Phage T4 SegB protein is a homing endonuclease required for the preferred inheritance of T4 tRNA gene region occurring in co-infection with a related phage.

PubMed

Brok-Volchanskaya, Vera S; Kadyrov, Farid A; Sivogrivov, Dmitry E; Kolosov, Peter M; Sokolov, Andrey S; Shlyapnikov, Michael G; Kryukov, Valentine M; Granovsky, Igor E

2008-04-01

Homing endonucleases initiate nonreciprocal transfer of DNA segments containing their own genes and the flanking sequences by cleaving the recipient DNA. Bacteriophage T4 segB gene, which is located in a cluster of tRNA genes, encodes a protein of unknown function, homologous to homing endonucleases of the GIY-YIG family. We demonstrate that SegB protein is a site-specific endonuclease, which produces mostly 3' 2-nt protruding ends at its DNA cleavage site. Analysis of SegB cleavage sites suggests that SegB recognizes a 27-bp sequence. It contains 11-bp conserved sequence, which corresponds to a conserved motif of tRNA TpsiC stem-loop, whereas the remainder of the recognition site is rather degenerate. T4-related phages T2L, RB1 and RB3 contain tRNA gene regions that are homologous to that of phage T4 but lack segB gene and several tRNA genes. In co-infections of phages T4 and T2L, segB gene is inherited with nearly 100% of efficiency. The preferred inheritance depends absolutely on the segB gene integrity and is accompanied by the loss of the T2L tRNA gene region markers. We suggest that SegB is a homing endonuclease that functions to ensure spreading of its own gene and the surrounding tRNA genes among T4-related phages.

Phage T4 SegB protein is a homing endonuclease required for the preferred inheritance of T4 tRNA gene region occurring in co-infection with a related phage

PubMed Central

Brok-Volchanskaya, Vera S.; Kadyrov, Farid A.; Sivogrivov, Dmitry E.; Kolosov, Peter M.; Sokolov, Andrey S.; Shlyapnikov, Michael G.; Kryukov, Valentine M.; Granovsky, Igor E.

2008-01-01

Homing endonucleases initiate nonreciprocal transfer of DNA segments containing their own genes and the flanking sequences by cleaving the recipient DNA. Bacteriophage T4 segB gene, which is located in a cluster of tRNA genes, encodes a protein of unknown function, homologous to homing endonucleases of the GIY-YIG family. We demonstrate that SegB protein is a site-specific endonuclease, which produces mostly 3′ 2-nt protruding ends at its DNA cleavage site. Analysis of SegB cleavage sites suggests that SegB recognizes a 27-bp sequence. It contains 11-bp conserved sequence, which corresponds to a conserved motif of tRNA TψC stem-loop, whereas the remainder of the recognition site is rather degenerate. T4-related phages T2L, RB1 and RB3 contain tRNA gene regions that are homologous to that of phage T4 but lack segB gene and several tRNA genes. In co-infections of phages T4 and T2L, segB gene is inherited with nearly 100% of efficiency. The preferred inheritance depends absolutely on the segB gene integrity and is accompanied by the loss of the T2L tRNA gene region markers. We suggest that SegB is a homing endonuclease that functions to ensure spreading of its own gene and the surrounding tRNA genes among T4-related phages. PMID:18281701

Creation of a type IIS restriction endonuclease with a long recognition sequence

PubMed Central

Lippow, Shaun M.; Aha, Patti M.; Parker, Matthew H.; Blake, William J.; Baynes, Brian M.; Lipovšek, Daša

2009-01-01

Type IIS restriction endonucleases cleave DNA outside their recognition sequences, and are therefore particularly useful in the assembly of DNA from smaller fragments. A limitation of type IIS restriction endonucleases in assembly of long DNA sequences is the relative abundance of their target sites. To facilitate ligation-based assembly of extremely long pieces of DNA, we have engineered a new type IIS restriction endonuclease that combines the specificity of the homing endonuclease I-SceI with the type IIS cleavage pattern of FokI. We linked a non-cleaving mutant of I-SceI, which conveys to the chimeric enzyme its specificity for an 18-bp DNA sequence, to the catalytic domain of FokI, which cuts DNA at a defined site outside the target site. Whereas previously described chimeric endonucleases do not produce type IIS-like precise DNA overhangs suitable for ligation, our chimeric endonuclease cleaves double-stranded DNA exactly 2 and 6 nt from the target site to generate homogeneous, 5′, four-base overhangs, which can be ligated with 90% fidelity. We anticipate that these enzymes will be particularly useful in manipulation of DNA fragments larger than a thousand bases, which are very likely to contain target sites for all natural type IIS restriction endonucleases. PMID:19304757

Selective inhibition by harmane of the apurinic apyrimidinic endonuclease activity of phage T4-induced UV endonuclease.

PubMed

Warner, H R; Persson, M L; Bensen, R J; Mosbaugh, D W; Linn, S

1981-11-25

1-Methyl-9H-pyrido-[3,4-b]indole (harmane) inhibits the apurinic/apyrimidinic (AP) endonuclease activity of the UV endonuclease induced by phage T4, whereas it stimulates the pyrimidine dimer-DNA glycosylase activity of that enzyme. E. coli endonuclease IV, E. coli endonuclease VI (the AP endonuclease activity associated with E. coli exonuclease III), and E. coli uracil-DNA glycosylase were not inhibited by harmane. Human fibroblast AP endonucleases I and II also were only slightly inhibited. Therefore, harmane is neither a general inhibitor of AP endonucleases, nor a general inhibitor of Class I AP endonucleases which incise DNA on the 3'-side of AP sites. However, E. coli endonuclease III and its associated dihydroxythymine-DNA glycosylase activity were both inhibited by harmane. This observation suggests that harmane may inhibit only AP endonucleases which have associated glycosylase activities.

Selective inhibition by harmane of the apurinic apyrimidinic endonuclease activity of phage T4-induced UV endonuclease.

PubMed Central

Warner, H R; Persson, M L; Bensen, R J; Mosbaugh, D W; Linn, S

1981-01-01

1-Methyl-9H-pyrido-[3,4-b]indole (harmane) inhibits the apurinic/apyrimidinic (AP) endonuclease activity of the UV endonuclease induced by phage T4, whereas it stimulates the pyrimidine dimer-DNA glycosylase activity of that enzyme. E. coli endonuclease IV, E. coli endonuclease VI (the AP endonuclease activity associated with E. coli exonuclease III), and E. coli uracil-DNA glycosylase were not inhibited by harmane. Human fibroblast AP endonucleases I and II also were only slightly inhibited. Therefore, harmane is neither a general inhibitor of AP endonucleases, nor a general inhibitor of Class I AP endonucleases which incise DNA on the 3'-side of AP sites. However, E. coli endonuclease III and its associated dihydroxythymine-DNA glycosylase activity were both inhibited by harmane. This observation suggests that harmane may inhibit only AP endonucleases which have associated glycosylase activities. PMID:6273822

Phylogenetic screening of a bacterial, metagenomic library using homing endonuclease restriction and marker insertion

PubMed Central

Yung, Pui Yi; Burke, Catherine; Lewis, Matt; Egan, Suhelen; Kjelleberg, Staffan; Thomas, Torsten

2009-01-01

Metagenomics provides access to the uncultured majority of the microbial world. The approaches employed in this field have, however, had limited success in linking functional genes to the taxonomic or phylogenetic origin of the organism they belong to. Here we present an efficient strategy to recover environmental DNA fragments that contain phylogenetic marker genes from metagenomic libraries. Our method involves the cleavage of 23S ribsosmal RNA (rRNA) genes within pooled library clones by the homing endonuclease I-CeuI followed by the insertion and selection of an antibiotic resistance cassette. This approach was applied to screen a library of 6500 fosmid clones derived from the microbial community associated with the sponge Cymbastela concentrica. Several fosmid clones were recovered after the screen and detailed phylogenetic and taxonomic assignment based on the rRNA gene showed that they belong to previously unknown organisms. In addition, compositional features of these fosmid clones were used to classify and taxonomically assign a dataset of environmental shotgun sequences. Our approach represents a valuable tool for the analysis of rapidly increasing, environmental DNA sequencing information. PMID:19767618

Problem-Solving Test: Restriction Endonuclease Mapping

ERIC Educational Resources Information Center

Szeberenyi, Jozsef

2011-01-01

The term "restriction endonuclease mapping" covers a number of related techniques used to identify specific restriction enzyme recognition sites on small DNA molecules. A method for restriction endonuclease mapping of a 1,000-basepair (bp)-long DNA molecule is described in the fictitious experiment of this test. The most important fact needed to…

An electrochemiluminescence biosensor for endonuclease EcoRI detection.

PubMed

Li, Yingjie; Li, Yuqin; Wu, Yaoyu; Lu, Fushen; Chen, Yaowen; Gao, Wenhua

2017-03-15

Endonucleases cleavage of DNA plays an important role in biological and medicinal chemistry. This work was going to develop a reliable and sensitive electrochemiluminescent (ECL) biosensor for detecting endonucleases by using gold nanoparticles graphene composite (GNPs-graphene) as a signal amplifier. Firstly, the GNPs and graphene were simultaneously deposited on the glassy carbon electrode (GCE) by cyclic voltammetry. Then a stem DNA was anchored on the surface of GCE. And with a modifying DNA introduced into the electrode by DNA assembly, a strong ECL signal was obtained. After a DNA modified with ferrocene assembly to the stem DNA, the ECL signal had a sharp decrease due to the quench effect of ferrocene to and the biosensor comes into being a "off" state. With the effect of endonuclease, the ECL signal had a recovery because of the ferrocene being released and the biosensor formed a "on" state. Moreover, the recovery of ECL signal was related to the concentration of endonucleases. Combining specific defined DNA and endonuclease, this method has a potential to detect different endonucleases. In this work, we took the EcoRI as an example to identify the feasibility of ECL biosensor in applying in sensitive detection of endonucleases using a GNPs-graphene signal amplifier. Under optimal condition, the proposed biosensor obtained a low limit of detection (LOD) 5.6×10 -5 UmL -1 . And the stability, selectivity and reproducibility of the biosensor also were researched. Copyright © 2016 Elsevier B.V. All rights reserved.

Expression of homing endonuclease gene and insertion-like element in sea anemone mitochondrial genomes: Lesson learned from Anemonia viridis.

PubMed

Chi, Sylvia Ighem; Urbarova, Ilona; Johansen, Steinar D

2018-04-30

The mitochondrial genomes of sea anemones are dynamic in structure. Invasion by genetic elements, such as self-catalytic group I introns or insertion-like sequences, contribute to sea anemone mitochondrial genome expansion and complexity. By using next generation sequencing we investigated the complete mtDNAs and corresponding transcriptomes of the temperate sea anemone Anemonia viridis and its closer tropical relative Anemonia majano. Two versions of fused homing endonuclease gene (HEG) organization were observed among the Actiniidae sea anemones; in-frame gene fusion and pseudo-gene fusion. We provided support for the pseudo-gene fusion organization in Anemonia species, resulting in a repressed HEG from the COI-884 group I intron. orfA, a putative protein-coding gene with insertion-like features, was present in both Anemonia species. Interestingly, orfA and COI expression were significantly up-regulated upon long-term environmental stress corresponding to low seawater pH conditions. This study provides new insights to the dynamics of sea anemone mitochondrial genome structure and function. Copyright © 2018 Elsevier B.V. All rights reserved.

Creating a monomeric endonuclease TALE-I-SceI with high specificity and low genotoxicity in human cells.

PubMed

Lin, Jianfei; Chen, He; Luo, Ling; Lai, Yongrong; Xie, Wei; Kee, Kehkooi

2015-01-01

To correct a DNA mutation in the human genome for gene therapy, homology-directed repair (HDR) needs to be specific and have the lowest off-target effects to protect the human genome from deleterious mutations. Zinc finger nucleases, transcription activator-like effector nuclease (TALEN) and CRISPR-CAS9 systems have been engineered and used extensively to recognize and modify specific DNA sequences. Although TALEN and CRISPR/CAS9 could induce high levels of HDR in human cells, their genotoxicity was significantly higher. Here, we report the creation of a monomeric endonuclease that can recognize at least 33 bp by fusing the DNA-recognizing domain of TALEN (TALE) to a re-engineered homing endonuclease I-SceI. After sequentially re-engineering I-SceI to recognize 18 bp of the human β-globin sequence, the re-engineered I-SceI induced HDR in human cells. When the re-engineered I-SceI was fused to TALE (TALE-ISVB2), the chimeric endonuclease induced the same HDR rate at the human β-globin gene locus as that induced by TALEN, but significantly reduced genotoxicity. We further demonstrated that TALE-ISVB2 specifically targeted at the β-globin sequence in human hematopoietic stem cells. Therefore, this monomeric endonuclease has the potential to be used in therapeutic gene targeting in human cells. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Linear nicking endonuclease-mediated strand-displacement DNA amplification.

PubMed

Joneja, Aric; Huang, Xiaohua

2011-07-01

We describe a method for linear isothermal DNA amplification using nicking endonuclease-mediated strand displacement by a DNA polymerase. The nicking of one strand of a DNA target by the endonuclease produces a primer for the polymerase to initiate synthesis. As the polymerization proceeds, the downstream strand is displaced into a single-stranded form while the nicking site is also regenerated. The combined continuous repetitive action of nicking by the endonuclease and strand-displacement synthesis by the polymerase results in linear amplification of one strand of the DNA molecule. We demonstrate that DNA templates up to 5000 nucleotides can be linearly amplified using a nicking endonuclease with 7-bp recognition sequence and Sequenase version 2.0 in the presence of single-stranded DNA binding proteins. We also show that a mixture of three templates of 500, 1000, and 5000 nucleotides in length is linearly amplified with the original molar ratios of the templates preserved. Moreover, we demonstrate that a complex library of hydrodynamically sheared genomic DNA from bacteriophage lambda can be amplified linearly. Copyright © 2011 Elsevier Inc. All rights reserved.

Linear nicking endonuclease-mediated strand displacement DNA amplification

PubMed Central

Joneja, Aric; Huang, Xiaohua

2011-01-01

We describe a method for linear isothermal DNA amplification using nicking endonuclease-mediated strand displacement by a DNA polymerase. The nicking of one strand of a DNA target by the endonuclease produces a primer for the polymerase to initiate synthesis. As the polymerization proceeds, the downstream strand is displaced into a single-stranded form while the nicking site is also regenerated. The combined continuous repetitive action of nicking by the endonuclease and strand displacement synthesis by the polymerase results in linear amplification of one strand of the DNA molecule. We demonstrate that DNA templates up to five thousand nucleotides can be linearly amplified using a nicking endonuclease with seven base-pair recognition sequence and Sequenase version 2.0 in the presence of single-stranded DNA binding proteins. We also show that a mixture of three templates of 500, 1000, and 5000 nucleotides in length are linearly amplified with the original molar ratios of the templates preserved. Moreover, we demonstrate that a complex library of hydrodynamically sheared genomic DNA from bacteriophage lambda can be amplified linearly. PMID:21342654

Homing at an extragenic locus mediated by VDE (PI-SceI) in Saccharomyces cerevisiae.

PubMed

Nogami, Satoru; Fukuda, Tomoyuki; Nagai, Yuri; Yabe, Shizu; Sugiura, Masako; Mizutani, Ryuta; Satow, Yoshinori; Anraku, Yasuhiro; Ohya, Yoshikazu

2002-06-30

PI-SceI (VDE), a homing endonuclease with protein splicing activity, is a genomic parasite in the VMA1 gene of Saccharomyces cerevisiae. In a heterozygous diploid of the VDE-less VMA1 allele and a VDE-containing VMA1 allele, VDE specifically cleaves its recognition sequence (VRS) in the VDE-less VMA1 allele at meiosis, followed by 'homing', i.e. a conversion to a VDE-containing allele. We found that upon VDE expression, homing of a marker gene at an extragenic locus occurs only when a 45 bp element containing the VRS is inserted at its allelic site, while mutants of VDE with no endonuclease activity lack authentic extragenic homing activity. Thus, both the VRS and VDE are required for homing. Insertion of the VRS in a homozygous diploid significantly lowered the spore germination ability, indicating that a template for gene repair at its allelic locus is essential for efficient homing and survival of yeast cells. Copyright 2002 John Wiley & Sons, Ltd.

The SalGI restriction endonuclease. Purification and properties

PubMed Central

Maxwell, Anthony; Halford, Stephen E.

1982-01-01

The type II restriction endonuclease SalGI has been purified to near homogeneity. At least 80% of the protein remaining after the final stage of the preparation is SalGI restriction endonuclease; no contaminating nucleases remain detectable. The principal form of the protein under both native and denaturing conditions is a monomer of Mr about 29000. The optimal conditions for both enzyme stability and enzyme activity have been determined. ImagesFig. 1. PMID:6285898

An antisense RNA in a lytic cyanophage links psbA to a gene encoding a homing endonuclease.

PubMed

Millard, Andrew D; Gierga, Gregor; Clokie, Martha R J; Evans, David J; Hess, Wolfgang R; Scanlan, David J

2010-09-01

Cyanophage genomes frequently possess the psbA gene, encoding the D1 polypeptide of photosystem II. This protein is believed to maintain host photosynthetic capacity during infection and enhance phage fitness under high-light conditions. Although the first documented cyanophage-encoded psbA gene contained a group I intron, this feature has not been widely reported since, despite a plethora of new sequences becoming available. In this study, we show that in cyanophage S-PM2, this intron is spliced during the entire infection cycle. Furthermore, we report the widespread occurrence of psbA introns in marine metagenomic libraries, and with psbA often adjacent to a homing endonuclease (HE). Bioinformatic analysis of the intergenic region between psbA and the adjacent HE gene F-CphI in S-PM2 showed the presence of an antisense RNA (asRNA) connecting these two separate genetic elements. The asRNA is co-regulated with psbA and F-CphI, suggesting its involvement with their expression. Analysis of scaffolds from global ocean survey datasets shows this asRNA to be commonly associated with the 3' end of cyanophage psbA genes, implying that this potential mechanism of regulating marine 'viral' photosynthesis is evolutionarily conserved. Although antisense transcription is commonly found in eukaryotic and increasingly also in prokaryotic organisms, there has been no indication for asRNAs in lytic phages so far. We propose that this asRNA also provides a means of preventing the formation of mobile group I introns within cyanophage psbA genes.

SLX4 Assembles a Telomere Maintenance Toolkit by Bridging Multiple Endonucleases with Telomeres

PubMed Central

Wan, Bingbing; Yin, Jinhu; Horvath, Kent; Sarkar, Jaya; Chen, Yong; Wu, Jian; Wan, Ke; Lu, Jian; Gu, Peili; Yu, Eun Young; Lue, Neal F.; Chang, Sandy

2014-01-01

Summary SLX4 interacts with several endonucleases to resolve structural barriers in DNA metabolism. SLX4 also interacts with telomeric protein TRF2 in human cells. The molecular mechanism of these interactions at telomeres remains unknown. Here, we report the crystal structure of the TRF2-binding motif of SLX4 (SLX4TBM) in complex with the TRFH domain of TRF2 (TRF2TRFH) and map the interactions of SLX4 with endonucleases SLX1, XPF, and MUS81. TRF2 recognizes a unique HxLxP motif on SLX4 via the peptide-binding site in its TRFH domain. Telomeric localization of SLX4 and associated nucleases depend on the SLX4-endonuclease and SLX4-TRF2 interactions and the protein levels of SLX4 and TRF2. SLX4 assembles an endonuclease toolkit that negatively regulates telomere length via SLX1-catalyzed nucleolytic resolution of telomere DNA structures. We propose that the SLX4-TRF2 complex serves as a double-layer scaffold bridging multiple endonucleases with telomeres for recombination-based telomere maintenance. PMID:24012755

Crystal structure of an avian influenza polymerase PA[subscript N] reveals an endonuclease active site

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

Yuan, Puwei; Bartlam, Mark; Lou, Zhiyong

2009-11-10

The heterotrimeric influenza virus polymerase, containing the PA, PB1 and PB2 proteins, catalyses viral RNA replication and transcription in the nucleus of infected cells. PB1 holds the polymerase active site and reportedly harbours endonuclease activity, whereas PB2 is responsible for cap binding. The PA amino terminus is understood to be the major functional part of the PA protein and has been implicated in several roles, including endonuclease and protease activities as well as viral RNA/complementary RNA promoter binding. Here we report the 2.2 angstrom (A) crystal structure of the N-terminal 197 residues of PA, termed PA(N), from an avian influenzamore » H5N1 virus. The PA(N) structure has an alpha/beta architecture and reveals a bound magnesium ion coordinated by a motif similar to the (P)DX(N)(D/E)XK motif characteristic of many endonucleases. Structural comparisons and mutagenesis analysis of the motif identified in PA(N) provide further evidence that PA(N) holds an endonuclease active site. Furthermore, functional analysis with in vivo ribonucleoprotein reconstitution and direct in vitro endonuclease assays strongly suggest that PA(N) holds the endonuclease active site and has critical roles in endonuclease activity of the influenza virus polymerase, rather than PB1. The high conservation of this endonuclease active site among influenza strains indicates that PA(N) is an important target for the design of new anti-influenza therapeutics.« less

Identification and characterization of influenza variants resistant to a viral endonuclease inhibitor

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

Song, Min-Suk; Kumar, Gyanendra; Shadrick, William R.

The influenza endonuclease is an essential subdomain of the viral RNA polymerase. It processes host pre-mRNAs to serve as primers for viral mRNA and is an attractive target for antiinfluenza drug discovery. Compound L-742,001 is a prototypical endonuclease inhibitor, and we found that repeated passaging of influenza virus in the presence of this drug did not lead to the development of resistant mutant strains. Reduced sensitivity to L-742,001 could only be induced by creating point mutations via a random mutagenesis strategy. Furthermore, these mutations mapped to the endonuclease active site where they can directly impact inhibitor binding. Engineered viruses containingmore » the mutations showed resistance to L-742,001 both in vitro and in vivo, with only a modest reduction in fitness. Introduction of the mutations into a second virus also increased its resistance to the inhibitor. When using the isolated wild-type and mutant endonuclease domains, we used kinetics, inhibitor binding and crystallography to characterize how the two most significant mutations elicit resistance to L-742,001. These studies lay the foundation for the development of a new class of influenza therapeutics with reduced potential for the development of clinical endonuclease inhibitor-resistant influenza strains.« less

Identification and characterization of influenza variants resistant to a viral endonuclease inhibitor

DOE PAGES

Song, Min-Suk; Kumar, Gyanendra; Shadrick, William R.; ...

2016-03-14

The influenza endonuclease is an essential subdomain of the viral RNA polymerase. It processes host pre-mRNAs to serve as primers for viral mRNA and is an attractive target for antiinfluenza drug discovery. Compound L-742,001 is a prototypical endonuclease inhibitor, and we found that repeated passaging of influenza virus in the presence of this drug did not lead to the development of resistant mutant strains. Reduced sensitivity to L-742,001 could only be induced by creating point mutations via a random mutagenesis strategy. Furthermore, these mutations mapped to the endonuclease active site where they can directly impact inhibitor binding. Engineered viruses containingmore » the mutations showed resistance to L-742,001 both in vitro and in vivo, with only a modest reduction in fitness. Introduction of the mutations into a second virus also increased its resistance to the inhibitor. When using the isolated wild-type and mutant endonuclease domains, we used kinetics, inhibitor binding and crystallography to characterize how the two most significant mutations elicit resistance to L-742,001. These studies lay the foundation for the development of a new class of influenza therapeutics with reduced potential for the development of clinical endonuclease inhibitor-resistant influenza strains.« less

Cloning and Characterization of a Wheat Homologue of Apurinic/Apyrimidinic Endonuclease Ape1L

PubMed Central

Grin, Inga R.; Zharkov, Dmitry O.; Ishenko, Alexander A.; Tudek, Barbara; Bissenbaev, Amangeldy K.; Saparbaev, Murat

2014-01-01

Background Apurinic/apyrimidinic (AP) endonucleases are key DNA repair enzymes involved in the base excision repair (BER) pathway. In BER, an AP endonuclease cleaves DNA at AP sites and 3′-blocking moieties generated by DNA glycosylases and/or oxidative damage. A Triticum aestivum cDNA encoding for a putative homologue of ExoIII family AP endonucleases which includes E. coli Xth, human APE1 and Arabidopsis thaliana AtApe1L has been isolated and its protein product purified and characterized. Methodology/Principal Findings We report that the putative wheat AP endonuclease, referred here as TaApe1L, contains AP endonuclease, 3′-repair phosphodiesterase, 3′-phosphatase and 3′→5′ exonuclease activities. Surprisingly, in contrast to bacterial and human AP endonucleases, addition of Mg2+ and Ca2+ (5–10 mM) to the reaction mixture inhibited TaApe1L whereas the presence of Mn2+, Co2+ and Fe2+ cations (0.1–1.0 mM) strongly stimulated all its DNA repair activities. Optimization of the reaction conditions revealed that the wheat enzyme requires low divalent cation concentration (0.1 mM), mildly acidic pH (6–7), low ionic strength (20 mM KCl) and has a temperature optimum at around 20°C. The steady-state kinetic parameters of enzymatic reactions indicate that TaApe1L removes 3′-blocking sugar-phosphate and 3′-phosphate groups with good efficiency (k cat/K M = 630 and 485 μM−1·min−1, respectively) but possesses a very weak AP endonuclease activity as compared to the human homologue, APE1. Conclusions/Significance Taken together, these data establish the DNA substrate specificity of the wheat AP endonuclease and suggest its possible role in the repair of DNA damage generated by endogenous and environmental factors. PMID:24667595

Structure of the endonuclease IV homologue from Thermotoga maritima in the presence of active-site divalent metal ions

PubMed Central

Tomanicek, Stephen J.; Hughes, Ronny C.; Ng, Joseph D.; Coates, Leighton

2010-01-01

The most frequent lesion in DNA is at apurinic/apyrimidinic (AP) sites resulting from DNA-base losses. These AP-site lesions can stall DNA replication and lead to genome instability if left unrepaired. The AP endonucleases are an important class of enzymes that are involved in the repair of AP-site intermediates during damage-general DNA base-excision repair pathways. These enzymes hydrolytically cleave the 5′-phosphodiester bond at an AP site to generate a free 3′-­hydroxyl group and a 5′-terminal sugar phosphate using their AP nuclease activity. Specifically, Thermotoga maritima endonuclease IV is a member of the second conserved AP endonuclease family that includes Escherichia coli endonuclease IV, which is the archetype of the AP endonuclease superfamily. In order to more fully characterize the AP endonuclease family of enzymes, two X-­ray crystal structures of the T. maritima endonuclease IV homologue were determined in the presence of divalent metal ions bound in the active-site region. These structures of the T. maritima endonuclease IV homologue further revealed the use of the TIM-barrel fold and the trinuclear metal binding site as important highly conserved structural elements that are involved in DNA-binding and AP-site repair processes in the AP endonuclease superfamily. PMID:20823514

The metabolic enhancer piracetam attenuates mitochondrion-specific endonuclease G translocation and oxidative DNA fragmentation.

PubMed

Gupta, Sonam; Verma, Dinesh Kumar; Biswas, Joyshree; Rama Raju, K Siva; Joshi, Neeraj; Wahajuddin; Singh, Sarika

2014-08-01

This study was performed to investigate the involvement of mitochondrion-specific endonuclease G in piracetam (P)-induced protective mechanisms. Studies have shown the antiapoptotic effects of piracetam but the mechanism of action of piracetam is still an enigma. To assess the involvement of endonuclease G in piracetam-induced protective effects, astrocyte glial cells were treated with lipopolysaccharide (LPS) and piracetam. LPS treatment caused significantly decreased viability, mitochondrial activity, oxidative stress, chromatin condensation, and DNA fragmentation, which were attenuated by piracetam cotreatment. Cotreatment of astrocytes with piracetam showed its significantly time-dependent absorption as observed with high-performance liquid chromatography. Astrocytes treated with piracetam alone showed enhanced mitochondrial membrane potential (MMP) in comparison to control astrocytes. However, in LPS-treated cells no significant alteration in MMP was observed in comparison to control cells. Protein and mRNA levels of the terminal executor of the caspase-mediated pathway, caspase-3, were not altered significantly in LPS or LPS + piracetam-treated astrocytes, whereas endonuclease G was significantly translocated to the nucleus in LPS-treated astrocytes. Piracetam cotreatment attenuated the LPS-induced endonuclease G translocation. In conclusion this study indicates that LPS treatment of astrocytes caused decreased viability, oxidative stress, mitochondrial dysfunction, chromatin condensation, DNA damage, and translocation of endonuclease G to the nucleus, which was inhibited by piracetam cotreatment, confirming that the mitochondrion-specific endonuclease G is one of the factors involved in piracetam-induced protective mechanisms. Copyright © 2014 Elsevier Inc. All rights reserved.

Endonuclease-independent LINE-1 retrotransposition at mammalian telomeres.

PubMed

Morrish, Tammy A; Garcia-Perez, José Luis; Stamato, Thomas D; Taccioli, Guillermo E; Sekiguchi, JoAnn; Moran, John V

2007-03-08

Long interspersed element-1 (LINE-1 or L1) elements are abundant, non-long-terminal-repeat (non-LTR) retrotransposons that comprise approximately 17% of human DNA. The average human genome contains approximately 80-100 retrotransposition-competent L1s (ref. 2), and they mobilize by a process that uses both the L1 endonuclease and reverse transcriptase, termed target-site primed reverse transcription. We have previously reported an efficient, endonuclease-independent L1 retrotransposition pathway (EN(i)) in certain Chinese hamster ovary (CHO) cell lines that are defective in the non-homologous end-joining (NHEJ) pathway of DNA double-strand-break repair. Here we have characterized EN(i) retrotransposition events generated in V3 CHO cells, which are deficient in DNA-dependent protein kinase catalytic subunit (DNA-PKcs) activity and have both dysfunctional telomeres and an NHEJ defect. Notably, approximately 30% of EN(i) retrotransposition events insert in an orientation-specific manner adjacent to a perfect telomere repeat (5'-TTAGGG-3'). Similar insertions were not detected among EN(i) retrotransposition events generated in controls or in XR-1 CHO cells deficient for XRCC4, an NHEJ factor that is required for DNA ligation but has no known function in telomere maintenance. Furthermore, transient expression of a dominant-negative allele of human TRF2 (also called TERF2) in XRCC4-deficient XR-1 cells, which disrupts telomere capping, enables telomere-associated EN(i) retrotransposition events. These data indicate that L1s containing a disabled endonuclease can use dysfunctional telomeres as an integration substrate. The findings highlight similarities between the mechanism of EN(i) retrotransposition and the action of telomerase, because both processes can use a 3' OH for priming reverse transcription at either internal DNA lesions or chromosome ends. Thus, we propose that EN(i) retrotransposition is an ancestral mechanism of RNA-mediated DNA repair associated with non

DNA Nucleotide Sequence Restricted by the RI Endonuclease

PubMed Central

Hedgpeth, Joe; Goodman, Howard M.; Boyer, Herbert W.

1972-01-01

The sequence of DNA base pairs adjacent to the phosphodiester bonds cleaved by the RI restriction endonuclease in unmodified DNA from coliphage λ has been determined. The 5′-terminal nucleotide labeled with 32P and oligonucleotides up to the heptamer were analyzed from a pancreatic DNase digest. The following sequence of nucleotides adjacent to the RI break made in λ DNA was deduced from these data and from the 3′-dinucleotide sequence and nearest-neighbor analysis obtained from repair synthesis with the DNA polymerase of Rous sarcoma virus [Formula: see text] The RI endonuclease cleavage of the phosphodiester bonds (indicated by arrows) generates 5′-phosphoryls and short cohesive termini of four nucleotides, pApApTpT. The most striking feature of the sequence is its symmetry. PMID:4343974

Generation of genetically-engineered animals using engineered endonucleases.

PubMed

Lee, Jong Geol; Sung, Young Hoon; Baek, In-Jeoung

2018-05-17

The key to successful drug discovery and development is to find the most suitable animal model of human diseases for the preclinical studies. The recent emergence of engineered endonucleases is allowing for efficient and precise genome editing, which can be used to develop potentially useful animal models for human diseases. In particular, zinc finger nucleases, transcription activator-like effector nucleases, and the clustered regularly interspaced short palindromic repeat systems are revolutionizing the generation of diverse genetically-engineered experimental animals including mice, rats, rabbits, dogs, pigs, and even non-human primates that are commonly used for preclinical studies of the drug discovery. Here, we describe recent advances in engineered endonucleases and their application in various laboratory animals. We also discuss the importance of genome editing in animal models for more closely mimicking human diseases.

Fragment-Based Identification of Influenza Endonuclease Inhibitors

PubMed Central

2016-01-01

The influenza virus is responsible for millions of cases of severe illness annually. Yearly variance in the effectiveness of vaccination, coupled with emerging drug resistance, necessitates the development of new drugs to treat influenza infections. One attractive target is the RNA-dependent RNA polymerase PA subunit. Herein we report the development of inhibitors of influenza PA endonuclease derived from lead compounds identified from a metal-binding pharmacophore (MBP) library screen. Pyromeconic acid and derivatives thereof were found to be potent inhibitors of endonuclease. Guided by modeling and previously reported structural data, several sublibraries of molecules were elaborated from the MBP hits. Structure–activity relationships were established, and more potent molecules were designed and synthesized using fragment growth and fragment merging strategies. This approach ultimately resulted in the development of a lead compound with an IC50 value of 14 nM, which displayed an EC50 value of 2.1 μM against H1N1 influenza virus in MDCK cells. PMID:27291165

A new restriction endonuclease from Citrobacter freundii

PubMed Central

Janulaitis, A.A.; Stakenas, P.S.; Lebedenko, E.N.; Berlin, Yu.A.

1982-01-01

CfrI, a new restriction endonuclease of unique substrate specificity, has been isolated from a Citrobacter freundii strain. The enzyme recognizes a degenerated sequence PyGGCCPu in double-strand DNA and cleaves it between Py and G residues to yield 5′ -protruding tetranucleotide ends GGCC. Images PMID:6294607

Analysis of class II (hydrolytic) and class I (beta-lyase) apurinic/apyrimidinic endonucleases with a synthetic DNA substrate.

PubMed Central

Levin, J D; Demple, B

1990-01-01

We have developed simple and sensitive assays that distinguish the main classes of apurinic/apyrimidinic (AP) endonucleases: Class I enzymes that cleave on the 3' side of AP sites by beta-elimination, and Class II enzymes that cleave by hydrolysis on the 5' side. The distinction of the two types depends on the use of a synthetic DNA polymer that contains AP sites with 5'-[32P]phosphate residues. Using this approach, we now show directly that Escherichia coli endonuclease IV and human AP endonuclease are Class II enzymes, as inferred previously on the basis of indirect assays. The assay method does not exhibit significant interference by nonspecific nucleases or primary amines, which allows the ready determination of different AP endonuclease activities in crude cell extracts. In this way, we show that virtually all of the Class II AP endonuclease activity in E. coli can be accounted for by two enzymes: exonuclease III and endonuclease IV. In the yeast Saccharomyces cerevisiae, the Class II AP endonuclease activity is totally dependent on a single enzyme, the Apn1 protein, but there are probably multiple Class I enzymes. The versatility and ease of our approach should be useful for characterizing this important class of DNA repair enzymes in diverse systems. PMID:1698278

Effect of site-specific modification on restriction endonucleases and DNA modification methyltransferases.

PubMed Central

McClelland, M; Nelson, M; Raschke, E

1994-01-01

Restriction endonucleases have site-specific interactions with DNA that can often be inhibited by site-specific DNA methylation and other site-specific DNA modifications. However, such inhibition cannot generally be predicted. The empirically acquired data on these effects are tabulated for over 320 restriction endonucleases. In addition, a table of known site-specific DNA modification methyltransferases and their specificities is presented along with EMBL database accession numbers for cloned genes. PMID:7937074

Comparison of genomes of malignant catarrhal fever-associated herpesviruses by restriction endonuclease analysis.

PubMed

Shih, L M; Zee, Y C; Castro, A E

1989-01-01

The restriction endonuclease DNA cleavage patterns of eight isolates of malignant catarrhal fever-associated herpesviruses were examined using the restriction endonucleases HindIII and EcoRI. The eight viruses could be assigned to two distinct groups. Virus isolates from a blue wildebeest, a sika deer and an ibex had restriction endonuclease DNA cleavage patterns that were in general similar to each other. The restriction pattern of these three viruses was distinct from the other five. Of these five, four were isolated from a greater kudu, a white tailed wildebeest, a white bearded wildebeest, and a cape hartebeest. The fifth isolate C500, was isolated from a domestic cow with malignant catarrhal fever. These five viruses had similar DNA cleavage patterns.

Endonuclease from Micrococcus luteus Which Has Activity Toward Ultraviolet-Irradiated Deoxyribonucleic Acid: Its Action on Transforming Deoxyribonucleic Acid

PubMed Central

Setlow, R. B.; Setlow, Jane K.; Carrier, W. L.

1970-01-01

An endonuclease purified from Micrococcus luteus makes single-strand breaks in ultraviolet (UV)-irradiated, native deoxyribonucleic acid (DNA). The purified endonuclease is able to reactivate UV-inactivated transforming DNA of Haemophilus influenzae, especially when the DNA is assayed on a UV-sensitive mutant of H. influenzae. After extensive endonuclease action, there is a loss of transforming DNA when assayed on both UV-sensitive and -resistant cells. The endonuclease does not affect unirradiated DNA. The results indicate that the endonuclease function is involved in the repair of biological damage resulting from UV irradiation and that the UV-sensitive mutant is deficient in this step. We interpret the data as indicating that the various steps in the repair of DNA must be well coordinated if repair is to be effective. PMID:4314478

Investigation of the mechanism of meiotic DNA cleavage by VMA1-derived endonuclease uncovers a meiotic alteration in chromatin structure around the target site.

PubMed

Fukuda, Tomoyuki; Ohta, Kunihiro; Ohya, Yoshikazu

2006-06-01

VMA1-derived endonuclease (VDE), a homing endonuclease in Saccharomyces cerevisiae, is encoded by the mobile intein-coding sequence within the nuclear VMA1 gene. VDE recognizes and cleaves DNA at the 31-bp VDE recognition sequence (VRS) in the VMA1 gene lacking the intein-coding sequence during meiosis to insert a copy of the intein-coding sequence at the cleaved site. The mechanism underlying the meiosis specificity of VMA1 intein-coding sequence homing remains unclear. We studied various factors that might influence the cleavage activity in vivo and found that VDE binding to the VRS can be detected only when DNA cleavage by VDE takes place, implying that meiosis-specific DNA cleavage is regulated by the accessibility of VDE to its target site. As a possible candidate for the determinant of this accessibility, we analyzed chromatin structure around the VRS and revealed that local chromatin structure near the VRS is altered during meiosis. Although the meiotic chromatin alteration exhibits correlations with DNA binding and cleavage by VDE at the VMA1 locus, such a chromatin alteration is not necessarily observed when the VRS is embedded in ectopic gene loci. This suggests that nucleosome positioning or occupancy around the VRS by itself is not the sole mechanism for the regulation of meiosis-specific DNA cleavage by VDE and that other mechanisms are involved in the regulation.

Investigation of the Mechanism of Meiotic DNA Cleavage by VMA1-Derived Endonuclease Uncovers a Meiotic Alteration in Chromatin Structure around the Target Site

PubMed Central

Fukuda, Tomoyuki; Ohta, Kunihiro; Ohya, Yoshikazu

2006-01-01

VMA1-derived endonuclease (VDE), a homing endonuclease in Saccharomyces cerevisiae, is encoded by the mobile intein-coding sequence within the nuclear VMA1 gene. VDE recognizes and cleaves DNA at the 31-bp VDE recognition sequence (VRS) in the VMA1 gene lacking the intein-coding sequence during meiosis to insert a copy of the intein-coding sequence at the cleaved site. The mechanism underlying the meiosis specificity of VMA1 intein-coding sequence homing remains unclear. We studied various factors that might influence the cleavage activity in vivo and found that VDE binding to the VRS can be detected only when DNA cleavage by VDE takes place, implying that meiosis-specific DNA cleavage is regulated by the accessibility of VDE to its target site. As a possible candidate for the determinant of this accessibility, we analyzed chromatin structure around the VRS and revealed that local chromatin structure near the VRS is altered during meiosis. Although the meiotic chromatin alteration exhibits correlations with DNA binding and cleavage by VDE at the VMA1 locus, such a chromatin alteration is not necessarily observed when the VRS is embedded in ectopic gene loci. This suggests that nucleosome positioning or occupancy around the VRS by itself is not the sole mechanism for the regulation of meiosis-specific DNA cleavage by VDE and that other mechanisms are involved in the regulation. PMID:16757746

Structural aspects of catalytic mechanisms of endonucleases and their binding to nucleic acids

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

Zhukhlistova, N. E.; Balaev, V. V.; Lyashenko, A. V.

2012-05-15

Endonucleases (EC 3.1) are enzymes of the hydrolase class that catalyze the hydrolytic cleavage of deoxyribonucleic and ribonucleic acids at any region of the polynucleotide chain. Endonucleases are widely used both in biotechnological processes and in veterinary medicine as antiviral agents. Medical applications of endonucleases in human cancer therapy hold promise. The results of X-ray diffraction studies of the spatial organization of endonucleases and their complexes and the mechanism of their action are analyzed and generalized. An analysis of the structural studies of this class of enzymes showed that the specific binding of enzymes to nucleic acids is characterized bymore » interactions with nitrogen bases and the nucleotide backbone, whereas the nonspecific binding of enzymes is generally characterized by interactions only with the nucleic-acid backbone. It should be taken into account that the specificity can be modulated by metal ions and certain low-molecular-weight organic compounds. To test the hypotheses about specific and nonspecific nucleic-acid-binding proteins, it is necessary to perform additional studies of atomic-resolution three-dimensional structures of enzyme-nucleic-acid complexes by methods of structural biology.« less

Structural aspects of catalytic mechanisms of endonucleases and their binding to nucleic acids

NASA Astrophysics Data System (ADS)

Zhukhlistova, N. E.; Balaev, V. V.; Lyashenko, A. V.; Lashkov, A. A.

2012-05-01

Endonucleases (EC 3.1) are enzymes of the hydrolase class that catalyze the hydrolytic cleavage of deoxyribonucleic and ribonucleic acids at any region of the polynucleotide chain. Endonucleases are widely used both in biotechnological processes and in veterinary medicine as antiviral agents. Medical applications of endonucleases in human cancer therapy hold promise. The results of X-ray diffraction studies of the spatial organization of endonucleases and their complexes and the mechanism of their action are analyzed and generalized. An analysis of the structural studies of this class of enzymes showed that the specific binding of enzymes to nucleic acids is characterized by interactions with nitrogen bases and the nucleotide backbone, whereas the nonspecific binding of enzymes is generally characterized by interactions only with the nucleic-acid backbone. It should be taken into account that the specificity can be modulated by metal ions and certain low-molecular-weight organic compounds. To test the hypotheses about specific and nonspecific nucleic-acid-binding proteins, it is necessary to perform additional studies of atomic-resolution three-dimensional structures of enzyme-nucleic-acid complexes by methods of structural biology.

A new endonuclease recognizing the deoxynucleotide sequence CCNNGG from the cyanobacterium Synechocystis 6701.

PubMed

Calléja, F; Tandeau de Marsac, N; Coursin, T; van Ormondt, H; de Waard, A

1985-09-25

A new sequence-specific endonuclease from the cyanobacterium Synechocystis species PCC 6701 has been purified and characterized. This enzyme, SecI, is unique in recognizing the nucleotide sequence: 5' -CCNNGG-3' 3' -GGNNCC-5' and cleaves it at the position indicated by the symbol. Two other restriction endonucleases, SecII and SecIII, found in this organism are isoschizomers of MspI and MstII, respectively.

PMS2 endonuclease activity has distinct biological functions and is essential for genome maintenance.

PubMed

van Oers, Johanna M M; Roa, Sergio; Werling, Uwe; Liu, Yiyong; Genschel, Jochen; Hou, Harry; Sellers, Rani S; Modrich, Paul; Scharff, Matthew D; Edelmann, Winfried

2010-07-27

The DNA mismatch repair protein PMS2 was recently found to encode a novel endonuclease activity. To determine the biological functions of this activity in mammals, we generated endonuclease-deficient Pms2E702K knock-in mice. Pms2EK/EK mice displayed increased genomic mutation rates and a strong cancer predisposition. In addition, class switch recombination, but not somatic hypermutation, was impaired in Pms2EK/EK B cells, indicating a specific role in Ig diversity. In contrast to Pms2-/- mice, Pms2EK/EK male mice were fertile, indicating that this activity is dispensable in spermatogenesis. Therefore, the PMS2 endonuclease activity has distinct biological functions and is essential for genome maintenance and tumor suppression.

A new endonuclease recognizing the deoxynucleotide sequence CCNNGG from the cyanobacterium Synechocystis 6701.

PubMed Central

Calléja, F; Tandeau de Marsac, N; Coursin, T; van Ormondt, H; de Waard, A

1985-01-01

A new sequence-specific endonuclease from the cyanobacterium Synechocystis species PCC 6701 has been purified and characterized. This enzyme, SecI, is unique in recognizing the nucleotide sequence: 5' -CCNNGG-3' 3' -GGNNCC-5' and cleaves it at the position indicated by the symbol. Two other restriction endonucleases, SecII and SecIII, found in this organism are isoschizomers of MspI and MstII, respectively. Images PMID:2997722

Crystal structure and DNA repair activities of the AP endonuclease from Leishmania major.

PubMed

Vidal, Antonio E; Harkiolaki, Maria; Gallego, Claribel; Castillo-Acosta, Victor M; Ruiz-Pérez, Luis M; Wilson, Keith; González-Pacanowska, Dolores

2007-11-02

Apurinic/apyrimidinic endonucleases initiate the repair of abasic sites produced either spontaneously, from attack of bases by reactive oxygen species or as intermediates during base excision repair. The catalytic properties and crystal structure of Leishmania major apurinic/apyrimidinic endonuclease are described and compared with those of human APE1 and bacterial exonuclease III. The purified enzyme is shown to possess apurinic/apyrimidinic endonuclease activity of the same order as eukaryotic and prokaryotic counterparts and an equally robust 3'-phosphodiesterase activity. Consistent with this, expression of the L. major endonuclease confers resistance to both methyl methane sulphonate and H2O2 in Escherichia coli repair-deficient mutants while expression of the human homologue only reverts methyl methane sulphonate sensitivity. Structural analyses and modelling of the enzyme-DNA complex demonstrates a high degree of conservation to previously characterized homologues, although subtle differences in the active site geometry might account for the high 3'-phosphodiesterase activity. Our results confirm that the L. major's enzyme is a key element in mediating repair of apurinic/apyrimidinic sites and 3'-blocked termini and therefore must play an important role in the survival of kinetoplastid parasites after exposure to the highly oxidative environment within the host macrophage.

Involvement of the VDE homing endonuclease and rapamycin in regulation of the Saccharomyces cerevisiae GSH11 gene encoding the high affinity glutathione transporter.

PubMed

Miyake, Tsuyoshi; Hiraishi, Hiroyuki; Sammoto, Hiroyuki; Ono, Bun-Ichiro

2003-10-10

The Saccharomyces cerevisiae gene HGT1/GSH11 encodes the high affinity glutathione transporter and is repressed by cysteine added to the culture medium. It has been found previously that a 5'-upstream cis-element, CCGCCACAC, is responsible for regulating GSH11 expression and that several proteins bind to this element (Miyake, T., Kanayama, M., Sammoto, H., and Ono, B. (2002) Mol. Genet. Genomics 266, 1004-1011). In this report we present evidence that the most prominent of these proteins is VDE, known previously as the homing endonuclease encoded by VMA1. We show also that GSH11 is not expressed in a VDE-deleted strain and that inability to express the GSH11 of this strain is overcome by introduction of the coding region of VDE or the entire VMA1 gene. It is also found that VDE does not cut DNA in the vicinity of the GSH11 cis-element. Rapamycin, an inhibitor of the target of rapamycin (TOR) signal-transduction system, is found to enhance expression of GSH11 in a VDE-dependent manner under conditions of sulfur starvation. These results indicate that GSH11 is regulated by a system sensitive to sulfur starvation (presumably via cysteine depletion) and a more general system involving the nutritional starvation signal mediated by the TOR system. Both systems need to be operational (inhibition of TOR and sulfur starvation) for full expression of GSH11.

PMS2 endonuclease activity has distinct biological functions and is essential for genome maintenance

PubMed Central

van Oers, Johanna M. M.; Roa, Sergio; Werling, Uwe; Liu, Yiyong; Genschel, Jochen; Sellers, Rani S.; Modrich, Paul; Scharff, Matthew D.; Edelmann, Winfried

2010-01-01

The DNA mismatch repair protein PMS2 was recently found to encode a novel endonuclease activity. To determine the biological functions of this activity in mammals, we generated endonuclease-deficient Pms2E702K knock-in mice. Pms2EK/EK mice displayed increased genomic mutation rates and a strong cancer predisposition. In addition, class switch recombination, but not somatic hypermutation, was impaired in Pms2EK/EK B cells, indicating a specific role in Ig diversity. In contrast to Pms2−/− mice, Pms2EK/EK male mice were fertile, indicating that this activity is dispensable in spermatogenesis. Therefore, the PMS2 endonuclease activity has distinct biological functions and is essential for genome maintenance and tumor suppression. PMID:20624957

Redesigning the specificity of protein-DNA interactions with Rosetta.

PubMed

Thyme, Summer; Baker, David

2014-01-01

Building protein tools that can selectively bind or cleave specific DNA sequences requires efficient technologies for modifying protein-DNA interactions. Computational design is one method for accomplishing this goal. In this chapter, we present the current state of protein-DNA interface design with the Rosetta macromolecular modeling program. The LAGLIDADG endonuclease family of DNA-cleaving enzymes, under study as potential gene therapy reagents, has been the main testing ground for these in silico protocols. At this time, the computational methods are most useful for designing endonuclease variants that can accommodate small numbers of target site substitutions. Attempts to engineer for more extensive interface changes will likely benefit from an approach that uses the computational design results in conjunction with a high-throughput directed evolution or screening procedure. The family of enzymes presents an engineering challenge because their interfaces are highly integrated and there is significant coordination between the binding and catalysis events. Future developments in the computational algorithms depend on experimental feedback to improve understanding and modeling of these complex enzymatic features. This chapter presents both the basic method of design that has been successfully used to modulate specificity and more advanced procedures that incorporate DNA flexibility and other properties that are likely necessary for reliable modeling of more extensive target site changes.

CNG site-specific and methyl-sensitive endonuclease WEN1 from wheat seedlings.

PubMed

Fedoreyeva, L I; Vanyushin, B F

2011-06-01

Endonuclease WEN1 with apparent molecular mass about 27 kDa isolated from cytoplasmic vesicular fraction of aging coleoptiles of wheat seedlings has expressed site specificity action. This is a first detection and isolation of a site-specific endonuclease from higher eukaryotes, in general, and higher plants, in particular. The enzyme hydrolyzes deoxyribooligonucleotides of different composition on CNG (N is G, A, C, or T) sites by splitting the phosphodiester bond between C and N nucleotide residues in CNG sequence independent from neighbor nucleotide context except for CCCG. WEN1 prefers to hydrolyze methylated λ phage DNA and double-stranded deoxyribooligonucleotides containing 5-methylcytosine sites (m(5)CAG, m(5)CTG) compared with unmethylated substrates. The enzyme is also able to hydrolyze single-stranded substrates, but in this case it splits unmethylated substrates predominantly. Detection in wheat seedlings of WEN1 endonuclease that is site specific, sensitive to the substrate methylation status, and modulated with S-adenosyl-L-methionine indicates that in higher plants restriction--modification systems or some of their elements, at least, may exist.

Salient Features of Endonuclease Platforms for Therapeutic Genome Editing.

PubMed

Certo, Michael T; Morgan, Richard A

2016-03-01

Emerging gene-editing technologies are nearing a revolutionary phase in genetic medicine: precisely modifying or repairing causal genetic defects. This may include any number of DNA sequence manipulations, such as knocking out a deleterious gene, introducing a particular mutation, or directly repairing a defective sequence by site-specific recombination. All of these edits can currently be achieved via programmable rare-cutting endonucleases to create targeted DNA breaks that can engage and exploit endogenous DNA repair pathways to impart site-specific genetic changes. Over the past decade, several distinct technologies for introducing site-specific DNA breaks have been developed, yet the different biological origins of these gene-editing technologies bring along inherent differences in parameters that impact clinical implementation. This review aims to provide an accessible overview of the various endonuclease-based gene-editing platforms, highlighting the strengths and weakness of each with respect to therapeutic applications.

Salient Features of Endonuclease Platforms for Therapeutic Genome Editing

PubMed Central

Certo, Michael T; Morgan, Richard A

2016-01-01

Emerging gene-editing technologies are nearing a revolutionary phase in genetic medicine: precisely modifying or repairing causal genetic defects. This may include any number of DNA sequence manipulations, such as knocking out a deleterious gene, introducing a particular mutation, or directly repairing a defective sequence by site-specific recombination. All of these edits can currently be achieved via programmable rare-cutting endonucleases to create targeted DNA breaks that can engage and exploit endogenous DNA repair pathways to impart site-specific genetic changes. Over the past decade, several distinct technologies for introducing site-specific DNA breaks have been developed, yet the different biological origins of these gene-editing technologies bring along inherent differences in parameters that impact clinical implementation. This review aims to provide an accessible overview of the various endonuclease-based gene-editing platforms, highlighting the strengths and weakness of each with respect to therapeutic applications. PMID:26796671

The major human AP endonuclease (Ape1) is involved in the nucleotide incision repair pathway

PubMed Central

Gros, Laurent; Ishchenko, Alexander A.; Ide, Hiroshi; Elder, Rhoderick H.; Saparbaev, Murat K.

2004-01-01

In nucleotide incision repair (NIR), an endonuclease nicks oxidatively damaged DNA in a DNA glycosylase-independent manner, providing the correct ends for DNA synthesis coupled to the repair of the remaining 5′-dangling modified nucleotide. This mechanistic feature is distinct from DNA glycosylase-mediated base excision repair. Here we report that Ape1, the major apurinic/apyrimidinic endonuclease in human cells, is the damage- specific endonuclease involved in NIR. We show that Ape1 incises DNA containing 5,6-dihydro-2′-deoxyuridine, 5,6-dihydrothymidine, 5-hydroxy-2′-deoxyuridine, alpha-2′-deoxyadenosine and alpha-thymidine adducts, generating 3′-hydroxyl and 5′-phosphate termini. The kinetic constants indicate that Ape1-catalysed NIR activity is highly efficient. The substrate specificity and protein conformation of Ape1 is modulated by MgCl2 concentrations, thus providing conditions under which NIR becomes a major activity in cell-free extracts. While the N-terminal region of Ape1 is not required for AP endonuclease function, we show that it regulates the NIR activity. The physiological relevance of the mammalian NIR pathway is discussed. PMID:14704345

Purification of Restriction Endonuclease EcoRII and its Co-Crystallization

NASA Technical Reports Server (NTRS)

Karpova, E. A.; Chen, L.; Meehan, E.; Pusey, M.; Rose, M. Franklin (Technical Monitor)

2000-01-01

Restriction endonuclease EcoRII (EcoRII) is a homodimeric DNA-binding protein. It belongs to the type II family of restriction-modification enzymes (subclass IIe). EcoRII recognizes the nucleotide sequence 5'-CCWGG (W=A or T) and cleaves the phosphodiester bond preceding the first cytosine. Methylation at C5 of the second cytosine inhibits cleavage. The enzyme has a unique ability to search for the presence of two substrate sites before cleavage. To the best of our knowledge no other subclass IIe restriction endonuclease has been crystallized yet, without or with a DNA-substrate. We have recently grown and characterized the crystals of this enzyme (1) Here we report on the result of co-crystallization experiments of EcoRII with an 11 b.p. oligonucleotide substrate. The dissociation constant (Kd) EcoRII: 11 b.p. was determined earlier (unpublished results). The needle-like crystals of oligonucleotide-EcoRII protein complex were obtained with this substrate by the technique of vapor diffusion hanging drops. The crystals obtained were washed and dissolved in an aliquot of 10 mM Tris-HCl buffer, pH=7.5. Running a portion of this solution on the SDS-get indicated the presence of endonuclease in the solution. A UV-spectrophotometric test of a second portion confirmed the presence of DNA. We are now working on improvement of the DNA-EcoRII protein crystals. Results obtained from these and ongoing efforts will be reported.

Studies of the Interaction of Influenza Virus RNA Polymerase PAN with Endonuclease Inhibitors.

PubMed

Dong, Li-Hua; Cao, Xiao-Rong

2018-06-01

Influenza virus is a major causative agent of respiratory viral infections, and RNA polymerase catalyzes its replication and transcription activities in infected cell nuclei. Since it is highly conserved in all virus strains, RNA polymerase becomes a key target of anti-influenza virus agents. Although experimental studies have revealed the good inhibitory activity of endonuclease inhibitors to RNA polymerase, the mechanism is still unclear. In this study, the docking and molecular dynamics simulations have been performed to explore the interaction of three kinds of endonuclease inhibitors with the subunit (PA N ) of RNA polymerase. Our calculations indicate that all these endonuclease inhibitors can bind to the binding pocket of PA N , in which the electronegative oxygen atoms of the inhibitors form a chelated structure with the two Mn 2+ cations of the active center. The most important interaction between these inhibitors and PA N is electrostatic interaction. The electron density of the chelate oxygen atoms determines the magnitude of the electrostatic energy, and the chelated structure and orientation of inhibitors depend largely on the distance between the chelate oxygen atoms.

PCNA function in the activation and strand direction of MutLα endonuclease in mismatch repair

PubMed Central

Pluciennik, Anna; Dzantiev, Leonid; Iyer, Ravi R.; Constantin, Nicoleta; Kadyrov, Farid A.; Modrich, Paul

2010-01-01

MutLα (MLH1–PMS2) is a latent endonuclease that is activated in a mismatch-, MutSα-, proliferating cell nuclear antigen (PCNA)-, replication factor C (RFC)-, and ATP-dependent manner, with nuclease action directed to the heteroduplex strand that contains a preexisting break. RFC depletion experiments and use of linear DNAs indicate that RFC function in endonuclease activation is limited to PCNA loading. Whereas nicked circular heteroduplex DNA is a good substrate for PCNA loading and for endonuclease activation on the incised strand, covalently closed, relaxed circular DNA is a poor substrate for both reactions. However, covalently closed supercoiled or bubble-containing relaxed heteroduplexes, which do support PCNA loading, also support MutLα activation, but in this case cleavage strand bias is largely abolished. Based on these findings we suggest that PCNA has two roles in MutLα function: The clamp is required for endonuclease activation, an effect that apparently involves interaction of the two proteins, and by virtue of its loading orientation, PCNA determines the strand direction of MutLα incision. These results also provide a potential mechanism for activation of mismatch repair on nonreplicating DNA, an effect that may have implications for the somatic phase of triplet repeat expansion. PMID:20713735

RNA-dependent DNA endonuclease Cas9 of the CRISPR system: Holy Grail of genome editing?

PubMed

Gasiunas, Giedrius; Siksnys, Virginijus

2013-11-01

Tailor-made nucleases for precise genome modification, such as zinc finger or TALE nucleases, currently represent the state-of-the-art for genome editing. These nucleases combine a programmable protein module which guides the enzyme to the target site with a nuclease domain which cuts DNA at the addressed site. Reprogramming of these nucleases to cut genomes at specific locations requires major protein engineering efforts. RNA-guided DNA endonuclease Cas9 of the type II (clustered regularly interspaced short palindromic repeat) CRISPR-Cas system uses CRISPR RNA (crRNA) as a guide to locate the DNA target and the Cas9 protein to cut DNA. Easy programmability of the Cas9 endonuclease using customizable RNAs brings unprecedented flexibility and versatility for targeted genome modification. We highlight the potential of the Cas9 RNA-guided DNA endonuclease as a novel tool for genome surgery, and discuss possible constraints and future prospects. Copyright © 2013 Elsevier Ltd. All rights reserved.

A Sequence-Specific Nicking Endonuclease from Streptomyces: Purification, Physical and Catalytic Properties

PubMed Central

Somyoonsap, Peechapack; Kitpreechavanich, Vichein

2013-01-01

A sequence-specific nicking endonuclease from Streptomyces designated as DC13 was purified to near homogeneity. Starting with 30 grams of wet cells, the enzyme was purified by ammonium sulfate fractionation, DEAE cellulose, and phenyl-Sepharose chromatography. The purified protein had a specific activity 1000 units/mg and migrated on SDS-PAGE gel with an estimated molecular weight of 71 kDa. Determination of subunit composition by gel filtration chromatography indicated that the native enzyme is a monomer. When incubated with different DNA substrates including pBluescript II KS, pUC118, pET-15b, and pET-26b, the enzyme converted these supercoiled plasmids to a mixture of open circular and linear DNA products, with the open circular DNA as the major cleavage product. Analysis of the kinetic of DNA cleavage showed that the enzyme appeared to cleave super-coiled plasmid in two distinct steps: a rapid cleavage of super-coiled plasmid to an open circular DNA followed a much slower step to linear DNA. The DNA cleavage reaction of the enzyme required Mg2+ as a cofactor. Based on the monomeric nature of the enzyme, the kinetics of DNA cleavage exhibited by the enzyme, and cofactor requirement, it is suggested here that the purified enzyme is a sequence-specific nicking endonuclease that is similar to type IIS restriction endonuclease. PMID:25937959

Endonuclease EEPD1 Is a Gatekeeper for Repair of Stressed Replication Forks*

PubMed Central

Kim, Hyun-Suk; Nickoloff, Jac A.; Wu, Yuehan; Williamson, Elizabeth A.; Sidhu, Gurjit Singh; Reinert, Brian L.; Jaiswal, Aruna S.; Srinivasan, Gayathri; Patel, Bhavita; Kong, Kimi; Burma, Sandeep; Lee, Suk-Hee; Hromas, Robert A.

2017-01-01

Replication is not as continuous as once thought, with DNA damage frequently stalling replication forks. Aberrant repair of stressed replication forks can result in cell death or genome instability and resulting transformation to malignancy. Stressed replication forks are most commonly repaired via homologous recombination (HR), which begins with 5′ end resection, mediated by exonuclease complexes, one of which contains Exo1. However, Exo1 requires free 5′-DNA ends upon which to act, and these are not commonly present in non-reversed stalled replication forks. To generate a free 5′ end, stalled replication forks must therefore be cleaved. Although several candidate endonucleases have been implicated in cleavage of stalled replication forks to permit end resection, the identity of such an endonuclease remains elusive. Here we show that the 5′-endonuclease EEPD1 cleaves replication forks at the junction between the lagging parental strand and the unreplicated DNA parental double strands. This cleavage creates the structure that Exo1 requires for 5′ end resection and HR initiation. We observed that EEPD1 and Exo1 interact constitutively, and Exo1 repairs stalled replication forks poorly without EEPD1. Thus, EEPD1 performs a gatekeeper function for replication fork repair by mediating the fork cleavage that permits initiation of HR-mediated repair and restart of stressed forks. PMID:28049724

Molecular mechanism of vde-initiated intein homing in yeast nuclear genome.

PubMed

Fukuda, Tomoyuki; Nagai, Yuri; Ohya, Yoshikazu

2004-01-01

In Saccharomyces cerevisiae, VMAI intein encodes a homing endonuclease termed VDE which is produced by an autocatalytic protein splicing reaction. VDE introduces a DSB at its recognition sequence on intein-minus allele, resulting in the lateral transfer of VMAI intein. In this review, we summarize a decade of in vitro study on VDE and describe our recent study on the in vivo behavior of both VDE and host proteins involved in intein mobility. Meiotic DSBs caused by VDE are repaired in the similar pathway to that working in meiotic recombination induced by Spollp-mediated DSBs. Meiosis-specific DNA cleavage and homing is shown to be guaranteed by the two distinct mechanisms, the subcellular localization of VDE and a requirement of premeiotic DNA replication. Based on these lines of evidence, we present the whole picture of molecular mechanism of VDEinitiated homing in yeast cells.

Human Fanconi Anemia Complementation Group A Protein Stimulates the 5’ Flap Endonuclease Activity of FEN1

PubMed Central

Qian, Liangyue; Yuan, Fenghua; Rodriguez-Tello, Paola; Padgaonkar, Suyog; Zhang, Yanbin

2013-01-01

In eukaryotic cells, Flap endonuclease 1 (FEN1) is a major structure-specific endonuclease that processes 5’ flapped structures during maturation of lagging strand DNA synthesis, long patch base excision repair, and rescue of stalled replication forks. Here we report that fanconi anemia complementation group A protein (FANCA), a protein that recognizes 5’ flap structures and is involved in DNA repair and maintenance of replication forks, constantly stimulates FEN1-mediated incision of both DNA and RNA flaps. Kinetic analyses indicate that FANCA stimulates FEN1 by increasing the turnover rate of FEN1 and altering its substrate affinity. More importantly, six pathogenic FANCA mutants are significantly less efficient than the wild-type at stimulating FEN1 endonuclease activity, implicating that regulation of FEN1 by FANCA contributes to the maintenance of genomic stability. PMID:24349332

The DNA repair endonuclease Mus81 facilitates fast DNA replication in the absence of exogenous damage

PubMed Central

Fu, Haiqing; Martin, Melvenia M.; Regairaz, Marie; Huang, Liang; You, Yang; Lin, Chi-Mei; Ryan, Michael; Kim, RyangGuk; Shimura, Tsutomu; Pommier, Yves; Aladjem, Mirit I.

2015-01-01

The Mus81 endonuclease resolves recombination intermediates and mediates cellular responses to exogenous replicative stress. Here, we show that Mus81 also regulates the rate of DNA replication during normal growth by promoting replication fork progression while reducing the frequency of replication initiation events. In the absence of Mus81 endonuclease activity, DNA synthesis is slowed and replication initiation events are more frequent. In addition, Mus81 deficient cells fail to recover from exposure to low doses of replication inhibitors and cell viability is dependent on the XPF endonuclease. Despite an increase in replication initiation frequency, cells lacking Mus81 use the same pool of replication origins as Mus81-expressing cells. Therefore, decelerated DNA replication in Mus81 deficient cells does not initiate from cryptic or latent origins not used during normal growth. These results indicate that Mus81 plays a key role in determining the rate of DNA replication without activating a novel group of replication origins. PMID:25879486

A model of EcoRII restriction endonuclease action: the active complex is most likely formed by one protein subunit and one DNA recognition site

NASA Technical Reports Server (NTRS)

Karpova, E. A.; Kubareva, E. A.; Shabarova, Z. A.

1999-01-01

To elucidate the mechanism of interaction of restriction endonuclease EcoRII with DNA, we studied by native gel electrophoresis the binding of this endonuclease to a set of synthetic DNA-duplexes containing the modified or canonical recognition sequence 5'-d(CCA/TGG)-3'. All binding substrate or substrate analogues tested could be divided into two major groups: (i) duplexes that, at the interaction with endonuclease EcoRII, form two types of stable complexes on native gel in the absence of Mg2+ cofactor; (ii) duplexes that form only one type of complex, observed both in the presence and absence of Mg2+. Unlike the latter, duplexes under the first group can be hydrolyzed by endonuclease. Data obtained suggest that the active complex is most likely formed by one protein subunit and one DNA recognition sequence. A model of EcoRII endonuclease action is presented.

The mismatch repair and meiotic recombination endonuclease Mlh1-Mlh3 is activated by polymer formation and can cleave DNA substrates in trans.

PubMed

Manhart, Carol M; Ni, Xiaodan; White, Martin A; Ortega, Joaquin; Surtees, Jennifer A; Alani, Eric

2017-04-01

Crossing over between homologs is initiated in meiotic prophase by the formation of DNA double-strand breaks that occur throughout the genome. In the major interference-responsive crossover pathway in baker's yeast, these breaks are resected to form 3' single-strand tails that participate in a homology search, ultimately forming double Holliday junctions (dHJs) that primarily include both homologs. These dHJs are resolved by endonuclease activity to form exclusively crossovers, which are critical for proper homolog segregation in Meiosis I. Recent genetic, biochemical, and molecular studies in yeast are consistent with the hypothesis of Mlh1-Mlh3 DNA mismatch repair complex acting as the major endonuclease activity that resolves dHJs into crossovers. However, the mechanism by which the Mlh1-Mlh3 endonuclease is activated is unknown. Here, we provide evidence that Mlh1-Mlh3 does not behave like a structure-specific endonuclease but forms polymers required to generate nicks in DNA. This conclusion is supported by DNA binding studies performed with different-sized substrates that contain or lack polymerization barriers and endonuclease assays performed with varying ratios of endonuclease-deficient and endonuclease-proficient Mlh1-Mlh3. In addition, Mlh1-Mlh3 can generate religatable double-strand breaks and form an active nucleoprotein complex that can nick DNA substrates in trans. Together these observations argue that Mlh1-Mlh3 may not act like a canonical, RuvC-like Holliday junction resolvase and support a novel model in which Mlh1-Mlh3 is loaded onto DNA to form an activated polymer that cleaves DNA.

Molecular mechanism of VDE-initiated intein homing in yeast nuclear genome.

PubMed

Fukuda, Tomoyuki; Nagai, Yuri; Ohya, Yoshikazu

2004-01-01

In Saccharomyces cerevisiae, VMA1 intein encodes a homing endonuclease termed VDE which is produced by an autocatalytic protein splicing reaction. VDE introduces a DSB at its recognition sequence on intein-minus allele, resulting in the lateral transfer of VMA1 intein. In this review, we summarize a decade of in vitro study on VDE and describe our recent study on the in vivo behavior of both VDE and host proteins involved in intein mobility. Meiotic DSBs caused by VDE are repaired in the similar pathway to that working in meiotic recombination induced by Spo11p-mediated DSBs. Meiosis-specific DNA cleavage and homing is shown to be guaranteed by the two distinct mechanisms, the subcellular localization of VDE and a requirement of premeiotic DNA replication. Based on these lines of evidence, we present the whole picture of molecular mechanism of VDE-initiated homing in yeast cells.

Identification of potential influenza virus endonuclease inhibitors through virtual screening based on the 3D-QSAR model.

PubMed

Kim, J; Lee, C; Chong, Y

2009-01-01

Influenza endonucleases have appeared as an attractive target of antiviral therapy for influenza infection. With the purpose of designing a novel antiviral agent with enhanced biological activities against influenza endonuclease, a three-dimensional quantitative structure-activity relationships (3D-QSAR) model was generated based on 34 influenza endonuclease inhibitors. The comparative molecular similarity index analysis (CoMSIA) with a steric, electrostatic and hydrophobic (SEH) model showed the best correlative and predictive capability (q(2) = 0.763, r(2) = 0.969 and F = 174.785), which provided a pharmacophore composed of the electronegative moiety as well as the bulky hydrophobic group. The CoMSIA model was used as a pharmacophore query in the UNITY search of the ChemDiv compound library to give virtual active compounds. The 3D-QSAR model was then used to predict the activity of the selected compounds, which identified three compounds as the most likely inhibitor candidates.

Magnesium-dependent RNA binding to the PA endonuclease domain of the avian influenza polymerase.

PubMed

Xiao, Shiyan; Klein, Michael L; LeBard, David N; Levine, Benjamin G; Liang, Haojun; MacDermaid, Christopher M; Alfonso-Prieto, Mercedes

2014-01-30

Influenza A viruses are highly pathogenic and pose an unpredictable public health danger to humans. An attractive target for developing new antiviral drugs is the PA N-terminal domain (PAN) of influenza polymerase, which is responsible for the endonuclease activity and essential for viral replication. Recently, the crystal structures of the holo form of PAN as well as PAN bound to different inhibitors have been reported, but the potency and selectivity of these inhibitors still need to be improved. New drug design can be guided by a better understanding of the endonuclease activity of PAN. However, this requires the structure of PAN in complex with the host mRNA, which has not been determined yet. In particular, divalent metal ions are known to be essential for RNA cleavage, but it is not clear whether there is either one or two Mg ions in the PAN active site. In the present work, we have modeled the complex of the PAN endonuclease domain with the host mRNA in the presence of either one or two Mg(2+) by using all-atom molecular dynamics. These simulations identify crucial interactions between the enzyme and the nucleic acid. Moreover, they validate a previous hypothesis that a second metal ion binds in the presence of the RNA substrate and therefore support a two-metal ion mechanism, in which K134 decreases the pKa of the nucleophilic water. Nevertheless, at low Mg concentrations an alternative, one-metal ion mechanism is possible, with K137 as the catalytic lysine and H41 as the general base, rationalizing previous unexpected mutagenesis results. The RNA-enzyme interactions determined here could likely be used to design more specific endonuclease inhibitors to fight influenza viral infections.

The mismatch repair and meiotic recombination endonuclease Mlh1-Mlh3 is activated by polymer formation and can cleave DNA substrates in trans

PubMed Central

Manhart, Carol M.; Ni, Xiaodan; White, Martin A.; Ortega, Joaquin; Surtees, Jennifer A.

2017-01-01

Crossing over between homologs is initiated in meiotic prophase by the formation of DNA double-strand breaks that occur throughout the genome. In the major interference-responsive crossover pathway in baker’s yeast, these breaks are resected to form 3' single-strand tails that participate in a homology search, ultimately forming double Holliday junctions (dHJs) that primarily include both homologs. These dHJs are resolved by endonuclease activity to form exclusively crossovers, which are critical for proper homolog segregation in Meiosis I. Recent genetic, biochemical, and molecular studies in yeast are consistent with the hypothesis of Mlh1-Mlh3 DNA mismatch repair complex acting as the major endonuclease activity that resolves dHJs into crossovers. However, the mechanism by which the Mlh1-Mlh3 endonuclease is activated is unknown. Here, we provide evidence that Mlh1-Mlh3 does not behave like a structure-specific endonuclease but forms polymers required to generate nicks in DNA. This conclusion is supported by DNA binding studies performed with different-sized substrates that contain or lack polymerization barriers and endonuclease assays performed with varying ratios of endonuclease-deficient and endonuclease-proficient Mlh1-Mlh3. In addition, Mlh1-Mlh3 can generate religatable double-strand breaks and form an active nucleoprotein complex that can nick DNA substrates in trans. Together these observations argue that Mlh1-Mlh3 may not act like a canonical, RuvC-like Holliday junction resolvase and support a novel model in which Mlh1-Mlh3 is loaded onto DNA to form an activated polymer that cleaves DNA. PMID:28453523

Specific action of T4 endonuclease V on damaged DNA in xeroderma pigmentosum cells in vivo. [UV radiation

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

Tanaka, K.; Hayakawa, H.; Sekiguchi, M.

1977-07-01

The specific action of T4 endonuclease V on damaged DNA in xeroderma pigmentosum cells was examined using an in vivo assay system with hemagglutinating virus of Japan (Sendai virus) inactivated by uv light. A clear dose response was observed between the level of uv-induced unscheduled DNA synthesis of xeroderma pigmentosum cells and the amount of T4 endonuclease V activity added. The T4 enzyme was unstable in human cells, and its half-life was 3 hr. Fractions derived from an extract of Escherichia coli infected with T4v/sub 1/, a mutant defective in the endonuclease V gene, showed no ability to restore themore » uv-induced unscheduled DNA synthesis of xeroderma pigmentosum cells. However, fractions derived from an extract of T4D-infected E. coli with endonuclease V activity were effective. The T4 enzyme was effective in xeroderma pigmentosum cells on DNA damaged by uv light but not in cells damaged by 4-nitroquinoline 1-oxide. The results of these experiments show that the T4 enzyme has a specific action on human cell DNA in vivo. Treatment with the T4 enzyme increased the survival of group A xeroderma pigmentosum cells after uv irradiation.« less

Repair Rate of Clustered Abasic DNA Lesions by Human Endonuclease: Molecular Bases of Sequence Specificity.

PubMed

Gattuso, Hugo; Durand, Elodie; Bignon, Emmanuelle; Morell, Christophe; Georgakilas, Alexandros G; Dumont, Elise; Chipot, Christophe; Dehez, François; Monari, Antonio

2016-10-06

In the present contribution, the interaction between damaged DNA and repair enzymes is examined by means of molecular dynamics simulations. More specifically, we consider clustered abasic DNA lesions processed by the primary human apurinic/apyrimidinic (AP) endonuclease, APE1. Our results show that, in stark contrast with the corresponding bacterial endonucleases, human APE1 imposes strong geometrical constraints on the DNA duplex. As a consequence, the level of recognition and, hence, the repair rate is higher. Important features that guide the DNA/protein interactions are the presence of an extended positively charged region and of a molecular tweezers that strongly constrains DNA. Our results are on very good agreement with the experimentally determined repair rate of clustered abasic lesions. The lack of repair for one particular arrangement of the two abasic sites is also explained considering the peculiar destabilizing interaction between the recognition region and the second lesion, resulting in a partial opening of the molecular tweezers and, thus, a less stable complex. This contribution cogently establishes the molecular bases for the recognition and repair of clustered DNA lesions by means of human endonucleases.

Endonuclease G promotes mitochondrial genome cleavage and replication

PubMed Central

Wiehe, Rahel Stefanie; Gole, Boris; Chatre, Laurent; Walther, Paul; Calzia, Enrico; Ricchetti, Miria; Wiesmüller, Lisa

2018-01-01

Endonuclease G (EndoG) is a nuclear-encoded endonuclease, mostly localised in mitochondria. In the nucleus EndoG participates in site-specific cleavage during replication stress and genome-wide DNA degradation during apoptosis. However, the impact of EndoG on mitochondrial DNA (mtDNA) metabolism is poorly understood. Here, we investigated whether EndoG is involved in the regulation of mtDNA replication and removal of aberrant copies. We applied the single-cell mitochondrial Transcription and Replication Imaging Protocol (mTRIP) and PCR-based strategies on human cells after knockdown/knockout and re-expression of EndoG. Our analysis revealed that EndoG stimulates both mtDNA replication initiation and mtDNA depletion, the two events being interlinked and dependent on EndoG's nuclease activity. Stimulation of mtDNA replication by EndoG was independent of 7S DNA processing at the replication origin. Importantly, both mtDNA-directed activities of EndoG were promoted by oxidative stress. Inhibition of base excision repair (BER) that repairs oxidative stress-induced DNA damage unveiled a pronounced effect of EndoG on mtDNA removal, reminiscent of recently discovered links between EndoG and BER in the nucleus. Altogether with the downstream effects on mitochondrial transcription, protein expression, redox status and morphology, this study demonstrates that removal of damaged mtDNA by EndoG and compensatory replication play a critical role in mitochondria homeostasis. PMID:29719607

A domain in human EXOG converts apoptotic endonuclease to DNA-repair exonuclease

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

Szymanski, Michal R.; Yu, Wangsheng; Gmyrek, Aleksandra M.

Human EXOG (hEXOG) is a 5'-exonuclease that is crucial for mitochondrial DNA repair; the enzyme belongs to a nonspecific nuclease family that includes the apoptotic endonuclease EndoG. Here we report biochemical and structural studies of hEXOG, including structures in its apo form and in a complex with DNA at 1.81 and 1.85 Å resolution, respectively. A Wing domain, absent in other ββα-Me members, suppresses endonuclease activity, but confers on hEXOG a strong 5'-dsDNA exonuclease activity that precisely excises a dinucleotide using an intrinsic ‘tape-measure’. The symmetrical apo hEXOG homodimer becomes asymmetrical upon binding to DNA, providing a structural basis formore » how substrate DNA bound to one active site allosterically regulates the activity of the other. These properties of hEXOG suggest a pathway for mitochondrial BER that provides an optimal substrate for subsequent gap-filling synthesis by DNA polymerase γ.« less

Molecular Phylogenetic Analysis of Archaeal Intron-Containing Genes Coding for rRNA Obtained from a Deep-Subsurface Geothermal Water Pool

PubMed Central

Takai, Ken; Horikoshi, Koki

1999-01-01

Molecular phylogenetic analysis of a naturally occurring microbial community in a deep-subsurface geothermal environment indicated that the phylogenetic diversity of the microbial population in the environment was extremely limited and that only hyperthermophilic archaeal members closely related to Pyrobaculum were present. All archaeal ribosomal DNA sequences contained intron-like sequences, some of which had open reading frames with repeated homing-endonuclease motifs. The sequence similarity analysis and the phylogenetic analysis of these homing endonucleases suggested the possible phylogenetic relationship among archaeal rRNA-encoded homing endonucleases. PMID:10584021

Recruitment of RecA homologs Dmc1p and Rad51p to the double-strand break repair site initiated by meiosis-specific endonuclease VDE (PI-SceI).

PubMed

Fukuda, Tomoyuki; Ohya, Yoshikazu

2006-02-01

During meiosis, VDE (PI-SceI), a homing endonuclease in Saccharomyces cerevisiae, introduces a double-strand break (DSB) at its recognition sequence and induces homologous recombinational repair, called homing. Meiosis-specific RecA homolog Dmc1p, as well as mitotic RecA homolog Rad51p, acts in the process of meiotic recombination, being required for strand invasion and exchange. In this study, recruitment of Dmc1p and Rad51p to the VDE-induced DSB repair site is investigated by chromatin immunoprecipitation assay. It is revealed that Dmc1p and Rad51p are loaded to the repair site in an independent manner. Association of Rad51p requires other DSB repair proteins of Rad52p, Rad55p, and Rad57p, while loading of Dmc1p is facilitated by the different protein, Sae3p. Absence of Tid1p, which can bind both RecA homologs, appears specifically to cause an abnormal distribution of Dmc1p. Lack of Hop2, Mnd1p, and Sae1p does not impair recruitment of both RecA homologs. These findings reveal the discrete functions of each strand invasion protein in VDE-initiated homing, confirm the similarity between VDE-initiated homing and Spo11p-initiated meiotic recombination, and demonstrate the availability of VDE-initiated homing for the study of meiotic recombination.

Purification and characterization of the restriction endonuclease RsrI, an isoschizomer of EcoRI.

PubMed

Greene, P J; Ballard, B T; Stephenson, F; Kohr, W J; Rodriguez, H; Rosenberg, J M; Boyer, H W

1988-08-15

Rhodobacter sphaeroides strain 630 produces restriction enzyme RsrI which is an isoschizomer of EcoRI. We have purified this enzyme and initiated a comparison with the EcoRI endonuclease. The properties of RsrI are consistent with a reaction mechanism similar to that of EcoRI: the position of cleavage within the -GAATTC-site is identical, the MgCl2 optimum for the cleavage is identical, and the pH profile is similar. Methylation of the substrate sequence by the EcoRI methylase protects the site from cleavage by the RsrI endonuclease. RsrI cross-reacts strongly with anti-EcoRI serum indicating three-dimensional structural similarities. We have determined the sequence of 34 N terminal amino acids for RsrI and this sequence possesses significant similarity to the EcoRI N terminus.

A detailed experimental study of a DNA computer with two endonucleases.

PubMed

Sakowski, Sebastian; Krasiński, Tadeusz; Sarnik, Joanna; Blasiak, Janusz; Waldmajer, Jacek; Poplawski, Tomasz

2017-07-14

Great advances in biotechnology have allowed the construction of a computer from DNA. One of the proposed solutions is a biomolecular finite automaton, a simple two-state DNA computer without memory, which was presented by Ehud Shapiro's group at the Weizmann Institute of Science. The main problem with this computer, in which biomolecules carry out logical operations, is its complexity - increasing the number of states of biomolecular automata. In this study, we constructed (in laboratory conditions) a six-state DNA computer that uses two endonucleases (e.g. AcuI and BbvI) and a ligase. We have presented a detailed experimental verification of its feasibility. We described the effect of the number of states, the length of input data, and the nondeterminism on the computing process. We also tested different automata (with three, four, and six states) running on various accepted input words of different lengths such as ab, aab, aaab, ababa, and of an unaccepted word ba. Moreover, this article presents the reaction optimization and the methods of eliminating certain biochemical problems occurring in the implementation of a biomolecular DNA automaton based on two endonucleases.

Unusual target site disruption by the rare-cutting HNH restriction endonuclease PacI

PubMed Central

Shen, Betty; Heiter, Daniel F.; Chan, Siu-Hong; Wang, Hua; Xu, Shuang-Yong; Morgan, Richard D.; Wilson, Geoffrey G.; Stoddard, Barry L.

2010-01-01

The crystal structure of the rare-cutting HNH restriction endonuclease PacI in complex with its eight base pair target recognition sequence 5'-TTAATTAA-3' has been determined to 1.9 Å resolution. The enzyme forms an extended homodimer, with each subunit containing two zinc-bound motifs surrounding a ββα-metal catalytic site. The latter is unusual in that a tyrosine residue likely initiates strand-cleavage. PacI dramatically distorts its target sequence from Watson-Crick duplex DNA basepairing, with every base separated from its original partner. Two bases on each strand are unpaired, four are engaged in non-canonical A:A and T:T base pairs, and the remaining two bases are matched with new Watson-Crick partners. This represents a highly unusual DNA binding mechanism for a restriction endonuclease, and implies that initial recognition of the target site might involve significantly different contacts from those visualized in the DNA-bound cocrystal structures. PMID:20541511

Expression, functionality, and localization of apurinic/apyrimidinic endonucleases in replicative and non-replicative forms of Trypanosoma cruzi.

PubMed

Sepúlveda, S; Valenzuela, L; Ponce, I; Sierra, S; Bahamondes, P; Ramirez, S; Rojas, V; Kemmerling, U; Galanti, N; Cabrera, G

2014-02-01

Trypanosoma cruzi is the etiological agent of Chagas disease. The parasite has to overcome oxidative damage by ROS/RNS all along its life cycle to survive and to establish a chronic infection. We propose that T. cruzi is able to survive, among other mechanisms of detoxification, by repair of its damaged DNA through activation of the DNA base excision repair (BER) pathway. BER is highly conserved in eukaryotes with apurinic/apirimidinic endonucleases (APEs) playing a fundamental role. Previous results showed that T. cruzi exposed to hydrogen peroxide and peroxinitrite significantly decreases its viability when co-incubated with methoxyamine, an AP endonuclease inhibitor. In this work the localization, expression and functionality of two T. cruzi APEs (TcAP1, Homo sapiens APE1 orthologous and TcAP2, orthologous to Homo sapiens APE2 and to Schizosaccaromyces pombe Apn2p) were determined. These enzymes are present and active in the two replicative parasite forms (epimastigotes and amastigotes) as well as in the non-replicative, infective trypomastigotes. TcAP1 and TcAP2 are located in the nucleus of epimastigotes and their expression is constitutive. Epimastigote AP endonucleases as well as recombinant TcAP1 and TcAP2 are inhibited by methoxyamine. Overexpression of TcAP1 increases epimastigotes viability when they are exposed to acute ROS/RNS attack. This protective effect is more evident when parasites are submitted to persistent ROS/RNS exposition, mimicking nature conditions. Our results confirm that the BER pathway is involved in T. cruzi resistance to DNA oxidative damage and points to the participation of DNA AP endonucleases in parasite survival. © 2013 Wiley Periodicals, Inc.

Genomic Disruption of VEGF-A Expression in Human Retinal Pigment Epithelial Cells Using CRISPR-Cas9 Endonuclease.

PubMed

Yiu, Glenn; Tieu, Eric; Nguyen, Anthony T; Wong, Brittany; Smit-McBride, Zeljka

2016-10-01

To employ type II clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 endonuclease to suppress ocular angiogenesis by genomic disruption of VEGF-A in human RPE cells. CRISPR sequences targeting exon 1 of human VEGF-A were computationally identified based on predicted Cas9 on- and off-target probabilities. Single guide RNA (gRNA) cassettes with these target sequences were cloned into lentiviral vectors encoding the Streptococcuspyogenes Cas9 endonuclease (SpCas9) gene. The lentiviral vectors were used to infect ARPE-19 cells, a human RPE cell line. Frequency of insertion or deletion (indel) mutations was assessed by T7 endonuclease 1 mismatch detection assay; mRNA levels were assessed with quantitative real-time PCR; and VEGF-A protein levels were determined by ELISA. In vitro angiogenesis was measured using an endothelial cell tube formation assay. Five gRNAs targeting VEGF-A were selected based on the highest predicted on-target probabilities, lowest off-target probabilities, or combined average of both scores. Lentiviral delivery of the top-scoring gRNAs with SpCas9 resulted in indel formation in the VEGF-A gene at frequencies up to 37.0% ± 4.0% with corresponding decreases in secreted VEGF-A protein up to 41.2% ± 7.4% (P < 0.001), and reduction of endothelial tube formation up to 39.4% ± 9.8% (P = 0.02). No significant indel formation in the top three putative off-target sites tested was detected. The CRISPR-Cas9 endonuclease system may reduce VEGF-A secretion from human RPE cells and suppress angiogenesis, supporting the possibility of employing gene editing for antiangiogenesis therapy in ocular diseases.

The RNA-induced silencing complex is a Mg2+-dependent endonuclease.

PubMed

Schwarz, Dianne S; Tomari, Yukihide; Zamore, Phillip D

2004-05-04

In the Drosophila and mammalian RNA interference (RNAi) pathways, target RNA destruction is catalyzed by the siRNA-guided, RNA-induced silencing complex (RISC). RISC has been proposed to be an siRNA-directed endonuclease, catalyzing cleavage of a single phosphodiester bond on the RNA target. Although 5' cleavage products are readily detected for RNAi in vitro, only 3' cleavage products have been observed in vivo. Proof that RISC acts as an endonuclease requires detection of both 5' and 3' cleavage products in a single experimental system. Here, we show that siRNA-programmed RISC generates both 5' and 3' cleavage products in vitro; cleavage requires Mg(2+), but not Ca(2+), and the cleavage product termini suggest a role for Mg(2+) in catalysis. Moreover, a single phosphorothioate in place of the scissile phosphate blocks cleavage; the phosphorothioate effect can be rescued by the thiophilic cation Mn(2+), but not by Ca(2+) or Mg(2+). We propose that during catalysis, a Mg(2+) ion is bound to the RNA substrate through a nonbridging oxygen of the scissile phosphate. The mechanism of endonucleolytic cleavage is not consistent with the mechanisms of the previously identified RISC nuclease, Tudor-SN. Thus, the RISC-component that mediates endonucleolytic cleavage of the target RNA remains to be identified.

Characterization of Arabidopsis thaliana mismatch specific endonucleases: application to mutation discovery by TILLING in pea.

PubMed

Triques, Karine; Sturbois, Bénédicte; Gallais, Stéphane; Dalmais, Marion; Chauvin, Stéphanie; Clepet, Christian; Aubourg, Sébastien; Rameau, Catherine; Caboche, Michel; Bendahmane, Abdelhafid

2007-09-01

Scanning DNA sequences for mutations and polymorphisms has become one of the most challenging, often expensive and time-consuming obstacles in many molecular genetic applications, including reverse genetic and clinical diagnostic applications. Enzymatic mutation detection methods are based on the cleavage of heteroduplex DNA at the mismatch sites. These methods are often limited by the availability of a mismatch-specific endonuclease, their sensitivity in detecting one allele in a pool of DNA and their costs. Here, we present detailed biochemical analysis of five Arabidopsis putative mismatch-specific endonucleases. One of them, ENDO1, is presented as the first endonuclease that recognizes and cleaves all types of mismatches with high efficiency. We report on a very simple protocol for the expression and purification of ENDO1. The ENDO1 system could be exploited in a wide range of mutation diagnostic tools. In particular, we report the use of ENDO1 for discovery of point mutations in the gibberellin 3beta-hydrolase gene of Pisum sativum. Twenty-one independent mutants were isolated, five of these were characterized and two new mutations affecting internodes length were identified. To further evaluate the quality of the mutant population we screened for mutations in four other genes and identified 5-21 new alleles per target. Based on the frequency of the obtained alleles we concluded that the pea population described here would be suitable for use in a large reverse-genetics project.

Biochemical characterization of a thermostable endonuclease V from the hyperthermophilic euryarchaeon Thermococcus barophilus Ch5.

PubMed

Wang, Yuxiao; Zhang, Likui; Zhu, Xinyuan; Li, Yuting; Shi, Haoqiang; Oger, Philippe; Yang, Zhihui

2018-05-22

Endonuclease V (Endo V) is an important enzyme for repairing deoxyinosine in DNA. While bacterial and eukaryotic endo Vs have been well studied, knowledge of archaeal endo Vs is limited. Here, we first presented biochemical characterization of a thermostable endonuclease V from the hyperthermophilic euryarchaeon Thermococcus barophilus Ch5 (Tba endo V). The recombinant enzyme possessed optimal endonuclease activity for cleaving deoxyinosine-containing DNA at 70-90 °C. Furthermore, Tba endo V can withstand 100 °C for 120 min without significant loss of its activity, suggesting the enzyme is thermostable. Tba endo V exhibited varying cleavage efficiencies at various pH levels from 6.0 to 11.0, among which an optimal pH for the enzyme was 8.0-9.0. In addition, a divalent metal ion was required for the enzyme to cleave DNA. Mn 2+ and Mg 2+ were optimal ions for the enzyme's activity whereas Ca 2+ , Zn 2+ and Co 2+ inhibited the enzyme activity. Moreover, the enzyme activity was suppressed by high NaCl concentration. Tba endo V bound to all DNA substrates; however, the enzyme exhibited a higher affinity for binding to deoxyinosine-containing DNA than normal DNA. Our work provides valuable information for revealing the role of Tba endo V in the base excision repair pathway for deoxyinosine repair in Thermococcus. Copyright © 2018. Published by Elsevier B.V.

Restriction endonuclease analysis of chloroplast DNA in interspecies somatic Hybrids of Petunia.

PubMed

Kumar, A; Cocking, E C; Bovenberg, W A; Kool, A J

1982-12-01

Restriction endonuclease cleavage pattern analysis of chloroplast DNA (cpDNA) of three different interspecific somatic hybrid plants revealed that the cytoplasms of the hybrids contained only cpDNA of P. parodii. The somatic hybrid plants analysed were those between P. parodii (wild type) + P. hybrida (wild type); P. parodii (wild type)+P. inflata (cytoplasmic albino mutant); P. parodii (wild type) + P. parviflora (nuclear albino mutant). The presence of only P. parodii chloroplasts in the somatic hybrid of P. parodii + P. inflata is possibly due to the stringent selection used for somatic hybrid production. However, in the case of the two other somatic hybrids P. parodii + P. hybrida and P. parodii + P. parviflora it was not possible to determine whether the presence of only P. parodii chloroplasts in these somatic hybrid plants was due to the nature of the selection schemes used or simply occurred by chance. The relevance of such somatic hybrid material for the study of genomic-cytoplasmic interaction is discussed, as well as the use of restriction endonuclease fragment patterns for the analysis of taxonomic and evolutionary inter-relationships in the genus Petunia.

The complex between a four-way DNA junction and T7 endonuclease I

PubMed Central

Déclais, Anne-Cécile; Fogg, Jonathan M.; Freeman, Alasdair D.J.; Coste, Franck; Hadden, Jonathan M.; Phillips, Simon E.V.; Lilley, David M.J.

2003-01-01

The junction-resolving enzyme endonuclease I is selective for the structure of the DNA four-way (Holliday) junction. The enzyme binds to a four-way junction in two possible orientations, with a 4:1 ratio, opening the DNA structure at the centre and changing the global structure into a 90° cross of approximately coaxial helices. The nuclease cleaves the continuous strands of the junction in each orientation. Binding leads to pronounced regions of protection of the DNA against hydroxyl radical attack. Using all this information together with the known structure of the enzyme and the structure of the BglI–DNA complex, we have constructed a model of the complex of endonuclease I and a DNA junction. This shows how the enzyme is selective for the structure of a four-way junction, such that both continuous strands can be accommodated into the two active sites so that a productive resolution event is possible. PMID:12628932

Determinants for DNA target structure selectivity of the human LINE-1 retrotransposon endonuclease.

PubMed

Repanas, Kostas; Zingler, Nora; Layer, Liliana E; Schumann, Gerald G; Perrakis, Anastassis; Weichenrieder, Oliver

2007-01-01

The human LINE-1 endonuclease (L1-EN) is the targeting endonuclease encoded by the human LINE-1 (L1) retrotransposon. L1-EN guides the genomic integration of new L1 and Alu elements that presently account for approximately 28% of the human genome. L1-EN bears considerable technological interest, because its target selectivity may ultimately be engineered to allow the site-specific integration of DNA into defined genomic locations. Based on the crystal structure, we generated L1-EN mutants to analyze and manipulate DNA target site recognition. Crystal structures and their dynamic and functional analysis show entire loop grafts to be feasible, resulting in altered specificity, while individual point mutations do not change the nicking pattern of L1-EN. Structural parameters of the DNA target seem more important for recognition than the nucleotide sequence, and nicking profiles on DNA oligonucleotides in vitro are less well defined than the respective integration site consensus in vivo. This suggests that additional factors other than the DNA nicking specificity of L1-EN contribute to the targeted integration of non-LTR retrotransposons.

Whole genome sequencing of Rhodotorula mucilaginosa isolated from the chewing stick (Distemonanthus benthamianus): insights into Rhodotorula phylogeny, mitogenome dynamics and carotenoid biosynthesis.

PubMed

Gan, Han Ming; Thomas, Bolaji N; Cavanaugh, Nicole T; Morales, Grace H; Mayers, Ashley N; Savka, Michael A; Hudson, André O

2017-01-01

In industry, the yeast Rhodotorula mucilaginosa is commonly used for the production of carotenoids. The production of carotenoids is important because they are used as natural colorants in food and some carotenoids are precursors of retinol (vitamin A). However, the identification and molecular characterization of the carotenoid pathway/s in species belonging to the genus Rhodotorula is scarce due to the lack of genomic information thus potentially impeding effective metabolic engineering of these yeast strains for improved carotenoid production. In this study, we report the isolation, identification, characterization and the whole nuclear genome and mitogenome sequence of the endophyte R. mucilaginosa RIT389 isolated from Distemonanthus benthamianus, a plant known for its anti-fungal and antibacterial properties and commonly used as chewing sticks. The assembled genome of R. mucilaginosa RIT389 is 19 Mbp in length with an estimated genomic heterozygosity of 9.29%. Whole genome phylogeny supports the species designation of strain RIT389 within the genus in addition to supporting the monophyly of the currently sequenced Rhodotorula species. Further, we report for the first time, the recovery of the complete mitochondrial genome of R. mucilaginosa using the genome skimming approach. The assembled mitogenome is at least 7,000 bases larger than that of Rhodotorula taiwanensis which is largely attributed to the presence of large intronic regions containing open reading frames coding for homing endonuclease from the LAGLIDADG and GIY-YIG families. Furthermore, genomic regions containing the key genes for carotenoid production were identified in R. mucilaginosa RIT389, revealing differences in gene synteny that may play a role in the regulation of the biotechnologically important carotenoid synthesis pathways in yeasts.

Evolution of group I introns in Porifera: new evidence for intron mobility and implications for DNA barcoding.

PubMed

Schuster, Astrid; Lopez, Jose V; Becking, Leontine E; Kelly, Michelle; Pomponi, Shirley A; Wörheide, Gert; Erpenbeck, Dirk; Cárdenas, Paco

2017-03-20

Mitochondrial introns intermit coding regions of genes and feature characteristic secondary structures and splicing mechanisms. In metazoans, mitochondrial introns have only been detected in sponges, cnidarians, placozoans and one annelid species. Within demosponges, group I and group II introns are present in six families. Based on different insertion sites within the cox1 gene and secondary structures, four types of group I and two types of group II introns are known, which can harbor up to three encoding homing endonuclease genes (HEG) of the LAGLIDADG family (group I) and/or reverse transcriptase (group II). However, only little is known about sponge intron mobility, transmission, and origin due to the lack of a comprehensive dataset. We analyzed the largest dataset on sponge mitochondrial group I introns to date: 95 specimens, from 11 different sponge genera which provided novel insights into the evolution of group I introns. For the first time group I introns were detected in four genera of the sponge family Scleritodermidae (Scleritoderma, Microscleroderma, Aciculites, Setidium). We demonstrated that group I introns in sponges aggregate in the most conserved regions of cox1. We showed that co-occurrence of two introns in cox1 is unique among metazoans, but not uncommon in sponges. However, this combination always associates an active intron with a degenerating one. Earlier hypotheses of HGT were confirmed and for the first time VGT and secondary losses of introns conclusively demonstrated. This study validates the subclass Spirophorina (Tetractinellida) as an intron hotspot in sponges. Our analyses confirm that most sponge group I introns probably originated from fungi. DNA barcoding is discussed and the application of alternative primers suggested.

Whole genome sequencing of Rhodotorula mucilaginosa isolated from the chewing stick (Distemonanthus benthamianus): insights into Rhodotorula phylogeny, mitogenome dynamics and carotenoid biosynthesis

PubMed Central

Thomas, Bolaji N.; Cavanaugh, Nicole T.; Morales, Grace H.; Mayers, Ashley N.; Savka, Michael A.

2017-01-01

In industry, the yeast Rhodotorula mucilaginosa is commonly used for the production of carotenoids. The production of carotenoids is important because they are used as natural colorants in food and some carotenoids are precursors of retinol (vitamin A). However, the identification and molecular characterization of the carotenoid pathway/s in species belonging to the genus Rhodotorula is scarce due to the lack of genomic information thus potentially impeding effective metabolic engineering of these yeast strains for improved carotenoid production. In this study, we report the isolation, identification, characterization and the whole nuclear genome and mitogenome sequence of the endophyte R. mucilaginosa RIT389 isolated from Distemonanthus benthamianus, a plant known for its anti-fungal and antibacterial properties and commonly used as chewing sticks. The assembled genome of R. mucilaginosa RIT389 is 19 Mbp in length with an estimated genomic heterozygosity of 9.29%. Whole genome phylogeny supports the species designation of strain RIT389 within the genus in addition to supporting the monophyly of the currently sequenced Rhodotorula species. Further, we report for the first time, the recovery of the complete mitochondrial genome of R. mucilaginosa using the genome skimming approach. The assembled mitogenome is at least 7,000 bases larger than that of Rhodotorula taiwanensis which is largely attributed to the presence of large intronic regions containing open reading frames coding for homing endonuclease from the LAGLIDADG and GIY-YIG families. Furthermore, genomic regions containing the key genes for carotenoid production were identified in R. mucilaginosa RIT389, revealing differences in gene synteny that may play a role in the regulation of the biotechnologically important carotenoid synthesis pathways in yeasts. PMID:29158974

Epigenetic Segregation of Microbial Genomes from Complex Samples Using Restriction Endonucleases HpaII and McrB.

PubMed

Liu, Guohong; Weston, Christopher Q; Pham, Long K; Waltz, Shannon; Barnes, Helen; King, Paula; Sphar, Dan; Yamamoto, Robert T; Forsyth, R Allyn

2016-01-01

We describe continuing work to develop restriction endonucleases as tools to enrich targeted genomes of interest from diverse populations. Two approaches were developed in parallel to segregate genomic DNA based on cytosine methylation. First, the methyl-sensitive endonuclease HpaII was used to bind non-CG methylated DNA. Second, a truncated fragment of McrB was used to bind CpG methylated DNA. Enrichment levels of microbial genomes can exceed 100-fold with HpaII allowing improved genomic detection and coverage of otherwise trace microbial genomes from sputum. Additionally, we observe interesting enrichment results that correlate with the methylation states not only of bacteria, but of fungi, viruses, a protist and plants. The methods presented here offer promise for testing biological samples for pathogens and global analysis of population methylomes.

Interstrand disulfide crosslinking of DNA bases supports a double nucleotide unpairing mechanism for flap endonucleases.

PubMed

Beddows, Amanda; Patel, Nikesh; Finger, L David; Atack, John M; Williams, David M; Grasby, Jane A

2012-09-14

Flap endonucleases (FENs) are proposed to select their target phosphate diester by unpairing the two terminal nucleotides of duplex. Interstrand disulfide crosslinks, introduced by oxidation of thiouracil and thioguanine bases, abolished the specificity of human FEN1 for hydrolysis one nucleotide into the 5'-duplex.

Mlh1-Mlh3, a Meiotic Crossover and DNA Mismatch Repair Factor, Is a Msh2-Msh3-stimulated Endonuclease*

PubMed Central

Rogacheva, Maria V.; Manhart, Carol M.; Chen, Cheng; Guarne, Alba; Surtees, Jennifer; Alani, Eric

2014-01-01

Crossing over between homologous chromosomes is initiated in meiotic prophase in most sexually reproducing organisms by the appearance of programmed double strand breaks throughout the genome. In Saccharomyces cerevisiae the double-strand breaks are resected to form three prime single-strand tails that primarily invade complementary sequences in unbroken homologs. These invasion intermediates are converted into double Holliday junctions and then resolved into crossovers that facilitate homolog segregation during Meiosis I. Work in yeast suggests that Msh4-Msh5 stabilizes invasion intermediates and double Holliday junctions, which are resolved into crossovers in steps requiring Sgs1 helicase, Exo1, and a putative endonuclease activity encoded by the DNA mismatch repair factor Mlh1-Mlh3. We purified Mlh1-Mlh3 and showed that it is a metal-dependent and Msh2-Msh3-stimulated endonuclease that makes single-strand breaks in supercoiled DNA. These observations support a direct role for an Mlh1-Mlh3 endonuclease activity in resolving recombination intermediates and in DNA mismatch repair. PMID:24403070

Mlh1-Mlh3, a meiotic crossover and DNA mismatch repair factor, is a Msh2-Msh3-stimulated endonuclease.

PubMed

Rogacheva, Maria V; Manhart, Carol M; Chen, Cheng; Guarne, Alba; Surtees, Jennifer; Alani, Eric

2014-02-28

Crossing over between homologous chromosomes is initiated in meiotic prophase in most sexually reproducing organisms by the appearance of programmed double strand breaks throughout the genome. In Saccharomyces cerevisiae the double-strand breaks are resected to form three prime single-strand tails that primarily invade complementary sequences in unbroken homologs. These invasion intermediates are converted into double Holliday junctions and then resolved into crossovers that facilitate homolog segregation during Meiosis I. Work in yeast suggests that Msh4-Msh5 stabilizes invasion intermediates and double Holliday junctions, which are resolved into crossovers in steps requiring Sgs1 helicase, Exo1, and a putative endonuclease activity encoded by the DNA mismatch repair factor Mlh1-Mlh3. We purified Mlh1-Mlh3 and showed that it is a metal-dependent and Msh2-Msh3-stimulated endonuclease that makes single-strand breaks in supercoiled DNA. These observations support a direct role for an Mlh1-Mlh3 endonuclease activity in resolving recombination intermediates and in DNA mismatch repair.

Spectroelectrochemical insights into structural and redox properties of immobilized endonuclease III and its catalytically inactive mutant

NASA Astrophysics Data System (ADS)

Moe, Elin; Rollo, Filipe; Silveira, Célia M.; Sezer, Murat; Hildebrandt, Peter; Todorovic, Smilja

2018-01-01

Endonuclease III is a Fe-S containing bifunctional DNA glycosylase which is involved in the repair of oxidation damaged DNA. Here we employ surface enhanced IR spectroelectrochemistry and electrochemistry to study the enzyme from the highly radiation- and desiccation-resistant bacterium Deinococcus radiodurans (DrEndoIII2). The experiments are designed to shed more light onto specific parameters that are currently proposed to govern damage search and recognition by endonucleases III. We demonstrate that electrostatic interactions required for the redox activation of DrEndoIII2 may result in high electric fields that alter its structural and thermodynamic properties. Analysis of inactive DrEndoIII2 (K132A/D150A double mutant) interacting with undamaged DNA, and the active enzyme interacting with damaged DNA also indicate that the electron transfer is modulated by subtle differences in the protein-DNA complex.

Dominant Mutations in S. cerevisiae PMS1 Identify the Mlh1-Pms1 Endonuclease Active Site and an Exonuclease 1-Independent Mismatch Repair Pathway

PubMed Central

Smith, Catherine E.; Mendillo, Marc L.; Bowen, Nikki; Hombauer, Hans; Campbell, Christopher S.; Desai, Arshad; Putnam, Christopher D.; Kolodner, Richard D.

2013-01-01

Lynch syndrome (hereditary nonpolypsis colorectal cancer or HNPCC) is a common cancer predisposition syndrome. Predisposition to cancer in this syndrome results from increased accumulation of mutations due to defective mismatch repair (MMR) caused by a mutation in one of the mismatch repair genes MLH1, MSH2, MSH6 or PMS2/scPMS1. To better understand the function of Mlh1-Pms1 in MMR, we used Saccharomyces cerevisiae to identify six pms1 mutations (pms1-G683E, pms1-C817R, pms1-C848S, pms1-H850R, pms1-H703A and pms1-E707A) that were weakly dominant in wild-type cells, which surprisingly caused a strong MMR defect when present on low copy plasmids in an exo1Δ mutant. Molecular modeling showed these mutations caused amino acid substitutions in the metal coordination pocket of the Pms1 endonuclease active site and biochemical studies showed that they inactivated the endonuclease activity. This model of Mlh1-Pms1 suggested that the Mlh1-FERC motif contributes to the endonuclease active site. Consistent with this, the mlh1-E767stp mutation caused both MMR and endonuclease defects similar to those caused by the dominant pms1 mutations whereas mutations affecting the predicted metal coordinating residue Mlh1-C769 had no effect. These studies establish that the Mlh1-Pms1 endonuclease is required for MMR in a previously uncharacterized Exo1-independent MMR pathway. PMID:24204293

Dominant mutations in S. cerevisiae PMS1 identify the Mlh1-Pms1 endonuclease active site and an exonuclease 1-independent mismatch repair pathway.

PubMed

Smith, Catherine E; Mendillo, Marc L; Bowen, Nikki; Hombauer, Hans; Campbell, Christopher S; Desai, Arshad; Putnam, Christopher D; Kolodner, Richard D

2013-10-01

Lynch syndrome (hereditary nonpolypsis colorectal cancer or HNPCC) is a common cancer predisposition syndrome. Predisposition to cancer in this syndrome results from increased accumulation of mutations due to defective mismatch repair (MMR) caused by a mutation in one of the mismatch repair genes MLH1, MSH2, MSH6 or PMS2/scPMS1. To better understand the function of Mlh1-Pms1 in MMR, we used Saccharomyces cerevisiae to identify six pms1 mutations (pms1-G683E, pms1-C817R, pms1-C848S, pms1-H850R, pms1-H703A and pms1-E707A) that were weakly dominant in wild-type cells, which surprisingly caused a strong MMR defect when present on low copy plasmids in an exo1Δ mutant. Molecular modeling showed these mutations caused amino acid substitutions in the metal coordination pocket of the Pms1 endonuclease active site and biochemical studies showed that they inactivated the endonuclease activity. This model of Mlh1-Pms1 suggested that the Mlh1-FERC motif contributes to the endonuclease active site. Consistent with this, the mlh1-E767stp mutation caused both MMR and endonuclease defects similar to those caused by the dominant pms1 mutations whereas mutations affecting the predicted metal coordinating residue Mlh1-C769 had no effect. These studies establish that the Mlh1-Pms1 endonuclease is required for MMR in a previously uncharacterized Exo1-independent MMR pathway.

Possibility of cytoplasmic pre-tRNA splicing: the yeast tRNA splicing endonuclease mainly localizes on the mitochondria.

PubMed

Yoshihisa, Tohru; Yunoki-Esaki, Kaori; Ohshima, Chie; Tanaka, Nobuyuki; Endo, Toshiya

2003-08-01

Pre-tRNA splicing has been believed to occur in the nucleus. In yeast, the tRNA splicing endonuclease that cleaves the exon-intron junctions of pre-tRNAs consists of Sen54p, Sen2p, Sen34p, and Sen15p and was thought to be an integral membrane protein of the inner nuclear envelope. Here we show that the majority of Sen2p, Sen54p, and the endonuclease activity are not localized in the nucleus, but on the mitochondrial surface. The endonuclease is peripherally associated with the cytosolic surface of the outer mitochondrial membrane. A Sen54p derivative artificially fixed on the mitochondria as an integral membrane protein can functionally replace the authentic Sen54p, whereas mutant proteins defective in mitochondrial localization are not fully active. sen2 mutant cells accumulate unspliced pre-tRNAs in the cytosol under the restrictive conditions, and this export of the pre-tRNAs partly depends on Los1p, yeast exportin-t. It is difficult to explain these results from the view of tRNA splicing in the nucleus. We rather propose a new possibility that tRNA splicing occurs on the mitochondrial surface in yeast.

Protein complexes formed during the incision reaction catalyzed by the Escherichia coli UvrABC endonuclease.

PubMed Central

Yeung, A T; Mattes, W B; Grossman, L

1986-01-01

An examination has been made into the nature of the nucleoprotein complexes formed during the incision reaction catalyzed by the Escherichia coli UvrABC endonuclease when acting on a pyrimidine dimer-containing fd RF-I DNA species. The complexes of proteins and DNA form in unique stages. The first stage of binding involves an ATP-stimulated interaction of the UvrA protein with duplex DNA containing pyrimidine dimer sites. The UvrB protein significantly stabilizes the UvrA-pyrimidine dimer containing DNA complex which, in turn, provides a foundation for the binding of UvrC to activate the UvrABC endonuclease. The binding of one molecule of UvrC to each UvrAB-damaged DNA complex is needed to catalyze incision in the vicinity of pyrimidine dimer sites. The UvrABC-DNA complex persists after the incision event suggesting that the lack of UvrABC turnover may be linked to other activities in the excision-repair pathway beyond the initial incision reaction. PMID:3960727

Probing the dynamics of restriction endonuclease NgoMIV-DNA interaction by single-molecule FRET.

PubMed

Tutkus, Marijonas; Sasnauskas, Giedrius; Rutkauskas, Danielis

2017-12-01

Many type II restriction endonucleases require two copies of their recognition sequence for optimal activity. Concomitant binding of two DNA sites by such an enzyme produces a DNA loop. Here we exploit single-molecule Förster resonance energy transfer (smFRET) of surface-immobilized DNA fragments to study the dynamics of DNA looping induced by tetrameric endonuclease NgoMIV. We have employed a DNA fragment with two NgoMIV recognition sites and a FRET dye pair such that upon protein-induced DNA looping the dyes are brought to close proximity resulting in a FRET signal. The dynamics of DNA-NgoMIV interactions proved to be heterogeneous, with individual smFRET trajectories exhibiting broadly different average looped state durations. Distinct types of the dynamics were attributed to different types of DNA-protein complexes, mediated either by one NgoMIV tetramer simultaneously bound to two specific sites ("slow" trajectories) or by semi-specific interactions of two DNA-bound NgoMIV tetramers ("fast" trajectories), as well as to conformational heterogeneity of individual NgoMIV molecules. © 2017 Wiley Periodicals, Inc.

RPA activates the XPF-ERCC1 endonuclease to initiate processing of DNA interstrand crosslinks.

PubMed

Abdullah, Ummi B; McGouran, Joanna F; Brolih, Sanja; Ptchelkine, Denis; El-Sagheer, Afaf H; Brown, Tom; McHugh, Peter J

2017-07-14

During replication-coupled DNA interstrand crosslink (ICL) repair, the XPF-ERCC1 endonuclease is required for the incisions that release, or "unhook", ICLs, but the mechanism of ICL unhooking remains largely unknown. Incisions are triggered when the nascent leading strand of a replication fork strikes the ICL Here, we report that while purified XPF-ERCC1 incises simple ICL-containing model replication fork structures, the presence of a nascent leading strand, modelling the effects of replication arrest, inhibits this activity. Strikingly, the addition of the single-stranded DNA (ssDNA)-binding replication protein A (RPA) selectively restores XPF-ERCC1 endonuclease activity on this structure. The 5'-3' exonuclease SNM1A can load from the XPF-ERCC1-RPA-induced incisions and digest past the crosslink to quantitatively complete the unhooking reaction. We postulate that these collaborative activities of XPF-ERCC1, RPA and SNM1A might explain how ICL unhooking is achieved in vivo . © 2017 The Authors. Published under the terms of the CC BY 4.0 license.

Spectroelectrochemical insights into structural and redox properties of immobilized endonuclease III and its catalytically inactive mutant.

PubMed

Moe, Elin; Rollo, Filipe; Silveira, Célia M; Sezer, Murat; Hildebrandt, Peter; Todorovic, Smilja

2018-01-05

Endonuclease III is a Fe-S containing bifunctional DNA glycosylase which is involved in the repair of oxidation damaged DNA. Here we employ surface enhanced IR spectroelectrochemistry and electrochemistry to study the enzyme from the highly radiation- and desiccation-resistant bacterium Deinococcus radiodurans (DrEndoIII 2 ). The experiments are designed to shed more light onto specific parameters that are currently proposed to govern damage search and recognition by endonucleases III. We demonstrate that electrostatic interactions required for the redox activation of DrEndoIII 2 may result in high electric fields that alter its structural and thermodynamic properties. Analysis of inactive DrEndoIII 2 (K132A/D150A double mutant) interacting with undamaged DNA, and the active enzyme interacting with damaged DNA also indicate that the electron transfer is modulated by subtle differences in the protein-DNA complex. Copyright © 2017 Elsevier B.V. All rights reserved.

An open reading frame in intron seven of the sea urchin DNA-methyltransferase gene codes for a functional AP1 endonuclease.

PubMed

Cioffi, Anna Valentina; Ferrara, Diana; Cubellis, Maria Vittoria; Aniello, Francesco; Corrado, Marcella; Liguori, Francesca; Amoroso, Alessandro; Fucci, Laura; Branno, Margherita

2002-08-01

Analysis of the genome structure of the Paracentrotus lividus (sea urchin) DNA methyltransferase (DNA MTase) gene showed the presence of an open reading frame, named METEX, in intron 7 of the gene. METEX expression is developmentally regulated, showing no correlation with DNA MTase expression. In fact, DNA MTase transcripts are present at high concentrations in the early developmental stages, while METEX is expressed at late stages of development. Two METEX cDNA clones (Met1 and Met2) that are different in the 3' end have been isolated in a cDNA library screening. The putative translated protein from Met2 cDNA clone showed similarity with Escherichia coli endonuclease III on the basis of sequence and predictive three-dimensional structure. The protein, overexpressed in E. coli and purified, had functional properties similar to the endonuclease specific for apurinic/apyrimidinic (AP) sites on the basis of the lyase activity. Therefore the open reading frame, present in intron 7 of the P. lividus DNA MTase gene, codes for a functional AP endonuclease designated SuAP1.

Activation of Saccharomyces cerevisiae Mlh1-Pms1 Endonuclease in a Reconstituted Mismatch Repair System.

PubMed

Smith, Catherine E; Bowen, Nikki; Graham, William J; Goellner, Eva M; Srivatsan, Anjana; Kolodner, Richard D

2015-08-28

Previous studies reported the reconstitution of an Mlh1-Pms1-independent 5' nick-directed mismatch repair (MMR) reaction using Saccharomyces cerevisiae proteins. Here we describe the reconstitution of a mispair-dependent Mlh1-Pms1 endonuclease activation reaction requiring Msh2-Msh6 (or Msh2-Msh3), proliferating cell nuclear antigen (PCNA), and replication factor C (RFC) and a reconstituted Mlh1-Pms1-dependent 3' nick-directed MMR reaction requiring Msh2-Msh6 (or Msh2-Msh3), exonuclease 1 (Exo1), replication protein A (RPA), RFC, PCNA, and DNA polymerase δ. Both reactions required Mg(2+) and Mn(2+) for optimal activity. The MMR reaction also required two reaction stages in which the first stage required incubation of Mlh1-Pms1 with substrate DNA, with or without Msh2-Msh6 (or Msh2-Msh3), PCNA, and RFC but did not require nicking of the substrate, followed by a second stage in which other proteins were added. Analysis of different mutant proteins demonstrated that both reactions required a functional Mlh1-Pms1 endonuclease active site, as well as mispair recognition and Mlh1-Pms1 recruitment by Msh2-Msh6 but not sliding clamp formation. Mutant Mlh1-Pms1 and PCNA proteins that were defective for Exo1-independent but not Exo1-dependent MMR in vivo were partially defective in the Mlh1-Pms1 endonuclease and MMR reactions, suggesting that both reactions reflect the activation of Mlh1-Pms1 seen in Exo1-independent MMR in vivo. The availability of this reconstituted MMR reaction should now make it possible to better study both Exo1-independent and Exo1-dependent MMR. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Activation of Saccharomyces cerevisiae Mlh1-Pms1 Endonuclease in a Reconstituted Mismatch Repair System*

PubMed Central

Smith, Catherine E.; Bowen, Nikki; Graham, William J.; Goellner, Eva M.; Srivatsan, Anjana; Kolodner, Richard D.

2015-01-01

Previous studies reported the reconstitution of an Mlh1-Pms1-independent 5′ nick-directed mismatch repair (MMR) reaction using Saccharomyces cerevisiae proteins. Here we describe the reconstitution of a mispair-dependent Mlh1-Pms1 endonuclease activation reaction requiring Msh2-Msh6 (or Msh2-Msh3), proliferating cell nuclear antigen (PCNA), and replication factor C (RFC) and a reconstituted Mlh1-Pms1-dependent 3′ nick-directed MMR reaction requiring Msh2-Msh6 (or Msh2-Msh3), exonuclease 1 (Exo1), replication protein A (RPA), RFC, PCNA, and DNA polymerase δ. Both reactions required Mg2+ and Mn2+ for optimal activity. The MMR reaction also required two reaction stages in which the first stage required incubation of Mlh1-Pms1 with substrate DNA, with or without Msh2-Msh6 (or Msh2-Msh3), PCNA, and RFC but did not require nicking of the substrate, followed by a second stage in which other proteins were added. Analysis of different mutant proteins demonstrated that both reactions required a functional Mlh1-Pms1 endonuclease active site, as well as mispair recognition and Mlh1-Pms1 recruitment by Msh2-Msh6 but not sliding clamp formation. Mutant Mlh1-Pms1 and PCNA proteins that were defective for Exo1-independent but not Exo1-dependent MMR in vivo were partially defective in the Mlh1-Pms1 endonuclease and MMR reactions, suggesting that both reactions reflect the activation of Mlh1-Pms1 seen in Exo1-independent MMR in vivo. The availability of this reconstituted MMR reaction should now make it possible to better study both Exo1-independent and Exo1-dependent MMR. PMID:26170454

Geographically diverse Australian isolates of Melissococcus pluton exhibit minimal genotypic diversity by restriction endonuclease analysis.

PubMed

Djordjevic, S P; Smith, L A; Forbes, W A; Hornitzky, M A

1999-04-15

Melissococcus pluton, the causative agent of European foulbrood is an economically significant disease of honey bees (Apis mellifera) across most regions of the world and is prevalent throughout most states of Australia. 49 Isolates of M. pluton recovered from diseased colonies or honey samples in New South Wales, Queensland, South Australia, Tasmania and Victoria were compared using SDS-PAGE, Western immunoblotting and restriction endonuclease analyses. DNA profiles of all 49 geographically diverse isolates showed remarkably similar AluI profiles although four isolates (one each from Queensland, South Australia, New South Wales and Victoria) displayed minor profile variations compared to AluI patterns of all other isolates. DNA from a subset of the 49 Australian and three isolates from the United Kingdom were digested separately with the restriction endonucleases CfoI, RsaI and DraI. Restriction endonuclease fragment patterns generated using these enzymes were also similar although minor variations were noted. SDS-PAGE of whole cell proteins from 13 of the 49 isolates from different states of Australia, including the four isolates which displayed minor profile variations (AluI) produced indistinguishable patterns. Major immunoreactive proteins of approximate molecular masses of 21, 24, 28, 30, 36, 40, 44, 56, 60, 71, 79 and 95 kDa were observed in immunoblots of whole cell lysates of 22 of the 49 isolates and reacted with rabbit hyperimmune antibodies raised against M. pluton whole cells. Neither SDS-PAGE or immunoblotting was capable of distinguishing differences between geographically diverse isolates of M. pluton. Collectively these data confirm that Australian isolates of M. pluton are genetically homogeneous and that this species may be clonal. Plasmid DNA was not detected in whole cell DNA profiles of any isolate resolved using agarose gel electrophoresis.

Characterization of Sulfolobus islandicus rod-shaped virus 2 gp19, a single-strand specific endonuclease.

PubMed

Gardner, Andrew F; Prangishvili, David; Jack, William E

2011-09-01

The hyperthermophilic Sulfolobus islandicus rod-shaped virus 2 (SIRV2) encodes a 25-kDa protein (SIRV2gp19) annotated as a hypothetical protein with sequence homology to the RecB nuclease superfamily. Even though SIRV2gp19 homologs are conserved throughout the rudivirus family and presumably play a role in the viral life cycle, SIRV2gp19 has not been functionally characterized. To define the minimal requirements for activity, SIRV2gp19 was purified and tested under varying conditions. SIRV2gp19 is a single-strand specific endonuclease that requires Mg(2+) for activity and is inactive on double-stranded DNA. A conserved aspartic acid in RecB nuclease superfamily Motif II (D89) is also essential for SIRV2gp19 activity and mutation to alanine (D89A) abolishes activity. Therefore, the SIRV2gp19 cleavage mechanism is similar to previously described RecB nucleases. Finally, SIRV2gp19 single-stranded DNA endonuclease activity could play a role in host chromosome degradation during SIRV2 lytic infection.

Purification and characterization of VDE, a site-specific endonuclease from the yeast Saccharomyces cerevisiae.

PubMed

Gimble, F S; Thorner, J

1993-10-15

The 119-kDa primary translation product of the VMA1 gene of Saccharomyces cerevisiae undergoes a self-catalyzed rearrangement ("protein splicing") that excises an internal 50-kDa segment of the polypeptide and joins the amino-terminal and carboxyl-terminal segments to generate the 69-kDa subunit of the vacuolar membrane-associated H(+)-ATPase. We have shown previously that the internal segment is a site-specific endonuclease (Gimble, F. S., and Thorner, J. (1992) Nature 357, 301-306). Here we describe methods for the high level expression and purification to near homogeneity of both the authentic VMA1-derived endonuclease (or VDE) from yeast (yield 18%) and a recombinant form of VDE made in bacteria (yield 29%). Detailed characterization of these preparations demonstrated that the yeast-derived and bacterially produced enzymes were indistinguishable, as judged by: (a) behavior during purification; (b) apparent native molecular mass (50 kDa); (c) immunological reactivity; and (d) catalytic properties (specific activity; cleavage site recognition; and optima for pH, temperature, divalent cation and ionic strength). The minimal site required for VDE cleavage was delimited to a 30-base pair sequence within its specific substrate (the VMA1 delta vde allele).

An ultrasensitive colorimeter assay strategy for p53 mutation assisted by nicking endonuclease signal amplification.

PubMed

Lin, Zhenyu; Yang, Weiqiang; Zhang, Guiyun; Liu, Qida; Qiu, Bin; Cai, Zongwei; Chen, Guonan

2011-08-28

A novel catalytic colorimetric assay assisted by nicking endonuclease signal amplification (NESA) was developed. With the signal amplification, the detection limit of the p53 target gene can be as low as 1 pM, which is nearly 5 orders of magnitude lower than that of other previously reported colorimetric DNA detection strategies based on catalytic DNAzyme.

Roles of Two Shewanella oneidensis MR-1 Extracellular Endonucleases ▿ †

PubMed Central

Gödeke, Julia; Heun, Magnus; Bubendorfer, Sebastian; Paul, Kristina; Thormann, Kai M.

2011-01-01

The dissimilatory iron-reducing bacterium Shewanella oneidensis MR-1 is capable of using extracellular DNA (eDNA) as the sole source of carbon, phosphorus, and nitrogen. In addition, we recently demonstrated that S. oneidensis MR-1 requires eDNA as a structural component during all stages of biofilm formation. In this study, we characterize the roles of two Shewanella extracellular endonucleases, ExeS and ExeM. While ExeS is likely secreted into the medium, ExeM is predicted to remain associated with the cell envelope. Both exeM and exeS are highly expressed under phosphate-limited conditions. Mutants lacking exeS and/or exeM exhibit decreased eDNA degradation; however, the capability of S. oneidensis MR-1 to use DNA as the sole source of phosphorus is only affected in mutants lacking exeM. Neither of the two endonucleases alleviates toxic effects of increased eDNA concentrations. The deletion of exeM and/or exeS significantly affects biofilm formation of S. oneidensis MR-1 under static conditions, and expression of exeM and exeS drastically increases during static biofilm formation. Under hydrodynamic conditions, a deletion of exeM leads to altered biofilms that consist of densely packed structures which are covered by a thick layer of eDNA. Based on these results, we hypothesize that a major role of ExeS and, in particular, ExeM of S. oneidensis MR-1, is to degrade eDNA as a matrix component during biofilm formation to improve nutrient supply and to enable detachment. PMID:21705528

Functional characterization of two flap endonuclease-1 homologues in rice.

PubMed

Kimura, Seisuke; Furukawa, Tomoyuki; Kasai, Nobuyuki; Mori, Yoko; Kitamoto, Hiroko K; Sugawara, Fumio; Hashimoto, Junji; Sakaguchi, Kengo

2003-09-18

Flap endonuclease-1 (FEN-1) is an important enzyme involved in DNA replication and repair. Previously, we isolated and characterized a complementary DNA (cDNA) from rice (Oryza sativa) encoding a protein which shows homology with the eukaryotic flap endonuclease-1 (FEN-1). In this report, we found that rice (O. sativa L. cv. Nipponbare) possessed two FEN-1 homologues designated as OsFEN-1a and OsFEN-1b. The OsFEN-1a and OsFEN-1b genes were mapped to chromosome 5 and 3, respectively. Both genes contained 17 exons and 16 introns. Alignment of OsFEN-1a protein with OsFEN-1b protein showed a high degree of sequence similarity, particularly around the N and I domains. Northern hybridization and in situ hybridization analysis demonstrated preferential expression of OsFEN-1a and OsFEN-1b in proliferating tissues such as the shoot apical meristem or young leaves. The levels of OsFEN-1a and OsFEN-1b expression were significantly reduced when cell proliferation was temporarily halted by the removal of sucrose from the growth medium. When the growth-halted cells began to regrow following the addition of sucrose to the medium, both OsFEN-1a and OsFEN-1b were again expressed at high level. These results suggested that OsFEN-1a and OsFEN-1b are required for cell proliferation. Functional complementation assay suggested that OsFEN-1a cDNA had the ability to complement Saccharomyces cerevisiae rad27 null mutant. On the other hand, OsFEN-1b cDNA could not complement the rad27 mutant. The roles of OsFEN-1a and OsFEN-1b in plant DNA replication and repair are discussed.

Comparison of the nucleotide and amino acid sequences of the RsrI and EcoRI restriction endonucleases.

PubMed

Stephenson, F H; Ballard, B T; Boyer, H W; Rosenberg, J M; Greene, P J

1989-12-21

The RsrI endonuclease, a type-II restriction endonuclease (ENase) found in Rhodobacter sphaeroides, is an isoschizomer of the EcoRI ENase. A clone containing an 11-kb BamHI fragment was isolated from an R. sphaeroides genomic DNA library by hybridization with synthetic oligodeoxyribonucleotide probes based on the N-terminal amino acid (aa) sequence of RsrI. Extracts of E. coli containing a subclone of the 11-kb fragment display RsrI activity. Nucleotide sequence analysis reveals an 831-bp open reading frame encoding a polypeptide of 277 aa. A 50% identity exists within a 266-aa overlap between the deduced aa sequences of RsrI and EcoRI. Regions of 75-100% aa sequence identity correspond to key structural and functional regions of EcoRI. The type-II ENases have many common properties, and a common origin might have been expected. Nevertheless, this is the first demonstration of aa sequence similarity between ENases produced by different organisms.

Apurinic/Apyrimidinic Endonuclease 1 Is the Essential Nuclease during Immunoglobulin Class Switch Recombination

PubMed Central

Masani, Shahnaz; Han, Li

2013-01-01

Immunoglobulin (Ig) class switch recombination (CSR) is initiated by activation-induced cytidine deaminase (AID) that catalyzes numerous DNA cytosine deaminations within switch regions. The resulting uracils are processed by uracil base excision and/or mismatch repair enzymes that ultimately generate switch region DNA double-strand breaks (DSBs). Uracil glycosylase 2 (UNG2) is required for CSR, most likely by removing uracils to generate abasic sites. Although it is presumed that the apurinic/apyrimidinic endonuclease 1 (APE1) generates DNA strand incisions (a prerequisite for CSR) at these abasic sites, a direct test of the requirement for APE1 in CSR has been difficult because of the embryonic lethality of APE1 ablation in mice. Here, we report the successful deletion of the APE1 gene in a mouse B cell line (CH12F3) capable of robust CSR in vitro. In contrast to the general assumption that APE1 is essential for cellular viability, deletion of APE1 in CH12F3 cells has no apparent effect on cell viability or growth. Moreover, CSR in APE1-null CH12F3 cells is drastically reduced, providing direct evidence for an essential role for APE1 in switch region cleavage and CSR. Finally, deletion of AP endonuclease 2 (APE2) has no effect on CSR in either APE1-proficient or -deficient cells. PMID:23382073

[Definition of the specificity of DNA-methyltransferase M.Bsc4I in cell lysate by blocking of restriction endonucleases and computer modeling].

PubMed

Dedkov, V S

2009-01-01

The specificity of DNA-methyltransferase M.Bsc4I was defined in cellular lysate of Bacillus schlegelii 4. For this purpose, we used methylation sensitivity of restriction endonucleases, and also modeling of methylation. The modeling consisted in editing sequences of DNA using replacements of methylated bases and their complementary bases. The substratum DNA processed by M.Bsc4I also were used for studying sensitivity of some restriction endonucleases to methylation. Thus, it was shown that M.Bsc4I methylated 5'-Cm4CNNNNNNNGG-3' and the overlapped dcm-methylation blocked its activity. The offered approach can appear universal enough and simple for definition of specificity of DNA-methyltransferases.

Atypical myxomatosis--virus isolation, experimental infection of rabbits and restriction endonuclease analysis of the isolate.

PubMed

Psikal, I; Smíd, B; Rodák, L; Valícek, L; Bendová, J

2003-08-01

Atypical form of myxomatosis, which caused non-lethal and clinically mild disease in domestic rabbits 1 month after immunization with a commercially available vaccine MXT, is described. The isolated myxoma virus designated as Litovel 2 (Li-2) did not induce systemic disease following subcutaneous and intradermal applications in susceptible experimental rabbits but led to the immune response demonstrated by ELISA. No severe disease was induced in those Li-2 inoculated rabbits by challenge with the virulent strains Lausanne (Lu) or Sanar (SA), while the control animals showed nodular form of myxomatosis with lethal course of the illness. Restriction fragment length polymorphism (RFLP) of genomic DNA with KpnI and BamHI endonucleases was used for genetic characterization of the Li-2 isolate, the vaccine strain MXT and both virulent strains Lu and SA, respectively. In general, RFLP analysis has shown to be informative for inferring genetic relatedness between myxoma viruses. Based on restriction endonuclease DNA fragment size distribution, it was evident that the pathogenic strain SA is genetically related to the reference strain Lu and the isolate Li-2 is more related, but not identical, to the vaccination strain MXT.

Single substitution in bacteriophage T4 RNase H alters the ratio between its exo- and endonuclease activities.

PubMed

Kholod, Natalia; Sivogrivov, Dmitry; Latypov, Oleg; Mayorov, Sergey; Kuznitsyn, Rafail; Kajava, Andrey V; Shlyapnikov, Mikhail; Granovsky, Igor

2015-11-01

The article describes substitutions in bacteriophage T4 RNase H which provide so called das-effect. Phage T4 DNA arrest suppression (das) mutations have been described to be capable of partially suppressing the phage DNA arrest phenotype caused by a dysfunction in genes 46 and/or 47 (also known as Mre11/Rad50 complex). Genetic mapping of das13 (one of the das mutations) has shown it to be in the region of the rnh gene encoding RNase H. Here we report that Das13 mutant of RNase H has substitutions of valine 43 and leucine 242 with isoleucines. To investigate the influence of these mutations on RNase H nuclease properties we have designed a novel in vitro assay that allows us to separate and quantify exo- or endonuclease activities of flap endonuclease. The nuclease assay in vitro showed that V43I substitution increased the ratio between exonuclease/endonuclease activities of RNase H whereas L242I substitution did not affect the nuclease activity of RNase H in vitro. However, both mutations were necessary for the full das effect in vivo. Molecular modelling of the nuclease structure suggests that V43I substitution may lead to disposition of H4 helix, responsible for the interaction with the first base pairs of 5'end of branched DNA. These structural changes may affect unwinding of the first base pairs of gapped or nicked DNA generating a short flap and therefore may stabilize the DNA-enzyme complex. L242I substitution did not affect the structure of RNase H and its role in providing das-effect remains unclear. Copyright © 2015 Elsevier B.V. All rights reserved.

Lucanthone and Its Derivative Hycanthone Inhibit Apurinic Endonuclease-1 (APE1) by Direct Protein Binding

PubMed Central

Naidu, Mamta D.; Agarwal, Rakhi; Pena, Louis A.; Cunha, Luis; Mezei, Mihaly; Shen, Min; Wilson, David M.; Liu, Yuan; Sanchez, Zina; Chaudhary, Pankaj; Wilson, Samuel H.; Waring, Michael J.

2011-01-01

Lucanthone and hycanthone are thioxanthenone DNA intercalators used in the 1980s as antitumor agents. Lucanthone is in Phase I clinical trial, whereas hycanthone was pulled out of Phase II trials. Their potential mechanism of action includes DNA intercalation, inhibition of nucleic acid biosyntheses, and inhibition of enzymes like topoisomerases and the dual function base excision repair enzyme apurinic endonuclease 1 (APE1). Lucanthone inhibits the endonuclease activity of APE1, without affecting its redox activity. Our goal was to decipher the precise mechanism of APE1 inhibition as a prerequisite towards development of improved therapeutics that can counteract higher APE1 activity often seen in tumors. The IC50 values for inhibition of APE1 incision of depurinated plasmid DNA by lucanthone and hycanthone were 5 µM and 80 nM, respectively. The KD values (affinity constants) for APE1, as determined by BIACORE binding studies, were 89 nM for lucanthone/10 nM for hycanthone. APE1 structures reveal a hydrophobic pocket where hydrophobic small molecules like thioxanthenones can bind, and our modeling studies confirmed such docking. Circular dichroism spectra uncovered change in the helical structure of APE1 in the presence of lucanthone/hycanthone, and notably, this effect was decreased (Phe266Ala or Phe266Cys or Trp280Leu) or abolished (Phe266Ala/Trp280Ala) when hydrophobic site mutants were employed. Reduced inhibition by lucanthone of the diminished endonuclease activity of hydrophobic mutant proteins (as compared to wild type APE1) supports that binding of lucanthone to the hydrophobic pocket dictates APE1 inhibition. The DNA binding capacity of APE1 was marginally inhibited by lucanthone, and not at all by hycanthone, supporting our hypothesis that thioxanthenones inhibit APE1, predominantly, by direct interaction. Finally, lucanthone-induced degradation was drastically reduced in the presence of short and long lived free radical scavengers, e.g., TRIS and DMSO

Bacterial persistence by RNA endonucleases

PubMed Central

Maisonneuve, Etienne; Shakespeare, Lana J.; Jørgensen, Mikkel Girke; Gerdes, Kenn

2011-01-01

Bacteria form persisters, individual cells that are highly tolerant to different types of antibiotics. Persister cells are genetically identical to nontolerant kin but have entered a dormant state in which they are recalcitrant to the killing activity of the antibiotics. The molecular mechanisms underlying bacterial persistence are unknown. Here, we show that the ubiquitous Lon (Long Form Filament) protease and mRNA endonucleases (mRNases) encoded by toxin-antitoxin (TA) loci are required for persistence in Escherichia coli. Successive deletion of the 10 mRNase-encoding TA loci of E. coli progressively reduced the level of persisters, showing that persistence is a phenotype common to TA loci. In all cases tested, the antitoxins, which control the activities of the mRNases, are Lon substrates. Consistently, cells lacking lon generated a highly reduced level of persisters. Moreover, Lon overproduction dramatically increased the levels of persisters in wild-type cells but not in cells lacking the 10 mRNases. These results support a simple model according to which mRNases encoded by TA loci are activated in a small fraction of growing cells by Lon-mediated degradation of the antitoxins. Activation of the mRNases, in turn, inhibits global cellular translation, and thereby induces dormancy and persistence. Many pathogenic bacteria known to enter dormant states have a plethora of TA genes. Therefore, in the future, the discoveries described here may lead to a mechanistic understanding of the persistence phenomenon in pathogenic bacteria. PMID:21788497

The Use of Bacterial Repair Endonucleases in the Comet Assay.

PubMed

Collins, Andrew R

2017-01-01

The comet assay is a sensitive electrophoretic method for measuring DNA breaks at the level of single cells, used widely in genotoxicity experiments, in biomonitoring, and in fundamental research. Its sensitivity and range of application are increased by the incorporation of an extra step, after lysis of agarose-embedded cells, in which the DNA is digested with lesion-specific endonucleases (DNA repair enzymes of bacterial or phage origin). Enzymes with specificity for oxidized purines, oxidized pyrimidines, alkylated bases, UV-induced cyclobutane pyrimidine dimers, and misincorporated uracil have been employed. The additional enzyme-sensitive sites, over and above the strand breaks detected in the standard comet assay, give a quantitative estimate of the number of specific lesions present in the cells.

A newly discovered Bordetella species carries a transcriptionally active CRISPR-Cas with a small Cas9 endonuclease

USDA-ARS?s Scientific Manuscript database

The Cas9 endonuclease of the Type II-a clustered regularly interspersed short palindromic repeats (CRISPR), of Streptococcus pyogenes (SpCas9) has been adapted as a widely used tool for genome editing and genome engineering. Herein, we describe a gene encoding a novel Cas9 ortholog (BpsuCas9) and th...

Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors

DOE PAGES

Jones, Jeremy C.; Kumar, Gyanendra; Barman, Subrata; ...

2018-04-24

ABSTRACT The clinical severity and annual occurrence of influenza virus epidemics, combined with the availability of just a single class of antivirals to treat infections, underscores the urgent need to develop new anti-influenza drugs. The endonuclease activity within the viral acidic polymerase (PA) protein is an attractive target for drug discovery due to the critical role it plays in viral gene transcription. RO-7 is a next-generation PA endonuclease inhibitor of influenza A and B viruses, but its drug resistance potential is unknown. Through serial passage of influenza A(H1N1) viruses in MDCK cells under selective pressure of RO-7, we identified anmore » I38T substitution within the PA endonuclease domain that conferred in vitro resistance to RO-7 (up to a 287-fold change in 50% effective concentration [EC 50 ]). I38T emerged between 5 and 10 passages, and when introduced into recombinant influenza A(H1N1) viruses, alone conferred RO-7 resistance (up to an 81-fold change in EC 50 ). Cocrystal structures of mutant and wild-type endonuclease domains with RO-7 provided the structural basis of resistance, where a key hydrophobic interaction between RO-7 and the Ile38 side chain is compromised when mutated to the polar threonine. While Ile38 does not have a crucial role in coordinating the endonuclease active site, the switch to threonine does affect the polymerase activity of some viruses and influences RO-7 affinity for the PA N target (i.e., the ≈200-residue N-terminal domain of PA). However, the change does not lead to a complete loss of replication activity in vitro . Our results predict that RO-7-resistant influenza viruses carrying the I38T substitution may emerge under treatment. This should be taken into consideration for clinical surveillance and in refinement of these drugs. IMPORTANCE The effectiveness of antiviral drugs can be severely compromised by the emergence of resistant viruses. Therefore, determination of the mechanisms by which viruses

Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors

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

Jones, Jeremy C.; Kumar, Gyanendra; Barman, Subrata

ABSTRACT The clinical severity and annual occurrence of influenza virus epidemics, combined with the availability of just a single class of antivirals to treat infections, underscores the urgent need to develop new anti-influenza drugs. The endonuclease activity within the viral acidic polymerase (PA) protein is an attractive target for drug discovery due to the critical role it plays in viral gene transcription. RO-7 is a next-generation PA endonuclease inhibitor of influenza A and B viruses, but its drug resistance potential is unknown. Through serial passage of influenza A(H1N1) viruses in MDCK cells under selective pressure of RO-7, we identified anmore » I38T substitution within the PA endonuclease domain that conferred in vitro resistance to RO-7 (up to a 287-fold change in 50% effective concentration [EC 50 ]). I38T emerged between 5 and 10 passages, and when introduced into recombinant influenza A(H1N1) viruses, alone conferred RO-7 resistance (up to an 81-fold change in EC 50 ). Cocrystal structures of mutant and wild-type endonuclease domains with RO-7 provided the structural basis of resistance, where a key hydrophobic interaction between RO-7 and the Ile38 side chain is compromised when mutated to the polar threonine. While Ile38 does not have a crucial role in coordinating the endonuclease active site, the switch to threonine does affect the polymerase activity of some viruses and influences RO-7 affinity for the PA N target (i.e., the ≈200-residue N-terminal domain of PA). However, the change does not lead to a complete loss of replication activity in vitro . Our results predict that RO-7-resistant influenza viruses carrying the I38T substitution may emerge under treatment. This should be taken into consideration for clinical surveillance and in refinement of these drugs. IMPORTANCE The effectiveness of antiviral drugs can be severely compromised by the emergence of resistant viruses. Therefore, determination of the mechanisms by which viruses

Ultrasensitive signal-on DNA biosensor based on nicking endonuclease assisted electrochemistry signal amplification.

PubMed

Liu, Zhongyuan; Zhang, Wei; Zhu, Shuyun; Zhang, Ling; Hu, Lianzhe; Parveen, Saima; Xu, Guobao

2011-11-15

Combining the advantages of signal-on strategy and nicking endonuclease assisted electrochemistry signal amplification (NEAESA), a new sensitive and signal-on electrochemical DNA biosensor for the sequence specific DNA detection based on NEAESA has been developed for the first time. A Hairpin-shape probe (HP), containing the target DNA recognition sequence, is thiol-modified at 5' end and immobilized on gold electrode via Au-S bonding. Subsequently, the HP modified electrode is hybridized with target DNA to form a duplex. Then the nicking endonuclease is added and nicks the HP strand in the duplex. After nicking, 3'-ferrocene (Fc)-labeled part complementary probe (Fc-PCP) is introduced on the electrode surface by hybridizing with the thiol-modified HP fragment, which results in the generation of electrochemical signal. Hence, the DNA biosensor is constructed successfully. The present DNA biosensor shows a wide linear range of 5.0×10(-13)-5.0×10(-8)M for detecting target DNA, with a low detection limit of 0.167pM. The proposed strategy does not require any amplifying labels (enzymes, DNAzymes, nanoparticles, etc.) for biorecognition events, which avoids false-positive results to occur frequently. Moreover, the strategy has the benefits of simple preparation, convenient operation, good selectivity, and high sensitivity. With the advantages mentioned above, this simple and sensitive strategy has the potential to be integrated in portable, low cost and simplified devices for diagnostic applications. Copyright © 2011 Elsevier B.V. All rights reserved.

Analysis of Endonuclease R·EcoRI Fragments of DNA from Lambdoid Bacteriophages and Other Viruses by Agarose-Gel Electrophoresis

PubMed Central

Helling, Robert B.; Goodman, Howard M.; Boyer, Herbert W.

1974-01-01

By means of agarose-gel electrophoresis, endonuclease R·EcoRI-generated fragments of DNA from various viruses were separated, their molecular weights were determined, and complete or partial fragment maps for lambda, φ80, and hybrid phages were constructed. Images PMID:4372397

BplI, a new BcgI-like restriction endonuclease, which recognizes a symmetric sequence.

PubMed Central

Vitkute, J; Maneliene, Z; Petrusyte, M; Janulaitis, A

1997-01-01

Bcg I and Bcg I-like restriction endonucleases cleave double stranded DNA specifically on both sides of their asymmetric recognition sequences which are interrupted by several ambiguous base pairs. Their heterosubunit structure, bifunctionality and stimulation by AdoMet make them different from other classified restriction enzymes. Here we report on a new Bcg I-like restriction endonuclease, Bpl I from Bacillus pumilus , which in contrast to all other Bcg I-like enzymes, recognizes a symmetric interrupted sequence, and which, like Bcg I, cleaves double stranded DNA upstream and downstream of its recognition sequence (8/13)GAGN5CTC(13/8). Like Bcg I, Bpl I is a bifunctional enzyme revealing both DNA cleavage and methyltransferase activities. There are two polypeptides in the homogeneous preparation of Bpl I with molecular masses of approximately 74 and 37 kDa. The sizes of the Bpl I subunits are close to those of Bcg I, but the proportion 1:1 in the final preparation is different from that of 2:1 in Bcg I. Low activity observed with Mg2+increases >100-fold in the presence of AdoMet. Even with AdoMet though, specific cleavage is incomplete. S -adenosylhomocysteine (AdoHcy) or sinefungin can replace AdoMet in the cleavage reaction. AdoHcy activated Bpl I yields complete cleavage of DNA. PMID:9358150

Multiplex, Rapid, and Sensitive Isothermal Detection of Nucleic-Acid Sequence by Endonuclease Restriction-Mediated Real-Time Multiple Cross Displacement Amplification.

PubMed

Wang, Yi; Wang, Yan; Zhang, Lu; Liu, Dongxin; Luo, Lijuan; Li, Hua; Cao, Xiaolong; Liu, Kai; Xu, Jianguo; Ye, Changyun

2016-01-01

We have devised a novel isothermal amplification technology, termed endonuclease restriction-mediated real-time multiple cross displacement amplification (ET-MCDA), which facilitated multiplex, rapid, specific and sensitive detection of nucleic-acid sequences at a constant temperature. The ET-MCDA integrated multiple cross displacement amplification strategy, restriction endonuclease cleavage and real-time fluorescence detection technique. In the ET-MCDA system, the functional cross primer E-CP1 or E-CP2 was constructed by adding a short sequence at the 5' end of CP1 or CP2, respectively, and the new E-CP1 or E-CP2 primer was labeled at the 5' end with a fluorophore and in the middle with a dark quencher. The restriction endonuclease Nb.BsrDI specifically recognized the short sequence and digested the newly synthesized double-stranded terminal sequences (5' end short sequences and their complementary sequences), which released the quenching, resulting on a gain of fluorescence signal. Thus, the ET-MCDA allowed real-time detection of single or multiple targets in only a single reaction, and the positive results were observed in as short as 12 min, detecting down to 3.125 fg of genomic DNA per tube. Moreover, the analytical specificity and the practical application of the ET-MCDA were also successfully evaluated in this study. Here, we provided the details on the novel ET-MCDA technique and expounded the basic ET-MCDA amplification mechanism.

Crystal structure of NucB, a biofilm-degrading endonuclease

PubMed Central

Baslé, Arnaud; Hewitt, Lorraine; Koh, Alan; Lamb, Heather K; Thompson, Paul; Burgess, J Grant; Hall, Michael J; Hawkins, Alastair R; Murray, Heath

2018-01-01

Abstract Bacterial biofilms are a complex architecture of cells that grow on moist interfaces, and are held together by a molecular glue of extracellular proteins, sugars and nucleic acids. Biofilms are particularly problematic in human healthcare as they can coat medical implants and are thus a potential source of disease. The enzymatic dispersal of biofilms is increasingly being developed as a new strategy to treat this problem. Here, we have characterized NucB, a biofilm-dispersing nuclease from a marine strain of Bacillus licheniformis, and present its crystal structure together with the biochemistry and a mutational analysis required to confirm its active site. Taken together, these data support the categorization of NucB into a unique subfamily of the ββα metal-dependent non-specific endonucleases. Understanding the structure and function of NucB will facilitate its future development into an anti-biofilm therapeutic agent. PMID:29165717

VDE-initiated intein homing in Saccharomyces cerevisiae proceeds in a meiotic recombination-like manner.

PubMed

Fukuda, Tomoyuki; Nogami, Satoru; Ohya, Yoshikazu

2003-07-01

Inteins and group I introns found in prokaryotic and eukaryotic organisms occasionally behave as mobile genetic elements. During meiosis of the yeast Saccharomyces cerevisiae, the site-specific endonuclease encoded by VMA1 intein, VDE, triggers a single double-strand break (DSB) at an inteinless allele, leading to VMA1 intein homing. Besides the accumulating information on the in vitro activity of VDE, very little has been known about the molecular mechanism of intein homing in yeast nucleus. We developed an assay to detect the product of VMA1 intein homing in yeast genome. We analysed mutant phenotypes of RecA homologs, Rad51p and Dmc1p, and their interacting proteins, Rad54p and Tid1p, and found that they all play critical roles in intein inheritance. The absence of DSB end processing proteins, Sae2p and those in the Mre11-Rad50-Xrs2 complex, also causes partial reduction in homing efficiency. As with meiotic recombination, crossover events are frequently observed during intein homing. We also observed that the absence of premeiotic DNA replication caused by hydroxyurea (HU) or clb5delta clb6delta mutation reduces VDE-mediated DSBs. The repairing system working in intein homing shares molecular machinery with meiotic recombination induced by Spo11p. Moreover, like Spo11p-induced DNA cleavage, premeiotic DNA replication is a prerequisite for a VDE-induced DSB. VMA1 intein thus utilizes several host factors involved in meiotic and recombinational processes to spread its genetic information and guarantee its progeny through establishment of a parasitic relationship with the organism.

Spectrophotometric, colorimetric and visually detection of Pseudomonas aeruginosa ETA gene based gold nanoparticles DNA probe and endonuclease enzyme

NASA Astrophysics Data System (ADS)

Amini, Bahram; Kamali, Mehdi; Salouti, Mojtaba; Yaghmaei, Parichehreh

2018-06-01

Colorimetric DNA detection is preferred over other methods for clinical molecular diagnosis because it does not require expensive equipment. In the present study, the colorimetric method based on gold nanoparticles (GNPs) and endonuclease enzyme was used for the detection of P. aeruginosa ETA gene. Firstly, the primers and probe for P. aeruginosa exotoxin A (ETA) gene were designed and checked for specificity by the PCR method. Then, GNPs were synthesized using the citrate reduction method and conjugated with the prepared probe to develop the new nano-biosensor. Next, the extracted target DNA of the bacteria was added to GNP-probe complex to check its efficacy for P. aeruginosa ETA gene diagnosis. A decrease in absorbance was seen when GNP-probe-target DNA cleaved into the small fragments of BamHI endonuclease due to the weakened electrostatic interaction between GNPs and the shortened DNA. The right shift of the absorbance peak from 530 to 562 nm occurred after adding the endonuclease. It was measured using a UV-VIS absorption spectroscopy that indicates the existence of the P. aeruginosa ETA gene. Sensitivity was determined in the presence of different concentrations of target DNA of P. aeruginosa. The results obtained from the optimized conditions showed that the absorbance value has linear correlation with concentration of target DNA (R: 0.9850) in the range of 10-50 ng mL-1 with the limit detection of 9.899 ng mL-1. Thus, the specificity of the new method for detection of P. aeruginosa was established in comparison with other bacteria. Additionally, the designed assay was quantitatively applied to detect the P. aeruginosa ETA gene from 103 to 108 CFU mL-1 in real samples with a detection limit of 320 CFU mL-1.

Spectrophotometric, colorimetric and visually detection of Pseudomonas aeruginosa ETA gene based gold nanoparticles DNA probe and endonuclease enzyme.

PubMed

Amini, Bahram; Kamali, Mehdi; Salouti, Mojtaba; Yaghmaei, Parichehreh

2018-06-15

Colorimetric DNA detection is preferred over other methods for clinical molecular diagnosis because it does not require expensive equipment. In the present study, the colorimetric method based on gold nanoparticles (GNPs) and endonuclease enzyme was used for the detection of P. aeruginosa ETA gene. Firstly, the primers and probe for P. aeruginosa exotoxin A (ETA) gene were designed and checked for specificity by the PCR method. Then, GNPs were synthesized using the citrate reduction method and conjugated with the prepared probe to develop the new nano-biosensor. Next, the extracted target DNA of the bacteria was added to GNP-probe complex to check its efficacy for P. aeruginosa ETA gene diagnosis. A decrease in absorbance was seen when GNP-probe-target DNA cleaved into the small fragments of BamHI endonuclease due to the weakened electrostatic interaction between GNPs and the shortened DNA. The right shift of the absorbance peak from 530 to 562nm occurred after adding the endonuclease. It was measured using a UV-VIS absorption spectroscopy that indicates the existence of the P. aeruginosa ETA gene. Sensitivity was determined in the presence of different concentrations of target DNA of P. aeruginosa. The results obtained from the optimized conditions showed that the absorbance value has linear correlation with concentration of target DNA (R: 0.9850) in the range of 10-50ngmL -1 with the limit detection of 9.899ngmL -1 . Thus, the specificity of the new method for detection of P. aeruginosa was established in comparison with other bacteria. Additionally, the designed assay was quantitatively applied to detect the P. aeruginosa ETA gene from 10 3 to 10 8 CFUmL -1 in real samples with a detection limit of 320CFUmL -1 . Copyright © 2018 Elsevier B.V. All rights reserved.

CgII cleaves DNA using a mechanism distinct from other ATP-dependent restriction endonucleases

PubMed Central

Toliusis, Paulius; Silanskas, Arunas; Szczelkun, Mark D.

2017-01-01

Abstract The restriction endonuclease CglI from Corynebacterium glutamicum recognizes an asymmetric 5′-GCCGC-3′ site and cleaves the DNA 7 and 6/7 nucleotides downstream on the top and bottom DNA strands, respectively, in an NTP-hydrolysis dependent reaction. CglI is composed of two different proteins: an endonuclease (R.CglI) and a DEAD-family helicase-like ATPase (H.CglI). These subunits form a heterotetrameric complex with R2H2 stoichiometry. However, the R2H2·CglI complex has only one nuclease active site sufficient to cut one DNA strand suggesting that two complexes are required to introduce a double strand break. Here, we report studies to evaluate the DNA cleavage mechanism of CglI. Using one- and two-site circular DNA substrates we show that CglI does not require two sites on the same DNA for optimal catalytic activity. However, one-site linear DNA is a poor substrate, supporting a mechanism where CglI complexes must communicate along the one-dimensional DNA contour before cleavage is activated. Based on experimental data, we propose that adenosine triphosphate (ATP) hydrolysis by CglI produces translocation on DNA preferentially in a downstream direction from the target, although upstream translocation is also possible. Our results are consistent with a mechanism of CglI action that is distinct from that of other ATP-dependent restriction-modification enzymes. PMID:28854738

Mitochondrial endonuclease G mediates breakdown of paternal mitochondria upon fertilization.

PubMed

Zhou, Qinghua; Li, Haimin; Li, Hanzeng; Nakagawa, Akihisa; Lin, Jason L J; Lee, Eui-Seung; Harry, Brian L; Skeen-Gaar, Riley Robert; Suehiro, Yuji; William, Donna; Mitani, Shohei; Yuan, Hanna S; Kang, Byung-Ho; Xue, Ding

2016-07-22

Mitochondria are inherited maternally in most animals, but the mechanisms of selective paternal mitochondrial elimination (PME) are unknown. While examining fertilization in Caenorhabditis elegans, we observed that paternal mitochondria rapidly lose their inner membrane integrity. CPS-6, a mitochondrial endonuclease G, serves as a paternal mitochondrial factor that is critical for PME. We found that CPS-6 relocates from the intermembrane space of paternal mitochondria to the matrix after fertilization to degrade mitochondrial DNA. It acts with maternal autophagy and proteasome machineries to promote PME. Loss of cps-6 delays breakdown of mitochondrial inner membranes, autophagosome enclosure of paternal mitochondria, and PME. Delayed removal of paternal mitochondria causes increased embryonic lethality, demonstrating that PME is important for normal animal development. Thus, CPS-6 functions as a paternal mitochondrial degradation factor during animal development. Copyright © 2016, American Association for the Advancement of Science.

Synthesis, Biological Evaluation and Structure-Activity Relationships of a Novel Class of Apurinic/Apyrimidinic Endonuclease 1 Inhibitors

PubMed Central

Rai, Ganesha; Vyjayanti, Vaddadi N.; Dorjsuren, Dorjbal; Simeonov, Anton; Jadhav, Ajit; Wilson, David M.; Maloney, David J.

2012-01-01

APE1 is an essential protein that operates in the base excision repair (BER) pathway and is responsible for ≥95% of the total apurinic/apyrimidinic (AP) endonuclease activity in human cells. BER is a major pathway that copes with DNA damage induced by several anti-cancer agents, including ionizing radiation and temozolomide. Overexpression of APE1 and enhanced AP endonuclease activity has been linked to increased resistance of tumor cells to treatment with monofunctional alkylators, implicating inhibition of APE1 as a valid strategy for cancer therapy. We report herein the results of a focused medicinal chemistry effort around a novel APE1 inhibitor, N-(3-(benzo[d]thiazol-2-yl)-6-isopropyl-4,5,6,7-tetrahydrothieno[2,3-c]pyridin-2-yl)acetamide (3). Compound 3 and related analogs exhibit single-digit µM activity against the purified APE1 enzyme, comparable activity in HeLa whole cell extract assays, and potentiate the cytotoxicity of the alkylating agents methylmethane sulfonate and temozolomide. Moreover, this class of compounds possesses a generally favorable in vitro ADME profile, along with good exposure levels in plasma and brain following intraperitoneal dosing (30 mg/kg body weight) in mice. PMID:22455312

Assembly of Francisella novicida Cpf1 endonuclease in complex with guide RNA and target DNA

PubMed Central

Montoya, Guillermo; Stella, Stefano

2017-01-01

Bacteria and archaea use the CRISPR–Cas system as an adaptive response against infection by foreign nucleic acids. Owing to its remarkable flexibility, this mechanism has been harnessed and adopted as a powerful tool for genome editing. The CRISPR–Cas system includes two classes that are subdivided into six types and 19 subtypes according to conservation of the cas gene and loci organization. Recently, a new protein with endonuclease activity belonging to class 2 type V has been identified. This endonuclease, termed Cpf1, in complex with a single CRISPR RNA (crRNA) is able to recognize and cleave a target DNA preceded by a 5′-TTN-3′ protospacer-adjacent motif (PAM) complementary to the RNA guide. To obtain structural insight into the inner workings of Cpf1, the crystallization of an active complex containing the full extent of the crRNA and a 31-nucleotide dsDNA target was attempted. The gene encoding Cpf1 from Francisella novicida was cloned, overexpressed and purified. The crRNA was transcribed and purified in vitro. Finally, the ternary FnCpf1–crRNA–DNA complex was assembled and purified by preparative electrophoresis before crystallization. Crystals belonging to space group C2221, with unit-cell parameters a = 85.2, b = 137.6, c = 320.5 Å, were obtained and subjected to preliminary diffraction experiments. PMID:28695850

A Mismatch EndoNuclease Array-Based Methodology (MENA) for Identifying Known SNPs or Novel Point Mutations.

PubMed

Comeron, Josep M; Reed, Jordan; Christie, Matthew; Jacobs, Julia S; Dierdorff, Jason; Eberl, Daniel F; Manak, J Robert

2016-04-05

Accurate and rapid identification or confirmation of single nucleotide polymorphisms (SNPs), point mutations and other human genomic variation facilitates understanding the genetic basis of disease. We have developed a new methodology (called MENA (Mismatch EndoNuclease Array)) pairing DNA mismatch endonuclease enzymology with tiling microarray hybridization in order to genotype both known point mutations (such as SNPs) as well as identify previously undiscovered point mutations and small indels. We show that our assay can rapidly genotype known SNPs in a human genomic DNA sample with 99% accuracy, in addition to identifying novel point mutations and small indels with a false discovery rate as low as 10%. Our technology provides a platform for a variety of applications, including: (1) genotyping known SNPs as well as confirming newly discovered SNPs from whole genome sequencing analyses; (2) identifying novel point mutations and indels in any genomic region from any organism for which genome sequence information is available; and (3) screening panels of genes associated with particular diseases and disorders in patient samples to identify causative mutations. As a proof of principle for using MENA to discover novel mutations, we report identification of a novel allele of the beethoven (btv) gene in Drosophila, which encodes a ciliary cytoplasmic dynein motor protein important for auditory mechanosensation.

Restriction of a bacteriophage of Streptomyces albus G involving endonuclease SalI.

PubMed Central

Chater, K F; Wilde, L C

1976-01-01

The bacteriophage Pa16, isolated from soil on Streptomyces albus G, was restricted when transferred from an alternative host back to S. albus G. Extracted unmodified Pa16 deoxyribonucleic acid was cleaved at a single site by a cell-free extract of S. albus G. Fractions cleaving Pal6 deoxyribonucleic acid contained the endonuclease SalI first described by J. Arrand, P. Myers, and R. J. Roberts (unpublished data). A mutant of S. albus G was isolated which was defective in both restriction and modification of Pal6. This mutant lacked SalI activity. It is concluded that SalI is the agent of restriction of Pal6 by S. albus G. Images PMID:977549

Restriction Endonucleases from Invasive Neisseria gonorrhoeae Cause Double-Strand Breaks and Distort Mitosis in Epithelial Cells during Infection

PubMed Central

Weyler, Linda; Engelbrecht, Mattias; Mata Forsberg, Manuel; Brehwens, Karl; Vare, Daniel; Vielfort, Katarina; Wojcik, Andrzej; Aro, Helena

2014-01-01

The host epithelium is both a barrier against, and the target for microbial infections. Maintaining regulated cell growth ensures an intact protective layer towards microbial-induced cellular damage. Neisseria gonorrhoeae infections disrupt host cell cycle regulation machinery and the infection causes DNA double strand breaks that delay progression through the G2/M phase. We show that intracellular gonococci upregulate and release restriction endonucleases that enter the nucleus and damage human chromosomal DNA. Bacterial lysates containing restriction endonucleases were able to fragment genomic DNA as detected by PFGE. Lysates were also microinjected into the cytoplasm of cells in interphase and after 20 h, DNA double strand breaks were identified by 53BP1 staining. In addition, by using live-cell microscopy and NHS-ester stained live gonococci we visualized the subcellular location of the bacteria upon mitosis. Infected cells show dysregulation of the spindle assembly checkpoint proteins MAD1 and MAD2, impaired and prolonged M-phase, nuclear swelling, micronuclei formation and chromosomal instability. These data highlight basic molecular functions of how gonococcal infections affect host cell cycle regulation, cause DNA double strand breaks and predispose cellular malignancies. PMID:25460012

Restriction endonucleases from invasive Neisseria gonorrhoeae cause double-strand breaks and distort mitosis in epithelial cells during infection.

PubMed

Weyler, Linda; Engelbrecht, Mattias; Mata Forsberg, Manuel; Brehwens, Karl; Vare, Daniel; Vielfort, Katarina; Wojcik, Andrzej; Aro, Helena

2014-01-01

The host epithelium is both a barrier against, and the target for microbial infections. Maintaining regulated cell growth ensures an intact protective layer towards microbial-induced cellular damage. Neisseria gonorrhoeae infections disrupt host cell cycle regulation machinery and the infection causes DNA double strand breaks that delay progression through the G2/M phase. We show that intracellular gonococci upregulate and release restriction endonucleases that enter the nucleus and damage human chromosomal DNA. Bacterial lysates containing restriction endonucleases were able to fragment genomic DNA as detected by PFGE. Lysates were also microinjected into the cytoplasm of cells in interphase and after 20 h, DNA double strand breaks were identified by 53BP1 staining. In addition, by using live-cell microscopy and NHS-ester stained live gonococci we visualized the subcellular location of the bacteria upon mitosis. Infected cells show dysregulation of the spindle assembly checkpoint proteins MAD1 and MAD2, impaired and prolonged M-phase, nuclear swelling, micronuclei formation and chromosomal instability. These data highlight basic molecular functions of how gonococcal infections affect host cell cycle regulation, cause DNA double strand breaks and predispose cellular malignancies.

Endonuclease G mediates α-synuclein cytotoxicity during Parkinson's disease.

PubMed

Büttner, Sabrina; Habernig, Lukas; Broeskamp, Filomena; Ruli, Doris; Vögtle, F Nora; Vlachos, Manolis; Macchi, Francesca; Küttner, Victoria; Carmona-Gutierrez, Didac; Eisenberg, Tobias; Ring, Julia; Markaki, Maria; Taskin, Asli Aras; Benke, Stefan; Ruckenstuhl, Christoph; Braun, Ralf; Van den Haute, Chris; Bammens, Tine; van der Perren, Anke; Fröhlich, Kai-Uwe; Winderickx, Joris; Kroemer, Guido; Baekelandt, Veerle; Tavernarakis, Nektarios; Kovacs, Gabor G; Dengjel, Jörn; Meisinger, Chris; Sigrist, Stephan J; Madeo, Frank

2013-11-27

Malfunctioning of the protein α-synuclein is critically involved in the demise of dopaminergic neurons relevant to Parkinson's disease. Nonetheless, the precise mechanisms explaining this pathogenic neuronal cell death remain elusive. Endonuclease G (EndoG) is a mitochondrially localized nuclease that triggers DNA degradation and cell death upon translocation from mitochondria to the nucleus. Here, we show that EndoG displays cytotoxic nuclear localization in dopaminergic neurons of human Parkinson-diseased patients, while EndoG depletion largely reduces α-synuclein-induced cell death in human neuroblastoma cells. Xenogenic expression of human α-synuclein in yeast cells triggers mitochondria-nuclear translocation of EndoG and EndoG-mediated DNA degradation through a mechanism that requires a functional kynurenine pathway and the permeability transition pore. In nematodes and flies, EndoG is essential for the α-synuclein-driven degeneration of dopaminergic neurons. Moreover, the locomotion and survival of α-synuclein-expressing flies is compromised, but reinstalled by parallel depletion of EndoG. In sum, we unravel a phylogenetically conserved pathway that involves EndoG as a critical downstream executor of α-synuclein cytotoxicity.

Digital detection of endonuclease mediated gene disruption in the HIV provirus

PubMed Central

Sedlak, Ruth Hall; Liang, Shu; Niyonzima, Nixon; De Silva Feelixge, Harshana S.; Roychoudhury, Pavitra; Greninger, Alexander L.; Weber, Nicholas D.; Boissel, Sandrine; Scharenberg, Andrew M.; Cheng, Anqi; Magaret, Amalia; Bumgarner, Roger; Stone, Daniel; Jerome, Keith R.

2016-01-01

Genome editing by designer nucleases is a rapidly evolving technology utilized in a highly diverse set of research fields. Among all fields, the T7 endonuclease mismatch cleavage assay, or Surveyor assay, is the most commonly used tool to assess genomic editing by designer nucleases. This assay, while relatively easy to perform, provides only a semi-quantitative measure of mutation efficiency that lacks sensitivity and accuracy. We demonstrate a simple droplet digital PCR assay that quickly quantitates a range of indel mutations with detection as low as 0.02% mutant in a wild type background and precision (≤6%CV) and accuracy superior to either mismatch cleavage assay or clonal sequencing when compared to next-generation sequencing. The precision and simplicity of this assay will facilitate comparison of gene editing approaches and their optimization, accelerating progress in this rapidly-moving field. PMID:26829887

The role of His-83 of yeast apurinic/apyrimidinic endonuclease Apn1 in catalytic incision of abasic sites in DNA.

PubMed

Dyakonova, Elena S; Koval, Vladimir V; Lomzov, Alexander A; Ishchenko, Alexander A; Fedorova, Olga S

2015-06-01

The apurinic/apyrimidinic (AP) endonuclease Apn1 from Saccharomyces cerevisiae is a key enzyme involved in the base excision repair (BER) at the cleavage stage of abasic sites (AP sites) in DNA. The crystal structure of Apn1 from S. cerevisiae is unresolved. Based on its high amino acid homology to Escherichia coli Endo IV, His-83 is believed to coordinate one of three Zn2+ ions in Apn1's active site similar to His-69 in Endo IV. Substituting His-83 with Ala is proposed to decrease the AP endonuclease activity of Apn1 owing to weak coordination of Zn2+ ions involved in enzymatic catalysis. The kinetics of recognition, binding, and incision of DNA substrates with the H83A Apn1 mutant was investigated. The stopped-flow method detecting fluorescence intensity changes of 2-aminopurine (2-aPu) was used to monitor the conformational dynamics of DNA at pre-steady-state conditions. We found substituting His-83 with Ala influenced catalytic complex formation and further incision of the damaged DNA strand. The H83A Apn1 catalysis depends not only on the location of the mismatch relative to the abasic site in DNA, but also on the nature of damage. We consider His-83 properly coordinates the active site Zn2+ ion playing a crucial role in catalytic incision stage. Our data prove suppressed enzymatic activity of H83A Apn1 results from the reduced number of active site Zn2+ ions. Our study provides insights into mechanistic specialty of AP site repair by yeast AP endonuclease Apn1 of Endo IV family, which members are not found in mammals, but are present in many microorganisms. The results will provide useful guidelines for design of new anti-fungal and anti-malarial agents. Copyright © 2015 Elsevier B.V. All rights reserved.

Peculiarities of Crystallization of the Restriction Endonuclease EcoRII

NASA Technical Reports Server (NTRS)

Karpove, Elizaveta; Pusey, M.arc L.

1998-01-01

Nucleases interfere with most standard molecular biology procedures. We have purified and crystallized the restriction endonuclease EcoRII, which belongs to the type II of restriction- modification enzyme, to study the protein crystallization process using a "non standard" macromolecule. A procedure for the purification of EcoRII was developed and 99% pure protein as determined by SDS PAGE electrophoresis obtained. Light scattering experiments were performed to assist in screening protein suitable crystallization conditions. The second virial coefficient was determined as a function of precipitating salt concentration, using sodium chloride, ammonium sulfate, and sodium sulfate. Small (maximum size approximately 0.2 mm) well shaped crystals have been obtained. Larger poorly formed crystals (ca 0.5 mm) have also been obtained, but we have been unable to mount them for diff-raction analysis due to their extreme fragility. Crystallization experiments with PEG have shown that using this precipitant, the best crystals are obtained from slightly over-saturated solutions. Use of higher precipitant concentration leads to dendritic crystal formation. EcoRII is difficult to solubilize and meticulous attention must be paid to the presence of reducing agents.

DNA interrogation by the CRISPR RNA-guided endonuclease Cas9.

PubMed

Sternberg, Samuel H; Redding, Sy; Jinek, Martin; Greene, Eric C; Doudna, Jennifer A

2014-03-06

The clustered regularly interspaced short palindromic repeats (CRISPR)-associated enzyme Cas9 is an RNA-guided endonuclease that uses RNA-DNA base-pairing to target foreign DNA in bacteria. Cas9-guide RNA complexes are also effective genome engineering agents in animals and plants. Here we use single-molecule and bulk biochemical experiments to determine how Cas9-RNA interrogates DNA to find specific cleavage sites. We show that both binding and cleavage of DNA by Cas9-RNA require recognition of a short trinucleotide protospacer adjacent motif (PAM). Non-target DNA binding affinity scales with PAM density, and sequences fully complementary to the guide RNA but lacking a nearby PAM are ignored by Cas9-RNA. Competition assays provide evidence that DNA strand separation and RNA-DNA heteroduplex formation initiate at the PAM and proceed directionally towards the distal end of the target sequence. Furthermore, PAM interactions trigger Cas9 catalytic activity. These results reveal how Cas9 uses PAM recognition to quickly identify potential target sites while scanning large DNA molecules, and to regulate scission of double-stranded DNA.

DNA interrogation by the CRISPR RNA-guided endonuclease Cas9

NASA Astrophysics Data System (ADS)

Sternberg, Samuel H.; Redding, Sy; Jinek, Martin; Greene, Eric C.; Doudna, Jennifer A.

2014-03-01

The clustered regularly interspaced short palindromic repeats (CRISPR)-associated enzyme Cas9 is an RNA-guided endonuclease that uses RNA-DNA base-pairing to target foreign DNA in bacteria. Cas9-guide RNA complexes are also effective genome engineering agents in animals and plants. Here we use single-molecule and bulk biochemical experiments to determine how Cas9-RNA interrogates DNA to find specific cleavage sites. We show that both binding and cleavage of DNA by Cas9-RNA require recognition of a short trinucleotide protospacer adjacent motif (PAM). Non-target DNA binding affinity scales with PAM density, and sequences fully complementary to the guide RNA but lacking a nearby PAM are ignored by Cas9-RNA. Competition assays provide evidence that DNA strand separation and RNA-DNA heteroduplex formation initiate at the PAM and proceed directionally towards the distal end of the target sequence. Furthermore, PAM interactions trigger Cas9 catalytic activity. These results reveal how Cas9 uses PAM recognition to quickly identify potential target sites while scanning large DNA molecules, and to regulate scission of double-stranded DNA.

Structural and functional characterization of two unusual endonuclease III enzymes from Deinococcus radiodurans.

PubMed

Sarre, Aili; Ökvist, Mats; Klar, Tobias; Hall, David R; Smalås, Arne O; McSweeney, Sean; Timmins, Joanna; Moe, Elin

2015-08-01

While most bacteria possess a single gene encoding the bifunctional DNA glycosylase Endonuclease III (EndoIII) in their genomes, Deinococcus radiodurans possesses three: DR2438 (DrEndoIII1), DR0289 (DrEndoIII2) and DR0982 (DrEndoIII3). Here we have determined the crystal structures of DrEndoIII1 and an N-terminally truncated form of DrEndoIII3 (DrEndoIII3Δ76). We have also generated a homology model of DrEndoIII2 and measured activity of the three enzymes. All three structures consist of two all α-helical domains, one of which exhibits a [4Fe-4S] cluster and the other a HhH-motif, separated by a DNA binding cleft, similar to previously determined structures of endonuclease III from Escherichia coli and Geobacillus stearothermophilus. However, both DrEndoIII1 and DrEndoIII3 possess an extended HhH motif with extra helical features and an altered electrostatic surface potential. In addition, the DNA binding cleft of DrEndoIII3 seems to be less accessible for DNA interactions, while in DrEndoIII1 it seems to be more open. Analysis of the enzyme activities shows that DrEndoIII2 is most similar to the previously studied enzymes, while DrEndoIII1 seems to be more distant with a weaker activity towards substrate DNA containing either thymine glycol or an abasic site. DrEndoIII3 is the most distantly related enzyme and displays no detectable activity towards these substrates even though the suggested catalytic residues are conserved. Based on a comparative structural analysis, we suggest that the altered surface potential, shape of the substrate-binding pockets and specific amino acid substitutions close to the active site and in the DNA interacting loops may underlie the unexpected differences in activity. Copyright © 2015 Elsevier Inc. All rights reserved.

Production and characterization of recombinant protein preparations of Endonuclease G-homologs from yeast, C. elegans and humans.

PubMed

Kieper, Jana; Lauber, Christiane; Gimadutdinow, Oleg; Urbańska, Anna; Cymerman, Iwona; Ghosh, Mahua; Szczesny, Bartosz; Meiss, Gregor

2010-09-01

Nuc1p, CPS-6, EndoG and EXOG are evolutionary conserved mitochondrial nucleases from yeast, Caenorhabditis elegans and humans, respectively. These enzymes play an important role in programmed cell death as well as mitochondrial DNA-repair and recombination. Whereas a significant interest has been given to the cell biology of these proteins, in particular their recruitment during caspase-independent apoptosis, determination of their biochemical properties has lagged behind. In part, biochemical as well as structural analysis of mitochondrial nucleases has been hampered by the fact that upon cloning and overexpression in Escherichia coli these enzymes can exert considerable toxicity and tend to aggregate and form inclusion bodies. We have, therefore, established a uniform E. coli expression system allowing us to obtain these four evolutionary related nucleases in active form from the soluble as well as insoluble fractions of E. coli cell lysates. Using preparations of recombinant Nuc1p, CPS-6, EndoG and EXOG we have compared biochemical properties and the substrate specificities of these related nucleases on selected substrates in parallel. Whereas Nuc1p and EXOG in addition to their endonuclease activity exert 5'-3'-exonuclease activity, CPS-6 and EndoG predominantly are endonucleases. These findings allow speculating that the mechanisms of action of these related nucleases in cell death as well as DNA-repair and recombination differ according to their enzyme activities and substrate specificities. Copyright 2010 Elsevier Inc. All rights reserved.

Genome editing and the next generation of antiviral therapy

PubMed Central

Stone, Daniel; Niyonzima, Nixon

2016-01-01

Engineered endonucleases such as homing endonucleases (HEs), zinc finger nucleases (ZFNs), Tal-effector nucleases (TALENS) and the RNA-guided engineered nucleases (RGENs or CRISPR/Cas9) can target specific DNA sequences for cleavage, and are proving to be valuable tools for gene editing. Recently engineered endonucleases have shown great promise as therapeutics for the treatment of genetic disease and infectious pathogens. In this review, we discuss recent efforts to use the HE, ZFN, TALEN and CRISPR/Cas9 gene-editing platforms as antiviral therapeutics. We also discuss the obstacles facing gene-editing antiviral therapeutics as they are tested in animal models of disease and transition towards human application. PMID:27272125

The Helicobacter pylori HpyAXII restriction–modification system limits exogenous DNA uptake by targeting GTAC sites but shows asymmetric conservation of the DNA methyltransferase and restriction endonuclease components

PubMed Central

Humbert, Olivier; Salama, Nina R.

2008-01-01

The naturally competent organism Helicobacter pylori encodes a large number of restriction–modification (R–M) systems that consist of a restriction endonuclease and a DNA methyltransferase. R–M systems are not only believed to limit DNA exchange among bacteria but may also have other cellular functions. We report a previously uncharacterized H. pylori type II R–M system, M.HpyAXII/R.HpyAXII. We show that this system targets GTAC sites, which are rare in the H. pylori chromosome but numerous in ribosomal RNA genes. As predicted, this type II R–M system showed attributes of a selfish element. Deletion of the methyltransferase M.HpyAXII is lethal when associated with an active endonuclease R.HpyAXII unless compensated by adaptive mutation or gene amplification. R.HpyAXII effectively restricted both unmethylated plasmid and chromosomal DNA during natural transformation and was predicted to belong to the novel ‘half pipe’ structural family of endonucleases. Analysis of a panel of clinical isolates revealed that R.HpyAXII was functional in a small number of H. pylori strains (18.9%, n = 37), whereas the activity of M.HpyAXII was highly conserved (92%, n = 50), suggesting that GTAC methylation confers a selective advantage to H. pylori. However, M.HpyAXII activity did not enhance H. pylori fitness during stomach colonization of a mouse infection model. PMID:18978016

Comparative studies of the endonucleases from two related Xenopus laevis retrotransposons, Tx1L and Tx2L: target site specificity and evolutionary implications.

PubMed

Christensen, S; Pont-Kingdon, G; Carroll, D

2000-01-01

In the genome of the South African frog, Xenopus laevis, there are two complex families of transposable elements, Tx1 and Tx2, that have identical overall structures, but distinct sequences. In each family there are approximately 1500 copies of an apparent DNA-based element (Tx1D and Tx2D). Roughly 10% of these elements in each family are interrupted by a non-LTR retrotransposon (Tx1L and Tx2L). Each retrotransposon is flanked by a 23-bp target duplication of a specific D element sequence. In earlier work, we showed that the endonuclease domain (Tx1L EN) located in the second open reading frame (ORF2) of Tx1L encodes a protein that makes a single-strand cut precisely at the expected site within its target sequence, supporting the idea that Tx1L is a site-specific retrotransposon. In this study, we express the endonuclease domain of Tx2L (Tx2L EN) and compare the target preferences of the two enzymes. Each endonuclease shows some preference for its cognate target, on the order of 5-fold over the non-cognate target. The observed discrimination is not sufficient, however, to explain the observation that no cross-occupancy is observed - that is, L elements of one family have never been found within D elements of the other family. Possible sources of additional specificity are discussed. We also compare two hypotheses regarding the genome duplication event that led to the contemporary pseudotetraploid character of Xenopus laevis in light of the Tx1L and Tx2L data.

Conformational Dynamics of DNA Repair by Escherichia coli Endonuclease III*

PubMed Central

Kuznetsov, Nikita A.; Kladova, Olga A.; Kuznetsova, Alexandra A.; Ishchenko, Alexander A.; Saparbaev, Murat K.; Zharkov, Dmitry O.; Fedorova, Olga S.

2015-01-01

Escherichia coli endonuclease III (Endo III or Nth) is a DNA glycosylase with a broad substrate specificity for oxidized or reduced pyrimidine bases. Endo III possesses two types of activities: N-glycosylase (hydrolysis of the N-glycosidic bond) and AP lyase (elimination of the 3′-phosphate of the AP-site). We report a pre-steady-state kinetic analysis of structural rearrangements of the DNA substrates and uncleavable ligands during their interaction with Endo III. Oligonucleotide duplexes containing 5,6-dihydrouracil, a natural abasic site, its tetrahydrofuran analog, and undamaged duplexes carried fluorescent DNA base analogs 2-aminopurine and 1,3-diaza-2-oxophenoxazine as environment-sensitive reporter groups. The results suggest that Endo III induces several fast sequential conformational changes in DNA during binding, lesion recognition, and adjustment to a catalytically competent conformation. A comparison of two fluorophores allowed us to distinguish between the events occurring in the damaged and undamaged DNA strand. Combining our data with the available structures of Endo III, we conclude that this glycosylase uses a multistep mechanism of damage recognition, which likely involves Gln41 and Leu81 as DNA lesion sensors. PMID:25869130

Effects of Dimerization of Serratia marcescens Endonuclease on Water Dynamics.

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

Chen, Chuanying; Beck, Brian W.; Krause, Kurt

2007-02-15

The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. The dynamics and structure of Serratia marcescens endonuclease and its neighboring solvent are investigated by molecular dynamics (MD). Comparisons are made with structural and biochemical experiments. The dimer form is physiologic and functions more processively than the monomer. We previously found a channel formed by connected clusters of waters from the active site to the dimer interface. Here, we showmore » that dimerization clearly changes correlations in the water structure and dynamics in the active site not seen in the monomer. Our results indicate that water at the active sites of the dimer is less affected compared with bulk solvent than in the monomer where it has much slower characteristic relaxation times. Given that water is a required participant in the reaction, this gives a clear advantage to dimerization in the absence of an apparent ability to use both active sites simultaneously.« less

A novel label-free fluorescence strategy for methyltransferase activity assay based on dsDNA-templated copper nanoparticles coupled with an endonuclease-assisted signal transduction system.

PubMed

Lai, Q Q; Liu, M D; Gu, C C; Nie, H G; Xu, X J; Li, Z H; Yang, Z; Huang, S M

2016-02-21

Evaluating DNA methyltransferase (MTase) activity has received considerable attention due to its significance in the fields of early cancer clinical diagnostics and drug discovery. Herein, we proposed a novel label-free fluorescence method for MTase activity assay by coupling double-stranded DNA (dsDNA)-templated copper nanoparticles (CuNPs) with an endonuclease-assisted signal transduction system. In this strategy, dsDNA molecules were first methylated by DNA adenine methylation (Dam) MTase and then cleaved by the methylation-sensitive restriction endonuclease DpnI. The cleaved DNA fragments could not act as efficient templates for the formation of fluorescent CuNPs and thus no fluorescence signal was produced. Under optimized experimental conditions, the developed strategy exhibited a sensitive fluorescence response to Dam MTase activity. This strategy was also demonstrated to provide an excellent platform to the inhibitor screening for Dam MTase. These results demonstrated the great potential for the practical applications of the proposed strategy for Dam MTase activity assay.

Crystallization and preliminary X-ray diffraction analysis of restriction endonuclease EcoRII

NASA Technical Reports Server (NTRS)

Karpova, E. A.; Meehan, E.; Pusey, M. L.; Chen, L.

1999-01-01

Crystals of the restriction endonuclease EcoRII have been obtained by the vapor-diffusion technique in the presence of ammonium sulfate or polyethylene glycol. The best crystals were grown with ammonium sulfate as a precipitant. Crystals with dimensions of up to 0.6 x 0. 6 x 0.6 mm have been observed. The crystals diffract to about 4.0 A resolution at a cryo-temperature of 100 K using a rotating-anode X-ray source and a Rigaku R-AXIS IV imaging-plate detector. The space group has been determined to be either I23 or I2(1)3, with unit-cell parameters a = b = c = 160.3 A, alpha = beta = gamma = 90 degrees. The crystal asymmetric unit contains two protein molecules, and self-rotation function analysis shows a pseudo-twofold symmetry relating the two monomers. Attempts to improve the resolution of crystal diffraction and to search for heavy-atom derivatives are under way.

Fractionated Radiation Exposure of Rat Spinal Cords Leads to Latent Neuro-Inflammation in Brain, Cognitive Deficits, and Alterations in Apurinic Endonuclease 1

DOE PAGES

Suresh Kumar, M. A.; Peluso, Michael; Chaudhary, Pankaj; ...

2015-07-24

Ionizing radiation causes degeneration of myelin, the insulating sheaths of neuronal axons, leading to neurological impairment. As radiation research on the central nervous system has predominantly focused on neurons, with few studies addressing the role of glial cells, we have focused our present research on identifying the latent effects of single/ fractionated -low dose of low/ high energy radiation on the role of base excision repair protein Apurinic Endonuclease-1, in the rat spinal cords oligodendrocyte progenitor cells ’ differentiation. Apurinic endonuclease-1 is predominantly upregulated in response to oxidative stress by low- energy radiation, and previous studies show significant induction ofmore » Apurinic Endonucle- ase-1 in neurons and astrocytes. Our studies show for the first time, that fractionation of pro- tons cause latent damage to spinal cord architecture while fractionation of HZE ( 28Si) induce increase in APE1 with single dose, which then decreased with fractionation. In conclusion, the oligoden- drocyte progenitor cells differentiation was skewed with increase in immature oligodendro- cytes and astrocytes, which likely cause the observed decrease in white matter, increased neuro-inflammation, together leading to the observed significant cognitive defects« less

Fractionated Radiation Exposure of Rat Spinal Cords Leads to Latent Neuro-Inflammation in Brain, Cognitive Deficits, and Alterations in Apurinic Endonuclease 1

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

Suresh Kumar, M. A.; Peluso, Michael; Chaudhary, Pankaj

Ionizing radiation causes degeneration of myelin, the insulating sheaths of neuronal axons, leading to neurological impairment. As radiation research on the central nervous system has predominantly focused on neurons, with few studies addressing the role of glial cells, we have focused our present research on identifying the latent effects of single/ fractionated -low dose of low/ high energy radiation on the role of base excision repair protein Apurinic Endonuclease-1, in the rat spinal cords oligodendrocyte progenitor cells ’ differentiation. Apurinic endonuclease-1 is predominantly upregulated in response to oxidative stress by low- energy radiation, and previous studies show significant induction ofmore » Apurinic Endonucle- ase-1 in neurons and astrocytes. Our studies show for the first time, that fractionation of pro- tons cause latent damage to spinal cord architecture while fractionation of HZE ( 28Si) induce increase in APE1 with single dose, which then decreased with fractionation. In conclusion, the oligoden- drocyte progenitor cells differentiation was skewed with increase in immature oligodendro- cytes and astrocytes, which likely cause the observed decrease in white matter, increased neuro-inflammation, together leading to the observed significant cognitive defects« less

Disruption or Excision of Provirus as an Approach to HIV Cure.

PubMed

Jerome, Keith R

2016-12-01

An effective approach to HIV cure will almost certainly require a combination of strategies, including some means of reducing the latent HIV reservoir. Because the integrated HIV provirus represents the major source of viral persistence and reactivation, one attractive approach is the direct targeting of provirus for disruption or excision using targeted endonucleases, such as CRISPR/Cas9, zinc finger nucleases, TAL effector nucleases, or meganucleases (homing endonucleases). This article highlights some of the challenges for successful endonuclease therapy for HIV, including optimization of enzyme activity and specificity, the possible emergence of viral resistance, and most importantly, efficient in vivo delivery of the enzymes to a sufficient portion of the latent reservoir.

Restoration of G1 chemo/radioresistance and double-strand-break repair proficiency by wild-type but not endonuclease-deficient Artemis.

PubMed

Mohapatra, Susovan; Kawahara, Misako; Khan, Imran S; Yannone, Steven M; Povirk, Lawrence F

2011-08-01

Deficiency in Artemis is associated with lack of V(D)J recombination, sensitivity to radiation and radiomimetic drugs, and failure to repair a subset of DNA double-strand breaks (DSBs). Artemis harbors an endonuclease activity that trims both 5'- and 3'-ends of DSBs. To examine whether endonucleolytic trimming of terminally blocked DSBs by Artemis is a biologically relevant function, Artemis-deficient fibroblasts were stably complemented with either wild-type Artemis or an endonuclease-deficient D165N mutant. Wild-type Artemis completely restored resistance to γ-rays, bleomycin and neocarzinostatin, and also restored DSB-repair proficiency in G0/G1 phase as measured by pulsed-field gel electrophoresis and repair focus resolution. In contrast, cells expressing the D165N mutant, even at very high levels, remained as chemo/radiosensitive and repair deficient as the parental cells, as evidenced by persistent γ-H2AX, 53BP1 and Mre11 foci that slowly increased in size and ultimately became juxtaposed with promyelocytic leukemia protein nuclear bodies. In normal fibroblasts, overexpression of wild-type Artemis increased radioresistance, while D165N overexpression conferred partial repair deficiency following high-dose radiation. Restoration of chemo/radioresistance by wild-type, but not D165N Artemis suggests that the lack of endonucleolytic trimming of DNA ends is the principal cause of sensitivity to double-strand cleaving agents in Artemis-deficient cells.

Site- and strand-specific nicking of DNA by fusion proteins derived from MutH and I-SceI or TALE repeats.

PubMed

Gabsalilow, Lilia; Schierling, Benno; Friedhoff, Peter; Pingoud, Alfred; Wende, Wolfgang

2013-04-01

Targeted genome engineering requires nucleases that introduce a highly specific double-strand break in the genome that is either processed by homology-directed repair in the presence of a homologous repair template or by non-homologous end-joining (NHEJ) that usually results in insertions or deletions. The error-prone NHEJ can be efficiently suppressed by 'nickases' that produce a single-strand break rather than a double-strand break. Highly specific nickases have been produced by engineering of homing endonucleases and more recently by modifying zinc finger nucleases (ZFNs) composed of a zinc finger array and the catalytic domain of the restriction endonuclease FokI. These ZF-nickases work as heterodimers in which one subunit has a catalytically inactive FokI domain. We present two different approaches to engineer highly specific nickases; both rely on the sequence-specific nicking activity of the DNA mismatch repair endonuclease MutH which we fused to a DNA-binding module, either a catalytically inactive variant of the homing endonuclease I-SceI or the DNA-binding domain of the TALE protein AvrBs4. The fusion proteins nick strand specifically a bipartite recognition sequence consisting of the MutH and the I-SceI or TALE recognition sequences, respectively, with a more than 1000-fold preference over a stand-alone MutH site. TALE-MutH is a programmable nickase.

The DNA repair endonuclease XPG interacts directly and functionally with the WRN helicase defective in Werner syndrome

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

Trego, Kelly S.; Chernikova, Sophia B.; Davalos, Albert R.

XPG is a structure-specific endonuclease required for nucleotide excision repair (NER). XPG incision defects result in the cancer-prone syndrome xeroderma pigmentosum, whereas truncating mutations of XPG cause the severe postnatal progeroid developmental disorder Cockayne syndrome. We show that XPG interacts directly with WRN protein, which is defective in the premature aging disorder Werner syndrome, and that the two proteins undergo similar sub-nuclear redistribution in S-phase and co-localize in nuclear foci. The co-localization was observed in mid- to late-S-phase, when WRN moves from nucleoli to nuclear foci that have been shown to contain protein markers of both stalled replication forks andmore » telomeric proteins. We mapped the interaction between XPG and WRN to the C-terminal domains of each and show that interaction with the C-terminal domain of XPG strongly stimulates WRN helicase activity. WRN also possesses a competing DNA single-strand annealing activity that, combined with unwinding, has been shown to coordinate regression of model replication forks to form Holliday junction/chicken foot intermediate structures. We tested whether XPG stimulated WRN annealing activity and found that XPG itself has intrinsic strand annealing activity that requires the unstructured R- and C-terminal domains, but not the conserved catalytic core or endonuclease activity. Annealing by XPG is cooperative, rather than additive, with WRN annealing. Taken together, our results suggest a novel function for XPG in S-phase that is at least in part carried out coordinately with WRN, and which may contribute to the severity of the phenotypes that occur upon loss of XPG.« less

Structure of the MazF-mt9 toxin, a tRNA-specific endonuclease from Mycobacterium tuberculosis.

PubMed

Chen, Ran; Tu, Jie; Liu, Zhihui; Meng, Fanrong; Ma, Pinyun; Ding, Zhishan; Yang, Chengwen; Chen, Lei; Deng, Xiangyu; Xie, Wei

2017-05-06

Tuberculosis (TB) is a severe disease caused by Mycobacterium tuberculosis (M. tb) and the well-characterized M. tb MazE/F proteins play important roles in stress adaptation. Recently, the MazF-mt9 toxin has been found to display endonuclease activities towards tRNAs but the mechanism is unknown. We hereby present the crystal structure of apo-MazF-mt9. The enzyme recognizes tRNA Lys with a central UUU motif within the anticodon loop, but is insensitive to the sequence context outside of the loop. Based on our crystallographic and biochemical studies, we identified key residues for catalysis and proposed the potential tRNA-binding site. Copyright © 2017 Elsevier Inc. All rights reserved.

Pre-steady-state fluorescence analysis of damaged DNA transfer from human DNA glycosylases to AP endonuclease APE1.

PubMed

Kuznetsova, Alexandra A; Kuznetsov, Nikita A; Ishchenko, Alexander A; Saparbaev, Murat K; Fedorova, Olga S

2014-10-01

DNA glycosylases remove the modified, damaged or mismatched bases from the DNA by hydrolyzing the N-glycosidic bonds. Some enzymes can further catalyze the incision of a resulting abasic (apurinic/apyrimidinic, AP) site through β- or β,δ-elimination mechanisms. In most cases, the incision reaction of the AP-site is catalyzed by special enzymes called AP-endonucleases. Here, we report the kinetic analysis of the mechanisms of modified DNA transfer from some DNA glycosylases to the AP endonuclease, APE1. The modified DNA contained the tetrahydrofurane residue (F), the analogue of the AP-site. DNA glycosylases AAG, OGG1, NEIL1, MBD4(cat) and UNG from different structural superfamilies were used. We found that all DNA glycosylases may utilise direct protein-protein interactions in the transient ternary complex for the transfer of the AP-containing DNA strand to APE1. We hypothesize a fast "flip-flop" exchange mechanism of damaged and undamaged DNA strands within this complex for monofunctional DNA glycosylases like MBD4(cat), AAG and UNG. Bifunctional DNA glycosylase NEIL1 creates tightly specific complex with DNA containing F-site thereby efficiently competing with APE1. Whereas APE1 fast displaces other bifunctional DNA glycosylase OGG1 on F-site thereby induces its shifts to undamaged DNA regions. Kinetic analysis of the transfer of DNA between human DNA glycosylases and APE1 allows us to elucidate the critical step in the base excision repair pathway. Copyright © 2014 Elsevier B.V. All rights reserved.

Cross index for improving cloning selectivity by partially filling in 5'-extensions of DNA produced by type II restriction endonucleases.

PubMed Central

Korch, C

1987-01-01

A cross index is presented for using the improved selectivity offered by the Hung and Wensink (Nucl. Acids Res. 12, 1863-1874, 1984) method of partially filling in 5'-extensions produced by type II restriction endonucleases. After this treatment, DNA fragments which normally cannot be ligated to one another, can be joined providing that complementary cohesive ends have been generated. The uses of this technique, which include the prevention of DNA fragments (both vector and insert) auto-annealing, are discussed. PMID:3033600

Binding affinity of the L-742,001 inhibitor to the endonuclease domain of A/H1N1/PA influenza virus variants: Molecular simulation approaches

NASA Astrophysics Data System (ADS)

Nguyen, Hung; Nguyen, Hoang Linh; Linh, Huynh Quang; Nguyen, Minh Tho

2018-01-01

The steered molecular dynamics (SMD), molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) and free energy perturbation (FEP) methods were used to determine the binding affinity of the L-742,001 inhibitor to the endonuclease domain of the A/H1N1/PA influenza viruses (including wild type (WT) and three mutations I79L, E119D and F105S for both pH1N1 PA and PR8 PA viruses). Calculated results showed that the L-742,001 inhibitor not only binds to the PR8 PAs (1934 A influenza virus) better than to the pH1N1 PAs (2009 A influenza virus) but also more strongly interacts with the WT endonuclease domain than with three mutant variants for both pH1N1 PA and PR8 PA viruses. The binding affinities obtained by the SMD, MM-PBSA and FEP methods attain high correlation with available experimental data. Here the FEP method appears to provide a more accurate determination of the binding affinity than the SMD and MM-PBSA counterparts.

Incision of trivalent chromium [Cr(III)]-induced DNA damage by Bacillus caldotenax UvrABC endonuclease.

PubMed

O'Brien, Travis J; Jiang, Guohui; Chun, Gina; Mandel, H George; Westphal, Craig S; Kahen, Kaveh; Montaser, Akbar; States, J Christopher; Patierno, Steven R

2006-11-07

Some hexavalent chromium [Cr(VI)]-containing compounds are lung carcinogens. Once within cells, Cr(VI) is reduced to trivalent chromium [Cr(III)] which displays an affinity for both DNA bases and the phosphate backbone. A diverse array of genetic lesions is produced by Cr including Cr-DNA monoadducts, DNA interstrand crosslinks (ICLs), DNA-Cr-protein crosslinks (DPCs), abasic sites, DNA strand breaks and oxidized bases. Despite the large amount of information available on the genotoxicity of Cr, little is known regarding the molecular mechanisms involved in the removal of these lesions from damaged DNA. Recent work indicates that nucleotide excision repair (NER) is involved in the processing of Cr-DNA adducts in human and rodent cells. In order to better understand this process at the molecular level and begin to identify the Cr-DNA adducts processed by NER, the incision of CrCl(3) [Cr(III)]-damaged plasmid DNA was studied using a thermal-resistant UvrABC NER endonuclease from Bacillus caldotenax (Bca). Treatment of plasmid DNA with Cr(III) (as CrCl(3)) increased DNA binding as a function of dose. For example, at a Cr(III) concentration of 1 microM we observed approximately 2 Cr(III)-DNA adducts per plasmid. At this same concentration of Cr(III) we found that approximately 17% of the plasmid DNA contained ICLs ( approximately 0.2 ICLs/plasmid). When plasmid DNA treated with Cr(III) (1 microM) was incubated with Bca UvrABC we observed approximately 0.8 incisions/plasmid. The formation of endonuclease IV-sensitive abasic lesions or Fpg-sensitive oxidized DNA bases was not detected suggesting that the incision of Cr(III)-damaged plasmid DNA by UvrABC was not related to the generation of oxidized DNA damage. Taken together, our data suggest that a sub-fraction of Cr(III)-DNA adducts is recognized and processed by the prokaryotic NER machinery and that ICLs are not necessarily the sole lesions generated by Cr(III) that are substrates for NER.

Purification and characterization of an endonuclease from calf thymus acting on irradiated DNA

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

Bacchetti, S.; Benne, R.

1974-01-01

An endonuclease acting on DNA exposed to ultraviolet light or gamma-rays was extensively purified from calf thymus. The enzyme has a pH optimum at pH 7.0 to 7.5, acts with equal efficiency in the presence of EDTA or divalent cations (Mg 2+ or Ca 2+), is inhibited by NaC1 and tRNA and is inactivated by incubation at 50 C. Its molecular weight, determined by Sephadex chromatography or SDS-gel electrophoresis, is + or - 30,000. The enzyme catalyzes the formation of single-strand breaks with 5'-phosphate termini in double-stranded DNA irradiated with ultraviolet or gamma-rays. It does not act on unirradiated DNAmore » or denatured DNA. The enzymatic activity on ultraviolet- and gamma-irradiated DNA is associated with the same protein. The site of action of the enzyme in ultraviolet-irradiated DNA is a photoproduct other than pyrimidine dimers, and can also be induced by irradiation of the DNA in vivo. (Author) (GRA)« less

The Methanothermobacter thermautotrophicus ExoIII homologue Mth212 is a DNA uridine endonuclease

PubMed Central

Georg, Jens; Schomacher, Lars; Chong, James P. J.; Majerník, Alan I.; Raabe, Monika; Urlaub, Henning; Müller, Sabine; Ciirdaeva, Elena; Kramer, Wilfried; Fritz, Hans-Joachim

2006-01-01

The genome of Methanothermobacter thermautotrophicus, as a hitherto unique case, is apparently devoid of genes coding for general uracil DNA glycosylases, the universal mediators of base excision repair following hydrolytic deamination of DNA cytosine residues. We have now identified protein Mth212, a member of the ExoIII family of nucleases, as a possible initiator of DNA uracil repair in this organism. This enzyme, in addition to bearing all the enzymological hallmarks of an ExoIII homologue, is a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5′-side of a 2′-d-uridine residue, irrespective of the nature of the opposing nucleotide. This type of activity has not been described before; it is absent from the ExoIII homologues of Escherichia coli, Homo sapiens and Methanosarcina mazei, all of which are equipped with uracil DNA repair glycosylases. The U-endo activity of Mth212 is served by the same catalytic center as its AP-endo activity. PMID:17012282

Primary processing of CRISPR RNA by the endonuclease Cas6 in Staphylococcus epidermidis.

PubMed

Wakefield, Noelle; Rajan, Rakhi; Sontheimer, Erik J

2015-10-07

In many bacteria and archaea, an adaptive immune system (CRISPR-Cas) provides immunity against foreign genetic elements. This system uses CRISPR RNAs (crRNAs) derived from the CRISPR array, along with CRISPR-associated (Cas) proteins, to target foreign nucleic acids. In most CRISPR systems, endonucleolytic processing of crRNA precursors (pre-crRNAs) is essential for the pathway. Here we study the Cas6 endonuclease responsible for crRNA processing in the Type III-A CRISPR-Cas system from Staphylococcus epidermidis RP62a, a model for Type III-A CRISPR-Cas systems, and define substrate requirements for SeCas6 activity. We find that SeCas6 is necessary and sufficient for full-length crRNA biogenesis in vitro, and that it relies on both sequence and stem-loop structure in the 3' half of the CRISPR repeat for recognition and processing. Copyright © 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Structure of an XPF endonuclease with and without DNA suggests a model for substrate recognition

PubMed Central

Newman, Matthew; Murray-Rust, Judith; Lally, John; Rudolf, Jana; Fadden, Andrew; Knowles, Philip P; White, Malcolm F; McDonald, Neil Q

2005-01-01

The XPF/Mus81 structure-specific endonucleases cleave double-stranded DNA (dsDNA) within asymmetric branched DNA substrates and play an essential role in nucleotide excision repair, recombination and genome integrity. We report the structure of an archaeal XPF homodimer alone and bound to dsDNA. Superposition of these structures reveals a large domain movement upon binding DNA, indicating how the (HhH)2 domain and the nuclease domain are coupled to allow the recognition of double-stranded/single-stranded DNA junctions. We identify two nonequivalent DNA-binding sites and propose a model in which XPF distorts the 3′ flap substrate in order to engage both binding sites and promote strand cleavage. The model rationalises published biochemical data and implies a novel role for the ERCC1 subunit of eukaryotic XPF complexes. PMID:15719018

Label-free and ultrasensitive fluorescence detection of cocaine based on a strategy that utilizes DNA-templated silver nanoclusters and the nicking endonuclease-assisted signal amplification method.

PubMed

Zhang, Kai; Wang, Ke; Zhu, Xue; Zhang, Jue; Xu, Lan; Huang, Biao; Xie, Minhao

2014-01-07

A general and reliable strategy for the detection of cocaine was proposed utilizing DNA-templated silver nanoclusters as signal indicators and the nicking endonuclease-assisted signal amplification method. This strategy can detect cocaine specifically with a detection limit as low as 2 nM by using a small volume of 5 μL.

Polyubiquitination of apurinic/apyrimidinic endonuclease 1 by Parkin.

PubMed

Scott, Timothy L; Wicker, Christina A; Suganya, Rangaswamy; Dhar, Bithika; Pittman, Thomas; Horbinski, Craig; Izumi, Tadahide

2017-02-01

Apurinic/apyrimidinic endonuclease 1 (APE1) is an essential protein crucial for repair of oxidized DNA damage not only in genomic DNA but also in mitochondrial DNA. Parkin, a tumor suppressor and Parkinson's disease (PD) associated gene, is an E3 ubiquitin ligase crucial for mitophagy. Although DNA damage is known to induce mitochondrial stress, Parkin's role in regulating DNA repair proteins has not been elucidated. In this study, we examined the possibility of Parkin-dependent ubiquitination of APE1. Ectopically expressed APE1 was degraded by Parkin and PINK1 via polyubiquitination in mouse embryonic fibroblast cells. PD-causing mutations in Parkin and PINK1 abrogated APE1 ubiquitination. Interaction of APE1 with Parkin was observed by co-immunoprecipitation, proximity ligation assay, and co-localization in the cytoplasm. N-terminal deletion of 41 amino acid residues in APE1 significantly reduced the Parkin-dependent APE1 degradation. These results suggested that Parkin directly ubiquitinated N-terminal Lys residues in APE1 in the cytoplasm. Modulation of Parkin and PINK1 activities under mitochondrial or oxidative stress caused moderate but statistically significant decrease of endogenous APE1 in human cell lines including SH-SY5Y, HEK293, and A549 cells. Analyses of glioblastoma tissues showed an inverse relation between the expression levels of APE1 and Parkin. These results suggest that degradation of endogenous APE1 by Parkin occur when cells are stressed to activate Parkin, and imply a role of Parkin in maintaining the quality of APE1, and loss of Parkin may contribute to elevated APE1 levels in glioblastoma. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Activation of apurinic/apyrimidinic endonuclease in human cells by reactive oxygen species and its correlation with their adaptive response to genotoxicity of free radicals

PubMed Central

Ramana, Chilakamarti V.; Boldogh, Istvan; Izumi, Tadahide; Mitra, Sankar

1998-01-01

Apurinic/apyrimidinic (AP) endonuclease (APE; EC 4.2.99.18) plays a central role in repair of DNA damage due to reactive oxygen species (ROS) because its DNA 3′-phosphoesterase activity removes 3′ blocking groups in DNA that are generated by DNA glycosylase/AP-lyases during removal of oxidized bases and by direct ROS reaction with DNA. The major human APE (APE-1) gene is activated selectively by sublethal levels of a variety of ROS and ROS generators, including ionizing radiation, but not by other genotoxicants—e.g., UV light and alkylating agents. Increased expression of APE mRNA and protein was observed both in the HeLa S3 tumor line and in WI 38 primary fibroblasts, and it was accompanied by translocation of the endonuclease to the nucleus. ROS-treated cells showed a significant increase in resistance to the cytotoxicity of such ROS generators as H2O2 and bleomycin, but not to UV light. This “adaptive response” appears to result from enhanced repair of cytotoxic DNA lesions due to an increased activity of APE-1, which may be limiting in the base excision repair process for ROS-induced toxic lesions. PMID:9560228

Diverse Small Molecule Inhibitors of Human Apurinic/Apyrimidinic Endonuclease APE1 Identified from a Screen of a Large Public Collection

PubMed Central

Dorjsuren, Dorjbal; Kim, Daemyung; Vyjayanti, Vaddadi N.; Maloney, David J.; Jadhav, Ajit; Wilson, David M.; Simeonov, Anton

2012-01-01

The major human apurinic/apyrimidinic endonuclease APE1 plays a pivotal role in the repair of base damage via participation in the DNA base excision repair (BER) pathway. Increased activity of APE1, often observed in tumor cells, is thought to contribute to resistance to various anticancer drugs, whereas down-regulation of APE1 sensitizes cells to DNA damaging agents. Thus, inhibiting APE1 repair endonuclease function in cancer cells is considered a promising strategy to overcome therapeutic agent resistance. Despite ongoing efforts, inhibitors of APE1 with adequate drug-like properties have yet to be discovered. Using a kinetic fluorescence assay, we conducted a fully-automated high-throughput screen (HTS) of the NIH Molecular Libraries Small Molecule Repository (MLSMR), as well as additional public collections, with each compound tested as a 7-concentration series in a 4 µL reaction volume. Actives identified from the screen were subjected to a panel of confirmatory and counterscreen tests. Several active molecules were identified that inhibited APE1 in two independent assay formats and exhibited potentiation of the genotoxic effect of methyl methanesulfonate with a concomitant increase in AP sites, a hallmark of intracellular APE1 inhibition; a number of these chemotypes could be good starting points for further medicinal chemistry optimization. To our knowledge, this represents the largest-scale HTS to identify inhibitors of APE1, and provides a key first step in the development of novel agents targeting BER for cancer treatment. PMID:23110144

The host-encoded RNase E endonuclease as the crRNA maturation enzyme in a CRISPR-Cas subtype III-Bv system.

PubMed

Behler, Juliane; Sharma, Kundan; Reimann, Viktoria; Wilde, Annegret; Urlaub, Henning; Hess, Wolfgang R

2018-03-01

Specialized RNA endonucleases for the maturation of clustered regularly interspaced short palindromic repeat (CRISPR)-derived RNAs (crRNAs) are critical in CRISPR-CRISPR-associated protein (Cas) defence mechanisms. The Cas6 and Cas5d enzymes are the RNA endonucleases in many class 1 CRISPR-Cas systems. In some class 2 systems, maturation and effector functions are combined within a single enzyme or maturation proceeds through the combined actions of RNase III and trans-activating CRISPR RNAs (tracrRNAs). Three separate CRISPR-Cas systems exist in the cyanobacterium Synechocystis sp. PCC 6803. Whereas Cas6-type enzymes act in two of these systems, the third, which is classified as subtype III-B variant (III-Bv), lacks cas6 homologues. Instead, the maturation of crRNAs proceeds through the activity of endoribonuclease E, leaving unusual 13- and 14-nucleotide-long 5'-handles. Overexpression of RNase E leads to overaccumulation and knock-down to the reduced accumulation of crRNAs in vivo, suggesting that RNase E is the limiting factor for CRISPR complex formation. Recognition by RNase E depends on a stem-loop in the CRISPR repeat, whereas base substitutions at the cleavage site trigger the appearance of secondary products, consistent with a two-step recognition and cleavage mechanism. These results suggest the adaptation of an otherwise very conserved housekeeping enzyme to accommodate new substrates and illuminate the impressive plasticity of CRISPR-Cas systems that enables them to function in particular genomic environments.

Diverse small molecule inhibitors of human apurinic/apyrimidinic endonuclease APE1 identified from a screen of a large public collection.

PubMed

Dorjsuren, Dorjbal; Kim, Daemyung; Vyjayanti, Vaddadi N; Maloney, David J; Jadhav, Ajit; Wilson, David M; Simeonov, Anton

2012-01-01

The major human apurinic/apyrimidinic endonuclease APE1 plays a pivotal role in the repair of base damage via participation in the DNA base excision repair (BER) pathway. Increased activity of APE1, often observed in tumor cells, is thought to contribute to resistance to various anticancer drugs, whereas down-regulation of APE1 sensitizes cells to DNA damaging agents. Thus, inhibiting APE1 repair endonuclease function in cancer cells is considered a promising strategy to overcome therapeutic agent resistance. Despite ongoing efforts, inhibitors of APE1 with adequate drug-like properties have yet to be discovered. Using a kinetic fluorescence assay, we conducted a fully-automated high-throughput screen (HTS) of the NIH Molecular Libraries Small Molecule Repository (MLSMR), as well as additional public collections, with each compound tested as a 7-concentration series in a 4 µL reaction volume. Actives identified from the screen were subjected to a panel of confirmatory and counterscreen tests. Several active molecules were identified that inhibited APE1 in two independent assay formats and exhibited potentiation of the genotoxic effect of methyl methanesulfonate with a concomitant increase in AP sites, a hallmark of intracellular APE1 inhibition; a number of these chemotypes could be good starting points for further medicinal chemistry optimization. To our knowledge, this represents the largest-scale HTS to identify inhibitors of APE1, and provides a key first step in the development of novel agents targeting BER for cancer treatment.

Evaluation of an Internally Controlled Multiplex Tth Endonuclease Cleavage Loop-Mediated Isothermal Amplification (TEC-LAMP) Assay for the Detection of Bacterial Meningitis Pathogens.

PubMed

Higgins, Owen; Clancy, Eoin; Cormican, Martin; Boo, Teck Wee; Cunney, Robert; Smith, Terry J

2018-02-09

Bacterial meningitis infection is a leading global health concern for which rapid and accurate diagnosis is essential to reduce associated morbidity and mortality. Loop-mediated isothermal amplification (LAMP) offers an effective low-cost diagnostic approach; however, multiplex LAMP is difficult to achieve, limiting its application. We have developed novel real-time multiplex LAMP technology, TEC-LAMP, using Tth endonuclease IV and a unique LAMP primer/probe. This study evaluates the analytical specificity, limit of detection (LOD) and clinical application of an internally controlled multiplex TEC-LAMP assay for detection of leading bacterial meningitis pathogens: Streptococcus pneumoniae , Neisseria meningitidis and Haemophilus influenzae . Analytical specificities were established by testing 168 bacterial strains, and LODs were determined using Probit analysis. The TEC-LAMP assay was 100% specific, with LODs for S. pneumoniae , N. meningitidis and H. influenzae of 39.5, 17.3 and 25.9 genome copies per reaction, respectively. Clinical performance was evaluated by testing 65 archived PCR-positive samples. Compared to singleplex real-time PCR, the multiplex TEC-LAMP assay demonstrated diagnostic sensitivity and specificity of 92.3% and 100%, respectively. This is the first report of a single-tube internally controlled multiplex LAMP assay for bacterial meningitis pathogen detection, and the first report of Tth endonuclease IV incorporation into nucleic acid amplification diagnostic technology.

Ab initio DNA synthesis by Bst polymerase in the presence of nicking endonucleases Nt.AlwI, Nb.BbvCI, and Nb.BsmI.

PubMed

Antipova, Valeriya N; Zheleznaya, Lyudmila A; Zyrina, Nadezhda V

2014-08-01

In the absence of added DNA, thermophilic DNA polymerases synthesize double-stranded DNA from free dNTPs, which consist of numerous repetitive units (ab initio DNA synthesis). The addition of thermophilic restriction endonuclease (REase), or nicking endonuclease (NEase), effectively stimulates ab initio DNA synthesis and determines the nucleotide sequence of reaction products. We have found that NEases Nt.AlwI, Nb.BbvCI, and Nb.BsmI with non-palindromic recognition sites stimulate the synthesis of sequences organized mainly as palindromes. Moreover, the nucleotide sequence of the palindromes appeared to be dependent on NEase recognition/cleavage modes. Thus, the heterodimeric Nb.BbvCI stimulated the synthesis of palindromes composed of two recognition sites of this NEase, which were separated by AT-reach sequences or (A)n (T)m spacers. Palindromic DNA sequences obtained in the ab initio DNA synthesis with the monomeric NEases Nb.BsmI and Nt.AlwI contained, along with the sites of these NEases, randomly synthesized sequences consisted of blocks of short repeats. These findings could help investigation of the potential abilities of highly productive ab initio DNA synthesis for the creation of DNA molecules with desirable sequence. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Alternative Nucleophilic Substrates for the Endonuclease Activities of Human Immunodeficiency Virus Type 1 Integrase

PubMed Central

Ealy, Julie B.; Sudol, Malgorzata; Krzeminski, Jacek; Amin, Shantu; Katzman, Michael

2012-01-01

Retroviral integrase can use water or some small alcohols as the attacking nucleophile to nick DNA. To characterize the range of compounds that human immunodeficiency virus type 1 integrase can accommodate for its endonuclease activities, we tested 45 potential electron donors (having varied size and number or spacing of nucleophilic groups) as substrates during site-specific nicking at viral DNA ends and during nonspecific nicking reactions. We found that integrase used 22 of the 45 compounds to nick DNA, but not all active compounds were used for both activities. In particular, 13 compounds were used for site-specific and nonspecific nicking, 5 only for site-specific nicking, and 4 only for nonspecific nicking; 23 other compounds were not used for either activity. Thus, integrase can accommodate a large number of nucleophilic substrates but has selective requirements for its different activities, underscoring its dynamic properties and providing new information for modeling and understanding integrase. PMID:22910593

alpha-Putrescinylthymine and the sensitivity of bacteriophage phi W-14 DNA to restriction endonucleases.

PubMed Central

Miller, P B; Wakarchuk, W W; Warren, R A

1985-01-01

The modified base alpha-putrescinylthymine (putT) in phi W-14 DNA blocks cleavage of the DNA by 17 of 32 Type II restriction endonucleases. The enzymes cleaving the DNA do so to widely varying extents. The frequencies of cleavage of three altered forms of the DNA show that putT blocks recognition sites either when it occurs within the site or when it is in a sequence flanking the site. The blocking is dependent on both charge and steric factors. The charge effects can be greater than the steric effects for some of the enzymes tested. All the enzymes cleaving phi W-14 DNA release discrete fragments, showing that the distribution of putT is ordered. The cleavage frequencies for different enzymes suggest that the sequence CAputTG occurs frequently in the DNA. Only TaqI of the enzymes tested appeared not to be blocked by putT, but it was slowed down. TaqI generated fragments are joinable by T4 DNA ligase. PMID:2987859

Comparative Structural and Functional Analysis of Bunyavirus and Arenavirus Cap-Snatching Endonucleases

PubMed Central

Reguera, Juan; Gerlach, Piotr; Rosenthal, Maria; Gaudon, Stephanie; Coscia, Francesca; Günther, Stephan; Cusack, Stephen

2016-01-01

Segmented negative strand RNA viruses of the arena-, bunya- and orthomyxovirus families uniquely carry out viral mRNA transcription by the cap-snatching mechanism. This involves cleavage of host mRNAs close to their capped 5′ end by an endonuclease (EN) domain located in the N-terminal region of the viral polymerase. We present the structure of the cap-snatching EN of Hantaan virus, a bunyavirus belonging to hantavirus genus. Hantaan EN has an active site configuration, including a metal co-ordinating histidine, and nuclease activity similar to the previously reported La Crosse virus and Influenza virus ENs (orthobunyavirus and orthomyxovirus respectively), but is more active in cleaving a double stranded RNA substrate. In contrast, Lassa arenavirus EN has only acidic metal co-ordinating residues. We present three high resolution structures of Lassa virus EN with different bound ion configurations and show in comparative biophysical and biochemical experiments with Hantaan, La Crosse and influenza ENs that the isolated Lassa EN is essentially inactive. The results are discussed in the light of EN activation mechanisms revealed by recent structures of full-length influenza virus polymerase. PMID:27304209

Nursing home queues and home health users.

PubMed

Swan, J H; Benjamin, A E

1993-01-01

Home health market growth suggests the need for models explaining home health utilization. We have previously explained state-level Medicare home health visits with reference to nursing home markets. Here we introduce a model whereby state-level Medicare home health use is a function of nursing home queues and other demand and supply factors. Medicare home health users per state population is negatively related to nursing home bed stock, positively to Medicaid eligibility levels and to Medicaid nursing home recipients per population, as well as to various other demand and supply measures. This explanation of home health users explains previously-reported findings for home health visits. The findings support the argument that home health use is explained by factors affecting lengths of nursing home queues.

[Endonuclease modified comet assay for oxidative DNA damage induced by detection of genetic toxicants].

PubMed

Zhao, Jian; Li, Hongli; Zhai, Qingfeng; Qiu, Yugang; Niu, Yong; Dai, Yufei; Zheng, Yuxin; Duan, Huawei

2014-03-01

The aim of this study was to investigate the use of the lesion-specific endonucleases-modified comet assay for analysis of DNA oxidation in cell lines. DNA breaks and oxidative damage were evaluated by normal alkaline and formamidopyrimidine-DNA-glycosylase (FPG) modified comet assays. Cytotoxicity were assessed by MTT method. The human bronchial epithelial cell (16HBE) were treated with benzo (a) pyrene (B(a)P), methyl methanesulfonate (MMS), colchicine (COL) and vincristine (VCR) respectively, and the dose is 20 µmol/L, 25 mg/ml, 5 mg/L and 0.5 mg/L for 24 h, respectively. Oxidative damage was also detected by levels of reactive oxygen species in treated cells. Four genotoxicants give higher cytotoxicity and no significant changes on parameters of comet assay treated by enzyme buffer. Cell survival rate were (59.69 ± 2.60) %, (54.33 ± 2.81) %, (53.11 ± 4.00) %, (51.43 ± 3.92) % in four groups, respectively. There was the direct DNA damage induced by test genotoxicants presented by tail length, Olive tail moment (TM) and tail DNA (%) in the comet assay. The presence of FPG in the assays increased DNA migration in treated groups when compared to those without it, and the difference was statistically significant which indicated that the clastogen and aneugen could induce oxidative damage in DNA strand. In the three parameters, the Olive TM was changed most obviously after genotoxicants treatment. In the contrast group, the Olive TM of B(a) P,MMS, COL,VCR in the contrast groups were 22.99 ± 17.33, 31.65 ± 18.86, 19.86 ± 9.56 and 17.02 ± 9.39, respectively, after dealing with the FPG, the Olive TM were 34.50 ± 17.29, 43.80 ± 10.06, 33.10 ± 12.38, 28.60 ± 10.53, increased by 58.94%, 38.48%, 66.86% and 68.21%, respectively (t value was 3.91, 3.89, 6.66 and 3.87, respectively, and all P < 0.05), and the correlation between Olive TM and reactive oxygen species was better than other parameters (r = 0.77, P < 0.05). This study indicates that FPG-comet assay

Evaluation of an Internally Controlled Multiplex Tth Endonuclease Cleavage Loop-Mediated Isothermal Amplification (TEC-LAMP) Assay for the Detection of Bacterial Meningitis Pathogens

PubMed Central

Clancy, Eoin; Cormican, Martin; Boo, Teck Wee; Cunney, Robert

2018-01-01

Bacterial meningitis infection is a leading global health concern for which rapid and accurate diagnosis is essential to reduce associated morbidity and mortality. Loop-mediated isothermal amplification (LAMP) offers an effective low-cost diagnostic approach; however, multiplex LAMP is difficult to achieve, limiting its application. We have developed novel real-time multiplex LAMP technology, TEC-LAMP, using Tth endonuclease IV and a unique LAMP primer/probe. This study evaluates the analytical specificity, limit of detection (LOD) and clinical application of an internally controlled multiplex TEC-LAMP assay for detection of leading bacterial meningitis pathogens: Streptococcus pneumoniae, Neisseria meningitidis and Haemophilus influenzae. Analytical specificities were established by testing 168 bacterial strains, and LODs were determined using Probit analysis. The TEC-LAMP assay was 100% specific, with LODs for S. pneumoniae, N. meningitidis and H. influenzae of 39.5, 17.3 and 25.9 genome copies per reaction, respectively. Clinical performance was evaluated by testing 65 archived PCR-positive samples. Compared to singleplex real-time PCR, the multiplex TEC-LAMP assay demonstrated diagnostic sensitivity and specificity of 92.3% and 100%, respectively. This is the first report of a single-tube internally controlled multiplex LAMP assay for bacterial meningitis pathogen detection, and the first report of Tth endonuclease IV incorporation into nucleic acid amplification diagnostic technology. PMID:29425124

Early endonuclease-mediated evasion of RNA sensing ensures efficient coronavirus replication

PubMed Central

Kindler, Eveline; Gil-Cruz, Cristina; Spanier, Julia; Li, Yize; Wilhelm, Jochen; Rabouw, Huib H.; Züst, Roland; Marti, Sabrina; Habjan, Matthias; Cervantes-Barragan, Luisa; Elliot, Ruth; Karl, Nadja; Gaughan, Christina; Silverman, Robert H.; Keller, Markus; Ludewig, Burkhard; Bergmann, Cornelia C.; Ziebuhr, John; Kalinke, Ulrich

2017-01-01

Coronaviruses are of veterinary and medical importance and include highly pathogenic zoonotic viruses, such as SARS-CoV and MERS-CoV. They are known to efficiently evade early innate immune responses, manifesting in almost negligible expression of type-I interferons (IFN-I). This evasion strategy suggests an evolutionary conserved viral function that has evolved to prevent RNA-based sensing of infection in vertebrate hosts. Here we show that the coronavirus endonuclease (EndoU) activity is key to prevent early induction of double-stranded RNA (dsRNA) host cell responses. Replication of EndoU-deficient coronaviruses is greatly attenuated in vivo and severely restricted in primary cells even during the early phase of the infection. In macrophages we found immediate induction of IFN-I expression and RNase L-mediated breakdown of ribosomal RNA. Accordingly, EndoU-deficient viruses can retain replication only in cells that are deficient in IFN-I expression or sensing, and in cells lacking both RNase L and PKR. Collectively our results demonstrate that the coronavirus EndoU efficiently prevents simultaneous activation of host cell dsRNA sensors, such as Mda5, OAS and PKR. The localization of the EndoU activity at the site of viral RNA synthesis–within the replicase complex—suggests that coronaviruses have evolved a viral RNA decay pathway to evade early innate and intrinsic antiviral host cell responses. PMID:28158275

RNA-cleaving properties of human apurinic/apyrimidinic endonuclease 1 (APE1)

PubMed Central

Kim, Wan-Cheol; King, Dustin; Lee, Chow H.

2010-01-01

We have recently identified apurinic/apyrimidinic endonuclease 1 (APE1) as an endoribonuclease that cleaves c-myc mRNA in vitro and regulates c-myc mRNA levels and half-life in cells. This study was undertaken to further unravel the RNA-cleaving properties of APE1. Here, we show that APE1 cleaves RNA in the absence of divalent metal ions and, at 2 mM, Zn2+, Ni2+, Cu2+, or Co2+ inhibited the endoribonuclease activity of APE1. APE1 is able to cleave CD44 mRNA, microRNAs (miR-21, miR-10b), and three RNA components of SARS-corona virus (orf1b, orf3, spike) suggesting that, when challenged, it can cleave any RNAs in vitro. APE1 does not cleave strong doublestranded regions of RNA and it has a strong preference for 3’ of pyrimidine, especially towards UA, CA, and UG sites at single-stranded or weakly paired regions. It also cleaves RNA weakly at UC, CU, AC, and AU sites in single-stranded or weakly paired regions. Finally, we found that APE1 can reduce the ability of the Dicer enzyme to process premiRNAs in vitro. Overall, this study has revealed some previously unknown biochemical properties of APE1 which has implications for its role in vivo. PMID:21968700

Home sweet home? Home physical environment and inflammation in children

PubMed Central

Schmeer, Kammi K.; Yoon, Aimee J.

2016-01-01

The home environment includes important social and physical contexts within which children develop. Poor physical home environments may be a potential source of stress for children through difficult daily experiences. Using a sub-sample from the Los Angeles Family and Neighborhood Survey (N = 425), we consider how the home physical environment affects stress-related immune system dysregulation in children ages 3–18 years. Results indicated that children in poorer quality homes had higher inflammation (measured by C-reactive protein). The associations were particularly strong for younger children. We also found that part of the home physical environment association with CRP worked through increased risk of obesity for children living in low-quality homes. Future research should assess how home physical environments could be improved to reduce stress and improve health outcomes in children. PMID:27712682

Single-molecule FRET unveils induced-fit mechanism for substrate selectivity in flap endonuclease 1

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

Rashid, Fahad; Harris, Paul D.; Zaher, Manal S.

Human flap endonuclease 1 (FEN1) and related structure-specific 5’nucleases precisely identify and incise aberrant DNA structures during replication, repair and recombination to avoid genomic instability. Yet, it is unclear how the 5’nuclease mechanisms of DNA distortion and protein ordering robustly mediate efficient and accurate substrate recognition and catalytic selectivity. Here, single-molecule sub-millisecond and millisecond analyses of FEN1 reveal a protein-DNA induced-fit mechanism that efficiently verifies substrate and suppresses off-target cleavage. FEN1 sculpts DNA with diffusion-limited kinetics to test DNA substrate. This DNA distortion mutually ‘locks’ protein and DNA conformation and enables substrate verification with extreme precision. Strikingly, FEN1 never missesmore » cleavage of its cognate substrate while blocking probable formation of catalytically competent interactions with noncognate substrates and fostering their pre-incision dissociation. These findings establish FEN1 has practically perfect precision and that separate control of induced-fit substrate recognition sets up the catalytic selectivity of the nuclease active site for genome stability.« less

Single-molecule FRET unveils induced-fit mechanism for substrate selectivity in flap endonuclease 1

DOE PAGES

Rashid, Fahad; Harris, Paul D.; Zaher, Manal S.; ...

2017-02-23

Human flap endonuclease 1 (FEN1) and related structure-specific 5’nucleases precisely identify and incise aberrant DNA structures during replication, repair and recombination to avoid genomic instability. Yet, it is unclear how the 5’nuclease mechanisms of DNA distortion and protein ordering robustly mediate efficient and accurate substrate recognition and catalytic selectivity. Here, single-molecule sub-millisecond and millisecond analyses of FEN1 reveal a protein-DNA induced-fit mechanism that efficiently verifies substrate and suppresses off-target cleavage. FEN1 sculpts DNA with diffusion-limited kinetics to test DNA substrate. This DNA distortion mutually ‘locks’ protein and DNA conformation and enables substrate verification with extreme precision. Strikingly, FEN1 never missesmore » cleavage of its cognate substrate while blocking probable formation of catalytically competent interactions with noncognate substrates and fostering their pre-incision dissociation. These findings establish FEN1 has practically perfect precision and that separate control of induced-fit substrate recognition sets up the catalytic selectivity of the nuclease active site for genome stability.« less

Resolution of model Holliday junctions by yeast endonuclease: effect of DNA structure and sequence.

PubMed Central

Parsons, C A; Murchie, A I; Lilley, D M; West, S C

1989-01-01

The resolution of Holliday junctions in DNA involves specific cleavage at or close to the site of the junction. A nuclease from Saccharomyces cerevisiae cleaves model Holliday junctions in vitro by the introduction of nicks in regions of duplex DNA adjacent to the crossover point. In previous studies [Parsons and West (1988) Cell, 52, 621-629] it was shown that cleavage occurred within homologous arm sequences with precise symmetry across the junction. In contrast, junctions with heterologous arm sequences were cleaved asymmetrically. In this work, we have studied the effect of sequence changes and base modification upon the site of cleavage. It is shown that the specificity of cleavage is unchanged providing that perfect homology is maintained between opposing arm sequences. However, in the absence of homology, cleavage depends upon sequence context and is affected by minor changes such as base modification. These data support the proposed mechanism for cleavage of a Holliday junction, which requires homologous alignment of arm sequences in an enzyme--DNA complex as a prerequisite for symmetrical cleavage by the yeast endonuclease. Images PMID:2653810

Single-molecule FRET unveils induced-fit mechanism for substrate selectivity in flap endonuclease 1

PubMed Central

Rashid, Fahad; Harris, Paul D; Zaher, Manal S; Sobhy, Mohamed A; Joudeh, Luay I; Yan, Chunli; Piwonski, Hubert; Tsutakawa, Susan E; Ivanov, Ivaylo; Tainer, John A; Habuchi, Satoshi; Hamdan, Samir M

2017-01-01

Human flap endonuclease 1 (FEN1) and related structure-specific 5’nucleases precisely identify and incise aberrant DNA structures during replication, repair and recombination to avoid genomic instability. Yet, it is unclear how the 5’nuclease mechanisms of DNA distortion and protein ordering robustly mediate efficient and accurate substrate recognition and catalytic selectivity. Here, single-molecule sub-millisecond and millisecond analyses of FEN1 reveal a protein-DNA induced-fit mechanism that efficiently verifies substrate and suppresses off-target cleavage. FEN1 sculpts DNA with diffusion-limited kinetics to test DNA substrate. This DNA distortion mutually ‘locks’ protein and DNA conformation and enables substrate verification with extreme precision. Strikingly, FEN1 never misses cleavage of its cognate substrate while blocking probable formation of catalytically competent interactions with noncognate substrates and fostering their pre-incision dissociation. These findings establish FEN1 has practically perfect precision and that separate control of induced-fit substrate recognition sets up the catalytic selectivity of the nuclease active site for genome stability. DOI: http://dx.doi.org/10.7554/eLife.21884.001 PMID:28230529

Recurrent invasion and extinction of a selfish gene.

PubMed

Goddard, M R; Burt, A

1999-11-23

Homing endonuclease genes show super-Mendelian inheritance, which allows them to spread in populations even when they are of no benefit to the host organism. To test the idea that regular horizontal transmission is necessary for the long-term persistence of these genes, we surveyed 20 species of yeasts for the omega-homing endonuclease gene and associated group I intron. The status of omega could be categorized into three states (functional, nonfunctional, or absent), and status was not clustered on the host phylogeny. Moreover, the phylogeny of omega differed significantly from that of the host, strong evidence of horizontal transmission. Further analyses indicate that horizontal transmission is more common than transposition, and that it occurs preferentially between closely related species. Parsimony analysis and coalescent theory suggest that there have been 15 horizontal transmission events in the ancestry of our yeast species, through simulations indicate that this value is probably an underestimate. Overall, the data support a cyclical model of invasion, degeneration, and loss, followed by reinvasion, and each of these transitions is estimated to occur about once every 2 million years. The data are thus consistent with the idea that frequent horizontal transmission is necessary for the long-term persistence of homing endonuclease genes, and further, that this requirement limits these genes to organisms with easily accessible germ lines. The data also show that mitochondrial DNA sequences are transferred intact between yeast species; if other genes do not show such high levels of horizontal transmission, it would be due to lack of selection, rather than lack of opportunity.

An intrinsic DFF40/CAD endonuclease deficiency impairs oligonucleosomal DNA hydrolysis during caspase-dependent cell death: a common trait in human glioblastoma cells

PubMed Central

Sánchez-Osuna, María; Martínez-Escardó, Laura; Granados-Colomina, Carla; Martínez-Soler, Fina; Pascual-Guiral, Sònia; Iglesias-Guimarais, Victoria; Velasco, Roser; Plans, Gerard; Vidal, Noemi; Tortosa, Avelina; Barcia, Carlos; Bruna, Jordi; Yuste, Victor J.

2016-01-01

Background Glioblastoma (GBM) or grade IV astrocytoma is one of the most devastating human cancers. The loss of DFF40/CAD, the key endonuclease that triggers oligonucleosomal DNA fragmentation during apoptosis, has been linked to genomic instability and cell survival after radiation. Despite the near inevitability of GBM tumor recurrence after treatment, the relationship between DFF40/CAD and GBM remains unexplored. Methods We studied the apoptotic behavior of human GBM-derived cells after apoptotic insult. We analyzed caspase activation and the protein levels and subcellular localization of DFF40/CAD apoptotic endonuclease. DFF40/CAD was also evaluated in histological sections from astrocytic tumors and nontumoral human brain. Results We showed that GBM cells undergo incomplete apoptosis without generating oligonucleosomal DNA degradation despite the correct activation of executioner caspases. The major defect of GBM cells relied on the improper accumulation of DFF40/CAD at the nucleoplasmic subcellular compartment. Supporting this finding, DFF40/CAD overexpression allowed GBM cells to display oligonucleosomal DNA degradation after apoptotic challenge. Moreover, the analysis of histological slices from astrocytic tumors showed that DFF40/CAD immunoreactivity in tumoral GFAP-positive cells was markedly reduced when compared with nontumoral samples. Conclusions Our data highlight the low expression levels of DFF40/CAD and the absence of DNA laddering as common molecular traits in GBM. These findings could be of major importance for understanding the malignant behavior of remaining tumor cells after radiochemotherapy. PMID:26755073

Interaction of the E. coli DNA G:T-mismatch endonuclease (vsr protein) with oligonucleotides containing its target sequence.

PubMed

Turner, D P; Connolly, B A

2000-12-15

The Escherichia coli vsr endonuclease recognises G:T base-pair mismatches in double-stranded DNA and initiates a repair pathway by hydrolysing the phosphate group 5' to the incorrectly paired T. The enzyme shows a preference for G:T mismatches within a particular sequence context, derived from the recognition site of the E. coli dcm DNA-methyltransferase (CC[A/T]GG). Thus, the preferred substrate for the vsr protein is (CT[A/T]GG), where the underlined T is opposed by a dG base. This paper provides quantitative data for the interaction of the vsr protein with a number of oligonucleotides containing G:T mismatches. Evaluation of specificity constant (k(st)/K(D); k(st)=rate constant for single turnover, K(D)=equilibrium dissociation constant) confirms vsr's preference for a G:T mismatch within a hemi-methylated dcm sequence, i.e. the best substrate is a duplex (both strands written in the 5'-3' orientation) composed of CT[A/T]GG and C(5Me)C[T/A]GG. Conversion of the mispaired T (underlined) to dU or the d(5Me)C to dC gave poorer substrates. No interaction was observed with oligonucleotides that lacked a G:T mismatch or did not possess a dcm sequence. An analysis of the fraction of active protein, by "reverse-titration" (i.e. adding increasing amounts of DNA to a fixed amount of protein followed by gel-mobility shift analysis) showed that less than 1% of the vsr endonuclease was able to bind to the substrate. This was confirmed using "competitive titrations" (where competitor oligonucleotides are used to displace a (32)P-labelled nucleic acid from the vsr protein) and burst kinetic analysis. This result is discussed in the light of previous in vitro and in vivo data which indicate that the MutL protein may be needed for full vsr activity. Copyright 2000 Academic Press.

Ultrasensitive apurinic/apyrimidinic endonuclease 1 immunosensing based on self-enhanced electrochemiluminescence of a Ru(II) complex.

PubMed

Zhuo, Ying; Liao, Ni; Chai, Ya-Qin; Gui, Guo-Feng; Zhao, Min; Han, Jing; Xiang, Yun; Yuan, Ruo

2014-01-21

An alternative "signal on" immunosensor for ultrasensitive detection of apurinic/apyrimidinic endonuclease 1 (APE-1) was designed utilizing the self-enhanced electrochemiluminescence (ECL) of a novel Ru(II) complex functionalized coil-like nanocomposite as signal labels. The desirable self-enhanced ECL luminophore was achieved by combining the coreactant of poly(ethylenimine) (PEI) and the luminophor of bis(2,2'-bipyridine)-5-amino-1,10-phenanthroline ruthenium(II) [Ru(bpy)2(5-NH2-1,10-phen)(2+)] to form one novel Ru(II) complex, which exhibited significantly enhanced ECL efficiency and stability. Moreover, the carbon nanotubes (CNTs) were employed as nanocarriers for self-enhanced Ru(II) complex loading via π-π stacking to obtain the coil-like nanocomposite to act as signal probe. Compared with traditional ECL immunoassay, our proposed strategy is simple and sensitive, avoiding the adding of any coreactant into testing solution for signal amplification, and shows a detection limit down to subfemtogram per milliliter level under the optimized experimental condition.

One-tube loop-mediated isothermal amplification combined with restriction endonuclease digestion and ELISA for colorimetric detection of resistance to isoniazid, ethambutol and streptomycin in Mycobacterium tuberculosis isolates.

PubMed

Lee, Mei-Feng; Chen, Yen-Hsu; Hsu, Hui-Jine; Peng, Chien-Fang

2010-10-01

In this study, we designed a simple and rapid colorimetric detection method, a one-tube loop-mediated isothermal amplification (LAMP)-PCR-hybridization-restriction endonuclease-ELISA [one-tube LAMP-PCR-HY-RE-ELISA] system, to detect resistance to isoniazid, ethambutol and streptomycin in strains of Mycobacterium tuberculosis isolated from clinical specimens. The clinical performance of this method for detecting isoniazid-resistant, ethambutol-resistant and streptomycin-resistant isolates of M. tuberculosis showed 98.9%, 94.3% and 93.8%, respectively. This assay is rapid and convenient that can be performed within one working day. One-tube LAMP-PCR-HY-RE-ELISA system was designed based on hot spot point mutations in target drug-resistant genes, using LAMP-PCR, hybridization, digestion with restriction endonuclease and colorimetric method of ELISA. In this study, LAMP assay was used to amplify DNA from drug-resistant M. tuberculosis, and ELISA was used for colorimetrical determination. This assay will be a useful tool for rapid diagnosis of mutant codons in strains of M. tuberculosis for isoniazid at katG 315 and katG 463, ethambutol at embB 306 and embB 497, and streptomycin at rpsL 43. Crown Copyright © 2010. Published by Elsevier B.V. All rights reserved.

Multipronged regulatory functions of a novel endonuclease (TieA) from Helicobacter pylori

PubMed Central

Devi, Savita; Ansari, Suhail A.; Tenguria, Shivendra; Kumar, Naveen; Ahmed, Niyaz

2016-01-01

Helicobacter pylori portrays a classical paradigm of persistent bacterial infections. A well balanced homeostasis of bacterial effector functions and host responses is purported to be the key in achieving long term colonization in specific hosts. H. pylori nucleases have been shown to assist in natural transformation, but their role in virulence and colonization remains elusive. Therefore, it is imperative to understand the involvement of these nucleases in the pathogenesis of H. pylori. Here, we report the multifaceted role of a TNFR-1 interacting endonuclease A (TieA) from H. pylori. tieA expression is differentially regulated in response to environmental stress and post adherence to gastric epithelial cells. Studies with isogenic knockouts of tieA revealed it to be a secretory protein which translocates into the host gastric epithelial cells independent of a type IV secretion system, gets phosphorylated by DNA-PK kinase and auto-phosphorylates as serine kinase. Furthermore, TieA binds to and cleaves DNA in a non-specific manner and promotes Fas mediated apoptosis in AGS cells. Additionally, TieA induced pro-inflammatory cytokine secretion via activation of transcription factor AP-1 and signaled through MAP kinase pathway. Collectively, TieA with its multipronged and moonlighting functions could facilitate H. pylori in maintaining a balance of bacterial adaptation, and elimination by the host responses. PMID:27550181

Association of Leukotrichia in Vitiligo and Asp148Glu Polymorphism of Apurinic/Apyrimidinic Endonuclease 1.

PubMed

Aydin, A Fatih; Aydıngöz, İkbal Esen; Doğru-Abbasoğlu, Semra; Vural, Pervin; Uysal, Müjdat

2017-01-01

Oxidative stress and increased DNA damage have been implicated in the etiopathogenesis of vitiligo. Oxidative DNA damage is mainly repaired by the base excision repair (BER) pathway. We sought to determine whether polymorphisms in DNA repair genes may have a role in the pathogenesis of vitiligo. We conducted a study including 100 patients with vitiligo and age- and sex-matched 193 control subjects to examine the role of single-nucleotide polymorphisms of BER genes, human 8-oxoG DNA N-glycosylase 1 (codon 326), apurinic/apyrimidinic endonuclease 1 (APE1) (codon 148), and X-ray repair cross-complementing group 1 (codon 399) as risk factors for vitiligo. These polymorphisms were determined by quantitative real-time polymerase chain reaction and melting curve analysis. No significant association was observed between the variant alleles of studied genes and vitiligo. However, we showed that the presence of APE1 148Glu variant allele is associated with leukotrichia. This preliminary study suggests that APE1 (codon 148) polymorphism may play a role in vitiligo pathogenesis.

An AP Endonuclease Functions in Active DNA Demethylation and Gene Imprinting in Arabidopsis

PubMed Central

Li, Yan; Córdoba-Cañero, Dolores; Qian, Weiqiang; Zhu, Xiaohong; Tang, Kai; Zhang, Huiming; Ariza, Rafael R.; Roldán-Arjona, Teresa; Zhu, Jian-Kang

2015-01-01

Active DNA demethylation in plants occurs through base excision repair, beginning with removal of methylated cytosine by the ROS1/DME subfamily of 5-methylcytosine DNA glycosylases. Active DNA demethylation in animals requires the DNA glycosylase TDG or MBD4, which functions after oxidation or deamination of 5-methylcytosine, respectively. However, little is known about the steps following DNA glycosylase action in the active DNA demethylation pathways in plants and animals. We show here that the Arabidopsis APE1L protein has apurinic/apyrimidinic endonuclease activities and functions downstream of ROS1 and DME. APE1L and ROS1 interact in vitro and co-localize in vivo. Whole genome bisulfite sequencing of ape1l mutant plants revealed widespread alterations in DNA methylation. We show that the ape1l/zdp double mutant displays embryonic lethality. Notably, the ape1l+/−zdp−/− mutant shows a maternal-effect lethality phenotype. APE1L and the DNA phosphatase ZDP are required for FWA and MEA gene imprinting in the endosperm and are important for seed development. Thus, APE1L is a new component of the active DNA demethylation pathway and, together with ZDP, regulates gene imprinting in Arabidopsis. PMID:25569774

How quantum entanglement in DNA synchronizes double-strand breakage by type II restriction endonucleases.

PubMed

Kurian, P; Dunston, G; Lindesay, J

2016-02-21

Macroscopic quantum effects in living systems have been studied widely in pursuit of fundamental explanations for biological energy transport and sensing. While it is known that type II endonucleases, the largest class of restriction enzymes, induce DNA double-strand breaks by attacking phosphodiester bonds, the mechanism by which simultaneous cutting is coordinated between the catalytic centers remains unclear. We propose a quantum mechanical model for collective electronic behavior in the DNA helix, where dipole-dipole oscillations are quantized through boundary conditions imposed by the enzyme. Zero-point modes of coherent oscillations would provide the energy required for double-strand breakage. Such quanta may be preserved in the presence of thermal noise by the enzyme's displacement of water surrounding the DNA recognition sequence. The enzyme thus serves as a decoherence shield. Palindromic mirror symmetry of the enzyme-DNA complex should conserve parity, because symmetric bond-breaking ceases when the symmetry of the complex is violated or when physiological parameters are perturbed from optima. Persistent correlations in DNA across longer spatial separations-a possible signature of quantum entanglement-may be explained by such a mechanism. Copyright © 2015 Elsevier Ltd. All rights reserved.

How quantum entanglement in DNA synchronizes double-strand breakage by type II restriction endonucleases

PubMed Central

Kurian, P.; Dunston, G.; Lindesay, J.

2015-01-01

Macroscopic quantum effects in living systems have been studied widely in pursuit of fundamental explanations for biological energy transport and sensing. While it is known that type II endonucleases, the largest class of restriction enzymes, induce DNA double-strand breaks by attacking phosphodiester bonds, the mechanism by which simultaneous cutting is coordinated between the catalytic centers remains unclear. We propose a quantum mechanical model for collective electronic behavior in the DNA helix, where dipole-dipole oscillations are quantized through boundary conditions imposed by the enzyme. Zero-point modes of coherent oscillations would provide the energy required for double-strand breakage. Such quanta may be preserved in the presence of thermal noise by the enzyme’s displacement of water surrounding the DNA recognition sequence. The enzyme thus serves as a decoherence shield. Palindromic mirror symmetry of the enzyme-DNA complex should conserve parity, because symmetric bond-breaking ceases when the symmetry of the complex is violated or when physiological parameters are perturbed from optima. Persistent correlations in DNA across longer spatial separations—a possible signature of quantum entanglement—may be explained by such a mechanism. PMID:26682627

Ambiguities: residents' experience of 'nursing home as my home'.

PubMed

Nakrem, Sigrid; Vinsnes, Anne G; Harkless, Gene E; Paulsen, Bård; Seim, Arnfinn

2013-09-01

Residential care in nursing homes continues to be necessary for those individuals who are no longer able to live at home. Uncovering what nursing home residents' view as quality of care in nursing homes will help further understanding of how best to provide high quality, person-centred care. To describe residents' experiences of living in a nursing home related to quality of care. The study utilises a descriptive exploratory design. In-depth interviews were undertaken with 15 residents who were not cognitively impaired, aged 65 and over and living in one of four nursing homes. The interviews were transcribed verbatim and analysed by categorising of meaning. Residents perceived the nursing home as their home, but at the same time not 'a home'. This essential ambiguity created the tension from which the categories of perceptions of quality emerged. Four main categories of quality of care experience were identified: 'Being at home in a nursing home', 'Paying the price for 24-hour care', 'Personal habits and institutional routines', and 'Meaningful activities for a meaningful day'. Ambiguities concerning the nursing home as a home and place to live, a social environment in which the residents experience most of their social life and the institution where professional health service is provided were uncovered. High-quality care was when ambiguities were managed well and a home could be created within the institution. Implication for practice. Achieving quality care in nursing homes requires reconciling the ambiguities of the nursing home as a home. This implies helping residents to create a private home distinct from the professional home, allowing residents' personal habits to guide institutional routines and supporting meaningful activities. Using these resident developed quality indicators is an important step in improving nursing home services. © 2012 Blackwell Publishing Ltd.

ERCC1-XPF Endonuclease Facilitates DNA Double-Strand Break Repair▿ †

PubMed Central

Ahmad, Anwaar; Robinson, Andria Rasile; Duensing, Anette; van Drunen, Ellen; Beverloo, H. Berna; Weisberg, David B.; Hasty, Paul; Hoeijmakers, Jan H. J.; Niedernhofer, Laura J.

2008-01-01

ERCC1-XPF endonuclease is required for nucleotide excision repair (NER) of helix-distorting DNA lesions. However, mutations in ERCC1 or XPF in humans or mice cause a more severe phenotype than absence of NER, prompting a search for novel repair activities of the nuclease. In Saccharomyces cerevisiae, orthologs of ERCC1-XPF (Rad10-Rad1) participate in the repair of double-strand breaks (DSBs). Rad10-Rad1 contributes to two error-prone DSB repair pathways: microhomology-mediated end joining (a Ku86-independent mechanism) and single-strand annealing. To determine if ERCC1-XPF participates in DSB repair in mammals, mutant cells and mice were screened for sensitivity to gamma irradiation. ERCC1-XPF-deficient fibroblasts were hypersensitive to gamma irradiation, and γH2AX foci, a marker of DSBs, persisted in irradiated mutant cells, consistent with a defect in DSB repair. Mutant mice were also hypersensitive to irradiation, establishing an essential role for ERCC1-XPF in protecting against DSBs in vivo. Mice defective in both ERCC1-XPF and Ku86 were not viable. However, Ercc1−/− Ku86−/− fibroblasts were hypersensitive to gamma irradiation compared to single mutants and accumulated significantly greater chromosomal aberrations. Finally, in vitro repair of DSBs with 3′ overhangs led to large deletions in the absence of ERCC1-XPF. These data support the conclusion that, as in yeast, ERCC1-XPF facilitates DSB repair via an end-joining mechanism that is Ku86 independent. PMID:18541667

Modulation of the Pyrococcus abyssi NucS Endonuclease Activity by Replication Clamp at Functional and Structural Levels*

PubMed Central

Creze, Christophe; Ligabue, Alessio; Laurent, Sébastien; Lestini, Roxane; Laptenok, Sergey P.; Khun, Joelle; Vos, Marten H.; Czjzek, Mirjam; Myllykallio, Hannu; Flament, Didier

2012-01-01

Pyrococcus abyssi NucS is the founding member of a new family of structure-specific DNA endonucleases that interact with the replication clamp proliferating cell nuclear antigen (PCNA). Using a combination of small angle x-ray scattering and surface plasmon resonance analyses, we demonstrate the formation of a stable complex in solution, in which one molecule of the PabNucS homodimer binds to the outside surface of the PabPCNA homotrimer. Using fluorescent labels, PCNA is shown to increase the binding affinity of NucS toward single-strand/double-strand junctions on 5′ and 3′ flaps, as well as to modulate the cleavage specificity on the branched DNA structures. Our results indicate that the presence of a single major contact between the PabNucS and PabPCNA proteins, together with the complex-induced DNA bending, facilitate conformational flexibility required for specific cleavage at the single-strand/double-strand DNA junction. PMID:22431731

Modulation of the Pyrococcus abyssi NucS endonuclease activity by replication clamp at functional and structural levels.

PubMed

Creze, Christophe; Ligabue, Alessio; Laurent, Sébastien; Lestini, Roxane; Laptenok, Sergey P; Khun, Joelle; Vos, Marten H; Czjzek, Mirjam; Myllykallio, Hannu; Flament, Didier

2012-05-04

Pyrococcus abyssi NucS is the founding member of a new family of structure-specific DNA endonucleases that interact with the replication clamp proliferating cell nuclear antigen (PCNA). Using a combination of small angle x-ray scattering and surface plasmon resonance analyses, we demonstrate the formation of a stable complex in solution, in which one molecule of the PabNucS homodimer binds to the outside surface of the PabPCNA homotrimer. Using fluorescent labels, PCNA is shown to increase the binding affinity of NucS toward single-strand/double-strand junctions on 5' and 3' flaps, as well as to modulate the cleavage specificity on the branched DNA structures. Our results indicate that the presence of a single major contact between the PabNucS and PabPCNA proteins, together with the complex-induced DNA bending, facilitate conformational flexibility required for specific cleavage at the single-strand/double-strand DNA junction.

[Effect of endonuclease G depletion on plasmid DNA uptake and levels of homologous recombination in hela cells].

PubMed

Misic, V; El-Mogy, M; Geng, S; Haj-Ahmad, Y

2016-01-01

Endonuclease G (EndoG) is a mitochondrial apoptosis regulator that also has roles outside of programmed cell death. It has been implicated as a defence DNase involved in the degradation of exogenous DNA after transfection of mammalian cells and in homologous recombination of viral and endogenous DNA. In this study, we looked at the effect of EndoG depletion on plasmid DNA uptake and the levels of homologous recombination in HeLa cells. We show that the proposed defence role of EndoG against uptake of non-viral DNA vectors does not extend to the cervical carcinoma HeLa cells, as targeting of EndoG expression by RNA interference failed to increase intracellular plasmid DNA levels. However, reducing EndoG levels in HeLa cells resulted in a statistically significant reduction of homologous recombination between two plasmid DNA substrates. These findings suggest that non-viral DNA vectors are also substrates for EndoG in its role in homologous recombination.

Multipronged regulatory functions of a novel endonuclease (TieA) from Helicobacter pylori.

PubMed

Devi, Savita; Ansari, Suhail A; Tenguria, Shivendra; Kumar, Naveen; Ahmed, Niyaz

2016-11-02

Helicobacter pylori portrays a classical paradigm of persistent bacterial infections. A well balanced homeostasis of bacterial effector functions and host responses is purported to be the key in achieving long term colonization in specific hosts. H. pylori nucleases have been shown to assist in natural transformation, but their role in virulence and colonization remains elusive. Therefore, it is imperative to understand the involvement of these nucleases in the pathogenesis of H. pylori Here, we report the multifaceted role of a TNFR-1 interacting endonuclease A (TieA) from H. pylori. tieA expression is differentially regulated in response to environmental stress and post adherence to gastric epithelial cells. Studies with isogenic knockouts of tieA revealed it to be a secretory protein which translocates into the host gastric epithelial cells independent of a type IV secretion system, gets phosphorylated by DNA-PK kinase and auto-phosphorylates as serine kinase. Furthermore, TieA binds to and cleaves DNA in a non-specific manner and promotes Fas mediated apoptosis in AGS cells. Additionally, TieA induced pro-inflammatory cytokine secretion via activation of transcription factor AP-1 and signaled through MAP kinase pathway. Collectively, TieA with its multipronged and moonlighting functions could facilitate H. pylori in maintaining a balance of bacterial adaptation, and elimination by the host responses. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

An intrinsic DFF40/CAD endonuclease deficiency impairs oligonucleosomal DNA hydrolysis during caspase-dependent cell death: a common trait in human glioblastoma cells.

PubMed

Sánchez-Osuna, María; Martínez-Escardó, Laura; Granados-Colomina, Carla; Martínez-Soler, Fina; Pascual-Guiral, Sònia; Iglesias-Guimarais, Victoria; Velasco, Roser; Plans, Gerard; Vidal, Noemi; Tortosa, Avelina; Barcia, Carlos; Bruna, Jordi; Yuste, Victor J

2016-07-01

Glioblastoma (GBM) or grade IV astrocytoma is one of the most devastating human cancers. The loss of DFF40/CAD, the key endonuclease that triggers oligonucleosomal DNA fragmentation during apoptosis, has been linked to genomic instability and cell survival after radiation. Despite the near inevitability of GBM tumor recurrence after treatment, the relationship between DFF40/CAD and GBM remains unexplored. We studied the apoptotic behavior of human GBM-derived cells after apoptotic insult. We analyzed caspase activation and the protein levels and subcellular localization of DFF40/CAD apoptotic endonuclease. DFF40/CAD was also evaluated in histological sections from astrocytic tumors and nontumoral human brain. We showed that GBM cells undergo incomplete apoptosis without generating oligonucleosomal DNA degradation despite the correct activation of executioner caspases. The major defect of GBM cells relied on the improper accumulation of DFF40/CAD at the nucleoplasmic subcellular compartment. Supporting this finding, DFF40/CAD overexpression allowed GBM cells to display oligonucleosomal DNA degradation after apoptotic challenge. Moreover, the analysis of histological slices from astrocytic tumors showed that DFF40/CAD immunoreactivity in tumoral GFAP-positive cells was markedly reduced when compared with nontumoral samples. Our data highlight the low expression levels of DFF40/CAD and the absence of DNA laddering as common molecular traits in GBM. These findings could be of major importance for understanding the malignant behavior of remaining tumor cells after radiochemotherapy. © The Author(s) 2016. Published by Oxford University Press on behalf of the Society for Neuro-Oncology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Phosphate steering by Flap Endonuclease 1 promotes 5'-flap specificity and incision to prevent genome instability

DOE PAGES

Tsutakawa, Susan E.; Thompson, Mark J.; Arvai, Andrew S.; ...

2017-06-27

DNA replication and repair enzyme Flap Endonuclease 1 (FEN1) is vital for genome integrity, and FEN1 mutations arise in multiple cancers. FEN1 precisely cleaves single-stranded (ss) 5'-flaps one nucleotide into duplex (ds) DNA. Yet, how FEN1 selects for but does not incise the ss 5'-flap was enigmatic. Here we combine crystallographic, biochemical and genetic analyses to show that two dsDNA binding sites set the 5'polarity and to reveal unexpected control of the DNA phosphodiester backbone by electrostatic interactions. Via phosphate steering', basic residues energetically steer an inverted ss 5'-flap through a gateway over FEN1's active site and shift dsDNA formore » catalysis. Mutations of these residues cause an 18,000-fold reduction in catalytic rate in vitro and large-scale trinucleotide (GAA) n repeat expansions in vivo, implying failed phosphate-steering promotes an unanticipated lagging-strand template-switch mechanism during replication. Thus, phosphate steering is an unappreciated FEN1 function that enforces 5'-flap specificity and catalysis, preventing genomic instability.« less

Phosphate steering by Flap Endonuclease 1 promotes 5'-flap specificity and incision to prevent genome instability

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

Tsutakawa, Susan E.; Thompson, Mark J.; Arvai, Andrew S.

DNA replication and repair enzyme Flap Endonuclease 1 (FEN1) is vital for genome integrity, and FEN1 mutations arise in multiple cancers. FEN1 precisely cleaves single-stranded (ss) 5'-flaps one nucleotide into duplex (ds) DNA. Yet, how FEN1 selects for but does not incise the ss 5'-flap was enigmatic. Here we combine crystallographic, biochemical and genetic analyses to show that two dsDNA binding sites set the 5'polarity and to reveal unexpected control of the DNA phosphodiester backbone by electrostatic interactions. Via phosphate steering', basic residues energetically steer an inverted ss 5'-flap through a gateway over FEN1's active site and shift dsDNA formore » catalysis. Mutations of these residues cause an 18,000-fold reduction in catalytic rate in vitro and large-scale trinucleotide (GAA) n repeat expansions in vivo, implying failed phosphate-steering promotes an unanticipated lagging-strand template-switch mechanism during replication. Thus, phosphate steering is an unappreciated FEN1 function that enforces 5'-flap specificity and catalysis, preventing genomic instability.« less

Adenomatous Polyposis Coli Interacts with Flap Endonuclease 1 to Block Its Nuclear Entry and Function1

PubMed Central

Jaiswal, Aruna S; Armas, Melissa L; Izumi, Tadahide; Strauss, Phyllis R; Narayan, Satya

2012-01-01

In previous studies, we found that adenomatous polyposis coli (APC) blocks the base excision repair (BER) pathway by interacting with 5′-flap endonuclease 1 (Fen1). In this study, we identify the molecular features that contribute to the formation and/or stabilization of the APC/Fen1 complex that determines the extent of BER inhibition, and the subsequent accumulation of DNA damage creates mutagenic lesions leading to transformation susceptibility. We show here that APC binds to the nuclear localization sequence of Fen1 (Lys365Lys366Lys367), which prevents entry of Fen1 into the nucleus and participation in Pol-β-directed long-patch BER. We also show that levels of the APC/Fen1 complex are higher in breast tumors than in the surrounding normal tissues. These studies demonstrate a novel role for APC in the suppression of Fen1 activity in the BER pathway and a new biomarker profile to be explored to identify individuals who may be susceptible to the development of mammary and other tumors. PMID:22787431

Nursing Homes

MedlinePlus

... our e-newsletter! Aging & Health A to Z Nursing Homes Basic Facts & Information Nursing homes have changed ... guide care in nursing homes. Who lives in nursing homes? Almost half of all people who live ...

Enabling at-homeness for residents living in a nursing home: Reflected experience of nursing home staff.

PubMed

Saarnio, Lotta; Boström, Anne-Marie; Hedman, Ragnhild; Gustavsson, Petter; Öhlén, Joakim

2017-12-01

Older people are often living the last period of their lives in institutions such as nursing homes. Knowledge of this period, specifically related to at-homeness which can be described as wellbeing in spite of illness and has been regarded as one of the goals in palliative care, has been very little researched in the context of nursing homes and the experience of nursing home staff. The aim of this study was to explore the experiences of nursing home staff of how to enable at-homeness for residents. Qualitative interpretive description methodology guided the design. The data generation was conducted in winter 2014-2015, when seven repetitive reflective group discussions with staff in a nursing home were held. The results show five patterns for how healthcare staff enabled at-homeness for the residents: Striving to know the resident, Showing respect for the resident's integrity, Creating and working in family-like relationships, Helping to find a new ordinariness and Preparing and making plans to ensure continuity. Nursing home staff seem to have collegial knowledge of how to enable at-homeness for the residents in a nursing home. Close relationships with respect for the resident's integrity stand out as enabling at-homeness. Copyright © 2017 Elsevier Inc. All rights reserved.

Factors predicting a home death among home palliative care recipients

PubMed Central

Ko, Ming-Chung; Huang, Sheng-Jean; Chen, Chu-Chieh; Chang, Yu-Ping; Lien, Hsin-Yi; Lin, Jia-Yi; Woung, Lin-Chung; Chan, Shang-Yih

2017-01-01

Abstract Awareness of factors affecting the place of death could improve communication between healthcare providers and patients and their families regarding patient preferences and the feasibility of dying in the preferred place. This study aimed to evaluate factors predicting home death among home palliative care recipients. This is a population-based study using a national representative sample retrieved from the National Health Insurance Research Database. Subjects receiving home palliative care, from 2010 to 2012, were analyzed to evaluate the association between a home death and various characteristics related to illness, individual, and health care utilization. A multiple-logistic regression model was used to assess the independent effect of various characteristics on the likelihood of a home death. The overall rate of a home death for home palliative care recipients was 43.6%. Age; gender; urbanization of the area where the patients lived; illness; the total number of home visits by all health care professionals; the number of home visits by nurses; utilization of nasogastric tube, endotracheal tube, or indwelling urinary catheter; the number of emergency department visits; and admission to intensive care unit in previous 1 year were not significantly associated with the risk of a home death. Physician home visits increased the likelihood of a home death. Compared with subjects without physician home visits (31.4%) those with 1 physician home visit (53.0%, adjusted odds ratio [AOR]: 3.23, 95% confidence interval [CI]: 1.93–5.42) and those with ≥2 physician home visits (43.9%, AOR: 2.23, 95% CI: 1.06–4.70) had higher likelihood of a home death. Compared with subjects with hospitalization 0 to 6 times in previous 1 year, those with hospitalization ≥7 times in previous 1 year (AOR: 0.57, 95% CI: 0.34–0.95) had lower likelihood of a home death. Among home palliative care recipients, physician home visits increased the likelihood of a home death

PAM-Dependent Target DNA Recognition and Cleavage by C2c1 CRISPR-Cas Endonuclease

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

Yang, Hui; Gao, Pu; Rajashankar, Kanagalaghatta R.

C2c1 is a newly identified guide RNA-mediated type V-B CRISPR-Cas endonuclease that site-specifically targets and cleaves both strands of target DNA. We have determined crystal structures of Alicyclobacillus acidoterrestris C2c1 (AacC2c1) bound to sgRNA as a binary complex and to target DNAs as ternary complexes, thereby capturing catalytically competent conformations of AacC2c1 with both target and non-target DNA strands independently positioned within a single RuvC catalytic pocket. Moreover, C2c1-mediated cleavage results in a staggered seven-nucleotide break of target DNA. crRNA adopts a pre-ordered five-nucleotide A-form seed sequence in the binary complex, with release of an inserted tryptophan, facilitating zippering upmore » of 20-bp guide RNA:target DNA heteroduplex on ternary complex formation. Notably, the PAM-interacting cleft adopts a “locked” conformation on ternary complex formation. Structural comparison of C2c1 ternary complexes with their Cas9 and Cpf1 counterparts highlights the diverse mechanisms adopted by these distinct CRISPR-Cas systems, thereby broadening and enhancing their applicability as genome editing tools.« less

Receptor-Mediated Delivery of CRISPR-Cas9 Endonuclease for Cell-Type-Specific Gene Editing.

PubMed

Rouet, Romain; Thuma, Benjamin A; Roy, Marc D; Lintner, Nathanael G; Rubitski, David M; Finley, James E; Wisniewska, Hanna M; Mendonsa, Rima; Hirsh, Ariana; de Oñate, Lorena; Compte Barrón, Joan; McLellan, Thomas J; Bellenger, Justin; Feng, Xidong; Varghese, Alison; Chrunyk, Boris A; Borzilleri, Kris; Hesp, Kevin D; Zhou, Kaihong; Ma, Nannan; Tu, Meihua; Dullea, Robert; McClure, Kim F; Wilson, Ross C; Liras, Spiros; Mascitti, Vincent; Doudna, Jennifer A

2018-05-30

CRISPR-Cas RNA-guided endonucleases hold great promise for disrupting or correcting genomic sequences through site-specific DNA cleavage and repair. However, the lack of methods for cell- and tissue-selective delivery currently limits both research and clinical uses of these enzymes. We report the design and in vitro evaluation of S. pyogenes Cas9 proteins harboring asialoglycoprotein receptor ligands (ASGPrL). In particular, we demonstrate that the resulting ribonucleoproteins (Cas9-ASGPrL RNP) can be engineered to be preferentially internalized into cells expressing the corresponding receptor on their surface. Uptake of such fluorescently labeled proteins in liver-derived cell lines HEPG2 (ASGPr+) and SKHEP (control; diminished ASGPr) was studied by live cell imaging and demonstrates increased accumulation of Cas9-ASGPrL RNP in HEPG2 cells as a result of effective ASGPr-mediated endocytosis. When uptake occurred in the presence of a peptide with endosomolytic properties, we observed receptor-facilitated and cell-type specific gene editing that did not rely on electroporation or the use of transfection reagents. Overall, these in vitro results validate the receptor-mediated delivery of genome-editing enzymes as an approach for cell-selective gene editing and provide a framework for future potential applications to hepatoselective gene editing in vivo.

The HOME network: an Australian national initiative for home therapies.

PubMed

Chow, Josephine; Fortnum, Debbie; Moodie, Jo-Anne; Simmonds, Rosemary; Tomlins, Melinda

2013-01-01

Longer, more frequent dialysis at home can improve life expectancy for patients with chronic kidney disease. Increased use of home dialysis therapies also benefits the hospital system, allowing for more efficient allocation of clinic resources. However, the Australian and New Zealand Data Registry statistics highlight the low uptake of home haemodialysis and peritoneal dialysis across Australia. In August 2009, the Australia's HOME Network was established as a national initiative to engage and empower healthcare professionals working in the home dialysis specialty. The aim was to develop solutions to advocate for and ultimately increase the use of home therapies. This paper describes the development, achievement and future plan of the Australian HOME Network. Achievements to date include: a survey of HOME Network members to assess the current state of patient and healthcare professional-targeted education resources; development of two patient case studies and activities addressing how to overcome the financial burden experienced by patients on home dialysis. Future projects aim to improve patient and healthcare professional education, and advocacy for home dialysis therapies. The HOME Network is supporting healthcare professionals working in the home dialysis specialty to develop solutions and tools that will help to facilitate greater utilisation of home dialysis therapies. © 2013 European Dialysis and Transplant Nurses Association/European Renal Care Association.

Location, Location, Location: Characteristics and Services of Long-Stay Home Care Recipients in Retirement Homes Compared to Others in Private Homes and Long-Term Care Homes

PubMed Central

Sinn, Chi-Ling Joanna; Grinchenko, Galina; Blums, Jane; Peirce, Tom; Hirdes, John

2017-01-01

We examine recipients of publicly funded ongoing care in a single Ontario jurisdiction who reside in three different settings: long-stay home care patients in private homes and apartments, other patients in retirement homes and residents of long-term care homes, using interRAI assessment instruments. Among home care patients, those in retirement homes have higher proportions of dementia and moderate cognitive impairment, less supportive informal care systems as well as more personal care and nursing services above those provided by the public home care system, more frequent but shorter home support visits and lower than expected public home care expenditures. These lower expenditures may be because of efficiency of care delivery or by retirement homes providing some services otherwise provided by the public home care system. Although persons in each setting are mostly older adults with high degrees of frailty and medical complexity, long-term care home residents show distinctly higher needs. We estimate that 40% of retirement home residents are long-stay home care patients, and they comprise about one in six of this Community Care Access Centre's long-stay patients. PMID:28277206

Location, Location, Location: Characteristics and Services of Long-Stay Home Care Recipients in Retirement Homes Compared to Others in Private Homes and Long-Term Care Homes.

PubMed

Poss, Jeffrey W; Sinn, Chi-Ling Joanna; Grinchenko, Galina; Blums, Jane; Peirce, Tom; Hirdes, John

2017-02-01

We examine recipients of publicly funded ongoing care in a single Ontario jurisdiction who reside in three different settings: long-stay home care patients in private homes and apartments, other patients in retirement homes and residents of long-term care homes, using interRAI assessment instruments. Among home care patients, those in retirement homes have higher proportions of dementia and moderate cognitive impairment, less supportive informal care systems as well as more personal care and nursing services above those provided by the public home care system, more frequent but shorter home support visits and lower than expected public home care expenditures. These lower expenditures may be because of efficiency of care delivery or by retirement homes providing some services otherwise provided by the public home care system. Although persons in each setting are mostly older adults with high degrees of frailty and medical complexity, long-term care home residents show distinctly higher needs. We estimate that 40% of retirement home residents are long-stay home care patients, and they comprise about one in six of this Community Care Access Centre's long-stay patients. Copyright © 2017 Longwoods Publishing.

Construction of an easy-to-use CRISPR-Cas9 system by patching a newly designed EXIT circuit.

PubMed

Tang, Qiang; Lou, Chunbo; Liu, Shuang-Jiang

2017-01-01

Plasmid-borne genetic editing tools, including the widely used CRISPR-Cas9 system, have greatly facilitated bacterial programming to obtain novel functionalities. However, the lack of effective post-editing plasmid elimination methods impedes follow-up genetic manipulation or application. Conventional strategies including exposure to physical and chemical treatments, or exploiting temperature-sensitive replication origins have several drawbacks (e.g., they are limited for efficiency and are time-consuming). Therefore, the demand is apparent for easy and rapid elimination of the tool plasmids from their bacterial hosts after genetic manipulation. To bridge this gap, we designed a novel EXIT circuit with the homing endonuclease, which can be exploited for rapid and efficient elimination of various plasmids with diverse replication origins. As a proof of concept, we validated the EXIT circuit in Escherichia coli by harnessing homing endonuclease I- Sce I and its cleavage site. When integrated into multiple plasmids with different origins, the EXIT circuit allowed them to be eliminated from the host cells, simultaneously. By combining the widely used plasmid-borne CRISPR-Cas9 system and the EXIT circuit, we constructed an easy-to-use CRISPR-Cas9 system that eliminated the Cas9- and the single-guide RNA (sgRNA)-encoding plasmids in one-step. Within 3 days, we successfully constructed an atrazine-degrading E. coli strain, thus further demonstrating the advantage of this new CRISPR-Cas9 system for bacterial genome editing. Our novel EXIT circuit, which exploits the homing endonuclease I- Sce I, enables plasmid(s) with different replication origins to be eliminated from their host cells rapidly and efficiently. We also developed an easy-to-use CRISPR-Cas9 system with the EXIT circuit, and this new system can be widely applied to bacterial genome editing.

Endonuclease G is a novel determinant of cardiac hypertrophy and mitochondrial function

PubMed Central

McDermott-Roe, Chris; Ye, Junmei; Ahmed, Rizwan; Sun, Xi-Ming; Serafín, Anna; Ware, James; Bottolo, Leonardo; Muckett, Phil; Cañas, Xavier; Zhang, Jisheng; Rowe, Glenn C.; Buchan, Rachel; Lu, Han; Braithwaite, Adam; Mancini, Massimiliano; Hauton, David; Martí, Ramon; García-Arumí, Elena; Hubner, Norbert; Jacob, Howard; Serikawa, Tadao; Zidek, Vaclav; Papousek, Frantisek; Kolar, Frantisek; Cardona, Maria; Ruiz-Meana, Marisol; García-Dorado, David; Comella, Joan X; Felkin, Leanne E; Barton, Paul JR; Arany, Zoltan; Pravenec, Michal; Petretto, Enrico; Sanchis, Daniel; Cook, Stuart A.

2011-01-01

Left ventricular mass (LVM) is a highly heritable trait1 and an independent risk factor for all-cause mortality2. To date, genome-wide association studies (GWASs) have not identified the genetic factors underlying LVM variation3 and the regulatory mechanisms for blood pressure (BP)-independent cardiac hypertrophy remain poorly understood4,5. Unbiased systems-genetics approaches in the rat6,7 now provide a powerful complementary tool to GWAS and we applied integrative genomics to dissect a highly replicated, BP-independent LVM locus on rat chromosome 3p. We identified endonuclease G (Endog), previously implicated in apoptosis8 but not hypertrophy, as the gene at the locus and demonstrated loss-of-function mutation in Endog associated with increased LVM and impaired cardiac function. Inhibition of Endog in cultured cardiomyocytes resulted in an increase in cell size and hypertrophic biomarkers in the absence of pro-hypertrophic stimulation. Genome-wide network analysis unexpectedly inferred ENDOG in fundamental mitochondrial processes unrelated to apoptosis. We showed direct regulation of ENDOG by ERRα and PGC1α, master regulators of mitochondrial and cardiac function9,10,11, interaction of ENDOG with the mitochondrial genome and ENDOG-mediated regulation of mitochondrial mass. At baseline, Endog deleted mouse heart had depleted mitochondria, mitochondrial dysfunction and elevated reactive oxygen species (ROS), which was associated with enlarged and steatotic cardiomyocytes. Our studies establish further the link between mitochondrial dysfunction, ROS and heart disease and demonstrate a new role for Endog in maladaptive cardiac hypertrophy. PMID:21979051

Aromatic residues located close to the active center are essential for the catalytic reaction of flap endonuclease-1 from hyperthermophilic archaeon Pyrococcus horikoshii.

PubMed

Matsui, Eriko; Abe, Junko; Yokoyama, Hideshi; Matsui, Ikuo

2004-04-16

Flap endonuclease-1 (FEN-1) possessing 5'-flap endonuclease and 5'-->3' exonuclease activity plays important roles in DNA replication and repair. In this study, the kinetic parameters of mutants at highly conserved aromatic residues, Tyr33, Phe35, Phe79, and Phe278-Phe279, in the vicinity of the catalytic centers of FEN-1 were examined. The substitution of these aromatic residues with alanine led to a large reduction in kcat values, although these mutants retained Km values similar to that of the wild-type enzyme. Notably, the kcat of Y33A and F79A decreased 333-fold and 71-fold, respectively, compared with that of the wild-type enzyme. The aromatic residues Tyr33 and Phe79, and the aromatic cluster Phe278-Phe279 mainly contributed to the recognition of the substrates without the 3' projection of the upstream strand (the nick, 5'-recess-end, single-flap, and pseudo-Y substrates) for the both exo- and endo-activities, but played minor roles in recognizing the substrates with the 3' projection (the double flap substrate and the nick substrate with the 3' projection). The replacement of Tyr33, Phe79, and Phe278-Phe279, with non-charged aromatic residues, but not with aliphatic hydrophobic residues, recovered the kcat values almost fully for the substrates without the 3' projection of the upstream strand, suggesting that the aromatic groups of Tyr33, Phe79, and Phe278-Phe279 might be involved in the catalytic reaction, probably via multiple stacking interactions with nucleotide bases. The stacking interactions of Tyr33 and Phe79 might play important roles in fixing the template strand and the downstream strand, respectively, in close proximity to the active center to achieve the productive transient state leading to the hydrolysis.

Family and home characteristics correlate with mold in homes.

PubMed

Reponen, Tiina; Levin, Linda; Zheng, Shu; Vesper, Stephen; Ryan, Patrick; Grinshpun, Sergey A; LeMasters, Grace

2013-07-01

Previously, we demonstrated that infants residing in homes with higher Environmental Relative Moldiness Index were at greater risk for developing asthma by age seven. The purpose of this analysis was to identify the family and home characteristics associated with higher moldiness index values in infants' homes at age one. Univariate linear regression of each characteristic determined that family factors associated with moldiness index were race and income. Home characteristics associated with the moldiness index values were: air conditioning, carpet, age of the home, season of home assessment, and house dust mite allergen. Parental history of asthma, use of dehumidifier, visible mold, dog and cat allergen levels were not associated with moldiness index. Results of multiple linear regression showed that older homes had 2.9 units higher moldiness index (95% confidence interval [CI]=0.4, 5.4), whereas homes with central air conditioning had 2.5 units lower moldiness index (95% CI=-4.7, -0.4). In addition, higher dust mite allergen levels and carpeting were positively and negatively associated with higher moldiness index, respectively. Because older homes and lack of air conditioning were also correlated with race and lower income, whereas carpeting was associated with newer homes, the multivariate analyses suggests that lower overall socioeconomic position is associated with higher moldiness index values. This may lead to increased asthma risk in homes inhabited by susceptible, vulnerable population subgroups. Further, age of the home was a surrogate of income, race and carpeting in our population; thus the use of these factors should carefully be evaluated in future studies. Copyright © 2013 Elsevier Inc. All rights reserved.

Home health care

MedlinePlus

... Skilled nursing - home health; Skilled nursing - home care; Physical therapy - at home; Occupational therapy - at home; Discharge - ... and any medicines that you may be taking. Physical and occupational therapists can make sure your home ...

Targeted DNA Mutagenesis for the Cure of Chronic Viral Infections

PubMed Central

Schiffer, Joshua T.; Aubert, Martine; Weber, Nicholas D.; Mintzer, Esther; Stone, Daniel

2012-01-01

Human immunodeficiency virus type 1 (HIV-1), hepatitis B virus (HBV), and herpes simplex virus (HSV) have been incurable to date because effective antiviral therapies target only replicating viruses and do not eradicate latently integrated or nonreplicating episomal viral genomes. Endonucleases that can target and cleave critical regions within latent viral genomes are currently in development. These enzymes are being engineered with high specificity such that off-target binding of cellular DNA will be absent or minimal. Imprecise nonhomologous-end-joining (NHEJ) DNA repair following repeated cleavage at the same critical site may permanently disrupt translation of essential viral proteins. We discuss the benefits and drawbacks of three types of DNA cleavage enzymes (zinc finger endonucleases, transcription activator-like [TAL] effector nucleases [TALENs], and homing endonucleases [also called meganucleases]), the development of delivery vectors for these enzymes, and potential obstacles for successful treatment of chronic viral infections. We then review issues regarding persistence of HIV-1, HBV, and HSV that are relevant to eradication with genome-altering approaches. PMID:22718830

24 CFR 982.612 - Group home: State approval of group home.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 24 Housing and Urban Development 4 2012-04-01 2012-04-01 false Group home: State approval of group home. 982.612 Section 982.612 Housing and Urban Development REGULATIONS RELATING TO HOUSING AND URBAN... Types Group Home § 982.612 Group home: State approval of group home. A group home must be licensed...

24 CFR 982.612 - Group home: State approval of group home.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 24 Housing and Urban Development 4 2011-04-01 2011-04-01 false Group home: State approval of group home. 982.612 Section 982.612 Housing and Urban Development REGULATIONS RELATING TO HOUSING AND URBAN... Types Group Home § 982.612 Group home: State approval of group home. A group home must be licensed...

24 CFR 982.612 - Group home: State approval of group home.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 24 Housing and Urban Development 4 2010-04-01 2010-04-01 false Group home: State approval of group home. 982.612 Section 982.612 Housing and Urban Development Regulations Relating to Housing and Urban... Types Group Home § 982.612 Group home: State approval of group home. A group home must be licensed...

24 CFR 982.612 - Group home: State approval of group home.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 24 Housing and Urban Development 4 2014-04-01 2014-04-01 false Group home: State approval of group home. 982.612 Section 982.612 Housing and Urban Development REGULATIONS RELATING TO HOUSING AND URBAN... Types Group Home § 982.612 Group home: State approval of group home. A group home must be licensed...

24 CFR 982.612 - Group home: State approval of group home.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 24 Housing and Urban Development 4 2013-04-01 2013-04-01 false Group home: State approval of group home. 982.612 Section 982.612 Housing and Urban Development REGULATIONS RELATING TO HOUSING AND URBAN... Types Group Home § 982.612 Group home: State approval of group home. A group home must be licensed...

DOE Zero Energy Ready Home Case Study: Palo Duro Homes — Palo Duro Homes, Albuquerque, NM

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

none,

2014-09-01

This builder was honored for Most DOE Zero Energy Ready Homes Built in the 2014 Housing Innovation Awards. By July 2014, Palo Duro had completed 152 homes since the program began in 2013 (under the original program title DOE Challenge Home), all of them certified to the stringent efficiency requirements of DOE’s Zero Energy Ready Home program.

Low Energy Technology. A Unit of Instruction in Housing and Home Environment. Single Family Homes--Multi-Family Homes--Mobile Homes.

ERIC Educational Resources Information Center

Beaulieu, Barbara; And Others

This unit of instruction on selection and living styles for energy conservation in single-family and multi-family housing and mobile homes was designed for use by home economics teachers in Florida high schools and by home economics extension agents as they work with their clientele. It is one of a series of 11 instructional units (see note)…

DOE Zero Energy Ready Home Case Study: Green Extreme Homes & Carl Franklin Homes — First DOE Zero Energy Ready Home Retrofit, Garland, TX

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

none,

This builder was honored with an Affordable Builder award in the 2014 Housing Innovation Awards, for the first retrofit home certified to the DOE Zero Energy Ready home requirements.The 60-year-old, three-bedroom ranch home is expected to save its homeowner more than $1,000 a year in utility bills compared to a home built to the current 2009 International Energy Conservation Code.

Associations Between Home Death and the Use and Type of Care at Home.

PubMed

McEwen, Rebecca; Asada, Yukiko; Burge, Frederick; Lawson, Beverley

2018-01-01

Despite wishes for and benefits of home deaths, a discrepancy between preferred and actual location of death persists. Provision of home care may be an effective policy response to support home deaths. Using the population-based mortality follow-back study conducted in Nova Scotia, we investigated the associations between home death and formal care at home and between home death and the type of formal care at home. We found (1) the use of formal care at home at the end of life was associated with home death and (2) the use of formal home support services at home was associated with home death among those whose symptoms were well managed.

DOE Zero Energy Ready Home Case Study: Thrive Home Builders, Lowry Plan

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

Pacific Northwest National Laboratory

Thrive Home Builders built this 4,119-ft2 home at the Lowry development in Denver, Colorado, to the high-performance criteria of the U.S. Department of Energy’s Zero Energy Ready Home Program. Despite the dense positioning of the homes, mono-plane roof designs afforded plenty of space for the 8.68 kW of photovoltaic panels. With the PV, the home achieves a Home Energy Rating System (HERS) score of 4 and the home owners should enjoy energy bills of about $-11 a year. Without the PV, the home would score a HERS 38 (far lower than the HERS 80 to 100 of typical new homes).

Home Rx: The Health Benefits of Home Performance

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

Wilson, Jonathan; Jacobs, David; Reddy, Amanda

Evidence in a new, groundbreaking U.S. Department of Energy report, Home Rx: The Health Benefits of Home Performance, shows that home performance upgrades can improve the quality of a home’s indoor environment by reducing the prevalence of harmful indoor air pollutants and contaminants. Until recently, no systematic review of this evidence had been conducted, limiting full understanding of the link between home performance and health. This new report summarizes current knowledge and identifies research gaps. The design characteristics and results of each of the 40 studies considered in the report are summarized in a searchable matrix.

Mother and Home Visitor Personality Characteristics, the Mother-Home-Visitor Relationship, and Home Visit Intensity.

ERIC Educational Resources Information Center

Ispa, Jean; Sharp, Elizabeth; Brookes, Sheila; Wolfenstein, Miriam; Thornburg, Kathy; Fine, Mark; Lane, Valeri

Noting that families in home visiting early intervention programs receive only about half the number of intended visits, this research used quantitative and qualitative methods to investigate how personality and other factors affect the mother-home visitor relationship and thereby, influence home visit intensity. Participating in the study were 5…

Restriction endonuclease analysis as a taxonomic tool in the study of pig isolates belonging to the Australis serogroup of Leptospira interrogans.

PubMed Central

Ellis, W A; Montgomery, J M; Thiermann, A B

1991-01-01

Restriction endonuclease analysis was performed on DNAs from the type strains of the Australis serogroup of Leptospira interrogans by using 20 restriction enzymes, and the electrophoretic patterns obtained were compared with patterns obtained from 162 Australis serogroup isolates from pigs. It proved to be a quick and reliable method for typing such strains. All of the pig isolates were identified as either serovar bratislava or muenchen. It also showed differences at the subserovar level which may be important in (i) understanding the epidemiology of the Australis serogroup, (ii) the development of suitable vaccines, and (iii) pathogenesis and pathogenicity studies. Two genotypes (B2b and M2) accounted for 92% of isolates from aborted or stillborn piglets, while a third genotype (B2a) was the only one recovered from the brains of piglets with meningitis. Images PMID:1647408

Restriction endonuclease analysis as a taxonomic tool in the study of pig isolates belonging to the Australis serogroup of Leptospira interrogans.

PubMed

Ellis, W A; Montgomery, J M; Thiermann, A B

1991-05-01

Restriction endonuclease analysis was performed on DNAs from the type strains of the Australis serogroup of Leptospira interrogans by using 20 restriction enzymes, and the electrophoretic patterns obtained were compared with patterns obtained from 162 Australis serogroup isolates from pigs. It proved to be a quick and reliable method for typing such strains. All of the pig isolates were identified as either serovar bratislava or muenchen. It also showed differences at the subserovar level which may be important in (i) understanding the epidemiology of the Australis serogroup, (ii) the development of suitable vaccines, and (iii) pathogenesis and pathogenicity studies. Two genotypes (B2b and M2) accounted for 92% of isolates from aborted or stillborn piglets, while a third genotype (B2a) was the only one recovered from the brains of piglets with meningitis.

Predictors of Home Care Expenditures and Death at Home for Cancer Patients in an Integrated Comprehensive Palliative Home Care Pilot Program

PubMed Central

Howell, Doris M.; Abernathy, Tom; Cockerill, Rhonda; Brazil, Kevin; Wagner, Frank; Librach, Larry

2011-01-01

Purpose: Empirical understanding of predictors for home care service use and death at home is important for healthcare planning. Few studies have examined these predictors in the context of the publicly funded Canadian home care system. This study examined predictors for home care use and home death in the context of a “gold standard” comprehensive palliative home care program pilot in Ontario where patients had equal access to home care services. Methods: Secondary clinical and administrative data sources were linked using a unique identifier to examine multivariate factors (predisposing, enabling, need) on total home care expenditures and home death for a cohort of cancer patients enrolled in the HPCNet pilot. Results: Subjects with gastrointestinal symptoms (OR: 1.64; p=0.03) and those with higher income had increased odds of dying at home (OR: 1.14; p<0.001), whereas age, number of GP visits, gastrointestinal symptoms (i.e., nausea, vomiting, bowel obstruction) and eating problems (i.e., anorexia/cachexia) predicted home care expenditures. Conclusions: Predictors of home death found in earlier studies appeared less important in this comprehensive palliative home care pilot. An income effect for home death observed in this study requires examination in future controlled studies. Relevance: Access to palliative home care that is adequately resourced and organized to address the multiple domains of issues that patients/families experience at the end of life has the potential to enable home death and shift care appropriately from limited acute care resources. PMID:22294993

Development of HIHM (Home Integrated Health Monitor) for ubiquitous home healthcare.

PubMed

Kim, Jung Soo; Kim, Beom Oh; Park, Kwang Suk

2007-01-01

Home Integrated Health Monitor (HIHM) was developed for ubiquitous home healthcare. From quantitative analysis, we have elicited modal of chair. The HIHM could detect Electrocardiogram (ECG) and Photoplethysmography (PPG) non-intrusively. Also, it could estimate blood pressure (BP) non-intrusively, measure blood glucose and ear temperature. Detected signals and information were transmitted to home gateway and home server through Zigbee communication technology. Home server carried them to Healthcare Center, and specialists such as medical doctors could monitor by Internet. There was also feedback system. This device has a potential to study about ubiquitous home healthcare.

Home Energy Assessments

ScienceCinema

Dispenza, Jason

2017-12-27

A home energy assessment, also known as a home energy audit, is the first step to assess how much energy your home consumes and to evaluate what measures you can take to make your home more energy efficient. An assessment will show you problems that may, when corrected, save you significant amounts of money over time. This video shows some of the ways that a contractor may test your home during an assessment, and helps you understand how an assessment can help you move toward energy savings. Find out more at: http://www.energysavers.gov/your_home/energy_audits/index.cfm/mytopic=11160

The GAN Exonuclease or the Flap Endonuclease Fen1 and RNase HII Are Necessary for Viability of Thermococcus kodakarensis.

PubMed

Burkhart, Brett W; Cubonova, Lubomira; Heider, Margaret R; Kelman, Zvi; Reeve, John N; Santangelo, Thomas J

2017-07-01

Many aspects of and factors required for DNA replication are conserved across all three domains of life, but there are some significant differences surrounding lagging-strand synthesis. In Archaea , a 5'-to-3' exonuclease, related to both bacterial RecJ and eukaryotic Cdc45, that associates with the replisome specifically through interactions with GINS was identified and designated GAN (for G INS- a ssociated n uclease). Despite the presence of a well-characterized flap endonuclease (Fen1), it was hypothesized that GAN might participate in primer removal during Okazaki fragment maturation, and as a Cdc45 homologue, GAN might also be a structural component of an archaeal CMG (Cdc45, MCM, and GINS) replication complex. We demonstrate here that, individually, either Fen1 or GAN can be deleted, with no discernible effects on viability and growth. However, deletion of both Fen1 and GAN was not possible, consistent with both enzymes catalyzing the same step in primer removal from Okazaki fragments in vivo RNase HII has also been proposed to participate in primer processing during Okazaki fragment maturation. Strains with both Fen1 and RNase HII deleted grew well. GAN activity is therefore sufficient for viability in the absence of both RNase HII and Fen1, but it was not possible to construct a strain with both RNase HII and GAN deleted. Fen1 alone is therefore insufficient for viability in the absence of both RNase HII and GAN. The ability to delete GAN demonstrates that GAN is not required for the activation or stability of the archaeal MCM replicative helicase. IMPORTANCE The mechanisms used to remove primer sequences from Okazaki fragments during lagging-strand DNA replication differ in the biological domains. Bacteria use the exonuclease activity of DNA polymerase I, whereas eukaryotes and archaea encode a flap endonuclease (Fen1) that cleaves displaced primer sequences. RNase HII and the GINS-associated exonuclease GAN have also been hypothesized to assist in primer

Hospice use among nursing home and non-nursing home patients.

PubMed

Unroe, Kathleen T; Sachs, Greg A; Dennis, M E; Hickman, Susan E; Stump, Timothy E; Tu, Wanzhu; Callahan, Christopher M

2015-02-01

For nursing home patients, hospice use and associated costs have grown dramatically. A better understanding of hospice in all care settings, especially how patients move across settings, is needed to inform debates about appropriateness of use and potential policy reform. Our aim was to describe characteristics and utilization of hospice among nursing home and non-nursing home patients. Medicare, Medicaid and Minimum Data Set data, 1999-2008, were merged for 3,771 hospice patients aged 65 years and above from a safety net health system. Patients were classified into four groups who received hospice: 1) only in nursing homes; 2) outside of nursing homes; 3) crossover patients utilizing hospice in both settings; and 4) "near-transition" patients who received hospice within 30 days of a nursing home stay. Differences in demographics, hospice diagnoses and length of stay, utilization and costs are presented with descriptive statistics. Nursing home hospice patients were older, and more likely to be women and to have dementia (p < 0.0001). Nearly one-third (32.3 %) of crossover patients had hospice stays > 6 months, compared with the other groups (16 % of nursing home hospice only, 10.7 % of non-nursing home hospice and 7.6 % of those with near transitions) (p < 0.0001). Overall, 27.7 % of patients had a hospice stay <1 week, but there were marked differences between groups-48 % of near-transition patients vs. 7.4 % of crossover patients had these short hospice stays (p < 0.0001). Crossover and near-transition hospice patients had higher costs to Medicare compared to other groups (p < 0.05). Dichotomizing hospice users only into nursing home vs. non-nursing home patients is difficult, due to transitions across settings. Hospice patients with transitions accrue higher costs. The impact of changes to the hospice benefit on patients who live or move through nursing homes near the end of life should be carefully considered.

IV treatment at home

MedlinePlus

... venous catheter - home; Port - home; PICC line - home; Infusion therapy - home; Home health care - IV treatment ... is given quickly, all at once. A slow infusion, which means the medicine is given slowly over ...

77 FR 72738 - Contracts and Provider Agreements for State Home Nursing Home Care

Federal Register 2010, 2011, 2012, 2013, 2014

2012-12-06

... State Home Nursing Home Care AGENCY: Department of Veterans Affairs. ACTION: Interim final rule. SUMMARY... into contracts or provider agreements with State homes for the nursing home care of certain disabled... submitted in response to ``RIN 2900-AO57--Contracts and Provider Agreements for State Home Nursing Home Care...

Shape-selective recognition of DNA abasic sites by metallohelices: inhibition of human AP endonuclease 1

PubMed Central

Malina, Jaroslav; Scott, Peter; Brabec, Viktor

2015-01-01

Loss of a base in DNA leading to creation of an abasic (AP) site leaving a deoxyribose residue in the strand, is a frequent lesion that may occur spontaneously or under the action of various physical and chemical agents. Progress in the understanding of the chemistry and enzymology of abasic DNA largely relies upon the study of AP sites in synthetic duplexes. We report here on interactions of diastereomerically pure metallo–helical ‘flexicate’ complexes, bimetallic triple-stranded ferro-helicates [Fe2(NN-NN)3]4+ incorporating the common NN–NN bis(bidentate) helicand, with short DNA duplexes containing AP sites in different sequence contexts. The results show that the flexicates bind to AP sites in DNA duplexes in a shape-selective manner. They preferentially bind to AP sites flanked by purines on both sides and their binding is enhanced when a pyrimidine is placed in opposite orientation to the lesion. Notably, the Λ-enantiomer binds to all tested AP sites with higher affinity than the Δ-enantiomer. In addition, the binding of the flexicates to AP sites inhibits the activity of human AP endonuclease 1, which is as a valid anticancer drug target. Hence, this finding indicates the potential of utilizing well-defined metallo–helical complexes for cancer chemotherapy. PMID:25940617

Nursing Home Checklist

MedlinePlus

Nursing home checklist Name of nursing home: ____________________________________________________ Address: ________________________________________________________________ Phone number: __________________________________________________________ Date of visit: _____________________________________________________________ Basic information Yes No Notes Is the nursing home Medicare certified? Is the nursing ...

16 CFR 460.16 - What new home sellers must tell new home buyers.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 16 Commercial Practices 1 2011-01-01 2011-01-01 false What new home sellers must tell new home... LABELING AND ADVERTISING OF HOME INSULATION § 460.16 What new home sellers must tell new home buyers. If you are a new home seller, you must put the following information in every sales contract: The type...

16 CFR 460.16 - What new home sellers must tell new home buyers.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 16 Commercial Practices 1 2013-01-01 2013-01-01 false What new home sellers must tell new home... LABELING AND ADVERTISING OF HOME INSULATION § 460.16 What new home sellers must tell new home buyers. If you are a new home seller, you must put the following information in every sales contract: The type...

16 CFR 460.16 - What new home sellers must tell new home buyers.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 16 Commercial Practices 1 2010-01-01 2010-01-01 false What new home sellers must tell new home... LABELING AND ADVERTISING OF HOME INSULATION § 460.16 What new home sellers must tell new home buyers. If you are a new home seller, you must put the following information in every sales contract: The type...

16 CFR 460.16 - What new home sellers must tell new home buyers.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 16 Commercial Practices 1 2012-01-01 2012-01-01 false What new home sellers must tell new home... LABELING AND ADVERTISING OF HOME INSULATION § 460.16 What new home sellers must tell new home buyers. If you are a new home seller, you must put the following information in every sales contract: The type...

16 CFR 460.16 - What new home sellers must tell new home buyers.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 16 Commercial Practices 1 2014-01-01 2014-01-01 false What new home sellers must tell new home... LABELING AND ADVERTISING OF HOME INSULATION § 460.16 What new home sellers must tell new home buyers. If you are a new home seller, you must put the following information in every sales contract: The type...

NGA: GNS Home

Science.gov Websites

NGA Home NGA Home NGA Home NGA Banner NGA Banner GNS Survey GNS Survey Label GNS Survey Tooltip Home News What's New? RSS for Headlines What's Coming? GNS Survey GNS Search OGC Viewer Page Text Based names, etc. This page will function properly with most modern browsers. GNS Offered Services GNS SURVEY

DOE Zero Energy Ready Home Case Study: Sterling Brook Custom Homes — Village Park Eco Home, Double Park, TX

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

none,

This builder won a Custom Builder honor in the 2014 Housing Innovation Awards for this showcase home that serves as an energy-efficient model home for the custom home builder: 1,300 visitors toured the home, thousands more learned about the home’s advanced construction via the webpage, YouTube, Twitter, Facebook, Instagram, and Pinterest.

Nursing perception of patient transitions from hospitals to home with home health.

PubMed

Smith, Shannon Bright; Alexander, Judith W

2012-01-01

The study's purpose was to determine nurses' opinions of sending patients from the hospital to home with home health services. The study occurred in the Charleston, South Carolina, Tricounty area (Berkeley, Charleston, and Dorchester counties). Home health agencies and hospitals were invited to participate. The study used a survey design to gather information on nursing perceptions of current practices and needed changes to improve transition of patients. The population was nurses (licensed practical nurses (LPNs) and registered nurses (RNs)) employed at inpatient hospitals or home health agencies in the area. Thirty-four RNs responded with no LPNs respondents. Agency administrators/chief nursing officers agreed for their agencies to participate and distributed the survey using a Research Electronic Data Capture (REDCap) Internet-based survey tool. Using the survey results and information from a literature review, the study developed a list of propositions, which participating administrators reviewed, for improving transitions to home. Both home health and hospital nurses reported a need to improve the process of sending patients from hospital to home with home health services. This study provides hospitals and home health agencies with propositions to facilitate the establishment of a process to communicate effectively patients care needs and streamline the discharging patients from the hospital to home health care; thus, improving patient transition. Case managers and discharge planners will need interagency collaboration along with evidence-based interventions to transition patients from the hospital to home with home health services with various populations. Direct patient care nurses in both hospital and home health settings should share the same accountability as case managers to ensure successful transitions.

Home Health Compare: Find a Home Health Agency

MedlinePlus

... page could not be loaded. The Medicare.gov Home page currently does not fully support browsers with " ... widget - Select to show Back to top Footer Home A federal government website managed and paid for ...

[Pharmacotherapy in nursing homes].

PubMed

Kersten, Hege; Ruths, Sabine; Wyller, Torgeir Bruun

2009-09-10

There is a high risk of drug-related problems in nursing homes due to polypharmacy, multi-morbidity and age-related changes. We describe the drug use and compare the pharmacotherapy in two nursing homes with different staffing of physicians. We included 48 long-term patients from two nursing homes in Oslo; i.e. nursing home A (24 patients) and nursing home B (24 patients). A pharmacist recorded information on patients' drug use, identified and classified drug-related problems, and classified the drugs used according to their anticholinergic burden. Two physicians (with experience in geriatrics and nursing home medicine) assessed the clinical importance of the drug-related problems independently from each other. The physicians were blinded with respect to which nursing home the patients came from. Patients in nursing home A used a median (interquartile range [IQR]) of 7.0 (5.3-11.0) drugs, and those in nursing home B used 9.5 (8.0-12.8); the median difference was 2.0, 95% CI 1.0-4.0, p = 0.006). Patients also had lower anticholinergic drug scores in nursing home A (1.0 [0.0-2.0]) than in nursing home B (2.0 [2.0-3.8]); median difference 1.0, 95% CI 0.0-2.0, p = 0.009). Patients in home A also had lower numbers of drug-related problems (3.0 [2.0-4.0]) than those in home B (5.5 [3.3-8.0]); median difference 1.0, 85% CI 0.0-3.0, p = 0.007. No significant differences were found between the nursing homes with regard to patients' age, co-morbidity, kidney function, or dementia state, but nursing home A had a better staffing of physicians. The number of drugs used as well as the quality indicators varied considerably between the nursing homes assessed. Differences in physician staffing might be one reasonable explanation. Our study highlights the importance of systematic multidisciplinary medication reviews for quality improvement in nursing homes.

No Jobs Like Homes: Careers in Helping Home Buyers and Sellers

ERIC Educational Resources Information Center

Torpey, Elka

2013-01-01

Millions of people buy and sell homes each year. And because these transactions are often complex, many home buyers and sellers turn to workers who can help with the search or the sale--or both. From preparing to put a home on the market to filing the sales documents, many workers are involved in helping a home change hands. Other key industries…

HomeADL for adaptive ADL monitoring within smart homes.

PubMed

Hong, Xin; Nugent, Chris D; Finlay, Dewar D; Mulvenna, Maurice

2008-01-01

In this paper we present homeADL: a representation standard for an inference hierarchy of activities of daily living which may be monitored in a sensor equipped smart home. The approach allows a free exchange of ADL monitoring structures between different communities who share the same concern of providing high quality healthcare to the elderly. Its ability of matching different ADL protocols enables a mapping between an ADL protocol to a suitable smart home which makes an effective management of smart homes within a community hence, not only being able to satisfy an individual's healthcare requirements but also efficiently using monitoring resources at hand.

Home Use Tests

MedlinePlus

... Medical Devices Radiation-Emitting Products Vaccines, Blood & Biologics Animal & Veterinary Cosmetics Tobacco Products Medical Devices Home Medical Devices Products and Medical Procedures In Vitro Diagnostics Home Use Tests Home Use Tests Share Tweet Linkedin Pin it ...

Ethics and safety in home care: perspectives on home support workers.

PubMed

Storch, Janet; Curry, Cherie Geering; Stevenson, Lynn; Macdonald, Marilyn; Lang, Ariella

2014-03-01

Home support workers (HSWs) encounter unique safety issues in their provision of home care. These issues raise ethical concerns, affecting the care workers provide to seniors and other recipients. This paper is derived from a subproject of a larger Canada-wide study, Safety at Home: A Pan-Canadian Home Care Safety Study, released in June 2013 by the Canadian Patient Safety Institute. Semi-structured, face-to-face, audiotaped interviews were conducted with providers, clients and informal caregivers in British Columbia, Manitoba and New Brunswick to better understand their perceptions of patient safety in home care. Using the BC data only, we then compared our findings to findings of other BC studies focusing on safety in home care that were conducted over the past decade. Through our interviews and comparative analyses it became clear that HSWs experienced significant inequities in providing home care. Utilizing a model depicting concerns of and for HSWs developed by Craven and colleagues (2012), we were able to illustrate the physical, spatial, interpersonal and temporal concerns set in the context of system design that emphasized the ethical dilemmas of HSWs in home care. Our data suggested the necessity of adding a fifth domain, organizational (system design). In this paper, we issue a call for stronger advocacy for home care and improved collaboration and resource equity between institutional care and community care.

Hospital at home: home-based end of life care

PubMed Central

Shepperd, Sasha; Wee, Bee; Straus, Sharon E

2014-01-01

Background The policy in a number of countries is to provide people with a terminal illness the choice of dying at home. This policy is supported by surveys indicating that the general public and patients with a terminal illness would prefer to receive end of life care at home. Objectives To determine if providing home-based end of life care reduces the likelihood of dying in hospital and what effect this has on patients’ symptoms, quality of life, health service costs and care givers compared with inpatient hospital or hospice care. Search methods We searched the Cochrane Central Register of Controlled Trials (CENTRAL) (The Cochrane Library) to October 2009, Ovid MED-LINE(R) 1950 to March 2011, EMBASE 1980 to October 2009, CINAHL 1982 to October 2009 and EconLit to October 2009. We checked the reference lists of articles identified for potentially relevant articles. Selection criteria Randomised controlled trials, interrupted time series or controlled before and after studies evaluating the effectiveness of home-based end of life care with inpatient hospital or hospice care for people aged 18 years and older. Data collection and analysis Two authors independently extracted data and assessed study quality. We combined the published data for dichotomous outcomes using fixed-effect Mantel-Haenszel meta-analysis. When combining outcome data was not possible we presented the data in narrative summary tables. Main results We included four trials in this review. Those receiving home-based end of life care were statistically significantly more likely to die at home compared with those receiving usual care (RR 1.33, 95% CI 1.14 to 1.55, P = 0.0002; Chi 2 = 1.72, df = 2, P = 0.42, I2 = 0% (three trials; N=652)). We detected no statistically significant differences for functional status (measured by the Barthel Index), psychological well-being or cognitive status, between patients receiving home-based end of life care compared with those receiving standard care (which

Smart homes and home health monitoring technologies for older adults: A systematic review.

PubMed

Liu, Lili; Stroulia, Eleni; Nikolaidis, Ioanis; Miguel-Cruz, Antonio; Rios Rincon, Adriana

2016-07-01

Around the world, populations are aging and there is a growing concern about ways that older adults can maintain their health and well-being while living in their homes. The aim of this paper was to conduct a systematic literature review to determine: (1) the levels of technology readiness among older adults and, (2) evidence for smart homes and home-based health-monitoring technologies that support aging in place for older adults who have complex needs. We identified and analyzed 48 of 1863 relevant papers. Our analyses found that: (1) technology-readiness level for smart homes and home health monitoring technologies is low; (2) the highest level of evidence is 1b (i.e., one randomized controlled trial with a PEDro score ≥6); smart homes and home health monitoring technologies are used to monitor activities of daily living, cognitive decline and mental health, and heart conditions in older adults with complex needs; (3) there is no evidence that smart homes and home health monitoring technologies help address disability prediction and health-related quality of life, or fall prevention; and (4) there is conflicting evidence that smart homes and home health monitoring technologies help address chronic obstructive pulmonary disease. The level of technology readiness for smart homes and home health monitoring technologies is still low. The highest level of evidence found was in a study that supported home health technologies for use in monitoring activities of daily living, cognitive decline, mental health, and heart conditions in older adults with complex needs. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Home Care Services

MedlinePlus

Home care is care that allows a person with special needs stay in their home. It might be for people who are getting ... chronically ill, recovering from surgery, or disabled. Home care services include Personal care, such as help with ...

Attitudes of palliative home care physicians towards palliative sedation at home in Italy.

PubMed

Mercadante, Sebastiano; Masedu, Francesco; Mercadante, Alessandro; Marinangeli, Franco; Aielli, Federica

2017-05-01

Information about the attitudes towards palliative sedation (PS) at home is limited. The aim of this survey was to assess the attitudes of palliative care physicians in Italy regarding PS at home. A questionnaire was submitted to a sample of palliative care physicians, asking information about their activity and attitudes towards PS at home. This is a survey of home care physicians in Italy who were involved in end-of-life care decisions at home. One hundred and fifty participants responded. A large heterogeneity of home care organizations that generate some problems was found. Indications, intention and monitoring of PS seem to be appropriate, although some cultural and logistic conditions were limiting the use of PS. Specialized home care physicians are almost involved to start PS at home. Midazolam was seldom available at home and opioids were more frequently used. These data should prompt health care agencies to make a minimal set of drugs easily available for home care. Further research is necessary to compare attitudes in countries with different sociocultural profiles.

Bringing Your Baby Home

MedlinePlus

... for Educators Search English Español Bringing Your Baby Home KidsHealth / For Parents / Bringing Your Baby Home What's ... recall your baby's seemingly endless crying episodes. The Home Front Introducing your baby to others at home ...

24 CFR 982.610 - Group home: Who may reside in a group home.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 24 Housing and Urban Development 4 2014-04-01 2014-04-01 false Group home: Who may reside in a group home. 982.610 Section 982.610 Housing and Urban Development REGULATIONS RELATING TO HOUSING AND... Housing Types Group Home § 982.610 Group home: Who may reside in a group home. (a) An elderly person or a...

24 CFR 982.610 - Group home: Who may reside in a group home.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 24 Housing and Urban Development 4 2010-04-01 2010-04-01 false Group home: Who may reside in a group home. 982.610 Section 982.610 Housing and Urban Development Regulations Relating to Housing and... Housing Types Group Home § 982.610 Group home: Who may reside in a group home. (a) An elderly person or a...

24 CFR 982.610 - Group home: Who may reside in a group home.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 24 Housing and Urban Development 4 2013-04-01 2013-04-01 false Group home: Who may reside in a group home. 982.610 Section 982.610 Housing and Urban Development REGULATIONS RELATING TO HOUSING AND... Housing Types Group Home § 982.610 Group home: Who may reside in a group home. (a) An elderly person or a...

24 CFR 982.610 - Group home: Who may reside in a group home.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 24 Housing and Urban Development 4 2011-04-01 2011-04-01 false Group home: Who may reside in a group home. 982.610 Section 982.610 Housing and Urban Development REGULATIONS RELATING TO HOUSING AND... Housing Types Group Home § 982.610 Group home: Who may reside in a group home. (a) An elderly person or a...

24 CFR 982.610 - Group home: Who may reside in a group home.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 24 Housing and Urban Development 4 2012-04-01 2012-04-01 false Group home: Who may reside in a group home. 982.610 Section 982.610 Housing and Urban Development REGULATIONS RELATING TO HOUSING AND... Housing Types Group Home § 982.610 Group home: Who may reside in a group home. (a) An elderly person or a...

A roundtable discussion: home healthcare-not a hospital in the home.

PubMed

Logan, Mary K; Parker, Chuck; Gardner-Bonneau, Daryle; Treu, Denny; Keller, James; Winstel, Lisa; Weick-Brady, Mary; Kramer, Nancy; Cyrus, Reginald; Thiel, Scott; Lewis, Vicki R; Rogers, Wendy

2013-01-01

Home healthcare is vital for a large percentage of the population. According to data from the U.S. Food and Drug Administration (FDA) and the Centers for Disease Control (CDC), 7 million people in the United States receive home healthcare annually. The use of medical devices in the home and other nonclinical environments is increasing dramatically. By the year 2050, an estimated 27 million people will need continuing care in the home or in the community and not in a controlled clinical environment. 1 The FDA recently announced its Home Use Devices Initiative and issued the document, "Draft Guidance for Industry and FDA Staff-Design Considerations for Devices Intended for Home Use" on Dec. 12, 2012. 2 The Center for Devices and Radiological Health (CDRH) regulates medical devices, but that regulatory authority alone is not enough to ensure safe and effective use of devices in the home. To address these and other issues, AAMI and FDA will co-host a summit on healthcare technology in nonclinical settings Oct. 9-10, 2013.

Quality of Life in Group Homes and Older Persons' Homes

ERIC Educational Resources Information Center

Higgins, Laura; Mansell, Jim

2009-01-01

Older people with intellectual disabilities sometimes live in older people's homes rather than homes for people with intellectual disabilities. Little is known about their quality of life in these homes. A non-equivalent comparison group design was used to compare the quality of life of 59 people in three groups; older people without an…

A novel regulatory circuit in base excision repair involving AP endonuclease 1, Creb1 and DNA polymerase β

PubMed Central

Pei, De-Sheng; Yang, Xiao-Jie; Liu, Wei; Guikema, Jeroen E. J.; Schrader, Carol E.; Strauss, Phyllis R.

2011-01-01

DNA repair is required to maintain genome stability in stem cells and early embryos. At critical junctures, oxidative damage to DNA requires the base excision repair (BER) pathway. Since early zebrafish embryos lack the major polymerase in BER, DNA polymerase ß, repair proceeds via replicative polymerases, even though there is ample polb mRNA. Here, we report that Polb protein fails to appear at the appropriate time in development when AP endonuclease 1 (Apex), the upstream protein in BER, is knocked down. Because polb contains a Creb1 binding site, we examined whether knockdown of Apex affects creb1. Apex knockdown results in loss of Creb1 and Creb complex members but not Creb1 phosphorylation. This effect is independent of p53. Although both apex and creb1 mRNA rescue Creb1 and Polb after Apex knockdown, Apex is not a co-activator of creb1 transcription. This observation has broad significance, as similar results occur when Apex is inhibited in B cells from apex+/− mice. These results describe a novel regulatory circuit involving Apex, Creb1 and Polb and provide a mechanism for lethality of Apex loss in higher eukaryotes. PMID:21172930

Double-stranded endonuclease activity in Bacillus halodurans clustered regularly interspaced short palindromic repeats (CRISPR)-associated Cas2 protein.

PubMed

Nam, Ki Hyun; Ding, Fran; Haitjema, Charles; Huang, Qingqiu; DeLisa, Matthew P; Ke, Ailong

2012-10-19

The CRISPR (clustered regularly interspaced short palindromic repeats) system is a prokaryotic RNA-based adaptive immune system against extrachromosomal genetic elements. Cas2 is a universally conserved core CRISPR-associated protein required for the acquisition of new spacers for CRISPR adaptation. It was previously characterized as an endoribonuclease with preference for single-stranded (ss)RNA. Here, we show using crystallography, mutagenesis, and isothermal titration calorimetry that the Bacillus halodurans Cas2 (Bha_Cas2) from the subtype I-C/Dvulg CRISPR instead possesses metal-dependent endonuclease activity against double-stranded (ds)DNA. This activity is consistent with its putative function in producing new spacers for insertion into the 5'-end of the CRISPR locus. Mutagenesis and isothermal titration calorimetry studies revealed that a single divalent metal ion (Mg(2+) or Mn(2+)), coordinated by a symmetric Asp pair in the Bha_Cas2 dimer, is involved in the catalysis. We envision that a pH-dependent conformational change switches Cas2 into a metal-binding competent conformation for catalysis. We further propose that the distinct substrate preferences among Cas2 proteins may be determined by the sequence and structure in the β1-α1 loop.

Roles for the Rad27 Flap Endonuclease in Mitochondrial Mutagenesis and Double-Strand Break Repair in Saccharomyces cerevisiae.

PubMed

Nagarajan, Prabha; Prevost, Christopher T; Stein, Alexis; Kasimer, Rachel; Kalifa, Lidza; Sia, Elaine A

2017-06-01

The structure-specific nuclease, Rad27p/FEN1, plays a crucial role in DNA repair and replication mechanisms in the nucleus. Genetic assays using the rad27-∆ mutant have shown altered rates of DNA recombination, microsatellite instability, and point mutation in mitochondria. In this study, we examined the role of Rad27p in mitochondrial mutagenesis and double-strand break (DSB) repair in Saccharomyces cerevisiae Our findings show that Rad27p is essential for efficient mitochondrial DSB repair by a pathway that generates deletions at a region flanked by direct repeat sequences. Mutant analysis suggests that both exonuclease and endonuclease activities of Rad27p are required for its role in mitochondrial DSB repair. In addition, we found that the nuclease activities of Rad27p are required for the prevention of mitochondrial DNA (mtDNA) point mutations, and in the generation of spontaneous mtDNA rearrangements. Overall, our findings underscore the importance of Rad27p in the maintenance of mtDNA, and demonstrate that it participates in multiple DNA repair pathways in mitochondria, unlinked to nuclear phenotypes. Copyright © 2017 by the Genetics Society of America.

Facilitating home birth.

PubMed

Finigan, Valerie; Chadderton, Diane

2015-06-01

The birth of a baby is a family experience. However, in the United Kingdom birth often occurs outside the family environment, in hospital. Both home and hospital births have risks and benefits, but research shows that, for most women, it is as safe to give birth at home as it is in hospital. Women report home-birth to be satisfying with lowered risks of intervention and less likelihood of being separated from their family. It is also more cost effective for the National Health Service. Yet, whilst midwives are working hard to promote home birth as an option, it remains controversial. The aim of this paper is to raise awareness of the safety of home birth and the needs of women and midwives when a home birth is chosen. It provides an overview of care required and the role of the midwife in the ensuring care is woman-centred and personalised.

Hospice and nursing homes.

PubMed

Castle, N G

1999-01-01

In this article a descriptive analysis of nursing homes with special care hospice units is provided. These are compared to nursing homes with other special care units and to nursing homes without any special care units. An analysis of the determinants of nursing homes with special care hospice units is also provided. Factors such as ownership, staffing levels, having other special care units, case-mix intensity, competitiveness of the nursing home market, and the state Medicaid reimbursement rate structure are examined. Finally, the influence of policies on hospice care in nursing homes is discussed.

Snails home

NASA Astrophysics Data System (ADS)

Dunstan, D. J.; Hodgson, D. J.

2014-06-01

Many gardeners and horticulturalists seek non-chemical methods to control populations of snails. It has frequently been reported that snails that are marked and removed from a garden are later found in the garden again. This phenomenon is often cited as evidence for a homing instinct. We report a systematic study of the snail population in a small suburban garden, in which large numbers of snails were marked and removed over a period of about 6 months. While many returned, inferring a homing instinct from this evidence requires statistical modelling. Monte Carlo techniques demonstrate that movements of snails are better explained by drift under the influence of a homing instinct than by random diffusion. Maximum likelihood techniques infer the existence of two groups of snails in the garden: members of a larger population that show little affinity to the garden itself, and core members of a local garden population that regularly return to their home if removed. The data are strongly suggestive of a homing instinct, but also reveal that snail-throwing can work as a pest management strategy.

Ultrasensitive electrochemical biosensor for detection of DNA from Bacillus subtilis by coupling target-induced strand displacement and nicking endonuclease signal amplification.

PubMed

Hu, Yuhua; Xu, Xueqin; Liu, Qionghua; Wang, Ling; Lin, Zhenyu; Chen, Guonan

2014-09-02

A simple, ultrasensitive, and specific electrochemical biosensor was designed to determine the given DNA sequence of Bacillus subtilis by coupling target-induced strand displacement and nicking endonuclease signal amplification. The target DNA (TD, the DNA sequence from the hypervarient region of 16S rDNA of Bacillus subtilis) could be detected by the differential pulse voltammetry (DPV) in a range from 0.1 fM to 20 fM with the detection limit down to 0.08 fM at the 3s(blank) level. This electrochemical biosensor exhibits high distinction ability to single-base mismatch, double-bases mismatch, and noncomplementary DNA sequence, which may be expected to detect single-base mismatch and single nucleotide polymorphisms (SNPs). Moreover, the applicability of the designed biosensor for detecting the given DNA sequence from Bacillus subtilis was investigated. The result obtained by electrochemical method is approximately consistent with that by a real-time quantitative polymerase chain reaction detecting system (QPCR) with SYBR Green.

[Home blood transfusion].

PubMed

Gay, V; Prévôt, G; Amico, I; Bonnet, B; Mansard, M-O

2010-12-01

The development of alternatives to hospitalization including home medical care (HAD), an aging population and a more secure transfusion raises the question of the feasibility of home blood transfusion. The legislation allows the home blood transfusion under specified conditions, but when they are met, the texts on nursing care and the transfusion gesture may hamper this progress. We report our experience of 3 years: a protocol was established to do home blood transfusions by trained transfusion nurses from the HAD. Six patients were eligible for transfusion at home but only three of them could be treated at home. Moreover, since late 2009, the Nursing Department no longer allows this practice for legal reasons. At the same time, a questionnaire was sent to 224 HAD to find out about their practice on the subject. In the light of practices in different countries, earnings for the quality of life of the patient, lack of space in hospitals and the aging population, it seems essential to change the law to permit a rational transfusion, thoughtful, safe for the patient at home and for caregivers who are involved. Copyright © 2010 Elsevier Masson SAS. All rights reserved.

Home range and travels

USGS Publications Warehouse

Stickel, L.F.; King, John A.

1968-01-01

The concept of home range was expressed by Seton (1909) in the term 'home region,' which Burr (1940, 1943) clarified with a definition of home range and exemplified in a definitive study of Peromyscus in the field. Burt pointed out the ever-changing characteristics of home-range area and the consequent absence of boundaries in the usual sense--a finding verified by investigators thereafter. In the studies summarized in this paper, sizes of home ranges of Peromyscus varied within two magnitudes, approximately from 0.1 acre to ten acres, in 34 studies conducted in a variety of habitats from the seaside dunes of Florida to the Alaskan forests. Variation in sizes of home ranges was correlated with both environmental and physiological factors; with habitat it was conspicuous, both in the same and different regions. Food supply also was related to size of home range, both seasonally and in relation to habitat. Home ranges generally were smallest in winter and largest in spring, at the onset of the breeding season. Activity and size also were affected by changes in weather. Activity was least when temperatures were low and nights were bright. Effects of rainfall were variable. Sizes varied according to sex and age; young mice remained in the parents' range until they approached maturity, when they began to travel more widely. Adult males commonly had larger home ranges than females, although there were a number of exceptions. An inverse relationship between population density and size of home range was shown in several studies and probably is the usual relationship. A basic need for activity and exploration also appeared to influence size of home range. Behavior within the home range was discussed in terms of travel patterns, travels in relation to home sites and refuges, territory, and stability of size of home range. Travels within the home range consisted of repeated use of well-worn trails to sites of food, shelter, and refuge, plus more random exploratory travels

Loss of mitochondrial exo/endonuclease EXOG affects mitochondrial respiration and induces ROS-mediated cardiomyocyte hypertrophy.

PubMed

Tigchelaar, Wardit; Yu, Hongjuan; de Jong, Anne Margreet; van Gilst, Wiek H; van der Harst, Pim; Westenbrink, B Daan; de Boer, Rudolf A; Silljé, Herman H W

2015-01-15

Recently, a locus at the mitochondrial exo/endonuclease EXOG gene, which has been implicated in mitochondrial DNA repair, was associated with cardiac function. The function of EXOG in cardiomyocytes is still elusive. Here we investigated the role of EXOG in mitochondrial function and hypertrophy in cardiomyocytes. Depletion of EXOG in primary neonatal rat ventricular cardiomyocytes (NRVCs) induced a marked increase in cardiomyocyte hypertrophy. Depletion of EXOG, however, did not result in loss of mitochondrial DNA integrity. Although EXOG depletion did not induce fetal gene expression and common hypertrophy pathways were not activated, a clear increase in ribosomal S6 phosphorylation was observed, which readily explains increased protein synthesis. With the use of a Seahorse flux analyzer, it was shown that the mitochondrial oxidative consumption rate (OCR) was increased 2.4-fold in EXOG-depleted NRVCs. Moreover, ATP-linked OCR was 5.2-fold higher. This increase was not explained by mitochondrial biogenesis or alterations in mitochondrial membrane potential. Western blotting confirmed normal levels of the oxidative phosphorylation (OXPHOS) complexes. The increased OCR was accompanied by a 5.4-fold increase in mitochondrial ROS levels. These increased ROS levels could be normalized with specific mitochondrial ROS scavengers (MitoTEMPO, mnSOD). Remarkably, scavenging of excess ROS strongly attenuated the hypertrophic response. In conclusion, loss of EXOG affects normal mitochondrial function resulting in increased mitochondrial respiration, excess ROS production, and cardiomyocyte hypertrophy. Copyright © 2015 the American Physiological Society.

DOE Challenge Home Case Study: e2 Homes – Winter Park, Florida

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

none,

2013-01-01

This Challenge Home case study describes the first certified DOE Challenge Home as constructed by e2 Homes. Completed in May 2012, the “Wilson Residence” in Winter Park, Florida, is a 4,305-ft2 custom home that scores a HERS 57 without solar and a better than zero net-energy HERS -7 with solar.

Home Sweet Home: Parent and Home Environmental Factors in Adolescent Consumption of Sugar-Sweetened Beverages.

PubMed

Bogart, Laura M; Elliott, Marc N; Ober, Allison J; Klein, David J; Hawes-Dawson, Jennifer; Cowgill, Burton O; Uyeda, Kimberly; Schuster, Mark A

2017-07-01

Sugar-sweetened beverages (SSBs) are key contributors to obesity among youth. We investigated associations among parental and home-related factors (parental attitudes and consumption; home availability) regarding 3 types of SSBs-soda, sports drinks, and fruit-flavored drinks-with consumption of each type of SSB in a general school-based sample of adolescents. Data were collected across 3 school semesters, from 2009 to 2011. A total of 1313 seventh grade student-parent dyads participated. Students completed in-class surveys across 9 schools in a large Los Angeles school district; their parents completed telephone interviews. Youth were asked about their SSB consumption (soda, sports drinks, and fruit-flavored drinks), and parents were asked about their attitudes, consumption, and home availability of SSBs. We estimated expected rates of youth SSB consumption for hypothetical parents at very low (5th) and very high (95th) percentiles for home/parental risk factors (ie, they consumed little, had negative attitudes, and did not keep SSBs in the home; or they consumed a lot, had positive attitudes, and did keep SSBs in the home). Youth of lower-risk parents (at the 5th percentile) were estimated to drink substantially less of each type of beverage than did youth of higher-risk parents (at the 95th percentile). For example, youth with higher-risk parents averaged nearly double the SSB consumption of youth of lower-risk parents (2.77 vs 1.37 glasses on the previous day; overall model significance F 22,1312  = 3.91, P < .001). Results suggest a need to focus on parental and home environmental factors when intervening to reduce youths' SSB consumption. Copyright © 2017 Academic Pediatric Association. Published by Elsevier Inc. All rights reserved.

Recruitment and positioning determine the specific role of the XPF-ERCC1 endonuclease in interstrand crosslink repair.

PubMed

Klein Douwel, Daisy; Hoogenboom, Wouter S; Boonen, Rick Acm; Knipscheer, Puck

2017-07-14

XPF-ERCC1 is a structure-specific endonuclease pivotal for several DNA repair pathways and, when mutated, can cause multiple diseases. Although the disease-specific mutations are thought to affect different DNA repair pathways, the molecular basis for this is unknown. Here we examine the function of XPF-ERCC1 in DNA interstrand crosslink (ICL) repair. We used Xenopus egg extracts to measure both ICL and nucleotide excision repair, and we identified mutations that are specifically defective in ICL repair. One of these separation-of-function mutations resides in the helicase-like domain of XPF and disrupts binding to SLX4 and recruitment to the ICL A small deletion in the same domain supports recruitment of XPF to the ICL, but inhibited the unhooking incisions most likely by disrupting a second, transient interaction with SLX4. Finally, mutation of residues in the nuclease domain did not affect localization of XPF-ERCC1 to the ICL but did prevent incisions on the ICL substrate. Our data support a model in which the ICL repair-specific function of XPF-ERCC1 is dependent on recruitment, positioning and substrate recognition. © 2017 The Authors. Published under the terms of the CC BY 4.0 license.

A comparative study of cold- and warm-adapted Endonucleases A using sequence analyses and molecular dynamics simulations.

PubMed

Michetti, Davide; Brandsdal, Bjørn Olav; Bon, Davide; Isaksen, Geir Villy; Tiberti, Matteo; Papaleo, Elena

2017-01-01

The psychrophilic and mesophilic endonucleases A (EndA) from Aliivibrio salmonicida (VsEndA) and Vibrio cholera (VcEndA) have been studied experimentally in terms of the biophysical properties related to thermal adaptation. The analyses of their static X-ray structures was no sufficient to rationalize the determinants of their adaptive traits at the molecular level. Thus, we used Molecular Dynamics (MD) simulations to compare the two proteins and unveil their structural and dynamical differences. Our simulations did not show a substantial increase in flexibility in the cold-adapted variant on the nanosecond time scale. The only exception is a more rigid C-terminal region in VcEndA, which is ascribable to a cluster of electrostatic interactions and hydrogen bonds, as also supported by MD simulations of the VsEndA mutant variant where the cluster of interactions was introduced. Moreover, we identified three additional amino acidic substitutions through multiple sequence alignment and the analyses of MD-based protein structure networks. In particular, T120V occurs in the proximity of the catalytic residue H80 and alters the interaction with the residue Y43, which belongs to the second coordination sphere of the Mg2+ ion. This makes T120V an amenable candidate for future experimental mutagenesis.

The contribution of DNA apurinic/apyrimidinic endonuclease genotype and smoking habit to Taiwan lung cancer risk.

PubMed

Chen, Wei-Chun; Tsai, Chia-Wen; Hsia, Te-Chun; Chang, Wen-Shin; Lin, Liang-Yi; Liang, Shinn-Jye; Tu, Chih-Yen; Cheng, Wei-Erh; Chen, Hung-Jen; Wang, Shu-Ming; Bau, da-Tian

2013-06-01

To evaluate the association and interaction of genotypic polymorphism the gene for DNA-apurinic/apyrimidinic endonuclease (APEX1) with personal smoking habit and lung cancer risk in Taiwan, the polymorphic variants of APEX1, Asp(148)Glu (rs1130409), were analyzed in association with lung cancer risk, and their joint effect with personal smoking habits on lung cancer susceptibility was discussed. In this hospital-based case-control study, 358 patients with lung cancer and 716 cancer-free controls, frequency-matched by age and sex, were recruited and genotyped by polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP). The results showed that the percentages of TT, TG and GG APEX1 Asp(148)Glu genotypes were not significantly different at 43.0%, 41.1% and 15.9% in the lung cancer patient group and 39.9%, 46.1% and 14.0% in non-cancer control group, respectively. We further analyzed the genetic-lifestyle effects on lung cancer risk and found the contribution of APEX1 Asp(148)Glu genotypes to lung cancer susceptibility was neither enhanced in the cigarette smokers nor in the non-smokers (p=0.3550 and 0.8019, respectively). Our results provide evidence that the non-synonymous polymorphism of APEX1 Asp(148)Glu may not be directly associated with lung cancer risk, nor enhance the effects of smoking habit on lung cancer development.

Shape-selective recognition of DNA abasic sites by metallohelices: inhibition of human AP endonuclease 1.

PubMed

Malina, Jaroslav; Scott, Peter; Brabec, Viktor

2015-06-23

Loss of a base in DNA leading to creation of an abasic (AP) site leaving a deoxyribose residue in the strand, is a frequent lesion that may occur spontaneously or under the action of various physical and chemical agents. Progress in the understanding of the chemistry and enzymology of abasic DNA largely relies upon the study of AP sites in synthetic duplexes. We report here on interactions of diastereomerically pure metallo-helical 'flexicate' complexes, bimetallic triple-stranded ferro-helicates [Fe2(NN-NN)3](4+) incorporating the common NN-NN bis(bidentate) helicand, with short DNA duplexes containing AP sites in different sequence contexts. The results show that the flexicates bind to AP sites in DNA duplexes in a shape-selective manner. They preferentially bind to AP sites flanked by purines on both sides and their binding is enhanced when a pyrimidine is placed in opposite orientation to the lesion. Notably, the Λ-enantiomer binds to all tested AP sites with higher affinity than the Δ-enantiomer. In addition, the binding of the flexicates to AP sites inhibits the activity of human AP endonuclease 1, which is as a valid anticancer drug target. Hence, this finding indicates the potential of utilizing well-defined metallo-helical complexes for cancer chemotherapy. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Cost-effectiveness implications based on a comparison of nursing home and home health case mix.

PubMed Central

Kramer, A M; Shaughnessy, P W; Pettigrew, M L

1985-01-01

Case-mix differences between 653 home health care patients and 650 nursing home patients, and between 455 Medicare home health patients and 447 Medicare nursing home patients were assessed using random samples selected from 20 home health agencies and 46 nursing homes in 12 states in 1982 and 1983. Home health patients were younger, had shorter lengths of stay, and were less functionally disabled than nursing home patients. Traditional long-term care problems requiring personal care were more common among nursing home patients, whereas problems requiring skilled nursing services were more prevalent among home health patients. Considering Medicare patients only, nursing home patients were much more likely to be dependent in activities of daily living (ADLs) than home health patients. Medicare nursing home and home health patients were relatively similar in terms of long-term care problems, and differences in medical problems were less pronounced than between all nursing home and all home health patients. From the standpoint of cost-effectiveness, it would appear that home health care might provide a substitute for acute care hospital use at the end of a hospital stay, and appears to be a more viable option in the care of patients who are not severely disabled and do not have profound functional problems. The Medicare skilled nursing facility, however, is likely to continue to have a crucial role in posthospital care as the treatment modality of choice for individuals who require both highly skilled care and functional assistance. PMID:3932258

Healthy Homes Tools

ERIC Educational Resources Information Center

Peek, Gina; Lyon, Melinda; Russ, Randall

2012-01-01

Extension is focusing on healthy homes programming. Extension educators are not qualified to diagnose consumers' medical problems as they relate to housing. We cannot give medical advice. Instead, we can help educate consumers about home conditions that may affect their well-being. Extension educators need appropriate healthy homes tools to…

Does hospital at home for palliative care facilitate death at home? Randomised controlled trial

PubMed Central

Grande, Gunn E; Todd, Chris J; Barclay, Stephen I G; Farquhar, Morag C

1999-01-01

Objective To evaluate the impact on place of death of a hospital at home service for palliative care. Design Pragmatic randomised controlled trial. Setting Former Cambridge health district. Participants 229 patients referred to the hospital at home service; 43 randomised to control group (standard care), 186 randomised to hospital at home. Intervention Hospital at home versus standard care. Main outcome measures Place of death. Results Twenty five (58%) control patients died at home compared with 124 (67%) patients allocated to hospital at home. This difference was not significant; intention to treat analysis did not show that hospital at home increased the number of deaths at home. Seventy three patients randomised to hospital at home were not admitted to the service. Patients admitted to hospital at home were significantly more likely to die at home (88/113; 78%) than control patients. It is not possible to determine whether this was due to hospital at home itself or other characteristics of the patients admitted to the service. The study attained less statistical power than initially planned. Conclusion In a locality with good provision of standard community care we could not show that hospital at home allowed more patients to die at home, although neither does the study refute this. Problems relating to recruitment, attrition, and the vulnerability of the patient group make randomised controlled trials in palliative care difficult. While these difficulties have to be recognised they are not insurmountable with the appropriate resourcing and setting. Key messagesTerminally ill patients allocated to hospital at home were no more likely to die at home than patients receiving standard careAlthough the subsample of patients actually admitted to hospital at home did show a significant increase in likelihood of dying at home, whether this was due to the service itself or the characteristics of patients admitted to hospital at home could not be determinedThe need to

Executive Views of Home Economists in Home Equipment and Related Industries.

ERIC Educational Resources Information Center

Michael, Carol M.

1991-01-01

From 32 responses of supervisors (91% male) of 87 female home economists employed in industry, it appeared executives had fairly accurate understanding of home economists' training and qualifications. Although they believed home economists had qualities for career advancement, executives rated them lower than women with business degrees. (SK)

Cell-autonomous progeroid changes in conditional mouse models for repair endonuclease XPG deficiency

DOE PAGES

Barnhoorn, Sander; Uittenboogaard, Lieneke M.; Jaarsma, Dick; ...

2014-10-09

As part of the Nucleotide Excision Repair (NER) process, the endonuclease XPG is involved in repair of helix-distorting DNA lesions, but the protein has also been implicated in several other DNA repair systems, complicating genotype-phenotype relationship in XPG patients. Defects in XPG can cause either the cancer-prone condition xeroderma pigmentosum (XP) alone, or XP combined with the severe neurodevelopmental disorder Cockayne Syndrome (CS), or the infantile lethal cerebro-oculo-facio-skeletal (COFS) syndrome, characterized by dramatic growth failure, progressive neurodevelopmental abnormalities and greatly reduced life expectancy. Here, we present a novel (conditional) Xpg -/- mouse model which—in a C57BL6/FVB F1 hybrid genetic background—displaysmore » many progeroid features, including cessation of growth, loss of subcutaneous fat, kyphosis, osteoporosis, retinal photoreceptor loss, liver aging, extensive neurodegeneration, and a short lifespan of 4–5 months. We show that deletion of XPG specifically in the liver reproduces the progeroid features in the liver, yet abolishes the effect on growth or lifespan. In addition, specific XPG deletion in neurons and glia of the forebrain creates a progressive neurodegenerative phenotype that shows many characteristics of human XPG deficiency. Our findings therefore exclude that both the liver as well as the neurological phenotype are a secondary consequence of derailment in other cell types, organs or tissues (e.g. vascular abnormalities) and support a cell-autonomous origin caused by the DNA repair defect itself. In addition they allow the dissection of the complex aging process in tissue- and cell-type-specific components. Moreover, our data highlight the critical importance of genetic background in mouse aging studies, establish the Xpg -/- mouse as a valid model for the severe form of human XPG patients and segmental accelerated aging, and strengthen the link between DNA damage and aging.« less

Cell-autonomous progeroid changes in conditional mouse models for repair endonuclease XPG deficiency

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

Barnhoorn, Sander; Uittenboogaard, Lieneke M.; Jaarsma, Dick

As part of the Nucleotide Excision Repair (NER) process, the endonuclease XPG is involved in repair of helix-distorting DNA lesions, but the protein has also been implicated in several other DNA repair systems, complicating genotype-phenotype relationship in XPG patients. Defects in XPG can cause either the cancer-prone condition xeroderma pigmentosum (XP) alone, or XP combined with the severe neurodevelopmental disorder Cockayne Syndrome (CS), or the infantile lethal cerebro-oculo-facio-skeletal (COFS) syndrome, characterized by dramatic growth failure, progressive neurodevelopmental abnormalities and greatly reduced life expectancy. Here, we present a novel (conditional) Xpg -/- mouse model which—in a C57BL6/FVB F1 hybrid genetic background—displaysmore » many progeroid features, including cessation of growth, loss of subcutaneous fat, kyphosis, osteoporosis, retinal photoreceptor loss, liver aging, extensive neurodegeneration, and a short lifespan of 4–5 months. We show that deletion of XPG specifically in the liver reproduces the progeroid features in the liver, yet abolishes the effect on growth or lifespan. In addition, specific XPG deletion in neurons and glia of the forebrain creates a progressive neurodegenerative phenotype that shows many characteristics of human XPG deficiency. Our findings therefore exclude that both the liver as well as the neurological phenotype are a secondary consequence of derailment in other cell types, organs or tissues (e.g. vascular abnormalities) and support a cell-autonomous origin caused by the DNA repair defect itself. In addition they allow the dissection of the complex aging process in tissue- and cell-type-specific components. Moreover, our data highlight the critical importance of genetic background in mouse aging studies, establish the Xpg -/- mouse as a valid model for the severe form of human XPG patients and segmental accelerated aging, and strengthen the link between DNA damage and aging.« less

Command Home Page

Science.gov Websites

Home Naval Special Warfare Home Subscribe to Navy News Service Search Navy.mil Advanced Search Home coordinator, explains details of the Montgomery G.I. Bill for active-duty service members to Naval Special fees, yearly books and supplies, and a monthly housing allowance to qualified service members. U.S

At Home in the Office. A Guide for the Home Worker.

ERIC Educational Resources Information Center

Thomas, Neil; And Others

This guide provides information to persons interested in establishing a work-at-home program, specifically those in clerical or support staff positions who use modern automated office equipment. The text is divided into two sections. The Home Worker section provides a summary of the At Home in the Office Project, personality characteristics…

Effectiveness of Home Study.

ERIC Educational Resources Information Center

Diehl, Grover E.; And Others

Home study has enjoyed a slow but steady growth in popularity and acceptance. The growth of independent home study may be attributed to both the realities of the present educational environment and the consistently positive results of the home study method. At least one researcher has suggested that the initially slow growth of home study may have…

[Home chemotherapy].

PubMed

Ichihara, Toshiaki

2010-12-01

We report the case of a male gastric cancer patient who had undergone outpatient chemotherapy with TAXOTAL+TS-1 for adrenal and lung metastases.The disease was in progress.Next, we performed home chemotherapy with TAXOL.However, this chemotherapy also was not effective either.Therefore, the patient was started on Campto with the premedication including NaseaOD, GasterD and Decadron.The 17-course was performed in the period of 12 months.However, his condition did not improve.He experienced delirium and was hospitalized and the chemotherapy was discontinued.Later, his disease was advanced further and he died.Because of our close relationship with the general hospital, this patient had undergone home chemotherapy as long as 13 months, so that if a seamless cooperation was insured, chemotherapy could have been more safely and effectively performed at the patient's home.This study suggests that home chemotherapy is an important treatment modality.

Nursing Home Staffing and Quality under the Nursing Home Reform Act

ERIC Educational Resources Information Center

Zhang, Xinzhi; Grabowski, David C.

2004-01-01

Purpose: We examine whether the Nursing Home Reform Act (NHRA) improved nursing home staffing and quality. Design and Methods: Data from 5,092 nursing homes were linked across the 1987 Medicare/Medicaid Automated Certification System and the 1993 Online Survey, Certification and Reporting system. A dummy-year model was used to examine the effects…

Lessons Learned from Home Visiting with Home-Based Child Care Providers

ERIC Educational Resources Information Center

McCabe, Lisa A.; Peterson, Shira M.; Baker, Amy C.; Dumka, Marsha; Brach, Mary Jo; Webb, Diana

2011-01-01

Caring for Quality and Partners in Family Child Care are home visiting programs designed to improve the quality of home-based child care. This article describes the experiences of two different home visitors to demonstrate how programs such as these can help providers improve the overall quality of care, increase children's development, and lead…

DOE Zero Energy Ready Home Case Study: Amaris Homes, Afton Model

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

Pacific Northwest National Laboratory

Amaris Homes built this 3,734-ft2 home in Afton, Minnesota, to the performance criteria of the DOE Zero Energy Ready Home (ZERH) program. A high-efficiency gas boiler provides hot water for the zoned radiant floor system as well as for faucets and showers. A high-efficiency heat pump provides zoned cooling.

At-home and away-from-home dietary patterns and BMI z-scores in Brazilian adolescents.

PubMed

Cunha, Diana Barbosa; Bezerra, Ilana Nogueira; Pereira, Rosangela Alves; Sichieri, Rosely

2018-01-01

Away-from-home food intake has been associated with high rates of overweight among children and adolescents. However, there are no studies comparing at-home and away-from-home eating patterns among adolescents. The objective of this paper was to identify at-home and away-from-home dietary patterns among adolescents in Brazil, and to evaluate the relationship between these patterns and body mass index (BMI) z-scores. Data from the Brazilian National Dietary Survey 2008-2009 were analyzed in this cross-sectional study. Dietary intake was assessed by completion of written food records on two non-consecutive days. Five thousand two hundred sixty-six adolescents 10-19 years of age living in urban areas of Brazil were included in the analysis. Thirty-two food groups were examined by factor analysis, stratified by at-home and away-from-home eating. The associations between the food patterns and BMI z-scores were ascertained using linear regression analysis. In general, mean at-home food intake was greater than away-from-home food intake, but the ratio of away-from-home/at-home was greater than 30% for baked and deep-fried snacks, soft drinks, sandwiches, pizza, and desserts, and was lower than 10% for rice and beans. Three main similar dietary patterns were identified both at-home and away-from-home: the "Traditional pattern", the "Bread and Butter pattern" and the "Western pattern"; however, away-from-home patterns encompassed more overall food items. Only the at-home "Western pattern" was positively associated with BMI z-scores (β = 0.0006; p < 0.001). Our results indicate that unhealthy dietary pattern consumed at home is associated to BMI z-score, while away-from-home food consumption is not associated. Copyright © 2017 Elsevier Ltd. All rights reserved.

Strategy Guideline. Demonstration Home

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

Hunt, A.; Savage, C.

2012-12-01

This guideline will provide a general overview of the different kinds of demonstration home projects, a basic understanding of the different roles and responsibilities involved in the successful completion of a demonstration home, and an introduction into some of the lessons learned from actual demonstration home projects. Also, this guideline will specifically look at the communication methods employed during demonstration home projects. And lastly, we will focus on how to best create a communication plan for including an energy efficient message in a demonstration home project and carry that message to successful completion.

Strategy Guideline: Demonstration Home

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

Savage, C.; Hunt, A.

2012-12-01

This guideline will provide a general overview of the different kinds of demonstration home projects, a basic understanding of the different roles and responsibilities involved in the successful completion of a demonstration home, and an introduction into some of the lessons learned from actual demonstration home projects. Also, this guideline will specifically look at the communication methods employed during demonstration home projects. And lastly, we will focus on how to best create a communication plan for including an energy efficient message in a demonstration home project and carry that message to successful completion.

A comparison of home care clients and nursing home residents: can community based care keep the elderly and disabled at home?

PubMed

Shugarman, L R; Fries, B E; James, M

1999-01-01

Admission cohorts from the Michigan Medicaid Home and Community-Based Waiver program and Ohio nursing homes were compared on measures of resource utilization including a modified Resource Utilization Groups (RUG-III) system, Activities of Daily Living (ADLs), and overall case mix. We found that, contrary to previous research, the two samples were remarkably similar across RUG-III categories. However, the nursing home sample was more functionally impaired on measures of ADL functioning and overall case mix. Results of this study may inform policymakers and providers of the potential for maintaining the appropriate population in the home with government-funded home care.

Negotiating and valuing spaces: The discourse of space and 'home' in care homes.

PubMed

Kenkmann, Andrea; Poland, Fiona; Burns, Diane; Hyde, Paula; Killett, Anne

2017-01-01

This paper examines how space in care homes is experienced and negotiated by people who live and work in them. The analysis of qualitative data of five in-depth case studies of care homes in England revealed three key ways in which space is negotiated: a) the way in which values affect interactions inside versus outside the care home environment, b) the negotiation of boundaries and domains within the homes, and c) the sense of being at 'home'. The paper illuminates how the design of the buildings and organisational factors can reinforce or bridge dichotomies between inside and outside spaces. Residents' abilities to re-negotiate boundaries, domains and communal spaces within homes are shown to be affected by organisational factors such as priorities of staff members. Despite 'home' being a common discourse, the spaces within care homes were often organised, ordered and experienced as two distinct, co-present worlds: the dwelling place of residents and the workplace of staff. Crown Copyright © 2016. Published by Elsevier Ltd. All rights reserved.

Alert management for home healthcare based on home automation analysis.

PubMed

Truong, T T; de Lamotte, F; Diguet, J-Ph; Said-Hocine, F

2010-01-01

Rising healthcare for elder and disabled people can be controlled by offering people autonomy at home by means of information technology. In this paper, we present an original and sensorless alert management solution which performs multimedia and home automation service discrimination and extracts highly regular home activities as sensors for alert management. The results of simulation data, based on real context, allow us to evaluate our approach before application to real data.

Identification of ATM mutations using extended RT-PCR and restriction endonuclease fingerprinting, and elucidation of the repertoire of A-T mutations in Israel.

PubMed

Gilad, S; Khosravi, R; Harnik, R; Ziv, Y; Shkedy, D; Galanty, Y; Frydman, M; Levi, J; Sanal, O; Chessa, L; Smeets, D; Shiloh, Y; Bar-Shira, A

1998-01-01

Ataxia-telangiectasia (A-T) is an autosomal recessive disorder characterized by neurodegeneration, immunodeficiency, cancer predisposition, and radiation sensitivity. The responsible gene, ATM, has an extensive genomic structure and encodes a large transcript with a 9.2 kb open reading frame (ORF). A-T mutations are extremely variable and most of them are private. We streamlined a high throughput protocol for the search for ATM mutations. The entire ATM ORF is amplified in a single RT-PCR step requiring a minimal amount of RNA. The product can serve for numerous nested PCRs in which overlapping portions of the ORF are further amplified and subjected to restriction endonuclease fingerprinting (REF) analysis. Splicing errors are readily detectable during the initial amplification of each portion. Using this protocol, we identified 5 novel A-T mutations and completed the elucidation of the molecular basis of A-T in the Israeli population.

Homes away from Home.

ERIC Educational Resources Information Center

Hansen, Laurel D.; And Others

1993-01-01

Describes the construction of a variety of inexpensive, escape-proof, and safe insect homes--each complete with window, ventilation screen, and cover--so students can observe firsthand the intriguing world of insects. (PR)

Family and home characteristics correlate with mold in homes

EPA Science Inventory

Previously, we demonstrated that infants exposed to higher Environmental Relative Moldiness Index (ERMI) value homes were more likely to develop asthma by age seven. The purpose of this analysis was to determine what family and home characteristics were associated with higher ER...

Predicting nursing home placement among home- and community-based services program participants.

PubMed

Greiner, Melissa A; Qualls, Laura G; Iwata, Isao; White, Heidi K; Molony, Sheila L; Sullivan, M Terry; Burke, Bonnie; Schulman, Kevin A; Setoguchi, Soko

2014-12-01

Several states offer publicly funded-care management programs to prevent long-term care placement of high-risk Medicaid beneficiaries. Understanding participant risk factors and services that may prevent long-term care placement can facilitate efficient allocation of program resources. To develop a practical prediction model to identify participants in a home- and community-based services program who are at highest risk for long-term nursing home placement, and to examine participant-level and program-level predictors of nursing home placement. In a retrospective observational study, we used deidentified data for participants in the Connecticut Home Care Program for Elders who completed an annual assessment survey between 2005 and 2010. We analyzed data on patient characteristics, use of program services, and short-term facility admissions in the previous year. We used logistic regression models with random effects to predict nursing home placement. The main outcome measures were long-term nursing home placement within 180 days or 1 year of assessment. Among 10,975 study participants, 1249 (11.4%) had nursing home placement within 1 year of annual assessment. Risk factors included Alzheimer's disease (odds ratio [OR], 1.30; 95% CI, 1.18-1.43), money management dependency (OR, 1.33; 95% CI, 1.18-1.51), living alone (OR, 1.53; 95% CI, 1.31-1.80), and number of prior short-term skilled nursing facility stays (OR, 1.46; 95% CI, 1.31-1.62). Use of a personal care assistance service was associated with 46% lower odds of nursing home placement. The model C statistic was 0.76 in the validation cohort. A model using information from a home- and community-based service program had strong discrimination to predict risk of long-term nursing home placement and can be used to identify high-risk participants for targeted interventions.

Volume of home- and community-based services and time to nursing-home placement.

PubMed

Sands, Laura P; Xu, Huiping; Thomas, Joseph; Paul, Sudeshna; Craig, Bruce A; Rosenman, Marc; Doebbeling, Caroline C; Weiner, Michael

2012-01-01

The purpose of this study was to determine whether the volume of Home- and Community-Based Services (HCBS) that target Activities of Daily Living disabilities, such as attendant care, homemaking services, and home-delivered meals, increases recipients' risk of transitioning from long-term care provided through HCBS to long-term care provided in a nursing home. Data are from the Indiana Medicaid enrollment, claims, and Insite databases. Insite is the software system that was developed for collecting and reporting data for In-Home Service Programs. Enrollees in Indiana Medicaid's Aged and Disabled Waiver program were followed forward from time of enrollment to assess the association between the volume of attendant care, homemaking services, home-delivered meals, and related covariates, and the risk for nursing-home placement. An extension of the Cox proportional hazard model was computed to determine the cumulative hazard of nursing-home placement in the presence of death as a competing risk. Of the 1354 Medicaid HCBS recipients followed in this study, 17% did not receive any attendant care, homemaking services, or home-delivered meals. Among recipients who survived through 24 months after enrollment, one in five transitioned from HCBS to a nursing-home. Risk for nursing-home placement was significantly lower for each five-hour increment in personal care (HR=0.95, 95% CI=0.92-0.98) and homemaking services (HR=0.87, 95% CI=0.77-0.99). Future policies and practices that are focused on optimizing long-term care outcomes should consider that a greater volume of HCBS for an individual is associated with reduced risk of nursing-home placement.

Asthma Home Environment Checklist

EPA Pesticide Factsheets

This checklist guides home care visitors in identifying environmental asthma triggers most commonly found in homes. It includes sections on the building, home interior and room interior and provides low-cost action steps for remediation.

A resource perspective on the work-home interface: the work-home resources model.

PubMed

ten Brummelhuis, Lieke L; Bakker, Arnold B

2012-10-01

The objective of this article is to provide a theoretical framework explaining positive and negative work-home processes integrally. Using insights from conservation of resources theory, we explain how personal resources (e.g., time, energy, and mood) link demanding and resourceful aspects of one domain to outcomes in the other domain. The resulting work-home resources (W-HR) model describes work-home conflict as a process whereby demands in one domain deplete personal resources and impede accomplishments in the other domain. Enrichment is described as a process of resource accumulation: Work and home resources increase personal resources. Those personal resources, in turn, can be utilized to improve home and work outcomes. Moreover, our resource approach to the work-home interface allows us to address two other issues that have thus far lacked a solid theoretical foundation. The W-HR model also explains how conditional factors such as personality and culture may influence the occurrence of work-home conflict and enrichment. Furthermore, the model allows us to examine how work-home conflict and enrichment develop over time. Finally, the model provides useful insights for other psychology subdisciplines, such as gender studies and developmental psychology.

Smart homes, private homes? An empirical study of technology researchers' perceptions of ethical issues in developing smart-home health technologies.

PubMed

Birchley, Giles; Huxtable, Richard; Murtagh, Madeleine; Ter Meulen, Ruud; Flach, Peter; Gooberman-Hill, Rachael

2017-04-04

Smart-home technologies, comprising environmental sensors, wearables and video are attracting interest in home healthcare delivery. Development of such technology is usually justified on the basis of the technology's potential to increase the autonomy of people living with long-term conditions. Studies of the ethics of smart-homes raise concerns about privacy, consent, social isolation and equity of access. Few studies have investigated the ethical perspectives of smart-home engineers themselves. By exploring the views of engineering researchers in a large smart-home project, we sought to contribute to dialogue between ethics and the engineering community. Either face-to-face or using Skype, we conducted in-depth qualitative interviews with 20 early- and mid-career smart-home researchers from a multi-centre smart-home project, who were asked to describe their own experience and to reflect more broadly about ethical considerations that relate to smart-home design. With participants' consent, interviews were audio-recorded, transcribed and analysed using a thematic approach. Two overarching themes emerged: in 'Privacy', researchers indicated that they paid close attention to negative consequences of potential unauthorised information sharing in their current work. However, when discussing broader issues in smart-home design beyond the confines of their immediate project, researchers considered physical privacy to a lesser extent, even though physical privacy may manifest in emotive concerns about being watched or monitored. In 'Choice', researchers indicated they often saw provision of choice to end-users as a solution to ethical dilemmas. While researchers indicated that choices of end-users may need to be restricted for technological reasons, ethical standpoints that restrict choice were usually assumed and embedded in design. The tractability of informational privacy may explain the greater attention that is paid to it. However, concerns about physical privacy may

Beyond tRNA cleavage: novel essential function for yeast tRNA splicing endonuclease unrelated to tRNA processing

PubMed Central

Dhungel, Nripesh; Hopper, Anita K.

2012-01-01

Pre-tRNA splicing is an essential process in all eukaryotes. In yeast and vertebrates, the enzyme catalyzing intron removal from pre-tRNA is a heterotetrameric complex (splicing endonuclease [SEN] complex). Although the SEN complex is conserved, the subcellular location where pre-tRNA splicing occurs is not. In yeast, the SEN complex is located at the cytoplasmic surface of mitochondria, whereas in vertebrates, pre-tRNA splicing is nuclear. We engineered yeast to mimic the vertebrate cell biology and demonstrate that all three steps of pre-tRNA splicing, as well as tRNA nuclear export and aminoacylation, occur efficiently when the SEN complex is nuclear. However, nuclear pre-tRNA splicing fails to complement growth defects of cells with defective mitochondrial-located splicing, suggesting that the yeast SEN complex surprisingly serves a novel and essential function in the cytoplasm that is unrelated to tRNA splicing. The novel function requires all four SEN complex subunits and the catalytic core. A subset of pre-rRNAs accumulates when the SEN complex is restricted to the nucleus, indicating that the SEN complex moonlights in rRNA processing. Thus, findings suggest that selection for the subcellular distribution of the SEN complex may reside not in its canonical, but rather in a novel, activity. PMID:22391451

Crystal structure and MD simulation of mouse EndoV reveal wedge motif plasticity in this inosine-specific endonuclease

NASA Astrophysics Data System (ADS)

Nawaz, Meh Sameen; Vik, Erik Sebastian; Ronander, Mia Elise; Solvoll, Anne Marthe; Blicher, Pernille; Bjørås, Magnar; Alseth, Ingrun; Dalhus, Bjørn

2016-04-01

Endonuclease V (EndoV) is an enzyme with specificity for deaminated adenosine (inosine) in nucleic acids. EndoV from Escherichia coli (EcEndoV) acts both on inosines in DNA and RNA, whereas the human homolog cleaves only at inosines in RNA. Inosines in DNA are mutagenic and the role of EndoV in DNA repair is well established. In contrast, the biological function of EndoV in RNA processing is largely unexplored. Here we have characterized a second mammalian EndoV homolog, mouse EndoV (mEndoV), and show that mEndoV shares the same RNA selectivity as human EndoV (hEndoV). Mouse EndoV cleaves the same inosine-containing substrates as hEndoV, but with reduced efficiencies. The crystal structure of mEndoV reveals a conformation different from the hEndoV and prokaryotic EndoV structures, particularly for the conserved tyrosine in the wedge motif, suggesting that this strand separating element has some flexibility. Molecular dynamics simulations of mouse and human EndoV reveal alternative conformations for the invariant tyrosine. The configuration of the active site, on the other hand, is very similar between the prokaryotic and mammalian versions of EndoV.

Double-stranded Endonuclease Activity in Bacillus halodurans Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated Cas2 Protein*

PubMed Central

Nam, Ki Hyun; Ding, Fran; Haitjema, Charles; Huang, Qingqiu; DeLisa, Matthew P.; Ke, Ailong

2012-01-01

The CRISPR (clustered regularly interspaced short palindromic repeats) system is a prokaryotic RNA-based adaptive immune system against extrachromosomal genetic elements. Cas2 is a universally conserved core CRISPR-associated protein required for the acquisition of new spacers for CRISPR adaptation. It was previously characterized as an endoribonuclease with preference for single-stranded (ss)RNA. Here, we show using crystallography, mutagenesis, and isothermal titration calorimetry that the Bacillus halodurans Cas2 (Bha_Cas2) from the subtype I-C/Dvulg CRISPR instead possesses metal-dependent endonuclease activity against double-stranded (ds)DNA. This activity is consistent with its putative function in producing new spacers for insertion into the 5′-end of the CRISPR locus. Mutagenesis and isothermal titration calorimetry studies revealed that a single divalent metal ion (Mg2+ or Mn2+), coordinated by a symmetric Asp pair in the Bha_Cas2 dimer, is involved in the catalysis. We envision that a pH-dependent conformational change switches Cas2 into a metal-binding competent conformation for catalysis. We further propose that the distinct substrate preferences among Cas2 proteins may be determined by the sequence and structure in the β1–α1 loop. PMID:22942283

Making the Transition from Traditional to Home Schooling: Home School Family Motivations

ERIC Educational Resources Information Center

Anthony, Kenneth Vance; Burroughs, Susie

2010-01-01

This study examined the motivations of families that operate home schools. Four intact, religiously conservative families were interviewed and observed over one year. Findings showed that families were motivated by multiple factors to leave traditional schooling and begin home schooling. Additionally, the motivations to home school influenced the…

Structure and specificity of the RNA-guided endonuclease Cas9 during DNA interrogation, target binding and cleavage

PubMed Central

Josephs, Eric A.; Kocak, D. Dewran; Fitzgibbon, Christopher J.; McMenemy, Joshua; Gersbach, Charles A.; Marszalek, Piotr E.

2015-01-01

CRISPR-associated endonuclease Cas9 cuts DNA at variable target sites designated by a Cas9-bound RNA molecule. Cas9's ability to be directed by single ‘guide RNA’ molecules to target nearly any sequence has been recently exploited for a number of emerging biological and medical applications. Therefore, understanding the nature of Cas9's off-target activity is of paramount importance for its practical use. Using atomic force microscopy (AFM), we directly resolve individual Cas9 and nuclease-inactive dCas9 proteins as they bind along engineered DNA substrates. High-resolution imaging allows us to determine their relative propensities to bind with different guide RNA variants to targeted or off-target sequences. Mapping the structural properties of Cas9 and dCas9 to their respective binding sites reveals a progressive conformational transformation at DNA sites with increasing sequence similarity to its target. With kinetic Monte Carlo (KMC) simulations, these results provide evidence of a ‘conformational gating’ mechanism driven by the interactions between the guide RNA and the 14th–17th nucleotide region of the targeted DNA, the stabilities of which we find correlate significantly with reported off-target cleavage rates. KMC simulations also reveal potential methodologies to engineer guide RNA sequences with improved specificity by considering the invasion of guide RNAs into targeted DNA duplex. PMID:26384421

Paramedic-Initiated Home Care Referrals and Use of Home Care and Emergency Medical Services.

PubMed

Verma, Amol A; Klich, John; Thurston, Adam; Scantlebury, Jordan; Kiss, Alex; Seddon, Gayle; Sinha, Samir K

2018-01-01

We examined the association between paramedic-initiated home care referrals and utilization of home care, 9-1-1, and Emergency Department (ED) services. This was a retrospective cohort study of individuals who received a paramedic-initiated home care referral after a 9-1-1 call between January 1, 2011 and December 31, 2012 in Toronto, Ontario, Canada. Home care, 9-1-1, and ED utilization were compared in the 6 months before and after home care referral. Nonparametric longitudinal regression was performed to assess changes in hours of home care service use and zero-inflated Poisson regression was performed to assess changes in the number of 9-1-1 calls and ambulance transports to ED. During the 24-month study period, 2,382 individuals received a paramedic-initiated home care referral. After excluding individuals who died, were hospitalized, or were admitted to a nursing home, the final study cohort was 1,851. The proportion of the study population receiving home care services increased from 18.2% to 42.5% after referral, representing 450 additional people receiving services. In longitudinal regression analysis, there was an increase of 17.4 hours in total services per person in the six months after referral (95% CI: 1.7-33.1, p = 0.03). The mean number of 9-1-1 calls per person was 1.44 (SD 9.58) before home care referral and 1.20 (SD 7.04) after home care referral in the overall study cohort. This represented a 10% reduction in 9-1-1 calls (95% CI: 7-13%, p < 0.001) in Poisson regression analysis. The mean number of ambulance transports to ED per person was 0.91 (SD 8.90) before home care referral and 0.79 (SD 6.27) after home care referral, representing a 7% reduction (95% CI: 3-11%, p < 0.001) in Poisson regression analysis. When only the participants with complete paramedic and home care records were included in the analysis, the reductions in 9-1-1 calls and ambulance transports to ED were attenuated but remained statistically significant. Paramedic

Home Hemodialysis

MedlinePlus

... home hemodialysis: You do this three times a week for three to four hours or longer each time. You and your care partner are trained to do dialysis safely and to handle any problems that may come up. Training may take from several weeks to a few months. 2. Short daily home ...

Type III restriction endonucleases are heterotrimeric: comprising one helicase–nuclease subunit and a dimeric methyltransferase that binds only one specific DNA

PubMed Central

Butterer, Annika; Pernstich, Christian; Smith, Rachel M.; Sobott, Frank; Szczelkun, Mark D.; Tóth, Júlia

2014-01-01

Fundamental aspects of the biochemistry of Type III restriction endonucleases remain unresolved despite being characterized by numerous research groups in the past decades. One such feature is the subunit stoichiometry of these hetero-oligomeric enzyme complexes, which has important implications for the reaction mechanism. In this study, we present a series of results obtained by native mass spectrometry and size exclusion chromatography with multi-angle light scattering consistent with a 1:2 ratio of Res to Mod subunits in the EcoP15I, EcoPI and PstII complexes as the main holoenzyme species and a 1:1 stoichiometry of specific DNA (sDNA) binding by EcoP15I and EcoPI. Our data are also consistent with a model where ATP hydrolysis activated by recognition site binding leads to release of the enzyme from the site, dissociation from the substrate via a free DNA end and cleavage of the DNA. These results are discussed critically in the light of the published literature, aiming to resolve controversies and discuss consequences in terms of the reaction mechanism. PMID:24510100

Technology Solutions Case Study: Southern Energy Homes, First DOE Zero Energy Ready Manufactured Home

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

None

The country’s first Zero Energy Ready manufactured home that is certified by the U.S. Department of Energy (DOE) is up and running in Russellville, Alabama. The manufactured home was built by a partnership between Southern Energy Homes and the Advanced Residential Integrated Energy Solutions Collaborative (ARIES), which is a DOE Building America team. The effort was part of a three-home study including a standard-code manufactured home and an ENERGY STAR® manufactured home. Cooling-season results showed that the building used half the space-conditioning energy of a manufactured home built to the U.S. Department of Housing and Urban Development’s (HUD’s) Manufactured Homemore » Construction and Safety Standards. These standards are known collectively as the HUD Code, which is the building standard for all U.S. manufactured housing.« less

There is no place like @home!: The value of home consultations in paediatric rehabilitation.

PubMed

van Maren-Suir, I; Ketelaar, M; Brouns, B; van der Sanden, K; Verhoef, M

2018-07-01

Family-centred services (FCS) is widely regarded as the best practice approach in early interventions. Creating a therapeutic environment, which also stimulates collaboration between parents and service professionals, is a way to conform to the principles of FCS. The present paper describes the project entitled @home, involving the implementation of home consultations by a specialized team working with children aged 0-5 years at our rehabilitation centre in the Netherlands. The objectives of this article are to (a) describe the development and implementation of home consultations as part of regular care and (b) share the experiences of parents and service providers with home consultations. The implementation process was divided into 3 steps: (1) interviewing experts, (2) adjusting current rehabilitation trajectories, and (3) service providers offering consultations to children at home. The experiences with the home consultations were immediately incorporated in the system, making the implementation an iterative process. In 82% of the 133 home conducted consultations, the service professionals reported that it was more valuable to offer home consultations than seeing the child at the rehabilitation centre. The semistructured interviews revealed that parents and service providers found that they received and provided more tailored advice, perceived a more equal partnership between service professionals and parents, and reported that the home consultations provided a good natural therapeutic environment where a child can be itself and where the child performs best. By using the @home system based on the 3 service models, home consultations are now part of the regular paediatric rehabilitation system at our rehabilitation centre. © 2018 John Wiley & Sons Ltd.

The determinants of nursing home costs in Nebraska's proprietary nursing homes.

PubMed

Palm, D W; Nelson, S

1984-01-01

In the past few years nursing home care expenditures in Nebraska and the U.S. have been the fastest growing component of total health care expenditures. This rate of increase is particularly alarming in view of the fact that nursing home care is financed primarily by the Medicaid program or direct out-of-pocket payments. In fact, given the cutbacks in federal and state funds for this program, consumers will be forced to allocate a larger share of their income to meet the costs of nursing home care. Although nursing home expenditures have grown at an extremely rapid rate, relatively few empirical studies exist which analyze the cost function of nursing home providers. The purpose of this study is to identify factors which have directly influenced the cost of nursing home care in Nebraska and to evaluate the current Nebraska Medicaid reimbursement system in terms of its impact upon nursing home costs. The study was limited to a sample of 40 nursing homes in Nebraska which represents 42% of the total proprietary nursing homes in the state. The sample was limited to those facilities licensed only as an Intermediate Care Facility--I and they had to be receiving some Medicaid revenue. The data were averaged over the period of 1977-79, but the year of analysis corresponded to 1978. Multiple regression analysis was used to measure the effect of the hypothesized independent variables upon two different measures of cost--the average total cost per patient day and the average variable cost per patient day. In the first regression model 76% of the variance was explained and 71% was explained in the second equation. The results of this analysis are basically consistent with the findings of other studies and indicate that the number of staffing hours, patient mix, facility age, administrator experience and administrative intensity are significant determinants of nursing home costs. The most important finding from a policy perspective is that the current retrospective cost

Home Safety, Safe Behaviors of Elderly People, and Fall Accidents At Home

ERIC Educational Resources Information Center

Erkal, Sibel

2010-01-01

The present study analyzed home safety and safe behaviors against fall accidents of elderly people living at home. The study group comprised 121 people aged 65+ living in the catchment area of Ankara Mamak Halil Ulgen Health Center. Data were collected via a personal information form and Home-Screen Scale. Statistical analysis used an independent…

The Science of Home Automation

NASA Astrophysics Data System (ADS)

Thomas, Brian Louis

Smart home technologies and the concept of home automation have become more popular in recent years. This popularity has been accompanied by social acceptance of passive sensors installed throughout the home. The subsequent increase in smart homes facilitates the creation of home automation strategies. We believe that home automation strategies can be generated intelligently by utilizing smart home sensors and activity learning. In this dissertation, we hypothesize that home automation can benefit from activity awareness. To test this, we develop our activity-aware smart automation system, CARL (CASAS Activity-aware Resource Learning). CARL learns the associations between activities and device usage from historical data and utilizes the activity-aware capabilities to control the devices. To help validate CARL we deploy and test three different versions of the automation system in a real-world smart environment. To provide a foundation of activity learning, we integrate existing activity recognition and activity forecasting into CARL home automation. We also explore two alternatives to using human-labeled data to train the activity learning models. The first unsupervised method is Activity Detection, and the second is a modified DBSCAN algorithm that utilizes Dynamic Time Warping (DTW) as a distance metric. We compare the performance of activity learning with human-defined labels and with automatically-discovered activity categories. To provide evidence in support of our hypothesis, we evaluate CARL automation in a smart home testbed. Our results indicate that home automation can be boosted through activity awareness. We also find that the resulting automation has a high degree of usability and comfort for the smart home resident.

Smart Home Test Bed: Examining How Smart Homes Interact with the Power Grid

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

This fact sheet highlights the Smart Home Test Bed capability at the Energy Systems Integration Facility. The National Renewable Energy Laboratory (NREL) is working on one of the new frontiers of smart home research: finding ways for smart home technologies and systems to enhance grid operations in the presence of distributed, clean energy technologies such as photovoltaics (PV). To help advance this research, NREL has developed a controllable, flexible, and fully integrated Smart Home Test Bed.

Protect Your Home from Wildfire!

ERIC Educational Resources Information Center

PTA Today, 1994

1994-01-01

Homes in wooded areas or in the wildland/urban interface are at special risk for wildfire. The article provides a checklist of what to keep on hand to make homes safer from wildfire, focusing on vegetation around the home and maintenance of the yard and home. (SM)

Safety Risks Among Home Infusion Nurses and Other Home Health Care Providers

PubMed Central

Galligan, Catherine; Quinn, Margaret

2017-01-01

In the United States, home health care (HHC) is a rapidly growing industry and home infusion therapy is a rapidly growing market. HHC can present substantial occupational safety and health (OSH) risks. This article summarizes major OSH risks relevant to home infusion therapy by illustrating them through real-life scenarios collected systematically using qualitative research methods by the National Institute for Occupational Safety and Health-funded research projects at the University of Massachusetts Lowell. The need for home infusion therapy will continue to grow in the future, and safety interventions to prevent or minimize OSH risks are essential. PMID:28683000

Depression in Home-Based Care: The Role of the Home Health Nurse.

PubMed

Groh, Carla J; Dumlao, Manuel S

2016-01-01

Depression is a major health issue among older adults receiving home-based services yet is underdiagnosed and undertreated, which can result in negative health outcomes. Despite the recognized need for improved mental health services, significant gaps and barriers exist that contribute to less than optimal home-based depression management interventions. Home healthcare clinicians are well positioned to drive this effort for improving depression care with enhanced learning. Thus, the purpose of this article is to provide guidelines on improving depression care in homebound older adults based on four clinical functions central to home healthcare: screening, assessment, medication management, and patient/family education.

Development and evaluation of human AP endonuclease inhibitors in melanoma and glioma cell lines.

PubMed

Mohammed, M Z; Vyjayanti, V N; Laughton, C A; Dekker, L V; Fischer, P M; Wilson, D M; Abbotts, R; Shah, S; Patel, P M; Hickson, I D; Madhusudan, S

2011-02-15

Modulation of DNA base excision repair (BER) has the potential to enhance response to chemotherapy and improve outcomes in tumours such as melanoma and glioma. APE1, a critical protein in BER that processes potentially cytotoxic abasic sites (AP sites), is a promising new target in cancer. In the current study, we aimed to develop small molecule inhibitors of APE1 for cancer therapy. An industry-standard high throughput virtual screening strategy was adopted. The Sybyl8.0 (Tripos, St Louis, MO, USA) molecular modelling software suite was used to build inhibitor templates. Similarity searching strategies were then applied using ROCS 2.3 (Open Eye Scientific, Santa Fe, NM, USA) to extract pharmacophorically related subsets of compounds from a chemically diverse database of 2.6 million compounds. The compounds in these subsets were subjected to docking against the active site of the APE1 model, using the genetic algorithm-based programme GOLD2.7 (CCDC, Cambridge, UK). Predicted ligand poses were ranked on the basis of several scoring functions. The top virtual hits with promising pharmaceutical properties underwent detailed in vitro analyses using fluorescence-based APE1 cleavage assays and counter screened using endonuclease IV cleavage assays, fluorescence quenching assays and radiolabelled oligonucleotide assays. Biochemical APE1 inhibitors were then subjected to detailed cytotoxicity analyses. Several specific APE1 inhibitors were isolated by this approach. The IC(50) for APE1 inhibition ranged between 30 nM and 50 μM. We demonstrated that APE1 inhibitors lead to accumulation of AP sites in genomic DNA and potentiated the cytotoxicity of alkylating agents in melanoma and glioma cell lines. Our study provides evidence that APE1 is an emerging drug target and could have therapeutic application in patients with melanoma and glioma.

Building America Top Innovations 2012: Affordable High Performance in Production Homes: Artistic Homes

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

none,

2013-01-01

This Building America Top Innovations profile describes Artistic Homes, a successful New Mexico production builder, who went from code-minimum to under HERS 50 standard on every home, with optional PV upgrades to HERS 35 or true net zero on every home plan offered.

Home Economics Cooperative Education.

ERIC Educational Resources Information Center

Texas Tech. Univ., Lubbock. School of Home Economics.

Prepared by home economics instructional materials center staff, this handbook is for use by home economics cooperative education teacher-coordinators in planning vocational home economics gainful employment programs and courses on the high school level. Contents include: (1) general information on the program, (2) approved occupations for the…

The effect of Channeling on in-home utilization and subsequent nursing home care: a simultaneous equation perspective.

PubMed Central

Rabiner, D J; Stearns, S C; Mutran, E

1994-01-01

OBJECTIVE. This study explored the relationship between participation in a home/community-based long-term care case management intervention (known as the Channeling demonstration), use of formal in-home care, and subsequent nursing home utilization. STUDY DESIGN. Structural analysis of the randomized Channeling intervention was conducted to decompose the total effects of Channeling on nursing home use into direct and indirect effects. DATA COLLECTION METHOD. Secondary data analysis of the National Long-Term Care Data Set. PRINCIPAL FINDINGS. The use of formal in-home care, which was increased by the Channeling intervention, was positively associated with nursing home utilization at 12 months. However, the negative direct effect of Channeling on nursing home use was of sufficient magnitude to offset this positive indirect effect, so that a small but significant negative total effect of Channeling on subsequent nursing home utilization was found. CONCLUSIONS. This study shows why Channeling did not have a large total impact on nursing home utilization. The analysis did not provide evidence of direct substitution of in-home care for nursing home care because the direct reductions in nursing home utilization due to other aspects of Channeling (including, but not limited to case management) were substantially offset by the indirect increases in nursing home utilization associated with additional home care use. PMID:8002352

On the Design of Smart Homes: A Framework for Activity Recognition in Home Environment.

PubMed

Cicirelli, Franco; Fortino, Giancarlo; Giordano, Andrea; Guerrieri, Antonio; Spezzano, Giandomenico; Vinci, Andrea

2016-09-01

A smart home is a home environment enriched with sensing, actuation, communication and computation capabilities which permits to adapt it to inhabitants preferences and requirements. Establishing a proper strategy of actuation on the home environment can require complex computational tasks on the sensed data. This is the case of activity recognition, which consists in retrieving high-level knowledge about what occurs in the home environment and about the behaviour of the inhabitants. The inherent complexity of this application domain asks for tools able to properly support the design and implementation phases. This paper proposes a framework for the design and implementation of smart home applications focused on activity recognition in home environments. The framework mainly relies on the Cloud-assisted Agent-based Smart home Environment (CASE) architecture offering basic abstraction entities which easily allow to design and implement Smart Home applications. CASE is a three layered architecture which exploits the distributed multi-agent paradigm and the cloud technology for offering analytics services. Details about how to implement activity recognition onto the CASE architecture are supplied focusing on the low-level technological issues as well as the algorithms and the methodologies useful for the activity recognition. The effectiveness of the framework is shown through a case study consisting of a daily activity recognition of a person in a home environment.

Prediction of Advisability of Returning Home Using the Home Care Score

PubMed Central

Matsugi, Akiyoshi; Tani, Keisuke; Tamaru, Yoshiki; Yoshioka, Nami; Yamashita, Akira; Mori, Nobuhiko; Oku, Kosuke; Ikeda, Masashi; Nagano, Kiyoshi

2015-01-01

Purpose. The aim of this study was to assess whether the home care score (HCS), which was developed by the Ministry of Health and Welfare in Japan in 1992, is useful for the prediction of advisability of home care. Methods. Subjects living at home and in assisted-living facilities were analyzed. Binominal logistic regression analyses, using age, sex, the functional independence measure score, and the HCS, along with receiver operating characteristic curve analyses, were conducted. Findings/Conclusions. Only HCS was selected for the regression equation. Receiver operating characteristic curve analysis revealed that the area under the curve (0.9), sensitivity (0.82), specificity (0.83), and positive predictive value (0.84) for HCS were higher than those for the functional independence measure, indicating that the HCS is a powerful predictor for advisability of home care. Clinical Relevance. Comprehensive measurements of the condition of provided care and the activities of daily living of the subjects, which are included in the HCS, are required for the prediction of advisability of home care. PMID:26491568

The Impact of Certificate-of-Need Laws on Nursing Home and Home Health Care Expenditures.

PubMed

Rahman, Momotazur; Galarraga, Omar; Zinn, Jacqueline S; Grabowski, David C; Mor, Vincent

2016-02-01

Over the past two decades, nursing homes and home health care agencies have been influenced by several Medicare and Medicaid policy changes including the adoption of prospective payment for Medicare-paid postacute care and Medicaid-paid long-term home and community-based care reforms. This article examines how spending growth in these sectors was affected by state certificate-of-need (CON) laws, which were designed to limit the growth of providers and have remained unchanged for several decades. Compared with states without CON laws, Medicare and Medicaid spending in states with CON laws grew faster for nursing home care and more slowly for home health care. In particular, we observed the slowest growth in community-based care in states with CON for both the nursing home and home health industries. Thus, controlling for other factors, public postacute and long-term care expenditures in CON states have become dominated by nursing homes. © The Author(s) 2015.

The Impact of Certificate-of-Need Laws on Nursing Home and Home Health Care Expenditures

PubMed Central

Rahman, Momotazur; Galarraga, Omar; Zinn, Jacqueline S.; Grabowski, David C.; Mor, Vincent

2016-01-01

Over the past two decades, nursing homes and home health care agencies have been influenced by several Medicare and Medicaid policy changes including the adoption of prospective payment for Medicare-paid postacute care and Medicaid-paid long-term home and community-based care reforms. This article examines how spending growth in these sectors was affected by state certificate-of-need (CON) laws, which were designed to limit the growth of providers and have remained unchanged for several decades. Compared with states without CON laws, Medicare and Medicaid spending in states with CON laws grew faster for nursing home care and more slowly for home health care. In particular, we observed the slowest growth in community-based care in states with CON for both the nursing home and home health industries. Thus, controlling for other factors, public postacute and long-term care expenditures in CON states have become dominated by nursing homes. PMID:26223431

Home Schooling Goes Mainstream

ERIC Educational Resources Information Center

Gaither, Milton

2009-01-01

This article reports that while home schooling may have particular appeal to celebrities, over the last decade families of all kinds have embraced the practice for widely varying reasons: no longer is home schooling exclusive to Christian fundamentalism and the countercultural Left. Along with growing acceptance of home schooling nationally has…

Association of Discharge Home with Home Health Care and 30-day Readmission after Pancreatectomy

PubMed Central

Sanford, Dominic E; Olsen, Margaret A; Bommarito, Kerry M; Shah, Manish; Fields, Ryan C; Hawkins, William G; Jaques, David P; Linehan, David C

2014-01-01

Background We sought to determine if discharge home with home health care (HHC) is an independent predictor of increased readmission following pancreatectomy. Study Design We examined 30-day readmissions in patients undergoing pancreatectomy using the Healthcare Cost and Utilization Project State Inpatient Database for California from 2009 to 2011. Readmissions were categorized as severe or non-severe using the Modified Accordion Severity Grading System. Multivariable logistic regression models were used to examine the association of discharge home with HHC and 30-day readmission using discharge home without HHC as the reference group. Propensity score matching was used as an additional analysis to compare the rate of 30-day readmission between patients discharged home with HHC to patients discharged home without HHC. Results 3,573 patients underwent pancreatectomy and 752 (21.0%) were readmitted within 30 days of discharge. In a multivariable logistic regression model, discharge home with HHC was an independent predictor of increased 30-day readmission (OR=1.37; 95%CI=1.11-1.69, p=0.004). Using propensity score matching, patients who received HHC had a significantly increased rate of 30-day readmission compared to patients discharged home without HHC (24.3% vs 19.8%, p<0.001). Patients discharged home with HHC had a significantly increased rate of non-severe readmission compared to those discharged home without HHC by univariate comparison (19.2% vs 13.9%, p<0.001), but not severe readmission (6.4% vs 4.7%, p= 0.08). In multivariable logistic regression models, excluding patients discharged to facilities, discharge home with HHC was an independent predictor of increased non-severe readmissions (OR=1.41; 95%CI=1.11-1.79, p=0.005), but not severe readmissions (OR=1.31; 95%CI=0.88-1.93, p=0.18). Conclusions Discharge home with HHC following pancreatectomy is an independent predictor of increased 30-day readmission; specifically, these services are associated with

Home Schooling: Parents as Educators.

ERIC Educational Resources Information Center

Mayberry, Maralee; And Others

Acknowledging the growing trend to educate school-aged children at home, this book provides a detailed account of home schooling, providing a vision of home education that reflects its multidimensional nature. The book consists of seven chapters: (1) "Learning about Home Schools" describes the research study from which this book is drawn…

Prescribing quality for older people in Norwegian nursing homes and home nursing services using multidose dispensed drugs.

PubMed

Halvorsen, Kjell H; Granas, Anne Gerd; Engeland, Anders; Ruths, Sabine

2012-09-01

To examine and compare the quality of drug prescribing for older patients in nursing homes and home nursing services. Cross-sectional study comprising 11,254 patients aged ≥ 65 years in nursing homes (n = 2986) and home nursing services (n = 8268). Potentially inappropriate medications were identified by using the Norwegian General Practice criteria and drug-drug interactions through a Norwegian Web-based tool. The impact of care setting on exposure to selected drug groups, potentially inappropriate medications, and drug interactions was calculated, adjusting for patients' age, gender, and number of drugs used. Patients in nursing homes and home nursing services used on average 5.7 (SD = 2.6) multidose dispensed regular drugs. Twenty-six percent used at least one potentially inappropriate medication, 31% in nursing homes and 25% in home nursing services, p < .001. Concomitant use of three or more psychotropic and/or opioid drugs was the criterion most commonly identified in nursing homes (18%) and home nursing services (9%), p < .001. Compared with nursing homes, more patients in home nursing services used cardiovascular drugs and fewer patients used psychotropic drugs. Altogether, 8615 drug-drug interactions were identified in 55% of patients, 48% in nursing homes and 57% in home nursing services, p < .001. There are significant differences in the quality of drug prescribing in nursing homes compared with home nursing services. Explanations as to why these differences exist need to be further explored. Copyright © 2011 John Wiley & Sons, Ltd.

Population Health and Tailored Medical Care in the Home: the Roles of Home-Based Primary Care and Home-Based Palliative Care.

PubMed

Ritchie, Christine S; Leff, Bruce

2018-03-01

With the growth of value-based care, payers and health systems have begun to appreciate the need to provide enhanced services to homebound adults. Recent studies have shown that home-based medical services for this high-cost, high-need population reduce costs and improve outcomes. Home-based medical care services have two flavors that are related to historical context and specialty background-home-based primary care (HBPC) and home-based palliative care (HBPalC). Although the type of services provided by HBPC and HBPalC (together termed "home-based medical care") overlap, HBPC tends to encompass longitudinal and preventive care, while HBPalC often provides services for shorter durations focused more on distress management and goals of care clarification. Given workforce constraints and growing demand, both HBPC and HBPalC will benefit from working together within a population health framework-where HBPC provides care to all patients who have trouble accessing traditional office practices and where HBPalC offers adjunctive care to patients with high symptom burden and those who need assistance with goals clarification. Policy changes that support provision of medical care in the home, population health strategies that tailor home-based medical care to the specific needs of the patients and their caregivers, and educational initiatives to assure basic palliative care competence for all home-based medical providers will improve access and reduce illness burden to this important and underrecognized population. Copyright © 2017 American Academy of Hospice and Palliative Medicine. Published by Elsevier Inc. All rights reserved.

DOE Zero Energy Ready Home Case Study: Amaris Custom Homes, St. Paul, Minnesota

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

None

For this project, Amaris worked with U.S. Department of Energy (DOE) team, NorthernSTAR Building America Partnership, to develop the first Zero Energy Ready Home (ZERH) in Minnesota's cold climate using reasonable, cost-effective, and replicable construction materials and practices. The result is a passive solar, super-efficient 3542-ft2 walkout ranch-style home with all the creature comforts. Along with meeting ZERH standards, Amaris also achieved certifications for Leadership in Energy & Environmental Design for Homes v4, MN Green Path Emerald, and a Builders Association of the Twin Cities Reggie Award of Excellence. The home achieves a HERS score of 41 without photovoltaics; withmore » PV, the home achieves a HERS score of 5.« less

An Analysis of Home Energy Score and REM/Rate Energy Simulation Results for Homes in Three Climates

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

Merket, Noel D

Energy ratings and scores for homes attempt to give homeowners a understandable metric to compare the energy efficiency of homes. Two rating systems in the marketplace include RESNET's Home Energy Rating System (HERS) and DOE's Home Energy Score (HEScore) and include differing energy calculation methodologies. This report compares the energy predictions from both REM/Rate and Home Energy Score for populations of real homes in three climates and determines some features of homes that lead to the greatest differences between energy predictions.

Engineered selective plant male sterility through pollen-specific expression of the EcoRI restriction endonuclease.

PubMed

Millwood, Reginald J; Moon, Hong S; Poovaiah, Charleson R; Muthukumar, Balasubramaniam; Rice, John Hollis; Abercrombie, Jason M; Abercrombie, Laura L; Green, William Derek; Stewart, Charles Neal

2016-05-01

Unintended gene flow from transgenic plants via pollen, seed and vegetative propagation is a regulatory concern because of potential admixture in food and crop systems, as well as hybridization and introgression to wild and weedy relatives. Bioconfinement of transgenic pollen would help address some of these concerns and enable transgenic plant production for several crops where gene flow is an issue. Here, we demonstrate the expression of the restriction endonuclease EcoRI under the control of the tomato pollen-specific LAT52 promoter is an effective method for generating selective male sterility in Nicotiana tabacum (tobacco). Of nine transgenic events recovered, four events had very high bioconfinement with tightly controlled EcoRI expression in pollen and negligible-to-no expression other plant tissues. Transgenic plants had normal morphology wherein vegetative growth and reproductivity were similar to nontransgenic controls. In glasshouse experiments, transgenic lines were hand-crossed to both male-sterile and emasculated nontransgenic tobacco varieties. Progeny analysis of 16 000-40 000 seeds per transgenic line demonstrated five lines approached (>99.7%) or attained 100% bioconfinement for one or more generations. Bioconfinement was again demonstrated at or near 100% under field conditions where four transgenic lines were grown in close proximity to male-sterile tobacco, and 900-2100 seeds per male-sterile line were analysed for transgenes. Based upon these results, we conclude EcoRI-driven selective male sterility holds practical potential as a safe and reliable transgene bioconfinement strategy. Given the mechanism of male sterility, this method could be applicable to any plant species. © 2015 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

Comparison of Long-term Care in Nursing Homes Versus Home Health: Costs and Outcomes in Alabama.

PubMed

Blackburn, Justin; Locher, Julie L; Kilgore, Meredith L

2016-04-01

To compare acute care outcomes and costs among nursing home residents with community-dwelling home health recipients. A matched retrospective cohort study of Alabamians aged more than or equal to 65 years admitted to a nursing home or home health between March 31, 2007 and December 31, 2008 (N = 1,291 pairs). Medicare claims were compared up to one year after admission into either setting. Death, emergency department and inpatient visits, inpatient length of stay, and acute care costs were compared using t tests. Medicaid long-term care costs were compared for a subset of matched beneficiaries. After one year, 77.7% of home health beneficiaries were alive compared with 76.2% of nursing home beneficiaries (p < .001). Home health beneficiaries averaged 0.2 hospital visits and 0.1 emergency department visits more than nursing home beneficiaries, differences that were statistically significant. Overall acute care costs were not statistically different; home health beneficiaries' costs averaged $31,423, nursing home beneficiaries' $32,239 (p = .5032). Among 426 dual-eligible pairs, Medicaid long-term care costs averaged $4,582 greater for nursing home residents (p < .001). Using data from Medicare claims, beneficiaries with similar functional status, medical diagnosis history, and demographics had similar acute care costs regardless of whether they were admitted to a nursing home or home health care. Additional research controlling for exogenous factors relating to long-term care decisions is needed. © The Author 2014. Published by Oxford University Press on behalf of The Gerontological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Home Away from Home: A Toolkit for Planning Home Visiting Partnerships with Family, Friend, and Neighbor Caregivers

ERIC Educational Resources Information Center

Johnson-Staub, Christine; Schmit, Stephanie

2012-01-01

Home visiting is one tool used to prevent child abuse and improve child well-being by providing education and services in families' homes through parent education and connection to community resources. This toolkit provides state policymakers and advocates with strategies for extending and expanding access to state- or federally-funded home…

Home Is where You Draw Strength and Rest: The Meanings of Home for Houseless Young People

ERIC Educational Resources Information Center

Kidd, Sean A.; Evans, Josh D.

2011-01-01

This qualitative study examined the meanings ascribed to the construct "home" by 208 youths defined by mainstream society as "homeless". Youth narratives on the topic of home ranged across a continuum with home as state at one end (i.e., home is a state of mind, comprised of one's friends) and home as place at the other (i.e.,…

Pervasive Home Environments

NASA Astrophysics Data System (ADS)

Bull, P.; Limb, R.; Payne, R.

An increasing number of computers and other equipment, such as games consoles and multimedia appliances for the home, have networking capability. The rapid growth of broadband in the home is also fuelling the demand for people to network their homes. In the near future we will see a number of market sectors trying to 'own' the home by providing gateways either from the traditional ISP or from games and other service providers. The consumer is bombarded with attractive advertising to acquire the latest technological advances, but is left with a plethora of different appliances, which have a bewildering range of requirements and features in terms of networking, user interface, and higher-level communications protocols. In many cases, these are proprietary, preventing interworking. Such technical and usability anarchy confuses the consumer and could ultimately suppress market adoption.

Vascular access for home haemodialysis.

PubMed

Al Shakarchi, Julien; Day, C; Inston, N

2018-03-01

Home haemodialysis has been advocated due to improved quality of life. However, there are very little data on the optimum vascular access for it. A retrospective cohort study was carried on all patients who initiated home haemodialysis between 2011 and 2016 at a large university hospital. Access-related hospital admissions and interventions were used as primary outcome measures. Our cohort consisted of 74 patients. On initiation of home haemodialysis, 62 individuals were using an arteriovenous fistula as vascular access, while the remaining were on a tunnelled dialysis catheter. Of the 12 patients who started on a tunnelled dialysis catheter, 5 were subsequently converted to either an arteriovenous fistula ( n = 4) or an arteriovenous graft ( n = 1). During the period of home haemodialysis use, four arteriovenous fistula failed or thrombosed with patients continuing on home haemodialysis using an arteriovenous graft ( n = 3) or a tunnelled dialysis catheter ( n = 1). To maintain uninterrupted home haemodialysis, interventional rates were 0.32 per arteriovenous fistula/arteriovenous graft access-year and 0.4 per tunnelled dialysis catheter access-year. Hospital admission rates for patients on home haemodialysis were 0.33 per patient-year. Our study has shown that home haemodialysis can be safely and independently performed at home within a closely managed home haemodialysis programme. The authors also advocate the use of arteriovenous fistulas for this cohort of patients due to both low complication and intervention rates.

[Markerless DNA deletion based on Red recombination and in vivo I-Sec I endonuclease cleavage in Escherichia coli chromosome].

PubMed

Zhu, Meiqin; Yu, Jian; Zhou, Changlin; Fang, Hongqing

2016-01-01

Red-based recombineering has been widely used in Escherichia coli genome modification through electroporating PCR fragments into electrocompetent cells to replace target sequences. Some mutations in the PCR fragments may be brought into the homologous regions near the target. To solve this problem in markeless gene deletion we developed a novel method characterized with two-step recombination and a donor plasmid. First, generated by PCR a linear DNA cassette which comprises a I-Sec I site-containing marker gene and homologous arms was electroporated into cells for marker-substitution deletion of the target sequence. Second, after a donor plasmid carrying the I-Sec I site-containing fusion homologous arm was chemically transformed into the marker-containing cells, the fusion arms and the marker was simultaneously cleaved by I-Sec I endonuclease and the marker-free deletion was stimulated by double-strand break-mediated intermolecular recombination. Eleven nonessential regions in E. coli DH1 genome were sequentially deleted by our method, resulting in a 10.59% reduced genome size. These precise deletions were also verified by PCR sequencing and genome resequencing. Though no change in the growth rate on the minimal medium, we found the genome-reduced strains have some alteration in the acid resistance and for the synthesis of lycopene.

A fluorescence method for detection of DNA and DNA methylation based on graphene oxide and restriction endonuclease HpaII.

PubMed

Wei, Wei; Gao, Chunyan; Xiong, Yanxiang; Zhang, Yuanjian; Liu, Songqin; Pu, Yuepu

2015-01-01

DNA methylation plays an important role in many biological events and is associated with various diseases. Most traditional methods for detection of DNA methylation are based on the complex and expensive bisulfite method. In this paper, we report a novel fluorescence method to detect DNA and DNA methylation based on graphene oxide (GO) and restriction endonuclease HpaII. The skillfully designed probe DNA labeled with 5-carboxyfluorescein (FAM) and optimized GO concentration keep the probe/target DNA still adsorbed on the GO. After the cleavage action of HpaII the labeled FAM is released from the GO surface and its fluorescence recovers, which could be used to detect DNA in the linear range of 50 pM-50 nM with a detection limit of 43 pM. DNA methylation induced by transmethylase (Mtase) or other chemical reagents prevents HpaII from recognizing and cleaving the specific site; as a result, fluorescence cannot recover. The fluorescence recovery efficiency is closely related to the DNA methylation level, which can be used to detect DNA methylation by comparing it with the fluorescence in the presence of intact target DNA. The method for detection of DNA and DNA methylation is simple, reliable and accurate. Copyright © 2014 Elsevier B.V. All rights reserved.

Early Childhood Home Visiting.

PubMed

Duffee, James H; Mendelsohn, Alan L; Kuo, Alice A; Legano, Lori A; Earls, Marian F

2017-09-01

High-quality home-visiting services for infants and young children can improve family relationships, advance school readiness, reduce child maltreatment, improve maternal-infant health outcomes, and increase family economic self-sufficiency. The American Academy of Pediatrics supports unwavering federal funding of state home-visiting initiatives, the expansion of evidence-based programs, and a robust, coordinated national evaluation designed to confirm best practices and cost-efficiency. Community home visiting is most effective as a component of a comprehensive early childhood system that actively includes and enhances a family-centered medical home. Copyright © 2017 by the American Academy of Pediatrics.

Ovulation home test

MedlinePlus

... test (home test); Ovulation prediction test; Ovulation predictor kit; Urinary LH immunoassays; At-home ovulation prediction test; ... Ovulation prediction test kits most often come with five to seven sticks. You may need to test for several days to detect a ...

Comparison of home and away-from-home physical activity using accelerometers and cellular network-based tracking devices.

PubMed

Ramulu, Pradeep Y; Chan, Emilie S; Loyd, Tara L; Ferrucci, Luigi; Friedman, David S

2012-08-01

Measuring physical at home and away from home is essential for assessing health and well-being, and could help design interventions to increase physical activity. Here, we describe how physical activity at home and away from home can be quantified by combining information from cellular network-based tracking devices and accelerometers. Thirty-five working adults wore a cellular network-based tracking device and an accelerometer for 6 consecutive days and logged their travel away from home. Performance of the tracking device was determined using the travel log for reference. Tracking device and accelerometer data were merged to compare physical activity at home and away from home. The tracking device detected 98.6% of all away-from-home excursions, accurately measured time away from home and demonstrated few prolonged signal drop-out periods. Most physical activity took place away from home on weekdays, but not on weekends. Subjects were more physically active per unit of time while away from home, particularly on weekends. Cellular network-based tracking devices represent an alternative to global positioning systems for tracking location, and provide information easily integrated with accelerometers to determine where physical activity takes place. Promoting greater time spent away from home may increase physical activity.

Rurality and Nursing Home Quality: Evidence from the 2004 National Nursing Home Survey

ERIC Educational Resources Information Center

Kang, Yu; Meng, Hongdao; Miller, Nancy A.

2011-01-01

Purpose of the Study: To evaluate the impact of rural geographic location on nursing home quality of care in the United States. Design and Methods: The study used cross-sectional observational design. We obtained resident- and facility-level data from 12,507 residents in 1,174 nursing homes from the 2004 National Nursing Home Survey. We used…

DOE Zero Energy Ready Home Case Study, Weiss Building & Development, LLC., System Home, River Forest, Illinois

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

none,

The Passive House Challenge Home located in River Forest, Illinois, is a 5-bedroom, 4.5-bath, 3,600 ft2 two-story home (plus basement) that costs about $237 less per month to operate than a similar sized home built to the 2009 IECC. For a home with no solar photovoltaic panels installed, it scored an amazingly low 27 on the Home Energy Rating System (HERS) score.An ENERGY STAR-rated dishwasher, clothes washer, and refrigerator; an induction cooktop, condensing clothes dryer, and LED lighting are among the energy-saving devices inside the home. All plumbing fixtures comply with EPA WaterSense criteria. The home was awarded a 2013more » Housing Innovation Award in the "systems builder" category.« less

Home is Where the Triggers Are: Increasing Asthma Control by Improving the Home Environment.

PubMed

Krieger, James

2010-06-01

Asthma remains the most common chronic condition of childhood. Strong evidence has linked exposure to allergens and other triggers commonly found in homes to allergen sensitization and asthma incidence and morbidity. A growing body of evidence has demonstrated that a home visit strategy that includes an environmental component that addresses multiple triggers through multiple interventions is effective. Such home visits reduce exposure to triggers, decrease symptoms and urgent health-care use, and increase quality of life. To make home visits widely available will require health-care payor reimbursement, government and health plan funding, training and certification of home visitors, and active referrals from health-care providers. However, a strategy based solely on education and behavior change is limited, because it cannot adequately reduce exposures due to adverse housing conditions. Therefore, approaches that address substandard housing are needed. These include remediation of existing housing and construction of new asthma-friendly homes. Most studies of remediation have made relatively narrow and focused improvements, such as insulation, heating, or ventilation. Outcomes have been mixed. Studies of new asthma-friendly homes are in their infancy, with promising pilot data. Further investigation is needed to establish the effectiveness of improving housing. A final strategy is improving housing quality through policy change, such as implementation of healthy housing guidelines for new construction, enhancement and increased enforcement of housing codes, and assuring smoke-free multi-unit homes. The combination of home visits, improved housing construction, and policy change has great potential for reducing the global burden of asthma.

Eldercare at Home: Dental Problems

MedlinePlus

... Nutrition Join our e-newsletter! Resources Eldercare at Home: Dental Problems Caregiving How Tos Understanding the Problem ... suggestions. Related Resources Caregiving How To's Eldercare at Home: Table of Contents Eldercare at Home covers over ...

Exploring workplace violence among home care workers in a consumer-driven home health care program.

PubMed

Nakaishi, Lindsay; Moss, Helen; Weinstein, Marc; Perrin, Nancy; Rose, Linda; Anger, W Kent; Hanson, Ginger C; Christian, Mervyn; Glass, Nancy

2013-10-01

Nominal research has examined sexual harassment and workplace violence against home care workers within consumer-driven home care models such as those offered in Oregon. This study examined home care workers' experiences of violence while providing care to consumer employers, the patients who hire and manage home care workers. Focus groups and interviews were conducted in Oregon with 83 home care workers, 99 Oregon Department of Human Services (DHS) employees, and 11 consumer employers. Home care workers reported incidents of workplace physical violence (44%), psychological abuse (65%), sexual harassment (41%), and sexual violence (14%). Further, three themes were identified that may increase the risk of workplace violence: (1) real and perceived barriers to reporting violence; (2) tolerance of violence; and (3) limited training to prevent violence. To ensure worker safety while maintaining quality care, safety policies and training for consumer employers, state DHS employees, and home care workers must be developed. Copyright 2013, SLACK Incorporated.

Protocols for Home Energy Upgrades

EPA Pesticide Factsheets

Remodeling or renovating an existing home not only has the potential to release pollutants into the home; it is also an opportunity to make changes that will improve the indoor air quality in your home.

FastStats: Home Health Care

MedlinePlus

... Submit What's this? Submit Button NCHS Home Home Health Care Recommend on Facebook Tweet Share Compartir Data are ... Data Alzheimer’s disease Characteristics and Use of Home Health Care by Men and Women Aged 65 and Over [ ...

Foraging optimally for home ranges

USGS Publications Warehouse

Mitchell, Michael S.; Powell, Roger A.

2012-01-01

Economic models predict behavior of animals based on the presumption that natural selection has shaped behaviors important to an animal's fitness to maximize benefits over costs. Economic analyses have shown that territories of animals are structured by trade-offs between benefits gained from resources and costs of defending them. Intuitively, home ranges should be similarly structured, but trade-offs are difficult to assess because there are no costs of defense, thus economic models of home-range behavior are rare. We present economic models that predict how home ranges can be efficient with respect to spatially distributed resources, discounted for travel costs, under 2 strategies of optimization, resource maximization and area minimization. We show how constraints such as competitors can influence structure of homes ranges through resource depression, ultimately structuring density of animals within a population and their distribution on a landscape. We present simulations based on these models to show how they can be generally predictive of home-range behavior and the mechanisms that structure the spatial distribution of animals. We also show how contiguous home ranges estimated statistically from location data can be misleading for animals that optimize home ranges on landscapes with patchily distributed resources. We conclude with a summary of how we applied our models to nonterritorial black bears (Ursus americanus) living in the mountains of North Carolina, where we found their home ranges were best predicted by an area-minimization strategy constrained by intraspecific competition within a social hierarchy. Economic models can provide strong inference about home-range behavior and the resources that structure home ranges by offering falsifiable, a priori hypotheses that can be tested with field observations.

Home advantage in Greek football.

PubMed

Armatas, Vasilis; Pollard, Richard

2014-01-01

Home advantage as it relates to team performance at football was examined in Superleague Greece using nine seasons of game-by-game performance data, a total of 2160 matches. After adjusting for team ability and annual fluctuations in home advantage, there were significant differences between teams. Previous findings regarding the role of territorial protection were strengthened by the fact that home advantage was above average for the team from Xanthi (P =0.015), while lower for teams from the capital city Athens (P =0.008). There were differences between home and away teams in the incidence of most of the 13 within-game match variables, but associated effect sizes were only moderate. In contrast, outcome ratios derived from these variables, and measuring shot success, had negligible effect sizes. This supported a previous finding that home and away teams differed in the incidence of on-the-ball behaviours, but not in their outcomes. By far the most important predictor of home advantage, as measured by goal difference, was the difference between home and away teams in terms of kicked shots from inside the penalty area. Other types of shots had little effect on the final score. The absence of a running track between spectators and the playing field was also a significant predictor of goal difference, worth an average of 0.102 goals per game to the home team. Travel distance did not affect home advantage.

Ensuring Quality Nursing Home Care

MedlinePlus

Ensuring Quality Nursing Home Care Before you choose a nursing home Expert information from Healthcare Professionals Who Specialize in the Care ... Nearly 1.6 million older Americans live in nursing homes in the United States. The move to ...

A Study of the Association Between Multidisciplinary Home Care and Home Death Among Thai Palliative Care Patients.

PubMed

Nagaviroj, Kittiphon; Anothaisintawee, Thunyarat

2017-06-01

Many terminally ill patients would prefer to stay and die in their own homes, but unfortunately, some may not be able to do so. Although there are many factors associated with successful home deaths, receiving palliative home visits from the multidisciplinary care teams is one of the key factors that enable patients to die at home. Our study was aimed to find whether there was any association between our palliative home care program and home death. A retrospective study was conducted in the Department of Family Medicine at Ramathibodi Hospital between January 2012 and May 2014. All of the patients who were referred to multidisciplinary palliative care teams were included. The data set comprised of patient's profile, disease status, functional status, patient's symptoms, preferred place of death, frequency of home visits, types of team interventions, and patient's actual place of death. Multiple logistic regression was applied in order to determine the association between the variables and the probability of dying at home. A total of 142 patients were included into the study. At the end of the study, 50 (35.2%) patients died at home and 92 (64.8%) patients died in the hospital. The multivariate logistic regression analysis demonstrated a strong association between multidisciplinary home care and home death (odds ratio 6.57, 95% confidence interval [CI] 2.48-17.38). Palliative home care was a significant factor enabling patients who want to die at home. We encourage health policy makers to promote the development of community-based palliative care programs in Thailand.

Perceived effects of home renovation on independence of physically disabled Koreans living at home.

PubMed

Lee, Yeunsook; Park, Jiyoung; Jang, Miseon

2017-06-06

This study aims to identify the potential effects of home renovation on independence promotion of physically disabled Koreans living at home. The method of the study is a survey with a questionnaire; subjects are physically disabled people living at home in rural and urban areas in Korea. The Functional Independence Measure was used to measure changes in subjects' levels of independence. It was expected that if homes were renovated according to individual needs, disabled people's independence level would be increased by one or more level compared to their current daily independence level in their existing homes. In particular, independence levels concerning bathing and locomotion, which are low in existing conditions, were expected to increase significantly with renovation. Such effects on independence level were conspicuous for disabled people in rural area. The results prove the positive effects of home renovations of disabled people's independence, thus providing meaningful academic evidence on home renovations for disabled people. Implication for rehabilitation Korea had a culture where support measures to aid the life independence of disabled persons relied heavily on human services, leading to a lack of diversity in support measures. By closing the gap between the resident's disability and the inadequacy in their prevailing environment, house remodeling can be a crucial intervention for improving the independence of disabled persons in their daily lives. Depending on the nature of their disabilities and their residential arrangements, disabled persons have diverse needs regarding home remodeling. Implementing home remodeling in such a manner that suits the resident's needs is crucial to boosting their independence. Because of this, remodeling personnel must interact with residents prior to the renovation while also strengthening their expertise.

Incentivizing the Medical Home

DTIC Science & Technology

2011-01-25

Outcomes of Implementing Patient -Centered Medical Home Interventions: A Review of the Evidence From Prospective Evaluation Studies in the United States...The Quadruple Aim: Working Together, Achieving Success 2011 Military Health System Conference Incentivizing the Medical Home 25 January 2011 CAPT...TITLE AND SUBTITLE Incentivizing the Medical Home 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER

The Future of Home Health project: developing the framework for health care at home.

PubMed

Lee, Teresa; Schiller, Jennifer

2015-02-01

In addition to providing high-quality care to vulnerable patient populations, home healthcare offers the least costly option for patients and the healthcare system, particularly in postacute care. As the baby boom generation ages, policymakers are expressing concerns about rising costs, variation in home healthcare service use, and program integrity. The Alliance for Home Health Quality and Innovation seeks to develop a research-based strategic framework for the future of home healthcare for older Americans and those with disabilities. This article describes the initiative and invites readers to provide comments and suggestions.

Home advantage in retractable-roof baseball stadia.

PubMed

Romanowich, Paul

2012-10-01

This study examined whether the home advantage varies for open-air, domed, or retractable-roof baseball stadia, and whether having the roof open or closed affects the home advantage in retractable-roof baseball stadia. Data from Major League Baseball (MLB) games played between 2001 and 2009 were analyzed for whether or not the presence of a home-advantage was dependent on the type of home stadium used. Home advantage was robust for all three types of stadia. A significant effect of stadium type on home advantage was found, with a greater home advantage for teams playing home games in domed stadia relative to open-air stadia, replicating a previous study. There was a greater home advantage for teams playing home games in domed stadia relative to retractable-roof stadia. No other differences in the home advantage were found; results are discussed in terms of familiarity with the facility.

The Future of Home Health Care

PubMed Central

Landers, Steven; Madigan, Elizabeth; Leff, Bruce; Rosati, Robert J.; McCann, Barbara A.; Hornbake, Rodney; MacMillan, Richard; Jones, Kate; Bowles, Kathryn; Dowding, Dawn; Lee, Teresa; Moorhead, Tracey; Rodriguez, Sally; Breese, Erica

2016-01-01

The Future of Home Health project sought to support transformation of home health and home-based care to meet the needs of patients in the evolving U.S. health care system. Interviews with key thought leaders and stakeholders resulted in key themes about the future of home health care. By synthesizing this qualitative research, a literature review, case studies, and the themes from a 2014 Institute of Medicine and National Research Council workshop on “The Future of Home Health Care,” the authors articulate a vision for home-based care and recommend a bold framework for the Medicare-certified home health agency of the future. The authors also identify challenges and recommendations for achievement of this framework. PMID:27746670

CareWatch: A Home Monitoring System for Use in Homes of Persons With Cognitive Impairment

PubMed Central

Rowe, Meredeth; Lane, Stephen; Phipps, Chad

2010-01-01

Currently, informal caregivers provide the bulk of care for persons with cognitive impairment who live in the home, often at significant cost in terms of their own physical, mental, and emotional health. This is a report of the development of a home monitoring system, CareWatch, designed for use in homes of persons with cognitive impairment such as Alzheimer’s disease. The purpose of CareWatch is to prevent unattended home exits, particularly during the night, and to improve caregiver sleep. We report on the development of CareWatch and on 2 clinical trials underway to test its effectiveness in the home setting. PMID:20454554

Introduction: shifting meanings of home.

PubMed

Hart, Mechthild; Ben-Yoseph, Miriam

2005-01-01

The studies and narratives collected in this special volume acknowledge "home" as a complex, ambiguous notion and reality. The contributors pay tribute to different ways of experiencing home, and to multiple connections to place and time. They illustrate how home is a social edifice, how it embodies different meanings and values, how it demarcates individual and social or national identities, and how a longing for home permeates experiences of homelessness as well as cultural, spatial, linguistic, and economic transitions.

Home Learning, Technology, and Tomorrow's Workplace.

ERIC Educational Resources Information Center

Rieseberg, Rhonda L.

1995-01-01

Discusses characteristics and trends of home schools and workplaces. Use of computers and computer applications (CD-ROMS, interactive software, and networking) in home schooling provides a compatible environment for future home-based businesses and telecommuting trends. Sidebars include information on home schools on line; standardized test…

National Nursing Home Survey

Cancer.gov

The National Nursing Home Survey provides includes characteristics such as size of nursing home facilities, ownership, Medicare/Medicaid certification, occupancy rate, number of days of care provided, and expenses.

Genetics Home Reference: SADDAN

MedlinePlus

... CLOSE navigation Home Page Search Home Health ... delay and acanthosis nigricans) is a rare disorder of bone growth characterized by skeletal, brain, and skin abnormalities. All people with this ...

Involvement in decisions about intravenous treatment for nursing home patients: nursing homes versus hospital wards.

PubMed

Klomstad, Kristin; Pedersen, Reidar; Førde, Reidun; Romøren, Maria

2018-05-08

Many of the elderly in nursing homes are very ill and have a reduced quality of life. Life expectancy is often hard to predict. Decisions about life-prolonging treatment should be based on a professional assessment of the patient's best interest, assessment of capacity to consent, and on the patient's own wishes. The purpose of this study was to investigate and compare how these types of decisions were made in nursing homes and in hospital wards. Using a questionnaire, we studied the decision-making process for 299 nursing home patients who were treated for dehydration using intravenous fluids, or for bacterial infections using intravenous antibiotics. We compared the 215 (72%) patients treated in nursing homes to the 84 (28%) nursing home patients treated in the hospital. The patients' capacity to consent was considered prior to treatment in 197 (92%) of the patients treated in nursing homes and 56 (67%) of the patients treated in hospitals (p < 0.001). The answers indicate that capacity to consent can be difficult to assess. Patients that were considered capable to consent, were more often involved in the decision-making in nursing homes than in hospital (90% vs. 52%). Next of kin and other health personnel were also more rarely involved when the nursing home patient was treated in hospital. Whether advance care planning had been carried out, was more often unknown in the hospital (69% vs. 17% in nursing homes). Hospital doctors expressed more doubt about the decision to admit the patient to the hospital than about the treatment itself. This study indicates a potential for improvement in decision-making processes in general, and in particular when nursing home patients are treated in a hospital ward. The findings corroborate that nursing home patients should be treated locally if adequate health care and treatment is available. The communication between the different levels of health care when hospitalization is necessary, must be better. Clinical

24 CFR 280.20 - Home quality.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 24 Housing and Urban Development 2 2011-04-01 2011-04-01 false Home quality. 280.20 Section 280.20... GRANT PROGRAMS NEHEMIAH HOUSING OPPORTUNITY GRANTS PROGRAM § 280.20 Home quality. (a) Generally. Except for manufactured homes, homes constructed or substantially rehabilitated under a program must comply...

24 CFR 280.20 - Home quality.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 24 Housing and Urban Development 2 2013-04-01 2013-04-01 false Home quality. 280.20 Section 280.20... GRANT PROGRAMS NEHEMIAH HOUSING OPPORTUNITY GRANTS PROGRAM § 280.20 Home quality. (a) Generally. Except for manufactured homes, homes constructed or substantially rehabilitated under a program must comply...

7 CFR 1755.509 - Mobile homes.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 7 Agriculture 11 2014-01-01 2014-01-01 false Mobile homes. 1755.509 Section 1755.509 Agriculture... homes. (a) Customer access location installations at mobile homes shall be treated the same whether the homes are mounted on permanent foundations or temporary foundations and shall be installed as specified...

7 CFR 1755.509 - Mobile homes.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 7 Agriculture 11 2012-01-01 2012-01-01 false Mobile homes. 1755.509 Section 1755.509 Agriculture... homes. (a) Customer access location installations at mobile homes shall be treated the same whether the homes are mounted on permanent foundations or temporary foundations and shall be installed as specified...

7 CFR 1755.509 - Mobile homes.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 7 Agriculture 11 2013-01-01 2013-01-01 false Mobile homes. 1755.509 Section 1755.509 Agriculture... homes. (a) Customer access location installations at mobile homes shall be treated the same whether the homes are mounted on permanent foundations or temporary foundations and shall be installed as specified...

24 CFR 280.20 - Home quality.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 24 Housing and Urban Development 2 2012-04-01 2012-04-01 false Home quality. 280.20 Section 280.20... GRANT PROGRAMS NEHEMIAH HOUSING OPPORTUNITY GRANTS PROGRAM § 280.20 Home quality. (a) Generally. Except for manufactured homes, homes constructed or substantially rehabilitated under a program must comply...

7 CFR 1755.509 - Mobile homes.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 7 Agriculture 11 2011-01-01 2011-01-01 false Mobile homes. 1755.509 Section 1755.509 Agriculture... homes. (a) Customer access location installations at mobile homes shall be treated the same whether the homes are mounted on permanent foundations or temporary foundations and shall be installed as specified...

24 CFR 280.20 - Home quality.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 24 Housing and Urban Development 2 2014-04-01 2014-04-01 false Home quality. 280.20 Section 280.20... GRANT PROGRAMS NEHEMIAH HOUSING OPPORTUNITY GRANTS PROGRAM § 280.20 Home quality. (a) Generally. Except for manufactured homes, homes constructed or substantially rehabilitated under a program must comply...

7 CFR 1755.509 - Mobile homes.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 11 2010-01-01 2010-01-01 false Mobile homes. 1755.509 Section 1755.509 Agriculture... homes. (a) Customer access location installations at mobile homes shall be treated the same whether the homes are mounted on permanent foundations or temporary foundations and shall be installed as specified...

24 CFR 280.20 - Home quality.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 24 Housing and Urban Development 2 2010-04-01 2010-04-01 false Home quality. 280.20 Section 280.20... GRANT PROGRAMS NEHEMIAH HOUSING OPPORTUNITY GRANTS PROGRAM § 280.20 Home quality. (a) Generally. Except for manufactured homes, homes constructed or substantially rehabilitated under a program must comply...

77 FR 5186 - Medical Foster Homes

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-02

... of these veterans are placed in nursing homes. Others, with the proper support, can continue to live in a residential setting and delay, or totally avoid, the need for nursing home care. VA's community... to a nursing home), while allowing veterans to live in a home-like [[Page 5187

78 FR 46421 - Proposed Information Collection (Per Diem for Nursing Home Care of Veterans in State Homes; Per...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-31

... Diem for Nursing Home Care of Veterans in State Homes; Per Diem for Adult Day Care of Veterans in State... information needed to ensure that nursing home and adult day health care facilities are providing high quality... State homes providing nursing home and adult day health services care to Veterans. VA requires...

Rate-determining Step of Flap Endonuclease 1 (FEN1) Reflects a Kinetic Bias against Long Flaps and Trinucleotide Repeat Sequences.

PubMed

Tarantino, Mary E; Bilotti, Katharina; Huang, Ji; Delaney, Sarah

2015-08-21

Flap endonuclease 1 (FEN1) is a structure-specific nuclease responsible for removing 5'-flaps formed during Okazaki fragment maturation and long patch base excision repair. In this work, we use rapid quench flow techniques to examine the rates of 5'-flap removal on DNA substrates of varying length and sequence. Of particular interest are flaps containing trinucleotide repeats (TNR), which have been proposed to affect FEN1 activity and cause genetic instability. We report that FEN1 processes substrates containing flaps of 30 nucleotides or fewer at comparable single-turnover rates. However, for flaps longer than 30 nucleotides, FEN1 kinetically discriminates substrates based on flap length and flap sequence. In particular, FEN1 removes flaps containing TNR sequences at a rate slower than mixed sequence flaps of the same length. Furthermore, multiple-turnover kinetic analysis reveals that the rate-determining step of FEN1 switches as a function of flap length from product release to chemistry (or a step prior to chemistry). These results provide a kinetic perspective on the role of FEN1 in DNA replication and repair and contribute to our understanding of FEN1 in mediating genetic instability of TNR sequences. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Increased sensitivity to mitochondrial permeability transition and myonuclear translocation of endonuclease G in atrophied muscle of physically active older humans.

PubMed

Gouspillou, Gilles; Sgarioto, Nicolas; Kapchinsky, Sophia; Purves-Smith, Fennigje; Norris, Brandon; Pion, Charlotte H; Barbat-Artigas, Sébastien; Lemieux, Francois; Taivassalo, Tanja; Morais, José A; Aubertin-Leheudre, Mylène; Hepple, Russell T

2014-04-01

Mitochondrial dysfunction is implicated in skeletal muscle atrophy and dysfunction with aging, with strong support for an increased mitochondrial-mediated apoptosis in sedentary rodent models. Whether this applies to aged human muscle is unknown, nor is it clear whether these changes are caused by sedentary behavior. Thus, we examined mitochondrial function [respiration, reactive oxygen species (ROS) emission, and calcium retention capacity (CRC)] in permeabilized myofibers obtained from vastus lateralis muscle biopsies of healthy physically active young (23.7±2.7 yr; mean±SD) and older (71.2±4.9 yr) men. Although mitochondrial ROS and maximal respiratory capacity were unaffected, the acceptor control ratio was reduced by 18% with aging, suggesting mild uncoupling of oxidative phosphorylation. CRC was reduced by 50% with aging, indicating sensitization of the mitochondrial permeability transition pore (mPTP) to apoptosis. Consistent with the mPTP sensitization, older muscles showed a 3-fold greater fraction of endonuclease G (a mitochondrial proapoptotic factor)-positive myonuclei. Aged muscles also had lower mitophagic potential, based on a 43% reduction in Parkin to the voltage-dependent anion channel (VDAC) protein ratio. Collectively, these results show that mitochondrial-mediated apoptotic signaling is increased in older human muscle and suggest that accumulation of dysfunctional mitochondria with exaggerated apoptotic sensitivity is due to impaired mitophagy.

A temporary home to nurture health: lived experiences of older nursing home residents in Taiwan.

PubMed

Tsai, Hsiu-Hsin; Tsai, Yun-Fang

2008-07-01

This study explored the lived experiences of older nursing home residents in Taiwan. With more long-term care institutions in Taiwan, older people are more often placed in nursing homes than in the past. Increased understanding of their lived experience is essential to assess residents' needs and determine the effectiveness of nursing interventions. A qualitative design was used to gain a deeper understanding of the lived experiences of older nursing home residents in Taiwan. Focus groups, followed by in-depth interviews, were used to gather information from 33 older residents at eight nursing homes in northern Taiwan. Participants were asked to describe what was important to them and what impressed them most in their daily lives in the nursing home. Participants (24 females and nine males) were on an average 75.3 years old. Verbatim transcripts of audiotaped focus groups and interviews were analysed by thematic analysis via ATLAS.ti software. The core theme of older residents' nursing home experience was 'a temporary home to nurture health'. This core theme was reflected in participants' descriptions of their overall life in the nursing home as a temporary experience to nurture their health. Their everyday experience was characterised by four subthemes: highly structured lifestyle, restricted activities, safety concerns and social interactions. Our findings may enhance policy makers' and healthcare providers' understanding of the lived experience of older nursing home residents, thus guiding the evaluation and development of nursing home services to improve residents' lives. For example, residents with the same characteristics could be placed in the same room or same floor, thus increasing their interactions with other residents. Residents' interactions with family members could also be developed using the Internet or mobile telephones.

Misalignment between Medicare Policies and Depression Care in Home Health Care: Home health provider perspectives

PubMed Central

Bao, Yuhua; Eggman, Ashley; Richardson, Joshua; Bruce, Martha

2013-01-01

Objective Depression affects one in four older adults receiving home health care. Medicare policies are influential in shaping home health practice. This study aims to identify Medicare policy areas that are aligned or misaligned with depression care quality improvement in home health care. Methods Qualitative study based on semi-structured interviews with nurses and administrators from five home health agencies in five states (n=20). Digitally recorded interviews were transcribed and analyzed using the grounded theory method. A multi-disciplinary team iteratively developed a codebook from interview data to identify themes. Results Several important Medicare policies are largely misaligned with depression care quality improvement in home health care: Medicare eligibility requirements for patients to remain homebound and to demonstrate a need for skilled care restrict nurses’ abilities to follow up with depressed patients for sufficient length of time; the lack of explicit recognition of nursing time and quality of care in the home health Prospective Payment System (PPS) provides misaligned incentives for depression care; incorporation of a two-item depression screening tool in Medicare-mandated comprehensive patient assessment raised clinician awareness of depression; however, inclusion of the tool at Start-of-Care only but not any other follow-up points limits its potential in assisting nurses with depression care management; under-development of clinical decision support for depression care in vendor-developed electronic health records constitutes an important barrier to depression quality improvement in home health care. Conclusions Several influential Medicare policies and regulations for home health practice may be misaligned with evidence-based depression care for home health patients. PMID:24632686

Vocational Home Economics Curriculum Guide for Occupational Home and Institutional Services.

ERIC Educational Resources Information Center

Dewald, Margaret R.

The training program outlined in this guide focuses upon the development of students for gainful employment through a two-year course of study in home and institutional services. Instructional topics are provided in nine areas: orientation to home and institutional services, cleaning supplies and equipment, cleaning surfaces, cleaning clothes and…

77 FR 45719 - Proposed Information Collection (Per Diem for Nursing Home Care of Veterans in State Homes; Per...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-01

... Diem for Nursing Home Care of Veterans in State Homes; Per Diem for Adult Day Care of Veterans in State... information needed to ensure that nursing home and adult day health care facilities are providing high quality... per diem to State homes providing nursing home and adult day health services care to Veterans. VA...

New Directions for Vocational Home Economics.

ERIC Educational Resources Information Center

Fane, Xenia F.

A 2-day conference jointly sponsored by the American Home Economics Association and the American Vocational Association was attended by approximately 400 home economists who sought to determine new directions for vocational home economics. Some presentations were: (1) -The Cooperative Role of AHEA" by D. Hanson, (2) "Vocational Home Economics in…

The HOME Inventory and Family Demographics.

ERIC Educational Resources Information Center

Bradley, Robert H.; Caldwell, Bettye M.

1984-01-01

Examines the relation between the Home Observation for Measurement of Environment (HOME) Inventory and sex, race, socioeconomic status, the amount of crowding in the home, and birth order. Performs multivariate analysis of covariance on an intact family sample using HOME subscales as criterion measures and status and structural variables as…

The Wiley Handbook of Home Education

ERIC Educational Resources Information Center

Gaither, Milton, Ed.

2016-01-01

"The Wiley Handbook of Home Education" is a comprehensive collection of the latest scholarship in all aspects of home education in the United States and abroad. This book presents the latest findings on academic achievement of home-schooled children, issues of socialization, and legal argumentation about home-schooling and government…

Engaging Parents in Early Head Start Home-Based Programs: How Do Home Visitors Do This?

PubMed

Shanti, Caroline

2017-01-01

Parental engagement is considered elemental to successful outcomes for parents and their children in early childhood home visiting programs. Engagement is that piece of parental involvement that refers to the working relationship between the parent and the home visitor. Multiple papers have called for research to pinpoint the ways in which home visitors work with parents to form these working relationships, and form partnerships to achieve positive outcomes. Analysis revealed that in individualizing their efforts to each family, home visitors follow semi-sequential steps in implementing engagement. This article presents a model of the process home visitors describe that resulted from analysis. Grounded theory techniques were used to analyze 29 interviews with Early Head Start (EHS) home visitors and 11 supervisors across four EHS programs in one region of the United States. The process of engagement as described emerges in three phases: (1) learning the parent's culture and style; (2) deepening the working partnership; and (3) balancing the ongoing work. Analysis further revealed specific strategies and goals that guide the work of home visitors in each of these three phases. This not only adds rich detail to the literature, but also provides a useful guide for programs and policy makers through identifying the areas where training and support will increase home visitor ability to engage parents.

Custodial Homes, Therapeutic Homes, and Parental Acceptance: Parental Experiences of Autism in Kerala, India and Atlanta, GA USA.

PubMed

Sarrett, Jennifer C

2015-06-01

The home is a critical place to learn about cultural values of childhood disability, including autism and intellectual disabilities. The current article describes how the introduction of autism into a home and the availability of intervention options change the structure and meaning of a home and reflect parental acceptance of a child's autistic traits. Using ethnographic data from Kerala, India and Atlanta, GA USA, a description of two types of homes are developed: the custodial home, which is primarily focused on caring for basic needs, and the therapeutic home, which is focused on changing a child's autistic traits. The type of home environment is respondent to cultural practices of child rearing in the home and influences daily activities, management, and care in the home. Further, these homes differ in parental acceptance of their autistic children's disabilities, which is critical to understand when engaging in international work related to autism and intellectual disability. It is proposed that parental acceptance can be fostered through the use of neurodiverse notions that encourage autism acceptance.

Home e-health system integration in the Smart Home through a common media server.

PubMed

Pau, I; Seoane, F; Lindecrantz, K; Valero, M A; Carracedo, J

2009-01-01

Home e-health systems and services are revealed as one of the most important challenges to promote Quality of Life related to Health in the Information Society. Leading companies have worked on e-health systems although the majority of them are addressed to hospital or primary care settings. The solution detailed in this paper offers a personal health system to be integrated with Smart Home services platform to support home based e-care. Thus, the home e-health system and architecture detailed in this research work is ready to supply a seamless personal care solution both from the biomedical data analysis, service provision, security guarantee and information management s point of view. The solution is ready to be integrated within the Accessible Digital Home, a living lab managed by Universidad Politécnica de Madrid for R&D activities.

Home Education: A Human Right?

ERIC Educational Resources Information Center

Monk, Daniel

2003-01-01

The right of parents to home educate is sometimes described as a "human right." Underlying this "rights claim" is the perception that attempts to restrict home education are both unnecessary and dangerous. "Unnecessary," because home education does not harm children or deprive them of the right to education and…

DNA and Protein Requirements for Substrate Conformational Changes Necessary for Human Flap Endonuclease-1-catalyzed Reaction*

PubMed Central

Algasaier, Sana I.; Exell, Jack C.; Bennet, Ian A.; Thompson, Mark J.; Gotham, Victoria J. B.; Shaw, Steven J.; Craggs, Timothy D.; Finger, L. David; Grasby, Jane A.

2016-01-01

Human flap endonuclease-1 (hFEN1) catalyzes the essential removal of single-stranded flaps arising at DNA junctions during replication and repair processes. hFEN1 biological function must be precisely controlled, and consequently, the protein relies on a combination of protein and substrate conformational changes as a prerequisite for reaction. These include substrate bending at the duplex-duplex junction and transfer of unpaired reacting duplex end into the active site. When present, 5′-flaps are thought to thread under the helical cap, limiting reaction to flaps with free 5′-termini in vivo. Here we monitored DNA bending by FRET and DNA unpairing using 2-aminopurine exciton pair CD to determine the DNA and protein requirements for these substrate conformational changes. Binding of DNA to hFEN1 in a bent conformation occurred independently of 5′-flap accommodation and did not require active site metal ions or the presence of conserved active site residues. More stringent requirements exist for transfer of the substrate to the active site. Placement of the scissile phosphate diester in the active site required the presence of divalent metal ions, a free 5′-flap (if present), a Watson-Crick base pair at the terminus of the reacting duplex, and the intact secondary structure of the enzyme helical cap. Optimal positioning of the scissile phosphate additionally required active site conserved residues Tyr40, Asp181, and Arg100 and a reacting duplex 5′-phosphate. These studies suggest a FEN1 reaction mechanism where junctions are bound and 5′-flaps are threaded (when present), and finally the substrate is transferred onto active site metals initiating cleavage. PMID:26884332

The first multicenter, randomized, controlled trial of home telemonitoring for Japanese patients with heart failure: home telemonitoring study for patients with heart failure (HOMES-HF).

PubMed

Kotooka, Norihiko; Kitakaze, Masafumi; Nagashima, Kengo; Asaka, Machiko; Kinugasa, Yoshiharu; Nochioka, Kotaro; Mizuno, Atsushi; Nagatomo, Daisuke; Mine, Daigo; Yamada, Yoko; Kuratomi, Akiko; Okada, Norihiro; Fujimatsu, Daisuke; Kuwahata, So; Toyoda, Shigeru; Hirotani, Shin-Ichi; Komori, Takahiro; Eguchi, Kazuo; Kario, Kazuomi; Inomata, Takayuki; Sugi, Kaoru; Yamamoto, Kazuhiro; Tsutsui, Hiroyuki; Masuyama, Tohru; Shimokawa, Hiroaki; Momomura, Shin-Ichi; Seino, Yoshihiko; Sato, Yasunori; Inoue, Teruo; Node, Koichi

2018-02-15

Home telemonitoring is becoming more important to home medical care for patients with heart failure. Since there are no data on home telemonitoring for Japanese patients with heart failure, we investigated its effect on cardiovascular outcomes. The HOMES-HF study was the first multicenter, open-label, randomized, controlled trial (RCT) to elucidate the effectiveness of home telemonitoring of physiological data, such as body weight, blood pressure, and pulse rate, for Japanese patients with heart failure (UMIN Clinical Trials Registry 000006839). The primary end-point was a composite of all-cause death or rehospitalization due to worsening heart failure. We analyzed 181 recently hospitalized patients with heart failure who were randomly assigned to a telemonitoring group (n = 90) or a usual care group (n = 91). The mean follow-up period was 15 (range 0-31) months. There was no statistically significant difference in the primary end-point between groups [hazard ratio (HR), 0.95; 95% confidence interval (CI), 0.548-1.648; p = 0.572]. Home telemonitoring for Japanese patients with heart failure was feasible; however, beneficial effects in addition to those of usual care were not demonstrated. Further investigation of more patients with severe heart failure, participation of home medical care providers, and use of a more integrated home telemonitoring system emphasizing communication as well as monitoring of symptoms and physiological data are required.

Case Study of Home-School Visits

ERIC Educational Resources Information Center

Aguerrebere, Yolanda

2009-01-01

This case study evaluated one site of a California teacher home visit program. Home visits have been an important means of connecting families and schooling. In 1999, California inaugurated a statewide home visit program to promote effective partnership between home and school for low-achieving schools. At this site, families in 3 kindergarten…

Nursing Home Administrators' Opinions of the Nursing Home Compare Web Site

ERIC Educational Resources Information Center

Castle, Nicholas G.

2005-01-01

Purpose: In November of 2002 the Centers for Medicare and Medicaid Services publicly reported on a national basis the quality of nursing homes on the Nursing Home Compare (NHC) Web site. This study examines administrators' opinions of this initiative and whether it has fostered quality improvement. Design and Methods: Data used in this…

Genetic Mediation of the Home Environment during Infancy: A Sibling Adoption Study of the HOME.

ERIC Educational Resources Information Center

Braungart, Julia M.; And Others

1992-01-01

The home environment of nonadoptive and adoptive sibling pairs was assessed using the Home Observation for Measurement of the Environment when each sibling was one and two years of age. Correlations between home environment scores for nonadoptive siblings were greater than those for adoptive siblings. (BC)

Randomized trial of the ForeseeHome monitoring device for early detection of neovascular age-related macular degeneration. The HOme Monitoring of the Eye (HOME) study design - HOME Study report number 1.

PubMed

Chew, Emily Y; Clemons, Traci E; Bressler, Susan B; Elman, Michael J; Danis, Ronald P; Domalpally, Amitha; Heier, Jeffrey S; Kim, Judy E; Garfinkel, Richard A

2014-03-01

To evaluate the effects of a home-monitoring device with tele-monitoring compared with standard care in detection of progression to choroidal neovascularization (CNV) associated with age-related macular degeneration (AMD), the leading cause of blindness in the US. Participants, aged 55 to 90 years, at high risk of developing CNV associated with AMD were recruited to the HOme Monitoring of Eye (HOME) Study, an unmasked, multi-center, randomized trial of the ForeseeHome (FH) device plus standard care vs. standard care alone. The FH device utilizes preferential hyperacuity perimetry and tele-monitoring to detect changes in vision function associated with development of CNV, potentially prior to symptom and visual acuity loss. After establishing baseline measurements, subsequent changes on follow-up are detected by the device, causing the monitoring center to alert the clinical center to recall participants for an exam. Standard care consists of instructions for self-monitoring visual changes with subsequent self-report to the clinical center. The primary objective of this study is to determine whether home monitoring plus standard care in comparison with standard care alone, results in earlier detection of incident CNV with better present visual acuity. The primary outcome is the decline in visual acuity at CNV diagnosis from baseline. Detection of CNV prior to substantial vision loss is critical as vision outcome following anti-angiogenic therapy is dependent on the visual acuity at initiation of treatment. HOME Study is the first large scale study to test the use of home tele-monitoring system in the management of AMD patients. Published by Elsevier Inc.

The incidence of depression and its risk factors in Dutch nursing homes and residential care homes.

PubMed

Boorsma, Marijke; Joling, Karlijn; Dussel, Martine; Ribbe, Miel; Frijters, Dinnus; van Marwijk, Harm W J; Nijpels, Giel; van Hout, Hein

2012-11-01

Although it is known that depression is highly prevalent in institutionalized older adults, little is known about its incidence and risk factors in nursing homes and residential care homes. The aim of this study was to investigate and compare the incidence and associated risk factors for depression in Dutch nursing homes and residential care homes. Data on depression were extracted from the Vrije Universiteit naturalistic cohort on routine care monitoring with the Minimum Data Set of the Resident Assessment Instrument. A total of 1,324 residents in six nursing homes and 1,723 residents in 23 residential care homes with an average follow-up of 1.2 years. Depression was defined as a clinical diagnosis according to Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition, criteria and the use of antidepressants. Residents with prevalent depression at baseline were excluded. The incidence rate was 13.6 per 100 person years in the nursing homes and 10.2 per 100 person years in the residential care homes. The independent risk factors for in-home depression for residents in nursing homes included dementia (OR: 1.7; 95% CI: 1.02-2.95) and a score of 3 or more on the Depression Rating Scale (odds ratio [OR]: 2.1; 95% confidence interval [CI]: 1.23-3.70). A protective effect was seen on the use of a hearing aid (OR: 0.3; 95% CI: 0.12-0.80). In the residential care homes, being male (OR: 2.1; 95% CI: 1.27-3.30), having cancer (OR: 2.9; 95% CI: 1.64-4.95), and a score of 2 or higher on the Cognitive Performance Scale (OR: 1.5; 95% CI: 1.05-2.22) increased the risk to develop depression. Age greater than 85 years (OR: 0.5; 95% CI: 0.31-0.67) and hearing impairment (OR: 0.8; 95% CI: 0.60-1.00) appeared to be protective. The incidence rate for depression in residents of Dutch nursing homes and residential care homes was high and the associated risk factors found may have important implications for staff. 2012 American Association for Geriatric Psychiatry

Inhibitors of nuclease and redox activity of apurinic/apyrimidinic endonuclease 1/redox effector factor 1 (APE1/Ref-1).

PubMed

Laev, Sergey S; Salakhutdinov, Nariman F; Lavrik, Olga I

2017-05-01

Human apurinic/apyrimidinic endonuclease 1/redox effector factor 1 (APE1/Ref-1) is a multifunctional protein which is essential in the base excision repair (BER) pathway of DNA lesions caused by oxidation and alkylation. This protein hydrolyzes DNA adjacent to the 5'-end of an apurinic/apyrimidinic (AP) site to produce a nick with a 3'-hydroxyl group and a 5'-deoxyribose phosphate moiety or activates the DNA-binding activity of certain transcription factors through its redox function. Studies have indicated a role for APE1/Ref-1 in the pathogenesis of cancer and in resistance to DNA-interactive drugs. Thus, this protein has potential as a target in cancer treatment. As a result, major efforts have been directed to identify small molecule inhibitors against APE1/Ref-1 activities. These agents have the potential to become anticancer drugs. The aim of this review is to present recent progress in studies of all published small molecule APE1/Ref-1 inhibitors. The structures and activities of APE1/Ref-1 inhibitors, that target both DNA repair and redox activities, are presented and discussed. To date, there is an urgent need for further development of the design and synthesis of APE1/Ref-1 inhibitors due to high importance of this protein target. Copyright © 2017 Elsevier Ltd. All rights reserved.

A molecular switch sensor for detection of PRSS1 genotype based on site-specific DNA cleavage of restriction endonuclease.

PubMed

Liu, Qicai; Gao, Feng; Weng, Shaohuang; Peng, Huaping; Lin, Liqing; Zhao, Chengfei; Lin, Xinhua

2015-01-01

PRSS1 mutations or polymorphism in the peripheral blood of patients can be used as susceptible molecular markers to pancreatic cancer. A sensor for selective electrochemical detection of PRSS1 genotypes was developed based on site-specific DNA cleavage of restriction endonuclease EcoRI. A mercapto-modified hairpin probe was immobilized on a gold electrode. The probe's neck can be cleaved by EcoRI in the absence of rs10273639 C/C of PRSS1 genotype, but it cannot be cleaved in the presence of T/T. The difference in quantity of electric charge was monitored by biosensors before and after enzymatic cleavage. Electrochemical signals are generated by differential pulse voltammetry interrogation of methylene blue (MB) that quantitatively binds to surface-confined hairpin probe via electrostatic interactions. The results suggested this method had a good specificity in distinguishing PRSS1 genotypes. There was a good linear relationship between the charge and the logarithmic function of PRSS1 rs10273639 T/T type DNA concentration (current=120.6303+8.8512log C, R=0.9942). The detection limit was estimated at 0.5 fM. The molecular switch sensor has several advantages, and it is possible to qualitatively, quantitatively, and noninvasively detect PRSS1 genotypes in the blood of patients with pancreatic cancer. © 2015 by the Association of Clinical Scientists, Inc.

Cardiomyocyte hypertrophy induced by Endonuclease G deficiency requires reactive oxygen radicals accumulation and is inhibitable by the micropeptide humanin.

PubMed

Blasco, Natividad; Cámara, Yolanda; Núñez, Estefanía; Beà, Aida; Barés, Gisel; Forné, Carles; Ruíz-Meana, Marisol; Girón, Cristina; Barba, Ignasi; García-Arumí, Elena; García-Dorado, David; Vázquez, Jesús; Martí, Ramon; Llovera, Marta; Sanchis, Daniel

2018-06-01

The endonuclease G gene (Endog), which codes for a mitochondrial nuclease, was identified as a determinant of cardiac hypertrophy. How ENDOG controls cardiomyocyte growth is still unknown. Thus, we aimed at finding the link between ENDOG activity and cardiomyocyte growth. Endog deficiency induced reactive oxygen species (ROS) accumulation and abnormal growth in neonatal rodent cardiomyocytes, altering the AKT-GSK3β and Class-II histone deacethylases (HDAC) signal transduction pathways. These effects were blocked by ROS scavengers. Lack of ENDOG reduced mitochondrial DNA (mtDNA) replication independently of ROS accumulation. Because mtDNA encodes several subunits of the mitochondrial electron transport chain, whose activity is an important source of cellular ROS, we investigated whether Endog deficiency compromised the expression and activity of the respiratory chain complexes but found no changes in these parameters nor in ATP content. MtDNA also codes for humanin, a micropeptide with possible metabolic functions. Nanomolar concentrations of synthetic humanin restored normal ROS levels and cell size in Endog-deficient cardiomyocytes. These results support the involvement of redox signaling in the control of cardiomyocyte growth by ENDOG and suggest a pathway relating mtDNA content to the regulation of cell growth probably involving humanin, which prevents reactive oxygen radicals accumulation and hypertrophy induced by Endog deficiency. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Home Energy Saver

Science.gov Websites

up zip code Case Studies Weatherization: Improving Home Safety and Reducing Your Energy Bill home energy efficient? Your House is a System Living Off The Sun, Or, No Electricity Bill Kermit was Cottage Energy Blogs 5 Most Effective Ways to Save on Your Energy Bill Updating Guest Bathroom With Energy

Home is Private…Do Not Enter! Introversion and Sensitivity to Work-Home Conflict.

PubMed

Baer, Stacy M; Jenkins, Jade S; Barber, Larissa K

2016-10-01

This study examined extraversion as a moderator of the relationship between negative work-home conflict and stress-related outcomes among US employees using conservation of resources theory and privacy regulation theory. Introverts only experienced stronger negative effects of negative work-home conflict on work-related resource depletion (job burnout, low engagement, low satisfaction with balance) rather than general resource depletion (personal burnout) and strain (physical and psychological). This finding suggests that introverts selectively withdraw from the work domain to conserve resources when privacy at home is threatened. Employers may want to consider ways to help introverts increase work-home segmentation, such as reducing workplace norms that encourage employees to be continuously accessible. Copyright © 2014 John Wiley & Sons, Ltd. Copyright © 2014 John Wiley & Sons, Ltd.

Implementing and Preparing for Home Visits

ERIC Educational Resources Information Center

McWilliam, R. A.

2012-01-01

The most common setting for early intervention services for infants and toddlers with disabilities and their families is the home. This article discusses home- and community-based early intervention and how the routines-based interview (RBI) can set the stage for successful home visits. It also addresses what has been learned about home visiting,…

Introduce Construction Technology through Home Inspection

ERIC Educational Resources Information Center

Wiggins, Enrique R.

2007-01-01

Introducing technology education students to the field of home inspection gives them a great opportunity to learn about and apply construction technology content. In working with his 8th-grade students, the author covers the purpose of a home inspection, the dynamic of home inspections, the process involved in inspecting schools and homes and…

Energy on the Home Front

NASA Astrophysics Data System (ADS)

Murphy, Thomas W.

2011-11-01

This article explores a variety of ways to measure, adjust, and augment home energy usage. Particular examples of using electricity and gas utility meters, power/energy meters for individual devices, whole-home energy monitoring, infrared cameras, and thermal measurements are discussed—leading to a factor-of-four reduction in home energy use in the case discussed. The net efficiency performance of a stand-alone photovoltaic system is also presented. Ideas for reducing one's energy/carbon footprint both within the home and in the larger community are quantitatively evaluated.

Apurinic/apyrimidinic endonuclease 1 regulates angiogenesis in a transforming growth factor β-dependent manner in human osteosarcoma.

PubMed

Jiang, Xuan; Shan, Jinlu; Dai, Nan; Zhong, Zhaoyang; Qing, Yi; Yang, Yuxing; Zhang, Shiheng; Li, Chongyi; Sui, Jiangdong; Ren, Tao; Li, Mengxia; Wang, Dong

2015-10-01

Angiogenesis plays an important role in tumor growth and metastasis and has been reported to be inversely correlated with overall survival of osteosarcoma patients. It has been shown that apurinic/apyrimidinic endonuclease 1 (APE1), a dually functional protein possessing both base excision repair and redox activities, is involved in tumor angiogenesis, although these mechanisms are not fully understood. Our previous study showed that the expression of transforming growth factor β (TGFβ) was significantly reduced in APE1-deficient osteosarcoma cells. Transforming growth factor β promotes cancer metastasis through various mechanisms including immunosuppression, angiogenesis, and invasion. In the current study, we initially revealed that APE1, TGFβ, and microvessel density (MVD) have pairwise correlation in osteosarcoma tissue samples, whereas TGFβ, tumor size, and MVD were inversely related to the prognosis of the cohort. We found that knocking down APE1 in osteosarcoma cells resulted in TGFβ downregulation. In addition, APE1-siRNA led to suppression of angiogenesis in vitro based on HUVECs in Transwell and Matrigel tube formation assays. Reduced secretory protein level of TGFβ of culture medium also resulted in decreased phosphorylation of Smad3 of HUVECs. In a mouse xenograft model, siRNA-mediated silencing of APE1 downregulated TGFβ expression, tumor size, and MVD. Collectively, the current evidence indicates that APE1 regulates angiogenesis in osteosarcoma by controlling the TGFβ pathway, suggesting a novel target for anti-angiogenesis therapy in human osteosarcoma. © 2015 The Authors. Cancer Science published by Wiley Publishing Asia Pty Ltd on behalf of Japanese Cancer Association.

Financing of pediatric home health care. Committee on Child Health Financing, Section on Home Care, American Academy of Pediatrics.

PubMed

2006-08-01

In certain situations, home health care has been shown to be a cost-effective alternative to inpatient hospital care. National health expenditures reveal that pediatric home health costs totaled $5.3 billion in 2000. Medicaid is the major payer for pediatric home health care (77%), followed by other public sources (22%). Private health insurance and families each paid less than 1% of pediatric home health expenses. The most important factors affecting access to home health care are the inadequate supply of clinicians and ancillary personnel, shortages of home health nurses with pediatric expertise, inadequate payment, and restrictive insurance and managed care policies. Many children must stay in the NICU, PICU, and other pediatric wards and intermediate care areas at a much higher cost because of inadequate pediatric home health care services. The main financing problem pertaining to Medicaid is low payment to home health agencies at rates that are insufficient to provide beneficiaries access to home health services. Although home care services may be a covered benefit under private health plans, most do not cover private-duty nursing (83%), home health aides (45%), or home physical, occupational, or speech therapy (33%) and/or impose visit or monetary limits or caps. To advocate for improvements in financing of pediatric home health care, the American Academy of Pediatrics has developed several recommendations for public policy makers, federal and state Medicaid offices, private insurers, managed care plans, Title V officials, and home health care professionals. These recommendations will improve licensing, payment, coverage, and research related to pediatric home health services.

Home-Use Tests - Cholesterol

MedlinePlus

... Medical Procedures In Vitro Diagnostics Home Use Tests Cholesterol Share Tweet Linkedin Pin it More sharing options ... a home-use test kit to measure total cholesterol. What cholesterol is: Cholesterol is a fat (lipid) ...

Alternatives to Nursing Homes

MedlinePlus

... this website may not be available. Alternatives to nursing homes Before you make any decisions about long ... live and what help you may need. A nursing home may not be your only choice. Discharge ...

The determinants of home and nursing home death: a systematic review and meta-analysis.

PubMed

Costa, Vania; Earle, Craig C; Esplen, Mary Jane; Fowler, Robert; Goldman, Russell; Grossman, Daphna; Levin, Leslie; Manuel, Douglas G; Sharkey, Shirlee; Tanuseputro, Peter; You, John J

2016-01-20

Most Canadians die in hospital, and yet, many express a preference to die at home. Place of death is the result of the interaction among sociodemographic, illness- and healthcare-related factors. Although home death is sometimes considered a potential indicator of end-of-life/palliative care quality, some determinants of place of death are more modifiable than others. The objective of this systematic review was to evaluate the determinants of home and nursing home death in adult patients diagnosed with an advanced, life-limiting illness. A systematic literature search was performed for studies in English published from January 1, 2004 to September 24, 2013 that evaluated the determinants of home or nursing home death compared to hospital death in adult patients with an advanced, life-limiting condition. The adjusted odds ratios, relative risks, and 95% confidence intervals of each determinant were extracted from the studies. Meta-analyses were performed if appropriate. The quality of individual studies was assessed using the Newcastle-Ottawa scale and the body of evidence was assessed according to the GRADE Working Group criteria. Of the 5,900 citations identified, 26 retrospective cohort studies were eligible. The risk of bias in the studies identified was considered low. Factors associated with an increased likelihood of home versus hospital death included multidisciplinary home palliative care, preference for home death, cancer as opposed to other diagnoses, early referral to palliative care, not living alone, having a caregiver, and the caregiver's coping skills. Knowledge about the determinants of place of death can be used to inform care planning between healthcare providers, patients and family members regarding the feasibility of dying in the preferred location and may help explain the incongruence between preferred and actual place of death. Modifiable factors such as early referral to palliative care, presence of a multidisciplinary home palliative care

Nursing Home Staff Turnover: Impact on Nursing Home Compare Quality Measures

ERIC Educational Resources Information Center

Castle, Nicholas G.; Engberg, John; Men, Aiju

2007-01-01

Purpose: We used data from a large sample of nursing homes to examine the association between staff turnover and quality. Design and Methods: The staff turnover measures came from primary data collected from 2,840 nursing homes in 2004 (representing a 71% response rate). Data collection included measures for nurse aides, licensed practical nurses,…

An Ontology-based Context-aware System for Smart Homes: E-care@home.

PubMed

Alirezaie, Marjan; Renoux, Jennifer; Köckemann, Uwe; Kristoffersson, Annica; Karlsson, Lars; Blomqvist, Eva; Tsiftes, Nicolas; Voigt, Thiemo; Loutfi, Amy

2017-07-06

Smart home environments have a significant potential to provide for long-term monitoring of users with special needs in order to promote the possibility to age at home. Such environments are typically equipped with a number of heterogeneous sensors that monitor both health and environmental parameters. This paper presents a framework called E-care@home, consisting of an IoT infrastructure, which provides information with an unambiguous, shared meaning across IoT devices, end-users, relatives, health and care professionals and organizations. We focus on integrating measurements gathered from heterogeneous sources by using ontologies in order to enable semantic interpretation of events and context awareness. Activities are deduced using an incremental answer set solver for stream reasoning. The paper demonstrates the proposed framework using an instantiation of a smart environment that is able to perform context recognition based on the activities and the events occurring in the home.

An Ontology-based Context-aware System for Smart Homes: E-care@home

PubMed Central

Alirezaie, Marjan; Köckemann, Uwe; Kristoffersson, Annica; Karlsson, Lars; Blomqvist, Eva; Voigt, Thiemo; Loutfi, Amy

2017-01-01

Smart home environments have a significant potential to provide for long-term monitoring of users with special needs in order to promote the possibility to age at home. Such environments are typically equipped with a number of heterogeneous sensors that monitor both health and environmental parameters. This paper presents a framework called E-care@home, consisting of an IoT infrastructure, which provides information with an unambiguous, shared meaning across IoT devices, end-users, relatives, health and care professionals and organizations. We focus on integrating measurements gathered from heterogeneous sources by using ontologies in order to enable semantic interpretation of events and context awareness. Activities are deduced using an incremental answer set solver for stream reasoning. The paper demonstrates the proposed framework using an instantiation of a smart environment that is able to perform context recognition based on the activities and the events occurring in the home. PMID:28684686

Home Visiting in Two Cultures

ERIC Educational Resources Information Center

Lamorey, Suzanne

2017-01-01

The home visiting component of early childhood education programs provides an important portal through which to observe family interactions as well as gain insights about the ethnotheories of the home visitor. Home visits were videotaped in the United States and in Turkey to analyze training and program effectiveness. One striking feature of this…

12 CFR 541.14 - Home.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 12 Banks and Banking 6 2014-01-01 2012-01-01 true Home. 541.14 Section 541.14 Banks and Banking OFFICE OF THRIFT SUPERVISION, DEPARTMENT OF THE TREASURY DEFINITIONS FOR REGULATIONS AFFECTING FEDERAL SAVINGS ASSOCIATIONS § 541.14 Home. The term home means real estate comprising a single-family dwelling(s...

12 CFR 541.14 - Home.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 12 Banks and Banking 6 2012-01-01 2012-01-01 false Home. 541.14 Section 541.14 Banks and Banking OFFICE OF THRIFT SUPERVISION, DEPARTMENT OF THE TREASURY DEFINITIONS FOR REGULATIONS AFFECTING FEDERAL SAVINGS ASSOCIATIONS § 541.14 Home. The term home means real estate comprising a single-family dwelling(s...

12 CFR 541.14 - Home.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 12 Banks and Banking 6 2013-01-01 2012-01-01 true Home. 541.14 Section 541.14 Banks and Banking OFFICE OF THRIFT SUPERVISION, DEPARTMENT OF THE TREASURY DEFINITIONS FOR REGULATIONS AFFECTING FEDERAL SAVINGS ASSOCIATIONS § 541.14 Home. The term home means real estate comprising a single-family dwelling(s...

12 CFR 541.14 - Home.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 12 Banks and Banking 5 2011-01-01 2011-01-01 false Home. 541.14 Section 541.14 Banks and Banking OFFICE OF THRIFT SUPERVISION, DEPARTMENT OF THE TREASURY DEFINITIONS FOR REGULATIONS AFFECTING FEDERAL SAVINGS ASSOCIATIONS § 541.14 Home. The term home means real estate comprising a single-family dwelling(s...

12 CFR 541.14 - Home.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 12 Banks and Banking 5 2010-01-01 2010-01-01 false Home. 541.14 Section 541.14 Banks and Banking OFFICE OF THRIFT SUPERVISION, DEPARTMENT OF THE TREASURY DEFINITIONS FOR REGULATIONS AFFECTING FEDERAL SAVINGS ASSOCIATIONS § 541.14 Home. The term home means real estate comprising a single-family dwelling(s...

Homing success in wintering sparrows

Treesearch

C. John Ralph; L. Richard Mewaldt

1976-01-01

The ability of birds to return "home" after displacement is generallywell known but poorly understood because of the multiplicity of variablesthat affect homing performance. These variables can include age andprevious experience of the bird, as well as the timing and distance of thedisplacement. The phenomenon of homing is also difficult to interpretbecause,...

Home Making Around the World.

ERIC Educational Resources Information Center

Extension Service (USDA), Washington, DC.

This book is designed to aid American home economists sent to other countries on technical assistance programs and home economists of other countries responsible for beginning such programs focused on the home and family. The information describes the pioneering experience of trained people in many countries and some ways in which basic principles…

Home Improvements Prevent Falls

MedlinePlus

... turn JavaScript on. Feature: Falls and Older Adults Home Improvements Prevent Falls Past Issues / Winter 2014 Table ... and ensure your safety. "Safe-ty-fy" Your Home Some Questions for Your Provider Will my medicines ...

Home Fires Involving Grills

MedlinePlus

... the home and from other things that can burn. f fEleven percent of home grill structure fires ... 200 or 49%) of the injuries were thermal burns, including burns both from fire and from contact ...

Paediatric home care in the UK.

PubMed Central

Tatman, M A; Woodroffe, C

1993-01-01

Paediatric home care services in the UK were ascertained in 1991 and 1992. Respondents from 209 (97%) UK health districts and boards identified 62 general and 124 specialist paediatric home care services by January 1993, 15% having opened in the previous year. Of all UK children, 30% lived in a district with a general home care service. Five health regions had only specialist services. Districts differed widely in the availability of home care for different disorders. The home care services were small, general services employing a mean (SD) of 2.5 (1.6) whole time equivalent (WTE) nurses, and specialist services 1.3 (0.8) WTE nurses. Few services were available 24 hours a day. Funding arrangements were diverse and some services had difficulties in obtaining consumables and equipment for home use. Despite rapid growth there remains considerable scope for the development of paediatric home care throughout the UK. PMID:8285782

The U.S. home infusion market.

PubMed

Monk-Tutor, M R

1998-10-01

Medicare legislation stimulated the development of home care services but also resulted in fragmentation of service components. In the 1980s, prospective pricing and diagnosis-related groups, and resulting pressures to reduce inpatient length of stay, prompted additional growth of the industry. Even so, in 1995 home care represented only 3% of total national expenditures on health care. The annual growth rate of the home infusion industry dropped from 64% in 1982-86 to 24% in 1986-93. While revenue per patient for home infusion is expected to decrease under managed care, an increasing number of patients will support continued market growth. The home infusion market is highly competitive, with only a few large national providers and many small local providers. In 1996, 29% of acute care hospitals provided or were developing a home care program. Community pharmacists' options in the home infusion area include independent services, partnerships, joint ventures, contracts with hospitals, and franchises. The home infusion market is being integrated into alternative sites, such as ambulatory infusion centers (AICs), as providers attempt to diversify to maintain managed care contracts. AICs provide infusion therapy and nursing to noninstitutionalized, nonhome-bound patients. Untapped sources for future growth of the infusion market include long-term-care facilities. More consistent studies of the home care market are needed. Despite slowed growth in recent years, home care has a strong market in the United States.

Home care decision support using an Arden engine--merging smart home and vital signs data.

PubMed

Marschollek, Michael; Bott, Oliver J; Wolf, Klaus-H; Gietzelt, Matthias; Plischke, Maik; Madiesh, Moaaz; Song, Bianying; Haux, Reinhold

2009-01-01

The demographic change with a rising proportion of very old people and diminishing resources leads to an intensification of the use of telemedicine and home care concepts. To provide individualized decision support, data from different sources, e.g. vital signs sensors and home environmental sensors, need to be combined and analyzed together. Furthermore, a standardized decision support approach is necessary. The aim of our research work is to present a laboratory prototype home care architecture that integrates data from different sources and uses a decision support system based on the HL7 standard Arden Syntax for Medical Logical Modules. Data from environmental sensors connected to a home bus system are stored in a data base along with data from wireless medical sensors. All data are analyzed using an Arden engine with the medical knowledge represented in Medical Logic Modules. Multi-modal data from four different sensors in the home environment are stored in a single data base and are analyzed using an HL7 standard conformant decision support system. Individualized home care decision support must be based on all data available, including context data from smart home systems and medical data from electronic health records. Our prototype implementation shows the feasibility of using an Arden engine for decision support in a home setting. Our future work will include the utilization of medical background knowledge for individualized decision support, as there is no one-size-fits-all knowledge base in medicine.

New Whole-House Solutions Case Study: Tommy Williams Homes Initial Performance of Two Zero Energy Homes, Gainesville, Florida

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

none,

2011-11-01

Tommy Williams Homes worked with PNNL, Florida HERO, Energy Smart Home Plans, and Florida Solar Energy Center to design and test two zero energy homes. Energy use was 30% lower in one home and 60% lower in the other.

12 CFR 141.14 - Home.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 12 Banks and Banking 1 2012-01-01 2012-01-01 false Home. 141.14 Section 141.14 Banks and Banking COMPTROLLER OF THE CURRENCY, DEPARTMENT OF THE TREASURY DEFINITIONS FOR REGULATIONS AFFECTING FEDERAL SAVINGS ASSOCIATIONS § 141.14 Home. The term home means real estate comprising a single-family dwelling(s) or a...

12 CFR 141.14 - Home.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 12 Banks and Banking 1 2014-01-01 2014-01-01 false Home. 141.14 Section 141.14 Banks and Banking COMPTROLLER OF THE CURRENCY, DEPARTMENT OF THE TREASURY DEFINITIONS FOR REGULATIONS AFFECTING FEDERAL SAVINGS ASSOCIATIONS § 141.14 Home. The term home means real estate comprising a single-family dwelling(s) or a...

12 CFR 141.14 - Home.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 12 Banks and Banking 1 2013-01-01 2013-01-01 false Home. 141.14 Section 141.14 Banks and Banking COMPTROLLER OF THE CURRENCY, DEPARTMENT OF THE TREASURY DEFINITIONS FOR REGULATIONS AFFECTING FEDERAL SAVINGS ASSOCIATIONS § 141.14 Home. The term home means real estate comprising a single-family dwelling(s) or a...

Music Therapy Clinical Practice in Hospice: Differences Between Home and Nursing Home Delivery.

PubMed

Liu, Xiaodi; Burns, Debra S; Hilliard, Russell E; Stump, Timothy E; Unroe, Kathleen T

2015-01-01

Hospice music therapy is delivered in both homes and nursing homes (NH). No studies to date have explored differences in music therapy delivery between home and NH hospice patients. To compare music therapy referral reasons and delivery for hospice patients living in NH versus home. A retrospective, electronic medical record review was conducted from a large U.S. hospice of patients receiving music therapy between January 1, 2006, and December 31, 2010. Among the 4,804 patients, 2,930 lived in an NH and 1,847 patients lived at home. Compared to home, NH hospice patients were more likely to be female, older, unmarried, and Caucasian. For home hospice patients, the top referral reasons were patient/family emotional and spiritual support, quality of life, and isolation. The most frequent referral reasons for NH hospice patients were isolation, quality of life, and patient/family emotional and spiritual support. Differences in music therapy delivery depended mainly on patients' primary diagnosis and location of care. Results suggest differences in referral reasons and delivery based on an interaction between location of care and patient characteristics. Delivery differences are likely a result of individualized assessment and care plans developed by the music therapist and other interdisciplinary team members to address the unique needs of the patient. Thus, it is important to have professionally trained music therapists assess and provide tailored music-based interventions for patients with different referral reasons and personal characteristics. This study also supports staffing decisions based on patient need rather than average daily census. © the American Music Therapy Association 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

On-line hemodiafiltration at home.

PubMed

Vega, Almudena; Abad, Soraya; Macías, Nicolás; Aragoncillo, Inés

2018-04-01

Survival with online hemodiafiltration (OL-HDF) is higher than with hemodialysis; frequent hemodialysis has also improved survival and quality of life. Home hemodialysis facilitates frequent therapy. We report our experience with 2 patients with stage 5 CKD who started home hemodialysis with OL-HDF in November 2016. After a training period at the hospital, they started home hemodialysis with OL-HDF after learning how to manage dialysis monitors and how to administer water treatment. We used the "5008-home" (FMC © ) monitor, and the Acqua C © (Fresenius Medical Care) for water treatment. Water conductivity was always checked before and during dialysis sessions and was always 2.5 to 3 mS/cm. Water cultures always fulfilled the criteria for ultrapurity. As far as we know, this is the first report on patients receiving OL-HDF at home. The technique proved to be safe and valid for renal replacement therapy and transfers the benefits of hospital convective therapy to the home setting. Future data will enable us to determine whether survival has also improved. © 2017 International Society for Hemodialysis.

"The home infusion patient": patient profiles for the home infusion therapy market.

PubMed

Westbrook, K W; Powers, T

1999-01-01

The authors review the relevant literature regarding home health care patient profiles. An empirical analysis is provided from archival data for a home infusion company servicing patients in urban and rural areas. The results are provided as a 2 x 2 matrix for patients in urban and rural areas seeing either a specialist or primary care physicians. A series of moderated regressions indicate that type of treating physician, patient's gender, geographic residence and level of acuity are cogent in predicting the complexity of prescribed infusion therapies. Managerial implications are provided for the home care marketer in segmenting patient markets for infusion services.

Nursing Home Nomads: A Study of Transfers.

ERIC Educational Resources Information Center

Retsinas, Joan

Researchers have divided nursing home residents into long-stayers and short-stayers. While long-stayers rarely return home, they do not necessarily stay long in one institution. Instead, they may transfer from nursing home to nursing home. Although many studies have examined the impact of relocation on nursing home residents, few studies have…

Reducing Energy Use in Existing Homes by 30%: Learning From Home Performance with ENERGY STAR

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

Liaukus, C.

2014-12-01

The improvement of existing homes in the United States can have a much greater impact on overall residential energy use than the construction of highly efficient new homes. There are over 130 million existing housing units in the U.S., while annually new construction represents less than two percent of the total supply (U.S. Census Bureau, 2013). Therefore, the existing housing stock presents a clear opportunity and responsibility for Building America (BA) to guide the remodeling and retrofit market toward higher performance existing homes. There are active programs designed to improve the energy performance of existing homes. Home Performance with ENERGYmore » STAR (HPwES) is a market-rate program among them. BARA's research in this project verified that the New Jersey HPwES program is achieving savings in existing homes that meet or exceed BA's goal of 30%. Among the 17 HPwES projects with utility data included in this report, 15 have actual energy savings ranging from 24% to 46%. Further, two of the homes achieved that level of energy savings without the costly replacement of heating and cooling equipment, which indicates that less costly envelope packages could be offered to consumers unable to invest in more costly mechanical packages, potentially creating broader market impact.« less

Patterns in Home Care Use in Manitoba

ERIC Educational Resources Information Center

Mitchell, Lori; Roos, Noralou, P.; Shapiro, Evelyn

2005-01-01

Administrative home care data from the Manitoba Support Services Payroll (MSSP) system for fiscal years 1995/1996 to 1998/1999 were utilized to study home care client characteristics and changes in home care use over time. Patterns in home care access and use after hospitalization, before admission to a nursing home, and before death were…

Head Start Home Visitor Handbook.

ERIC Educational Resources Information Center

Administration for Children, Youth, and Families (DHHS), Washington, DC. Head Start Bureau.

Developed to provide assistance in the building of an effective home-based program for Head Start children and their families, this handbook may serve as a blueprint for parent-focused home visits that assist the child and family to meet their special needs. Chapter one focuses on the home visitation model for providing services to families and…

Can Intimacy Justify Home Education?

ERIC Educational Resources Information Center

Merry, Michael S.; Howell, Charles

2009-01-01

Many parents cite intimacy as one of their reasons for deciding to educate at home. It seems intuitively obvious that home education is conducive to intimacy because of the increased time families spend together. Yet what is not clear is whether intimacy can provide justification for one's decision to home educate. To see whether this is so, we…

[Maintaining patients' autonomy at home].

PubMed

Niang, Bénédicte; Coudre, Jean Pierre

2015-01-01

To maintain the flow of hospital discharges, the patient's return home with support from a home nursing service is important. If any difficulties are identified, there are various programmes or good practices which can be put into place. The future law on adapting society to ageing also comprises a scheme combining home assistance and nursing care.

Activities of daily living in nursing home and home care settings: a retrospective 1-year cohort study.

PubMed

Lee, Tae Wha; Cho, Eunhee; Yim, Eun Shil; Lee, Hye Sun; Ko, Yu Kyung; Kim, Bok Nam; Kim, Sinhye

2015-02-01

Korea introduced universal long-term care insurance (LTCI) for physically dependent older adults in 2008. Older adults, their family members, and policy makers in Korea want to know patient outcomes in different care modalities because older adults who have a similar functional status and LTC needs can choose either nursing home care or home care. The aim of this study was to compare activities of daily living (ADLs) in nursing home care and home care settings for physically dependent older adults in Korea. A retrospective 1-year cohort study using national LTCI data. This study used the LTCI dataset from the National Health Insurance Service in Korea. Participants were identified from among those in the LTCI dataset who enrolled from July 2008 to June 2010. We extracted a sample consisting of 22,557 older adults who consistently received either nursing home care (n = 11,678) or home care (n = 10,879) for 1 year. The outcome variable was change in ADLs after 1 year. Covariates were an older adult's home geographical region, LTC level, age, sex, primary caregiver, Medicaid beneficiary status, bedridden status, medical diagnosis, baseline ADLs, cognitive function, behavioral problems, nursing and special treatment, and rehabilitation needs. Multiple regression analysis of all participants unmatched and a paired t-test with a propensity-score-matched cohort were performed to explain the association of changes in ADLs with the types of LTC. Multiple regression analysis with all participants (n = 22,557) unmatched showed that compared with older adults who received home care, those who received nursing home care had deteriorated further in terms of ADLs after 1 year (β = 0.44108, P < .0001). After propensity-score matching, paired t-test analysis also found that the ADLs of older adults had deteriorated less in the home care group compared with the nursing home group after 1 year (P < .0001). The ADLs of older adults who received home care showed significantly less

Brain Computer Interface on Track to Home.

PubMed

Miralles, Felip; Vargiu, Eloisa; Dauwalder, Stefan; Solà, Marc; Müller-Putz, Gernot; Wriessnegger, Selina C; Pinegger, Andreas; Kübler, Andrea; Halder, Sebastian; Käthner, Ivo; Martin, Suzanne; Daly, Jean; Armstrong, Elaine; Guger, Christoph; Hintermüller, Christoph; Lowish, Hannah

2015-01-01

The novel BackHome system offers individuals with disabilities a range of useful services available via brain-computer interfaces (BCIs), to help restore their independence. This is the time such technology is ready to be deployed in the real world, that is, at the target end users' home. This has been achieved by the development of practical electrodes, easy to use software, and delivering telemonitoring and home support capabilities which have been conceived, implemented, and tested within a user-centred design approach. The final BackHome system is the result of a 3-year long process involving extensive user engagement to maximize effectiveness, reliability, robustness, and ease of use of a home based BCI system. The system is comprised of ergonomic and hassle-free BCI equipment; one-click software services for Smart Home control, cognitive stimulation, and web browsing; and remote telemonitoring and home support tools to enable independent home use for nonexpert caregivers and users. BackHome aims to successfully bring BCIs to the home of people with limited mobility to restore their independence and ultimately improve their quality of life.

Ownership conversions and nursing home performance.

PubMed

Grabowski, David C; Stevenson, David G

2008-08-01

To examine the effects of ownership conversions on nursing home performance. Online Survey, Certification, and Reporting system data from 1993 to 2004, and the Minimum Data Set (MDS) facility reports from 1998 to 2004. Regression specification incorporating facility fixed effects, with terms to identify trends in the pre- and postconversion periods. The annual rate of nursing home conversions almost tripled between 1994 and 2004. Our regression results indicate converting facilities are generally different throughout the pre/postconversion years, suggesting little causal effect of ownership conversions on nursing home performance. Before and after conversion, nursing homes converting from nonprofit to for-profit status generally exhibit deterioration in their performance, while nursing homes converting from for-profit to nonprofit status generally exhibit improvement. Policy makers have expressed concern regarding the implications of ownership conversions for nursing home performance. Our results imply that regulators and policy makers should not only monitor the outcomes of nursing home conversions, but also the targets of these conversions.

Haemodialysis: hospital or home?

PubMed

Power, Albert; Ashby, Damien

2014-02-01

Healthcare costs associated with the provision of dialysis therapy are escalating globally as the number of patients developing end-stage renal disease increases. In this setting, there has been heightened interest in the application and potential benefit of home haemodialysis therapies compared with the conventional approach of thrice weekly, incentre treatments. Increasingly, national healthcare systems are financially incentivising the expansion of home haemodialysis programmes with observational studies demonstrating better patient survival, superior control of circulating volume and blood pressure, greater patient satisfaction and lower running costs compared with incentre dialysis. Nonetheless, increasing the prevalence of home haemodialysis is challenged by the technological complexity of conventional dialysis systems, the need for significant adaptations to the home as well as suboptimal clinician and patient education about the feasibility and availability of this modality. In addition, enthusiasm about frequent as well as nocturnal (extended-hours) haemodialysis has been tempered by results from the recent Frequent Haemodialysis Network randomised controlled trials comparing these schedules with a conventional incentre regime. An increasing emphasis on empowering patient choice and promoting self-management of chronic illness is a powerful driver for the expansion of home haemodialysis programmes in the UK and internationally.

Home destruction within the Hayman Fire perimeter

Treesearch

Jack Cohen; Rick Stratton

2003-01-01

The Hayman Fire report on home destruction examines the following four questions: 1. How many homes were destroyed out of the total number of homes within the Hayman Fire perimeter? 2. What was the relative wildland fire intensity associated with the destroyed homes? 3. What was the categorical cause of home ignition suggested by the associated wildland fire intensity...

Music@Home: A novel instrument to assess the home musical environment in the early years.

PubMed

Politimou, Nina; Stewart, Lauren; Müllensiefen, Daniel; Franco, Fabia

2018-01-01

The majority of children under the age of 5 appear to show spontaneous enjoyment of singing, being exposed to music and interacting with musical instruments, but whether variations in engaging in such activities in the home could contribute to developmental outcomes is still largely unknown. Critically, researchers lack a comprehensive instrument with good psychometric properties to assess the home musical environment from infancy to the preschool years. To address this gap, this paper presents two studies that describe the development and validation of the Music@Home questionnaire, which comprises two versions: Infant and Preschool. In Study 1, an initial pool of items was generated and administered to a wide audience of parents (n = 287 for the Infant, n = 347 for the Preschool version). Exploratory factor analysis was used to identify different dimensions comprising the home musical environment of both infants and pre-schoolers, and to reduce the initial pool of items to a smaller number of meaningful items. In Study 2, convergent and divergent validity and internal and test-retest reliability of the new instrument were established, using data from a different sample of participants (n = 213 for the Infant, n = 213 for the Preschool version). The second study also investigated associations between the Music@Home and musical characteristics of the parents, such as their musical education and personal engagement with music. Overall, the Music@Home constitutes a novel, valid and reliable instrument that allows for the systematic assessment of distinct aspects of the home musical environment in families with children under the age of 5. Furthermore, the Infant and Preschool versions of the Music@Home present differential associations with musical characteristics of the parents opening a new area of inquiry into how musical exposure and interaction in the home may vary across different developmental stages.

Music@Home: A novel instrument to assess the home musical environment in the early years

PubMed Central

Stewart, Lauren; Müllensiefen, Daniel; Franco, Fabia

2018-01-01

The majority of children under the age of 5 appear to show spontaneous enjoyment of singing, being exposed to music and interacting with musical instruments, but whether variations in engaging in such activities in the home could contribute to developmental outcomes is still largely unknown. Critically, researchers lack a comprehensive instrument with good psychometric properties to assess the home musical environment from infancy to the preschool years. To address this gap, this paper presents two studies that describe the development and validation of the Music@Home questionnaire, which comprises two versions: Infant and Preschool. In Study 1, an initial pool of items was generated and administered to a wide audience of parents (n = 287 for the Infant, n = 347 for the Preschool version). Exploratory factor analysis was used to identify different dimensions comprising the home musical environment of both infants and pre-schoolers, and to reduce the initial pool of items to a smaller number of meaningful items. In Study 2, convergent and divergent validity and internal and test-retest reliability of the new instrument were established, using data from a different sample of participants (n = 213 for the Infant, n = 213 for the Preschool version). The second study also investigated associations between the Music@Home and musical characteristics of the parents, such as their musical education and personal engagement with music. Overall, the Music@Home constitutes a novel, valid and reliable instrument that allows for the systematic assessment of distinct aspects of the home musical environment in families with children under the age of 5. Furthermore, the Infant and Preschool versions of the Music@Home present differential associations with musical characteristics of the parents opening a new area of inquiry into how musical exposure and interaction in the home may vary across different developmental stages. PMID:29641607

Xerostomia among older home care clients.

PubMed

Viljakainen, Sari; Nykänen, Irma; Ahonen, Riitta; Komulainen, Kaija; Suominen, Anna Liisa; Hartikainen, Sirpa; Tiihonen, Miia

2016-06-01

The purpose of this study was to examine drug use and other factors associated with xerostomia in home care clients aged 75 years or older. The study sample included 270 home care clients aged ≥75 years living in Eastern and Central Finland. The home care clients underwent in-home interviews carried out by trained home care nurses, nutritionists, dental hygienists and pharmacists. The collected data contained information on sociodemographic factors, health and oral health status, drug use, depressive symptoms (GDS-15), cognitive functioning (MMSE), functional ability (Barthel Index, IADL) and nutrition (MNA). The primary outcome was xerostomia status (never, occasionally or continuously). Among the home care clients, 56% (n = 150) suffered from xerostomia. Persons with continuous xerostomia used more drugs and had more depressive symptoms and a higher number of comorbidities than other home care clients. In multivariate analyses, excessive polypharmacy (OR = 1.83, 95% Cl 1.08-3.10) and depressive symptoms (OR = 1.12, 95% Cl 1.03-1.22) were associated with xerostomia. Xerostomia is a common problem among old home care clients. Excessive polypharmacy, use of particular drug groups and depressive symptoms were associated with xerostomia. The findings support the importance of a multidisciplinary approach in the care of older home care clients. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Implementing Home Health Standards in Clinical Practice.

PubMed

Gorski, Lisa A

2016-02-01

In 1986, the American Nurses Association (ANA) published the first Standards of Home Health Practice. Revised in 1992 and expanded in 1999 to become Home Health Nursing: Scope and Standards of Practice, it was revised in 2008 and again in 2014. In the 2014 edition, there are 6 standards of home healthcare nursing practice and 10 standards of professional performance for home healthcare nursing. The focus of this article is to describe the home healthcare standards and to provide guidance for implementation in clinical practice. It is strongly encouraged that home healthcare administrators, educators, and staff obtain a copy of the standards and fully read this essential home healthcare resource.

Smart Secure Homes: A Survey of Smart Home Technologies that Sense, Assess, and Respond to Security Threats.

PubMed

Dahmen, Jessamyn; Cook, Diane J; Wang, Xiaobo; Honglei, Wang

2017-08-01

Smart home design has undergone a metamorphosis in recent years. The field has evolved from designing theoretical smart home frameworks and performing scripted tasks in laboratories. Instead, we now find robust smart home technologies that are commonly used by large segments of the population in a variety of settings. Recent smart home applications are focused on activity recognition, health monitoring, and automation. In this paper, we take a look at another important role for smart homes: security. We first explore the numerous ways smart homes can and do provide protection for their residents. Next, we provide a comparative analysis of the alternative tools and research that has been developed for this purpose. We investigate not only existing commercial products that have been introduced but also discuss the numerous research that has been focused on detecting and identifying potential threats. Finally, we close with open challenges and ideas for future research that will keep individuals secure and healthy while in their own homes.

Factors related to the provision of home-based end-of-life care among home-care nursing, home help, and care management agencies in Japan.

PubMed

Igarashi, Ayumi; Kurinobu, Takeshi; Ko, Ayako; Okamoto, Yuko; Matsuura, Shino; Feng, Mei; Yamamoto-Mitani, Noriko

2015-09-12

To promote home death, it is necessary to clarify the institutional barriers to conducting end-of-life (EOL) care and consider strategies to deal with this process. This study aims to clarify institution-related factors associated with the provision of home-based EOL care cases, and to compare them among three different types of home-care agencies. We administered a cross-sectional survey throughout Japan to investigate the number and characteristics of EOL cases of home-care nursing (HN), home-help (HH) and care management (CM) agencies. Bivariate and multivariate analyses were performed for each type of agency to examine factors related to the provision of EOL care. 378 HN agencies, 274 HH agencies, and 452 CM agencies responded to the distributed questionnaire. HN agencies had on average 2.1 (SD = 4.0; range 0-60) home-based EOL cases in the last 3 months, while HH agencies had 0.9 (SD = 1.3; range 0-7) and CM agencies had 1.5 (SD = 2.2; range 0-18) in the last 6 months. In a multivariable analysis of HN agencies, a large number of staff (OR: 1.52; p < 0.001) and a large number of collaborating CM agencies (OR: 1.08; p = 0.008) were positively associated with the provision of EOL care; in HH agencies, accepting EOL clients in the agency (OR: 3.29; p < 0.001) was positively associated with the provision of EOL care; in CM agencies, the number of staff (OR: 1.21; p = 0.037), the number of collaborating HH agencies (OR: 1.07; p = 0.032), and whether home-care nurses and home helpers visit clients together (OR: 1.89; p = 0.007) were positively associated with the provision of EOL care. The agency's size and the inter-agency collaborative system seemed most important among HN agencies and CM agencies, while institutional preparedness for EOL was most important for HH agencies. These findings represent important new information for targeting different effective strategies in the promotion of home-based EOL care, depending on the agency type.

Business Solutions Case Study: Marketing Zero Energy Homes: LifeStyle Homes, Melbourne, Florida

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

None

Building America research has shown that high-performance homes can potentially give builders an edge in the marketplace and can boost sales. But it doesn't happen automatically. It requires a tailored, easy to understand marketing campaign and sometimes a little flair. This case study highlights LifeStyle Homes’ successful marketing approach for their SunSmart home package, which has helped to boost sales for the company. SunSmart marketing includes a modified logo, weekly blog, social media, traditional advertising, website, and sales staff training. Marketing focuses on quality, durability, healthy indoor air, and energy efficiency with an emphasis on the surety of third-party verificationmore » and the scientific approach to developing the SunSmart package. With the introduction of SunSmart, LifeStyle began an early recovery, nearly doubling sales in 2010; SunSmart sales now exceed 300 homes, including more than 20 zero energy homes. Completed homes in 2014 far outpaced the national (19%) and southern census region (27%) recovery rates for the same period. As technology improves and evolves, this builder will continue to collaborate with Building America.« less