RECS Data Show Decreased Energy Consumption per Household

EIA Publications

2012-01-01

Total United States energy consumption in homes has remained relatively stable for many years as increased energy efficiency has offset the increase in the number and average size of housing units, according to the newly released data from the Residential Energy Consumption Survey (RECS). The average household consumed 90 million British thermal units (Btu) in 2009 based on RECS. This continues the downward trend in average residential energy consumption of the last 30 years. Despite increases in the number and the average size of homes plus increased use of electronics, improvements in efficiency for space heating, air conditioning, and major appliances have all led to decreased consumption per household. Newer homes also tend to feature better insulation and other characteristics, such as double-pane windows, that improve the building envelope.

The amino-terminal domain of ORF149 of koi herpesvirus is preferentially targeted by IgM from carp populations surviving infection.

PubMed

Torrent, F; Villena, A; Lee, P A; Fuchs, W; Bergmann, S M; Coll, J M

2016-10-01

Recombinantly expressed fragments of the protein encoded by ORF149 (pORF149), a structural protein from the common- and koi-carp-infecting cyprinid herpesvirus-3 (CyHV-3) that was previously shown to be antigenic, were used to obtain evidence that its amino-terminal part contains immunodominant epitopes in fish populations that survived the infection. To obtain such evidence, nonspecific binding of carp serum tetrameric IgM had to be overcome by a novel ELISA protocol (rec2-ELISA). Rec2-ELISA involved pre-adsorption of carp sera with a heterologous recombinant fragment before incubation with pORF149 fragments and detection with anti-carp IgM monoclonal antibodies. Only in this way was it possible to distinguish between sera from uninfected and survivor carp populations. Although IgM from survivors recognised pORF149 fragments to a lesser degree than whole virus, specificity was confirmed by correlation of rec2- and CyHV-3-ELISAs, inhibition of rec2-ELISA by an excess of frgIIORF149, ELISA using IgM-capture, Western blotting, and reduction of reactivity in CyHV-3-ELISA by pre-adsorption of sera with frgIIORF149. The similarity of IgM-binding profiles between frgIORF149 (amino acid residues 42-629) and frgIIORF149 (42-159) and their reactivities with previously described anti-CyHV-3 monoclonal antibodies confirmed that most pORF149 epitopes were localised in its amino-terminal part.

Single Molecule Visualization of Protein-DNA Complexes: Watching Machines at Work

NASA Astrophysics Data System (ADS)

Kowalczykowski, Stephen

2013-03-01

We can now watch individual proteins acting on single molecules of DNA. Such imaging provides unprecedented interrogation of fundamental biophysical processes. Visualization is achieved through the application of two complementary procedures. In one, single DNA molecules are attached to a polystyrene bead and are then captured by an optical trap. The DNA, a worm-like coil, is extended either by the force of solution flow in a micro-fabricated channel, or by capturing the opposite DNA end in a second optical trap. In the second procedure, DNA is attached by one end to a glass surface. The coiled DNA is elongated either by continuous solution flow or by subsequently tethering the opposite end to the surface. Protein action is visualized by fluorescent reporters: fluorescent dyes that bind double-stranded DNA (dsDNA), fluorescent biosensors for single-stranded DNA (ssDNA), or fluorescently-tagged proteins. Individual molecules are imaged using either epifluorescence microscopy or total internal reflection fluorescence (TIRF) microscopy. Using these approaches, we imaged the search for DNA sequence homology conducted by the RecA-ssDNA filament. The manner by which RecA protein finds a single homologous sequence in the genome had remained undefined for almost 30 years. Single-molecule imaging revealed that the search occurs through a mechanism termed ``intersegmental contact sampling,'' in which the randomly coiled structure of DNA is essential for reiterative sampling of DNA sequence identity: an example of parallel processing. In addition, the assembly of RecA filaments on single molecules of single-stranded DNA was visualized. Filament assembly requires nucleation of a protein dimer on DNA, and subsequent growth occurs via monomer addition. Furthermore, we discovered a class of proteins that catalyzed both nucleation and growth of filaments, revealing how the cell controls assembly of this protein-DNA complex.

Experimental demonstration of distributed feedback semiconductor lasers based on reconstruction-equivalent-chirp technology.

PubMed

Li, Jingsi; Wang, Huan; Chen, Xiangfei; Yin, Zuowei; Shi, Yuechun; Lu, Yanqing; Dai, Yitang; Zhu, Hongliang

2009-03-30

In this paper we report, to the best of our knowledge, the first experimental realization of distributed feedback (DFB) semiconductor lasers based on reconstruction-equivalent-chirp (REC) technology. Lasers with different lasing wavelengths are achieved simultaneously on one chip, which shows a potential for the REC technology in combination with the photonic integrated circuits (PIC) technology to be a possible method for monolithic integration, in that its fabrication is as powerful as electron beam technology and the cost and time-consuming are almost the same as standard holographic technology.

The RecF protein antagonizes RecX function via direct interaction

PubMed Central

Lusetti, Shelley L.; Hobbs, Michael D.; Stohl, Elizabeth A.; Chitteni-Pattu, Sindhu; Inman, Ross B.; Seifert, H. Steven; Cox, Michael M.

2014-01-01

Summary The RecX protein inhibits RecA filament extension leading to net filament disassembly. The RecF protein physically interacts with the RecX protein and protects RecA from the inhibitory effects of RecX. In vitro, efficient RecA filament formation onto SSB-coated circular single-stranded DNA in the presence of RecX occurs only when all of the RecFOR proteins are present. The RecOR proteins contribute only to RecA filament nucleation onto SSB-coated single-stranded DNA and are unable to counter the inhibitory effects of RecX on RecA filaments. RecF protein uniquely supports substantial RecA filament extension in the presence of RecX. In vivo, RecF protein counters a RecX-mediated inhibition of plasmid recombination. Thus, a significant positive contribution of RecF to RecA filament assembly is to antagonize the effects of the negative modulator, RecX, specifically during the extension phase. PMID:16387652

AN/SLQ-32 EW System Model: and Expandable, Object-Oriented, Process- Based Simulation

DTIC Science & Technology

1992-09-01

CONST threshold = 0.1; timetol = 0.01; orientol = 5.8; VAR rec, recLast :BufferBeamRecType; time,power : REAL; powerl,orientation : REAL; BEGIN NEW...PulseGroup); rec:-ASK BufferBeam Removed; time: =rec. time; orientation: =rec. orientation; OUTPUT ( "ORIENREFI, orientation); recLast :=ASK BufferBeam Last...TO Add(rec); IF (rec= recLast ) EXIT; END IF; rec :=ASK BufferBeam Remove o; ELSE ASK BufferBeam TO Add(rec); IF (rec = recLast ) EXIT; END IF; rec

Attainment of Electron Beam Suitable for Medium Energy Electron Cooling

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

Seletskiy, Sergei M.

Electron cooling of charged particle beams is a well-established technique at electron energies of up to 300 keV. However, up to the present time the advance of electron cooling to the MeV-range energies has remained a purely theoretical possibility. The electron cooling project at Fermilab has recently demonstrated the ¯rst cooling of 8.9 GeV/c antiprotons in the Recycler ring, and therefore, has proved the validity of the idea of relativistic electron cool- ing. The Recycler Electron Cooler (REC) is the key component of the Teva- tron Run II luminosity upgrade project. Its performance depends critically on the quality of electronmore » beam. A stable electron beam of 4.3 MeV car- rying 0.5 A of DC current is required. The beam suitable for the Recycler Electron Cooler must have an angular spread not exceeding 200 ¹rad. The full-scale prototype of the REC was designed, built and tested at Fermilab in the Wideband laboratory to study the feasibility of attaining the high-quality electron beam. In this thesis I describe various aspects of development of the Fermilab electron cooling system, and the techniques used to obtain the electron beam suitable for the cooling process. In particular I emphasize those aspects of the work for which I was principally responsible.« less

Suppression of the UV-sensitive phenotype of Escherichia coli recF mutants by recA(Srf) and recA(Tif) mutations requires recJ+.

PubMed Central

Thoms, B; Wackernagel, W

1988-01-01

Mutations in recA, such as recA801(Srf) (suppressor of RecF) or recA441(Tif) (temperature-induced filamentation) partially suppress the deficiency in postreplication repair of UV damage conferred by recF mutations. We observed that spontaneous recA(Srf) mutants accumulated in cultures of recB recC sbcB sulA::Mu dX(Ap lac) lexA51 recF cells because they grew faster than the parental strain. We show that in a uvrA recB+ recC+ genetic background there are two prerequisites for the suppression by recA(Srf) of the UV-sensitive phenotype of recF mutants. (i) The recA(Srf) protein must be provided in increased amounts either by SOS derepression or by a recA operator-constitutive mutation in a lexA(Ind) (no induction of SOS functions) genetic background. (ii) The gene recJ, which has been shown previously to be involved in the recF pathway of recombination and repair, must be functional. The level of expression of recJ in a lexA(Ind) strain suffices for full suppression. Suppression by recA441 at 30 degrees C also depends on recJ+. The hampered induction by UV of the SOS gene uvrA seen in a recF mutant was improved by a recA(Srf) mutation. This improvement did not require recJ+. We suggest that recA(Srf) and recA(Tif) mutant proteins can operate in postreplication repair independent of recF by using the recJ+ function. PMID:2841294

3' Homologous Free Ends are Required for Stable Joint Molecule Formation by the RecA and Single-Stranded Binding Proteins of Escherichia coli

NASA Astrophysics Data System (ADS)

Konforti, Boyana B.; Davis, Ronald W.

1987-02-01

The RecA protein of Escherichia coli is important for genetic recombination in vivo and can promote synapsis and strand exchange in vitro. The DNA pairing and strand exchange reactions have been well characterized in reactions with circular single strands and linear duplexes, but little is known about these two processes using substrates more characteristic of those likely to exist in the cell. Single-stranded linear DNAs were prepared by separating strands of duplex molecules or by cleaving single-stranded circles at a unique restriction site created by annealing a short defined oligonucleotide to the circle. Analysis by gel electrophoresis and electron microscopy revealed that, in the presence of RecA and single-stranded binding proteins, a free 3' homologous end is essential for stable joint molecule formation between linear single-stranded and circular duplex DNA.

The RecX protein interacts with the RecA protein and modulates its activity in Herbaspirillum seropedicae

PubMed Central

Galvão, C.W.; Souza, E.M.; Etto, R.M.; Pedrosa, F.O.; Chubatsu, L.S.; Yates, M.G.; Schumacher, J.; Buck, M.; Steffens, M.B.R.

2012-01-01

DNA repair is crucial to the survival of all organisms. The bacterial RecA protein is a central component in the SOS response and in recombinational and SOS DNA repairs. The RecX protein has been characterized as a negative modulator of RecA activity in many bacteria. The recA and recX genes of Herbaspirillum seropedicae constitute a single operon, and evidence suggests that RecX participates in SOS repair. In the present study, we show that the H. seropedicae RecX protein (RecXHs) can interact with the H. seropedicae RecA protein (RecAHs) and that RecAHs possesses ATP binding, ATP hydrolyzing and DNA strand exchange activities. RecXHs inhibited 90% of the RecAHs DNA strand exchange activity even when present in a 50-fold lower molar concentration than RecAHs. RecAHs ATP binding was not affected by the addition of RecX, but the ATPase activity was reduced. When RecXHs was present before the formation of RecA filaments (RecA-ssDNA), inhibition of ATPase activity was substantially reduced and excess ssDNA also partially suppressed this inhibition. The results suggest that the RecXHs protein negatively modulates the RecAHs activities by protein-protein interactions and also by DNA-protein interactions. PMID:23044625

Implementing a Social Knowledge Networking (SKN) system to enable meaningful use of an EHR medication reconciliation system.

PubMed

Rangachari, Pavani

2018-01-01

Despite the regulatory impetus toward meaningful use of electronic health record (EHR) Medication Reconciliation (MedRec) to prevent medication errors during care transitions, hospital adherence has lagged for one chief reason: low physician engagement, stemming from lack of consensus about which physician is responsible for managing a patient's medication list. In October 2016, Augusta University received a 2-year grant from the Agency for Healthcare Research and Quality to implement a Social Knowledge Networking (SKN) system for enabling its health system (AU Health) to progress from "limited use" of EHR MedRec technology to "meaningful use." The hypothesis is that SKN would bring together a diverse group of practitioners, to facilitate tacit knowledge exchange on issues related to EHR MedRec, which in turn is expected to increase practitioners' engagement in addressing those issues and enable meaningful use of EHR. The specific aims are to examine: 1) user-engagement in the SKN system, and 2) associations between "SKN use" and "meaningful use" of EHR. The 2-year project uses an exploratory mixed-method design and consists of three phases: 1) development; 2) SKN implementation; and 3) analysis. Phase 1, completed in May 2017, sought to identify a comprehensive set of issues related to EHR MedRec from practitioners directly involved in the MedRec process. This process facilitated development of a "Reporting Tool" on issues related to EHR MedRec, which, along with an existing "SKN/Discussion Tool," was integrated into the EHR at AU Health. Phase 2 (launched in June 2017) involves implementing the EHR-integrated SKN system over a 52-week period in inpatient and outpatient medicine units. The prospective implementation design is expected to generate context-sensitive strategies for meaningful use and successful implementation of EHR MedRec and thereby make substantial contributions to the patient safety and risk management literature. From a health care policy perspective, if the hypothesis holds, federal vendors could be encouraged to incorporate SKN features into EHR systems.

Electronic noses and tongues: Applications for the food and pharmaceutical industries

USDA-ARS?s Scientific Manuscript database

The electronic nose (enose) is designed to crudely mimic the human brain in that most contain sensors that non-selectively interact with odor molecules to produce some sort of signal that is then sent to a computer that uses multivariate statistics to determine patterns in the data. This pattern rec...

The RecX protein interacts with the RecA protein and modulates its activity in Herbaspirillum seropedicae.

PubMed

Galvão, C W; Souza, E M; Etto, R M; Pedrosa, F O; Chubatsu, L S; Yates, M G; Schumacher, J; Buck, M; Steffens, M B R

2012-12-01

DNA repair is crucial to the survival of all organisms. The bacterial RecA protein is a central component in the SOS response and in recombinational and SOS DNA repairs. The RecX protein has been characterized as a negative modulator of RecA activity in many bacteria. The recA and recX genes of Herbaspirillum seropedicae constitute a single operon, and evidence suggests that RecX participates in SOS repair. In the present study, we show that the H. seropedicae RecX protein (RecX Hs) can interact with the H. seropedicaeRecA protein (RecA Hs) and that RecA Hs possesses ATP binding, ATP hydrolyzing and DNA strand exchange activities. RecX Hs inhibited 90% of the RecA Hs DNA strand exchange activity even when present in a 50-fold lower molar concentration than RecA Hs. RecA Hs ATP binding was not affected by the addition of RecX, but the ATPase activity was reduced. When RecX Hs was present before the formation of RecA filaments (RecA-ssDNA), inhibition of ATPase activity was substantially reduced and excess ssDNA also partially suppressed this inhibition. The results suggest that the RecX Hs protein negatively modulates the RecA Hs activities by protein-protein interactions and also by DNA-protein interactions.

Replication restart in UV-irradiated Escherichia coli involving pols II, III, V, PriA, RecA and RecFOR proteins.

PubMed

Rangarajan, Savithri; Woodgate, Roger; Goodman, Myron F

2002-02-01

In Escherichia coli, UV-irradiated cells resume DNA synthesis after a transient inhibition by a process called replication restart. To elucidate the role of several key proteins involved in this process, we have analysed the time dependence of replication restart in strains carrying a combination of mutations in lexA, recA, polB (pol II), umuDC (pol V), priA, dnaC, recF, recO or recR. We find that both pol II and the origin-independent primosome-assembling function of PriA are essential for the immediate recovery of DNA synthesis after UV irradiation. In their absence, translesion replication or 'replication readthrough' occurs approximately 50 min after UV and is pol V-dependent. In a wild-type, lexA+ background, mutations in recF, recO or recR block both pathways. Similar results were obtained with a lexA(Def) recF strain. However, lexA(Def) recO or lexA(Def) recR strains, although unable to facilitate PriA-pol II-dependent restart, were able to perform pol V-dependent readthrough. The defects in restart attributed to mutations in recF, recO or recR were suppressed in a recA730 lexA(Def) strain expressing constitutively activated RecA (RecA*). Our data suggest that in a wild-type background, RecF, O and R are important for the induction of the SOS response and the formation of RecA*-dependent recombination intermediates necessary for PriA/Pol II-dependent replication restart. In con-trast, only RecF is required for the activation of RecA that leads to the formation of pol V (UmuD'2C) and facilitates replication readthrough.

Genetic requirements for high constitutive SOS expression in recA730 mutants of Escherichia coli.

PubMed

Vlašić, Ignacija; Šimatović, Ana; Brčić-Kostić, Krunoslav

2011-09-01

The RecA protein in its functional state is in complex with single-stranded DNA, i.e., in the form of a RecA filament. In SOS induction, the RecA filament functions as a coprotease, enabling the autodigestion of the LexA repressor. The RecA filament can be formed by different mechanisms, but all of them require three enzymatic activities essential for the processing of DNA double-stranded ends. These are helicase, 5'-3' exonuclease, and RecA loading onto single-stranded DNA (ssDNA). In some mutants, the SOS response can be expressed constitutively during the process of normal DNA metabolism. The RecA730 mutant protein is able to form the RecA filament without the help of RecBCD and RecFOR mediators since it better competes with the single-strand binding (SSB) protein for ssDNA. As a consequence, the recA730 mutants show high constitutive SOS expression. In the study described in this paper, we studied the genetic requirements for constitutive SOS expression in recA730 mutants. Using a β-galactosidase assay, we showed that the constitutive SOS response in recA730 mutants exhibits different requirements in different backgrounds. In a wild-type background, the constitutive SOS response is partially dependent on RecBCD function. In a recB1080 background (the recB1080 mutation retains only helicase), constitutive SOS expression is partially dependent on RecBCD helicase function and is strongly dependent on RecJ nuclease. Finally, in a recB-null background, the constitutive SOS expression of the recA730 mutant is dependent on the RecJ nuclease. Our results emphasize the importance of the 5'-3' exonuclease for high constitutive SOS expression in recA730 mutants and show that RecBCD function can further enhance the excellent intrinsic abilities of the RecA730 protein in vivo. Copyright © 2011, American Society for Microbiology. All Rights Reserved.

The recX gene product is involved in the SOS response in Herbaspirillum seropedicae.

PubMed

Galvão, Carolina W; Pedrosa, Fábio O; Souza, Emanuel M; Yates, M Geoffrey; Chubatsu, Leda S; Steffens, Maria Berenice R

2003-02-01

The recA and the recX genes of Herbaspirillum seropedicae were sequenced. The recX is located 359 bp downstream from recA. Sequence analysis indicated the presence of a putative operator site overlapping a probable sigma70-dependent promoter upstream of recA and a transcription terminator downstream from recX, with no apparent promoter sequence in the intergenic region. Transcriptional analysis using lacZ promoter fusions indicated that recA expression increased three- to fourfold in the presence of methyl methanesulfonate (MMS). The roles of recA and recX genes in the SOS response were determined from studies of chromosomal mutants. The recA mutant showed the highest sensitivity to MMS and UV, and the recX mutant had an intermediate sensitivity, compared with the wild type (SMR1), confirming the essential role of the RecA protein in cell viability in the presence of mutagenic agents and also indicating a role for RecX in the SOS response.

Circadian clock protein KaiC forms ATP-dependent hexameric rings and binds DNA

PubMed Central

Mori, Tetsuya; Saveliev, Sergei V.; Xu, Yao; Stafford, Walter F.; Cox, Michael M.; Inman, Ross B.; Johnson, Carl H.

2002-01-01

KaiC from Synechococcus elongatus PCC 7942 (KaiC) is an essential circadian clock protein in cyanobacteria. Previous sequence analyses suggested its inclusion in the RecA/DnaB superfamily. A characteristic of the proteins of this superfamily is that they form homohexameric complexes that bind DNA. We show here that KaiC also forms ring complexes with a central pore that can be visualized by electron microscopy. A combination of analytical ultracentrifugation and chromatographic analyses demonstrates that these complexes are hexameric. The association of KaiC molecules into hexamers depends on the presence of ATP. The KaiC sequence does not include the obvious DNA-binding motifs found in RecA or DnaB. Nevertheless, KaiC binds forked DNA substrates. These data support the inclusion of KaiC into the RecA/DnaB superfamily and have important implications for enzymatic activity of KaiC in the circadian clock mechanism that regulates global changes in gene expression patterns. PMID:12477935

Circadian clock protein KaiC forms ATP-dependent hexameric rings and binds DNA.

PubMed

Mori, Tetsuya; Saveliev, Sergei V; Xu, Yao; Stafford, Walter F; Cox, Michael M; Inman, Ross B; Johnson, Carl H

2002-12-24

KaiC from Synechococcus elongatus PCC 7942 (KaiC) is an essential circadian clock protein in cyanobacteria. Previous sequence analyses suggested its inclusion in the RecADnaB superfamily. A characteristic of the proteins of this superfamily is that they form homohexameric complexes that bind DNA. We show here that KaiC also forms ring complexes with a central pore that can be visualized by electron microscopy. A combination of analytical ultracentrifugation and chromatographic analyses demonstrates that these complexes are hexameric. The association of KaiC molecules into hexamers depends on the presence of ATP. The KaiC sequence does not include the obvious DNA-binding motifs found in RecA or DnaB. Nevertheless, KaiC binds forked DNA substrates. These data support the inclusion of KaiC into the RecADnaB superfamily and have important implications for enzymatic activity of KaiC in the circadian clock mechanism that regulates global changes in gene expression patterns.

Deinococcus radiodurans RecA nucleoprotein filaments characterized at the single-molecule level with optical tweezers

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

Pobegalov, Georgii, E-mail: george.pobegalov@nanobio.spbstu.ru; Cherevatenko, Galina; Alekseev, Aleksandr

2015-10-23

Deinococcus radiodurans can survive extreme doses of ionizing radiation due to the very efficient DNA repair mechanisms that are able to cope even with hundreds of double-strand breaks. RecA, the critical protein of homologous recombination in bacteria, is one of the key components of the DNA-repair system. Repair of double-strand breaks requires RecA binding to DNA and assembly of the RecA nucleoprotein helical filaments. The Escherichia coli RecA protein (EcRecA) and its interactions with DNA have been extensively studied using various approaches including single-molecule techniques, while the D. radiodurans RecA (DrRecA) remains much less characterized. However, DrRecA shows some remarkable differencesmore » from E. coli homolog. Here we combine microfluidics and single-molecule DNA manipulation with optical tweezers to follow the binding of DrRecA to long double-stranded DNA molecules and probe the mechanical properties of DrRecA nucleoprotein filaments at physiological pH. Our data provide a direct comparison of DrRecA and EcRecA binding to double-stranded DNA under identical conditions. We report a significantly faster filaments assembly as well as lower values of persistence length and contour length for DrRecA nucleoprotein filaments compared to EcRecA. Our results support the existing model of DrRecA forming more frequent and less continuous filaments relative to those of EcRecA. - Highlights: • We investigate Deinococcus radiodurans RecA interactions with long double-stranded DNA at the single-molecule level. • At physiological pH D. radiodurans RecA forms nucleoprotein filaments significantly faster relative to Escherichia coli RecA. • D. radiodurans RecA-dsDNA nucleoprotein filaments are more flexible and slightly shorter compared to those of E. coli RecA.« less

Differential requirements of two recA mutants for constitutive SOS expression in Escherichia coli K-12.

PubMed

Long, Jarukit Edward; Renzette, Nicholas; Centore, Richard C; Sandler, Steven J

2008-01-01

Repairing DNA damage begins with its detection and is often followed by elicitation of a cellular response. In E. coli, RecA polymerizes on ssDNA produced after DNA damage and induces the SOS Response. The RecA-DNA filament is an allosteric effector of LexA auto-proteolysis. LexA is the repressor of the SOS Response. Not all RecA-DNA filaments, however, lead to an SOS Response. Certain recA mutants express the SOS Response (recA(C)) in the absence of external DNA damage in log phase cells. Genetic analysis of two recA(C) mutants was used to determine the mechanism of constitutive SOS (SOS(C)) expression in a population of log phase cells using fluorescence of single cells carrying an SOS reporter system (sulAp-gfp). SOS(C) expression in recA4142 mutants was dependent on its initial level of transcription, recBCD, recFOR, recX, dinI, xthA and the type of medium in which the cells were grown. SOS(C) expression in recA730 mutants was affected by none of the mutations or conditions tested above. It is concluded that not all recA(C) alleles cause SOS(C) expression by the same mechanism. It is hypothesized that RecA4142 is loaded on to a double-strand end of DNA and that the RecA filament is stabilized by the presence of DinI and destabilized by RecX. RecFOR regulate the activity of RecX to destabilize the RecA filament. RecA730 causes SOS(C) expression by binding to ssDNA in a mechanism yet to be determined.

Exposure Assessment in a Single-Walled Carbon Nanotube Primary Manufacturer.

PubMed

Kouassi, Serge; Catto, Cyril; Ostiguy, Claude; L'Espérance, Gilles; Kroeger, Jens; Debia, Maximilien

2017-03-01

This study was aimed at documenting and characterizing occupational exposure to single-walled carbon nanotubes (SWCNTs) generated in a primary manufacturing plant. It also compared various strategies of exposure monitoring. A 6-day measurement protocol was scheduled (D1-D6) including both (i) quasi-personal monitoring with an array of direct reading instruments (DRIs) and (ii) offline electron microscopy analyses of surface and breathing zone filter-based samples. The first step (D1 and D2) consisted of contamination screenings resulting from the various SWCNT production tasks using a multimetric approach. Surface sampling was also carried out to assess workplace cross-contamination. The second step (D3-D6) focused on the exposure monitoring during recovery/cleaning task, by comparing three personal elemental carbon (EC) measurements [respirable EC using a cyclone following the NIOSH 5040 method (REC-CYC), respirable and thoracic EC using parallel particle impactors [REC-PPI and TEC-PPI, respectively)] and gravimetric mass concentration measurements. DustTrak DRX and electrical low-pressure impactor measurements indicated that particles were released during weighing, transferring, and recovery/cleaning tasks of the manufacturing process. Electron microscopy revealed the presence of agglomerated SWCNTs only during the recovery/cleaning task. REC-CYC concentrations remained under the limits of quantification; REC-PPI showed levels up to 58 µg m-3; and TEC-PPI ranged from 40 to 70 µg m-3. Ratios calculated between gravimetric measurements and estimated DustTrak mass concentrations ranged from 2.8 to 4.9. Cross-contamination appeared to be limited since SWCNTs was only found on surface samples collected close to the reactor in the production room. This case study showed that the DustTrak DRX should be the preferred device among DRIs to identify potential exposure to SWCNTs. However, there is a risk of false positive since it is a non-specific instrument; therefore, the actual release of SWCNTs must be confirmed with scanning electron microscopy/transmission electron microscopy analyses. Besides, using EC measurements as a proxy for SWCNT exposure assessments, as suggested by the NIOSH, is still challenging since interferences can occur with other EC sources such as carbon black, which is also present in the workplace. © The Author 2017. Published by Oxford University Press on behalf of the British Occupational Hygiene Society.

The Incidence and Survival of Rare Cancers of the Thyroid, Parathyroid, Adrenal, and Pancreas.

PubMed

James, Benjamin C; Aschebrook-Kilfoy, Briseis; Cipriani, Nicole; Kaplan, Edwin L; Angelos, Peter; Grogan, Raymon H

2016-02-01

With the exception of papillary and follicular thyroid cancer, malignant cancers of the thyroid, parathyroid, adrenal, and endocrine pancreas are uncommon. These rare malignancies present a challenge to both the clinician and patient, because few data exist on their incidence or survival. We analyzed the incidence and survival of these rare endocrine cancers (RECs), as well as the trends in incidence over time. We used the NCI's SEER 18 database (2000-2012) to investigate incidence and survival of rare cancers of the thyroid, parathyroid, adrenal, and endocrine pancreas. Cancers were categorized using the WHO classification systems. We collected data on incidence, gender, stage, size, and survival. Time trends were evaluated from 2000-2002 to 2010-2012. We identified 36 types of rare cancers in the endocrine organs captured in the SEER database. RECs of the thyroid had the highest combined incidence rate (IR8.26), followed by pancreas (IR 3.24), adrenal (IR 2.71), and parathyroid (IR 0.41). The incidence rate for all rare endocrine organs combined increased 32.4 % during the study period. The majority of the increase was attributable to rare cancers of thyroid, which increased in not only microcarcinomas, but in all sizes. The mean 5-year survival for RECs is 59.56 % (range 2.49–100 %). This study is a comprehensive analysis ofthe incidence and survival for rare malignant endocrine cancers. There has been an increase in incidence rate of almost all RECs and their survival is low. We hope that our data will serve as a source of information for clinicians as well as bring awareness regarding these uncommon cancers.

Structural and Functional Studies of H. seropedicae RecA Protein - Insights into the Polymerization of RecA Protein as Nucleoprotein Filament.

PubMed

Leite, Wellington C; Galvão, Carolina W; Saab, Sérgio C; Iulek, Jorge; Etto, Rafael M; Steffens, Maria B R; Chitteni-Pattu, Sindhu; Stanage, Tyler; Keck, James L; Cox, Michael M

2016-01-01

The bacterial RecA protein plays a role in the complex system of DNA damage repair. Here, we report the functional and structural characterization of the Herbaspirillum seropedicae RecA protein (HsRecA). HsRecA protein is more efficient at displacing SSB protein from ssDNA than Escherichia coli RecA protein. HsRecA also promotes DNA strand exchange more efficiently. The three dimensional structure of HsRecA-ADP/ATP complex has been solved to 1.7 Å resolution. HsRecA protein contains a small N-terminal domain, a central core ATPase domain and a large C-terminal domain, that are similar to homologous bacterial RecA proteins. Comparative structural analysis showed that the N-terminal polymerization motif of archaeal and eukaryotic RecA family proteins are also present in bacterial RecAs. Reconstruction of electrostatic potential from the hexameric structure of HsRecA-ADP/ATP revealed a high positive charge along the inner side, where ssDNA is bound inside the filament. The properties of this surface may explain the greater capacity of HsRecA protein to bind ssDNA, forming a contiguous nucleoprotein filament, displace SSB and promote DNA exchange relative to EcRecA. Our functional and structural analyses provide insight into the molecular mechanisms of polymerization of bacterial RecA as a helical nucleoprotein filament.

An electrochemical aptasensor for multiplex antibiotics detection based on metal ions doped nanoscale MOFs as signal tracers and RecJf exonuclease-assisted targets recycling amplification.

PubMed

Chen, Meng; Gan, Ning; Zhou, You; Li, Tianhua; Xu, Qing; Cao, Yuting; Chen, Yinji

2016-12-01

An ultrasensitive electrochemical aptasensor for simultaneous detection of oxytetracycline (OTC) and kanamycin (KAN) has been developed based on metal ions doped metal organic frame materials (MOFs) as signal tracers and RecJ f exonuclease-catalyzed targets recycling amplification. The aptasensor consists of capture beads (the anti-single-stranded DNA Antibody, as anti-ssDNA Ab, labeled on Dynabeads) and nanoscale MOF (NMOF) based signal tracers (simplified as Apts-MNM, the NMOF labeled with metal ions and the aptamers). Particularly, the MOF (UiO-66-NH 2 ), with large internal surface areas, ultrahigh porosity and abundant amine groups in the pores, was employed as substrates to carry plenty of metal ions (Pb 2+ or Cd 2+ ) and label aptamers of OTC or KAN. Thus, the aptasensor is formed by the specific recognition between anti-ssDNA Ab and aptamers. In the presence of targets (OTC and KAN), aptamers prefer to form targets-Apts-MNM complexes in lieu of anti-ssDNA Ab-aptamer complexes, which results in the dissociation of Apts-MNM from capture beads. With the employment of RecJ f exonuclease, targets-Apts-MNM in supernatant was digested into mononucleotides and liberated the target, which can further participate in the next reaction cycling to produce more signal tracers. After magnetic separation, the enhanced square wave voltammetry (SWV) signals were produced from signal tracers. The aptasensor exhibited a linear correlation in the range from 0.5pM to 50nM, with detection limits of 0.18pM and 0.15pM (S/N=3) toward OTC and KAN respectively. This strategy provides specificity and sensitive approach for multiplex antibiotics detection and has promising applications in food analysis. Copyright © 2016 Elsevier B.V. All rights reserved.

Mechanical force antagonizes the inhibitory effects of RecX on RecA filament formation in Mycobacterium tuberculosis

PubMed Central

Le, Shimin; Chen, Hu; Zhang, Xinghua; Chen, Jin; Patil, K. Neelakanteshwar; Muniyappa, Kalappa; Yan, Jie

2014-01-01

Efficient bacterial recombinational DNA repair involves rapid cycles of RecA filament assembly and disassembly. The RecX protein plays a crucial inhibitory role in RecA filament formation and stability. As the broken ends of DNA are tethered during homologous search, RecA filaments assembled at the ends are likely subject to force. In this work, we investigated the interplay between RecX and force on RecA filament formation and stability. Using magnetic tweezers, at single molecular level, we found that Mycobacterium tuberculosis (Mt) RecX could catalyze stepwise de-polymerization of preformed MtRecA filament in the presence of ATP hydrolysis at low forces (<7 pN). However, applying larger forces antagonized the inhibitory effects of MtRecX, and a partially de-polymerized MtRecA filament could re-polymerize in the presence of MtRecX, which cannot be explained by previous models. Theoretical analysis of force-dependent conformational free energies of naked ssDNA and RecA nucleoprotein filament suggests that mechanical force stabilizes RecA filament, which provides a possible mechanism for the observation. As the antagonizing effect of force on the inhibitory function of RecX takes place in a physiological range; these findings broadly suggest a potential mechanosensitive regulation during homologous recombination. PMID:25294832

Implementing a Social Knowledge Networking (SKN) system to enable meaningful use of an EHR medication reconciliation system

PubMed Central

Rangachari, Pavani

2018-01-01

Background Despite the regulatory impetus toward meaningful use of electronic health record (EHR) Medication Reconciliation (MedRec) to prevent medication errors during care transitions, hospital adherence has lagged for one chief reason: low physician engagement, stemming from lack of consensus about which physician is responsible for managing a patient’s medication list. In October 2016, Augusta University received a 2-year grant from the Agency for Healthcare Research and Quality to implement a Social Knowledge Networking (SKN) system for enabling its health system (AU Health) to progress from “limited use” of EHR MedRec technology to “meaningful use.” The hypothesis is that SKN would bring together a diverse group of practitioners, to facilitate tacit knowledge exchange on issues related to EHR MedRec, which in turn is expected to increase practitioners’ engagement in addressing those issues and enable meaningful use of EHR. The specific aims are to examine: 1) user-engagement in the SKN system, and 2) associations between “SKN use” and “meaningful use” of EHR. Methods The 2-year project uses an exploratory mixed-method design and consists of three phases: 1) development; 2) SKN implementation; and 3) analysis. Phase 1, completed in May 2017, sought to identify a comprehensive set of issues related to EHR MedRec from practitioners directly involved in the MedRec process. This process facilitated development of a “Reporting Tool” on issues related to EHR MedRec, which, along with an existing “SKN/Discussion Tool,” was integrated into the EHR at AU Health. Phase 2 (launched in June 2017) involves implementing the EHR-integrated SKN system over a 52-week period in inpatient and outpatient medicine units. Discussion The prospective implementation design is expected to generate context-sensitive strategies for meaningful use and successful implementation of EHR MedRec and thereby make substantial contributions to the patient safety and risk management literature. From a health care policy perspective, if the hypothesis holds, federal vendors could be encouraged to incorporate SKN features into EHR systems. PMID:29618941

Structural and Functional Studies of H. seropedicae RecA Protein – Insights into the Polymerization of RecA Protein as Nucleoprotein Filament

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

Leite, Wellington C.; Galvão, Carolina W.; Saab, Sérgio C.

The bacterial RecA protein plays a role in the complex system of DNA damage repair. Here, we report the functional and structural characterization of the Herbaspirillum seropedicae RecA protein (HsRecA). HsRecA protein is more efficient at displacing SSB protein from ssDNA than Escherichia coli RecA protein. HsRecA also promotes DNA strand exchange more efficiently. The three dimensional structure of HsRecA-ADP/ATP complex has been solved to 1.7 Å resolution. HsRecA protein contains a small N-terminal domain, a central core ATPase domain and a large C-terminal domain, that are similar to homologous bacterial RecA proteins. Comparative structural analysis showed that the N-terminalmore » polymerization motif of archaeal and eukaryotic RecA family proteins are also present in bacterial RecAs. Reconstruction of electrostatic potential from the hexameric structure of HsRecA-ADP/ATP revealed a high positive charge along the inner side, where ssDNA is bound inside the filament. The properties of this surface may explain the greater capacity of HsRecA protein to bind ssDNA, forming a contiguous nucleoprotein filament, displace SSB and promote DNA exchange relative to EcRecA. In conclusion, our functional and structural analyses provide insight into the molecular mechanisms of polymerization of bacterial RecA as a helical nucleoprotein filament.« less

Structural and Functional Studies of H. seropedicae RecA Protein – Insights into the Polymerization of RecA Protein as Nucleoprotein Filament

PubMed Central

Galvão, Carolina W.; Saab, Sérgio C.; Iulek, Jorge; Etto, Rafael M.; Steffens, Maria B. R.; Chitteni-Pattu, Sindhu; Stanage, Tyler; Keck, James L.; Cox, Michael M.

2016-01-01

The bacterial RecA protein plays a role in the complex system of DNA damage repair. Here, we report the functional and structural characterization of the Herbaspirillum seropedicae RecA protein (HsRecA). HsRecA protein is more efficient at displacing SSB protein from ssDNA than Escherichia coli RecA protein. HsRecA also promotes DNA strand exchange more efficiently. The three dimensional structure of HsRecA-ADP/ATP complex has been solved to 1.7 Å resolution. HsRecA protein contains a small N-terminal domain, a central core ATPase domain and a large C-terminal domain, that are similar to homologous bacterial RecA proteins. Comparative structural analysis showed that the N-terminal polymerization motif of archaeal and eukaryotic RecA family proteins are also present in bacterial RecAs. Reconstruction of electrostatic potential from the hexameric structure of HsRecA-ADP/ATP revealed a high positive charge along the inner side, where ssDNA is bound inside the filament. The properties of this surface may explain the greater capacity of HsRecA protein to bind ssDNA, forming a contiguous nucleoprotein filament, displace SSB and promote DNA exchange relative to EcRecA. Our functional and structural analyses provide insight into the molecular mechanisms of polymerization of bacterial RecA as a helical nucleoprotein filament. PMID:27447485

Characterization of biochemical properties of Bacillus subtilis RecQ helicase.

PubMed

Qin, Wei; Liu, Na-Nv; Wang, Lijun; Zhou, Min; Ren, Hua; Bugnard, Elisabeth; Liu, Jie-Lin; Zhang, Lin-Hu; Vendôme, Jeremie; Hu, Jin-Shan; Xi, Xu Guang

2014-12-01

RecQ family helicases function as safeguards of the genome. Unlike Escherichia coli, the Gram-positive Bacillus subtilis bacterium possesses two RecQ-like homologues, RecQ[Bs] and RecS, which are required for the repair of DNA double-strand breaks. RecQ[Bs] also binds to the forked DNA to ensure a smooth progression of the cell cycle. Here we present the first biochemical analysis of recombinant RecQ[Bs]. RecQ[Bs] binds weakly to single-stranded DNA (ssDNA) and blunt-ended double-stranded DNA (dsDNA) but strongly to forked dsDNA. The protein exhibits a DNA-stimulated ATPase activity and ATP- and Mg(2+)-dependent DNA helicase activity with a 3' → 5' polarity. Molecular modeling shows that RecQ[Bs] shares high sequence and structure similarity with E. coli RecQ. Surprisingly, RecQ[Bs] resembles the truncated Saccharomyces cerevisiae Sgs1 and human RecQ helicases more than RecQ[Ec] with regard to its enzymatic activities. Specifically, RecQ[Bs] unwinds forked dsDNA and DNA duplexes with a 3'-overhang but is inactive on blunt-ended dsDNA and 5'-overhung duplexes. Interestingly, RecQ[Bs] unwinds blunt-ended DNA with structural features, including nicks, gaps, 5'-flaps, Kappa joints, synthetic replication forks, and Holliday junctions. We discuss these findings in the context of RecQ[Bs]'s possible functions in preserving genomic stability. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Properties of a mutant recA-encoded protein reveal a possible role for Escherichia coli recF-encoded protein in genetic recombination

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

Madiraju, M.V.; Templin, A.; Clark, A.J.

A mutation partially suppressing the UV sensitivity caused by recF143 in a uvrA6 background was located at codon 37 of recA where GTG (valine) became ATG (methionine). This mutation, originally named srf-803, was renamed recA803. Little if any suppression of the recF143 defect in UV induction of a lexA regulon promoter was detected. This led to the hypothesis that a defect in recombination repair of UV damage was suppressed by recA803. The mutant RecA protein (RecA803) was purified and compared with wild-type protein (RecA+) as a catalyst of formation of joint molecules. Under suboptimal conditions, RecA803 produces both a highermore » rate of formation and a higher yield of joint molecules. The suboptimal conditions tested included addition of single-stranded DNA binding protein to single-stranded DNA prior to addition of RecA. We hypothesize that the ability of RecA803 to overcome interference by single-stranded DNA binding protein is the property that allows recA803 to suppress partially the deficiency in repair caused by recF mutations in the uvrA6 background. Implications of this hypothesis for the function of RecF protein in recombination are discussed.« less

Ring-shaped architecture of RecR: implications for its role in homologous recombinational DNA repair

PubMed Central

Lee, Byung Il; Kim, Kyoung Hoon; Park, Soo Jeong; Eom, Soo Hyun; Song, Hyun Kyu; Suh, Se Won

2004-01-01

RecR, together with RecF and RecO, facilitates RecA loading in the RecF pathway of homologous recombinational DNA repair in procaryotes . The human Rad52 protein is a functional counterpart of RecFOR. We present here the crystal structure of RecR from Deinococcus radiodurans (DR RecR). A monomer of DR RecR has a two-domain structure: the N-terminal domain with a helix–hairpin–helix (HhH) motif and the C-terminal domain with a Cys4 zinc-finger motif, a Toprim domain and a Walker B motif. Four such monomers form a ring-shaped tetramer of 222 symmetry with a central hole of 30−35 Å diameter. In the crystal, two tetramers are concatenated, implying that the RecR tetramer is capable of opening and closing. We also show that DR RecR binds to both dsDNA and ssDNA, and that its HhH motif is essential for DNA binding. PMID:15116069

Materials Data on K3ReC4(N2O)2 (SG:2) by Materials Project

DOE Data Explorer

Kristin Persson

2016-02-11

Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

Factors Limiting SOS Expression in Log-Phase Cells of Escherichia coli

PubMed Central

Massoni, Shawn C.; Leeson, Michael C.; Long, Jarukit Edward; Gemme, Kristin; Mui, Alice

2012-01-01

In Escherichia coli, RecA–single-stranded DNA (RecA-ssDNA) filaments catalyze DNA repair, recombination, and induction of the SOS response. It has been shown that, while many (15 to 25%) log-phase cells have RecA filaments, few (about 1%) are induced for SOS. It is hypothesized that RecA's ability to induce SOS expression in log-phase cells is repressed because of the potentially detrimental effects of SOS mutagenesis. To test this, mutations were sought to produce a population where the number of cells with SOS expression more closely equaled the number of RecA filaments. Here, it is shown that deleting radA (important for resolution of recombination structures) and increasing recA transcription 2- to 3-fold with a recAo1403 operator mutation act independently to minimally satisfy this condition. This allows 24% of mutant cells to have elevated levels of SOS expression, a percentage similar to that of cells with RecA-green fluorescent protein (RecA-GFP) foci. In an xthA (exonuclease III gene) mutant where there are 3-fold more RecA loading events, recX (a destabilizer of RecA filaments) must be additionally deleted to achieve a population of cells where the percentage having elevated SOS expression (91%) nearly equals the percentage with at least one RecA-GFP focus (83%). It is proposed that, in the xthA mutant, there are three independent mechanisms that repress SOS expression in log-phase cells. These are the rapid processing of RecA filaments by RadA, maintaining the concentration of RecA below a critical level, and the destabilizing of RecA filaments by RecX. Only the first two mechanisms operate independently in a wild-type cell. PMID:22843848

Factors limiting SOS expression in log-phase cells of Escherichia coli.

PubMed

Massoni, Shawn C; Leeson, Michael C; Long, Jarukit Edward; Gemme, Kristin; Mui, Alice; Sandler, Steven J

2012-10-01

In Escherichia coli, RecA-single-stranded DNA (RecA-ssDNA) filaments catalyze DNA repair, recombination, and induction of the SOS response. It has been shown that, while many (15 to 25%) log-phase cells have RecA filaments, few (about 1%) are induced for SOS. It is hypothesized that RecA's ability to induce SOS expression in log-phase cells is repressed because of the potentially detrimental effects of SOS mutagenesis. To test this, mutations were sought to produce a population where the number of cells with SOS expression more closely equaled the number of RecA filaments. Here, it is shown that deleting radA (important for resolution of recombination structures) and increasing recA transcription 2- to 3-fold with a recAo1403 operator mutation act independently to minimally satisfy this condition. This allows 24% of mutant cells to have elevated levels of SOS expression, a percentage similar to that of cells with RecA-green fluorescent protein (RecA-GFP) foci. In an xthA (exonuclease III gene) mutant where there are 3-fold more RecA loading events, recX (a destabilizer of RecA filaments) must be additionally deleted to achieve a population of cells where the percentage having elevated SOS expression (91%) nearly equals the percentage with at least one RecA-GFP focus (83%). It is proposed that, in the xthA mutant, there are three independent mechanisms that repress SOS expression in log-phase cells. These are the rapid processing of RecA filaments by RadA, maintaining the concentration of RecA below a critical level, and the destabilizing of RecA filaments by RecX. Only the first two mechanisms operate independently in a wild-type cell.

Directed Evolution of RecA Variants with Enhanced Capacity for Conjugational Recombination

PubMed Central

Kim, Taejin; Chitteni-Pattu, Sindhu; Cox, Benjamin L.; Wood, Elizabeth A.; Sandler, Steven J.; Cox, Michael M.

2015-01-01

The recombination activity of Escherichia coli (E. coli) RecA protein reflects an evolutionary balance between the positive and potentially deleterious effects of recombination. We have perturbed that balance, generating RecA variants exhibiting improved recombination functionality via random mutagenesis followed by directed evolution for enhanced function in conjugation. A recA gene segment encoding a 59 residue segment of the protein (Val79-Ala137), encompassing an extensive subunit-subunit interface region, was subjected to degenerate oligonucleotide-mediated mutagenesis. An iterative selection process generated at least 18 recA gene variants capable of producing a higher yield of transconjugants. Three of the variant proteins, RecA I102L, RecA V79L and RecA E86G/C90G were characterized based on their prominence. Relative to wild type RecA, the selected RecA variants exhibited faster rates of ATP hydrolysis, more rapid displacement of SSB, decreased inhibition by the RecX regulator protein, and in general displayed a greater persistence on DNA. The enhancement in conjugational function comes at the price of a measurable RecA-mediated cellular growth deficiency. Persistent DNA binding represents a barrier to other processes of DNA metabolism in vivo. The growth deficiency is alleviated by expression of the functionally robust RecX protein from Neisseria gonorrhoeae. RecA filaments can be a barrier to processes like replication and transcription. RecA regulation by RecX protein is important in maintaining an optimal balance between recombination and other aspects of DNA metabolism. PMID:26047498

A RecA Protein Surface Required for Activation of DNA Polymerase V

PubMed Central

Gruber, Angela J.; Erdem, Aysen L.; Sabat, Grzegorz; Karata, Kiyonobu; Jaszczur, Malgorzata M.; Vo, Dan D.; Olsen, Tayla M.; Woodgate, Roger; Goodman, Myron F.; Cox, Michael M.

2015-01-01

DNA polymerase V (pol V) of Escherichia coli is a translesion DNA polymerase responsible for most of the mutagenesis observed during the SOS response. Pol V is activated by transfer of a RecA subunit from the 3'-proximal end of a RecA nucleoprotein filament to form a functional complex called DNA polymerase V Mutasome (pol V Mut). We identify a RecA surface, defined by residues 112-117, that either directly interacts with or is in very close proximity to amino acid residues on two distinct surfaces of the UmuC subunit of pol V. One of these surfaces is uniquely prominent in the active pol V Mut. Several conformational states are populated in the inactive and active complexes of RecA with pol V. The RecA D112R and RecA D112R N113R double mutant proteins exhibit successively reduced capacity for pol V activation. The double mutant RecA is specifically defective in the ATP binding step of the activation pathway. Unlike the classic non-mutable RecA S117F (recA1730), the RecA D112R N113R variant exhibits no defect in filament formation on DNA and promotes all other RecA activities efficiently. An important pol V activation surface of RecA protein is thus centered in a region encompassing amino acid residues 112, 113, and 117, a surface exposed at the 3'-proximal end of a RecA filament. The same RecA surface is not utilized in the RecA activation of the homologous and highly mutagenic RumA'2B polymerase encoded by the integrating-conjugative element (ICE) R391, indicating a lack of structural conservation between the two systems. The RecA D112R N113R protein represents a new separation of function mutant, proficient in all RecA functions except SOS mutagenesis. PMID:25811184

Modulating Cellular Recombination Potential through Alterations in RecA Structure and Regulation

PubMed Central

Bakhlanova, Irina V.; Dudkina, Alexandra V.; Baitin, Dima M.; Knight, Kendall L.; Cox, Michael M.; Lanzov, Vladislav A.

2010-01-01

The wild type E. coli RecA protein is a recombinase platform with unrealized recombination potential. We have explored the factors affecting recombination during conjugation with a quantitative assay. Regulatory proteins that affect RecA function have the capacity to increase or decrease recombination frequencies by factors up to 6 fold. Autoinhibition by the RecA C-terminus can affect recombination frequency by factors up to 4 fold. The greatest changes in recombination frequency measured here are brought about by point mutations in the recA gene. RecA variants can increase recombination frequencies by more than 50 fold. The RecA protein thus possesses an inherently broad functional range. The RecA protein of Escherichia coli (EcRecA) is not optimized for recombination function. Instead, much of the recombination potential of EcRecA is structurally suppressed, probably reflecting cellular requirements. One point mutation in EcRecA with a particularly dramatic effect on recombination frequency, D112R, exhibits an enhanced capacity to load onto SSB-coated ssDNA, overcome the effects of regulatory proteins such as PsiB and RecX, and to pair homologous DNAs. Comparisons of key RecA protein mutants reveal two components to RecA recombination function – filament formation and the inherent DNA pairing activity of the formed filaments. PMID:21143322

Nucleotide sequence and further characterization of the Synechococcus sp. strain PCC 7002 recA gene: complementation of a cyanobacterial recA mutation by the Escherichia coli recA gene.

PubMed Central

Murphy, R C; Gasparich, G E; Bryant, D A; Porter, R D

1990-01-01

The nucleotide sequence and transcript initiation site of the Synechococcus sp. strain PCC 7002 recA gene have been determined. The deduced amino acid sequence of the RecA protein of this cyanobacterium is 56% identical and 73% similar to the Escherichia coli RecA protein. Northern (RNA) blot analysis indicates that the Synechococcus strain PCC 7002 recA gene is transcribed as a monocistronic transcript 1,200 bases in length. The 5' endpoint of the recA mRNA was mapped by primer extension by using synthetic oligonucleotides of 17 and 27 nucleotides as primers. The nucleotide sequence 5' to the mapped endpoint contained sequence motifs bearing a striking resemblance to the heat shock (sigma 32-specific) promoters of E. coli but did not contain sequences similar to the E. coli SOS operator recognized by the LexA repressor. An insertion mutation introduced into the recA locus of Synechococcus strain PCC 7002 via homologous recombination resulted in the formation of diploids carrying both mutant and wild-type recA alleles. A variety of growth regimens and transformation procedures failed to produce a recA Synechococcus strain PCC 7002 mutant. However, introduction into these diploid cells of the E. coli recA gene in trans on a biphasic shuttle vector resulted in segregation of the cyanobacterial recA alleles, indicating that the E. coli recA gene was able to provide a function required for growth of recA Synechococcus strain PCC 7002 cells. This interpretation is supported by the observation that the E. coli recA gene is maintained in these cells when antibiotic selection for the shuttle vector is removed. Images FIG. 3 FIG. 4 FIG. 6 PMID:2105307

Creating a foundation for implementing an electronic health records (EHR)-integrated Social Knowledge Networking (SKN) system on medication reconciliation.

PubMed

Rangachari, P; Dellsperger, K C; Fallaw, D; Davis, I; Sumner, M; Ray, W; Fiedler, S; Nguyen, T; Rethemeyer, R

2018-04-01

In fall 2016, Augusta University received a two-year grant from AHRQ, to implement a Social Knowledge Networking (SKN) system for enabling its health system, AU-Health, to progress from "limited use" of EHR Medication Reconciliation (MedRec) Technology, to "meaningful use." Phase 1 sought to identify a comprehensive set of issues related to EHR MedRec encountered by practitioners at AU-Health. These efforts helped develop a Reporting Tool , which, along with a Discussion Tool , was incorporated into the AU-Health EHR, at the end of Phase 1. Phase 2 (currently underway), comprises a 52-week pilot of the EHR-integrated SKN system in outpatient and inpatient medicine units. The purpose of this paper is to describe the methods and results of Phase 1. Phase 1 utilized an exploratory mixed-method approach, involving two rounds of data collection. This included 15 individual interviews followed by a survey of 200 practitioners, i.e., physicians, nurses, and pharmacists, based in the outpatient and inpatient medicine service at AU Health. Thematic analysis of interviews identified 55 issue-items related to EHR MedRec under 9 issue-categories. The survey sought practitioners' importance-rating of all issue-items identified from interviews. A total of 127 (63%) survey responses were received. Factor analysis served to validate the following 6 of the 9 issue-categories, all of which, were rated "Important" or higher (on average), by over 70% of all respondents: 1) Care-Coordination (CCI); 2) Patient-Education (PEI); 3) Ownership-and-Accountability (OAI); 4) Processes-of-Care (PCI); 5) IT-Related (ITRI); and 6) Workforce-Training (WTI). Significance-testing of importance-rating by professional affiliation revealed no statistically significant differences for CCI and PEI; and some statistically significant differences for OAI, PCI, ITRI, and WTI. There were two key gleanings from the issues related to EHR MedRec unearthed by this study: 1) there was an absence of shared understanding among practitioners, of the value of EHR MedRec in promoting patient safety, which contributed to workarounds, and suboptimal use of the EHR MedRec system; and 2) there was a socio-technical dimension to many of the issues, creating an added layer of complexity. These gleanings in turn, provide insights into best practices for managing both clinical transitions-of-care in the EHR MedRec process; and socio-technical challenges encountered in EHR MedRec implementation.

Creating a foundation for implementing an electronic health records (EHR)-integrated Social Knowledge Networking (SKN) system on medication reconciliation

PubMed Central

Rangachari, P.; Dellsperger, K.C; Fallaw, D.; Davis, I.; Sumner, M.; Ray, W.; Fiedler, S.; Nguyen, T.; Rethemeyer, R.

2018-01-01

Background In fall 2016, Augusta University received a two-year grant from AHRQ, to implement a Social Knowledge Networking (SKN) system for enabling its health system, AU-Health, to progress from “limited use” of EHR Medication Reconciliation (MedRec) Technology, to “meaningful use.” Phase 1 sought to identify a comprehensive set of issues related to EHR MedRec encountered by practitioners at AU-Health. These efforts helped develop a Reporting Tool, which, along with a Discussion Tool, was incorporated into the AU-Health EHR, at the end of Phase 1. Phase 2 (currently underway), comprises a 52-week pilot of the EHR-integrated SKN system in outpatient and inpatient medicine units. The purpose of this paper is to describe the methods and results of Phase 1. Methods Phase 1 utilized an exploratory mixed-method approach, involving two rounds of data collection. This included 15 individual interviews followed by a survey of 200 practitioners, i.e., physicians, nurses, and pharmacists, based in the outpatient and inpatient medicine service at AU Health. Results Thematic analysis of interviews identified 55 issue-items related to EHR MedRec under 9 issue-categories. The survey sought practitioners’ importance-rating of all issue-items identified from interviews. A total of 127 (63%) survey responses were received. Factor analysis served to validate the following 6 of the 9 issue-categories, all of which, were rated “Important” or higher (on average), by over 70% of all respondents: 1) Care-Coordination (CCI); 2) Patient-Education (PEI); 3) Ownership-and-Accountability (OAI); 4) Processes-of-Care (PCI); 5) IT-Related (ITRI); and 6) Workforce-Training (WTI). Significance-testing of importance-rating by professional affiliation revealed no statistically significant differences for CCI and PEI; and some statistically significant differences for OAI, PCI, ITRI, and WTI. Conclusion There were two key gleanings from the issues related to EHR MedRec unearthed by this study: 1) there was an absence of shared understanding among practitioners, of the value of EHR MedRec in promoting patient safety, which contributed to workarounds, and suboptimal use of the EHR MedRec system; and 2) there was a socio-technical dimension to many of the issues, creating an added layer of complexity. These gleanings in turn, provide insights into best practices for managing both clinical transitions-of-care in the EHR MedRec process; and socio-technical challenges encountered in EHR MedRec implementation. PMID:29682132

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

Heeter, J.; Armstrong, P.; Bird, L.

This report documents the status and trends of U.S. 'voluntary' markets -- those in which consumers and institutions purchase renewable energy to match their electricity needs on a voluntary basis. Voluntary REC markets continue to exhibit growth and spur renewable energy development. Voluntary green power markets provide an additional revenue stream for renewable energy projects and raise consumer awareness of the benefits of renewable energy. Although a full estimate of the size of the voluntary market is not available for 2011, this review uses indicative metrics to capture 2011 voluntary market trends.

Asymmetric Regulation of Bipolar Single-stranded DNA Translocation by the Two Motors within Escherichia coli RecBCD Helicase*

PubMed Central

Xie, Fuqian; Wu, Colin G.; Weiland, Elizabeth; Lohman, Timothy M.

2013-01-01

Repair of double-stranded DNA breaks in Escherichia coli is initiated by the RecBCD helicase that possesses two superfamily-1 motors, RecB (3′ to 5′ translocase) and RecD (5′ to 3′ translocase), that operate on the complementary DNA strands to unwind duplex DNA. However, it is not known whether the RecB and RecD motors act independently or are functionally coupled. Here we show by directly monitoring ATP-driven single-stranded DNA translocation of RecBCD that the 5′ to 3′ rate is always faster than the 3′ to 5′ rate on DNA without a crossover hotspot instigator site and that the translocation rates are coupled asymmetrically. That is, RecB regulates both 3′ to 5′ and 5′ to 3′ translocation, whereas RecD only regulates 5′ to 3′ translocation. We show that the recently identified RecBC secondary translocase activity functions within RecBCD and that this contributes to the coupling. This coupling has implications for how RecBCD activity is regulated after it recognizes a crossover hotspot instigator sequence during DNA unwinding. PMID:23192341

Requirement of RecBC enzyme and an elevated level of activated RecA for induced stable DNA replication in Escherichia coli.

PubMed Central

Magee, T R; Kogoma, T

1990-01-01

During SOS induction, Escherichia coli cells acquire the ability to replicate DNA in the absence of protein synthesis, i.e., induced stable DNA replication (iSDR). Initiation of iSDR can occur in the absence of transcription and DnaA protein activity, which are both required for initiation of normal DNA replication at the origin of replication, oriC. In this study we examined the requirement of recB, recC, and recA for the induction and maintenance of iSDR. We found that recB and recC mutations blocked the induction of iSDR by UV irradiation and nalidixic acid treatment. In recB(Ts) strains, iSDR activity induced at 30 degrees C was inhibited by subsequent incubation at 42 degrees C. In addition, iSDR that was induced after heat activation of the RecA441 protein was abolished by the recB21 mutation. These results indicated that the RecBC enzyme was essential not only for SOS signal generation but also for the reinitiation of DNA synthesis following DNA damage. recAo(Con) lexA3(Ind-) strains were found to be capable of iSDR after nalidixic acid treatment, indicating that the derepression of the recA gene and the activation of the elevated level of RecA protein were the necessary and sufficient conditions for the induction of iSDR. PMID:2180906

Rat embryo cells immortalized with transfected oncogenes are transformed by gamma irradiation.

PubMed

Endlich, B; Salavati, R; Sullivan, T; Ling, C C

1992-12-01

Cesium-137 gamma rays were used to transform rat embryo cells (REC) which were first transfected with activated c-myc or c-Ha-ras oncogenes to produce immortal cell lines (REC:myc and REC:ras). When exposed to 6 Gy of 137Cs gamma rays, some cells became morphologically transformed with focus formation frequencies of approximately 3 x 10(-4) for REC:myc and approximately 1 x 10(-4) for REC:ras, respectively. Cells isolated from foci of gamma-ray-transformed REC:myc (REC:myc:gamma) formed anchorage-independent colonies and were tumorigenic in nude mice, but foci from gamma-ray-transformed REC:ras (REC:ras:gamma) did not exhibit either of these criteria of transformation. Similar to the results with gamma irradiation, we observed a sequence-dependent phenomenon when myc and ras were transfected into REC, one at a time. REC immortalized by ras transfection were not converted to a tumorigenic phenotype by secondary transfection with myc, but REC transfected with myc were very susceptible to transformation by subsequent ras transfection. This suggests that myc-immortalized cells are more permissive to transformation via secondary treatments. In sequentially transfected REC, myc expression was high whether it was transfected first or second, whereas ras expression was highest when the ras gene was transfected secondarily into myc-containing REC. Molecular analysis of REC:ras:gamma transformants showed no alterations in structure of the transfected ras or of the endogenous ras, myc, p53, or fos genes. The expression of ras and p53 was increased in some isolates of REC:ras:gamma, but myc and fos expression were not affected. Similarly, REC:myc:gamma transformants did not demonstrate rearrangement or amplification of the transfected or the endogenous myc genes, or of the potentially cooperating Ha-, Ki-, or N-ras genes. Northern hybridization analysis revealed increased expression of N-ras in two isolates, REC:myc:gamma 33 and gamma 41, but no alterations in the expression of myc, raf, Ha-ras, or Ki-ras genes in any REC:myc transformant. DNA from several transformed REC:myc:gamma cell lines induced focus formation in recipient C3H 10T1/2 and NIH 3T3 cells. The NIH 3T3 foci tested positive when hybridized to a probe for rat repetitive DNA. A detailed analysis of the NIH 3T3 transformants generated from REC:myc:gamma 33 and gamma 41 DNA failed to detect Ha-ras, Ki-ras, raf, neu, trk, abl, fms, or src oncogenes of rat origin.(ABSTRACT TRUNCATED AT 400 WORDS)

tif-1 mutation alters polynucleotide recognition by the recA protein of Escherichia coli.

PubMed Central

McEntee, K; Weinstock, G M

1981-01-01

The requirements for polynucleotide-dependent hydrolysis of ATP and for proteolytic cleavage of phage lambda repressor have been examined for both the wild-type (recA+ protein) and the tif-1 mutant form [tif(recA) protein] of the recA gene product. The recA+ and tif(recA) proteins catalyze both reactions in the presence of long single-stranded DNAs or certain deoxyhomopolymers. However, short oligonucleotides [(dT)12, (dA)14] stimulate neither the protease nor the ATPase activities of the recA+ protein. In contrast, these short oligonucleotides activate tif(recA) protein to cleave lambda repressor without stimulating its ATPase activity. Moreover, both the ATPase and protease activities of the tif(recA) protein are stimulated by poly(rU) and poly(rC) whereas the recA+ protein does not respond to these ribopolymers. We have purified the recA protein from a strain in which the tif mutation is intragenically suppressed. This mutant protein (recA629) is inactive in the presence of (dT)12, (dA)14, poly(rU), and poly(rC) for lambda repressor cleavage and ATP hydrolysis. These results argue that the tif-1 mutation (or mutations) alters the DNA binding site of the recA protein. We suggest that in vivo the tif(recA) protein is activated for cleaving repressors of SOS genes by complex formation with short single-stranded regions or gaps that normally occur near the growing fork of replicating chromosomes and are too short for activating the recA+ enzyme. This mechanism can account for the expression of SOS functions in the absence of DNA damage in tif mutant strains. Images PMID:7031642

Two distinct modes of RecA action are required for DNA polymerase V-catalyzed translesion synthesis.

PubMed

Pham, Phuong; Seitz, Erica M; Saveliev, Sergei; Shen, Xuan; Woodgate, Roger; Cox, Michael M; Goodman, Myron F

2002-08-20

SOS mutagenesis in Escherichia coli requires DNA polymerase V (pol V) and RecA protein to copy damaged DNA templates. Here we show that two distinct biochemical modes for RecA protein are necessary for pol V-catalyzed translesion synthesis. One RecA mode is characterized by a strong stimulation in nucleotide incorporation either directly opposite a lesion or at undamaged template sites, but by the absence of lesion bypass. A separate RecA mode is necessary for translesion synthesis. The RecA1730 mutant protein, which was identified on the basis of its inability to promote pol V (UmuD'(2)C)-dependent UV-mutagenesis, appears proficient for the first mode of RecA action but is deficient in the second mode. Data are presented suggesting that the two RecA modes are "nonfilamentous". That is, contrary to current models for SOS mutagenesis, formation of a RecA nucleoprotein filament may not be required for copying damaged DNA templates. Instead, SOS mutagenesis occurs when pol V interacts with two RecA molecules, first at a 3' primer end, upstream of a template lesion, where RecA mode 1 stimulates pol V activity, and subsequently at a site immediately downstream of the lesion, where RecA mode 2 cocatalyzes lesion bypass. We posit that in vivo assembly of a RecA nucleoprotein filament may be required principally to target pol V to a site of DNA damage and to stabilize the pol V-RecA interaction at the lesion. However, it is only a RecA molecule located at the 3' filament tip, proximal to a damaged template base, that is directly responsible for translesion synthesis.

Two distinct modes of RecA action are required for DNA polymerase V-catalyzed translesion synthesis

PubMed Central

Pham, Phuong; Seitz, Erica M.; Saveliev, Sergei; Shen, Xuan; Woodgate, Roger; Cox, Michael M.; Goodman, Myron F.

2002-01-01

SOS mutagenesis in Escherichia coli requires DNA polymerase V (pol V) and RecA protein to copy damaged DNA templates. Here we show that two distinct biochemical modes for RecA protein are necessary for pol V-catalyzed translesion synthesis. One RecA mode is characterized by a strong stimulation in nucleotide incorporation either directly opposite a lesion or at undamaged template sites, but by the absence of lesion bypass. A separate RecA mode is necessary for translesion synthesis. The RecA1730 mutant protein, which was identified on the basis of its inability to promote pol V (UmuD′2C)-dependent UV-mutagenesis, appears proficient for the first mode of RecA action but is deficient in the second mode. Data are presented suggesting that the two RecA modes are “nonfilamentous”. That is, contrary to current models for SOS mutagenesis, formation of a RecA nucleoprotein filament may not be required for copying damaged DNA templates. Instead, SOS mutagenesis occurs when pol V interacts with two RecA molecules, first at a 3′ primer end, upstream of a template lesion, where RecA mode 1 stimulates pol V activity, and subsequently at a site immediately downstream of the lesion, where RecA mode 2 cocatalyzes lesion bypass. We posit that in vivo assembly of a RecA nucleoprotein filament may be required principally to target pol V to a site of DNA damage and to stabilize the pol V-RecA interaction at the lesion. However, it is only a RecA molecule located at the 3′ filament tip, proximal to a damaged template base, that is directly responsible for translesion synthesis. PMID:12177433

A unified REC market and composite RPO scheme for promotion of renewable energy in India

NASA Astrophysics Data System (ADS)

Shereef, R. M.; Khaparde, S. A.

2017-07-01

In India, uniform price was assigned to renewable energy certificate (REC) irrespective of renewable energy (RE) type, technology, and location. Moreover REC price bands are higher than existing preferential tariff. There are distinct renewable purchase obligations (RPOs) specified for various RE types, whereas there is lack of efficient tools to check RPO compliance. Because of these reasons, REC market stabilisation is getting delayed. This paper proposes a method using plant performance multiplier to convert non-solar and solar REC to single equivalent REC with competitive REC pricing, which can be traded on unified REC market. The method combines solar and non-solar RPOs into a single composite RPO, to make RPO compliance and its checking simple and efficient. A sample illustration of the proposed method is given. The benefits offered by the proposed method in REC pricing, REC trading and RPO compliance are discussed. A comparative economic analysis of present and proposed method is reported.

The Walker A motif mutation recA4159 abolishes the SOS response and recombination in a recA730 mutant of Escherichia coli.

PubMed

Šimatović, Ana; Mitrikeski, Petar T; Vlašić, Ignacija; Sopta, Mary; Brčić-Kostić, Krunoslav

2016-01-01

In bacteria, the RecA protein forms recombinogenic filaments required for the SOS response and DNA recombination. In order to form a recombinogenic filament, wild type RecA needs to bind ATP and to interact with mediator proteins. The RecA730 protein is a mutant version of RecA with superior catalytic abilities, allowing filament formation without the help of mediator proteins. The mechanism of RecA730 filament formation is not well understood, and the question remains as to whether the RecA730 protein requires ATP binding in order to become competent for filament formation. We examined two mutants, recA730,4159 (presumed to be defective for ATP binding) and recA730,2201 (defective for ATP hydrolysis), and show that they have different properties with respect to SOS induction, conjugational recombination and double-strand break repair. We show that ATP binding is essential for all RecA730 functions, while ATP hydrolysis is required only for double-strand break repair. Our results emphasize the similarity of the SOS response and conjugational recombination, neither of which requires ATP hydrolysis by RecA730. Copyright © 2016 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Survival and SOS response induction in ultraviolet B irradiated Escherichia coli cells with defective repair mechanisms.

PubMed

Prada Medina, Cesar Augusto; Aristizabal Tessmer, Elke Tatjana; Quintero Ruiz, Nathalia; Serment-Guerrero, Jorge; Fuentes, Jorge Luis

2016-06-01

Purpose In this paper, the contribution of different genes involved in DNA repair for both survival and SOS induction in Escherichia coli mutants exposed to ultraviolet B radiation (UVB, [wavelength range 280-315 nm]) was evaluated. Materials and methods E. coli strains defective in uvrA, oxyR, recO, recN, recJ, exoX, recB, recD or xonA genes were used to determine cell survival. All strains also had the genetic sulA::lacZ fusion, which allowed for the quantification of SOS induction through the SOS Chromotest. Results Five gene products were particularly important for survival, as follows: UvrA > RecB > RecO > RecJ > XonA. Strains defective in uvrA and recJ genes showed elevated SOS induction compared with the wild type, which remained stable for up to 240 min after UVB-irradiation. In addition, E. coli strains carrying the recO or recN mutation showed no SOS induction. Conclusions The nucleotide excision and DNA recombination pathways were equally used to repair UVB-induced DNA damage in E. coli cells. The sulA gene was not turned off in strains defective in UvrA and RecJ. RecO protein was essential for processing DNA damage prior to SOS induction. In this study, the roles of DNA repair proteins and their contributions to the mechanisms that induce SOS genes in E. coli are proposed.

Health Research Ethics Committees in South Africa 12 years into democracy

PubMed Central

Moodley, Keymanthri; Myer, Landon

2007-01-01

Background Despite the growth of biomedical research in South Africa, there are few insights into the operation of Research Ethics Committees (RECs) in this setting. We investigated the composition, operations and training needs of health RECs in South Africa against the backdrop of national and international guidelines. Methods The 12 major health RECs in South Africa were surveyed using semi-structured questionnaires that investigated the composition and functions of each REC as well as the operational issues facing committees. Results Health RECs in SA have an average of 16 members and REC members are predominantly male and white. Overall, there was a large discrepancy in findings between under-resourced RECs and well resourced RECs. The majority of members (56%) are scientists or clinicians who are typically affiliated to the same institution as the health REC. Community representatives account for only 8% of membership. Training needs for health REC members varied widely. Conclusion Most major health RECs in South Africa are well organized given the resource constraints that exist in relation to research ethics in developing countries. However, the gender, racial and occupational diversity of most of these RECs is suboptimal, and most RECs are not constituted in accordance with South African guidelines. Variability in the operations and training needs of RECs is a reflection of apartheid-entrenched influences in tertiary education in SA. While legislation now exists to enforce standardization of research ethics review systems, no provision has been made for resources or capacity development, especially to support historically-disadvantaged institutions. Perpetuation of this legacy of apartheid represents a violation of the principles of justice and equity. PMID:17254335

Human RecQL4 helicase plays multifaceted roles in the genomic stability of normal and cancer cells.

PubMed

Mo, Dongliang; Zhao, Yongliang; Balajee, Adayabalam S

2018-01-28

Human RecQ helicases that share homology with E. coli RecQ helicase play critical roles in diverse biological activities such as DNA replication, transcription, recombination and repair. Mutations in three of the five human RecQ helicases (RecQ1, WRN, BLM, RecQL4 and RecQ5) result in autosomal recessive syndromes characterized by accelerated aging symptoms and cancer incidence. Mutational inactivation of Werner (WRN) and Bloom (BLM) genes results in Werner syndrome (WS) and Bloom syndrome (BS) respectively. However, mutations in RecQL4 result in three human disorders: (I) Rothmund-Thomson syndrome (RTS), (II) RAPADILINO and (III) Baller-Gerold syndrome (BGS). Cells from WS, BS and RTS are characterized by a unique chromosomal anomaly indicating that each of the RecQ helicases performs specialized function(s) in a non-redundant manner. Elucidating the biological functions of RecQ helicases will enable us to understand not only the aging process but also to determine the cause for age-associated human diseases. Recent biochemical and molecular studies have given new insights into the multifaceted roles of RecQL4 that range from genomic stability to carcinogenesis and beyond. This review summarizes some of the existing and emerging knowledge on diverse biological functions of RecQL4 and its significance as a potential molecular target for cancer therapy. Copyright © 2017 Elsevier B.V. All rights reserved.

Efficacy of periodontal plastic surgery procedures in the treatment of localized facial gingival recessions. A systematic review.

PubMed

Cairo, Francesco; Nieri, Michele; Pagliaro, Umberto

2014-04-01

The aim of this Systematic Review (SR) was to assess the clinical efficacy of periodontal plastic surgery procedures in the treatment of localized gingival recessions (Rec) with or without inter-dental clinical attachment loss (iCAL). Electronic and hand searches were performed to identify randomized clinical trials (RCTs) on treatment of single gingival recessions with at least 6 months of follow-up. Primary outcome variable was complete root coverage (CRC). Secondary outcome variables were recession reduction (RecRed) and keratinized tissue (KT) gain. To evaluate treatment effect, Odds Ratios were combined for dichotomous data and mean differences in continuous data using a random-effect model. Fifty-one RCTs (53 articles) with a total of 1574 treated patients (1744 recessions) were included in this SR. Finally, 30 groups of comparisons were identified and a total of 80 meta-analyses were performed. Coronally Advanced Flap (CAF) was associated with higher probability of CRC and higher amount of RecRed than Semilunar Coronal Positioned Flap (SCPF). The combination CAF plus Connective Tissue Graft (CAF+CTG) or CAF plus Enamel Matrix Derivative (CAF+EMD) was more effective than CAF alone in terms of CRC and RecRed. The combination CAF plus Collagen Matrix (CAF+CM) achieved higher RecRed than CAF alone. In addition, CAF+CTG achieved CRC more frequently than CAF+EMD, SCPF, Free Gingival Graft (FGG) and Laterally Positioned Flap (LPS). CAF+CTG was also associated with higher RecRed than Barrier Membranes (CAF+GTR), CAF+EMD and CAF+CM. GTR was not able to improve the clinical efficacy of CAF. Studies adding Acellular Dermal Matrix (ADM) under CAF showed a large heterogeneity and not significant benefits compared with CAF alone. Multiple combinations, using more than a single graft/biomaterial under the flap, usually provide similar or less benefits than simpler, control procedures in term of root coverage outcomes. CAF procedures alone or with CTG, EMD are supported by large evidence in modern periodontal plastic surgery. CAF+CTG achieved the best clinical outcomes in single gingival recessions with or without iCAL. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Expression, purification, and DNA-binding activity of the Herbaspirillum seropedicae RecX protein.

PubMed

Galvão, Carolina W; Pedrosa, Fábio O; Souza, Emanuel M; Yates, M Geoffrey; Chubatsu, Leda S; Steffens, Maria Berenice R

2004-06-01

The Herbaspirillum seropedicae RecX protein participates in the SOS response: a process in which the RecA protein plays a central role. The RecX protein of the H. seropedicae, fused to a His-tag sequence (RecX His-tagged), was over-expressed in Escherichia coli and purified by metal-affinity chromatography to yield a highly purified and active protein. DNA band-shift assays showed that the RecX His-tagged protein bound to both circular and linear double-stranded DNA and also to circular single-stranded DNA. The apparent affinity of RecX for DNA decreased in the presence of Mg(2+) ions. The ability of RecX to bind DNA may be relevant to its function in the SOS response.

Status and Trends in U.S. Compliance and Voluntary Renewable Energy Certificate Markets (2010 Data)

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

Heeter, J.; Bird, L.

2011-10-01

This report documents the status and trends of 'compliance'--renewable energy certificate (REC) markets used to meet state renewable portfolio standard (RPS) requirements--and 'voluntary' markets--those in which consumers and institutions purchase renewable energy to match their electricity needs on a voluntary basis. Today, 29 states and the District of Columbia have an RPS, more than half of all U.S. electricity customers have an option to purchase some type of green power product directly from a retail electricity provider, and all consumers have the option to purchase RECs. This report documents REC activities and trends in the United States. The compliance RECmore » market analysis includes analysis of REC trading, regional REC markets, REC tracking systems, types of compliance RECs, compliance REC pricing trends, and an overview of compliance with RPS polices. The voluntary REC analysis presents data and analysis on voluntary market sales and customer participation, products and premiums, green pricing marketing and administrative expenses, voluntary REC pricing, and the voluntary carbon offsets market. The report concludes with a discussion of upcoming guidance from the Federal Trade Commission on green marketing claims, the emergence of community solar programs, and the potential impact of Dodd-Frank regulations on the REC market.« less

Crystal structure of RecBCD enzyme reveals a machine for processing DNA breaks

NASA Astrophysics Data System (ADS)

Singleton, Martin R.; Dillingham, Mark S.; Gaudier, Martin; Kowalczykowski, Stephen C.; Wigley, Dale B.

2004-11-01

RecBCD is a multi-functional enzyme complex that processes DNA ends resulting from a double-strand break. RecBCD is a bipolar helicase that splits the duplex into its component strands and digests them until encountering a recombinational hotspot (Chi site). The nuclease activity is then attenuated and RecBCD loads RecA onto the 3' tail of the DNA. Here we present the crystal structure of RecBCD bound to a DNA substrate. In this initiation complex, the DNA duplex has been split across the RecC subunit to create a fork with the separated strands each heading towards different helicase motor subunits. The strands pass along tunnels within the complex, both emerging adjacent to the nuclease domain of RecB. Passage of the 3' tail through one of these tunnels provides a mechanism for the recognition of a Chi sequence by RecC within the context of double-stranded DNA. Gating of this tunnel suggests how nuclease activity might be regulated.

Dynamics and Regulation of RecA Polymerization and De-Polymerization on Double-Stranded DNA

PubMed Central

Muniyappa, Kalappa; Yan, Jie

2013-01-01

The RecA filament formed on double-stranded (ds) DNA is proposed to be a functional state analogous to that generated during the process of DNA strand exchange. RecA polymerization and de-polymerization on dsDNA is governed by multiple physiological factors. However, a comprehensive understanding of how these factors regulate the processes of polymerization and de-polymerization of RecA filament on dsDNA is still evolving. Here, we investigate the effects of temperature, pH, tensile force, and DNA ends (in particular ssDNA overhang) on the polymerization and de-polymerization dynamics of the E. coli RecA filament at a single-molecule level. Our results identified the optimal conditions that permitted spontaneous RecA nucleation and polymerization, as well as conditions that could maintain the stability of a preformed RecA filament. Further examination at a nano-meter spatial resolution, by stretching short DNA constructs, revealed a striking dynamic RecA polymerization and de-polymerization induced saw-tooth pattern in DNA extension fluctuation. In addition, we show that RecA does not polymerize on S-DNA, a recently identified novel base-paired elongated DNA structure that was previously proposed to be a possible binding substrate for RecA. Overall, our studies have helped to resolve several previous single-molecule studies that reported contradictory and inconsistent results on RecA nucleation, polymerization and stability. Furthermore, our findings also provide insights into the regulatory mechanisms of RecA filament formation and stability in vivo. PMID:23825559

Investigating Deinococcus radiodurans RecA protein filament formation on dsDNA by a real-time single-molecule approach

PubMed Central

Hsu, Hsin-Fang; Ngo, Khanh V.; Chitteni-Pattu, Sindhu; Cox, Michael M.; Li, Hung-Wen

2011-01-01

With the aid of an efficient, precise, and almost error-free DNA repair system, Deinococcus radiodurans can survive hundreds of double strand breaks inflicted by high doses of irradiation or desiccation. The RecA of Deinococcus radiodurans (DrRecA) plays a central role both in the early phase of repair by an extended synthesis-dependent strand annealing process and in the later more general homologous recombination phase. Both roles likely require DrRecA filament formation on duplex DNA. We have developed single-molecule tethered particle motion (TPM) experiments to study the assembly dynamics of RecA proteins on individual duplex DNA molecules by observing changes in DNA tether length resulting from RecA binding. We demonstrate that DrRecA nucleation on dsDNA is much faster than Escherichia coli (Ec) RecA protein, but the extension is slower. This combination of attributes would tend to increase the number and decrease the length of DrRecA filaments relative to those of EcRecA, a feature that may reflect the requirement to repair hundreds of genomic double strand breaks concurrently in irradiated Deinococcus cells. PMID:21853996

Genes involved in transitory recombination between phage M13 and plasmid pHV33.

PubMed Central

Dagert, M; Ehrlich, S D

1984-01-01

Plasmid pHV33 and phage M13 combine in Escherichia coli cells to form a chimera, which decombines to regenerate two parental genomes. Combination can occur via two genetic pathways, one defined by the recBC genes, the other by recA, recF and possibly recL genes. Decombination can also occur via two pathways, one defined again by the recBC genes, the other by a gene not identified, but active only in the absence of the recL gene product. PMID:6323172

Evidence that the recA441 (tif-1) mutant of Escherichia coli K-12 contains a thermosensitive intragenic suppressor of RecA constitutive protease activity.

PubMed Central

Wang, W B; Tessman, E S

1985-01-01

The recA441 mutant of Escherichia coli, which has been thought to have thermoinducible constitutive RecA protease activity, is known to have two mutations within recA. We show here that the mutation that alters codon 38 actually confers temperature-independent constitutive protease activity; the second mutation in recA441, which is at codon 298, appears to be acting as a temperature-sensitive suppressor of the protease activity. Images PMID:3891740

Evidence that the recA441 (tif-1) mutant of Escherichia coli K-12 contains a thermosensitive intragenic suppressor of RecA constitutive protease activity.

PubMed

Wang, W B; Tessman, E S

1985-07-01

The recA441 mutant of Escherichia coli, which has been thought to have thermoinducible constitutive RecA protease activity, is known to have two mutations within recA. We show here that the mutation that alters codon 38 actually confers temperature-independent constitutive protease activity; the second mutation in recA441, which is at codon 298, appears to be acting as a temperature-sensitive suppressor of the protease activity.

Elemental composition of strawberry plants inoculated with the plant growth-promoting bacterium Azospirillum brasilense REC3, assessed with scanning electron microscopy and energy dispersive X-ray analysis.

PubMed

Guerrero-Molina, M F; Lovaisa, N C; Salazar, S M; Díaz-Ricci, J C; Pedraza, R O

2014-07-01

The elemental composition of strawberry plants (Fragaria ananassa cv. Macarena) inoculated with the plant growth-promoting bacterium Azospirillum brasilense REC3, and non-inoculated controls, was studied using scanning electron microscopy (SEM) and energy dispersive X-ray (EDS) analysis. This allowed simultaneous semi-quantification of different elements in a small, solid sample. Plants were inoculated and grown hydroponically in 50% or 100% Hoagland solution, corresponding to limited or optimum nutrient medium, respectively. Bacteria-inoculated plants increased the growth index 45% and 80% compared to controls when grown in 100% and 50% Hoagland solution, respectively. Thus, inoculation with A. brasilense REC3 in a nutrient-limited medium had the strongest effect in terms of increasing both shoot and root biomass and growth index, as already described for Azospirillum inoculated into nutrient-poor soils. SEM-EDS spectra and maps showed the elemental composition and relative distribution of nutrients in strawberry tissues. Leaves contained C, O, N, Na, P, K, Ca and Cu, while roots also had Si and Cl. The organic fraction (C, O and N) accounted for over 96.3% of the total chemical composition; of the mineral fraction, Na had higher accumulation in both leaves and roots. Azospirillum-inoculated and control plants had similar elemental quantities; however, in bacteria-inoculated roots, P was significantly increased (34.33%), which constitutes a major benefit for plant nutrition, while Cu content decreased (35.16%). © 2013 German Botanical Society and The Royal Botanical Society of the Netherlands.

Triple-Negative or HER2-Positive Status Predicts Higher Rates of Locoregional Recurrence in Node-Positive Breast Cancer Patients After Mastectomy

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

Wang Shulian; Li Yexiong, E-mail: yexiong@yahoo.com; Song Yongwen

2011-07-15

Purpose: To evaluate the prognostic value of determining estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor 2 (HER2) expression in node-positive breast cancer patients treated with mastectomy. Methods and Materials: The records of 835 node-positive breast cancer patients who had undergone mastectomy between January 2000 and December 2004 were analyzed retrospectively. Of these, 764 patients (91.5%) received chemotherapy; 68 of 398 patients (20.9%) with T1-2N1 disease and 352 of 437 patients (80.5%) with T3-4 or N2-3 disease received postoperative radiotherapy. Patients were classified into four subgroups according to hormone receptor (Rec+ or Rec-) and HER2 expression profiles:more » Rec-/HER2- (triple negative; n = 141), Rec-/HER2+ (n = 99), Rec+/HER2+ (n = 157), and Rec+/HER2- (n = 438). The endpoints were the duration of locoregional recurrence-free survival, distant metastasis-free survival, disease-free survival, and overall survival. Results: Patients with triple-negative, Rec-/HER2+, and Rec+/HER2+ expression profiles had a significantly lower 5-year locoregional recurrence-free survival than those with Rec+/HER2- profiles (86.5% vs. 93.6%, p = 0.002). Compared with those with Rec+/HER2+ and Rec+/HER2- profiles, patients with Rec-/HER2- and Rec-/HER2+ profiles had significantly lower 5-year distant metastasis-free survival (69.1% vs. 78.5%, p = 0.000), lower disease-free survival (66.6% vs. 75.6%, p = 0.000), and lower overall survival (71.4% vs. 84.2%, p = 0.000). Triple-negative or Rec-/HER2+ breast cancers had an increased likelihood of relapse and death within the first 3 years after treatment. Conclusions: Triple-negative and HER2-positive profiles are useful markers of prognosis for locoregional recurrence and survival in node-positive breast cancer patients treated with mastectomy.« less

ATP-dependent RecG Helicase Is Required for the Transcriptional Regulator OxyR Function in Pseudomonas species*

PubMed Central

Yeom, Jinki; Lee, Yunho; Park, Woojun

2012-01-01

The oxyR gene appears to reside in an operon with the recG helicase gene in many bacteria, including pathogenic Pseudomonas aeruginosa and Pseudomonas putida. Analysis of P. putida transcriptomes shows that many OxyR-controlled genes are regulated by the ATP-dependent RecG helicase and that RecG alone modulates the expression of many genes. We found that purified RecG binds to the promoters of many OxyR-controlled genes and that expression of these genes was not induced under conditions of oxidative stress in recG mutants of P. aeruginosa, P. putida, and Escherichia coli. In vitro data revealed that promoters containing palindromic sequences are essential for RecG binding and that single-strand binding proteins and ATP are also needed for RecG to promote transcription, whereas a magnesium ion has the opposite effect. The OxyR tetramer preferentially binds to promoters after RecG has generated linear DNA in the presence of ATP; otherwise, the OxyR dimer has higher affinity. This study provides new insights into the mechanism of bacterial transcription by demonstrating that RecG might be required for the induction of the OxyR regulon by unwinding palindromic DNA for transcription. This work describes a novel bacterial transcriptional function by RecG helicase with OxyR and may provide new targets for controlling Pseudomonas species pathogen. PMID:22621928

Identification of the recA (tif) gene product of Escherichia coli

PubMed Central

Gudas, Lorraine J.; Mount, David W.

1977-01-01

Treatments that inhibit DNA synthesis in recA+lexA+Escherichia coli stimulate synthesis of a 40,000 molecular weight protein species (protein X). The protein X molecules produced by wild-type and mutant E. coli strains have been compared by two-dimensional gel electrophoresis. One recA mutant (DM1415 spr recA1) produced a protein X with a more acidic isoelectric point than protein X from the wild type, demonstrating that protein X is probably the product of the recA gene. Additional mutants carrying the recA-linked tif-1 mutation yielded a protein X that was more basic than the wild-type protein, indicating that the tif-1 mutation also alters the recA protein. Protein X molecules from the above mutants and wild-type E. coli have been shown to yield similar partial products upon limited proteolysis in sodium dodecyl sulfate, indicating they are the same protein species. These and additional studies suggest that (i) the tif-1 mutation alters a site on the recA protein that is sensitive to DNA synthesis inhibition, (ii) synthesis of recA protein is self-regulated, and (iii) synthesis of recA protein is also regulated by the lexA product with lexA-suppressor mutations such as spr resulting in constitutive synthesis of recA protein. Images PMID:341152

Reanalysis of Diesel Engine Exhaust and Lung Cancer Mortality in the Diesel Exhaust in Miners Study Cohort Using Alternative Exposure Estimates and Radon Adjustment.

PubMed

Chang, Ellen T; Lau, Edmund C; Van Landingham, Cynthia; Crump, Kenny S; McClellan, Roger O; Moolgavkar, Suresh H

2018-06-01

The Diesel Exhaust in Miners Study (DEMS) (United States, 1947-1997) reported positive associations between diesel engine exhaust exposure, estimated as respirable elemental carbon (REC), and lung cancer mortality. This reanalysis of the DEMS cohort used an alternative estimate of REC exposure incorporating historical data on diesel equipment, engine horsepower, ventilation rates, and declines in particulate matter emissions per horsepower. Associations with cumulative REC and average REC intensity using the alternative REC estimate and other exposure estimates were generally attenuated compared with original DEMS REC estimates. Most findings were statistically nonsignificant; control for radon exposure substantially weakened associations with the original and alternative REC estimates. No association with original or alternative REC estimates was detected among miners who worked exclusively underground. Positive associations were detected among limestone workers, whereas no association with REC or radon was found among workers in the other 7 mines. The differences in results based on alternative exposure estimates, control for radon, and stratification by worker location or mine type highlight areas of uncertainty in the DEMS data.

Causality links among renewable energy consumption, CO2 emissions, and economic growth in Africa: evidence from a panel ARDL-PMG approach.

PubMed

Attiaoui, Imed; Toumi, Hassen; Ammouri, Bilel; Gargouri, Ilhem

2017-05-01

This research examines the causality (For the remainder of the paper, the notion of causality refers to Granger causality.) links among renewable energy consumption (REC), CO 2 emissions (CE), non-renewable energy consumption (NREC), and economic growth (GDP) using an autoregressive distributed lag model based on the pooled mean group estimation (ARDL-PMG) and applying Granger causality tests for a panel consisting of 22 African countries for the period between 1990 and 2011. There is unidirectional and irreversible short-run causality from CE to GDP. The causal direction between CE and REC is unobservable over the short-term. Moreover, we find unidirectional, short-run causality from REC to GDP. When testing per pair of variables, there are short-run bidirectional causalities among REC, CE, and GDP. However, if we add CE to the variables REC and NREC, the causality to GDP is observable, and causality from the pair REC and NREC to economic growth is neutral. Likewise, if we add NREC to the variables GDP and REC, there is causality. There are bidirectional long-run causalities among REC, CE, and GDP, which supports the feedback assumption. Causality from GDP to REC is not strong for the panel. If we test per pair of variables, the strong causality from GDP and CE to REC is neutral. The long-run PMG estimates show that NREC and gross domestic product increase CE, whereas REC decreases CE.

A Case-Study of the Resources and Functioning of Two Research Ethics Committees in Western India.

PubMed

Chenneville, Tiffany; Menezes, Lynette; Kosambiya, Jayendrakumar; Baxi, Rajendra

2016-12-01

Assessing the resources and functioning of research ethics committees (RECs) in low-resource settings poses many challenges. We conducted a case study of two medical college RECs (A and B) in Western India utilizing the Research Ethics Committee Quality Assurance Self-Assessment Tool (RECQASAT) as well as in-depth interviews with representative members to evaluate REC effectiveness. REC A and B obtained 62% and 67% of allowable points on the RECQASAT. These scores together with findings from the in-depth interviews suggest the need for significant improvement in REC effectiveness particularly in the areas of membership and educational training, organizational aspects, recording minutes, communicating decisions, and REC resources. Developing evidence-based best practices and strengthening infrastructure are essential to enhancing REC efficacy in low-resource countries.

A soluble RecN homologue provides means for biochemical and genetic analysis of DNA double-strand break repair in Escherichia coli.

PubMed

Grove, Jane I; Wood, Stuart R; Briggs, Geoffrey S; Oldham, Neil J; Lloyd, Robert G

2009-12-03

RecN is a highly conserved, SMC-like protein in bacteria. It plays an important role in the repair of DNA double-strand breaks and is therefore a key factor in maintaining genome integrity. The insolubility of Escherichia coli RecN has limited efforts to unravel its function. We overcame this limitation by replacing the resident coding sequence with that of Haemophilus influenzae RecN. The heterologous construct expresses Haemophilus RecN from the SOS-inducible E. coli promoter. The hybrid gene is fully functional, promoting survival after I-SceI induced DNA breakage, gamma irradiation or exposure to mitomycin C as effectively as the native gene, indicating that the repair activity is conserved between these two species. H. influenzae RecN is quite soluble, even when expressed at high levels, and is readily purified. Its analysis by ionisation-mass spectrometry, gel filtration and glutaraldehyde crosslinking indicates that it is probably a dimer under physiological conditions, although a higher multimer cannot be excluded. The purified protein displays a weak ATPase activity that is essential for its DNA repair function in vivo. However, no DNA-binding activity was detected, which contrasts with RecN from Bacillus subtilis. RecN proteins from Aquifex aeolicus and Bacteriodes fragilis also proved soluble. Neither binds DNA, but the Aquifex RecN has weak ATPase activity. Our findings support studies indicating that RecN, and the SOS response in general, behave differently in E. coli and B. subtilis. The hybrid recN reported provides new opportunities to study the genetics and biochemistry of how RecN operates in E. coli.

High-sensitivity chemiluminescence immunoassays for detection of growth hormone doping in sports.

PubMed

Bidlingmaier, Martin; Suhr, Jennifer; Ernst, Andrea; Wu, Zida; Keller, Alexandra; Strasburger, Christian J; Bergmann, Andreas

2009-03-01

Recombinant human growth hormone (rhGH) is abused in sports, but adequate routine doping tests are lacking. Analysis of serum hGH isoform composition has been shown to be effective in detecting rhGH doping. We developed and validated selective immunoassays for isoform analysis with potential utility for screening and confirmation in doping tests. Monoclonal antibodies with preference for pituitary hGH (phGH) or rhGH were used to establish 2 pairs of sandwich-type chemiluminescence assays with differential recognition of rhGH (recA and recB) and phGH (pitA and pitB). We analyzed specimens from volunteers before and after administration of rhGH and calculated ratios between the respective rec- and pit-assay results. Functional sensitivities were <0.05 microg/L, with intra- and interassay imprecision < or =8.4% and < or =13.7%, respectively. In 2 independent cohorts of healthy subjects, rec/pit ratios (median range) were 0.84 (0.09-1.32)/0.81 (0.27-1.21) (recA/pitA) and 0.68 (0.08-1.20)/0.80 (0.25-1.36) (recB/pitB), with no sex difference. In 20 recreational athletes, ratios (median SD) increased after a single injection of rhGH, reaching 350% (73%) (recA/pitA) and 400% (93%) (recB/pitB) of baseline ratios. At a moderate dose (0.033 mg/kg), mean recA/pitA and recB/pitB ratios remained significantly increased for 18 h (men) and 26 h (women). After high-dose rhGH (0.083 mg/kg), mean rec/pit ratios remained increased for 32 h (recA/pitA) and 34 h (recB/pitB) in men and were still increased after 36 h in women. Using sensitive chemiluminescence assays with preferential recognition of phGH or rhGH, detection of a single injection of rhGH was possible for up to 36 h.

The recA gene from the thermophile Thermus aquaticus YT-1: cloning, expression, and characterization.

PubMed Central

Angov, E; Camerini-Otero, R D

1994-01-01

We have cloned, expressed, and purified the RecA analog from the thermophilic eubacterium Thermus aquaticus YT-1. Analysis of the deduced amino acid sequence indicates that the T. aquaticus RecA is structurally similar to the Escherichia coli RecA and suggests that RecA-like function has been conserved in thermophilic organisms. Preliminary biochemical analysis indicates that the protein has an ATP-dependent single-stranded DNA binding activity and can pair and carry out strand exchange to form a heteroduplex DNA under reaction conditions previously described for E. coli RecA, but at 55 to 65 degrees C. Further characterization of a thermophilically derived RecA protein should yield important information concerning DNA-protein interactions at high temperatures. In addition, a thermostable RecA protein may have some general applicability in stabilizing DNA-protein interactions in reactions which occur at high temperatures by increasing the specificity (stringency) of annealing reactions. Images PMID:8113181

Probing the structure of RecA-DNA filaments. Advantages of a fluorescent guanine analog.

PubMed

Singleton, Scott F; Roca, Alberto I; Lee, Andrew M; Xiao, Jie

2007-04-23

The RecA protein of Escherichia coli plays a crucial roles in DNA recombination and repair, as well as various aspects of bacterial pathogenicity. The formation of a RecA-ATP-ssDNA complex initiates all RecA activities and yet a complete structural and mechanistic description of this filament has remained elusive. An analysis of RecA-DNA interactions was performed using fluorescently labeled oligonucleotides. A direct comparison was made between fluorescein and several fluorescent nucleosides. The fluorescent guanine analog 6-methylisoxanthopterin (6MI) demonstrated significant advantages over the other fluorophores and represents an important new tool for characterizing RecA-DNA interactions.

RecQL5 promotes genome stabilization through two parallel mechanisms--interacting with RNA polymerase II and acting as a helicase.

PubMed

Islam, M Nurul; Fox, David; Guo, Rong; Enomoto, Takemi; Wang, Weidong

2010-05-01

The RecQL5 helicase is essential for maintaining genome stability and reducing cancer risk. To elucidate its mechanism of action, we purified a RecQL5-associated complex and identified its major component as RNA polymerase II (Pol II). Bioinformatics and structural modeling-guided mutagenesis revealed two conserved regions in RecQL5 as KIX and SRI domains, already known in transcriptional regulators for Pol II. The RecQL5-KIX domain binds both initiation (Pol IIa) and elongation (Pol IIo) forms of the polymerase, whereas the RecQL5-SRI domain interacts only with the elongation form. Fully functional RecQL5 requires both helicase activity and associations with the initiation polymerase, because mutants lacking either activity are partially defective in the suppression of sister chromatid exchange and resistance to camptothecin-induced DNA damage, and mutants lacking both activities are completely defective. We propose that RecQL5 promotes genome stabilization through two parallel mechanisms: by participation in homologous recombination-dependent DNA repair as a RecQ helicase and by regulating the initiation of Pol II to reduce transcription-associated replication impairment and recombination.

Reanalysis of Diesel Engine Exhaust and Lung Cancer Mortality in the Diesel Exhaust in Miners Study Cohort Using Alternative Exposure Estimates and Radon Adjustment

PubMed Central

Chang, Ellen T; Lau, Edmund C; Van Landingham, Cynthia; Crump, Kenny S; McClellan, Roger O; Moolgavkar, Suresh H

2018-01-01

Abstract The Diesel Exhaust in Miners Study (DEMS) (United States, 1947–1997) reported positive associations between diesel engine exhaust exposure, estimated as respirable elemental carbon (REC), and lung cancer mortality. This reanalysis of the DEMS cohort used an alternative estimate of REC exposure incorporating historical data on diesel equipment, engine horsepower, ventilation rates, and declines in particulate matter emissions per horsepower. Associations with cumulative REC and average REC intensity using the alternative REC estimate and other exposure estimates were generally attenuated compared with original DEMS REC estimates. Most findings were statistically nonsignificant; control for radon exposure substantially weakened associations with the original and alternative REC estimates. No association with original or alternative REC estimates was detected among miners who worked exclusively underground. Positive associations were detected among limestone workers, whereas no association with REC or radon was found among workers in the other 7 mines. The differences in results based on alternative exposure estimates, control for radon, and stratification by worker location or mine type highlight areas of uncertainty in the DEMS data. PMID:29522073

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

Berendt, Christopher B.

RECs are the currency driving the growth of renewable energy markets and the sale of RECs from renewable energy generation projects could promise a predictable return. But the existing REC markets in the U.S. sorely lack the liquidity needed to make good on that promise. The author proposes a Renewable Energy Certificate Exchange program rooted in the construction of a national trading platform for RECs in tandem with the execution of a new agreement among the states with REC-based renewable portfolio standards. (author)

Mechanism of the formation of the RecA-ssDNA nucleoprotein filament structure: a coarse-grained approach.

PubMed

Mukherjee, Goutam; Pal, Arumay; Levy, Yaakov

2017-11-21

In prokaryotes, the RecA protein catalyzes the repair and strand exchange of double-stranded DNA. RecA binds to single-stranded DNA (ssDNA) and forms a presynaptic complex in which the protein polymerizes around the ssDNA to form a right-handed helical nucleoprotein filament structure. In the present work, the mechanism for the formation of the RecA-ssDNA filament structure is modeled using coarse-grained molecular dynamics simulations. Information from the X-ray structure was used to model the protein itself but not its interactions; the interactions between the protein and the ssDNA were modeled solely by electrostatic, aromatic, and repulsive energies. For the present study, the monomeric, dimeric, and trimeric units of RecA and 4, 8, and 11 NT-long ssDNA, respectively, were studied. Our results indicate that monomeric RecA is not sufficient for nucleoprotein filament formation; rather, dimeric RecA is the elementary binding unit, with higher multimeric units of RecA facilitating filament formation. Our results reveal that loop region flexibility at the primary binding site of RecA is essential for it to bind the incoming ssDNA, that the aromatic residues present in the loop region play an important role in ssDNA binding, and that ATP may play a role in guiding the ssDNA by changing the electrostatic potential of the RecA protein.

Molecular determinants of the DprA−RecA interaction for nucleation on ssDNA

PubMed Central

Lisboa, Johnny; Andreani, Jessica; Sanchez, Dyana; Boudes, Marion; Collinet, Bruno; Liger, Dominique; van Tilbeurgh, Herman; Guérois, Raphael; Quevillon-Cheruel, Sophie

2014-01-01

Natural transformation is a major mechanism of horizontal gene transfer in bacteria that depends on DNA recombination. RecA is central to the homologous recombination pathway, catalyzing DNA strand invasion and homology search. DprA was shown to be a key binding partner of RecA acting as a specific mediator for its loading on the incoming exogenous ssDNA. Although the 3D structures of both RecA and DprA have been solved, the mechanisms underlying their cross-talk remained elusive. By combining molecular docking simulations and experimental validation, we identified a region on RecA, buried at its self-assembly interface and involving three basic residues that contact an acidic triad of DprA previously shown to be crucial for the interaction. At the core of these patches, DprAM238 and RecAF230 are involved in the interaction. The other DprA binding regions of RecA could involve the N-terminal α-helix and a DNA-binding region. Our data favor a model of DprA acting as a cap of the RecA filament, involving a DprA−RecA interplay at two levels: their own oligomeric states and their respective interaction with DNA. Our model forms the basis for a mechanistic explanation of how DprA can act as a mediator for the loading of RecA on ssDNA. PMID:24782530

Biochemistry of homologous recombination in Escherichia coli.

PubMed Central

Kowalczykowski, S C; Dixon, D A; Eggleston, A K; Lauder, S D; Rehrauer, W M

1994-01-01

Homologous recombination is a fundamental biological process. Biochemical understanding of this process is most advanced for Escherichia coli. At least 25 gene products are involved in promoting genetic exchange. At present, this includes the RecA, RecBCD (exonuclease V), RecE (exonuclease VIII), RecF, RecG, RecJ, RecN, RecOR, RecQ, RecT, RuvAB, RuvC, SbcCD, and SSB proteins, as well as DNA polymerase I, DNA gyrase, DNA topoisomerase I, DNA ligase, and DNA helicases. The activities displayed by these enzymes include homologous DNA pairing and strand exchange, helicase, branch migration, Holliday junction binding and cleavage, nuclease, ATPase, topoisomerase, DNA binding, ATP binding, polymerase, and ligase, and, collectively, they define biochemical events that are essential for efficient recombination. In addition to these needed proteins, a cis-acting recombination hot spot known as Chi (chi: 5'-GCTGGTGG-3') plays a crucial regulatory function. The biochemical steps that comprise homologous recombination can be formally divided into four parts: (i) processing of DNA molecules into suitable recombination substrates, (ii) homologous pairing of the DNA partners and the exchange of DNA strands, (iii) extension of the nascent DNA heteroduplex; and (iv) resolution of the resulting crossover structure. This review focuses on the biochemical mechanisms underlying these steps, with particular emphases on the activities of the proteins involved and on the integration of these activities into likely biochemical pathways for recombination. Images PMID:7968921

Blocking the RecA activity and SOS-response in bacteria with a short α-helical peptide.

PubMed

Yakimov, Alexander; Pobegalov, Georgii; Bakhlanova, Irina; Khodorkovskii, Mikhail; Petukhov, Michael; Baitin, Dmitry

2017-09-19

The RecX protein, a very active natural RecA protein inhibitor, can completely disassemble RecA filaments at nanomolar concentrations that are two to three orders of magnitude lower than that of RecA protein. Based on the structure of RecX protein complex with the presynaptic RecA filament, we designed a short first in class α-helical peptide that both inhibits RecA protein activities in vitro and blocks the bacterial SOS-response in vivo. The peptide was designed using SEQOPT, a novel method for global sequence optimization of protein α-helices. SEQOPT produces artificial peptide sequences containing only 20 natural amino acids with the maximum possible conformational stability at a given pH, ionic strength, temperature, peptide solubility. It also accounts for restrictions due to known amino acid residues involved in stabilization of protein complexes under consideration. The results indicate that a few key intermolecular interactions inside the RecA protein presynaptic complex are enough to reproduce the main features of the RecX protein mechanism of action. Since the SOS-response provides a major mechanism of bacterial adaptation to antibiotics, these results open new ways for the development of antibiotic co-therapy that would not cause bacterial resistance. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Roles of Bacillus subtilis DprA and SsbA in RecA-mediated genetic recombination.

PubMed

Yadav, Tribhuwan; Carrasco, Begoña; Serrano, Ester; Alonso, Juan C

2014-10-03

Bacillus subtilis competence-induced RecA, SsbA, SsbB, and DprA are required to internalize and to recombine single-stranded (ss) DNA with homologous resident duplex. RecA, in the ATP · Mg(2+)-bound form (RecA · ATP), can nucleate and form filament onto ssDNA but is inactive to catalyze DNA recombination. We report that SsbA or SsbB bound to ssDNA blocks the RecA filament formation and fails to activate recombination. DprA facilitates RecA filamentation; however, the filaments cannot engage in DNA recombination. When ssDNA was preincubated with SsbA, but not SsbB, DprA was able to activate DNA strand exchange dependent on RecA · ATP. This work demonstrates that RecA · ATP, in concert with SsbA and DprA, catalyzes DNA strand exchange, and SsbB is an accessory factor in the reaction. In contrast, RecA · dATP efficiently catalyzes strand exchange even in the absence of single-stranded binding proteins or DprA, and addition of the accessory factors marginally improved it. We proposed that the RecA-bound nucleotide (ATP and to a lesser extent dATP) might dictate the requirement for accessory factors. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

REC-1 and HIM-5 distribute meiotic crossovers and function redundantly in meiotic double-strand break formation in Caenorhabditis elegans

PubMed Central

Chung, George; Rose, Ann M.; Petalcorin, Mark I.R.; Martin, Julie S.; Kessler, Zebulin; Sanchez-Pulido, Luis; Ponting, Chris P.; Yanowitz, Judith L.; Boulton, Simon J.

2015-01-01

The Caenorhabditis elegans gene rec-1 was the first genetic locus identified in metazoa to affect the distribution of meiotic crossovers along the chromosome. We report that rec-1 encodes a distant paralog of HIM-5, which was discovered by whole-genome sequencing and confirmed by multiple genome-edited alleles. REC-1 is phosphorylated by cyclin-dependent kinase (CDK) in vitro, and mutation of the CDK consensus sites in REC-1 compromises meiotic crossover distribution in vivo. Unexpectedly, rec-1; him-5 double mutants are synthetic-lethal due to a defect in meiotic double-strand break formation. Thus, we uncovered an unexpected robustness to meiotic DSB formation and crossover positioning that is executed by HIM-5 and REC-1 and regulated by phosphorylation. PMID:26385965

Transcriptomic analysis and mutational status of IDH1 in paired primary-recurrent intrahepatic cholangiocarcinoma.

PubMed

Peraldo-Neia, C; Ostano, P; Cavalloni, G; Pignochino, Y; Sangiolo, D; De Cecco, L; Marchesi, E; Ribero, D; Scarpa, A; De Rose, A M; Giuliani, A; Calise, F; Raggi, C; Invernizzi, P; Aglietta, M; Chiorino, G; Leone, F

2018-06-05

Effective target therapies for intrahepatic cholangiocarcinoma (ICC) have not been identified so far. One of the reasons may be the genetic evolution from primary (PR) to recurrent (REC) tumors. We aim to identify peculiar characteristics and to select potential targets specific for recurrent tumors. Eighteen ICC paired PR and REC tumors were collected from 5 Italian Centers. Eleven pairs were analyzed for gene expression profiling and 16 for mutational status of IDH1. For one pair, deep mutational analysis by Next Generation Sequencing was also carried out. An independent cohort of patients was used for validation. Two class-paired comparison yielded 315 differentially expressed genes between REC and PR tumors. Up-regulated genes in RECs are involved in RNA/DNA processing, cell cycle, epithelial to mesenchymal transition (EMT), resistance to apoptosis, and cytoskeleton remodeling. Down-regulated genes participate to epithelial cell differentiation, proteolysis, apoptotic, immune response, and inflammatory processes. A 24 gene signature is able to discriminate RECs from PRs in an independent cohort; FANCG is statistically associated with survival in the chol-TCGA dataset. IDH1 was mutated in the RECs of five patients; 4 of them displayed the mutation only in RECs. Deep sequencing performed in one patient confirmed the IDH1 mutation in REC. RECs are enriched for genes involved in EMT, resistance to apoptosis, and cytoskeleton remodeling. Key players of these pathways might be considered druggable targets in RECs. IDH1 is mutated in 30% of RECs, becoming both a marker of progression and a target for therapy.

Rhenium Mechanical Properties and Joining Technology

NASA Technical Reports Server (NTRS)

Reed, Brian D.; Biaglow, James A.

1996-01-01

Iridium-coated rhenium (Ir/Re) provides thermal margin for high performance and long life radiation cooled rockets. Two issues that have arisen in the development of flight Ir/Re engines are the sparsity of rhenium (Re) mechanical property data (particularly at high temperatures) required for engineering design, and the inability to directly electron beam weld Re chambers to C103 nozzle skirts. To address these issues, a Re mechanical property database is being established and techniques for creating Re/C103 transition joints are being investigated. This paper discusses the tensile testing results of powder metallurgy Re samples at temperatures from 1370 to 2090 C. Also discussed is the evaluation of Re/C103 transition pieces joined by both, explosive and diffusion bonding. Finally, the evaluation of full size Re transition pieces, joined by inertia welding, as well as explosive and diffusion bonding, is detailed.

REC-1 and HIM-5 distribute meiotic crossovers and function redundantly in meiotic double-strand break formation in Caenorhabditis elegans.

PubMed

Chung, George; Rose, Ann M; Petalcorin, Mark I R; Martin, Julie S; Kessler, Zebulin; Sanchez-Pulido, Luis; Ponting, Chris P; Yanowitz, Judith L; Boulton, Simon J

2015-09-15

The Caenorhabditis elegans gene rec-1 was the first genetic locus identified in metazoa to affect the distribution of meiotic crossovers along the chromosome. We report that rec-1 encodes a distant paralog of HIM-5, which was discovered by whole-genome sequencing and confirmed by multiple genome-edited alleles. REC-1 is phosphorylated by cyclin-dependent kinase (CDK) in vitro, and mutation of the CDK consensus sites in REC-1 compromises meiotic crossover distribution in vivo. Unexpectedly, rec-1; him-5 double mutants are synthetic-lethal due to a defect in meiotic double-strand break formation. Thus, we uncovered an unexpected robustness to meiotic DSB formation and crossover positioning that is executed by HIM-5 and REC-1 and regulated by phosphorylation. © 2015 Chung et al.; Published by Cold Spring Harbor Laboratory Press.

RecA-mediated SOS response provides a geraniol tolerance in Escherichia coli.

PubMed

Shah, Asad Ali; Wang, Chonglong; Yoon, Sang-Hwal; Kim, Jae-Yean; Choi, Eui-Sung; Kim, Seon-Won

2013-09-20

Geraniol is an important industrial material and a potential candidate of advanced biofuels. One challenge of microbial geraniol production is the toxicity to hosts. However, the poor understanding on geraniol tolerance mechanism is an obstacle for developing geraniol tolerant host. This study genome-widely screened a shot-gun DNA library of Escherichia coli and found that recA is able to confer geraniol tolerance in E. coli. The recA knockout mutant was found extremely sensitive to geraniol. Based on our data, it was deciphered that recA provided tolerance through SOS response network responding to DNA damage caused by geraniol. RecA-mediated SOS response activates the homologous recombinational repair by RecB and RecN for corrective DNA maintenance. This protection mechanism suggests an effective strategy to combat geraniol toxicity in E. coli. Copyright © 2013 Elsevier B.V. All rights reserved.

DNA compaction in the early part of the SOS response is dependent on RecN and RecA.

PubMed

Odsbu, Ingvild; Skarstad, Kirsten

2014-05-01

The nucleoids of undamaged Escherichia coli cells have a characteristic shape and number, which is dependent on the growth medium. Upon induction of the SOS response by a low dose of UV irradiation an extensive reorganization of the nucleoids occurred. Two distinct phases were observed by fluorescence microscopy. First, the nucleoids were found to change shape and fuse into compact structures at midcell. The compaction of the nucleoids lasted for 10-20 min and was followed by a phase where the DNA was dispersed throughout the cells. This second phase lasted for ~1 h. The compaction was found to be dependent on the recombination proteins RecA, RecO and RecR as well as the SOS-inducible, SMC (structural maintenance of chromosomes)-like protein RecN. RecN protein is produced in high amounts during the first part of the SOS response. It is possible that the RecN-mediated 'compact DNA' stage at the beginning of the SOS response serves to stabilize damaged DNA prior to recombination and repair.

Creating Directed Double-strand Breaks with the Ref Protein: A Novel Rec A-Dependent Nuclease from Bacteriophage P1

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

Gruenig, Marielle C.; Lu, Duo; Won, Sang Joon

2012-03-16

The bacteriophage P1-encoded Ref protein enhances RecA-dependent recombination in vivo by an unknown mechanism. We demonstrate that Ref is a new type of enzyme; that is, a RecA-dependent nuclease. Ref binds to ss- and dsDNA but does not cleave any DNA substrate until RecA protein and ATP are added to form RecA nucleoprotein filaments. Ref cleaves only where RecA protein is bound. RecA functions as a co-nuclease in the Ref/RecA system. Ref nuclease activity can be limited to the targeted strands of short RecA-containing D-loops. The result is a uniquely programmable endonuclease activity, producing targeted double-strand breaks at any chosenmore » DNA sequence in an oligonucleotide-directed fashion. We present evidence indicating that cleavage occurs in the RecA filament groove. The structure of the Ref protein has been determined to 1.4 {angstrom} resolution. The core structure, consisting of residues 77-186, consists of a central 2-stranded {beta}-hairpin that is sandwiched between several {alpha}-helical and extended loop elements. The N-terminal 76 amino acid residues are disordered; this flexible region is required for optimal activity. The overall structure of Ref, including several putative active site histidine residues, defines a new subclass of HNH-family nucleases. We propose that enhancement of recombination by Ref reflects the introduction of directed, recombinogenic double-strand breaks.« less

Molecular determinants of the DprA-RecA interaction for nucleation on ssDNA.

PubMed

Lisboa, Johnny; Andreani, Jessica; Sanchez, Dyana; Boudes, Marion; Collinet, Bruno; Liger, Dominique; van Tilbeurgh, Herman; Guérois, Raphael; Quevillon-Cheruel, Sophie

2014-06-01

Natural transformation is a major mechanism of horizontal gene transfer in bacteria that depends on DNA recombination. RecA is central to the homologous recombination pathway, catalyzing DNA strand invasion and homology search. DprA was shown to be a key binding partner of RecA acting as a specific mediator for its loading on the incoming exogenous ssDNA. Although the 3D structures of both RecA and DprA have been solved, the mechanisms underlying their cross-talk remained elusive. By combining molecular docking simulations and experimental validation, we identified a region on RecA, buried at its self-assembly interface and involving three basic residues that contact an acidic triad of DprA previously shown to be crucial for the interaction. At the core of these patches, (DprA)M238 and (RecA)F230 are involved in the interaction. The other DprA binding regions of RecA could involve the N-terminal α-helix and a DNA-binding region. Our data favor a model of DprA acting as a cap of the RecA filament, involving a DprA-RecA interplay at two levels: their own oligomeric states and their respective interaction with DNA. Our model forms the basis for a mechanistic explanation of how DprA can act as a mediator for the loading of RecA on ssDNA. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Evaluation of the work of hospital districts' research ethics committees in Finland.

PubMed

Halila, Ritva

2014-12-01

The main task of research ethics committees (RECs) is to assess research studies before their start. In this study, 24 RECs that evaluate medical research were sent questionnaires about their structure and functions. The RECs were divided into two separate groups: those working in university hospital districts (uRECs) and those in central hospital districts (non-uRECs). The two groups were different in many respects: the uRECs were bigger in size, covered a wider range of disciplines (both medical and non-medical), had better resources and more frequent and regular meetings. After the survey was performed and analysed, the Medical Research Act was amended so that only hospital districts with a medical faculty in their region had a duty to establish ethics committees. After the amendment, the number of RECs evaluating medical research in Finland decreased from 25 to 9. The ethics committees that remained had wider expertise and were better equipped already by the time of this survey. Only one non-uREC was continuing its work, and this was being done under the governance of a university hospital district. Simple measures were used for qualitative analysis of the work of RECs that evaluate medical research. These showed differences between RECs. This may be helpful in establishing an ethics committee network in a research field or administrational area. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Molecular Interaction and Cellular Location of RecA and CheW Proteins in Salmonella enterica during SOS Response and Their Implication in Swarming.

PubMed

Irazoki, Oihane; Aranda, Jesús; Zimmermann, Timo; Campoy, Susana; Barbé, Jordi

2016-01-01

In addition to its role in DNA damage repair and recombination, the RecA protein, through its interaction with CheW, is involved in swarming motility, a form of flagella-dependent movement across surfaces. In order to better understand how SOS response modulates swarming, in this work the location of RecA and CheW proteins within the swarming cells has been studied by using super-resolution microscopy. Further, and after in silico docking studies, the specific RecA and CheW regions associated with the RecA-CheW interaction have also been confirmed by site-directed mutagenesis and immunoprecipitation techniques. Our results point out that the CheW distribution changes, from the cell poles to foci distributed in a helical pattern along the cell axis when SOS response is activated or RecA protein is overexpressed. In this situation, the CheW presents the same subcellular location as that of RecA, pointing out that the previously described RecA storage structures may be modulators of swarming motility. Data reported herein not only confirmed that the RecA-CheW pair is essential for swarming motility but it is directly involved in the CheW distribution change associated to SOS response activation. A model explaining not only the mechanism by which DNA damage modulates swarming but also how both the lack and the excess of RecA protein impair this motility is proposed.

Managing the SOS Response for Enhanced CRISPR-Cas-Based Recombineering in E. coli through Transient Inhibition of Host RecA Activity.

PubMed

Moreb, Eirik Adim; Hoover, Benjamin; Yaseen, Adam; Valyasevi, Nisakorn; Roecker, Zoe; Menacho-Melgar, Romel; Lynch, Michael D

2017-12-15

Phage-derived "recombineering" methods are utilized for bacterial genome editing. Recombineering results in a heterogeneous population of modified and unmodified chromosomes, and therefore selection methods, such as CRISPR-Cas9, are required to select for edited clones. Cells can evade CRISPR-Cas-induced cell death through recA-mediated induction of the SOS response. The SOS response increases RecA dependent repair as well as mutation rates through induction of the umuDC error prone polymerase. As a result, CRISPR-Cas selection is more efficient in recA mutants. We report an approach to inhibiting the SOS response and RecA activity through the expression of a mutant dominant negative form of RecA, which incorporates into wild type RecA filaments and inhibits activity. Using a plasmid-based system in which Cas9 and recA mutants are coexpressed, we can achieve increased efficiency and consistency of CRISPR-Cas9-mediated selection and recombineering in E. coli, while reducing the induction of the SOS response. To date, this approach has been shown to be independent of recA genotype and host strain lineage. Using this system, we demonstrate increased CRISPR-Cas selection efficacy with over 10 000 guides covering the E. coli chromosome. The use of dominant negative RecA or homologues may be of broad use in bacterial CRISPR-Cas-based genome editing where the SOS pathways are present.

Budding Yeast ATM/ATR Control Meiotic Double-Strand Break (DSB) Levels by Down-Regulating Rec114, an Essential Component of the DSB-machinery

PubMed Central

Carballo, Jesús A.; Panizza, Silvia; Serrentino, Maria Elisabetta; Johnson, Anthony L.; Geymonat, Marco; Borde, Valérie; Klein, Franz; Cha, Rita S.

2013-01-01

An essential feature of meiosis is Spo11 catalysis of programmed DNA double strand breaks (DSBs). Evidence suggests that the number of DSBs generated per meiosis is genetically determined and that this ability to maintain a pre-determined DSB level, or “DSB homeostasis”, might be a property of the meiotic program. Here, we present direct evidence that Rec114, an evolutionarily conserved essential component of the meiotic DSB-machinery, interacts with DSB hotspot DNA, and that Tel1 and Mec1, the budding yeast ATM and ATR, respectively, down-regulate Rec114 upon meiotic DSB formation through phosphorylation. Mimicking constitutive phosphorylation reduces the interaction between Rec114 and DSB hotspot DNA, resulting in a reduction and/or delay in DSB formation. Conversely, a non-phosphorylatable rec114 allele confers a genome-wide increase in both DSB levels and in the interaction between Rec114 and the DSB hotspot DNA. These observations strongly suggest that Tel1 and/or Mec1 phosphorylation of Rec114 following Spo11 catalysis down-regulates DSB formation by limiting the interaction between Rec114 and DSB hotspots. We also present evidence that Ndt80, a meiosis specific transcription factor, contributes to Rec114 degradation, consistent with its requirement for complete cessation of DSB formation. Loss of Rec114 foci from chromatin is associated with homolog synapsis but independent of Ndt80 or Tel1/Mec1 phosphorylation. Taken together, we present evidence for three independent ways of regulating Rec114 activity, which likely contribute to meiotic DSBs-homeostasis in maintaining genetically determined levels of breaks. PMID:23825959

Oral immunisation of naive and primed animals with transgenic potato tubers expressing LT-B.

PubMed

Lauterslager, T G; Florack, D E; van der Wal, T J; Molthoff, J W; Langeveld, J P; Bosch, D; Boersma, W J; Hilgers, L A

2001-03-21

The efficacy of edible vaccines produced in potato tubers was examined in mice. Transgenic plants were developed by Agrobacterium tumefaciens-mediated transformation. The antigen selected was the non-toxic B subunit of the Escherichia coli enterotoxin (recLT-B). A synthetic gene coding for recLT-B was made and optimised for expression in potato tubers and accumulation in the endoplasmic reticulum. Introduction of this gene under control of the tuber-specific patatin promoter in potato plants resulted in the production of functional, i.e. Gm1-binding, recLT-B pentamers in tubers. Selected tubers containing about 13 microg of recLT-B per gram fresh weight were used for immunisation. Subcutaneous immunisation with an extract of recLT-B tubers yielded high antibody titres in serum that were similar to those obtained with bacterial recLT-B. The efficacy of oral administration of recLT-B tubers was determined by measuring mucosal and systemic immune responses in naive and primed mice. Animals were primed by subcutaneous injection of an extract of recLT-B tuber plus adjuvant. Naive and primed mice were fed 5 g of tubers ( approximately 65 microg of recLT-B) or were intubated intragastrically with 0.4 ml of tuber extract ( approximately 2 microg of recLT-B). In naive mice, feeding recLT-B tubers or intubation of tuber extract did not induce detectable anti-LT antibody titres. In primed animals, however, oral immunisation resulted in significant anti-LT IgA antibody responses in serum and faeces. Intragastric intubation of tuber extract revealed higher responses than feeding of tubers. These results indicate clearly that functional recLT-B can be produced in potato tubers, that this recombinant protein is immunogenic and that oral administration thereof elicits both systemic and local IgA responses in parentally primed, but not naive, animals.

Dissociation of tsl-tif-Induced Filamentation and recA Protein Synthesis in Escherichia coli K-12

PubMed Central

Huisman, Olivier; D'Ari, Richard; George, Jacqueline

1980-01-01

In Escherichia coli, expression of the tif-1 mutation (in the recA gene) induces the “SOS response” at 40°C, including massive synthesis of the recA(tif) protein, cell filamentation, appearance of new repair and mutagenic activities, and prophage induction. Expression of the tsl-1 mutation (in the lexA gene) induces massive synthesis of the recA protein and cell filamentation at 42°C, although other SOS functions are not induced. In this paper we show that the septation inhibition induced in tif and tsl strains at 42°C is not due to the presence of a high concentration of recA protein since (i) no recA mutants (≤10−8) were isolated among thermoresistant nonfilamenting revertants of a tif-1 tsl-1 strain, (ii) in a tsl-1 zab-53 strain, only the low basal level of recA protein was synthesized at 42°C, yet cell division was inhibited, and (iii) in a tsl-1 recA99 (amber) strain, no recA protein could be detected at 42°C, yet cell division was inhibited. Among suppressors of tsl-tif-induced lethality are mutations at a locus which we call infB, located in the 66- to 83-min region. The infB1 mutation confers a highly pleiotropic phenotype, which is suggestive of a regulatory defect; it suppressed tsl-tif-induced filamentation but not recA protein synthesis, it did not suppress ultraviolet-induced filamentation (in a lon derivative), and it reduced but did not abolish tif-mediated induction of λ prophage and bacterial mutagenesis. The dissociation of tsl-tif-induced septation inhibition and recA protein synthesis in the tif-1 tsl-1 infB1 strain suggests that the control of SOS filamentation may not be strictly identical to the control of recA protein synthesis. Images PMID:6445897

Brown spider phospholipase-D containing a conservative mutation (D233E) in the catalytic site: identification and functional characterization.

PubMed

Vuitika, Larissa; Gremski, Luiza Helena; Belisário-Ferrari, Matheus Regis; Chaves-Moreira, Daniele; Ferrer, Valéria Pereira; Senff-Ribeiro, Andrea; Chaim, Olga Meiri; Veiga, Silvio Sanches

2013-11-01

Brown spider (Loxosceles genus) bites have been reported worldwide. The venom contains a complex composition of several toxins, including phospholipases-D. Native or recombinant phospholipase-D toxins induce cutaneous and systemic loxoscelism, particularly necrotic lesions, inflammatory response, renal failure, and hematological disturbances. Herein, we describe the cloning, heterologous expression and purification of a novel phospholipase-D toxin, LiRecDT7 in reference to six other previously described in phospholipase-D toxin family. The complete cDNA sequence of this novel brown spider phospholipase-D isoform was obtained and the calculated molecular mass of the predicted mature protein is 34.4 kDa. Similarity analyses revealed that LiRecDT7 is homologous to the other dermonecrotic toxin family members particularly to LiRecDT6, sharing 71% sequence identity. LiRecDT7 possesses the conserved amino acid residues involved in catalysis except for a conservative mutation (D233E) in the catalytic site. Purified LiRecDT7 was detected as a soluble 36 kDa protein using anti-whole venom and anti-LiRecDT1 sera, indicating immunological cross-reactivity and evidencing sequence-epitopes identities similar to those of other phospholipase-D family members. Also, LiRecDT7 exhibits sphingomyelinase activity in a concentration dependent-manner and induces experimental skin lesions with swelling, erythema and dermonecrosis. In addition, LiRecDT7 induced a massive inflammatory response in rabbit skin dermis, which is a hallmark of brown spider venom phospholipase-D toxins. Moreover, LiRecDT7 induced in vitro hemolysis in human erythrocytes and increased blood vessel permeability. These features suggest that this novel member of the brown spider venom phospholipase-D family, which naturally contains a mutation (D233E) in the catalytic site, could be useful for future structural and functional studies concerning loxoscelism and lipid biochemistry. 1- Novel brown spider phospholipase-D recombinant toxin contains a conservative mutation (D233E) on the catalytic site. 2-LiRecDT7 shares high identity level with isoforms of Loxosceles genus. 3-LiRecDT7 is a recombinant protein immunodetected by specific antibodies to native and recombinant phospholipase-D toxins. 4-LiRecDT7 shows sphingomyelinase-D activity in a concentration-dependent manner, but less intense than other isoforms. 5-LiRecDT7 induces dermonecrosis and inflammatory response in rabbit skin. 6-LiRecDT7 increases vascular permeability in mice. 7-LiRecDT7 triggers direct complement-independent hemolysis in erythrocytes. © 2013 Wiley Periodicals, Inc.

Market Brief. Status of the Voluntary Renewable Energy Certificate Market (2011 Data)

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

Heeter, Jenny; Armstrong, Philip; Bird, Lori

2012-09-01

This report documents the status and trends of U.S. 'voluntary' markets -- those in which consumers and institutions purchase renewable energy to match their electricity needs on a voluntary basis. Voluntary REC markets continue to exhibit growth and spur renewable energy development. Voluntary green power markets provide an additional revenue stream for renewable energy projects and raise consumer awareness of the benefits of renewable energy. Although a full estimate of the size of the voluntary market is not available for 2011, this review uses indicative metrics to capture 2011 voluntary market trends.

Genotyping of Chromobacterium violaceum isolates by recA PCR-RFLP analysis.

PubMed

Scholz, Holger Christian; Witte, Angela; Tomaso, Herbert; Al Dahouk, Sascha; Neubauer, Heinrich

2005-03-15

Intraspecies variation of Chromobacterium violaceum was examined by comparative sequence - and by restriction fragment length polymorphism analysis of the recombinase A gene (recA-PCR-RFLP). Primers deduced from the known recA gene sequence of the type strain C. violaceum ATCC 12472(T) allowed the specific amplification of a 1040bp recA fragment from each of the 13 C. violaceum strains investigated, whereas other closely related organisms tested negative. HindII-PstI-recA RFLP analysis generated from 13 representative C. violaceum strains enabled us to identify at least three different genospecies. In conclusion, analysis of the recA gene provides a rapid and robust nucleotide sequence-based approach to specifically identify and classify C. violaceum on genospecies level.

Rad51 and RecA juxtapose dsDNA ends ready for DNA ligase-catalyzed end-joining under recombinase-suppressive conditions

PubMed Central

Konomura, Naoto; Arai, Naoto; Shinohara, Takeshi; Kobayashi, Jun; Iwasaki, Wakana; Ikawa, Shukuko; Kusano, Kohji; Shibata, Takehiko

2017-01-01

RecA-family recombinase-catalyzed ATP-dependent homologous joint formation is critical for homologous recombination, in which RecA or Rad51 binds first to single-stranded (ss)DNA and then interacts with double-stranded (ds)DNA. However, when RecA or Rad51 interacts with dsDNA before binding to ssDNA, the homologous joint-forming activity of RecA or Rad51 is quickly suppressed. We found that under these and adenosine diphosphate (ADP)-generating suppressive conditions for the recombinase activity, RecA or Rad51 at similar optimal concentrations enhances the DNA ligase-catalyzed dsDNA end-joining (DNA ligation) about 30- to 40-fold. The DNA ligation enhancement by RecA or Rad51 transforms most of the substrate DNA into multimers within 2–5 min, and for this enhancement, ADP is the common and best cofactor. Adenosine triphosphate (ATP) is effective for RecA, but not for Rad51. Rad51/RecA-enhanced DNA ligation depends on dsDNA-binding, as shown by a mutant, and is independent of physical interactions with the DNA ligase. These observations demonstrate the common and unique activities of RecA and Rad51 to juxtapose dsDNA-ends in preparation for covalent joining by a DNA ligase. This new in vitro function of Rad51 provides a simple explanation for our genetic observation that Rad51 plays a role in the fidelity of the end-joining of a reporter plasmid DNA, by yeast canonical non-homologous end-joining (NHEJ) in vivo. PMID:27794044

Renewable Energy Certificate Monetization

EPA Pesticide Factsheets

The Toolbox for Renewable Energy Project Development's Renewable Energy Certificate (REC) Monetization page provides an overview of REC monetization strategies and resources and how RECs impact the financing and economics of solar projects.

Heterologous expression, purification and characterization of nitrilase from Aspergillus niger K10.

PubMed

Kaplan, Ondřej; Bezouška, Karel; Plíhal, Ondřej; Ettrich, Rüdiger; Kulik, Natallia; Vaněk, Ondřej; Kavan, Daniel; Benada, Oldřich; Malandra, Anna; Sveda, Ondřej; Veselá, Alicja B; Rinágelová, Anna; Slámová, Kristýna; Cantarella, Maria; Felsberg, Jürgen; Dušková, Jarmila; Dohnálek, Jan; Kotik, Michael; Křen, Vladimír; Martínková, Ludmila

2011-01-06

Nitrilases attract increasing attention due to their utility in the mild hydrolysis of nitriles. According to activity and gene screening, filamentous fungi are a rich source of nitrilases distinct in evolution from their widely examined bacterial counterparts. However, fungal nitrilases have been less explored than the bacterial ones. Nitrilases are typically heterogeneous in their quaternary structures, forming short spirals and extended filaments, these features making their structural studies difficult. A nitrilase gene was amplified by PCR from the cDNA library of Aspergillus niger K10. The PCR product was ligated into expression vectors pET-30(+) and pRSET B to construct plasmids pOK101 and pOK102, respectively. The recombinant nitrilase (Nit-ANigRec) expressed in Escherichia coli BL21-Gold(DE3)(pOK101/pTf16) was purified with an about 2-fold increase in specific activity and 35% yield. The apparent subunit size was 42.7 kDa, which is approx. 4 kDa higher than that of the enzyme isolated from the native organism (Nit-ANigWT), indicating post-translational cleavage in the enzyme's native environment. Mass spectrometry analysis showed that a C-terminal peptide (Val327 - Asn₃₅₆) was present in Nit-ANigRec but missing in Nit-ANigWT and Asp₂₉₈-Val₃₁₃ peptide was shortened to Asp₂₉₈-Arg₃₁₀ in Nit-ANigWT. The latter enzyme was thus truncated by 46 amino acids. Enzymes Nit-ANigRec and Nit-ANigWT differed in substrate specificity, acid/amide ratio, reaction optima and stability. Refolded recombinant enzyme stored for one month at 4°C was fractionated by gel filtration, and fractions were examined by electron microscopy. The late fractions were further analyzed by analytical centrifugation and dynamic light scattering, and shown to consist of a rather homogeneous protein species composed of 12-16 subunits. This hypothesis was consistent with electron microscopy and our modelling of the multimeric nitrilase, which supports an arrangement of dimers into helical segments as a plausible structural solution. The nitrilase from Aspergillus niger K10 is highly homologous (≥86%) with proteins deduced from gene sequencing in Aspergillus and Penicillium genera. As the first of these proteins, it was shown to exhibit nitrilase activity towards organic nitriles. The comparison of the Nit-ANigRec and Nit-ANigWT suggested that the catalytic properties of nitrilases may be changed due to missing posttranslational cleavage of the former enzyme. Nit-ANigRec exhibits a lower tendency to form filaments and, moreover, the sample homogeneity can be further improved by in vitro protein refolding. The homogeneous protein species consisting of short spirals is expected to be more suitable for structural studies.

RNA-Mediated cis Regulation in Acinetobacter baumannii Modulates Stress-Induced Phenotypic Variation

PubMed Central

Ching, Carly; Gozzi, Kevin; Heinemann, Björn; Chai, Yunrong

2017-01-01

ABSTRACT In the nosocomial opportunistic pathogen Acinetobacter baumannii, RecA-dependent mutagenesis, which causes antibiotic resistance acquisition, is linked to the DNA damage response (DDR). Notably, unlike the Escherichia coli paradigm, recA and DDR gene expression in A. baumannii is bimodal. Namely, there is phenotypic variation upon DNA damage, which may provide a bet-hedging strategy for survival. Thus, understanding recA gene regulation is key to elucidate the yet unknown DDR regulation in A. baumannii. Here, we identify a structured 5′ untranslated region (UTR) in the recA transcript which serves as a cis-regulatory element. We show that a predicted stem-loop structure in this 5′ UTR affects mRNA half-life and underlies bimodal gene expression and thus phenotypic variation in response to ciprofloxacin treatment. We furthermore show that the stem-loop structure of the recA 5′ UTR influences intracellular RecA protein levels and, in vivo, impairing the formation of the stem-loop structure of the recA 5′ UTR lowers cell survival of UV treatment and decreases rifampin resistance acquisition from DNA damage-induced mutagenesis. We hypothesize that the 5′ UTR allows for stable recA transcripts during stress, including antibiotic treatment, enabling cells to maintain suitable RecA levels for survival. This innovative strategy to regulate the DDR in A. baumannii may contribute to its success as a pathogen. IMPORTANCE Acinetobacter baumannii is an opportunistic pathogen quickly gaining antibiotic resistances. Mutagenesis and antibiotic resistance acquisition are linked to the DNA damage response (DDR). However, how the DDR is regulated in A. baumannii remains unknown, since unlike most bacteria, A. baumannii does not follow the regulation of the Escherichia coli paradigm. In this study, we have started to uncover the mechanisms regulating the novel A. baumannii DDR. We have found that a cis-acting 5′ UTR regulates recA transcript stability, RecA protein levels, and DNA damage-induced phenotypic variation. Though 5′ UTRs are known to provide stability to transcripts in bacteria, this is the first example in which it regulates a bimodal DDR response through recA transcript stabilization, potentially enabling cells to have enough RecA for survival and genetic variability. PMID:28320880

Redefining RECs: Additionality in the voluntary Renewable Energy Certificate market

NASA Astrophysics Data System (ADS)

Gillenwater, Michael Wayne

In the United States, electricity consumers are told that they can "buy" electricity from renewable energy projects, versus fossil fuel-fired facilities, through participation in a voluntary green power program. The marketing messages communicate to consumers that their participation and premium payments for a green label will cause additional renewable energy generation and thereby allow them to claim they consume electricity that is absent pollution as well as reduce pollutant emissions. Renewable Energy Certificates (RECs) and wind energy are the basis for the majority of the voluntary green power market in the United States. This dissertation addresses the question: Do project developers respond to the voluntary REC market in the United States by altering their decisions to invest in wind turbines? This question is investigated by modeling and probabilistically quantifying the effect of the voluntary REC market on a representative wind power investor in the United States using data from formal expert elicitations of active participants in the industry. It is further explored by comparing the distribution of a sample of wind power projects supplying the voluntary green power market in the United States against an economic viability model that incorporates geographic factors. This dissertation contributes the first quantitative analysis of the effect of the voluntary REC market on project investment. It is found that 1) RECs should be not treated as equivalent to emission offset credits, 2) there is no clearly credible role for voluntary market RECs in emissions trading markets without dramatic restructuring of one or both markets and the environmental commodities they trade, and 3) the use of RECs in entity-level GHG emissions accounting (i.e., "carbon footprinting") leads to double counting of emissions and therefore is not justified. The impotence of the voluntary REC market was, at least in part, due to the small magnitude of the REC price signal and lack of long-term contracts that would reduce the risk of relying on revenue the voluntary green power market. Although no simple solutions are identified, a proposal for integrating RECs into a load based cap-and-trade system is presented. Keywords: Renewable Energy Certificate (REC); Renewable Portfolio Standard (RPS); emission offset; additionality; attributes

Apoptosis-like death, an extreme SOS response in Escherichia coli.

PubMed

Erental, Ariel; Kalderon, Ziva; Saada, Ann; Smith, Yoav; Engelberg-Kulka, Hanna

2014-07-15

In bacteria, SOS is a global response to DNA damage, mediated by the recA-lexA genes, resulting in cell cycle arrest, DNA repair, and mutagenesis. Previously, we reported that Escherichia coli responds to DNA damage via another recA-lexA-mediated pathway resulting in programmed cell death (PCD). We called it apoptosis-like death (ALD) because it is characterized by membrane depolarization and DNA fragmentation, which are hallmarks of eukaryotic mitochondrial apoptosis. Here, we show that ALD is an extreme SOS response that occurs only under conditions of severe DNA damage. Furthermore, we found that ALD is characterized by additional hallmarks of eukaryotic mitochondrial apoptosis, including (i) rRNA degradation by the endoribonuclease YbeY, (ii) upregulation of a unique set of genes that we called extensive-damage-induced (Edin) genes, (iii) a decrease in the activities of complexes I and II of the electron transport chain, and (iv) the formation of high levels of OH˙ through the Fenton reaction, eventually resulting in cell death. Our genetic and molecular studies on ALD provide additional insight for the evolution of mitochondria and the apoptotic pathway in eukaryotes. Importance: The SOS response is the first described and the most studied bacterial response to DNA damage. It is mediated by a set of two genes, recA-lexA, and it results in DNA repair and thereby in the survival of the bacterial culture. We have shown that Escherichia coli responds to DNA damage by an additional recA-lexA-mediated pathway resulting in an apoptosis-like death (ALD). Apoptosis is a mode of cell death that has previously been reported only in eukaryotes. We found that E. coli ALD is characterized by several hallmarks of eukaryotic mitochondrial apoptosis. Altogether, our results revealed that recA-lexA is a DNA damage response coordinator that permits two opposite responses: life, mediated by the SOS, and death, mediated by the ALD. The choice seems to be a function of the degree of DNA damage in the cell. Copyright © 2014 Erental et al.

Is recurrence in major depressive disorder related to bipolarity and mixed features? Results from the BRIDGE-II-Mix study.

PubMed

Mazzarini, Lorenzo; Kotzalidis, Georgios D; Piacentino, Daria; Rizzato, Salvatore; Angst, Jules; Azorin, Jean-Michel; Bowden, Charles L; Mosolov, Sergey; Young, Allan H; Vieta, Eduard; Girardi, Paolo; Perugi, Giulio

2018-03-15

Current classifications separate Bipolar (BD) from Major Depressive Disorder (MDD) based on polarity rather than recurrence. We aimed to determine bipolar/mixed feature frequency in a large MDD multinational sample with (High-Rec) and without (Low-Rec) >3 recurrences, comparing the two subsamples. We measured frequency of bipolarity/hypomanic features during current depressive episodes (MDEs) in 2347 MDD patients from the BRIDGE-II-mix database, comparing High-Rec with Low-Rec. We used Bonferroni-corrected Student's t-test for continuous, and chi-squared test, for categorical variables. Logistic regression estimated the size of the association between clinical characteristics and High-Rec MDD. Compared to Low-Rec (n = 1084, 46.2%), High-Rec patients (n = 1263, 53.8%) were older, with earlier depressive onset, had more family history of BD, more atypical features, suicide attempts, hospitalisations, and treatment resistance and (hypo)manic switches when treated with antidepressants, higher comorbidity with borderline personality disorder, and more hypomanic symptoms during current MDE, resulting in higher rates of mixed depression according to both DSM-5 and research-based diagnostic (RBDC) criteria. Logistic regression showed age at first symptoms < 30 years, current MDE duration ≤ 1 month, hypomania/mania among first-degree relatives, past suicide attempts, treatment-resistance, antidepressant-induced swings, and atypical, mixed, or psychotic features during MDE to associate with High-Rec. Number of MDEs for defining recurrence was arbitrary; cross-sectionality did not allow assessment of conversion from MDD to BD. High-Rec MDD differed from Low-Rec group for several clinical/epidemiological variables, including bipolar/mixed features. Bipolarity specifier and RBDC were more sensitive than DSM-5 criteria in detecting bipolar and mixed features in MDD. Copyright © 2017. Published by Elsevier B.V.

A homozygous recA mutant of Synechocystis PCC6803: construction strategy and characteristics eliciting a novel RecA independent UVC resistance in dark.

PubMed

Minda, Renu; Ramchandani, Jyoti; Joshi, Vasudha P; Bhattacharjee, Swapan Kumar

2005-12-01

We report here the construction of a homozygous recA460::cam insertion mutant of Synechocystis sp. PCC 6803 that may be useful for plant molecular genetics by providing a plant like host free of interference from homologous recombination. The homozygous recA460::cam mutant is highly sensitive to UVC under both photoreactivating and non-photoreactivating conditions compared to the wild type (WT). The liquid culture of the mutant growing in approximately 800 lx accumulates nonviable cells to the tune of 86% as estimated by colony counts on plates incubated at the same temperature and light intensity. The generation time of recA mutant in standard light intensity (2,500 lx) increases to 50 h compared to 28 h in lower light intensity (approximately 800 lx) that was used for selection, thus explaining the earlier failures to obtain a homozygous recA mutant. The WT, in contrast, grows at faster rate (23 h generation time) in standard light intensity compared to that at approximately 800 lx (26 h). The Synechocystis RecA protein supports homologous recombination during conjugation in recA (-) mutant of Escherichia coli, but not the SOS response as measured by UV sensitivity. It is suggested that using this homozygous recA460::cam mutant, investigations can now be extended to dissect the network of DNA repair pathways involved in housekeeping activities that may be more active in cyanobacteria than in heterotrophs. Using this mutant for the first time we provide a genetic evidence of a mechanism independent of RecA that causes enhanced UVC resistance on light to dark transition.

Alkaline phosphatase protects against renal inflammation through dephosphorylation of lipopolysaccharide and adenosine triphosphate.

PubMed

Peters, E; Geraci, S; Heemskerk, S; Wilmer, M J; Bilos, A; Kraenzlin, B; Gretz, N; Pickkers, P; Masereeuw, R

2015-10-01

Recently, two phase-II trials demonstrated improved renal function in critically ill patients with sepsis-associated acute kidney injury treated with the enzyme alkaline phosphatase. Here, we elucidated the dual active effect on renal protection of alkaline phosphatase. The effect of human recombinant alkaline phosphatase (recAP) on LPS-induced renal injury was studied in Sprague-Dawley rats. Renal function was assessed by transcutaneous measurement of FITC-sinistrin elimination in freely moving, awake rats. The mechanism of action of recAP was further investigated in vitro using conditionally immortalized human proximal tubular epithelial cells (ciPTEC). In vivo, LPS administration significantly prolonged FITC-sinistrin half-life and increased fractional urea excretion, which was prevented by recAP co-administration. Moreover, recAP prevented LPS-induced increase in proximal tubule injury marker, kidney injury molecule-1 expression and excretion. In vitro, LPS-induced production of TNF-α, IL-6 and IL-8 was significantly attenuated by recAP. This effect was linked to dephosphorylation, as enzymatically inactive recAP had no effect on LPS-induced cytokine production. RecAP-mediated protection resulted in increased adenosine levels through dephosphorylation of LPS-induced extracellular ADP and ATP. Also, recAP attenuated LPS-induced increased expression of adenosine A2A receptor. However, the A2A receptor antagonist ZM-241385 did not diminish the effects of recAP. These results indicate that the ability of recAP to reduce renal inflammation may account for the beneficial effect observed in septic acute kidney injury patients, and that dephosphorylation of ATP and LPS are responsible for this protective effect. © 2015 The British Pharmacological Society.

Evidence for the role of Mycobacterium tuberculosis RecG helicase in DNA repair and recombination.

PubMed

Thakur, Roshan S; Basavaraju, Shivakumar; Somyajit, Kumar; Jain, Akshatha; Subramanya, Shreelakshmi; Muniyappa, Kalappa; Nagaraju, Ganesh

2013-04-01

In order to survive and replicate in a variety of stressful conditions during its life cycle, Mycobacterium tuberculosis must possess mechanisms to safeguard the integrity of the genome. Although DNA repair and recombination related genes are thought to play key roles in the repair of damaged DNA in all organisms, so far only a few of them have been functionally characterized in the tubercle bacillus. In this study, we show that M. tuberculosis RecG (MtRecG) expression was induced in response to different genotoxic agents. Strikingly, expression of MtRecG in Escherichia coli ∆recG mutant strain provided protection against mitomycin C, methyl methane sulfonate and UV induced cell death. Purified MtRecG exhibited higher binding affinity for the Holliday junction (HJ) compared with a number of canonical recombinational DNA repair intermediates. Notably, although MtRecG binds at the core of the mobile and immobile HJs, and with higher binding affinity for the immobile HJ, branch migration was evident only in the case of the mobile HJ. Furthermore, immobile HJs stimulate MtRecG ATPase activity less efficiently than mobile HJs. In addition to HJ substrates, MtRecG exhibited binding affinity for a variety of branched DNA structures including three-way junctions, replication forks, flap structures, forked duplex and a D-loop structure, but demonstrated strong unwinding activity on replication fork and flap DNA structures. Together, these results support that MtRecG plays an important role in processes related to DNA metabolism under normal as well as stress conditions. © 2013 The Authors Journal compilation © 2013 FEBS.

Implication of RuvABC and RecG in homologous recombination in Streptomyces ambofaciens.

PubMed

Hoff, Grégory; Bertrand, Claire; Piotrowski, Emilie; Thibessard, Annabelle; Leblond, Pierre

2017-01-01

Most bacterial organisms rely on homologous recombination to repair DNA double-strand breaks and for the post-replicative repair of DNA single-strand gaps. Homologous recombination can be divided into three steps: (i) a pre-synaptic step in which the DNA 3'-OH ends are processed, (ii) a recA-dependent synaptic step allowing the invasion of an intact copy and the formation of Holliday junctions, and (iii) a post-synaptic step consisting of migration and resolution of these junctions. Currently, little is known about factors involved in homologous recombination, especially for the post-synaptic step. In Escherichia coli, branch migration and resolution are performed by the RuvABC complex, but could also rely on the RecG helicase in a redundant manner. In this study, we show that recG and ruvABC are well-conserved among Streptomyces. ΔruvABC, ΔrecG and ΔruvABC ΔrecG mutant strains were constructed. ΔruvABC ΔrecG is only slightly affected by exposure to DNA damage (UV). We also show that conjugational recombination decreases in the absence of RuvABC and RecG, but that intra-chromosomal recombination is not affected. These data suggest that RuvABC and RecG are indeed involved in homologous recombination in Streptomyces ambofaciens and that alternative factors are able to take over Holliday junction in Streptomyces. Copyright © 2016 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Aviation System Safety Risk Management Tool Analysis. Volume 2: Appendices

DTIC Science & Technology

1993-10-01

Part Number FY AMC Case Number BATERY BB433AA 81 E 810421201 E’ BATTERY BB433AA 81 E 810421181 [’ BATTERY BB433AA 81 E 810514141 [’ BATIERY BB433AA 81...830520061 [- BAT=ERY NOT REC 83 E 830514071 -l BATTERY NOT REC 82 E 811102131 El BATERY NOT REC 82 E 820715191 " BATTERY NOT REC 82 E 820902051 "- BATERY NOT

40 CFR Table 3 to Subpart II of... - Summary of Recordkeeping and Reporting Requirements abc

Code of Federal Regulations, 2012 CFR

2012-07-01

... abc Requirement All Opts. Rec Rep Option 1 Rec Rep Option 2 Rec Rep Option 3 Rec Rep Notification (§ 63.9(a)-(d)) X X Implementation plan (§ 63.787(b)) d X X Volume of coating applied at unaffected major sources (§ 63.781(b)) X Volume of each low-usage-exempt coating applied at affected sources (§ 63...

40 CFR Table 3 to Subpart II of... - Summary of Recordkeeping and Reporting Requirements abc

Code of Federal Regulations, 2011 CFR

2011-07-01

... abc Requirement All Opts. Rec Rep Option 1 Rec Rep Option 2 Rec Rep Option 3 Rec Rep Notification (§ 63.9(a)-(d)) X X Implementation plan (§ 63.787(b)) d X X Volume of coating applied at unaffected major sources (§ 63.781(b)) X Volume of each low-usage-exempt coating applied at affected sources (§ 63...

40 CFR Table 3 to Subpart II of... - Summary of Recordkeeping and Reporting Requirements abc

Code of Federal Regulations, 2010 CFR

2010-07-01

... abc Requirement All Opts. Rec Rep Option 1 Rec Rep Option 2 Rec Rep Option 3 Rec Rep Notification (§ 63.9(a)-(d)) X X Implementation plan (§ 63.787(b)) d X X Volume of coating applied at unaffected major sources (§ 63.781(b)) X Volume of each low-usage-exempt coating applied at affected sources (§ 63...

40 CFR Table 3 to Subpart II of... - Summary of Recordkeeping and Reporting Requirements abc

Code of Federal Regulations, 2013 CFR

2013-07-01

... abc Requirement All Opts. Rec Rep Option 1 Rec Rep Option 2 Rec Rep Option 3 Rec Rep Notification (§ 63.9(a)-(d)) X X Implementation plan (§ 63.787(b)) d X X Volume of coating applied at unaffected major sources (§ 63.781(b)) X Volume of each low-usage-exempt coating applied at affected sources (§ 63...

40 CFR Table 3 to Subpart II of... - Summary of Recordkeeping and Reporting Requirements abc

Code of Federal Regulations, 2014 CFR

2014-07-01

... abc Requirement All Opts. Rec Rep Option 1 Rec Rep Option 2 Rec Rep Option 3 Rec Rep Notification (§ 63.9(a)-(d)) X X Implementation plan (§ 63.787(b)) d X X Volume of coating applied at unaffected major sources (§ 63.781(b)) X Volume of each low-usage-exempt coating applied at affected sources (§ 63...

Bacteroides fragilis RecA protein overexpression causes resistance to metronidazole

PubMed Central

Steffens, Laura S.; Nicholson, Samantha; Paul, Lynthia V.; Nord, Carl Erik; Patrick, Sheila; Abratt, Valerie R.

2010-01-01

Bacteroides fragilis is a human gut commensal and an opportunistic pathogen causing anaerobic abscesses and bacteraemias which are treated with metronidazole (Mtz), a DNA damaging agent. This study examined the role of the DNA repair protein, RecA, in maintaining endogenous DNA stability and its contribution to resistance to Mtz and other DNA damaging agents. RT-PCR of B. fragilis genomic DNA showed that the recA gene was co-transcribed as an operon together with two upstream genes, putatively involved in repairing oxygen damage. A B. fragilis recA mutant was generated using targeted gene inactivation. Fluorescence microscopy using DAPI staining revealed increased numbers of mutant cells with reduced intact double-stranded DNA. Alkaline gel electrophoresis of the recA mutant DNA showed increased amounts of strand breaks under normal growth conditions, and the recA mutant also showed less spontaneous mutagenesis relative to the wild type strain. The recA mutant was sensitive to Mtz, ultraviolet light and hydrogen peroxide. A B. fragilis strain overexpressing the RecA protein exhibited increased resistance to Mtz compared to the wild type. This is the first study to show that overexpression of a DNA repair protein in B. fragilis increases Mtz resistance. This represents a novel drug resistance mechanism in this bacterium. PMID:20435137

Role of Renewable Energy Certificates in Developing New Renewable Energy Projects

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

Holt, E.; Sumner, J.; Bird, L.

2011-06-01

For more than a decade, renewable energy certificates (RECs) have grown in use, becoming a common way to track ownership of the renewable and environmental attributes of renewable electricity generation. In recent years, however, questions have risen about the role RECs play in the decision to build new renewable energy projects. Information from a variety of market participants suggests that the importance of RECs in building new projects varies depending on a number of factors, including electricity market prices, the cost-competitiveness of the project, the presence or absence of public policies supportive of new projects, contract duration, and the perspectivemore » of different market participants. While there is no single answer to the role that RECs play, there are situations in which REC revenues are essential to project economics, as well as some where REC revenues may have little impact. To strengthen the role RECs play in both compliance and voluntary markets, there are a number of options that could be considered. In compliance markets, lawmakers or regulators would have to adopt measures that strengthen the role of RECs in the development of new projects, while in voluntary markets, it would be up to program leaders and market participants themselves to implement measures.« less

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

Holt, E.; Bird, L.

Renewable energy certificates (RECs) represent the attributes of electricity generated from renewable energy sources. These attributes are unbundled from the physical electricity, and the two products-the attributes embodied in the certificates and the commodity electricity-may be sold or traded separately. RECs are quickly becoming the currency of renewable energy markets because of their flexibility and the fact that they are not subject to the geographic and physical limitations of commodity electricity. RECs are currently used by utilities and marketers to supply renewable energy products to end-use customers as well as to demonstrate compliance with regulatory requirements, such as renewable energymore » mandates. The purpose of this report is to describe and analyze the emerging market for renewable energy certificates. It describes how RECs are marketed, examines RECs markets including scope and prices, and identifies and describes the key challenges facing the growth and success of RECs markets.« less

Arrangement of RecA protein in its active filament determined by polarized-light spectroscopy.

PubMed

Morimatsu, Katsumi; Takahashi, Masayuki; Nordén, Bengt

2002-09-03

Linear dichroism (LD) polarized-light spectroscopy is used to determine the arrangement of RecA in its large filamentous complex with DNA, active in homologous recombination. Angular orientation data for two tryptophan and seven tyrosine residues, deduced from differential LD of wild-type RecA vs. mutants that were engineered to attenuate the UV absorption of selected residues, revealed a rotation by some 40 degrees of the RecA subunits relative to the arrangement in crystal without DNA. In addition, conformational changes are observed for tyrosine residues assigned to be involved in DNA binding and in RecA-RecA contacts, thus potentially related to the global structure of the filament and its biological function. The presented spectroscopic approach, called "Site-Specific Linear Dichroism" (SSLD), may find forceful applications also to other biologically important fibrous complexes not amenable to x-ray crystallographic or NMR structural analysis.

Structural mechanisms of DNA binding and unwinding in bacterial RecQ helicases

DOE PAGES

Manthei, Kelly A.; Hill, Morgan C.; Burke, Jordan E.; ...

2015-03-23

RecQ helicases unwind remarkably diverse DNA structures as key components of many cellular processes. How RecQ enzymes accommodate different substrates in a unified mechanism that couples ATP hydrolysis to DNA unwinding is unknown. In this paper, the X-ray crystal structure of the Cronobacter sakazakii RecQ catalytic core domain bound to duplex DNA with a 3' single-stranded extension identifies two DNA-dependent conformational rearrangements: a winged-helix domain pivots ~90° to close onto duplex DNA, and a conserved aromatic-rich loop is remodeled to bind ssDNA. These changes coincide with a restructuring of the RecQ ATPase active site that positions catalytic residues for ATPmore » hydrolysis. Complex formation also induces a tight bend in the DNA and melts a portion of the duplex. Finally, this bending, coupled with translocation, could provide RecQ with a mechanism for unwinding duplex and other DNA structures.« less

Loop L1 governs the DNA-binding specificity and order for RecA-catalyzed reactions in homologous recombination and DNA repair

PubMed Central

Shinohara, Takeshi; Ikawa, Shukuko; Iwasaki, Wakana; Hiraki, Toshiki; Hikima, Takaaki; Mikawa, Tsutomu; Arai, Naoto; Kamiya, Nobuo; Shibata, Takehiko

2015-01-01

In all organisms, RecA-family recombinases catalyze homologous joint formation in homologous genetic recombination, which is essential for genome stability and diversification. In homologous joint formation, ATP-bound RecA/Rad51-recombinases first bind single-stranded DNA at its primary site and then interact with double-stranded DNA at another site. The underlying reason and the regulatory mechanism for this conserved binding order remain unknown. A comparison of the loop L1 structures in a DNA-free RecA crystal that we originally determined and in the reported DNA-bound active RecA crystals suggested that the aspartate at position 161 in loop L1 in DNA-free RecA prevented double-stranded, but not single-stranded, DNA-binding to the primary site. This was confirmed by the effects of the Ala-replacement of Asp-161 (D161A), analyzed directly by gel-mobility shift assays and indirectly by DNA-dependent ATPase activity and SOS repressor cleavage. When RecA/Rad51-recombinases interact with double-stranded DNA before single-stranded DNA, homologous joint-formation is suppressed, likely by forming a dead-end product. We found that the D161A-replacement reduced this suppression, probably by allowing double-stranded DNA to bind preferentially and reversibly to the primary site. Thus, Asp-161 in the flexible loop L1 of wild-type RecA determines the preference for single-stranded DNA-binding to the primary site and regulates the DNA-binding order in RecA-catalyzed recombinase reactions. PMID:25561575

Human endogenous retrovirus HERV-K(HML-2) encodes a stable signal peptide with biological properties distinct from Rec

PubMed Central

Ruggieri, Alessia; Maldener, Esther; Sauter, Marlies; Mueller-Lantzsch, Nikolaus; Meese, Eckart; Fackler, Oliver T; Mayer, Jens

2009-01-01

Background The human endogenous retrovirus HERV-K(HML-2) family is associated with testicular germ cell tumors (GCT). Various HML-2 proviruses encode viral proteins such as Env and Rec. Results We describe here that HML-2 Env gives rise to a 13 kDa signal peptide (SP) that harbors a different C-terminus compared to Rec. Subsequent to guiding Env to the endoplasmatic reticulum (ER), HML-2 SP is released into the cytosol. Biochemical analysis and confocal microscopy demonstrated that similar to Rec, SP efficiently translocates to the granular component of nucleoli. Unlike Rec, SP does not shuttle between nucleus and cytoplasm. SP is less stable than Rec as it is subjected to proteasomal degradation. Moreover, SP lacks export activity towards HML-2 genomic RNA, the main function of Rec in the original viral context, and SP does not interfere with Rec's RNA export activity. Conclusion SP is a previously unrecognized HML-2 protein that, besides targeting and translocation of Env into the ER lumen, may exert biological functions distinct from Rec. HML-2 SP represents another functional similarity with the closely related Mouse Mammary Tumor Virus that encodes an Env-derived SP named p14. Our findings furthermore support the emerging concept of bioactive SPs as a conserved retroviral strategy to modulate their host cell environment, evidenced here by a "retroviral fossil". While the specific role of HML-2 SP remains to be elucidated in the context of human biology, we speculate that it may be involved in immune evasion of GCT cells or tumorigenesis. PMID:19220907

Orbital electron capture by the nucleus

NASA Technical Reports Server (NTRS)

Bambynek, W.; Behrens, H.; Chen, M. H.; Crasemann, B.; Fitzpatrick, M. L.; Ledingham, K. W. D.; Genz, H.; Mutterer, M.; Intemann, R. L.

1976-01-01

The theory of nuclear electron capture is reviewed in the light of current understanding of weak interactions. Experimental methods and results regarding capture probabilities, capture ratios, and EC/Beta(+) ratios are summarized. Radiative electron capture is discussed, including both theory and experiment. Atomic wave function overlap and electron exchange effects are covered, as are atomic transitions that accompany nuclear electron capture. Tables are provided to assist the reader in determining quantities of interest for specific cases.

Structural ensembles reveal intrinsic disorder for the multi-stimuli responsive bio-mimetic protein Rec1-resilin

PubMed Central

Balu, Rajkamal; Knott, Robert; Cowieson, Nathan P.; Elvin, Christopher M.; Hill, Anita J.; Choudhury, Namita R.; Dutta, Naba K.

2015-01-01

Rec1-resilin is the first recombinant resilin-mimetic protein polymer, synthesized from exon-1 of the Drosophila melanogaster gene CG15920 that has demonstrated unusual multi-stimuli responsiveness in aqueous solution. Crosslinked hydrogels of Rec1-resilin have also displayed remarkable mechanical properties including near-perfect rubber-like elasticity. The structural basis of these extraordinary properties is not clearly understood. Here we combine a computational and experimental investigation to examine structural ensembles of Rec1-resilin in aqueous solution. The structure of Rec1-resilin in aqueous solutions is investigated experimentally using circular dichroism (CD) spectroscopy and small angle X-ray scattering (SAXS). Both bench-top and synchrotron SAXS are employed to extract structural data sets of Rec1-resilin and to confirm their validity. Computational approaches have been applied to these experimental data sets in order to extract quantitative information about structural ensembles including radius of gyration, pair-distance distribution function, and the fractal dimension. The present work confirms that Rec1-resilin is an intrinsically disordered protein (IDP) that displays equilibrium structural qualities between those of a structured globular protein and a denatured protein. The ensemble optimization method (EOM) analysis reveals a single conformational population with partial compactness. This work provides new insight into the structural ensembles of Rec1-resilin in solution. PMID:26042819

Structural ensembles reveal intrinsic disorder for the multi-stimuli responsive bio-mimetic protein Rec1-resilin.

PubMed

Balu, Rajkamal; Knott, Robert; Cowieson, Nathan P; Elvin, Christopher M; Hill, Anita J; Choudhury, Namita R; Dutta, Naba K

2015-06-04

Rec1-resilin is the first recombinant resilin-mimetic protein polymer, synthesized from exon-1 of the Drosophila melanogaster gene CG15920 that has demonstrated unusual multi-stimuli responsiveness in aqueous solution. Crosslinked hydrogels of Rec1-resilin have also displayed remarkable mechanical properties including near-perfect rubber-like elasticity. The structural basis of these extraordinary properties is not clearly understood. Here we combine a computational and experimental investigation to examine structural ensembles of Rec1-resilin in aqueous solution. The structure of Rec1-resilin in aqueous solutions is investigated experimentally using circular dichroism (CD) spectroscopy and small angle X-ray scattering (SAXS). Both bench-top and synchrotron SAXS are employed to extract structural data sets of Rec1-resilin and to confirm their validity. Computational approaches have been applied to these experimental data sets in order to extract quantitative information about structural ensembles including radius of gyration, pair-distance distribution function, and the fractal dimension. The present work confirms that Rec1-resilin is an intrinsically disordered protein (IDP) that displays equilibrium structural qualities between those of a structured globular protein and a denatured protein. The ensemble optimization method (EOM) analysis reveals a single conformational population with partial compactness. This work provides new insight into the structural ensembles of Rec1-resilin in solution.

Structural ensembles reveal intrinsic disorder for the multi-stimuli responsive bio-mimetic protein Rec1-resilin

NASA Astrophysics Data System (ADS)

Balu, Rajkamal; Knott, Robert; Cowieson, Nathan P.; Elvin, Christopher M.; Hill, Anita J.; Choudhury, Namita R.; Dutta, Naba K.

2015-06-01

Rec1-resilin is the first recombinant resilin-mimetic protein polymer, synthesized from exon-1 of the Drosophila melanogaster gene CG15920 that has demonstrated unusual multi-stimuli responsiveness in aqueous solution. Crosslinked hydrogels of Rec1-resilin have also displayed remarkable mechanical properties including near-perfect rubber-like elasticity. The structural basis of these extraordinary properties is not clearly understood. Here we combine a computational and experimental investigation to examine structural ensembles of Rec1-resilin in aqueous solution. The structure of Rec1-resilin in aqueous solutions is investigated experimentally using circular dichroism (CD) spectroscopy and small angle X-ray scattering (SAXS). Both bench-top and synchrotron SAXS are employed to extract structural data sets of Rec1-resilin and to confirm their validity. Computational approaches have been applied to these experimental data sets in order to extract quantitative information about structural ensembles including radius of gyration, pair-distance distribution function, and the fractal dimension. The present work confirms that Rec1-resilin is an intrinsically disordered protein (IDP) that displays equilibrium structural qualities between those of a structured globular protein and a denatured protein. The ensemble optimization method (EOM) analysis reveals a single conformational population with partial compactness. This work provides new insight into the structural ensembles of Rec1-resilin in solution.

Suppression of the E. coli SOS response by dNTP pool changes.

PubMed

Maslowska, Katarzyna H; Makiela-Dzbenska, Karolina; Fijalkowska, Iwona J; Schaaper, Roel M

2015-04-30

The Escherichia coli SOS system is a well-established model for the cellular response to DNA damage. Control of SOS depends largely on the RecA protein. When RecA is activated by single-stranded DNA in the presence of a nucleotide triphosphate cofactor, it mediates cleavage of the LexA repressor, leading to expression of the 30(+)-member SOS regulon. RecA activation generally requires the introduction of DNA damage. However, certain recA mutants, like recA730, bypass this requirement and display constitutive SOS expression as well as a spontaneous (SOS) mutator effect. Presently, we investigated the possible interaction between SOS and the cellular deoxynucleoside triphosphate (dNTP) pools. We found that dNTP pool changes caused by deficiencies in the ndk or dcd genes, encoding nucleoside diphosphate kinase and dCTP deaminase, respectively, had a strongly suppressive effect on constitutive SOS expression in recA730 strains. The suppression of the recA730 mutator effect was alleviated in a lexA-deficient background. Overall, the findings suggest a model in which the dNTP alterations in the ndk and dcd strains interfere with the activation of RecA, thereby preventing LexA cleavage and SOS induction. Published by Oxford University Press on behalf of Nucleic Acids Research 2015. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Roles of Type 1A Topoisomerases in Genome Maintenance in Escherichia coli

PubMed Central

Usongo, Valentine; Drolet, Marc

2014-01-01

In eukaryotes, type 1A topoisomerases (topos) act with RecQ-like helicases to maintain the stability of the genome. Despite having been the first type 1A enzymes to be discovered, much less is known about the involvement of the E. coli topo I (topA) and III (topB) enzymes in genome maintenance. These enzymes are thought to have distinct cellular functions: topo I regulates supercoiling and R-loop formation, and topo III is involved in chromosome segregation. To better characterize their roles in genome maintenance, we have used genetic approaches including suppressor screens, combined with microscopy for the examination of cell morphology and nucleoid shape. We show that topA mutants can suffer from growth-inhibitory and supercoiling-dependent chromosome segregation defects. These problems are corrected by deleting recA or recQ but not by deleting recJ or recO, indicating that the RecF pathway is not involved. Rather, our data suggest that RecQ acts with a type 1A topo on RecA-generated recombination intermediates because: 1-topo III overproduction corrects the defects and 2-recQ deletion and topo IIII overproduction are epistatic to recA deletion. The segregation defects are also linked to over-replication, as they are significantly alleviated by an oriC::aph suppressor mutation which is oriC-competent in topA null but not in isogenic topA+ cells. When both topo I and topo III are missing, excess supercoiling triggers growth inhibition that correlates with the formation of extremely long filaments fully packed with unsegregated and diffuse DNA. These phenotypes are likely related to replication from R-loops as they are corrected by overproducing RNase HI or by genetic suppressors of double topA rnhA mutants affecting constitutive stable DNA replication, dnaT::aph and rne::aph, which initiates from R-loops. Thus, bacterial type 1A topos maintain the stability of the genome (i) by preventing over-replication originating from oriC (topo I alone) and R-loops and (ii) by acting with RecQ. PMID:25102178

Genetic Interactions Between the Meiosis-Specific Cohesin Components, STAG3, REC8, and RAD21L.

PubMed

Ward, Ayobami; Hopkins, Jessica; Mckay, Matthew; Murray, Steve; Jordan, Philip W

2016-06-01

Cohesin is an essential structural component of chromosomes that ensures accurate chromosome segregation during mitosis and meiosis. Previous studies have shown that there are cohesin complexes specific to meiosis, required to mediate homologous chromosome pairing, synapsis, recombination, and segregation. Meiosis-specific cohesin complexes consist of two structural maintenance of chromosomes proteins (SMC1α/SMC1β and SMC3), an α-kleisin protein (RAD21, RAD21L, or REC8), and a stromal antigen protein (STAG1, 2, or 3). STAG3 is exclusively expressed during meiosis, and is the predominant STAG protein component of cohesin complexes in primary spermatocytes from mouse, interacting directly with each α-kleisin subunit. REC8 and RAD21L are also meiosis-specific cohesin components. Stag3 mutant spermatocytes arrest in early prophase ("zygotene-like" stage), displaying failed homolog synapsis and persistent DNA damage, as a result of unstable loading of cohesin onto the chromosome axes. Interestingly, Rec8, Rad21L double mutants resulted in an earlier "leptotene-like" arrest, accompanied by complete absence of STAG3 loading. To assess genetic interactions between STAG3 and α-kleisin subunits RAD21L and REC8, our lab generated Stag3, Rad21L, and Stag3, Rec8 double knockout mice, and compared them to the Rec8, Rad21L double mutant. These double mutants are phenotypically distinct from one another, and more severe than each single knockout mutant with regards to chromosome axis formation, cohesin loading, and sister chromatid cohesion. The Stag3, Rad21L, and Stag3, Rec8 double mutants both progress further into prophase I than the Rec8, Rad21L double mutant. Our genetic analysis demonstrates that cohesins containing STAG3 and REC8 are the main complex required for centromeric cohesion, and RAD21L cohesins are required for normal clustering of pericentromeric heterochromatin. Furthermore, the STAG3/REC8 and STAG3/RAD21L cohesins are the primary cohesins required for axis formation. Copyright © 2016 Ward et al.

Whole body protection against lethal ionizing radiation in mice by REC-2001: a semi-purified fraction of Podophyllum hexandrum.

PubMed

Lata, M; Prasad, J; Singh, S; Kumar, R; Singh, L; Chaudhary, P; Arora, R; Chawla, R; Tyagi, S; Soni, N L; Sagar, R K; Devi, M; Sharma, R K; Puri, S C; Tripathi, R P

2009-01-01

The current study has concentrated on assessment of the radioprotective potential of REC-2001, a semi-purified fraction of rhizomes of Podophyllum hexandrum, in Swiss albino Strain 'A' mice exposed to 10 Gy whole-body gamma radiation. Animals were treated with 10 and 15 mg/kg b wt (i.p.) of REC-2001 1h prior to exposure to a lethal dose of gamma-radiation (10 Gy) and observed upto 30 days. For analysis of maximum tolerable dose (MTD), LD(50) and acute toxic dose, different concentrations of the extract were administered to animals and their mortality and morbidity status was observed upto 72 h and one week, respectively. Dose reduction factor (DRF) was determined by exposing REC-2001 pre-treated mice to supra-lethal doses of gamma-radiation. Endogenous spleen colony forming units (CFU), DNA strand breaks in thymocytes (alkaline halo assay) and lipid degradation was studied to understand the mechanism of radioprotection. A single dose of REC-2001 (10 and 15 mg/kg b wt i.p.) exhibited >90% survival in the pre-treated irradiated group versus no survival in radiation control group. Single doses of upto 75 mg/kg b wt (i.p.) did not cause any mortality (MTD) in mice. REC-2001, a dose of 90 mg/kg b wt, resulted in 50% mortality (LD(50)), while the LD(100) was 115 mg/kg b wt REC-2001 exhibited a DRF of 1.62. CFU counts in the REC-2001 treated group were found significantly high (5.33/spleen) as compared to controls. Exposure of thymocytes to 10 Gy radiation resulted in increased halo diameter (45+/-3 microm) in comparison to untreated controls (8+/-1 microm). REC-2001 administration (500 microg/ml) decreased the halo diameter to 15+/-2 microm. Radiation-induced lipid degradation was also inhibited by REC-2001. The present study has revealed that REC-2001 is a promising radioprotective fraction that can be effectively used against lethal doses of gamma-radiation after further investigations in higher animal models.

Ship Tracks

NASA Image and Video Library

2017-12-08

Ship tracks above the northern Pacific Ocean. NASA image captured July 3, 2010. Satellite: Aqua NASA/GSFC/Jeff Schmaltz/MODIS Land Rapid Response Team To learn more about MODIS go to: rapidfire.sci.gsfc.nasa.gov/gallery/?latest To learn more about ship tracks go to: visibleearth.nasa.gov/view_rec.php?id=2370 To watch a video on ship tracks go to: www.youtube.com/watch?v=Vsri2sOAjWo&feature=player_em...! NASA Goddard Space Flight Center is home to the nation's largest organization of combined scientists, engineers and technologists that build spacecraft, instruments and new technology to study the Earth, the sun, our solar system, and the universe.

Effects of a human recombinant alkaline phosphatase on renal hemodynamics, oxygenation and inflammation in two models of acute kidney injury

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

Peters, Esther, E-mail: esther.peters@radboudumc.n

Two small clinical trials indicated that administration of bovine intestinal alkaline phosphatase (AP) improves renal function in critically ill patients with sepsis-associated acute kidney injury (AKI), for which the mechanism of action is not completely understood. Here, we investigated the effects of a newly developed human recombinant AP (recAP) on renal oxygenation and hemodynamics and prevention of kidney damage and inflammation in two in vivo AKI models. To induce AKI, male Wistar rats (n = 18) were subjected to renal ischemia (30 min) and reperfusion (I/R), or sham-operated. In a second model, rats (n = 18) received a 30 minmore » infusion of lipopolysaccharide (LPS; 2.5 mg/kg), or saline, and fluid resuscitation. In both models, recAP (1000 U/kg) was administered intravenously (15 min before reperfusion, or 90 min after LPS). Following recAP treatment, I/R-induced changes in renal blood flow, renal vascular resistance and oxygen delivery at early, and cortical microvascular oxygen tension at late reperfusion were no longer significantly affected. RecAP did not influence I/R-induced effects on mean arterial pressure. During endotoxemia, recAP treatment did not modulate the LPS-induced changes in systemic hemodynamics and renal oxygenation. In both models, recAP did exert a clear renal protective anti-inflammatory effect, demonstrated by attenuated immunostaining of inflammatory, tubular injury and pro-apoptosis markers. Whether this renal protective effect is sufficient to improve outcome of patients suffering from sepsis-associated AKI is being investigated in a large clinical trial. - Highlights: • Human recombinant alkaline phosphatase (recAP) is a potential new therapy for sepsis-associated acute kidney injury (AKI). • RecAP can modulate renal oxygenation and hemodynamics immediately following I/R-induced AKI. • RecAP did not modulate endotoxemia-induced changes in systemic hemodynamics and renal oxygenation. • RecAP did exert a clear renal protective anti-inflammatory effect in both models.« less

Can an ethics officer role reduce delays in research ethics approval? A mixed-method evaluation of an improvement project

PubMed Central

Dixon-Woods, Mary; Foy, Chris; Hayden, Charlotte; Al-Shahi Salman, Rustam; Tebbutt, Stephen; Schroter, Sara

2016-01-01

Objective Frustration continues to be directed at delays in gaining approvals for undertaking health research in the UK. We aimed to evaluate the impact of an ethics officer intervention on rates of favourable opinions (approval) and provisional opinions (requiring revision and resubmission) and on the time taken to reach a final opinion by research ethics committees (RECs), to characterise how the role operated in practice, and to investigate applicants' views. Design Mixed-method study involving (i) a 2-group, non-randomised before-and-after intervention study of RECs assigned an ethics officer and a matched comparator group; (ii) a process evaluation involving a survey of applicants and documentary analysis. Participants 6 RECs and 3 associated ethics officers; 18 comparator RECs; REC applicants. Results Rates of provisional and favourable opinions between ethics officer and comparator RECs did not show a statistically significant effect of the intervention (logistic regression, p=0.26 for favourable opinions and p=0.31 for provisional opinions). Mean time to reach a decision showed a non-significant reduction (ANOVA, p=0.22) from 33.3 to 32.0 days in the ethics officer RECs compared with the comparator RECs (32.6 to 32.9 days). The survey (30% response rate) indicated applicant satisfaction and also suggested that ethics officer support might be more useful before submission. Ethics officers were successful in identifying many issues with applications, but the intervention did not function exactly as designed: in 31% of applicants, no contact between the applicants and the ethics officer took place before REC review. Limitations This study was a non-randomised comparison cohort study. Some data were missing. Conclusions An ethics officer intervention, as designed and implemented in this study, did not increase the proportion of applications to RECs that were approved on first review and did not reduce the time to a committee decision. PMID:27580832

BIGH3 protein and macrophages in retinal endothelial cell apoptosis.

PubMed

Mondragon, Albert A; Betts-Obregon, Brandi S; Moritz, Robert J; Parvathaneni, Kalpana; Navarro, Mary M; Kim, Hong Seok; Lee, Chi Fung; LeBaron, Richard G; Asmis, Reto; Tsin, Andrew T

2015-01-01

Diabetes is a pandemic disease with a higher occurrence in minority populations. The molecular mechanism to initiate diabetes-associated retinal angiogenesis remains largely unknown. We propose an inflammatory pathway of diabetic retinopathy in which macrophages in the diabetic eye provide TGFβ to retinal endothelial cells (REC) in the retinal microvasculature. In response to TGFβ, REC synthesize and secrete a pro-apoptotic BIGH3 (TGFβ-Induced Gene Human Clone 3) protein, which acts in an autocrine loop to induce REC apoptosis. Rhesus monkey retinal endothelial cells (RhREC) were treated with dMCM (cell media of macrophages treated with high glucose and LDL) and assayed for apoptosis (TUNEL), BIGH3 mRNA (qPCR), and protein (Western blots) expressions. Cells were also treated with ΤGFβ1 and 2 for BIGH3 mRNA and protein expression. Inhibition assays were carried out using antibodies for TGFβ1 and for BIGH3 to block apoptosis and mRNA expression. BIGH3 in cultured RhREC cells were identified by immunohistochemistry (IHC). Distribution of BIGH3 and macrophages in the diabetic mouse retina was examined with IHC. RhRECs treated with dMCM or TGFβ showed a significant increase in apoptosis and BIGH3 protein expression. Recombinant BIGH3 added to RhREC culture medium led to a dose-dependent increase in apoptosis. Antibodies (Ab) directed against BIGH3 and TGFβ, as well as TGFβ receptor blocker resulted in a significant reduction in apoptosis induced by either dMCM, TGFβ or BIGH3. IHC showed that cultured RhREC constitutively expressed BIGH3. Macrophage and BIGH3 protein were co-localized to the inner retina of the diabetic mouse eye. Our results support a novel inflammatory pathway for diabetic retinopathy. This pathway is initiated by TGFβ released from macrophages, which promotes synthesis and release of BIGH3 protein by REC and REC apoptosis.

The effects of buffers and pH on the thermal stability, unfolding and substrate binding of RecA.

PubMed

Metrick, Michael A; Temple, Joshua E; MacDonald, Gina

2013-12-31

The Escherichia coli protein RecA is responsible for catalysis of the strand transfer reaction used in DNA repair and recombination. Previous studies in our lab have shown that high concentrations of salts stabilize RecA in a reverse-anionic Hofmeister series. Here we investigate how changes in pH and buffer alter the thermal unfolding and cofactor binding. RecA in 20mM HEPES, MES, Tris and phosphate buffers was studied in the pH range from 6.5 to 8.5 using circular dichroism (CD), infrared (IR) and fluorescence spectroscopies. The results show all of the buffers studied stabilize RecA up to 50°C above the Tris melting temperature and influence RecA's ability to nucleate on double-stranded DNA. Infrared and CD spectra of RecA in the different buffers do not show that secondary structural changes are associated with increased stability or decreased ability to nucleate on dsDNA. These results suggest the differences in stability arise from decreasing positive charge and/or buffer interactions. © 2013. Published by Elsevier B.V. All rights reserved.

Varying ethics rules in clinical research and routine patient care – research ethics committee chairpersons’ views in Finland

PubMed Central

2014-01-01

Background To present empirical data on how the variation in regulating clinical research and patient care was perceived in Finland between 2009 and 2012. Methods Notes of interviews with 22 research ethics committee (REC) chairpersons were analyzed to identify whether differences in the regulation of clinical research and patient care were addressed. REC chairpersons’ opinions on three imaginary cases of clinical research projects challenging current research ethics rules (vignettes) were requested with a questionnaire; 18 of the 22 interviewed chairpersons responded. Results Based on REC chairpersons’ interviews, the differences between care and research regulation were not considered important issues in Finland. In the vignettes, REC chairpersons’ assumptions on how their REC would decide varied in regard to allowing research without informed consent, while solutions that are not allowed by current law were even anticipated. Mostly, but not always, the chairpersons’ own personal view agreed with their REC. Conclusions The distinction between care and research regulation has not been publicly challenged by Finnish RECs, even though it is a challenge when research relevant to health care is carried out. There is a need for debate and changes in laws and practices. PMID:24666735

The Diesel Exhaust in Miners Study: III. Interrelations between respirable elemental carbon and gaseous and particulate components of diesel exhaust derived from area sampling in underground non-metal mining facilities.

PubMed

Vermeulen, Roel; Coble, Joseph B; Yereb, Daniel; Lubin, Jay H; Blair, Aaron; Portengen, Lützen; Stewart, Patricia A; Attfield, Michael; Silverman, Debra T

2010-10-01

Diesel exhaust (DE) has been implicated as a potential lung carcinogen. However, the exact components of DE that might be involved have not been clearly identified. In the past, nitrogen oxides (NO(x)) and carbon oxides (CO(x)) were measured most frequently to estimate DE, but since the 1990s, the most commonly accepted surrogate for DE has been elemental carbon (EC). We developed quantitative estimates of historical exposure levels of respirable elemental carbon (REC) for an epidemiologic study of mortality, particularly lung cancer, among diesel-exposed miners by back-extrapolating 1998-2001 REC exposure levels using historical measurements of carbon monoxide (CO). The choice of CO was based on the availability of historical measurement data. Here, we evaluated the relationship of REC with CO and other current and historical components of DE from side-by-side area measurements taken in underground operations of seven non-metal mining facilities. The Pearson correlation coefficient of the natural log-transformed (Ln)REC measurements with the Ln(CO) measurements was 0.4. The correlation of REC with the other gaseous, organic carbon (OC), and particulate measurements ranged from 0.3 to 0.8. Factor analyses indicated that the gaseous components, including CO, together with REC, loaded most strongly on a presumed 'Diesel exhaust' factor, while the OC and particulate agents loaded predominantly on other factors. In addition, the relationship between Ln(REC) and Ln(CO) was approximately linear over a wide range of REC concentrations. The fact that CO correlated with REC, loaded on the same factor, and increased linearly in log-log space supported the use of CO in estimating historical exposure levels to DE.

Mycobacterium leprae RecA is structurally analogous but functionally distinct from Mycobacterium tuberculosis RecA protein.

PubMed

Patil, K Neelakanteshwar; Singh, Pawan; Harsha, Sri; Muniyappa, K

2011-12-01

Mycobacterium leprae is closely related to Mycobacterium tuberculosis, yet causes a very different illness. Detailed genomic comparison between these two species of mycobacteria reveals that the decaying M. leprae genome contains less than half of the M. tuberculosis functional genes. The reduction of genome size and accumulation of pseudogenes in the M. leprae genome is thought to result from multiple recombination events between related repetitive sequences, which provided the impetus to investigate the recombination-like activities of RecA protein. In this study, we have cloned, over-expressed and purified M. leprae RecA and compared its activities with that of M. tuberculosis RecA. Both proteins, despite being 91% identical at the amino acid level, exhibit strikingly different binding profiles for single-stranded DNA with varying GC contents, in the ability to catalyze the formation of D-loops and to promote DNA strand exchange. The kinetics and the extent of single-stranded DNA-dependent ATPase and coprotease activities were nearly equivalent between these two recombinases. However, the degree of inhibition exerted by a range of ATP:ADP ratios was greater on strand exchange promoted by M. leprae RecA compared to its M. tuberculosis counterpart. Taken together, our results provide insights into the mechanistic aspects of homologous recombination and coprotease activity promoted by M. lepare RecA, and further suggests that it differs from the M. tuberculosis counterpart. These results are consistent with an emerging concept of DNA-sequence influenced structural differences in RecA nucleoprotein filaments and how these differences reflect on the multiple activities associated with RecA protein. Copyright © 2011 Elsevier B.V. All rights reserved.

The Diesel Exhaust in Miners Study: III. Interrelations between Respirable Elemental Carbon and Gaseous and Particulate Components of Diesel Exhaust derived from Area Sampling in Underground Non-metal Mining Facilities

PubMed Central

Vermeulen, Roel; Coble, Joseph B.; Yereb, Daniel; Lubin, Jay H.; Blair, Aaron; Portengen, Lützen; Stewart, Patricia A.; Attfield, Michael; Silverman, Debra T.

2010-01-01

Diesel exhaust (DE) has been implicated as a potential lung carcinogen. However, the exact components of DE that might be involved have not been clearly identified. In the past, nitrogen oxides (NOx) and carbon oxides (COx) were measured most frequently to estimate DE, but since the 1990s, the most commonly accepted surrogate for DE has been elemental carbon (EC). We developed quantitative estimates of historical exposure levels of respirable elemental carbon (REC) for an epidemiologic study of mortality, particularly lung cancer, among diesel-exposed miners by back-extrapolating 1998–2001 REC exposure levels using historical measurements of carbon monoxide (CO). The choice of CO was based on the availability of historical measurement data. Here, we evaluated the relationship of REC with CO and other current and historical components of DE from side-by-side area measurements taken in underground operations of seven non-metal mining facilities. The Pearson correlation coefficient of the natural log-transformed (Ln)REC measurements with the Ln(CO) measurements was 0.4. The correlation of REC with the other gaseous, organic carbon (OC), and particulate measurements ranged from 0.3 to 0.8. Factor analyses indicated that the gaseous components, including CO, together with REC, loaded most strongly on a presumed ‘Diesel exhaust’ factor, while the OC and particulate agents loaded predominantly on other factors. In addition, the relationship between Ln(REC) and Ln(CO) was approximately linear over a wide range of REC concentrations. The fact that CO correlated with REC, loaded on the same factor, and increased linearly in log–log space supported the use of CO in estimating historical exposure levels to DE. PMID:20876234

The evaluation of complex clinical trial protocols: resources available to research ethics committees and the use of clinical trial registries--a case study.

PubMed

Homedes, Núria; Ugalde, Antonio

2015-06-01

To assess the potential role of clinical trial (CT) registries and other resources available to research ethics committees (RECs) in the evaluation of complex CT protocols in low-income and middle-income countries. Using a case study approach, the authors examined the decision-making process of a REC in Argentina and its efforts to use available resources to decide on a complex protocol. We also analysed the information in the USA and other CT registries and consulted 24 CT experts in seven countries. Information requested by the Argentinean REC from other national RECs and ethics' experts was not useful to verify the adequacy of the REC's decision whether or not to approve the CT. The responses from the national regulatory agency and the sponsor were not helpful either. The identification of international resources that could assist was beyond the REC's capability. The information in the USA and other CT registries is limited, and at times misleading; and its accuracy is not verified by register keepers. RECs have limited access to experts and institutions that could assist them in their deliberations. Sponsors do not always answer RECs' request for information to properly conduct the ethical and methodological assessment of CT protocols. The usefulness of the CT registries is curtailed by the lack of appropriate codes and by data errors. Information about reasons for rejection, withdrawal or suspension of the trial should be included in the registries. Establishing formal channels of communication among national and foreign RECs and with independent international reference centres could strengthen the ethical review of CT protocols. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Radiation damage and repair in cells and cell components. Progress report, 1980-1981

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

Not Available

1981-01-01

One aim has been to see whether, in E.coli, the various phenomena which were ascribed to the induction of the recA gene produce (p-recA) are really manifestations of one process. It was concluded that this is true for septum inhibition, Weigle-reactivation, induced inhibition of post radiation DNA degradation, and with the additional concept of a premutational lesion, for uv mutagenesis. lambda prophage induction may perhaps be brought into line with p-recA induction with the consideration of the additional secondary aspects of (a) activation of p-recA to make it enzymatically active and (b) the need to have the concentration of activatedmore » p-recA high enough to keep up with the rate of production of lambda-repressors. Revertants seem to be in more than one class and two of these can not easily be explained by the idea that p-recA contains an error-prone repair enzyme that makes errors at mutagenic lesions.« less

Meiotic recombination protein Rec12: functional conservation, crossover homeostasis and early crossover/non-crossover decision

PubMed Central

Kan, Fengling; Davidson, Mari K.; Wahls, Wayne P.

2011-01-01

In fission yeast and other eukaryotes, Rec12 (Spo11) is thought to catalyze the formation of dsDNA breaks (DSBs) that initiate homologous recombination in meiosis. Rec12 is orthologous to the catalytic subunit of topoisomerase VI (Top6A). Guided by the crystal structure of Top6A, we engineered the rec12 locus to encode Rec12 proteins each with a single amino acid substitution in a conserved residue. Of 21 substitutions, 10 significantly reduced or abolished meiotic DSBs, gene conversion, crossover recombination and the faithful segregation of chromosomes. Critical residues map within the metal ion-binding pocket toprim (E179A, D229A, D231A), catalytic region 5Y-CAP (R94A, D95A, Y98F) and the DNA-binding interface (K201A, G202E, R209A, K242A). A subset of substitutions reduced DSBs but maintained crossovers, demonstrating crossover homeostasis. Furthermore, a strong separation of function mutation (R304A) suggests that the crossover/non-crossover decision is established early by a protein–protein interaction surface of Rec12. Fission yeast has multiple crossovers per bivalent, and chromosome segregation was robust above a threshold of about one crossover per bivalent, below which non-disjunction occurred. These results support structural and functional conservation among Rec12/Spo11/Top6A family members for the catalysis of DSBs, and they reveal how Rec12 regulates other features of meiotic chromosome dynamics. PMID:21030440

Annealing Vs. Invasion in Phage λ Recombination

PubMed Central

Stahl, M. M.; Thomason, L.; Poteete, A. R.; Tarkowski, T.; Kuzminov, A.; Stahl, F. W.

1997-01-01

Genetic recombination catalyzed by λ's Red pathway was studied in rec(+) and recA mutant bacteria by examining both intracellular λ DNA and mature progeny particles. Recombination of nonreplicating phage chromosomes was induced by double-strand breaks delivered at unique sites in vivo. In rec(+) cells, cutting only one chromosome gave nearly maximal stimulation of recombination; the recombinants formed contained relatively short hybrid regions, suggesting strand invasion. In contrast, in recA mutant cells, cutting the two parental chromosomes at non-allelic sites was required for maximal stimulation; the recombinants formed tended to be hybrid over the entire region between the two cuts, implying strand annealing. We conclude that, in the absence of RecA and the presence of non-allelic DNA ends, the Red pathway of λ catalyzes recombination primarily by annealing. PMID:9383045

Description and Evaluation of the Research Ethics Review Process in Japan: Proposed Measures for Improvement.

PubMed

Suzuki, Mika; Sato, Keiko

2016-07-01

Research Ethics Committees (RECs) are designed to protect human subjects in research. It is essential to recognize whether the RECs are achieving this goal. Several studies have reported on RECs; however, detailed data regarding the quality of research protocols and the review process of RECs have not been reported in Japan. We examine research protocols reviewed by RECs and the review processes at three institutions using a novel checklist we developed. The data show that approximately half of all examined protocols lacked a clearly written "Background" section that defines the study rationale and design. These results reiterate suggestions made in previous research regarding educational programs and support departments that could enhance responsible conduct in clinical research to protect human subjects in Japan. © The Author(s) 2016.

Research ethics consultation: ethical and professional practice challenges and recommendations.

PubMed

Sharp, Richard R; Taylor, Holly A; Brinich, Margaret A; Boyle, Mary M; Cho, Mildred; Coors, Marilyn; Danis, Marion; Havard, Molly; Magnus, David; Wilfond, Benjamin

2015-05-01

The complexity of biomedical research has increased considerably in the last decade, as has the pace of translational research. This complexity has generated a number of novel ethical issues for clinical investigators, institutional review boards (IRBs), and other oversight committees. In response, many academic medical centers have created formal research ethics consultation (REC) services to help clinical investigators and IRBs navigate ethical issues in biomedical research. Key functions of a REC service include assisting with research design and implementation, providing a forum for deliberative exploration of ethical issues, and supplementing regulatory oversight. As increasing numbers of academic research institutions establish REC services, there is a pressing need for consensus about the primary aims and policies that should guide these activities. Establishing clear expectations about the aims and policies of REC services is important if REC programs are to achieve their full potential. Drawing on the experiences of a Clinical and Translational Science Award Research Ethics Consultation Working Group, this article describes three major ethical and professional practice challenges associated with the provision of REC: (1) managing multiple institutional roles and responsibilities, (2) managing sensitive information, and (3) communicating with consultation requestors about how these issues are managed. The paper also presents several practical strategies for addressing these challenges and enhancing the quality of REC services.

Research Ethics Consultation: Ethical and Professional Practice Challenges and Recommendations

PubMed Central

Sharp, Richard R.; Taylor, Holly A.; Brinich, Margaret A.; Boyle, Mary M.; Cho, Mildred; Coors, Marilyn; Danis, Marion; Havard, Molly; Magnus, David; Wilfond, Benjamin

2015-01-01

The complexity of biomedical research has increased considerably in the last decade, as has the pace of translational research. This complexity has generated a number of novel ethical issues for clinical investigators, institutional review boards (IRBs), and other oversight committees. In response, many academic medical centers have created formal research ethics consultation (REC) services to help clinical investigators and IRBs navigate ethical issues in biomedical research. Key functions of a REC service include: assisting with research design and implementation, providing a forum for deliberative exploration of ethical issues, and supplementing regulatory oversight. As increasing numbers of academic research institutions establish REC services, there is a pressing need for consensus about the primary aims and policies that should guide these activities. Establishing clear expectations about the aims and policies of REC services is important if REC programs are to achieve their full potential. Drawing on the experiences of a Clinical Translational Science Award (CTSA) Research Ethics Consultation Working Group, this article describes three major ethical and professional practice challenges associated with the provision of REC: 1) managing multiple institutional roles and responsibilities, 2) managing sensitive information, and 3) communicating with consultation requestors about how these issues are managed. The paper also presents several practical strategies for addressing these challenges and enhancing the quality of REC services. PMID:25607942

A Structure-Function Study of RecA: The Structural Basis for ATP Specificity in the Strand Exchange Reaction

NASA Astrophysics Data System (ADS)

Gegner, Julie; Spruill, Natalie; Plesniak, Leigh A.

1999-11-01

The terms "structure" and "function" can assume a variety of meanings. In biochemistry, the "structure" of a protein can refer to its sequence of amino acids, the three-dimensional arrangement of atoms within a subunit, or the arrangement of subunits into a larger oligomeric or filamentous state. Likewise, the function of biological macromolecules can be examined at many levels. The function of a protein can be described by its role in an organism's survival or by a chemical reaction that it promotes. We have designed a three-part biochemical laboratory experiment that characterizes the structure and function of the Escherichia coli RecA protein. The first part examines the importance of RecA in the survival of bacteria that have been exposed to UV light. This is the broadest view of function of the enzyme. Second, the students use an in vitro assay of RecA whereby the protein promotes homologous recombination. Because RecA functions not catalytically, but rather stoichiometrically, in this recombination reaction, the oligomeric state of RecA in complex with DNA must also be discussed. Finally, through molecular modeling of X-ray crystallographic structures, students identify functionally important features of the ATP cofactor binding site of RecA.

Efficacy of species-specific recA PCR tests in the identification of Burkholderia cepacia complex environmental isolates.

PubMed

Dalmastri, Claudia; Pirone, Luisa; Tabacchioni, Silvia; Bevivino, Annamaria; Chiarini, Luigi

2005-05-01

In this study, we evaluated if recA species-specific PCR assays could be successfully applied to identify environmental isolates of the widespread Burkholderia cepacia complex (Bcc) species. A total of 729 Bcc rhizosphere isolates collected in different samplings were assigned to the species B. cepacia genomovar I (61), B. cenocepacia recA lineage IIIB (514), B. ambifaria (124) and B. pyrrocinia (30), by means of recA (RFLP) analysis, and PCR tests were performed to assess sensitivity and specificity of recA species-specific primers pairs. B. cepacia genomovar I specific primers produced the expected amplicon with all isolates of the corresponding species (sensitivity, 100%), and cross-reacted with all B. pyrrocinia isolates. On the contrary, B. cenocepacia IIIB primers did not give the expected amplicon in 164 B. cenocepacia IIIB isolates (sensitivity, 68.1%), and isolates of distinct populations showed different sensitivity. B. ambifaria primers failed to amplify a recA-specific fragment only in a few isolates of this species (sensitivity, 93.5%). The absence of specific amplification in a high number of B. cenocepacia rhizosphere isolates indicates that recA specific PCR assays can lead to an underestimation of environmental microorganisms belonging to this bacterial species.

Isotope separation by photoselective dissociative electron capture

DOEpatents

Stevens, C.G.

1978-08-29

Disclosed is a method of separating isotopes based on photoselective electron capture dissociation of molecules having an electron capture cross section dependence on the vibrational state of the molecule. A molecular isotope source material is irradiated to selectively excite those molecules containing a desired isotope to a predetermined vibrational state having associated therewith an electron capture energy region substantially non-overlapping with the electron capture energy ranges associated with the lowest vibration states of the molecules. The isotope source is also subjected to electrons having an energy corresponding to the non-overlapping electron capture region whereby the selectively excited molecules preferentially capture electrons and dissociate into negative ions and neutrals. The desired isotope may be in the negative ion product or in the neutral product depending upon the mechanism of dissociation of the particular isotope source used. The dissociation product enriched in the desired isotope is then separated from the reaction system by conventional means. Specifically, [sup 235]UF[sub 6] is separated from a UF[sub 6] mixture by selective excitation followed by dissociative electron capture into [sup 235]UF[sub 5]- and F. 2 figs.

Isotope separation by photoselective dissociative electron capture

DOEpatents

Stevens, Charles G. [Pleasanton, CA

1978-08-29

A method of separating isotopes based on photoselective electron capture dissociation of molecules having an electron capture cross section dependence on the vibrational state of the molecule. A molecular isotope source material is irradiated to selectively excite those molecules containing a desired isotope to a predetermined vibrational state having associated therewith an electron capture energy region substantially non-overlapping with the electron capture energy ranges associated with the lowest vibration states of the molecules. The isotope source is also subjected to electrons having an energy corresponding to the non-overlapping electron capture region whereby the selectively excited molecules preferentially capture electrons and dissociate into negative ions and neutrals. The desired isotope may be in the negative ion product or in the neutral product depending upon the mechanism of dissociation of the particular isotope source used. The dissociation product enriched in the desired isotope is then separated from the reaction system by conventional means. Specifically, .sup.235 UF.sub.6 is separated from a UF.sub.6 mixture by selective excitation followed by dissociative electron capture into .sup.235 UF.sub.5 - and F.

Structure of human Cdc45 and implications for CMG helicase function

PubMed Central

Simon, Aline C.; Sannino, Vincenzo; Costanzo, Vincenzo; Pellegrini, Luca

2016-01-01

Cell division cycle protein 45 (Cdc45) is required for DNA synthesis during genome duplication, as a component of the Cdc45-MCM-GINS (CMG) helicase. Despite its essential biological function, its biochemical role in DNA replication has remained elusive. Here we report the 2.1-Å crystal structure of human Cdc45, which confirms its evolutionary link with the bacterial RecJ nuclease and reveals several unexpected features that underpin its function in eukaryotic DNA replication. These include a long-range interaction between N- and C-terminal DHH domains, blocking access to the DNA-binding groove of its RecJ-like fold, and a helical insertion in its N-terminal DHH domain, which appears poised for replisome interactions. In combination with available electron microscopy data, we validate by mutational analysis the mechanism of Cdc45 association with the MCM ring and GINS co-activator, critical for CMG assembly. These findings provide an indispensable molecular basis to rationalize the essential role of Cdc45 in genomic duplication. PMID:27189187

Can an ethics officer role reduce delays in research ethics approval? A mixed-method evaluation of an improvement project.

PubMed

Dixon-Woods, Mary; Foy, Chris; Hayden, Charlotte; Al-Shahi Salman, Rustam; Tebbutt, Stephen; Schroter, Sara

2016-08-31

Frustration continues to be directed at delays in gaining approvals for undertaking health research in the UK. We aimed to evaluate the impact of an ethics officer intervention on rates of favourable opinions (approval) and provisional opinions (requiring revision and resubmission) and on the time taken to reach a final opinion by research ethics committees (RECs), to characterise how the role operated in practice, and to investigate applicants' views. Mixed-method study involving (i) a 2-group, non-randomised before-and-after intervention study of RECs assigned an ethics officer and a matched comparator group; (ii) a process evaluation involving a survey of applicants and documentary analysis. 6 RECs and 3 associated ethics officers; 18 comparator RECs; REC applicants. Rates of provisional and favourable opinions between ethics officer and comparator RECs did not show a statistically significant effect of the intervention (logistic regression, p=0.26 for favourable opinions and p=0.31 for provisional opinions). Mean time to reach a decision showed a non-significant reduction (ANOVA, p=0.22) from 33.3 to 32.0 days in the ethics officer RECs compared with the comparator RECs (32.6 to 32.9 days). The survey (30% response rate) indicated applicant satisfaction and also suggested that ethics officer support might be more useful before submission. Ethics officers were successful in identifying many issues with applications, but the intervention did not function exactly as designed: in 31% of applicants, no contact between the applicants and the ethics officer took place before REC review. This study was a non-randomised comparison cohort study. Some data were missing. An ethics officer intervention, as designed and implemented in this study, did not increase the proportion of applications to RECs that were approved on first review and did not reduce the time to a committee decision. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

RecFOR Is Not Required for Pneumococcal Transformation but Together with XerS for Resolution of Chromosome Dimers Frequently Formed in the Process

PubMed Central

Johnston, Calum; Mortier-Barrière, Isabelle; Granadel, Chantal; Polard, Patrice; Martin, Bernard; Claverys, Jean-Pierre

2015-01-01

Homologous recombination (HR) is required for both genome maintenance and generation of diversity in eukaryotes and prokaryotes. This process initiates from single-stranded (ss) DNA and is driven by a universal recombinase, which promotes strand exchange between homologous sequences. The bacterial recombinase, RecA, is loaded onto ssDNA by recombinase loaders, RecBCD and RecFOR for genome maintenance. DprA was recently proposed as a third loader dedicated to genetic transformation. Here we assessed the role of RecFOR in transformation of the human pathogen Streptococcus pneumoniae. We firstly established that RecFOR proteins are not required for plasmid transformation, strongly suggesting that DprA ensures annealing of plasmid single-strands internalized in the process. We then observed no reduction in chromosomal transformation using a PCR fragment as donor, contrasting with the 10,000-fold drop in dprA - cells and demonstrating that RecFOR play no role in transformation. However, a ∼1.45-fold drop in transformation was observed with total chromosomal DNA in recFOR mutants. To account for this limited deficit, we hypothesized that transformation with chromosomal DNA stimulated unexpectedly high frequency (>30% of cells) formation of chromosome dimers as an intermediate in the generation of tandem duplications, and that RecFOR were crucial for dimer resolution. We validated this hypothesis, showing that the site-specific recombinase XerS was also crucial for dimer resolution. An even higher frequency of dimer formation (>80% of cells) was promoted by interspecies transformation with Streptococcus mitis chromosomal DNA, which contains numerous inversions compared to pneumococcal chromosome, each potentially promoting dimerization. In the absence of RecFOR and XerS, dimers persist, as confirmed by DAPI staining, and can limit the efficiency of transformation, since resulting in loss of transformant chromosome. These findings strengthen the view that different HR machineries exist for genome maintenance and transformation in pneumococci. These observations presumably apply to most naturally transformable species. PMID:25569614

The Value of Perioperative Levels of ACTH, DHEA, and DHEA-S and Tumor Size in Predicting Recurrence of Cushing Disease.

PubMed

El Asmar, Nadine; Rajpal, Aman; Selman, Warren R; Arafah, Baha M

2018-02-01

Despite the development of hypocortisolemia after corticotroph surgical adenomectomy, 15% to 20% patients have recurrence of Cushing disease (CD). In this study, we investigated the effect of tumor size and the value of perioperative assessment of corticotropin (ACTH) and adrenal steroid levels in predicting recurrence. Perioperatively, no glucocorticoids were administered until the serum cortisol was ≤3 μg/dL. Blood samples were obtained before and repeatedly after adenomectomy in 79 patients with CD. Of these, 66 had a nadir serum cortisol of ≤3.0 μg/dL and clinical and biochemical remissions. During a median follow-up of 131 months, 11 of 66 had disease recurrence (REC), whereas 55 of 66 did not (NO-REC). Preoperative hormone levels in the REC and NO-REC groups were similar. After adenomectomy, a brief and similar increase in ACTH, cortisol, and dehydroepiandrosterone (DHEA) levels was observed in both groups followed by gradual decline in those levels. Although REC and NO-REC patients had similar cortisol levels (3.4 ± 1.7 μg/dL vs 2.9 ± 2.2 μg/dL) at the 36th postoperative hour, their respective ACTH (33 ± 7.1 ng/L vs 12.1 ± 5.4 ng/L; P < 0.0001), DHEA (3.8 ± 1.7 ng/mL vs 1.2 ± 1.1 ng/mL; P = 0.005), and dehydroepiandrosterone sulphate (DHEA-S) (143.9 ± 45.2 μg/dL vs 48.9 ± 38.2 μg/dL; P < 0.0001) were higher. At nadir hypocortisolemia, perioperative ACTH levels were >20 in all REC patients and <20 ng/L in the NO-REC group. Patients with REC had larger tumors than those with NO-REC. Recurrent CD is characterized by persistent perioperative ACTH secretion after adenomectomy. Higher perioperative levels of ACTH, DHEA, and DHEA-S are highly predictive of future disease recurrence, particularly in those with profound hypocortisolemia. Copyright © 2017 Endocrine Society

Gender equality in the work of local research ethics committees in Europe: a study of practice in five countries.

PubMed

Moerman, C J; Haafkens, J A; Söderström, M; Rásky, E; Maguire, P; Maschewsky-Schneider, U; Norstedt, M; Hahn, D; Reinerth, H; McKevitt, N

2007-02-01

Funding organisations and research ethics committees (RECs) should play a part in strengthening attention to gender equality in clinical research. In the research policy of European Union (EU), funding measures have been taken to realise this, but such measures are lacking in the EU policy regarding RECs. To explore how RECs in Austria, Germany, Ireland, The Netherlands and Sweden deal with gender equality issues by asking two questions: (1) Do existing procedures promote representation of women and gender expertise in the committee? (2) How are sex and gender issues dealt with in protocol evaluation? Two RECs were selected from each country. Data were obtained through interviews with key informants and content analysis of relevant documents (regulations, guidelines and review tools in use in 2003). All countries have rules (mostly informal) to ensure the presence of women on RECs; gender expertise is not required. Drug study protocols are carefully evaluated, sometimes on a formal basis, as regards the inclusion of women of childbearing age. The reason for excluding either one of the sexes or including specific groups of women or making a gender-specific risk-benefit analysis are investigated by some RECs. Such measures are, however, neither defined in the regulations nor integrated in review tools. The RECs investigated in five European member states are found to pay limited attention to gender equality in their working methods and, in particular in protocol evaluation. Policy and regulations of EU are needed to strengthen attention to gender equality in the work of RECs.

Decisions by Finnish Medical Research Ethics Committees: A Nationwide Study of Process and Outcomes.

PubMed

Hemminki, Elina; Virtanen, Jorma I; Regushevskaya, Elena

2015-10-01

Review by research ethics committees (RECs) is the key in medical research regulation. Data from meeting notes and project summaries were abstracted from all projects submitted in 2002 (n = 1,004) and 2007 (n = 1,045) to the official medical RECs in Finland. Data from consecutive submissions were combined per project. When comparing RECs, logistic regression was used to adjust for application characteristics. The number of projects handled varied notably by REC. In the first handling, 85% of applications in 2002 and 77% in 2007 were approved, while 13% and 20% were tabled. For 61% of the projects, the review time was <30 days, 16% had >89 days, and 6% had 6 months or longer. The variation by REC in approval rates, number of handlings, or long review times was not explained by project characteristics. In the last handling, 94% of the projects in both years were approved or concluded not to need a statement from that REC. The most common reason for tabling or not approving an application was patient autonomy, usually centered on the patient leaflet. The next most common reasons were requests for further information and dissatisfaction with the scientific aspects of the project. The reasons classified as "ethics" in the narrow sense were rare. The REC focus was to assure that researchers follow the various rules on medical research and to improve the quality of research and project documents. REC considerations could be divided into decisions based on ethics and recommendations covering other aspects. © The Author(s) 2015.

Research ethics committees in the regulation of clinical research: comparison of Finland to England, Canada, and the United States.

PubMed

Hemminki, Elina

2016-01-19

The aim of this paper is to compare common features and variation in the work of research ethics committees (RECs) in Finland to three other countries - England, Canada, the United States of America (USA) - in the late 2000s. Several approaches and data sources were used, including semi- or unstructured interviews of experts, documents, previous reports, presentations in meetings and observations. A theoretical framework was created and data from various sources synthesized. In Finland, RECs were regulated by a medical research law, whereas in the other countries many related laws and rules guided RECs; drug trials had specific additional rules. In England and the USA, there was a REC control body. In all countries, members were voluntary and included lay-persons, and payment arrangements varied. Patient protection was the main ethics criteria, but other criteria (research advancement, availability of results, payments, detailed fulfilment of legislation) varied. In all countries, RECs had been given administrative duties. Variations by country included the mandate, practical arrangements, handling of multi-site research, explicitness of proportionate handlings, judging scientific quality, time-limits for decisions, following of projects, role in institute protection, handling conflicts of interests, handling of projects without informed consent, and quality assurance research. The division of work between REC members and secretariats varied in checking of formalities. In England, quality assurance of REC work was thorough, fairly thorough in the USA, and not performed in Finland. The work of RECs in the four countries varied notably. Various deficiencies in the system require action, for which international comparison can provide useful insights.

DNA repair properties of Escherichia coli tif-1, recAo281 and lexA1 strains deficient in single-strand DNA binding protein.

PubMed

Whittier, R F; Chase, J W

1983-01-01

Mutations affecting single-strand DNA binding protein (SSB) impair induction of mutagenic (SOS) repair. To further investigate the role of SSB in SOS induction and DNA repair, isogenic strains were constructed combining the ssb+, ssb-1 or ssb-113 alleles with one or more mutations known to alter regulation of damage inducible functions. As is true in ssb+ strains tif-1 (recA441) was found to allow thermal induction of prophage lambda + and Weigle reactivation in ssb-1 and ssb-113 strains. Furthermore, tif-1 decreased the UV sensitivity of the ssb-113 strain slightly and permitted UV induction of prophage lambda + at 30 degrees C. Strains carrying the recAo281 allele were also constructed. This mutation causes high constitutive levels of RecA protein synthesis and relieves much of the UV sensitivity conferred by lexA- alleles without restoring SOS (error-prone) repair. In contrast, the recAo281 allele failed to alleviate the UV sensitivity associated with either ssb- mutation. In a lexA1 recAo281 background the ssb-1 mutation increased the extent of postirradiation DNA degradation and concommitantly increased UV sensitivity 20-fold to the level exhibited by a recA1 strain. The ssb-113 mutation also increased UV sensitivity markedly in this background but did so without greatly increasing postirradiation DNA degradation. These results suggest a direct role for SSB in recombinational repair apart from and in addition to its role in facilitating induction of the recA-lexA regulon.

Factors affecting expression of the recF gene of Escherichia coli K-12.

PubMed

Sandler, S J; Clark, A J

1990-01-31

This report describes four factors which affect expression of the recF gene from strong upstream lambda promoters under temperature-sensitive cIAt2-encoded repressor control. The first factor was the long mRNA leader sequence consisting of the Escherichia coli dnaN gene and 95% of the dnaA gene and lambda bet, N (double amber) and 40% of the exo gene. When most of this DNA was deleted, RecF became detectable in maxicells. The second factor was the vector, pBEU28, a runaway replication plasmid. When we substituted pUC118 for pBEU28, RecF became detectable in whole cells by the Coomassie blue staining technique. The third factor was the efficiency of initiation of translation. We used site-directed mutagenesis to change the mRNA leader, ribosome-binding site and the 3 bp before and after the translational start codon. Monitoring the effect of these mutational changes by translational fusion to lacZ, we discovered that the efficiency of initiation of translation was increased 30-fold. Only an estimated two- or threefold increase in accumulated levels of RecF occurred, however. This led us to discover the fourth factor, namely sequences in the recF gene itself. These sequences reduce expression of the recF-lacZ fusion genes 100-fold. The sequences responsible for this decrease in expression occur in four regions in the N-terminal half of recF. Expression is reduced by some sequences at the transcriptional level and by others at the translational level.

From Recreational Mathematics to Recreational Programming, and Back

ERIC Educational Resources Information Center

Ruiz Jimenez, B. C.; Ruiz Munoz, M.

2011-01-01

Recreational Programming (RecPro) is the discipline that encourages the study of computer programming through ludic problems. Problems that are typically studied within this discipline are similar to those of Recreational Mathematics (RecMat), which sometimes leads to the confusion of these two disciplines. The objective for RecPro is to write…

75 FR 38866 - Submission for OMB Review; Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-06

... collection. Title: Principal Place of Business on Beer Labels. TTB REC 5130/5. Abstract: TTB regulations... beer, their ``principal place of business'' address. This label option may be used in lieu of showing... Equipment and Structures (TTB REC 5130/3) and Marks and Labels on Containers of Beer (TTB REC 5130/4...

Disintegration of Nascent Replication Bubbles during Thymine Starvation Triggers RecA- and RecBCD-dependent Replication Origin Destruction*

PubMed Central

Kuong, Kawai J.; Kuzminov, Andrei

2012-01-01

Thymineless death strikes cells unable to synthesize DNA precursor dTTP, with the nature of chromosomal damage still unclear. Thymine starvation stalls replication forks, whereas accumulating evidence indicates the replication origin is also affected. Using a novel DNA labeling technique, here we show that replication slowly continues in thymine-starved cells, but the newly synthesized DNA becomes fragmented and degraded. This degradation apparently releases enough thymine to sustain initiation of new replication bubbles from the chromosomal origin, which destabilizes the origin in a RecA-dependent manner. Marker frequency analysis with gene arrays 1) reveals destruction of the origin-centered chromosomal segment in RecA+ cells; 2) confirms origin accumulation in the recA mutants; and 3) identifies the sites around the origin where destruction initiates in the recBCD mutants. We propose that thymineless cells convert persistent single-strand gaps behind replication forks into double-strand breaks, using the released thymine for new initiations, whereas subsequent disintegration of small replication bubbles causes replication origin destruction. PMID:22621921

DNA polymerase V activity is autoregulated by a novel intrinsic DNA-dependent ATPase

PubMed Central

Erdem, Aysen L; Jaszczur, Malgorzata; Bertram, Jeffrey G; Woodgate, Roger; Cox, Michael M; Goodman, Myron F

2014-01-01

Escherichia coli DNA polymerase V (pol V), a heterotrimeric complex composed of UmuD′2C, is marginally active. ATP and RecA play essential roles in the activation of pol V for DNA synthesis including translesion synthesis (TLS). We have established three features of the roles of ATP and RecA. (1) RecA-activated DNA polymerase V (pol V Mut), is a DNA-dependent ATPase; (2) bound ATP is required for DNA synthesis; (3) pol V Mut function is regulated by ATP, with ATP required to bind primer/template (p/t) DNA and ATP hydrolysis triggering dissociation from the DNA. Pol V Mut formed with an ATPase-deficient RecA E38K/K72R mutant hydrolyzes ATP rapidly, establishing the DNA-dependent ATPase as an intrinsic property of pol V Mut distinct from the ATP hydrolytic activity of RecA when bound to single-stranded (ss)DNA as a nucleoprotein filament (RecA*). No similar ATPase activity or autoregulatory mechanism has previously been found for a DNA polymerase. DOI: http://dx.doi.org/10.7554/eLife.02384.001 PMID:24843026

Biochemical characterization of RecA variants that contribute to extreme resistance to ionizing radiation

PubMed Central

Piechura, Joseph R.; Tseng, Tzu-Ling; Hsu, Hsin-Fang; Byrne, Rose T.; Windgassen, Tricia A.; Chitteni-Pattu, Sindhu; Battista, John R.; Li, Hung-Wen; Cox, Michael M.

2015-01-01

Among strains of Escherichia coli that have evolved to survive extreme exposure to ionizing radiation, mutations in the recA gene are prominent and contribute substantially to the acquired phenotype. Changes at amino acid residue 276, D276A and D276N, occur repeatedly and in separate evolved populations. RecA D276A and RecA D276N exhibit unique adaptations to an environment that can require the repair of hundreds of double strand breaks. These two RecA protein variants (a) exhibit a faster rate of filament nucleation on DNA, as well as a slower extension under at least some conditions, leading potentially to a distribution of the protein among a higher number of shorter filaments, (b) promote DNA strand exchange more efficiently in the context of a shorter filament, and (c) are markedly less inhibited by ADP. These adaptations potentially allow RecA protein to address larger numbers of double strand DNA breaks in an environment where ADP concentrations are higher due to a compromised cellular metabolism. PMID:25559557

Particle Methods for Electromagnetic Wave Propagation Problems

DTIC Science & Technology

2014-09-15

operation with respect to the underlying jump process. Using (8), (9), (12), (13), and the commutation of the expectation and differential operators (18...F’03) received the B.S. degree in electronics and communications engi- neering from REC-Warangal (now NIT Warangal), Warangal, India , in 1981, the...M.S. degree in mi- crowave and radar engineering from IIT-Kharagpur, Kharagpur, India , in 1983, and the Ph.D. degree in electrical engineering from the

Clinical research ethics review process in Lebanon: efficiency and functions of research ethics committees - results from a descriptive questionnaire-based study.

PubMed

Atallah, David; Moubarak, Malak; El Kassis, Nadine; Abboud, Sara

2018-01-11

Clinical trials conducted in Lebanon are increasing. However, little is known about the performance of research ethics committees (RECs) in charge of reviewing the research protocols. This study aimed to assess the level of adherence to the ethics surrounding the conduct of clinical trials and perceptions of team members regarding roles of the RECs during the conduct of clinical trials in Lebanon. The research question was: Are RECs adherent to the ethics surrounding the conduct of clinical trials (chapters II and IV in 'Standards and Operational Guidance for Ethics Review of Health-related Research with Human Participants' in Lebanon?' This was a quantitative and descriptive questionnaire-based study conducted among RECs of university hospitals in Lebanon. The questionnaire had to be completed online and included general questions in addition to items reflecting the different aspects of a REC performance and effectiveness. All the questionnaire was assigned a total score of 175 points. General information and questions assigned point values/scores were analysed using descriptive statistics: frequency and percentage, mean score ± standard deviation. Ten RECs participated in the study (52 persons: four chairs, one vice-president, 47 ordinary members). Forty-seven (90.4%) had previous experience with clinical research and 30 (57.7%) had a diploma or had done a training in research ethics. Forty-one percent confirmed that they were required to have a training in research ethics. All RECs had a policy for disclosing and managing potential conflicts of interest for its members, but 71.8% of participants reported the existence of such a policy for researchers. Thirty-three point three percent reported that the RECs had an anti-bribery policy. The questionnaire mean score was 129.6 ± 22.3/175 points reflecting thus an excellent adherence to international standards. Inadequate training of REC members and the lack of anti-bribery policies should be resolved to improve their performance.

Human recombinant alkaline phosphatase inhibits ex vivo platelet activation in humans.

PubMed

Tunjungputri, Rahajeng N; Peters, Esther; van der Ven, André; de Groot, Philip G; de Mast, Quirijn; Pickkers, Peter

2016-11-30

Sepsis-associated acute kidney injury (AKI) is associated with high morbidity and mortality. Excessive platelet activation contributes to AKI through the formation of microthrombi and amplification of systemic inflammation. Two phase II trials demonstrated that bovine-intestinal alkaline phosphatase (AP) improved renal function in critically ill patients with sepsis-associated AKI. In this study, we characterised the platelet-inhibiting effects of a human recombinant AP. Whole blood and platelet-rich plasma (PRP) of healthy volunteers (n=6) was pre-treated ex vivo with recAP, whereafter platelet reactivity to ADP, collagen-related peptide (CRP-XL) and Pam3CSK4 was determined by flow cytometry. RecAP (40 U/ml) reduced the platelet reactivity to ADP (inhibition with a median of 47 %, interquartile range 43-49 %; p<0.001) and tended to reduce platelet reactivity to CRP-XL (9 %, 2-25 %; p=0.08) in whole blood. The platelet-inhibiting effects of recAP were more pronounced in PRP both for ADP- (64 %, 54-68 %; p=0.002) and CRP-XL-stimulated samples (60 %, 46-71 %; p=0.002). RecAP rapidly converted ADP into adenosine, whereas antagonism of the A2A adenosine receptor partially reversed the platelet inhibitory effects of recAP. Platelets of septic shock patients (n=5) showed a 31% (22-34%; p=0.03) more pronounced reactivity compared to healthy volunteers, and this was completely reversed by recAP treatment. In conclusion, we demonstrate that recAP inhibits ex vivo human platelet activation through dephosphorylation of ADP and formation of adenosine as its turnover product. RecAP is able to reverse the platelet hyperreactivity present in septic shock patients. These effects may contribute to the beneficial effects of recAP as a new therapeutic candidate for sepsis-associated AKI.

Sequence-dependent nanometer-scale conformational dynamics of individual RecBCD–DNA complexes

PubMed Central

Carter, Ashley R.; Seaberg, Maasa H.; Fan, Hsiu-Fang; Sun, Gang; Wilds, Christopher J.; Li, Hung-Wen; Perkins, Thomas T.

2016-01-01

RecBCD is a multifunctional enzyme that possesses both helicase and nuclease activities. To gain insight into the mechanism of its helicase function, RecBCD unwinding at low adenosine triphosphate (ATP) (2–4 μM) was measured using an optical-trapping assay featuring 1 base-pair (bp) precision. Instead of uniformly sized steps, we observed forward motion convolved with rapid, large-scale (∼4 bp) variations in DNA length. We interpret this motion as conformational dynamics of the RecBCD–DNA complex in an unwinding-competent state, arising, in part, by an enzyme-induced, back-and-forth motion relative to the dsDNA that opens and closes the duplex. Five observations support this interpretation. First, these dynamics were present in the absence of ATP. Second, the onset of the dynamics was coupled to RecBCD entering into an unwinding-competent state that required a sufficiently long 5′ strand to engage the RecD helicase. Third, the dynamics were modulated by the GC-content of the dsDNA. Fourth, the dynamics were suppressed by an engineered interstrand cross-link in the dsDNA that prevented unwinding. Finally, these dynamics were suppressed by binding of a specific non-hydrolyzable ATP analog. Collectively, these observations show that during unwinding, RecBCD binds to DNA in a dynamic mode that is modulated by the nucleotide state of the ATP-binding pocket. PMID:27220465

Conservation of an ATP-binding domain among recA proteins from Proteus vulgaris, erwinia carotovora, Shigella flexneri, and Escherichia coli K-12 and B/r

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

Knight, K.L.; Hess, R.M.; McEntee, K.

1988-06-01

The purified RecA proteins encoded by the cloned genes from Proteus vulgaris, Erwinia carotovora, Shigella flexneri, and Escherichia coli B/r were compared with the RecA protein from E. coli K-12. Each of the proteins hydrolyzed ATP in the presence of single-stranded DNA, and each was covalently modified with the photoaffinity ATP analog 8-azidoadenosine 5'-triphosphate (8N/sub 3/ATP). Two-dimensional tryptic maps of the four heterologous RecA proteins demonstrated considerable structural conservation among these bacterial genera. Moreover, when the (..cap alpha..-/sup 32/P)8N/sub 3/ATP-modified proteins were digested with trypsin and analyzed by high-performance liquid chromatography, a single peak of radioactivity was detected in eachmore » of the digests and these peptides eluted identically with the tryptic peptide T/sub 31/ of the E. coli K-12 RecA protein, which was the unique site of 8N/sub 3/ATP photolabeling. Each of the heterologous recA genes hybridized to oligonucleotide probes derived from the ATP-binding domain sequence of the E. coli K-12 gene. These last results demonstrate that the ATP-binding domain of the RecA protein has been strongly conserved for greater than 10/sup 7/ years.« less

APC/C-Cdc20 mediates deprotection of centromeric cohesin at meiosis II in yeast.

PubMed

Jonak, Katarzyna; Zagoriy, Ievgeniia; Oz, Tugce; Graf, Peter; Rojas, Julie; Mengoli, Valentina; Zachariae, Wolfgang

2017-06-18

Cells undergoing meiosis produce haploid gametes through one round of DNA replication followed by 2 rounds of chromosome segregation. This requires that cohesin complexes, which establish sister chromatid cohesion during S phase, are removed in a stepwise manner. At meiosis I, the separase protease triggers the segregation of homologous chromosomes by cleaving cohesin's Rec8 subunit on chromosome arms. Cohesin persists at centromeres because the PP2A phosphatase, recruited by the shugoshin protein, dephosphorylates Rec8 and thereby protects it from cleavage. While chromatids disjoin upon cleavage of centromeric Rec8 at meiosis II, it was unclear how and when centromeric Rec8 is liberated from its protector PP2A. One proposal is that bipolar spindle forces separate PP2A from Rec8 as cells enter metaphase II. We show here that sister centromere biorientation is not sufficient to "deprotect" Rec8 at meiosis II in yeast. Instead, our data suggest that the ubiquitin-ligase APC/C Cdc20 removes PP2A from centromeres by targeting for degradation the shugoshin Sgo1 and the kinase Mps1. This implies that Rec8 remains protected until entry into anaphase II when it is phosphorylated concurrently with the activation of separase. Here, we provide further support for this model and speculate on its relevance to mammalian oocytes.

APC/C-Cdc20 mediates deprotection of centromeric cohesin at meiosis II in yeast

PubMed Central

Jonak, Katarzyna; Oz, Tugce; Graf, Peter; Rojas, Julie; Mengoli, Valentina; Zachariae, Wolfgang

2017-01-01

ABSTRACT Cells undergoing meiosis produce haploid gametes through one round of DNA replication followed by 2 rounds of chromosome segregation. This requires that cohesin complexes, which establish sister chromatid cohesion during S phase, are removed in a stepwise manner. At meiosis I, the separase protease triggers the segregation of homologous chromosomes by cleaving cohesin's Rec8 subunit on chromosome arms. Cohesin persists at centromeres because the PP2A phosphatase, recruited by the shugoshin protein, dephosphorylates Rec8 and thereby protects it from cleavage. While chromatids disjoin upon cleavage of centromeric Rec8 at meiosis II, it was unclear how and when centromeric Rec8 is liberated from its protector PP2A. One proposal is that bipolar spindle forces separate PP2A from Rec8 as cells enter metaphase II. We show here that sister centromere biorientation is not sufficient to “deprotect” Rec8 at meiosis II in yeast. Instead, our data suggest that the ubiquitin-ligase APC/CCdc20 removes PP2A from centromeres by targeting for degradation the shugoshin Sgo1 and the kinase Mps1. This implies that Rec8 remains protected until entry into anaphase II when it is phosphorylated concurrently with the activation of separase. Here, we provide further support for this model and speculate on its relevance to mammalian oocytes. PMID:28514186

The role of meiotic cohesin REC8 in chromosome segregation in gamma irradiation-induced endopolyploid tumour cells.

PubMed

Erenpreisa, Jekaterina; Cragg, Mark S; Salmina, Kristine; Hausmann, Michael; Scherthan, Harry

2009-09-10

Escape from mitotic catastrophe and generation of endopolyploid tumour cells (ETCs) represents a potential survival strategy of tumour cells in response to genotoxic treatments. ETCs that resume the mitotic cell cycle have reduced ploidy and are often resistant to these treatments. In search for a mechanism for genome reduction, we previously observed that ETCs express meiotic proteins among which REC8 (a meiotic cohesin component) is of particular interest, since it favours reductional cell division in meiosis. In the present investigation, we induced endopolyploidy in p53-dysfunctional human tumour cell lines (Namalwa, WI-L2-NS, HeLa) by gamma irradiation, and analysed the sub-cellular localisation of REC8 in the resulting ETCs. We observed by RT-PCR and Western blot that REC8 is constitutively expressed in these tumour cells, along with SGOL1 and SGOL2, and that REC8 becomes modified after irradiation. REC8 localised to paired sister centromeres in ETCs, the former co-segregating to opposite poles. Furthermore, REC8 localised to the centrosome of interphase ETCs and to the astral poles in anaphase cells where it colocalised with the microtubule-associated protein NuMA. Altogether, our observations indicate that radiation-induced ETCs express features of meiotic cell divisions and that these may facilitate chromosome segregation and genome reduction.

Genome Sequence of Azospirillum brasilense REC3, Isolated from Strawberry Plants.

PubMed

Fontana, Cecilia Alejandra; Salazar, Sergio Miguel; Bassi, Daniela; Puglisi, Edoardo; Lovaisa, Nadia; Toffoli, Lucía Mercedes; Pedraza, Raúl; Cocconcelli, Pier Sandro

2018-02-22

The genome sequence of a plant growth-promoting bacterium and biocontrol agent, Azospirillum brasilense REC3, isolated from strawberry roots, is reported here. The A. brasilense REC3 total genome contains 7,229,924 bp and has a G+C content of 68.7 mol%. Copyright © 2018 Fontana et al.

Genome-wide association study for cheese yield and curd nutrient recovery in dairy cows.

PubMed

Dadousis, C; Biffani, S; Cipolat-Gotet, C; Nicolazzi, E L; Rosa, G J M; Gianola, D; Rossoni, A; Santus, E; Bittante, G; Cecchinato, A

2017-02-01

Cheese production and consumption are increasing in many countries worldwide. As a result, interest has increased in strategies for genetic selection of individuals for technological traits of milk related to cheese yield (CY) in dairy cattle breeding. However, little is known about the genetic background of a cow's ability to produce cheese. Recently, a relatively large panel (1,264 cows) of different measures of individual cow CY and milk nutrient and energy recoveries in the cheese (REC) became available. Genetic analyses showed considerable variation for CY and for aptitude to retain high proportions of fat, protein, and water in the coagulum. For the dairy industry, these characteristics are of major economic importance. Nevertheless, use of this knowledge in dairy breeding is hampered by high costs, intense labor requirement, and lack of appropriate technology. However, in the era of genomics, new possibilities are available for animal breeding and genetic improvement. For example, identification of genomic regions involved in cow CY might provide potential for marker-assisted selection. The objective of this study was to perform genome-wide association studies on different CY and REC measures. Milk and DNA samples from 1,152 Italian Brown Swiss cows were used. Three CY traits expressing the weight (wt) of fresh curd (%CY CURD ), curd solids (%CY SOLIDS ), and curd moisture (%CY WATER ) as a percentage of weight of milk processed, and 4 REC (REC FAT , REC PROTEIN , REC SOLIDS , and REC ENERGY , calculated as the % ratio between the nutrient in curd and the corresponding nutrient in processed milk) were analyzed. Animals were genotyped with the Illumina BovineSNP50 Bead Chip v.2. Single marker regressions were fitted using the GenABEL R package (genome-wide association using mixed model and regression-genomic control). In total, 103 significant associations (88 single nucleotide polymorphisms) were identified in 10 chromosomes (2, 6, 9, 11, 12, 14, 18, 19, 27, 28). For REC FAT and REC PROTEIN , high significance peaks were identified in Bos taurus autosome (BTA) 6 and BTA11, respectively. Marker ARS-BFGL-NGS-104610 (∼104.3 Mbp) was highly associated with REC PROTEIN and Hapmap52348-rs29024684 (∼87.4 Mbp), closely located to the casein genes on BTA6, with REC FAT . Genomic regions identified may enhance marker-assisted selection in bovine cheese breeding beyond the use of protein (casein) and fat contents, whereas new knowledge will help to unravel the genomic background of a cow's ability for cheese production. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Internalization of Rat FSH and LH/CG Receptors by rec-eCG in CHO-K1 Cells.

PubMed

Park, Jong-Ju; Seong, Hun-Ki; Kim, Jeong-Soo; Munkhzaya, Byambaragchaa; Kang, Myung-Hwa; Min, Kwan-Sik

2017-06-01

Equine chorionic gonadotropin (eCG) is a unique molecule that elicits the response characteristics of both follicle-stimulating hormone (FSH) and luteinizing hormone (LH) in other species. Previous studies from this laboratory had demonstrated that recombinant eCG (rec-eCG) from Chinese hamster ovary (CHO-K1) cells exhibited both FSH- and LH-like activity in rat granulosa and Leydig cells. In this study, we analyzed receptor internalization through rec-eCGs, wild type eCG (eCGβ/α) and mutant eCG (eCGβ/αΔ56) with an N-linked oligosaccharide at Asn 56 of the α-subunit. Both the rec-eCGs were obtained from CHO-K1 cells. The agonist activation of receptors was analyzed by measuring stimulation time and concentrations of rec-eCGs. Internalization values in the stably selected rat follicle-stimulating hormone receptor (rFSHR) and rat luteinizing/chorionic gonadotropin receptor (rLH/CGR) were highest at 50 min after stimulation with 10 ng of rec-eCGβ/α. The dose-dependent response was highest when 10 ng of rec-eCGβ/α was used. The deglycosylated eCGβ/αΔ56 mutant did not enhance the agonist-stimulated internalization. We concluded that the state of activation of rFSHR and rLH/CGR could be modulated through agonist-stimulated internalization. Our results suggested that the eLH/CGRs are mostly internalized within 60 min by agonist-stimulation by rec-eCG. We also suggested that the lack of responsiveness of the deglycosylated eCGβ/ αΔ56 was likely because the site of glycosylation played a pivotal role in agonist-stimulated internalization in cells expressing rFSHR and rLH/CGR.

Temperature dependent characteristics of a recombinant infectious hematopoietic necrosis virus glycoprotein produced in insect cells.

PubMed

Cain, K D; Byrne, K M; Brassfield, A L; LaPatra, S E; Ristow, S S

1999-04-15

A recombinant infectious hematopoietic necrosis virus (IHNV) glycoprotein (G protein) was produced in insect cells using a baculovirus vector (Autographa californica nuclear polyhedrosis virus). Characteristics of this protein were evaluated in relation to native viral G protein. A full-length (1.6 kb) cDNA copy of the glycoprotein gene of IHNV was inserted into the baculovirus vector under control of the polyhedrin promoter. High levels of G protein (approximately 0.5 microgram/1 x 10(5) cells) were produced in Spodoptera frugiperda (Sf9) cells following recombinant baculovirus infection. Analysis of cell lysates by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and Western blot revealed a recombinant IHNV G of slightly higher mobility on the gel than the viral G protein. Differences in mobility were abrogated by endoglycosidase treatment. When the recombinant G protein was produced in insect cells at 20 degrees C (RecGlow), immunostaining and cell fusion activity demonstrated surface localization of the protein. In contrast, when recombinant protein was produced at 27 degrees C (RecGhigh), G protein was sequestered within the cell, suggesting that at the 2 different temperatures processing differences may exist. Eleven monoclonal antibodies (MAbs) were tested by immunoblotting for reactivity to the recombinant G protein. All 11 MAbs reacted to the reduced proteins. Four MAbs recognized both RecGhigh and RecGlow under non-reducing conditions; however, 1 neutralizing MAb (92A) recognized RecGlow but failed to react to RecGhigh under non-reducing conditions. This suggests that differences exist between RecGlow and RecGhigh which may have implications in the development of a properly folded recombinant G protein with the ability to elicit protective immunity in fish.

The Challenge of Timely, Responsive and Rigorous Ethics Review of Disaster Research: Views of Research Ethics Committee Members.

PubMed

Hunt, Matthew; Tansey, Catherine M; Anderson, James; Boulanger, Renaud F; Eckenwiler, Lisa; Pringle, John; Schwartz, Lisa

2016-01-01

Research conducted following natural disasters such as earthquakes, floods or hurricanes is crucial for improving relief interventions. Such research, however, poses ethical, methodological and logistical challenges for researchers. Oversight of disaster research also poses challenges for research ethics committees (RECs), in part due to the rapid turnaround needed to initiate research after a disaster. Currently, there is limited knowledge available about how RECs respond to and appraise disaster research. To address this knowledge gap, we investigated the experiences of REC members who had reviewed disaster research conducted in low- or middle-income countries. We used interpretive description methodology and conducted in-depth interviews with 15 respondents. Respondents were chairs, members, advisors, or coordinators from 13 RECs, including RECs affiliated with universities, governments, international organizations, a for-profit REC, and an ad hoc committee established during a disaster. Interviews were analyzed inductively using constant comparative techniques. Through this process, three elements were identified as characterizing effective and high-quality review: timeliness, responsiveness and rigorousness. To ensure timeliness, many RECs rely on adaptations of review procedures for urgent protocols. Respondents emphasized that responsive review requires awareness of and sensitivity to the particularities of disaster settings and disaster research. Rigorous review was linked with providing careful assessment of ethical considerations related to the research, as well as ensuring independence of the review process. Both the frequency of disasters and the conduct of disaster research are on the rise. Ensuring effective and high quality review of disaster research is crucial, yet challenges, including time pressures for urgent protocols, exist for achieving this goal. Adapting standard REC procedures may be necessary. However, steps should be taken to ensure that ethics review of disaster research remains diligent and thorough.

Ultrasound Scoring of Endometrial Pattern for Fast-Track Identification or Exclusion of Endometrial Cancer in Women with Postmenopausal Bleeding.

PubMed

Dueholm, Margit; Hjorth, Ina Marie Dueholm; Dahl, Katja; Hansen, Estrid Stær; Ørtoft, Gitte

2018-06-23

To evaluate the Risk of Endometrial Cancer (REC) scoring system for the prediction of high and low probability of endometrial cancer (EC) in women with postmenopausal bleeding (PMB). Prospective study (Canadian Task Force classification II-1). Academic hospital. Nine hundred and fifty consecutive patients with PMB underwent transvaginal ultrasonography (TVS) and REC scoring between November 2013 and December 2015. Obstetrics and gynecology residents, supervised by trained physicians, scored endometrial patterns according to the previously established REC scoring system. The reference standard was endometrial samples, endometrial thickness (ET; 4-4.9 mm), operative hysteroscopy, or hysterectomy (ET ≥5 mm), and one-year follow-up in all patients presenting with ET <4 mm. Diagnostic performance for prediction of probability of malignancy was assessed using the REC scoring system. The area under the receiver operating characteristic (ROC) curve (AUC) of the TVS REC score system was 97% (range: 95-98) for prediction of malignancy. In 656 patients with ET ≥4 mm, REC scoring effectively predicted high probability of malignancy: sensitivity (95% confidence interval): 92% (range: 87%-95%); specificity: 94% (range: 91%-96%). An REC score of 0 was present in 206 (32%) patients with ET ≥4 mm and was associated with a low negative likelihood ratio of 0.026 for EC. Only 7 patients with EC/atypical hyperplasia were seen among these 206 patients. The REC scoring system identified or ruled out most ECs, clearly demonstrating that more specific image analysis at first-line TVS can accelerate the diagnosis of EC in patients with PMB and may allow for improved selection of second-line strategies in patients with ET ≥4 mm. Copyright © 2018. Published by Elsevier Inc.

The Challenge of Timely, Responsive and Rigorous Ethics Review of Disaster Research: Views of Research Ethics Committee Members

PubMed Central

Hunt, Matthew; Tansey, Catherine M.

2016-01-01

Background Research conducted following natural disasters such as earthquakes, floods or hurricanes is crucial for improving relief interventions. Such research, however, poses ethical, methodological and logistical challenges for researchers. Oversight of disaster research also poses challenges for research ethics committees (RECs), in part due to the rapid turnaround needed to initiate research after a disaster. Currently, there is limited knowledge available about how RECs respond to and appraise disaster research. To address this knowledge gap, we investigated the experiences of REC members who had reviewed disaster research conducted in low- or middle-income countries. Methods We used interpretive description methodology and conducted in-depth interviews with 15 respondents. Respondents were chairs, members, advisors, or coordinators from 13 RECs, including RECs affiliated with universities, governments, international organizations, a for-profit REC, and an ad hoc committee established during a disaster. Interviews were analyzed inductively using constant comparative techniques. Results Through this process, three elements were identified as characterizing effective and high-quality review: timeliness, responsiveness and rigorousness. To ensure timeliness, many RECs rely on adaptations of review procedures for urgent protocols. Respondents emphasized that responsive review requires awareness of and sensitivity to the particularities of disaster settings and disaster research. Rigorous review was linked with providing careful assessment of ethical considerations related to the research, as well as ensuring independence of the review process. Conclusion Both the frequency of disasters and the conduct of disaster research are on the rise. Ensuring effective and high quality review of disaster research is crucial, yet challenges, including time pressures for urgent protocols, exist for achieving this goal. Adapting standard REC procedures may be necessary. However, steps should be taken to ensure that ethics review of disaster research remains diligent and thorough. PMID:27327165

Can Temperate-Water Immersion Effectively Reduce Rectal Temperature in Exertional Heat Stroke? A Critically Appraised Topic.

PubMed

Truxton, Tyler T; Miller, Kevin C

2017-09-01

Clinical Scenario: Exertional heat stroke (EHS) is a medical emergency which, if left untreated, can result in death. The standard of care for EHS patients includes confirmation of hyperthermia via rectal temperature (T rec ) and then immediate cold-water immersion (CWI). While CWI is the fastest way to reduce T rec , it may be difficult to lower and maintain water bath temperature in the recommended ranges (1.7°C-15°C [35°F-59°F]) because of limited access to ice and/or the bath being exposed to high ambient temperatures for long periods of time. Determining if T rec cooling rates are acceptable (ie, >0.08°C/min) when significantly hyperthermic humans are immersed in temperate water (ie, ≥20°C [68°F]) has applications for how EHS patients are treated in the field. Are T rec cooling rates acceptable (≥0.08°C/min) when significantly hyperthermic humans are immersed in temperate water? T rec cooling rates of hyperthermic humans immersed in temperate water (≥20°C [68°F]) ranged from 0.06°C/min to 0.19°C/min. The average T rec cooling rate for all examined studies was 0.11±0.06°C/min. Clinical Bottom Line: Temperature water immersion (TWI) provides acceptable (ie, >0.08°C/min) T rec cooling rates for hyperthermic humans post-exercise. However, CWI cooling rates are higher and should be used if feasible (eg, access to ice, shaded treatment areas). Strength of Recommendation: The majority of evidence (eg, Level 2 studies with PEDro scores ≥5) suggests TWI provides acceptable, though not ideal, T rec cooling. If possible, CWI should be used instead of TWI in EHS scenarios.

Specificity in suppression of SOS expression by recA4162 and uvrD303

PubMed Central

Massoni, Shawn C.; Sandler, Steven J.

2013-01-01

Detection and repair of DNA damage is essential in all organisms and depends on the ability of proteins recognizing and processing specific DNA substrates. In E. coli, the RecA protein forms a filament on single-stranded DNA (ssDNA) produced by DNA damage and induces the SOS response. Previous work has shown that one type of recA mutation (e.g., recA4162 (I298V)) and one type of uvrD mutation (e.g., uvrD303 (D403A, D404A)) can differentially decrease SOS expression depending on the type of inducing treatments (UV damage versus RecA mutants that constitutively express SOS). Here it is tested using other SOS inducing conditions if there is a general feature of ssDNA generated during these treatments that allows recA4162 and uvrD303 to decrease SOS expression. The SOS inducing conditions tested include growing cells containing temperature-sensitive DNA replication mutations (dnaE486, dnaG2903, dnaN159, dnaZ2016 (at 37°C)), a del(polA)501 mutation and induction of Double-Strand Breaks (DSBs). uvrD303 could decrease SOS expression under all conditions, while recA4162 could decrease SOS expression under all conditions except in the polA strain or when DSBs occur. It is hypothesized that recA4162 suppresses SOS expression best when the ssDNA occurs at a gap and that uvrD303 is able to decrease SOS expression when the ssDNA is either at a gap or when it is generated at a DSB (but does so better at a gap). PMID:24084169

Specificity in suppression of SOS expression by recA4162 and uvrD303.

PubMed

Massoni, Shawn C; Sandler, Steven J

2013-12-01

Detection and repair of DNA damage is essential in all organisms and depends on the ability of proteins recognizing and processing specific DNA substrates. In E. coli, the RecA protein forms a filament on single-stranded DNA (ssDNA) produced by DNA damage and induces the SOS response. Previous work has shown that one type of recA mutation (e.g., recA4162 (I298V)) and one type of uvrD mutation (e.g., uvrD303 (D403A, D404A)) can differentially decrease SOS expression depending on the type of inducing treatments (UV damage versus RecA mutants that constitutively express SOS). Here it is tested using other SOS inducing conditions if there is a general feature of ssDNA generated during these treatments that allows recA4162 and uvrD303 to decrease SOS expression. The SOS inducing conditions tested include growing cells containing temperature-sensitive DNA replication mutations (dnaE486, dnaG2903, dnaN159, dnaZ2016 (at 37°C)), a del(polA)501 mutation and induction of Double-Strand Breaks (DSBs). uvrD303 could decrease SOS expression under all conditions, while recA4162 could decrease SOS expression under all conditions except in the polA strain or when DSBs occur. It is hypothesized that recA4162 suppresses SOS expression best when the ssDNA occurs at a gap and that uvrD303 is able to decrease SOS expression when the ssDNA is either at a gap or when it is generated at a DSB (but does so better at a gap). Copyright © 2013 Elsevier B.V. All rights reserved.

Process mapping evaluation of medication reconciliation in academic teaching hospitals: a critical step in quality improvement.

PubMed

Holbrook, Anne; Bowen, James M; Patel, Harsit; O'Brien, Chris; You, John J; Tahavori, Roshan; Doleweerd, Jeff; Berezny, Tim; Perri, Dan; Nieuwstraten, Carmine; Troyan, Sue; Patel, Ameen

2016-12-30

Medication reconciliation (MedRec) has been a mandated or recommended activity in Canada, the USA and the UK for nearly 10 years. Accreditation bodies in North America will soon require MedRec for every admission, transfer and discharge of every patient. Studies of MedRec have revealed unintentional discrepancies in prescriptions but no clear evidence that clinically important outcomes are improved, leading to widely variable practices. Our objective was to apply process mapping methodology to MedRec to clarify current processes and resource usage, identify potential efficiencies and gaps in care, and make recommendations for improvement in the light of current literature evidence of effectiveness. Process engineers observed and recorded all MedRec activities at 3 academic teaching hospitals, from initial emergency department triage to patient discharge, for general internal medicine patients. Process maps were validated with frontline staff, then with the study team, managers and patient safety leads to summarise current problems and discuss solutions. Across all of the 3 hospitals, 5 general problem themes were identified: lack of use of all available medication sources, duplication of effort creating inefficiency, lack of timeliness of completion of the Best Possible Medication History, lack of standardisation of the MedRec process, and suboptimal communication of MedRec issues between physicians, pharmacists and nurses. MedRec as practised in this environment requires improvements in quality, timeliness, consistency and dissemination. Further research exploring efficient use of resources, in terms of personnel and costs, is required. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

RecA: Regulation and Mechanism of a Molecular Search Engine.

PubMed

Bell, Jason C; Kowalczykowski, Stephen C

2016-06-01

Homologous recombination maintains genomic integrity by repairing broken chromosomes. The broken chromosome is partially resected to produce single-stranded DNA (ssDNA) that is used to search for homologous double-stranded DNA (dsDNA). This homology driven 'search and rescue' is catalyzed by a class of DNA strand exchange proteins that are defined in relation to Escherichia coli RecA, which forms a filament on ssDNA. Here, we review the regulation of RecA filament assembly and the mechanism by which RecA quickly and efficiently searches for and identifies a unique homologous sequence among a vast excess of heterologous DNA. Given that RecA is the prototypic DNA strand exchange protein, its behavior affords insight into the actions of eukaryotic RAD51 orthologs and their regulators, BRCA2 and other tumor suppressors. Copyright © 2016 Elsevier Ltd. All rights reserved.

Comparative analysis of the effects of electron and hole capture on the power characteristics of a semiconductor quantum-well laser

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

Sokolova, Z. N., E-mail: Zina.Sokolova@mail.ioffe.ru; Pikhtin, N. A.; Tarasov, I. S.

The operating characteristics of a semiconductor quantum-well laser calculated using three models are compared. These models are (i) a model not taking into account differences between the electron and hole parameters and using the electron parameters for both types of charge carriers; (ii) a model, which does not take into account differences between the electron and hole parameters and uses the hole parameters for both types of charge carriers; and (iii) a model taking into account the asymmetry between the electron and hole parameters. It is shown that, at the same velocity of electron and hole capture into an unoccupiedmore » quantum well, the laser characteristics, obtained using the three models, differ considerably. These differences are due to a difference between the filling of the electron and hole subbands in a quantum well. The electron subband is more occupied than the hole subband. As a result, at the same velocities of electron and hole capture into an empty quantum well, the effective electron-capture velocity is lower than the effective hole-capture velocity. Specifically, it is shown that for the laser structure studied the hole-capture velocity of 5 × 10{sup 5} cm/s into an empty quantum well and the corresponding electron-capture velocity of 3 × 10{sup 6} cm/s into an empty quantum well describe the rapid capture of these carriers, at which the light–current characteristic of the laser remains virtually linear up to high pump-current densities. However, an electron-capture velocity of 5 × 10{sup 5} cm/s and a corresponding hole-capture velocity of 8.4 × 10{sup 4} cm/s describe the slow capture of these carriers, causing significant sublinearity in the light–current characteristic.« less

Mississippi | Midmarket Solar Policies in the United States | Solar

Science.gov Websites

DG adder of $0.025/kWh (total estimated 7 to 7.5 cents per kWh) RECs: The customer retains ownership of RECs. If the customer receives benefits from the DG adder while selling electricity to the utility , then the RECs are transferred from the customer to the utility. Meter aggregation: Not specified

Realizing Rec. 2020 color gamut with quantum dot displays.

PubMed

Zhu, Ruidong; Luo, Zhenyue; Chen, Haiwei; Dong, Yajie; Wu, Shin-Tson

2015-09-07

We analyze how to realize Rec. 2020 wide color gamut with quantum dots. For photoluminescence, our simulation indicates that we are able to achieve over 97% of the Rec. 2020 standard with quantum dots by optimizing the emission spectra and redesigning the color filters. For electroluminescence, by optimizing the emission spectra of quantum dots is adequate to render over 97% of the Rec. 2020 standard. We also analyze the efficiency and angular performance of these devices, and then compare results with LCDs using green and red phosphors-based LED backlight. Our results indicate that quantum dot display is an outstanding candidate for achieving wide color gamut and high optical efficiency.

Saccharomyces cerevisiae Hrq1 requires a long 3'-tailed DNA substrate for helicase activity.

PubMed

Kwon, Sung-Hun; Choi, Do-Hee; Lee, Rina; Bae, Sung-Ho

2012-10-26

RecQ helicases are well conserved proteins from bacteria to human and function in various DNA metabolism for maintenance of genome stability. Five RecQ helicases are found in humans, whereas only one RecQ helicase has been described in lower eukaryotes. However, recent studies predicted the presence of a second RecQ helicase, Hrq1, in fungal genomes and verified it as a functional gene in fission yeast. Here we show that 3'-5' helicase activity is intrinsically associated with Hrq1 of Saccharomyces cerevisiae. We also determined several biochemical properties of Hrq1 helicase distinguishable from those of other RecQ helicase members. Hrq1 is able to unwind relatively long duplex DNA up to 120-bp and is significantly stimulated by a preexisting fork structure. Further, the most striking feature of Hrq1 is its absolute requirement for a long 3'-tail (⩾70-nt) for efficient unwinding of duplex DNA. We also found that Hrq1 has potent DNA strand annealing activity. Our results indicate that Hrq1 has vigorous helicase activity that deserves further characterization to expand our understanding of RecQ helicases. Copyright © 2012 Elsevier Inc. All rights reserved.

Casein Kinase 1 and Phosphorylation of Cohesin Subunit Rec11 (SA3) Promote Meiotic Recombination through Linear Element Formation.

PubMed

Phadnis, Naina; Cipak, Lubos; Polakova, Silvia; Hyppa, Randy W; Cipakova, Ingrid; Anrather, Dorothea; Karvaiova, Lucia; Mechtler, Karl; Smith, Gerald R; Gregan, Juraj

2015-05-01

Proper meiotic chromosome segregation, essential for sexual reproduction, requires timely formation and removal of sister chromatid cohesion and crossing-over between homologs. Early in meiosis cohesins hold sisters together and also promote formation of DNA double-strand breaks, obligate precursors to crossovers. Later, cohesin cleavage allows chromosome segregation. We show that in fission yeast redundant casein kinase 1 homologs, Hhp1 and Hhp2, previously shown to regulate segregation via phosphorylation of the Rec8 cohesin subunit, are also required for high-level meiotic DNA breakage and recombination. Unexpectedly, these kinases also mediate phosphorylation of a different meiosis-specific cohesin subunit Rec11. This phosphorylation in turn leads to loading of linear element proteins Rec10 and Rec27, related to synaptonemal complex proteins of other species, and thereby promotes DNA breakage and recombination. Our results provide novel insights into the regulation of chromosomal features required for crossing-over and successful reproduction. The mammalian functional homolog of Rec11 (STAG3) is also phosphorylated during meiosis and appears to be required for fertility, indicating wide conservation of the meiotic events reported here.

Image charge effects on electron capture by dust grains in dusty plasmas.

PubMed

Jung, Y D; Tawara, H

2001-07-01

Electron-capture processes by negatively charged dust grains from hydrogenic ions in dusty plasmas are investigated in accordance with the classical Bohr-Lindhard model. The attractive interaction between the electron in a hydrogenic ion and its own image charge inside the dust grain is included to obtain the total interaction energy between the electron and the dust grain. The electron-capture radius is determined by the total interaction energy and the kinetic energy of the released electron in the frame of the projectile dust grain. The classical straight-line trajectory approximation is applied to the motion of the ion in order to visualize the electron-capture cross section as a function of the impact parameter, kinetic energy of the projectile ion, and dust charge. It is found that the image charge inside the dust grain plays a significant role in the electron-capture process near the surface of the dust grain. The electron-capture cross section is found to be quite sensitive to the collision energy and dust charge.

Genetic parameters of different measures of cheese yield and milk nutrient recovery from an individual model cheese-manufacturing process.

PubMed

Bittante, G; Cipolat-Gotet, C; Cecchinato, A

2013-01-01

Cheese yield (CY) is an important technological trait in the dairy industry, and the objective of this study was to estimate the genetic parameters of cheese yield in a dairy cattle population using an individual model-cheese production procedure. A total of 1,167 Brown Swiss cows belonging to 85 herds were sampled once (a maximum of 15 cows were sampled per herd on a single test day, 1 or 2 herds per week). From each cow, 1,500 mL of milk was processed according to the following steps: milk sampling and heating, culture addition, rennet addition, gelation-time recording, curd cutting, whey draining and sampling, wheel formation, pressing, salting in brine, weighing, and cheese sampling. The compositions of individual milk, whey, and curd samples were determined. Three measures of percentage cheese yield (%CY) were calculated: %CY(CURD), %CY(SOLIDS), and %CY(WATER), which represented the ratios between the weight of fresh curd, the total solids of the curd, and the water content of the curd, respectively, and the weight of the milk processed. In addition, 3 measures of daily cheese yield (dCY, kg/d) were defined, considering the daily milk yield. Three measures of nutrient recovery (REC) were computed: REC(FAT), REC(PROTEIN), and REC(SOLIDS), which represented the ratio between the weights of the fat, protein, and total solids in the curd, respectively, and the corresponding nutrient in the milk. Energy recovery, REC(ENERGY), represented the energy content of the cheese versus that in the milk. For statistical analysis, a Bayesian animal model was implemented via Gibbs sampling. The effects of parity (1 to ≥4), days in milk (6 classes), and laboratory vat (15 vats) were assigned flat priors; those of herd-test-date, animal, and residual were given Gaussian prior distributions. Intra-herd heritability estimates of %CY(CURD), %CY(SOLIDS), and %CY(WATER) ranged from 0.224 to 0.267; these were larger than the estimates obtained for milk yield (0.182) and milk fat content (0.122), and similar to that for protein content (0.275). Daily cheese yields showed heritability estimates similar to those of daily milk yield. The trait %CY(WATER) showed a highly positive genetic correlation with %CY(SOLIDS) (0.87), whereas their phenotypic correlation was moderate (0.37), and the fat and protein contents of milk showed high genetic correlations with %CY traits. The heritability estimates of REC(PROTEIN) and REC(FAT) were larger (0.490 and 0.208, respectively) than those obtained for the protein and fat contents of milk, and the genetic relationships between REC(PROTEIN) and REC(FAT) with milk protein and fat content were low or moderate; REC(PROTEIN) and REC(FAT) were moderately correlated with the %CY traits and highly correlated with REC(SOLIDS) and REC(ENERGY). Both REC(SOLIDS) and REC(ENERGY) were heritable (0.274 and 0.232), and showed high correlations with each other (0.96) and with the %CY traits (0.83 to 0.97). Together, these findings demonstrate the existence of economically important, genetically determined variability in cheese yield that does not depend solely upon the fat and protein contents of milk, but also relies on the ability of the coagulum to retain the highest possible proportions of the available protein, fat, and water. Exploitation of this interesting genetic variation does not seem to be feasible through direct measurement of the phenotype in cows at the population level. Instead, further research is warranted to examine possible means for indirect prediction, such as through assessing the mid-infrared spectra of milk samples. Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Bogolon-mediated electron capture by impurities in hybrid Bose-Fermi systems

NASA Astrophysics Data System (ADS)

Boev, M. V.; Kovalev, V. M.; Savenko, I. G.

2018-04-01

We investigate the processes of electron capture by a Coulomb impurity center residing in a hybrid system consisting of spatially separated two-dimensional layers of electron and Bose-condensed dipolar exciton gases coupled via the Coulomb forces. We calculate the probability of the electron capture accompanied by the emission of a single Bogoliubov excitation (bogolon), similar to regular phonon-mediated scattering in solids. Furthermore, we study the electron capture mediated by the emission of a pair of bogolons in a single capture event and show that these processes not only should be treated in the same order of the perturbation theory, but also they give a more important contribution than single-bogolon-mediated capture, in contrast with regular phonon scattering.

Testing COBOL Programs by Mutation. Volume I. Introduction to the CMS.1 System.

DTIC Science & Technology

1980-02-01

ALTER-OCCURS><SYMBOL TABLE location><code><x> where code = 0 means "add 1 to occurs", = 1 means "subtract 1 from occurs". 4 Insert a filler ( PIC X) in...REC. 31 01 OLD-REC. 32 03 FILLER PIC X. 33 03 OLD-KEY PIC X(12). 34 03 FILLER PIC X(67). 35S to NEdETF 36 RECORD CONTATS 90 CHARACTERS 37 LABEL RECORDS...ARE STANDARD 3S DATA RECORD IS NEd-REC. 39 01 NEd-REC. AO 03 FILLER PIC 1. Al 03 NEW-(FY PIC X(12). A2 03 FILLER PIC 1(6?). 43 ED PMTHR 44 RECORD

Trapping of Embolic Particles in a Vessel Phantom by Cavitation-Enhanced Acoustic Streaming

PubMed Central

Maxwell, Adam D.; Park, Simone; Vaughan, Benjamin L.; Cain, Charles A.; Grotberg, James B.; Xu, Zhen

2014-01-01

Cavitation clouds generated by short, high-amplitude, focused ultrasound pulses were previously observed to attract, trap, and erode thrombus fragments in a vessel phantom. This phenomenon may offer a noninvasive method to capture and eliminate embolic fragments flowing through the bloodstream during a cardiovascular intervention. In this article, the mechanism of embolus trapping was explored by particle image velocimetry (PIV). PIV was used to examine the fluid streaming patterns generated by ultrasound in a vessel phantom with and without crossflow of blood-mimicking fluid. Cavitation enhanced streaming, which generated fluid vortices adjacent to the focus. The focal streaming velocity, uf, was as high as 120 cm/s, while mean crossflow velocities, uc, were imposed up to 14 cm/s. When a solid particle 3-4 mm diameter was introduced into crossflow, it was trapped near the focus. Increasing uf promoted particle trapping while increasing uc promoted particle escape. The maximum crossflow Reynolds number at which particles could be trapped, Rec, was approximately linear with focal streaming number, Ref, i.e. Rec = 0.25Ref + 67.44 (R2=0.76) corresponding to dimensional velocities uc=0.084uf + 3.122 for 20 < uf < 120 cm/s. The fluidic pressure map was estimated from PIV and indicated a negative pressure gradient towards the focus, trapping the embolus near this location. PMID:25109407

NASA Ares I Launch Vehicle Roll and Reaction Control Systems Lessons Learned

NASA Technical Reports Server (NTRS)

Butt, Adam; Popp, Chris G.; Jernigan, Frankie R.; Paseur, Lila F.; Pitts, Hank M.

2011-01-01

On April 15, 2010 President Barak Obama made the official announcement that the Constellation Program, which included the Ares I launch vehicle, would be canceled. NASA s Ares I launch vehicle was being designed to launch the Orion Crew Exploration Vehicle, returning humans to the moon, Mars, and beyond. It consisted of a First Stage (FS) five segment solid rocket booster and a liquid J-2X Upper Stage (US) engine. Roll control for the FS was planned to be handled by a dedicated Roll Control System (RoCS), located on the connecting interstage. Induced yaw or pitch moments experienced during FS ascent would have been handled by vectoring of the booster nozzle. After FS booster separation, the US Reaction Control System (ReCS) would have provided the US Element with three degrees of freedom control as needed. The lessons learned documented in this paper will be focused on the technical designs and producibility of both systems along with the partnership between NASA and Boeing, who was on contract to build the Ares I US Element, which included the FS RoCS and US ReCS. In regards to partnership, focus will be placed on integration along with technical work accomplished by Boeing with special emphasis on each task order. In summary, this paper attempts to capture key lessons learned that should be helpful in the development of future launch vehicle RCS designs.

Payment of research participants: current practice and policies of Irish research ethics committees.

PubMed

Roche, Eric; King, Romaine; Mohan, Helen M; Gavin, Blanaid; McNicholas, Fiona

2013-09-01

Payment of research participants helps to increase recruitment for research studies, but can pose ethical dilemmas. Research ethics committees (RECs) have a centrally important role in guiding this practice, but standardisation of the ethical approval process in Ireland is lacking. Our aim was to examine REC policies, experiences and concerns with respect to the payment of participants in research projects in Ireland. Postal survey of all RECs in Ireland. Response rate was 62.5% (n=50). 80% of RECs reported not to have any established policy on the payment of research subjects while 20% had refused ethics approval to studies because the investigators proposed to pay research participants. The most commonly cited concerns were the potential for inducement and undermining of voluntary consent. There is considerable variability among RECs on the payment of research participants and a lack of clear consensus guidelines on the subject. The development of standardised guidelines on the payment of research subjects may enhance recruitment of research participants.

Consistency in decision making by research ethics committees: a controlled comparison.

PubMed

Angell, E; Sutton, A J; Windridge, K; Dixon-Woods, M

2006-11-01

There has been longstanding interest in the consistency of decisions made by research ethics committees (RECs) in the UK, but most of the evidence has come from single studies submitted to multiple committees. A systematic comparison was carried out of the decisions made on 18 purposively selected applications, each of which was reviewed independently by three different RECs in a single strategic health authority. Decisions on 11 applications were consistent, but disparities were found among RECs on decisions on seven applications. An analysis of the agreement between decisions of RECs yielded an overall measure of agreement of kappa = 0.286 (95% confidence interval -0.06 to 0.73), indicating a level of agreement that, although probably better than chance, may be described as "slight". The small sample size limits the robustness of these findings. Further research on reasons for inconsistencies in decision making between RECs, and on the importance of such inconsistencies for a range of arguments, is needed.

The transcription fidelity factor GreA impedes DNA break repair.

PubMed

Sivaramakrishnan, Priya; Sepúlveda, Leonardo A; Halliday, Jennifer A; Liu, Jingjing; Núñez, María Angélica Bravo; Golding, Ido; Rosenberg, Susan M; Herman, Christophe

2017-10-12

Homologous recombination repairs DNA double-strand breaks and must function even on actively transcribed DNA. Because break repair prevents chromosome loss, the completion of repair is expected to outweigh the transcription of broken templates. However, the interplay between DNA break repair and transcription processivity is unclear. Here we show that the transcription factor GreA inhibits break repair in Escherichia coli. GreA restarts backtracked RNA polymerase and hence promotes transcription fidelity. We report that removal of GreA results in markedly enhanced break repair via the classic RecBCD-RecA pathway. Using a deep-sequencing method to measure chromosomal exonucleolytic degradation, we demonstrate that the absence of GreA limits RecBCD-mediated resection. Our findings suggest that increased RNA polymerase backtracking promotes break repair by instigating RecA loading by RecBCD, without the influence of canonical Chi signals. The idea that backtracked RNA polymerase can stimulate recombination presents a DNA transaction conundrum: a transcription fidelity factor that compromises genomic integrity.

Decision-making and planning in full recovery of anorexia nervosa.

PubMed

Lindner, Susanne E; Fichter, Manfred M; Quadflieg, Norbert

2012-11-01

Based on findings of persisting neuropsychological impairments in women recovered from anorexia nervosa (rec AN), this study examined decision-making and planning, for achieving a desired goal, as central executive functions in a large sample of rec AN. The definition of recovery included physiological, behavioral, and psychological variables. A total of 100 rec AN women were compared to 100 healthy women, 1:1 matched for age and educational level. Decision-making was assessed with the Iowa Gambling Task and planning with the Tower of London. Expert interviews and self-ratings were used for assessing the inclusion/exclusion criteria and control variables. Compared to healthy controls, rec AN women were better in decision-making and worse in planning even after considering control variables. This study does not support results from other studies showing that rec AN participants perform better in decision-making. Results from this study show that planning is impaired even after full recovery from AN. Copyright © 2012 Wiley Periodicals, Inc.

A homolog of Escherichia coli RecA in mitochondria of the cellular slime mold Dictyostelium discoideum.

PubMed

Hasegawa, Yasuna; Wakabayashi, Masayuki; Nakamura, Shogo; Kodaira, Ken-ichi; Shinohara, Hiroaki; Yasukawa, Hiro

2004-05-04

The cellular slime mold Dictyostelium discoideum expresses a gene encoding a 452-amino-acid polypeptide that is 47% identical to Escherichia coli RecA. A recA-deficient E. coli, JE6651, was transformed by pYSN1, which was designed to express the truncated form of the D. discoideum gene, and used in suppression assays. The viability of the transformant, JE6651(pYSN1), increased following UV irradiation or mitomycin C treatment. Phage lambda (red(-) gam(-)), which required RecA activity for DNA packaging, formed plaques on a lawn of JE6651(pYSN1). These results indicate that the gene product has a DNA recombination activity. Fluorescence of D. discoideum protein fused with GFP was detected in mitochondria. The gene disruption mutant was hypersensitive to UV-light (254nm), mitomycin C and H(2)O(2), indicating that D. discoideum recA is important for survival following exposure to DNA damaging agents.

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

Erenpreisa, Jekaterina; Cragg, Mark S.; Salmina, Kristine

Escape from mitotic catastrophe and generation of endopolyploid tumour cells (ETCs) represents a potential survival strategy of tumour cells in response to genotoxic treatments. ETCs that resume the mitotic cell cycle have reduced ploidy and are often resistant to these treatments. In search for a mechanism for genome reduction, we previously observed that ETCs express meiotic proteins among which REC8 (a meiotic cohesin component) is of particular interest, since it favours reductional cell division in meiosis. In the present investigation, we induced endopolyploidy in p53-dysfunctional human tumour cell lines (Namalwa, WI-L2-NS, HeLa) by gamma irradiation, and analysed the sub-cellular localisationmore » of REC8 in the resulting ETCs. We observed by RT-PCR and Western blot that REC8 is constitutively expressed in these tumour cells, along with SGOL1 and SGOL2, and that REC8 becomes modified after irradiation. REC8 localised to paired sister centromeres in ETCs, the former co-segregating to opposite poles. Furthermore, REC8 localised to the centrosome of interphase ETCs and to the astral poles in anaphase cells where it colocalised with the microtubule-associated protein NuMA. Altogether, our observations indicate that radiation-induced ETCs express features of meiotic cell divisions and that these may facilitate chromosome segregation and genome reduction.« less

The Aspartate-Less Receiver (ALR) Domains: Distribution, Structure and Function

PubMed Central

Weiner, Joshua J.; Han, Lanlan; Peterson, Francis C.; Volkman, Brian F.; Silvaggi, Nicholas R.; Ulijasz, Andrew T.

2015-01-01

Two-component signaling systems are ubiquitous in bacteria, Archaea and plants and play important roles in sensing and responding to environmental stimuli. To propagate a signaling response the typical system employs a sensory histidine kinase that phosphorylates a Receiver (REC) domain on a conserved aspartate (Asp) residue. Although it is known that some REC domains are missing this Asp residue, it remains unclear as to how many of these divergent REC domains exist, what their functional roles are and how they are regulated in the absence of the conserved Asp. Here we have compiled all deposited REC domains missing their phosphorylatable Asp residue, renamed here as the Aspartate-Less Receiver (ALR) domains. Our data show that ALRs are surprisingly common and are enriched for when attached to more rare effector outputs. Analysis of our informatics and the available ALR atomic structures, combined with structural, biochemical and genetic data of the ALR archetype RitR from Streptococcus pneumoniae presented here suggest that ALRs have reorganized their active pockets to instead take on a constitutive regulatory role or accommodate input signals other than Asp phosphorylation, while largely retaining the canonical post-phosphorylation mechanisms and dimeric interface. This work defines ALRs as an atypical REC subclass and provides insights into shared mechanisms of activation between ALR and REC domains. PMID:25875291

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

Larkin, Robert M.; Stefano, Giovanni; Ruckle, Michael E.

Eukaryotic cells require mechanisms to establish the proportion of cellular volume devoted to particular organelles. These mechanisms are poorly understood. From a screen for plastid-to-nucleus signaling mutants in Arabidopsis thaliana, we cloned a mutant allele of a gene that encodes a protein of unknown function that is homologous to two other Arabidopsis genes of unknown function and Arabidopsis. In contrast to FRIENDLY, these three homologs of FRIENDLY are found only in photosynthetic organisms. Based on these data, we proposed that FRIENDLY expanded into a small gene family to help regulate the energy metabolism of cells that contain both mitochondria andmore » chloroplasts. Indeed, we found that knocking out these genes caused a number of chloroplast phenotypes, including a reduction in the proportion of cellular volume devoted to chloroplasts to 50% of wild type. Thus, we refer to these genes as REDUCED CHLOROPLAST COVERAGE (REC). The size of the chloroplast compartment was reduced most in rec1 mutants. The REC1 protein accumulated in the cytosol and the nucleus. REC1 was excluded from the nucleus when plants were treated with amitrole, which inhibits cell expansion and chloroplast function. Finally, we conclude that REC1 is an extraplastidic protein that helps to establish the size of the chloroplast compartment, and that signals derived from cell expansion or chloroplasts may regulate REC1.« less

A programmable Cas9-serine recombinase fusion protein that operates on DNA sequences in mammalian cells

PubMed Central

Chaikind, Brian; Bessen, Jeffrey L.; Thompson, David B.; Hu, Johnny H.; Liu, David R.

2016-01-01

We describe the development of ‘recCas9’, an RNA-programmed small serine recombinase that functions in mammalian cells. We fused a catalytically inactive dCas9 to the catalytic domain of Gin recombinase using an optimized fusion architecture. The resulting recCas9 system recombines DNA sites containing a minimal recombinase core site flanked by guide RNA-specified sequences. We show that these recombinases can operate on DNA sites in mammalian cells identical to genomic loci naturally found in the human genome in a manner that is dependent on the guide RNA sequences. DNA sequencing reveals that recCas9 catalyzes guide RNA-dependent recombination in human cells with an efficiency as high as 32% on plasmid substrates. Finally, we demonstrate that recCas9 expressed in human cells can catalyze in situ deletion between two genomic sites. Because recCas9 directly catalyzes recombination, it generates virtually no detectable indels or other stochastic DNA modification products. This work represents a step toward programmable, scarless genome editing in unmodified cells that is independent of endogenous cellular machinery or cell state. Current and future generations of recCas9 may facilitate targeted agricultural breeding, or the study and treatment of human genetic diseases. PMID:27515511

Identification of Bacillus Probiotics Isolated from Soil Rhizosphere Using 16S rRNA, recA, rpoB Gene Sequencing and RAPD-PCR.

PubMed

Mohkam, Milad; Nezafat, Navid; Berenjian, Aydin; Mobasher, Mohammad Ali; Ghasemi, Younes

2016-03-01

Some Bacillus species, especially Bacillus subtilis and Bacillus pumilus groups, have highly similar 16S rRNA gene sequences, which are hard to identify based on 16S rDNA sequence analysis. To conquer this drawback, rpoB, recA sequence analysis along with randomly amplified polymorphic (RAPD) fingerprinting was examined as an alternative method for differentiating Bacillus species. The 16S rRNA, rpoB and recA genes were amplified via a polymerase chain reaction using their specific primers. The resulted PCR amplicons were sequenced, and phylogenetic analysis was employed by MEGA 6 software. Identification based on 16S rRNA gene sequencing was underpinned by rpoB and recA gene sequencing as well as RAPD-PCR technique. Subsequently, concatenation and phylogenetic analysis showed that extent of diversity and similarity were better obtained by rpoB and recA primers, which are also reinforced by RAPD-PCR methods. However, in one case, these approaches failed to identify one isolate, which in combination with the phenotypical method offsets this issue. Overall, RAPD fingerprinting, rpoB and recA along with concatenated genes sequence analysis discriminated closely related Bacillus species, which highlights the significance of the multigenic method in more precisely distinguishing Bacillus strains. This research emphasizes the benefit of RAPD fingerprinting, rpoB and recA sequence analysis superior to 16S rRNA gene sequence analysis for suitable and effective identification of Bacillus species as recommended for probiotic products.

Biochemical Characterization of a Mycobacteriophage Derived DnaB Ortholog Reveals New Insight into the Evolutionary Origin of DnaB Helicases

PubMed Central

Bhowmik, Priyanka; Das Gupta, Sujoy K.

2015-01-01

The bacterial replicative helicases known as DnaB are considered to be members of the RecA superfamily. All members of this superfamily, including DnaB, have a conserved C- terminal domain, known as the RecA core. We unearthed a series of mycobacteriophage encoded proteins in which the RecA core domain alone was present. These proteins were phylogenetically related to each other and formed a distinct clade within the RecA superfamily. A mycobacteriophage encoded protein, Wildcat Gp80 that roots deep in the DnaB family, was found to possess a core domain having significant sequence homology (Expect value < 10-5) with members of this novel cluster. This indicated that Wildcat Gp80, and by extrapolation, other members of the DnaB helicase family, may have evolved from a single domain RecA core polypeptide belonging to this novel group. Biochemical investigations confirmed that Wildcat Gp80 was a helicase. Surprisingly, our investigations also revealed that a thioredoxin tagged truncated version of the protein in which the N-terminal sequences were removed was fully capable of supporting helicase activity, although its ATP dependence properties were different. DnaB helicase activity is thus, primarily a function of the RecA core although additional N-terminal sequences may be necessary for fine tuning its activity and stability. Based on sequence comparison and biochemical studies we propose that DnaB helicases may have evolved from single domain RecA core proteins having helicase activities of their own, through the incorporation of additional N-terminal sequences. PMID:26237048

Discrimination of the Lactobacillus acidophilus group using sequencing, species-specific PCR and SNaPshot mini-sequencing technology based on the recA gene.

PubMed

Huang, Chien-Hsun; Chang, Mu-Tzu; Huang, Mu-Chiou; Wang, Li-Tin; Huang, Lina; Lee, Fwu-Ling

2012-10-01

To clearly identify specific species and subspecies of the Lactobacillus acidophilus group using phenotypic and genotypic (16S rDNA sequence analysis) techniques alone is difficult. The aim of this study was to use the recA gene for species discrimination in the L. acidophilus group, as well as to develop a species-specific primer and single nucleotide polymorphism primer based on the recA gene sequence for species and subspecies identification. The average sequence similarity for the recA gene among type strains was 80.0%, and most members of the L. acidophilus group could be clearly distinguished. The species-specific primer was designed according to the recA gene sequencing, which was employed for polymerase chain reaction with the template DNA of Lactobacillus strains. A single 231-bp species-specific band was found only in L. delbrueckii. A SNaPshot mini-sequencing assay using recA as a target gene was also developed. The specificity of the mini-sequencing assay was evaluated using 31 strains of L. delbrueckii species and was able to unambiguously discriminate strains belonging to the subspecies L. delbrueckii subsp. bulgaricus. The phylogenetic relationships of most strains in the L. acidophilus group can be resolved using recA gene sequencing, and a novel method to identify the species and subspecies of the L. delbrueckii and L. delbrueckii subsp. bulgaricus was developed by species-specific polymerase chain reaction combined with SNaPshot mini-sequencing. Copyright © 2012 Society of Chemical Industry.

Physiological, structural and molecular traits activated in strawberry plants after inoculation with the plant growth-promoting bacterium Azospirillum brasilense REC3.

PubMed

Guerrero-Molina, M F; Lovaisa, N C; Salazar, S M; Martínez-Zamora, M G; Díaz-Ricci, J C; Pedraza, R O

2015-05-01

The plant growth-promoting strain REC3 of Azospirillum brasilense, isolated from strawberry roots, prompts growth promotion and systemic protection against anthracnose disease in this crop. Hence, we hypothesised that A. brasilense REC3 can induce different physiological, structural and molecular responses in strawberry plants. Therefore, the aim of this work was to study these traits activated in Azospirillum-colonised strawberry plants, which have not been assessed until now. Healthy, in vitro micropropagated plants were root-inoculated with REC3 under hydroponic conditions; root and leaf tissues were sampled at different times, and oxidative burst, phenolic compound content, malondialdehyde (MDA) concentration, callose deposition, cell wall fortification and gene expression were evaluated. Azospirillum inoculation enhanced levels of soluble phenolic compounds after 12 h post-inoculation (hpi), while amounts of cell wall bound phenolics were similar in inoculated and control plants. Other early responses activated by REC3 (at 24 hpi) were a decline of lipid peroxidation and up-regulation of strawberry genes involved in defence (FaPR1), bacterial recognition (FaFLS2) and H₂O₂ depuration (FaCAT and FaAPXc). The last may explain the apparent absence of oxidative burst in leaves after bacterial inoculation. Also, REC3 inoculation induced delayed structural responses such as callose deposition and cell wall fortification (at 72 hpi). Results showed that A. brasilense REC3 is capable of exerting beneficial effects on strawberry plants, reinforcing their physiological and cellular characteristics, which in turns contribute to improve plant performance. © 2014 German Botanical Society and The Royal Botanical Society of the Netherlands.

Hot-spot identification on a broad class of proteins and RNA suggest unifying principles of molecular recognition

PubMed Central

Kulp, John L.; Cloudsdale, Ian S.; Kulp, John L.

2017-01-01

Chemically diverse fragments tend to collectively bind at localized sites on proteins, which is a cornerstone of fragment-based techniques. A central question is how general are these strategies for predicting a wide variety of molecular interactions such as small molecule-protein, protein-protein and protein-nucleic acid for both experimental and computational methods. To address this issue, we recently proposed three governing principles, (1) accurate prediction of fragment-macromolecule binding free energy, (2) accurate prediction of water-macromolecule binding free energy, and (3) locating sites on a macromolecule that have high affinity for a diversity of fragments and low affinity for water. To test the generality of these concepts we used the computational technique of Simulated Annealing of Chemical Potential to design one small fragment to break the RecA-RecA protein-protein interaction and three fragments that inhibit peptide-deformylase via water-mediated multi-body interactions. Experiments confirm the predictions that 6-hydroxydopamine potently inhibits RecA and that PDF inhibition quantitatively tracks the water-mediated binding predictions. Additionally, the principles correctly predict the essential bound waters in HIV Protease, the surprisingly extensive binding site of elastase, the pinpoint location of electron transfer in dihydrofolate reductase, the HIV TAT-TAR protein-RNA interactions, and the MDM2-MDM4 differential binding to p53. The experimental confirmations of highly non-obvious predictions combined with the precise characterization of a broad range of known phenomena lend strong support to the generality of fragment-based methods for characterizing molecular recognition. PMID:28837642

Hot-spot identification on a broad class of proteins and RNA suggest unifying principles of molecular recognition.

PubMed

Kulp, John L; Cloudsdale, Ian S; Kulp, John L; Guarnieri, Frank

2017-01-01

Chemically diverse fragments tend to collectively bind at localized sites on proteins, which is a cornerstone of fragment-based techniques. A central question is how general are these strategies for predicting a wide variety of molecular interactions such as small molecule-protein, protein-protein and protein-nucleic acid for both experimental and computational methods. To address this issue, we recently proposed three governing principles, (1) accurate prediction of fragment-macromolecule binding free energy, (2) accurate prediction of water-macromolecule binding free energy, and (3) locating sites on a macromolecule that have high affinity for a diversity of fragments and low affinity for water. To test the generality of these concepts we used the computational technique of Simulated Annealing of Chemical Potential to design one small fragment to break the RecA-RecA protein-protein interaction and three fragments that inhibit peptide-deformylase via water-mediated multi-body interactions. Experiments confirm the predictions that 6-hydroxydopamine potently inhibits RecA and that PDF inhibition quantitatively tracks the water-mediated binding predictions. Additionally, the principles correctly predict the essential bound waters in HIV Protease, the surprisingly extensive binding site of elastase, the pinpoint location of electron transfer in dihydrofolate reductase, the HIV TAT-TAR protein-RNA interactions, and the MDM2-MDM4 differential binding to p53. The experimental confirmations of highly non-obvious predictions combined with the precise characterization of a broad range of known phenomena lend strong support to the generality of fragment-based methods for characterizing molecular recognition.

The Effect of Recovery Duration on Vastus Lateralis Oxygenation, Heart Rate, Perceived Exertion and Time Motion Descriptors during Small Sided Football Games.

PubMed

McLean, Scott; Kerhervé, Hugo; Lovell, Geoff P; Gorman, Adam D; Solomon, Colin

2016-01-01

Small sided games (SSG) of football are an effective and efficient format to simultaneously train the physiological, technical, and tactical components of football. The duration of the recovery period between bouts of SSG will affect the physiological response to subsequent bouts. It was hypothesised that decreasing the duration of recovery periods separating serial SSG bouts would increase physiological, and perceptual responses, and decrease high speed running, and distance during SSG bouts. Twelve experienced footballers (mean ± SD; age 21 ± 3 yrs; VO2peak 64 ± 7 ml·min·kg-1; playing experience 15 ± 3 yrs) completed two SSG sessions. Each SSG consisted of 3 vs. 3 players and 6 bouts of 2 min duration, with bouts separated by either 30 s recovery (REC-30) or 120 s recovery (REC-120). Deoxygenated haemoglobin (HHb) in the vastus lateralis (VL) (using near infrared spectroscopy), heart rate (HR) and time motion descriptors (TMD) (speed and distance) were measured continuously during the SSG sessions and perceived exertion (RPE) was measured for each bout. During the recovery periods, in REC-30 compared to REC-120, there was a significant (p < 0.05) main effect of a higher HHb and HR. During the bouts, in REC-30 compared to REC-120, there were no significant differences in HHb, HR, RPE, or TMD, but within both REC-30 and REC-120 there were significant increases as a function of bout number in RPE. Although a four-fold increase in recovery period allowed a significant increase in the recovery of HHb and HR, this did not increase the physiological, and perceptual responses, or time motion descriptors during the bouts. These results could have been due to the regulation of effort (pacing), in these experienced players performing an exercise task to which they were well adapted.

The Effect of Recovery Duration on Vastus Lateralis Oxygenation, Heart Rate, Perceived Exertion and Time Motion Descriptors during Small Sided Football Games

PubMed Central

McLean, Scott; Kerhervé, Hugo; Lovell, Geoff P.; Gorman, Adam D.; Solomon, Colin

2016-01-01

Purpose Small sided games (SSG) of football are an effective and efficient format to simultaneously train the physiological, technical, and tactical components of football. The duration of the recovery period between bouts of SSG will affect the physiological response to subsequent bouts. It was hypothesised that decreasing the duration of recovery periods separating serial SSG bouts would increase physiological, and perceptual responses, and decrease high speed running, and distance during SSG bouts. Methods Twelve experienced footballers (mean ± SD; age 21 ± 3 yrs; VO2peak 64 ± 7 ml·min·kg−1; playing experience 15 ± 3 yrs) completed two SSG sessions. Each SSG consisted of 3 vs. 3 players and 6 bouts of 2 min duration, with bouts separated by either 30 s recovery (REC-30) or 120 s recovery (REC-120). Deoxygenated haemoglobin (HHb) in the vastus lateralis (VL) (using near infrared spectroscopy), heart rate (HR) and time motion descriptors (TMD) (speed and distance) were measured continuously during the SSG sessions and perceived exertion (RPE) was measured for each bout. Results During the recovery periods, in REC-30 compared to REC-120, there was a significant (p < 0.05) main effect of a higher HHb and HR. During the bouts, in REC-30 compared to REC-120, there were no significant differences in HHb, HR, RPE, or TMD, but within both REC-30 and REC-120 there were significant increases as a function of bout number in RPE. Conclusions Although a four-fold increase in recovery period allowed a significant increase in the recovery of HHb and HR, this did not increase the physiological, and perceptual responses, or time motion descriptors during the bouts. These results could have been due to the regulation of effort (pacing), in these experienced players performing an exercise task to which they were well adapted. PMID:26919064

A Summary of Transonic Natural Laminar Flow Airfoil Development at NAE (Resume Des Recherches de l’Ena sur des Profils Aerodynamiques A Ecoulements Laminaires Naturels Transsoniques)

DTIC Science & Technology

1990-05-01

Transition Free Drag Polars at Re/c=6.7 X 106 11 2.3.1.2 Transition Fixed Drag Polars at Re/c= 6.7 X 106 13 2.3.1.3 Transition Free Drag Polars at Re...c=12.5 X 106 14 2.3.1.4 Transition Fixed Drag Polars at Re/c=12.5 X 106 14 2.3.2 Drag versus Mach number 15 2.4 DRAG COMPARISON AGAINST OTHER...4. Coefficient of lift versus angle of attack CLB versus a 38 5. Lift curve slope versus Mach Number aCL/aa versus M, Re= 6.7 X 106 (Free Transition

RecA family proteins in archaea: RadA and its cousins.

PubMed

Haldenby, Sam; White, Malcolm F; Allers, Thorsten

2009-02-01

Recombinases of the RecA family are essential for homologous recombination and underpin genome stability, by promoting the repair of double-stranded DNA breaks and the rescue of collapsed DNA replication forks. Until now, our understanding of homologous recombination has relied on studies of bacterial and eukaryotic model organisms. Archaea provide new opportunities to study how recombination operates in a lineage distinct from bacteria and eukaryotes. In the present paper, we focus on RadA, the archaeal RecA family recombinase, and its homologues in archaea and other domains. On the basis of phylogenetic analysis, we propose that a family of archaeal proteins with a single RecA domain, which are currently annotated as KaiC, be renamed aRadC.

Does RecA have a role in Borrelia recurrentis?

PubMed

Cutler, S J; Rinky, I J; Bonilla, E M

2011-02-01

Genomic sequencing of two relapsing fever spirochaetes showed truncation of recA in Borrelia recurrentis, but not in Borrelia duttonii. RecA has an important role among bacteria; we investigated whether this characteristic was representative of B. recurrentis, or an artefact following in vitro cultivation. We sequenced recA directly from samples of patient with louse-borne relapsing fever (B. recurrentis) or tick-borne relapsing fever (B. duttonii). We confirmed the premature stop codon in seven louse-borne relapsing fever samples, and its absence from three tick-borne relapsing fever samples. Furthermore, specific signature polymorphisms were found that could differentiate between these highly similar spirochaetes. © 2010 The Authors. Journal Compilation © 2010 European Society of Clinical Microbiology and Infectious Diseases.

Neuroanatomy of the Pig Cardiac Ventricles. A Stereomicroscopic, Confocal and Electron Microscope Study.

PubMed

Pauziene, Neringa; Rysevaite-Kyguoliene, Kristina; Alaburda, Paulius; Pauza, Audrys G; Skukauskaite, Monika; Masaityte, Aiste; Laucaityte, Goda; Saburkina, Inga; Inokaitis, Hermanas; Plisiene, Jurgita; Pauza, Dainius H

2017-10-01

Although the pig is a model for heart disease, the neuroanatomy of cardiac ventricles (CV) in this species remains undetailed. We aimed to define the innervation pattern of pig CV, combining histochemistry for acetylcholinesterase, immunofluorescent labeling and electron microscopy. Forty nine examined pig hearts show that the major nerves supplying the ventral side of CV descend from the venous part of the heart hilum. Fewer in number and smaller in size, epicardial nerves supply the dorsal half of the CV. Epicardial nerves on the left ventricle are thicker than those on the right. Ventricular ganglia of various sizes distribute at the basal level of both CV. Averagely, we found 3,848 ventricular neuronal somata per heart. The majority of somata were cholinergic, although ganglionic cells of different neurochemical phenotypes (positive for nNOS, ChAT/nNOS, or ChAT/TH) were also observed. Large and most numerous nerves proceeded within the epicardium. Most of endocardium and myocardium contained a network of nerve bundles and nerve fibers (NFs). But, a large number of thin nerves extended along the bundle of His and its branches. The majority of NFs were adrenergic, while cholinergic NFs were scarce yet more abundant than nitrergic ones. Sensory NFs positive for CGRP were the second most abundant phenotype after adrenergic NFs in all layers of the ventricular wall. Electron microscopy elucidated that ultrastructure of nerves varied between different areas of CV. The described structural organization of CV provides an anatomical basis for further functional and pathophysiological studies in the pig heart. Anat Rec, 2017. © 2017 Wiley Periodicals, Inc. Anat Rec, 300:1756-1780, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Dual fluorescence from an isonido ReIII rhenacarborane phosphine complex, [7,10-mu-H-7-CO-7,7-(PPh3)2-isonido-7,8,9-ReC2B7H9].

PubMed

Buckner, Steven W; Fischer, Matthew J; Jelliss, Paul A; Luo, Rensheng; Minteer, Shelley D; Rath, Nigam P; Siemiarczuk, Aleksander

2006-09-04

The complex [7,10-mu-H-7-CO-7,7-(PPh3)2-isonido-7,8,9-ReC2B7H9] has been synthesized by treatment of the complex salt [NHMe3][3,3-Cl2-3,3-(CO)2-closo-3,1,2-ReC2B9H11] with PPh3 in refluxing THF (tetrahydrofuran) and isolated as intensely colored orange-red microcrystals. Spectroscopic NMR and IR data have suggested that the product has a highly asymmetric structure with two inequivalent PPh3 ligands and a single CO ligand. Measurement of 11B NMR spectra in particular have indicated seven distinct boron vertexes, although the resulting cage degradation by removal of two BH vertexes was confirmed only following X-ray crystallographic analysis, which revealed the pentadecahedral isonido-7,8,9-ReC2B7 architecture. The 11B NMR resonances span an enormous chemical shift range (Deltadelta = 113), and this appears to be a direct consequence of the deshielding of the boron vertex directly opposite the quadrilateral |ReCCB| aperture. The new complex has been shown by electrochemical measurements to undergo a reversible one-electron oxidation. Digitally simulated cyclic voltammograms support a proposed square scheme (E(1/2) = 0.58, 0.69 V vs ferrocene) involving a reversible isonido-closo transition of the metallacarborane cage. Most unusually for a metallacarborane complex, ambient temperature solutions in CH2Cl2 and DMF have been shown to be intensely turquoise-blue fluorescent (lambda(em) = 442 nm, Phi = 0.012). Fluorescence spectroscopy measurements in MeTHF (2-methyltetrahydrofuran) glass at 77 K have indicated that the likely cause of such a broad emission is dual fluorescence (lambda(em) = 404, 505 nm), with both emissions displaying vibronic structure. Following excited-state lifetime decay analysis, the emissive behavior has been accredited to metal-perturbed 1IL states, with the lower energy emission arising from a slight geometric distortion of the initially excited complex.

Effect of various methods for rectum delineation on relative and absolute dose-volume histograms for prostate IMRT treatment planning

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

Kusumoto, Chiaki; Ohira, Shingo; Department of Medical Physics and Engineering, Osaka University Graduate School of Medicine, Suita

2016-07-01

Several reports have dealt with correlations of late rectal toxicity with rectal dose-volume histograms (DVHs) for high dose levels. There are 2 techniques to assess rectal volume for reception of a specific dose: relative-DVH (R-DVH, %) that indicates relative volume for a vertical axis, and absolute-DVH (A-DVH, cc) with its vertical axis showing absolute volume of the rectum. The parameters of DVH vary depending on the rectum delineation method, but the literature does not present any standardization of such methods. The aim of the present study was to evaluate the effects of different delineation methods on rectal DVHs. The enrollmentmore » for this study comprised 28 patients with high-risk localized prostate cancer, who had undergone intensity-modulated radiation therapy (IMRT) with the prescription dose of 78 Gy. The rectum was contoured with 4 different methods using 2 lengths, short (Sh) and long (Lg), and 2 cross sections, rectum (Rec) and rectal wall (Rw). Sh means the length from 1 cm above the seminal vesicles to 1 cm below the prostate and Lg the length from the rectosigmoid junction to the anus. Rec represents the entire rectal volume including the rectal contents and Rw the rectal volume of the area with a wall thickness of 4 mm. We compared dose-volume parameters by using 4 rectal contour methods for the same plan with the R-DVHs as well as the A-DVHs. For the high dose levels, the R-DVH parameters varied widely. The mean of V{sub 70} for Sh-Rw was the highest (19.4%) and nearly twice as high as that for Lg-Rec (10.4%). On the contrary, only small variations were observed in the A-DVH parameters (4.3, 4.3, 5.5, and 5.5 cc for Sh-Rw, Lg-Rw, Sh-Rec, and Lg-Rec, respectively). As for R-DVHs, the parameters of V{sub 70} varied depending on the rectal lengths (Sh-Rec vs Lg-Rec: R = 0.76; Sh-Rw vs Lg-Rw: R = 0.85) and cross sections (Sh-Rec vs Sh-Rw: R = 0.49; Lg-Rec vs Lg-Rw: R = 0.65). For A-DVHs, however, the parameters of Sh rectal A-DVHs hardly changed regardless of differences in rectal length at all dose levels. Moreover, at high dose levels (V{sub 70}), the parameters of A-DVHs showed less dependence on rectal cross sections (Sh-Rec vs Sh-Rw: R = 0.66; Lg-Rec vs Lg-Rw: R = 0.59). This study showed that A-DVHs were less dependent on the delineation methods than R-DVHs, especially for evaluating the rectal dose at higher dose levels. It can therefore be assumed that, in addition to R-DVHs, A-DVHs can be used for evaluating rectal toxicity.« less

SOS response in bacteria: Inhibitory activity of lichen secondary metabolites against Escherichia coli RecA protein.

PubMed

Bellio, Pierangelo; Di Pietro, Letizia; Mancini, Alisia; Piovano, Marisa; Nicoletti, Marcello; Brisdelli, Fabrizia; Tondi, Donatella; Cendron, Laura; Franceschini, Nicola; Amicosante, Gianfranco; Perilli, Mariagrazia; Celenza, Giuseppe

2017-06-15

RecA is a bacterial multifunctional protein essential to genetic recombination, error-prone replicative bypass of DNA damages and regulation of SOS response. The activation of bacterial SOS response is directly related to the development of intrinsic and/or acquired resistance to antimicrobials. Although recent studies directed towards RecA inactivation via ATP binding inhibition described a variety of micromolar affinity ligands, inhibitors of the DNA binding site are still unknown. Twenty-seven secondary metabolites classified as anthraquinones, depsides, depsidones, dibenzofurans, diphenyl-butenolides, paraconic acids, pseudo-depsidones, triterpenes and xanthones, were investigated for their ability to inhibit RecA from Escherichia coli. They were isolated in various Chilean regions from 14 families and 19 genera of lichens. The ATP hydrolytic activity of RecA was quantified detecting the generation of free phosphate in solution. The percentage of inhibition was calculated fixing at 100µM the concentration of the compounds. Deeper investigations were reserved to those compounds showing an inhibition higher than 80%. To clarify the mechanism of inhibition, the semi-log plot of the percentage of inhibition vs. ATP and vs. ssDNA, was evaluated. Only nine compounds showed a percentage of RecA inhibition higher than 80% (divaricatic, perlatolic, alpha-collatolic, lobaric, lichesterinic, protolichesterinic, epiphorellic acids, sphaerophorin and tumidulin). The half-inhibitory concentrations (IC 50 ) calculated for these compounds were ranging from 14.2µM for protolichesterinic acid to 42.6µM for sphaerophorin. Investigations on the mechanism of inhibition showed that all compounds behaved as uncompetitive inhibitors for ATP binding site, with the exception of epiphorellic acid which clearly acted as non-competitive inhibitor of the ATP site. Further investigations demonstrated that epiphorellic acid competitively binds the ssDNA binding site. Kinetic data were confirmed by molecular modelling binding predictions which shows that epiphorellic acid is expected to bind the ssDNA site into the L2 loop of RecA protein. In this paper the first RecA ssDNA binding site ligand is described. Our study sets epiphorellic acid as a promising hit for the development of more effective RecA inhibitors. In our drug discovery approach, natural products in general and lichen in particular, represent a successful source of active ligands and structural diversity. Copyright © 2017 Elsevier GmbH. All rights reserved.

Determination of the electron-capture coefficients and the concentration of free electrons in GaN from time-resolved photoluminescence

PubMed Central

Reshchikov, M. A.; McNamara, J. D.; Toporkov, M.; Avrutin, V.; Morkoç, H.; Usikov, A.; Helava, H.; Makarov, Yu.

2016-01-01

Point defects in high-purity GaN layers grown by hydride vapor phase epitaxy are studied by steady-state and time-resolved photoluminescence (PL). The electron-capture coefficients for defects responsible for the dominant defect-related PL bands in this material are found. The capture coefficients for all the defects, except for the green luminescence (GL1) band, are independent of temperature. The electron-capture coefficient for the GL1 band significantly changes with temperature because the GL1 band is caused by an internal transition in the related defect, involving an excited state acting as a giant trap for electrons. By using the determined electron-capture coefficients, the concentration of free electrons can be found at different temperatures by a contactless method. A new classification system is suggested for defect-related PL bands in undoped GaN. PMID:27901025

Deletion of the Clostridium thermocellum recA gene reveals that it is required for thermophilic plasmid replication but not plasmid integration at homologous DNA sequences.

PubMed

Groom, Joseph; Chung, Daehwan; Kim, Sun-Ki; Guss, Adam; Westpheling, Janet

2018-05-28

A limitation to the engineering of cellulolytic thermophiles is the availability of functional, thermostable (≥ 60 °C) replicating plasmid vectors for rapid expression and testing of genes that provide improved or novel fuel molecule production pathways. A series of plasmid vectors for genetic manipulation of the cellulolytic thermophile Caldicellulosiruptor bescii has recently been extended to Clostridium thermocellum, another cellulolytic thermophile that very efficiently solubilizes plant biomass and produces ethanol. While the C. bescii pBAS2 replicon on these plasmids is thermostable, the use of homologous promoters, signal sequences and genes led to undesired integration into the bacterial chromosome, a result also observed with less thermostable replicating vectors. In an attempt to overcome undesired plasmid integration in C. thermocellum, a deletion of recA was constructed. As expected, C. thermocellum ∆recA showed impaired growth in chemically defined medium and an increased susceptibility to UV damage. Interestingly, we also found that recA is required for replication of the C. bescii thermophilic plasmid pBAS2 in C. thermocellum, but it is not required for replication of plasmid pNW33N. In addition, the C. thermocellum recA mutant retained the ability to integrate homologous DNA into the C. thermocellum chromosome. These data indicate that recA can be required for replication of certain plasmids, and that a recA-independent mechanism exists for the integration of homologous DNA into the C. thermocellum chromosome. Understanding thermophilic plasmid replication is not only important for engineering of these cellulolytic thermophiles, but also for developing genetic systems in similar new potentially useful non-model organisms.

Comparison of ovulation induction and pregnacy outcomes in IVF patients with normal ovarian reserve who underwent long protocol with recombinant-FSH and highly purified-hMG.

PubMed

Celik, Cem; Sofuoğlu, Kenan; Selçuk, Selçuk; Asoğlu, Mehmet Reşit; Abalı, Remzi; Cetingöz, Elçin; Baykal, Bahar; Uludoğan, Mehmet

2011-01-01

Gonadotropins used in controlled ovarian stimulation have been increasing in number. Beside the recombinant preparations such as rec-FSH, rec-LH and h-hMG human-derived preparations have entered the market. We decided to compare the effects of rec-FSH and HP-hMG with GnRHa on embryo quality and pregnancy outcome in women undergoing an IVF cycle. In this study, data of 87 patients who had applied to our center from 2007 to 2008 and who had met all inclusion criteria, were analyzed. The patients underwent controlled ovarian hyperstimulation with HP-hMG, rec-FSH following down-regulation with a GnRHa in a long protocol, selected according to determined criteria and acquired embryo via IVF transfer. Of the 87 patients, 44 were stimulated with rec-FSH and 43 with HP-hMG. Distribution of infertility causes was similar between the groups. Duration of gonadotropin administration (p=0.677, Student's t-test) and the total dose of gonadotropin received (p=0.392, Student's t-test) were similar between the two groups. The fertilization rate of the rec-FSH group was significantly higher than the HP-hMG group (p=0.001, Mann-Whitney U test). No significant differences were observed between the study groups in biochemical, clinical and ongoing pregnancy parameters. The higher oocyte yield with rec-FSH does not result in higher quality embryos. LH activity in combination with FSH activity positively affected the oocyte and embryo maturation. Therefore, when we consider the clinical and ongoing pregnancy rates there is no inferiority of HP-hMG in controlled ovarian stimulation.

Comparison of ovulation induction and pregnacy outcomes in IVF patients with normal ovarian reserve who underwent long protocol with recombinant-FSH and highly purified-hMG

PubMed Central

Çelik, Cem; Sofuoğlu, Kenan; Selçuk, Selçuk; Asoğlu, Mehmet Reşit; Abalı, Remzi; Çetingöz, Elçin; Baykal, Bahar; Uludoğan, Mehmet

2011-01-01

Objective Gonadotropins used in controlled ovarian stimulation have been increasing in number. Beside the recombinant preparations such as rec-FSH, rec-LH and h-hMG human-derived preparations have entered the market. We decided to compare the effects of rec-FSH and HP-hMG with GnRHa on embryo quality and pregnancy outcome in women undergoing an IVF cycle. Material and Methods In this study, data of 87 patients who had applied to our center from 2007 to 2008 and who had met all inclusion criteria, were analyzed. The patients underwent controlled ovarian hyperstimulation with HP-hMG, rec-FSH following down-regulation with a GnRHa in a long protocol, selected according to determined criteria and acquired embryo via IVF transfer. Results Of the 87 patients, 44 were stimulated with rec-FSH and 43 with HP-hMG. Distribution of infertility causes was similar between the groups. Duration of gonadotropin administration (p=0.677, Student’s t-test) and the total dose of gonadotropin received (p=0.392, Student’s t-test) were similar between the two groups. The fertilization rate of the rec-FSH group was significantly higher than the HP-hMG group (p=0.001, Mann-Whitney U test). No significant differences were observed between the study groups in biochemical, clinical and ongoing pregnancy parameters. Conclusion The higher oocyte yield with rec-FSH does not result in higher quality embryos. LH activity in combination with FSH activity positively affected the oocyte and embryo maturation. Therefore, when we consider the clinical and ongoing pregnancy rates there is no inferiority of HP-hMG in controlled ovarian stimulation. PMID:24591951

Deletion of the Clostridium thermocellum recA Gene Reveals that it is Required for Thermophilic Plasmid Replication but not Plasmid Integration at Homologous DNA Sequences

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

Chung, Daehwan; Groom, Joseph; Kim, Sun-Ki

A limitation to the engineering of cellulolytic thermophiles is the availability of functional, thermostable (>/= 60 degrees C) replicating plasmid vectors for rapid expression and testing of genes that provide improved or novel fuel molecule production pathways. A series of plasmid vectors for genetic manipulation of the cellulolytic thermophile Caldicellulosiruptor bescii has recently been extended to Clostridium thermocellum, another cellulolytic thermophile that very efficiently solubilizes plant biomass and produces ethanol. While the C. bescii pBAS2 replicon on these plasmids is thermostable, the use of homologous promoters, signal sequences and genes led to undesired integration into the bacterial chromosome, a resultmore » also observed with less thermostable replicating vectors. In an attempt to overcome undesired plasmid integration in C. thermocellum, a deletion of recA was constructed. As expected, C. thermocellum ..delta..recA showed impaired growth in chemically defined medium and an increased susceptibility to UV damage. Interestingly, we also found that recA is required for replication of the C. bescii thermophilic plasmid pBAS2 in C. thermocellum, but it is not required for replication of plasmid pNW33N. In addition, the C. thermocellum recA mutant retained the ability to integrate homologous DNA into the C. thermocellum chromosome. These data indicate that recA can be required for replication of certain plasmids, and that a recA-independent mechanism exists for the integration of homologous DNA into the C. thermocellum chromosome. Understanding thermophilic plasmid replication is not only important for engineering of these cellulolytic thermophiles, but also for developing genetic systems in similar new potentially useful non-model organisms.« less

Nucleotide excision repair and recombination are engaged in repair of trans-4-hydroxy-2-nonenal adducts to DNA bases in Escherichia coli.

PubMed

Janowska, Beata; Komisarski, Marek; Prorok, Paulina; Sokołowska, Beata; Kuśmierek, Jarosław; Janion, Celina; Tudek, Barbara

2009-09-23

One of the major products of lipid peroxidation is trans-4-hydroxy-2-nonenal (HNE). HNE forms highly mutagenic and genotoxic adducts to all DNA bases. Using M13 phage lacZ system, we studied the mutagenesis and repair of HNE treated phage DNA in E. coli wild-type or uvrA, recA, and mutL mutants. These studies revealed that: (i) nucleotide excision and recombination, but not mismatch repair, are engaged in repair of HNE adducts when present in phage DNA replicating in E. coli strains; (ii) in the single uvrA mutant, phage survival was drastically decreased while mutation frequency increased, and recombination events constituted 48% of all mutations; (iii) in the single recA mutant, the survival and mutation frequency of HNE-modified M13 phage was slightly elevated in comparison to that in the wild-type bacteria. The majority of mutations in recA(-) strain were G:C --> T:A transversions, occurring within the sequence which in recA(+) strains underwent RecA-mediated recombination, and the entire sequence was deleted; (iv) in the double uvrA recA mutant, phage survival was the same as in the wild-type although the mutation frequency was higher than in the wild-type and recA single mutant, but lower than in the single uvrA mutant. The majority of mutations found in the latter strain were base substitutions, with G:C --> A:T transitions prevailing. These transitions could have resulted from high reactivity of HNE with G and C, and induction of SOS-independent mutations.

Nucleotide excision repair and recombination are engaged in repair of trans-4-hydroxy-2-nonenal adducts to DNA bases in Escherichia coli

PubMed Central

Janowska, Beata; Komisarski, Marek; Prorok, Paulina; Sokołowska, Beata; Kuśmierek, Jarosław; Janion, Celina; Tudek, Barbara

2009-01-01

One of the major products of lipid peroxidation is trans-4-hydroxy-2-nonenal (HNE). HNE forms highly mutagenic and genotoxic adducts to all DNA bases. Using M13 phage lacZ system, we studied the mutagenesis and repair of HNE treated phage DNA in E. coli wild-type or uvrA, recA, and mutL mutants. These studies revealed that: (i) nucleotide excision and recombination, but not mismatch repair, are engaged in repair of HNE adducts when present in phage DNA replicating in E. coli strains; (ii) in the single uvrA mutant, phage survival was drastically decreased while mutation frequency increased, and recombination events constituted 48 % of all mutations; (iii) in the single recA mutant, the survival and mutation frequency of HNE-modified M13 phage was slightly elevated in comparison to that in the wild-type bacteria. The majority of mutations in recA- strain were G:C → T:A transversions, occurring within the sequence which in recA+ strains underwent RecA-mediated recombination, and the entire sequence was deleted; (iv) in the double uvrA recA mutant, phage survival was the same as in the wild-type although the mutation frequency was higher than in the wild-type and recA single mutant, but lower than in the single uvrA mutant. The majority of mutations found in the latter strain were base substitutions, with G:C → A:T transitions prevailing. These transitions could have resulted from high reactivity of HNE with G and C, and induction of SOS-independent mutations. PMID:19834545

Follicular development and hormonal levels following highly purified or recombinant follicle-stimulating hormone administration in ovulatory women undergoing ovarian stimulation after pituitary suppression for in vitro fertilization: implications for implantation potential.

PubMed

Balasch, J; Fábregues, F; Creus, M; Peñarrubia, J; Vidal, E; Carmona, F; Puerto, B; Vanrell, J A

2000-01-01

The main goal in the present study was to compare follicular development and estradiol levels after ovarian stimulation in pituitary suppressed normally ovulating women undergoing IVF, using highly purified urinary follicle stimulating hormone (FSH) (u-FSH-HP) and recombinant FSH (rec-FSH). A secondary variable in our study was embryo implantation potential, which is closely related to appropriate follicular development and oocyte competence. For the main purpose of this study, 30 IVF patients (group 1) were treated during IVF consecutive cycles, using the same stimulation protocol, with u-FSH-HP in the first treatment study cycle and rec-FSH in the second one. As a control group (group 2) for implantation rates obtained in cycles treated with rec-FSH, 30 additional IVF patients were included who underwent a second IVF attempt again with u-FSH-HP. The total dose of FSH used and ovarian response obtained in terms of estradiol plasma levels and the total number of growing follicles on the day of human chronic gonadotropin (HCG) injection were similar in both treatment cycles in group 1 but better follicular dynamics and oocyte maturity were obtained with rec-FSH. The implantation rate was significantly higher in rec-FSH treated cycles in patients in group 1 than in control women (group 2). rec-FSH is more efficacious than u-FSH-HP when used in the same patient in inducing multiple follicular development in down-regulated cycles as indicated by ovarian performance and oocyte maturity. In addition, rec-FSH yields significantly higher implantation rates than u-FSH-HP when used in patients undergoing their second IVF attempt.

Chitosan-rectorite nanospheres immobilized on polystyrene fibrous mats via alternate electrospinning/electrospraying techniques for copper ions adsorption

NASA Astrophysics Data System (ADS)

Tu, Hu; Huang, Mengtian; Yi, Yang; Li, Zhenshun; Zhan, Yingfei; Chen, Jiajia; Wu, Yang; Shi, Xiaowen; Deng, Hongbing; Du, Yumin

2017-12-01

Chitosan (CS), as a kind of well characterized biopolymer, has been used for heavy metal adsorption due to its low cost and high efficacy. However, when used directly, chitosan particles had small surface area and weak mechanical strength which is unfavorable to metal adsorption and reused. Besides, it cannot be easily recycled that may cause a secondary pollution. In this paper, CS and layered silicate rectorite (REC) were fully mixed and the mixtures were subsequently electrosprayed nano-sized spheres, which were immobilized on the surface of electrospun polystyrene (PS) mats for metal adsorption. The morphology analysis taken from SEM confirmed that CS-REC nanospheres were loaded on the surface of PS fibrous mats. Small Angle X-ray diffraction patterns showed that the interlayer distance of REC in composite mats was enlarged by the intercalation of CS chains; such structure meant bigger surface area which was helpful for metal adsorption. The data of contact angle implied that PS mats coated with CS-REC nanospheres exhibited better hydrophilicity than PS mats, which was conductive to adsorption rate. Besides, the copper ions adsorption of composite mats was tested at different conditions including the adsorption time, the initial pH and the initial concentration of copper ion. The results demonstrated that PS mats coated with CS-REC nanospheres had the adsorption capacity up to 134 mg/g. In addition, the addition of REC containing Ca2+ could also improve the metal adsorption because of cation exchange. The desorption assay indicated that PS mats immobilized with CS and CS-REC still kept high adsorption ability which retained 74% and 78% after three adsorption-desorption cycles.

CT Imaging Biomarkers Predict Clinical Outcomes After Pancreatic Cancer Surgery

PubMed Central

Zhu, Liang; Shi, Xiaohua; Xue, Huadan; Wu, Huanwen; Chen, Ge; Sun, Hao; He, Yonglan; Jin, Zhengyu; Liang, Zhiyong; Zhang, Zhuoli

2016-01-01

Abstract This study aimed to determine whether changes in contrast-enhanced computed tomography (CT) parameters could predict postsurgery overall and progression-free survival (PFS) in pancreatic cancer patients. Seventy-nine patients with a final pathological diagnosis of pancreatic adenocarcinoma were included in this study from June 2008 to August 2012. Dynamic contrast-enhanced (DCE) CT of tumors was obtained before curative-intent surgery. Absolute enhancement change (AEC) and relative enhancement change (REC) were evaluated on DCE-CT. PFS and overall survival (OS) were compared based on CT enhancement patterns. The markers of fibrogenic alpha-smooth muscle antigen (α-SMA) and periostin in tumor specimens were evaluated by immunohistochemical staining. The χ2 test was performed to determine whether CT enhancement patterns were associated with α-SMA-periostin expression levels (recorded as positive or negative). Lower REC (<0.9) was associated with shorter PFS (HR 0.51, 95% CI: 0.31–0.89) and OS (HR 0.44, 95% CI: 0.25–0.78). The α-SMA and periostin expression level were negatively correlated with REC (both P = 0). Among several CT enhancement parameters, REC was the best predictor of patient postsurgery survival. Low REC was associated with a short progression-free time and poor survival. The pathological studies suggested that REC might be a reflection of cancer fibrogenic potential. PMID:26844495

Physical and Functional Interactions of Human Endogenous Retrovirus Proteins Np9 and Rec with the Promyelocytic Leukemia Zinc Finger Protein▿

PubMed Central

Denne, Miriam; Sauter, Marlies; Armbruester, Vivienne; Licht, Jonathan D.; Roemer, Klaus; Mueller-Lantzsch, Nikolaus

2007-01-01

Only few of the human endogenous retrovirus (HERV) sequences in the human genome can produce proteins. We have previously reported that (i) patients with germ cell tumors often make antibodies against proteins encoded by HERV-K elements, (ii) expression of the HERV-K rec gene in transgenic mice can interfere with germ cell development and induce carcinoma in situ, and (iii) HERV-K np9 transcript is overproduced in many tumors including breast cancers. Here we document that both Np9 and Rec physically and functionally interact with the promyelocytic leukemia zinc finger (PLZF) tumor suppressor, a transcriptional repressor and chromatin remodeler implicated in cancer and the self-renewal of spermatogonial stem cells. Interaction is mediated via two different central and C-terminal domains of Np9 and Rec and the C-terminal zinc fingers of PLZF. One major target of PLZF is the c-myc proto-oncogene. Coexpression of Np9 and Rec with PLZF abrogates the transcriptional repression of the c-myc gene promoter by PLZF and results in c-Myc overproduction, altered expression of c-Myc-regulated genes, and corresponding effects on cell proliferation and survival. Thus, the human endogenous retrovirus proteins Np9 and Rec may act oncogenically by derepressing c-myc through the inhibition of PLZF. PMID:17360752

The Effect of Recovery Duration on Technical Proficiency during Small Sided Games of Football.

PubMed

McLean, Scott; Kerhervé, Hugo; Naughton, Mitchell; Lovell, Geoff P; Gorman, Adam D; Solomon, Colin

2016-07-08

The aim of this study was to determine the effect of increasing the duration of the recovery periods separating serial bouts of small sided games (SSG) of football on technical skills (TS). Twelve semi-professional footballers (mean ± SD; age 21 ± 3 years; VO 2peak 64 ± 7 mL∙min∙kg -1 ; playing experience 15 ± 3 years) completed two SSG sessions, consisting of 3 vs. 3 players and 6 bouts of 2 min, separated by either 30 s recovery (REC-30) or 120 s recovery (REC-120). Sixteen TS, including passing, possession, and defensive related variables, and exercise intensity (heart rate, rating of perceived exertion, time motion descriptors) during the bouts were measured. Repeated measures ANOVA were used to determine differences between-conditions, for TS. The number of successful tackles was significantly higher, and the average time each team maintained possession was significantly lower in REC-120 compared to REC-30. There were no significant differences for all other TS variables, or exercise intensity measures between REC-30 and REC-120. Overall, a four-fold increase in the duration of recovery separating SSG bouts did not alter the technical skill execution of players. The experience and skill level of the players, combined with an apparent regulation of effort through pacing, may have assisted in the maintenance of technical skill execution.

Rec.2100 color gamut revelation using spectrally ultranarrow emitters

NASA Astrophysics Data System (ADS)

Genc, Sinan; Uguz, Mustafa; Yilmaz, Osman; Mutlugun, Evren

2017-11-01

We theoretically simulate the performance of ultranarrow emitters for the first time to achieve record high coverage for the International Telecommunication Union Radiocommunication Sector BT.2100 (Rec.2100) and National Television System Committee (NTSC) color gamut. Our results, employing more than 130-m parameter sets, include the investigation into peak emission wavelength and full width at half maximum (FWHM) values for three primaries that show ultranarrow emitters, i.e., nanoplatelets are potentially promising materials to fully cover the Rec.2100 color gamut. Using ultranarrow emitters having FWHM as low as 6 nm can provide the ability to attain 99.7% coverage area of the Rec.2100 color gamut as well as increasing the NTSC triangle to 133.7% with full coverage. The parameter set that provides possibility to fully reach Rec.2100 also has been shown to match with D65 white light by making use of the correct combination of those three primaries. Furthermore, we investigate the effect of the fourth color component on the CIE 1931 color space without sacrificing the achieved coverage percentages. The investigation into the fourth color component, cyan, is shown for the first time to enhance the Rec.2100 gamut area to 127.7% with 99.9% coverage. The fourth color component also provides an NTSC coverage ratio of 171.5%. The investigation into the potential of emitters with ultranarrow emission bandwidth holds great promise for future display applications.

Using the Emanuel et al. framework to assess ethical issues raised by a biomedical research ethics committee in South Africa.

PubMed

Tsoka-Gwegweni, Joyce M; Wassenaar, Douglas R

2014-12-01

The Emanuel, Wendler, and Grady framework was designed as a universal tool for use in many settings including developing countries. However, it is not known whether the work of African health research ethics committees (RECs) is compatible with this framework. The absence of any normative or empirical weighting of the eight principles within this framework suggests that different health RECs may raise some ethical issues more frequently than others when reviewing protocols. We used the Emanuel et al. framework to assess, code, and rank the most frequent ethical issues considered by a biomedical REC during review of research protocols for the years 2008 to 2012. We extracted data from the recorded minutes of a South African biomedical REC for the years 2008 to 2012, designed the data collection sheet according to the Emanuel et al. framework, and removed all identifiers during data processing and analysis. From the 98 protocols that we assessed, the most frequent issues that emerged were the informed consent, scientific validity, fair participant selection, and ongoing respect for participants. This study represents the first known attempt to analyze REC responses/minutes using the Emanuel et al. framework, and suggests that this framework may be useful in describing and categorizing the core activities of an REC. © The Author(s) 2014.

SparRec: An effective matrix completion framework of missing data imputation for GWAS

NASA Astrophysics Data System (ADS)

Jiang, Bo; Ma, Shiqian; Causey, Jason; Qiao, Linbo; Hardin, Matthew Price; Bitts, Ian; Johnson, Daniel; Zhang, Shuzhong; Huang, Xiuzhen

2016-10-01

Genome-wide association studies present computational challenges for missing data imputation, while the advances of genotype technologies are generating datasets of large sample sizes with sample sets genotyped on multiple SNP chips. We present a new framework SparRec (Sparse Recovery) for imputation, with the following properties: (1) The optimization models of SparRec, based on low-rank and low number of co-clusters of matrices, are different from current statistics methods. While our low-rank matrix completion (LRMC) model is similar to Mendel-Impute, our matrix co-clustering factorization (MCCF) model is completely new. (2) SparRec, as other matrix completion methods, is flexible to be applied to missing data imputation for large meta-analysis with different cohorts genotyped on different sets of SNPs, even when there is no reference panel. This kind of meta-analysis is very challenging for current statistics based methods. (3) SparRec has consistent performance and achieves high recovery accuracy even when the missing data rate is as high as 90%. Compared with Mendel-Impute, our low-rank based method achieves similar accuracy and efficiency, while the co-clustering based method has advantages in running time. The testing results show that SparRec has significant advantages and competitive performance over other state-of-the-art existing statistics methods including Beagle and fastPhase.

REDUCED CHLOROPLAST COVERAGE genes from Arabidopsis thaliana help to establish the size of the chloroplast compartment

DOE PAGES

Larkin, Robert M.; Stefano, Giovanni; Ruckle, Michael E.; ...

2016-02-09

Eukaryotic cells require mechanisms to establish the proportion of cellular volume devoted to particular organelles. These mechanisms are poorly understood. From a screen for plastid-to-nucleus signaling mutants in Arabidopsis thaliana, we cloned a mutant allele of a gene that encodes a protein of unknown function that is homologous to two other Arabidopsis genes of unknown function and Arabidopsis. In contrast to FRIENDLY, these three homologs of FRIENDLY are found only in photosynthetic organisms. Based on these data, we proposed that FRIENDLY expanded into a small gene family to help regulate the energy metabolism of cells that contain both mitochondria andmore » chloroplasts. Indeed, we found that knocking out these genes caused a number of chloroplast phenotypes, including a reduction in the proportion of cellular volume devoted to chloroplasts to 50% of wild type. Thus, we refer to these genes as REDUCED CHLOROPLAST COVERAGE (REC). The size of the chloroplast compartment was reduced most in rec1 mutants. The REC1 protein accumulated in the cytosol and the nucleus. REC1 was excluded from the nucleus when plants were treated with amitrole, which inhibits cell expansion and chloroplast function. Finally, we conclude that REC1 is an extraplastidic protein that helps to establish the size of the chloroplast compartment, and that signals derived from cell expansion or chloroplasts may regulate REC1.« less

RuvAB and RecG are not essential for the recovery of DNA synthesis following UV-induced DNA damage in Escherichia coli.

PubMed Central

Donaldson, Janet R; Courcelle, Charmain T; Courcelle, Justin

2004-01-01

Ultraviolet light induces DNA lesions that block the progression of the replication machinery. Several models speculate that the resumption of replication following disruption by UV-induced DNA damage requires regression of the nascent DNA or migration of the replication machinery away from the blocking lesion to allow repair or bypass of the lesion to occur. Both RuvAB and RecG catalyze branch migration of three- and four-stranded DNA junctions in vitro and are proposed to catalyze fork regression in vivo. To examine this possibility, we characterized the recovery of DNA synthesis in ruvAB and recG mutants. We found that in the absence of either RecG or RuvAB, arrested replication forks are maintained and DNA synthesis is resumed with kinetics that are similar to those in wild-type cells. The data presented here indicate that RecG- or RuvAB-catalyzed fork regression is not essential for DNA synthesis to resume following arrest by UV-induced DNA damage in vivo. PMID:15126385

RecQL4 is required for the association of Mcm10 and Ctf4 with replication origins in human cells

PubMed Central

Im, Jun-Sub; Park, Soon-Young; Cho, Won-Ho; Bae, Sung-Ho; Hurwitz, Jerard; Lee, Joon-Kyu

2015-01-01

Though RecQL4 was shown to be essential for the initiation of DNA replication in mammalian cells, its role in initiation is poorly understood. Here, we show that RecQL4 is required for the origin binding of Mcm10 and Ctf4, and their physical interactions and association with replication origins are controlled by the concerted action of both CDK and DDK activities. Although RecQL4-dependent binding of Mcm10 and Ctf4 to chromatin can occur in the absence of pre-replicative complex, their association with replication origins requires the presence of the pre-replicative complex and CDK and DDK activities. Their association with replication origins and physical interactions are also targets of the DNA damage checkpoint pathways which prevent initiation of DNA replication at replication origins. Taken together, the RecQL4-dependent association of Mcm10 and Ctf4 with replication origins appears to be the first important step controlled by S phase promoting kinases and checkpoint pathways for the initiation of DNA replication in human cells. PMID:25602958

SOS System Induction Inhibits the Assembly of Chemoreceptor Signaling Clusters in Salmonella enterica

PubMed Central

Irazoki, Oihane; Mayola, Albert; Campoy, Susana; Barbé, Jordi

2016-01-01

Swarming, a flagellar-driven multicellular form of motility, is associated with bacterial virulence and increased antibiotic resistance. In this work we demonstrate that activation of the SOS response reversibly inhibits swarming motility by preventing the assembly of chemoreceptor-signaling polar arrays. We also show that an increase in the concentration of the RecA protein, generated by SOS system activation, rather than another function of this genetic network impairs chemoreceptor polar cluster formation. Our data provide evidence that the molecular balance between RecA and CheW proteins is crucial to allow polar cluster formation in Salmonella enterica cells. Thus, activation of the SOS response by the presence of a DNA-injuring compound increases the RecA concentration, thereby disturbing the equilibrium between RecA and CheW and resulting in the cessation of swarming. Nevertheless, when the DNA-damage decreases and the SOS response is no longer activated, basal RecA levels and thus polar cluster assembly are reestablished. These results clearly show that bacterial populations moving over surfaces make use of specific mechanisms to avoid contact with DNA-damaging compounds. PMID:26784887

SOS System Induction Inhibits the Assembly of Chemoreceptor Signaling Clusters in Salmonella enterica.

PubMed

Irazoki, Oihane; Mayola, Albert; Campoy, Susana; Barbé, Jordi

2016-01-01

Swarming, a flagellar-driven multicellular form of motility, is associated with bacterial virulence and increased antibiotic resistance. In this work we demonstrate that activation of the SOS response reversibly inhibits swarming motility by preventing the assembly of chemoreceptor-signaling polar arrays. We also show that an increase in the concentration of the RecA protein, generated by SOS system activation, rather than another function of this genetic network impairs chemoreceptor polar cluster formation. Our data provide evidence that the molecular balance between RecA and CheW proteins is crucial to allow polar cluster formation in Salmonella enterica cells. Thus, activation of the SOS response by the presence of a DNA-injuring compound increases the RecA concentration, thereby disturbing the equilibrium between RecA and CheW and resulting in the cessation of swarming. Nevertheless, when the DNA-damage decreases and the SOS response is no longer activated, basal RecA levels and thus polar cluster assembly are reestablished. These results clearly show that bacterial populations moving over surfaces make use of specific mechanisms to avoid contact with DNA-damaging compounds.

A Distinct Class of Genome Rearrangements Driven by Heterologous Recombination.

PubMed

León-Ortiz, Ana María; Panier, Stephanie; Sarek, Grzegorz; Vannier, Jean-Baptiste; Patel, Harshil; Campbell, Peter J; Boulton, Simon J

2018-01-18

Erroneous DNA repair by heterologous recombination (Ht-REC) is a potential threat to genome stability, but evidence supporting its prevalence is lacking. Here we demonstrate that recombination is possible between heterologous sequences and that it is a source of chromosomal alterations in mitotic and meiotic cells. Mechanistically, we find that the RTEL1 and HIM-6/BLM helicases and the BRCA1 homolog BRC-1 counteract Ht-REC in Caenorhabditis elegans, whereas mismatch repair does not. Instead, MSH-2/6 drives Ht-REC events in rtel-1 and brc-1 mutants and excessive crossovers in rtel-1 mutant meioses. Loss of vertebrate Rtel1 also causes a variety of unusually large and complex structural variations, including chromothripsis, breakage-fusion-bridge events, and tandem duplications with distant intra-chromosomal insertions, whose structure are consistent with a role for RTEL1 in preventing Ht-REC during break-induced replication. Our data establish Ht-REC as an unappreciated source of genome instability that underpins a novel class of complex genome rearrangements that likely arise during replication stress. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Developing Single-Molecule TPM Experiments for Direct Observation of Successful RecA-Mediated Strand Exchange Reaction

PubMed Central

Fan, Hsiu-Fang; Cox, Michael M.; Li, Hung-Wen

2011-01-01

RecA recombinases play a central role in homologous recombination. Once assembled on single-stranded (ss) DNA, RecA nucleoprotein filaments mediate the pairing of homologous DNA sequences and strand exchange processes. We have designed two experiments based on tethered particle motion (TPM) to investigate the fates of the invading and the outgoing strands during E. coli RecA-mediated pairing and strand exchange at the single-molecule level in the absence of force. TPM experiments measure the tethered bead Brownian motion indicative of the DNA tether length change resulting from RecA binding and dissociation. Experiments with beads labeled on either the invading strand or the outgoing strand showed that DNA pairing and strand exchange occurs successfully in the presence of either ATP or its non-hydrolyzable analog, ATPγS. The strand exchange rates and efficiencies are similar under both ATP and ATPγS conditions. In addition, the Brownian motion time-courses suggest that the strand exchange process progresses uni-directionally in the 5′-to-3′ fashion, using a synapse segment with a wide and continuous size distribution. PMID:21765895

78 FR 16531 - Certain Electronic Devices for Capturing and Transmitting Images, and Components Thereof...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-15

... INTERNATIONAL TRADE COMMISSION [Investigation No. 337-TA-831] Certain Electronic Devices for Capturing and Transmitting Images, and Components Thereof; Commission Determination Not To Review an Initial... certain electronic devices for capturing and transmitting images, and components thereof. The complaint...

Development of Holmium-163 electron-capture spectroscopy with transition-edge sensors

DOE PAGES

Croce, Mark Philip; Rabin, Michael W.; Mocko, Veronika; ...

2016-08-01

Calorimetric decay energy spectroscopy of electron-capture-decaying isotopes is a promising method to achieve the sensitivity required for electron neutrino mass measurement. The very low total nuclear decay energy (Q EC < 3 keV) and short half-life (4570 years) of 163Ho make it attractive for high-precision electron-capture spectroscopy (ECS) near the kinematic endpoint, where the neutrino momentum goes to zero. In the ECS approach, an electron-capture-decaying isotope is embedded inside a microcalorimeter designed to capture and measure the energy of all the decay radiation except that of the escaping neutrino. We have developed a complete process for proton irradiation-based isotope production,more » isolation, and purification of 163Ho. We have developed transition-edge sensors for this measurement and methods for incorporating 163Ho into high-resolution microcalorimeters, and have measured the electron-capture spectrum of 163Ho. Finally, we present our work in these areas and discuss the measured spectrum and its comparison to current theory.« less

Development of Holmium-163 electron-capture spectroscopy with transition-edge sensors

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

Croce, Mark Philip; Rabin, Michael W.; Mocko, Veronika

Calorimetric decay energy spectroscopy of electron-capture-decaying isotopes is a promising method to achieve the sensitivity required for electron neutrino mass measurement. The very low total nuclear decay energy (Q EC < 3 keV) and short half-life (4570 years) of 163Ho make it attractive for high-precision electron-capture spectroscopy (ECS) near the kinematic endpoint, where the neutrino momentum goes to zero. In the ECS approach, an electron-capture-decaying isotope is embedded inside a microcalorimeter designed to capture and measure the energy of all the decay radiation except that of the escaping neutrino. We have developed a complete process for proton irradiation-based isotope production,more » isolation, and purification of 163Ho. We have developed transition-edge sensors for this measurement and methods for incorporating 163Ho into high-resolution microcalorimeters, and have measured the electron-capture spectrum of 163Ho. Finally, we present our work in these areas and discuss the measured spectrum and its comparison to current theory.« less

Renewable Energy Certificates (RECs)

EPA Pesticide Factsheets

Renewable Energy Certificates (RECs), are tradable, non-tangible energy commodities in the United States that represent proof that 1 megawatt-hour (MWh) of electricity was generated from an eligible renewable energy resource.

Distinct functions of human RecQ helicases during DNA replication.

PubMed

Urban, Vaclav; Dobrovolna, Jana; Janscak, Pavel

2017-06-01

DNA replication is the most vulnerable process of DNA metabolism in proliferating cells and therefore it is tightly controlled and coordinated with processes that maintain genomic stability. Human RecQ helicases are among the most important factors involved in the maintenance of replication fork integrity, especially under conditions of replication stress. RecQ helicases promote recovery of replication forks being stalled due to different replication roadblocks of either exogenous or endogenous source. They prevent generation of aberrant replication fork structures and replication fork collapse, and are involved in proper checkpoint signaling. The essential role of human RecQ helicases in the genome maintenance during DNA replication is underlined by association of defects in their function with cancer predisposition. Copyright © 2016 Elsevier B.V. All rights reserved.

Recognizing Risk and Vulnerability in Research Ethics: Imagining the "What Ifs?"

PubMed

Peter, Elizabeth; Friedland, Judith

2017-04-01

Research ethics committees (RECs) may misunderstand the vulnerability of participants, given their distance from the field. What RECs identify as the vulnerabilities that were not adequately recognized in protocols and how they attempt to protect the perceived vulnerability of participants and mitigate risks were examined using the response letters sent to researchers by three university-based RECs. Using a critical qualitative method informed by feminist ethics, we identified an overarching theme of recognizing and responding to cascading vulnerabilities and four subthemes: identifying vulnerable groups, recognizing potentially risky research, imagining the "what ifs," and mitigating perceived risks. An ethics approach that is up-close, as opposed to distant, is needed to foster closer relationships among participants, researchers, and RECs and to understand participant vulnerability and strength better.

Ultra-fast electron capture by electrosterically-stabilized gold nanoparticles.

PubMed

Ghandi, Khashayar; Findlater, Alexander D; Mahimwalla, Zahid; MacNeil, Connor S; Awoonor-Williams, Ernest; Zahariev, Federico; Gordon, Mark S

2015-07-21

Ultra-fast pre-solvated electron capture has been observed for aqueous solutions of room-temperature ionic liquid (RTIL) surface-stabilized gold nanoparticles (AuNPs; ∼9 nm). The extraordinarily large inverse temperature dependent rate constants (k(e)∼ 5 × 10(14) M(-1) s(-1)) measured for the capture of electrons in solution suggest electron capture by the AuNP surface that is on the timescale of, and therefore in competition with, electron solvation and electron-cation recombination reactions. The observed electron transfer rates challenge the conventional notion that radiation induced biological damage would be enhanced in the presence of AuNPs. On the contrary, AuNPs stabilized by non-covalently bonded ligands demonstrate the potential to quench radiation-induced electrons, indicating potential applications in fields ranging from radiation therapy to heterogeneous catalysis.

Helical filaments of human Dmc1 protein on single-stranded DNA: a cautionary tale.

PubMed

Yu, Xiong; Egelman, Edward H

2010-08-20

Proteins in the RecA/Rad51/RadA family form nucleoprotein filaments on DNA that catalyze a strand exchange reaction as part of homologous genetic recombination. Because of the centrality of this system to many aspects of DNA repair, the generation of genetic diversity, and cancer when this system fails or is not properly regulated, these filaments have been the object of many biochemical and biophysical studies. A recent paper has argued that the human Dmc1 protein, a meiotic homolog of bacterial RecA and human Rad51, forms filaments on single-stranded DNA with approximately 9 subunits per turn in contrast to the filaments formed on double-stranded DNA with approximately 6.4 subunits per turn and that the stoichiometry of DNA binding is different between these two filaments. We show using scanning transmission electron microscopy that the Dmc1 filament formed on single-stranded DNA has a mass per unit length expected from approximately 6.5 subunits per turn. More generally, we show how ambiguities in helical symmetry determination can generate incorrect solutions and why one sometimes must use other techniques, such as biochemistry, metal shadowing, or scanning transmission electron microscopy, to resolve these ambiguities. While three-dimensional reconstruction of helical filaments from EM images is a powerful tool, the intrinsic ambiguities that may be present with limited resolution are not sufficiently appreciated. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

Measurement of the beta+ and orbital electron-capture decay rates in fully ionized, hydrogenlike, and heliumlike 140Pr ions.

PubMed

Litvinov, Yu A; Bosch, F; Geissel, H; Kurcewicz, J; Patyk, Z; Winckler, N; Batist, L; Beckert, K; Boutin, D; Brandau, C; Chen, L; Dimopoulou, C; Fabian, B; Faestermann, T; Fragner, A; Grigorenko, L; Haettner, E; Hess, S; Kienle, P; Knöbel, R; Kozhuharov, C; Litvinov, S A; Maier, L; Mazzocco, M; Montes, F; Münzenberg, G; Musumarra, A; Nociforo, C; Nolden, F; Pfützner, M; Plass, W R; Prochazka, A; Reda, R; Reuschl, R; Scheidenberger, C; Steck, M; Stöhlker, T; Torilov, S; Trassinelli, M; Sun, B; Weick, H; Winkler, M

2007-12-31

We report on the first measurement of the beta+ and orbital electron-capture decay rates of 140Pr nuclei with the simplest electron configurations: bare nuclei, hydrogenlike, and heliumlike ions. The measured electron-capture decay constant of hydrogenlike 140Pr58+ ions is about 50% larger than that of heliumlike 140Pr57+ ions. Moreover, 140Pr ions with one bound electron decay faster than neutral 140Pr0+ atoms with 59 electrons. To explain this peculiar observation one has to take into account the conservation of the total angular momentum, since only particular spin orientations of the nucleus and of the captured electron can contribute to the allowed decay.

Accelerated Electron-Beam Formation with a High Capture Coefficient in a Parallel Coupled Accelerating Structure

NASA Astrophysics Data System (ADS)

Chernousov, Yu. D.; Shebolaev, I. V.; Ikryanov, I. M.

2018-01-01

An electron beam with a high (close to 100%) coefficient of electron capture into the regime of acceleration has been obtained in a linear electron accelerator based on a parallel coupled slow-wave structure, electron gun with microwave-controlled injection current, and permanent-magnet beam-focusing system. The high capture coefficient was due to the properties of the accelerating structure, beam-focusing system, and electron-injection system. Main characteristics of the proposed systems are presented.

RecA: a universal drug target in pathogenic bacteria.

PubMed

Pavlopoulou, Athanasia

2018-01-01

The spread of bacterial infectious diseases due to the development of resistance to antibiotic drugs in pathogenic bacteria is an emerging global concern. Therefore, the efficacious management and prevention of bacterial infections are major public health challenges. RecA is a pleiotropic recombinase protein that has been demonstrated to be implicated strongly in the bacterial drug resistance, survival and pathogenicity. In this minireview, RecA's role in the development of antibiotic resistance and its potential as an antimicrobial drug target are discussed.

Simulation of spiral instabilities in wide-gap spherical Couette flow

NASA Astrophysics Data System (ADS)

Abbas, Suhail; Yuan, Li; Shah, Abdullah

2018-04-01

We numerically study the wide-gap spherical Couette flow between two concentric spheres with the inner sphere rotating and the outer one stationary. Two wide-gap clearance ratios, β =({R}2-{R}1)/{R}1=0.33 and 0.50, are chosen to investigate the transition scenarios of the spiral instabilities with increasing Reynolds number ({{Re}}). For β =0.33, we first obtain the steady 1-vortex flow at {{Re}} = 700 by using the 1-vortex flow for a medium gap β =0.18 at {{Re}} = 700 as the initial condition. The 1-vortex flow for β =0.33 exists for {Re} \\in [450,2050] and it collapses back to the basic flow when {Re} > 2050. We then detect spiral instabilities by increasing the Reynolds number gradually. The basic flow becomes unstable at {{Re}}{{c}1} = 2900 where spiral waves of wavenumber m = 6 appear first. Increasing the Reynolds number further, the wavenumber decreases to 5 and 4 at {{Re}}{{c}2} = 3000 and {{Re}}{{c}3} = 4000 respectively. The flow becomes turbulent when {Re} > 4500. For β =0.50, no Taylor vortices are found. The basic flow becomes unstable at {{Re}}{{c}1} = 1280 where spiral waves of wavenumber m = 5 occur first. As the Reynolds number is increased, the wavenumber becomes 4 at {{Re}}{{c}2} = 1700, 5 again at {{Re}}{{c}3} = 1800, 4 at {{Re}}{{c}4} = 2000, and becomes 3 at {{Re}}{{c}5} = 2200 while the flow becomes turbulent for {Re} > 2200. The computed rotational frequencies as a function of the Reynolds number for spiral waves of wavenumber m = 5, 4 and 3 are in good agreement with previous experimental results. The present transition scenario of the spiral wavenumber with increasing Reynolds number for β =0.33 is the same as that of Egbers and Rath (1995 Acta Mech. 111 125-40), while for β =0.50, it is only partially similar to those of Wulf et al (1999 Phys. Fluids 11 1359-72) and Egbers and Rath (1995 Acta Mech. 111 125-40).

Immunogenicity of a recombinant infectious hematopoietic necrosis virus glycoprotein produced in insect cells.

PubMed

Cain, K D; LaPatra, S E; Shewmaker, B; Jones, J; Byrne, K M; Ristow, S S

1999-04-15

A recombinant infectious hematopoietic necrosis virus (IHNV) glycoprotein (G protein), produced in Spodoptera frugiperda (Sf9) cells following infection with a baculovirus vector containing the full-length (1.6 kb) glycoprotein gene, provided very limited protection in rainbow trout Oncorhynchus mykiss challenged with IHNV. Fish were injected intraperitoneally (i.p.) with Sf9 cells grown at 20 degrees C (RecGlow) or 27 degrees C (RecGhigh) expressing the glycoprotein gene. Various antigen (Ag) preparations were administered to adult rainbow trout or rainbow trout fry. Sera collected from adult fish were evaluated for IHNV neutralization activity by a complement-dependent neutralization assay. Anti-IHNV neutralizing activity was observed in sera, but the percent of fish responding was significantly lower (p < 0.05) in comparison to fish immunized with a low virulence strain of IHNV (LV-IHNV). A small number of fish immunized with RecGlow or RecGhigh possessed IHNV G protein specific antibodies (Abs) in their serum. Cumulative mortality (CM) of rainbow trout fry (mean weight, 1 g) vaccinated by i.p. injection of freeze/thawed Sf9 cells producing RecGlow was 18% in initial trials following IHNV challenge. This level of protection was significant (p < 0.05) but was not long lasting, and neutralizing Abs were not detected in pooled serum samples. When trout fry (mean weight, 0.6 g) were vaccinated with supernatant collected from sonicated Sf9 cells, Sf9 cells producing RecGlow, or Sf9 cells producing RecGhigh, CM averaged 46%. Protection was enhanced over negative controls, but not the positive controls (2% CM), suggesting that in the first trial soluble cellular proteins may have provided some level of non-specific protection, regardless of recombinant protein expression. Although some immunity was elicited in fish, and RecGlow provided short-term protection from IHNV, Ab-mediated protection could not be demonstrated. The results suggest that recombinant G proteins produced in insect cells lack the immunogenicity associated with vaccination of fish with an attenuated strain of IHNV.

APPLYING RESEARCH ETHICS GUIDELINES: THE VIEW FROM A SUB-SAHARAN RESEARCH ETHICS COMMITTEE

PubMed Central

Henderson, Gail E.; Corneli, Amy L.; Mahoney, David B.; Nelson, Daniel K.; Mwansambo, Charles

2009-01-01

Considerable variation has been demonstrated in applying regulations across research ethics committees (RECs) in the U.S., U.K., and European nations. With the rise of international research collaborations, RECs in developing countries apply a variety of international regulations. We conducted a qualitative descriptive pilot study with members of the national REC in Malawi to determine criteria they use to review research, and their views on international collaborations. Qualitative content analysis demonstrated that international guidelines are interpreted in light of local African conditions such that emphasis is placed on examining benefit to the community and ensuring the informed consent process translates concepts in locally-meaningful ways. Members suggest that RECs often must comply with regulations that do not fit local conditions. Recommendations are provided for improving such international collaborations. PMID:19385794

Use of RecA protein to enrich for homologous genes in a genomic library

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

Taidi-Laskowski, B.; Grumet, F.C.; Tyan, D.

1988-08-25

RecA protein-coated probe has been utilized to enrich genomic digests for desired genes in order to facilitate cloning from genomic libraries. Using a previously cloned HLA-B27 gene as the recA-coated enrichment probe, the authors obtained a mean 108x increase in the ratio of specific to nonspecific plaques in lambda libraries screened for B27 variant alleles of estimated 99% homology to the probe. Class I genes of lesser homology were less enriched. Loss of genomic DNA during the enrichment procedure can, however, restrict application of this technique whenever starting genomic DNA is very limited. Nevertheless, the impressive reduction in cloning effortmore » and material makes recA enrichment a useful new tool for cloning homologous genes from genomic DNA.« less

From "a Fair Game" to "a Form of Covert Research": Research Ethics Committee Members' Differing Notions of Consent and Potential Risk to Participants Within Social Media Research.

PubMed

Hibbin, R A; Samuel, G; Derrick, G E

2018-04-01

Social media (SM) research presents new challenges for research ethics committees (RECs) who must balance familiar ethical principles with new notions of public availability. This article qualitatively examines how U.K. REC members view this balance in terms of risk and consent. While it found significant variance overall, there were discernible experience-based trends. REC members with less experience of reviewing SM held inflexible notions of consent and risk that could be categorized as either relying on traditional notions of requiring direct consent, or viewing publicly available data as "fair game." More experienced REC members took a more nuanced approach to data use and consent. We conclude that the more nuanced approach should be best practice during ethical review of SM research.

Exploring Modality Compatibility in the Response-Effect Compatibility Paradigm.

PubMed

Földes, Noémi; Philipp, Andrea M; Badets, Arnaud; Koch, Iring

2017-01-01

According to ideomotor theory , action planning is based on anticipatory perceptual representations of action-effects. This aspect of action control has been investigated in studies using the response-effect compatibility (REC) paradigm, in which responses have been shown to be facilitated if ensuing perceptual effects share codes with the response based on dimensional overlap (i.e., REC). Additionally, according to the notion of ideomotor compatibility, certain response-effect (R-E) mappings will be stronger than others because some response features resemble the anticipated sensory response effects more strongly than others (e.g., since vocal responses usually produce auditory effects, an auditory stimulus should be anticipated in a stronger manner following vocal responses rather than following manual responses). Yet, systematic research on this matter is lacking. In the present study, two REC experiments aimed to explore the influence of R-E modality mappings. In Experiment 1, vocal number word responses produced visual effects on the screen (digits vs. number words; i.e., visual-symbolic vs. visual-verbal effect codes). The REC effect was only marginally larger for visual-verbal than for visual-symbolic effects. Using verbal effect codes in Experiment 2, we found that the REC effect was larger with auditory-verbal R-E mapping than with visual-verbal R-E mapping. Overall, the findings support the hypothesis of a role of R-E modality mappings in REC effects, suggesting both further evidence for ideomotor accounts as well as code-specific and modality-specific contributions to effect anticipation.

A genomic island integrated into recA of Vibrio cholerae contains a divergent recA and provides multi-pathway protection from DNA damage.

PubMed

Rapa, Rita A; Islam, Atiqul; Monahan, Leigh G; Mutreja, Ankur; Thomson, Nicholas; Charles, Ian G; Stokes, Harold W; Labbate, Maurizio

2015-04-01

Lateral gene transfer (LGT) has been crucial in the evolution of the cholera pathogen, Vibrio cholerae. The two major virulence factors are present on two different mobile genetic elements, a bacteriophage containing the cholera toxin genes and a genomic island (GI) containing the intestinal adhesin genes. Non-toxigenic V. cholerae in the aquatic environment are a major source of novel DNA that allows the pathogen to morph via LGT. In this study, we report a novel GI from a non-toxigenic V. cholerae strain containing multiple genes involved in DNA repair including the recombination repair gene recA that is 23% divergent from the indigenous recA and genes involved in the translesion synthesis pathway. This is the first report of a GI containing the critical gene recA and the first report of a GI that targets insertion into a specific site within recA. We show that possession of the island in Escherichia coli is protective against DNA damage induced by UV-irradiation and DNA targeting antibiotics. This study highlights the importance of genetic elements such as GIs in the evolution of V. cholerae and emphasizes the importance of environmental strains as a source of novel DNA that can influence the pathogenicity of toxigenic strains. © 2014 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Combining two open source tools for neural computation (BioPatRec and Netlab) improves movement classification for prosthetic control.

PubMed

Prahm, Cosima; Eckstein, Korbinian; Ortiz-Catalan, Max; Dorffner, Georg; Kaniusas, Eugenijus; Aszmann, Oskar C

2016-08-31

Controlling a myoelectric prosthesis for upper limbs is increasingly challenging for the user as more electrodes and joints become available. Motion classification based on pattern recognition with a multi-electrode array allows multiple joints to be controlled simultaneously. Previous pattern recognition studies are difficult to compare, because individual research groups use their own data sets. To resolve this shortcoming and to facilitate comparisons, open access data sets were analysed using components of BioPatRec and Netlab pattern recognition models. Performances of the artificial neural networks, linear models, and training program components were compared. Evaluation took place within the BioPatRec environment, a Matlab-based open source platform that provides feature extraction, processing and motion classification algorithms for prosthetic control. The algorithms were applied to myoelectric signals for individual and simultaneous classification of movements, with the aim of finding the best performing algorithm and network model. Evaluation criteria included classification accuracy and training time. Results in both the linear and the artificial neural network models demonstrated that Netlab's implementation using scaled conjugate training algorithm reached significantly higher accuracies than BioPatRec. It is concluded that the best movement classification performance would be achieved through integrating Netlab training algorithms in the BioPatRec environment so that future prosthesis training can be shortened and control made more reliable. Netlab was therefore included into the newest release of BioPatRec (v4.0).

Inhibitors of LexA Autoproteolysis and the Bacterial SOS Response Discovered by an Academic-Industry Partnership.

PubMed

Mo, Charlie Y; Culyba, Matthew J; Selwood, Trevor; Kubiak, Jeffrey M; Hostetler, Zachary M; Jurewicz, Anthony J; Keller, Paul M; Pope, Andrew J; Quinn, Amy; Schneck, Jessica; Widdowson, Katherine L; Kohli, Rahul M

2018-03-09

The RecA/LexA axis of the bacterial DNA damage (SOS) response is a promising, yet nontraditional, drug target. The SOS response is initiated upon genotoxic stress, when RecA, a DNA damage sensor, induces LexA, the SOS repressor, to undergo autoproteolysis, thereby derepressing downstream genes that can mediate DNA repair and accelerate mutagenesis. As genetic inhibition of the SOS response sensitizes bacteria to DNA damaging antibiotics and decreases acquired resistance, inhibitors of the RecA/LexA axis could potentiate our current antibiotic arsenal. Compounds targeting RecA, which has many mammalian homologues, have been reported; however, small-molecules targeting LexA autoproteolysis, a reaction unique to the prokaryotic SOS response, have remained elusive. Here, we describe the logistics and accomplishments of an academic-industry partnership formed to pursue inhibitors against the RecA/LexA axis. A novel fluorescence polarization assay reporting on RecA-induced self-cleavage of LexA enabled the screening of 1.8 million compounds. Follow-up studies on select leads show distinct activity patterns in orthogonal assays, including several with activity in cell-based assays reporting on SOS activation. Mechanistic assays demonstrate that we have identified first-in-class small molecules that specifically target the LexA autoproteolysis step in SOS activation. Our efforts establish a realistic example for navigating academic-industry partnerships in pursuit of anti-infective drugs and offer starting points for dedicated lead optimization of SOS inhibitors that could act as adjuvants for current antibiotics.

Evaluation of an exposure assessment used in epidemiological studies of diesel exhaust and lung cancer in underground mines

PubMed Central

Crump, Kenny; Van Landingham, Cynthia

2012-01-01

NIOSH/NCI (National Institute of Occupational Safety and Health and National Cancer Institute) developed exposure estimates for respirable elemental carbon (REC) as a surrogate for exposure to diesel exhaust (DE) for different jobs in eight underground mines by year beginning in the 1940s—1960s when diesel equipment was first introduced into these mines. These estimates played a key role in subsequent epidemiological analyses of the potential relationship between exposure to DE and lung cancer conducted in these mines. We report here on a reanalysis of some of the data from this exposure assessment. Because samples of REC were limited primarily to 1998–2001, NIOSH/NCI used carbon monoxide (CO) as a surrogate for REC. In addition, because CO samples were limited, particularly in the earlier years, they used the ratio of diesel horsepower (HP) to the mine air exhaust rate as a surrogate for CO. There are considerable uncertainties connected with each of these surrogate-based steps. The estimates of HP appear to involve considerable uncertainty, although we had no data upon which to evaluate the magnitude of this uncertainty. A sizable percentage (45%) of the CO samples used in the HP to CO model was below the detection limit which required NIOSH/NCI to assign CO values to these samples. In their preferred REC estimates, NIOSH/NCI assumed a linear relation between C0 and REC, although they provided no credible support for that assumption. Their assumption of a stable relationship between HP and CO also is questionable, and our reanalysis found a statistically significant relationship in only one-half of the mines. We re-estimated yearly REC exposures mainly using NIOSH/NCI methods but with some important differences: (i) rather than simply assuming a linear relationship, we used data from the mines to estimate the CO—REC relationship; (ii) we used a different method for assigning values to nondetect CO measurements; and (iii) we took account of statistical uncertainty to estimate bounds for REC exposures. This exercise yielded significantly different exposure estimates than estimated by NIOSH/NCI. However, this analysis did not incorporate the full range of uncertainty in REC exposures because of additional uncertainties in the assumptions underlying the modeling and in the underlying data (e.g. HP and mine exhaust rates). Estimating historical exposures in a cohort is generally a very difficult undertaking. However, this should not prevent one from recognizing the uncertainty in the resulting estimates in any use made of them. PMID:22594934

Dynamics of heart rate variability analysed through nonlinear and linear dynamics is already impaired in young type 1 diabetic subjects.

PubMed

Souza, Naiara M; Giacon, Thais R; Pacagnelli, Francis L; Barbosa, Marianne P C R; Valenti, Vitor E; Vanderlei, Luiz C M

2016-10-01

Autonomic diabetic neuropathy is one of the most common complications of type 1 diabetes mellitus, and studies using heart rate variability to investigate these individuals have shown inconclusive results regarding autonomic nervous system activation. Aims To investigate the dynamics of heart rate in young subjects with type 1 diabetes mellitus through nonlinear and linear methods of heart rate variability. We evaluated 20 subjects with type 1 diabetes mellitus and 23 healthy control subjects. We obtained the following nonlinear indices from the recurrence plot: recurrence rate (REC), determinism (DET), and Shanon entropy (ES), and we analysed indices in the frequency (LF and HF in ms2 and normalised units - nu - and LF/HF ratio) and time domains (SDNN and RMSSD), through analysis of 1000 R-R intervals, captured by a heart rate monitor. There were reduced values (p<0.05) for individuals with type 1 diabetes mellitus compared with healthy subjects in the following indices: DET, REC, ES, RMSSD, SDNN, LF (ms2), and HF (ms2). In relation to the recurrence plot, subjects with type 1 diabetes mellitus demonstrated lower recurrence and greater variation in their plot, inter-group and intra-group, respectively. Young subjects with type 1 diabetes mellitus have autonomic nervous system behaviour that tends to randomness compared with healthy young subjects. Moreover, this behaviour is related to reduced sympathetic and parasympathetic activity of the autonomic nervous system.

Ethics committees and the legality of research

PubMed Central

Douglas, T M

2007-01-01

One role of research ethics committees (RECs) is to assess the ethics of proposed health research. In some countries, RECs are also instructed to assess its legality. However, in other countries they are explicitly instructed not to do so. In this paper, I defend the claim that public policy should instruct RECs not to assess the legality of proposed research (“the Claim”). I initially defend a presumption in favour of the Claim, citing reasons for making research institutions solely responsible for assessing the legality of their own research. I then consider three arguments against the Claim which may over‐ride this presumption—namely, that policy should instruct RECs to assess the legality of research because (1) doing so would minimise the costs of assessing the legality of research, (2) whether research is legal may partly determine whether it is ethical and (3) whether research is legal may constitute evidence for whether it is ethical. I reject the first two arguments and note that whether the third succeeds depends on the answer to a more fundamental question about the appropriate nature of REC ethical deliberation. I end with a brief discussion of this question, tentatively concluding that the third argument also fails. PMID:18055906

Direct Single-Molecule Observation of Mode and Geometry of RecA-Mediated Homology Search.

PubMed

Lee, Andrew J; Endo, Masayuki; Hobbs, Jamie K; Wälti, Christoph

2018-01-23

Genomic integrity, when compromised by accrued DNA lesions, is maintained through efficient repair via homologous recombination. For this process the ubiquitous recombinase A (RecA), and its homologues such as the human Rad51, are of central importance, able to align and exchange homologous sequences within single-stranded and double-stranded DNA in order to swap out defective regions. Here, we directly observe the widely debated mechanism of RecA homology searching at a single-molecule level using high-speed atomic force microscopy (HS-AFM) in combination with tailored DNA origami frames to present the reaction targets in a way suitable for AFM-imaging. We show that RecA nucleoprotein filaments move along DNA substrates via short-distance facilitated diffusions, or slides, interspersed with longer-distance random moves, or hops. Importantly, from the specific interaction geometry, we find that the double-stranded substrate DNA resides in the secondary DNA binding-site within the RecA nucleoprotein filament helical groove during the homology search. This work demonstrates that tailored DNA origami, in conjunction with HS-AFM, can be employed to reveal directly conformational and geometrical information on dynamic protein-DNA interactions which was previously inaccessible at an individual single-molecule level.

A non-canonical DNA structure enables homologous recombination in various genetic systems.

PubMed

Masuda, Tokiha; Ito, Yutaka; Terada, Tohru; Shibata, Takehiko; Mikawa, Tsutomu

2009-10-30

Homologous recombination, which is critical to genetic diversity, depends on homologous pairing (HP). HP is the switch from parental to recombinant base pairs, which requires expansion of inter-base pair spaces. This expansion unavoidably causes untwisting of the parental double-stranded DNA. RecA/Rad51-catalyzed ATP-dependent HP is extensively stimulated in vitro by negative supercoils, which compensates for untwisting. However, in vivo, double-stranded DNA is relaxed by bound proteins and thus is an unfavorable substrate for RecA/Rad51. In contrast, Mhr1, an ATP-independent HP protein required for yeast mitochondrial homologous recombination, catalyzes HP without the net untwisting of double-stranded DNA. Therefore, we questioned whether Mhr1 uses a novel strategy to promote HP. Here, we found that, like RecA, Mhr1 induced the extension of bound single-stranded DNA. In addition, this structure was induced by all evolutionarily and structurally distinct HP proteins so far tested, including bacterial RecO, viral RecT, and human Rad51. Thus, HP includes the common non-canonical DNA structure and uses a common core mechanism, independent of the species of HP proteins. We discuss the significance of multiple types of HP proteins.

The establishment of research ethics consultation services (RECS): an emerging research resource.

PubMed

McCormick, Jennifer B; Sharp, Richard R; Ottenberg, Abigale L; Reider, Carson R; Taylor, Holly A; Wilfond, Benjamin S

2013-02-01

Emphasis on translational research to facilitate progression from the laboratory into the community also creates a dynamic in which ethics and social policy questions and solutions are ever pressing. In response, academic institutions are creating Research Ethics Consultation Services (RECS). All Clinical Translational Science Award institutions were surveyed in early 2010 to determine which institutions have a RECS in operation and what is their composition and function. Of the 46 institutions surveyed, 33 (70%) have a RECS. Only 15 RECS have received any consult requests in the last year. Issues that are common among these relatively nascent services include relationships with institutional oversight committees, balancing requestor concerns about confidentiality with research integrity and human subjects protection priorities, tracking consult data and outcomes, and developing systems for internal evaluation. There is variability in how these issues are approached. It will be important to be attentive to the institutional context to develop an appropriate approach. Further data about the issues raised by requestors and the recommendations provided are necessary to build a community of scholars who can navigate and resolve ethical issues encountered along the translational research pathway. © 2012 Wiley Periodicals, Inc.

Eye and Ear Temperature Using Infrared Thermography Are Related to Rectal Temperature in Dogs at Rest or With Exercise.

PubMed

Zanghi, Brian M

2016-01-01

Rectal body temperature (BT) has been documented in exercising dogs to monitor thermoregulation, heat stress risk, and performance during physical activity. Eye (BT eye ) and ear (BT ear ) temperature measured with infrared thermography (IRT) were compared to rectal (BT rec ) temperature as the reference method and assess alternative sites to track hyperthermia, possibly to establish BT eye IRT as a passive and non-contact method. BT measures were recorded at 09:00, 11:30, 12:30, and 02:30 from Labrador Retrievers ( N  = 16) and Beagles ( N  = 16) while sedentary and with 30-min play-exercise (pre- and 0, 15, 30-min post-exercise). Total exercise locomotor activity counts were recorded to compare relative intensity of play-exercise between breeds. BT rec , BT eye , and BT ear were measured within 5 min of the target time. Each BT method was analyzed by analysis of variance for main effects of breed and time. Method differences were compared using Bland-Altman plots and linear regression. Sedentary BT differed by breed for BT rec ( p  < 0.0001), BT ear ( p  < 0.0001), and BT eye ( p  = 0.06) with Labs having on average 0.3-0.8°C higher BT compared to Beagles. Readings also declined over time for BT eye ( p  < 0.0001) and BT ear ( p  < 0.0001), but not for BT rec ( p  = 0.63) for both breeds. Total exercise (30-min) activity counts did not differ ( p  = 0.53) between breeds. Time and breed interaction was significant in response to exercise for both BT rec and BT ear ( p  = 0.035 and p  = 0.005, respectively), with a marginal interaction ( p  = 0.09) for BT eye . All the three methods detected hyperthermia with Labs having a higher increase compared to Beagles. Both BT ear and BT eye were significantly ( p  < 0.0001) related to BT rec in all dogs with sedentary or exercise activity. The relationship between BT eye and BT rec improved when monitoring exercise hyperthermia ( r  = 0.674) versus measures at rest ( r  = 0.381), whereas BT ear was significantly related to BT rec regardless of activity ( r  = 0.615-0.735). Although BT readings were significantly related, method bias ( p  < 0.02) was observed for BT eye to slightly underestimate BT rec , whereas no bias was observed between BT ear and BT rec . This study demonstrates that IRT technology effectively measures both ear and eye temperature and enables effective monitoring of BT changes at rest, with exercise, and between breeds. However, ear, and not eye, temperature is a better reflection of rectal temperature.

The Diesel Exhaust in Miners Study: IV. Estimating historical exposures to diesel exhaust in underground non-metal mining facilities.

PubMed

Vermeulen, Roel; Coble, Joseph B; Lubin, Jay H; Portengen, Lützen; Blair, Aaron; Attfield, Michael D; Silverman, Debra T; Stewart, Patricia A

2010-10-01

We developed quantitative estimates of historical exposures to respirable elemental carbon (REC) for an epidemiologic study of mortality, including lung cancer, among diesel-exposed miners at eight non-metal mining facilities [the Diesel Exhaust in Miners Study (DEMS)]. Because there were no historical measurements of diesel exhaust (DE), historical REC (a component of DE) levels were estimated based on REC data from monitoring surveys conducted in 1998-2001 as part of the DEMS investigation. These values were adjusted for underground workers by carbon monoxide (CO) concentration trends in the mines derived from models of historical CO (another DE component) measurements and DE determinants such as engine horsepower (HP; 1 HP = 0.746 kW) and mine ventilation. CO was chosen to estimate historical changes because it was the most frequently measured DE component in our study facilities and it was found to correlate with REC exposure. Databases were constructed by facility and year with air sampling data and with information on the total rate of airflow exhausted from the underground operations in cubic feet per minute (CFM) (1 CFM = 0.0283 m³ min⁻¹), HP of the diesel equipment in use (ADJ HP), and other possible determinants. The ADJ HP purchased after 1990 (ADJ HP₁₉₉₀(+)) was also included to account for lower emissions from newer, cleaner engines. Facility-specific CO levels, relative to those in the DEMS survey year for each year back to the start of dieselization (1947-1967 depending on facility), were predicted based on models of observed CO concentrations and log-transformed (Ln) ADJ HP/CFM and Ln(ADJ HP₁₉₉₀(+)). The resulting temporal trends in relative CO levels were then multiplied by facility/department/job-specific REC estimates derived from the DEMS surveys personal measurements to obtain historical facility/department/job/year-specific REC exposure estimates. The facility-specific temporal trends of CO levels (and thus the REC estimates) generated from these models indicated that CO concentrations had been generally greater in the past than during the 1998-2001 DEMS surveys, with the highest levels ranging from 100 to 685% greater (median: 300%). These levels generally occurred between 1970 and the early 1980s. A comparison of the CO facility-specific model predictions with CO air concentration measurements from a 1976-1977 survey external to the modeling showed that our model predictions were slightly lower than those observed (median relative difference of 29%; range across facilities: 49 to -25%). In summary, we successfully modeled past CO concentration levels using selected determinants of DE exposure to derive retrospective estimates of REC exposure. The results suggested large variations in REC exposure levels both between and within the underground operations of the facilities and over time. These REC exposure estimates were in a plausible range and were used in the investigation of exposure-response relationships in epidemiologic analyses.

EPA's Role with the Regional Environmental Center (REC) for Central and Eastern Europe

EPA Pesticide Factsheets

The Regional Environmental Center (REC) for Central and Eastern Europe provides assistance in solving environmental problems in Central and Eastern Europe by promoting cooperation among governments, non-governmental organizations, businesses and others.

From “a Fair Game” to “a Form of Covert Research”: Research Ethics Committee Members’ Differing Notions of Consent and Potential Risk to Participants Within Social Media Research

PubMed Central

Derrick, G. E.

2018-01-01

Social media (SM) research presents new challenges for research ethics committees (RECs) who must balance familiar ethical principles with new notions of public availability. This article qualitatively examines how U.K. REC members view this balance in terms of risk and consent. While it found significant variance overall, there were discernible experience-based trends. REC members with less experience of reviewing SM held inflexible notions of consent and risk that could be categorized as either relying on traditional notions of requiring direct consent, or viewing publicly available data as “fair game.” More experienced REC members took a more nuanced approach to data use and consent. We conclude that the more nuanced approach should be best practice during ethical review of SM research. PMID:29350083

GAP-REACH

PubMed Central

Lewis-Fernández, Roberto; Raggio, Greer A.; Gorritz, Magdaliz; Duan, Naihua; Marcus, Sue; Cabassa, Leopoldo J.; Humensky, Jennifer; Becker, Anne E.; Alarcón, Renato D.; Oquendo, María A.; Hansen, Helena; Like, Robert C.; Weiss, Mitchell; Desai, Prakash N.; Jacobsen, Frederick M.; Foulks, Edward F.; Primm, Annelle; Lu, Francis; Kopelowicz, Alex; Hinton, Ladson; Hinton, Devon E.

2015-01-01

Growing awareness of health and health care disparities highlights the importance of including information about race, ethnicity, and culture (REC) in health research. Reporting of REC factors in research publications, however, is notoriously imprecise and unsystematic. This article describes the development of a checklist to assess the comprehensiveness and the applicability of REC factor reporting in psychiatric research publications. The 16-itemGAP-REACH© checklist was developed through a rigorous process of expert consensus, empirical content analysis in a sample of publications (N = 1205), and interrater reliability (IRR) assessment (N = 30). The items assess each section in the conventional structure of a health research article. Data from the assessment may be considered on an item-by-item basis or as a total score ranging from 0% to 100%. The final checklist has excellent IRR (κ = 0.91). The GAP-REACH may be used by multiple research stakeholders to assess the scope of REC reporting in a research article. PMID:24080673

Efficient mouse airway transduction following recombination between AAV vectors carrying parts of a larger gene.

PubMed

Halbert, Christine L; Allen, James M; Miller, A Dusty

2002-07-01

The small packaging capacity of adeno-associated virus (AAV) vectors limits the utility of this promising vector system for transfer of large genes. We explored the possibility that larger genes could be reconstituted following homologous recombination between AAV vectors carrying overlapping gene fragments. An alkaline phosphatase (AP) gene was split between two such AAV vectors (rec vectors) and packaged using AAV2 or AAV6 capsid proteins. Rec vectors having either capsid protein recombined to express AP in cultured cells at about 1-2% of the rate observed for an intact vector. Surprisingly, the AAV6 rec vectors transduced lung cells in mice almost as efficiently as did an intact vector, with 10% of airway epithelial cells, the target for treatment of cystic fibrosis (CF), being positive. Thus AAV rec vectors may be useful for diseases such as CF that require transfer of large genes.

A second case of inv(4)pat with both recombinants in the offspring: rec dup(4q) in a girl with Wolf-Hirschhorn syndrome and rec dup(4p).

PubMed

Dufke, A; Eggermann, K; Balg, S; Stengel-Rutkowski, S; Enders, H; Kaiser, P

2000-01-01

In a girl presenting with features of Wolf-Hirschhorn syndrome, cytogenetic and molecular cytogenetic analysis revealed a rearranged chromosome 4 with monosomy of the distal bands 4pter-->4p16.2 and trisomy of the distal bands 4q35.1-->4qter [rec dup(4q)] due to a large, paternal pericentric inversion. In the following two pregnancies, prenatal diagnosis showed the same imbalance in one fetus and a reverse segmental imbalance [rec dup(4p)] in the other. We discuss the recombination risk of the given inversion with respect to the size of the inverted segment and the viability of the recombinants. The high frequency of recombinants in this family and others suggests a high recurrence risk in similar cases with large pericentric inversions comprising almost entire chromosomes. Copyright 2001 S. Karger AG, Basel.

What is the role of the research ethics committee? Paternalism, inducements, and harm in research ethics

PubMed Central

Garrard, E; Dawson, A

2005-01-01

In a recent paper Edwards, Kirchin, and Huxtable have argued that research ethics committees (RECs) are often wrongfully paternalistic in their approach to medical research. They argue that it should be left to competent potential research subjects to make judgments about the acceptability of harms and benefits relating to research, and that this is not a legitimate role for any REC. They allow an exception to their overall antipaternalism, however, in that they think RECs should have the power to prohibit the use of financial inducements to recruit research subjects into trials. In this paper it is argued that these claims are unjustified and implausible. A sketch is provided of an alternative model of the role of the REC as an expert body making judgments about the acceptability of research proposals through a consensual weighing of different moral considerations. PMID:15994364

Construction of horizontal stratum landform-like composite foams and their methyl orange adsorption capacity

NASA Astrophysics Data System (ADS)

Chen, Jiajia; Shi, Xiaowen; Zhan, Yingfei; Qiu, Xiaodan; Du, Yumin; Deng, Hongbing

2017-03-01

Chitosan (CS)/rectorite (REC)/carbon nanotubes (CNTs) composite foams with good mechanical properties were successfully fabricated by unidirectional freeze-casting technique. The morphology of the foam showed the well-ordered porous three-dimensional layers and horizontal stratum landform-like structure. The holes on the layers looked like the wings of butterfly. Additionally, the X-ray photoelectron spectroscopy and energy-dispersive X-ray spectroscopy results indicated the successful addition of CNTs and REC. The intercalated REC with CS chains was confirmed by small-angle X-ray diffraction. The surface structure of the foams was also analyzed by Raman spectroscopy. The adsorption experiments showed that when the mass ratio of CS to REC was 10:1 and CNTs content was 20%, the composite foam performed best in adsorbing low concentration methyl orange, and the largest adsorption capacity was 41.65 mg/g.

Apoptosis-Like Death, an Extreme SOS Response in Escherichia coli

PubMed Central

Erental, Ariel; Kalderon, Ziva; Saada, Ann; Smith, Yoav

2014-01-01

ABSTRACT In bacteria, SOS is a global response to DNA damage, mediated by the recA-lexA genes, resulting in cell cycle arrest, DNA repair, and mutagenesis. Previously, we reported that Escherichia coli responds to DNA damage via another recA-lexA-mediated pathway resulting in programmed cell death (PCD). We called it apoptosis-like death (ALD) because it is characterized by membrane depolarization and DNA fragmentation, which are hallmarks of eukaryotic mitochondrial apoptosis. Here, we show that ALD is an extreme SOS response that occurs only under conditions of severe DNA damage. Furthermore, we found that ALD is characterized by additional hallmarks of eukaryotic mitochondrial apoptosis, including (i) rRNA degradation by the endoribonuclease YbeY, (ii) upregulation of a unique set of genes that we called extensive-damage-induced (Edin) genes, (iii) a decrease in the activities of complexes I and II of the electron transport chain, and (iv) the formation of high levels of OH˙ through the Fenton reaction, eventually resulting in cell death. Our genetic and molecular studies on ALD provide additional insight for the evolution of mitochondria and the apoptotic pathway in eukaryotes. PMID:25028428

Evaluation of radioprotective activities Rhodiola imbricata Edgew--a high altitude plant.

PubMed

Arora, Rajesh; Chawla, Raman; Sagar, Ravinder; Prasad, Jagdish; Singh, Surendar; Kumar, Raj; Sharma, Ashok; Singh, Shikha; Sharma, Rakesh Kumar

2005-05-01

The present study reports the radioprotective properties of a hydro-alcoholic rhizome extract of Rhodiola imbricata (code named REC-7004), a plant native to the high-altitude Himalayas. The radioprotective effect, along with its relevant superoxide ion scavenging, metal chelation, antioxidant, anti-lipid peroxidation and anti-hemolytic activities was evaluated under both in vitro and in vivo conditions. Chemical analysis showed the presence of high content of polyphenolics (0.971 +/- 0.01 mg% of quercetin). Absorption spectra analysis revealed constituents that absorb in the range of 220-290 nm, while high-performance liquid chromatography (HPLC) analysis confirmed the presence of four major peaks with retention times of 4.780, 5.767, 6.397 and 7.577 min. REC-7004 was found to lower lipid oxidation significantly (p < 0.05) at concentrations viz., 8 and 80 microg/ml respectively as compared to reduced glutathione, although the optimally protective dose was 80 microg/ml, which showed 59.5% inhibition of induction of linoleic acid degradation within first 24 h. The metal chelation activity of REC-7004 was found to increase concomitantly from 1 to 50 microg/ml. REC-7004 (10-50 microg/ml) exhibited significant metal chelation activity (p < 0.05), as compared to control, and maximum percentage inhibition (30%) of formation of iron-2,2'-bi-pyridyl complex was observed at 50 microg/ml, which correlated well with quercetin (34.9%), taken as standard. The reducing power of REC-7004 increased in a dose-dependent manner. The absorption unit value of REC-7004 was significantly lower (0.0183 +/- 0.0033) as compared to butylated hydroxy toluene, a standard antioxidant (0.230 +/- 0.091), confirming its high reducing ability. Superoxide ion scavenging ability of REC-7004 exhibited a dose-dependent increase (1-100 microg/ml) and was significantly higher (p < 0.05) than that of quercetin at lower concentrations (1-10 microg/ml), while at 100 microg/ml, both quercetin and REC-7004 scavenged over 90% superoxide anions. MTT assay in U87 cell line revealed an increase in percent survival of cells at doses between 25 and 125 microg/ml in case of drug + radiation group. In vivo evaluation of radio-protective efficacy in mice revealed that intraperitoneal administration of REC-7004 (maximally effective dose: 400 mg/kg b.w.) 30 min prior to lethal (10 Gy) total-body gamma-irradiation rendered 83.3% survival. The ability of REC-7004 to inhibit lipid peroxidation induced by iron/ascorbate, radiation (250 Gy) and their combination [i.e., iron/ascorbate and radiation (250 Gy)], was also investigated and was found to decrease in a dose-dependent manner (0.05-2 mg/ml). The maximum percent inhibition of formation of MDA-TBA complex at 2 mg/ml in case of iron/ascorbate, radiation (250 Gy) and both i.e., iron/ascorbate with radiation (250 Gy) was 53.78, 63.07, and 51.76% respectively and were found to be comparable to that of quercetin. REC-7004 (1 microg/ml) also exhibited significant anti-hemolytic capacity by preventing radiation-induced membrane degeneration of human erythrocytes. In conclusion, Rhodiola renders in vitro and in vivo radioprotection via multifarious mechanisms that act in a synergistic manner.

Exploring the representational basis of response-effect compatibility: Evidence from bilingual verbal response-effect mappings.

PubMed

Földes, Noémi; Philipp, Andrea M; Badets, Arnaud; Koch, Iring

2018-05-01

The ideomotor principle states that actions are represented by their anticipated sensory effects. This notion is often tested using the response-effect compatibility (REC) paradigm, where participants' responses are followed either by a compatible or incompatible response effect (e.g., an effect on the right side after a right-hand response is considered R-E compatible due to the spatial overlap, whereas an effect on the left side after the right-hand response is considered incompatible). Shorter reaction times are typically observed in the compatible condition compared to the incompatible condition (i.e., REC effect), suggesting that effect anticipation plays a role in action control. Previous evidence from verbal REC suggested that effect anticipation can be due to conceptual R-E overlap, but there was also phonological overlap (i.e., anticipated reading of a word preceded by the vocal response of saying that very word). To examine the representational basis of REC, in three experiments, we introduced a bilingual R-E mapping to exclude phonological R-E overlap (i.e., in the R-E compatible condition, the translation equivalent of the response word is presented as an effect word in a different language). Our findings show that the REC effect is obtained when presenting the effect word in the same language as the response (i.e., monolingual condition), but the compatibility effect was not found when the semantically same word is presented in a different language, suggesting no conceptually generalized REC in a bilingual setting. (232 words). Copyright © 2018 Elsevier B.V. All rights reserved.

Holliday junction trap shows how cells use recombination and a junction-guardian role of RecQ helicase.

PubMed

Xia, Jun; Chen, Li-Tzu; Mei, Qian; Ma, Chien-Hui; Halliday, Jennifer A; Lin, Hsin-Yu; Magnan, David; Pribis, John P; Fitzgerald, Devon M; Hamilton, Holly M; Richters, Megan; Nehring, Ralf B; Shen, Xi; Li, Lei; Bates, David; Hastings, P J; Herman, Christophe; Jayaram, Makkuni; Rosenberg, Susan M

2016-11-01

DNA repair by homologous recombination (HR) underpins cell survival and fuels genome instability, cancer, and evolution. However, the main kinds and sources of DNA damage repaired by HR in somatic cells and the roles of important HR proteins remain elusive. We present engineered proteins that trap, map, and quantify Holliday junctions (HJs), a central DNA intermediate in HR, based on catalytically deficient mutant RuvC protein of Escherichia coli . We use RuvCDefGFP (RDG) to map genomic footprints of HR at defined DNA breaks in E. coli and demonstrate genome-scale directionality of double-strand break (DSB) repair along the chromosome. Unexpectedly, most spontaneous HR-HJ foci are instigated, not by DSBs, but rather by single-stranded DNA damage generated by replication. We show that RecQ, the E. coli ortholog of five human cancer proteins, nonredundantly promotes HR-HJ formation in single cells and, in a novel junction-guardian role, also prevents apparent non-HR-HJs promoted by RecA overproduction. We propose that one or more human RecQ orthologs may act similarly in human cancers overexpressing the RecA ortholog RAD51 and find that cancer genome expression data implicate the orthologs BLM and RECQL4 in conjunction with EME1 and GEN1 as probable HJ reducers in such cancers. Our results support RecA-overproducing E. coli as a model of the many human tumors with up-regulated RAD51 and provide the first glimpses of important, previously elusive reaction intermediates in DNA replication and repair in single living cells.

Effects of a human recombinant alkaline phosphatase on renal hemodynamics, oxygenation and inflammation in two models of acute kidney injury.

PubMed

Peters, Esther; Ergin, Bülent; Kandil, Asli; Gurel-Gurevin, Ebru; van Elsas, Andrea; Masereeuw, Rosalinde; Pickkers, Peter; Ince, Can

2016-12-15

Two small clinical trials indicated that administration of bovine intestinal alkaline phosphatase (AP) improves renal function in critically ill patients with sepsis-associated acute kidney injury (AKI), for which the mechanism of action is not completely understood. Here, we investigated the effects of a newly developed human recombinant AP (recAP) on renal oxygenation and hemodynamics and prevention of kidney damage and inflammation in two in vivo AKI models. To induce AKI, male Wistar rats (n=18) were subjected to renal ischemia (30min) and reperfusion (I/R), or sham-operated. In a second model, rats (n=18) received a 30min infusion of lipopolysaccharide (LPS; 2.5mg/kg), or saline, and fluid resuscitation. In both models, recAP (1000U/kg) was administered intravenously (15min before reperfusion, or 90min after LPS). Following recAP treatment, I/R-induced changes in renal blood flow, renal vascular resistance and oxygen delivery at early, and cortical microvascular oxygen tension at late reperfusion were no longer significantly affected. RecAP did not influence I/R-induced effects on mean arterial pressure. During endotoxemia, recAP treatment did not modulate the LPS-induced changes in systemic hemodynamics and renal oxygenation. In both models, recAP did exert a clear renal protective anti-inflammatory effect, demonstrated by attenuated immunostaining of inflammatory, tubular injury and pro-apoptosis markers. Whether this renal protective effect is sufficient to improve outcome of patients suffering from sepsis-associated AKI is being investigated in a large clinical trial. Copyright © 2016. Published by Elsevier Inc.

Cytotoxic and radioprotective effects of Podophyllum hexandrum.

PubMed

Shukla, Sandeep Kumar; Chaudhary, Pankaj; Prem Kumar, Indracanti; Afrin, Farhat; Puri, Satish Chandra; Qazi, Ghulam Nabi; Sharma, Rakesh Kumar

2006-07-01

Podophyllum hexandrum, a herb thriving in Himalayas has already been reported to exhibit antitumor and radioprotective properties. Present study was undertaken to unravel the possible mechanism responsible for the cytotoxic and radioprotective properties of REC-2001, a fraction isolated from the rhizome of P. hexandrum using murine peritoneal macrophages and plasmid DNA as model systems. Cell death, levels of intracellular reactive oxygen species (ROS) and apoptosis were studied employing trypan blue exclusion assay, dichlorofluorescein diacetate and DNA fragmentation assay, respectively. Superoxide anions, hydroxyl radicals and DNA damage were estimated following nitroblue tetrazolium, 2-deoxyribose degradation and plasmid DNA relaxation assays, respectively. Pre-irradiation administration of REC-2001 to peritoneal macrophages in the concentration range of 25-200μg/ml significantly reduced radiation induced ROS generation, DNA damage, apoptosis and cell killing in comparison to radiation control group indicating radioprotective potential. Studies with plasmid DNA indicated the ability of REC-2001 to inhibit 20Gy induced single and double strand breaks further supporting the antioxidative potential. However, REC-2001 in a dose-dependent fashion induced cell death, ROS and DNA fragmentation indicating the cytotoxic nature. REC-2001, in presence of 100μM copper sulfate, generated significant amount of hydroxyl radicals and superoxide anions indicating ability to act as a pro-oxidant in presence of metal ions. The superoxide anion generation was found to be sensitive to metal chelators like EDTA and deferoxamine mesylate (DFR). These results suggest that the ability of REC-2001 to act as a pro-oxidant in presence of metal ions and antioxidant in presence of free radicals might be responsible for cytotoxic and radioprotective properties.

Holliday junction trap shows how cells use recombination and a junction-guardian role of RecQ helicase

PubMed Central

Xia, Jun; Chen, Li-Tzu; Mei, Qian; Ma, Chien-Hui; Halliday, Jennifer A.; Lin, Hsin-Yu; Magnan, David; Pribis, John P.; Fitzgerald, Devon M.; Hamilton, Holly M.; Richters, Megan; Nehring, Ralf B.; Shen, Xi; Li, Lei; Bates, David; Hastings, P. J.; Herman, Christophe; Jayaram, Makkuni; Rosenberg, Susan M.

2016-01-01

DNA repair by homologous recombination (HR) underpins cell survival and fuels genome instability, cancer, and evolution. However, the main kinds and sources of DNA damage repaired by HR in somatic cells and the roles of important HR proteins remain elusive. We present engineered proteins that trap, map, and quantify Holliday junctions (HJs), a central DNA intermediate in HR, based on catalytically deficient mutant RuvC protein of Escherichia coli. We use RuvCDefGFP (RDG) to map genomic footprints of HR at defined DNA breaks in E. coli and demonstrate genome-scale directionality of double-strand break (DSB) repair along the chromosome. Unexpectedly, most spontaneous HR-HJ foci are instigated, not by DSBs, but rather by single-stranded DNA damage generated by replication. We show that RecQ, the E. coli ortholog of five human cancer proteins, nonredundantly promotes HR-HJ formation in single cells and, in a novel junction-guardian role, also prevents apparent non-HR–HJs promoted by RecA overproduction. We propose that one or more human RecQ orthologs may act similarly in human cancers overexpressing the RecA ortholog RAD51 and find that cancer genome expression data implicate the orthologs BLM and RECQL4 in conjunction with EME1 and GEN1 as probable HJ reducers in such cancers. Our results support RecA-overproducing E. coli as a model of the many human tumors with up-regulated RAD51 and provide the first glimpses of important, previously elusive reaction intermediates in DNA replication and repair in single living cells. PMID:28090586

Genotyping of bacteria belonging to the former Erwinia genus by PCR-RFLP analysis of a recA gene fragment.

PubMed

Waleron, Małgorzata; Waleron, Krzysztof; Podhajska, Anna J; Lojkowska, Ewa

2002-02-01

Genotypic characterization, based on the analysis of restriction fragment length polymorphism of the recA gene fragment PCR product (recA PCR-RFLP), was performed on members of the former Erwinia genus. PCR primers deduced from published recA gene sequences of Erwinia carotovora allowed the amplification of an approximately 730 bp DNA fragment from each of the 19 Erwinia species tested. Amplified recA fragments were compared using RFLP analysis with four endonucleases (AluI, HinfI, TasI and Tru1I), allowing the detection of characteristic patterns of RFLP products for most of the Erwinia species. Between one and three specific RFLP groups were identified among most of the species tested (Erwinia amylovora, Erwinia ananas, Erwinia cacticida, Erwinia cypripedii, Erwinia herbicola, Erwinia mallotivora, Erwinia milletiae, Erwinia nigrifluens, Erwinia persicina, Erwinia psidii, Erwinia quercina, Erwinia rhapontici, Erwinia rubrifaciens, Erwinia salicis, Erwinia stewartii, Erwinia tracheiphila, Erwinia uredovora, Erwinia carotovora subsp. atroseptica, Erwinia carotovora subsp. betavasculorum, Erwinia carotovora subsp. odorifera and Erwinia carotovora subsp. wasabiae). However, in two cases, Erwinia chrysanthemi and Erwinia carotovora subsp. carotovora, 15 and 18 specific RFLP groups were detected, respectively. The variability of genetic patterns within these bacteria could be explained in terms of their geographic origin and/or wide host-range. The results indicated that PCR-RFLP analysis of the recA gene fragment is a useful tool for identification of species and subspecies belonging to the former Erwinia genus, as well as for differentiation of strains within E. carotovora subsp. carotovora and E. chrysanthemi.

Associations of pre-pregnancy body mass index and gestational weight gain with pregnancy outcome and postpartum weight retention: a prospective observational cohort study

PubMed Central

2014-01-01

Background Excessive gestational weight gain (GWG) is associated with pregnancy complications, and Norwegian Health Authorities have adopted the GWG recommendations of the US Institute of Medicine and National Research Council (IOM). The aim of this study was to evaluate if a GWG outside the IOM recommendation in a Norwegian population is associated with increased risk of pregnancy complications like hypertension, low and high birth weight, preeclampsia, emergency caesarean delivery, and maternal post-partum weight retention (PPWR) at 6 and 18 months. Methods This study was performed in 56 101 pregnant women included in the prospective national Norwegian Mother and Child Cohort Study (MoBa) in the years 1999 to 2008. Women who delivered a singleton live born child during gestational week 37 to 42 were included. Maternal prepregnant and postpartum weight was collected from questionnaires at 17th week of gestation and 6 and 18 months postpartum. Results A weight gain less than the IOM recommendations (GWG < IOM rec.) increased the risk for giving birth to a low weight baby among normal weight nulliparous women. A weight gain higher than the IOM recommendations (GWG > IOM rec.) significantly increased the risk of pregnancy hypertension, a high birth weight baby, preeclampsia and emergency cesarean delivery in both nulliparous and parous normal weight women. Similar results were found for overweight women except for no increased risk for gestational hypertension in parous women with GWG > IOM rec. Seventy-four percent of the overweight nulliparous women and 66% of the obese women had a GWG > IOM rec. A GWG > IOM rec. resulted in increased risk of PPWR > 2 kg in all weight classes, but most women attained their prepregnant weight class by 18 months post-partum. Conclusions For prepregnant normal weight and overweight women a GWG > IOM rec. increased the risk for unfavorable birth outcomes in both nulliparous and parous women. A GWG > IOM rec. increased the risk of a PPWR > 2 kg at 18 months in all weight classes. This large study supports the Norwegian Health authorities’ recommendations for normal weight and overweight women to comply with the IOM rec. PMID:24917037

Comparative Genomics of DNA Recombination and Repair in Cyanobacteria: Biotechnological Implications

PubMed Central

Cassier-Chauvat, Corinne; Veaudor, Théo; Chauvat, Franck

2016-01-01

Cyanobacteria are fascinating photosynthetic prokaryotes that are regarded as the ancestors of the plant chloroplast; the purveyors of oxygen and biomass for the food chain; and promising cell factories for an environmentally friendly production of chemicals. In colonizing most waters and soils of our planet, cyanobacteria are inevitably challenged by environmental stresses that generate DNA damages. Furthermore, many strains engineered for biotechnological purposes can use DNA recombination to stop synthesizing the biotechnological product. Hence, it is important to study DNA recombination and repair in cyanobacteria for both basic and applied research. This review reports what is known in a few widely studied model cyanobacteria and what can be inferred by mining the sequenced genomes of morphologically and physiologically diverse strains. We show that cyanobacteria possess many E. coli-like DNA recombination and repair genes, and possibly other genes not yet identified. E. coli-homolog genes are unevenly distributed in cyanobacteria, in agreement with their wide genome diversity. Many genes are extremely well conserved in cyanobacteria (mutMS, radA, recA, recFO, recG, recN, ruvABC, ssb, and uvrABCD), even in small genomes, suggesting that they encode the core DNA repair process. In addition to these core genes, the marine Prochlorococcus and Synechococcus strains harbor recBCD (DNA recombination), umuCD (mutational DNA replication), as well as the key SOS genes lexA (regulation of the SOS system) and sulA (postponing of cell division until completion of DNA reparation). Hence, these strains could possess an E. coli-type SOS system. In contrast, several cyanobacteria endowed with larger genomes lack typical SOS genes. For examples, the two studied Gloeobacter strains lack alkB, lexA, and sulA; and Synechococcus PCC7942 has neither lexA nor recCD. Furthermore, the Synechocystis PCC6803 lexA product does not regulate DNA repair genes. Collectively, these findings indicate that not all cyanobacteria have an E. coli-type SOS system. Also interestingly, several cyanobacteria possess multiple copies of E. coli-like DNA repair genes, such as Acaryochloris marina MBIC11017 (2 alkB, 3 ogt, 7 recA, 3 recD, 2 ssb, 3 umuC, 4 umuD, and 8 xerC), Cyanothece ATCC51142 (2 lexA and 4 ruvC), and Nostoc PCC7120 (2 ssb and 3 xerC). PMID:27881980

Identification of 2-keto-3-deoxy-d-Gluconate Kinase and 2-keto-3-deoxy-d-Phosphogluconate Aldolase in an Alginate-Assimilating Bacterium, Flavobacterium sp. Strain UMI-01

PubMed Central

Nishiyama, Ryuji; Inoue, Akira; Ojima, Takao

2017-01-01

Recently, we identified an alginate-assimilating gene cluster in the genome of Flavobacterium sp. strain UMI-01, a member of Bacteroidetes. Alginate lyase genes and a 4-deoxy-l-erythro-5-hexoseulose uronic acid (DEH) reductase gene in the cluster have already been characterized; however, 2-keto-3-deoxy-d-gluconate (KDG) kinase and 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase genes, i.e., flkin and flald, still remained uncharacterized. The amino acid sequences deduced from flkin and flald showed low identities with those of corresponding enzymes of Saccharophagus degradans 2-40T, a member of Proteobacteria (Kim et al., Process Biochem., 2016). This led us to consider that the DEH-assimilating enzymes of Bacteroidetes species are somewhat deviated from those of Proteobacteria species. Thus, in the present study, we first assessed the characteristics in the primary structures of KDG kinase and KDG aldolase of the strain UMI-01, and then investigated the enzymatic properties of recombinant enzymes, recFlKin and recFlAld, expressed by an Escherichia coli expression system. Multiple-sequence alignment among KDG kinases and KDG aldolases from several Proteobacteria and Bacteroidetes species indicated that the strain UMI-01 enzymes showed considerably low sequence identities (15%–25%) with the Proteobacteria enzymes, while they showed relatively high identities (47%–68%) with the Bacteroidetes enzymes. Phylogenetic analyses for these enzymes indicated the distant relationship between the Proteobacteria enzymes and the Bacteroidetes enzymes, i.e., they formed distinct clusters in the phylogenetic tree. recFlKin and recFlAld produced with the genes flkin and flald, respectively, were confirmed to show KDG kinase and KDPG aldolase activities. Namely, recFlKin produced 1.7 mM KDPG in a reaction mixture containing 2.5 mM KDG and 2.5 mM ATP in a 90-min reaction, while recFlAld produced 1.2 mM pyruvate in the reaction mixture containing 5 mM KDPG at the equilibrium state. An in vitro alginate-metabolizing system constructed from recFlKin, recFlAld, and previously reported alginate lyases and DEH reductase of the strain UMI-01 could convert alginate to pyruvate and glyceraldehyde-3-phosphate with an efficiency of 38%. PMID:28216576

Associations of pre-pregnancy body mass index and gestational weight gain with pregnancy outcome and postpartum weight retention: a prospective observational cohort study.

PubMed

Haugen, Margaretha; Brantsæter, Anne Lise; Winkvist, Anna; Lissner, Lauren; Alexander, Jan; Oftedal, Bente; Magnus, Per; Meltzer, Helle Margrete

2014-06-11

Excessive gestational weight gain (GWG) is associated with pregnancy complications, and Norwegian Health Authorities have adopted the GWG recommendations of the US Institute of Medicine and National Research Council (IOM). The aim of this study was to evaluate if a GWG outside the IOM recommendation in a Norwegian population is associated with increased risk of pregnancy complications like hypertension, low and high birth weight, preeclampsia, emergency caesarean delivery, and maternal post-partum weight retention (PPWR) at 6 and 18 months. This study was performed in 56 101 pregnant women included in the prospective national Norwegian Mother and Child Cohort Study (MoBa) in the years 1999 to 2008. Women who delivered a singleton live born child during gestational week 37 to 42 were included. Maternal prepregnant and postpartum weight was collected from questionnaires at 17th week of gestation and 6 and 18 months postpartum. A weight gain less than the IOM recommendations (GWG < IOM rec.) increased the risk for giving birth to a low weight baby among normal weight nulliparous women. A weight gain higher than the IOM recommendations (GWG > IOM rec.) significantly increased the risk of pregnancy hypertension, a high birth weight baby, preeclampsia and emergency cesarean delivery in both nulliparous and parous normal weight women. Similar results were found for overweight women except for no increased risk for gestational hypertension in parous women with GWG > IOM rec. Seventy-four percent of the overweight nulliparous women and 66% of the obese women had a GWG > IOM rec. A GWG > IOM rec. resulted in increased risk of PPWR > 2 kg in all weight classes, but most women attained their prepregnant weight class by 18 months post-partum. For prepregnant normal weight and overweight women a GWG > IOM rec. increased the risk for unfavorable birth outcomes in both nulliparous and parous women. A GWG > IOM rec. increased the risk of a PPWR > 2 kg at 18 months in all weight classes. This large study supports the Norwegian Health authorities' recommendations for normal weight and overweight women to comply with the IOM rec.

Impact of electron-captures on nuclei near N = 50 on core-collapse supernovae

NASA Astrophysics Data System (ADS)

Titus, R.; Sullivan, C.; Zegers, R. G. T.; Brown, B. A.; Gao, B.

2018-01-01

The sensitivity of the late stages of stellar core collapse to electron-capture rates on nuclei is investigated, with a focus on electron-capture rates on 74 nuclei with neutron number close to 50, just above doubly magic 78Ni. It is demonstrated that variations in key characteristics of the evolution, such as the lepton fraction, electron fraction, entropy, stellar density, and in-fall velocity are about 50% due to uncertainties in the electron-capture rates on nuclei in this region, although thousands of nuclei are included in the simulations. The present electron-capture rate estimates used for the nuclei in this high-sensitivity region of the chart of isotopes are primarily based on a simple approximation, and it is shown that the estimated rates are likely too high, by an order of magnitude or more. Electron-capture rates based on Gamow-Teller strength distributions calculated in microscopic theoretical models will be required to obtain better estimates. Gamow-Teller distributions extracted from charge-exchange experiments performed at intermediate energies serve to guide the development and benchmark the models. A previously compiled weak-rate library that is used in the astrophysical simulations was updated as part of the work presented here, by adding additional rate tables for nuclei near stability for mass numbers between 60 and 110.

Current oscillations in semi-insulating GaAs associated with field-enhanced capture of electrons by the major deep donor EL2

NASA Technical Reports Server (NTRS)

Kaminska, M.; Parsey, J. M.; Lagowski, J.; Gatos, H. C.

1982-01-01

Current oscillations thermally activated by the release of electrons from deep levels in undoped semiinsulating GaAs were observed for the first time. They were attributed to electric field-enhanced capture of electrons by the dominant deep donor EL2 (antisite AsGa defect). This enhanced capture is due to the configurational energy barrier of EL2, which is readily penetrated by hot electrons.

Limit on the radiative neutrinoless double electron capture of ^{36}Ar from GERDA Phase I

NASA Astrophysics Data System (ADS)

Agostini, M.; Allardt, M.; Bakalyarov, A. M.; Balata, M.; Barabanov, I.; Barros, N.; Baudis, L.; Bauer, C.; Bellotti, E.; Belogurov, S.; Belyaev, S. T.; Benato, G.; Bettini, A.; Bezrukov, L.; Bode, T.; Borowicz, D.; Brudanin, V.; Brugnera, R.; Caldwell, A.; Cattadori, C.; Chernogorov, A.; D'Andrea, V.; Demidova, E. V.; di Vacri, A.; Domula, A.; Doroshkevich, E.; Egorov, V.; Falkenstein, R.; Fedorova, O.; Freund, K.; Frodyma, N.; Gangapshev, A.; Garfagnini, A.; Gooch, C.; Grabmayr, P.; Gurentsov, V.; Gusev, K.; Hakenmüller, J.; Hegai, A.; Heisel, M.; Hemmer, S.; Heusser, G.; Hofmann, W.; Hult, M.; Inzhechik, L. V.; Csáthy, J. Janicskó; Jochum, J.; Junker, M.; Kazalov, V.; Kihm, T.; Kirpichnikov, I. V.; Kirsch, A.; Kish, A.; Klimenko, A.; Kneißl, R.; Knöpfle, K. T.; Kochetov, O.; Kornoukhov, V. N.; Kuzminov, V. V.; Laubenstein, M.; Lazzaro, A.; Lebedev, V. I.; Lehnert, B.; Liao, H. Y.; Lindner, M.; Lippi, I.; Lubashevskiy, A.; Lubsandorzhiev, B.; Lutter, G.; Macolino, C.; Majorovits, B.; Maneschg, W.; Medinaceli, E.; Miloradovic, M.; Mingazheva, R.; Misiaszek, M.; Moseev, P.; Nemchenok, I.; Palioselitis, D.; Panas, K.; Pandola, L.; Pelczar, K.; Pullia, A.; Riboldi, S.; Rumyantseva, N.; Sada, C.; Salamida, F.; Salathe, M.; Schmitt, C.; Schneider, B.; Schönert, S.; Schreiner, J.; Schütz, A.-K.; Schulz, O.; Schwingenheuer, B.; Selivanenko, O.; Shirchenko, M.; Simgen, H.; Smolnikov, A.; Stanco, L.; Stepaniuk, M.; Vanhoefer, L.; Vasenko, A. A.; Veresnikova, A.; von Sturm, K.; Wagner, V.; Walter, M.; Wegmann, A.; Wester, T.; Wiesinger, C.; Wilsenach, H.; Wojcik, M.; Yanovich, E.; Zhitnikov, I.; Zhukov, S. V.; Zinatulina, D.; Zuber, K.; Zuzel, G.

2016-12-01

Neutrinoless double electron capture is a process that, if detected, would give evidence of lepton number violation and the Majorana nature of neutrinos. A search for neutrinoless double electron capture of ^{36}Ar has been performed with germanium detectors installed in liquid argon using data from Phase I of the GERmanium Detector Array ( Gerda) experiment at the Gran Sasso Laboratory of INFN, Italy. No signal was observed and an experimental lower limit on the half-life of the radiative neutrinoless double electron capture of ^{36}Ar was established: T_{1/2} > 3.6 × 10^{21} years at 90% CI.

Limit on the radiative neutrinoless double electron capture of 36Ar from GERDA Phase I

DOE PAGES

Agostini, M.; Allardt, M.; Bakalyarov, A. M.; ...

2016-11-28

Neutrinoless double electron capture is a process that, if detected, would give evidence of lepton number violation and the Majorana nature of neutrinos. Here, a search for neutrinoless double electron capture of 36Ar has been performed with germanium detectors installed in liquid argon using data from Phase I of the GERmanium Detector Array (Gerda) experiment at the Gran Sasso Laboratory of INFN, Italy. No signal was observed and an experimental lower limit on the half-life of the radiative neutrinoless double electron capture of 36 Ar was established: T 1/2 > 3.6 × 10 21 years at 90% CI.

Electron capture from circular Rydberg atoms

NASA Astrophysics Data System (ADS)

Lundsgaard, M. F. V.; Chen, Z.; Lin, C. D.; Toshima, N.

1995-02-01

Electron capture cross sections from circular Rydberg states as a function of the angle cphi between the ion velocity and the angular momentum of the circular orbital have been reported recently by Hansen et al. [Phys. Rev. Lett. 71, 1522 (1993)]. We show that the observed cphi dependence can be explained in terms of the propensity rule that governs the dependence of electron capture cross sections on the magnetic quantum numbers of the initial excited states. We also carried out close-coupling calculations to show that electron capture from the circular H(3d,4f,5g) states by protons at the same scaled velocity has nearly the same cphi dependence.

College Student Life & Experience | Nova Southeastern University

Science.gov Websites

creative spirit at NSU Campus Rec...Work hard, Play hard Living on Campus...Create memories and friendships Performing Arts...Nurture your creative spirit at NSU Campus Rec...Work hard, Play hard Shark Athletics....17

Where Does RECS Square Footage Data Come From?

EIA Publications

2012-01-01

The size of a home is a fixed characteristic strongly associated with the amount of energy consumed within it, particularly for space heating, air conditioning, lighting, and other appliances. As a part of the Residential Energy Consumption Survey (RECS), trained interviewers measure the square footage of each housing unit. RECS square footage data allow comparison of homes with varying characteristics. In-person measurements are vital because many alternate data sources, including property tax records, real estate listings, and, respondent estimates use varying definitions and under-estimate square footage as defined for the purposes of evaluating residential energy consumption.

Effect of Variables Independent of Performance on Promotion Rates to Major, Lieutenant Colonel, and Colonel in the Marine Corps

DTIC Science & Technology

1992-09-01

1 54. 1 71. 50s css/3:Cfautsbulation (count) tables For ALS-N &MARSTAT-M &SOURCE-USNA & DEGREE-UNDRG3RAD SELECTED DUrYSTA QUA FMF NON HOM REC 104 3...MARS1’AT-M & SOURCE- USNA __________________& DEGREE-UNDRGRAD ____ ________ SELECTED DUTrYSTA QUA FMF NON HQM REC 104 1 2.9 29. 62. 6.7 0 N so 33...M & SOURCE-OCS ___________________& DEGREE-ADVANCED ____ ________ SELECrED DUTrYSTA QUA FMF NON HOM REC N 72 7 2241 1 1 Y 198 471 104 16 3 X~SELECMD

Evaluation of DCS III Transmission Alternatives. Phase 1A Report. Appendix A. Transmission Media.

DTIC Science & Technology

1980-05-26

macNV to40 NOTES: Numbers in box indicate max. channel capacity. (No. of voice channels pier rf channel). (0 CCI R Rec. 383 and Rec. 387 channel capacity...is 1800 telephone channels. (2 MCR Rec. 384 channel capacity is 2700 or 1 260 telephone Channels. (3) CCIR Plec . 386 lAnneet chainel Capacity is 960...R + R" Rt + Rr +- (A.11-2)2 where R and Rr or R and Rr are distances from one end or the other end of the zone to the transmitter and receiver

Electrical Capacitance as a Predictor of Root Dry Weight in Shrub Willow ( Salix; Salicaceae) Parents and Progeny

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

Carlson, Craig H.; Smart, Lawrence B.

Here, the root biomass is an important trait often disregarded in woody perennial selection due to the challenge and expense of accurately and efficiently measuring large populations. In this study, we aim to develop a simple method that can predict root dry weight within a diverse shrub willow ( Salix) breeding population representing species hybrids and their parents using root electrical capacitance (REC). The REC method was tested on plants started from cuttings and grown in pots with potting mix in the greenhouse for 11 wk to assess the relationship of REC with 24 biomass traits and its usefulness inmore » allometric models for root and stem dry biomass. As a result, strong linear and positive correlations were found between REC and root dry biomass (r = 0.88). The total proportion of variance of root and stem dry biomass explained by predictors in multiple regression was 85% and 69%, respectively. The relative importance of predictor variables in allometric models was dominated by the contribution of REC. Here, this work provides an efficient and nondestructive technique to indirectly quantify root biomass of genetically diverse shrub willow progeny, which has great promise for selection of genotypes with varying root biomass and for the accurate estimation of belowground carbon sequestration.« less

Real-time Responsiveness for Ethics Oversight During Disaster Research.

PubMed

Eckenwiler, Lisa; Pringle, John; Boulanger, Renaud; Hunt, Matthew

2015-11-01

Disaster research has grown in scope and frequency. Research in the wake of disasters and during humanitarian crises--particularly in resource-poor settings--is likely to raise profound and unique ethical challenges for local communities, crisis responders, researchers, and research ethics committees (RECs). Given the ethical challenges, many have questioned how best to provide research ethics review and oversight. We contribute to the conversation concerning how best to ensure appropriate ethical oversight in disaster research and argue that ethical disaster research requires of researchers and RECs a particular sort of ongoing, critical engagement which may not be warranted in less exceptional research. We present two cases that typify the concerns disaster researchers and RECs may confront, and elaborate upon what this ongoing engagement might look like--how it might be conceptualized and utilized--using the concept of real-time responsiveness (RTR). The central aim of RTR, understood here as both an ethical ideal and practice, is to lessen the potential for research conducted in the wake of disasters to create, perpetuate, or exacerbate vulnerabilities and contribute to injustices suffered by disaster-affected populations. Well cultivated and deployed, we believe that RTR may enhance the moral capacities of researchers and REC members, and RECs as institutions where moral agency is nurtured and sustained. © 2015 John Wiley & Sons Ltd.

Electrical Capacitance as a Predictor of Root Dry Weight in Shrub Willow ( Salix; Salicaceae) Parents and Progeny

DOE PAGES

Carlson, Craig H.; Smart, Lawrence B.

2016-08-19

Here, the root biomass is an important trait often disregarded in woody perennial selection due to the challenge and expense of accurately and efficiently measuring large populations. In this study, we aim to develop a simple method that can predict root dry weight within a diverse shrub willow ( Salix) breeding population representing species hybrids and their parents using root electrical capacitance (REC). The REC method was tested on plants started from cuttings and grown in pots with potting mix in the greenhouse for 11 wk to assess the relationship of REC with 24 biomass traits and its usefulness inmore » allometric models for root and stem dry biomass. As a result, strong linear and positive correlations were found between REC and root dry biomass (r = 0.88). The total proportion of variance of root and stem dry biomass explained by predictors in multiple regression was 85% and 69%, respectively. The relative importance of predictor variables in allometric models was dominated by the contribution of REC. Here, this work provides an efficient and nondestructive technique to indirectly quantify root biomass of genetically diverse shrub willow progeny, which has great promise for selection of genotypes with varying root biomass and for the accurate estimation of belowground carbon sequestration.« less

Residential Energy Consumption Survey (RECS)

EIA Publications

2028-01-01

EIA administers the Residential Energy Consumption Survey (RECS) to a nationally representative sample of housing units. Traditionally, specially trained interviewers collect energy characteristics on the housing unit, usage patterns, and household demographics. Data include energy costs and usage for heating, cooling, appliances and other end uses.

Recombinant PrPSc shares structural features with brain-derived PrPSc: Insights from limited proteolysis.

PubMed

Sevillano, Alejandro M; Fernández-Borges, Natalia; Younas, Neelam; Wang, Fei; R Elezgarai, Saioa; Bravo, Susana; Vázquez-Fernández, Ester; Rosa, Isaac; Eraña, Hasier; Gil, David; Veiga, Sonia; Vidal, Enric; Erickson-Beltran, Melissa L; Guitián, Esteban; Silva, Christopher J; Nonno, Romolo; Ma, Jiyan; Castilla, Joaquín; R Requena, Jesús

2018-01-01

Very solid evidence suggests that the core of full length PrPSc is a 4-rung β-solenoid, and that individual PrPSc subunits stack to form amyloid fibers. We recently used limited proteolysis to map the β-strands and connecting loops that make up the PrPSc solenoid. Using high resolution SDS-PAGE followed by epitope analysis, and mass spectrometry, we identified positions ~116/118, 133-134, 141, 152-153, 162, 169 and 179 (murine numbering) as Proteinase K (PK) cleavage sites in PrPSc. Such sites likely define loops and/or borders of β-strands, helping us to predict the threading of the β-solenoid. We have now extended this approach to recombinant PrPSc (recPrPSc). The term recPrPSc refers to bona fide recombinant prions prepared by PMCA, exhibiting infectivity with attack rates of ~100%. Limited proteolysis of mouse and bank vole recPrPSc species yielded N-terminally truncated PK-resistant fragments similar to those seen in brain-derived PrPSc, albeit with varying relative yields. Along with these fragments, doubly N- and C-terminally truncated fragments, in particular ~89/97-152, were detected in some recPrPSc preparations; similar fragments are characteristic of atypical strains of brain-derived PrPSc. Our results suggest a shared architecture of recPrPSc and brain PrPSc prions. The observed differences, in particular the distinct yields of specific PK-resistant fragments, are likely due to differences in threading which result in the specific biochemical characteristics of recPrPSc. Furthermore, recombinant PrPSc offers exciting opportunities for structural studies unachievable with brain-derived PrPSc.

tif-dependent induction of colicin E1, prophage lambda, and filamentation in Escherichia coli K-12.

PubMed

Tessman, E S; Peterson, P K

1980-09-01

To help understand how the tif-1 mutation of the recA gene of Escherichia coli confers adenine activability on the recA protein, we used the fact that cytidine plus guanosine inhibits induction of prophage lambda and cell filamentation in a tif-1 mutant, and that adenine reverses this inhibition. We varied the amount of adenine in agar plates containing a fixed amount of cytidine and scored for survivors of three different tif-dependent lethal induction processes. Much more adenine was required for cell killing when cytidine was present than when it was absent. Therefore adenine does not override cytidine inhibition, but instead appears to compete with it for a site of action which may be on the recA protein. The competition is not at the cell transport level. Our results lead to a model in which the tif form of the recA protein is an allosteric enzyme that binds both negative and positive modulators. By varying the adenine-cytidine ratio of the medium it is possible to control the degree of induction in a tif-1 cell. For the three different tif-dependent inductions studied here, least adenine was required for lambda induction and most for lethal filamentation, presumably reflecting requirements for different amounts of activated recA protein in each process. Varying the adenine-cytidine ratio revealed two stable intermediate stages in lambda induction, as well as a stage of colicin E1 induction in which the cells produced colicin without cell death. The rate of filament formation could be similarly controlled. Experiments with tif (ColE1, lambda) gave evidence of a competition between colicin repressor and lambda repressor for activated recA protein.

Validity of field expedient devices to assess core temperature during exercise in the cold.

PubMed

Bagley, James R; Judelson, Daniel A; Spiering, Barry A; Beam, William C; Bartolini, J Albert; Washburn, Brian V; Carney, Keven R; Muñoz, Colleen X; Yeargin, Susan W; Casa, Douglas J

2011-12-01

Exposure to cold environments affects human performance and physiological function. Major medical organizations recommend rectal temperature (TREC) to evaluate core body temperature (TcORE) during exercise in the cold; however, other field expedient devices claim to measure TCORE. The purpose of this study was to determine if field expedient devices provide valid measures of TcRE during rest and exercise in the cold. Participants included 13 men and 12 women (age = 24 +/- 3 yr, height = 170.7 +/- 10.6 cm, mass = 73.4 +/- 16.7 kg, body fat = 18 +/- 7%) who reported being healthy and at least recreationally active. During 150 min of cold exposure, subjects sequentially rested for 30 min, cycled for 90 min (heart rate = 120-140 bpm), and rested for an additional 30 min. Investigators compared aural (T(AUR)), expensive axillary (T(AXLe)), inexpensive axillary (T(AXLi)), forehead (T(FOR)), gastrointestinal (T(GI)), expensive oral (T(ORLe)), inexpensive oral (T(ORLi)), and temporal (T(TEM)) temperatures to T(REc) every 15 min. Researchers used mean difference between each device and T(REC) (i.e., mean bias) as the primary criterion for validity. T(AUR), T(AXLe), T(AXLi), T(FOR), TORLe, T(ORLi), and TTEM provided significantly lower measures compared to T(REC) and fell below our validity criterion. T(GI) significantly exceeded T(REC) at three of eleven time points, but no significant difference existed between mean T(REC) and T(GI) across time. Only T(GI) achieved our validity criterion and compared favorably to T(REC). T(GI) offers a valid measurement with which to assess T(CORE) during rest and exercise in the cold; athletic trainers, mountain rescuers, and military medical personnel should avoid other field expedient devices in similar conditions.

Physiological temperatures reduce dimerization of dengue and Zika virus recombinant envelope proteins.

PubMed

Kudlacek, Stephan T; Premkumar, Lakshmanane; Metz, Stefan W; Tripathy, Ashutosh; Bobkov, Andrey A; Payne, Alexander Matthew; Graham, Stephen; Brackbill, James A; Miley, Michael J; de Silva, Aravinda M; Kuhlman, Brian

2018-06-08

The spread of dengue (DENV) and Zika virus (ZIKV) is a major public health concern. The primary target of antibodies that neutralize DENV and ZIKV is the envelope (E) glycoprotein, and there is interest in using soluble recombinant E (sRecE) proteins as subunit vaccines. However, the most potent neutralizing antibodies against DENV and ZIKV recognize epitopes on the virion surface that span two or more E proteins. Therefore, to create effective DENV and ZIKV vaccines, presentation of these quaternary epitopes may be necessary. The sRecE proteins from DENV and ZIKV crystallize as native-like dimers, but studies in solution suggest that these dimers are marginally stable. To better understand the challenges associated with creating stable sRecE dimers, we characterized the thermostability of sRecE proteins from ZIKV and three DENV serotypes, DENV2-4. All four proteins irreversibly unfolded at moderate temperatures (46-53 °C). At 23 °C and low micromolar concentrations, DENV2 and ZIKV were primarily dimeric, and DENV3-4 were primarily monomeric, whereas at 37 °C, all four proteins were predominantly monomeric. We further show that the dissociation constant for DENV2 dimerization is very temperature-sensitive, ranging from <1 μm at 25 °C to 50 μm at 41 °C, due to a large exothermic enthalpy of binding of -79 kcal/mol. We also found that quaternary epitope antibody binding to DENV2-4 and ZIKV sRecE is reduced at 37 °C. Our observation of reduced sRecE dimerization at physiological temperature highlights the need for stabilizing the dimer as part of its development as a subunit vaccine. © 2018 Kudlacek et al.

Heart-Rate Recovery Index Is Impaired in Behçet's Disease

PubMed Central

Kaya, Ergun Baris; Yorgun, Hikmet; Akdogan, Ali; Ates, Ahmet Hakan; Canpolat, Ugur; Sunman, Hamza; Aytemir, Kudret; Tokgozoglu, Lale; Kabakci, Giray; Calguneri, Meral; Ozkutlu, Hilmi; Oto, Ali

2009-01-01

Behçet's disease, a multisystemic inflammatory disorder, has been associated with a number of cardiovascular dysfunctions, including ventricular arrhythmias and sudden cardiac death. Heart-rate recovery after exercise can provide both an estimate of impaired parasympathetic tone and a prognosis in regard to all-cause and cardiovascular death. The aim of our study was to evaluate heart-rate recovery in Behçet's disease From January through July 2008, we examined at our outpatient clinic and prospectively enrolled 30 consecutive patients with Behçet's disease and 50 healthy control participants who were matched for age and sex. Basal electrocardiography, echocardiography, and treadmill exercise testing were performed in all patients and control participants. The heart-rate recovery index was calculated in the usual manner, by subtracting the 1st-minute (Rec1), 2nd-minute (Rec2), and 3rd-minute (Rec3) recovery heart rates from the maximal heart rate after exercise stress testing. Patients with Behçet's disease exhibited significantly lower heart-rate recovery numbers, compared with healthy control participants: Rec1, 24.28 ± 8.2 vs 34.4 ± 7.6, P = 0.002; Rec2, 49.28 ± 11.2 vs 57.5 ± 7.0, P < 0.05; and Rec3, 56.2 ± 12.11 vs 67.4 ± 8.7, P = 0.014. To our knowledge, this is the 1st study that shows an impaired heart-rate recovery index (indicative of reduced parasympathetic activity) among patients with Behçet's disease. Given the independent prognostic value of the heart-rate recovery index, our results may explain the increased occurrence of arrhythmias and sudden cardiac death in Behçet's patients. Therefore, this index may be clinically useful in the identification of high-risk patients. PMID:19693299

Conventional and novel body temperature measurement during rest and exercise induced hyperthermia.

PubMed

Towey, Colin; Easton, Chris; Simpson, Robert; Pedlar, Charles

2017-01-01

Despite technological advances in thermal sensory equipment, few core temperature (T CORE ) measurement techniques have met the established validity criteria in exercise science. Additionally, there is debate as to what method serves as the most practically viable, yet upholds the proposed measurement accuracy. This study assessed the accuracy of current and novel T CORE measurement techniques in comparison to rectal temperature (T REC ) as a reference standard. Fifteen well-trained subjects (11 male, 4 female) completed 60min of exercise at an intensity equating to the lactate threshold; measured via a discontinuous exercise test. T REC was significantly elevated from resting values (37.2±0.3°C) at the end of moderate intensity exercise (39.6±0.04°C; P=0.001). Intestinal telemetric pill (T PILL ) temperature and temporal artery temperature (T TEM ) did not differ significantly from T REC at rest or during exercise (P>0.05). However, aural canal temperature (T AUR ) and thermal imaging temperature (T IMA ) were both significantly lower than T REC (P<0.05). Bland Altman analysis revealed only T PILL was within acceptable limits of agreement (mean bias; 0.04°C), while T TEM , T AUR and T IMA demonstrated mean bias values outside of the acceptable range (>0.27°C). Against T REC , these results support the use of T PILL over all other techniques as a valid measure of T CORE at rest and during exercise induced hyperthermia. Novel findings illustrate that T IMA (when measured at the inner eye canthus) shows poor agreement to T REC during rest and exercise, which is similar to other 'surface' measures. Crown Copyright © 2016. Published by Elsevier Ltd. All rights reserved.

Analysis of total copper, cadmium and lead in refuse-derived fuels (RDF): study on analytical errors using synthetic samples.

PubMed

Skutan, Stefan; Aschenbrenner, Philipp

2012-12-01

Components with extraordinarily high analyte contents, for example copper metal from wires or plastics stabilized with heavy metal compounds, are presumed to be a crucial source of errors in refuse-derived fuel (RDF) analysis. In order to study the error generation of those 'analyte carrier components', synthetic samples spiked with defined amounts of carrier materials were mixed, milled in a high speed rotor mill to particle sizes <1 mm, <0.5 mm and <0.2 mm, respectively, and analyzed repeatedly. Copper (Cu) metal and brass were used as Cu carriers, three kinds of polyvinylchloride (PVC) materials as lead (Pb) and cadmium (Cd) carriers, and paper and polyethylene as bulk components. In most cases, samples <0.2 mm delivered good recovery rates (rec), and low or moderate relative standard deviations (rsd), i.e. metallic Cu 87-91% rec, 14-35% rsd, Cd from flexible PVC yellow 90-92% rec, 8-10% rsd and Pb from rigid PVC 92-96% rec, 3-4% rsd. Cu from brass was overestimated (138-150% rec, 13-42% rsd), Cd from flexible PVC grey underestimated (72-75% rec, 4-7% rsd) in <0.2 mm samples. Samples <0.5 mm and <1 mm spiked with Cu or brass produced errors of up to 220% rsd (<0.5 mm) and 370% rsd (<1 mm). In the case of Pb from rigid PVC, poor recoveries (54-75%) were observed in spite of moderate variations (rsd 11-29%). In conclusion, time-consuming milling to <0.2 mm can reduce variation to acceptable levels, even given the presence of analyte carrier materials. Yet, the sources of systematic errors observed (likely segregation effects) remain uncertain.

Genomic features of intertypic recombinant sabin poliovirus strains excreted by primary vaccinees.

PubMed

Cuervo, N S; Guillot, S; Romanenkova, N; Combiescu, M; Aubert-Combiescu, A; Seghier, M; Caro, V; Crainic, R; Delpeyroux, F

2001-07-01

The trivalent oral poliomyelitis vaccine (OPV) contains three different poliovirus serotypes. It use therefore creates particularly favorable conditions for mixed infection of gut cells, and indeed intertypic vaccine-derived recombinants (VdRec) have been frequently found in patients with vaccine-associated paralytic poliomyelitis. Nevertheless, there have not been extensive searches for VdRec in healthy vaccinees following immunization with OPV. To determine the incidence of VdRec and their excretion kinetics in primary vaccinees, and to establish the general genomic features of the corresponding recombinant genomes, we characterized poliovirus isolates excreted by vaccinees following primary immunization with OPV. Isolates were collected from 67 children 2 to 60 days following vaccination. Recombinant strains were identified by multiple restriction fragment length polymorphism assays. The localization of junction sites in recombinant genomes was also determined. VdRec excreted by vaccinees were first detected 2 to 4 days after vaccination. The highest rate of recombinants was on day 14. The frequency of VdRec depends strongly on the serotype of the analyzed isolates (2, 53, and 79% of recombinant strains in the last-excreted type 1, 2, and 3 isolates, respectively). Particular associations of genomic segments were preferred in the recombinant genomes, and recombination junctions were found in the genomic region encoding the nonstructural proteins. Recombination junctions generally clustered in particular subgenomic regions that were dependent on the serotype of the isolate and/or on the associations of genomic segments in recombinants. Thus, VdRec are frequently excreted by vaccinees, and the poliovirus replication machinery requirements or selection factors appear to act in vivo to shape the features of the recombinant genomes.

Differences in the motor unit firing rates and amplitudes in relation to recruitment thresholds during submaximal contractions of the first dorsal interosseous between chronically resistance trained and physically active men.

PubMed

Sterczala, Adam J; Miller, Jonathan D; Trevino, Michael A; Dimmick, Hannah L; Herda, Trent J

2018-02-26

Previous investigations report no changes in motor unit (MU) firing rates during submaximal contractions following resistance training. These investigations did not account for MU recruitment or examine firing rates as a function of recruitment threshold (REC).Therefore, MU recruitment and firing rates in chronically resistance trained (RT) and physically active controls (CON) were examined. Surface electromyography signals were collected from the first dorsal interosseous (FDI) during isometric muscle actions at 40% and 70% maximal voluntary contraction (MVC). For each MU, force at REC, mean firing rate (MFR) during the steady force, and MU action potential amplitude (MUAP_AMP) were analyzed. For each individual and contraction, the MFRs were linearly regressed against REC, whereas, exponential models were applied to the MFR vs. MUAP_AMP and MUAP_AMP vs. REC relationships with the y-intercepts and slopes (linear) and A and B terms (exponential) calculated. For the 40% MVC, the RT group had less negative slopes (p=0.001) and lower y-intercepts (p=0.006) of the MFR vs. REC relationships and lower B terms (p=0.011) of the MUAP_AMP vs. REC relationships. There were no differences in either relationship between groups for the 70% MVC. During the 40% MVC, the RT had a smaller range of MFRs and MUAP_AMPS in comparison to the CON, likely due to reduced MU recruitment. The RT had lower MFRs and recruitment during the 40% MVC that may indicate a leftward shift in the force-frequency relationship, and thus require less excitation to the motoneuron pool to match the same relative force.

Mutation analysis of Australasian Gaucher disease patients

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

Nelson, P.V.; Carey, W.F.; Morris, C.P.

1995-09-25

We have previously reported phenotype and genotype analyses in 28 Australasian Gaucher patients who were screened for several of the common Gaucher mutations: N370S, L444P, 84GG, and R463C. Horowitz and Zimran have reported that the complex alleles recNciI and recTL, which contain several point mutations including L444P, are relatively common, especially in non-Jewish Gaucher patients. Zimran and Horowitz have also stated that these recombinant alleles could easily be missed by laboratories testing only for the common Gaucher point mutations. Failure to correctly identify these mutations would influence any attempt to correlate genotype with phenotype. We have therefore retested our Gauchermore » patients for recNciI (L444P, A456P, and V46OV) and recTL (D409H, L444P, A456P, and V46OV) by PCR amplification, followed by hybridization with allele-specific oligonucleotides. 4 refs.« less

RecA binding to a single double-stranded DNA molecule: A possible role of DNA conformational fluctuations

PubMed Central

Leger, J. F.; Robert, J.; Bourdieu, L.; Chatenay, D.; Marko, J. F.

1998-01-01

Most genetic regulatory mechanisms involve protein–DNA interactions. In these processes, the classical Watson–Crick DNA structure sometimes is distorted severely, which in turn enables the precise recognition of the specific sites by the protein. Despite its key importance, very little is known about such deformation processes. To address this general question, we have studied a model system, namely, RecA binding to double-stranded DNA. Results from micromanipulation experiments indicate that RecA binds strongly to stretched DNA; based on this observation, we propose that spontaneous thermal stretching fluctuations may play a role in the binding of RecA to DNA. This has fundamental implications for the protein–DNA binding mechanism, which must therefore rely in part on a combination of flexibility and thermal fluctuations of the DNA structure. We also show that this mechanism is sequence sensitive. Theoretical simulations support this interpretation of our experimental results, and it is argued that this is of broad relevance to DNA–protein interactions. PMID:9770480

GAP-REACH: a checklist to assess comprehensive reporting of race, ethnicity, and culture in psychiatric publications.

PubMed

Lewis-Fernández, Roberto; Raggio, Greer A; Gorritz, Magdaliz; Duan, Naihua; Marcus, Sue; Cabassa, Leopoldo J; Humensky, Jennifer; Becker, Anne E; Alarcón, Renato D; Oquendo, María A; Hansen, Helena; Like, Robert C; Weiss, Mitchell; Desai, Prakash N; Jacobsen, Frederick M; Foulks, Edward F; Primm, Annelle; Lu, Francis; Kopelowicz, Alex; Hinton, Ladson; Hinton, Devon E

2013-10-01

Growing awareness of health and health care disparities highlights the importance of including information about race, ethnicity, and culture (REC) in health research. Reporting of REC factors in research publications, however, is notoriously imprecise and unsystematic. This article describes the development of a checklist to assess the comprehensiveness and the applicability of REC factor reporting in psychiatric research publications. The 16-item GAP-REACH checklist was developed through a rigorous process of expert consensus, empirical content analysis in a sample of publications (N = 1205), and interrater reliability (IRR) assessment (N = 30). The items assess each section in the conventional structure of a health research article. Data from the assessment may be considered on an item-by-item basis or as a total score ranging from 0% to 100%. The final checklist has excellent IRR (κ = 0.91). The GAP-REACH may be used by multiple research stakeholders to assess the scope of REC reporting in a research article.

Packaging and testing of multi-wavelength DFB laser array using REC technology

NASA Astrophysics Data System (ADS)

Ni, Yi; Kong, Xuan; Gu, Xiaofeng; Chen, Xiangfei; Zheng, Guanghui; Luan, Jia

2014-02-01

Packaging of distributed feedback (DFB) laser array based on reconstruction-equivalent-chirp (REC) technology is a bridge from chip to system, and influences the practical process of REC chip. In this paper, DFB laser arrays of 4-channel @1310 nm and 8-channel @1550 nm are packaged. Our experimental results show that both these laser arrays have uniform wavelength spacing and larger than 35 dB average Side Mode Suppression Ratio (SMSR). When I=35 mA, we obtain the total output power of 1 mW for 4-channel @1310 nm, and 227 μw for 8-channel @1550 nm respectively. The high frequency characteristics of the packaged chips are also obtained, and the requirements for 4×10 G or even 8×10 G systems can be reached. Our results demonstrate the practical and low cost performance of REC technology and indicate its potential in the future fiber-to-the-home (FTTH) application.

Set-shifting and its relation to clinical and personality variables in full recovery of anorexia nervosa.

PubMed

Lindner, Susanne E; Fichter, Manfred M; Quadflieg, Norbert

2014-07-01

First, this study aimed to explore whether set-shifting is inefficient after full recovery of anorexia nervosa (recAN). Second, this study wanted to explore the relation of set-shifting to clinical and personality variables. A total of 100 recAN women were compared with 100 healthy women. Set-shifting was assessed with Berg's Card Sorting Test. Expert interviews yielded assessments for the inclusion/exclusion criteria, self-ratings for clinical and personality variables. Compared with the healthy control group, the recAN participants achieved fewer categories, showed more perseverations and spent less time for shifting set. Perfectionism is correlated with set-shifting but in converse directions in the two groups. Our study supports the findings of inefficiencies in set-shifting after full recovery from AN. Higher perfectionism in the recAN group is associated with better set-shifting ability, whereas higher perfectionism in the healthy control group is related to worse set-shifting ability. Copyright © 2014 John Wiley & Sons, Ltd and Eating Disorders Association.

RecA Inhibitors Potentiate Antibiotic Activity and Block Evolution of Antibiotic Resistance.

PubMed

Alam, Md Kausar; Alhhazmi, Areej; DeCoteau, John F; Luo, Yu; Geyer, C Ronald

2016-03-17

Antibiotic resistance arises from the maintenance of resistance mutations or genes acquired from the acquisition of adaptive de novo mutations or the transfer of resistance genes. Antibiotic resistance is acquired in response to antibiotic therapy by activating SOS-mediated DNA repair and mutagenesis and horizontal gene transfer pathways. Initiation of the SOS pathway promotes activation of RecA, inactivation of LexA repressor, and induction of SOS genes. Here, we have identified and characterized phthalocyanine tetrasulfonic acid RecA inhibitors that block antibiotic-induced activation of the SOS response. These inhibitors potentiate the activity of bactericidal antibiotics, including members of the quinolone, β-lactam, and aminoglycoside families in both Gram-negative and Gram-positive bacteria. They reduce the ability of bacteria to acquire antibiotic resistance mutations and to transfer mobile genetic elements conferring resistance. This study highlights the advantage of including RecA inhibitors in bactericidal antibiotic therapies and provides a new strategy for prolonging antibiotic shelf life. Copyright © 2016 Elsevier Ltd. All rights reserved.

Shortcomings of protocols of drug trials in relation to sponsorship as identified by Research Ethics Committees: analysis of comments raised during ethical review.

PubMed

van Lent, Marlies; Rongen, Gerard A; Out, Henk J

2014-12-10

Submission of study protocols to research ethics committees (RECs) constitutes one of the earliest stages at which planned trials are documented in detail. Previous studies have investigated the amendments requested from researchers by RECs, but the type of issues raised during REC review have not been compared by sponsor type. The objective of this study was to identify recurring shortcomings in protocols of drug trials based on REC comments and to assess whether these were more common among industry-sponsored or non-industry trials. Retrospective analysis of 226 protocols of drug trials approved in 2010-2011 by three RECs affiliated to academic medical centres in The Netherlands. For each protocol, information on sponsorship, number of participating centres, participating countries, study phase, registration status of the study drug, and type and number of subjects was retrieved. REC comments were extracted from decision letters sent to investigators after review and were classified using a predefined checklist that was based on legislation and guidelines on clinical drug research and previous literature. Most protocols received comments regarding participant information and consent forms (n = 182, 80.5%), methodology and statistical analyses (n = 160, 70.8%), and supporting documentation, including trial agreements and certificates of insurance (n = 154, 68.1%). Of the submitted protocols, 122 (54.0%) were non-industry and 104 (46.0%) were industry-sponsored trials. Non-industry trials more often received comments on subject selection (n = 44, 36.1%) than industry-sponsored trials (n = 18, 17.3%; RR, 1.58; 95% CI, 1.01 to 2.47), and on methodology and statistical analyses (n = 95, 77.9% versus n = 65, 62.5%, respectively; RR, 1.18; 95% CI, 1.01 to 1.37). Non-industry trials less often received comments on supporting documentation (n = 72, 59.0%) than industry-sponsored trials (n = 82, 78.8%; RR, 0.83; 95% CI, 0.72 to 0.95). RECs identified important ethical and methodological shortcomings in protocols of both industry-sponsored and non-industry drug trials. Investigators, especially of non-industry trials, should better prepare their research protocols in order to facilitate the ethical review process.

The Establishment of a Formal Midwest Renewable Energy Tracking System (M-RETS) Organization

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

Maria Redmond; Chela Bordas O'Connor

2010-06-30

The objectives identified in requesting and utilizing this funding has been met. The goal was to establish a formal, multi-jurisdictional organization to: (1) ensure the policy objectives of the participating jurisdictions are addressed through increased tradability of the Renewable Energy Credits (RECs) from M-RETS and to eliminate the possibility that a single jurisdiction will be the sole arbiter of the operation of the system; (2) facilitate the establishment of REC standards including the attributes related to, the creation, trading, and interaction with other trading and tracking systems; and (3) have a centralized and established organization that will be responsible formore » the contracting and governance responsibilities of a multi-jurisdictional tracking system. The M-RETS Inc. Board ensures that the system remains policy neutral; that the attributes of generation are tracked in a way that allows the system users to easily identify and trade relevant RECs; that the system can add jurisdictions as needed or desired; and that the tracking system operate in such a way to allow for the greatest access possible for those participating in other tracking or trading systems by allowing those systems to negotiate with a single M-RETS entity for the import and export of RECs. M-RETS as an organizational body participates and often leads the discussions related to the standardization of RECs and increasing the tradability of M-RETS RECs. M-RETS is a founding member of the Environmental Trading Network of North America (ETNNA) and continues to take a leadership role in the development of processes to facilitate trading among tracking systems and to standardize REC definitions. The Board of Directors of M-RETS, Inc., the non-profit corporation, continues to hold telephone/internet Board meetings. Legal counsel continues working with the board and APX management on a new agreement with APX. The board expects to have an agreement and corresponding fee structure in place by January 2011. The Board has recently approved exports to three other tracking systems and is in discussions about imports to the system. Below are the tasks outlined in the request and attached you will find the relevant documentation.« less

TSAR (Theater Simulation of Airbase Resources) Database Dictionary F-4G.

DTIC Science & Technology

1987-06-05

REC/TRANS RT-1159 388 71ZDO CNTL UNIT C- 10062 /A 391 71320 CNTL ARN-127 393 723A0 REC/TRANS RT-689 394 723B0 INDIC, HEIGHT TOTAL NUMBER OF PART REPAIR...PROCEDURES - 2 LOU " 4"p" IW qg t~l pb i.go stanc E lm FIGURE 98 111-260 S.. RESOURCE REQUIREMENTS 111.1.5.25 LIU’S #45 - #49 - *LRU PART TIME...RT-1159 AG 386 71ZBO ADAPTER MX9577 AG 387 71ZCO MOUNT (REC/TRANS) AG 388 71ZDO CNTL UNIT C- 10062 /A AG 389 71ZEO MOUNT (DIG TO ANALOG CONVERTER) AG

Detecting potential teratogenic alkaloids from blue cohosh rhizomes using an in vitro rat embryo culture.

PubMed

Kennelly, E J; Flynn, T J; Mazzola, E P; Roach, J A; McCloud, T G; Danford, D E; Betz, J M

1999-10-01

The novel alkaloid thalictroidine (1), as well as the known alkaloids taspine (2), magnoflorine (3), anagyrine (4), baptifoline (5), 5,6-dehydro-alpha-isolupanine (6), alpha-isolupanine (7), lupanine (8), N-methylcytisine (9), and sparteine (10), were identified from an extract of Caulophyllum thalictroides rhizomes. N-Methylcytisine exhibited teratogenic activity in the rat embryo culture (REC), an in vitro method to detect potential teratogens. The structure of 1 was elucidated using various spectroscopic methods, primarily by NMR techniques. Thalictroidine, anagyrine, and alpha-isolupanine were not teratogenic in the REC at tested concentrations. Taspine (2) showed high embryotoxicity, but no teratogenic activity, in the REC.

Best Practices from the Design and Development of the Ares I Launch Vehicle Roll and Reaction Control Systems

NASA Technical Reports Server (NTRS)

Butt, Adam; Paseur, Lila F.; Pitts, Hank M.

2012-01-01

On April 15, 2010 President Barak Obama made the official announcement that the Constellation Program, which included the Ares I launch vehicle, would be canceled. NASA s Ares I launch vehicle was being designed to launch the Orion Crew Exploration Vehicle, returning humans to the moon, Mars, and beyond. It consisted of a First Stage (FS) five segment solid rocket booster and a liquid J-2X Upper Stage (US) engine. Roll control for the FS was planned to be handled by a dedicated Roll Control System (RoCS), located on the connecting interstage. Induced yaw or pitch moments experienced during FS ascent would have been handled by vectoring of the booster nozzle. After FS booster separation, the US Reaction Control System (ReCS) would have provided the US Element with three degrees of freedom control as needed. The best practices documented in this paper will be focused on the technical designs and producibility of both systems along with the partnership between NASA and Boeing, who was on contract to build the Ares I US Element, which included the FS RoCS and US ReCS. In regards to partnership, focus will be placed on integration along with technical work accomplished by Boeing. This will include detailed emphasis on task orders developed between NASA and Boeing that were used to direct specific work that needed to be accomplished. In summary, this paper attempts to capture key best practices that should be helpful in the development of future launch vehicle and spacecraft RCS designs.

Debris extrusion and foraminal deformation produced by reciprocating instruments made of thermally treated NiTi wires.

PubMed

Frota, Myrna Maria Arcanjo; Bernardes, Ricardo Affonso; Vivan, Rodrigo Ricci; Vivacqua-Gomes, Nilton; Duarte, Marco Antonio Hungaro; Vasconcelos, Bruno Carvalho de

2018-01-18

To evaluate the amount of apically extruded debris, percentage of foraminal enlargement and apical foramen (AF) deformation that occurred during root canal preparation with different reciprocation systems: Reciproc, WaveOne (M-Wire), and ProDesign R (Shape Memory Technology Wire) at two different working lengths (WLs): 0.0 and 1.0 mm beyond the AF. The AF of 120 root canals in 60 mesial roots of mandibular molars were photographed with stereomicroscope and randomly assigned into four groups: manual, Reciproc (REC), WaveOne (WO), and ProDesign R (PDR); subsequently, they were further subdivided according to the WL (n=15). Teeth were instrumented, coupled to a dual collecting chamber, and then another photograph of each AF was captured. Extrusion was analysed by determining the weight of extruded debris. Each AF diameter was measured in pre- and post-instrumentation images to determine deformation, which was analysed, and afterwards the final format of AFs was classified (circular/oval/deformed). We found no significant differences when analysing each system at different WLs. When considering each WL, REC and WO showed highest extrusion values (P<.05); for AF enlargement, differences were observed only for WO, when it was used beyond the AF; differences were observed among M-Wire groups beyond the AF (P<.05). AF deformation was observed in all groups; PDR showed the lowest AF deformation values at both WLs; M-Wire groups showed 50% strain beyond the AF. Authors concluded that beyond the apical limit, the alloy and taper are important aspects when considering extrusion and deformation.

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the identification of Burkholderia pseudomallei from Asia and Australia and differentiation between Burkholderia species

PubMed Central

Suttisunhakul, Vichaya; Pumpuang, Apinya; Ekchariyawat, Peeraya; Wuthiekanun, Vanaporn; Elrod, Mindy G.; Turner, Paul; Currie, Bart J.; Phetsouvanh, Rattanaphone; Dance, David A. B.; Limmathurotsakul, Direk; Peacock, Sharon J.

2017-01-01

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is increasingly used for rapid bacterial identification. Studies of Burkholderia pseudomallei identification have involved small isolate numbers drawn from a restricted geographic region. There is a need to expand the reference database and evaluate B. pseudomallei from a wider geographic distribution that more fully captures the extensive genetic diversity of this species. Here, we describe the evaluation of over 650 isolates. Main spectral profiles (MSP) for 26 isolates of B. pseudomallei (N = 5) and other Burkholderia species (N = 21) were added to the Biotyper database. MALDI-TOF MS was then performed on 581 B. pseudomallei, 19 B. mallei, 6 B. thailandensis and 23 isolates representing a range of other bacterial species. B. pseudomallei originated from northeast and east Thailand (N = 524), Laos (N = 12), Cambodia (N = 14), Hong Kong (N = 4) and Australia (N = 27). All 581 B. pseudomallei were correctly identified, with 100% sensitivity and specificity. Accurate identification required a minimum inoculum of 5 x 107 CFU/ml, and identification could be performed on spiked blood cultures after 24 hours of incubation. Comparison between a dendrogram constructed from MALDI-TOF MS main spectrum profiles and a phylogenetic tree based on recA gene sequencing demonstrated that MALDI-TOF MS distinguished between B. pseudomallei and B. mallei, while the recA tree did not. MALDI-TOF MS is an accurate method for the identification of B. pseudomallei, and discriminates between this and other related Burkholderia species. PMID:28384252

Recombineering using RecET from Pseudomonas syringae

USDA-ARS?s Scientific Manuscript database

Here we report the identification of functions that promote genomic recombination of linear DNA introduced into Pseudomonas cells by electroporation. The genes encoding these functions were identified in Pseudomonas syringae pv. syringae B728a based on similarity to the lambda Red Exo/Beta and RecE...

Rec and Read Mentor Programs

ERIC Educational Resources Information Center

Johnson, Amy Carpenter; Halas, Joannie

2011-01-01

For the past six years in Winnipeg, Canada, young people from diverse Aboriginal backgrounds have been volunteering their time, energy, and talents to develop and deliver after-school physical activity, nutrition, and education programs for children in their school's neighbourhood. Known as "Rec and Read," the after-school activities are…

32 CFR Appendix B to Part 651 - Categorical Exclusions

Code of Federal Regulations, 2014 CFR

2014-07-01

... local permits), and erosion control and stormwater control structures (REC required). (3) Implementation..., smoke bombs, etc.) for military police and crowd control activities where there is no change from the... areas to the underlying fee owner (REC required). (3) Transfer of real property administrative control...

A defect in homologous recombination leads to increased translesion synthesis in E. coli

PubMed Central

Naiman, Karel; Pagès, Vincent; Fuchs, Robert P.

2016-01-01

DNA damage tolerance pathways allow cells to duplicate their genomes despite the presence of replication blocking lesions. Cells possess two major tolerance strategies, namely translesion synthesis (TLS) and homology directed gap repair (HDGR). TLS pathways involve specialized DNA polymerases that are able to synthesize past DNA lesions with an intrinsic risk of causing point mutations. In contrast, HDGR pathways are essentially error-free as they rely on the recovery of missing information from the sister chromatid by RecA-mediated homologous recombination. We have investigated the genetic control of pathway choice between TLS and HDGR in vivo in Escherichia coli. In a strain with wild type RecA activity, the extent of TLS across replication blocking lesions is generally low while HDGR is used extensively. Interestingly, recA alleles that are partially impaired in D-loop formation confer a decrease in HDGR and a concomitant increase in TLS. Thus, partial defect of RecA's capacity to invade the homologous sister chromatid increases the lifetime of the ssDNA.RecA filament, i.e. the ‘SOS signal’. This increase favors TLS by increasing both the TLS polymerase concentration and the lifetime of the TLS substrate, before it becomes sequestered by homologous recombination. In conclusion, the pathway choice between error-prone TLS and error-free HDGR is controlled by the efficiency of homologous recombination. PMID:27257075

Research ethics committee auditing: the experience of a university hospital.

PubMed

Marchetti, Daniela; Spagnolo, Angelico; Cicerone, Marina; Cascini, Fidelia; La Monaca, Giuseppe; Spagnolo, Antonio G

2013-09-01

The authors report the first Italian experience of a research ethics committee (REC) audit focused on the evaluation of the REC's compliance with standard operating procedures, requirements in insurance coverage, informed consent, protection of privacy and confidentiality, predictable risks/harms, selection of subjects, withdrawal criteria and other issues, such as advertisement details and justification of placebo. The internal audit was conducted over a two-year period (March 2009-February 2011) divided into quarters to better value the influence of the new insurance coverage regulation that came into effect in March 2010 (Ministerial Decree of 14 July, 2009) and expand the requirements to safeguard participants in clinical drug trials including other critical items as information and consent and the risks to benefits ratio. Out of a total of 639 REC's opinions and research studies, 316 were reviewed. Regarding the insurance policy requirements, Auditor/REC non-compliance occurred only in one case. The highest number of Auditor/REC non-compliance was in regard to information and consent, which should have incurred a suspended decision rather than a favorable opinion. This internal audit shows the importance and the difficulty of the review process. For this reason, specific courses for members of the research ethics committee and for those who aspire to become auditors will be provided. There may also be efforts to improve the standard operating procedures already in place.

Effects of a human recombinant alkaline phosphatase during impaired mitochondrial function in human renal proximal tubule epithelial cells.

PubMed

Peters, Esther; Schirris, Tom; van Asbeck, Alexander H; Gerretsen, Jelle; Eymael, Jennifer; Ashikov, Angel; Adjobo-Hermans, Merel J W; Russel, Frans; Pickkers, Peter; Masereeuw, Rosalinde

2017-02-05

Sepsis-associated acute kidney injury is a multifactorial syndrome in which inflammation and renal microcirculatory dysfunction play a profound role. Subsequently, renal tubule mitochondria reprioritize cellular functions to prevent further damage. Here, we investigated the putative protective effects of human recombinant alkaline phosphatase (recAP) during inhibition of mitochondrial respiration in conditionally immortalized human proximal tubule epithelial cells (ciPTEC). Full inhibition of mitochondrial oxygen consumption was obtained after 24h antimycin A treatment, which did not affect cell viability. While recAP did not affect the antimycin A-induced decreased oxygen consumption and increased hypoxia-inducible factor-1α or adrenomedullin gene expression levels, the antimycin A-induced increase of pro-inflammatory cytokines IL-6 and IL-8 was attenuated. Antimycin A tended to induce the release of detrimental purines ATP and ADP, which reached statistical significance when antimycin A was co-incubated with lipopolysaccharide, and were completely converted into cytoprotective adenosine by recAP. As the adenosine A 2A receptor was up-regulated after antimycin A exposure, an adenosine A 2A receptor knockout ciPTEC cell line was generated in which recAP still provided protection. Together, recAP did not affect oxygen consumption but attenuated the inflammatory response during impaired mitochondrial function, an effect suggested to be mediated by dephosphorylating ATP and ADP into adenosine. Copyright © 2016 Elsevier B.V. All rights reserved.

Diabetes-Induced Superoxide Anion and Breakdown of the Blood-Retinal Barrier: Role of the VEGF/uPAR Pathway

PubMed Central

El-Remessy, Azza B.; Franklin, Telina; Ghaley, Nagla; Yang, Jinling; Brands, Michael W.; Caldwell, Ruth B.; Behzadian, Mohamed Ali

2013-01-01

Diabetes-induced breakdown of the blood-retinal barrier (BRB) has been linked to hyperglycemia-induced expression of vascular endothelial growth factor (VEGF) and is likely mediated by an increase in oxidative stress. We have shown that VEGF increases permeability of retinal endothelial cells (REC) by inducing expression of urokinase plasminogen activator receptor (uPAR). The purpose of this study was to define the role of superoxide anion in VEGF/uPAR expression and BRB breakdown in diabetes. Studies were performed in streptozotocin diabetic rats and mice and high glucose (HG) treated REC. The superoxide dismutase (SOD) mimetic tempol blocked diabetes-induced permeability and uPAR expression in rats and the cell permeable SOD inhibited HG-induced expression of uPAR and VEGF in REC. Inhibiting VEGFR blocked HG-induced expression of VEGF and uPAR and GSK-3β phosphorylation in REC. HG caused β-catenin translocation from the plasma membrane into the cytosol and nucleus. Treatment with HG-conditioned media increased REC paracellular permeability that was blocked by anti-uPA or anti-uPAR antibodies. Moreover, deletion of uPAR blocked diabetes-induced BRB breakdown and activation of MMP-9 in mice. Together, these data indicate that diabetes-induced oxidative stress triggers BRB breakdown by a mechanism involving uPAR expression through VEGF-induced activation of the GSK3β/β-catenin signaling pathway. PMID:23951261

Variable pressure ionization detector for gas chromatography

DOEpatents

Buchanan, Michelle V.; Wise, Marcus B.

1988-01-01

Method and apparatus for differentiating organic compounds based on their electron affinity. An electron capture detector cell (ECD) is operated at pressures ranging from atmospheric to less than 1 torr. Through variation of the pressure within the ECD cell, the organic compounds are induced to either capture or emit electrons. Differentiation of isomeric compounds can be obtianed when, at a given pressure, one isomer is in the emission mode and the other is in the capture mode. Output of the ECD is recorded by chromatogram. The invention also includes a method for obtaining the zero-crossing pressure of a compound, defined as the pressure at which the competing emission and capture reactions are balanced and which may be correlated to the electron affinity of a compound.

77 FR 4059 - Certain Electronic Devices for Capturing and Transmitting Images, and Components Thereof; Receipt...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-01-26

... Images, and Components Thereof; Receipt of Complaint; Solicitation of Comments Relating to the Public... Devices for Capturing and Transmitting Images, and Components Thereof, DN 2869; the Commission is... importation of certain electronic devices for capturing and transmitting images, and components thereof. The...

North Carolina | Midmarket Solar Policies in the United States | Solar

Science.gov Websites

impose standby charges consistent with approved standby rates applicable to other customer-owned utilities without customer compensation. RECs: Utilities owns renewable energy certificates (RECs), unless customer chooses to net meter under a time of use tariff with demand charges. Meter aggregation: Not

Factors affecting variation of different measures of cheese yield and milk nutrient recovery from an individual model cheese-manufacturing process.

PubMed

Cipolat-Gotet, C; Cecchinato, A; De Marchi, M; Bittante, G

2013-01-01

Cheese yield (CY) is the most important technological trait of milk, because cheese-making uses a very high proportion of the milk produced worldwide. Few studies have been carried out at the level of individual milk-producing animals due to a scarcity of appropriate procedures for model-cheese production, the complexity of cheese-making, and the frequent use of the fat and protein (or casein) contents of milk as a proxy for cheese yield. Here, we report a high-throughput cheese manufacturing process that mimics all phases of cheese-making, uses 1.5-L samples of milk from individual animals, and allows the simultaneous processing of 15 samples per run. Milk samples were heated (35°C for 40 min), inoculated with starter culture (90 min), mixed with rennet (51.2 international milk-clotting units/L of milk), and recorded for gelation time. Curds were cut twice (10 and 15 min after gelation), separated from the whey, drained (for 30 min), pressed (3 times, 20 min each, with the wheel turned each time), salted in brine (for 60 min), weighed, and sampled. Whey was collected, weighed, and sampled. Milk, curd, and whey samples were analyzed for pH, total solids, fat content, and protein content, and energy content was estimated. Three measures of percentage cheese yield (%CY) were calculated: %CY(CURD), %CY(SOLIDS), and %CY(WATER), representing the ratios between the weight of fresh curd, the total solids of the curd, and the water content of the curd, respectively, and the weight of the milk processed. In addition, 3 measures of daily cheese yield (dCY, kg/d) were defined, considering the daily milk yield. Three measures of nutrient recovery (REC) were computed: REC(FAT), REC(PROTEIN), and REC(SOLIDS), which represented the ratio between the weights of the fat, protein, and total solids in the curd, respectively, and the corresponding components in the milk. Energy recovery, REC(ENERGY), represented the energy content of the cheese compared with that in the milk. This procedure was used to process individual milk samples obtained from 1,167 Brown Swiss cows reared in 85 herds of the province of Trento (Italy). The assessed traits exhibited almost normal distributions, with the exception of REC(FAT). The average values (± SD) were as follows: %CY(CURD)=14.97±1.86, %CY(SOLIDS)=7.18±0.92, %CY(WATER)=7.77±1.27, dCY(CURD)=3.63±1.17, dCY(SOLIDS)=1.74±0.57, dCY(WATER)=1.88±0.63, REC(FAT)=89.79±3.55, REC(PROTEIN)=78.08±2.43, REC(SOLIDS)=51.88±3.52, and REC(ENERGY)=67.19±3.29. All traits were highly influenced by herd-test-date and days in milk of the cow, moderately influenced by parity, and weakly influenced by the utilized vat. Both %CY(CURD) and dCY(CURD) depended not only on the fat and protein (casein) contents of the milk, but also on their proportions retained in the curd; the water trapped in curd presented an higher variability than that of %CY(SOLIDS). All REC traits were variable and affected by days in milk and parity of the cows. The described model cheese-making procedure and the results obtained provided new insight into the phenotypic variation of cheese yield and recovery traits at the individual level. Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

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

Dillon, Heather E.; Antonopoulos, Chrissi A.; Solana, Amy E.

As the model energy codes are improved to reach efficiency levels 50 percent greater than current codes, use of on-site renewable energy generation is likely to become a code requirement. This requirement will be needed because traditional mechanisms for code improvement, including envelope, mechanical and lighting, have been pressed to the end of reasonable limits. Research has been conducted to determine the mechanism for implementing this requirement (Kaufman 2011). Kaufmann et al. determined that the most appropriate way to structure an on-site renewable requirement for commercial buildings is to define the requirement in terms of an installed power density permore » unit of roof area. This provides a mechanism that is suitable for the installation of photovoltaic (PV) systems on future buildings to offset electricity and reduce the total building energy load. Kaufmann et al. suggested that an appropriate maximum for the requirement in the commercial sector would be 4 W/ft{sup 2} of roof area or 0.5 W/ft{sup 2} of conditioned floor area. As with all code requirements, there must be an alternative compliance path for buildings that may not reasonably meet the renewables requirement. This might include conditions like shading (which makes rooftop PV arrays less effective), unusual architecture, undesirable roof pitch, unsuitable building orientation, or other issues. In the short term, alternative compliance paths including high performance mechanical equipment, dramatic envelope changes, or controls changes may be feasible. These options may be less expensive than many renewable systems, which will require careful balance of energy measures when setting the code requirement levels. As the stringency of the code continues to increase however, efficiency trade-offs will be maximized, requiring alternative compliance options to be focused solely on renewable electricity trade-offs or equivalent programs. One alternate compliance path includes purchase of Renewable Energy Credits (RECs). Each REC represents a specified amount of renewable electricity production and provides an offset of environmental externalities associated with non-renewable electricity production. The purpose of this paper is to explore the possible issues with RECs and comparable alternative compliance options. Existing codes have been examined to determine energy equivalence between the energy generation requirement and the RECs alternative over the life of the building. The price equivalence of the requirement and the alternative are determined to consider the economic drivers for a market decision. This research includes case studies that review how the few existing codes have incorporated RECs and some of the issues inherent with REC markets. Section 1 of the report reviews compliance options including RECs, green energy purchase programs, shared solar agreements and leases, and other options. Section 2 provides detailed case studies on codes that include RECs and community based alternative compliance methods. The methods the existing code requirements structure alternative compliance options like RECs are the focus of the case studies. Section 3 explores the possible structure of the renewable energy generation requirement in the context of energy and price equivalence. The price of RECs have shown high variation by market and over time which makes it critical to for code language to be updated frequently for a renewable energy generation requirement or the requirement will not remain price-equivalent over time. Section 4 of the report provides a maximum case estimate for impact to the PV market and the REC market based on the Kaufmann et al. proposed requirement levels. If all new buildings in the commercial sector complied with the requirement to install rooftop PV arrays, nearly 4,700 MW of solar would be installed in 2012, a major increase from EIA estimates of 640 MW of solar generation capacity installed in 2009. The residential sector could contribute roughly an additional 2,300 MW based on the same code requirement levels of 4 W/ft{sup 2} of roof area. Section 5 of the report provides a basic framework for draft code language recommendations based on the analysis of the alternative compliance levels.« less

Electron capture in collisions of Al2+ ions with He atoms at intermediate energies

NASA Astrophysics Data System (ADS)

Watanabe, A.; Sato, H.; Gu, J. P.; Hirsch, G.; Buenker, R. J.; Kimura, M.

2001-09-01

Electron capture resulting from collisions of Al2+ ions with He atoms from 0.15 to 1000 keV/u is investigated using a molecular-orbital representation within a semiclassical frame. Molecular electronic states and corresponding couplings are determined by the ALCHEMY program. Sixteen molecular states all connecting to single-electron-capture processes are included, and hence radial and rotational couplings among these channels are fully considered. The trajectory effect arising from the straight-line, Coulomb, and ground-state potential trajectories for electron-capture and excitation processes is carefully assessed. The electron-capture cross section by ground-state Al2+(2S) ions slowly increases before it reaches a maximum of 1.3×10-16 cm2 at 100 keV/u. Those for metastable Al2+(2P) ions sharply increase with increasing energy, and reach a peak at 1 keV/u with a value of 1.5×10-16 cm2. The earlier experimental data are found to be larger by an order of magnitude although their energy dependence is in good accord with the present result. Excitation cross sections for both the ground and metastable states are found to be much larger by a factor of 2-3 than corresponding capture cross sections above 1 keV/u although they become comparable below this energy.

Electronic case report forms and electronic data capture within clinical trials and pharmacoepidemiology.

PubMed

Rorie, David A; Flynn, Robert W V; Grieve, Kerr; Doney, Alexander; Mackenzie, Isla; MacDonald, Thomas M; Rogers, Amy

2017-09-01

Researchers in clinical and pharmacoepidemiology fields have adopted information technology (IT) and electronic data capture, but these remain underused despite the benefits. This review discusses electronic case report forms and electronic data capture, specifically within pharmacoepidemiology and clinical research. The review used PubMed and the Institute of Electrical and Electronic Engineers library. Search terms used were agreed by the authors and documented. PubMed is medical and health based, whereas Institute of Electrical and Electronic Engineers is technology based. The review focuses on electronic case report forms and electronic data capture, but briefly considers other relevant topics; consent, ethics and security. There were 1126 papers found using the search terms. Manual filtering and reviewing of abstracts further condensed this number to 136 relevant manuscripts. The papers were further categorized: 17 contained study data; 40 observational data; 27 anecdotal data; 47 covering methodology or design of systems; one case study; one literature review; two feasibility studies; and one cost analysis. Electronic case report forms, electronic data capture and IT in general are viewed with enthusiasm and are seen as a cost-effective means of improving research efficiency, educating participants and improving trial recruitment, provided concerns about how data will be protected from misuse can be addressed. Clear operational guidelines and best practises are key for healthcare providers, and researchers adopting IT, and further work is needed on improving integration of new technologies with current systems. A robust method of evaluation for technical innovation is required. © 2017 The Authors. British Journal of Clinical Pharmacology published by John Wiley & Sons Ltd on behalf of British Pharmacological Society.

Electronic case report forms and electronic data capture within clinical trials and pharmacoepidemiology

PubMed Central

Flynn, Robert W. V.; Grieve, Kerr; Doney, Alexander; Mackenzie, Isla; MacDonald, Thomas M.; Rogers, Amy

2017-01-01

Aims Researchers in clinical and pharmacoepidemiology fields have adopted information technology (IT) and electronic data capture, but these remain underused despite the benefits. This review discusses electronic case report forms and electronic data capture, specifically within pharmacoepidemiology and clinical research. Methods The review used PubMed and the Institute of Electrical and Electronic Engineers library. Search terms used were agreed by the authors and documented. PubMed is medical and health based, whereas Institute of Electrical and Electronic Engineers is technology based. The review focuses on electronic case report forms and electronic data capture, but briefly considers other relevant topics; consent, ethics and security. Results There were 1126 papers found using the search terms. Manual filtering and reviewing of abstracts further condensed this number to 136 relevant manuscripts. The papers were further categorized: 17 contained study data; 40 observational data; 27 anecdotal data; 47 covering methodology or design of systems; one case study; one literature review; two feasibility studies; and one cost analysis. Conclusion Electronic case report forms, electronic data capture and IT in general are viewed with enthusiasm and are seen as a cost‐effective means of improving research efficiency, educating participants and improving trial recruitment, provided concerns about how data will be protected from misuse can be addressed. Clear operational guidelines and best practises are key for healthcare providers, and researchers adopting IT, and further work is needed on improving integration of new technologies with current systems. A robust method of evaluation for technical innovation is required. PMID:28276585

Studies on the genotoxic properties of essential oils with Bacillus subtilis rec-assay and Salmonella/microsome reversion assay.

PubMed

Zani, F; Massimo, G; Benvenuti, S; Bianchi, A; Albasini, A; Melegari, M; Vampa, G; Bellotti, A; Mazza, P

1991-06-01

Genotoxic properties of essential oils from Anthemis nobilis L., Artemisia dracunculus L., Salvia officinalis L., Salvia sclarea L., Satureja hortensis L., Satureja montana L., Thymus capitatus L., Thymus citriodorus Schreb., Thymus vulgaris L., Citrus bergamia Risso, were studied with Bacillus subtilis rec-assay and Salmonella/microsome reversion assay. The essential oil of Artemisia dracunculus L. "Piemontese" turned out to be active in the rec-assay but not in the Salmonella test. DNA-damaging activity was demonstrated to be due to the estragol component of the oil. Advantages of the combined use of these two short-term microbial assays in genotoxic studies are discussed.

In situ expression of nifD in Geobacteraceae in subsurface sediments

USGS Publications Warehouse

Holmes, Dawn E.; Nevin, Kelly P.; Lovely, Derek R.

2004-01-01

In order to determine whether the metabolic state of Geobacteraceae involved in bioremediation of subsurface sediments might be inferred from levels of mRNA for key genes, in situ expression of nifD, a highly conserved gene involved in nitrogen fixation, was investigated. When Geobacter sulfurreducens was grown without a source of fixed nitrogen in chemostats with acetate provided as the limiting electron donor and Fe(III) as the electron acceptor, levels of nifD transcripts were 4 to 5 orders of magnitude higher than in chemostat cultures provided with ammonium. In contrast, the number of transcripts of recA and the 16S rRNA gene were slightly lower in the absence of ammonium. The addition of acetate to organic- and nitrogen-poor subsurface sediments stimulated the growth of Geobacteraceae and Fe(III) reduction, as well as the expression of nifD in Geobacteraceae. Levels of nifD transcripts in Geobacteraceae decreased more than 100-fold within 2 days after the addition of 100 μM ammonium, while levels of recA and total bacterial 16S rRNA in Geobacteraceae remained relatively constant. Ammonium amendments had no effect on rates of Fe(III) reduction in acetate-amended sediments or toluene degradation in petroleum-contaminated sediments, suggesting that other factors, such as the rate that Geobacteraceae could access Fe(III) oxides, limited Fe(III) reduction. These results demonstrate that it is possible to monitor one aspect of the in situ metabolic state of Geobacteraceae species in subsurface sediments via analysis of mRNA levels, which is the first step toward a more global analysis of in situ gene expression related to nutrient status and stress response during bioremediation by Geobacteraceae.

Scaling of cross sections for K-electron capture by high-energy protons and alpha-particles from the multielectron atoms

NASA Technical Reports Server (NTRS)

Omidvar, K.

1976-01-01

Electron capture by protons from H, He, and the K-shell of Ar, and alpha particles from He are considered. It is shown that when a certain function of the experimental cross sections is plotted versus the inverse of the collision energy, at high energies the function falls on a straight line. At lower energies the function concaves up or down, depending on the charge of the projectile, the effective charge and the ionization potential of the electron that is being captured. The plot can be used to predict cross sections where experimental data are not available, and as a guide in future experiments. High energy scaling formulas for K-electron capture by low-charge projectiles are given.

Whose Ethics, Whose Accountability? A Debate about University Research Ethics Committees

ERIC Educational Resources Information Center

Hoecht, Andreas

2011-01-01

Research ethics approval procedures and research ethics committees (RECs) are now well-established in most Western Universities. RECs base their judgements on an ethics code that has been developed by the health and biomedical sciences research community and that is widely considered to be universally valid regardless of discipline. On the other…

Nevada | Midmarket Solar Policies in the United States | Solar Research |

Science.gov Websites

the retail rate. RECs: Customer retain the ownership of renewable energy certificates (RECs). Meter Interconnection standards were adopted by PUCN in 2003 for customer-generators of Nevada Power and Sierra Pacific Utilities Commission of Nevada Customer-generators who do not avail renewable energy rebates from other

State Fact Sheets on Household Energy Use

EIA Publications

2013-01-01

The Residential Energy Consumption Survey (RECS) gathers information through personal interviews with a nationwide sample of homes and energy suppliers. The 2009 survey was the largest RECS to date and the larger sample size allowed for the release of data for 16 individual states, in addition to national, regional, and division-level estimates.

Some Life History Narratives of Religious Education Coordinators in Catholic Schools

ERIC Educational Resources Information Center

Rymarz, Richard; Belmonte, Angelo

2014-01-01

This paper seeks to gain a better understanding of religious education coordinators (RECs) in contemporary Catholic schools. This is done by using life history narratives to explore how participants came to be RECs. This study takes place in a wider cultural context that sees strong religious commitment, manifested by taking leadership positions…

Kentucky | Midmarket Solar Policies in the United States | Solar Research |

Science.gov Websites

NREL Kentucky Kentucky No renewable portfolio standard Carve-out: None Tracking system Attribute Tracking System (PJM-GATS) Kentucky currently has no state renewable portfolio standard or goal and no demand for renewable energy certificates (RECs). However, solar customers may sell RECs to the

EdREC: Design and Development of Adaptive Platform for Scaling-up Flipped Mastery Learning

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

Gautam, Thakur

EdREC is an adaptive learning and management platform designed to enhance the adoption of differential classroom and mastery flipped learning in K-12 school system. The platform is an innovative approach to teaching and learning that addresses education needs of each student separately by providing customized education plans and adaptive learning methodologies that tunes to the students abilities as well as giving students freedom to learn in their own way. On one side, EdREC provides innovative ways to help students learn; on the other side, it reduces educators' workload and empowers them to understand their students better. EdREC comes with amore » state-of-the-art computer algorithm package that enables educators to store and retrieve their students' information and augment their abilities to individualize student attention, get real-time feedback about student education progress, and provide corrective actions. The platform provides approaches to design and develop a differential classroom concept that frees much needed time by the teachers to focus more on the students at the individual level and to increase communication and collaboration opportunities among them.« less

Thermoresistant revertants of an Escherichia coli strain carrying tif-1 and ruv mutations: non-suppressibility of ruv by sfi.

PubMed Central

Otsuji, N; Iyehara-Ogawa, H

1979-01-01

Spontaneous thermoresistant revertants were isolated from Tif1 Ruv- and Tif1 Ruv+ strains of Escherichia coli K-12. They were divided into five groups; backmutants to tif+ and recA structural gene mutants accounted for at least two of these groups. Mutations with an unconditional RecA- phenyotype were detected at a higher frequency in the Tif1 Ruv- strains (65%) than in the Tif1 Ruv+ strains (25%). A third group consisted of revertants exhibiting a RecA- phenotype at low temperature. Revertants with normal recombination ability and UV resistance, but with a thermosensitive defect in propagating lambda bio11 phage, were also isolated (group 4). The alleles responsible for this property were cotransducible with the srl gene, suggesting that they are located at the recA locus. Other revertants, which might carry lex, LEXB, or zab mutations, were UV sensitive and were able to propagate lambda bio11 phage (group 5). The sfi mutation, which suppresses filamentation in the Tif1 and UV-sensitive Lon- strains, does not restore UV resistance of the Ruv- mutant. PMID:374356

21 CFR 172.860 - Fatty acids.

Code of Federal Regulations, 2013 CFR

2013-04-01

... the gas chromatographic-electron capture method prescribed in paragraph (c)(3) of this section. If..._locations.html. (3) The gas chromatographic-electron capture method for testing fatty acids for chick-edema...

21 CFR 172.860 - Fatty acids.

Code of Federal Regulations, 2012 CFR

2012-04-01

... the gas chromatographic-electron capture method prescribed in paragraph (c)(3) of this section. If..._locations.html. (3) The gas chromatographic-electron capture method for testing fatty acids for chick-edema...

Photon structure studied at an electron ion collider

DOE PAGES

Chu, X.; Aschenauer, E. C.; Lee, J. H.; ...

2017-10-30

We report that a future electron ion collider (EIC) will be able to provide collisions of polarized electrons with protons and heavy ions over a wide range of center-of-mass energies (20 GeV to 140 GeV) at an instantaneous luminosity of 10 33 - 10 34cm -2s -1. One of its promising physics programs is the study of the partonic structure of quasireal photons. Measuring dijets in quasireal photoproduction events, one can effectively access the underlying parton dynamics of the photons. In this paper, we discuss the feasibility of tagging resolved photon processes and measuring the dijet cross section as a function of jet transverse momentum in the range of 0.01 < xmore » $$rec\\atop{γ}$$ < 1 at an EIC. Finally, it will be shown that both unpolarized and polarized parton distributions in the photon can be extracted, and that the flavor of the parton can be tagged at an EIC.« less

Molecular characterization of Plum pox virus Rec isolates from Russia suggests a new insight into evolution of the strain.

PubMed

Chirkov, Sergei; Ivanov, Peter; Sheveleva, Anna; Kudryavtseva, Anna; Mitrofanova, Irina

2018-04-01

Field isolates of Plum pox virus (PPV), belonging to the strain Rec, have been found for the first time in Russia. Full-size genomes of the isolates K28 and Kisl-1pl from myrobalan and plum, respectively, were sequenced on the 454 platform. Analysis of all known PPV-Rec complete genomes using the Recombination Detection Program (RDP4) revealed yet another recombination event in the 5'-terminal region. This event was detected by seven algorithms, implemented in the RDP4, with statistically significant P values and supported by a phylogenetic analysis with the bootstrap value of 87%. A putative PPV-M-derived segment, encompassing the C-terminus of the P1 gene and approximately two-thirds of the HcPro gene, is bordered by breakpoints at positions 760-940 and 1838-1964, depending on the recombinant isolate. The predicted 5'-distal breakpoint for the isolate Valjevka is located at position 2804. The Dideron (strain D) and SK68 (strain M) isolates were inferred as major and minor parents, respectively. Finding of another recombination event suggests more complex evolutionary history of PPV-Rec than previously assumed. Perhaps the first recombination event led to the formation of a PPV-D variant harboring the PPV-M-derived fragment within the 5'-proximal part of the genome. Subsequent recombination of its descendant with PPV-M in the 3'-proximal genomic region resulted in the emergence of the evolutionary successful strain Rec.

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.

The Cdc45/RecJ-like protein forms a complex with GINS and MCM, and is important for DNA replication in Thermococcus kodakarensis

PubMed Central

Nagata, Mariko; Yamagami, Takeshi; Ogino, Hiromi; Simons, Jan-Robert; Kanai, Tamotsu; Atomi, Haruyuki

2017-01-01

Abstract The archaeal minichromosome maintenance (MCM) has DNA helicase activity, which is stimulated by GINS in several archaea. In the eukaryotic replicative helicase complex, Cdc45 forms a complex with MCM and GINS, named as CMG (Cdc45-MCM-GINS). Cdc45 shares sequence similarity with bacterial RecJ. A Cdc45/RecJ-like protein from Thermococcus kodakarensis shows a bacterial RecJ-like exonuclease activity, which is stimulated by GINS in vitro. Therefore, this archaeal Cdc45/RecJ is designated as GAN, from GINS-associated nuclease. In this study, we identified the CMG-like complex in T. kodakarensis cells. The GAN·GINS complex stimulated the MCM helicase, but MCM did not affect the nuclease activity of GAN in vitro. The gene disruption analysis showed that GAN was non-essential for its viability but the Δgan mutant did not grow at 93°C. Furthermore, the Δgan mutant showed a clear retardation in growth as compared with the parent cells under optimal conditions at 85°C. These deficiencies were recovered by introducing the gan gene encoding the nuclease deficient GAN protein back to the genome. These results suggest that the replicative helicase complex without GAN may become unstable and ineffective in replication fork progression. The nuclease activity of GAN is not related to the growth defects of the Δgan mutant cells. PMID:28977567

Non-therapeutic research with minors: how do chairpersons of German research ethics committees decide?

PubMed Central

Lenk, C; Radenbach, K; Dahl, M; Wiesemann, C

2004-01-01

Objectives: Clinical trials in humans in Germany—as in many other countries—must be approved by local research ethics committees (RECs). The current study has been designed to document and evaluate decisions of chairpersons of RECs in the problematic field of non-therapeutic research with minors. The authors' purpose was to examine whether non-therapeutic research was acceptable for chairpersons at all, and whether there was certainty on how to decide in research trials involving more than minimal risk. Design: In a questionnaire, REC chairpersons had to evaluate five different scenarios with (in parts) non-therapeutic research. The scenarios described realistic potential research projects with minors, involving increasing levels of risk for the research participants. The chairpersons had to decide whether the respective projects should be approved. Methods: A total of 49 German REC chairpersons were sent questionnaires; 29 questionnaires were returned. The main measurements were approval or rejection of research scenarios. Results: Chairpersons of German RECs generally tend to accept non-therapeutic research with minors if the apparent risk for the participating children is low. If the risk is clearly higher than "minimal", the chairpersons' decisions differ widely. Conclusion: The fact that there seem to be different attitudes of chairpersons to non-therapeutic research with minors is problematic from an ethical point of view. It suggests a general uncertainty about the standards of protection for minor research participants in Germany. Therefore, further ethical and legal regulation of non-therapeutic research with minors in Germany seems necessary. PMID:14872082

Identification of Cell Adhesive Sequences in the N-terminal Region of the Laminin α2 Chain*

PubMed Central

Hozumi, Kentaro; Ishikawa, Masaya; Hayashi, Takemitsu; Yamada, Yuji; Katagiri, Fumihiko; Kikkawa, Yamato; Nomizu, Motoyoshi

2012-01-01

The laminin α2 chain is specifically expressed in the basement membrane surrounding muscle and nerve. We screened biologically active sequences in the mouse laminin N-terminal region of α2 chain using 216 soluble peptides and three recombinant proteins (rec-a2LN, rec-a2LN+, and rec-a2N) by both the peptide- or protein-coated plate and the peptide-conjugated Sepharose bead assays. Ten peptides showed cell attachment activity in the plate assay, and 8 peptides were active in the bead assay. Seven peptides were active in the both assays. Five peptides promoted neurite outgrowth with PC12 cells. To clarify the cellular receptors, we examined the effects of heparin and EDTA on cell attachment to 11 active peptides. Heparin inhibited cell attachment to 10 peptides, and EDTA significantly affected only A2-8 peptide (YHYVTITLDLQQ, mouse laminin α2 chain, 117–128)-mediated cell attachment. Cell attachment to A2-8 was also specifically inhibited by anti-integrin β1 and anti-integrin α2β1 antibodies. These results suggest that A2-8 promotes an integrin α2β1-mediated cell attachment. The rec-a2LN protein, containing the A2-8 sequence, bound to integrin α2β1 and cell attachment to rec-a2LN was inhibited by A2-8 peptide. Further, alanine substitution analysis of both the A2-8 peptide and the rec-a2LN+ protein revealed that the amino acids Ile-122, Leu-124, and Asp-125 were involved in integrin α2β1-mediated cell attachment, suggesting that the A2-8 site plays a functional role as an integrin α2β1 binding site in the LN module. These active peptides may provide new insights on the molecular mechanism of laminin-receptor interactions. PMID:22654118

A pH-responsive interface derived from resilin-mimetic protein Rec1-resilin.

PubMed

Truong, My Y; Dutta, Naba K; Choudhury, Namita R; Kim, Misook; Elvin, Christopher M; Hill, Anita J; Thierry, Benjamin; Vasilev, Krasimir

2010-05-01

In this investigation, for the first time we report the effects of pH on the molecular orientation, packing density, structural properties, adsorption characteristics and viscoelastic behaviour of resilin-mimetic protein rec1-resilin at the solid-liquid interface using quartz crystal microbalance with dissipation monitoring (QCM-D) and surface plasmon resonance (SPR) spectroscopy. QCM-D and SPR data confirm that the binding ability of rec1-resilin on a substrate is strongly pH-dependent the protein packing density on a gold surface is calculated to be 4.45 x 10(13) per cm(2) at the isoelectric point (IEP approximately 4.9), 8.79 x 10(11) per cm(2) at pH 2 and 9.90 x 10(11) per cm(2) at pH 12, respectively. Our findings based on the thickness, dissipation and viscoelasticity of the rec1-resilin adlayer also indicate that it is adsorbed onto the gold substrate with different orientation depending on pH, such as back-on adsorption at acidic pH of 2, compact end-on bilayer adsorption at the IEP and side-on at high alkaline pH of 12. When rec1-resilin is 'pinned' to the substrate at IEP and subsequently exposed to an electrolyte solution adjusted to different pH, it switches from a compact globular conformation of the bio-macromolecule at the IEP to a coil conformation at pH between IEP to IED (IED = pKa value of tyrosine amino acid residue) and an extended coil conformation at pH > IED. This transformation from globule to coil to extended coil conformation is kinetically fast, robust and completely reversible. Such responsive surfaces created using 'smart' biomimetic rec1-resilin have the potential to find applications in many areas including biotechnology, medicine, sensors, controlled drug delivery systems and engineering. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

Role of allosteric switch residue histidine 195 in maintaining active-site asymmetry in presynaptic filaments of bacteriophage T4 UvsX recombinase.

PubMed

Farb, Joshua N; Morrical, Scott W

2009-01-16

Recombinases of the highly conserved RecA/Rad51 family play central roles in homologous recombination and DNA double-stranded break repair. RecA/Rad51 enzymes form presynaptic filaments on single-stranded DNA (ssDNA) that are allosterically activated to catalyze ATPase and DNA strand-exchange reactions. Information is conveyed between DNA- and ATP-binding sites, in part, by a highly conserved glutamine residue (Gln194 in Escherichia coli RecA) that acts as an allosteric switch. The T4 UvsX protein is a divergent RecA ortholog and contains histidine (His195) in place of glutamine at the allosteric switch position. UvsX and RecA catalyze similar strand-exchange reactions, but differ in other properties. UvsX produces both ADP and AMP as products of its ssDNA-dependent ATPase activity--a property that is unique among characterized recombinases. Details of the kinetics of ssDNA-dependent ATP hydrolysis reactions indicate that UvsX-ssDNA presynaptic filaments are asymmetric and contain two classes of ATPase active sites: one that generates ADP, and another that generates AMP. Active-site asymmetry is reduced by mutations at the His195 position, since UvsX-H195Q and UvsX-H195A mutants both exhibit stronger ssDNA-dependent ATPase activity, with lower cooperativity and markedly higher ADP/AMP product ratios, than wild-type UvsX. Reduced active-site asymmetry correlates strongly with reduced ssDNA-binding affinity and DNA strand-exchange activity in both H195Q and H195A mutants. These and other results support a model in which allosteric switch residue His195 controls the formation of an asymmetric conformation of UvsX-ssDNA filaments that is active in DNA strand exchange. The implications of our findings for UvsX recombination functions, and for RecA functions in general, are discussed.

Evolution of Exchangeable Copper and Relative Exchangeable Copper through the Course of Wilson's Disease in the Long Evans Cinnamon Rat

PubMed Central

Schmitt, Françoise; Podevin, Guillaume; Poupon, Joël; Roux, Jérôme; Legras, Pierre; Trocello, Jean-Marc; Woimant, France; Laprévote, Olivier; NGuyen, Tuan Huy; Balkhi, Souleiman El

2013-01-01

Background Wilson's disease (WD) is an inherited disorder of copper metabolism leading to liver failure and/or neurological impairment. Its diagnosis often remains difficult even with genetic testing. Relative exchangeable copper (REC) has recently been described as a reliable serum diagnostic marker for WD. Methodology/Principal Findings The aim of this study was to validate the use of REC in the Long Evans Cinnamon (LEC) rat, an animal model for WD, and to study its relevance under different conditions in comparison with conventional markers. Two groups of LEC rats and one group of Long-Evans (LE) rats were clinically and biologically monitored from 6 to 28 weeks of age. One group of LEC rats was given copper-free food. The other groups had normal food. Blood samples were collected each month and different serum markers for WD (namely ceruloplasmin oxidase activity, exchangeable copper (CuEXC), total serum copper and REC) and acute liver failure (serum transaminases and bilirubinemia) were tested. Every LEC rat under normal food developed acute liver failure (ALF), with 40% global mortality. Serum transaminases and bilirubinemia along with total serum copper and exchangeable copper levels increased with the onset of acute liver failure. A correlation was observed between CuEXC values and the severity of ALF. Cut-off values were different between young and adult rats and evolved because of age and/or liver failure. Only REC, with values >19%, was able to discriminate LEC groups from the LE control group at every time point in the study. REC sensitivity and specificity reached 100% in adults rats. Conclusions/Significance REC appears to be independent of demographic or clinical data in LEC rats. It is a very simple and reliable blood test for the diagnosis of copper toxicosis owing to a lack of ATP7B function. CuEXC can be used as an accurate biomarker of copper overload. PMID:24358170

Bacterial RecA Protein Promotes Adenoviral Recombination during In Vitro Infection

PubMed Central

Lee, Jeong Yoon; Lee, Ji Sun; Materne, Emma C.; Rajala, Rahul; Ismail, Ashrafali M.; Seto, Donald; Dyer, David W.

2018-01-01

ABSTRACT Adenovirus infections in humans are common and sometimes lethal. Adenovirus-derived vectors are also commonly chosen for gene therapy in human clinical trials. We have shown in previous work that homologous recombination between adenoviral genomes of human adenovirus species D (HAdV-D), the largest and fastest growing HAdV species, is responsible for the rapid evolution of this species. Because adenovirus infection initiates in mucosal epithelia, particularly at the gastrointestinal, respiratory, genitourinary, and ocular surfaces, we sought to determine a possible role for mucosal microbiota in adenovirus genome diversity. By analysis of known recombination hot spots across 38 human adenovirus genomes in species D (HAdV-D), we identified nucleotide sequence motifs similar to bacterial Chi sequences, which facilitate homologous recombination in the presence of bacterial Rec enzymes. These motifs, referred to here as ChiAD, were identified immediately 5′ to the sequence encoding penton base hypervariable loop 2, which expresses the arginine-glycine-aspartate moiety critical to adenoviral cellular entry. Coinfection with two HAdV-Ds in the presence of an Escherichia coli lysate increased recombination; this was blocked in a RecA mutant strain, E. coli DH5α, or upon RecA depletion. Recombination increased in the presence of E. coli lysate despite a general reduction in viral replication. RecA colocalized with viral DNA in HAdV-D-infected cell nuclei and was shown to bind specifically to ChiAD sequences. These results indicate that adenoviruses may repurpose bacterial recombination machinery, a sharing of evolutionary mechanisms across a diverse microbiota, and unique example of viral commensalism. IMPORTANCE Adenoviruses are common human mucosal pathogens of the gastrointestinal, respiratory, and genitourinary tracts and ocular surface. Here, we report finding Chi-like sequences in adenovirus recombination hot spots. Adenovirus coinfection in the presence of bacterial RecA protein facilitated homologous recombination between viruses. Genetic recombination led to evolution of an important external feature on the adenoviral capsid, namely, the penton base protein hypervariable loop 2, which contains the arginine-glycine-aspartic acid motif critical to viral internalization. We speculate that free Rec proteins present in gastrointestinal secretions upon bacterial cell death facilitate the evolution of human adenoviruses through homologous recombination, an example of viral commensalism and the complexity of virus-host interactions, including regional microbiota. PMID:29925671

A Comparison of the Performance Capabilities of Radioisotope Energy Conversion Systems, Betavoltaic Cells, and other Nuclear Batteries

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

Steinfelds, Eric V; Prelas, Mark A.; Sudarshan, Loyalka K.

2006-07-01

In this paper we compare the potential performance capabilities of several types of nuclear batteries to the Radioisotope Thermocouple Generators (RTG's) currently in use. There have been theoretical evaluations of, and some experimental testing of, several types of nuclear batteries including Radioisotope Energy Conversion Systems (RECS), Direct Energy Conversion (DEC) systems, and Betavoltaic Power Cells (BPC's). It has been theoretically shown, and to some extent experimentally demonstrated, that RECS, capacitive DEC systems, and possibly BPC's are all potentially capable of efficiencies well above the 9% maximum efficiency demonstrated to date in RTG's customized for deep space probe applications. Even thoughmore » RTG's have proven their reliability and have respectable power to mass ratios, it is desirable to attain efficiencies of at least 25% in typical applications. High fuel efficiency is needed to minimize the quantities of radioisotopic or nuclear fuels in the systems, to maximize power to mass ratios, and to minimize housing requirements. It has been shown that RECS can attain electric power generation efficiencies greater than 18% for devices which use Sr-90 fuel and where the accompanying material is less than roughly twice the mass of the Sr-90 fuel. Other radioisotopic fuels such as Pu-238 or Kr-85 can also be placed into RECS in order to attain efficiencies over 18%. With the likely exception of one fuel investigated by the authors, all of the promising candidates for RECS fuels can attain electric power to mass ratios greater than 15 W kg{sup -1}. It has been claimed recently [1] that the efficiency of tritium-fueled BPC's can be as high as 25%. While this is impressive and tritium has the benefit of being a 'soft' radioisotopic fuel, the silicon wafer that holds the tritium would have to be considerably more massive than the tritium contained within it and immediately adjacent to the wafer. Considering realistic mass requirements for the presence of silicon in the bulk of the wafer, a tritium cell would thus be limited to power to mass ratios <3 W kg{sup -1}. Even RECS designs with more energetic fuels and higher shielding burdens can attain >3 W kg{sup -1} and efficiencies exceeding 20%. Capacitive DEC systems can also offer significant benefits. With larger fuel quantities and larger dimensions, DEC systems can attain power efficiencies >50%. For small nuclear batteries of low or medium power, RECS appear highly desirable since the efficiency of a RECS does not vary with the amount of fuel present nor does it vary with temperature to any significant degree. (authors)« less

Duration of time that beef cattle are fed a high-grain diet affects the recovery from a bout of ruminal acidosis: short-chain fatty acid and lactate absorption, saliva production, and blood metabolites.

PubMed

Schwaiger, T; Beauchemin, K A; Penner, G B

2013-12-01

This study was conducted to determine if the duration of time that beef cattle are fed a high-grain diet affects short-chain fatty acid (SCFA) absorption, saliva production, and blood metabolites before, during, and following an induced bout of ruminal acidosis. Sixteen Angus heifers were assigned to 1 of 4 blocks and within block to 1 of 2 treatments designated as long adapted (LA) or short adapted (SA). Long adapted and SA heifers were fed a backgrounding diet [forage:concentrate (F:C) = 60:40] for 33 and 7 d, respectively, and then transitioned over 20 d to a high-grain diet (F:C = 9:91) with the timing of dietary transition staggered such that the LA and SA heifers were fed the high-grain diet for 34 and 8 d, respectively, before inducing ruminal acidosis. Ruminal acidosis was induced by restricting feed to 50% of DMI:BW for 24 h followed by an intraruminal infusion of ground barley at 10% DMI:BW. Heifers were then given their regular diet allocation 1 h after the intraruminal infusion. Data were collected during an 8 d baseline period (BASE), on the day of the acidosis challenge (CHAL), and during 2 consecutive 8 d recovery periods (REC1 and REC2). When pooled across periods, the fractional rates of propionate (42 vs. 34%/h; P = 0.045) and butyrate (45 vs. 36%/h; P = 0.019) absorption, measured using the isolated and washed reticulorumen technique, were greater for LA than SA heifers. Moreover, overall, LA heifers tended to have greater absolute rates of butyrate absorption (94 vs. 79 mmol/h; P = 0.087) and fractional rates of total SCFA absorption (37 vs. 32%/h; P = 0.100). Treatment × period interactions for lactate absorption (P = 0.024) and serum D-lactate concentration (P = 0.003) were detected with LA heifers having greater D-lactate concentrations during CHAL and greater fractional rates of lactate absorption during REC1 than SA. The absolute and fractional absorption of acetate, propionate, and butyrate increased between REC1 and REC2, with intermediate values for BASE (P ≤ 0.05). Although fractional rates of SCFA absorption were low during REC1, saliva production (P = 0.018) increased between BASE and REC1, with intermediate values for REC2. These results suggest that the duration of time that animals are fed a high-grain diet may increase propionate, butyrate, and lactate absorption, and that cattle may decrease SCFA absorption and increase saliva production shortly after an acute bout of ruminal acidosis.

Natural Resources Research Program: Summary of the 1986-87 Campground Receipt Study

DTIC Science & Technology

1991-03-01

can sum to more than 100 percent because parties can use multiple pieces of equipment. B16 Table BI5 1987 Shenango Lake (Shenango Rec Area) User...table represent actual camping use. ** Percent of camping parties. t Percent of camping permits. B17 Table Bl6 1987 Shenango Lake (Shenango Rec Area

Dimensions of belonging as an aspect of racial-ethnic-cultural identity: an exploration of indigenous Australians.

PubMed

Neville, Helen A; Oyama, Kathleen E; Odunewu, Latifat O; Huggins, Jackie G

2014-07-01

Sense of belonging is a key aspect of racial and ethnic identity. Interestingly, there is little exploration of the multiple characteristics of belongingness within the racial and ethnic identity literature. Through individual interviews and a focus group, we explored the sense of racial-ethnic-cultural (REC) belonging among 19 self-identified Black Indigenous Australians (Aborigines and Torres Strait Islanders). Using dimensional analysis, we uncovered 5 core interrelated dimensions of REC belonging: History/Memory, Place, and Peoplehood; Sense of Community; Acceptance and Pride; Shared Language and Culture; and Interconnections. We also uncovered 3 main barriers undermining participants' sense of REC belonging: phenotype, social identity, and history of colonization. PsycINFO Database Record (c) 2014 APA, all rights reserved.

Drag reduction in the turbulent Kolmogorov flow.

PubMed

Boffetta, Guido; Celani, Antonio; Mazzino, Andrea

2005-03-01

We investigate the phenomenon of drag reduction in a viscoelastic fluid model of dilute polymer solutions. By means of direct numerical simulations of the three-dimensional turbulent Kolmogorov flow we show that drag reduction takes place above a critical Reynolds number Re(c). An explicit expression for the dependence of Re(c) on polymer elasticity and diffusivity is derived. The values of the drag coefficient obtained for different fluid parameters collapse onto a universal curve when plotted as a function of the rescaled Reynolds number Re/ Re(c). The analysis of the momentum budget allows us to gain some insight on the physics of drag reduction, and suggests the existence of a Re-independent value of the drag cofficient--lower than the Newtonian one--for large Reynolds numbers.

New Crocodyliform specimens from Recôncavo-Tucano Basin (Early Cretaceous) of Bahia, Brazil.

PubMed

Souza, Rafael G DE; Campos, Diogenes A

2018-04-16

In 1940, L.I. Price and A. Oliveira recovered four crocodyliform specimens from the Early Cretaceous Bahia Supergroup (Recôncavo-Tucano Basin). In the present work, we describe four different fossil specimens: an osteoderm, a fibula, a tibia, and some autopodial bones. No further identification besides Mesoeucrocodylia was made due to their fragmentary nature and the reduced number of recognized synapomorphies for more inclusive clades. With exception of the fibula, all other specimens have at least one particular feature, which with new specimens could represent new species. The new specimens described here increase the known diversity of Early Cretaceous crocodyliforms from Brazil. This work highlights the great fossiliferous potential of Recôncavo-Tucano Basin with regard to crocodyliform remains.

Perspectives of Egyptian research ethics committees regarding their effective functioning.

PubMed

Matar, Amal; Silverman, Henry

2013-02-01

The recent increase in research in the Middle East has been associated with the establishment of research ethics committees (RECs). Our aim was to obtain perspectives of RECs regarding the challenges that impede their effective functioning. We conducted in-depth interviews using a semi-structured interview guide. We transcribed and analyzed the interviews to uncover major themes and subthemes. We identified the following themes: membership composition; training needs of members; availability of human and capital resources; role of the national government; concerns with the informed consent process; government scrutiny of research; investigator-related issues; and concerns with transfer of biological samples to other countries. Our interview study revealed several barriers that need to be considered by appropriate stakeholders to enhance adequate functioning of RECs.

Residential Energy Consumption Survey (RECS): Household screener survey, 1979-1980, household characteristics and annualized consumption

NASA Astrophysics Data System (ADS)

Windell, P.

1981-08-01

This document provides basic information and technical specifications necessary for using the machine-readable magnetic tape containing data from the Household Screener Survey of the Residential Energy Consumption Survey (RECS). Included in this document are an overview of the RECS and a brief description of the Household Screener Survey. The next section contains technical specifications for reading the tape and descriptions of the contents of each of the files contained on the tape. The remaining four sections are devoted to technical topics of special interest to users of the data. Appended to this document are copies of the fieldwork instruments used in the survey and a listing of the contents of a portion of the SPSS labels information.

Superconductivity and the periodic table: from elements to materials.

PubMed

Simon, Arndt

2015-03-13

Based on the normal-state electronic band structure, the necessary condition for a metal to become a superconductor is the simultaneous occurrence of flat and steep bands at the Fermi level. The sufficient condition at least for conventional superconductors is a strong enough coupling of the flat band states to the lattice, e.g. via phonons. Selected elements (Te) and compounds of the rare earth metals (RE(2)C(3), REC(2), RE(2)X(2)C(2) with X=halogen) and MgB(2) serve as examples to illustrate the idea. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

A Benign, Low Z Electron Capture Agent for Negative Ion TPCs

NASA Technical Reports Server (NTRS)

Martoff, C. J.; Dion, M. P.; Hosack, M.; Barton, D.; Black, J. K.

2008-01-01

We have identified nitromethane (CH3NO2) as an effective electron capture agent for negative ion TPCs (NITPCs). We present drift velocity and longitudinal diffusion measurements for negative ion gas mixtures using nitromethane as the capture agent. Not only is nitromethane substantially more benign than the only other identified capture agent, CS2, but its low atomic number will enable the use of the NITPC as a photoelectric X-ray polarimeter in the 1-10 keV band.

2013 R&D 100 Award: Movie-mode electron microscope captures nanoscale

ScienceCinema

Lagrange, Thomas; Reed, Bryan

2018-01-26

A new instrument developed by LLNL scientists and engineers, the Movie Mode Dynamic Transmission Electron Microscope (MM-DTEM), captures billionth-of-a-meter-scale images with frame rates more than 100,000 times faster than those of conventional techniques. The work was done in collaboration with a Pleasanton-based company, Integrated Dynamic Electron Solutions (IDES) Inc. Using this revolutionary imaging technique, a range of fundamental and technologically important material and biological processes can be captured in action, in complete billionth-of-a-meter detail, for the first time. The primary application of MM-DTEM is the direct observation of fast processes, including microstructural changes, phase transformations and chemical reactions, that shape real-world performance of nanostructured materials and potentially biological entities. The instrument could prove especially valuable in the direct observation of macromolecular interactions, such as protein-protein binding and host-pathogen interactions. While an earlier version of the technology, Single Shot-DTEM, could capture a single snapshot of a rapid process, MM-DTEM captures a multiframe movie that reveals complex sequences of events in detail. It is the only existing technology that can capture multiple electron microscopy images in the span of a single microsecond.

2013 R&D 100 Award: Movie-mode electron microscope captures nanoscale

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

Lagrange, Thomas; Reed, Bryan

2014-04-03

A new instrument developed by LLNL scientists and engineers, the Movie Mode Dynamic Transmission Electron Microscope (MM-DTEM), captures billionth-of-a-meter-scale images with frame rates more than 100,000 times faster than those of conventional techniques. The work was done in collaboration with a Pleasanton-based company, Integrated Dynamic Electron Solutions (IDES) Inc. Using this revolutionary imaging technique, a range of fundamental and technologically important material and biological processes can be captured in action, in complete billionth-of-a-meter detail, for the first time. The primary application of MM-DTEM is the direct observation of fast processes, including microstructural changes, phase transformations and chemical reactions, that shapemore » real-world performance of nanostructured materials and potentially biological entities. The instrument could prove especially valuable in the direct observation of macromolecular interactions, such as protein-protein binding and host-pathogen interactions. While an earlier version of the technology, Single Shot-DTEM, could capture a single snapshot of a rapid process, MM-DTEM captures a multiframe movie that reveals complex sequences of events in detail. It is the only existing technology that can capture multiple electron microscopy images in the span of a single microsecond.« less

Quasiclassical treatment of the Auger effect in slow ion-atom collisions

NASA Astrophysics Data System (ADS)

Frémont, F.

2017-09-01

A quasiclassical model based on the resolution of Hamilton equations of motion is used to get evidence for Auger electron emission following double-electron capture in 150-keV N e10 ++He collisions. Electron-electron interaction is taken into account during the collision by using pure Coulombic potential. To make sure that the helium target is stable before the collision, phenomenological potentials for the electron-nucleus interactions that simulate the Heisenberg principle are included in addition to the Coulombic potential. First, single- and double-electron captures are determined and compared with previous experiments and theories. Then, integration time evolution is calculated for autoionizing and nonautoionizing double capture. In contrast with single capture, the number of electrons originating from autoionization slowly increases with integration time. A fit of the calculated cross sections by means of an exponential function indicates that the average lifetime is 4.4 ×10-3a .u . , in very good agreement with the average lifetime deduced from experiments and a classical model introduced to calculate individual angular momentum distributions. The present calculation demonstrates the ability of classical models to treat the Auger effect, which is a pure quantum effect.

Debris extrusion and foraminal deformation produced by reciprocating instruments made of thermally treated NiTi wires

PubMed Central

Frota, Myrna Maria Arcanjo; Bernardes, Ricardo Affonso; Vivan, Rodrigo Ricci; Vivacqua-Gomes, Nilton; Duarte, Marco Antonio Hungaro; de Vasconcelos, Bruno Carvalho

2018-01-01

Abstract Objective To evaluate the amount of apically extruded debris, percentage of foraminal enlargement and apical foramen (AF) deformation that occurred during root canal preparation with different reciprocation systems: Reciproc, WaveOne (M-Wire), and ProDesign R (Shape Memory Technology Wire) at two different working lengths (WLs): 0.0 and 1.0 mm beyond the AF. Material and methods The AF of 120 root canals in 60 mesial roots of mandibular molars were photographed with stereomicroscope and randomly assigned into four groups: manual, Reciproc (REC), WaveOne (WO), and ProDesign R (PDR); subsequently, they were further subdivided according to the WL (n=15). Teeth were instrumented, coupled to a dual collecting chamber, and then another photograph of each AF was captured. Extrusion was analysed by determining the weight of extruded debris. Each AF diameter was measured in pre- and post-instrumentation images to determine deformation, which was analysed, and afterwards the final format of AFs was classified (circular/oval/deformed). Results We found no significant differences when analysing each system at different WLs. When considering each WL, REC and WO showed highest extrusion values (P<.05); for AF enlargement, differences were observed only for WO, when it was used beyond the AF; differences were observed among M-Wire groups beyond the AF (P<.05). AF deformation was observed in all groups; PDR showed the lowest AF deformation values at both WLs; M-Wire groups showed 50% strain beyond the AF. Conclusion Authors concluded that beyond the apical limit, the alloy and taper are important aspects when considering extrusion and deformation. PMID:29364346

Using tree diversity to compare phylogenetic heuristics.

PubMed

Sul, Seung-Jin; Matthews, Suzanne; Williams, Tiffani L

2009-04-29

Evolutionary trees are family trees that represent the relationships between a group of organisms. Phylogenetic heuristics are used to search stochastically for the best-scoring trees in tree space. Given that better tree scores are believed to be better approximations of the true phylogeny, traditional evaluation techniques have used tree scores to determine the heuristics that find the best scores in the fastest time. We develop new techniques to evaluate phylogenetic heuristics based on both tree scores and topologies to compare Pauprat and Rec-I-DCM3, two popular Maximum Parsimony search algorithms. Our results show that although Pauprat and Rec-I-DCM3 find the trees with the same best scores, topologically these trees are quite different. Furthermore, the Rec-I-DCM3 trees cluster distinctly from the Pauprat trees. In addition to our heatmap visualizations of using parsimony scores and the Robinson-Foulds distance to compare best-scoring trees found by the two heuristics, we also develop entropy-based methods to show the diversity of the trees found. Overall, Pauprat identifies more diverse trees than Rec-I-DCM3. Overall, our work shows that there is value to comparing heuristics beyond the parsimony scores that they find. Pauprat is a slower heuristic than Rec-I-DCM3. However, our work shows that there is tremendous value in using Pauprat to reconstruct trees-especially since it finds identical scoring but topologically distinct trees. Hence, instead of discounting Pauprat, effort should go in improving its implementation. Ultimately, improved performance measures lead to better phylogenetic heuristics and will result in better approximations of the true evolutionary history of the organisms of interest.

Characterization of an Escherichia coli mutant (radB101) sensitive to. gamma. and uv radiation, and methyl methanesulfonate

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

Sargentini, N.J.; Smith, K.C.

1983-03-01

After N-methyl-N'-nitro-N-nitrosoguanidine mutagenesis of Escherichia coli K-12 (xthA14), an X-ray-sensitive mutant was isolated. This sensitivity is due to a mutation, radB101, which is located at 56.5 min on the E.coli K-12 linkage map. The radB101 mutation sensitized wild-type cells to ..gamma.. and uv radiation, and to methyl methanesulfonate. When known DNA repair-deficient mutants were ranked for their ..gamma..-radiation sensitivity relative to their uv-radiation sensitivity, their order was (starting with the most selectively ..gamma..-radiation-sensitive strain): recB21, radB101, wild type, polA1, recF143, lexA101, recA56, uvrD3, and uvrA6. The radB mutant was normal for ..gamma..- and uv-radiation mutagenesis, it showed only a slightmore » enhancement of ..gamma..- and uv-radiation-induced DNA degradation, and it was approx. 60% deficient in recombination ability. The radB gene is suggested to play a role in the recA gene-dependent (Type III) repair of DNA single-strand breaks after ..gamma.. irradiation and in postreplication repair after uv irradiation for the following reasons: the radB strain was normal for the host-cell reactivation of ..gamma..- and uv-irradiated bacteriophage lambda; the radB mutation did not sensitize a recA strain, but did sensitize a polA strain to ..gamma.. and uv radiation; the radB mutation sensitized a uvrB strain to uv radiation.« less

Research Ethics Review and Aboriginal Community Values: Can the Two be Reconciled?

PubMed

Glass, Kathleen Cranley; Kaufert, Joseph

2007-06-01

CONTEMPORARY RESEARCH ETHICS REVIEW COMMITTEES (RECs) are heavily influenced by the established academic or health care institutional frameworks in which they operate, sharing a cultural, methodological and ethical perspective on the conduct of research involving humans. The principle of autonomous choice carries great weight in what is a highly individualistic decision-making process in medical practice and research. This assumes that the best protection lies in the ability of patients or research participants to make competent, voluntary, informed choices, evaluating the risks and benefits from a personal perspective. Over the past two decades, North American and international indigenous researchers, policy makers and communities have identified key issues of relevance to them, but ignored by most institutional or university-based RECs. They critique the current research review structure, and propose changes on a variety of levels in an attempt to develop more community sensitive research ethics review processes. In doing so, they have emphasized recognition of collective rights including community consent. Critics see alternative policy guidelines and community-based review bodies as challenging the current system of ethics review. Some view them as reflecting a fundamental difference in values. In this paper, we explore these developments in the context of the political, legal and ethical frameworks that have informed REC review. We examine the process and content of these frameworks and ask how this contrasts with emerging Aboriginal proposals for community-based research ethics review. We follow this with recommendations on how current REC review models might accommodate the requirements of both communities and RECs.

The Cdc45/RecJ-like protein forms a complex with GINS and MCM, and is important for DNA replication in Thermococcus kodakarensis.

PubMed

Nagata, Mariko; Ishino, Sonoko; Yamagami, Takeshi; Ogino, Hiromi; Simons, Jan-Robert; Kanai, Tamotsu; Atomi, Haruyuki; Ishino, Yoshizumi

2017-10-13

The archaeal minichromosome maintenance (MCM) has DNA helicase activity, which is stimulated by GINS in several archaea. In the eukaryotic replicative helicase complex, Cdc45 forms a complex with MCM and GINS, named as CMG (Cdc45-MCM-GINS). Cdc45 shares sequence similarity with bacterial RecJ. A Cdc45/RecJ-like protein from Thermococcus kodakarensis shows a bacterial RecJ-like exonuclease activity, which is stimulated by GINS in vitro. Therefore, this archaeal Cdc45/RecJ is designated as GAN, from GINS-associated nuclease. In this study, we identified the CMG-like complex in T. kodakarensis cells. The GAN·GINS complex stimulated the MCM helicase, but MCM did not affect the nuclease activity of GAN in vitro. The gene disruption analysis showed that GAN was non-essential for its viability but the Δgan mutant did not grow at 93°C. Furthermore, the Δgan mutant showed a clear retardation in growth as compared with the parent cells under optimal conditions at 85°C. These deficiencies were recovered by introducing the gan gene encoding the nuclease deficient GAN protein back to the genome. These results suggest that the replicative helicase complex without GAN may become unstable and ineffective in replication fork progression. The nuclease activity of GAN is not related to the growth defects of the Δgan mutant cells. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Identification and analysis of recombineering functions from Gram-negative and Gram-positive bacteria and their phages

PubMed Central

Datta, Simanti; Costantino, Nina; Zhou, Xiaomei; Court, Donald L.

2008-01-01

We report the identification and functional analysis of nine genes from Gram-positive and Gram-negative bacteria and their phages that are similar to lambda (λ) bet or Escherichia coli recT. Beta and RecT are single-strand DNA annealing proteins, referred to here as recombinases. Each of the nine other genes when expressed in E. coli carries out oligonucleotide-mediated recombination. To our knowledge, this is the first study showing single-strand recombinase activity from diverse bacteria. Similar to bet and recT, most of these other recombinases were found to be associated with putative exonuclease genes. Beta and RecT in conjunction with their cognate exonucleases carry out recombination of linear double-strand DNA. Among four of these foreign recombinase/exonuclease pairs tested for recombination with double-strand DNA, three had activity, albeit barely detectable. Thus, although these recombinases can function in E. coli to catalyze oligonucleotide recombination, the double-strand DNA recombination activities with their exonuclease partners were inefficient. This study also demonstrated that Gam, by inhibiting host RecBCD nuclease activity, helps to improve the efficiency of λ Red-mediated recombination with linear double-strand DNA, but Gam is not absolutely essential. Thus, in other bacterial species where Gam analogs have not been identified, double-strand DNA recombination may still work in the absence of a Gam-like function. We anticipate that at least some of the recombineering systems studied here will potentiate oligonucleotide and double-strand DNA-mediated recombineering in their native or related bacteria. PMID:18230724

Study of photon emission by electron capture during solar nuclei acceleration. 2: Delimitation of conditions for charge transfert establishment

NASA Technical Reports Server (NTRS)

Perez-Peraza, J.; Alvarez, M.; Gallegos, A.

1985-01-01

The conditions for establishment of charge transfer during acceleration of nuclei up to Fe, for typical conditions of solar flare regions T = 5 x 10 to the 3rd power to 2.5 x 10 to the 8th power degrees K were explored. Results show that such conditions are widely assorted, depending on the acceleration mechanism, the kind of projections and their velocity, the target elements, the source temperature and consequently on the degree of ionization of matter and the local charge state of the accelerated ions. Nevertheless, in spite of that assorted behavior, there are some general tendencies that can be summarized as follows. In atomic H electron capture is systematically established from thermal energies up to high energies, whatever the element and for both acceleration process. For a given element and fixed temperature (T), the probability and energy domain of electron capture and loss with Fermi are higher than with Betatron acceleration. For a given acceleration process the heavier the ion the higher the probability and the wider the energy range for electron capture and loss. For given acceleration mechanism and fixed element the importance and energy domain of capture and loss increase with T: for those reasons, the energy range of charge equilibrium (illustrated with solid lines on the next figs.) is wider with Fermi and increases with temperature and atomic number of projectiles. For the same reasons, electron loss is smaller while the lighter the element, the lower the temperature and the Betatron process, such that there are conditions for which electron loss is not allowed at low energies, but only electron capture is established.

Development of an Electron-capture Technique Specific for Explosives Detection

DOT National Transportation Integrated Search

1974-07-01

This document contains information on the design, fabrication, and testing of a prototype detector specific for explosives which employs electron-capture sensors. The technique used exploits the observation that the electronegative vapors from explos...

Search for neutrinoless double-electron capture of 156Dy

NASA Astrophysics Data System (ADS)

Finch, S. W.; Tornow, W.

2015-12-01

Background: Multiple large collaborations are currently searching for neutrinoless double-β decay, with the ultimate goal of differentiating the Majorana-Dirac nature of the neutrino. Purpose: Investigate the feasibility of resonant neutrinoless double-electron capture, an experimental alternative to neutrinoless double-β decay. Method: Two clover germanium detectors were operated underground in coincidence to search for the de-excitation γ rays of 156Gd following the neutrinoless double-electron capture of 156Dy. 231.95 d of data were collected at the Kimballton underground research facility with a 231.57 mg enriched 156Dy sample. Results: No counts were seen above background and half-life limits are set at O (1016-1018) yr for the various decay modes of 156Dy. Conclusion: Low background spectra were efficiently collected in the search for neutrinoless double-electron capture of 156Dy, although the low natural abundance and associated lack of large quantities of enriched samples hinders the experimental reach.

Measuring double-electron capture with liquid xenon experiments

NASA Astrophysics Data System (ADS)

Mei, D.-M.; Marshall, I.; Wei, W.-Z.; Zhang, C.

2014-01-01

We investigate the possibilities of observing the decay mode for 124Xe in which two electrons are captured, two neutrinos are emitted, and the final daughter nucleus is in its ground state, using dark matter experiments with liquid xenon. The first upper limit of the decay half-life is calculated to be 1.66 × 1021 years at a 90% confidence level (C.L.) obtained with the published background data from the XENON100 experiment. Employing a known background model from the large underground xenon (LUX) experiment, we predict that the detection of double-electron capture of 124Xe to the ground state of 124Te with LUX will have approximately 115 events, assuming a half-life of 2.9 × 1021 years. We conclude that measuring 124Xe 2ν double-electron capture to the ground state of 124Te can be performed more precisely with the proposed LUX-Zeplin (LZ) experiment.

Search for two-neutrino double electron capture of 124Xe with XENON100

NASA Astrophysics Data System (ADS)

Aprile, E.; Aalbers, J.; Agostini, F.; Alfonsi, M.; Amaro, F. D.; Anthony, M.; Arneodo, F.; Barrow, P.; Baudis, L.; Bauermeister, B.; Benabderrahmane, M. L.; Berger, T.; Breur, P. A.; Brown, A.; Brown, E.; Bruenner, S.; Bruno, G.; Budnik, R.; Bütikofer, L.; Calvén, J.; Cardoso, J. M. R.; Cervantes, M.; Cichon, D.; Coderre, D.; Colijn, A. P.; Conrad, J.; Cussonneau, J. P.; Decowski, M. P.; de Perio, P.; di Gangi, P.; di Giovanni, A.; Diglio, S.; Duchovni, E.; Fei, J.; Ferella, A. D.; Fieguth, A.; Franco, D.; Fulgione, W.; Gallo Rosso, A.; Galloway, M.; Gao, F.; Garbini, M.; Geis, C.; Goetzke, L. W.; Greene, Z.; Grignon, C.; Hasterok, C.; Hogenbirk, E.; Itay, R.; Kaminsky, B.; Kessler, G.; Kish, A.; Landsman, H.; Lang, R. F.; Lellouch, D.; Levinson, L.; Le Calloch, M.; Levy, C.; Lin, Q.; Lindemann, S.; Lindner, M.; Lopes, J. A. M.; Manfredini, A.; Marrodán Undagoitia, T.; Masbou, J.; Massoli, F. V.; Masson, D.; Mayani, D.; Meng, Y.; Messina, M.; Micheneau, K.; Miguez, B.; Molinario, A.; Murra, M.; Naganoma, J.; Ni, K.; Oberlack, U.; Orrigo, S. E. A.; Pakarha, P.; Pelssers, B.; Persiani, R.; Piastra, F.; Pienaar, J.; Piro, M.-C.; Plante, G.; Priel, N.; Rauch, L.; Reichard, S.; Reuter, C.; Rizzo, A.; Rosendahl, S.; Rupp, N.; Dos Santos, J. M. F.; Sartorelli, G.; Scheibelhut, M.; Schindler, S.; Schreiner, J.; Schumann, M.; Scotto Lavina, L.; Selvi, M.; Shagin, P.; Silva, M.; Simgen, H.; Sivers, M. V.; Stein, A.; Thers, D.; Tiseni, A.; Trinchero, G.; Tunnell, C. D.; Wall, R.; Wang, H.; Weber, M.; Wei, Y.; Weinheimer, C.; Wulf, J.; Zhang, Y.; Xenon Collaboration

2017-02-01

Two-neutrino double electron capture is a rare nuclear decay where two electrons are simultaneously captured from the atomic shell. For 124Xe this process has not yet been observed and its detection would provide a new reference for nuclear matrix element calculations. We have conducted a search for two-neutrino double electron capture from the K shell of 124Xe using 7636 kg d of data from the XENON100 dark matter detector. Using a Bayesian analysis we observed no significant excess above background, leading to a lower 90% credibility limit on the half-life T1 /2>6.5 ×1020 yr. We have also evaluated the sensitivity of the XENON1T experiment, which is currently being commissioned, and found a sensitivity of T1 /2>6.1 ×1022 yr after an exposure of 2 t yr .

75 FR 31762 - Foreign-Trade Zone 203; Application for Subzone Authority; REC Silicon; Invitation for Public...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-04

... orders. A key consideration in this request is the cumulative effect on domestic silicon metal prices and... applications to avoid AD/CVD duties on silicon metal for export production. In addition to the REC Silicon... those of the other U.S. producers, the ripple effect on silicon metal suppliers would be significant and...

Thiols, recA induction and radiosensitivity in Escherichia coli.

PubMed

Naslund, M; Anderstam, B; Granath, F; Ehrenberg, L

1996-01-01

Induction by gamma-radiation, UV radiation or hydroxyurea of RecA gene product synthesis in Escherichia coli, monitored as beta-D-galactosidase in recA-lacZ fusion strains, was shown to be inhibited if 2-mercaptoethylamine (MEA) was added before treatment with the inducing agents. If cysteine (Cys) at low concentrations was added at the same time as MEA it counteracted the action of MEA. The effect of MEA may be described as a competitive inhibition of an inducing or conducting effect of Cys. In E. coli GE499 (uvrA+), complete inhibition by 30-mmol dm-3 MEA of recA induction was associated with about five times higher radio-resistence. Both of these effects of MEA were completely reversed by 0.3-mmol dm-3 Cys. As shown in parallel experiments with E. coli GE500 (uvrA-), these effects of MEA and Cys were shown to be independent of excision-repair proficiency. Treatment of bacteria with MEA and/or Cys was shown not to lead to increased intracellular concentrations of these thiols. Instead, treatment with them appeared to provoke conspicuous increases in glutathione levels, which are, however, probably not directly involved in the studied action of MEA and Cys.

The Vacuolar-Type H+-ATPase in Ovine Rumen Epithelium is Regulated by Metabolic Signals

PubMed Central

Kuzinski, Judith; Zitnan, Rudolf; Warnke-Gurgel, Christina; Schweigel, Monika

2010-01-01

In this study, the effect of metabolic inhibition (MI) by glucose substitution with 2-deoxyglucose (2-DOG) and/or application of antimycin A on ovine rumen epithelial cells (REC) vacuolar-type H+-ATPase (vH+-ATPase) activity was investigated. Using fluorescent spectroscopy, basal pHi of REC was measured to be 7.3 ± 0.1 in HCO3−-free, glucose-containing NaCl medium. MI induced a strong pHi reduction (−0.44 ± 0.04 pH units) with a more pronounced effect of 2-DOG compared to antimycin A (−0.30 ± 0.03 versus −0.21 ± 0.03 pH units). Treatment with foliomycin, a specific vH+-ATPase inhibitor, decreased REC pHi by 0.21 ± 0.05 pH units. After MI induction, this effect was nearly abolished (−0.03 ± 0.02 pH units). In addition, membrane-associated localization of vH+-ATPase B subunit disappeared. Metabolic control of vH+-ATPase involving regulation of its assembly state by elements of the glycolytic pathway could provide a means to adapt REC ATP consumption according to energy availability. PMID:20069127

Novel recA-Independent Horizontal Gene Transfer in Escherichia coli K-12.

PubMed

Kingston, Anthony W; Roussel-Rossin, Chloé; Dupont, Claire; Raleigh, Elisabeth A

2015-01-01

In bacteria, mechanisms that incorporate DNA into a genome without strand-transfer proteins such as RecA play a major role in generating novelty by horizontal gene transfer. We describe a new illegitimate recombination event in Escherichia coli K-12: RecA-independent homologous replacements, with very large (megabase-length) donor patches replacing recipient DNA. A previously uncharacterized gene (yjiP) increases the frequency of RecA-independent replacement recombination. To show this, we used conjugal DNA transfer, combining a classical conjugation donor, HfrH, with modern genome engineering methods and whole genome sequencing analysis to enable interrogation of genetic dependence of integration mechanisms and characterization of recombination products. As in classical experiments, genomic DNA transfer begins at a unique position in the donor, entering the recipient via conjugation; antibiotic resistance markers are then used to select recombinant progeny. Different configurations of this system were used to compare known mechanisms for stable DNA incorporation, including homologous recombination, F'-plasmid formation, and genome duplication. A genome island of interest known as the immigration control region was specifically replaced in a minority of recombinants, at a frequency of 3 X 10(-12) CFU/recipient per hour.

Analysis of strand transfer and template switching mechanisms of DNA gap repair by homologous recombination in Escherichia coli: predominance of strand transfer.

PubMed

Izhar, Lior; Goldsmith, Moshe; Dahan, Ronny; Geacintov, Nicholas; Lloyd, Robert G; Livneh, Zvi

2008-09-12

Daughter strand gaps formed upon interruption of replication at DNA lesions in Escherichia coli can be repaired by either translesion DNA synthesis or homologous recombination (HR) repair. Using a plasmid-based assay system that enables discrimination between strand transfer and template switching (information copying) modes of HR gap repair, we found that approximately 80% of strand gaps were repaired by physical strand transfer from the donor, whereas approximately 20% appear to be repaired by template switching. HR gap repair operated on both small and bulky lesions and largely depended on RecA and RecF but not on the RecBCD nuclease. In addition, we found that HR was mildly reduced in cells lacking the RuvABC and RecG proteins involved in resolution of Holliday junctions. These results, obtained for the first time under conditions that detect the two HR gap repair mechanisms, provide in vivo high-resolution molecular evidence for the predominance of the strand transfer mechanism in HR gap repair. A small but significant portion of HR gap repair appears to occur via a template switching mechanism.

The adnAB Locus, Encoding a Putative Helicase-Nuclease Activity, Is Essential in Streptomyces

PubMed Central

Zhang, Lingli; Nguyen, Hoang Chuong; Chipot, Ludovic; Piotrowski, Emilie; Bertrand, Claire

2014-01-01

Homologous recombination is a crucial mechanism that repairs a wide range of DNA lesions, including the most deleterious ones, double-strand breaks (DSBs). This multistep process is initiated by the resection of the broken DNA ends by a multisubunit helicase-nuclease complex exemplified by Escherichia coli RecBCD, Bacillus subtilis AddAB, and newly discovered Mycobacterium tuberculosis AdnAB. Here we show that in Streptomyces, neither recBCD nor addAB homologues could be detected. The only putative helicase-nuclease-encoding genes identified were homologous to M. tuberculosis adnAB genes. These genes are conserved as a single copy in all sequenced genomes of Streptomyces. The disruption of adnAB in Streptomyces ambofaciens and Streptomyces coelicolor could not be achieved unless an ectopic copy was provided, indicating that adnAB is essential for growth. Both adnA and adnB genes were shown to be inducible in response to DNA damage (mitomycin C) and to be independently transcribed. Introduction of S. ambofaciens adnAB genes in an E. coli recB mutant restored viability and resistance to UV light, suggesting that Streptomyces AdnAB could be a functional homologue of RecBCD and be involved in DNA damage resistance. PMID:24837284

Effect of collective response on electron capture and excitation in collisions of highly charged ions with fullerenes.

PubMed

Kadhane, U; Misra, D; Singh, Y P; Tribedi, Lokesh C

2003-03-07

Projectile deexcitation Lyman x-ray emission following electron capture and K excitation has been studied in collisions of bare and Li-like sulphur ions (of energy 110 MeV) with fullerenes (C(60)/C(70)) and different gaseous targets. The intensity ratios of different Lyman x-ray lines in collisions with fullerenes are found to be substantially lower than those for the gas targets, both for capture and excitation. This has been explained in terms of a model based on "solidlike" effect, namely, wakefield induced stark mixing of the excited states populated via electron capture or K excitation: a collective phenomenon of plasmon excitation in the fullerenes under the influence of heavy, highly charged ions.

Status and Trends in the U.S. Voluntary Green Power Market (2013 Data)

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

Heeter, J.; Belyeu, K.; Kuskova-Burns, K.

Voluntary green power markets are those in which consumers and institutions voluntarily purchase renewable energy to match their electricity needs. This report surveys utilities, competitive suppliers, renewable energy certificate (REC) marketers, and, for the first time, the community choice aggregation market. This report finds that the voluntary market totaled 62 million megawatt-hours in 2013. Approximately 5.4 million customers are purchasing green power. This report presents data and analysis on voluntary market sales and customer participation, products and premiums, green pricing marketing, and administrative expenses. The report also details trends in REC tracking systems, REC pricing in voluntary and compliance markets,more » community and crowd-funded solar, and interest in renewable energy by the information and communication technologies sector.« less

Helical filaments of human Dmc1 protein on single-stranded DNA: a cautionary tale

PubMed Central

Yu, Xiong; Egelman, Edward H.

2010-01-01

Proteins in the RecA/Rad51/RadA family form nucleoprotein filaments on DNA that catalyze a strand exchange reaction as part of homologous genetic recombination. Because of the centrality of this system to many aspects of DNA repair, the generation of genetic diversity, and cancer when this system fails or is not properly regulated, these filaments have been the object of many biochemical and biophysical studies. A recent paper has argued that the human Dmc1 protein, a meiotic homolog of bacterial RecA and human Rad51, forms filaments on single stranded DNA with ∼ 9 subunits per turn in contrast to the filaments formed on double stranded DNA with ∼ 6.4 subunits per turn, and that the stoichiometry of DNA binding is different between these two filaments. We show using scanning transmission electron microscopy (STEM) that the Dmc1 filament formed on single stranded DNA has a mass per unit length expected from ∼ 6.5 subunits per turn. More generally, we show how ambiguities in helical symmetry determination can generate incorrect solutions, and why one sometimes must use other techniques, such as biochemistry, metal shadowing, or STEM to resolve these ambiguities. While three-dimensional reconstruction of helical filaments from EM images is a powerful tool, the intrinsic ambiguities that may be present with limited resolution are not sufficiently appreciated. PMID:20600108

Equilibration kinetics in isolated and membrane-bound photosynthetic reaction centers upon illumination: a method to determine the photoexcitation rate.

PubMed

Manzo, Anthony J; Goushcha, Alexander O; Barabash, Yuri M; Kharkyanen, Valery N; Scott, Gary W

2009-07-01

Kinetics of electron transfer, following variation of actinic light intensity, for photosynthetic reaction centers (RCs) of purple bacteria (isolated and membrane-bound) were analyzed by measuring absorbance changes in the primary photoelectron donor absorption band at 865 nm. The bleaching of the primary photoelectron donor absorption band in RCs, following a sudden increase of illumination from the dark to an actinic light intensity of I(exp), obeys a simple exponential law with the rate constant alphaI(exp) + k(rec), in which alpha is a parameter relating the light intensity, measured in mW/cm(2), to a corresponding theoretical rate in units of reciprocal seconds, and k(rec) is the effective rate constant of the charge recombination in the photosynthetic RCs. In this work, a method for determining the alpha parameter value is developed and experimentally verified for isolated and membrane-bound RCs, allowing for rigorous modeling of RC macromolecule dynamics under varied photoexcitation conditions. Such modeling is necessary for RCs due to alterations of the forward photoexcitation rates and relaxation rates caused by illumination history and intramolecular structural dynamics effects. It is demonstrated that the classical Bouguer-Lambert-Beer formalism can be applied for the samples with relatively low scattering, which is not necessarily the case with strongly scattering media or high light intensity excitation.

DNA recombination activity in soybean mitochondria.

PubMed

Manchekar, Medha; Scissum-Gunn, Karyn; Song, Daqing; Khazi, Fayaz; McLean, Stephanie L; Nielsen, Brent L

2006-02-17

Mitochondrial genomes in higher plants are much larger and more complex as compared to animal mitochondrial genomes. There is growing evidence that plant mitochondrial genomes exist predominantly as a collection of linear and highly branched DNA molecules and replicate by a recombination-dependent mechanism. However, biochemical evidence of mitochondrial DNA (mtDNA) recombination activity in plants has previously been lacking. We provide the first report of strand-invasion activity in plant mitochondria. Similar to bacterial RecA, this activity from soybean is dependent on the presence of ATP and Mg(2+). Western blot analysis using an antibody against the Arabidopsis mitochondrial RecA protein shows cross-reaction with a soybean protein of about 44 kDa, indicating conservation of this protein in at least these two plant species. mtDNA structure was analyzed by electron microscopy of total soybean mtDNA and molecules recovered after field-inversion gel electrophoresis (FIGE). While most molecules were found to be linear, some molecules contained highly branched DNA structures and a small but reproducible proportion consisted of circular molecules (many with tails) similar to recombination intermediates. The presence of recombination intermediates in plant mitochondria preparations is further supported by analysis of mtDNA molecules by 2-D agarose gel electrophoresis, which indicated the presence of complex recombination structures along with a considerable amount of single-stranded DNA. These data collectively provide convincing evidence for the occurrence of homologous DNA recombination in plant mitochondria.

Ecology and Population Structure of Vibrionaceae in the Coastal Ocean

DTIC Science & Technology

2010-02-01

population is closest to V. gazogenes at atpA (Fig. 2) and V. kanoleae at gyrB (Fig. 3). The relationship with other species at all genetic loci is...Closest named relative varies by gene: V pacinii (recA), V kanaloae (gyrB) and V gazogenes (atpA) F11 L V. splendidus cluster 1 atpA, gyrB, pyrH, recA

Chromosomal Fragmentation in "Escherichia Coli": Its Absence in "mutT" Mutants and Its Mechanisms in "seqA" Mutants

ERIC Educational Resources Information Center

Rotman, Ella Rose

2009-01-01

Chromosomal fragmentation in "Escherichia coli" is a lethal event for the cell unless mended by the recombinational repair proteins RecA, RecBCD, and RuvABC. Certain mutations exacerbate problems that cause the cell to be dependent on the recombinational repair proteins for viability. We tested whether the absence of the MutT protein caused…

Familiar ethical issues amplified: how members of research ethics committees describe ethical distinctions between disaster and non-disaster research.

PubMed

Tansey, Catherine M; Anderson, James; Boulanger, Renaud F; Eckenwiler, Lisa; Pringle, John; Schwartz, Lisa; Hunt, Matthew

2017-06-28

The conduct of research in settings affected by disasters such as hurricanes, floods and earthquakes is challenging, particularly when infrastructures and resources were already limited pre-disaster. However, since post-disaster research is essential to the improvement of the humanitarian response, it is important that adequate research ethics oversight be available. We aim to answer the following questions: 1) what do research ethics committee (REC) members who have reviewed research protocols to be conducted following disasters in low- and middle-income countries (LMICs) perceive as the key ethical concerns associated with disaster research?, and 2) in what ways do REC members understand these concerns to be distinct from those arising in research conducted in non-crisis situations? This qualitative study was developed using interpretative description methodology; 15 interviews were conducted with REC members. Four key ethical issues were identified as presenting distinctive considerations for disaster research to be implemented in LMICs, and were described by participants as familiar research ethics issues that were amplified in these contexts. First, REC members viewed disaster research as having strong social value due to its potential for improving disaster response, but also as requiring a higher level of justification compared to other research settings. Second, they identified vulnerability as an overarching concern for disaster research ethics, and a feature that required careful and critical appraisal when assessing protocols. They noted that research participants' vulnerabilities frequently change in the aftermath of a disaster and often in unpredictable ways. Third, they identified concerns related to promoting and maintaining safety, confidentiality and data security in insecure or austere environments. Lastly, though REC members endorsed the need and usefulness of community engagement, they noted that there are significant challenges in a disaster setting over and above those typically encountered in global health research to achieve meaningful community engagement. Disaster research presents distinctive ethical considerations that require attention to ensure that participants are protected. As RECs review disaster research protocols, they should address these concerns and consider how justification, vulnerability, security and confidentially, and community engagement are shaped by the realities of conducting research in a disaster.

Functions that Protect Escherichia coli from Tightly Bound DNA-Protein Complexes Created by Mutant EcoRII Methyltransferase.

PubMed

Henderson, Morgan L; Kreuzer, Kenneth N

2015-01-01

Expression of mutant EcoRII methyltransferase protein (M.EcoRII-C186A) in Escherichia coli leads to tightly bound DNA-protein complexes (TBCs), located sporadically on the chromosome rather than in tandem arrays. The mechanisms behind the lethality induced by such sporadic TBCs are not well studied, nor is it clear whether very tight binding but non-covalent complexes are processed in the same way as covalent DNA-protein crosslinks (DPCs). Using 2D gel electrophoresis, we found that TBCs induced by M.EcoRII-C186A block replication forks in vivo. Specific bubble molecules were detected as spots on the 2D gel, only when M.EcoRII-C186A was induced, and a mutation that eliminates a specific EcoRII methylation site led to disappearance of the corresponding spot. We also performed a candidate gene screen for mutants that are hypersensitive to TBCs induced by M.EcoRII-C186A. We found several gene products necessary for protection against these TBCs that are known to also protect against DPCs induced with wild-type M.EcoRII (after 5-azacytidine incorporation): RecA, RecBC, RecG, RuvABC, UvrD, FtsK, XerCD and SsrA (tmRNA). In contrast, the RecFOR pathway and Rep helicase are needed for protection against TBCs but not DPCs induced by M.EcoRII. We propose that stalled fork processing by RecFOR and RecA promotes release of tightly bound (but non-covalent) blocking proteins, perhaps by licensing Rep helicase-driven dissociation of the blocking M.EcoRII-C186A. Our studies also argued against the involvement of several proteins that might be expected to protect against TBCs. We took the opportunity to directly compare the sensitivity of all tested mutants to two quinolone antibiotics, which target bacterial type II topoisomerases and induce a unique form of DPC. We uncovered rep, ftsK and xerCD as novel quinolone hypersensitive mutants, and also obtained evidence against the involvement of a number of functions that might be expected to protect against quinolones.

Influence of nutrient intake on antioxidant capacity, muscle damage and white blood cell count in female soccer players

PubMed Central

2012-01-01

Background Soccer is a form of exercise that induces inflammatory response, as well as an increase in free radicals potentially leading to muscle injury. Balanced nutritional intake provides important antioxidant vitamins, including vitamins A, C and E, which may assist in preventing exercise-related muscle damage. The purpose of the present study was to determine the effect of macro/micronutrient intake on markers of oxidative stress, muscle damage, inflammatory and immune response in female soccer players. Methods Twenty-eight female players belonging to two soccer teams of the same professional soccer club participated in this study after being informed about the aims and procedures and after delivering written consent. Each team completed an 8-day dietary record and played one competition match the same week. Participants were divided into two groups: the REC group (who complied with recommended intakes) and the NO-REC group (who were not compliant). Laboratory blood tests were carried out to determine hematological, electrolytic and hormonal variables, as well as to monitor markers of cell damage and oxidative stress. Blood samples were obtained 24 h before, immediately after and 18 h after official soccer matches. Student t-test or Mann–Whitney U-test was used to compare both groups throughout the match. Results At rest, we observed that the REC group had higher levels of total antioxidant status (TAS), glutathione peroxidase (GPx), and lower levels of creatine kinase (CK) and lactate dehydrogenase (LDH) in comparison to the NO-REC group. Immediately after the match, levels of TAS, GPx, superoxide dismutase (SOD), LDH and % lymphocytes were higher and the % of neutrophils were lower in the REC group compared to the NO-REC group. These differences were also maintained 18 h post-match, only for TAS and GPx. Conclusions Our data reveal an association between nutritional intake and muscle damage, oxidative stress, immunity and inflammation markers. The benefit of the intake of specific nutrients may contribute to preventing the undesirable physiological effects provoked by soccer matches. PMID:22812729

An Evaluation of Time-Trial-Based Predictions of V[Combining Dot Above]O2max and Recommended Training Paces for Collegiate and Recreational Runners.

PubMed

Scudamore, Eric M; Barry, Vaughn W; Coons, John M

2018-04-01

Scudamore, EM, Barry, VW, and Coons, JM. An Evaluation of time-trial-based predictions of V[Combining Dot Above]O2max and recommended training paces for collegiate and recreational runners. J Strength Cond Res 32(4): 1137-1143, 2018-The purpose of the current study was to determine the accuracy of Jack Daniels' VDOT Running Calculator for the prediction of V[Combining Dot Above]O2max, and recommendations of interval and training paces (pIN and pTH) in samples of National Collegiate Athletic Association Division 1 track athletes (ATH, n = 11) and recreational runners (REC; n = 9). Predicted variable data were obtained using results from indoor 5-km time-trials. Data from the VDOT Calculator were compared with laboratory-tested V[Combining Dot Above]O2max, pace at V[Combining Dot Above]O2max (V[Combining Dot Above]O2maxpace), and lactate threshold pace (LTpace). Results indicated that VDOT underestimated V[Combining Dot Above]O2max in ATH (t(10) = -6.00, p < 0.001, d = 1.75) and REC (t(8) = -8.96, p < 0.001, d = 3.44). Follow-up between-groups analysis indicated that the difference between VDOT and V[Combining Dot Above]O2max was significantly greater in REC than in ATH (p = 0.0031, d = 1.59). pIN was slower than V[Combining Dot Above]O2maxpace in REC (t(8) = -4.26, p = 0.003, d = 1.76), but not different in ATH (t(10) = 0.52, p = 0.614, d = 0.14). Conversely, pTH was faster than LTpace in ATH (t(8) = -4.17, p = 0.003, d = 1.49), but not different in REC (t(8) = 1.64, p = 0.139, d = 0.57). Practically, pTH can be confidently used for threshold training regardless of the ability level. pIN also seemed to be accurate for ATH, but may be not be optimal for improving V[Combining Dot Above]O2max in REC. Practitioners should interpret VDOT with caution as it may underestimate V[Combining Dot Above]O2max.

Treatment of gingival recession defects using coronally advanced flap with a porcine collagen matrix compared to coronally advanced flap with connective tissue graft: a randomized controlled clinical trial.

PubMed

Cardaropoli, Daniele; Tamagnone, Lorenzo; Roffredo, Alessandro; Gaveglio, Lorena

2012-03-01

Connective tissue graft (CTG) plus coronally advanced flap (CAF) is the reference therapy for root coverage. The aim of the present study is to evaluate the use of a porcine collagen matrix (PCM) plus CAF as an alternative to CTG+CAF for the treatment of gingival recessions (REC), in a prospective randomized, controlled clinical trial. Eighteen adult patients participated in this study. The patients presented 22 single Miller's Class I or II REC, randomly assigned to the test (PCM+CAF) or control (CTG+CAF) group. REC, probing depth, clinical attachment level (CAL), and width of keratinized tissue (KG) were evaluated at 12 months. In addition, the gingival thickness (GT) was measured 1mm apical to the bottom of the sulcus. At 12 months, mean REC was 0.23 mm for test sites and 0.09 mm for control sites (P <0.01), whereas percentage of root coverage was 94.32% and 96.97%, respectively. CAL gain was 2.41 mm in test sites and 2.95 mm in control sites (P <0.01). KG gain was 1.23 mm in the test group and 1.27 mm in the control group (P <0.01). In test sites, GT changed from 0.82 to 1.82 mm, and in control sites, from 0.86 to 2.09 mm (P <0.01). Within the limits of the study, both treatment procedures resulted in significant reduction in REC at 12 months. No statistically significant differences were found between PCM+CAF and CTG+CAF with regard to any clinical parameter. The collagen matrix represents a possible alternative to CTG.

Recombinant vaccine displaying the loop-neutralizing determinant from protective antigen completely protects rabbits from experimental inhalation anthrax.

PubMed

Oscherwitz, Jon; Yu, Fen; Jacobs, Jana L; Cease, Kemp B

2013-03-01

We previously showed that a multiple antigenic peptide (MAP) vaccine displaying amino acids (aa) 304 to 319 from the 2β2-2β3 loop of protective antigen was capable of protecting rabbits from an aerosolized spore challenge with Bacillus anthracis Ames strain. Antibodies to this sequence, referred to as the loop-neutralizing determinant (LND), are highly potent at neutralizing lethal toxin yet are virtually absent in rabbit and human protective antigen (PA) antiserum. While the MAP vaccine was protective against anthrax, it contains a single heterologous helper T cell epitope which may be suboptimal for stimulating an outbred human population. We therefore engineered a recombinant vaccine (Rec-LND) containing two tandemly repeated copies of the LND fused to maltose binding protein, with enhanced immunogenicity resulting from the p38/P4 helper T cell epitope from Schistosoma mansoni. Rec-LND was found to be highly immunogenic in four major histocompatibility complex (MHC)-diverse strains of mice. All (7/7) rabbits immunized with Rec-LND developed high-titer antibody, 6 out of 7 developed neutralizing antibody, and all rabbits were protected from an aerosolized spore challenge of 193 50% lethal doses (LD(50)) of the B. anthracis Ames strain. Survivor serum from Rec-LND-immunized rabbits revealed significantly increased neutralization titers and specific activity compared to prechallenge levels yet lacked PA or lethal factor (LF) antigenemia. Control rabbits immunized with PA, which were also completely protected, appeared sterilely immune, exhibiting significant declines in neutralization titer and specific activity compared to prechallenge levels. We conclude that Rec-LND may represent a prototype anthrax vaccine for use alone or potentially combined with PA-containing vaccines.

Characteristics of Drug and Dietary Supplement Inquiries by College Athletes

PubMed Central

Ambrose, Peter J.; Tsourounis, Candy; Olander, Rachel; Uryasz, Frank

2010-01-01

Background: In the United States, the National Center for Drug Free Sport manages the drug-testing programs for athletes of the National Collegiate Athletic Association (NCAA). Through its Resource Exchange Center (REC), Drug Free Sport supports athletic staff and athletes with information regarding drugs and dietary supplements. Purpose: To characterize the types of drug-related and dietary supplement–related inquiries submitted to Drug Free Sport through the REC. Study Design: Cross-sectional study. Methods: All inquiries submitted to the REC for the period of September 1, 2005, through June 30, 2006, were reviewed. The data were categorized by the method of inquiry submission; the name of the substance in question; the sex, sport, and NCAA division of the athlete involved; the nature of the inquiry; and the response provided by the REC regarding the NCAA’s status of the substance in question. Results: Pseudoephedrine, acetaminophen/hydrocodone, and albuterol were the most commonly self-searched medications; stimulants accounted for the majority of banned medications. Dietary supplements accounted for 80% of all inquiries submitted to the REC via the Banned Drug Inquiry Form. Among all dietary supplements, creatine was the most commonly inquired. Banned substances accounted for 29% of all inquiries. Conclusions: There were more than 10 000 inquiries regarding the status of medications, dietary supplements, and other substances for NCAA athletes during the 2005-2006 academic year. It is helpful for athletes to have resources that help them navigate banned-substance lists and so avoid the inadvertent use of banned substances. Clinical Relevance: Educating athletes regarding the stimulant content of various dietary supplements and addressing the lack of clinical trials to support stated claims and safety appear critical. PMID:23015919

Division-induced DNA double strand breaks in the chromosome terminus region of Escherichia coli lacking RecBCD DNA repair enzyme

PubMed Central

Durand, Adeline; Desfontaines, Jean-Michel; Iurchenko, Ielyzaveta; Auger, Hélène; Leach, David R. F.

2017-01-01

Marker frequency analysis of the Escherichia coli recB mutant chromosome has revealed a deficit of DNA in a specific zone of the terminus, centred on the dif/TerC region. Using fluorescence microscopy of a marked chromosomal site, we show that the dif region is lost after replication completion, at the time of cell division, in one daughter cell only, and that the phenomenon is transmitted to progeny. Analysis by marker frequency and microscopy shows that the position of DNA loss is not defined by the replication fork merging point since it still occurs in the dif/TerC region when the replication fork trap is displaced in strains harbouring ectopic Ter sites. Terminus DNA loss in the recB mutant is also independent of dimer resolution by XerCD at dif and of Topo IV action close to dif. It occurs in the terminus region, at the point of inversion of the GC skew, which is also the point of convergence of specific sequence motifs like KOPS and Chi sites, regardless of whether the convergence of GC skew is at dif (wild-type) or a newly created sequence. In the absence of FtsK-driven DNA translocation, terminus DNA loss is less precisely targeted to the KOPS convergence sequence, but occurs at a similar frequency and follows the same pattern as in FtsK+ cells. Importantly, using ftsIts, ftsAts division mutants and cephalexin treated cells, we show that DNA loss of the dif region in the recB mutant is decreased by the inactivation of cell division. We propose that it results from septum-induced chromosome breakage, and largely contributes to the low viability of the recB mutant. PMID:28968392

Reduction in body temperature using hand cooling versus passive rest after exercise in the heat.

PubMed

Adams, William M; Hosokawa, Yuri; Adams, Elizabeth L; Belval, Luke N; Huggins, Robert A; Casa, Douglas J

2016-11-01

To examine the effects of hydration and hand cooling on lowering body temperature after exercise in the heat. Randomized cross-over design. Nine recreationally active male participants (mean±SD; age, 24±4; height, 177.3±9.9cm; body mass, 76.7±11.6kg; body fat, 14.7±5.8%) completed a bout of treadmill exercise in a hot environment. After completion of exercise, participants were assigned to the following trials for post-exercise cooling: (1) hydrated with passive rest (HY), (2) hydrated with hand cooling on both hands (HY+2HC), (3) dehydrated with passive rest (DY), and (4) dehydrated with hand cooling on both hands (DY+2HC). Within subject differences were assessed using a three-way (Hydration×Condition×Time) repeated measures ANOVA with Tukey's post hoc analysis if significant interactions were found. Irrespective of hydration status, hand cooling on both hands resulted in significantly greater reductions in T REC than passive cooling at minute 20 (0.27°C [0.05, 0.49], ES=2.08, p=0.017) (Fig. 1). The reduction in T REC at minute 18 trended towards statistical significance (0.21°C [.003, .42], ES=1.59, p=0.053). Hydration status alone and when differentiated among modes of cooling showed no differences on changes of T REC or heart rate across all conditions during post exercise recovery (p>0.05). Hand cooling on both hands reduced T REC more than passive cooling, however, the cooling rates observed render hand cooling a poor option for cooling. Greater reductions in T REC after exercise or between bouts of exercise may enhance recovery and subsequent performance. Copyright © 2016 Sports Medicine Australia. Published by Elsevier Ltd. All rights reserved.

Interaction of caffeine with the SOS response pathway in Escherichia coli.

PubMed

Whitney, Alyssa K; Weir, Tiffany L

2015-01-01

Previous studies have highlighted the antimicrobial activity of caffeine, both individually and in combination with other compounds. A proposed mechanism for caffeine's antimicrobial effects is inhibition of bacterial DNA repair pathways. The current study examines the influence of sub-lethal caffeine levels on the growth and morphology of SOS response pathway mutants of Escherichia coli. Growth inhibition after treatment with caffeine and methyl methane sulfonate (MMS), a mutagenic agent, was determined for E. coli mutants lacking key genes in the SOS response pathway. The persistence of caffeine's effects was explored by examining growth and morphology of caffeine and MMS-treated bacterial isolates in the absence of selective pressure. Caffeine significantly reduced growth of E. coli recA- and uvrA-mutants treated with MMS. However, there was no significant difference in growth between umuC-isolates treated with MMS alone and MMS in combination with caffeine after 48 h of incubation. When recA-isolates from each treatment group were grown in untreated medium, bacterial isolates that had been exposed to MMS or MMS with caffeine showed increased growth relative to controls and caffeine-treated isolates. Morphologically, recA-isolates that had been treated with caffeine and both caffeine and MMS together had begun to display filamentous growth. Caffeine treatment further reduced growth of recA- and uvrA-mutants treated with MMS, despite a non-functional SOS response pathway. However, addition of caffeine had very little effect on MMS inhibition of umuC-mutants. Thus, growth inhibition of E. coli with caffeine treatment may be driven by caffeine interaction with UmuC, but also appears to induce damage by additional mechanisms as evidenced by the additive effects of caffeine in recA- and uvrA-mutants.

Overexpression of Salmonella enterica serovar Typhi recA gene confers fluoroquinolone resistance in Escherichia coli DH5α.

PubMed

Yassien, M A M; Elfaky, M A

2015-11-01

A spontaneous fluoroquinolone-resistant mutant (STM1) was isolated from its parent Salmonella enterica serovar Typhi (S. Typhi) clinical isolate. Unlike its parent isolate, this mutant has selective resistance to fluoroquinolones without any change in its sensitivity to various other antibiotics. DNA gyrase assays revealed that the fluoroquinolone resistance phenotype of the STM1 mutant did not result from alteration of the fluoroquinolone sensitivity of the DNA gyrase isolated from it. To study the mechanism of fluoroquinolone resistance, a genomic library from the STM1 mutant was constructed in Escherichia coli DH5α and two recombinant plasmids were obtained. Only one of these plasmids (STM1-A) conferred the selective fluoroquinolone resistance phenotype to E. coli DH5α. The chromosomal insert from STM1-A, digested with EcoRI and HindIII restriction endonucleases, produced two DNA fragments and these were cloned separately into pUC19 thereby generating two new plasmids, STM1-A1 and STM1-A2. Only STM1-A1 conferred the selective fluoroquinolone resistance phenotype to E. coli DH5α. Sequence and subcloning analyses of STM1-A1 showed the presence of an intact RecA open reading frame. Unlike that of the wild-type E. coli DH5α, protein analysis of a crude STM1-A1 extract showed overexpression of a 40 kDa protein. Western blotting confirmed the 40 kDa protein band to be RecA. When a RecA PCR product was cloned into pGEM-T and introduced into E. coli DH5α, the STM1-A11 subclone retained fluoroquinolone resistance. These results suggest that overexpression of RecA causes selective fluoroquinolone resistance in E. coli DH5α.

12. VIEW OF OPERATING ROOMRCA COMMUNICATION REC STATION (THIS ROOM ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

12. VIEW OF OPERATING ROOM-RCA COMMUNICATION REC STATION (THIS ROOM WAS ORIGINALLY A MOTOR GENERATOR FACILITY AND SUPPLIED DC POWER TO AN EARLIER GENERATION OF POINT-TO-POINT RECEIVERS ON SECOND FLOOR). VIEW SHOWS TRANSMITTER CONTROL STATION AND AUDIO CONTROL STATION (LEFT, WATKINS-JOHNSON WJ-8718-23. HP RECEIVERS AND KENWOOD R-5000 COMMUNICATIONS RECEIVERS (220 DEGREES). - Marconi Radio Sites, Receiving, Point Reyes Station, Marin County, CA

Genetic Engineering of Single-Domain Magnetic Bacteria.

DTIC Science & Technology

1992-09-25

siderophore produc- cient but modification-proficient for all the three modifi- tion have been demonstrated in Serratia marcescens cation systems of S...characterization of 3-dehydroquinase cally novel iron(llll) transport system in Serratia marcescens . J from Eschenchia co/i. Biochem J 239: 699-704...should provide valuable infor- lion of rec.c4 mutants. rec.4-independen’t instabilit\\ of alciinatc mnation about the history of the evolution of this

"Dentinal microcracks after root canal preparation" a comparative evaluation with hand, rotary and reciprocating instrumentation.

PubMed

Priya, N Tulasi; Chandrasekhar, Veeramachaneni; Anita, S; Tummala, Muralidhar; Raj, T B Phanindhar; Badami, Vijetha; Kumar, Pradeep; Soujanya, E

2014-12-01

The purpose of this study was to compare the incidence of dentinal micro cracks after instrumentation with various types of NiTi files in rotary and reciprocating motion. One hundred human extracted mandibular central incisors were taken and divided into 10 groups (n=10 teeth per group). Group 1- No preparation, Group 2 - Hand instrumentation, Groups 3,4 - ProTaper files in rotary and reciprocating motion, Groups 5,6 - ProTaper Next files in rotary and reciprocating motion, Groups 7,8 - Oneshape files in rotary and reciprocating motion, Groups 9,10 - Reciproc files in rotary and reciprocating motion. Specimens were sectioned horizontally at 3,6 and 9 mm from the apex and dentinal micro cracks were observed under a stereomicroscope. There was a statistically significant difference between the groups (p<0.05). There were no significant differences in crack formation between the groups (Protaper Next - Rot, Protaper Next - Rec, Reciproc - Rec); (ProTaper - Rot, ProTaper - Rec, Oneshape - Rot), (Oneshape - Rot, Reciproc - Rot), (One shape Reciproc, Reciproc - Rec); (p >.05). Least cracks were seen in canals instrumented with Pro Taper Next files both in rotary and reciprocating motion. Full sequence rotary systems showed less cracks than single file systems and full sequence rotary systems showed less cracks in reciprocating motion than in rotary motion.

WASP (Write a Scientific Paper): Ethics approval for a research study (2).

PubMed

Mallia, Pierre

2018-05-03

Research Ethics Committees are composed of a minimum of five members which include a lay person, a member from a different institution and at least another three members which should be versed in ethics. Legal and expert advisors can be sought by the committee. The REC will require a detailed protocol from the researcher including the curriculum of the principal investigator and all other researchers under him/her. The protocol should include all details of the research to be undertaken including a detailed description, the reasons for the research, literature pertaining to the research, a clear description of the target population, the actual consent form including what information is to be given to the participants, a declaration where necessary that things prohibited by the law (such as use of embryonic stem cells if this is the case in the country [2] will not be researchers, and a declaration that the relevant directives and rules and procedures which the REC falls under will be followed. The REC will also require a description of any risks and what actions are to be undertaken to eliminate hazards. The researchers must adhere only to the protocol given and any changes, minor or major, must be reported to the REC and approved. Copyright © 2018. Published by Elsevier B.V.

The RECG1 DNA Translocase Is a Key Factor in Recombination Surveillance, Repair, and Segregation of the Mitochondrial DNA in Arabidopsis[OPEN

PubMed Central

Le Ret, Monique; Bergdoll, Marc; Bichara, Marc; Dietrich, André

2015-01-01

The mitochondria of flowering plants have considerably larger and more complex genomes than the mitochondria of animals or fungi, mostly due to recombination activities that modulate their genomic structures. These activities most probably participate in the repair of mitochondrial DNA (mtDNA) lesions by recombination-dependent processes. Rare ectopic recombination across short repeats generates new genomic configurations that contribute to mtDNA heteroplasmy, which drives rapid evolution of the sequence organization of plant mtDNAs. We found that Arabidopsis thaliana RECG1, an ortholog of the bacterial RecG translocase, is an organellar protein with multiple roles in mtDNA maintenance. RECG1 targets to mitochondria and plastids and can complement a bacterial recG mutant that shows defects in repair and replication control. Characterization of Arabidopsis recG1 mutants showed that RECG1 is required for recombination-dependent repair and for suppression of ectopic recombination in mitochondria, most likely because of its role in recovery of stalled replication forks. The analysis of alternative mitotypes present in a recG1 line and of their segregation following backcross allowed us to build a model to explain how a new stable mtDNA configuration, compatible with normal plant development, can be generated by stoichiometric shift. PMID:26462909

[Impact of the economic crisis on the activity of a clinical research ethics committee].

PubMed

Redondo Capafons, S; Arcenillas, Paula; Giménez, Nuria; March López, Pablo; Soriano, Laura; Pla, Ramon; Quintana, Salvador

2014-11-03

Analyze the impact of economic and social crisis in volume and funding of clinical trials (CT) and observational studies (ES) from the activity of an Research Ethics Committee (REC). REC memories 2003-2012 were reviewed. Financing of evaluated projects, CT and OS were analyzed classifying them into four groups: 1) promoted by pharmaceutical industry, 2) by scientific societies with industry support, 3) by scientific societies with government support and 4) unfunding.Two periods were compared: pre-crisis (2003-2007) and crisis (2008-2012). During 10 studied years, 744 protocols were evaluated: a 71% of group 1, a 9% of group 2, a 3% of group 3 and a 17% was no funding. Regarding OS, 40%, 5,4%, 8,6% and 46% were the groups 1, 2, 3 and 4 respectively. Analyzing crisis versus pre-crisis period, statistically significant differences were observed in the decreasing of number of CT phase 2 and 3 and in the rising EO. Comparing crisis related to the pre-crisis period, the Group 4 increased statistically significantly. Evolution of total number of studies evaluated by REC tends to be maintained and even increased over time. REC maintains its activity and even increased at the expense of financing and unfunded OS. Copyright AULA MEDICA EDICIONES 2014. Published by AULA MEDICA. All rights reserved.

Scanning electron microscopy of Ancylostoma spp. dog infective larvae captured and destroyed by the nematophagous fungus Duddingtonia flagrans.

PubMed

Maciel, A S; Araújo, J V; Campos, A K; Benjamin, L A; Freitas, L G

2009-06-01

The interaction between the nematode-trapping fungus Duddingtonia flagrans (isolate CG768) against Ancylostoma spp. dog infective larvae (L(3)) was evaluated by means of scanning electron microscopy. Adhesive network trap formation was observed 6h after the beginning of the interaction, and the capture of Ancylostoma spp. L(3) was observed 8h after the inoculation these larvae on the cellulose membranes colonized by the fungus. Scanning electron micrographs were taken at 0, 12, 24, 36 and 48 h, where 0 is the time when Ancylostoma spp. L(3) was first captured by the fungus. Details of the capture structure formed by the fungus were described. Nematophagous Fungus Helper Bacteria (NHB) were found at interactions points between the D. flagrans and Ancylostoma spp. L(3). The cuticle penetration by the differentiated fungal hyphae with the exit of nematode internal contents was observed 36 h after the capture. Ancylostoma spp. L(3) were completely destroyed after 48 h of interaction with the fungus. The scanning electron microscopy technique was efficient on the study of this interaction, showing that the nematode-trapping fungus D. flagrans (isolate CG768) is a potential exterminator of Ancylostoma spp. L(3).

Methods of analysis by the U.S. Geological Survey National Water Quality Laboratory; determination of chlorinated pesticides in aquatic tissue by capillary-column gas chromatography with electron-capture detection

USGS Publications Warehouse

Leiker, Thomas J.; Madsen, J.E.; Deacon, J.R.; Foreman, W.T.

1995-01-01

A method for the determination of chlorinated organic compounds in aquatic tissue by dual capillary-column gas chromatography with electron-capture detection is described. Whole-body-fish or corbicula tissue is homogenized, Soxhlet extracted, lipid removed by gel permeation chromatography, and fractionated using alumina/silica adsorption chromatography. The extracts are analyzed by dissimilar capillary-column gas chromatography with electron-capture detection. The method reporting limits are 5 micrograms per kilogram (μg/kg) for chlorinated compounds, 50 μg/kg for polychlorinated biphenyls, and 200 μg/kg for toxaphene.

The Diesel Exhaust in Miners Study: II. Exposure monitoring surveys and development of exposure groups.

PubMed

Coble, Joseph B; Stewart, Patricia A; Vermeulen, Roel; Yereb, Daniel; Stanevich, Rebecca; Blair, Aaron; Silverman, Debra T; Attfield, Michael

2010-10-01

Air monitoring surveys were conducted between 1998 and 2001 at seven non-metal mining facilities to assess exposure to respirable elemental carbon (REC), a component of diesel exhaust (DE), for an epidemiologic study of miners exposed to DE. Personal exposure measurements were taken on workers in a cross-section of jobs located underground and on the surface. Air samples taken to measure REC were also analyzed for respirable organic carbon (ROC). Concurrent measurements to assess exposure to nitric oxide (NO) and nitrogen dioxide (NO₂), two gaseous components of DE, were also taken. The REC measurements were used to develop quantitative estimates of average exposure levels by facility, department, and job title for the epidemiologic analysis. Each underground job was assigned to one of three sets of exposure groups from specific to general: (i) standardized job titles, (ii) groups of standardized job titles combined based on the percentage of time in the major underground areas, and (iii) larger groups based on similar area carbon monoxide (CO) air concentrations. Surface jobs were categorized based on their use of diesel equipment and proximity to DE. A total of 779 full-shift personal measurements were taken underground. The average REC exposure levels for underground jobs with five or more measurements ranged from 31 to 58 μg m⁻³ at the facility with the lowest average exposure levels and from 313 to 488 μg m⁻³ at the facility with the highest average exposure levels. The average REC exposure levels for surface workers ranged from 2 to 6 μg m⁻³ across the seven facilities. There was much less contrast in the ROC compared with REC exposure levels measured between surface and underground workers within each facility, as well as across the facilities. The average ROC levels underground ranged from 64 to 195 μg m⁻³, while on the surface, the average ROC levels ranged from 38 to 71 μg m⁻³ by facility, an ∼2- to 3-fold difference. The average NO and NO₂ levels underground ranged from 0.20 to 1.49 parts per million (ppm) and from 0.10 to 0.60 ppm, respectively, and were ∼10 times higher than levels on the surface, which ranged from 0.02 to 0.11 ppm and from 0.01 to 0.06 ppm, respectively. The ROC, NO, and NO₂ concentrations underground were correlated with the REC levels (r = 0.62, 0.71, and 0.62, respectively). A total of 80% of the underground jobs were assigned an exposure estimate based on measurements taken for the specific job title or for other jobs with a similar percentage of time spent in the major underground work areas. The average REC exposure levels by facility were from 15 to 64 times higher underground than on the surface. The large contrast in exposure levels measured underground versus on the surface, along with the differences between the mining facilities and between underground jobs within the facilities resulted in a wide distribution in the exposure estimates for evaluation of exposure-response relationships in the epidemiologic analyses.

The Diesel Exhaust in Miners Study: II. Exposure Monitoring Surveys and Development of Exposure Groups

PubMed Central

Coble, Joseph B.; Stewart, Patricia A.; Vermeulen, Roel; Yereb, Daniel; Stanevich, Rebecca; Blair, Aaron; Silverman, Debra T.; Attfield, Michael

2010-01-01

Air monitoring surveys were conducted between 1998 and 2001 at seven non-metal mining facilities to assess exposure to respirable elemental carbon (REC), a component of diesel exhaust (DE), for an epidemiologic study of miners exposed to DE. Personal exposure measurements were taken on workers in a cross-section of jobs located underground and on the surface. Air samples taken to measure REC were also analyzed for respirable organic carbon (ROC). Concurrent measurements to assess exposure to nitric oxide (NO) and nitrogen dioxide (NO2), two gaseous components of DE, were also taken. The REC measurements were used to develop quantitative estimates of average exposure levels by facility, department, and job title for the epidemiologic analysis. Each underground job was assigned to one of three sets of exposure groups from specific to general: (i) standardized job titles, (ii) groups of standardized job titles combined based on the percentage of time in the major underground areas, and (iii) larger groups based on similar area carbon monoxide (CO) air concentrations. Surface jobs were categorized based on their use of diesel equipment and proximity to DE. A total of 779 full-shift personal measurements were taken underground. The average REC exposure levels for underground jobs with five or more measurements ranged from 31 to 58 μg m−3 at the facility with the lowest average exposure levels and from 313 to 488 μg m−3 at the facility with the highest average exposure levels. The average REC exposure levels for surface workers ranged from 2 to 6 μg m−3 across the seven facilities. There was much less contrast in the ROC compared with REC exposure levels measured between surface and underground workers within each facility, as well as across the facilities. The average ROC levels underground ranged from 64 to 195 μg m−3, while on the surface, the average ROC levels ranged from 38 to 71 μg m−3 by facility, an ∼2- to 3-fold difference. The average NO and NO2 levels underground ranged from 0.20 to 1.49 parts per million (ppm) and from 0.10 to 0.60 ppm, respectively, and were ∼10 times higher than levels on the surface, which ranged from 0.02 to 0.11 ppm and from 0.01 to 0.06 ppm, respectively. The ROC, NO, and NO2 concentrations underground were correlated with the REC levels (r = 0.62, 0.71, and 0.62, respectively). A total of 80% of the underground jobs were assigned an exposure estimate based on measurements taken for the specific job title or for other jobs with a similar percentage of time spent in the major underground work areas. The average REC exposure levels by facility were from 15 to 64 times higher underground than on the surface. The large contrast in exposure levels measured underground versus on the surface, along with the differences between the mining facilities and between underground jobs within the facilities resulted in a wide distribution in the exposure estimates for evaluation of exposure–response relationships in the epidemiologic analyses. PMID:20876232

Alkali metal mediated C-C bond coupling reaction

NASA Astrophysics Data System (ADS)

Tachikawa, Hiroto

2015-02-01

Metal catalyzed carbon-carbon (C-C) bond formation is one of the important reactions in pharmacy and in organic chemistry. In the present study, the electron and hole capture dynamics of a lithium-benzene sandwich complex, expressed by Li(Bz)2, have been investigated by means of direct ab-initio molecular dynamics method. Following the electron capture of Li(Bz)2, the structure of [Li(Bz)2]- was drastically changed: Bz-Bz parallel form was rapidly fluctuated as a function of time, and a new C-C single bond was formed in the C1-C1' position of Bz-Bz interaction system. In the hole capture, the intermolecular vibration between Bz-Bz rings was only enhanced. The mechanism of C-C bond formation in the electron capture was discussed on the basis of theoretical results.

Resonant electron capture by aspartame and aspartic acid molecules.

PubMed

Muftakhov, M V; Shchukin, P V

2016-12-30

The processes for dissociative electron capture are the key mechanisms for decomposition of biomolecules, proteins in particular, under interaction with low-energy electrons. Molecules of aspartic acid and aspartame, i.e. modified dipeptides, were studied herein to define the impact of the side functional groups on peptide chain decomposition in resonant electron-molecular reactions. The processes of formation and decomposition of negative ions of both aspartame and aspartic acid were studied by mass spectrometry of negative ions under resonant electron capture. The obtained mass spectra were interpreted under thermochemical analysis by quantum chemical calculations. Main channels of negative molecular ions fragmentation were found and characteristic fragment ions were identified. The СООН fragment of the side chain in aspartic acid is shown to play a key role like the carboxyl group in amino acids and aliphatic oligopeptides. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Electron capture strength for Ni60,62 and Ni58,60,62,64(p, n)Cu58,60,62,64 reactions at 134.3 MeV

NASA Astrophysics Data System (ADS)

Anantaraman, N.; Austin, Sam M.; Brown, B. A.; Crawley, G. M.; Galonsky, A.; Zegers, R. G. T.; Anderson, B. D.; Baldwin, A. R.; Flanders, B. S.; Madey, R.; Watson, J. W.; Foster, C. C.

2008-12-01

Background: The strength of electron capture for medium mass nuclei has a significant effect on the evolution of supernovae. There is insufficient knowledge of these strengths and very little data for important radioactive nuclei. Purpose: Determine whether it is feasible to obtain EC strength from studies of To+1 excitations in (p, n) reactions, and whether this might yield information for radioactive nuclei. Methods: Cross sections for the Ni58,60,62,64(p, n)Cu58,60,62,64 reactions were measured over the angular range of 0.3∘ to 11.6∘ at 134.3 MeV using the IUCF neutron time-of-flight facility. Results: The To+1 excitations in Ni60,62 were identified by comparison with inelastic proton scattering spectra, their B(GT) were extracted, and the corresponding electron capture rates in supernovae were calculated. Data from the TRIUMF (n, p) experiments at 198 MeV were reanalyzed; the electron capture rates for the reanalyzed data are in moderately good agreement with the higher resolution (p, n) results, but differ in detail. The possibility of future measurements with radioactive nuclei was considered. Conclusions: It may be possible to obtain low-lying electron capture strength for radioactive nuclei by studying (p, n) reactions in inverse kinematics.

Nuclear structure and weak rates of heavy waiting point nuclei under rp-process conditions

NASA Astrophysics Data System (ADS)

Nabi, Jameel-Un; Böyükata, Mahmut

2017-01-01

The structure and the weak interaction mediated rates of the heavy waiting point (WP) nuclei 80Zr, 84Mo, 88Ru, 92Pd and 96Cd along N = Z line were studied within the interacting boson model-1 (IBM-1) and the proton-neutron quasi-particle random phase approximation (pn-QRPA). The energy levels of the N = Z WP nuclei were calculated by fitting the essential parameters of IBM-1 Hamiltonian and their geometric shapes were predicted by plotting potential energy surfaces (PESs). Half-lives, continuum electron capture rates, positron decay rates, electron capture cross sections of WP nuclei, energy rates of β-delayed protons and their emission probabilities were later calculated using the pn-QRPA. The calculated Gamow-Teller strength distributions were compared with previous calculation. We present positron decay and continuum electron capture rates on these WP nuclei under rp-process conditions using the same model. For the rp-process conditions, the calculated total weak rates are twice the Skyrme HF+BCS+QRPA rates for 80Zr. For remaining nuclei the two calculations compare well. The electron capture rates are significant and compete well with the corresponding positron decay rates under rp-process conditions. The finding of the present study supports that electron capture rates form an integral part of the weak rates under rp-process conditions and has an important role for the nuclear model calculations.

Extraction of highly charged ions from the Berlin Electron Beam Ion Trap for interactions with a gas target

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

Allen, F.I.; Biedermann, C.; Radtke, R.

2006-03-15

Highly charged ions are extracted from the Berlin Electron Beam Ion Trap for investigations of charge exchange with a gas target. The classical over-the-barrier model for slow highly charged ions describes this process, whereby one or more electrons are captured from the target into Rydberg states of the ion. The excited state relaxes via a radiative cascade of the electron to ground energy. The cascade spectra are characteristic of the capture state. We investigate x-ray photons emitted as a result of interactions between Ar{sup 17+} ions at energies {<=}5q keV with Ar atoms. Of particular interest is the velocity dependencemore » of the angular momentum capture state l{sub c}.« less

Developing the Digital Kyoto Collection in Education and Research.

PubMed

Hill, Mark Anthony

2018-04-16

The Kyoto embryo collection was begun in 1961 by Dr. Hideo Nishimura. The collection has been continuously developed and currently contains over 44,000 human normal and abnormal specimens. Beginning online in 1997, the internet provided an opportunity to make embryos from the collection widely available for research and educational purposes (http://tiny.cc/Embryo). These embryonic development resources have been continuously published and available from that time until today. Published in Japanese as an Atlas of Embryonic Development. Published online as the Kyoto Human Embryo Visualization Project (http://atlas.cac.med.kyoto-u.ac.jp) and also as the Human Embryo Atlas (http://tiny.cc/Human_Embryo_Atlas). Published now electronically as a digital eBook (http://tiny.cc/Kyoto_Collection_eBook). This new digital format allows incorporation of whole embryo and histology manipulable images, labels, and a linked glossary. New imaging modalities of magnetic resonance imaging (MRI) and episcopic fluorescence image capture (EFIC) can also be easily displayed as animations. For research, the collection specimens and histological sections have been extensively studied and published in several hundred papers, discussed here and elsewhere in this special edition. I will also describe how the Kyoto collection will now form a major partner of a new international embryology research group, the Digital Embryology Consortium (https://human-embryology.org). The digital Kyoto collection will be made available for remote researcher access, analysis, and comparison with other collections allowing new research and educational applications. This work was presented at the 40th Anniversary Commemoration Symposium of the Congenital Anomaly Research Center, Graduate School of Medicine, Kyoto University, Japan, November, 2015. Anat Rec, 2018. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Conductive Graphitic Carbon Nitride as an Ideal Material for Electrocatalytically Switchable CO2 Capture

PubMed Central

Tan, Xin; Kou, Liangzhi; Tahini, Hassan A.; Smith, Sean C.

2015-01-01

Good electrical conductivity and high electron mobility of the sorbent materials are prerequisite for electrocatalytically switchable CO2 capture. However, no conductive and easily synthetic sorbent materials are available until now. Here, we examined the possibility of conductive graphitic carbon nitride (g-C4N3) nanosheets as sorbent materials for electrocatalytically switchable CO2 capture. Using first-principle calculations, we found that the adsorption energy of CO2 molecules on g-C4N3 nanosheets can be dramatically enhanced by injecting extra electrons into the adsorbent. At saturation CO2 capture coverage, the negatively charged g-C4N3 nanosheets achieve CO2 capture capacities up to 73.9 × 1013 cm−2 or 42.3 wt%. In contrast to other CO2 capture approaches, the process of CO2 capture/release occurs spontaneously without any energy barriers once extra electrons are introduced or removed, and these processes can be simply controlled and reversed by switching on/off the charging voltage. In addition, these negatively charged g-C4N3 nanosheets are highly selective for separating CO2 from mixtures with CH4, H2 and/or N2. These predictions may prove to be instrumental in searching for a new class of experimentally feasible high-capacity CO2 capture materials with ideal thermodynamics and reversibility. PMID:26621618

Ethical Issues Surrounding the Use of Modern Human Remains for Research in South Africa.

PubMed

Briers, N; Dempers, J J

2017-02-01

Chapter 8 of the South African National Health Act 61 of 2003 (NHA) that deals with the donation of human tissue was promulgated in 2012. The new Act is perceived to impose restrictions on low-risk research involving human remains. This study aimed to identify the issues raised by a research ethics committee (REC) when reviewing protocols where human remains are used as data source. REC minutes from 2009 to 2014 were reviewed, and issues raised by the committee were categorized. In total, 127 protocols submitted to the committee over 6 years involved human remains. Queries relating to science (22.2%) and administration (18.9%) were the most common, whereas queries relating to legal issues constituted only 10.2%. Ethical issues centered on informed consent regarding sensitive topics such as HIV, DNA, and deceased children. The change in legislation did not change the number or type of legal issues identified by the REC.

Nucleotide sequence analysis of the recA gene and discrimination of the three isolates of urease-positive thermophilic Campylobacter (UPTC) isolated from seagulls (Larus spp.) in Northern Ireland.

PubMed

Matsuda, M; Tai, K; Moore, J E; Millar, B C; Murayama, O

2004-01-01

Nucleotide sequencing after TA cloning of the amplicon of the almost-full length recA gene from three strains of UPTC (A1, A2, and A3) isolated from seagulls in Northern Ireland, the phenotypical and genotypical characteristics of which have been demonstrated to be indistinguishable, clarified nucleotide differences at three nucleotide positions among the three strains. In conclusion, the nucleotide sequences of the recA gene were found to discriminate among the three strains of UPTC, A1, A2, and A3, which are indistinguishable phenotypically and genotypically. Thus, the present study strongly suggests that nucleotide sequence data of the amplicon of a suitable gene or region could aid in discriminating among isolates of the UPTC group, which are indistinguishable phenotypically and genotypically. Copyright 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

An inclusive Research Education Community (iREC): Impact of the SEA-PHAGES program on research outcomes and student learning.

PubMed

Hanauer, David I; Graham, Mark J; Betancur, Laura; Bobrownicki, Aiyana; Cresawn, Steven G; Garlena, Rebecca A; Jacobs-Sera, Deborah; Kaufmann, Nancy; Pope, Welkin H; Russell, Daniel A; Jacobs, William R; Sivanathan, Viknesh; Asai, David J; Hatfull, Graham F

2017-12-19

Engaging undergraduate students in scientific research promises substantial benefits, but it is not accessible to all students and is rarely implemented early in college education, when it will have the greatest impact. An inclusive Research Education Community (iREC) provides a centralized scientific and administrative infrastructure enabling engagement of large numbers of students at different types of institutions. The Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) is an iREC that promotes engagement and continued involvement in science among beginning undergraduate students. The SEA-PHAGES students show strong gains correlated with persistence relative to those in traditional laboratory courses regardless of academic, ethnic, gender, and socioeconomic profiles. This persistent involvement in science is reflected in key measures, including project ownership, scientific community values, science identity, and scientific networking. Copyright © 2017 the Author(s). Published by PNAS.

Human endogenous retrovirus rec interferes with germ cell development in mice and may cause carcinoma in situ, the predecessor lesion of germ cell tumors.

PubMed

Galli, Uwe M; Sauter, Marlies; Lecher, Bernd; Maurer, Simone; Herbst, Hermann; Roemer, Klaus; Mueller-Lantzsch, Nikolaus

2005-04-28

Germ cell tumors (GCTs) are among the most common malignancies in young men. We have previously documented that patients with GCT frequently produce serum antibodies directed against proteins encoded by human endogenous retrovirus (HERV) type K sequences. Transcripts originating from the env gene of HERV-K, including the rec-relative of human immunodeficiency virus rev, are highly expressed in GCTs. We report here that mice that inducibly express HERV-K rec show a disturbed germ cell development and may exhibit, by 19 months of age, changes reminiscent of carcinoma in situ, the predecessor lesion of classic seminoma in humans. This provides the first direct evidence that the expression of a human endogenous retroviral gene previously established as a marker in human germ cell tumors may contribute to organ-specific tumorigenesis in a transgenic mouse model.

Possibilities in identification of genomic species of Burkholderia cepacia complex by PCR and RFLP.

PubMed

Navrátilová, Lucie; Chromá, Magdalena; Hanulík, Vojtech; Raclavský, Vladislav

2013-01-01

The strains belonging to Burkholderia cepacia complex are important opportunistic pathogens in immunocompromised patients and cause serious diseases. It is possible to obtain isolates from soil, water, plants and human samples. Taxonomy of this group is difficult. Burkholderia cepacia complex consists of seventeen genomic species and the genetic scheme is based on recA gene. Commonly, first five genomovars occurre in humans, mostly genomovars II and III, subdivision IIIA. Within this study we tested identification of first five genomovars by PCR with following melting analysis and RFLP. The experiments were targeted on eubacterial 16S rDNA and specific gene recA, which allowed identification of all five genomovars. RecA gene appeared as more suitable than 16S rDNA, which enabled direct identification of only genomovars II and V; genomovars I, III and IV were similar within 16S rDNA sequence.

An inclusive Research Education Community (iREC): Impact of the SEA-PHAGES program on research outcomes and student learning

PubMed Central

Hanauer, David I.; Graham, Mark J.; Betancur, Laura; Bobrownicki, Aiyana; Cresawn, Steven G.; Garlena, Rebecca A.; Jacobs-Sera, Deborah; Kaufmann, Nancy; Pope, Welkin H.; Russell, Daniel A.; Jacobs, William R.; Sivanathan, Viknesh; Asai, David J.

2017-01-01

Engaging undergraduate students in scientific research promises substantial benefits, but it is not accessible to all students and is rarely implemented early in college education, when it will have the greatest impact. An inclusive Research Education Community (iREC) provides a centralized scientific and administrative infrastructure enabling engagement of large numbers of students at different types of institutions. The Science Education Alliance–Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) is an iREC that promotes engagement and continued involvement in science among beginning undergraduate students. The SEA-PHAGES students show strong gains correlated with persistence relative to those in traditional laboratory courses regardless of academic, ethnic, gender, and socioeconomic profiles. This persistent involvement in science is reflected in key measures, including project ownership, scientific community values, science identity, and scientific networking. PMID:29208718

The Diesel Exhaust in Miners Study: I. Overview of the Exposure Assessment Process

PubMed Central

Stewart, Patricia A.; Coble, Joseph B.; Vermeulen, Roel; Schleiff, Patricia; Blair, Aaron; Lubin, Jay; Attfield, Michael; Silverman, Debra T.

2010-01-01

This report provides an overview of the exposure assessment process for an epidemiologic study that investigated mortality, with a special focus on lung cancer, associated with diesel exhaust (DE) exposure among miners. Details of several components are provided in four other reports. A major challenge for this study was the development of quantitative estimates of historical exposures to DE. There is no single standard method for assessing the totality of DE, so respirable elemental carbon (REC), a component of DE, was selected as the primary surrogate in this study. Air monitoring surveys at seven of the eight study mining facilities were conducted between 1998 and 2001 and provided reference personal REC exposure levels and measurements for other agents and DE components in the mining environment. (The eighth facility had closed permanently prior to the surveys.) Exposure estimates were developed for mining facility/department/job/year combinations. A hierarchical grouping strategy was developed for assigning exposure levels to underground jobs [based on job titles, on the amount of time spent in various areas of the underground mine, and on similar carbon monoxide (CO, another DE component) concentrations] and to surface jobs (based on the use of, or proximity to, diesel-powered equipment). Time trends in air concentrations for underground jobs were estimated from mining facility-specific prediction models using diesel equipment horsepower, total air flow rates exhausted from the underground mines, and, because there were no historical REC measurements, historical measurements of CO. Exposures to potentially confounding agents, i.e. respirable dust, silica, radon, asbestos, and non-diesel sources of polycyclic aromatic hydrocarbons, also were assessed. Accuracy and reliability of the estimated REC exposures levels were evaluated by comparison with several smaller datasets and by development of alternative time trend models. During 1998–2001, the average measured REC exposure level by facility ranged from 40 to 384 μg m−3 for the underground workers and from 2 to 6 μg m−3 for the surface workers. For one prevalent underground job, ‘miner operator’, the maximum annual REC exposure estimate by facility ranged up to 685% greater than the corresponding 1998–2001 value. A comparison of the historical CO estimates from the time trend models with 1976–1977 CO measurements not used in the modeling found an overall median relative difference of 29%. Other comparisons showed similar levels of agreement. The assessment process indicated large differences in REC exposure levels over time and across the underground operations. Method evaluations indicated that the final estimates were consistent with those from alternative time trend models and demonstrated moderate to high agreement with external data. PMID:20876233

The diesel exhaust in miners study: I. Overview of the exposure assessment process.

PubMed

Stewart, Patricia A; Coble, Joseph B; Vermeulen, Roel; Schleiff, Patricia; Blair, Aaron; Lubin, Jay; Attfield, Michael; Silverman, Debra T

2010-10-01

This report provides an overview of the exposure assessment process for an epidemiologic study that investigated mortality, with a special focus on lung cancer, associated with diesel exhaust (DE) exposure among miners. Details of several components are provided in four other reports. A major challenge for this study was the development of quantitative estimates of historical exposures to DE. There is no single standard method for assessing the totality of DE, so respirable elemental carbon (REC), a component of DE, was selected as the primary surrogate in this study. Air monitoring surveys at seven of the eight study mining facilities were conducted between 1998 and 2001 and provided reference personal REC exposure levels and measurements for other agents and DE components in the mining environment. (The eighth facility had closed permanently prior to the surveys.) Exposure estimates were developed for mining facility/department/job/year combinations. A hierarchical grouping strategy was developed for assigning exposure levels to underground jobs [based on job titles, on the amount of time spent in various areas of the underground mine, and on similar carbon monoxide (CO, another DE component) concentrations] and to surface jobs (based on the use of, or proximity to, diesel-powered equipment). Time trends in air concentrations for underground jobs were estimated from mining facility-specific prediction models using diesel equipment horsepower, total air flow rates exhausted from the underground mines, and, because there were no historical REC measurements, historical measurements of CO. Exposures to potentially confounding agents, i.e. respirable dust, silica, radon, asbestos, and non-diesel sources of polycyclic aromatic hydrocarbons, also were assessed. Accuracy and reliability of the estimated REC exposures levels were evaluated by comparison with several smaller datasets and by development of alternative time trend models. During 1998-2001, the average measured REC exposure level by facility ranged from 40 to 384 μg m⁻³ for the underground workers and from 2 to 6 μg m⁻³ for the surface workers. For one prevalent underground job, 'miner operator', the maximum annual REC exposure estimate by facility ranged up to 685% greater than the corresponding 1998-2001 value. A comparison of the historical CO estimates from the time trend models with 1976-1977 CO measurements not used in the modeling found an overall median relative difference of 29%. Other comparisons showed similar levels of agreement. The assessment process indicated large differences in REC exposure levels over time and across the underground operations. Method evaluations indicated that the final estimates were consistent with those from alternative time trend models and demonstrated moderate to high agreement with external data.

ELECTRON-CAPTURE AND β-DECAY RATES FOR sd-SHELL NUCLEI IN STELLAR ENVIRONMENTS RELEVANT TO HIGH-DENSITY O–NE–MG CORES

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

Suzuki, Toshio; Toki, Hiroshi; Nomoto, Ken’ichi, E-mail: suzuki@phys.chs.nihon-u.ac.jp

Electron-capture and β-decay rates for nuclear pairs in the sd-shell are evaluated at high densities and high temperatures relevant to the final evolution of electron-degenerate O–Ne–Mg cores of stars with initial masses of 8–10 M{sub ⊙}. Electron capture induces a rapid contraction of the electron-degenerate O–Ne–Mg core. The outcome of rapid contraction depends on the evolutionary changes in the central density and temperature, which are determined by the competing processes of contraction, cooling, and heating. The fate of the stars is determined by these competitions, whether they end up with electron-capture supernovae or Fe core-collapse supernovae. Since the competing processes aremore » induced by electron capture and β-decay, the accurate weak rates are crucially important. The rates are obtained for pairs with A = 20, 23, 24, 25, and 27 by shell-model calculations in the sd-shell with the USDB Hamiltonian. Effects of Coulomb corrections on the rates are evaluated. The rates for pairs with A = 23 and 25 are important for nuclear Urca processes that determine the cooling rate of the O–Ne–Mg core, while those for pairs with A = 20 and 24 are important for the core contraction and heat generation rates in the core. We provide these nuclear rates at stellar environments in tables with fine enough meshes at various densities and temperatures for studies of astrophysical processes sensitive to the rates. In particular, the accurate rate tables are crucially important for the final fates of not only O–Ne–Mg cores but also a wider range of stars, such as C–O cores of lower-mass stars.« less

Multilocus sequence analysis (MLSA) of Bradyrhizobium strains: revealing high diversity of tropical diazotrophic symbiotic bacteria.

PubMed

Delamuta, Jakeline Renata Marçon; Ribeiro, Renan Augusto; Menna, Pâmela; Bangel, Eliane Villamil; Hungria, Mariangela

2012-04-01

Symbiotic association of several genera of bacteria collectively called as rhizobia and plants belonging to the family Leguminosae (=Fabaceae) results in the process of biological nitrogen fixation, playing a key role in global N cycling, and also bringing relevant contributions to the agriculture. Bradyrhizobium is considered as the ancestral of all nitrogen-fixing rhizobial species, probably originated in the tropics. The genus encompasses a variety of diverse bacteria, but the diversity captured in the analysis of the 16S rRNA is often low. In this study, we analyzed twelve Bradyrhizobium strains selected from previous studies performed by our group for showing high genetic diversity in relation to the described species. In addition to the 16S rRNA, five housekeeping genes (recA, atpD, glnII, gyrB and rpoB) were analyzed in the MLSA (multilocus sequence analysis) approach. Analysis of each gene and of the concatenated housekeeping genes captured a considerably higher level of genetic diversity, with indication of putative new species. The results highlight the high genetic variability associated with Bradyrhizobium microsymbionts of a variety of legumes. In addition, the MLSA approach has proved to represent a rapid and reliable method to be employed in phylogenetic and taxonomic studies, speeding the identification of the still poorly known diversity of nitrogen-fixing rhizobia in the tropics.

Interactions and Localization of Escherichia coli Error-Prone DNA Polymerase IV after DNA Damage.

PubMed

Mallik, Sarita; Popodi, Ellen M; Hanson, Andrew J; Foster, Patricia L

2015-09-01

Escherichia coli's DNA polymerase IV (Pol IV/DinB), a member of the Y family of error-prone polymerases, is induced during the SOS response to DNA damage and is responsible for translesion bypass and adaptive (stress-induced) mutation. In this study, the localization of Pol IV after DNA damage was followed using fluorescent fusions. After exposure of E. coli to DNA-damaging agents, fluorescently tagged Pol IV localized to the nucleoid as foci. Stepwise photobleaching indicated ∼60% of the foci consisted of three Pol IV molecules, while ∼40% consisted of six Pol IV molecules. Fluorescently tagged Rep, a replication accessory DNA helicase, was recruited to the Pol IV foci after DNA damage, suggesting that the in vitro interaction between Rep and Pol IV reported previously also occurs in vivo. Fluorescently tagged RecA also formed foci after DNA damage, and Pol IV localized to them. To investigate if Pol IV localizes to double-strand breaks (DSBs), an I-SceI endonuclease-mediated DSB was introduced close to a fluorescently labeled LacO array on the chromosome. After DSB induction, Pol IV localized to the DSB site in ∼70% of SOS-induced cells. RecA also formed foci at the DSB sites, and Pol IV localized to the RecA foci. These results suggest that Pol IV interacts with RecA in vivo and is recruited to sites of DSBs to aid in the restoration of DNA replication. DNA polymerase IV (Pol IV/DinB) is an error-prone DNA polymerase capable of bypassing DNA lesions and aiding in the restart of stalled replication forks. In this work, we demonstrate in vivo localization of fluorescently tagged Pol IV to the nucleoid after DNA damage and to DNA double-strand breaks. We show colocalization of Pol IV with two proteins: Rep DNA helicase, which participates in replication, and RecA, which catalyzes recombinational repair of stalled replication forks. Time course experiments suggest that Pol IV recruits Rep and that RecA recruits Pol IV. These findings provide in vivo evidence that Pol IV aids in maintaining genomic stability not only by bypassing DNA lesions but also by participating in the restoration of stalled replication forks. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Alkali metal mediated C–C bond coupling reaction

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

Tachikawa, Hiroto, E-mail: hiroto@eng.hokudai.ac.jp

2015-02-14

Metal catalyzed carbon-carbon (C–C) bond formation is one of the important reactions in pharmacy and in organic chemistry. In the present study, the electron and hole capture dynamics of a lithium-benzene sandwich complex, expressed by Li(Bz){sub 2}, have been investigated by means of direct ab-initio molecular dynamics method. Following the electron capture of Li(Bz){sub 2}, the structure of [Li(Bz){sub 2}]{sup −} was drastically changed: Bz–Bz parallel form was rapidly fluctuated as a function of time, and a new C–C single bond was formed in the C{sub 1}–C{sub 1}′ position of Bz–Bz interaction system. In the hole capture, the intermolecular vibrationmore » between Bz–Bz rings was only enhanced. The mechanism of C–C bond formation in the electron capture was discussed on the basis of theoretical results.« less

2D or Not 2D? Testing the Utility of 2D Vs. 3D Landmark Data in Geometric Morphometrics of the Sculpin Subfamily Oligocottinae (Pisces; Cottoidea).

PubMed

Buser, Thaddaeus J; Sidlauskas, Brian L; Summers, Adam P

2018-05-01

We contrast 2D vs. 3D landmark-based geometric morphometrics in the fish subfamily Oligocottinae by using 3D landmarks from CT-generated models and comparing the morphospace of the 3D landmarks to one based on 2D landmarks from images. The 2D and 3D shape variables capture common patterns across taxa, such that the pairwise Procrustes distances among taxa correspond and the trends captured by principal component analysis are similar in the xy plane. We use the two sets of landmarks to test several ecomorphological hypotheses from the literature. Both 2D and 3D data reject the hypothesis that head shape correlates significantly with the depth at which a species is commonly found. However, in taxa where shape variation in the z-axis is high, the 2D shape variables show sufficiently strong distortion to influence the outcome of the hypothesis tests regarding the relationship between mouth size and feeding ecology. Only the 3D data support previous studies which showed that large mouth sizes correlate positively with high percentages of elusive prey in the diet. When used to test for morphological divergence, 3D data show no evidence of divergence, while 2D data show that one clade of oligocottines has diverged from all others. This clade shows the greatest degree of z-axis body depth within Oligocottinae, and we conclude that the inability of the 2D approach to capture this lateral body depth causes the incongruence between 2D and 3D analyses. Anat Rec, 301:806-818, 2018. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Many functions of the meiotic cohesin.

PubMed

Bardhan, Amit

2010-12-01

Sister chromatids are held together from the time of their formation in S phase until they segregate in anaphase by the cohesin complex. In meiosis of most organisms, the mitotic Mcd1/Scc1/Rad21 subunit of the cohesin complex is largely replaced by its paralog named Rec8. This article reviews the specialized functions of Rec8 that are crucial for diverse aspects of chromosome dynamics in meiosis, and presents some speculations relating to meiotic chromosome organization.

Mechanisms of Mutation in Non-Dividing Cells

DTIC Science & Technology

2003-05-01

which cells with a lac +1 frameshift allele on an F’ plasmid generate Lac+ mutants upon starvation on lactose medium (3). The stationary-phase mutations...starved on lactose . The accumulation of ampD mutants requires RecA, and is promoted at a greater frequency in RecG-deficient cells, similar to Lac...stationary-phase cells after they are starved in the presence of lactose . In studies performed to date by our lab and others, mutation in stationary-phase

The Role of recA Protein in the Multiplicity Reactivation Pathway of Phage T4.

DTIC Science & Technology

1983-01-01

shown below: HARRIS BERNSTEIN DATE Professor of Medical Molecular Microbiology i To Jane and Brian they make it all worthwhile Aeoession For NTiSi...Department of Molecular and Medical Microbiology , University of Arizona College of Medicine, Tucson, Arizona, 85724. Media The following growth media...M. and Prescott , C. (1983) Inducable expression of a gene specific to the recF pathway for recombination in Escherichia coli K12. Mol Gen Genet 190

recA and catalase in H sub 2 O sub 2 -mediated toxicity in Neisseria gonorrhoeae

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

Hassett, D.J.; Charniga, L.; Cohen, M.S.

1990-12-01

Neisseria gonorrhoeae cells defective in the biosynthesis of the recA gene product are no more sensitive to hydrogen peroxide than wild-type cells. Although gonococci possess nearly 100-fold-greater catalase levels than Escherichia coli, they are more susceptible to hydrogen peroxide than this organism. The natural niche of gonococci undoubtedly results in exposure to oxidant stress; however, they do not demonstrate particularly efficient antioxidant defense systems.

Electron removal from H and He atoms in collisions with C q+ , O q+ ions

NASA Astrophysics Data System (ADS)

Janev, R. K.; McDowell, M. R. C.

1984-06-01

Cross sections for electron capture and ionisation in collision of partially and completely stripped C q+ , N q+ and O q+ ions with hydrogen and helium atoms have been calculated at selected energies. The classical trajectory Monte Carlo method was used with a variable-charge pseudopotential to describe the interaction of the active electron with the projectile ion. A scalling relationship has been derived for the electron removal (capture and ionisation) cross section which allows a unifield representation of the data.

Correlated motion of protein subdomains and large-scale conformational flexibility of RecA protein filament

NASA Astrophysics Data System (ADS)

Yu, Garmay; A, Shvetsov; D, Karelov; D, Lebedev; A, Radulescu; M, Petukhov; V, Isaev-Ivanov

2012-02-01

Based on X-ray crystallographic data available at Protein Data Bank, we have built molecular dynamics (MD) models of homologous recombinases RecA from E. coli and D. radiodurans. Functional form of RecA enzyme, which is known to be a long helical filament, was approximated by a trimer, simulated in periodic water box. The MD trajectories were analyzed in terms of large-scale conformational motions that could be detectable by neutron and X-ray scattering techniques. The analysis revealed that large-scale RecA monomer dynamics can be described in terms of relative motions of 7 subdomains. Motion of C-terminal domain was the major contributor to the overall dynamics of protein. Principal component analysis (PCA) of the MD trajectories in the atom coordinate space showed that rotation of C-domain is correlated with the conformational changes in the central domain and N-terminal domain, that forms the monomer-monomer interface. Thus, even though C-terminal domain is relatively far from the interface, its orientation is correlated with large-scale filament conformation. PCA of the trajectories in the main chain dihedral angle coordinate space implicates a co-existence of a several different large-scale conformations of the modeled trimer. In order to clarify the relationship of independent domain orientation with large-scale filament conformation, we have performed analysis of independent domain motion and its implications on the filament geometry.

Production of thick uniform-coating films containing rectorite on nanofibers through the use of an automated coating machine.

PubMed

Wu, Yang; Li, Xueyong; Shi, Xiaowen; Zhan, Yingfei; Tu, Hu; Du, Yumin; Deng, Hongbing; Jiang, Linbin

2017-01-01

When an efficient automated coating machine is used to process layer-by-layer (LBL) deposited nanofibrous mats, it causes an obvious planar effect on the surface of the mats, which can be eliminated through ultimate immersion. During this process, chitosan (CS) - rectorite (REC) intercalated composite films are built on the surface of cellulose acetate (CA) nanofibrous mats by a coating machine. Then, the immersion process is utilized to allow positively charged CS or CS-REC intercalated composites to uniformly assemble on the surface of negatively charged CA nanofibers. An investigation into the morphology of the resultant scaffolds confirms that the uniquely small pore size, high specific surface area and typically three-dimensional (3D) structure of nanofibrous mats remain present. The results of Fourier transform infrared (FT-IR) and X-ray photoelectron spectroscopy (XPS) indicate that it is feasible to assemble nanofibrous mats using a coating machine. The intercalated structure of CS-REC is confirmed by the results of small-angle X-ray diffraction (SAXRD) and wide-angle X-ray diffraction (WAXRD). The results of the cell experiment and antibacterial test demonstrate that the addition of REC not only has little impact on the cytocompatibility of the mats but also enhances their ability to inhibit bacteria. Copyright © 2016 Elsevier B.V. All rights reserved.

Electron capture in collisions of Si3+ ions with atomic hydrogen from low to intermediate energies

NASA Astrophysics Data System (ADS)

Liu, C. H.; Liu, L.; Wang, J. G.

2014-07-01

The electron capture process for the Si3+(3s) + H(1s) collisions is investigated by the quantum-mechanical molecular orbital close-coupling (MOCC) method and by the two-center atomic orbital close-coupling (AOCC) method in the energy range of 10-5-10 keV/u and 0.8-200 keV/u, respectively. Total and state-selective cross sections are presented and compared with the available theoretical and experimental results. The present MOCC and AOCC results agree well with the experimental measurements, but show some discrepancy with the calculations of Wang et al. [Phys. Rev. A 74, 052709 (2006), 10.1103/PhysRevA.74.052709] at E > 40 eV/u because of the inclusion of rotational couplings, which play important roles in the electron capture process. At lower energies, the present results are about three to five times smaller than those of Wang et al. due to the difference in the molecular data at large internuclear distances. The energy behaviors of the electron capture cross sections are discussed on the basis of identified reaction mechanisms.

Atypical behavior in the electron capture induced dissociation of biologically relevant transition metal ion complexes of the peptide hormone oxytocin

NASA Astrophysics Data System (ADS)

Kleinnijenhuis, Anne J.; Mihalca, Romulus; Heeren, Ron M. A.; Heck, Albert J. R.

2006-07-01

Doubly protonated ions of the disulfide bond containing nonapeptide hormone oxytocin and oxytocin complexes with different transition metal ions, that have biological relevance under physiological conditions, were subjected to electron capture dissociation (ECD) to probe their structural features in the gas phase. Although, all the ECD spectra were strikingly different, typical ECD behavior was observed for complexes of the nonapeptide hormone oxytocin with Ni2+, Co2+ and Zn2+, i.e., abundant c/z' and a'/y backbone cleavages and ECD characteristic S-S and S-C bond cleavages were observed. We propose that, although in the oxytocin-transition metal ion complexes the metal ions serve as the main initial capture site, the captured electron is transferred to other sites in the complex to form a hydrogen radical, which drives the subsequent typical ECD fragmentations. The complex of oxytocin with Cu2+ displayed noticeably different ECD behavior. The fragment ions were similar to fragment ions typically observed with low-energy collision induced dissociation (CID). We propose that the electrons captured by the oxytocin-Cu2+ complex might be favorably involved in reducing the Cu2+ metal ion to Cu+. Subsequent energy redistribution would explain the observed low-energy CID-type fragmentations. Electron capture resulted also in quite different specific cleavage sites for the complexes of oxytocin with Ni2+, Co2+ and Zn2+. This is an indication for structural differences in these complexes possibly linked to their significantly different biological effects on oxytocin-receptor binding, and suggests that ECD may be used to study subtle structural differences in transition metal ion-peptide complexes.

Capture and Emission of Charge Carriers by Quantum Well

NASA Astrophysics Data System (ADS)

Davydov, V. N.; Karankevich, O. A.

2018-06-01

The interaction of electrons from the conduction band of the barrier layer of a LED heterostructure with the quantum well size-quantization level described by the capture time and emission time of charge carriers is considered. Relaxation of an excess energy upon capture and emission of charge carriers occurs as a result of their collisions with phonons of the quantum well substance and the "barrier layer-quantum well" interface. Analytical expressions are obtained for the interaction times, taking into account the depth of the sizequantization level, involved in the interaction with electrons, and the width of the well. Numerical estimates show that in real conditions, the capture time is shorter than the emission time, and this difference increases with increasing depth of the level. At shallow depths, the capture and emission times are comparable.

Comparative study of the double-K -shell-vacancy production in single- and double-electron-capture decay

NASA Astrophysics Data System (ADS)

Ratkevich, S. S.; Gangapshev, A. M.; Gavrilyuk, Yu. M.; Karpeshin, F. F.; Kazalov, V. V.; Kuzminov, V. V.; Panasenko, S. I.; Trzhaskovskaya, M. B.; Yakimenko, S. P.

2017-12-01

Background: A double-K -electron capture is a rare nuclear-atomic process in which two K electrons are captured simultaneously from the atomic shell. A "hollow atom" is created as a result of this process. In single-K -shell electron-capture decays, there is a small probability that the second electron in the K shell is excited to an unoccupied level or can (mostly) be ejected to the continuum. In either case, a double vacancy is created in the K shell. The relaxation of the double-K -shell vacancy, accompanied by the emission of two K -fluorescence photons, makes it possible to perform experimental studies of such rare processes with the large-volume proportional gas chamber. Purpose: The purpose of the present analysis is to estimate a double-K -shell vacancy creation probability per K -shell electron capture PK K of 81Kr, as well as to measure the half-life of 78Kr relative to 2 ν 2 K capture. Method: Time-resolving current pulse from the large low-background proportional counter (LPC), filled with the krypton sample, was applied to detect triple coincidences of "shaked" electrons and two fluorescence photons. Results: The number of K -shell vacancies per the K -electron capture, produced as a result of the shake-off process, has been measured for the decay of 81Kr. The probability for this decay was found to be PK K=(5.7 ±0.8 ) ×10-5 with a systematic error of (ΔPKK) syst=±0.4 ×10-5 . For the 78Kr(2 ν 2 K ) decay, the comparative study of single- and double-capture decays allowed us to obtain the signal-to-background ratio up to 15/1. The half-life T1/2 2 ν 2 K(g .s .→g .s .) =[1 .9-0.7+1.3(stat) ±0.3 (syst) ] ×1022 y is determined from the analysis of data that have been accumulated over 782 days of live measurements in the experiment that used samples consisted of 170.6 g of 78Kr. Conclusions: The data collected during low background measurements using the LPC were analyzed to search the rare atomic and nuclear processes. We have determined PKK exp for the E C decay of 81Kr, which are in satisfactory agreement with Z-2 dependence of PK K predicted by Primakoff and Porter. This made possible to more accurately determine the background contribution in the energy region of our interest for the search for the 2 K capture in 78Kr. The general procedure of data analysis allowed us to determine the half-life of 78Kr relative to 2 ν 2 K transition with a greater statistical accuracy than in our previous works.

Planck 2013 results. XXVI. Background geometry and topology of the Universe

NASA Astrophysics Data System (ADS)

Planck Collaboration; Ade, P. A. R.; Aghanim, N.; Armitage-Caplan, C.; Arnaud, M.; Ashdown, M.; Atrio-Barandela, F.; Aumont, J.; Baccigalupi, C.; Banday, A. J.; Barreiro, R. B.; Bartlett, J. G.; Battaner, E.; Benabed, K.; Benoît, A.; Benoit-Lévy, A.; Bernard, J.-P.; Bersanelli, M.; Bielewicz, P.; Bobin, J.; Bock, J. J.; Bonaldi, A.; Bonavera, L.; Bond, J. R.; Borrill, J.; Bouchet, F. R.; Bridges, M.; Bucher, M.; Burigana, C.; Butler, R. C.; Cardoso, J.-F.; Catalano, A.; Challinor, A.; Chamballu, A.; Chiang, H. C.; Chiang, L.-Y.; Christensen, P. R.; Church, S.; Clements, D. L.; Colombi, S.; Colombo, L. P. L.; Couchot, F.; Coulais, A.; Crill, B. P.; Curto, A.; Cuttaia, F.; Danese, L.; Davies, R. D.; Davis, R. J.; de Bernardis, P.; de Rosa, A.; de Zotti, G.; Delabrouille, J.; Delouis, J.-M.; Désert, F.-X.; Diego, J. M.; Dole, H.; Donzelli, S.; Doré, O.; Douspis, M.; Dupac, X.; Efstathiou, G.; Enßlin, T. A.; Eriksen, H. K.; Fabre, O.; Finelli, F.; Forni, O.; Frailis, M.; Franceschi, E.; Galeotta, S.; Ganga, K.; Giard, M.; Giardino, G.; Giraud-Héraud, Y.; González-Nuevo, J.; Górski, K. M.; Gratton, S.; Gregorio, A.; Gruppuso, A.; Hansen, F. K.; Hanson, D.; Harrison, D. L.; Henrot-Versillé, S.; Hernández-Monteagudo, C.; Herranz, D.; Hildebrandt, S. R.; Hivon, E.; Hobson, M.; Holmes, W. A.; Hornstrup, A.; Hovest, W.; Huffenberger, K. M.; Jaffe, A. H.; Jaffe, T. R.; Jones, W. C.; Juvela, M.; Keihänen, E.; Keskitalo, R.; Kisner, T. S.; Knoche, J.; Knox, L.; Kunz, M.; Kurki-Suonio, H.; Lagache, G.; Lähteenmäki, A.; Lamarre, J.-M.; Lasenby, A.; Laureijs, R. J.; Lawrence, C. R.; Leahy, J. P.; Leonardi, R.; Leroy, C.; Lesgourgues, J.; Liguori, M.; Lilje, P. B.; Linden-Vørnle, M.; López-Caniego, M.; Lubin, P. M.; Macías-Pérez, J. F.; Maffei, B.; Maino, D.; Mandolesi, N.; Maris, M.; Marshall, D. J.; Martin, P. G.; Martínez-González, E.; Masi, S.; Massardi, M.; Matarrese, S.; Matthai, F.; Mazzotta, P.; McEwen, J. D.; Melchiorri, A.; Mendes, L.; Mennella, A.; Migliaccio, M.; Mitra, S.; Miville-Deschênes, M.-A.; Moneti, A.; Montier, L.; Morgante, G.; Mortlock, D.; Moss, A.; Munshi, D.; Murphy, J. A.; Naselsky, P.; Nati, F.; Natoli, P.; Netterfield, C. B.; Nørgaard-Nielsen, H. U.; Noviello, F.; Novikov, D.; Novikov, I.; Osborne, S.; Oxborrow, C. A.; Paci, F.; Pagano, L.; Pajot, F.; Paoletti, D.; Pasian, F.; Patanchon, G.; Peiris, H. V.; Perdereau, O.; Perotto, L.; Perrotta, F.; Piacentini, F.; Piat, M.; Pierpaoli, E.; Pietrobon, D.; Plaszczynski, S.; Pogosyan, D.; Pointecouteau, E.; Polenta, G.; Ponthieu, N.; Popa, L.; Poutanen, T.; Pratt, G. W.; Prézeau, G.; Prunet, S.; Puget, J.-L.; Rachen, J. P.; Rebolo, R.; Reinecke, M.; Remazeilles, M.; Renault, C.; Riazuelo, A.; Ricciardi, S.; Riller, T.; Ristorcelli, I.; Rocha, G.; Rosset, C.; Roudier, G.; Rowan-Robinson, M.; Rusholme, B.; Sandri, M.; Santos, D.; Savini, G.; Scott, D.; Seiffert, M. D.; Shellard, E. P. S.; Spencer, L. D.; Starck, J.-L.; Stolyarov, V.; Stompor, R.; Sudiwala, R.; Sureau, F.; Sutton, D.; Suur-Uski, A.-S.; Sygnet, J.-F.; Tauber, J. A.; Tavagnacco, D.; Terenzi, L.; Toffolatti, L.; Tomasi, M.; Tristram, M.; Tucci, M.; Tuovinen, J.; Valenziano, L.; Valiviita, J.; Van Tent, B.; Varis, J.; Vielva, P.; Villa, F.; Vittorio, N.; Wade, L. A.; Wandelt, B. D.; Yvon, D.; Zacchei, A.; Zonca, A.

2014-11-01

The new cosmic microwave background (CMB) temperature maps from Planck provide the highest-quality full-sky view of the surface of last scattering available to date. This allows us to detect possible departures from the standard model of a globally homogeneous and isotropic cosmology on the largest scales. We search for correlations induced by a possible non-trivial topology with a fundamental domain intersecting, or nearly intersecting, the last scattering surface (at comoving distance χrec), both via a direct search for matched circular patterns at the intersections and by an optimal likelihood search for specific topologies. For the latter we consider flat spaces with cubic toroidal (T3), equal-sided chimney (T2) and slab (T1) topologies, three multi-connected spaces of constant positive curvature (dodecahedral, truncated cube and octahedral) and two compact negative-curvature spaces. These searches yield no detection of the compact topology with the scale below the diameter of the last scattering surface. For most compact topologies studied the likelihood maximized over the orientation of the space relative to the observed map shows some preference for multi-connected models just larger than the diameter of the last scattering surface. Since this effect is also present in simulated realizations of isotropic maps, we interpret it as the inevitable alignment of mild anisotropic correlations with chance features in a single sky realization; such a feature can also be present, in milder form, when the likelihood is marginalized over orientations. Thus marginalized, the limits on the radius ℛi of the largest sphere inscribed in topological domain (at log-likelihood-ratio Δln ℒ > -5 relative to a simply-connected flat Planck best-fit model) are: in a flat Universe, ℛi> 0.92χrec for the T3 cubic torus; ℛi> 0.71χrec for the T2 chimney; ℛi> 0.50χrec for the T1 slab; and in a positively curved Universe, ℛi> 1.03χrec for the dodecahedral space; ℛi> 1.0χrec for the truncated cube; and ℛi> 0.89χrec for the octahedral space. The limit for a wider class of topologies, i.e., those predicting matching pairs of back-to-back circles, among them tori and the three spherical cases listed above, coming from the matched-circles search, is ℛi> 0.94χrec at 99% confidence level. Similar limits apply to a wide, although not exhaustive, range of topologies. We also perform a Bayesian search for an anisotropic global Bianchi VIIh geometry. In the non-physical setting where the Bianchi cosmology is decoupled from the standard cosmology, Planck data favour the inclusion of a Bianchi component with a Bayes factor of at least 1.5 units of log-evidence. Indeed, the Bianchi pattern is quite efficient at accounting for some of the large-scale anomalies found in Planck data. However, the cosmological parameters that generate this pattern are in strong disagreement with those found from CMB anisotropy data alone. In the physically motivated setting where the Bianchi parameters are coupled and fitted simultaneously with the standard cosmological parameters, we find no evidence for a Bianchi VIIh cosmology and constrain the vorticity of such models to (ω/H)0< 8.1 × 10-10 (95% confidence level).

A RecET-assisted CRISPR-Cas9 genome editing in Corynebacterium glutamicum.

PubMed

Wang, Bo; Hu, Qitiao; Zhang, Yu; Shi, Ruilin; Chai, Xin; Liu, Zhe; Shang, Xiuling; Zhang, Yun; Wen, Tingyi

2018-04-23

Extensive modification of genome is an efficient manner to regulate the metabolic network for producing target metabolites or non-native products using Corynebacterium glutamicum as a cell factory. Genome editing approaches by means of homologous recombination and counter-selection markers are laborious and time consuming due to multiple round manipulations and low editing efficiencies. The current two-plasmid-based CRISPR-Cas9 editing methods generate false positives due to the potential instability of Cas9 on the plasmid, and require a high transformation efficiency for co-occurrence of two plasmids transformation. Here, we developed a RecET-assisted CRISPR-Cas9 genome editing method using a chromosome-borne Cas9-RecET and a single plasmid harboring sgRNA and repair templates. The inducible expression of chromosomal RecET promoted the frequencies of homologous recombination, and increased the efficiency for gene deletion. Due to the high transformation efficiency of a single plasmid, this method enabled 10- and 20-kb region deletion, 2.5-, 5.7- and 7.5-kb expression cassette insertion and precise site-specific mutation, suggesting a versatility of this method. Deletion of argR and farR regulators as well as site-directed mutation of argB and pgi genes generated the mutant capable of accumulating L-arginine, indicating the stability of chromosome-borne Cas9 for iterative genome editing. Using this method, the model-predicted target genes were modified to redirect metabolic flux towards 1,2-propanediol biosynthetic pathway. The final engineered strain produced 6.75 ± 0.46 g/L of 1,2-propanediol that is the highest titer reported in C. glutamicum. Furthermore, this method is available for Corynebacterium pekinense 1.563, suggesting its universal applicability in other Corynebacterium species. The RecET-assisted CRISPR-Cas9 genome editing method will facilitate engineering of metabolic networks for the synthesis of interested bio-based products from renewable biomass using Corynebacterium species as cell factories.

Reactivity of IgE to the allergen hyaluronidase from Polybia paulista (Hymenoptera, Vespidae) venom.

PubMed

Justo Jacomini, Débora Laís; Gomes Moreira, Susana Margarida; Campos Pereira, Franco Dani; Zollner, Ricardo de Lima; Brochetto Braga, Márcia Regina

2014-05-01

To date, there are no allergenic extracts or components available in Brazil to diagnosis and treatment of patients with venom allergy from social wasp (Vespidae Family; Polistinae Subfamily) despite of the great number of existing species. We evaluated the immunogenic potential of the Hyal recombinant protein (Pp-Hyal-rec) which was expressed in an insoluble form in comparison with the allergenic native protein (Pp-Hyal-nat) for recognition of immunoglobulin E (IgE) in the serum of allergic patients to venom of the endemic social wasp Polybia paulista from São Paulo State, Brazil. Hyal cDNA from the venom of the social wasp P. paulista (Pp-Hyal) (GI: 302201582) was cloned into the expression vector pET-28a in Escherichia coli DE3 (BL21) cells. Solubilization and purification of Pp-Hyal-rec from inclusion bodies were performed using Ni(2+) affinity chromatography (Ni-NTA-Agarose) under denaturing conditions. Both the native (Pp-Hyal-nat) and the recombinant (Pp-Hyal-rec) purified allergens were used for Western blotting to assess the levels of Pp-Hyal-IgE specific in the serum of 10 patients exclusively reactive to the venom of the social wasp P. paulista. The immune sera specifically recognized the band corresponding to the Pp-Hyal-rec protein (40 kDa) at a higher intensity than the native allergen (39 kDa). The sera recognized other proteins in P. paulista crude venom extract to a lesser extent, likely corresponding to other venom allergens such as phospholipase (34 kDa), Antigen 5 (25 kDa), and proteases. The recognition pattern of the immune sera to the Pp-Hyal-rec allergen strongly suggests that this recombinant antigen could be used for developing a diagnostic allergy test as well as for specific immunotherapy (IT). Copyright © 2014 Elsevier Ltd. All rights reserved.

REC-2006-A Fractionated Extract of Podophyllum hexandrum Protects Cellular DNA from Radiation-Induced Damage by Reducing the Initial Damage and Enhancing Its Repair In Vivo.

PubMed

Chaudhary, Pankaj; Shukla, Sandeep Kumar; Sharma, Rakesh Kumar

2011-01-01

Podophyllum hexandrum, a perennial herb commonly known as the Himalayan May Apple, is well known in Indian and Chinese traditional systems of medicine. P. hexandrum has been widely used for the treatment of venereal warts, skin infections, bacterial and viral infections, and different cancers of the brain, lung and bladder. This study aimed at elucidating the effect of REC-2006, a bioactive fractionated extract from the rhizome of P. hexandrum, on the kinetics of induction and repair of radiation-induced DNA damage in murine thymocytes in vivo. We evaluated its effect on non-specific radiation-induced DNA damage by the alkaline halo assay in terms of relative nuclear spreading factor (RNSF) and gene-specific radiation-induced DNA damage via semi-quantitative polymerase chain reaction. Whole body exposure of animals with gamma rays (10 Gy) caused a significant amount of DNA damage in thymocytes (RNSF values 17.7 ± 0.47, 12.96 ± 1.64 and 3.3 ± 0.014) and a reduction in the amplification of β-globin gene to 0, 28 and 43% at 0, 15 and 60 min, respectively. Administrating REC-2006 at a radioprotective concentration (15 mg kg(-1) body weight) 1 h before irradiation resulted in time-dependent reduction of DNA damage evident as a decrease in RNSF values 6.156 ± 0.576, 1.647 ± 0.534 and 0.496 ± 0.012, and an increase in β-globin gene amplification 36, 95 and 99%, at 0, 15 and 60 min, respectively. REC-2006 scavenged radiation-induced hydroxyl radicals in a dose-dependent manner stabilized DPPH free radicals and also inhibited superoxide anions. Various polyphenols and flavonoides present in REC-2006 might contribute to scavenging of radiation-induced free radicals, thereby preventing DNA damage and stimulating its repair.

REC-2006—A Fractionated Extract of Podophyllum hexandrum Protects Cellular DNA from Radiation-Induced Damage by Reducing the Initial Damage and Enhancing Its Repair In Vivo

PubMed Central

Chaudhary, Pankaj; Shukla, Sandeep Kumar; Sharma, Rakesh Kumar

2011-01-01

Podophyllum hexandrum, a perennial herb commonly known as the Himalayan May Apple, is well known in Indian and Chinese traditional systems of medicine. P. hexandrum has been widely used for the treatment of venereal warts, skin infections, bacterial and viral infections, and different cancers of the brain, lung and bladder. This study aimed at elucidating the effect of REC-2006, a bioactive fractionated extract from the rhizome of P. hexandrum, on the kinetics of induction and repair of radiation-induced DNA damage in murine thymocytes in vivo. We evaluated its effect on non-specific radiation-induced DNA damage by the alkaline halo assay in terms of relative nuclear spreading factor (RNSF) and gene-specific radiation-induced DNA damage via semi-quantitative polymerase chain reaction. Whole body exposure of animals with gamma rays (10 Gy) caused a significant amount of DNA damage in thymocytes (RNSF values 17.7 ± 0.47, 12.96 ± 1.64 and 3.3 ± 0.014) and a reduction in the amplification of β-globin gene to 0, 28 and 43% at 0, 15 and 60 min, respectively. Administrating REC-2006 at a radioprotective concentration (15 mg kg−1 body weight) 1 h before irradiation resulted in time-dependent reduction of DNA damage evident as a decrease in RNSF values 6.156 ± 0.576, 1.647 ± 0.534 and 0.496 ± 0.012, and an increase in β-globin gene amplification 36, 95 and 99%, at 0, 15 and 60 min, respectively. REC-2006 scavenged radiation-induced hydroxyl radicals in a dose-dependent manner stabilized DPPH free radicals and also inhibited superoxide anions. Various polyphenols and flavonoides present in REC-2006 might contribute to scavenging of radiation-induced free radicals, thereby preventing DNA damage and stimulating its repair. PMID:20008078

Effect of a carbohydrate-electrolyte beverage, lemon tea, or water on rehydration during short-term recovery from exercise.

PubMed

Wong, Stephen Heung-Sang; Chen, Yajun

2011-08-01

This study examined the rehydration achieved by drinking different beverages during a short-term recovery period (REC) after exercise-induced dehydration. Thirteen well-trained men (age 22.1 ± 3.3 yr, body mass 61.2 ± 9.1 kg, VO(2max) 64.9 ± 4.0 ml · kg-1 · min-1, maximum heart rate 198 ± 7 beats/min) ran for 60 min on 3 occasions on a level treadmill at 70% VO(2max). All trials were performed in thermoneutral conditions (21 °C, 71% relative humidity) and were separated by at least 7 d. During 4 hr REC, the subjects consumed either a volume of a carbohydrate-electrolyte beverage (CE), lemon tea (LT), or distilled water (DW) equal to 150% of the body weight (BW) lost during the previous run. The fluid was consumed in 6 equal volumes at 30, 60, 90, 120, 150, and 180 min of REC. After the completion of the 60-min run, the subjects lost ~2.0% of their preexercise BW in all trials, and no differences were observed in these BW changes between trials. At the end of REC, the greatest fraction of the retained drink occurred when the CE drink was consumed (CE vs. LT vs. DW: 52% ± 18% vs. 36% ± 15% vs. 30% ± 14%, p < .05). The CE drink also caused the least diuretic effect (CE vs. LT vs. DW: 638 ± 259 vs. 921 ± 323 vs. 915 ± 210 ml, p < .05) and produced the optimal restoration of plasma volume (CE vs. LT vs. DW: 11.2% ± 2.0% vs. -3.1% ± 1.8% vs. 0.2% ± 2.1%, p < .05). The results of this study suggest that CE drinks are more effective than DW or LT in restoring fluid balance during short-term REC after exercise-induced dehydration.

Diesel motor exhaust and lung cancer mortality: reanalysis of a cohort study in potash miners.

PubMed

Möhner, Matthias; Kersten, Norbert; Gellissen, Johannes

2013-02-01

The aim of the reanalysis is to reassess lung cancer risk associated with occupational exposure to diesel motor exhaust in potash miners, while controlling for potential confounders such as smoking and previous occupational history. Our investigation is based on a cohort study of nearly 6,000 German potash miners, who were followed up from 1970 to 2001. The reanalysis also takes into account the employment periods before potash mining, in particular uranium mining. Different approaches (nested case-control study and Cox model) were used to adjust for confounding. The exposure estimates were recalculated, lagging the exposure by 5 years. Exposure groups were defined by tertiles of cumulative respirable elemental carbon (REC) exposure estimates and occupational categories, where exposure was estimated originally by representative measurements of total carbon for different occupations. The highest REC concentration was measured for production workers, about twice as much as for other occupations. The reanalysis revealed that while about 4 % of all study subjects had worked earlier in uranium mines, 10.3 % of later lung cancer cases did so. Although their absolute number was small, the corresponding relative risk estimator was significantly elevated. Our analysis did not show any notable association between cumulative REC exposure and lung cancer risk. Introducing cumulative REC exposure as a continuous variable into the conditional logistic regression model yielded an odds ratio of OR = 1.04 [0.70-1.53]95 % adjusted for smoking and previous employment. The study results give no evidence for an association between REC exposure and lung cancer risk. Only for very high cumulative dose, corresponding to at least 20 years of exposure in the production area, some weak hints for a possible risk increase could be detected. The study underlines the importance of assessing the entire occupational history in occupational studies, especially if the supposed dose-response-relationship is weak.

Escherichia coli DinB inhibits replication fork progression without significantly inducing the SOS response.

PubMed

Mori, Tetsuya; Nakamura, Tatsuro; Okazaki, Naoto; Furukohri, Asako; Maki, Hisaji; Akiyama, Masahiro Tatsumi

2012-01-01

The SOS response is readily triggered by replication fork stalling caused by DNA damage or a dysfunctional replicative apparatus in Escherichia coli cells. E. coli dinB encodes DinB DNA polymerase and its expression is upregulated during the SOS response. DinB catalyzes translesion DNA synthesis in place of a replicative DNA polymerase III that is stalled at a DNA lesion. We showed previously that DNA replication was suppressed without exogenous DNA damage in cells overproducing DinB. In this report, we confirm that this was due to a dose-dependent inhibition of ongoing replication forks by DinB. Interestingly, the DinB-overproducing cells did not significantly induce the SOS response even though DNA replication was perturbed. RecA protein is activated by forming a nucleoprotein filament with single-stranded DNA, which leads to the onset of the SOS response. In the DinB-overproducing cells, RecA was not activated to induce the SOS response. However, the SOS response was observed after heat-inducible activation in strain recA441 (encoding a temperature-sensitive RecA) and after replication blockage in strain dnaE486 (encoding a temperature-sensitive catalytic subunit of the replicative DNA polymerase III) at a non-permissive temperature when DinB was overproduced in these cells. Furthermore, since catalytically inactive DinB could avoid the SOS response to a DinB-promoted fork block, it is unlikely that overproduced DinB takes control of primer extension and thus limits single-stranded DNA. These observations suggest that DinB possesses a feature that suppresses DNA replication but does not abolish the cell's capacity to induce the SOS response. We conclude that DinB impedes replication fork progression in a way that does not activate RecA, in contrast to obstructive DNA lesions and dysfunctional replication machinery.

Destruction of Peptides and Nucleosides in Reactions with Low-Energy Electrons

NASA Astrophysics Data System (ADS)

Muftakhov, M. V.; Shchukin, P. V.

2018-05-01

Mass-spectrometry of negative ions is used to study dissociative electron capture by molecules of several nucleosides, simplest di- and tripeptides, and modified dipeptides. Energy domains and efficiencies of dissociative capture are determined for the objects under study, and threshold energies of several fragmentation processes are estimated. It is shown that cytidine and peptides are stable against fragmentation due to simple bond breaking at electron energies ranging from 0 to 1 eV.

New developments in electron microscopy for serial image acquisition of neuronal profiles.

PubMed

Kubota, Yoshiyuki

2015-02-01

Recent developments in electron microscopy largely automate the continuous acquisition of serial electron micrographs (EMGs), previously achieved by laborious manual serial ultrathin sectioning using an ultramicrotome and ultrastructural image capture process with transmission electron microscopy. The new systems cut thin sections and capture serial EMGs automatically, allowing for acquisition of large data sets in a reasonably short time. The new methods are focused ion beam/scanning electron microscopy, ultramicrotome/serial block-face scanning electron microscopy, automated tape-collection ultramicrotome/scanning electron microscopy and transmission electron microscope camera array. In this review, their positive and negative aspects are discussed. © The Author 2015. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

A Real-Time Air Dispersion Modeling System.

DTIC Science & Technology

1984-04-01

8217 UNFORMATTED’) READ (SUNITI, REC=I) HD 5 ICNT=2 FLAGI-. FALSE. DO 20 I=2,HD,1 IF (.NOT. FLA6i) FLAG1-.TRUE. READ(SUNIT1, REC-I) HEAD, HDR ICHECK =0 DO 13 JG=1,9...lt IF (HDR(JG) NE. 0) ICHECKI1 13 CONTINUE IF ( ICHECK .EQ. 0) SOTO 28 IF (SKEY(2) .NE. ’*’) THEN IF (SKEY(2 .NE. 𔄁’) THEN DO 12 K-1,9,1 IF (HDR(K) .EQ

General features of the dissociative recombination of polyatomic molecules

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

Pratt, S. T.; Jungen, Ch.; Schneider, I. F.

We discuss some aspects of a simple expression for the low-energy dissociative recombination cross section that applies when the recombination process is dominated by the indirect mechanism. In most previous applications, this expression has been applied to capture into vibrationally excited Rydberg states with the assumption that capture is always followed by prompt dissociation. Here we consider the dissociative recombination of larger polyatomic ions and electrons. More specifically, we consider capture into electronically core-excited Rydberg states, and begin to assess its potential importance for larger systems.

General features of the dissociative recombination of polyatomic molecules

DOE PAGES

Pratt, S. T.; Jungen, Ch.; Schneider, I. F.; ...

2015-01-29

We discuss some aspects of a simple expression for the low-energy dissociative recombination cross section that applies when the recombination process is dominated by the indirect mechanism. In most previous applications, this expression has been applied to capture into vibrationally excited Rydberg states with the assumption that capture is always followed by prompt dissociation. Here we consider the dissociative recombination of larger polyatomic ions and electrons. More specifically, we consider capture into electronically core-excited Rydberg states, and begin to assess its potential importance for larger systems.

The Diesel Exhaust in Miners Study: A Nested Case–Control Study of Lung Cancer and Diesel Exhaust

PubMed Central

Samanic, Claudine M.; Lubin, Jay H.; Blair, Aaron E.; Stewart, Patricia A.; Vermeulen, Roel; Coble, Joseph B.; Rothman, Nathaniel; Schleiff, Patricia L.; Travis, William D.; Ziegler, Regina G.; Wacholder, Sholom; Attfield, Michael D.

2012-01-01

Background Most studies of the association between diesel exhaust exposure and lung cancer suggest a modest, but consistent, increased risk. However, to our knowledge, no study to date has had quantitative data on historical diesel exposure coupled with adequate sample size to evaluate the exposure–response relationship between diesel exhaust and lung cancer. Our purpose was to evaluate the relationship between quantitative estimates of exposure to diesel exhaust and lung cancer mortality after adjustment for smoking and other potential confounders. Methods We conducted a nested case–control study in a cohort of 12 315 workers in eight non-metal mining facilities, which included 198 lung cancer deaths and 562 incidence density–sampled control subjects. For each case subject, we selected up to four control subjects, individually matched on mining facility, sex, race/ethnicity, and birth year (within 5 years), from all workers who were alive before the day the case subject died. We estimated diesel exhaust exposure, represented by respirable elemental carbon (REC), by job and year, for each subject, based on an extensive retrospective exposure assessment at each mining facility. We conducted both categorical and continuous regression analyses adjusted for cigarette smoking and other potential confounding variables (eg, history of employment in high-risk occupations for lung cancer and a history of respiratory disease) to estimate odds ratios (ORs) and 95% confidence intervals (CIs). Analyses were both unlagged and lagged to exclude recent exposure such as that occurring in the 15 years directly before the date of death (case subjects)/reference date (control subjects). All statistical tests were two-sided. Results We observed statistically significant increasing trends in lung cancer risk with increasing cumulative REC and average REC intensity. Cumulative REC, lagged 15 years, yielded a statistically significant positive gradient in lung cancer risk overall (P trend = .001); among heavily exposed workers (ie, above the median of the top quartile [REC ≥ 1005 μg/m3-y]), risk was approximately three times greater (OR = 3.20, 95% CI = 1.33 to 7.69) than that among workers in the lowest quartile of exposure. Among never smokers, odd ratios were 1.0, 1.47 (95% CI = 0.29 to 7.50), and 7.30 (95% CI = 1.46 to 36.57) for workers with 15-year lagged cumulative REC tertiles of less than 8, 8 to less than 304, and 304 μg/m3-y or more, respectively. We also observed an interaction between smoking and 15-year lagged cumulative REC (P interaction = .086) such that the effect of each of these exposures was attenuated in the presence of high levels of the other. Conclusion Our findings provide further evidence that diesel exhaust exposure may cause lung cancer in humans and may represent a potential public health burden. PMID:22393209

The Diesel Exhaust in Miners study: a nested case-control study of lung cancer and diesel exhaust.

PubMed

Silverman, Debra T; Samanic, Claudine M; Lubin, Jay H; Blair, Aaron E; Stewart, Patricia A; Vermeulen, Roel; Coble, Joseph B; Rothman, Nathaniel; Schleiff, Patricia L; Travis, William D; Ziegler, Regina G; Wacholder, Sholom; Attfield, Michael D

2012-06-06

Most studies of the association between diesel exhaust exposure and lung cancer suggest a modest, but consistent, increased risk. However, to our knowledge, no study to date has had quantitative data on historical diesel exposure coupled with adequate sample size to evaluate the exposure-response relationship between diesel exhaust and lung cancer. Our purpose was to evaluate the relationship between quantitative estimates of exposure to diesel exhaust and lung cancer mortality after adjustment for smoking and other potential confounders. We conducted a nested case-control study in a cohort of 12 315 workers in eight non-metal mining facilities, which included 198 lung cancer deaths and 562 incidence density-sampled control subjects. For each case subject, we selected up to four control subjects, individually matched on mining facility, sex, race/ethnicity, and birth year (within 5 years), from all workers who were alive before the day the case subject died. We estimated diesel exhaust exposure, represented by respirable elemental carbon (REC), by job and year, for each subject, based on an extensive retrospective exposure assessment at each mining facility. We conducted both categorical and continuous regression analyses adjusted for cigarette smoking and other potential confounding variables (eg, history of employment in high-risk occupations for lung cancer and a history of respiratory disease) to estimate odds ratios (ORs) and 95% confidence intervals (CIs). Analyses were both unlagged and lagged to exclude recent exposure such as that occurring in the 15 years directly before the date of death (case subjects)/reference date (control subjects). All statistical tests were two-sided. We observed statistically significant increasing trends in lung cancer risk with increasing cumulative REC and average REC intensity. Cumulative REC, lagged 15 years, yielded a statistically significant positive gradient in lung cancer risk overall (P (trend) = .001); among heavily exposed workers (ie, above the median of the top quartile [REC ≥ 1005 μg/m(3)-y]), risk was approximately three times greater (OR = 3.20, 95% CI = 1.33 to 7.69) than that among workers in the lowest quartile of exposure. Among never smokers, odd ratios were 1.0, 1.47 (95% CI = 0.29 to 7.50), and 7.30 (95% CI = 1.46 to 36.57) for workers with 15-year lagged cumulative REC tertiles of less than 8, 8 to less than 304, and 304 μg/m(3)-y or more, respectively. We also observed an interaction between smoking and 15-year lagged cumulative REC (P (interaction) = .086) such that the effect of each of these exposures was attenuated in the presence of high levels of the other. Our findings provide further evidence that diesel exhaust exposure may cause lung cancer in humans and may represent a potential public health burden.

Differential Mobility Spectrometry: Preliminary Findings on Determination of Fundamental Constants

NASA Technical Reports Server (NTRS)

Limero, Thomas; Cheng, Patti; Boyd, John

2007-01-01

The electron capture detector (ECD) has been used for 40+ years (1) to derive fundamental constants such as a compound's electron affinity. Given this historical perspective, it is not surprising that differential mobility spectrometry (DMS) might be used in a like manner. This paper will present data from a gas chromatography (GC)-DMS instrument that illustrates the potential capability of this device to derive fundamental constants for electron-capturing compounds. Potential energy curves will be used to provide possible explanation of the data.

IN VITRO EVALUATION OF BIOLOGICAL ACTIVITY OF CINNAMIC, CAFFEIC, FERULIC AND CHLOROGENIC ACIDS WITH USE OF ESCHERICHIA COLI K-12 RECA::GFP BIOSENSOR STRAIN.

PubMed

Matejczyk, Marzena; Swislocka, Renata; Kalinowska, Monika; Widerskp, Grzegorz; Lewandowsk, Wlodzimierz; Jablonska-Trypuo, Agata; Rosochacki, Stanislaw Jozef

2017-05-01

Cinnamic acid and its derivatives are important and promising compounds in cancer therapy, because of its broad spectrum of anicancer and antioxidative ability, and with high potential for development into new generation drugs. The aim of this study was to compare the cyto- and genotoxic effects of cinnamic acid and its derivatives with the use of4Escherichia coli K-12 recA::gfp microbial biosensor strain with plasmid fusion of recA promoter and gfp gene as reporter. Obtained results indicate that recA::gfpmut2 genetic system was a sensitive biosensor to the most chemicals tested in our experiments. The cinnamic acid and its derivatives modulated the reactivity of wcA promoter in relation to control sample and significantly inhibited bacteria cells growth. In the light of our results only chlorogenic and ferulic acids at higher concentrations demonstrated cyto and genotoxic activity toward to E. coli K-12 mcA::gfp cells.

[Vitamin para-aminobenzoic acid inhibits development of SOS function in tif-1 mutants of Escherichia coli at nonpermissive temperatures].

PubMed

Vasil'eva, S V; Gorb, T E; Rapoport, I A

1983-12-01

The development of "SOS" inducible functions in lysogenic and non-lysogenic strains of Escherichia coli tif-1 sfiA11 (lambda) at nonpermissive temperature of 42 degrees C was strongly suppressed by para-aminobenzoic acid (PABA). The rate of prophage lambda induction decreased 400 times, as compared to the control level; the efficiency of W-reactivation of UV-irradiated phage lambda decreased 37.5 to 16%. PABA also inhibited to some extent (1.5 times) the process of inducible recombination on the RecF pathway. The processes of spontaneous lambda induction and W-reactivation, as well as spontaneous recombination on RecBC and RecF pathways, were not influenced by PABA. The above data are in accordance with previous studies of PABA action when the manifestation of "SOS" functions was induced by chemical mutagens. The action of PABA has been tentatively interpreted on the basis of negative control of "SOS" repair pathway.

Characterization of the Caenorhabditis elegans HIM-6/BLM helicase: unwinding recombination intermediates.

PubMed

Jung, Hana; Lee, Jin A; Choi, Seoyoon; Lee, Hyunwoo; Ahn, Byungchan

2014-01-01

Mutations in three human RecQ genes are implicated in heritable human syndromes. Mutations in BLM, a RecQ gene, cause Bloom syndrome (BS), which is characterized by short stature, cancer predisposition, and sensitivity to sunlight. BLM is a RecQ DNA helicase that, with interacting proteins, is able to dissolve various DNA structures including double Holliday junctions. A BLM ortholog, him-6, has been identified in Caenorhabditis elegans, but little is known about its enzymatic activities or its in vivo roles. By purifying recombinant HIM-6 and performing biochemical assays, we determined that the HIM-6 has DNA-dependent ATPase activity HIM-6 and helicase activity that proceeds in the 3'-5' direction and needs at least five 3' overhanging nucleotides. HIM-6 is also able to unwind DNA structures including D-loops and Holliday junctions. Worms with him-6 mutations were defective in recovering the cell cycle arrest after HU treatment. These activities strongly support in vivo roles for HIM-6 in processing recombination intermediates.

Characterization of the Caenorhabditis elegans HIM-6/BLM Helicase: Unwinding Recombination Intermediates

PubMed Central

Choi, Seoyoon; Lee, Hyunwoo; Ahn, Byungchan

2014-01-01

Mutations in three human RecQ genes are implicated in heritable human syndromes. Mutations in BLM, a RecQ gene, cause Bloom syndrome (BS), which is characterized by short stature, cancer predisposition, and sensitivity to sunlight. BLM is a RecQ DNA helicase that, with interacting proteins, is able to dissolve various DNA structures including double Holliday junctions. A BLM ortholog, him-6, has been identified in Caenorhabditis elegans, but little is known about its enzymatic activities or its in vivo roles. By purifying recombinant HIM-6 and performing biochemical assays, we determined that the HIM-6 has DNA-dependent ATPase activity HIM-6 and helicase activity that proceeds in the 3'-5' direction and needs at least five 3' overhanging nucleotides. HIM-6 is also able to unwind DNA structures including D-loops and Holliday junctions. Worms with him-6 mutations were defective in recovering the cell cycle arrest after HU treatment. These activities strongly support in vivo roles for HIM-6 in processing recombination intermediates. PMID:25036527

Salivary sIg-A response against the recombinant Ag38 antigen of Mycobacterium tuberculosis Indonesian strain.

PubMed

Raras, Tri Yudani Mardining; Sholeh, Gamal; Lyrawati, Diana

2014-01-01

An evaluation of the humoral response based on secretory immunoglobulin A levels in the saliva of pulmonary tuberculosis (TB) acid-fast bacillus-positive (TB-AFB+) patients against a recombinant 38 kDa antigen (Ag38-rec) is reported. A total of 60 saliva samples consist of 30 TB-AFB+ patients and 30 healthy controls were tested against 500 ng of semi-purified antigen using the dot blot method. Results showed that the protein antigen could differentiate between healthy individuals and TB-AFB(+) patients. Whole saliva demonstrated better reactivity than centrifuged saliva. The Ag38-rec protein indicated statistically comparable sensitivity (80% versus 90%), but lower specificity (36.6% versus 70%) compared with purified protein derivative (PPD). Surprisingly, both antigens similarly recognized secretory immunoglobulin A in the saliva of the healthy group (50% versus 50%, respectively). These findings suggest that the Ag38-rec protein originating from a local strain of Mycobacterium tuberculosis may be used for TB screening, however require purity improvement.

Protein Determinants of Meiotic DNA Break Hotspots

PubMed Central

Fowler, Kyle R.; Gutiérrez-Velasco, Susana

2013-01-01

SUMMARY Meiotic recombination, crucial for proper chromosome segregation and genome evolution, is initiated by programmed DNA double-strand breaks (DSBs) in yeasts and likely all sexually reproducing species. In fission yeast, DSBs occur up to hundreds of times more frequently at special sites, called hotspots, than in other regions of the genome. What distinguishes hotspots from cold regions is an unsolved problem, although transcription factors determine some hotspots. We report the discovery that three coiled-coil proteins – Rec25, Rec27, and Mug20 – bind essentially all hotspots with unprecedented specificity even without DSB formation. These small proteins are components of linear elements, are related to synaptonemal complex proteins, and are essential for nearly all DSBs at most hotspots. Our results indicate these hotspot determinants activate or stabilize the DSB-forming protein Rec12 (Spo11 homolog) rather than promote its binding to hotspots. We propose a new paradigm for hotspot determination and crossover control by linear element proteins. PMID:23395004

Research Ethics Committees and Participatory Action Research With Young People: The Politics of Voice.

PubMed

Yanar, Zeynep M; Fazli, Mehria; Rahman, Jahanara; Farthing, Rys

2016-04-01

Participatory action research (PAR) is a methodological approach that seeks to maximize the participation of people whose lives it researches. It is underpinned by an ethical concern to research "with" people, rather than "on" people. However, this ethical approach to research is often, paradoxically, problematized by universities' research ethics committees (RECs). This article explores one site of tension between PAR and RECs-the requirement for anonymity for below 18-year-olds. It explores this tension by exploring a case study of a peer-to-peer research project undertaken by young women in East London, and using our own experiences and perspectives, it argues that anonymity can be unjust, disempowering, and unnecessary, and can reduce "pride." Without wanting to develop specific recommendations, given the limited scope of our case study, this article uses firsthand experiences to add weight to the broader discussions calling for a critical rethink of REC guidelines. © The Author(s) 2016.

Electron capture and excitation processes in H+-H collisions in dense quantum plasmas

NASA Astrophysics Data System (ADS)

Jakimovski, D.; Markovska, N.; Janev, R. K.

2016-10-01

Electron capture and excitation processes in proton-hydrogen atom collisions taking place in dense quantum plasmas are studied by employing the two-centre atomic orbital close-coupling (TC-AOCC) method. The Debye-Hückel cosine (DHC) potential is used to describe the plasma screening effects on the Coulomb interaction between charged particles. The properties of a hydrogen atom with DHC potential are investigated as a function of the screening strength of the potential. It is found that the decrease in binding energy of nl levels with increasing screening strength is considerably faster than in the case of the Debye-Hückel (DH) screening potential, appropriate for description of charged particle interactions in weakly coupled classical plasmas. This results in a reduction in the number of bound states in the DHC potential with respect to that in the DH potential for the same plasma screening strength, and is reflected in the dynamics of excitation and electron capture processes for the two screened potentials. The TC-AOCC cross sections for total and state-selective electron capture and excitation cross sections with the DHC potential are calculated for a number of representative screening strengths in the 1-300 keV energy range and compared with those for the DH and pure Coulomb potential. The total capture cross sections for a selected number of screening strengths are compared with the available results from classical trajectory Monte Carlo calculations.

Diesel engine exhaust and lung cancer mortality: time-related factors in exposure and risk.

PubMed

Moolgavkar, Suresh H; Chang, Ellen T; Luebeck, Georg; Lau, Edmund C; Watson, Heather N; Crump, Kenny S; Boffetta, Paolo; McClellan, Roger

2015-04-01

To develop a quantitative exposure-response relationship between concentrations and durations of inhaled diesel engine exhaust (DEE) and increases in lung cancer risks, we examined the role of temporal factors in modifying the estimated effects of exposure to DEE on lung cancer mortality and characterized risk by mine type in the Diesel Exhaust in Miners Study (DEMS) cohort, which followed 12,315 workers through December 1997. We analyzed the data using parametric functions based on concepts of multistage carcinogenesis to directly estimate the hazard functions associated with estimated exposure to a surrogate marker of DEE, respirable elemental carbon (REC). The REC-associated risk of lung cancer mortality in DEMS is driven by increased risk in only one of four mine types (limestone), with statistically significant heterogeneity by mine type and no significant exposure-response relationship after removal of the limestone mine workers. Temporal factors, such as duration of exposure, play an important role in determining the risk of lung cancer mortality following exposure to REC, and the relative risk declines after exposure to REC stops. There is evidence of effect modification of risk by attained age. The modifying impact of temporal factors and effect modification by age should be addressed in any quantitative risk assessment (QRA) of DEE. Until there is a better understanding of why the risk appears to be confined to a single mine type, data from DEMS cannot reliably be used for QRA. © 2015 Society for Risk Analysis.

Exploring optimization parameters to increase ssDNA recombineering in Lactococcus lactis and Lactobacillus reuteri

PubMed Central

van Pijkeren, Jan-Peter; Neoh, Kar Mun; Sirias, Denise; Findley, Anthony S.; Britton, Robert A.

2012-01-01

Single-stranded DNA (ssDNA) recombineering is a technology which is used to make subtle changes in the chromosome of several bacterial genera. Cells which express a single-stranded DNA binding protein (RecT or Bet) are transformed with an oligonucleotide which is incorporated via an annealing and replication-dependent mechanism. By in silico analysis we identified ssDNA binding protein homologs in the genus Lactobacillus and Lactococcus lactis. To assess whether we could further improve the recombineering efficiency in Lactobacillus reuteri ATCC PTA 6475 we expressed several RecT homologs in this strain. RecT derived from Enterococcus faecalis CRMEN 19 yielded comparable efficiencies compared with a native RecT protein, but none of the other proteins further increased the recombineering efficiency. We successfully improved recombineering efficiency 10-fold in L. lactis by increasing oligonucleotide concentration combined with the use of oligonucleotides containing phosphorothioate-linkages (PTOs). Surprisingly, neither increased oligonucleotide concentration nor PTO linkages enhanced recombineering in L. reuteri 6475. To emphasize the utility of this technology in improving probiotic features we modified six bases in a transcriptional regulatory element region of the pdu-operon of L. reuteri 6475, yielding a 3-fold increase in the production of the antimicrobial compound reuterin. Directed genetic modification of lactic acid bacteria through ssDNA recombineering will simplify strain improvement in a way that, when mutating a single base, is genetically indistinguishable from strains obtained through directed evolution. PMID:22750793

Establishment of a rat model of thrombosis induced by intravenous injection of anti-phosphatidylserine-prothrombin complex antibody.

PubMed

Yamada, Mai; Kawakami, Tamihiro; Takashima, Kohei; Nishioka, Yusuke; Nishibata, Yuka; Masuda, Sakiko; Yoshida, Shigeru; Tomaru, Utano; Ishizu, Akihiro

2017-06-01

Recent studies have suggested that aPS-PT antibody is one of the most relevant autoantibodies to APS. This study aimed to demonstrate the pathogenicity of aPS-PT antibody in vivo . At first, cultured rat vascular endothelial cells (RECs) were exposed to calf thymus-derived histones. Two hours later, lactate dehydrogenase release from the RECs and expression of PS on the cell surface were assessed. Next, we administered an i.v. injection of calf thymus-derived histones into Wistar rats (12.5 µg/g weight of 8-week-old female rats), and 2 h later they were given an i.v. injection of aPS-PT mAb (1.25 mg/g weight, n = 6) or an equal dose of rat IgM as controls (n = 5). Three days later, histological examination was conducted. Calf thymus-derived histones (>12.5 µg/ml) could injure RECs in vitro . Simultaneously, annexin V could bind to the RECs; thereby, this result indicated that cell-free histone exposure of vascular endothelial cells induced cell surface expression of PS, which is naturally present inside the plasma membrane. Thrombosis developed with higher frequency in the rats given an i.v. injection of aPS-PT mAb than in controls. We established a rat model of thrombosis induced by i.v. injection of aPS-PT mAb. © The Author 2017. Published by Oxford University Press on behalf of the British Society for Rheumatology.

Thymineless death is inhibited by CsrA in Escherichia coli lacking the SOS response.

PubMed

Hamilton, Holly M; Wilson, Ray; Blythe, Martin; Nehring, Ralf B; Fonville, Natalie C; Louis, Edward J; Rosenberg, Susan M

2013-11-01

Thymineless death (TLD) is the rapid loss of colony-forming ability in bacterial, yeast and human cells starved for thymine, and is the mechanism of action of common chemotherapeutic drugs. In Escherichia coli, significant loss of viability during TLD requires the SOS replication-stress/DNA-damage response, specifically its role in inducing the inhibitor of cell division, SulA. An independent RecQ- and RecJ-dependent TLD pathway accounts for a similarly large additional component of TLD, and a third SOS- and RecQ/J-independent TLD pathway has also been observed. Although two groups have implicated the SOS-response in TLD, an SOS-deficient mutant strain from an earlier study was found to be sensitive to thymine deprivation. We performed whole-genome resequencing on that SOS-deficient strain and find that, compared with the SOS-proficient control strain, it contains five mutations in addition to the SOS-blocking lexA(Ind(-)) mutation. One of the additional mutations, csrA, confers TLD sensitivity specifically in SOS-defective strains. We find that CsrA, a carbon storage regulator, reduces TLD in SOS- or SulA-defective cells, and that the increased TLD that occurs in csrA(-) SOS-defective cells is dependent on RecQ. We consider a hypothesis in which the modulation of nucleotide pools by CsrA might inhibit TLD specifically in SOS-deficient (SulA-deficient) cells. Copyright © 2013 Elsevier B.V. All rights reserved.

The cell pole: the site of cross talk between the DNA uptake and genetic recombination machinery.

PubMed

Kidane, Dawit; Ayora, Silvia; Sweasy, Joann B; Graumann, Peter L; Alonso, Juan C

2012-01-01

Natural transformation is a programmed mechanism characterized by binding of free double-stranded (ds) DNA from the environment to the cell pole in rod-shaped bacteria. In Bacillus subtilis some competence proteins, which process the dsDNA and translocate single-stranded (ss) DNA into the cytosol, recruit a set of recombination proteins mainly to one of the cell poles. A subset of single-stranded binding proteins, working as "guardians", protects ssDNA from degradation and limit the RecA recombinase loading. Then, the "mediators" overcome the inhibitory role of guardians, and recruit RecA onto ssDNA. A RecA·ssDNA filament searches for homology on the chromosome and, in a process that is controlled by "modulators", catalyzes strand invasion with the generation of a displacement loop (D-loop). A D-loop resolvase or "resolver" cleaves this intermediate, limited DNA replication restores missing information and a DNA ligase seals the DNA ends. However, if any step fails, the "rescuers" will repair the broken end to rescue chromosomal transformation. If the ssDNA does not share homology with resident DNA, but it contains information for autonomous replication, guardian and mediator proteins catalyze plasmid establishment after inhibition of RecA. DNA replication and ligation reconstitute the molecule (plasmid transformation). In this review, the interacting network that leads to a cross talk between proteins of the uptake and genetic recombination machinery will be placed into prospective.

The cell pole: The site of cross talk between the DNA uptake and genetic recombination machinery

PubMed Central

Kidane, Dawit; Ayora, Silvia; Sweasy, Joann; Graumann, Peter L.; Alonso, Juan C.

2012-01-01

Natural transformation is a programmed mechanism characterized by binding of free double-stranded (ds) DNA from the environment to the cell pole in rod-shaped bacteria. In Bacillus subtilis some competence proteins, which process the dsDNA and translocate single-stranded (ss) DNA into the cytosol, recruit a set of recombination proteins mainly to one of the cell poles. A subset of single-stranded binding proteins, working as “guardians”, protect ssDNA from degradation and limit the RecA recombinase loading. Then, the “mediators” overcome the inhibitory role of guardians, and recruit RecA onto ssDNA. A RecA·ssDNA filament searches for homology on the chromosome and, in a process that is controlled by “modulators”, catalyzes strand invasion with the generation of a displacement loop (D-loop). A D-loop resolvase or “resolver” cleaves this intermediate, limited DNA replication restores missing information and a DNA ligase seals the DNA ends. However, if any step fails, the “rescuers” will repair the broken end to rescue chromosomal transformation. If the ssDNA does not share homology with resident DNA, but it contains information for autonomous replication, guardian and mediator proteins catalyze plasmid establishment after inhibition of RecA. DNA replication and ligation reconstitute the molecule (plasmid transformation). In this review, the interacting network that leads to a cross talk between proteins of the uptake and genetic recombination machinery will be placed into prospective. PMID:23046409

Recombinant Protein p30 for Serological Diagnosis of African Swine Fever by Immunoblotting Assay.

PubMed

Kazakova, A S; Imatdinov, I R; Dubrovskaya, O A; Imatdinov, A R; Sidlik, M V; Balyshev, V M; Krasochko, P A; Sereda, A D

2017-10-01

This article is devoted to the development and evaluation of the immunoblotting test system for serological diagnosis of African swine fever (ASF), based on the highly purified recombinant p30 of ASF virus (ASFV) strain Stavropol 01/08 (Stavropol 2008), representative of the ASFV currently circulating in the Russian Federation. The main project stages are as follows: (i) cloning of the central hydrophilic region of the ASFV gene CP204L (p30) into a prokaryotic vector; (ii) expression and chromatographic purification of the recombinant product p30 with thioredoxin and poly-histidine site (p30e1_TrxA_6xHis); (iii) development of the immunoblotting test system (Rec p30-IB) using the highly purified recombinant p30; and (iv) evaluation of Rec p30-IB using sera and organ samples from domestic pigs and wild boars experimentally or naturally infected by ASFV. Testing of the Rec p30-IB showed the diagnostic specificity and sensitivity of the assay to be 98.75% and 100.00%, respectively. High sensitivity of the Rec p30-IB allowed the detection of ASFV-specific antibodies in samples of organs of the immune system and blood sera, collected from domestic pigs and wild boars, starting from 6 to 8 days post-infection, regardless of virus virulence, seroimmunotype and geographic origin of the samples (East Europe, South Europe, West Europe, Central and south-east Africa). © 2016 Blackwell Verlag GmbH.

Relatives with opposite chromosome constitutions, rec(10)dup(10p)inv(10)(p15.1q26.12) and rec(10)dup(10q)inv(10)(p15.1q26.12), due to a familial pericentric inversion.

PubMed

Ciuladaite, Zivile; Preiksaitiene, Egle; Utkus, Algirdas; Kučinskas, Vaidutis

2014-01-01

Large pericentric inversions in chromosome 10 are rare chromosomal aberrations with only few cases of familial inheritance. Such chromosomal rearrangements may lead to production of unbalanced gametes. As a result of a recombination event in the inversion loop, 2 recombinants with duplicated and deficient chromosome segments, including the regions distal to the inversion, may be produced. We report on 2 relatives in a family with opposite terminal chromosomal rearrangements of chromosome 10, i.e. rec(10)dup(10p)inv(10) and rec(10)dup(10q)inv(10), due to familial pericentric inversion inv(10)(p15.1q26.12). Based on array-CGH results, we characterized the exact genomic regions involved and compared the clinical features of both patients with previous reports on similar pericentric inversions and regional differences within 10p and 10q. The fact that both products of recombination are viable indicates a potentially high recurrence risk of unbalanced offspring. This report of unbalanced rearrangements in chromosome 10 in 2 generations confirms the importance of screening for terminal imbalances in patients with idiopathic intellectual disability by molecular cytogenetic techniques such as FISH, MLPA or microarrays. It also underlines the necessity for FISH to define structural characteristics of such cryptic intrachromosomal rearrangements and the underlying cytogenetic mechanisms. © 2014 S. Karger AG, Basel.