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

PubMed Central

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

2010-01-01

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

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

PubMed Central

McClelland, M; Nelson, M; Raschke, E

1994-01-01

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

Type III restriction-modification enzymes: a historical perspective.

PubMed

Rao, Desirazu N; Dryden, David T F; Bheemanaik, Shivakumara

2014-01-01

Restriction endonucleases interact with DNA at specific sites leading to cleavage of DNA. Bacterial DNA is protected from restriction endonuclease cleavage by modifying the DNA using a DNA methyltransferase. Based on their molecular structure, sequence recognition, cleavage position and cofactor requirements, restriction-modification (R-M) systems are classified into four groups. Type III R-M enzymes need to interact with two separate unmethylated DNA sequences in inversely repeated head-to-head orientations for efficient cleavage to occur at a defined location (25-27 bp downstream of one of the recognition sites). Like the Type I R-M enzymes, Type III R-M enzymes possess a sequence-specific ATPase activity for DNA cleavage. ATP hydrolysis is required for the long-distance communication between the sites before cleavage. Different models, based on 1D diffusion and/or 3D-DNA looping, exist to explain how the long-distance interaction between the two recognition sites takes place. Type III R-M systems are found in most sequenced bacteria. Genome sequencing of many pathogenic bacteria also shows the presence of a number of phase-variable Type III R-M systems, which play a role in virulence. A growing number of these enzymes are being subjected to biochemical and genetic studies, which, when combined with ongoing structural analyses, promise to provide details for mechanisms of DNA recognition and catalysis.

A general mixture equation of state for double bonding carboxylic acids with ≥2 association sites

NASA Astrophysics Data System (ADS)

Marshall, Bennett D.

2018-05-01

In this paper, we obtain the first general multi-component solution to Wertheim's thermodynamic perturbation theory for the case that molecules can participate in cyclic double bonds. In contrast to previous authors, we do not restrict double bonding molecules to a 2-site association scheme. Each molecule in a multi-component mixture can have an arbitrary number of donor and acceptor association sites. The one restriction on the theory is that molecules can have at most one pair of double bonding sites. We also incorporate the effect of hydrogen bond cooperativity in cyclic double bonds. We then apply this new association theory to 2-site and 3-site models for carboxylic acids within the polar perturbed chain statistical associating fluid theory equation of state. We demonstrate the accuracy of the approach by comparison to both pure and multi-component phase equilibria data. It is demonstrated that the 3-site association model gives substantially a different hydrogen bonding structure than a 2-site approach. We also demonstrate that inclusion of hydrogen bond cooperativity has a substantial effect on a liquid phase hydrogen bonding structure.

Discrimination of SHV β-Lactamase Genes by Restriction Site Insertion-PCR

PubMed Central

Chanawong, Aroonwadee; M'Zali, Fatima Hannachi; Heritage, John; Lulitanond, Aroonlug; Hawkey, Peter Michael

2001-01-01

Restriction site insertion-PCR (RSI-PCR) is a simple, rapid technique for detection of point mutations. This technique exploits primers with one to three base mismatches near the 3′ end to modulate a restriction site. We have developed this technique to identify described mutations of the blaSHV genes for differentiation of SHV variants that cannot be distinguished easily by other techniques. To validate this method, eight standard strains were used, each producing a different SHV β-lactamase: SHV-1, SHV-2, SHV-3, SHV-4, SHV-5, SHV-6, SHV-8, and SHV-18. Mismatch primers were designed to detect mutations affecting amino acids at positions 8 (SspI), 179 (HinfI), 205 (PstI), 238 (Gly→Ala) (BsrI), and 240 (NruI) of blaSHV genes. All amplimers of the blaSHV genes used in this study yielded the predicted restriction endonuclease digestion products. In addition, this study also makes theoretical identification of blaSHV-6, blaSHV-8, and 12 novel blaSHV variants using the PCR-restriction fragment length polymorphism (RFLP) technique possible. By using a combination of PCR-RFLP and RSI-PCR techniques, up to 27 SHV variants can now be distinguished rapidly and reliably. These simple techniques are readily applied to epidemiological studies of the SHV β-lactamases and may be extended to the characterisation of other resistance determinants. PMID:11408231

Response of estuarine biofilm microbial community development to changes in dissolved oxygen and nutrient concentrations.

PubMed

Nocker, Andreas; Lepo, Joe Eugene; Martin, Linda Lin; Snyder, Richard Allan

2007-10-01

The information content and responsiveness of microbial biofilm community structure, as an integrative indicator of water quality, was assessed against short-term changes in oxygen and nutrient loading in an open-water estuarine setting. Biofilms were grown for 7-day periods on artificial substrates in the Pensacola Bay estuary, Florida, in the vicinity of a wastewater treatment plant (WWTP) outfall and a nearby reference site. Substrates were deployed floating at the surface and near the benthos in 5.4 m of water. Three sampling events covered a 1-month period coincident with declining seasonal WWTP flow and increasing dissolved oxygen (DO) levels in the bottom waters. Biomass accumulation in benthic biofilms appeared to be controlled by oxygen rather than nutrients. The overriding effect of DO was also seen in DNA fingerprints of community structure by terminal restriction fragment length polymorphism (T-RFLP) of amplified 16S rRNA genes. Ribotype diversity in benthic biofilms at both sites dramatically increased during the transition from hypoxic to normoxic. Terminal restriction fragment length polymorphism patterns showed pronounced differences between benthic and surface biofilm communities from the same site in terms of signal type, strength, and diversity, but minor differences between sites. Sequencing of 16S rRNA gene clone libraries from benthic biofilms at the WWTP site suggested that low DO levels favored sulfate-reducing prokaryotes (SRP), which decreased with rising oxygen levels and increasing overall diversity. A 91-bp ribotype in the CfoI-restricted 16S rRNA gene T-RFLP profiles, indicative of SRP, tracked the decrease in relative SRP abundance over time.

Optimizing Restriction Site Placement for Synthetic Genomes

NASA Astrophysics Data System (ADS)

Montes, Pablo; Memelli, Heraldo; Ward, Charles; Kim, Joondong; Mitchell, Joseph S. B.; Skiena, Steven

Restriction enzymes are the workhorses of molecular biology. We introduce a new problem that arises in the course of our project to design virus variants to serve as potential vaccines: we wish to modify virus-length genomes to introduce large numbers of unique restriction enzyme recognition sites while preserving wild-type function by substitution of synonymous codons. We show that the resulting problem is NP-Complete, give an exponential-time algorithm, and propose effective heuristics, which we show give excellent results for five sample viral genomes. Our resulting modified genomes have several times more unique restriction sites and reduce the maximum gap between adjacent sites by three to nine-fold.

Detection of possible restriction sites for type II restriction enzymes in DNA sequences.

PubMed

Gagniuc, P; Cimponeriu, D; Ionescu-Tîrgovişte, C; Mihai, Andrada; Stavarachi, Monica; Mihai, T; Gavrilă, L

2011-01-01

In order to make a step forward in the knowledge of the mechanism operating in complex polygenic disorders such as diabetes and obesity, this paper proposes a new algorithm (PRSD -possible restriction site detection) and its implementation in Applied Genetics software. This software can be used for in silico detection of potential (hidden) recognition sites for endonucleases and for nucleotide repeats identification. The recognition sites for endonucleases may result from hidden sequences through deletion or insertion of a specific number of nucleotides. Tests were conducted on DNA sequences downloaded from NCBI servers using specific recognition sites for common type II restriction enzymes introduced in the software database (n = 126). Each possible recognition site indicated by the PRSD algorithm implemented in Applied Genetics was checked and confirmed by NEBcutter V2.0 and Webcutter 2.0 software. In the sequence NG_008724.1 (which includes 63632 nucleotides) we found a high number of potential restriction sites for ECO R1 that may be produced by deletion (n = 43 sites) or insertion (n = 591 sites) of one nucleotide. The second module of Applied Genetics has been designed to find simple repeats sizes with a real future in understanding the role of SNPs (Single Nucleotide Polymorphisms) in the pathogenesis of the complex metabolic disorders. We have tested the presence of simple repetitive sequences in five DNA sequence. The software indicated exact position of each repeats detected in the tested sequences. Future development of Applied Genetics can provide an alternative for powerful tools used to search for restriction sites or repetitive sequences or to improve genotyping methods.

Digital Biological Converter

DTIC Science & Technology

2013-06-28

of cuts that each fragment should be cut into so the fragments are no greater than a specific length threshold. Additionally, vector sequences and...restriction sites are attached to each fragment while ensuring the restriction sites are unique to each sequence. The vector sequences serve as hooks...for assembly into vector for cloning purposes, and also as primer binding domains for PCR ampl ification. The restriction sites are added to

Deoxyribonucleic acid restriction and modification systems in Salmonella: chromosomally located systems of different serotypes.

PubMed Central

Bullas, L R; Colson, C; Neufeld, B

1980-01-01

With the use of four different phages, Salmonella strains representing 85 different serotypes were examined to determine their restriction-modification phenotype. They fell into one of three groups on this basis: group 1, those which lacked the common LT system; group 2, those in which only the LT system could be recognized; and group 3. those which possessed the LT system and at least one other system shown with some serotypes to be closely linked to serB. The specificity of the serB-linked restriction-modification system was unique for each serotype, but different strains of the same serotype expressed the same specificity. Two of the systems were shown to behave in genetic crosses as functional alleles of the S. typhimurium SB system. It is possible that these serB-linked restriction-modification systems constitute a large multiallelic series of genes extending throughout the Salmonella genus and Escherichia coli. We suggest that the division of the Salmonella into the three restriction-modification groups may be significant in defining a "biological grouping" of the different serotypes within the genus which may ultimately be useful in describing the Salmonella species. From the genetic relatedness between the genes of some of the Salmonella restriction-modification systems with those of the E. coli systems, we deduce that the restriction endonuclases produced by the Salmonella serB-linked systems are of type 1. Determination of the nucleotide sequences of the recognition sites of the restriction endonucleases of selected Salmonella systems should further our understanding of specificity with these enzymes. PMID:6243623

Evaluation of simultaneous binding of Chromomycin A3 to the multiple sites of DNA by the new restriction enzyme assay.

PubMed

Murase, Hirotaka; Noguchi, Tomoharu; Sasaki, Shigeki

2018-06-01

Chromomycin A3 (CMA3) is an aureolic acid-type antitumor antibiotic. CMA3 forms dimeric complexes with divalent cations, such as Mg 2+ , which strongly binds to the GC rich sequence of DNA to inhibit DNA replication and transcription. In this study, the binding property of CMA3 to the DNA sequence containing multiple GC-rich binding sites was investigated by measuring the protection from hydrolysis by the restriction enzymes, AccII and Fnu4HI, for the center of the CGCG site and the 5'-GC↓GGC site, respectively. In contrast to the standard DNase I footprinting method, the DNA substrates are fully hydrolyzed by the restriction enzymes, therefore, the full protection of DNA at all the cleavable sites indicates that CMA3 simultaneously binds to all the binding sites. The restriction enzyme assay has suggested that CMA3 has a high tendency to bind the successive CGCG sites and the CGG repeat. Copyright © 2018 Elsevier Ltd. All rights reserved.

Regional Control of Tumor Growth

PubMed Central

Zaslavsky, Alexander; Chen, Catherine; Grillo, Jenny; Baek, Kwan-Hyuck; Holmgren, Lars; Yoon, Sam S.; Folkman, Judah; Ryeom, Sandra

2010-01-01

Tumors implanted near the scapulae have been shown to grow four-times faster than the same tumors implanted at the iliac crest. While there were marked differences in the vascularization of tumors from these two different sites, the mechanism controlling regional angiogenesis was not identified. Here we demonstrate site-specific growth of intraperitoneal tumor implants in the mouse abdomen. Our data indicate that the angiogenic response of the host differs significantly between the upper and lower sites in the mouse abdomen and reveals that the expansion of tumor mass is restricted at sites with low angiogenic responses such as the bowel mesentery in the lower abdomen. We show that in this model, this suppression of angiogenesis is due to an expression gradient of thrombospondin-1, a potent endogenous angiogenesis inhibitor. Mice with a targeted deletion of thrombospondin-1 no longer demonstrate regional restriction of tumor growth. The physiological relevance of these findings may be seen in patients with peritoneal carcinomatosis, whereby tumors spread within the peritoneal cavity and show differential growth in the upper and lower abdomen. We hypothesize that the difference in tumor growth in these patients may be due to a gradient of thrombospondin-1 expression in stroma. Finally, our studies suggest that upregulation of thrombospondin-1 in tumor cells is one method to suppress the growth of tumors in the upper abdomen. PMID:20736295

Detection of the Single Nucleotide Polymorphism at Position rs2735940 in the Human Telomerase Reverse Transcriptase Gene by the Introduction of a New Restriction Enzyme Site for the PCR-RFLP Assay.

PubMed

Wang, Sihua; Ding, Mingcui; Duan, Xiaoran; Wang, Tuanwei; Feng, Xiaolei; Wang, Pengpeng; Yao, Wu; Wu, Yongjun; Yan, Zhen; Feng, Feifei; Yu, Songcheng; Wang, Wei

2017-09-01

It has been shown that the single nucleotide polymorphism (SNP) of the rs2735940 site in the human telomerase reverse transcriptase ( hTERT ) gene is associated with increased cancer risk. The traditional method to detect SNP genotypes is polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). However, there is a limitation to utilizing PCR-RFLP due to a lack of proper restriction enzyme sites at many polymorphic loci. This study used an improved PCR-RFLP method with a mismatched base for detection of the SNP rs2735940. A new restriction enzyme cutting site was created by created restriction site PCR (CRS-PCR), and in addition, the restriction enzyme Msp I for CRS-PCR was cheaper than other enzymes. We used this novel assay to determine the allele frequencies in 552 healthy Chinese Han individuals, and found the allele frequencies to be 63% for allele C and 37% for allele T In summary, the modified PCR-RFLP can be used to detect the SNP of rs2735940 with low cost and high efficiency. © 2017 by the Association of Clinical Scientists, Inc.

Growth data for 29 elevational transect years from the California study of ponderosa pine

Treesearch

M. Thompson Conkle

1973-01-01

Ponderosa pine progenies from parents restricted in latitude but spanning 7.000 feet of elevation show significant growth differences in plantations at low-, mid-, and high-elevation test sites. At low- and mid-elevation sites tree heights and diameters of progenies from high-elevation parents were the smallest; those from the low-elevation parents, intermediate; and...

'DNA Strider': a 'C' program for the fast analysis of DNA and protein sequences on the Apple Macintosh family of computers.

PubMed Central

Marck, C

1988-01-01

DNA Strider is a new integrated DNA and Protein sequence analysis program written with the C language for the Macintosh Plus, SE and II computers. It has been designed as an easy to learn and use program as well as a fast and efficient tool for the day-to-day sequence analysis work. The program consists of a multi-window sequence editor and of various DNA and Protein analysis functions. The editor may use 4 different types of sequences (DNA, degenerate DNA, RNA and one-letter coded protein) and can handle simultaneously 6 sequences of any type up to 32.5 kB each. Negative numbering of the bases is allowed for DNA sequences. All classical restriction and translation analysis functions are present and can be performed in any order on any open sequence or part of a sequence. The main feature of the program is that the same analysis function can be repeated several times on different sequences, thus generating multiple windows on the screen. Many graphic capabilities have been incorporated such as graphic restriction map, hydrophobicity profile and the CAI plot- codon adaptation index according to Sharp and Li. The restriction sites search uses a newly designed fast hexamer look-ahead algorithm. Typical runtime for the search of all sites with a library of 130 restriction endonucleases is 1 second per 10,000 bases. The circular graphic restriction map of the pBR322 plasmid can be therefore computed from its sequence and displayed on the Macintosh Plus screen within 2 seconds and its multiline restriction map obtained in a scrolling window within 5 seconds. PMID:2832831

76 FR 30027 - Land Disposal Restrictions: Site-Specific Treatment Variance for Hazardous Selenium-Bearing Waste...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-24

... Restrictions: Site-Specific Treatment Variance for Hazardous Selenium-Bearing Waste Treated by U.S. Ecology.... Ecology Nevada in Beatty, Nevada and withdrew an existing site- specific treatment variance issued to... 268.44(o)) by granting a site-specific treatment variance to U.S. Ecology Nevada in Beatty, Nevada and...

Differences in the second internal transcribed spacer of four species of Nematodirus (Nematoda: Molineidae).

PubMed

Newton, L A; Chilton, N B; Beveridge, I; Gasser, R B

1998-02-01

Genetic differences among Nematodirus spathiger, Nematodirus filicollis, Nematodirus helvetianus and Nematodirus battus in the nucleotide sequence of the second internal transcribed spacer (ITS-2) of ribosomal DNA ranged from 3.9 to 24.7%. Pairwise comparisons of their ITS-2 sequences indicated that the most genetically similar species were N. spathiger and N. helvetianus. N. battus was the most genetically distinct species, with differences ranging from 22.8 to 24.7% with respect to the other three species. Some of the nucleotide differences among species provided different endonuclease restriction sites that could be used in restriction fragment length polymorphism studies. The ITS-2 sequence data may prove useful in studies of the systematics of molineid nematodes.

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

PubMed

Tutkus, Marijonas; Sasnauskas, Giedrius; Rutkauskas, Danielis

2017-12-01

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

CO2 and CH4 fluxes in a Spartina salt marsh and brackish Phragmites marsh in Massachusetts

NASA Astrophysics Data System (ADS)

Tang, J.; Wang, F.; Kroeger, K. D.; Gonneea, M. E.

2017-12-01

Coastal salt marshes play an important role in global and regional carbon cycling. Tidally restricted marshes reduce salinity and provide a habitat suitable for Phragmites invasion. We measured greenhouse gas (GHG) emissions (CO2 and CH4) continuously with the eddy covariance method and biweekly with the static chamber method in a Spartina salt marsh and a Phragmites marsh on Cape Cod, Massachusetts, USA. We did not find significant difference in CO2 fluxes between the two sites, but the CH4 fluxes were much higher in the Phragmites site than the Spartina marsh. Temporally, tidal cycles influence the CO2 and CH4 fluxes in both sites. We found that the salt marsh was a significant carbon sink when CO2 and CH4 fluxes were combined. Restoring tidally restricted marshes will significantly reduce CH4 emissions and provide a strong ecosystem carbon service.

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

PubMed Central

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

2017-01-01

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

Evolutionary genomics and HIV restriction factors.

PubMed

Pyndiah, Nitisha; Telenti, Amalio; Rausell, Antonio

2015-03-01

To provide updated insights into innate antiviral immunity and highlight prototypical evolutionary features of well characterized HIV restriction factors. Recently, a new HIV restriction factor, Myxovirus resistance 2, has been discovered and the region/residue responsible for its activity identified using an evolutionary approach. Furthermore, IFI16, an innate immunity protein known to sense several viruses, has been shown to contribute to the defense to HIV-1 by causing cell death upon sensing HIV-1 DNA. Restriction factors against HIV show characteristic signatures of positive selection. Different patterns of accelerated sequence evolution can distinguish antiviral strategies--offense or defence--as well as the level of specificity of the antiviral properties. Sequence analysis of primate orthologs of restriction factors serves to localize functional domains and sites responsible for antiviral action. We use recent discoveries to illustrate how evolutionary genomic analyses help identify new antiviral genes and their mechanisms of action.

Comparison of Methods of Detection of Exceptional Sequences in Prokaryotic Genomes.

PubMed

Rusinov, I S; Ershova, A S; Karyagina, A S; Spirin, S A; Alexeevski, A V

2018-02-01

Many proteins need recognition of specific DNA sequences for functioning. The number of recognition sites and their distribution along the DNA might be of biological importance. For example, the number of restriction sites is often reduced in prokaryotic and phage genomes to decrease the probability of DNA cleavage by restriction endonucleases. We call a sequence an exceptional one if its frequency in a genome significantly differs from one predicted by some mathematical model. An exceptional sequence could be either under- or over-represented, depending on its frequency in comparison with the predicted one. Exceptional sequences could be considered biologically meaningful, for example, as targets of DNA-binding proteins or as parts of abundant repetitive elements. Several methods to predict frequency of a short sequence in a genome, based on actual frequencies of certain its subsequences, are used. The most popular are methods based on Markov chain models. But any rigorous comparison of the methods has not previously been performed. We compared three methods for the prediction of short sequence frequencies: the maximum-order Markov chain model-based method, the method that uses geometric mean of extended Markovian estimates, and the method that utilizes frequencies of all subsequences including discontiguous ones. We applied them to restriction sites in complete genomes of 2500 prokaryotic species and demonstrated that the results depend greatly on the method used: lists of 5% of the most under-represented sites differed by up to 50%. The method designed by Burge and coauthors in 1992, which utilizes all subsequences of the sequence, showed a higher precision than the other two methods both on prokaryotic genomes and randomly generated sequences after computational imitation of selective pressure. We propose this method as the first choice for detection of exceptional sequences in prokaryotic genomes.

Microgravity

NASA Image and Video Library

1998-12-01

Type II restriction enzymes, such as Eco R1 endonulease, present a unique advantage for the study of sequence-specific recognition because they leave a record of where they have been in the form of the cleaved ends of the DNA sites where they were bound. The differential behavior of a sequence -specific protein at sites of differing base sequence is the essence of the sequence-specificity; the core question is how do these proteins discriminate between different DNA sequences especially when the two sequences are very similar. Principal Investigator: Dan Carter/New Century Pharmaceuticals

Protein Crystal Eco R1 Endonulease-DNA Complex

NASA Technical Reports Server (NTRS)

1998-01-01

Type II restriction enzymes, such as Eco R1 endonulease, present a unique advantage for the study of sequence-specific recognition because they leave a record of where they have been in the form of the cleaved ends of the DNA sites where they were bound. The differential behavior of a sequence -specific protein at sites of differing base sequence is the essence of the sequence-specificity; the core question is how do these proteins discriminate between different DNA sequences especially when the two sequences are very similar. Principal Investigator: Dan Carter/New Century Pharmaceuticals

Identification of the "A" genome of finger millet using chloroplast DNA.

PubMed

Hilu, K W

1988-01-01

Finger millet (Eleusine corocana subsp. coracana), an important cereal in East Africa and India, is a tetraploid species with unknown genomic components. A recent cytogenetic study confirmed the direct origin of this millet from the tetraploid E. coracana subsp. africana but questioned Eleusine indica as a genomic donor. Chloroplast (ct) DNA sequence analysis using restriction fragment pattern was used to examine the phylogenetic relationships between E. coracana subsp. coracana (domesticated finger millet), E. coracana subspecies africana (wild finger millet), and E. indica. Eleusine tristachya was included since it is the only other annual diploid species in the genus with a basic chromosome number of x = 9 like finger millet. Eight of the ten restriction endonucleases used had 16 to over 30 restriction sites per genome and were informative. E. coracana subsp. coracana and subsp. africana and E. indica were identical in all the restriction sites surveyed, while the ct genome of E, tristachya differed consistently by at least one mutational event for each restriction enzyme surveyed. This random survey of the ct genomes of these species points out E. indica as one of the genome donors (maternal genome donor) of domesticated finger millet contrary to a previous cytogenetic study. The data also substantiate E. coracana subsp. africana as the progenitor of domesticated finger millet. The disparity between the cytogenetic and the molecular approaches is discussed in light of the problems associated with chromosome pairing and polyploidy.

Alteration of gene expression by restriction enzymes electroporated into plant cells.

PubMed

Ashraf, M; Altschuler, M; Galasinski, S; Griffiths, T D

1993-06-01

The alteration in the expression of a beta-glucuronidase (GUS) reporter gene was used to monitor the effect of restriction endonucleases electroporated into the tobacco (Nicotiana tabacum L.) protoplasts. Restriction enzyme (RE) Hind III which does not have a recognition site within the gene cassette, had little effect on enzyme activity. In contrast restriction endonucleases Hae III and Sau3A1 which possess 8 and 16 recognition sites in the GUS cassette, were found to reduce the enzyme activity by 89% and 94% respectively when compared to control electroporations. Restriction-site mutation analysis (RSM) and Southern blot analysis indicated the enzymatic degradation of GUS coding sequence by the REs Hae III and Sau3A1. Results of this study suggest that on electroporation, REs can enter into plant cells and alter the expression of the GUS gene. The alteration of gene expression is thus correlated with the digestion of GUS template DNA. Future applications of this technique could include addressing fundamental questions with regard to DNA repair, site-specific recombination, identifying mutations, insertional mutagenesis, enhancement of stable transformation and gene tagging in plants.

Public opinion on nutrition-related policies to combat child obesity, Los Angeles County, 2011.

PubMed

Simon, Paul A; Chiang, Choiyuk; Lightstone, Amy S; Shih, Margaret

2014-06-05

We assessed public opinion on nutrition-related policies to address child obesity: a soda tax, restrictions on advertising unhealthy foods and beverages to children, and restrictions on siting fast food restaurants and convenience stores near schools. We analyzed data from 998 adults (aged ≥18 years) in the 2011 Los Angeles County Health Survey. Support was highest for advertising restrictions (74%), intermediate for a soda tax (60%), and lowest for siting restrictions on fast food restaurants and convenience stores (44% and 37%, respectively). Support for food and beverage advertising restrictions and soda taxation is promising for future policy efforts to address child obesity.

Restrictions on surgical resident shift length does not impact type of medical errors.

PubMed

Anderson, Jamie E; Goodman, Laura F; Jensen, Guy W; Salcedo, Edgardo S; Galante, Joseph M

2017-05-15

In 2011, resident duty hours were restricted in an attempt to improve patient safety and resident education. With the goal of reducing fatigue, shorter shift length leads to more patient handoffs, raising concerns about adverse effects on patient safety. This study seeks to determine whether differences in duty-hour restrictions influence types of errors made by residents. This is a nested retrospective cohort study at a surgery department in an academic medical center. During 2013-14, standard 2011 duty hours were in place for residents. In 2014-15, duty-hour restrictions at the study site were relaxed ("flexible") with no restrictions on shift length. We reviewed all morbidity and mortality submissions from July 1, 2013-June 30, 2015 and compared differences in types of errors between these periods. A total of 383 patients experienced adverse events, including 59 deaths (15.4%). Comparing standard versus flexible periods, there was no difference in mortality (15.7% versus 12.6%, P = 0.479) or complication rates (2.6% versus 2.5%, P = 0.696). There was no difference in types of errors between periods (P = 0.050-0.808). The most number of errors were due to cognitive failures (229, 59.6%), whereas the fewest number of errors were due to team failure (127, 33.2%). By subset, technical errors resulted in the highest number of errors (169, 44.1%). There were no differences between types of errors of cases that were nonelective, at night, or involving residents. Among adverse events reported in this departmental surgical morbidity and mortality, there were no differences in types of errors when resident duty hours were less restrictive. Copyright © 2017 Elsevier Inc. All rights reserved.

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

PubMed Central

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

2009-01-01

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

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

PubMed Central

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

1985-01-01

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

Brownfield to Brightfield Initiative in Oak Ridge, TN - 12346

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

Hough, Gil; Fairless, Chad

Experience characterizing, permitting, and restoring 'Brownfield' sites-government or industrial sites with restricted future use due to the presence or potential presence of hazardous substances, pollutants, or contaminants-is being leveraged to identify opportunities for redevelopment into solar power generating facilities which, in this context, are called 'Brightfields'. Brownfield sites offer the expansive land necessary for large photovoltaic (PV) solar farms, but require an in-depth working knowledge of complicated regulatory restrictions and environmental constraints to develop them. As a part of the effort to identify opportunities for redevelopment of Brownfield sites for solar applications, a technical guide, was composed specifically for themore » development of solar generation on restricted use sites. The basis of the technical guide gives specific consideration to environmental requirements and installation methods breaking that into three areas for assessing: 1) levels of contamination, 2) ground penetration requirements, and 3) the requirements for aesthetics and maintenance. Brightfield projects are underway to support the technical guide and expand re-industrialization efforts for the former DOE Gaseous Diffusion Plant in Oak Ridge, TN. There are exciting opportunities to turn Brownfields into Brightfield solar energy solutions for meeting the future renewable energy needs of our country. Brownfields that offer the large surface area required for solar PV farms coupled with the technical guide for the installation of solar farms on restricted use sites supports efforts to develop the solar capacities and expertise to tap this future market. The initial projects designed following the technical guide will provide verification of the installation requirements and beneficial reuse of restricted use sites. (authors)« less

Global methylation screening in the Arabidopsis thaliana and Mus musculus genome: applications of virtual image restriction landmark genomic scanning (Vi-RLGS)

PubMed Central

Matsuyama, Tomoki; Kimura, Makoto T.; Koike, Kuniaki; Abe, Tomoko; Nakano, Takeshi; Asami, Tadao; Ebisuzaki, Toshikazu; Held, William A.; Yoshida, Shigeo; Nagase, Hiroki

2003-01-01

Understanding the role of ‘epigenetic’ changes such as DNA methylation and chromatin remodeling has now become critical in understanding many biological processes. In order to delineate the global methylation pattern in a given genomic DNA, computer software has been developed to create a virtual image of restriction landmark genomic scanning (Vi-RLGS). When using a methylation- sensitive enzyme such as NotI as the restriction landmark, the comparison between real and in silico RLGS profiles of the genome provides a methylation map of genomic NotI sites. A methylation map of the Arabidopsis genome was created that could be confirmed by a methylation-sensitive PCR assay. The method has also been applied to the mouse genome. Although a complete methylation map has not been completed, a region of methylation difference between two tissues has been tested and confirmed by bisulfite sequencing. Vi-RLGS in conjunction with real RLGS will make it possible to develop a more complete map of genomic sites that are methylated or demethylated as a consequence of normal or abnormal development. PMID:12888509

Comprehensive restriction enzyme lists to update any DNA sequence computer program.

PubMed

Raschke, E

1993-04-01

Restriction enzyme lists are presented for the practical working geneticist to update any DNA computer program. These lists combine formerly scattered information and contain all presently known restriction enzymes with a unique recognition sequence, a cut site, or methylation (in)sensitivity. The lists are in the shortest possible form to also be functional with small DNA computer programs, and will produce clear restriction maps without any redundancy or loss of information. The lists discern between commercial and noncommercial enzymes, and prototype enzymes and different isoschizomers are cross-referenced. Differences in general methylation sensitivities and (in)sensitivities against Dam and Dcm methylases of Escherichia coli are indicated. Commercial methylases and intron-encoded endonucleases are included. An address list is presented to contact commercial suppliers. The lists are constantly updated and available in electronic form as pure US ASCII files, and in formats for the DNA computer programs DNA-Strider for Apple Macintosh, and DNAsis for IBM personal computers or compatibles via e-mail from the internet address: NETSERV@EMBL-HEIDELBERG.DE by sending only the message HELP RELIBRARY.

Mannan-Binding Lectin Is Involved in the Protection against Renal Ischemia/Reperfusion Injury by Dietary Restriction

PubMed Central

Shushimita, Shushimita; van der Pol, Pieter; W.F. de Bruin, Ron; N. M. Ijzermans, Jan; van Kooten, Cees; Dor, Frank J. M. F.

2015-01-01

Preoperative fasting and dietary restriction offer robust protection against renal ischemia/reperfusion injury (I/RI) in mice. We recently showed that Mannan-binding lectin (MBL), the initiator of the lectin pathway of complement activation, plays a pivotal role in renal I/RI. Based on these findings, we investigated the effect of short-term DR (30% reduction of total food intake) or three days of water only fasting on MBL in 10–12 weeks old male C57/Bl6 mice. Both dietary regimens significantly reduce the circulating levels of MBL as well as its mRNA expression in liver, the sole production site of MBL. Reconstitution of MBL abolished the protection afforded by dietary restriction, whereas in the fasting group the protection persisted. These data show that modulation of MBL is involved in the protection against renal I/RI induced by dietary restriction, and suggest that the mechanisms of protection induced by dietary restriction and fasting may be different. PMID:26367533

Evolutionary Pressure on Mitochondrial Cytochrome b Is Consistent with a Role of CytbI7T Affecting Longevity during Caloric Restriction

PubMed Central

Beckstead, Wesley A.; Ebbert, Mark T. W.; Rowe, Mark J.; McClellan, David A.

2009-01-01

Background Metabolism of energy nutrients by the mitochondrial electron transport chain (ETC) is implicated in the aging process. Polymorphisms in core ETC proteins may have an effect on longevity. Here we investigate the cytochrome b (cytb) polymorphism at amino acid 7 (cytbI7T) that distinguishes human mitochondrial haplogroup H from haplogroup U. Principal Findings We compared longevity of individuals in these two haplogroups during historical extremes of caloric intake. Haplogroup H exhibits significantly increased longevity during historical caloric restriction compared to haplogroup U (p = 0.02) while during caloric abundance they are not different. The historical effects of natural selection on the cytb protein were estimated with the software TreeSAAP using a phylogenetic reconstruction for 107 mammal taxa from all major mammalian lineages using 13 complete protein-coding mitochondrial gene sequences. With this framework, we compared the biochemical shifts produced by cytbI7T with historical evolutionary pressure on and near this polymorphic site throughout mammalian evolution to characterize the role cytbI7T had on the ETC during times of restricted caloric intake. Significance Our results suggest the relationship between caloric restriction and increased longevity in human mitochondrial haplogroup H is determined by cytbI7T which likely enhances the ability of water to replenish the Qi binding site and decreases the time ubisemiquinone is at the Qo site, resulting in a decrease in the average production rate of radical oxygen species (ROS). PMID:19503808

DNA cleavage site selection by Type III restriction enzymes provides evidence for head-on protein collisions following 1D bidirectional motion

PubMed Central

Schwarz, Friedrich W.; van Aelst, Kara; Tóth, Júlia; Seidel, Ralf; Szczelkun, Mark D.

2011-01-01

DNA cleavage by the Type III Restriction–Modification enzymes requires communication in 1D between two distant indirectly-repeated recognitions sites, yet results in non-specific dsDNA cleavage close to only one of the two sites. To test a recently proposed ATP-triggered DNA sliding model, we addressed why one site is selected over another during cleavage. We examined the relative cleavage of a pair of identical sites on DNA substrates with different distances to a free or protein blocked end, and on a DNA substrate using different relative concentrations of protein. Under these conditions a bias can be induced in the cleavage of one site over the other. Monte-Carlo simulations based on the sliding model reproduce the experimentally observed behaviour. This suggests that cleavage site selection simply reflects the dynamics of the preceding stochastic enzyme events that are consistent with bidirectional motion in 1D and DNA cleavage following head-on protein collision. PMID:21724613

Atomic layer deposition overcoating: tuning catalyst selectivity for biomass conversion.

PubMed

Zhang, Hongbo; Gu, Xiang-Kui; Canlas, Christian; Kropf, A Jeremy; Aich, Payoli; Greeley, Jeffrey P; Elam, Jeffrey W; Meyers, Randall J; Dumesic, James A; Stair, Peter C; Marshall, Christopher L

2014-11-03

The terraces, edges, and facets of nanoparticles are all active sites for heterogeneous catalysis. These different active sites may cause the formation of various products during the catalytic reaction. Here we report that the step sites of Pd nanoparticles (NPs) can be covered precisely by the atomic layer deposition (ALD) method, whereas the terrace sites remain as active component for the hydrogenation of furfural. Increasing the thickness of the ALD-generated overcoats restricts the adsorption of furfural onto the step sites of Pd NPs and increases the selectivity to furan. Furan selectivities and furfural conversions are linearly correlated for samples with or without an overcoating, though the slopes differ. The ALD technique can tune the selectivity of furfural hydrogenation over Pd NPs and has improved our understanding of the reaction mechanism. The above conclusions are further supported by density functional theory (DFT) calculations. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

10 CFR 862.6 - Voluntary minimum altitude.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 4 2011-01-01 2011-01-01 false Voluntary minimum altitude. 862.6 Section 862.6 Energy DEPARTMENT OF ENERGY RESTRICTIONS ON AIRCRAFT LANDING AND AIR DELIVERY AT DEPARTMENT OF ENERGY NUCLEAR SITES... designated site. Applicable FAA prohibitions or restrictions take precedence over this voluntary minimum...

Right Filter for the Wrong Addresses: Regulating Net Access.

ERIC Educational Resources Information Center

Simpson, Carol

1996-01-01

Guides librarians in evaluating "filtering" software which schools may purchase for restricting access to potentially inappropriate Internet sites. This article discusses the workings of filtering programs and practical and ethical questions such as: how sites are restricted, who decides, and whether transactions are monitored.…

Identification of the ``a'' Genome of Finger Millet Using Chloroplast DNA

PubMed Central

Hilu, K. W.

1988-01-01

Finger millet (Eleusine corocana subsp. coracana), an important cereal in East Africa and India, is a tetraploid species with unknown genomic components. A recent cytogenetic study confirmed the direct origin of this millet from the tetraploid E. coracana subsp. africana but questioned Eleusine indica as a genomic donor. Chloroplast (ct) DNA sequence analysis using restriction fragment pattern was used to examine the phylogenetic relationships between E. coracana subsp. coracana (domesticated finger millet), E. coracana subspecies africana (wild finger millet), and E. indica. Eleusine tristachya was included since it is the only other annual diploid species in the genus with a basic chromosome number of x = 9 like finger millet. Eight of the ten restriction endonucleases used had 16 to over 30 restriction sites per genome and were informative. E. coracana subsp. coracana and subsp. africana and E. indica were identical in all the restriction sites surveyed, while the ct genome of E. tristachya differed consistently by at least one mutational event for each restriction enzyme surveyed. This random survey of the ct genomes of these species points out E. indica as one of the genome donors (maternal genome donor) of domesticated finger millet contrary to a previous cytogenetic study. The data also substantiate E. coracana subsp. africana as the progenitor of domesticated finger millet. The disparity between the cytogenetic and the molecular approaches is discussed in light of the problems associated with chromosome pairing and polyploidy. PMID:8608927

Secure Web-Site Access with Tickets and Message-Dependent Digests

USGS Publications Warehouse

Donato, David I.

2008-01-01

Although there are various methods for restricting access to documents stored on a World Wide Web (WWW) site (a Web site), none of the widely used methods is completely suitable for restricting access to Web applications hosted on an otherwise publicly accessible Web site. A new technique, however, provides a mix of features well suited for restricting Web-site or Web-application access to authorized users, including the following: secure user authentication, tamper-resistant sessions, simple access to user state variables by server-side applications, and clean session terminations. This technique, called message-dependent digests with tickets, or MDDT, maintains secure user sessions by passing single-use nonces (tickets) and message-dependent digests of user credentials back and forth between client and server. Appendix 2 provides a working implementation of MDDT with PHP server-side code and JavaScript client-side code.

Terminal Restriction Fragment Length Polymorphism Analysis Program, a Web-Based Research Tool for Microbial Community Analysis

PubMed Central

Marsh, Terence L.; Saxman, Paul; Cole, James; Tiedje, James

2000-01-01

Rapid analysis of microbial communities has proven to be a difficult task. This is due, in part, to both the tremendous diversity of the microbial world and the high complexity of many microbial communities. Several techniques for community analysis have emerged over the past decade, and most take advantage of the molecular phylogeny derived from 16S rRNA comparative sequence analysis. We describe a web-based research tool located at the Ribosomal Database Project web site (http://www.cme.msu.edu/RDP/html/analyses.html) that facilitates microbial community analysis using terminal restriction fragment length polymorphism of 16S ribosomal DNA. The analysis function (designated TAP T-RFLP) permits the user to perform in silico restriction digestions of the entire 16S sequence database and derive terminal restriction fragment sizes, measured in base pairs, from the 5′ terminus of the user-specified primer to the 3′ terminus of the restriction endonuclease target site. The output can be sorted and viewed either phylogenetically or by size. It is anticipated that the site will guide experimental design as well as provide insight into interpreting results of community analysis with terminal restriction fragment length polymorphisms. PMID:10919828

Problem-Solving Test: Restriction Endonuclease Mapping

ERIC Educational Resources Information Center

Szeberenyi, Jozsef

2011-01-01

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

30 CFR 56.9306 - Warning devices for restricted clearances.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 30 Mineral Resources 1 2012-07-01 2012-07-01 false Warning devices for restricted clearances. 56... Loading and Dumping Sites § 56.9306 Warning devices for restricted clearances. Where restricted clearance creates a hazard to persons on mobile equipment, warning devices shall be installed in advance of the...

30 CFR 57.9306 - Warning devices for restricted clearances.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 30 Mineral Resources 1 2014-07-01 2014-07-01 false Warning devices for restricted clearances. 57... Loading and Dumping Sites § 57.9306 Warning devices for restricted clearances. Where restricted clearance creates a hazard to persons on mobile equipment, warning devices shall be installed in advance of the...

30 CFR 56.9306 - Warning devices for restricted clearances.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 30 Mineral Resources 1 2014-07-01 2014-07-01 false Warning devices for restricted clearances. 56... Loading and Dumping Sites § 56.9306 Warning devices for restricted clearances. Where restricted clearance creates a hazard to persons on mobile equipment, warning devices shall be installed in advance of the...

30 CFR 57.9306 - Warning devices for restricted clearances.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 30 Mineral Resources 1 2012-07-01 2012-07-01 false Warning devices for restricted clearances. 57... Loading and Dumping Sites § 57.9306 Warning devices for restricted clearances. Where restricted clearance creates a hazard to persons on mobile equipment, warning devices shall be installed in advance of the...

30 CFR 57.9306 - Warning devices for restricted clearances.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Warning devices for restricted clearances. 57... Loading and Dumping Sites § 57.9306 Warning devices for restricted clearances. Where restricted clearance creates a hazard to persons on mobile equipment, warning devices shall be installed in advance of the...

30 CFR 57.9306 - Warning devices for restricted clearances.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Warning devices for restricted clearances. 57... Loading and Dumping Sites § 57.9306 Warning devices for restricted clearances. Where restricted clearance creates a hazard to persons on mobile equipment, warning devices shall be installed in advance of the...

30 CFR 56.9306 - Warning devices for restricted clearances.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Warning devices for restricted clearances. 56... Loading and Dumping Sites § 56.9306 Warning devices for restricted clearances. Where restricted clearance creates a hazard to persons on mobile equipment, warning devices shall be installed in advance of the...

30 CFR 56.9306 - Warning devices for restricted clearances.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 30 Mineral Resources 1 2013-07-01 2013-07-01 false Warning devices for restricted clearances. 56... Loading and Dumping Sites § 56.9306 Warning devices for restricted clearances. Where restricted clearance creates a hazard to persons on mobile equipment, warning devices shall be installed in advance of the...

30 CFR 57.9306 - Warning devices for restricted clearances.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 30 Mineral Resources 1 2013-07-01 2013-07-01 false Warning devices for restricted clearances. 57... Loading and Dumping Sites § 57.9306 Warning devices for restricted clearances. Where restricted clearance creates a hazard to persons on mobile equipment, warning devices shall be installed in advance of the...

30 CFR 56.9306 - Warning devices for restricted clearances.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Warning devices for restricted clearances. 56... Loading and Dumping Sites § 56.9306 Warning devices for restricted clearances. Where restricted clearance creates a hazard to persons on mobile equipment, warning devices shall be installed in advance of the...

SfiI genomic cleavage map of Escherichia coli K-12 strain MG1655.

PubMed Central

Perkins, J D; Heath, J D; Sharma, B R; Weinstock, G M

1992-01-01

An SfiI restriction map of Escherichia coli K-12 strain MG1655 is presented. The map contains thirty-one cleavage sites separating fragments ranging in size from 407 kb to 3.7 kb. Several techniques were used in the construction of this map, including CHEF pulsed field gel electrophoresis; physical analysis of a set of twenty-six auxotrophic transposon insertions; correlation with the restriction map of Kohara and coworkers using the commercially available E. coli Gene Mapping Membranes; analysis of publicly available sequence information; and correlation of the above data with the combined genetic and physical map developed by Rudd, et al. The combination of these techniques has yielded a map in which all but one site can be localized within a range of +/- 2 kb, and over half the sites can be localized precisely by sequence data. Two sites present in the EcoSeq5 sequence database are not cleaved in MG1655 and four sites are noted to be sensitive to methylation by the dcm methylase. This map, combined with the NotI physical map of MG1655, can aid in the rapid, precise mapping of several different types of genetic alterations, including transposon mediated mutations and other insertions, inversions, deletions and duplications. Images PMID:1312707

5-Methyldeoxycytidine in the Physarum minichromosome containing the ribosomal RNA genes.

PubMed Central

Cooney, C A; Matthews, H R; Bradbury, E M

1984-01-01

5-Methyldeoxycytidine (5MC) was analyzed by high pressure liquid chromatography (HPLC) and by restriction enzyme digestion in rDNA isolated from Physarum polycephalum. rDNA from Physarum M3C strain microplasmodia has a significant 5MC content (about half that of the whole genomic DNA). This rDNA contains many C5MCGG sites because it is clearly digested further by Msp I than by Hpa II. However, most 5MC is in other sites. In particular, alternating CG sequences appear to be highly methylated. HPLC of deoxyribonucleosides shows tha most of the transcribed regions contain little or no 5MC. Restriction digestion indicates that there is little or no 5MC in any of the transcribed regions including the transcription origin and adjacent sequences. Over 90% of the total 5MC is in or near the central nontranscribed spacer and most methylated restriction sites are in inverted repeats of this spacer. rDNA is very heterogeneous with respect to 5MC. The 5MC pattern doesn't appear to change with inactivation of the rRNA genes during reversible differentiation from microplasmodia (growing) to microsclerotia (dormant), showing that inactivation is due to changes in other chromatin variables. The 5MC pattern is different between Physarum strains. The possible involvement of this 5MC in rDNA chromatin structure and in cruciform and Z-DNA formation is discussed. Images PMID:6322108

Polarity of recombination in transformation of Streptococcus pneumoniae

PubMed Central

Pasta, Franck; Sicard, Michel A.

1999-01-01

In transformation of Streptococcus pneumoniae DNA enters the cell as single-strand fragments and integrates into the chromosome by homologous recombination. Deletions and insertions of a few hundred base pairs frequently stop the recombination process of a donor strand. In this work we took advantage of such interruptions of recombination to compare the transformation efficiencies of the segments 5′- and 3′-ward from a deletion. The deletion was created in the center of a fragment of the ami locus, and sites around the deletion were labeled by a frameshift generating a restriction site. Heteroduplexes were constructed containing two restriction sites on one strand and two different ones on the complementary strand. ami+ bacteria were transformed with such heteroduplexes. ami− transformants were isolated and individually underwent amplification of the transformed ami region. We have obtained two kinds of amplification products: short when the deletion was integrated, long when recombination stops at the deletion. Each long fragment was tested by the four restriction enzymes to detect which strand and which side of the deletion had recombined. We found that 80% of the cuts were located 5′ to the deletion, showing that, in vivo, the 5′ side is strongly favored by recombination. Further results suggest that exchanges occurring from 5′ to 3′ relative to the donor strand are more efficient than in the opposite direction, thus accounting for the 5′ preference. PMID:10077616

Polarity of recombination in transformation of Streptococcus pneumoniae.

PubMed

Pasta, F; Sicard, M A

1999-03-16

In transformation of Streptococcus pneumoniae DNA enters the cell as single-strand fragments and integrates into the chromosome by homologous recombination. Deletions and insertions of a few hundred base pairs frequently stop the recombination process of a donor strand. In this work we took advantage of such interruptions of recombination to compare the transformation efficiencies of the segments 5'- and 3'-ward from a deletion. The deletion was created in the center of a fragment of the ami locus, and sites around the deletion were labeled by a frameshift generating a restriction site. Heteroduplexes were constructed containing two restriction sites on one strand and two different ones on the complementary strand. ami+ bacteria were transformed with such heteroduplexes. ami- transformants were isolated and individually underwent amplification of the transformed ami region. We have obtained two kinds of amplification products: short when the deletion was integrated, long when recombination stops at the deletion. Each long fragment was tested by the four restriction enzymes to detect which strand and which side of the deletion had recombined. We found that 80% of the cuts were located 5' to the deletion, showing that, in vivo, the 5' side is strongly favored by recombination. Further results suggest that exchanges occurring from 5' to 3' relative to the donor strand are more efficient than in the opposite direction, thus accounting for the 5' preference.

Leaf margin phenotype-specific restriction-site-associated DNA-derived markers for pineapple (Ananas comosus L.)

PubMed Central

Urasaki, Naoya; Goeku, Satoko; Kaneshima, Risa; Takamine, Tomonori; Tarora, Kazuhiko; Takeuchi, Makoto; Moromizato, Chie; Yonamine, Kaname; Hosaka, Fumiko; Terakami, Shingo; Matsumura, Hideo; Yamamoto, Toshiya; Shoda, Moriyuki

2015-01-01

To explore genome-wide DNA polymorphisms and identify DNA markers for leaf margin phenotypes, a restriction-site-associated DNA sequencing analysis was employed to analyze three bulked DNAs of F1 progeny from a cross between a ‘piping-leaf-type’ cultivar, ‘Yugafu’, and a ‘spiny-tip-leaf-type’ variety, ‘Yonekura’. The parents were both Ananas comosus var. comosus. From the analysis, piping-leaf and spiny-tip-leaf gene-specific restriction-site-associated DNA sequencing tags were obtained and designated as PLSTs and STLSTs, respectively. The five PLSTs and two STSLTs were successfully converted to cleaved amplified polymorphic sequence (CAPS) or simple sequence repeat (SSR) markers using the sequence differences between alleles. Based on the genotyping of the F1 with two SSR and three CAPS markers, the five PLST markers were mapped in the vicinity of the P locus, with the closest marker, PLST1_SSR, being located 1.5 cM from the P locus. The two CAPS markers from STLST1 and STLST3 perfectly assessed the ‘spiny-leaf type’ as homozygotes of the recessive s allele of the S gene. The recombination value between the S locus and STLST loci was 2.4, and STLSTs were located 2.2 cM from the S locus. SSR and CAPS markers are applicable to marker-assisted selection of leaf margin phenotypes in pineapple breeding. PMID:26175625

Leaf margin phenotype-specific restriction-site-associated DNA-derived markers for pineapple (Ananas comosus L.).

PubMed

Urasaki, Naoya; Goeku, Satoko; Kaneshima, Risa; Takamine, Tomonori; Tarora, Kazuhiko; Takeuchi, Makoto; Moromizato, Chie; Yonamine, Kaname; Hosaka, Fumiko; Terakami, Shingo; Matsumura, Hideo; Yamamoto, Toshiya; Shoda, Moriyuki

2015-06-01

To explore genome-wide DNA polymorphisms and identify DNA markers for leaf margin phenotypes, a restriction-site-associated DNA sequencing analysis was employed to analyze three bulked DNAs of F1 progeny from a cross between a 'piping-leaf-type' cultivar, 'Yugafu', and a 'spiny-tip-leaf-type' variety, 'Yonekura'. The parents were both Ananas comosus var. comosus. From the analysis, piping-leaf and spiny-tip-leaf gene-specific restriction-site-associated DNA sequencing tags were obtained and designated as PLSTs and STLSTs, respectively. The five PLSTs and two STSLTs were successfully converted to cleaved amplified polymorphic sequence (CAPS) or simple sequence repeat (SSR) markers using the sequence differences between alleles. Based on the genotyping of the F1 with two SSR and three CAPS markers, the five PLST markers were mapped in the vicinity of the P locus, with the closest marker, PLST1_SSR, being located 1.5 cM from the P locus. The two CAPS markers from STLST1 and STLST3 perfectly assessed the 'spiny-leaf type' as homozygotes of the recessive s allele of the S gene. The recombination value between the S locus and STLST loci was 2.4, and STLSTs were located 2.2 cM from the S locus. SSR and CAPS markers are applicable to marker-assisted selection of leaf margin phenotypes in pineapple breeding.

Sanitation, Stress, and Life Stage: A Systematic Data Collection Study among Women in Odisha, India.

PubMed

Hulland, Kristyna R S; Chase, Rachel P; Caruso, Bethany A; Swain, Rojalin; Biswal, Bismita; Sahoo, Krushna Chandra; Panigrahi, Pinaki; Dreibelbis, Robert

2015-01-01

Emerging evidence demonstrates how inadequate access to water and sanitation is linked to psychosocial stress, especially among women, forcing them to navigate social and physical barriers during their daily sanitation routines. We examine sanitation-related psychosocial stress (SRPS) across women's reproductive lives in three distinct geographic sites (urban slums, rural villages, and rural tribal villages) in Odisha, India. We explored daily sanitation practices of adolescent, newly married, pregnant, and established adult women (n = 60) and identified stressors encountered during sanitation. Responding to structured data collection methods, women ranked seven sanitation activities (defecation, urination, menstruation, bathing, post-defecation cleaning, carrying water, and changing clothes) based on stress (high to low) and level of freedom (associated with greatest freedom to having the most restrictions). Women then identified common stressors they encountered when practicing sanitation and sorted stressors in constrained piles based on frequency and severity of each issue. The constellation of factors influencing SRPS varies by life stage and location. Overall, sanitation behaviors that were most restricted (i.e., menstruation) were the most stressful. Women in different sites encountered different stressors, and the level of perceived severity varied based on site and life stage. Understanding the influence of place and life stage on SRPS provides a nuanced understanding of sanitation, and may help identify areas for intervention.

77 FR 50622 - Land Disposal Restrictions: Site-Specific Treatment Variance for Hazardous Selenium-Bearing Waste...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-22

... Restrictions: Site-Specific Treatment Variance for Hazardous Selenium-Bearing Waste Treated by U.S. Ecology... program, to U.S. Ecology Nevada in Beatty, Nevada for the treatment of a hazardous selenium- bearing waste.... Ecology Nevada located in Beatty, Nevada. B. Table of Contents I. Background [[Page 50623

Assessment of association of D3 dopamine receptor MscI polymorphism with schizophrenia: Analysis of symptom ratings, family history, age at onset, and movement disorders

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

Gaitonde, E.J.; Mollon, J.D.; McKenna, P.J.

Several studies have reported an association between schizophrenia and homozygosity for the MscI restriction site in exon 1 of the D3 dopamine receptor gene, but other studies have failed to find this association. Recent reports have suggested that the association is most salient in male patients with a family history of schizophrenia. We examined this restriction site in a group of schizophrenic patients (n = 84) and in normal controls (n = 77). Patients were subdivided according to demographic and clinical features, particular attention being paid to movement disorders. No significant difference in allelic or genotypic distribution was seen betweenmore » the two groups. No association was seen between homozygosity and a positive family history, age at onset of illness, clinical subtype, negative symptom score, or movement disorder scores. 33 refs., 2 tabs.« less

Mapping DNA cleavage by the Type ISP restriction-modification enzymes following long-range communication between DNA sites in different orientations

PubMed Central

van Aelst, Kara; Saikrishnan, Kayarat; Szczelkun, Mark D.

2015-01-01

The prokaryotic Type ISP restriction-modification enzymes are single-chain proteins comprising an Mrr-family nuclease, a superfamily 2 helicase-like ATPase, a coupler domain, a methyltransferase, and a DNA-recognition domain. Upon recognising an unmodified DNA target site, the helicase-like domain hydrolyzes ATP to cause site release (remodeling activity) and to then drive downstream translocation consuming 1–2 ATP per base pair (motor activity). On an invading foreign DNA, double-strand breaks are introduced at random wherever two translocating enzymes form a so-called collision complex following long-range communication between a pair of target sites in inverted (head-to-head) repeat. Paradoxically, structural models for collision suggest that the nuclease domains are too far apart (>30 bp) to dimerise and produce a double-strand DNA break using just two strand-cleavage events. Here, we examined the organisation of different collision complexes and how these lead to nuclease activation. We mapped DNA cleavage when a translocating enzyme collides with a static enzyme bound to its site. By following communication between sites in both head-to-head and head-to-tail orientations, we could show that motor activity leads to activation of the nuclease domains via distant interactions of the helicase or MTase-TRD. Direct nuclease dimerization is not required. To help explain the observed cleavage patterns, we also used exonuclease footprinting to demonstrate that individual Type ISP domains can swing off the DNA. This study lends further support to a model where DNA breaks are generated by multiple random nicks due to mobility of a collision complex with an overall DNA-binding footprint of ∼30 bp. PMID:26507855

The association between measurement sites of visceral adipose tissue and cardiovascular risk factors after caloric restriction in obese Korean women.

PubMed

Lee, Hye-Ok; Yim, Jung-Eun; Lee, Jeong-Sook; Kim, Young-Seol; Choue, Ryowon

2013-02-01

Quantities as well as distributions of adipose tissue (AT) are significantly related to cardiovascular disease (CVD) risk factors and can be altered with caloric restriction. This study investigated which cross-sectional slice location of AT is most strongly correlated with changes in CVD risk factors after caloric restriction in obese Korean women. Thirty-three obese pre-menopausal Korean women (32.4 ± 8.5 yrs, BMI 27.1 ± 2.3 kg/m(2)) participated in a 12 weeks caloric restriction program. Subcutaneous adipose tissue (SAT) and visceral adipose tissue (VAT) were measured using computed tomography (CT) scans at the sites of L2-L3, L3-L4, and L4-L5. Fasting serum levels of glucose, insulin, triglyceride, total cholesterol (TC), low density lipoprotein cholesterol (LDL-C), high density lipoprotein cholesterol (HDL-C), leptin and homeostasis model assessment-insulin resistance (HOMA-IR) were observed. Pearson's partial correlation coefficients were used to assess the relationship between AT measurement sites and changes in CVD risk factors after calorie restriction. When calories were reduced by 350 kcal/day for 12 weeks, body weight (-2.7%), body fat mass (-8.2%), and waist circumference (-5.8%) all decreased (P < 0.05). In addition, following caloric restriction, serum levels of glucose (-4.6%), TC (-6.2%), LDL-C (-5.3%), leptin (-17.6%) and HOMA-IR (-18.2%) decreased significantly (P < 0.05) as well. Changes in VAT at the level of L3-L4 were significantly greater than those at other abdominal sites, and these changes were correlated with changes in TC (P < 0.05), LDL-C (P < 0.001), SBP (P < 0.001) and HOMA-IR (P < 0.01). These results show that VAT at L3-L4 had a stronger correlation with CVD risk factors than with other AT measurement sites after caloric restriction.

Eastern and Central Kansas Country Schools. Country School Legacy: Humanities on the Frontier.

ERIC Educational Resources Information Center

Judge, Sara E.

Country schools in eastern and central Kansas are explored from six different aspects: country schools as historic sites; teachers (their roles, rules, and restrictions); reading, writing, arithmetic, and recitation (a day in a rural school); country schools and the Americanization of ethnic groups; country schools as community centers; and…

Switchgrass (Panicum virgatum L.) genotypes differ between coastal sites and inland road corridors in the Northeastern US

USDA-ARS?s Scientific Manuscript database

Switchgrass (Panicum virgatum L.) is a North American grass that exhibits vast genetic diversity across its geographic range. In the Northeast, switchgrass was restricted to a narrow zone adjacent to the coastal salt marsh, but current populations inhabit inland road verges raising questions about t...

Methylation Pattern of Radish (Raphanus sativus) Nuclear Ribosomal RNA Genes 1

PubMed Central

Delseny, Michel; Laroche, Monique; Penon, Paul

1984-01-01

The methylation pattern of radish Raphanus sativus nuclear rDNA has been investigated using the Hpa II, Msp I, and Hha I restriction enzymes. The presence of numerous target sites for these enzymes has been shown using cloned rDNA fragments. A large fraction of the numerous rDNA units are heavily methylated, being completely resistant to Hpa II and Hpa I. However, specific sites are constantly available in another fraction of the units and are therefore unmethylated. The use of different probes allowed us to demonstrate that hypomethylated sites are present in different regions. Major hypomethylated Hha I sites have been mapped in the 5′ portion of 25S rRNA coding sequence. Among the hypomethylated fraction, different methylation patterns coexist. It has been possible to demonstrate that methylation patterns are specific for particular units. The Hha I pattern of rDNA in tissues of different developmental stages was analyzed. Evidence for possible tissue specific differences in the methylation pattern is reported. Images Fig. 2 Fig. 3 Fig. 5 PMID:16663896

An A-T linker adapter polymerase chain reaction method for chromosome walking without restriction site cloning bias.

PubMed

Trinh, Quoclinh; Xu, Wentao; Shi, Hui; Luo, Yunbo; Huang, Kunlun

2012-06-01

A-T linker adapter polymerase chain reaction (PCR) was modified and employed for the isolation of genomic fragments adjacent to a known DNA sequence. The improvements in the method focus on two points. The first is the modification of the PO(4) and NH(2) groups in the adapter to inhibit the self-ligation of the adapter or the generation of nonspecific products. The second improvement is the use of the capacity of rTaq DNA polymerase to add an adenosine overhang at the 3' ends of digested DNA to suppress self-ligation in the digested DNA and simultaneously resolve restriction site clone bias. The combination of modifications in the adapter and in the digested DNA leads to T/A-specific ligation, which enhances the flexibility of this method and makes it feasible to use many different restriction enzymes with a single adapter. This novel A-T linker adapter PCR overcomes the inherent limitations of the original ligation-mediated PCR method such as low specificity and a lack of restriction enzyme choice. Moreover, this method also offers higher amplification efficiency, greater flexibility, and easier manipulation compared with other PCR methods for chromosome walking. Experimental results from 143 Arabidopsis mutants illustrate that this method is reliable and efficient in high-throughput experiments. Copyright © 2012 Elsevier Inc. All rights reserved.

Leveraging Technology and Social Media for Information Sharing

DTIC Science & Technology

2009-04-01

praised as a "gift to humanity the benefits of social networking sites such as Facebook and MySpace in forging friendships and understanding.2” The...is relatively easy to sign-up to and access. It should be noted that many DoD installations and agencies restrict access to social networking sites for...to sign-up to and access. As with facebook, many DoD installations and agencies restrict access to social networking sites . Users of Twitter are

Electrostatic potential of human immunodeficiency virus type 2 and rhesus macaque simian immunodeficiency virus capsid proteins.

PubMed

Bozek, Katarzyna; Nakayama, Emi E; Kono, Ken; Shioda, Tatsuo

2012-01-01

Human immunodeficiency virus type 2 (HIV-2) and simian immunodeficiency virus isolated from a macaque monkey (SIVmac) are assumed to have originated from simian immunodeficiency virus isolated from sooty mangabey (SIVsm). Despite their close similarity in genome structure, HIV-2 and SIVmac show different sensitivities to TRIM5α, a host restriction factor against retroviruses. The replication of HIV-2 strains is potently restricted by rhesus (Rh) monkey TRIM5α, while that of SIVmac strain 239 (SIVmac239) is not. Viral capsid protein is the determinant of this differential sensitivity to TRIM5α, as the HIV-2 mutant carrying SIVmac239 capsid protein evaded Rh TRIM5α-mediated restriction. However, the molecular determinants of this restriction mechanism are unknown. Electrostatic potential on the protein-binding site is one of the properties regulating protein-protein interactions. In this study, we investigated the electrostatic potential on the interaction surface of capsid protein of HIV-2 strain GH123 and SIVmac239. Although HIV-2 GH123 and SIVmac239 capsid proteins share more than 87% amino acid identity, we observed a large difference between the two molecules with the HIV-2 GH123 molecule having predominantly positive and SIVmac239 predominantly negative electrostatic potential on the surface of the loop between α-helices 4 and 5 (L4/5). As L4/5 is one of the major determinants of Rh TRIM5α sensitivity of these viruses, the present results suggest that the binding site of the Rh TRIM5α may show complementarity to the HIV-2 GH123 capsid surface charge distribution.

Homologous species restriction of the complement-mediated killing of nucleated cells.

PubMed Central

Yamamoto, H; Blaas, P; Nicholson-Weller, A; Hänsch, G M

1990-01-01

The homologous restriction of complement (C) lysis is attributed to membrane proteins: decay-accelerating factor (DAF), C8 binding protein (C8bp) and P18/CD59. Since these proteins are also expressed on peripheral blood cells, species restriction was tested for in the complement-mediated killing of antibody-coated human leucocytes by human or rabbit complement. Killing was more efficient when rabbit complement was used. Preincubation of cells with an antibody to DAF abolished the difference. When C1-7 sites were first attached to the cells and either rabbit or human C8, C9 were added, the killing of monocytes and lymphocytes was equally efficient; only in polymorphonuclear neutrophils was a higher efficiency of rabbit C8, C9 seen. Thus, in contrast to haemolysis, restriction occurred predominantly at the C3 level and the action of the terminal complement components was not inhibited. Since C8bp isolated from peripheral blood cells showed essentially similar characteristics as the erythrocyte-derived C8bp, the failure of C8bp to inhibit the action of the terminal components on nucleated cells might reflect differences of the complement membrane interactions between erythrocytes or nucleated cells, respectively. Images Figure 5 PMID:1697561

mTOR kinase structure, mechanism and regulation by the rapamycin-binding domain

PubMed Central

Yang, Haijuan; Rudge, Derek G.; Koos, Joseph D.; Vaidialingam, Bhamini; Yang, Hyo J.; Pavletich, Nikola P.

2015-01-01

The mammalian target of rapamycin (mTOR), a phosphoinositide 3-kinase related protein kinase, controls cell growth in response to nutrients and growth factors and is frequently deregulated in cancer. Here we report co-crystal structures of a truncated mTOR-mLST8 complex with an ATP transition state mimic and with ATP-site inhibitors. The structures reveal an intrinsically active kinase conformation, with catalytic residues and mechanism remarkably similar to canonical protein kinases. The active site is highly recessed due to the FKBP12-Rapamycin binding (FRB) domain and an inhibitory helix protruding from the catalytic cleft. mTOR activating mutations map to the structural framework that holds these elements in place, indicating the kinase is controlled by restricted access. In vitro biochemistry indicates that the FRB domain acts as a gatekeeper, with its rapamycin-binding site interacting with substrates to grant them access to the restricted active site. FKBP12-rapamycin inhibits by directly blocking substrate recruitment and by further restricting active site access. The structures also reveal active site residues and conformational changes that underlie inhibitor potency and specificity. PMID:23636326

Restricted Mandibular Movement Attributed to Ossification of Mandibular Depressors and Medial Pterygoid Muscles in Patients With Fibrodysplasia Ossificans Progressiva: A Report of 3 Cases.

PubMed

Okuno, Tetsuko; Suzuki, Hitoshi; Inoue, Akio; Kusukawa, Jingo

2017-09-01

Fibrodysplasia ossificans progressiva (FOP) is an extremely rare genetic condition characterized by congenital malformation and progressive heterotopic ossification (HO) caused by a recurrent single nucleotide substitution at position 617 in the ACVR1 gene. As the condition progresses, HO leads to joint ankylosis, breathing difficulties, and mouth-opening restriction, and it can shorten the patient's lifespan. This report describes 3 cases of FOP confirmed by genetic testing in patients with restricted mouth opening. Each patient presented a different onset and degree of jaw movement restriction. The anatomic ossification site of the mandibular joint was examined in each patient using reconstructed computed tomographic (CT) images and 3-dimensional reconstructed CT (3D-CT) images. A 29-year-old woman complained of jaw movement restriction since 13 years of age. 3D-CT image of the mandibular joint showed an osseous bridge, formed by the mandibular depressors that open the mouth, between the hyoid bone and the mentum of the mandible. A 39-year-old man presented with jaw movement restriction that developed at 3 years of age after a mouth injury. 3D-CT image of the jaw showed ankylosis of the jaw from ossification of the mandibular depressors that was worse than in patient 1. CT images showed no HO findings of the masticatory muscles. To the authors' knowledge, these are the first 2 case descriptions of the anatomic site of ankylosis involving HO of the mandibular depressors in the jaw resulting from FOP. In contrast, a 62-year-old bedridden woman with an interincisal distance longer than 10 mm (onset, 39 years of age) had no HO of the mandibular depressors and slight HO of the medial pterygoid muscle on the right and left sides. These findings suggest that restricted mouth opening varies according to the presence or absence of HO of the mandibular depressors. Copyright © 2017. Published by Elsevier Inc.

Dominant petroleum hydrocarbon-degrading bacteria in the Archipelago Sea in South-West Finland (Baltic Sea) belong to different taxonomic groups than hydrocarbon degraders in the oceans.

PubMed

Reunamo, Anna; Riemann, Lasse; Leskinen, Piia; Jørgensen, Kirsten S

2013-07-15

The natural petroleum hydrocarbon degrading capacity of the Archipelago Sea water in S-W Finland was studied in a microcosm experiment. Pristine and previously oil exposed sites were examined. Bacterial community fingerprinting was performed using terminal restriction fragment length polymorphism (T-RFLP) and samples from selected microcosms were sequenced. The abundance of PAH degradation genes was measured by quantitative PCR. Bacterial communities in diesel exposed microcosms diverged from control microcosms during the experiment. Gram positive PAH degradation genes dominated at both sites in situ, whereas gram negative PAH degrading genes became enriched in diesel microcosms. The dominant bacterial groups after a 14 days of diesel exposure were different depending on the sampling site, belonging to the class Actinobacteria (32%) at a pristine site and Betaproteobacteria (52%) at a previously oil exposed site. The hydrocarbon degrading bacteria in the Baltic Sea differ from those in the oceans, where most hydrocarbon degraders belong to Gammaproteobacteria. Copyright © 2013 Elsevier Ltd. All rights reserved.

Don’t Judge a (Face)Book by its Cover: A Critical Review of the Implications of Social Networking Sites

DTIC Science & Technology

2011-05-01

It is vital to emphasise the possible risks, reinforce the restrictions to use, and stress the consequences of a failure to comply. This should...and the most popular sites now have in excess of 300 million members. Although these sites are currently most popular with teenagers and young adults...any necessary restrictions to use, and stress the consequences associated with a failure to comply. Evidence also suggests that education is most

Restriction enzyme body doubles and PCR cloning: on the general use of type IIs restriction enzymes for cloning.

PubMed

Tóth, Eszter; Huszár, Krisztina; Bencsura, Petra; Kulcsár, Péter István; Vodicska, Barbara; Nyeste, Antal; Welker, Zsombor; Tóth, Szilvia; Welker, Ervin

2014-01-01

The procedure described here allows the cloning of PCR fragments containing a recognition site of the restriction endonuclease (Type IIP) used for cloning in the sequence of the insert. A Type IIS endonuclease--a Body Double of the Type IIP enzyme--is used to generate the same protruding palindrome. Thus, the insert can be cloned to the Type IIP site of the vector without digesting the PCR product with the same Type IIP enzyme. We achieve this by incorporating the recognition site of a Type IIS restriction enzyme that cleaves the DNA outside of its recognition site in the PCR primer in such a way that the cutting positions straddle the desired overhang sequence. Digestion of the PCR product by the Body Double generates the required overhang. Hitherto the use of Type IIS restriction enzymes in cloning reactions has only been used for special applications, the approach presented here makes Type IIS enzymes as useful as Type IIP enzymes for general cloning purposes. To assist in finding Body Double enzymes, we summarised the available Type IIS enzymes which are potentially useful for Body Double cloning and created an online program (http://group.szbk.u-szeged.hu/welkergr/body_double/index.html) for the selection of suitable Body Double enzymes and the design of the appropriate primers.

A theory that may explain the Hayflick limit--a means to delete one copy of a repeating sequence during each cell cycle in certain human cells such as fibroblasts.

PubMed

Naveilhan, P; Baudet, C; Jabbour, W; Wion, D

1994-09-01

A model that may explain the limited division potential of certain cells such as human fibroblasts in culture is presented. The central postulate of this theory is that there exists, prior to certain key exons that code for materials needed for cell division, a unique sequence of specific repeating segments of DNA. One copy of such repeating segments is deleted during each cell cycle in cells that are not protected from such deletion through methylation of their cytosine residues. According to this theory, the means through which such repeated sequences are removed, one per cycle, is through the sequential action of enzymes that act much as bacterial restriction enzymes do--namely to produce scissions in both strands of DNA in areas that correspond to the DNA base sequence recognition specificities of such enzymes. After the first scission early in a replicative cycle, that enzyme becomes inhibited, but the cleavage of the first site exposes the closest site in the repetitive element to the action of a second restriction enzyme after which that enzyme also becomes inhibited. Then repair occurs, regenerating the original first site. Through this sequential activation and inhibition of two different restriction enzymes, only one copy of the repeating sequence is deleted during each cell cycle. In effect, the repeating sequence operates as a precise counter of the numbers of cell doubling that have occurred since the cells involved differentiated during development.

Nutrient loading on subsoils from on-site wastewater effluent, comparing septic tank and secondary treatment systems.

PubMed

Gill, L W; O'Luanaigh, N; Johnston, P M; Misstear, B D R; O'Suilleabhain, C

2009-06-01

The performance of six separate percolation areas was intensively monitored to ascertain the attenuation effects of unsaturated subsoils with respect to on-site wastewater effluent: three sites receiving septic tank effluent, the other three sites receiving secondary treated effluent. The development of a biomat across the percolation areas receiving secondary treated effluent was restricted on these sites compared to those sites receiving septic tank effluent and this created significant differences in terms of the potential nitrogen loading to groundwater. The average nitrogen loading per capita at 1.0m depth of unsaturated subsoil equated to 3.9 g total-N/d for the sites receiving secondary treated effluent, compared to 2.1 g total-N/d for the sites receiving septic tank effluent. Relatively high nitrogen loading was, however, found on the septic tank sites discharging effluent into highly permeable subsoil that counteracted any significant denitrification. Phosphorus removal was generally very good on all of the sites although a clear relationship to the soil mineralogy was determined.

HIV-1 Vpu Antagonizes CD317/Tetherin by Adaptor Protein-1-Mediated Exclusion from Virus Assembly Sites

PubMed Central

Pujol, François M.; Laketa, Vibor; Schmidt, Florian; Mukenhirn, Markus; Müller, Barbara; Boulant, Steeve; Grimm, Dirk; Keppler, Oliver T.

2016-01-01

ABSTRACT The host cell restriction factor CD317/tetherin traps virions at the surface of producer cells to prevent their release. The HIV-1 accessory protein Vpu antagonizes this restriction. Vpu reduces the cell surface density of the restriction factor and targets it for degradation; however, these activities are dispensable for enhancing particle release. Instead, Vpu has been suggested to antagonize CD317/tetherin by preventing recycling of internalized CD317/tetherin to the cell surface, blocking anterograde transport of newly synthesized CD317/tetherin, and/or displacing the restriction factor from virus assembly sites at the plasma membrane. At the molecular level, antagonism relies on the physical interaction of Vpu with CD317/tetherin. Recent findings suggested that phosphorylation of a diserine motif enables Vpu to bind to adaptor protein 1 (AP-1) trafficking complexes via two independent interaction motifs and to couple CD317/tetherin to the endocytic machinery. Here, we used a panel of Vpu proteins with specific mutations in individual interaction motifs to define which interactions are required for antagonism of CD317/tetherin. Impairing recycling or anterograde transport of CD317/tetherin to the plasma membrane was insufficient for antagonism. In contrast, excluding CD317/tetherin from HIV-1 assembly sites depended on Vpu motifs for interaction with AP-1 and CD317/tetherin and correlated with antagonism of the particle release restriction. Consistently, interference with AP-1 function or its expression blocked these Vpu activities. Our results define displacement from HIV-1 assembly sites as active principle of CD317/tetherin antagonism by Vpu and support a role of tripartite complexes between Vpu, AP-1, and CD317/tetherin in this process. IMPORTANCE CD317/tetherin poses an intrinsic barrier to human immunodeficiency virus type 1 (HIV-1) replication in human cells by trapping virus particles at the surface of producer cells and thereby preventing their release. The viral protein Vpu antagonizes this restriction, and molecular interactions with the restriction factor and adaptor protein complex 1 (AP-1) were suggested to mediate this activity. Vpu modulates intracellular trafficking of CD317/tetherin and excludes the restriction factor from HIV-1 assembly sites at the plasma membrane, but the relative contribution of these effects to antagonism remain elusive. Using a panel of Vpu mutants, as well as interference with AP-1 function and expression, we show here that Vpu antagonizes CD317/tetherin by blocking its recruitment to viral assembly sites in an AP-1-dependent manner. These results refine our understanding of the molecular mechanisms of CD317/tetherin antagonism and suggest complexes of Vpu with the restriction factor and AP-1 as targets for potential therapeutic intervention. PMID:27170757

Sanitation, Stress, and Life Stage: A Systematic Data Collection Study among Women in Odisha, India

PubMed Central

Hulland, Kristyna R. S.; Chase, Rachel P.; Caruso, Bethany A.; Swain, Rojalin; Biswal, Bismita; Sahoo, Krushna Chandra; Panigrahi, Pinaki; Dreibelbis, Robert

2015-01-01

Emerging evidence demonstrates how inadequate access to water and sanitation is linked to psychosocial stress, especially among women, forcing them to navigate social and physical barriers during their daily sanitation routines. We examine sanitation-related psychosocial stress (SRPS) across women’s reproductive lives in three distinct geographic sites (urban slums, rural villages, and rural tribal villages) in Odisha, India. We explored daily sanitation practices of adolescent, newly married, pregnant, and established adult women (n = 60) and identified stressors encountered during sanitation. Responding to structured data collection methods, women ranked seven sanitation activities (defecation, urination, menstruation, bathing, post-defecation cleaning, carrying water, and changing clothes) based on stress (high to low) and level of freedom (associated with greatest freedom to having the most restrictions). Women then identified common stressors they encountered when practicing sanitation and sorted stressors in constrained piles based on frequency and severity of each issue. The constellation of factors influencing SRPS varies by life stage and location. Overall, sanitation behaviors that were most restricted (i.e., menstruation) were the most stressful. Women in different sites encountered different stressors, and the level of perceived severity varied based on site and life stage. Understanding the influence of place and life stage on SRPS provides a nuanced understanding of sanitation, and may help identify areas for intervention. PMID:26551866

indCAPS: A tool for designing screening primers for CRISPR/Cas9 mutagenesis events.

PubMed

Hodgens, Charles; Nimchuk, Zachary L; Kieber, Joseph J

2017-01-01

Genetic manipulation of organisms using CRISPR/Cas9 technology generally produces small insertions/deletions (indels) that can be difficult to detect. Here, we describe a technique to easily and rapidly identify such indels. Sequence-identified mutations that alter a restriction enzyme recognition site can be readily distinguished from wild-type alleles using a cleaved amplified polymorphic sequence (CAPS) technique. If a restriction site is created or altered by the mutation such that only one allele contains the restriction site, a polymerase chain reaction (PCR) followed by a restriction digest can be used to distinguish the two alleles. However, in the case of most CRISPR-induced alleles, no such restriction sites are present in the target sequences. In this case, a derived CAPS (dCAPS) approach can be used in which mismatches are purposefully introduced in the oligonucleotide primers to create a restriction site in one, but not both, of the amplified templates. Web-based tools exist to aid dCAPS primer design, but when supplied sequences that include indels, the current tools often fail to suggest appropriate primers. Here, we report the development of a Python-based, species-agnostic web tool, called indCAPS, suitable for the design of PCR primers used in dCAPS assays that is compatible with indels. This tool should have wide utility for screening editing events following CRISPR/Cas9 mutagenesis as well as for identifying specific editing events in a pool of CRISPR-mediated mutagenesis events. This tool was field-tested in a CRISPR mutagenesis experiment targeting a cytokinin receptor (AHK3) in Arabidopsis thaliana. The tool suggested primers that successfully distinguished between wild-type and edited alleles of a target locus and facilitated the isolation of two novel ahk3 null alleles. Users can access indCAPS and design PCR primers to employ dCAPS to identify CRISPR/Cas9 alleles at http://indcaps.kieber.cloudapps.unc.edu/.

CAPRRESI: Chimera Assembly by Plasmid Recovery and Restriction Enzyme Site Insertion.

PubMed

Santillán, Orlando; Ramírez-Romero, Miguel A; Dávila, Guillermo

2017-06-25

Here, we present chimera assembly by plasmid recovery and restriction enzyme site insertion (CAPRRESI). CAPRRESI benefits from many strengths of the original plasmid recovery method and introduces restriction enzyme digestion to ease DNA ligation reactions (required for chimera assembly). For this protocol, users clone wildtype genes into the same plasmid (pUC18 or pUC19). After the in silico selection of amino acid sequence regions where chimeras should be assembled, users obtain all the synonym DNA sequences that encode them. Ad hoc Perl scripts enable users to determine all synonym DNA sequences. After this step, another Perl script searches for restriction enzyme sites on all synonym DNA sequences. This in silico analysis is also performed using the ampicillin resistance gene (ampR) found on pUC18/19 plasmids. Users design oligonucleotides inside synonym regions to disrupt wildtype and ampR genes by PCR. After obtaining and purifying complementary DNA fragments, restriction enzyme digestion is accomplished. Chimera assembly is achieved by ligating appropriate complementary DNA fragments. pUC18/19 vectors are selected for CAPRRESI because they offer technical advantages, such as small size (2,686 base pairs), high copy number, advantageous sequencing reaction features, and commercial availability. The usage of restriction enzymes for chimera assembly eliminates the need for DNA polymerases yielding blunt-ended products. CAPRRESI is a fast and low-cost method for fusing protein-coding genes.

24 CFR 200.72 - Zoning, deed and building restrictions.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 24 Housing and Urban Development 2 2010-04-01 2010-04-01 false Zoning, deed and building... Zoning, deed and building restrictions. The project when completed shall not violate any material zoning or deed restrictions applicable to the project site, and shall comply with all applicable building...

Re-evaluating the kinetics of ATP hydrolysis during initiation of DNA sliding by Type III restriction enzymes

PubMed Central

Tóth, Júlia; Bollins, Jack; Szczelkun, Mark D.

2015-01-01

DNA cleavage by the Type III restriction enzymes requires long-range protein communication between recognition sites facilitated by thermally-driven 1D diffusion. This ‘DNA sliding’ is initiated by hydrolysis of multiple ATPs catalysed by a helicase-like domain. Two distinct ATPase phases were observed using short oligoduplex substrates; the rapid consumption of ∼10 ATPs coupled to a protein conformation switch followed by a slower phase, the duration of which was dictated by the rate of dissociation from the recognition site. Here, we show that the second ATPase phase is both variable and only observable when DNA ends are proximal to the recognition site. On DNA with sites more distant from the ends, a single ATPase phase coupled to the conformation switch was observed and subsequent site dissociation required little or no further ATP hydrolysis. The overall DNA dissociation kinetics (encompassing site release, DNA sliding and escape via a DNA end) were not influenced by the second phase. Although the data simplifies the ATP hydrolysis scheme for Type III restriction enzymes, questions remain as to why multiple ATPs are hydrolysed to prepare for DNA sliding. PMID:26538601

Mojo Hand, a TALEN design tool for genome editing applications.

PubMed

Neff, Kevin L; Argue, David P; Ma, Alvin C; Lee, Han B; Clark, Karl J; Ekker, Stephen C

2013-01-16

Recent studies of transcription activator-like (TAL) effector domains fused to nucleases (TALENs) demonstrate enormous potential for genome editing. Effective design of TALENs requires a combination of selecting appropriate genetic features, finding pairs of binding sites based on a consensus sequence, and, in some cases, identifying endogenous restriction sites for downstream molecular genetic applications. We present the web-based program Mojo Hand for designing TAL and TALEN constructs for genome editing applications (http://www.talendesign.org). We describe the algorithm and its implementation. The features of Mojo Hand include (1) automatic download of genomic data from the National Center for Biotechnology Information, (2) analysis of any DNA sequence to reveal pairs of binding sites based on a user-defined template, (3) selection of restriction-enzyme recognition sites in the spacer between the TAL monomer binding sites including options for the selection of restriction enzyme suppliers, and (4) output files designed for subsequent TALEN construction using the Golden Gate assembly method. Mojo Hand enables the rapid identification of TAL binding sites for use in TALEN design. The assembly of TALEN constructs, is also simplified by using the TAL-site prediction program in conjunction with a spreadsheet management aid of reagent concentrations and TALEN formulation. Mojo Hand enables scientists to more rapidly deploy TALENs for genome editing applications.

A Pronounced Inflammatory Activity Characterizes the Early Fracture Healing Phase in Immunologically Restricted Patients

PubMed Central

Hoff, Paula; Gaber, Timo; Strehl, Cindy; Jakstadt, Manuela; Hoff, Holger; Schmidt-Bleek, Katharina; Lang, Annemarie; Röhner, Eric; Huscher, Dörte; Matziolis, Georg; Burmester, Gerd-Rüdiger; Schmidmaier, Gerhard; Perka, Carsten; Duda, Georg N.; Buttgereit, Frank

2017-01-01

Immunologically restricted patients such as those with autoimmune diseases or malignancies often suffer from delayed or insufficient fracture healing. In human fracture hematomas and the surrounding bone marrow obtained from immunologically restricted patients, we analyzed the initial inflammatory phase on cellular and humoral level via flow cytometry and multiplex suspension array. Compared with controls, we demonstrated higher numbers of immune cells like monocytes/macrophages, natural killer T (NKT) cells, and activated T helper cells within the fracture hematomas and/or the surrounding bone marrow. Also, several pro-inflammatory cytokines such as Interleukin (IL)-6 and Tumor necrosis factor α (TNFα), chemokines (e.g., Eotaxin and RANTES), pro-angiogenic factors (e.g., IL-8 and Macrophage migration inhibitory factor: MIF), and regulatory cytokines (e.g., IL-10) were found at higher levels within the fracture hematomas and/or the surrounding bone marrow of immunologically restricted patients when compared to controls. We conclude here that the inflammatory activity on cellular and humoral levels at fracture sites of immunologically restricted patients considerably exceeds that of control patients. The initial inflammatory phase profoundly differs between these patient groups and is probably one of the reasons for prolonged or insufficient fracture healing often occurring within immunologically restricted patients. PMID:28282868

SDM-Assist software to design site-directed mutagenesis primers introducing “silent” restriction sites

PubMed Central

2013-01-01

Background Over the past decades site-directed mutagenesis (SDM) has become an indispensable tool for biological structure-function studies. In principle, SDM uses modified primer pairs in a PCR reaction to introduce a mutation in a cDNA insert. DpnI digestion of the reaction mixture is used to eliminate template copies before amplification in E. coli; however, this process is inefficient resulting in un-mutated clones which can only be distinguished from mutant clones by sequencing. Results We have developed a program – ‘SDM-Assist’ which creates SDM primers adding a specific identifier: through additional silent mutations a restriction site is included or a previous one removed which allows for highly efficient identification of ‘mutated clones’ by a simple restriction digest. Conclusions The direct identification of SDM clones will save time and money for researchers. SDM-Assist also scores the primers based on factors such as Tm, GC content and secondary structure allowing for simplified selection of optimal primer pairs. PMID:23522286

40 CFR 228.15 - Dumping sites designated on a final basis.

Code of Federal Regulations, 2011 CFR

2011-07-01

... designation to establish different or additional standards. The EPA will act on any such petition within 120...) Disposal not subject to the restrictions in paragraphs (b)(4)(vi)(C) through (G) or (b)(4)(vi)(I) of this... prior to the completion of the DMMP and completed within two years after the completion of the DMMP. (J...

Chloroplast DNA Diversity among Trees, Populations and Species in the California Closed-Cone Pines (Pinus Radiata, Pinus Muricata and Pinus Attenuata)

PubMed Central

Hong, Y. P.; Hipkins, V. D.; Strauss, S. H.

1993-01-01

The amount, distribution and mutational nature of chloroplast DNA polymorphisms were studied via analysis of restriction fragment length polymorphisms in three closely related species of conifers, the California closed-cone pines-knobcone pine: Pinus attenuata Lemm.; bishop pine: Pinus muricata D. Don; and Monterey pine: Pinus radiata D. Don. Genomic DNA from 384 trees representing 19 populations were digested with 9-20 restriction enzymes and probed with cloned cpDNA fragments from Douglas-fir [Pseudotsuga menziesii (Mirb.) Franco] that comprise 82% of the chloroplast genome. Up to 313 restriction sites were surveyed, and 25 of these were observed to be polymorphic among or within species. Differences among species accounted for the majority of genetic (haplotypic) diversity observed [G(st) = 84(+/-13)%]; nucleotide diversity among species was estimated to be 0.3(+/-0.1)%. Knobcone pine and Monterey pine displayed almost no genetic variation within or among populations. Bishop pine also showed little variability within populations, but did display strong population differences [G(st) = 87(+/-8)%] that were a result of three distinct geographic groups. Mean nucleotide diversity within populations was 0.003(+/-0.002)%; intrapopulation polymorphisms were found in only five populations. This pattern of genetic variation contrasts strongly with findings from study of nuclear genes (allozymes) in the group, where most genetic diversity resides within populations rather than among populations or species. Regions of the genome subject to frequent length mutations were identified; estimates of subdivision based on length variant frequencies in one region differed strikingly from those based on site mutations or allozymes. Two trees were identified with a major chloroplast DNA inversion that closely resembled one documented between Pinus and Pseudotsuga. PMID:7905846

A new detection method for the K variant of butyrylcholinesterase based on PCR primer introduced restriction analysis (PCR-PIRA).

PubMed Central

Shibuta, K; Abe, M; Suzuki, T

1994-01-01

The K variant of human butyrylcholinesterase is caused by a G/A transition in the butyrylcholinesterase gene, which neither creates nor destroys any restriction site. In an attempt to detect the K variant both simply and rapidly, we developed a two step method of "PCR primer introduced restriction analysis" (PCR-PIRA). The first step was used to introduce a new Fun4HI site into the normal allele for a screening test, while the second step was performed to create a new MaeIII site on the variant allele for a specific test. This method thus enabled us to distinguish clearly the K variant from the normal allele, and also showed that the frequency of the K variant allele is 0.164 in the Japanese population. Images PMID:7966197

Phylogeographic population structure of Red-winged Blackbirds assessed by mitochondrial DNA

PubMed Central

Ball, R. Martin; Freeman, Scott; James, Frances C.; Bermingham, Eldredge; Avise, John C.

1988-01-01

A continent-wide survey of restriction-site variation in mitochondrial DNA (mtDNA) of the Red-winged Blackbird (Agelaius phoeniceus) was conducted to assess the magnitude of phylogeographic population structure in an avian species. A total of 34 mtDNA genotypes was observed among the 127 specimens assayed by 18 restriction endonucleases. Nonetheless, population differentiation was minor, as indicated by (i) small genetic distances in terms of base substitutions per nucleotide site between mtDNA genotypes (maximum P ≈ 0.008) and by (ii) the widespread geographic distributions of particular mtDNA clones and phylogenetic arrays of clones. Extensive morphological differentiation among redwing populations apparently has occurred in the context of relatively little phylogenetic separation. A comparison between mtDNA data sets for Red-winged Blackbirds and deermice (Peromyscus maniculatus) also sampled from across North America shows that intraspecific population structures of these two species differ dramatically. The lower phylogeographic differentiation in redwings is probably due to historically higher levels of gene flow. PMID:16593914

Evaluating Sex and Age Differences in ADI-R and ADOS Scores in a Large European Multi-site Sample of Individuals with Autism Spectrum Disorder.

PubMed

Tillmann, J; Ashwood, K; Absoud, M; Bölte, S; Bonnet-Brilhault, F; Buitelaar, J K; Calderoni, S; Calvo, R; Canal-Bedia, R; Canitano, R; De Bildt, A; Gomot, M; Hoekstra, P J; Kaale, A; McConachie, H; Murphy, D G; Narzisi, A; Oosterling, I; Pejovic-Milovancevic, M; Persico, A M; Puig, O; Roeyers, H; Rommelse, N; Sacco, R; Scandurra, V; Stanfield, A C; Zander, E; Charman, T

2018-02-21

Research on sex-related differences in Autism Spectrum Disorder (ASD) has been impeded by small samples. We pooled 28 datasets from 18 sites across nine European countries to examine sex differences in the ASD phenotype on the ADI-R (376 females, 1763 males) and ADOS (233 females, 1187 males). On the ADI-R, early childhood restricted and repetitive behaviours were lower in females than males, alongside comparable levels of social interaction and communication difficulties in females and males. Current ADI-R and ADOS scores showed no sex differences for ASD severity. There were lower socio-communicative symptoms in older compared to younger individuals. This large European ASD sample adds to the literature on sex and age variations of ASD symptomatology.

Differentiating the persistency and permanency of some two stages DNA splicing language via Yusof-Goode (Y-G) approach

NASA Astrophysics Data System (ADS)

Mudaber, M. H.; Yusof, Y.; Mohamad, M. S.

2017-09-01

Predicting the existence of restriction enzymes sequences on the recombinant DNA fragments, after accomplishing the manipulating reaction, via mathematical approach is considered as a convenient way in terms of DNA recombination. In terms of mathematics, for this characteristic of the recombinant DNA strands, which involve the recognition sites of restriction enzymes, is called persistent and permanent. Normally differentiating the persistency and permanency of two stages recombinant DNA strands using wet-lab experiment is expensive and time-consuming due to running the experiment at two stages as well as adding more restriction enzymes on the reaction. Therefore, in this research, by using Yusof-Goode (Y-G) model the difference between persistent and permanent splicing language of some two stages is investigated. Two theorems were provided, which show the persistency and non-permanency of two stages DNA splicing language.

Classification of European Mtdnas from an Analysis of Three European Populations

PubMed Central

Torroni, A.; Huoponen, K.; Francalacci, P.; Petrozzi, M.; Morelli, L.; Scozzari, R.; Obinu, D.; Savontaus, M. L.; Wallace, D. C.

1996-01-01

Mitochondrial DNA (mtDNA) sequence variation was examined in Finns, Swedes and Tuscans by PCR amplification and restriction analysis. About 99% of the mtDNAs were subsumed within 10 mtDNA haplogroups (H, I, J, K, M, T, U, V, W, and X) suggesting that the identified haplogroups could encompass virtually all European mtDNAs. Because both hypervariable segments of the mtDNA control region were previously sequenced in the Tuscan samples, the mtDNA haplogroups and control region sequences could be compared. Using a combination of haplogroup-specific restriction site changes and control region nucleotide substitutions, the distribution of the haplogroups was surveyed through the published restriction site polymorphism and control region sequence data of Caucasoids. This supported the conclusion that most haplogroups observed in Europe are Caucasoid-specific, and that at least some of them occur at varying frequencies in different Caucasoid populations. The classification of almost all European mtDNA variation in a number of well defined haplogroups could provide additional insights about the origin and relationships of Caucasoid populations and the process of human colonization of Europe, and is valuable for the definition of the role played by mtDNA backgrounds in the expression of pathological mtDNA mutations PMID:8978068

Compensatory Mitigation Site Protection Instrument Handbook and Fact Sheet

EPA Pesticide Factsheets

The site protection instrument is a written description of the legal arrangements including site ownership, management, and enforcement of any use restrictions that will be used to ensure the long-term protection of the compensatory mitigation project site

47 CFR 54.637 - Off-site data centers and off-site administrative offices.

Code of Federal Regulations, 2013 CFR

2013-10-01

... Healthcare Connect Fund § 54.637 Off-site data centers and off-site administrative offices. (a) The... the Healthcare Connect Fund, subject to the conditions and restrictions set forth in paragraph (b) of...

47 CFR 54.637 - Off-site data centers and off-site administrative offices.

Code of Federal Regulations, 2014 CFR

2014-10-01

... Healthcare Connect Fund § 54.637 Off-site data centers and off-site administrative offices. (a) The... the Healthcare Connect Fund, subject to the conditions and restrictions set forth in paragraph (b) of...

Restrictive versus Liberal Fluid Therapy for Major Abdominal Surgery.

PubMed

Myles, Paul S; Bellomo, Rinaldo; Corcoran, Tomas; Forbes, Andrew; Peyton, Philip; Story, David; Christophi, Chris; Leslie, Kate; McGuinness, Shay; Parke, Rachael; Serpell, Jonathan; Chan, Matthew T V; Painter, Thomas; McCluskey, Stuart; Minto, Gary; Wallace, Sophie

2018-05-09

Background Guidelines to promote the early recovery of patients undergoing major surgery recommend a restrictive intravenous-fluid strategy for abdominal surgery. However, the supporting evidence is limited, and there is concern about impaired organ perfusion. Methods In a pragmatic, international trial, we randomly assigned 3000 patients who had an increased risk of complications while undergoing major abdominal surgery to receive a restrictive or liberal intravenous-fluid regimen during and up to 24 hours after surgery. The primary outcome was disability-free survival at 1 year. Key secondary outcomes were acute kidney injury at 30 days, renal-replacement therapy at 90 days, and a composite of septic complications, surgical-site infection, or death. Results During and up to 24 hours after surgery, 1490 patients in the restrictive fluid group had a median intravenous-fluid intake of 3.7 liters (interquartile range, 2.9 to 4.9), as compared with 6.1 liters (interquartile range, 5.0 to 7.4) in 1493 patients in the liberal fluid group (P<0.001). The rate of disability-free survival at 1 year was 81.9% in the restrictive fluid group and 82.3% in the liberal fluid group (hazard ratio for death or disability, 1.05; 95% confidence interval, 0.88 to 1.24; P=0.61). The rate of acute kidney injury was 8.6% in the restrictive fluid group and 5.0% in the liberal fluid group (P<0.001). The rate of septic complications or death was 21.8% in the restrictive fluid group and 19.8% in the liberal fluid group (P=0.19); rates of surgical-site infection (16.5% vs. 13.6%, P=0.02) and renal-replacement therapy (0.9% vs. 0.3%, P=0.048) were higher in the restrictive fluid group, but the between-group difference was not significant after adjustment for multiple testing. Conclusions Among patients at increased risk for complications during major abdominal surgery, a restrictive fluid regimen was not associated with a higher rate of disability-free survival than a liberal fluid regimen and was associated with a higher rate of acute kidney injury. (Funded by the Australian National Health and Medical Research Council and others; RELIEF ClinicalTrials.gov number, NCT01424150 .).

Nucleic acid indexing

DOEpatents

Guilfoyle, Richard A.; Guo, Zhen

2001-01-01

A restriction site indexing method for selectively amplifying any fragment generated by a Class II restriction enzyme includes adaptors specific to fragment ends containing adaptor indexing sequences complementary to fragment indexing sequences near the termini of fragments generated by Class II enzyme cleavage. A method for combinatorial indexing facilitates amplification of restriction fragments whose sequence is not known.

Nucleic acid indexing

DOEpatents

Guilfoyle, Richard A.; Guo, Zhen

1999-01-01

A restriction site indexing method for selectively amplifying any fragment generated by a Class II restriction enzyme includes adaptors specific to fragment ends containing adaptor indexing sequences complementary to fragment indexing sequences near the termini of fragments generated by Class II enzyme cleavage. A method for combinatorial indexing facilitates amplification of restriction fragments whose sequence is not known.

75 FR 66303 - Revocation of Restricted Areas R-3807 Glencoe, LA, and R-6320 Matagorda, TX

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-28

... restricted areas were originally established to contain aerostat balloons used in detecting illegal entry across the southern border of the United States. The aerostat balloons have not been operational for... restricted areas, which were originally established as Tethered Air Radar Sites (TARS) to contain aerostat...

From Agrobacterium to viral vectors: genome modification of plant cells by rare cutting restriction enzymes.

PubMed

Marton, Ira; Honig, Arik; Omid, Ayelet; De Costa, Noam; Marhevka, Elena; Cohen, Barry; Zuker, Amir; Vainstein, Alexander

2013-01-01

Researchers and biotechnologists require methods to accurately modify the genome of higher eukaryotic cells. Such modifications include, but are not limited to, site-specific mutagenesis, site-specific insertion of foreign DNA, and replacement and deletion of native sequences. Accurate genome modifications in plant species have been rather limited, with only a handful of plant species and genes being modified through the use of early genome-editing techniques. The development of rare-cutting restriction enzymes as a tool for the induction of site-specific genomic double-strand breaks and their introduction as a reliable tool for genome modification in animals, animal cells and human cell lines have paved the way for the adaptation of rare-cutting restriction enzymes to genome editing in plant cells. Indeed, the number of plant species and genes which have been successfully edited using zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and engineered homing endonucleases is on the rise. In our review, we discuss the basics of rare-cutting restriction enzyme-mediated genome-editing technology with an emphasis on its application in plant species.

Systematic prediction of control proteins and their DNA binding sites

PubMed Central

Sorokin, Valeriy; Severinov, Konstantin; Gelfand, Mikhail S.

2009-01-01

We present here the results of a systematic bioinformatics analysis of control (C) proteins, a class of DNA-binding regulators that control time-delayed transcription of their own genes as well as restriction endonuclease genes in many type II restriction-modification systems. More than 290 C protein homologs were identified and DNA-binding sites for ∼70% of new and previously known C proteins were predicted by a combination of phylogenetic footprinting and motif searches in DNA upstream of C protein genes. Additional analysis revealed that a large proportion of C protein genes are translated from leaderless RNA, which may contribute to time-delayed nature of genetic switches operated by these proteins. Analysis of genetic contexts of newly identified C protein genes revealed that they are not exclusively associated with restriction-modification genes; numerous instances of associations with genes originating from mobile genetic elements were observed. These instances might be vestiges of ancient horizontal transfers and indicate that during evolution ancestral restriction-modification system genes were the sites of mobile elements insertions. PMID:19056824

Reversible geminate recombination of hydrogen-bonded water molecule pair

NASA Astrophysics Data System (ADS)

Markovitch, Omer; Agmon, Noam

2008-08-01

The (history independent) autocorrelation function for a hydrogen-bonded water molecule pair, calculated from classical molecular dynamics trajectories of liquid water, exhibits a t-3/2 asymptotic tail. Its whole time dependence agrees quantitatively with the solution for reversible diffusion-influenced geminate recombination derived by Agmon and Weiss [J. Chem. Phys. 91, 6937 (1989)]. Agreement with diffusion theory is independent of the precise definition of the bound state. Given the water self-diffusion constant, this theory enables us to determine the dissociation and bimolecular recombination rate parameters for a water dimer. (The theory is indispensable for obtaining the bimolecular rate coefficient.) Interestingly, the activation energies obtained from the temperature dependence of these rate coefficients are similar, rather than differing by the hydrogen-bond (HB) strength. This suggests that recombination requires displacing another water molecule, which meanwhile occupied the binding site. Because these activation energies are about twice the HB strength, cleavage of two HBs may be required to allow pair separation. The autocorrelation function without the HB angular restriction yields a recombination rate coefficient that is larger than that for rebinding to all four tetrahedral water sites (with angular restrictions), suggesting the additional participation of interstitial sites. Following dissociation, the probability of the pair to be unbound but within the reaction sphere rises more slowly than expected, possibly because binding to the interstitial sites delays pair separation. An extended diffusion model, which includes an additional binding site, can account for this behavior.

Owned and unowned dog population estimation, dog management and dog bites to inform rabies prevention and response on Lombok Island, Indonesia.

PubMed

Mustiana, Ana; Toribio, Jenny-Ann; Abdurrahman, Muktasam; Suadnya, I Wayan; Hernandez-Jover, Marta; Putra, Anak Agung Gde; Ward, Michael P

2015-01-01

Although Indonesia has been rabies-infected since at least the 1880s, some islands remain rabies-free, such as Lombok. However, due to its adjacency to rabies-infected islands such as Bali and Flores, there is considerable risk of a rabies incursion. As part of a rabies risk assessment project, surveys were conducted to estimate the size of the dog population and to describe dog management practices of households belonging to different ethnic groups. A photographic-recapture method was employed and the number of unowned dogs was estimated. A total of 400 dog owning households were interviewed, 300 at an urban site and 100 at a rural site. The majority of the interviewed households belonged to the Balinese ethnic group. Owned dogs were more likely male, and non-pedigree or local breed. These households kept their dogs either fully restricted, semi-free roaming or free-roaming but full restriction was reported only at the urban site. Dog bite cases were reported to be higher at the urban site, and commonly affected children/young adults to 20 years old and males. A higher number of unowned dogs was observed at the urban site than at the rural site. Data generated within these surveys can inform rabies risk assessment models to quantify the probability of rabies being released into Lombok and resulting in the infection of the local dog population. The information gained is critical for efforts to educate dog owners about rabies, as a component of preparedness to prevent the establishment of rabies should an incursion occur.

Owned and Unowned Dog Population Estimation, Dog Management and Dog Bites to Inform Rabies Prevention and Response on Lombok Island, Indonesia

PubMed Central

Mustiana, Ana; Toribio, Jenny-Ann; Abdurrahman, Muktasam; Suadnya, I. Wayan; Hernandez-Jover, Marta; Putra, Anak Agung Gde; Ward, Michael P.

2015-01-01

Although Indonesia has been rabies-infected since at least the 1880s, some islands remain rabies-free, such as Lombok. However, due to its adjacency to rabies-infected islands such as Bali and Flores, there is considerable risk of a rabies incursion. As part of a rabies risk assessment project, surveys were conducted to estimate the size of the dog population and to describe dog management practices of households belonging to different ethnic groups. A photographic-recapture method was employed and the number of unowned dogs was estimated. A total of 400 dog owning households were interviewed, 300 at an urban site and 100 at a rural site. The majority of the interviewed households belonged to the Balinese ethnic group. Owned dogs were more likely male, and non-pedigree or local breed. These households kept their dogs either fully restricted, semi-free roaming or free-roaming but full restriction was reported only at the urban site. Dog bite cases were reported to be higher at the urban site, and commonly affected children/young adults to 20 years old and males. A higher number of unowned dogs was observed at the urban site than at the rural site. Data generated within these surveys can inform rabies risk assessment models to quantify the probability of rabies being released into Lombok and resulting in the infection of the local dog population. The information gained is critical for efforts to educate dog owners about rabies, as a component of preparedness to prevent the establishment of rabies should an incursion occur. PMID:25932916

An isoleucine to leucine mutation that switches the cofactor requirement of the EcoRV restriction endonuclease from magnesium to manganese.

PubMed

Vipond, I B; Moon, B J; Halford, S E

1996-02-13

The EcoRV restriction endonuclease cleaves DNA at its recognition sequence more readily with Mg2+ as the cofactor than with Mn2+ but, at noncognate sequences that differ from the EcoRV site by one base pair, Mn2+ gives higher rates than Mg2+. A mutant of EcoRV, in which an isoleucine near the active site was replaced by leucine, showed the opposite behavior. It had low activity with Mg2+, but, in the presence of Mn2+ ions, it cleaved the recognition site faster than wild-type EcoRV with either Mn2+ or Mg2+. The mutant was also more specific for the recognition sequence than the native enzyme: the noncognate DNA cleavages by wild-type EcoRV and Mn2+ were not detected with the mutant. Further mutagenesis showed that the protein required the same acidic residues at its active site as wild-type EcoRV. The Ile-->Leu mutation seems to perturb the configuration of the metal-binding ligands at the active site so that the protein has virtually no affinity for Mg2+ yet it can still bind Mn2+ ions, though the latter only occurs when the protein is at the recognition site. This contrasts to wild-type EcoRV, where Mn2+ ions bind readily to complexes with either cognate and noncognate DNA and only Mg2+ shows the discrimination between the complexes. The structural perturbation is a specific consequence of leucine in place of isoleucine, since mutants with valine or alanine were similar to wild-type EcoRV.

Clonality and diversity of the fish pathogen Lactococcus garvieae in Mediterranean countries.

PubMed

Eyngor, Marina; Zlotkin, Amir; Ghittino, Claudio; Prearo, Marino; Douet, Diane-Gaëlle; Chilmonczyk, Stefan; Eldar, Avi

2004-09-01

Infection with Lactococcus garvieae is considered the most important risk factor for the European trout industry, and the losses are approximately 50% of the total production. To improve our understanding of the genetic links among strains originating from different countries, we examined the population structure of L. garvieae by comparing 81 strains isolated from different sources and ecosystems (41 farms in six countries) in which the bacterium is commonly found. Genetic similarities (as assessed with molecular tools, including restriction fragment length polymorphism ribotyping with two endonucleases) were compared with serological data. The combined results reveal that in endemic sites the bacterial population displays a clonal structure, whereas bacterial diversity characterizes sites where the infection is sporadic.

Molecular Analysis of Bacterial Community Dynamics During Bioaugmentation Studies in a Soil Column and at a Field Test Site

DTIC Science & Technology

2004-06-03

82 4.14 A GelComparII-generated UPGMA clustering dendrogram and corresponding normalized restriction...A GelComparII-generated UPGMA clustering dendrogram and corresponding normalized restriction profiles from the community...A GelComparII-generated UPGMA clustering dendrogram and corresponding normalized restriction profiles from the community

Fast and Efficient Drosophila melanogaster Gene Knock-Ins Using MiMIC Transposons

PubMed Central

Vilain, Sven; Vanhauwaert, Roeland; Maes, Ine; Schoovaerts, Nils; Zhou, Lujia; Soukup, Sandra; da Cunha, Raquel; Lauwers, Elsa; Fiers, Mark; Verstreken, Patrik

2014-01-01

Modern molecular genetics studies necessitate the manipulation of genes in their endogenous locus, but most of the current methodologies require an inefficient donor-dependent homologous recombination step to locally modify the genome. Here we describe a methodology to efficiently generate Drosophila knock-in alleles by capitalizing on the availability of numerous genomic MiMIC transposon insertions carrying recombinogenic attP sites. Our methodology entails the efficient PhiC31-mediated integration of a recombination cassette flanked by unique I-SceI and/or I-CreI restriction enzyme sites into an attP-site. These restriction enzyme sites allow for double-strand break−mediated removal of unwanted flanking transposon sequences, while leaving the desired genomic modifications or recombination cassettes. As a proof-of-principle, we mutated LRRK, tau, and sky by using different MiMIC elements. We replaced 6 kb of genomic DNA encompassing the tau locus and 35 kb encompassing the sky locus with a recombination cassette that permits easy integration of DNA at these loci and we also generated a functional LRRKHA knock in allele. Given that ~92% of the Drosophila genes are located within the vicinity (<35 kb) of a MiMIC element, our methodology enables the efficient manipulation of nearly every locus in the fruit fly genome without the need for inefficient donor-dependent homologous recombination events. PMID:25298537

Fast and efficient Drosophila melanogaster gene knock-ins using MiMIC transposons.

PubMed

Vilain, Sven; Vanhauwaert, Roeland; Maes, Ine; Schoovaerts, Nils; Zhou, Lujia; Soukup, Sandra; da Cunha, Raquel; Lauwers, Elsa; Fiers, Mark; Verstreken, Patrik

2014-10-08

Modern molecular genetics studies necessitate the manipulation of genes in their endogenous locus, but most of the current methodologies require an inefficient donor-dependent homologous recombination step to locally modify the genome. Here we describe a methodology to efficiently generate Drosophila knock-in alleles by capitalizing on the availability of numerous genomic MiMIC transposon insertions carrying recombinogenic attP sites. Our methodology entails the efficient PhiC31-mediated integration of a recombination cassette flanked by unique I-SceI and/or I-CreI restriction enzyme sites into an attP-site. These restriction enzyme sites allow for double-strand break-mediated removal of unwanted flanking transposon sequences, while leaving the desired genomic modifications or recombination cassettes. As a proof-of-principle, we mutated LRRK, tau, and sky by using different MiMIC elements. We replaced 6 kb of genomic DNA encompassing the tau locus and 35 kb encompassing the sky locus with a recombination cassette that permits easy integration of DNA at these loci and we also generated a functional LRRK(HA) knock in allele. Given that ~92% of the Drosophila genes are located within the vicinity (<35 kb) of a MiMIC element, our methodology enables the efficient manipulation of nearly every locus in the fruit fly genome without the need for inefficient donor-dependent homologous recombination events. Copyright © 2014 Vilain et al.

Chronic obstructive pulmonary disease mortality and prevalence: the associations with smoking and poverty--a BOLD analysis.

PubMed

Burney, Peter; Jithoo, Anamika; Kato, Bernet; Janson, Christer; Mannino, David; Nizankowska-Mogilnicka, Ewa; Studnicka, Michael; Tan, Wan; Bateman, Eric; Koçabas, Ali; Vollmer, William M; Gislason, Thorarrin; Marks, Guy; Koul, Parvaiz A; Harrabi, Imed; Gnatiuc, Louisa; Buist, Sonia

2014-05-01

Chronic obstructive pulmonary disease (COPD) is a commonly reported cause of death and associated with smoking. However, COPD mortality is high in poor countries with low smoking rates. Spirometric restriction predicts mortality better than airflow obstruction, suggesting that the prevalence of restriction could explain mortality rates attributed to COPD. We have studied associations between mortality from COPD and low lung function, and between both lung function and death rates and cigarette consumption and gross national income per capita (GNI). National COPD mortality rates were regressed against the prevalence of airflow obstruction and spirometric restriction in 22 Burden of Obstructive Lung Disease (BOLD) study sites and against GNI, and national smoking prevalence. The prevalence of airflow obstruction and spirometric restriction in the BOLD sites were regressed against GNI and mean pack years smoked. National COPD mortality rates were more strongly associated with spirometric restriction in the BOLD sites (<60 years: men rs=0.73, p=0.0001; women rs=0.90, p<0.0001; 60+ years: men rs=0.63, p=0.0022; women rs=0.37, p=0.1) than obstruction (<60 years: men rs=0.28, p=0.20; women rs=0.17, p<0.46; 60+ years: men rs=0.28, p=0.23; women rs=0.22, p=0.33). Obstruction increased with mean pack years smoked, but COPD mortality fell with increased cigarette consumption and rose rapidly as GNI fell below US$15 000. Prevalence of restriction was not associated with smoking but also increased rapidly as GNI fell below US$15 000. Smoking remains the single most important cause of obstruction but a high prevalence of restriction associated with poverty could explain the high 'COPD' mortality in poor countries.

Establishing physico-chemical reference conditions in Mediterranean streams according to the European Water Framework Directive.

PubMed

Sánchez-Montoya, María del Mar; Arce, Maria Isabel; Vidal-Abarca, María Rosario; Suárez, María Luisa; Prat, Narcís; Gómez, Rosa

2012-05-01

Type-specific physico-chemical reference conditions are required for the assessment of ecological status in the Water Framework Directive context, similarly to the biological and hydro-morphological elements. This directive emphasises that natural variability of quality elements in high status (reference condition) needs to be quantified. Mediterranean streams often present a marked seasonal pattern in hydrological, biological and geochemical processes which could affect physico-chemical reference conditions. This study establishes general physico-chemical reference conditions (oxygenation, nutrient, salinity and acidification conditions) for different Mediterranean stream types. 116 potential reference sites located in 23 Mediterranean catchments in Spain were sampled in spring, summer and autumn in 2003. All sites were subjected to a screening method for the selection of reference sites in Mediterranean streams (Mediterranean Reference Criteria) and classified using a pre-established stream typology that establishes five different stream types (temporary streams, evaporite-calcareous at medium altitude, siliceous headwaters, calcareous headwaters and large watercourses). Reference conditions (reference value and reference threshold equivalents to high-good class boundary) were calculated using two different methods according to the availability of reference sites: the reference site 75th percentile approach of all reference sites and the 25th percentile of the population approach. The majority of the studied potential reference sites (76 out of 116) were selected as reference sites. Regarding type-specific reference conditions, only siliceous headwaters could be considered different from the rest of stream types because lower conductivity and pH. All reference stream types presented seasonal differences as regards some parameters, except for temporary streams due to the high natural variation of this stream type. For those parameters which presented seasonal differences in a specific stream type, the least restrictive values were proposed as reference conditions. Copyright © 2012 Elsevier Ltd. All rights reserved.

Visible, Durable, Enforceable Institutional Controls: Weldon Spring Site - A 10-Year Journey - 13190

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

Uhlmeyer, Terri; Thompson, Randy; Starr, Ken

2013-07-01

The DOE Office of Legacy Management's (LM's) mission is to manage the DOE's post-closure responsibilities and ensure the future protection of human health and the environment. LM has control and custody of legacy land, structures, and facilities and is responsible for maintaining them at levels suitable for their long-term use. This includes all engineered and institutional controls (ICs) designed as another level of assurance to prevent exposure to residual contamination and waste. The development and management of ICs has been, and continues to be, a critical component to the success of LM surveillance and maintenance activities. Many major federal laws,more » Executive Orders, regulations, and various other drivers influence the establishment and use of ICs at LM sites. LM uses a wide range of ICs to appropriately limit access to, or uses of, land, facilities, and other real and personal properties; protect the environment; maintain the physical safety and security of DOE facilities; and prevent or limit inadvertent human and environmental exposure to residual contaminants and other hazards. The ICs at the Weldon Spring, Missouri, Site were developed in close coordination with federal and state regulators. An Explanation of Significant Differences (ESD) was issued in February 2005, which clarified the use restrictions necessary for the remedial actions specified in the Records of Decision for the separate operable units to remain protective over the long-term. The operable units included the Chemical Plant Operable Unit, the Chemical Plant Groundwater Operable Unit, and the Quarry Residuals Operable Unit. The ESD clarified specific requirements for each site area that needed use restrictions and established how DOE would implement, maintain, and monitor the specific requirements. DOE developed the Long-Term Surveillance and Maintenance Plan for the U.S. Department of Energy Weldon Spring, Missouri, Site (LTS and M Plan) that addressed the full scope of the site management activities necessary to ensure that the Weldon Spring Site remains protective over the long-term. The LTS and M Plan is revised periodically to ensure its applicability to changing site, regulatory, or procedural conditions. In addition to addressing such activities as long-term groundwater monitoring and disposal cell maintenance, the LTS and M Plan was developed and issued to ensure that the use restrictions identified in the ESD were properly imposed and maintained. The LTS and M Plan included a detailed IC Implementation Plan, which includes a process for evaluating and identifying specific IC mechanisms that best accomplish the objectives set out in the ESD. Consistent with EPA guidance on selecting ICs, various IC mechanisms were evaluated, including government controls, proprietary controls, enforcement tools, and informational devices. Where appropriate, redundant mechanisms were employed to increase the effectiveness of the ICs. Information in the IC Implementation Plan includes: (1) a discussion of current site conditions (reflecting post-remedial action conditions for the Chemical Plant and Quarry Areas and the risk-basis for why use restrictions are needed); (2) the objectives of, or performance expectations for, the use restrictions; (3) specific ICs already in place and additional mechanisms identified for implementation; (4) a schedule for implementing additional ICs; (5) procedures for maintaining the ICs and for conducting periodic inspections; and (6) general provisions for the implementing ICs for the site. The actual agreements and documentation of the various ICs are included in an appendix of the LTS and M Plan. These documents are also available via the internet from the authorizing agencies (County, Missouri Department of Natural Resources, EPA, etc.) The Weldon Spring Site personnel have been successful in finalizing each of the ICs that were established for the site. The planning, establishment, and implementation of the ICs was a long and detailed process with several lessons-learned that were identified along the way. (authors)« less

Fragment length polymorphisms among independent isolates of Epstein-Barr virus from immunocompromised and normal hosts.

PubMed

Katz, B Z; Niederman, J C; Olson, B A; Miller, G

1988-02-01

DNA restriction fragment length polymorphisms of Epstein-Barr virus (EBV) DNA were used as a molecular epidemiological tool to study multiple isolates of virus from the same and different individuals. We studied 35 EBV isolates: 19 from seven immunocompromised children and 16 from seven college students with mononucleosis. Analysis of the fragment length polymorphisms in this collection of isolates permitted several conclusions. Sites of polymorphism were most often encountered in regions with repetitive DNA. Epidemiologically unrelated patients harbored viruses that could be readily distinguished; by contrast, two infants and their mothers harbored similar viruses. Isolates from different sites in the same patient were similar. Variations between different clinical isolates of EBV mimic those found between different laboratory strains of the virus. Fragment length polymorphisms thus provide a useful marker for studying transmission and pathogenesis of EBV infections.

State preemption of local smoke-free laws in government work sites, private work sites, and restaurants - United States, 2005-2009.

PubMed

2010-02-05

Smoke-free policies (i.e., policies that completely eliminate smoking in indoor workplaces and public places) result in health benefits, including preventing heart attacks. Preemptive legislation at the state level prohibits localities from enacting laws that vary from state law or are more stringent. A Healthy People 2010 objective (27-19) is to eliminate state laws that preempt stronger local tobacco control laws. A 2005 CDC review found that little progress was being made toward reducing the number of state laws preempting local smoking restrictions in three indoor settings: government work sites, private-sector work sites, and restaurants. These three settings were selected for analysis because they are settings that often are addressed by state and local smoking restrictions and because they are major settings where nonsmoking workers and patrons are exposed to secondhand smoke. This report updates the previous analysis and summarizes changes that occurred from December 31, 2004, to December 31, 2009, in state laws that preempt local smoke-free laws for the same three settings. During that period, the number of states preempting local smoking restrictions in at least one of these three settings decreased from 19 to 12. In contrast with the 2005 findings, this decrease indicates progress toward achieving the goal of eliminating state laws preempting local smoking restrictions. Further progress could result in additional reductions in secondhand smoke exposure.

10 CFR 862.7 - Designation of sites.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 4 2011-01-01 2011-01-01 false Designation of sites. 862.7 Section 862.7 Energy DEPARTMENT OF ENERGY RESTRICTIONS ON AIRCRAFT LANDING AND AIR DELIVERY AT DEPARTMENT OF ENERGY NUCLEAR SITES § 862.7 Designation of sites. (a) DOE shall designate sites covered by this part as deemed necessary...

10 CFR 862.7 - Designation of sites.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 4 2010-01-01 2010-01-01 false Designation of sites. 862.7 Section 862.7 Energy DEPARTMENT OF ENERGY RESTRICTIONS ON AIRCRAFT LANDING AND AIR DELIVERY AT DEPARTMENT OF ENERGY NUCLEAR SITES § 862.7 Designation of sites. (a) DOE shall designate sites covered by this part as deemed necessary...

Characterization of a restriction-modification system of the thermotolerant methylotroph Bacillus methanolicus.

PubMed Central

Cue, D; Lam, H; Hanson, R S; Flickinger, M C

1996-01-01

We report the isolation of a restriction endonuclease, BmeTI, an isoschizomer of BclI, that recognizes the DNA sequence 5' TGATCA 3'. We also report that BmeTI sites are modified to TGm6ATCA. These findings provide the basis for devising strategies to prevent BmeTI restriction of any DNA introduced into Bacillus methanolicus. PMID:8975604

Chemical restrictions of roots in Ultisol subsoils lessened by long-term management

NASA Technical Reports Server (NTRS)

Hardy, D. H.; Raper, C. D. Jr; Miner, G. S.; Raper CD, J. r. (Principal Investigator)

1990-01-01

Exchangeable Al in subsoils of Ultisols in the southeastern USA can restrict rooting depth. Downward movement of basic cations (Ca, Mg, and K), applied as lime and fertilizer, may diminish that restriction over time. Materials from the argillic horizon were collected from three paired sites, having managed (long-term cropping) and nonmanaged topsoils (Typic Paleudults and Hapludults). One managed site was cropped continuously for 15 yr while the others were cultivated for more than 30 yr. Concentrations of extractable cations and other nutrients from the paired sites were compared to determine the magnitude of change due to management. The ability of the subsoils to support plant growth was evaluated in a missing-nutrient greenhouse experiment with sorghum [Sorghum bicolor (L.) Moench]. Subsoils of managed sites had greater effective cation-exchange capacity (CEC) and base saturation than those of non-managed sites. While availabilities of Ca, Mg, and K in subsoils of nonmanaged sites were inadequate to support maximal plant growth, they were adequate in subsoils of managed sites. Compared with nonmanaged sites, KCl-exchangeable Al in subsoils of managed sites was 23% lower at the 15-yr location and 65 and 100% lower at the two other locations. In the absence of lime, sorghum growth was almost totally inhibited on nonmanaged subsoils amended with optimum nutrients. On the managed subsoils, where 100, 65, and 23% of the nonmanaged exchangeable Al had been neutralized by topsoil fertilization and liming, growth reductions under the same conditions were 0, 50, and 100%, respectively. Thus, relatively long-term management had improved these Ultisol subsoils for root growth and development.

25 CFR 248.9 - Camping and use restrictions.

Code of Federal Regulations, 2011 CFR

2011-04-01

... beverages, setting or use of fires, use of the sites for cleaning of fish, the deposit of any garbage, paper... Area Director may prescribe and cause to be posted on the site or sites to which said regulations are...

25 CFR 248.9 - Camping and use restrictions.

Code of Federal Regulations, 2014 CFR

2014-04-01

... beverages, setting or use of fires, use of the sites for cleaning of fish, the deposit of any garbage, paper... Area Director may prescribe and cause to be posted on the site or sites to which said regulations are...

25 CFR 248.9 - Camping and use restrictions.

Code of Federal Regulations, 2012 CFR

2012-04-01

... beverages, setting or use of fires, use of the sites for cleaning of fish, the deposit of any garbage, paper... Area Director may prescribe and cause to be posted on the site or sites to which said regulations are...

25 CFR 248.9 - Camping and use restrictions.

Code of Federal Regulations, 2013 CFR

2013-04-01

... beverages, setting or use of fires, use of the sites for cleaning of fish, the deposit of any garbage, paper... Area Director may prescribe and cause to be posted on the site or sites to which said regulations are...

25 CFR 248.9 - Camping and use restrictions.

Code of Federal Regulations, 2010 CFR

2010-04-01

... beverages, setting or use of fires, use of the sites for cleaning of fish, the deposit of any garbage, paper... Area Director may prescribe and cause to be posted on the site or sites to which said regulations are...

25 CFR 141.31 - Trade by Indian Affairs employees restricted.

Code of Federal Regulations, 2010 CFR

2010-04-01

... organization. (b) Lease or sale of home sites or allotments on trust or restricted Indian land to or from... (or affirm) that I have not exercised any undue influence nor used any special knowledge received by...

25 CFR 247.17 - What are the restrictions on fires?

Code of Federal Regulations, 2010 CFR

2010-04-01

... TREATY FISHING ACCESS SITES § 247.17 What are the restrictions on fires? (a) You cannot burn timber, trees, slash, brush or grass unless you have a permit issued by the Area Director or his designee. (b...

25 CFR 247.17 - What are the restrictions on fires?

Code of Federal Regulations, 2012 CFR

2012-04-01

... TREATY FISHING ACCESS SITES § 247.17 What are the restrictions on fires? (a) You cannot burn timber, trees, slash, brush or grass unless you have a permit issued by the Area Director or his designee. (b...

25 CFR 247.17 - What are the restrictions on fires?

Code of Federal Regulations, 2011 CFR

2011-04-01

... TREATY FISHING ACCESS SITES § 247.17 What are the restrictions on fires? (a) You cannot burn timber, trees, slash, brush or grass unless you have a permit issued by the Area Director or his designee. (b...

25 CFR 247.17 - What are the restrictions on fires?

Code of Federal Regulations, 2013 CFR

2013-04-01

... TREATY FISHING ACCESS SITES § 247.17 What are the restrictions on fires? (a) You cannot burn timber, trees, slash, brush or grass unless you have a permit issued by the Area Director or his designee. (b...

25 CFR 247.17 - What are the restrictions on fires?

Code of Federal Regulations, 2014 CFR

2014-04-01

... TREATY FISHING ACCESS SITES § 247.17 What are the restrictions on fires? (a) You cannot burn timber, trees, slash, brush or grass unless you have a permit issued by the Area Director or his designee. (b...

Assessing the Efficacy of Restricting Access to Barbecue Charcoal for Suicide Prevention in Taiwan: A Community-Based Intervention Trial

PubMed Central

Chen, Ying-Yeh; Chen, Feng; Chang, Shu-Sen; Wong, Jacky; Yip, Paul S F

2015-01-01

Objective Charcoal-burning suicide has recently been spreading to many Asian countries. There have also been several cases involving this new method of suicide in Western countries. Restricting access to suicide means is one of the few suicide-prevention measures that have been supported by empirical evidence. The current study aims to assess the effectiveness of a community intervention program that restricts access to charcoal to prevent suicide in Taiwan. Methods and Findings A quasi-experimental design is used to compare method-specific (charcoal-burning suicide, non-charcoal-burning suicide) and overall suicide rates in New Taipei City (the intervention site, with a population of 3.9 million) with two other cities (Taipei City and Kaohsiung City, the control sites, each with 2.7 million residents) before (Jan 1st 2009- April 30th 2012) and after (May 1st 2012-Dec. 31st 2013) the initiation of a charcoal-restriction program on May 1st 2012. The program mandates the removal of barbecue charcoal from open shelves to locked storage in major retail stores in New Taipei City. No such restriction measure was implemented in the two control sites. Generalized linear regression models incorporating secular trends were used to compare the changes in method-specific and overall suicide rates before and after the initiation of the restriction measure. A simulation approach was used to estimate the number of lives saved by the intervention. Compared with the pre-intervention period, the estimated rate reduction of charcoal-burning suicide in New Taipei City was 37% (95% CI: 17%, 50%) after the intervention. Taking secular trends into account, the reduction was 30% (95% CI: 14%, 44%). No compensatory rise in non-charcoal-burning suicide was observed in New Taipei City. No significant reduction in charcoal-burning suicide was observed in the other two control sites. The simulation approach estimated that 91 (95%CI [55, 128]) lives in New Taipei City were saved during the 20 months of the intervention. Conclusion Our results demonstrate that the charcoal-restriction program reduced method-specific and overall suicides. This study provides strong empirical evidence that restricting the accessibility of common lethal methods of suicide can effectively reduce suicide rates. PMID:26305374

Facilitated diffusion in chromatin lattices: mechanistic diversity and regulatory potential.

PubMed

Kampmann, Martin

2005-08-01

The interaction between a protein and a specific DNA site is the molecular basis for vital processes in all organisms. Location of the DNA target site by the protein commonly involves facilitated diffusion. Mechanisms of facilitated diffusion vary among proteins; they include one- and two-dimensional sliding along DNA, direct transfer between uncorrelated sites, as well as combinations of these mechanisms. Facilitated diffusion has almost exclusively been studied in vitro. This review discusses facilitated diffusion in the context of the living cell and proposes a theoretical model for facilitated diffusion in chromatin lattices. Chromatin structure differentially affects proteins in different modes of diffusion. The interplay of facilitated diffusion and chromatin structure can determine the rate of protein association with the target site, the frequency of association-dissociation events at the target site, and, under particular conditions, the occupancy of the target site. Facilitated diffusion is required in vivo for efficient DNA repair and bacteriophage restriction and has potential roles in fine-tuning gene regulatory networks and kinetically compartmentalizing the eukaryotic nucleus.

COBRA-Seq: Sensitive and Quantitative Methylome Profiling

PubMed Central

Varinli, Hilal; Statham, Aaron L.; Clark, Susan J.; Molloy, Peter L.; Ross, Jason P.

2015-01-01

Combined Bisulfite Restriction Analysis (COBRA) quantifies DNA methylation at a specific locus. It does so via digestion of PCR amplicons produced from bisulfite-treated DNA, using a restriction enzyme that contains a cytosine within its recognition sequence, such as TaqI. Here, we introduce COBRA-seq, a genome wide reduced methylome method that requires minimal DNA input (0.1–1.0 μg) and can either use PCR or linear amplification to amplify the sequencing library. Variants of COBRA-seq can be used to explore CpG-depleted as well as CpG-rich regions in vertebrate DNA. The choice of enzyme influences enrichment for specific genomic features, such as CpG-rich promoters and CpG islands, or enrichment for less CpG dense regions such as enhancers. COBRA-seq coupled with linear amplification has the additional advantage of reduced PCR bias by producing full length fragments at high abundance. Unlike other reduced representative methylome methods, COBRA-seq has great flexibility in the choice of enzyme and can be multiplexed and tuned, to reduce sequencing costs and to interrogate different numbers of sites. Moreover, COBRA-seq is applicable to non-model organisms without the reference genome and compatible with the investigation of non-CpG methylation by using restriction enzymes containing CpA, CpT, and CpC in their recognition site. PMID:26512698

Modification-dependent restriction endonuclease, MspJI, flips 5-methylcytosine out of the DNA helix

DOE PAGES

Horton, J. R.; Wang, H.; Mabuchi, M. Y.; ...

2014-09-27

MspJI belongs to a family of restriction enzymes that cleave DNA containing 5-methylcytosine (5mC) or 5-hydroxymethylcytosine (5hmC). MspJI is specific for the sequence 5(h)mC-N-N-G or A and cleaves with some variability 9/13 nucleotides downstream. Earlier, we reported the crystal structure of MspJI without DNA and proposed how it might recognize this sequence and catalyze cleavage. Here we report its co-crystal structure with a 27-base pair oligonucleotide containing 5mC. This structure confirms that MspJI acts as a homotetramer and that the modified cytosine is flipped from the DNA helix into an SRA-like-binding pocket. We expected the structure to reveal two DNAmore » molecules bound specifically to the tetramer and engaged with the enzyme's two DNA-cleavage sites. A coincidence of crystal packing precluded this organization, however. We found that each DNA molecule interacted with two adjacent tetramers, binding one specifically and the other non-specifically. The latter interaction, which prevented cleavage-site engagement, also involved base flipping and might represent the sequence-interrogation phase that precedes specific recognition. MspJI is unusual in that DNA molecules are recognized and cleaved by different subunits. Such interchange of function might explain how other complex multimeric restriction enzymes act.« less

Generation of HIV-1 based bi-cistronic lentiviral vectors for stable gene expression and live cell imaging.

PubMed

Sehgal, Lalit; Budnar, Srikanth; Bhatt, Khyati; Sansare, Sneha; Mukhopadhaya, Amitabha; Kalraiya, Rajiv D; Dalal, Sorab N

2012-10-01

The study of protein-protein interactions, protein localization, protein organization into higher order structures and organelle dynamics in live cells, has greatly enhanced the understanding of various cellular processes. Live cell imaging experiments employ plasmid or viral vectors to express the protein/proteins of interest fused to a fluorescent protein. Unlike plasmid vectors, lentiviral vectors can be introduced into both dividing and non dividing cells, can be pseudotyped to infect a broad or narrow range of cells, and can be used to generate transgenic animals. However, the currently available lentiviral vectors are limited by the choice of fluorescent protein tag, choice of restriction enzyme sites in the Multiple Cloning Sites (MCS) and promoter choice for gene expression. In this report, HIV-1 based bi-cistronic lentiviral vectors have been generated that drive the expression of multiple fluorescent tags (EGFP, mCherry, ECFP, EYFP and dsRed), using two different promoters. The presence of a unique MCS with multiple restriction sites allows the generation of fusion proteins with the fluorescent tag of choice, allowing analysis of multiple fusion proteins in live cell imaging experiments. These novel lentiviral vectors are improved delivery vehicles for gene transfer applications and are important tools for live cell imaging in vivo.

DNA looping by FokI: the impact of synapse geometry on loop topology at varied site orientations

PubMed Central

Rusling, David A.; Laurens, Niels; Pernstich, Christian; Wuite, Gijs J. L.; Halford, Stephen E.

2012-01-01

Most restriction endonucleases, including FokI, interact with two copies of their recognition sequence before cutting DNA. On DNA with two sites they act in cis looping out the intervening DNA. While many restriction enzymes operate symmetrically at palindromic sites, FokI acts asymmetrically at a non-palindromic site. The directionality of its sequence means that two FokI sites can be bridged in either parallel or anti-parallel alignments. Here we show by biochemical and single-molecule biophysical methods that FokI aligns two recognition sites on separate DNA molecules in parallel and that the parallel arrangement holds for sites in the same DNA regardless of whether they are in inverted or repeated orientations. The parallel arrangement dictates the topology of the loop trapped between sites in cis: the loop from inverted sites has a simple 180° bend, while that with repeated sites has a convoluted 360° turn. The ability of FokI to act at asymmetric sites thus enabled us to identify the synapse geometry for sites in trans and in cis, which in turn revealed the relationship between synapse geometry and loop topology. PMID:22362745

25 CFR 247.11 - What other restrictions apply to use of the sites?

Code of Federal Regulations, 2012 CFR

2012-04-01

... Area Director may prescribe and post at the sites regulations covering: (a) Camping; (b) Picnicking; (c) Use of alcoholic beverages; (d) Setting or use of fires; (e) Use of the sites for cleaning fish; (f...

25 CFR 247.11 - What other restrictions apply to use of the sites?

Code of Federal Regulations, 2010 CFR

2010-04-01

... Area Director may prescribe and post at the sites regulations covering: (a) Camping; (b) Picnicking; (c) Use of alcoholic beverages; (d) Setting or use of fires; (e) Use of the sites for cleaning fish; (f...

25 CFR 247.11 - What other restrictions apply to use of the sites?

Code of Federal Regulations, 2013 CFR

2013-04-01

... Area Director may prescribe and post at the sites regulations covering: (a) Camping; (b) Picnicking; (c) Use of alcoholic beverages; (d) Setting or use of fires; (e) Use of the sites for cleaning fish; (f...

25 CFR 247.11 - What other restrictions apply to use of the sites?

Code of Federal Regulations, 2011 CFR

2011-04-01

... Area Director may prescribe and post at the sites regulations covering: (a) Camping; (b) Picnicking; (c) Use of alcoholic beverages; (d) Setting or use of fires; (e) Use of the sites for cleaning fish; (f...

25 CFR 247.11 - What other restrictions apply to use of the sites?

Code of Federal Regulations, 2014 CFR

2014-04-01

... Area Director may prescribe and post at the sites regulations covering: (a) Camping; (b) Picnicking; (c) Use of alcoholic beverages; (d) Setting or use of fires; (e) Use of the sites for cleaning fish; (f...

Quercus rubra-associated ectomycorrhizal fungal communities of disturbed urban sites and mature forests.

PubMed

Karpati, Amy S; Handel, Steven N; Dighton, John; Horton, Thomas R

2011-08-01

The presence and quality of the belowground mycorrhizal fungal community could greatly influence plant community structure and host species response. This study tests whether mycorrhizal fungal communities in areas highly impacted by anthropogenic disturbance and urbanization are less species rich or exhibit lower host root colonization rates when compared to those of less disturbed systems. Using a soil bioassay, we sampled the ectomycorrhizal fungal (EMF) communities associating with Quercus rubra (northern red oak) seedlings in soil collected from seven sites: two mature forest reference sites and five urban sites of varying levels of disturbance. Morphological and polymerase chain reaction-restriction fragment length polymorphism analyses of fungi colonizing root tips revealed that colonization rates and fungal species richness were significantly lower on root systems of seedlings grown in disturbed site soils. Analysis of similarity showed that EMF community composition was not significantly different among several urban site soils but did differ significantly between mature forest sites and all but one urban site. We identified a suite of fungal species that occurred across several urban sites. Lack of a diverse community of belowground mutualists could be a constraint on urban plant community development, especially of late-successional woodlands. Analysis of urban EMF communities can add to our understanding of urban plant community structure and should be addressed during ecological assessment before pragmatic decisions to restore habitats are framed.

Recombination between bacteriophage lambda and plasmid pBR322 in Escherichia coli.

PubMed Central

Pogue-Geile, K L; Dassarma, S; King, S R; Jaskunas, S R

1980-01-01

Recombinant lambda phages were isolated that resulted from recombination between the lambda genome and plasmid pBR322 in Escherichia coli, even though these deoxyribonucleic acids (DNAs) did not share extensive regions of homology. The characterization of these recombinant DNAs by heteroduplex analysis and restriction endonucleases is described. All but one of the recombinants appeared to have resulted from reciprocal recombination between a site on lambda DNA and a site on the plasmid. In general, there were two classes of recombinants. One class appeared to have resulted from recombination at the phage attachment site that probably resulted from lambda integration into secondary attachment sites on the plasmid. Seven different secondary attachment sites on pBR322 were found. The other class resulted from plasmid integration at other sites that were widely scattered on the lambda genome. For this second class of recombinants, more than one site on the plasmid could recombine with lambda DNA. Thus, the recombination did not appear to be site specific with respect to lambda or the plasmid. Possible mechanisms for generating these recombinants are discussed. Images PMID:6247334

Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data.

PubMed

Excoffier, L; Smouse, P E; Quattro, J M

1992-06-01

We present here a framework for the study of molecular variation within a single species. Information on DNA haplotype divergence is incorporated into an analysis of variance format, derived from a matrix of squared-distances among all pairs of haplotypes. This analysis of molecular variance (AMOVA) produces estimates of variance components and F-statistic analogs, designated here as phi-statistics, reflecting the correlation of haplotypic diversity at different levels of hierarchical subdivision. The method is flexible enough to accommodate several alternative input matrices, corresponding to different types of molecular data, as well as different types of evolutionary assumptions, without modifying the basic structure of the analysis. The significance of the variance components and phi-statistics is tested using a permutational approach, eliminating the normality assumption that is conventional for analysis of variance but inappropriate for molecular data. Application of AMOVA to human mitochondrial DNA haplotype data shows that population subdivisions are better resolved when some measure of molecular differences among haplotypes is introduced into the analysis. At the intraspecific level, however, the additional information provided by knowing the exact phylogenetic relations among haplotypes or by a nonlinear translation of restriction-site change into nucleotide diversity does not significantly modify the inferred population genetic structure. Monte Carlo studies show that site sampling does not fundamentally affect the significance of the molecular variance components. The AMOVA treatment is easily extended in several different directions and it constitutes a coherent and flexible framework for the statistical analysis of molecular data.

Mumps Hoshino and Torii vaccine strains were distinguished from circulating wild strains.

PubMed

Sawada, Akihito; Yamaji, Yoshiaki; Nakayama, Tetsuo

2013-06-01

Aseptic meningitis and acute parotitis have been observed after mumps vaccination. Mumps outbreaks have been reported in Japan because of low vaccine coverage, and molecular differentiation is required to determine whether these cases are vaccine associated. RT-nested PCR was performed in the small hydrophobic gene region, and viruses were differentiated by restriction fragment length polymorphism assay. A total of 584 nucleotides were amplified. The PCR product of the Hoshino strain was cut into two fragments (313 and 271 nucleotides) by MfeI; that of the Torii strain was digested with EcoT22I, resulting in 332- and 252-nucleotide fragments. Both strains were genotype B and had an XbaI site, resulting in two fragments: 299 and 285 nucleotides. Current circulating wild types were cut only by XbaI or MfeI. However, the MfeI site of the wild types was different from that of the Hoshino strain, resulting in 451- and 133-nucleotide fragments. Using three restriction enzymes, two mumps vaccine strains were distinguished from wild types, and this separation was applied to the identification of vaccine-related adverse events.

Secondary Growth and Carbohydrate Storage Patterns Differ between Sexes in Juniperus thurifera

PubMed Central

DeSoto, Lucía; Olano, José M.; Rozas, Vicente

2016-01-01

Differences in reproductive costs between male and female plants have been shown to foster sex-related variability in growth and C-storage patterns. The extent to which differential secondary growth in dioecious trees is associated with changes in stem carbohydrate storage patterns, however, has not been fully assessed. We explored the long-term radial growth and the seasonal variation of non-structural carbohydrate (NSC) content in sapwood of 40 males and 40 females Juniperus thurifera trees at two sites. NSC content was analyzed bimonthly for 1 year, and tree-ring width was measured for the 1931–2010 period. Sex-related differences in secondary growth and carbohydrate storage were site-dependent. Under less restrictive environmental conditions females grew more and stored more non-soluble sugars than males. Our results reinforce that sex-related differences in growth and resource storage may be a consequence of local adaptation to environmental conditions. Seasonal variation in soluble sugars concentration was opposite to cambial activity, with minima seen during periods of maximal secondary growth, and did not differ between the sexes or sites. Trees with higher stem NSC levels at critical periods showed higher radial growth, suggesting a common mechanism irrespective of site or sex. Sex-related patterns of secondary growth were linked to differences in non-soluble sugars content indicating sex-specific strategies of long-term performance. PMID:27303418

Genetic differentiation of Colletotrichum gloeosporioides and C. truncatum associated with Anthracnose disease of papaya (Carica papaya L.) and bell pepper (Capsium annuum L.) based on ITS PCR-RFLP fingerprinting.

PubMed

Maharaj, Ariana; Rampersad, Sephra N

2012-03-01

Members of the genus Colletotrichum include some of the most economically important fungal pathogens in the world. Accurate diagnosis is critical to devising disease management strategies. Two species, Colletotrichum gloeosporioides and C. truncatum, are responsible for anthracnose disease in papaya (Carica papaya L.) and bell pepper (Capsicum annuum L.) in Trinidad. The ITS1-5.8S-ITS2 region of 48 Colletotrichum isolates was sequenced, and the ITS PCR products were analyzed by PCR-RFLP analysis. Restriction site polymorphisms generated from 11 restriction enzymes enabled the identification of specific enzymes that were successful in distinguishing between C. gloeosporioides and C. truncatum isolates. Species-specific restriction fragment length polymorphisms generated by the enzymes AluI, HaeIII, PvuII, RsaI, and Sau3A were used to consistently resolve C. gloeosporioides and C. truncatum isolates from papaya. AluI, ApaI, PvuII, RsaI, and SmaI reliably separated isolates of C. gloeosporioides and C. truncatum from bell pepper. PvuII, RsaI, and Sau3A were also capable of distinguishing among the C. gloeosporioides isolates from papaya based on the different restriction patterns that were obtained as a result of intra-specific variation in restriction enzyme recognition sites in the ITS1-5.8S-ITS2 rDNA region. Of all the isolates tested, C. gloeosporioides from papaya also had the highest number of PCR-RFLP haplotypes. Cluster analysis of sequence and PCR-RFLP data demonstrated that all C. gloeosporioides and C. truncatum isolates clustered separately into species-specific clades regardless of host species. Phylograms also revealed consistent topologies which suggested that the genetic distances for PCR-RFLP-generated data were comparable to that of ITS sequence data. ITS PCR-RFLP fingerprinting is a rapid and reliable method to identify and differentiate between Colletotrichum species.

Long-term experimental warming alters nitrogen-cycling communities but site factors remain the primary drivers of community structure in high arctic tundra soils.

PubMed

Walker, Jennifer K M; Egger, Keith N; Henry, Gregory H R

2008-09-01

Arctic air temperatures are expected to rise significantly over the next century. Experimental warming of arctic tundra has been shown to increase plant productivity and cause community shifts and may also alter microbial community structure. Hence, the objective of this study was to determine whether experimental warming caused shifts in soil microbial communities by measuring changes in the frequency, relative abundance and/or richness of nosZ and nifH genotypes. Five sites at a high arctic coastal lowland were subjected to a 13-year warming experiment using open-top chambers (OTCs). Sites differed by dominant plant community, soil parent material and/or moisture regimen. Six soil cores were collected from each of four replicate OTC and ambient plots at each site and subdivided into upper and lower samples. Differences in frequency and relative abundance of terminal restriction fragments were assessed graphically by two-way cluster analysis and tested statistically with permutational multivariate analysis of variance (ANOVA). Genotypic richness was compared using factorial ANOVA. The genotype frequency, relative abundance and genotype richness of both nosZ and nifH communities differed significantly by site, and by OTC treatment and/or depth at some sites. The site that showed the most pronounced treatment effect was a wet sedge meadow, where community structure and genotype richness of both nosZ and nifH were significantly affected by warming. Although warming was an important factor affecting these communities at some sites at this high arctic lowland, overall, site factors were the main determinants of community structure.

Segmental expression of Hoxb2 in r4 requires two separate sites that integrate cooperative interactions between Prep1, Pbx and Hox proteins.

PubMed

Ferretti, E; Marshall, H; Pöpperl, H; Maconochie, M; Krumlauf, R; Blasi, F

2000-01-01

Direct auto- and cross-regulatory interactions between Hox genes serve to establish and maintain segmentally restricted patterns in the developing hindbrain. Rhombomere r4-specific expression of both Hoxb1 and Hoxb2 depends upon bipartite cis Hox response elements for the group 1 paralogous proteins, Hoxal and Hoxbl. The DNA-binding ability and selectivity of these proteins depend upon the formation of specific heterodimeric complexes with members of the PBC homeodomain protein family (Pbx genes). The r4 enhancers from Hoxb1 and Hoxb2 have the same activity, but differ with respect to the number and organisation of bipartite Pbx/Hox (PH) sites required, suggesting the intervention of other components/sequences. We report here that another family of homeodomain proteins (TALE, Three-Amino acids-Loop-Extension: Prep1, Meis, HTH), capable of dimerizing with Pbx/EXD, is involved in the mechanisms of r4-restricted expression. We show that: (1) the r4-specific Hoxb1 and Hoxb2 enhancers are complex elements containing separate PH and Prep/Meis (PM) sites; (2) the PM site of the Hoxb2, but not Hoxb1, enhancer is essential in vivo for r4 expression and also influences other sites of expression; (3) both PM and PH sites are required for in vitro binding of Prepl-Pbx and formation and binding of a ternary Hoxbl-Pbxla (or 1b)-Prepl complex. (4) A similar ternary association forms in nuclear extracts from embryonal P19 cells, but only upon retinoic acid induction. This requires synthesis of Hoxbl and also contains Pbx with either Prepl or Meisl. Together these findings highlight the fact that PM sites are found in close proximity to bipartite PH motifs in several Hox responsive elements shown to be important in vivo and that such sites play an essential role in potentiating regulatory activity in combination with the PH motifs.

Silencing Effect of Hominoid Highly Conserved Noncoding Sequences on Embryonic Brain Development

PubMed Central

Mahmoudi Saber, Morteza

2017-01-01

Abstract Superfamily Hominoidea, which consists of Hominidae (humans and great apes) and Hylobatidae (gibbons), is well-known for sharing human-like characteristics, however, the genomic origins of these shared unique phenotypes have mainly remained elusive. To decipher the underlying genomic basis of Hominoidea-restricted phenotypes, we identified and characterized Hominoidea-restricted highly conserved noncoding sequences (HCNSs) that are a class of potential regulatory elements which may be involved in evolution of lineage-specific phenotypes. We discovered 679 such HCNSs from human, chimpanzee, gorilla, orangutan and gibbon genomes. These HCNSs were demonstrated to be under purifying selection but with lineage-restricted characteristics different from old CNSs. A significant proportion of their ancestral sequences had accelerated rates of nucleotide substitutions, insertions and deletions during the evolution of common ancestor of Hominoidea, suggesting the intervention of positive Darwinian selection for creating those HCNSs. In contrary to enhancer elements and similar to silencer sequences, these Hominoidea-restricted HCNSs are located in close proximity of transcription start sites. Their target genes are enriched in the nervous system, development and transcription, and they tend to be remotely located from the nearest coding gene. Chip-seq signals and gene expression patterns suggest that Hominoidea-restricted HCNSs are likely to be functional regulatory elements by imposing silencing effects on their target genes in a tissue-restricted manner during fetal brain development. These HCNSs, emerged through adaptive evolution and conserved through purifying selection, represent a set of promising targets for future functional studies of the evolution of Hominoidea-restricted phenotypes. PMID:28633494

Autoinhibitory regulation of S100A8/S100A9 alarmin activity locally restricts sterile inflammation.

PubMed

Vogl, Thomas; Stratis, Athanasios; Wixler, Viktor; Völler, Tom; Thurainayagam, Sumita; Jorch, Selina K; Zenker, Stefanie; Dreiling, Alena; Chakraborty, Deblina; Fröhling, Mareike; Paruzel, Peter; Wehmeyer, Corinna; Hermann, Sven; Papantonopoulou, Olympia; Geyer, Christiane; Loser, Karin; Schäfers, Michael; Ludwig, Stephan; Stoll, Monika; Leanderson, Tomas; Schultze, Joachim L; König, Simone; Pap, Thomas; Roth, Johannes

2018-05-01

Autoimmune diseases, such as psoriasis and arthritis, show a patchy distribution of inflammation despite systemic dysregulation of adaptive immunity. Thus, additional tissue-derived signals, such as danger-associated molecular patterns (DAMPs), are indispensable for manifestation of local inflammation. S100A8/S100A9 complexes are the most abundant DAMPs in many autoimmune diseases. However, regulatory mechanisms locally restricting DAMP activities are barely understood. We now unravel for the first time, to our knowledge, a mechanism of autoinhibition in mice and humans restricting S100-DAMP activity to local sites of inflammation. Combining protease degradation, pull-down assays, mass spectrometry, and targeted mutations, we identified specific peptide sequences within the second calcium-binding EF-hands triggering TLR4/MD2-dependent inflammation. These binding sites are free when S100A8/S100A9 heterodimers are released at sites of inflammation. Subsequently, S100A8/S100A9 activities are locally restricted by calcium-induced (S100A8/S100A9)2 tetramer formation hiding the TLR4/MD2-binding site within the tetramer interphase, thus preventing undesirable systemic effects. Loss of this autoinhibitory mechanism in vivo results in TNF-α-driven fatal inflammation, as shown by lack of tetramer formation in crossing S100A9-/- mice with 2 independent TNF-α-transgene mouse strains. Since S100A8/S100A9 is the most abundant DAMP in many inflammatory diseases, specifically blocking the TLR4-binding site of active S100 dimers may represent a promising approach for local suppression of inflammatory diseases, avoiding systemic side effects.

Biodiversity Sampling Using a Global Acoustic Approach: Contrasting Sites with Microendemics in New Caledonia

PubMed Central

Gasc, Amandine; Sueur, Jérôme; Pavoine, Sandrine; Pellens, Roseli; Grandcolas, Philippe

2013-01-01

New Caledonia is a Pacific island with a unique biodiversity showing an extreme microendemism. Many species distributions observed on this island are extremely restricted, localized to mountains or rivers making biodiversity evaluation and conservation a difficult task. A rapid biodiversity assessment method based on acoustics was recently proposed. This method could help to document the unique spatial structure observed in New Caledonia. Here, this method was applied in an attempt to reveal differences among three mountain sites (Mandjélia, Koghis and Aoupinié) with similar ecological features and species richness level, but with high beta diversity according to different microendemic assemblages. In each site, several local acoustic communities were sampled with audio recorders. An automatic acoustic sampling was run on these three sites for a period of 82 successive days. Acoustic properties of animal communities were analysed without any species identification. A frequency spectral complexity index (NP) was used as an estimate of the level of acoustic activity and a frequency spectral dissimilarity index (Df) assessed acoustic differences between pairs of recordings. As expected, the index NP did not reveal significant differences in the acoustic activity level between the three sites. However, the acoustic variability estimated by the index Df, could first be explained by changes in the acoustic communities along the 24-hour cycle and second by acoustic dissimilarities between the three sites. The results support the hypothesis that global acoustic analyses can detect acoustic differences between sites with similar species richness and similar ecological context, but with different species assemblages. This study also demonstrates that global acoustic methods applied at broad spatial and temporal scales could help to assess local biodiversity in the challenging context of microendemism. The method could be deployed over large areas, and could help to compare different sites and determine conservation priorities. PMID:23734245

Biodiversity sampling using a global acoustic approach: contrasting sites with microendemics in New Caledonia.

PubMed

Gasc, Amandine; Sueur, Jérôme; Pavoine, Sandrine; Pellens, Roseli; Grandcolas, Philippe

2013-01-01

New Caledonia is a Pacific island with a unique biodiversity showing an extreme microendemism. Many species distributions observed on this island are extremely restricted, localized to mountains or rivers making biodiversity evaluation and conservation a difficult task. A rapid biodiversity assessment method based on acoustics was recently proposed. This method could help to document the unique spatial structure observed in New Caledonia. Here, this method was applied in an attempt to reveal differences among three mountain sites (Mandjélia, Koghis and Aoupinié) with similar ecological features and species richness level, but with high beta diversity according to different microendemic assemblages. In each site, several local acoustic communities were sampled with audio recorders. An automatic acoustic sampling was run on these three sites for a period of 82 successive days. Acoustic properties of animal communities were analysed without any species identification. A frequency spectral complexity index (NP) was used as an estimate of the level of acoustic activity and a frequency spectral dissimilarity index (Df ) assessed acoustic differences between pairs of recordings. As expected, the index NP did not reveal significant differences in the acoustic activity level between the three sites. However, the acoustic variability estimated by the index Df , could first be explained by changes in the acoustic communities along the 24-hour cycle and second by acoustic dissimilarities between the three sites. The results support the hypothesis that global acoustic analyses can detect acoustic differences between sites with similar species richness and similar ecological context, but with different species assemblages. This study also demonstrates that global acoustic methods applied at broad spatial and temporal scales could help to assess local biodiversity in the challenging context of microendemism. The method could be deployed over large areas, and could help to compare different sites and determine conservation priorities.

Appliation of rad-sequencing to linkage mapping in citrus

USDA-ARS?s Scientific Manuscript database

High density linkage maps can be developed for modest cost using high-throughput DNA sequencing to genotype a defined fraction (representation) of the genome. We developed linkage maps in two citrus populations using the RAD (Restriction site Associated DNA) genotyping method which involves restrict...

Restricted growth of U-type infectious haematopoietic necrosis virus (IHNV) in rainbow trout cells may be linked to casein kinase II activity

USGS Publications Warehouse

Park, J.-W.; Moon, C.H.; Harmache, A.; Wargo, A.R.; Purcell, M.K.; Bremont, M.; Kurath, G.

2011-01-01

Previously, we demonstrated that a representative M genogroup type strain of infectious haematopoietic necrosis virus (IHNV) from rainbow trout grows well in rainbow trout-derived RTG-2 cells, but a U genogroup type strain from sockeye salmon has restricted growth, associated with reduced genome replication and mRNA transcription. Here, we analysed further the mechanisms for this growth restriction of U-type IHNV in RTG-2 cells, using strategies that assessed differences in viral genes, host immune regulation and phosphorylation. To determine whether the viral glycoprotein (G) or non-virion (NV) protein was responsible for the growth restriction, four recombinant IHNV viruses were generated in which the G gene of an infectious IHNV clone was replaced by the G gene of U- or M-type IHNV and the NV gene was replaced by NV of U- or M-type IHNV. There was no significant difference in the growth of these recombinants in RTG-2 cells, indicating that G and NV proteins are not major factors responsible for the differential growth of the U- and M-type strains. Poly I:C pretreatment of RTG-2 cells suppressed the growth of both U- and M-type IHNV, although the M virus continued to replicate at a reduced level. Both viruses induced type 1 interferon (IFN1) and the IFN1 stimulated gene Mx1, but the expression levels in M-infected cells were significantly higher than in U-infected cells and an inhibitor of the IFN1-inducible protein kinase PKR, 2-aminopurine (2-AP), did not affect the growth of U- or M-type IHNV in RTG-2 cells. These data did not indicate a role for the IFN1 system in the restricted growth of U-type IHNV in RTG-2 cells. Prediction of kinase-specific phosphorylation sites in the viral phosphoprotein (P) using the NetPhosK program revealed differences between U- and M-type P genes at five phosphorylation sites. Pretreatment of RTG-2 cells with a PKC inhibitor or a p38MAPK inhibitor did not affect the growth of the U- and M-type viruses. However, 100 μm of the casein kinase II (CKII) inhibitor, 5,6-dichloro-1-β-d-ribofuranosylbenzimidazole (DRB), reduced the titre of the U type 8.3-fold at 24 h post-infection. In contrast, 100 μm of the CKII inhibitor reduced the titre of the M type only 1.3-fold at 48 h post-infection. Our data suggest that the different growth of U- and M-type IHNV in RTG-2 cells may be linked to a differential requirement for cellular protein kinases such as CKII for their growth.

Restriction Site Tiling Analysis: accurate discovery and quantitative genotyping of genome-wide polymorphisms using nucleotide arrays

PubMed Central

2010-01-01

High-throughput genotype data can be used to identify genes important for local adaptation in wild populations, phenotypes in lab stocks, or disease-related traits in human medicine. Here we advance microarray-based genotyping for population genomics with Restriction Site Tiling Analysis. The approach simultaneously discovers polymorphisms and provides quantitative genotype data at 10,000s of loci. It is highly accurate and free from ascertainment bias. We apply the approach to uncover genomic differentiation in the purple sea urchin. PMID:20403197

Cloning vector

DOEpatents

Guilfoyle, Richard A.; Smith, Lloyd M.

1994-01-01

A vector comprising a filamentous phage sequence containing a first copy of filamentous phage gene X and other sequences necessary for the phage to propagate is disclosed. The vector also contains a second copy of filamentous phage gene X downstream from a promoter capable of promoting transcription in a bacterial host. In a preferred form of the present invention, the filamentous phage is M13 and the vector additionally includes a restriction endonuclease site located in such a manner as to substantially inactivate the second gene X when a DNA sequence is inserted into the restriction site.

Cloning vector

DOEpatents

Guilfoyle, R.A.; Smith, L.M.

1994-12-27

A vector comprising a filamentous phage sequence containing a first copy of filamentous phage gene X and other sequences necessary for the phage to propagate is disclosed. The vector also contains a second copy of filamentous phage gene X downstream from a promoter capable of promoting transcription in a bacterial host. In a preferred form of the present invention, the filamentous phage is M13 and the vector additionally includes a restriction endonuclease site located in such a manner as to substantially inactivate the second gene X when a DNA sequence is inserted into the restriction site. 2 figures.

SNP-RFLPing 2: an updated and integrated PCR-RFLP tool for SNP genotyping.

PubMed

Chang, Hsueh-Wei; Cheng, Yu-Huei; Chuang, Li-Yeh; Yang, Cheng-Hong

2010-04-08

PCR-restriction fragment length polymorphism (RFLP) assay is a cost-effective method for SNP genotyping and mutation detection, but the manual mining for restriction enzyme sites is challenging and cumbersome. Three years after we constructed SNP-RFLPing, a freely accessible database and analysis tool for restriction enzyme mining of SNPs, significant improvements over the 2006 version have been made and incorporated into the latest version, SNP-RFLPing 2. The primary aim of SNP-RFLPing 2 is to provide comprehensive PCR-RFLP information with multiple functionality about SNPs, such as SNP retrieval to multiple species, different polymorphism types (bi-allelic, tri-allelic, tetra-allelic or indels), gene-centric searching, HapMap tagSNPs, gene ontology-based searching, miRNAs, and SNP500Cancer. The RFLP restriction enzymes and the corresponding PCR primers for the natural and mutagenic types of each SNP are simultaneously analyzed. All the RFLP restriction enzyme prices are also provided to aid selection. Furthermore, the previously encountered updating problems for most SNP related databases are resolved by an on-line retrieval system. The user interfaces for functional SNP analyses have been substantially improved and integrated. SNP-RFLPing 2 offers a new and user-friendly interface for RFLP genotyping that can be used in association studies and is freely available at http://bio.kuas.edu.tw/snp-rflping2.

10 CFR 862.2 - Scope.

Code of Federal Regulations, 2011 CFR

2011-01-01

... RESTRICTIONS ON AIRCRAFT LANDING AND AIR DELIVERY AT DEPARTMENT OF ENERGY NUCLEAR SITES § 862.2 Scope. (a) This...) Aircraft in the process of landing on a DOE site due to circumstances beyond the control of the operator... section are within the scope of this part upon landing at a DOE designated site. ...

10 CFR 862.4 - Prohibitions and penalties.

Code of Federal Regulations, 2011 CFR

2011-01-01

... DEPARTMENT OF ENERGY RESTRICTIONS ON AIRCRAFT LANDING AND AIR DELIVERY AT DEPARTMENT OF ENERGY NUCLEAR SITES...) Operation or use of aircraft on lands or waters of designated sites. (2) Air delivery to or from designated sites. (3) Removal or movement of downed aircraft, or participation in the removal or movement of downed...

Estimating red pine site index in northern Minnesota.

Treesearch

1976-01-01

Methods are presented for estimating red pine site index from the height growth of red pine, site index of several associated species (jack pine, white pine, white spruce, or quaking aspen), and from easily measured soil properties. The restrictions and limitations of each method and their relative precision are discussed.

Site preferences of actinide cations in [NZP] compounds

NASA Astrophysics Data System (ADS)

Hawkins, H. T.; Spearing, D. R.; Smith, D. M.; Hampel, F. G.; Veirs, D. K.; Scheetz, B. E.

2000-07-01

Compounds adopting the sodium dizirconium tris(phosphate) (NaZr2(PO4)3) structure type belong to the [NZP] structural family of compounds. [NZP] compounds possess desirable properties that would permit their application as hosts for the actinides. These properties include compositional flexibility (i.e., three structural sites that can accommodate a variety of different cations), high thermal stability, negligible thermal expansion, and resistance to radiation damage. Experimental data indicate that [NZP] compounds resist dissolution and release of constituents over a wide range of experimental conditions. Moreover, [NZP] compounds may be synthesized by both conventional and novel methods and may be heat treated or sintered at modest temperatures (800 °C-1350 °C) in open or restricted systems.

An evaluation of the current radiative forcing benefit of the Montreal Protocol at the high-Alpine site Jungfraujoch.

PubMed

Steinbacher, M; Vollmer, M K; Buchmann, B; Reimann, S

2008-03-01

A combination of reconstructed histories, long-term time series and recent quasi-continuous observations of non-CO2 greenhouse gases at the high-Alpine site Jungfraujoch is used to assess their current global radiative forcing budget and the influence of regulations due to the Montreal Protocol on Substances that Deplete the Ozone Layer in terms of climate change. Extrapolated atmospheric greenhouse gases trends from 1989 assuming a business-as-usual scenario, i.e. no Montreal Protocol restriction, are presented and compared to the observations. The largest differences between hypothetical business-as-usual mixing ratios and current atmospheric observations over the last 16 years were found for chlorinated species, in particular methyl chloroform (CH3CCl3) at 167 to 203 ppt and chlorofluorocarbon-12 (CFC-12) at 121 to 254 ppt. These prevented increases were used to estimate the effects of their restrictions on the radiative forcing budget. The net direct effect due to the Montreal Protocol regulations reduces global warming and offsets about 14 to 30% of the positive greenhouse effect related to the major greenhouse gases CO2, CH4, N2O and also SF6, and about 12 to 22% of the hypothetical current radiative forcing increase without Montreal Protocol restrictions. Thus, the Montreal Protocol succeeded not only in reducing the atmospheric chlorine content in the atmosphere but also dampened global warming. Nevertheless, the Montreal Protocol controlled species still add to global warming.

Mouse mammary tumor virus chromatin in human breast cancer cells is constitutively hypersensitive and exhibits steroid hormone-independent loading of transcription factors in vivo.

PubMed Central

Mymryk, J S; Berard, D; Hager, G L; Archer, T K

1995-01-01

We have stably introduced a reporter gene under the control of the mouse mammary tumor virus (MMTV) long terminal repeat (LTR) into human T47D breast cancer cells to study the action of the progesterone receptor (PR) on transcription from a chromatin template. Unexpectedly, the chromatin organization of the MMTV LTR in these human breast cancer cells differed markedly from what we have observed previously. The region adjacent to the transcription start site (-221 to -75) was found to be constitutively hypersensitive to restriction enzyme cleavage in the absence of hormone. This region is normally encompassed within the second nucleosome of a phased array of six nucleosomes that is assembled when the MMTV LTR is stably maintained in mouse cells. Characteristically, in these rodent cells, the identical DNA sequences show increased restriction enzyme cleavage only in the presence of glucocorticoid. The increased access of restriction enzymes observed in the human PR+ cells was not observed in adjacent nucleosomes and was unaffected by treatment with the progesterone antagonist RU486. In addition, exonuclease III-dependent stops corresponding to the binding sites for nuclear factor 1 and the PR were observed before and after hormone treatment. These results indicate that MMTV chromatin replicated in these cells is organized into a constitutively open architecture and that this open chromatin state is accompanied by hormone-independent loading of a transcription factor complex that is normally excluded from uninduced chromatin. PMID:7799933

Mouse mammary tumor virus chromatin in human breast cancer cells is constitutively hypersensitive and exhibits steroid hormone-independent loading of transcription factors in vivo.

PubMed

Mymryk, J S; Berard, D; Hager, G L; Archer, T K

1995-01-01

We have stably introduced a reporter gene under the control of the mouse mammary tumor virus (MMTV) long terminal repeat (LTR) into human T47D breast cancer cells to study the action of the progesterone receptor (PR) on transcription from a chromatin template. Unexpectedly, the chromatin organization of the MMTV LTR in these human breast cancer cells differed markedly from what we have observed previously. The region adjacent to the transcription start site (-221 to -75) was found to be constitutively hypersensitive to restriction enzyme cleavage in the absence of hormone. This region is normally encompassed within the second nucleosome of a phased array of six nucleosomes that is assembled when the MMTV LTR is stably maintained in mouse cells. Characteristically, in these rodent cells, the identical DNA sequences show increased restriction enzyme cleavage only in the presence of glucocorticoid. The increased access of restriction enzymes observed in the human PR+ cells was not observed in adjacent nucleosomes and was unaffected by treatment with the progesterone antagonist RU486. In addition, exonuclease III-dependent stops corresponding to the binding sites for nuclear factor 1 and the PR were observed before and after hormone treatment. These results indicate that MMTV chromatin replicated in these cells is organized into a constitutively open architecture and that this open chromatin state is accompanied by hormone-independent loading of a transcription factor complex that is normally excluded from uninduced chromatin.

Phylogenomics of Phrynosomatid Lizards: Conflicting Signals from Sequence Capture versus Restriction Site Associated DNA Sequencing

PubMed Central

Leaché, Adam D.; Chavez, Andreas S.; Jones, Leonard N.; Grummer, Jared A.; Gottscho, Andrew D.; Linkem, Charles W.

2015-01-01

Sequence capture and restriction site associated DNA sequencing (RADseq) are popular methods for obtaining large numbers of loci for phylogenetic analysis. These methods are typically used to collect data at different evolutionary timescales; sequence capture is primarily used for obtaining conserved loci, whereas RADseq is designed for discovering single nucleotide polymorphisms (SNPs) suitable for population genetic or phylogeographic analyses. Phylogenetic questions that span both “recent” and “deep” timescales could benefit from either type of data, but studies that directly compare the two approaches are lacking. We compared phylogenies estimated from sequence capture and double digest RADseq (ddRADseq) data for North American phrynosomatid lizards, a species-rich and diverse group containing nine genera that began diversifying approximately 55 Ma. Sequence capture resulted in 584 loci that provided a consistent and strong phylogeny using concatenation and species tree inference. However, the phylogeny estimated from the ddRADseq data was sensitive to the bioinformatics steps used for determining homology, detecting paralogs, and filtering missing data. The topological conflicts among the SNP trees were not restricted to any particular timescale, but instead were associated with short internal branches. Species tree analysis of the largest SNP assembly, which also included the most missing data, supported a topology that matched the sequence capture tree. This preferred phylogeny provides strong support for the paraphyly of the earless lizard genera Holbrookia and Cophosaurus, suggesting that the earless morphology either evolved twice or evolved once and was subsequently lost in Callisaurus. PMID:25663487

Epidemiologic analysis of prevalence of the hyperhidrosis.

PubMed

Estevan, Fernanda Alvarenga; Wolosker, Marina Borri; Wolosker, Nelson; Puech-Leão, Pedro

2017-01-01

The present paper aims to study the prevalence of the various manifestations of hyperhidrosis in patients who sought treatment in a specialized ambulatory in the state of São Paulo. Opposite to previous studies, this paper studies the different combinations of sweating sites, not being restricted to the main complaint site of the patients, but taking into consideration secondary complaints patients may present. This was a retrospective approach of a database containing more than 1200 patients in which were mapped: combination of sweating sites, age of onset, age spectrum, mean age, body mass index and gender of patients. Patients were categorized into four groups based on their main sweating site - palmar, plantar, axillary and facial. We concluded that hyperhidrosis appears frequently in more than one site, being the main complaint that affects the most patients palmar hyperhidrosis, which appears early in the patients during adolescence. When there are two sites of sweating, the most frequent combination is palmar + plantar, and when there are three sites of sweating the most frequent combinations are palmar + plantar + axillary and axillary + palmar + plantar. This research has casuistics limited to a single care service for patients with hyperhidrosis. It is necessary to keep in mind that the disease manifests itself mainly in more than one location, with different intensities in each of the patients, generating a significant impairment of their quality of life.

Epidemiologic analysis of prevalence of the hyperhidrosis*

PubMed Central

Estevan, Fernanda Alvarenga; Wolosker, Marina Borri; Wolosker, Nelson; Puech-Leão, Pedro

2017-01-01

Background The present paper aims to study the prevalence of the various manifestations of hyperhidrosis in patients who sought treatment in a specialized ambulatory in the state of São Paulo. Objectives Opposite to previous studies, this paper studies the different combinations of sweating sites, not being restricted to the main complaint site of the patients, but taking into consideration secondary complaints patients may present. Methods This was a retrospective approach of a database containing more than 1200 patients in which were mapped: combination of sweating sites, age of onset, age spectrum, mean age, body mass index and gender of patients. Patients were categorized into four groups based on their main sweating site - palmar, plantar, axillary and facial. Results We concluded that hyperhidrosis appears frequently in more than one site, being the main complaint that affects the most patients palmar hyperhidrosis, which appears early in the patients during adolescence. When there are two sites of sweating, the most frequent combination is palmar + plantar, and when there are three sites of sweating the most frequent combinations are palmar + plantar + axillary and axillary + palmar + plantar. Study limitations This research has casuistics limited to a single care service for patients with hyperhidrosis. Conclusion It is necessary to keep in mind that the disease manifests itself mainly in more than one location, with different intensities in each of the patients, generating a significant impairment of their quality of life. PMID:29166497

Different Mechanisms Regulate Productive Herpes Simplex Virus 1 (HSV-1) and HSV-2 Infections in Adult Trigeminal Neurons

PubMed Central

Ma, AyeAye; Margolis, Mathew S.

2013-01-01

Herpes simplex virus 1 (HSV-1) and HSV-2 establish latency in different neuronal subtypes (A5+ and KH10+) in murine trigeminal ganglia, results which correlate with restricted productive infection in these neurons in vitro. HSV-2 latency-associated transcript (LAT) contains a cis-acting regulatory element near the transcription start site that promotes productive infection in A5+ neurons and a second element in exon 1 that inhibits productive infection in KH10+ neurons. HSV-1 contains no such regulatory sequences, demonstrating different mechanisms for regulating productive HSV infection in neurons. PMID:23514893

Strain of Escherichia coli with a temperature-sensitive mutation affecting ribosomal ribonucleic acid accumulation.

PubMed Central

Frey, T; Newlin, L L; Atherly, A G

1975-01-01

A mutant of Escherichia coli has been isolated that has a temperature-sensitive mutation that results in specific loss of ribosomal ribonucleic acid (RNA) synthesis and some reduction in messenger RNA synthesis. When the strain was grown in glucose medium at a restrictive temperature, RNA accumulation ceased, but both messenger RNA and protein synthesis continued for an extended time. Because carbon metabolism was slowed drastically when strain AA-157 was placed at the restrictive temperature, this phenotype can be compared with carbon depletion conditions present during diauxic lag. However, the phenotype of mutant AA-157 differs from shift-down conditions in that guanosine-3',5'-tetraphosphate levels are unaffected; therefore, a different site is affected. This mutant strain (AA-157) thus shows many characteristics similar to an aldolase mutant previously reported (Böck and Neidhardt, 1966). However, the mutation occurred in a different position on the E. coli genetic map, and furthermore, aldolase was not temperature sensitive in strain AA-157. In this paper we present a study of macromolecular biosynthesis in this mutant. PMID:1090609

A comparison of campfire impacts and policies in seven protected areas

USGS Publications Warehouse

Reid, S.E.; Marion, J.L.

2005-01-01

Using resource-monitoring data from seven protected areas, the effectiveness of three campfire policies-campfire ban, designated campfires, and unregulated campfires-were assessed based on the number of fire sites and the amount of tree damage. Results indicate that unregulated campfire policies permitted substantial numbers of fire sites and tree damage in campsites, although fire bans did not eliminate or even substantially decrease these problems. A designated campfire policy was effective in decreasing number of fire sites, but little difference was found among policies regarding tree damage. Given the importance of campfires to visitor experiences, campfire prohibitions could be viewed as unnecessarily restrictive based on their limited success in preventing resource damage. Conclusions encourage protected-area managers to consider designated campfire policies and prohibitions on axes, hatchets, and saws to better meet resource protection and visitor experience mandates.

Nest-location and nest-survival of black-chinned hummingbirds in New Mexico: A comparison between rivers with differing levels of regulation and invasion of nonnative plants

Treesearch

D. Max Smith; Deborah M. Finch; Scott H. Stoleson

2014-01-01

We compared plants used as sites for nests and survival of nests of black-chinned hummingbirds (Archilochus alexandri) along two rivers in New Mexico. Along the free-flowing Gila River which was dominated by native plants, most nests were constructed in boxelder (Acer negundo). Along the flow-restricted Middle Rio Grande which was dominated by nonnative plants, most...

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

PubMed

Fedoreyeva, L I; Vanyushin, B F

2011-06-01

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

Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution.

PubMed

Kobayashi, I

2001-09-15

Restriction-modification (RM) systems are composed of genes that encode a restriction enzyme and a modification methylase. RM systems sometimes behave as discrete units of life, like viruses and transposons. RM complexes attack invading DNA that has not been properly modified and thus may serve as a tool of defense for bacterial cells. However, any threat to their maintenance, such as a challenge by a competing genetic element (an incompatible plasmid or an allelic homologous stretch of DNA, for example) can lead to cell death through restriction breakage in the genome. This post-segregational or post-disturbance cell killing may provide the RM complexes (and any DNA linked with them) with a competitive advantage. There is evidence that they have undergone extensive horizontal transfer between genomes, as inferred from their sequence homology, codon usage bias and GC content difference. They are often linked with mobile genetic elements such as plasmids, viruses, transposons and integrons. The comparison of closely related bacterial genomes also suggests that, at times, RM genes themselves behave as mobile elements and cause genome rearrangements. Indeed some bacterial genomes that survived post-disturbance attack by an RM gene complex in the laboratory have experienced genome rearrangements. The avoidance of some restriction sites by bacterial genomes may result from selection by past restriction attacks. Both bacteriophages and bacteria also appear to use homologous recombination to cope with the selfish behavior of RM systems. RM systems compete with each other in several ways. One is competition for recognition sequences in post-segregational killing. Another is super-infection exclusion, that is, the killing of the cell carrying an RM system when it is infected with another RM system of the same regulatory specificity but of a different sequence specificity. The capacity of RM systems to act as selfish, mobile genetic elements may underlie the structure and function of RM enzymes.

An industry perspective on commercial radioactive waste disposal conditions and trends.

PubMed

Romano, Stephen A

2006-11-01

The United States is presently served by Class-A, -B and -C low-level radioactive waste and naturally-occurring and accelerator-produced radioactive material disposal sites in Washington and South Carolina; a Class-A and mixed waste disposal site in Utah that also accepts naturally-occurring radioactive material; and hazardous and solid waste facilities and uranium mill tailings sites that accept certain radioactive materials on a site-specific basis. The Washington site only accepts low-level radioactive waste from 11 western states due to interstate Compact restrictions on waste importation. The South Carolina site will be subject to geographic service area restrictions beginning 1 July 2008, after which only three states will have continued access. The Utah site dominates the commercial Class-A and mixed waste disposal market due to generally lower state fees than apply in South Carolina. To expand existing commercial services, an existing hazardous waste site in western Texas is seeking a Class-A, -B and -C and mixed waste disposal license. With that exception, no new Compact facilities are proposed. This fluid, uncertain situation has inspired national level rulemaking initiatives and policy studies, as well as alternative disposal practices for certain low-activity materials.

Columbus Closure Project Released without Radiological Restrictions

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

Henderson, G.

2007-07-01

The Columbus Closure Project (CCP), a historic radiological research complex, was cleaned up for future use without radiological restriction in 2006. The CCP research and development site contributed to national defense, nuclear fuel fabrication, and the development of safe nuclear reactors in the United States until 1988 when research activities were concluded for site decommissioning. In November of 2003, the Ohio Field Office of the U.S. Department of Energy contracted ECC/E2 Closure Services, LLC (Closure Services) to complete the removal of radioactive contamination from of a 1955 era nuclear sciences area consisting of a large hot cell facility, research reactormore » building and underground piping. The project known as the Columbus Closure Project (CCP) was completed in 27 months and brought to a close 16 years of D and D in Columbus, Ohio. This paper examines the project innovations and challenges presented during the Columbus Closure Project. The examination of the CCP includes the project regulatory environment, the CS safety program, accelerated clean up innovation, project execution strategies and management of project waste issues and the regulatory approach to site release 'without radiological restrictions'. (authors)« less

Programmable DNA-Guided Artificial Restriction Enzymes.

PubMed

Enghiad, Behnam; Zhao, Huimin

2017-05-19

Restriction enzymes are essential tools for recombinant DNA technology that have revolutionized modern biological research. However, they have limited sequence specificity and availability. Here we report a Pyrococcus furiosus Argonaute (PfAgo) based platform for generating artificial restriction enzymes (AREs) capable of recognizing and cleaving DNA sequences at virtually any arbitrary site and generating defined sticky ends of varying length. Short DNA guides are used to direct PfAgo to target sites for cleavage at high temperatures (>87 °C) followed by reannealing of the cleaved single stranded DNAs. We used this platform to generate over 18 AREs for DNA fingerprinting and molecular cloning of PCR-amplified or genomic DNAs. These AREs work as efficiently as their naturally occurring counterparts, and some of them even do not have any naturally occurring counterparts, demonstrating easy programmability, generality, versatility, and high efficiency for this new technology.

Site and incidence of birth canal lacerations from instrumental delivery with mediolateral episiotomy.

PubMed

Chikazawa, Kenro; Ushijima, Junko; Takagi, Kenjiro; Nakamura, Eishin; Samejima, Koki; Kadowaki, Kanako; Horiuchi, Isao

2016-12-01

Instrument-assisted vaginal delivery is a significant risk factor for birth canal lacerations. Although many obstetricians recently are recommending restrictive rather than a routine episiotomy, reports have shown restrictive episiotomy to be associated with more extensive anterior birth canal trauma compared with routine episiotomy. We retrospectively reviewed 110 cases of forceps and vacuum deliveries and investigated the site of birth canal lacerations. Birth canal lacerations were divided into four sites according to direction-anterior, ipsilateral, contralateral, and posterior. The frequency of lacerations were, from most to least, posterior (34%), lateral (21.7%), and anterior (1.9%). Moreover, among the lateral lacerations, they were more frequent in the contralateral side of episiotomy than the ipsilateral side (18.9% vs. 4.7%, p < 0.01). Our results indicate that caution is also needed concerning not only the anterior site, but also the contralateral site of an episiotomy to prevent laceration in an instrument-assisted vaginal delivery. Copyright © 2016. Published by Elsevier B.V.

The active site of O-GlcNAc transferase imposes constraints on substrate sequence

PubMed Central

Rafie, Karim; Blair, David E.; Borodkin, Vladimir S.; Albarbarawi, Osama; van Aalten, Daan M. F.

2016-01-01

O-GlcNAc transferase (OGT) glycosylates a diverse range of intracellular proteins with O-linked N-acetylglucosamine (O-GlcNAc), an essential and dynamic post-translational modification in metazoa. Although this enzyme modifies hundreds of proteins with O-GlcNAc, it is not understood how OGT achieves substrate specificity. In this study, we describe the application of a high-throughput OGT assay on a library of peptides. The sites of O-GlcNAc modification were mapped by ETD-mass spectrometry, and found to correlate with previously detected O-GlcNAc sites. Crystal structures of four acceptor peptides in complex with human OGT suggest that a combination of size and conformational restriction defines sequence specificity in the −3 to +2 subsites. This work reveals that while the N-terminal TPR repeats of hOGT may play a role in substrate recognition, the sequence restriction imposed by the peptide-binding site makes a significant contribution to O-GlcNAc site specificity. PMID:26237509

Restricted versus continued standard caloric intake during the management of refeeding syndrome in critically ill adults: a randomised, parallel-group, multicentre, single-blind controlled trial.

PubMed

Doig, Gordon S; Simpson, Fiona; Heighes, Philippa T; Bellomo, Rinaldo; Chesher, Douglas; Caterson, Ian D; Reade, Michael C; Harrigan, Peter W J

2015-12-01

Equipoise exists regarding the benefits of restricting caloric intake during electrolyte replacement for refeeding syndrome, with half of intensive care specialists choosing to continue normal caloric intake. We aimed to assess whether energy restriction affects the duration of critical illness, and other measures of morbidity, compared with standard care. We did a randomised, multicentre, single-blind clinical trial in 13 hospital intensive care units (ICUs) in Australia (11 sites) and New Zealand (two sites). Adult critically ill patients who developed refeeding syndrome within 72 h of commencing nutritional support in the ICU were enrolled and allocated to receive continued standard nutritional support or protocolised caloric restriction. 1:1 computer-based randomisation was done in blocks of variable size, stratified by enrolment serum phosphate concentration (>0·32 mmol/L vs ≤0·32 mmol/L) and body-mass index (BMI; >18 kg/m(2)vs ≤18 kg/m(2)). The primary outcome was the number of days alive after ICU discharge, with 60 day follow-up, in a modified intention-to-treat population of all randomly allocated patients except those mistakenly enrolled. Days alive after ICU discharge was a composite outcome based on ICU length of stay, overall survival time, and mortality. The Refeeding Syndrome Trial was registered with the Australian and New Zealand Clinical Trials Registry (ANZCTR number 12609001043224). Between Dec 3, 2010, and Aug 13, 2014, we enrolled 339 adult critically ill patients: 170 were randomly allocated to continued standard nutritional support and 169 to protocolised caloric restriction. During the 60 day follow-up, the mean number of days alive after ICU discharge in 165 assessable patients in the standard care group was 39·9 (95% CI 36·4-43·7) compared with 44·8 (95% CI 40·9-49·1) in 166 assessable patients in the caloric restriction group (difference 4·9 days, 95% CI -2·3 to 13·6, p=0·19). Nevertheless, protocolised caloric restriction improved key individual components of the primary outcome: more patients were alive at day 60 (128 [78%] of 163 vs 149 [91%] of 164, p=0·002) and overall survival time was increased (48·9 [SD 1·46] days vs 53·65 [0·97] days, log-rank p=0·002). Protocolised caloric restriction is a suitable therapeutic option for critically ill adults who develop refeeding syndrome. We did not identify any safety concerns associated with the use of protocolised caloric restriction. National Health and Medical Research Council of Australia. Copyright © 2015 Elsevier Ltd. All rights reserved.

Outcomes of PCI at hospitals with or without on-site cardiac surgery.

PubMed

Aversano, Thomas; Lemmon, Cynthia C; Liu, Li

2012-05-10

Performance of percutaneous coronary intervention (PCI) is usually restricted to hospitals with cardiac surgery on site. We conducted a noninferiority trial to compare the outcomes of PCI performed at hospitals without and those with on-site cardiac surgery. We randomly assigned participants to undergo PCI at a hospital with or without on-site cardiac surgery. Patients requiring primary PCI were excluded. The trial had two primary end points: 6-week mortality and 9-month incidence of major adverse cardiac events (the composite of death, Q-wave myocardial infarction, or target-vessel revascularization). Noninferiority margins for the risk difference were 0.4 percentage points for mortality at 6 weeks and 1.8 percentage points for major adverse cardiac events at 9 months. A total of 18,867 patients were randomly assigned in a 3:1 ratio to undergo PCI at a hospital without on-site cardiac surgery (14,149 patients) or with on-site cardiac surgery (4718 patients). The 6-week mortality rate was 0.9% at hospitals without on-site surgery versus 1.0% at those with on-site surgery (difference, -0.04 percentage points; 95% confidence interval [CI], -0.31 to 0.23; P=0.004 for noninferiority). The 9-month rates of major adverse cardiac events were 12.1% and 11.2% at hospitals without and those with on-site surgery, respectively (difference, 0.92 percentage points; 95% CI, 0.04 to 1.80; P=0.05 for noninferiority). The rate of target-vessel revascularization was higher in hospitals without on-site surgery (6.5% vs. 5.4%, P=0.01). We found that PCI performed at hospitals without on-site cardiac surgery was noninferior to PCI performed at hospitals with on-site cardiac surgery with respect to mortality at 6 weeks and major adverse cardiac events at 9 months. (Funded by the Cardiovascular Patient Outcomes Research Team [C-PORT] participating sites; ClinicalTrials.gov number, NCT00549796.).

Spatial variation in reproductive effort of a southern Australian seagrass.

PubMed

Smith, Timothy M; York, Paul H; Macreadie, Peter I; Keough, Michael J; Ross, D Jeff; Sherman, Craig D H

2016-09-01

In marine environments characterised by habitat-forming plants, the relative allocation of resources into vegetative growth and flowering is an important indicator of plant condition and hence ecosystem health. In addition, the production and abundance of seeds can give clues to local resilience. Flowering density, seed bank, biomass and epiphyte levels were recorded for the temperate seagrass Zostera nigricaulis in Port Phillip Bay, south east Australia at 14 sites chosen to represent several regions with different physicochemical conditions. Strong regional differences were found within the large bay. Spathe and seed density were very low in the north of the bay (3 sites), low in the centre of the bay (2 sites) intermediate in the Outer Geelong Arm (2 sites), high in Swan Bay (2 sites) and very high in the Inner Geelong Arm (3 sites). In the south (2 sites) seed density was low and spathe density was high. These regional patterns were largely consistent for the 5 sites sampled over the three year period. Timing of flowering was consistent across sites, occurring from August until December with peak production in October, except during the third year of monitoring when overall densities were lower and peaked in November. Seagrass biomass, epiphyte load, canopy height and stem density showed few consistent spatial and temporal patterns. Variation in spathe and seed density and morphology across Port Phillip Bay reflects varying environmental conditions and suggests that northern sites may be restricted in their ability to recover from disturbance through sexual reproduction. In contrast, sites in the west and south of the bay have greater potential to recover from disturbances due to a larger seed bank and these sites could act as source populations for sites where seed production is low. Copyright © 2016 Elsevier Ltd. All rights reserved.

Rapid discrimination of sequences flanking and within T-DNA insertions in the Arabidopsis genome.

PubMed

Ponce, M R; Quesada, V; Micol, J L

1998-05-01

An improvement to previous methods for recovering Arabidopsis thaliana genomic DNA flanking T-DNA insertions is presented that allows for the avoidance of some of the cloning difficulties caused by the concatameric nature of T-DNA inserts. The principle of the procedure is to categorize by size restriction fragments of mutant DNA, produced in separate digestions with NdeI and Bst1107I. Given that the sites for these two enzymes are contiguous within the pGV3850:1003 T-DNA construct, the restriction fragments obtained fall into two categories: those showing identical size in both digestions, which correspond to sequences internal to T-DNA concatamers; and those of different sizes, that contain the junctions between plant DNA and the T-DNA insert. Such a criterion makes it possible to easily distinguish the digestion products corresponding to internal T-DNA parts, which do not deserve further attention, and those which presumably include a segment of the locus of interest. Discrimination between restriction fragments of genomic mutant DNA can be made on rescued plasmids, inverse PCR amplification products or bands in a genomic blot.

Molecular cloning and physical mapping of the genome of fish lymphocystis disease virus.

PubMed

Darai, G; Delius, H; Clarke, J; Apfel, H; Schnitzler, P; Flügel, R M

1985-10-30

A defined and complete gene library of the fish lymphocystis disease virus (FLDV) genome was established. FLDV DNA was cleaved with EcoRI, BamHI, EcoRI/BamHI and EcoRI/HindIII and the resulting fragments were inserted into the corresponding sites of the pACYC184 or pAT153 plasmid vectors using T4 DNA ligase. Since FLDV DNA is highly methylated at CpG sequences (Darai et al., 1983; Wagner et al., 1985), an Escherichia coli GC-3 strain was required to amplify the recombinant plasmids harboring the FLDV DNA fragments. Bacterial colonies harboring recombinant plasmids were selected. All cloned fragments were individually identified by digestion of the recombinant plasmid DNA with different restriction enzymes and screened by hybridization of recombinant plasmid DNA to viral DNA. This analysis revealed that sequences representing 100% of the viral genome were cloned. Using these recombinant plasmids, the physical maps of the genome were constructed for BamHI, EcoRI, BestEII, and PstI restriction endonucleases. Although the FLDV genome is linear, due to circular permutation the restriction maps are circular.

Taking It Like a Man: Masculine Role Norms as Moderators of the Racial Discrimination–Depressive Symptoms Association Among African American Men

PubMed Central

2012-01-01

Objectives. I examined the association between everyday racial discrimination and depressive symptoms and explored the moderating role of 2 dimensions of masculine role norms, restrictive emotionality and self-reliance. Methods. Cross-sectional survey data from 674 African American men aged 18 years and older recruited primarily from barbershops in 4 US regions (2003–2010) were used. Direct and moderated associations were assessed with multivariate linear regression analyses for the overall sample and different age groups. Models were adjusted for recruitment site, sociodemographics, masculine role norms salience, and general social stress. Results. Everyday racial discrimination was associated with more depressive symptoms across all age groups. Higher restrictive emotionality was associated with more depressive symptoms among men aged 18 to 29 and 30 to 39 years. Self-reliance was associated with fewer depressive symptoms among men aged 18 to 29 years and 40 years and older. The positive association between everyday racial discrimination and depressive symptoms was stronger among men with high restrictive emotionality, but this moderated effect was limited to men older than 30 years. Conclusions. Interventions designed to reduce African American men’s depression instigated by racism should be life-course specific and address masculine role norms that encourage emotion restriction. PMID:22401515

Taking it like a man: masculine role norms as moderators of the racial discrimination-depressive symptoms association among African American men.

PubMed

Hammond, Wizdom Powell

2012-05-01

I examined the association between everyday racial discrimination and depressive symptoms and explored the moderating role of 2 dimensions of masculine role norms, restrictive emotionality and self-reliance. Cross-sectional survey data from 674 African American men aged 18 years and older recruited primarily from barbershops in 4 US regions (2003-2010) were used. Direct and moderated associations were assessed with multivariate linear regression analyses for the overall sample and different age groups. Models were adjusted for recruitment site, sociodemographics, masculine role norms salience, and general social stress. Everyday racial discrimination was associated with more depressive symptoms across all age groups. Higher restrictive emotionality was associated with more depressive symptoms among men aged 18 to 29 and 30 to 39 years. Self-reliance was associated with fewer depressive symptoms among men aged 18 to 29 years and 40 years and older. The positive association between everyday racial discrimination and depressive symptoms was stronger among men with high restrictive emotionality, but this moderated effect was limited to men older than 30 years. Interventions designed to reduce African American men's depression instigated by racism should be life-course specific and address masculine role norms that encourage emotion restriction.

1999 Report on Hanford Site land disposal restriction for mixed waste

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

BLACK, D.G.

This report was submitted to meet the requirements of Hanford Federal Facility Agreement and Consent Order (Tri-Party Agreement) Milestone M-26-011. This milestone requires the preparation of an annual report that covers characterization, treatment, storage, minimization, and other aspects of managing land-disposal-restricted mixed waste at the Hanford Facility.

22 CFR 103.3 - Requirement to provide a sample.

Code of Federal Regulations, 2010 CFR

2010-04-01

... will notify appropriate site representatives of any request by an Inspection Team to take a sample. At... Inspection Team of the Technical Secretariat. (f) Person to take a sample. If a sample is required, the owner... restrict activities regarding sampling, e.g., conditions that restrict where, when, and how samples are...

Regional comparisons of on-site solar potential in the residential and industrial sectors

NASA Astrophysics Data System (ADS)

Gatzke, A. E.; Skewes-Cox, A. O.

1980-10-01

Regional and subregional differences in the potential development of decentralized solar technologies are studied. Two sectors of the economy were selected for intensive analysis: the residential and industrial sectors. The sequence of analysis follows the same general steps: (1) selection of appropriate prototypes within each land use sector disaggregated by census region; (2) characterization of the end-use energy demand of each prototype in order to match an appropriate decentralized solar technology to the energy demand; (3) assessment of the energy conservation potential within each prototype limited by land use patterns, technology efficiency, and variation in solar insolation; and (4) evaluation of the regional and subregional differences in the land use implications of decentralized energy supply technologies that result from the combination of energy demand, energy supply potential, and the subsequent addition of increasingly more restrictive policies to increase the percent contribution of on-site solar energy.

Soil Bacteria and Fungi Respond on Different Spatial Scales to Invasion by the Legume Lespedeza cuneata

DTIC Science & Technology

2011-05-24

of 230   community similarity (Legendre and Legendre 1998). 231   232   Permutational Multivariate Analysis of Variance ( PerMANOVA ) (McArdle...241   null hypothesis can be rejected with a type I error rate of a. We used an implementation 242   of PerMANOVA that involved sequential removal...TEXTURE, and 249   HABITAT. 250   251   The null distribution for PerMANOVA tests for site-scale effects was generated 252   using a restricted

The impact of landscape disturbance on spatial genetic structure in the Guanacaste tree, Enterolobium cyclocarpum (Fabaceae).

PubMed

Gonzales, Eva; Hamrick, James L; Smouse, Peter E; Trapnell, Dorset W; Peakall, Rod

2010-01-01

We examined spatial genetic structure (SGS) in Enterolobium cyclocarpum (the Guanacaste tree), a dominant tree of Central American dry forests in 4 sites in Guanacaste Province, Costa Rica. In disturbed dry forest sites (e.g., pastures), E. cyclocarpum is primarily dispersed by cattle and horses, whose movements are restricted by pasture boundaries. The study sites varied in tree densities and disturbance. Allozyme analyses of adult trees demonstrated significant levels of SGS in 3 of 4 sites. SGS was primarily due to clusters of young adults located along seasonal streams, rocky areas, and in abandoned pastures. SGS was highest in the first distance class in the least disturbed population, which also had the lowest density of large adults. Low, but significant SGS characterized the site with the highest number of large adults located in individual pastures. The semiurban site, had no clusters of young adults and, probably as a result, failed to exhibit SGS. Our results demonstrate that disturbance can strongly influence SGS patterns and are consistent with a landscape model in which the location of potential recruitment sites, restricted seed disperser movements, and the number and location of maternal individuals dictate the level and pattern of SGS.

Analysis of DNA methylation in Arabidopsis thaliana based on methylation-sensitive AFLP markers.

PubMed

Cervera, M T; Ruiz-García, L; Martínez-Zapater, J M

2002-12-01

AFLP analysis using restriction enzyme isoschizomers that differ in their sensitivity to methylation of their recognition sites has been used to analyse the methylation state of anonymous CCGG sequences in Arabidopsis thaliana. The technique was modified to improve the quality of fingerprints and to visualise larger numbers of scorable fragments. Sequencing of amplified fragments indicated that detection was generally associated with non-methylation of the cytosine to which the isoschizomer is sensitive. Comparison of EcoRI/ HpaII and EcoRI/ MspI patterns in different ecotypes revealed that 35-43% of CCGG sites were differentially digested by the isoschizomers. Interestingly, the pattern of digestion among different plants belonging to the same ecotype is highly conserved, with the rate of intra-ecotype methylation-sensitive polymorphisms being less than 1%. However, pairwise comparisons of methylation patterns between samples belonging to different ecotypes revealed differences in up to 34% of the methylation-sensitive polymorphisms. The lack of correlation between inter-ecotype similarity matrices based on methylation-insensitive or methylation-sensitive polymorphisms suggests that whatever the mechanisms regulating methylation may be, they are not related to nucleotide sequence variation.

The sustainable management of ameliorated peatlands on changed land use conditions; scenarios of constrains and possibilities

NASA Astrophysics Data System (ADS)

Shanskiy, , Merrit; Vollmer, Elis; Penu, Priit

2015-04-01

The utilization of organic soils for forestry or agriculture requires the land amelioration that could result on the peat losses from 15 to 20 t ha-1 in a year on following five years. After five years, the peat losses will be 5 - 15 t ha-1 in a year. The agricultural land resource on different types of organic soils (including ameliorated bogs) in Estonia is 360 000 ha that comprises 41% of total agricultural land area. The landscape iself is a valuable resource that considered to be a set of characteristics that satisfy needs of people using the landscape: economical or non-economical value; ecological, social, recreational, aesthetical, educational, scientific or even protective value. More diverse landscapes have higher biodiversity and yield more services to public, they are also seen as more sustainable and resilient to short-term changes. In order to maintain landscape diversity, sustainable maintenance is important. The purpose of current study was to estimate the land use potential on three different ameliorated peat areas and to develop the methodology for the futher sustainable utilization in order to secure the best ecological functioning of soil while taking into account maintaining and increasing landscape value. Therefore, site specific soil sampling (n=77) was carried out on predetermined eight study sites. Soil samples were analyzed for main agrochemical parameters (n=17; pHKCl, P, K, C%, N%, S%, ash, main anions and cations). This enables determing site-specific best suitable crops and land use scenarios. For the land resource description (soils type, topology) the digital soil map (1: 10,000) and field sudy based database were used for describing the model areas. For more specific identification of the field layers the Agricultural Registers and Information Board (ARIB) and databases of the Common Agricultural Policy (CAP) payments were used for subsidy schemes chekout. Estonian Nature Information System map tool was used to specify the restrictions on study sites by nature conversation on the maps data about nature protected objects and buffer zones or forming restricted areas around those objects. The results will indicate the utilization possibility and most sustainable scenarios for different land use cases. Moreover, the possible changes in soil functioning accordingly to site specific soil conditions will be discussed and presented.

Bioinorganic Chemistry of Parkinson's Disease: Affinity and Structural Features of Cu(I) Binding to the Full-Length β-Synuclein Protein.

PubMed

Miotto, Marco C; Pavese, Mayra D; Quintanar, Liliana; Zweckstetter, Markus; Griesinger, Christian; Fernández, Claudio O

2017-09-05

Alterations in the levels of copper in brain tissue and formation of α-synuclein (αS)-copper complexes might play a key role in the amyloid aggregation of αS and the onset of Parkinson's disease (PD). Recently, we demonstrated that formation of the high-affinity Cu(I) complex with the N-terminally acetylated form of the protein αS substantially increases and stabilizes local conformations with α-helical secondary structure and restricted motility. In this work, we performed a detailed NMR-based structural characterization of the Cu(I) complexes with the full-length acetylated form of its homologue β-synuclein (βS), which is colocalized with αS in vivo and can bind copper ions. Our results show that, similarly to αS, the N-terminal region of βS constitutes the preferential binding interface for Cu(I) ions, encompassing two independent and noninteractive Cu(I) binding sites. According to these results, βS binds the metal ion with higher affinity than αS, in a coordination environment that involves the participation of Met-1, Met-5, and Met-10 residues (site 1). Compared to αS, the shift of His from position 50 to 65 in the N-terminal region of βS does not change the Cu(I) affinity features at that site (site 2). Interestingly, the formation of the high-affinity βS-Cu(I) complex at site 1 in the N-terminus promotes a short α-helix conformation that is restricted to the 1-5 segment of the AcβS sequence, which differs with the substantial increase in α-helix conformations seen for N-terminally acetylated αS upon Cu(I) complexation. Our NMR data demonstrate conclusively that the differences observed in the conformational transitions triggered by Cu(I) binding to AcαS and AcβS find a correlation at the level of their backbone dynamic properties; added to the potential biological implications of these findings, this fact opens new avenues of investigations into the bioinorganic chemistry of PD.

Enzymatic synthesis of long double-stranded DNA labeled with haloderivatives of nucleobases in a precisely pre-determined sequence

PubMed Central

2011-01-01

Background Restriction endonucleases are widely applied in recombinant DNA technology. Among them, enzymes of class IIS, which cleave DNA beyond recognition sites, are especially useful. We use BsaI enzyme for the pinpoint introduction of halogen nucleobases into DNA. This has been done for the purpose of anticancer radio- and phototherapy that is our long-term objective. Results An enzymatic method for synthesizing long double-stranded DNA labeled with the halogen derivatives of nucleobases (Hal-NBs) with 1-bp accuracy has been put forward and successfully tested on three different DNA fragments containing the 5-bromouracil (5-BrU) residue. The protocol assumes enzymatic cleavage of two Polymerase-Chain-Reaction (PCR) fragments containing two recognition sequences for the same or different class IIS restriction endonucleases, where each PCR fragment has a partially complementary cleavage site. These sites are introduced using synthetic DNA primers or are naturally present in the sequence used. The cleavage sites are not compatible, and therefore not susceptible to ligation until they are partially filled with a Hal-NB or original nucleobase, resulting in complementary cohesive end formation. Ligation of these fragments ultimately leads to the required Hal-NB-labeled DNA duplex. With this approach, a synthetic, extremely long DNA fragment can be obtained by means of a multiple assembly reaction (n × maximum PCR product length: n × app. 50 kb). Conclusions The long, precisely labeled DNA duplexes obtained behave in very much the same manner as natural DNA and are beyond the range of chemical synthesis. Moreover, the conditions of synthesis closely resemble the natural ones, and all the artifacts accompanying the chemical synthesis of DNA are thus eliminated. The approach proposed seems to be completely general and could be used to label DNA at multiple pre-determined sites and with halogen derivatives of any nucleobase. Access to DNAs labeled with Hal-NBs at specific position is an indispensable condition for the understanding and optimization of DNA photo- and radio-degradation, which are prerequisites for clinical trials of Hal-NBs in anticancer therapy. PMID:21864341

Enzymatic synthesis of long double-stranded DNA labeled with haloderivatives of nucleobases in a precisely pre-determined sequence.

PubMed

Sobolewski, Ireneusz; Polska, Katarzyna; Zylicz-Stachula, Agnieszka; Jeżewska-Frąckowiak, Joanna; Rak, Janusz; Skowron, Piotr

2011-08-24

Restriction endonucleases are widely applied in recombinant DNA technology. Among them, enzymes of class IIS, which cleave DNA beyond recognition sites, are especially useful. We use BsaI enzyme for the pinpoint introduction of halogen nucleobases into DNA. This has been done for the purpose of anticancer radio- and phototherapy that is our long-term objective. An enzymatic method for synthesizing long double-stranded DNA labeled with the halogen derivatives of nucleobases (Hal-NBs) with 1-bp accuracy has been put forward and successfully tested on three different DNA fragments containing the 5-bromouracil (5-BrU) residue. The protocol assumes enzymatic cleavage of two Polymerase-Chain-Reaction (PCR) fragments containing two recognition sequences for the same or different class IIS restriction endonucleases, where each PCR fragment has a partially complementary cleavage site. These sites are introduced using synthetic DNA primers or are naturally present in the sequence used. The cleavage sites are not compatible, and therefore not susceptible to ligation until they are partially filled with a Hal-NB or original nucleobase, resulting in complementary cohesive end formation. Ligation of these fragments ultimately leads to the required Hal-NB-labeled DNA duplex. With this approach, a synthetic, extremely long DNA fragment can be obtained by means of a multiple assembly reaction (n × maximum PCR product length: n × app. 50 kb). The long, precisely labeled DNA duplexes obtained behave in very much the same manner as natural DNA and are beyond the range of chemical synthesis. Moreover, the conditions of synthesis closely resemble the natural ones, and all the artifacts accompanying the chemical synthesis of DNA are thus eliminated. The approach proposed seems to be completely general and could be used to label DNA at multiple pre-determined sites and with halogen derivatives of any nucleobase. Access to DNAs labeled with Hal-NBs at specific position is an indispensable condition for the understanding and optimization of DNA photo- and radio-degradation, which are prerequisites for clinical trials of Hal-NBs in anticancer therapy.

Accounting for unsearched areas in estimating wind turbine-caused fatality

USGS Publications Warehouse

Huso, Manuela M.P.; Dalthorp, Dan

2014-01-01

With wind energy production expanding rapidly, concerns about turbine-induced bird and bat fatality have grown and the demand for accurate estimation of fatality is increasing. Estimation typically involves counting carcasses observed below turbines and adjusting counts by estimated detection probabilities. Three primary sources of imperfect detection are 1) carcasses fall into unsearched areas, 2) carcasses are removed or destroyed before sampling, and 3) carcasses present in the searched area are missed by observers. Search plots large enough to comprise 100% of turbine-induced fatality are expensive to search and may nonetheless contain areas unsearchable because of dangerous terrain or impenetrable brush. We evaluated models relating carcass density to distance from the turbine to estimate the proportion of carcasses expected to fall in searched areas and evaluated the statistical cost of restricting searches to areas near turbines where carcass density is highest and search conditions optimal. We compared 5 estimators differing in assumptions about the relationship of carcass density to distance from the turbine. We tested them on 6 different carcass dispersion scenarios at each of 3 sites under 2 different search regimes. We found that even simple distance-based carcass-density models were more effective at reducing bias than was a 5-fold expansion of the search area. Estimators incorporating fitted rather than assumed models were least biased, even under restricted searches. Accurate estimates of fatality at wind-power facilities will allow critical comparisons of rates among turbines, sites, and regions and contribute to our understanding of the potential environmental impact of this technology.

Homing endonucleases: from basics to therapeutic applications.

PubMed

Marcaida, Maria J; Muñoz, Inés G; Blanco, Francisco J; Prieto, Jesús; Montoya, Guillermo

2010-03-01

Homing endonucleases (HE) are double-stranded DNAses that target large recognition sites (12-40 bp). HE-encoding sequences are usually embedded in either introns or inteins. Their recognition sites are extremely rare, with none or only a few of these sites present in a mammalian-sized genome. However, these enzymes, unlike standard restriction endonucleases, tolerate some sequence degeneracy within their recognition sequence. Several members of this enzyme family have been used as templates to engineer tools to cleave DNA sequences that differ from their original wild-type targets. These custom HEs can be used to stimulate double-strand break homologous recombination in cells, to induce the repair of defective genes with very low toxicity levels. The use of tailored HEs opens up new possibilities for gene therapy in patients with monogenic diseases that can be treated ex vivo. This review provides an overview of recent advances in this field.

hisT is part of a multigene operon in Escherichia coli K-12.

PubMed Central

Marvel, C C; Arps, P J; Rubin, B C; Kammen, H O; Penhoet, E E; Winkler, M E

1985-01-01

The Escherichia coli K-12 hisT gene has been cloned, and its organization and expression have been analyzed on multicopy plasmids. The hisT gene, which encodes tRNA pseudouridine synthase I (PSUI), was isolated on a Clarke-Carbon plasmid known to contain the purF gene. The presence of the hisT gene on this plasmid was suggested by its ability to restore both production of PSUI enzymatic activity and suppression of amber mutations in a hisT mutant strain. A 2.3-kilobase HindIII-ClaI restriction fragment containing the hisT gene was subcloned into plasmid pBR322, and the resulting plasmid (designated psi 300) was mapped with restriction enzymes. Complementation analysis with different kinds of hisT mutations and tRNA structural analysis confirmed that plasmid psi 300 contained the hisT structural gene. Enzyme assays showed that plasmid psi 300 overproduced PSUI activity by ca. 20-fold compared with the wild-type level. Subclones containing restriction fragments from plasmid psi 300 inserted downstream from the lac promoter established that the hisT gene is oriented from the HindIII site toward the ClaI site. Other subclones and derivatives of plasmid psi 300 containing insertion or deletion mutations were constructed and assayed for production of PSUI activity and production of proteins in minicells. These experiments showed that: (i) the proximal 1.3-kilobase HindIII-BssHII restriction fragment contains a promoter for the hisT gene and encodes a 45,000-dalton polypeptide that is not PSUI; (ii) the distal 1.0-kilobase BssHII-ClaI restriction fragment encodes the 31,000-dalton PSUI polypeptide; (iii) the 45,000-dalton polypeptide is synthesized in an approximately eightfold excess compared with PSUI; and (iv) synthesis of the two polypeptides is coupled, suggesting that the two genes are part of an operon. Insertion of mini-Mu d1 (lac Km) phage into plasmid psi 300 confirmed that the hisT gene is the downstream gene in the operon. Images PMID:2981810

Impact of Helminth Infections and Nutritional Constraints on the Small Intestine Microbiota

PubMed Central

Cattadori, Isabella M.; Albert, Istvan; Eilertson, Kirsten E.; Kapur, Vivek; Pathak, Ashutosh; Mitchell, Susan

2016-01-01

Helminth infections and nutrition can independently alter the composition and abundance of the gastrointestinal microbiota, however, their combined effect is poorly understood. Here, we used the T. retortaeformis-rabbit system to examine how the helminth infection and host restriction from coprophagy/ready-to-absorb nutrients affected the duodenal microbiota, and how these changes related to the acquired immune response at the site of infection. A factorial experiment was performed where the bacterial community, its functionality and the immune response were examined in four treatments (Infect, Infect+Collar, Control+Collar and Control). Helminths reduced the diversity and abundance of the microbiota while the combination of parasites and coprophagic restriction led to a more diversified and abundant microbiota than infected cases, without significantly affecting the intensity of infection. Animals restricted from coprophagy and free from parasites exhibited the richest and most abundant bacterial community. By forcing the individuals to absorb nutrients from less digested food, the coprophagic restriction appears to have facilitated the diversity and proliferation of bacteria in the duodenum. Changes in the microbiota were more clearly associated with changes in the immune response for the infected than the nutrient restricted animals. The functional and metabolic characteristics of the duodenal microbiota were not significantly different between treatments. Overall, infection and diet affect the gut microbiota but their interactions and outcome can be complex. These findings can have important implications for the development of control measures to helminth infections where poor nutrition/malnutrition can also be a concern. PMID:27438701

Impact of Helminth Infections and Nutritional Constraints on the Small Intestine Microbiota.

PubMed

Cattadori, Isabella M; Sebastian, Aswathy; Hao, Han; Katani, Robab; Albert, Istvan; Eilertson, Kirsten E; Kapur, Vivek; Pathak, Ashutosh; Mitchell, Susan

2016-01-01

Helminth infections and nutrition can independently alter the composition and abundance of the gastrointestinal microbiota, however, their combined effect is poorly understood. Here, we used the T. retortaeformis-rabbit system to examine how the helminth infection and host restriction from coprophagy/ready-to-absorb nutrients affected the duodenal microbiota, and how these changes related to the acquired immune response at the site of infection. A factorial experiment was performed where the bacterial community, its functionality and the immune response were examined in four treatments (Infect, Infect+Collar, Control+Collar and Control). Helminths reduced the diversity and abundance of the microbiota while the combination of parasites and coprophagic restriction led to a more diversified and abundant microbiota than infected cases, without significantly affecting the intensity of infection. Animals restricted from coprophagy and free from parasites exhibited the richest and most abundant bacterial community. By forcing the individuals to absorb nutrients from less digested food, the coprophagic restriction appears to have facilitated the diversity and proliferation of bacteria in the duodenum. Changes in the microbiota were more clearly associated with changes in the immune response for the infected than the nutrient restricted animals. The functional and metabolic characteristics of the duodenal microbiota were not significantly different between treatments. Overall, infection and diet affect the gut microbiota but their interactions and outcome can be complex. These findings can have important implications for the development of control measures to helminth infections where poor nutrition/malnutrition can also be a concern.

76 FR 19003 - Land Disposal Restrictions: Nevada and California; Site Specific Treatment Variances for...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-04-06

... both a site-specific treatment variance to U.S. Ecology Nevada (USEN) located in Beatty, Nevada and... site-specific treatment variance to U.S. Ecology Nevada (USEN) located in Beatty, Nevada and withdraw... section of this document. II. Does this action apply to me? This proposal applies only to U. S. Ecology...

Nature and function of insulator protein binding sites in the Drosophila genome

PubMed Central

Schwartz, Yuri B.; Linder-Basso, Daniela; Kharchenko, Peter V.; Tolstorukov, Michael Y.; Kim, Maria; Li, Hua-Bing; Gorchakov, Andrey A.; Minoda, Aki; Shanower, Gregory; Alekseyenko, Artyom A.; Riddle, Nicole C.; Jung, Youngsook L.; Gu, Tingting; Plachetka, Annette; Elgin, Sarah C.R.; Kuroda, Mitzi I.; Park, Peter J.; Savitsky, Mikhail; Karpen, Gary H.; Pirrotta, Vincenzo

2012-01-01

Chromatin insulator elements and associated proteins have been proposed to partition eukaryotic genomes into sets of independently regulated domains. Here we test this hypothesis by quantitative genome-wide analysis of insulator protein binding to Drosophila chromatin. We find distinct combinatorial binding of insulator proteins to different classes of sites and uncover a novel type of insulator element that binds CP190 but not any other known insulator proteins. Functional characterization of different classes of binding sites indicates that only a small fraction act as robust insulators in standard enhancer-blocking assays. We show that insulators restrict the spreading of the H3K27me3 mark but only at a small number of Polycomb target regions and only to prevent repressive histone methylation within adjacent genes that are already transcriptionally inactive. RNAi knockdown of insulator proteins in cultured cells does not lead to major alterations in genome expression. Taken together, these observations argue against the concept of a genome partitioned by specialized boundary elements and suggest that insulators are reserved for specific regulation of selected genes. PMID:22767387

Changes in the chemistry of precipitation in the United States, 1981-1998

USGS Publications Warehouse

Nilles, M.A.; Conley, B.E.

2001-01-01

Regulatory measures in the United States, such as Title IV of the Clean Air Act Amendments of 1990, have primarily restricted sulfur dioxide emissions as a way to control acidic deposition. These restrictions, coupled with increasing concentrations of NH4+ in wet deposition in some regions of the U.S. and continued high emissions of nitrogen oxides have generated a significant shift in the chemistry of precipitation as measured at National Atmospheric Deposition Program/National Trends Network sites. Trends in precipitation chemistry at NADP/NTN sites were evaluated for statistical significance for the period 1981-1998 using a Seasonal Mann-Kendall Test, a robust non-parametric test for detection of monotonic trends. SO42- declines were detected at 100 of the 147 sites examined while no sites exhibited increasing SO42- trends. On average, SO42- declined 35% over the period 1981-1998 with downward SO42- trends being most pronounced in the northeastern United States. In contrast, no consistent trends in NO3- concentrations were observed in precipitation in any major region of the United States. Although the majority of sites did not exhibit significant trends in NH4+ concentration, 30 sites exhibited upward trends. For Ca2+ concentration in precipitation, 64 sites exhibited a significant decreasing trend and no sites exhibited an upward trend.

Effect of weather, subsurface topography and fertilizer type on corn yields at the BARC experimental OPE3 site

USDA-ARS?s Scientific Manuscript database

Availability of soil water is critical for plant growth and development. In shallow groundwater conditions, this availability may vary with the depth to the restrictive layer that is found beneath groundwater. The restrictive layer is not flat, and the presence of the relief of this layer leads to t...

Evaluation of Movement Restriction Zone Sizes in Controlling Classical Swine Fever Outbreaks

PubMed Central

Yadav, Shankar; Olynk Widmar, Nicole; Lay, Donald C.; Croney, Candace; Weng, Hsin-Yi

2017-01-01

The objective of this study was to compare the impacts of movement restriction zone sizes of 3, 5, 9, and 11 km with that of 7 km (the recommended zone size in the United States) in controlling a classical swine fever (CSF) outbreak. In addition to zone size, different compliance assumptions and outbreak types (single site and multiple site) were incorporated in the study. Three assumptions of compliance level were simulated: baseline, baseline ± 10%, and baseline ± 15%. The compliance level was held constant across all zone sizes in the baseline simulation. In the baseline ± 10% and baseline ± 15% simulations, the compliance level was increased for 3 and 5 km and decreased for 9 and 11 km from the baseline by the indicated percentages. The compliance level remained constant in all simulations for the 7-km zone size. Four single-site (i.e., with one index premises at the onset of outbreak) and four multiple-site (i.e., with more than one index premises at the onset of outbreak) CSF outbreak scenarios in Indiana were simulated incorporating various zone sizes and compliance assumptions using a stochastic between-premises disease spread model to estimate epidemic duration, percentage of infected, and preemptively culled swine premises. Furthermore, a risk assessment model that incorporated the results from the disease spread model was developed to estimate the number of swine premises under movement restrictions that would experience animal welfare outcomes of overcrowding or feed interruption during a CSF outbreak in Indiana. Compared with the 7-km zone size, the 3-km zone size resulted in a longer median epidemic duration, larger percentages of infected premises, and preemptively culled premises (P’s < 0.001) across all compliance assumptions and outbreak types. With the assumption of a higher compliance level, the 5-km zone size significantly (P < 0.001) reduced the epidemic duration and percentage of swine premises that would experience animal welfare outcomes in both outbreak types, whereas assumption of a lower compliance level for 9- and 11-km zone sizes significantly (P < 0.001) increased the epidemic duration and percentage of swine premises with animal welfare outcomes compared with the 7-km zone size. The magnitude of impact due to a zone size varied across the outbreak types (single site and multiple site). Overall, the 7-km zone size was found to be most effective in controlling CSF outbreaks, whereas the 5-km zone size was comparable to the 7-km zone size in some circumstances. PMID:28119920

Frequency of TERT promoter mutations in primary tumors of the liver.

PubMed

Quaas, Alexander; Oldopp, Theresa; Tharun, Lars; Klingenfeld, Catina; Krech, Till; Sauter, Guido; Grob, Tobias J

2014-12-01

Transcriptional regulation of the TERT gene is a major cause of the cancer-specific increase in telomerase activity. Recently, frequent somatic mutations in the TERT promoter have been described in several tumor entities such as melanoma, glioblastoma, bladder cancer, and hepatocellular carcinoma. By generating a putative consensus binding site for ETS transcription factors within the TERT promoter, these mutations are predicted to increase promoter activity and TERT transcription. In order to improve the understanding of the role of TERT promoter mutation in liver tumorigenesis, the mutational status of the TERT promoter was analyzed in 78 hepatocellular carcinomas, 15 hepatocellular adenomas, and 52 intrahepatic cholangiocarciomas. The promoter region of TERT was screened for the two hotspot mutations using PCR and restriction fragment length analysis, utilizing the introduction of novel restriction sites by the somatic mutations. TERT promoter mutation was found in 37 of 78 hepatocellular carcinomas (47 %) and was restricted to the -124C>T mutation. Frequency of mutations was associated with grade of differentiation ranging from 39 % in well-differentiated tumors to 73 % in high-grade hepatocellular carcinomas. TERT promoter mutations were not found in 15 hepatocellular adenomas and 52 intrahepatic cholangiocarcinomas. These data show that TERT promoter mutation is the most frequent genetic alteration in hepatocellular carcinoma known at this time. The striking predominance of the -124C>T mutation compared with other tumor entities suggest a biological difference of the two hotspot mutations. Analysis of TERT promoter mutation might become a diagnostic tool distinguishing hepatocellular adenoma from well-differentiated hepatocellular carcinoma.

Effect of NaeI-L43K mutation on protein dynamics and DNA conformation: Insights from molecular dynamics simulations.

PubMed

Ramachandrakurup, Sreelakshmi; Ramakrishnan, Vigneshwar

2017-09-01

Protein-DNA interactions are an important class of biomolecular interactions inside the cell. Delineating the mechanisms of protein-DNA interactions and more specifically, how proteins search and bind to their specific cognate sequences has been the quest of many in the scientific community. Restriction enzymes have served as useful model systems to this end. In this work, we have investigated using molecular dynamics simulations the effect of L43K mutation on NaeI, a type IIE restriction enzyme. NaeI has two domains, the Topo and the Endo domains, each binding to identical strands of DNA sequences (GCCGGC) 2 . The binding of the DNA to the Topo domain is thought to enhance the binding and cleavage of DNA at the Endo domain. Interestingly, it has been found that the mutation of an amino acid that is distantly-located from the DNA cleavage site (L43K) converts the restriction endonuclease to a topoisomerase. Our investigations reveal that the L43K mutation not only induces local structural changes (as evidenced by changes in hydrogen bond propensities and differences in the percentage of secondary structure assignments of the residues in the ligase-like domain) but also alters the overall protein dynamics and DNA conformation which probably leads to the loss of specific cleavage of the recognition site. In a larger context, our study underscores the importance of considering the role of distantly-located amino acids in understanding protein-DNA interactions. Copyright © 2017 Elsevier Inc. All rights reserved.

Molecular analysis of bacterial microbiota associated with oysters (Crassostrea gigas and Crassostrea corteziensis) in different growth phases at two cultivation sites.

PubMed

Trabal, Natalia; Mazón-Suástegui, José M; Vázquez-Juárez, Ricardo; Asencio-Valle, Felipe; Morales-Bojórquez, Enrique; Romero, Jaime

2012-08-01

Microbiota presumably plays an essential role in inhibiting pathogen colonization and in the maintenance of health in oysters, but limited data exist concerning their different growth phases and conditions. We analyzed the bacterial microbiota composition of two commercial oysters: Crassostrea gigas and Crassostrea corteziensis. Differences in microbiota were assayed in three growth phases: post-larvae at the hatchery, juvenile, and adult at two grow-out cultivation sites. Variations in the microbiota were assessed by PCR analysis of the 16S rRNA gene in DNA extracted from depurated oysters. Restriction fragment length polymorphism (RFLP) profiles were studied using Dice's similarity coefficient (Cs) and statistical principal component analysis (PCA). The microbiota composition was determined by sequencing temperature gradient gel electrophoresis (TGGE) bands. The RFLP analysis of post-larvae revealed homology in the microbiota of both oyster species (Cs > 88 %). Dice and PCA analyses of C. corteziensis but not C. gigas showed differences in the microbiota according to the cultivation sites. The sequencing analysis revealed low bacterial diversity (primarily β-Proteobacteria, Firmicutes, and Spirochaetes), with Burkholderia cepacia being the most abundant bacteria in both oyster species. This study provides the first description of the microbiota in C. corteziensis, which was shown to be influenced by cultivation site conditions. During early growth, we observed that B. cepacia colonized and remained strongly associated with the two oysters, probably in a symbiotic host-bacteria relationship. This association was maintained in the three growth phases and was not altered by environmental conditions or the management of the oysters at the grow-out site.

An Introduction to the Cost of Engineering and Institutional Controls at Brownfield Properties

EPA Pesticide Factsheets

This fact sheet introduces and explores the costs of site cleanup and, where cleanup leaves site contamination that restricts reuse, outlines the engineering and institutional controls and their monitoring and maintenance costs over a longer time frame.

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

Li, Dongfang; Voigt, Thomas B.; Kent, Angela D.

Here, bacterial assemblages, especially diazotroph assemblages residing in the rhizomes and the rhizosphere soil of Miscanthus × giganteus, contribute to plant growth and nitrogen use efficiency. However, the composition of these microbial communities has not been adequately explored nor have the potential ecological drivers for these communities been sufficiently studied. This knowledge is needed for understanding and potentially improving M. × giganteus – microbe interactions, and further enhancing sustainability of M. × giganteus production. In this study, cultivated M. × giganteus from four sites in Illinois, Kentucky, Nebraska, and New Jersey were collected to examine the relative influences of soilmore » conditions and plant compartments on assembly of the M. × giganteus-associated microbiome. Automated ribosomal intergenic spacer (ARISA) and terminal restriction fragment length polymorphism (T-RFLP) targeting the nifH gene were applied to examine the total bacterial communities and diazotroph assemblages that reside in the rhizomes and the rhizosphere. Distinct microbial assemblages were detected in the endophytic and rhizosphere compartments. Site soil conditions had strong correlation with both total bacterial and diazotroph assemblages, but in different ways. Nitrogen treatments showed no significant effect on the composition of diazotroph assemblages in most sites. Endophytic compartments of different M. × giganteus plants tended to harbor similar microbial communities across all sites, whereas the rhizosphere soil of different plant tended to harbor diverse microbial assemblages that were distinct among sites. These observations offer insight into better understanding of the associative interactions between M. × giganteus and diazotrophs, and how this relationship is influenced by agronomic and edaphic factors.« less

Environmenal analysis of the Bayo Canyon (TA-10) Site, Los Alamos, New Mexico

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

Ferenbaugh, R.W.; Buhl, T.E.; Stoker, A.K.

1982-05-01

The radiological survey of the old TA-10 site in Bayo Canyon found low levels of surface contamination in the vicinity of the firing sites and subsurface contamination in the old waste disposal area. The three alternatives proposed for the site are: (1) to take no action; (2) to restrict usage of the area of subsurface contamination to activities that cause no subsurface disturbance (minimal action); and (3) to remove the subsurface conamination to levels below the working criteria. Dose calculations indicate that doses from surface contamination for recreational users of the canyon, permanent residents, and construction workers and doses formore » workers involved in excavation of contaminated soil under the clean up alternative are only small percentages of applicable guidelines. No environmental impacts are associated with either the no-action or minimal action alternatives. The impact associated with the cleanup alternative is small, especially considering that the area already has been affected by the original TA-10 decommissioning action, but nevertheless, the preferred alternative is the minimal action alternative, where 0.6 hectare of land is restricted to surface activities. This leaves the rest of the canyon available for development with up to 400 homes. The restricted area can be used for a park, tennis courts, etc., and the /sup 90/Sr activity will decay to levels permitting unrestricted usage in about 160 y.« less

Validation of the high-throughput marker technology DArT using the model plant Arabidopsis thaliana.

PubMed

Wittenberg, Alexander H J; van der Lee, Theo; Cayla, Cyril; Kilian, Andrzej; Visser, Richard G F; Schouten, Henk J

2005-08-01

Diversity Arrays Technology (DArT) is a microarray-based DNA marker technique for genome-wide discovery and genotyping of genetic variation. DArT allows simultaneous scoring of hundreds of restriction site based polymorphisms between genotypes and does not require DNA sequence information or site-specific oligonucleotides. This paper demonstrates the potential of DArT for genetic mapping by validating the quality and molecular basis of the markers, using the model plant Arabidopsis thaliana. Restriction fragments from a genomic representation of the ecotype Landsberg erecta (Ler) were amplified by PCR, individualized by cloning and spotted onto glass slides. The arrays were then hybridized with labeled genomic representations of the ecotypes Columbia (Col) and Ler and of individuals from an F(2) population obtained from a Col x Ler cross. The scoring of markers with specialized software was highly reproducible and 107 markers could unambiguously be ordered on a genetic linkage map. The marker order on the genetic linkage map coincided with the order on the DNA sequence map. Sequencing of the Ler markers and alignment with the available Col genome sequence confirmed that the polymorphism in DArT markers is largely a result of restriction site polymorphisms.

The Gene Construction Kit: a new computer program for manipulating and presenting DNA constructs.

PubMed

Gross, R H

1990-06-01

The Gene Construction Kit is a new tool for manipulating and displaying DNA sequence information. Constructs can be displayed either graphically or as formatted sequence. Segments of DNA can be cut out with restriction enzymes and pasted into other sites. The program keeps track of staggered ends and notifies the user of incompatibilities and offers a choice of ligation options. Each segment of a construct can have its own defined thickness, pattern, direction and color. The sequence listing can be displayed in any font and style in user defined grouping. Nucleotide positions can be displayed as can restriction sites and protein sequences. The DNA can be displayed as either single- or double-stranded. Restriction sites can be readily marked. Alternative views of the DNA can be maintained and the history of the construct automatically stored. Gel electrophoresis patterns can be generated and can be used in cloning project design. Extensive comments can be stored with the construct and can be searched rapidly for key words. High quality illustrations showing multiple editable constructs with added graphics and text information can be generated for slides, posters or publication.

Evidence of host-associated divergence from coral-eating snails (genus Coralliophila) in the Coral Triangle

NASA Astrophysics Data System (ADS)

Simmonds, Sara E.; Chou, Vincent; Cheng, Samantha H.; Rachmawati, Rita; Calumpong, Hilconida P.; Ngurah Mahardika, G.; Barber, Paul H.

2018-06-01

We studied how host-associations and geography shape the genetic structure of sister species of marine snails Coralliophila radula (A. Adams, 1853) and C. violacea (Kiener, 1836). These obligate ectoparasites prey upon corals and are sympatric throughout much of their ranges in coral reefs of the tropical and subtropical Indo-Pacific. We tested for population genetic structure of snails in relation to geography and their host corals using mtDNA (COI) sequences in minimum spanning trees and AMOVAs. We also examined the evolutionary relationships of their Porites host coral species using maximum likelihood trees of RAD-seq (restriction site-associated DNA sequencing) loci mapped to a reference transcriptome. A maximum likelihood tree of host corals revealed three distinct clades. Coralliophila radula showed a pronounced genetic break across the Sunda Shelf ( Φ CT = 0.735) but exhibited no genetic structure with respect to host. C. violacea exhibited significant geographic structure ( Φ CT = 0.427), with divergence among Hawaiian populations, the Coral Triangle and the Indian Ocean. Notably, C. violacea showed evidence of ecological divergence; two lineages were associated with different groups of host coral species, one widespread found at all sites, and the other restricted to the Coral Triangle. Sympatric populations of C. violacea found on different suites of coral species were highly divergent ( Φ CT = 0.561, d = 5.13%), suggesting that symbiotic relationships may contribute to lineage diversification in the Coral Triangle.

Relationship between peripheral insertion site and catheter-related phlebitis in adult hospitalized patients: a systematic review.

PubMed

Comparcini, Dania; Simonetti, Valentina; Blot, Stijn; Tomietto, Marco; Cicolini, Giancarlo

2017-01-01

To explore the relationship between the anatomical site of peripheral venous catheterization and risk of catheter-related phlebitis. Peripheral venous catheterization is frequently associated with phlebitis. Recent guidelines, recommend the use of an upper-extremity site for catheter insertion but no univocal consensus exists on the anatomical site with lower risk of phlebitis. Systematic review. We searched Medline (PubMed) and CINAHL (EBSCOhost) databases until the end of January 2017. We also reviewed the reference lists of retrieved articles and gray literature was excluded. Searches were limited to articles published in English with no restriction imposed to date of publication. The primary outcome was the incidence of phlebitis associated with anatomical site of peripheral catheterization. We included randomized controlled trials and observational studies on adult patients who required a peripheral catheter for the administration of medi- cation, intermittent or continuous fluid infusion. Antecubital fossa veins are associated with lower phlebitis rates, while hands veins are the most risky sites to develop phlebitis. There is no consensus regarding vein in forearm. Choosing the right anatomical site to insert a peripheral venous catheter is important to decrease phlebitis rate. Further studies should compare indwelling time in different anatomical sites with phlebitis rate. A more standardized approach in defining and assessing phlebitis among studies is recommended.

Identification of distinct movement patterns in Pacific leatherback turtle populations influenced by ocean conditions.

PubMed

Bailey, Helen; Benson, Scott R; Shillinger, George L; Bograd, Steven J; Dutton, Peter H; Eckert, Scott A; Morreale, Stephen J; Paladino, Frank V; Eguchi, Tomoharu; Foley, David G; Block, Barbara A; Piedra, Rotney; Hitipeuw, Creusa; Tapilatu, Ricardo F; Spotila, James R

2012-04-01

Interactions with fisheries are believed to be a major cause of mortality for adult leatherback turtles (Dermochelys coriacea), which is of particular concern in the Pacific Ocean, where they have been rapidly declining. In order to identify where these interactions are occurring and how they may be reduced, it is essential first to understand the movements and behavior of leatherback turtles. There are two regional nesting populations in the East Pacific (EP) and West Pacific (WP), comprising multiple nesting sites. We synthesized tracking data from the two populations and compared their movement patterns. A switching state-space model was applied to 135 Argos satellite tracks to account for observation error, and to distinguish between migratory and area-restricted search behaviors. The tracking data, from the largest leatherback data set ever assembled, indicated that there was a high degree of spatial segregation between EP and WP leatherbacks. Area-restricted search behavior mainly occurred in the southeast Pacific for the EP leatherbacks, whereas the WP leatherbacks had several different search areas in the California Current, central North Pacific, South China Sea, off eastern Indonesia, and off southeastern Australia. We also extracted remotely sensed oceanographic data and applied a generalized linear mixed model to determine if leatherbacks exhibited different behavior in relation to environmental variables. For the WP population, the probability of area-restricted search behavior was positively correlated with chlorophyll-a concentration. This response was less strong in the EP population, but these turtles had a higher probability of search behavior where there was greater Ekman upwelling, which may increase the transport of nutrients and consequently prey availability. These divergent responses to oceanographic conditions have implications for leatherback vulnerability to fisheries interactions and to the effects of climate change. The occurrence of leatherback turtles within both coastal and pelagic areas means they have a high risk of exposure to many different fisheries, which may be very distant from their nesting sites. The EP leatherbacks have more limited foraging grounds than the WP leatherbacks, which could make them more susceptible to any temperature or prey changes that occur in response to climate change.

Single-Stranded γPNAs for In Vivo Site-Specific Genome Editing via Watson-Crick Recognition

PubMed Central

Bahal, Raman; Quijano, Elias; McNeer, Nicole Ali; Liu, Yanfeng; Bhunia, Dinesh C.; López-Giráldez, Francesco; Fields, Rachel J.; Saltzman, W. Mark; Ly, Danith H.; Glazer, Peter M.

2014-01-01

Triplex-forming peptide nucleic acids (PNAs) facilitate gene editing by stimulating recombination of donor DNAs within genomic DNA via site-specific formation of altered helical structures that further stimulate DNA repair. However, PNAs designed for triplex formation are sequence restricted to homopurine sites. Herein we describe a novel strategy where next generation single-stranded gamma PNAs (γPNAs) containing miniPEG substitutions at the gamma position can target genomic DNA in mouse bone marrow at mixed-sequence sites to induce targeted gene editing. In addition to enhanced binding, γPNAs confer increased solubility and improved formulation into poly(lactic-co-glycolic acid) (PLGA) nanoparticles for efficient intracellular delivery. Single-stranded γPNAs induce targeted gene editing at frequencies of 0.8% in mouse bone marrow cells treated ex vivo and 0.1% in vivo via IV injection, without detectable toxicity. These results suggest that γPNAs may provide a new tool for induced gene editing based on Watson-Crick recognition without sequence restriction. PMID:25174576

Single-stranded γPNAs for in vivo site-specific genome editing via Watson-Crick recognition.

PubMed

Bahal, Raman; Quijano, Elias; McNeer, Nicole A; Liu, Yanfeng; Bhunia, Dinesh C; Lopez-Giraldez, Francesco; Fields, Rachel J; Saltzman, William M; Ly, Danith H; Glazer, Peter M

2014-01-01

Triplex-forming peptide nucleic acids (PNAs) facilitate gene editing by stimulating recombination of donor DNAs within genomic DNA via site-specific formation of altered helical structures that further stimulate DNA repair. However, PNAs designed for triplex formation are sequence restricted to homopurine sites. Herein we describe a novel strategy where next generation single-stranded gamma PNAs (γPNAs) containing miniPEG substitutions at the gamma position can target genomic DNA in mouse bone marrow at mixed-sequence sites to induce targeted gene editing. In addition to enhanced binding, γPNAs confer increased solubility and improved formulation into poly(lactic-co-glycolic acid) (PLGA) nanoparticles for efficient intracellular delivery. Single-stranded γPNAs induce targeted gene editing at frequencies of 0.8% in mouse bone marrow cells treated ex vivo and 0.1% in vivo via IV injection, without detectable toxicity. These results suggest that γPNAs may provide a new tool for induced gene editing based on Watson-Crick recognition without sequence restriction.

Calorie restriction suppresses subgenomic mink cytopathic focus-forming murine leukemia virus transcription and frequency of genomic expression while impairing lymphoma formation.

PubMed Central

Shields, B A; Engelman, R W; Fukaura, Y; Good, R A; Day, N K

1991-01-01

Calorie restriction suppresses mammary proviral mRNA expression and protooncogene activation in breast tumor-prone C3H/Ou mice while inhibiting tumor formation. To determine whether the beneficial effects of chronic energy-intake restriction (CEIR) can be extended to an organ site of retrovirus-induced tumorigenesis where the dynamics of growth and sexual maturity are not paramount as they are in breast tissue, calorie restriction of 40% was imposed on thymic lymphoma-prone AKR mice when 4 weeks old. Recombination between various murine leukemia virus (MuLV) mRNAs, resulting in the generation of an 8.4-kilobase genomic-length transcript with mink cytopathic focus-forming (MCF) characteristics, is considered the proximal retroviral event in AKR lymphomagenesis. Thymic expression of subgenomic MCF MuLV mRNA was uniformly suppressed among 6- and 8-week-old CEIR mice (P less than 0.02). This suppression of MuLV transcription preceded a 25% reduction in the appearance of genomic-length MCF transcripts among CEIR mice and a 28% reduction in cumulative lymphoma mortality. The latency to median tumor incidence was extended greater than 3 months by calorie restriction, and median lifespan was extended approximately 50%. Survival curves for the full-fed and CEIR dietary cohorts were found to be significantly different (P less than 0.0001), with full-fed mice experiencing a 3 times greater risk of lymphoma mortality. These findings extend the known range of pathologic states influenced by CEIR in inbred mice and show that retroviral mechanisms involved in generation of lymphoid malignancy can be significantly impaired by calorie restriction. Images PMID:1763029

Phylogenetic relationships among anuran trypanosomes as revealed by riboprinting.

PubMed

Clark, C G; Martin, D S; Diamond, L S

1995-01-01

Twenty trypanosome isolates from Anura (frogs and toads) assigned to several species were characterized by riboprinting-restriction enzyme digestion of polymerase chain reaction amplified small subunit ribosomal RNA genes. Restriction site polymorphisms allowed distinction of all the recognized species and no intraspecific variation in riboprint patterns was detected. Phylogenetic reconstruction using parsimony and distance estimates based on restriction fragment comigration showed Trypanosoma chattoni to be only distantly related to the other species, while T. ranarum and T. fallisi appear to be sister taxa despite showing non-overlapping host specificities.

Protected areas mitigate diseases of reef-building corals by reducing damage from fishing.

PubMed

Lamb, Joleah B; Williamson, David H; Russ, Garry R; Willis, Bette L

2015-09-01

Parks and protected areas have been instrumental in reducing anthropogenic sources of damage in terrestrial and aquatic environments. Pathogen invasion often succeeds physical wounding and injury, yet links between the reduction of damage and the moderation of disease have not been assessed. Here, we examine the utility of no-take marine reserves as tools for mitigating diseases that affect reef-building corals. We found that sites located within reserves had fourfold reductions in coral disease prevalence compared to non-reserve sites (80466 corals surveyed). Of 31 explanatory variables assessed, coral damage and the abundance of derelict fishing line best explained differences in disease assemblages between reserves and non-reserves. Unexpectedly, we recorded significantly higher levels of disease, coral damage, and derelict fishing line in non-reserves with fishing gear restrictions than in those without gear restrictions. Fishers targeting stocks perceived to be less depleted, coupled with enhanced site access from immediately adjacent boat moorings, may explain these unexpected patterns. Significant correlations between the distance from mooring sites and prevalence values for a ciliate disease known to infest wounded tissue (r = -0.65), coral damage (r = -0.64), and the abundance of derelict fishing line (r = -0.85) corroborate this interpretation. This is the first study to link disease with recreational use intensity in a park, emphasizing the need to evaluate the placement of closures and their direct relationship to ecosystem health. Since corals are modular, ecological processes that govern reproductive and competitive fitness are frequently related to colony surface area therefore, even low levels of cumulative tissue loss from progressing diseases pose significant threats to reef coral persistence. Disease mitigation through reductions in physical injury in areas where human activities are concentrated is another mechanism by which protected areas may improve ecosystem resilience in a changing climate.

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

PubMed Central

Chater, K F; Wilde, L C

1976-01-01

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

Hybridization Capture Using RAD Probes (hyRAD), a New Tool for Performing Genomic Analyses on Collection Specimens

PubMed Central

Suchan, Tomasz; Pitteloud, Camille; Gerasimova, Nadezhda S.; Kostikova, Anna; Schmid, Sarah; Arrigo, Nils; Pajkovic, Mila; Ronikier, Michał; Alvarez, Nadir

2016-01-01

In the recent years, many protocols aimed at reproducibly sequencing reduced-genome subsets in non-model organisms have been published. Among them, RAD-sequencing is one of the most widely used. It relies on digesting DNA with specific restriction enzymes and performing size selection on the resulting fragments. Despite its acknowledged utility, this method is of limited use with degraded DNA samples, such as those isolated from museum specimens, as these samples are less likely to harbor fragments long enough to comprise two restriction sites making possible ligation of the adapter sequences (in the case of double-digest RAD) or performing size selection of the resulting fragments (in the case of single-digest RAD). Here, we address these limitations by presenting a novel method called hybridization RAD (hyRAD). In this approach, biotinylated RAD fragments, covering a random fraction of the genome, are used as baits for capturing homologous fragments from genomic shotgun sequencing libraries. This simple and cost-effective approach allows sequencing of orthologous loci even from highly degraded DNA samples, opening new avenues of research in the field of museum genomics. Not relying on the restriction site presence, it improves among-sample loci coverage. In a trial study, hyRAD allowed us to obtain a large set of orthologous loci from fresh and museum samples from a non-model butterfly species, with a high proportion of single nucleotide polymorphisms present in all eight analyzed specimens, including 58-year-old museum samples. The utility of the method was further validated using 49 museum and fresh samples of a Palearctic grasshopper species for which the spatial genetic structure was previously assessed using mtDNA amplicons. The application of the method is eventually discussed in a wider context. As it does not rely on the restriction site presence, it is therefore not sensitive to among-sample loci polymorphisms in the restriction sites that usually causes loci dropout. This should enable the application of hyRAD to analyses at broader evolutionary scales. PMID:26999359

Superfund record of decision (EPA Region 3): Ohio River Park Site, Operable Unit 3, Neville Island, PA, September 17, 1998

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

NONE

1998-10-01

This Record of Decision (ROD) presents the selected remedial action plan for the Ohio River Park Superfund Site (the Site) in Allegheny County, Pennsylvania. The remedial action plan in this document is presented as the permanent remedy for controlling the groundwater at the Site. This remedy is comprised of: monitoring of natural attenuation processes to measure changes in contaminant concentrations in groundwater plume at the Site until the cleanup levels are achieved; deed restriction preventing residential use of groundwater at the Site.

Reserve selection with minimum contiguous area restrictions: An application to open space protection planning in suburban Chicago

Treesearch

Sandor F. Toth; Robert Haight; Stephanie A. Snyder; Sonney George; James R. Miller; Mark S. Gregory; Adam M. Skibbe

2009-01-01

Conservation efforts often require site or parcel selection strategies that lead to spatially cohesive reserves. Although habitat contiguity is thought to be conducive to the persistence of many sensitive species, availability of funding and suitable land may restrict the extent to which this spatial attribute can be pursued in land management or conservation. Using...

How Building Principals Made Sense of Free and Appropriate Public Education in the Least Restrictive Environment

ERIC Educational Resources Information Center

Sumbera, Meagan J.; Pazey, Barbara L.; Lashley, Carl

2014-01-01

Confusion among school leaders regarding how to interpret and implement special education legislation, and specific federal and state policies and mandates such as a free and appropriate public education (FAPE), in the least restrictive environment (LRE) at the school-site level has existed since the 1970s and continues to exist. This…

A mitochondrial mutator plasmid that causes senescence under dietary restricted conditions

PubMed Central

Maas, Marc FPM; Hoekstra, Rolf F; Debets, Alfons JM

2007-01-01

Background Calorie or dietary restriction extends life span in a wide range of organisms including the filamentous fungus Podospora anserina. Under dietary restricted conditions, P. anserina isolates are several-fold longer lived. This is however not the case in isolates that carry one of the pAL2-1 homologous mitochondrial plasmids. Results We show that the pAL2-1 homologues act as 'insertional mutators' of the mitochondrial genome, which may explain their negative effect on life span extension. Sequencing revealed at least fourteen unique plasmid integration sites, of which twelve were located within the mitochondrial genome and two within copies of the plasmid itself. The plasmids were able to integrate in their entirety, via a non-homologous mode of recombination. Some of the integrated plasmid copies were truncated, which probably resulted from secondary, post-integrative, recombination processes. Integration sites were predominantly located within and surrounding the region containing the mitochondrial rDNA loci. Conclusion We propose a model for the mechanism of integration, based on innate modes of mtDNA recombination, and discuss its possible link with the plasmid's negative effect on dietary restriction mediated life span extension. PMID:17407571

Laser mass spectrometry for DNA fingerprinting for forensic applications

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

Chen, C.H.; Tang, K.; Taranenko, N.I.

The application of DNA fingerprinting has become very broad in forensic analysis, patient identification, diagnostic medicine, and wildlife poaching, since every individual`s DNA structure is identical within all tissues of their body. DNA fingerprinting was initiated by the use of restriction fragment length polymorphisms (RFLP). In 1987, Nakamura et al. found that a variable number of tandem repeats (VNTR) often occurred in the alleles. The probability of different individuals having the same number of tandem repeats in several different alleles is very low. Thus, the identification of VNTR from genomic DNA became a very reliable method for identification of individuals.more » DNA fingerprinting is a reliable tool for forensic analysis. In DNA fingerprinting, knowledge of the sequence of tandem repeats and restriction endonuclease sites can provide the basis for identification. The major steps for conventional DNA fingerprinting include (1) specimen processing (2) amplification of selected DNA segments by PCR, and (3) gel electrophoresis to do the final DNA analysis. In this work we propose to use laser desorption mass spectrometry for fast DNA fingerprinting. The process and advantages are discussed.« less

TALE-PvuII fusion proteins--novel tools for gene targeting.

PubMed

Yanik, Mert; Alzubi, Jamal; Lahaye, Thomas; Cathomen, Toni; Pingoud, Alfred; Wende, Wolfgang

2013-01-01

Zinc finger nucleases (ZFNs) consist of zinc fingers as DNA-binding module and the non-specific DNA-cleavage domain of the restriction endonuclease FokI as DNA-cleavage module. This architecture is also used by TALE nucleases (TALENs), in which the DNA-binding modules of the ZFNs have been replaced by DNA-binding domains based on transcription activator like effector (TALE) proteins. Both TALENs and ZFNs are programmable nucleases which rely on the dimerization of FokI to induce double-strand DNA cleavage at the target site after recognition of the target DNA by the respective DNA-binding module. TALENs seem to have an advantage over ZFNs, as the assembly of TALE proteins is easier than that of ZFNs. Here, we present evidence that variant TALENs can be produced by replacing the catalytic domain of FokI with the restriction endonuclease PvuII. These fusion proteins recognize only the composite recognition site consisting of the target site of the TALE protein and the PvuII recognition sequence (addressed site), but not isolated TALE or PvuII recognition sites (unaddressed sites), even at high excess of protein over DNA and long incubation times. In vitro, their preference for an addressed over an unaddressed site is > 34,000-fold. Moreover, TALE-PvuII fusion proteins are active in cellula with minimal cytotoxicity.

Comprehensive sieve analysis of breakthrough HIV-1 sequences in the RV144 vaccine efficacy trial.

PubMed

Edlefsen, Paul T; Rolland, Morgane; Hertz, Tomer; Tovanabutra, Sodsai; Gartland, Andrew J; deCamp, Allan C; Magaret, Craig A; Ahmed, Hasan; Gottardo, Raphael; Juraska, Michal; McCoy, Connor; Larsen, Brendan B; Sanders-Buell, Eric; Carrico, Chris; Menis, Sergey; Kijak, Gustavo H; Bose, Meera; Arroyo, Miguel A; O'Connell, Robert J; Nitayaphan, Sorachai; Pitisuttithum, Punnee; Kaewkungwal, Jaranit; Rerks-Ngarm, Supachai; Robb, Merlin L; Kirys, Tatsiana; Georgiev, Ivelin S; Kwong, Peter D; Scheffler, Konrad; Pond, Sergei L Kosakovsky; Carlson, Jonathan M; Michael, Nelson L; Schief, William R; Mullins, James I; Kim, Jerome H; Gilbert, Peter B

2015-02-01

The RV144 clinical trial showed the partial efficacy of a vaccine regimen with an estimated vaccine efficacy (VE) of 31% for protecting low-risk Thai volunteers against acquisition of HIV-1. The impact of vaccine-induced immune responses can be investigated through sieve analysis of HIV-1 breakthrough infections (infected vaccine and placebo recipients). A V1/V2-targeted comparison of the genomes of HIV-1 breakthrough viruses identified two V2 amino acid sites that differed between the vaccine and placebo groups. Here we extended the V1/V2 analysis to the entire HIV-1 genome using an array of methods based on individual sites, k-mers and genes/proteins. We identified 56 amino acid sites or "signatures" and 119 k-mers that differed between the vaccine and placebo groups. Of those, 19 sites and 38 k-mers were located in the regions comprising the RV144 vaccine (Env-gp120, Gag, and Pro). The nine signature sites in Env-gp120 were significantly enriched for known antibody-associated sites (p = 0.0021). In particular, site 317 in the third variable loop (V3) overlapped with a hotspot of antibody recognition, and sites 369 and 424 were linked to CD4 binding site neutralization. The identified signature sites significantly covaried with other sites across the genome (mean = 32.1) more than did non-signature sites (mean = 0.9) (p < 0.0001), suggesting functional and/or structural relevance of the signature sites. Since signature sites were not preferentially restricted to the vaccine immunogens and because most of the associations were insignificant following correction for multiple testing, we predict that few of the genetic differences are strongly linked to the RV144 vaccine-induced immune pressure. In addition to presenting results of the first complete-genome analysis of the breakthrough infections in the RV144 trial, this work describes a set of statistical methods and tools applicable to analysis of breakthrough infection genomes in general vaccine efficacy trials for diverse pathogens.

Comprehensive Sieve Analysis of Breakthrough HIV-1 Sequences in the RV144 Vaccine Efficacy Trial

PubMed Central

Edlefsen, Paul T.; Rolland, Morgane; Hertz, Tomer; Tovanabutra, Sodsai; Gartland, Andrew J.; deCamp, Allan C.; Magaret, Craig A.; Ahmed, Hasan; Gottardo, Raphael; Juraska, Michal; McCoy, Connor; Larsen, Brendan B.; Sanders-Buell, Eric; Carrico, Chris; Menis, Sergey; Bose, Meera; Arroyo, Miguel A.; O’Connell, Robert J.; Nitayaphan, Sorachai; Pitisuttithum, Punnee; Kaewkungwal, Jaranit; Rerks-Ngarm, Supachai; Robb, Merlin L.; Kirys, Tatsiana; Georgiev, Ivelin S.; Kwong, Peter D.; Scheffler, Konrad; Pond, Sergei L. Kosakovsky; Carlson, Jonathan M.; Michael, Nelson L.; Schief, William R.; Mullins, James I.; Kim, Jerome H.; Gilbert, Peter B.

2015-01-01

The RV144 clinical trial showed the partial efficacy of a vaccine regimen with an estimated vaccine efficacy (VE) of 31% for protecting low-risk Thai volunteers against acquisition of HIV-1. The impact of vaccine-induced immune responses can be investigated through sieve analysis of HIV-1 breakthrough infections (infected vaccine and placebo recipients). A V1/V2-targeted comparison of the genomes of HIV-1 breakthrough viruses identified two V2 amino acid sites that differed between the vaccine and placebo groups. Here we extended the V1/V2 analysis to the entire HIV-1 genome using an array of methods based on individual sites, k-mers and genes/proteins. We identified 56 amino acid sites or “signatures” and 119 k-mers that differed between the vaccine and placebo groups. Of those, 19 sites and 38 k-mers were located in the regions comprising the RV144 vaccine (Env-gp120, Gag, and Pro). The nine signature sites in Env-gp120 were significantly enriched for known antibody-associated sites (p = 0.0021). In particular, site 317 in the third variable loop (V3) overlapped with a hotspot of antibody recognition, and sites 369 and 424 were linked to CD4 binding site neutralization. The identified signature sites significantly covaried with other sites across the genome (mean = 32.1) more than did non-signature sites (mean = 0.9) (p < 0.0001), suggesting functional and/or structural relevance of the signature sites. Since signature sites were not preferentially restricted to the vaccine immunogens and because most of the associations were insignificant following correction for multiple testing, we predict that few of the genetic differences are strongly linked to the RV144 vaccine-induced immune pressure. In addition to presenting results of the first complete-genome analysis of the breakthrough infections in the RV144 trial, this work describes a set of statistical methods and tools applicable to analysis of breakthrough infection genomes in general vaccine efficacy trials for diverse pathogens. PMID:25646817

47 CFR 64.1200 - Delivery restrictions.

Code of Federal Regulations, 2014 CFR

2014-10-01

.... The notice must be clear and conspicuous and include, at a minimum, the Internet address and toll-free... established business relationship; or (B) A directory, advertisement, or site on the Internet to which the... obtains the facsimile number from the recipient's own directory, advertisement, or Internet site, it will...

47 CFR 64.1200 - Delivery restrictions.

Code of Federal Regulations, 2012 CFR

2012-10-01

.... The notice must be clear and conspicuous and include, at a minimum, the Internet address and toll-free... established business relationship; or (B) A directory, advertisement, or site on the Internet to which the... obtains the facsimile number from the recipient's own directory, advertisement, or Internet site, it will...

47 CFR 64.1200 - Delivery restrictions.

Code of Federal Regulations, 2013 CFR

2013-10-01

.... The notice must be clear and conspicuous and include, at a minimum, the Internet address and toll-free... established business relationship; or (B) A directory, advertisement, or site on the Internet to which the... obtains the facsimile number from the recipient's own directory, advertisement, or Internet site, it will...

ELECTROFISHING IN BOATABLE RIVERS: DOES SAMPLING DESIGN AFFECT BIOASSESSMENT METRICS?

EPA Science Inventory

Data were collected from 60 boatable sites using an electrofishing design that permitted comparisons of the effects of designs and distances on fish assemblage metrics. Sites were classified a priori as Run-of-the-River (ROR) or Restricted Flow (RF). Data representing four diff...

Patterns and trends of chlorinated hydrocarbons in nestling bald eagle (Haliaeetus leucocephalus) plasma in British Columbia and Southern California.

PubMed

Cesh, Lillian S; Williams, Tony D; Garcelon, David K; Elliott, John E

2008-10-01

Patterns and trends of chlorinated hydrocarbons were assessed in bald eagle nestling plasma from sites along the west coast of North America. Eagle plasma was sampled from four areas in southwestern British Columbia (BC), a reference site in northern BC, and from Santa Catalina Island, off the coast of California. Sites were chosen to reflect variation in contaminant exposure due to differing recent and/or historic anthropogenic activities. Santa Catalina Island had significantly greater mean concentrations of p,p'-DDE, 41.3 microg/kg wet weight (ww), than other sites, and Nanaimo/Crofton, BC had the greatest mean concentration of total PCBs, 28.9 microg/kg ww. Contaminant levels measured in 2003 in BC were compared to levels measured in 1993; over that ten year span, concentrations and patterns of chlorinated hydrocarbons have not significantly changed. There were no significant differences in levels of p,p'-DDE or hexachlorobenzene between 1993 and 2003, but significant decreases were found for trans-nonachlor and PCBs at BC sites. Levels of total PCBs and trans-nonachlor in the central Fraser Valley and Nanaimo/Crofton area have significantly decreased. Mean concentrations of p,p'-DDE measured in bald eagle nestling plasma samples in 2003 exceeded published criteria for effects on bald eagle reproduction at Santa Catalina Island and Barkley Sound, more than 30 years since heavy usage restrictions were imposed.

Diversity of the small subunit ribosomal RNA gene of the arbuscular mycorrhizal fungi colonizing Clintonia borealis from a mixed-wood boreal forest.

PubMed

DeBellis, Tonia; Widden, Paul

2006-11-01

Arbuscular mycorrhizal fungi (AMF) communities in Clintonia borealis roots from a boreal mixed forests in northwestern Québec were investigated. Roots were sampled from 100 m2 plots whose overstory was dominated by either trembling aspen (Populus tremuloides Michx.), white birch (Betula papyrifera Marsh.), or mixed white spruce (Picea glauca (Moench) Voss) and balsam fir (Abies balsamea (L.) Mill.). Part of the 18S ribosomal gene of the AMF was amplified and the resulting PCR products were cloned. Restriction analysis of the 576 resulting clones yielded 92 different restriction patterns which were then sequenced. Fifty-two sequences closely matched other Glomus sequences from Genbank. Phylogenetic analysis revealed 10 different AMF sequence types, most of which clustered with other uncultured AM sequences from plant roots from various field sites. Compared with other AMF communities from comparable studies, richness and diversity were higher than observed in an arable field, but lower than seen in a tropical forest and a temperate wetland. The AMF communities from Clintonia roots under the different canopy types did not differ significantly and the dominant sequence type, which clustered with AM sequences from a variety of environments and hosts at distant geographical locations, represented 66.9% of all the clones analyzed.

DNA-based differentiation of the Ecuadorian cocoa types CCN-51 and Arriba based on sequence differences in the chloroplast genome.

PubMed

Herrmann, Luise; Haase, Ilka; Blauhut, Maike; Barz, Nadine; Fischer, Markus

2014-12-17

Two cocoa types, Arriba and CCN-51, are being cultivated in Ecuador. With regard to the unique aroma, Arriba is considered a fine cocoa type, while CCN-51 is a bulk cocoa because of its weaker aroma. Because it is being assumed that Arriba is mixed with CCN-51, there is an interest in the analytical differentiation of the two types. Two methods to identify CCN-51 adulterations in Arriba cocoa were developed on the basis of differences in the chloroplast DNA. On the one hand, a different repeat of the sequence TAAAG in the inverted repeat region results in a different length of amplicons for the two cocoa types, which can be detected by agarose gel electrophoresis, capillary gel electrophoresis, and denaturing high-performance liquid chromatography. On the other hand, single nucleotide polymorphisms (SNPs) between the CCN-51 and Arriba sequences represent restriction sites, which can be used for restriction fragment length polymorphism analysis. A semi-quantitative analysis based on these SNPs is feasible. A method for an exact quantitation based on these results is not realizable. These sequence variations were confirmed for a comprehensive cultivar collection of Arriba and CCN-51, for both bean and leaf samples.

Arabidopsis AIP1-2 restricted by WER-mediated patterning modulates planar polarity

PubMed Central

Kiefer, Christian S.; Claes, Andrea R.; Nzayisenga, Jean-Claude; Pietra, Stefano; Stanislas, Thomas; Hüser, Anke; Ikeda, Yoshihisa; Grebe, Markus

2015-01-01

The coordination of cell polarity within the plane of the tissue layer (planar polarity) is crucial for the development of diverse multicellular organisms. Small Rac/Rho-family GTPases and the actin cytoskeleton contribute to planar polarity formation at sites of polarity establishment in animals and plants. Yet, upstream pathways coordinating planar polarity differ strikingly between kingdoms. In the root of Arabidopsis thaliana, a concentration gradient of the phytohormone auxin coordinates polar recruitment of Rho-of-plant (ROP) to sites of polar epidermal hair initiation. However, little is known about cytoskeletal components and interactions that contribute to this planar polarity or about their relation to the patterning machinery. Here, we show that ACTIN7 (ACT7) represents a main actin isoform required for planar polarity of root hair positioning, interacting with the negative modulator ACTIN-INTERACTING PROTEIN1-2 (AIP1-2). ACT7, AIP1-2 and their genetic interaction are required for coordinated planar polarity of ROP downstream of ethylene signalling. Strikingly, AIP1-2 displays hair cell file-enriched expression, restricted by WEREWOLF (WER)-dependent patterning and modified by ethylene and auxin action. Hence, our findings reveal AIP1-2, expressed under control of the WER-dependent patterning machinery and the ethylene signalling pathway, as a modulator of actin-mediated planar polarity. PMID:25428588

Multi-element compound specific stable isotope analysis of chlorinated aliphatic contaminants derived from chlorinated pitches.

PubMed

Filippini, Maria; Nijenhuis, Ivonne; Kümmel, Steffen; Chiarini, Veronica; Crosta, Giovanni; Richnow, Hans H; Gargini, Alessandro

2018-05-30

Tetrachloroethene and trichloroethene are typical by-products of the industrial production of chloromethanes. These by-products are known as "chlorinated pitches" and were often dumped in un-contained waste disposal sites causing groundwater contaminations. Previous research showed that a strongly depleted stable carbon isotope signature characterizes chlorinated compounds associated with chlorinated pitches whereas manufactured commercial compounds have more enriched carbon isotope ratios. The findings were restricted to a single case study and one element (i.e. carbon). This paper presents a multi-element Compound-Specific Stable Isotope Analysis (CSIA, including carbon, chlorine and hydrogen) of chlorinated aliphatic contaminants originated from chlorinated pitches at two sites with different hydrogeology and different producers of chloromethanes. The results show strongly depleted carbon signatures at both sites whereas the chlorine and the hydrogen signatures are comparable to those presented in the literature for manufactured commercial compounds. Multi-element CSIA allowed the identification of sources and site-specific processes affecting chloroethene transformation in groundwater as a result of emergency remediation measures. CSIA turned out to be an effective forensic tool to address the liability for the contamination, leading to a conviction for the crimes of unintentional aggravated public water supply poisoning and environmental disaster. Copyright © 2018 Elsevier B.V. All rights reserved.

Antigenic regions within the hepatitis C virus envelope 1 and non-structural proteins: identification of an IgG3-restricted recognition site with the envelope 1 protein.

PubMed Central

Sällberg, M; Rudén, U; Wahren, B; Magnius, L O

1993-01-01

Antibody binding to antigenic regions of hepatitis C virus (HCV) envelope 1 (E1; residues 183-380, E2/non-structural (NS) 1 (residues 380-437), NS1 (residues 643-690), and NS4 (1684-1751) proteins were assayed for 50 sera with antibodies to HCV (anti-HCV) and for 46 sera without anti-HCV. Thirty-four peptides, 18 residues long with an eight-amino acid overlap within each HCV region, were synthesized and tested with all 96 sera. Within the E region 183-380, the major binding site was located to residues 203-220, and was recognized by eight sera. Within the E2/NS1 region 380-437, the peptide covering residues 410-427 was recognized by two sera, and within the NS1 region 643-690, peptides covering residues 663-690 were recognized by four sera. Within the NS4 region 1684-1751, 27 sera were reactive to one or more of the NS4 peptides, and 21 out of these were reactive with peptide 1694-1711. One part of the major binding site could be located to residues 1701-1704, with the sequence Leu-Tyr-Arg-Glu. The IgG1, IgG3 and IgG4 subclasses were reactive with the five antigenic regions of HCV core, residues 1-18, 11-28, 21-38, 51-68 and 101-118. Reactivity to the major envelope site consisted almost exclusively of IgG3, and reactivity to the major site of NS4 consisted only of IgG1. Thus, a non-restricted IgG response to linear HCV-encoded binding sites was found to the core protein, whereas IgG subclass-restricted linear binding sites were found within the E1 protein, and within the NS4 protein. PMID:7680297

Social Media and the Army

DTIC Science & Technology

2010-04-01

certain social networking sites such as YouTube and MySpace, though commanders can still restrict access due to security concerns or bandwidth... social networking sites is almost always linked back to traditional Army websites, lending validity to the news. The goal is a conversation and... networking sites , including Facebook, You- Tube, Twitter, and Flickr. Leaders at the highest levels are embracing social media. 65MILITARY REVIEW

Multispecies spawning sites for fishes on a low-latitude coral reef: spatial and temporal patterns.

PubMed

Claydon, J A B; McCormick, M I; Jones, G P

2014-04-01

Spawning sites used by one or more species were located by intensively searching nearshore coral reefs of Kimbe Bay (New Britain, Papua New Guinea). Once identified, the spawning sites were surveyed repeatedly within fixed 5 m radius circular areas, for  > 2000 h of observations ranging from before dawn to after dusk spanning 190 days between July 2001 and May 2004. A total of 38 spawning sites were identified on the seven study reefs distributed at an average of one site every 60 m of reef edge. Pelagic spawning was observed in 41 fish species from six families. On three intensively studied reefs, all 17 spawning sites identified were used by at least three species, with a maximum of 30 different species observed spawning at a single site. Spawning was observed during every month of the study, on all days of the lunar month, at all states of the tide and at most hours of the day studied. Nevertheless, the majority of species were observed spawning on proportionately more days from December to April, on more days around the new moon and in association with higher tides. The strongest temporal association, however, was with species-specific diel spawning times spanning < 3 h for most species. While dawn spawning, afternoon spawning and dusk spawning species were differentiated, the time of spawning for the striated surgeonfish Ctenochaetus striatus also differed significantly among sites. The large number of species spawning at the same restricted locations during predictable times suggests that these sites are extremely important on this low-latitude coral reef. © 2014 The Fisheries Society of the British Isles.

Comparison of US EPA and European emission standards for combustion and incineration technologies

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

Licata, A.; Hartenstein, H.U.; Terracciano, L.

1997-12-01

There has been considerable debate, misunderstanding, and controversy when comparing emission standards used in Europe and the United States. One of the first questions you hear whenever U.S. EPA publishes a new emission standard is, {open_quotes}Is it as restrictive or is it the same as the German standard{close_quotes}. Although both systems of regulation call for the use of CEMS for compliance, there are substantial differences in how emission standards are structured in Europe and in the U.S. They include reference points, averaging times, sampling methods, and technology. Generally, the European standards tend to be more restrictive, due in part tomore » the fact that the facilities are of necessity sited in close proximity to residential areas. In Germany, for example, regulations in general are comprehensive and include both design standards and emission limits while U.S. EPA`s rules are source specific and, in most cases, limited to numerical emission standards. In some cases, comparisons can be made between emission standards and, in some cases, comparisons can only be made with restrictive caveats. The paper will present a comprehensive overview of the emission standards and how they are applied.« less

The Chthonomonas calidirosea Genome Is Highly Conserved across Geographic Locations and Distinct Chemical and Microbial Environments in New Zealand's Taupō Volcanic Zone.

PubMed

Lee, Kevin C; Stott, Matthew B; Dunfield, Peter F; Huttenhower, Curtis; McDonald, Ian R; Morgan, Xochitl C

2016-06-15

Chthonomonas calidirosea T49(T) is a low-abundance, carbohydrate-scavenging, and thermophilic soil bacterium with a seemingly disorganized genome. We hypothesized that the C. calidirosea genome would be highly responsive to local selection pressure, resulting in the divergence of its genomic content, genome organization, and carbohydrate utilization phenotype across environments. We tested this hypothesis by sequencing the genomes of four C. calidirosea isolates obtained from four separate geothermal fields in the Taupō Volcanic Zone, New Zealand. For each isolation site, we measured physicochemical attributes and defined the associated microbial community by 16S rRNA gene sequencing. Despite their ecological and geographical isolation, the genome sequences showed low divergence (maximum, 1.17%). Isolate-specific variations included single-nucleotide polymorphisms (SNPs), restriction-modification systems, and mobile elements but few major deletions and no major rearrangements. The 50-fold variation in C. calidirosea relative abundance among the four sites correlated with site environmental characteristics but not with differences in genomic content. Conversely, the carbohydrate utilization profiles of the C. calidirosea isolates corresponded to the inferred isolate phylogenies, which only partially paralleled the geographical relationships among the sample sites. Genomic sequence conservation does not entirely parallel geographic distance, suggesting that stochastic dispersal and localized extinction, which allow for rapid population homogenization with little restriction by geographical barriers, are possible mechanisms of C. calidirosea distribution. This dispersal and extinction mechanism is likely not limited to C. calidirosea but may shape the populations and genomes of many other low-abundance free-living taxa. This study compares the genomic sequence variations and metabolisms of four strains of Chthonomonas calidirosea, a rare thermophilic bacterium from the phylum Armatimonadetes It additionally compares the microbial communities and chemistry of each of the geographically distinct sites from which the four C. calidirosea strains were isolated. C. calidirosea was previously reported to possess a highly disorganized genome, but it was unclear whether this reflected rapid evolution. Here, we show that each isolation site has a distinct chemistry and microbial community, but despite this, the C. calidirosea genome is highly conserved across all isolation sites. Furthermore, genomic sequence differences only partially paralleled geographic distance, suggesting that C. calidirosea genotypes are not primarily determined by adaptive evolution. Instead, the presence of C. calidirosea may be driven by stochastic dispersal and localized extinction. This ecological mechanism may apply to many other low-abundance taxa. Copyright © 2016 Lee et al.

The Chthonomonas calidirosea Genome Is Highly Conserved across Geographic Locations and Distinct Chemical and Microbial Environments in New Zealand's Taupō Volcanic Zone

PubMed Central

Lee, Kevin C.; Stott, Matthew B.; Dunfield, Peter F.; Huttenhower, Curtis; McDonald, Ian R.

2016-01-01

ABSTRACT Chthonomonas calidirosea T49T is a low-abundance, carbohydrate-scavenging, and thermophilic soil bacterium with a seemingly disorganized genome. We hypothesized that the C. calidirosea genome would be highly responsive to local selection pressure, resulting in the divergence of its genomic content, genome organization, and carbohydrate utilization phenotype across environments. We tested this hypothesis by sequencing the genomes of four C. calidirosea isolates obtained from four separate geothermal fields in the Taupō Volcanic Zone, New Zealand. For each isolation site, we measured physicochemical attributes and defined the associated microbial community by 16S rRNA gene sequencing. Despite their ecological and geographical isolation, the genome sequences showed low divergence (maximum, 1.17%). Isolate-specific variations included single-nucleotide polymorphisms (SNPs), restriction-modification systems, and mobile elements but few major deletions and no major rearrangements. The 50-fold variation in C. calidirosea relative abundance among the four sites correlated with site environmental characteristics but not with differences in genomic content. Conversely, the carbohydrate utilization profiles of the C. calidirosea isolates corresponded to the inferred isolate phylogenies, which only partially paralleled the geographical relationships among the sample sites. Genomic sequence conservation does not entirely parallel geographic distance, suggesting that stochastic dispersal and localized extinction, which allow for rapid population homogenization with little restriction by geographical barriers, are possible mechanisms of C. calidirosea distribution. This dispersal and extinction mechanism is likely not limited to C. calidirosea but may shape the populations and genomes of many other low-abundance free-living taxa. IMPORTANCE This study compares the genomic sequence variations and metabolisms of four strains of Chthonomonas calidirosea, a rare thermophilic bacterium from the phylum Armatimonadetes. It additionally compares the microbial communities and chemistry of each of the geographically distinct sites from which the four C. calidirosea strains were isolated. C. calidirosea was previously reported to possess a highly disorganized genome, but it was unclear whether this reflected rapid evolution. Here, we show that each isolation site has a distinct chemistry and microbial community, but despite this, the C. calidirosea genome is highly conserved across all isolation sites. Furthermore, genomic sequence differences only partially paralleled geographic distance, suggesting that C. calidirosea genotypes are not primarily determined by adaptive evolution. Instead, the presence of C. calidirosea may be driven by stochastic dispersal and localized extinction. This ecological mechanism may apply to many other low-abundance taxa. PMID:27060125

A simple algorithm for quantifying DNA methylation levels on multiple independent CpG sites in bisulfite genomic sequencing electropherograms.

PubMed

Leakey, Tatiana I; Zielinski, Jerzy; Siegfried, Rachel N; Siegel, Eric R; Fan, Chun-Yang; Cooney, Craig A

2008-06-01

DNA methylation at cytosines is a widely studied epigenetic modification. Methylation is commonly detected using bisulfite modification of DNA followed by PCR and additional techniques such as restriction digestion or sequencing. These additional techniques are either laborious, require specialized equipment, or are not quantitative. Here we describe a simple algorithm that yields quantitative results from analysis of conventional four-dye-trace sequencing. We call this method Mquant and we compare it with the established laboratory method of combined bisulfite restriction assay (COBRA). This analysis of sequencing electropherograms provides a simple, easily applied method to quantify DNA methylation at specific CpG sites.

The interaction of the Eco R1 restriction enzyme E.coli with nucleotides

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

Hollis, Donald F.

1979-11-01

The Eco R1 restriction enzyme can be shown to be inhibited by nucleotides which correspond to any part of its known site of phosphodiesterase activity. A series of di-, tetra-, and hexa-nucleotide fragments were synthesized and their effect on the activity of the enzyme upon superhelical Co1 E1 DNA studied. The inhibition caused by the individual mononucleotides were also studied. In general all the nucleotide fragments showed some form of interaction with the enzyme system. Tetranucleotides were stronger inhibitors than dinucleotides, which in turn were stronger inhibitors than the mononucleotides. Within each category of inhibitors, those containing the phosphodiester bondmore » which is acted upon by the enzyme were the strongest inhibitors. Only those fragments which were consistent with the enzymes site of activity showed competitive inhibition kinetics. Nucleotides which do not fit within the site of phosphodiesterase activity show non-competitive inhibition kinetics.« less

Mitochondrial DNA variation in bull trout (Salvelinus confluentus) from northwestern North America: implications for zoogeography and conservation.

PubMed

Taylor, E B; Pollard, S; Louie, D

1999-07-01

Bull trout, Salvelinus confluentus (Salmonidae), are distributed in northwestern North America from Nevada to Yukon Territory, largely in interior drainages. The species is of conservation concern owing to declines in abundance, particularly in southern portions of its range. To investigate phylogenetic structure within bull trout that might form the basis for the delineation of major conservation units, we conducted a mitochondrial DNA (mtDNA) survey in bull trout from throughout its range. Restriction fragment length polymorphism (RFLP) analysis of four segments of the mtDNA genome with 11 restriction enzymes resolved 21 composite haplotypes that differed by an average of 0.5% in sequence. One group of haplotypes predominated in 'coastal' areas (west of the coastal mountain ranges) while another predominated in 'interior' regions (east of the coastal mountains). The two putative lineages differed by 0.8% in sequence and were also resolved by sequencing a portion of the ND1 gene in a representative of each RFLP haplotype. Significant variation existed within individual sample sites (12% of total variation) and among sites within major geographical regions (33%), but most variation (55%) was associated with differences between coastal and interior regions. We concluded that: (i) bull trout are subdivided into coastal and interior lineages; (ii) this subdivision reflects recent historical isolation in two refugia south of the Cordilleran ice sheet during the Pleistocene: the Chehalis and Columbia refugia; and (iii) most of the molecular variation resides at the interpopulation and inter-region levels. Conservation efforts, therefore, should focus on maintaining as many populations as possible across as many geographical regions as possible within both coastal and interior lineages.

Misconceptions on Missing Data in RAD-seq Phylogenetics with a Deep-scale Example from Flowering Plants.

PubMed

Eaton, Deren A R; Spriggs, Elizabeth L; Park, Brian; Donoghue, Michael J

2017-05-01

Restriction-site associated DNA (RAD) sequencing and related methods rely on the conservation of enzyme recognition sites to isolate homologous DNA fragments for sequencing, with the consequence that mutations disrupting these sites lead to missing information. There is thus a clear expectation for how missing data should be distributed, with fewer loci recovered between more distantly related samples. This observation has led to a related expectation: that RAD-seq data are insufficiently informative for resolving deeper scale phylogenetic relationships. Here we investigate the relationship between missing information among samples at the tips of a tree and information at edges within it. We re-analyze and review the distribution of missing data across ten RAD-seq data sets and carry out simulations to determine expected patterns of missing information. We also present new empirical results for the angiosperm clade Viburnum (Adoxaceae, with a crown age >50 Ma) for which we examine phylogenetic information at different depths in the tree and with varied sequencing effort. The total number of loci, the proportion that are shared, and phylogenetic informativeness varied dramatically across the examined RAD-seq data sets. Insufficient or uneven sequencing coverage accounted for similar proportions of missing data as dropout from mutation-disruption. Simulations reveal that mutation-disruption, which results in phylogenetically distributed missing data, can be distinguished from the more stochastic patterns of missing data caused by low sequencing coverage. In Viburnum, doubling sequencing coverage nearly doubled the number of parsimony informative sites, and increased by >10X the number of loci with data shared across >40 taxa. Our analysis leads to a set of practical recommendations for maximizing phylogenetic information in RAD-seq studies. [hierarchical redundancy; phylogenetic informativeness; quartet informativeness; Restriction-site associated DNA (RAD) sequencing; sequencing coverage; Viburnum.]. © The authors 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For permissions, please e-mail: journals.permission@oup.com.

47 CFR 64.1200 - Delivery restrictions.

Code of Federal Regulations, 2011 CFR

2011-10-01

.... The notice must be clear and conspicuous and include, at a minimum, the Internet address and toll-free...; or (B) A directory, advertisement, or site on the Internet to which the recipient voluntarily agreed... number from the recipient's own directory, advertisement, or Internet site, it will be presumed that the...

47 CFR 64.1200 - Delivery restrictions.

Code of Federal Regulations, 2010 CFR

2010-10-01

.... The notice must be clear and conspicuous and include, at a minimum, the Internet address and toll-free...; or (B) A directory, advertisement, or site on the Internet to which the recipient voluntarily agreed... number from the recipient's own directory, advertisement, or Internet site, it will be presumed that the...

Savannah River Site Approved Site Treatment Plan, 2001 Annual Update (Volumes I and II)

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

Lawrence, B.

2001-04-30

The Compliance Plan Volume (Volume I) identifies project activity scheduled milestones for achieving compliance with Land Disposal Restrictions. Information regarding the technical evaluation of treatment options for SRS mixed wastes is contained in the Background Volume (Volume II) and is provided for information.

Subsurface Water Flow and its Subsequent Impact on Chemical Behavior

USDA-ARS?s Scientific Manuscript database

The impact of the subsurface stratigraphy on crop growth and agrichemical behavior has been studied for several years at the OPE3 research site located at the USDA-ARS Beltsville Agricultural Research Center, in Beltsville Maryland. This site contains subsurface restricting layers that have been id...

Active site remodeling switches HIV specificity of antiretroviral TRIMCyp

PubMed Central

Price, Amanda J; Marzetta, Flavia; Lammers, Michael; Ylinen, Laura M J; Schaller, Torsten; Wilson, Sam J; Towers, Greg J; James, Leo C

2011-01-01

TRIMCyps are primate antiretroviral proteins that potently inhibit HIV replication. Here we describe how rhesus macaque TRIMCyp (RhTC) has evolved to target and restrict HIV-2. We show that the ancestral cyclophilin A (CypA) domain of RhTC targets HIV-2 capsid with weak affinity, which is strongly increased in RhTC by two mutations (D66N and R69H) at the expense of HIV-1 binding. These mutations disrupt a constraining intramolecular interaction in CypA, triggering the complete restructuring (>16 Å) of an active site loop. This new configuration discriminates between divergent HIV-1 and HIV-2 loop conformations mediated by capsid residue 88. Viral sensitivity to RhTC restriction can be conferred or abolished by mutating position 88. Furthermore, position 88 determines the susceptibility of naturally occurring HIV-1 sequences to restriction. Our results reveal the complex molecular, structural and thermodynamic changes that underlie the ongoing evolutionary race between virus and host. PMID:19767750

Three-Dimensional Structural Characterization of HIV-1 Tethered to Human Cells

PubMed Central

Strauss, Joshua D.; Hammonds, Jason E.; Yi, Hong; Ding, Lingmei

2015-01-01

ABSTRACT Tetherin (BST2, CD317, or HM1.24) is a host cellular restriction factor that prevents the release of enveloped viruses by mechanically linking virions to the plasma membrane. The precise arrangement of tetherin molecules at the plasma membrane site of HIV-1 assembly, budding, and restriction is not well understood. To gain insight into the biophysical mechanism underlying tetherin-mediated restriction of HIV-1, we utilized cryo-electron tomography (cryo-ET) to directly visualize HIV-1 virus-like particles (VLPs) and virions tethered to human cells in three dimensions (3D). Rod-like densities that we refer to as tethers were seen connecting HIV-1 virions to each other and to the plasma membrane. Native immunogold labeling showed tetherin molecules located on HIV-1 VLPs and virions in positions similar to those of the densities observed by cryo-ET. The location of the tethers with respect to the ordered immature Gag lattice or mature conical core was random. However, tethers were not uniformly distributed on the viral membrane but rather formed clusters at sites of contact with the cell or other virions. Chains of tethered HIV-1 virions often were arranged in a linear fashion, primarily as single chains and, to a lesser degree, as branched chains. Distance measurements support the extended tetherin model, in which the coiled-coil ectodomains are oriented perpendicular with respect to the viral and plasma membranes. IMPORTANCE Tetherin is a cellular factor that restricts HIV-1 release by directly cross-linking the virus to the host cell plasma membrane. We used cryo-electron tomography to visualize HIV-1 tethered to human cells in 3D. We determined that tetherin-restricted HIV-1 virions were physically connected to each other or to the plasma membrane by filamentous tethers that resembled rods ∼15 nm in length, which is consistent with the extended tetherin model. In addition, we found the position of the tethers to be arbitrary relative to the ordered immature Gag lattice or the mature conical cores. However, when present as multiple copies, the tethers clustered at the interface between virions. Tethered HIV-1 virions were arranged in a linear fashion, with the majority as single chains. This study advances our understanding of tetherin-mediated HIV-1 restriction by defining the spatial arrangement and orientation of tetherin molecules at sites of HIV-1 restriction. PMID:26582000

Lesion of the Olfactory Epithelium Accelerates Prion Neuroinvasion and Disease Onset when Prion Replication Is Restricted to Neurons

PubMed Central

Crowell, Jenna; Wiley, James A.; Bessen, Richard A.

2015-01-01

Natural prion diseases of ruminants are moderately contagious and while the gastrointestinal tract is the primary site of prion agent entry, other mucosae may be entry sites in a subset of infections. In the current study we examined prion neuroinvasion and disease induction following disruption of the olfactory epithelium in the nasal mucosa since this site contains environmentally exposed olfactory sensory neurons that project directly into the central nervous system. Here we provide evidence for accelerated prion neuroinvasion and clinical onset from the olfactory mucosa after disruption and regeneration of the olfactory epithelium and when prion replication is restricted to neurons. In transgenic mice with neuron restricted replication of prions, there was a reduction in survival when the olfactory epithelium was disrupted prior to intranasal inoculation and there was >25% decrease in the prion incubation period. In a second model, the neurotropic DY strain of transmissible mink encephalopathy was not pathogenic in hamsters by the nasal route, but 50% of animals exhibited brain infection and/or disease when the olfactory epithelium was disrupted prior to intranasal inoculation. A time course analysis of prion deposition in the brain following loss of the olfactory epithelium in models of neuron-restricted prion replication suggests that neuroinvasion from the olfactory mucosa is via the olfactory nerve or brain stem associated cranial nerves. We propose that induction of neurogenesis after damage to the olfactory epithelium can lead to prion infection of immature olfactory sensory neurons and accelerate prion spread to the brain. PMID:25822718

CisSERS: Customizable in silico sequence evaluation for restriction sites

DOE PAGES

Sharpe, Richard M.; Koepke, Tyson; Harper, Artemus; ...

2016-04-12

High-throughput sequencing continues to produce an immense volume of information that is processed and assembled into mature sequence data. Here, data analysis tools are urgently needed that leverage the embedded DNA sequence polymorphisms and consequent changes to restriction sites or sequence motifs in a high-throughput manner to enable biological experimentation. CisSERS was developed as a standalone open source tool to analyze sequence datasets and provide biologists with individual or comparative genome organization information in terms of presence and frequency of patterns or motifs such as restriction enzymes. Predicted agarose gel visualization of the custom analyses results was also integrated tomore » enhance the usefulness of the software. CisSERS offers several novel functionalities, such as handling of large and multiple datasets in parallel, multiple restriction enzyme site detection and custom motif detection features, which are seamlessly integrated with real time agarose gel visualization. Using a simple fasta-formatted file as input, CisSERS utilizes the REBASE enzyme database. Results from CisSERSenable the user to make decisions for designing genotyping by sequencing experiments, reduced representation sequencing, 3’UTR sequencing, and cleaved amplified polymorphic sequence (CAPS) molecular markers for large sample sets. CisSERS is a java based graphical user interface built around a perl backbone. Several of the applications of CisSERS including CAPS molecular marker development were successfully validated using wet-lab experimentation. Here, we present the tool CisSERSand results from in-silico and corresponding wet-lab analyses demonstrating that CisSERS is a technology platform solution that facilitates efficient data utilization in genomics and genetics studies.« less

Restriction-Site-Specific PCR as a Rapid Test To Detect Enterohemorrhagic Escherichia coli O157:H7 Strains in Environmental Samples

PubMed Central

Kimura, Richard; Mandrell, Robert E.; Galland, John C.; Hyatt, Doreene; Riley, Lee W.

2000-01-01

Enterohemorrhagic Escherichia coli (EHEC) O157:H7 is an important food-borne pathogen in industrialized countries. We developed a rapid and simple test for detecting E. coli O157:H7 using a method based on restriction site polymorphisms. Restriction-site-specific PCR (RSS-PCR) involves the amplification of DNA fragments using primers based on specific restriction enzyme recognition sequences, without the use of endonucleases, to generate a set of amplicons that yield “fingerprint” patterns when resolved electrophoretically on an agarose gel. The method was evaluated in a blinded study of E. coli isolates obtained from environmental samples collected at beef cattle feedyards. The 54 isolates were all initially identified by a commonly used polyclonal antibody test as belonging to O157:H7 serotype. They were retested by anti-O157 and anti-H7 monoclonal antibody enzyme-linked immunosorbent assay (ELISA). The RSS-PCR method identified all 28 isolates that were shown to be E. coli O157:H7 by the monoclonal antibody ELISA as belonging to the O157:H7 serotype. Of the remaining 26 ELISA-confirmed non-O157:H7 strains, the method classified 25 strains as non-O157:H7. The specificity of the RSS-PCR results correlated better with the monoclonal antibody ELISA than with the polyclonal antibody latex agglutination tests. The RSS-PCR method may be a useful test to distinguish E. coli O157:H7 from a large number of E. coli isolates from environmental samples. PMID:10831431

CisSERS: Customizable in silico sequence evaluation for restriction sites

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

Sharpe, Richard M.; Koepke, Tyson; Harper, Artemus

High-throughput sequencing continues to produce an immense volume of information that is processed and assembled into mature sequence data. Here, data analysis tools are urgently needed that leverage the embedded DNA sequence polymorphisms and consequent changes to restriction sites or sequence motifs in a high-throughput manner to enable biological experimentation. CisSERS was developed as a standalone open source tool to analyze sequence datasets and provide biologists with individual or comparative genome organization information in terms of presence and frequency of patterns or motifs such as restriction enzymes. Predicted agarose gel visualization of the custom analyses results was also integrated tomore » enhance the usefulness of the software. CisSERS offers several novel functionalities, such as handling of large and multiple datasets in parallel, multiple restriction enzyme site detection and custom motif detection features, which are seamlessly integrated with real time agarose gel visualization. Using a simple fasta-formatted file as input, CisSERS utilizes the REBASE enzyme database. Results from CisSERSenable the user to make decisions for designing genotyping by sequencing experiments, reduced representation sequencing, 3’UTR sequencing, and cleaved amplified polymorphic sequence (CAPS) molecular markers for large sample sets. CisSERS is a java based graphical user interface built around a perl backbone. Several of the applications of CisSERS including CAPS molecular marker development were successfully validated using wet-lab experimentation. Here, we present the tool CisSERSand results from in-silico and corresponding wet-lab analyses demonstrating that CisSERS is a technology platform solution that facilitates efficient data utilization in genomics and genetics studies.« less

Variation in biological properties of cauliflower mosaic virus clones.

PubMed

al-Kaff, N; Covey, S N

1994-11-01

Infectious clones were prepared from virion DNA of three cauliflower mosaic virus (CaMV) isolates, 11/3, Xinjiang (XJ), and Aust, to investigate pathogenic variation in virus populations. Of 10 infectious clones obtained for isolate 11/3, four pathotypes were identified, each producing symptoms in turnip that differed from those of the 11/3 wild-type. Virus from two clonal groups of 11/3 was transmissible by aphids whereas that from two others was not. Of the five infectious clones obtained from isolate XJ, two groups were identified, one of which differed symptomatically from the wild-type. Only one infectious clone was obtained from isolate Aust and this had properties similar to the wild-type. Restriction enzyme polymorphisms were found in some clonal groups and these correlated with symptoms. Other groups with different pathogenic properties could not be distinguished apart by restriction site polymorphisms. Further variation was observed in the nucleotide sequences of gene II (coding for aphid transmission factor) from these viruses as compared with other CaMV isolates. In the aphid non-transmissible clones of isolate 11/3, one had a Gly to Arg mutation in gene II similar to that of other non-deleted non-transmissible CaMV isolates. The second had a 322 bp deletion at the site of a small direct repeat similar to that of isolate CM4-184 although occurring in a different position. The gene II deletion of isolate 11/3 produced a frame-shift that separated genes II and III by 60 bp. Most CaMV clones studied remained biologically stable producing similar symptoms during subsequent passages. However, one clone (11/3-7) produced two new biotypes during its first passage suggesting that it was relatively unstable. Our results show that wild-type populations of CaMV contain a range of infectious genome variants with contrasting biological properties and differing stability. We suggest that a variety of significant viral phenotypic changes can occur during each infection cycle resulting from relatively small genome changes.

Methylated site display (MSD)-AFLP, a sensitive and affordable method for analysis of CpG methylation profiles.

PubMed

Aiba, Toshiki; Saito, Toshiyuki; Hayashi, Akiko; Sato, Shinji; Yunokawa, Harunobu; Maruyama, Toru; Fujibuchi, Wataru; Kurita, Hisaka; Tohyama, Chiharu; Ohsako, Seiichiroh

2017-03-09

It has been pointed out that environmental factors or chemicals can cause diseases that are developmental in origin. To detect abnormal epigenetic alterations in DNA methylation, convenient and cost-effective methods are required for such research, in which multiple samples are processed simultaneously. We here present methylated site display (MSD), a unique technique for the preparation of DNA libraries. By combining it with amplified fragment length polymorphism (AFLP) analysis, we developed a new method, MSD-AFLP. Methylated site display libraries consist of only DNAs derived from DNA fragments that are CpG methylated at the 5' end in the original genomic DNA sample. To test the effectiveness of this method, CpG methylation levels in liver, kidney, and hippocampal tissues of mice were compared to examine if MSD-AFLP can detect subtle differences in the levels of tissue-specific differentially methylated CpGs. As a result, many CpG sites suspected to be tissue-specific differentially methylated were detected. Nucleotide sequences adjacent to these methyl-CpG sites were identified and we determined the methylation level by methylation-sensitive restriction endonuclease (MSRE)-PCR analysis to confirm the accuracy of AFLP analysis. The differences of the methylation level among tissues were almost identical among these methods. By MSD-AFLP analysis, we detected many CpGs showing less than 5% statistically significant tissue-specific difference and less than 10% degree of variability. Additionally, MSD-AFLP analysis could be used to identify CpG methylation sites in other organisms including humans. MSD-AFLP analysis can potentially be used to measure slight changes in CpG methylation level. Regarding the remarkable precision, sensitivity, and throughput of MSD-AFLP analysis studies, this method will be advantageous in a variety of epigenetics-based research.

Protecting intellectual property associated with Canadian academic clinical trials - approaches and impact

PubMed Central

2012-01-01

Intellectual property is associated with the creative work needed to design clinical trials. Two approaches have developed to protect the intellectual property associated with multicentre trial protocols prior to site initiation. The ‘open access’ approach involves publishing the protocol, permitting easy access to the complete protocol. The main advantages of the open access approach are that the protocol is freely available to all stakeholders, permitting them to discuss the protocol widely with colleagues, assess the quality and rigour of the protocol, determine the feasibility of conducting the trial at their centre, and after trial completion, to evaluate the reported findings based on a full understanding of the protocol. The main potential disadvantage of this approach is the potential for plagiarism; however if that occurred, it should be easy to identify because of the open access to the original trial protocol, as well as ensure that appropriate sanctions are used to deal with plagiarism. The ‘restricted access’ approach involves the use of non-disclosure agreements, legal documents that must be signed between the trial lead centre and collaborative sites. Potential sites must guarantee they will not disclose any details of the study before they are permitted to access the protocol. The main advantages of the restricted access approach are for the lead institution and nominated principal investigator, who protect their intellectual property associated with the trial. The main disadvantages are that ownership of the protocol and intellectual property is assigned to the lead institution; defining who ‘needs to know’ about the study protocol is difficult; and the use of non-disclosure agreements involves review by lawyers and institutional representatives at each site before access is permitted to the protocol, significantly delaying study implementation and adding substantial indirect costs to research institutes. This extra step may discourage sites from joining a trial. It is possible that the restricted access approach may contribute to the failure of well-designed trials without any significant benefit in protecting intellectual property. Funding agencies should formalize rules around open versus restricted access to the study protocol just as they have around open access to results. PMID:23270486

Protecting intellectual property associated with Canadian academic clinical trials--approaches and impact.

PubMed

Ross, Sue; Magee, Laura; Walker, Mark; Wood, Stephen

2012-12-27

Intellectual property is associated with the creative work needed to design clinical trials. Two approaches have developed to protect the intellectual property associated with multicentre trial protocols prior to site initiation. The 'open access' approach involves publishing the protocol, permitting easy access to the complete protocol. The main advantages of the open access approach are that the protocol is freely available to all stakeholders, permitting them to discuss the protocol widely with colleagues, assess the quality and rigour of the protocol, determine the feasibility of conducting the trial at their centre, and after trial completion, to evaluate the reported findings based on a full understanding of the protocol. The main potential disadvantage of this approach is the potential for plagiarism; however if that occurred, it should be easy to identify because of the open access to the original trial protocol, as well as ensure that appropriate sanctions are used to deal with plagiarism. The 'restricted access' approach involves the use of non-disclosure agreements, legal documents that must be signed between the trial lead centre and collaborative sites. Potential sites must guarantee they will not disclose any details of the study before they are permitted to access the protocol. The main advantages of the restricted access approach are for the lead institution and nominated principal investigator, who protect their intellectual property associated with the trial. The main disadvantages are that ownership of the protocol and intellectual property is assigned to the lead institution; defining who 'needs to know' about the study protocol is difficult; and the use of non-disclosure agreements involves review by lawyers and institutional representatives at each site before access is permitted to the protocol, significantly delaying study implementation and adding substantial indirect costs to research institutes. This extra step may discourage sites from joining a trial. It is possible that the restricted access approach may contribute to the failure of well-designed trials without any significant benefit in protecting intellectual property. Funding agencies should formalize rules around open versus restricted access to the study protocol just as they have around open access to results.

Can ecological history influence immunomarker responses and antioxidant enzyme activities in bivalves that have been experimentally exposed to contaminants? A new subject for discussion in "eco-immunology" studies.

PubMed

Matozzo, Valerio; Giacomazzo, Matteo; Finos, Livio; Marin, Maria Gabriella; Bargelloni, Luca; Milan, Massimo

2013-07-01

Numerous studies have demonstrated that environmental parameters affect bivalve immunomarkers. In the present study, we tested the hypothesis that clams (Venerupis philippinarum) collected in sites with different environmental conditions respond differently to experimental contaminant exposure. Clams were collected at two sites within the Lagoon of Venice that are influenced differently by both anthropogenic impact and natural conditions: Marghera, which is characterised by relatively high contamination levels and restricted clam fishing, and Chioggia, which is inside a licensed clam culture area that is characterised by lower contamination levels. Total haemocyte count, haemocyte diameter and volume, lysozyme activity in both haemocyte lysate and cell-free haemolymph, superoxide dismutase and catalase activities in gills and digestive glands were measured at time 0 (clam sampling time), after 7 days of acclimation in the laboratory and after 1, 3 and 7 days of copper exposure. Interestingly, statistical analyses (three-way ANOVA and Canonical Correlation Analysis) revealed persistent differences in the biological responses of clams from the two sampling sites before and after copper exposure. Conversely, the influence of copper on cellular and biochemical parameters was negligible. Overall, the results obtained indicated that animals with a different ecological history respond differently to experimental contaminant exposure. In addition, this study suggested that immunomarkers and other biomarkers might be used to determine the origin of fishing products. Copyright © 2013 Elsevier Ltd. All rights reserved.

Post-Closure Strategy for Use-Restricted Sites on the Nevada National Security Site, Nevada Test and Training Range, and Tonopah Test Range, Nevada

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

Silvas, A. J.

The purpose of this Post-Closure Strategy is to provide a consistent methodology for continual evaluation of post-closure requirements for use-restricted areas on the Nevada National Security Site (NNSS), Nevada Test and Training Range (NTTR), and Tonopah Test Range (TTR) to consolidate, modify, or streamline the program. In addition, this document stipulates the creation of a single consolidated Post-Closure Plan that will detail the current post-closure requirements for all active use restrictions (URs) and outlines its implementation and subsequent revision. This strategy will ensure effective management and control of the post-closure sites. There are currently over 200 URs located on themore » NNSS, NTTR, and TTR. Post-closure requirements were initially established in the Closure Report for each site. In some cases, changes to the post-closure requirements have been implemented through addenda, errata sheets, records of technical change, or letters. Post-closure requirements have been collected from these multiple sources and consolidated into several formats, such as summaries and databases. This structure increases the possibility of inconsistencies and uncertainty. As more URs are established and the post-closure program is expanded, the need for a comprehensive approach for managing the program will increase. Not only should the current requirements be obtainable from a single source that supersedes all previous requirements, but the strategy for modifying the requirements should be standardized. This will enable more effective management of the program into the future. This strategy document and the subsequent comprehensive plan are to be implemented under the assumption that the NNSS and outlying sites will be under the purview of the U.S. Department of Energy, National Nuclear Security Administration for the foreseeable future. This strategy was also developed assuming that regulatory control of the sites remains static. The comprehensive plan is not intended to be a permanent long-term stewardship plan. However, it is intended to clarify requirements and identify components to effectively manage the sites until regulatory requirements are met or management of the site changes. The Environmental Management Program is required to manage these sites until the NNSS Environmental Restoration program is completed, currently planned for 2030. Prior to completion of the Environmental Restoration program, additional planning will be conducted to ensure that long-term stewardship of the sites is maintained. A comprehensive post-closure plan can be transitioned effectively into any future site-wide long-term stewardship program that may be developed. Therefore, the post-closure plan will include current aspects of the post-closure program that are also important aspects of long-term stewardship, including the following: • Management of physical and engineering controls such as fences, signs, and soil covers • Management of institutional and administrative controls such as use restrictions and real estate systems • Management of monitoring and maintenance programs • Management of information related to the sites such as geographic information system data and related documentation The strategy will also allow for periodic review and modification of any aspect of the program to ensure continued effectiveness.« less

Removal of either N-glycan site from the envelope receptor binding domain of Moloney and Friend but not AKV mouse ecotropic gammaretroviruses alters receptor usage

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

Knoper, Ryan C.; Ferrarone, John; Yan Yuhe

2009-09-01

Three N-linked glycosylation sites were removed from the envelope glycoproteins of Friend, Moloney, and AKV mouse ecotropic gammaretroviruses: gs1 and gs2, in the receptor binding domain; and gs8, in a region implicated in post-binding cell fusion. Mutants were tested for their ability to infect rodent cells expressing 4 CAT-1 receptor variants. Three mutants (Mo-gs1, Mo-gs2, and Fr-gs1) infect NIH 3T3 and rat XC cells, but are severely restricted in Mus dunni cells and Lec8, a Chinese hamster cell line susceptible to ecotropic virus. This restriction is reproduced in ferret cells expressing M. dunni dCAT-1, but not in cells expressing NIHmore » 3T3 mCAT-1. Virus binding assays, pseudotype assays, and the use of glycosylation inhibitors further suggest that restriction is primarily due to receptor polymorphism and, in M. dunni cells, to glycosylation of cellular proteins. Virus envelope glycan size or type does not affect infectivity. Thus, host range variation due to N-glycan deletion is receptor variant-specific, cell-specific, virus type-specific, and glycan site-specific.« less

Isolation and Characterization of Five Erwinia amylovora Bacteriophages and Assessment of Phage Resistance in Strains of Erwinia amylovora

PubMed Central

Schnabel, Elise L.; Jones, Alan L.

2001-01-01

Phages able to infect the fire blight pathogen Erwinia amylovora were isolated from apple, pear, and raspberry tissues and from soil samples collected at sites displaying fire blight symptoms. Among a collection of 50 phage isolates, 5 distinct phages, including relatives of the previously described phages φEa1 and φEa7 and 3 novel phages named φEa100, φEa125, and φEa116C, were identified based on differences in genome size and restriction fragment pattern. φEa1, the phage distributed most widely, had an approximately 46-kb genome which exhibited some restriction site variability between isolates. Phages φEa100, φEa7, and φEa125 each had genomes of approximately 35 kb and could be distinguished by their EcoRI restriction fragment patterns. φEa116C contained an approximately 75-kb genome. φEa1, φEa7, φEa100, φEa125, and φEa116C were able to infect 39, 36, 16, 20, and 40, respectively, of 40 E. amylovora strains isolated from apple orchards in Michigan and 8, 12, 10, 10, and 12, respectively, of 12 E. amylovora strains isolated from raspberry fields (Rubus spp.) in Michigan. Only 22 of 52 strains were sensitive to all five phages, and 23 strains exhibited resistance to more than one phage. φEa116C was more effective than the other phages at lysing E. amylovora strain Ea110 in liquid culture, reducing the final titer of Ea110 by >95% when added at a ratio of 1 PFU per 10 CFU and by 58 to 90% at 1 PFU per 105 CFU. PMID:11133428

Plant and soil effects on bacterial communities associated with Miscanthus  ×  giganteus rhizosphere and rhizomes

DOE PAGES

Li, Dongfang; Voigt, Thomas B.; Kent, Angela D.

2015-02-11

Here, bacterial assemblages, especially diazotroph assemblages residing in the rhizomes and the rhizosphere soil of Miscanthus × giganteus, contribute to plant growth and nitrogen use efficiency. However, the composition of these microbial communities has not been adequately explored nor have the potential ecological drivers for these communities been sufficiently studied. This knowledge is needed for understanding and potentially improving M. × giganteus – microbe interactions, and further enhancing sustainability of M. × giganteus production. In this study, cultivated M. × giganteus from four sites in Illinois, Kentucky, Nebraska, and New Jersey were collected to examine the relative influences of soilmore » conditions and plant compartments on assembly of the M. × giganteus-associated microbiome. Automated ribosomal intergenic spacer (ARISA) and terminal restriction fragment length polymorphism (T-RFLP) targeting the nifH gene were applied to examine the total bacterial communities and diazotroph assemblages that reside in the rhizomes and the rhizosphere. Distinct microbial assemblages were detected in the endophytic and rhizosphere compartments. Site soil conditions had strong correlation with both total bacterial and diazotroph assemblages, but in different ways. Nitrogen treatments showed no significant effect on the composition of diazotroph assemblages in most sites. Endophytic compartments of different M. × giganteus plants tended to harbor similar microbial communities across all sites, whereas the rhizosphere soil of different plant tended to harbor diverse microbial assemblages that were distinct among sites. These observations offer insight into better understanding of the associative interactions between M. × giganteus and diazotrophs, and how this relationship is influenced by agronomic and edaphic factors.« less

Conserved DNA methylation patterns in healthy blood cells and extensive changes in leukemia measured by a new quantitative technique

PubMed Central

Jelinek, Jaroslav; Liang, Shoudan; Lu, Yue; He, Rong; Ramagli, Louis S.; Shpall, Elizabeth J.; Estecio, Marcos R.H.; Issa, Jean-Pierre J.

2012-01-01

Genome wide analysis of DNA methylation provides important information in a variety of diseases, including cancer. Here, we describe a simple method, Digital Restriction Enzyme Analysis of Methylation (DREAM), based on next generation sequencing analysis of methylation-specific signatures created by sequential digestion of genomic DNA with SmaI and XmaI enzymes. DREAM provides information on 150,000 unique CpG sites, of which 39,000 are in CpG islands and 30,000 are at transcription start sites of 13,000 RefSeq genes. We analyzed DNA methylation in healthy white blood cells and found methylation patterns to be remarkably uniform. Inter individual differences > 30% were observed only at 227 of 28,331 (0.8%) of autosomal CpG sites. Similarly, > 30% differences were observed at only 59 sites when we comparing the cord and adult blood. These conserved methylation patterns contrasted with extensive changes affecting 18–40% of CpG sites in a patient with acute myeloid leukemia and in two leukemia cell lines. The method is cost effective, quantitative (r2 = 0.93 when compared with bisulfite pyrosequencing) and reproducible (r2 = 0.997). Using 100-fold coverage, DREAM can detect differences in methylation greater than 10% or 30% with a false positive rate below 0.05 or 0.001, respectively. DREAM can be useful in quantifying epigenetic effects of environment and nutrition, correlating developmental epigenetic variation with phenotypes, understanding epigenetics of cancer and chronic diseases, measuring the effects of drugs on DNA methylation or deriving new biological insights into mammalian genomes. PMID:23075513

Plant and soil effects on bacterial communities associated with Miscanthus  ×  giganteus rhizosphere and rhizomes

DOE PAGES

Li, Dongfang; Voigt, Thomas B.; Kent, Angela D.

2015-04-30

Here, bacterial assemblages, especially diazotroph assemblages residing in the rhizomes and the rhizosphere soil of Miscanthus × giganteus, contribute to plant growth and nitrogen use efficiency. However, the composition of these microbial communities has not been adequately explored nor have the potential ecological drivers for these communities been sufficiently studied. This knowledge is needed for understanding and potentially improving M. × giganteus – microbe interactions, and further enhancing sustainability of M. × giganteus production. In this study, cultivated M. × giganteus from four sites in Illinois, Kentucky, Nebraska, and New Jersey were collected to examine the relative influences of soilmore » conditions and plant compartments on assembly of the M. × giganteus-associated microbiome. Automated ribosomal intergenic spacer (ARISA) and terminal restriction fragment length polymorphism (T-RFLP) targeting the nifH gene were applied to examine the total bacterial communities and diazotroph assemblages that reside in the rhizomes and the rhizosphere. Distinct microbial assemblages were detected in the endophytic and rhizosphere compartments. Site soil conditions had strong correlation with both total bacterial and diazotroph assemblages, but in different ways. Nitrogen treatments showed no significant effect on the composition of diazotroph assemblages in most sites. Endophytic compartments of different M. × giganteus plants tended to harbor similar microbial communities across all sites, whereas the rhizosphere soil of different plant tended to harbor diverse microbial assemblages that were distinct among sites. These observations offer insight into better understanding of the associative interactions between M. × giganteus and diazotrophs, and how this relationship is influenced by agronomic and edaphic factors.« less

Differential Transcription Factor Use by the KIR2DL4 Promoter Under Constitutive and IL-2/15-Treated Conditions

PubMed Central

Presnell, Steven R.; Zhang, Lei; Chlebowy, Corrin N.; Al-Attar, Ahmad; Lutz, Charles T.

2012-01-01

KIR2DL4 is unique among human KIR genes in expression, cellular localization, structure, and function, yet the transcription factors required for its expression have not been identified. Using mutagenesis, electrophoretic mobility shift assay, and co-transfection assays, we identified two redundant Runx binding sites in the 2DL4 promoter as essential for constitutive 2DL4 transcription, with contributions by a CRE site and initiator elements. IL-2-and IL-15-stimulated human NK cell lines increased 2DL4 promoter activity, which required functional Runx, CRE, and Ets sites. Chromatin immunoprecipitation experiments show that Runx3 and Ets1 bind the 2DL4 promoter in situ. 2DL4 promoter activity had similar transcription factor requirements in T cells. Runx, CRE, and Ets binding motifs are present in 2DL4 promoters from across primate species, but other postulated transcription factor binding sites are not preserved. Differences between 2DL4 and clonally-restricted KIR promoters suggest a model that explains the unique 2DL4 expression pattern in human NK cells. PMID:22467658

The importance of fetal gender in intrauterine growth restriction

PubMed Central

Radulescu, L; Ferechide, D; Popa, F

2013-01-01

One of the most important causes of perinatal mortality and morbidity complicating significant percentage pregnancies is intrauterine growth restriction (IUGR). Fetal growth restriction is the main cause of intrauterine fetal death and the second leading cause of death in the neonatal period. Numerous studies in different populations reveal an association between intrauterine growth restriction and perinatal and postnatal developments, which differ according to the sex of newborns with intrauterine growth restriction. However, the mechanisms of intrauterine programming, the critical time necessary to cause injury and involvement of other factors are unclear and although several authors’ opinions differ, it seems that females are more likely to develop intrauterine growth restriction. Abbreviations: IUGR=intrauterine growth restriction PMID:23599816

A field study using the fungicide benomyl to investigate the effect of mycorrhizal fungi on plant fitness.

PubMed

Carey, Peter D; Fitter, Alastair H; Watkinson, Andrew R

1992-07-01

The effect of vesicular-arbuscular mycorrhiza (VAM) on the fecundity ofVulpia ciliata ssp.ambigua was investigated at two field sites in eastern England by applying the fungicide benomyl to reduce VAM infection. The application of benomyl at the two sites produced very different results. At one site the application of the fungicide reduced the fecundity of plants whereas at the other fecundity was increased. At the first site the reduction in fecundity was linked to a significant reduction in VAM infection on the sprayed plants. The mechanism of the benefit associated with the VAM infection is however unclear: there was no treatment effect on morphology or on phosphorus inflow. At the second site, where fecundity was increased, there was only a negligible amount of VAM infection amongst the unsprayed plants and it is suggested that the increase in fecundity with the application of benomyl may have resulted from a reduction in infection by other, presumably pathogenic, fungi. The value of VAM fungi to the host plant may therefore not be restricted to physiological benefits. They may also provide protection to the plant by competing for space with other species of pathogenic fungi.

Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences.

PubMed

Colonna, Vincenza; Ayub, Qasim; Chen, Yuan; Pagani, Luca; Luisi, Pierre; Pybus, Marc; Garrison, Erik; Xue, Yali; Tyler-Smith, Chris; Abecasis, Goncalo R; Auton, Adam; Brooks, Lisa D; DePristo, Mark A; Durbin, Richard M; Handsaker, Robert E; Kang, Hyun Min; Marth, Gabor T; McVean, Gil A

2014-06-30

Population differentiation has proved to be effective for identifying loci under geographically localized positive selection, and has the potential to identify loci subject to balancing selection. We have previously investigated the pattern of genetic differentiation among human populations at 36.8 million genomic variants to identify sites in the genome showing high frequency differences. Here, we extend this dataset to include additional variants, survey sites with low levels of differentiation, and evaluate the extent to which highly differentiated sites are likely to result from selective or other processes. We demonstrate that while sites with low differentiation represent sampling effects rather than balancing selection, sites showing extremely high population differentiation are enriched for positive selection events and that one half may be the result of classic selective sweeps. Among these, we rediscover known examples, where we actually identify the established functional SNP, and discover novel examples including the genes ABCA12, CALD1 and ZNF804, which we speculate may be linked to adaptations in skin, calcium metabolism and defense, respectively. We identify known and many novel candidate regions for geographically restricted positive selection, and suggest several directions for further research.

Identification of the structural mutation responsible for the dibucaine-resistant (atypical) variant form of human serum cholinesterase.

PubMed Central

McGuire, M C; Nogueira, C P; Bartels, C F; Lightstone, H; Hajra, A; Van der Spek, A F; Lockridge, O; La Du, B N

1989-01-01

A point mutation in the gene for human serum cholinesterase was identified that changes Asp-70 to Gly in the atypical form of serum cholinesterase. The mutation in nucleotide 209, which changes codon 70 from GAT to GGT, was found by sequencing a genomic clone and sequencing selected regions of DNA amplified by the polymerase chain reaction. The entire coding sequences for usual and atypical cholinesterases were compared, and no other consistent base differences were found. A polymorphic site near the C terminus of the coded region was detected, but neither allele at this locus segregated consistently with the atypical trait. The nucleotide-209 mutation was detected in all five atypical cholinesterase families examined. There was complete concordance between this mutation and serum cholinesterase phenotypes for all 14 heterozygous and 6 homozygous atypical subjects tested. The mutation causes the loss of a Sau3A1 restriction site; the resulting DNA fragment length polymorphism was verified by electrophoresis of 32P-labeled DNA restriction fragments from usual and atypical subjects. Dot-blot hybridization analysis with a 19-mer allele-specific probe to the DNA amplified by the polymerase chain reaction distinguished between the usual and atypical genotypes. We conclude that the Asp-70----Gly mutation (acidic to neutral amino acid substitution) accounts for reduced affinity of atypical cholinesterase for choline esters and that Asp-70 must be an important component of the anionic site. Heterogeneity in atypical alleles may exist, but the Asp-70 point mutation may represent an appreciable portion of the atypical gene pool. Images PMID:2915989

The Effect of Different Type of Herbivores, Grazing Types and Grazing Intensities on Alpine Basiphillous Vegetation of the Romanian Carpathians

NASA Astrophysics Data System (ADS)

Ballová, Zuzana; Pekárik, Ladislav; Šibík, Jozef

2017-04-01

The major purpose of the present study was to test the hypothesis that there are significant differences in vegetation structure, plant species composition, and soil chemical properties in relation to type of grazing animals, various levels of grazing intensity and grazing type, and if potential differences alter with ecosystem productivity (increase in more productive ecosystems). The study was conducted in three mountain ranges of the Romanian Carpathians with a predominance of alkaline substrates (the Bucegi Mts, the Little Retezat Mts and the Ceahlău Massif). Statistical analyses were performed in R statistical software environment. The effects of grazing animals (cattle, horses and sheep), grazing types (fence, regular, irregular) and grazing intensity (low, medium, high) on the community structure were tested using ordination methods. In the case of soil properties, General Linear Mixed Model was applied. Special statistical approach eliminated the differences between the examined mountains and sites. Type of grazing animal does not significantly influence species cover but it is related to specific species occurrence. According to our results, grazing horses had similar effects as cattle compared to sheep. Grazing in restricted areas (surrounded by fence) and regular unrestricted grazing were more similar if compared to irregular grazing. When comparing the intensity of grazing, high and medium intensity were more similar to each other than to the low intensity grazing. Cattle grazed sites had significantly higher lichens cover, while the sheep patches were covered with increased overall herb layer (forbs, graminoids and low shrubs together). Medium grazing intensity decreased the lichens cover, cover of overall herb layer, and total vegetation cover compared to high and low grazing intensity. Grazing type had important impact on the lichens cover and cover of overall herb layer. The lichens cover appeared to decrease while the cover of overall herb layer increased the most in restricted areas compared to irregularly and regularly grazed sites. When analyzing soil properties, Generalized mixed models revealed reliable results in the differences among categories of grazing types and intensity. These differences were only noticeable in calcium concentration being calcium the most decreased by medium grazing intensity and the most increased by irregular grazing. Grazing had significant effects on individual plant species occurrences and covers. Horses decreased presence of Anthoxanthum odoratum and regular grazing sites as well as fences had significantly higher occurrence of trampling tolerant species Nardus stricta compared to sites with irregular grazing. The type of grazing herbivores influenced covers of Agrostis capillaris, A. rupestris, Campanula rotundifolia, Festuca supina, Luzula multiflora, and Ranunculus pseudomontanus. The grazing types significantly altered covers of Agrostis capillaris, Alchemilla sp. div., Campanula rotundifolia, Festuca supina, Luzula multiflora, Nardus stricta, and Potentilla ternata (Potentilla aurea subsp. chrysocraspeda). The intensity of grazing had important impact on covers of Agrostis rupestris, Alchemilla sp. div., Campanula rotundifolia, Festuca supina, Luzula multiflora, Poa alpina, Potentilla ternata, and Ranunculus pseudomontanus. Key words: alpine meadows; pastures; GLMM; NMDS; (nested) PERMANOVA

New restriction enzymes discovered from Escherichia coli clinical strains using a plasmid transformation method

PubMed Central

Kasarjian, Julie K. A.; Iida, Masatake; Ryu, Junichi

2003-01-01

The presence of restriction enzymes in bacterial cells has been predicted by either classical phage restriction-modification (R-M) tests, direct in vitro enzyme assays or more recently from bacterial genome sequence analysis. We have applied phage R-M test principles to the transformation of plasmid DNA and established a plasmid R-M test. To validate this test, six plasmids that contain BamHI fragments of phage lambda DNA were constructed and transformed into Escherichia coli strains containing known R-M systems including: type I (EcoBI, EcoAI, Eco124I), type II (HindIII) and type III (EcoP1I). Plasmid DNA with a single recognition site showed a reduction of relative efficiency of transformation (EOT = 10–1–10–2). When multiple recognition sites were present, greater reductions in EOT values were observed. Once established in the cell, the plasmids were subjected to modification (EOT = 1.0). We applied this test to screen E.coli clinical strains and detected the presence of restriction enzymes in 93% (14/15) of cells. Using additional subclones and the computer program, RM Search, we identified four new restriction enzymes, Eco377I, Eco585I, Eco646I and Eco777I, along with their recognition sequences, GGA(8N)ATGC, GCC(6N)TGCG, CCA(7N)CTTC, and GGA(6N)TATC, respectively. Eco1158I, an isoschizomer of EcoBI, was also found in this study. PMID:12595571

TALE-PvuII Fusion Proteins – Novel Tools for Gene Targeting

PubMed Central

Yanik, Mert; Alzubi, Jamal; Lahaye, Thomas; Cathomen, Toni; Pingoud, Alfred; Wende, Wolfgang

2013-01-01

Zinc finger nucleases (ZFNs) consist of zinc fingers as DNA-binding module and the non-specific DNA-cleavage domain of the restriction endonuclease FokI as DNA-cleavage module. This architecture is also used by TALE nucleases (TALENs), in which the DNA-binding modules of the ZFNs have been replaced by DNA-binding domains based on transcription activator like effector (TALE) proteins. Both TALENs and ZFNs are programmable nucleases which rely on the dimerization of FokI to induce double-strand DNA cleavage at the target site after recognition of the target DNA by the respective DNA-binding module. TALENs seem to have an advantage over ZFNs, as the assembly of TALE proteins is easier than that of ZFNs. Here, we present evidence that variant TALENs can be produced by replacing the catalytic domain of FokI with the restriction endonuclease PvuII. These fusion proteins recognize only the composite recognition site consisting of the target site of the TALE protein and the PvuII recognition sequence (addressed site), but not isolated TALE or PvuII recognition sites (unaddressed sites), even at high excess of protein over DNA and long incubation times. In vitro, their preference for an addressed over an unaddressed site is > 34,000-fold. Moreover, TALE-PvuII fusion proteins are active in cellula with minimal cytotoxicity. PMID:24349308

Clinical relevance of the breakpoint sites within the M-BCR in 50 patients from Argentina with chronic myeloid leukemia.

PubMed

Giere, I A; Larripa, I B

1996-08-01

Fifty patients from Argentina with chronic myeloid leukemia (CML) were studied in order to characterize the breakpoint site within the major breakpoint cluster region (M-BCR) and its relationship with the duration of the chronic phase (CP). The DNA digestion with the restriction enzymes: Bgl II, BAM HI and Hind III and hybridization with the 1.2Kb Hind III-Bgl II bcr probe showed that 56% of cases had the breakpoint in 5'M-bcr region and the remaining 44% in 3'M-bcr region. The duration of chronic phase from diagnosis to the onset of the blast crisis (BC) was correlated with the location of the breakpoint within the M-bcr and no statistical differences were observed between the 5' and the 3' groups. These data indicate that the breakpoint site within the bcr gene is not a prognostic indicator of the duration of CP of the disease.

One Paradox in District Accountability and Site-Based Management.

ERIC Educational Resources Information Center

Shellman, David W.

The paradox of site-based school management with use of standardized tests or instructional management systems that restrict teacher choices was evident in one school district in North Carolina in which measurement of student success has centered on student performance on state-mandated tests. A study was conducted to see if students whose…

10 CFR 862.1 - Purpose.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 4 2011-01-01 2011-01-01 false Purpose. 862.1 Section 862.1 Energy DEPARTMENT OF ENERGY RESTRICTIONS ON AIRCRAFT LANDING AND AIR DELIVERY AT DEPARTMENT OF ENERGY NUCLEAR SITES § 862.1 Purpose. The... aircraft and air delivery on nuclear sites under the jurisdiction of DOE pursuant to the Atomic Energy Act...

43 CFR 2094.2 - Waiver of 160-rod limitation.

Code of Federal Regulations, 2011 CFR

2011-10-01

... necessary for harborage, landing, and wharf purposes. The act does not authorize the waiver of the 80-rod restriction, mentioned in § 2094.0-3. (b) Except as to trade and manufacturing sites, and home and headquarters sites, any applications to enter and notices of settlement which cover lands extending more than...

77 FR 52397 - Federal Property Suitable as Facilities To Assist the Homeless

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-29

...: 26305, 40132 Comments: Off-site removal only; sf. varies; use varies; fair conditions; restricted area..., 912, 913 Comments: Off-site removal only; sf varies; housing; fair to poor conditions; asbestos and...; office space; fair to poor conditions; secured area; prior approval to access property 258 7th Division...

10 CFR 862.1 - Purpose.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 4 2010-01-01 2010-01-01 false Purpose. 862.1 Section 862.1 Energy DEPARTMENT OF ENERGY RESTRICTIONS ON AIRCRAFT LANDING AND AIR DELIVERY AT DEPARTMENT OF ENERGY NUCLEAR SITES § 862.1 Purpose. The... aircraft and air delivery on nuclear sites under the jurisdiction of DOE pursuant to the Atomic Energy Act...

76 FR 66961 - National Register of Historic Places; Notification of Pending Nominations and Related Actions

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-28

...., Waterloo, 11000813 Buena Vista County Danish Lutheran Church, 113 W. 4th St., Alta, 11000814 Carroll County..., 11000824 NEW MEXICO Eddy County LA 157206--White Oaks Pictograph Site (Guadalupe Mountains Rock Art MPS), Address Restricted, Queen, 11000829 LA 158783--Ambush Site (Guadalupe Mountains Rock Art MPS), Address...

50 CFR 32.49 - New Jersey.

Code of Federal Regulations, 2010 CFR

2010-10-01

... through the end of the State common snipe season. 5. You may only possess approved nontoxic shot while in... Division, we restrict hunting to designated sites, with each site limited to one party of hunters. 5. In.... We require persons hunting on the refuge for the first time to attend one of the four refuge-specific...

77 FR 24760 - Safety Advisory 2012-02; Restricted Speed

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-25

... recommend that FRA: \\1\\ Available online at NTSB's Web site: http://www.ntsb.gov/doclib/recletters/2011/R-11... bulletins on [FRA's Web site], advise all railroads of the occurrences of the following five recent rear end... intermodal train. The intermodal train was following the rock train, and had passed a dark (non-illuminated...

Alternative models of recreational off-highway vehicle site demand

Treesearch

Jeffrey Englin; Thomas Holmes; Rebecca Niell

2006-01-01

A controversial recreation activity is off-highway vehicle use. Off-highway vehicle use is controversial because it is incompatible with most other activities and is extremely hard on natural eco-systems. This study estimates utility theoretic incomplete demand systems for four off-highway vehicle sites. Since two sets of restrictions are equally consistent with...

Groundwater similarity across a watershed derived from time-warped and flow-corrected time series

NASA Astrophysics Data System (ADS)

Rinderer, M.; McGlynn, B. L.; van Meerveld, H. J.

2017-05-01

Information about catchment-scale groundwater dynamics is necessary to understand how catchments store and release water and why water quantity and quality varies in streams. However, groundwater level monitoring is often restricted to a limited number of sites. Knowledge of the factors that determine similarity between monitoring sites can be used to predict catchment-scale groundwater storage and connectivity of different runoff source areas. We used distance-based and correlation-based similarity measures to quantify the spatial and temporal differences in shallow groundwater similarity for 51 monitoring sites in a Swiss prealpine catchment. The 41 months long time series were preprocessed using Dynamic Time-Warping and a Flow-corrected Time Transformation to account for small timing differences and bias toward low-flow periods. The mean distance-based groundwater similarity was correlated to topographic indices, such as upslope contributing area, topographic wetness index, and local slope. Correlation-based similarity was less related to landscape position but instead revealed differences between seasons. Analysis of variance and partial Mantel tests showed that landscape position, represented by the topographic wetness index, explained 52% of the variability in mean distance-based groundwater similarity, while spatial distance, represented by the Euclidean distance, explained only 5%. The variability in distance-based similarity and correlation-based similarity between groundwater and streamflow time series was significantly larger for midslope locations than for other landscape positions. This suggests that groundwater dynamics at these midslope sites, which are important to understand runoff source areas and hydrological connectivity at the catchment scale, are most difficult to predict.

COLD-WATER CORALS AND HYDROCHEMISTRY - is there a unifying link?

NASA Astrophysics Data System (ADS)

Flögel, Sascha; Rüggeberg, Andres; Mienis, Furu; Dullo, Wolf-Christian

2010-05-01

Physical and chemical parameters were measured in five different regions of the Northeast Atlantic with known occurrences of cold-water coral reefs and mounds and in the Mediterranean, where these corals form living carpets over existing morphologies. In this study we analyzed 282 bottom water samples regarding delta13CDIC, delta18O, and DIC. The hydrochemical data reveal characteristic patterns and differences for cold-water coral sites with living coral communities and ongoing reef and mound growth at the Irish and Norwegian sites. While the localities in the Mediterranean, in the Gulf of Cadiz, and off Mauritania show only patchy coral growth on mound-like reliefs and various substrates. The analysis of delta13C/delta18O reveals distinct clusters for the different regions and the respective bottom water masses bathing the delta18O, and especially between delta13CDIC and DIC shows that DIC is a parameter with high sensitivity to the mixing of bottom water masses. It varies distinctively between sites with living reefs/mounds and sites with restricted patchy growth or dead corals. Results suggest that DIC and delta13CDIC can provide additional insights into the mixing of bottom water masses. Prolific cold-water coral growth forming giant biogenic structures plot into a narrow geochemical window characterized by a variation of delta13CDIC between 0.45 and 0.79 per mille being associated with the water mass having a density of sigma-theta of 27.5±0.15 kg m-3.

Microbial decomposers not constrained by climate history along a Mediterranean climate gradient in southern California.

PubMed

Baker, Nameer R; Khalili, Banafshe; Martiny, Jennifer B H; Allison, Steven D

2018-06-01

Microbial decomposers mediate the return of CO 2 to the atmosphere by producing extracellular enzymes to degrade complex plant polymers, making plant carbon available for metabolism. Determining if and how these decomposer communities are constrained in their ability to degrade plant litter is necessary for predicting how carbon cycling will be affected by future climate change. We analyzed mass loss, litter chemistry, microbial biomass, extracellular enzyme activities, and enzyme temperature sensitivities in grassland litter transplanted along a Mediterranean climate gradient in southern California. Microbial community composition was manipulated by caging litter within bags made of nylon membrane that prevent microbial immigration. To test whether grassland microbes were constrained by climate history, half of the bags were inoculated with local microbial communities native to each gradient site. We determined that temperature and precipitation likely interact to limit microbial decomposition in the extreme sites along our gradient. Despite their unique climate history, grassland microbial communities were not restricted in their ability to decompose litter under different climate conditions across the gradient, although microbial communities across our gradient may be restricted in their ability to degrade different types of litter. We did find some evidence that local microbial communities were optimized based on climate, but local microbial taxa that proliferated after inoculation into litterbags did not enhance litter decomposition. Our results suggest that microbial community composition does not constrain C-cycling rates under climate change in our system, but optimization to particular resource environments may act as more general constraints on microbial communities. © 2018 by the Ecological Society of America.

Cellular architecture mediates DivIVA ultrastructure and regulates min activity in Bacillus subtilis | Center for Cancer Research

Cancer.gov

The Min system in rod-shaped bacteria restricts improper assembly of the division septum. In Escherichia coli, the Min system localizes to the cell poles, but in Bacillus subtilis, it is recruited to nascent cell division sites at mid-cell to prevent aberrant septation events immediately adjacent to a constricting septum. How does the cell spatially and temporally restrict the

Comparison of allele-specific PCR, created restriction-site PCR, and PCR with primer-introduced restriction analysis methods used for screening complex vertebral malformation carriers in Holstein cattle

PubMed Central

Altınel, Ahmet

2017-01-01

Complex vertebral malformation (CVM) is an inherited, autosomal recessive disorder of Holstein cattle. The aim of this study was to compare sensitivity, specificity, positive and negative predictive values, accuracy, and rapidity of allele-specific polymerase chain reaction (AS-PCR), created restriction-site PCR (CRS-PCR), and PCR with primer-introduced restriction analysis (PCR-PIRA), three methods used in identification of CVM carriers in a Holstein cattle population. In order to screen for the G>T mutation in the solute carrier family 35 member A3 (SLC35A3) gene, DNA sequencing as the gold standard method was used. The prevalence of carriers and the mutant allele frequency were 3.2% and 0.016, respectively, among Holstein cattle in the Thrace region of Turkey. Among the three methods, the fastest but least accurate was AS-PCR. Although the rapidity of CRS-PCR and PCR-PIRA were nearly equal, the accuracy of PCR-PIRA was higher than that of CRS-PCR. Therefore, among the three methods, PCR-PIRA appears to be the most efficacious for screening of mutant alleles when identifying CVM carriers in a Holstein cattle population. PMID:28927256

Transformable Rhodobacter strains, method for producing transformable Rhodobacter strains

DOEpatents

Laible, Philip D.; Hanson, Deborah K.

2018-05-08

The invention provides an organism for expressing foreign DNA, the organism engineered to accept standard DNA carriers. The genome of the organism codes for intracytoplasmic membranes and features an interruption in at least one of the genes coding for restriction enzymes. Further provided is a system for producing biological materials comprising: selecting a vehicle to carry DNA which codes for the biological materials; determining sites on the vehicle's DNA sequence susceptible to restriction enzyme cleavage; choosing an organism to accept the vehicle based on that organism not acting upon at least one of said vehicle's sites; engineering said vehicle to contain said DNA; thereby creating a synthetic vector; and causing the synthetic vector to enter the organism so as cause expression of said DNA.

Temperature responses of tropical to warm temperate Cladophora species in relation to their distribution in the North Atlantic Ocean

NASA Astrophysics Data System (ADS)

Cambridge, M. L.; Breeman, A. M.; Kraak, S.; van den Hoek, C.

1987-09-01

The relationship between distribution boundaries and temperature responses of some North Atlantic Cladophora species (Chlorophyta) was experimentally examined under various regimes of temperature, light and daylength. Experimentally determined critical temperature intervals, in which survival, growth or reproduction was limited, were compared with annual temperature regimes (monthly means and extremes) at sites inside and outside distribution boundaries. The species tested belonged to two phytogeographic groups: (1) the tropical West Atlantic group ( C. submarina: isolate from Curaçao) and (2) the amphiatlantic tropical to warm temperate group ( C. prolifera: isolate from Corsica; C. coelothrix: isolates from Brittany and Curaçao; and C. laetevirens: isolates from deep and shallow water in Corsica and from Brittany). In accordance with distribution from tropical to warm temperate regions, each of the species grew well between 20 30°C and reproduction and growth were limited at and below 15°C. The upper survival limit in long days was <35°C in all species but high or maximum growth rates occurred at 30°C. C. prolifera, restricted to the tropical margins, had the most limited survival at 35°C. Experimental evidence suggests that C. submarina is restricted to the Caribbean and excluded from the more northerly American mainland and Gulf of Mexico coasts by sporadic low winter temperatures in the nearshore waters, when cold northerly weather penetrates far south every few years. Experimental evidence suggests that C. prolifera, C. coelothrix and C. laetevirens are restricted to their northern European boundaries by summer temperatures too low for sufficient growth and/or reproduction. Their progressively more northerly located boundaries were accounted for by differences in growth rates over the critical 10 15°C interval. C. prolifera and C. coelothrix are excluded or restricted in distribution on North Sea coasts by lethal winter temperatures, again differences in cold tolerance accounting for differences in their distribution patterns. On the American coast, species were probably restricted by lethal winter temperatures in the nearshore and, in some cases, by the absence of suitable hard substrates in the more equable offshore waters. Isolates from two points along the European coast (Brittany, Corsica) of C. laetevirens showed no marked differences in their temperature tolerance but the Caribbean and European isolates of C. coelothrix differed markedly in their tolerance to low temperatures, the lethal limit of the Caribbean isolate lying more than 5°C higher (at ca 5°C).

Intergenerational equity and long-term stewardship plans.

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

Hocking, E. K.

2002-02-05

For an untold number of contaminated sites throughout the world, stewardship will be inevitable. For many such sites, stewardship will be a reasonable approach because of the uncertainties associated with present and future site conditions and site contaminants, the limited performance of available technologies, the nonavailability of technologies, and the risk and cost associated with complete cleanup. Regardless of whether stewardship is a realistic approach to site situations or simply a convenient default, it could be required at most contaminated sites for multiple generations. Because the stewardship plan is required to protect the release of hazardous contaminants to the environment,more » some use restrictions will be put in place to provide that protection. These use restrictions will limit access to resources for as long as the protection is required. The intergenerational quality of long-term stewardship plans and their inherent limitations on resource use require that they be designed to achieve equity among the affected generations. Intergenerational equity, defined here as the fairness of access to resources across generations, could be achieved through a well-developed stewardship plan that provides future generations with the information they need to make wise decisions about resource use. Developing and implementing such a plan would take into account the failure mechanisms of the plan's components, feature short stewardship time blocks that would allow for periodic reassessments of the site and of the stewardship program's performance, and provide present and future generations with necessary site information.« less

The response of epiphytic microbes to habitat and growth status of Potamogeton malaianus Miq. in Lake Taihu.

PubMed

Cai, Xianlei; Gao, Guang; Tang, Xiangming; Dong, Baili; Dai, Jiangyu; Chen, Dan; Song, Yuzhi

2013-10-01

To investigate the effects of different habitats and plant growth status on abundance, biomass and community structure of epiphytic microbes, Potamogeton malaianus Miq. at two different habitats (Gonghu Bay and East Taihu) in Lake Taihu were collected in June, August and November (corresponding to the period of development of submerged macrophytes). The relative abundance of major epiphytic algae groups was determined with high performance liquid chromatography (HPLC), and the structures and dynamics of epiphytic bacteria were assessed by terminal restriction fragment length polymorphism (T-RFLP) analysis. Results showed that the biomass of epiphytic microbes was not significant difference between the two sites, and the analysis of similarity found no significant intra-lake heterogeneity in community structure, but the temporal heterogeneity of epiphytic microbes was significant, which linked to the growth state of submerged macrophytes and water temperature. The difference in community structure between June and August was larger than that between August and November at each site, indicating that the growth status of submerged macrophytes has a greater impact on the community structure of epiphytic microbes than the seasonal variation of environmental conditions. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Niche specificity of two Glypthelmins (Trematoda) congeners infecting Leptodactylus chaquensis (Anura: Leptodactylidae) from Argentina.

PubMed

Hamann, M I; Kehr, A I; González, C E

2009-08-01

Sixty-five specimens of the frog Leptodactylus chaquensis were infected by 2 Glypthelmins species (Glypthelmins repandum: 41%, and Glypthelmins palmipedis: 38%) in the small intestine. This study was designed to determine the site specificity of both species along the length of the small intestine by analyzing the distribution, niche overlap, morphological characteristics, and population dynamics. The location of G. palmipedis is very restricted, with the core infection site in the anterior small intestine. In contrast, G. repandum can be characterized as having an expanded niche within the small intestine. In single infections and with different intensities, individuals of both parasitic species showed preference for the anterior small intestine. In concurrent infections and with different intensities, the distribution of G. palmipedis did not change when G. repandum was present; however, displacement of G. repandum toward the middle of the small intestine was observed. Glypthelmins species used the same microhabitat and presumably the same food resource and were generally found to overlap more than expected by chance. This finding suggests the possibility of different feeding mechanisms given by differences in their pharynx size by 37%. Also, the coexistence of these could be associated with the differentiation of realized niches.

Children's Internet use in a family context: influence on family relationships and parental mediation.

PubMed

Lee, Sook-Jung; Chae, Young-Gil

2007-10-01

We conducted a survey of 222 fourth-, fifth-, and sixth-grade Korean children to examine (a) whether children's Internet use influences declines in family time and family communication and (b) how parental mediation techniques are related to children's online activities. According to the findings, total time using the Internet was related to perceived declines in family time but not related to family communication. The influence of the Internet on family time and family communication differed by the type of children's online activities. The analysis of the relationship between parental mediation techniques and children's online activities indicated that parents' recommendation of useful Web sites and co-using were positively related to frequency of children's educational online activities. However, parental restrictions on time and Web sites did not alter children's actual Internet usage.

Genetic diversity in Echinococcus shiquicus from the plateau pika (Ochotona curzoniae) in Darlag County, Qinghai, China.

PubMed

Fan, Yan-Lei; Lou, Zhong-Zi; Li, Li; Yan, Hong-Bin; Liu, Quan-Yuan; Zhan, Fang; Li, Jian-Qiu; Liu, Cong-Nuan; Cai, Jin-Zhong; Lei, Meng-Tong; Shi, Wan-Gui; Yang, Yu-Rong; McManus, Donald P; Jia, Wan-Zhong

2016-11-01

The metacestode of Echinococcus shiquicus has been recorded previously in the lung and liver of its intermediate host, the plateau pika (Ochotona curzoniae), but there is limited information regarding other organ sites. There is also limited evidence of intra-specific genetic variation within E. shiquicus. A PCR-amplified mitochondrial (mt) nad1 gene fragment (approximately 1400bp in size), with unique EcoRI and SspI restriction sites, was used to distinguish cysts or cyst-like lesions of E. shiquicus from E. multilocularis. Then, the complete mt nad1 and cox1 genes for the E. shiquicus isolates were amplified and sequenced. Phylogenetic tree and haplotype network analyses for the isolates were then generated based on a concatenated dataset of the nad1 and cox1 genes using the neighbour-joining (NJ) method and TCS1.21 software. Nineteen of eighty trapped pikas were found to harbor cysts (71 in total) when dissected at the survey site. Seventeen animals had cysts (fertile) present only in the lungs, one animal had fertile cysts in the lungs and spleen, and one individual had an infertile kidney cyst. Restriction endonuclease analysis of a fragment of the nad1 gene indicated all the cysts were due to E. shiquicus. Genetic diversity analysis revealed that the nad1 and cox1 genes varied by 0.1-1.2% and 0.1-1.0%, respectively. Haplotype network analysis of the concatenated nad1 and cox1 sequences of the isolates showed they were classified into at least 6 haplotypes, and different haplotype percentages ranged from 4.2% to 29.6%. Although, high haplotype diversity was evident in the study area, the complete nad1 and cox1 gene sequences obtained indicated that all samples represented isolates of E. shiquicus. The study has also provided a new PCR-restriction endonuclease-based method to rapidly distinguish E. shiquicus from E. multilocularis which provides a useful tool for epidemiological investigations where the two species overlap. Copyright © 2016. Published by Elsevier B.V.

Trace elements have limited utility for studying migratory connectivity in shorebirds that winter in Argentina

USGS Publications Warehouse

Torres-Dowdall, J.; Farmer, A.H.; Abril, M.; Bucher, E.H.; Ridley, I.

2010-01-01

Trace-element analysis has been suggested as a tool for the study of migratory connectivity because (1) trace-element abundance varies spatially in the environment, (2) trace elements are assimilated into animals' tissues through the diet, and (3) current technology permits the analysis of multiple trace elements in a small tissue sample, allowing the simultaneous exploration of several elements. We explored the potential of trace elements (B, Na, Mg, Al, Si, P, S, K, Ca, Ti, Cr, Mn, Ni, Cu, Zn, As, Sr, Cs, Hg, Tl, Pb, Bi, Th, and U) to clarify the migratory connectivity of shorebirds that breed in North America and winter in southern South America. We collected 66 recently replaced secondary feathers from Red Knots (Calidris canutus) at three sites in Patagonia and 76 from White-rumped Sandpipers (C. fuscicollis) at nine sites across Argentina. There were significant differences in trace-element abundance in shorebird feathers grown at different nonbreeding sites, and annual variability within a site was small compared to variability among sites. Across Argentina, there was no large-scale gradient in trace elements. The lack of such a gradient restricts the application of this technique to questions concerning the origin of shorebirds to a small number of discrete sites. Furthermore, our results including three additional species, the Pectoral Sandpiper (C. melanotos), Wilson's Phalarope (Phalaropus tricolor), and Collared Plover (Charadrius collaris), suggest that trace-element profiles change as feathers age. Temporal instability of trace-element values could undermine their application to the study of migratory connectivity in shorebirds. ?? The Cooper Ornithological Society 2010.

Factors controlling the establishment of Fremont cottonwood seedlings on the Upper Green River, USA

USGS Publications Warehouse

Cooper, David J.; Merritt, David M.; Andersen, Douglas C.; Chimner, Rodney A.

1999-01-01

Declines in cottonwood (Populus spp.) recruitment along alluvial reaches of large rivers in arid regions of the western United States have been attributed to modified flow regimes, lack of suitable substrate, insufficient seed rain, and increased interspecific competition. We evaluated whether and how these factors were operating during 1993–1996 to influence demographics of Fremont cottonwood (P. deltoides Marshall subsp. wislizenii (Watson) Eckenwalder) along reaches of the Green and Yampa Rivers near their confluence in northwestern Colorado. We examined seedling establishment, defined as survival through three growing seasons, at three alluvial reaches that differed primarily in the level of flow regulation: a site on the unregulated Yampa, an upper Green River site regulated by Flaming Gorge Dam, and a lower Green River site below the Green–Yampa confluence. Seed rain was abundant in all sites, and led to large numbers of germinants (first-year seedlings) appearing each year at all sites. The regulated flow in the upper Green River reach restricted germination to islands and cut banks that were later inundated or eroded; no seedlings survived there. Mortality at the lower Green River site was due largely to desiccation or substrate erosion; 23% of 1993 germinants survived their first growing season, but at most 2% survived through their second. At the Yampa River site, germinants appeared on vegetated and unvegetated surfaces up to 2.5 m above base flow stage, but survived to autumn only on bare surfaces at least 1.25 m above base flow stage, and where at least 10 of the upper 40 cm of the alluvium was fine-textured. Our studies of rooting depths and the stable isotopic composition of xylem water showed that seedlings in the most favorable locations for establishment at the Yampa site do not become phreatophytic until their third or fourth growing season. Further, the results of experimental field studies examining effects of shade and competition supported the hypothesis that insufficient soil moisture, possibly in combination with insufficient light, restricts establishment to unvegetated sites. Collectively, the demographic and experimental studies suggest that, in arid regions, soil water availability is at least as important as light level in limiting establishment of Fremont cottonwood seedlings. We hypothesize that in cases where arid land rivers experience large spring stage changes, recruitment is further constrained within bare areas to those sites that contain sufficient fine-textured alluvium, saturated during the spring flood, to provide the flood-derived soil moisture normally necessary for late-summer seedling survival.

Gene Inactivation by CRISPR-Cas9 in Nicotiana tabacum BY-2 Suspension Cells.

PubMed

Mercx, Sébastien; Tollet, Jérémie; Magy, Bertrand; Navarre, Catherine; Boutry, Marc

2016-01-01

Plant suspension cells are interesting hosts for the heterologous production of pharmacological proteins such as antibodies. They have the advantage to facilitate the containment and the application of good manufacturing practices. Furthermore, antibodies can be secreted to the extracellular medium, which makes the purification steps much simpler. However, improvements are still to be made regarding the quality and the production yield. For instance, the inactivation of proteases and the humanization of glycosylation are both important targets which require either gene silencing or gene inactivation. To this purpose, CRISPR-Cas9 is a very promising technique which has been used recently in a series of plant species, but not yet in plant suspension cells. Here, we sought to use the CRISPR-Cas9 system for gene inactivation in Nicotiana tabacum BY-2 suspension cells. We transformed a transgenic line expressing a red fluorescent protein (mCherry) with a binary vector containing genes coding for Cas9 and three guide RNAs targeting mCherry restriction sites, as well as a bialaphos-resistant (bar) gene for selection. To demonstrate gene inactivation in the transgenic lines, the mCherry gene was PCR-amplified and analyzed by electrophoresis. Seven out of 20 transformants displayed a shortened fragment, indicating that a deletion occurred between two target sites. We also analyzed the transformants by restriction fragment length polymorphism and observed that the three targeted restriction sites were hit. DNA sequencing of the PCR fragments confirmed either deletion between two target sites or single nucleotide deletion. We therefore conclude that CRISPR-Cas9 can be used in N. tabacum BY2 cells.

1995 Report on Hanford site land disposal restrictions for mixed waste

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

Black, D.G.

This report was submitted to meet the requirements of Hanford Federal Facility Agreement and Consent Order Milestone M-26-01E. This milestone requires the preparation of an annual report that covers characterization, treatment, storage, minimization, and other aspects of land disposal restricted mixed waste at the Hanford Site. The U.S. Department of Energy, its predecessors, and contractors at the Hanford Site were involved in the production and purification of nuclear defense materials from the early 1940s to the late 1980s. These production activities have generated large quantities of liquid and solid radioactive mixed waste. This waste is subject to regulation under authoritymore » of both the Resource Conservation and Recovery Act of 1976 and Atomic Energy Act of 1954. This report covers mixed waste only. The Washington State Department of Ecology, U.S. Environmental Protection Agency, and U.S. Department of Energy have entered into an agreement, the Hanford Federal Facility Agreement and Consent Order (commonly referred to as the Tri-Party Agreement) to bring the Hanford Site operations into compliance with dangerous waste regulations. The Tri-Party Agreement required development of the original land disposal restrictions (LDRs) plan and its annual updates to comply with LDR requirements for radioactive mixed waste. This report is the fifth update of the plan first issued in 1990. Tri-Party Agreement negotiations completed in 1993 and approved in January 1994 changed and added many new milestones. Most of the changes were related to the Tank Waste Remediation System and these changes are incorporated into this report.« less

Health assessment for Midwest Industrial Waste Disposal Company, Inc. (Midco II) NPL (National Priorities List) Site, 5900 Industrial Highway, Gary, Indiana, Region 5. CERCLIS No. IND980679559. Final report

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

Not Available

1989-04-12

The 7-acre Midco II Site is located at 5900 Industrial Highway, Gary, Indiana. The site is listed on the National Priorities List. Various heavy metals, inorganic, and organic compounds were found in the media on-site. The environmental media of concern at the site are ground water, surface water, and soil. Although access to the Midco II site is restricted, the contaminants detected on-site will continue to migrate and may pose health threats until remedial activities are completed. Therefore, the Midco II site poses a potential health concern until an evaluation of the site is completed and remedial activities are chosen.

Land Use Withdrawal, McGregor Range, Fort Bliss, Texas

DTIC Science & Technology

1977-08-01

Range by armoured vehicles to existing maneuver areas south of McGregor Range Camp. j. Cease joint training exercises requiring the use of the basin...Maneuvers: Site Avoidance a. Implement all measures called for in Alternative 1 except i. and j., restriction of armoured vehicle use. b. Define...Maneuvers. District Avcidance a. Implement all measures called for in Alternative 1 except i. and j. restriction of armoured vehicle use. b. Define

How Public Is the Web?: Robots, Access, and Scholarly Communication.

ERIC Educational Resources Information Center

Snyder, Herbert; Rosenbaum, Howard

1998-01-01

Examines the use of Robot Exclusion Protocol (REP) to restrict the access of search engine robots to 10 major United States university Web sites. An analysis of Web site searching and interviews with Web server administrators shows that the decision to use this procedure is largely technical and is typically made by the Web server administrator.…

Sequence analysis of serum albumins reveals the molecular evolution of ligand recognition properties.

PubMed

Fanali, Gabriella; Ascenzi, Paolo; Bernardi, Giorgio; Fasano, Mauro

2012-01-01

Serum albumin (SA) is a circulating protein providing a depot and carrier for many endogenous and exogenous compounds. At least seven major binding sites have been identified by structural and functional investigations mainly in human SA. SA is conserved in vertebrates, with at least 49 entries in protein sequence databases. The multiple sequence analysis of this set of entries leads to the definition of a cladistic tree for the molecular evolution of SA orthologs in vertebrates, thus showing the clustering of the considered species, with lamprey SAs (Lethenteron japonicum and Petromyzon marinus) in a separate outgroup. Sequence analysis aimed at searching conserved domains revealed that most SA sequences are made up by three repeated domains (about 600 residues), as extensively characterized for human SA. On the contrary, lamprey SAs are giant proteins (about 1400 residues) comprising seven repeated domains. The phylogenetic analysis of the SA family reveals a stringent correlation with the taxonomic classification of the species available in sequence databases. A focused inspection of the sequences of ligand binding sites in SA revealed that in all sites most residues involved in ligand binding are conserved, although the versatility towards different ligands could be peculiar of higher organisms. Moreover, the analysis of molecular links between the different sites suggests that allosteric modulation mechanisms could be restricted to higher vertebrates.

Are women aware of religious restrictions on reproductive health at Catholic hospitals? A survey of women's expectations and preferences for family planning care.

PubMed

Guiahi, Maryam; Sheeder, Jeanelle; Teal, Stephanie

2014-10-01

To understand if women anticipate a difference in reproductive healthcare when attending a Catholic institution. A convenience sample of reproductive-aged women in the Denver metro area completed an online survey. Women were randomized to hypothetical women's health clinics at either a secular or Catholic hospital and asked about expectations for family planning care. Questions covered contraception and management of abnormal or unintended pregnancy. We subsequently assessed provider/site preferences for care. We analyzed 236 surveys. The majority of participants expected their gynecologist to provide all family planning services presented. The only difference based on institution was that participants randomized to the Catholic hospital were more likely to expect natural family planning advice. At least half of respondents reported they would seek care from their gynecologist for the services surveyed with the exceptions of emergency contraception and elective abortion. Overall, this cohort of women did not anticipate differences in reproductive healthcare based on institution. If women who enroll at Catholic hospitals do not receive information related to potential healthcare restrictions, their ability to act as informed healthcare consumers may be constrained. Women did not anticipate differences in reproductive healthcare based on institution type (Catholic vs. secular) and, thus, their ability to act as informed healthcare consumers may be constrained. Copyright © 2014 Elsevier Inc. All rights reserved.

Investigations of α-helix↔β-sheet transition pathways in a miniprotein using the finite-temperature string method

PubMed Central

Ovchinnikov, Victor; Karplus, Martin

2014-01-01

A parallel implementation of the finite-temperature string method is described, which takes into account the invariance of coordinates with respect to rigid-body motions. The method is applied to the complex α-helix↔β-sheet transition in a β-hairpin miniprotein in implicit solvent, which exhibits much of the complexity of conformational changes in proteins. Two transition paths are considered, one derived from a linear interpolant between the endpoint structures and the other derived from a targeted dynamics simulation. Two methods for computing the conformational free energy (FE) along the string are compared, a restrained method, and a tessellation method introduced by E. Vanden-Eijnden and M. Venturoli [J. Chem. Phys. 130, 194103 (2009)]. It is found that obtaining meaningful free energy profiles using the present atom-based coordinates requires restricting sampling to a vicinity of the converged path, where the hyperplanar approximation to the isocommittor surface is sufficiently accurate. This sampling restriction can be easily achieved using restraints or constraints. The endpoint FE differences computed from the FE profiles are validated by comparison with previous calculations using a path-independent confinement method. The FE profiles are decomposed into the enthalpic and entropic contributions, and it is shown that the entropy difference contribution can be as large as 10 kcal/mol for intermediate regions along the path, compared to 15–20 kcal/mol for the enthalpy contribution. This result demonstrates that enthalpic barriers for transitions are offset by entropic contributions arising from the existence of different paths across a barrier. The possibility of using systematically coarse-grained representations of amino acids, in the spirit of multiple interaction site residue models, is proposed as a means to avoid ad hoc sampling restrictions to narrow transition tubes. PMID:24811667

Investigations of α-helix↔β-sheet transition pathways in a miniprotein using the finite-temperature string method

NASA Astrophysics Data System (ADS)

Ovchinnikov, Victor; Karplus, Martin

2014-05-01

A parallel implementation of the finite-temperature string method is described, which takes into account the invariance of coordinates with respect to rigid-body motions. The method is applied to the complex α-helix↔β-sheet transition in a β-hairpin miniprotein in implicit solvent, which exhibits much of the complexity of conformational changes in proteins. Two transition paths are considered, one derived from a linear interpolant between the endpoint structures and the other derived from a targeted dynamics simulation. Two methods for computing the conformational free energy (FE) along the string are compared, a restrained method, and a tessellation method introduced by E. Vanden-Eijnden and M. Venturoli [J. Chem. Phys. 130, 194103 (2009)]. It is found that obtaining meaningful free energy profiles using the present atom-based coordinates requires restricting sampling to a vicinity of the converged path, where the hyperplanar approximation to the isocommittor surface is sufficiently accurate. This sampling restriction can be easily achieved using restraints or constraints. The endpoint FE differences computed from the FE profiles are validated by comparison with previous calculations using a path-independent confinement method. The FE profiles are decomposed into the enthalpic and entropic contributions, and it is shown that the entropy difference contribution can be as large as 10 kcal/mol for intermediate regions along the path, compared to 15-20 kcal/mol for the enthalpy contribution. This result demonstrates that enthalpic barriers for transitions are offset by entropic contributions arising from the existence of different paths across a barrier. The possibility of using systematically coarse-grained representations of amino acids, in the spirit of multiple interaction site residue models, is proposed as a means to avoid ad hoc sampling restrictions to narrow transition tubes.

RNA viruses can hijack vertebrate microRNAs to suppress innate immunity

NASA Astrophysics Data System (ADS)

Trobaugh, Derek W.; Gardner, Christina L.; Sun, Chengqun; Haddow, Andrew D.; Wang, Eryu; Chapnik, Elik; Mildner, Alexander; Weaver, Scott C.; Ryman, Kate D.; Klimstra, William B.

2014-02-01

Currently, there is little evidence for a notable role of the vertebrate microRNA (miRNA) system in the pathogenesis of RNA viruses. This is primarily attributed to the ease with which these viruses mutate to disrupt recognition and growth suppression by host miRNAs. Here we report that the haematopoietic-cell-specific miRNA miR-142-3p potently restricts the replication of the mosquito-borne North American eastern equine encephalitis virus in myeloid-lineage cells by binding to sites in the 3' non-translated region of its RNA genome. However, by limiting myeloid cell tropism and consequent innate immunity induction, this restriction directly promotes neurologic disease manifestations characteristic of eastern equine encephalitis virus infection in humans. Furthermore, the region containing the miR-142-3p binding sites is essential for efficient virus infection of mosquito vectors. We propose that RNA viruses can adapt to use antiviral properties of vertebrate miRNAs to limit replication in particular cell types and that this restriction can lead to exacerbation of disease severity.

Games, Simulations and Virtual Labs for Science Education: a Compendium and Some Examples

NASA Astrophysics Data System (ADS)

Russell, R. M.

2012-12-01

We have assembled a list of computer-based simulations, games, and virtual labs for science education. This list, with links to the sources of these resources, is available online. The entries span a broad range of science, math, and engineering topics. They also span a range of target student ages, from elementary school to university students. We will provide a brief overview of this web site and the resources found on it. We will also briefly demonstrate some of our own educational simulations and games. Computer-based simulations and virtual labs are valuable resources for science educators in various settings, allowing learners to experiment and explore "what if" scenarios. Educational computer games can motivate learners in both formal and informal settings, encouraging them to spend much more time exploring a topic than they might otherwise be inclined to do. Part of this presentation is effectively a "literature review" of numerous sources of simulations, games, and virtual labs. Although we have encountered several nice collections of such resources, those collections seem to be restricted in scope. They either represent materials developed by a specific group or agency (e.g. NOAA's games web site) or are restricted to a specific discipline (e.g. geology simulations and virtual labs). This presentation directs viewers to games, simulations, and virtual labs from many different sources and spanning a broad range of STEM disciplines.

Arabidopsis AIP1-2 restricted by WER-mediated patterning modulates planar polarity.

PubMed

Kiefer, Christian S; Claes, Andrea R; Nzayisenga, Jean-Claude; Pietra, Stefano; Stanislas, Thomas; Hüser, Anke; Ikeda, Yoshihisa; Grebe, Markus

2015-01-01

The coordination of cell polarity within the plane of the tissue layer (planar polarity) is crucial for the development of diverse multicellular organisms. Small Rac/Rho-family GTPases and the actin cytoskeleton contribute to planar polarity formation at sites of polarity establishment in animals and plants. Yet, upstream pathways coordinating planar polarity differ strikingly between kingdoms. In the root of Arabidopsis thaliana, a concentration gradient of the phytohormone auxin coordinates polar recruitment of Rho-of-plant (ROP) to sites of polar epidermal hair initiation. However, little is known about cytoskeletal components and interactions that contribute to this planar polarity or about their relation to the patterning machinery. Here, we show that ACTIN7 (ACT7) represents a main actin isoform required for planar polarity of root hair positioning, interacting with the negative modulator ACTIN-INTERACTING PROTEIN1-2 (AIP1-2). ACT7, AIP1-2 and their genetic interaction are required for coordinated planar polarity of ROP downstream of ethylene signalling. Strikingly, AIP1-2 displays hair cell file-enriched expression, restricted by WEREWOLF (WER)-dependent patterning and modified by ethylene and auxin action. Hence, our findings reveal AIP1-2, expressed under control of the WER-dependent patterning machinery and the ethylene signalling pathway, as a modulator of actin-mediated planar polarity. © 2015. Published by The Company of Biologists Ltd.

A molecular switch sensor for detection of PRSS1 genotype based on site-specific DNA cleavage of restriction endonuclease.

PubMed

Liu, Qicai; Gao, Feng; Weng, Shaohuang; Peng, Huaping; Lin, Liqing; Zhao, Chengfei; Lin, Xinhua

2015-01-01

PRSS1 mutations or polymorphism in the peripheral blood of patients can be used as susceptible molecular markers to pancreatic cancer. A sensor for selective electrochemical detection of PRSS1 genotypes was developed based on site-specific DNA cleavage of restriction endonuclease EcoRI. A mercapto-modified hairpin probe was immobilized on a gold electrode. The probe's neck can be cleaved by EcoRI in the absence of rs10273639 C/C of PRSS1 genotype, but it cannot be cleaved in the presence of T/T. The difference in quantity of electric charge was monitored by biosensors before and after enzymatic cleavage. Electrochemical signals are generated by differential pulse voltammetry interrogation of methylene blue (MB) that quantitatively binds to surface-confined hairpin probe via electrostatic interactions. The results suggested this method had a good specificity in distinguishing PRSS1 genotypes. There was a good linear relationship between the charge and the logarithmic function of PRSS1 rs10273639 T/T type DNA concentration (current=120.6303+8.8512log C, R=0.9942). The detection limit was estimated at 0.5 fM. The molecular switch sensor has several advantages, and it is possible to qualitatively, quantitatively, and noninvasively detect PRSS1 genotypes in the blood of patients with pancreatic cancer. © 2015 by the Association of Clinical Scientists, Inc.

Genetic consequences of Quaternary climatic oscillations in the Himalayas: Primula tibetica as a case study based on restriction site-associated DNA sequencing.

PubMed

Ren, Guangpeng; Mateo, Rubén G; Liu, Jianquan; Suchan, Tomasz; Alvarez, Nadir; Guisan, Antoine; Conti, Elena; Salamin, Nicolas

2017-02-01

The effects of Quaternary climatic oscillations on the demography of organisms vary across regions and continents. In taxa distributed in Europe and North America, several paradigms regarding the distribution of refugia have been identified. By contrast, less is known about the processes that shaped the species' spatial genetic structure in areas such as the Himalayas, which is considered a biodiversity hotspot. Here, we investigated the phylogeographic structure and population dynamics of Primula tibetica by combining genomic phylogeography and species distribution models (SDMs). Genomic data were obtained for 293 samples of P. tibetica using restriction site-associated DNA sequencing (RADseq). Ensemble SDMs were carried out to predict potential present and past distribution ranges. Four distinct lineages were identified. Approximate Bayesian computation analyses showed that each of them have experienced both expansions and bottlenecks since their divergence, which occurred during or across the Quaternary glacial cycles. The two lineages at both edges of the distribution were found to be more vulnerable and responded in different ways to past climatic changes. These results illustrate how past climatic changes affected the demographic history of Himalayan organisms. Our findings highlight the significance of combining genomic approaches with environmental data when evaluating the effects of past climatic changes. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

The value of Web-based library services at Cedars-Sinai Health System.

PubMed

Halub, L P

1999-07-01

Cedars-Sinai Medical Library/Information Center has maintained Web-based services since 1995 on the Cedars-Sinai Health System network. In that time, the librarians have found the provision of Web-based services to be a very worthwhile endeavor. Library users value the services that they access from their desktops because the services save time. They also appreciate being able to access services at their convenience, without restriction by the library's hours of operation. The library values its Web site because it brings increased visibility within the health system, and it enables library staff to expand services when budget restrictions have forced reduced hours of operation. In creating and maintaining the information center Web site, the librarians have learned the following lessons: consider the design carefully; offer what services you can, but weigh the advantages of providing the services against the time required to maintain them; make the content as accessible as possible; promote your Web site; and make friends in other departments, especially information services.

The value of Web-based library services at Cedars-Sinai Health System.

PubMed Central

Halub, L P

1999-01-01

Cedars-Sinai Medical Library/Information Center has maintained Web-based services since 1995 on the Cedars-Sinai Health System network. In that time, the librarians have found the provision of Web-based services to be a very worthwhile endeavor. Library users value the services that they access from their desktops because the services save time. They also appreciate being able to access services at their convenience, without restriction by the library's hours of operation. The library values its Web site because it brings increased visibility within the health system, and it enables library staff to expand services when budget restrictions have forced reduced hours of operation. In creating and maintaining the information center Web site, the librarians have learned the following lessons: consider the design carefully; offer what services you can, but weigh the advantages of providing the services against the time required to maintain them; make the content as accessible as possible; promote your Web site; and make friends in other departments, especially information services. PMID:10427423

Simulation of Tracer Concentration Data in the Brush Creek Drainage Flow Using an Integrated Puff Model.

NASA Astrophysics Data System (ADS)

Rao, K. Shankar; Eckman, Richard M.; Hosker, Rayford P., Jr.

1989-07-01

During the 1984 ASCOT field study in Brush Creek Valley, two perfluorocarbon tracers were released into the nocturnal drainage flow at two different heights. The resulting surface concentrations were sampled at 90 sites, and vertical concentration profiles at 11 sites. These detailed tracer measurements provide a valuable dataset for developing and testing models of pollutant transport and dispersion in valleys.In this paper, we present the results of Gaussian puff model simulations of the tracer releases in Brush Creek Valley. The model was modified to account for the restricted lateral dispersion in the valley, and for the gross elevation differences between the release site and the receptors. The variable wind fields needed to transport the puffs were obtained by interpolation between wind profiles measured using tethered balloons at five along-valley sites. Direct turbulence measurements were used to estimate diffusion. Subsidence in the valley flow was included for elevated releases.Two test simulations-covering different nights, tracers, and release heights-were performed. The predicted hourly concentrations were compared with observations at 51 ground-level locations. At most sites, the predicted and observed concentrations agree within a factor of 2 to 6. For the elevated release simulation, the observed mean concentration is 40 pL/L, the predicted mean is 21 pL/L, the correlation coefficient between the observed and predicted concentrations is 0.24, and the index of agreement is 0.46. For the surface release simulation, the observed mean is 85 pL/L, and the predicted mean is 73 pL/L. The correlation coefficient is 0.23, and the index of agreement is 0.42. The results suggest that this modified puff model can be used as a practical tool for simulating pollutant transport and dispersion in deep valleys.

Superfund record of decision (EPA Region 4): USMC Camp Lejeune Military Reservation, operable unit 4, Jacksonville, NC, January 16, 1996

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

NONE

1996-05-01

This operable unit consists of Sites 41 and 74. The remedial actions are designed to prevent future potential exposure by implementing institutional controls. These controls include: (1) designate the sites as `restricted` or `limited use` areas, within the base master plan; (2) prohibit the installation of potable water supply wells within the vicinity of the sites: and (3) implement a groundwater, surface water and sediment monitoring program.

Shifts in phylogenetic diversity of archaeal communities in mangrove sediments at different sites and depths in southeastern Brazil.

PubMed

Mendes, Lucas William; Taketani, Rodrigo Gouvêa; Navarrete, Acácio Aparecido; Tsai, Siu Mui

2012-06-01

This study focused on the structure and composition of archaeal communities in sediments of tropical mangroves in order to obtain sufficient insight into two Brazilian sites from different locations (one pristine and another located in an urban area) and at different depth levels from the surface. Terminal restriction fragment length polymorphism (T-RFLP) of PCR-amplified 16S rRNA gene fragments was used to scan the archaeal community structure, and 16S rRNA gene clone libraries were used to determine the community composition. Redundancy analysis of T-RFLP patterns revealed differences in archaeal community structure according to location, depth and soil attributes. Parameters such as pH, organic matter, potassium and magnesium presented significant correlation with general community structure. Furthermore, phylogenetic analysis revealed a community composition distributed differently according to depth where, in shallow samples, 74.3% of sequences were affiliated with Euryarchaeota and 25.7% were shared between Crenarchaeota and Thaumarchaeota, while for the deeper samples, 24.3% of the sequences were affiliated with Euryarchaeota and 75.7% with Crenarchaeota and Thaumarchaeota. Archaeal diversity measurements based on 16S rRNA gene clone libraries decreased with increasing depth and there was a greater difference between depths (<18% of sequences shared) than sites (>25% of sequences shared). Taken together, our findings indicate that mangrove ecosystems support a diverse archaeal community; it might possibly be involved in nutrient cycles and are affected by sediment properties, depth and distinct locations. Copyright © 2012 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Null effect of dietary restriction on prostate carcinogenesis in the Wistar-Unilever rat.

PubMed

McCormick, David L; Johnson, William D; Haryu, Todd M; Bosland, Maarten C; Lubet, Ronald A; Steele, Vernon E

2007-01-01

Chronic dietary restriction inhibits carcinogenesis in several sites in laboratory animals. To determine the effects of dietary restriction on prostate carcinogenesis, prostate cancers were induced in male Wistar-Unilever rats by a sequential regimen of cyproterone acetate (50 mg/day; 21 days); testosterone propionate (100 mg/kg/day; 3 days); N-methyl-N-nitrosourea [MNU; 30 mg/kg; single dose]; and testosterone (subcutaneous implants of 2 pellets containing 40 mg each). Dietary restriction (0% [ad libitum control], 15%, or 30%) was initiated 2 wk post-MNU, and continued until study termination at 12 mo. Dietary restriction induced a rapid suppression of body weight gain but conferred no protection against prostate carcinogenesis. 74% of carcinogen-treated ad libitum controls developed accessory sex gland cancers, versus cancer incidences of 64% and 72% in groups restricted by 15% and 30%, respectively. Similarly, 44% of dietary controls developed cancers limited to the dorsolateral/prostate, versus incidences of 45% and 53% in groups restricted by 15% and 30%. The results of the present study do not support the hypothesis that prostate carcinogenesis can be prevented by reducing caloric intake. Reducing mean body weight by up to 25% through chronic dietary restriction has no effect on the induction of prostate cancers in the Wistar-Unilever rat model.

JUBA (Joint UAS-Balloon Activities) Final Campaign Report.

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

Dexheimer, Darielle; Apple, Monty; Callow, Diane Schafer

Using internal investment funds within Sandia National Laboratories’ (SNL) Division 6000, JUBA was a collaborative exercise between SNL Orgs. 6533 & 6913 (later 8863) to demonstrate simultaneous flights of tethered balloons and UAS on the North Slope of Alaska. JUBA UAS and tethered balloon flights were conducted within the Restricted Airspace associated with the ARM AMF3 site at Oliktok Point, Alaska. The Restricted Airspace occupies a 2 nautical mile radius around Oliktok Point. JUBA was conducted at the Sandia Arctic Site, which is approximately 2 km east-southeast of the AMF3. JUBA activities occurred from 08/08/17 – 08/10/17. Atmospheric measurements frommore » tethered balloons can occur for a long duration, but offer limited spatial variation. Measurements from UAS could offer increased spatial variability.« less

Variation in Ribosomal DNA among Isolates of the Mycorrhizal Fungus Cenococcum Geophilum FR.

NASA Astrophysics Data System (ADS)

Lobuglio, Katherine Frances

1990-01-01

Cenococcum geophilum Fr., a cosmopolitan mycorrhizal fungus, is well-known for its extremely wide host and habitat range. The ecological diversity of C. geophilum sharply contrasts its present taxonomic status as a monotypic form -genus. Restriction fragment length polymorphisms (RFLPs) in nuclear ribosomal DNA (rDNA) was used to assess the degree of genetic variation among 72 isolates of C. geophilum. The probe used in this study was the rDNA repeat cloned from C. geophilum isolate A145 (pCG15). Length of the rDNA repeat was approximately 9 kb. The rDNA clone was mapped for 5 restriction endonucleases. Hybridization with cloned Saccharomyces cerevisiae rDNA (pSR118, and pSR125 containing the 18S, and 5.8-25S rRNA genes respectively), and alignment of restriction endonuclease sites conserved in the rDNA genes of other fungi, were used to position the corresponding rDNAs of C. geophilum. Southern hybridizations with EcoRI, HindIII, XhoI, and PstI digested DNAs indicated extensive variation among the C. geophilum isolates, greater than has been previously reported to occur within a fungal species. Most of the rDNA polymorphisms occurred in the IGS region. Restriction endonuclease site and length polymorphisms were also observed in the 5.8S-26S genic regions. Sixteen size categories of length mutations, 6 restriction endonuclease site additions, and 4 restriction endonuclease site deletions were determined using isolate A145 as a reference. The rDNA repeat length among the isolates varied from approximately 8.5 to 10.2 kb. RFLPs were also observed in the mitochondrial (mt) 24S rRNA gene and flanking regions of HindIII digested DNAs of C. geophilum isolates representing both geographically distinct and similar origins. Among the C. geophilum isolates analyzed there were fewer RFLPs in mt-DNA than in nuclear rDNA. EcoRI rDNA phenotypes between C. geophilum and Elaphomyces anthracinus, its proposed teleomorph or sexual state, did not correspond. In addition, the four Elaphomyces species examined had smaller rDNA repeat sizes (approximately 7.3 to 8.0 kb) than that observed among C. geophilum isolates. UPGMA cluster analysis grouped C. geophilum isolates, on the basis of shared nuclear rDNA phenotypes, into a broad range of clusters ranging from 100% to 44% similarity. Limited correlation was observed among nuclear rDNA phenotypes and culture morphology, mycorrhizal characteristics, or geographic origins of the isolates. The amount of genetic variation demonstrated in this study indicates that C. geophilum is either an extremely heterogenous species or it represents more than one species and possibly more than one genus.

Estimating the scale of adverse animal welfare consequences of movement restriction and mitigation strategies in a classical swine fever outbreak.

PubMed

Yadav, Shankar; Weng, Hsin-Yi

2017-04-04

The study aim was to quantify the impact of movement restriction on the well-being of pigs and the associated mitigation responses during a classical swine fever (CSF) outbreak. We developed a stochastic risk assessment model and incorporated Indiana swine industry statistics to estimate the timing and number of swine premises that would encounter overcrowding or feed interruption resulting from movement restriction. Our model also quantified the amount of on-farm euthanasia and movement of pigs to slaughter plants required to alleviate those conditions. We simulated various single-site (i.e., an outbreak initiated from one location) and multiple-site (i.e., an outbreak initiated from more than one location) outbreak scenarios in Indiana to estimate outputs. The study estimated that 14% of the swine premises in Indiana would encounter overcrowding or feed interruption due to movement restriction implemented during a CSF outbreak. The number of premises that would experience animal welfare conditions was about 2.5 fold of the number of infected premises. On-farm euthanasia needed to be performed on 33% of those swine premises to alleviate adverse animal welfare conditions, and more than 90% of on-farm euthanasia had to be carried out within 2 weeks after the implementation of movement restriction. Conversely, movement of pigs to slaughter plants could alleviate 67% of adverse animal welfare conditions due to movement restriction, and only less than 1% of movement of pigs to slaughter plants had to be initiated in the first 2 weeks of movement restrictions. The risk of secondary outbreaks due to movement of pigs from movement restriction areas to slaughter plants was low and only seven pigs from each shipment needed to be tested for CSF infection to prevent a secondary outbreak. We found that the scale of adverse animal welfare consequences of movement restriction during a CSF outbreak in Indiana was substantial, and controlled movement of pigs to slaughter plants was an efficient and low-risk alternative mitigation response to on-farm euthanasia. The output estimates generated from this study provide empirical evidence for decision makers to properly incorporate required resources for mitigating adverse animal welfare conditions in CSF outbreak management strategic planning.

2009 Defense Supply Center Columbus Land and Maritime Supply Chains: Business Conference and Exhibition

DTIC Science & Technology

2009-08-19

DSN: 388-7453 CSCASSIG@CSD.DISA.MIL  DFAS eCommerce web site http://www.dfas.mil/contractorpay/electroniccommerce.html  DFAS Customer Service...M-ATV is a separate category within the MRAP family of vehicles. ►Mission: Small-unit combat operations in highly restricted rural , mountainous...vehicles. ►Mission: Small-unit combat operations in highly restricted rural , mountainous and urban environments. ► Troop Transport: Carry up to five

2009 Defense Supply Center Columbus Land and Maritime Supply Chains Business Conference and Exhibition

DTIC Science & Technology

2009-08-19

DSN: 388-7453 CSCASSIG@CSD.DISA.MIL  DFAS eCommerce web site http://www.dfas.mil/contractorpay/electroniccommerce.html  DFAS Customer Service...M-ATV is a separate category within the MRAP family of vehicles. ►Mission: Small-unit combat operations in highly restricted rural , mountainous...vehicles. ►Mission: Small-unit combat operations in highly restricted rural , mountainous and urban environments. ► Troop Transport: Carry up to five

D1/D2 domain of large-subunit ribosomal DNA for differentiation of Orpinomyces spp.

PubMed

Dagar, Sumit S; Kumar, Sanjay; Mudgil, Priti; Singh, Rameshwar; Puniya, Anil K

2011-09-01

This study presents the suitability of D1/D2 domain of large-subunit (LSU) ribosomal DNA (rDNA) for differentiation of Orpinomyces joyonii and Orpinomyces intercalaris based on PCR-restriction fragment length polymorphism (RFLP). A variation of G/T in O. intercalaris created an additional restriction site for AluI, which was used as an RFLP marker. The results demonstrate adequate heterogeneity in the LSU rDNA for species-level differentiation.

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

Graaff, E. de; Willemsen, R.; Zhong, N.

The molecular mechanism of the fragile X syndrome is based on the expansion of an CGG repeat in the 5{prime} UTR of the FMR1 gene in the majority of fragile X patients. This repeat displays instability both between individuals and within an individual. We studied the instability of the CGG repeat and the expression of the FMR1 protein (FMRP) in several different tissues derived from a male fragile X patient. Using Southern blot analysis, only a full mutation is detected in 9 of the 11 tissues tested. The lung tumor contains a methylated premutation of 160 repeats, whereas in themore » testis, besides the full mutation, a premutation of 60 CGG repeats is detected. Immunohistochemistry of the testis revealed expression of FMR1 in the spermatogonia only, confirming the previous finding that, in the sperm cells of fragile X patients with a full mutation in their blood cells, only a premutation is present. Immunohistochemistry of brain and lung tissue revealed that 1% of the cells are expressing the FMRP. PCR analysis demonstrated the presence of a premutation of 160 repeats in these FMR1-expressing cells. This indicates that the tumor was derived from a lung cell containing a premutation. Remarkably, despite the methylation of the EagI and BssHII sites, FMRP expression is detected in the tumor. Methylation of both restriction sites has thus far resulted in a 100% correlation with the lack of FMR1 expression, but the results found in the tumor suggest that the CpGs in these restriction sites are not essential for regulation of FMR1 expression. This indicates a need for a more accurate study of the exact promoter of FMR1. 54 refs., 4 figs.« less

Vitamin K Acupuncture Point Injection for Severe Primary Dysmenorrhea: An International Pilot Study

PubMed Central

Wang, Li; Zhao, Wenjie; Yu, Jin; Cardini, Francesco; Forcella, Emanuela; Regalia, Anna Laura; Wade, Christine

2004-01-01

Context Vitamin K acupuncture point injection, a menstrual pain treatment derived from traditional Chinese medicine, has been a standard treatment in some hospitals in China since the 1980s. Objectives To investigate the effects of vitamin K acupuncture point injection on menstrual pain in young women aged 14 to 25 from different countries and cultural backgrounds who have had unmitigated severe primary dysmenorrhea for 6 months or more Design Prospective, observational, clinical pilot study Settings One site in China (a hospital outpatient clinic in Shanghai) and 2 sites in Italy (a hospital clinic in Milan and a private gynecology practice in Verona) Interventions All subjects were treated with bilateral acupuncture point injection of vitamin K on the first or second day of menstrual pain. Vitamin K3 was used in China and vitamin K4 in Italy. Main Outcome Measures Pain intensity, total duration, and average intensity of menstrual distress, hours in bed, normal daily activity restrictions, and numbers of analgesic tablets taken to relieve pain were recorded before the treatment and for 4 subsequent menstrual cycles. Results Noticeable pain relief was observed 2 minutes after treatment, and subsequent pain reduction occurred at 30 minutes (P < .001). Subjects reported significantly fewer daily life restrictions, fewer hours in bed, less consumption of analgesic tablets, and lower scores of menstrual pain duration and intensity (P < .001). There were no adverse events. Some women experienced mild, self-limited pain at the injection site. Conclusion Acupuncture point injection with vitamin K alleviated acute menstrual pain, and relief extended through the nontreatment follow-up cycles in this uncontrolled pilot study conducted in 2 countries. Further investigation employing controlled experimental designs is warranted. PMID:15775872

Unfulfilled translation opportunities in industry sponsored clinical trials.

PubMed

Smed, Marie; Getz, Kenneth A

2013-05-01

Knowledge generated by site representatives through their participation in clinical trials is valuable for testing new products in use and obtaining final market approval. The leverage of this important knowledge is however challenged as the former direct relationships between in-house staff in the industry and site representatives are changing. The process of clinical trials has increased in complexity over the years, resulting in additional management layers. Besides an increase in internal management layers, sponsors often also outsource various tasks related to clinical trials to a CRO (Contract Research Organization) and thereby adding another link in the relationships between site and sponsor. These changes are intended to optimize the time-consuming and costly trial phases; however, there is a need to study whether valuable knowledge and experience is compromised in the process. Limited research exists on the full range of clinical practice insights obtained by investigators during and after clinical trials and how well these insights are transferred to study sponsors. This study explores the important knowledge-transfer processes between sites and sponsors and to what extent sites' knowledge gained in clinical trials is utilized by the industry. Responses from 451 global investigative site representatives are included in the study. The analysis of the extensive dataset reveals that the current processes of collaboration between sites and the industry restrict the leverage of valuable knowledge gained by physicians in the process of clinical trials. These restrictions to knowledge-transfer between site and sponsor are further challenged if CRO partners are integrated in the trial process. Copyright © 2013 Elsevier Inc. All rights reserved.

30 CFR 46.11 - Site-specific hazard awareness training.

Code of Federal Regulations, 2011 CFR

2011-07-01

... environmental conditions, recognition and avoidance of hazards such as electrical and powered-haulage hazards, traffic patterns and control, and restricted areas; and warning and evacuation signals, evacuation and...

44 CFR 80.21 - Closeout requirements.

Code of Federal Regulations, 2010 CFR

2010-10-01

... HOMELAND SECURITY INSURANCE AND HAZARD MITIGATION National Flood Insurance Program PROPERTY ACQUISITION AND... restriction language to meet the requirements of this part; (b) A photo of each property site after project...

44 CFR 80.21 - Closeout requirements.

Code of Federal Regulations, 2012 CFR

2012-10-01

... HOMELAND SECURITY INSURANCE AND HAZARD MITIGATION National Flood Insurance Program PROPERTY ACQUISITION AND... restriction language to meet the requirements of this part; (b) A photo of each property site after project...

44 CFR 80.21 - Closeout requirements.

Code of Federal Regulations, 2011 CFR

2011-10-01

... HOMELAND SECURITY INSURANCE AND HAZARD MITIGATION National Flood Insurance Program PROPERTY ACQUISITION AND... restriction language to meet the requirements of this part; (b) A photo of each property site after project...

44 CFR 80.21 - Closeout requirements.

Code of Federal Regulations, 2014 CFR

2014-10-01

... HOMELAND SECURITY INSURANCE AND HAZARD MITIGATION National Flood Insurance Program PROPERTY ACQUISITION AND... restriction language to meet the requirements of this part; (b) A photo of each property site after project...

44 CFR 80.21 - Closeout requirements.

Code of Federal Regulations, 2013 CFR

2013-10-01

... HOMELAND SECURITY INSURANCE AND HAZARD MITIGATION National Flood Insurance Program PROPERTY ACQUISITION AND... restriction language to meet the requirements of this part; (b) A photo of each property site after project...

Adopting Social Networking Sites (SNSs) as Interactive Communities among English Foreign Language (EFL) Learners in Writing: Opportunities and Challenges

ERIC Educational Resources Information Center

Razak, Norizan Abdul; Saeed, Murad; Ahmad, Zulkifli

2013-01-01

As most traditional classroom environments in English as Foreign Language (EFL) still restrict learners' collaboration and interaction in college writing classes, today, the majority of EFL learners are accessing Social Networking Sites (SNSs) as online communities of practice (CoPs) for adopting informal collaborative learning as a way of…

Tree hazard control on recreation sites...estimating local budgets

Treesearch

Lee A. Paine

1967-01-01

Tree hazard control efforts on recreation sites are subject to budget and administrative restrictions. To make the most effective use of available control funds, priorities should be assigned to various classes of tree defects and a budget set up. With the method provided, local priorities are based on cost effectiveness. Some guide lines and a worksheet for planning a...

76 FR 18921 - Land Disposal Restrictions: Nevada and California; Site Specific Treatment Variances for...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-04-06

... final actions to both issue a site- specific treatment variance to U.S. Ecology Nevada (USEN) in Beatty... me? This action applies only to U.S. Ecology Nevada located in Beatty, Nevada and to Chemical Waste... This Variance A. U.S. Ecology Nevada Petition B. What Type and How Much Waste Will be Subject to This...

Argonaute-based programmable RNase as a tool for cleavage of highly-structured RNA.

PubMed

Dayeh, Daniel M; Cantara, William A; Kitzrow, Jonathan P; Musier-Forsyth, Karin; Nakanishi, Kotaro

2018-06-12

The recent identification and development of RNA-guided enzymes for programmable cleavage of target nucleic acids offers exciting possibilities for both therapeutic and biotechnological applications. However, critical challenges such as expensive guide RNAs and inability to predict the efficiency of target recognition, especially for highly-structured RNAs, remain to be addressed. Here, we introduce a programmable RNA restriction enzyme, based on a budding yeast Argonaute (AGO), programmed with cost-effective 23-nucleotide (nt) single-stranded DNAs as guides. DNA guides offer the advantage that diverse sequences can be easily designed and purchased, enabling high-throughput screening to identify optimal recognition sites in the target RNA. Using this DNA-induced slicing complex (DISC) programmed with 11 different guide DNAs designed to span the sequence, sites of cleavage were identified in the 352-nt human immunodeficiency virus type 1 5'-untranslated region. This assay, coupled with primer extension and capillary electrophoresis, allows detection and relative quantification of all DISC-cleavage sites simultaneously in a single reaction. Comparison between DISC cleavage and RNase H cleavage reveals that DISC not only cleaves solvent-exposed sites, but also sites that become more accessible upon DISC binding. This study demonstrates the advantages of the DISC system for programmable cleavage of highly-structured, functional RNAs.

Site Safety Plan for Lawrence Livermore National Laboratory CERCLA investigations

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

Bainer, R.; Duarte, J.

1993-07-01

The safety policy of LLNL is to take every reasonable precaution in the performance of work to protect the environment and the health and safety of employees and the public, and to prevent property damage. With respect to hazardous agents, this protection is provided by limiting human exposures, releases to the environment, and contamination of property to levels that are as low as reasonably achievable (ALARA). It is the intent of this Plan to supply the broad outline for completing environmental investigations within ALARA guidelines. It may not be possible to determine actual working conditions in advance of the work;more » therefore, planning must allow the opportunity to provide a range of protection based upon actual working conditions. Requirements will be the least restrictive possible for a given set of circumstances, such that work can be completed in an efficient and timely fashion. Due to the relatively large size of the LLNL Site and the different types of activities underway, site-specific Operational Safety Procedures (OSPs) will be prepared to supplement activities not covered by this Plan. These site-specific OSPs provide the detailed information for each specific activity and act as an addendum to this Plan, which provides the general plan for LLNL Main Site operation.« less

Construction of New Campylobacter Cloning Vectors and a New Mutational Cat Cassette

DTIC Science & Technology

1993-01-01

mutational cat cassette PE - 61102A PR - 3M161102 6. AUTHOR(S) TA - BS13AK Yao R, Aim RA, Trust TJ, Guerry P WU- 1291 7. PERFORMING ORGANIZATION NAME(S) AND...mutational cat cassette %~ccesion For (Site-specific mutagenesis; recombinant DNA; multiple cloning site; PCR; shuttle vectors) NTIS CRA&I OTIC TAB E...campylobacter portion of these vectors, only three CAT , Cm acetyllraaseriase; car, gene encoding CAT , Cm, restriction sites in the IacZ MCS remain unique

Novel Immune Modulating Cellular Vaccine for Prostate Cancer

DTIC Science & Technology

2014-10-01

restriction sites. Murine PSMA : The cDNA encoding mPSMA was purchased from Sino Biologicals and was cloned into the HindIII and BamHI sites of pSP73-Sph/A64...sequence) and reverse primer 5’-TATATAGAGCTCTCAGATGTTCCGATACACATCTC-3’ Murine PSMA no signal sequence (mPSMA-SS): Murine PSMA minus the signal sequence...contains a HindIII site for cloning and utilizes an ATG that lies downstream of the signal sequence as the start codon in PSMA -SS ( PSMA without signal

Facile Site-Directed Mutagenesis of Large Constructs Using Gibson Isothermal DNA Assembly.

PubMed

Yonemoto, Isaac T; Weyman, Philip D

2017-01-01

Site-directed mutagenesis is a commonly used molecular biology technique to manipulate biological sequences, and is especially useful for studying sequence determinants of enzyme function or designing proteins with improved activity. We describe a strategy using Gibson Isothermal DNA Assembly to perform site-directed mutagenesis on large (>~20 kbp) constructs that are outside the effective range of standard techniques such as QuikChange II (Agilent Technologies), but more reliable than traditional cloning using restriction enzymes and ligation.

β-globin haplotypes in normal and hemoglobinopathic individuals from Reconcavo Baiano, State of Bahia, Brazil.

PubMed

Dos Santos Silva, Wellington; de Nazaré Klautau-Guimarães, Maria; Grisolia, Cesar Koppe

2010-07-01

Five restriction site polymorphisms in the β-globin gene cluster (HincII-5' ε, HindIII-(G) γ, HindIII-(A) γ, HincII- ψβ1 and HincII-3' ψβ1) were analyzed in three populations (n = 114) from Reconcavo Baiano, State of Bahia, Brazil. The groups included two urban populations from the towns of Cachoeira and Maragojipe and one rural Afro-descendant population, known as the "quilombo community", from Cachoeira municipality. The number of haplotypes found in the populations ranged from 10 to 13, which indicated higher diversity than in the parental populations. The haplotypes 2 (+ - - - -), 3 (- - - - +), 4 (- + - - +) and 6 (- + + - +) on the β(A) chromosomes were the most common, and two haplotypes, 9 (- + + + +) and 14 (+ + - - +), were found exclusively in the Maragojipe population. The other haplotypes (1, 5, 9, 11, 12, 13, 14 and 16) had lower frequencies. Restriction site analysis and the derived haplotypes indicated homogeneity among the populations. Thirty-two individuals with hemoglobinopathies (17 sickle cell disease, 12 HbSC disease and 3 HbCC disease) were also analyzed. The haplotype frequencies of these patients differed significantly from those of the general population. In the sickle cell disease subgroup, the predominant haplotypes were BEN (Benin) and CAR (Central African Republic), with frequencies of 52.9% and 32.4%, respectively. The high frequency of the BEN haplotype agreed with the historical origin of the afro-descendant population in the state of Bahia. However, this frequency differed from that of Salvador, the state capital, where the CAR and BEN haplotypes have similar frequencies, probably as a consequence of domestic slave trade and subsequent internal migrations to other regions of Brazil.

β-globin haplotypes in normal and hemoglobinopathic individuals from Reconcavo Baiano, State of Bahia, Brazil

PubMed Central

2010-01-01

Five restriction site polymorphisms in the β-globin gene cluster (HincII-5‘ ε, HindIII-G γ, HindIII-A γ, HincII- ψβ1 and HincII-3‘ ψβ1) were analyzed in three populations (n = 114) from Reconcavo Baiano, State of Bahia, Brazil. The groups included two urban populations from the towns of Cachoeira and Maragojipe and one rural Afro-descendant population, known as the “quilombo community”, from Cachoeira municipality. The number of haplotypes found in the populations ranged from 10 to 13, which indicated higher diversity than in the parental populations. The haplotypes 2 (+ - - - -), 3 (- - - - +), 4 (- + - - +) and 6 (- + + - +) on the βA chromosomes were the most common, and two haplotypes, 9 (- + + + +) and 14 (+ + - - +), were found exclusively in the Maragojipe population. The other haplotypes (1, 5, 9, 11, 12, 13, 14 and 16) had lower frequencies. Restriction site analysis and the derived haplotypes indicated homogeneity among the populations. Thirty-two individuals with hemoglobinopathies (17 sickle cell disease, 12 HbSC disease and 3 HbCC disease) were also analyzed. The haplotype frequencies of these patients differed significantly from those of the general population. In the sickle cell disease subgroup, the predominant haplotypes were BEN (Benin) and CAR (Central African Republic), with frequencies of 52.9% and 32.4%, respectively. The high frequency of the BEN haplotype agreed with the historical origin of the afro-descendant population in the state of Bahia. However, this frequency differed from that of Salvador, the state capital, where the CAR and BEN haplotypes have similar frequencies, probably as a consequence of domestic slave trade and subsequent internal migrations to other regions of Brazil. PMID:21637405

Coupled simulations and comparison with multi-lidar measurements of the wind flow over a double-ridge

NASA Astrophysics Data System (ADS)

Veiga Rodrigues, C.; Palma, JMLM; Vasiljević, N.; Courtney, M.; Mann, J.

2016-09-01

The wind flow over a double-ridge site has been numerically simulated with a nested model- chain coupling, down to horizontal resolutions of 40 m. The results were compared with field measurements attained using a triple-lidar instrument, the long-range WindScanner system, which allowed measurements up to 500 m height and the mapping of the wind speed onto a two-dimensional transect crossing the valley. The site, known as Serra do Perdigão, is located in central Portugal and consists of two parallel ridges 1.4 km apart with height differences of 200 m in between, being characterized by rough terrain and forested areas. The analysis was restricted to June 10th 2015, for which measurements and simulations both predicted gravity wave activity, the later showing formation of rotors in the lee of both ridges and some events of wave breaking above the ridge top.

Directing Reaction Pathways through Controlled Reactant Binding at Pd-TiO2 Interfaces.

PubMed

Zhang, Jing; Wang, Bingwen; Nikolla, Eranda; Medlin, J Will

2017-06-01

Recent efforts to design selective catalysts for multi-step reactions, such as hydrodeoxygenation (HDO), have emphasized the preparation of active sites at the interface between two materials having different properties. However, achieving precise control over interfacial properties, and thus reaction selectivity, has remained a challenge. Here, we encapsulated Pd nanoparticles (NPs) with TiO 2 films of regulated porosity to gain a new level of control over catalyst performance, resulting in essentially 100 % HDO selectivity for two biomass-derived alcohols. This catalyst also showed exceptional reaction specificity in HDO of furfural and m-cresol. In addition to improving HDO activity by maximizing the interfacial contact between the metal and metal oxide sites, encapsulation by the nanoporous oxide film provided a significant selectivity boost by restricting the accessible conformations of aromatics on the surface. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

[Urban industrial contaminated sites: a new issue in the field of environmental remediation in China].

PubMed

Liao, Xiao-Yong; Chong, Zhong-Yi; Yan, Xiu-Lan; Zhao, Dan

2011-03-01

Contamination of urban industrial lands is a new environmental problem in China during the process of upgrade of industrial structure and adjustment of urban layout. It restricts the safe re-use of urban land resources, and threatens the health of surrounding inhabitants. In the paper, the market potential of contaminated-site remediation was known through analysis of spatial distribution of urban industrial sites in China. Remediation technologies in the Occident which were suitable for urban industrial contaminated sites were discussed and compared to evaluate their superiority and inferiority. And then, some advices of remediation technologies for urban industrial contaminated sites in China were proposed.

36 CFR 261.52 - Fire.

Code of Federal Regulations, 2010 CFR

2010-07-01

.... (c) Smoking. (d) Smoking, except within an enclosed vehicle or building, a developed recreation site... concerning burning, fires or which is for the purpose of preventing, or restricting the spread of fires. [42...

Can captive orangutans (Pongo pygmaeus abelii) be coaxed into cumulative build-up of techniques?

PubMed

Lehner, Stephan R; Burkart, Judith M; Schaik, Carel P van

2011-11-01

While striking cultural variation in behavior from one site to another has been described in chimpanzees and orangutans, cumulative culture might be unique to humans. Captive chimpanzees were recently found to be rather conservative, sticking to the technique they had mastered, even after more effective alternatives were demonstrated. Behavioral flexibility in problem solving, in the sense of acquiring new solutions after having learned another one earlier, is a vital prerequisite for cumulative build-up of techniques. Here, we experimentally investigate whether captive orangutans show such flexibility, and if so, whether they show techniques that cumulatively build up (ratchet) on previous ones after conditions of the task are changed. We provided nine Sumatran orangutans (Pongo pygmaeus abelii) with two types of transparent tubes partly filled with syrup, along with potential tools such as sticks, twigs, wood wool and paper. In the first phase, the orangutans could reach inside the tubes with their hands (Regular Condition), but in the following phase, tubes had been made too narrow for their hands to fit in (Restricted Condition 1), or in addition the setup lacked their favorite materials (Restricted Condition 2). The orangutans showed high behavioral flexibility, applying nine different techniques under the regular condition in total. Individuals abandoned preferred techniques and switched to different techniques under restricted conditions when this was advantageous. We show for two of these techniques how they cumulatively built up on earlier ones. This suggests that the near-absence of cumulative culture in wild orangutans is not due to a lack of flexibility when existing solutions to tasks are made impossible.

Study of the location and function of N/sup 6/-methyladenosine in Rous sarcoma virus genomic RNA

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

Kane, S.E.

1986-01-01

N/sup 6/-methyladenosine (m/sup 6/A) residues are present as internal base modifications in most higher eukaryotic mRNAs; however, the biological function of this modification is not known. A method is described for localizing and quantitating m/sup 6/A within a large RNA molecule, the genomic RNA of Rous sarcoma virus (RSV). Specific fragments of /sup 32/P-labeled RSV RNA were isolated by hybridizations with complementary DNA restriction fragments spanning nucleotides 6185 and 8050. RNA was digested with RNAse and fingerprinted, and individual oligonucleotides were analyzed for the presence of m/sup 6/A by thin layer chromatography. With this technique, seven sites of methylation inmore » this region of the RSV genome were localized at nucleotides 6394, 6447, 6507, 6718, 7414, 7424, and 8014. Further, m/sup 6/A was observed at two additional sites whose nucleotide assignments remain ambiguous. A clustering of two or more m/sup 6/A residues was seen at three positions within the RNA analyzed. Modification at certain sites was found to be heterogeneous, in that different molecules of RNA appeared to be methylated differently. An approach for directly studying the function of m/sup 6/A in RNA is presented.« less

[Evaluating the Stability of Loop-Mediated Isothermal Amplification Reagents at Irregular Storage Temperatures for On-Site Diagnosis].

PubMed

Inoshima, Yasuo; Ishiguro, Naotaka

2015-01-01

Temperature-stability of loop-mediated isothermal amplification (LAMP) reagents was determined for their use in on-site diagnosis, such as in farms/pastures. Bst and Csa DNA polymerases and the reagents that were stored at different temperatures (4 or 25°C) for 1, 2, or 4 days were used for the LAMP assay to detect orf virus DNA as a model. After storage at 4 and 25°C for 2 days, the enzymes and reagents were found to retain sufficient activity to carry out successful DNA amplification. Visual diagnosis was also possible with the reagents (Loopamp Fluorescent Detection Reagent or hydroxy naphthol blue, as well as DNA amplification checker, D-Quick) that were stored for 2 days at different temperatures. Although the time taken to obtain the positive/negative results were delayed, the enzymes and reagents, stored at 25°C for 4 days, were active and had the ability to efficiently amplify DNA in less than 50 min. These results indicate that LAMP assay can be successfully utilized for the diagnosis of infectious diseases under non-clinical settings such as for on-site diagnosis in farms/pastures, owing to the fact that the relevant enzymes and reagents does not require restricted temperature storage.

Characterization of proviruses cloned from mink cell focus-forming virus-infected cellular DNA.

PubMed Central

Khan, A S; Repaske, R; Garon, C F; Chan, H W; Rowe, W P; Martin, M A

1982-01-01

Two proviruses were cloned from EcoRI-digested DNA extracted from mink cells chronically infected with AKR mink cell focus-forming (MCF) 247 murine leukemia virus (MuLV), using a lambda phage host vector system. One cloned MuLV DNA fragment (designated MCF 1) contained sequences extending 6.8 kilobases from an EcoRI restriction site in the 5' long terminal repeat (LTR) to an EcoRI site located in the envelope (env) region and was indistinguishable by restriction endonuclease mapping for 5.1 kilobases (except for the EcoRI site in the LTR) from the 5' end of AKR ecotropic proviral DNA. The DNA segment extending from 5.1 to 6.8 kilobases contained several restriction sites that were not present in the AKR ecotropic provirus. A 0.5-kilobase DNA segment located at the 3' end of MCF 1 DNA contained sequences which hybridized to a xenotropic env-specific DNA probe but not to labeled ecotropic env-specific DNA. This dual character of MCF 1 proviral DNA was also confirmed by analyzing heteroduplex molecules by electron microscopy. The second cloned proviral DNA (designated MCF 2) was a 6.9-kilobase EcoRI DNA fragment which contained LTR sequences at each end and a 2.0-kilobase deletion encompassing most of the env region. The MCF 2 proviral DNA proved to be a useful reagent for detecting LTRs electron microscopically due to the presence of nonoverlapping, terminally located LTR sequences which effected its circularization with DNAs containing homologous LTR sequences. Nucleotide sequence analysis demonstrated the presence of a 104-base-pair direct repeat in the LTR of MCF 2 DNA. In contrast, only a single copy of the reiterated component of the direct repeat was present in MCF 1 DNA. Images PMID:6281459

Site preparation for switchgrass intercropping in loblolly pine plantations reduces retained trees and snags, but maintains downed woody debris

USGS Publications Warehouse

Loman, Zachary G.; Riffell, Samuel K.; Miller, Darrin A.; Martin, James A.; Vilella, Francisco

2013-01-01

Within young pine (Pinus spp.) plantations, coarse woody debris (CWD) and green trees are important habitat structures that may be impacted by the production of biofuel feedstock. Therefore, we compared site preparation procedures associated with switchgrass (Panicum virgatum L.) intercropping to determine effects on CWD and green trees in stands (n = 24) site-prepared for intercropping, with switchgrass only, or pine plantation in Mississippi, USA. Following site preparation, CWD dispersal or volume did not differ between intercropped and control stands. Intercropped stands had significantly fewer retained trees and snags. Switchgrass monocultures had no retained trees or piles and significantly fewer pieces and less volume of CWD than the other treatments. Our results suggest switchgrass intercropping may provide similar habitat quality to traditional pine plantations for wildlife species using these areas in the year following disturbance, but may provide a less suitable habitat for species that require snags. However, the relationship between snag reduction and wildlife population response in an intercropped setting is not clear and should be further investigated. Regardless, if retaining snags is a desired outcome, site preparation for switchgrass should be restricted to the interbed area where it will be cultivated as opposed to extensive debris removal from the entire site.                   

Genetic diversity of rice tungro spherical virus in tungro-endemic provinces of the Philippines and Indonesia.

PubMed

Azzam, O; Yambao, M L; Muhsin, M; McNally, K L; Umadhay, K M

2000-01-01

The two adjacent genes of coat protein 1 and 2 of rice tungro spherical virus (RTSV) were amplified from total RNA extracts of serologically indistinguishable field isolates from the Philippines and Indonesia, using reverse transcriptase polymerase chain reaction (RT-PCR). Digestion with HindIII and BstYI restriction endonucleases differentiated the amplified DNA products into eight distinct coat protein genotypes. These genotypes were then used as indicators of virus diversity in the field. Inter- and intra-site diversities were determined over three cropping seasons. At each of the sites surveyed, one or two main genotypes prevailed together with other related minor or mixed genotypes that did not replace the main genotype over the sampling time. The cluster of genotypes found at the Philippines sites was significantly different from the one at the Indonesia sites, suggesting geographic isolation for virus populations. Phylogenetic studies based on the nucleotide sequences of 38 selected isolates confirm the spatial distribution of RTSV virus populations but show that gene flow may occur between populations. Under the present conditions, rice varieties do not seem to exert selective pressure on the virus populations. Based on the selective constraints in the coat protein amino acid sequences and the virus genetic composition per site, a negative selection model followed by random-sampling events due to vector transmissions is proposed to explain the inter-site diversity observed.

Behavior of restriction–modification systems as selfish mobile elements and their impact on genome evolution

PubMed Central

Kobayashi, Ichizo

2001-01-01

Restriction–modification (RM) systems are composed of genes that encode a restriction enzyme and a modification methylase. RM systems sometimes behave as discrete units of life, like viruses and transposons. RM complexes attack invading DNA that has not been properly modified and thus may serve as a tool of defense for bacterial cells. However, any threat to their maintenance, such as a challenge by a competing genetic element (an incompatible plasmid or an allelic homologous stretch of DNA, for example) can lead to cell death through restriction breakage in the genome. This post-segregational or post-disturbance cell killing may provide the RM complexes (and any DNA linked with them) with a competitive advantage. There is evidence that they have undergone extensive horizontal transfer between genomes, as inferred from their sequence homology, codon usage bias and GC content difference. They are often linked with mobile genetic elements such as plasmids, viruses, transposons and integrons. The comparison of closely related bacterial genomes also suggests that, at times, RM genes themselves behave as mobile elements and cause genome rearrangements. Indeed some bacterial genomes that survived post-disturbance attack by an RM gene complex in the laboratory have experienced genome rearrangements. The avoidance of some restriction sites by bacterial genomes may result from selection by past restriction attacks. Both bacteriophages and bacteria also appear to use homologous recombination to cope with the selfish behavior of RM systems. RM systems compete with each other in several ways. One is competition for recognition sequences in post-segregational killing. Another is super-infection exclusion, that is, the killing of the cell carrying an RM system when it is infected with another RM system of the same regulatory specificity but of a different sequence specificity. The capacity of RM systems to act as selfish, mobile genetic elements may underlie the structure and function of RM enzymes. PMID:11557807

77 FR 76509 - Federal Property Suitable as Facilities To Assist the Homeless

Federal Register 2010, 2011, 2012, 2013, 2014

2012-12-28

... Register publication; off-site removal only, sf. varies, fair conditions, asbestos, restricted area...; moderate conditions; asbestos; access by appt. only Unsuitable Properties Building FLORIDA Building 11 NAS...

Emotion regulation in bereavement: searching for and finding emotional support in social network sites

NASA Astrophysics Data System (ADS)

Döveling, Katrin

2015-04-01

In an age of rising impact of online communication in social network sites (SNS), emotional interaction is neither limited nor restricted by time or space. Bereavement extends to the anonymity of cyberspace. What role does virtual interaction play in SNS in dealing with the basic human emotion of grief caused by the loss of a beloved person? The analysis laid out in this article provides answers in light of an interdisciplinary perspective on online bereavement. Relevant lines of research are scrutinized. After laying out the theoretical spectrum for the study, hypotheses based on a prior in-depth qualitative content analysis of 179 postings in three different German online bereavement platforms are proposed and scrutinized in a quantitative content analysis (2127 postings from 318 users). Emotion regulation patterns in SNS and similarities as well as differences in online bereavement of children, adolescents and adults are revealed. Large-scale quantitative findings into central motives, patterns, and restorative effects of online shared bereavement in regulating distress, fostering personal empowerment, and engendering meaning are presented. The article closes with implications for further analysis in memorialization practices.

New edge-centered photonic square lattices with flat bands

NASA Astrophysics Data System (ADS)

Zhang, Da; Zhang, Yiqi; Zhong, Hua; Li, Changbiao; Zhang, Zhaoyang; Zhang, Yanpeng; Belić, Milivoj R.

2017-07-01

We report a new class of edge-centered photonic square lattices with multiple flat bands, and consider in detail two examples: the Lieb-5 and Lieb-7 lattices. In these lattices, there are 5 and 7 sites in the unit cell and in general, the number is restricted to odd integers. The number of flat bands m in the new Lieb lattices is related to the number of sites N in the unit cell by a simple formula m =(N - 1) / 2. The flat bands reported here are independent of the pseudomagnetic field. The properties of lattices with even and odd number of flat bands are different. We consider the localization of light in such Lieb lattices. If the input beam excites the flat-band mode, it will not diffract during propagation, owing to the strong mode localization. In the Lieb-7 lattice, the beam will also oscillate during propagation and still not diffract. The period of oscillation is determined by the energy difference between the two flat bands. This study provides a new platform for investigating light trapping, photonic topological insulators, and pseudospin-mediated vortex generation.

Localization of the human mitochondrial citrate transporter protein gene to chromosome 22q11 in the DiGeorge syndrome critical region

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

Heisterkamp, N.; Hoeve, J.T.; Groffen, J.

A high percentage of patients with DiGeorge syndrome and velo-cardio-facial syndrome have interstitial deletions on chromosome 22q11. The shortest region of overlap is currently estimated to be around 500 kb. Two segments of DNA from chromosome 22q11, located 160 kb apart, were cloned because they contained NotI restriction enzyme sites. In the current study we demonstrate that these segments are absent from chromosomes 22 carrying microdeletions of two different DiGeorge patients. Fluorescence in situ and Southern blot hybridization was further used to show that this locus is within the DiGeorge critical region. Phylogenetically conserved sequences adjacent to one of themore » two NotI sites hybridized to mRNAs in different human cell lines. cDNAs isolated with a probe from this segment showed it to contain the gene for the human mitochondrial citrate transporter protein. Deletion of this gene in DiGeorge may contribute to the mental deficiency seen in the patients. 35 refs., 5 figs.« less

Human immune cells' behavior and survival under bioenergetically restricted conditions in an in vitro fracture hematoma model

PubMed Central

Hoff, Paula; Maschmeyer, Patrick; Gaber, Timo; Schütze, Tabea; Raue, Tobias; Schmidt-Bleek, Katharina; Dziurla, René; Schellmann, Saskia; Lohanatha, Ferenz Leonard; Röhner, Eric; Ode, Andrea; Burmester, Gerd-Rüdiger; Duda, Georg N; Perka, Carsten; Buttgereit, Frank

2013-01-01

The initial inflammatory phase of bone fracture healing represents a critical step for the outcome of the healing process. However, both the mechanisms initiating this inflammatory phase and the function of immune cells present at the fracture site are poorly understood. In order to study the early events within a fracture hematoma, we established an in vitro fracture hematoma model: we cultured hematomas forming during an osteotomy (artificial bone fracture) of the femur during total hip arthroplasty (THA) in vitro under bioenergetically controlled conditions. This model allowed us to monitor immune cell populations, cell survival and cytokine expression during the early phase following a fracture. Moreover, this model enabled us to change the bioenergetical conditions in order to mimic the in vivo situation, which is assumed to be characterized by hypoxia and restricted amounts of nutrients. Using this model, we found that immune cells adapt to hypoxia via the expression of angiogenic factors, chemoattractants and pro-inflammatory molecules. In addition, combined restriction of oxygen and nutrient supply enhanced the selective survival of lymphocytes in comparison with that of myeloid derived cells (i.e., neutrophils). Of note, non-restricted bioenergetical conditions did not show any similar effects regarding cytokine expression and/or different survival rates of immune cell subsets. In conclusion, we found that the bioenergetical conditions are among the crucial factors inducing the initial inflammatory phase of fracture healing and are thus a critical step for influencing survival and function of immune cells in the early fracture hematoma. PMID:23396474

INM Integrated Noise Model Version 2. Programmer’s Guide

DTIC Science & Technology

1979-09-01

cost, turnaround time, and system-dependent limitations. 3.2 CONVERSION PROBLEMS Item Item Item No. Desciption Category 1 BLOCK DATA Initialization IBM ...Restricted 2 Boolean Operations Differences Call Statement Parameters Extensions 4 Data Initialization IBM Restricted 5 ENTRY Differences 6 EQUIVALENCE...Machine Dependent 7 Format: A CDC Extension 8 Hollerith Strings IBM Restricted 9 Hollerith Variables IBM Restricted 10 Identifier Names CDC Extension

D1/D2 Domain of Large-Subunit Ribosomal DNA for Differentiation of Orpinomyces spp.▿

PubMed Central

Dagar, Sumit S.; Kumar, Sanjay; Mudgil, Priti; Singh, Rameshwar; Puniya, Anil K.

2011-01-01

This study presents the suitability of D1/D2 domain of large-subunit (LSU) ribosomal DNA (rDNA) for differentiation of Orpinomyces joyonii and Orpinomyces intercalaris based on PCR-restriction fragment length polymorphism (RFLP). A variation of G/T in O. intercalaris created an additional restriction site for AluI, which was used as an RFLP marker. The results demonstrate adequate heterogeneity in the LSU rDNA for species-level differentiation. PMID:21784906

Long-Term Management Strategy for Dredged Material Disposal for Naval Facilities at Pearl Harbor, Hawaii Phase III - Analysis of Alternatives and Development of an LTMS

DTIC Science & Technology

2000-03-01

are needed to restrict contaminants losses via the leachate and volatilization pathways. Plant uptake testing indicated a potential need to restrict...or control future use of the site, to amend the material with soil additives, to phytoremediate , or to provide a final surface cover of clean...initial release including toxicity and bioaccumulation, effluent, runoff, leachate , plant uptake, upland and aquatic animal uptake, and

Integrins are required for tissue organization and restriction of neurogenesis in regenerating planarians

PubMed Central

Seebeck, Florian; März, Martin; Meyer, Anna-Wiebke; Reuter, Hanna; Vogg, Matthias C.; Stehling, Martin; Mildner, Karina; Zeuschner, Dagmar; Rabert, Franziska

2017-01-01

Tissue regeneration depends on proliferative cells and on cues that regulate cell division, differentiation, patterning and the restriction of these processes once regeneration is complete. In planarians, flatworms with high regenerative potential, muscle cells express some of these instructive cues. Here, we show that members of the integrin family of adhesion molecules are required for the integrity of regenerating tissues, including the musculature. Remarkably, in regenerating β1-integrin RNAi planarians, we detected increased numbers of mitotic cells and progenitor cell types, as well as a reduced ability of stem cells and lineage-restricted progenitor cells to accumulate at wound sites. These animals also formed ectopic spheroid structures of neural identity in regenerating heads. Interestingly, those polarized assemblies comprised a variety of neural cells and underwent continuous growth. Our study indicates that integrin-mediated cell adhesion is required for the regenerative formation of organized tissues and for restricting neurogenesis during planarian regeneration. PMID:28137894

Elevation as a barrier: genetic structure for an Atlantic rain forest tree (Bathysa australis) in the Serra do Mar mountain range, SE Brazil.

PubMed

Reis, Talita Soares; Ciampi-Guillardi, Maísa; Bajay, Miklos Maximiliano; de Souza, Anete Pereira; Dos Santos, Flavio Antonio Maës

2015-05-01

Distance and discrete geographic barriers play a role in isolating populations, as seed and pollen dispersal become limited. Nearby populations without any geographic barrier between them may also suffer from ecological isolation driven by habitat heterogeneity, which may promote divergence by local adaptation and drift. Likewise, elevation gradients may influence the genetic structure and diversity of populations, particularly those marginally distributed. Bathysa australis (Rubiaceae) is a widespread tree along the elevation gradient of the Serra do Mar, SE Brazil. This self-compatible species is pollinated by bees and wasps and has autochoric seeds, suggesting restricted gene dispersal. We investigated the distribution of genetic diversity in six B. australis populations at two extreme sites along an elevation gradient: a lowland site (80-216 m) and an upland site (1010-1100 m.a.s.l.). Nine microsatellite loci were used to test for genetic structure and to verify differences in genetic diversity between sites. We found a marked genetic structure on a scale as small as 6 km (F ST = 0.21), and two distinct clusters were identified, each corresponding to a site. Although B. australis is continuously distributed along the elevation gradient, we have not observed a gene flow between the extreme populations. This might be related to B. australis biological features and creates a potential scenario for adaptation to the different conditions imposed by the elevation gradient. We failed to find an isolation-by-distance pattern; although on the fine scale, all populations showed spatial autocorrelation until ∼10-20 m. Elevation difference was a relevant factor though, but we need further sampling effort to check its correlation with genetic distance. The lowland populations had a higher allelic richness and showed higher rare allele counts than the upland ones. The upland site may be more selective, eliminating rare alleles, as we did not find any evidence for bottleneck.

Relationship between mRNA secondary structure and sequence variability in Chloroplast genes: possible life history implications.

PubMed

Krishnan, Neeraja M; Seligmann, Hervé; Rao, Basuthkar J

2008-01-28

Synonymous sites are freer to vary because of redundancy in genetic code. Messenger RNA secondary structure restricts this freedom, as revealed by previous findings in mitochondrial genes that mutations at third codon position nucleotides in helices are more selected against than those in loops. This motivated us to explore the constraints imposed by mRNA secondary structure on evolutionary variability at all codon positions in general, in chloroplast systems. We found that the evolutionary variability and intrinsic secondary structure stability of these sequences share an inverse relationship. Simulations of most likely single nucleotide evolution in Psilotum nudum and Nephroselmis olivacea mRNAs, indicate that helix-forming propensities of mutated mRNAs are greater than those of the natural mRNAs for short sequences and vice-versa for long sequences. Moreover, helix-forming propensity estimated by the percentage of total mRNA in helices increases gradually with mRNA length, saturating beyond 1000 nucleotides. Protection levels of functionally important sites vary across plants and proteins: r-strategists minimize mutation costs in large genes; K-strategists do the opposite. Mrna length presumably predisposes shorter mRNAs to evolve under different constraints than longer mRNAs. The positive correlation between secondary structure protection and functional importance of sites suggests that some sites might be conserved due to packing-protection constraints at the nucleic acid level in addition to protein level constraints. Consequently, nucleic acid secondary structure a priori biases mutations. The converse (exposure of conserved sites) apparently occurs in a smaller number of cases, indicating a different evolutionary adaptive strategy in these plants. The differences between the protection levels of functionally important sites for r- and K-strategists reflect their respective molecular adaptive strategies. These converge with increasing domestication levels of K-strategists, perhaps because domestication increases reproductive output.

Molecular characterization of diazotrophic and denitrifying bacteria associated with mangrove roots.

PubMed

Flores-Mireles, Ana L; Winans, Stephen C; Holguin, Gina

2007-11-01

An analysis of the molecular diversity of N(2) fixers and denitrifiers associated with mangrove roots was performed using terminal restriction length polymorphism (T-RFLP) of nifH (N(2) fixation) and nirS and nirK (denitrification), and the compositions and structures of these communities among three sites were compared. The number of operational taxonomic units (OTU) for nifH was higher than that for nirK or nirS at all three sites. Site 3, which had the highest organic matter and sand content in the rhizosphere sediment, as well as the lowest pore water oxygen concentration, had the highest nifH diversity. Principal component analysis of biogeochemical parameters identified soil texture, organic matter content, pore water oxygen concentration, and salinity as the main variables that differentiated the sites. Nonmetric multidimensional scaling (MDS) analyses of the T-RFLP data using the Bray-Curtis coefficient, group analyses, and pairwise comparisons between the sites clearly separated the OTU of site 3 from those of sites 1 and 2. For nirS, there were statistically significant differences in the composition of OTU among the sites, but the variability was less than for nifH. OTU defined on the basis of nirK were highly similar, and the three sites were not clearly separated on the basis of these sequences. The phylogenetic trees of nifH, nirK, and nirS showed that most of the cloned sequences were more similar to sequences from the rhizosphere isolates than to those from known strains or from other environments.

Molecular Characterization of Diazotrophic and Denitrifying Bacteria Associated with Mangrove Roots▿

PubMed Central

Flores-Mireles, Ana L.; Winans, Stephen C.; Holguin, Gina

2007-01-01

An analysis of the molecular diversity of N2 fixers and denitrifiers associated with mangrove roots was performed using terminal restriction length polymorphism (T-RFLP) of nifH (N2 fixation) and nirS and nirK (denitrification), and the compositions and structures of these communities among three sites were compared. The number of operational taxonomic units (OTU) for nifH was higher than that for nirK or nirS at all three sites. Site 3, which had the highest organic matter and sand content in the rhizosphere sediment, as well as the lowest pore water oxygen concentration, had the highest nifH diversity. Principal component analysis of biogeochemical parameters identified soil texture, organic matter content, pore water oxygen concentration, and salinity as the main variables that differentiated the sites. Nonmetric multidimensional scaling (MDS) analyses of the T-RFLP data using the Bray-Curtis coefficient, group analyses, and pairwise comparisons between the sites clearly separated the OTU of site 3 from those of sites 1 and 2. For nirS, there were statistically significant differences in the composition of OTU among the sites, but the variability was less than for nifH. OTU defined on the basis of nirK were highly similar, and the three sites were not clearly separated on the basis of these sequences. The phylogenetic trees of nifH, nirK, and nirS showed that most of the cloned sequences were more similar to sequences from the rhizosphere isolates than to those from known strains or from other environments. PMID:17827324

Association Between Scalp Laxity, Elasticity, and Glidability and Donor Strip Scar Width in Hair Transplantation and a New Elasticity Measuring Method.

PubMed

Park, Jae Hyun

2017-04-01

Hair transplantation requires precise evaluation of donor site laxity, elasticity, and glidability. The purpose of this study was to examine the relationship between donor strip scar width and preoperative laxity, elasticity, and glidability. Preoperative measurements of scalp laxity, elasticity, and glidability and of donor site scar width 10 months postoperatively were evaluated in 88 patients who underwent hair transplantation with strip harvesting. Elasticity was measured by firmly pressing the scalp with the fingertips of one hand at 2 points to restrict dermis movement while stretching the skin with the other hand. Glidability was calculated as laxity minus elasticity. Scar width positively correlated with laxity (p < .01) and elasticity (p < .05) but had no relationship with glidability. There was a significant difference between patients in the upper 30th percentile of elasticity (≥10 mm) versus others (<10 mm) in scar width. Scalp laxity, elasticity, and glidability are of great clinical importance in hair transplantation. The authors' novel method of measuring elasticity will assist surgeons in predicting donor site scar width.

15 CFR 744.21 - Restrictions on certain military end-uses in the People's Republic of China (PRC).

Code of Federal Regulations, 2010 CFR

2010-01-01

... Wassenaar Arrangement Web site at http://www.wassenaar.org); incorporation into items listed under ECCNs...: product engineering, manufacturing, integration, assembly (mounting), inspection, testing, quality...

15 CFR 744.21 - Restrictions on certain military end-uses in the People's Republic of China (PRC).

Code of Federal Regulations, 2011 CFR

2011-01-01

... Wassenaar Arrangement Web site at http://www.wassenaar.org); incorporation into items listed under ECCNs...: product engineering, manufacturing, integration, assembly (mounting), inspection, testing, quality...

76 FR 79230 - Advisory Committee on Small and Emerging Companies

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-21

... Commission on relaxing current restrictions on general solicitation and advertising in exempt offerings of.../acsec.shtml. Statements also will be available for Web site viewing and printing in the Commission's...

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

PubMed

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

1988-08-15

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

Lack of Effectiveness of Neutropenic Diet and Social Restrictions as Anti-Infective Measures in Children With Acute Myeloid Leukemia: An Analysis of the AML-BFM 2004 Trial

PubMed Central

Tramsen, Lars; Salzmann-Manrique, Emilia; Bochennek, Konrad; Klingebiel, Thomas; Reinhardt, Dirk; Creutzig, Ursula; Sung, Lillian

2016-01-01

Purpose Although nonpharmacologic anti-infective measures are widely used in children treated for acute myeloid leukemia (AML), there is little evidence of their effectiveness. Patients and Methods We analyzed infectious complications in children during intensive treatment of AML according to the AML-BFM 2004 trial and surveyed sites on institutional standards regarding recommended restrictions of social contacts (six items), pets (five items), and food (eight items). A scoring system was developed with a restriction score for each item. Multivariable Poisson regression adjusted for sex, age, weight group, risk stratification, and prophylactic antibiotics was used to estimate the impact of the restrictions on the incidence ratios of fever of unknown origin, bacteremia, pneumonia, and gastroenteritis. Results Data on recommendations of nonpharmacologic anti-infective measures and infectious complications were available in 339 patients treated in 37 institutions. Analyses did not demonstrate a significant benefit of any of the restrictions regarding food, social contacts, and pets on the risk of fever, bacteremia, pneumonia, and gastroenteritis. In contrast, age, weight group, risk stratification, and nonabsorbable antibiotics had some influence on infections complications. Conclusion The lack of effectiveness of dietary restrictions and restrictions regarding social contacts and pets should result in reconsideration of anti-infective policies. PMID:27269945

Lack of Effectiveness of Neutropenic Diet and Social Restrictions as Anti-Infective Measures in Children With Acute Myeloid Leukemia: An Analysis of the AML-BFM 2004 Trial.

PubMed

Tramsen, Lars; Salzmann-Manrique, Emilia; Bochennek, Konrad; Klingebiel, Thomas; Reinhardt, Dirk; Creutzig, Ursula; Sung, Lillian; Lehrnbecher, Thomas

2016-08-10

Although nonpharmacologic anti-infective measures are widely used in children treated for acute myeloid leukemia (AML), there is little evidence of their effectiveness. We analyzed infectious complications in children during intensive treatment of AML according to the AML-BFM 2004 trial and surveyed sites on institutional standards regarding recommended restrictions of social contacts (six items), pets (five items), and food (eight items). A scoring system was developed with a restriction score for each item. Multivariable Poisson regression adjusted for sex, age, weight group, risk stratification, and prophylactic antibiotics was used to estimate the impact of the restrictions on the incidence ratios of fever of unknown origin, bacteremia, pneumonia, and gastroenteritis. Data on recommendations of nonpharmacologic anti-infective measures and infectious complications were available in 339 patients treated in 37 institutions. Analyses did not demonstrate a significant benefit of any of the restrictions regarding food, social contacts, and pets on the risk of fever, bacteremia, pneumonia, and gastroenteritis. In contrast, age, weight group, risk stratification, and nonabsorbable antibiotics had some influence on infections complications. The lack of effectiveness of dietary restrictions and restrictions regarding social contacts and pets should result in reconsideration of anti-infective policies. © 2016 by American Society of Clinical Oncology.

Effects of restriction on children’s intake differ by child temperament, food reinforcement, and parent’s chronic use of restriction.

PubMed

Rollins, Brandi Y; Loken, Eric; Savage, Jennifer S; Birch, Leann L

2014-02-01

Parents’ use of restrictive feeding practices is counterproductive, increasing children’s intake of restricted foods and risk for excessive weight gain. The aims of this research were to replicate Fisher and Birch’s (1999b) original findings that short-term restriction increases preschool children’s (3–5 y) selection, intake, and behavioral response to restricted foods, and to identify characteristics of children who were more susceptible to the negative effects of restriction. The experiment used a within-subjects design; 37 children completed the food reinforcement task and heights/weights were measured. Parents reported on their use of restrictive feeding practices and their child’s inhibitory control and approach. Overall, the findings replicated those of and revealed that the effects of restriction differed by children’s regulatory and appetitive tendencies. Greater increases in intake in response to restriction were observed among children lower in inhibitory control, higher in approach, who found the restricted food highly reinforcing, and who had previous experience with parental use of restriction. Results confirm that the use of restriction does not reduce children’s consumption of these foods, particularly among children with lower regulatory or higher appetitive tendencies.

Effect of traffic restriction on reducing ambient volatile organic compounds (VOCs): Observation-based evaluation during a traffic restriction drill in Guangzhou, China

NASA Astrophysics Data System (ADS)

Huang, Xinyu; Zhang, Yanli; Yang, Weiqiang; Huang, Zuzhao; Wang, Yujun; Zhang, Zhou; He, Quanfu; Lü, Sujun; Huang, Zhonghui; Bi, Xinhui; Wang, Xinming

2017-07-01

Traffic restriction (TR) is a widely adopted control measure in case of heavy air pollution particularly in urban areas, yet it is hard to evaluate the effect of TR on reducing VOC emissions based on monitoring data since ambient VOC mixing ratios are influenced not only by source emissions but also by meteorological conditions and atmospheric degradation. Here we collected air samples for analysis of VOCs before, during and after a TR drill carried out in Guangzhou in September 2010 at both a roadside and a rooftop (∼50 m above the ground) site. TR measures mainly included the "odd-even license" rule and banning high-emitting "yellow label" vehicles. The mixing ratios of non-methane hydrocarbons (NMHCs) did not show significant changes at the roadside site with total NMHCs of 39.0 ± 11.8 ppbv during non-TR period and 39.1 ± 14.8 ppbv during TR period, whereas total NMHCs decreased from 30.4 ± 14.3 ppbv during the non-TR period to 22.1 ± 10.6 ppbv during the TR period at rooftop site. However, the ratios of methyl tert-butyl ether (MTBE), benzene and toluene against carbon monoxide (MTBE/CO, T/CO and B/CO) at the both sampling sites dropped significantly. The ratios of toluene to benzene (T/B) instead increased significantly. Changes in these ratios all consistently indicated reduced input from traffic emissions particularly gasoline vehicles. Source attribution by positive matrix factorization (PMF) confirmed that during the TR period gasoline vehicles contributed less VOCs in percentages while industrial sources, biomass burning and LPG shared larger percentages. Assuming that emissions from industrial sources remained unchanged during the TR and non-TR periods, we further used the PMF-retrieved contribution percentages to deduce the reduction rate of traffic-related VOC emissions, and obtained a reduction rate of 31% based on monitoring data at the roadside site and of 34% based on the monitoring data at the rooftop site. Considering VOC emissions from all sources in Guangzhou city, the TR control measures adopted could reduce VOC up to 15%.

Microbiological characterization and probiotic potential of koko and koko sour water, African spontaneously fermented millet porridge and drink.

PubMed

Lei, V; Jakobsen, M

2004-01-01

To identify and examine the diversity of predominant lactic acid bacteria (LAB) in koko and koko sour water (KSW) from different Ghanaian production sites with regard to pattern of fermentation (API 50 CHL), genotype, antimicrobial activity, and resistance to low pH and bile salts. In total 215 LAB were isolated from koko and KSW. The isolates were identified using intergenic transcribed spacers (ITS)-PCR restriction fragment length polymorphism (RFLP), API 50 CHL, restriction enzyme analysis with pulsed-field gel electrophoresis (REA-PFGE) and sequencing of the 16S rRNA gene. The dominating micro-organisms in koko was found to be Weisella confusa and Lactobacillus fermentum, followed by Lact. salivarius and Pediococcus spp. Chemometric data analysis were used to link the LAB species to the different production stages and production sites. At intra-species level the isolates were found to have a great diversity. The isolates were investigated for antimicrobial activity using agar diffusion assays, and acid and bile tolerance. Most isolates showed low levels of antimicrobial activity towards the indicator strain Listeria innocua, but not towards the bacteriocin-sensitive Lact. sakei. Growth of all LAB isolates was unaffected by the presence of 0.3% (v/v) oxgall bile. The isolates were able to survive, but were not able to grow in growth medium adjusted to pH 2.5. The dominating LAB of koko and KSW were W. confusa and Lact. fermentum showing a pronounced taxonomic biodiversity at sub-species level between stages within the production as well as between production sites. Other species observed in KSW were Lact. salivarius, Ped. pentosaceus, Ped. acidilactici and Lact. paraplantarum. They occurred in levels of 108 CFU ml-1 in fresh KSW and showed uniform antimicrobial activity, and acid and bile tolerance. The present study gives a detailed picture of the taxonomy and diversity of LAB in an African-fermented millet product that may have potential as a probiotic product for the local population. The chemometric tools Principal Component Analysis and anova Partial Least Squares Regression were proven to be useful in the analysis of microbial groupings and associations with specific sites and stages in the production of koko and KSW.

Honey Bee Location- and Time-Linked Memory Use in Novel Foraging Situations: Floral Color Dependency

PubMed Central

Amaya-Márquez, Marisol; Hill, Peggy S. M.; Abramson, Charles I.; Wells, Harrington

2014-01-01

Learning facilitates behavioral plasticity, leading to higher success rates when foraging. However, memory is of decreasing value with changes brought about by moving to novel resource locations or activity at different times of the day. These premises suggest a foraging model with location- and time-linked memory. Thus, each problem is novel, and selection should favor a maximum likelihood approach to achieve energy maximization results. Alternatively, information is potentially always applicable. This premise suggests a different foraging model, one where initial decisions should be based on previous learning regardless of the foraging site or time. Under this second model, no problem is considered novel, and selection should favor a Bayesian or pseudo-Bayesian approach to achieve energy maximization results. We tested these two models by offering honey bees a learning situation at one location in the morning, where nectar rewards differed between flower colors, and examined their behavior at a second location in the afternoon where rewards did not differ between flower colors. Both blue-yellow and blue-white dimorphic flower patches were used. Information learned in the morning was clearly used in the afternoon at a new foraging site. Memory was not location-time restricted in terms of use when visiting either flower color dimorphism. PMID:26462587

Deep mutational scanning identifies sites in influenza nucleoprotein that affect viral inhibition by MxA

PubMed Central

Ashenberg, Orr; Padmakumar, Jai

2017-01-01

The innate-immune restriction factor MxA inhibits influenza replication by targeting the viral nucleoprotein (NP). Human influenza virus is more resistant than avian influenza virus to inhibition by human MxA, and prior work has compared human and avian viral strains to identify amino-acid differences in NP that affect sensitivity to MxA. However, this strategy is limited to identifying sites in NP where mutations that affect MxA sensitivity have fixed during the small number of documented zoonotic transmissions of influenza to humans. Here we use an unbiased deep mutational scanning approach to quantify how all single amino-acid mutations to NP affect MxA sensitivity in the context of replication-competent virus. We both identify new sites in NP where mutations affect MxA resistance and re-identify mutations known to have increased MxA resistance during historical adaptations of influenza to humans. Most of the sites where mutations have the greatest effect are almost completely conserved across all influenza A viruses, and the amino acids at these sites confer relatively high resistance to MxA. These sites cluster in regions of NP that appear to be important for its recognition by MxA. Overall, our work systematically identifies the sites in influenza nucleoprotein where mutations affect sensitivity to MxA. We also demonstrate a powerful new strategy for identifying regions of viral proteins that affect inhibition by host factors. PMID:28346537

Population Genomics of Daphnia pulex

PubMed Central

Lynch, Michael; Gutenkunst, Ryan; Ackerman, Matthew; Spitze, Ken; Ye, Zhiqiang; Maruki, Takahiro; Jia, Zhiyuan

2017-01-01

Using data from 83 isolates from a single population, the population genomics of the microcrustacean Daphnia pulex are described and compared to current knowledge for the only other well-studied invertebrate, Drosophila melanogaster. These two species are quite similar with respect to effective population sizes and mutation rates, although some features of recombination appear to be different, with linkage disequilibrium being elevated at short (<100 bp) distances in D. melanogaster and at long distances in D. pulex. The study population adheres closely to the expectations under Hardy–Weinberg equilibrium, and reflects a past population history of no more than a twofold range of variation in effective population size. Fourfold redundant silent sites and a restricted region of intronic sites appear to evolve in a nearly neutral fashion, providing a powerful tool for population genetic analyses. Amino acid replacement sites are predominantly under strong purifying selection, as are a large fraction of sites in UTRs and intergenic regions, but the majority of SNPs at such sites that rise to frequencies >0.05 appear to evolve in a nearly neutral fashion. All forms of genomic sites (including replacement sites within codons, and intergenic and UTR regions) appear to be experiencing an ∼2× higher level of selection scaled to the power of drift in D. melanogaster, but this may in part be a consequence of recent demographic changes. These results establish D. pulex as an excellent system for future work on the evolutionary genomics of natural populations. PMID:27932545

Timing and magnitude of Broad-winged Hawk migration at Montclair Hawk Lookout, New Jersey, and Hawk Mountain Sanctuary, Pennsylvania

USGS Publications Warehouse

Miller, M.W.; Greenstone, E.M.; Greenstone, W.; Bildstein, K.L.

2002-01-01

The Broad-winged Hawk (Buteo platypterus) breeds in eastern and central Canada and the United States, and winters in Central America and northern and central South America. Birders and ornithologists count migrating Broad-winged Hawks at dozens of traditional watch sites throughout the northeastern United States. We modeled counts of migrating Broad-winged Hawks from two raptor migration watch sites: Montclair Hawk Lookout, New Jersey, and Hawk Mountain Sanctuary, Pennsylvania, to determine whether annual abundance and trend estimates from individual sites within the mid-Atlantic states are representative of the region as a whole. We restricted ourselves to counts made between 10:00 and 16:00 EST during September to standardize count effort between sites. We created one model set for annual counts and another model set for daily counts. When modeling daily counts we incorporated weather and identity of individual observers. Akaike's Information Criteria were used to select the best model from an initial set of competing models. Annual counts declined at both sites during 1979-1998. Broad-winged Hawk migration began, peaked, and ended later at Montclair than at Hawk Mountain, even though Hawk Mountain is 155 km west-southwest of Montclair. Mean annual counts of hawks at Montclair were more than twice those at Hawk Mountain, but were not correlated. Broad-winged Hawks counted at Montclair may not be the same birds as those counted at Hawk Mountain. Rather, the two sites may be monitoring different regional subpopulations. Broad-winged Hawks counted at the two sites may use different migration tactics, with those counted at Hawk Mountain being more likely to slope soar, and those at Montclair more likely to use thermal soaring. A system of multiple watch sites is needed to monitor various breeding populations of this widely dispersed migrant.

A combined EPR and MD simulation study of a nitroxyl spin label with restricted internal mobility sensitive to protein dynamics.

PubMed

Oganesyan, Vasily S; Chami, Fatima; White, Gaye F; Thomson, Andrew J

2017-01-01

EPR studies combined with fully atomistic Molecular Dynamics (MD) simulations and an MD-EPR simulation method provide evidence for intrinsic low rotameric mobility of a nitroxyl spin label, Rn, compared to the more widely employed label MTSL (R1). Both experimental and modelling results using two structurally different sites of attachment to Myoglobin show that the EPR spectra of Rn are more sensitive to the local protein environment than that of MTSL. This study reveals the potential of using the Rn spin label as a reporter of protein motions. Copyright © 2016 Elsevier Inc. All rights reserved.

Caffeine inhibition of aflatoxin synthesis: probable site of action.

PubMed Central

Buchanan, R L; Lewis, D F

1984-01-01

Aflatoxin production by pregrown cultures of Aspergillus parasiticus was completely inhibited by incorporation of 2 mg of caffeine per ml into the medium. This was accompanied by a decrease in glucose utilization and an inhibition of oxygen uptake and carbon dioxide evolution. Enzyme analyses indicated no significant differences in specific activities on glucose-6-phosphate dehydrogenase, mannitol dehydrogenase, phosphofructokinase, fructose 1,6-diphosphatase, pyruvate kinase, or malate dehydrogenase. Glucose uptake kinetics indicated a linear dose-related inhibition of glucose uptake. It appears likely that caffeine inhibits aflatoxin synthesis by restricting the uptake of carbohydrates which are ultimately used by the mold to synthesize this family of mycotoxins. PMID:6331311

Evaluation of Microbial Diversity in Wetland through Polymerase Chain Reaction (PCR) and Restriction Fragment Length Polymorphism (RFLP)

DTIC Science & Technology

2006-06-01

51 Appendix C. Promega Restriction Digest Protocol ....................................................53...Rsa1 Restriction Digest Results............................................................................180 9. DNA Base Pair Comparison...particular restriction endonuclease, the length of the fragments produced will differ when the DNA is digested with a restriction enzyme (Edwards

Estimating restricted mean treatment effects with stacked survival models

PubMed Central

Wey, Andrew; Vock, David M.; Connett, John; Rudser, Kyle

2016-01-01

The difference in restricted mean survival times between two groups is a clinically relevant summary measure. With observational data, there may be imbalances in confounding variables between the two groups. One approach to account for such imbalances is estimating a covariate-adjusted restricted mean difference by modeling the covariate-adjusted survival distribution, and then marginalizing over the covariate distribution. Since the estimator for the restricted mean difference is defined by the estimator for the covariate-adjusted survival distribution, it is natural to expect that a better estimator of the covariate-adjusted survival distribution is associated with a better estimator of the restricted mean difference. We therefore propose estimating restricted mean differences with stacked survival models. Stacked survival models estimate a weighted average of several survival models by minimizing predicted error. By including a range of parametric, semi-parametric, and non-parametric models, stacked survival models can robustly estimate a covariate-adjusted survival distribution and, therefore, the restricted mean treatment effect in a wide range of scenarios. We demonstrate through a simulation study that better performance of the covariate-adjusted survival distribution often leads to better mean-squared error of the restricted mean difference although there are notable exceptions. In addition, we demonstrate that the proposed estimator can perform nearly as well as Cox regression when the proportional hazards assumption is satisfied and significantly better when proportional hazards is violated. Finally, the proposed estimator is illustrated with data from the United Network for Organ Sharing to evaluate post-lung transplant survival between large and small-volume centers. PMID:26934835

Different Levels of Food Restriction Reveal Genotype-Specific Differences in Learning a Visual Discrimination Task

PubMed Central

Makowiecki, Kalina; Hammond, Geoff; Rodger, Jennifer

2012-01-01

In behavioural experiments, motivation to learn can be achieved using food rewards as positive reinforcement in food-restricted animals. Previous studies reduce animal weights to 80–90% of free-feeding body weight as the criterion for food restriction. However, effects of different degrees of food restriction on task performance have not been assessed. We compared learning task performance in mice food-restricted to 80 or 90% body weight (BW). We used adult wildtype (WT; C57Bl/6j) and knockout (ephrin-A2−/−) mice, previously shown to have a reverse learning deficit. Mice were trained in a two-choice visual discrimination task with food reward as positive reinforcement. When mice reached criterion for one visual stimulus (80% correct in three consecutive 10 trial sets) they began the reverse learning phase, where the rewarded stimulus was switched to the previously incorrect stimulus. For the initial learning and reverse phase of the task, mice at 90%BW took almost twice as many trials to reach criterion as mice at 80%BW. Furthermore, WT 80 and 90%BW groups significantly differed in percentage correct responses and learning strategy in the reverse learning phase, whereas no differences between weight restriction groups were observed in ephrin-A2−/− mice. Most importantly, genotype-specific differences in reverse learning strategy were only detected in the 80%BW groups. Our results indicate that increased food restriction not only results in better performance and a shorter training period, but may also be necessary for revealing behavioural differences between experimental groups. This has important ethical and animal welfare implications when deciding extent of diet restriction in behavioural studies. PMID:23144936

Different levels of food restriction reveal genotype-specific differences in learning a visual discrimination task.

PubMed

Makowiecki, Kalina; Hammond, Geoff; Rodger, Jennifer

2012-01-01

In behavioural experiments, motivation to learn can be achieved using food rewards as positive reinforcement in food-restricted animals. Previous studies reduce animal weights to 80-90% of free-feeding body weight as the criterion for food restriction. However, effects of different degrees of food restriction on task performance have not been assessed. We compared learning task performance in mice food-restricted to 80 or 90% body weight (BW). We used adult wildtype (WT; C57Bl/6j) and knockout (ephrin-A2⁻/⁻) mice, previously shown to have a reverse learning deficit. Mice were trained in a two-choice visual discrimination task with food reward as positive reinforcement. When mice reached criterion for one visual stimulus (80% correct in three consecutive 10 trial sets) they began the reverse learning phase, where the rewarded stimulus was switched to the previously incorrect stimulus. For the initial learning and reverse phase of the task, mice at 90%BW took almost twice as many trials to reach criterion as mice at 80%BW. Furthermore, WT 80 and 90%BW groups significantly differed in percentage correct responses and learning strategy in the reverse learning phase, whereas no differences between weight restriction groups were observed in ephrin-A2⁻/⁻ mice. Most importantly, genotype-specific differences in reverse learning strategy were only detected in the 80%BW groups. Our results indicate that increased food restriction not only results in better performance and a shorter training period, but may also be necessary for revealing behavioural differences between experimental groups. This has important ethical and animal welfare implications when deciding extent of diet restriction in behavioural studies.

Cigars, youth, and the Internet link.

PubMed Central

Malone, R E; Bero, L A

2000-01-01

OBJECTIVES: This study examined the accessibility and appeal to youth of cigar marketing sites on the Internet. METHODS: Sites marketing cigars (n = 141) were examined for age restrictions, prices, health warnings, and other elements. RESULTS: Although it is illegal for minors to purchase tobacco, only 36 sites (25.5%) prohibited purchases by minors. Sites offered low prices, and 32% accepted money orders, cashier's checks, or cash-on-delivery (COD) orders. Almost 30% of the sites included elements with potential youth appeal; only 3.5% displayed health warnings. CONCLUSIONS: The unregulated promotion of cigars on the Internet has the potential to attract youth, and there are few barriers to Internet tobacco purchases by minors. PMID:10800432

Population structure of Columbia spotted frogs (Rana luteiventris) is strongly affected by the landscape

USGS Publications Warehouse

Funk, W.C.; Blouin, M.S.; Corn, P.S.; Maxell, B.A.; Pilliod, D.S.; Amish, S.; Allendorf, F.W.

2005-01-01

Landscape features such as mountains, rivers, and ecological gradients may strongly affect patterns of dispersal and gene flow among populations and thereby shape population dynamics and evolutionary trajectories. The landscape may have a particularly strong effect on patterns of dispersal and gene flow in amphibians because amphibians are thought to have poor dispersal abilities. We examined genetic variation at six microsatellite loci in Columbia spotted frogs (Rana luteiventris) from 28 breeding ponds in western Montana and Idaho, USA, in order to investigate the effects of landscape structure on patterns of gene flow. We were particularly interested in addressing three questions: (i) do ridges act as barriers to gene flow? (ii) is gene flow restricted between low and high elevation ponds? (iii) does a pond equal a 'randomly mating population' (a deme)? We found that mountain ridges and elevational differences were associated with increased genetic differentiation among sites, suggesting that gene flow is restricted by ridges and elevation in this species. We also found that populations of Columbia spotted frogs generally include more than a single pond except for very isolated ponds. There was also evidence for surprisingly high levels of gene flow among low elevation sites separated by large distances. Moreover, genetic variation within populations was strongly negatively correlated with elevation, suggesting effective population sizes are much smaller at high elevation than at low elevation. Our results show that landscape features have a profound effect on patterns of genetic variation in Columbia spotted frogs.

Simulations, Games, and Virtual Labs for Science Education: a Compendium and Some Examples

NASA Astrophysics Data System (ADS)

Russell, R. M.

2011-12-01

We have assembled a list of computer-based simulations, games, and virtual labs for science education. This list, with links to the sources of these resources, is available online. The entries span a broad range of science, math, and engineering topics. They also span a range of target student ages, from elementary school to university students. We will provide a brief overview of this web site and the resources found on it. We will also briefly demonstrate some of our own educational simulations, including the "Very, Very Simple Climate Model", and report on formative evaluations of these resources. Computer-based simulations and virtual labs are valuable resources for science educators in various settings, allowing learners to experiment and explore "what if" scenarios. Educational computer games can motivate learners in both formal and informal settings, encouraging them to spend much more time exploring a topic than they might otherwise be inclined to do. Part of this presentation is effectively a "literature review" of numerous sources of simulations, games, and virtual labs. Although we have encountered several nice collections of such resources, those collections seem to be restricted in scope. They either represent materials developed by a specific group or agency (e.g. NOAA's games web site) or are restricted to a specific discipline (e.g. geology simulations and virtual labs). This presentation directs viewers to games, simulations, and virtual labs from many different sources and spanning a broad range of STEM disciplines.

Identification of the structural mutation responsible for the dibucaine-resistant (atypical) variant form of human serum cholinesterase

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

McGuire, M.C.; Nogueira, C.P.; Bartels, C.F.

1989-02-01

A point mutation in the gene for human serum cholinesterase was identified that changes Asp-70 to Gly in the atypical form of serum cholinesterase. The mutation in nucleotide 209, which changes codon 70 from GAT to GGT, was found by sequencing a genomic clone and sequencing selected regions of DNA amplified by the polymerase chain reaction. The entire coding sequences for usual and atypical cholinesterases were compared, and no other consistent base differences were found. The nucleotide-209 mutation was detected in all five atypical cholinesterase families examined. There was complete concordance between this mutation and serum cholinesterase phenotypes for allmore » 14 heterozygous and 6 homozygous atypical subjects tested. The mutation causes the loss of a Sau3A1 restriction site; the resulting DNA fragment length polymorphism was verified by electrophoresis of {sup 32}P-labeled DNA restriction fragments from usual and atypical subjects. Dot-blot hybridization analysis with a 19-mer allele-specific probe to the DNA amplified by the polymerase chain reaction distinguished between the usual and atypical genotypes. The authors conclude that the Asp-70 {yields} Gly mutation accounts for reduced affinity of atypical cholinesterase for choline esters and that Asp-70 must be an important component of the anionic site. Heterogeneity in atypical alleles may exist, but the Asp-70 point mutation may represent an appreciable portion of the atypical gene pool.« less

Path-preference cellular-automaton model for traffic flow through transit points and its application to the transcription process in human cells.

PubMed

Ohta, Yoshihiro; Nishiyama, Akinobu; Wada, Yoichiro; Ruan, Yijun; Kodama, Tatsuhiko; Tsuboi, Takashi; Tokihiro, Tetsuji; Ihara, Sigeo

2012-08-01

We all use path routing everyday as we take shortcuts to avoid traffic jams, or by using faster traffic means. Previous models of traffic flow of RNA polymerase II (RNAPII) during transcription, however, were restricted to one dimension along the DNA template. Here we report the modeling and application of traffic flow in transcription that allows preferential paths of different dimensions only restricted to visit some transit points, as previously introduced between the 5' and 3' end of the gene. According to its position, an RNAPII protein molecule prefers paths obeying two types of time-evolution rules. One is an asymmetric simple exclusion process (ASEP) along DNA, and the other is a three-dimensional jump between transit points in DNA where RNAPIIs are staying. Simulations based on our model, and comparison experimental results, reveal how RNAPII molecules are distributed at the DNA-loop-formation-related protein binding sites as well as CTCF insulator proteins (or exons). As time passes after the stimulation, the RNAPII density at these sites becomes higher. Apparent far-distance jumps in one dimension are realized by short-range three-dimensional jumps between DNA loops. We confirm the above conjecture by applying our model calculation to the SAMD4A gene by comparing the experimental results. Our probabilistic model provides possible scenarios for assembling RNAPII molecules into transcription factories, where RNAPII and related proteins cooperatively transcribe DNA.

Analysis of bacterial communities associated with the benthic amphipod Diporeia in the Laurentian Great Lakes Basin.

PubMed

Winters, Andrew D; Marsh, Terence L; Brenden, Travis O; Faisal, Mohamed

2015-01-01

Bacterial communities play important roles in the biological functioning of crustaceans, yet little is known about their diversity, structure, and dynamics. This study was conducted to investigate the bacterial communities associated with the benthic amphipod Diporeia, an important component in the Great Lakes foodweb that has been declining over the past 3 decades. In this study, the combination of 16S rRNA gene sequencing and terminal restriction fragment length polymorphism revealed a total of 175 and 138 terminal restriction fragments (T-RFs) in Diporeia samples following treatment with the endonucleases HhaI and MspI, respectively. Relatively abundant and prevalent T-RFs were affiliated with the genera Flavobacterium and Pseudomonas and the class Betaproteobacteria. T-RFs affiliated with the order Rickettsiales were also detected. A significant difference in T-RF presence and abundance (P = 0.035) was detected among profiles generated for Diporeia collected from 4 sites in Lake Michigan. Comparison of profiles generated for Diporeia samples collected in 2 years from lakes Superior and Michigan showed a significant change in diversity for Lake Superior Diporeia but not Lake Michigan Diporeia. Profiles from one Lake Michigan site contained multiple unique T-RFs compared with other Lake Michigan Diporeia profiles, most notably one that represents the genus Methylotenera. This study generated the most extensive list of bacteria associated with Diporeia and sheds useful insights on the microbiome of Great Lakes Diporeia that may help to reveal potential causes of the decline of Diporeia populations.

Divergence, differential methylation and interspersion of melon satellite DNA sequences.

PubMed Central

Shmookler Reis, R; Timmis, J N; Ingle, J

1981-01-01

Melon (Cucumis melo) satellite DNA consists of two components, Q and S, each with a buoyant density in CsCl of 1.707 g/ml, but differing by 9 degrees C in "melting" temperature. These physical properties appear to be in contradiction, since both depend on G + C content. In order to resolve this anomaly, base compositions were directly determined for isolated fractions. the low-"melting" component S contains 41.8% G + C, with 6% of C present as 5-methylcytosine, whereas Q DNA contains 54% G + C, with 41% of C methylated. Analyses of restriction site loss agreed well with the direct determinations of methylation and divergence, and indicated some clustering of methylated sites in Q DNA. Analysis of restricted main-band DNA by hydridization with RNA complementary to Q satellite DNA ("Southern transfer") showed satellite Q tandem arrays interspersed in DNA of main-band density. Sequence divergence and extent of methylation did not appear to depend on whether a repeat array was present as satellite or interspersed in main-band DNA. Hydridization in situ indicated considerable heterogeneity in the genomic proportion of the Q-DNA sequences in melon fruit nuclei, implying over- and under-representation consistent with extensive unequal recombination in satellite Q tandem arrays. The cucumber, Cucumis sativus, contains less than 8% as much Q-homologous DNA per genome as the melon, suggesting rapid evolutionary gain or loss of these tandem repeat sequences. Images Fig. 2. PLATE 1 Fig. 4. Fig. 10. PMID:6172117

Biodiversity study of wine yeasts belonging to the "terroir" of Montepulciano d'Abruzzo "Colline Teramane" revealed Saccharomyces cerevisiae strains exhibiting atypical and unique 5.8S-ITS restriction patterns.

PubMed

Tofalo, Rosanna; Perpetuini, Giorgia; Fasoli, Giuseppe; Schirone, Maria; Corsetti, Aldo; Suzzi, Giovanna

2014-05-01

The Montepulciano d'Abruzzo "Colline Teramane" premium wine DOCG is produced in the Teramo province (Abruzzo, Italy). This region has a great tradition in winemaking and the wine is produced by a spontaneous fermentation so it could represent a reservoir of wine natural yeasts with important oenological features. The aim of this study was to characterize the yeast community of this wine grape growing region in order to create a Saccharomyces cerevisiae bank, providing data on oenological properties for potential industrial applications. A total of 430 yeasts were isolated at the end of spontaneous fermentation. PCR-RFLP was applied for the identification at the species level and underlined that 14 strains exhibited unusual and characteristic restriction patterns different from those typical of the species S. cerevisiae. This difference was due to the insertion of base C at a position 138 in the ITS1 region that determined an additional cleavage site for the enzyme HaeIII. This insertion could be associated to the fermentative performance and associated to the relationship existing between yeasts and a viticulture region or 'terroir'. Copyright © 2013 Elsevier Ltd. All rights reserved.

Isolation and Identification of Pathogenicity Mutant of Curvularia lunata via Restriction Enzyme-Mediated Integration.

PubMed

Wang, Y J; Liu, T; Hou, J M; Zuo, Y H

2013-09-01

In this report, 156 hygromycin-resistant mutants were generated via restriction enzyme-mediated insertional (REMI) mutagenesis. All mutants were subjected to a bioassay on detached leaves. Five mutants (T4, T39, T71, T91, and T135) showed reduced symptom development, whereas one mutant (T120) did not exhibit any symptoms on the leaves compared with the wild type. The pathogenicity of these mutants was further assayed through the spray inoculation of whole seedlings. The results demonstrated that the pathogenicity of the T4, T39, T71, T91, and T135 mutants was reduced, whereas the T120 mutant lost its pathogenicity. Southern blot analysis revealed that the plasmids were inserted at different sites in the genome with different copy numbers. Flanking sequences approximately 550, 860, and 150 bp were obtained from T7, T91, and T120, respectively through plasmids rescue. Sequence analysis of the flanking sequences from T7 and T91 showed no homology to any known sequences in GenBank. The flanking sequence from the T120 mutant was highly homologous to MAPKK kinases, which regulates sexual/asexual development, melanization, pathogenicity from Cochliobolus heterostrophus. These results indicate that REMI and plasmids rescue have great potential for finding pathogenicity genes.

Restricted gene flow and fine-scale population structuring in tool using New Caledonian crows

NASA Astrophysics Data System (ADS)

Rutz, C.; Ryder, T. B.; Fleischer, R. C.

2012-04-01

New Caledonian crows Corvus moneduloides are the most prolific avian tool users. It has been suggested that some aspects of their complex tool use behaviour are under the influence of cultural processes, involving the social transmission—and perhaps even progressive refinement—of tool designs. Using microsatellite and mt-haplotype profiling of crows from three distinct habitats (dry forest, farmland and beachside habitat), we show that New Caledonian crow populations can exhibit significant fine-scale genetic structuring. Our finding that some sites of <10 km apart were highly differentiated demonstrates considerable potential for genetic and/or cultural isolation of crow groups. Restricted movement of birds between local populations at such small spatial scales, especially across habitat boundaries, illustrates how specific tool designs could be preserved over time, and how tool technologies of different crow groups could diverge due to drift and local selection pressures. Young New Caledonian crows have an unusually long juvenile dependency period, during which they acquire complex tool-related foraging skills. We suggest that the resulting delayed natal dispersal drives population-divergence patterns in this species. Our work provides essential context for future studies that examine the genetic makeup of crow populations across larger geographic areas, including localities with suspected cultural differences in crow tool technologies.

RADseq provides unprecedented insights into molecular ecology and evolutionary genetics: comment on Breaking RAD by Lowry et al. (2016).

PubMed

McKinney, Garrett J; Larson, Wesley A; Seeb, Lisa W; Seeb, James E

2017-05-01

In their recently corrected manuscript, "Breaking RAD: An evaluation of the utility of restriction site associated DNA sequencing for genome scans of adaptation", Lowry et al. argue that genome scans using RADseq will miss many loci under selection due to a combination of sparse marker density and low levels of linkage disequilibrium in most species. We agree that marker density and levels of LD are important considerations when designing a RADseq study; however, we dispute that RAD-based genome scans are as prone to failure as Lowry et al. suggest. Their arguments ignore the flexible nature of RADseq; the availability of different restriction enzymes and capacity for combining restriction enzymes ensures that a well-designed study should be able to generate enough markers for efficient genome coverage. We further believe that simplifying assumptions about linkage disequilibrium in their simulations are invalid in many species. Finally, it is important to note that the alternative methods proposed by Lowry et al. have limitations equal to or greater than RADseq. The wealth of studies with positive impactful findings that have used RAD genome scans instead supports the argument that properly conducted RAD genome scans are an effective method for gaining insight into ecology and evolution, particularly for non-model organisms and those with large or complex genomes. © 2016 John Wiley & Sons Ltd.

A Novel Tool for Microbial Genome Editing Using the Restriction-Modification System.

PubMed

Bai, Hua; Deng, Aihua; Liu, Shuwen; Cui, Di; Qiu, Qidi; Wang, Laiyou; Yang, Zhao; Wu, Jie; Shang, Xiuling; Zhang, Yun; Wen, Tingyi

2018-01-19

Scarless genetic manipulation of genomes is an essential tool for biological research. The restriction-modification (R-M) system is a defense system in bacteria that protects against invading genomes on the basis of its ability to distinguish foreign DNA from self DNA. Here, we designed an R-M system-mediated genome editing (RMGE) technique for scarless genetic manipulation in different microorganisms. For bacteria with Type IV REase, an RMGE technique using the inducible DNA methyltransferase gene, bceSIIM (RMGE-bceSIIM), as the counter-selection cassette was developed to edit the genome of Escherichia coli. For bacteria without Type IV REase, an RMGE technique based on a restriction endonuclease (RMGE-mcrA) was established in Bacillus subtilis. These techniques were successfully used for gene deletion and replacement with nearly 100% counter-selection efficiencies, which were higher and more stable compared to conventional methods. Furthermore, precise point mutation without limiting sites was achieved in E. coli using RMGE-bceSIIM to introduce a single base mutation of A128C into the rpsL gene. In addition, the RMGE-mcrA technique was applied to delete the CAN1 gene in Saccharomyces cerevisiae DAY414 with 100% counter-selection efficiency. The effectiveness of the RMGE technique in E. coli, B. subtilis, and S. cerevisiae suggests the potential universal usefulness of this technique for microbial genome manipulation.

Uncoupling metallonuclease metal ion binding sites via nudge mutagenesis.

PubMed

Papadakos, Grigorios A; Nastri, Horacio; Riggs, Paul; Dupureur, Cynthia M

2007-05-01

The hydrolysis of phosphodiester bonds by nucleases is critical to nucleic acid processing. Many nucleases utilize metal ion cofactors, and for a number of these enzymes two active-site metal ions have been detected. Testing proposed mechanistic roles for individual bound metal ions has been hampered by the similarity between the sites and cooperative behavior. In the homodimeric PvuII restriction endonuclease, the metal ion dependence of DNA binding is sigmoidal and consistent with two classes of coupled metal ion binding sites. We reasoned that a conservative active-site mutation would perturb the ligand field sufficiently to observe the titration of individual metal ion binding sites without significantly disturbing enzyme function. Indeed, mutation of a Tyr residue 5.5 A from both metal ions in the enzyme-substrate crystal structure (Y94F) renders the metal ion dependence of DNA binding biphasic: two classes of metal ion binding sites become distinct in the presence of DNA. The perturbation in metal ion coordination is supported by 1H-15N heteronuclear single quantum coherence spectra of enzyme-Ca(II) and enzyme-Ca(II)-DNA complexes. Metal ion binding by free Y94F is basically unperturbed: through multiple experiments with different metal ions, the data are consistent with two alkaline earth metal ion binding sites per subunit of low millimolar affinity, behavior which is very similar to that of the wild type. The results presented here indicate a role for the hydroxyl group of Tyr94 in the coupling of metal ion binding sites in the presence of DNA. Its removal causes the affinities for the two metal ion binding sites to be resolved in the presence of substrate. Such tuning of metal ion affinities will be invaluable to efforts to ascertain the contributions of individual bound metal ions to metallonuclease function.

Ecological Origins of Freedom: Pathogens, Heat Stress, and Frontier Topography Predict More Vertical but Less Horizontal Governmental Restriction.

PubMed

Conway, Lucian Gideon; Bongard, Kate; Plaut, Victoria; Gornick, Laura Janelle; Dodds, Daniel P; Giresi, Thomas; Tweed, Roger G; Repke, Meredith A; Houck, Shannon C

2017-10-01

What kinds of physical environments make for free societies? The present research investigates the effect of three different types of ecological stressors (climate stress, pathogen stress, and frontier topography) on two measurements of governmental restriction: Vertical restriction involves select persons imposing asymmetrical laws on others, while horizontal restriction involves laws that restrict most members of a society equally. Investigation 1 validates our measurements of vertical and horizontal restriction. Investigation 2 demonstrates that, across both U.S. states and a sample of nations, ecological stressors tend to cause more vertically restrictive societies but less horizontally restrictive societies. Investigation 3 demonstrates that assortative sociality partially mediates ecological stress→restriction relationships across nations, but not in U.S. states. Although some stressor-specific effects emerged (most notably, cold stress consistently showed effects in the opposite direction), these results in the main suggest that ecological stress simultaneously creates opposing pressures that push freedom in two different directions.

Effects of restriction on children’s intake differ by child temperament, food reinforcement, and parent’s chronic use of restriction

PubMed Central

Rollins, Brandi Y.; Loken, Eric; Savage, Jennifer S.; Birch, Leann L.

2014-01-01

Parents’ use of restrictive feeding practices is counterproductive, increasing children’s intake of restricted foods and risk for excessive weight gain. The aims of this research were to replicate Fisher and Birch’s (1999b) original findings that short-term restriction increases preschool children’s (3–5 y) selection, intake, and behavioral response to restricted foods, and to identify characteristics of children who were more susceptible to the negative effects of restriction. The experiment used a within-subjects design; 37 children completed the food reinforcement task and heights/weights were measured. Parents reported on their use of restrictive feeding practices and their child’s inhibitory control and approach. Overall, the findings replicated those of Fisher and Birch (1999b) and revealed that the effects of restriction differed by children’s regulatory and appetitive tendencies. Greater increases in intake in response to restriction were observed among children lower in inhibitory control, higher in approach, who found the restricted food highly reinforcing, and who had previous experience with parental use of restriction. Results confirm that parents’ use of restriction does not moderate children’s consumption of these foods, particularly among children with lower regulatory or higher appetitive tendencies. PMID:24511616

Summer carbon dioxide and water vapor fluxes across a range of northern peatlands

NASA Astrophysics Data System (ADS)

Humphreys, Elyn R.; Lafleur, Peter M.; Flanagan, Lawrence B.; Hedstrom, Newell; Syed, Kamran H.; Glenn, Aaron J.; Granger, Raoul

2006-12-01

Northern peatlands are a diverse group of ecosystems varying along a continuum of hydrological, chemical, and vegetation gradients. These ecosystems contain about one third of the global soil carbon pool, but it is uncertain how carbon and water cycling processes and response to climate change differ among peatland types. This study examines midsummer CO2 and H2O fluxes measured using the eddy covariance technique above seven northern peatlands including a low-shrub bog, two open poor fens, two wooded moderately rich fens, and two open extreme-rich fens. Gross ecosystem production and ecosystem respiration correlated positively with vegetation indices and with each other. Consequently, 24-hour net ecosystem CO2 exchange was similar among most of the sites (an average net carbon sink of 1.5 ± 0.2 g C m-2 d-1) despite large differences in water table depth, water chemistry, and plant communities. Evapotranspiration was primarily radiatively driven at all sites but a decline in surface conductance with increasing water vapor deficit indicated physiological restrictions to transpiration, particularly at the peatlands with woody vegetation and less at the peatlands with 100% Sphagnum cover. Despite these differences, midday evapotranspiration ranged only from 0.21 to 0.34 mm h-1 owing to compensation among the factors controlling evapotranspiration. Water use efficiency varied among sites primarily as a result of differences in productivity and plant functional type. Although peatland classification includes a great variety of ecosystem characteristics, peatland type may not be an effective way to predict the magnitude and characteristics of midsummer CO2 and water vapor exchanges.

Installation Restoration Program. Phase 1: Records Search, Sheppard AFB, Texas

DTIC Science & Technology

1984-02-01

Environmental Response, Compensation, and Liability Act (CIERA) of 1980, by Executive Order 12316, and 40 Ci 300 Subpart F (National Contingency Plan). CCLA...hensive Environmental Response, Compensation, and Liability Act of 1980 (CURCLA). A potentially hazardous waste is one which is suspected of being...site for agricultural purposes to prevent food chain contamination. Silvicultural use Restrict the use of the site for silvi- cultural uses (root

Department of the Navy Explosives Safety Site Approval Process Improvement Initiative

DTIC Science & Technology

2010-07-01

All applicable existing land-use restrictions, such as explosives safety quantity distance (ESQD) arcs, Hazards of Electromagnetic Radiation to... Ordnance ( HERO ) zones, air field safety zones, and munitions response program sites are noted in the ESAR.  PWO will have in place a written...N547) Naval Ordnance Safety and Security Activity Farragut Hall, 3817 Strauss Ave, Suite 108 Indian Head, MD 20640-5151 (301) 744-6059

Organization of the BcgI restriction-modification protein for the cleavage of eight phosphodiester bonds in DNA

PubMed Central

Smith, Rachel M.; Marshall, Jacqueline J. T.; Jacklin, Alistair J.; Retter, Susan E.; Halford, Stephen E.; Sobott, Frank

2013-01-01

Type IIB restriction-modification systems, such as BcgI, feature a single protein with both endonuclease and methyltransferase activities. Type IIB nucleases require two recognition sites and cut both strands on both sides of their unmodified sites. BcgI cuts all eight target phosphodiester bonds before dissociation. The BcgI protein contains A and B polypeptides in a 2:1 ratio: A has one catalytic centre for each activity; B recognizes the DNA. We show here that BcgI is organized as A2B protomers, with B at its centre, but that these protomers self-associate to assemblies containing several A2B units. Moreover, like the well known FokI nuclease, BcgI bound to its site has to recruit additional protomers before it can cut DNA. DNA-bound BcgI can alternatively be activated by excess A subunits, much like the activation of FokI by its catalytic domain. Eight A subunits, each with one centre for nuclease activity, are presumably needed to cut the eight bonds cleaved by BcgI. Its nuclease reaction may thus involve two A2B units, each bound to a recognition site, with two more A2B units bridging the complexes by protein–protein interactions between the nuclease domains. PMID:23147005

Differences in antigen presentation to MHC class I-and class II- restricted influenza virus-specific cytolytic T lymphocyte clones

PubMed Central

1986-01-01

We have examined requirements for antigen presentation to a panel of MHC class I-and class II-restricted, influenza virus-specific CTL clones by controlling the form of virus presented on the target cell surface. Both H-2K/D- and I region-restricted CTL recognize target cells exposed to infectious virus, but only the I region-restricted clones efficiently lysed histocompatible target cells pulsed with inactivated virus preparations. The isolated influenza hemagglutinin (HA) polypeptide also could sensitize target cells for recognition by class II-restricted, HA-specific CTL, but not by class I-restricted, HA- specific CTL. Inhibition of nascent viral protein synthesis abrogated the ability of target cells to present viral antigen relevant for class I-restricted CTL recognition. Significantly, presentation for class II- restricted recognition was unaffected in target cells exposed to preparations of either inactivated or infectious virus. This differential sensitivity suggested that these H-2I region-restricted CTL recognized viral polypeptides derived from the exogenously introduced virions, rather than viral polypeptides newly synthesized in the infected cell. In support of this contention, treatment of the target cells with the lysosomotropic agent chloroquine abolished recognition of infected target cells by class II-restricted CTL without diminishing class I-restricted recognition of infected target cells. Furthermore, when the influenza HA gene was introduced into target cells without exogenous HA polypeptide, the target cells that expressed the newly synthesized protein product of the HA gene were recognized only by H-2K/D-restricted CTL. These observations suggest that important differences may exist in requirements for antigen presentation between H-2K/D and H-2I region-restricted CTL. These differences may reflect the nature of the antigenic epitopes recognized by these two CTL subsets. PMID:3485173

Supporting the Future Air Traffic Control Projection Process

NASA Technical Reports Server (NTRS)

Davison, Hayley J.; Hansman, R. John, Jr.

2002-01-01

In air traffic control, projecting what the air traffic situation will be over the next 30 seconds to 30 minutes is a key process in identifying conflicts that may arise so that evasive action can be taken upon discovery of these conflicts. A series of field visits in the Boston and New York terminal radar approach control (TRACON) facilities and in the oceanic air traffic control facilities in New York and Reykjavik, Iceland were conducted to investigate the projection process in two different ATC domains. The results from the site visits suggest that two types of projection are currently used in ATC tasks, depending on the type of separation minima and/or traffic restriction and information display used by the controller. As technologies improve and procedures change, care should be taken by designers to support projection through displays, automation, and procedures. It is critical to prevent time/space mismatches between interfaces and restrictions. Existing structure in traffic dynamics could be utilized to provide controllers with useful behavioral models on which to build projections. Subtle structure that the controllers are unable to internalize could be incorporated into an ATC projection aid.

AMPK and vacuole-associated Atg14p orchestrate μ-lipophagy for energy production and long-term survival under glucose starvation

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

Seo, Arnold Y.; Lau, Pick -Wei; Feliciano, Daniel

Dietary restriction increases the longevity of many organisms, but the cell signaling and organellar mechanisms underlying this capability are unclear. We demonstrate that to permit long-term survival in response to sudden glucose depletion, yeast cells activate lipid-droplet (LD) consumption through micro-lipophagy (µ-lipophagy), in which fat is metabolized as an alternative energy source. AMP-activated protein kinase (AMPK) activation triggered this pathway, which required Atg14p. More gradual glucose starvation, amino acid deprivation or rapamycin did not trigger µ-lipophagy and failed to provide the needed substitute energy source for long-term survival. During acute glucose restriction, activated AMPK was stabilized from degradation and interactedmore » with Atg14p. This prompted Atg14p redistribution from ER exit sites onto liquid-ordered vacuole membrane domains, initiating µ-lipophagy. Our findings that activated AMPK and Atg14p are required to orchestrate µ-lipophagy for energy production in starved cells is relevant for studies on aging and evolutionary survival strategies of different organisms.« less

AMPK and vacuole-associated Atg14p orchestrate μ-lipophagy for energy production and long-term survival under glucose starvation

DOE PAGES

Seo, Arnold Y.; Lau, Pick -Wei; Feliciano, Daniel; ...

2017-04-10

Dietary restriction increases the longevity of many organisms, but the cell signaling and organellar mechanisms underlying this capability are unclear. We demonstrate that to permit long-term survival in response to sudden glucose depletion, yeast cells activate lipid-droplet (LD) consumption through micro-lipophagy (µ-lipophagy), in which fat is metabolized as an alternative energy source. AMP-activated protein kinase (AMPK) activation triggered this pathway, which required Atg14p. More gradual glucose starvation, amino acid deprivation or rapamycin did not trigger µ-lipophagy and failed to provide the needed substitute energy source for long-term survival. During acute glucose restriction, activated AMPK was stabilized from degradation and interactedmore » with Atg14p. This prompted Atg14p redistribution from ER exit sites onto liquid-ordered vacuole membrane domains, initiating µ-lipophagy. Our findings that activated AMPK and Atg14p are required to orchestrate µ-lipophagy for energy production in starved cells is relevant for studies on aging and evolutionary survival strategies of different organisms.« less

Bipartite Structure of the 5s Ribosomal Gene Family in a Drosophila Melanogaster Strain, and Its Evolutionary Implications

PubMed Central

Samson, M. L.; Wegnez, M.

1988-01-01

Knowledge of multigenic family organization should provide insight into their mode of evolution. Accordingly, we characterized the 5S ribosomal gene family in the Drosophila melanogaster strain ry(506). The 5S genes in this strain display a striking HindIII restriction difference compared to the ``standard'' D. melanogaster 5S genes. The sequence of three ry(506) 5S genes was determined. We show that the HindIII restriction site heterogeneity within the ry(506) 5S family most probably results from the same point mutation, suggesting that a single 5S variant was propagated into the 5S cluster of this strain. Furthermore, we demonstrate that the structural organization of the 5S genes in ry(506) is a bipartite structure, i.e., that about 40% of the 5S genes constitute a HindIII(+)/HindIII(-) mixed cluster, while those remaining constitute an homogeneous HindIII(-) cluster. The events which might lead to such an heterogeneous pattern are discussed from an evolutionary point of view. PMID:2835290

Distribution of Candida albicans genotypes among family members

NASA Technical Reports Server (NTRS)

Mehta, S. K.; Stevens, D. A.; Mishra, S. K.; Feroze, F.; Pierson, D. L.

1999-01-01

Thirty-three families (71 subjects) were screened for the presence of Candida albicans in mouthwash or stool specimens; 12 families (28 subjects) were culture-positive for this yeast. An enrichment procedure provided a twofold increase in the recovery of C. albicans from mouthwash specimens. Nine of the twelve culture-positive families had two positive members each, two families had three positive members each, and one family had four positive members. Genetic profiles were obtained by three methods: pulsed-field gel electrophoresis; restriction endonuclease analysis, and random amplification of polymorphic DNA analysis. DNA fingerprinting of C. albicans isolated from one body site three consecutive times revealed that each of the 12 families carried a distinct genotype. No two families shared the same strain, and two or more members of a family commonly shared the same strain. Intrafamily genotypic identity (i.e., each member within the family harbored the same strain) was demonstrated in six families. Genotypes of isolates from husband and wife differed from one another in five families. All three methods were satisfactory in determining genotypes; however, we concluded that restriction endonuclease analysis provided adequate resolving power.

New insights into gill chemoreception: receptor distribution and roles in water and air breathing fish.

PubMed

Milsom, William K

2012-12-01

The location (gills, oro-branchial cavity or elsewhere) and orientation (external (water) or internal (blood) sensing) of the receptors involved in reflex changes in each of the different components of the cardiorespiratory response (breathing frequency, breath amplitude, heart rate, systemic vascular resistance) to hypoxia and hypercarbia are highly variable between species of water and air breathing fish. Although not universal, the receptors involved in eliciting changes in heart rate and breathing frequency in response to hypoxia and hypercarbia tend to be restricted exclusively to the gills while those producing increases in breath amplitude are more wide spread, frequently also being found at extrabranchial sites. The distribution of the chemoreceptors sensitive to CO(2) in the gills involved in producing ventilatory responses tend to be more restricted than that of the O(2)-sensitive chemoreceptors and the specific location of the receptors involved in the various components of the cardiorespiratory response can vary from those of the O(2)-sensitive chemoreceptors. Copyright © 2012 Elsevier B.V. All rights reserved.

[Mitochondrial DNA genetic differentiation of the muksun Coregonus muksun (Pallas) and related Siberian species of Coregonus (Coredonidae, Salmoniformes)].

PubMed

Baldina, S N; Gordon, N Iu; Politov, D V

2008-07-01

Restriction enzyme analysis of the mitochondrial DNA (mtDNA) fragment encoding subunit 1 of the NADH dehydrogenase complex (ND-1) amplified via polymerase chain reaction (PCR) has been used to obtain data on genetic differentiation of muksun Coregonus muksun (Pallas) populations. Population polymorphism with respect to the restriction sites of 18 endonucleases has been described. It has been demonstrated that the muksun is genetically related to the pidschian C. pidschian (Gmelin), its sympatric species in Siberian waters. Analysis of the median network of mtDNA haplotypes has shown that haplotypes of muksun from various Siberian basins form a common group with haplotypes of pidschian of the Arctic Ocean basin, some frequent haplotypes been found in both forms. This raises the question as to the validity of the muksun as a species. Differences within this group of haplotypes are much smaller than those typical of species of the genus Coregonus. The possibility of a hybrid origin of the muksun from a pidschian-like ancestor and species of the cisco-peled (C. sardinella-C. peled) complex is discussed.

Using PCR-RFLP technology to teach single nucleotide polymorphism for undergraduates.

PubMed

Zhang, Bo; Wang, Yan; Xu, Xiaofeng; Guan, Xingying; Bai, Yun

2013-01-01

Recent studies indicated that the aberrant gene expression of peroxiredoxin-6 (prdx6) was found in various kinds of cancers. Because of its biochemical function and gene expression pattern in cancer cells, the association between genetic polymorphism of Prdx6 and cancer onset is interesting. In this report, we have developed and implemented a serial experiment in molecular biology laboratory course to teach single nucleotide polymorphism (SNP) to undergraduate students majoring in molecular biology or genetics. The flanking sequence of rs4382766 was located in Prdx6 gene, which contained a restriction site of SspI, and was used as a target in this lab course. The students could mimic real research by integrating different techniques, such as database retrieving, genomic DNA isolation, PCR, and restriction enzyme assay. This serial experiment of PCR-RFLP helps students set up intact idea of molecular biology and understand the relation among individual experiments. Students were found to be more enthusiastic during the laboratory classes than those in the former curriculum. Copyright © 2013 Wiley Periodicals, Inc.

Environmental Factors Affect Acidobacterial Communities below the Subgroup Level in Grassland and Forest Soils

PubMed Central

Naether, Astrid; Foesel, Bärbel U.; Naegele, Verena; Wüst, Pia K.; Weinert, Jan; Bonkowski, Michael; Alt, Fabian; Oelmann, Yvonne; Polle, Andrea; Lohaus, Gertrud; Gockel, Sonja; Hemp, Andreas; Kalko, Elisabeth K. V.; Linsenmair, Karl Eduard; Pfeiffer, Simone; Renner, Swen; Schöning, Ingo; Weisser, Wolfgang W.; Wells, Konstans; Fischer, Markus; Overmann, Jörg

2012-01-01

In soil, Acidobacteria constitute on average 20% of all bacteria, are highly diverse, and are physiologically active in situ. However, their individual functions and interactions with higher taxa in soil are still unknown. Here, potential effects of land use, soil properties, plant diversity, and soil nanofauna on acidobacterial community composition were studied by cultivation-independent methods in grassland and forest soils from three different regions in Germany. The analysis of 16S rRNA gene clone libraries representing all studied soils revealed that grassland soils were dominated by subgroup Gp6 and forest soils by subgroup Gp1 Acidobacteria. The analysis of a large number of sites (n = 57) by 16S rRNA gene fingerprinting methods (terminal restriction fragment length polymorphism [T-RFLP] and denaturing gradient gel electrophoresis [DGGE]) showed that Acidobacteria diversities differed between grassland and forest soils but also among the three different regions. Edaphic properties, such as pH, organic carbon, total nitrogen, C/N ratio, phosphorus, nitrate, ammonium, soil moisture, soil temperature, and soil respiration, had an impact on community composition as assessed by fingerprinting. However, interrelations with environmental parameters among subgroup terminal restriction fragments (T-RFs) differed significantly, e.g., different Gp1 T-RFs correlated positively or negatively with nitrogen content. Novel significant correlations of Acidobacteria subpopulations (i.e., individual populations within subgroups) with soil nanofauna and vascular plant diversity were revealed only by analysis of clone sequences. Thus, for detecting novel interrelations of environmental parameters with Acidobacteria, individual populations within subgroups have to be considered. PMID:22885760

Impact of Demographic Siting Criteria and Environmental Suitability on Land Availability for Nuclear Reactor Siting

NASA Technical Reports Server (NTRS)

Hansen, K. L.

1982-01-01

The effect of population and certain environmental characteristics on the availability of land for siting nuclear power plants was assessed. The study area, consisting of the 48 contiguous states, was divided into 5 kilometer (km) square grid cells yielding a total of 600,000 cells. Through the use of a modern geographic information system, it was possible to provide a detailed analysis of a quite large area. Numerous maps and statistical tables were produced, the detail of which were limited only by available data. Evaluation issues included population density, restricted lands, seismic hardening, site preparation, water availability, and cost factors.

GeMS: an advanced software package for designing synthetic genes.

PubMed

Jayaraj, Sebastian; Reid, Ralph; Santi, Daniel V

2005-01-01

A user-friendly, advanced software package for gene design is described. The software comprises an integrated suite of programs-also provided as stand-alone tools-that automatically performs the following tasks in gene design: restriction site prediction, codon optimization for any expression host, restriction site inclusion and exclusion, separation of long sequences into synthesizable fragments, T(m) and stem-loop determinations, optimal oligonucleotide component design and design verification/error-checking. The output is a complete design report and a list of optimized oligonucleotides to be prepared for subsequent gene synthesis. The user interface accommodates both inexperienced and experienced users. For inexperienced users, explanatory notes are provided such that detailed instructions are not necessary; for experienced users, a streamlined interface is provided without such notes. The software has been extensively tested in the design and successful synthesis of over 400 kb of genes, many of which exceeded 5 kb in length.

Evaluating the effect of aging on interference resolution with time-varying complex networks analysis

PubMed Central

Ariza, Pedro; Solesio-Jofre, Elena; Martínez, Johann H.; Pineda-Pardo, José A.; Niso, Guiomar; Maestú, Fernando; Buldú, Javier M.

2015-01-01

In this study we used graph theory analysis to investigate age-related reorganization of functional networks during the active maintenance of information that is interrupted by external interference. Additionally, we sought to investigate network differences before and after averaging network parameters between both maintenance and interference windows. We compared young and older adults by measuring their magnetoencephalographic recordings during an interference-based working memory task restricted to successful recognitions. Data analysis focused on the topology/temporal evolution of functional networks during both the maintenance and interference windows. We observed that: (a) Older adults require higher synchronization between cortical brain sites in order to achieve a successful recognition, (b) The main differences between age groups arise during the interference window, (c) Older adults show reduced ability to reorganize network topology when interference is introduced, and (d) Averaging network parameters leads to a loss of sensitivity to detect age differences. PMID:26029079

Effects of protein restriction, melatonin administration, and short daylength on brain benzodiazepine receptors in prepubertal male rats

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

Kennaway, D.J.; Royles, P.; Webb, H.

The possibility that there are changes in brain benzodiazepine binding sites controlled by photoperiod was investigated in two strains of male rats. The hypothesis was tested by 3H-diazepam binding studies in various brain regions of prepubertal rats maintained in 14 or 10 h of light or treated with late-afternoon injections of melatonin (50 micrograms/day). Protein restriction was applied during the experiment to sensitize the animals to the treatments. Under the conditions employed, rats kept in short daylength throughout or kept on long photoperiod and given late-afternoon melatonin injections showed evidence of delayed puberty (seminal vesicle, ventral prostate, and testis weightmore » decreased by 45%, 55%, and 60% respectively, compared to control rats). Binding measurements were made 1 h before and 2 and 5 h after the onset of darkness in the pubertal (42-day-old) or experimentally prepubertal rats. In the rats of the Porton strain (for which protein restriction was obligatory for the gonadal response) there was no consistent treatment or time effects on specific binding of 3H-diazepam to washed membranes of the hypothalamus, midbrain, or striatum. Similarly, there were no differences in the stimulation of 3H-diazepam binding by 100 microM GABA or the inhibition of binding by 50 microM N-acetyl 5 methoxy kynurenamine. By contrast, in Wistar rats, specific binding to midbrain membranes was reduced 5 h after dark compared to 2 h (37% saline; 20% melatonin) and the extent of stimulation by GABA in the hypothalamus was increased 5 h after darkness (35.6% to 46.7% saline; 37.4% to 50% melatonin). Melatonin treatment resulted in significantly higher specific binding in the hypothalamus 2 h after dark (10%, control fed; 20%, protein restricted) but reduced the GABA induced stimulation of binding in the midbrain (35.5% to 25%, control fed; 33.7% to 23.5%, protein restricted).« less

Equations for estimating horizontal response spectra and peak acceleration from western North American earthquakes: A summary of recent work

USGS Publications Warehouse

Boore, D.M.; Joyner, W.B.; Fumal, T.E.

1997-01-01

In this paper we summarize our recently-published work on estimating horizontal response spectra and peak acceleration for shallow earthquakes in western North America. Although none of the sets of coefficients given here for the equations are new, for the convenience of the reader and in keeping with the style of this special issue, we provide tables for estimating random horizontal-component peak acceleration and 5 percent damped pseudo-acceleration response spectra in terms of the natural, rather than common, logarithm of the ground-motion parameter. The equations give ground motion in terms of moment magnitude, distance, and site conditions for strike-slip, reverse-slip, or unspecified faulting mechanisms. Site conditions are represented by the shear velocity averaged over the upper 30 m, and recommended values of average shear velocity are given for typical rock and soil sites and for site categories used in the National Earthquake Hazards Reduction Program's recommended seismic code provisions. In addition, we stipulate more restrictive ranges of magnitude and distance for the use of our equations than in our previous publications. Finally, we provide tables of input parameters that include a few corrections to site classifications and earthquake magnitude (the corrections made a small enough difference in the ground-motion predictions that we chose not to change the coefficients of the prediction equations).

Increased energy intake following sleep restriction in men and women: A one-size-fits-all conclusion?

PubMed

McNeil, Jessica; St-Onge, Marie-Pierre

2017-06-01

This study assessed the degree of interindividual responses in energy intake (EI) to an imposed sleep restriction versus habitual sleep duration protocol. It also investigated participant (age, sex, ethnicity, and BMI) and study (study site and protocol order) characteristics as potential contributors to the variance in EI responses to sleep restriction between individuals. Data from two randomized crossover trials were combined. All participants (n = 43; age: 31 ± 7 years, BMI: 23 ± 2 kg/m 2 ) were free of medical/sleep conditions, were nonsmokers, reported not performing shift work, and had an average sleep duration of 7 to 9 hours per night. Ad libitum, 24-hour EI was objectively assessed following sleep restriction (3.5-4 hours in bed per night) and habitual sleep (7-9 hours in bed per night) conditions. Large interindividual variations in EI change (ΔEI) between restricted and habitual sleep conditions were noted (-813 to 1437 kcal/d). Only phase order was associated with ΔEI (β = -568 kcal/d, 95% confidence interval for β = -921 to -215 kcal/d; P = 0.002); participants randomized to the habitual sleep condition first had greater increases in EI when sleep was restricted (P = 0.01). Large interindividual variations in ΔEI following sleep restriction were noted, suggesting that not all participants were negatively impacted by the effects of sleep restriction. © 2017 The Obesity Society.

Analysis of Alternative (Low Impact) Development on a Theoretical Residential Development in North Central Florida

NASA Astrophysics Data System (ADS)

Wise, W. R.

2001-05-01

Research currently in progress will evaluate land development options on a 161 +/- HA site in North Central Florida lying within a 292+/- HA watershed that contributes to Bullfrog Creek in the Camp Blanding Wildlife Management Area. The research analyzes aspects of an emerging storm-water management philosophy, called low-impact development (LID) by Prince Georges County, Maryland. LID seeks to preserve site hydrology by reducing the area of disturbance on the site, preserving natural drainage features on the site and by utilizing BMPs that promote infiltration and slower transport of runoff. This research investigates the benefits and problems associated with this design philosophy, particularly in Florida. Two scenarios will be investigated: Low density residential and Medium density residential. Within each scenario the hydrologic response of the site under conventional and LID will be explored. Furthermore, the impact of using cluster developments in LIDs will be investigated. Parameters to be measured include: peak flow, runoff volume, pollutant load generated/removed by BMPs, peak-flow timing and base flow. HEC-HMS will be used for hydrologic modeling (soil moisture accounting module). Pollutant loads generated and removed will be based on published data for land use and BMPs. An economic analysis, based on the estimated construction costs of conventional and LID, will also be done. Further sensitivity analyses will be conducted on the effect that various watershed conditions have on the hydrologic response of the site developed as a LID. This research will provide insight to several questions. In the most general sense it will indicate whether this emerging design philosophy, much of which was developed in other regions of the country, is beneficial to Florida watersheds "as it is" and what, if any, alterations should be considered. Secondly, this research will show the impact of development with different site-planning options, for example cluster development versus deed restrictions on lots. Thirdly, the research will give insight to the applicability of this land-development approach under different allowable residential densities. Lastly, the effect of different physical characteristics on the watershed can be explored.

Preferences, specialization, and management attitudes of trout anglers fishing in Tennessee tailwaters

USGS Publications Warehouse

Hutt, C.P.; Bettoli, P.W.

2007-01-01

Efforts to manage several trout fisheries in Tennessee have been stymied by conflicts between management agencies and angler groups. To assist in preventing such conflicts in the future, we examined attitudes and motivations of trout anglers who fished eight tailwater fisheries in Tennessee during 2001-2002. Using a stratified random sampling design, anglers were contacted and interviewed on site (n = 2,643). Those anglers who agreed to complete a questionnaire (n = 1,942) were mailed a 10-page survey. Response rate to the mail survey was 55% after excluding surveys that were undeliverable. Angler subgroups were created using hierarchical cluster analyses of 14 variables related to experience, resource use, investment, and centrality of fishing to their lifestyle. Five subgroups of minimally to highly specialized anglers were identified, and nonhierarchical cluster analysis determined the size of each group (n = 178-369 anglers/group). Subgroups differed in the importance they attached to harvesting trout and catching trophy trout. The most disparate mean ratings among subgroups were for the motive of "obtaining fish to eat." Specialized anglers placed greater importance on catching a trophy fish, experiencing the catch, developing their skills, releasing fish, and restrictive regulations than did less-specialized anglers. Mean ratings for most of nine fishing regulations presented to anglers differed among tailwaters; however, bait restrictions and closed seasons received little support across all rivers. The Caney Fork, Clinch, and Hiwassee rivers had the most uniform distributions of anglers among the five subgroups and thus had a relatively high potential for conflicts over management decisions. The fisheries on the Elk, South Fork Holston, and Watauga rivers were dominated by the most specialized subgroups, indicating that the majority of anglers on those rivers would accept restrictive regulations. ?? Copyright by the American Fisheries Society 2007.

A Rapid Method to Test for Chloroplast DNA Involvement in Atrazine Resistance

PubMed Central

McNally, Sheila; Bettini, Priscilla; Sevignac, Mireille; Darmency, Henry; Gasquez, Jacques; Dron, Michel

1987-01-01

A point mutation in the chloroplast psbA gene at codon 264 resulting in an animo acid substitution (ser-gly) manifests itself as atrazine resistance in all recognized weed species studied to date. The single base substitution overlaps a highly conserved Mae1 restriction site which is present in susceptible but not in resistant plants. This restriction enzyme, recently commercialized, has been used to show that it is now possible to discriminate rapidly between the two biotypes without the need for DNA sequencing. Images Fig. 1 PMID:16665229

Superfund record of decision (EPA Region 3): US Defense General Supply Center (DLA), operable unit 3, Chesterfield County, Richmond, VA, September 29, 1995

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

NONE

This decision document presents the selected remedial action for the National Guard Source Area (NGA), Operable Unit (OU3) at the Defense General Supply Center (DGSC) in Richmond, Virginia. Operable Unit 3 addresses the contaminated soils at the National Guard . The selected alternative requires that institutional controls, including access restriction, property transfer restriction, and preconstruction assessment, be implemented or continued at the site. Also, contaminated soils posing human health risks will be excavated and disposed of.

Manipulating vineyard nitrogen on a saline site: 1. Effect of nitrogen on growth, grape yield and nutrients of Vitis vinifera L. cv Shiraz.

PubMed

Bell, Sally-Jean; Francis, I Leigh

2013-08-15

With increased prevalence of saline irrigation water applied to vines worldwide, the issue of appropriate nitrogen management is of concern. Different rates of nitrogen per vine as urea were applied to Shiraz vines on own roots over four seasons in a low-rainfall, saline growing environment. Application of nitrogen in the vineyard early in the season not only altered the vine nitrogen status but also increased some other elements in the petioles, notably chloride and sodium but also manganese and magnesium. In contrast, nitrogen application decreased petiole phosphorus. In comparison with the majority of nitrogen studies on non-saline sites, nitrogen-induced growth responses were restricted under the saline conditions in this study. While some changes in canopy density in response to nitrogen were observed, this did not affect light interception in the fruit zone. Yield responses were varied and could be related to the nutritional conditions under which bud development and flowering took place. This study demonstrated that current best practice guidelines, in terms of rate of nitrogen applied, for correcting a nitrogen deficiency on a non-saline site may not be appropriate for saline sites and that application of nitrogen can increase the potential for salt toxicity in vines. © 2013 Society of Chemical Industry.

Binding Sites Analyser (BiSA): Software for Genomic Binding Sites Archiving and Overlap Analysis

PubMed Central

Khushi, Matloob; Liddle, Christopher; Clarke, Christine L.; Graham, J. Dinny

2014-01-01

Genome-wide mapping of transcription factor binding and histone modification reveals complex patterns of interactions. Identifying overlaps in binding patterns by different factors is a major objective of genomic studies, but existing methods to archive large numbers of datasets in a personalised database lack sophistication and utility. Therefore we have developed transcription factor DNA binding site analyser software (BiSA), for archiving of binding regions and easy identification of overlap with or proximity to other regions of interest. Analysis results can be restricted by chromosome or base pair overlap between regions or maximum distance between binding peaks. BiSA is capable of reporting overlapping regions that share common base pairs; regions that are nearby; regions that are not overlapping; and average region sizes. BiSA can identify genes located near binding regions of interest, genomic features near a gene or locus of interest and statistical significance of overlapping regions can also be reported. Overlapping results can be visualized as Venn diagrams. A major strength of BiSA is that it is supported by a comprehensive database of publicly available transcription factor binding sites and histone modifications, which can be directly compared to user data. The documentation and source code are available on http://bisa.sourceforge.net PMID:24533055

Paleosecular Variation and Time-Averaged Field Behavior: Global and Regional Signatures

NASA Astrophysics Data System (ADS)

Johnson, C. L.; Cromwell, G.; Tauxe, L.; Constable, C.

2012-12-01

We use an updated global dataset of directional and intensity data from lava flows to investigate time-averaged field (TAF) and paleosecular variation (PSV) signatures regionally and globally. The data set includes observations from the past 10 Ma, but we focus our investigations on the field structure over past 5 Ma, in particular during the Brunhes and Matuyama. We restrict our analyses to sites with at least 5 samples (all of which have been stepwise demagnetized), and for which the estimate of the Fisher precision parameter, k, is at least 50. The data set comprises 1572 sites from the past 5 Ma that span latitudes 78oS to 71oN; of these ˜40% are from the Brunhes chron and ˜20% are from the Matuyama chron. Age control at the site level is variable because radiometric dates are available for only about one third of our sites. New TAF models for the Brunhes show longitudinal structure. In particular, high latitude flux lobes are observed, constrained by improved data sets from N. and S. America, Japan, and New Zealand. We use resampling techniques to examine possible biases in the TAF and PSV incurred by uneven temporal sampling, and the limited age information available for many sites. Results from Hawaii indicate that resampling of the paleodirectional data onto a uniform temporal distribution, incorporating site ages and age errors leads to a TAF estimate for the Brunhes that is close to that reported for the actual data set, but a PSV estimate (virtual geomagnetic pole dispersion) that is increased relative to that obtained from the unevenly sampled data. The global distribution of sites in our dataset allows us to investigate possible hemispheric asymmetries in field structure, in particular differences between north and south high latitude field behavior and low latitude differences between the Pacific and Atlantic hemispheres.

Risk assessment of imidacloprid use in forest settings on the aquatic macroinvertebrate community.

PubMed

Benton, Elizabeth P; Grant, Jerome F; Nichols, Rebecca J; Webster, R Jesse; Schwartz, John S; Bailey, Joseph K

2017-11-01

The isolated effects of a single insecticide can be difficult to assess in natural settings because of the presence of numerous pollutants in many watersheds. Imidacloprid use for suppressing hemlock woolly adelgid, Adelges tsugae (Annand) (Hemiptera: Adelgidae), in forests offers a rare opportunity to assess potential impacts on aquatic macroinvertebrates in relatively pristine landscapes. Aquatic macroinvertebrate communities were assessed in 9 streams in Great Smoky Mountains National Park (southern Appalachian Mountains, USA). The streams flow through hemlock conservation areas where imidacloprid soil drench treatments were applied for hemlock woolly adelgid suppression. Sites were located upstream and downstream of the imidacloprid treatments. Baseline species presence data (pre-imidacloprid treatment) were available from previous sample collections at downstream sites. Downstream and upstream sites did not vary in numerous community measures. Although comparisons of paired upstream and downstream sites showed differences in diversity in 7 streams, higher diversity was found more often in downstream sites. Macroinvertebrate functional feeding groups and life habits were similar between downstream and upstream sites. Downstream and baseline stream samples were similar. While some functional feeding group and life habit species richness categories varied, variations did not indicate poorer quality downstream communities. Imidacloprid treatments applied according to US Environmental Protection Agency federal restrictions did not result in negative effects to aquatic macroinvertebrate communities, which indicates that risks of imidacloprid use in forest settings are low. Environ Toxicol Chem 2017;36:3108-3119. © 2017 SETAC. © 2017 SETAC.

Correlation between the development of calcium oxalate stones and polymorphisms in the fibronectin gene in the Uighur population of the Xinjiang region of China.

PubMed

Murat, M; Aekeper, A; Yuan, L Y; Alim, T; Du, G J; Abdusamat, A; Wu, G W; Aniwer, Y

2015-10-29

Here, we have investigated the correlation between calcium oxalate stone formation and Fn gene polymorphisms in urinary calculi patients among the Uighur population (Xinjiang region). In this case control study, genomic DNA extracted from the peripheral blood of 129 patients with calcium oxalate stones (patient group) and 94 normal people (control group) was used to genotype polymorphisms in the rs6725958, rs10202709, and rs35343655 sites of the Fn gene by polymerase chain reaction-restriction fragment length polymorphism. Subsequently, the association between different genotypes and susceptibility to calcium oxalate stone formation was compared among the patient and control groups. Single nucleotide polymorphisms (SNPs) were detected in the rs6725958, rs10202709, and rs35343655 sites of the Fn gene among the patient and control groups. The genotype distributions of the three loci complied with the Hardy-Weinberg equilibrium. The results of allele frequencies of the patient/control group for polymorphisms in the rs6725958 site of the Fn gene were C = 179 (69.92%)/119 (63.30%) and A = 77 (30.08%)/69 (36.70%), in the rs10202709 site were C = 245 (95.70%)/176 (93.63%) and T = 11 (4.30%)/12 (6.38%), and in the rs35343655 site of the Fn gene were A = 139 (54.30%)/87 (46.28%) and G = 117 (45.70%)/101 (53.72%). We observed no significant differences between the three SNPs and development of calcium oxalate stones. Polymorphisms in rs6725958, rs10202709, and rs35343655 of the Fn gene had no obvious effect on the susceptibility to the development of calcium oxalate stones in the Uighur population, residing in the Xinjiang region of China.

Construction of a high-density genetic map for grape using next generation restriction-site associated DNA sequencing

PubMed Central

2012-01-01

Background Genetic mapping and QTL detection are powerful methodologies in plant improvement and breeding. Construction of a high-density and high-quality genetic map would be of great benefit in the production of superior grapes to meet human demand. High throughput and low cost of the recently developed next generation sequencing (NGS) technology have resulted in its wide application in genome research. Sequencing restriction-site associated DNA (RAD) might be an efficient strategy to simplify genotyping. Combining NGS with RAD has proven to be powerful for single nucleotide polymorphism (SNP) marker development. Results An F1 population of 100 individual plants was developed. In-silico digestion-site prediction was used to select an appropriate restriction enzyme for construction of a RAD sequencing library. Next generation RAD sequencing was applied to genotype the F1 population and its parents. Applying a cluster strategy for SNP modulation, a total of 1,814 high-quality SNP markers were developed: 1,121 of these were mapped to the female genetic map, 759 to the male map, and 1,646 to the integrated map. A comparison of the genetic maps to the published Vitis vinifera genome revealed both conservation and variations. Conclusions The applicability of next generation RAD sequencing for genotyping a grape F1 population was demonstrated, leading to the successful development of a genetic map with high density and quality using our designed SNP markers. Detailed analysis revealed that this newly developed genetic map can be used for a variety of genome investigations, such as QTL detection, sequence assembly and genome comparison. PMID:22908993

Biological Functionalization of Drug Delivery Carriers to Bypass Size Restrictions of Receptor-Mediated Endocytosis Independently from Receptor Targeting

PubMed Central

Ansar, Maria; Serrano, Daniel; Papademetriou, Iason; Bhowmick, Tridib Kumar; Muro, Silvia

2014-01-01

Targeting of drug carriers to cell-surface receptors involved in endocytosis is commonly used for intracellular drug delivery. However, most endocytic receptors mediate uptake via clathrin or caveolar pathways associated with ≤200-nm vesicles, restricting carrier design. We recently showed that endocytosis mediated by intercellular adhesion molecule 1 (ICAM-1), which differs from clathrin- and caveolar-mediated pathways, allows uptake of nano- and micro-carriers in cell culture and in vivo due to recruitment of cellular sphingomyelinases to the plasmalemma. This leads to ceramide generation at carrier binding sites and formation of actin stress-fibers, enabling engulfment and uptake of a wide size-range of carriers. Here we adapted this paradigm to enhance uptake of drug carriers targeted to receptors associated with size-restricted pathways. We coated sphingomyelinase onto model (polystyrene) submicro- and micro-carriers targeted to clathrin-associated mannose-6-phosphate receptor. In endothelial cells, this provided ceramide enrichment at the cell surface and actin stress-fiber formation, modifying the uptake pathway and enhancing carrier endocytosis without affecting targeting, endosomal transport, cell-associated degradation, or cell viability. This improvement depended on the carrier size and enzyme dose, and similar results were observed for other receptors (transferrin receptor) and cell types (epithelial cells). This phenomenon also enhanced tissue accumulation of carriers after intravenous injection in mice. Hence, it is possible to maintain targeting toward a selected receptor while bypassing natural size-restrictions of its associated endocytic route by functionalization of drug carriers with biological elements mimicking the ICAM-1 pathway. This strategy holds considerable promise to enhance flexibility of design of targeted drug delivery systems. PMID:24237309

Biological functionalization of drug delivery carriers to bypass size restrictions of receptor-mediated endocytosis independently from receptor targeting.

PubMed

Ansar, Maria; Serrano, Daniel; Papademetriou, Iason; Bhowmick, Tridib Kumar; Muro, Silvia

2013-12-23

Targeting of drug carriers to cell-surface receptors involved in endocytosis is commonly used for intracellular drug delivery. However, most endocytic receptors mediate uptake via clathrin or caveolar pathways associated with ≤200-nm vesicles, restricting carrier design. We recently showed that endocytosis mediated by intercellular adhesion molecule 1 (ICAM-1), which differs from clathrin- and caveolae-mediated pathways, allows uptake of nano- and microcarriers in cell culture and in vivo due to recruitment of cellular sphingomyelinases to the plasmalemma. This leads to ceramide generation at carrier binding sites and formation of actin stress-fibers, enabling engulfment and uptake of a wide size-range of carriers. Here we adapted this paradigm to enhance uptake of drug carriers targeted to receptors associated with size-restricted pathways. We coated sphingomyelinase onto model (polystyrene) submicro- and microcarriers targeted to clathrin-associated mannose-6-phosphate receptor. In endothelial cells, this provided ceramide enrichment at the cell surface and actin stress-fiber formation, modifying the uptake pathway and enhancing carrier endocytosis without affecting targeting, endosomal transport, cell-associated degradation, or cell viability. This improvement depended on the carrier size and enzyme dose, and similar results were observed for other receptors (transferrin receptor) and cell types (epithelial cells). This phenomenon also enhanced tissue accumulation of carriers after intravenous injection in mice. Hence, it is possible to maintain targeting toward a selected receptor while bypassing natural size restrictions of its associated endocytic route by functionalization of drug carriers with biological elements mimicking the ICAM-1 pathway. This strategy holds considerable promise to enhance flexibility of design of targeted drug delivery systems.

Predictors of outcome at 1 year in adolescents with DSM-5 restrictive eating disorders: report of the national eating disorders quality improvement collaborative.

PubMed

Forman, Sara F; McKenzie, Nicole; Hehn, Rebecca; Monge, Maria C; Kapphahn, Cynthia J; Mammel, Kathleen A; Callahan, S Todd; Sigel, Eric J; Bravender, Terrill; Romano, Mary; Rome, Ellen S; Robinson, Kelly A; Fisher, Martin; Malizio, Joan B; Rosen, David S; Hergenroeder, Albert C; Buckelew, Sara M; Jay, M Susan; Lindenbaum, Jeffrey; Rickert, Vaughn I; Garber, Andrea; Golden, Neville H; Woods, Elizabeth R

2014-12-01

The National Eating Disorders Quality Improvement Collaborative evaluated data of patients with restrictive eating disorders to analyze demographics of diagnostic categories and predictors of weight restoration at 1 year. Fourteen Adolescent Medicine eating disorder programs participated in a retrospective review of 700 adolescents aged 9-21 years with three visits, with DSM-5 categories of restrictive eating disorders including anorexia nervosa (AN), atypical AN, and avoidant/restrictive food intake disorder (ARFID). Data including demographics, weight and height at intake and follow-up, treatment before intake, and treatment during the year of follow-up were analyzed. At intake, 53.6% met criteria for AN, 33.9% for atypical AN, and 12.4% for ARFID. Adolescents with ARFID were more likely to be male, younger, and had a longer duration of illness before presentation. All sites had a positive change in mean percentage median body mass index (%MBMI) for their population at 1-year follow-up. Controlling for age, gender, duration of illness, diagnosis, and prior higher level of care, only %MBMI at intake was a significant predictor of weight recovery. In the model, there was a 12.7% change in %MBMI (interquartile range, 6.5-19.3). Type of treatment was not predictive, and there were no significant differences between programs in terms of weight restoration. The National Eating Disorders Quality Improvement Collaborative provides a description of the patient population presenting to a national cross-section of 14 Adolescent Medicine eating disorder programs and categorized by DSM-5. Treatment modalities need to be further evaluated to assess for more global aspects of recovery. Copyright © 2014 Society for Adolescent Health and Medicine. Published by Elsevier Inc. All rights reserved.

Restrictions for Medicaid Reimbursement of Sofosbuvir for the Treatment of Hepatitis C Virus Infection in the United States.

PubMed

Barua, Soumitri; Greenwald, Robert; Grebely, Jason; Dore, Gregory J; Swan, Tracy; Taylor, Lynn E

2015-08-04

The aim of this study was to systematically evaluate state Medicaid policies for the treatment of hepatitis C virus (HCV) infection with sofosbuvir in the United States. Medicaid reimbursement criteria for sofosbuvir were evaluated in all 50 states and the District of Columbia. The authors searched state Medicaid Web sites between 23 June and 7 December 2014 and extracted data in duplicate. Any differences were resolved by consensus. Data were extracted on whether sofosbuvir was covered and the criteria for coverage based on the following categories: liver disease stage, HIV co-infection, prescriber type, and drug or alcohol use. Of the 42 states with known Medicaid reimbursement criteria for sofosbuvir, 74% limit sofosbuvir access to persons with advanced fibrosis (Meta-Analysis of Histologic Data in Viral Hepatitis [METAVIR] fibrosis stage F3) or cirrhosis (F4). One quarter of states require persons co-infected with HCV and HIV to be receiving antiretroviral therapy or to have suppressed HIV RNA levels. Two thirds of states have restrictions based on prescriber type, and 88% include drug or alcohol use in their sofosbuvir eligibility criteria, with 50% requiring a period of abstinence and 64% requiring urine drug screening. Heterogeneity is present in Medicaid reimbursement criteria for sofosbuvir with respect to liver disease staging, HIV co-infection, prescriber type, and drug or alcohol use across the United States. Restrictions do not seem to conform with recommendations from professional organizations, such as the Infectious Diseases Society of America and the American Association for the Study of Liver Diseases. Current restrictions seem to violate federal Medicaid law, which requires states to cover drugs consistent with their U.S. Food and Drug Administration labels.

Superfund record of decision (EPA Region 3): Allegany Ballistics Laboratory (USNavy) Site 10, Mineral, WV, June 30, 1998

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

NONE

1998-12-01

This decision document presents the selected remedial action for Site 10 (the Site) Groundwater at the Allegany Ballistics Laboratory (ABL), Rocket Center, West Virginia. The major components of the selected remedy are: Institutional controls, including land use restrictions imposed through appropriate administrative mechanisms to prevent groundwater use; Groundwater pumping from a minimum of three extraction wells to capture the hot spot of the VOC contaminant plume; Installation of a pipeline to transport groundwater from Site 10 to the Site 1 treatment plant; Discharge to the North Branch Potomac River; and Groundwater monitoring on a timely basis, quarterly to semi-annually, willmore » evaluate groundwater quality, contaminant migration, and degradation for inclusion in the 5-year site reviews.« less

DNA methylation profiles of donor nuclei cells and tissues of cloned bovine fetuses.

PubMed

Kremenskoy, Maksym; Kremenska, Yuliya; Suzuki, Masako; Imai, Kei; Takahashi, Seiya; Hashizume, Kazuyoshi; Yagi, Shintaro; Shiota, Kunio

2006-04-01

Methylation of DNA in CpG islands plays an important role during fetal development and differentiation because CpG islands are preferentially located in upstream regions of mammalian genomic DNA, including the transcription start site of housekeeping genes and are also associated with tissue-specific genes. Somatic nuclear transfer (NT) technology has been used to generate live clones in numerous mammalian species, but only a low percentage of nuclear transferred animals develop to term. Abnormal epigenetic changes in the CpG islands of donor nuclei after nuclear transfer could contribute to a high rate of abortion during early gestation and increase perinatal death. These changes have yet to be explored. Thus, we investigated the genome-wide DNA methylation profiles of CpG islands in nuclei donor cells and NT animals. Using Restriction Landmark Genomic Scanning (RLGS), we showed, for the first time, the epigenetic profile formation of tissues from NT bovine fetuses produced from cumulus cells. From approximately 2600 unmethylated NotI sites visualized on the RLGS profile, at least 35 NotI sites showed different methylation statuses. Moreover, we proved that fetal and placental tissues from artificially inseminated and cloned cattle have tissue-specific differences in the genome-wide methylation profiles of the CpG islands. We also found that possible abnormalities occurred in the fetal brain and placental tissues of cloned animals.

Hypervariability of ribosomal DNA at multiple chromosomal sites in lake trout (Salvelinus namaycush).

PubMed

Zhuo, L; Reed, K M; Phillips, R B

1995-06-01

Variation in the intergenic spacer (IGS) of the ribosomal DNA (rDNA) of lake trout (Salvelinus namaycush) was examined. Digestion of genomic DNA with restriction enzymes showed that almost every individual had a unique combination of length variants with most of this variation occurring within rather than between populations. Sequence analysis of a 2.3 kilobase (kb) EcoRI-DraI fragment spanning the 3' end of the 28S coding region and approximately 1.8 kb of the IGS revealed two blocks of repetitive DNA. Putative transcriptional termination sites were found approximately 220 bases (b) downstream from the end of the 28S coding region. Comparison of the 2.3-kb fragments with two longer (3.1 kb) fragments showed that the major difference in length resulted from variation in the number of short (89 b) repeats located 3' to the putative terminator. Repeat units within a single nucleolus organizer region (NOR) appeared relatively homogeneous and genetic analysis found variants to be stably inherited. A comparison of the number of spacer-length variants with the number of NORs found that the number of length variants per individual was always less than the number of NORs. Examination of spacer variants in five populations showed that populations with more NORs had more spacer variants, indicating that variants are present at different rDNA sites on nonhomologous chromosomes.

Short-term intermittent energy restriction interventions for weight management: a systematic review and meta-analysis.

PubMed

Harris, L; McGarty, A; Hutchison, L; Ells, L; Hankey, C

2018-01-01

This systematic review synthesized the available evidence on the effect of short-term periods of intermittent energy restriction (weekly intermittent energy restriction; ≥7-d energy restriction) in comparison with usual care (daily continuous energy restriction), in the treatment of overweight and obesity in adults. Six electronic databases were searched from inception to October 2016. Only randomized controlled trials of interventions (≥12 weeks) in adults with overweight and obesity were included. Five studies were included in this review. Weekly intermittent energy restriction periods ranged from an energy intake between 1757 and 6276 kJ/d -1 . The mean duration of the interventions was 26 (range 14 to 48) weeks. Meta-analysis demonstrated no significant difference in weight loss between weekly intermittent energy restriction and continuous energy restriction post-intervention (weighted mean difference: -1.36 [-3.23, 0.51], p = 0.15) and at follow-up (weighted mean difference: -0.82 [-3.76, 2.11], p = 0.58). Both interventions achieved comparable weight loss of >5 kg and therefore were associated with clinical benefits to health. The findings support the use of weekly intermittent energy restriction as an alternative option for the treatment of obesity. Currently, there is insufficient evidence to support the long-term sustainable effects of weekly intermittent energy restriction on weight management. © 2017 The Authors. Obesity Reviews published by John Wiley & Sons Ltd on behalf of World Obesity.

Directional, seamless, and restriction enzyme-free construction of random-primed complementary DNA libraries using phosphorothioate-modified primers.

PubMed

Howland, Shanshan W; Poh, Chek-Meng; Rénia, Laurent

2011-09-01

Directional cloning of complementary DNA (cDNA) primed by oligo(dT) is commonly achieved by appending a restriction site to the primer, whereas the second strand is synthesized through the combined action of RNase H and Escherichia coli DNA polymerase I (PolI). Although random primers provide more uniform and complete coverage, directional cloning with the same strategy is highly inefficient. We report that phosphorothioate linkages protect the tail sequence appended to random primers from the 5'→3' exonuclease activity of PolI. We present a simple strategy for constructing a random-primed cDNA library using the efficient, size-independent, and seamless In-Fusion cloning method instead of restriction enzymes. Copyright © 2011 Elsevier Inc. All rights reserved.

In vivo Elimination of Parental Clones in General and Site-directed Mutagenesis

PubMed Central

Holland, Erika G.; Acca, Felicity E.; Belanger, Kristina M.; Bylo, Mary E.; Kay, Brian K.; Weiner, Michael P.; Kiss, Margaret M.

2015-01-01

The Eco29k I restriction endonuclease is a Sac II isoschizomer that recognizes the sequence 5’-CCGCGG-3’ and is encoded, along with the Eco29k I methylase, in the Escherichia coli strain 29k. We have expressed the Eco29k I restriction-methylation system (RM2) in E. coli strain TG1 to produce the strain AXE688. We have developed a directed molecular evolution (DME) mutagenesis method that uses Eco29k I to restrict incoming parental DNA in transformed cells. Using our DME method, we have demonstrated that our AXE688 strain results in mutated directed molecular evolution libraries with diversity greater than 107 from a single transformation and with greater than 90% recombinant clones. PMID:25523926

In vivo elimination of parental clones in general and site-directed mutagenesis.

PubMed

Holland, Erika G; Acca, Felicity E; Belanger, Kristina M; Bylo, Mary E; Kay, Brian K; Weiner, Michael P; Kiss, Margaret M

2015-02-01

The Eco29k I restriction endonuclease is a Sac II isoschizomer that recognizes the sequence 5'-CCGCGG-3' and is encoded, along with the Eco29k I methylase, in the Escherichia coli strain 29k. We have expressed the Eco29k I restriction-methylation system (RM2) in E. coli strain TG1 to produce the strain AXE688. We have developed a directed molecular evolution (DME) mutagenesis method that uses Eco29k I to restrict incoming parental DNA in transformed cells. Using our DME method, we have demonstrated that our AXE688 strain results in mutated directed molecular evolution libraries with diversity greater than 10(7) from a single transformation and with greater than 90% recombinant clones. Copyright © 2014 Elsevier B.V. All rights reserved.

10 CFR 2.1013 - Use of the electronic docket during the proceeding.

Code of Federal Regulations, 2014 CFR

2014-01-01

.... Information contained in hyperlinks to a Web site on the Internet or to another PDF file, that is necessary... to the filing. (vii) All electronic submissions must be free of author-imposed security restrictions...

Genetic diversity and differentiation of the Critically Endangered Hispaniolan palm Coccothrinax jimenezii M.M. Mejía & M.M. García based on novel SSR markers

USDA-ARS?s Scientific Manuscript database

The palm species Coccothrinax jimenezii M.M. Mejía & M.M. García is a Critically Endangered species (sensu IUCN) restricted to two populations from Haiti (one site on coastal areas near the city of Gonaïves with 43 individuals) and the Dominican Republic (one site on the shores of Lago Enriquillo ...

Derived concentration guideline levels for Argonne National Laboratory's building 310 area.

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

Kamboj, S., Dr.; Yu, C ., Dr.

2011-08-12

The derived concentration guideline level (DCGL) is the allowable residual radionuclide concentration that can remain in soil after remediation of the site without radiological restrictions on the use of the site. It is sometimes called the single radionuclide soil guideline or the soil cleanup criteria. This report documents the methodology, scenarios, and parameters used in the analysis to support establishing radionuclide DCGLs for Argonne National Laboratory's Building 310 area.

Calorie for calorie, dietary fat restriction results in more body fat loss than carbohydrate restriction in people with obesity

PubMed Central

Hall, Kevin D.; Bemis, Thomas; Brychta, Robert; Chen, Kong Y.; Courville, Amber; Crayner, Emma J.; Goodwin, Stephanie; Guo, Juen; Howard, Lilian; Knuth, Nicolas D.; Miller, Bernard V.; Prado, Carla M.; Siervo, Mario; Skarulis, Monica C.; Walter, Mary; Walter, Peter J.; Yannai, Laura

2015-01-01

Summary Dietary carbohydrate restriction has been purported to cause endocrine adaptations that promote body fat loss more than dietary fat restriction. We selectively restricted dietary carbohydrate versus fat for 6 days following a 5 day baseline diet in 19 adults with obesity confined to a metabolic ward where they exercised daily. Subjects received both isocaloric diets in random order during each of two inpatient stays. Body fat loss was calculated as the difference between daily fat intake and net fat oxidation measured while residing in a metabolic chamber. Whereas carbohydrate restriction led to sustained increases in fat oxidation and loss of 53±6 g/d of body fat, fat oxidation was unchanged by fat restriction leading to 89±6 g/d of fat loss and was significantly greater than carbohydrate restriction (p=0.002). Mathematical model simulations agreed with these data, but predicted that the body acts to minimize body fat differences with isocaloric diets varying in carbohydrate and fat. PMID:26278052

Treatment of PCR products with exonuclease I and heat-labile alkaline phosphatase improves the visibility of combined bisulfite restriction analysis

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

Watanabe, Kousuke; Emoto, Noriko; Sunohara, Mitsuhiro

2010-08-27

Research highlights: {yields} Incubating PCR products at a high temperature causes smears in gel electrophoresis. {yields} Smears interfere with the interpretation of methylation analysis using COBRA. {yields} Treatment with exonuclease I and heat-labile alkaline phosphatase eliminates smears. {yields} The elimination of smears improves the visibility of COBRA. -- Abstract: DNA methylation plays a vital role in the regulation of gene expression. Abnormal promoter hypermethylation is an important mechanism of inactivating tumor suppressor genes in human cancers. Combined bisulfite restriction analysis (COBRA) is a widely used method for identifying the DNA methylation of specific CpG sites. Here, we report that exonucleasemore » I and heat-labile alkaline phosphatase can be used for PCR purification for COBRA, improving the visibility of gel electrophoresis after restriction digestion. This improvement is observed when restriction digestion is performed at a high temperature, such as 60 {sup o}C or 65 {sup o}C, with BstUI and TaqI, respectively. This simple method can be applied instead of DNA purification using spin columns or phenol/chloroform extraction. It can also be applied to other situations when PCR products are digested by thermophile-derived restriction enzymes, such as PCR restriction fragment length polymorphism (RFLP) analysis.« less

Assessing restrictiveness of national alcohol marketing policies.

PubMed

Esser, Marissa B; Jernigan, David H

2014-01-01

To develop an approach for monitoring national alcohol marketing policies globally, an area of the World Health Organization's (WHO) Global Alcohol Strategy. Data on restrictiveness of alcohol marketing policies came from the 2002 and 2008 WHO Global Surveys on Alcohol and Health. We included four scales in a sensitivity analysis to determine optimal weights to score countries on their marketing policies and applied the selected scale to assess national marketing policy restrictiveness. Nearly, 36% of countries had no marketing restrictions. The overall restrictiveness levels were not significantly different between 2002 and 2008. The number of countries with strict marketing regulations did not differ across years. This method of monitoring alcohol marketing restrictiveness helps track progress towards implementing WHO'S Global Alcohol Strategy. Findings indicate a consistent lack of restrictive policies over time, making this a priority area for national and global action. © The Author 2014. Medical Council on Alcohol and Oxford University Press. All rights reserved.

Fish communities of the Buffalo River Basin and nearby basins of Arkansas and their relation to selected environmental factors, 2001-2002

USGS Publications Warehouse

Petersen, James C.

2004-01-01

The Buffalo River lies in north-central Arkansas and is a tributary of the White River. Most of the length of the Buffalo River lies within the boundaries of Buffalo National River, a unit of the National Park Service; the upper 24 river kilometers lie within the boundary of the Ozark National Forest. Much of the upper and extreme lower parts of the basin on the south side of the Buffalo River is within the Ozark National Forest. During the summers of 2001 and 2002, fish communities were sampled at 52 sites in the study area that included the Buffalo River Basin and selected smaller nearby basins within the White River Basin in north-central Arkansas. Water quality (including nutrient and bacteria concentrations) and several other environmental factors (such as stream size, land use, substrate size, and riparian shading) also were measured. A total of 56 species of fish were collected from sites within the Buffalo River Basin in 2001 and 2002. All 56 species also were collected from within the boundaries of Buffalo National River. Twenty-two species were collected from headwater sites on tributaries of the Buffalo River; 27 species were collected from sites within or immediately adjacent to the Ozark National Forest. The list of species collected from Buffalo National River is similar to the list of species reported by previous investigators. Species richness at sites on the mainstem of the Buffalo River generally increased in a downstream direction. The number of species collected (both years combined) increased from 17 at the most upstream site to 38 near the mouth of the Buffalo River. In 2001 and 2002, a total of 53 species of fish were collected from sites outside the Buffalo River Basin. Several fish community metrics varied among sites in different site categories (mainstem, large tributary, small tributary, headwater, and developed out-of-basin sites). Median relative abundances of stonerollers ranged from about 25 to 55 percent and were highest at headwater and developed out-of-basin sites and lowest at mainstem sites. The relative abundances at the headwater and developed out-of-basin sites were significantly different from the relative abundances at the mainstem sites. Percentages of individuals of algivorous/herbivorous, invertivorous, and piscivorous species at headwater sites were significantly lower than values at mainstem and developed out-of-basin sites. Percentages of individuals of invertivorous species at mainstem sites were significantly higher than values at small tributary, headwater, and developed out-of-basin sites. Percentages of top carnivores at mainstem sites were significantly higher than values at tributary and headwater sites. The numbers of darter, sculpin, plus madtom species at mainstem, large tributary, and developed out-of-basin sites were significantly higher than values at other sites, and the values at small tributary sites and headwater sites were each significantly different from values at the other four types of sites. The number of lithophilic spawning species at large tributary sites was not significantly different from values at mainstem and developed out-of-basin sites, but values for small tributary and headwater sites each were significantly different from values for all other categories. Index of biotic integrity scores varied among the site categories. Scores for mainstem sites were significantly larger than all but large tributary site scores. Scores for headwater sites were significantly smaller than mainstem and large tributary site scores. Several analyses of the data described in this report suggest that drainage area is the most important single factor influencing fish communities of the Buffalo River Basin and nearby basins. Species richness increases with increasing drainage area and some species are restricted to smaller streams while other species are more common in larger streams. Some community metrics also are related to land use and related factors

Closure Report (CR) for Corrective Action Unit (CAU) 91: Area 3 U-3fi Injection Well with Errata Sheet and Certification, Revision 0

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

Navarro Nevada Environmental Services

The closure report for CAU 91 has no Use Restriction Form or drawing/map included in the document to describe the use restricted area, however, Section 3.3.3 states that the site will be fenced and signage placed indicating the area as a Resource Conservation and Recovery Act (RCRA) Unit. The drawing that was placed in the FFACO indicating the use restricted area lists the coordinates for the RCRA Unit in Nevada State Plan Coordinates - North American Datum of 1983. In the ensuing years the reporting of coordinates has been standardized so that all coordinates are reported in the same manner,more » which is: NAD 27 UTM Zone 11 N, meters. This Errata Sheet updates the coordinate reporting to the currently accepted method and includes an aerial photo showing the RCRA Unit with the coordinates listed showing the use restricted area.« less

Does Non-Targeted Community CPR Training Increase Bystander CPR Frequency?

PubMed

Uber, Amy; Sadler, Richard C; Chassee, Todd; Reynolds, Joshua C

2018-05-01

Only 37% of out-of-hospital cardiac arrests (OHCA) receive bystander Cardiopulmonary resuscitation (CPR) in Kent County, MI. In May 2014, prehospital providers offered one-time, point-of-contact compression-only CPR training to 2,253 passersby at 7 public locations in Grand Rapids, Michigan. To assess the impact of this intervention, we compared bystander CPR frequency and clinical outcomes in regions surrounding training sites before and after the intervention, adjusting for prehospital covariates. We aimed to assess the effect of this broad, non-targeted intervention on bystander CPR frequency, type of CPR utilized, and clinical outcomes. We also tested for differences in geospatial variation of bystander CPR and clinical outcomes clustered around training sites. Retrospective, observational, before-after study of adult, EMS-treated OHCA in Kent County from January 1, 2010 to December 31, 2015. We generated a 5-kilometer radius surrounding each training site to estimate any geospatial influence that training sites might have on bystander CPR frequency in nearby OHCA cases. Chi-squared, Fisher's exact, and t-tests assessed differences in subject features. Difference-in-differences analysis with generalized estimating equation (GEE) modeling assessed bystander CPR frequency, adjusting for training site, covariates (age, sex, witnessed, shockable rhythm, public location), and clustering around training sites. Similar modeling tested for changes in bystander CPR type, return of spontaneous circulation (ROSC), survival to hospital discharge, and cerebral performance category (CPC) of 1-2 at hospital discharge. We included 899 cases before and 587 cases post-intervention. Overall, we observed no increase in the frequency of bystander CPR or favorable clinical outcomes. We did observe an increase in compression-only CPR, but this was paradoxically restricted to OHCA cases falling outside radii around training sites. In adjusted modeling, the bystander CPR training intervention was not associated with bystander CPR frequency (β -0.002; 95% CI -0.16, 0.15), compression-only CPR (β -0.06; 95% CI -0.15, 0.02), ROSC (β -0.06; 95% CI -0.21, 0.25), survival (β -0.02; 95% CI -0.11, 0.06), or favorable neurologic outcome (β -0.01; 95% CI -0.07, 0.09). We observed no impact in bystander CPR performance or outcomes from a blanket, non-targeted approach to community CPR education. The effect of targeted CPR education in locales with known low bystander CPR rates should be tested in this region.

The development of a code of practice for single house on-site wastewater treatment in Ireland.

PubMed

Gill, L W

2011-01-01

The performance of six separate percolation areas was intensively monitored to ascertain the attenuation effects of unsaturated subsoils with respect to on-site wastewater effluent: three sites receiving septic tank effluent, the other three sites receiving secondary treated effluent. The development of a biomat across the percolation areas receiving secondary treated effluent was restricted on these sites compared to those sites receiving septic tank effluent. This created significant differences in terms of the hydraulic loading on the percolation areas with implications for the transport and attenuation of indicator microorganisms and nitrogen down through the subsoils and into the groundwater. The results of this work have formed a large input into the production of a new Code of Practice Wastewater Treatment and Disposal Systems Serving Single Houses. This has led to changes in the design of on-site hydraulic loading from 180 L per capita per day (L/c.d) down to 150 L/c.d. The range of acceptable subsoils receiving septic tank effluent has narrowed for more highly permeable subsoils following a series of tracer studies using bacteriophages. However, the range has been extended for lower permeability subsoils (range 0.08 down to 0.06 m/d) receiving secondary treated effluent in order to encourage the effluent to spread further along the trenches. The maximum individual length of percolation trenches receiving secondary effluent has also been reduced to 10 m to encourage dispersion on a wider area. This paper thus highlights how research can directly feed into a Code of Practice.

GIS and the Analytic Hierarchy Process for Regional Landfill Site Selection in Transitional Countries: A Case Study From Serbia

NASA Astrophysics Data System (ADS)

Zelenović Vasiljević, Tamara; Srdjević, Zorica; Bajčetić, Ratko; Vojinović Miloradov, Mirjana

2012-02-01

The Serbian National Waste Management Strategy for the Period 2010-2019, harmonized with the European Union Directives, mandates new and very strict requirements for landfill sites. To enable analysis of a number of required qualitative and quantitative factors for landfill site selection, the traditional method of site selection must be replaced with a new approach. The combination of GIS and the Analytic Hierarchy Process (AHP) was selected to solve this complex problem. The Srem region in northern Serbia, being one of the most environmentally sensitive areas, was chosen as a case study. Seventeen factors selected as criteria/sub-criteria were recognized as most important, divided into geo-natural, environmental, social and techno-economic factors, and were evaluated by experts from different fields using an AHP extension in Arc GIS. Weighted spatial layers were combined into a landfill suitability map which was then overlapped with four restriction maps, resulting in a final suitability map. According to the results, 82.65% of the territory of Srem is unsuitable for regional landfill siting. The most suitable areas cover 9.14%, suitable areas 5.24%, while areas with low and very low suitability cover 2.21 and 0.76% of the territory, respectively. Based on these findings, five sites close to two large urban agglomerations were suggested as possible locations for a regional landfill site in Srem. However, the final decision will require further field investigation, a public acceptance survey, and consideration of ownership status and price of the land.

R Factor-Controlled Restriction and Modification of Deoxyribonucleic Acid: Restriction Mutants

PubMed Central

Yoshimori, Robert; Roulland-Dussoix, Daisy; Boyer, Herbert W.

1972-01-01

Restriction mutants of two different R factor-controlled host specificities (RI and RII) were isolated. All of the restriction mutants examined had a normal modification phenotype. No complementation was observed between the RI and RII host specificities. It is concluded that for each host specificity no protein subunit is shared by the restriction endonuclease and modification methylase. PMID:4565538

Enhanced summer warming reduces fungal decomposer diversity and litter mass loss more strongly in dry than in wet tundra.

PubMed

Christiansen, Casper T; Haugwitz, Merian S; Priemé, Anders; Nielsen, Cecilie S; Elberling, Bo; Michelsen, Anders; Grogan, Paul; Blok, Daan

2017-01-01

Many Arctic regions are currently experiencing substantial summer and winter climate changes. Litter decomposition is a fundamental component of ecosystem carbon and nutrient cycles, with fungi being among the primary decomposers. To assess the impacts of seasonal climatic changes on litter fungal communities and their functioning, Betula glandulosa leaf litter was surface-incubated in two adjacent low Arctic sites with contrasting soil moisture regimes: dry shrub heath and wet sedge tundra at Disko Island, Greenland. At both sites, we investigated the impacts of factorial combinations of enhanced summer warming (using open-top chambers; OTCs) and deepened snow (using snow fences) on surface litter mass loss, chemistry and fungal decomposer communities after approximately 1 year. Enhanced summer warming significantly restricted litter mass loss by 32% in the dry and 17% in the wet site. Litter moisture content was significantly reduced by summer warming in the dry, but not in the wet site. Likewise, fungal total abundance and diversity were reduced by OTC warming at the dry site, while comparatively modest warming effects were observed in the wet site. These results suggest that increased evapotranspiration in the OTC plots lowered litter moisture content to the point where fungal decomposition activities became inhibited. In contrast, snow addition enhanced fungal abundance in both sites but did not significantly affect litter mass loss rates. Across sites, control plots only shared 15% of their fungal phylotypes, suggesting strong local controls on fungal decomposer community composition. Nevertheless, fungal community functioning (litter decomposition) was negatively affected by warming in both sites. We conclude that although buried soil organic matter decomposition is widely expected to increase with future summer warming, surface litter decay and nutrient turnover rates in both xeric and relatively moist tundra are likely to be significantly restricted by the evaporative drying associated with warmer air temperatures. © 2016 John Wiley & Sons Ltd.

Undocumented Youth Living Between the Lines: Urban Governance, Social Policy, and the Boundaries of Legality in New York City and Paris

NASA Astrophysics Data System (ADS)

Ruszczyk, Stephen P.

This dissertation compares the transition to adulthood of undocumented youth in New York and Paris, along with analysis of the construction of illegality in each city. In both the United States and France, national restrictions against undocumented immigrants increasingly take the form of deportations and limiting access to social rights. New York City and Paris, however, mitigate the national restrictions in important but different ways. They construct "illegality" differently, leading to different young adult outcomes and lived experiences of "illegality." This project uses seven years of multi-site ethnographic data to trace the effects of these mitigated "illegalities" on two dozen (male) youth. We can begin to understand the variation in these undocumented young men's social lives within and between cities by centering on (1) governance structure, the labyrinth of obtaining rights associated with citizenship, (2) citizenship, the possibility of gaining a legal status, steered in particular by civil society actors, and (3) identity, here centered on youths' negotiation of social mobility with the fear of enforcement. Biographical narratives show the shifts in social memberships as youth transition to new countries, new restrictions at adulthood, and new, limiting work. In New York, most social prospects are flattened as future possibilities are whittled down to ones focusing on family and wages. Undocumented status propels New York informants into an accelerated transition to adulthood, as they take on adult responsibilities of work, paying bills, and developing families. In Paris, youth experience more divergent processes of transitioning to adulthood. Those who are more socially integrated use a civil society actor to garner a (temporary) legal status, which does not lead to work opportunities. Those who are less socially integrated face isolation as they wait to gain status and access to better jobs. Paris undocumented youth are thus characterized by a decelerated transition to adulthood as most lack sufficient resources for adult responsibilities. The comparison of Paris and New York shows how different institutional, social, and political contexts---including different systems of state and local governance, political culture and labor market characteristics---produce specific contours of social life for undocumented youth, with varying outcomes. Using boundary theory to represent these different socio-legal and socio-economic contexts over time, we see the more flexible regularization practices in Paris helping youth cross the legal boundary but remaining stratified vis-a-vis the social boundary. With a low deportation risk, New York's legal boundary is blurred. Federal restrictions, however, mean youth also end up stratified vis-a-vis the social boundary. A key difference, however, lies in the family and romantic relationship benefits of available low-end work in New York.

Placentomal differentiation may compensate for maternal nutrient restriction in ewes adapted to harsh range conditions.

PubMed

Vonnahme, K A; Hess, B W; Nijland, M J; Nathanielsz, P W; Ford, S P

2006-12-01

Maternal nutrient restriction from early to midgestation can lead to fetal growth retardation, with long-term impacts on offspring growth, physiology, and metabolism. We hypothesized that ewes from flocks managed under markedly different environmental conditions and levels of nutrition might differ in their ability to protect their own fetus from a bout of maternal nutrient restriction. We utilized multiparous ewes of similar breeding, age, and parity from 2 flocks managed as 1) ewes adapted to a nomadic existence and year-long, limited nutrition near Baggs, WY (Baggs ewes), and 2) University of Wyoming ewes with a sedentary lifestyle and continuous provision of more than adequate nutrition (UW ewes). Groups of Baggs ewes and UW ewes were fed 50 (nutrient restricted) or 100% (control fed) of National Research Council recommendations from d 28 to 78 of gestation, then necropsied, and fetal and placental data were obtained. Although there was a marked decrease (P < 0.05) in fetal weight and blood glucose concentrations in nutrient-restricted vs. control fed UW ewes, there was no difference in these fetal measurements between nutrient-restricted and control-fed Baggs ewes. Nutrient-restricted and control-fed UW ewes exhibited predominantly type A placentomes on d 78, but there were fewer (P c0.05) type A and greater (P < 0.05) numbers of type B, C, and D placentomes in nutrient-restricted than control-fed Baggs ewes. Placental efficiency (fetal weight/placentomal weight) was reduced (P = 0.04) in d 78 nutrient-restricted UW ewes when compared with control-fed UW ewes. In contrast, nutrient-restricted and control-fed Baggs ewes exhibited similar placental efficiencies on d 78. This is the first report of different placental responses to a nutritional challenge during pregnancy when ewes were selected under different management systems. These data are consistent with the concept that Baggs ewes or their conceptuses, which were adapted to both harsh environments and limited nutrition, initiated conversion of type A placentomes to other placentomal types when subjected to an early to mid-gestational nutrient restriction, whereas this conversion failed to occur in UW ewes. This early placentomal conversion in the Baggs ewes may function to maintain normal nutrient delivery to their developing fetuses during maternal nutrient restriction.

Sensorimotor restriction affects complex movement topography and reachable space in the rat motor cortex.

PubMed

Budri, Mirco; Lodi, Enrico; Franchi, Gianfranco

2014-01-01

Long-duration intracortical microstimulation (ICMS) studies with 500 ms of current pulses suggest that the forelimb area of the motor cortex is organized into several spatially distinct functional zones that organize movements into complex sequences. Here we studied how sensorimotor restriction modifies the extent of functional zones, complex movements, and reachable space representation in the rat forelimb M1. Sensorimotor restriction was achieved by means of whole-forelimb casting of 30 days duration. Long-duration ICMS was carried out 12 h and 14 days after cast removal. Evoked movements were measured using a high-resolution 3D optical system. Long-term cast caused: (i) a reduction in the number of sites where complex forelimb movement could be evoked; (ii) a shrinkage of functional zones but no change in their center of gravity; (iii) a reduction in movement with proximal/distal coactivation; (iv) a reduction in maximal velocity, trajectory and vector length of movement, but no changes in latency or duration; (v) a large restriction of reachable space. Fourteen days of forelimb freedom after casting caused: (i) a recovery of the number of sites where complex forelimb movement could be evoked; (ii) a recovery of functional zone extent and movement with proximal/distal coactivation; (iii) an increase in movement kinematics, but only partial restoration of control rat values; (iv) a slight increase in reachability parameters, but these remained far below baseline values. We pose the hypothesis that specific aspects of complex movement may be stored within parallel motor cortex re-entrant systems.

Sensorimotor restriction affects complex movement topography and reachable space in the rat motor cortex

PubMed Central

Budri, Mirco; Lodi, Enrico; Franchi, Gianfranco

2014-01-01

Long-duration intracortical microstimulation (ICMS) studies with 500 ms of current pulses suggest that the forelimb area of the motor cortex is organized into several spatially distinct functional zones that organize movements into complex sequences. Here we studied how sensorimotor restriction modifies the extent of functional zones, complex movements, and reachable space representation in the rat forelimb M1. Sensorimotor restriction was achieved by means of whole-forelimb casting of 30 days duration. Long-duration ICMS was carried out 12 h and 14 days after cast removal. Evoked movements were measured using a high-resolution 3D optical system. Long-term cast caused: (i) a reduction in the number of sites where complex forelimb movement could be evoked; (ii) a shrinkage of functional zones but no change in their center of gravity; (iii) a reduction in movement with proximal/distal coactivation; (iv) a reduction in maximal velocity, trajectory and vector length of movement, but no changes in latency or duration; (v) a large restriction of reachable space. Fourteen days of forelimb freedom after casting caused: (i) a recovery of the number of sites where complex forelimb movement could be evoked; (ii) a recovery of functional zone extent and movement with proximal/distal coactivation; (iii) an increase in movement kinematics, but only partial restoration of control rat values; (iv) a slight increase in reachability parameters, but these remained far below baseline values. We pose the hypothesis that specific aspects of complex movement may be stored within parallel motor cortex re-entrant systems. PMID:25565987

Mosquito abundance and behavior in the influence area of the hydroelectric complex on the Madeira River, Western Amazon, Brazil.

PubMed

Cruz, Rafael Mesquita Bastos; Gil, Luiz Herman Soares; de Almeida e Silva, Alexandre; da Silva Araújo, Maisa; Katsuragawa, Tony Hiroshi

2009-11-01

Malaria is currently highly prevalent and restricted to the north of Brazil, and its dynamics are severely affected by human environmental changes, such as the large dam construction recently approved by the Brazilian Government in Rondônia. We studied the mosquito fauna and behavior before hydroelectric construction. Mosquitoes were captured by human landing catches on the riversides of the Madeira River in Porto Velho, Rondônia. A total of 3121 mosquitoes from eight different genera were collected; only Mansonia and Anopheles darlingi were found in all 21 collection sites throughout the night. These results suggest that the riverines of the study area are exposed to malaria.

Localization of cholinesterases in the chicken nervous system and the problem of the selective neurotoxicity of organophosphorus compounds

PubMed Central

Cavanagh, J. B.; Holland, P.

1961-01-01

Using the thiocholine method, a restricted survey has been made of cholinesterases in the spinal cord and brain stem of the chicken. No simple relation between sites of selective damage in organophosphorus neurotoxicity and centres of cholinesterase activity could be adduced. Moreover, no significant differences between species susceptible and insusceptible to poisoning by these compounds were found by this method. It is concluded that, while cholinesterase may well play an intermediary role in the intoxication, other factors determine the selective damage to certain neurones and their processes. ImagesFig. 1Fig. 2Fig. 3Fig. 4Fig. 5Fig. 6 PMID:13691740

[Construction of thr461 --> Asn461 and Ile462 --> Val462 mutation vector of P4501A1 gene].

PubMed

Wei, Qing; Liu, Yi-Min; Wang, Hui; Zhao, Xiao-Lin; Ren, Tie-ling; Xiao, Yong-mei

2006-09-01

To construct Thr461 --> Asn461 and Ile462 --> Val462 mutation vector of P4501A1 gene and to provide scientific base for deeply researching on the function of cytochrome 1A1 gene (CYP1A1) and the mechanism of carcinogenesis. According to cDNA sequence of human CYP1A1 gene, universal primers (Pm3/Pm4) and mutant primers (Pt15/Pt16 and Pt17/Pt18) containing restriction enzyme site and mutation site were designed. The first set of primers involving Pm3/Pt16 and Pm3/Pt18 amplified a forward 1.5kb fragment from pGEM-T-CYP1A1 plasmid. The second set of primers involving Pt15/Pm4 and Pt17/Pm4 amplified a reverse 177-bp fragment from 10ng pGEM-T-CYP1A1 plasmid. The third set of primers involving Pm3/Pm4 amplified a 1.5kb fragment from the fomer PCR amplifications. The third PCR products were separated, purified and recovered from 1% agarose gel, then inserted into pMD-T vector. Subsequently the conjunct products were transformed into E. coil strain DH-5alpha., then the single clone was screened out and plasmids were extracted from such clone finally verified by restriction endonuclease analysis and sequencing. A 1.5kb fragment of tricycle PCR amplifications were digested by restriction endonucleases (BamHI and SailI) and sequenced bidirectionally by universal primers(T7p and SP6). The results verified that the cloned fragment including Asn461 and Val462 mutant site had 99.9% homology with the human cDNA of CYP1A1 gene in Genebank. The objective fragment containing Asn461 and Va462 mutant site with cDNA of the CYP1A1 gene has been successfully constructed in this experiment.

A New Glycan-Dependent CD4-Binding Site Neutralizing Antibody Exerts Pressure on HIV-1 In Vivo

PubMed Central

Freund, Natalia T.; Horwitz, Joshua A.; Nogueira, Lilian; Sievers, Stuart A.; Scharf, Louise; Scheid, Johannes F.; Gazumyan, Anna; Liu, Cassie; Velinzon, Klara; Goldenthal, Ariel; Sanders, Rogier W.; Moore, John P.; Bjorkman, Pamela J.; Seaman, Michael S.; Walker, Bruce D.; Klein, Florian; Nussenzweig, Michel C.

2015-01-01

The CD4 binding site (CD4bs) on the envelope glycoprotein is a major site of vulnerability that is conserved among different HIV-1 isolates. Many broadly neutralizing antibodies (bNAbs) to the CD4bs belong to the VRC01 class, sharing highly restricted origins, recognition mechanisms and viral escape pathways. We sought to isolate new anti-CD4bs bNAbs with different origins and mechanisms of action. Using a gp120 2CC core as bait, we isolated antibodies encoded by IGVH3-21 and IGVL3-1 genes with long CDRH3s that depend on the presence of the N-linked glycan at position-276 for activity. This binding mode is similar to the previously identified antibody HJ16, however the new antibodies identified herein are more potent and broad. The most potent variant, 179NC75, had a geometric mean IC80 value of 0.42 μg/ml against 120 Tier-2 HIV-1 pseudoviruses in the TZM.bl assay. Although this group of CD4bs glycan-dependent antibodies can be broadly and potently neutralizing in vitro, their in vivo activity has not been tested to date. Here, we report that 179NC75 is highly active when administered to HIV-1-infected humanized mice, where it selects for escape variants that lack a glycan site at position-276. The same glycan was absent from the virus isolated from the 179NC75 donor, implying that the antibody also exerts selection pressure in humans. PMID:26516768

Differential Maternal Feeding Practices, Eating Self-Regulation, and Adiposity in Young Twins

PubMed Central

Tripicchio, Gina L.; Keller, Kathleen L.; Johnson, Cassandra; Pietrobelli, Angelo; Heo, Moonseong

2014-01-01

OBJECTIVE: Restrictive feeding is associated with childhood obesity; however, this could be due to other factors that drive children to overeat and parents to restrict (eg, child genetics). Using a twin design to better control for confounders, we tested differences in restrictive feeding within families in relation to differences in twins’ self-regulatory eating and weight status. METHODS: Sixty-four same-gender twin pairs (4–7 years old) were studied with their mothers. Child caloric compensation ability (COMPX% index) was assessed by using a laboratory-based protocol. The Child Feeding Questionnaire assessed mothers’ self-reported feeding styles toward each twin. Child BMI (kg/m2) and BMI z score were calculated by using measured weight and height; percent body fat and waist circumference were also assessed. Partial correlations examined within-twin pair differences in Child Feeding Questionnaire subscales in relation to within-twin pair differences in anthropometry and caloric compensation (COMPX%). RESULTS: Differences in maternal restriction were significantly associated with within-pair differences in child COMPX% and BMI z score. Mothers reported more restriction toward the heavier and more poorly compensating twin. Additionally, within-pair differences in parental pressure to eat were associated with significant differences in BMI z score, percent body fat, and waist circumference. Mothers were more pressuring toward the lighter twin. CONCLUSIONS: Mothers vary in their feeding practices, even among same-gender twin pairs, which might influence differences in adiposity. Future research needs to elucidate cause-and-effect and intervention implications regarding parental restriction and pressure-to-eat prompts. PMID:25311601

Gauging state-level and user group views of oyster reef restoration activities in the northern Gulf of Mexico

USGS Publications Warehouse

LaPeyre, Megan K.; Nix, Ashby; Laborde, Luke; Piazza, Bryan P.

2012-01-01

Successful oyster reef restoration, like many conservation challenges, requires not only biological understanding of the resource, but also stakeholder cooperation and political support. To measure perceptions of oyster reef restoration activities and priorities for future restoration along the northern Gulf of Mexico coast, a survey of 1500 individuals representing 4 user groups (oyster harvesters, shrimpers, environmental organization members, professionals), across 5 states (Texas, Louisiana, Mississippi, Alabama, Florida) was conducted in 2011. All respondents highly supported reef restoration efforts, but there was a dichotomy in preferred restoration goals with commercial fishermen more likely to support oyster reef restoration for stock enhancement, while professionals and environmental organization members were more likely to support oyster reef restoration to enhance ecosystem services. All user groups identified enforcement, funding, and appropriate site selection as basic requirements for successful reef restoration. For management of restored oyster reefs, oyster harvesters and shrimpers were less likely to support options that restricted the use of reefs, including gear restrictions and permanent closures, but did support rotating annual reef closures, while other stakeholders were willing to consider all options, including annual reef closures and sanctuary reefs. Overall, there were clear differences in management and communication preferences across user groups, but few differences across states. Understanding these key differences in stakeholder support for, and willingness to accept specific management actions is critical in moving management and restoration forward while minimizing conflict.

Response of soybean rhizosphere communities to human hygiene water addition as determined by community level physiological profiling (CLPP) and terminal restriction fragment length polymorphism (TRFLP) analysis

NASA Technical Reports Server (NTRS)

Kerkhof, L.; Santoro, M.; Garland, J.

2000-01-01

In this report, we describe an experiment conducted at Kennedy Space Center in the biomass production chamber (BPC) using soybean plants for purification and processing of human hygiene water. Specifically, we tested whether it was possible to detect changes in the root-associated bacterial assemblage of the plants and ultimately to identify the specific microorganism(s) which differed when plants were exposed to hygiene water and other hydroponic media. Plants were grown in hydroponics media corresponding to four different treatments: control (Hoagland's solution), artificial gray water (Hoagland's+surfactant), filtered gray water collected from human subjects on site, and unfiltered gray water. Differences in rhizosphere microbial populations in all experimental treatments were observed when compared to the control treatment using both community level physiological profiles (BIOLOG) and molecular fingerprinting of 16S rRNA genes by terminal restriction fragment length polymorphism analysis (TRFLP). Furthermore, screening of a clonal library of 16S rRNA genes by TRFLP yielded nearly full length SSU genes associated with the various treatments. Most 16S rRNA genes were affiliated with the Klebsiella, Pseudomonas, Variovorax, Burkholderia, Bordetella and Isosphaera groups. This molecular approach demonstrated the ability to rapidly detect and identify microorganisms unique to experimental treatments and provides a means to fingerprint microbial communities in the biosystems being developed at NASA for optimizing advanced life support operations.

Soil factors involved in the diversity and structure of soil bacterial communities in commercial organic olive orchards in Southern Spain.

PubMed

Landa, B B; Montes-Borrego, M; Aranda, S; Soriano, M A; Gómez, J A; Navas-Cortés, J A

2014-04-01

Nowadays, there is a tendency in olive production systems to reduce tillage or keep a vegetative cover to reduce soil erosion and degradation. However, there is scarce information on the effects of different soil management systems (SMS) in soil bacterial community composition of olive groves. In this study, we have evaluated the effects of soil type and different SMS implemented to control weeds in the structure and diversity of bacterial communities of 58 soils in the two geographic areas that best represent the organic olive production systems in Spain. Bacterial community composition assessed by frequency and intensity of occurrence of terminal restriction profiles (TRFs) derived from terminal restriction fragment length polymorphism (T-RFLP) analysis of amplified 16S ribosomal deoxyribonucleic acid were strongly correlated with soil type/field site (Eutric/Calcaric) that differed mainly in soil particle size distribution and soil pH, followed by a strong effect of SMS, in that order. Canonical discriminant (CD) analysis of TRFs properly classified all of the olive orchard soils as belonging to their respective soil type or SMS. Furthermore, only a small set of TRFs were enough to clearly and significantly differentiate soil samples according to soil type or SMS. Those specific TRFs could be used as bioindicators to assess the effect of changes in SMS aimed to enhance soil quality in olive production systems. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Activity and Diversity of Methanotrophic Bacteria at Methane Seeps in Eastern Lake Constance Sediments ▿

PubMed Central

Deutzmann, Jörg S.; Wörner, Susanne; Schink, Bernhard

2011-01-01

The activity and community structure of aerobic methanotrophic communities were investigated at methane seeps (pockmarks) in the littoral and profundal zones of an oligotrophic freshwater lake (Lake Constance, Germany). Measurements of potential methane oxidation rates showed that sediments inside littoral pockmarks are hot spots of methane oxidation. Potential methane oxidation rates at littoral pockmark sites exceeded the rates of the surrounding sediment by 2 orders of magnitude. Terminal restriction fragment length polymorphism (T-RFLP) analysis of the pmoA gene revealed major differences in the methanotrophic community composition between littoral pockmarks and the surrounding sediments. Clone library analysis confirmed that one distinct Methylobacter-related group dominates the community at littoral pockmarks. In profundal sediments, the differences between pockmarks and surrounding sediments were found to be less pronounced. PMID:21335392

Reduction of atmospheric fine particle level by restricting the idling vehicles around a sensitive area.

PubMed

Lee, Yen-Yi; Lin, Sheng-Lun; Yuan, Chung-Shin; Lin, Ming-Yeng; Chen, Kang-Shin

2018-07-01

Atmospheric particles are a major problem that could lead to harmful effects on human health, especially in densely populated urban areas. Chiayi is a typical city with very high population and traffic density, as well as being located at the downwind side of several pollution sources. Multiple contributors for PM 2.5 (particulate matter with an aerodynamic diameter ≥2.5 μm) and ultrafine particles cause complicated air quality problems. This study focused on the inhibition of local emission sources by restricting the idling vehicles around a school area and evaluating the changes in surrounding atmospheric PM conditions. Two stationary sites were monitored, including a background site on the upwind side of the school and a campus site inside the school, to monitor the exposure level, before and after the idling prohibition. In the base condition, the PM 2.5  mass concentrations were found to increase 15% from the background, whereas the nitrate (NO 3 - ) content had a significant increase at the campus site. The anthropogenic metal contents in PM 2.5 were higher at the campus site than the background site. Mobile emissions were found to be the most likely contributor to the school hot spot area by chemical mass balance modeling (CMB8.2). On the other hand, the PM 2.5 in the school campus fell to only 2% after idling vehicle control, when the mobile source contribution reduced from 42.8% to 36.7%. The mobile monitoring also showed significant reductions in atmospheric PM 2.5 , PM 0.1 , polycyclic aromatic hydrocarbons (PAHs), and black carbon (BC) levels by 16.5%, 33.3%, 48.0%, and 11.5%, respectively. Consequently, the restriction of local idling emission was proven to significantly reduce PM and harmful pollutants in the hot spots around the school environment. The emission of idling vehicles strongly affects the levels of particles and relative pollutants in near-ground air around a school area. The PM 2.5 mass concentration at a campus site increased from the background site by 15%, whereas NO 3 - and anthropogenic metals also significantly increased. Meanwhile, the PM 2.5 contribution from mobile source in the campus increased 6.6% from the upwind site. An idling prohibition took place and showed impressive results. Reductions of PM 2.5 , ionic component, and non-natural metal contents were found after the idling prohibition. The mobile monitoring also pointed out a significant improvement with the spatial analysis of PM 2.5 , PM 0.1 , PAH, and black carbon concentrations. These findings are very useful to effectively improve the local air quality of a densely city during the rush hour.

Vortex Sensing Tests at Logan and Kennedy Airports

DOT National Transportation Integrated Search

1972-12-01

The report describes a series of tests of wake vortex sensing systems at Logan and Kennedy Airports. Two systems, a pulsed acoustic radar (acdar) and an array of ground level pressure sensors, were tested. Site restrictions limited the Logan work to ...

Clean Water Act Section 404(c) Factsheet

EPA Pesticide Factsheets

404(c) authorizes EPA to restrict, prohibit, deny, or withdraw the use of an area as a disposal site for dredged or fill material if the discharge will have unacceptable adverse effects on municipal water supplies, shellfish beds, fishery areas, etc.