SINEs, evolution and genome structure in the opossum.

PubMed

Gu, Wanjun; Ray, David A; Walker, Jerilyn A; Barnes, Erin W; Gentles, Andrew J; Samollow, Paul B; Jurka, Jerzy; Batzer, Mark A; Pollock, David D

2007-07-01

Short INterspersed Elements (SINEs) are non-autonomous retrotransposons, usually between 100 and 500 base pairs (bp) in length, which are ubiquitous components of eukaryotic genomes. Their activity, distribution, and evolution can be highly informative on genomic structure and evolutionary processes. To determine recent activity, we amplified more than one hundred SINE1 loci in a panel of 43 M. domestica individuals derived from five diverse geographic locations. The SINE1 family has expanded recently enough that many loci were polymorphic, and the SINE1 insertion-based genetic distances among populations reflected geographic distance. Genome-wide comparisons of SINE1 densities and GC content revealed that high SINE1 density is associated with high GC content in a few long and many short spans. Young SINE1s, whether fixed or polymorphic, showed an unbiased GC content preference for insertion, indicating that the GC preference accumulates over long time periods, possibly in periodic bursts. SINE1 evolution is thus broadly similar to human Alu evolution, although it has an independent origin. High GC content adjacent to SINE1s is strongly correlated with bias towards higher AT to GC substitutions and lower GC to AT substitutions. This is consistent with biased gene conversion, and also indicates that like chickens, but unlike eutherian mammals, GC content heterogeneity (isochore structure) is reinforced by substitution processes in the M. domestica genome. Nevertheless, both high and low GC content regions are apparently headed towards lower GC content equilibria, possibly due to a relative shift to lower recombination rates in the recent Monodelphis ancestral lineage. Like eutherians, metatherian (marsupial) mammals have evolved high CpG substitution rates, but this is apparently a convergence in process rather than a shared ancestral state.

[The primary structure of a vaccine strain of tobacco mosaic virus V-69].

PubMed

Shiian, A N; Mil'shina, N V; Snegireva, P B; Pukhal'skiĭ, V A

1994-12-01

A random set of cDNA fragments were synthesized on genomic RNA of TMV vaccine strain V-69, using random primers and reverse transcriptase. Following synthesis of double-stranded cDNA, they were cloned into the pUC-19 plasmid; and 28 clones were sequenced (insert size 100-500 bp). High nucleotide sequence homology of V-69 (more than 95%) was shown only with tomato strain TMV-L [1]. Sequenced clones represent 54% of the genome (50% of the replicase gene, 98% of the transport protein gene, and 60% of the coat protein gene). In this genome region, 24 base substitutions were revealed, as compared to the wild-type TMV-L sequence. Six base substitutions resulted in changes in corresponding amino acid codons. No substitutions coincided with those discovered in the related TMV vaccine strain L11A [2], while two substitutions in the replicase gene were identical to those found in TMV strain Lta1 [3], which is capable of overcoming protection in tomatoes with the resistance gene Tm-1.

Genome-Wide Spectra of Transcription Insertions and Deletions Reveal That Slippage Depends on RNA:DNA Hybrid Complementarity

PubMed Central

Traverse, Charles C.

2017-01-01

ABSTRACT Advances in sequencing technologies have enabled direct quantification of genome-wide errors that occur during RNA transcription. These errors occur at rates that are orders of magnitude higher than rates during DNA replication, but due to technical difficulties such measurements have been limited to single-base substitutions and have not yet quantified the scope of transcription insertions and deletions. Previous reporter gene assay findings suggested that transcription indels are produced exclusively by elongation complex slippage at homopolymeric runs, so we enumerated indels across the protein-coding transcriptomes of Escherichia coli and Buchnera aphidicola, which differ widely in their genomic base compositions and incidence of repeat regions. As anticipated from prior assays, transcription insertions prevailed in homopolymeric runs of A and T; however, transcription deletions arose in much more complex sequences and were rarely associated with homopolymeric runs. By reconstructing the relocated positions of the elongation complex as inferred from the sequences inserted or deleted during transcription, we show that continuation of transcription after slippage hinges on the degree of nucleotide complementarity within the RNA:DNA hybrid at the new DNA template location. PMID:28851848

Guanidinoacetate methyltransferase deficiency: the first inborn error of creatine metabolism in man.

PubMed Central

Stöckler, S.; Isbrandt, D.; Hanefeld, F.; Schmidt, B.; von Figura, K.

1996-01-01

In two children with an accumulation of guanidinoacetate in brain and a deficiency of creatine in blood, a severe deficiency of guanidinoacetate methyltransferase (GAMT) activity was detected in the liver. Two mutant GAMT alleles were identified that carried a single base substitution within a 5' splice site or a 13-nt insertion and gave rise to four mutant transcripts. Three of the transcripts encode truncated polypeptides that lack a residue known to be critical for catalytic activity of GAMT. Deficiency of GAMT is the first inborn error of creatine metabolism. It causes a severe developmental delay and extrapyramidal symptoms in early infancy and is treatable by oral substitution with creatine. Images Figure 2 PMID:8651275

Phylogenetic Conflict in Bears Identified by Automated Discovery of Transposable Element Insertions in Low-Coverage Genomes

PubMed Central

Gallus, Susanne; Janke, Axel

2017-01-01

Abstract Phylogenetic reconstruction from transposable elements (TEs) offers an additional perspective to study evolutionary processes. However, detecting phylogenetically informative TE insertions requires tedious experimental work, limiting the power of phylogenetic inference. Here, we analyzed the genomes of seven bear species using high-throughput sequencing data to detect thousands of TE insertions. The newly developed pipeline for TE detection called TeddyPi (TE detection and discovery for Phylogenetic Inference) identified 150,513 high-quality TE insertions in the genomes of ursine and tremarctine bears. By integrating different TE insertion callers and using a stringent filtering approach, the TeddyPi pipeline produced highly reliable TE insertion calls, which were confirmed by extensive in vitro validation experiments. Analysis of single nucleotide substitutions in the flanking regions of the TEs shows that these substitutions correlate with the phylogenetic signal from the TE insertions. Our phylogenomic analyses show that TEs are a major driver of genomic variation in bears and enabled phylogenetic reconstruction of a well-resolved species tree, despite strong signals for incomplete lineage sorting and introgression. The analyses show that the Asiatic black, sun, and sloth bear form a monophyletic clade, in which phylogenetic incongruence originates from incomplete lineage sorting. TeddyPi is open source and can be adapted to various TE and structural variation callers. The pipeline makes it possible to confidently extract thousands of TE insertions even from low-coverage genomes (∼10×) of nonmodel organisms. This opens new possibilities for biologists to study phylogenies and evolutionary processes as well as rates and patterns of (retro-)transposition and structural variation. PMID:28985298

Evaluation of second-generation sequencing of 19 dilated cardiomyopathy genes for clinical applications.

PubMed

Gowrisankar, Sivakumar; Lerner-Ellis, Jordan P; Cox, Stephanie; White, Emily T; Manion, Megan; LeVan, Kevin; Liu, Jonathan; Farwell, Lisa M; Iartchouk, Oleg; Rehm, Heidi L; Funke, Birgit H

2010-11-01

Medical sequencing for diseases with locus and allelic heterogeneities has been limited by the high cost and low throughput of traditional sequencing technologies. "Second-generation" sequencing (SGS) technologies allow the parallel processing of a large number of genes and, therefore, offer great promise for medical sequencing; however, their use in clinical laboratories is still in its infancy. Our laboratory offers clinical resequencing for dilated cardiomyopathy (DCM) using an array-based platform that interrogates 19 of more than 30 genes known to cause DCM. We explored both the feasibility and cost effectiveness of using PCR amplification followed by SGS technology for sequencing these 19 genes in a set of five samples enriched for known sequence alterations (109 unique substitutions and 27 insertions and deletions). While the analytical sensitivity for substitutions was comparable to that of the DCM array (98%), SGS technology performed better than the DCM array for insertions and deletions (90.6% versus 58%). Overall, SGS performed substantially better than did the current array-based testing platform; however, the operational cost and projected turnaround time do not meet our current standards. Therefore, efficient capture methods and/or sample pooling strategies that shorten the turnaround time and decrease reagent and labor costs are needed before implementing this platform into routine clinical applications.

Characterization of 2-Oxindole Forming Heme Enzyme MarE, Expanding the Functional Diversity of the Tryptophan Dioxygenase Superfamily.

PubMed

Zhang, Yuyang; Zou, Yi; Brock, Nelson L; Huang, Tingting; Lan, Yingxia; Wang, Xiaozheng; Deng, Zixin; Tang, Yi; Lin, Shuangjun

2017-08-30

3-Substituted 2-oxindoles are important structural motifs found in many biologically active natural products and pharmaceutical lead compounds. Here, we report an enzymatic formation of the 3-substituted 2-oxindoles catalyzed by MarE in the maremycin biosynthetic pathway in Streptomyces sp. B9173. MarE is a homologue of Fe II /heme-dependent tryptophan 2,3-dioxygenases (TDOs). Typical TDOs usually catalyze the insertion of two oxygen atoms from O 2 into an indole ring to generate N-formylkynurenine (NFK)-like products. In contrast, MarE catalyzes the insertion of a single oxygen atom from O 2 into an indole ring, to probably generate an epoxyindole intermediate that undergoes an unprecedented 2,3-hydride migration to form 2-oxindole structure. MarE shows substrate robustness to catalyze the conversion of a series of 3-substituted indoles into their corresponding 3-substituted 2-oxindoles. Although containing most key amino acid residues conserved in well-known TDO homologues, MarE falls into a separate new subgroup in the phylogenetic tree. The characterization of MarE and its homologue enriches the functional diversities of TDO superfamily and provides a new strategy for discovering novel natural products containing 3-substituted 2-oxindole pharmacophores by genome mining.

Probing the mechanistic role of the long α-helix in subunit L of respiratory Complex I from Escherichia coli by site-directed mutagenesis

PubMed Central

Belevich, Galina; Knuuti, Juho; Verkhovsky, Michael I; Wikström, Mårten; Verkhovskaya, Marina

2011-01-01

The C-terminus of the NuoL subunit of Complex I includes a long amphipathic α-helix positioned parallel to the membrane, which has been considered to function as a piston in the proton pumping machinery. Here, we have introduced three types of mutations into the nuoL gene to test the piston-like function. First, NuoL was truncated at its C- and N-termini, which resulted in low production of a fragile Complex I with negligible activity. Second, we mutated three partially conserved residues of the amphipathic α-helix: Asp and Lys residues and a Pro were substituted for acidic, basic or neutral residues. All these variants exhibited almost a wild-type phenotype. Third, several substitutions and insertions were made to reduce rigidity of the amphipathic α-helix, and/or to change its geometry. Most insertions/substitutions resulted in a normal growth phenotype, albeit often with reduced stability of Complex I. In contrast, insertion of six to seven amino acids at a site of the long α-helix between NuoL and M resulted in substantial loss of proton pumping efficiency. The implications of these results for the proton pumping mechanism of Complex I are discussed. PMID:22060017

Phylogenetic Conflict in Bears Identified by Automated Discovery of Transposable Element Insertions in Low-Coverage Genomes.

PubMed

Lammers, Fritjof; Gallus, Susanne; Janke, Axel; Nilsson, Maria A

2017-10-01

Phylogenetic reconstruction from transposable elements (TEs) offers an additional perspective to study evolutionary processes. However, detecting phylogenetically informative TE insertions requires tedious experimental work, limiting the power of phylogenetic inference. Here, we analyzed the genomes of seven bear species using high-throughput sequencing data to detect thousands of TE insertions. The newly developed pipeline for TE detection called TeddyPi (TE detection and discovery for Phylogenetic Inference) identified 150,513 high-quality TE insertions in the genomes of ursine and tremarctine bears. By integrating different TE insertion callers and using a stringent filtering approach, the TeddyPi pipeline produced highly reliable TE insertion calls, which were confirmed by extensive in vitro validation experiments. Analysis of single nucleotide substitutions in the flanking regions of the TEs shows that these substitutions correlate with the phylogenetic signal from the TE insertions. Our phylogenomic analyses show that TEs are a major driver of genomic variation in bears and enabled phylogenetic reconstruction of a well-resolved species tree, despite strong signals for incomplete lineage sorting and introgression. The analyses show that the Asiatic black, sun, and sloth bear form a monophyletic clade, in which phylogenetic incongruence originates from incomplete lineage sorting. TeddyPi is open source and can be adapted to various TE and structural variation callers. The pipeline makes it possible to confidently extract thousands of TE insertions even from low-coverage genomes (∼10×) of nonmodel organisms. This opens new possibilities for biologists to study phylogenies and evolutionary processes as well as rates and patterns of (retro-)transposition and structural variation. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

V-insertion in Li(Fe,Mn)FePO4

NASA Astrophysics Data System (ADS)

Wu, T.; Liu, J.; Sun, L.; Cong, L.; Xie, H.; Abdel-Ghany, A.; Mauger, A.; Julien, C. M.

2018-04-01

Insertion of 3% vanadium in LiMn1-yFeyPO4 has been investigated, with y = 0.2 corresponding to the highest manganese concentration before the stress/strain field degrades the electrochemical performance. V substitutes for Fe2+ in the trivalent state V3+. This substitution is accompanied with the formation of Fe vacancies while Mn remains in the Mn2+ valence state, leading to a composition LiMn0.8Fe0.2-0.045V0.03□0.015PO4 where □ is a Fe vacancy. The comparison between electrochemical properties of a pristine sample and a sample with 3 mol.% vanadium made of particles with the same morphology (spherical particles with the same dispersion 100-150 nm in size) and same carbon coating (same conductivity of the carbon layer) is reported. Although the vanadium is in the V3+ state at open circuit voltage (2.6 V) before cycling, a reversible V3+/V2+ is observed when the potential of the half-cell is lowered below the redox potential of 1.8 V vs Li+/Li, due to Li-vacancies. The V-insertion improves the electrochemical properties, due to a synergetic effect of an increase of the lithium diffusion coefficient by a factor two and an increase of the electric conductivity at any Li-concentration during the cycling process, in contradiction with prior claims that attributed the increase of conductivity to V-based impurities.

The origin of the ligand-controlled regioselectivity in Rh-catalyzed [(2 + 2) + 2] carbocyclizations: steric vs. stereoelectronic effects† †Electronic supplementary information (ESI) available: Computational details, Cartesian coordinates and vibrational frequencies of all optimized structures. See DOI: 10.1039/c5sc02307f Click here for additional data file.

PubMed Central

Crandell, Douglas W.; Mazumder, Shivnath

2015-01-01

Density functional theory calculations demonstrate that the reversal of regiochemical outcome of the addition for substituted methyl propiolates in the rhodium-catalyzed [(2 + 2) + 2] carbocyclization with PPh3 and (S)-xyl-binap as ligands is both electronically and sterically controlled. For example, the ester functionality polarizes the alkyne π* orbital to favor overlap of the methyl-substituted terminus of the alkyne with the pπ-orbital of the alkenyl fragment of the rhodacycle during alkyne insertion with PPh3 as the ligand. In contrast, the sterically demanding xyl-binap ligand cannot accommodate the analogous alkyne orientation, thereby forcing insertion to occur at the sterically preferred ester terminus, overriding the electronically preferred orientation for alkyne insertion. PMID:28757978

Primary stability of different plate positions and the role of bone substitute in open wedge high tibial osteotomy.

PubMed

Takeuchi, Ryohei; Woon-Hwa, Jung; Ishikawa, Hiroyuki; Yamaguchi, Yuichiro; Osawa, Katsunari; Akamatsu, Yasushi; Kuroda, Koichi

2017-12-01

The purpose of this study was to compare the mechanical fixation strengths of anteromedial and medial plate positions in osteotomy, and clarify the effects of bone substitute placement into the osteotomy site. Twenty-eight sawbone tibia models were used. Four different models were prepared: Group A, the osteotomy site was open and the plate position was anteromedial; Group B, bone substitutes were inserted into the osteotomy site and the plate position was anteromedial; Group C, the osteotomy site was open and the plate position was medial; and Group D, bone substitutes were inserted into the osteotomy site and the plate position was medial. The loading condition ranged from 0 to 800N and one hertz cycles were applied. Changes of the tibial posterior slope angle (TPS), stress on the plate and lateral hinge were measured. The changes in the TPS and the stress on the plate were significantly larger in Group A than in Group C. These were significantly larger in Group A than in Group B, and in Group C than in Group D. There was no significant difference between Group B and Group D, and no significant difference between knee flexion angles of 0° and 10°. Stress on the lateral hinge was significantly smaller when bone substitute was used. A medial plate position was biomechanically superior to an anteromedial position if bone substitute was not used. Bone substitute distributed the stress concentration around the osteotomy gap and prevented an increase in TPS angle regardless of the plate position. Copyright © 2017. Published by Elsevier B.V.

Identify OH groups in TiOF{sub 2} and their impact on the lithium intercalation properties

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

Li, Wei; Body, Monique; Legein, Christophe

A detailed investigation on the chemical composition of the cubic form of titanium oxyfluoride-based compound reveals the presence of OH groups substituting the oxide/ fluoride sublattice. The substitution of oxide by hydroxyl groups induces the presence of titanium vacancies (□) which were characterized by {sup 1}H and {sup 19}F solid-state NMR. {sup 1}H NMR shows that OH groups are present as bridging Ti-OH-Ti or terminal OH groups, i.e. sitting close to a titanium vacancy Ti-OH-□. The electrochemical properties vs. Li{sup +}/Li indicates that the presence of OH groups prevents the intercalation of lithium in the upper voltage region (1.2–3 Vmore » vs. Li{sup +}/Li). Indeed, a partial dehydroxylation of the framework enables to improve the reversibility of the lithium insertion/de-insertion processes. Since the presence of OH groups in this type of compounds is usual and depends on the synthesis method employed, this work enables to rationalize the different electrochemical behaviors reported in the literature and further highlights the importance of a good knowledge of the chemical composition with regard to the physico-chemical properties. - Graphical abstract: The substitution of oxide by hydroxyl groups inducing the formation of titanium vacancies (□), i.e., Ti{sub 1−x}□{sub x}O{sub 1-4x}(OH){sub 4x+y}F{sub 2−y}, was characterized by solid-state {sup 1}H and {sup 19}F NMR. - Highlights: • Evidences of the presence of OH groups and titanium vacancies in titanium oxyfluoride. • {sup 1}H NMR showed the presence of Ti-OH-Ti and Ti-OH-□ species. • The presence of OH groups limits the insertion of lithium within the interstitial sites.« less

Nanocrystalline hydroxyapatite bone substitute leads to sufficient bone tissue formation already after 3 months: histological and histomorphometrical analysis 3 and 6 months following human sinus cavity augmentation.

PubMed

Ghanaati, Shahram; Barbeck, Mike; Willershausen, Ines; Thimm, Benjamin; Stuebinger, Stefan; Korzinskas, Tadas; Obreja, Karina; Landes, Constantin; Kirkpatrick, Charles J; Sader, Robert A

2013-12-01

In this study the de novo bone formation capacity of a nanocrystalline hydroxyapatite bone substitute was assessed 3 and 6 months after its insertion into the human sinus cavity. Sinus cavity augmentation was performed in a total of 14 patients (n = 7 implantation after 3 months; n = 7 implantation after 6 months) with severely atrophic maxillary bone. The specimens obtained after 3 and 6 months were analyzed histologically and histomorphometrically with special focus on bone metabolism within the residual bone and the augmented region. This study revealed that bone tissue formation started from the bone-biomaterial-interface and was directed into the most cranial parts of the augmented region. There was no statistically significant difference in new bone formation after 3 and 6 months (24.89 ± 10.22% vs 31.29 ± 2.29%), respectively. Within the limits of the present study and according to previously published data, implant insertion in regions augmented with this bone substitute material could be considered already after 3 months. Further clinical studies with bone substitute materials are necessary to validate these findings. © 2012 Wiley Periodicals, Inc.

Assessment of Passive Intestinal Permeability Using an Artificial Membrane Insert System.

PubMed

Berben, Philippe; Brouwers, Joachim; Augustijns, Patrick

2018-01-01

Despite reasonable predictive power of current cell-based and cell-free absorption models for the assessment of intestinal drug permeability, high costs and lengthy preparation steps hamper their use. The use of a simple artificial membrane (without any lipids present) as intestinal barrier substitute would overcome these hurdles. In the present study, a set of 14 poorly water-soluble drugs, dissolved in 2 different media (fasted state simulated/human intestinal fluids [FaSSIF/FaHIF]), were applied to the donor compartment of an artificial membrane insert system (AMI-system) containing a regenerated cellulose membrane. Furthermore, to investigate the predictive capacity of the AMI-system as substitute for the well-established Caco-2 system to assess intestinal permeability, the same set of 14 drugs dissolved in FaHIF were applied to the donor compartment of a Caco-2 system. For 14 drugs, covering a broad range of physicochemical parameters, a reasonable correlation between both absorption systems was observed, characterized by a Pearson correlation coefficient r of 0.95 (FaHIF). Using the AMI-system, an excellent predictive capacity of FaSSIF as surrogate medium for FaHIF was demonstrated (r = 0.96). Based on the acquired data, the AMI-system appears to be a time- and cost-effective tool for the early-stage estimation of passive intestinal permeability for poorly water-soluble drugs. Copyright © 2018 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

Local structure and structural rigidity of the green phosphor β -SiAlON:Eu 2+

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

Brgoch, J.; Gaultois, M. W.; Balasubramanian, M.

Eu2+ inserted in beta-Si3-xAlxOxN4-x is a material that shows exceptional promise as a green-emitting phosphor. Synchrotron X-ray and neutron scattering, in conjunction with first-principles calculations and Eu L-3 X-ray absorption measurements, yield a consistent picture of the composition, and the favorable position for Eu2+ substitution in the crystal structure. The Debye temperature Theta(D), which is a proxy for structural rigidity relating to effectiveness as a phosphor, is very high for the starting beta-Si3N4 framework and is determined to decrease only slightly for the small amounts of Al3+ and O2- co-substitution that are required for charge balance associated with Eu2+ insertion.more » (C) 2014 AIP Publishing LLC.« less

Photochemical insertion of alkynes into Cp sub 2 Fe sub 2 (CO) sub 2 (. mu. -CO) sub 2 : A mechanistic study by laser flash photolysis

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

Bursten, B.E.; McKee, S.D.; Platz, M.S.

1989-04-26

Cp{sub 2}Fe{sub 2}(CO){sub 2}({mu}-CO){sub 2} (1: Cp = {eta}{sup 5}-C{sub 5}H{sub 5}) has a rich and diverse photochemistry, as evidenced by the plethora of synthetic and mechanistic studies of it in the literature. Early photochemical studies of 1 have demonstrated homolysis to the radical Cp(CO){sub 2}Fe{sup {sm bullet}} (2). Recent work on metal dimers indicates that a dinuclear species is formed concomitantly. Tyler, Schmidt, and Gray (TSG) first proposed that irradiation of 1 leads to the dinuclear species 3, which they suggested was the intermediate responsible for phosphine substitution. Research by other individuals has indicated that the substitutionally active speciesmore » is the CO-loss photoproduct CpFe({mu}-CO){sub 3}FeCp (4). The authors interest in the photochemistry of 1 stemmed from their theoretical studies on piano-stool dimers. One reaction of particular concern is the photochemical insertion of alkynes into 1 to yield dimetallacyclopentenone 5. On the basis of MO calculations, the authors proposed a possible LUMO-controlled mechanism for this reaction that involved alkyne addition to the TSG transition state 3, followed by CO loss. In this contribution, they report initial experimental studies which demonstrate that 4 is the photochemical intermediate responsible for this reaction. They consider this reaction to be a paradigm for photochemical substitution and insertion reaction in such systems.« less

Whole-Gene Positive Selection, Elevated Synonymous Substitution Rates, Duplication, and Indel Evolution of the Chloroplast clpP1 Gene

PubMed Central

Erixon, Per; Oxelman, Bengt

2008-01-01

Background Synonymous DNA substitution rates in the plant chloroplast genome are generally relatively slow and lineage dependent. Non-synonymous rates are usually even slower due to purifying selection acting on the genes. Positive selection is expected to speed up non-synonymous substitution rates, whereas synonymous rates are expected to be unaffected. Until recently, positive selection has seldom been observed in chloroplast genes, and large-scale structural rearrangements leading to gene duplications are hitherto supposed to be rare. Methodology/Principle Findings We found high substitution rates in the exons of the plastid clpP1 gene in Oenothera (the Evening Primrose family) and three separate lineages in the tribe Sileneae (Caryophyllaceae, the Carnation family). Introns have been lost in some of the lineages, but where present, the intron sequences have substitution rates similar to those found in other introns of their genomes. The elevated substitution rates of clpP1 are associated with statistically significant whole-gene positive selection in three branches of the phylogeny. In two of the lineages we found multiple copies of the gene. Neighboring genes present in the duplicated fragments do not show signs of elevated substitution rates or positive selection. Although non-synonymous substitutions account for most of the increase in substitution rates, synonymous rates are also markedly elevated in some lineages. Whereas plant clpP1 genes experiencing negative (purifying) selection are characterized by having very conserved lengths, genes under positive selection often have large insertions of more or less repetitive amino acid sequence motifs. Conclusions/Significance We found positive selection of the clpP1 gene in various plant lineages to correlated with repeated duplication of the clpP1 gene and surrounding regions, repetitive amino acid sequences, and increase in synonymous substitution rates. The present study sheds light on the controversial issue of whether negative or positive selection is to be expected after gene duplications by providing evidence for the latter alternative. The observed increase in synonymous substitution rates in some of the lineages indicates that the detection of positive selection may be obscured under such circumstances. Future studies are required to explore the functional significance of the large inserted repeated amino acid motifs, as well as the possibility that synonymous substitution rates may be affected by positive selection. PMID:18167545

TRAP-Positive Multinucleated Giant Cells Are Foreign Body Giant Cells Rather Than Osteoclasts: Results From a Split-Mouth Study in Humans.

PubMed

Lorenz, Jonas; Kubesch, Alica; Korzinskas, Tadas; Barbeck, Mike; Landes, Constantin; Sader, Robert A; Kirkpatrick, Charles J; Ghanaati, Shahram

2015-12-01

This study compared the material-specific tissue response to the synthetic, hydroxyapatite-based bone substitute material NanoBone (NB) with that of the xenogeneic, bovine-based bone substitute material Bio-Oss (BO). The sinus cavities of 14 human patients were augmented with NB and BO in a split-mouth design. Six months after augmentation, bone biopsies were extracted for histological and histomorphometric investigation prior to dental implant insertion. The following were evaluated: the cellular inflammatory pattern, the induction of multinucleated giant cells, vascularization, the relative amounts of newly formed bone, connective tissue, and the remaining bone substitute material. NB granules were well integrated in the peri-implant tissue and were surrounded by newly formed bone tissue. Multinucleated giant cells were visible on the surfaces of the remaining granules. BO granules were integrated into the newly formed bone tissue, which originated from active osteoblasts on their surface. Histomorphometric analysis showed a significantly higher number of multinucleated giant cells and blood vessels in the NB group compared to the BO group. No statistical differences were observed in regard to connective tissue, remaining bone substitute, and newly formed bone. The results of this study highlight the different cellular reactions to synthetic and xenogeneic bone substitute materials. The significantly higher number of multinucleated giant cells within the NB implantation bed seems to have no effect on its biodegradation. Accordingly, the multinucleated giant cells observed within the NB implantation bed have characteristics more similar to those of foreign body giant cells than to those of osteoclasts.

Japanese Wolves are Genetically Divided into Two Groups Based on an 8-Nucleotide Insertion/Deletion within the mtDNA Control Region.

PubMed

Ishiguro, Naotaka; Inoshima, Yasuo; Yanai, Tokuma; Sasaki, Motoki; Matsui, Akira; Kikuchi, Hiroki; Maruyama, Masashi; Hongo, Hitomi; Vostretsov, Yuri E; Gasilin, Viatcheslav; Kosintsev, Pavel A; Quanjia, Chen; Chunxue, Wang

2016-02-01

The mitochondrial DNA (mtDNA) control region (198- to 598-bp) of four ancient Canis specimens (two Canis mandibles, a cranium, and a first phalanx) was examined, and each specimen was genetically identified as Japanese wolf. Two unique nucleotide substitutions, the 78-C insertion and the 482-G deletion, both of which are specific for Japanese wolf, were observed in each sample. Based on the mtDNA sequences analyzed, these four specimens and 10 additional Japanese wolf samples could be classified into two groups- Group A (10 samples) and Group B (4 samples)-which contain or lack an 8-bp insertion/deletion (indel), respectively. Interestingly, three dogs (Akita-b, Kishu 25, and S-husky 102) that each contained Japanese wolf-specific features were also classified into Group A or B based on the 8-bp indel. To determine the origin or ancestor of the Japanese wolf, mtDNA control regions of ancient continental Canis specimens were examined; 84 specimens were from Russia, and 29 were from China. However, none of these 113 specimens contained Japanese wolf-specific sequences. Moreover, none of 426 Japanese modern hunting dogs examined contained these Japanese wolf-specific mtDNA sequences. The mtDNA control region sequences of Groups A and B appeared to be unique to grey wolf and dog populations.

Synthesis, characterization and modelling of zinc and silicate co-substituted hydroxyapatite

PubMed Central

Friederichs, Robert J.; Chappell, Helen F.; Shepherd, David V.; Best, Serena M.

2015-01-01

Experimental chemistry and atomic modelling studies were performed here to investigate a novel ionic co-substitution in hydroxyapatite (HA). Zinc, silicate co-substituted HA (ZnSiHA) remained phase pure after heating to 1100°C with Zn and Si amounts of 0.6 wt% and 1.2 wt%, respectively. Unique lattice expansions in ZnSiHA, silicate Fourier transform infrared peaks and changes to the hydroxyl IR stretching region suggested Zn and silicate co-substitution in ZnSiHA. Zn and silicate insertion into HA was modelled using density functional theory (DFT). Different scenarios were considered where Zn substituted for different calcium sites or at a 2b site along the c-axis, which was suspected in singly substituted ZnHA. The most energetically favourable site in ZnSiHA was Zn positioned at a previously unreported interstitial site just off the c-axis near a silicate tetrahedron sitting on a phosphate site. A combination of experimental chemistry and DFT modelling provided insight into these complex co-substituted calcium phosphates that could find biomedical application as a synthetic bone mineral substitute. PMID:26040597

Structural effects in the interstitial solid solution system (La,Ce)(Fe,Si)13Cx-H: Correlation with hydrogenation kinetics

NASA Astrophysics Data System (ADS)

Hai, X.; Porcher, F.; Mayer, C.; Miraglia, S.

2018-02-01

Steady state and in-situ neutron powder diffraction on selected compositions of the magneto-caloric (La,Ce)(Fe,Si)13CxHy compounds has been used to locate the sites accommodated by the interstitial species and to reveal the structural modifications (breathing) that occur upon metal substitution and/or interstitial insertion. The latter type of measurement in which the sequential filling of interstitial sites is followed allows one to extract some useful hydrogenation kinetics data. This structural investigation has allowed to precise the deformations undergone by the complex metallic alloys La(Fe,Si)13 when subjected to light interstitial insertion or rare earth substitution at the cation site of the NaZn13-structure type. We attempt to correlate hydrogenation kinetics variations (depression or enhancement of the hydrogen absorption rate) with a particular inhomogeneous cell variation (breathing) and bonding of the NaZn13 structure-type.

Local structure and structural rigidity of the green phosphor β-SiAlON:Eu{sup 2+}

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

Brgoch, J., E-mail: jbrgoch@uh.edu; Gaultois, M. W., E-mail: mgaultois@mrl.ucsb.edu; Seshadri, R.

Eu{sup 2+} inserted in β-Si{sub 3−x}Al{sub x}O{sub x}N{sub 4−x} is a material that shows exceptional promise as a green-emitting phosphor. Synchrotron X-ray and neutron scattering, in conjunction with first-principles calculations and Eu L{sub 3} X-ray absorption measurements, yield a consistent picture of the composition, and the favorable position for Eu{sup 2+} substitution in the crystal structure. The Debye temperature Θ{sub D}, which is a proxy for structural rigidity relating to effectiveness as a phosphor, is very high for the starting β-Si{sub 3}N{sub 4} framework and is determined to decrease only slightly for the small amounts of Al{sup 3+} and O{supmore » 2−} co-substitution that are required for charge balance associated with Eu{sup 2+} insertion.« less

Kagomé lattices as cathode: Effect of particle size and fluoride substitution on electrochemical lithium insertion in sodium- and ammonium Jarosites

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

Sandineni, Prashanth; Yaghoobnejad Asl, Hooman; Choudhury, Amitava, E-mail: choudhurya@mst.edu

Highly crystalline sodium and ammonium Jarosites, NaFe{sub 3}(SO{sub 4}){sub 2}(OH){sub 6} and NH{sub 4}Fe{sub 3}(SO{sub 4}){sub 2}(OH){sub 6}, have been synthesized employing hydrothermal synthesis routes. The structures consist of anionic layers of vertex-sharing FeO{sub 6} octahedra and SO{sub 4} tetrahedral units with interlayer space occupied by Na and ammonium ions, respectively. The corner-sharing FeO{sub 6} octahedral units form six and three rings similar to hexagonal tungsten bronze sheets also known as kagomé lattice. These sodium and ammonium Jarosites are thermally stable up to 400 °C and undergo facile electrochemical lithium insertion through the reduction of Fe{sup 3+} to Fe{sup 2+}.more » Galvanostatic charge–discharge indicates that up to 2.25 and 2 lithium ions per formula unit can be inserted at an average voltage of 2.49 and 2.26 V to the sodium and the ammonium Jarosites, respectively, under slow discharge rate of C/50. The cycle-life and experimental achievable capacity show strong dependence on particle sizes and synthesis conditions. A small amount of fluoride substitution improves both achievable capacity and average voltage. - Graphical abstract: Discharge capacity of jarosite phases as a function of particle size and fluoride substitution. - Highlights: • Synthesis of natro- and ammonium Jarosites. • Jarosites as cathodes for lithium ion batteries. • Li-ion electrochemistry of Jarosites. • Mössbauer spectroscopy of Jarosites.« less

LenVarDB: database of length-variant protein domains.

PubMed

Mutt, Eshita; Mathew, Oommen K; Sowdhamini, Ramanathan

2014-01-01

Protein domains are functionally and structurally independent modules, which add to the functional variety of proteins. This array of functional diversity has been enabled by evolutionary changes, such as amino acid substitutions or insertions or deletions, occurring in these protein domains. Length variations (indels) can introduce changes at structural, functional and interaction levels. LenVarDB (freely available at http://caps.ncbs.res.in/lenvardb/) traces these length variations, starting from structure-based sequence alignments in our Protein Alignments organized as Structural Superfamilies (PASS2) database, across 731 structural classification of proteins (SCOP)-based protein domain superfamilies connected to 2 730 625 sequence homologues. Alignment of sequence homologues corresponding to a structural domain is available, starting from a structure-based sequence alignment of the superfamily. Orientation of the length-variant (indel) regions in protein domains can be visualized by mapping them on the structure and on the alignment. Knowledge about location of length variations within protein domains and their visual representation will be useful in predicting changes within structurally or functionally relevant sites, which may ultimately regulate protein function. Non-technical summary: Evolutionary changes bring about natural changes to proteins that may be found in many organisms. Such changes could be reflected as amino acid substitutions or insertions-deletions (indels) in protein sequences. LenVarDB is a database that provides an early overview of observed length variations that were set among 731 protein families and after examining >2 million sequences. Indels are followed up to observe if they are close to the active site such that they can affect the activity of proteins. Inclusion of such information can aid the design of bioengineering experiments.

Cruciate retaining and cruciate substituting ultra-congruent insert

PubMed Central

Deledda, Davide; Rosso, Federica; Ratto, Nicola; Bruzzone, Matteo; Bonasia, Davide Edoardo; Rossi, Roberto

2016-01-01

The posterior cruciate ligament (PCL) conservation and the polyethylene insert constraint in total knee arthroplasty (TKA) are still debated. The PCL is one of the primary stabilizers of the joint, but cruciate retaining (CR) implants have the disadvantage of a difficult balancing of the PCL. Postero-stabilized (PS) implants were introduced to reduce this problem. However, also the PS implants have some disadvantages, due to the cam-mechanism, such as high risk of cam-mechanism polyethylene wear. To minimize the polyethylene wear of the cam-mechanism and the bone sacrifice due to the intercondylar box, different types of inserts were developed, trying to increase the implant conformity and to reduce stresses on the bone-implant interface. In this scenario ultra-congruent (UC) inserts were developed. Those inserts are characterized by a high anterior wall and a deep-dished plate. This conformation should guarantee a good stability without the posterior cam. Few studies on both kinematic and clinical outcomes of UC inserts are available. Clinical and radiological outcomes, as well as kinematic data are similar between UC mobile bearing (MB) and standard PS MB inserts at short to mid-term follow-up. In this manuscript biomechanics and clinical outcomes of UC inserts will be described, and they will be compared to standard PS or CR inserts. PMID:26855938

Synthesis, characterization and modelling of zinc and silicate co-substituted hydroxyapatite.

PubMed

Friederichs, Robert J; Chappell, Helen F; Shepherd, David V; Best, Serena M

2015-07-06

Experimental chemistry and atomic modelling studies were performed here to investigate a novel ionic co-substitution in hydroxyapatite (HA). Zinc, silicate co-substituted HA (ZnSiHA) remained phase pure after heating to 1100 °C with Zn and Si amounts of 0.6 wt% and 1.2 wt%, respectively. Unique lattice expansions in ZnSiHA, silicate Fourier transform infrared peaks and changes to the hydroxyl IR stretching region suggested Zn and silicate co-substitution in ZnSiHA. Zn and silicate insertion into HA was modelled using density functional theory (DFT). Different scenarios were considered where Zn substituted for different calcium sites or at a 2b site along the c-axis, which was suspected in singly substituted ZnHA. The most energetically favourable site in ZnSiHA was Zn positioned at a previously unreported interstitial site just off the c-axis near a silicate tetrahedron sitting on a phosphate site. A combination of experimental chemistry and DFT modelling provided insight into these complex co-substituted calcium phosphates that could find biomedical application as a synthetic bone mineral substitute. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Transition-Metal-Catalyzed Laboratory-Scale Carbon–Carbon Bond-Forming Reactions of Ethylene

PubMed Central

Saini, Vaneet; Stokes, Benjamin J.; Sigman, Matthew S.

2014-01-01

Ethylene, the simplest alkene, is the most abundantly synthesized organic molecule by volume. It is readily incorporated into transitionmetal–catalyzed carbon-carbon bond-forming reactions through migratory insertions into alkylmetal intermediates. Because of its D2h symmetry, only one insertion outcome is possible. This limits byproduct formation and greatly simplifies analysis. As described within this Minireview, many carbon–carbon bond-forming reactions incorporate a molecule (or more) of ethylene at ambient pressure and temperature. In many cases, a useful substituted alkene is incorporated into the product. PMID:24105881

Electrocatalytic oxidation of hydrogen peroxide on a platinum electrode in the imitation of oxidative drug metabolism of lidocaine.

PubMed

Nouri-Nigjeh, Eslam; Bruins, Andries P; Bischoff, Rainer; Permentier, Hjalmar P

2012-10-21

Electrochemistry in combination with mass spectrometry has shown promise as a versatile technique not only in the analytical assessment of oxidative drug metabolism, but also for small-scale synthesis of drug metabolites. However, electrochemistry is generally limited to reactions initiated by direct electron transfer. In the case of substituted-aromatic compounds, oxidation proceeds through a Wheland-type intermediate where resonance stabilization of the positive charge determines the regioselectivity of the anodic substitution reaction, and hence limits the extent of generating drug metabolites in comparison with in vivo oxygen insertion reactions. In this study, we show that the electrocatalytic oxidation of hydrogen peroxide on a platinum electrode generates reactive oxygen species, presumably surface-bound platinum-oxo species, which are capable of oxygen insertion reactions in analogy to oxo-ferryl radical cations in the active site of Cytochrome P450. Electrochemical oxidation of lidocaine at constant potential in the presence of hydrogen peroxide produces both 3- and 4-hydroxylidocaine, suggesting reaction via an arene oxide rather than a Wheland-type intermediate. No benzylic hydroxylation was observed, thus freely diffusing radicals do not appear to be present. The results of the present study extend the possibilities of electrochemical imitation of oxidative drug metabolism to oxygen insertion reactions.

Twisted trees and inconsistency of tree estimation when gaps are treated as missing data - The impact of model mis-specification in distance corrections.

PubMed

McTavish, Emily Jane; Steel, Mike; Holder, Mark T

2015-12-01

Statistically consistent estimation of phylogenetic trees or gene trees is possible if pairwise sequence dissimilarities can be converted to a set of distances that are proportional to the true evolutionary distances. Susko et al. (2004) reported some strikingly broad results about the forms of inconsistency in tree estimation that can arise if corrected distances are not proportional to the true distances. They showed that if the corrected distance is a concave function of the true distance, then inconsistency due to long branch attraction will occur. If these functions are convex, then two "long branch repulsion" trees will be preferred over the true tree - though these two incorrect trees are expected to be tied as the preferred true. Here we extend their results, and demonstrate the existence of a tree shape (which we refer to as a "twisted Farris-zone" tree) for which a single incorrect tree topology will be guaranteed to be preferred if the corrected distance function is convex. We also report that the standard practice of treating gaps in sequence alignments as missing data is sufficient to produce non-linear corrected distance functions if the substitution process is not independent of the insertion/deletion process. Taken together, these results imply inconsistent tree inference under mild conditions. For example, if some positions in a sequence are constrained to be free of substitutions and insertion/deletion events while the remaining sites evolve with independent substitutions and insertion/deletion events, then the distances obtained by treating gaps as missing data can support an incorrect tree topology even given an unlimited amount of data. Copyright © 2015 Elsevier Inc. All rights reserved.

Training alignment parameters for arbitrary sequencers with LAST-TRAIN.

PubMed

Hamada, Michiaki; Ono, Yukiteru; Asai, Kiyoshi; Frith, Martin C

2017-03-15

LAST-TRAIN improves sequence alignment accuracy by inferring substitution and gap scores that fit the frequencies of substitutions, insertions, and deletions in a given dataset. We have applied it to mapping DNA reads from IonTorrent and PacBio RS, and we show that it reduces reference bias for Oxford Nanopore reads. the source code is freely available at http://last.cbrc.jp/. mhamada@waseda.jp or mcfrith@edu.k.u-tokyo.ac.jp. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Ultra-superovulation for the CRISPR-Cas9-mediated production of gene-knockout, single-amino-acid-substituted, and floxed mice.

PubMed

Nakagawa, Yoshiko; Sakuma, Tetsushi; Nishimichi, Norihisa; Yokosaki, Yasuyuki; Yanaka, Noriyuki; Takeo, Toru; Nakagata, Naomi; Yamamoto, Takashi

2016-08-15

Current advances in producing genetically modified mice using genome-editing technologies have indicated the need for improvement of limiting factors including zygote collection for microinjection and their cryopreservation. Recently, we developed a novel superovulation technique using inhibin antiserum and equine chorionic gonadotropin to promote follicle growth. This method enabled the increased production of fertilized oocytes via in vitro fertilization compared with the conventional superovulation method. Here, we verify that the ultra-superovulation technique can be used for the efficient generation of clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9)-mediated knockout mice by microinjection of plasmid vector or ribonucleoprotein into zygotes. We also investigated whether single-amino-acid-substituted mice and conditional knockout mice could be generated. Founder mice bearing base substitutions were generated more efficiently by co-microinjection of Cas9 protein, a guide RNA and single-stranded oligodeoxynucleotide (ssODN) than by plasmid microinjection with ssODN. The conditional allele was successfully introduced by the one-step insertion of an ssODN designed to carry an exon flanked by two loxP sequences and homology arms using a double-cut CRISPR-Cas9 strategy. Our study presents a useful method for the CRISPR-Cas9-based generation of genetically modified mice from the viewpoints of animal welfare and work efficiency. © 2016. Published by The Company of Biologists Ltd.

Investigation of real tissue water equivalent path lengths using an efficient dose extinction method

NASA Astrophysics Data System (ADS)

Zhang, Rongxiao; Baer, Esther; Jee, Kyung-Wook; Sharp, Gregory C.; Flanz, Jay; Lu, Hsiao-Ming

2017-07-01

For proton therapy, an accurate conversion of CT HU to relative stopping power (RSP) is essential. Validation of the conversion based on real tissue samples is more direct than the current practice solely based on tissue substitutes and can potentially address variations over the population. Based on a novel dose extinction method, we measured water equivalent path lengths (WEPL) on animal tissue samples to evaluate the accuracy of CT HU to RSP conversion and potential variations over a population. A broad proton beam delivered a spread out Bragg peak to the samples sandwiched between a water tank and a 2D ion-chamber detector. WEPLs of the samples were determined from the transmission dose profiles measured as a function of the water level in the tank. Tissue substitute inserts and Lucite blocks with known WEPLs were used to validate the accuracy. A large number of real tissue samples were measured. Variations of WEPL over different batches of tissue samples were also investigated. The measured WEPLs were compared with those computed from CT scans with the Stoichiometric calibration method. WEPLs were determined within  ±0.5% percentage deviation (% std/mean) and  ±0.5% error for most of the tissue surrogate inserts and the calibration blocks. For biological tissue samples, percentage deviations were within  ±0.3%. No considerable difference (<1%) in WEPL was observed for the same type of tissue from different sources. The differences between measured WEPLs and those calculated from CT were within 1%, except for some bony tissues. Depending on the sample size, each dose extinction measurement took around 5 min to produce ~1000 WEPL values to be compared with calculations. This dose extinction system measures WEPL efficiently and accurately, which allows the validation of CT HU to RSP conversions based on the WEPL measured for a large number of samples and real tissues.

Basecalling with LifeTrace

PubMed Central

Walther, Dirk; Bartha, Gábor; Morris, Macdonald

2001-01-01

A pivotal step in electrophoresis sequencing is the conversion of the raw, continuous chromatogram data into the actual sequence of discrete nucleotides, a process referred to as basecalling. We describe a novel algorithm for basecalling implemented in the program LifeTrace. Like Phred, currently the most widely used basecalling software program, LifeTrace takes processed trace data as input. It was designed to be tolerant to variable peak spacing by means of an improved peak-detection algorithm that emphasizes local chromatogram information over global properties. LifeTrace is shown to generate high-quality basecalls and reliable quality scores. It proved particularly effective when applied to MegaBACE capillary sequencing machines. In a benchmark test of 8372 dye-primer MegaBACE chromatograms, LifeTrace generated 17% fewer substitution errors, 16% fewer insertion/deletion errors, and 2.4% more aligned bases to the finished sequence than did Phred. For two sets totaling 6624 dye-terminator chromatograms, the performance improvement was 15% fewer substitution errors, 10% fewer insertion/deletion errors, and 2.1% more aligned bases. The processing time required by LifeTrace is comparable to that of Phred. The predicted quality scores were in line with observed quality scores, permitting direct use for quality clipping and in silico single nucleotide polymorphism (SNP) detection. Furthermore, we introduce a new type of quality score associated with every basecall: the gap-quality. It estimates the probability of a deletion error between the current and the following basecall. This additional quality score improves detection of single basepair deletions when used for locating potential basecalling errors during the alignment. We also describe a new protocol for benchmarking that we believe better discerns basecaller performance differences than methods previously published. PMID:11337481

[Study of the functional role of mutation in the guinea pig-adapted Ebola virus genome on a Drosophila melanogaster model].

PubMed

Shelemba-Chepurnova, A A; Omel'ianchuk, L V; Chepurnov, A A

2011-01-01

Ebola virus virulence in guinea pigs, which appears through virus adaptation to this animal host, correlates with substitutions in the gene encoding vp24 protein. In particular, the substitution His-->Tyr186 was found when obtaining strain 8 ms. An attempt was made to clarify the functional role of this substitution in a transgenic fruit fly model. Using the drosophila transformation technique provided transgenic strains that contained genomic insertions of wild-type Ebola virus vp24 gene and the mutant gene with the His-->Tyr substitution at the above position. Thus, the drosophila strains carrying the sequences encoding for the vp24 proteins of Ebola virus Zaire and 8 ms in pUAST vector were obtained. This makes it possible to study the expression of transgenic constructs in various D. melanogaster organs and tissues.

A novel dihydropyridine with 3-aryl meta-hydroxyl substitution blocks L-type calcium channels in rat cardiomyocytes.

PubMed

Galvis-Pareja, David; Zapata-Torres, Gerald; Hidalgo, Jorge; Ayala, Pedro; Pedrozo, Zully; Ibarra, Cristián; Diaz-Araya, Guillermo; Hall, Andrew R; Vicencio, Jose Miguel; Nuñez-Vergara, Luis; Lavandero, Sergio

2014-08-15

Dihydropyridines are widely used for the treatment of several cardiac diseases due to their blocking activity on L-type Ca(2+) channels and their renowned antioxidant properties. We synthesized six novel dihydropyridine molecules and performed docking studies on the binding site of the L-type Ca(2+) channel. We used biochemical techniques on isolated adult rat cardiomyocytes to assess the efficacy of these molecules on their Ca(2+) channel-blocking activity and antioxidant properties. The Ca(2+) channel-blocking activity was evaluated by confocal microscopy on fluo-3AM loaded cardiomyocytes, as well as using patch clamp experiments. Antioxidant properties were evaluated by flow cytometry using the ROS sensitive dye 1,2,3 DHR. Our docking studies show that a novel compound with 3-OH substitution inserts into the active binding site of the L-type Ca(2+) channel previously described for nitrendipine. In biochemical assays, the novel meta-OH group in the aryl in C4 showed a high blocking effect on L-type Ca(2+) channel as opposed to para-substituted compounds. In the tests we performed, none of the molecules showed antioxidant properties. Only substitutions in C2, C3 and C5 of the aryl ring render dihydropyridine compounds with the capacity of blocking LTCC. Based on our docking studies, we postulate that the antioxidant activity requires a larger group than the meta-OH substitution in C2, C3 or C5 of the dihydropyridine ring. Copyright © 2014 Elsevier Inc. All rights reserved.

Stereoselective 1,3-Insertions of Rhodium(II) Azavinyl Carbenes

PubMed Central

Chuprakov, Stepan; Worrell, Brady T.; Selander, Nicklas; Sit, Rakesh K.; Fokin, Valery V.

2014-01-01

Rhodium(II) azavinyl carbenes, conveniently generated from 1-sulfonyl-1,2,3-triazoles, undergo a facile, mild and convergent formal 1,3-insertion into N–H and O–H bonds of primary and secondary amides, various alcohols, and carboxylic acids to afford a wide range of vicinally bis-functionalized Z-olefins with perfect regio- and stereoselectively. Utilizing the distinctive functionality installed through these reactions, a number of subsequent rearrangements and cyclizations expand the repertoire of valuable organic building blocks constructed by reactions of transition metal carbene complexes, including α-allenyl ketones and amino-substituted heterocycles. PMID:24295389

Engineering antimicrobial peptides with improved antimicrobial and hemolytic activities.

PubMed

Zhao, Jun; Zhao, Chao; Liang, Guizhao; Zhang, Mingzhen; Zheng, Jie

2013-12-23

The rapid rise of antibiotic resistance in pathogens becomes a serious and growing threat to medicine and public health. Naturally occurring antimicrobial peptides (AMPs) are an important line of defense in the immune system against invading bacteria and microbial infection. In this work, we present a combined computational and experimental study of the biological activity and membrane interaction of the computationally designed Bac2A-based peptide library. We used the MARTINI coarse-grained molecular dynamics with adaptive biasing force method and the umbrella sampling technique to investigate the translocation of a total of 91 peptides with different amino acid substitutions through a mixed anionic POPE/POPG (3:1) bilayer and a neutral POPC bilayer, which mimic the bacterial inner membrane and the human red blood cell (hRBC) membrane, respectively. Potential of mean force (PMF, free energy profile) was obtained to measure the free energy barrier required to transfer the peptides from the bulk water phase to the water-membrane interface and to the bilayer interior. Different PMF profiles can indeed identify different membrane insertion scenarios by mapping out peptide-lipid energy landscapes, which are correlated with antimicrobial activity and hemolytic activity. Computationally designed peptides were further tested experimentally for their antimicrobial and hemolytic activities using bacteria growth inhibition assay and hemolysis assay. Comparison of PMF data with cell assay results reveals a good correlation of the peptides between predictive transmembrane activity and antimicrobial/hemolytic activity. Moreover, the most active mutants with the balanced substitutions of positively charged Arg and hydrophobic Trp residues at specific positions were discovered to achieve the improved antimicrobial activity while minimizing red blood cell lysis. Such substitutions provide more effective and cooperative interactions to distinguish the peptide interaction with different lipid bilayers. This work provides a useful computational tool to better understand the mechanism and energetics of membrane insertion of AMPs and to rationally design more effective AMPs.

Inter-individual and intragenomic variations in the ITS region of Clonorchis sinensis (Trematoda: Opisthorchiidae) from Russia and Vietnam.

PubMed

Tatonova, Yulia V; Chelomina, Galina N; Nguyen, Hung Manh

2017-11-01

Here we examined the intraspecific genetic variability of Clonorchis sinensis from Russia and Vietnam using nuclear DNA sequences (the 5.8S gene and two internal transcribed spacers of the ribosomal cluster). Despite the low level of variability in the ITS1 region, this marker has revealed some features of C. sinensis across multiple geographic regions. The genetic diversity levels for the Russian and Vietnamese populations were similar (0.1 and 0.09%, respectively) but were significantly lower than the C. sinensis from China (0.31%). About half of the sequences of the Chinese (53%) and Korean (47%) populations and about a tenth of the Vietnamese (12%) and Russian (8%) sequences included a 5bp insertion. No sequences with nucleotide substitutions both upstream and downstream of the 5bp insertion were found within the whole data set. The population of northern China had both sequence variants (with substitutions either upstream or downstream of the insertion), while only one of these variants was presented at the other localities. The Vietnamese population had a higher frequency of intragenomic polymorphism than the Russian population (69% vs. 46% and 23% vs. 3% at the 114bp and 339bp positions, respectively). These data are discussed in connection with parasite origin and adaptation, and also its invasive capacity and drug-resistance. Copyright © 2017 Elsevier B.V. All rights reserved.

A simple and efficient method to visualize and quantify the efficiency of chromosomal mutations from genome editing

PubMed Central

Fu, Liezhen; Wen, Luan; Luu, Nga; Shi, Yun-Bo

2016-01-01

Genome editing with designer nucleases such as TALEN and CRISPR/Cas enzymes has broad applications. Delivery of these designer nucleases into organisms induces various genetic mutations including deletions, insertions and nucleotide substitutions. Characterizing those mutations is critical for evaluating the efficacy and specificity of targeted genome editing. While a number of methods have been developed to identify the mutations, none other than sequencing allows the identification of the most desired mutations, i.e., out-of-frame insertions/deletions that disrupt genes. Here we report a simple and efficient method to visualize and quantify the efficiency of genomic mutations induced by genome-editing. Our approach is based on the expression of a two-color fusion protein in a vector that allows the insertion of the edited region in the genome in between the two color moieties. We show that our approach not only easily identifies developing animals with desired mutations but also efficiently quantifies the mutation rate in vivo. Furthermore, by using LacZα and GFP as the color moieties, our approach can even eliminate the need for a fluorescent microscope, allowing the analysis with simple bright field visualization. Such an approach will greatly simplify the screen for effective genome-editing enzymes and identify the desired mutant cells/animals. PMID:27748423

Mutational Dynamics of Aroid Chloroplast Genomes

PubMed Central

Ahmed, Ibrar; Biggs, Patrick J.; Matthews, Peter J.; Collins, Lesley J.; Hendy, Michael D.; Lockhart, Peter J.

2012-01-01

A characteristic feature of eukaryote and prokaryote genomes is the co-occurrence of nucleotide substitution and insertion/deletion (indel) mutations. Although similar observations have also been made for chloroplast DNA, genome-wide associations have not been reported. We determined the chloroplast genome sequences for two morphotypes of taro (Colocasia esculenta; family Araceae) and compared these with four publicly available aroid chloroplast genomes. Here, we report the extent of genome-wide association between direct and inverted repeats, indels, and substitutions in these aroid chloroplast genomes. We suggest that alternative but not mutually exclusive hypotheses explain the mutational dynamics of chloroplast genome evolution. PMID:23204304

A novel dihydropyridine with 3-aryl meta-hydroxyl substitution blocks L-type calcium channels in rat cardiomyocytes

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

Galvis-Pareja, David; Centro Estudios Moleculares de la Célula; Zapata-Torres, Gerald

2014-08-15

Rationale: Dihydropyridines are widely used for the treatment of several cardiac diseases due to their blocking activity on L-type Ca{sup 2+} channels and their renowned antioxidant properties. Methods: We synthesized six novel dihydropyridine molecules and performed docking studies on the binding site of the L-type Ca{sup 2+} channel. We used biochemical techniques on isolated adult rat cardiomyocytes to assess the efficacy of these molecules on their Ca{sup 2+} channel-blocking activity and antioxidant properties. The Ca{sup 2+} channel-blocking activity was evaluated by confocal microscopy on fluo-3AM loaded cardiomyocytes, as well as using patch clamp experiments. Antioxidant properties were evaluated by flowmore » cytometry using the ROS sensitive dye 1,2,3 DHR. Results: Our docking studies show that a novel compound with 3-OH substitution inserts into the active binding site of the L-type Ca{sup 2+} channel previously described for nitrendipine. In biochemical assays, the novel meta-OH group in the aryl in C4 showed a high blocking effect on L-type Ca{sup 2+} channel as opposed to para-substituted compounds. In the tests we performed, none of the molecules showed antioxidant properties. Conclusions: Only substitutions in C2, C3 and C5 of the aryl ring render dihydropyridine compounds with the capacity of blocking LTCC. Based on our docking studies, we postulate that the antioxidant activity requires a larger group than the meta-OH substitution in C2, C3 or C5 of the dihydropyridine ring. - Highlights: • Dihydropyridine (DHP) molecules are widely used in cardiovascular disease. • DHPs block Ca{sup 2+} entry through LTCC—some DHPs have antioxidant activity as well. • We synthesized 6 new DHPs and tested their Ca{sup 2+} blocking and antioxidant activities. • 3-Aryl meta-hydroxyl substitution strongly increases their Ca{sup 2+} blocking activity. • 3-Aryl meta-hydroxyl substitution did not affect the antioxidant properties.« less

Comparison of Insertional RNA Editing in Myxomycetes

PubMed Central

Chen, Cai; Frankhouser, David; Bundschuh, Ralf

2012-01-01

RNA editing describes the process in which individual or short stretches of nucleotides in a messenger or structural RNA are inserted, deleted, or substituted. A high level of RNA editing has been observed in the mitochondrial genome of Physarum polycephalum. The most frequent editing type in Physarum is the insertion of individual Cs. RNA editing is extremely accurate in Physarum; however, little is known about its mechanism. Here, we demonstrate how analyzing two organisms from the Myxomycetes, namely Physarum polycephalum and Didymium iridis, allows us to test hypotheses about the editing mechanism that can not be tested from a single organism alone. First, we show that using the recently determined full transcriptome information of Physarum dramatically improves the accuracy of computational editing site prediction in Didymium. We use this approach to predict genes in the mitochondrial genome of Didymium and identify six new edited genes as well as one new gene that appears unedited. Next we investigate sequence conservation in the vicinity of editing sites between the two organisms in order to identify sites that harbor the information for the location of editing sites based on increased conservation. Our results imply that the information contained within only nine or ten nucleotides on either side of the editing site (a distance previously suggested through experiments) is not enough to locate the editing sites. Finally, we show that the codon position bias in C insertional RNA editing of these two organisms is correlated with the selection pressure on the respective genes thereby directly testing an evolutionary theory on the origin of this codon bias. Beyond revealing interesting properties of insertional RNA editing in Myxomycetes, our work suggests possible approaches to be used when finding sequence motifs for any biological process fails. PMID:22383871

Improvement of single detector proton radiography by incorporating intensity of time-resolved dose rate functions

NASA Astrophysics Data System (ADS)

Zhang, Rongxiao; Jee, Kyung-Wook; Cascio, Ethan; Sharp, Gregory C.; Flanz, Jacob B.; Lu, Hsiao-Ming

2018-01-01

Proton radiography, which images patients with the same type of particles as those with which they are to be treated, is a promising approach to image guidance and water equivalent path length (WEPL) verification in proton radiation therapy. We have shown recently that proton radiographs could be obtained by measuring time-resolved dose rate functions (DRFs) using an x-ray amorphous silicon flat panel. The WEPL values were derived solely from the root-mean-square (RMS) of DRFs, while the intensity information in the DRFs was filtered out. In this work, we explored the use of such intensity information for potential improvement in WEPL accuracy and imaging quality. Three WEPL derivation methods based on, respectively, the RMS only, the intensity only, and the intensity-weighted RMS were tested and compared in terms of the quality of obtained radiograph images and the accuracy of WEPL values. A Gammex CT calibration phantom containing inserts made of various tissue substitute materials with independently measured relative stopping powers (RSP) was used to assess the imaging performances. Improved image quality with enhanced interfaces was achieved while preserving the accuracy by using intensity information in the calibration. Other objects, including an anthropomorphic head phantom, a proton therapy range compensator, a frozen lamb’s head and an ‘image quality phantom’ were also imaged. Both the RMS only and the intensity-weighted RMS methods derived RSPs within  ±  1% for most of the Gammex phantom inserts, with a mean absolute percentage error of 0.66% for all inserts. In the case of the insert with a titanium rod, the method based on RMS completely failed, whereas that based on the intensity-weighted RMS was qualitatively valid. The use of intensity greatly enhanced the interfaces between different materials in the obtained WEPL images, suggesting the potential for image guidance in areas such as patient positioning and tumor tracking by proton radiography.

The evolution of small insertions and deletions in the coding genes of Drosophila melanogaster.

PubMed

Chong, Zechen; Zhai, Weiwei; Li, Chunyan; Gao, Min; Gong, Qiang; Ruan, Jue; Li, Juan; Jiang, Lan; Lv, Xuemei; Hungate, Eric; Wu, Chung-I

2013-12-01

Studies of protein evolution have focused on amino acid substitutions with much less systematic analysis on insertion and deletions (indels) in protein coding genes. We hence surveyed 7,500 genes between Drosophila melanogaster and D. simulans, using D. yakuba as an outgroup for this purpose. The evolutionary rate of coding indels is indeed low, at only 3% of that of nonsynonymous substitutions. As coding indels follow a geometric distribution in size and tend to fall in low-complexity regions of proteins, it is unclear whether selection or mutation underlies this low rate. To resolve the issue, we collected genomic sequences from an isogenic African line of D. melanogaster (ZS30) at a high coverage of 70× and analyzed indel polymorphism between ZS30 and the reference genome. In comparing polymorphism and divergence, we found that the divergence to polymorphism ratio (i.e., fixation index) for smaller indels (size ≤ 10 bp) is very similar to that for synonymous changes, suggesting that most of the within-species polymorphism and between-species divergence for indels are selectively neutral. Interestingly, deletions of larger sizes (size ≥ 11 bp and ≤ 30 bp) have a much higher fixation index than synonymous mutations and 44.4% of fixed middle-sized deletions are estimated to be adaptive. To our surprise, this pattern is not found for insertions. Protein indel evolution appear to be in a dynamic flux of neutrally driven expansion (insertions) together with adaptive-driven contraction (deletions), and these observations provide important insights for understanding the fitness of new mutations as well as the evolutionary driving forces for genomic evolution in Drosophila species.

Analysis of conserved noncoding DNA in Drosophila reveals similar constraints in intergenic and intronic sequences.

PubMed

Bergman, C M; Kreitman, M

2001-08-01

Comparative genomic approaches to gene and cis-regulatory prediction are based on the principle that differential DNA sequence conservation reflects variation in functional constraint. Using this principle, we analyze noncoding sequence conservation in Drosophila for 40 loci with known or suspected cis-regulatory function encompassing >100 kb of DNA. We estimate the fraction of noncoding DNA conserved in both intergenic and intronic regions and describe the length distribution of ungapped conserved noncoding blocks. On average, 22%-26% of noncoding sequences surveyed are conserved in Drosophila, with median block length approximately 19 bp. We show that point substitution in conserved noncoding blocks exhibits transition bias as well as lineage effects in base composition, and occurs more than an order of magnitude more frequently than insertion/deletion (indel) substitution. Overall, patterns of noncoding DNA structure and evolution differ remarkably little between intergenic and intronic conserved blocks, suggesting that the effects of transcription per se contribute minimally to the constraints operating on these sequences. The results of this study have implications for the development of alignment and prediction algorithms specific to noncoding DNA, as well as for models of cis-regulatory DNA sequence evolution.

Formation of a Ruthenium-Arene Complex, Cyclometallation with a Substituted Benzylamine, and Insertion of an Alkyne

ERIC Educational Resources Information Center

Chetcuti, Michael J.; Ritleng, Vincent

2007-01-01

The three step synthesis is presented to allow the functionalization of an aromatic amine by forming new C-C and C-N bonds via an intramolecular C-H activation under mild conditions. The reactions are stoichiometric and allow the students to isolate the different organometallic intermediates.

Detection of mitochondrial DNA mutations in primary breast cancer and fine-needle aspirates.

PubMed

Parrella, P; Xiao, Y; Fliss, M; Sanchez-Cespedes, M; Mazzarelli, P; Rinaldi, M; Nicol, T; Gabrielson, E; Cuomo, C; Cohen, D; Pandit, S; Spencer, M; Rabitti, C; Fazio, V M; Sidransky, D

2001-10-15

To determine the frequency and distribution of mitochondrial DNA mutations in breast cancer, 18 primary breast tumors were analyzed by direct sequencing. Twelve somatic mutations not present in matched lymphocytes and normal breast tissues were detected in 11 of the tumors screened (61%). Of these mutations, five (42%) were deletions or insertions in a homopolymeric C-stretch between nucleotides 303-315 (D310) within the D-loop. The remaining seven mutations (58%) were single-base substitutions in the coding (ND1, ND4, ND5, and cytochrome b genes) or noncoding regions (D-loop) of the mitochondrial genome. In three cases (25%), the mutations detected in coding regions led to amino acid substitutions in the protein sequence. We then screened an additional 46 primary breast tumors with a rapid PCR-based assay to identify poly-C alterations in D310, and we found seven more cancers with alterations. Using D310 mutations as clonal marker, we detected identical changes in five of five matched fine-needle aspirates and in four of four metastases-positive lymph nodes. The high frequency of D310 alterations in primary breast cancer combined with the high sensitivity of the PCR-based assays provides a new molecular tool for cancer detection.

Intralayer magnetic ordering in Ge/Mn digital alloys

NASA Astrophysics Data System (ADS)

Otrokov, M. M.; Ernst, A.; Ostanin, S.; Fischer, G.; Buczek, P.; Sandratskii, L. M.; Hergert, W.; Mertig, I.; Kuznetsov, V. M.; Chulkov, E. V.

2011-04-01

We present a first-principles investigation of the electronic properties of Ge/Mn digital alloys obtained by the insertion of Mn monolayers in the Ge host. The main attention is devoted to the study of the magnetic properties of the Mn layers for various types of ordering of the Mn atoms. Depending on the type of Mn position three different structures are considered: substitutional, interstitial, and combined substitutional-interstitial. In all three cases numerical structural relaxation of the atomic positions has been performed. We find that the intralayer exchange parameters depend strongly on the crystal structure. For the substitutional and interstitial types of structure the stable magnetic order was found to be ferromagnetic. For the mixed substitutional-interstitial structure the ferromagnetic configuration appears unstable and a complex ferrimagnetic structure forms. The spin-wave excitations are calculated within the Heisenberg model. The critical temperatures of the magnetic phase transitions are determined using Monte Carlo simulations with interatomic exchange parameters obtained for two different magnetic reference states: a ferromagnetic and a disordered local moment state.

Replication infidelity via a mismatch with Watson-Crick geometry.

PubMed

Bebenek, Katarzyna; Pedersen, Lars C; Kunkel, Thomas A

2011-02-01

In describing the DNA double helix, Watson and Crick suggested that "spontaneous mutation may be due to a base occasionally occurring in one of its less likely tautomeric forms." Indeed, among many mispairing possibilities, either tautomerization or ionization of bases might allow a DNA polymerase to insert a mismatch with correct Watson-Crick geometry. However, despite substantial progress in understanding the structural basis of error prevention during polymerization, no DNA polymerase has yet been shown to form a natural base-base mismatch with Watson-Crick-like geometry. Here we provide such evidence, in the form of a crystal structure of a human DNA polymerase λ variant poised to misinsert dGTP opposite a template T. All atoms needed for catalysis are present at the active site and in positions that overlay with those for a correct base pair. The mismatch has Watson-Crick geometry consistent with a tautomeric or ionized base pair, with the pH dependence of misinsertion consistent with the latter. The results support the original idea that a base substitution can originate from a mismatch having Watson-Crick geometry, and they suggest a common catalytic mechanism for inserting a correct and an incorrect nucleotide. A second structure indicates that after misinsertion, the now primer-terminal G • T mismatch is also poised for catalysis but in the wobble conformation seen in other studies, indicating the dynamic nature of the pathway required to create a mismatch in fully duplex DNA.

Gene replacements and insertions in rice by intron targeting using CRISPR-Cas9.

PubMed

Li, Jun; Meng, Xiangbing; Zong, Yuan; Chen, Kunling; Zhang, Huawei; Liu, Jinxing; Li, Jiayang; Gao, Caixia

2016-09-12

Sequence-specific nucleases have been exploited to create targeted gene knockouts in various plants(1), but replacing a fragment and even obtaining gene insertions at specific loci in plant genomes remain a serious challenge. Here, we report efficient intron-mediated site-specific gene replacement and insertion approaches that generate mutations using the non-homologous end joining (NHEJ) pathway using the clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) system. Using a pair of single guide RNAs (sgRNAs) targeting adjacent introns and a donor DNA template including the same pair of sgRNA sites, we achieved gene replacements in the rice endogenous gene 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) at a frequency of 2.0%. We also obtained targeted gene insertions at a frequency of 2.2% using a sgRNA targeting one intron and a donor DNA template including the same sgRNA site. Rice plants harbouring the OsEPSPS gene with the intended substitutions were glyphosate-resistant. Furthermore, the site-specific gene replacements and insertions were faithfully transmitted to the next generation. These newly developed approaches can be generally used to replace targeted gene fragments and to insert exogenous DNA sequences into specific genomic sites in rice and other plants.

Crystal structures and electronic properties for the over-lithiated and Li–Ag substituted phases of Li{sub 9}V{sub 3}(P{sub 2}O{sub 7}){sub 3}(PO{sub 4}){sub 2} insertion electrode system

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

Onoda, Masashige, E-mail: onoda.masashige.ft@u.tsukuba.ac.jp; Inagaki, Makoto; Saito, Hiroaki

2014-11-15

For the Li{sub 9}V{sub 3}(P{sub 2}O{sub 7}){sub 3}(PO{sub 4}){sub 2} insertion electrode system with a multiple-electron reaction, the over-lithiated phase Li{sub x}V{sub 3}(P{sub 2}O{sub 7}){sub 3}(PO{sub 4}){sub 2} with 99) and Li{sub 9−y}Ag{sub y}V{sub 3}(P{sub 2}O{sub 7}){sub 3}(PO{sub 4}){sub 2} (0

Synergistic Diazo-OH Insertion/Conia-Ene Cascade Catalysis for the Stereoselective Synthesis of γ-Butyrolactones and Tetrahydrofurans.

PubMed

Hunter, Arianne C; Schlitzer, Steven C; Sharma, Indrajeet

2016-11-02

A novel and highly efficient diazo-OH insertion/Conia-ene cascade reaction of readily available homopropargylic acids and alcohols with diazo carbonyl compounds is described. The cascade reaction involves a synergistic Rh/Ag/Au catalyst cocktail and proceeds instantly with a variety of substituted diazo compounds and acids/alcohols to provide functionalized γ-butyrolactones and tetrahydrofurans with complete regio- and stereoselectivity. The unprecedented rate-enhancement, complete stereoselectivity, and the enabling of new Conia-ene cyclizations suggest a concerted [4+1]-cycloaddition reaction pathway under synergistic (Rh/Ag/Au)-catalysis conditions. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Statistical Physics Approaches to RNA Editing

NASA Astrophysics Data System (ADS)

Bundschuh, Ralf

2012-02-01

The central dogma of molecular Biology states that DNA is transcribed base by base into RNA which is in turn translated into proteins. However, some organisms edit their RNA before translation by inserting, deleting, or substituting individual or short stretches of bases. In many instances the mechanisms by which an organism recognizes the positions at which to edit or by which it performs the actual editing are unknown. One model system that stands out by its very high rate of on average one out of 25 bases being edited are the Myxomycetes, a class of slime molds. In this talk we will show how the computational methods and concepts from statistical Physics can be used to analyze DNA and protein sequence data to predict editing sites in these slime molds and to guide experiments that identified previously unknown types of editing as well as the complete set of editing events in the slime mold Physarum polycephalum.

Masking as an effective quality control method for next-generation sequencing data analysis.

PubMed

Yun, Sajung; Yun, Sijung

2014-12-13

Next generation sequencing produces base calls with low quality scores that can affect the accuracy of identifying simple nucleotide variation calls, including single nucleotide polymorphisms and small insertions and deletions. Here we compare the effectiveness of two data preprocessing methods, masking and trimming, and the accuracy of simple nucleotide variation calls on whole-genome sequence data from Caenorhabditis elegans. Masking substitutes low quality base calls with 'N's (undetermined bases), whereas trimming removes low quality bases that results in a shorter read lengths. We demonstrate that masking is more effective than trimming in reducing the false-positive rate in single nucleotide polymorphism (SNP) calling. However, both of the preprocessing methods did not affect the false-negative rate in SNP calling with statistical significance compared to the data analysis without preprocessing. False-positive rate and false-negative rate for small insertions and deletions did not show differences between masking and trimming. We recommend masking over trimming as a more effective preprocessing method for next generation sequencing data analysis since masking reduces the false-positive rate in SNP calling without sacrificing the false-negative rate although trimming is more commonly used currently in the field. The perl script for masking is available at http://code.google.com/p/subn/. The sequencing data used in the study were deposited in the Sequence Read Archive (SRX450968 and SRX451773).

Replication infidelity via a mismatch with Watson–Crick geometry

PubMed Central

Bebenek, Katarzyna; Pedersen, Lars C.; Kunkel, Thomas A.

2011-01-01

In describing the DNA double helix, Watson and Crick suggested that “spontaneous mutation may be due to a base occasionally occurring in one of its less likely tautomeric forms.” Indeed, among many mispairing possibilities, either tautomerization or ionization of bases might allow a DNA polymerase to insert a mismatch with correct Watson–Crick geometry. However, despite substantial progress in understanding the structural basis of error prevention during polymerization, no DNA polymerase has yet been shown to form a natural base–base mismatch with Watson–Crick-like geometry. Here we provide such evidence, in the form of a crystal structure of a human DNA polymerase λ variant poised to misinsert dGTP opposite a template T. All atoms needed for catalysis are present at the active site and in positions that overlay with those for a correct base pair. The mismatch has Watson–Crick geometry consistent with a tautomeric or ionized base pair, with the pH dependence of misinsertion consistent with the latter. The results support the original idea that a base substitution can originate from a mismatch having Watson–Crick geometry, and they suggest a common catalytic mechanism for inserting a correct and an incorrect nucleotide. A second structure indicates that after misinsertion, the now primer-terminal G•T mismatch is also poised for catalysis but in the wobble conformation seen in other studies, indicating the dynamic nature of the pathway required to create a mismatch in fully duplex DNA. PMID:21233421

Spectra of spontaneous frameshift mutations at the hisD3052 allele of Salmonella typhimurium in four DNA repair backgrounds.

PubMed Central

DeMarini, D M; Shelton, M L; Abu-Shakra, A; Szakmary, A; Levine, J G

1998-01-01

To characterize the hisD3052 -1 frameshift allele of Salmonella typhimurium, we analyzed approximately 6000 spontaneous revertants (rev) for a 2-base deletion hotspot within the sequence (CG)4, and we sequenced approximately 500 nonhotspot rev. The reversion target is a minimum of 76 bases (nucleotides 843-918) that code for amino acids within a nonconserved region of the histidinol dehydrogenase protein. Only 0.4-3.9% were true rev. Of the following classes, 182 unique second-site mutations were identified: hotspot, complex frameshifts requiring DeltauvrB + pKM101 (TA98-specific) or not (concerted), 1-base insertions, duplications, and nonhotspot deletions. The percentages of hotspot mutations were 13.8% in TA1978 (wild type), 24.5% in UTH8413 (pKM101), 31.6% in TA1538 (DeltauvrB), and 41.0% in TA98 (DeltauvrB, pKM101). The DeltauvrB allele decreased by three times the mutant frequency (MF, rev/10(8) survivors) of duplications and increased by about two times the MF of deletions. Separately, the DeltauvrB allele or pKM101 plasmid increased by two to three times the MF of hotspot mutations; combined, they increased this MF by five times. The percentage of 1-base insertions was not influenced by either DeltauvrB or pKM101. Hotspot deletions and TA98-specific complex frameshifts are inducible by some mutagens; concerted complex frameshifts and 1-base insertions are not; and there is little evidence for mutagen-induced duplications and nonhotspot deletions. Except for the base substitutions in TA98-specific complex frameshifts, all spontaneous mutations of the hisD3052 allele are likely templated. The mechanisms may involve (1) the potential of direct and inverted repeats to undergo slippage and misalignment and to form quasi-palindromes and (2) the interaction of these sequences with DNA replication and repair proteins. PMID:9584083

Time-resolved fluorescent properties of 8-vinyl-deoxyadenosine and 2-amino-deoxyribosylpurine exhibit different sensitivity to their opposite base in duplexes.

PubMed

Kenfack, Cyril A; Piémont, Etienne; Ben Gaied, Nouha; Burger, Alain; Mély, Yves

2008-08-14

8-Vinyl-deoxyadenosine (8VA) has been recently introduced as a fluorescent analogue of adenosine that is less perturbing and less quenched than the well-established 2-amino-deoxyribosylpurine (2AP) probe when inserted in oligonucleotides. To further validate 8VA as a fluorescent substitute of A, we compared the ability of 8VA and 2AP in sequences of the type d(CGT TTT XNX TTT TGC) (with N=8VA or 2AP and X=T and C) to discriminate the nature of the opposite base (Y) in duplexes. For both probes, systematic variations in the amplitudes of the short- and long-lived lifetimes of the fluorescence intensity decays as well as in the amplitude of the fast rotational correlation time of the fluorescence anisotropy decays were observed as a function of the nature of Y. From these parameters, we inferred a stability order 8VA-T > 8VA-G > 8VA-A > 8VA-C, similar to the stability order with the native A base, but different from the stability order with 2AP. Using a combination of molecular mechanics and ab initio calculations, we found that the time-resolved parameters of 8VA, but not the 2AP ones, correlate well with the geometry and the strength of the A-Y base-pairing interaction. This may be rationalized by the smaller structural and electronic perturbations induced by the vinyl group in position 8 as compared to the amino group at position 2. As a consequence, substitution of A by 8VA in a base pair was found to only minimally modify the structure and interaction energy of the base pair. Thus, 8VA can be used as a fluorescent substitute of the natural A, to straightforwardly discriminate the nature of the opposite base. This may find interesting applications notably in the elucidation of the mechanisms and dynamics of the DNA mismatch repair system.

Probing the role of helix α1 in the acid-tolerance and thermal stability of the Streptomyces sp. SK Glucose Isomerase by site-directed mutagenesis.

PubMed

Hajer, Ben Hlima; Dorra, Zouari Ayadi; Monia, Mezghani; Samir, Bejar; Nushin, Aghajari

2014-03-10

In order to investigate the role of helix α1 in the different biochemical properties between class I and class II Glucose Isomerases, a histidine and a phenylalanine residue were inserted at position 17 and 19 of Streptomyces sp. SK Glucose Isomerase (SKGI). In addition, W16 was substituted by a histidine. The H17/F19 insertion displaced the optimal pH of SKGI from 6.5 to 7-8 and slightly decreased the thermostability. As for the W16H mutant, a shift in optimal pH of SKGI from 6.5 to 6 was observed along with a decrease in the enzyme thermostability at 85°C with a half-life time reduced twice compared to the wild-type enzyme. Three-dimensional structure analysis suggested that the insertion of a histidine at position 17 results in the formation of new hydrogen bond with D287, thereby preventing it from deprotonating the O2 hydroxyl of the sugar at low pH, while the substitution W16H induced opposite effect by preventing hydrogen bond formation between D287 and W16 and thereby probably facilitating the hydrogen transfer during the isomerization reaction. The findings highlight the essential role of helix α1, which bears the three introduced mutations, in the acid-tolerance and the thermostability of SKGI and of glucose isomerases in general. Copyright © 2014 Elsevier B.V. All rights reserved.

Precision-engineering the Pseudomonas aeruginosa genome with two-step allelic exchange

PubMed Central

Hmelo, Laura R.; Borlee, Bradley R.; Almblad, Henrik; Love, Michelle E.; Randall, Trevor E.; Tseng, Boo Shan; Lin, Chuyang; Irie, Yasuhiko; Storek, Kelly M.; Yang, Jaeun Jane; Siehnel, Richard J.; Howell, P. Lynne; Singh, Pradeep K.; Tolker-Nielsen, Tim; Parsek, Matthew R.; Schweizer, Herbert P.; Harrison, Joe J.

2016-01-01

Allelic exchange is an efficient method of bacterial genome engineering. This protocol describes the use of this technique to make gene knockouts and knockins, as well as single nucleotide insertions, deletions and substitutions in Pseudomonas aeruginosa. Unlike other approaches to allelic exchange, this protocol does not require heterologous recombinases to insert or excise selective markers from the target chromosome. Rather, positive and negative selection are enabled solely by suicide vector-encoded functions and host cell proteins. Here, mutant alleles, which are flanked by regions of homology to the recipient chromosome, are synthesized in vitro and then cloned into allelic exchange vectors using standard procedures. These suicide vectors are then introduced into recipient cells by conjugation. Homologous recombination then results in antibiotic resistant single-crossover mutants in which the plasmid has integrated site-specifically into the chromosome. Subsequently, unmarked double-crossover mutants are isolated directly using sucrose-mediated counter-selection. This two-step process yields seamless mutations that are precise to a single base pair of DNA. The entire procedure requires ~2 weeks. PMID:26492139

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

"rsed" is an R package that contains tools for stream editing: manipulating text files by making insertions, replacements, deletions, substitutions, or commenting. It hails from the powerful Unix command, "sed". While the "rsed" package is not nearly as powerful as "see", it is much simpler to use. R programmers often write scripts that may require simple manipulation of text files. "rsed" addresses that need.

Equivalent Indels – Ambiguous Functional Classes and Redundancy in Databases

PubMed Central

Assmus, Jens; Kleffe, Jürgen; Schmitt, Armin O.; Brockmann, Gudrun A.

2013-01-01

There is considerable interest in studying sequenced variations. However, while the positions of substitutions are uniquely identifiable by sequence alignment, the location of insertions and deletions still poses problems. Each insertion and deletion causes a change of sequence. Yet, due to low complexity or repetitive sequence structures, the same indel can sometimes be annotated in different ways. Two indels which differ in allele sequence and position can be one and the same, i.e. the alternative sequence of the whole chromosome is identical in both cases and, therefore, the two deletions are biologically equivalent. In such a case, it is impossible to identify the exact position of an indel merely based on sequence alignment. Thus, variation entries in a mutation database are not necessarily uniquely defined. We prove the existence of a contiguous region around an indel in which all deletions of the same length are biologically identical. Databases often show only one of several possible locations for a given variation. Furthermore, different data base entries can represent equivalent variation events. We identified 1,045,590 such problematic entries of insertions and deletions out of 5,860,408 indel entries in the current human database of Ensembl. Equivalent indels are found in sequence regions of different functions like exons, introns or 5' and 3' UTRs. One and the same variation can be assigned to several different functional classifications of which only one is correct. We implemented an algorithm that determines for each indel database entry its complete set of equivalent indels which is uniquely characterized by the indel itself and a given interval of the reference sequence. PMID:23658777

An insight into the dopant selection for CeO2-based resistive-switching memory system: a DFT and experimental study

NASA Astrophysics Data System (ADS)

Hussain, Fayyaz; Imran, Muhammad; Rana, Anwar Manzoor; Khalil, R. M. Arif; Khera, Ejaz Ahmad; Kiran, Saira; Javid, M. Arshad; Sattar, M. Atif; Ismail, Muhammad

2018-03-01

The aim of this study is to figure out better metal dopants for CeO2 for designing highly efficient non-volatile memory (NVM) devices. The present DFT work involves four different metals doped interstitially and substitutionally in CeO2 thin films. First principle calculations involve electron density of states (DOS) and partial density of states (PDOS), and isosurface charge densities are carried out within the plane-wave density functional theory using GGA and GGA + U approach by employing the Vienna ab initio simulation package VASP. Isosurface charge density plots confirmed that interstitial doping of Zr and Ti metals truly assists in generating conduction filaments (CFs), while substitutional doping of these metals cannot do so. Substitutional doping of W may contribute in generating CFs in CeO2 directly, but its interstitial doping improves conductivity of CeO2. However, Ni-dopant is capable of directly generating CFs both as substitutional and interstitial dopants in ceria. Such a capability of Ni appears acting as top electrode in Ni/CeO2/Pt memory devices, but its RS behavior is not so good. On inserting Zr layer to make Ni/Zr:CeO2/Pt memory stacks, Ni does not contribute in RS characteristics, but Zr plays a vital role in forming CFs by creating oxygen vacancies and forming ZrO2 interfacial layer. Therefore, Zr-doped devices exhibit high-resistance ratio of 104 and good endurance as compared to undoped devices suitable for RRAM applications.

3-methyl-2-phenyl-1-substituted-indole derivatives as indomethacin analogs: design, synthesis and biological evaluation as potential anti-inflammatory and analgesic agents.

PubMed

Abdellatif, Khaled R A; Lamie, Phoebe F; Omar, Hany A

2016-01-01

In a new group of 3-methyl-2-phenyl-1-substituted-indole derivatives (10a-f), the indomethacin analogs were prepared via the Fisher indole synthesis reaction of propiophenone with appropriately substituted phenylhydrazine hydrochloride. This is followed by the insertion of the appropriate benzyl or benzoyl fragment. All the synthesized compounds were evaluated for their anti-inflammatory (in vitro and in vivo) and analgesic activities. The methanesulphonyl derivatives 10d, e and f showed the highest anti-inflammatory (in vitro and in vivo) and analgesic activities. In addition, molecular docking studies were performed on compounds 10a-f and the results were in agreement with that obtained from the in vitro COX inhibition assays. The significant anti-inflammatory and analgesic activities exhibited by 10d and 10e warrant continued preclinical development as potential anti-inflammatory and analgesic agents.

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.

Characterization of highly efficient heavy-ion mutagenesis in Arabidopsis thaliana.

PubMed

Kazama, Yusuke; Hirano, Tomonari; Saito, Hiroyuki; Liu, Yang; Ohbu, Sumie; Hayashi, Yoriko; Abe, Tomoko

2011-11-15

Heavy-ion mutagenesis is recognised as a powerful technology to generate new mutants, especially in higher plants. Heavy-ion beams show high linear energy transfer (LET) and thus more effectively induce DNA double-strand breaks than other mutagenic techniques. Previously, we determined the most effective heavy-ion LET (LETmax: 30.0 keV μm(-1)) for Arabidopsis mutagenesis by analysing the effect of LET on mutation induction. However, the molecular structure of mutated DNA induced by heavy ions with LETmax remains unclear. Knowledge of the structure of mutated DNA will contribute to the effective exploitation of heavy-ion beam mutagenesis. Dry Arabidopsis thaliana seeds were irradiated with carbon (C) ions with LETmax at a dose of 400 Gy and with LET of 22.5 keV μm(-1) at doses of 250 Gy or 450 Gy. The effects on mutation frequency and alteration of DNA structure were compared. To characterise the structure of mutated DNA, we screened the well-characterised mutants elongated hypocotyls (hy) and glabrous (gl) and identified mutated DNA among the resulting mutants by high-resolution melting curve, PCR and sequencing analyses. The mutation frequency induced by C ions with LETmax was two-fold higher than that with 22.5 keV μm(-1) and similar to the mutation frequency previously induced by ethyl methane sulfonate. We identified the structure of 22 mutated DNAs. Over 80% of the mutations caused by C ions with both LETs were base substitutions or deletions/insertions of less than 100 bp. The other mutations involved large rearrangements. The C ions with LETmax showed high mutation efficiency and predominantly induced base substitutions or small deletions/insertions, most of which were null mutations. These small alterations can be determined by single-nucleotide polymorphism (SNP) detection systems. Therefore, C ions with LETmax might be useful as a highly efficient reverse genetic system in conjunction with SNP detection systems, and will be beneficial for forward genetics and plant breeding.

Complete Genome Sequence of ER2796, a DNA Methyltransferase-Deficient Strain of Escherichia coli K-12.

PubMed

Anton, Brian P; Mongodin, Emmanuel F; Agrawal, Sonia; Fomenkov, Alexey; Byrd, Devon R; Roberts, Richard J; Raleigh, Elisabeth A

2015-01-01

We report the complete sequence of ER2796, a laboratory strain of Escherichia coli K-12 that is completely defective in DNA methylation. Because of its lack of any native methylation, it is extremely useful as a host into which heterologous DNA methyltransferase genes can be cloned and the recognition sequences of their products deduced by Pacific Biosciences Single-Molecule Real Time (SMRT) sequencing. The genome was itself sequenced from a long-insert library using the SMRT platform, resulting in a single closed contig devoid of methylated bases. Comparison with K-12 MG1655, the first E. coli K-12 strain to be sequenced, shows an essentially co-linear relationship with no major rearrangements despite many generations of laboratory manipulation. The comparison revealed a total of 41 insertions and deletions, and 228 single base pair substitutions. In addition, the long-read approach facilitated the surprising discovery of four gene conversion events, three involving rRNA operons and one between two cryptic prophages. Such events thus contribute both to genomic homogenization and to bacteriophage diversification. As one of relatively few laboratory strains of E. coli to be sequenced, the genome also reveals the sequence changes underlying a number of classical mutant alleles including those affecting the various native DNA methylation systems.

Complete Genome Sequence of ER2796, a DNA Methyltransferase-Deficient Strain of Escherichia coli K-12

PubMed Central

Anton, Brian P.; Mongodin, Emmanuel F.; Agrawal, Sonia; Fomenkov, Alexey; Byrd, Devon R.; Roberts, Richard J.; Raleigh, Elisabeth A.

2015-01-01

We report the complete sequence of ER2796, a laboratory strain of Escherichia coli K-12 that is completely defective in DNA methylation. Because of its lack of any native methylation, it is extremely useful as a host into which heterologous DNA methyltransferase genes can be cloned and the recognition sequences of their products deduced by Pacific Biosciences Single-Molecule Real Time (SMRT) sequencing. The genome was itself sequenced from a long-insert library using the SMRT platform, resulting in a single closed contig devoid of methylated bases. Comparison with K-12 MG1655, the first E. coli K-12 strain to be sequenced, shows an essentially co-linear relationship with no major rearrangements despite many generations of laboratory manipulation. The comparison revealed a total of 41 insertions and deletions, and 228 single base pair substitutions. In addition, the long-read approach facilitated the surprising discovery of four gene conversion events, three involving rRNA operons and one between two cryptic prophages. Such events thus contribute both to genomic homogenization and to bacteriophage diversification. As one of relatively few laboratory strains of E. coli to be sequenced, the genome also reveals the sequence changes underlying a number of classical mutant alleles including those affecting the various native DNA methylation systems. PMID:26010885

Entropy Beacon: A Hairpin-Free DNA Amplification Strategy for Efficient Detection of Nucleic Acids

PubMed Central

2015-01-01

Here, we propose an efficient strategy for enzyme- and hairpin-free nucleic acid detection called an entropy beacon (abbreviated as Ebeacon). Different from previously reported DNA hybridization/displacement-based strategies, Ebeacon is driven forward by increases in the entropy of the system, instead of free energy released from new base-pair formation. Ebeacon shows high sensitivity, with a detection limit of 5 pM target DNA in buffer and 50 pM in cellular homogenate. Ebeacon also benefits from the hairpin-free amplification strategy and zero-background, excellent thermostability from 20 °C to 50 °C, as well as good resistance to complex environments. In particular, based on the huge difference between the breathing rate of a single base pair and two adjacent base pairs, Ebeacon also shows high selectivity toward base mutations, such as substitution, insertion, and deletion and, therefore, is an efficient nucleic acid detection method, comparable to most reported enzyme-free strategies. PMID:26505212

V-doped SnS2: a new intermediate band material for a better use of the solar spectrum.

PubMed

Wahnón, Perla; Conesa, José C; Palacios, Pablo; Lucena, Raquel; Aguilera, Irene; Seminovski, Yohanna; Fresno, Fernando

2011-12-07

Intermediate band materials can boost photovoltaic efficiency through an increase in photocurrent without photovoltage degradation thanks to the use of two sub-bandgap photons to achieve a full electronic transition from the valence band to the conduction band of a semiconductor structure. After having reported in previous works several transition metal-substituted semiconductors as able to achieve the electronic structure needed for this scheme, we propose at present carrying out this substitution in sulfides that have bandgaps of around 2.0 eV and containing octahedrally coordinated cations such as In or Sn. Specifically, the electronic structure of layered SnS(2) with Sn partially substituted by vanadium is examined here with first principles quantum methods and seen to give favourable characteristics in this respect. The synthesis of this material in nanocrystalline powder form is then undertaken and achieved using solvothermal chemical methods. The insertion of vanadium in SnS(2) is found to produce an absorption spectrum in the UV-Vis-NIR range that displays a new sub-bandgap feature in agreement with the quantum calculations. A photocatalytic reaction-based test verifies that this sub-bandgap absorption produces highly mobile electrons and holes in the material that may be used for the solar energy conversion, giving experimental support to the quantum calculations predictions.

Rh(II)-catalyzed reactions of differentially substituted bis(diazo) functionalities.

PubMed

Bonderoff, Sara A; Padwa, Albert

2013-08-16

The chemoselective reaction of donor/acceptor (D/A) and acceptor/acceptor (A/A) diazo moieties in the same molecule was examined using 3-diazo-1-(ethyl 2-diazomalonyl)indolin-2-one under rhodium(II) catalysis. The D/A diazo group undergoes selective cyclopropanation as well as XH-insertion, leaving behind the second diazo group for a further intramolecular dipolar cycloaddition reaction.

Rh(I)–Bisphosphine-Catalyzed Asymmetric, Intermolecular Hydroheteroarylation of α-Substituted Acrylate Derivatives

PubMed Central

2015-01-01

Asymmetric hydroheteroarylation of alkenes represents a convenient entry to elaborated heterocyclic motifs. While chiral acids are known to mediate asymmetric addition of electron-rich heteroarenes to Michael acceptors, very few methods exploit transition metals to catalyze alkylation of heterocycles with olefins via a C–H activation, migratory insertion sequence. Herein, we describe the development of an asymmetric, intermolecular hydroheteroarylation reaction of α-substituted acrylates with benzoxazoles. The reaction provides 2-substitued benzoxazoles in moderate to excellent yields and good to excellent enantioselectivities. Notably, a series of mechanistic studies appears to contradict a pathway involving enantioselective protonation of a Rh(I)–enolate, despite the fact that such a mechanism is invoked almost unanimously in the related addition of aryl boronic acids to methacrylate derivatives. Evidence suggests instead that migratory insertion or beta-hydride elimination is enantiodetermining and that isomerization of a Rh(I)–enolate to a Rh(I)–heterobenzyl species insulates the resultant α-stereocenter from epimerization. A bulky ligand, CTH-(R)-Xylyl-P-Phos, is crucial for reactivity and enantioselectivity, as it likely discourages undesired ligation of benzoxazole substrates or intermediates to on- or off-cycle rhodium complexes and attenuates coordination-promoted product epimerization. PMID:25545834

Method to optimize optical switch topology for photonic network-on-chip

NASA Astrophysics Data System (ADS)

Zhou, Ting; Jia, Hao

2018-04-01

In this paper, we propose a method to optimize the optical switch by substituting optical waveguide crossings for optical switching units and an optimizing algorithm to complete the optimization automatically. The functionality of the optical switch remains constant under optimization. With this method, we simplify the topology of optical switch, which means the insertion loss and power consumption of the whole optical switch can be effectively minimized. Simulation result shows that the number of switching units of the optical switch based on Spanke-Benes can be reduced by 16.7%, 20%, 20%, 19% and 17.9% for the scale from 4 × 4 to 8 × 8 respectively. As a proof of concept, the experimental demonstration of an optimized six-port optical switch based on Spanke-Benes structure by means of silicon photonics chip is reported.

Scope and mechanism in palladium-catalyzed isomerizations of highly substituted allylic, homoallylic, and alkenyl alcohols.

PubMed

Larionov, Evgeny; Lin, Luqing; Guénée, Laure; Mazet, Clément

2014-12-03

Herein we report the palladium-catalyzed isomerization of highly substituted allylic alcohols and alkenyl alcohols by means of a single catalytic system. The operationally simple reaction protocol is applicable to a broad range of substrates and displays a wide functional group tolerance, and the products are usually isolated in high chemical yield. Experimental and computational mechanistic investigations provide complementary and converging evidence for a chain-walking process consisting of repeated migratory insertion/β-H elimination sequences. Interestingly, the catalyst does not dissociate from the substrate in the isomerization of allylic alcohols, whereas it disengages during the isomerization of alkenyl alcohols when additional substituents are present on the alkyl chain.

Mutational effects of γ-rays and carbon ion beams on Arabidopsis seedlings

PubMed Central

Yoshihara, Ryouhei; Nozawa, Shigeki; Hase, Yoshihiro; Narumi, Issay; Hidema, Jun; Sakamoto, Ayako N.

2013-01-01

To assess the mutational effects of radiation on vigorously proliferating plant tissue, the mutation spectrum was analyzed with Arabidopsis seedlings using the plasmid-rescue method. Transgenic plants containing the Escherichia coli rpsL gene were irradiated with γ-rays and carbon ion beams (320-MeV 12C6+), and mutations in the rpsL gene were analyzed. Mutant frequency increased significantly following irradiation by γ-rays, but not by 320-MeV 12C6+. Mutation spectra showed that both radiations increased the frequency of frameshifts and other mutations, including deletions and insertions, but only γ-rays increased the frequency of total base substitutions. These results suggest that the type of DNA lesions which cause base substitutions were less often induced by 320-MeV 12C6+ than by γ-rays in Arabidopsis seedlings. Furthermore, γ-rays never increased the frequencies of G:C to T:A or A:T to C:G transversions, which are caused by oxidized guanine; 320-MeV 12C6+, however, produced a slight increase in both transversions. Instead, γ-rays produced a significant increase in the frequency of G:C to A:T transitions. These results suggest that 8-oxoguanine has little effect on mutagenesis in Arabidopsis cells. PMID:23728320

Ester versus polyketone formation in the palladium-diphosphine catalyzed carbonylation of ethene.

PubMed

Zuidema, Erik; Bo, Carles; van Leeuwen, Piet W N M

2007-04-04

The origin of the chemoselectivity of palladium catalysts containing bidentate phosphine ligands toward either methoxycarbonylation of ethene or the copolymerization of ethene and carbon monoxide was investigated using density functional theory based calculations. For a palladium catalyst containing the electron-donating bis(dimethylphosphino)ethane (dmpe) ligand, the rate determining step for chain propagation is shown to be the insertion of ethene into the metal-acyl bond. The high barrier for chain propagation is attributed to the low stability of the ethene intermediate, (dmpe)Pd(ethene)(C(O)CH3). For the competing methanolysis process, the most likely pathway involves the formation of (dmpe)Pd(CH3OH)(C(O)CH3) via dissociative ligand exchange, followed by a solvent mediated proton-transfer/reductive- elimination process. The overall barrier for this process is higher than the barrier for ethene insertion into the palladium-acetyl bond, in line with the experimentally observed preference of this type of catalyst toward the formation of polyketone. Electronic bite angle effects on the rates of ethene insertion and ethanoyl methanolysis were evaluated using four electronically and sterically related ligands (Me)2P(CH2)nP(Me)2 (n = 1-4). Steric effects were studied for larger tert-butyl substituted ligands using a QM/MM methodology. The results show that ethene coordination to the metal center and subsequent insertion into the palladium-ethanoyl bond are disfavored by the addition of steric bulk around the metal center. Key intermediates in the methanolysis mechanism, on the other hand, are stabilized because of electronic effects caused by increasing the bite angle of the diphosphine ligand. The combined effects explain successfully which ligands give polymer and which ones give methyl propionate as the major products of the reaction.

Genome Editing in Escherichia coli with Cas9 and synthetic CRISPRs

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

Peng, Ze; Richardson, Sarah; Robinson, David

Recently, the Cas9-CRISPR system has proven to be a useful tool for genome editing in eukaryotes, which repair the double stranded breaks made by Cas9 with non-homologous end joining or homologous recombination. Escherichia coli lacks non-homologous end joining and has a very low homologous recombination rate, effectively rendering targeted Cas9 activity lethal. We have developed a heat curable, serializable, plasmid based system for selectionless Cas9 editing in arbitrary E. coli strains that uses synthetic CRISPRs for targeting and -red to effect repairs of double stranded breaks. We have demonstrated insertions, substitutions, and multi-target deletions with our system, which we havemore » tested in several strains.« less

Robust one-Tube Ω-PCR Strategy Accelerates Precise Sequence Modification of Plasmids for Functional Genomics

PubMed Central

Chen, Letian; Wang, Fengpin; Wang, Xiaoyu; Liu, Yao-Guang

2013-01-01

Functional genomics requires vector construction for protein expression and functional characterization of target genes; therefore, a simple, flexible and low-cost molecular manipulation strategy will be highly advantageous for genomics approaches. Here, we describe a Ω-PCR strategy that enables multiple types of sequence modification, including precise insertion, deletion and substitution, in any position of a circular plasmid. Ω-PCR is based on an overlap extension site-directed mutagenesis technique, and is named for its characteristic Ω-shaped secondary structure during PCR. Ω-PCR can be performed either in two steps, or in one tube in combination with exonuclease I treatment. These strategies have wide applications for protein engineering, gene function analysis and in vitro gene splicing. PMID:23335613

Engineered, axially-vascularized osteogenic grafts from human adipose-derived cells to treat avascular necrosis of bone in a rat model.

PubMed

Ismail, Tarek; Osinga, Rik; Todorov, Atanas; Haumer, Alexander; Tchang, Laurent A; Epple, Christian; Allafi, Nima; Menzi, Nadia; Largo, René D; Kaempfen, Alexandre; Martin, Ivan; Schaefer, Dirk J; Scherberich, Arnaud

2017-11-01

Avascular necrosis of bone (AVN) leads to sclerosis and collapse of bone and joints. The standard of care, vascularized bone grafts, is limited by donor site morbidity and restricted availability. The aim of this study was to generate and test engineered, axially vascularized SVF cells-based bone substitutes in a rat model of AVN. SVF cells were isolated from lipoaspirates and cultured onto porous hydroxyapatite scaffolds within a perfusion-based bioreactor system for 5days. The resulting constructs were inserted into devitalized bone cylinders mimicking AVN-affected bone. A ligated vascular bundle was inserted upon subcutaneous implantation of constructs in nude rats. After 1 and 8weeks in vivo, bone formation and vascularization were analyzed. Newly-formed bone was found in 80% of SVF-seeded scaffolds after 8weeks but not in unseeded controls. Human ALU+cells in the bone structures evidenced a direct contribution of SVF cells to bone formation. A higher density of regenerative, M2 macrophages was observed in SVF-seeded constructs. In both experimental groups, devitalized bone was revitalized by vascularized tissue after 8 weeks. SVF cells-based osteogenic constructs revitalized fully necrotic bone in a challenging AVN rat model of clinically-relevant size. SVF cells contributed to accelerated initial vascularization, to bone formation and to recruitment of pro-regenerative endogenous cells. Avascular necrosis (AVN) of bone often requires surgical treatment with autologous bone grafts, which is surgically demanding and restricted by significant donor site morbidity and limited availability. This paper describes a de novo engineered axially-vascularized bone graft substitute and tests the potential to revitalize dead bone and provide efficient new bone formation in a rat model. The engineering of an osteogenic/vasculogenic construct of clinically-relevant size with stromal vascular fraction of human adipose, combined to an arteriovenous bundle is described. This construct revitalized and generated new bone tissue. This successful approach proposes a novel paradigm in the treatment of AVN, in which an engineered, vascularized osteogenic graft would be used as a germ to revitalize large volumes of necrotic bone. Copyright © 2017 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Reconstitution of wild type viral DNA in simian cells transfected with early and late SV40 defective genomes.

PubMed

O'Neill, F J; Gao, Y; Xu, X

1993-11-01

The DNAs of polyomaviruses ordinarily exist as a single circular molecule of approximately 5000 base pairs. Variants of SV40, BKV and JCV have been described which contain two complementing defective DNA molecules. These defectives, which form a bipartite genome structure, contain either the viral early region or the late region. The defectives have the unique property of being able to tolerate variable sized reiterations of regulatory and terminus region sequences, and portions of the coding region. They can also exchange coding region sequences with other polyomaviruses. It has been suggested that the bipartite genome structure might be a stage in the evolution of polyomaviruses which can uniquely sustain genome and sequence diversity. However, it is not known if the regulatory and terminus region sequences are highly mutable. Also, it is not known if the bipartite genome structure is reversible and what the conditions might be which would favor restoration of the monomolecular genome structure. We addressed the first question by sequencing the reiterated regulatory and terminus regions of E- and L-SV40 DNAs. This revealed a large number of mutations in the regulatory regions of the defective genomes, including deletions, insertions, rearrangements and base substitutions. We also detected insertions and base substitutions in the T-antigen gene. We addressed the second question by introducing into permissive simian cells, E- and L-SV40 genomes which had been engineered to contain only a single regulatory region. Analysis of viral DNA from transfected cells demonstrated recombined genomes containing a wild type monomolecular DNA structure. However, the complete defectives, containing reiterated regulatory regions, could often compete away the wild type genomes. The recombinant monomolecular genomes were isolated, cloned and found to be infectious. All of the DNA alterations identified in one of the regulatory regions of E-SV40 DNA were present in the recombinant monomolecular genomes. These and other findings indicate that the bipartite genome state can sustain many mutations which wtSV40 cannot directly sustain. However, the mutations can later be introduced into the wild type genomes when the E- and L-SV40 DNAs recombine to generate a new monomolecular genome structure.

Design and testing of microfabricated surgical tools for large animal probe insertion

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

Jorgensen, Shelly

Neural probes provide therapeutic stimulation for neuropsychiatric disorders or record neural activity to investigate the workings of the brain. Researchers utilize 6 mm long temporary silicon stiffeners attached with biodissolvable adhesive to insert flexible neural probes into rat brains, but increasing the probe length fivefold makes inserting large animal probes a significant challenge because of an increased potential for buckling. This study compared the insertion success rates of 6 mm and 30 mm long silicon stiffeners that were 80 μm wide and 30 μm thick, and ascertained the material thickness and modulus of elasticity that would provide successful insertion formore » a 30 mm probe. Using a microdrive, stiffeners were inserted into an agarose brain phantom at controlled insertion speeds while being video-recorded. Twenty-five percent of the 30 mm silicon stiffeners fully inserted at speeds approximately four times higher than the target rate of 0.13 mm/s, while 100 percent of the 6 mm silicon stiffeners inserted successfully at target speed. Critical buckling loads (P cr) were calculated for the 6 mm and 30 mm silicon stiffeners, and for 30 mm diamond and tungsten stiffeners, with thicknesses varying from 30-80 μm. Increasing the thickness of the material by 10 μm, 20 μm and 30 μm improved the P cr by 2.4, 4.7 and 8.2 times, respectively, independent of the material, and substituting diamond for silicon multiplied the buckling capacity by 5.0 times. Stiffeners made of silicon for large animal probe insertion are not strong enough to withstand buckling upon insertion without a significant increase in thickness. Replacing silicon with diamond and increasing the thickness of the stiffener to 50 μm would afford a stiffener with the same P cr capacity as the 6 mm silicon stiffener that had a 100 percent insertion success rate. Experiments should continue with diamond to determine a minimum thickness that will ensure successful insertions and provide an adequate margin of safety.« less

A novel forward projection-based metal artifact reduction method for flat-detector computed tomography.

PubMed

Prell, Daniel; Kyriakou, Yiannis; Beister, Marcel; Kalender, Willi A

2009-11-07

Metallic implants generate streak-like artifacts in flat-detector computed tomography (FD-CT) reconstructed volumetric images. This study presents a novel method for reducing these disturbing artifacts by inserting discarded information into the original rawdata using a three-step correction procedure and working directly with each detector element. Computation times are minimized by completely implementing the correction process on graphics processing units (GPUs). First, the original volume is corrected using a three-dimensional interpolation scheme in the rawdata domain, followed by a second reconstruction. This metal artifact-reduced volume is then segmented into three materials, i.e. air, soft-tissue and bone, using a threshold-based algorithm. Subsequently, a forward projection of the obtained tissue-class model substitutes the missing or corrupted attenuation values directly for each flat detector element that contains attenuation values corresponding to metal parts, followed by a final reconstruction. Experiments using tissue-equivalent phantoms showed a significant reduction of metal artifacts (deviations of CT values after correction compared to measurements without metallic inserts reduced typically to below 20 HU, differences in image noise to below 5 HU) caused by the implants and no significant resolution losses even in areas close to the inserts. To cover a variety of different cases, cadaver measurements and clinical images in the knee, head and spine region were used to investigate the effectiveness and applicability of our method. A comparison to a three-dimensional interpolation correction showed that the new approach outperformed interpolation schemes. Correction times are minimized, and initial and corrected images are made available at almost the same time (12.7 s for the initial reconstruction, 46.2 s for the final corrected image compared to 114.1 s and 355.1 s on central processing units (CPUs)).

Molecular Population Genetics of the Alcohol Dehydrogenase Gene Region of DROSOPHILA MELANOGASTER

PubMed Central

Aquadro, Charles F.; Desse, Susan F.; Bland, Molly M.; Langley, Charles H.; Laurie-Ahlberg, Cathy C.

1986-01-01

Variation in the DNA restriction map of a 13-kb region of chromosome II including the alcohol dehydrogenase structural gene (Adh) was examined in Drosophila melanogaster from natural populations. Detailed analysis of 48 D. melanogaster lines representing four eastern United States populations revealed extensive DNA sequence variation due to base substitutions, insertions and deletions. Cloning of this region from several lines allowed characterization of length variation as due to unique sequence insertions or deletions [nine sizes; 21–200 base pairs (bp)] or transposable element insertions (several sizes, 340 bp to 10.2 kb, representing four different elements). Despite this extensive variation in sequences flanking the Adh gene, only one length polymorphism is clearly associated with altered Adh expression (a copia element approximately 250 bp 5' to the distal transcript start site). Nonetheless, the frequency spectra of transposable elements within and between Drosophila species suggests they are slightly deleterious. Strong nonrandom associations are observed among Adh region sequence variants, ADH allozyme (Fast vs. Slow), ADH enzyme activity and the chromosome inversion ln(2L) t. Phylogenetic analysis of restriction map haplotypes suggest that the major twofold component of ADH activity variation (high vs. low, typical of Fast and Slow allozymes, respectively) is due to sequence variation tightly linked to and possibly distinct from that underlying the allozyme difference. The patterns of nucleotide and haplotype variation for Fast and Slow allozyme lines are consistent with the recent increase in frequency and spread of the Fast haplotype associated with high ADH activity. These data emphasize the important role of evolutionary history and strong nonrandom associations among tightly linked sequence variation as determinants of the patterns of variation observed in natural populations. PMID:3026893

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

Rechkoblit, Olga; Delaney, James C.; Essigmann, John M.

DNA is susceptible to alkylation damage by a number of environmental agents that modify the Watson-Crick edge of the bases. Such lesions, if not repaired, may be bypassed by Y-family DNA polymerases. The bypass polymerase Dpo4 is strongly inhibited by 1-methylguanine (m1G) and 3-methylcytosine (m3C), with nucleotide incorporation opposite these lesions being predominantly mutagenic. Further, extension after insertion of both correct and incorrect bases, introduces additional base substitution and deletion errors. Crystal structures of the Dpo4 ternary extension complexes with correct and mismatched 3'-terminal primer bases opposite the lesions reveal that both m1G and m3C remain positioned within the DNAmore » template/primer helix. However, both correct and incorrect pairing partners exhibit pronounced primer terminal nucleotide distortion, being primarily evicted from the DNA helix when opposite m1G or misaligned when pairing with m3C. Our studies provide insights into mechanisms related to hindered and mutagenic bypass of methylated lesions and models associated with damage recognition by repair demethylases.« less

Production of Mutated Porcine Embryos Using Zinc Finger Nucleases and a Reporter-based Cell Enrichment System.

PubMed

Koo, Ok Jae; Park, Sol Ji; Lee, Choongil; Kang, Jung Taek; Kim, Sujin; Moon, Joon Ho; Choi, Ji Yei; Kim, Hyojin; Jang, Goo; Kim, Jin-Soo; Kim, Seokjoong; Lee, Byeong-Chun

2014-03-01

To facilitate the construction of genetically-modified pigs, we produced cloned embryos derived from porcine fibroblasts transfected with a pair of engineered zinc finger nuclease (ZFN) plasmids to create targeted mutations and enriched using a reporter plasmid system. The reporter expresses RFP and eGFP simultaneously when ZFN-mediated site-specific mutations occur. Thus, double positive cells (RFP(+)/eGFP(+)) were selected and used for somatic cell nuclear transfer. Two types of reporter based enrichment systems were used in this study; the cloned embryos derived from cells enriched using a magnetic sorting-based system showed better developmental competence than did those derived from cells enriched by flow cytometry. Mutated sequences, such as insertions, deletions, or substitutions, together with the wild-type sequence, were found in the cloned porcine blastocysts. Therefore, genetic mutations can be achieved in cloned porcine embryos reconstructed with ZFN-treated cells that were enriched by a reporter-based system.

Algorithm for detection of steganographic inserts type LSB-substitution on the basis of an analysis of the zero layer

NASA Astrophysics Data System (ADS)

Belim, S. V.; Vilkhovskiy, D. E.

2018-01-01

All articles must contain an abstract. The abstract text should be formatted using 10 point Times or Times New Roman and indented 25 mm from the left margin. Leave 10 mm space after the abstract before you begin the main text of your article, starting on the same page as the abstract. The abstract should give readers concise information about the content of the article and indicate the main results obtained and conclusions drawn. The abstract is not part of the text and should be complete in itself; no table numbers, figure numbers, references or displayed mathematical expressions should be included. It should be suitable for direct inclusion in abstracting services and should not normally exceed 200 words in a single paragraph. Since contemporary information-retrieval systems rely heavily on the content of titles and abstracts to identify relevant articles in literature searches, great care should be taken in constructing both. Keywords - search for LSB-inserts, analysis of steganography container, revealing of steganography inserts.

Defects in ion-implanted hcp-titanium: A first-principles study of electronic structures

NASA Astrophysics Data System (ADS)

Raji, Abdulrafiu T.; Mazzarello, Riccardo; Scandolo, Sandro; Nsengiyumva, Schadrack; Härting, Margit; Britton, David T.

2011-12-01

The electronic structures of hexagonal closed-packed (h.c.p) titanium containing a vacancy and krypton impurity atoms at various insertion sites are calculated by first-principles methods in the framework of the density-functional theory (DFT). The density of states (DOS) for titanium containing a vacancy defect shows resonance-like features. Also, the bulk electron density decreases from ˜0.15/Å 3 to ˜0.05/Å 3 at the vacancy centre. Electronic structure calculations have been performed to investigate what underlies the krypton site preference in titanium. The DOS of the nearest-neighbour (NN) titanium atoms to the octahedral krypton appears to be less distorted (relative to pure titanium) when compared to the NN titanium atoms to the tetrahedral krypton. The electronic density deformation maps show that polarization of the titanium atoms is stronger when the krypton atom is located at the tetrahedral site. Since krypton is a closed-shell atom, thus precluding any bonding with the titanium atoms, we may conclude that the polarization of the electrons in the vicinity of the inserted krypton atoms and the distortion of the DOS of the NN titanium atoms to the krypton serve to indicate which defect site is preferred when a krypton atom is inserted into titanium. Based on these considerations, we conclude that the substitutional site is the most favourable one, and the octahedral is the preferred interstitial site, in agreement with recent DFT calculations of the energetics of krypton impurity sites.

Surveyor Nuclease: a new strategy for a rapid identification of heteroplasmic mitochondrial DNA mutations in patients with respiratory chain defects.

PubMed

Bannwarth, Sylvie; Procaccio, Vincent; Paquis-Flucklinger, Veronique

2005-06-01

Molecular analysis of mitochondrial DNA (mtDNA) is a critical step in diagnosis and genetic counseling of respiratory chain defects. No fast method is currently available for the identification of unknown mtDNA point mutations. We have developed a new strategy based on complete mtDNA PCR amplification followed by digestion with a mismatch-specific DNA endonuclease, Surveyor Nuclease. This enzyme, a member of the CEL nuclease family of plant DNA endonucleases, cleaves double-strand DNA at any mismatch site including base substitutions and small insertions/deletions. After digestion, cleavage products are separated and analyzed by agarose gel electrophoresis. The size of the digestion products indicates the location of the mutation, which is then confirmed and characterized by sequencing. Although this method allows the analysis of 2 kb mtDNA amplicons and the detection of multiple mutations within the same fragment, it does not lead to the identification of homoplasmic base substitutions. Homoplasmic pathogenic mutations have been described. Nevertheless, most homoplasmic base substitutions are neutral polymorphisms while deleterious mutations are typically heteroplasmic. Here, we report that this method can be used to detect mtDNA mutations such as m.3243A>G tRNA(Leu) and m.14709T>C tRNA(Glu) even when they are present at levels as low as 3% in DNA samples derived from patients with respiratory chain defects. Then, we tested five patients suffering from a mitochondrial respiratory chain defect and we identified a variant (m.16189T>C) in two of them, which was previously associated with susceptibility to diabetes and cardiomyopathy. In conclusion, this method can be effectively used to rapidly and completely screen the entire human mitochondrial genome for heteroplasmic mutations and in this context represents an important advance for the diagnosis of mitochondrial diseases.

Supraclavicular Approach to Ultrasound-Guided Brachiocephalic Vein Cannulation in Children and Neonates

PubMed Central

Merchaoui, Zied; Lausten-Thomsen, Ulrik; Pierre, Florence; Ben Laiba, Maher; Le Saché, Nolwenn; Tissieres, Pierre

2017-01-01

The correct choice of intra vascular access in critically ill neonates should be individualized depending on the type and duration of therapy, gestational and chronological age, weight and/or size, diagnosis, clinical status, and venous system patency. Accordingly, there is an ongoing demand for optimization of catheterization. Recently, the use of ultrasound (US)-guided cannulation of the subclavian vein (SCV) has been described in children and neonates. This article gives an overview of the current use of US for achieving central venous catheter placement in the SCV or the brachiocephalic vein (BCV) in neonates. More than 1,250 catheters have been reported inserted in children and neonates for a cumulated success rate of 98.4% and the complication rate is reported to be low. The technical aspects of various approaches are discussed, and we offer our recommendation of an US-guided technique for SCV and BCV cannulation based on our experience in a large NICU setting. Although the cannulation the SCV or BCV does not substitute the use of peripherally inserted central catheters or umbilical venous central catheters in neonates, it is a feasible route in very small children who are in need of a large caliber central venous access. PMID:29051889

On Utilizing Optimal and Information Theoretic Syntactic Modeling for Peptide Classification

NASA Astrophysics Data System (ADS)

Aygün, Eser; Oommen, B. John; Cataltepe, Zehra

Syntactic methods in pattern recognition have been used extensively in bioinformatics, and in particular, in the analysis of gene and protein expressions, and in the recognition and classification of bio-sequences. These methods are almost universally distance-based. This paper concerns the use of an Optimal and Information Theoretic (OIT) probabilistic model [11] to achieve peptide classification using the information residing in their syntactic representations. The latter has traditionally been achieved using the edit distances required in the respective peptide comparisons. We advocate that one can model the differences between compared strings as a mutation model consisting of random Substitutions, Insertions and Deletions (SID) obeying the OIT model. Thus, in this paper, we show that the probability measure obtained from the OIT model can be perceived as a sequence similarity metric, using which a Support Vector Machine (SVM)-based peptide classifier, referred to as OIT_SVM, can be devised.

The topography of mutational processes in breast cancer genomes.

PubMed

Morganella, Sandro; Alexandrov, Ludmil B; Glodzik, Dominik; Zou, Xueqing; Davies, Helen; Staaf, Johan; Sieuwerts, Anieta M; Brinkman, Arie B; Martin, Sancha; Ramakrishna, Manasa; Butler, Adam; Kim, Hyung-Yong; Borg, Åke; Sotiriou, Christos; Futreal, P Andrew; Campbell, Peter J; Span, Paul N; Van Laere, Steven; Lakhani, Sunil R; Eyfjord, Jorunn E; Thompson, Alastair M; Stunnenberg, Hendrik G; van de Vijver, Marc J; Martens, John W M; Børresen-Dale, Anne-Lise; Richardson, Andrea L; Kong, Gu; Thomas, Gilles; Sale, Julian; Rada, Cristina; Stratton, Michael R; Birney, Ewan; Nik-Zainal, Serena

2016-05-02

Somatic mutations in human cancers show unevenness in genomic distribution that correlate with aspects of genome structure and function. These mutations are, however, generated by multiple mutational processes operating through the cellular lineage between the fertilized egg and the cancer cell, each composed of specific DNA damage and repair components and leaving its own characteristic mutational signature on the genome. Using somatic mutation catalogues from 560 breast cancer whole-genome sequences, here we show that each of 12 base substitution, 2 insertion/deletion (indel) and 6 rearrangement mutational signatures present in breast tissue, exhibit distinct relationships with genomic features relating to transcription, DNA replication and chromatin organization. This signature-based approach permits visualization of the genomic distribution of mutational processes associated with APOBEC enzymes, mismatch repair deficiency and homologous recombinational repair deficiency, as well as mutational processes of unknown aetiology. Furthermore, it highlights mechanistic insights including a putative replication-dependent mechanism of APOBEC-related mutagenesis.

Novel Tay-Sachs disease mutations from China.

PubMed

Akalin, N; Shi, H P; Vavougios, G; Hechtman, P; Lo, W; Scriver, C R; Mahuran, D; Kaplan, F

1992-01-01

We describe three HEXA mutations associated with infantile Tay-Sachs disease (TSD) in three unrelated nonconsanguineous Chinese families. Novel mutations were found in two of these families. The third is a previously reported mutation (G-->A transition at nt 1444) (Nakano et al., 1988). Direct sequencing of PCR products identified a novel insertion of an A after nt 547 in family 1. This change generates an early termination codon 6 bp downstream from the insertion site. Allele-specific oligonucleotide hybridization confirmed homozygosity in the proband. Single strand conformational polymorphism analysis and direct sequencing of amplified exon 13 revealed a T-->C transition at nt 1453 with the corresponding amino acid substitution W485R in the second family. This mutation creates an Fnu4HI restriction site. The proband is homozygous for this allele. When the site-specific mutagenized alpha cDNA carrying the T-->C transition at nt 1453 was expressed in COS 1 cells hexosaminidase S activity was not detectable above background. A G-->A transition at nt 1444 (exon 13) corresponding to the E482K substitution was found in the third family. This mutation occurs at a CpG dinucleotide. It has been reported in an Italian TSD proband and causes defective intracellular transport of the alpha-subunit from the rough endoplasmic reticulum to the Golgi apparatus.

Prospective short-term feasibility study of perioperative suprapubic catheters in laparoscopic colectomy.

PubMed

Nagao, Sayaka; Saida, Yoshihisa; Enomoto, Toshiyuki; Takahashi, Asako; Higuchi, Tadashi; Moriyama, Hodaka; Niituma, Toru; Watanabe, Manabu; Asai, Koji; Kusachi, Shinya

2018-05-16

Here we report a prospective study on whether a temporary suprapubic catheter (SPC) can be safely inserted as a substitute for transurethral balloon catheterization during laparoscopy-assisted colectomy. Our subjects included 52 cases who gave informed consent to have an SPC inserted. These subjects were selected from cases who underwent laparoscopy-assisted surgery for primary colorectal cancer from October 2014 to August 2015. An SPC was inserted into 45 of the original 52 cases. The median surgical duration was 220 min (range, 11-438 min), and the SPC insertion was performed at a median of 133 min (range, 9-384 min) after the start of surgery. Insertion required a median duration of 116 s. In one case (2.2%), the bladder was perforated by the paracentesis needle, and in two cases (4.4%), hematuria was observed at the time of insertion; however, surgery was completed without any incident in these three cases. Six of the remaining 42 cases (13.3%) demonstrated neither micturition desire nor independent urination on the day the catheter was clamped. In these cases, the clamp was released two to four times, and draining of an average of 586-mL urine, micturition desire, and independent urination were confirmed 2-4 days later. Transurethral balloon catheterization is a simple procedure that is commonly used on surgical patients, but it can cause pain, discomfort, and infection. In contrast, SPC insertion is a procedure that avoids crossing the urethra and its associated disadvantages. Here we were able to demonstrate that the procedure can be safely used in laparoscopic surgery patients. © 2018 Japan Society for Endoscopic Surgery, Asia Endosurgery Task Force and John Wiley & Sons Australia, Ltd.

Genomic gigantism: DNA loss is slow in mountain grasshoppers.

PubMed

Bensasson, D; Petrov, D A; Zhang, D X; Hartl, D L; Hewitt, G M

2001-02-01

Several studies have shown DNA loss to be inversely correlated with genome size in animals. These studies include a comparison between Drosophila and the cricket, Laupala, but there has been no assessment of DNA loss in insects with very large genomes. Podisma pedestris, the brown mountain grasshopper, has a genome over 100 times as large as that of Drosophila and 10 times as large as that of Laupala. We used 58 paralogous nuclear pseudogenes of mitochondrial origin to study the characteristics of insertion, deletion, and point substitution in P. pedestris and Italopodisma. In animals, these pseudogenes are "dead on arrival"; they are abundant in many different eukaryotes, and their mitochondrial origin simplifies the identification of point substitutions accumulated in nuclear pseudogene lineages. There appears to be a mononucleotide repeat within the 643-bp pseudogene sequence studied that acts as a strong hot spot for insertions or deletions (indels). Because the data for other insect species did not contain such an unusual region, hot spots were excluded from species comparisons. The rate of DNA loss relative to point substitution appears to be considerably and significantly lower in the grasshoppers studied than in Drosophila or Laupala. This suggests that the inverse correlation between genome size and the rate of DNA loss can be extended to comparisons between insects with large or gigantic genomes (i.e., Laupala and Podisma). The low rate of DNA loss implies that in grasshoppers, the accumulation of point mutations is a more potent force for obscuring ancient pseudogenes than their loss through indel accumulation, whereas the reverse is true for Drosophila. The main factor contributing to the difference in the rates of DNA loss estimated for grasshoppers, crickets, and Drosophila appears to be deletion size. Large deletions are relatively rare in Podisma and Italopodisma.

The honey insertion cladding to improve the sensitivity of temperature polymer optical fiber sensor

NASA Astrophysics Data System (ADS)

Arwani, M.; Kuswanto, H.

2018-04-01

The sensitivity of temperature polymer optical fiber (POF) sensor has been studied. Part of cladding (9 cm) was substituted with honey. Polymer cladding was stripped mechanically and the honey inserted into the tube. Plastic gel closed the two end sides of the tubes. The optical power output was detected by Optical Power Meter (OPM). Honey cladding and temperature changing effect to the internal reflection and optical fiber output intensity. Highest output intensity changing at 20°C was shown by optical fiber coated by longan honey as cladding. The range of 10-50° C, as the rise of surroundings temperature, the attenuation was getting smaller. Best sensitivity was fiber with sensing part coated by Longan honey. Best linearity was sensing fiber with sensing part coated by Pracimantoro honey.

DCJ-indel and DCJ-substitution distances with distinct operation costs

PubMed Central

2013-01-01

Background Classical approaches to compute the genomic distance are usually limited to genomes with the same content and take into consideration only rearrangements that change the organization of the genome (i.e. positions and orientation of pieces of DNA, number and type of chromosomes, etc.), such as inversions, translocations, fusions and fissions. These operations are generically represented by the double-cut and join (DCJ) operation. The distance between two genomes, in terms of number of DCJ operations, can be computed in linear time. In order to handle genomes with distinct contents, also insertions and deletions of fragments of DNA – named indels – must be allowed. More powerful than an indel is a substitution of a fragment of DNA by another fragment of DNA. Indels and substitutions are called content-modifying operations. It has been shown that both the DCJ-indel and the DCJ-substitution distances can also be computed in linear time, assuming that the same cost is assigned to any DCJ or content-modifying operation. Results In the present study we extend the DCJ-indel and the DCJ-substitution models, considering that the content-modifying cost is distinct from and upper bounded by the DCJ cost, and show that the distance in both models can still be computed in linear time. Although the triangular inequality can be disrupted in both models, we also show how to efficiently fix this problem a posteriori. PMID:23879938

A Modified Rabbit Ulna Defect Model for Evaluating Periosteal Substitutes in Bone Engineering: A Pilot Study

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

El Backly, Rania M.; IRCCS AOU San Martino–IST Istituto Nazionale per la Ricerca sul Cancro, Genova; Faculty of Dentistry, Alexandria University, Alexandria

The present work defines a modified critical size rabbit ulna defect model for bone regeneration in which a non-resorbable barrier membrane was used to separate the radius from the ulna to create a valid model for evaluation of tissue-engineered periosteal substitutes. Eight rabbits divided into two groups were used. Critical defects (15 mm) were made in the ulna completely eliminating periosteum. For group I, defects were filled with a nanohydroxyapatite poly(ester urethane) scaffold soaked in PBS and left as such (group Ia) or wrapped with a tissue-engineered periosteal substitute (group Ib). For group II, an expanded-polytetrafluoroethylene (e-PTFE) (GORE-TEX{sup ®}) membranemore » was inserted around the radius then the defects received either scaffold alone (group IIa) or scaffold wrapped with periosteal substitute (group IIb). Animals were euthanized after 12–16 weeks, and bone regeneration was evaluated by radiography, computed microtomography (μCT), and histology. In the first group, we observed formation of radio-ulnar synostosis irrespective of the treatment. This was completely eliminated upon placement of the e-PTFE (GORE-TEX{sup ®}) membrane in the second group of animals. In conclusion, modification of the model using a non-resorbable e-PTFE membrane to isolate the ulna from the radius was a valuable addition allowing for objective evaluation of the tissue-engineered periosteal substitute.« less

HIV evolution in early infection: selection pressures, patterns of insertion and deletion, and the impact of APOBEC.

PubMed

Wood, Natasha; Bhattacharya, Tanmoy; Keele, Brandon F; Giorgi, Elena; Liu, Michael; Gaschen, Brian; Daniels, Marcus; Ferrari, Guido; Haynes, Barton F; McMichael, Andrew; Shaw, George M; Hahn, Beatrice H; Korber, Bette; Seoighe, Cathal

2009-05-01

The pattern of viral diversification in newly infected individuals provides information about the host environment and immune responses typically experienced by the newly transmitted virus. For example, sites that tend to evolve rapidly across multiple early-infection patients could be involved in enabling escape from common early immune responses, could represent adaptation for rapid growth in a newly infected host, or could represent reversion from less fit forms of the virus that were selected for immune escape in previous hosts. Here we investigated the diversification of HIV-1 env coding sequences in 81 very early B subtype infections previously shown to have resulted from transmission or expansion of single viruses (n = 78) or two closely related viruses (n = 3). In these cases, the sequence of the infecting virus can be estimated accurately, enabling inference of both the direction of substitutions as well as distinction between insertion and deletion events. By integrating information across multiple acutely infected hosts, we find evidence of adaptive evolution of HIV-1 env and identify a subset of codon sites that diversified more rapidly than can be explained by a model of neutral evolution. Of 24 such rapidly diversifying sites, 14 were either i) clustered and embedded in CTL epitopes that were verified experimentally or predicted based on the individual's HLA or ii) in a nucleotide context indicative of APOBEC-mediated G-to-A substitutions, despite having excluded heavily hypermutated sequences prior to the analysis. In several cases, a rapidly evolving site was embedded both in an APOBEC motif and in a CTL epitope, suggesting that APOBEC may facilitate early immune escape. Ten rapidly diversifying sites could not be explained by CTL escape or APOBEC hypermutation, including the most frequently mutated site, in the fusion peptide of gp41. We also examined the distribution, extent, and sequence context of insertions and deletions, and we provide evidence that the length variation seen in hypervariable loop regions of the envelope glycoprotein is a consequence of selection and not of mutational hotspots. Our results provide a detailed view of the process of diversification of HIV-1 following transmission, highlighting the role of CTL escape and hypermutation in shaping viral evolution during the establishment of new infections.

HIV Evolution in Early Infection: Selection Pressures, Patterns of Insertion and Deletion, and the Impact of APOBEC

PubMed Central

Wood, Natasha; Bhattacharya, Tanmoy; Keele, Brandon F.; Giorgi, Elena; Liu, Michael; Gaschen, Brian; Daniels, Marcus; Ferrari, Guido; Haynes, Barton F.; McMichael, Andrew; Shaw, George M.; Hahn, Beatrice H.; Korber, Bette; Seoighe, Cathal

2009-01-01

The pattern of viral diversification in newly infected individuals provides information about the host environment and immune responses typically experienced by the newly transmitted virus. For example, sites that tend to evolve rapidly across multiple early-infection patients could be involved in enabling escape from common early immune responses, could represent adaptation for rapid growth in a newly infected host, or could represent reversion from less fit forms of the virus that were selected for immune escape in previous hosts. Here we investigated the diversification of HIV-1 env coding sequences in 81 very early B subtype infections previously shown to have resulted from transmission or expansion of single viruses (n = 78) or two closely related viruses (n = 3). In these cases, the sequence of the infecting virus can be estimated accurately, enabling inference of both the direction of substitutions as well as distinction between insertion and deletion events. By integrating information across multiple acutely infected hosts, we find evidence of adaptive evolution of HIV-1 env and identify a subset of codon sites that diversified more rapidly than can be explained by a model of neutral evolution. Of 24 such rapidly diversifying sites, 14 were either i) clustered and embedded in CTL epitopes that were verified experimentally or predicted based on the individual's HLA or ii) in a nucleotide context indicative of APOBEC-mediated G-to-A substitutions, despite having excluded heavily hypermutated sequences prior to the analysis. In several cases, a rapidly evolving site was embedded both in an APOBEC motif and in a CTL epitope, suggesting that APOBEC may facilitate early immune escape. Ten rapidly diversifying sites could not be explained by CTL escape or APOBEC hypermutation, including the most frequently mutated site, in the fusion peptide of gp41. We also examined the distribution, extent, and sequence context of insertions and deletions, and we provide evidence that the length variation seen in hypervariable loop regions of the envelope glycoprotein is a consequence of selection and not of mutational hotspots. Our results provide a detailed view of the process of diversification of HIV-1 following transmission, highlighting the role of CTL escape and hypermutation in shaping viral evolution during the establishment of new infections. PMID:19424423

A Coupling of Benzamides and Donor/Acceptor Diazo–Compounds to form γ-Lactams via Rh(III)–Catalyzed C–H Activation

PubMed Central

Hyster, Todd K.; Ruhl, Kyle E.; Rovis, Tomislav

2013-01-01

The coupling of O-pivaloyl benzhydroxamic acids with donor/acceptor diazo compounds provides iso-indolones in high yield. The reaction tolerates a broad range of benzhydroxamic acids and diazo compounds including substituted 2,2,2-trifluorodiazo ethanes. Mechanistic experiments suggest that C–H activation is turnover limiting and irreversible, while insertion of the diazo compound favors electron deficient substrates. PMID:23548055

Role of the 2 adenine (g.11293_11294insAA) insertion polymorphism in the 3' untranslated region of the factor VII (FVII) gene: molecular characterization of a patient with severe FVII deficiency.

PubMed

Peyvandi, F; Garagiola, I; Palla, R; Marziliano, N; Mannucci, P M

2005-11-01

Polymorphic variants in the gene encoding factor VII (F7) affect the plasma levels of this coagulation protein and modify the clinical phenotype of FVII deficiency in some patients. In this study we report the in vitro functional analysis of a novel polymorphic variant located in the 3' untranslated region of F7: g.11293_11294insAA. To determine whether this variant regulates FVII expression, we initially compared an expression vector containing FVII cDNA with g.11293_11294insAA with the FVII wild-type (WT) construct. The kinetics of mRNA production showed that the insertion decreases the steady-state FVII mRNA levels. To assess whether the insertion influences the phenotype of FVII-deficient patients, we evaluated its effect on the expression of FVII in a patient with severe FVII deficiency (undetectable FVII activity and antigen) carrying two additional homozygous missense variations (p.Arg277Cys and p.Arg353Gln). The two substitutions alone reduced the expression of FVII activity and antigen in vitro, but with the insertion polymorphism in our expression vector the patient's phenotype of undetectable plasma FVII was recapitulated. The insertion polymorphism in the 3' untranslated region of F7 is another modifier of FVII expression that might explain the poor genotype-phenotype correlation in some FVII-deficient patients. Copyright 2005 Wiley-Liss, Inc.

Does impaction of titanium-coated interbody fusion cages into the disc space cause wear debris or delamination?

PubMed

Kienle, Annette; Graf, Nicolas; Wilke, Hans-Joachim

2016-02-01

A large number of interbody fusion cages are made of polyetheretherketone (PEEK). To improve bone on-growth, some are coated with a thin layer of titanium. This coating may fail when subjected to shear loading. The purpose of this testing was to investigate whether impaction of titanium-coated PEEK cages into the disc space can result in wear or delamination of the coating, and whether titanium cages with subtractive surface etching (no coating) are less susceptible to such failure. A biomechanical study was carried out to simulate the impaction process in clinical practice and to evaluate if wear or delamination may result from impaction. Two groups of posterior lumbar interbody fusion cages with a similar geometry were tested: n=6 titanium-coated PEEK and n=6 surface-etched titanium cages. The cages were impacted into the space in between two vertebral body substitutes (polyurethane foam blocks). The two vertebral body substitutes were fixed in a device, through which a standardized axial preload of 390 N was applied. The anterior tip of the cage was positioned at the posterior border of the space between the two vertebral body substitutes. The cages were then inserted using a drop weight with a mass representative of a surgical hammer. The drop weight impacted the insertion instrument at a maximum speed of about 2.6 m/s, which is in the range of the impaction speed in vivo. This was repeated until the cages were fully inserted. The wear particles were captured and analyzed according to the pertinent standards. The surface-etched titanium cages did not show any signs of wear debris or surface damage. In contrast, the titanium-coated PEEK cages resulted in detached wear particles of different sizes (1-191 µm). Over 50% of these particles had a size <10 µm. In median, on 26% of the implants' teeth, the coating was abraded. Full delamination was not observed. In contrast to the surface-etched implants, the titanium-coated PEEK implants lost some coating material. This was visible to the naked eye. More than half of all particles were of a size range that allows phagocytosis. This study shows that titanium-coated implants are susceptible to impaction-related wear debris. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Using whole genome sequencing to identify resistance determinants and predict antimicrobial resistance phenotypes for year 2015 invasive pneumococcal disease isolates recovered in the United States.

PubMed

Metcalf, B J; Chochua, S; Gertz, R E; Li, Z; Walker, H; Tran, T; Hawkins, P A; Glennen, A; Lynfield, R; Li, Y; McGee, L; Beall, B

2016-12-01

Our whole genome sequence (WGS) pipeline was assessed for accurate prediction of antimicrobial phenotypes. For 2316 invasive pneumococcal isolates recovered during 2015 we compared WGS pipeline data to broth dilution testing (BDT) for 18 antimicrobials. For 11 antimicrobials categorical discrepancies were assigned when WGS-predicted MICs and BDT MICs predicted different categorizations for susceptibility, intermediate resistance or resistance, ranging from 0.9% (tetracycline) to 2.9% (amoxicillin). For β-lactam antibiotics, the occurrence of at least four-fold differences in MIC ranged from 0.2% (meropenem) to 1.0% (penicillin), although phenotypic retesting resolved 25%-78% of these discrepancies. Non-susceptibility to penicillin, predicted by penicillin-binding protein types, was 2.7% (non-meningitis criteria) and 23.8% (meningitis criteria). Other common resistance determinants included mef (475 isolates), ermB (191 isolates), ermB + mef (48 isolates), tetM (261 isolates) and cat (51 isolates). Additional accessory resistance genes (tetS, tet32, aphA-3, sat4) were rarely detected (one to three isolates). Rare core genome mutations conferring erythromycin-resistance included a two-codon rplD insertion (rplD69-KG-70) and the 23S rRNA A2061G substitution (six isolates). Intermediate cotrimoxazole-resistance was associated with one or two codon insertions within folP (238 isolates) or the folA I100L substitution (38 isolates), whereas full cotrimoxazole-resistance was attributed to alterations in both genes (172 isolates). The two levofloxacin-resistant isolates contained parC and/or gyrA mutations. Of 11 remaining isolates with moderately elevated MICs to both ciprofloxacin and levofloxacin, seven contained parC or gyrA mutations. The two rifampin-resistant isolates contained rpoB mutations. WGS-based antimicrobial phenotype prediction was an informative alternative to BDT for invasive pneumococci. Published by Elsevier Ltd.

On measurement of the acoustic nonlinearity parameter using the finite amplitude insertion substitution (FAIS) technique

NASA Astrophysics Data System (ADS)

Zeqiri, Bajram; Cook, Ashley; Rétat, Lise; Civale, John; ter Haar, Gail

2015-04-01

The acoustic nonlinearity parameter, B/A, is an important parameter which defines the way a propagating finite amplitude acoustic wave progressively distorts when travelling through any medium. One measurement technique used to determine its value is the finite amplitude insertion substitution (FAIS) method which has been applied to a range of liquid, tissue and tissue-like media. Importantly, in terms of the achievable measurement uncertainties, it is a relative technique. This paper presents a detailed study of the method, employing a number of novel features. The first of these is the use of a large area membrane hydrophone (30 mm aperture) which is used to record the plane-wave component of the acoustic field. This reduces the influence of diffraction on measurements, enabling studies to be carried out within the transducer near-field, with the interrogating transducer, test cell and detector positioned close to one another, an attribute which assists in controlling errors arising from nonlinear distortion in any intervening water path. The second feature is the development of a model which estimates the influence of finite-amplitude distortion as the acoustic wave travels from the rear surface of the test cell to the detector. It is demonstrated that this can lead to a significant systematic error in B/A measurement whose magnitude and direction depends on the acoustic property contrast between the test material and the water-filled equivalent cell. Good qualitative agreement between the model and experiment is reported. B/A measurements are reported undertaken at (20 ± 0.5) °C for two fluids commonly employed as reference materials within the technical literature: Corn Oil and Ethylene Glycol. Samples of an IEC standardised agar-based tissue-mimicking material were also measured. A systematic assessment of measurement uncertainties is presented giving expanded uncertainties in the range ±7% to ±14%, expressed at a confidence level close to 95%, dependent on specimen details.

Novel poly-uridine insertion in the 3'UTR and E2 amino acid substitutions in a low virulent classical swine fever virus.

PubMed

Coronado, Liani; Liniger, Matthias; Muñoz-González, Sara; Postel, Alexander; Pérez, Lester Josue; Pérez-Simó, Marta; Perera, Carmen Laura; Frías-Lepoureau, Maria Teresa; Rosell, Rosa; Grundhoff, Adam; Indenbirken, Daniela; Alawi, Malik; Fischer, Nicole; Becher, Paul; Ruggli, Nicolas; Ganges, Llilianne

2017-03-01

In this study, we compared the virulence in weaner pigs of the Pinar del Rio isolate and the virulent Margarita strain. The latter caused the Cuban classical swine fever (CSF) outbreak of 1993. Our results showed that the Pinar del Rio virus isolated during an endemic phase is clearly of low virulence. We analysed the complete nucleotide sequence of the Pinar del Rio virus isolated after persistence in newborn piglets, as well as the genome sequence of the inoculum. The consensus genome sequence of the Pinar del Rio virus remained completely unchanged after 28days of persistent infection in swine. More importantly, a unique poly-uridine tract was discovered in the 3'UTR of the Pinar del Rio virus, which was not found in the Margarita virus or any other known CSFV sequences. Based on RNA secondary structure prediction, the poly-uridine tract results in a long single-stranded intervening sequence (SS) between the stem-loops I and II of the 3'UTR, without major changes in the stem- loop structures when compared to the Margarita virus. The possible implications of this novel insertion on persistence and attenuation remain to be investigated. In addition, comparison of the amino acid sequence of the viral proteins E rns , E1, E2 and p7 of the Margarita and Pinar del Rio viruses showed that all non-conservative amino acid substitutions acquired by the Pinar del Rio isolate clustered in E2, with two of them being located within the B/C domain. Immunisation and cross-neutralisation experiments in pigs and rabbits suggest differences between these two viruses, which may be attributable to the amino acid differences observed in E2. Altogether, these data provide fresh insights into viral molecular features which might be associated with the attenuation and adaptation of CSFV for persistence in the field. Copyright © 2017 Elsevier B.V. All rights reserved.

Key diffusion mechanisms involved in regulating bidirectional water permeation across E. coli outer membrane lectin

PubMed Central

Sachdeva, Shivangi; Kolimi, Narendar; Nair, Sanjana Anilkumar; Rathinavelan, Thenmalarchelvi

2016-01-01

Capsular polysaccharides (CPSs) are major bacterial virulent determinants that facilitate host immune evasion. E. coli group1 K30CPS is noncovalently attached to bacterial surface by Wzi, a lectin. Intriguingly, structure based phylogenetic analysis indicates that Wzi falls into porin superfamily. Molecular dynamics (MD) simulations further shed light on dual role of Wzi as it also functions as a bidirectional passive water specific porin. Such a functional role of Wzi was not realized earlier, due to the occluded pore. While five water specific entry points distributed across extracellular & periplasmic faces regulate the water diffusion involving different mechanisms, a luminal hydrophobic plug governs water permeation across the channel. Coincidently, MD observed open state structure of “YQF” triad is seen in sugar-binding site of sodium-galactose cotransporters, implicating its involvement in K30CPS surface anchorage. Importance of Loop 5 (L5) in membrane insertion is yet another highlight. Change in water diffusion pattern of periplasmic substitution mutants suggests Wzi’s role in osmoregulation by aiding in K30CPS hydration, corroborating earlier functional studies. Water molecules located inside β-barrel of Wzi crystal structure further strengthens the role of Wzi in osmoregulation. Thus, interrupting water diffusion or L5 insertion may reduce bacterial virulence. PMID:27320406

Use of Metallic Endosseous Implants as a Tooth Substitute.

DTIC Science & Technology

1979-06-01

exposed in the oral cavity and placed in function with the opposing dentition iBACKGROUND The development of a dental implant that will serve as a...contract year was spent in testing the dental implant as a single tooth replacement. The ultimate goal of this implant study was to develop a free-standing...to read and sign an informed consent form. SURGICAL PROCEDURES The dental implant was inserted into the edentulous area using the exact procedures as

Propensities of Aromatic Amino Acids versus Leucine and Proline to Induce Residual Structure in the Denatured State Ensemble of Iso-1-cytochrome c

PubMed Central

Finnegan, Michaela L.; Bowler, Bruce E.

2010-01-01

Histidine-heme loop formation in the denatured state of a protein is a sensitive means to probe for residual structure under unfolding conditions. In this study, we use a host-guest approach to investigate the relative tendencies of different amino acids to promote residual structure under denaturing conditions. The host for this work is a 6 amino acid insert of five alanines followed by a lysine engineered immediately following a unique histidine near the N-terminus of yeast iso-1-cytochrome c. We substitute the 4th alanine in this sequence, HAAAXAK, with X = Trp, Phe, Tyr and Leu. The effects of proline are tested with substitutions at positions 1 and 5 in the insert, HPAAAAK and HAAAAPK, respectively. Thermodynamic studies on His-heme loop formation in 3 M guanidine hydrochloride reveal significant stabilization of residual structure by aromatic amino acids, particularly, Trp and Phe, and minimal stabilization of residual structure by Leu. Prolines disfavor His-heme loop formation slightly, presumably due to enhanced chain stiffness. Kinetic studies reveal that much of the change in His-heme loop stability for the aromatic amino acids is caused by a slowing of the rate of His-heme loop breakage, indicating that residual structure is preferentially stabilized in the closed-loop form of the denatured state. PMID:20850458

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

Pecchi, Gina; Campos, Claudia; Pena, Octavio

Thermal and reduction-oxidation stability of substituted LaMn{sub 1-y}Co{sub y}O{sub 3} perovskite-type oxides (0.0 {<=} y{sub Co} {<=} 1.0) prepared by the citrate route have been studied by means of surface area, X-ray diffraction, FTIR spectroscopy and magnetic properties. The perovskite orthorhombic structure is found for y{sub Co} {<=} 0.5, with the exception of y{sub Co} = 0.1, which corresponds better to rhombohedral LaMnO{sub 3.15}. For y{sub Co} > 0.5 the diffraction profiles are quite similar to the cobaltite's rhombohedral structure. Magnetic iso-field studies (ZFC-FC) reveal that, for y{sub Co} {<=} 0.50, the system presents an antiferromagnetic canted-like ordering of themore » Mn/Co sublattice, in which the presence of divalent Co ion creates Mn{sup 3+}-Mn{sup 4+} pairs that interact ferromagnetically through the oxygen orbital. This interpretation is confirmed by the magnetization loops, in which the magnetic moment increases when substituting Mn for Co. Therefore, the general trend is: for y{sub Co} {<=} 0.5, the Co ions are inserted in the manganite structure and for y{sub Co} > 0.5, the Mn ions are inserted in cobaltite structure. The enhancement of the ferromagnetic properties and the thermal stability against reduction for y{sub Co} = 0.5 is attributed to optimized Co{sup 2+}-Mn{sup 4+} interactions.« less

Automated startup of the MIT research reactor

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

Kwok, K.S.

1992-01-01

This summary describes the development, implementation, and testing of a generic method for performing automated startups of nuclear reactors described by space-independent kinetics under conditions of closed-loop digital control. The technique entails first obtaining a reliable estimate of the reactor's initial degree of subcriticality and then substituting that estimate into a model-based control law so as to permit a power increase from subcritical on a demanded trajectory. The estimation of subcriticality is accomplished by application of the perturbed reactivity method. The shutdown reactor is perturbed by the insertion of reactivity at a known rate. Observation of the resulting period permitsmore » determination of the initial degree of subcriticality. A major advantage to this method is that repeated estimates are obtained of the same quantity. Hence, statistical methods can be applied to improve the quality of the calculation.« less

The comparative chloroplast genomic analysis of photosynthetic orchids and developing DNA markers to distinguish Phalaenopsis orchids.

PubMed

Jheng, Cheng-Fong; Chen, Tien-Chih; Lin, Jhong-Yi; Chen, Ting-Chieh; Wu, Wen-Luan; Chang, Ching-Chun

2012-07-01

The chloroplast genome of Phalaenopsis equestris was determined and compared to those of Phalaenopsis aphrodite and Oncidium Gower Ramsey in Orchidaceae. The chloroplast genome of P. equestris is 148,959 bp, and a pair of inverted repeats (25,846 bp) separates the genome into large single-copy (85,967 bp) and small single-copy (11,300 bp) regions. The genome encodes 109 genes, including 4 rRNA, 30 tRNA and 75 protein-coding genes, but loses four ndh genes (ndhA, E, F and H) and seven other ndh genes are pseudogenes. The rate of inter-species variation between the two moth orchids was 0.74% (1107 sites) for single nucleotide substitution and 0.24% for insertions (161 sites; 1388 bp) and deletions (189 sites; 1393 bp). The IR regions have a lower rate of nucleotide substitution (3.5-5.8-fold) and indels (4.3-7.1-fold) than single-copy regions. The intergenic spacers are the most divergent, and based on the length variation of the three intergenic spacers, 11 native Phalaenopsis orchids could be successfully distinguished. The coding genes, IR junction and RNA editing sites are relatively more conserved between the two moth orchids than between those of Phalaenopsis and Oncidium spp. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Mucoadhesive ocular insert based on thiolated poly(acrylic acid): development and in vivo evaluation in humans.

PubMed

Hornof, Margit; Weyenberg, Wim; Ludwig, Annick; Bernkop-Schnürch, Andreas

2003-05-20

The aim of the study was to develop a mucoadhesive ocular insert for the controlled delivery of ophthalmic drugs and to evaluate its efficacy in vivo. The inserts tested were based either on unmodified or thiolated poly(acrylic acid). Water uptake and swelling behavior of the inserts as well as the drug release rates of the model drugs fluorescein and two diclofenac salts with different solubility properties were evaluated in vitro. Fluorescein was used as fluorescent tracer to study the drug release from the insert in humans. The mean fluorescein concentration in the cornea/tearfilm compartment as a function of time was determined after application of aqueous eye drops and inserts composed of unmodified and of thiolated poly(acrylic acid). The acceptability of the inserts by the volunteers was also evaluated. Inserts based on thiolated poly(acrylic acid) were not soluble and had good cohesive properties. A controlled release was achieved for the incorporated model drugs. The in vivo study showed that inserts based on thiolated poly(acrylic acid) provide a fluorescein concentration on the eye surface for more than 8 h, whereas the fluorescein concentration rapidly decreased after application of aqueous eye drops or inserts based on unmodified poly(acrylic acid). Moreover, these inserts were well accepted by the volunteers. The present study indicates that ocular inserts based on thiolated poly(acrylic acid) are promising new solid devices for ocular drug delivery.

The topography of mutational processes in breast cancer genomes

DOE PAGES

Morganella, Sandro; Alexandrov, Ludmil B.; Glodzik, Dominik; ...

2016-01-01

Somatic mutations in human cancers show unevenness in genomic distribution that correlate with aspects of genome structure and function. These mutations are, however, generated by multiple mutational processes operating through the cellular lineage between the fertilized egg and the cancer cell, each composed of specific DNA damage and repair components and leaving its own characteristic mutational signature on the genome. Using somatic mutation catalogues from 560 breast cancer whole-genome sequences, here we show that each of 12 base substitution, 2 insertion/deletion (indel) and 6 rearrangement mutational signatures present in breast tissue, exhibit distinct relationships with genomic features relating to transcription,more » DNA replication and chromatin organization. This signature-based approach permits visualization of the genomic distribution of mutational processes associated with APOBEC enzymes, mismatch repair deficiency and homologous recombinational repair deficiency, as well as mutational processes of unknown aetiology. Lastly, it highlights mechanistic insights including a putative replication-dependent mechanism of APOBEC-related mutagenesis.« less

Germline mutations in the proof-reading domains of POLE and POLD1 predispose to colorectal adenomas and carcinomas

PubMed Central

Palles, Claire; Cazier, Jean-Baptiste; Howarth, Kimberley M; Domingo, Enric; Jones, Angela M.; Broderick, Peter; Kemp, Zoe; Spain, Sarah L; Almeida, Estrella Guarino; Salguero, Israel; Sherborne, Amy; Chubb, Daniel; Carvajal-Carmona, Luis G; Ma, Yusanne; Kaur, Kulvinder; Dobbins, Sara; Barclay, Ella; Gorman, Maggie; Martin, Lynn; Kovac, Michal B; Humphray, Sean; Lucassen, Anneke; Holmes, Christopher; Bentley, David; Donnelly, Peter; Taylor, Jenny; Petridis, Christos; Roylance, Rebecca; Sawyer, Elinor J; Kerr, David J.; Clark, Susan; Grimes, Jonathan; Kearsey, Stephen E; Thomas, Huw JW; McVean, Gilean; Houlston, Richard S; Tomlinson, Ian

2013-01-01

Many individuals with multiple or large colorectal adenomas, or early-onset colorectal cancer (CRC), have no detectable germline mutations in the known cancer predisposition genes. Using whole-genome sequencing, supplemented by linkage and association analysis, we identified specific heterozygous POLE or POLD1 germline variants in several multiple adenoma and/or CRC cases, but in no controls. The susceptibility variants appear to have high penetrance. POLD1 is also associated with endometrial cancer predisposition. The mutations map to equivalent sites in the proof-reading (exonuclease) domain of DNA polymerases ε and δ, and are predicted to impair correction of mispaired bases inserted during DNA replication. In agreement with this prediction, mutation carriers’ tumours were microsatellite-stable, but tended to acquire base substitution mutations, as confirmed by yeast functional assays. Further analysis of published data showed that the recently-described group of hypermutant, microsatellite-stable CRCs is likely to be caused by somatic POLE exonuclease domain mutations. PMID:23263490

A shifting mutational landscape in 6 nutritional states: Stress-induced mutagenesis as a series of distinct stress input-mutation output relationships.

PubMed

Maharjan, Ram P; Ferenci, Thomas

2017-06-01

Environmental stresses increase genetic variation in bacteria, plants, and human cancer cells. The linkage between various environments and mutational outcomes has not been systematically investigated, however. Here, we established the influence of nutritional stresses commonly found in the biosphere (carbon, phosphate, nitrogen, oxygen, or iron limitation) on both the rate and spectrum of mutations in Escherichia coli. We found that each limitation was associated with a remarkably distinct mutational profile. Overall mutation rates were not always elevated, and nitrogen, iron, and oxygen limitation resulted in major spectral changes but no net increase in rate. Our results thus suggest that stress-induced mutagenesis is a diverse series of stress input-mutation output linkages that is distinct in every condition. Environment-specific spectra resulted in the differential emergence of traits needing particular mutations in these settings. Mutations requiring transpositions were highest under iron and oxygen limitation, whereas base-pair substitutions and indels were highest under phosphate limitation. The unexpected diversity of input-output effects explains some important phenomena in the mutational biases of evolving genomes. The prevalence of bacterial insertion sequence transpositions in the mammalian gut or in anaerobically stored cultures is due to environmentally determined mutation availability. Likewise, the much-discussed genomic bias towards transition base substitutions in evolving genomes can now be explained as an environment-specific output. Altogether, our conclusion is that environments influence genetic variation as well as selection.

A shifting mutational landscape in 6 nutritional states: Stress-induced mutagenesis as a series of distinct stress input–mutation output relationships

PubMed Central

Maharjan, Ram P.

2017-01-01

Environmental stresses increase genetic variation in bacteria, plants, and human cancer cells. The linkage between various environments and mutational outcomes has not been systematically investigated, however. Here, we established the influence of nutritional stresses commonly found in the biosphere (carbon, phosphate, nitrogen, oxygen, or iron limitation) on both the rate and spectrum of mutations in Escherichia coli. We found that each limitation was associated with a remarkably distinct mutational profile. Overall mutation rates were not always elevated, and nitrogen, iron, and oxygen limitation resulted in major spectral changes but no net increase in rate. Our results thus suggest that stress-induced mutagenesis is a diverse series of stress input–mutation output linkages that is distinct in every condition. Environment-specific spectra resulted in the differential emergence of traits needing particular mutations in these settings. Mutations requiring transpositions were highest under iron and oxygen limitation, whereas base-pair substitutions and indels were highest under phosphate limitation. The unexpected diversity of input–output effects explains some important phenomena in the mutational biases of evolving genomes. The prevalence of bacterial insertion sequence transpositions in the mammalian gut or in anaerobically stored cultures is due to environmentally determined mutation availability. Likewise, the much-discussed genomic bias towards transition base substitutions in evolving genomes can now be explained as an environment-specific output. Altogether, our conclusion is that environments influence genetic variation as well as selection. PMID:28594817

Nonsense mutation in the phosphofructokinase muscle subunit gene associated with retention of intron 10 in one of the isolated transcripts in Ashkenazi Jewish patients with Tarui disease.

PubMed Central

Vasconcelos, O; Sivakumar, K; Dalakas, M C; Quezado, M; Nagle, J; Leon-Monzon, M; Dubnick, M; Gajdusek, D C; Goldfarb, L G

1995-01-01

Mutations in the human phosphofructokinase muscle subunit gene (PFKM) are known to cause myopathy classified as glycogenosis type VII (Tarui disease). Previously described molecular defects include base substitutions altering encoded amino acids or resulting in abnormal splicing. We report a mutation resulting in phosphofructokinase deficiency in three patients from an Ashkenazi Jewish family. Using a reverse transcription PCR assay, PFKM subunit transcripts differing by length were detected in skeletal muscle tissue of all three affected subjects. In the longer transcript, an insertion of 252 nucleotides totally homologous to the structure of the 10th intron of the PFKM gene was found separating exon 10 from exon 11. In addition, two single base transitions were identified by direct sequencing: [exon 6; codon 95; CGA (Arg) to TGA (stop)] and [exon 7; codon 172; ACC (Thr) to ACT (Thr)] in either transcript. Single-stranded conformational polymorphism and restriction enzyme analyses confirmed the presence of these point substitutions in genomic DNA and strongly suggested homozygosity for the pathogenic allele. The nonsense mutation at codon 95 appeared solely responsible for the phenotype in these patients, further expanding genetic heterogeneity of Tarui disease. Transcripts with and without intron 10 arising from identical mutant alleles probably resulted from differential pre-mRNA processing and may represent a novel message from the PFKM gene. Images Fig. 2 Fig. 4 Fig. 5 PMID:7479776

Total synthesis of (+)-ileabethoxazole via an iron-mediated Pauson-Khand [2 + 2 + 1] carbocyclization.

PubMed

Williams, David R; Shah, Akshay A

2014-06-18

Studies describe the total synthesis of (+)-ileabethoxazole (1) using a Stille cross-coupling reaction of propargylic stannanes with 5-iodo-1,3-oxazoles to produce 1,1-disubstituted allenes (11). An iron-mediated [2 + 2 + 1] carbocyclization yields a novel cyclopentenone for elaboration to 1. Site-selective palladium insertion reactions allow for regiocontrolled substitutions of the heterocycle. Asymmetric copper hydride reductions are examined, and strategies for the formation of the central aromatic ring are discussed.

Asymmetric intermolecular Pauson-Khand reaction of symmetrically substituted alkynes.

PubMed

Ji, Yining; Riera, Antoni; Verdaguer, Xavier

2009-10-01

The asymmetric intermolecular Pauson-Khand reaction of symmetric alkynes has been accomplished for the first time. N-Phosphino-p-tolylsulfinamide (PNSO) ligands have been identified as efficient ligands in this process. The chirality of the cobalt S-bonded sulfinyl moiety was found to direct olefin insertion into one of the two possible cobalt-carbon bonds in the alkyne complex. Reaction of symmetric alkynes allows for a simplified experimental protocol since there is no need for separation of diastereomeric complexes.

A two-in-one Faraday rotator mirror exempt of active optical alignment.

PubMed

Wan, Qiong; Wan, Zhujun; Liu, Hai; Liu, Deming

2014-02-10

A two-in-one Faraday rotator mirror was presented, which functions as two independent Faraday rotation mirrors with a single device. With the introduction of a reflection lens as substitution of the mirror in traditional structure, this device is characterized by exemption of active optical alignment for the designers and manufacturers of Faraday rotator mirrors. A sample was fabricated by passive mechanical assembly. The insertion loss was measured as 0.46 dB/0.50 dB for the two independent ports, respectively.

Comparative Efficacy of the Air-Q Intubating Laryngeal Airway during General Anesthesia in Pediatric Patients: A Systematic Review and Meta-Analysis.

PubMed

Ahn, Eun Jin; Choi, Geun Joo; Kang, Hyun; Baek, Chong Wha; Jung, Yong Hun; Woo, Young Cheol; Bang, Si Ra

2016-01-01

Air-Q® (air-Q) is a supraglottic airway device which can be used as a guidance of intubation in pediatric as well as in adult patients. We evaluated the efficacy and safety of air-Q compared to other airway devices during general anesthesia in pediatric patients by conducting a systematic review and meta-analysis. A total of 10 studies including 789 patients were included in the final analysis. Compared with other supraglottic airway devices, air-Q showed no evidence for a difference in leakage pressure and insertion time. The ease of insertion was significantly lower than other supraglottic airway devices. The success rate of intubation was significantly lower than other airway devices. However, fiberoptic view was better through the air-Q than other supraglottic airway devices. Therefore, air-Q could be a safe substitute for other airway devices and may provide better fiberoptic bronchoscopic view.

MCMC genome rearrangement.

PubMed

Miklós, István

2003-10-01

As more and more genomes have been sequenced, genomic data is rapidly accumulating. Genome-wide mutations are believed more neutral than local mutations such as substitutions, insertions and deletions, therefore phylogenetic investigations based on inversions, transpositions and inverted transpositions are less biased by the hypothesis on neutral evolution. Although efficient algorithms exist for obtaining the inversion distance of two signed permutations, there is no reliable algorithm when both inversions and transpositions are considered. Moreover, different type of mutations happen with different rates, and it is not clear how to weight them in a distance based approach. We introduce a Markov Chain Monte Carlo method to genome rearrangement based on a stochastic model of evolution, which can estimate the number of different evolutionary events needed to sort a signed permutation. The performance of the method was tested on simulated data, and the estimated numbers of different types of mutations were reliable. Human and Drosophila mitochondrial data were also analysed with the new method. The mixing time of the Markov Chain is short both in terms of CPU times and number of proposals. The source code in C is available on request from the author.

The A-chain of insulin contacts the insert domain of the insulin receptor. Photo-cross-linking and mutagenesis of a diabetes-related crevice.

PubMed

Huang, Kun; Chan, Shu Jin; Hua, Qing-xin; Chu, Ying-Chi; Wang, Run-ying; Klaproth, Birgit; Jia, Wenhua; Whittaker, Jonathan; De Meyts, Pierre; Nakagawa, Satoe H; Steiner, Donald F; Katsoyannis, Panayotis G; Weiss, Michael A

2007-11-30

The contribution of the insulin A-chain to receptor binding is investigated by photo-cross-linking and nonstandard mutagenesis. Studies focus on the role of Val(A3), which projects within a crevice between the A- and B-chains. Engineered receptor alpha-subunits containing specific protease sites ("midi-receptors") are employed to map the site of photo-cross-linking by an analog containing a photoactivable A3 side chain (para-azido-Phe (Pap)). The probe cross-links to a C-terminal peptide (residues 703-719 of the receptor A isoform, KTFEDYLHNVVFVPRPS) containing side chains critical for hormone binding (underlined); the corresponding segment of the holoreceptor was shown previously to cross-link to a Pap(B25)-insulin analog. Because Pap is larger than Val and so may protrude beyond the A3-associated crevice, we investigated analogs containing A3 substitutions comparable in size to Val as follows: Thr, allo-Thr, and alpha-aminobutyric acid (Aba). Substitutions were introduced within an engineered monomer. Whereas previous studies of smaller substitutions (Gly(A3) and Ser(A3)) encountered nonlocal conformational perturbations, NMR structures of the present analogs are similar to wild-type insulin; the variant side chains are accommodated within a native-like crevice with minimal distortion. Receptor binding activities of Aba(A3) and allo-Thr(A3) analogs are reduced at least 10-fold; the activity of Thr(A3)-DKP-insulin is reduced 5-fold. The hormone-receptor interface is presumably destabilized either by a packing defect (Aba(A3)) or by altered polarity (allo-Thr(A3) and Thr(A3)). Our results provide evidence that Val(A3), a site of mutation causing diabetes mellitus, contacts the insert domain-derived tail of the alpha-subunit in a hormone-receptor complex.

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

Dinh, Phat X.; Panda, Debasis; Das, Phani B.

Using a recombinant vesicular stomatitis virus encoding eGFP fused in-frame with an essential viral replication protein, the phosphoprotein P, we show that during passage in culture, the virus mutates the nucleotide C289 within eGFP of the fusion protein PeGFP to A or T, resulting in R97S/C amino acid substitution and loss of fluorescence. The resultant non-fluorescent virus exhibits increased fitness and growth advantage over its fluorescent counterpart. The growth advantage of the non-fluorescent virus appears to be due to increased transcription and replication activities of the PeGFP protein carrying the R97S/C substitution. Further, our results show that the R97S/C mutationmore » occurs prior to accumulation of mutations that can result in loss of expression of the gene inserted at the G-L gene junction. These results suggest that fitness gain is more important for the recombinant virus than elimination of expression of the heterologous gene.« less

Reactivity measurement in estimation of benzoquinone and benzoquinone derivatives’ allergenicity

PubMed Central

Mbiya, Wilbes; Chipinda, Itai; Simoyi, Reuben H.; Siegel, Paul D.

2015-01-01

Benzoquinone (BQ) and benzoquinone derivatives (BQD) are used in the production of dyes and cosmetics. While BQ, an extreme skin sensitizer, is an electrophile known to covalently modify proteins via Michael Addition (MA) reaction whilst halogen substituted BQD undergo nucleophilic vinylic substitution (SNV) mechanism onto amine and thiol moieties on proteins, the allergenic effects of adding substituents on BQ have not been reported. The effects of inserting substituents on the BQ ring has not been studied in animal assays. However, mandated reduction/elimination of animals used in cosmetics testing in Europe has led to an increased need for alternatives for the prediction of skin sensitization potential. Electron withdrawing and electron donating substituents on BQ were assessed for effects on BQ reactivity toward nitrobenzene thiol (NBT). The NBT binding studies demonstrated that addition of EWG to BQ as exemplified by the chlorine substituted BQDs increased reactivity while addition of EDG as in the methyl substituted BQDs reduced reactivity. BQ and BQD skin allerginicity was evaluated in the murine local lymph node assay (LLNA). BQD with electron withdrawing groups had the highest chemical potency followed by unsubstituted BQ and the least potent were the BQD with electron donating groups. The BQD results demonstrate the impact of inductive effects on both BQ reactivity and allergenicity, and suggest the potential utility of chemical reactivity data for electrophilic allergen identification and potency ranking. PMID:26612505

Analysis of Impingement between Patella Bone and Bearing Post in Cruciate-Substituting High-Flexion Total Knee Arthroplasty

PubMed Central

Chon, Jegyun; Shin, Sangyeop; Jang, Gunil; Jeon, Taehyeon

2016-01-01

Background We investigated the causes of impingement between the patella bone and the bearing post during high flexion in cruciate-substituting total knee arthroplasty and proposed a treatment strategy. Methods This prospective cohort study included 218 cases that had undergone cruciate-substituting total knee arthroplasty from February 2014 to January 2015; a single surgeon performed the operation using the same method without patellar resurfacing in all patients. Results In these patients, the occurrence of impingement was determined by performing more than 120° high knee flexion after inserting a bearing perioperatively. The incidence of impingement was significantly associated with bearing design, femoral implant size, patella bone length, and patella inferior pole angle (p < 0.05). The impingement was resolved by resection of the lower articular side of the patella bone. Conclusions In the cruciate-substituting high-flexion total knee arthroplasty, impingement between the patella bone and bearing post was more common in patients with mobile bearing, small-size femoral component, and a long patella or a large inferior pole angle. In cases of intraoperative impingement between the patella bone and the bearing post, resection in the lower portion of the patella prevented impingement of the bearing with soft tissue or the patella by widening the space between the patella and the bearing post, which in turn prevented postoperative reduction in range of motion. PMID:27247740

Coevolution between Nuclear-Encoded DNA Replication, Recombination, and Repair Genes and Plastid Genome Complexity

PubMed Central

Zhang, Jin; Ruhlman, Tracey A.; Sabir, Jamal S. M.; Blazier, John Chris; Weng, Mao-Lun; Park, Seongjun; Jansen, Robert K.

2016-01-01

Disruption of DNA replication, recombination, and repair (DNA-RRR) systems has been hypothesized to cause highly elevated nucleotide substitution rates and genome rearrangements in the plastids of angiosperms, but this theory remains untested. To investigate nuclear–plastid genome (plastome) coevolution in Geraniaceae, four different measures of plastome complexity (rearrangements, repeats, nucleotide insertions/deletions, and substitution rates) were evaluated along with substitution rates of 12 nuclear-encoded, plastid-targeted DNA-RRR genes from 27 Geraniales species. Significant correlations were detected for nonsynonymous (dN) but not synonymous (dS) substitution rates for three DNA-RRR genes (uvrB/C, why1, and gyrA) supporting a role for these genes in accelerated plastid genome evolution in Geraniaceae. Furthermore, correlation between dN of uvrB/C and plastome complexity suggests the presence of nucleotide excision repair system in plastids. Significant correlations were also detected between plastome complexity and 13 of the 90 nuclear-encoded organelle-targeted genes investigated. Comparisons revealed significant acceleration of dN in plastid-targeted genes of Geraniales relative to Brassicales suggesting this correlation may be an artifact of elevated rates in this gene set in Geraniaceae. Correlation between dN of plastid-targeted DNA-RRR genes and plastome complexity supports the hypothesis that the aberrant patterns in angiosperm plastome evolution could be caused by dysfunction in DNA-RRR systems. PMID:26893456

Analysis of Impingement between Patella Bone and Bearing Post in Cruciate-Substituting High-Flexion Total Knee Arthroplasty.

PubMed

Chon, Jegyun; Lee, Bongju; Shin, Sangyeop; Jang, Gunil; Jeon, Taehyeon

2016-06-01

We investigated the causes of impingement between the patella bone and the bearing post during high flexion in cruciate-substituting total knee arthroplasty and proposed a treatment strategy. This prospective cohort study included 218 cases that had undergone cruciate-substituting total knee arthroplasty from February 2014 to January 2015; a single surgeon performed the operation using the same method without patellar resurfacing in all patients. In these patients, the occurrence of impingement was determined by performing more than 120° high knee flexion after inserting a bearing perioperatively. The incidence of impingement was significantly associated with bearing design, femoral implant size, patella bone length, and patella inferior pole angle (p < 0.05). The impingement was resolved by resection of the lower articular side of the patella bone. In the cruciate-substituting high-flexion total knee arthroplasty, impingement between the patella bone and bearing post was more common in patients with mobile bearing, small-size femoral component, and a long patella or a large inferior pole angle. In cases of intraoperative impingement between the patella bone and the bearing post, resection in the lower portion of the patella prevented impingement of the bearing with soft tissue or the patella by widening the space between the patella and the bearing post, which in turn prevented postoperative reduction in range of motion.

Differentiation of highly virulent strains of Streptococcus suis serotype 2 according to glutamate dehydrogenase electrophoretic and sequence type.

PubMed

Kutz, Russell; Okwumabua, Ogi

2008-10-01

The glutamate dehydrogenase (GDH) enzymes of 19 Streptococcus suis serotype 2 strains, consisting of 18 swine isolates and 1 human clinical isolate from a geographically varied collection, were analyzed by activity staining on a nondenaturing gel. All seven (100%) of the highly virulent strains tested produced an electrophoretic type (ET) distinct from those of moderately virulent and nonvirulent strains. By PCR and nucleotide sequence determination, the gdh genes of the 19 strains and of 2 highly virulent strains involved in recent Chinese outbreaks yielded a 1,820-bp fragment containing an open reading frame of 1,344 nucleotides, which encodes a protein of 448 amino acid residues with a calculated molecular mass of approximately 49 kDa. The nucleotide sequences contained base pair differences, but most were silent. Cluster analysis of the deduced amino acid sequences separated the isolates into three groups. Group I (ETI) consisted of the seven highly virulent isolates and the two Chinese outbreak strains, containing Ala(299)-to-Ser, Glu(305)-to-Lys, and Glu(330)-to-Lys amino acid substitutions compared with groups II and III (ETII). Groups II and III consisted of moderately virulent and nonvirulent strains, which are separated from each other by Tyr(72)-to-Asp and Thr(296)-to-Ala substitutions. Gene exchange studies resulted in the change of ETI to ETII and vice versa. A spectrophotometric activity assay for GDH did not show significant differences between the groups. These results suggest that the GDH ETs and sequence types may serve as useful markers in predicting the pathogenic behavior of strains of this serotype and that the molecular basis for the observed differences in the ETs was amino acid substitutions and not deletion, insertion, or processing uniqueness.

Correlation of Local Effects of DNA Sequence and Position of Beta-Alanine Inserts with Polyamide-DNA Complex Binding Affinities and Kinetics

PubMed Central

Wang, Shuo; Nanjunda, Rupesh; Aston, Karl; Bashkin, James K.; Wilson, W. David

2012-01-01

In order to better understand the effects of β-alanine (β) substitution and the number of heterocycles on DNA binding affinity and selectivity, the interactions of an eight-ring hairpin polyamide (PA) and two β derivatives as well as a six-heterocycle analog have been investigated with their cognate DNA sequence, 5′-TGGCTT-3′. Binding selectivity and the effects of β have been investigated with the cognate and five mutant DNAs. A set of powerful and complementary methods have been employed for both energetic and structural evaluations: UV-melting, biosensor-surface plasmon resonance, isothermal titration calorimetry, circular dichroism and a DNA ligation ladder global structure assay. The reduced number of heterocycles in the six-ring PA weakens the binding affinity; however, the smaller PA aggregates significantly less than the larger PAs, and allows us to obtain the binding thermodynamics. The PA-DNA binding enthalpy is large and negative with a large negative ΔCp, and is the primary driving component of the Gibbs free energy. The complete SPR binding results clearly show that β substitutions can substantially weaken the binding affinity of hairpin PAs in a position-dependent manner. More importantly, the changes in PA binding to the mutant DNAs further confirm the position-dependent effects on PA-DNA interaction affinity. Comparison of mutant DNA sequences also shows a different effect in recognition of T•A versus A•T base pairs. The effects of DNA mutations on binding of a single PA as well as the effects of the position of β substitution on binding tell a clear and very important story about sequence dependent binding of PAs to DNA. PMID:23167504

Rubella virus: first calcium-requiring viral fusion protein.

PubMed

Dubé, Mathieu; Rey, Felix A; Kielian, Margaret

2014-12-01

Rubella virus (RuV) infection of pregnant women can cause fetal death, miscarriage, or severe fetal malformations, and remains a significant health problem in much of the underdeveloped world. RuV is a small enveloped RNA virus that infects target cells by receptor-mediated endocytosis and low pH-dependent membrane fusion. The structure of the RuV E1 fusion protein was recently solved in its postfusion conformation. RuV E1 is a member of the class II fusion proteins and is structurally related to the alphavirus and flavivirus fusion proteins. Unlike the other known class II fusion proteins, however, RuV E1 contains two fusion loops, with a metal ion complexed between them by the polar residues N88 and D136. Here we demonstrated that RuV infection specifically requires Ca(2+) during virus entry. Other tested cations did not substitute. Ca(2+) was not required for virus binding to cell surface receptors, endocytic uptake, or formation of the low pH-dependent E1 homotrimer. However, Ca(2+) was required for low pH-triggered E1 liposome insertion, virus fusion and infection. Alanine substitution of N88 or D136 was lethal. While the mutant viruses were efficiently assembled and endocytosed by host cells, E1-membrane insertion and fusion were specifically blocked. Together our data indicate that RuV E1 is the first example of a Ca(2+)-dependent viral fusion protein and has a unique membrane interaction mechanism.

Genetic variation in the 3’ untranslated region of dengue virus serotype 3 strains isolated from mosquitoes and humans in Brazil

PubMed Central

2013-01-01

Summary Background Dengue, a mosquito-borne viral infection caused by one of the four dengue virus (DENV) serotypes (DENV-1 to 4), replicate alternately on the mosquito vector and human host and are responsible for infections throughout tropical and subtropical regions of the world. In Brazil, the disease has become a major public health problem and the introduction of DENV-3 in 2000 in Rio de Janeiro (RJ) was associated with severe dengue epidemics. The potential emergence of strains associated with severe disease highlights the need for the surveillance of DENV in human host and vectors. Methods Aiming to contribute for DENV phylogenetic and vector-virus-human host studies, we sequenced the entire genome of one DENV-3 isolated from naturally infected Aedes aegypti from RJ in 2001 and characterized the 3’ UTR from strains isolated from mosquitoes and humans. Mosquitoes were pooled and submitted to virus isolation in Ae. albopictus C6/36 cells and the infecting serotype was identified by immunofluorescence using type-specific monoclonal antibody. Sequence analysis was performed using BioEdit software, the multiple alignments were performed using CLUSTAL W and the phylogenetic analysis by MEGA 5, using the Neighbor-joining method. Secondary structure prediction was performed by using the MFOLD program. Results Exclusive substitutions and a substitution leading to a stop codon on the NS5 gene were observed in the DENV-3 isolated from a naturally infected Ae. aegypti and fully sequenced. As an 8- nucleotides deletion was observed within the 11- nucleotides (nts) insertion on the variable region (VR) from the 3′UTR in this isolate, we further sequenced other DENV-3 from both mosquitoes and humans. The majority of DENV-3 from RJ analyzed were characterized by the 11-nts insertion in the VR of the 3′UTR, despite the observation of strains carrying the 8-nts deletion. The latter presented similar secondary structures, however not all strains presenting the 11-nts insertion were similar in the predicted secondary structure. Conclusions The phylogeny based on the analysis of the complete genome and 3′UTR characterized the DENV-3 isolated from both vector and human host as belonging to Genotype III (GIII), despite the differences observed on the 3’ UTR. Further studies are needed to address the role of those mutations in the transmission of the different viral populations and vector competence. PMID:23282086

GASP: Gapped Ancestral Sequence Prediction for proteins

PubMed Central

Edwards, Richard J; Shields, Denis C

2004-01-01

Background The prediction of ancestral protein sequences from multiple sequence alignments is useful for many bioinformatics analyses. Predicting ancestral sequences is not a simple procedure and relies on accurate alignments and phylogenies. Several algorithms exist based on Maximum Parsimony or Maximum Likelihood methods but many current implementations are unable to process residues with gaps, which may represent insertion/deletion (indel) events or sequence fragments. Results Here we present a new algorithm, GASP (Gapped Ancestral Sequence Prediction), for predicting ancestral sequences from phylogenetic trees and the corresponding multiple sequence alignments. Alignments may be of any size and contain gaps. GASP first assigns the positions of gaps in the phylogeny before using a likelihood-based approach centred on amino acid substitution matrices to assign ancestral amino acids. Important outgroup information is used by first working down from the tips of the tree to the root, using descendant data only to assign probabilities, and then working back up from the root to the tips using descendant and outgroup data to make predictions. GASP was tested on a number of simulated datasets based on real phylogenies. Prediction accuracy for ungapped data was similar to three alternative algorithms tested, with GASP performing better in some cases and worse in others. Adding simple insertions and deletions to the simulated data did not have a detrimental effect on GASP accuracy. Conclusions GASP (Gapped Ancestral Sequence Prediction) will predict ancestral sequences from multiple protein alignments of any size. Although not as accurate in all cases as some of the more sophisticated maximum likelihood approaches, it can process a wide range of input phylogenies and will predict ancestral sequences for gapped and ungapped residues alike. PMID:15350199

Composite cervical skin and cartilage flap provides a novel large airway substitute after long-segment tracheal resection.

PubMed

Fabre, Dominique; Singhal, Sunil; De Montpreville, Vincent; Decante, Benoit; Mussot, Sacha; Chataigner, Olivier; Mercier, Olaf; Kolb, Frederic; Dartevelle, Philippe G; Fadel, Elie

2009-07-01

Airway replacement after long-segment tracheal resection for benign and malignant disease remains a challenging problem because of the lack of a substitute conduit. Ideally, an airway substitute should be well vascularized, rigid, and autologous to avoid infections, airway stenosis, and the need for immunosuppression. We report the development of an autologous tracheal substitute for long-segment tracheal resection that satisfies these criteria and demonstrates excellent short-term functional results in a large-animal study. Twelve adult pigs underwent long-segment (6 cm, 60% of total length) tracheal resection. Autologous costal cartilage strips measuring 6 cm x 2 mm were harvested from the chest wall and inserted at regular 0.5-cm intervals between dermal layers of a cervical skin flap. The neotrachea was then scaffolded by rotating the composite cartilage skin flap around a silicone stent measuring 6 cm in length and 1.4 cm in diameter. The neotrachea replaced the long segment of tracheal resection, and the donor flap site was closed with a double-Z plasty. Animals were killed at 1 week (group I, n = 4), 2 weeks (group II, n = 4), and 5 weeks (group III, n = 4). In group III the stent was removed 1 week before death. Viability of the neotrachea was monitored by means of daily flexible bronchoscopy and histologic examination at autopsy. Long-term morbidity and mortality were determined by monitoring weight gain, respiratory distress, and survival. There was no mortality during the study period. Weight gain was appropriate in all animals. Daily bronchoscopy and postmortem histologic evaluation confirmed excellent viability of the neotrachea. There was no evidence of suture-line dehiscence. Five animals had distal granulomas that were removed by using rigid bronchoscopy. In group III 1 animal had tracheomalacia, which was successfully managed by means of insertion of a silicon stent. Airway reconstruction with autologous cervical skin flaps scaffolded with costal cartilages is a novel approach to replace long segments of resected trachea. This preliminary study demonstrates excellent respiratory function and survival in large animals undergoing resection of more than 50% of their native trachea. Use of cervical skin flaps buttressed with costal cartilage is a promising solution for long-segment tracheal replacement.

Sugar Substitutes

MedlinePlus

... Substitutes Share Print Sugar substitutes are chemical or plant-based substances used to sweeten or enhance the ... made with saccharin. Stevia sweeteners Stevia is a plant-based sugar substitute that has no calories. The ...

Multiplex screening for RB1 germline mutations in 106 patients with hereditary retinoblastoma

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

Lohmann, D.R.; Brandt, B.; Passarge, E.

1994-09-01

The identification of germline mutations in the retinoblastoma susceptibility gene (RB1) is important for genetic counseling in hereditary retinoblastoma. Due to the complex genomic organization of this gene and the heterogeneity of mutations, efficient screening procedures are important for rapid mutation detection. We have developed methods based on simultaneous analysis of multiple regions of this gene in an ABI automated DNA fragment analyzer to examine 106 patients with hereditary retinoblastoma in which no alteration was identified by Southern blot hybridization. Primers for the amplification of all 27 exons of the RB1 gene as well as the promoter and poly(A) signalmore » sequences were labelled with distinct fluorescent dyes (FAM, HEX, TAMRA) to enable simultaneous electrophoretic analysis of PCR products with similar mobility. PCR fragments distinguishable by size or color were co-amplified by multiplex PCR and analyzed for length by GENESCAN analysis. Using this approach, small deletions ranging from 1 bp to 22 bp were identified in 24 patients (23%). Short sequence repeats or polypyrimidine runs were present in the vicinity of most of these deletions. In 4 patients (4%), insertions from 1 bp to 4 bp were found. The majority of length mutations resulted in a truncated gene product due to frameshift and premature termination. No mutation was identified in exons 25 to 27 possibly indicating that the encoded protein domains have minor functional importance. In order to screen for base substitutions that are not detectable by fragment length analysis, we adapted heteroduplex analysis for the use in the DNA fragment analyzer. During the optimization of this method we detected 10 single base substitutions most of which generated stop codons. Intriguingly, two identical missense mutations were identified in two unrelated families with a low-penetrance phenotype.« less

Requirement for Msh6, but not for Swi4 (Msh3), in Msh2-dependent repair of base-base mismatches and mononucleotide loops in Schizosaccharomyces pombe.

PubMed

Tornier, C; Bessone, S; Varlet, I; Rudolph, C; Darmon, M; Fleck, O

2001-05-01

The msh6 mismatch repair gene of Schizosaccharomyces pombe was cloned, sequenced, and inactivated. Strains bearing all combinations of inactivated msh6, msh2, and swi4 (the S. pombe MSH3 ortholog) alleles were tested for their defects in mitotic and meiotic mismatch repair. Mitotic mutation rates were similarly increased in msh6 and msh2 mutants, both for reversion of a base-base substitution as well as of an insertion of one nucleotide in a mononucleotide run. Tetrad analysis and intragenic two-factor crosses revealed that meiotic mismatch repair was affected in msh6 to the same extent as in msh2 background. In contrast, loss of Swi4 likely did not cause a defect in mismatch repair, but rather resulted in reduced recombination frequency. Consistently, a mutated swi4 caused a two- to threefold reduction of recombinants in intergenic crosses, while msh2 and msh6 mutants were not significantly different from wild type. In summary, our study showed that Msh6 plays the same important role as Msh2 in the major mismatch repair pathway of S. pombe, while Swi4 rather functions in recombination.

SSR allelic variation in almond (Prunus dulcis Mill.).

PubMed

Xie, Hua; Sui, Yi; Chang, Feng-Qi; Xu, Yong; Ma, Rong-Cai

2006-01-01

Sixteen SSR markers including eight EST-SSR and eight genomic SSRs were used for genetic diversity analysis of 23 Chinese and 15 international almond cultivars. EST- and genomic SSR markers previously reported in species of Prunus, mainly peach, proved to be useful for almond genetic analysis. DNA sequences of 117 alleles of six of the 16 SSR loci were analysed to reveal sequence variation among the 38 almond accessions. For the four SSR loci with AG/CT repeats, no insertions or deletions were observed in the flanking regions of the 98 alleles sequenced. Allelic size variation of these loci resulted exclusively from differences in the structures of repeat motifs, which involved interruptions or occurrences of new motif repeats in addition to varying number of AG/CT repeats. Some alleles had a high number of uninterrupted repeat motifs, indicating that SSR mutational patterns differ among alleles at a given SSR locus within the almond species. Allelic homoplasy was observed in the SSR loci because of base substitutions, interruptions or compound repeat motifs. Substitutions in the repeat regions were found at two SSR loci, suggesting that point mutations operate on SSRs and hinder the further SSR expansion by introducing repeat interruptions to stabilize SSR loci. Furthermore, it was shown that some potential point mutations in the flanking regions are linked with new SSR repeat motif variation in almond and peach.

Evidence for Watson-Crick and not Hoogsteen or wobble base pairing in the selection of nucleotides for insertion opposite pyrimidines and a thymine dimer by yeast DNA pol eta.

PubMed

Hwang, Hanshin; Taylor, John-Stephen

2005-03-29

We have recently reported that pyrene nucleotide is preferentially inserted opposite an abasic site, the 3'-T of a thymine dimer, and most undamaged bases by yeast DNA polymerase eta (pol eta). Because pyrene is a nonpolar molecule with no H-bonding ability, the unusually high efficiencies of dPMP insertion are ascribed to its superior base stacking ability, and underscore the importance of base stacking in the selection of nucleotides by pol eta. To investigate the role of H-bonding and base pair geometry in the selection of nucleotides by pol eta, we determined the insertion efficiencies of the base-modified nucleotides 2,6-diaminopurine, 2-aminopurine, 6-chloropurine, and inosine which would make a different number of H-bonds with the template base depending on base pair geometry. Watson-Crick base pairing appears to play an important role in the selection of nucleotide analogues for insertion opposite C and T as evidenced by the decrease in the relative insertion efficiencies with a decrease in the number of Watson-Crick H-bonds and an increase in the number of donor-donor and acceptor-acceptor interactions. The selectivity of nucleotide insertion is greater opposite the 5'-T than the 3'-T of the thymine dimer, in accord with previous work suggesting that the 5'-T is held more rigidly than the 3'-T. Furthermore, insertion of A opposite both Ts of the dimer appears to be mediated by Watson-Crick base pairing and not by Hoogsteen base pairing based on the almost identical insertion efficiencies of A and 7-deaza-A, the latter of which lacks H-bonding capability at N7. The relative efficiencies for insertion of nucleotides that can form Watson-Crick base pairs parallel those for the Klenow fragment, whereas the Klenow fragment more strongly discriminates against mismatches, in accord with its greater shape selectivity. These results underscore the importance of H-bonding and Watson-Crick base pair geometry in the selection of nucleotides by both pol eta and the Klenow fragment, and the lesser role of shape selection in insertion by pol eta due to its more open and less constrained active site.

Short template switch events explain mutation clusters in the human genome.

PubMed

Löytynoja, Ari; Goldman, Nick

2017-06-01

Resequencing efforts are uncovering the extent of genetic variation in humans and provide data to study the evolutionary processes shaping our genome. One recurring puzzle in both intra- and inter-species studies is the high frequency of complex mutations comprising multiple nearby base substitutions or insertion-deletions. We devised a generalized mutation model of template switching during replication that extends existing models of genome rearrangement and used this to study the role of template switch events in the origin of short mutation clusters. Applied to the human genome, our model detects thousands of template switch events during the evolution of human and chimp from their common ancestor and hundreds of events between two independently sequenced human genomes. Although many of these are consistent with a template switch mechanism previously proposed for bacteria, our model also identifies new types of mutations that create short inversions, some flanked by paired inverted repeats. The local template switch process can create numerous complex mutation patterns, including hairpin loop structures, and explains multinucleotide mutations and compensatory substitutions without invoking positive selection, speculative mechanisms, or implausible coincidence. Clustered sequence differences are challenging for current mapping and variant calling methods, and we show that many erroneous variant annotations exist in human reference data. Local template switch events may have been neglected as an explanation for complex mutations because of biases in commonly used analyses. Incorporation of our model into reference-based analysis pipelines and comparisons of de novo assembled genomes will lead to improved understanding of genome variation and evolution. © 2017 Löytynoja and Goldman; Published by Cold Spring Harbor Laboratory Press.

Total prosthetic replacement of atrioventricular valves in the dog

PubMed Central

Den Otter, G.

1968-01-01

The free-floating cone and cage valve, described in a previous study as being successful as a substitute for the right atrioventricular valve, does not perform well when it is inserted in the mitral ostium. A tilting cone or disc was constructed and tested in a series of 15 dogs. This prosthesis gave excellent results in 12 animals. The reasons for its failure in the remaining three is discussed. The prosthesis presented has advantages over any ball and cage valve, mainly because of its smaller volume. Images PMID:5654076

α-Diazo-β-ketonitriles: uniquely reactive substrates for arene and alkene cyclopropanation.

PubMed

Nani, Roger R; Reisman, Sarah E

2013-05-15

An investigation of the intramolecular cyclopropanation reactions of α-diazo-β-ketonitriles is reported. These studies reveal that α-diazo-β-ketonitriles exhibit unique reactivity in their ability to undergo arene cyclopropanation reactions; other similar acceptor-acceptor-substituted diazo substrates instead produce mixtures of C-H insertion and dimerization products. α-Diazo-β-ketonitriles also undergo highly efficient intramolecular cyclopropanation of tri- and tetrasubstituted alkenes. In addition, the α-cyano-α-ketocyclopropane products are demonstrated to serve as substrates for SN2, SN2', and aldehyde cycloaddition reactions.

The Paramecium germline genome provides a niche for intragenic parasitic DNA: evolutionary dynamics of internal eliminated sequences.

PubMed

Arnaiz, Olivier; Mathy, Nathalie; Baudry, Céline; Malinsky, Sophie; Aury, Jean-Marc; Denby Wilkes, Cyril; Garnier, Olivier; Labadie, Karine; Lauderdale, Benjamin E; Le Mouël, Anne; Marmignon, Antoine; Nowacki, Mariusz; Poulain, Julie; Prajer, Malgorzata; Wincker, Patrick; Meyer, Eric; Duharcourt, Sandra; Duret, Laurent; Bétermier, Mireille; Sperling, Linda

2012-01-01

Insertions of parasitic DNA within coding sequences are usually deleterious and are generally counter-selected during evolution. Thanks to nuclear dimorphism, ciliates provide unique models to study the fate of such insertions. Their germline genome undergoes extensive rearrangements during development of a new somatic macronucleus from the germline micronucleus following sexual events. In Paramecium, these rearrangements include precise excision of unique-copy Internal Eliminated Sequences (IES) from the somatic DNA, requiring the activity of a domesticated piggyBac transposase, PiggyMac. We have sequenced Paramecium tetraurelia germline DNA, establishing a genome-wide catalogue of -45,000 IESs, in order to gain insight into their evolutionary origin and excision mechanism. We obtained direct evidence that PiggyMac is required for excision of all IESs. Homology with known P. tetraurelia Tc1/mariner transposons, described here, indicates that at least a fraction of IESs derive from these elements. Most IES insertions occurred before a recent whole-genome duplication that preceded diversification of the P. aurelia species complex, but IES invasion of the Paramecium genome appears to be an ongoing process. Once inserted, IESs decay rapidly by accumulation of deletions and point substitutions. Over 90% of the IESs are shorter than 150 bp and present a remarkable size distribution with a -10 bp periodicity, corresponding to the helical repeat of double-stranded DNA and suggesting DNA loop formation during assembly of a transpososome-like excision complex. IESs are equally frequent within and between coding sequences; however, excision is not 100% efficient and there is selective pressure against IES insertions, in particular within highly expressed genes. We discuss the possibility that ancient domestication of a piggyBac transposase favored subsequent propagation of transposons throughout the germline by allowing insertions in coding sequences, a fraction of the genome in which parasitic DNA is not usually tolerated.

The Paramecium Germline Genome Provides a Niche for Intragenic Parasitic DNA: Evolutionary Dynamics of Internal Eliminated Sequences

PubMed Central

Arnaiz, Olivier; Mathy, Nathalie; Baudry, Céline; Malinsky, Sophie; Aury, Jean-Marc; Denby Wilkes, Cyril; Garnier, Olivier; Labadie, Karine; Lauderdale, Benjamin E.; Le Mouël, Anne; Marmignon, Antoine; Nowacki, Mariusz; Poulain, Julie; Prajer, Malgorzata; Wincker, Patrick; Meyer, Eric; Duharcourt, Sandra; Duret, Laurent; Bétermier, Mireille; Sperling, Linda

2012-01-01

Insertions of parasitic DNA within coding sequences are usually deleterious and are generally counter-selected during evolution. Thanks to nuclear dimorphism, ciliates provide unique models to study the fate of such insertions. Their germline genome undergoes extensive rearrangements during development of a new somatic macronucleus from the germline micronucleus following sexual events. In Paramecium, these rearrangements include precise excision of unique-copy Internal Eliminated Sequences (IES) from the somatic DNA, requiring the activity of a domesticated piggyBac transposase, PiggyMac. We have sequenced Paramecium tetraurelia germline DNA, establishing a genome-wide catalogue of ∼45,000 IESs, in order to gain insight into their evolutionary origin and excision mechanism. We obtained direct evidence that PiggyMac is required for excision of all IESs. Homology with known P. tetraurelia Tc1/mariner transposons, described here, indicates that at least a fraction of IESs derive from these elements. Most IES insertions occurred before a recent whole-genome duplication that preceded diversification of the P. aurelia species complex, but IES invasion of the Paramecium genome appears to be an ongoing process. Once inserted, IESs decay rapidly by accumulation of deletions and point substitutions. Over 90% of the IESs are shorter than 150 bp and present a remarkable size distribution with a ∼10 bp periodicity, corresponding to the helical repeat of double-stranded DNA and suggesting DNA loop formation during assembly of a transpososome-like excision complex. IESs are equally frequent within and between coding sequences; however, excision is not 100% efficient and there is selective pressure against IES insertions, in particular within highly expressed genes. We discuss the possibility that ancient domestication of a piggyBac transposase favored subsequent propagation of transposons throughout the germline by allowing insertions in coding sequences, a fraction of the genome in which parasitic DNA is not usually tolerated. PMID:23071448

Spin dependent transport properties of Mn-Ga/MgO/Mn-Ga magnetic tunnel junctions with metal(Mg, Co, Cr) insertion layer

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

Liang, S. H.; Tao, L. L.; Liu, D. P., E-mail: dpliu@iphy.ac.cn

We report a first principles theoretical investigation of spin polarized quantum transport in Mn{sub 2}Ga/MgO/Mn{sub 2}Ga and Mn{sub 3}Ga/MgO/Mn{sub 3}Ga magnetic tunneling junctions (MTJs) with the consideration of metal(Mg, Co, Cr) insertion layer effect. By changing the concentration of Mn, our calculation shows a considerable disparity in transport properties: A tunneling magnetoresistance (TMR) ratio of 852% was obtained for Mn{sub 2}Ga-based MTJs, however, only a 5% TMR ratio for Mn{sub 3}Ga-based MTJs. In addition, the influence of insertion layer has been considered in our calculation. We found the Co insertion layer can increase the TMR of Mn{sub 2}Ga-based MTJ tomore » 904%; however, the Cr insertion layer can decrease the TMR by 668%; A negative TMR ratio can be obtained with Mg insertion layer. Our work gives a comprehensive understanding of the influence of different insertion layer in Mn-Ga based MTJs. It is proved that, due to the transmission can be modulated by the interfacial electronic structure of insertion, the magnetoresistance ratio of Mn{sub 2}Ga/MgO/Mn{sub 2}Ga MTJ can be improved by inserting Co layer.« less

Germline mutations affecting the proofreading domains of POLE and POLD1 predispose to colorectal adenomas and carcinomas.

PubMed

Palles, Claire; Cazier, Jean-Baptiste; Howarth, Kimberley M; Domingo, Enric; Jones, Angela M; Broderick, Peter; Kemp, Zoe; Spain, Sarah L; Guarino, Estrella; Guarino Almeida, Estrella; Salguero, Israel; Sherborne, Amy; Chubb, Daniel; Carvajal-Carmona, Luis G; Ma, Yusanne; Kaur, Kulvinder; Dobbins, Sara; Barclay, Ella; Gorman, Maggie; Martin, Lynn; Kovac, Michal B; Humphray, Sean; Lucassen, Anneke; Holmes, Christopher C; Bentley, David; Donnelly, Peter; Taylor, Jenny; Petridis, Christos; Roylance, Rebecca; Sawyer, Elinor J; Kerr, David J; Clark, Susan; Grimes, Jonathan; Kearsey, Stephen E; Thomas, Huw J W; McVean, Gilean; Houlston, Richard S; Tomlinson, Ian

2013-02-01

Many individuals with multiple or large colorectal adenomas or early-onset colorectal cancer (CRC) have no detectable germline mutations in the known cancer predisposition genes. Using whole-genome sequencing, supplemented by linkage and association analysis, we identified specific heterozygous POLE or POLD1 germline variants in several multiple-adenoma and/or CRC cases but in no controls. The variants associated with susceptibility, POLE p.Leu424Val and POLD1 p.Ser478Asn, have high penetrance, and POLD1 mutation was also associated with endometrial cancer predisposition. The mutations map to equivalent sites in the proofreading (exonuclease) domain of DNA polymerases ɛ and δ and are predicted to cause a defect in the correction of mispaired bases inserted during DNA replication. In agreement with this prediction, the tumors from mutation carriers were microsatellite stable but tended to acquire base substitution mutations, as confirmed by yeast functional assays. Further analysis of published data showed that the recently described group of hypermutant, microsatellite-stable CRCs is likely to be caused by somatic POLE mutations affecting the exonuclease domain.

Molecular spectrum of somaclonal variation in regenerated rice revealed by whole-genome sequencing.

PubMed

Miyao, Akio; Nakagome, Mariko; Ohnuma, Takako; Yamagata, Harumi; Kanamori, Hiroyuki; Katayose, Yuichi; Takahashi, Akira; Matsumoto, Takashi; Hirochika, Hirohiko

2012-01-01

Somaclonal variation is a phenomenon that results in the phenotypic variation of plants regenerated from cell culture. One of the causes of somaclonal variation in rice is the transposition of retrotransposons. However, many aspects of the mechanisms that result in somaclonal variation remain undefined. To detect genome-wide changes in regenerated rice, we analyzed the whole-genome sequences of three plants independently regenerated from cultured cells originating from a single seed stock. Many single-nucleotide polymorphisms (SNPs) and insertions and deletions (indels) were detected in the genomes of the regenerated plants. The transposition of only Tos17 among 43 transposons examined was detected in the regenerated plants. Therefore, the SNPs and indels contribute to the somaclonal variation in regenerated rice in addition to the transposition of Tos17. The observed molecular spectrum was similar to that of the spontaneous mutations in Arabidopsis thaliana. However, the base change ratio was estimated to be 1.74 × 10(-6) base substitutions per site per regeneration, which is 248-fold greater than the spontaneous mutation rate of A. thaliana.

Coevolution between Nuclear-Encoded DNA Replication, Recombination, and Repair Genes and Plastid Genome Complexity.

PubMed

Zhang, Jin; Ruhlman, Tracey A; Sabir, Jamal S M; Blazier, John Chris; Weng, Mao-Lun; Park, Seongjun; Jansen, Robert K

2016-02-17

Disruption of DNA replication, recombination, and repair (DNA-RRR) systems has been hypothesized to cause highly elevated nucleotide substitution rates and genome rearrangements in the plastids of angiosperms, but this theory remains untested. To investigate nuclear-plastid genome (plastome) coevolution in Geraniaceae, four different measures of plastome complexity (rearrangements, repeats, nucleotide insertions/deletions, and substitution rates) were evaluated along with substitution rates of 12 nuclear-encoded, plastid-targeted DNA-RRR genes from 27 Geraniales species. Significant correlations were detected for nonsynonymous (dN) but not synonymous (dS) substitution rates for three DNA-RRR genes (uvrB/C, why1, and gyrA) supporting a role for these genes in accelerated plastid genome evolution in Geraniaceae. Furthermore, correlation between dN of uvrB/C and plastome complexity suggests the presence of nucleotide excision repair system in plastids. Significant correlations were also detected between plastome complexity and 13 of the 90 nuclear-encoded organelle-targeted genes investigated. Comparisons revealed significant acceleration of dN in plastid-targeted genes of Geraniales relative to Brassicales suggesting this correlation may be an artifact of elevated rates in this gene set in Geraniaceae. Correlation between dN of plastid-targeted DNA-RRR genes and plastome complexity supports the hypothesis that the aberrant patterns in angiosperm plastome evolution could be caused by dysfunction in DNA-RRR systems. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

INS studies of Cobalt-Copper Catalyst for the Conversion of Syngas to Higher Oxygenates

NASA Astrophysics Data System (ADS)

Sprunger, Phillip; Wang, Zi; Patterson, Matthew; Kurtz, Richard; Spivey, James

Cobalt-copper catalysts have been proposed for the synthesis of ethanol and higher oxygenates as a substitute of Rh and other high-cost noble metal catalysts. Two types of sites with atomic proximity are needed to form higher oxygenates: one to dissociate CO and a second to insert CO to the intermediates to form the CHxCO intermediate. Metallic cobalt is responsible for CO dissociation, while the nature of the site for CO insertion is still under study. We have utilized inelastic neutron scattering (INS) at the VISION beamline at SNS to probe intermediate surface species of this cobalt-copper catalyst. This unique technique allows for elucidation of mechanistic details of the CO insertion and subsequent CHxCO intermediate formation on the metal surfaces (Co0, Co2C and/or Cu0) . In addition to XRD and EXAFS which show a unique surface Co-C carbide formation, a combination of both INS and computational modeling indicate that the active site for CHxCO intermediates. Sponsored through the Louisiana Consortium for Neutron Scattering, DOE No. DE-SC0012432 with additional support from the LA BOR; also ORNL's Spallation Neutron Source (VISION Beamline), DOE-BES under Contract No. DE-AC0500OR22725.

Accuracy of pedicle screw insertion by AIRO® intraoperative CT in complex spinal deformity assessed by a new classification based on technical complexity of screw insertion.

PubMed

Rajasekaran, S; Bhushan, Manindra; Aiyer, Siddharth; Kanna, Rishi; Shetty, Ajoy Prasad

2018-01-09

To develop a classification based on the technical complexity encountered during pedicle screw insertion and to evaluate the performance of AIRO ® CT navigation system based on this classification, in the clinical scenario of complex spinal deformity. 31 complex spinal deformity correction surgeries were prospectively analyzed for performance of AIRO ® mobile CT-based navigation system. Pedicles were classified according to complexity of insertion into five types. Analysis was performed to estimate the accuracy of screw placement and time for screw insertion. Breach greater than 2 mm was considered for analysis. 452 pedicle screws were inserted (T1-T6: 116; T7-T12: 171; L1-S1: 165). The average Cobb angle was 68.3° (range 60°-104°). We had 242 grade 2 pedicles, 133 grade 3, and 77 grade 4, and 44 pedicles were unfit for pedicle screw insertion. We noted 27 pedicle screw breach (medial: 10; lateral: 16; anterior: 1). Among lateral breach (n = 16), ten screws were planned for in-out-in pedicle screw insertion. Among lateral breach (n = 16), ten screws were planned for in-out-in pedicle screw insertion. Average screw insertion time was 1.76 ± 0.89 min. After accounting for planned breach, the effective breach rate was 3.8% resulting in 96.2% accuracy for pedicle screw placement. This classification helps compare the accuracy of screw insertion in range of conditions by considering the complexity of screw insertion. Considering the clinical scenario of complex pedicle anatomy in spinal deformity AIRO ® navigation showed an excellent accuracy rate of 96.2%.

Teleoperated master-slave needle insertion.

PubMed

Abolhassani, Niki; Patel, Rajni V

2009-12-01

Accuracy of needle tip placement and needle tracking in soft tissue are of particular importance in many medical procedures. In recent years, developing autonomous and teleoperated systems for needle insertion has become an active area of research. In this study, needle insertion was performed using a master-slave set-up with multi-degrees of freedom. The effect of force feedback on the accuracy of needle insertion was investigated. In addition, this study compared autonomous, teleoperated and semi-autonomous needle insertion. The results of this study show that incorporation of force feedback can improve teleoperated needle insertion. However, autonomous and semi-autonomous needle insertions, which use feedback from a deflection model, provide significantly better performance. Development of a haptic master-slave needle insertion system, which is capable of performing some autonomous tasks based on feedback from tissue deformation and needle deflection models, can improve the performance of autonomous robotics-based insertions as well as non-autonomous teleoperated manual insertions. Copyright (c) 2009 John Wiley & Sons, Ltd.

Treatment Using the SpyGlass Digital System in a Patient with Hepatolithiasis after a Whipple Procedure.

PubMed

Harima, Hirofumi; Hamabe, Kouichi; Hisano, Fusako; Matsuzaki, Yuko; Itoh, Tadahiko; Sanuki, Kazutoshi; Sakaida, Isao

2018-05-23

An 89-year-old man was referred to our hospital for treatment of hepatolithiasis causing recurrent cholangitis. He had undergone a prior Whipple procedure. Computed tomography demonstrated left-sided hepatolithiasis. First, we conducted peroral direct cholangioscopy (PDCS) using an ultraslim endoscope. Although PDCS was successfully conducted, it was unsuccessful in removing all the stones. The stones located in the B2 segment were difficult to remove because the endoscope could not be inserted deeply into this segment due to the small size of the intrahepatic bile duct. Next, we substituted the endoscope with an upper gastrointestinal endoscope. After positioning the endoscope, the SpyGlass digital system (SPY-DS) was successfully inserted deep into the B2 segment. Upon visualizing the residual stones, we conducted SPY-DS-guided electrohydraulic lithotripsy. The stones were disintegrated and completely removed. In cases of PDCS failure, a treatment strategy using the SPY-DS can be considered for patients with hepatolithiasis after a Whipple procedure.

Retrotransposon Tf1 is targeted to pol II promoters by transcription activators

PubMed Central

Leem, Young-Eun; Ripmaster, Tracy; Kelly, Felice; Ebina, Hirotaka; Heincelman, Marc; Zhang, Ke; Grewal, Shiv I. S.; Hoffman, Charles S.; Levin, Henry L.

2008-01-01

SUMMARY The LTR-retrotransposon Tf1 preserves the coding capacity of its host Schizosaccharomyces pombe by integrating upstream of open reading frames (ORFs). To determine which features of the target sites were recognized by the transposon, we introduced plasmids containing candidate insertion sites into S. pombe and mapped the positions of integration. We found that Tf1 was targeted specifically to the promoters of pol II transcribed genes. A detailed analysis of integration in plasmids that contained either ade6 or fbp1 revealed insertions occurred in the promoters at positions where transcription factors bound. Further experiments revealed that the activator Atf1p and its binding site were required for directing integration to the promoter of fbp1. An interaction between Tf1 integrase and Atf1p was observed indicating that integration at fbp1 was mediated by the activator bound to its promoter. Surprisingly we found Tf1 contained sequences that activated transcription and these substituted for elements of the ade6 promoter disrupted by integration. PMID:18406330

Retrotransposon Tf1 is targeted to Pol II promoters by transcription activators.

PubMed

Leem, Young-Eun; Ripmaster, Tracy L; Kelly, Felice D; Ebina, Hirotaka; Heincelman, Marc E; Zhang, Ke; Grewal, Shiv I S; Hoffman, Charles S; Levin, Henry L

2008-04-11

The LTR-retrotransposon Tf1 preserves the coding capacity of its host Schizosaccharomyces pombe by integrating upstream of open reading frames (ORFs). To determine which features of the target sites were recognized by the transposon, we introduced plasmids containing candidate insertion sites into S. pombe and mapped the positions of integration. We found that Tf1 was targeted specifically to the promoters of Pol II-transcribed genes. A detailed analysis of integration in plasmids that contained either ade6 or fbp1 revealed insertions occurred in the promoters at positions where transcription factors bound. Further experiments revealed that the activator Atf1p and its binding site were required for directing integration to the promoter of fbp1. An interaction between Tf1 integrase and Atf1p was observed, indicating that integration at fbp1 was mediated by the activator bound to its promoter. Surprisingly, we found Tf1 contained sequences that activated transcription, and these substituted for elements of the ade6 promoter disrupted by integration.

Anomalous Hall hysteresis in T m3F e5O12/Pt with strain-induced perpendicular magnetic anisotropy

NASA Astrophysics Data System (ADS)

Tang, Chi; Sellappan, Pathikumar; Liu, Yawen; Xu, Yadong; Garay, Javier E.; Shi, Jing

2016-10-01

We demonstrate robust interface strain-induced perpendicular magnetic anisotropy in atomically flat ferrimagnetic insulator T m3F e5O12 (TIG) films grown with pulsed laser deposition on a substituted G d3G a5O12 substrate which maximizes the tensile strain at the interface. In bilayers consisting of Pt and TIG, we observe large squared Hall hysteresis loops over a wide range of thicknesses of Pt at room temperature. When a thin Cu layer is inserted between Pt and TIG, the Hall hysteresis magnitude decays but stays finite as the thickness of Cu increases up to 5 nm. However, if the Cu layer is placed atop Pt instead, the Hall hysteresis magnitude is consistently larger than when the Cu layer with the same thickness is inserted in between for all Cu thicknesses. These results suggest that both the proximity-induced ferromagnetism and spin current contribute to the anomalous Hall effect.

Thin-film magnetless Faraday rotators for compact heterogeneous integrated optical isolators

NASA Astrophysics Data System (ADS)

Karki, Dolendra; Stenger, Vincent; Pollick, Andrea; Levy, Miguel

2017-06-01

This report describes the fabrication, characterization, and transfer of ultra-compact thin-film magnetless Faraday rotators to silicon photonic substrates. Thin films of magnetization latching bismuth-substituted rare-earth iron garnets were produced from commercially available materials by mechanical lapping, dice polishing, and crystal-ion-slicing. Eleven- μ m -thick films were shown to retain the 45 ° Faraday rotation of the bulk material to within 2 ° at 1.55 μ m wavelength without re-poling. Anti-reflection coated films evince 0.09 dB insertion loses and better than -20 dB extinction ratios. Lower extinction ratios than the bulk are ascribed to multimode propagation. Significantly larger extinction ratios are predicted for single-mode waveguides. Faraday rotation, extinction ratios, and insertion loss tests on He-ion implanted slab waveguides of the same material yielded similar results. The work culminated with bond alignment and transfer of 7 μ m -thick crystal-ion-sliced 50 × 480 μ m 2 films onto silicon photonic substrates.

MODEST: a web-based design tool for oligonucleotide-mediated genome engineering and recombineering

PubMed Central

Bonde, Mads T.; Klausen, Michael S.; Anderson, Mads V.; Wallin, Annika I.N.; Wang, Harris H.; Sommer, Morten O.A.

2014-01-01

Recombineering and multiplex automated genome engineering (MAGE) offer the possibility to rapidly modify multiple genomic or plasmid sites at high efficiencies. This enables efficient creation of genetic variants including both single mutants with specifically targeted modifications as well as combinatorial cell libraries. Manual design of oligonucleotides for these approaches can be tedious, time-consuming, and may not be practical for larger projects targeting many genomic sites. At present, the change from a desired phenotype (e.g. altered expression of a specific protein) to a designed MAGE oligo, which confers the corresponding genetic change, is performed manually. To address these challenges, we have developed the MAGE Oligo Design Tool (MODEST). This web-based tool allows designing of MAGE oligos for (i) tuning translation rates by modifying the ribosomal binding site, (ii) generating translational gene knockouts and (iii) introducing other coding or non-coding mutations, including amino acid substitutions, insertions, deletions and point mutations. The tool automatically designs oligos based on desired genotypic or phenotypic changes defined by the user, which can be used for high efficiency recombineering and MAGE. MODEST is available for free and is open to all users at http://modest.biosustain.dtu.dk. PMID:24838561

[A study of PDE6B gene mutation and phenotype in Chinese cases with retinitis pigmentosa].

PubMed

Cui, Yun; Zhao, Kan-xing; Wang, Li; Wang, Qing; Zhang, Wei; Chen, Wei-ying; Wang, Li-ming

2003-01-01

To identify the mutation spectrum of phosphodiesterase beta subunit (PDE6B) gene, the incidence in Chinese patients with retinitis pigmentosa (RP) and their clinical phenotypic characteristics. Screening of mutations within PDE6B gene was performed using polymerase chain reaction-heteroduplex-single strand conformation polymorphism (PCR-SSCP) and DNA sequence in 35 autosomal recessive (AR) RP and 55 sporadic RP cases. The phenotypes of the patients with the gene mutation were examined and analyzed. Novel complex heterozygous variants of PDE6B gene in a sporadic case, a T to C transversion in codon 323 resulting in the substitution of Gly by Ser and 2 base pairs (bp: G and T) insert between the 27th-28th bp upstream of the 5'-end of exon 10 were both present in a same isolate RP. But they are not found in 100 unrelated healthy individuals. Ocular findings showed diffuse pigmentary retinal degeneration in the midperipheral and peripheral fundi, optic atrophy and vessel attenuation. Multi-focal ERG indicated that the rod function was more severely deteriorated. A mutation was found in a case with RP in a ARRP family, a G to A transversion at 19th base upstream 5'-end of exon 11 (within intron 10) of PDE6B gene. A sporadic RP carried a sequence variant of PDE6B gene, a G to C transition, at the 15th base adjacent to the 3'-end of exon l8. In another isolate case with RP was found 2 bp (GT) insert between 31st and 32nd base upstream 5'-end of exon 4 (in intron 3) of PDE6B gene. There are novel complex heterozygous mutations of PDE6B gene responsible for a sporadic RP patient in China. This gene mutation associated with rod deterioration and RP. Several DNA variants were found in introns of PDE6B gene in national population.

Use of simulation-based education to reduce catheter-related bloodstream infections.

PubMed

Barsuk, Jeffrey H; Cohen, Elaine R; Feinglass, Joe; McGaghie, William C; Wayne, Diane B

2009-08-10

Simulation-based education improves procedural competence in central venous catheter (CVC) insertion. The effect of simulation-based education in CVC insertion on the incidence of catheter-related bloodstream infection (CRBSI) is unknown. The aim of this study was to determine if simulation-based training in CVC insertion reduces CRBSI. This was an observational education cohort study set in an adult intensive care unit (ICU) in an urban teaching hospital. Ninety-two internal medicine and emergency medicine residents completed a simulation-based mastery learning program in CVC insertion skills. Rates of CRBSI from CVCs inserted by residents in the ICU before and after the simulation-based educational intervention were compared over a 32-month period. There were fewer CRBSIs after the simulator-trained residents entered the intervention ICU (0.50 infections per 1000 catheter-days) compared with both the same unit prior to the intervention (3.20 per 1000 catheter-days) (P = .001) and with another ICU in the same hospital throughout the study period (5.03 per 1000 catheter-days) (P = .001). An educational intervention in CVC insertion significantly improved patient outcomes. Simulation-based education is a valuable adjunct in residency education.

The novel cytochrome c6 of chloroplasts: a case of evolutionary bricolage?

PubMed

Howe, Christopher J; Schlarb-Ridley, Beatrix G; Wastl, Juergen; Purton, Saul; Bendall, Derek S

2006-01-01

Cytochrome c6 has long been known as a redox carrier of the thylakoid lumen of cyanobacteria and some eukaryotic algae that can substitute for plastocyanin in electron transfer. Until recently, it was widely accepted that land plants lack a cytochrome c6. However, a homologue of the protein has now been identified in several plant species together with an additional isoform in the green alga Chlamydomonas reinhardtii. This form of the protein, designated cytochrome c6A, differs from the 'conventional' cytochrome c6 in possessing a conserved insertion of 12 amino acids that includes two absolutely conserved cysteine residues. There are conflicting reports of whether cytochrome c6A can substitute for plastocyanin in photosynthetic electron transfer. The evidence for and against this is reviewed and the likely evolutionary history of cytochrome c6A is discussed. It is suggested that it has been converted from a primary role in electron transfer to one in regulation within the chloroplast, and is an example of evolutionary 'bricolage'.

Evolutionary mechanisms involved in the virulence of infectious salmon anaemia virus (ISAV), a piscine orthomyxovirus

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

Markussen, Turhan; Jonassen, Christine Monceyron; Numanovic, Sanela

2008-05-10

Infectious salmon anaemia virus (ISAV) is an orthomyxovirus causing a multisystemic, emerging disease in Atlantic salmon. Here we present, for the first time, detailed sequence analyses of the full-genome sequence of a presumed avirulent isolate displaying a full-length hemagglutinin-esterase (HE) gene (HPR0), and compare this with full-genome sequences of 11 Norwegian ISAV isolates from clinically diseased fish. These analyses revealed the presence of a virulence marker right upstream of the putative cleavage site R{sub 267} in the fusion (F) protein, suggesting a Q{sub 266} {yields} L{sub 266} substitution to be a prerequisite for virulence. To gain virulence in isolates lackingmore » this substitution, a sequence insertion near the cleavage site seems to be required. This strongly suggests the involvement of a protease recognition pattern at the cleavage site of the fusion protein as a determinant of virulence, as seen in highly pathogenic influenza A virus H5 or H7 and the paramyxovirus Newcastle disease virus.« less

A novel mutation affecting the arginine-137 residue of AVPR2 in dizygous twins leads to nephrogenic diabetes insipidus and attenuated urine exosome aquaporin-2.

PubMed

Hinrichs, Gitte R; Hansen, Louise H; Nielsen, Maria R; Fagerberg, Christina; Dieperink, Hans; Rittig, Søren; Jensen, Boye L

2016-04-01

Mutations in the vasopressin V2 receptor gene AVPR2 may cause X-linked nephrogenic diabetes insipidus by defective apical insertion of aquaporin-2 in the renal collecting duct principal cell. Substitution mutations with exchange of arginine at codon 137 can cause nephrogenic syndrome of inappropriate antidiuresis or congenital X-linked nephrogenic diabetes insipidus. We present a novel mutation in codon 137 within AVPR2 with substitution of glycine for arginine in male dizygotic twins. Nephrogenic diabetes insipidus was demonstrated by water deprivation test and resistance to vasopressin administration. While a similar urine exosome release rate was shown between probands and controls by western blotting for the marker ALIX, there was a selective decrease in exosome aquaporin-2 versus aquaporin-1 protein in probands compared to controls. © 2016 The Authors. Physiological Reports published by Wiley Periodicals, Inc. on behalf of the American Physiological Society and The Physiological Society.

Effect of cobalt on Escherichia coli metabolism and metalloporphyrin formation

PubMed Central

Majtan, Tomas; Frerman, Frank E.

2011-01-01

Toxicity in Escherichia coli resulting from high concentrations of cobalt has been explained by competition of cobalt with iron in various metabolic processes including Fe–S cluster assembly, sulfur assimilation, production of free radicals and reduction of free thiol pool. Here we present another aspect of increased cobalt concentrations in the culture medium resulting in the production of cobalt protoporphyrin IX (CoPPIX), which was incorporated into heme proteins including membrane-bound cytochromes and an expressed human cystathionine beta-synthase (CBS). The presence of CoPPIX in cytochromes inhibited their electron transport capacity and resulted in a substantially decreased respiration. Bacterial cells adapted to the increased cobalt concentration by inducing a modified mixed acid fermentative pathway under aerobiosis. We capitalized on the ability of E. coli to insert cobalt into PPIX to carry out an expression of CoPPIX-substituted heme proteins. The level of CoPPIX-substitution increased with the number of passages of cells in a cobalt-containing medium. This approach is an inexpensive method to prepare cobalt-substituted heme proteins compared to in vitro enzyme reconstitution or in vivo replacement using metalloporphyrin heme analogs and seems to be especially suitable for complex heme proteins with an additional coenzyme, such as human CBS. PMID:21184140

An SRY mutation causing human sex reversal resolves a general mechanism of structure-specific DNA recognition: application to the four-way DNA junction.

PubMed

Peters, R; King, C Y; Ukiyama, E; Falsafi, S; Donahoe, P K; Weiss, M A

1995-04-11

SRY, a genetic "master switch" for male development in mammals, exhibits two biochemical activities: sequence-specific recognition of duplex DNA and sequence-independent binding to the sharp angles of four-way DNA junctions. Here, we distinguish between these activities by analysis of a mutant SRY associated with human sex reversal (46, XY female with pure gonadal dysgenesis). The substitution (168T in human SRY) alters a nonpolar side chain in the minor-groove DNA recognition alpha-helix of the HMG box [Haqq, C.M., King, C.-Y., Ukiyama, E., Haqq, T.N., Falsalfi, S., Donahoe, P.K., & Weiss, M.A. (1994) Science 266, 1494-1500]. The native (but not mutant) side chain inserts between specific base pairs in duplex DNA, interrupting base stacking at a site of induced DNA bending. Isotope-aided 1H-NMR spectroscopy demonstrates that analogous side-chain insertion occurs on binding of SRY to a four-way junction, establishing a shared mechanism of sequence- and structure-specific DNA binding. Although the mutant DNA-binding domain exhibits > 50-fold reduction in sequence-specific DNA recognition, near wild-type affinity for four-way junctions is retained. Our results (i) identify a shared SRY-DNA contact at a site of either induced or intrinsic DNA bending, (ii) demonstrate that this contact is not required to bind an intrinsically bent DNA target, and (iii) rationalize patterns of sequence conservation or diversity among HMG boxes. Clinical association of the I68T mutation with human sex reversal supports the hypothesis that specific DNA recognition by SRY is required for male sex determination.

Development and comparison of projection and image space 3D nodule insertion techniques

NASA Astrophysics Data System (ADS)

Robins, Marthony; Solomon, Justin; Sahbaee, Pooyan; Samei, Ehsan

2016-04-01

This study aimed to develop and compare two methods of inserting computerized virtual lesions into CT datasets. 24 physical (synthetic) nodules of three sizes and four morphologies were inserted into an anthropomorphic chest phantom (LUNGMAN, KYOTO KAGAKU). The phantom was scanned (Somatom Definition Flash, Siemens Healthcare) with and without nodules present, and images were reconstructed with filtered back projection and iterative reconstruction (SAFIRE) at 0.6 mm slice thickness using a standard thoracic CT protocol at multiple dose settings. Virtual 3D CAD models based on the physical nodules were virtually inserted (accounting for the system MTF) into the nodule-free CT data using two techniques. These techniques include projection-based and image-based insertion. Nodule volumes were estimated using a commercial segmentation tool (iNtuition, TeraRecon, Inc.). Differences were tested using paired t-tests and R2 goodness of fit between the virtually and physically inserted nodules. Both insertion techniques resulted in nodule volumes very similar to the real nodules (<3% difference) and in most cases the differences were not statistically significant. Also, R2 values were all <0.97 for both insertion techniques. These data imply that these techniques can confidently be used as a means of inserting virtual nodules in CT datasets. These techniques can be instrumental in building hybrid CT datasets composed of patient images with virtually inserted nodules.

Double-double bend achromat cell upgrade at the Diamond Light Source: From design to commissioning

NASA Astrophysics Data System (ADS)

Bartolini, R.; Abraham, C.; Apollonio, M.; Bailey, C. P.; Cox, M. P.; Day, A.; Fielder, R. T.; Hammond, N. P.; Heron, M. T.; Holdsworth, R.; Kay, J.; Martin, I. P. S.; Mhaskar, S.; Miller, A.; Pulampong, T.; Rehm, G.; Rial, E. C. M.; Rose, A.; Shahveh, A.; Singh, B.; Thomson, A.; Walker, R. P.

2018-05-01

Diamond has recently successfully commissioned a major change in the lattice consisting of the substitution of a standard double-bend achromat (DBA) cell with a modified four-bend achromat (4BA) cell called "double-double bend achromat" (DDBA). This work stems from the original studies initiated in 2012 towards a Diamond upgrade and provides the benefit of an additional straight section in the ring available for insertion devices. This paper reviews the DDBA design and layout, the implications for technical subsystems, the associated engineering challenges and the main results of the commissioning completed in April 2017.

Spelling Errors of Dyslexic Children in Bosnian Language With Transparent Orthography.

PubMed

Duranović, Mirela

The purpose of this study was to explore the nature of spelling errors made by children with dyslexia in Bosnian language with transparent orthography. Three main error categories were distinguished: phonological, orthographic, and grammatical errors. An analysis of error type showed 86% of phonological errors,10% of orthographic errors, and 4% of grammatical errors. Furthermore, the majority errors were the omissions and substitutions, followed by the insertions, omission of rules of assimilation by voicing, and errors with utilization of suffix. We can conclude that phonological errors were dominant in children with dyslexia at all grade levels.

Cryogenic expansion machine

DOEpatents

Pallaver, Carl B.; Morgan, Michael W.

1978-01-01

A cryogenic expansion engine includes intake and exhaust poppet valves each controlled by a cam having adjustable dwell, the valve seats for the valves being threaded inserts in the valve block. Each cam includes a cam base and a ring-shaped cam insert disposed at an exterior corner of the cam base, the cam base and cam insert being generally circular but including an enlarged cam dwell, the circumferential configuration of the cam base and cam dwell being identical, the cam insert being rotatable with respect to the cam base. GI CONTRACTUAL ORIGIN OF THE INVENTION The invention described herein was made in the course of, or under, a contract with the UNITED STATES ENERGY RESEARCH AND DEVELOPMENT ADMINISTRATION.

Molecular design toward highly efficient photovoltaic polymers based on two-dimensional conjugated benzodithiophene.

PubMed

Ye, Long; Zhang, Shaoqing; Huo, Lijun; Zhang, Maojie; Hou, Jianhui

2014-05-20

As researchers continue to develop new organic materials for solar cells, benzo[1,2-b:4,5-b']dithiophene (BDT)-based polymers have come to the fore. To improve the photovoltaic properties of BDT-based polymers, researchers have developed and applied various strategies leading to the successful molecular design of highly efficient photovoltaic polymers. Novel polymer materials composed of two-dimensional conjugated BDT (2D-conjugated BDT) have boosted the power conversion efficiency of polymer solar cells (PSCs) to levels that exceed 9%. In this Account, we summarize recent progress related to the design and synthesis of 2D-conjugated BDT-based polymers and discuss their applications in highly efficient photovoltaic devices. We introduce the basic considerations for the construction of 2D-conjugated BDT-based polymers and systematic molecular design guidelines. For example, simply modifying an alkoxyl-substituted BDT to form an alkylthienyl-substituted BDT can improve the polymer hole mobilities substantially with little effect on their molecular energy level. Secondly, the addition of a variety of chemical moieties to the polymer can produce a 2D-conjugated BDT unit with more functions. For example, the introduction of a conjugated side chain with electron deficient groups (such as para-alkyl-phenyl, meta-alkoxyl-phenyl, and 2-alkyl-3-fluoro-thienyl) allowed us to modulate the molecular energy levels of 2D-conjugated BDT-based polymers. Through the rational design of BDT analogues such as dithienobenzodithiophene (DTBDT) or the insertion of larger π bridges, we can tune the backbone conformations of these polymers and modulate their photovoltaic properties. We also discuss the influence of 2D-conjugated BDT on polymer morphology and the blends of these polymers with phenyl-C61 (or C71)-butyric acid methyl ester (PCBM). Finally, we summarize the various applications of the 2D-conjugated BDT-based polymers in highly efficient PSC devices. Overall, this Account correlates the molecular structures of the 2D-conjugated BDT-based polymers with their photovoltaic properties. As a result, this Account can guide the molecular design of organic photovoltaic materials and the development of organic materials for other types of optoelectronic devices.

Comprehensive genomic profiling of 295 cases of clinically advanced urothelial carcinoma of the urinary bladder reveals a high frequency of clinically relevant genomic alterations.

PubMed

Ross, Jeffrey S; Wang, Kai; Khaira, Depinder; Ali, Siraj M; Fisher, Huge A G; Mian, Badar; Nazeer, Tipu; Elvin, Julia A; Palma, Norma; Yelensky, Roman; Lipson, Doron; Miller, Vincent A; Stephens, Philip J; Subbiah, Vivek; Pal, Sumanta K

2016-03-01

In the current study, the authors present a comprehensive genomic profile (CGP)-based study of advanced urothelial carcinoma (UC) designed to detect clinically relevant genomic alterations (CRGAs). DNA was extracted from 40 µm of formalin-fixed, paraffin-embedded sections from 295 consecutive cases of recurrent/metastatic UC. CGP was performed on hybridization-captured, adaptor ligation-based libraries to a mean coverage depth of 688X for all coding exons of 236 cancer-related genes plus 47 introns from 19 genes frequently rearranged in cancer, using process-matched normal control samples as a reference. CRGAs were defined as GAs linked to drugs on the market or currently under evaluation in mechanism-driven clinical trials. All 295 patients assessed were classified with high-grade (International Society of Urological Pathology classification) and advanced stage (stage III/IV American Joint Committee on Cancer) disease, and 294 of 295 patients (99.7%) had at least 1 GA on CGP with a mean of 6.4 GAs per UC (61% substitutions/insertions/deletions, 37% copy number alterations, and 2% fusions). Furthermore, 275 patients (93%) had at least 1 CRGA involving 75 individual genes with a mean of 2.6 CRGAs per UC. The most common CRGAs involved cyclin-dependent kinase inhibitor 2A (CDKN2A) (34%), fibroblast growth factor receptor 3 (FGFR3) (21%), phosphatidylinositol 3-kinase catalytic subunit alpha (PIK3CA) (20%), and ERBB2 (17%). FGFR3 GAs were diverse types and included 10% fusions. ERBB2 GAs were equally divided between amplifications and substitutions. ERBB2 substitutions were predominantly within the extracellular domain and were highly enriched in patients with micropapillary UC (38% of 32 cases vs 5% of 263 nonmicropapillary UC cases; P<.0001). Using a CGP assay capable of detecting all classes of GA simultaneously, an extraordinarily high frequency of CRGA was identified in a large series of patients with advanced UC. Cancer 2016;122:702-711. © 2015 American Cancer Society. © 2015 American Cancer Society.

A mutant (‘lab strain’) of the hyperthermophilic archaeon Pyrococcus furiosus, lacking flagella, has unusual growth physiology

DOE PAGES

Lewis, Derrick L.; Notey, Jaspreet S.; Chandrayan, Sanjeev K.; ...

2014-12-04

In this paper, a mutant (‘lab strain’) of the hyperthermophilic archaeon Pyrococcus furiosus DSM3638 exhibited an extended exponential phase and atypical cell aggregation behavior. Genomic DNA from the mutant culture was sequenced and compared to wild-type (WT) DSM3638, revealing 145 genes with one or more insertions, deletions, or substitutions (12 silent, 33 amino acid substitutions, and 100 frame shifts). Approximately, half of the mutated genes were transposases or hypothetical proteins. The WT transcriptome revealed numerous changes in amino acid and pyrimidine biosynthesis pathways coincidental with growth phase transitions, unlike the mutant whose transcriptome reflected the observed prolonged exponential phase. Targetedmore » gene deletions, based on frame-shifted ORFs in the mutant genome, in a genetically tractable strain of P. furiosus (COM1) could not generate the extended exponential phase behavior observed for the mutant. For example, a putative radical SAM family protein (PF2064) was the most highly up-regulated ORF (>25-fold) in the WT between exponential and stationary phase, although this ORF was unresponsive in the mutant; deletion of this gene in P. furiosus COM1 resulted in no apparent phenotype. On the other hand, frame-shifting mutations in the mutant genome negatively impacted transcription of a flagellar biosynthesis operon (PF0329-PF0338).Consequently, cells in the mutant culture lacked flagella and, unlike the WT, showed minimal evidence of exopolysaccharide-based cell aggregation in post-exponential phase. Finally, electron microscopy of PF0331-PF0337 deletions in P. furiosus COM1 showed that absence of flagella impacted normal cell aggregation behavior and, furthermore, indicated that flagella play a key role, beyond motility, in the growth physiology of P. furiosus.« less

A mutant (‘lab strain’) of the hyperthermophilic archaeon Pyrococcus furiosus, lacking flagella, has unusual growth physiology

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

Lewis, Derrick L.; Notey, Jaspreet S.; Chandrayan, Sanjeev K.

In this paper, a mutant (‘lab strain’) of the hyperthermophilic archaeon Pyrococcus furiosus DSM3638 exhibited an extended exponential phase and atypical cell aggregation behavior. Genomic DNA from the mutant culture was sequenced and compared to wild-type (WT) DSM3638, revealing 145 genes with one or more insertions, deletions, or substitutions (12 silent, 33 amino acid substitutions, and 100 frame shifts). Approximately, half of the mutated genes were transposases or hypothetical proteins. The WT transcriptome revealed numerous changes in amino acid and pyrimidine biosynthesis pathways coincidental with growth phase transitions, unlike the mutant whose transcriptome reflected the observed prolonged exponential phase. Targetedmore » gene deletions, based on frame-shifted ORFs in the mutant genome, in a genetically tractable strain of P. furiosus (COM1) could not generate the extended exponential phase behavior observed for the mutant. For example, a putative radical SAM family protein (PF2064) was the most highly up-regulated ORF (>25-fold) in the WT between exponential and stationary phase, although this ORF was unresponsive in the mutant; deletion of this gene in P. furiosus COM1 resulted in no apparent phenotype. On the other hand, frame-shifting mutations in the mutant genome negatively impacted transcription of a flagellar biosynthesis operon (PF0329-PF0338).Consequently, cells in the mutant culture lacked flagella and, unlike the WT, showed minimal evidence of exopolysaccharide-based cell aggregation in post-exponential phase. Finally, electron microscopy of PF0331-PF0337 deletions in P. furiosus COM1 showed that absence of flagella impacted normal cell aggregation behavior and, furthermore, indicated that flagella play a key role, beyond motility, in the growth physiology of P. furiosus.« less

Molecular analysis of hprt mutations induced by chromium picolinate in CHO AA8 cells.

PubMed

Coryell, Virginia H; Stearns, Diane M

2006-11-07

Chromium picolinate (CrPic) is a popular dietary supplement, marketed to the public for weight loss, bodybuilding, and control of blood sugar. Recommendations for long-term use at high dosages have led to questions regarding its safety. Previous studies have reported that CrPic can cause chromosomal aberrations and mutations. The purpose of the current work was to compare the mutagenicity of CrPic as a suspension in acetone versus a solution in DMSO, and to characterize the hprt mutations induced by CrPic in CHO AA8 cells. Treatments of 2% acetone or 2% DMSO alone produced no significant increase in 6-thioguanine (6-TG)-resistant mutants after 48 h exposures. Mutants resistant to 6-TG were generated by exposing cells for 48 h to 80 microg/cm(2) CrPic in acetone or to 1.0mM CrPic in DMSO. CrPic in acetone produced an average induced mutation frequency (MF) of 56 per 10(6) surviving cells relative to acetone solvent. CrPic in acetone was 3.5-fold more mutagenic than CrPic in DMSO, which produced an MF of 16.2. Characterization of 61 total mutations in 48 mutants generated from exposure to CrPic in acetone showed that base substitutions comprised 33% of the mutations, with transversions being predominant; deletions made up 62% of the mutations, with one-exon deletions predominating; and 1-4 bp insertions made up 5% of the characterized mutations. CrPic induced a statistically greater number of deletions and a statistically smaller number of base substitutions than have been measured in spontaneously generated mutants. These data confirm previous studies showing that CrPic is mutagenic, and support the contention that further study is needed to verify the safety of CrPic for human consumption.

[Genetic Characteristics of Type 2 Vaccine-derived Poliovirus in Shanxi Province (China) in 2014].

PubMed

Yan, Dongrei; Li, Xiaolei; Zhang, Yong; Yang, Jianfang; Zhu, Shuangli; Wang, Dongyan; Zhang, Chuangye; Zhu, Hui; Xu, Wenbo

2015-03-01

The World Health Organization redefined the type 2 vaccine-derived poliovirus (VDPV) in 2010. To study the genetic characteristics and evolution of type 2 VDPV under this new definition, we conducted genome sequencing and analyses of type 2 VDPVs isolated from one patient with acute flaccid paralysis in Shanxi province (China) in 2014. Nucleotide sequencing revealed that the full-length of type 2 VDPV is 7439 bases encoding 2207 amino acids with no insertion or deletion of nucleotides compared with Sabin2. One nucleotide substitution identified as a key determinant of the attenuated phenotype of the Sabin 2 strain (A-G reversion at nucleotide nt 481 in the 5-end of the untranslated region) had reverted in the Shanxi type 2 VDPV. The other known key determinant of the attenuated phenotype of the Sabin 2 strain (U-->C reversion at nt2909 in the VP1 coding region that caused a Ile143Thr substitution in VP1) had not reverted in the Shanxi VDPV. The Shanxi type 2 VDPV was S2/S1 recombinant, the crossover site of which mapped to the 3-end of the 3D region (between nt 6247 and nt 6281). A phylogentic tree based on the VP1 coding region showed that evolution of the Shanxi type 2 VDPV was independent of other type 2 VDPVs detected worldwide. We estimated that the strain circulated for approximately = 11 months in the population according to the known evolution rate. The present study confirmed that the Chinese Polio Laboratory Network could discover the VDPV promptly and that it played an important part in maintenance of a polio-free China.

The Fate of Arabidopsis thaliana Homeologous CNSs and Their Motifs in the Paleohexaploid Brassica rapa

PubMed Central

Subramaniam, Sabarinath; Wang, Xiaowu; Freeling, Michael; Pires, J. Chris

2013-01-01

Following polyploidy, duplicate genes are often deleted, and if they are not, then duplicate regulatory regions are sometimes lost. By what mechanism is this loss and what is the chance that such a loss removes function? To explore these questions, we followed individual Arabidopsis thaliana–A. thaliana conserved noncoding sequences (CNSs) into the Brassica ancestor, through a paleohexaploidy and into Brassica rapa. Thus, a single Brassicaceae CNS has six potential orthologous positions in B. rapa; a single Arabidopsis CNS has three potential homeologous positions. We reasoned that a CNS, if present on a singlet Brassica gene, would be unlikely to lose function compared with a more redundant CNS, and this is the case. Redundant CNSs go nondetectable often. Using this logic, each mechanism of CNS loss was assigned a metric of functionality. By definition, proved deletions do not function as sequence. Our results indicated that CNSs that go nondetectable by base substitution or large insertion are almost certainly still functional (redundancy does not matter much to their detectability frequency), whereas those lost by inferred deletion or indels are approximately 75% likely to be nonfunctional. Overall, an average nondetectable, once-redundant CNS more than 30 bp in length has a 72% chance of being nonfunctional, and that makes sense because 97% of them sort to a molecular mechanism with “deletion” in its description, but base substitutions do cause loss. Similarly, proved-functional G-boxes go undetectable by deletion 82% of the time. Fractionation mutagenesis is a procedure that uses polyploidy as a mutagenic agent to genetically alter RNA expression profiles, and then to construct testable hypotheses as to the function of the lost regulatory site. We show fractionation mutagenesis to be a “deletion machine” in the Brassica lineage. PMID:23493633

Host plant-dependent phenotypic reversion of Ralstonia solanacearum from non-pathogenic to pathogenic forms via alterations in the phcA gene.

PubMed

Poussier, Stéphane; Thoquet, Philippe; Trigalet-Demery, Danièle; Barthet, Séverine; Meyer, Damien; Arlat, Matthieu; Trigalet, André

2003-08-01

Ralstonia solanacearum is a plant pathogenic bacterium that undergoes a spontaneous phenotypic conversion (PC) from a wild-type pathogenic to a non-pathogenic form. PC is often associated with mutations in phcA, which is a key virulence regulatory gene. Until now, reversion to the wild-type pathogenic form has not been observed for PC variants and the biological significance of PC has been questioned. In this study, we characterized various alterations in phcA (eight IS element insertions, three tandem duplications, seven deletions and a base substitution) in 19 PC mutants from the model strain GMI1000. In five of these variants, reversion to the pathogenic form was observed in planta, while no reversion was ever noticed in vitro whatever culture media used. However, reversion was observed for a 64 bp tandem duplication in vitro in the presence of tomato root exudate. This is the first report showing a complete cycle of phenotypic conversion/reversion in a plant pathogenic bacterium.

A soft, transparent, freely accessible cranial window for chronic imaging and electrophysiology

PubMed Central

Heo, Chaejeong; Park, Hyejin; Kim, Yong-Tae; Baeg, Eunha; Kim, Yong Ho; Kim, Seong-Gi; Suh, Minah

2016-01-01

Chronic in vivo imaging and electrophysiology are important for better understanding of neural functions and circuits. We introduce the new cranial window using soft, penetrable, elastic, and transparent, silicone-based polydimethylsiloxane (PDMS) as a substitute for the skull and dura in both rats and mice. The PDMS can be readily tailored to any size and shape to cover large brain area. Clear and healthy cortical vasculatures were observed up to 15 weeks post-implantation. Real-time hemodynamic responses were successfully monitored during sensory stimulation. Furthermore, the PDMS window allowed for easy insertion of microelectrodes and micropipettes into the cortical tissue for electrophysiological recording and chemical injection at any location without causing any fluid leakage. Longitudinal two-photon microscopic imaging of Cx3Cr1+/− GFP transgenic mice was comparable with imaging via a conventional glass-type cranial window, even immediately following direct intracortical injection. This cranial window will facilitate direct probing and mapping for long-term brain studies. PMID:27283875

Investigation of the tone-burst tube for duct lining attenuation measurement

NASA Technical Reports Server (NTRS)

Soffel, A. R.; Morrow, P. F.

1972-01-01

The tone burst technique makes practical the laboratory evaluation of potential inlet and discharge duct treatments. Tone burst apparatus requires only simple machined parts and standard components. Small, simply made, lining samples are quickly and easily installed in the system. Two small electromagnetric loudspeaker drivers produce peak sound pressure level of over 166 db in the 3-square-inch sample duct. Air pump available in most laboratories can produce air flows of over plus and minus Mach 0.3 in the sample duct. The technique uses short shaped pulses of sound propagated down a progressive wave tube containing the sample duct. The peak pressure level output of the treated duct is compared with the peak pressure level output of a substituted reference duct. The difference between the levels is the attenuation or insertion loss of the treated duct. Evaluations of resonant absorber linings by the tone burst technique check attenuation values predicted by empirical formulas based on full scale ducts.

Characterization of frequencies and distribution of single nucleotide insertions/deletions in the human genome.

PubMed

Tan, Ene-Choo; Li, Haixia

2006-07-19

Most of the studies on single nucleotide variations are on substitutions rather than insertions/deletions. In this study, we examined the distribution and characteristics of single nucleotide insertions/deletions (SNindels), using data available from dbSNP for all the human chromosomes. There are almost 300,000 SNindels in the database, of which only 0.8% are validated. They occur at the frequency of 0.887 per 10 kb on average for the whole genome, or approximately 1 for every 11,274 bp. More than half occur in regions with mononucleotide repeats the longest of which is 47 bases. Overall the mononucleotide repeats involving C and G are much shorter than those for A and T. About 12% are surrounded by palindromes. There is general correlation between chromosome size and total number for each chromosome. Inter-chromosomal variation in density ranges from 0.6 to 21.7 per kilobase. The overall spectrum shows very high proportion of SNindel of types -/A and -/T at over 81%. The proportion of -/A and -/T SNindels for each chromosome is correlated to its AT content. Less than half of the SNindels are within or near known genes and even fewer (<0.183%) in coding regions, and more than 1.4% of -/C and -/G are in coding compared to 0.2% for -/A and -/T types. SNindels of -/A and -/T types make up 80% of those found within untranslated regions but less than 40% of those within coding regions. A separate analysis using the subset of 2324 validated SNindels showed slightly less AT bias of 74%, SNindels not within mononucleotide repeats showed even less AT bias at 58%. Density of validated SNindels is 0.007/10 kb overall and 90% are found within or near genes. Among all chromosomes, Y has the lowest numbers and densities for all SNindels, validated SNindels, and SNindels not within repeats.

Risk-based screening for Chlamydia trachomatis and Neisseria gonorrhoeae prior to intrauterine device insertion.

PubMed

Grentzer, Jaclyn M; Peipert, Jeffrey F; Zhao, Qiuhong; McNicholas, Colleen; Secura, Gina M; Madden, Tessa

2015-10-01

The objective was to compare three strategies for Chlamydia trachomatis and Neisseria gonorrhoeae screening prior to intrauterine device (IUD) insertion. This was a secondary analysis of the Contraceptive CHOICE Project. We measured the prevalence of C. trachomatis and/or N. gonorrhoeae at the time of IUD insertion. We then compared sensitivity, specificity, negative and positive predictive values, and likelihood ratios for three screening strategies for C. trachomatis and N. gonorrhoeae prior to IUD insertion: (a) "age-based" — age ≤25 years alone; (b) "age/partner-based" — age ≤25 and/or multiple sexual partners; and (c) "risk-based" — age ≤25, multiple sexual partners, inconsistent condom use and/or history of prior sexually transmitted infection (STI). Among 5087 IUD users, 140 (2.8%) tested positive for C. trachomatis, 16 (0.3%) tested positive for N. gonorrhoeae, and 6 (0.1%) were positive for both at the time of IUD insertion. The "risk-based" screening strategy had the highest sensitivity (99.3%) compared to "age-based" and "age/partner-based" screening (80.7% and 84.7%, respectively.) Only one (0.7%) woman with a chlamydia or gonorrhea infection would not have been screened using "risk-based" screening. A risk-based strategy to screen for C. trachomatis and N. gonorrhoeae prior to IUD insertion has higher sensitivity than screening based on age alone or age and multiple sexual partners. Using a risk-based screening strategy (age≤25, multiple sexual partners, inconsistent condom use and/or history of an STI) to determine who should be screened for C. trachomatis and N. gonorrhoeae prior to IUD insertion will miss very few cases of infection and obviates the need for universal screening. Copyright © 2015 Elsevier Inc. All rights reserved.

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

K Kucera; A Koblansky; L Saunders

Profilins promote actin polymerization by exchanging ADP for ATP on monomeric actin and delivering ATP-actin to growing filament barbed ends. Apicomplexan protozoa such as Toxoplasma gondii invade host cells using an actin-dependent gliding motility. Toll-like receptor (TLR) 11 generates an innate immune response upon sensing T. gondii profilin (TgPRF). The crystal structure of TgPRF reveals a parasite-specific surface motif consisting of an acidic loop, followed by a long {beta}-hairpin. A series of structure-based profilin mutants show that TLR11 recognition of the acidic loop is responsible for most of the interleukin (IL)-12 secretion response to TgPRF in peritoneal macrophages. Deletion ofmore » both the acidic loop and the {beta}-hairpin completely abrogates IL-12 secretion. Insertion of the T. gondii acidic loop and {beta}-hairpin into yeast profilin is sufficient to generate TLR11-dependent signaling. Substitution of the acidic loop in TgPRF with the homologous loop from the apicomplexan parasite Cryptosporidium parvum does not affect TLR11-dependent IL-12 secretion, while substitution with the acidic loop from Plasmodium falciparum results in reduced but significant IL-12 secretion. We conclude that the parasite-specific motif in TgPRF is the key molecular pattern recognized by TLR11. Unlike other profilins, TgPRF slows nucleotide exchange on monomeric rabbit actin and binds rabbit actin weakly. The putative TgPRF actin-binding surface includes the {beta}-hairpin and diverges widely from the actin-binding surfaces of vertebrate profilins.« less

Society already achieves economic benefits from generic substitution but fails to do the same for therapeutic substitution.

PubMed

Gumbs, Pearl D; Verschuren, W M Monique; Souverein, Patrick C; Mantel-Teeuwisse, Aukje K; de Wit, G Ardine; de Boer, Anthonius; Klungel, Olaf H

2007-11-01

To assess the potential annual savings due to generic and therapeutic substitution of statin therapy for the general Dutch population, taking the patients medical history into account. We conducted a population-based costing study using the PHARMO Record Linkage System (RLS). PHARMO RLS contains drug dispensing records from a representative sample of pharmacies located in more than 50 regions in the Netherlands. We selected all statin users in the database since 2003. The cost-savings of generic substitution of statin therapy for all simvastatin and pravastatin users, and of therapeutic substitution of statin therapy for other statin users were calculated. Substituting current users and new users of statins were considered separately. Therapeutic substitution was based on the medical history of the individual patient. Patients were only substituted if there was an appropriate substitute available. The appropriateness of substitution was based on drug-drug interactions between statins and possible comedication and the availability of an equipotent alternative. Substituting (generic and therapeutic) statin therapy for all current users would lead to potential annual savings of approximately 87 million euros. Substituting (generic and therapeutic) all starters on statin therapy would lead to potential annual savings of around 51 million euros. In the case of generic substitution only, the potential annual savings for all current simvastatin and pravastatin users would be 2.4 million euros and for the new users about 1.8 million euros. From an economic point of view, society could gain a lot from substituting statin therapy, especially from therapeutic substitution.

Rearrangement of the distal pocket accompanying E7 His yields Gln substitution in elephant carbonmonoxy- and oxymyoglobin: sup 1 H NMR identification of a new aromatic residue in the heme pocket

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

Yu, L.P.; La Mar, G.N.; Mizukami, H.

1990-03-13

Two-dimensional {sup 1}H NMR methods have been used to assign side-chain resonances for the residues in the distal heme pocket of elephant carbonmonoxymyoglobin (MbCO) and oxymyoglobin (MbO{sub 2}). It is shown that, while the other residues in the heme pocket are minimally perturbed, the Phe CD4 residue in elephant MbCO and MbO{sub 2} resonates considerably upfield compared to the corresponding residue in sperm whale MbCO. The new NOE connectivities to Val E11 and heme-induced ring current calculations indicate that Phe CD4 has been inserted into the distal heme pocket by reorienting the aromatic side chain and moving the CD cornermore » closer to the heme. The C{zeta}H proton of the Phe CD4 was found to move toward the iron of the heme by {approximately}4 {angstrom} relative to the position in sperm whale MbCO, requiring minimally a 3-{angstrom} movement of the CD helical backbone. The significantly altered distal conformation in elephant myoglobin, rather than the single distal E7 substitution, forms a plausible basis for its altered functional properties of lower autoxidation rate, higher redox potential, and increased affinity for CO ligand. These results demonstrate that one-to-one interpretation of amino acid residue substitution (E7 His {yields} Gln) is oversimplified and that conformational changes of substituted proteins which are not readily predicted have to be considered for interpretation of their functional properties.« less

Evolution-based Virtual Content Insertion with Visually Virtual Interactions in Videos

NASA Astrophysics Data System (ADS)

Chang, Chia-Hu; Wu, Ja-Ling

With the development of content-based multimedia analysis, virtual content insertion has been widely used and studied for video enrichment and multimedia advertising. However, how to automatically insert a user-selected virtual content into personal videos in a less-intrusive manner, with an attractive representation, is a challenging problem. In this chapter, we present an evolution-based virtual content insertion system which can insert virtual contents into videos with evolved animations according to predefined behaviors emulating the characteristics of evolutionary biology. The videos are considered not only as carriers of message conveyed by the virtual content but also as the environment in which the lifelike virtual contents live. Thus, the inserted virtual content will be affected by the videos to trigger a series of artificial evolutions and evolve its appearances and behaviors while interacting with video contents. By inserting virtual contents into videos through the system, users can easily create entertaining storylines and turn their personal videos into visually appealing ones. In addition, it would bring a new opportunity to increase the advertising revenue for video assets of the media industry and online video-sharing websites.

Novel insertion mutation in a non-Jewish Caucasian type 1 Gaucher disease patient

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

Choy, F.Y.M.; Humphries, M.L.; Ferreira, P.

1997-01-20

Gaucher disease is the most prevalent lysosomal storage disorder. It is autosomal recessive, resulting in lysosomal glucocerebrosidase deficiency. Three clinical forms of Gaucher disease have been described: type 1 (nonneuronopathic), type 2 (acute neuronopathic), and type 3 (subacute neuronopathic). We performed PCR-thermal cycle sequence analysis of glucocerebrosidase genomic DNA and identified a novel mutation in a non-Jewish type 1 Gaucher disease patient. It is a C insertion in exon 3 at cDNA nucleotide position 122 and genomic nucleotide position 1626. This mutation causes a frameshift and, subsequently, four of the five codons immediately downstream of the insertion were changed whilemore » the sixth was converted to a stop codon, resulting in premature termination of protein translation. The 122CC insertion abolishes a Cac81 restriction endonuclease cleavage site, allowing a convenient and reliable method for detection using RFLP analysis of PCR-amplified glucocerebrosidase genomic DNA. The mutation in the other Gaucher allele was found to be an A{r_arrow}G substitution at glucocerebrosidase cDNA nucleotide position 1226 that so far has only been reported among type 1 Gaucher disease patients. Since mutation 122CC causes a frameshift and early termination of protein translation, it most likely results in a meaningless transcript and subsequently no residual glucocerebrosidase enzyme activity. We speculate that mutation 122CC may result in a worse prognosis than mutations associated with partial activity. When present in the homozygous form, it could be a lethal allele similar to what has been postulated for the other known insertion mutation, 84GG. Our patient, who is a compound heterozygote 122CC/1226G, has moderately severe type 1 Gaucher disease. Her clinical response to Ceredase{reg_sign} therapy that began 31 months ago has been favorable, though incomplete. 30 refs., 3 figs., 2 tabs.« less

Fatal mitochondrial encephalopathy caused by fumarase deficiency: A molecular-genetic study

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

Gellera, C.; Cavadini, P.; Baratta, S.

Fumarase deficiency is a rare autosomal recessive disorder of the citric acid cycle resulting in severe organic aciduria and encephalopathy. Mammalian cells contain two fumarase isoenzymes, one mitochondrial and one cytosolic. In rat, the two proteins are encoded by the same gene and are synthesized by alternative initiation of translation at two in-phase AUG codons. One single fumarase gene locus has been identified on human chromosome 1. In most of the patients so far described, the activities of both isozymes are severely affected, suggesting that mutations within a single gene may underlie the disease. Here, we report the molecular studymore » of fumarase deficiency in a patient exhibiting compound heterozygosity for two different allelic mutations affecting the amino acid composition of both isoforms. The proband, an Italian boy of nonconsanguineous parents, died at 7 months of age of a progressive encephalopathy. Immunoblot demonstrated absence of cross-reacting material in both cytosolic and mitochondrial fraction of all tissues examined. Molecular analysis of the patient`s fumarase cDNA amplified by RT-PCR showed the presence of two mutations affecting the amino acid composition of both isoforms, a missense mutation resulting in the nonconservative amino acid substitution at codon 190 (Arg190Cys) and an amino acid in-frame insertion at codon 434 (Lys434ins). SSCP analysis of genomic PCR fragments encompassing the mutations demonstrated that the patient was heterozygous for both mutations, having inherited the Arg-to-Cys substitution from the father and the in-frame insertion from the mother. Finally, the effects of the mutations on enzyme function were investigated by expressing both normal and mutated fumarase cDNAs in a fumarase-deficient ({delta}FUM1) S. cerevisiae strain.« less

Experimental model of bone response to collagenized xenografts of porcine origin (OsteoBiol® mp3): a radiological and histomorphometric study.

PubMed

Calvo Guirado, Jose Luis; Ramírez Fernández, Maria Piedad; Negri, Bruno; Delgado Ruiz, Rafael Arcesio; Maté Sánchez de-Val, José Eduardo; Gómez-Moreno, Gerardo

2013-02-01

Adequate alveolar ridges are fundamental to successful rehabilitation with implants. There are diverse techniques for reconstructing atrophied ridges, of which bone substitute grafts is one possibility. The aim of this study was to carry out radiological and histomorphometric evaluations of bone response to collagenized porcine bone xenografts over a 4-month period following their insertion in rabbits' tibiae. Twenty New Zealand rabbits were used. Twenty collagenized porcine bone xenografts (Osteobiol® mp3, Tecnoss Dental s.r.l., Torino, Italy), in granulated form of 600 to 1,000 µm, were inserted in the proximal metaphyseal area of the animals' tibiae and 20 control areas were created. Following implantation, the animals were sacrificed in four groups of five, after 1, 2, 3, and 4 months, respectively. Radiological and histomorphometric studies were made. After 4 months, radiological images revealed bone defects with a decrease in graft volume and the complete repair of the osseous defect. No healed or residual bone alterations attributable to the presence of the implants were observed. Histomorphometric analysis at 4 months found mean values for newly formed bone, residual graft material, and non-mineralized connective tissue of 25.4 ± 1.8%, 36.37 ± 3.0%, and 38.22 ± 2.5%, respectively. There were no statistical differences in the length of cortical formation with collagenized porcine xenograft (98.9 ± 1.1%) compared with the control samples (99.1 ± 0.7%) at the end of the study period. The biomaterial used proved to be biocompatible, bioabsorbable, and osteoconductive and as such, a possible bone substitute that did not interfere with the bone's normal reparative processes. © 2011 Wiley Periodicals, Inc.

Nature and Recurrence of AVPR2 Mutations in X-linked Nephrogenic Diabetes Insipidus

PubMed Central

Bichet, Daniel G.; Birnbaumer, Mariel; Lonergan, Michèle; Arthus, Marie-Françoise; Rosenthal, Walter; Goodyer, Paul; Nivet, Hubert; Benoit, Stéphane; Giampietro, Philip; Simonetti, Simonetta; Fish, Alfred; Whitley, Chester B.; Jaeger, Philippe; Gertner, Joseph; New, Maria; DiBona, Francis J.; Kaplan, Bernard S.; Robertson, Gary L.; Hendy, Geoffrey N.; Fujiwara, T. Mary; Morgan, Kenneth

1994-01-01

X-linked nephrogenic diabetes insipidus (NDI) is a rare disease with defective renal and extrarenal arginine-vasopressin V2 receptor responses due to mutations in the AVPR2 gene in Xq28. We analyzed 31 independent NDI families to determine the nature and recurrence of AVPR2 mutations. Twenty-one new putative disease-causing mutations were identified: 113delCT, 253del35, 255del9, 274insG, V88M, R106C, 402delCT, C112R, Y124X, S126F, W164S, S167L, 684delTA, 804insG, W284X, A285P, W293X, R337X, and three large deletions or gene rearrangements. Five other mutations—R113W, Y128S, R137H, R181C, and R202C—that previously had been reported in other families were detected. There was evidence for recurrent mutation for four mutations (R113W, R137H, S167L, and R337X). Eight de novo mutation events were detected (274insG, R106C, Y128S, 167L [twice], R202C, 684delTA, and R337X). The origins were maternal (one), grandmaternal (one), and grandpaternal (six). In the 31 NDI families and 6 families previously reported by us, there is evidence both for mutation hot spots for nucleotide substitutions and for small deletions and insertions. More than half (58%) of the nucleotide substitutions in 26 families could be a consequence of 5-methylcytosine deamination at a CpG dinucleotide. Most of the small deletions and insertions could be attributed to slipped mispairing during DNA replication. PMID:8037205

The chlorophyll-deficient golden leaf mutation in cucumber is due to a single nucleotide substitution in CsChlI for magnesium chelatase I subunit.

PubMed

Gao, Meiling; Hu, Liangliang; Li, Yuhong; Weng, Yiqun

2016-10-01

The cucumber chlorophyll-deficient golden leaf mutation is due to a single nucleotide substitution in the CsChlI gene for magnesium chelatase I subunit which plays important roles in the chlorophyll biosynthesis pathway. The Mg-chelatase catalyzes the insertion of Mg(2+) into the protoporphyrin IX in the chlorophyll biosynthesis pathway, which is a protein complex encompassing three subunits CHLI, CHLD, and CHLH. Chlorophyll-deficient mutations in genes encoding the three subunits have played important roles in understanding the structure, function and regulation of this important enzyme. In an EMS mutagenesis population, we identified a chlorophyll-deficient mutant C528 with golden leaf color throughout its development which was viable and able to set fruits and seeds. Segregation analysis in multiple populations indicated that this leaf color mutation was recessively inherited and the green color showed complete dominance over golden color. Map-based cloning identified CsChlI as the candidate gene for this mutation which encoded the CHLI subunit of cucumber Mg-chelatase. The 1757-bp CsChlI gene had three exons and a single nucleotide change (G to A) in its third exon resulted in an amino acid substitution (G269R) and the golden leaf color in C528. This mutation occurred in the highly conserved nucleotide-binding domain of the CHLI protein in which chlorophyll-deficient mutations have been frequently identified. The mutant phenotype, CsChlI expression pattern and the mutated residue in the CHLI protein suggested the mutant allele in C528 is unique among mutations identified so far in different species. This golden leaf mutant not only has its potential in cucumber breeding, but also provides a useful tool in understanding the CHLI function and its regulation in the chlorophyll biosynthesis pathway as well as chloroplast development.

Small Changes in the Primary Structure of Transportan 10 Alter the Thermodynamics and Kinetics of its Interaction with Phospholipid Vesicles

PubMed Central

2008-01-01

The kinetics and thermodynamics of binding of transportan 10 (tp10) and four of its variants to phospholipid vesicles, and the kinetics of peptide-induced dye efflux, were compared. Tp10 is a 21-residue, amphipathic, cationic, cell-penetrating peptide similar to helical antimicrobial peptides. The tp10 variants examined include amidated and free peptides, and replacements of tyrosine by tryptophan. Carboxy-terminal amidation or substitution of tryptophan for tyrosine enhance binding and activity. The Gibbs energies of peptide binding to membranes determined experimentally and calculated from the interfacial hydrophobicity scale are in good agreement. The Gibbs energy for insertion into the bilayer core was calculated using hydrophobicity scales of residue transfer from water to octanol and to the membrane/water interface. Peptide-induced efflux becomes faster as the Gibbs energies for binding and insertion of the tp10 variants decrease. If anionic lipids are included, binding and efflux rate increase, as expected because all tp10 variants are cationic and an electrostatic component is added. Whether the most important effect of peptide amidation is the change in charge or an enhancement of helical structure, however, still needs to be established. Nevertheless, it is clear that the changes in efflux rate reflect the differences in the thermodynamics of binding and insertion of the free and amidated peptide groups. PMID:18260641

Large-scale aeroacoustic research feasibility and conceptual design of test-section inserts for the Ames 80- by 120-foot wind tunnel

NASA Technical Reports Server (NTRS)

Soderman, Paul T.; Olsen, Larry E.

1990-01-01

An engineering feasibility study was made of aeroacoustic inserts designed for large-scale acoustic research on aircraft models in the 80 by 120 foot Wind Tunnel at NASA Ames Research Center. The advantages and disadvantages of likely designs were analyzed. Results indicate that the required maximum airspeed leads to the design of a particular insert. Using goals of 200, 150, and 100 knots airspeed, the analysis indicated a 30 x 60 ft open-jet test section, a 40 x 80 ft open jet test section, and a 70 x 100 ft closed test section with enhanced wall lining, respectively. The open-jet inserts would be composed of a nozzle, collector, diffuser, and acoutic wedges incorporated in the existing 80 x 120 test section. The closed test section would be composed of approximately 5 ft acoustic wedges covered by a porous plate attached to the test section walls of the existing 80 x 120. All designs would require a double row of acoustic vanes between the test section and fan drive to attenuate fan noise and, in the case of the open-jet designs, to control flow separation at the diffuser downstream end. The inserts would allow virtually anechoic acoustic studies of large helicopter models, jets, and V/STOL aircraft models in simulated flight. Model scale studies would be necessary to optimize the aerodynamic and acoustic performance of any of the designs. In all designs studied, the existing structure would have to be reinforced. Successful development of acoustically transparent walls, though not strictly necessary to the project, would lead to a porous-wall test section that could be substituted for any of the open-jet designs, and thereby eliminate many aerodynamic and acoustic problems characteristic of open-jet shear layers. The larger size of the facility would make installation and removal of the insert components difficult. Consequently, scheduling of the existing 80 x 120 aerodynamic test section and scheduling of the open-jet test section would likely be made on an annual or longer basis. The enhanced wall-lining insert would likely be permanent. Although the modifications are technically feasible, the economic practicality of the project was not evaluated.

Improvement of the insertion axis for cochlear implantation with a robot-based system.

PubMed

Torres, Renato; Kazmitcheff, Guillaume; De Seta, Daniele; Ferrary, Evelyne; Sterkers, Olivier; Nguyen, Yann

2017-02-01

It has previously reported that alignment of the insertion axis along the basal turn of the cochlea was depending on surgeon' experience. In this experimental study, we assessed technological assistances, such as navigation or a robot-based system, to improve the insertion axis during cochlear implantation. A preoperative cone beam CT and a mastoidectomy with a posterior tympanotomy were performed on four temporal bones. The optimal insertion axis was defined as the closest axis to the scala tympani centerline avoiding the facial nerve. A neuronavigation system, a robot assistance prototype, and software allowing a semi-automated alignment of the robot were used to align an insertion tool with an optimal insertion axis. Four procedures were performed and repeated three times in each temporal bone: manual, manual navigation-assisted, robot-based navigation-assisted, and robot-based semi-automated. The angle between the optimal and the insertion tool axis was measured in the four procedures. The error was 8.3° ± 2.82° for the manual procedure (n = 24), 8.6° ± 2.83° for the manual navigation-assisted procedure (n = 24), 5.4° ± 3.91° for the robot-based navigation-assisted procedure (n = 24), and 3.4° ± 1.56° for the robot-based semi-automated procedure (n = 12). A higher accuracy was observed with the semi-automated robot-based technique than manual and manual navigation-assisted (p < 0.01). Combination of a navigation system and a manual insertion does not improve the alignment accuracy due to the lack of friendly user interface. On the contrary, a semi-automated robot-based system reduces both the error and the variability of the alignment with a defined optimal axis.

37 CFR 2.35 - Adding, deleting, or substituting bases.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 37 Patents, Trademarks, and Copyrights 1 2013-07-01 2013-07-01 false Adding, deleting, or substituting bases. 2.35 Section 2.35 Patents, Trademarks, and Copyrights UNITED STATES PATENT AND TRADEMARK..., deleting, or substituting bases. (a) In an application under section 66(a) of the Act, an applicant may not...

37 CFR 2.35 - Adding, deleting, or substituting bases.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 37 Patents, Trademarks, and Copyrights 1 2011-07-01 2011-07-01 false Adding, deleting, or substituting bases. 2.35 Section 2.35 Patents, Trademarks, and Copyrights UNITED STATES PATENT AND TRADEMARK..., deleting, or substituting bases. (a) In an application under section 66(a) of the Act, an applicant may not...

37 CFR 2.35 - Adding, deleting, or substituting bases.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 37 Patents, Trademarks, and Copyrights 1 2012-07-01 2012-07-01 false Adding, deleting, or substituting bases. 2.35 Section 2.35 Patents, Trademarks, and Copyrights UNITED STATES PATENT AND TRADEMARK..., deleting, or substituting bases. (a) In an application under section 66(a) of the Act, an applicant may not...

37 CFR 2.35 - Adding, deleting, or substituting bases.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 37 Patents, Trademarks, and Copyrights 1 2010-07-01 2010-07-01 false Adding, deleting, or substituting bases. 2.35 Section 2.35 Patents, Trademarks, and Copyrights UNITED STATES PATENT AND TRADEMARK..., deleting, or substituting bases. (a) In an application under section 66(a) of the Act, an applicant may not...

Binding, folding and insertion of a β-hairpin peptide at a lipid bilayer surface: Influence of electrostatics and lipid tail packing.

PubMed

Reid, Keon A; Davis, Caitlin M; Dyer, R Brian; Kindt, James T

2018-03-01

Antimicrobial peptides (AMPs) act as host defenses against microbial pathogens. Here we investigate the interactions of SVS-1 (KVKVKVKV d P l PTKVKVKVK), an engineered AMP and anti-cancer β-hairpin peptide, with lipid bilayers using spectroscopic studies and atomistic molecular dynamics simulations. In agreement with literature reports, simulation and experiment show preferential binding of SVS-1 peptides to anionic over neutral bilayers. Fluorescence and circular dichroism studies of a Trp-substituted SVS-1 analogue indicate, however, that it will bind to a zwitterionic DPPC bilayer under high-curvature conditions and folds into a hairpin. In bilayers formed from a 1:1 mixture of DPPC and anionic DPPG lipids, curvature and lipid fluidity are also observed to promote deeper insertion of the fluorescent peptide. Simulations using the CHARMM C36m force field offer complementary insight into timescales and mechanisms of folding and insertion. SVS-1 simulated at an anionic mixed POPC/POPG bilayer folded into a hairpin over a microsecond, the final stage in folding coinciding with the establishment of contact between the peptide's valine sidechains and the lipid tails through a "flip and dip" mechanism. Partial, transient folding and superficial bilayer contact are seen in simulation of the peptide at a zwitterionic POPC bilayer. Only when external surface tension is applied does the peptide establish lasting contact with the POPC bilayer. Our findings reveal the influence of disruption to lipid headgroup packing (via curvature or surface tension) on the pathway of binding and insertion, highlighting the collaborative effort of electrostatic and hydrophobic interactions on interaction of SVS-1 with lipid bilayers. Copyright © 2017 Elsevier B.V. All rights reserved.

Corneal sensitivity, ocular surface health and tear film stability after punctal plug therapy of aqueous deficient dry eye

PubMed Central

Said, Azza Mohamed Ahmed; Farag, Mona Elsayed; Abdulla, Tarek Mohamed; Ziko, Othman Ali Othman; Osman, Wesam Mohamed

2016-01-01

AIM To evaluate the effect of punctal occlusion using thermosensitive (smart plug) versus silicone plug for management of aqueous deficient dry eye on corneal sensitivity, ocular surface health and tear film stability. METHODS A comparative prospective interventional case study included 45 patients with bilateral severe form of aqueous deficient dry eye. In each patient, the smart plug was inserted in the lower punctum of the right eye which was considered as study group 1 and silicone plug was inserted in the lower punctum of the left eye of the same patient which was considered as study group 2. All patients were subjected to careful history taking and questionnaire for subjective assessment of severity of symptoms. Corneal sensitivity, corneal fluorescein, rose bengal staining, Schirmer's I test, tear film break up time and conjunctival impression cytology were performed pre and 1, 3 and 6mo post plug insertion. RESULTS A statistically significant improvement in subjective and objective manifestations occurred following treatment with both types of plugs (P<0.01). The thermosensitive plug caused significant overall improvement, decrease in frequency of application of tear substitutes and improvement of conjunctival impression cytology parameters in the inserted side (P<0.01). Canaliculitis was reported in two eyes (4.4%) following punctal occlusion using thermosensitive plug (study group 1). Spontaneous plug loss occurred in 21 eyes (46.6%) in the silicone plug group (study group 2). CONCLUSION Improvement of subjective and objective manifestations of aqueous deficient dry eye occurs following punctal plug occlusion. Thermosensitive plug has good patient's compliance with fewer complications and lower rates of loss compared to the silicone plug. PMID:27990362

Bone response to hydroxyapatites with open porosity of animal origin (porcine [OsteoBiol mp3] and bovine [Endobon]): a radiological and histomorphometric study.

PubMed

Ramírez-Fernández, MaPiedad; Calvo-Guirado, Jose Luis; Delgado-Ruiz, Rafael Arcesio; Maté-Sánchez Del Val, José Eduardo; Vicente-Ortega, Vicente; Meseguer-Olmos, Luis

2011-07-01

To carry out a radiological and histomorphometric evaluation of bone response to two xenografts of animal origin, one porcine, and the other bovine, inserted in rabbits' tibiae. Twenty New Zealand rabbits weighing 3900-4500 g were used. Twenty bovine bone grafts (Endobon) in granulated form of 500-1000 μm granulometry were inserted in the proximal metaphyseal area of the animals' right tibia, and 20 porcine bone grafts (OsteoBiol mp3) in granulated form of 600-1000 μm granulometry were inserted in the proximal metaphyseal area of the animals' left tibia. Following graft insertion, the animals were sacrificed in four groups of five, after 1, 2, 3 and 4 months, respectively. Anteroposterior and lateral radiographs were taken. Samples were processed for observation under light microscopy. Histomorphometric measurements were presented as mean values ± standard deviations. At 4 months after treatment, the bone defects displayed radiological images that showed complete repair of osseous defects. Histomorphometric evaluation showed that for the porcine xenograft, the study averages for newly formed bone represented 22.8 ± 1.8%, for residual graft material 23.6 ± 3% and for connective tissue 53.5 ± 2.5%, while for the bovine xenograft newly formed bone represented 23.1 ± 1.8%, residual graft material 39.4 ± 3% and non-mineralized connective tissue 37.5 ± 2.5%. The biomaterials assessed in the study were shown to be biocompatible and osteoconductive. Collagenized porcine xenografts proved more resorbable than bovine xenografts. Both can be used as possible bone substitutes without interfering with normal reparative bone processes. © 2011 John Wiley & Sons A/S.

Rectal suppository: commonsense and mode of insertion.

PubMed

Abd-el-Maeboud, K H; el-Naggar, T; el-Hawi, E M; Mahmoud, S A; Abd-el-Hay, S

1991-09-28

Rectal suppository is a well-known form of medication and its use is increasing. The commonest shape is one with an apex (pointed end) tapering to a base (blunt end). Because of a general lack of information about mode of insertion, we asked 360 lay subjects (Egyptians and non-Egyptians) and 260 medical personnel (physicians, pharmacists, and nurses) by questionnaire which end they inserted foremost. Apart from 2 individuals, all subjects suggested insertion with the apex foremost. Commonsense was the most frequent basis for this practice (86.9% of lay subjects and 84.6% of medical personnel) followed by information from a relative, a friend, or medical personnel, or from study at medical school. Suppository insertion with the base or apex foremost was compared in 100 subjects (60 adults, 40 infants and children). Retention with the former method was more easily achieved in 98% of the cases, with no need to introduce a finger in the anal canal (1% vs 83%), and lower expulsion rate (0% vs 3%). The designer of the "torpedo-shaped" suppository suggested its insertion with apex foremost. Our data suggest that a suppository is better inserted with the base foremost. Reversed vermicular contractions or pressure gradient of the anal canal might press it inwards.

Transition-state charge transfer reveals electrophilic, ambiphilic, and nucleophilic carbon-hydrogen bond activation.

PubMed

Ess, Daniel H; Nielsen, Robert J; Goddard, William A; Periana, Roy A

2009-08-26

Absolutely localized molecular orbital energy decomposition analysis of C-H activation transition states (TSs), including Pt, Au, Ir, Ru, W, Sc, and Re metal centers, shows an electrophilic, ambiphilic, and nucleophilic charge transfer (CT) continuum irrespective of the bonding paradigm (oxidative addition, sigma-bond metathesis, oxidative hydrogen migration, 1,2-substitution). Pt(II) insertion and Au(III) substitution TSs are highly electrophilic and dominated by C-H bond to metal/ligand orbital stabilization, while Ir-X and Ru-X (X = R, NH(2), OR, or BOR(2)) substitution TSs are ambiphilic in nature. In this ambiphilic activation regime, an increase in one direction of CT typically leads to a decrease in the reverse direction. Comparison of Tp(CO)Ru-OH and Tp(CO)Ru-NH(2) complexes showed no evidence for the classic d(pi)-p(pi) repulsion model. Complexes such as and Cp(CO)(2)W-B(OR)(2), (PNP)Ir(I), Cp(2)ScMe, and (acac-kappaO,kappaO)(2)Re(III)-OH were found to mediate nucleophilic C-H activation, where the CT is dominated by the metal/ligand orbital to C-H antibonding orbital interaction. This CT continuum ultimately affects the metal-alkyl intermediate polarization and possible functionalization reactions. This analysis will impact the design of new activation reactions and stimulate the discovery of more nucleophilic activation complexes.

Alternative splicing by participation of the group II intron ORF in extremely halotolerant and alkaliphilic Oceanobacillus iheyensis.

PubMed

Chee, Gab-Joo; Takami, Hideto

2011-01-01

Group II introns inserted into genes often undergo splicing at unexpected sites, and participate in the transcription of host genes. We identified five copies of a group II intron, designated Oi.Int, in the genome of an extremely halotolerant and alkaliphilic bacillus, Oceanobacillus iheyensis. The Oi.Int4 differs from the Oi.Int3 at four bases. The ligated exons of the Oi.Int4 could not be detected by RT-PCR assays in vivo or in vitro although group II introns can generally self-splice in vitro without the involvement of an intron-encoded open reading frame (ORF). In the Oi.Int4 mutants with base substitutions within the ORF, ligated exons were detected by in vitro self-splicing. It was clear that the ligation of exons during splicing is affected by the sequence of the intron-encoded ORF since the splice sites corresponded to the joining sites of the intron. In addition, the mutant introns showed unexpected multiple products with alternative 5' splice sites. These findings imply that alternative 5' splicing which causes a functional change of ligated exons presumably has influenced past adaptations of O. iheyensis to various environmental changes.

Discriminative Prediction of A-To-I RNA Editing Events from DNA Sequence

PubMed Central

Sun, Jiangming; Singh, Pratibha; Bagge, Annika; Valtat, Bérengère; Vikman, Petter; Spégel, Peter; Mulder, Hindrik

2016-01-01

RNA editing is a post-transcriptional alteration of RNA sequences that, via insertions, deletions or base substitutions, can affect protein structure as well as RNA and protein expression. Recently, it has been suggested that RNA editing may be more frequent than previously thought. A great impediment, however, to a deeper understanding of this process is the paramount sequencing effort that needs to be undertaken to identify RNA editing events. Here, we describe an in silico approach, based on machine learning, that ameliorates this problem. Using 41 nucleotide long DNA sequences, we show that novel A-to-I RNA editing events can be predicted from known A-to-I RNA editing events intra- and interspecies. The validity of the proposed method was verified in an independent experimental dataset. Using our approach, 203 202 putative A-to-I RNA editing events were predicted in the whole human genome. Out of these, 9% were previously reported. The remaining sites require further validation, e.g., by targeted deep sequencing. In conclusion, the approach described here is a useful tool to identify potential A-to-I RNA editing events without the requirement of extensive RNA sequencing. PMID:27764195

Occurrence and characterization of hitherto unknown Streptomyces species in semi-arid soils.

PubMed

Kumar, Surendra; Priya, E; Singh Solanki, Dilip; Sharma, Ruchika; Gehlot, Praveen; Pathak, Rakesh; Singh, S K

2016-09-01

Streptomyces the predominant genus of Actinobacteria and plays an important role in the recycling of soil organic matter and production of important secondary metabolites. The occurrence and diversity assessment of Streptomyces species revealed alkaline and poor nutrient status of soils of semi-arid region of Jodhpur, Rajasthan. The morphological and biochemical characterization of 21 Streptomyces isolates facilitated Genus level identification but were insufficient to designate species. Species designation based on 16S rRNA gene delineated 21 isolates into 14 Streptomyces species. Upon BLAST search, the test isolates exhibited 98 to 100% identities with that of the best aligned sequences of the NCBI database. The GC content of 16S rRNA gene sequences of all the Streptomyces isolates tested ranged from 59.03% to 60.94%. The multiple sequence alignment of all the 21 Streptomyces isolates generated a phylogram with high bootstrap values indicating reliable grouping of isolates based on nucleotide sequence variations by way of insertion, deletion and substitutions and 16S rRNA length polymorphism. Some of the Streptomyces species molecularly identified under present study are reported for the first time from semi-arid region of Jodhpur.

Quantitation of base substitutions in eukaryotic 5S rRNA: selection for the maintenance of RNA secondary structure.

PubMed

Curtiss, W C; Vournakis, J N

1984-01-01

Eukaryotic 5S rRNA sequences from 34 diverse species were compared by the following method: (1) The sequences were aligned; (2) the positions of substitutions were located by comparison of all possible pairs of sequences; (3) the substitution sites were mapped to an assumed general base pairing model; and (4) the R-Y model of base stacking was used to study stacking pattern relationships in the structure. An analysis of the sequence and structure variability in each region of the molecule is presented. It was found that the degree of base substitution varies over a wide range, from absolute conservation to occurrence of over 90% of the possible observable substitutions. The substitutions are located primarily in stem regions of the 5S rRNA secondary structure. More than 88% of the substitutions in helical regions maintain base pairing. The disruptive substitutions are primarily located at the edges of helical regions, resulting in shortening of the helical regions and lengthening of the adjacent nonpaired regions. Base stacking patterns determined by the R-Y model are mapped onto the general secondary structure. Intrastrand and interstrand stacking could stabilize alternative coaxial structures and limit the conformational flexibility of nonpaired regions. Two short contiguous regions are 100% conserved in all species. This may reflect evolutionary constraints imposed at the DNA level by the requirement for binding of a 5S gene transcription initiation factor during gene expression.

Diazo Reagents with Small Steric Footprints for Simultaneous Arming/SAR Studies of Alcohol-Containing Natural Products via O–H Insertion

PubMed Central

Chamni, Supakarn; He, Qing-Li; Dang, Yongjun; Bhat, Shridhar; Liu, Jun O.; Romo, Daniel

2011-01-01

Natural products are essential tools for basic cellular studies leading to the identification of medically relevant protein targets and the discovery of potential therapeutic leads. The development of methods that enable mild and selective derivatization of natural products continues to be of significant interest for mining their information-rich content. Herein, we describe novel diazo reagents for simultaneous arming and structure-activity relationship (SAR) studies of alcohol-containing natural products with a small steric footprint, namely an α-trifluoroethyl (HTFB) substituted reagent. The Rh(II)-catalyzed O–H insertion reaction of several natural products, including the potent translation inhibitor lactimidomycin, was investigated and useful reactivity and both chemo- and site (chemosite) selectivities were observed. Differential binding to the known protein targets of both FK506 and fumagillol was demonstrated, validating the advantage of the smaller steric footprint of trifluoroethyl derivatives. A p-azidophenyl diazo reagent is also described that will prove useful for photoaffinity labeling of low affinity small molecule protein receptors. PMID:21894934

Introducing Aliphatic Substitution with a Discovery Experiment Using Competing Electrophiles

ERIC Educational Resources Information Center

Curran, Timothy P.; Mostovoy, Amelia J.; Curran, Margaret E.; Berger, Clara

2016-01-01

A facile, discovery-based experiment is described that introduces aliphatic substitution in an introductory undergraduate organic chemistry curriculum. Unlike other discovery-based experiments that examine substitution using two competing nucleophiles with a single electrophile, this experiment compares two isomeric, competing electrophiles…

Cobalt ferrite based magnetostrictive materials for magnetic stress sensor and actuator applications

NASA Technical Reports Server (NTRS)

Jiles, David C. (Inventor); Paulsen, Jason A. (Inventor); Snyder, John E. (Inventor); Lo, Chester C. H. (Inventor); Ring, Andrew P. (Inventor); Bormann, Keith A. (Inventor)

2008-01-01

Magnetostrictive material based on cobalt ferrite is described. The cobalt ferrite is substituted with transition metals (such manganese (Mn), chromium (Cr), zinc (Zn) and copper (Cu) or mixtures thereof) by substituting the transition metals for iron or cobalt to form substituted cobalt ferrite that provides mechanical properties that make the substituted cobalt ferrite material effective for use as sensors and actuators. The substitution of transition metals lowers the Curie temperature of the material (as compared to cobalt ferrite) while maintaining a suitable magnetostriction for stress sensing applications.

Study of methyl- and phenyl-substituted thermostable polysiloxane-silarylene motionless phases for capillary gas chromatography

NASA Astrophysics Data System (ADS)

Komarova, A. O.; Shashkov, M. V.; Sidel'nikov, V. N.

2017-11-01

Capillary columns based on a number of thermostable polysiloxane-silarylene motionless phases are prepared and their properties are studied. Three polymers with different contents of methyl and phenyl groups are synthesized: dimethylsiloxanesilarylene (DMS), methylphenylsiloxanesilarylene (MPhS), and diphenylsiloxanesilarylene (DPhS). Studies of their thermostability show that the level of the background current of these columns upon heating to 350°C is several times lower than that of a column based on polydimethylsiloxane. Based on McReynolds' studies of polarity and Abraham's studies of the selectivity of prepared columns according to the parameters of intermolecular interactions, it is found that silarylene MLPs are more affected by the contributions from specific interactions (especially for dipole-dipole, π-π-, and n-π-interactions) than MLPs with no phenylene inserts. The effect on the selectivity of a phenyl group inside a chain differs from the one produced by the phenyl groups in side MLP chains. The effect on the selectivity of a phenyl group inside a chain differs from the one produced by the phenyl groups in side MLP chains. Examples of the separation of test mixtures of aromatic and oxygen-containing compounds are obtained, along with an extract of thistle oil containing tocopherols and phytosterols at a final temperature of analysis of 350°C.

In Silico Olefin Metathesis with Ru-Based Catalysts Containing N-Heterocyclic Carbenes Bearing C60 Fullerenes.

PubMed

Martínez, Juan Pablo; Vummaleti, Sai Vikrama Chaitanya; Falivene, Laura; Nolan, Steven P; Cavallo, Luigi; Solà, Miquel; Poater, Albert

2016-05-04

Density functional theory calculations have been used to explore the potential of Ru-based complexes with 1,3-bis(2,4,6-trimethylphenyl)imidazolin-2-ylidene (SIMes) ligand backbone (A) being modified in silico by the insertion of a C60 molecule (B and C), as olefin metathesis catalysts. To this end, we investigated the olefin metathesis reaction catalyzed by complexes A, B, and C using ethylene as the substrate, focusing mainly on the thermodynamic stability of all possible reaction intermediates. Our results suggest that complex B bearing an electron-withdrawing N-heterocyclic carbene improves the performance of unannulated complex A. The efficiency of complex B is only surpassed by complex A when the backbone of the N-heterocyclic carbene of complex A is substituted by two amino groups. The particular performance of complexes B and C has to be attributed to electronic factors, that is, the electronic-donating capacity of modified SIMes ligand rather than steric effects, because the latter are predicted to be almost identical for complexes B and C when compared to those of A. Overall, this study indicates that such Ru-based complexes B and C might have the potential to be effective olefin metathesis catalysts. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Full-length genome analysis of two genetically distinct variants of porcine epidemic diarrhea virus in Thailand.

PubMed

Cheun-Arom, Thaniwan; Temeeyasen, Gun; Tripipat, Thitima; Kaewprommal, Pavita; Piriyapongsa, Jittima; Sukrong, Suchada; Chongcharoen, Wanchai; Tantituvanont, Angkana; Nilubol, Dachrit

2016-10-01

Porcine epidemic diarrhea virus (PEDV) has continued to cause sporadic outbreaks in Thailand since 2007 and a pandemic variant containing an insertion and deletion in the spike gene was responsible for outbreaks. In 2014, there were further outbreaks of the disease occurring within four months of each other. In this study, the full-length genome sequences of two genetically distinct PEDV isolates from the outbreaks were characterized. The two PEDV isolates, CBR1/2014 and EAS1/2014, were 28,039 and 28,033 nucleotides in length and showed 96.2% and 93.6% similarities at nucleotide and amino acid levels respectively. In total, we have observed 1048 nucleotide substitutions throughout the genome. Compared to EAS1/2014, CBR1/2014 has 2 insertions of 4 ((56)GENQ(59)) and 1 ((140)N) amino acid positions 56-59 and 140, and 2 deletions of 2 ((160)DG(161)) and 1 ((1199)Y) amino acid positions 160-161 and 1199. The phylogenetic analysis based on full-length genome of CBR1/2014 isolate has grouped the virus with the pandemic variants. In contrast, EAS1/2014 isolate was grouped with CV777, LZC and SM98, a classical variant. Our findings demonstrated the emergence of EAS1/2014, a classical variant which is novel to Thailand and genetically distinct from the currently circulating endemic variants. This study warrants further investigations into molecular epidemiology and genetic evolution of the PEDV in Thailand. Copyright © 2016 Elsevier B.V. All rights reserved.

Recent insertion/deletion (reINDEL) mutations: increasing awareness to boost molecular-based research in ecology and evolution

PubMed Central

Schlick-Steiner, Birgit C; Arthofer, Wolfgang; Moder, Karl; Steiner, Florian M

2015-01-01

Today, the comparative analysis of DNA molecules mainly uses information inferred from nucleotide substitutions. Insertion/deletion (INDEL) mutations, in contrast, are largely considered uninformative and discarded, due to our lacking knowledge on their evolution. However, including rather than discarding INDELs would be relevant to any research area in ecology and evolution that uses molecular data. As a practical approach to better understanding INDEL evolution in general, we propose the study of recent INDEL (reINDEL) mutations – mutations where both ancestral and derived state are seen in the sample. The precondition for reINDEL identification is knowledge about the pedigree of the individuals sampled. Sound reINDEL knowledge will allow the improved modeling needed for including INDELs in the downstream analysis of molecular data. Both microsatellites, currently still the predominant marker system in the analysis of populations, and sequences generated by next-generation sequencing, a promising and rapidly developing range of technologies, offer the opportunity for reINDEL identification. However, a 2013 sample of animal microsatellite studies contained unexpectedly few reINDELs identified. As most likely explanation, we hypothesize that reINDELs are underreported rather than absent and that this underreporting stems from common reINDEL unawareness. If our hypothesis applies, increased reINDEL awareness should allow gathering data rapidly. We recommend the routine reporting of either the absence or presence of reINDELs together with standardized key information on the nature of mutations when they are detected and the use of the keyword “reINDEL” to increase visibility in both instances of successful and unsuccessful search. PMID:25628861

Refunctionalization of the ancient rice blast disease resistance gene Pit by the recruitment of a retrotransposon as a promoter.

PubMed

Hayashi, Keiko; Yoshida, Hitoshi

2009-02-01

The plant genome contains a large number of disease resistance (R) genes that have evolved through diverse mechanisms. Here, we report that a long terminal repeat (LTR) retrotransposon contributed to the evolution of the rice blast resistance gene Pit. Pit confers race-specific resistance against the fungal pathogen Magnaporthe grisea, and is a member of the nucleotide-binding site leucine-rich repeat (NBS-LRR) family of R genes. Compared with the non-functional allele Pit(Npb), the functional allele Pit(K59) contains four amino acid substitutions, and has the LTR retrotransposon Renovator inserted upstream. Pathogenesis assays using chimeric constructs carrying the various regions of Pit(K59) and Pit(Npb) suggest that amino acid substitutions might have a potential effect in Pit resistance; more importantly, the upregulated promoter activity conferred by the Renovator sequence is essential for Pit function. Our data suggest that transposon-mediated transcriptional activation may play an important role in the refunctionalization of additional 'sleeping' R genes in the plant genome.

Silicon incorporation in GaAs: From delta-doping to monolayer insertion

NASA Astrophysics Data System (ADS)

Wagner, J.; Newman, R. C.; Roberts, C.

1995-08-01

Raman spectroscopy was used to study the incorporation of Si into doping layers in GaAs, grown by molecular beam epitaxy at a temperature of 400 °C, for Si concentrations ranging from the δ-doping level to a ML coverage. The strength of the scattering by local vibrational modes of substitutional Si was almost constant for Si areal concentration [Si]A in the range 5×1012<[Si]A<5×1013 cm-2 but then decreased, dropping below the detection limit for [Si]A≳3×1014 cm-2. At these concentrations a new vibrational band emerged at a frequency close to 470 cm-1 and developed into the optic zone center phonon of a coherently strained epitaxial layer of Si embedded in GaAs when a coverage of ≊1.5 ML (9.3×1014 cm-2) was reached. These findings strongly indicate that the observed saturation and the eventual decrease of the concentration of substitutional silicon is caused by an increasing incorporation of deposited Si into two-dimensional islands of covalently bonded Si.

Crystal Structure of Cockroach Allergen Bla g 2, an Unusual Zinc Binding Aspartic Protease with a Novel Mode of Self-inhibition

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

Gustchina, Alla; Li, Mi; Wunschmann, Sabina

2010-07-19

The crystal structure of Bla g 2 was solved in order to investigate the structural basis for the allergenic properties of this unusual protein. This is the first structure of an aspartic protease in which conserved glycine residues, in two canonical DTG triads, are substituted by different amino acid residues. Another unprecedented feature revealed by the structure is the single phenylalanine residue insertion on the tip of the flap, with the side-chain occupying the S1 binding pocket. This and other important amino acid substitutions in the active site region of Bla g 2 modify the interactions in the vicinity ofmore » the catalytic aspartate residues, increasing the distance between them to {approx}4 {angstrom} and establishing unique direct contacts between the flap and the catalytic residues. We attribute the absence of substantial catalytic activity in Bla g 2 to these unusual features of the active site. Five disulfide bridges and a Zn-binding site confer stability to the protein, which may contribute to sensitization at lower levels of exposure than other allergens.« less

Quantitative Analysis of the Mutagenic Potential of 1-Aminopyrene-DNA Adduct Bypass Catalyzed by Y-Family DNA Polymerases

PubMed Central

Sherrer, Shanen M.; Taggart, David J.; Pack, Lindsey R.; Malik, Chanchal K.; Basu, Ashis K.; Suo, Zucai

2012-01-01

N- (deoxyguanosin-8-yl)-1-aminopyrene (dGAP) is the predominant nitro polyaromatic hydrocarbon product generated from the air pollutant 1-nitropyrene reacting with DNA. Previous studies have shown that dGAP induces genetic mutations in bacterial and mammalian cells. One potential source of these mutations is the error-prone bypass of dGAP lesions catalyzed by the low-fidelity Y-family DNA polymerases. To provide a comparative analysis of the mutagenic potential of the translesion DNA synthesis (TLS) of dGAP, we employed short oligonucleotide sequencing assays (SOSAs) with the model Y-family DNA polymerase from Sulfolobus solfataricus, DNA Polymerase IV (Dpo4), and the human Y-family DNA polymerases eta (hPolη), kappa (hPolκ), and iota (hPolι). Relative to undamaged DNA, all four enzymes generated far more mutations (base deletions, insertions, and substitutions) with a DNA template containing a site-specifically placed dGAP. Opposite dGAP and at an immediate downstream template position, the most frequent mutations made by the three human enzymes were base deletions and the most frequent base substitutions were dAs for all enzymes. Based on the SOSA data, Dpo4 was the least error-prone Y-family DNA polymerase among the four enzymes during the TLS of dGAP. Among the three human Y-family enzymes, hPolκ made the fewest mutations at all template positions except opposite the lesion site. hPolκ was significantly less error-prone than hPolι and hPolη during the extension of dGAP bypass products. Interestingly, the most frequent mutations created by hPolι at all template positions were base deletions. Although hRev1, the fourth human Y-family enzyme, could not extend dGAP bypass products in our standing start assays, it preferentially incorporated dCTP opposite the bulky lesion. Collectively, these mutagenic profiles suggest that hPolkk and hRev1 are the most suitable human Y-family DNA polymerases to perform TLS of dGAP in humans. PMID:22917544

The influence of specific neighboring bases on substitution bias in noncoding regions of the plant chloroplast genome.

PubMed

Morton, B R; Oberholzer, V M; Clegg, M T

1997-09-01

Substitutions occurring in noncoding sequences of the plant chloroplast genome violate the independence of sites that is assumed by substitution models in molecular evolution. The probability that a substitution at a site is a transversion, as opposed to a transition, increases significantly with increasing A + T content of the two adjacent nucleotides. In the present study, this dependency of substitutions on local context is examined further in a number of noncoding regions from the chloroplast genome of members of the grass family (Poaceae). Two features were examined; the influence of specific neighboring bases, as opposed to the general A + T content, on transversion proportion and an influence on substitutions by nucleotides other than the two immediately adjacent to the site of substitution. In both cases, a significant effect was found. In the case of specific nucleotides, transversion proportion is significantly higher at sites with a pyrimidine immediately 5' on either strand. Substitutions at sites of the type YNR, where N is the site of substitution, have the highest rate of transversion. This specific effect is secondary to the A + T content effect such that, in terms of proportion of substitutions that are transversions, the nucleotides are ranked T > A > C > G as to their effect when they are immediately 5' to the site of substitution. In the case of nucleotides other than the immediate neighbors, a significant influence on substitution dynamics is observed in the case where the two neighboring bases are both A and/or T. Thus, substitutions are primarily, but not exclusively, influenced by the composition of the two nucleotides that are immediately adjacent. These results indicate that the pattern of molecular evolution of the plant chloroplast genome is extremely complex as a result of a variety of inter-site dependencies.

Dynamic soft tissue deformation estimation based on energy analysis

NASA Astrophysics Data System (ADS)

Gao, Dedong; Lei, Yong; Yao, Bin

2016-10-01

The needle placement accuracy of millimeters is required in many needle-based surgeries. The tissue deformation, especially that occurring on the surface of organ tissue, affects the needle-targeting accuracy of both manual and robotic needle insertions. It is necessary to understand the mechanism of tissue deformation during needle insertion into soft tissue. In this paper, soft tissue surface deformation is investigated on the basis of continuum mechanics, where a geometry model is presented to quantitatively approximate the volume of tissue deformation. The energy-based method is presented to the dynamic process of needle insertion into soft tissue based on continuum mechanics, and the volume of the cone is exploited to quantitatively approximate the deformation on the surface of soft tissue. The external work is converted into potential, kinetic, dissipated, and strain energies during the dynamic rigid needle-tissue interactive process. The needle insertion experimental setup, consisting of a linear actuator, force sensor, needle, tissue container, and a light, is constructed while an image-based method for measuring the depth and radius of the soft tissue surface deformations is introduced to obtain the experimental data. The relationship between the changed volume of tissue deformation and the insertion parameters is created based on the law of conservation of energy, with the volume of tissue deformation having been obtained using image-based measurements. The experiments are performed on phantom specimens, and an energy-based analytical fitted model is presented to estimate the volume of tissue deformation. The experimental results show that the energy-based analytical fitted model can predict the volume of soft tissue deformation, and the root mean squared errors of the fitting model and experimental data are 0.61 and 0.25 at the velocities 2.50 mm/s and 5.00 mm/s. The estimating parameters of the soft tissue surface deformations are proven to be useful for compensating the needle-targeting error in the rigid needle insertion procedure, especially for percutaneous needle insertion into organs.

Descemet's Stripping Automated Endothelial Keratoplasty Tissue Insertion Devices

PubMed Central

Khan, Salman Nasir; Shiakolas, Panos S.; Mootha, Venkateswara Vinod

2015-01-01

This review study provides information regarding the construction, design, and use of six commercially available endothelial allograft insertion devices applied for Descemet's stripping automated endothelial keratoplasty (DSAEK). We also highlight issues being faced in DSAEK and discuss the methods through which medical devices such as corneal inserters may alleviate these issues. Inserter selection is of high importance in the DSAEK procedure since overcoming the learning curve associated with the use of an insertion device is a time and energy consuming process. In the present review, allograft insertion devices were compared in terms of design, construction material, insertion technique, dimensions, incision requirements and endothelial cell loss to show their relative merits and capabilities based on available data in the literature. Moreover, the advantages/disadvantages of various insertion devices used for allograft insertion in DSAEK are reviewed and compared. The information presented in this review can be utilized for better selection of an insertion device for DSAEK. PMID:27051492

Combined micro computed tomography and histology study of bone augmentation and distraction osteogenesis

NASA Astrophysics Data System (ADS)

Ilgenstein, Bernd; Deyhle, Hans; Jaquiery, Claude; Kunz, Christoph; Stalder, Anja; Stübinger, Stefan; Jundt, Gernot; Beckmann, Felix; Müller, Bert; Hieber, Simone E.

2012-10-01

Bone augmentation is a vital part of surgical interventions of the oral and maxillofacial area including dental implantology. Prior to implant placement, sufficient bone volume is needed to reduce the risk of peri-implantitis. While augmentation using harvested autologous bone is still considered as gold standard, many surgeons prefer bone substitutes to reduce operation time and to avoid donor site morbidity. To assess the osteogenic efficacy of commercially available augmentation materials we analyzed drill cores extracted before implant insertion. In younger patients, distraction osteogenesis is successfully applied to correct craniofacial deformities through targeted bone formation. To study the influence of mesenchymal stem cells on bone regeneration during distraction osteogenesis, human mesenchymal stem cells were injected into the distraction gap of nude rat mandibles immediately after osteotomy. The distraction was performed over eleven days to reach a distraction gap of 6 mm. Both the rat mandibles and the drill cores were scanned using synchrotron radiation-based micro computed tomography. The three-dimensional data were manually registered and compared with corresponding two-dimensional histological sections to assess bone regeneration and its morphology. The analysis of the rat mandibles indicates that bone formation is enhanced by mesenchymal stem cells injected before distraction. The bone substitutes yielded a wide range of bone volume and degree of resorption. The volume fraction of the newly formed bone was determined to 34.4% in the computed tomography dataset for the augmentation material Geistlich Bio-Oss®. The combination of computed tomography and histology allowed a complementary assessment for both bone augmentation and distraction osteogenesis.

Synthesis, characterization, molecular docking and biological studies of self assembled transition metal dithiocarbamates of substituted pyrrole-2-carboxaldehyde.

PubMed

Nami, Shahab A A; Ullah, Irfan; Alam, Mahboob; Lee, Dong-Ung; Sarikavakli, Nursabah

2016-07-01

A series of self assembled 3d transition metal dithiocarbamate, M(pdtc) [where M=Mn(II), Fe(II), Co(II), Ni(II) and Cu(II)] have been synthesized and spectroscopically characterized. The bidentate dithiocarbamate ligand Na2pdtc (Disodium-1,4-phenyldiaminobis (pyrrole-1-sulfino)dithioate) was prepared by insertion reaction of carbondisulfide with Schiff base, N,N'-bis-(1H-pyrrol-2-ylmethylene)-benzene-1,4-diamine (L1) in basic medium. The simple substitution reaction between the metal halide and Na2pdtc yielded the title complexes in moderate yields. However, the in situ procedure gives high yield with the formation of single product as evident by TLC. Elemental analysis, IR, (1)H and (13)C NMR spectra, UV-vis., magnetic susceptibility and conductance measurements were done to characterize the complexes, M(pdtc). All the evidences suggest that the complexes have tetrahedral geometry excepting Cu(II) which is found to be square planar. A symmetrical bidentate coordination of the dithiocarbamato moiety has been observed in all the complexes. The conductivity data show that the complexes are non-electrolyte in nature. The anti-oxidant activity of the ligand, Na2pdtc and its transition metal complexes, M(pdtc) have been carried out using DPPH and Cu(pdtc) was found to be most effective. The anti-microbial activity of the Na2pdtc and M(pdtc) complexes have been carried out and on this basis the molecular docking study of the most effective complex, Cu(pdtc) has also been reported. Copyright © 2016 Elsevier B.V. All rights reserved.

CE: Original Research: Does Certification in Vascular Access Matter? An Analysis of the PICC1 Survey.

PubMed

Chopra, Vineet; Kuhn, Latoya; Vaughn, Valerie; Ratz, David; Winter, Suzanne; Moureau, Nancy; Meyer, Britt; Krein, Sarah

2017-12-01

: Background: Although certification by an accredited agency is often a practice prerequisite in health care, it is not required of vascular access specialists who insert peripherally inserted central catheters (PICCs). Whether certification is associated with differences in practice among inserters is unknown. The purpose of this study was to gather information regarding whether certified and noncertified PICC inserters differ with respect to their practices and views about PICC use. We conducted a national survey of vascular access specialists, identifying certified PICC inserters as those who had received board certification from the Association for Vascular Access, the Infusion Nurses Society, or both. The 76-item survey asked about PICC policies and procedures at respondents' facilities, use of insertion technologies, device management, management of complications, perceptions about PICC use, and relationships with other health care providers. Additional data about respondents, including years in practice and primary practice settings, were also gathered. Bivariable comparisons were made using χ tests; two-sided α with P ≤ 0.05 was considered statistically significant. Of the 1,450 respondents in the final sample, 1,007 (69%) said they were certified inserters and 443 (31%) said they were not. Significantly higher percentages of certified than noncertified inserters reported having practiced for five or more years (78% versus 54%) and having placed 1,000 or more PICCs (58% versus 32%). Significantly more certified than noncertified inserters also reported being the vascular access lead for their facility (56% versus 44%). Reported practice patterns for insertion, care, and management of PICCs varied based on certification status. Some evidence-based practices (such as the use of ultrasound to measure catheter-to-vein ratios) were more often reported by certified inserters, while others (such as the use of maximal sterile barriers during PICC insertion) were not. Asked about their perceptions of PICC use at their institution, certified inserters reported higher percentages of inappropriate insertion and removal than noncertified inserters. Certified PICC inserters appear to be a distinct group of vascular access specialists. A better understanding of how and why practices differ between certified and noncertified inserters is necessary to ensuring safer, high-quality patient care.

Role of blood ribosomal protein S19 in coagulum resorption: a study using Gln137Glu-ribosomal protein S19 gene knock-in mouse.

PubMed

Chen, Jun; Fujino, Rika; Zhao, Rui; Semba, Umeko; Araki, Kimi; Yamamoto, Tetsuro

2014-11-01

Sera of human, guinea pig or mouse contain a strong monocyte chemoattractant capacity that is attributed to the ribosomal protein S19 (RP S19) oligomers generated during blood coagulation. In contrast, sera prepared from Gln137Glu-RP S19 gene knock-in mice contained negligible chemoattractant capacity. When coagula that had been pre-formed from the blood of both the wild type and knock-in mice were intraperitoneally inserted into host mice, after 3 days of recovery, the knock-in mouse coagula remained larger than the wild type mouse coagula. The wild type mouse coagula were covered by multiple macrophage layers at the surface and were infiltrated inside by macrophages. Knock-in mouse coagula exhibited less macrophage involvement. When coagula of knock-in mice and coagula of knock-in mice containing C5a/RP S19, an artificial substitute of the RP S19 oligomers, were intraperitoneally inserted as pairs, the C5a/RP S19 containing coagulum was more rapidly absorbed, concomitant with increased macrophage involvement. Finally, when the knock-in mouse and wild type mouse coagula pairs were inserted into mice in which macrophages had been depleted using clodronate liposome, the size difference of recovered coagula was reversed. These results indicate the importance of the RP S19 oligomer-induced macrophage recruitment in coagulum resorption. © 2014 Japanese Society of Pathology and Wiley Publishing Asia Pty Ltd.

A Defect in DNA Ligase4 Enhances the Frequency of TALEN-Mediated Targeted Mutagenesis in Rice1[OPEN

PubMed Central

Cermak, Tomas; Sugimoto, Kazuhiko; Saika, Hiroaki; Mori, Akiko; Osakabe, Keishi; Hamada, Masao; Katayose, Yuichi; Voytas, Daniel F.

2016-01-01

We have established methods for site-directed mutagenesis via transcription activator-like effector nucleases (TALENs) in the endogenous rice (Oryza sativa) waxy gene and demonstrated stable inheritance of TALEN-induced somatic mutations to the progeny. To analyze the role of classical nonhomologous end joining (cNHEJ) and alternative nonhomologous end joining (altNHEJ) pathways in TALEN-induced mutagenesis in plant cells, we investigated whether a lack of DNA Ligase4 (Lig4) affects the kinetics of TALEN-induced double-strand break repair in rice cells. Deep-sequencing analysis revealed that the frequency of all types of mutations, namely deletion, insertion, combination of insertion with deletion, and substitution, in lig4 null mutant calli was higher than that in a lig4 heterozygous mutant or the wild type. In addition, the ratio of large deletions (greater than 10 bp) and deletions repaired by microhomology-mediated end joining (MMEJ) to total deletion mutations in lig4 null mutant calli was higher than that in the lig4 heterozygous mutant or wild type. Furthermore, almost all insertions (2 bp or greater) were shown to be processed via copy and paste of one or more regions around the TALENs cleavage site and rejoined via MMEJ regardless of genetic background. Taken together, our findings indicate that the dysfunction of cNHEJ leads to a shift in the repair pathway from cNHEJ to altNHEJ or synthesis-dependent strand annealing. PMID:26668331

Acid-triggered membrane insertion of Pseudomonas exotoxin A involves an original mechanism based on pH-regulated tryptophan exposure.

PubMed

Méré, Jocelyn; Morlon-Guyot, Juliette; Bonhoure, Anne; Chiche, Laurent; Beaumelle, Bruno

2005-06-03

Exposure to low endosomal pH during internalization of Pseudomonas exotoxin A (PE) triggers membrane insertion of its translocation domain. This process is a prerequisite for PE translocation to the cytosol where it inactivates protein synthesis. Although hydrophobic helices enable membrane insertion of related bacterial toxins such as diphtheria toxin, the PE translocation domain is devoid of hydrophobic stretches and the structural features triggering acid-induced membrane insertion of PE are not known. Here we have identified a molecular device that enables PE membrane insertion. This process is promoted by exposure of a key tryptophan residue. At neutral pH, this Trp is buried in a hydrophobic pocket closed by the smallest alpha-helix of the translocation domain. Upon acidification, protonation of the Asp that is the N-cap residue of the helix leads to its destabilization, enabling Trp side chain insertion into the endosome membrane. This tryptophan-based membrane insertion system is surprisingly similar to the membrane-anchoring mechanism of human annexin-V and could be used by other proteins as well.

Nucleophilic substitution reaction for post-functionalization of polyoxometalates

DOE PAGES

Yin, Panchao; Li, Qiang; Zhang, Jin; ...

2015-07-06

In this study, a hexamolybdate-based organic inorganic hybrid molecule containing a chloralkane fragment is synthesized and its Cl atom can be substituted by iodine and nitrate through nucleophilic substitution reactions in high yields, which provide a post-functionalization protocol to bring in various additional functional groups into polyoxometalate-based hybrid materials under mild conditions.

Composition and structure of porcine digital flexor tendon-bone insertion tissues.

PubMed

Chandrasekaran, Sandhya; Pankow, Mark; Peters, Kara; Huang, Hsiao-Ying Shadow

2017-11-01

Tendon-bone insertion is a functionally graded tissue, transitioning from 200 MPa tensile modulus at the tendon end to 20 GPa tensile modulus at the bone, across just a few hundred micrometers. In this study, we examine the porcine digital flexor tendon insertion tissue to provide a quantitative description of its collagen orientation and mineral concentration by using Fast Fourier Transform (FFT) based image analysis and mass spectrometry, respectively. Histological results revealed uniformity in global collagen orientation at all depths, indicative of mechanical anisotropy, although at mid-depth, the highest fiber density, least amount of dispersion, and least cellular circularity were evident. Collagen orientation distribution obtained through 2D FFT of histological imaging data from fluorescent microscopy agreed with past measurements based on polarized light microscopy. Results revealed global fiber orientation across the tendon-bone insertion to be preserved along direction of physiologic tension. Gradation in the fiber distribution orientation index across the insertion was reflective of a decrease in anisotropy from the tendon to the bone. We provided elemental maps across the fibrocartilage for its organic and inorganic constituents through time-of-flight secondary ion mass spectrometry (TOF-SIMS). The apatite intensity distribution from the tendon to bone was shown to follow a linear trend, supporting past results based on Raman microprobe analysis. The merit of this study lies in the image-based simplified approach to fiber distribution quantification and in the high spatial resolution of the compositional analysis. In conjunction with the mechanical properties of the insertion tissue, fiber, and mineral distribution results for the insertion from this may potentially be incorporated into the development of a structural constitutive approach toward computational modeling. Characterizing the properties of the native insertion tissue would provide the microstructural basis for developing biomimetic scaffolds to recreate the graded morphology of a fibrocartilaginous insertion. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 105A: 3050-3058, 2017. © 2017 Wiley Periodicals, Inc.

Effectiveness of the surgical torque limiter: a model comparing drill- and hand-based screw insertion into locking plates.

PubMed

Ioannou, Christopher; Knight, Matthew; Daniele, Luca; Flueckiger, Lee; Tan, Ezekiel S L

2016-10-17

The objective of this study is to analyse the effectiveness of the surgical torque limiter during operative use. The study also investigates the potential differences in torque between hand and drill-based screw insertion into locking plates using a standardised torque limiter. Torque for both hand and power screw insertion was measured through a load cell, registering 6.66 points per second. This was performed in a controlled environment using synthetic bone, a locking plate and locking screws to simulate plate fixation. Screws were inserted by hand and by drill with torque values measured. The surgical torque limiter (1.5 Nm) was effective as the highest recorded reading in the study was 1.409 Nm. Comparatively, there is a statistically significant difference between screw insertion methods. Torque produced for manually driven screw insertion into locking plates was 1.289 Nm (95 % CI 1.269-1.308) with drill-powered screw insertion at 0.740 Nm (95 % CI 0.723-0.757). The surgical torque limiter proved to be effective as per product specifications. Screws inserted under power produce significantly less torque when compared to manual insertion by hand. This is likely related to the mechanism of the torque limiter when being used at higher speeds for which it was designed. We conclude that screws may be inserted using power to the plate with the addition of a torque limiter. It is recommended that all screws inserted by drill be hand tightened to achieve adequate torque values.

Shoe inserts and orthotics for sport and physical activities.

PubMed

Nigg, B M; Nurse, M A; Stefanyshyn, D J

1999-07-01

The purposes of this paper were to discuss the perceived benefits of inserts and orthotics for sport activities and to propose a new concept for inserts and orthotics. There is evidence that inserts or orthotics reduce or prevent movement-related injuries. However, there is limited knowledge about the specific functioning an orthotic or insert provides. The same orthotic or insert is often proposed for different problems. Changes in skeletal movement due to inserts or orthotics seem to be small and not systematic. Based on the results of a study using bone pins, one may question the idea that a major function of orthotics or inserts consists in aligning the skeleton. Impact cushioning with shoe inserts or orthotics is typically below 10%. Such small reductions might not be important for injury reduction. It has been suggested that changes in material properties might produce adjustments in the muscular response of the locomotor system. The foot has various sensors to detect input signals with subject specific thresholds. Subjects with similar sensitivity threshold levels seem to respond in their movement pattern in a similar way. Comfort is an important variable. From a biomechanical point of view, comfort may be related to fit, additional stabilizing muscle work, fatigue, and damping of soft tissue vibrations. Based on the presented evidence, the concept of minimizing muscle work is proposed when using orthotics or inserts. A force signal acts as an input variable on the shoe. The shoe sole acts as a first filter, the insert or orthotic as a second filter, the plantar surface of the foot as a third filter for the force input signal. The filtered information is transferred to the central nervous system that provides a subject specific dynamic response. The subject performs the movement for the task at hand. For a given movement task, the skeleton has a preferred path. If an intervention supports/counteracts the preferred movement path, muscle activity can/must be reduced/increased. Based on this concept, an optimal insert or orthotic would reduce muscle activity, feel comfortable, and should increase performance.

Bidding Agents That Perpetrate Auction Fraud

NASA Astrophysics Data System (ADS)

Trevathan, Jarrod; McCabe, Alan; Read, Wayne

This paper presents a software bidding agent that inserts fake bids on the seller's behalf to inflate an auction's price. This behaviour is referred to as shill bidding. Shill bidding is strictly prohibited by online auctioneers, as it defrauds unsuspecting buyers by forcing them to pay more for the item. The malicious bidding agent was constructed to aid in developing shill detection techniques. We have previously documented a simple shill bidding agent that incrementally increases the auction price until it reaches the desired profit target, or it becomes too risky to continue bidding. This paper presents an adaptive shill bidding agent which when used over a series of auctions with substitutable items, can revise its strategy based on bidding behaviour in past auctions. The adaptive agent applies a novel prediction technique referred to as the Extremum Consistency (EC) algorithm, to determine the optimal price to aspire for. The EC algorithm has successfully been used in handwritten signature verification for determining the maximum and minimum values in an input stream. The agent's ability to inflate the price has been tested in a simulated marketplace and experimental results are presented.

Theoretical and experimental study of electron-deficient core substitution effect of diketopyrrolopyrrole derivatives on optoelectrical and charge transport properties

NASA Astrophysics Data System (ADS)

Ding, Guodong; Mahmood, Asif; Tang, Ailing; Chen, Fan; Zhou, Erjun

2018-01-01

Three new diketopyrrolopyrrole based compounds with Acceptor-Donor-Acceptor-Donor-Acceptor (A-D-A-D-A) skeletons were designed and synthesized through varying the electron-deficient core from diphenylquinoxaline (DP-Qx), thieno[3,4-c]pyrrole-4,6-dione (DP-TPD) to 2-dodecyl-6,7-diphenyl-2H-[1,2,3]triazole[4,5-g]quinoxaline (DP-TQx). We have calculated and studied the effect of central acceptor units on electronic, optical and non-optical properties. As well as, we have predicted the charge transport properties. Results indicate that change of central acceptor unit remarkably affects the molecular electronic, optical and non-optical properties. And the molecular band gap and UV/vis adsorption spectra are significantly changed. It should be noted that Compound 3 with 2-dodecyl-6,7-diphenyl-2H-[1,2,3]triazole[4,5-g]quinoxaline as core show superior non-optical properties as compare to other compounds. Our study here indicate that inserting the strong electron-deficient moieties improves intramolecular charge transfer (ICT) and charge transport properties dramatically.

Removing nickel from nickel-coated carbon fibers

NASA Astrophysics Data System (ADS)

Hardianto, A.; Hertleer, C.; De Mey, G.; Van Langenhove, L.

2017-10-01

Conductive fibers/yarns are one of the most important materials for smart textiles because of their electrically conductive functionality combined with flexibility and light weight. They can be applied in many fields such as the medical sector, electronics, sensors and even as thermoelectric generators. Temperature sensors, for example, can be made using the thermocouple or thermopile principle which usually uses two different metal wires that can produce a temperature-dependent voltage. However, if metal wires are inserted into a textile structure, they will decrease the flexibility properties of the textile product. Nickel-coated Carbon Fiber (NiCF), a conductive textile yarn, has a potential use as a textile-based thermopile if we can create an alternating region of carbon and nickel along the fiber which in turn it can be used for substituting the metallic thermopile. The idea was to remove nickel from NiCF in order to obtain a yarn that contains alternating zones of carbon and nickel. Due to no literature reporting on how to remove nickel from NiCF, in this paper we investigated some chemicals to remove nickel from NiCF.

Soy-based polyols

DOEpatents

Suppes, Galen; Lozada, Zueica; Lubguban, Arnold

2013-06-25

The invention provides processes for preparing soy-based oligomeric polyols or substituted oligomeric polyols, as well as urethane bioelasteromers comprising the oligomeric polyols or substituted oligomeric polyols.

Estimating needle tip deflection in biological tissue from a single transverse ultrasound image: application to brachytherapy.

PubMed

Rossa, Carlos; Sloboda, Ron; Usmani, Nawaid; Tavakoli, Mahdi

2016-07-01

This paper proposes a method to predict the deflection of a flexible needle inserted into soft tissue based on the observation of deflection at a single point along the needle shaft. We model the needle-tissue as a discretized structure composed of several virtual, weightless, rigid links connected by virtual helical springs whose stiffness coefficient is found using a pattern search algorithm that only requires the force applied at the needle tip during insertion and the needle deflection measured at an arbitrary insertion depth. Needle tip deflections can then be predicted for different insertion depths. Verification of the proposed method in synthetic and biological tissue shows a deflection estimation error of [Formula: see text]2 mm for images acquired at 35 % or more of the maximum insertion depth, and decreases to 1 mm for images acquired closer to the final insertion depth. We also demonstrate the utility of the model for prostate brachytherapy, where in vivo needle deflection measurements obtained during early stages of insertion are used to predict the needle deflection further along the insertion process. The method can predict needle deflection based on the observation of deflection at a single point. The ultrasound probe can be maintained at the same position during insertion of the needle, which avoids complications of tissue deformation caused by the motion of the ultrasound probe.

Efficiency and droop improvement in a blue InGaN-based light emitting diode with a p-InGaN layer inserted in the GaN barriers

NASA Astrophysics Data System (ADS)

Wang, Xing-Fu; Tong, Jin-Hui; Zhao, Bi-Jun; Chen, Xin; Ren, Zhi-Wei; Li, Dan-Wei; Zhuo, Xiang-Jing; Zhang, Jun; Yi, Han-Xiang; Li, Shu-Ti

2013-09-01

The advantages of a blue InGaN-based light-emitting diode with a p-InGaN layer inserted in the GaN barriers is studied. The carrier concentration in the quantum well, radiative recombination rate in the active region, output power, and internal quantum efficiency are investigated. The simulation results show that the InGaN-based light-emitting diode with a p-InGaN layer inserted in the barriers has better performance over its conventional counterpart and the light emitting diode with p-GaN inserted in the barriers. The improvement is due to enhanced Mg acceptor activation and enhanced hole injection into the quantum wells.

Improving the assessment of prescribing: use of a 'substitution index'.

PubMed

Kunisawa, Susumu; Otsubo, Tetsuya; Lee, Jason; Imanaka, Yuichi

2013-07-01

To analyse the current and potential utilization of generic drugs in Japan, to examine the maximum possible cost savings from generic drug use and to develop a fairer measure to assess the level of generic drug substitution. We conducted a cross-sectional retrospective analysis of nine million dispensing records during January to March 2010 in Kyoto Prefecture. Maximum potential quantity-based shares were defined as the quantity of generic drugs used plus the quantity of branded drugs that could have been replaced by generic drugs divided by the quantity of all drugs dispensed. We developed a 'substitution index', defined as the proportion of generic drugs out of the total drugs substitutable with generic drugs (based on quantity rather than cost). Generic drugs had a quantity-based share of 17.9%, a cost-based share of 8.9% and a maximum potential quantity-based share of 50.1%, which is lower than the actual generic drug shares of some other countries. The maximum possible cost savings as a result of generic drug substitution was 16.5%. We also observed wide variations in maximum potential quantity-based shares between health care sectors and health care institutions. Simple comparisons based on quantity-based shares may misrepresent the actual generic drug use. A substitution index that takes into account the maximum potential quantity-based share of generic drugs as a fairer measure may promote more realistic goals and encourage generic drug usage.

Torsional Dynamics of Steerable Needles: Modeling and Fluoroscopic Guidance

PubMed Central

Swensen, John P.; Lin, MingDe; Okamura, Allison M.; Cowan, Noah J.

2017-01-01

Needle insertions underlie a diversity of medical interventions. Steerable needles provide a means by which to enhance existing needle-based interventions and facilitate new ones. Tip-steerable needles follow a curved path and can be steered by twisting the needle base during insertion, but this twisting excites torsional dynamics that introduce a discrepancy between the base and tip twist angles. Here, we model the torsional dynamics of a flexible rod—such as a tip-steerable needle—during subsurface insertion and develop a new controller based on the model. The torsional model incorporates time-varying mode shapes to capture the changing boundary conditions inherent during insertion. Numerical simulations and physical experiments using two distinct setups—stereo camera feedback in semi-transparent artificial tissue and feedback control with real-time X-ray imaging in optically opaque artificial tissue— demonstrate the need to account for torsional dynamics in control of the needle tip. PMID:24860026

[The ISP (Safe Insertion of PICCs) protocol: a bundle of 8 recommendations to minimize the complications related to the peripherally inserted central venous catheters (PICC)].

PubMed

Emoli, Alessandro; Cappuccio, Serena; Marche, Bruno; Musarò, Andrea; Scoppettuolo, Giancarlo; Pittiruti, Mauro

2014-01-01

The ISP (Safe Insertion of PICCs) protocol: a bundle of 8 recommendations to minimize the complications related to the peripherally inserted central venous catheters (PICC). The insertion of a peripherally inserted central venous catheter (PICC) is not without risks. The Italian Group for the Study of Long-Term Central Venous Access Devices (GAVeCeLT) has developed a protocol (SIP: Safe Implantation of PICCs) with the aim of minimizing the risks which may be associated with the placement of PICCs. The protocol is based on recommendations available in the literature and on the main clinical practice guidelines. The SIP protocol, a bundle of evidence-based recommendations, it is is easy to use, inexpensive, and cost-effective. If routinely used and carefully inplemented, it greatly reduces complications such as failure of venipuncture, accidental arterial puncture, damage of median nerve, infection and catheter related venous thrombosis.

Characterization of GM events by insert knowledge adapted re-sequencing approaches

PubMed Central

Yang, Litao; Wang, Congmao; Holst-Jensen, Arne; Morisset, Dany; Lin, Yongjun; Zhang, Dabing

2013-01-01

Detection methods and data from molecular characterization of genetically modified (GM) events are needed by stakeholders of public risk assessors and regulators. Generally, the molecular characteristics of GM events are incomprehensively revealed by current approaches and biased towards detecting transformation vector derived sequences. GM events are classified based on available knowledge of the sequences of vectors and inserts (insert knowledge). Herein we present three insert knowledge-adapted approaches for characterization GM events (TT51-1 and T1c-19 rice as examples) based on paired-end re-sequencing with the advantages of comprehensiveness, accuracy, and automation. The comprehensive molecular characteristics of two rice events were revealed with additional unintended insertions comparing with the results from PCR and Southern blotting. Comprehensive transgene characterization of TT51-1 and T1c-19 is shown to be independent of a priori knowledge of the insert and vector sequences employing the developed approaches. This provides an opportunity to identify and characterize also unknown GM events. PMID:24088728

Characterization of GM events by insert knowledge adapted re-sequencing approaches.

PubMed

Yang, Litao; Wang, Congmao; Holst-Jensen, Arne; Morisset, Dany; Lin, Yongjun; Zhang, Dabing

2013-10-03

Detection methods and data from molecular characterization of genetically modified (GM) events are needed by stakeholders of public risk assessors and regulators. Generally, the molecular characteristics of GM events are incomprehensively revealed by current approaches and biased towards detecting transformation vector derived sequences. GM events are classified based on available knowledge of the sequences of vectors and inserts (insert knowledge). Herein we present three insert knowledge-adapted approaches for characterization GM events (TT51-1 and T1c-19 rice as examples) based on paired-end re-sequencing with the advantages of comprehensiveness, accuracy, and automation. The comprehensive molecular characteristics of two rice events were revealed with additional unintended insertions comparing with the results from PCR and Southern blotting. Comprehensive transgene characterization of TT51-1 and T1c-19 is shown to be independent of a priori knowledge of the insert and vector sequences employing the developed approaches. This provides an opportunity to identify and characterize also unknown GM events.

Synthesis and biological activity of lipophilic analogs of the cationic antimicrobial active peptide anoplin.

PubMed

Chionis, Kostas; Krikorian, Dimitrios; Koukkou, Anna-Irini; Sakarellos-Daitsiotis, Maria; Panou-Pomonis, Eugenia

2016-11-01

Anoplin is a short natural cationic antimicrobial peptide which is derived from the venom sac of the solitary wasp, Anoplius samariensis. Due to its short sequence G 1 LLKR 5 IKT 8 LL-NH 2 , it is ideal for research tests. In this study, novel analogs of anoplin were prepared and examined for their antimicrobial, hemolytic activity, and proteolytic stability. Specific substitutions were introduced in amino acids Gly 1 , Arg 5 , and Thr 8 and lipophilic groups with different lengths in the N-terminus in order to investigate how these modifications affect their antimicrobial activity. These cationic analogs exhibited higher antimicrobial activity than the native peptide; they are also nontoxic at their minimum inhibitory concentration (MIC) values and resistant to enzymatic degradation. The substituted peptide GLLKF 5 IKK 8 LL-NH 2 exhibited high activity against Gram-negative bacterium Zymomonas mobilis (MIC = 7 µg/ml), and the insertion of octanoic, decanoic, and dodecanoic acid residues in its N-terminus increased the antimicrobial activity against Gram-positive and Gram-negative bacteria (MIC = 5 µg/ml). The conformational characteristics of the peptide analogs were studied by circular dichroism. Structure activity studies revealed that the substitution of specific amino acids and the incorporation of lipophilic groups enhanced the amphipathic α-helical conformation inducing better antimicrobial effects. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.

Ultra-Deep Sequencing Analysis of the Hepatitis A Virus 5'-Untranslated Region among Cases of the Same Outbreak from a Single Source

PubMed Central

Wu, Shuang; Nakamoto, Shingo; Kanda, Tatsuo; Jiang, Xia; Nakamura, Masato; Miyamura, Tatsuo; Shirasawa, Hiroshi; Sugiura, Nobuyuki; Takahashi-Nakaguchi, Azusa; Gonoi, Tohru; Yokosuka, Osamu

2014-01-01

Hepatitis A virus (HAV) is a causative agent of acute viral hepatitis for which an effective vaccine has been developed. Here we describe ultra-deep pyrosequences (UDPSs) of HAV 5'-untranslated region (5'UTR) among cases of the same outbreak, which arose from a single source, associated with a revolving sushi bar. We determined the reference sequence from HAV-derived clone from an attendant by the Sanger method. Sixteen UDPSs from this outbreak and one from another sporadic case were compared with this reference. Nucleotide errors yielded a UDPS error rate of < 1%. This study confirmed that nucleotide substitutions of this region are transition mutations in outbreak cases, that insertion was observed only in non-severe cases, and that these nucleotide substitutions were different from those of the sporadic case. Analysis of UDPSs detected low-prevalence HAV variations in 5'UTR, but no specific mutations associated with severity in these outbreak cases. To our surprise, HAV strains in this outbreak conserved HAV IRES sequence even if we performed analysis of UDPSs. UDPS analysis of HAV 5'UTR gave us no association between the disease severity of hepatitis A and HAV 5'UTR substitutions. It might be more interesting to perform ultra-deep sequencing of full length HAV genome in order to reveal possible unknown genomic determinants associated with disease severity. Further studies will be needed. PMID:24396287

Genetic and Biochemical characterization of OXA-519, a novel OXA-48-like β-lactamase.

PubMed

Dabos, Laura; Bogaerts, Pierre; Bonnin, Remy A; Zavala, Agustin; Sacré, Pierre; Iorga, Bogdan I; Huang, Daniel T; Glupczynski, Youri; Naas, Thierry

2018-06-04

A multidrug-resistant K. pneumoniae 1210 isolate with reduced carbapenem susceptibility revealed the presence of a novel plasmid-encoded bla OXA-48-like gene, named bla OXA-519. The 60.7-kb plasmid (pOXA-519) was similar to the IncL-OXA-48 prototypical plasmid except for a ca. 2-kb deletion due to an IS 1R insertion. OXA-519 differed from OXA-48 by a Val120Leu substitution, which resulted in an overall reduced ß-lactam-hydrolysis profile, except for ertapenem and meropenem that was increased. Thus, detection of OXA-519-producers using biochemical tests monitoring imipenem-hydrolysis will be difficult. Copyright © 2018 American Society for Microbiology.

O2 and CO binding to tetraaza-tripodal-capped iron(II) porphyrins.

PubMed

Ruzié, Christian; Even, Pascale; Ricard, David; Roisnel, Thierry; Boitrel, Bernard

2006-02-06

A series of tris(2-aminoethylamine) (tren) capped iron(II) porphyrins has been synthesized and characterized and their affinities for dioxygen and carbon monoxide measured. The X-ray structure of the basic scaffold with nickel inserted in the porphyrin is also reported. All the ligands differ by the nature of the group(s) attached to the secondary amine functions of the cap. These various substitutions were introduced to probe if a hydrogen bond with these secondary amine groups acting as the donor could rationalize the high affinity of these myoglobin models. This work clearly indicates that the cage structure of the tren predominates over all the other appended groups with the exception of p-nitrophenol.

Computerized planning of prostate cryosurgery using variable cryoprobe insertion depth.

PubMed

Rossi, Michael R; Tanaka, Daigo; Shimada, Kenji; Rabin, Yoed

2010-02-01

The current study presents a computerized planning scheme for prostate cryosurgery using a variable insertion depth strategy. This study is a part of an ongoing effort to develop computerized tools for cryosurgery. Based on typical clinical practices, previous automated planning schemes have required that all cryoprobes be aligned at a single insertion depth. The current study investigates the benefit of removing this constraint, in comparison with results based on uniform insertion depth planning as well as the so-called "pullback procedure". Planning is based on the so-called "bubble-packing method", and its quality is evaluated with bioheat transfer simulations. This study is based on five 3D prostate models, reconstructed from ultrasound imaging, and cryoprobe active length in the range of 15-35 mm. The variable insertion depth technique is found to consistently provide superior results when compared to the other placement methods. Furthermore, it is shown that both the optimal active length and the optimal number of cryoprobes vary among prostate models, based on the size and shape of the target region. Due to its low computational cost, the new scheme can be used to determine the optimal cryoprobe layout for a given prostate model in real time. Copyright 2008 Elsevier Inc. All rights reserved.

Genetic variants of uncoupling proteins-2 and -3 in relation to maximal oxygen uptake in different sports.

PubMed

Holdys, Joanna; Gronek, Piotr; Kryściak, Jakub; Stanisławski, Daniel

2013-01-01

Uncoupling proteins 2 and 3 (UCP2 and UCP3) as mitochondrial electron transporters are involved in regulation of ATP production and energy dissipation as heat. Energy efficiency plays an important role in physical performance, especially in aerobic fitness. The aim of this study was to examine the association between maximal oxygen uptake and genetic variants of the UCP2 and UCP3 genes. The studies were carried out in a group of 154 men and 85 women, professional athletes representing various sports and fitness levels and students of the University of Physical Education in Poznań. Physiological and molecular procedures were used, i.e. direct measurement of maximum oxygen uptake (VO₂max) and analysis of an insertion/deletion (I/D) polymorphism in the 3'untranslated region of exon 8 of the UCP2 gene and a C>T substitution in exon 5 (Y210Y) of the UCP3 gene. No statistically significant associations were found, only certain trends. Insertion allele (I) of the I/D UCP2 and the T allele of the UCP3 gene were favourable in obtaining higher VO₂max level and might be considered as endurance-related alleles.

Evolutionary inference via the Poisson Indel Process.

PubMed

Bouchard-Côté, Alexandre; Jordan, Michael I

2013-01-22

We address the problem of the joint statistical inference of phylogenetic trees and multiple sequence alignments from unaligned molecular sequences. This problem is generally formulated in terms of string-valued evolutionary processes along the branches of a phylogenetic tree. The classic evolutionary process, the TKF91 model [Thorne JL, Kishino H, Felsenstein J (1991) J Mol Evol 33(2):114-124] is a continuous-time Markov chain model composed of insertion, deletion, and substitution events. Unfortunately, this model gives rise to an intractable computational problem: The computation of the marginal likelihood under the TKF91 model is exponential in the number of taxa. In this work, we present a stochastic process, the Poisson Indel Process (PIP), in which the complexity of this computation is reduced to linear. The Poisson Indel Process is closely related to the TKF91 model, differing only in its treatment of insertions, but it has a global characterization as a Poisson process on the phylogeny. Standard results for Poisson processes allow key computations to be decoupled, which yields the favorable computational profile of inference under the PIP model. We present illustrative experiments in which Bayesian inference under the PIP model is compared with separate inference of phylogenies and alignments.

Evolutionary inference via the Poisson Indel Process

PubMed Central

Bouchard-Côté, Alexandre; Jordan, Michael I.

2013-01-01

We address the problem of the joint statistical inference of phylogenetic trees and multiple sequence alignments from unaligned molecular sequences. This problem is generally formulated in terms of string-valued evolutionary processes along the branches of a phylogenetic tree. The classic evolutionary process, the TKF91 model [Thorne JL, Kishino H, Felsenstein J (1991) J Mol Evol 33(2):114–124] is a continuous-time Markov chain model composed of insertion, deletion, and substitution events. Unfortunately, this model gives rise to an intractable computational problem: The computation of the marginal likelihood under the TKF91 model is exponential in the number of taxa. In this work, we present a stochastic process, the Poisson Indel Process (PIP), in which the complexity of this computation is reduced to linear. The Poisson Indel Process is closely related to the TKF91 model, differing only in its treatment of insertions, but it has a global characterization as a Poisson process on the phylogeny. Standard results for Poisson processes allow key computations to be decoupled, which yields the favorable computational profile of inference under the PIP model. We present illustrative experiments in which Bayesian inference under the PIP model is compared with separate inference of phylogenies and alignments. PMID:23275296

CMV-promoter driven codon-optimized expression alters the assembly type and morphology of a reconstituted HERV-K(HML-2).

PubMed

Hohn, Oliver; Hanke, Kirsten; Lausch, Veronika; Zimmermann, Anja; Mostafa, Saeed; Bannert, Norbert

2014-11-11

The HERV-K(HML-2) family contains the most recently integrated and best preserved endogenized proviral sequences in the human genome. All known elements have nevertheless been subjected to mutations or deletions that render expressed particles non-infectious. Moreover, these post-insertional mutations hamper the analysis of the general biological properties of this ancient virus family. The expression of consensus sequences and sequences of elements with reverted post-insertional mutations has therefore been very instrumental in overcoming this limitation. We investigated the particle morphology of a recently reconstituted HERV-K113 element termed oriHERV-K113 using thin-section electron microscopy (EM) and could demonstrate that strong overexpression by substitution of the 5'LTR for a CMV promoter and partial codon optimization altered the virus assembly type and morphology. This included a conversion from the regular C-type to an A-type morphology with a mass of cytoplasmic immature cores tethered to the cell membrane and the membranes of vesicles. Overexpression permitted the release and maturation of virions but reduced the envelope content. A weaker boost of virus expression by Staufen-1 was not sufficient to induce these morphological alterations.

CMV-Promoter Driven Codon-Optimized Expression Alters the Assembly Type and Morphology of a Reconstituted HERV-K(HML-2)

PubMed Central

Hohn, Oliver; Hanke, Kirsten; Lausch, Veronika; Zimmermann, Anja; Mostafa, Saeed; Bannert, Norbert

2014-01-01

The HERV-K(HML-2) family contains the most recently integrated and best preserved endogenized proviral sequences in the human genome. All known elements have nevertheless been subjected to mutations or deletions that render expressed particles non-infectious. Moreover, these post-insertional mutations hamper the analysis of the general biological properties of this ancient virus family. The expression of consensus sequences and sequences of elements with reverted post-insertional mutations has therefore been very instrumental in overcoming this limitation. We investigated the particle morphology of a recently reconstituted HERV-K113 element termed oriHERV-K113 using thin-section electron microscopy (EM) and could demonstrate that strong overexpression by substitution of the 5'LTR for a CMV promoter and partial codon optimization altered the virus assembly type and morphology. This included a conversion from the regular C-type to an A-type morphology with a mass of cytoplasmic immature cores tethered to the cell membrane and the membranes of vesicles. Overexpression permitted the release and maturation of virions but reduced the envelope content. A weaker boost of virus expression by Staufen-1 was not sufficient to induce these morphological alterations. PMID:25393897

Inherited Creutzfeldt-Jakob disease in a British family associated with a novel 144 base pair insertion of the prion protein gene.

PubMed Central

Nicholl, D; Windl, O; de Silva, R; Sawcer, S; Dempster, M; Ironside, J W; Estibeiro, J P; Yuill, G M; Lathe, R; Will, R G

1995-01-01

A case of familial Creutzfeldt-Jakob disease associated with a 144 base pair insertion in the open reading frame of the prion protein gene is described. Sequencing of the mutated allele showed an arrangement of six octapeptide repeats, distinct from that of a recently described British family with an insertion of similar size. Thirteen years previously the brother of the proband had died from "Huntington's disease", but re-examination of his neuropathology revealed spongiform encephalopathy and anti-prion protein immunocytochemistry gave a positive result. The independent evolution of at least two distinct pathological 144 base pair insertions in Britain is proposed. The importance of maintaining a high index of suspicion of inherited Creutzfeldt-Jakob disease in cases of familial neurodegenerative disease is stressed. Images PMID:7823070

Pressure redistribution by molded inserts in diabetic footwear: a pilot study.

PubMed

Lord, M; Hosein, R

1994-08-01

A small-scale trial is described to demonstrate and evaluate the redistribution of plantar pressure resulting from the use of custom-molded inserts in the orthopedic shoes of diabetic patients at risk of plantar ulceration. A pressure-measuring insole based on force-sensitive resistor technology enabled the load distribution to be compared using molded inserts and flat inserts fitted into the same shoes. An analysis of the 12 peaks of pressure that could be identified under a discrete metatarsal head of six subjects in the trial showed that the pressure was significantly reduced with the use of molded inserts (flat inserts: 305 +/- 79 kPa; molded inserts: 216 +/- 70 kPa; n = 6 p < 0.005). Technical limitations of the equipment and the difficult choice of match of flat insert to molded for comparison suggest that further studies are required for a definitive result.

A comparison of somatic mutational spectra in healthy study populations from Russia, Sweden and USA

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

Noori, P; Hou, S; Jones, I M

Comparison of mutation spectra at the hypoxanthine-phosphoribosyl transferase (HPRT) gene of peripheral blood T lymphocytes may provide insight into the aetiology of somatic mutation contributing to carcinogenesis and other diseases. To increase knowledge of mutation spectra in healthy people, we have analyzed HPRT mutant T-cells of 50 healthy Russians originally recruited as controls for a study of Chernobyl clean-up workers (Jones et al. Radiation Res. 158, 2002, 424). Reverse transcriptase polymerase chain reactions and DNA sequencing identified 161 independent mutations among 176 thioguanine resistant mutants. Forty (40) mutations affected splicing mechanisms and 27 deletions or insertions of 1 to 60more » nucleotides were identified. Ninety four (94) single base substitutions were identified, including 62 different mutations at 55 different nucleotide positions, of which 19 had not previously been reported in human T-cells. Comparison of this base substitution spectrum with mutation spectra in a USA (Burkhart-Schultz et al. Carcinogenesis 17, 1996, 1871) and two Swedish populations (Podlutsky et al, Carcinogenesis 19, 1998, 557, Podlutsky et al. Mutation Res. 431, 1999, 325) revealed similarity in the type, frequency and distribution of mutations in the four spectra, consistent with aetiologies inherent in human metabolism. There were 15-19 identical mutations in the three pair-wise comparisons of Russian with USA and Swedish spectra. Intriguingly, there were 21 mutations unique to the Russian spectrum, and comparison by the Monte Carlo method of Adams and Skopek (J. Mol. Biol. 194, 1987, 391) indicated that the Russian spectrum was different from both Swedish spectra (P=0.007, 0.002) but not different from the USA spectrum (P=0.07), when Bonferroni correction for multiple comparisons was made (p < 0.008 required for significance). Age and smoking did not account for these differences. Other factors causing mutational differences need to be explored.« less

Severity-Based Adaptation with Limited Data for ASR to Aid Dysarthric Speakers

PubMed Central

Mustafa, Mumtaz Begum; Salim, Siti Salwah; Mohamed, Noraini; Al-Qatab, Bassam; Siong, Chng Eng

2014-01-01

Automatic speech recognition (ASR) is currently used in many assistive technologies, such as helping individuals with speech impairment in their communication ability. One challenge in ASR for speech-impaired individuals is the difficulty in obtaining a good speech database of impaired speakers for building an effective speech acoustic model. Because there are very few existing databases of impaired speech, which are also limited in size, the obvious solution to build a speech acoustic model of impaired speech is by employing adaptation techniques. However, issues that have not been addressed in existing studies in the area of adaptation for speech impairment are as follows: (1) identifying the most effective adaptation technique for impaired speech; and (2) the use of suitable source models to build an effective impaired-speech acoustic model. This research investigates the above-mentioned two issues on dysarthria, a type of speech impairment affecting millions of people. We applied both unimpaired and impaired speech as the source model with well-known adaptation techniques like the maximum likelihood linear regression (MLLR) and the constrained-MLLR(C-MLLR). The recognition accuracy of each impaired speech acoustic model is measured in terms of word error rate (WER), with further assessments, including phoneme insertion, substitution and deletion rates. Unimpaired speech when combined with limited high-quality speech-impaired data improves performance of ASR systems in recognising severely impaired dysarthric speech. The C-MLLR adaptation technique was also found to be better than MLLR in recognising mildly and moderately impaired speech based on the statistical analysis of the WER. It was found that phoneme substitution was the biggest contributing factor in WER in dysarthric speech for all levels of severity. The results show that the speech acoustic models derived from suitable adaptation techniques improve the performance of ASR systems in recognising impaired speech with limited adaptation data. PMID:24466004

Hot Spots of Recombination in Fission Yeast: Inactivation of the M26 Hot Spot by Deletion of the Ade6 Promoter and the Novel Hotspot Ura4-Aim

PubMed Central

Zahn-Zabal, M.; Lehmann, E.; Kohli, J.

1995-01-01

The M26 mutation in the ade6 gene of Schizosaccharomyces pombe creates a hot spot of meiotic recombination. A single base substitution, the M26 mutation is situated within the open reading frame, near the 5' end. It has previously been shown that the heptanucleotide sequence 5' ATGACGT 3', which includes the M26 mutation, is required for hot spot activity. The 510-bp ade6-delXB deletion encompasses the promoter and the first 23 bp of the open reading frame, ending 112 bp upstream of M26. Deletion of the promoter in cis to M26 abolishes hot spot activity, while deletion in trans to M26 has no effect. Homozygous deletion of the promoter also eliminates M26 hot spot activity, indicating that the heterology created through deletion of the promoter per se is not responsible for the loss of hot spot activity. Thus, DNA sequences other than the heptanucleotide 5' ATGACGT 3', which must be located at the 5' end of the ade6 gene, appear to be required for hot spot activity. While the M26 hotspot stimulates crossovers associated with M26 conversion, it does not affect the crossover frequency in the intervals adjacent to ade6. The flanking marker ura4-aim, a heterology created by insertion of the ura4(+) gene upstream of ade6, turned out to be a hot spot itself. It shows disparity of conversion with preferential loss of the insertion. The frequency of conversion at ura4-aim is reduced when the M26 hot spot is active 15 kb away, indicating competition for recombination factors by hot spots in close proximity. PMID:7498729

An Unbiased Genome-Wide View of the Mutation Rate and Spectrum of the Endosymbiotic Bacterium Teredinibacter turnerae.

PubMed

Senra, Marcus V X; Sung, Way; Ackerman, Matthew; Miller, Samuel F; Lynch, Michael; Soares, Carlos Augusto G

2018-03-01

Mutations contribute to genetic variation in all living systems. Thus, precise estimates of mutation rates and spectra across a diversity of organisms are required for a full comprehension of evolution. Here, a mutation-accumulation (MA) assay was carried out on the endosymbiotic bacterium Teredinibacter turnerae. After ∼3,025 generations, base-pair substitutions (BPSs) and insertion-deletion (indel) events were characterized by whole-genome sequencing analysis of 47 independent MA lines, yielding a BPS rate of 1.14 × 10-9 per site per generation and indel rate of 1.55 × 10-10 events per site per generation, which are among the highest within free-living and facultative intracellular bacteria. As in other endosymbionts, a significant bias of BPSs toward A/T and an excess of deletion mutations over insertion mutations are observed for these MA lines. However, even with a deletion bias, the genome remains relatively large (∼5.2 Mb) for an endosymbiotic bacterium. The estimate of the effective population size (Ne) in T. turnerae is quite high and comparable to free-living bacteria (∼4.5 × 107), suggesting that the heavy bottlenecking associated with many endosymbiotic relationships is not prevalent during the life of this endosymbiont. The efficiency of selection scales with increasing Ne and such strong selection may have been operating against the deletion bias, preventing genome erosion. The observed mutation rate in this endosymbiont is of the same order of magnitude of those with similar Ne, consistent with the idea that population size is a primary determinant of mutation-rate evolution within endosymbionts, and that not all endosymbionts have low Ne.

Identification and Characterization of Crr1a, a Gene for Resistance to Clubroot Disease (Plasmodiophora brassicae Woronin) in Brassica rapa L.

PubMed Central

Hatakeyama, Katsunori; Suwabe, Keita; Tomita, Rubens Norio; Kato, Takeyuki; Nunome, Tsukasa; Fukuoka, Hiroyuki; Matsumoto, Satoru

2013-01-01

Clubroot disease, caused by the obligate biotrophic protist Plasmodiophora brassicae Woronin, is one of the most economically important diseases of Brassica crops in the world. Although many clubroot resistance (CR) loci have been identified through genetic analysis and QTL mapping, the molecular mechanisms of defense responses against P. brassicae remain unknown. Fine mapping of the Crr1 locus, which was originally identified as a single locus, revealed that it comprises two gene loci, Crr1a and Crr1b. Here we report the map-based cloning and characterization of Crr1a, which confers resistance to clubroot in Brassica rapa. Crr1aG004, cloned from the resistant line G004, encodes a Toll-Interleukin-1 receptor/nucleotide-binding site/leucine-rich repeat (TIR-NB-LRR) protein expressed in the stele and cortex of hypocotyl and roots, where secondary infection of the pathogen occurs, but not in root hairs, where primary infection occurs. Gain-of-function analysis proved that Crr1aG004 alone conferred resistance to isolate Ano-01 in susceptible Arabidopsis and B. rapa. In comparison, the susceptible allele Crr1aA9709 encodes a truncated NB-LRR protein, which lacked more than half of the TIR domain on account of the insertion of a solo-long terminal repeat (LTR) in exon 1 and included several substitutions and insertion-deletions in the LRR domain. This study provides a basis for further molecular analysis of defense mechanisms against P. brassicae and will contribute to the breeding of resistant cultivars of Brassica vegetables by marker-assisted selection. Data deposition The sequence reported in this paper has been deposited in the GenBank database (accession no. AB605024). PMID:23382954

High-resolution definition of the Vibrio cholerae essential gene set with hidden Markov model–based analyses of transposon-insertion sequencing data

PubMed Central

Chao, Michael C.; Pritchard, Justin R.; Zhang, Yanjia J.; Rubin, Eric J.; Livny, Jonathan; Davis, Brigid M.; Waldor, Matthew K.

2013-01-01

The coupling of high-density transposon mutagenesis to high-throughput DNA sequencing (transposon-insertion sequencing) enables simultaneous and genome-wide assessment of the contributions of individual loci to bacterial growth and survival. We have refined analysis of transposon-insertion sequencing data by normalizing for the effect of DNA replication on sequencing output and using a hidden Markov model (HMM)-based filter to exploit heretofore unappreciated information inherent in all transposon-insertion sequencing data sets. The HMM can smooth variations in read abundance and thereby reduce the effects of read noise, as well as permit fine scale mapping that is independent of genomic annotation and enable classification of loci into several functional categories (e.g. essential, domain essential or ‘sick’). We generated a high-resolution map of genomic loci (encompassing both intra- and intergenic sequences) that are required or beneficial for in vitro growth of the cholera pathogen, Vibrio cholerae. This work uncovered new metabolic and physiologic requirements for V. cholerae survival, and by combining transposon-insertion sequencing and transcriptomic data sets, we also identified several novel noncoding RNA species that contribute to V. cholerae growth. Our findings suggest that HMM-based approaches will enhance extraction of biological meaning from transposon-insertion sequencing genomic data. PMID:23901011

REDO: RNA Editing Detection in Plant Organelles Based on Variant Calling Results.

PubMed

Wu, Shuangyang; Liu, Wanfei; Aljohi, Hasan Awad; Alromaih, Sarah A; Alanazi, Ibrahim O; Lin, Qiang; Yu, Jun; Hu, Songnian

2018-05-01

RNA editing is a post-transcriptional or cotranscriptional process that changes the sequence of the precursor transcript by substitutions, insertions, or deletions. Almost all of the land plants undergo RNA editing in organelles (plastids and mitochondria). Although several software tools have been developed to identify RNA editing events, there has been a great challenge to distinguish true RNA editing events from genome variation, sequencing errors, and other factors. Here we introduce REDO, a comprehensive application tool for identifying RNA editing events in plant organelles based on variant call format files from RNA-sequencing data. REDO is a suite of Perl scripts that illustrate a bunch of attributes of RNA editing events in figures and tables. REDO can also detect RNA editing events in multiple samples simultaneously and identify the significant differential proportion of RNA editing loci. Comparing with similar tools, such as REDItools, REDO runs faster with higher accuracy, and more specificity at the cost of slightly lower sensitivity. Moreover, REDO annotates each RNA editing site in RNAs, whereas REDItools reports only possible RNA editing sites in genome, which need additional steps to obtain RNA editing profiles for RNAs. Overall, REDO can identify potential RNA editing sites easily and provide several functions such as detailed annotations, statistics, figures, and significantly differential proportion of RNA editing sites among different samples.

The Sequences of 1504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies

PubMed Central

Pham, Nikki T.; Wei, Tong; Schackwitz, Wendy S.; Lipzen, Anna M.; Duong, Phat Q.; Jones, Kyle C.; Ruan, Deling; Bauer, Diane; Peng, Yi; Schmutz, Jeremy

2017-01-01

The availability of a whole-genome sequenced mutant population and the cataloging of mutations of each line at a single-nucleotide resolution facilitate functional genomic analysis. To this end, we generated and sequenced a fast-neutron-induced mutant population in the model rice cultivar Kitaake (Oryza sativa ssp japonica), which completes its life cycle in 9 weeks. We sequenced 1504 mutant lines at 45-fold coverage and identified 91,513 mutations affecting 32,307 genes, i.e., 58% of all rice genes. We detected an average of 61 mutations per line. Mutation types include single-base substitutions, deletions, insertions, inversions, translocations, and tandem duplications. We observed a high proportion of loss-of-function mutations. We identified an inversion affecting a single gene as the causative mutation for the short-grain phenotype in one mutant line. This result reveals the usefulness of the resource for efficient, cost-effective identification of genes conferring specific phenotypes. To facilitate public access to this genetic resource, we established an open access database called KitBase that provides access to sequence data and seed stocks. This population complements other available mutant collections and gene-editing technologies. This work demonstrates how inexpensive next-generation sequencing can be applied to generate a high-density catalog of mutations. PMID:28576844

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

Li, Guotian; Jain, Rashmi; Chern, Mawsheng

The availability of a whole-genome sequenced mutant population and the cataloging of mutations of each line at a single-nucleotide resolution facilitate functional genomic analysis. To this end, we generated and sequenced a fast-neutron-induced mutant population in the model rice cultivar Kitaake (Oryza sativa ssp japonica), which completes its life cycle in 9 weeks. We sequenced 1504 mutant lines at 45-fold coverage and identified 91,513 mutations affecting 32,307 genes, i.e., 58% of all rice genes. We detected an average of 61 mutations per line. Mutation types include single-base substitutions, deletions, insertions, inversions, translocations, and tandem duplications. We observed a high proportionmore » of loss-of-function mutations. We identified an inversion affecting a single gene as the causative mutation for the short-grain phenotype in one mutant line. This result reveals the usefulness of the resource for efficient, cost-effective identification of genes conferring specific phenotypes. To facilitate public access to this genetic resource, we established an open access database called KitBase that provides access to sequence data and seed stocks. This population complements other available mutant collections and gene-editing technologies. In conclusion, this work demonstrates how inexpensive next-generation sequencing can be applied to generate a high-density catalog of mutations.« less

A gene duplication/loss event in the ribulose-1,5-bisphosphate-carboxylase/oxygenase (rubisco) small subunit gene family among accessions of Arabidopsis thaliana.

PubMed

Schwarte, Sandra; Tiedemann, Ralph

2011-06-01

Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase; EC 4.1.1.39), the most abundant protein in nature, catalyzes the assimilation of CO(2) (worldwide about 10(11) t each year) by carboxylation of ribulose-1,5-bisphosphate. It is a hexadecamer consisting of eight large and eight small subunits. Although the Rubisco large subunit (rbcL) is encoded by a single gene on the multicopy chloroplast genome, the Rubisco small subunits (rbcS) are encoded by a family of nuclear genes. In Arabidopsis thaliana, the rbcS gene family comprises four members, that is, rbcS-1a, rbcS-1b, rbcS-2b, and rbcS-3b. We sequenced all Rubisco genes in 26 worldwide distributed A. thaliana accessions. In three of these accessions, we detected a gene duplication/loss event, where rbcS-1b was lost and substituted by a duplicate of rbcS-2b (called rbcS-2b*). By screening 74 additional accessions using a specific polymerase chain reaction assay, we detected five additional accessions with this duplication/loss event. In summary, we found the gene duplication/loss in 8 of 100 A. thaliana accessions, namely, Bch, Bu, Bur, Cvi, Fei, Lm, Sha, and Sorbo. We sequenced an about 1-kb promoter region for all Rubisco genes as well. This analysis revealed that the gene duplication/loss event was associated with promoter alterations (two insertions of 450 and 850 bp, one deletion of 730 bp) in rbcS-2b and a promoter deletion (2.3 kb) in rbcS-2b* in all eight affected accessions. The substitution of rbcS-1b by a duplicate of rbcS-2b (i.e., rbcS-2b*) might be caused by gene conversion. All four Rubisco genes evolve under purifying selection, as expected for central genes of the highly conserved photosystem of green plants. We inferred a single positive selected site, a tyrosine to aspartic acid substitution at position 72 in rbcS-1b. Exactly the same substitution compromises carboxylase activity in the cyanobacterium Anacystis nidulans. In A. thaliana, this substitution is associated with an inferred recombination. Functional implications of the substitution remain to be evaluated.

Olodaterol Oral Inhalation

MedlinePlus

... not be all the way in the inhaler. Push the cartridge against a firm surface to ensure that it is correctly inserted. Do not remove the cartridge once it has been inserted into the inhaler. Put the clear base back into place. Do not remove the clear base ...

FROG - Fingerprinting Genomic Variation Ontology

PubMed Central

Bhardwaj, Anshu

2015-01-01

Genetic variations play a crucial role in differential phenotypic outcomes. Given the complexity in establishing this correlation and the enormous data available today, it is imperative to design machine-readable, efficient methods to store, label, search and analyze this data. A semantic approach, FROG: “FingeRprinting Ontology of Genomic variations” is implemented to label variation data, based on its location, function and interactions. FROG has six levels to describe the variation annotation, namely, chromosome, DNA, RNA, protein, variations and interactions. Each level is a conceptual aggregation of logically connected attributes each of which comprises of various properties for the variant. For example, in chromosome level, one of the attributes is location of variation and which has two properties, allosomes or autosomes. Another attribute is variation kind which has four properties, namely, indel, deletion, insertion, substitution. Likewise, there are 48 attributes and 278 properties to capture the variation annotation across six levels. Each property is then assigned a bit score which in turn leads to generation of a binary fingerprint based on the combination of these properties (mostly taken from existing variation ontologies). FROG is a novel and unique method designed for the purpose of labeling the entire variation data generated till date for efficient storage, search and analysis. A web-based platform is designed as a test case for users to navigate sample datasets and generate fingerprints. The platform is available at http://ab-openlab.csir.res.in/frog. PMID:26244889

The PROGINS polymorphism of the human progesterone receptor diminishes the response to progesterone.

PubMed

Romano, Andrea; Delvoux, Bert; Fischer, Dagmar-Christiane; Groothuis, Patrick

2007-02-01

The human progesterone receptor (PR) is a ligand-dependent transcription factor and two isoforms, (PRA and PRB), can be distinguished. PROGINS, a PR polymorphic variant, affects PRA and PRB and acts as a risk-modulating factor in several gynaecological disorders. Little is known about the functional consequences of this variant. Here, we characterise the properties of PROGINS with respect to transcription, mRNA maturation, protein activity and proliferation. PROGINS is characterised by a 320 bp PV/HS-1 Alu insertion in intron G and two point mutations, V660L in exon 4 and H770H (silent substitution) in exon 5. The Alu element contains a half oestrogen-response element/Sp1-binding site (Alu-ERE/Sp1), which acts as an in-cis intronic enhancer leading to increased transcription of the PROGINS allele in response to 17beta-oestradiol. Moreover, Alu insertions in the human genome are frequently methylated. Our data indicate that the PROGINS-Alu does not affect gene transcription due to DNA methylation. However, the Alu element reduced the stability of the PROGINS transcript compared with the CP allele and does not generate splice variants. The amino acid substitution (V600L) in exon 4 leads to differences in PR phosphorylation and degradation in the two PR variants upon ligand binding, most likely as a result of differences in the three-dimensional structures of the two PR variants. As a consequence, the PR-L660 (PROGINS) variant (1) displays decreased transactivation activity in a luciferase reporter system and (2) is less efficient in opposing cell proliferation in hamster ovarian cells expressing human PRA, when compared with the PR-V660 (most common variant). Taken together, our results indicate that the PROGINS variant of PR is less responsive to progestin compared with the most common PR because of (i) reduced amounts of gene transcript and (ii) decreased protein activity.

Implant placement after marsupialization of a dentigerous cyst.

PubMed

Karamanis, S; Kitharas, T; Tsoukalas, D; Parissis, N

2006-01-01

This paper presents a case of a dentigerous cyst accompanied by a history of inflammation, resorption of the roots of the first molar and the lingual aspect of the distal root of the second molar, and devitalization of the 2 premolars. The treatment option chosen was marsupialization of the cyst, extraction of the involved teeth, endodontic treatment of both premolars, and implant insertion in the area of the first mandibular molar at a later stage. Twelve months postsurgery the area of interest was almost flattened and the radiographic examination revealed total disappearance of the radiolucency. An implant of 15 x 4 mm was inserted in the area of the first mandibular molar. Despite the excellent implant stability achieved, a thin central zone of the defect remained void of bone. After complete excision of soft tissue the defect was filled with an alloplastic bone substitute. Eight months later (20 months postsurgery), the implant was uncovered and the restorative procedure completed. The implant and the crown have been functioning sign and symptom free for 48 months. Marsupialization was preferred instead of enucleation due to (1) proximity of the cyst to the mandibular canal; (2) need for apicectomy of both premolars to gain good access for enucleation; (3) refusal of the patient to undergo a second surgery for bone harvesting; (4) lower probability for postoperative contamination; (5) need of small quantity of bone substitute; (6) easier extraction of the impacted second molar due to its coronal movement. The disadvantages of the treatment were the long healing period and the discomfort of the patient at the early stages of marsupialization. It was judged that the advantages outweighed the disadvantages in this case. We discuss the findings of other authors who support the conservative approach to jaw cysts in a young population, and the concerns that exist in the literature about the ability of osseoconductive graft materials to generate vital bone and achieve implant-to-bone contact.

Podoplanin immunopositive lymphatic vessels at the implant interface in a rat model of osteoporotic fractures.

PubMed

Lips, Katrin Susanne; Kauschke, Vivien; Hartmann, Sonja; Thormann, Ulrich; Ray, Seemun; Kampschulte, Marian; Langheinrich, Alexander; Schumacher, Matthias; Gelinsky, Michael; Heinemann, Sascha; Hanke, Thomas; Kautz, Armin R; Schnabelrauch, Matthias; Schnettler, Reinhard; Heiss, Christian; Alt, Volker; Kilian, Olaf

2013-01-01

Insertion of bone substitution materials accelerates healing of osteoporotic fractures. Biodegradable materials are preferred for application in osteoporotic patients to avoid a second surgery for implant replacement. Degraded implant fragments are often absorbed by macrophages that are removed from the fracture side via passage through veins or lymphatic vessels. We investigated if lymphatic vessels occur in osteoporotic bone defects and whether they are regulated by the use of different materials. To address this issue osteoporosis was induced in rats using the classical method of bilateral ovariectomy and additional calcium and vitamin deficient diet. In addition, wedge-shaped defects of 3, 4, or 5 mm were generated in the distal metaphyseal area of femur via osteotomy. The 4 mm defects were subsequently used for implantation studies where bone substitution materials of calcium phosphate cement, composites of collagen and silica, and iron foams with interconnecting pores were inserted. Different materials were partly additionally functionalized by strontium or bisphosphonate whose positive effects in osteoporosis treatment are well known. The lymphatic vessels were identified by immunohistochemistry using an antibody against podoplanin. Podoplanin immunopositive lymphatic vessels were detected in the granulation tissue filling the fracture gap, surrounding the implant and growing into the iron foam through its interconnected pores. Significant more lymphatic capillaries were counted at the implant interface of composite, strontium and bisphosphonate functionalized iron foam. A significant increase was also observed in the number of lymphatics situated in the pores of strontium coated iron foam. In conclusion, our results indicate the occurrence of lymphatic vessels in osteoporotic bone. Our results show that lymphatic vessels are localized at the implant interface and in the fracture gap where they might be involved in the removal of lymphocytes, macrophages, debris and the implants degradation products. Therefore the lymphatic vessels are involved in implant integration and fracture healing.

Podoplanin Immunopositive Lymphatic Vessels at the Implant Interface in a Rat Model of Osteoporotic Fractures

PubMed Central

Lips, Katrin Susanne; Kauschke, Vivien; Hartmann, Sonja; Thormann, Ulrich; Ray, Seemun; Kampschulte, Marian; Langheinrich, Alexander; Schumacher, Matthias; Gelinsky, Michael; Heinemann, Sascha; Hanke, Thomas; Kautz, Armin R.; Schnabelrauch, Matthias; Schnettler, Reinhard; Heiss, Christian; Alt, Volker; Kilian, Olaf

2013-01-01

Insertion of bone substitution materials accelerates healing of osteoporotic fractures. Biodegradable materials are preferred for application in osteoporotic patients to avoid a second surgery for implant replacement. Degraded implant fragments are often absorbed by macrophages that are removed from the fracture side via passage through veins or lymphatic vessels. We investigated if lymphatic vessels occur in osteoporotic bone defects and whether they are regulated by the use of different materials. To address this issue osteoporosis was induced in rats using the classical method of bilateral ovariectomy and additional calcium and vitamin deficient diet. In addition, wedge-shaped defects of 3, 4, or 5 mm were generated in the distal metaphyseal area of femur via osteotomy. The 4 mm defects were subsequently used for implantation studies where bone substitution materials of calcium phosphate cement, composites of collagen and silica, and iron foams with interconnecting pores were inserted. Different materials were partly additionally functionalized by strontium or bisphosphonate whose positive effects in osteoporosis treatment are well known. The lymphatic vessels were identified by immunohistochemistry using an antibody against podoplanin. Podoplanin immunopositive lymphatic vessels were detected in the granulation tissue filling the fracture gap, surrounding the implant and growing into the iron foam through its interconnected pores. Significant more lymphatic capillaries were counted at the implant interface of composite, strontium and bisphosphonate functionalized iron foam. A significant increase was also observed in the number of lymphatics situated in the pores of strontium coated iron foam. In conclusion, our results indicate the occurrence of lymphatic vessels in osteoporotic bone. Our results show that lymphatic vessels are localized at the implant interface and in the fracture gap where they might be involved in the removal of lymphocytes, macrophages, debris and the implants degradation products. Therefore the lymphatic vessels are involved in implant integration and fracture healing. PMID:24130867

Transposon insertion libraries for the characterization of mutants from the kiwifruit pathogen Pseudomonas syringae pv. actinidiae

PubMed Central

Mesarich, Carl H.; Rees-George, Jonathan; Gardner, Paul P.; Ghomi, Fatemeh Ashari; Gerth, Monica L.; Andersen, Mark T.; Rikkerink, Erik H. A.; Fineran, Peter C.

2017-01-01

Pseudomonas syringae pv. actinidiae (Psa), the causal agent of kiwifruit canker, is one of the most devastating plant diseases of recent times. We have generated two mini-Tn5-based random insertion libraries of Psa ICMP 18884. The first, a ‘phenotype of interest’ (POI) library, consists of 10,368 independent mutants gridded into 96-well plates. By replica plating onto selective media, the POI library was successfully screened for auxotrophic and motility mutants. Lipopolysaccharide (LPS) biosynthesis mutants with ‘Fuzzy-Spreader’-like morphologies were also identified through a visual screen. The second, a ‘mutant of interest’ (MOI) library, comprises around 96,000 independent mutants, also stored in 96-well plates, with approximately 200 individuals per well. The MOI library was sequenced on the Illumina MiSeq platform using Transposon-Directed Insertion site Sequencing (TraDIS) to map insertion sites onto the Psa genome. A grid-based PCR method was developed to recover individual mutants, and using this strategy, the MOI library was successfully screened for a putative LPS mutant not identified in the visual screen. The Psa chromosome and plasmid had 24,031 and 1,236 independent insertion events respectively, giving insertion frequencies of 3.65 and 16.6 per kb respectively. These data suggest that the MOI library is near saturation, with the theoretical probability of finding an insert in any one chromosomal gene estimated to be 97.5%. However, only 47% of chromosomal genes had insertions. This surprisingly low rate cannot be solely explained by the lack of insertions in essential genes, which would be expected to be around 5%. Strikingly, many accessory genes, including most of those encoding type III effectors, lacked insertions. In contrast, 94% of genes on the Psa plasmid had insertions, including for example, the type III effector HopAU1. These results suggest that some chromosomal sites are rendered inaccessible to transposon insertion, either by DNA-binding proteins or by the architecture of the nucleoid. PMID:28249011

Anatomical Footprint of the Tibialis Anterior Tendon: Surgical Implications for Foot and Ankle Reconstructions.

PubMed

Willegger, Madeleine; Seyidova, Nargiz; Schuh, Reinhard; Windhager, Reinhard; Hirtler, Lena

2017-01-01

This study aimed to analyze precisely the dimensions, shapes, and variations of the insertional footprints of the tibialis anterior tendon (TAT) at the medial cuneiform (MC) and first metatarsal (MT1) base. Forty-one formalin-fixed human cadaveric specimens were dissected. After preparation of the TAT footprint, standardized photographs were made and the following parameters were evaluated: the footprint length, width, area of insertion, dorsoplantar location, shape, and additional tendon slips. Twenty feet (48.8%) showed an equal insertion at the MC and MT1, another 20 feet (48.8%) had a wide insertion at the MC and a narrow insertion at the MT1, and 1 foot (2.4%) demonstrated a narrow insertion at the MC and a wide insertion at the MT1. Additional tendon slips inserting at the metatarsal shaft were found in two feet (4.8%). Regarding the dorsoplantar orientation, the footprints were located medial in 29 feet (70.7%) and medioplantar in 12 feet (29.3%). The most common shape at the MT1 base was the crescent type (75.6%) and the oval type at the MC (58.5%). The present study provided more detailed data on the dimensions and morphologic types of the tibialis anterior tendon footprint. The established anatomical data may allow for a safer surgical preparation and a more anatomical reconstruction.

Spectrum of FANCA mutations in Italian Fanconi anemia patients: identification of six novel alleles and phenotypic characterization of the S858R variant.

PubMed

Savino, Maria; Borriello, Adriana; D'Apolito, Maria; Criscuolo, Maria; Del Vecchio, Maria; Bianco, Anna Monica; Di Perna, Michele; Calzone, Rita; Nobili, Bruno; Zatterale, Adriana; Zelante, Leopoldo; Joenje, Hans; Della Ragione, Fulvio; Savoia, Anna

2003-10-01

Fanconi anemia (FA) is an autosomal recessive disorder characterized by genomic instability, bone marrow failure, congenital malformations, and cancer predisposition. FA is a genetically heterogeneous disease with at least seven genes so far identified. The role of FA proteins is unknown although they interact in a common functional pathway. Here, we report six novel FANCA sequence changes and review all the mutations identified in Italy. Except for two missense substitutions, all are expected to cause a premature termination of the FANCA protein at various sites throughout the molecule. The premature terminations are due to nonsense and splice site mutations, as well as small insertions and deletions, and large genomic rearrangements. The expected truncated proteins were not detectable on Western blot analyses. The FANCA-S858R variant is instead expressed at lower level than that seen in normal cell lines and is associated with a non-ubiquinated FANCD2 protein, strongly suggesting that the amino acid substitution is a disease-causing mutation. The spectrum of FA mutations is widely in agreement with the heterogeneous ethnic origin of the Italian population. Copyright 2003 Wiley-Liss, Inc.

In search of a new class of stable nitroxide: synthesis and reactivity of a peri-substituted N,N-bissulfonylhydroxylamine.

PubMed

Patel, Bhaven; Carlisle, Julie; Bottle, Steven E; Hanson, Graeme R; Kariuki, Benson M; Male, Louise; McMurtrie, John C; Spencer, Neil; Grainger, Richard S

2011-04-07

Acyclic bissulfonylnitroxides have never been isolated, and degrade through fragmentation. In an approach to stabilising a bissulfonylnitroxide radical, the cyclic, peri-substituted N,N-bissulfonylhydroxylamine, 2-hydroxynaphtho[1,8-de][1,3,2]dithiazine 1,1,3,3-tetraoxide (1), has been prepared by formal nitrogen insertion into the sulfur-sulfur bond of a sulfinylsulfone, naphtho[1,8-cd][1,2]dithiole 1,1,2-trioxide. The heterocyclic ring of 1 is shown to adopt a sofa conformation by X-ray crystallography, with a pseudo-axial hydroxyl group. N,N-Bissulfonylhydroxylamine 1 displays high thermal, photochemical and hydrolytic stability compared to acyclic systems. EPR analysis reveals formation of the corresponding bissulfonylnitroxide 2 upon oxidation of 1 with the Ce(IV) salts CAN and CTAN. Although 2 does not undergo fragmentation, it cannot be isolated, since hydrogen atom abstraction to reform 1 occurs in situ. The stability and reactivity of 1 and 2 are compared with the known cyclic benzo-fused N,N-bissulfonylhydroxylamine, N-hydroxy-O-benzenedisulfonimide (6), for which the X-ray data, and EPR of the corresponding nitroxide 10, are also reported for the first time.

Evidence for a Catalytically and Kinetically Competent Enzyme–Substrate Cross-Linked Intermediate in Catalysis by Lipoyl Synthase

PubMed Central

2015-01-01

Lipoyl synthase (LS) catalyzes the final step in lipoyl cofactor biosynthesis: the insertion of two sulfur atoms at C6 and C8 of an (N6-octanoyl)-lysyl residue on a lipoyl carrier protein (LCP). LS is a member of the radical SAM superfamily, enzymes that use a [4Fe–4S] cluster to effect the reductive cleavage of S-adenosyl-l-methionine (SAM) to l-methionine and a 5′-deoxyadenosyl 5′-radical (5′-dA•). In the LS reaction, two equivalents of 5′-dA• are generated sequentially to abstract hydrogen atoms from C6 and C8 of the appended octanoyl group, initiating sulfur insertion at these positions. The second [4Fe–4S] cluster on LS, termed the auxiliary cluster, is proposed to be the source of the inserted sulfur atoms. Herein, we provide evidence for the formation of a covalent cross-link between LS and an LCP or synthetic peptide substrate in reactions in which insertion of the second sulfur atom is slowed significantly by deuterium substitution at C8 or by inclusion of limiting concentrations of SAM. The observation that the proteins elute simultaneously by anion-exchange chromatography but are separated by aerobic SDS-PAGE is consistent with their linkage through the auxiliary cluster that is sacrificed during turnover. Generation of the cross-linked species with a small, unlabeled (N6-octanoyl)-lysyl-containing peptide substrate allowed demonstration of both its chemical and kinetic competence, providing strong evidence that it is an intermediate in the LS reaction. Mössbauer spectroscopy of the cross-linked intermediate reveals that one of the [4Fe–4S] clusters, presumably the auxiliary cluster, is partially disassembled to a 3Fe-cluster with spectroscopic properties similar to those of reduced [3Fe–4S]0 clusters. PMID:24901788

Alu Insertions and Genetic Diversity: A Preliminary Investigation by an Undergraduate Bioinformatics Class

ERIC Educational Resources Information Center

Elwess, Nancy L.; Duprey, Stephen L.; Harney, Lindesay A.; Langman, Jessie E.; Marino, Tara C.; Martinez, Carolina; McKeon, Lauren L.; Moss, Chantel I. E.; Myrie, Sasha S.; Taylor, Luke Ryan

2008-01-01

"Alu"-insertion polymorphisms were used by an undergraduate Bioinformatics class to study how these insertion sites could be the basis for an investigation in human population genetics. Based on the students' investigation, both allele and genotype "Alu" frequencies were determined for African-American and Japanese populations as well as a…

Effectiveness of electrocardiographic guidance in CVAD tip placement.

PubMed

Walker, Graham; Chan, Raymond J; Alexandrou, Evan; Webster, Joan; Rickard, Claire

International standard practice for the correct confirmation of the central venous access device is the chest X-ray. The intracavitary electrocardiogram-based insertion method is radiation-free, and allows real-time placement verification, providing immediate treatment and reduced requirement for post-procedural repositioning. Relevant databases were searched for prospective randomised controlled trials (RCTs) or quasi RCTs that compared the effectiveness of electrocardiogram-guided catheter tip positioning with placement using surface-anatomy-guided insertion plus chest X-ray confirmation. The primary outcome was accurate catheter tip placement. Secondary outcomes included complications, patient satisfaction and costs. Five studies involving 729 participants were included. Electrocardiogram-guided insertion was more accurate than surface anatomy guided insertion (odds ratio: 8.3; 95% confidence interval (CI) 1.38; 50.07; p=0.02). There was a lack of reporting on complications, patient satisfaction and costs. The evidence suggests that intracavitary electrocardiogram-based positioning is superior to surface-anatomy-guided positioning of central venous access devices, leading to significantly more successful placements. This technique could potentially remove the requirement for post-procedural chest X-ray, especially during peripherally inserted central catheter (PICC) line insertion.

Rapid molecular sexing of three-spined sticklebacks, Gasterosteus aculeatus L., based on large Y-chromosomal insertions.

PubMed

Bakker, Theo C M; Giger, Thomas; Frommen, Joachim G; Largiadèr, Carlo R

2017-08-01

There is a need for rapid and reliable molecular sexing of three-spined sticklebacks, Gasterosteus aculeatus, the supermodel species for evolutionary biology. A DNA region at the 5' end of the sex-linked microsatellite Gac4202 was sequenced for the X chromosome of six females and the Y chromosome of five males from three populations. The Y chromosome contained two large insertions, which did not recombine with the phenotype of sex in a cross of 322 individuals. Genetic variation (SNPs and indels) within the insertions was smaller than on flanking DNA sequences. Three molecular PCR-based sex tests were developed, in which the first, the second or both insertions were covered. In five European populations (from DE, CH, NL, GB) of three-spined sticklebacks, tests with both insertions combined showed two clearly separated bands on agarose minigels in males and one band in females. The tests with the separate insertions gave similar results. Thus, the new molecular sexing method gave rapid and reliable results for sexing three-spined sticklebacks and is an improvement and/or alternative to existing methods.

Fine-scale genetic mapping of a hybrid sterility factor between Drosophila simulans and D. mauritiana: the varied and elusive functions of "speciation genes".

PubMed

Araripe, Luciana O; Montenegro, Horácio; Lemos, Bernardo; Hartl, Daniel L

2010-12-14

Hybrid male sterility (HMS) is a usual outcome of hybridization between closely related animal species. It arises because interactions between alleles that are functional within one species may be disrupted in hybrids. The identification of genes leading to hybrid sterility is of great interest for understanding the evolutionary process of speciation. In the current work we used marked P-element insertions as dominant markers to efficiently locate one genetic factor causing a severe reduction in fertility in hybrid males of Drosophila simulans and D. mauritiana. Our mapping effort identified a region of 9 kb on chromosome 3, containing three complete and one partial coding sequences. Within this region, two annotated genes are suggested as candidates for the HMS factor, based on the comparative molecular characterization and public-source information. Gene Taf1 is partially contained in the region, but yet shows high polymorphism with four fixed non-synonymous substitutions between the two species. Its molecular functions involve sequence-specific DNA binding and transcription factor activity. Gene agt is a small, intronless gene, whose molecular function is annotated as methylated-DNA-protein-cysteine S-methyltransferase activity. High polymorphism and one fixed non-synonymous substitution suggest this is a fast evolving gene. The gene trees of both genes perfectly separate D. simulans and D. mauritiana into monophyletic groups. Analysis of gene expression using microarray revealed trends that were similar to those previously found in comparisons between whole-genome hybrids and parental species. The identification following confirmation of the HMS candidate gene will add another case study leading to understanding the evolutionary process of hybrid incompatibility.

Refining the chemical composition of the inner core with multicomponent alloys: from first-principles to thermodynamics and seismology

NASA Astrophysics Data System (ADS)

Caracas, R.; Asimow, P. D.; Wolf, A. S.; Harvey, J. P.; Martin, A.; Torrent, M.

2015-12-01

We compute the solubility limits of Si in the hexagonal-close packed (hcp) phase of iron using standard thermodynamical treatment of solid solutions with data obtained from first-principles calculations. For this, we consider the system with end-members hcp Fe and the B2 phase of FeSi. Si and Fe enter both structures in substitution of one another. The system is characterized by an immiscibility gap, which according to our results widens with pressure. At core conditions about 5 wt.% Si can be dissolved into the hcp phase of Fe. Comparatively there is much more Fe that can enter the FeSi B2 phase. In a second step we start with the hcp Fe-Si alloys and add the most probable light elements found in the core: H, C, O, and S. The light elements can enter the hcp structure either as interstitial impurities, in case of H, C, O, or in substitution of Fe, in case of S. We consider several insertion patterns with the light elements both adjacent and far apart. For each of these new phases we compute the elastic constants tensors and the seismic properties. Based on our theoretical results and the comparisons with PREM we discuss in detail the possible composition of the Earth's inner core, we rule out certain light elements, like H, and we show that the distribution pattern is not important. This is also the first time the elastic constants tensor is computed from lattice dynamics using the response function in the Planar Augmented Wavefunction approach of the Density Functional Theory [1]. [1] A. Martin, M. Torrent, R. Caracas, submitted (2015); A. Martin, PhD thesis (2015).

Football boot insoles and sensitivity to extent of ankle inversion movement.

PubMed

Waddington, G; Adams, R

2003-04-01

The capacity of the plantar sole of the foot to convey information about foot position is reduced by conventional smooth boot insoles, compared with barefoot surface contact. To test the hypothesis that movement discrimination may be restored by inserting textured replacement insoles, achieved by changing footwear conditions and measuring the accuracy of judgments of the extent of ankle inversion movement. An automated testing device, the ankle movement extent discrimination apparatus (AMEDA), developed to assess active ankle function in weight bearing without a balance demand, was used to test the effects of sole inserts in soccer boots. Seventeen elite soccer players, the members of the 2000 Australian Women's soccer squad (34 ankles), took part in the study. Subjects were randomly allocated to start testing in: bare feet, their own football boots, own football boot and replacement insole, and on the left or right side. Subjects underwent six 50 trial blocks, in which they completed all footwear conditions. The sole inserts were cut to size for each foot from textured rubber "finger profile" sheeting. Movement discrimination scores were significantly worse when subjects wore their football boots and socks, compared with barefoot data collected at the same time. The substitution of textured insoles for conventional smooth insoles in the football boots was found to restore movement discrimination to barefoot levels. The lower active movement discrimination scores of athletes when wearing football boots with smooth insoles suggest that the insole is one aspect of football boot and sport shoe design that could be modified to provide the sensory feedback needed for accurate foot positioning.

Lentiviral vector-based insertional mutagenesis identifies genes associated with liver cancer

PubMed Central

Ranzani, Marco; Cesana, Daniela; Bartholomae, Cynthia C.; Sanvito, Francesca; Pala, Mauro; Benedicenti, Fabrizio; Gallina, Pierangela; Sergi, Lucia Sergi; Merella, Stefania; Bulfone, Alessandro; Doglioni, Claudio; von Kalle, Christof; Kim, Yoon Jun; Schmidt, Manfred; Tonon, Giovanni; Naldini, Luigi; Montini, Eugenio

2013-01-01

Transposons and γ-retroviruses have been efficiently used as insertional mutagens in different tissues to identify molecular culprits of cancer. However, these systems are characterized by recurring integrations that accumulate in tumor cells, hampering the identification of early cancer-driving events amongst bystander and progression-related events. We developed an insertional mutagenesis platform based on lentiviral vectors (LVV) by which we could efficiently induce hepatocellular carcinoma (HCC) in 3 different mouse models. By virtue of LVV’s replication-deficient nature and broad genome-wide integration pattern, LVV-based insertional mutagenesis allowed identification of 4 new liver cancer genes from a limited number of integrations. We validated the oncogenic potential of all the identified genes in vivo, with different levels of penetrance. Our newly identified cancer genes are likely to play a role in human disease, since they are upregulated and/or amplified/deleted in human HCCs and can predict clinical outcome of patients. PMID:23314173

Tunable ferromagnetic resonance in La-Co substituted barium hexaferrites at millimeter wave frequencies

NASA Astrophysics Data System (ADS)

Korolev, Konstantin A.; Wu, Chuanjian; Yu, Zhong; Sun, Ke; Afsar, Mohammed N.; Harris, Vincent G.

2018-05-01

Transmittance measurements have been performed on La-Co substituted barium hexaferrites in millimeter waves. Broadband millimeter-wave measurements have been carried out using the free space quasi-optical spectrometer, equipped with a set of high power backward wave oscillators covering the frequency range of 30 - 120 GHz. Strong absorption zones have been observed in the millimeter-wave transmittance spectra of all La-Co substituted barium hexaferrites due to the ferromagnetic resonance. Linear shift of ferromagnetic resonance frequency as functions of La-Co substitutions have been found. Real and imaginary parts of dielectric permittivity of La-Co substituted barium hexaferrites have been calculated using the analysis of recorded high precision transmittance spectra. Frequency dependences of magnetic permeability of La-Co substituted barium hexaferrites, as well as saturation magnetization and anisotropy field have been determined based on Schlömann's theory for partially magnetized ferrites. La-Co substituted barium hexaferrites have been further investigated by DC magnetization to assess magnetic behavior and compare with millimeter wave data. Consistency of saturation magnetization determined independently by both millimeter wave absorption and DC magnetization have been found for all La-Co substituted barium hexaferrites. These materials seem to be quite promising as tunable millimeter wave absorbers, filters, circulators, based on the adjusting of their substitution parameters.

Impacts of Vehicle Weight Reduction via Material Substitution on Life-Cycle Greenhouse Gas Emissions.

PubMed

Kelly, Jarod C; Sullivan, John L; Burnham, Andrew; Elgowainy, Amgad

2015-10-20

This study examines the vehicle-cycle and vehicle total life-cycle impacts of substituting lightweight materials into vehicles. We determine part-based greenhouse gas (GHG) emission ratios by collecting material substitution data and evaluating that alongside known mass-based GHG ratios (using and updating Argonne National Laboratory's GREET model) associated with material pair substitutions. Several vehicle parts are lightweighted via material substitution, using substitution ratios from a U.S. Department of Energy report, to determine GHG emissions. We then examine fuel-cycle GHG reductions from lightweighting. The fuel reduction value methodology is applied using FRV estimates of 0.15-0.25, and 0.25-0.5 L/(100km·100 kg), with and without powertrain adjustments, respectively. GHG breakeven values are derived for both driving distance and material substitution ratio. While material substitution can reduce vehicle weight, it often increases vehicle-cycle GHGs. It is likely that replacing steel (the dominant vehicle material) with wrought aluminum, carbon fiber reinforced plastic (CRFP), or magnesium will increase vehicle-cycle GHGs. However, lifetime fuel economy benefits often outweigh the vehicle-cycle, resulting in a net total life-cycle GHG benefit. This is the case for steel replaced by wrought aluminum in all assumed cases, and for CFRP and magnesium except for high substitution ratio and low FRV.

Comparative Assessment of Cutting Inserts and Optimization during Hard Turning: Taguchi-Based Grey Relational Analysis

NASA Astrophysics Data System (ADS)

Venkata Subbaiah, K.; Raju, Ch.; Suresh, Ch.

2017-08-01

The present study aims to compare the conventional cutting inserts with wiper cutting inserts during the hard turning of AISI 4340 steel at different workpiece hardness. Type of insert, hardness, cutting speed, feed, and depth of cut are taken as process parameters. Taguchi’s L18 orthogonal array was used to conduct the experimental tests. Parametric analysis carried in order to know the influence of each process parameter on the three important Surface Roughness Characteristics (Ra, Rz, and Rt) and Material Removal Rate. Taguchi based Grey Relational Analysis (GRA) used to optimize the process parameters for individual response and multi-response outputs. Additionally, the analysis of variance (ANOVA) is also applied to identify the most significant factor.

Laparoscopic insertion of the Moss feeding tube.

PubMed

Albrink, M H; Hagan, K; Rosemurgy, A S

1993-12-01

Placement of enteral feeding tubes is an important part of a surgeon's skill base. Surgical insertion of feeding tubes has been performed safely for many years with very few modifications. With the recent surge in interest and applicability of other laparoscopic procedures, it is well within the skills of the average laparoscopic surgeon to insert feeding tubes. We describe herein a simple technique for the insertion of the Moss feeding tube. The procedure described has a minimum of invasion, along with simplicity, safety, and accuracy.

An ab initio mechanism for efficient population of triplet states in cytotoxic sulfur substituted DNA bases: the case of 6-thioguanine.

PubMed

Martínez-Fernández, Lara; González, Leticia; Corral, Inés

2012-02-18

The deactivation mechanism of the cytotoxic 6-thioguanine, the 6-sulfur-substituted analogue of the canonical DNA base, is unveiled by ab initio calculations. Oxygen-by-sulfur substitution leads to efficient population of triplet states-the first step for generating singlet oxygen-which is responsible for its cytotoxicity. This journal is © The Royal Society of Chemistry 2012

Nucleotide sequence analysis establishes the role of endogenous murine leukemia virus DNA segments in formation of recombinant mink cell focus-forming murine leukemia viruses.

PubMed Central

Khan, A S

1984-01-01

The sequence of 363 nucleotides near the 3' end of the pol gene and 564 nucleotides from the 5' terminus of the env gene in an endogenous murine leukemia viral (MuLV) DNA segment, cloned from AKR/J mouse DNA and designated as A-12, was obtained. For comparison, the nucleotide sequence in an analogous portion of AKR mink cell focus-forming (MCF) 247 MuLV provirus was also determined. Sequence features unique to MCF247 MuLV DNA in the 3' pol and 5' env regions were identified by comparison with nucleotide sequences in analogous regions of NFS -Th-1 xenotropic and AKR ecotropic MuLV proviruses. These included (i) an insertion of 12 base pairs encoding four amino acids located 60 base pairs from the 3' terminus of the pol gene and immediately preceding the env gene, (ii) the deletion of 12 base pairs (encoding four amino acids) and the insertion of 3 base pairs (encoding one amino acid) in the 5' portion of the env gene, and (iii) single base substitutions resulting in 2 MCF247 -specific amino acids in the 3' pol and 23 in the 5' env regions. Nucleotide sequence comparison involving the 3' pol and 5' env regions of AKR MCF247 , NFS xenotropic, and AKR ecotropic MuLV proviruses with the cloned endogenous MuLV DNA indicated that MCF247 proviral DNA sequences were conserved in the cloned endogenous MuLV proviral segment. In fact, total nucleotide sequence identity existed between the endogenous MuLV DNA and the MCF247 MuLV provirus in the 3' portion of the pol gene. In the 5' env region, only 4 of 564 nucleotides were different, resulting in three amino acid changes between AKR MCF247 MuLV DNA and the endogenous MuLV DNA present in clone A-12. In addition, nucleotide sequence comparison indicated that Moloney-and Friend-MCF MuLVs were also highly related in the 3' pol and 5' env regions to the cloned endogenous MuLV DNA. These results establish the role of endogenous MuLV DNA segments in generation of recombinant MCF viruses. PMID:6328017

A Web service substitution method based on service cluster nets

NASA Astrophysics Data System (ADS)

Du, YuYue; Gai, JunJing; Zhou, MengChu

2017-11-01

Service substitution is an important research topic in the fields of Web services and service-oriented computing. This work presents a novel method to analyse and substitute Web services. A new concept, called a Service Cluster Net Unit, is proposed based on Web service clusters. A service cluster is converted into a Service Cluster Net Unit. Then it is used to analyse whether the services in the cluster can satisfy some service requests. Meanwhile, the substitution methods of an atomic service and a composite service are proposed. The correctness of the proposed method is proved, and the effectiveness is shown and compared with the state-of-the-art method via an experiment. It can be readily applied to e-commerce service substitution to meet the business automation needs.

Design and characterisation of a polyethylene oxide matrix with the potential use as a teat insert for prevention/treatment of bovine mastitis.

PubMed

Bhattarai, Sushila; Alany, Raid G; Bunt, Craig R; Abdelkader, Hamdy; Rathbone, Michael J

2015-01-01

This manuscript reports (for the first time) on antibiotic-free polymeric inserts for the prevention and/or treatment of bovine mastitis. Polyethylene oxide (PEO)-based inserts were prepared using different concentrations of various hydrophilic polymers and water-soluble and water-insoluble drug-release-modifying excipients. A simple and scalable melt-extrusion method was employed to prepare the inserts. The prepared inserts were characterised for their dimension, rheological and mechanical properties. The in vitro release of a model bacteriostatic drug (salicylic acid) from the prepared inserts was studied to demonstrate the effectiveness and reproducibility of the melt-extrusion manufacturing method. Further, the in vitro stability of the inserts was evaluated using gel permeation chromatography (GPC) to monitor any change in molecular weight under real-time and accelerated storage conditions. The investigated inserts were stable at accelerated storage conditions over a period of 6 months. PEO inserts have the potential to serve a dual purpose, act as a physical barrier against pathogens invading the teat canal of cows and possibly control the release of a drug.

Fracture of Reduced-Diameter Zirconia Dental Implants Following Repeated Insertion.

PubMed

Karl, Matthias; Scherg, Stefan; Grobecker-Karl, Tanja

Achievement of high insertion torque values indicating good primary stability is a goal during dental implant placement. The objective of this study was to evaluate whether or not two-piece implants made from zirconia ceramic may be damaged as a result of torque application. A total of 10 two-piece zirconia implants were repeatedly inserted into polyurethane foam material with increasing density and decreasing osteotomy size. The insertion torque applied was measured, and implants were checked for fractures by applying the fluorescent penetrant method. Weibull probability of failure was calculated based on the recorded insertion torque values. Catastrophic failures could be seen in five of the implants from two different batches at insertion torques ranging from 46.0 to 70.5 Ncm, while the remaining implants (all belonging to one batch) survived. Weibull probability of failure seems to be low at the manufacturer-recommended maximum insertion torque of 35 Ncm. Chipping fractures at the thread tips as well as tool marks were the only otherwise observed irregularities. While high insertion torques may be desirable for immediate loading protocols, zirconia implants may fracture when manufacturer-recommended insertion torques are exceeded. Evaluating bone quality prior to implant insertion may be useful.

Data entry and error embedding system

NASA Technical Reports Server (NTRS)

Woo, Daniel N. (Inventor); Woo, Jr., John (Inventor)

1998-01-01

A data entry and error embedding system in which, first, a document is bitmapped and recorded in a first memory. Then, it is displayed, and portions of it to be replicated by data entry are underlayed by a window, into which window replicated data is entered in location and size such that it is juxtaposed just below that which is replicated, enhancing the accuracy of replication. Second, with this format in place, selected portions of the replicated data are altered by the insertion of character or word substitutions, thus the embedding of errors. Finally, a proofreader would endeavor to correct the error embedded data and a record of his or her changes recorded. In this manner, the skill level of the proofreader and accuracy of the data are computed.

Surface and bulk modified high capacity layered oxide cathodes with low irreversible capacity loss

NASA Technical Reports Server (NTRS)

Manthiram, Arumugam (Inventor); Wu, Yan (Inventor)

2010-01-01

The present invention includes compositions, surface and bulk modifications, and methods of making of (1-x)Li[Li.sub.1/3Mn.sub.2/3]O.sub.2.xLi[Mn.sub.0.5-yNi.sub.0.5-yCo.sub.2- y]O.sub.2 cathode materials having an O3 crystal structure with a x value between 0 and 1 and y value between 0 and 0.5, reducing the irreversible capacity loss in the first cycle by surface modification with oxides and bulk modification with cationic and anionic substitutions, and increasing the reversible capacity to close to the theoretical value of insertion/extraction of one lithium per transition metal ion (250-300 mAh/g).

Mild Aromatic Palladium-Catalyzed Protodecarboxylation: Kinetic Assessment of the Decarboxylative Palladation and the Protodepalladation Steps

PubMed Central

Dickstein, Joshua S.; Curto, John M.; Gutierrez, Osvaldo; Mulrooney, Carol A.; Kozlowski, Marisa C.

2013-01-01

Mechanism studies of a mild palladium catalyzed decarboxylation of aromatic carboxylic acids are described. In particular, reaction orders and activation parameters for the two stages of the transformation were determined. These studies guided development of a catalytic system capable of turnover. Further evidence reinforces that the second stage, protonation of the aryl palladium intermediate, is the rate-determining step of the reaction. The first step, decarboxylative palladation is proposed to occur through an intramolecular electrophilic palladation pathway, which is supported by computational and mechansim studies. In contrast to the reverse reaction (C-H insertion), the data support an electrophilic aromatic substitution mechanism involving a stepwise intramolecular protonation sequence for the protodepalladation portion of the reaction. PMID:23590518

Regulating Ion Transport in Peptide Nanotubes by Tailoring the Nanotube Lumen Chemistry.

PubMed

Ruiz, Luis; Benjamin, Ari; Sullivan, Matthew; Keten, Sinan

2015-05-07

We use atomistic nonequilibrium molecular dynamics simulations to demonstrate how specific ionic flux in peptide nanotubes can be regulated by tailoring the lumen chemistry through single amino acid substitutions. By varying the size and polarity of the functional group inserted into the nanotube interior, we are able to adjust the Na(+) flux by over an order of magnitude. Cl(-) is consistently denied passage. Bulky, nonpolar groups encourage interactions between the Na(+) and the peptide backbone carbonyl groups, disrupting the Na(+) solvation shell and slowing the transport of Na(+). Small groups have the opposite effect and accelerate flow. These results suggest that relative ion flux and selectivity can be precisely regulated in subnanometer pores by molecularly defining the lumen according to biological principles.

Surface and bulk modified high capacity layered oxide cathodes with low irreversible capacity loss

DOEpatents

Manthiram, Arumugam; Wu, Yan

2010-03-16

The present invention includes compositions, surface and bulk modifications, and methods of making of (1-x)Li[Li.sub.1/3Mn.sub.2/3]O.sub.2.xLi[Mn.sub.0.5-yNi.sub.0.5-yCo.sub.2- y]O.sub.2 cathode materials having an O3 crystal structure with a x value between 0 and 1 and y value between 0 and 0.5, reducing the irreversible capacity loss in the first cycle by surface modification with oxides and bulk modification with cationic and anionic substitutions, and increasing the reversible capacity to close to the theoretical value of insertion/extraction of one lithium per transition metal ion (250-300 mAh/g).

Molecular Epidemiology of Colistin-Resistant, Carbapenemase-Producing Klebsiella pneumoniae in Serbia from 2013 to 2016

PubMed Central

Novović, Katarina; Trudić, Anika; Brkić, Snežana; Vasiljević, Zorica; Kojić, Milan; Medić, Deana; Ćirković, Ivana

2017-01-01

ABSTRACT Twenty-seven colistin-resistant, carbapenemase-producing Klebsiella pneumoniae isolates were identified from hospitals in Serbia. All isolates were blaCTX-M-15 positive; ST101, ST888, ST437, ST336, and ST307 were blaOXA-48 positive; and ST340 was blaNDM-1 positive. ST307 had an insertion, and ST336 had a premature stop codon in the mgrB gene. Amino acid substitutions were detected in PmrAB of isolates ST101, ST888, ST336, and ST307. The mcr-1 and mcr-2 were not detected. An increase in phoP, phoQ, and pmrK gene transcription was detected for all sequence types. PMID:28242665

Evolving together: the biology of symbiosis, part 2

PubMed Central

2000-01-01

Symbiotic trade-offs dominate the world of biology and medicine in colonist-host relationships and between separate, mutually dependent organisms of different species. Infectious and parasitic diseases can be better understood by exploring the dynamic continuum between pathogenicity and mutualism, between antagonism and cooperation—the sliding scale along which microorganisms can move in a moment's notice with a single nucleotide substitution. Organisms practicing piracy or pastoralism may be close genetic relatives. Mergers occur not only between cells but also between genomes; viruses co-opt host genes and in turn insert themselves into host genomes. Separate organisms, from ants to fungi to plants, establish symbiotic ties with each other that bind over deep time, generating much of the diversity we see in nature. PMID:16389348

Ferrocene-Alkynyl Conjugated Molecular Wires: Synthesis, Characterization, and Conductance Properties.

PubMed

Yuan, Ye; Yan, Jian-Feng; Lin, Da-Qiang; Mao, Bing-Wei; Yuan, Yao-Feng

2018-03-07

A novel series of 1,2,3-substituted ferrocene-based wires a1-a2 and b4-b5 have been synthesized by using an iterative Pd-mediated Sonogashira cross-coupling methodology. The molecular structures of a2 and b3 were determined by single-crystal X-ray analysis. Electrochemical data showed that there was a strong electronic communication among the ferrocenyl moieties in b1-b5. The UV absorption spectra indicated that replacing the 1,1'-substituted ferrocene unit with a 1,2,3-substituted ferrocene moiety causes delocalization of electrons in the extended π orbitals. The self-assembled monolayers of wire a1 and a2 on Au surfaces have been comprehensively characterized by electrochemistry and scanning tunneling microscopy break junction. The data demonstrated that 1,2,3-substituted ferrocene-based wires reduced the intermolecular π-π stacking, and furthermore solved the rotation problem in the 1,1'-substituted ferrocene-based wires. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

Explicit Substitutions and All That

NASA Technical Reports Server (NTRS)

Ayala-Rincon, Mauricio; Munoz, Cesar

2000-01-01

Explicit substitution calculi are extensions of the lambda-calculus where the substitution mechanism is internalized into the theory. This feature makes them suitable for implementation and theoretical study of logic-based tools such as strongly typed programming languages and proof assistant systems. In this paper we explore new developments on two of the most successful styles of explicit substitution calculi: the lambda sigma- and lambda S(e)-calculi.

Explicit Substitutions and All That

NASA Technical Reports Server (NTRS)

Ayala-Rincon, Mauricio; Munoz, Cesar; Busnell, Dennis M. (Technical Monitor)

2000-01-01

Explicit substitution calculi are extensions of the Lambda-calculus where the substitution mechanism is internalized into the theory. This feature makes them suitable for implementation and theoretical study of logic-based tools such as strongly typed programming languages and proof assistant systems. In this paper we explore new developments on two of the most successful styles of explicit substitution calculi: the lambda(sigma)- and lambda(s(e))-calculi.

Aluminium substitution in iron(II-III)-layered double hydroxides: Formation and cationic order

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

Ruby, Christian; Abdelmoula, Mustapha; Aissa, Rabha

The formation and the modifications of the structural properties of an aluminium-substituted iron(II-III)-layered double hydroxide (LDH) of formula Fe{sub 4}{sup II}Fe{sub (2-6y)}{sup III}Al{sub 6y}{sup III} (OH){sub 12} SO{sub 4}, 8H{sub 2}O are followed by pH titration curves, Moessbauer spectroscopy and high-resolution X-ray powder diffraction using synchrotron radiation. Rietveld refinements allow to build a structural model for hydroxysulphate green rust, GR(SO{sub 4}{sup 2-}), i.e. y=0, in which a bilayer of sulphate anions points to the Fe{sup 3+} species. A cationic order is proposed to occur in both GR(SO{sub 4}{sup 2-}) and aluminium-substituted hydroxysulphate green rust when y<0.08. Variation of the cellmore » parameters and a sharp decrease in average crystal size and anisotropy are detected for an aluminium content as low as y=0.01. The formation of Al-GR(SO{sub 4}{sup 2-}) is preceded by the successive precipitation of Fe{sup III} and Al{sup III} (oxy)hydroxides. Adsorption of more soluble Al{sup III} species onto the initially formed ferric oxyhydroxide may be responsible for this slowdown of crystal growth. Therefore, the insertion of low aluminium amount (y{approx}0.01) could be an interesting way for increasing the surface reactivity of iron(II-III) LDH that maintains constant the quantity of the reactive Fe{sup II} species of the material. - Graphical abstract: (a) Crystallographical structure of sulphated green rust: SO{sub 4}{sup 2-} point to the Fe{sup 3+} cations (red) that form an ordered array with the Fe{sup 2+} cations (green). (b) Width and asymmetry of the synchrotron XRD peaks increase rapidly when some Al{sup 3+} species substitute the Fe{sup 3+} cations; z is molar ratio Al{sup 3+}/Fe{sup 3+}.« less

Raman study of the Hg0.7Cr0.3Sr2CuO4+δ superconductors

NASA Astrophysics Data System (ADS)

Lee, S.-Y.; Chang, B.-Y.; Yang, I.-S.; Gwak, J.-H.; Kim, S.-J.; Choi, J.-H.; Lee, S.-I.; Yakhmi, J. V.; Mandal, J. B.; Bandyopadhyay, B.; Ghosh, B.

1997-08-01

The local environment of the apical oxygens (OA) in the Sr-substituted mercury-based superconductor Hg0.7Cr0.3Sr2CuO4+δ is investigated using Raman spectroscopy. Raman spectra from the Sr-substituted Hg-1201 samples show broad OA A1g double peaks at 553 and 583 cm-l, which are 10 - 20 cm-1 lower than the pristine Hg-1201. The existence of, and lower shift of, the double peaks in the Raman spectra of the Sr-substituted Hg-1201 superconductors indicate changes in the environment of OA in the Sr-substituted mercury-based superconductors.

Influence of Screw Length and Bone Thickness on the Stability of Temporary Implants

PubMed Central

Fernandes, Daniel Jogaib; Elias, Carlos Nelson; Ruellas, Antônio Carlos de Oliveira

2015-01-01

The purpose of this work was to study the influence of screw length and bone thickness on the stability of temporary implants. A total of 96 self-drilling temporary screws with two different lengths were inserted into polyurethane blocks (n = 66), bovine femurs (n = 18) and rabbit tibia (n = 12) with different cortical thicknesses (1 to 8 mm). Screws insertion in polyurethane blocks was assisted by a universal testing machine, torque peaks were collected by a digital torquemeter and bone thickness was monitored by micro-CT. The results showed that the insertion torque was significantly increased with the thickness of cortical bone from polyurethane (p < 0.0001), bovine (p = 0.0035) and rabbit (p < 0.05) sources. Cancellous bone improved significantly the mechanical implant stability. Insertion torque and insertion strength was successfully moduled by equations, based on the cortical/cancellous bone behavior. Based on the results, insertion torque and bone strength can be estimate in order to prevent failure of the cortical layer during temporary screw placement. The stability provided by a cortical thickness of 2 or 1 mm coupled to cancellous bone was deemed sufficient for temporary implants stability. PMID:28793582

Managing Substitute Teaching.

ERIC Educational Resources Information Center

Jones, Kevin R.

1999-01-01

This news brief presents information on managing substitute teaching. The information is based on issues discussed at a summit meeting which included public school administrators and personnel directors from around the nation. The main topics of concern focused around four core components related to the management of substitute teaching:…

Structural and catalytic effects of an invariant purine substitution in the hammerhead ribozyme: implications for the mechanism of acid–base catalysis

PubMed Central

Schultz, Eric P.; Vasquez, Ernesto E.; Scott, William G.

2014-01-01

The hammerhead ribozyme catalyzes RNA cleavage via acid–base catalysis. Whether it does so by general acid–base catalysis, in which the RNA itself donates and abstracts protons in the transition state, as is typically assumed, or by specific acid–base catalysis, in which the RNA plays a structural role and proton transfer is mediated by active-site water molecules, is unknown. Previous biochemical and crystallographic experiments implicate an invariant purine in the active site, G12, as the general base. However, G12 may play a structural role consistent with specific base catalysis. To better understand the role of G12 in the mechanism of hammerhead catalysis, a 2.2 Å resolution crystal structure of a hammerhead ribozyme from Schistosoma mansoni with a purine substituted for G12 in the active site of the ribozyme was obtained. Comparison of this structure (PDB entry 3zd4), in which A12 is substituted for G, with three previously determined structures that now serve as important experimental controls, allows the identification of structural perturbations that are owing to the purine substitution itself. Kinetic measurements for G12 purine-substituted schistosomal hammerheads confirm a previously observed dependence of rate on the pK a of the substituted purine; in both cases inosine, which is similar to G in pK a and hydrogen-bonding properties, is unexpectedly inactive. Structural comparisons indicate that this may primarily be owing to the lack of the exocyclic 2-amino group in the G12A and G12I substitutions and its structural effect upon both the nucleotide base and phosphate of A9. The latter involves the perturbation of a previously identified and well characterized metal ion-binding site known to be catalytically important in both minimal and full-length hammerhead ribozyme sequences. The results permit it to be suggested that G12 plays an important role in stabilizing the active-site structure. This result, although not inconsistent with the potential role of G12 as a general base, indicates that an alternative hammerhead cleavage mechanism involving specific base catalysis may instead explain the observed rate dependence upon purine substitutions at G12. The crystallographic results, contrary to previous assumptions, therefore cannot be interpreted to favor the general base catalysis mecahnism over the specific base catalysis mechanism. Instead, both of these mutually exclusive mechanistic alternatives must be considered in light of the current structural and biochemical data. PMID:25195740

Structural and catalytic effects of an invariant purine substitution in the hammerhead ribozyme: implications for the mechanism of acid-base catalysis.

PubMed

Schultz, Eric P; Vasquez, Ernesto E; Scott, William G

2014-09-01

The hammerhead ribozyme catalyzes RNA cleavage via acid-base catalysis. Whether it does so by general acid-base catalysis, in which the RNA itself donates and abstracts protons in the transition state, as is typically assumed, or by specific acid-base catalysis, in which the RNA plays a structural role and proton transfer is mediated by active-site water molecules, is unknown. Previous biochemical and crystallographic experiments implicate an invariant purine in the active site, G12, as the general base. However, G12 may play a structural role consistent with specific base catalysis. To better understand the role of G12 in the mechanism of hammerhead catalysis, a 2.2 Å resolution crystal structure of a hammerhead ribozyme from Schistosoma mansoni with a purine substituted for G12 in the active site of the ribozyme was obtained. Comparison of this structure (PDB entry 3zd4), in which A12 is substituted for G, with three previously determined structures that now serve as important experimental controls, allows the identification of structural perturbations that are owing to the purine substitution itself. Kinetic measurements for G12 purine-substituted schistosomal hammerheads confirm a previously observed dependence of rate on the pK(a) of the substituted purine; in both cases inosine, which is similar to G in pK(a) and hydrogen-bonding properties, is unexpectedly inactive. Structural comparisons indicate that this may primarily be owing to the lack of the exocyclic 2-amino group in the G12A and G12I substitutions and its structural effect upon both the nucleotide base and phosphate of A9. The latter involves the perturbation of a previously identified and well characterized metal ion-binding site known to be catalytically important in both minimal and full-length hammerhead ribozyme sequences. The results permit it to be suggested that G12 plays an important role in stabilizing the active-site structure. This result, although not inconsistent with the potential role of G12 as a general base, indicates that an alternative hammerhead cleavage mechanism involving specific base catalysis may instead explain the observed rate dependence upon purine substitutions at G12. The crystallographic results, contrary to previous assumptions, therefore cannot be interpreted to favor the general base catalysis mecahnism over the specific base catalysis mechanism. Instead, both of these mutually exclusive mechanistic alternatives must be considered in light of the current structural and biochemical data.

Feature-based classification of amino acid substitutions outside conserved functional protein domains.

PubMed

Gemovic, Branislava; Perovic, Vladimir; Glisic, Sanja; Veljkovic, Nevena

2013-01-01

There are more than 500 amino acid substitutions in each human genome, and bioinformatics tools irreplaceably contribute to determination of their functional effects. We have developed feature-based algorithm for the detection of mutations outside conserved functional domains (CFDs) and compared its classification efficacy with the most commonly used phylogeny-based tools, PolyPhen-2 and SIFT. The new algorithm is based on the informational spectrum method (ISM), a feature-based technique, and statistical analysis. Our dataset contained neutral polymorphisms and mutations associated with myeloid malignancies from epigenetic regulators ASXL1, DNMT3A, EZH2, and TET2. PolyPhen-2 and SIFT had significantly lower accuracies in predicting the effects of amino acid substitutions outside CFDs than expected, with especially low sensitivity. On the other hand, only ISM algorithm showed statistically significant classification of these sequences. It outperformed PolyPhen-2 and SIFT by 15% and 13%, respectively. These results suggest that feature-based methods, like ISM, are more suitable for the classification of amino acid substitutions outside CFDs than phylogeny-based tools.

Unexpected formal insertion of CO 2 into the C-Si bonds of a zinc compound

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

Kemp, Richard A.; McGrew, Genette I.; Khatri, Pathik A.

Reaction of [κ 2-PR 2C(SiMe 3)Py] 2Zn (R = Ph, 2a; iPr, 2b) with CO 2 affords the products of formal insertion at the C–Si bond, [κ 2-PR 2CC(O)O(SiMe 3)Py] 2Zn (R = Ph, 3a; iPr, 3b). Insertion product 3b was structurally characterized. As a result, the reaction appears to be a stepwise insertion and rearrangement of CO 2 based on kinetic data.

Unexpected formal insertion of CO 2 into the C-Si bonds of a zinc compound

DOE PAGES

Kemp, Richard A.; McGrew, Genette I.; Khatri, Pathik A.; ...

2015-09-08

Reaction of [κ 2-PR 2C(SiMe 3)Py] 2Zn (R = Ph, 2a; iPr, 2b) with CO 2 affords the products of formal insertion at the C–Si bond, [κ 2-PR 2CC(O)O(SiMe 3)Py] 2Zn (R = Ph, 3a; iPr, 3b). Insertion product 3b was structurally characterized. As a result, the reaction appears to be a stepwise insertion and rearrangement of CO 2 based on kinetic data.

End Restraints for Impact-Energy-Absorbing Tube Specimens

NASA Technical Reports Server (NTRS)

Farley, G. L.; Modlin, J. T.

1985-01-01

Inexpensive device developed that eliminates tipping problem without affecting crushing process. Device consists of soft sponge-rubber insert approximately 0.5 inches (1.3 centimeters) thick, cut to same diameter as internal diameter of tube specimen. Metal washer, slightly smaller than internal diameter of tube, placed on top of rubber insert. Screw passed through washer and rubber insert and threaded into base of test machine. As screw tightened against washer, rubber insert compressed and expands radially. Radial expansion applies pressure against internal wall of tube specimen, which provides sufficient support to tube to prevent tipping.

Perfluorinated Polyalkylether Based Lubricant Composition.

DTIC Science & Technology

phosphorus atoms are substituted by aromatic groups and the carbon atom is substituted by a perfluoroalkyl or perfluoroalkylether moiety. (Author)...A lubricant composition comprising a perfluorinated polyalkylether base fluid and a minor amount of a diphospha-s-triazine in which the two

Electronic structure of Pt-substituted clathrate silicides Ba{sub 8}Pt{sub x}Si{sub 46–x}(x = 4–6)

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

Borshch, N. A., E-mail: n.a.borshch@ya.ru

The results of calculation of the electronic structure of Si-based Pt-substituted clathrates are reported. Calculation is carried out by the linearized-augmented-plane-wave method. The effect of the number of substitutions and their crystallographic position in the unit cell on the electron-energy spectrum and the electronic properties of Pt-substituted clathrates is analyzed.

Base-promoted one-pot tandem reaction of 3-(1-alkynyl)chromones under microwave irradiation to functionalized amino-substituted xanthones.

PubMed

Liu, Yang; Huang, Liping; Xie, Fuchun; Hu, Youhong

2010-09-17

A base-promoted one-pot tandem reaction has been developed from 3-(1-alkynyl)chromones with various acetonitriles to afford functionalized amino-substituted xanthones 3 under microwave irradiation. This tandem process involves multiple reactions, such as Michael addition/cyclization/1,2-addition, without a transition metal catalyst. This method provides an efficient approach to build up natural product-like diversified amino-substituted xanthone scaffolds rapidly.

Strength of inserts in titanium alloy machining

NASA Astrophysics Data System (ADS)

Kozlov, V.; Huang, Z.; Zhang, J.

2016-04-01

In this paper, a stressed state of a non-worn cutting wedge in a machined titanium alloy (Ti6Al2Mo2Cr) is analyzed. The distribution of contact loads on the face of a cutting tool was obtained experimentally with the use of a ‘split cutting tool’. Calculation of internal stresses in the indexable insert made from cemented carbide (WC8Co) was carried out with the help of ANSYS 14.0 software. Investigations showed that a small thickness of the cutting insert leads to extremely high compressive stresses near the cutting edge, stresses that exceed the ultimate compressive strength of cemented carbide. The face and the base of the insert experience high tensile stresses, which approach the ultimate tensile strength of cemented carbide and increase a probability of cutting insert destruction. If the thickness of the cutting insert is bigger than 5 mm, compressive stresses near the cutting edge decrease, and tensile stresses on the face and base decrease to zero. The dependences of the greatest normal and tangential stresses on thickness of the cutting insert were found. Abbreviation and symbols: m/s - meter per second (cutting speed v); mm/r - millimeter per revolution (feed rate f); MPa - mega Pascal (dimension of specific contact loads and stresses); γ - rake angle of the cutting tool [°] α - clearance angle of the sharp cutting tool [°].

Nontraumatic tibial polyethylene insert cone fracture in mobile-bearing posterior-stabilized total knee arthroplasty.

PubMed

Tanikake, Yohei; Hayashi, Koji; Ogawa, Munehiro; Inagaki, Yusuke; Kawate, Kenji; Tomita, Tetsuya; Tanaka, Yasuhito

2016-12-01

A 72-year-old male patient underwent mobile-bearing posterior-stabilized total knee arthroplasty for osteoarthritis. He experienced a nontraumatic polyethylene tibial insert cone fracture 27 months after surgery. Scanning electron microscopy of the fracture surface of the tibial insert cone suggested progress of ductile breaking from the posterior toward the anterior of the cone due to repeated longitudinal bending stress, leading to fatigue breaking at the anterior side of the cone, followed by the tibial insert cone fracture at the anterior side of the cone, resulting in fracture at the base of the cone. This analysis shows the risk of tibial insert cone fracture due to longitudinal stress in mobile-bearing posterior-stabilized total knee arthroplasty in which an insert is designed to highly conform to the femoral component.

[The development and operation of a package inserts service system for electronic medical records].

PubMed

Yamada, Hidetoshi; Nishimura, Sachiho; Shimamori, Yoshimitsu; Sato, Seiji; Hayase, Yukitoshi

2003-03-01

To promote the appropriate use of pharmaceuticals and to prevent side effects, physicians need package inserts on medicinal drugs as soon as possible. A medicinal drug information service system was established for electronic medical records to speed up and increase the efficiency of package insert communications within a medical institution. Development of this system facilitates access to package inserts by, for example, physicians. The time required to maintain files of package inserts was shortened, and the efficiency of the drug information service increased. As a source of package inserts for this system, package inserts using a standard generalized markup language (SGML) form were used, which are accessible to the public on the homepage of the Organization for Pharmaceutical Safety and Research (OPSR). This study found that a delay occurred in communicating revised package inserts from pharmaceutical companies to the OPSR. Therefore a pharmaceutical department page was set up as part of the homepage of the medical institution for electronic medical records to shorten the delay in the revision of package inserts posted on the medicinal drug information service homepage of the OPSR. The usefulness of this package insert service system for electronic medical records is clear. For more effective use of this system based on the OPSR homepage pharmaceutical companies have been requested to provide quicker updating of package inserts.

Detection of novel polymorphisms in the ckit gene of canine patients with lymphoma, melanoma, haemangiosarcoma, and osteosarcoma.

PubMed

Gramer, Irina; Kessler, Martin; Geyer, Joachim

2016-06-01

Tyrosine kinase inhibitors (TKIs) that specifically target cKIT represent a therapeutic approach for non-resectable canine mast cell tumours (MCTs) grade II/III. The therapeutic benefit of TKIs has been investigated in other tumours based on clinical response rates and identification of gain-of-function mutations. In the present study, cKIT expression in 14 dogs with osteosarcoma, melanoma, haemangiosarcoma, lymphoma, and fibrosarcoma was analysed. Tissue samples were used for cKIT sequencing to (I) detect the cKIT transcript and to (II) identify gain-of-function mutations. The cKIT transcript was detected in ten patients. Four novel amino acid substitutions and five silent polymorphisms were identified. Furthermore, an insertion mutation (GNSK) was discovered in the tissue, but not in the blood sample of one dog. CKIT expression was identified in a variety of canine tumours and, therefore, TKIs might have a broader therapeutic indication apart from treatment of MCTs. Further investigations will be necessary to localize the cKIT protein in the respective tumours and to evaluate the functional consequence of the cKIT variants identified in the present study.

Comparison of self-written waveguide techniques and bulk index matching for low-loss polymer waveguide interconnects

NASA Astrophysics Data System (ADS)

Burrell, Derek; Middlebrook, Christopher

2016-03-01

Polymer waveguides (PWGs) are used within photonic interconnects as inexpensive and versatile substitutes for traditional optical fibers. The PWGs are typically aligned to silica-based optical fibers for coupling. An epoxide elastomer is then applied and cured at the interface for index matching and rigid attachment. Self-written waveguides (SWWs) are proposed as an alternative to further reduce connection insertion loss (IL) and alleviate marginal misalignment issues. Elastomer material is deposited after the initial alignment, and SWWs are formed by injecting ultraviolet (UV) light into the fiber or waveguide. The coupled UV light cures a channel between the two differing structures. A suitable cladding layer can be applied after development. Such factors as longitudinal gap distance, UV cure time, input power level, polymer material selection and choice of solvent affect the resulting SWWs. Experimental data are compared between purely index-matched samples and those with SWWs at the fiber-PWG interface. It is shown that < 1 dB IL per connection can be achieved by either method and results indicate lowest potential losses associated with a fine-tuned self-writing process. Successfully fabricated SWWs reduce overall processing time and enable an effectively continuous low-loss rigid interconnect.

REDIdb: the RNA editing database.

PubMed

Picardi, Ernesto; Regina, Teresa Maria Rosaria; Brennicke, Axel; Quagliariello, Carla

2007-01-01

The RNA Editing Database (REDIdb) is an interactive, web-based database created and designed with the aim to allocate RNA editing events such as substitutions, insertions and deletions occurring in a wide range of organisms. The database contains both fully and partially sequenced DNA molecules for which editing information is available either by experimental inspection (in vitro) or by computational detection (in silico). Each record of REDIdb is organized in a specific flat-file containing a description of the main characteristics of the entry, a feature table with the editing events and related details and a sequence zone with both the genomic sequence and the corresponding edited transcript. REDIdb is a relational database in which the browsing and identification of editing sites has been simplified by means of two facilities to either graphically display genomic or cDNA sequences or to show the corresponding alignment. In both cases, all editing sites are highlighted in colour and their relative positions are detailed by mousing over. New editing positions can be directly submitted to REDIdb after a user-specific registration to obtain authorized secure access. This first version of REDIdb database stores 9964 editing events and can be freely queried at http://biologia.unical.it/py_script/search.html.

U.S. Selected Practice Recommendations for Contraceptive Use, 2016.

PubMed

Curtis, Kathryn M; Jatlaoui, Tara C; Tepper, Naomi K; Zapata, Lauren B; Horton, Leah G; Jamieson, Denise J; Whiteman, Maura K

2016-07-29

The 2016 U.S. Selected Practice Recommendations for Contraceptive Use (U.S. SPR) addresses a select group of common, yet sometimes controversial or complex, issues regarding initiation and use of specific contraceptive methods. These recommendations for health care providers were updated by CDC after review of the scientific evidence and consultation with national experts who met in Atlanta, Georgia, during August 26-28, 2015. The information in this report updates the 2013 U.S. SPR (CDC. U.S. selected practice recommendations for contraceptive use, 2013. MMWR 2013;62[No. RR-5]). Major updates include 1) revised recommendations for starting regular contraception after the use of emergency contraceptive pills and 2) new recommendations for the use of medications to ease insertion of intrauterine devices. The recommendations in this report are intended to serve as a source of clinical guidance for health care providers and provide evidence-based guidance to reduce medical barriers to contraception access and use. Health care providers should always consider the individual clinical circumstances of each person seeking family planning services. This report is not intended to be a substitute for professional medical advice for individual patients. Persons should seek advice from their health care providers when considering family planning options.

Ca/Alq3 hybrid cathode buffer layer for the optimization of organic solar cells based on a planar heterojunction

NASA Astrophysics Data System (ADS)

El Jouad, Z.; Barkat, L.; Stephant, N.; Cattin, L.; Hamzaoui, N.; Khelil, A.; Ghamnia, M.; Addou, M.; Morsli, M.; Béchu, S.; Cabanetos, C.; Richard-Plouet, M.; Blanchard, P.; Bernède, J. C.

2016-11-01

Use of efficient anode cathode buffer layer (CBL) is crucial to improve the efficiency of organic photovoltaic cells. Here we show that using a double CBL, Ca/Alq3, allows improving significantly cell performances. The insertion of Ca layer facilitates electron harvesting and blocks hole collection, leading to improved charge selectivity and reduced leakage current, whereas Alq3 blocks excitons. After optimisation of this Ca/Alq3 CBL using CuPc as electron donor, it is shown that it is also efficient when SubPc is substituted to CuPc in the cells. In that case we show that the morphology of the SubPc layer, and therefore the efficiency of the cells, strongly depends on the deposition rate of the SubPc film. It is necessary to deposit slowly (0.02 nm/s) the SubPc films because at higher deposition rate (0.06 nm/s) the films are porous, which induces leakage currents and deterioration of the cell performances. The SubPc layers whose formations are kinetically driven at low deposition rates are more uniform, whereas those deposited faster exhibit high densities of pinholes.

Retention-error patterns in complex alphanumeric serial-recall tasks.

PubMed

Mathy, Fabien; Varré, Jean-Stéphane

2013-01-01

We propose a new method based on an algorithm usually dedicated to DNA sequence alignment in order to both reliably score short-term memory performance on immediate serial-recall tasks and analyse retention-error patterns. There can be considerable confusion on how performance on immediate serial list recall tasks is scored, especially when the to-be-remembered items are sampled with replacement. We discuss the utility of sequence-alignment algorithms to compare the stimuli to the participants' responses. The idea is that deletion, substitution, translocation, and insertion errors, which are typical in DNA, are also typical putative errors in short-term memory (respectively omission, confusion, permutation, and intrusion errors). We analyse four data sets in which alphanumeric lists included a few (or many) repetitions. After examining the method on two simple data sets, we show that sequence alignment offers 1) a compelling method for measuring capacity in terms of chunks when many regularities are introduced in the material (third data set) and 2) a reliable estimator of individual differences in short-term memory capacity. This study illustrates the difficulty of arriving at a good measure of short-term memory performance, and also attempts to characterise the primary factors underpinning remembering and forgetting.

Parsimony and Model-Based Analyses of Indels in Avian Nuclear Genes Reveal Congruent and Incongruent Phylogenetic Signals

PubMed Central

Yuri, Tamaki; Kimball, Rebecca T.; Harshman, John; Bowie, Rauri C. K.; Braun, Michael J.; Chojnowski, Jena L.; Han, Kin-Lan; Hackett, Shannon J.; Huddleston, Christopher J.; Moore, William S.; Reddy, Sushma; Sheldon, Frederick H.; Steadman, David W.; Witt, Christopher C.; Braun, Edward L.

2013-01-01

Insertion/deletion (indel) mutations, which are represented by gaps in multiple sequence alignments, have been used to examine phylogenetic hypotheses for some time. However, most analyses combine gap data with the nucleotide sequences in which they are embedded, probably because most phylogenetic datasets include few gap characters. Here, we report analyses of 12,030 gap characters from an alignment of avian nuclear genes using maximum parsimony (MP) and a simple maximum likelihood (ML) framework. Both trees were similar, and they exhibited almost all of the strongly supported relationships in the nucleotide tree, although neither gap tree supported many relationships that have proven difficult to recover in previous studies. Moreover, independent lines of evidence typically corroborated the nucleotide topology instead of the gap topology when they disagreed, although the number of conflicting nodes with high bootstrap support was limited. Filtering to remove short indels did not substantially reduce homoplasy or reduce conflict. Combined analyses of nucleotides and gaps resulted in the nucleotide topology, but with increased support, suggesting that gap data may prove most useful when analyzed in combination with nucleotide substitutions. PMID:24832669

Transcriptional regulatory elements in the noncoding region of human papillomavirus type 6

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

Wu, Tzyy-Choou.

1989-01-01

The structure and function of the transcriptional regulatory region of human papillomavirus type 6 (HPV-6) has been investigated. To investigate tissue specific gene expression, a sensitive method to detect and localize HPV-6 viral DNA, mRNA and protein in plastic-embedded tissue sections of genital and respiratory tract papillomata by using in situ hybridization and immunoperoxidase assays has been developed. This method, using ultrathin sections and strand-specific {sup 3}H labeled riboprobes, offers the advantages of superior morphological preservation and detection of viral genomes at low copy number with good resolution, and the modified immunocytochemistry provides better sensitivity. The results suggest that genitalmore » tract epithelium is more permissive for HPV-6 replication than respiratory tract epithelium. To study the tissue tropism of HPV-6 at the level of regulation of viral gene expression, the polymerase chain reaction was used to isolate the noncoding region (NCR) of HPV-6 in independent isolates. Nucleotide sequence analysis of molecularly cloned DNA identified base substitutions, deletions/insertions and tandem duplications. Transcriptional regulatory elements in the NCR were assayed in recombinant plasmids containing the bacterial gene for chloramphenicol acetyl transferase.« less

Zethrene biradicals: How pro-aromaticity is expressed in the ground electronic state and in the lowest energy singlet, triplet, and ionic states

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

Zafra, José Luis; González Cano, Rafael C.; Ruiz Delgado, M. Carmen

A analysis of the electronic and molecular structures of new molecular materials based on zethrene is presented with particular attention to those systems having a central benzo-quinoidal core able to generate Kekulé biradicals whose stability is provided by the aromaticity recovery in this central unit. These Kekulé biradicals display singlet ground electronic states thanks to double spin polarization and have low-energy lying triplet excited states also featured by the aromaticity gain. Pro-aromatization is also the driving force for the stabilization of the ionized species. Moreover, the low energy lying singlet excited states also display a profound biradical fingerprint allowing tomore » singlet exciton fission. These properties are discussed in the context of the size of the zethrene core and of its substitution. The work encompasses all known long zethrenes and makes use of a variety of experimental techniques, such as Raman, UV-Vis-NIR absorption, transient absorption, in situ spectroelectrochemistry and quantum chemical calculations. This study reveals how the insertion of suitable molecular modules (i.e., quinoidal) opens the door to new intriguing molecular properties exploitable in organic electronics.« less

Synthetic versatility of 2-substituted-6-methyl 2,3-dihydropyridinones in the synthesis of polyfunctional piperidine-based compounds and related β amino acid derivatives.

PubMed

Yang, Yang; Hardman, Clayton

2017-10-18

Chiral 2-substituted-6-methyl 2,3-dihydropyidinones 9, which can be facilely obtained from an asymmetric vinylogous Mannich reaction (VMR) with 1,3-bis-trimethysily enol ether, were used as versatile intermediates in constructing chiral polyfunctional piperidine-based compounds. The 6-methyl group of such compounds can be conveniently functionalized via alkylation and acylation reactions to provide efficient entries to the synthesis of a variety of chiral multi-substituted piperidine-based compounds. Further elaboration of the corresponding intermediates also provided access to polyfunctional indolizidine-based compounds. These methods were showcased in an asymmetric synthesis of 2,6-di-substituted piperidine compound 13, reported as the key intermediate in the synthesis of (+)-calvine and a natural alkaloid (-)-indolizidine 209D. Furthermore, selective C5 iodination of compound 9 enabled the installation of additional functional groups at this position. Finally, we demonstrated that the oxidative cleavage of 2-substituted-6-methyl-2,3-dihydropyidinones is a practical and efficient method for the enantioselective synthesis of β-amino acids, which can undergo further intra-molecular cyclization to give the corresponding chiral four-membered β-lactam derivatives.

An experimental investigation on heat transfer enhancement in the laminar flow of water/TiO2 nanofluid through a tube heat exchanger fitted with modified butterfly inserts

NASA Astrophysics Data System (ADS)

Venkitaraj, K. P.; Suresh, S.; Alwin Mathew, T.; Bibin, B. S.; Abraham, Jisa

2018-03-01

Nanofluids are advanced heat transfer fluids that exhibit thermal properties superior than that of the conventional fluids such as water, oil etc. This paper reports the experimental study on convective heat transfer characteristics of water based titanium dioxide nanofluids in fully developed flow through a uniformly heated pipe heat exchanger fitted with modified butterfly inserts. Nanofluids are prepared by dispersing TiO2 nanoparticles of average particle size 29 nm in deionized water. The heat transfer experiments are performed in laminar regime using nanofluids prepared with 0.1% and 0.3% volume fractions of TiO2 nanoparticles. The thermal performance characteristics of conventional butterfly inserts and modified butterfly inserts are also compared using TiO2 nanofluid. The inserts with different pitches 6 cm, 9 cm and 12 cm are tested to determine the effect of pitch distance of inserts in the heat transfer and friction. The experimental results showed that the modification made in the butterfly inserts were able to produce higher heat transfer than conventional butterfly inserts.

A study of a tissue equivalent gelatine based tissue substitute

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

Spence, J.L.

1992-11-01

A study of several tissue substitutes for use as volumetric dosimeters was performed. The tissue substitutes studied included tissue substitutes from previous studies and from ICRU 44. The substitutes were evaluated for an overall match to Reference Man which was used as a basis for this study. The evaluation was based on the electron stopping power, the mass attenuation coefficient, the electron density, and the specific gravity. The tissue substitute chosen also had to be capable of changing from a liquid into a solid form to maintain an even distribution of thermoluminesent dosimetry (TLD) powder and then back to amore » liquid for recovery of the TLD powder without adversely effecting the TLD powder. The gelatine mixture provided the closest match to the data from Reference Man tissue. The gelatine mixture was put through a series of test to determine it's usefulness as a reliable tissue substitute. The TLD powder was cast in the gelatine mixture and recovered to determine if the TLD powder was adversely effected. The distribution of the TLD powder after being cast into the gelatin mixture was tested in insure an even was maintained.« less

A study of a tissue equivalent gelatine based tissue substitute

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

Spence, Jody L.

1992-11-01

A study of several tissue substitutes for use as volumetric dosimeters was performed. The tissue substitutes studied included tissue substitutes from previous studies and from ICRU 44. The substitutes were evaluated for an overall match to Reference Man which was used as a basis for this study. The evaluation was based on the electron stopping power, the mass attenuation coefficient, the electron density, and the specific gravity. The tissue substitute chosen also had to be capable of changing from a liquid into a solid form to maintain an even distribution of thermoluminesent dosimetry (TLD) powder and then back to amore » liquid for recovery of the TLD powder without adversely effecting the TLD powder. The gelatine mixture provided the closest match to the data from Reference Man tissue. The gelatine mixture was put through a series of test to determine it`s usefulness as a reliable tissue substitute. The TLD powder was cast in the gelatine mixture and recovered to determine if the TLD powder was adversely effected. The distribution of the TLD powder after being cast into the gelatin mixture was tested in insure an even was maintained.« less

A multi-material coating containing chemically-modified apatites for combined enhanced bioactivity and reduced infection via a drop-on-demand micro-dispensing technique.

PubMed

Lim, Poon Nian; Wang, Zuyong; Chang, Lei; Konishi, Toshiisa; Choong, Cleo; Ho, Bow; Thian, Eng San

2017-01-01

Prevention of infection and enhanced osseointegration are closely related, and required for a successful orthopaedic implant, which necessitate implant designs to consider both criteria in tandem. A multi-material coating containing 1:1 ratio of silicon-substituted hydroxyapatite and silver-substituted hydroxyapatite as the top functional layer, and hydroxyapatite as the base layer, was produced via the drop-on-demand micro-dispensing technique, as a strategic approach in the fight against infection along with the promotion of bone tissue regeneration. The homogeneous distribution of silicon-substituted hydroxyapatite and silver-substituted hydroxyapatite micro-droplets at alternate position in silicon-substituted hydroxyapatite-silver-substituted hydroxyapatite/hydroxyapatite coating delayed the exponential growth of Staphylococcus aureus for up to 24 h, and gave rise to up-regulated expression of alkaline phosphatase activity, type I collagen and osteocalcin as compared to hydroxyapatite and silver-substituted hydroxyapatite coatings. Despite containing reduced amounts of silicon-substituted hydroxyapatite and silver-substituted hydroxyapatite micro-droplets over the coated area than silicon-substituted hydroxyapatite and silver-substituted hydroxyapatite coatings, silicon-substituted hydroxyapatite-silver-substituted hydroxyapatite/hydroxyapatite coating exhibited effective antibacterial property with enhanced bioactivity. By exhibiting good controllability of distributing silicon-substituted hydroxyapatite, silver-substituted hydroxyapatite and hydroxyapatite micro-droplets, it was demonstrated that drop-on-demand micro-dispensing technique was capable in harnessing the advantages of silver-substituted hydroxyapatite, silicon-substituted hydroxyapatite and hydroxyapatite to produce a multi-material coating along with enhanced bioactivity and reduced infection.

Simulator trials to determine the wear of the combination aluminium oxide ceramic-carbon fibre reinforced plastic (CFRP) used as an insert in a hip socket.

PubMed

Scheller, G; Schwarz, M; Früh, H J; Jani, L

1999-01-01

Hip simulator trials were conducted to determine the initial wear between alumina femoral heads and carbon fibre reinforced plastic (CFRP, CAPROMAN) insert in a titanium socket. A force of 2500 N and a frequency of 0.857 H were applied. Using surface and sphericity measurement techniques, the amount of wear was determined. After 500,000 cycles, the centre of the head had moved by 10 microm into the insert, and the average radius increased by 2 microm. After 1 million cycles, the additional changes were less than 1 microm. Based on an examination of retrieved implants (wear rate: 6.1 microm/year) and based on the simulator results, the combination alumina-CFRP inserts could be approved for total hip replacement.

Management of computed tomography-detected pneumothorax in patients with blunt trauma: experience from a community-based hospital

PubMed Central

Hefny, Ashraf F; Kunhivalappil, Fathima T; Matev, Nikolay; Avila, Norman A; Bashir, Masoud O; Abu-Zidan, Fikri M

2018-01-01

INTRODUCTION Diagnoses of pneumothorax, especially occult pneumothorax, have increased as the use of computed tomography (CT) for imaging trauma patients becomes near-routine. However, the need for chest tube insertion remains controversial. We aimed to study the management of pneumothorax detected on CT among patients with blunt trauma, including the decision for tube thoracostomy, in a community-based hospital. METHODS Chest CT scans of patients with blunt trauma treated at Al Rahba Hospital, Abu Dhabi, United Arab Emirates, from October 2010 to October 2014 were retrospectively studied. Variables studied included demography, mechanism of injury, endotracheal intubation, pneumothorax volume, chest tube insertion, Injury Severity Score, hospital length of stay and mortality. RESULTS CT was performed in 703 patients with blunt trauma. Overall, pneumothorax was detected on CT for 74 (10.5%) patients. Among the 65 patients for whom pneumothorax was detected before chest tube insertion, 25 (38.5%) needed chest tube insertion, while 40 (61.5%) did not. Backward stepwise likelihood regression showed that independent factors that significantly predicted chest tube insertion were endotracheal intubation (p = 0.01), non-United Arab Emirates nationality (p = 0.01) and pneumothorax volume (p = 0.03). The receiver operating characteristic curve showed that the best pneumothorax volume that predicted chest tube insertion was 30 mL. CONCLUSION Chest tube was inserted in less than half of the patients with blunt trauma for whom pneumothorax was detected on CT. Pneumothorax volume should be considered in decision-making regarding chest tube insertion. Conservative treatment may be sufficient for pneumothorax of volume < 30 mL. PMID:28741012

Management of computed tomography-detected pneumothorax in patients with blunt trauma: experience from a community-based hospital.

PubMed

Hefny, Ashraf F; Kunhivalappil, Fathima T; Matev, Nikolay; Avila, Norman A; Bashir, Masoud O; Abu-Zidan, Fikri M

2018-03-01

Diagnoses of pneumothorax, especially occult pneumothorax, have increased as the use of computed tomography (CT) for imaging trauma patients becomes near-routine. However, the need for chest tube insertion remains controversial. We aimed to study the management of pneumothorax detected on CT among patients with blunt trauma, including the decision for tube thoracostomy, in a community-based hospital. Chest CT scans of patients with blunt trauma treated at Al Rahba Hospital, Abu Dhabi, United Arab Emirates, from October 2010 to October 2014 were retrospectively studied. Variables studied included demography, mechanism of injury, endotracheal intubation, pneumothorax volume, chest tube insertion, Injury Severity Score, hospital length of stay and mortality. CT was performed in 703 patients with blunt trauma. Overall, pneumothorax was detected on CT for 74 (10.5%) patients. Among the 65 patients for whom pneumothorax was detected before chest tube insertion, 25 (38.5%) needed chest tube insertion, while 40 (61.5%) did not. Backward stepwise likelihood regression showed that independent factors that significantly predicted chest tube insertion were endotracheal intubation (p = 0.01), non-United Arab Emirates nationality (p = 0.01) and pneumothorax volume (p = 0.03). The receiver operating characteristic curve showed that the best pneumothorax volume that predicted chest tube insertion was 30 mL. Chest tube was inserted in less than half of the patients with blunt trauma for whom pneumothorax was detected on CT. Pneumothorax volume should be considered in decision-making regarding chest tube insertion. Conservative treatment may be sufficient for pneumothorax of volume < 30 mL. Copyright: © Singapore Medical Association.

A new allele of flower color gene W1 encoding flavonoid 3'5'-hydroxylase is responsible for light purple flowers in wild soybean Glycine soja.

PubMed

Takahashi, Ryoji; Dubouzet, Joseph G; Matsumura, Hisakazu; Yasuda, Kentaro; Iwashina, Tsukasa

2010-07-28

Glycine soja is a wild relative of soybean that has purple flowers. No flower color variant of Glycine soja has been found in the natural habitat. B09121, an accession with light purple flowers, was discovered in southern Japan. Genetic analysis revealed that the gene responsible for the light purple flowers was allelic to the W1 locus encoding flavonoid 3'5'-hydroxylase (F3'5'H). The new allele was designated as w1-lp. The dominance relationship of the locus was W1 >w1-lp >w1. One F2 plant and four F3 plants with purple flowers were generated in the cross between B09121 and a Clark near-isogenic line with w1 allele. Flower petals of B09121 contained lower amounts of four major anthocyanins (malvidin 3,5-di-O-glucoside, petunidin 3,5-di-O-glucoside, delphinidin 3,5-di-O-glucoside and delphinidin 3-O-glucoside) common in purple flowers and contained small amounts of the 5'-unsubstituted versions of the above anthocyanins, peonidin 3,5-di-O-glucoside, cyanidin 3,5-di-O-glucoside and cyanidin 3-O-glucoside, suggesting that F3'5'H activity was reduced and flavonoid 3'-hydroxylase activity was increased. F3'5'H cDNAs were cloned from Clark and B09121 by RT-PCR. The cDNA of B09121 had a unique base substitution resulting in the substitution of valine with methionine at amino acid position 210. The base substitution was ascertained by dCAPS analysis. The polymorphism associated with the dCAPS markers co-segregated with flower color in the F2 population. F3 progeny test, and dCAPS and indel analyses suggested that the plants with purple flowers might be due to intragenic recombination and that the 65 bp insertion responsible for gene dysfunction might have been eliminated in such plants. B09121 may be the first example of a flower color variant found in nature. The light purple flower was controlled by a new allele of the W1 locus encoding F3'5'H. The flower petals contained unique anthocyanins not found in soybean and G. soja. B09121 may be a useful tool for studies of the structural and functional properties of F3'5'H genes as well as investigations on the role of flower color in relation to adaptation of G. soja to natural habitats.

Designing robust watermark barcodes for multiplex long-read sequencing.

PubMed

Ezpeleta, Joaquín; Krsticevic, Flavia J; Bulacio, Pilar; Tapia, Elizabeth

2017-03-15

To attain acceptable sample misassignment rates, current approaches to multiplex single-molecule real-time sequencing require upstream quality improvement, which is obtained from multiple passes over the sequenced insert and significantly reduces the effective read length. In order to fully exploit the raw read length on multiplex applications, robust barcodes capable of dealing with the full single-pass error rates are needed. We present a method for designing sequencing barcodes that can withstand a large number of insertion, deletion and substitution errors and are suitable for use in multiplex single-molecule real-time sequencing. The manuscript focuses on the design of barcodes for full-length single-pass reads, impaired by challenging error rates in the order of 11%. The proposed barcodes can multiplex hundreds or thousands of samples while achieving sample misassignment probabilities as low as 10-7 under the above conditions, and are designed to be compatible with chemical constraints imposed by the sequencing process. Software tools for constructing watermark barcode sets and demultiplexing barcoded reads, together with example sets of barcodes and synthetic barcoded reads, are freely available at www.cifasis-conicet.gov.ar/ezpeleta/NS-watermark . ezpeleta@cifasis-conicet.gov.ar. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Sequence diversity of NanA manifests in distinct enzyme kinetics and inhibitor susceptibility

NASA Astrophysics Data System (ADS)

Xu, Zhongli; von Grafenstein, Susanne; Walther, Elisabeth; Fuchs, Julian E.; Liedl, Klaus R.; Sauerbrei, Andreas; Schmidtke, Michaela

2016-04-01

Streptococcus pneumoniae is the leading pathogen causing bacterial pneumonia and meningitis. Its surface-associated virulence factor neuraminidase A (NanA) promotes the bacterial colonization by removing the terminal sialyl residues from glycoconjugates on eukaryotic cell surface. The predominant role of NanA in the pathogenesis of pneumococci renders it an attractive target for therapeutic intervention. Despite the highly conserved activity of NanA, our alignment of the 11 NanAs revealed the evolutionary diversity of this enzyme. The amino acid substitutions we identified, particularly those in the lectin domain and in the insertion domain next to the catalytic centre triggered our special interest. We synthesised the representative NanAs and the mutagenized derivatives from E. coli for enzyme kinetics study and neuraminidase inhibitor susceptibility test. Via molecular docking we got a deeper insight into the differences between the two major variants of NanA and their influence on the ligand-target interactions. In addition, our molecular dynamics simulations revealed a prominent intrinsic flexibility of the linker between the active site and the insertion domain, which influences the inhibitor binding. Our findings for the first time associated the primary sequence diversity of NanA with the biochemical properties of the enzyme and with the inhibitory efficiency of neuraminidase inhibitors.

Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 with improved proof-reading enhances homology-directed repair.

PubMed

Kato-Inui, Tomoko; Takahashi, Gou; Hsu, Szuyin; Miyaoka, Yuichiro

2018-05-18

Genome editing using clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) predominantly induces non-homologous end joining (NHEJ), which generates random insertions or deletions, whereas homology-directed repair (HDR), which generates precise recombination products, is useful for wider applications. However, the factors that determine the ratio of HDR to NHEJ products after CRISPR/Cas9 editing remain unclear, and methods by which the proportion of HDR products can be increased have not yet been fully established. We systematically analyzed the HDR and NHEJ products after genome editing using various modified guide RNAs (gRNAs) and Cas9 variants with an enhanced conformational checkpoint to improve the fidelity at endogenous gene loci in HEK293T cells and HeLa cells. We found that these modified gRNAs and Cas9 variants were able to enhance HDR in both single-nucleotide substitutions and a multi-kb DNA fragment insertion. Our results suggest that the original CRISPR/Cas9 system from the bacterial immune system is not necessarily the best option for the induction of HDR in genome editing and indicate that the modulation of the kinetics of conformational checkpoints of Cas9 can optimize the HDR/NHEJ ratio.

Precise and heritable genome editing in evolutionarily diverse nematodes using TALENs and CRISPR/Cas9 to engineer insertions and deletions.

PubMed

Lo, Te-Wen; Pickle, Catherine S; Lin, Steven; Ralston, Edward J; Gurling, Mark; Schartner, Caitlin M; Bian, Qian; Doudna, Jennifer A; Meyer, Barbara J

2013-10-01

Exploitation of custom-designed nucleases to induce DNA double-strand breaks (DSBs) at genomic locations of choice has transformed our ability to edit genomes, regardless of their complexity. DSBs can trigger either error-prone repair pathways that induce random mutations at the break sites or precise homology-directed repair pathways that generate specific insertions or deletions guided by exogenously supplied DNA. Prior editing strategies using site-specific nucleases to modify the Caenorhabditis elegans genome achieved only the heritable disruption of endogenous loci through random mutagenesis by error-prone repair. Here we report highly effective strategies using TALE nucleases and RNA-guided CRISPR/Cas9 nucleases to induce error-prone repair and homology-directed repair to create heritable, precise insertion, deletion, or substitution of specific DNA sequences at targeted endogenous loci. Our robust strategies are effective across nematode species diverged by 300 million years, including necromenic nematodes (Pristionchus pacificus), male/female species (Caenorhabditis species 9), and hermaphroditic species (C. elegans). Thus, genome-editing tools now exist to transform nonmodel nematode species into genetically tractable model organisms. We demonstrate the utility of our broadly applicable genome-editing strategies by creating reagents generally useful to the nematode community and reagents specifically designed to explore the mechanism and evolution of X chromosome dosage compensation. By developing an efficient pipeline involving germline injection of nuclease mRNAs and single-stranded DNA templates, we engineered precise, heritable nucleotide changes both close to and far from DSBs to gain or lose genetic function, to tag proteins made from endogenous genes, and to excise entire loci through targeted FLP-FRT recombination.

Unique and redundant functional domains of APETALA1 and CAULIFLOWER, two recently duplicated Arabidopsis thaliana floral MADS-box genes.

PubMed

Alvarez-Buylla, Elena R; García-Ponce, Berenice; Garay-Arroyo, Adriana

2006-01-01

APETALA1 (AP1) and CAULIFLOWER (CAL) are closely related MADS box genes that are partially redundant during Arabidopsis thaliana floral meristem determination. AP1 is able to fully substitute for CAL functions, but not vice versa, and AP1 has unique sepal and petal identity specification functions. In this study, the unique and redundant functions of these two genes has been mapped to the four protein domains that characterize type-II MADS-domain proteins by expressing all 15 chimeric combinations of AP1 and CAL cDNA regions under control of the AP1 promoter in ap1-1 loss-of-function plants. The "in vivo" function of these chimeric genes was analysed in Arabidopsis plants by expressing the chimeras. Rescue of flower meristem and sepal/petal identities was scored in single and multiple insert homozygous transgenic lines. Using these chimeric lines, it was found that distinct residues of the AP1 K domain not shared by the same CAL domain are necessary and sufficient for complete recovery of floral meristem identity, in the context of the CAL protein sequence, while both AP1 COOH and K domains are indispensable for complete rescue of sepal identity. By contrast, either one of these two AP1 domains is necessary and sufficient for complete petal identity recovery. It was also found that there were positive and negative synergies among protein domains and their combinations, and that multiple-insert lines showed relatively better rescue than equivalent single-insert lines. Finally, several lines had flowers with extra sepals and petals suggesting that chimeric proteins yield abnormal transcriptional complexes that may alter the expression or regulation of genes that control floral organ number under normal conditions.

Post-modification of preformed liposomes with novel non-phospholipid poly(ethylene glycol)-conjugated hexadecylcarbamoylmethyl hexadecanoic acid for enhanced circulation persistence in vivo

PubMed Central

Nag, Okhil K; Yadav, Vivek R; Hedrick, Andria; Awasthi, Vibhudutta

2013-01-01

We report synthesis and characterization of a novel PEG2000-conjugated hexadecylcarbamoylmethyl hexadecanoate (HDAS-PEG) as a PEG-phospholipid substitute for enhancing circulation persistence of liposomes. HDAS-PEG showed critical micelle concentration of 4.25 μM. We used post-insertion technique to introduce HDAS-PEG in outer lipid layer of the preformed liposomes. The presence of surface HDAS-PEG was confirmed by altered electrophoretic mobility, confocal microscopy and PEG estimation by ELISA. The post-inserted HDAS-PEG desorbed at approximately half the rate at which post-inserted DSPE-PEG desorbed from the liposome surface. HDAS-PEG significantly reduced liposome-induced complement activation (C4d, Bb and SC5b); HDAS-PEG was more effective than more commonly used DSPE-PEG in this capacity. For studying circulation persistence, the liposomes were labeled with 99mTc radionuclide and administered in rats. 99mTc-HDAS-PEG-liposomes showed prolonged persistence in blood as compared to that shown by 99mTc-plain liposomes. After 24 h of administration, < 1% of 99mTc-plain liposomes remained in blood, whereas approximately 28% of injected 99mTc-HDAS-PEG-liposomes were present in blood. In comparison, only 4.8% of 99mTc-DSPE-PEG-liposomes was measured in blood after 24 h. As expected, the clearance route of the liposomes was through liver and spleen. These results demonstrate the potential of a novel non-phosphoryl HDAS-PEG for surface modification of preformed liposomes with a goal of prolonging their circulation persistence and more effective inhibition of complement activation. PMID:23419666

Characterization of three Agrobacterium tumefaciens avirulent mutants with chromosomal mutations that affect induction of vir genes.

PubMed

Metts, J; West, J; Doares, S H; Matthysse, A G

1991-02-01

Three Agrobacterium tumefaciens mutants with chromosomal mutations that affect bacterial virulence were isolated by transposon mutagenesis. Two of the mutants were avirulent on all hosts tested. The third mutant, Ivr-211, was a host range mutant which was avirulent on Bryophyllum diagremontiana, Nicotiana tabacum, N. debneyi, N. glauca, and Daucus carota but was virulent on Zinnia elegans and Lycopersicon esculentum (tomato). That the mutant phenotype was due to the transposon insertion was determined by cloning the DNA containing the transposon insertion and using the cloned DNA to replace the wild-type DNA in the parent bacterial strain by marker exchange. The transposon insertions in the three mutants mapped at three widely separated locations on the bacterial chromosome. The effects of the mutations on various steps in tumor formation were examined. All three mutants showed no alteration in binding to carrot cells. However, none of the mutants showed any induction of vir genes by acetosyringone under conditions in which the parent strain showed vir gene induction. When the mutant bacteria were examined for changes in surface components, it was found that all three of the mutants showed a similar alteration in lipopolysaccharide (LPS). LPS from the mutants was larger in size and more heavily saccharide substituted than LPS from the parent strain. Two of the mutants showed no detectable alteration in outer membrane and periplasmic space proteins. The third mutant, Ivr-225, was missing a 79-kDa surface peptide. The reason(s) for the failure of vir gene induction in these mutants and its relationship, if any, to the observed alteration in LPS are unknown.

Foods for Special Dietary Needs: Non-dairy Plant-based Milk Substitutes and Fermented Dairy-type Products.

PubMed

Mäkinen, Outi Elina; Wanhalinna, Viivi; Zannini, Emanuele; Arendt, Elke Karin

2016-01-01

A growing number of consumers opt for plant-based milk substitutes for medical reasons or as a lifestyle choice. Medical reasons include lactose intolerance, with a worldwide prevalence of 75%, and cow's milk allergy. Also, in countries where mammal milk is scarce and expensive, plant milk substitutes serve as a more affordable option. However, many of these products have sensory characteristics objectionable to the mainstream western palate. Technologically, plant milk substitutes are suspensions of dissolved and disintegrated plant material in water, resembling cow's milk in appearance. They are manufactured by extracting the plant material in water, separating the liquid, and formulating the final product. Homogenization and thermal treatments are necessary to improve the suspension and microbial stabilities of commercial products that can be consumed as such or be further processed into fermented dairy-type products. The nutritional properties depend on the plant source, processing, and fortification. As some products have extremely low protein and calcium contents, consumer awareness is important when plant milk substitutes are used to replace cow's milk in the diet, e.g. in the case of dairy intolerances. If formulated into palatable and nutritionally adequate products, plant-based substitutes can offer a sustainable alternative to dairy products.

Kinetic measurement of 2-aminopurine X cytosine and 2-aminopurine X thymine base pairs as a test of DNA polymerase fidelity mechanisms.

PubMed Central

Watanabe, S M; Goodman, M F

1982-01-01

Enzyme kinetic measurements are presented showing that Km rather than maximum velocity (Vmax) discrimination governs the frequency of forming 2-aminopurine X cytosine base mispairs by DNA polymerase alpha. An in vitro system is used in which incorporation of dTMP or dCMP occurs opposite a template 2-aminopurine, and values for Km and Vmax are obtained. Results from a previous study in which dTTP and dCTP were competing simultaneously for insertion opposite 2-aminopurine indicated that dTMP is inserted 22 times more frequently than dCMP. We now report that the ratio of Km values KCm/KTm = 25 +/- 6, which agrees quantitatively with the dTMP/dCMP incorporation ratio obtained previously. We also report that VCmax is indistinguishable from VTmax. These Km and Vmax data are consistent with predictions from a model, the Km discrimination model, in which replication fidelity is determined by free energy differences between matched and mismatched base pairs. Central to this model is the prediction that the ratio of Km values for insertion of correct and incorrect nucleotides specifies the insertion fidelity, and the maximum velocities of insertion are the same for both nucleotides. PMID:6959128

Chronic behavior evaluation of a micro-machined neural implant with optimized design based on an experimentally derived model.

PubMed

Andrei, Alexandru; Welkenhuysen, Marleen; Ameye, Lieveke; Nuttin, Bart; Eberle, Wolfgang

2011-01-01

Understanding the mechanical interactions between implants and the surrounding tissue is known to have an important role for improving the bio-compatibility of such devices. Using a recently developed model, a particular micro-machined neural implant design aiming the reduction of insertion forces dependence on the insertion speed was optimized. Implantations with 10 and 100 μm/s insertion speeds showed excellent agreement with the predicted behavior. Lesion size, gliosis (GFAP), inflammation (ED1) and neuronal cells density (NeuN) was evaluated after 6 week of chronic implantation showing no insertion speed dependence.

MutAid: Sanger and NGS Based Integrated Pipeline for Mutation Identification, Validation and Annotation in Human Molecular Genetics.

PubMed

Pandey, Ram Vinay; Pabinger, Stephan; Kriegner, Albert; Weinhäusel, Andreas

2016-01-01

Traditional Sanger sequencing as well as Next-Generation Sequencing have been used for the identification of disease causing mutations in human molecular research. The majority of currently available tools are developed for research and explorative purposes and often do not provide a complete, efficient, one-stop solution. As the focus of currently developed tools is mainly on NGS data analysis, no integrative solution for the analysis of Sanger data is provided and consequently a one-stop solution to analyze reads from both sequencing platforms is not available. We have therefore developed a new pipeline called MutAid to analyze and interpret raw sequencing data produced by Sanger or several NGS sequencing platforms. It performs format conversion, base calling, quality trimming, filtering, read mapping, variant calling, variant annotation and analysis of Sanger and NGS data under a single platform. It is capable of analyzing reads from multiple patients in a single run to create a list of potential disease causing base substitutions as well as insertions and deletions. MutAid has been developed for expert and non-expert users and supports four sequencing platforms including Sanger, Illumina, 454 and Ion Torrent. Furthermore, for NGS data analysis, five read mappers including BWA, TMAP, Bowtie, Bowtie2 and GSNAP and four variant callers including GATK-HaplotypeCaller, SAMTOOLS, Freebayes and VarScan2 pipelines are supported. MutAid is freely available at https://sourceforge.net/projects/mutaid.

MutAid: Sanger and NGS Based Integrated Pipeline for Mutation Identification, Validation and Annotation in Human Molecular Genetics

PubMed Central

Pandey, Ram Vinay; Pabinger, Stephan; Kriegner, Albert; Weinhäusel, Andreas

2016-01-01

Traditional Sanger sequencing as well as Next-Generation Sequencing have been used for the identification of disease causing mutations in human molecular research. The majority of currently available tools are developed for research and explorative purposes and often do not provide a complete, efficient, one-stop solution. As the focus of currently developed tools is mainly on NGS data analysis, no integrative solution for the analysis of Sanger data is provided and consequently a one-stop solution to analyze reads from both sequencing platforms is not available. We have therefore developed a new pipeline called MutAid to analyze and interpret raw sequencing data produced by Sanger or several NGS sequencing platforms. It performs format conversion, base calling, quality trimming, filtering, read mapping, variant calling, variant annotation and analysis of Sanger and NGS data under a single platform. It is capable of analyzing reads from multiple patients in a single run to create a list of potential disease causing base substitutions as well as insertions and deletions. MutAid has been developed for expert and non-expert users and supports four sequencing platforms including Sanger, Illumina, 454 and Ion Torrent. Furthermore, for NGS data analysis, five read mappers including BWA, TMAP, Bowtie, Bowtie2 and GSNAP and four variant callers including GATK-HaplotypeCaller, SAMTOOLS, Freebayes and VarScan2 pipelines are supported. MutAid is freely available at https://sourceforge.net/projects/mutaid. PMID:26840129

Interface thermal conductance characterization by infrared thermography: A tool for the study of insertions in bronze ancient Statuary

NASA Astrophysics Data System (ADS)

Mercuri, F.; Caruso, G.; Orazi, N.; Zammit, U.; Cicero, C.; Colacicchi Alessandri, O.; Ferretti, M.; Paoloni, S.

2018-05-01

In this paper, a new method based on the use of infrared thermography is proposed for the characterization of repairs and inserted parts on ancient bronzes. In particular, the quality of the contact between different kind of insertions and the main body of bronze statues is investigated by analysing the heat conduction process occurring across the interface between them. The thermographic results have been used to establish the nature of these inserted elements and the way they have been coupled to the main body of the statue during and after the manufacturing process. A model for the heat conduction based on the numerical finite elements method has been applied to compare the obtained results to the theoretical predictions. Measurements have been first carried out on test samples and then in the field on the Boxer at Rest (Museo Nazionale Romano in Rome), a masterpiece of the Greek Statuary, which contains a large variety of inserted items and repairs which are typical of the manufacturing process of bronze artefacts in general.

Determination of Membrane-Insertion Free Energies by Molecular Dynamics Simulations

PubMed Central

Gumbart, James; Roux, Benoît

2012-01-01

The accurate prediction of membrane-insertion probability for arbitrary protein sequences is a critical challenge to identifying membrane proteins and determining their folded structures. Although algorithms based on sequence statistics have had moderate success, a complete understanding of the energetic factors that drive the insertion of membrane proteins is essential to thoroughly meeting this challenge. In the last few years, numerous attempts to define a free-energy scale for amino-acid insertion have been made, yet disagreement between most experimental and theoretical scales persists. However, for a recently resolved water-to-bilayer scale, it is found that molecular dynamics simulations that carefully mimic the conditions of the experiment can reproduce experimental free energies, even when using the same force field as previous computational studies that were cited as evidence of this disagreement. Therefore, it is suggested that experimental and simulation-based scales can both be accurate and that discrepancies stem from disparities in the microscopic processes being considered rather than methodological errors. Furthermore, these disparities make the development of a single universally applicable membrane-insertion free energy scale difficult. PMID:22385850

A Risk Based Approach to Node Insertion Within Social Networks

DTIC Science & Technology

2015-03-26

changes to enemy networks, tactical involvement must evolve, beginning with the intelligent use of network infiltration through the application of the...counterterrorism begins with the intelligent use of network infiltration, or the covert insertion of assets into a network, otherwise known as node insertion. The...Federal Bureau of Intelligence (FBI) defines an undercover operation as “an investigation involving a series of related undercover activities over a

Membrane Insertion Profiles of Peptides Probed by Molecular Dynamics Simulations

DTIC Science & Technology

2008-07-17

Membrane insertion profiles of peptides probed by molecular dynamics simulations In-Chul Yeh,* Mark A. Olson,# Michael S. Lee,*#§ and Anders...a methodology based on molecular dynamics simulation techniques to probe the insertion profiles of small peptides across the membrane interface. The...profiles of peptides probed by molecular dynamics simulations 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d

App-based serious gaming for training of chest tube insertion: study protocol for a randomized controlled trial.

PubMed

Friedrich, Mirco; Bergdolt, Christian; Haubruck, Patrick; Bruckner, Thomas; Kowalewski, Karl-Friedrich; Müller-Stich, Beat Peter; Tanner, Michael C; Nickel, Felix

2017-02-06

Chest tube insertion is a standard intervention for management of various injuries of the thorax. Quick and accurate execution facilitates efficient therapy without further complications. Here, we propose a new training concept comprised of e-learning elements as well as continuous rating using an objective structured assessment of technical skills (OSATS) tool. The study protocol is presented for a randomized trial to evaluate e-learning with app-based serious gaming for chest drain insertion. The proposed randomized trial will be carried out at the Department of Orthopedics and Traumatology at Heidelberg University in the context of regular curricular teaching for medical students (n = 90, 3rd to 6th year). The intervention group will use e-learning with the serious gaming app Touch Surgery (TM) for chest drain insertion, whereas the control group uses serious gaming for an unrelated procedure. Primary endpoint is operative performance of chest drain insertion in a porcine cadaveric model according to OSATS. The randomized trial will help determine the value of e-learning with the serious gaming app Touch Surgery (TM) for chest drain insertion by using the OSATS score. The study will improve surgical training for trauma situations. Trial Registration Number, DRKS00009994 . Registered on 27 May 2016.

Applying School Administrators' Authentic Leadership Skills in Conflict Situations: The Perceptions of Substitute Teachers

ERIC Educational Resources Information Center

Demirdag, Seyithan; Kalafat, Sezai

2016-01-01

This study mainly aimed to determine the relationships between conflict management strategies and authentic leadership attitudes of primary school administrators based on the perception of substitute teachers, who were in pedagogical proficiency classes at a university. This quantitative study included 456 substitute teachers. Two instruments were…

Brooke-Spiegler syndrome: report of 10 patients from 8 families with novel germline mutations: evidence of diverse somatic mutations in the same patient regardless of tumor type.

PubMed

Sima, Radek; Vanecek, Tomas; Kacerovska, Denisa; Trubac, Pavel; Cribier, Bernard; Rutten, Arno; Vazmitel, Marina; Spagnolo, Dominic V; Litvik, Radek; Vantuchova, Yvetta; Weyers, Wolfgang; Pearce, Robert L; Pearn, John; Michal, Michal; Kazakov, Dmitry V

2010-06-01

Brooke-Spiegler syndrome (BSS) is an inherited autosomal dominant disease characterized by the development of multiple adnexal cutaneous neoplasms including spiradenoma, cylindroma, spiradenocylindroma, and trichoepithelioma (cribriform trichoblastoma). BSS patients have various mutations in the CYLD gene, a tumor suppressor gene located on chromosome 16q. Our search of the literature revealed 51 germline CYLD mutations reported to date. Somatic CYLD mutations have rarely been investigated. We studied 10 patients from 8 families with BSS. Analysis of germline mutations of the CYLD gene was performed using either peripheral blood or nontumorous tissue. In addition, 19 formalin-fixed paraffin-embedded tumor samples were analyzed for somatic mutations, including loss of heterozygosity studies. A total of 38 tumors were available for histopathologic review. We have identified 8 novel germline mutations, all of which consisted of substitutions, deletions, and insertions/duplications and all except one led to premature stop codons. The substitution mutation in a single case was also predicted to disrupt protein function and seems causally implicated in tumor formation. We demonstrate for the first time that somatic events, loss of heterozygosity, or sequence mutations may differ among multiple neoplasms even of the same histologic type, occurring in the same patient.

Evolution of the Male-Determining Gene SRY Within the Cat Family Felidae

PubMed Central

King, V.; Goodfellow, P. N.; Wilkerson, A. J. Pearks; Johnson, W. E.; O'Brien, S. J.; Pecon-Slattery, J.

2007-01-01

In most placental mammals, SRY is a single-copy gene located on the Y chromosome and is the trigger for male sex determination during embryonic development. Here, we present comparative genomic analyses of SRY (705 bp) along with the adjacent noncoding 5′ flank (997 bp) and 3′ flank (948 bp) in 36 species of the cat family Felidae. Phylogenetic analyses indicate that the noncoding genomic flanks and SRY closely track species divergence. However, several inconsistencies are observed in SRY. Overall, the gene exhibits purifying selection to maintain function (ω = 0.815) yet SRY is under positive selection in two of the eight felid lineages. SRY has low numbers of nucleotide substitutions, yet most encode amino acid changes between species, and four different species have significantly altered SRY due to insertion/deletions. Moreover, fixation of nonsynonymous substitutions between sister taxa is not consistent and may occur rapidly, as in the case of domestic cat, or not at all over long periods of time, as observed within the Panthera lineage. The former resembles positive selection during speciation, and the latter purifying selection to maintain function. Thus, SRY evolution in cats likely reflects the different phylogeographic histories, selection pressures, and patterns of speciation in modern felids. PMID:17277366

Targeted mutagenesis in cotton (Gossypium hirsutum L.) using the CRISPR/Cas9 system

PubMed Central

Chen, Xiugui; Lu, Xuke; Shu, Na; Wang, Shuai; Wang, Junjuan; Wang, Delong; Guo, Lixue; Ye, Wuwei

2017-01-01

The CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas9 system has been widely used for genome editing in various plants because of its simplicity, high efficiency and design flexibility. However, to our knowledge, there is no report on the application of CRISPR/Cas9-mediated targeted mutagenesis in cotton. Here, we report the genome editing and targeted mutagenesis in upland cotton (Gossypium hirsutum L., hereafter cotton) using the CRISPR/Cas9 system. We designed two guide RNAs to target distinct sites of the cotton Cloroplastos alterados 1 (GhCLA1) and vacuolar H+-pyrophosphatase (GhVP) genes. Mutations in these two genes were detected in cotton protoplasts. Most of the mutations were nucleotide substitutions, with one nucleotide insertion and one substitution found in GhCLA1 and one deletion found in GhVP in cotton protoplasts. Subsequently, the two vectors were transformed into cotton shoot apexes through Agrobacterium-mediated transformation, resulting in efficient target gene editing. Most of the mutations were nucleotide deletions, and the mutation efficiencies were 47.6–81.8% in transgenic cotton plants. Evaluation using restriction-enzyme-PCR assay and sequence analysis detected no off-target mutations. Our results indicated that the CRISPR/Cas9 system was an efficient and specific tool for targeted mutagenesis of the cotton genome. PMID:28287154

Targeted mutagenesis in cotton (Gossypium hirsutum L.) using the CRISPR/Cas9 system.

PubMed

Chen, Xiugui; Lu, Xuke; Shu, Na; Wang, Shuai; Wang, Junjuan; Wang, Delong; Guo, Lixue; Ye, Wuwei

2017-03-13

The CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas9 system has been widely used for genome editing in various plants because of its simplicity, high efficiency and design flexibility. However, to our knowledge, there is no report on the application of CRISPR/Cas9-mediated targeted mutagenesis in cotton. Here, we report the genome editing and targeted mutagenesis in upland cotton (Gossypium hirsutum L., hereafter cotton) using the CRISPR/Cas9 system. We designed two guide RNAs to target distinct sites of the cotton Cloroplastos alterados 1 (GhCLA1) and vacuolar H + -pyrophosphatase (GhVP) genes. Mutations in these two genes were detected in cotton protoplasts. Most of the mutations were nucleotide substitutions, with one nucleotide insertion and one substitution found in GhCLA1 and one deletion found in GhVP in cotton protoplasts. Subsequently, the two vectors were transformed into cotton shoot apexes through Agrobacterium-mediated transformation, resulting in efficient target gene editing. Most of the mutations were nucleotide deletions, and the mutation efficiencies were 47.6-81.8% in transgenic cotton plants. Evaluation using restriction-enzyme-PCR assay and sequence analysis detected no off-target mutations. Our results indicated that the CRISPR/Cas9 system was an efficient and specific tool for targeted mutagenesis of the cotton genome.

Extracting atomic numbers and electron densities from a dual source dual energy CT scanner: experiments and a simulation model.

PubMed

Landry, Guillaume; Reniers, Brigitte; Granton, Patrick Vincent; van Rooijen, Bart; Beaulieu, Luc; Wildberger, Joachim E; Verhaegen, Frank

2011-09-01

Dual energy CT (DECT) imaging can provide both the electron density ρ(e) and effective atomic number Z(eff), thus facilitating tissue type identification. This paper investigates the accuracy of a dual source DECT scanner by means of measurements and simulations. Previous simulation work suggested improved Monte Carlo dose calculation accuracy when compared to single energy CT for low energy photon brachytherapy, but lacked validation. As such, we aim to validate our DECT simulation model in this work. A cylindrical phantom containing tissue mimicking inserts was scanned with a second generation dual source scanner (SOMATOM Definition FLASH) to obtain Z(eff) and ρ(e). A model of the scanner was designed in ImaSim, a CT simulation program, and was used to simulate the experiment. Accuracy of measured Z(eff) (labelled Z) was found to vary from -10% to 10% from low to high Z tissue substitutes while the accuracy on ρ(e) from DECT was about 2.5%. Our simulation reproduced the experiments within ±5% for both Z and ρ(e). A clinical DECT scanner was able to extract Z and ρ(e) of tissue substitutes. Our simulation tool replicates the experiments within a reasonable accuracy. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Bone tissue reactions to biomimetic ion-substituted apatite surfaces on titanium implants.

PubMed

Ballo, Ahmed M; Xia, Wei; Palmquist, Anders; Lindahl, Carl; Emanuelsson, Lena; Lausmaa, Jukka; Engqvist, Håkan; Thomsen, Peter

2012-07-07

The aim of this study was to evaluate the bone tissue response to strontium- and silicon-substituted apatite (Sr-HA and Si-HA) modified titanium (Ti) implants. Sr-HA, Si-HA and HA were grown on thermally oxidized Ti implants by a biomimetic process. Oxidized implants were used as controls. Surface properties, i.e. chemical composition, surface thickness, morphology/pore characteristics, crystal structure and roughness, were characterized with various analytical techniques. The implants were inserted in rat tibiae and block biopsies were prepared for histology, histomorphometry and scanning electron microscopy analysis. Histologically, new bone formed on all implant surfaces. The bone was deposited directly onto the Sr-HA and Si-HA implants without any intervening soft tissue. The statistical analysis showed significant higher amount of bone-implant contact (BIC) for the Si-doped HA modification (P = 0.030), whereas significant higher bone area (BA) for the Sr-doped HA modification (P = 0.034), when compared with the non-doped HA modification. The differences were most pronounced at the early time point. The healing time had a significant impact for both BA and BIC (P < 0.001). The present results show that biomimetically prepared Si-HA and Sr-HA on Ti implants provided bioactivity and promoted early bone formation.

HIP1 propagates in cyanobacterial DNA via nucleotide substitutions but promotes excision at similar frequencies in Escherichia coli and Synechococcus PCC 7942.

PubMed

Robinson, P J; Cranenburgh, R M; Head, I M; Robinson, N J

1997-04-01

The sequence 5'-GCGATCGC-3', designated HIP1, for highly iterated palindrome, was first identified at the borders of a gene-deletion event and subsequently shown to constitute up to 2.5% of the DNA in some cyanobacteria. It is now reported that HIP1 is polyphyletic, occurring in several distinct cyanobacterial lineages and not defining a clade. HIP1 does not introduce gaps into sequence alignments. It aligns with partial HIP1 sites in related sequences showing that it propagates by nucleotide substitutions rather than insertion. Constructs have been created to determine the frequencies at which deletion events occur between palindromes located within the selectable marker neo. Deletion between HIP1 sites was more frequent in Synechococcus PCC 7942 than deletion between control palindromes, 5'-CCGATCGG-3', designated PAL0. However, this is not due to a recombinase that recognises HIP1 and is peculiar to cyanobacteria because similar deletion frequencies were detected in Escherichia coli. Furthermore, the frequency of deletion of DNA flanked asymmetrically by one HIP1 site and one PAL0 site was less than the frequency of deletion of DNA flanked asymmetrically by identical copies of either palindrome. This is consistent with deletion by copy-choice.

Mitochondrial DNA sequence analysis of four Alzheimer`s and Parkinson`s disease patients

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

Brown, M.D.; Shoffner, J.M.; Wallace, D.C.

1996-01-22

The mitochondrial DNA (mtDNA) sequence was determined on 3 patients with Alzheimer`s disease (AD) exhibiting AD plus Parkinson`s disease (PD) neuropathologic changes and one patient with PD. Patient mtDNA sequences were compared to the standard Cambridge sequence to identify base changes. In the first AD + PD patient, 2 of the 15 nucleotide substitutions may contribute to the neuropathology, a nucleotide pair (np) 4336 transition in the tRNA{sup Gln} gene found 7.4 times more frequently in patients than in controls, and a unique np 721 transition in the 12S rRNA gene which was not found in 70 other patients ormore » 905 controls. In the second AD + PD patient, 27 nucleotide substitutions were detected, including an np 3397 transition in the ND1 gene which converts a conserved methionine to a valine. In the third AD + PD patient, 2 polymorphic base substitutions frequently found at increased frequency in Leber`s hereditary optic neuropathy patients were observed, an np 4216 transition in ND1 and an np 13708 transition in the ND5 gene. For the PD patient, 2 novel variants were observed among 25 base substitutions, an np 1709 substitution in the 16S rRNA gene and an np 15851 missense mutation in the cytb gene. Further studies will be required to demonstrate a casual role for these base substitutions in neurodegenerative disease. 68 refs., 2 tabs.« less

The Sequences of 1504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies.

PubMed

Li, Guotian; Jain, Rashmi; Chern, Mawsheng; Pham, Nikki T; Martin, Joel A; Wei, Tong; Schackwitz, Wendy S; Lipzen, Anna M; Duong, Phat Q; Jones, Kyle C; Jiang, Liangrong; Ruan, Deling; Bauer, Diane; Peng, Yi; Barry, Kerrie W; Schmutz, Jeremy; Ronald, Pamela C

2017-06-01

The availability of a whole-genome sequenced mutant population and the cataloging of mutations of each line at a single-nucleotide resolution facilitate functional genomic analysis. To this end, we generated and sequenced a fast-neutron-induced mutant population in the model rice cultivar Kitaake ( Oryza sativa ssp japonica ), which completes its life cycle in 9 weeks. We sequenced 1504 mutant lines at 45-fold coverage and identified 91,513 mutations affecting 32,307 genes, i.e., 58% of all rice genes. We detected an average of 61 mutations per line. Mutation types include single-base substitutions, deletions, insertions, inversions, translocations, and tandem duplications. We observed a high proportion of loss-of-function mutations. We identified an inversion affecting a single gene as the causative mutation for the short-grain phenotype in one mutant line. This result reveals the usefulness of the resource for efficient, cost-effective identification of genes conferring specific phenotypes. To facilitate public access to this genetic resource, we established an open access database called KitBase that provides access to sequence data and seed stocks. This population complements other available mutant collections and gene-editing technologies. This work demonstrates how inexpensive next-generation sequencing can be applied to generate a high-density catalog of mutations. © 2017 American Society of Plant Biologists. All rights reserved.

The Sequences of 1,504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies

DOE PAGES

Li, Guotian; Jain, Rashmi; Chern, Mawsheng; ...

2017-06-02

The availability of a whole-genome sequenced mutant population and the cataloging of mutations of each line at a single-nucleotide resolution facilitate functional genomic analysis. To this end, we generated and sequenced a fast-neutron-induced mutant population in the model rice cultivar Kitaake (Oryza sativa ssp japonica), which completes its life cycle in 9 weeks. We sequenced 1504 mutant lines at 45-fold coverage and identified 91,513 mutations affecting 32,307 genes, i.e., 58% of all rice genes. We detected an average of 61 mutations per line. Mutation types include single-base substitutions, deletions, insertions, inversions, translocations, and tandem duplications. We observed a high proportionmore » of loss-of-function mutations. We identified an inversion affecting a single gene as the causative mutation for the short-grain phenotype in one mutant line. This result reveals the usefulness of the resource for efficient, cost-effective identification of genes conferring specific phenotypes. To facilitate public access to this genetic resource, we established an open access database called KitBase that provides access to sequence data and seed stocks. This population complements other available mutant collections and gene-editing technologies. In conclusion, this work demonstrates how inexpensive next-generation sequencing can be applied to generate a high-density catalog of mutations.« less

Targeted gene knock-in by homology-directed genome editing using Cas9 ribonucleoprotein and AAV donor delivery.

PubMed

Gaj, Thomas; Staahl, Brett T; Rodrigues, Gonçalo M C; Limsirichai, Prajit; Ekman, Freja K; Doudna, Jennifer A; Schaffer, David V

2017-06-20

Realizing the full potential of genome editing requires the development of efficient and broadly applicable methods for delivering programmable nucleases and donor templates for homology-directed repair (HDR). The RNA-guided Cas9 endonuclease can be introduced into cells as a purified protein in complex with a single guide RNA (sgRNA). Such ribonucleoproteins (RNPs) can facilitate the high-fidelity introduction of single-base substitutions via HDR following co-delivery with a single-stranded DNA oligonucleotide. However, combining RNPs with transgene-containing donor templates for targeted gene addition has proven challenging, which in turn has limited the capabilities of the RNP-mediated genome editing toolbox. Here, we demonstrate that combining RNP delivery with naturally recombinogenic adeno-associated virus (AAV) donor vectors enables site-specific gene insertion by homology-directed genome editing. Compared to conventional plasmid-based expression vectors and donor templates, we show that combining RNP and AAV donor delivery increases the efficiency of gene addition by up to 12-fold, enabling the creation of lineage reporters that can be used to track the conversion of striatal neurons from human fibroblasts in real time. These results thus illustrate the potential for unifying nuclease protein delivery with AAV donor vectors for homology-directed genome editing. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Muver, a computational framework for accurately calling accumulated mutations.

PubMed

Burkholder, Adam B; Lujan, Scott A; Lavender, Christopher A; Grimm, Sara A; Kunkel, Thomas A; Fargo, David C

2018-05-09

Identification of mutations from next-generation sequencing data typically requires a balance between sensitivity and accuracy. This is particularly true of DNA insertions and deletions (indels), that can impart significant phenotypic consequences on cells but are harder to call than substitution mutations from whole genome mutation accumulation experiments. To overcome these difficulties, we present muver, a computational framework that integrates established bioinformatics tools with novel analytical methods to generate mutation calls with the extremely low false positive rates and high sensitivity required for accurate mutation rate determination and comparison. Muver uses statistical comparison of ancestral and descendant allelic frequencies to identify variant loci and assigns genotypes with models that include per-sample assessments of sequencing errors by mutation type and repeat context. Muver identifies maximally parsimonious mutation pathways that connect these genotypes, differentiating potential allelic conversion events and delineating ambiguities in mutation location, type, and size. Benchmarking with a human gold standard father-son pair demonstrates muver's sensitivity and low false positive rates. In DNA mismatch repair (MMR) deficient Saccharomyces cerevisiae, muver detects multi-base deletions in homopolymers longer than the replicative polymerase footprint at rates greater than predicted for sequential single-base deletions, implying a novel multi-repeat-unit slippage mechanism. Benchmarking results demonstrate the high accuracy and sensitivity achieved with muver, particularly for indels, relative to available tools. Applied to an MMR-deficient Saccharomyces cerevisiae system, muver mutation calls facilitate mechanistic insights into DNA replication fidelity.

A deep intronic mutation in the SLC12A3 gene leads to Gitelman syndrome.

PubMed

Nozu, Kandai; Iijima, Kazumoto; Nozu, Yoshimi; Ikegami, Ei; Imai, Takehide; Fu, Xue Jun; Kaito, Hiroshi; Nakanishi, Koichi; Yoshikawa, Norishige; Matsuo, Masafumi

2009-11-01

Many mutations have been detected in the SLC12A3 gene of Gitelman syndrome (GS, OMIM 263800) patients. In previous studies, only one mutant allele was detected in approximately 20 to 41% of patients with GS; however, the exact reason for the nonidentification has not been established. In this study, we used RT-PCR using mRNA to investigate for the first time transcript abnormalities caused by deep intronic mutation. Direct sequencing analysis of leukocyte DNA identified one base insertion in exon 6 (c.818_819insG), but no mutation was detected in another allele. We analyzed RNA extracted from leukocytes and urine sediments and detected unknown sequence containing 238bp between exons 13 and 14. The genomic DNA analysis of intron 13 revealed a single-base substitution (c.1670-191C>T) that creates a new donor splice site within the intron resulting in the inclusion of a novel cryptic exon in mRNA. This is the first report of creation of a splice site by a deep intronic single-nucleotide change in GS and the first report to detect the onset mechanism in a patient with GS and missing mutation in one allele. This molecular onset mechanism may partly explain the poor success rate of mutation detection in both alleles of patients with GS.

Minimal domain of bacterial phytochrome required for chromophore binding and fluorescence

NASA Astrophysics Data System (ADS)

Rumyantsev, Konstantin A.; Shcherbakova, Daria M.; Zakharova, Natalia I.; Emelyanov, Alexander V.; Turoverov, Konstantin K.; Verkhusha, Vladislav V.

2015-12-01

Fluorescent proteins (FP) are used to study various biological processes. Recently, a series of near-infrared (NIR) FPs based on bacterial phytochromes was developed. Finding ways to improve NIR FPs is becoming progressively important. By applying rational design and molecular evolution we have engineered R. palustris bacterial phytochrome into a single-domain NIR FP of 19.6 kDa, termed GAF-FP, which is 2-fold and 1.4-fold smaller than bacterial phytochrome-based NIR FPs and GFP-like proteins, respectively. Engineering of GAF-FP involved a substitution of 15% of its amino acids and a deletion of the knot structure. GAF-FP covalently binds two tetrapyrrole chromophores, biliverdin (BV) and phycocyanobilin (PCB). With the BV chromophore GAF-FP absorbs at 635 nm and fluoresces at 670 nm. With the PCB chromophore GAF-FP becomes blue-shifted and absorbs at 625 nm and fluoresces at 657 nm. The GAF-FP structure has a high tolerance to small peptide insertions. The small size of GAF-FP and its additional absorbance band in the violet range has allowed for designing a chimeric protein with Renilla luciferase. The chimera exhibits efficient non-radiative energy transfer from luciferase to GAF-FP, resulting in NIR bioluminescence. This study opens the way for engineering of small NIR FPs and NIR luciferases from bacterial phytochromes.

A data-driven soft sensor for needle deflection in heterogeneous tissue using just-in-time modelling.

PubMed

Rossa, Carlos; Lehmann, Thomas; Sloboda, Ronald; Usmani, Nawaid; Tavakoli, Mahdi

2017-08-01

Global modelling has traditionally been the approach taken to estimate needle deflection in soft tissue. In this paper, we propose a new method based on local data-driven modelling of needle deflection. External measurement of needle-tissue interactions is collected from several insertions in ex vivo tissue to form a cloud of data. Inputs to the system are the needle insertion depth, axial rotations, and the forces and torques measured at the needle base by a force sensor. When a new insertion is performed, the just-in-time learning method estimates the model outputs given the current inputs to the needle-tissue system and the historical database. The query is compared to every observation in the database and is given weights according to some similarity criteria. Only a subset of historical data that is most relevant to the query is selected and a local linear model is fit to the selected points to estimate the query output. The model outputs the 3D deflection of the needle tip and the needle insertion force. The proposed approach is validated in ex vivo multilayered biological tissue in different needle insertion scenarios. Experimental results in five different case studies indicate an accuracy in predicting needle deflection of 0.81 and 1.24 mm in the horizontal and vertical lanes, respectively, and an accuracy of 0.5 N in predicting the needle insertion force over 216 needle insertions.

A MEMS disk resonator-based band pass filter electrical equivalent circuit simulation

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

Sundaram, G. M.; Angira, Mahesh; Gupta, Navneet

In this paper, coupled beam bandpass Disk filter is designed for 1 MHz bandwidth. Filter electrical equivalent circuit simulation is performed using circuit simulators. Important filter parameters such as insertion loss, shape factor and Q factor aresetimated using coventorware simulation. Disk resonator based radial contour mode filter provides 1.5 MHz bandwidth and unloaded quality factor of resonator and filter as 233480, 21797 respectively. From the simulation result it’s found that insertion loss minimum is 151.49 dB, insertion loss maximum is 213.94 dB, and 40 dB shape factor is 4.17.

Alternative method for predicting optimal insertion depth of the laryngeal tube in children.

PubMed

Kim, J T; Jeon, S Y; Kim, C S; Kim, S D; Kim, H S

2007-11-01

Little information is available about the accuracy of the teeth mark on the laryngeal tube (LT) as a guide to correct placement in children. The aim of this crossover study was to evaluate three methods for optimal insertion depth of the size (#) 2 tube in children weighing 12-25 kg. In 24 children, the LT #2 was consecutively inserted by three different methods: (A) until the thick teeth mark on the tube was aligned with the upper incisors, (B) until resistance was felt, and (C) by inserting to a depth, previously measured, of the curved distance between the cricoid cartilage and the upper incisor. In each case, the depth of insertion, the degree of effective ventilation, the presence of leakage, and the fibreoptic view were assessed. Insertion based on the teeth mark led to a shorter insertion depth and a greater incidence of inadequate ventilation compared with the other two methods. There was no difference in the adequacy of ventilation between methods B and C. The vocal cords were more easily identified with methods B (62.5%) and C (75%) than with method A (12.5%). Insertion of the LT #2 aligned with the teeth mark can result in a shallow insertion depth and inadequate ventilation. The measured distance from the cricoid cartilage to the upper incisor offers alternative guidance for correct LT insertion.

Human Kinematics of Cochlear Implant Surgery: An Investigation of Insertion Micro-Motions and Speed Limitations.

PubMed

Kesler, Kyle; Dillon, Neal P; Fichera, Loris; Labadie, Robert F

2017-09-01

Objectives Document human motions associated with cochlear implant electrode insertion at different speeds and determine the lower limit of continuous insertion speed by a human. Study Design Observational. Setting Academic medical center. Subjects and Methods Cochlear implant forceps were coupled to a frame containing reflective fiducials, which enabled optical tracking of the forceps' tip position in real time. Otolaryngologists (n = 14) performed mock electrode insertions at different speeds based on recommendations from the literature: "fast" (96 mm/min), "stable" (as slow as possible without stopping), and "slow" (15 mm/min). For each insertion, the following metrics were calculated from the tracked position data: percentage of time at prescribed speed, percentage of time the surgeon stopped moving forward, and number of direction reversals (ie, going from forward to backward motion). Results Fast insertion trials resulted in better adherence to the prescribed speed (45.4% of the overall time), no motion interruptions, and no reversals, as compared with slow insertions (18.6% of time at prescribed speed, 15.7% stopped time, and an average of 18.6 reversals per trial). These differences were statistically significant for all metrics ( P < .01). The metrics for the fast and stable insertions were comparable; however, stable insertions were performed 44% slower on average. The mean stable insertion speed was 52 ± 19.3 mm/min. Conclusion Results indicate that continuous insertion of a cochlear implant electrode at 15 mm/min is not feasible for human operators. The lower limit of continuous forward insertion is 52 mm/min on average. Guidelines on manual insertion kinematics should consider this practical limit of human motion.

Target-matched insertion gain derived from three different hearing aid selection procedures.

PubMed

Punch, J L; Shovels, A H; Dickinson, W W; Calder, J H; Snead, C

1995-11-01

Three hearing aid selection procedures were compared to determine if any one was superior in producing prescribed real-ear insertion gain. For each of three subject groups, 12 in-the-ear style hearing aids with Class D circuitry and similar dispenser controls were ordered from one of three manufacturers. Subject groups were classified based on the type of information included on the hearing aid order form: (1) the subject's audiogram, (2) a three-part matrix specifying the desired maximum output, full-on gain, and frequency response slope of the hearing aid, or (3) the desired 2-cc coupler full-in grain of the hearing aid, based on real-ear coupler difference (RECD) measurements. Following electroacoustic adjustments aimed at approximating a commonly used target insertion gain formula, results revealed no significant differences among any of the three selection procedures with respect to obtaining acceptable insertion gain values.

Review: Potential Strength of Fly Ash-Based Geopolymer Paste with Substitution of Local Waste Materials with High-Temperature Effect

NASA Astrophysics Data System (ADS)

Subekti, S.; Bayuaji, R.; Darmawan, M. S.; Husin, N. A.; Wibowo, B.; Anugraha, B.; Irawan, S.; Dibiantara, D.

2017-11-01

This research provided an overview of the potential fly ash based geopolymer paste for application in building construction. Geopolymer paste with various variations of fly ash substitution with local waste material and high-temperature influence exploited with the fresh and hardened condition. The local waste material which utilized for this study were sandblasting waste, carbide waste, shell powder, bagasse ash, rice husk and bottom ash. The findings of this study indicated that fly-based geopolymer paste with local waste material substitution which had high-temperature influence ash showed a similar nature of OPC binders potentially used in civil engineering applications.

Fabrication and evaluation of an improved polymer-based cochlear electrode array for atraumatic insertion.

PubMed

Gwon, Tae Mok; Min, Kyou Sik; Kim, Jin Ho; Oh, Seung Ha; Lee, Ho Sun; Park, Min-Hyun; Kim, Sung June

2015-04-01

An atraumatic cochlear electrode array has become indispensable to high-performance cochlear implants such as electric acoustic stimulation (EAS), wherein the preservation of residual hearing is significant. For an atraumatic implantation, we propose and demonstrate a new improved design of a cochlear electrode array based on liquid crystal polymer (LCP), which can be fabricated by precise batch processes and a thermal lamination process, in contrast to conventional wire-based cochlear electrode arrays. Using a thin-film process of LCP-film-mounted silicon wafer and thermal press lamination, we devise a multi-layered structure with variable layers of LCP films to achieve a sufficient degree of basal rigidity and a flexible tip. A peripheral blind via and self-aligned silicone elastomer molding process can reduce the width of the array. Measuring the insertion and extraction forces in a human scala tympani model, we investigate five human temporal bone insertion trials and record electrically evoked auditory brainstem responses (EABR) acutely in a guinea pig model. The diameters of the finalized electrode arrays are 0.3 mm (tip) and 0.75 mm (base). The insertion force with a displacement of 8 mm from a round window and the maximum extraction force are 2.4 mN and 34.0 mN, respectively. The electrode arrays can be inserted from 360° to 630° without trauma at the basal turn. The EABR data confirm the efficacy of the array. A new design of LCP-based cochlear electrode array for atraumatic implantation is fabricated. Verification indicates that foretells the development of an atraumatic cochlear electrode array and clinical implant.

Ventricular flow dynamics with varying LVAD inflow cannula lengths: In-silico evaluation in a multiscale model.

PubMed

Liao, Sam; Neidlin, Michael; Li, Zhiyong; Simpson, Benjamin; Gregory, Shaun D

2018-04-27

Left ventricular assist devices are associated with thromboembolic events, which are potentially caused by altered intraventricular flow. Due to patient variability, differences in apical wall thickness affects cannula insertion lengths, potentially promoting unfavourable intraventricular flow patterns which are thought to be correlated to the risk of thrombosis. This study aimed to present a 3D multiscale computational fluid dynamic model of the left ventricle (LV) developed using a commercial software, Ansys, and evaluate the risk of thrombosis with varying inflow cannula insertion lengths in a severely dilated LV. Based on a HeartWare HVAD inflow cannula, insertion lengths of 5, 19, 24 and 50 mm represented cases of apical hypertrophy, typical ranges of apical thicknesses and an experimental length, respectively. The risk of thrombosis was evaluated based on blood washout, residence time, instantaneous blood stagnation and a pulsatility index. By introducing fresh blood to displace pre-existing blood in the LV, after 5 cardiac cycles, 46.7%, 45.7%, 45.1% and 41.8% of pre-existing blood remained for insertion lengths of 5, 19, 24 and 50 mm, respectively. Compared to the 50 mm insertion, blood residence time was at least 9%, 7% and 6% higher with the 5, 19 and 24 mm insertion lengths, respectively. No instantaneous stagnation at the apex was observed directly after the E-wave. Pulsatility indices adjacent to the cannula increased with shorter insertion lengths. For the specific scenario studied, a longer insertion length, relative to LV size, may be advantageous to minimise thrombosis by increasing LV washout and reducing blood residence time. Copyright © 2018 Elsevier Ltd. All rights reserved.

Amphiphilic interactions of ionic liquids with lipid biomembranes: a molecular simulation study.

PubMed

Yoo, Brian; Shah, Jindal K; Zhu, Yingxi; Maginn, Edward J

2014-11-21

Current bottlenecks in the large-scale commercial use of many ionic liquids (ILs) include their high costs, low biodegradability, and often unknown toxicities. As a proactive effort to better understand the molecular mechanisms of ionic liquid toxicities, the work herein presents a comprehensive molecular simulation study on the interactions of 1-n-alkyl-3-methylimidazolium-based ILs with a phosphatidylcholine (PC) lipid bilayer. We explore the effects of increasing alkyl chain length (n = 4, 8, and 12) in the cation and anion hydrophobicity on the interactions with the lipid bilayer. Bulk atomistic molecular dynamics (MD) simulations performed at millimolar (mM) IL concentrations show spontaneous insertion of cations into the lipid bilayer regardless of the alkyl chain length and a favorable orientational preference once a cation is inserted. Cations also exhibit the ability to "flip" inside the lipid bilayer (as is common for amphiphiles) if partially inserted with an unfavorable orientation. Moreover, structural analysis of the lipid bilayer show that cationic insertion induces roughening of the bilayer surface, which may be a precursor to bilayer disruption. To overcome the limitation in the timescale of our simulations, free energies for a single IL cation and anion insertion have been determined based on potential of mean force calculations. These results show a decrease in free energy in response to both short and long alkyl chain IL cation insertion, and likewise for a single hydrophobic anion insertion, but an increase in free energy for the insertion of a hydrophilic chloride anion. Both bulk MD simulations and free energy calculations suggest that toxicity mechanisms toward biological systems are likely caused by ILs behaving as ionic surfactants. [Yoo et al., Soft Matter, 2014].

The Novel Bacterial N-Demethylase PdmAB Is Responsible for the Initial Step of N,N-Dimethyl-Substituted Phenylurea Herbicide Degradation

PubMed Central

Gu, Tao; Zhou, Chaoyang; Sørensen, Sebastian R.; Zhang, Ji; He, Jian; Yu, Peiwen; Li, Shunpeng

2013-01-01

The environmental fate of phenylurea herbicides has received considerable attention in recent decades. The microbial metabolism of N,N-dimethyl-substituted phenylurea herbicides can generally be initiated by mono-N-demethylation. In this study, the molecular basis for this process was revealed. The pdmAB genes in Sphingobium sp. strain YBL2 were shown to be responsible for the initial mono-N-demethylation of commonly used N,N-dimethyl-substituted phenylurea herbicides. PdmAB is the oxygenase component of a bacterial Rieske non-heme iron oxygenase (RO) system. The genes pdmAB, encoding the α subunit PdmA and the β subunit PdmB, are organized in a transposable element flanked by two direct repeats of an insertion element resembling ISRh1. Furthermore, this transposable element is highly conserved among phenylurea herbicide-degrading sphingomonads originating from different areas of the world. However, there was no evidence of a gene for an electron carrier (a ferredoxin or a reductase) located in the immediate vicinity of pdmAB. Without its cognate electron transport components, expression of PdmAB in Escherichia coli, Pseudomonas putida, and other sphingomonads resulted in a functional enzyme. Moreover, coexpression of a putative [3Fe-4S]-type ferredoxin from Sphingomonas sp. strain RW1 greatly enhanced the catalytic activity of PdmAB in E. coli. These data suggested that PdmAB has a low specificity for electron transport components and that its optimal ferredoxin may be the [3Fe-4S] type. PdmA exhibited low homology to the α subunits of previously characterized ROs (less than 37% identity) and did not cluster with the RO group involved in O- or N-demethylation reactions, indicating that PdmAB is a distinct bacterial RO N-demethylase. PMID:24123738

Guided bone regeneration with a synthetic biodegradable membrane: a comparative study in dogs.

PubMed

Jung, Ronald E; Kokovic, Vladimir; Jurisic, Milan; Yaman, Duygu; Subramani, Karthikeyan; Weber, Franz E

2011-08-01

The aim of the present study was to compare a newly developed biodegradable polylactide/polyglycolide/N-methyl-2-pyrrolidone (PLGA/NMP) membrane with a standard resorbable collagen membrane (RCM) in combination with and without the use of a bone substitute material (deproteinized bovine bone mineral [DBBM]) looking at the proposed tenting effect and bone regeneration. In five adult German sheepdogs, the mandibular premolars P2, P3, P4, and the molar M1 were bilaterally extracted creating two bony defects on each site. A total of 20 dental implants were inserted and allocated to four different treatment modalities within each dog: PLGA/NMP membrane only (Test 1), PLGA/NMP membrane with DBBM (Test 2), RCM only (negative control), and RCM with DBBM (positive control). A histomorphometric analysis was performed 12 weeks after implantation. For statistical analysis, a Friedman test and subsequently a Wilcoxon signed ranks test were applied. In four out of five PLGA/NMP membrane-treated defects, the membranes had broken into pieces without the support of DBBM. This led to a worse outcome than in the RCM group. In combination with DBBM, both membranes revealed similar amounts of area of bone regeneration and bone-to-implant contact without significant differences. On the level of the third implant thread, the PLGA/NMP membrane induced more horizontal bone formation beyond the graft than the RCM. The newly developed PLGA/NMP membrane performs equally well as the RCM when applied in combination with DBBM. Without bone substitute material, the PLGA/NMP membrane performed worse than the RCM in challenging defects, and therefore, a combination with a bone substitute material is recommended. © 2010 John Wiley & Sons A/S.

Alpha S1-casein polymorphisms in camel (Camelus dromedarius) and descriptions of biological active peptides and allergenic epitopes.

PubMed

Erhardt, Georg; Shuiep, El Tahir Salih; Lisson, Maria; Weimann, Christina; Wang, Zhaoxin; El Zubeir, Ibtisam El Yas Mohamed; Pauciullo, Alfredo

2016-06-01

Milk samples of 193 camels (Camelus dromedarius) from different regions of Sudan were screened for casein variability by isoelectric focusing. Kappa-casein and beta-casein were monomorphic, whereas three protein patterns named αs1-casein A, C, and D were identified. The major allele A revealed frequencies of 0.79 (Lahaoi), 0.75 (Shanbali), 0.90 (Arabi Khali), and 0.88 (Arabi Gharbawi) in the different ecotypes. CSN1S1*C shows a single G > T nucleotide substitution in the exon 5, leading to a non-synonymous amino acid exchange (p.Glu30 > Asp30) in comparison to CSN1S1*A and D. At cDNA level, no further single nucleotide polymorphisms could be identified in CSN1S1* A, C, and D, whereas the variants CSN1S1*A and CSN1S1*C are characterized by missing of exon 18 compared to the already described CSN1S1*B, as consequence of DNA insertion of 11 bp at intron 17 which alter the pre-mRNA spliceosome machinery. A polymerase chain-restriction fragment length polymorphism method (PCR-RFLP) was established to type for G > T nucleotide substitution at genomic DNA level. The occurrence and differences of IgE-binding epitopes and bioactive peptides between αs1-casein A, C, and D after digestion were analyzed in silico. The amino acid substitutions and deletion affected the arising peptide pattern and thus modifications between IgE-binding epitopes and bioactive peptides of the variants were found. The allergenic potential of these different peptides will be investigated by microarray immunoassay using sera from milk-sensitized individuals, as it was already demonstrated for bovine αs1-casein variants.

Mutation signature in neuraminidase gene of avian influenza H9N2/G1 in Egypt.

PubMed

Mosaad, Zienab; Arafa, Abdelsatar; Hussein, Hussein A; Shalaby, Mohamed A

2017-06-01

The low pathogenic avian influenza (LPAI) H9N2 subtype has become the most prevalent and widespread in many Asian and Middle Eastern countries. It causes an enzootic situation in commercial poultry and known as a potential facilitator virus that can be transmitted to human from birds. The neuraminidase (NA) gene plays an important role the release and spread of the virus from infected cells and throughout the bird. The complete nucleotide sequences of the NA gene of seven H9N2 viruses collected from apparent healthy chicken and quail flocks in Egypt during 2014-2015, were amplified and sequenced. The phylogenetic relationships were investigated and all viruses were belonging to the A/Q/HK/G1/97 strain (G1-like). There were no insertions or deletions or shortening in NA stalk regions when compared to Y280-lineage and the human H9N2 isolates. No obvious changes NA interactions with antiviral drugs. We found that the Egyptian H9N2 viruses have seven glycosylation sites like the most recorded H9N2 viruses in the country, except A/Q/Egypt/14864V/2014 virus which has only six. The NA has four amino acid substitutions distributed in different parts of the hemadsorbing site. The most characteristic substitutions in this site were S372A and W403R these substitutions were a distinctive feature resembling to human H9N2, H2N2 and H3N2 viruses but differs from the other avian influenza viruses. These Special features of surface glycoproteins of LPAI-H9N2 viruses refer to the tendency for enhanced introductions into humans and ensuring the importance of poultry in the transfer influenza viruses.

The Application of a Homologous Recombination Assay Revealed Amino Acid Residues in an LTR-Retrotransposon That Were Critical for Integration

PubMed Central

Atwood, Angela; Choi, Jeannie; Levin, Henry L.

1998-01-01

Retroviruses and their relatives, the LTR-retrotransposons, possess an integrase protein (IN) that is required for the insertion of reverse transcripts into the genome of host cells. Schizosaccharomyces pombe is the host of Tf1, an LTR-retrotransposon with integration activity that can be studied by using techniques of yeast genetics. In this study, we sought to identify amino acid substitutions in Tf1 that specifically affected the integration step of transposition. In addition to seeking amino acid substitutions in IN, we also explored the possibility that other Tf1 proteins contributed to integration. By comparing the results of genetic assays that monitored both transposition and reverse transcription, we were able to seek point mutations throughout Tf1 that blocked transposition but not the synthesis of reverse transcripts. These mutant versions of Tf1 were candidates of elements that possessed defects in the integration step of transposition. Five mutations in Tf1 that resulted in low levels of integration were found to be located in the IN protein: two substitutions in the N-terminal Zn domain, two in the catalytic core, and one in the C-terminal domain. These results suggested that each of the three IN domains was required for Tf1 transposition. The potential role of these five amino acid residues in the function of IN is discussed. Two of the mutations that reduced integration mapped to the RNase H (RH) domain of Tf1 reverse transcriptase. The Tf1 elements with the RH mutations produced high levels of reverse transcripts, as determined by recombination and DNA blot analysis. These results indicated that the RH of Tf1 possesses a function critical for transposition that is independent of the accumulation of reverse transcripts. PMID:9445033

Novel high contrast electrochromic polymer materials based on 3,4-propylenedioxythiophene

NASA Astrophysics Data System (ADS)

Sahoo, Rabindra; Mishra, Sarada P.; Kumar, Anil; Sindhu, S.; Narasimha Rao, K.; Gopal, E. S. R.

2007-09-01

Mono and di allyl and napthyl substituted 3,4-propylenedioxythiophenes were synthesized and polymerized electrochemically. All the monomers were characterized for their molecular structures, and the polymers were characterized for their electrochemical properties. The disubstituted derivatives showed higher contrast than the corresponding mono substituted derivatives. The allyl substituted polymers showed higher contrast and faster switching time than corresponding napthyl substituted derivatives. The presence of the allyl group as the pendant can be used for further functionalization of the polymer.

Influence of mandatory generic substitution on pharmaceutical sales patterns: a national study over five years.

PubMed

Andersson, Karolina A; Petzold, Max G; Allebeck, Peter; Carlsten, Anders

2008-02-29

Mandatory generic substitution was introduced in Sweden in October 2002 in order to try to curb escalating pharmaceutical expenditure. The aim of this study was to investigate how sales patterns for substitutable and non-substitutable pharmaceuticals have developed since the introduction of mandatory generic substitution; furthermore, to compare sales patterns in different groups of the population, based on patients' age and gender. Five therapeutic groups comprising both substitutable and non-substitutable pharmaceuticals were included. The study period was from January 2000 to June 2005. National sales data were used, covering volumes of dispensed prescription medicines (expressed in defined daily doses per 1000 inhabitants and day) of each pharmacological substance in the therapeutic groups for each age and gender group. Sales patterns for substitutable and non-substitutable pharmaceuticals were compared using a descriptive approach. In most therapeutic groups there has been an increase in the volumes of substitutable pharmaceuticals sold since the introduction of the reform, ranging from one third to three times the initial volume; whereas the volumes of non-substitutable pharmaceuticals have levelled out or declined. There were few gender differences in sales patterns of substitutable and non-substitutable drugs. In three therapeutic groups, sales patterns differed across different age groups, and there was a tendency for volumes of recently introduced non-substitutable pharmaceuticals to be proportionally higher in the youngest age groups. Since the introduction of the reform, there has been a proportionally larger increase in sales of substitutable pharmaceuticals compared with sales of non-substitutable pharmaceuticals. This indicates that the reform might have contributed to larger sales of less expensive pharmaceuticals.

16 CFR 322.2 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-01-01

..., such as the Internet, online services, and software, the required disclosures shall: (i) Be consistent... television, radio, or Internet-based multi-media commercial communications, the required disclosures shall be..., brochure, newspaper, magazine, pamphlet, leaflet, circular, mailer, book insert, free standing insert...

16 CFR 322.2 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-01-01

..., such as the Internet, online services, and software, the required disclosures shall: (i) Be consistent... television, radio, or Internet-based multi-media commercial communications, the required disclosures shall be..., brochure, newspaper, magazine, pamphlet, leaflet, circular, mailer, book insert, free standing insert...

12 CFR 1015.2 - Definitions.

Code of Federal Regulations, 2013 CFR

2013-01-01

... duration of the oral disclosure; (4) In communications made through interactive media, such as the internet..., or internet-based multimedia commercial communications, the required disclosures shall be made at the..., newspaper, magazine, pamphlet, leaflet, circular, mailer, book insert, free standing insert, letter...

12 CFR 1015.2 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-01-01

... duration of the oral disclosure; (4) In communications made through interactive media, such as the internet..., or internet-based multimedia commercial communications, the required disclosures shall be made at the..., newspaper, magazine, pamphlet, leaflet, circular, mailer, book insert, free standing insert, letter...

12 CFR 1015.2 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-01-01

... duration of the oral disclosure; (4) In communications made through interactive media, such as the internet..., or internet-based multimedia commercial communications, the required disclosures shall be made at the..., newspaper, magazine, pamphlet, leaflet, circular, mailer, book insert, free standing insert, letter...

Synthesis of Aryl-Substituted 2,4-Dinitrophenylamines: Nucleophilic Aromatic Substitution as a Problem-Solving and Collaborative-Learning Approach

ERIC Educational Resources Information Center

Santos, Elvira Santos; Garcia, Irma Cruz Gavilan; Gomez, Eva Florencia Lejarazo; Vilchis-Reyes, Miguel Angel

2010-01-01

A series of experiments based on problem-solving and collaborative-learning pedagogies are described that encourage students to interpret results and draw conclusions from data. Different approaches including parallel library synthesis, solvent variation, and leaving group variation are used to study a nucleophilic aromatic substitution of…

A Simulation-Based Blended Curriculum for Short Peripheral Intravenous Catheter Insertion: An Industry-Practice Collaboration.

PubMed

Glover, Kevin R; Stahl, Brian R; Murray, Connie; LeClair, Matthew; Gallucci, Susan; King, Mary Anne; Labrozzi, Laura J; Schuster, Catherine; Keleekai, Nowai L

2017-09-01

Despite peripheral intravenous catheter (PIVC) insertion being a commonly performed skill, practicing nurses may receive little substantive education, training, or opportunities to practice this skill at a competent level. This article describes a collaboration between private industry and a hospital to modify, implement, and evaluate a simulation-based blended PIVC insertion continuing education program for staff nurses. Included is an overview of the practical and theoretical rationale for the initial development of the curriculum to address an identified PIVC insertion education gap, the collaborative modification and implementation of the program, and an evaluation of the program. The curriculum combined self-paced e-learning and classroom-based deliberate practice with simulation tools of varying fidelity in a peer-to-peer learning environment. Given the mutual challenges of resource allocation in industry training and clinical nursing education departments, interprofessional partnerships may be an effective option for sharing instructional knowledge and resources to promote innovation and improve patient care. J Contin Educ Nurs. 2017;48(9):397-406. Copyright 2017, SLACK Incorporated.

A novel adaptive needle insertion sequencing for robotic, single needle MR-guided high-dose-rate prostate brachytherapy

NASA Astrophysics Data System (ADS)

Borot de Battisti, M.; de Senneville, B. Denis; Hautvast, G.; Binnekamp, D.; Lagendijk, J. J. W.; Maenhout, M.; Moerland, M. A.

2017-05-01

MR-guided high-dose-rate (HDR) brachytherapy has gained increasing interest as a treatment for patients with localized prostate cancer because of the superior value of MRI for tumor and surrounding tissues localization. To enable needle insertion into the prostate with the patient in the MR bore, a single needle MR-compatible robotic system involving needle-by-needle dose delivery has been developed at our institution. Throughout the intervention, dose delivery may be impaired by: (1) sub-optimal needle positioning caused by e.g. needle bending, (2) intra-operative internal organ motion such as prostate rotations or swelling, or intra-procedural rectum or bladder filling. This may result in failure to reach clinical constraints. To assess the first aforementioned challenge, a recent study from our research group demonstrated that the deposited dose may be greatly improved by real-time adaptive planning with feedback on the actual needle positioning. However, the needle insertion sequence is left to the doctor and therefore, this may result in sub-optimal dose delivery. In this manuscript, a new method is proposed to determine and update automatically the needle insertion sequence. This strategy is based on the determination of the most sensitive needle track. The sensitivity of a needle track is defined as its impact on the dose distribution in case of sub-optimal positioning. A stochastic criterion is thus presented to determine each needle track sensitivity based on needle insertion simulations. To assess the proposed sequencing strategy, HDR prostate brachytherapy was simulated on 11 patients with varying number of needle insertions. Sub-optimal needle positioning was simulated at each insertion (modeled by typical random angulation errors). In 91% of the scenarios, the dose distribution improved when the needle was inserted into the most compared to the least sensitive needle track. The computation time for sequencing was less than 6 s per needle track. The proposed needle insertion sequencing can therefore assist in delivering an optimal dose in HDR prostate brachytherapy.

Automatic Multiple-Needle Surgical Planning of Robotic-Assisted Microwave Coagulation in Large Liver Tumor Therapy

PubMed Central

Liu, Shaoli; Xia, Zeyang; Liu, Jianhua; Xu, Jing; Ren, He; Lu, Tong; Yang, Xiangdong

2016-01-01

The “robotic-assisted liver tumor coagulation therapy” (RALTCT) system is a promising candidate for large liver tumor treatment in terms of accuracy and speed. A prerequisite for effective therapy is accurate surgical planning. However, it is difficult for the surgeon to perform surgical planning manually due to the difficulties associated with robot-assisted large liver tumor therapy. These main difficulties include the following aspects: (1) multiple needles are needed to destroy the entire tumor, (2) the insertion trajectories of the needles should avoid the ribs, blood vessels, and other tissues and organs in the abdominal cavity, (3) the placement of multiple needles should avoid interference with each other, (4) an inserted needle will cause some deformation of liver, which will result in changes in subsequently inserted needles’ operating environment, and (5) the multiple needle-insertion trajectories should be consistent with the needle-driven robot’s movement characteristics. Thus, an effective multiple-needle surgical planning procedure is needed. To overcome these problems, we present an automatic multiple-needle surgical planning of optimal insertion trajectories to the targets, based on a mathematical description of all relevant structure surfaces. The method determines the analytical expression of boundaries of every needle “collision-free reachable workspace” (CFRW), which are the feasible insertion zones based on several constraints. Then, the optimal needle insertion trajectory within the optimization criteria will be chosen in the needle CFRW automatically. Also, the results can be visualized with our navigation system. In the simulation experiment, three needle-insertion trajectories were obtained successfully. In the in vitro experiment, the robot successfully achieved insertion of multiple needles. The proposed automatic multiple-needle surgical planning can improve the efficiency and safety of robot-assisted large liver tumor therapy, significantly reduce the surgeon’s workload, and is especially helpful for an inexperienced surgeon. The methodology should be easy to adapt in other body parts. PMID:26982341

A Safer, Discovery-Based Nucleophilic Substitution Experiment

ERIC Educational Resources Information Center

Horowitz, Gail

2009-01-01

A discovery-based nucleophilic substitution experiment is described in which students compare the reactivity of chloride and iodide ions in an S[subscript N]2 reaction. This experiment improves upon the well-known "Competing Nucleophiles" experiment in that it does not involve the generation of hydrogen halide gas. The experiment also introduces…

Pediatric, Adolescent, and Young Adult Thyroid Carcinoma Harbors Frequent and Diverse Targetable Genomic Alterations, Including Kinase Fusions

PubMed Central

Schrock, Alexa B.; Anderson, Peter M.; Morris, John C.; Heilmann, Andreas M.; Holmes, Oliver; Wang, Kai; Johnson, Adrienne; Waguespack, Steven G.; Ou, Sai‐Hong Ignatius; Khan, Saad; Fung, Kar‐Ming; Stephens, Philip J.; Erlich, Rachel L.; Miller, Vincent A.; Ross, Jeffrey S.; Ali, Siraj M.

2017-01-01

Background. Thyroid carcinoma, which is rare in pediatric patients (age 0–18 years) but more common in adolescent and young adult (AYA) patients (age 15–39 years), carries the potential for morbidity and mortality. Methods. Hybrid‐capture‐based comprehensive genomic profiling (CGP) was performed prospectively on 512 consecutively submitted thyroid carcinomas, including 58 from pediatric and AYA (PAYA) patients, to identify genomic alterations (GAs), including base substitutions, insertions/deletions, copy number alterations, and rearrangements. This PAYA data series includes 41 patients with papillary thyroid carcinoma (PTC), 3 with anaplastic thyroid carcinoma (ATC), and 14 with medullary thyroid carcinoma (MTC). Results. GAs were detected in 93% (54/58) of PAYA cases, with a mean of 1.4 GAs per case. In addition to BRAF V600E mutations, detected in 46% (19/41) of PAYA PTC cases and in 1 of 3 AYA ATC cases, oncogenic fusions involving RET, NTRK1, NTRK3, and ALK were detected in 37% (15/41) of PAYA PTC and 33% (1/3) of AYA ATC cases. Ninety‐three percent (13/14) of MTC patients harbored RET alterations, including 3 novel insertions/deletions in exons 6 and 11. Two of these MTC patients with novel alterations in RET experienced clinical benefit from vandetanib treatment. Conclusion. CGP identified diverse clinically relevant GAs in PAYA patients with thyroid carcinoma, including 83% (34/41) of PTC cases harboring activating kinase mutations or activating kinase rearrangements. These genomic observations and index cases exhibiting clinical benefit from targeted therapy suggest that young patients with advanced thyroid carcinoma can benefit from CGP and rationally matched targeted therapy. Implications for Practice. The detection of diverse clinically relevant genomic alterations in the majority of pediatric, adolescent, and young adult patients with thyroid carcinoma in this study suggests that comprehensive genomic profiling may be beneficial for young patients with papillary, anaplastic, or medullary thyroid carcinoma, particularly for advanced or refractory cases for which clinical trials involving molecularly targeted therapies may be appropriate. PMID:28209747

Templated sequence insertion polymorphisms in the human genome

NASA Astrophysics Data System (ADS)

Onozawa, Masahiro; Aplan, Peter

2016-11-01

Templated Sequence Insertion Polymorphism (TSIP) is a recently described form of polymorphism recognized in the human genome, in which a sequence that is templated from a distant genomic region is inserted into the genome, seemingly at random. TSIPs can be grouped into two classes based on nucleotide sequence features at the insertion junctions; Class 1 TSIPs show features of insertions that are mediated via the LINE-1 ORF2 protein, including 1) target-site duplication (TSD), 2) polyadenylation 10-30 nucleotides downstream of a “cryptic” polyadenylation signal, and 3) preference for insertion at a 5’-TTTT/A-3’ sequence. In contrast, class 2 TSIPs show features consistent with repair of a DNA double-strand break via insertion of a DNA “patch” that is derived from a distant genomic region. Survey of a large number of normal human volunteers demonstrates that most individuals have 25-30 TSIPs, and that these TSIPs track with specific geographic regions. Similar to other forms of human polymorphism, we suspect that these TSIPs may be important for the generation of human diversity and genetic diseases.

Experimental evaluation of neural probe’s insertion induced injury based on digital image correlation method

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

Zhang, Wenguang, E-mail: zhwg@sjtu.edu.cn; Ma, Yakun; Li, Zhengwei

Purpose: The application of neural probes in clinic has been challenged by probes’ short lifetime when implanted into brain tissue. The primary goal is to develop an evaluation system for testing brain tissue injury induced by neural probe’s insertion using microscope based digital image correlation method. Methods: A brain tissue phantom made of silicone rubber with speckle pattern on its surface was fabricated. To obtain the optimal speckle pattern, mean intensity gradient parameter was used for quality assessment. The designed testing system consists of three modules: (a) load module for simulating neural electrode implantation process; (b) data acquisition module tomore » capture micrographs of speckle pattern and to obtain reactive forces during the insertion of the probe; (c) postprocessing module for extracting tissue deformation information from the captured speckle patterns. On the basis of the evaluation system, the effects of probe wedge angle, insertion speed, and probe streamline on insertion induced tissue injury were investigated. Results: The optimal quality speckle pattern can be attained by the following fabrication parameters: spin coating rate—1000 r/min, silicone rubber component A: silicone rubber component B: softener: graphite = 5 ml: 5 ml: 2 ml: 0.6 g. The probe wedge angle has a significant effect on tissue injury. Compared to wedge angle 40° and 20°, maximum principal strain of 60° wedge angle was increased by 40.3% and 87.5%, respectively; compared with a relatively higher speed (500 μm/s), the maximum principle strain within the tissue induced by slow insertion speed (100 μm/s) was increased by 14.3%; insertion force required by probe with convex streamline was smaller than the force of traditional probe. Based on the experimental results, a novel neural probe that has a rounded tip covered by a biodegradable silk protein coating with convex streamline was proposed, which has both lower insertion and micromotion induced tissue injury. Conclusions: The established evaluation system has provided a simulation environment for testing brain tissue injury produced by various insertion conditions. At the same time, it eliminates the adverse effect of biological factors on tissue deformation during the experiment, improving the repeatability of measurement results. As a result, the evaluation system will provide support on novel neural probe design that can reduce the acute tissue injury during the implantation of the probe.« less

A combined calorimetric and computational study of the energetics of rare earth substituted UO 2 systems

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

Zhang, Lei; Solomon, Jonathan M.; Asta, Mark

2015-09-01

The energetics of rare earth substituted UO2 solid solutions (U1-xLnxO2-0.5x+y, where Ln = La, Y, and Nd) are investigated employing a combination of calorimetric measurements and density functional theory based computations. Calculated and measured formation enthalpies agree within 10 kJ/mol for stoichiometric oxygen/metal compositions. To better understand the factors governing the stability and defect binding in rare earth substituted urania solid solutions, systematic trends in the energetics are investigated based on the present results and previous computational and experimental thermochemical studies of rare earth substituted fluorite oxides (A1-xLnxO2-0.5x, where A = Hf, Zr, Ce, and Th). A consistent trend towardsmore » increased energetic stability with larger size mismatch between the smaller host tetravalent cation and the larger rare earth trivalent cation is found for both actinide and non-actinide fluorite oxide systems where aliovalent substitution of Ln cations is compensated by oxygen vacancies. However, the large exothermic oxidation enthalpy in the UO2 based systems favors oxygen rich compositions where charge compensation occurs through the formation of uranium cations with higher oxidation states.« less

Use of a national continuing medical education meeting to provide simulation-based training in temporary hemodialysis catheter insertion skills: a pre-test post-test study.

PubMed

Clark, Edward G; Paparello, James J; Wayne, Diane B; Edwards, Cedric; Hoar, Stephanie; McQuillan, Rory; Schachter, Michael E; Barsuk, Jeffrey H

2014-01-01

Simulation-based-mastery-learning (SBML) is an effective method to train nephrology fellows to competently insert temporary, non-tunneled hemodialysis catheters (NTHCs). Previous studies of SBML for NTHC-insertion have been conducted at a local level. Determine if SBML for NTHC-insertion can be effective when provided at a national continuing medical education (CME) meeting. Describe the correlation of demographic factors, prior experience with NTHC-insertion and procedural self-confidence with simulated performance of the procedure. Pre-test - post-test study. 2014 Canadian Society of Nephrology annual meeting. Nephrology fellows, internal medicine residents and medical students. Participants were surveyed regarding demographics, prior NTHC-insertion experience, procedural self-confidence and attitudes regarding the training they received. NTHC-insertion skills were assessed using a 28-item checklist. Participants underwent a pre-test of their NTHC-insertion skills at the internal jugular site using a realistic patient simulator and ultrasound machine. Participants then had a training session that included a didactic presentation and 2 hours of deliberate practice using the simulator. On the following day, trainees completed a post-test of their NTHC-insertion skills. All participants were required to meet or exceed a minimum passing score (MPS) previously set at 79%. Trainees who did not reach the MPS were required to perform more deliberate practice until the MPS was achieved. Twenty-two individuals participated in SBML training. None met or exceeded the MPS at baseline with a median checklist score of 20 (IQR, 7.25 to 21). Seventeen of 22 participants (77%) completed post-testing and improved their scores to a median of 27 (IQR, 26 to 28; p < 0.001). All met or exceeded the MPS on their first attempt. There were no significant correlations between demographics, prior experience or procedural self-confidence with pre-test performance. Small sample-size and self-selection of participants. Costs could limit the long-term feasibility of providing this type of training at a CME conference. Despite most participants reporting having previously inserted NTHCs in clinical practice, none met the MPS at baseline; this suggests their prior training may have been inadequate.

Readability assessment of package inserts of biological medicinal products from the European medicines agency website.

PubMed

Piñero-López, Ma Ángeles; Modamio, Pilar; Lastra, Cecilia F; Mariño, Eduardo L

2014-07-01

Package inserts that accompany medicines are a common source of information aimed at patients and should match patient abilities in terms of readability. Our objective was to determine the degree of readability of the package inserts for biological medicinal products commercially available in 2007 and compare them with the readability of the same package inserts in 2010. A total of 33 package inserts were selected and classified into five groups according to the type of medicine: monoclonal antibody-based products, cytokines, therapeutic enzymes, recombinant blood factors and other blood-related products, and recombinant hormones. The package inserts were downloaded from the European Medicines Agency website in 2007 and 2010. Readability was evaluated for the entire text of five of the six sections of the package inserts and for the 'Annex' when there was one. Three readability formulas were used: SMOG (Simple Measure of Gobbledygook) grade, Flesh-Kincaid grade level, and Szigriszt's perspicuity index. No significant differences were found between the readability results for the 2007 package inserts and those from 2010 according to any of the three readability indices studied (p>0.05). However, there were significant differences (p<0.05) between the readability scores of the sections of the package inserts in both 2007 and 2010. The readability of the package inserts was above the recommended sixth grade reading level (ages 11-12) and may lead to difficulties of understanding for people with limited literacy. All the sections should be easy to read and, therefore, the readability of the medicine package inserts studied should be improved.

A Predictive Model of Intein Insertion Site for Use in the Engineering of Molecular Switches

PubMed Central

Apgar, James; Ross, Mary; Zuo, Xiao; Dohle, Sarah; Sturtevant, Derek; Shen, Binzhang; de la Vega, Humberto; Lessard, Philip; Lazar, Gabor; Raab, R. Michael

2012-01-01

Inteins are intervening protein domains with self-splicing ability that can be used as molecular switches to control activity of their host protein. Successfully engineering an intein into a host protein requires identifying an insertion site that permits intein insertion and splicing while allowing for proper folding of the mature protein post-splicing. By analyzing sequence and structure based properties of native intein insertion sites we have identified four features that showed significant correlation with the location of the intein insertion sites, and therefore may be useful in predicting insertion sites in other proteins that provide native-like intein function. Three of these properties, the distance to the active site and dimer interface site, the SVM score of the splice site cassette, and the sequence conservation of the site showed statistically significant correlation and strong predictive power, with area under the curve (AUC) values of 0.79, 0.76, and 0.73 respectively, while the distance to secondary structure/loop junction showed significance but with less predictive power (AUC of 0.54). In a case study of 20 insertion sites in the XynB xylanase, two features of native insertion sites showed correlation with the splice sites and demonstrated predictive value in selecting non-native splice sites. Structural modeling of intein insertions at two sites highlighted the role that the insertion site location could play on the ability of the intein to modulate activity of the host protein. These findings can be used to enrich the selection of insertion sites capable of supporting intein splicing and hosting an intein switch. PMID:22649521

High molecular weight glutenin subunits in some durum wheat cultivars investigated by means of mass spectrometric techniques.

PubMed

Muccilli, Vera; Lo Bianco, Marisol; Cunsolo, Vincenzo; Saletti, Rosaria; Gallo, Giulia; Foti, Salvatore

2011-11-23

The primary structures of high molecular weight glutenin subunits (HMW-GS) of 5 Triticum durum Desf. cultivars (Simeto, Svevo, Duilio, Bronte, and Sant'Agata), largely cultivated in the south of Italy, and of 13 populations of the old spring Sicilian durum wheat landrace Timilia (Triticum durum Desf.) (accession nos. 1, 2, 3, 4, 7, 8, 9, 13, 14, 15, SG1, SG2, and SG3) were investigated using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) and reversed-phase high performance liquid chromatography/nanoelectrospray ionization mass spectrometry (RP-HPLC/nESI-MS/MS). M(r) of the intact proteins determined by MALDI mass spectrometry showed that all the 13 populations of Timilia contained the same two HMW-GS with 75.2 kDa and 86.4 kDa, whereas the other durum wheat cultivars showed the presence of the expected HMW-GS 1By8 and 1Bx7 at 75.1 kDa and 83.1 kDa, respectively. By MALDI mass spectrometry of the tryptic digestion peptides of the isolated HMW-GS of Timilia, the 1Bx and 1By subunits were identified as the NCBInr Acc. No AAQ93629, and AAQ93633, respectively. Sequence verification for HMW-GS 1Bx and 1By both in Simeto and Timilia was obtained by MALDI mass mapping and HPLC/nESI-MSMS of the tryptic peptides. The Bx subunit of Timila presents a sequence similarity of 96% with respect to Simeto, with differences in the insertion of 3 peptides of 5, 9, and 15 amino acids, for a total insertion of 29 amino acids and 25 amino acid substitutions. These differences in the amino acidic sequence account for the determined Δm of 3294 Da between the M(r) of the 1Bx subunits in Timilia and Simeto. Sequence alignment between the two By subunits shows 10 amino acid substitutions and is consistent with the Δm of 148 Da found in the MALDI mass spectra of the intact subunits.

Ultrasound-guided three-dimensional needle steering in biological tissue with curved surfaces

PubMed Central

Abayazid, Momen; Moreira, Pedro; Shahriari, Navid; Patil, Sachin; Alterovitz, Ron; Misra, Sarthak

2015-01-01

In this paper, we present a system capable of automatically steering a bevel-tipped flexible needle under ultrasound guidance toward a physical target while avoiding a physical obstacle embedded in gelatin phantoms and biological tissue with curved surfaces. An ultrasound pre-operative scan is performed for three-dimensional (3D) target localization and shape reconstruction. A controller based on implicit force control is developed to align the transducer with curved surfaces to assure the maximum contact area, and thus obtain an image of sufficient quality. We experimentally investigate the effect of needle insertion system parameters such as insertion speed, needle diameter and bevel angle on target motion to adjust the parameters that minimize the target motion during insertion. A fast sampling-based path planner is used to compute and periodically update a feasible path to the target that avoids obstacles. We present experimental results for target reconstruction and needle insertion procedures in gelatin-based phantoms and biological tissue. Mean targeting errors of 1.46 ± 0.37 mm, 1.29 ± 0.29 mm and 1.82 ± 0.58 mm are obtained for phantoms with inclined, curved and combined (inclined and curved) surfaces, respectively, for insertion distance of 86–103 mm. The achieved targeting errors suggest that our approach is sufficient for targeting lesions of 3 mm radius that can be detected using clinical ultrasound imaging systems. PMID:25455165

Functional Studies and Homology Modeling of Msh2-Msh3 Predict that Mispair Recognition Involves DNA Bending and Strand Separation▿ †

PubMed Central

Dowen, Jill M.; Putnam, Christopher D.; Kolodner, Richard D.

2010-01-01

The Msh2-Msh3 heterodimer recognizes various DNA mispairs, including loops of DNA ranging from 1 to 14 nucleotides and some base-base mispairs. Homology modeling of the mispair-binding domain (MBD) of Msh3 using the related Msh6 MBD revealed that mismatch recognition must be different, even though the MBD folds must be similar. Model-based point mutation alleles of Saccharomyces cerevisiae msh3 designed to disrupt mispair recognition fell into two classes. One class caused defects in repair of both small and large insertion/deletion mispairs, whereas the second class caused defects only in the repair of small insertion/deletion mispairs; mutations of the first class also caused defects in the removal of nonhomologous tails present at the ends of double-strand breaks (DSBs) during DSB repair, whereas mutations of the second class did not cause defects in the removal of nonhomologous tails during DSB repair. Thus, recognition of small insertion/deletion mispairs by Msh3 appears to require a greater degree of interactions with the DNA conformations induced by small insertion/deletion mispairs than with those induced by large insertion/deletions that are intrinsically bent and strand separated. Mapping of the two classes of mutations onto the Msh3 MBD model appears to distinguish mispair recognition regions from DNA stabilization regions. PMID:20421420

Functional studies and homology modeling of Msh2-Msh3 predict that mispair recognition involves DNA bending and strand separation.

PubMed

Dowen, Jill M; Putnam, Christopher D; Kolodner, Richard D

2010-07-01

The Msh2-Msh3 heterodimer recognizes various DNA mispairs, including loops of DNA ranging from 1 to 14 nucleotides and some base-base mispairs. Homology modeling of the mispair-binding domain (MBD) of Msh3 using the related Msh6 MBD revealed that mismatch recognition must be different, even though the MBD folds must be similar. Model-based point mutation alleles of Saccharomyces cerevisiae msh3 designed to disrupt mispair recognition fell into two classes. One class caused defects in repair of both small and large insertion/deletion mispairs, whereas the second class caused defects only in the repair of small insertion/deletion mispairs; mutations of the first class also caused defects in the removal of nonhomologous tails present at the ends of double-strand breaks (DSBs) during DSB repair, whereas mutations of the second class did not cause defects in the removal of nonhomologous tails during DSB repair. Thus, recognition of small insertion/deletion mispairs by Msh3 appears to require a greater degree of interactions with the DNA conformations induced by small insertion/deletion mispairs than with those induced by large insertion/deletions that are intrinsically bent and strand separated. Mapping of the two classes of mutations onto the Msh3 MBD model appears to distinguish mispair recognition regions from DNA stabilization regions.

Standardized, Interdepartmental, Simulation-Based Central Line Insertion Course Closes an Educational Gap and Improves Intern Comfort with the Procedure.

PubMed

Grudziak, Joanna; Herndon, Blair; Dancel, Ria D; Arora, Harendra; Tignanelli, Christopher J; Phillips, Michael R; Crowner, Jason R; True, Nicholas A; Kiser, Andy C; Brown, Rebecca F; Goodell, Harry P; Murty, Neil; Meyers, Michael O; Montgomery, Sean P

2017-06-01

Central line placement is a common procedure, routinely performed by junior residents in medical and surgical departments. Before this project, no standardized instructional course on the insertion of central lines existed at our institution, and few interns had received formal ultrasound training. Interns from five departments participated in a simulation-based central line insertion course. Intern familiarity with the procedure and with ultrasound, as well as their prior experience with line placement and their level of comfort, was assessed. Of the 99 interns in participating departments, 45 per cent had been trained as of October 2015. Forty-one per cent were female. The majority (59.5%) had no prior formal ultrasound training, and 46.0 per cent had never placed a line as primary operator. Scores increased significantly, from a precourse score mean of 13.7 to a postcourse score mean of 16.1, P < 0.001. All three of the self-reported measures of comfort with ultrasound also improved significantly. All interns reported the course was "very much" helpful, and 100 per cent reported they felt "somewhat" or "much" more comfortable with the procedure after attendance. To our knowledge, this is the first hospital-wide, standardized, simulation-based central line insertion course in the United States. Preliminary results indicate overwhelming satisfaction with the course, better ultrasound preparedness, and improved comfort with central line insertion.

Fluid delivery manifolds and microfluidic systems

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

Renzi, Ronald F.; Sommer, Gregory J.; Singh, Anup K.

2017-02-28

Embodiments of fluid distribution manifolds, cartridges, and microfluidic systems are described herein. Fluid distribution manifolds may include an insert member and a manifold base and may define a substantially closed channel within the manifold when the insert member is press-fit into the base. Cartridges described herein may allow for simultaneous electrical and fluidic interconnection with an electrical multiplex board and may be held in place using magnetic attraction.

Analysis of the breast milk of giant pandas (Ailuropoda melanoleuca) and the preparation of substitutes

PubMed Central

ZHANG, Zhihe; HOU, Rong; LAN, Jingchao; WANG, Hairui; KUROKAWA, Hiroyuki; TAKATSU, Zenta; KOBAYASHI, Toyokazu; KOIE, Hiroshi; KAMATA, Hiroshi; KANAYAMA, Kiichi; WATANABE, Toshi

2016-01-01

The first milk substitute for giant panda cubs was developed in 1988 based on limited data about giant panda breast milk and that of certain types of bear. Mixtures of other formulas have also been fed to cubs at some facilities. However, they are not of sufficient nutritional quality for promoting growth in panda cubs. Here, we report analysis of giant panda breast milk and propose new milk substitutes for cubs, which were developed based on the results of our analysis. The Chengdu Research Base of Giant Panda Breeding obtained breast milk samples from three giant pandas. Up to 30 ml of breast milk were collected from each mother by hand. Then, the milk samples were frozen and sent to Nihon University. The levels of protein, fat, carbohydrates, ash, moisture, vitamins, minerals, total amino acids, fatty acids, lactose and other carbohydrates in the milk were analyzed. The breast milk samples exhibited the following nutritional values: protein: 6.6–8.5%, fat: 6.9–16.4%, carbohydrates: 2.5–9.1%, ash: 0.9–1.0% and moisture: 67–83%. We designed two kinds of milk substitutes based on the data obtained and the nutritional requirements of dogs, cats and rodents. The nutritional composition of the milk substitutes for the first and second stages was as follows: protein: 38 and 26%, fat: 40 and 40%, carbohydrates: 13 and 25%, ash: 6 and 6% and moisture: 3 and 3%, respectively. In addition, the substitutes contained vitamins, minerals, taurine, docosahexaenoic acid, lactoferrin, nucleotides and other nutrients. PMID:26781707

Vitreous Substitutes: Old and New Materials in Vitreoretinal Surgery

PubMed Central

Panico, Claudio; Eandi, Chiara M.

2017-01-01

Recent developments in vitreoretinal surgery have increased the need for suitable vitreous substitutes. A successful substitute should maintain all the physical and biochemical properties of the original vitreous, be easy to manipulate, and be long lasting. Substitutes can be gaseous or liquid, both of which have associated advantages and disadvantages related to their physical properties and use. Furthermore, new surgical techniques with smaller vitreoretinal instruments have driven the use of more viscous substitutes. In this review, we analyze and discuss the most frequently used vitreous substitutes and look ahead to future alternatives. We classify these compounds based on their composition and structure, discuss their clinical use with respect to their associated advantages and disadvantages, and analyze how new vitreoretinal surgical techniques have modified their use. PMID:28785482

Organ-specific SPECT activity calibration using 3D printed phantoms for molecular radiotherapy dosimetry.

PubMed

Robinson, Andrew P; Tipping, Jill; Cullen, David M; Hamilton, David; Brown, Richard; Flynn, Alex; Oldfield, Christopher; Page, Emma; Price, Emlyn; Smith, Andrew; Snee, Richard

2016-12-01

Patient-specific absorbed dose calculations for molecular radiotherapy require accurate activity quantification. This is commonly derived from Single-Photon Emission Computed Tomography (SPECT) imaging using a calibration factor relating detected counts to known activity in a phantom insert. A series of phantom inserts, based on the mathematical models underlying many clinical dosimetry calculations, have been produced using 3D printing techniques. SPECT/CT data for the phantom inserts has been used to calculate new organ-specific calibration factors for (99m) Tc and (177)Lu. The measured calibration factors are compared to predicted values from calculations using a Gaussian kernel. Measured SPECT calibration factors for 3D printed organs display a clear dependence on organ shape for (99m) Tc and (177)Lu. The observed variation in calibration factor is reproduced using Gaussian kernel-based calculation over two orders of magnitude change in insert volume for (99m) Tc and (177)Lu. These new organ-specific calibration factors show a 24, 11 and 8 % reduction in absorbed dose for the liver, spleen and kidneys, respectively. Non-spherical calibration factors from 3D printed phantom inserts can significantly improve the accuracy of whole organ activity quantification for molecular radiotherapy, providing a crucial step towards individualised activity quantification and patient-specific dosimetry. 3D printed inserts are found to provide a cost effective and efficient way for clinical centres to access more realistic phantom data.

TM-pass polarizer based on multilayer graphene polymer waveguide

NASA Astrophysics Data System (ADS)

Cai, Ke-su; Li, Yue-e.; Wei, Wen-jing; Mu, Xi-jiao; Ma, A.-ning; Wang, Zhong; Song, Dan-ming

2018-05-01

A TM-pass polarizer based on multilayer graphene polymer waveguide is proposed and theoretically analyzed. The mode properties, the extinction ratio, the insertion loss and the bandwidth are also discussed. The results show that a TM-pass polarizer, which only guides the TM mode, can be achieved by multilayer graphene polymer waveguide. With length of 150 μm, the proposed polarizer can achieve extinction ratio of 33 dB and insertion loss of 0.5 dB at optical wavelength of 1.55 μm. This device has an excellent performance, including large extinction ratio and low insertion loss within the spectral range from 1.45 μm to 1.6 μm.

Performance Analysis of Water Based Copper Oxide Nano Fluids in Heat Exchanger with Twisted Insert

NASA Astrophysics Data System (ADS)

Ashok Reddy, K.; Hanmanthu, Bhukya

2018-03-01

A new experimental setup has been designed for conducting experiments in a copper round pipe heat exchanger with inner diameter di=14.5mm and outer diameter do=16mm and length L = 1720 mm . By using two copper oxide nano concentrations of 0.1% and 0.3% with water as based fluid, the heat transfer rates have been obtained with helical twisted insert H/D=5 in turbulent flow condition. Reynolds number and friction factor with pressure gradient have been evaluated. The heat transfer rates of 0.1% conc. Nano-fluid with insert was found to be 13.77% more when compared to water.

Peripherally Inserted Central Catheters in Pediatric Oncology Patients: A 15-Year Population-based Review From Maritimes, Canada.

PubMed

Borretta, Lisa; MacDonald, Tamara; Digout, Carol; Smith, Nadine; Fernandez, Conrad V; Kulkarni, Ketan

2018-01-01

The present population-based study evaluates the management and complications of peripherally inserted central catheters (PICC) in all pediatric oncology patients diagnosed in Maritimes, Canada from 2000 to 2014. A total of 107 PICCs were placed in 87 (10.1%) pediatric oncology patients. A high percentage (33% and 44%, respectively) of the first and second PICC lines was associated with complications. Thrombosis, occlusion, and infection were the most frequent complications. Age above 10 years and left body side of insertion were significantly associated with PICC complications. Given the frequent use of PICCs and the high incidence (>33%) of complications, there is a need to mitigate PICC line complications.

Imaging, Virtual Planning, Design, and Production of Patient-Specific Implants and Clinical Validation in Craniomaxillofacial Surgery

PubMed Central

Dérand, Per; Rännar, Lars-Erik; Hirsch, Jan-M

2012-01-01

The purpose of this article was to describe the workflow from imaging, via virtual design, to manufacturing of patient-specific titanium reconstruction plates, cutting guide and mesh, and its utility in connection with surgical treatment of acquired bone defects in the mandible using additive manufacturing by electron beam melting (EBM). Based on computed tomography scans, polygon skulls were created. Following that virtual treatment plans entailing free microvascular transfer of fibula flaps using patient-specific reconstruction plates, mesh, and cutting guides were designed. The design was based on the specification of a Compact UniLOCK 2.4 Large (Synthes®, Switzerland). The obtained polygon plates were bent virtually round the reconstructed mandibles. Next, the resections of the mandibles were planned virtually. A cutting guide was outlined to facilitate resection, as well as plates and titanium mesh for insertion of bone or bone substitutes. Polygon plates and meshes were converted to stereolithography format and used in the software Magics for preparation of input files for the successive step, additive manufacturing. EBM was used to manufacture the customized implants in a biocompatible titanium grade, Ti6Al4V ELI. The implants and the cutting guide were cleaned and sterilized, then transferred to the operating theater, and applied during surgery. Commercially available software programs are sufficient in order to virtually plan for production of patient-specific implants. Furthermore, EBM-produced implants are fully usable under clinical conditions in reconstruction of acquired defects in the mandible. A good compliance between the treatment plan and the fit was demonstrated during operation. Within the constraints of this article, the authors describe a workflow for production of patient-specific implants, using EBM manufacturing. Titanium cutting guides, reconstruction plates for fixation of microvascular transfer of osteomyocutaneous bone grafts, and mesh to replace resected bone that can function as a carrier for bone or bone substitutes were designed and tested during reconstructive maxillofacial surgery. A clinically fit, well within the requirements for what is needed and obtained using traditional free hand bending of commercially available devices, or even higher precision, was demonstrated in ablative surgery in four patients. PMID:23997858

Imaging, virtual planning, design, and production of patient-specific implants and clinical validation in craniomaxillofacial surgery.

PubMed

Dérand, Per; Rännar, Lars-Erik; Hirsch, Jan-M

2012-09-01

The purpose of this article was to describe the workflow from imaging, via virtual design, to manufacturing of patient-specific titanium reconstruction plates, cutting guide and mesh, and its utility in connection with surgical treatment of acquired bone defects in the mandible using additive manufacturing by electron beam melting (EBM). Based on computed tomography scans, polygon skulls were created. Following that virtual treatment plans entailing free microvascular transfer of fibula flaps using patient-specific reconstruction plates, mesh, and cutting guides were designed. The design was based on the specification of a Compact UniLOCK 2.4 Large (Synthes(®), Switzerland). The obtained polygon plates were bent virtually round the reconstructed mandibles. Next, the resections of the mandibles were planned virtually. A cutting guide was outlined to facilitate resection, as well as plates and titanium mesh for insertion of bone or bone substitutes. Polygon plates and meshes were converted to stereolithography format and used in the software Magics for preparation of input files for the successive step, additive manufacturing. EBM was used to manufacture the customized implants in a biocompatible titanium grade, Ti6Al4V ELI. The implants and the cutting guide were cleaned and sterilized, then transferred to the operating theater, and applied during surgery. Commercially available software programs are sufficient in order to virtually plan for production of patient-specific implants. Furthermore, EBM-produced implants are fully usable under clinical conditions in reconstruction of acquired defects in the mandible. A good compliance between the treatment plan and the fit was demonstrated during operation. Within the constraints of this article, the authors describe a workflow for production of patient-specific implants, using EBM manufacturing. Titanium cutting guides, reconstruction plates for fixation of microvascular transfer of osteomyocutaneous bone grafts, and mesh to replace resected bone that can function as a carrier for bone or bone substitutes were designed and tested during reconstructive maxillofacial surgery. A clinically fit, well within the requirements for what is needed and obtained using traditional free hand bending of commercially available devices, or even higher precision, was demonstrated in ablative surgery in four patients.

PD-L1 Is Not Constitutively Expressed on Tasmanian Devil Facial Tumor Cells but Is Strongly Upregulated in Response to IFN-γ and Can Be Expressed in the Tumor Microenvironment

PubMed Central

Flies, Andrew S.; Lyons, A. Bruce; Corcoran, Lynn M.; Papenfuss, Anthony T.; Murphy, James M.; Knowles, Graeme W.; Woods, Gregory M.; Hayball, John D.

2016-01-01

The devil facial tumor disease (DFTD) is caused by clonal transmissible cancers that have led to a catastrophic decline in the wild Tasmanian devil (Sarcophilus harrisii) population. The first transmissible tumor, now termed devil facial tumor 1 (DFT1), was first discovered in 1996 and has been continually transmitted to new hosts for at least 20 years. In 2015, a second transmissible cancer [devil facial tumor 2 (DFT2)] was discovered in wild devils, and the DFT2 is genetically distinct and independent from the DFT1. Despite the estimated 136,559 base pair substitutions and 14,647 insertions/deletions in the DFT1 genome as compared to two normal devil reference genomes, the allograft tumors are not rejected by the host immune system. Additionally, genome sequencing of two sub-strains of DFT1 detected greater than 15,000 single-base substitutions that were found in only one of the DFT1 sub-strains, demonstrating the transmissible tumors are evolving and that generation of neoantigens is likely ongoing. Recent evidence in human clinical trials suggests that blocking PD-1:PD-L1 interactions promotes antitumor immune responses and is most effective in cancers with a high number of mutations. We hypothesized that DFTD cells could exploit the PD-1:PD-L1 inhibitory pathway to evade antitumor immune responses. We developed recombinant proteins and monoclonal antibodies (mAbs) to provide the first demonstration that PD-1 binds to both PD-L1 and PD-L2 in a non-placental mammal and show that PD-L1 is upregulated in DFTD cells in response to IFN-γ. Immunohistochemistry showed that PD-L1 is rarely expressed in primary tumor masses, but low numbers of PD-L1+ non-tumor cells were detected in the microenvironment of several metastatic tumors. Importantly, in vitro testing suggests that PD-1 binding to PD-L1 and PD-L2 can be blocked by mAbs, which could be critical to understanding how the DFT allografts evade the immune system. PMID:28018348

Synthesis of substituted pyrazines

DOEpatents

Pagoria, Philip F.; Zhang, Mao Xi

2016-10-04

A method for synthesizing a pyrazine-containing material according to one embodiment includes contacting an iminodiacetonitrile derivative with a base and a reagent selected from a group consisting of hydroxylamine, a hydroxylamine salt, an aliphatic primary amine, a secondary amine, an aryl-substituted alkylamine a heteroaryl-substituted alkyl amine, an alcohol, an alkanolamine and an aryl alcoholamine. Additional methods and several reaction products are presented. ##STR00001##

Classification of group B streptococci with reduced β-lactam susceptibility (GBS-RBS) based on the amino acid substitutions in PBPs.

PubMed

Kimura, Kouji; Nagano, Noriyuki; Arakawa, Yoshichika

2015-01-01

All clinical isolates of group B Streptococcus (GBS; Streptococcus agalactiae) are considered uniformly susceptible to β-lactams, including penicillins. However, GBS with reduced penicillin susceptibility (PRGBS) were first identified by our group in Japan and have also been reported from North America. PRGBS are non-susceptible to penicillin because of acquisition of amino acid substitutions near the conserved active-site motifs in PBP2X. In particular, V405A and Q557E are considered the key amino acid substitutions responsible for penicillin non-susceptibility. We revealed that in addition to the substitutions in PBP2X, an amino acid substitution in PBP1A confers high-level cephalosporin resistance in GBS. As the number of publications on GBS with reduced β-lactam susceptibility (GBS-RBS), especially PRGBS, and concomitantly the need for a systematic classification of GBS-RBS is increasing, we propose here a classification of GBS-RBS based on the amino acid substitutions in their PBPs. © The Author 2015. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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

Kelly, Jarod C.; Sullivan, John L.; Burnham, Andrew

This study examines the vehicle-cycle impacts associated with substituting lightweight materials for those currently found in light-duty passenger vehicles. We determine part-based energy use and greenhouse gas (GHG) emission ratios by collecting material substitution data from both the literature and automotive experts and evaluating that alongside known mass-based energy use and GHG emission ratios associated with material pair substitutions. Several vehicle parts, along with full vehicle systems, are examined for lightweighting via material substitution to observe the associated impact on GHG emissions. Results are contextualized by additionally examining fuel-cycle GHG reductions associated with mass reductions relative to the baseline vehiclemore » during the use phase and also determining material pair breakeven driving distances for GHG emissions. The findings show that, while material substitution is useful in reducing vehicle weight, it often increases vehicle-cycle GHGs depending upon the material substitution pair. However, for a vehicle’s total life cycle, fuel economy benefits are greater than the increased burdens associated with the vehicle manufacturing cycle, resulting in a net total life-cycle GHG benefit. The vehicle cycle will become increasingly important in total vehicle life-cycle GHGs, since fuel-cycle GHGs will be gradually reduced as automakers ramp up vehicle efficiency to meet fuel economy standards.« less

Predeployment validation of fault-tolerant systems through software-implemented fault insertion

NASA Technical Reports Server (NTRS)

Czeck, Edward W.; Siewiorek, Daniel P.; Segall, Zary Z.

1989-01-01

Fault injection-based automated testing (FIAT) environment, which can be used to experimentally characterize and evaluate distributed realtime systems under fault-free and faulted conditions is described. A survey is presented of validation methodologies. The need for fault insertion based on validation methodologies is demonstrated. The origins and models of faults, and motivation for the FIAT concept are reviewed. FIAT employs a validation methodology which builds confidence in the system through first providing a baseline of fault-free performance data and then characterizing the behavior of the system with faults present. Fault insertion is accomplished through software and allows faults or the manifestation of faults to be inserted by either seeding faults into memory or triggering error detection mechanisms. FIAT is capable of emulating a variety of fault-tolerant strategies and architectures, can monitor system activity, and can automatically orchestrate experiments involving insertion of faults. There is a common system interface which allows ease of use to decrease experiment development and run time. Fault models chosen for experiments on FIAT have generated system responses which parallel those observed in real systems under faulty conditions. These capabilities are shown by two example experiments each using a different fault-tolerance strategy.

Dynamic analysis of a needle insertion for soft materials: Arbitrary Lagrangian-Eulerian-based three-dimensional finite element analysis.

PubMed

Yamaguchi, Satoshi; Tsutsui, Kihei; Satake, Koji; Morikawa, Shigehiro; Shirai, Yoshiaki; Tanaka, Hiromi T

2014-10-01

Our goal was to develop a three-dimensional finite element model that enables dynamic analysis of needle insertion for soft materials. To demonstrate large deformation and fracture, we used the arbitrary Lagrangian-Eulerian (ALE) method for fluid analysis. We performed ALE-based finite element analysis for 3% agar gel and three types of copper needle with bevel tips. To evaluate simulation results, we compared the needle deflection and insertion force with corresponding experimental results acquired with a uniaxial manipulator. We studied the shear stress distribution of agar gel on various time scales. For 30°, 45°, and 60°, differences in deflections of each needle between both sets of results were 2.424, 2.981, and 3.737mm, respectively. For the insertion force, there was no significant difference for mismatching area error (p<0.05) between simulation and experimental results. Our results have the potential to be a stepping stone to develop pre-operative surgical planning to estimate an optimal needle insertion path for MR image-guided microwave coagulation therapy and for analyzing large deformation and fracture in biological tissues. Copyright © 2014 Elsevier Ltd. All rights reserved.

Vaginal inserts based on chitosan and carboxymethylcellulose complexes for local delivery of chlorhexidine: preparation, characterization and antimicrobial activity.

PubMed

Bigucci, Federica; Abruzzo, Angela; Vitali, Beatrice; Saladini, Bruno; Cerchiara, Teresa; Gallucci, Maria Caterina; Luppi, Barbara

2015-01-30

The aim of this work was to prepare vaginal inserts based on chitosan/carboxymethylcellulose polyelectrolyte complexes for local delivery of chlorhexidine digluconate. Complexes were prepared with different chitosan/carboxymethylcellulose molar ratios at a pH value close to pKa interval of the polymers and were characterized in terms of physico-chemical properties, complexation yield and drug loading. Then complexes were used to prepare inserts as vaginal dosage forms and their physical handling, morphology, water-uptake ability and drug release properties as well as antimicrobial activity toward Candida albicans and Escherichia coli were evaluated. Results confirmed the ionic interaction between chitosan and carboxymethylcellulose and the influence of the charge amount on the complexation yield. Complexes were characterized by high values of drug loading and showed increasing water-uptake ability with the increase of carboxymethylcellulose amount. The selection of appropriate chitosan/carboxymethylcellulose molar ratios allowed to obtain cone-like shaped solid inserts, easy to handle and able to hydrate releasing the drug over time. Finally, the formulated inserts showed antimicrobial activity against common pathogens responsible for vaginal infections. Copyright © 2014 Elsevier B.V. All rights reserved.

Model-based assist feature insertion for sub-40nm memory device

NASA Astrophysics Data System (ADS)

Suh, Sungsoo; Lee, Suk-joo; Choi, Seong-woon; Lee, Sung-Woo; Park, Chan-hoon

2009-04-01

Many issues need to be resolved for a production-worthy model based assist feature insertion flow for single and double exposure patterning process to extend low k1 process at 193 nm immersion technology. Model based assist feature insertion is not trivial to implement either for single and double exposure patterning compared to rule based methods. As shown in Fig. 1, pixel based mask inversion technology in itself has difficulties in mask writing and inspection although it presents as one of key technology to extend single exposure for contact layer. Thus far, inversion technology is tried as a cooptimization of target mask to simultaneously generate optimized main and sub-resolution assists features for a desired process window. Alternatively, its technology can also be used to optimize for a target feature after an assist feature types are inserted in order to simplify the mask complexity. Simplification of inversion mask is one of major issue with applying inversion technology to device development even if a smaller mask feature can be fabricated since the mask writing time is also a major factor. As shown in Figure 2, mask writing time may be a limiting factor in determining whether or not an inversion solution is viable. It can be reasoned that increased number of shot counts relates to increase in margin for inversion methodology. On the other hand, there is a limit on how complex a mask can be in order to be production worthy. There is also source and mask co-optimization which influences the final mask patterns and assist feature sizes and positions for a given target. In this study, we will discuss assist feature insertion methods for sub 40-nm technology.

The Study of Substitution and Elimination Reactions Using Gas Chromatography: An Examination of the Effects of Alkane and Base Structure on Product Distributions

ERIC Educational Resources Information Center

Wharry, Donald L.

2011-01-01

An experiment that compares product distribution obtained by either substitution or elimination utilizing alkyl bromides and methoxide, ethoxide, or t-butoxide as the base (or nucleophile) is described. The change in product distribution caused by steric effects of the base and substrate are readily apparent. Prior work on this experiment focused…

24 CFR 290.21 - Computing annual number of units eligible for substitution of tenant-based assistance or...

Code of Federal Regulations, 2010 CFR

2010-04-01

... PROPERTIES DISPOSITION OF MULTIFAMILY PROJECTS AND SALE OF HUD-HELD MULTIFAMILY MORTGAGES Disposition of Multifamily Projects § 290.21 Computing annual number of units eligible for substitution of tenant-based... the fiscal year, taking into consideration the total number of units in multifamily housing projects...

24 CFR 290.21 - Computing annual number of units eligible for substitution of tenant-based assistance or...

Code of Federal Regulations, 2011 CFR

2011-04-01

... PROPERTIES DISPOSITION OF MULTIFAMILY PROJECTS AND SALE OF HUD-HELD MULTIFAMILY MORTGAGES Disposition of Multifamily Projects § 290.21 Computing annual number of units eligible for substitution of tenant-based... the fiscal year, taking into consideration the total number of units in multifamily housing projects...

24 CFR 290.21 - Computing annual number of units eligible for substitution of tenant-based assistance or...

Code of Federal Regulations, 2012 CFR

2012-04-01

... PROPERTIES DISPOSITION OF MULTIFAMILY PROJECTS AND SALE OF HUD-HELD MULTIFAMILY MORTGAGES Disposition of Multifamily Projects § 290.21 Computing annual number of units eligible for substitution of tenant-based... the fiscal year, taking into consideration the total number of units in multifamily housing projects...

24 CFR 290.21 - Computing annual number of units eligible for substitution of tenant-based assistance or...

Code of Federal Regulations, 2014 CFR

2014-04-01

... PROPERTIES DISPOSITION OF MULTIFAMILY PROJECTS AND SALE OF HUD-HELD MULTIFAMILY MORTGAGES Disposition of Multifamily Projects § 290.21 Computing annual number of units eligible for substitution of tenant-based... the fiscal year, taking into consideration the total number of units in multifamily housing projects...

Wood Substitutes; A Base Syllabus on Wood Technology.

ERIC Educational Resources Information Center

Eastern Kentucky Univ., Richmond.

This curriculum guide is for use by college instructors concerned with expanding traditional woodworking programs. It was developed in a National Defense Education Act summer institute and is based on an outline provided by members of a previous institute. The content concerns wood substitutes which are made to resemble wood and are often used…

Development of navy bean-soybean milk substitute beverages and evaluation of its nutritional and physical properties

USDA-ARS?s Scientific Manuscript database

As health-conscious consumers are increasingly looking for plant-based milk substitute beverages for weight management, cancer prevention, and overall cardiovascular health, we are exploring pulse based healthful beverages with soybean-navy bean blends of 100:0, 80:20, 60:40, 20:80, and 0:100 ratios...

Rotary slot dog

DOEpatents

Cutburth, Ronald W.; Smauley, David A.

1987-01-01

A clamp or dog is disclosed which preferably comprises a slotted stepped cylindrical body which is inserted into a hole in a workpiece and then fastened to a base or fixture using a screw which is inserted through the slot. The stepped configuration provides an annular clamping surface which securely clamps the workpiece against the base or fixture. The slotted cylindrical configuration permits adjustment of the workpiece and retaining clamp in any direction, i.e., over 360.degree., relative to the mounting position of the screw in the base or fixture.

The Effect of 24c-site (A) Cation Substitution on the Tetragonal-Cubic Phase Transition in Li7-xLa3-xAxZr2O12 Garnet-Based Ceramic Electrolyte

DTIC Science & Technology

2012-12-27

Another super-valent substitution scheme involves either Nb (5þ) or Ta (5þ) on the 16a site ( Zr 4þ), that reduces the Li content and/or increases Li...substitution for Zr are as follows [20,22,23]: Ta$ Zr ¼ V0Li (3) Nb $ Zr ¼ V0Li (4) Likewise, super-valent substitution on the 24c (La 3þ) is...Substitution of La with Ce stabilizes the cubic LLZO garnet phase. < CeO2 precipitation at grain boundaries increases grain boundary resistance . < Super

Rechargeable Aluminum-Ion Batteries Based on an Open-Tunnel Framework.

PubMed

Kaveevivitchai, Watchareeya; Huq, Ashfia; Wang, Shaofei; Park, Min Je; Manthiram, Arumugam

2017-09-01

Rechargeable batteries based on an abundant metal such as aluminum with a three-electron transfer per atom are promising for large-scale electrochemical energy storage. Aluminum can be handled in air, thus offering superior safety, easy fabrication, and low cost. However, the development of Al-ion batteries has been challenging due to the difficulties in identifying suitable cathode materials. This study presents the use of a highly open framework Mo 2.5 +  y VO 9 +  z as a cathode for Al-ion batteries. The open-tunnel oxide allows a facile diffusion of the guest species and provides sufficient redox centers to help redistribute the charge within the local host lattice during the multivalent-ion insertion, thus leading to good rate capability with a specific capacity among the highest reported in the literature for Al-based batteries. This study also presents the use of Mo 2.5 +  y VO 9 +  z as a model host to develop a novel ultrafast technique for chemical insertion of Al ions into host structures. The microwave-assisted method employing diethylene glycol and aluminum diacetate (Al(OH)(C 2 H 3 O 2 ) 2 ) can be performed in air in as little as 30 min, which is far superior to the traditional chemical insertion techniques involving moisture-sensitive organometallic reagents. The Al-inserted Al x Mo 2.5 +  y VO 9 +  z obtained by the microwave-assisted chemical insertion can be used in Al-based rechargeable batteries. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Prediction of the translocon-mediated membrane insertion free energies of protein sequences.

PubMed

Park, Yungki; Helms, Volkhard

2008-05-15

Helical membrane proteins (HMPs) play crucial roles in a variety of cellular processes. Unlike water-soluble proteins, HMPs need not only to fold but also get inserted into the membrane to be fully functional. This process of membrane insertion is mediated by the translocon complex. Thus, it is of great interest to develop computational methods for predicting the translocon-mediated membrane insertion free energies of protein sequences. We have developed Membrane Insertion (MINS), a novel sequence-based computational method for predicting the membrane insertion free energies of protein sequences. A benchmark test gives a correlation coefficient of 0.74 between predicted and observed free energies for 357 known cases, which corresponds to a mean unsigned error of 0.41 kcal/mol. These results are significantly better than those obtained by traditional hydropathy analysis. Moreover, the ability of MINS to reasonably predict membrane insertion free energies of protein sequences allows for effective identification of transmembrane (TM) segments. Subsequently, MINS was applied to predict the membrane insertion free energies of 316 TM segments found in known structures. An in-depth analysis of the predicted free energies reveals a number of interesting findings about the biogenesis and structural stability of HMPs. A web server for MINS is available at http://service.bioinformatik.uni-saarland.de/mins

Laryngeal electromyography: electrode guidance based on 3-dimensional magnetic resonance tomography images of the larynx.

PubMed

Storck, Claudio; Gehrer, Raphael; Hofer, Michael; Neumayer, Bernhard; Stollberger, Rudolf; Schumacher, Ralf; Gugatschka, Markus; Friedrich, Gerhard; Wolfensberger, Markus

2012-01-01

Laryngeal electromyography (LEMG) is an important tool for the assessment of laryngeal nerve and muscle functioning. The purpose of the study was to determine electrode insertion angle and insertion depth for the various laryngeal muscles. Twenty-three cadaver larynges were examined with magnetic resonance tomography (MRT) and Materialize Interactive Medical Image Control System (Leuven, Belgium) 3-dimensional (3D) imaging software. Geometrical analysis was used to calculate the electrode insertion angles. All laryngeal muscles could be identified and 3D visualized on MRT scans. Although the insertion angles were the same in male and female larynges, the insertion depth was significantly larger in male than in female larynges (P<0.05). Of particular clinical importance is the fact that the electrode has to be directed lateral and upward for the thyroarytenoid muscle but lateral and downward for the lateral cricoarytenoid muscle (insertion point=midline lower border of the thyroid). This is the first study that analyzes electrode insertion angles and insertion depths for each laryngeal muscle using 3D imaging. We hope that the information gained from this study will help clinicians performing LEMG to localize the individual laryngeal muscles. Copyright © 2012 The Voice Foundation. Published by Mosby, Inc. All rights reserved.

Impact of protease and amylase treatment on proteins and the product quality of a quinoa-based milk substitute.

PubMed

Jeske, Stephanie; Zannini, Emanuele; Cronin, Michael F; Arendt, Elke K

2018-06-12

Plant proteins are often characterized by low solubilities and impaired functionalities e.g. emulsifying properties. In products like milk substitutes, these protein properties are of great importance to ensure good product quality. In this study proteolytic enzymes were used as a tool to increase protein solubility and alter their properties gently. A plant-based milk substitute based on quinoa was produced and treated with different enzymes. One α-amylase and three commercial proteases were selected: Hitempase 2XP, Profix 100L, Bioprotease N100L, and Flavourzyme 1000L. The protein solubility of the samples was initially low with 48.02% and was improved with the increasing degree of hydrolysis up to a value of 75.82% for Profix. These results were supported by SDS-PAGE and circular dichroism analysis: especially Profix degraded the proteins extensively. Quality characteristics, such as foaming, and emulsifying properties were not influenced considerably by the protease treatment. The results of this study provide an in-depth understanding of the effects of different enzymes in a complex system of a plant-based milk substitute and contribute to the development of protein based products.

Determinants of Base-Pair Substitution Patterns Revealed by Whole-Genome Sequencing of DNA Mismatch Repair Defective Escherichia coli.

PubMed

Foster, Patricia L; Niccum, Brittany A; Popodi, Ellen; Townes, Jesse P; Lee, Heewook; MohammedIsmail, Wazim; Tang, Haixu

2018-06-15

Mismatch repair (MMR) is a major contributor to replication fidelity, but its impact varies with sequence context and the nature of the mismatch. Mutation accumulation experiments followed by whole-genome sequencing of MMR-defective E. coli strains yielded ≈30,000 base-pair substitutions, revealing mutational patterns across the entire chromosome. The base-pair substitution spectrum was dominated by A:T > G:C transitions, which occurred predominantly at the center base of 5'N A C3'+5'G T N3' triplets. Surprisingly, growth on minimal medium or at low temperature attenuated these mutations. Mononucleotide runs were also hotspots for base-pair substitutions, and the rate at which these occurred increased with run length. Comparison with ≈2000 base-pair substitutions accumulated in MMR-proficient strains revealed that both kinds of hotspots appeared in the wild-type spectrum and so are likely to be sites of frequent replication errors. In MMR-defective strains transitions were strand biased, occurring twice as often when A and C rather than T and G were on the lagging-strand template. Loss of nucleotide diphosphate kinase increases the cellular concentration of dCTP, which resulted in increased rates of mutations due to misinsertion of C opposite A and T. In an mmr ndk double mutant strain, these mutations were more frequent when the template A and T were on the leading strand, suggesting that lagging-strand synthesis was more error-prone or less well corrected by proofreading than was leading strand synthesis. Copyright © 2018, Genetics.

3D kinematics of mobile-bearing total knee arthroplasty using X-ray fluoroscopy.

PubMed

Yamazaki, Takaharu; Futai, Kazuma; Tomita, Tetsuya; Sato, Yoshinobu; Yoshikawa, Hideki; Tamura, Shinichi; Sugamoto, Kazuomi

2015-04-01

Total knee arthroplasty (TKA) 3D kinematic analysis requires 2D/3D image registration of X-ray fluoroscopic images and a computer-aided design (CAD) model of the knee implant. However, these techniques cannot provide information on the radiolucent polyethylene insert, since the insert silhouette does not appear clearly in X-ray images. Therefore, it is difficult to obtain the 3D kinematics of the polyethylene insert, particularly the mobile-bearing insert. A technique for 3D kinematic analysis of a mobile-bearing insert used in TKA was developed using X-ray fluoroscopy. The method was tested and a clinical application was evaluated. Tantalum beads and a CAD model of the mobile-bearing TKA insert are used for 3D pose estimation of the mobile-bearing insert used in TKA using X-ray fluoroscopy. The insert model was created using four identical tantalum beads precisely located at known positions in a polyethylene insert using a specially designed insertion device. Finally, the 3D pose of the insert model was estimated using a feature-based 2D/3D registration technique, using the silhouette of beads in fluoroscopic images and the corresponding CAD insert model. In vitro testing for the repeatability of the positioning of the tantalum beads and computer simulations for 3D pose estimation of the mobile-bearing insert were performed. The pose estimation accuracy achieved was sufficient for analyzing mobile-bearing TKA kinematics (RMS error: within 1.0 mm and 1.0°, except for medial-lateral translation). In a clinical application, nine patients with mobile-bearing TKA were investigated and analyzed with respect to a deep knee bending motion. A 3D kinematic analysis technique was developed that enables accurate quantitative evaluation of mobile-bearing TKA kinematics. This method may be useful for improving implant design and optimizing TKA surgical techniques.

Extreme primary and secondary protein structure variability in the chimeric male-transmitted cytochrome c oxidase subunit II protein in freshwater mussels: Evidence for an elevated amino acid substitution rate in the face of domain-specific purifying selection

PubMed Central

2008-01-01

Background Freshwater unionoidean bivalves, and species representing two marine bivalve orders (Mytiloida and Veneroida), exhibit a mode of mtDNA inheritance involving distinct maternal (F) and paternal (M) transmission routes concomitant with highly divergent gender-associated mtDNA genomes. Additionally, male unionoidean bivalves have a ~550 bp 3' coding extension to the cox2 gene (Mcox2e), that is apparently absent from all other metazoan taxa. Results Our molecular sequence analyses of MCOX2e indicate that both the primary and secondary structures of the MCOX2e region are evolving much faster than other regions of the F and M COX2-COX1 gene junction. The near N-terminus ~2/3 of the MCOX2e region contains an interspecifically variable number of predicted transmembrane helices (TMH) and interhelical loops (IHL) whereas the C-terminus ~1/3 is relatively conserved and hydrophilic while containing conserved functional motifs. MCOX2e displays an overall pattern of purifying selection that leads to the preservation of TMH/IHL and C-terminus tail sub-regions. However, 14 amino acid positions in the MCOX2e TMH/IHL sub-region might be targeted by diversifying selection, each representing a site where there exists interspecific variation for the constituent amino acids residing in a TMH or IHL. Conclusion Our results indicate that Mcox2e is unique to unionoidean bivalves, likely the result of a single insertion event that took place over 65 MYA and that MCOX2e is functional. The predicted TMH number, length and position variability likely stems from substitution-based processes rather than the typically implicated insertion/deletion events. MCOX2e has relatively high rates of primary and secondary structure evolution, with some amino acid residues potentially subjected to site-specific positive selection, yet an overall pattern of purifying selection leading to the preservation of the TMH/IHL and hydrophilic C-terminus tail subregions. The more conserved C-terminus tail (relative to the TMH/IHL sub-region of MCOX2e) is likely biologically active because it contains functional motifs. The rapid evolution of primary and secondary structure in MCOX2e, combined with the action of both positive and purifying selection, provide supporting evidence for the hypothesis that MCOX2e has a novel reproductive function within unionoidean bivalves. All tolled, our data indicate that unionoidean bivalve MCOX2 is the first reported chimeric animal mtDNA-encoded protein. PMID:18513440

Teaching aseptic technique for central venous access under ultrasound guidance: a randomized trial comparing didactic training alone to didactic plus simulation-based training.

PubMed

Latif, Rana K; Bautista, Alexander F; Memon, Saima B; Smith, Elizabeth A; Wang, Chenxi; Wadhwa, Anupama; Carter, Mary B; Akca, Ozan

2012-03-01

Our goal was to determine whether simulation combined with didactic training improves sterile technique during ultrasound (US)-guided central venous catheter (CVC) insertion compared with didactic training alone among novices. We hypothesized that novices who receive combined didactic and simulation-based training would perform similarly to experienced residents in aseptic technique, knowledge, and perception of comfort during US-guided CVC insertion on a simulator. Seventy-two subjects were enrolled in a randomized, controlled trial of an educational intervention. Fifty-four novices were randomized into either the didactic group or the simulation combined with didactic group. Both groups received didactic training but the simulation combined with didactic group also received simulation-based CVC insertion training. Both groups were tested by demonstrating US-guided CVC insertion on a simulator. Aseptic technique was scored on 8 steps as "yes/no" and also using a 7-point Likert scale with 7 being "excellent technique" by a rater blinded to subject randomization. After initial testing, the didactic group was offered simulation-based training and retesting. Both groups also took a pre- and posttraining test of knowledge and rated their comfort with US and CVC insertion pre- and posttraining on a 5-point Likert scale. Subsequently, 18 experienced residents also took the test of knowledge, rated their comfort level, and were scored while performing aseptic US-guided CVC insertion using a simulator. The simulation combined with didactic group achieved a 167% (95% confidence interval [CI] 133%-167%) incremental increase in yes/no scores and 115% (CI 112%-127%) incremental increase in Likert scale ratings on aseptic technique compared with novices in the didactic group. Compared with experienced residents, simulation combined with didactic trained novices achieved an increase in aseptic scores with a 33.3% (CI 16.7%-50%) increase in yes/no ratings and a 20% (CI 13.3%-40%) increase in Likert scaled ratings, and scored 2.5-fold higher on the test of knowledge. There was a 3-fold increase in knowledge and 2-fold increase in comfort level among all novices (P < 0.001) after combined didactic and simulation-based training. Simulation combined with didactic training is superior to didactic training alone for acquisition of clinical skills such as US-guided CVC insertion. After combined didactic and simulation-based training, novices can outperform experienced residents in aseptic technique as well as in measurements of knowledge.

Genome editing using CRISPR/Cas9-based knock-in approaches in zebrafish.

PubMed

Albadri, Shahad; Del Bene, Filippo; Revenu, Céline

2017-05-15

With its variety of applications, the CRISPR/Cas9 genome editing technology has been rapidly evolving in the last few years. In the zebrafish community, knock-out reports are constantly increasing but insertion studies have been so far more challenging. With this review, we aim at giving an overview of the homologous directed repair (HDR)-based knock-in generation in zebrafish. We address the critical points and limitations of the procedure such as cutting efficiency of the chosen single guide RNA, use of cas9 mRNA or Cas9 protein, homology arm size etc. but also ways to circumvent encountered issues with HDR insertions by the development of non-homologous dependent strategies. While imprecise, these homology-independent mechanisms based on non-homologous-end-joining (NHEJ) repair have been employed in zebrafish to generate reporter lines or to accurately edit an open reading frame by the use of intron-targeting modifications. Therefore, with higher efficiency and insertion rate, NHEJ-based knock-in seems to be a promising approach to target endogenous loci and to circumvent the limitations of HDR whenever it is possible and appropriate. In this perspective, we propose new strategies to generate cDNA edited or tagged insertions, which once established will constitute a new and versatile toolbox for CRISPR/Cas9-based knock-ins in zebrafish. Copyright © 2017 Elsevier Inc. All rights reserved.

Visual attention distracter insertion for improved EEG rapid serial visual presentation (RSVP) target stimuli detection

NASA Astrophysics Data System (ADS)

Khosla, Deepak; Huber, David J.; Martin, Kevin

2017-05-01

This paper† describes a technique in which we improve upon the prior performance of the Rapid Serial Visual Presentation (RSVP) EEG paradigm for image classification though the insertion of visual attention distracters and overall sequence reordering based upon the expected ratio of rare to common "events" in the environment and operational context. Inserting distracter images maintains the ratio of common events to rare events at an ideal level, maximizing the rare event detection via P300 EEG response to the RSVP stimuli. The method has two steps: first, we compute the optimal number of distracters needed for an RSVP stimuli based on the desired sequence length and expected number of targets and insert the distracters into the RSVP sequence, and then we reorder the RSVP sequence to maximize P300 detection. We show that by reducing the ratio of target events to nontarget events using this method, we can allow RSVP sequences with more targets without sacrificing area under the ROC curve (azimuth).

Beamline Insertions Manager at Jefferson Lab

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

Johnson, Michael C.

2015-09-01

The beam viewer system at Jefferson Lab provides operators and beam physicists with qualitative and quantitative information on the transverse electron beam properties. There are over 140 beam viewers installed on the 12 GeV CEBAF accelerator. This paper describes an upgrade consisting of replacing the EPICS-based system tasked with managing all viewers with a mixed system utilizing EPICS and high-level software. Most devices, particularly the beam viewers, cannot be safely inserted into the beam line during high-current beam operations. Software is partly responsible for protecting the machine from untimely insertions. The multiplicity of beam-blocking and beam-vulnerable devices motivates us tomore » try a data-driven approach. The beamline insertions application components are centrally managed and configured through an object-oriented software framework created for this purpose. A rules-based engine tracks the configuration and status of every device, along with the beam status of the machine segment containing the device. The application uses this information to decide on which device actions are allowed at any given time.« less

Biocomposite Plasma-Sprayed Coatings Based on Zinc-Substituted Hydroxyapatite: Structure, Properties, and Prospects of Application

NASA Astrophysics Data System (ADS)

Lyasnikova, A. V.; Markelova, O. A.; Lyasnikov, V. N.; Dudareva, O. A.

2016-01-01

The method of synthesis of a zinc-substituted hydroxyapatite powder is presented, and the technology of creating coatings by its spraying is described. The results of studies on the morphological, physical, and chemical parameters of a zinc-substituted hydroxyapatite coating by using X-ray analysis, infrared spectroscopy, transmission electron microscopy, optical microscopy, SEM, and other methods are given.

Principal component analysis of binding energies for single-point mutants of hT2R16 bound to an agonist correlate with experimental mutant cell response.

PubMed

Chen, Derek E; Willick, Darryl L; Ruckel, Joseph B; Floriano, Wely B

2015-01-01

Directed evolution is a technique that enables the identification of mutants of a particular protein that carry a desired property by successive rounds of random mutagenesis, screening, and selection. This technique has many applications, including the development of G protein-coupled receptor-based biosensors and designer drugs for personalized medicine. Although effective, directed evolution is not without challenges and can greatly benefit from the development of computational techniques to predict the functional outcome of single-point amino acid substitutions. In this article, we describe a molecular dynamics-based approach to predict the effects of single amino acid substitutions on agonist binding (salicin) to a human bitter taste receptor (hT2R16). An experimentally determined functional map of single-point amino acid substitutions was used to validate the whole-protein molecular dynamics-based predictive functions. Molecular docking was used to construct a wild-type agonist-receptor complex, providing a starting structure for single-point substitution simulations. The effects of each single amino acid substitution in the functional response of the receptor to its agonist were estimated using three binding energy schemes with increasing inclusion of solvation effects. We show that molecular docking combined with molecular mechanics simulations of single-point mutants of the agonist-receptor complex accurately predicts the functional outcome of single amino acid substitutions in a human bitter taste receptor.

The nature of chemical innovation: new enzymes by evolution.

PubMed

Arnold, Frances H

2015-11-01

I describe how we direct the evolution of non-natural enzyme activities, using chemical intuition and information on structure and mechanism to guide us to the most promising reaction/enzyme systems. With synthetic reagents to generate new reactive intermediates and just a few amino acid substitutions to tune the active site, a cytochrome P450 can catalyze a variety of carbene and nitrene transfer reactions. The cyclopropanation, N-H insertion, C-H amination, sulfimidation, and aziridination reactions now demonstrated are all well known in chemical catalysis but have no counterparts in nature. The new enzymes are fully genetically encoded, assemble and function inside of cells, and can be optimized for different substrates, activities, and selectivities. We are learning how to use nature's innovation mechanisms to marry some of the synthetic chemists' favorite transformations with the exquisite selectivity and tunability of enzymes.

Model for Codon Position Bias in RNA Editing

NASA Astrophysics Data System (ADS)

Liu, Tsunglin; Bundschuh, Ralf

2005-08-01

RNA editing can be crucial for the expression of genetic information via inserting, deleting, or substituting a few nucleotides at specific positions in an RNA sequence. Within coding regions in an RNA sequence, editing usually occurs with a certain bias in choosing the positions of the editing sites. In the mitochondrial genes of Physarum polycephalum, many more editing events have been observed at the third codon position than at the first and second, while in some plant mitochondria the second codon position dominates. Here we propose an evolutionary model that explains this bias as the basis of selection at the protein level. The model predicts a distribution of the three positions rather close to the experimental observation in Physarum. This suggests that the codon position bias in Physarum is mainly a consequence of selection at the protein level.

A model for codon position bias in RNA editing

NASA Astrophysics Data System (ADS)

Bundschuh, Ralf; Liu, Tsunglin

2006-03-01

RNA editing can be crucial for the expression of genetic information via inserting, deleting, or substituting a few nucleotides at specific positions in an RNA sequence. Within coding regions in an RNA sequence, editing usually occurs with a certain bias in choosing the positions of the editing sites. In the mitochondrial genes of Physarum polycephalum, many more editing events have been observed at the third codon position than at the first and second, while in some plant mitochondria the second codon position dominates. Here we propose an evolutionary model that explains this bias as the basis of selection at the protein level. The model predicts a distribution of the three positions rather close to the experimental observation in Physarum. This suggests that the codon position bias in Physarum is mainly a consequence of selection at the protein level.

Efficient parallel algorithms for string editing and related problems

NASA Technical Reports Server (NTRS)

Apostolico, Alberto; Atallah, Mikhail J.; Larmore, Lawrence; Mcfaddin, H. S.

1988-01-01

The string editing problem for input strings x and y consists of transforming x into y by performing a series of weighted edit operations on x of overall minimum cost. An edit operation on x can be the deletion of a symbol from x, the insertion of a symbol in x or the substitution of a symbol x with another symbol. This problem has a well known O((absolute value of x)(absolute value of y)) time sequential solution (25). The efficient Program Requirements Analysis Methods (PRAM) parallel algorithms for the string editing problem are given. If m = ((absolute value of x),(absolute value of y)) and n = max((absolute value of x),(absolute value of y)), then the CREW bound is O (log m log n) time with O (mn/log m) processors. In all algorithms, space is O (mn).

A series of spinel phase cathode materials prepared by a simple hydrothermal process for rechargeable lithium batteries

NASA Astrophysics Data System (ADS)

Liang, Yan-Yu; Bao, Shu-Juan; Li, Hu-Lin

2006-07-01

A series of spinel-structured materials have been prepared by a simple hydrothermal procedure in an aqueous medium. The new synthetic method is time and energy saving i.e., no further thermal treatment and extended grinding. The main experimental process involved the insertion of lithium into electrolytic manganese dioxide with glucose as a mild reductant in an autoclave. Both the hydrothermal temperature and the presence of glucose play the critical roles in determining the final spinel integrity. Particular electrochemical performance has also been systematically explored, and the results show that Al 3+, F - co-substituted spinels have the best combination of initial capacity and capacity retention among all these samples, exhibited the initial capacity of 115 mAh/g and maintained more than 90% of the initial value at the 50th cycle.

Classification of rare missense substitutions, using risk surfaces, with genetic- and molecular-epidemiology applications.

PubMed

Tavtigian, Sean V; Byrnes, Graham B; Goldgar, David E; Thomas, Alun

2008-11-01

Many individually rare missense substitutions are encountered during deep resequencing of candidate susceptibility genes and clinical mutation screening of known susceptibility genes. BRCA1 and BRCA2 are among the most resequenced of all genes, and clinical mutation screening of these genes provides an extensive data set for analysis of rare missense substitutions. Align-GVGD is a mathematically simple missense substitution analysis algorithm, based on the Grantham difference, which has already contributed to classification of missense substitutions in BRCA1, BRCA2, and CHEK2. However, the distribution of genetic risk as a function of Align-GVGD's output variables Grantham variation (GV) and Grantham deviation (GD) has not been well characterized. Here, we used data from the Myriad Genetic Laboratories database of nearly 70,000 full-sequence tests plus two risk estimates, one approximating the odds ratio and the other reflecting strength of selection, to display the distribution of risk in the GV-GD plane as a series of surfaces. We abstracted contours from the surfaces and used the contours to define a sequence of missense substitution grades ordered from greatest risk to least risk. The grades were validated internally using a third, personal and family history-based, measure of risk. The Align-GVGD grades defined here are applicable to both the genetic epidemiology problem of classifying rare missense substitutions observed in known susceptibility genes and the molecular epidemiology problem of analyzing rare missense substitutions observed during case-control mutation screening studies of candidate susceptibility genes. (c) 2008 Wiley-Liss, Inc.

Evaluation of Different Oligonucleotide Base Substitutions at CpG Binding sites in Multiplex Bisulfite-PCR sequencing.

PubMed

Lu, Jennifer; Ru, Kelin; Candiloro, Ida; Dobrovic, Alexander; Korbie, Darren; Trau, Matt

2017-03-22

Multiplex bisulfite-PCR sequencing is a convenient and scalable method for the quantitative determination of the methylation state of target DNA regions. A challenge of this application is the presence of CpGs in the same region where primers are being placed. A common solution to the presence of CpGs within a primer-binding region is to substitute a base degeneracy at the cytosine position. However, the efficacy of different substitutions and the extent to which bias towards methylated or unmethylated templates may occur has never been evaluated in bisulfite multiplex sequencing applications. In response, we examined the performance of four different primer substitutions at the cytosine position of CpG's contained within the PCR primers. In this study, deoxyinosine-, 5-nitroindole-, mixed-base primers and primers with an abasic site were evaluated across a series of methylated controls. Primers that contained mixed- or deoxyinosine- base modifications performed most robustly. Mixed-base primers were further selected to determine the conditions that induce bias towards methylated templates. This identified an optimized set of conditions where the methylated state of bisulfite DNA templates can be accurately assessed using mixed-base primers, and expands the scope of bisulfite resequencing assays when working with challenging templates.

Therapy of vaginismus by hypnotic desensitization.

PubMed

Fuchs, K

1980-05-01

Fear and anxiety are of tremendous importance in the production and maintenance of a symptom. Vaginismus, as a reaction of avoidance of an anxiety-producing situation, is readily amenable to treatment by systematic desensitization. This may proceed mainly in two ways: "in vitro" or "in vivo." In order to strengthen and speed up the densensitization process, we used hypnotic techniques in a dynamic approach. The "in vitro" treatment proceeds with imagery, under hypnosis, of an "anxiety hierarchy" of increasingly erotic and sexually intimate situations which will be reproduced at home with the partner, until sexual intercourse is achieved. In the "in vivo" method the patient learns self-hypnosis and then inserts in the vagina first a finger, and then Hegar dilators of gradually increasing sizes. The partner, the patient, and the physician will then successively proceed to insertion, forming a team-referred work situation. This continues until the "female superior position," practiced first with the largest dilator, is reproduced at home by intercourse. Between 1965 and 1974 we treated 71 women with this method. Good results were obtained in 16 of 18 by the "in vitro" technique and in 53 of 54 by the "in vivo" technique. One patient was referred from the "in vitro" group to the "in vivo" group. In follow-up of 2 to 5 years there was no relapse or symptom substitution.

Comparative Mitogenomic Analysis of Damsel Bugs Representing Three Tribes in the Family Nabidae (Insecta: Hemiptera)

PubMed Central

Song, Fan; Shi, Aimin; Zhou, Xuguo; Cai, Wanzhi

2012-01-01

Background Nabidae, a family of predatory heteropterans, includes two subfamilies and five tribes. We previously reported the complete mitogenome of Alloeorhynchus bakeri, a representative of the tribe Prostemmatini in the subfamily Prostemmatinae. To gain a better understanding of architecture and evolution of mitogenome in Nabidae, mitogenomes of five species representing two tribes (Gorpini and Nabini) in the subfamily Nabinae were sequenced, and a comparative mitogenomic analysis of three nabid tribes in two subfamilies was carried out. Methodology/Principal Findings Nabid mitogenomes share a similar nucleotide composition and base bias, except for the control region, where differences are observed at the subfamily level. In addition, the pattern of codon usage is influenced by the GC content and consistent with the standard invertebrate mitochondrial genetic code and the preference for A+T-rich codons. The comparison among orthologous protein-coding genes shows that different genes have been subject to different rates of molecular evolution correlated with the GC content. The stems and anticodon loops of tRNAs are extremely conserved, and the nucleotide substitutions are largely restricted to TψC and DHU loops and extra arms, with insertion-deletion polymorphisms. Comparative analysis shows similar rates of substitution between the two rRNAs. Long non-coding regions are observed in most Gorpini and Nabini mtDNAs in-between trnI-trnQ and/or trnS2-nad1. The lone exception, Nabis apicalis, however, has lost three tRNAs. Overall, phylogenetic analysis using mitogenomic data is consistent with phylogenies constructed mainly form morphological traits. Conclusions/Significance This comparative mitogenomic analysis sheds light on the architecture and evolution of mitogenomes in the family Nabidae. Nucleotide diversity and mitogenomic traits are phylogenetically informative at subfamily level. Furthermore, inclusion of a broader range of samples representing various taxonomic levels is critical for the understanding of mitogenomic evolution in damsel bugs. PMID:23029320

[Inserts for foot deformities].

PubMed

Stinus, H; Weber, F

2005-08-01

Inserts are orthopedic aids in the treatment of foot disorders that result from changes of the static or dynamic situation. Provision of appropriate orthopedic devices can relieve the pain caused by forefoot deformities either in lieu of surgical intervention or in rare cases also following surgical treatment to improve the symptoms of residual pain.Available materials provide support, padding, and cushioning. Inserts are custom-made to measure and/or based on a plaster impression. Determining the indication, prescribing the inlay, and checking the orthosis are the tasks of the physician. One treatment option for relieving the pain of forefoot deformities consists in conservative therapy with an insert combining features of padding and support as well as adjusting a ready-made shoe. The shoe and inlay should constitute a functional unit since often the optimal effect is only achieved with a combination of insert and orthopedic adjustment of the ready-made shoe.

Accelerated hydrolysis of substituted cellulose for potential biofuel production: kinetic study and modeling.

PubMed

Mu, Bingnan; Xu, Helan; Yang, Yiqi

2015-11-01

In this work, kinetics of substitution accelerated cellulose hydrolysis with multiple reaction stages was investigated to lay foundation for mechanism study and molecular design of substituting compounds. High-efficiency hydrolysis of cellulose is critical for cellulose-based bioethanol production. It is known that, substitution could substantially decrease activation energy and increase reaction rate of acidic hydrolysis of glycosidic bonds in cellulose. However, reaction kinetics and mechanism of the accelerated hydrolysis were not fully revealed. In this research, it was proved that substitution therefore accelerated hydrolysis only occurred in amorphous regions of cellulose fibers, and was a process with multiple reaction stages. With molar ratio of substitution less than 1%, the overall hydrolysis rate could be increased for around 10 times. We also quantified the relationship between the hydrolysis rate of individual reaction stage and its major influences, including molar ratio of substitution, activation energy of acidic hydrolysis, pH and temperature. Copyright © 2015 Elsevier Ltd. All rights reserved.

Clinical outcomes of VNS therapy with AspireSR® (including cardiac-based seizure detection) at a large complex epilepsy and surgery centre.

PubMed

Hamilton, Preci; Soryal, Imad; Dhahri, Prince; Wimalachandra, Welege; Leat, Anna; Hughes, Denise; Toghill, Nicole; Hodson, James; Sawlani, Vijay; Hayton, Tom; Samarasekera, Shanika; Bagary, Manny; McCorry, Dougall; Chelvarajah, Ramesh

2018-05-01

To compare the efficacy of AspireSR ® to preceding VNS battery models for battery replacements, and to determine the efficacy of the AspireSR ® for new implants. Data were collected retrospectively from patients with epilepsy who had VNS AspireSR ® implanted over a three-year period between June 2014 and June 2017 by a single surgeon. Cases were divided into two cohorts, those in whom the VNS was a new insertion, and those in whom the VNS battery was changed from a previous model to AspireSR ® . Within each group, the seizure burden was compared between the periods before and after insertion of AspireSR ® . Fifty-one patients with a newly inserted AspireSR ® VNS model had a significant reduction in seizure frequency (p < 0.001), with 59% (n = 30) reporting ≥50% reduction. Of the 62 patients who had an existing VNS, 53% (n = 33) reported ≥50% reduction in seizure burden when the original VNS was inserted. After the battery was changed to the AspireSR ® , 71% (n = 44) reported a further reduction of ≥50% in their seizure burden. The size of this reduction was at least as large as that resulting from the insertion of their existing VNS in 98% (61/62) of patients. The results suggest that approximately 70% of patients with existing VNS insertions could have significant additional benefit from cardiac based seizure detection and closed loop stimulation from the AspireSR ® device. For new insertions, the AspireSR ® device has efficacy in 59% of patients. The 'rule of thirds' used in counseling patients may need to be modified accordingly. Crown Copyright © 2018. Published by Elsevier Ltd. All rights reserved.

The influence of cholinesterase inhibitor therapy for dementia on risk of cardiac pacemaker insertion: a retrospective, population-based, health administrative databases study in Ontario, Canada.

PubMed

Huang, Allen R; Redpath, Calum J; van Walraven, Carl

2015-04-28

Cholinesterase inhibitors are used to treat the symptoms of dementia and can theoretically cause bradycardia. Previous studies suggest that patients taking these medications have an increased risk of undergoing pacemaker insertion. Since these drugs have a marginal impact on patient outcomes, it might be preferable to change drug treatment rather than implant a pacemaker. This population-based study determined the association of people with dementia exposed to cholinesterase inhibitor medication and pacemaker insertion. We used data from the Ontario health administrative databases from January 1, 1993 to June 30, 2012. We included all community-dwelling seniors who had a code for dementia and were exposed to cholinesterase inhibitors (donezepil, galantamine, and rivastigmine) and/or drugs used to treat co-morbidities of hypertension, diabetes, depression and hypothyroidism. We controlled for exposure to anti-arrhythmic drugs. Observation started at first exposure to any medication and continued until the earliest of pacemaker insertion, death, or end of study. 2,353,909 people were included with 96,000 (4.1%) undergoing pacemaker insertion during the observation period. Case-control analysis showed that pacemaker patients were less likely to be coded with dementia (unadjusted OR 0.42 [95%CI 0.41-0.42]) or exposed to cholinesterase inhibitors (unadjusted OR 0.39 [95%CI 0.37-0.41]). That Cohort analysis showed patients with dementia taking cholinesterase inhibitors had a decreased risk of pacemaker insertion (unadj-HR 0.58 [0.55-0.61]). Adjustment for patient age, sex, and other medications did not notably change results, as did restricting the analysis to incident users. Patients taking cholinesterase inhibitors rarely undergo, and have a significantly reduced risk of, cardiac pacemaker insertion.

Insertion characteristics and placement of the Mid-Scala electrode array in human temporal bones using detailed cone beam computed tomography.

PubMed

Dietz, Aarno; Gazibegovic, Dzemal; Tervaniemi, Jyrki; Vartiainen, Veli-Matti; Löppönen, Heikki

2016-12-01

The aim of this study was to evaluate the insertion results and placement of the new Advanced Bionics HiFocus Mid-Scala (HFms) electrode array, inserted through the round window membrane, in eight fresh human temporal bones using cone beam computed tomography (CBCT). Pre- and post-insertion CBCT scans were registered to create a 3D reconstruction of the cochlea with the array inserted. With an image fusion technique both the bony edges of the cochlea and the electrode array in situ could accurately be determined, thus enabling to identify the exact position of the electrode array within the scala tympani. Vertical and horizontal scalar location was measured at four points along the cochlea base at an angular insertion depth of 90°, 180° and 270° and at electrode 16, the most basal electrode. Smooth insertion through the round window membrane was possible in all temporal bones. The imaging results showed that there were no dislocations from the scala tympani into the scala vestibule. The HFms electrode was positioned in the middle of the scala along the whole electrode array in three out of the eight bones and in 62 % of the individual locations measured along the base of the cochlea. In only one cochlea a close proximity of the electrode with the basilar membrane was observed, indicating possible contact with the basilar membrane. The results and assessments presented in this study appear to be highly accurate. Although a further validation including histopathology is needed, the image fusion technique described in this study represents currently the most accurate method for intracochlear electrode assessment obtainable with CBCT.

Can we cut out the meat of the dish? Constructing consumer-oriented pathways towards meat substitution.

PubMed

Schösler, Hanna; de Boer, Joop; Boersema, Jan J

2012-02-01

The shift towards a more sustainable diet necessitates less reliance on foods of animal origin. This study presents data from a representative survey of Dutch consumers on their practices related to meat, meat substitution and meat reduction. The practices reflected a cultural gradient of meat substitution options running from other products of animal origin and conventional meat free meals to real vegetarian meals. To investigate feasible substitution options, a variety of meals without meat were presented using photos, which were rated by the participants in terms of attractiveness and chances that they would prepare a similar meal at home. The results demonstrated the influence of meal formats, product familiarity, cooking skills, preferences for plant-based foods and motivational orientations towards food. In particular, a lack of familiarity and skill hampered the preparation of real vegetarian meals. Based on the findings we propose a diversified understanding of meat substitution and we specify four policy-relevant pathways for a transition towards a more plant-based diet, including an incremental change towards more health-conscious vegetarian meals, a pathway that utilizes the trend towards convenience, a pathway of reduced portion size, and practice-oriented change towards vegetarian meals. Copyright © 2011 Elsevier Ltd. All rights reserved.

Microneedle-based minimally-invasive measurement of puncture resistance and fracture toughness of sclera.

PubMed

Park, Seung Hyun; Lee, Kang Ju; Lee, JiYong; Yoon, Jae Hyoung; Jo, Dong Hyun; Kim, Jeong Hun; Kang, Keonwook; Ryu, WonHyoung

2016-10-15

The sclera provides the structural support of the eye and protects the intraocular contents. Since it covers a large portion of the eye surface and has relatively high permeability for most drugs, the sclera has been used as a major pathway for drug administration. Recently, microneedle (MN) technology has shown the possibility of highly local and minimally-invasive drug delivery to the eye by MN insertion through the sclera or the suprachoroidal space. Although ocular MN needs to be inserted through the sclera, there has been no systematic study to understand the mechanical properties of the sclera, which are important to design ocular MNs. In this study, we investigated a MN-based method to measure the puncture resistance and fracture toughness of the sclera. To reflect the conditions of MN insertion into the sclera, force-displacement curves obtained from MN-insertion tests were used to estimate the puncture resistance and fracture toughness of sclera tissue. To understand the effect of the insertion conditions, dependency of the mechanical properties on insertion speeds, pre-strain of the sclera, and MN sizes were analyzed and discussed. Measurement of mechanical property of soft biological tissue is challenging due to variations between tissue samples or lack of well-defined measurement techniques. Although non-invasive measurement techniques such as nano/micro indentation were employed to locally measure the elastic modulus of soft biological materials, mechanical properties such as puncture resistance or fracture toughness, which requires "invasive" measurement and is important for the application of "microneedles or hypodermic needles", has not been well studied. In this work, we report minimally-invasive measurement of puncture resistance and fracture toughness of sclera using a double MN insertion method. Parametric studies showed that use of MN proved to be advantageous because of minimally-invasive insertion into tissue as well as higher sensitivity to sub-tissue architecture during the measurement. Copyright © 2016 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

MR Performance Comparison of a PET/MR System Before and After SiPM-Based Time-of-Flight PET Detector Insertion

NASA Astrophysics Data System (ADS)

Khalighi, Mohammad Mehdi; Delso, Gaspar; Maramraju, Sri Harsha; Deller, Timothy W.; Levin, Craig S.; Glover, Gary H.

2016-10-01

A silicon photomultiplier (SiPM)-based time-of-flight capable PET detector has been integrated with a 70 cm wide-bore 3T MR scanner for simultaneous whole-body imaging (MR750w, GE Healthcare, Waukesha, WI). After insertion of the PET detector, the final PET/MR bore is 60 cm wide (SIGNA PET/MR, GE Healthcare, Waukesha, WI). The MR performance was compared before and after the PET ring insertion. B0 homogeneity, B1+ uniformity of the body coil along with peak B1+, coherent noise, and FBIRN (Function Biomedical Informatics Research Network) tests are used to compare the MR performance. It is shown that B0 homogeneity and coherent noise have not changed according to the system specifications. Peak B1+ is increased by 33% and B1+ inhomogeneity is increased by 4% after PET ring insertion due to a smaller diameter body coil design. The FBIRN test shows similar temporal stability before and after PET ring insertion. Due to a smaller body coil on the PET/MR system, the signal fluctuation to noise ratio (SFNR) and SNR for body receive coil, are improved by 40% and 160% for Echo Planar Imaging (EPI) and spiral sequences respectively. Comparison using RF- and gradient-intensive clinical sequences shows inserting the PET detectors into the wide-bore MRI has not compromised the MR image quality according to these tests.

A virtual reality based simulator for learning nasogastric tube placement.

PubMed

Choi, Kup-Sze; He, Xuejian; Chiang, Vico Chung-Lim; Deng, Zhaohong

2015-02-01

Nasogastric tube (NGT) placement is a common clinical procedure where a plastic tube is inserted into the stomach through the nostril for feeding or drainage. However, the placement is a blind process in which the tube may be mistakenly inserted into other locations, leading to unexpected complications or fatal incidents. The placement techniques are conventionally acquired by practising on unrealistic rubber mannequins or on humans. In this paper, a virtual reality based training simulation system is proposed to facilitate the training of NGT placement. It focuses on the simulation of tube insertion and the rendering of the feedback forces with a haptic device. A hybrid force model is developed to compute the forces analytically or numerically under different conditions, including the situations when the patient is swallowing or when the tube is buckled at the nostril. To ensure real-time interactive simulations, an offline simulation approach is adopted to obtain the relationship between the insertion depth and insertion force using a non-linear finite element method. The offline dataset is then used to generate real-time feedback forces by interpolation. The virtual training process is logged quantitatively with metrics that can be used for assessing objective performance and tracking progress. The system has been evaluated by nursing professionals. They found that the haptic feeling produced by the simulated forces is similar to their experience during real NGT insertion. The proposed system provides a new educational tool to enhance conventional training in NGT placement. Copyright © 2014 Elsevier Ltd. All rights reserved.

Comparison of mechanical behavior between implant-simulated bone tissue and implant-jaw bone tissue interfaces based on Pull Out testing

NASA Astrophysics Data System (ADS)

Lopez, C.; Muñoz, J. C.; Pinillos, J. C.

2013-11-01

The main purpose of this research was to achieve a better understanding of the relationship within the mechanical properties of human cadaver jaw bone with kind D2 density regarding a substitute polymer to simulate bone tissue, proposed by the ASTM, to evaluate orthopedic implants. However, despite the existence of several densities of foams and his mechanical characterization has been classified into different degrees of tissue densities to simulate cancellous and cortical bone, the value of the densities are different contrasted with the densities of bone tissue, making difficult to establish direct relationship about mechanical behavior between the polymer and the bone material, and therefore no clear criteria known for choosing the polymeric foam which describes the mechanical behavior of tissue for a specific or particular study. To understand such behavior from bone tissue regarding the polymer samples, on this research was a dental implant inserted into the samples, and subjected to destructive Pull Out test according to ASTM F543The Pull Out strength was compared between implant-jawbone and implant-rigid polyurethane foam interfaces. Thus, the test pieces with mechanical behavior similar to bone tissue, enabling an approximation to choose degree appropriate of polymer to replace the bone tissue in future trials biomechanical.

Osseointegration of zirconia implants: an SEM observation of the bone-implant interface.

PubMed

Depprich, Rita; Zipprich, Holger; Ommerborn, Michelle; Mahn, Eduardo; Lammers, Lydia; Handschel, Jörg; Naujoks, Christian; Wiesmann, Hans-Peter; Kübler, Norbert R; Meyer, Ulrich

2008-11-06

The successful use of zirconia ceramics in orthopedic surgery led to a demand for dental zirconium-based implant systems. Because of its excellent biomechanical characteristics, biocompatibility, and bright tooth-like color, zirconia (zirconium dioxide, ZrO2) has the potential to become a substitute for titanium as dental implant material. The present study aimed at investigating the osseointegration of zirconia implants with modified ablative surface at an ultrastructural level. A total of 24 zirconia implants with modified ablative surfaces and 24 titanium implants all of similar shape and surface structure were inserted into the tibia of 12 Göttinger minipigs. Block biopsies were harvested 1 week, 4 weeks or 12 weeks (four animals each) after surgery. Scanning electron microscopy (SEM) analysis was performed at the bone implant interface. Remarkable bone attachment was already seen after 1 week which increased further to intimate bone contact after 4 weeks, observed on both zirconia and titanium implant surfaces. After 12 weeks, osseointegration without interposition of an interfacial layer was detected. At the ultrastructural level, there was no obvious difference between the osseointegration of zirconia implants with modified ablative surfaces and titanium implants with a similar surface topography. The results of this study indicate similar osseointegration of zirconia and titanium implants at the ultrastructural level.

Spectrum of benzo[a]pyrene-induced mutations in the Pig-a gene of L5178YTk+/- cells identified with next generation sequencing.

PubMed

Revollo, Javier; Wang, Yiying; McKinzie, Page; Dad, Azra; Pearce, Mason; Heflich, Robert H; Dobrovolsky, Vasily N

2017-12-01

We used Sanger sequencing and next generation sequencing (NGS) for analysis of mutations in the endogenous X-linked Pig-a gene of clonally expanded L5178YTk +/- cells. The clones developed from single cells that were sorted on a flow cytometer based upon the expression pattern of the GPI-anchored marker, CD90, on their surface. CD90-deficient and CD90-proficient cells were sorted from untreated cultures and CD90-deficient cells were sorted from cultures treated with benzo[a]pyrene (B[a]P). Pig-a mutations were identified in all clones developed from CD90-deficient cells; no Pig-a mutations were found in clones of CD90-proficient cells. The spectrum of B[a]P-induced Pig-a mutations was dominated by basepair substitutions, small insertions and deletions at G:C, or at sequences rich in G:C content. We observed high concordance between Pig-a mutations determined by Sanger sequencing and by NGS, but NGS was able to identify mutations in samples that were difficult to analyze by Sanger sequencing (e.g., mixtures of two mutant clones). Overall, the NGS method is a cost and labor efficient high throughput approach for analysis of a large number of mutant clones. Published by Elsevier B.V.

Dysgraphia in Patients with Primary Lateral Sclerosis: A Speech-Based Rehearsal Deficit?

PubMed Central

Zago, S.; Poletti, B.; Corbo, M.; Adobbati, L.; Silani, V.

2008-01-01

The present study aims to demonstrate that errors when writing are more common than expected in patients affected by primary lateral sclerosis (PLS) with severe dysarthria or complete mutism, independent of spasticity. Sixteen patients meeting Pringle’s et al. [34] criteria for PLS underwent standard neuropsychological tasks and evaluation of writing. We assessed writing abilities in spelling through dictation in which a set of words, non-words and short phrases were presented orally and by composing words using a set of preformed letters. Finally, a written copying task was performed with the same words. Relative to controls, PLS patients made a greater number of spelling errors in all writing conditions, but not in copy task. The error types included: omissions, transpositions, insertions and letter substitutions. These were equally distributed on the writing task and the composition of words with a set of preformed letters. This pattern of performance is consistent with a spelling impairment. The results are consistent with the concept that written production is critically dependent on the subvocal articulatory mechanism of rehearsal, perhaps at the level of retaining the sequence of graphemes in a graphemic buffer. In PLS patients a disturbance in rehearsal opportunity may affect the correct sequencing/assembly of an orthographic representation in the written process. PMID:19096141

Catalog of genetic progression of human cancers: breast cancer.

PubMed

Desmedt, Christine; Yates, Lucy; Kulka, Janina

2016-03-01

With the rapid development of next-generation sequencing, deeper insights are being gained into the molecular evolution that underlies the development and clinical progression of breast cancer. It is apparent that during evolution, breast cancers acquire thousands of mutations including single base pair substitutions, insertions, deletions, copy number aberrations, and structural rearrangements. As a consequence, at the whole genome level, no two cancers are identical and few cancers even share the same complement of "driver" mutations. Indeed, two samples from the same cancer may also exhibit extensive differences due to constant remodeling of the genome over time. In this review, we summarize recent studies that extend our understanding of the genomic basis of cancer progression. Key biological insights include the following: subclonal diversification begins early in cancer evolution, being detectable even in in situ lesions; geographical stratification of subclonal structure is frequent in primary tumors and can include therapeutically targetable alterations; multiple distant metastases typically arise from a common metastatic ancestor following a "metastatic cascade" model; systemic therapy can unmask preexisting resistant subclones or influence further treatment sensitivity and disease progression. We conclude the review by describing novel approaches such as the analysis of circulating DNA and patient-derived xenografts that promise to further our understanding of the genomic changes occurring during cancer evolution and guide treatment decision making.

Genetic variation in the chloroplast genome suggests multiple domestication of cultivated Asian rice (Oryza sativa L.).

PubMed

Kawakami, Shin-ichi; Ebana, Kaworu; Nishikawa, Tomotaro; Sato, Yo-ichiro; Vaughan, Duncan A; Kadowaki, Koh-ichi

2007-02-01

Two hundred and seventy-five accessions of cultivated Asian rice and 44 accessions of AA genome Oryza species were classified into 8 chloroplast (cp) genome types (A-H) based on insertion-deletion events at 3 regions (8K, 57K, and 76K) of the cp genome. The ancestral cp genome type was determined according to the frequency of occurrence in Oryza species and the likely evolution of the variable 57K region of the cp genome. When 2 nucleotide substitutions (AA or TT) were taken into account, these 8 cp types were subdivided into 11 cp types. Most indica cultivars had 1 of 3 cp genome types that were also identified in the wild relatives of rice, O. nivara and O. rufipogon, suggesting that the 3 indica cp types had evolved from distinct gene pools of the O. rufipogon - O. nivara complex. The majority of japonica cultivars had 1 of 3 different cp genome types. One of these 3 was identified in O. rufipogon, suggesting that at least 1 japonica type is derived from O. rufipogon with the same cp genome type. These results provide evidence to support a polyphyletic origin of cultivated Asian rice from at least 4 principal lineages in the O. rufipogon - O. nivara complex.

Cement As a Waste Form for Nuclear Fission Products: The Case of (90)Sr and Its Daughters.

PubMed

Dezerald, Lucile; Kohanoff, Jorge J; Correa, Alfredo A; Caro, Alfredo; Pellenq, Roland J-M; Ulm, Franz J; Saúl, Andrés

2015-11-17

One of the main challenges faced by the nuclear industry is the long-term confinement of nuclear waste. Because it is inexpensive and easy to manufacture, cement is the material of choice to store large volumes of radioactive materials, in particular the low-level medium-lived fission products. It is therefore of utmost importance to assess the chemical and structural stability of cement containing radioactive species. Here, we use ab initio calculations based on density functional theory (DFT) to study the effects of (90)Sr insertion and decay in C-S-H (calcium-silicate-hydrate) in order to test the ability of cement to trap and hold this radioactive fission product and to investigate the consequences of its β-decay on the cement paste structure. We show that (90)Sr is stable when it substitutes the Ca(2+) ions in C-S-H, and so is its daughter nucleus (90)Y after β-decay. Interestingly, (90)Zr, daughter of (90)Y and final product in the decay sequence, is found to be unstable compared to the bulk phase of the element at zero K but stable when compared to the solvated ion in water. Therefore, cement appears as a suitable waste form for (90)Sr storage.

Mendel’s Genes: Toward a Full Molecular Characterization

PubMed Central

Reid, James B.; Ross, John J.

2011-01-01

The discipline of classical genetics is founded on the hereditary behavior of the seven genes studied by Gregor Mendel. The advent of molecular techniques has unveiled much about the identity of these genes. To date, four genes have been sequenced: A (flower color), LE (stem length), I (cotyledon color), and R (seed shape). Two of the other three genes, GP (pod color) and FA (fasciation), are amenable to candidate gene approaches on the basis of their function, linkage relationships, and synteny between the pea and Medicago genomes. However, even the gene (locus) identity is not known for certain for the seventh character, the pod form, although it is probably V. While the nature of the mutations used by Mendel cannot be determined with certainty, on the basis of the varieties available in Europe in the 1850s, we can speculate on their nature. It turns out that these mutations are attributable to a range of causes—from simple base substitutions and changes to splice sites to the insertion of a transposon-like element. These findings provide a fascinating connection between Mendelian genetics and molecular biology that can be used very effectively in teaching new generations of geneticists. Mendel’s characters also provide novel insights into the nature of the genes responsible for characteristics of agronomic and consumer importance. PMID:21908742

Early-progressive dilated cardiomyopathy in a family with Becker muscular dystrophy related to a novel frameshift mutation in the dystrophin gene exon 27.

PubMed

Tsuda, Takeshi; Fitzgerald, Kristi; Scavena, Mena; Gidding, Samuel; Cox, Mary O; Marks, Harold; Flanigan, Kevin M; Moore, Steven A

2015-03-01

We report a family in which two male siblings with Becker muscular dystrophy (BMD) developed severe dilated cardiomyopathy (DCM) and progressive heart failure (HF) at age 11 years; one died at age 14 years while awaiting heart transplant and the other underwent left ventricular assist device implantation at the same age. Genetic analysis of one sibling showed a novel frameshift mutation in exon 27 of Duchenne muscular dystrophy (DMD) gene (c.3779_3785delCTTTGGAinsGG), in which seven base pairs are deleted and two are inserted. Although this predicts an amino-acid substitution and premature termination (p.Thr1260Argfs*8), muscle biopsy dystrophin immunostaining instead indicates that the mutation is more likely to alter splicing. Despite relatively preserved skeletal muscular performance, both the siblings developed progressive HF secondary to early-onset DCM. In addition, their 7-year-old nephew with delayed gross motor development, mild proximal muscle weakness and markedly elevated serum creatine kinase level (>13 000 IU l(-1)) at 16 months was recently demonstrated to have the familial DMD mutation. Here, we report a novel genotype of BMD with early-onset DCM and progressive lethal HF during early adolescence.

Bulk-heterojunction organic solar cells sandwiched by solution processed molybdenum oxide and titania nanosheet layers

NASA Astrophysics Data System (ADS)

Itoh, Eiji; Goto, Yoshinori; Fukuda, Katsutoshi

2014-02-01

The contributions of ultrathin titania nanosheet (TN) crystallites were studied in both an inverted bulk-heterojunction (BHJ) cell in an indium-tin oxide (ITO)/titania nanosheet (TN)/poly(3-hexylthiophene) (P3HT):phenyl-C61-butyric acid methylester (PCBM) active layer/MoOx/Ag multilayered photovoltaic device and a conventional BHJ cell in ITO/MoOx/P3HT:PCBM active layer/TN/Al multilayered photovoltaic device. The insertion of only one or two layers of poly(diallyldimethylammonium chloride) (PDDA) and TN multilayered film prepared by the layer-by-layer deposition technique effectively decreased the leakage current and increased the open circuit voltage (VOC), fill factor (FF), and power conversion efficiency (η). The conventional cell sandwiched between a solution-processed, partially crystallized molybdenum oxide hole-extracting buffer layer and a TN electron extracting buffer layer showed comparable cell performance to a device sandwiched between vacuum-deposited molybdenum oxide and TN layers, whereas the inverted cell with solution-processed molybdenum oxide showed a poorer performance probably owing to the increment in the leakage current across the film. The abnormal S-shaped curves observed in the inverted BHJ cell above VOC disappeared with the use of a polyfluorene-based cationic semiconducting polymer as a substitute for an insulating PDDA film, resulting in the improved cell performance.

Oxidized nucleotide insertion by pol β confounds ligation during base excision repair

PubMed Central

Çağlayan, Melike; Horton, Julie K.; Dai, Da-Peng; Stefanick, Donna F.; Wilson, Samuel H.

2017-01-01

Oxidative stress in cells can lead to accumulation of reactive oxygen species and oxidation of DNA precursors. Oxidized purine nucleotides can be inserted into DNA during replication and repair. The main pathway for correcting oxidized bases in DNA is base excision repair (BER), and in vertebrates DNA polymerase β (pol β) provides gap filling and tailoring functions. Here we report that the DNA ligation step of BER is compromised after pol β insertion of oxidized purine nucleotides into the BER intermediate in vitro. These results suggest the possibility that BER mediated toxic strand breaks are produced in cells under oxidative stress conditions. We observe enhanced cytotoxicity in oxidizing-agent treated pol β expressing mouse fibroblasts, suggesting formation of DNA strand breaks under these treatment conditions. Increased cytotoxicity following MTH1 knockout or treatment with MTH1 inhibitor suggests the oxidation of precursor nucleotides. PMID:28067232

Read count-based method for high-throughput allelic genotyping of transposable elements and structural variants.

PubMed

Kuhn, Alexandre; Ong, Yao Min; Quake, Stephen R; Burkholder, William F

2015-07-08

Like other structural variants, transposable element insertions can be highly polymorphic across individuals. Their functional impact, however, remains poorly understood. Current genome-wide approaches for genotyping insertion-site polymorphisms based on targeted or whole-genome sequencing remain very expensive and can lack accuracy, hence new large-scale genotyping methods are needed. We describe a high-throughput method for genotyping transposable element insertions and other types of structural variants that can be assayed by breakpoint PCR. The method relies on next-generation sequencing of multiplex, site-specific PCR amplification products and read count-based genotype calls. We show that this method is flexible, efficient (it does not require rounds of optimization), cost-effective and highly accurate. This method can benefit a wide range of applications from the routine genotyping of animal and plant populations to the functional study of structural variants in humans.

Techniques for virtual lung nodule insertion: volumetric and morphometric comparison of projection-based and image-based methods for quantitative CT

NASA Astrophysics Data System (ADS)

Robins, Marthony; Solomon, Justin; Sahbaee, Pooyan; Sedlmair, Martin; Choudhury, Kingshuk Roy; Pezeshk, Aria; Sahiner, Berkman; Samei, Ehsan

2017-09-01

Virtual nodule insertion paves the way towards the development of standardized databases of hybrid CT images with known lesions. The purpose of this study was to assess three methods (an established and two newly developed techniques) for inserting virtual lung nodules into CT images. Assessment was done by comparing virtual nodule volume and shape to the CT-derived volume and shape of synthetic nodules. 24 synthetic nodules (three sizes, four morphologies, two repeats) were physically inserted into the lung cavity of an anthropomorphic chest phantom (KYOTO KAGAKU). The phantom was imaged with and without nodules on a commercial CT scanner (SOMATOM Definition Flash, Siemens) using a standard thoracic CT protocol at two dose levels (1.4 and 22 mGy CTDIvol). Raw projection data were saved and reconstructed with filtered back-projection and sinogram affirmed iterative reconstruction (SAFIRE, strength 5) at 0.6 mm slice thickness. Corresponding 3D idealized, virtual nodule models were co-registered with the CT images to determine each nodule’s location and orientation. Virtual nodules were voxelized, partial volume corrected, and inserted into nodule-free CT data (accounting for system imaging physics) using two methods: projection-based Technique A, and image-based Technique B. Also a third Technique C based on cropping a region of interest from the acquired image of the real nodule and blending it into the nodule-free image was tested. Nodule volumes were measured using a commercial segmentation tool (iNtuition, TeraRecon, Inc.) and deformation was assessed using the Hausdorff distance. Nodule volumes and deformations were compared between the idealized, CT-derived and virtual nodules using a linear mixed effects regression model which utilized the mean, standard deviation, and coefficient of variation (Mea{{n}RHD} , ST{{D}RHD} and C{{V}RHD}{) }~ of the regional Hausdorff distance. Overall, there was a close concordance between the volumes of the CT-derived and virtual nodules. Percent differences between them were less than 3% for all insertion techniques and were not statistically significant in most cases. Correlation coefficient values were greater than 0.97. The deformation according to the Hausdorff distance was also similar between the CT-derived and virtual nodules with minimal statistical significance in the (C{{V}RHD} ) for Techniques A, B, and C. This study shows that both projection-based and image-based nodule insertion techniques yield realistic nodule renderings with statistical similarity to the synthetic nodules with respect to nodule volume and deformation. These techniques could be used to create a database of hybrid CT images containing nodules of known size, location and morphology.

Techniques for virtual lung nodule insertion: volumetric and morphometric comparison of projection-based and image-based methods for quantitative CT

PubMed Central

Robins, Marthony; Solomon, Justin; Sahbaee, Pooyan; Sedlmair, Martin; Choudhury, Kingshuk Roy; Pezeshk, Aria; Sahiner, Berkman; Samei, Ehsan

2017-01-01

Virtual nodule insertion paves the way towards the development of standardized databases of hybrid CT images with known lesions. The purpose of this study was to assess three methods (an established and two newly developed techniques) for inserting virtual lung nodules into CT images. Assessment was done by comparing virtual nodule volume and shape to the CT-derived volume and shape of synthetic nodules. 24 synthetic nodules (three sizes, four morphologies, two repeats) were physically inserted into the lung cavity of an anthropomorphic chest phantom (KYOTO KAGAKU). The phantom was imaged with and without nodules on a commercial CT scanner (SOMATOM Definition Flash, Siemens) using a standard thoracic CT protocol at two dose levels (1.4 and 22 mGy CTDIvol). Raw projection data were saved and reconstructed with filtered back-projection and sinogram affirmed iterative reconstruction (SAFIRE, strength 5) at 0.6 mm slice thickness. Corresponding 3D idealized, virtual nodule models were co-registered with the CT images to determine each nodule’s location and orientation. Virtual nodules were voxelized, partial volume corrected, and inserted into nodule-free CT data (accounting for system imaging physics) using two methods: projection-based Technique A, and image-based Technique B. Also a third Technique C based on cropping a region of interest from the acquired image of the real nodule and blending it into the nodule-free image was tested. Nodule volumes were measured using a commercial segmentation tool (iNtuition, TeraRecon, Inc.) and deformation was assessed using the Hausdorff distance. Nodule volumes and deformations were compared between the idealized, CT-derived and virtual nodules using a linear mixed effects regression model which utilized the mean, standard deviation, and coefficient of variation (MeanRHD, and STDRHD CVRHD) of the regional Hausdorff distance. Overall, there was a close concordance between the volumes of the CT-derived and virtual nodules. Percent differences between them were less than 3% for all insertion techniques and were not statistically significant in most cases. Correlation coefficient values were greater than 0.97. The deformation according to the Hausdorff distance was also similar between the CT-derived and virtual nodules with minimal statistical significance in the (CVRHD) for Techniques A, B, and C. This study shows that both projection-based and image-based nodule insertion techniques yield realistic nodule renderings with statistical similarity to the synthetic nodules with respect to nodule volume and deformation. These techniques could be used to create a database of hybrid CT images containing nodules of known size, location and morphology. PMID:28786399

Rapid construction of a Bacterial Artificial Chromosomal (BAC) expression vector using designer DNA fragments.

PubMed

Chen, Chao; Zhao, Xinqing; Jin, Yingyu; Zhao, Zongbao Kent; Suh, Joo-Won

2014-11-01

Bacterial artificial chromosomal (BAC) vectors are increasingly being used in cloning large DNA fragments containing complex biosynthetic pathways to facilitate heterologous production of microbial metabolites for drug development. To express inserted genes using Streptomyces species as the production hosts, an integration expression cassette is required to be inserted into the BAC vector, which includes genetic elements encoding a phage-specific attachment site, an integrase, an origin of transfer, a selection marker and a promoter. Due to the large sizes of DNA inserted into the BAC vectors, it is normally inefficient and time-consuming to assemble these fragments by routine PCR amplifications and restriction-ligations. Here we present a rapid method to insert fragments to construct BAC-based expression vectors. A DNA fragment of about 130 bp was designed, which contains upstream and downstream homologous sequences of both BAC vector and pIB139 plasmid carrying the whole integration expression cassette. In-Fusion cloning was performed using the designer DNA fragment to modify pIB139, followed by λ-RED-mediated recombination to obtain the BAC-based expression vector. We demonstrated the effectiveness of this method by rapid construction of a BAC-based expression vector with an insert of about 120 kb that contains the entire gene cluster for biosynthesis of immunosuppressant FK506. The empty BAC-based expression vector constructed in this study can be conveniently used for construction of BAC libraries using either microbial pure culture or environmental DNA, and the selected BAC clones can be directly used for heterologous expression. Alternatively, if a BAC library has already been constructed using a commercial BAC vector, the selected BAC vectors can be manipulated using the method described here to get the BAC-based expression vectors with desired gene clusters for heterologous expression. The rapid construction of a BAC-based expression vector facilitates heterologous expression of large gene clusters for drug discovery. Copyright © 2014 Elsevier Inc. All rights reserved.

Synthesis and antimalarial activity study of some new Mannich bases of 7-chloro-4-aminoquinoline.

PubMed

Roy, Susanta; Chetia, Dipak; Rudrapal, Mithun; Prakash, Anil

2013-05-01

New derivatives of 7-chloro-4-aminoquinoline Mannich base were prepared by selectively modifying the aliphatic diethyl amino function of isoquine with different aliphatic/aromatic heterocyclic primary amino moieties at Mannich side chain. The synthesized compounds were characterized by their analytical and spectral data, and screened for in-vitro antimalarial activity against a chloroquine-sensitive 3D7 strain of Plasmodium falciparum. All the compounds showed in-vitro antimalarial activity at the tested dose; which, however, was considerably less than that of the standard reference drug, chloroquine. Among synthesized compounds, compounds with cyclohexyl (2f), methyl (2c) substitutions showed better activity than compounds substituted with n-octyl (2a), propyl (2b), 3-aminopropyl (2d) and furan-2- ylmethyl (2e) moieties at aminomethyl side chain. The results clearly demonstrate that the compound substituted with saturated cycloalkyl moiety (cyclohexyl) exhibited to some extent increased activity as compared to the compound containing heterocyclic moiety (furan-2-ylmethyl), and compounds with short chain alkyl substitutions (methyl, propyl) were found to be more active than that of compounds with long chain alkyl substitution (n-octyl).

High-Temperature Thermoelectric and Microstructural Characteristics of Cobalt-Based Oxides with Ga Substituted on the Co-Site

NASA Astrophysics Data System (ADS)

Nong, N. V.; Yanagiya, S.; Monica, S.; Pryds, N.; Ohtaki, M.

2011-05-01

The effects of Ga substitution on the Co-site on the high-temperature thermoelectric properties and microstructure are investigated for the misfitlayered Ca3Co4O9 and the complex perovskite-related Sr3RECo4O10.5 (RE = rare earth) cobalt-based oxides. For both systems, substitution of Ga for Co results in a simultaneous increase in the Seebeck coefficient ( S) and the electrical conductivity ( σ), and the influence is more significant in the high temperature region. The power factor ( S 2 σ) is thereby remarkably improved by Ga substitution, particularly at high temperatures. Texture factor calculations using x-ray diffraction pattern data for pressed and powder samples reveal that the Ga-doped samples are highly textured. Microstructure observed by scanning electron microscopy shows very well-crystallized grains for the samples with Ga substitution for Co. Among the Ga-doped samples, Ca3Co3.95Ga0.05O9 shows the best ZT value of 0.45 at 1200 K, which is about 87.5% higher than the nondoped one, a considerable improvement.

A System for Discovering Bioengineered Threats by Knowledge Base Driven Mining of Toxin Data

DTIC Science & Technology

2004-08-01

RMSD cut - off and select a residue substitution matrix. The user is also allowed...in the sense that after super-positioning, the RMSD between the substructures is no more than the cut - off RMSD . * Residue substitutions are allowed...during super-positioning. Default RMSD cut - off and residue substitution matrix are provided. Users can specify their own RMSD cut - offs as well as

Epistatic interactions influence terrestrial–marine functional shifts in cetacean rhodopsin

PubMed Central

2017-01-01

Like many aquatic vertebrates, whales have blue-shifting spectral tuning substitutions in the dim-light visual pigment, rhodopsin, that are thought to increase photosensitivity in underwater environments. We have discovered that known spectral tuning substitutions also have surprising epistatic effects on another function of rhodopsin, the kinetic rates associated with light-activated intermediates. By using absorbance spectroscopy and fluorescence-based retinal release assays on heterologously expressed rhodopsin, we assessed both spectral and kinetic differences between cetaceans (killer whale) and terrestrial outgroups (hippo, bovine). Mutation experiments revealed that killer whale rhodopsin is unusually resilient to pleiotropic effects on retinal release from key blue-shifting substitutions (D83N and A292S), largely due to a surprisingly specific epistatic interaction between D83N and the background residue, S299. Ancestral sequence reconstruction indicated that S299 is an ancestral residue that predates the evolution of blue-shifting substitutions at the origins of Cetacea. Based on these results, we hypothesize that intramolecular epistasis helped to conserve rhodopsin's kinetic properties while enabling blue-shifting spectral tuning substitutions as cetaceans adapted to aquatic environments. Trade-offs between different aspects of molecular function are rarely considered in protein evolution, but in cetacean and other vertebrate rhodopsins, may underlie multiple evolutionary scenarios for the selection of specific amino acid substitutions. PMID:28250185