of oligomers that has remained elusive thus far.

Emerging Technologies for Assembly of Microscale Hydrogels

PubMed Central

Kavaz, Doga; Demirel, Melik C.; Demirci, Utkan

2013-01-01

Assembly of cell encapsulating building blocks (i.e., microscale hydrogels) has significant applications in areas including regenerative medicine, tissue engineering, and cell-based in vitro assays for pharmaceutical research and drug discovery. Inspired by the repeating functional units observed in native tissues and biological systems (e.g., the lobule in liver, the nephron in kidney), assembly technologies aim to generate complex tissue structures by organizing microscale building blocks. Novel assembly technologies enable fabrication of engineered tissue constructs with controlled properties including tunable microarchitectural and predefined compositional features. Recent advances in micro- and nano-scale technologies have enabled engineering of microgel based three dimensional (3D) constructs. There is a need for high-throughput and scalable methods to assemble microscale units with a complex 3D micro-architecture. Emerging assembly methods include novel technologies based on microfluidics, acoustic and magnetic fields, nanotextured surfaces, and surface tension. In this review, we survey emerging microscale hydrogel assembly methods offering rapid, scalable microgel assembly in 3D, and provide future perspectives and discuss potential applications. PMID:23184717

Expression, purification and crystallization of the C-terminal LRR domain of Streptococcus pyogenes protein 0843.

PubMed

Haikarainen, Teemu; Loimaranta, Vuokko; Prieto-Lopez, Carlos; Battula, Pradeep; Finne, Jukka; Papageorgiou, Anastassios C

2013-05-01

Streptococcus pyogenes protein 0843 (Spy0843) is a recently identified protein with a potential adhesin function. Sequence analysis has shown that Spy0843 contains two leucine-rich repeat (LRR) domains that mediate interactions with the gp340 receptor. Here, the C-terminal LRR domain was overexpressed in Escherichia coli, purified and crystallized in the presence of 1.7-1.8 M ammonium sulfate pH 7.4 as precipitant. Data were collected from a single crystal to 1.59 Å resolution at 100 K at a synchrotron-radiation source. The crystal was found to belong to space group I41, with unit-cell parameters a = b = 121.4, c = 51.5 Å and one molecule in the asymmetric unit. Elucidation of the crystal structure will provide insights into the interactions of Spy0843 with the gp340 receptor and a better understanding of the role of Spy0843 in streptococcal infections.

Expression, purification and crystallization of the C-terminal LRR domain of Streptococcus pyogenes protein 0843

PubMed Central

Haikarainen, Teemu; Loimaranta, Vuokko; Prieto-Lopez, Carlos; Battula, Pradeep; Finne, Jukka; Papageorgiou, Anastassios C.

2013-01-01

Streptococcus pyogenes protein 0843 (Spy0843) is a recently identified protein with a potential adhesin function. Sequence analysis has shown that Spy0843 contains two leucine-rich repeat (LRR) domains that mediate interactions with the gp340 receptor. Here, the C-terminal LRR domain was overexpressed in Escherichia coli, purified and crystallized in the presence of 1.7–1.8 M ammonium sulfate pH 7.4 as precipitant. Data were collected from a single crystal to 1.59 Å resolution at 100 K at a synchrotron-radiation source. The crystal was found to belong to space group I41, with unit-cell parameters a = b = 121.4, c = 51.5 Å and one molecule in the asymmetric unit. Elucidation of the crystal structure will provide insights into the interactions of Spy0843 with the gp340 receptor and a better understanding of the role of Spy0843 in streptococcal infections. PMID:23695577

Improving psychotropic drug prescription in nursing home patients with dementia: design of a cluster randomized controlled trial

PubMed Central

2013-01-01

Background Neuropsychiatric symptoms are highly prevalent in nursing home patients with dementia. Despite modest effectiveness and considerable side effects, psychotropic drugs are frequently prescribed for these neuropsychiatric symptoms. This raises questions whether psychotropic drugs are appropriately prescribed. The aim of the PROPER (PRescription Optimization of Psychotropic drugs in Elderly nuRsing home patients with dementia) II study is to investigate the efficacy of an intervention for improving the appropriateness of psychotropic drug prescription in nursing home patients with dementia. Methods/design The PROPER II study is a multi-center cluster randomized controlled, pragmatic trial using parallel groups. It has a duration of eighteen months and four six-monthly assessments. Six nursing homes will participate in the intervention and six will continue care as usual. The nursing homes will be located throughout the Netherlands, each participating with two dementia special care units with an average of fifteen patients per unit, resulting in 360 patients. The intervention consists of a structured and repeated multidisciplinary medication review supported by education and continuous evaluation. It is conducted by pharmacists, physicians, and nurses and consists of three components: 1) preparation and education, 2) conduct, and 3) evaluation/guidance. The primary outcome is the proportion of patients with appropriate psychotropic drug use. Secondary outcomes are the overall frequency of psychotropic drug use, neuropsychiatric symptoms, quality of life, activities of daily living, psychotropic drug side effects and adverse events (including cognition, comorbidity, and mortality). Besides, a process analysis on the intervention will be carried out. Discussion This study is expected to improve the appropriateness of psychotropic drug prescription for neuropsychiatric symptoms in nursing home patients with dementia by introducing a structured and repeated multidisciplinary medication review supported by education and continuous evaluation. Trial registration Netherlands Trial Registry (NTR): NTR3569. PMID:24180295

Always look on both sides: Phylogenetic information conveyed by simple sequence repeat allele sequences

USDA-ARS?s Scientific Manuscript database

Simple sequence repeat (SSR) markers are widely used tools for inferences about genetic diversity, phylogeography and spatial genetic structure. Their applications assume that variation among alleles is essentially caused by an expansion or contraction of the number of repeats and that, accessorily,...

Supramolecular structures of halogenated oligothiophenes on the Si(111)-√3 ×√3-Ag surface

NASA Astrophysics Data System (ADS)

Liu, R.; Fu, C.; Perepichka, D. F.; Gallagher, M. C.

2016-05-01

We have studied the adsorption of brominated tetrathienoanthracene (TBTTA) molecules onto the Si(111)-√3 × √ 3-Ag surface at room temperature. The two-dimensional √ 3 silver adlayer acts to passivate the silicon surface and provides a high-mobility template for TBTTA adsorption. Scanning tunneling microscopy (STM) images reveal that at low coverage, the molecules readily migrate to step edges and defects in the √ 3 overlayer. With increasing coverage, the molecules eventually form compact supramolecular structures. In terms of the hexagonal √ 3 lattice vectors (a√ 3 and b√ 3), the oblique unit cell of these structures can be defined by lattice vectors am = 3a√ 3 + 2b√ 3, and bm = - a√ 3 + b√ 3. The structures are quite fragile and can decompose under repeated STM imaging. This is particularly true at higher bias and suggests an electric field-induced dissociation in these instances. With increasing molecular dose, the size and stability of the structures increases. At higher coverage, the spatial extent of the supramolecular structures is often limited by defects in the underlying √ 3 layer. Our results suggest that the √ 3-Ag surface provides a relatively inert substrate for the adsorption of TBTTA molecules, and that the supramolecular structures are held together by relatively weak intermolecular forces.

Development of Electrochemical Supercapacitors for EMA Applications

NASA Technical Reports Server (NTRS)

Kosek, John A.; Dunning, Thomas; LaConti, Anthony B.

1996-01-01

A limitation of the typical electrochemical capacitor is the maximum available power and energy density, and an improvement in capacitance per unit weight and volume is needed. A solid-ionomer electrochemical capacitor having a unit cell capacitance greater than 2 F/sq cm and a repeating element thickness of 6 mils has been developed. This capacitor could provide high-current pulses for electromechanical actuation (EMA). Primary project objectives were to develop high-capacitance particulates, to increase capacitor gravimetric and volumetric energy densities above baseline and to fabricate a 10-V capacitor with a repeating element thickness of 6 mils or less. Specific EMA applications were identified and capacitor weight and volume projections made.

The United States Army’s Full-Spectrum Training Strategy Challenge

DTIC Science & Technology

2012-05-17

the high operational tempo for deployed and deploying units. Soldiers and units conducted repeat deployments to both Iraq and Afghanistan with little...prevalent in Strategic Operational Design and associated variations of design. Further complicating Israeli ideas of warfare was the notion that...Army to develop an overarching operational framework that finally replaces Airland Battle, like EBO or some variation of operational design. But one

Understanding the new HbA1c units for the diagnosis of Type 2 diabetes.

PubMed

Braatvedt, Geoff D; Cundy, Tim; Crooke, Michael; Florkowski, Chris; Mann, Jim I; Lunt, Helen; Jackson, Rod; Orr-Walker, Brandon; Kenealy, Timothy; Drury, Paul L

2012-09-21

In New Zealand laboratories the measurement of glycated haemoglobin (HbA1c) for diagnosis of diabetes is now only reported in SI units of mmol/mol. HbA1c is now recommended as the preferred test to diagnose diabetes in most circumstances. The requirement for a second positive test in asymptomatic individuals is retained. An HbA1c greater than and equal to 50 mmol/mol (repeated on a second occasion in asymptomatic patients) is diagnostic of diabetes and a value less than and equal to 40 mmol/mol represents normal glucose tolerance. For patients with an initial HbA1c result of 41-49 mmol/mol, cardiovascular risk assessment and lifestyle interventions are recommended with repeat HbA1c screening in 6-12 months. For patients whose HbA1c is less than and equal to 40 mmol/mol, repeat screening (including for CVD risk) at intermittent intervals is recommended as per published guidelines.

40 CFR 59.405 - Container labeling requirements.

Code of Federal Regulations, 2012 CFR

2012-07-01

...) Repeated (frequent) heavy abrasion, including mechanical wear and repeated (frequent) scrubbing with industrial solvents, cleansers, or scouring agents; or (v) Exterior exposure of metal structures and...

Molecular Dynamics Simulations of DNA-Free and DNA-Bound TAL Effectors

PubMed Central

Wan, Hua; Hu, Jian-ping; Li, Kang-shun; Tian, Xu-hong; Chang, Shan

2013-01-01

TAL (transcriptional activator-like) effectors (TALEs) are DNA-binding proteins, containing a modular central domain that recognizes specific DNA sequences. Recently, the crystallographic studies of TALEs revealed the structure of DNA-recognition domain. In this article, molecular dynamics (MD) simulations are employed to study two crystal structures of an 11.5-repeat TALE, in the presence and absence of DNA, respectively. The simulated results indicate that the specific binding of RVDs (repeat-variable diresidues) with DNA leads to the markedly reduced fluctuations of tandem repeats, especially at the two ends. In the DNA-bound TALE system, the base-specific interaction is formed mainly by the residue at position 13 within a TAL repeat. Tandem repeats with weak RVDs are unfavorable for the TALE-DNA binding. These observations are consistent with experimental studies. By using principal component analysis (PCA), the dominant motions are open-close movements between the two ends of the superhelical structure in both DNA-free and DNA-bound TALE systems. The open-close movements are found to be critical for the recognition and binding of TALE-DNA based on the analysis of free energy landscape (FEL). The conformational analysis of DNA indicates that the 5′ end of DNA target sequence has more remarkable structural deformability than the other sites. Meanwhile, the conformational change of DNA is likely associated with the specific interaction of TALE-DNA. We further suggest that the arrangement of N-terminal repeats with strong RVDs may help in the design of efficient TALEs. This study provides some new insights into the understanding of the TALE-DNA recognition mechanism. PMID:24130757

Response of soricid populations to repeated fire and fuel reduction treatments in the southern Appalachain Mountains

Treesearch

Charlotte E Matthews; Christopher E Moorman; Cathryn H Greenberg

2009-01-01

Fuel hazards have increased in forests across the United States because offire exclusion during the 20th century. Treatments used to reduce fuel buildup Illay affect wildlife. such as shrews. living 011 the forest floor. especially when treatments are applied repeatedly. From mid-May to mid-August 2006 and 2007.  we used drift fences...

Certificates Count: An Analysis of Sub-Baccalaureate Certificates

ERIC Educational Resources Information Center

Bosworth, Brian

2010-01-01

Since President Obama took office, he has repeatedly called for the United States to significantly improve its postsecondary education performance. One goal in particular has gained wide attention: the President's declaration that in an ever more competitive global marketplace, the United States must once again lead the world in college…

Drastic stability change of X-X mismatch in d(CXG) trinucleotide repeat disorders under molecular crowding condition.

PubMed

Teng, Ye; Pramanik, Smritimoy; Tateishi-Karimata, Hisae; Ohyama, Tatsuya; Sugimoto, Naoki

2018-02-05

The trinucleotide repeat d(CXG) (X = A, C, G or T) is the most common sequence causing repeat expansion disorders. The formation of non-canonical structures, such as hairpin structures with X-X mismatches, has been proposed to affect gene expression and regulation, which are important in pathological studies of these devastating neurological diseases. However, little information is available regarding the thermodynamics of the repeat sequence under crowded cellular conditions where many non-canonical structures such as G-quadruplexes are highly stabilized, while duplexes are destabilised. In this study, we investigated the different stabilities of X-X mismatches in the context of internal d(CXG) self-complementary sequences in an environment with a high concentration of cosolutes to mimic the crowding conditions in cells. The stabilities of full-matched duplexes and duplexes with A-A, G-G, and T-T mismatched base pairs under molecular crowding conditions were notably decreased compared to under dilute conditions. However, the stability of the DNA duplex with a C-C mismatch base pair was only slightly destabilised. Investigating different stabilities of X-X mismatches in d(CXG) sequences is important for improving our understanding of the formation and transition of multiple non-canonical structures in trinucleotide repeat diseases, and may provide insights for pathological studies and drug development. Copyright © 2018 Elsevier Inc. All rights reserved.

SSRscanner: a program for reporting distribution and exact location of simple sequence repeats.

PubMed

Anwar, Tamanna; Khan, Asad U

2006-02-20

Simple sequence repeats (SSRs) have become important molecular markers for a broad range of applications, such as genome mapping and characterization, phenotype mapping, marker assisted selection of crop plants and a range of molecular ecology and diversity studies. These repeated DNA sequences are found in both prokaryotes and eukaryotes. They are distributed almost at random throughout the genome, ranging from mononucleotide to trinucleotide repeats. They are also found at longer lengths (> 6 repeating units) of tracts. Most of the computer programs that find SSRs do not report its exact position. A computer program SSRscanner was written to find out distribution, frequency and exact location of each SSR in the genome. SSRscanner is user friendly. It can search repeats of any length and produce outputs with their exact position on chromosome and their frequency of occurrence in the sequence. This program has been written in PERL and is freely available for non-commercial users by request from the authors. Please contact the authors by E-mail: huzzi99@hotmail.com.

Children's Conceptions of Bullying and Repeated Conventional Transgressions: Moral, Conventional, Structuring and Personal-Choice Reasoning

ERIC Educational Resources Information Center

Thornberg, Robert; Thornberg, Ulrika Birberg; Alamaa, Rebecca; Daud, Noor

2016-01-01

This study examined 307 elementary school children's judgements and reasoning about bullying and other repeated transgressions when school rules regulating these transgressions have been removed in hypothetical school situations. As expected, children judged bullying (repeated moral transgressions) as wrong independently of rules and as more wrong…

A divergent Pumilio repeat protein family for pre-rRNA processing and mRNA localization

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

Qiu, Chen; McCann, Kathleen L.; Wine, Robert N.

Pumilio/feminization of XX and XO animals (fem)-3 mRNA-binding factor (PUF) proteins bind sequence specifically to mRNA targets using a single-stranded RNA-binding domain comprising eight Pumilio (PUM) repeats. PUM repeats have now been identified in proteins that function in pre-rRNA processing, including human Puf-A and yeast Puf6. This is a role not previously ascribed to PUF proteins. In this paper we present crystal structures of human Puf-A that reveal a class of nucleic acid-binding proteins with 11 PUM repeats arranged in an “L”-like shape. In contrast to classical PUF proteins, Puf-A forms sequence-independent interactions with DNA or RNA, mediated by conservedmore » basic residues. We demonstrate that equivalent basic residues in yeast Puf6 are important for RNA binding, pre-rRNA processing, and mRNA localization. Finally, PUM repeats can be assembled into alternative folds that bind to structured nucleic acids in addition to forming canonical eight-repeat crescent-shaped RNA-binding domains found in classical PUF proteins.« less

A divergent Pumilio repeat protein family for pre-rRNA processing and mRNA localization

DOE PAGES

Qiu, Chen; McCann, Kathleen L.; Wine, Robert N.; ...

2014-12-15

Pumilio/feminization of XX and XO animals (fem)-3 mRNA-binding factor (PUF) proteins bind sequence specifically to mRNA targets using a single-stranded RNA-binding domain comprising eight Pumilio (PUM) repeats. PUM repeats have now been identified in proteins that function in pre-rRNA processing, including human Puf-A and yeast Puf6. This is a role not previously ascribed to PUF proteins. In this paper we present crystal structures of human Puf-A that reveal a class of nucleic acid-binding proteins with 11 PUM repeats arranged in an “L”-like shape. In contrast to classical PUF proteins, Puf-A forms sequence-independent interactions with DNA or RNA, mediated by conservedmore » basic residues. We demonstrate that equivalent basic residues in yeast Puf6 are important for RNA binding, pre-rRNA processing, and mRNA localization. Finally, PUM repeats can be assembled into alternative folds that bind to structured nucleic acids in addition to forming canonical eight-repeat crescent-shaped RNA-binding domains found in classical PUF proteins.« less

Fine typing of methicillin-resistant Staphylococcus aureus isolates using direct repeat unit and staphylococcal interspersed repeat unit typing methods.

PubMed

Ho, Cheng-Mao; Ho, Mao-Wang; Li, Chi-Yuan; Lu, Jang-Jih

2015-08-01

Methicillin-resistant Staphylococcus aureus (MRSA) typing is an important epidemiologic tool for monitoring trends and preventing outbreaks. However, the efficiency of various MRSA typing methods for each SCCmec MRSA isolate is rarely evaluated. A total of 157 MRSA isolates from four different regions in Taiwan were typed with five different molecular methods, including SCCmec typing, multilocus sequence typing (MLST), spa typing, mec-associated direct repeat unit (dru) copy number determination, and staphylococcal interspersed repeat unit (SIRU) profiling. There were four SCCmec types, eight MLST types, 15 spa types, 11 dru types, and 31 SIRU profiles. The most common type determined by each molecular typing method was SCCmec III (115 isolates, 73.2%), ST239 (99 isolates, 63.1%), t037 (107 isolates, 68.2%), 14 dru copies (76 isolates, 48.4%), and SIRU profile 3013722 (102 isolates, 65%), respectively. When using the combination of MLST, spa typing, and dru copy number, ST5-t002-4 (n = 8), ST239-t037-14 (n = 68), ST59-t437-9 (n = 9), and ST59-t437-11 (n = 6) were found to be the most common types of SCCmec types II (n = 9), III (n = 115), IV (n = 21), and VT (n = 11) isolates, respectively. SCCmec type III isolates were further classified into 11 dru types. Of the 21 SCCmec type IV isolates, 14 SIRU profiles were found. Seven SIRU patterns were observed in the 11 SCCmec type VT isolates. Different typing methods showed a similar Hunter-Gaston discrimination index among the 157 MRSA isolates. However, dru and SIRU typing methods had a better discriminatory power for SCCmec type III and SCCmec types IV and VT isolates, respectively, suggesting that dru and SIRU can be used to further type these isolates. Copyright © 2013. Published by Elsevier B.V.

Elongated fibrillar structure of a streptococcal adhesin assembled by the high-affinity association of [alpha]- and PPII-helices

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

Larson, Matthew R.; Rajashankar, Kanagalaghatta R.; Patel, Manisha H.

2010-08-18

Streptococcus mutans antigen I/II (AgI/II) is a cell surface-localized protein adhesin that interacts with salivary components within the salivary pellicle. AgI/II contributes to virulence and has been studied as an immunological and structural target, but a fundamental understanding of its underlying architecture has been lacking. Here we report a high-resolution (1.8 {angstrom}) crystal structure of the A{sub 3}VP{sub 1} fragment of S. mutans AgI/II that demonstrates a unique fibrillar form (155 {angstrom}) through the interaction of two noncontiguous regions in the primary sequence. The A{sub 3} repeat of the alanine-rich domain adopts an extended {alpha}-helix that intertwines with the P{submore » 1} repeat polyproline type II (PPII) helix to form a highly extended stalk-like structure heretofore unseen in prokaryotic or eukaryotic protein structures. Velocity sedimentation studies indicate that full-length AgI/II that contains three A/P repeats extends over 50 nanometers in length. Isothermal titration calorimetry revealed that the high-affinity association between the A{sub 3} and P{sub 1} helices is enthalpically driven. Two distinct binding sites on AgI/II to the host receptor salivary agglutinin (SAG) were identified by surface plasmon resonance (SPR). The current crystal structure reveals that AgI/II family proteins are extended fibrillar structures with the number of alanine- and proline-rich repeats determining their length.« less

Crystal structures of three lead(II) acetate-bridged di-amino-benzene coordination polymers.

PubMed

Geiger, David K; Parsons, Dylan E; Zick, Patricia L

2014-12-01

Poly[tris-(acetato-κ(2) O,O')(μ2-acetato-κ(3) O,O':O)tetra-kis-(μ3-acetato-κ(4) O,O':O:O')bis-(benzene-1,2-di-amine-κN)tetra-lead(II)], [Pb4(CH3COO)8(C6H8N2)2] n , (I), poly[(acetato-κ(2) O,O')(μ3-acetato-κ(4) O,O':O:O')(4-chloro-benzene-1,2-diamine-κN)lead(II)], [Pb(CH3COO)2(C6H7ClN2)] n , (II), and poly[(κ(2) O,O')(μ3-acetato-κ(4) O,O':O:O')(3,4-di-amino-benzo-nitrile-κN)lead(II)], [Pb(CH3COO)2(C7H7N3)] n , (III), have polymeric structures in which monomeric units are joined by bridging acetate ligands. All of the Pb(II) ions exhibit hemidirected coordination. The repeating unit in (I) is composed of four Pb(II) ions having O6, O6N, O7 and O6N coordination spheres, respectively, where N represents a monodentate benzene-1,2-di-amine ligand and O acetate O atoms. Chains along [010] are joined by bridging acetate ligands to form planes parallel to (10-1). (II) and (III) are isotypic and have one Pb(II) ion in the asymmetric unit that has an O6N coordination sphere. Pb2O2 units result from a symmetry-imposed inversion center. Polymeric chains parallel to [100] exhibit hydrogen bonding between the amine and acetate ligands. In (III), additional hydrogen bonds between cyano groups and non-coordinating amines join the chains by forming R 2 (2)(14) rings.

Examination of the Potential of Structure-from-Motion (SfM) Photogrammetry and Terrestrial Laser Scanning (TLS) for Rapid Nondestructive Field Measurement of Grass Biomass

NASA Astrophysics Data System (ADS)

Cooper, S. D.; Roy, D. P.; Sathyachandran, S. K.

2016-12-01

Quantifying the above ground biomass of grasslands is needed for a number of applications including monitoring grass productivity, wildlife habitat, carbon storage, and fuel bed characteristics. Destructive biomass measurements, although highly accurate, are time consuming and are not easily undertaken on a repeat basis or over large areas. A number of non-destructive techniques have been developed that relate vegetation structural properties to above ground biomass. Conventionally, the disc pasture meter is used for rapid grass biomass estimation and uses the settling height of a disk placed on the grass and allometry. Structure-from-Motion (SfM) photogrammetry and Terrestrial Laser Scanning (TLS) are two technologies that have the potential to yield highly precise three-dimensional (3D) structural measurements of vegetation quite rapidly. Recent advances in computing and data acquisition technologies have led to the successful application of TLS and SfM in woody biomass estimation, but application in grassland systems remains largely untested. The Canopy Biomass Lidar (CBL) is one such advance and is a highly portable and relatively inexpensive TLS unit allowing for rapid and widespread data collection. We investigated the efficacy of a CBL unit as well as SfM in allometric estimation of grassland biomass from volumetric measurements derived from these two technologies, both separately and through the merging of the two independently generated 3D point clouds. The results are compared to biomass estimation from a pasture disc meter. Best use practices for grassland applications of these technologies are also presented.

Crystal structure of the second fibronectin type III (FN3) domain from human collagen α1 type XX.

PubMed

Zhao, Jingfeng; Ren, Jixia; Wang, Nan; Cheng, Zhong; Yang, Runmei; Lin, Gen; Guo, Yi; Cai, Dayong; Xie, Yong; Zhao, Xiaohong

2017-12-01

Collagen α1 type XX, which contains fibronectin type III (FN3) repeats involving six FN3 domains (referred to as the FN#1-FN#6 domains), is an unusual member of the fibril-associated collagens with interrupted triple helices (FACIT) subfamily of collagens. The results of standard protein BLAST suggest that the FN3 repeats might contribute to collagen α1 type XX acting as a cytokine receptor. To date, solution NMR structures of the FN#3, FN#4 and FN#6 domains have been determined. To obtain further structural evidence to understand the relationship between the structure and function of the FN3 repeats from collagen α1 type XX, the crystal structure of the FN#2 domain from human collagen α1 type XX (residues Pro386-Pro466; referred to as FN2-HCXX) was solved at 2.5 Å resolution. The crystal structure of FN2-HCXX shows an immunoglobulin-like fold containing a β-sandwich structure, which is formed by a three-stranded β-sheet (β1, β2 and β5) packed onto a four-stranded β-sheet (β3, β4, β6 and β7). Two consensus domains, tencon and fibcon, are structural analogues of FN2-HCXX. Fn8, an FN3 domain from human oncofoetal fibronectin, is the closest structural analogue of FN2-HCXX derived from a naturally occurring sequence. Based solely on the structural similarity of FN2-HCXX to other FN3 domains, the detailed functions of FN2-HCXX and the FN3 repeats in collagen α1 type XX cannot be identified.

Programmable DNA-Mediated Multitasking Processor.

PubMed

Shu, Jian-Jun; Wang, Qi-Wen; Yong, Kian-Yan; Shao, Fangwei; Lee, Kee Jin

2015-04-30

Because of DNA appealing features as perfect material, including minuscule size, defined structural repeat and rigidity, programmable DNA-mediated processing is a promising computing paradigm, which employs DNAs as information storing and processing substrates to tackle the computational problems. The massive parallelism of DNA hybridization exhibits transcendent potential to improve multitasking capabilities and yield a tremendous speed-up over the conventional electronic processors with stepwise signal cascade. As an example of multitasking capability, we present an in vitro programmable DNA-mediated optimal route planning processor as a functional unit embedded in contemporary navigation systems. The novel programmable DNA-mediated processor has several advantages over the existing silicon-mediated methods, such as conducting massive data storage and simultaneous processing via much fewer materials than conventional silicon devices.

Structural determination of the capsular polysaccharide produced by Klebsiella pneumoniae serotype K40. NMR studies of the oligosaccharide obtained upon depolymerisation of the polysaccharide with a bacteriophage-associated endoglycanase.

PubMed

Cescutti, P; Toffanin, R; Kvam, B J; Paoletti, S; Dutton, G G

1993-04-01

The Klebsiella pneumoniae K40 capsular polysaccharide has been isolated and investigated by use of methylation analysis, specific degradations and NMR spectroscopy. The polysaccharide was depolymerised by a bacteriophage-associated endogalactosidase, and the resulting oligosaccharide was characterised by one-dimensional and two-dimensional NMR spectroscopy and direct chemical ionisation MS. The repeating unit of the K40 capsular polysaccharide was shown to be a linear hexasaccharide with the composition-->3)- alpha-L-Rhap-(1-->2)-alpha-L-Rhap-(1-->4)-alpha-D-GlcpA++ +-(1-->2-)- alpha-D-Manp-(1-->2)-alpha-D-Manp-(1-->3)-alpha-D-Galp-(1--> (Rha, rhamnose).

Impact of Repeated Exposures on Information Spreading in Social Networks

PubMed Central

Zhou, Cangqi; Zhao, Qianchuan; Lu, Wenbo

2015-01-01

Clustered structure of social networks provides the chances of repeated exposures to carriers with similar information. It is commonly believed that the impact of repeated exposures on the spreading of information is nontrivial. Does this effect increase the probability that an individual forwards a message in social networks? If so, to what extent does this effect influence people’s decisions on whether or not to spread information? Based on a large-scale microblogging data set, which logs the message spreading processes and users’ forwarding activities, we conduct a data-driven analysis to explore the answer to the above questions. The results show that an overwhelming majority of message samples are more probable to be forwarded under repeated exposures, compared to those under only a single exposure. For those message samples that cover various topics, we observe a relatively fixed, topic-independent multiplier of the willingness of spreading when repeated exposures occur, regardless of the differences in network structure. We believe that this finding reflects average people’s intrinsic psychological gain under repeated stimuli. Hence, it makes sense that the gain is associated with personal response behavior, rather than network structure. Moreover, we find that the gain is robust against the change of message popularity. This finding supports that there exists a relatively fixed gain brought by repeated exposures. Based on the above findings, we propose a parsimonious model to predict the saturated numbers of forwarding activities of messages. Our work could contribute to better understandings of behavioral psychology and social media analytics. PMID:26465749

Repeating Patterns: Strategies to Assist Young Students to Generalise the Mathematical Structure

ERIC Educational Resources Information Center

Warren, Elizabeth; Miller, Jodie; Cooper, Thomas

2012-01-01

This paper focuses on very young students' ability to engage in repeating pattern tasks and identifying strategies that assist them to ascertain the structure of the pattern. It describes results of a study which is part of the Early Years Generalising Project (EYGP) and involves Australian students in Years 1 to 4 (ages 5-10). This paper reports…