Efficient and simpler method to construct normalized cDNA libraries with improved representations of full-length cDNAs

DOEpatents

Soares, M.B.; Fatima Bonaldo, M. de

1998-12-08

This invention provides a method to normalize a cDNA library comprising: (a) constructing a directionally cloned library containing cDNA inserts wherein the insert is capable of being amplified by polymerase chain reaction; (b) converting a double-stranded cDNA library into single-stranded DNA circles; (c) generating single-stranded nucleic acid molecules complementary to the single-stranded DNA circles converted in step (b) by polymerase chain reaction with appropriate primers; (d) hybridizing the single-stranded DNA circles converted in step (b) with the complementary single-stranded nucleic acid molecules generated in step (c) to produce partial duplexes to an appropriate Cot; and (e) separating the unhybridized single-stranded DNA circles from the hybridized DNA circles, thereby generating a normalized cDNA library. This invention also provides a method to normalize a cDNA library wherein the generating of single-stranded nucleic acid molecules complementary to the single-stranded DNA circles converted in step (b) is by excising cDNA inserts from the double-stranded cDNA library; purifying the cDNA inserts from cloning vectors; and digesting the cDNA inserts with an exonuclease. This invention further provides a method to construct a subtractive cDNA library following the steps described above. This invention further provides normalized and/or subtractive cDNA libraries generated by the above methods. 25 figs.

Direct cloning from enrichment cultures, a reliable strategy for isolation of complete operons and genes from microbial consortia.

PubMed

Entcheva, P; Liebl, W; Johann, A; Hartsch, T; Streit, W R

2001-01-01

Enrichment cultures of microbial consortia enable the diverse metabolic and catabolic activities of these populations to be studied on a molecular level and to be explored as potential sources for biotechnology processes. We have used a combined approach of enrichment culture and direct cloning to construct cosmid libraries with large (>30-kb) inserts from microbial consortia. Enrichment cultures were inoculated with samples from five environments, and high amounts of avidin were added to the cultures to favor growth of biotin-producing microbes. DNA was extracted from three of these enrichment cultures and used to construct cosmid libraries; each library consisted of between 6,000 and 35,000 clones, with an average insert size of 30 to 40 kb. The inserts contained a diverse population of genomic DNA fragments isolated from the consortia organisms. These three libraries were used to complement the Escherichia coli biotin auxotrophic strain ATCC 33767 Delta(bio-uvrB). Initial screens resulted in the isolation of seven different complementing cosmid clones, carrying biotin biosynthesis operons. Biotin biosynthesis capabilities and growth under defined conditions of four of these clones were studied. Biotin measured in the different culture supernatants ranged from 42 to 3,800 pg/ml/optical density unit. Sequencing the identified biotin synthesis genes revealed high similarities to bio operons from gram-negative bacteria. In addition, random sequencing identified other interesting open reading frames, as well as two operons, the histidine utilization operon (hut), and the cluster of genes involved in biosynthesis of molybdopterin cofactors in bacteria (moaABCDE).

Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome

PubMed Central

2011-01-01

Background One of the key goals of oak genomics research is to identify genes of adaptive significance. This information may help to improve the conservation of adaptive genetic variation and the management of forests to increase their health and productivity. Deep-coverage large-insert genomic libraries are a crucial tool for attaining this objective. We report herein the construction of a BAC library for Quercus robur, its characterization and an analysis of BAC end sequences. Results The EcoRI library generated consisted of 92,160 clones, 7% of which had no insert. Levels of chloroplast and mitochondrial contamination were below 3% and 1%, respectively. Mean clone insert size was estimated at 135 kb. The library represents 12 haploid genome equivalents and, the likelihood of finding a particular oak sequence of interest is greater than 99%. Genome coverage was confirmed by PCR screening of the library with 60 unique genetic loci sampled from the genetic linkage map. In total, about 20,000 high-quality BAC end sequences (BESs) were generated by sequencing 15,000 clones. Roughly 5.88% of the combined BAC end sequence length corresponded to known retroelements while ab initio repeat detection methods identified 41 additional repeats. Collectively, characterized and novel repeats account for roughly 8.94% of the genome. Further analysis of the BESs revealed 1,823 putative genes suggesting at least 29,340 genes in the oak genome. BESs were aligned with the genome sequences of Arabidopsis thaliana, Vitis vinifera and Populus trichocarpa. One putative collinear microsyntenic region encoding an alcohol acyl transferase protein was observed between oak and chromosome 2 of V. vinifera. Conclusions This BAC library provides a new resource for genomic studies, including SSR marker development, physical mapping, comparative genomics and genome sequencing. BES analysis provided insight into the structure of the oak genome. These sequences will be used in the assembly of a future genome sequence for oak. PMID:21645357

From the ORFeome concept to highly comprehensive, full-genome screening libraries.

PubMed

Rid, Raphaela; Abdel-Hadi, Omar; Maier, Richard; Wagner, Martin; Hundsberger, Harald; Hintner, Helmut; Bauer, Johann; Onder, Kamil

2013-02-01

Recombination-based cloning techniques have in recent times facilitated the establishment of genome-scale single-gene ORFeome repositories. Their further handling and downstream application in systematic fashion is, however, practically impeded because of logistical plus economic challenges. At this juncture, simultaneously transferring entire gene collections in compiled pool format could represent an advanced compromise between systematic ORFeome (an organism's entire set of protein-encoding open reading frames) projects and traditional random library approaches, but has not yet been considered in great detail. In our endeavor to merge the comprehensiveness of ORFeomes with a basically simple, streamlined, and easily executable single-tube design, we have here produced five different pooled screening-ready libraries for both Staphylococcus aureus and Homo sapiens. By evaluating the parallel transfer efficiencies of differentially sized genes from initial polymerase chain reaction (PCR) product amplification to entry and final destination library construction via quantitative real-time PCR, we found that the complexity of the gene population is fairly stably maintained once an entry resource has been successfully established, and that no apparent size-selection bias loss of large inserts takes place. Recombinational transfer processes are hence robust enough for straightforwardly achieving such pooled screening libraries.

Construction of random sheared fosmid library from Chinese cabbage and its use for Brassica rapa genome sequencing project.

PubMed

Park, Tae-Ho; Park, Beom-Seok; Kim, Jin-A; Hong, Joon Ki; Jin, Mina; Seol, Young-Joo; Mun, Jeong-Hwan

2011-01-01

As a part of the Multinational Genome Sequencing Project of Brassica rapa, linkage group R9 and R3 were sequenced using a bacterial artificial chromosome (BAC) by BAC strategy. The current physical contigs are expected to cover approximately 90% euchromatins of both chromosomes. As the project progresses, BAC selection for sequence extension becomes more limited because BAC libraries are restriction enzyme-specific. To support the project, a random sheared fosmid library was constructed. The library consists of 97536 clones with average insert size of approximately 40 kb corresponding to seven genome equivalents, assuming a Chinese cabbage genome size of 550 Mb. The library was screened with primers designed at the end of sequences of nine points of scaffold gaps where BAC clones cannot be selected to extend the physical contigs. The selected positive clones were end-sequenced to check the overlap between the fosmid clones and the adjacent BAC clones. Nine fosmid clones were selected and fully sequenced. The sequences revealed two completed gap filling and seven sequence extensions, which can be used for further selection of BAC clones confirming that the fosmid library will facilitate the sequence completion of B. rapa. Copyright © 2011. Published by Elsevier Ltd.

Using PATIMDB to Create Bacterial Transposon Insertion Mutant Libraries

PubMed Central

Urbach, Jonathan M.; Wei, Tao; Liberati, Nicole; Grenfell-Lee, Daniel; Villanueva, Jacinto; Wu, Gang; Ausubel, Frederick M.

2015-01-01

PATIMDB is a software package for facilitating the generation of transposon mutant insertion libraries. The software has two main functions: process tracking and automated sequence analysis. The process tracking function specifically includes recording the status and fates of multiwell plates and samples in various stages of library construction. Automated sequence analysis refers specifically to the pipeline of sequence analysis starting with ABI files from a sequencing facility and ending with insertion location identifications. The protocols in this unit describe installation and use of PATIMDB software. PMID:19343706

Large exon size does not limit splicing in vivo.

PubMed

Chen, I T; Chasin, L A

1994-03-01

Exon sizes in vertebrate genes are, with a few exceptions, limited to less than 300 bases. It has been proposed that this limitation may derive from the exon definition model of splice site recognition. In this model, a downstream donor site enhances splicing at the upstream acceptor site of the same exon. This enhancement may require contact between factors bound to each end of the exon; an exon size limitation would promote such contact. To test the idea that proximity was required for exon definition, we inserted random DNA fragments from Escherichia coli into a central exon in a three-exon dihydrofolate reductase minigene and tested whether the expanded exons were efficiently spliced. DNA from a plasmid library of expanded minigenes was used to transfect a CHO cell deletion mutant lacking the dhfr locus. PCR analysis of DNA isolated from the pooled stable cotransfectant populations displayed a range of DNA insert sizes from 50 to 1,500 nucleotides. A parallel analysis of the RNA from this population by reverse transcription followed by PCR showed a similar size distribution. Central exons as large as 1,400 bases could be spliced into mRNA. We also tested individual plasmid clones containing exon inserts of defined sizes. The largest exon included in mRNA was 1,200 bases in length, well above the 300-base limit implied by the survey of naturally occurring exons. We conclude that a limitation in exon size is not part of the exon definition mechanism.

Genomic resources for gene discovery, functional genome annotation, and evolutionary studies of maize and its close relatives.

PubMed

Wang, Chao; Shi, Xue; Liu, Lin; Li, Haiyan; Ammiraju, Jetty S S; Kudrna, David A; Xiong, Wentao; Wang, Hao; Dai, Zhaozhao; Zheng, Yonglian; Lai, Jinsheng; Jin, Weiwei; Messing, Joachim; Bennetzen, Jeffrey L; Wing, Rod A; Luo, Meizhong

2013-11-01

Maize is one of the most important food crops and a key model for genetics and developmental biology. A genetically anchored and high-quality draft genome sequence of maize inbred B73 has been obtained to serve as a reference sequence. To facilitate evolutionary studies in maize and its close relatives, much like the Oryza Map Alignment Project (OMAP) (www.OMAP.org) bacterial artificial chromosome (BAC) resource did for the rice community, we constructed BAC libraries for maize inbred lines Zheng58, Chang7-2, and Mo17 and maize wild relatives Zea mays ssp. parviglumis and Tripsacum dactyloides. Furthermore, to extend functional genomic studies to maize and sorghum, we also constructed binary BAC (BIBAC) libraries for the maize inbred B73 and the sorghum landrace Nengsi-1. The BAC/BIBAC vectors facilitate transfer of large intact DNA inserts from BAC clones to the BIBAC vector and functional complementation of large DNA fragments. These seven Zea Map Alignment Project (ZMAP) BAC/BIBAC libraries have average insert sizes ranging from 92 to 148 kb, organellar DNA from 0.17 to 2.3%, empty vector rates between 0.35 and 5.56%, and genome equivalents of 4.7- to 8.4-fold. The usefulness of the Parviglumis and Tripsacum BAC libraries was demonstrated by mapping clones to the reference genome. Novel genes and alleles present in these ZMAP libraries can now be used for functional complementation studies and positional or homology-based cloning of genes for translational genomics.

Construction of the BAC Library of Small Abalone (Haliotis diversicolor) for Gene Screening and Genome Characterization.

PubMed

Jiang, Likun; You, Weiwei; Zhang, Xiaojun; Xu, Jian; Jiang, Yanliang; Wang, Kai; Zhao, Zixia; Chen, Baohua; Zhao, Yunfeng; Mahboob, Shahid; Al-Ghanim, Khalid A; Ke, Caihuan; Xu, Peng

2016-02-01

The small abalone (Haliotis diversicolor) is one of the most important aquaculture species in East Asia. To facilitate gene cloning and characterization, genome analysis, and genetic breeding of it, we constructed a large-insert bacterial artificial chromosome (BAC) library, which is an important genetic tool for advanced genetics and genomics research. The small abalone BAC library includes 92,610 clones with an average insert size of 120 Kb, equivalent to approximately 7.6× of the small abalone genome. We set up three-dimensional pools and super pools of 18,432 BAC clones for target gene screening using PCR method. To assess the approach, we screened 12 target genes in these 18,432 BAC clones and identified 16 positive BAC clones. Eight positive BAC clones were then sequenced and assembled with the next generation sequencing platform. The assembled contigs representing these 8 BAC clones spanned 928 Kb of the small abalone genome, providing the first batch of genome sequences for genome evaluation and characterization. The average GC content of small abalone genome was estimated as 40.33%. A total of 21 protein-coding genes, including 7 target genes, were annotated into the 8 BACs, which proved the feasibility of PCR screening approach with three-dimensional pools in small abalone BAC library. One hundred fifty microsatellite loci were also identified from the sequences for marker development in the future. The BAC library and clone pools provided valuable resources and tools for genetic breeding and conservation of H. diversicolor.

Generation and analysis of a barcode-tagged insertion mutant library in the fission yeast Schizosaccharomyces pombe.

PubMed

Chen, Bo-Ruei; Hale, Devin C; Ciolek, Peter J; Runge, Kurt W

2012-05-03

Barcodes are unique DNA sequence tags that can be used to specifically label individual mutants. The barcode-tagged open reading frame (ORF) haploid deletion mutant collections in the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe allow for high-throughput mutant phenotyping because the relative growth of mutants in a population can be determined by monitoring the proportions of their associated barcodes. While these mutant collections have greatly facilitated genome-wide studies, mutations in essential genes are not present, and the roles of these genes are not as easily studied. To further support genome-scale research in S. pombe, we generated a barcode-tagged fission yeast insertion mutant library that has the potential of generating viable mutations in both essential and non-essential genes and can be easily analyzed using standard molecular biological techniques. An insertion vector containing a selectable ura4+ marker and a random barcode was used to generate a collection of 10,000 fission yeast insertion mutants stored individually in 384-well plates and as six pools of mixed mutants. Individual barcodes are flanked by Sfi I recognition sites and can be oligomerized in a unique orientation to facilitate barcode sequencing. Independent genetic screens on a subset of mutants suggest that this library contains a diverse collection of single insertion mutations. We present several approaches to determine insertion sites. This collection of S. pombe barcode-tagged insertion mutants is well-suited for genome-wide studies. Because insertion mutations may eliminate, reduce or alter the function of essential and non-essential genes, this library will contain strains with a wide range of phenotypes that can be assayed by their associated barcodes. The design of the barcodes in this library allows for barcode sequencing using next generation or standard benchtop cloning approaches.

Bioproduction and characterization of extracellular melanin-like pigment from industrially polluted metagenomic library equipped Escherichia coli.

PubMed

Amin, Shivani; Rastogi, Rajesh P; Sonani, Ravi R; Ray, Arabinda; Sharma, Rakesh; Madamwar, Datta

2018-04-15

To explore the potential genes from the industrially polluted Amlakhadi canal, located in Ankleshwar, Gujarat, India, its community genome was extracted and cloned into E. coli EPI300™-T1 R using a fosmid vector (pCC2 FOS™) generating a library of 3,92,000 clones with average size of 40kb of DNA-insert. From this library, the clone DM1 producing brown colored melanin-like pigment was isolated and characterized. For over expression of the pigment, further sub-cloning of the clone DM1 was done. Sub-clone containing 10kb of the insert was sequenced for gene identification. The amino acids sequence of a protein 4-Hydroxyphenylpyruvate dioxygenase (HPPD), which is know to be involved in melanin biosynthesis was obtained from the gene sequence. The sequence-homology based 3D structure model of HPPD was constructed and analyzed. The physico-chemical nature of pigment was further analysed using 1 H and 13 C NMR, LC-MS, FTIR and UV-visible spectroscopy. The pigment was readily soluble in DMSO with an absorption maximum around 290nm. Based on the genetic and chemical characterization, the compound was confirmed as melanin-like pigment. The present results indicate that the metagenomic library from industrially polluted environment generated a microbial tool for the production of melanin-like pigment. Copyright © 2018 Elsevier B.V. All rights reserved.

A novel helper phage enabling construction of genome-scale ORF-enriched phage display libraries.

PubMed

Gupta, Amita; Shrivastava, Nimisha; Grover, Payal; Singh, Ajay; Mathur, Kapil; Verma, Vaishali; Kaur, Charanpreet; Chaudhary, Vijay K

2013-01-01

Phagemid-based expression of cloned genes fused to the gIIIP coding sequence and rescue using helper phages, such as VCSM13, has been used extensively for constructing large antibody phage display libraries. However, for randomly primed cDNA and gene fragment libraries, this system encounters reading frame problems wherein only one of 18 phages display the translated foreign peptide/protein fused to phagemid-encoded gIIIP. The elimination of phages carrying out-of-frame inserts is vital in order to improve the quality of phage display libraries. In this study, we designed a novel helper phage, AGM13, which carries trypsin-sensitive sites within the linker regions of gIIIP. This renders the phage highly sensitive to trypsin digestion, which abolishes its infectivity. For open reading frame (ORF) selection, the phagemid-borne phages are rescued using AGM13, so that clones with in-frame inserts express fusion proteins with phagemid-encoded trypsin-resistant gIIIP, which becomes incorporated into the phages along with a few copies of AGM13-encoded trypsin-sensitive gIIIP. In contrast, clones with out-of-frame inserts produce phages carrying only AGM13-encoded trypsin-sensitive gIIIP. Trypsin treatment of the phage population renders the phages with out-of-frame inserts non-infectious, whereas phages carrying in-frame inserts remain fully infectious and can hence be enriched by infection. This strategy was applied efficiently at a genome scale to generate an ORF-enriched whole genome fragment library from Mycobacterium tuberculosis, in which nearly 100% of the clones carried in-frame inserts after selection. The ORF-enriched libraries were successfully used for identification of linear and conformational epitopes for monoclonal antibodies specific to mycobacterial proteins.

Construction of a nurse shark (Ginglymostoma cirratum) bacterial artificial chromosome (BAC) library and a preliminary genome survey.

PubMed

Luo, Meizhong; Kim, Hyeran; Kudrna, Dave; Sisneros, Nicholas B; Lee, So-Jeong; Mueller, Christopher; Collura, Kristi; Zuccolo, Andrea; Buckingham, E Bryan; Grim, Suzanne M; Yanagiya, Kazuyo; Inoko, Hidetoshi; Shiina, Takashi; Flajnik, Martin F; Wing, Rod A; Ohta, Yuko

2006-05-03

Sharks are members of the taxonomic class Chondrichthyes, the oldest living jawed vertebrates. Genomic studies of this group, in comparison to representative species in other vertebrate taxa, will allow us to theorize about the fundamental genetic, developmental, and functional characteristics in the common ancestor of all jawed vertebrates. In order to obtain mapping and sequencing data for comparative genomics, we constructed a bacterial artificial chromosome (BAC) library for the nurse shark, Ginglymostoma cirratum. The BAC library consists of 313,344 clones with an average insert size of 144 kb, covering ~4.5 x 1010 bp and thus providing an 11-fold coverage of the haploid genome. BAC end sequence analyses revealed, in addition to LINEs and SINEs commonly found in other animal and plant genomes, two new groups of nurse shark-specific repetitive elements, NSRE1 and NSRE2 that seem to be major components of the nurse shark genome. Screening the library with single-copy or multi-copy gene probes showed 6-28 primary positive clones per probe of which 50-90% were true positives, demonstrating that the BAC library is representative of the different regions of the nurse shark genome. Furthermore, some BAC clones contained multiple genes, making physical mapping feasible. We have constructed a deep-coverage, high-quality, large insert, and publicly available BAC library for a cartilaginous fish. It will be very useful to the scientific community interested in shark genomic structure, comparative genomics, and functional studies. We found two new groups of repetitive elements specific to the nurse shark genome, which may contribute to the architecture and evolution of the nurse shark genome.

Comparison of large-insert, small-insert and pyrosequencing libraries for metagenomic analysis.

PubMed

Danhorn, Thomas; Young, Curtis R; DeLong, Edward F

2012-11-01

The development of DNA sequencing methods for characterizing microbial communities has evolved rapidly over the past decades. To evaluate more traditional, as well as newer methodologies for DNA library preparation and sequencing, we compared fosmid, short-insert shotgun and 454 pyrosequencing libraries prepared from the same metagenomic DNA samples. GC content was elevated in all fosmid libraries, compared with shotgun and 454 libraries. Taxonomic composition of the different libraries suggested that this was caused by a relative underrepresentation of dominant taxonomic groups with low GC content, notably Prochlorales and the SAR11 cluster, in fosmid libraries. While these abundant taxa had a large impact on library representation, we also observed a positive correlation between taxon GC content and fosmid library representation in other low-GC taxa, suggesting a general trend. Analysis of gene category representation in different libraries indicated that the functional composition of a library was largely a reflection of its taxonomic composition, and no additional systematic biases against particular functional categories were detected at the level of sequencing depth in our samples. Another important but less predictable factor influencing the apparent taxonomic and functional library composition was the read length afforded by the different sequencing technologies. Our comparisons and analyses provide a detailed perspective on the influence of library type on the recovery of microbial taxa in metagenomic libraries and underscore the different uses and utilities of more traditional, as well as contemporary 'next-generation' DNA library construction and sequencing technologies for exploring the genomics of the natural microbial world.

Generation and analysis of a barcode-tagged insertion mutant library in the fission yeast Schizosaccharomyces pombe

PubMed Central

2012-01-01

Background Barcodes are unique DNA sequence tags that can be used to specifically label individual mutants. The barcode-tagged open reading frame (ORF) haploid deletion mutant collections in the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe allow for high-throughput mutant phenotyping because the relative growth of mutants in a population can be determined by monitoring the proportions of their associated barcodes. While these mutant collections have greatly facilitated genome-wide studies, mutations in essential genes are not present, and the roles of these genes are not as easily studied. To further support genome-scale research in S. pombe, we generated a barcode-tagged fission yeast insertion mutant library that has the potential of generating viable mutations in both essential and non-essential genes and can be easily analyzed using standard molecular biological techniques. Results An insertion vector containing a selectable ura4+ marker and a random barcode was used to generate a collection of 10,000 fission yeast insertion mutants stored individually in 384-well plates and as six pools of mixed mutants. Individual barcodes are flanked by Sfi I recognition sites and can be oligomerized in a unique orientation to facilitate barcode sequencing. Independent genetic screens on a subset of mutants suggest that this library contains a diverse collection of single insertion mutations. We present several approaches to determine insertion sites. Conclusions This collection of S. pombe barcode-tagged insertion mutants is well-suited for genome-wide studies. Because insertion mutations may eliminate, reduce or alter the function of essential and non-essential genes, this library will contain strains with a wide range of phenotypes that can be assayed by their associated barcodes. The design of the barcodes in this library allows for barcode sequencing using next generation or standard benchtop cloning approaches. PMID:22554201

A Blumeria graminisf.sp. hordei BAC library--contig building and microsynteny studies.

PubMed

Pedersen, Carsten; Wu, Boqian; Giese, Henriette

2002-11-01

A bacterial artificial chromosome (BAC) library of Blumeria graminis f.sp. hordei, containing 12,000 clones with an average insert size of 41 kb, was constructed. The library represents about three genome equivalents and BAC-end sequencing showed a high content of repetitive sequences, making contig-building difficult. To identify overlapping clones, several strategies were used: colony hybridisation, PCR screening, fingerprinting techniques and the use of single-copy expressed sequence tags. The latter proved to be the most efficient method for identification of overlapping clones. Two contigs, at or close to avirulence loci, were constructed. Single nucleotide polymorphism (SNP) markers were developed from BAC-end sequences to link the contigs to the genetic maps. Two other BAC contigs were used to study microsynteny between B. graminis and two other ascomycetes, Neurospora crassa and Aspergillus fumigatus. The library provides an invaluable tool for the isolation of avirulence genes from B. graminis and for the study of gene synteny between this fungus and other fungi.

Construction, Characterization, and Preliminary BAC-End Sequence Analysis of a Bacterial Artificial Chromosome Library of the Tea Plant (Camellia sinensis)

PubMed Central

Lin, Jinke; Kudrna, Dave; Wing, Rod A.

2011-01-01

We describe the construction and characterization of a publicly available BAC library for the tea plant, Camellia sinensis. Using modified methods, the library was constructed with the aim of developing public molecular resources to advance tea plant genomics research. The library consists of a total of 401,280 clones with an average insert size of 135 kb, providing an approximate coverage of 13.5 haploid genome equivalents. No empty vector clones were observed in a random sampling of 576 BAC clones. Further analysis of 182 BAC-end sequences from randomly selected clones revealed a GC content of 40.35% and low chloroplast and mitochondrial contamination. Repetitive sequence analyses indicated that LTR retrotransposons were the most predominant sequence class (86.93%–87.24%), followed by DNA retrotransposons (11.16%–11.69%). Additionally, we found 25 simple sequence repeats (SSRs) that could potentially be used as genetic markers. PMID:21234344

Assembling short reads from jumping libraries with large insert sizes.

PubMed

Vasilinetc, Irina; Prjibelski, Andrey D; Gurevich, Alexey; Korobeynikov, Anton; Pevzner, Pavel A

2015-10-15

Advances in Next-Generation Sequencing technologies and sample preparation recently enabled generation of high-quality jumping libraries that have a potential to significantly improve short read assemblies. However, assembly algorithms have to catch up with experimental innovations to benefit from them and to produce high-quality assemblies. We present a new algorithm that extends recently described exSPAnder universal repeat resolution approach to enable its applications to several challenging data types, including jumping libraries generated by the recently developed Illumina Nextera Mate Pair protocol. We demonstrate that, with these improvements, bacterial genomes often can be assembled in a few contigs using only a single Nextera Mate Pair library of short reads. Described algorithms are implemented in C++ as a part of SPAdes genome assembler, which is freely available at bioinf.spbau.ru/en/spades. ap@bioinf.spbau.ru Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

[Construction of fetal mesenchymal stem cell cDNA subtractive library].

PubMed

Yang, Li; Wang, Dong-Mei; Li, Liang; Bai, Ci-Xian; Cao, Hua; Li, Ting-Yu; Pei, Xue-Tao

2002-04-01

To identify differentially expressed genes between fetal mesenchymal stem cell (MSC) and adult MSC, especially specified genes expressed in fetal MSC, a cDNA subtractive library of fetal MSC was constructed using suppression subtractive hybridization (SSH) technique. At first, total RNA was isolated from fetal and adult MSC. Using SMART PCR synthesis method, single-strand and double-strand cDNAs were synthesized. After Rsa I digestion, fetal MSC cDNAs were divided into two groups and ligated to adaptor 1 and adaptor 2 respectively. Results showed that the amplified library contains 890 clones. Analysis of 890 clones with PCR demonstrated that 768 clones were positive. The positive rate is 86.3%. The size of inserted fragments in these positive clones was between 0.2 - 1 kb, with an average of 400 - 600 bp. SSH is a convenient and effective method for screening differentially expressed genes. The constructed cDNA subtractive library of fetal MSC cDNA lays solid foundation for screening and cloning new and specific function related genes of fetal MSC.

Construction of High-Quality Camel Immune Antibody Libraries.

PubMed

Romão, Ema; Poignavent, Vianney; Vincke, Cécile; Ritzenthaler, Christophe; Muyldermans, Serge; Monsion, Baptiste

2018-01-01

Single-domain antibodies libraries of heavy-chain only immunoglobulins from camelids or shark are enriched for high-affinity antigen-specific binders by a short in vivo immunization. Thus, potent binders are readily retrieved from relatively small-sized libraries of 10 7 -10 8 individual transformants, mostly after phage display and panning on a purified target. However, the remaining drawback of this strategy arises from the need to generate a dedicated library, for nearly every envisaged target. Therefore, all the procedures that shorten and facilitate the construction of an immune library of best possible quality are definitely a step forward. In this chapter, we provide the protocol to generate a high-quality immune VHH library using the Golden Gate Cloning strategy employing an adapted phage display vector where a lethal ccdB gene has to be substituted by the VHH gene. With this procedure, the construction of the library can be shortened to less than a week starting from bleeding the animal. Our libraries exceed 10 8 individual transformants and close to 100% of the clones harbor a phage display vector having an insert with the length of a VHH gene. These libraries are also more economic to make than previous standard approaches using classical restriction enzymes and ligations. The quality of the Nanobodies that are retrieved from immune libraries obtained by Golden Gate Cloning is identical to those from immune libraries made according to the classical procedure.

Genomic clones for human cholinesterase

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

Kott, M.; Venta, P.J.; Larsen, J.

1987-05-01

A human genomic library was prepared from peripheral white blood cells from a single donor by inserting an MboI partial digest into BamHI poly-linker sites of EMBL3. This library was screened using an oligolabeled human cholinesterase cDNA probe over 700 bp long. The latter probe was obtained from a human basal ganglia cDNA library. Of approximately 2 million clones screened with high stringency conditions several positive clones were identified; two have been plaque purified. One of these clones has been partially mapped using restriction enzymes known to cut within the coded region of the cDNA for human serum cholinesterase. Hybridizationmore » of the fragments and their sizes are as expected if the genomic clone is cholinesterase. Sequencing of the DNA fragments in M13 is in progress to verify the identify of the clone and the location of introns.« less

[Construction of dengue virus-specific full-length fully human antibody libraries by mammalian display technology].

PubMed

Wen, Yangming; Lan, Kaijian; Wang, Junjie; Yu, Jingyi; Qu, Yarong; Zhao, Wei; Zhang, Fuchun; Tan, Wanlong; Cao, Hong; Zhou, Chen

2013-06-01

To construct dengue virus-specific full-length fully human antibody libraries using mammalian cell surface display technique. Total RNA was extracted from peripheral blood mononuclear cells (PBMCs) from convalescent patients with dengue fever. The reservoirs of the light chain and heavy chain variable regions (LCκ and VH) of the antibody genes were amplified by RT-PCR and inserted into the vector pDGB-HC-TM separately to construct the light chain and heavy chain libraries. The library DNAs were transfected into CHO cells and the expression of full-length fully human antibodies on the surface of CHO cells was analyzed by flow cytometry. Using 1.2 µg of the total RNA isolated from the PBMCs as the template, the LCκ and VH were amplified and the full-length fully human antibody mammalian display libraries were constructed. The kappa light chain gene library had a size of 1.45×10(4) and the heavy chain gene library had a size of 1.8×10(5). Sequence analysis showed that 8 out of the 10 light chain clones and 7 out of the 10 heavy chain clones randomly picked up from the constructed libraries contained correct open reading frames. FACS analysis demonstrated that all the 15 clones with correct open reading frames expressed full-length antibodies, which could be detected on CHO cell surfaces. After co-transfection of the heavy chain and light chain gene libraries into CHO cells, the expression of full-length antibodies on CHO cell surfaces could be detected by FACS analysis with an expressible diversity of the antibody library reaching 1.46×10(9) [(1.45×10(4)×80%)×(1.8×10(5)×70%)]. Using 1.2 µg of total RNA as template, the LCκ and VH full-length fully human antibody libraries against dengue virus have been successfully constructed with an expressible diversity of 10(9).

Scaling up the 454 Titanium Library Construction and Pooling of Barcoded Libraries

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

Phung, Wilson; Hack, Christopher; Shapiro, Harris

2009-03-23

We have been developing a high throughput 454 library construction process at the Joint Genome Institute to meet the needs of de novo sequencing a large number of microbial and eukaryote genomes, EST, and metagenome projects. We have been focusing efforts in three areas: (1) modifying the current process to allow the construction of 454 standard libraries on a 96-well format; (2) developing a robotic platform to perform the 454 library construction; and (3) designing molecular barcodes to allow pooling and sorting of many different samples. In the development of a high throughput process to scale up the number ofmore » libraries by adapting the process to a 96-well plate format, the key process change involves the replacement of gel electrophoresis for size selection with Solid Phase Reversible Immobilization (SPRI) beads. Although the standard deviation of the insert sizes increases, the overall quality sequence and distribution of the reads in the genome has not changed. The manual process of constructing 454 shotgun libraries on 96-well plates is a time-consuming, labor-intensive, and ergonomically hazardous process; we have been experimenting to program a BioMek robot to perform the library construction. This will not only enable library construction to be completed in a single day, but will also minimize any ergonomic risk. In addition, we have implemented a set of molecular barcodes (AKA Multiple Identifiers or MID) and a pooling process that allows us to sequence many targets simultaneously. Here we will present the testing of pooling a set of selected fosmids derived from the endomycorrhizal fungus Glomus intraradices. By combining the robotic library construction process and the use of molecular barcodes, it is now possible to sequence hundreds of fosmids that represent a minimal tiling path of this genome. Here we present the progress and the challenges of developing these scaled-up processes.« less

Construction and Analysis of Siberian Tiger Bacterial Artificial Chromosome Library with Approximately 6.5-Fold Genome Equivalent Coverage

PubMed Central

Liu, Changqing; Bai, Chunyu; Guo, Yu; Liu, Dan; Lu, Taofeng; Li, Xiangchen; Ma, Jianzhang; Ma, Yuehui; Guan, Weijun

2014-01-01

Bacterial artificial chromosome (BAC) libraries are extremely valuable for the genome-wide genetic dissection of complex organisms. The Siberian tiger, one of the most well-known wild primitive carnivores in China, is an endangered animal. In order to promote research on its genome, a high-redundancy BAC library of the Siberian tiger was constructed and characterized. The library is divided into two sub-libraries prepared from blood cells and two sub-libraries prepared from fibroblasts. This BAC library contains 153,600 individually archived clones; for PCR-based screening of the library, BACs were placed into 40 superpools of 10 × 384-deep well microplates. The average insert size of BAC clones was estimated to be 116.5 kb, representing approximately 6.46 genome equivalents of the haploid genome and affording a 98.86% statistical probability of obtaining at least one clone containing a unique DNA sequence. Screening the library with 19 microsatellite markers and a SRY sequence revealed that each of these markers were present in the library; the average number of positive clones per marker was 6.74 (range 2 to 12), consistent with 6.46 coverage of the tiger genome. Additionally, we identified 72 microsatellite markers that could potentially be used as genetic markers. This BAC library will serve as a valuable resource for physical mapping, comparative genomic study and large-scale genome sequencing in the tiger. PMID:24608928

Design and pitch scaling for affordable node transition and EUV insertion scenario

NASA Astrophysics Data System (ADS)

Kim, Ryoung-han; Ryckaert, Julien; Raghavan, Praveen; Sherazi, Yasser; Debacker, Peter; Trivkovic, Darko; Gillijns, Werner; Tan, Ling Ee; Drissi, Youssef; Blanco, Victor; Bekaert, Joost; Mao, Ming; Larivière, Stephane; McIntyre, Greg

2017-04-01

imec's DTCO and EUV achievement toward imec 7nm (iN7) technology node which is industry 5nm node equivalent is reported with a focus on cost and scaling. Patterning-aware design methodology supports both iArF multiple patterning and EUV under one compliant design rule. FinFET device with contacted poly pitch of 42nm and metal pitch of 32nm with 7.5-track, 6.5-track, and 6-track standard cell library are explored. Scaling boosters are used to provide additional scaling and die cost benefit while lessening pitch shrink burden, and it makes EUV insertion more affordable. EUV pattern fidelity is optimized through OPC, SMO, M3D, mask sizing and SRAF. Processed wafers were characterized and edge-placement-error (EPE) variability is validated for EUV insertion. Scale-ability and cost of ownership of EUV patterning in aligned with iN7 standard cell design, integration and patterning specification are discussed.

Construction of an 800-kb contig in the near-centromeric region of the rice blast resistance gene Pi-ta2 using a highly representative rice BAC library.

PubMed

Nakamura, S; Asakawa, S; Ohmido, N; Fukui, K; Shimizu, N; Kawasaki, S

1997-05-01

We constructed a rice Bacterial Artificial Chromosome (BAC) library from green leaf protoplasts of the cultivar Shimokita harboring the rice blast resistance gene Pi-ta. The average insert size of 155 kb and the library size of seven genome equivalents make it one of the most comprehensive BAC libraries available, and larger than many plant YAC libraries. The library clones were plated on seven high density membranes of microplate size, enabling efficient colony identification in colony hybridization experiments. Seven percent of clones carried chloroplast DNA. By probing with markers close to the blast resistance genes Pi-ta2(closely linked to Pi-ta) and Pi-b, respectively located in the centromeric region of chromosome 12 and near the telomeric end of chromosome 2, on average 2.2 +/- 1.3 and 8.0 +/- 2.6 BAC clones/marker were isolated. Differences in chromosomal structures may contribute to this wide variation in yield. A contig of about 800 kb, consisting of 19 clones, was constructed in the Pi-ta2 region. This region had a high frequency of repetitive sequences. To circumvent this difficulty, we devised a "two-step walking" method. The contig spanned a 300 kb region between markers located at 0 cM and 0.3 cM from Pi-ta. The ratio of physical to genetic distances (> 1,000 kb/cM) was more than three times larger than the average of rice (300 kb/cM). The low recombination rate and high frequency of repetitive sequences may also be related to the near centromeric character of this region. Fluorescent in situ hybridization (FISH) with a BAC clone from the Pi-b region yielded very clear signals on the long arm of chromosome 2, while a clone from the Pi-ta2 region showed various cross-hybridizing signals near the centromeric regions of all chromosomes.

Physical mapping of complex genomes

DOEpatents

Evans, G.A.

1993-06-15

A method for the simultaneous identification of overlapping cosmid clones among multiple cosmid clones and the use of the method for mapping complex genomes are provided. A library of cosmid clones that contains the DNA to be mapped is constructed and arranged in a manner such that individual clones can be identified and replicas of the arranged clones prepared. In preferred embodiments, the clones are arranged in a two dimensional matrix. In such embodiments, the cosmid clones in a row are pooled, mixed probes complementary to the ends of the DNA inserts in the pooled clones are synthesized, hybridized to a first replica of the library. Hybridizing clones, which include the pooled row, are identified. A second portion of clones is prepared by pooling cosmid clones that correspond to a column in the matrix. The second pool thereby includes one clone from the first portion pooled clones. This common clone is located on the replica at the intersection of the column and row. Mixed probes complementary to the ends of the DNA inserts in the second pooled portion of clones are prepared and hybridized to a second replica of the library. The hybridization pattern on the first and second replicas of the library are compared and cross-hybridizing clones, other than the clones in the pooled column and row, that hybridize to identical clones in the first and second replicas are identified. These clones necessarily include DNA inserts that overlap with the DNA insert in the common clone located at the intersection of the pooled row and pooled column. The DNA in the entire library may be mapped by pooling the clones in each of the rows and columns of the matrix, preparing mixed end-specific probes and hybridizing the probes from each row or column to a replica of the library. Since all clones in the library are located at the intersection of a column and a row, the overlapping clones for all clones in the library may be identified and a physical map constructed.

Toward functional genomics in bacteria: Analysis of gene expression in Escherichia coli from a bacterial artificial chromosome library of Bacillus cereus

PubMed Central

Rondon, Michelle R.; Raffel, Sandra J.; Goodman, Robert M.; Handelsman, Jo

1999-01-01

As the study of microbes moves into the era of functional genomics, there is an increasing need for molecular tools for analysis of a wide diversity of microorganisms. Currently, biological study of many prokaryotes of agricultural, medical, and fundamental scientific interest is limited by the lack of adequate genetic tools. We report the application of the bacterial artificial chromosome (BAC) vector to prokaryotic biology as a powerful approach to address this need. We constructed a BAC library in Escherichia coli from genomic DNA of the Gram-positive bacterium Bacillus cereus. This library provides 5.75-fold coverage of the B. cereus genome, with an average insert size of 98 kb. To determine the extent of heterologous expression of B. cereus genes in the library, we screened it for expression of several B. cereus activities in the E. coli host. Clones expressing 6 of 10 activities tested were identified in the library, namely, ampicillin resistance, zwittermicin A resistance, esculin hydrolysis, hemolysis, orange pigment production, and lecithinase activity. We analyzed selected BAC clones genetically to identify rapidly specific B. cereus loci. These results suggest that BAC libraries will provide a powerful approach for studying gene expression from diverse prokaryotes. PMID:10339608

Construction of cDNA library and preliminary analysis of expressed sequence tags from Siberian tiger

PubMed Central

Liu, Chang-Qing; Lu, Tao-Feng; Feng, Bao-Gang; Liu, Dan; Guan, Wei-Jun; Ma, Yue-Hui

2010-01-01

In this study we successfully constructed a full-length cDNA library from Siberian tiger, Panthera tigris altaica, the most well-known wild Animal. Total RNA was extracted from cultured Siberian tiger fibroblasts in vitro. The titers of primary and amplified libraries were 1.30×106 pfu/ml and 1.62×109 pfu/ml respectively. The proportion of recombinants from unamplified library was 90.5% and average length of exogenous inserts was 1.13 kb. A total of 282 individual ESTs with sizes ranging from 328 to 1,142bps were then analyzed the BLASTX score revealed that 53.9% of the sequences were classified as strong match, 38.6% as nominal and 7.4% as weak match. 28.0% of them were found to be related to enzyme/catalytic protein, 20.9% ESTs to metabolism, 13.1% ESTs to transport, 12.1% ESTs to signal transducer/cell communication, 9.9% ESTs to structure protein, 3.9% ESTs to immunity protein/defense metabolism, 3.2% ESTs to cell cycle, and 8.9 ESTs classified as novel genes. These results demonstrated that the reliability and representativeness of the cDNA library attained to the requirements of a standard cDNA library. This library provided a useful platform for the functional genomic research of Siberian tigers. PMID:20941376

Rapid construction of a Bacterial Artificial Chromosomal (BAC) expression vector using designer DNA fragments.

PubMed

Chen, Chao; Zhao, Xinqing; Jin, Yingyu; Zhao, Zongbao Kent; Suh, Joo-Won

2014-11-01

Bacterial artificial chromosomal (BAC) vectors are increasingly being used in cloning large DNA fragments containing complex biosynthetic pathways to facilitate heterologous production of microbial metabolites for drug development. To express inserted genes using Streptomyces species as the production hosts, an integration expression cassette is required to be inserted into the BAC vector, which includes genetic elements encoding a phage-specific attachment site, an integrase, an origin of transfer, a selection marker and a promoter. Due to the large sizes of DNA inserted into the BAC vectors, it is normally inefficient and time-consuming to assemble these fragments by routine PCR amplifications and restriction-ligations. Here we present a rapid method to insert fragments to construct BAC-based expression vectors. A DNA fragment of about 130 bp was designed, which contains upstream and downstream homologous sequences of both BAC vector and pIB139 plasmid carrying the whole integration expression cassette. In-Fusion cloning was performed using the designer DNA fragment to modify pIB139, followed by λ-RED-mediated recombination to obtain the BAC-based expression vector. We demonstrated the effectiveness of this method by rapid construction of a BAC-based expression vector with an insert of about 120 kb that contains the entire gene cluster for biosynthesis of immunosuppressant FK506. The empty BAC-based expression vector constructed in this study can be conveniently used for construction of BAC libraries using either microbial pure culture or environmental DNA, and the selected BAC clones can be directly used for heterologous expression. Alternatively, if a BAC library has already been constructed using a commercial BAC vector, the selected BAC vectors can be manipulated using the method described here to get the BAC-based expression vectors with desired gene clusters for heterologous expression. The rapid construction of a BAC-based expression vector facilitates heterologous expression of large gene clusters for drug discovery. Copyright © 2014 Elsevier Inc. All rights reserved.

Begin at the beginning: A BAC-end view of the passion fruit (Passiflora) genome.

PubMed

Santos, Anselmo Azevedo; Penha, Helen Alves; Bellec, Arnaud; Munhoz, Carla de Freitas; Pedrosa-Harand, Andrea; Bergès, Hélène; Vieira, Maria Lucia Carneiro

2014-09-26

The passion fruit (Passiflora edulis) is a tropical crop of economic importance both for juice production and consumption as fresh fruit. The juice is also used in concentrate blends that are consumed worldwide. However, very little is known about the genome of the species. Therefore, improving our understanding of passion fruit genomics is essential and to some degree a pre-requisite if its genetic resources are to be used more efficiently. In this study, we have constructed a large-insert BAC library and provided the first view on the structure and content of the passion fruit genome, using BAC-end sequence (BES) data as a major resource. The library consisted of 82,944 clones and its levels of organellar DNA were very low. The library represents six haploid genome equivalents, and the average insert size was 108 kb. To check its utility for gene isolation, successful macroarray screening experiments were carried out with probes complementary to eight Passiflora gene sequences available in public databases. BACs harbouring those genes were used in fluorescent in situ hybridizations and unique signals were detected for four BACs in three chromosomes (n=9). Then, we explored 10,000 BES and we identified reads likely to contain repetitive mobile elements (19.6% of all BES), simple sequence repeats and putative proteins, and to estimate the GC content (~42%) of the reads. Around 9.6% of all BES were found to have high levels of similarity to plant genes and ontological terms were assigned to more than half of the sequences analysed (940). The vast majority of the top-hits made by our sequences were to Populus trichocarpa (24.8% of the total occurrences), Theobroma cacao (21.6%), Ricinus communis (14.3%), Vitis vinifera (6.5%) and Prunus persica (3.8%). We generated the first large-insert library for a member of Passifloraceae. This BAC library provides a new resource for genetic and genomic studies, as well as it represents a valuable tool for future whole genome study. Remarkably, a number of BAC-end pair sequences could be mapped to intervals of the sequenced Arabidopsis thaliana, V. vinifera and P. trichocarpa chromosomes, and putative collinear microsyntenic regions were identified.

Construction of Signature-tagged Mutant Library in Mesorhizobium loti as a Powerful Tool for Functional Genomics

PubMed Central

Shimoda, Yoshikazu; Mitsui, Hisayuki; Kamimatsuse, Hiroko; Minamisawa, Kiwamu; Nishiyama, Eri; Ohtsubo, Yoshiyuki; Nagata, Yuji; Tsuda, Masataka; Shinpo, Sayaka; Watanabe, Akiko; Kohara, Mitsuyo; Yamada, Manabu; Nakamura, Yasukazu; Tabata, Satoshi; Sato, Shusei

2008-01-01

Rhizobia are nitrogen-fixing soil bacteria that establish endosymbiosis with some leguminous plants. The completion of several rhizobial genome sequences provides opportunities for genome-wide functional studies of the physiological roles of many rhizobial genes. In order to carry out genome-wide phenotypic screenings, we have constructed a large mutant library of the nitrogen-fixing symbiotic bacterium, Mesorhizobium loti, by transposon mutagenesis. Transposon insertion mutants were generated using the signature-tagged mutagenesis (STM) technique and a total of 29 330 independent mutants were obtained. Along with the collection of transposon mutants, we have determined the transposon insertion sites for 7892 clones, and confirmed insertions in 3680 non-redundant M. loti genes (50.5% of the total number of M. loti genes). Transposon insertions were randomly distributed throughout the M. loti genome without any bias toward G+C contents of insertion target sites and transposon plasmids used for the mutagenesis. We also show the utility of STM mutants by examining the specificity of signature tags and test screenings for growth- and nodulation-deficient mutants. This defined mutant library allows for genome-wide forward- and reverse-genetic functional studies of M. loti and will serve as an invaluable resource for researchers to further our understanding of rhizobial biology. PMID:18658183

Creation of BAC genomic resources for cocoa ( Theobroma cacao L.) for physical mapping of RGA containing BAC clones.

PubMed

Clément, D; Lanaud, C; Sabau, X; Fouet, O; Le Cunff, L; Ruiz, E; Risterucci, A M; Glaszmann, J C; Piffanelli, P

2004-05-01

We have constructed and validated the first cocoa ( Theobroma cacao L.) BAC library, with the aim of developing molecular resources to study the structure and evolution of the genome of this perennial crop. This library contains 36,864 clones with an average insert size of 120 kb, representing approximately ten haploid genome equivalents. It was constructed from the genotype Scavina-6 (Sca-6), a Forastero clone highly resistant to cocoa pathogens and a parent of existing mapping populations. Validation of the BAC library was carried out with a set of 13 genetically-anchored single copy and one duplicated markers. An average of nine BAC clones per probe was identified, giving an initial experimental estimation of the genome coverage represented in the library. Screening of the library with a set of resistance gene analogues (RGAs), previously mapped in cocoa and co-localizing with QTL for resistance to Phytophthora traits, confirmed at the physical level the tight clustering of RGAs in the cocoa genome and provided the first insights into the relationships between genetic and physical distances in the cocoa genome. This library represents an available BAC resource for structural genomic studies or map-based cloning of genes corresponding to important QTLs for agronomic traits such as resistance genes to major cocoa pathogens like Phytophthora spp ( palmivora and megakarya), Crinipellis perniciosa and Moniliophthora roreri.

Development and validation of novel AAV2 random libraries displaying peptides of diverse lengths and at diverse capsid positions.

PubMed

Naumer, Matthias; Ying, Ying; Michelfelder, Stefan; Reuter, Antje; Trepel, Martin; Müller, Oliver J; Kleinschmidt, Jürgen A

2012-05-01

Libraries based on the insertion of random peptide ligands into the capsid of adeno-associated virus type 2 (AAV2) have been widely used to improve the efficiency and selectivity of the AAV vector system. However, so far only libraries of 7-mer peptide ligands have been inserted at one well-characterized capsid position. Here, we expanded the combinatorial AAV2 display system to a panel of novel AAV libraries, displaying peptides of 5, 7, 12, 19, or 26 amino acids in length at capsid position 588 or displaying 7-mer peptides at position 453, the most prominently exposed region of the viral capsid. Library selections on two unrelated cell types-human coronary artery endothelial cells and rat cardiomyoblasts-revealed the isolation of cell type-characteristic peptides of different lengths mediating strongly improved target-cell transduction, except for the 26-mer peptide ligands. Characterization of vector selectivity by transduction of nontarget cells and comparative gene-transduction analysis using a panel of 44 human tumor cell lines revealed that insertion of different-length peptides allows targeting of distinct cellular receptors for cell entry with similar efficiency, but with different selectivity. The application of such novel AAV2 libraries broadens the spectrum of targetable receptors by capsid-modified AAV vectors and provides the opportunity to choose the best suited targeting ligand for a certain application from a number of different candidates.

A Comprehensive Analysis of In Vitro and In Vivo Genetic Fitness of Pseudomonas aeruginosa Using High-Throughput Sequencing of Transposon Libraries

PubMed Central

Aschard, Hugues; Cattoir, Vincent; Yoder-Himes, Deborah; Lory, Stephen; Pier, Gerald B.

2013-01-01

High-throughput sequencing of transposon (Tn) libraries created within entire genomes identifies and quantifies the contribution of individual genes and operons to the fitness of organisms in different environments. We used insertion-sequencing (INSeq) to analyze the contribution to fitness of all non-essential genes in the chromosome of Pseudomonas aeruginosa strain PA14 based on a library of ∼300,000 individual Tn insertions. In vitro growth in LB provided a baseline for comparison with the survival of the Tn insertion strains following 6 days of colonization of the murine gastrointestinal tract as well as a comparison with Tn-inserts subsequently able to systemically disseminate to the spleen following induction of neutropenia. Sequencing was performed following DNA extraction from the recovered bacteria, digestion with the MmeI restriction enzyme that hydrolyzes DNA 16 bp away from the end of the Tn insert, and fractionation into oligonucleotides of 1,200–1,500 bp that were prepared for high-throughput sequencing. Changes in frequency of Tn inserts into the P. aeruginosa genome were used to quantify in vivo fitness resulting from loss of a gene. 636 genes had <10 sequencing reads in LB, thus defined as unable to grow in this medium. During in vivo infection there were major losses of strains with Tn inserts in almost all known virulence factors, as well as respiration, energy utilization, ion pumps, nutritional genes and prophages. Many new candidates for virulence factors were also identified. There were consistent changes in the recovery of Tn inserts in genes within most operons and Tn insertions into some genes enhanced in vivo fitness. Strikingly, 90% of the non-essential genes were required for in vivo survival following systemic dissemination during neutropenia. These experiments resulted in the identification of the P. aeruginosa strain PA14 genes necessary for optimal survival in the mucosal and systemic environments of a mammalian host. PMID:24039572

Anatomy of the Medial Patello-Femoral Ligament: a systematic review of the last 20 years literature.

PubMed

Placella, G; Tei, M; Sebastiani, E; Speziali, A; Antinolfi, P; Delcogliano, M; Georgoulis, A; Cerulli, G

2015-08-01

Although many studies have investigated the anatomy of the Medial Patello-Femoral Ligament (MPFL), some studies have even questioned its existence. In the last 20 years, there is a renewed interest on the role of the MPFL in patello-femoral instability. As a result, several studies have been published that describe the anatomy, function and possible surgical reconstruction of the MPFL. Despite the large amount of literature produced, there is still a lack of consensus on what is its real anatomy as there are currently no systematic reviews on this topic. Thus, the aim of this review is to systematically report the results in literature regarding in anatomical papers, the existence, size, insertion sites and relationships of this ligament with the other medial structures of the knee. We have systematically analyzed anatomical studies currently available in literature between 1980 and December 2012. The search was carried out on Medline, Embase, Cochrane Library and Google Scholar. We checked reference lists of articles, reviews and textbooks identified by the search strategy for other possible relevant studies. The outcomes examined are the presence of the ligament, its size (length, width, thickness), and its patellar and femoral insertions. A total of 312 cadaveric knees were included in the 17 studies; the MPFL was identified in 99% of cases (309). The consensus is that the MPFL is almost always present in the dissected knees. The size and insertions of the ligament demonstrate great variation between cadavers. Systematic review of anatomical study, Level 1.

Physical mapping of complex genomes

DOEpatents

Evans, Glen A.

1993-01-01

Method for simultaneous identification of overlapping cosmid clones among multiple cosmid clones and the use of the method for mapping complex genomes are provided. A library of cosmid clones that contains the DNA to be mapped is constructed and arranged in a manner such that individual clones can be identified and replicas of the arranged clones prepared. In preferred embodiments, the clones are arranged in a two dimensional matrix. In such embodiments, the cosmid clones in a row are pooled, mixed probes complementary to the ends of the DNA inserts int he pooled clones are synthesized, hybridized to a first replica of the library. Hybridizing clones, which include the pooled row, are identified. A second portion of clones is prepared by pooling cosmid clones that correspond to a column in the matrix. The second pool thereby includes one clone from the first portion pooled clones. This common clone is located on the replica at the intersection of the column and row. Mixed probes complementary to the ends of the DNA inserts in the second pooled portion of clones are prepared and hybridized to a second replica of the library. The hybridization pattern on the first and second replicas of the library are compared and cross-hybridizing clones, other than the clones in the pooled column and row, that hybridize to identical clones in the first and second replicas are identified. These clones necessarily include DNA inserts that overlap with the DNA insert int he common clone located at the intersection of the pooled row and pooled column. The DNA in the entire library may be mapped by pooling the clones in each of the rows and columns of the matrix, preparing mixed end-specific probes and hybridizing the probes from each row or column to a replica of the library. Since all clones in the library are located at the intersection of a column and a row, the overlapping clones for all clones in the library may be identified and a physical map constructed. In other preferred embodiments, the cosmid clones are arranged in a three dimensional matrix, pooled and compared in threes according to intersecting planes of the three dimensional matrix. Arrangements corresponding to geometries of higher dimensions may also be prepared and used to simultaneously identify overlapping clones in highly complex libraries with relatively few hybridization reactions.

Gene-targeted Random Mutagenesis to Select Heterochromatin-destabilizing Proteasome Mutants in Fission Yeast.

PubMed

Seo, Hogyu David; Lee, Daeyoup

2018-05-15

Random mutagenesis of a target gene is commonly used to identify mutations that yield the desired phenotype. Of the methods that may be used to achieve random mutagenesis, error-prone PCR is a convenient and efficient strategy for generating a diverse pool of mutants (i.e., a mutant library). Error-prone PCR is the method of choice when a researcher seeks to mutate a pre-defined region, such as the coding region of a gene while leaving other genomic regions unaffected. After the mutant library is amplified by error-prone PCR, it must be cloned into a suitable plasmid. The size of the library generated by error-prone PCR is constrained by the efficiency of the cloning step. However, in the fission yeast, Schizosaccharomyces pombe, the cloning step can be replaced by the use of a highly efficient one-step fusion PCR to generate constructs for transformation. Mutants of desired phenotypes may then be selected using appropriate reporters. Here, we describe this strategy in detail, taking as an example, a reporter inserted at centromeric heterochromatin.

Alignment of the Genomes of Brachypodium distachyon and Temperate Cereals and Grasses Using Bacterial Artificial Chromosome Landing With Fluorescence in Situ Hybridization

PubMed Central

Hasterok, Robert; Marasek, Agnieszka; Donnison, Iain S.; Armstead, Ian; Thomas, Ann; King, Ian P.; Wolny, Elzbieta; Idziak, Dominika; Draper, John; Jenkins, Glyn

2006-01-01

As part of an initiative to develop Brachypodium distachyon as a genomic “bridge” species between rice and the temperate cereals and grasses, a BAC library has been constructed for the two diploid (2n = 2x = 10) genotypes, ABR1 and ABR5. The library consists of 9100 clones, with an approximate average insert size of 88 kb, representing 2.22 genome equivalents. To validate the usefulness of this species for comparative genomics and gene discovery in its larger genome relatives, the library was screened by PCR using primers designed on previously mapped rice and Poaceae sequences. Screening indicated a degree of synteny between these species and B. distachyon, which was confirmed by fluorescent in situ hybridization of the marker-selected BACs (BAC landing) to the 10 chromosome arms of the karyotype, with most of the BACs hybridizing as single loci on known chromosomes. Contiguous BACs colocalized on individual chromosomes, thereby confirming the conservation of genome synteny and proving that B. distachyon has utility as a temperate grass model species alternative to rice. PMID:16489232

Alignment of the genomes of Brachypodium distachyon and temperate cereals and grasses using bacterial artificial chromosome landing with fluorescence in situ hybridization.

PubMed

Hasterok, Robert; Marasek, Agnieszka; Donnison, Iain S; Armstead, Ian; Thomas, Ann; King, Ian P; Wolny, Elzbieta; Idziak, Dominika; Draper, John; Jenkins, Glyn

2006-05-01

As part of an initiative to develop Brachypodium distachyon as a genomic "bridge" species between rice and the temperate cereals and grasses, a BAC library has been constructed for the two diploid (2n = 2x = 10) genotypes, ABR1 and ABR5. The library consists of 9100 clones, with an approximate average insert size of 88 kb, representing 2.22 genome equivalents. To validate the usefulness of this species for comparative genomics and gene discovery in its larger genome relatives, the library was screened by PCR using primers designed on previously mapped rice and Poaceae sequences. Screening indicated a degree of synteny between these species and B. distachyon, which was confirmed by fluorescent in situ hybridization of the marker-selected BACs (BAC landing) to the 10 chromosome arms of the karyotype, with most of the BACs hybridizing as single loci on known chromosomes. Contiguous BACs colocalized on individual chromosomes, thereby confirming the conservation of genome synteny and proving that B. distachyon has utility as a temperate grass model species alternative to rice.

Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community

DOE PAGES

Bowers, Robert M.; Clum, Alicia; Tice, Hope; ...

2015-10-24

Background: The rapid development of sequencing technologies has provided access to environments that were either once thought inhospitable to life altogether or that contain too few cells to be analyzed using genomics approaches. While 16S rRNA gene microbial community sequencing has revolutionized our understanding of community composi tion and diversity over time and space, it only provides a crude estimate of microbial functional and metabolic potential. Alternatively, shotgun metagenomics allows comprehensive sampling of all genetic material in an environment, without any underlying primer biases. Until recently, one of the major bottlenecks of shotgun metagenomics has been the requirement for largemore » initial DNA template quantities during library preparation. Results: Here, we investigate the effects of varying template concentrations across three low biomass library preparation protocols on their ability to accurately reconstruct a mock microbial community of known composition. We analyze the effects of input DNA quantity and library preparation method on library insert size, GC content, community composition, assembly quality and metagenomic binning. We found that library preparation method and the amount of starting material had significant impacts on the mock community metagenomes. In particular, GC content shifted towards more GC rich sequences at the lower input quantities regardless of library prep method, the number of low quality reads that could not be mapped to the reference genomes increased with decreasing input quantities, and the different library preparation methods had an impact on overall metagenomic community composition. Conclusions: This benchmark study provides recommendations for library creation of representative and minimally biased metagenome shotgun sequencing, enabling insights into functional attributes of low biomass ecosystem microbial communities.« less

Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community

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

Bowers, Robert M.; Clum, Alicia; Tice, Hope

Background: The rapid development of sequencing technologies has provided access to environments that were either once thought inhospitable to life altogether or that contain too few cells to be analyzed using genomics approaches. While 16S rRNA gene microbial community sequencing has revolutionized our understanding of community composi tion and diversity over time and space, it only provides a crude estimate of microbial functional and metabolic potential. Alternatively, shotgun metagenomics allows comprehensive sampling of all genetic material in an environment, without any underlying primer biases. Until recently, one of the major bottlenecks of shotgun metagenomics has been the requirement for largemore » initial DNA template quantities during library preparation. Results: Here, we investigate the effects of varying template concentrations across three low biomass library preparation protocols on their ability to accurately reconstruct a mock microbial community of known composition. We analyze the effects of input DNA quantity and library preparation method on library insert size, GC content, community composition, assembly quality and metagenomic binning. We found that library preparation method and the amount of starting material had significant impacts on the mock community metagenomes. In particular, GC content shifted towards more GC rich sequences at the lower input quantities regardless of library prep method, the number of low quality reads that could not be mapped to the reference genomes increased with decreasing input quantities, and the different library preparation methods had an impact on overall metagenomic community composition. Conclusions: This benchmark study provides recommendations for library creation of representative and minimally biased metagenome shotgun sequencing, enabling insights into functional attributes of low biomass ecosystem microbial communities.« less

Development of novel metabolite-responsive transcription factors via transposon-mediated protein fusion.

PubMed

Younger, Andrew K D; Su, Peter Y; Shepard, Andrea J; Udani, Shreya V; Cybulski, Thaddeus R; Tyo, Keith E J; Leonard, Joshua N

2018-02-01

Naturally evolved metabolite-responsive biosensors enable applications in metabolic engineering, ranging from screening large genetic libraries to dynamically regulating biosynthetic pathways. However, there are many metabolites for which a natural biosensor does not exist. To address this need, we developed a general method for converting metabolite-binding proteins into metabolite-responsive transcription factors-Biosensor Engineering by Random Domain Insertion (BERDI). This approach takes advantage of an in vitro transposon insertion reaction to generate all possible insertions of a DNA-binding domain into a metabolite-binding protein, followed by fluorescence activated cell sorting to isolate functional biosensors. To develop and evaluate the BERDI method, we generated a library of candidate biosensors in which a zinc finger DNA-binding domain was inserted into maltose binding protein, which served as a model well-studied metabolite-binding protein. Library diversity was characterized by several methods, a selection scheme was deployed, and ultimately several distinct and functional maltose-responsive transcriptional biosensors were identified. We hypothesize that the BERDI method comprises a generalizable strategy that may ultimately be applied to convert a wide range of metabolite-binding proteins into novel biosensors for applications in metabolic engineering and synthetic biology. © The Author(s) 2018. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Construction of cDNA expression library of watermelon for isolation of ClWRKY1 transcription factors gene involved in resistance to Fusarium wilt.

PubMed

Yang, Bing-Yan; Huo, Xiu-Ai; Li, Peng-Fei; Wang, Cui-Xia; Duan, Hui-Jun

2014-08-01

Full-length cDNAs are very important for genome annotation and functional analysis of genes. The number of full-length cDNAs from watermelon remains limited. Here we report first the construction of a full-length enriched cDNA library from Fusarium wilt stressed watermelon (Citrullus lanatus Thunb.) cultivar PI296341 root tissues using the SMART method. The titer of primary cDNA library and amplified library was 2.21 x 10(6) and 2.0 x 10(10) pfu/ml, respectively and the rate of recombinant was above 85%. The size of insert fragment ranged from 0.3 to 2.0 kb. In this study, we first cloned a gene named ClWRKY1, which was 1981 bp long and encoded a protein consisting of 394 amino acids. It contained two characteristic WRKY domains and two zinc finger motifs. Quantitative real-time PCR showed that ClWRKY1 expression levels reached maximum level at 12 h after inoculation with Fusarium oxysporum f. sp. niveum. The full-length cDNA library of watermelon root tissues is not only essential for the cloning of genes which are known, but also an initial key for the screening and cloning of new genes that might be involved in resistance to Fusarium wilt.

Construction of C35 gene bait recombinants and T47D cell cDNA library.

PubMed

Yin, Kun; Xu, Chao; Zhao, Gui-Hua; Liu, Ye; Xiao, Ting; Zhu, Song; Yan, Ge

2017-11-20

C35 is a novel tumor biomarker associated with metastasis progression. To investigate the interaction factors of C35 in its high expressed breast cancer cell lines, we constructed bait recombinant plasmids of C35 gene and T47D cell cDNA library for yeast two-hybrid screening. Full length C35 sequences were subcloned using RT-PCR from cDNA template extracted from T47D cells. Based on functional domain analysis, the full-length C35 1-348bp was also truncated into two fragments C351-153bp and C35154-348bp to avoid auto-activation. The three kinds of C35 genes were successfully amplified and inserted into pGBKT7 to construct bait recombinant plasmids pGBKT7-C351-348bp, pGBKT7-C351-153bp and pGBKT7-C35154-348bp, then transformed into Y187 yeast cells by the lithium acetate method. Auto-activation and toxicity of C35 baits were detected using nutritional deficient medium and X-α-Gal assays. The T47D cell ds cDNA was generated by SMART TM technology and the library was constructed using in vivo recombination-mediated cloning in the AH109 yeast strain using a pGADT7-Rec plasmid. The transformed Y187/pGBKT7-C351-348bp line was intensively inhibited while the truncated Y187/pGBKT7-C35 lines had no auto-activation and toxicity in yeast cells. The titer of established cDNA library was 2 × 10 7 pfu/mL with high transformation efficiency of 1.4 × 10 6 , and the insert size of ds cDNA was distributed homogeneously between 0.5-2.0 kb. Our research generated a T47D cell cDNA library with high titer, and the constructed two C35 "baits" contained a respective functional immunoreceptor tyrosine based activation motif (ITAM) and the conserved last four amino acids Cys-Ile-Leu-Val (CILV) motif, and therefore laid a foundation for screening the C35 interaction factors in a BC cell line.

A Semiautomated Journal Check-In and Binding System; or Variations on a Common Theme

PubMed Central

Livingston, Frances G.

1967-01-01

The journal check-in project described here, though based on a computerized system, uses only unit-record equipment and is designed for the medium-sized library. The frequency codes used are based on the date printed on the journal rather than on the expected date of receipt, which allows for more stability in the coding scheme. The journal's volume number and issue number, which in other systems are usually predetermined by a computer, are inserted at the time of check-in. Routine claiming of overdue issues and a systematic binding schedule have also been developed as by-products. PMID:6041836

Microdissection and molecular manipulation of single chromosomes in woody fruit trees with small chromosomes using pomelo (Citrus grandis) as a model. I. Construction of single chromosomal DNA libraries.

PubMed

Huang, D; Wu, W; Zhou, Y; Hu, Z; Lu, L

2004-05-01

Construction of single chromosomal DNA libraries by means of chromosome microdissection and microcloning will be useful for genomic research, especially for those species that have not been extensively studied genetically. Application of the technology of microdissection and microcloning to woody fruit plants has not been reported hitherto, largely due to the generally small sizes of metaphase chromosomes and the difficulty of chromosome preparation. The present study was performed to establish a method for single chromosome microdissection and microcloning in woody fruit species using pomelo as a model. The standard karyotype of a pomelo cultivar ( Citrus grandis cv. Guanxi) was established based on 20 prometaphase photomicrographs. According to the standard karyotype, chromosome 1 was identified and isolated with fine glass microneedles controlled by a micromanipulator. DNA fragments ranging from 0.3 kb to 2 kb were acquired from the isolated single chromosome 1 via two rounds of PCR mediated by Sau3A linker adaptors and then cloned into T-easy vectors to generate a DNA library of chromosome 1. Approximately 30,000 recombinant clones were obtained. Evaluation based on 108 randomly selected clones showed that the sizes of the cloned inserts varied from 0.5 kb to 1.5 kb with an average of 860 bp. Our research suggests that microdissection and microcloning of single small chromosomes in woody plants is feasible.

Construction of BAC Libraries from Flow-Sorted Chromosomes.

PubMed

Šafář, Jan; Šimková, Hana; Doležel, Jaroslav

2016-01-01

Cloned DNA libraries in bacterial artificial chromosome (BAC) are the most widely used form of large-insert DNA libraries. BAC libraries are typically represented by ordered clones derived from genomic DNA of a particular organism. In the case of large eukaryotic genomes, whole-genome libraries consist of a hundred thousand to a million clones, which make their handling and screening a daunting task. The labor and cost of working with whole-genome libraries can be greatly reduced by constructing a library derived from a smaller part of the genome. Here we describe construction of BAC libraries from mitotic chromosomes purified by flow cytometric sorting. Chromosome-specific BAC libraries facilitate positional gene cloning, physical mapping, and sequencing in complex plant genomes.

Discovering novel enzymes by functional screening of plurigenomic libraries from alga-associated Flavobacteriia and Gammaproteobacteria.

PubMed

Martin, Marjolaine; Vandermies, Marie; Joyeux, Coline; Martin, Renée; Barbeyron, Tristan; Michel, Gurvan; Vandenbol, Micheline

2016-01-01

Alga-associated microorganisms, in the context of their numerous interactions with the host and the complexity of the marine environment, are known to produce diverse hydrolytic enzymes with original biochemistry. We recently isolated several macroalgal-polysaccharide-degrading bacteria from the surface of the brown alga Ascophyllum nodosum. These active isolates belong to two classes: the Flavobacteriia and the Gammaproteobacteria. In the present study, we constructed two "plurigenomic" (with multiple bacterial genomes) libraries with the 5 most interesting isolates (regarding their phylogeny and their enzymatic activities) of each class (Fv and Gm libraries). Both libraries were screened for diverse hydrolytic activities. Five activities, out of the 48 previously identified in the natural polysaccharolytic isolates, were recovered by functional screening: a xylanase (GmXyl7), a beta-glucosidase (GmBg1), an esterase (GmEst7) and two iota-carrageenases (Fvi2.5 and Gmi1.3). We discuss here the potential role of the used host-cell, the average DNA insert-sizes and the used restriction enzymes on the divergent screening yields obtained for both libraries and get deeper inside the "great screen anomaly". Interestingly, the discovered esterase probably stands for a novel family of homoserine o-acetyltransferase-like-esterases, while the two iota-carrageenases represent new members of the poorly known GH82 family (containing only 19 proteins since its description in 2000). These original results demonstrate the efficiency of our uncommon "plurigenomic" library approach and the underexplored potential of alga-associated cultivable microbiota for the identification of novel and algal-specific enzymes. Copyright © 2016 Elsevier GmbH. All rights reserved.

Comparative genomic data of the Avian Phylogenomics Project.

PubMed

Zhang, Guojie; Li, Bo; Li, Cai; Gilbert, M Thomas P; Jarvis, Erich D; Wang, Jun

2014-01-01

The evolutionary relationships of modern birds are among the most challenging to understand in systematic biology and have been debated for centuries. To address this challenge, we assembled or collected the genomes of 48 avian species spanning most orders of birds, including all Neognathae and two of the five Palaeognathae orders, and used the genomes to construct a genome-scale avian phylogenetic tree and perform comparative genomics analyses (Jarvis et al. in press; Zhang et al. in press). Here we release assemblies and datasets associated with the comparative genome analyses, which include 38 newly sequenced avian genomes plus previously released or simultaneously released genomes of Chicken, Zebra finch, Turkey, Pigeon, Peregrine falcon, Duck, Budgerigar, Adelie penguin, Emperor penguin and the Medium Ground Finch. We hope that this resource will serve future efforts in phylogenomics and comparative genomics. The 38 bird genomes were sequenced using the Illumina HiSeq 2000 platform and assembled using a whole genome shotgun strategy. The 48 genomes were categorized into two groups according to the N50 scaffold size of the assemblies: a high depth group comprising 23 species sequenced at high coverage (>50X) with multiple insert size libraries resulting in N50 scaffold sizes greater than 1 Mb (except the White-throated Tinamou and Bald Eagle); and a low depth group comprising 25 species sequenced at a low coverage (~30X) with two insert size libraries resulting in an average N50 scaffold size of about 50 kb. Repetitive elements comprised 4%-22% of the bird genomes. The assembled scaffolds allowed the homology-based annotation of 13,000 ~ 17000 protein coding genes in each avian genome relative to chicken, zebra finch and human, as well as comparative and sequence conservation analyses. Here we release full genome assemblies of 38 newly sequenced avian species, link genome assembly downloads for the 7 of the remaining 10 species, and provide a guideline of genomic data that has been generated and used in our Avian Phylogenomics Project. To the best of our knowledge, the Avian Phylogenomics Project is the biggest vertebrate comparative genomics project to date. The genomic data presented here is expected to accelerate further analyses in many fields, including phylogenetics, comparative genomics, evolution, neurobiology, development biology, and other related areas.

Construction of naïve camelids VHH repertoire in phage display-based library.

PubMed

Sabir, Jamal S M; Atef, Ahmed; El-Domyati, Fotouh M; Edris, Sherif; Hajrah, Nahid; Alzohairy, Ahmed M; Bahieldin, Ahmed

2014-04-01

Camelids have unique antibodies, namely HCAbs (VHH) or commercially named Nanobodies(®) (Nb) that are composed only of a heavy-chain homodimer. As libraries based on immunized camelids are time-consuming, costly and likely redundant for certain antigens, we describe the construction of a naïve camelid VHHs library from blood serum of non-immunized camelids with affinity in the subnanomolar range and suitable for standard immune applications. This approach is rapid and recovers VHH repertoire with the advantages of being more diverse, non-specific and devoid of subpopulations of specific antibodies, which allows the identification of binders for any potential antigen (or pathogen). RNAs from a number of camelids from Saudi Arabia were isolated and cDNAs of the diverse vhh gene were amplified; the resulting amplicons were cloned in the phage display pSEX81 vector. The size of the library was found to be within the required range (10(7)) suitable for subsequent applications in disease diagnosis and treatment. Two hundred clones were randomly selected and the inserted gene library was either estimated for redundancy or sequenced and aligned to the reference camelid vhh gene (acc. No. ADE99145). Results indicated complete non-specificity of this small library in which no single event of redundancy was detected. These results indicate the efficacy of following this approach in order to yield a large and diverse enough gene library to secure the presence of the required version encoding the required antibodies for any target antigen. This work is a first step towards the construction of phage display-based biosensors useful in disease (e.g., TB or tuberculosis) diagnosis and treatment. Copyright © 2014 Académie des sciences. Published by Elsevier SAS. All rights reserved.

Engineering Complex Microbial Phenotypes with Continuous Genetic Integration and Plasmid Based Multi-gene Library

DTIC Science & Technology

2013-10-09

have desirable traits. We aim to enlarge the E. coli genome using Lactobacillusplantarum genes to build cells tolerant to EtOH and BT. L. plantarum is...chemicals III. Approach Objective 1 & la: Integrated heterologous (L. plantarum ) DNA into the E. coli chromosome and selected for insertions that...developed in combination with genes identified from screening L. plantarum libraries. Additionally, we have screened heterologous libraries for

[Construction of human phage antibody library and screening for human monoclonal antibodies of amylin].

PubMed

Gong, Qian; Li, Chang-ying; Chang, Ji-wu; Zhu, Tie-hong

2012-06-01

To screen monoclonal antibodies to amylin from a constructed human phage antibody library and identify their antigenic specificity and combining activities. The heavy chain Fd fragment and light chain of human immunoglobulin genes were amplified from peripheral blood lymphocytes of healthy donors using RT-PCR, and then inserted into phagemid pComb3XSS to generate a human phage antibody library. The insertion of light chain or heavy chain Fd genes were identified by PCR after the digestion of Sac I, Xba I, Xho Iand Spe I. One of positive clones was analyzed by DNA sequencing. The specific anti-amylin clones were screened from antibody library against human amylin antigens and then the positive clones were determined by Phage-ELISA analysis. A Fab phage antibody library with 0.8×10(8); members was constructed with the efficacy of about 70%. DNA sequence analysis indicated V(H); gene belonged to V(H);3 gene family and V(λ); gene belonged to the V(λ); gene family. Using human amylin as panning antigen, specific anti-amylin Fab antibodies were enriched by screening the library for three times. Phage-ELISA assay showed the positive clones had very good specificity to amylin antigen. The successful construction of a phage antibody library and the identification of anti-amylin Fab antibodies provide a basis for further study and preparation of human anti-amylin antibodies.

Comprehensive discovery of noncoding RNAs in acute myeloid leukemia cell transcriptomes.

PubMed

Zhang, Jin; Griffith, Malachi; Miller, Christopher A; Griffith, Obi L; Spencer, David H; Walker, Jason R; Magrini, Vincent; McGrath, Sean D; Ly, Amy; Helton, Nichole M; Trissal, Maria; Link, Daniel C; Dang, Ha X; Larson, David E; Kulkarni, Shashikant; Cordes, Matthew G; Fronick, Catrina C; Fulton, Robert S; Klco, Jeffery M; Mardis, Elaine R; Ley, Timothy J; Wilson, Richard K; Maher, Christopher A

2017-11-01

To detect diverse and novel RNA species comprehensively, we compared deep small RNA and RNA sequencing (RNA-seq) methods applied to a primary acute myeloid leukemia (AML) sample. We were able to discover previously unannotated small RNAs using deep sequencing of a library method using broader insert size selection. We analyzed the long noncoding RNA (lncRNA) landscape in AML by comparing deep sequencing from multiple RNA-seq library construction methods for the sample that we studied and then integrating RNA-seq data from 179 AML cases. This identified lncRNAs that are completely novel, differentially expressed, and associated with specific AML subtypes. Our study revealed the complexity of the noncoding RNA transcriptome through a combined strategy of strand-specific small RNA and total RNA-seq. This dataset will serve as an invaluable resource for future RNA-based analyses. Copyright © 2017 ISEH – Society for Hematology and Stem Cells. Published by Elsevier Inc. All rights reserved.

The carnegie protein trap library: a versatile tool for Drosophila developmental studies.

PubMed

Buszczak, Michael; Paterno, Shelley; Lighthouse, Daniel; Bachman, Julia; Planck, Jamie; Owen, Stephenie; Skora, Andrew D; Nystul, Todd G; Ohlstein, Benjamin; Allen, Anna; Wilhelm, James E; Murphy, Terence D; Levis, Robert W; Matunis, Erika; Srivali, Nahathai; Hoskins, Roger A; Spradling, Allan C

2007-03-01

Metazoan physiology depends on intricate patterns of gene expression that remain poorly known. Using transposon mutagenesis in Drosophila, we constructed a library of 7404 protein trap and enhancer trap lines, the Carnegie collection, to facilitate gene expression mapping at single-cell resolution. By sequencing the genomic insertion sites, determining splicing patterns downstream of the enhanced green fluorescent protein (EGFP) exon, and analyzing expression patterns in the ovary and salivary gland, we found that 600-900 different genes are trapped in our collection. A core set of 244 lines trapped different identifiable protein isoforms, while insertions likely to act as GFP-enhancer traps were found in 256 additional genes. At least 8 novel genes were also identified. Our results demonstrate that the Carnegie collection will be useful as a discovery tool in diverse areas of cell and developmental biology and suggest new strategies for greatly increasing the coverage of the Drosophila proteome with protein trap insertions.

76 FR 60013 - Combined Notice of Filings #1

Federal Register 2010, 2011, 2012, 2013, 2014

2011-09-28

... per 35.17(b): Amendment--docket number inserted 09192011 to be effective 10/11/2011. Filed Date: 09/19... Northeast LLC submits tariff filing per 35.17(b): Amendment--docket number inserted 09192011 to be effective... Commission's eLibrary system by clicking on the links or querying the docket number. Any person desiring to...

Various mutations compensate for a deleterious lacZα insert in the replication enhancer of M13 bacteriophage

PubMed Central

Zygiel, Emily M.; Noren, Karen A.; Adamkiewicz, Marta A.; Aprile, Richard J.; Bowditch, Heather K.; Carroll, Christine L.; Cerezo, Maria Abigail S.; Dagher, Adelle M.; Hebert, Courtney R.; Hebert, Lauren E.; Mahame, Gloria M.; Milne, Stephanie C.; Silvestri, Kelly M.; Sutherland, Sara E.; Sylvia, Alexandria M.; Taveira, Caitlyn N.; VanValkenburgh, David J.; Noren, Christopher J.

2017-01-01

M13 and other members of the Ff class of filamentous bacteriophages have been extensively employed in myriad applications. The Ph.D. series of phage-displayed peptide libraries were constructed from the M13-based vector M13KE. As a direct descendent of M13mp19, M13KE contains the lacZα insert in the intergenic region between genes IV and II, where it interrupts the replication enhancer of the (+) strand origin. Phage carrying this 816-nucleotide insert are viable, but propagate in E. coli at a reduced rate compared to wild-type M13 phage, presumably due to a replication defect caused by the insert. We have previously reported thirteen compensatory mutations in the 5’-untranslated region of gene II, which encodes the replication initiator protein gIIp. Here we report several additional mutations in M13KE that restore a wild-type propagation rate. Several clones from constrained-loop variable peptide libraries were found to have ejected the majority of lacZα gene in order to reconstruct the replication enhancer, albeit with a small scar. In addition, new point mutations in the gene II 5’-untranslated region or the gene IV coding sequence have been spontaneously observed or synthetically engineered. Through phage propagation assays, we demonstrate that all these genetic modifications compensate for the replication defect in M13KE and restore the wild-type propagation rate. We discuss the mechanisms by which the insertion and ejection of the lacZα gene, as well as the mutations in the regulatory region of gene II, influence the efficiency of replication initiation at the (+) strand origin. We also examine the presence and relevance of fast-propagating mutants in phage-displayed peptide libraries. PMID:28445507

Various mutations compensate for a deleterious lacZα insert in the replication enhancer of M13 bacteriophage.

PubMed

Zygiel, Emily M; Noren, Karen A; Adamkiewicz, Marta A; Aprile, Richard J; Bowditch, Heather K; Carroll, Christine L; Cerezo, Maria Abigail S; Dagher, Adelle M; Hebert, Courtney R; Hebert, Lauren E; Mahame, Gloria M; Milne, Stephanie C; Silvestri, Kelly M; Sutherland, Sara E; Sylvia, Alexandria M; Taveira, Caitlyn N; VanValkenburgh, David J; Noren, Christopher J; Hall, Marilena Fitzsimons

2017-01-01

M13 and other members of the Ff class of filamentous bacteriophages have been extensively employed in myriad applications. The Ph.D. series of phage-displayed peptide libraries were constructed from the M13-based vector M13KE. As a direct descendent of M13mp19, M13KE contains the lacZα insert in the intergenic region between genes IV and II, where it interrupts the replication enhancer of the (+) strand origin. Phage carrying this 816-nucleotide insert are viable, but propagate in E. coli at a reduced rate compared to wild-type M13 phage, presumably due to a replication defect caused by the insert. We have previously reported thirteen compensatory mutations in the 5'-untranslated region of gene II, which encodes the replication initiator protein gIIp. Here we report several additional mutations in M13KE that restore a wild-type propagation rate. Several clones from constrained-loop variable peptide libraries were found to have ejected the majority of lacZα gene in order to reconstruct the replication enhancer, albeit with a small scar. In addition, new point mutations in the gene II 5'-untranslated region or the gene IV coding sequence have been spontaneously observed or synthetically engineered. Through phage propagation assays, we demonstrate that all these genetic modifications compensate for the replication defect in M13KE and restore the wild-type propagation rate. We discuss the mechanisms by which the insertion and ejection of the lacZα gene, as well as the mutations in the regulatory region of gene II, influence the efficiency of replication initiation at the (+) strand origin. We also examine the presence and relevance of fast-propagating mutants in phage-displayed peptide libraries.

Versatile Cosmid Vectors for the Isolation, Expression, and Rescue of Gene Sequences: Studies with the Human α -globin Gene Cluster

NASA Astrophysics Data System (ADS)

Lau, Yun-Fai; Kan, Yuet Wai

1983-09-01

We have developed a series of cosmids that can be used as vectors for genomic recombinant DNA library preparations, as expression vectors in mammalian cells for both transient and stable transformations, and as shuttle vectors between bacteria and mammalian cells. These cosmids were constructed by inserting one of the SV2-derived selectable gene markers-SV2-gpt, SV2-DHFR, and SV2-neo-in cosmid pJB8. High efficiency of genomic cloning was obtained with these cosmids and the size of the inserts was 30-42 kilobases. We isolated recombinant cosmids containing the human α -globin gene cluster from these genomic libraries. The simian virus 40 DNA in these selectable gene markers provides the origin of replication and enhancer sequences necessary for replication in permissive cells such as COS 7 cells and thereby allows transient expression of α -globin genes in these cells. These cosmids and their recombinants could also be stably transformed into mammalian cells by using the respective selection systems. Both of the adult α -globin genes were more actively expressed than the embryonic zeta -globin genes in these transformed cell lines. Because of the presence of the cohesive ends of the Charon 4A phage in the cosmids, the transforming DNA sequences could readily be rescued from these stably transformed cells into bacteria by in vitro packaging of total cellular DNA. Thus, these cosmid vectors are potentially useful for direct isolation of structural genes.

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

PubMed Central

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

2009-01-01

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

Transposon mutagenesis in Bifidobacterium breve: construction and characterization of a Tn5 transposon mutant library for Bifidobacterium breve UCC2003.

PubMed

Ruiz, Lorena; Motherway, Mary O'Connell; Lanigan, Noreen; van Sinderen, Douwe

2013-01-01

Bifidobacteria are claimed to contribute positively to human health through a range of beneficial or probiotic activities, including amelioration of gastrointestinal and metabolic disorders, and therefore this particular group of gastrointestinal commensals has enjoyed increasing industrial and scientific attention in recent years. However, the molecular mechanisms underlying these probiotic mechanisms are still largely unknown, mainly due to the fact that molecular tools for bifidobacteria are rather poorly developed, with many strains lacking genetic accessibility. In this work, we describe the generation of transposon insertion mutants in two bifidobacterial strains, B. breve UCC2003 and B. breve NCFB2258. We also report the creation of the first transposon mutant library in a bifidobacterial strain, employing B. breve UCC2003 and a Tn5-based transposome strategy. The library was found to be composed of clones containing single transposon insertions which appear to be randomly distributed along the genome. The usefulness of the library to perform phenotypic screenings was confirmed through identification and analysis of mutants defective in D-galactose, D-lactose or pullulan utilization abilities.

Genome-wide transposon insertion scanning of environmental survival functions in the polycyclic aromatic hydrocarbon degrading bacterium Sphingomonas wittichii RW1.

PubMed

Roggo, Clémence; Coronado, Edith; Moreno-Forero, Silvia K; Harshman, Keith; Weber, Johann; van der Meer, Jan Roelof

2013-10-01

Sphingomonas wittichii RW1 is a dibenzofuran and dibenzodioxin-degrading bacterium with potentially interesting properties for bioaugmentation of contaminated sites. In order to understand the capacity of the microorganism to survive in the environment we used a genome-wide transposon scanning approach. RW1 transposon libraries were generated with around 22,000 independent insertions. Libraries were grown for an average of 50 generations (five successive passages in batch liquid medium) with salicylate as sole carbon and energy source in presence or absence of salt stress at -1.5 MPa. Alternatively, libraries were grown in sand with salicylate, at 50% water holding capacity, for 4 and 10 days (equivalent to 7 generations). Library DNA was recovered from the different growth conditions and scanned by ultrahigh throughput sequencing for the positions and numbers of inserted transposed kanamycin resistance gene. No transposon reads were recovered in 579 genes (10% of all annotated genes in the RW1 genome) in any of the libraries, suggesting those to be essential for survival under the used conditions. Libraries recovered from sand differed strongly from those incubated in liquid batch medium. In particular, important functions for survival of cells in sand at the short term concerned nutrient scavenging, energy metabolism and motility. In contrast to this, fatty acid metabolism and oxidative stress response were essential for longer term survival of cells in sand. Comparison to transcriptome data suggested important functions in sand for flagellar movement, pili synthesis, trehalose and polysaccharide synthesis and putative cell surface antigen proteins. Interestingly, a variety of genes were also identified, interruption of which cause significant increase in fitness during growth on salicylate. One of these was an Lrp family transcription regulator and mutants in this gene covered more than 90% of the total library after 50 generations of growth on salicylate. Our results demonstrate the power of genome-wide transposon scanning approaches for analysis of complex traits. © 2013 John Wiley & Sons Ltd and Society for Applied Microbiology.

Library Involvement in State Government Information Policy Development in the United States.

ERIC Educational Resources Information Center

Weaver, Barbara F.

This paper focuses on efforts by library groups and individuals to influence the development of state government information policy in various states in the United States, and emphasizes the need for librarians to make sure they either initiate such development or insert themselves into any existing policy development processes. Emphasis is given…

Isolation and characterization of novel lipases/esterases from a bovine rumen metagenome.

PubMed

Privé, Florence; Newbold, C Jamie; Kaderbhai, Naheed N; Girdwood, Susan G; Golyshina, Olga V; Golyshin, Peter N; Scollan, Nigel D; Huws, Sharon A

2015-07-01

Improving the health beneficial fatty acid content of meat and milk is a major challenge requiring an increased understanding of rumen lipid metabolism. In this study, we isolated and characterized rumen bacterial lipases/esterases using functional metagenomics. Metagenomic libraries were constructed from DNA extracted from strained rumen fluid (SRF), solid-attached bacteria (SAB) and liquid-associated rumen bacteria (LAB), ligated into a fosmid vector and subsequently transformed into an Escherichia coli host. Fosmid libraries consisted of 7,744; 8,448; and 7,680 clones with an average insert size of 30 to 35 kbp for SRF, SAB and LAB, respectively. Transformants were screened on spirit blue agar plates containing tributyrin for lipase/esterase activity. Five SAB and four LAB clones exhibited lipolytic activity, and no positive clones were found in the SRF library. Fosmids from positive clones were pyrosequenced and twelve putative lipase/esterase genes and two phospholipase genes retrieved. Although the derived proteins clustered into diverse esterase and lipase families, a degree of novelty was seen, with homology ranging from 40 to 78% following BlastP searches. Isolated lipases/esterases exhibited activity against mostly short- to medium-chain substrates across a range of temperatures and pH. The function of these novel enzymes recovered in ruminal metabolism needs further investigation, alongside their potential industrial uses.

Identification of Novel Virulence Determinants in Mycobacterium paratuberculosis by Screening a Library of Insertional Mutants†

PubMed Central

Shin, Sung Jae; Wu, Chia-wei; Steinberg, Howard; Talaat, Adel M.

2006-01-01

Johne's disease, caused by Mycobacterium paratuberculosis infection, is a worldwide problem for the dairy industry and has a possible involvement in Crohn's disease in humans. To identify virulence determinants of this economically important pathogen, a library of 5,060 transposon mutants was constructed using Tn5367 insertion mutagenesis, followed by large-scale sequencing to identify disrupted genes. In this report, 1,150 mutants were analyzed and 970 unique insertion sites were identified. Sequence analysis of the disrupted genes indicated that the insertion of Tn5367 was more prevalent in genomic regions with G+C content (50.5 to 60.5%) lower than the average G+C content (69.3%) of the rest of the genome. Phenotypic screening of the library identified disruptions of genes involved in iron, tryptophan, or mycolic acid metabolic pathways that displayed unique growth characteristics. Bioinformatic analysis of disrupted genes identified a list of potential virulence determinants for further testing with animals. Mouse infection studies showed a significant decrease in tissue colonization by mutants with a disruption in the gcpE, pstA, kdpC, papA2, impA, umaA1, or fabG2_2 gene. Attenuation phenotypes were tissue specific (e.g., for the umaA1 mutant) as well as time specific (e.g., for the impA mutant), suggesting that those genes may be involved in different virulence mechanisms. The identified potential virulence determinants represent novel functional classes that could be necessary for mycobacterial survival during infection and could provide suitable targets for vaccine and drug development against Johne's and Crohn's diseases. PMID:16790754

Novel transcripts of the estrogen receptor α gene in channel catfish

USGS Publications Warehouse

Patino, Reynaldo; Xia, Zhenfang; Gale, William L.; Wu, Chunfa; Maule, Alec G.; Chang, Xiaotian

2000-01-01

Complementary DNA libraries from liver and ovary of an immature female channel catfish were screened with a homologous ERα cDNA probe. The hepatic library yielded two new channel catfish ER cDNAs that encode N-terminal ERα variants of different sizes. Relative to the catfish ERα (medium size; 581 residues) previously reported, these new cDNAs encode Long-ERα (36 residues longer) and Short-ERα (389 residues shorter). The 5′-end of Long-ERα cDNA is identical to that of Medium-ERα but has an additional 503-bp segment with an upstream, in-frame translation-start codon. Recombinant Long-ERα binds estrogen with high affinity (Kd = 3.4 nM), similar to that previously reported for Medium-ERα but lower than reported for catfish ERβ. Short-ERα cDNA encodes a protein that lacks most of the receptor protein and does not bind estrogen. Northern hybridization confirmed the existence of multiple hepatic ERα RNAs that include the size range of the ERα cDNAs obtained from the libraries as well as additional sizes. Using primers for RT-PCR that target locations internal to the protein-coding sequence, we also established the presence of several ERα cDNA variants with in-frame insertions in the ligand-binding and DNA-binding domains and in-frame or out-of-frame deletions in the ligand-binding domain. These internal variants showed patterns of expression that differed between the ovary and liver. Further, the ovarian library yielded a full-length, ERα antisense cDNA containing a poly(A) signal and tail. A limited survey of histological preparations from juvenile catfish by in situ hybridization using directionally synthesized cRNA probes also suggested the expression of ERα antisense RNA in a tissue-specific manner. In conclusion, channel catfish seemingly have three broad classes of ERα mRNA variants: those encoding N-terminal truncated variants, those encoding internal variants (including C-terminal truncated variants), and antisense mRNA. The sense variants may encode functional ERα or related proteins that modulate ERα or ERβ activity. The existence of ER antisense mRNA is reported in this study for the first time. Its role may be to participate in the regulation of ER gene expression.

The Carnegie Protein Trap Library: A Versatile Tool for Drosophila Developmental Studies

PubMed Central

Buszczak, Michael; Paterno, Shelley; Lighthouse, Daniel; Bachman, Julia; Planck, Jamie; Owen, Stephenie; Skora, Andrew D.; Nystul, Todd G.; Ohlstein, Benjamin; Allen, Anna; Wilhelm, James E.; Murphy, Terence D.; Levis, Robert W.; Matunis, Erika; Srivali, Nahathai; Hoskins, Roger A.; Spradling, Allan C.

2007-01-01

Metazoan physiology depends on intricate patterns of gene expression that remain poorly known. Using transposon mutagenesis in Drosophila, we constructed a library of 7404 protein trap and enhancer trap lines, the Carnegie collection, to facilitate gene expression mapping at single-cell resolution. By sequencing the genomic insertion sites, determining splicing patterns downstream of the enhanced green fluorescent protein (EGFP) exon, and analyzing expression patterns in the ovary and salivary gland, we found that 600–900 different genes are trapped in our collection. A core set of 244 lines trapped different identifiable protein isoforms, while insertions likely to act as GFP-enhancer traps were found in 256 additional genes. At least 8 novel genes were also identified. Our results demonstrate that the Carnegie collection will be useful as a discovery tool in diverse areas of cell and developmental biology and suggest new strategies for greatly increasing the coverage of the Drosophila proteome with protein trap insertions. PMID:17194782

Development of genomic resources for the narrow-leafed lupin (Lupinus angustifolius): construction of a bacterial artificial chromosome (BAC) library and BAC-end sequencing

PubMed Central

2011-01-01

Background Lupinus angustifolius L, also known as narrow-leafed lupin (NLL), is becoming an important grain legume crop that is valuable for sustainable farming and is becoming recognised as a potential human health food. Recent interest is being directed at NLL to improve grain production, disease and pest management and health benefits of the grain. However, studies have been hindered by a lack of extensive genomic resources for the species. Results A NLL BAC library was constructed consisting of 111,360 clones with an average insert size of 99.7 Kbp from cv Tanjil. The library has approximately 12 × genome coverage. Both ends of 9600 randomly selected BAC clones were sequenced to generate 13985 BAC end-sequences (BESs), covering approximately 1% of the NLL genome. These BESs permitted a preliminary characterisation of the NLL genome such as organisation and composition, with the BESs having approximately 39% G:C content, 16.6% repetitive DNA and 5.4% putative gene-encoding regions. From the BESs 9966 simple sequence repeat (SSR) motifs were identified and some of these are shown to be potential markers. Conclusions The NLL BAC library and BAC-end sequences are powerful resources for genetic and genomic research on lupin. These resources will provide a robust platform for future high-resolution mapping, map-based cloning, comparative genomics and assembly of whole-genome sequencing data for the species. PMID:22014081

The Essential Genome of Escherichia coli K-12

PubMed Central

2018-01-01

ABSTRACT Transposon-directed insertion site sequencing (TraDIS) is a high-throughput method coupling transposon mutagenesis with short-fragment DNA sequencing. It is commonly used to identify essential genes. Single gene deletion libraries are considered the gold standard for identifying essential genes. Currently, the TraDIS method has not been benchmarked against such libraries, and therefore, it remains unclear whether the two methodologies are comparable. To address this, a high-density transposon library was constructed in Escherichia coli K-12. Essential genes predicted from sequencing of this library were compared to existing essential gene databases. To decrease false-positive identification of essential genes, statistical data analysis included corrections for both gene length and genome length. Through this analysis, new essential genes and genes previously incorrectly designated essential were identified. We show that manual analysis of TraDIS data reveals novel features that would not have been detected by statistical analysis alone. Examples include short essential regions within genes, orientation-dependent effects, and fine-resolution identification of genome and protein features. Recognition of these insertion profiles in transposon mutagenesis data sets will assist genome annotation of less well characterized genomes and provides new insights into bacterial physiology and biochemistry. PMID:29463657

Automated construction of an intraoperative high-dose-rate treatment plan library for the Varian brachytherapy treatment planning system.

PubMed

Deufel, Christopher L; Furutani, Keith M; Dahl, Robert A; Haddock, Michael G

2016-01-01

The ability to create treatment plans for intraoperative high-dose-rate (IOHDR) brachytherapy is limited by lack of imaging and time constraints. An automated method for creation of a library of high-dose-rate brachytherapy plans that can be used with standard planar applicators in the intraoperative setting is highly desirable. Nonnegative least squares algebraic methods were used to identify dwell time values for flat, rectangular planar applicators. The planar applicators ranged in length and width from 2 cm to 25 cm. Plans were optimized to deliver an absorbed dose of 10 Gy to three different depths from the patient surface: 0 cm, 0.5 cm, and 1.0 cm. Software was written to calculate the optimized dwell times and insert dwell times and positions into a .XML plan template that can be imported into the Varian brachytherapy treatment planning system. The user may import the .XML template into the treatment planning system in the intraoperative setting to match the patient applicator size and prescribed treatment depth. A total of 1587 library plans were created for IOHDR brachytherapy. Median plan generation time was approximately 1 minute per plan. Plan dose was typically 100% ± 1% (mean, standard deviation) of the prescribed dose over the entire length and width of the applicator. Plan uniformity was best for prescription depths of 0 cm and 0.5 cm from the patient surface. An IOHDR plan library may be created using automated methods. Thousands of plan templates may be optimized and prepared in a few hours to accommodate different applicator sizes and treatment depths and reduce treatment planning time. The automated method also enforces dwell time symmetry for symmetrical applicator geometries, which simplifies quality assurance. Copyright © 2016 American Brachytherapy Society. Published by Elsevier Inc. All rights reserved.

Small but Pristine--Lessons for Small Library Automation.

ERIC Educational Resources Information Center

Clement, Russell; Robertson, Dane

1990-01-01

Compares the more positive library automation experiences of a small public library with those of a large research library. Topics addressed include collection size; computer size and the need for outside control of a data processing center; staff size; selection process for hardware and software; and accountability. (LRW)

Designing deep sequencing experiments: detecting structural variation and estimating transcript abundance.

PubMed

Bashir, Ali; Bansal, Vikas; Bafna, Vineet

2010-06-18

Massively parallel DNA sequencing technologies have enabled the sequencing of several individual human genomes. These technologies are also being used in novel ways for mRNA expression profiling, genome-wide discovery of transcription-factor binding sites, small RNA discovery, etc. The multitude of sequencing platforms, each with their unique characteristics, pose a number of design challenges, regarding the technology to be used and the depth of sequencing required for a particular sequencing application. Here we describe a number of analytical and empirical results to address design questions for two applications: detection of structural variations from paired-end sequencing and estimating mRNA transcript abundance. For structural variation, our results provide explicit trade-offs between the detection and resolution of rearrangement breakpoints, and the optimal mix of paired-read insert lengths. Specifically, we prove that optimal detection and resolution of breakpoints is achieved using a mix of exactly two insert library lengths. Furthermore, we derive explicit formulae to determine these insert length combinations, enabling a 15% improvement in breakpoint detection at the same experimental cost. On empirical short read data, these predictions show good concordance with Illumina 200 bp and 2 Kbp insert length libraries. For transcriptome sequencing, we determine the sequencing depth needed to detect rare transcripts from a small pilot study. With only 1 Million reads, we derive corrections that enable almost perfect prediction of the underlying expression probability distribution, and use this to predict the sequencing depth required to detect low expressed genes with greater than 95% probability. Together, our results form a generic framework for many design considerations related to high-throughput sequencing. We provide software tools http://bix.ucsd.edu/projects/NGS-DesignTools to derive platform independent guidelines for designing sequencing experiments (amount of sequencing, choice of insert length, mix of libraries) for novel applications of next generation sequencing.

Construction of a Full-Length Enriched cDNA Library and Preliminary Analysis of Expressed Sequence Tags from Bengal Tiger Panthera tigris tigris

PubMed Central

Liu, Changqing; Liu, Dan; Guo, Yu; Lu, Taofeng; Li, Xiangchen; Zhang, Minghai; Ma, Jianzhang; Ma, Yuehui; Guan, Weijun

2013-01-01

In this study, a full-length enriched cDNA library was successfully constructed from Bengal tiger, Panthera tigris tigris, the most well-known wild Animal. Total RNA was extracted from cultured Bengal tiger fibroblasts in vitro. The titers of primary and amplified libraries were 1.28 × 106 pfu/mL and 1.56 × 109 pfu/mL respectively. The percentage of recombinants from unamplified library was 90.2% and average length of exogenous inserts was 0.98 kb. A total of 212 individual ESTs with sizes ranging from 356 to 1108 bps were then analyzed. The BLASTX score revealed that 48.1% of the sequences were classified as a strong match, 45.3% as nominal and 6.6% as a weak match. Among the ESTs with known putative function, 26.4% ESTs were found to be related to all kinds of metabolisms, 19.3% ESTs to information storage and processing, 11.3% ESTs to posttranslational modification, protein turnover, chaperones, 11.3% ESTs to transport, 9.9% ESTs to signal transducer/cell communication, 9.0% ESTs to structure protein, 3.8% ESTs to cell cycle, and only 6.6% ESTs classified as novel genes. By EST sequencing, a full-length gene coding ferritin was identified and characterized. The recombinant plasmid pET32a-TAT-Ferritin was constructed, coded for the TAT-Ferritin fusion protein with two 6× His-tags in N and C-terminal. After BCA assay, the concentration of soluble Trx-TAT-Ferritin recombinant protein was 2.32 ± 0.12 mg/mL. These results demonstrated that the reliability and representativeness of the cDNA library attained to the requirements of a standard cDNA library. This library provided a useful platform for the functional genome and transcriptome research of Bengal tigers. PMID:23708105

Construction of a full-length enriched cDNA library and preliminary analysis of expressed sequence tags from Bengal Tiger Panthera tigris tigris.

PubMed

Liu, Changqing; Liu, Dan; Guo, Yu; Lu, Taofeng; Li, Xiangchen; Zhang, Minghai; Ma, Jianzhang; Ma, Yuehui; Guan, Weijun

2013-05-24

In this study, a full-length enriched cDNA library was successfully constructed from Bengal tiger, Panthera tigris tigris, the most well-known wild Animal. Total RNA was extracted from cultured Bengal tiger fibroblasts in vitro. The titers of primary and amplified libraries were 1.28 × 106 pfu/mL and 1.56 × 109 pfu/mL respectively. The percentage of recombinants from unamplified library was 90.2% and average length of exogenous inserts was 0.98 kb. A total of 212 individual ESTs with sizes ranging from 356 to 1108 bps were then analyzed. The BLASTX score revealed that 48.1% of the sequences were classified as a strong match, 45.3% as nominal and 6.6% as a weak match. Among the ESTs with known putative function, 26.4% ESTs were found to be related to all kinds of metabolisms, 19.3% ESTs to information storage and processing, 11.3% ESTs to posttranslational modification, protein turnover, chaperones, 11.3% ESTs to transport, 9.9% ESTs to signal transducer/cell communication, 9.0% ESTs to structure protein, 3.8% ESTs to cell cycle, and only 6.6% ESTs classified as novel genes. By EST sequencing, a full-length gene coding ferritin was identified and characterized. The recombinant plasmid pET32a-TAT-Ferritin was constructed, coded for the TAT-Ferritin fusion protein with two 6× His-tags in N and C-terminal. After BCA assay, the concentration of soluble Trx-TAT-Ferritin recombinant protein was 2.32 ± 0.12 mg/mL. These results demonstrated that the reliability and representativeness of the cDNA library attained to the requirements of a standard cDNA library. This library provided a useful platform for the functional genome and transcriptome research of Bengal tigers.

Construction of a scFv Library with Synthetic, Non-combinatorial CDR Diversity.

PubMed

Bai, Xuelian; Shim, Hyunbo

2017-01-01

Many large synthetic antibody libraries have been designed, constructed, and successfully generated high-quality antibodies suitable for various demanding applications. While synthetic antibody libraries have many advantages such as optimized framework sequences and a broader sequence landscape than natural antibodies, their sequence diversities typically are generated by random combinatorial synthetic processes which cause the incorporation of many undesired CDR sequences. Here, we describe the construction of a synthetic scFv library using oligonucleotide mixtures that contain predefined, non-combinatorially synthesized CDR sequences. Each CDR is first inserted to a master scFv framework sequence and the resulting single-CDR libraries are subjected to a round of proofread panning. The proofread CDR sequences are assembled to produce the final scFv library with six diversified CDRs.

Library Webmasters in Medium-Sized Academic Libraries

ERIC Educational Resources Information Center

Kneip, Jason

2007-01-01

Library webmasters in medium-sized academic libraries were surveyed about their educational backgrounds, job responsibilities, and training and experience levels in Web development. The article summarizes the findings of the survey with recommendations for libraries and library and information science programs. (Contains 7 tables, 5 figures,and 5…

Species richness in soil bacterial communities: a proposed approach to overcome sample size bias.

PubMed

Youssef, Noha H; Elshahed, Mostafa S

2008-09-01

Estimates of species richness based on 16S rRNA gene clone libraries are increasingly utilized to gauge the level of bacterial diversity within various ecosystems. However, previous studies have indicated that regardless of the utilized approach, species richness estimates obtained are dependent on the size of the analyzed clone libraries. We here propose an approach to overcome sample size bias in species richness estimates in complex microbial communities. Parametric (Maximum likelihood-based and rarefaction curve-based) and non-parametric approaches were used to estimate species richness in a library of 13,001 near full-length 16S rRNA clones derived from soil, as well as in multiple subsets of the original library. Species richness estimates obtained increased with the increase in library size. To obtain a sample size-unbiased estimate of species richness, we calculated the theoretical clone library sizes required to encounter the estimated species richness at various clone library sizes, used curve fitting to determine the theoretical clone library size required to encounter the "true" species richness, and subsequently determined the corresponding sample size-unbiased species richness value. Using this approach, sample size-unbiased estimates of 17,230, 15,571, and 33,912 were obtained for the ML-based, rarefaction curve-based, and ACE-1 estimators, respectively, compared to bias-uncorrected values of 15,009, 11,913, and 20,909.

Isolation of CYP3A5P cDNA from human liver: a reflection of a novel cytochrome P-450 pseudogene.

PubMed

Schuetz, J D; Guzelian, P S

1995-03-14

We have isolated, from a human liver cDNA library, a 1627 bp CYP3A5 cDNA variant (CYP3A5P) that contains several large insertions, deletions, and in-frame termination codons. By comparison with the genomic structure of other CYP3A genes, the major insertions in CYP3A5P cDNA demarcate the inferred sites of several CYP3A5 exons. The segments inserted in CYP3A5P have no homology with splice donor acceptor sites. It is unlikely that CYP3A5P cDNA represents an artifact of the cloning procedures since Southern blot analysis of human genomic DNA disclosed that CYP3A5P cDNA hybridized with a DNA fragment distinct from fragments that hybridized with either CYP3A5, CYP3A3 or CYP3A4. Moreover, analysis of adult human liver RNA on Northern blots hybridized with a CYP3A5P cDNA fragment revealed the presence of an mRNA with the predicted size of CYP3A5P. We conclude that CYP3A5P cDNA was derived from a separate gene, CYP3A5P, most likely a pseudogene evolved from CYP3A5.

Optimizing doped libraries by using genetic algorithms

NASA Astrophysics Data System (ADS)

Tomandl, Dirk; Schober, Andreas; Schwienhorst, Andreas

1997-01-01

The insertion of random sequences into protein-encoding genes in combination with biologicalselection techniques has become a valuable tool in the design of molecules that have usefuland possibly novel properties. By employing highly effective screening protocols, a functionaland unique structure that had not been anticipated can be distinguished among a hugecollection of inactive molecules that together represent all possible amino acid combinations.This technique is severely limited by its restriction to a library of manageable size. Oneapproach for limiting the size of a mutant library relies on `doping schemes', where subsetsof amino acids are generated that reveal only certain combinations of amino acids in a proteinsequence. Three mononucleotide mixtures for each codon concerned must be designed, suchthat the resulting codons that are assembled during chemical gene synthesis represent thedesired amino acid mixture on the level of the translated protein. In this paper we present adoping algorithm that `reverse translates' a desired mixture of certain amino acids into threemixtures of mononucleotides. The algorithm is designed to optimally bias these mixturestowards the codons of choice. This approach combines a genetic algorithm with localoptimization strategies based on the downhill simplex method. Disparate relativerepresentations of all amino acids (and stop codons) within a target set can be generated.Optional weighing factors are employed to emphasize the frequencies of certain amino acidsand their codon usage, and to compensate for reaction rates of different mononucleotidebuilding blocks (synthons) during chemical DNA synthesis. The effect of statistical errors thataccompany an experimental realization of calculated nucleotide mixtures on the generatedmixtures of amino acids is simulated. These simulations show that the robustness of differentoptima with respect to small deviations from calculated values depends on their concomitantfitness. Furthermore, the calculations probe the fitness landscape locally and allow apreliminary assessment of its structure.

In vitro optimization of truncated stem-loop II variants of the hammerhead ribozyme for cleavage in low concentrations of magnesium under non-turnover conditions.

PubMed Central

Zillmann, M; Limauro, S E; Goodchild, J

1997-01-01

By truncating helix II to two base pairs in a hammerhead ribozyme having long flanking sequences (greater than 30 bases), the rate of cleavage in 1 mM magnesium can be increased roughly 100-fold. Replacing most of the nucleotides in a typical stem-loop II with 1-4 randomized nucleotides gave an RNA library that, even before selection, was more active in 1 mM magnesium than the parent ribozyme, but considerably less active than the truncated stem-loop II ribozyme. A novel, multiround selection for intermolecular cleavage was exploited to optimize this library for cleavage in low concentrations of magnesium. After three rounds of selection at sequentially lower concentrations of magnesium, the library cleaved substrate RNA 20-fold faster than the initial pool and was cloned. This pool was heavily enriched for one particular sequence (5'-CGUG-3') that represented 16 of 52 isolates (the next most common sequence was represented only six times). This sequence also represented the most active sequence, exceeding the activity of the short helix II variant under the conditions of the selection, thereby demonstrating the effectiveness of the selection technique. Analysis of the cleavage rates of RNAs made from eight isolates having different four-base insert sequences allowed assignment of highly preferred bases at each position in the insert. Analysis of pool clones having insert of differing lengths showed that, in general, activity decreased as the length of the insert decreased from 4 to 1. This supports the suggested role of stem-loop II in stabilizing the non-Watson-Crick interactions between the conserved bases of the catalytic core. PMID:9214657

Genetic Control of Plant Root Colonization by the Biocontrol agent, Pseudomonas fluorescens

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

Cole, Benjamin J.; Fletcher, Meghan; Waters, Jordan

Plant growth promoting rhizobacteria (PGPR) are a critical component of plant root ecosystems. PGPR promote plant growth by solubilizing inaccessible minerals, suppressing pathogenic microorganisms in the soil, and directly stimulating growth through hormone synthesis. Pseudomonas fluorescens is a well-established PGPR isolated from wheat roots that can also colonize the root system of the model plant, Arabidopsis thaliana. We have created barcoded transposon insertion mutant libraries suitable for genome-wide transposon-mediated mutagenesis followed by sequencing (TnSeq). These libraries consist of over 105 independent insertions, collectively providing loss-of-function mutants for nearly all genes in the P.fluorescens genome. Each insertion mutant can be unambiguouslymore » identified by a randomized 20 nucleotide sequence (barcode) engineered into the transposon sequence. We used these libraries in a gnotobiotic assay to examine the colonization ability of P.fluorescens on A.thaliana roots. Taking advantage of the ability to distinguish individual colonization events using barcode sequences, we assessed the timing and microbial concentration dependence of colonization of the rhizoplane niche. These data provide direct insight into the dynamics of plant root colonization in an in vivo system and define baseline parameters for the systematic identification of the bacterial genes and molecular pathways using TnSeq assays. Having determined parameters that facilitate potential colonization of roots by thousands of independent insertion mutants in a single assay, we are currently establishing a genome-wide functional map of genes required for root colonization in P.fluorescens. Importantly, the approach developed and optimized here for P.fluorescens>A.thaliana colonization will be applicable to a wide range of plant-microbe interactions, including biofuel feedstock plants and microbes known or hypothesized to impact on biofuel-relevant traits including biomass productivity and pathogen resistance.« less

Estimating P-coverage of biosynthetic pathways in DNA libraries and screening by genetic selection: biotin biosynthesis in the marine microorganism Chromohalobacter.

PubMed

Kim, Eun Jin; Angell, Scott; Janes, Jeff; Watanabe, Coran M H

2008-06-01

Traditional approaches to natural product discovery involve cell-based screening of natural product extracts followed by compound isolation and characterization. Their importance notwithstanding, continued mining leads to depletion of natural resources and the reisolation of previously identified metabolites. Metagenomic strategies aimed at localizing the biosynthetic cluster genes and expressing them in surrogate hosts offers one possible alternative. A fundamental question that naturally arises when pursuing such a strategy is, how large must the genomic library be to effectively represent the genome of an organism(s) and the biosynthetic gene clusters they harbor? Such an issue is certainly augmented in the absence of expensive robotics to expedite colony picking and/or screening of clones. We have developed an algorism, named BPC (biosynthetic pathway coverage), supported by molecular simulations to deduce the number of BAC clones required to achieve proper coverage of the genome and their respective biosynthetic pathways. The strategy has been applied to the construction of a large-insert BAC library from a marine microorganism, Hon6 (isolated from Honokohau, Maui) thought to represent a new species. The genomic library is constructed with a BAC yeast shuttle vector pClasper lacZ paving the way for the culturing of libraries in both prokaryotic and eukaryotic hosts. Flow cytometric methods are utilized to estimate the genome size of the organism and BPC implemented to assess P-coverage or percent coverage. A genetic selection strategy is illustrated, applications of which could expedite screening efforts in the identification and localization of biosynthetic pathways from marine microbial consortia, offering a powerful complement to genome sequencing and degenerate probe strategies. Implementing this approach, we report on the biotin biosynthetic pathway from the marine microorganism Hon6.

Occurrence of Phlebitis: A Systematic Review and Meta-analysis.

PubMed

Chang, Wen P; Peng, Yu X

Peripheral venous catheters (PVCs) are commonly used in clinical practice. However, varying degrees of phlebitis often occur in patients receiving intravenous injections. The relevant literature suggests that phlebitis occurrence is highly associated with the catheter gauge, insertion site, and catheterization duration. Nevertheless, no meta-analysis has been performed on the influence of these three factors on the occurrence of phlebitis. The objective of this study was to determine whether any significant differences exist in the occurrence of phlebitis between catheters of 20 gauge or smaller and those larger than 20 gauge, between catheters inserted in the antecubital fossa and those inserted in other locations on the upper limbs, or between catheters inserted for more than 96 hours and those inserted for 96 hours or less. Using a systematic approach, we searched for literature published between 2006 and 2017 in the Cumulative Index to Nursing and Allied Health Literature (CINAHL), PubMed, ProQuest, and Cochrane Library databases. We used Comprehensive Meta-analysis Version 2 to perform our meta-analysis. After the screening and review processes, we identified 17 studies that met our selection conditions. Among these studies, 14 contained complete data for meta-analysis. These studies involved 4,343 patients and 5,846 PVCs. Regarding the overall effect size in the meta-analysis, the results of the forest plot comparing catheters of 20 gauge or smaller and those larger than 20 gauge presented a risk ratio (RR) of 0.88 (95% confidence interval [0.67, 1.17], p = .380), indicating no statistically significant difference in the occurrence of phlebitis between catheters of the aforementioned gauges. The results of the forest plot comparing catheters inserted in the antecubital fossa and those inserted in other locations on the upper limbs presented an RR of 1.05 (95% confidence interval [0.82, 1.34], p = .696), indicating no statistically significant difference in the occurrence of phlebitis between catheters inserted in the aforementioned locations. The results of the forest plot comparing catheters inserted for more than 96 hours and those inserted for 96 hours or less presented an RR of 1.13 (95% confidence interval [0.49, 2.61], p = .779), indicating no statistically significant difference in the occurrence of phlebitis between catheters inserted for the aforementioned durations. The empirical results of this meta-analysis can serve as a reference for hospital management for selecting the PVC gauge, insertion site, and catheterization duration. In addition to the three factors that we analyzed, whether any other factors influence the occurrence of phlebitis in patients with catheter implantation is worth investigating in future research.

Method of generating ploynucleotides encoding enhanced folding variants

DOEpatents

Bradbury, Andrew M.; Kiss, Csaba; Waldo, Geoffrey S.

2017-05-02

The invention provides directed evolution methods for improving the folding, solubility and stability (including thermostability) characteristics of polypeptides. In one aspect, the invention provides a method for generating folding and stability-enhanced variants of proteins, including but not limited to fluorescent proteins, chromophoric proteins and enzymes. In another aspect, the invention provides methods for generating thermostable variants of a target protein or polypeptide via an internal destabilization baiting strategy. Internally destabilization a protein of interest is achieved by inserting a heterologous, folding-destabilizing sequence (folding interference domain) within DNA encoding the protein of interest, evolving the protein sequences adjacent to the heterologous insertion to overcome the destabilization (using any number of mutagenesis methods), thereby creating a library of variants. The variants in the library are expressed, and those with enhanced folding characteristics selected.

Modular Polyethylene Inserts for Total Knee Arthroplasty: Can Surgeons Detect 1-mm Thickness Increments?

PubMed

Yoo, Joanne Y; Cai, Jenny; Chen, Antonia F; Austin, Matthew S; Sharkey, Peter F

2016-05-01

Some manufacturers have introduced polyethylene (PE) inserts in 1-mm increment thickness options to allow for finer adjustments in total knee arthroplasty kinematics. Two surgeons with extensive experience performed 88 total knee arthroplasties using implants with 1-mm PE inserts. After trial components were inserted and the optimal PE thickness was selected, the insert was removed and a trial insert size was randomly chosen from opaque envelopes (1-mm smaller, same size, and 1-mm larger). The knee was re-examined and the surgeon determined which size PE had been placed. Surgeons reliably determined insert thicknesses in 62.5% (55 of 88; P = .050) of trials. Surgeons were not able to accurately detect 1-mm incremental changes of trial PE implants on a consistent basis. The potential clinical usefulness of this concept should be further evaluated. Copyright © 2016 Elsevier Inc. All rights reserved.

Construction of a filamentous phage display peptide library.

PubMed

Fagerlund, Annette; Myrset, Astrid Hilde; Kulseth, Mari Ann

2014-01-01

The concept of phage display is based on insertion of random oligonucleotides at an appropriate location within a structural gene of a bacteriophage. The resulting phage will constitute a library of random peptides displayed on the surface of the bacteriophages, with the encoding genotype packaged within each phage particle. Using a phagemid/helper phage system, the random peptides are interspersed between wild-type coat proteins. Libraries of phage-expressed peptides may be used to search for novel peptide ligands to target proteins. The success of finding a peptide with a desired property in a given library is highly dependent on the diversity and quality of the library. The protocols in this chapter describe the construction of a high-diversity library of phagemid vector encoding fusions of the phage coat protein pVIII with random peptides, from which a phage library displaying random peptides can be prepared.

Construction of a normalized full-length cDNA library of cephalopod Amphioctopus fangsiao and development of microsatellite markers

NASA Astrophysics Data System (ADS)

Feng, Yanwei; Liu, Wenfen; Xu, Xin; Yang, Jianmin; Wang, Weijun; Wei, Xiumei; Liu, Xiangquan; Sun, Guohua

2017-10-01

Amphioctopus fangsiao is one of the most economically important species and has been considered to be a candidate for aquaculture. In order to facilitate its fine-scale genetic analyses, we constructed a normalized full-length library successfully and developed a set of microsatellite markers in this study. The normalized full-length library had a storage capacity of 6.9×105 independent clones. The recombination efficiency was 95% and the average size of inserted fragments was longer than 1000 bp. A total of 3440 high quality ESTs were obtained, which were assembled into 1803 unigenes. Of these unigenes, 450 (25%) were assigned into 33 Gene Ontology terms, 576 (31.9%) into 153 Kyoto Encyclopedia of Genes and Genomes pathways, and 275 (15.3%) into 22 Clusters of Orthologous Groups. Seventy-six polymorphic microsatellite markers were identified. The number of alleles per locus ranged from 4 to 17, and the observed and expected heterozygosities varied between 0.167 and 0.967 and between 0.326 and 0.944, respectively. Twelve loci were significantly deviated from Hardy-Weinberg equilibrium after Bonferroni correction and no linkage disequilibrium was found between different loci. This study provided not only a useful resource for the isolation of the functional genes, but also a set of informative microsatellites for the assessment of population structure and conservation genetics of A. fangsiao.

Next-generation sequencing library preparation method for identification of RNA viruses on the Ion Torrent Sequencing Platform.

PubMed

Chen, Guiqian; Qiu, Yuan; Zhuang, Qingye; Wang, Suchun; Wang, Tong; Chen, Jiming; Wang, Kaicheng

2018-05-09

Next generation sequencing (NGS) is a powerful tool for the characterization, discovery, and molecular identification of RNA viruses. There were multiple NGS library preparation methods published for strand-specific RNA-seq, but some methods are not suitable for identifying and characterizing RNA viruses. In this study, we report a NGS library preparation method to identify RNA viruses using the Ion Torrent PGM platform. The NGS sequencing adapters were directly inserted into the sequencing library through reverse transcription and polymerase chain reaction, without fragmentation and ligation of nucleic acids. The results show that this method is simple to perform, able to identify multiple species of RNA viruses in clinical samples.

A filtering method to generate high quality short reads using illumina paired-end technology.

PubMed

Eren, A Murat; Vineis, Joseph H; Morrison, Hilary G; Sogin, Mitchell L

2013-01-01

Consensus between independent reads improves the accuracy of genome and transcriptome analyses, however lack of consensus between very similar sequences in metagenomic studies can and often does represent natural variation of biological significance. The common use of machine-assigned quality scores on next generation platforms does not necessarily correlate with accuracy. Here, we describe using the overlap of paired-end, short sequence reads to identify error-prone reads in marker gene analyses and their contribution to spurious OTUs following clustering analysis using QIIME. Our approach can also reduce error in shotgun sequencing data generated from libraries with small, tightly constrained insert sizes. The open-source implementation of this algorithm in Python programming language with user instructions can be obtained from https://github.com/meren/illumina-utils.

Dinucleotide repeat polymorphisms in waterfowl (family Anatidae): Characterization of a sex-linked (Z-specific) and 14 autosomal loci

USGS Publications Warehouse

Buchholz, W.G.; Pearce, J.M.; Pierson, B.J.; Scribner, K.T.

1998-01-01

Canada goose (Branta Canadensis) and harlequin duck (Histrionicus histrionicus) DNAs were digested with Sau3AI, and size selected (300-700 bp) fragments were ligated into BamHI-digested pBluscriptII KS+. The enrichment protocol of Ostrander et al.1 was followed. The resulting libraries were screened using a [ƴ-32P]ATP end-labelled (CA)20 oligonucleotides as a hybridization probe. Positive clones were sequenced using cycle-sequencing protocols (Epicentre Technologies, Madison, WI) and primers flanking the inserts. PCR primers were designed to amplify the repeat and yield amplification products of ≈100-200 bp. DNA  samples were screened for variation at these loci using [ƴ-32P]ATP end-labelled primers. The products were resolved using 6% denaturing polyacrylamide gels and autoradiography.

Circulation policies in health science libraries.

PubMed

Watkins, C; Coker, N C

1970-10-01

There is general agreement that library policies have considerable influence on the use of libraries. Medical school (health science) libraries of this country were surveyed as to their policies in respect to whether faculty and student use were regulated by a single policy, circulation regulations, hours library was accessible to users, accessibility of reserve material, interlibrary loan, policy on overdue material, and exit control. THE LIBRARIES WERE THEN DIVIDED INTO THREE GROUPS, HIGH, MIDDLE, AND LOW ACCORDING TO THE FOLLOWING CHARACTERISTICS: size of student body, size of faculty, size of holdings, size of library staff, annual budget, and annual circulation. Our findings would indicate that schools falling in a high category based upon these criteria tend to be more restrictive in their policies and to have different regulations for faculty and students than do schools in the low category.These findings warrant further study.

Attitudes about OCLC in Small and Medium-Sized Libraries. Illinois Valley Library System OCLC Experimental Project. Report No. 4.

ERIC Educational Resources Information Center

Bills, Linda G.; Wilford, Valerie

A project was conducted from 1980 to 1982 to determine the costs and benefits of OCLC use in 29 small and medium-sized member libraries of the Illinois Valley Library System (IVLS). Academic, school, public, and special libraries participated in the project. Based on written attitude surveys of and interviews with library directors, staff,…

A Deep-Coverage Tomato BAC Library and Prospects Toward Development of an STC Framework for Genome Sequencing

PubMed Central

Budiman, Muhammad A.; Mao, Long; Wood, Todd C.; Wing, Rod A.

2000-01-01

Recently a new strategy using BAC end sequences as sequence-tagged connectors (STCs) was proposed for whole-genome sequencing projects. In this study, we present the construction and detailed characterization of a 15.0 haploid genome equivalent BAC library for the cultivated tomato, Lycopersicon esculentum cv. Heinz 1706. The library contains 129,024 clones with an average insert size of 117.5 kb and a chloroplast content of 1.11%. BAC end sequences from 1490 ends were generated and analyzed as a preliminary evaluation for using this library to develop an STC framework to sequence the tomato genome. A total of 1205 BAC end sequences (80.9%) were obtained, with an average length of 360 high-quality bases, and were searched against the GenBank database. Using a cutoff expectation value of <10−6, and combining the results from BLASTN, BLASTX, and TBLASTX searches, 24.3% of the BAC end sequences were similar to known sequences, of which almost half (48.7%) share sequence similarities to retrotransposons and 7% to known genes. Some of the transposable element sequences were the first reported in tomato, such as sequences similar to maize transposon Activator (Ac) ORF and tobacco pararetrovirus-like sequences. Interestingly, there were no BAC end sequences similar to the highly repeated TGRI and TGRII elements. However, the majority (70.3%) of STCs did not share significant sequence similarities to any sequences in GenBank at either the DNA or predicted protein levels, indicating that a large portion of the tomato genome is still unknown. Our data demonstrate that this BAC library is suitable for developing an STC database to sequence the tomato genome. The advantages of developing an STC framework for whole-genome sequencing of tomato are discussed. [The BAC end sequences described in this paper have been deposited in the GenBank data library under accession nos. AQ367111–AQ368361.] PMID:10645957

Simultaneous digital quantification and fluorescence-based size characterization of massively parallel sequencing libraries.

PubMed

Laurie, Matthew T; Bertout, Jessica A; Taylor, Sean D; Burton, Joshua N; Shendure, Jay A; Bielas, Jason H

2013-08-01

Due to the high cost of failed runs and suboptimal data yields, quantification and determination of fragment size range are crucial steps in the library preparation process for massively parallel sequencing (or next-generation sequencing). Current library quality control methods commonly involve quantification using real-time quantitative PCR and size determination using gel or capillary electrophoresis. These methods are laborious and subject to a number of significant limitations that can make library calibration unreliable. Herein, we propose and test an alternative method for quality control of sequencing libraries using droplet digital PCR (ddPCR). By exploiting a correlation we have discovered between droplet fluorescence and amplicon size, we achieve the joint quantification and size determination of target DNA with a single ddPCR assay. We demonstrate the accuracy and precision of applying this method to the preparation of sequencing libraries.

A High-Throughput Arabidopsis Reverse Genetics System

PubMed Central

Sessions, Allen; Burke, Ellen; Presting, Gernot; Aux, George; McElver, John; Patton, David; Dietrich, Bob; Ho, Patrick; Bacwaden, Johana; Ko, Cynthia; Clarke, Joseph D.; Cotton, David; Bullis, David; Snell, Jennifer; Miguel, Trini; Hutchison, Don; Kimmerly, Bill; Mitzel, Theresa; Katagiri, Fumiaki; Glazebrook, Jane; Law, Marc; Goff, Stephen A.

2002-01-01

A collection of Arabidopsis lines with T-DNA insertions in known sites was generated to increase the efficiency of functional genomics. A high-throughput modified thermal asymetric interlaced (TAIL)-PCR protocol was developed and used to amplify DNA fragments flanking the T-DNA left borders from ∼100,000 transformed lines. A total of 85,108 TAIL-PCR products from 52,964 T-DNA lines were sequenced and compared with the Arabidopsis genome to determine the positions of T-DNAs in each line. Predicted T-DNA insertion sites, when mapped, showed a bias against predicted coding sequences. Predicted insertion mutations in genes of interest can be identified using Arabidopsis Gene Index name searches or by BLAST (Basic Local Alignment Search Tool) search. Insertions can be confirmed by simple PCR assays on individual lines. Predicted insertions were confirmed in 257 of 340 lines tested (76%). This resource has been named SAIL (Syngenta Arabidopsis Insertion Library) and is available to the scientific community at www.tmri.org. PMID:12468722

Area of the tibial insertion site of the anterior cruciate ligament as a predictor for graft size.

PubMed

Guenther, Daniel; Irarrázaval, Sebastian; Albers, Marcio; Vernacchia, Cara; Irrgang, James J; Musahl, Volker; Fu, Freddie H

2017-05-01

To determine the distribution of different sizes of the area of the tibial insertion site among the population and to evaluate whether preoperative MRI measurements correlate with intraoperative findings to enable preoperative planning of the required graft size to cover the tibial insertion site sufficiently. The hypothesis was that the area of the tibial insertion site varies among individuals and that there is good agreement between MRI and intraoperative measurements. Intraoperative measurements of the tibial insertion site were taken on 117 patients. Three measurements were taken in each plane building a grid to cover the tibial insertion site as closely as possible. The mean of the three measurements in each plane was used for determination of the area. Two orthopaedic surgeons, who were blinded to the intraoperative measurements, took magnetic resonance imaging (MRI) measurements of the area of the tibial insertion site at two different time points. The intraoperative measured mean area was 123.8 ± 21.5 mm 2 . The mean area was 132.8 ± 15.7 mm 2 (rater 1) and 136.7 ± 15.4 mm 2 (rater 2) when determined using MRI. The size of the area was approximately normally distributed. Inter-rater (0.89; 95 % CI 0.84, 0.92; p < 0.001) and intrarater reliability (rater 1: 0.97; 95 % CI 0.95, 0.98; p < 0.001; rater 2: 0.95; 95 % CI 0.92, 0.96; p < 0.001) demonstrated excellent test-retest reliability. There was good agreement between MRI and intraoperative measurement of tibial insertion site area (ICCs rater 1: 0.80; 95 % CI 0.71, 0.87; p < 0.001; rater 2: 0.87; 95 % CI 0.81, 0.91; p < 0.001). The tibial insertion site varies in size and shape. Preoperative determination of the area using MRI is repeatable and enables planning of graft choice and size to optimally cover the tibial insertion site. III.

Improved gap size estimation for scaffolding algorithms.

PubMed

Sahlin, Kristoffer; Street, Nathaniel; Lundeberg, Joakim; Arvestad, Lars

2012-09-01

One of the important steps of genome assembly is scaffolding, in which contigs are linked using information from read-pairs. Scaffolding provides estimates about the order, relative orientation and distance between contigs. We have found that contig distance estimates are generally strongly biased and based on false assumptions. Since erroneous distance estimates can mislead in subsequent analysis, it is important to provide unbiased estimation of contig distance. In this article, we show that state-of-the-art programs for scaffolding are using an incorrect model of gap size estimation. We discuss why current maximum likelihood estimators are biased and describe what different cases of bias we are facing. Furthermore, we provide a model for the distribution of reads that span a gap and derive the maximum likelihood equation for the gap length. We motivate why this estimate is sound and show empirically that it outperforms gap estimators in popular scaffolding programs. Our results have consequences both for scaffolding software, structural variation detection and for library insert-size estimation as is commonly performed by read aligners. A reference implementation is provided at https://github.com/SciLifeLab/gapest. Supplementary data are availible at Bioinformatics online.

Versatile P(acman) BAC Libraries for Transgenesis Studies in Drosophila melanogaster

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

Venken, Koen J.T.; Carlson, Joseph W.; Schulze, Karen L.

2009-04-21

We constructed Drosophila melanogaster BAC libraries with 21-kb and 83-kb inserts in the P(acman) system. Clones representing 12-fold coverage and encompassing more than 95percent of annotated genes were mapped onto the reference genome. These clones can be integrated into predetermined attP sites in the genome using Phi C31 integrase to rescue mutations. They can be modified through recombineering, for example to incorporate protein tags and assess expression patterns.

Technical Note: Computer-Manufactured Inserts for Prosthetic Sockets

PubMed Central

Sanders, Joan E.; McLean, Jake B.; Cagle, John C.; Gardner, David W.; Allyn, Katheryn J.

2016-01-01

The objective of this research was to use computer-aided design software and a tabletop 3-D additive manufacturing system to design and fabricate custom plastic inserts for trans-tibial prosthesis users. Shape quality of inserts was tested right after they were inserted into participant’s test sockets and again after four weeks of wear. Inserts remained properly positioned and intact throughout testing. Right after insertion the inserts caused the socket to be slightly under-sized, by a mean of 0.11 mm, approximately 55% of the thickness of a nylon sheath. After four weeks of wear the under-sizing was less, averaging 0.03 mm, approximately 15% of the thickness of a nylon sheath. Thus the inserts settled into the sockets over time. If existing prosthetic design software packages were enhanced to conduct insert design and to automatically generate fabrication files for manufacturing, then computer manufactured inserts may offer advantages over traditional methods in terms of speed of fabrication, ease of design, modification, and record keeping. PMID:27212209

Construction of a plant-transformation-competent BIBAC library and genome sequence analysis of polyploid Upland cotton (Gossypium hirsutum L.)

PubMed Central

2013-01-01

Background Cotton, one of the world’s leading crops, is important to the world’s textile and energy industries, and is a model species for studies of plant polyploidization, cellulose biosynthesis and cell wall biogenesis. Here, we report the construction of a plant-transformation-competent binary bacterial artificial chromosome (BIBAC) library and comparative genome sequence analysis of polyploid Upland cotton (Gossypium hirsutum L.) with one of its diploid putative progenitor species, G. raimondii Ulbr. Results We constructed the cotton BIBAC library in a vector competent for high-molecular-weight DNA transformation in different plant species through either Agrobacterium or particle bombardment. The library contains 76,800 clones with an average insert size of 135 kb, providing an approximate 99% probability of obtaining at least one positive clone from the library using a single-copy probe. The quality and utility of the library were verified by identifying BIBACs containing genes important for fiber development, fiber cellulose biosynthesis, seed fatty acid metabolism, cotton-nematode interaction, and bacterial blight resistance. In order to gain an insight into the Upland cotton genome and its relationship with G. raimondii, we sequenced nearly 10,000 BIBAC ends (BESs) randomly selected from the library, generating approximately one BES for every 250 kb along the Upland cotton genome. The retroelement Gypsy/DIRS1 family predominates in the Upland cotton genome, accounting for over 77% of all transposable elements. From the BESs, we identified 1,269 simple sequence repeats (SSRs), of which 1,006 were new, thus providing additional markers for cotton genome research. Surprisingly, comparative sequence analysis showed that Upland cotton is much more diverged from G. raimondii at the genomic sequence level than expected. There seems to be no significant difference between the relationships of the Upland cotton D- and A-subgenomes with the G. raimondii genome, even though G. raimondii contains a D genome (D5). Conclusions The library represents the first BIBAC library in cotton and related species, thus providing tools useful for integrative physical mapping, large-scale genome sequencing and large-scale functional analysis of the Upland cotton genome. Comparative sequence analysis provides insights into the Upland cotton genome, and a possible mechanism underlying the divergence and evolution of polyploid Upland cotton from its diploid putative progenitor species, G. raimondii. PMID:23537070

Construction and characterization of two BAC libraries representing a deep-coverage of the genome of chicory (Cichorium intybus L., Asteraceae)

PubMed Central

2010-01-01

Background The Asteraceae represents an important plant family with respect to the numbers of species present in the wild and used by man. Nonetheless, genomic resources for Asteraceae species are relatively underdeveloped, hampering within species genetic studies as well as comparative genomics studies at the family level. So far, six BAC libraries have been described for the main crops of the family, i.e. lettuce and sunflower. Here we present the characterization of BAC libraries of chicory (Cichorium intybus L.) constructed from two genotypes differing in traits related to sexual and vegetative reproduction. Resolving the molecular mechanisms underlying traits controlling the reproductive system of chicory is a key determinant for hybrid development, and more generally will provide new insights into these traits, which are poorly investigated so far at the molecular level in Asteraceae. Findings Two bacterial artificial chromosome (BAC) libraries, CinS2S2 and CinS1S4, were constructed from HindIII-digested high molecular weight DNA of the contrasting genotypes C15 and C30.01, respectively. C15 was hermaphrodite, non-embryogenic, and S2S2 for the S-locus implicated in self-incompatibility, whereas C30.01 was male sterile, embryogenic, and S1S4. The CinS2S2 and CinS1S4 libraries contain 89,088 and 81,408 clones. Mean insert sizes of the CinS2S2 and CinS1S4 clones are 90 and 120 kb, respectively, and provide together a coverage of 12.3 haploid genome equivalents. Contamination with mitochondrial and chloroplast DNA sequences was evaluated with four mitochondrial and four chloroplast specific probes, and was estimated to be 0.024% and 1.00% for the CinS2S2 library, and 0.028% and 2.35% for the CinS1S4 library. Using two single copy genes putatively implicated in somatic embryogenesis, screening of both libraries resulted in detection of 12 and 13 positive clones for each gene, in accordance with expected numbers. Conclusions This indicated that both BAC libraries are valuable tools for molecular studies in chicory, one goal being the positional cloning of the S-locus in this Asteraceae species. PMID:20701751

Construction and characterization of two BAC libraries representing a deep-coverage of the genome of chicory (Cichorium intybus L., Asteraceae).

PubMed

Gonthier, Lucy; Bellec, Arnaud; Blassiau, Christelle; Prat, Elisa; Helmstetter, Nicolas; Rambaud, Caroline; Huss, Brigitte; Hendriks, Theo; Bergès, Hélène; Quillet, Marie-Christine

2010-08-11

The Asteraceae represents an important plant family with respect to the numbers of species present in the wild and used by man. Nonetheless, genomic resources for Asteraceae species are relatively underdeveloped, hampering within species genetic studies as well as comparative genomics studies at the family level. So far, six BAC libraries have been described for the main crops of the family, i.e. lettuce and sunflower. Here we present the characterization of BAC libraries of chicory (Cichorium intybus L.) constructed from two genotypes differing in traits related to sexual and vegetative reproduction. Resolving the molecular mechanisms underlying traits controlling the reproductive system of chicory is a key determinant for hybrid development, and more generally will provide new insights into these traits, which are poorly investigated so far at the molecular level in Asteraceae. Two bacterial artificial chromosome (BAC) libraries, CinS2S2 and CinS1S4, were constructed from HindIII-digested high molecular weight DNA of the contrasting genotypes C15 and C30.01, respectively. C15 was hermaphrodite, non-embryogenic, and S2S2 for the S-locus implicated in self-incompatibility, whereas C30.01 was male sterile, embryogenic, and S1S4. The CinS2S2 and CinS1S4 libraries contain 89,088 and 81,408 clones. Mean insert sizes of the CinS2S2 and CinS1S4 clones are 90 and 120 kb, respectively, and provide together a coverage of 12.3 haploid genome equivalents. Contamination with mitochondrial and chloroplast DNA sequences was evaluated with four mitochondrial and four chloroplast specific probes, and was estimated to be 0.024% and 1.00% for the CinS2S2 library, and 0.028% and 2.35% for the CinS1S4 library. Using two single copy genes putatively implicated in somatic embryogenesis, screening of both libraries resulted in detection of 12 and 13 positive clones for each gene, in accordance with expected numbers. This indicated that both BAC libraries are valuable tools for molecular studies in chicory, one goal being the positional cloning of the S-locus in this Asteraceae species.

BACCardI--a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison.

PubMed

Bartels, Daniela; Kespohl, Sebastian; Albaum, Stefan; Drüke, Tanja; Goesmann, Alexander; Herold, Julia; Kaiser, Olaf; Pühler, Alfred; Pfeiffer, Friedhelm; Raddatz, Günter; Stoye, Jens; Meyer, Folker; Schuster, Stephan C

2005-04-01

We provide the graphical tool BACCardI for the construction of virtual clone maps from standard assembler output files or BLAST based sequence comparisons. This new tool has been applied to numerous genome projects to solve various problems including (a) validation of whole genome shotgun assemblies, (b) support for contig ordering in the finishing phase of a genome project, and (c) intergenome comparison between related strains when only one of the strains has been sequenced and a large insert library is available for the other. The BACCardI software can seamlessly interact with various sequence assembly packages. Genomic assemblies generated from sequence information need to be validated by independent methods such as physical maps. The time-consuming task of building physical maps can be circumvented by virtual clone maps derived from read pair information of large insert libraries.

A library of MiMICs allows tagging of genes and reversible, spatial and temporal knockdown of proteins in Drosophila

DOE PAGES

Nagarkar-Jaiswal, Sonal; Lee, Pei-Tseng; Campbell, Megan E.; ...

2015-03-31

Here, we document a collection of ~7434 MiMIC (Minos Mediated Integration Cassette) insertions of which 2854 are inserted in coding introns. They allowed us to create a library of 400 GFP-tagged genes. We show that 72% of internally tagged proteins are functional, and that more than 90% can be imaged in unfixed tissues. Moreover, the tagged mRNAs can be knocked down by RNAi against GFP (iGFPi), and the tagged proteins can be efficiently knocked down by deGradFP technology. The phenotypes associated with RNA and protein knockdown typically correspond to severe loss of function or null mutant phenotypes. Finally, we demonstratemore » reversible, spatial, and temporal knockdown of tagged proteins in larvae and adult flies. This new strategy and collection of strains allows unprecedented in vivo manipulations in flies for many genes. These strategies will likely extend to vertebrates.« less

Construction and Screening of Marine Metagenomic Large Insert Libraries.

PubMed

Weiland-Bräuer, Nancy; Langfeldt, Daniela; Schmitz, Ruth A

2017-01-01

The marine environment covers more than 70 % of the world's surface. Marine microbial communities are highly diverse and have evolved during extended evolutionary processes of physiological adaptations under the influence of a variety of ecological conditions and selection pressures. They harbor an enormous diversity of microbes with still unknown and probably new physiological characteristics. In the past, marine microbes, mostly bacteria of microbial consortia attached to marine tissues of multicellular organisms, have proven to be a rich source of highly potent bioactive compounds, which represent a considerable number of drug candidates. However, to date, the biodiversity of marine microbes and the versatility of their bioactive compounds and metabolites have not been fully explored. This chapter describes sampling in the marine environment, construction of metagenomic large insert libraries from marine habitats, and exemplarily one function based screen of metagenomic clones for identification of quorum quenching activities.

Construction of a large-scale Burkholderia cenocepacia J2315 transposon mutant library

NASA Astrophysics Data System (ADS)

Wong, Yee-Chin; Pain, Arnab; Nathan, Sheila

2014-09-01

Burkholderia cenocepacia, a pathogenic member of the Burkholderia cepacia complex (Bcc), has emerged as a significant threat towards cystic fibrosis patients, where infection often leads to the fatal clinical manifestation known as cepacia syndrome. Many studies have investigated the pathogenicity of B. cenocepacia as well as its ability to become highly resistant towards many of the antibiotics currently in use. In addition, studies have also been undertaken to understand the pathogen's capacity to adapt and survive in a broad range of environments. Transposon based mutagenesis has been widely used in creating insertional knock-out mutants and coupled with recent advances in sequencing technology, robust tools to study gene function in a genome-wide manner have been developed based on the assembly of saturated transposon mutant libraries. In this study, we describe the construction of a large-scale library of B. cenocepacia transposon mutants. To create transposon mutants of B. cenocepacia strain J2315, electrocompetent bacteria were electrotransformed with the EZ-Tn5 transposome. Tetracyline resistant colonies were harvested off selective agar and pooled. Mutants were generated in multiple batches with each batch consisting of ˜20,000 to 40,000 mutants. Transposon insertion was validated by PCR amplification of the transposon region. In conclusion, a saturated B. cenocepacia J2315 transposon mutant library with an estimated total number of 500,000 mutants was successfully constructed. This mutant library can now be further exploited as a genetic tool to assess the function of every gene in the genome, facilitating the discovery of genes important for bacterial survival and adaptation, as well as virulence.

Viral morphogenesis is the dominant source of sequence censorship in M13 combinatorial peptide phage display.

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

Rodi, D. J.; Soares, A. S.; Makowski, L.

Novel statistical methods have been developed and used to quantitate and annotate the sequence diversity within combinatorial peptide libraries on the basis of small numbers (1-200) of sequences selected at random from commercially available M13 p3-based phage display libraries. These libraries behave statistically as though they correspond to populations containing roughly 4.0{+-}1.6% of the random dodecapeptides and 7.9{+-}2.6% of the random constrained heptapeptides that are theoretically possible within the phage populations. Analysis of amino acid residue occurrence patterns shows no demonstrable influence on sequence censorship by Escherichia coli tRNA isoacceptor profiles or either overall codon or Class II codon usagemore » patterns, suggesting no metabolic constraints on recombinant p3 synthesis. There is an overall depression in the occurrence of cysteine, arginine and glycine residues and an overabundance of proline, threonine and histidine residues. The majority of position-dependent amino acid sequence bias is clustered at three positions within the inserted peptides of the dodecapeptide library, +1, +3 and +12 downstream from the signal peptidase cleavage site. Conformational tendency measures of the peptides indicate a significant preference for inserts favoring a {beta}-turn conformation. The observed protein sequence limitations can primarily be attributed to genetic codon degeneracy and signal peptidase cleavage preferences. These data suggest that for applications in which maximal sequence diversity is essential, such as epitope mapping or novel receptor identification, combinatorial peptide libraries should be constructed using codon-corrected trinucleotide cassettes within vector-host systems designed to minimize morphogenesis-related censorship.« less

Optimization of design and production strategies for novel adeno-associated viral display peptide libraries.

PubMed

Körbelin, J; Hunger, A; Alawi, M; Sieber, T; Binder, M; Trepel, M

2017-08-01

Libraries displaying random peptides on the surface of adeno-associated virus (AAV) are powerful tools for the generation of target-specific gene therapy vectors. However, for unknown reasons the success rate of AAV library screenings is variable and the influence of the production procedure has not been thoroughly evaluated. During library screenings, the capsid variants with the most favorable tropism are enriched over several selection rounds on a target of choice and identified by subsequent sequencing of the encapsidated viral genomes encoding the library capsids with targeting peptide insertions. Thus, a high capsid-genome correlation is crucial to obtain the correct information about the selected capsid variants. Producing AAV libraries by a two-step protocol with pseudotyped library transfer shuttles has been proposed as one way to ensure such a correlation. Here we show that AAV2 libraries produced by such a protocol via transfer shuttles display an unexpected additional bias in the amino-acid composition which confers increased heparin affinity and thus similarity to wildtype AAV2 tropism. This bias may fundamentally impair the intended use of AAV libraries, discouraging the use of transfer shuttles for the production of AAV libraries in the future.

A cohort evaluation of the pediatric ProSeal laryngeal mask airway in 100 children.

PubMed

Kelly, Fiona; Sale, Steven; Bayley, Guy; Cook, Tim; Stoddart, Peter; White, Michelle

2008-10-01

The ProSeal laryngeal mask airway (PLMA) has been available in pediatric sizes in the UK since 2007. Although several non-UK studies have evaluated PLMAs in children, there are little published data regarding their use in this country. Having decided to introduce the pediatric PLMA into our practice, we chose to prospectively audit the first 100 uses as part of our clinical governance. We studied children undergoing elective surgery who were considered suitable for a supraglottic airway. We recorded patient, surgical and insertion details, device performance data and complications. Patient management was not altered by inclusion in this audit. Twenty size 1.5, 55 size 2.0, 15 size 2.5 and 10 size 3.0 PLMAs were inserted in 100 consecutive children [median age 2 years (range 2 months to 10 years) and median weight 15 kg (range 4.9-60 kg)]. The overall first attempt success rate was 93% (size 1.5, 100%; size 2.0, 100%; size 2.5, 87%; size 3.0, 90%) and overall successful insertion rate was 99%. Median leak pressure was 25 cmH(2)O. Outright failure was seen in one patient; complications were seen in another six patients (partial airway obstruction in five patients and mild laryngospasm in one patient), all of whom were transient and none of whom required intubation. No episodes of regurgitation were recorded. Even without prior experience and using nonconventional insertion, pediatric PLMAs (including size 1.5) can be easily inserted and provide an effective airway.

Construction of cDNA library from intestine, mesentery and coelomocyte of Apostichopus japonicus Selenka infected with Vibrio sp. and a preliminary analysis of immunity-related genes

NASA Astrophysics Data System (ADS)

Liu, Hongzhan; Zheng, Fengrong; Sun, Xiuqin; Cai, Yimei

2012-06-01

The aquaculture of sea cucumber Apostichopus japonicus (Echinodermata, Holothuroidea) has grown rapidly during recent years and has become an important sector of the marine industry in Northern China. However, with the rapid growth of the industry and the use of non-standard culture techniques, epidemic diseases of A. japonicus now pose increasing problems to the industry. To screen the genes with stress response to bacterial infection in sea cucumber at a genome wide level, we constructed a cDNA library from A. japonicus Selenka (Aspidochirotida: Stichopodidae) after infecting them with Vibrio sp. for 48 h. Total RNA was extracted from the intestine, mesentery and coelomocyte of infected sea cucumber using Trizol and mRNA was isolated by Oligotex mRNA Kits. The ligated cDNAs were transformed into DH5α, and a library of 3.24×105 clones (3.24×105 cfu mL-1) was obtained with the sizes of inserted fragments ranging from 0.8 to 2.5 kb. Sequencing the cDNA clones resulted in a total of 1106 ESTs that passed the quality control. BlastX and BlastN searches have identified 168 (31.5%) ESTs sharing significant homology with known sequences in NCBI protein or nucleotide databases. Among a panel of 25 putative immunity-related genes, serum lectin isoform, complement component 3, complement component 3-like genes were further studied by real-time PCR and they all increased more than 5 fold in response to Vibrio sp. challenge. Our library provides a valuable molecular tool for future study of invertebrate immunity against bacterial infection and our gene expression data indicates the importance of the immune system in the evolution and development of sea cucumber.

A genomic library-based amplification approach (GL-PCR) for the mapping of multiple IS6110 insertion sites and strain differentiation of Mycobacterium tuberculosis.

PubMed

Namouchi, Amine; Mardassi, Helmi

2006-11-01

Evidence suggests that insertion of the IS6110 element is not without consequence to the biology of Mycobacterium tuberculosis complex strains. Thus, mapping of multiple IS6110 insertion sites in the genome of biomedically relevant clinical isolates would result in a better understanding of the role of this mobile element, particularly with regard to transmission, adaptability and virulence. In the present paper, we describe a versatile strategy, referred to as GL-PCR, that amplifies IS6110-flanking sequences based on the construction of a genomic library. M. tuberculosis chromosomal DNA is fully digested with HincII and then ligated into a plasmid vector between T7 and T3 promoter sequences. The ligation reaction product is transformed into Escherichia coli and selective PCR amplification targeting both 5' and 3' IS6110-flanking sequences are performed on the plasmid library DNA. For this purpose, four separate PCR reactions are performed, each combining an outward primer specific for one IS6110 end with either T7 or T3 primer. Determination of the nucleotide sequence of the PCR products generated from a single ligation reaction allowed mapping of 21 out of the 24 IS6110 copies of two 12 banded M. tuberculosis strains, yielding an overall sensitivity of 87,5%. Furthermore, by simply comparing the migration pattern of GL-PCR-generated products, the strategy proved to be as valuable as IS6110 RFLP for molecular typing of M. tuberculosis complex strains. Importantly, GL-PCR was able to discriminate between strains differing by a single IS6110 band.

Continuous air monitor filter changeout apparatus

DOEpatents

Rodgers, John C [Santa Fe, NM

2008-07-15

An apparatus and corresponding method for automatically changing out a filter cartridge in a continuous air monitor. The apparatus includes: a first container sized to hold filter cartridge replacements; a second container sized to hold used filter cartridges; a transport insert connectively attached to the first and second containers; a shuttle block, sized to hold the filter cartridges that is located within the transport insert; a transport driver mechanism means used to supply a motive force to move the shuttle block within the transport insert; and, a control means for operating the transport driver mechanism.

How AACR2 Will Affect a Medium Sized Library.

ERIC Educational Resources Information Center

Pang, Isabel S.

1980-01-01

Measures the impact of AACR2 on the catalog of a medium sized college library, using data collected from the Library of Congress announced changes. How to deal with these changes and estimate their costs is discussed. (Author/RAA)

Analysis of Environmental Friendly Library Based on the Satisfaction and Service Quality: study at Library “X”

NASA Astrophysics Data System (ADS)

Herdiansyah, Herdis; Satriya Utama, Andre; Safruddin; Hidayat, Heri; Gema Zuliana Irawan, Angga; Immanuel Tjandra Muliawan, R.; Mutia Pratiwi, Diana

2017-10-01

One of the factor that influenced the development of science is the existence of the library, which in this case is the college libraries. Library, which is located in the college environment, aims to supply collections of literatures to support research activities as well as educational for students of the college. Conceptually, every library now starts to practice environmental principles. For example, “X” library as a central library claims to be an environmental friendly library for practicing environmental friendly management, but the X library has not inserted the satisfaction and service aspect to the users, including whether it is true that environmental friendly process is perceived by library users. Satisfaction can be seen from the comparison between expectations and reality of library users. This paper analyzes the level of library user satisfaction with library services in the campus area and the gap between expectations and reality felt by the library users. The result of the research shows that there is a disparity between the hope of library management, which is sustainable and environmentally friendly with the reality in the management of the library, so that it has not given satisfaction to the users yet. The gap value of satisfaction that has the biggest difference is in the library collection with the value of 1.57; while for the smallest gap value is in the same service to all students with a value of 0.67.

Technical note: Computer-manufactured inserts for prosthetic sockets.

PubMed

Sanders, Joan E; McLean, Jake B; Cagle, John C; Gardner, David W; Allyn, Katheryn J

2016-08-01

The objective of this research was to use computer-aided design software and a tabletop 3-D additive manufacturing system to design and fabricate custom plastic inserts for trans-tibial prosthesis users. Shape quality of inserts was tested right after they were inserted into participant's test sockets and again after four weeks of wear. Inserts remained properly positioned and intact throughout testing. Right after insertion the inserts caused the socket to be slightly under-sized, by a mean of 0.11mm, approximately 55% of the thickness of a nylon sheath. After four weeks of wear the under-sizing was less, averaging 0.03mm, approximately 15% of the thickness of a nylon sheath. Thus the inserts settled into the sockets over time. If existing prosthetic design software packages were enhanced to conduct insert design and to automatically generate fabrication files for manufacturing, then computer manufactured inserts may offer advantages over traditional methods in terms of speed of fabrication, ease of design, modification, and record keeping. Copyright © 2016 IPEM. Published by Elsevier Ltd. All rights reserved.

Spectrum-to-Spectrum Searching Using a Proteome-wide Spectral Library*

PubMed Central

Yen, Chia-Yu; Houel, Stephane; Ahn, Natalie G.; Old, William M.

2011-01-01

The unambiguous assignment of tandem mass spectra (MS/MS) to peptide sequences remains a key unsolved problem in proteomics. Spectral library search strategies have emerged as a promising alternative for peptide identification, in which MS/MS spectra are directly compared against a reference library of confidently assigned spectra. Two problems relate to library size. First, reference spectral libraries are limited to rediscovery of previously identified peptides and are not applicable to new peptides, because of their incomplete coverage of the human proteome. Second, problems arise when searching a spectral library the size of the entire human proteome. We observed that traditional dot product scoring methods do not scale well with spectral library size, showing reduction in sensitivity when library size is increased. We show that this problem can be addressed by optimizing scoring metrics for spectrum-to-spectrum searches with large spectral libraries. MS/MS spectra for the 1.3 million predicted tryptic peptides in the human proteome are simulated using a kinetic fragmentation model (MassAnalyzer version2.1) to create a proteome-wide simulated spectral library. Searches of the simulated library increase MS/MS assignments by 24% compared with Mascot, when using probabilistic and rank based scoring methods. The proteome-wide coverage of the simulated library leads to 11% increase in unique peptide assignments, compared with parallel searches of a reference spectral library. Further improvement is attained when reference spectra and simulated spectra are combined into a hybrid spectral library, yielding 52% increased MS/MS assignments compared with Mascot searches. Our study demonstrates the advantages of using probabilistic and rank based scores to improve performance of spectrum-to-spectrum search strategies. PMID:21532008

Identification of immune protective genes of Eimeria maxima through cDNA expression library screening.

PubMed

Yang, XinChao; Li, MengHui; Liu, JianHua; Ji, YiHong; Li, XiangRui; Xu, LiXin; Yan, RuoFeng; Song, XiaoKai

2017-02-16

Eimeria maxima is one of the most prevalent Eimeria species causing avian coccidiosis, and results in huge economic loss to the global poultry industry. Current control strategies, such as anti-coccidial medication and live vaccines have been limited because of their drawbacks. The third generation anticoccidial vaccines including the recombinant vaccines as well as DNA vaccines have been suggested as a promising alternative strategy. To date, only a few protective antigens of E. maxima have been reported. Hence, there is an urgent need to identify novel protective antigens of E. maxima for the development of neotype anticoccidial vaccines. With the aim of identifying novel protective genes of E. maxima, a cDNA expression library of E. maxima sporozoites was constructed using Gateway technology. Subsequently, the cDNA expression library was divided into 15 sub-libraries for cDNA expression library immunization (cDELI) using parasite challenged model in chickens. Protective sub-libraries were selected for the next round of screening until individual protective clones were obtained, which were further sequenced and analyzed. Adopting the Gateway technology, a high-quality entry library was constructed, containing 9.2 × 10 6 clones with an average inserted fragments length of 1.63 kb. The expression library capacity was 2.32 × 10 7 colony-forming units (cfu) with an average inserted fragments length of 1.64 Kb. The expression library was screened using parasite challenged model in chickens. The screening yielded 6 immune protective genes including four novel protective genes of EmJS-1, EmRP, EmHP-1 and EmHP-2, and two known protective genes of EmSAG and EmCKRS. EmJS-1 is the selR domain-containing protein of E. maxima whose function is unknown. EmHP-1 and EmHP-2 are the hypothetical proteins of E. maxima. EmRP and EmSAG are rhomboid-like protein and surface antigen glycoproteins of E. maxima respectively, and involved in invasion of the parasite. Our results provide a cDNA expression library for further screening of T cell stimulating or inhibiting antigens of E. maxima. Moreover, our results provide six candidate protective antigens for developing new vaccines against E. maxima.

In vivo insertion pool sequencing identifies virulence factors in a complex fungal–host interaction

PubMed Central

Uhse, Simon; Pflug, Florian G.; Stirnberg, Alexandra; Ehrlinger, Klaus; von Haeseler, Arndt

2018-01-01

Large-scale insertional mutagenesis screens can be powerful genome-wide tools if they are streamlined with efficient downstream analysis, which is a serious bottleneck in complex biological systems. A major impediment to the success of next-generation sequencing (NGS)-based screens for virulence factors is that the genetic material of pathogens is often underrepresented within the eukaryotic host, making detection extremely challenging. We therefore established insertion Pool-Sequencing (iPool-Seq) on maize infected with the biotrophic fungus U. maydis. iPool-Seq features tagmentation, unique molecular barcodes, and affinity purification of pathogen insertion mutant DNA from in vivo-infected tissues. In a proof of concept using iPool-Seq, we identified 28 virulence factors, including 23 that were previously uncharacterized, from an initial pool of 195 candidate effector mutants. Because of its sensitivity and quantitative nature, iPool-Seq can be applied to any insertional mutagenesis library and is especially suitable for genetically complex setups like pooled infections of eukaryotic hosts. PMID:29684023

Using Phage Display to Create Recombinant Antibodies.

PubMed

Dasch, James R; Dasch, Amy L

2017-09-01

A variety of phage display technologies have been developed since the approach was first described for antibodies. The most widely used approaches incorporate antibody sequences into the minor coat protein pIII of the nonlytic filamentous phage fd or M13. Libraries of variable gene sequences, encoding either scFv or Fab fragments, are made by incorporating sequences into phagemid vectors. The phagemid is packaged into phage particles with the assistance of a helper phage to produce the antibody display phage. This protocol describes a method for creating a phagemid library. The multiple cloning site (MCS) of the pBluescript KS(-) phagemid vector is replaced by digestion with the restriction enzyme BssHII, followed by the insertion of four overlapping oligonucleotides to create a new MCS within the vector. Next, the 3' portion of gene III (from M13mp18) is amplified and combined with an antibody sequence using overlap extension PCR. This product is inserted into the phagemid vector to create pPDS. Two helper plasmids are also created from the modified pBluescript vector: pLINK provides the linker between the heavy and light chains, and pFABC provides the CH1 domain of the heavy chain. An antibody cDNA library is constructed from the RNA of interest and ligated into pPDS. The phagemid library is electroporated into Escherichia coli cells along with the VCS-M13 helper phage. © 2017 Cold Spring Harbor Laboratory Press.

Direct and inverted reciprocal chromosome insertions between chromosomes 7 and 14 in a woman with recurrent miscarriages

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

Ying-Tai Wang; Zhao-Cai Wang; Bajalica, S.

We present the first case of direct and inverted reciprocal chromosome insertions between human chromosomes 7 and 14, ascertained because of repeated spontaneous abortions. Prometaphase GTG banding analysis showed the karyotype to be 46, XX, inv ins (7;14)(7pter {yields} 7q11.23::14q32.2 {yields} 14q22::7q21.2 {yields} 7qter), dir ins(14;7)(14pter {yields} 14q22::7q11.23 {yields} 7q21.2::14q32.2 {yields} 14qter). Origins of the insertion have been confirmed by chromosome painting with libraries specific for chromosomes 7 and 14 using fluorescence in situ hybridization. 5 refs., 3 figs.

Generation of mariner-based transposon insertion mutant library of Bacillus sphaericus 2297 and investigation of genes involved in sporulation and mosquito-larvicidal crystal protein synthesis.

PubMed

Wu, Yiming; Hu, Xiaomin; Ge, Yong; Zheng, Dasheng; Yuan, Zhiming

2012-05-01

Bacillus sphaericus has been used with great success in mosquito control programs worldwide. Under conditions of nutrient limitation, it undergoes sporulation via a series of well defined morphological stages. However, only a small number of genes involved in sporulation have been identified. To identify genes associated with sporulation, and to understand the relationship between sporulation and crystal protein synthesis, a random mariner-based transposon insertion mutant library of B. sphaericus strain 2297 was constructed and seven sporulation-defective mutants were selected. Sequencing of the DNA flanking of the transposon insertion identified several genes involved in sporulation. The morphologies of mutants were determined by electron microscopy and synthesis of crystal proteins was analyzed by SDS-PAGE and Western blot. Four mutants blocked at early stages of sporulation failed to produce crystal proteins and had lower larvicidal activity. However, the other three mutants were blocked at later stages and were able to form crystal proteins, and the larvicidal activity was similar to wild type. These results indicated that crystal protein synthesis in B. sphaericus is dependent on sporulation initiation. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

PERMutation Using Transposase Engineering (PERMUTE): A Simple Approach for Constructing Circularly Permuted Protein Libraries.

PubMed

Jones, Alicia M; Atkinson, Joshua T; Silberg, Jonathan J

2017-01-01

Rearrangements that alter the order of a protein's sequence are used in the lab to study protein folding, improve activity, and build molecular switches. One of the simplest ways to rearrange a protein sequence is through random circular permutation, where native protein termini are linked together and new termini are created elsewhere through random backbone fission. Transposase mutagenesis has emerged as a simple way to generate libraries encoding different circularly permuted variants of proteins. With this approach, a synthetic transposon (called a permuteposon) is randomly inserted throughout a circularized gene to generate vectors that express different permuted variants of a protein. In this chapter, we outline the protocol for constructing combinatorial libraries of circularly permuted proteins using transposase mutagenesis, and we describe the different permuteposons that have been developed to facilitate library construction.

Sequencing cDNAs: An Introduction to DNA Sequence Analysis in the Undergraduate Molecular Genetics Course.

ERIC Educational Resources Information Center

Galewsky, Samuel

2000-01-01

Introduces a series of molecular genetics laboratories where students pick a single colony from a Drosophila melanogester embryo cDNA library and purify the plasmid, then analyze the insert through restriction digests and gel electrophoresis. (Author/YDS)

Genome-wide mutant profiling predicts the mechanism of a Lipid II binding antibiotic.

PubMed

Santiago, Marina; Lee, Wonsik; Fayad, Antoine Abou; Coe, Kathryn A; Rajagopal, Mithila; Do, Truc; Hennessen, Fabienne; Srisuknimit, Veerasak; Müller, Rolf; Meredith, Timothy C; Walker, Suzanne

2018-06-01

Identifying targets of antibacterial compounds remains a challenging step in the development of antibiotics. We have developed a two-pronged functional genomics approach to predict mechanism of action that uses mutant fitness data from antibiotic-treated transposon libraries containing both upregulation and inactivation mutants. We treated a Staphylococcus aureus transposon library containing 690,000 unique insertions with 32 antibiotics. Upregulation signatures identified from directional biases in insertions revealed known molecular targets and resistance mechanisms for the majority of these. Because single-gene upregulation does not always confer resistance, we used a complementary machine-learning approach to predict the mechanism from inactivation mutant fitness profiles. This approach suggested the cell wall precursor Lipid II as the molecular target of the lysocins, a mechanism we have confirmed. We conclude that docking to membrane-anchored Lipid II precedes the selective bacteriolysis that distinguishes these lytic natural products, showing the utility of our approach for nominating the antibiotic mechanism of action.

A library of MiMICs allows tagging of genes and reversible, spatial and temporal knockdown of proteins in Drosophila

PubMed Central

Nagarkar-Jaiswal, Sonal; Lee, Pei-Tseng; Campbell, Megan E; Chen, Kuchuan; Anguiano-Zarate, Stephanie; Cantu Gutierrez, Manuel; Busby, Theodore; Lin, Wen-Wen; He, Yuchun; Schulze, Karen L; Booth, Benjamin W; Evans-Holm, Martha; Venken, Koen JT; Levis, Robert W; Spradling, Allan C; Hoskins, Roger A; Bellen, Hugo J

2015-01-01

Here, we document a collection of ∼7434 MiMIC (Minos Mediated Integration Cassette) insertions of which 2854 are inserted in coding introns. They allowed us to create a library of 400 GFP-tagged genes. We show that 72% of internally tagged proteins are functional, and that more than 90% can be imaged in unfixed tissues. Moreover, the tagged mRNAs can be knocked down by RNAi against GFP (iGFPi), and the tagged proteins can be efficiently knocked down by deGradFP technology. The phenotypes associated with RNA and protein knockdown typically correspond to severe loss of function or null mutant phenotypes. Finally, we demonstrate reversible, spatial, and temporal knockdown of tagged proteins in larvae and adult flies. This new strategy and collection of strains allows unprecedented in vivo manipulations in flies for many genes. These strategies will likely extend to vertebrates. DOI: http://dx.doi.org/10.7554/eLife.05338.001 PMID:25824290

Constructing high complexity synthetic libraries of long ORFs using in vitro selection

NASA Technical Reports Server (NTRS)

Cho, G.; Keefe, A. D.; Liu, R.; Wilson, D. S.; Szostak, J. W.

2000-01-01

We present a method that can significantly increase the complexity of protein libraries used for in vitro or in vivo protein selection experiments. Protein libraries are often encoded by chemically synthesized DNA, in which part of the open reading frame is randomized. There are, however, major obstacles associated with the chemical synthesis of long open reading frames, especially those containing random segments. Insertions and deletions that occur during chemical synthesis cause frameshifts, and stop codons in the random region will cause premature termination. These problems can together greatly reduce the number of full-length synthetic genes in the library. We describe a strategy in which smaller segments of the synthetic open reading frame are selected in vitro using mRNA display for the absence of frameshifts and stop codons. These smaller segments are then ligated together to form combinatorial libraries of long uninterrupted open reading frames. This process can increase the number of full-length open reading frames in libraries by up to two orders of magnitude, resulting in protein libraries with complexities of greater than 10(13). We have used this methodology to generate three types of displayed protein library: a completely random sequence library, a library of concatemerized oligopeptide cassettes with a propensity for forming amphipathic alpha-helical or beta-strand structures, and a library based on one of the most common enzymatic scaffolds, the alpha/beta (TIM) barrel. Copyright 2000 Academic Press.

Taxonomic and functional assignment of cloned sequences from high Andean forest soil metagenome.

PubMed

Montaña, José Salvador; Jiménez, Diego Javier; Hernández, Mónica; Angel, Tatiana; Baena, Sandra

2012-02-01

Total metagenomic DNA was isolated from high Andean forest soil and subjected to taxonomical and functional composition analyses by means of clone library generation and sequencing. The obtained yield of 1.7 μg of DNA/g of soil was used to construct a metagenomic library of approximately 20,000 clones (in the plasmid p-Bluescript II SK+) with an average insert size of 4 Kb, covering 80 Mb of the total metagenomic DNA. Metagenomic sequences near the plasmid cloning site were sequenced and them trimmed and assembled, obtaining 299 reads and 31 contigs (0.3 Mb). Taxonomic assignment of total sequences was performed by BLASTX, resulting in 68.8, 44.8 and 24.5% classification into taxonomic groups using the metagenomic RAST server v2.0, WebCARMA v1.0 online system and MetaGenome Analyzer v3.8 software, respectively. Most clone sequences were classified as Bacteria belonging to phlya Actinobacteria, Proteobacteria and Acidobacteria. Among the most represented orders were Actinomycetales (34% average), Rhizobiales, Burkholderiales and Myxococcales and with a greater number of sequences in the genus Mycobacterium (7% average), Frankia, Streptomyces and Bradyrhizobium. The vast majority of sequences were associated with the metabolism of carbohydrates, proteins, lipids and catalytic functions, such as phosphatases, glycosyltransferases, dehydrogenases, methyltransferases, dehydratases and epoxide hydrolases. In this study we compared different methods of taxonomic and functional assignment of metagenomic clone sequences to evaluate microbial diversity in an unexplored soil ecosystem, searching for putative enzymes of biotechnological interest and generating important information for further functional screening of clone libraries.

The protein structure prediction problem could be solved using the current PDB library

PubMed Central

Zhang, Yang; Skolnick, Jeffrey

2005-01-01

For single-domain proteins, we examine the completeness of the structures in the current Protein Data Bank (PDB) library for use in full-length model construction of unknown sequences. To address this issue, we employ a comprehensive benchmark set of 1,489 medium-size proteins that cover the PDB at the level of 35% sequence identity and identify templates by structure alignment. With homologous proteins excluded, we can always find similar folds to native with an average rms deviation (RMSD) from native of 2.5 Å with ≈82% alignment coverage. These template structures often contain a significant number of insertions/deletions. The tasser algorithm was applied to build full-length models, where continuous fragments are excised from the top-scoring templates and reassembled under the guide of an optimized force field, which includes consensus restraints taken from the templates and knowledge-based statistical potentials. For almost all targets (except for 2/1,489), the resultant full-length models have an RMSD to native below 6 Å (97% of them below 4 Å). On average, the RMSD of full-length models is 2.25 Å, with aligned regions improved from 2.5 Å to 1.88 Å, comparable with the accuracy of low-resolution experimental structures. Furthermore, starting from state-of-the-art structural alignments, we demonstrate a methodology that can consistently bring template-based alignments closer to native. These results are highly suggestive that the protein-folding problem can in principle be solved based on the current PDB library by developing efficient fold recognition algorithms that can recover such initial alignments. PMID:15653774

[Construction of forward and reverse subtracted cDNA libraries between muscle tissue of Meishan and Landrace pigs].

PubMed

Xu, De-Quan; Zhang, Yi-Bing; Xiong, Yuan-Zhu; Gui, Jian-Fang; Jiang, Si-Wen; Su, Yu-Hong

2003-07-01

Using suppression subtractive hybridization (SSH) technique, forward and reverse subtracted cDNA libraries were constructed between Longissimus muscles from Meishan and Landrace pigs. A housekeeping gene, G3PDH, was used to estimate the efficiency of subtractive cDNA. In two cDNA libraries, G3PDH was subtracted very efficiently at appropriate 2(10) and 2(5) folds, respectively, indicating that some differentially expressed genes were also enriched at the same folds and the two subtractive cDNA libraries were very successful. A total of 709 and 673 positive clones were isolated from forward and reverse subtracted cDNA libraries, respectively. Analysis of PCR showed that most of all plasmids in the clones contained 150-750 bp inserts. The construction of subtractive cDNA libraries between muscle tissue from different pig breeds laid solid foundations for isolating and identifying the genes determining muscle growth and meat quality, which will be important to understand the mechanism of muscle growth, determination of meat quality and practice of molecular breeding.

Survey of microsatellite DNA in pine

Treesearch

C. S. Echt; P. May-Marquardt

1997-01-01

A large insert genomic library from eastern white pine (Pinus strobus) was probed for the microsatellite motifs (AC)n and (AG)n, all 10 trinucleotide motifs, and 22 of the 33 possible tetranucleotide motifs. For comparison with a species from a different subgenus, a loblolly pine (Pinus taeda...

Survey of microsatellite DNA in pine

Treesearch

Craig S. Echt; P. May-Marquardt

1997-01-01

A large insert genomic library from eastern white pine (Pinus strobus) was probed for the microsatellite motifs (AC)n and (AG)n, all 10 trinucleotide motifs, and 22 of the 33 possible tetranucleotide motifs. For comparison with a species from a different subgenus, a loblolly pine (Pinus taeda) genomic...

Practice variation in surgical procedures and IUD-insertions among general practitioners in Norway - a longitudinal study.

PubMed

Pahle, Andreas Saxlund; Sørli, Daniel; Kristiansen, Ivar Sønbø; Deraas, Trygve S; Halvorsen, Peder A

2017-01-21

Studies of Primary Health Care (PHC) reveal considerable practice variations in terms of the range of services provided. In Norway, general practitioners (GPs) are traditionally expected to perform IUD-insertions and several surgical procedures as a part of comprehensive PHC. We aimed to investigate variation in the provision of surgical procedures and IUD-insertions across GPs and over time and explore determinants of such variation. Retrospective registry study of Norwegian GPs. From a comprehensive database of GPs' reimbursement claims, we obtained procedure codes and GP characteristics such as age, gender, list size and municipality characteristics from 2006 through 2013. Multivariable logistic regression models were fitted to explore determinants of practice variation. We extracted data from 4,828 GPs. In 2013, 91.0, 76.1 and 74.8% were reimbursed at least once for minor and major surgical procedures and IUD-insertion, respectively. Female GPs had lower odds for performing major surgical procedures (OR 0.38, 95% CI 0.32-0.45) and higher odds for performing IUD-insertions (OR 6.28, 95% CI 4.47-8.82) than male GPs. Older GPs and GPs with shorter patient lists were less likely to perform surgical procedures. GPs with longer patient lists had higher odds for performing IUD-insertions. The proportion of GPs performing surgical procedures increased over time, while the proportion decreased for IUD-insertions. The number of IUD-insertions in specialist care increased from 12,575 in 2011 to 15 216 (+21.0%) in 2014. We observed a large variation in the provision of surgical procedures and IUD-insertions amongst GPs in Norway. The GPs' age, gender, list size and size of municipality were associated with performing the procedures. Our findings suggest a shift of IUD-insertions from primary to specialist care.

Retrotransposon Capture Sequencing (RC-Seq): A Targeted, High-Throughput Approach to Resolve Somatic L1 Retrotransposition in Humans.

PubMed

Sanchez-Luque, Francisco J; Richardson, Sandra R; Faulkner, Geoffrey J

2016-01-01

Mobile genetic elements (MGEs) are of critical importance in genomics and developmental biology. Polymorphic and somatic MGE insertions have the potential to impact the phenotype of an individual, depending on their genomic locations and functional consequences. However, the identification of polymorphic and somatic insertions among the plethora of copies residing in the genome presents a formidable technical challenge. Whole genome sequencing has the potential to address this problem; however, its efficacy depends on the abundance of cells carrying the new insertion. Robust detection of somatic insertions present in only a subset of cells within a given sample can also be prohibitively expensive due to a requirement for high sequencing depth. Here, we describe retrotransposon capture sequencing (RC-seq), a sequence capture approach in which Illumina libraries are enriched for fragments containing the 5' and 3' termini of specific MGEs. RC-seq allows the detection of known polymorphic insertions present in an individual, as well as the identification of rare or private germline insertions not previously described. Furthermore, RC-seq can be used to detect and characterize somatic insertions, providing a valuable tool to elucidate the extent and characteristics of MGE activity in healthy tissues and in various disease states.

Identification of Mycobacterial Genes Involved in Antibiotic Sensitivity: Implications for the Treatment of Tuberculosis with β-Lactam-Containing Regimens

PubMed Central

Viswanathan, Gopinath; Yadav, Sangya

2017-01-01

ABSTRACT In a Mycobacterium smegmatis mutant library screen, transposon mutants with insertions in fhaA, dprE2, rpsT, and parA displayed hypersusceptibility to antibiotics, including the β-lactams meropenem, ampicillin, amoxicillin, and cefotaxime. Sub-MIC levels of octoclothepin, a psychotic drug inhibiting ParA, phenocopied the parA insertion and enhanced the bactericidal activity of meropenem against Mycobacterium tuberculosis in combination with clavulanate. Our study identifies novel factors associated with antibiotic resistance, with implications in repurposing β-lactams for tuberculosis treatment. PMID:28438925

Reaching High Bookshelves From a Wheelchair

NASA Technical Reports Server (NTRS)

Walch, A. J.

1982-01-01

"Book retriever" allows people confined to wheelchairs to remove or replace books from upper shelves of library stacks. Retriever is mechanical device composed of aluminum tube approximately 5 feet long with two jaws at upper end. Jaws securely clamp selected book; they are thin enough to be inserted between adjacent books.

Development of microsatellites from Fothergilla xintermedia (Hamamelidaceae) and cross transfer to four other genera within Hamamelidaceae

USDA-ARS?s Scientific Manuscript database

Premise of the study: Develop microsatellites from Fothergilla ×intermedia to establish loci capable of distinguishing species and cultivars, and assess genetic diversity for use by ornamental breeders, and for transfer within Hamamelidaceae. Methods and Results: A small insert genomic library enric...

Identification of genes differentially expressed in association with acquired cisplatin resistance

PubMed Central

Johnsson, A; Zeelenberg, I; Min, Y; Hilinski, J; Berry, C; Howell, S B; Los, G

2000-01-01

The goal of this study was to identify genes whose mRNA levels are differentially expressed in human cells with acquired cisplatin (cDDP) resistance. Using the parental UMSCC10b head and neck carcinoma cell line and the 5.9-fold cDDP-resistant subline, UMSCC10b/Pt-S15, two suppressive subtraction hybridization (SSH) cDNA libraries were prepared. One library represented mRNAs whose levels were increased in the cDDP resistant variant (the UP library), the other one represented mRNAs whose levels were decreased in the resistant cells (the DOWN library). Arrays constructed with inserts recovered from these libraries were hybridized with SSH products to identify truly differentially expressed elements. A total of 51 cDNA fragments present in the UP library and 16 in the DOWN library met the criteria established for differential expression. The sequences of 87% of these cDNA fragments were identified in Genbank. Among the mRNAs in the UP library that were frequently isolated and that showed high levels of differential expression were cytochrome oxidase I, ribosomal protein 28S, elongation factor 1α, α-enolase, stathmin, and HSP70. The approach taken in this study permitted identification of many genes never before linked to the cDDP-resistant phenotype. © 2000 Cancer Research Campaign PMID:10993653

Final incision size after cataract surgery with toric intraocular lens implantation using 2 techniques.

PubMed

Guarnieri, Adriano; Moreno-Montañés, Javier; Sabater, Alfonso L; Gosende-Chico, Inmaculada; Bonet-Farriol, Elvira

2013-11-01

To analyze the changes in incision sizes after implantation of a toric intraocular lens (IOL) using 2 methods. Department of Ophthalmology, Clínica Universidad de Navarra, Pamplona, Spain. Prospective case series. Coaxial phacoemulsification and IOL implantation through a 2.2 mm clear corneal incision using a cartridge injector were performed. Wound-assisted or cartridge-insertion techniques were used to implant the IOLs. The results were analyzed according to IOL spherical and cylindrical powers. Corneal hysteresis (CH) and the corneal resistance factor (CRF) were measured and evaluated based on the changes in incision size. Incision size increased in 30 (41.7%) of 72 eyes in the wound-assisted group and 71 (98.6%) of 72 eyes in the cartridge-insertion group. The mean incision size after IOL implantation was 2.27 mm ± 0.06 (SD) and 2.37 ± 0.05 mm, respectively (P<.01). The final incision size and IOL spherical power in the wound-assisted technique group (P=.02) and the cartridge-insertion technique group (P=.03) were correlated significantly; IOL toricity was not (P=.19 and P=.28, respectively). The CH and CRF values were not correlated with the final incision size. The final incision size and the changes in incision size after IOL implantation were greater with the cartridge-insertion technique than with the wound-assisted technique. The increase was related to IOL spherical power in both groups but not to IOL toricity. Corneal biomechanical properties were not correlated with the final incision size. Copyright © 2013 ASCRS and ESCRS. Published by Elsevier Inc. All rights reserved.

Inter and intra-system size variability of reverse shoulder arthroplasty polyethylene inserts

PubMed Central

Teeter, Matthew G.; Dawson, Matthew T.; Athwal, George S.

2016-01-01

Background: As the incidence of reverse shoulder arthroplasty (RSA) increases, so will the revision burden. At times, the revision surgeon may be faced with a well-fixed component on one side of the joint and revision implants from a different manufacturer. The ability to use glenoid and humeral implants from different manufacturers could simplify the revision procedure. This study hypothesized that across a range of RSA systems, some implants would demonstrate high size compatibility and others would demonstrate low compatibility. Materials and Methods: Six polyethylene inserts each from eight reverse total shoulder arthroplasty systems were examined (48 total inserts). All inserts were scanned using a laboratory micro-computed tomography scanner at 50 μm isotropic voxel spacing, and their surface geometries were reconstructed. The different implant geometries were co-registered, and the three-dimensional (3D) variability between the articular surfaces of the different implant systems was measured. Intrasystem manufacturing variability was also determined by measuring the 3D variability of inserts from the same system. Results: The intersystem polyethylene articular surface deviations between same-size systems were not significantly different (P = 0.61) and were a mean maximum of 60 ± 16 μm (range: 30-80 μm). Intrasystem manufacturing variability was equivalent between all but two models, averaging 49 ± 17 μm (range: 23-99 μm). Discussion: Differences in articular geometry between same-size inserts from different systems were on the same scale as intrasystem manufacturing variability, suggesting that different implant systems of the same nominal diameter could potentially be used interchangeably in revision or extenuating circumstances. Conclusion: The results of this study suggest that surgeons can theoretically interchange same-sized implant components from the different RSA systems tested when conducting revisions. PMID:26980984

Amino acid Alphabet Size in Protein Evolution Experiments: Better to Search a Small library Thoroughly or a Large Library Sparsely?

PubMed Central

Muñoz, Enrique

2015-01-01

We compare the results obtained from searching a smaller library thoroughly versus searching a more diverse, larger library sparsely. We study protein evolution with reduced amino acid alphabets, by simulating directed evolution experiments at three different alphabet sizes: 20, 5 and 2. We employ a physical model for evolution, the generalized NK model, that has proved successful in modeling protein evolution, antibody evolution, and T cell selection. We find that antibodies with higher affinity are found by searching a library with a larger alphabet sparsely than by searching a smaller library thoroughly, even with well-designed reduced libraries. We find ranked amino acid usage frequencies in agreement with observations of the CDR-H3 variable region of human antibodies. PMID:18375453

The State of Planning of Automation Projects in the Libraries of Canada.

ERIC Educational Resources Information Center

Clement, Hope E. A.

Library automation in Canada is complicated by the large size, dispersed population, and cultural diversity of the country. The National Library of Canada is actively planning a Canadian library network based on national bibliographic services for which the library is now developing automated systems. Canadian libraries are involved in the…

Analysis of Current DNA Encoded Library Screening Data Indicates Higher False Negative Rates for Numerically Larger Libraries.

PubMed

Satz, Alexander L; Hochstrasser, Remo; Petersen, Ann C

2017-04-10

To optimize future DNA-encoded library design, we have attempted to quantify the library size at which the signal becomes undetectable. To accomplish this we (i) have calculated that percent yields of individual library members following a screen range from 0.002 to 1%, (ii) extrapolated that ∼1 million copies per library member are required at the outset of a screen, and (iii) from this extrapolation predict that false negative rates will begin to outweigh the benefit of increased diversity at library sizes >10 8 . The above analysis is based upon a large internal data set comprising multiple screens, targets, and libraries; we also augmented our internal data with all currently available literature data. In theory, high false negative rates may be overcome by employing larger amounts of library; however, we argue that using more than currently reported amounts of library (≫10 nmoles) is impractical. The above conclusions may be generally applicable to other DNA encoded library platforms, particularly those platforms that do not allow for library amplification.

Evaluation and optimisation of preparative semi-automated electrophoresis systems for Illumina library preparation.

PubMed

Quail, Michael A; Gu, Yong; Swerdlow, Harold; Mayho, Matthew

2012-12-01

Size selection can be a critical step in preparation of next-generation sequencing libraries. Traditional methods employing gel electrophoresis lack reproducibility, are labour intensive, do not scale well and employ hazardous interchelating dyes. In a high-throughput setting, solid-phase reversible immobilisation beads are commonly used for size-selection, but result in quite a broad fragment size range. We have evaluated and optimised the use of two semi-automated preparative DNA electrophoresis systems, the Caliper Labchip XT and the Sage Science Pippin Prep, for size selection of Illumina sequencing libraries. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

SAR by Oxime-Containing Peptide Libraries: Application to Tsg101 Ligand Optimization

PubMed Central

Liu, Fa; Stephen, Andrew G.; Waheed, Abdul A.; Aman, M. Javad; Freed, Eric O.; Fisher, Robert J.; Burke, Terrence R.

2008-01-01

HIV-1 viral assembly requires a direct interaction between a Pro-Thr-Ala-Pro (“PTAP”) motif in the viral protein Gag-p6 and the cellular endosomal sorting factor Tsg101. In an effort to develop competitive inhibitors of this interaction, an SAR study was conducted based on the application of post solid-phase oxime formation involving the sequential insertion of aminooxy-containing residues within a nonamer parent peptide followed by reaction with libraries of aldehydes. Approximately 15–20-fold enhancement in binding affinity was achieved by this approach. PMID:18655064

Going, going, gone: predicting the fate of genomic insertions in plant RNA viruses.

PubMed

Willemsen, Anouk; Carrasco, José L; Elena, Santiago F; Zwart, Mark P

2018-05-10

Horizontal gene transfer is common among viruses, while they also have highly compact genomes and tend to lose artificial genomic insertions rapidly. Understanding the stability of genomic insertions in viral genomes is therefore relevant for explaining and predicting their evolutionary patterns. Here, we revisit a large body of experimental research on a plant RNA virus, tobacco etch potyvirus (TEV), to identify the patterns underlying the stability of a range of homologous and heterologous insertions in the viral genome. We obtained a wide range of estimates for the recombination rate-the rate at which deletions removing the insertion occur-and these appeared to be independent of the type of insertion and its location. Of the factors we considered, recombination rate was the best predictor of insertion stability, although we could not identify the specific sequence characteristics that would help predict insertion instability. We also considered experimentally the possibility that functional insertions lead to higher mutational robustness through increased redundancy. However, our observations suggest that both functional and non-functional increases in genome size decreased the mutational robustness. Our results therefore demonstrate the importance of recombination rates for predicting the long-term stability and evolution of viral RNA genomes and suggest that there are unexpected drawbacks to increases in genome size for mutational robustness.

Systematic cloning of human minisatellites from ordered array charomid libraries.

PubMed

Armour, J A; Povey, S; Jeremiah, S; Jeffreys, A J

1990-11-01

We present a rapid and efficient method for the isolation of minisatellite loci from human DNA. The method combines cloning a size-selected fraction of human MboI DNA fragments in a charomid vector with hybridization screening of the library in ordered array. Size-selection of large MboI fragments enriches for the longer, more variable minisatellites and reduces the size of the library required. The library was screened with a series of multi-locus probes known to detect a large number of hypervariable loci in human DNA. The gridded library allowed both the rapid processing of positive clones and the comparative evaluation of the different multi-locus probes used, in terms of both the relative success in detecting hypervariable loci and the degree of overlap between the sets of loci detected. We report 23 new human minisatellite loci isolated by this method, which map to 14 autosomes and the sex chromosomes.

Suppressive subtractive hybridization approach revealed differential expression of hypersensitive response and reactive oxygen species production genes in tea (Camellia sinensis (L.) O. Kuntze) leaves during Pestalotiopsis thea infection.

PubMed

Senthilkumar, Palanisamy; Thirugnanasambantham, Krishnaraj; Mandal, Abul Kalam Azad

2012-12-01

Tea (Camellia sinensis (L.) O. Kuntze) is an economically important plant cultivated for its leaves. Infection of Pestalotiopsis theae in leaves causes gray blight disease and enormous loss to the tea industry. We used suppressive subtractive hybridization (SSH) technique to unravel the differential gene expression pattern during gray blight disease development in tea. Complementary DNA from P. theae-infected and uninfected leaves of disease tolerant cultivar UPASI-10 was used as tester and driver populations respectively. Subtraction efficiency was confirmed by comparing abundance of β-actin gene. A total of 377 and 720 clones with insert size >250 bp from forward and reverse library respectively were sequenced and analyzed. Basic Local Alignment Search Tool analysis revealed 17 sequences in forward SSH library have high degree of similarity with disease and hypersensitive response related genes and 20 sequences with hypothetical proteins while in reverse SSH library, 23 sequences have high degree of similarity with disease and stress response-related genes and 15 sequences with hypothetical proteins. Functional analysis indicated unknown (61 and 59 %) or hypothetical functions (23 and 18 %) for most of the differentially regulated genes in forward and reverse SSH library, respectively, while others have important role in different cellular activities. Majority of the upregulated genes are related to hypersensitive response and reactive oxygen species production. Based on these expressed sequence tag data, putative role of differentially expressed genes were discussed in relation to disease. We also demonstrated the efficiency of SSH as a tool in enriching gray blight disease related up- and downregulated genes in tea. The present study revealed that many genes related to disease resistance were suppressed during P. theae infection and enhancing these genes by the application of inducers may impart better disease tolerance to the plants.

Some Observations On the Architectural Style, Size and Cost of Libraries

ERIC Educational Resources Information Center

Ellsworth, Ralph E.

1975-01-01

The architectural style of academic library buildings of today reflect as accurately the status of the library and the state of building technology as did the academic libraries of 80 to 100 years ago. (Author/PF)

Transposable element distribution, abundance and role in genome size variation in the genus Oryza.

PubMed

Zuccolo, Andrea; Sebastian, Aswathy; Talag, Jayson; Yu, Yeisoo; Kim, HyeRan; Collura, Kristi; Kudrna, Dave; Wing, Rod A

2007-08-29

The genus Oryza is composed of 10 distinct genome types, 6 diploid and 4 polyploid, and includes the world's most important food crop - rice (Oryza sativa [AA]). Genome size variation in the Oryza is more than 3-fold and ranges from 357 Mbp in Oryza glaberrima [AA] to 1283 Mbp in the polyploid Oryza ridleyi [HHJJ]. Because repetitive elements are known to play a significant role in genome size variation, we constructed random sheared small insert genomic libraries from 12 representative Oryza species and conducted a comprehensive study of the repetitive element composition, distribution and phylogeny in this genus. Particular attention was paid to the role played by the most important classes of transposable elements (Long Terminal Repeats Retrotransposons, Long interspersed Nuclear Elements, helitrons, DNA transposable elements) in shaping these genomes and in their contributing to genome size variation. We identified the elements primarily responsible for the most strikingly genome size variation in Oryza. We demonstrated how Long Terminal Repeat retrotransposons belonging to the same families have proliferated to very different extents in various species. We also showed that the pool of Long Terminal Repeat Retrotransposons is substantially conserved and ubiquitous throughout the Oryza and so its origin is ancient and its existence predates the speciation events that originated the genus. Finally we described the peculiar behavior of repeats in the species Oryza coarctata [HHKK] whose placement in the Oryza genus is controversial. Long Terminal Repeat retrotransposons are the major component of the Oryza genomes analyzed and, along with polyploidization, are the most important contributors to the genome size variation across the Oryza genus. Two families of Ty3-gypsy elements (RIRE2 and Atlantys) account for a significant portion of the genome size variations present in the Oryza genus.

Designing using manufacturing features

NASA Astrophysics Data System (ADS)

Szecsi, T.; Hoque, A. S. M.

2012-04-01

This paper presents a design system that enables the composition of a part using manufacturing features. Features are selected from feature libraries. Upon insertion, the system ensures that the feature does not contradict the design-for-manufacture rules. This helps eliminating costly manufacturing problems. The system is developed as an extension to a commercial CAD/CAM system Pro/Engineer.

Development and characterization of simple sequence repeats for Bipolaris sokiniana and cross transferability to related species

USDA-ARS?s Scientific Manuscript database

Simple sequence repeats (SSR) markers were developed from a small insert genomic library for Bipolaris sorokiniana, a mitosporic fungal pathogen that causes spot blotch and root rot in switchgrass. About 59% of sequenced clones (n=384) harbored various SSR motifs. After eliminating the redundant seq...

High-Throughput Sequencing of Campylobacter jejuni Insertion Mutant Libraries Reveals mapA as a Fitness Factor for Chicken Colonization

PubMed Central

Johnson, Jeremiah G.; Livny, Jonathan

2014-01-01

Campylobacter jejuni is a leading cause of gastrointestinal infections worldwide, due primarily to its ability to asymptomatically colonize the gastrointestinal tracts of agriculturally relevant animals, including chickens. Infection often occurs following consumption of meat that was contaminated by C. jejuni during harvest. Because of this, much interest lies in understanding the mechanisms that allow C. jejuni to colonize the chicken gastrointestinal tract. To address this, we generated a C. jejuni transposon mutant library that is amenable to insertion sequencing and introduced this mutant pool into day-of-hatch chicks. Following deep sequencing of C. jejuni mutants in the cecal outputs, several novel factors required for efficient colonization of the chicken gastrointestinal tract were identified, including the predicted outer membrane protein MapA. A mutant strain lacking mapA was constructed and found to be significantly reduced for chicken colonization in both competitive infections and monoinfections. Further, we found that mapA is required for in vitro competition with wild-type C. jejuni but is dispensable for growth in monoculture. PMID:24633877

High-throughput sequencing of Campylobacter jejuni insertion mutant libraries reveals mapA as a fitness factor for chicken colonization.

PubMed

Johnson, Jeremiah G; Livny, Jonathan; Dirita, Victor J

2014-06-01

Campylobacter jejuni is a leading cause of gastrointestinal infections worldwide, due primarily to its ability to asymptomatically colonize the gastrointestinal tracts of agriculturally relevant animals, including chickens. Infection often occurs following consumption of meat that was contaminated by C. jejuni during harvest. Because of this, much interest lies in understanding the mechanisms that allow C. jejuni to colonize the chicken gastrointestinal tract. To address this, we generated a C. jejuni transposon mutant library that is amenable to insertion sequencing and introduced this mutant pool into day-of-hatch chicks. Following deep sequencing of C. jejuni mutants in the cecal outputs, several novel factors required for efficient colonization of the chicken gastrointestinal tract were identified, including the predicted outer membrane protein MapA. A mutant strain lacking mapA was constructed and found to be significantly reduced for chicken colonization in both competitive infections and monoinfections. Further, we found that mapA is required for in vitro competition with wild-type C. jejuni but is dispensable for growth in monoculture.

A transposase strategy for creating libraries of circularly permuted proteins.

PubMed

Mehta, Manan M; Liu, Shirley; Silberg, Jonathan J

2012-05-01

A simple approach for creating libraries of circularly permuted proteins is described that is called PERMutation Using Transposase Engineering (PERMUTE). In PERMUTE, the transposase MuA is used to randomly insert a minitransposon that can function as a protein expression vector into a plasmid that contains the open reading frame (ORF) being permuted. A library of vectors that express different permuted variants of the ORF-encoded protein is created by: (i) using bacteria to select for target vectors that acquire an integrated minitransposon; (ii) excising the ensemble of ORFs that contain an integrated minitransposon from the selected vectors; and (iii) circularizing the ensemble of ORFs containing integrated minitransposons using intramolecular ligation. Construction of a Thermotoga neapolitana adenylate kinase (AK) library using PERMUTE revealed that this approach produces vectors that express circularly permuted proteins with distinct sequence diversity from existing methods. In addition, selection of this library for variants that complement the growth of Escherichia coli with a temperature-sensitive AK identified functional proteins with novel architectures, suggesting that PERMUTE will be useful for the directed evolution of proteins with new functions.

A transposase strategy for creating libraries of circularly permuted proteins

PubMed Central

Mehta, Manan M.; Liu, Shirley; Silberg, Jonathan J.

2012-01-01

A simple approach for creating libraries of circularly permuted proteins is described that is called PERMutation Using Transposase Engineering (PERMUTE). In PERMUTE, the transposase MuA is used to randomly insert a minitransposon that can function as a protein expression vector into a plasmid that contains the open reading frame (ORF) being permuted. A library of vectors that express different permuted variants of the ORF-encoded protein is created by: (i) using bacteria to select for target vectors that acquire an integrated minitransposon; (ii) excising the ensemble of ORFs that contain an integrated minitransposon from the selected vectors; and (iii) circularizing the ensemble of ORFs containing integrated minitransposons using intramolecular ligation. Construction of a Thermotoga neapolitana adenylate kinase (AK) library using PERMUTE revealed that this approach produces vectors that express circularly permuted proteins with distinct sequence diversity from existing methods. In addition, selection of this library for variants that complement the growth of Escherichia coli with a temperature-sensitive AK identified functional proteins with novel architectures, suggesting that PERMUTE will be useful for the directed evolution of proteins with new functions. PMID:22319214

An integrated runtime and compile-time approach for parallelizing structured and block structured applications

NASA Technical Reports Server (NTRS)

Agrawal, Gagan; Sussman, Alan; Saltz, Joel

1993-01-01

Scientific and engineering applications often involve structured meshes. These meshes may be nested (for multigrid codes) and/or irregularly coupled (called multiblock or irregularly coupled regular mesh problems). A combined runtime and compile-time approach for parallelizing these applications on distributed memory parallel machines in an efficient and machine-independent fashion was described. A runtime library which can be used to port these applications on distributed memory machines was designed and implemented. The library is currently implemented on several different systems. To further ease the task of application programmers, methods were developed for integrating this runtime library with compilers for HPK-like parallel programming languages. How this runtime library was integrated with the Fortran 90D compiler being developed at Syracuse University is discussed. Experimental results to demonstrate the efficacy of our approach are presented. A multiblock Navier-Stokes solver template and a multigrid code were experimented with. Our experimental results show that our primitives have low runtime communication overheads. Further, the compiler parallelized codes perform within 20 percent of the code parallelized by manually inserting calls to the runtime library.

Health sciences library building projects, 1998 survey.

PubMed Central

Bowden, V M

1999-01-01

Twenty-eight health sciences library building projects are briefly described, including twelve new buildings and sixteen additions, remodelings, and renovations. The libraries range in size from 2,144 square feet to 190,000 gross square feet. Twelve libraries are described in detail. These include three hospital libraries, one information center sponsored by ten institutions, and eight academic health sciences libraries. Images PMID:10550027

Libraries Achieving Greatness: Technology at the Helm

ERIC Educational Resources Information Center

Muir, Scott P.

2009-01-01

Libraries have been around for thousands of years. Many of them are considered great because of their magnificent architecture or because of the size of their collections. This paper offers ten case studies of libraries that have used technology to achieve greatness. Because almost any library can implement technology, a library does not have to…

Transposon tagging of genes for cell-cell interactions in Myxococcus xanthus.

PubMed Central

Kalos, M; Zissler, J

1990-01-01

The prokaryote Myxococcus xanthus is a model for cell interactions important in multicellular behavior. We used the transposon TnphoA to specifically identify genes for cell-surface factors involved in cell interactions. From a library of 10,700 insertions of TnphoA, we isolated 36 that produced alkaline phosphatase activity. Three TnphoA insertions tagged cell motility genes, called cgl, which control the adventurous movement of cells. The products of the tagged cgl genes could function in trans upon other cells and were localized primarily in the cell envelope and extracellular space, consistent with TnphoA tagging genes for extracellular factors controlling motility. Images PMID:2172982

A genome-wide BAC-end sequence survey provides first insights into sweetpotato (Ipomoea batatas (L.) Lam.) genome composition.

PubMed

Si, Zengzhi; Du, Bing; Huo, Jinxi; He, Shaozhen; Liu, Qingchang; Zhai, Hong

2016-11-21

Sweetpotato, Ipomoea batatas (L.) Lam., is an important food crop widely grown in the world. However, little is known about the genome of this species because it is a highly heterozygous hexaploid. Gaining a more in-depth knowledge of sweetpotato genome is therefore necessary and imperative. In this study, the first bacterial artificial chromosome (BAC) library of sweetpotato was constructed. Clones from the BAC library were end-sequenced and analyzed to provide genome-wide information about this species. The BAC library contained 240,384 clones with an average insert size of 101 kb and had a 7.93-10.82 × coverage of the genome, and the probability of isolating any single-copy DNA sequence from the library was more than 99%. Both ends of 8310 BAC clones randomly selected from the library were sequenced to generate 11,542 high-quality BAC-end sequences (BESs), with an accumulative length of 7,595,261 bp and an average length of 658 bp. Analysis of the BESs revealed that 12.17% of the sweetpotato genome were known repetitive DNA, including 7.37% long terminal repeat (LTR) retrotransposons, 1.15% Non-LTR retrotransposons and 1.42% Class II DNA transposons etc., 18.31% of the genome were identified as sweetpotato-unique repetitive DNA and 10.00% of the genome were predicted to be coding regions. In total, 3,846 simple sequences repeats (SSRs) were identified, with a density of one SSR per 1.93 kb, from which 288 SSRs primers were designed and tested for length polymorphism using 20 sweetpotato accessions, 173 (60.07%) of them produced polymorphic bands. Sweetpotato BESs had significant hits to the genome sequences of I. trifida and more matches to the whole-genome sequences of Solanum lycopersicum than those of Vitis vinifera, Theobroma cacao and Arabidopsis thaliana. The first BAC library for sweetpotato has been successfully constructed. The high quality BESs provide first insights into sweetpotato genome composition, and have significant hits to the genome sequences of I. trifida and more matches to the whole-genome sequences of Solanum lycopersicum. These resources as a robust platform will be used in high-resolution mapping, gene cloning, assembly of genome sequences, comparative genomics and evolution for sweetpotato.

Microcomputers in the Anesthesia Library.

ERIC Educational Resources Information Center

Wright, A. J.

The combination of computer technology and library operation is helping to alleviate such library problems as escalating costs, increasing collection size, deteriorating materials, unwieldy arrangement schemes, poor subject control, and the acquisition and processing of large numbers of rarely used documents. Small special libraries such as…

Isolation of a complementary DNA clone for thyroid microsomal antigen. Homology with the gene for thyroid peroxidase.

PubMed Central

Seto, P; Hirayu, H; Magnusson, R P; Gestautas, J; Portmann, L; DeGroot, L J; Rapoport, B

1987-01-01

The thyroid microsomal antigen (MSA) in autoimmune thyroid disease is a protein of approximately 107 kD. We screened a human thyroid cDNA library constructed in the expression vector lambda gt11 with anti-107-kD monoclonal antibodies. Of five clones obtained, the recombinant beta-galactosidase fusion protein from one clone (PM-5) was confirmed to react with the monoclonal antiserum. The complementary DNA (cDNA) insert from PM-5 (0.8 kb) was used as a probe on Northern blot analysis to estimate the size of the mRNA coding for the MSA. The 2.9-kb messenger RNA (mRNA) species observed was the same size as that coding for human thyroid peroxidase (TPO). The probe did not bind to human liver mRNA, indicating the thyroid-specific nature of the PM-5-related mRNA. The nucleotide sequence of PM-5 (842 bp) was determined and consisted of a single open reading frame. Comparison of the nucleotide sequence of PM-5 with that presently available for pig TPO indicates 84% homology. In conclusion, a cDNA clone representing part of the microsomal antigen has been isolated. Sequence homology with porcine TPO, as well as identity in the size of the mRNA species for both the microsomal antigen and TPO, indicate that the microsomal antigen is, at least in part, TPO. Images PMID:3654979

Essential Genes for In Vitro Growth of the Endophyte Herbaspirillum seropedicae SmR1 as Revealed by Transposon Insertion Site Sequencing

PubMed Central

Rosconi, Federico; de Vries, Stefan P. W.; Baig, Abiyad; Fabiano, Elena

2016-01-01

ABSTRACT The interior of plants contains microorganisms (referred to as endophytes) that are distinct from those present at the root surface or in the surrounding soil. Herbaspirillum seropedicae strain SmR1, belonging to the betaproteobacteria, is an endophyte that colonizes crops, including rice, maize, sugarcane, and sorghum. Different approaches have revealed genes and pathways regulated during the interactions of H. seropedicae with its plant hosts. However, functional genomic analysis of transposon (Tn) mutants has been hampered by the lack of genetic tools. Here we successfully employed a combination of in vivo high-density mariner Tn mutagenesis and targeted Tn insertion site sequencing (Tn-seq) in H. seropedicae SmR1. The analysis of multiple gene-saturating Tn libraries revealed that 395 genes are essential for the growth of H. seropedicae SmR1 in tryptone-yeast extract medium. A comparative analysis with the Database of Essential Genes (DEG) showed that 25 genes are uniquely essential in H. seropedicae SmR1. The Tn mutagenesis protocol developed and the gene-saturating Tn libraries generated will facilitate elucidation of the genetic mechanisms of the H. seropedicae endophytic lifestyle. IMPORTANCE A focal point in the study of endophytes is the development of effective biofertilizers that could help to reduce the input of agrochemicals in croplands. Besides the ability to promote plant growth, a good biofertilizer should be successful in colonizing its host and competing against the native microbiota. By using a systematic Tn-based gene-inactivation strategy and massively parallel sequencing of Tn insertion sites (Tn-seq), it is possible to study the fitness of thousands of Tn mutants in a single experiment. We have applied the combination of these techniques to the plant-growth-promoting endophyte Herbaspirillum seropedicae SmR1. The Tn mutant libraries generated will enable studies into the genetic mechanisms of H. seropedicae-plant interactions. The approach that we have taken is applicable to other plant-interacting bacteria. PMID:27590816

Validation of an improved abnormality insertion method for medical image perception investigations

NASA Astrophysics Data System (ADS)

Madsen, Mark T.; Durst, Gregory R.; Caldwell, Robert T.; Schartz, Kevin M.; Thompson, Brad H.; Berbaum, Kevin S.

2009-02-01

The ability to insert abnormalities in clinical tomographic images makes image perception studies with medical images practical. We describe a new insertion technique and its experimental validation that uses complementary image masks to select an abnormality from a library and place it at a desired location. The method was validated using a 4-alternative forced-choice experiment. For each case, four quadrants were simultaneously displayed consisting of 5 consecutive frames of a chest CT with a pulmonary nodule. One quadrant was unaltered, while the other 3 had the nodule from the unaltered quadrant artificially inserted. 26 different sets were generated and repeated with order scrambling for a total of 52 cases. The cases were viewed by radiology staff and residents who ranked each quadrant by realistic appearance. On average, the observers were able to correctly identify the unaltered quadrant in 42% of cases, and identify the unaltered quadrant both times it appeared in 25% of cases. Consensus, defined by a majority of readers, correctly identified the unaltered quadrant in only 29% of 52 cases. For repeats, the consensus observer successfully identified the unaltered quadrant only once. We conclude that the insertion method can be used to reliably place abnormalities in perception experiments.

The Major Cold Shock Gene, cspA, Is Involved in the Susceptibility of Staphylococcus aureus to an Antimicrobial Peptide of Human Cathepsin G

PubMed Central

Katzif, Samuel; Danavall, Damien; Bowers, Samera; Balthazar, Jacqueline T.; Shafer, William M.

2003-01-01

A Tn551 insertional library of Staphylococcus aureus strain ISP479 was challenged with an antimicrobial peptide (CG 117-136) derived from human neutrophil cathepsin G (CG). After repeated selection and screening of surviving colonies, a mutant was identified that expressed increased resistance to CG 117-136. Southern hybridization analysis revealed that the Tn551 insert in this mutant (SK1) was carried on a 10.6-kb EcoRI chromosomal DNA fragment. Subsequent physical mapping of this Tn551 insert revealed that it was positioned between a putative promoter sequence and the translational start codon of the cspA gene, which encodes a protein (CspA) highly similar to the major cold shock proteins CspA and CspB of Escherichia coli and Bacillus subtilis, respectively. This Tn551 insertion as well as a separate deletion-insertion mutation in cspA decreased the capacity of S. aureus to respond to the stress of cold shock and increased resistance to CG 117-136. The results indicate for the first time that a physiologic link exists between bacterial susceptibility to an antimicrobial peptide and a stress response system. PMID:12874306

The major cold shock gene, cspA, is involved in the susceptibility of Staphylococcus aureus to an antimicrobial peptide of human cathepsin G.

PubMed

Katzif, Samuel; Danavall, Damien; Bowers, Samera; Balthazar, Jacqueline T; Shafer, William M

2003-08-01

A Tn551 insertional library of Staphylococcus aureus strain ISP479 was challenged with an antimicrobial peptide (CG 117-136) derived from human neutrophil cathepsin G (CG). After repeated selection and screening of surviving colonies, a mutant was identified that expressed increased resistance to CG 117-136. Southern hybridization analysis revealed that the Tn551 insert in this mutant (SK1) was carried on a 10.6-kb EcoRI chromosomal DNA fragment. Subsequent physical mapping of this Tn551 insert revealed that it was positioned between a putative promoter sequence and the translational start codon of the cspA gene, which encodes a protein (CspA) highly similar to the major cold shock proteins CspA and CspB of Escherichia coli and Bacillus subtilis, respectively. This Tn551 insertion as well as a separate deletion-insertion mutation in cspA decreased the capacity of S. aureus to respond to the stress of cold shock and increased resistance to CG 117-136. The results indicate for the first time that a physiologic link exists between bacterial susceptibility to an antimicrobial peptide and a stress response system.

Leisure reading collections in academic health sciences and science libraries: results of visits to seven libraries.

PubMed

Watson, Erin M

2014-03-01

To visit leisure reading collections in academic science and health sciences libraries to determine how they function and what role they play in their libraries. The author visited seven libraries with leisure reading collections and carried out a semistructured interview with those responsible either for selection of materials or for the establishment of the collection. These collections contained a variety of materials, with some libraries focusing on health-science-related materials and others on providing recreational reading. The size of the collections also varied, from 186 to 9700 books, with corresponding differences in budget size. All collections were housed apart, with the same loan period as the regular collection. No collections contained electronic materials. Although there was little comparable statistical data on usage, at the six libraries at which active selection was occurring, librarians and library staff felt that the collection was well used and felt that it provided library users with benefits such as stress relief and relaxation and exposure to other perspectives. Librarians and library staff at the libraries that undertook active selection felt that their leisure reading collection was worthwhile. It would be interesting for future work to focus on the user experience of such collections. © 2013 The author. Health Information and Libraries Journal © 2013 Health Libraries Group.

Characterization of full-length sequenced cDNA inserts (FLIcs) from Atlantic salmon (Salmo salar)

PubMed Central

Andreassen, Rune; Lunner, Sigbjørn; Høyheim, Bjørn

2009-01-01

Background Sequencing of the Atlantic salmon genome is now being planned by an international research consortium. Full-length sequenced inserts from cDNAs (FLIcs) are an important tool for correct annotation and clustering of the genomic sequence in any species. The large amount of highly similar duplicate sequences caused by the relatively recent genome duplication in the salmonid ancestor represents a particular challenge for the genome project. FLIcs will therefore be an extremely useful resource for the Atlantic salmon sequencing project. In addition to be helpful in order to distinguish between duplicate genome regions and in determining correct gene structures, FLIcs are an important resource for functional genomic studies and for investigation of regulatory elements controlling gene expression. In contrast to the large number of ESTs available, including the ESTs from 23 developmental and tissue specific cDNA libraries contributed by the Salmon Genome Project (SGP), the number of sequences where the full-length of the cDNA insert has been determined has been small. Results High quality full-length insert sequences from 560 pre-smolt white muscle tissue specific cDNAs were generated, accession numbers [GenBank: BT043497 - BT044056]. Five hundred and ten (91%) of the transcripts were annotated using Gene Ontology (GO) terms and 440 of the FLIcs are likely to contain a complete coding sequence (cCDS). The sequence information was used to identify putative paralogs, characterize salmon Kozak motifs, polyadenylation signal variation and to identify motifs likely to be involved in the regulation of particular genes. Finally, conserved 7-mers in the 3'UTRs were identified, of which some were identical to miRNA target sequences. Conclusion This paper describes the first Atlantic salmon FLIcs from a tissue and developmental stage specific cDNA library. We have demonstrated that many FLIcs contained a complete coding sequence (cCDS). This suggests that the remaining cDNA libraries generated by SGP represent a valuable cCDS FLIc source. The conservation of 7-mers in 3'UTRs indicates that these motifs are functionally important. Identity between some of these 7-mers and miRNA target sequences suggests that they are miRNA targets in Salmo salar transcripts as well. PMID:19878547

Assembly of YAC contigs on the long arm of human chromosome 2

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

Liu, J.; Fujiwara, T.M.; Wang, J.X.

1994-09-01

We have previously identified approximately 2,000 chromosome 2-specific YACs by screening the CEPH Mark I YAC library (`Midi- YACs`). Using STS content mapping, we have been able to order groups of these YACs along chromosome 2q. The four biggest YAC groups were associated with VIL (2q35), FN (2q34), PAX3 (2q36), ALPI (2q37) and contained 113, 107, 79, and 63 YACs, respectively. We have identified the minimal tiling paths for most YAC groups and determined the insert sizes of over 300 YACs. Furthermore, on human chromosome 2q31-q37, 15 microsatellite markers were linked to various expressed genes through overlapping YACs and themore » physical distance of microsatellites to expressed genes was determined. The precise mapping of a set of highly informative microsatellite markers with respect to known genes provides a useful tool for linkage studies and the identification of disease genes from the long arm of human chromosome 2.« less

New library buildings: the Health Sciences Library, Memorial University of Newfoundland, St. John's.

PubMed Central

Fredericksen, R B

1979-01-01

The new Health Sciences Library of Memorial University of Newfoundland is described and illustrated. A library facility that forms part of a larger health sciences center, this is a medium-sized academic health sciences library built on a single level. Along with a physical description of the library and its features, the concepts of single-level libraries, phased occupancy, and the project management approach to building a large health center library are discussed in detail. Images PMID:476319

The influence of the insertion technique on the pullout force of pedicle screws: an experimental study.

PubMed

Chatzistergos, Panagiotis E; Sapkas, George; Kourkoulis, Stavros K

2010-04-20

The pullout strength of a typical pedicle screw was evaluated experimentally for different screw insertion techniques. OBJECTIVE.: To conclude whether the self-tapping insertion technique is indeed the optimum one for self-tapping screws, with respect to the pullout strength. It is reported in the literature that the size of the pilot-hole significantly influences the pullout strength of a self-tapping screw. In addition it is accepted that an optimum value of the diameter of the pilot-hole exists. For non self-tapping screw insertion it is reported that undertapping of the pilot-hole can increase its pullout strength. Finally it is known that in some cases orthopedic surgeons open the threaded holes, using another screw instead of a tap. A typical commercial self-tapping pedicle screw was inserted into blocks of Solid Rigid Polyurethane Foam (simulating osteoporotic cancellous bone), following different insertion techniques. The pullout force was measured according to the ASTM-F543-02 standard. The screw was inserted into previously prepared holes of different sizes, either threaded or cylindrical, to conclude whether an optimum size of the pilot-hole exists and whether tapping can increase the pullout strength. The case where the tapping is performed using another screw was also studied. For screw insertion with tapping, decreasing the outer radius of the threaded hole from 1.00 to 0.87 of the screw's outer radius increased the pullout force 9%. For insertion without tapping, decreasing the pilot-hole's diameter from 0.87 to 0.47 of the screw's outer diameter increased its pullout force 75%. Finally, tapping using another screw instead of a tap, gave results similar to those of conventional tapping. Undertapping of a pilot-hole either using a tap or another screw can increase the pullout strength of self-tapping pedicle screws.

Effects of imidazolium-based ionic surfactants on the size and dynamics of phosphatidylcholine bilayers with saturated and unsaturated chains.

PubMed

Lee, Hwankyu

2015-07-01

Imidazolium-based ionic surfactants of different sizes were simulated with 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), and 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) bilayers. Regardless of the phospholipid type, larger surfactants at higher concentrations more significantly insert into the bilayer and increase the bilayer-surface size, in agreement with experiments and previous simulations. Insertion of surfactants only slightly decreases the bilayer thickness, as also observed in experiments. Although the surfactant insertion and its effect on the bilayer size and thickness are similar in different types of bilayers, the volume fractions of surfactants in the bilayer are higher for DMPC bilayers than for POPC and DOPC bilayers. In particular, ionic surfactants with four hydrocarbons yield their volume fractions of 4.6% and 8.7%, respectively, in POPC and DMPC bilayers, in quantitative agreement with experimental values of ∼5% and ∼10%. Also, the inserted surfactants increase the lateral diffusivity of the bilayer, which depends on the bilayer type. These findings indicate that although the surfactant insertion does not depend on the bilayer type, the effects of surfactants on the volume fraction and bilayer dynamics occur more significantly in the DMPC bilayer because of the smaller area per lipid and shorter saturated tails, which helps explain the experimental observations regarding different volume fractions of surfactants in POPC and DMPC bilayers. Copyright © 2015 Elsevier Inc. All rights reserved.

Easy preparation of a large-size random gene mutagenesis library in Escherichia coli.

PubMed

You, Chun; Percival Zhang, Y-H

2012-09-01

A simple and fast protocol for the preparation of a large-size mutant library for directed evolution in Escherichia coli was developed based on the DNA multimers generated by prolonged overlap extension polymerase chain reaction (POE-PCR). This protocol comprised the following: (i) a linear DNA mutant library was generated by error-prone PCR or shuffling, and a linear vector backbone was prepared by regular PCR; (ii) the DNA multimers were generated based on these two DNA templates by POE-PCR; and (iii) the one restriction enzyme-digested DNA multimers were ligated to circular plasmids, followed by transformation to E. coli. Because the ligation efficiency of one DNA fragment was several orders of magnitude higher than that of two DNA fragments for typical mutant library construction, it was very easy to generate a mutant library with a size of more than 10(7) protein mutants per 50 μl of the POE-PCR product. Via this method, four new fluorescent protein mutants were obtained based on monomeric cherry fluorescent protein. This new protocol was simple and fast because it did not require labor-intensive optimizations in restriction enzyme digestion and ligation, did not involve special plasmid design, and enabled constructing a large-size mutant library for directed enzyme evolution within 1 day. Copyright © 2012 Elsevier Inc. All rights reserved.

General Economic and Demographic Background and Projections for Indiana Library Services.

ERIC Educational Resources Information Center

Foust, James D.; Tower, Carl B.

Before future library needs can be estimated, economic and demographic variables that influence the demand for library services must be projected and estimating equations relating library needs to economic and demographic parameters developed. This study considers the size, location and age-sex characteristics of Indiana's current population and…

Planning the School Library.

ERIC Educational Resources Information Center

Babcock, Ruth E.; And Others

This report consists of recommendations for library facilities in either new or existing school buildings. Suggestions are made for the location and size of the library. Also included are considerations for library acoustics, heating and interior finish. It is considered to be of critical importance that adequate and separate space should be…

An efficient Agrobacterium-mediated transformation method for aflatoxin generation fungus Aspergillus flavus.

PubMed

Han, Guomin; Shao, Qian; Li, Cuiping; Zhao, Kai; Jiang, Li; Fan, Jun; Jiang, Haiyang; Tao, Fang

2018-05-01

Aspergillus flavus often invade many important corps and produce harmful aflatoxins both in preharvest and during storage stages. The regulation mechanism of aflatoxin biosynthesis in this fungus has not been well explored mainly due to the lack of an efficient transformation method for constructing a genome-wide gene mutant library. This challenge was resolved in this study, where a reliable and efficient Agrobacterium tumefaciens-mediated transformation (ATMT) protocol for A. flavus NRRL 3357 was established. The results showed that removal of multinucleate conidia, to collect a homogenous sample of uninucleate conidia for use as the transformation material, is the key step in this procedure. A. tumefaciens strain AGL-1 harboring the ble gene for zeocin resistance under the control of the gpdA promoter from A. nidulans is suitable for genetic transformation of this fungus. We successfully generated A. flavus transformants with an efficiency of ∼ 60 positive transformants per 10 6 conidia using our protocol. A small-scale insertional mutant library (∼ 1,000 mutants) was constructed using this method and the resulting several mutants lacked both production of conidia and aflatoxin biosynthesis capacity. Southern blotting analysis demonstrated that the majority of the transformants contained a single T-DNA insert on the genome. To the best of our knowledge, this is the first report of genetic transformation of A. flavus via ATMT and our protocol provides an effective tool for construction of genome-wide gene mutant libraries for functional analysis of important genes in A. flavus.

[Isolation and function of genes regulating aphB expression in Vibrio cholerae].

PubMed

Chen, Haili; Zhu, Zhaoqin; Zhong, Zengtao; Zhu, Jun; Kan, Biao

2012-02-04

We identified genes that regulate the expression of aphB, the gene encoding a key virulence regulator in Vibrio cholerae O1 E1 Tor C6706(-). We constructed a transposon library in V. cholerae C6706 strain containing a P(aphB)-luxCDABE and P(aphB)-lacZ transcriptional reporter plasmids. Using a chemiluminescence imager system, we rapidly detected aphB promoter expression level at a large scale. We then sequenced the transposon insertion sites by arbitrary PCR and sequencing analysis. We obtained two candidate mutants T1 and T2 which displayed reduced aphB expression from approximately 40,000 transposon insertion mutants. Sequencing analysis shows that Tn inserted in vc1585 reading frame in the T1 mutant and Tn inserted in the end of coding sequence of vc1602 in the T2 mutant. By using a genetic screen, we identified two potential genes that may involve in regulation of the expression of the key virulence regulator AphB. This study sheds light on our further investigation to fully understand V. cholerae virulence gene regulatory cascades.

Automated synthesis of a 96 product-sized library of triazole derivatives using a solid phase supported copper catalyst.

PubMed

Jlalia, Ibtissem; Beauvineau, Claire; Beauvière, Sophie; Onen, Esra; Aufort, Marie; Beauvineau, Aymeric; Khaba, Eihab; Herscovici, Jean; Meganem, Faouzi; Girard, Christian

2010-04-28

This article deal with the parallel synthesis of a 96 product-sized library using a polymer-based copper catalyst that we developed which can be easily separated from the products by simple filtration. This gave us the opportunity to use this catalyst in an automated chemical synthesis station (Chemspeed ASW-2000). Studies and results about the preparation of the catalyst, its use in different solvent systems, its recycling capabilities and its scope and limitations in the synthesis of this library will be addressed. The synthesis of the triazole library and the very good results obtained will finally be discussed.

Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes

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

Gihring, Thomas; Green, Stefan; Schadt, Christopher Warren

2011-01-01

Technologies for massively parallel sequencing are revolutionizing microbial ecology and are vastly increasing the scale of ribosomal RNA (rRNA) gene studies. Although pyrosequencing has increased the breadth and depth of possible rRNA gene sampling, one drawback is that the number of reads obtained per sample is difficult to control. Pyrosequencing libraries typically vary widely in the number of sequences per sample, even within individual studies, and there is a need to revisit the behaviour of richness estimators and diversity indices with variable gene sequence library sizes. Multiple reports and review papers have demonstrated the bias in non-parametric richness estimators (e.g.more » Chao1 and ACE) and diversity indices when using clone libraries. However, we found that biased community comparisons are accumulating in the literature. Here we demonstrate the effects of sample size on Chao1, ACE, CatchAll, Shannon, Chao-Shen and Simpson's estimations specifically using pyrosequencing libraries. The need to equalize the number of reads being compared across libraries is reiterated, and investigators are directed towards available tools for making unbiased diversity comparisons.« less

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.

Specific insertions of zinc finger domains into Gag-Pol yield engineered retroviral vectors with selective integration properties

PubMed Central

Lim, Kwang-il; Klimczak, Ryan; Yu, Julie H.; Schaffer, David V.

2010-01-01

Retroviral vectors offer benefits of efficient delivery and stable gene expression; however, their clinical use raises the concerns of insertional mutagenesis and potential oncogenesis due to genomic integration preferences in transcriptional start sites (TSS). We have shifted the integration preferences of retroviral vectors by generating a library of viral variants with a DNA-binding domain inserted at random positions throughout murine leukemia virus Gag-Pol, then selecting for variants that are viable and exhibit altered integration properties. We found seven permissive zinc finger domain (ZFD) insertion sites throughout Gag-Pol, including within p12, reverse transcriptase, and integrase. Comprehensive genome integration analysis showed that several ZFD insertions yielded retroviral vector variants with shifted integration patterns that did not favor TSS. Furthermore, integration site analysis revealed selective integration for numerous mutants. For example, two retroviral variants with a given ZFD at appropriate positions in Gag-Pol strikingly integrated primarily into four common sites out of 3.1 × 109 possible human genome locations (P = 4.6 × 10-29). Our findings demonstrate that insertion of DNA-binding motifs into multiple locations in Gag-Pol can make considerable progress toward engineering safer retroviral vectors that integrate into a significantly narrowed pool of sites on human genome and overcome the preference for TSS. PMID:20616052

Automated design of degenerate codon libraries.

PubMed

Mena, Marco A; Daugherty, Patrick S

2005-12-01

Degenerate codon libraries are frequently used in protein engineering and evolution studies but are often limited to targeting a small number of positions to adequately limit the search space. To mitigate this, codon degeneracy can be limited using heuristics or previous knowledge of the targeted positions. To automate design of libraries given a set of amino acid sequences, an algorithm (LibDesign) was developed that generates a set of possible degenerate codon libraries, their resulting size, and their score relative to a user-defined scoring function. A gene library of a specified size can then be constructed that is representative of the given amino acid distribution or that includes specific sequences or combinations thereof. LibDesign provides a new tool for automated design of high-quality protein libraries that more effectively harness existing sequence-structure information derived from multiple sequence alignment or computational protein design data.

A universal phage display system for the seamless construction of Fab libraries.

PubMed

Nelson, Renae S; Valadon, Philippe

2017-11-01

The construction of Fab phage libraries requires the cloning of domains from both the light and the heavy chain of antibodies. Despite the advent of powerful strategies such as splicing-by-overlap extension PCR, obtaining high quality libraries with excellent coverage remains challenging. Here, we explored the use of type IIS restriction enzymes for the seamless cloning of Fab libraries. We analyzed human, murine and rabbit germline antibody repertoires and identified combinations of restriction enzymes that exhibit very few or no recognition sites in the antibody sequences. We describe three phagemid vectors, pUP-22Hb, pUP-22Mc and pUP-22Rc, which were employed for cloning the Fab repertoire of these hosts using BsmBI and SapI (human) or SapI alone (mouse and rabbit). Using human serum albumin as a model immunization, we built a mouse/human chimeric Fab library and a mouse Fab library in a single step ligation and successfully panned multiple cognate antibodies. The overall process is highly scalable and faster than PCR-based techniques, with a Fab insertion success rate of around 80%. By using carefully chosen overhangs on each end of the antibody domains, this approach paves the way to the universal, sequence- and vector-independent cloning and reformatting of antibody libraries. Copyright © 2017 Elsevier B.V. All rights reserved.

Rambrain - a library for virtually extending physical memory

NASA Astrophysics Data System (ADS)

Imgrund, Maximilian; Arth, Alexander

2017-08-01

We introduce Rambrain, a user space library that manages memory consumption of your code. Using Rambrain you can overcommit memory over the size of physical memory present in the system. Rambrain takes care of temporarily swapping out data to disk and can handle multiples of the physical memory size present. Rambrain is thread-safe, OpenMP and MPI compatible and supports Asynchronous IO. The library was designed to require minimal changes to existing programs and to be easy to use.

The Special Challenges for National Libraries

ERIC Educational Resources Information Center

Breeding, Marshall

2011-01-01

Managing a library collection at the national level follows quite a different set of assumptions than hold for typical academic or public libraries. These collections, often comprehensive of all materials published in a country, press the limits of scale in terms of the sizes of collections. A national library collection might, for example, stand…

The Practicing Librarian: Public Library Parking Needs.

ERIC Educational Resources Information Center

Galvin, Hoyt

1978-01-01

Suggests standards for the numbers of parking spaces needed for a public library. From the annual Library Journal public library construction questionnaires, data were available on the number of parking spaces and the square foot size of the buildings reported; information on estimated needs was collected from the librarians in charge of each…

Reexamining Content-Enriched Access: Its Effect on Usage and Discovery

ERIC Educational Resources Information Center

Tosaka, Yuji; Weng, Cathy

2011-01-01

Content-enriched metadata in bibliographic records is considered helpful to library users in identifying and selecting library materials for their needs. The paper presents a study, using circulation data from a medium-sized academic library, of the effect of content-enriched records on library materials usage. The study also examines OPAC search…

Wisconsin Library Trustee Reference Manual.

ERIC Educational Resources Information Center

Opinion Research Corp., Princeton, NJ.

This newly updated and revised expansion of the Wisconsin Library Trustee's Manual serves as a comprehensive resource and how-to guide for board members of public libraries that range in size and scope from small to large communities in both urban and rural areas. The manual includes basic information to which every Wisconsin library trustee…

Electronic Resource Expenditure and the Decline in Reference Transaction Statistics in Academic Libraries

ERIC Educational Resources Information Center

Dubnjakovic, Ana

2012-01-01

The current study investigates factors influencing increase in reference transactions in a typical week in academic libraries across the United States of America. Employing multiple regression analysis and general linear modeling, variables of interest from the "Academic Library Survey (ALS) 2006" survey (sample size 3960 academic libraries) were…

Design of focused and restrained subsets from extremely large virtual libraries.

PubMed

Jamois, Eric A; Lin, Chien T; Waldman, Marvin

2003-11-01

With the current and ever-growing offering of reagents along with the vast palette of organic reactions, virtual libraries accessible to combinatorial chemists can reach sizes of billions of compounds or more. Extracting practical size subsets for experimentation has remained an essential step in the design of combinatorial libraries. A typical approach to computational library design involves enumeration of structures and properties for the entire virtual library, which may be unpractical for such large libraries. This study describes a new approach termed as on the fly optimization (OTFO) where descriptors are computed as needed within the subset optimization cycle and without intermediate enumeration of structures. Results reported herein highlight the advantages of coupling an ultra-fast descriptor calculation engine to subset optimization capabilities. We also show that enumeration of properties for the entire virtual library may not only be unpractical but also wasteful. Successful design of focused and restrained subsets can be achieved while sampling only a small fraction of the virtual library. We also investigate the stability of the method and compare results obtained from simulated annealing (SA) and genetic algorithms (GA).

Construction and Evaluation of Normalized cDNA Libraries Enriched with Full-Length Sequences for Rapid Discovery of New Genes from Sisal (Agave sisalana Perr.) Different Developmental Stages

PubMed Central

Zhou, Wen-Zhao; Zhang, Yan-Mei; Lu, Jun-Ying; Li, Jun-Feng

2012-01-01

To provide a resource of sisal-specific expressed sequence data and facilitate this powerful approach in new gene research, the preparation of normalized cDNA libraries enriched with full-length sequences is necessary. Four libraries were produced with RNA pooled from Agave sisalana multiple tissues to increase efficiency of normalization and maximize the number of independent genes by SMART™ method and the duplex-specific nuclease (DSN). This procedure kept the proportion of full-length cDNAs in the subtracted/normalized libraries and dramatically enhanced the discovery of new genes. Sequencing of 3875 cDNA clones of libraries revealed 3320 unigenes with an average insert length about 1.2 kb, indicating that the non-redundancy of libraries was about 85.7%. These unigene functions were predicted by comparing their sequences to functional domain databases and extensively annotated with Gene Ontology (GO) terms. Comparative analysis of sisal unigenes and other plant genomes revealed that four putative MADS-box genes and knotted-like homeobox (knox) gene were obtained from a total of 1162 full-length transcripts. Furthermore, real-time PCR showed that the characteristics of their transcripts mainly depended on the tight expression regulation of a number of genes during the leaf and flower development. Analysis of individual library sequence data indicated that the pooled-tissue approach was highly effective in discovering new genes and preparing libraries for efficient deep sequencing. PMID:23202944

A high-coverage draft genome of the mycalesine butterfly Bicyclus anynana.

PubMed

Nowell, Reuben W; Elsworth, Ben; Oostra, Vicencio; Zwaan, Bas J; Wheat, Christopher W; Saastamoinen, Marjo; Saccheri, Ilik J; Van't Hof, Arjen E; Wasik, Bethany R; Connahs, Heidi; Aslam, Muhammad L; Kumar, Sujai; Challis, Richard J; Monteiro, Antónia; Brakefield, Paul M; Blaxter, Mark

2017-07-01

The mycalesine butterfly Bicyclus anynana, the "Squinting bush brown," is a model organism in the study of lepidopteran ecology, development, and evolution. Here, we present a draft genome sequence for B. anynana to serve as a genomics resource for current and future studies of this important model species. Seven libraries with insert sizes ranging from 350 bp to 20 kb were constructed using DNA from an inbred female and sequenced using both Illumina and PacBio technology; 128 Gb of raw Illumina data was filtered to 124 Gb and assembled to a final size of 475 Mb (∼×260 assembly coverage). Contigs were scaffolded using mate-pair, transcriptome, and PacBio data into 10 800 sequences with an N50 of 638 kb (longest scaffold 5 Mb). The genome is comprised of 26% repetitive elements and encodes a total of 22 642 predicted protein-coding genes. Recovery of a BUSCO set of core metazoan genes was almost complete (98%). Overall, these metrics compare well with other recently published lepidopteran genomes. We report a high-quality draft genome sequence for Bicyclus anynana. The genome assembly and annotated gene models are available at LepBase (http://ensembl.lepbase.org/index.html). © The Authors 2017. Published by Oxford University Press.

A high-coverage draft genome of the mycalesine butterfly Bicyclus anynana

PubMed Central

Elsworth, Ben; Oostra, Vicencio; Zwaan, Bas J.; Wheat, Christopher W.; Saastamoinen, Marjo; Saccheri, Ilik J.; van’t Hof, Arjen E.; Wasik, Bethany R.; Connahs, Heidi; Aslam, Muhammad L.; Kumar, Sujai; Challis, Richard J.; Monteiro, Antónia; Brakefield, Paul M.

2017-01-01

Abstract The mycalesine butterfly Bicyclus anynana, the “Squinting bush brown,” is a model organism in the study of lepidopteran ecology, development, and evolution. Here, we present a draft genome sequence for B. anynana to serve as a genomics resource for current and future studies of this important model species. Seven libraries with insert sizes ranging from 350 bp to 20 kb were constructed using DNA from an inbred female and sequenced using both Illumina and PacBio technology; 128 Gb of raw Illumina data was filtered to 124 Gb and assembled to a final size of 475 Mb (∼×260 assembly coverage). Contigs were scaffolded using mate-pair, transcriptome, and PacBio data into 10 800 sequences with an N50 of 638 kb (longest scaffold 5 Mb). The genome is comprised of 26% repetitive elements and encodes a total of 22 642 predicted protein-coding genes. Recovery of a BUSCO set of core metazoan genes was almost complete (98%). Overall, these metrics compare well with other recently published lepidopteran genomes. We report a high-quality draft genome sequence for Bicyclus anynana. The genome assembly and annotated gene models are available at LepBase (http://ensembl.lepbase.org/index.html). PMID:28486658

VdCYC8, encoding CYC8 glucose repression mediator protein, is required for microsclerotia formation and full virulence in Verticillium dahliae

USDA-ARS?s Scientific Manuscript database

Verticillium dahliae is the primary causal agent for Verticillium wilt disease on a diverse array of economically important crops, including cotton. In previous research, we screened a T-DNA insertional mutant library of the highly virulent isolate Vd080 derived from cotton. In this study, the targ...

[Construction and characterization of a cDNA library from human liver tissue of cirrhosis].

PubMed

Chen, Xiao-hong; Chen, Zhi; Chen, Feng; Zhu, Hai-hong; Zhou, Hong-juan; Yao, Hang-ping

2005-03-01

To construct a cDNA library from human liver tissue of cirrhosis. The total RNA from human liver tissue of cirrhosis was extracted using Trizol method, and the mRNA was purified using mRNA purification kit. SMART technique and CDSIII/3' primer were used for first-strand cDNA synthesis. Long distance PCR was then used to synthesize the double-strand cDNA that was then digested by proteinase K and Sfi I, and was fractionated by CHOMA SPIN-400 column. The cDNA fragments longer than 0.4 kb were collected and ligated to lambdaTripl Ex2 vector. Then lambda-phage packaging reaction and library amplification were performed. The qualities of both unamplified and amplified cDNA libraries was strictly checked by conventional titer determination. Eleven plaques were randomly picked and tested using PCR with universal primers derived from the sequence flanking the vector. The titers of unamplifed and amplified libraries were 1.03 x 10(6) pfu/ml and 1.36 x 10(9) pfu/ml respectively. The percentages of recombinants from both libraries were 97.24 % in unamplified library and 99.02 % in amplified library. The lengths of the inserts were 1.02 kb in average (36.36 % 1 approximately equals 2 kb and 63.64 % 0.5 approximately equals 1.0 kb). A high quality cDNA library from human liver tissue of cirrhosis was constructed successfully, which can be used for screening and cloning new special genes associated with the occurrence of cirrhosis.

Analysis of plastid and mitochondrial DNA insertions in the nucleus (NUPTs and NUMTs) of six plant species: size, relative age and chromosomal localization.

PubMed

Michalovova, M; Vyskot, B; Kejnovsky, E

2013-10-01

We analysed the size, relative age and chromosomal localization of nuclear sequences of plastid and mitochondrial origin (NUPTs-nuclear plastid DNA and NUMTs-nuclear mitochondrial DNA) in six completely sequenced plant species. We found that the largest insertions showed lower divergence from organelle DNA than shorter insertions in all species, indicating their recent origin. The largest NUPT and NUMT insertions were localized in the vicinity of the centromeres in the small genomes of Arabidopsis and rice. They were also present in other chromosomal regions in the large genomes of soybean and maize. Localization of NUPTs and NUMTs correlated positively with distribution of transposable elements (TEs) in Arabidopsis and sorghum, negatively in grapevine and soybean, and did not correlate in rice or maize. We propose a model where new plastid and mitochondrial DNA sequences are inserted close to centromeres and are later fragmented by TE insertions and reshuffled away from the centromere or removed by ectopic recombination. The mode and tempo of TE dynamism determines the turnover of NUPTs and NUMTs resulting in their species-specific chromosomal distributions.

Spotlight on SLA Members: An Interview with Paul O'Pecko, Librarian at the Mystic Seaport G.W. Blunt White Library.

ERIC Educational Resources Information Center

Information Outlook, 1999

1999-01-01

Discusses the collection of this special library that contains materials concerning maritime commerce and related topics and is part of the Mystic Seaport Museum. Highlights include users; research; budgeting; staff; library collection size; vendors; online projects; marketing; and views on the Special Library Association. (LRW)

Collection overlap in hospital health sciences libraries: a case study.

PubMed

Stroyan, S

1985-10-01

Given similar demographics (age, size, and user population), to what extent do community hospital libraries differ in collection content? It is sometimes assumed that hospital libraries are relatively homogeneous and therefore subject to standardized procedures and collection development guides. This study compares the holdings of two community hospital libraries in Illinois to determine similarities and differences.

A Model for Service to the Elderly by the Small/Medium Sized Public Library.

ERIC Educational Resources Information Center

Jeffries, Stephen R.

Citing the American Library Association's 1964 statement of libraries' responsibilities to the aging, this paper presents a needs assessment of the elderly and suggests methods by which public libraries can attempt to meet some of these needs, e.g., barrier-free design, programs, materials, and services. The needs assessment of older users…

Technique for joining metal tubing

NASA Technical Reports Server (NTRS)

Wright, H. W.

1976-01-01

Uniform wall thickness and uninterrupted heat transfer is achieved by using shaped metal insert as wall material for joint. Insert acts as support during brazing, after which excess material is ground away to bring joint to original tubing size.

SU-F-207-16: CT Protocols Optimization Using Model Observer

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

Tseng, H; Fan, J; Kupinski, M

2015-06-15

Purpose: To quantitatively evaluate the performance of different CT protocols using task-based measures of image quality. This work studies the task of size and the contrast estimation of different iodine concentration rods inserted in head- and body-sized phantoms using different imaging protocols. These protocols are designed to have the same dose level (CTDIvol) but using different X-ray tube voltage settings (kVp). Methods: Different concentrations of iodine objects inserted in a head size phantom and a body size phantom are imaged on a 64-slice commercial CT scanner. Scanning protocols with various tube voltages (80, 100, and 120 kVp) and current settingsmore » are selected, which output the same absorbed dose level (CTDIvol). Because the phantom design (size of the iodine objects, the air gap between the inserted objects and the phantom) is not ideal for a model observer study, the acquired CT images are used to generate simulation images with four different sizes and five different contracts iodine objects. For each type of the objects, 500 images (100 x 100 pixels) are generated for the observer study. The observer selected in this study is the channelized scanning linear observer which could be applied to estimate the size and the contrast. The figure of merit used is the correct estimation ratio. The mean and the variance are estimated by the shuffle method. Results: The results indicate that the protocols with 100 kVp tube voltage setting provides the best performance for iodine insert size and contrast estimation for both head and body phantom cases. Conclusion: This work presents a practical and robust quantitative approach using channelized scanning linear observer to study contrast and size estimation performance from different CT protocols. Different protocols at same CTDIvol setting could Result in different image quality performance. The relationship between the absorbed dose and the diagnostic image quality is not linear.« less

How do geometry-related parameters influence the clinical performance of orthodontic mini-implants? A systematic review and meta-analysis.

PubMed

Cunha, A C; da Veiga, A M A; Masterson, D; Mattos, C T; Nojima, L I; Nojima, M C G; Maia, L C

2017-12-01

The aim of this systematic review and meta-analysis was to investigate how parameters related to geometry influence the clinical performance of orthodontic mini-implants (MIs). Systematic searches were performed in electronic databases including MEDLINE, Scopus, Web of Science, Virtual Health Library, and Cochrane Library and reference lists up to March 2016. Eligibility criteria comprised clinical studies involving patients who received MIs for orthodontic anchorage, with data for categories of MI dimension, shape, and thread design and insertion site, and evaluated by assessment of primary and secondary stability. Study selection, data extraction, quality assessment, and a meta-analysis were carried out. Twenty-seven studies were included in the qualitative synthesis: five randomized, eight prospective, and 14 retrospective clinical studies. One study with a serious risk of bias was later excluded. Medium and short MIs (1.4-1.9mm diameter and 5-8mm length) presented the highest success rates (0.87, 95% CI 0.80-0.92). A maximum insertion torque of 13.28Ncm (standard error 0.34) was observed for tapered self-drilling MIs in the mandible, whereas cylindrical MIs in the maxilla presented a maximum removal torque of 10.01Ncm (standard error 0.17). Moderate evidence indicates that the clinical performance of MIs is influenced by implant geometry parameters and is also related to properties of the insertion site. However, further research is necessary to support these associations. Copyright © 2017 International Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.

Comprehensive identification of Vibrio vulnificus genes required for growth in human serum.

PubMed

Carda-Diéguez, M; Silva-Hernández, F X; Hubbard, T P; Chao, M C; Waldor, M K; Amaro, C

2018-12-31

Vibrio vulnificus can be a highly invasive pathogen capable of spreading from an infection site to the bloodstream, causing sepsis and death. To survive and proliferate in blood, the pathogen requires mechanisms to overcome the innate immune defenses and metabolic limitations of this host niche. We created a high-density transposon mutant library in YJ016, a strain representative of the most virulent V. vulnificus lineage (or phylogroup) and used transposon insertion sequencing (TIS) screens to identify loci that enable the pathogen to survive and proliferate in human serum. Initially, genes underrepresented for insertions were used to estimate the V. vulnificus essential gene set; comparisons of these genes with similar TIS-based classification of underrepresented genes in other vibrios enabled the compilation of a common Vibrio essential gene set. Analysis of the relative abundance of insertion mutants in the library after exposure to serum suggested that genes involved in capsule biogenesis are critical for YJ016 complement resistance. Notably, homologues of two genes required for YJ016 serum-resistance and capsule biogenesis were not previously linked to capsule biogenesis and are largely absent from other V. vulnificus strains. The relative abundance of mutants after exposure to heat inactivated serum was compared with the findings from the serum screen. These comparisons suggest that in both conditions the pathogen relies on its Na + transporting NADH-ubiquinone reductase (NQR) complex and type II secretion system to survive/proliferate within the metabolic constraints of serum. Collectively, our findings reveal the potency of comparative TIS screens to provide knowledge of how a pathogen overcomes the diverse limitations to growth imposed by serum.

Comprehensive MALDI-TOF biotyping of the non-redundant Harvard Pseudomonas aeruginosa PA14 transposon insertion mutant library.

PubMed

Oumeraci, Tonio; Jensen, Vanessa; Talbot, Steven R; Hofmann, Winfried; Kostrzewa, Markus; Schlegelberger, Brigitte; von Neuhoff, Nils; Häussler, Susanne

2015-01-01

Pseudomonas aeruginosa is a gram-negative bacterium that is ubiquitously present in the aerobic biosphere. As an antibiotic-resistant facultative pathogen, it is a major cause of hospital-acquired infections. Its rapid and accurate identification is crucial in clinical and therapeutic environments. In a large-scale MALDI-TOF mass spectrometry-based screen of the Harvard transposon insertion mutant library of P. aeruginosa strain PA14, intact-cell proteome profile spectra of 5547 PA14 transposon mutants exhibiting a plethora of different phenotypes were acquired and analyzed. Of all P. aeruginosa PA14 mutant profiles 99.7% were correctly identified as P. aeruginosa with the Biotyper software on the species level. On the strain level, 99.99% of the profiles were mapped to five different individual P. aeruginosa Biotyper database entries. A principal component analysis-based approach was used to determine the most important discriminatory mass features between these Biotyper groups. Although technical replicas were consistently categorized to specific Biotyper groups in 94.2% of the mutant profiles, biological replicas were not, indicating that the distinct proteotypes are affected by growth conditions. The PA14 mutant profile collection presented here constitutes the largest coherent P. aeruginosa MALDI-TOF spectral dataset publicly available today. Transposon insertions in thousands of different P. aeruginosa genes did not affect species identification from MALDI-TOF mass spectra, clearly demonstrating the robustness of the approach. However, the assignment of the individual spectra to sub-groups proved to be non-consistent in biological replicas, indicating that the differentiation between biotyper groups in this nosocomial pathogen is unassured.

Identification of human antibody fragment clones specific for tetanus toxoid in a bacteriophage. lambda. immunoexpression library

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

Mullinax, R.L.; Gross, E.A.; Amberg, J.R.

1990-10-01

The authors have applied a molecular biology approach to the identification of human monoclonal antibodies. Human peripheral blood lymphocyte mRNA was converted to cDNA and a select subset was amplified by the polymerase chain reaction. These products, containing coding sequences for numerous immunoglobulin heavy- and {kappa} light-chain variable and constant region domains, were inserted into modified bacteriophase {lambda} expression vectors and introduced into Escherichia coli by infection to yield a combinatorial immunoexpression library. Clones with binding activity to tetanus toxoid were identified by filter hybridization with radiolabeled antigen and appeared at a frequency of 0.2{percent} in the library. These humanmore » antigen binding fragments, consisting of a heavy-chain fragment covalently linked to a light chain, displayed high affinity of binding to tetanus toxoid with equilibrium constants in the nanomolar range but did not cross-react with other proteins tested. They estimate that this human immunoexpression library contains 20,000 clones with high affinity and specificity to our chosen antigen.« less

The Essential Genome of Escherichia coli K-12.

PubMed

Goodall, Emily C A; Robinson, Ashley; Johnston, Iain G; Jabbari, Sara; Turner, Keith A; Cunningham, Adam F; Lund, Peter A; Cole, Jeffrey A; Henderson, Ian R

2018-02-20

Transposon-directed insertion site sequencing (TraDIS) is a high-throughput method coupling transposon mutagenesis with short-fragment DNA sequencing. It is commonly used to identify essential genes. Single gene deletion libraries are considered the gold standard for identifying essential genes. Currently, the TraDIS method has not been benchmarked against such libraries, and therefore, it remains unclear whether the two methodologies are comparable. To address this, a high-density transposon library was constructed in Escherichia coli K-12. Essential genes predicted from sequencing of this library were compared to existing essential gene databases. To decrease false-positive identification of essential genes, statistical data analysis included corrections for both gene length and genome length. Through this analysis, new essential genes and genes previously incorrectly designated essential were identified. We show that manual analysis of TraDIS data reveals novel features that would not have been detected by statistical analysis alone. Examples include short essential regions within genes, orientation-dependent effects, and fine-resolution identification of genome and protein features. Recognition of these insertion profiles in transposon mutagenesis data sets will assist genome annotation of less well characterized genomes and provides new insights into bacterial physiology and biochemistry. IMPORTANCE Incentives to define lists of genes that are essential for bacterial survival include the identification of potential targets for antibacterial drug development, genes required for rapid growth for exploitation in biotechnology, and discovery of new biochemical pathways. To identify essential genes in Escherichia coli , we constructed a transposon mutant library of unprecedented density. Initial automated analysis of the resulting data revealed many discrepancies compared to the literature. We now report more extensive statistical analysis supported by both literature searches and detailed inspection of high-density TraDIS sequencing data for each putative essential gene for the E. coli model laboratory organism. This paper is important because it provides a better understanding of the essential genes of E. coli , reveals the limitations of relying on automated analysis alone, and provides a new standard for the analysis of TraDIS data. Copyright © 2018 Goodall et al.

Measuring Effectiveness in a Virtual Library

ERIC Educational Resources Information Center

Finch, Jannette L.

2010-01-01

Measuring quality of service in academic libraries traditionally includes quantifiable data such as collection size, staff counts, circulation numbers, reference service statistics, qualitative analyses of customer satisfaction, shelving accuracy, and building comfort. In the libraries of the third millennium, virtual worlds, Web content and…

DNA-encoded chemical libraries: advancing beyond conventional small-molecule libraries.

PubMed

Franzini, Raphael M; Neri, Dario; Scheuermann, Jörg

2014-04-15

DNA-encoded chemical libraries (DECLs) represent a promising tool in drug discovery. DECL technology allows the synthesis and screening of chemical libraries of unprecedented size at moderate costs. In analogy to phage-display technology, where large antibody libraries are displayed on the surface of filamentous phage and are genetically encoded in the phage genome, DECLs feature the display of individual small organic chemical moieties on DNA fragments serving as amplifiable identification barcodes. The DNA-tag facilitates the synthesis and allows the simultaneous screening of very large sets of compounds (up to billions of molecules), because the hit compounds can easily be identified and quantified by PCR-amplification of the DNA-barcode followed by high-throughput DNA sequencing. Several approaches have been used to generate DECLs, differing both in the methods used for library encoding and for the combinatorial assembly of chemical moieties. For example, DECLs can be used for fragment-based drug discovery, displaying a single molecule on DNA or two chemical moieties at the extremities of complementary DNA strands. DECLs can vary substantially in the chemical structures and the library size. While ultralarge libraries containing billions of compounds have been reported containing four or more sets of building blocks, also smaller libraries have been shown to be efficient for ligand discovery. In general, it has been found that the overall library size is a poor predictor for library performance and that the number and diversity of the building blocks are rather important indicators. Smaller libraries consisting of two to three sets of building blocks better fulfill the criteria of drug-likeness and often have higher quality. In this Account, we present advances in the DECL field from proof-of-principle studies to practical applications for drug discovery, both in industry and in academia. DECL technology can yield specific binders to a variety of target proteins and is likely to become a standard tool for pharmaceutical hit discovery, lead expansion, and Chemical Biology research. The introduction of new methodologies for library encoding and for compound synthesis in the presence of DNA is an exciting research field and will crucially contribute to the performance and the propagation of the technology.

Critical Features of Fragment Libraries for Protein Structure Prediction

PubMed Central

dos Santos, Karina Baptista

2017-01-01

The use of fragment libraries is a popular approach among protein structure prediction methods and has proven to substantially improve the quality of predicted structures. However, some vital aspects of a fragment library that influence the accuracy of modeling a native structure remain to be determined. This study investigates some of these features. Particularly, we analyze the effect of using secondary structure prediction guiding fragments selection, different fragments sizes and the effect of structural clustering of fragments within libraries. To have a clearer view of how these factors affect protein structure prediction, we isolated the process of model building by fragment assembly from some common limitations associated with prediction methods, e.g., imprecise energy functions and optimization algorithms, by employing an exact structure-based objective function under a greedy algorithm. Our results indicate that shorter fragments reproduce the native structure more accurately than the longer. Libraries composed of multiple fragment lengths generate even better structures, where longer fragments show to be more useful at the beginning of the simulations. The use of many different fragment sizes shows little improvement when compared to predictions carried out with libraries that comprise only three different fragment sizes. Models obtained from libraries built using only sequence similarity are, on average, better than those built with a secondary structure prediction bias. However, we found that the use of secondary structure prediction allows greater reduction of the search space, which is invaluable for prediction methods. The results of this study can be critical guidelines for the use of fragment libraries in protein structure prediction. PMID:28085928

Critical Features of Fragment Libraries for Protein Structure Prediction.

PubMed

Trevizani, Raphael; Custódio, Fábio Lima; Dos Santos, Karina Baptista; Dardenne, Laurent Emmanuel

2017-01-01

The use of fragment libraries is a popular approach among protein structure prediction methods and has proven to substantially improve the quality of predicted structures. However, some vital aspects of a fragment library that influence the accuracy of modeling a native structure remain to be determined. This study investigates some of these features. Particularly, we analyze the effect of using secondary structure prediction guiding fragments selection, different fragments sizes and the effect of structural clustering of fragments within libraries. To have a clearer view of how these factors affect protein structure prediction, we isolated the process of model building by fragment assembly from some common limitations associated with prediction methods, e.g., imprecise energy functions and optimization algorithms, by employing an exact structure-based objective function under a greedy algorithm. Our results indicate that shorter fragments reproduce the native structure more accurately than the longer. Libraries composed of multiple fragment lengths generate even better structures, where longer fragments show to be more useful at the beginning of the simulations. The use of many different fragment sizes shows little improvement when compared to predictions carried out with libraries that comprise only three different fragment sizes. Models obtained from libraries built using only sequence similarity are, on average, better than those built with a secondary structure prediction bias. However, we found that the use of secondary structure prediction allows greater reduction of the search space, which is invaluable for prediction methods. The results of this study can be critical guidelines for the use of fragment libraries in protein structure prediction.

Intracellular screen to identify metagenomic clones that induce or inhibit a quorum-sensing biosensor.

PubMed

Williamson, Lynn L; Borlee, Bradley R; Schloss, Patrick D; Guan, Changhui; Allen, Heather K; Handelsman, Jo

2005-10-01

The goal of this study was to design and evaluate a rapid screen to identify metagenomic clones that produce biologically active small molecules. We built metagenomic libraries with DNA from soil on the floodplain of the Tanana River in Alaska. We extracted DNA directly from the soil and cloned it into fosmid and bacterial artificial chromosome vectors, constructing eight metagenomic libraries that contain 53,000 clones with inserts ranging from 1 to 190 kb. To identify clones of interest, we designed a high throughput "intracellular" screen, designated METREX, in which metagenomic DNA is in a host cell containing a biosensor for compounds that induce bacterial quorum sensing. If the metagenomic clone produces a quorum-sensing inducer, the cell produces green fluorescent protein (GFP) and can be identified by fluorescence microscopy or captured by fluorescence-activated cell sorting. Our initial screen identified 11 clones that induce and two that inhibit expression of GFP. The intracellular screen detected quorum-sensing inducers among metagenomic clones that a traditional overlay screen would not. One inducing clone carries a LuxI homologue that directs the synthesis of an N-acyl homoserine lactone quorum-sensing signal molecule. The LuxI homologue has 62% amino acid sequence identity to its closest match in GenBank, AmfI from Pseudomonas fluorescens, and is on a 78-kb insert that contains 67 open reading frames. Another inducing clone carries a gene with homology to homocitrate synthase. Our results demonstrate the power of an intracellular screen to identify functionally active clones and biologically active small molecules in metagenomic libraries.

Polymorphic human (CTAT)n microsatellite provides a conserved linkage marker for mouse mutants causing cleft palate, vestibular defects, obesity and ataxia

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

Griffith, A.J.; Burgess, D.L.; Kohrman, D.

1994-09-01

The Twirler mutation (Tw) causing cleft palate {plus_minus} cleft lip, vestibular defects and obesity is located within 0.5 cM of an ataxia locus (ax) on mouse chromosome 18. We identified a transgene-induced insertional mutation with vestibular and craniofacial defects that appears to be a new allele of Twirler. Mouse DNA flanking the transgene insertion site was isolated from a cosmid library. An evolutionarily conserved, zoo blot positive cosmid subclone was used to probe a human {lambda} genomic library. From the sequence of a highly homologous human {lambda} clone, we designed STS primers and screened a human P1 library. DNA frommore » two positive P1 clones was hybridized with simple sequence probes, and a (CTAT){sub 12} repeat was detected. Analysis of 62 CEPH parents with primers flanking the repeat identified six alleles containing 9 to 14 copies of the repeat, at frequencies of 0.17, 0.17, 0.17, 0.27, 0.15 and 0.07, respectively. The observed heterozygosity was 49/62 with a calculated PIC value of 0.76. This polymorphic microsatellite marker, designated Umi3, was mapped to the predicted conserved human linkage group by analysis of somatic cell hybrid panels. The anticipated short distance between Umi3 and the disease genes will facilitate detection of linkage in small families. We would like to type appropriate human pedigrees with Umi3 in order to identify patients with inherited disorders homologous to the mouse mutations Twirler and ataxia.« less

Illinois Public Library Statistics: A Guide for Librarians and Trustees, 1990-1991.

ERIC Educational Resources Information Center

Illinois Univ., Urbana. Graduate School of Library and Information Science.

The fourth in a series, this publication presents a statistical picture of Illinois Public Libraries during the 1990-1991 fiscal year. Its purpose is to provide librarians and trustees with statistics that can be compared to those of other libraries of similar size and environment to determine whether the library is above or below the average for…

Collection overlap in hospital health sciences libraries: a case study.

PubMed Central

Stroyan, S

1985-01-01

Given similar demographics (age, size, and user population), to what extent do community hospital libraries differ in collection content? It is sometimes assumed that hospital libraries are relatively homogeneous and therefore subject to standardized procedures and collection development guides. This study compares the holdings of two community hospital libraries in Illinois to determine similarities and differences. PMID:4052675

The Impact of the Economic Downturn on Libraries: With Special Reference to University Libraries

ERIC Educational Resources Information Center

Nicholas, David; Rowlands, Ian; Jubb, Michael; Jamali, Hamid R.

2010-01-01

Evidence is presented of the extent to which libraries from around the world are experiencing financial hardship as a result of the world-wide economic downturn. Comparative analyses are provides on the grounds of country, sector and size of institution. The article concentrates on the situation of UK and US university libraries and is based on…

How Much Space Does a Library Need? Justifying Collections Space in an Electronic Age

ERIC Educational Resources Information Center

Butkovich, Nancy J.

2010-01-01

In 2002, plans to merge Penn State's Physical Sciences Library and Mathematics Library provoked a controversy in the Eberly College of Science over the size of the library needed to support its departments. The College contended that a physical collection no more than 5 years old was adequate. A study of astronomy, chemistry, mathematics, physics,…

Consultants' Corner: System Performance. A Forum.

ERIC Educational Resources Information Center

Drabenstott, John, Ed.

1986-01-01

Five library consultants address issues that affect online system performance: options in system design that relate to diverse library requirements; criteria that most affect performance; benchmark tests and sizing criteria; minimalizing the risks of miscalculation; and the roles and responsibilities of vendors, libraries, and consultants.…

An Examination of Library World Wide Web Sites at Medium-Sized Universities.

ERIC Educational Resources Information Center

Tolppanen, Bradley P.; Miller, Joan; Wooden, Martha H.

2000-01-01

Presents the results of a study of Web sites for 133 academic libraries serving medium-sized universities. Suggests that navigational and design aspects need improvement; information should not be included unless it will be accessed and used; and greater use should be made of online tutorials and virtual tours to supplement regular bibliographic…

On Compact Book Storage in Libraries.

ERIC Educational Resources Information Center

Ravindran, Arunachalam

The optimal storage of books by size in libraries is considered in this paper. It is shown that for a given collection of books of various sizes, the optimum number of shelf heights to use can be determined by finding the shortest path in an equivalent network. Applications of this model to inventory control, assortment and packaging problems are…

USER SERVICES AND EXTENSION SERVICES IN SELECTED SPECIAL LIBRARIES AND INFORMATION CENTERS IN THE UNITED STATES.

ERIC Educational Resources Information Center

NONINI, CERISE

A SURVEY BY QUESTIONNAIRE WAS MADE OF THE PROBLEM OF USER SERVICES AND EXTENSION SERVICES USED IN THE DISSEMINATION OF MATERIALS AND INFORMATION TO A SELECTED NUMBER OF INDUSTRIAL LIBRARIES. THE SURVEY RESULTED IN DATA CONCERNING STAFF SIZE, PROFESSIONAL-TO-CLERICAL RATIO, SIZE OF BOOK, DOCUMENT, PERIODICAL AND MICROFORM COLLECTIONS, LIBRARY…

78 FR 58300 - Texas Eastern Transmission, LP; Notice of Availability of the Environmental Assessment for the...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-23

... Mississippi. \\2\\ A ``pig'' is a tool that is inserted into and moves through the pipeline, and is used for... Web site ( www.ferc.gov ) using the eLibrary link. A limited number of copies of the EA are available... using the eComment feature on the Commission's Web site ( www.ferc.gov ) under the link to Documents and...

76 FR 51966 - Texas Eastern Transmission, LP; Notice of Intent To Prepare an Environmental Assessment for the...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-08-19

... using the link called ``eLibrary'' or from the Commission's Public Reference Room, 888 First Street, NE... transportation service of 27,000 dekatherms per day of natural gas. \\2\\ A ``pig'' is a tool that is inserted into... all those receiving this notice in the mail and are available at http://www.ferc.gov using the link...

75 FR 24938 - Questar Pipeline Company; Notice of Intent to Prepare an Environmental Assessment for the Planned...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-06

.../receivers; \\2\\ \\2\\ A ``pig'' is a tool that is inserted into and moves through the pipeline, and is used for...://www.ferc.gov using the link called ``eLibrary'' or from the Commission's Public Reference Room, 888... feature, which is located at http://www.ferc.gov under the link called ``Documents and Filings''. A Quick...

EcpA, an extracellular protease, is a specific virulence factor required by Xanthomonas oryzae pv. oryzicola but not by X. oryzae pv. oryzae in rice

USDA-ARS?s Scientific Manuscript database

Previously, twelve protease-deficient mutants of Xanthomonas oryzae pv. oryzicola (Xoc) RS105 strain were recovered from a Tn5-tagged mutant library. In the current study, the Tn5 insertion site in each mutant was mapped. Mutations in genes encoding components of the type II secretion apparatus, cAM...

Essential Genes for In Vitro Growth of the Endophyte Herbaspirillum seropedicae SmR1 as Revealed by Transposon Insertion Site Sequencing.

PubMed

Rosconi, Federico; de Vries, Stefan P W; Baig, Abiyad; Fabiano, Elena; Grant, Andrew J

2016-11-15

The interior of plants contains microorganisms (referred to as endophytes) that are distinct from those present at the root surface or in the surrounding soil. Herbaspirillum seropedicae strain SmR1, belonging to the betaproteobacteria, is an endophyte that colonizes crops, including rice, maize, sugarcane, and sorghum. Different approaches have revealed genes and pathways regulated during the interactions of H. seropedicae with its plant hosts. However, functional genomic analysis of transposon (Tn) mutants has been hampered by the lack of genetic tools. Here we successfully employed a combination of in vivo high-density mariner Tn mutagenesis and targeted Tn insertion site sequencing (Tn-seq) in H. seropedicae SmR1. The analysis of multiple gene-saturating Tn libraries revealed that 395 genes are essential for the growth of H. seropedicae SmR1 in tryptone-yeast extract medium. A comparative analysis with the Database of Essential Genes (DEG) showed that 25 genes are uniquely essential in H. seropedicae SmR1. The Tn mutagenesis protocol developed and the gene-saturating Tn libraries generated will facilitate elucidation of the genetic mechanisms of the H. seropedicae endophytic lifestyle. A focal point in the study of endophytes is the development of effective biofertilizers that could help to reduce the input of agrochemicals in croplands. Besides the ability to promote plant growth, a good biofertilizer should be successful in colonizing its host and competing against the native microbiota. By using a systematic Tn-based gene-inactivation strategy and massively parallel sequencing of Tn insertion sites (Tn-seq), it is possible to study the fitness of thousands of Tn mutants in a single experiment. We have applied the combination of these techniques to the plant-growth-promoting endophyte Herbaspirillum seropedicae SmR1. The Tn mutant libraries generated will enable studies into the genetic mechanisms of H. seropedicae-plant interactions. The approach that we have taken is applicable to other plant-interacting bacteria. Copyright © 2016 Rosconi et al.

Ecomorphology of parasite attachment: experiments with feather lice.

PubMed

Bush, Sarah E; Sohn, Edward; Clayton, Dale H

2006-02-01

The host specificity of some parasites can be reinforced by morphological specialization for attachment to mobile hosts. For example, ectoparasites with adaptations for attaching to hosts of a particular size might not be able to remain attached to larger or smaller hosts. This hypothesis is suggested by the positive correlation documented between the body sizes of many parasites and their hosts. We adopted an ecomorphological approach to test the attachment hypothesis. We tested the ability of host-specific feather lice (Phthiraptera: Ischnocera) to attach to 6 novel species of pigeons and doves that vary in size by nearly 2 orders of magnitude. Surprisingly, Rock Pigeon lice (Columbicola columbae) remained attached equally well to all 6 novel host species. We tested the relative importance of 3 factors that could facilitate louse attachment: whole-body insertion, tarsal claw use, and mandible use. Insertion, per se, was not necessary for attachment. However, insertion on coarse feathers of large hosts allowed lice to access feather barbules with their mandibles. Mandible use was a key component of attachment regardless of feather size. Attachment constraints do not appear to reinforce host specificity in this system.

Flexible CRISPR library construction using parallel oligonucleotide retrieval

PubMed Central

Read, Abigail; Gao, Shaojian; Batchelor, Eric

2017-01-01

Abstract CRISPR/Cas9-based gene knockout libraries have emerged as a powerful tool for functional screens. We present here a set of pre-designed human and mouse sgRNA sequences that are optimized for both high on-target potency and low off-target effect. To maximize the chance of target gene inactivation, sgRNAs were curated to target both 5΄ constitutive exons and exons that encode conserved protein domains. We describe here a robust and cost-effective method to construct multiple small sized CRISPR library from a single oligo pool generated by array synthesis using parallel oligonucleotide retrieval. Together, these resources provide a convenient means for individual labs to generate customized CRISPR libraries of variable size and coverage depth for functional genomics application. PMID:28334828

Health sciences library building projects, 1996-1997 survey.

PubMed Central

Bowden, V M

1998-01-01

Nine building projects are briefly described, including four new libraries, two renovations, and three combined renovations and additions. The libraries range in size from 657 square feet to 136,832 square feet, with seating varying from 14 to 635. Three hospital libraries and four academic health sciences libraries are described in more detail. In each case an important consideration was the provision for computer access. Two of the libraries expanded their space for historical collections. Three of the libraries added mobile shelving as a way of storing print materials while providing space for other activities. Images PMID:9549012

Droplet Digital™ PCR Next-Generation Sequencing Library QC Assay.

PubMed

Heredia, Nicholas J

2018-01-01

Digital PCR is a valuable tool to quantify next-generation sequencing (NGS) libraries precisely and accurately. Accurately quantifying NGS libraries enable accurate loading of the libraries on to the sequencer and thus improve sequencing performance by reducing under and overloading error. Accurate quantification also benefits users by enabling uniform loading of indexed/barcoded libraries which in turn greatly improves sequencing uniformity of the indexed/barcoded samples. The advantages gained by employing the Droplet Digital PCR (ddPCR™) library QC assay includes the precise and accurate quantification in addition to size quality assessment, enabling users to QC their sequencing libraries with confidence.

Automated System Marketplace 1988: Focused on Fulfilling Commitments.

ERIC Educational Resources Information Center

Walton, Robert A.; Bridge, Frank R.

1989-01-01

Analyzes trends in the library automation marketplace. Market shares for online vendors are examined in terms of total installations, academic libraries, public libraries, revenues, differently sized systems, and foreign installations. Hardware availability, operating systems, and interfaces with MARC are also discussed for each vendor. A source…

An Integrated Library System: Preliminary Considerations.

ERIC Educational Resources Information Center

Neroda, Edward

Noting difficulties experienced by small to medium sized colleges in acquiring integrated library computer systems, this position paper outlines issues related to the subject with the intention of increasing familiarity and interest in integrated library systems. The report includes: a brief review of technological advances as they relate to…

Cataloging Before and After OCLC. Illinois Valley Library System OCLC Experimental Project. Report No. 3.

ERIC Educational Resources Information Center

Bills, Linda G.

A project was conducted from 1980 to 1982 to determine the costs and benefits of OCLC use in 29 small and medium-sized member libraries of the Illinois Valley Library System (IVLS). Academic, school, public, and special libraries participated by recording the time and staffing levels used for and the cost of OCLC and pre-OCLC cataloging (by…

Maine School Library Survey. Statistics of Public School Libraries in Maine Serving Grades K-12, from Data Gathered February 1990.

ERIC Educational Resources Information Center

Soule, Margaret

This survey of the current status of public school libraries in Maine was intended to provide statistical data as a basis for improving the school library media center program in these schools. Information was gathered that detailed how resources and delivery of services differed across grade level; across variation in size of school; between…

Clinic on Library Applications of Data Processing, 1972. Proceedings: Applications of On-Line Computers to Library Problems.

ERIC Educational Resources Information Center

Lancaster, F. Wilfrid, Ed.

In planning this ninth annual clinic an attempt was made to include papers on a wide range of library applications of on-line computers, as well as to include libraries of various types and various sizes. Two papers deal with on-line circulation control (the Ohio State University system, described by Hugh C. Atkinson, and the Northwestern…

Mobile elements reveal small population size in the ancient ancestors of Homo sapiens.

PubMed

Huff, Chad D; Xing, Jinchuan; Rogers, Alan R; Witherspoon, David; Jorde, Lynn B

2010-02-02

The genealogies of different genetic loci vary in depth. The deeper the genealogy, the greater the chance that it will include a rare event, such as the insertion of a mobile element. Therefore, the genealogy of a region that contains a mobile element is on average older than that of the rest of the genome. In a simple demographic model, the expected time to most recent common ancestor (TMRCA) is doubled if a rare insertion is present. We test this expectation by examining single nucleotide polymorphisms around polymorphic Alu insertions from two completely sequenced human genomes. The estimated TMRCA for regions containing a polymorphic insertion is two times larger than the genomic average (P < <10(-30)), as predicted. Because genealogies that contain polymorphic mobile elements are old, they are shaped largely by the forces of ancient population history and are insensitive to recent demographic events, such as bottlenecks and expansions. Remarkably, the information in just two human DNA sequences provides substantial information about ancient human population size. By comparing the likelihood of various demographic models, we estimate that the effective population size of human ancestors living before 1.2 million years ago was 18,500, and we can reject all models where the ancient effective population size was larger than 26,000. This result implies an unusually small population for a species spread across the entire Old World, particularly in light of the effective population sizes of chimpanzees (21,000) and gorillas (25,000), which each inhabit only one part of a single continent.

A Case Study and Analysis of a Successful and Collaborative Student-Centered Textbook Reserve Program in a Mid-Size Academic Library

ERIC Educational Resources Information Center

Schlak, Timothy M.; Johnston, Bruce

2018-01-01

This article presents an innovative textbook reserve program at a mid-sized academic library. Research conducted subsequent to the program's launch showed a positive correlation between students' use of the program and their perceived academic success. In addition, the program has proved effective at helping students with college affordability.…

Installing a Microcomputer Lab in a Medium-Sized Academic Library.

ERIC Educational Resources Information Center

Hallman, Clark N.; And Others

Designed to serve as a blueprint for other libraries developing plans for microcomputer facilities, this report describes the planning and implementation of a microcomputer laboratory at South Dakota State University's Hilton M. Briggs Library. The university's plan for installing microcomputer labs on campus and the initial planning process…

Perceptions of Library Leadership in a Time of Change.

ERIC Educational Resources Information Center

Deekle, Peter V.; de Klerk, Ann

1992-01-01

Reports on a survey of chief academic officers and library directors at over 250 small- and medium-sized private colleges and universities. Responses indicate that institution administrators were aware of new trends in information management but did not recognize library directors' qualifications for broader administrative participation. (11…

Signs of the Times: Signage in the Library.

ERIC Educational Resources Information Center

Johnson, Carolyn

1993-01-01

Discusses the use of signs in libraries and lists 12 steps to create successful signage. Highlights include consistency, location, color, size, lettering, types of material, user needs, signage policy, planning, in-house fabrication versus vendors, and evaluation, A selected bibliography of 24 sources of information on library signage is included.…

Are We There Yet? Evaluating Library Collections, Reference Services, Programs, and Personnel.

ERIC Educational Resources Information Center

Robbins-Carter, Jane; Zweizig, Douglas L.

1985-01-01

This second in a five-lesson tutorial on library evaluation focuses on the evaluation of library collections. Highlights include the seven-step evaluation process described in lesson one; quantitative methods (total size, unfilled requests, circulation, turnover rate); and qualitative methods (impressionistic, list-checking). One required and…

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

Lin, Qingqing; Li, Huilin; Wang, Tong

Perfringolysin O (PFO) is a transmembrane (TM) β-barrel protein that inserts into mammalian cell membranes. Once inserted into membranes, PFO assembles into pore-forming oligomers containing 30–50 PFO monomers. These form a pore of up to 300 Å, far exceeding the size of most other proteinaceous pores. In this study, we found that altering PFO TM segment length can alter the size of PFO pores. A PFO mutant with lengthened TM segments oligomerized to a similar extent as wild-type PFO, and exhibited pore-forming activity and a pore size very similar to wild-type PFO as measured by electron microscopy and a leakagemore » assay. In contrast, PFO with shortened TM segments exhibited a large reduction in pore-forming activity and pore size. This suggests that the interaction between TM segments can greatly affect the size of pores formed by TM β-barrel proteins. PFO may be a promising candidate for engineering pore size for various applications.« less

A physical map of a BAC clone contig covering the entire autosome insertion between ovine MHC Class IIa and IIb

PubMed Central

2012-01-01

Background The ovine Major Histocompatibility Complex (MHC) harbors genes involved in overall resistance/susceptibility of the host to infectious diseases. Compared to human and mouse, the ovine MHC is interrupted by a large piece of autosome insertion via a hypothetical chromosome inversion that constitutes ~25% of ovine chromosome 20. The evolutionary consequence of such an inversion and an insertion (inversion/insertion) in relation to MHC function remains unknown. We previously constructed a BAC clone physical map for the ovine MHC exclusive of the insertion region. Here we report the construction of a high-density physical map covering the autosome insertion in order to address the question of what the inversion/insertion had to do with ruminants during the MHC evolution. Results A total of 119 pairs of comparative bovine oligo primers were utilized to screen an ovine BAC library for positive clones and the orders and overlapping relationships of the identified clones were determined by DNA fingerprinting, BAC-end sequencing, and sequence-specific PCR. A total of 368 positive BAC clones were identified and 108 of the effective clones were ordered into an overlapping BAC contig to cover the consensus region between ovine MHC class IIa and IIb. Therefore, a continuous physical map covering the entire ovine autosome inversion/insertion region was successfully constructed. The map confirmed the bovine sequence assembly for the same homologous region. The DNA sequences of 185 BAC-ends have been deposited into NCBI database with the access numbers HR309252 through HR309068, corresponding to dbGSS ID 30164010 through 30163826. Conclusions We have constructed a high-density BAC clone physical map for the ovine autosome inversion/insertion between the MHC class IIa and IIb. The entire ovine MHC region is now fully covered by a continuous BAC clone contig. The physical map we generated will facilitate MHC functional studies in the ovine, as well as the comparative MHC evolution in ruminants. PMID:22897909

Construction and screening of marine metagenomic libraries.

PubMed

Weiland, Nancy; Löscher, Carolin; Metzger, Rebekka; Schmitz, Ruth

2010-01-01

Marine microbial communities are highly diverse and have evolved during extended evolutionary processes of physiological adaptations under the influence of a variety of ecological conditions and selection pressures. They harbor an enormous diversity of microbes with still unknown and probably new physiological characteristics. Besides, the surfaces of marine multicellular organisms are typically covered by a consortium of epibiotic bacteria and act as barriers, where diverse interactions between microorganisms and hosts take place. Thus, microbial diversity in the water column of the oceans and the microbial consortia on marine tissues of multicellular organisms are rich sources for isolating novel bioactive compounds and genes. Here we describe the sampling, construction of large-insert metagenomic libraries from marine habitats and exemplarily one function based screen of metagenomic clones.

NEBNext Direct: A Novel, Rapid, Hybridization-Based Approach for the Capture and Library Conversion of Genomic Regions of Interest.

PubMed

Emerman, Amy B; Bowman, Sarah K; Barry, Andrew; Henig, Noa; Patel, Kruti M; Gardner, Andrew F; Hendrickson, Cynthia L

2017-07-05

Next-generation sequencing (NGS) is a powerful tool for genomic studies, translational research, and clinical diagnostics that enables the detection of single nucleotide polymorphisms, insertions and deletions, copy number variations, and other genetic variations. Target enrichment technologies improve the efficiency of NGS by only sequencing regions of interest, which reduces sequencing costs while increasing coverage of the selected targets. Here we present NEBNext Direct ® , a hybridization-based, target-enrichment approach that addresses many of the shortcomings of traditional target-enrichment methods. This approach features a simple, 7-hr workflow that uses enzymatic removal of off-target sequences to achieve a high specificity for regions of interest. Additionally, unique molecular identifiers are incorporated for the identification and filtering of PCR duplicates. The same protocol can be used across a wide range of input amounts, input types, and panel sizes, enabling NEBNext Direct to be broadly applicable across a wide variety of research and diagnostic needs. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

Population-based structural variation discovery with Hydra-Multi.

PubMed

Lindberg, Michael R; Hall, Ira M; Quinlan, Aaron R

2015-04-15

Current strategies for SNP and INDEL discovery incorporate sequence alignments from multiple individuals to maximize sensitivity and specificity. It is widely accepted that this approach also improves structural variant (SV) detection. However, multisample SV analysis has been stymied by the fundamental difficulties of SV calling, e.g. library insert size variability, SV alignment signal integration and detecting long-range genomic rearrangements involving disjoint loci. Extant tools suffer from poor scalability, which limits the number of genomes that can be co-analyzed and complicates analysis workflows. We have developed an approach that enables multisample SV analysis in hundreds to thousands of human genomes using commodity hardware. Here, we describe Hydra-Multi and measure its accuracy, speed and scalability using publicly available datasets provided by The 1000 Genomes Project and by The Cancer Genome Atlas (TCGA). Hydra-Multi is written in C++ and is freely available at https://github.com/arq5x/Hydra. aaronquinlan@gmail.com or ihall@genome.wustl.edu Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

Quantifying and resolving multiple vector transformants in S. cerevisiae plasmid libraries.

PubMed

Scanlon, Thomas C; Gray, Elizabeth C; Griswold, Karl E

2009-11-20

In addition to providing the molecular machinery for transcription and translation, recombinant microbial expression hosts maintain the critical genotype-phenotype link that is essential for high throughput screening and recovery of proteins encoded by plasmid libraries. It is known that Escherichia coli cells can be simultaneously transformed with multiple unique plasmids and thusly complicate recombinant library screening experiments. As a result of their potential to yield misleading results, bacterial multiple vector transformants have been thoroughly characterized in previous model studies. In contrast to bacterial systems, there is little quantitative information available regarding multiple vector transformants in yeast. Saccharomyces cerevisiae is the most widely used eukaryotic platform for cell surface display, combinatorial protein engineering, and other recombinant library screens. In order to characterize the extent and nature of multiple vector transformants in this important host, plasmid-born gene libraries constructed by yeast homologous recombination were analyzed by DNA sequencing. It was found that up to 90% of clones in yeast homologous recombination libraries may be multiple vector transformants, that on average these clones bear four or more unique mutant genes, and that these multiple vector cells persist as a significant proportion of library populations for greater than 24 hours during liquid outgrowth. Both vector concentration and vector to insert ratio influenced the library proportion of multiple vector transformants, but their population frequency was independent of transformation efficiency. Interestingly, the average number of plasmids born by multiple vector transformants did not vary with their library population proportion. These results highlight the potential for multiple vector transformants to dominate yeast libraries constructed by homologous recombination. The previously unrecognized prevalence and persistence of multiply transformed yeast cells have important implications for yeast library screens. The quantitative information described herein should increase awareness of this issue, and the rapid sequencing approach developed for these studies should be widely useful for identifying multiple vector transformants and avoiding complications associated with cells that have acquired more than one unique plasmid.

Preload-Release Mechanism For Mounting Electronics Boxes

NASA Technical Reports Server (NTRS)

Generoli, Robert M.; Young, Harry J.

1995-01-01

Proposed mechanism applies spring preload to electrical connector only while needed during insertion of electronics box into supporting frame. Once connector fully mated, mechanism relieves preload. As result, supporting structure sized to handle only individual load applied briefly by each connector on box during insertion.

Computerized tomography calibrator

NASA Technical Reports Server (NTRS)

Engel, Herbert P. (Inventor)

1991-01-01

A set of interchangeable pieces comprising a computerized tomography calibrator, and a method of use thereof, permits focusing of a computerized tomographic (CT) system. The interchangeable pieces include a plurality of nestable, generally planar mother rings, adapted for the receipt of planar inserts of predetermined sizes, and of predetermined material densities. The inserts further define openings therein for receipt of plural sub-inserts. All pieces are of known sizes and densities, permitting the assembling of different configurations of materials of known sizes and combinations of densities, for calibration (i.e., focusing) of a computerized tomographic system through variation of operating variables thereof. Rather than serving as a phanton, which is intended to be representative of a particular workpiece to be tested, the set of interchangeable pieces permits simple and easy standardized calibration of a CT system. The calibrator and its related method of use further includes use of air or of particular fluids for filling various openings, as part of a selected configuration of the set of pieces.

Using scientific evidence to improve hospital library services: Southern Chapter/Medical Library Association journal usage study.

PubMed

Dee, C R; Rankin, J A; Burns, C A

1998-07-01

Journal usage studies, which are useful for budget management and for evaluating collection performance relative to library use, have generally described a single library or subject discipline. The Southern Chapter/Medical Library Association (SC/MLA) study has examined journal usage at the aggregate data level with the long-term goal of developing hospital library benchmarks for journal use. Thirty-six SC/MLA hospital libraries, categorized for the study by size as small, medium, or large, reported current journal title use centrally for a one-year period following standardized data collection procedures. Institutional and aggregate data were analyzed for the average annual frequency of use, average costs per use and non-use, and average percent of non-used titles. Permutation F-type tests were used to measure difference among the three hospital groups. Averages were reported for each data set analysis. Statistical tests indicated no significant differences between the hospital groups, suggesting that benchmarks can be derived applying to all types of hospital libraries. The unanticipated lack of commonality among heavily used titles pointed to a need for uniquely tailored collections. Although the small sample size precluded definitive results, the study's findings constituted a baseline of data that can be compared against future studies.

Using scientific evidence to improve hospital library services: Southern Chapter/Medical Library Association journal usage study.

PubMed Central

Dee, C R; Rankin, J A; Burns, C A

1998-01-01

BACKGROUND: Journal usage studies, which are useful for budget management and for evaluating collection performance relative to library use, have generally described a single library or subject discipline. The Southern Chapter/Medical Library Association (SC/MLA) study has examined journal usage at the aggregate data level with the long-term goal of developing hospital library benchmarks for journal use. METHODS: Thirty-six SC/MLA hospital libraries, categorized for the study by size as small, medium, or large, reported current journal title use centrally for a one-year period following standardized data collection procedures. Institutional and aggregate data were analyzed for the average annual frequency of use, average costs per use and non-use, and average percent of non-used titles. Permutation F-type tests were used to measure difference among the three hospital groups. RESULTS: Averages were reported for each data set analysis. Statistical tests indicated no significant differences between the hospital groups, suggesting that benchmarks can be derived applying to all types of hospital libraries. The unanticipated lack of commonality among heavily used titles pointed to a need for uniquely tailored collections. CONCLUSION: Although the small sample size precluded definitive results, the study's findings constituted a baseline of data that can be compared against future studies. PMID:9681164

An improved yeast transformation method for the generation of very large human antibody libraries.

PubMed

Benatuil, Lorenzo; Perez, Jennifer M; Belk, Jonathan; Hsieh, Chung-Ming

2010-04-01

Antibody library selection by yeast display technology is an efficient and highly sensitive method to identify binders to target antigens. This powerful selection tool, however, is often hampered by the typically modest size of yeast libraries (approximately 10(7)) due to the limited yeast transformation efficiency, and the full potential of the yeast display technology for antibody discovery and engineering can only be realized if it can be coupled with a mean to generate very large yeast libraries. We describe here a yeast transformation method by electroporation that allows for the efficient generation of large antibody libraries up to 10(10) in size. Multiple components and conditions including CaCl(2), MgCl(2), sucrose, sorbitol, lithium acetate, dithiothreitol, electroporation voltage, DNA input and cell volume have been tested to identify the best combination. By applying this developed protocol, we have constructed a 1.4 x 10(10) human spleen antibody library essentially in 1 day with a transformation efficiency of 1-1.5 x 10(8) transformants/microg vector DNA. Taken together, we have developed a highly efficient yeast transformation method that enables the generation of very large and productive human antibody libraries for antibody discovery, and we are now routinely making 10(9) libraries in a day for antibody engineering purposes.

76 FR 51965 - National Fuel Gas Supply Corporation; Notice of Intent To Prepare an Environmental Assessment for...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-08-19

... crossings south of the Buffalo Compressor Station. \\1\\ A ``pig'' is a tool that is inserted into and moves... receiving this notice in the mail and are available at http://www.ferc.gov using the link called ``eLibrary... Commission's Web site at http://www.ferc.gov under the link to Documents and Filings. An eComment is an easy...

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

PubMed Central

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

1998-01-01

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

Chapter 7. Cloning and analysis of natural product pathways.

PubMed

Gust, Bertolt

2009-01-01

The identification of gene clusters of natural products has lead to an enormous wealth of information about their biosynthesis and its regulation, and about self-resistance mechanisms. Well-established routine techniques are now available for the cloning and sequencing of gene clusters. The subsequent functional analysis of the complex biosynthetic machinery requires efficient genetic tools for manipulation. Until recently, techniques for the introduction of defined changes into Streptomyces chromosomes were very time-consuming. In particular, manipulation of large DNA fragments has been challenging due to the absence of suitable restriction sites for restriction- and ligation-based techniques. The homologous recombination approach called recombineering (referred to as Red/ET-mediated recombination in this chapter) has greatly facilitated targeted genetic modifications of complex biosynthetic pathways from actinomycetes by eliminating many of the time-consuming and labor-intensive steps. This chapter describes techniques for the cloning and identification of biosynthetic gene clusters, for the generation of gene replacements within such clusters, for the construction of integrative library clones and their expression in heterologous hosts, and for the assembly of entire biosynthetic gene clusters from the inserts of individual library clones. A systematic approach toward insertional mutation of a complete Streptomyces genome is shown by the use of an in vitro transposon mutagenesis procedure.

A Bayesian nonparametric method for prediction in EST analysis

PubMed Central

Lijoi, Antonio; Mena, Ramsés H; Prünster, Igor

2007-01-01

Background Expressed sequence tags (ESTs) analyses are a fundamental tool for gene identification in organisms. Given a preliminary EST sample from a certain library, several statistical prediction problems arise. In particular, it is of interest to estimate how many new genes can be detected in a future EST sample of given size and also to determine the gene discovery rate: these estimates represent the basis for deciding whether to proceed sequencing the library and, in case of a positive decision, a guideline for selecting the size of the new sample. Such information is also useful for establishing sequencing efficiency in experimental design and for measuring the degree of redundancy of an EST library. Results In this work we propose a Bayesian nonparametric approach for tackling statistical problems related to EST surveys. In particular, we provide estimates for: a) the coverage, defined as the proportion of unique genes in the library represented in the given sample of reads; b) the number of new unique genes to be observed in a future sample; c) the discovery rate of new genes as a function of the future sample size. The Bayesian nonparametric model we adopt conveys, in a statistically rigorous way, the available information into prediction. Our proposal has appealing properties over frequentist nonparametric methods, which become unstable when prediction is required for large future samples. EST libraries, previously studied with frequentist methods, are analyzed in detail. Conclusion The Bayesian nonparametric approach we undertake yields valuable tools for gene capture and prediction in EST libraries. The estimators we obtain do not feature the kind of drawbacks associated with frequentist estimators and are reliable for any size of the additional sample. PMID:17868445

Fabrication of robust tooling for mass production of polymeric microfluidic devices

NASA Astrophysics Data System (ADS)

Fu, G.; Tor, S. B.; Loh, N. H.; Hardt, D. E.

2010-08-01

Polymer microfluidic devices are gaining popularity for bio-applications. In both commonly used methods for the fabrication of polymer microfluidic devices, i.e. injection molding and hot-embossing, the quality of a mold insert is of high importance. Micro powder injection molding (μPIM) provides a suitable option for metal mold insert fabrication. In this paper, two mold inserts with micro-features of different patterns and sizes were produced using 316L stainless steel powder and an in-house binder system. The mold inserts were successfully used to produce cyclic olefin copolymer (COC, trade name TOPAS) micromixer plates with micro-channels of widths 100 µm and 50 µm. Compared with CNC-machined hot work steel mold inserts, the quality of the micro-channels is better as far as geometrical quality and dimensional tolerance are concerned. However, surface finish and flatness of the μPIM mold inserts are inferior to those of CNC-machined mold inserts.

Estimating live fuels for shrubs and herbs with BIOPAK.

Treesearch

Joseph E. Means; Olga N Krankina; Hao Jiang; Hongyan Li

1996-01-01

This paper describes use of BIOPAK to calculate size classes of live fuels for shrubs and herbs. A library of equations to estimate such fuels in the Pacific Northwest and northern Rocky Mountains is presented and used in an example. These methods can be used in other regions if the user first enters fuel size-class equations for a given region into a new library by...

The Soviet Union and Eastern Europe: A Bibliographic Guide to Recommended Books for Small and Medium-Sized Libraries and School Media Centers.

ERIC Educational Resources Information Center

Horak, Stephan M.

Intended to aid librarians in small- and medium-sized libraries and media centers, this annotated bibliography lists 1,555 books focusing on the Soviet Union and Eastern Europe. The book is divided into four parts: (1) "General and Interrelated Themes--Union of the Soviet Socialist Republics and Eastern European Countries"; (2)…

Chronic behavior evaluation of a micro-machined neural implant with optimized design based on an experimentally derived model.

PubMed

Andrei, Alexandru; Welkenhuysen, Marleen; Ameye, Lieveke; Nuttin, Bart; Eberle, Wolfgang

2011-01-01

Understanding the mechanical interactions between implants and the surrounding tissue is known to have an important role for improving the bio-compatibility of such devices. Using a recently developed model, a particular micro-machined neural implant design aiming the reduction of insertion forces dependence on the insertion speed was optimized. Implantations with 10 and 100 μm/s insertion speeds showed excellent agreement with the predicted behavior. Lesion size, gliosis (GFAP), inflammation (ED1) and neuronal cells density (NeuN) was evaluated after 6 week of chronic implantation showing no insertion speed dependence.

Public Library Directors: A Career and Managerial Profile.

ERIC Educational Resources Information Center

Mech, Terrence

1989-01-01

Develops a career and managerial profile of directors of Northeastern medium-sized public libraries based on the responses of 217 directors. The results confirm the existence of many of the gender-based career patterns found among directors of academic and larger public libraries together with an emphasis on internal administrator roles. (16…

Automation Challenges of the 80's: What to Do until Your Integrated Library System Arrives.

ERIC Educational Resources Information Center

Allan, Ferne C.; Shields, Joyce M.

1986-01-01

A medium-sized aerospace library has developed interim solutions to automation needs by using software and equipment that were available in-house in preparation for an expected integrated library system. Automated processes include authors' file of items authored by employees, journal routing (including routing slips), statistics, journal…

Supervisory Rotation: Impact on an Academic Library Reference Staff.

ERIC Educational Resources Information Center

Perdue, Bob; Piotrowski, Chris

1986-01-01

Presents results of managerial rotation program (librarians take turns on two-year cycle serving as department head) in medium-sized academic library reference department. An assessment of both the advantages and disadvantages of such a plan examines impact of this innovative and collegial management technique on staff, library, and patrons. (7…

2004 National Awards for Museum & Library Service

ERIC Educational Resources Information Center

Institute of Museum and Library Services, 2004

2004-01-01

The National Awards for Museum and Library Service give national recognition to institutions that play an integral and essential part in our learning society. The awards celebrate the efforts of libraries and museums of all sizes to connect with their increasingly diverse communities and to serve as centers of lifelong learning. As the pace of…

The Elusive Cost of Library Software

ERIC Educational Resources Information Center

Breeding, Marshall

2009-01-01

Software pricing is not a straightforward issue, since each procurement involves a special business arrangement between a library and its chosen vendor. The author thinks that it is reasonable to scale the cost of a product to such factors as the size of the library, the complexity of the installation, the number of simultaneous users, or the…

Single Service Points in Libraries: A Review

ERIC Educational Resources Information Center

Frederiksen, Linda; Wilkinson, Brandon

2016-01-01

As libraries of all types and sizes continue to re-envision themselves to remain relevant in a rapidly changing information landscape, the single service point is visible evidence of this effort. In a complex environment, combining formerly disparate functional or service units is for many libraries both an innovative and effective way to manage…

InfoQUEST: An Online Catalog for Small Libraries.

ERIC Educational Resources Information Center

Campbell, Bonnie

1984-01-01

InfoQUEST is a microcomputer-based online public access catalog, designed for the small library handling file sizes up to 25,000 records. Based on the IBM-PC, or compatible machines, the system will accept downloading, in batch mode, of records from the library's file on the UTLAS Catalog Support System. (Author/EJS)

A study of hospital and medical libraries in Riyadh, Kingdom of Saudi Arabia.

PubMed Central

al-Ogla, S

1998-01-01

The study reported examined the status of hospital libraries, their sponsoring organizations, their staff, the academic qualifications of the head of the library, collection size, available space, buildings, and services. The study was limited to the hospitals with libraries for staff in Riyadh, the capital of Saudi Arabia. The data were collected through questionnaires sent to a sample of fifteen hospitals with medical libraries. Twelve libraries responded. This is the first study of its kind in Saudi Arabia, and it is hoped that similar surveys will be done covering the whole kingdom. PMID:9549013

The AHEC library program and consortia development in California.

PubMed

Jensen, M A; Maddalena, B

1986-07-01

A brief history of the first Area Health Education Center (AHEC) Library Program in California is presented, with a description of methodology and results. The goals of this program were to develop and improve hospital library resources and services, to train hospital library personnel, and to promote resource sharing in a medically underserved area. The health sciences library consortium that evolved became a model for the ten other library consortia in the state. Based on AHEC's twelve years' experience with consortia, from 1973 to 1985, recommendations are made as to size, composition, leadership, outside funding, group participation, publicity, and linkages.

Difficulties in spinal needle use. Insertion characteristics and failure rates associated with 25-, 27- and 29-gauge Quincke-type spinal needles.

PubMed

Tarkkila, P; Huhtala, J; Salminen, U

1994-08-01

The effect of different size (25-, 27- and 29-gauge) Quincke-type spinal needles on the incidence of insertion difficulties and failure rates was investigated in a randomised, prospective study with 300 patients. The needle size was randomised but the insertion procedure was standardised. The time to achieve dural puncture was significantly longer with the 29-gauge spinal needle compared with the larger bore needles and was due to the greater flexibility of the thin needle. However, the difference was less than 1 min and cannot be considered clinically significant. There were no significant differences between groups in the number of insertion attempts or failures and the same sensory level of analgesia was reached with all the needle sizes studied. Postoperatively, no postdural puncture headaches occurred in the 29-gauge spinal needle group, whilst in the 25- and 27-gauge needle groups, the postdural puncture headache rates were 7.4% and 2.1% respectively. The incidence of backache was similar in all study groups. We conclude that dural puncture with a 29-gauge spinal needle is clinically as easy as with larger bore needles and its use is indicated in patients who have a high risk of postdural puncture headache.

Decreasing transmembrane segment length greatly decreases perfringolysin O pore size

DOE PAGES

Lin, Qingqing; Li, Huilin; Wang, Tong; ...

2015-04-08

Perfringolysin O (PFO) is a transmembrane (TM) β-barrel protein that inserts into mammalian cell membranes. Once inserted into membranes, PFO assembles into pore-forming oligomers containing 30–50 PFO monomers. These form a pore of up to 300 Å, far exceeding the size of most other proteinaceous pores. In this study, we found that altering PFO TM segment length can alter the size of PFO pores. A PFO mutant with lengthened TM segments oligomerized to a similar extent as wild-type PFO, and exhibited pore-forming activity and a pore size very similar to wild-type PFO as measured by electron microscopy and a leakagemore » assay. In contrast, PFO with shortened TM segments exhibited a large reduction in pore-forming activity and pore size. This suggests that the interaction between TM segments can greatly affect the size of pores formed by TM β-barrel proteins. PFO may be a promising candidate for engineering pore size for various applications.« less

Reference quality assembly of the 3.5-Gb genome of Capsicum annuum from a single linked-read library.

PubMed

Hulse-Kemp, Amanda M; Maheshwari, Shamoni; Stoffel, Kevin; Hill, Theresa A; Jaffe, David; Williams, Stephen R; Weisenfeld, Neil; Ramakrishnan, Srividya; Kumar, Vijay; Shah, Preyas; Schatz, Michael C; Church, Deanna M; Van Deynze, Allen

2018-01-01

Linked-Read sequencing technology has recently been employed successfully for de novo assembly of human genomes, however, the utility of this technology for complex plant genomes is unproven. We evaluated the technology for this purpose by sequencing the 3.5-gigabase (Gb) diploid pepper ( Capsicum annuum ) genome with a single Linked-Read library. Plant genomes, including pepper, are characterized by long, highly similar repetitive sequences. Accordingly, significant effort is used to ensure that the sequenced plant is highly homozygous and the resulting assembly is a haploid consensus. With a phased assembly approach, we targeted a heterozygous F 1 derived from a wide cross to assess the ability to derive both haplotypes and characterize a pungency gene with a large insertion/deletion. The Supernova software generated a highly ordered, more contiguous sequence assembly than all currently available C. annuum reference genomes. Over 83% of the final assembly was anchored and oriented using four publicly available  de novo linkage maps. A comparison of the annotation of conserved eukaryotic genes indicated the completeness of assembly. The validity of the phased assembly is further demonstrated with the complete recovery of both 2.5-Kb insertion/deletion haplotypes of the PUN1 locus in the F 1 sample that represents pungent and nonpungent peppers, as well as nearly full recovery of the BUSCO2 gene set within each of the two haplotypes. The most contiguous pepper genome assembly to date has been generated which demonstrates that Linked-Read library technology provides a tool to de novo assemble complex highly repetitive heterozygous plant genomes. This technology can provide an opportunity to cost-effectively develop high-quality genome assemblies for other complex plants and compare structural and gene differences through accurate haplotype reconstruction.

Metagenomes of complex microbial consortia derived from different soils as sources for novel genes conferring formation of carbonyls from short-chain polyols on Escherichia coli.

PubMed

Knietsch, Anja; Waschkowitz, Tanja; Bowien, Susanne; Henne, Anke; Daniel, Rolf

2003-01-01

Metagenomic DNA libraries from three different soil samples (meadow, sugar beet field, cropland) were constructed. The three unamplified libraries comprised approximately 1267000 independent clones and harbored approximately 4.05 Gbp of environmental DNA. Approximately 300000 recombinant Escherichia coli strains of each library per test substrate were screened for the production of carbonyls from short-chain (C2 to C4) polyols such as 1,2-ethanediol, 2,3-butanediol, and a mixture of glycerol and 1,2-propanediol on indicator agar. Twenty-four positive E. COLI clones were obtained during the initial screen. Fifteen of them contained recombinant plasmids, designated pAK201-215, which conferred a stable carbonyl-forming phenotype on E. coli Sequencing revealed that the inserts of pAK201-215 encoded 26 complete and 14 incomplete predicted protein-encoding genes. Most of these genes were similar to genes with unknown functions from other microorganisms or unrelated to any other known gene. The further analysis was focused on the 7 plasmids (pAK204, pAK206, pAK208, and pAK210-213) recovered from the positive clones, which exhibited an NAD(H)-dependent alcohol oxidoreductase activity with polyols or the correlating carbonyls as substrates in crude extracts. Three genes (ORF6, ORF24, and ORF25) conferring this activity were identified during subcloning of the inserts of pAK204, pAK211, and pAK212. The sequences of the three deduced gene products revealed no significant similarities to known alcohol oxidoreductases, but contained putative glycine-rich regions, which are characteristic for binding of nicotinamide cofactors. Copyright 2003 S. Karger AG, Basel

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

PubMed

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

2013-12-01

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

The Contemporary Medical Society Library

PubMed Central

Crawford, Susan; Michel, Carol; Waligorski, Conrad

1965-01-01

Four hundred sixty-eight medical societies in the United States were surveyed to determine those which sponsor libraries. Seventy-eight libraries were identified, of which eighteen are “marginal” and nine are jointly supported by a medical school and a society, leaving fifty-one relatively “substantial” libraries whose major support is through society membership. Characteristics measured include size of collection, types of media, staff, budget, services, and sources of support. Questions are raised concerning the role of the medical library as one institution which participates in the continuing education of the physician. PMID:14271112

Toward a Molecular Cytogenetic Map for Cultivated Sunflower (Helianthus annuus L.) by Landed BAC/BIBAC Clones

PubMed Central

Feng, Jiuhuan; Liu, Zhao; Cai, Xiwen; Jan, Chao-Chien

2013-01-01

Conventional karyotypes and various genetic linkage maps have been established in sunflower (Helianthus annuus L., 2n = 34). However, the relationship between linkage groups and individual chromosomes of sunflower remains unknown and has considerable relevance for the sunflower research community. Recently, a set of linkage group-specific bacterial /binary bacterial artificial chromosome (BAC/BIBAC) clones was identified from two complementary BAC and BIBAC libraries constructed for cultivated sunflower cv. HA89. In the present study, we used these linkage group-specific clones (∼100 kb in size) as probes to in situ hybridize to HA89 mitotic chromosomes at metaphase using the BAC- fluorescence in situ hybridization (FISH) technique. Because a characteristic of the sunflower genome is the abundance of repetitive DNA sequences, a high ratio of blocking DNA to probe DNA was applied to hybridization reactions to minimize the background noise. As a result, all sunflower chromosomes were anchored by one or two BAC/BIBAC clones with specific FISH signals. FISH analysis based on tandem repetitive sequences, such as rRNA genes, has been previously reported; however, the BAC-FISH technique developed here using restriction fragment length polymorphism (RFLP)−derived BAC/BIBAC clones as probes to apply genome-wide analysis is new for sunflower. As chromosome-specific cytogenetic markers, the selected BAC/BIBAC clones that encompass the 17 linkage groups provide a valuable tool for identifying sunflower cytogenetic stocks (such as trisomics) and tracking alien chromosomes in interspecific crosses. This work also demonstrates the potential of using a large-insert DNA library for the development of molecular cytogenetic resources. PMID:23316437

Assembly of ordered contigs of cosmids selected with YACs of human chromosome 13

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

Fischer, S.G.; Cayanis, E.; Boukhgalter, B.

1994-06-01

The authors have developed an efficient method for assembling ordered cosmid contigs aligned to mega-YACs and midi-YACs (average insert sizes of 1.0 and 0.35 Mb, respectively) and used this general method to initiate high-resolution physical mapping of human chromosome 13 (Chr 13). Chr 13-enriched midi-YAC (mYAC) and mega-YAC (MYAC) sublibraries were obtained from corresponding CEPH total human YAC libraries by selecting colonies with inter-Alu PCR probes derived from Chr 13 monochromosomal cell hybrid DNA. These sublibraries were arrayed on filters at high density. In this approach, the MYAC 13 sublibrary is screened by hybridization with cytogenetically assigned Chr 13 DNAmore » probes to select one or a small subset of MYACs. Inter-Alu PCR products from each mYAC are then hybridized to the MYAC and mYAC sublibraries to identify overlapping YACs and to an arrayed Chr 13-specific cosmid library to select corresponding cosmids. The set of selected cosmids, gridded on filters at high density, is hybridized with inter-Alu PCR products from each of the overlapping YACs to identify subsets of cosmids and also with riboprobes from each cosmid of the arrayed set ({open_quotes}cosmid matrix cross-hybridization{close_quotes}). From these data, cosmid contigs are assembled by a specifically designed computer program. Application of this method generates cosmid contigs spanning the length of a MYAC with few gaps. To provide a high-resolution map, ends of cosmids are sequenced at preselected sites to position densely spaced sequence-tagged sites. 33 refs., 7 figs., 1 tab.« less

A Computerized Cataloging System for an Outdoor Program Library or Resource Center.

ERIC Educational Resources Information Center

Watters, Ron

The Outdoor Resource Library Cataloging System is a computer software program designed primarily for outdoor programs with small to medium-sized resource centers. The software is free to nonprofit organizations and is available from the Idaho State University Outdoor Program. The software is used to construct a database of library materials, which…

A Methodology for Estimating the Size of Subject Collections, Using African Studies as an Example.

ERIC Educational Resources Information Center

Lauer, Joseph J.

1983-01-01

Provides formula for estimating number of Africana titles in large libraries using Library of Congress classification schedule. To determine percentage of Africana falling in DT section, distribution of titles in two academic libraries with separate shelflists is analyzed. Core categories of Africana and distribution of northern African titles are…

The Library Manager's Deskbook: 102 Expert Solutions to 101 Common Dilemmas.

ERIC Educational Resources Information Center

Carson, Paula Phillips; And Others

This is a handbook of advice for handling the everyday problems encountered in all types and sizes of libraries. It is designed to assist managers before, during, and after crises develop. Organized in an question-and-answer format, it tackles many dilemmas that can occur in the library, then offers solutions drawn from actual experience. The…

BAC Libraries from Wheat Chromosome 7D – Efficient Tool for Positional Cloning of Aphid Resistance Genes

USDA-ARS?s Scientific Manuscript database

Positional cloning in bread wheat is a tedious task due to its huge genome size (~17 Gbp) and polyploid character. BAC libraries represent an essential tool for positional cloning. However, wheat BAC libraries comprise more than million clones, which make their screening very laborious. Here we pres...

Southeast Asia: A Bibliography for Undergraduate Libraries. Occasional Publication Number Thirteen.

ERIC Educational Resources Information Center

Johnson, Donald Clay, Ed.; And Others

Southeast Asian library resources primarily for the humanities and social sciences are listed in this bibliography that is one of a series. The volume furnishes a basic and balanced bibliography on all the countries of Southeast Asia, of manageable size for the undergraduate library. Selections include: 1) few works in languages other than…

The Management of Change and Improvement in Academic Library Performance.

ERIC Educational Resources Information Center

Webster, Duane

As academic libraries increase in size and become more complex, their organization tends to become more bureaucratic in nature and resistant to change. This paper describes a range of both internal and external strategies which have been used to introduce constructive change into the management of academic libraries in North America and the major…

The Responsive Public Library: How to Develop and Market a Winning Collection. Second Edition.

ERIC Educational Resources Information Center

Baker, Sharon L.; Wallace, Karen L.

This book provides a broad, introductory overview of issues affecting the marketing of public library collections, with examples and research results from more than 200 libraries of all sizes. This new edition of the work updates and expands the original, referencing new studies (published since 1992), encompassing more of the literature from…

Cloning and expression of 130-kd mosquito-larvicidal delta-endotoxin gene of Bacillus thuringiensis var. Israelensis in Escherichia coli.

PubMed

Angsuthanasombat, C; Chungjatupornchai, W; Kertbundit, S; Luxananil, P; Settasatian, C; Wilairat, P; Panyim, S

1987-07-01

Five recombinant E. coli clones exhibiting toxicity to Aedes aegypti larvae were obtained from a library of 800 clones containing XbaI DNA fragments of 110 kb plasmid from B. thuringiensis var. israelensis. All the five clones (pMU 14/258/303/388/679) had the same 3.8-kb insert and encoded a major protein of 130 kDa which was highly toxic to A. aegypti larvae. Three clones (pMU 258/303/388) transcribed the 130 kD a gene in the same direction as that of lac Z promoter of pUC12 vector whereas the transcription of the other two (pMU 14/679) was in the opposite direction. A 1.9-kb fragment of the 3.8 kb insert coded for a protein of 65 kDa. Partial DNA sequence of the 3.8 kb insert, corresponding to the 5'-terminal of the 130 kDa gene, revealed a continuous reading frame, a Shine-Dalgarno sequence and a tentative 5'-regulatory region. These results demonstrated that the 3.8 kb insert is a minimal DNA fragment containing a regulatory region plus the coding sequence of the 130 kDa protein that is highly toxic to mosquito larvae.

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

PubMed

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

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

Genome-Wide Transposon Mutagenesis in Pathogenic Leptospira Species▿ ‡

PubMed Central

Murray, Gerald L.; Morel, Viviane; Cerqueira, Gustavo M.; Croda, Julio; Srikram, Amporn; Henry, Rebekah; Ko, Albert I.; Dellagostin, Odir A.; Bulach, Dieter M.; Sermswan, Rasana W.; Adler, Ben; Picardeau, Mathieu

2009-01-01

Leptospira interrogans is the most common cause of leptospirosis in humans and animals. Genetic analysis of L. interrogans has been severely hindered by a lack of tools for genetic manipulation. Recently we developed the mariner-based transposon Himar1 to generate the first defined mutants in L. interrogans. In this study, a total of 929 independent transposon mutants were obtained and the location of insertion determined. Of these mutants, 721 were located in the protein coding regions of 551 different genes. While sequence analysis of transposon insertion sites indicated that transposition occurred in an essentially random fashion in the genome, 25 unique transposon mutants were found to exhibit insertions into genes encoding 16S or 23S rRNAs, suggesting these genes are insertional hot spots in the L. interrogans genome. In contrast, loci containing notionally essential genes involved in lipopolysaccharide and heme biosynthesis showed few transposon insertions. The effect of gene disruption on the virulence of a selected set of defined mutants was investigated using the hamster model of leptospirosis. Two attenuated mutants with disruptions in hypothetical genes were identified, thus validating the use of transposon mutagenesis for the identification of novel virulence factors in L. interrogans. This library provides a valuable resource for the study of gene function in L. interrogans. Combined with the genome sequences of L. interrogans, this provides an opportunity to investigate genes that contribute to pathogenesis and will provide a better understanding of the biology of L. interrogans. PMID:19047402

Genome-wide transposon mutagenesis in pathogenic Leptospira species.

PubMed

Murray, Gerald L; Morel, Viviane; Cerqueira, Gustavo M; Croda, Julio; Srikram, Amporn; Henry, Rebekah; Ko, Albert I; Dellagostin, Odir A; Bulach, Dieter M; Sermswan, Rasana W; Adler, Ben; Picardeau, Mathieu

2009-02-01

Leptospira interrogans is the most common cause of leptospirosis in humans and animals. Genetic analysis of L. interrogans has been severely hindered by a lack of tools for genetic manipulation. Recently we developed the mariner-based transposon Himar1 to generate the first defined mutants in L. interrogans. In this study, a total of 929 independent transposon mutants were obtained and the location of insertion determined. Of these mutants, 721 were located in the protein coding regions of 551 different genes. While sequence analysis of transposon insertion sites indicated that transposition occurred in an essentially random fashion in the genome, 25 unique transposon mutants were found to exhibit insertions into genes encoding 16S or 23S rRNAs, suggesting these genes are insertional hot spots in the L. interrogans genome. In contrast, loci containing notionally essential genes involved in lipopolysaccharide and heme biosynthesis showed few transposon insertions. The effect of gene disruption on the virulence of a selected set of defined mutants was investigated using the hamster model of leptospirosis. Two attenuated mutants with disruptions in hypothetical genes were identified, thus validating the use of transposon mutagenesis for the identification of novel virulence factors in L. interrogans. This library provides a valuable resource for the study of gene function in L. interrogans. Combined with the genome sequences of L. interrogans, this provides an opportunity to investigate genes that contribute to pathogenesis and will provide a better understanding of the biology of L. interrogans.

46 CFR 160.052-5 - Construction-standard vests.

Code of Federal Regulations, 2011 CFR

2011-10-01

...) Buoyant inserts. The unicellular plastic foam buoyant inserts shall be cut and formed as shown on Dwg. 160...: SPECIFICATIONS AND APPROVAL LIFESAVING EQUIPMENT Specification for a Buoyant Vest, Unicellular Plastic Foam.... Two pieces of fabric shall be cut to the pattern shown on Dwg. No. 160.052-1, Sheet 1 for adult size...

46 CFR 160.052-5 - Construction-standard vests.

Code of Federal Regulations, 2012 CFR

2012-10-01

...) Buoyant inserts. The unicellular plastic foam buoyant inserts shall be cut and formed as shown on Dwg. 160...: SPECIFICATIONS AND APPROVAL LIFESAVING EQUIPMENT Specification for a Buoyant Vest, Unicellular Plastic Foam.... Two pieces of fabric shall be cut to the pattern shown on Dwg. No. 160.052-1, Sheet 1 for adult size...

46 CFR 160.052-5 - Construction-standard vests.

Code of Federal Regulations, 2014 CFR

2014-10-01

...) Buoyant inserts. The unicellular plastic foam buoyant inserts shall be cut and formed as shown on Dwg. 160...: SPECIFICATIONS AND APPROVAL LIFESAVING EQUIPMENT Specification for a Buoyant Vest, Unicellular Plastic Foam.... Two pieces of fabric shall be cut to the pattern shown on Dwg. No. 160.052-1, Sheet 1 for adult size...

46 CFR 160.052-5 - Construction-standard vests.

Code of Federal Regulations, 2013 CFR

2013-10-01

...) Buoyant inserts. The unicellular plastic foam buoyant inserts shall be cut and formed as shown on Dwg. 160...: SPECIFICATIONS AND APPROVAL LIFESAVING EQUIPMENT Specification for a Buoyant Vest, Unicellular Plastic Foam.... Two pieces of fabric shall be cut to the pattern shown on Dwg. No. 160.052-1, Sheet 1 for adult size...

Library Automation.

ERIC Educational Resources Information Center

Husby, Ole

1990-01-01

The challenges and potential benefits of automating university libraries are reviewed, with special attention given to cooperative systems. Aspects discussed include database size, the role of the university computer center, storage modes, multi-institutional systems, resource sharing, cooperative system management, networking, and intelligent…

Impact of New Nuclear Data Libraries on Small Sized Long Life CANDLE HTGR Design Parameters

NASA Astrophysics Data System (ADS)

Liem, Peng Hong; Hartanto, Donny; Tran, Hoai Nam

2017-01-01

The impact of new evaluated nuclear data libraries (JENDL-4.0, ENDF/B-VII.0 and JEFF-3.1) on the core characteristics of small-sized long-life CANDLE High Temperature Gas-Cooled Reactors (HTGRs) with uranium and thorium fuel cycles was investigated. The most important parameters of the CANDLE core characteristics investigated here covered (1) infinite multiplication factor of the fresh fuel containing burnable poison, (2) the effective multiplication factor of the equilibrium core, (3) the moving velocity of the burning region, (4) the attained discharge burnup, and (5) the maximum power density. The reference case was taken from the current JENDL-3.3 results. For the uranium fuel cycle, the impact of the new libraries was small, while significant impact was found for thorium fuel cycle. The findings indicated the needs of more accurate nuclear data libraries for nuclides involved in thorium fuel cycle in the future.

An experimental investigation on heat transfer enhancement in the laminar flow of water/TiO2 nanofluid through a tube heat exchanger fitted with modified butterfly inserts

NASA Astrophysics Data System (ADS)

Venkitaraj, K. P.; Suresh, S.; Alwin Mathew, T.; Bibin, B. S.; Abraham, Jisa

2018-03-01

Nanofluids are advanced heat transfer fluids that exhibit thermal properties superior than that of the conventional fluids such as water, oil etc. This paper reports the experimental study on convective heat transfer characteristics of water based titanium dioxide nanofluids in fully developed flow through a uniformly heated pipe heat exchanger fitted with modified butterfly inserts. Nanofluids are prepared by dispersing TiO2 nanoparticles of average particle size 29 nm in deionized water. The heat transfer experiments are performed in laminar regime using nanofluids prepared with 0.1% and 0.3% volume fractions of TiO2 nanoparticles. The thermal performance characteristics of conventional butterfly inserts and modified butterfly inserts are also compared using TiO2 nanofluid. The inserts with different pitches 6 cm, 9 cm and 12 cm are tested to determine the effect of pitch distance of inserts in the heat transfer and friction. The experimental results showed that the modification made in the butterfly inserts were able to produce higher heat transfer than conventional butterfly inserts.

The effects of substrate size, surface area, and density on coat thickness of multi-particulate dosage forms.

PubMed

Heinicke, Grant; Matthews, Frank; Schwartz, Joseph B

2005-01-01

Drugs layering experiments were performed in a fluid bed fitted with a rotor granulator insert using diltiazem as a model drug. The drug was applied in various quantities to sugar spheres of different mesh sizes to give a series of drug-layered sugar spheres (cores) of different potency, size, and weight per particle. The drug presence lowered the bulk density of the cores in proportion to the quantity of added drug. Polymer coating of each core lot was performed in a fluid bed fitted with a Wurster insert. A series of polymer-coated cores (pellets) was removed from each coating experiment. The mean diameter of each core and each pellet sample was determined by image analysis. The rate of change of diameter on polymer addition was determined for each starting size of core and compared to calculated values. The core diameter was displaced from the line of best fit through the pellet diameter data. Cores of different potency with the same size distribution were made by layering increasing quantities of drug onto sugar spheres of decreasing mesh size. Equal quantities of polymer were applied to the same-sized core lots and coat thickness was measured. Weight/weight calculations predict equal coat thickness under these conditions, but measurable differences were found. Simple corrections to core charge weight in the Wurster insert were successfully used to manufacture pellets having the same coat thickness. The sensitivity of the image analysis technique in measuring particle size distributions (PSDs) was demonstrated by measuring a displacement in PSD after addition of 0.5% w/w talc to a pellet sample.

Novel mutants of Erwinia carotovora subsp. carotovora defective in the production of plant cell wall degrading enzymes generated by Mu transpososome-mediated insertion mutagenesis.

PubMed

Laasik, Eve; Ojarand, Merli; Pajunen, Maria; Savilahti, Harri; Mäe, Andres

2005-02-01

As in Erwinia carotovora subsp. carotovora the regulation details of the main virulence factors, encoding extracellular enzymes that degrade the plant cell wall, is only rudimentally understood, we performed a genetic screen to identify novel candidate genes involved in the process. Initially, we used Mu transpososome-mediated mutagenesis approach to generate a comprehensive transposon insertion mutant library of ca. 10000 clones and screened the clones for the loss of extracellular enzyme production. Extracellular enzymes production was abolished by mutations in the chromosomal helEcc, trkAEcc yheLEcc, glsEcc, igaAEcc and cysQEcc genes. The findings reported here demonstrate that we have isolated six new representatives that belong to the pool of genes modulating the production of virulence factors in E. carotovora.

Subtraction of cap-trapped full-length cDNA libraries to select rare transcripts.

PubMed

Hirozane-Kishikawa, Tomoko; Shiraki, Toshiyuki; Waki, Kazunori; Nakamura, Mari; Arakawa, Takahiro; Kawai, Jun; Fagiolini, Michela; Hensch, Takao K; Hayashizaki, Yoshihide; Carninci, Piero

2003-09-01

The normalization and subtraction of highly expressed cDNAs from relatively large tissues before cloning dramatically enhanced the gene discovery by sequencing for the mouse full-length cDNA encyclopedia, but these methods have not been suitable for limited RNA materials. To normalize and subtract full-length cDNA libraries derived from limited quantities of total RNA, here we report a method to subtract plasmid libraries excised from size-unbiased amplified lambda phage cDNA libraries that avoids heavily biasing steps such as PCR and plasmid library amplification. The proportion of full-length cDNAs and the gene discovery rate are high, and library diversity can be validated by in silico randomization.

Engineering Complex Microbial Phenotypes with Continuous Genetic Integration and Plasmid Based Multi-Gene Library

DTIC Science & Technology

2010-01-01

genes from strains that have desirable traits. Here, we aim to enlarge the E. coli genome using Lactobacillus plantarum genes to build cells tolerant to...EtOH and BT. L. plantarum is an organism with established high tolerance to alcohols and solvents more broadly. Objective 2: Build a stress...heterologous (here: L. plantarum ; abbreviated as L. pl) DNA into the E. coli chromosome while selecting for insertions that enhance ethanol tolerance (which

Primary structure and mapping of the hupA gene of Salmonella typhimurium.

PubMed Central

Higgins, N P; Hillyard, D

1988-01-01

In bacteria, the complex nucleoid structure is folded and maintained by negative superhelical tension and a set of type II DNA-binding proteins, also called histonelike proteins. The most abundant type II DNA-binding protein is HU. Southern blot analysis showed that Salmonella typhimurium contained two HU genes that corresponded to Escherichia coli genes hupA (encoding HU-2 protein) and hupB (encoding HU-1). Salmonella hupA was cloned, and the nucleotide sequence of the gene was determined. Comparison of hupA of E. coli and S. typhimurium revealed that the HU-2 proteins were identical and that there was high conservation of nucleotide sequences outside the coding frames of the genes. A 300-member genomic library of S. typhimurium was constructed by using random transposition of MudP, a specialized chimeric P22-Mu phage that packages chromosomal DNA unidirectionally from its insertion point. Oligonucleotide hybridization against the library identified one MudP insertion that lies within 28 kilobases of hupA; the MudP was 12% linked to purH at 90.5 min on the standard map. Plasmids expressing HU-2 had a surprising phenotype; they caused growth arrest when they were introduced into E. coli strains bearing a himA or hip mutation. These results suggest that IHF and HU have interactive roles in bacteria. Images PMID:3056912

[Screening and identification of anoikis-resistant gene UBCH7 in esophageal cancer cells].

PubMed

Yang, Yang; Wang, Bo-Shi; Wang, Xiao-Min; Zhang, Yu; Wang, Ming-Rong; Jia, Xue-Mei

2012-02-01

Anoikis is a kind of programmed cell death induced by loss of extracellular matrix (ECM) adhesion, which is one of key factors for homestasis. Resistance to anoikis is required for tumor cell metastasis. We have previously shown several anoikis-resistance genes in esophageal squamous cell carcinoma (ESCC). In order to find novel anoikis-resistant genes in ESCC, we constructed retroviral cDNA library using total RNA from ESCC cell lines. NIH 3T3 cells, which are sensitive to anoikis, were infected with the library constructed. The cells were cultured in soft agar, and the clones which can survive in detached states were selected. The cDNAs inserted into the anoikis-resistant NIH3T3 clones were amplified using retroviral specific primers. Sequencing analysis showed that a cDNA fragment inserted into the anoikis-resistant clone contains full coding sequence (ORF) of human UBCH7/UBE2L3 gene. By infection with retrovirus encoding UBCH7 ORF (pMSCV-UBCH7), forced expression of UBCH7 increased the anoikis-resistance of NIH3T3 cells. More importantly, knockdown of UBCH7 expression by siRNA transfection reduced the anoikis-resistant ability of esophageal cancer MLuC1 cells. The data suggest that UBCH7/UBE2L3 gene would be involved in anoikis-resistance in ESCC.

A genome-wide inducible phenotypic screen identifies antisense RNA constructs silencing Escherichia coli essential genes

PubMed Central

Meng, Jia; Kanzaki, Gregory; Meas, Diane; Lam, Christopher K.; Crummer, Heather; Tain, Justina; Xu, H. Howard

2013-01-01

Regulated antisense RNA (asRNA) expression has been employed successfully in Gram-positive bacteria for genome-wide essential gene identification and drug target determination. However, there have been no published reports describing the application of asRNA gene silencing for comprehensive analyses of essential genes in Gram-negative bacteria. In this study, we report the first genome-wide identification of asRNA constructs for essential genes in Escherichia coli. We screened 250,000 library transformants for conditional growth-inhibitory recombinant clones from two shot-gun genomic libraries of E. coli using a paired-termini expression vector (pHN678). After sequencing plasmid inserts of 675 confirmed inducer-sensitive cell clones, we identified 152 separate asRNA constructs of which 134 inserts came from essential genes while 18 originated from non-essential genes (but share operons with essential genes). Among the 79 individual essential genes silenced by these asRNA constructs, 61 genes (77%) engage in processes related to protein synthesis. The cell-based assays of an asRNA clone targeting fusA (encoding elongation factor G) showed that the induced cells were sensitized 12 fold to fusidic acid, a known specific inhibitor. Our results demonstrate the utility of the paired-termini expression vector and feasibility of large-scale gene silencing in E. coli using regulated asRNA expression. PMID:22268863

SU-G-201-04: Can the Dynamic Library of Flap Applicators Replace Treatment Planning in Surface Brachytherapy?

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

Buzurovic, I; Devlin, P; Hansen, J

Purpose: Contemporary brachytherapy treatment planning systems-(TPS) include the applicator model libraries to improve digitization; however, the library of surface-flap-applicators-(SFA) is not incorporated into the commercial TPS. We propose the dynamic library-(DL) for SFA and investigate if such library can eliminate applicator reconstruction, source activation and dose normalization. Methods: DL was generated for the SFA using the C++class libraries of the Visualization Toolkit-(VTK) and Qt-application framework for complete abstraction of the graphical interface. DL was designed such that the user can initially choose the size of the applicator that corresponds to the one clinically placed to the patient. The virtual applicator-(VA)more » has an elastic property so that it can be registered to the clinical CT images with a real applicator-(RA) on it. The VA and RA matching is performed by adjusting the position and curvature of the VA. The VA does not elongate or change its size so each catheter could always be at a distance of 5mm from the skin and 10mm apart from the closest catheter maintaining the physical accuracy of the clinical setup. Upon the applicator placement, the dwell positions were automatically activated, and the dose is normalized to the prescription depth. The accuracy of source positioning was evaluated using various applicator sizes. Results: The accuracy of the applicator placement was in the sub-millimeter range. The time-study reveals that up to 50% of the planning time can be saved depending on the complexity of the clinical setup. Unlike in the classic approach, the planning time was not highly dependent on the applicator size. Conclusion: The practical benefits of the DL of the SFA were demonstrated. The time demanding planning processes can be partially automated. Consequently, the planner can dedicate effort to fine tuning, which can result in the improvement of the quality of treatment plans in surface brachytherapy.« less

Lean and Efficient Software: Whole-Program Optimization of Executables

DTIC Science & Technology

2015-09-30

libraries. Many levels of library interfaces—where some libraries are dynamically linked and some are provided in binary form only—significantly limit...software at build time. The opportunity: Our objective in this project is to substantially improve the performance, size, and robustness of binary ...executables by using static and dynamic binary program analysis techniques to perform whole-program optimization directly on compiled programs

Lecturers and Postgraduates Perception of Libraries as Promoters of Teaching, Learning, and Research at the University of Ibadan, Nigeria

ERIC Educational Resources Information Center

Oyewole, Olawale; Adetimirin, Airen

2015-01-01

Lecturers and postgraduates are among the users of the university libraries and their perception of the libraries has influence on utilization of the information resources, hence the need for this study. Survey method was adopted for the study and simple random sampling method was used to select sample size of 38 lecturers and 233 postgraduates.…

Complete genome sequence of the phenanthrene-degrading soil bacterium Delftia acidovorans Cs1-4

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

Shetty, Ameesha R.; de Gannes, Vidya; Obi, Chioma C.

Polycyclic aromatic hydrocarbons (PAH) are ubiquitous environmental pollutants and microbial biodegradation is an important means of remediation of PAH-contaminated soil. Delftia acidovorans Cs1-4 (formerly Delftia sp. Cs1-4) was isolated by using phenanthrene as the sole carbon source from PAH contaminated soil in Wisconsin. Its full genome sequence was determined to gain insights into a mechanisms underlying biodegradation of PAH. Three genomic libraries were constructed and sequenced: an Illumina GAii shotgun library (916,416,493 reads), a 454 Titanium standard library (770,171 reads) and one paired-end 454 library (average insert size of 8 kb, 508,092 reads). The initial assembly contained 40 contigs inmore » two scaffolds. The 454 Titanium standard data and the 454 paired end data were assembled together and the consensus sequences were computationally shredded into 2 kb overlapping shreds. Illumina sequencing data was assembled, and the consensus sequence was computationally shredded into 1.5 kb overlapping shreds. Gaps between contigs were closed by editing in Consed, by PCR and by Bubble PCR primer walks. A total of 182 additional reactions were needed to close gaps and to raise the quality of the finished sequence. The final assembly is based on 253.3 Mb of 454 draft data (averaging 38.4 X coverage) and 590.2 Mb of Illumina draft data (averaging 89.4 X coverage). The genome of strain Cs1-4 consists of a single circular chromosome of 6,685,842 bp (66.7 %G+C) containing 6,028 predicted genes; 5,931 of these genes were protein-encoding and 4,425 gene products were assigned to a putative function. Genes encoding phenanthrene degradation were localized to a 232 kb genomic island (termed the phn island), which contained near its 3’ end a bacteriophage P4-like integrase, an enzyme often associated with chromosomal integration of mobile genetic elements. Other biodegradation pathways reconstructed from the genome sequence included: benzoate (by the acetyl-CoA pathway), styrene, nicotinic acid (by the maleamate pathway) and the pesticides Dicamba and Fenitrothion. Lastly, determination of the complete genome sequence of D. acidovorans Cs1-4 has provided new insights the microbial mechanisms of PAH biodegradation that may shape the process in the environment.« less

Complete genome sequence of the phenanthrene-degrading soil bacterium Delftia acidovorans Cs1-4

DOE PAGES

Shetty, Ameesha R.; de Gannes, Vidya; Obi, Chioma C.; ...

2015-08-15

Polycyclic aromatic hydrocarbons (PAH) are ubiquitous environmental pollutants and microbial biodegradation is an important means of remediation of PAH-contaminated soil. Delftia acidovorans Cs1-4 (formerly Delftia sp. Cs1-4) was isolated by using phenanthrene as the sole carbon source from PAH contaminated soil in Wisconsin. Its full genome sequence was determined to gain insights into a mechanisms underlying biodegradation of PAH. Three genomic libraries were constructed and sequenced: an Illumina GAii shotgun library (916,416,493 reads), a 454 Titanium standard library (770,171 reads) and one paired-end 454 library (average insert size of 8 kb, 508,092 reads). The initial assembly contained 40 contigs inmore » two scaffolds. The 454 Titanium standard data and the 454 paired end data were assembled together and the consensus sequences were computationally shredded into 2 kb overlapping shreds. Illumina sequencing data was assembled, and the consensus sequence was computationally shredded into 1.5 kb overlapping shreds. Gaps between contigs were closed by editing in Consed, by PCR and by Bubble PCR primer walks. A total of 182 additional reactions were needed to close gaps and to raise the quality of the finished sequence. The final assembly is based on 253.3 Mb of 454 draft data (averaging 38.4 X coverage) and 590.2 Mb of Illumina draft data (averaging 89.4 X coverage). The genome of strain Cs1-4 consists of a single circular chromosome of 6,685,842 bp (66.7 %G+C) containing 6,028 predicted genes; 5,931 of these genes were protein-encoding and 4,425 gene products were assigned to a putative function. Genes encoding phenanthrene degradation were localized to a 232 kb genomic island (termed the phn island), which contained near its 3’ end a bacteriophage P4-like integrase, an enzyme often associated with chromosomal integration of mobile genetic elements. Other biodegradation pathways reconstructed from the genome sequence included: benzoate (by the acetyl-CoA pathway), styrene, nicotinic acid (by the maleamate pathway) and the pesticides Dicamba and Fenitrothion. Lastly, determination of the complete genome sequence of D. acidovorans Cs1-4 has provided new insights the microbial mechanisms of PAH biodegradation that may shape the process in the environment.« less

Comparison of 2 cuff inflation methods of laryngeal mask airway Classic for safe use without cuff manometer in adults.

PubMed

Kim, Min-Soo; Lee, Jeong-Rim; Shin, Yang-Sik; Chung, Ji-Won; Lee, Kyu-Ho; Ahn, Ki Ryang

2014-03-01

This single-center, prospective, randomized, double-blind, 2-arm, parallel group comparison trial was performed to establish whether the adult-sized laryngeal mask airway (LMA) Classic (The Laryngeal Mask Company Ltd, Henley-on-Thames, UK) could be used safely without any consideration of cuff hyperinflation when a cuff of the LMA Classic was inflated using half the maximum inflation volume or the resting volume before insertion of device. Eighty patients aged 20 to 70 years scheduled for general anesthesia using the LMA Classic were included. Before insertion, the cuff was partially filled with half the maximum inflation volume in the half volume group or the resting volume created by opening the pilot balloon valve to equalize with atmospheric pressure in the resting volume group. Several parameters regarding insertion, intracuff pressure, airway leak pressure, and leakage volume/fraction were collected after LMA insertion. The LMA Classic with a partially inflated cuff was successfully inserted in all enrolled patients. Both groups had the same success rate of 95% at the first insertion attempt. The half volume group had a lower mean intracuff pressure compared with the resting volume group (54.5 ± 16.1 cm H2O vs 61.8 ± 16.1 cm H2O; P = .047). There was no difference in airway leak pressure or leakage volume/fraction between the 2 groups under mechanical ventilation. The partially inflated cuff method using half the maximum recommended inflation volume or the resting volume is feasible with the adult-sized LMA Classic, resulting in a high success rate of insertion and adequate range of intracuff pressures. Copyright © 2014 Elsevier Inc. All rights reserved.

Plantar Fibroma

MedlinePlus

... size. Orthotic devices. If the fibroma is stable, meaning it is not changing in size, custom orthotic devices (shoe inserts) may relieve the pain by distributing the patient’s weight away from the fibroma. Physical therapy. The pain is sometimes treated through physical ...

Functional Screening of Antibiotic Resistance Genes from a Representative Metagenomic Library of Food Fermenting Microbiota

PubMed Central

Devirgiliis, Chiara; Barile, Simona; Perozzi, Giuditta

2014-01-01

Lactic acid bacteria (LAB) represent the predominant microbiota in fermented foods. Foodborne LAB have received increasing attention as potential reservoir of antibiotic resistance (AR) determinants, which may be horizontally transferred to opportunistic pathogens. We have previously reported isolation of AR LAB from the raw ingredients of a fermented cheese, while AR genes could be detected in the final, marketed product only by PCR amplification, thus pointing at the need for more sensitive microbial isolation techniques. We turned therefore to construction of a metagenomic library containing microbial DNA extracted directly from the food matrix. To maximize yield and purity and to ensure that genomic complexity of the library was representative of the original bacterial population, we defined a suitable protocol for total DNA extraction from cheese which can also be applied to other lipid-rich foods. Functional library screening on different antibiotics allowed recovery of ampicillin and kanamycin resistant clones originating from Streptococcus salivarius subsp. thermophilus and Lactobacillus helveticus genomes. We report molecular characterization of the cloned inserts, which were fully sequenced and shown to confer AR phenotype to recipient bacteria. We also show that metagenomics can be applied to food microbiota to identify underrepresented species carrying specific genes of interest. PMID:25243126

Identification and characterization of mutant clones with enhanced propagation rates from phage-displayed peptide libraries.

PubMed

Nguyen, Kieu T H; Adamkiewicz, Marta A; Hebert, Lauren E; Zygiel, Emily M; Boyle, Holly R; Martone, Christina M; Meléndez-Ríos, Carola B; Noren, Karen A; Noren, Christopher J; Hall, Marilena Fitzsimons

2014-10-01

A target-unrelated peptide (TUP) can arise in phage display selection experiments as a result of a propagation advantage exhibited by the phage clone displaying the peptide. We previously characterized HAIYPRH, from the M13-based Ph.D.-7 phage display library, as a propagation-related TUP resulting from a G→A mutation in the Shine-Dalgarno sequence of gene II. This mutant was shown to propagate in Escherichia coli at a dramatically faster rate than phage bearing the wild-type Shine-Dalgarno sequence. We now report 27 additional fast-propagating clones displaying 24 different peptides and carrying 14 unique mutations. Most of these mutations are found either in or upstream of the gene II Shine-Dalgarno sequence, but still within the mRNA transcript of gene II. All 27 clones propagate at significantly higher rates than normal library phage, most within experimental error of wild-type M13 propagation, suggesting that mutations arise to compensate for the reduced virulence caused by the insertion of a lacZα cassette proximal to the replication origin of the phage used to construct the library. We also describe an efficient and convenient assay to diagnose propagation-related TUPS among peptide sequences selected by phage display. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

The effects of variable sample biomass on comparative metagenomics.

PubMed

Chafee, Meghan; Maignien, Loïs; Simmons, Sheri L

2015-07-01

Longitudinal studies that integrate samples with variable biomass are essential to understand microbial community dynamics across space or time. Shotgun metagenomics is widely used to investigate these communities at the functional level, but little is known about the effects of combining low and high biomass samples on downstream analysis. We investigated the interacting effects of DNA input and library amplification by polymerase chain reaction on comparative metagenomic analysis using dilutions of a single complex template from an Arabidopsis thaliana-associated microbial community. We modified the Illumina Nextera kit to generate high-quality large-insert (680 bp) paired-end libraries using a range of 50 pg to 50 ng of input DNA. Using assembly-based metagenomic analysis, we demonstrate that DNA input level has a significant impact on community structure due to overrepresentation of low-GC genomic regions following library amplification. In our system, these differences were largely superseded by variations between biological replicates, but our results advocate verifying the influence of library amplification on a case-by-case basis. Overall, this study provides recommendations for quality filtering and de-replication prior to analysis, as well as a practical framework to address the issue of low biomass or biomass heterogeneity in longitudinal metagenomic surveys. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

New drug information resources for pharmacists at the National Library of Medicine.

PubMed

Knoben, James E; Phillips, Steven J

2014-01-01

To provide an overview of selected drug information-related databases of the National Library of Medicine (NLM), with a focus on newer resources that support the professional information needs of pharmacists and other health care providers. NLM, which is the world's largest medical library, provides an array of bibliographic, factual, and evidence-based drug, herbal remedy, and dietary supplement information resources. Five of the more recently introduced online resources include areas of particular importance to pharmacists, including a repository of current product labeling/package inserts, with automated search links to associated information resources; a portal to drug information that allows pharmacists to search multiple databases simultaneously and link to related medication and health care information resources; authoritative information on the effects of medications, herbal remedies, and dietary supplements in nursing infants and their mothers; comprehensive information, including a case registry, on the potential for liver toxicity due to drugs, herbal remedies, and dietary supplements; and a pill identification system with two intuitive search methodologies. NLM provides several clinical-scientific drug information resources that are particularly useful in meeting the professional information needs of pharmacists.

Antibody phage display: overview of a powerful technology that has quickly translated to the clinic.

PubMed

Kotlan, Beatrix; Glassy, Mark C

2009-01-01

Antibody-based immunologic reagents are useful for identifying, isolating, or eliminating cells with particular characteristics related to different diseases. Phage display is a highly valuable technique for antibody selection related to this purpose. In brief, a diverse group of antibody genes prepared from a patient or generated in vitro are inserted into a phagemid vector or the phage genome so that when the protein is expressed, it becomes anchored on the surface of the phage by fusion to a coat protein. A diverse library of recombinant antibodies is generated in this way and can then be exposed or panned on the antigen of interest, typically, this being a molecule associated with a particular pathological condition. Phage that carry proteins or peptides bind preferentially to the target and can thus be isolated from the library. The viruses that are recovered in this way also carry the gene for the binding moiety facilitating its over-expression or manipulation. Recent reviews highlight key milestones in the development of antibody libraries and their screening by phage display, and the impact of these technologies on drug discovery seems assured.

Vendors' Corner: System Performance. A Forum.

ERIC Educational Resources Information Center

Sugnet, Chris, Ed.

1986-01-01

Representatives of six vendors of online library systems address key issues related to system performance: designing, configuring and sizing systems; establishing performance criteria; using benchmark and acceptance tests; the risks of miscalculations; vendor, consultant, and library roles; and related topics. (Author/EM)

A resource for the assessment of lung nodule size estimation methods: database of thoracic CT scans of an anthropomorphic phantom◊

PubMed Central

Gavrielides, Marios A.; Kinnard, Lisa M.; Myers, Kyle J.; Peregoy, Jennifer; Pritchard, William F.; Zeng, Rongping; Esparza, Juan; Karanian, John; Petrick, Nicholas

2010-01-01

A number of interrelated factors can affect the precision and accuracy of lung nodule size estimation. To quantify the effect of these factors, we have been conducting phantom CT studies using an anthropomorphic thoracic phantom containing a vasculature insert to which synthetic nodules were inserted or attached. Ten repeat scans were acquired on different multi-detector scanners, using several sets of acquisition and reconstruction protocols and various nodule characteristics (size, shape, density, location). This study design enables both bias and variance analysis for the nodule size estimation task. The resulting database is in the process of becoming publicly available as a resource to facilitate the assessment of lung nodule size estimation methodologies and to enable comparisons between different methods regarding measurement error. This resource complements public databases of clinical data and will contribute towards the development of procedures that will maximize the utility of CT imaging for lung cancer screening and tumor therapy evaluation. PMID:20640011

Size-Dependency of the Surface Ligand Density of Liposomes Prepared by Post-insertion.

PubMed

Lee, Shang-Hsuan; Sato, Yusuke; Hyodo, Mamoru; Harashima, Hideyoshi

2017-01-01

In the active targeting of a drug delivery system (DDS), the density of the ligand on the functionalized liposome determines its affinity for binding to the target. To evaluate these densities on the surface of different sized liposomes, 4 liposomes with various diameters (188, 137, 70, 40 nm) were prepared and their surfaces were modified with fluorescently labeled ligand-lipid conjugates by the post-insertion method. Each liposomal mixture was fractionated into a series of fractions using size exclusion chromatography (SEC), and the resulting liposome fractions were precisely analyzed and the surface ligand densities calculated. The data collected using this methodology indicate that the density of the ligand on a particle is greatly dependent on the size of the liposome. This, in turn, indicates that smaller liposomes (75-40 nm) tend to possess higher densities. For developing active targeting systems, size and the density of the ligands are two important and independent factors that can affect the efficiency of a system as it relates to medical use.

Surgical implications of perimodiolar cochlear implant electrode design: avoiding intracochlear damage and scala vestibuli insertion.

PubMed

Briggs, R J; Tykocinski, M; Saunders, E; Hellier, W; Dahm, M; Pyman, B; Clark, G M

2001-09-01

To review the mechanisms and nature of intracochlear damage associated with cochlear implant electrode array insertion, in particular, the various perimodiolar electrode designs. Make recommendations regarding surgical techniques for the Nucleus Contour electrode to ensure correct position and minimal insertion trauma. The potential advantages of increased modiolar proximity of intracochlear multichannel electrode arrays are a reduction in stimulation thresholds, an increase in dynamic range and more localized neural excitation. This may improve speech perception and reduce power consumption. These advantages may be negated if increased intracochlear damage results from the method used to position the electrodes close to the modiolus. A review of the University of Melbourne Department of Otolaryngology experience with temporal bone safety studies using the Nucleus standard straight electrode array and a variety of perimodiolar electrode array designs; comparison with temporal bone insertion studies from other centres and postmortem histopathology studies reported in the literature. Review of our initial clinical experience using the Nucleus Contour electrode array. The nature of intracochlear damage resulting from electrode insertion trauma ranges from minor, localized, spiral ligament tear to diffuse organ of Corti disruption and osseous spiral lamina fracture. The type of damage depends on the mechanical characteristics of the electrode array, the stiffness, curvature and size of the electrode in relation to the scala, and the surgical technique. The narrow, flexible, straight arrays are the least traumatic. Pre-curved or stiffer arrays are associated with an incidence of basilar membrane perforation. The cochleostomy must be correctly sited in relation to the round window to ensure scala tympani insertion. A cochleostomy anterior to the round window rather than inferior may lead to scala media or scala vestibuli insertion. Proximity of electrodes to the modiolus can be achieved without intracochlear damage provided the electrode array is a free fit within the scala, of appropriate size and shape, and accurate scala tympani insertion is performed.

Penile Lengthening, Girth, and Size Preservation at the Time of Penile Prosthesis Insertion.

PubMed

Tran, Henry; Goldfarb, Robert; Ackerman, Anika; Valenzuela, Robert J

2017-07-01

Penile prosthetic devices are the gold standard treatment of medication-refractory erectile dysfunction. Inflatable penile prosthetic (IPP) devices have been available and used for more than four decades. Oftentimes, medical conditions causing erectile dysfunction also cause penile shortening, causing decreased patient quality of life. To identify and review all available penile lengthening procedures that can be performed at time of IPP insertion. An extensive, systematic literature review was performed using PubMed searching for key terms penile lengthening, inflatable penile prosthesis, penile girth, corporoplasty, glans augmentation, and penile enhancement; all articles with subjective and/or objective penile length outcomes were reviewed. A review of various techniques for penile length and girth preservation and enhancement during penile prosthesis insertion. Several advanced and novel techniques were found for penile length preservation and enhancement at time of IPP insertion, including the sub-coronal IPP insertion technique, and adjuvant maneuvers during insertion, such as the sliding technique, modified sliding technique, multiple slice technique, and circumferential incision and grafting. Other adjuvant techniques that can enhance perception of increased length include ventral phalloplasty, suprapubic lipectomy, and suspensory ligament release. Further enhancement can be obtained using augmentation corporoplasty and glans augmentation with hyaluronic acid and other fillers. The different techniques vary in complexity and could require specialized training and experience. Maximum length gain appears to be limited by the length of the neurovascular bundles. Overall, surgical penile lengthening procedures at time of IPP insertion appear safe and effective for treatment of patients with penile shortening and severe erectile dysfunction. These therapies can significantly improve patient self-esteem and quality of life in properly selected patients. Tran H, Goldfarb R, Ackerman A, Valenxuela RJ. Penile Lengthening, Girth and Size Preservation at the Time of Penile Prosthesis Insertion. Sex Med Rev 2017;5:403-412. Copyright © 2017 International Society for Sexual Medicine. Published by Elsevier Inc. All rights reserved.

Interlibrary loan in primary access libraries: challenging the traditional view.

PubMed

Dudden, R F; Coldren, S; Condon, J E; Katsh, S; Reiter, C M; Roth, P L

2000-10-01

Primary access libraries serve as the foundation of the National Network of Libraries of Medicine (NN/LM) interlibrary loan (ILL) hierarchy, yet few published reports directly address the important role these libraries play in the ILL system. This may reflect the traditional view that small, primary access libraries are largely users of ILL, rather than important contributors to the effectiveness and efficiency of the national ILL system. This study was undertaken to test several commonly held beliefs regarding ILL system use by primary access libraries. Three hypotheses were developed. HI: Colorado and Wyoming primary access libraries comply with the recommended ILL guideline of adhering to a hierarchical structure, emphasizing local borrowing. H2: The closures of two Colorado Council of Medical Librarians (CCML) primary access libraries in 1996 resulted in twenty-three Colorado primary access libraries' borrowing more from their state resource library in 1997. H3: The number of subscriptions held by Colorado and Wyoming primary access libraries is positively correlated with the number of items they loan and negatively correlated with the number of items they borrow. The hypotheses were tested using the 1992 and 1997 DOCLINE and OCLC data of fifty-four health sciences libraries, including fifty primary access libraries, two state resource libraries, and two general academic libraries in Colorado and Wyoming. The ILL data were obtained electronically and analyzed using Microsoft Word 98, Microsoft Excel 98, and JMP 3.2.2. CCML primary access libraries comply with the recommended guideline to emphasize local borrowing by supplying each other with the majority of their ILLs, instead of overburdening libraries located at higher levels in the ILL hierarchy (H1). The closures of two CCML primary access libraries appear to have affected the entire ILL system, resulting in a greater volume of ILL activity for the state resource library and other DOCLINE libraries higher up in the ILL hierarchy and highlighting the contribution made by CCML primary access libraries (H2). CCML primary access libraries borrow and lend in amounts that are proportional to their collection size, rather than overtaxing libraries at higher levels in the ILL hierarchy with large numbers of requests (H3). The main limitations of this study were the small sample size and the use of data collected for another purpose, the CCML ILL survey. The findings suggest that there is little evidence to support several commonly held beliefs regarding ILL system use by primary access libraries. In addition to validating the important contributions made by primary access libraries to the national ILL system, baseline data that can be used to benchmark current practice performance are provided.

Interlibrary loan in primary access libraries: challenging the traditional view

PubMed Central

Dudden, Rosalind Farnam; Coldren, Sue; Condon, Joyce Elizabeth; Katsh, Sara; Reiter, Catherine Morton; Roth, Pamela Lynn

2000-01-01

Introduction: Primary access libraries serve as the foundation of the National Network of Libraries of Medicine (NN/LM) interlibrary loan (ILL) hierarchy, yet few published reports directly address the important role these libraries play in the ILL system. This may reflect the traditional view that small, primary access libraries are largely users of ILL, rather than important contributors to the effectiveness and efficiency of the national ILL system. Objective: This study was undertaken to test several commonly held beliefs regarding ILL system use by primary access libraries. Hypotheses: Three hypotheses were developed. H1: Colorado and Wyoming primary access libraries comply with the recommended ILL guideline of adhering to a hierarchical structure, emphasizing local borrowing. H2: The closures of two Colorado Council of Medical Librarians (CCML) primary access libraries in 1996 resulted in twenty-three Colorado primary access libraries' borrowing more from their state resource library in 1997. H3: The number of subscriptions held by Colorado and Wyoming primary access libraries is positively correlated with the number of items they loan and negatively correlated with the number of items they borrow. Methods: The hypotheses were tested using the 1992 and 1997 DOCLINE and OCLC data of fifty-four health sciences libraries, including fifty primary access libraries, two state resource libraries, and two general academic libraries in Colorado and Wyoming. The ILL data were obtained electronically and analyzed using Microsoft Word 98, Microsoft Excel 98, and JMP 3.2.2. Results: CCML primary access libraries comply with the recommended guideline to emphasize local borrowing by supplying each other with the majority of their ILLs, instead of overburdening libraries located at higher levels in the ILL hierarchy (H1). The closures of two CCML primary access libraries appear to have affected the entire ILL system, resulting in a greater volume of ILL activity for the state resource library and other DOCLINE libraries higher up in the ILL hierarchy and highlighting the contribution made by CCML primary access libraries (H2). CCML primary access libraries borrow and lend in amounts that are proportional to their collection size, rather than overtaxing libraries at higher levels in the ILL hierarchy with large numbers of requests (H3). Limitations: The main limitations of this study were the small sample size and the use of data collected for another purpose, the CCML ILL survey. Conclusions: The findings suggest that there is little evidence to support several commonly held beliefs regarding ILL system use by primary access libraries. In addition to validating the important contributions made by primary access libraries to the national ILL system, baseline data that can be used to benchmark current practice performance are provided. PMID:11055297

48 CFR 52.247-61 - F.o.b. Origin-Minimum Size of Shipments.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 48 Federal Acquisition Regulations System 2 2010-10-01 2010-10-01 false F.o.b. Origin-Minimum Size... Clauses 52.247-61 F.o.b. Origin—Minimum Size of Shipments. As prescribed in 47.305-16(c), insert the following clause in solicitations and contracts when volume rates may apply: F.o.b. Origin—Minimum Size of...

TRADOC Library and Information Network (TRALINET)

DTIC Science & Technology

1979-03-01

by the Library of Congress, Dewey materials that have beer photographically reduced Decimal , or any other classification scheme adopted in size for...sites at Forts Hood, TX; Gordon, GA; Monroe, VA; Knox, KY, and Leavenworth, KS. DTIC, formally Defense Documentation Center ( DDC ), serves as the primary...locally expanded subject schedules, whether schedules aic for Dewey , Library of Congress, etc., particularly in the are& of Military Arts and Sciences. 1 4

A Comparative Analysis of the Availability of Information Resources on Ibibio Culture in the University of Uyo and Akwa Ibom State Public Library

ERIC Educational Resources Information Center

Okon, Henry Itohowo; Simon, Jehu S.; Akai, Iniobong

2015-01-01

This study reports the results of a survey of the available holdings of information resources on Ibibio culture in the University of Uyo Library and Akwa Ibom State Library. The specific objectives of the study were to determine the different size of information resources on funeral, fattening (Mbobo), taboos, myths as well as dissemination in the…

Trends in Public Library Buildings.

ERIC Educational Resources Information Center

Holt, Raymond M.

1987-01-01

Review of trends in public library buildings covers cycles in building activity; financial support; site selection; expansion, remodeling, or conversion of existing buildings; size of buildings; and such architectural concerns as flexible space, lighting, power, accommodation of computer systems, heat and ventilation, fire protection, security,…

Theoretical distribution of gutta-percha within root canals filled using cold lateral compaction based on numeric calculus.

PubMed

Min, Yi; Song, Ying; Gao, Yuan; Dummer, Paul M H

2016-08-01

This study aimed to present a new method based on numeric calculus to provide data on the theoretical volume ratio of voids when using the cold lateral compaction technique in canals with various diameters and tapers. Twenty-one simulated mathematical root canal models were created with different tapers and sizes of apical diameter, and were filled with defined sizes of standardized accessory gutta-percha cones. The areas of each master and accessory gutta-percha cone as well as the depth of their insertion into the canals were determined mathematically in Microsoft Excel. When the first accessory gutta-percha cone had been positioned, the residual area of void was measured. The areas of the residual voids were then measured repeatedly upon insertion of additional accessary cones until no more could be inserted in the canal. The volume ratio of voids was calculated through measurement of the volume of the root canal and mass of gutta-percha cones. The theoretical volume ratio of voids was influenced by the taper of canal, the size of apical preparation and the size of accessory gutta-percha cones. Greater apical preparation size and larger taper together with the use of smaller accessory cones reduced the volume ratio of voids in the apical third. The mathematical model provided a precise method to determine the theoretical volume ratio of voids in root-filled canals when using cold lateral compaction.

A novel suicide shuttle plasmid for Streptococcus suis serotype 2 and Streptococcus equi ssp. zooepidemicus gene mutation

PubMed Central

Liu, Rui; Zhang, Ping; Su, Yiqi; Lin, Huixing; Zhang, Hui; Yu, Lei; Ma, Zhe; Fan, Hongjie

2016-01-01

The mariner-based Himar1 system has been utilized for creating mutant libraries of many Gram-positive bacteria. Streptococcus suis serotype 2 (SS2) and Streptococcus equi ssp. zooepidemicus (SEZ) are primary pathogens of swine that threaten the swine industry in China. To provide a forward-genetics technology for finding virulent phenotype-related genes in these two pathogens, we constructed a novel temperature-sensitive suicide shuttle plasmid, pMar4s, which contains the Himar1 system transposon, TnYLB-1, and the Himar1 C9 transposase from pMarA and the repTAs temperature-sensitive fragment from pSET4s. The kanamycin (Kan) resistance gene was in the TnYLB-1 transposon. Temperature sensitivity and Kan resistance allowed the selection of mutant strains and construction of the mutant library. The SS2 and SEZ mutant libraries were successfully constructed using the pMar4s plasmid. Inverse-Polymerase Chain Reaction (Inverse-PCR) results revealed large variability in transposon insertion sites and that the library could be used for phenotype alteration screening. The thiamine biosynthesis gene apbE was screened for its influence on SS2 anti-phagocytosis; likewise, the sagF gene was identified to be a hemolytic activity-related gene in SEZ. pMar4s was suitable for mutant library construction, providing more information regarding SS2 and SEZ virulence factors and illustrating the pathogenesis of swine streptococcosis. PMID:27256117

Draft genome of the gayal, Bos frontalis

PubMed Central

Wang, Ming-Shan; Zeng, Yan; Wang, Xiao; Nie, Wen-Hui; Wang, Jin-Huan; Su, Wei-Ting; Xiong, Zi-Jun; Wang, Sheng; Qu, Kai-Xing; Yan, Shou-Qing; Yang, Min-Min; Wang, Wen; Dong, Yang; Zhang, Ya-Ping

2017-01-01

Abstract Gayal (Bos frontalis), also known as mithan or mithun, is a large endangered semi-domesticated bovine that has a limited geographical distribution in the hill-forests of China, Northeast India, Bangladesh, Myanmar, and Bhutan. Many questions about the gayal such as its origin, population history, and genetic basis of local adaptation remain largely unresolved. De novo sequencing and assembly of the whole gayal genome provides an opportunity to address these issues. We report a high-depth sequencing, de novo assembly, and annotation of a female Chinese gayal genome. Based on the Illumina genomic sequencing platform, we have generated 350.38 Gb of raw data from 16 different insert-size libraries. A total of 276.86 Gb of clean data is retained after quality control. The assembled genome is about 2.85 Gb with scaffold and contig N50 sizes of 2.74 Mb and 14.41 kb, respectively. Repetitive elements account for 48.13% of the genome. Gene annotation has yielded 26 667 protein-coding genes, of which 97.18% have been functionally annotated. BUSCO assessment shows that our assembly captures 93% (3183 of 4104) of the core eukaryotic genes and 83.1% of vertebrate universal single-copy orthologs. We provide the first comprehensive de novo genome of the gayal. This genetic resource is integral for investigating the origin of the gayal and performing comparative genomic studies to improve understanding of the speciation and divergence of bovine species. The assembled genome could be used as reference in future population genetic studies of gayal. PMID:29048483

Genome-Wide Mutagenesis in Borrelia burgdorferi.

PubMed

Lin, Tao; Gao, Lihui

2018-01-01

Signature-tagged mutagenesis (STM) is a functional genomics approach to identify bacterial virulence determinants and virulence factors by simultaneously screening multiple mutants in a single host animal, and has been utilized extensively for the study of bacterial pathogenesis, host-pathogen interactions, and spirochete and tick biology. The signature-tagged transposon mutagenesis has been developed to investigate virulence determinants and pathogenesis of Borrelia burgdorferi. Mutants in genes important in virulence are identified by negative selection in which the mutants fail to colonize or disseminate in the animal host and tick vector. STM procedure combined with Luminex Flex ® Map™ technology and next-generation sequencing (e.g., Tn-seq) are the powerful high-throughput tools for the determination of Borrelia burgdorferi virulence determinants. The assessment of multiple tissue sites and two DNA resources at two different time points using Luminex Flex ® Map™ technology provides a robust data set. B. burgdorferi transposon mutant screening indicates that a high proportion of genes are the novel virulence determinants that are required for mouse and tick infection. In this protocol, an effective signature-tagged Himar1-based transposon suicide vector was developed and used to generate a sequence-defined library of nearly 4800 mutants in the infectious B. burgdorferi B31 clone. In STM, signature-tagged suicide vectors are constructed by inserting unique DNA sequences (tags) into the transposable elements. The signature-tagged transposon mutants are generated when transposon suicide vectors are transformed into an infectious B. burgdorferi clone, and the transposable element is transposed into the 5'-TA-3' sequence in the B. burgdorferi genome with the signature tag. The transposon library is created and consists of many sub-libraries, each sub-library has several hundreds of mutants with same tags. A group of mice or ticks are infected with a mixed population of mutants with different tags, after recovered from different tissues of infected mice and ticks, mutants from output pool and input pool are detected using high-throughput, semi-quantitative Luminex ® FLEXMAP™ or next-generation sequencing (Tn-seq) technologies. Thus far, we have created a high-density, sequence-defined transposon library of over 6600 STM mutants for the efficient genome-wide investigation of genes and gene products required for wild-type pathogenesis, host-pathogen interactions, in vitro growth, in vivo survival, physiology, morphology, chemotaxis, motility, structure, metabolism, gene regulation, plasmid maintenance and replication, etc. The insertion sites of 4480 transposon mutants have been determined. About 800 predicted protein-encoding genes in the genome were disrupted in the STM transposon library. The infectivity and some functions of 800 mutants in 500 genes have been determined. Analysis of these transposon mutants has yielded valuable information regarding the genes and gene products important in the pathogenesis and biology of B. burgdorferi and its tick vectors.

Probing and Tapping: Are We Inserting Pedicle Screws Correctly?

PubMed

Prasad, Vishal; Mesfin, Addisu; Lee, Robert; Reigrut, Julie; Schmidt, John

2016-11-01

Although there are a significant number of research publications on the topic of bone morphology and the strength of bone, the clinical significance of a failed pedicle screw is often revision surgery and the potential for further postoperative complications; especially in elderly patients with osteoporotic bone. The purpose of this report is to quantify the mechanical strength of the foam-screw interface by assessing probe/pilot hole diameter and tap sizes using statistically relevant sample sizes under highly controlled test conditions. The study consisted of two experiments and used up to three different densities of reference-grade polyurethane foam (ASTM 1839), including 0.16, 0.24, and 0.32 g/cm 3 . All screws and rods were provided by K2M Inc. and screws were inserted to a depth of 25 mm. A series of pilot holes, 1.5, 2.2, 2.7, 3.2, 3.7, 4.2, 5.0, and 6.0 mm in diameter were drilled through the entire depth of the material. A 6.5 × 45-mm pedicle screw was inserted and axially pulled from the material (n = 720). A 3.0-mm pilot hole was drilled and tapped with: no tap, 3.5-, 4.5-, 5.5-, and 6.5-mm taps. A 6.5 × 45-mm pedicle screw was inserted and axially pulled from the material (n = 300). The size of the probe/pilot hole had a nonlinear, parabolic effect on pullout strength. This shape suggests an optimum-sized probe hole for a given size pedicle screw. Too large or too small of a probe hole causes a rapid falloff in pullout strength. The tap data demonstrated that not tapping and undertapping by two or three sizes did not significantly alter the pullout strength of the screws. The data showed an exponential falloff of pullout strength when as tap size increased to the diameter of the screw. In the current study, the data show that an ideal pilot hole size half the diameter of the screw is a starting point. Also, that if tapping was necessary, to use a tap two sizes smaller than the screw being implanted. A similar optimum pilot hole or tap size may be expected in the clinical scenario, however, it may not be the same as seen with the uniform density polyurethane foam tested in the current study. Copyright © 2016 Scoliosis Research Society. Published by Elsevier Inc. All rights reserved.

Enhanced heat transfer and frictional losses in heat exchanger tube with modified helical coiled inserts

NASA Astrophysics Data System (ADS)

Verma, Aditya; Kumar, Manoj; Patil, Anil Kumar

2018-04-01

The application of compact heat exchangers in any thermal system improves overall performance with a considerable reduction in size and weight. Inserts of different geometrical features have been used as turbulence promoting devices to increase the heat transfer rates. The present study deals with the experimental investigation of heat transfer and fluid flow characteristics of a tubular heat exchanger fitted with modified helical coiled inserts. Experiments have been carried out for a smooth tube without insert, tube fitted with helical coiled inserts, and modified helical coiled inserts. The helical coiled inserts are tested by varying the pitch ratio and wire diameter ratio from 0.5-1.5, and 0.063-0.125, respectively for the Reynolds number range of 1400 to 11,000. Experimental data have also been collected for the modified helical coiled inserts with gradually increasing pitch (GIP) and gradually decreasing pitch (GDP) configurations. The Nusselt number and friction factor values for helical coiled inserts are enhanced in the range of 1.42-2.62, 3.4-27.4, relative to smooth tube, respectively. The modified helical coiled insert showed enhancements in Nusselt number and friction factor values in the range of 1.49-3.14, 11.2-19.9, relative to smooth tube, respectively. The helical coiled and modified helical coiled inserts have thermo-hydraulic performance factor in the range of 0.59-1.29, 0.6-1.39, respectively. The empirical correlations of Nusselt number and friction factor for helical coiled inserts are proposed.

Combat Identification Systems COMO Integrated Air Defense Model Evaluation (CISE) Study

DTIC Science & Technology

1989-02-01

use K or IR , whichever one applies) E-6 CAA-SR-89- 3 Subroutine PDECLR 1/21/88 Before label 1000 Insert: IF (IR.GT.10) IR a 10 These changes were made...Internal Distribution: Unclassified Library 2 F-2 CAA-SR-89- 3 GLOSSARY 1. ABBREVIATIONS, ACRONYMS, AND SHORT TERMS ADM2 Air Defense Models Modification...STUDY REPORT ’ , CAA-Sn-89- 3 i , .- CD o COMBAT IDENTIFICATION SYSTEMS N COMO INTEGRATED AIR DEFENSE MODEL EVALUATION (CISE) STUDY FEBRUARY 1989

METHOD FOR MAKING FUEL ELEMENTS

DOEpatents

Kates, L.W.; Campbell, R.W.; Heartel, R.H.W.

1960-08-01

A method is given for making zirconium-clad uranium wire. A tube of zirconium is closed with a zirconium plug, after which a chilled uranium core is inserted in the tube to rest against the plug. Additional plugs and cores are inserted alternately as desired. The assembly is then sheathed with iron, hot worked to the desired size, and the iron sheath removed.

An analysis of absorbing image on the Indonesian text by using color matching

NASA Astrophysics Data System (ADS)

Hutagalung, G. A.; Tulus; Iryanto; Lubis, Y. F. A.; Khairani, M.; Suriati

2018-03-01

The insertion of messages in an image is performed by inserting per character message in some pixels. One way of inserting a message into an image is by inserting the ASCII decimal value of a character to the decimal value of the primary color of the image. Messages that use characters in letters, numbers or symbols, where the use of letters of each word is different in number and frequency of use, as well as the use of letters in various messages within each language. In Indonesian language, the use of the letter A to be the most widely used, and the use of other letters greatly affect the clarity of a message or text presented in the language. This study aims to determine the capacity to absorb the message in Indonesian language from an image and what are the things that affect the difference. The data used in this study consists of several images in JPG or JPEG format can be obtained from the image drawing software or hardware of the image makers at different image sizes. The results of testing on four samples of a color image have been obtained by using an image size of 1200 X 1920.

Improvement of perpendicular anisotropy of columnar FePt-ZrO2-C films with FePt insert layer

NASA Astrophysics Data System (ADS)

Dong, Kaifeng; Mo, Wenqin; Jin, Fang; Song, Junlei; Cheng, Weimin; Wang, Haiwei

2018-05-01

The effects of various thicknesses of FePt insert layer on the microstructure and magnetic properties of FePt-ZrO2-C thin films have been investigated. It is found that with inserting 0.4 nm FePt films between the TiON intermediate layer and FePt-ZrO2-C layer, the perpendicular anisotropy indicated by Hc⊥/Hc//ratio would increase from 4 to 13.1, suggesting the perpendicular anisotropy could be improved a lot with using FePt insert layer. Simultaneously, the FePt grains of FePt-ZrO2-C thin films maintained columnar structure and the grain isolation could also be improved in a certain degree. With further increase of the FePt insert layer thickness, although the perpendicular anisotropy was still larger than that without FePt insert layer, the grain size of the FePt-ZrO2-C films would increase and the isolation would be deteriorated.

Additive Manufacturing for Highly Efficient Window Inserts CRADA Report

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

Roschli, Alex C.; Chesser, Phillip C.; Love, Lonnie J.

ORNL partnered with the Mackinac Technology Company to demonstrate how additive manufacturing can be used to create highly energy efficient window inserts for retrofit in pre-existing buildings. Many early iterations of the window inserts were fabricated using carbon fiber reinforced thermoplastics and polycarbonate films as a stand in for the low-e coated films produced by the Mackinac Technology Company. After demonstration of the proof of concept, i.e. custom window inserts with tensioned film, the materials used for the manufacture of the frames was more closely examined. Hollow particle-filled syntactic foam and low-density polymer composites formed by expandable microspheres were exploredmore » as the materials used to additively manufacture the frames of the inserts. It was concluded that low-cost retrofit window inserts in custom sizes could be easily fabricated using large scale additive manufacturing. Furthermore, the syntactic and expanded foams developed and tested satisfy the mechanical performance requirements for the application.« less

Recurrence, submicroscopic complexity, and potential clinical relevance of copy gains detected by array CGH that are shown to be unbalanced insertions by FISH.

PubMed

Neill, Nicholas J; Ballif, Blake C; Lamb, Allen N; Parikh, Sumit; Ravnan, J Britt; Schultz, Roger A; Torchia, Beth S; Rosenfeld, Jill A; Shaffer, Lisa G

2011-04-01

Insertions occur when a segment of one chromosome is translocated and inserted into a new region of the same chromosome or a non-homologous chromosome. We report 71 cases with unbalanced insertions identified using array CGH and FISH in 4909 cases referred to our laboratory for array CGH and found to have copy-number abnormalities. Although the majority of insertions were non-recurrent, several recurrent unbalanced insertions were detected, including three der(Y)ins(Y;18)(q?11.2;p11.32p11.32)pat inherited from parents carrying an unbalanced insertion. The clinical significance of these recurrent rearrangements is unclear, although the small size, limited gene content, and inheritance pattern of each suggests that the phenotypic consequences may be benign. Cryptic, submicroscopic duplications were observed at or near the insertion sites in two patients, further confounding the clinical interpretation of these insertions. Using FISH, linear amplification, and array CGH, we identified a 126-kb duplicated region from 19p13.3 inserted into MECP2 at Xq28 in a patient with symptoms of Rett syndrome. Our results demonstrate that although the interpretation of most non-recurrent insertions is unclear without high-resolution insertion site characterization, the potential for an otherwise benign duplication to result in a clinically relevant outcome through the disruption of a gene necessitates the use of FISH to determine whether copy-number gains detected by array CGH represent tandem duplications or unbalanced insertions. Further follow-up testing using techniques such as linear amplification or sequencing should be used to determine gene involvement at the insertion site after FISH has identified the presence of an insertion.

Investigation into the sequence structure of 23 Y chromosomal STR loci using massively parallel sequencing.

PubMed

Kwon, So Yeun; Lee, Hwan Young; Kim, Eun Hye; Lee, Eun Young; Shin, Kyoung-Jin

2016-11-01

Next-generation sequencing (NGS) can produce massively parallel sequencing (MPS) data for many targeted regions with a high depth of coverage, suggesting its successful application to the amplicons of forensic genetic markers. In the present study, we evaluated the practical utility of MPS in Y-chromosome short tandem repeat (Y-STR) analysis using a multiplex polymerase chain reaction (PCR) system. The multiplex PCR system simultaneously amplified 24 Y-chromosomal markers, including the PowerPlex ® Y23 loci (DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS481, DYS533, DYS549, DYS570, DYS576, DYS635, DYS643, and YGATAH4) and the M175 marker with the small-sized amplicons ranging from 85 to 253bp. The barcoded libraries for the amplicons of the 24 Y-chromosomal markers were produced using a simplified PCR-based library preparation method and successfully sequenced using MPS on a MiSeq ® System with samples from 250 unrelated Korean males. The genotyping concordance between MPS and the capillary electrophoresis (CE) method, as well as the sequence structure of the 23 Y-STRs, were investigated. Three samples exhibited discordance between the MPS and CE results at DYS385, DYS439, and DYS576. There were 12 Y-STR loci that showed sequence variations in the alleles by a fragment size determination, and the most varied alleles occurred in DYS389II with a different sequence structure in the repeat region. The largest increase in gene diversity between the CE and MPS results was in DYS437 at +34.41%. Single nucleotide polymorphisms (SNPs), insertions, and deletions (indels) were observed in the flanking regions of DYS481, DYS576, and DYS385, respectively. Stutter and noise ratios of the 23 Y-STRs using the developed MPS system were also investigated. Based on these results, the MPS analysis system used in this study could facilitate the investigation into the sequences of the 23 Y-STRs in forensic genetics laboratories. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Insertion of GaAs MMICs into EW systems

NASA Astrophysics Data System (ADS)

Schineller, E. R.; Pospishil, A.; Grzyb, J.

1989-09-01

Development activities on a microwave/mm-wave monolithic IC (MIMIC) program are described, as well as the methodology for inserting these GaAs IC chips into several EW systems. The generic EW chip set developed on the MIMIC program consists of 23 broadband chip types, including amplifiers, oscillators, mixers, switches, variable attenuators, power dividers, and power combiners. These chips are being designed for fabrication using the multifunction self-aligned gate process. The benefits from GaAs IC insertion are quantified by a comparison of hardware units fabricated with existing MIC and digital ECL technology and the same units manufactured with monolithic technology. It is found that major improvements in cost, reliability, size, weight, and performance can be realized. Examples illustrating the methodology for technology insertion are presented.

Biomathematical Description of Synthetic Peptide Libraries

PubMed Central

Trepel, Martin

2015-01-01

Libraries of randomised peptides displayed on phages or viral particles are essential tools in a wide spectrum of applications. However, there is only limited understanding of a library's fundamental dynamics and the influences of encoding schemes and sizes on their quality. Numeric properties of libraries, such as the expected number of different peptides and the library's coverage, have long been in use as measures of a library's quality. Here, we present a graphical framework of these measures together with a library's relative efficiency to help to describe libraries in enough detail for researchers to plan new experiments in a more informed manner. In particular, these values allow us to answer-in a probabilistic fashion-the question of whether a specific library does indeed contain one of the "best" possible peptides. The framework is implemented in a web-interface based on two packages, discreteRV and peptider, to the statistical software environment R. We further provide a user-friendly web-interface called PeLiCa (Peptide Library Calculator, http://www.pelica.org), allowing scientists to plan and analyse their peptide libraries. PMID:26042419

Mechanization of library procedures in the medium-sized medical library. 8. Computer applications in hospital departmental libraries.

PubMed

Howard, E; Kharibian, G

1972-07-01

To test the hypothesis that a standard library system could be designed for hospital departmental libraries, a system was developed and partially tested for four departmental libraries in the Washington University School of Medicine and Associated Hospitals. The system from determination of needs through design and evaluation, is described. The system was limited by specific constraints to control of the monograph collection. Products of control include catalog cards, accessions list, new book list, location list, fund list, missing book list, and discard book list. Sample data form and pages from a procedure manual are given, and conversion from a manual to an automated system is outlined. The question of standardization of library records and procedures is discussed, with indications of the way in which modular design, as utilized in this system, could contribute to greater flexibility in design of future systems. Reference is made to anticipating needs for organizing departmental libraries in developing regional medical library programs and to exploring the role of the departmental library in a medical library network.

The Quiet Room: A Cyber-Free Haven in the Community Library.

ERIC Educational Resources Information Center

Jacob, Bernard; Morphew, Carol

1997-01-01

Because community libraries are becoming centers of suburban and "exurban" activity, quiet study rooms are being constructed for customers intent on concentrated study. Discusses functional (size, location, furniture) and physical (acoustic, heating, ventilation, air conditioning, lighting, electronic support) considerations of quiet…

The Adoption of Innovations over Time: Structural Determinants and Consequences in Library Organizations.

ERIC Educational Resources Information Center

Damanpour, Fariborz; Evan, William M.

1992-01-01

This study used a sampling of empirical data from public libraries to examine organizational characteristics (i.e., specialization, horizontal differentiation, vertical differentiation, professionalism, administrative intensity, organizational slack, and organizational size) and performance levels of three groups of organizations delineated…

A thermal emission spectral library of rock-forming minerals

NASA Astrophysics Data System (ADS)

Christensen, Philip R.; Bandfield, Joshua L.; Hamilton, Victoria E.; Howard, Douglas A.; Lane, Melissa D.; Piatek, Jennifer L.; Ruff, Steven W.; Stefanov, William L.

2000-04-01

A library of thermal infrared spectra of silicate, carbonate, sulfate, phosphate, halide, and oxide minerals has been prepared for comparison to spectra obtained from planetary and Earth-orbiting spacecraft, airborne instruments, and laboratory measurements. The emphasis in developing this library has been to obtain pure samples of specific minerals. All samples were hand processed and analyzed for composition and purity. The majority are 710-1000 μm particle size fractions, chosen to minimize particle size effects. Spectral acquisition follows a method described previously, and emissivity is determined to within 2% in most cases. Each mineral spectrum is accompanied by descriptive information in database form including compositional information, sample quality, and a comments field to describe special circumstances and unique conditions. More than 150 samples were selected to include the common rock-forming minerals with an emphasis on igneous and sedimentary minerals. This library is available in digital form and will be expanded as new, well-characterized samples are acquired.

Small RNA Library Preparation Method for Next-Generation Sequencing Using Chemical Modifications to Prevent Adapter Dimer Formation.

PubMed

Shore, Sabrina; Henderson, Jordana M; Lebedev, Alexandre; Salcedo, Michelle P; Zon, Gerald; McCaffrey, Anton P; Paul, Natasha; Hogrefe, Richard I

2016-01-01

For most sample types, the automation of RNA and DNA sample preparation workflows enables high throughput next-generation sequencing (NGS) library preparation. Greater adoption of small RNA (sRNA) sequencing has been hindered by high sample input requirements and inherent ligation side products formed during library preparation. These side products, known as adapter dimer, are very similar in size to the tagged library. Most sRNA library preparation strategies thus employ a gel purification step to isolate tagged library from adapter dimer contaminants. At very low sample inputs, adapter dimer side products dominate the reaction and limit the sensitivity of this technique. Here we address the need for improved specificity of sRNA library preparation workflows with a novel library preparation approach that uses modified adapters to suppress adapter dimer formation. This workflow allows for lower sample inputs and elimination of the gel purification step, which in turn allows for an automatable sRNA library preparation protocol.

[A research of letter color visibility in package insert information using simulator].

PubMed

Kamimura, Naoki; Kinoshita, Noriyuki; Onaga, Midori; Watanabe, Yurika; Ijuin, Kazushige; Shikamura, Yoshiaki; Negishi, Kenichi; Kaiho, Fusao; Ohta, Takafumi

2012-01-01

Package insert of pharmaceutical drug is one of the most prioritized information for pharmacists to secure safety of patients. However, the color of character, size, font and so on are various company by company product to product from a viewpoint of visibility. It may be cause a serious accident in case visibility is unclear, although it is the most important information. Moreover, package insert with high visibility is required for color vision defectives from a viewpoint of a universal design. Then, the authors selected the package insert which has the boxed warning in the ethical pharmaceutical currently stored mostly in the present health insurance pharmacy and quantified the red color using the color meter. We advocate the state of a suitable package insert from a viewpoint of a universal design, whether the red color is high visible or not for color vision defectives using simulator.

Atmospheric particulate analysis using angular light scattering

NASA Technical Reports Server (NTRS)

Hansen, M. Z.

1980-01-01

Using the light scattering matrix elements measured by a polar nephelometer, a procedure for estimating the characteristics of atmospheric particulates was developed. A theoretical library data set of scattering matrices derived from Mie theory was tabulated for a range of values of the size parameter and refractive index typical of atmospheric particles. Integration over the size parameter yielded the scattering matrix elements for a variety of hypothesized particulate size distributions. A least squares curve fitting technique was used to find a best fit from the library data for the experimental measurements. This was used as a first guess for a nonlinear iterative inversion of the size distributions. A real index of 1.50 and an imaginary index of -0.005 are representative of the smoothed inversion results for the near ground level atmospheric aerosol in Tucson.

Acute myeloid leukaemia (FAB AML-M4Eo) with cryptic insertion of cbfb resulting in cbfb-Myh11 fusion.

PubMed

Douet-Guilbert, Nathalie; Chauveau, Aurelie; Gueganic, Nadia; Guillerm, Gaëlle; Tous, Corine; Le Bris, Marie-Josee; Basinko, Audrey; Morel, Frederic; Ugo, Valerie; De Braekeleer, Marc

2017-09-01

Inv(16)(p13q22) and t(16;16)(p13;q22) are cytogenetic hallmarks of acute myelomonoblastic leukaemia, most of them associated with abnormal bone marrow eosinophils [acute myeloid leukaemia French-American-British classification M4 with eosinophilia (FAB AML-M4Eo)] and a relatively favourable clinical course. They generate a 5'CBFB-3'MYH11 fusion gene. However, in a few cases, although RT-PCR identified a CBFB-MYH11 transcript, normal karyotype and/or fluorescent in situ hybridization (FISH) analyses using commercially available probes are found. We identified a 32-year-old woman with AML-M4Eo and normal karyotype and FISH results. Using two libraries of Bacterial Artificial Chromosome clones on 16p13 and 16q22, FISH analyses identified an insertion of 16q22 material in band 16p13, generating a CBFB-MYH11 type A transcript. Although very rare, insertions should be searched for in patients with discordant cytological and cytogenetic features because of the therapeutic consequences. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

Alternative method for predicting optimal insertion depth of the laryngeal tube in children.

PubMed

Kim, J T; Jeon, S Y; Kim, C S; Kim, S D; Kim, H S

2007-11-01

Little information is available about the accuracy of the teeth mark on the laryngeal tube (LT) as a guide to correct placement in children. The aim of this crossover study was to evaluate three methods for optimal insertion depth of the size (#) 2 tube in children weighing 12-25 kg. In 24 children, the LT #2 was consecutively inserted by three different methods: (A) until the thick teeth mark on the tube was aligned with the upper incisors, (B) until resistance was felt, and (C) by inserting to a depth, previously measured, of the curved distance between the cricoid cartilage and the upper incisor. In each case, the depth of insertion, the degree of effective ventilation, the presence of leakage, and the fibreoptic view were assessed. Insertion based on the teeth mark led to a shorter insertion depth and a greater incidence of inadequate ventilation compared with the other two methods. There was no difference in the adequacy of ventilation between methods B and C. The vocal cords were more easily identified with methods B (62.5%) and C (75%) than with method A (12.5%). Insertion of the LT #2 aligned with the teeth mark can result in a shallow insertion depth and inadequate ventilation. The measured distance from the cricoid cartilage to the upper incisor offers alternative guidance for correct LT insertion.

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

NASA Astrophysics Data System (ADS)

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

2016-04-01

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

Design and preliminary analysis of a vaginal inserter for speculum-free cervical cancer screening

PubMed Central

Agudogo, Júlia; Krieger, Marlee S.; Miros, Robert; Proeschold-Bell, Rae Jean; Schmitt, John W.; Ramanujam, Nimmi

2017-01-01

Objective Cervical cancer screening usually requires use of a speculum to provide a clear view of the cervix. The speculum is one potential barrier to screening due to fear of pain, discomfort and embarrassment. The aim of this paper is to present and demonstrate the feasibility of a tampon-sized inserter and the POCkeT Colposcope, a miniature pen sized-colposcope, for comfortable, speculum-free and potentially self-colposcopy. Study design We explored different designs using 3D computer-aided design (CAD) software and performed mechanical testing simulations on each. Designs were rapid prototyped and tested using a custom vaginal phantom across a range of vaginal pressures and uterine tilts to select an optimal design. Two final designs were tested with fifteen volunteers to assess cervix visualization, comfort and usability compared to the speculum and the optimal design, the curved-tip inserter, was selected for testing in volunteers. Results We present a vaginal inserter as an alternative to the standard speculum for use with the POCkeT Colposcope. The device has a slim tubular body with a funnel-like curved tip measuring approximately 2.5 cm in diameter. The inserter has a channel through which a 2 megapixel (MP) mini camera with LED illumination fits to enable image capture. Mechanical finite element testing simulations with an applied pressure of 15 cm H2O indicated a high factor of safety (90.9) for the inserter. Testing of the device with a custom vaginal phantom, across a range of supine vaginal pressures and uterine tilts (retroverted, anteverted and sideverted), demonstrated image capture with a visual area comparable to the speculum for a normal/axial positioned uteri and significantly better than the speculum for anteverted and sideverted uteri (p<0.00001). Volunteer studies with self-insertion and physician-assisted cervix image capture showed adequate cervix visualization for 83% of patients. In addition, questionnaire responses from volunteers indicated a 92.3% overall preference for the inserter over the speculum and all indicated that the inserter was more comfortable than the speculum. The inserter provides a platform for self-cervical cancer screening and also enables acetic acid/Lugol’s iodine application and insertion of swabs for Pap smear sample collection. Conclusion This study demonstrates the feasibility of an inserter and miniature-imaging device for comfortable cervical image capture of women with potential for synergistic HPV and Pap smear sample collection. PMID:28562669

Performance comparison analysis library communication cluster system using merge sort

NASA Astrophysics Data System (ADS)

Wulandari, D. A. R.; Ramadhan, M. E.

2018-04-01

Begins by using a single processor, to increase the speed of computing time, the use of multi-processor was introduced. The second paradigm is known as parallel computing, example cluster. The cluster must have the communication potocol for processing, one of it is message passing Interface (MPI). MPI have many library, both of them OPENMPI and MPICH2. Performance of the cluster machine depend on suitable between performance characters of library communication and characters of the problem so this study aims to analyze the comparative performances libraries in handling parallel computing process. The case study in this research are MPICH2 and OpenMPI. This case research execute sorting’s problem to know the performance of cluster system. The sorting problem use mergesort method. The research method is by implementing OpenMPI and MPICH2 on a Linux-based cluster by using five computer virtual then analyze the performance of the system by different scenario tests and three parameters for to know the performance of MPICH2 and OpenMPI. These performances are execution time, speedup and efficiency. The results of this study showed that the addition of each data size makes OpenMPI and MPICH2 have an average speed-up and efficiency tend to increase but at a large data size decreases. increased data size doesn’t necessarily increased speed up and efficiency but only execution time example in 100000 data size. OpenMPI has a execution time greater than MPICH2 example in 1000 data size average execution time with MPICH2 is 0,009721 and OpenMPI is 0,003895 OpenMPI can customize communication needs.

Synthesis of a Stereochemically Diverse Library of Medium-Sized Lactams and Sultams via SNAr Cycloetherification

PubMed Central

Gerard, Baudouin; Duvall, Jeremy R.; Lowe, Jason T.; Murillo, Tiffanie; Wei, Jingqiang; Akella, Lakshmi B.; Marcaurelle, Lisa A.

2011-01-01

We have implemented an aldol-based ‘build/couple/pair’ (B/C/P) strategy for the synthesis of stereochemically diverse 8-membered lactam and sultam scaffolds via SNAr cycloetherification. Each scaffold contains two handles, an amine and aryl bromide, for solid-phase diversification via N-capping and Pd-mediated cross coupling. A sparse matrix design strategy that achieves the dual objective of controlling physicochemical properties and selecting diverse library members was implemented. The production of two 8000-membered libraries is discussed including a full analysis of library purity and property distribution. Library diversity was evaluated in comparison to the Molecular Library Small Molecule Repository (MLSMR) through the use of a multi-fusion similarity (MFS) map and principal component analysis (PCA). PMID:21526820

Identification and characterization of a chitin deacetylase from a metagenomic library of deep-sea sediments of the Arctic Ocean.

PubMed

Liu, Jinlin; Jia, Zhijuan; Li, Sha; Li, Yan; You, Qiang; Zhang, Chunyan; Zheng, Xiaotong; Xiong, Guomei; Zhao, Jin; Qi, Chao; Yang, Jihong

2016-09-15

The chemical and biological compositions of deep-sea sediments are interesting because of the underexplored diversity when it comes to bioprospecting. The special geographical location and climates make Arctic Ocean a unique ocean area containing an abundance of microbial resources. A metagenomic library was constructed based on the deep-sea sediments of Arctic Ocean. Part of insertion fragments of this library were sequenced. A chitin deacetylase gene, cdaYJ, was identified and characterized. A metagenomic library with 2750 clones was obtained and ten clones were sequenced. Results revealed several interesting genes, including a chitin deacetylase coding sequence, cdaYJ. The CdaYJ is homologous to some known chitin deacetylases and contains conserved chitin deacetylase active sites. CdaYJ protein exhibits a long N-terminal and a relative short C-terminal. Phylogenetic analysis revealed that CdaYJ showed highest homology to CDAs from Alphaproteobacteria. The cdaYJ gene was subcloned into the pET-28a vector and the recombinant CdaYJ (rCdaYJ) was expressed in Escherichia coli BL21 (DE3). rCdaYJ showed a molecular weight of 43kDa, and exhibited deacetylation activity by using p-nitroacetanilide as substrate. The optimal pH and temperature of rCdaYJ were tested as pH7.4 and 28°C, respectively. The construction of metagenomic library of the Arctic deep-sea sediments provides us an opportunity to look into the microbial communities and exploiting valuable gene resources. A chitin deacetylase CdaYJ was identified from the library. It showed highest deacetylation activity under slight alkaline and low temperature conditions. CdaYJ might be a candidate chitin deacetylase that possesses industrial and pharmaceutical potentials. Copyright © 2016 Elsevier B.V. All rights reserved.

[Construction of a phage antibody library and screening of anti-epidermal growth factor receptor variant III single chain antibody].

PubMed

Han, Dong-gang; Duan, Xiao-yi; Guo, You-min; Zhou, Qi; Wang, Quan-ying; Yang, Guang-xiao

2010-01-01

To obtain specific anti-epidermal growth factor receptor variant III (EGFRvIII) single chain antibody (ScFv) by phage antibody library display system. The total RNA was extracted from the spleen B cells of BALB/c mice immunized with pep-3-OVA protein, and the first-strand cDNA was synthesized by reverse transcription. Antibody VH and VL gene fragments were amplified and joined to a ScFv gene with the linker. The ScFv gene was ligated into the phagemid vector pCANTAB5E, which was transformed into competent E. coli TG1. The transformed cells were then infected with M13KO7 helper phage to yield the recombinant phage to construct the phage ScFv library. Pep-3-BSA protein was used to screen the phage antibody library and ELISA carried out to characterize the activity of the antibody. The VH and VL gene fragments of the antibody were about 350 bp and 320 bp in length as analyzed by agarose gel electrophoresis. The ScFv gene was 780 bp, consistent with the expected length. The recombinant phagemid with ScFv gene insert was rescued, and an immune phage ScFv library with the content of 5.0x10(6) was constructed. The recombinant ScFv phage had a titer of 3.0x10(4) cfu/ml, and the fourth phage harvest yielded 56 times as much as that of the first one. SDS-PAGE demonstrated a molecular mass of the soluble ScFv of about 28 kD. ELISA results indicated good specificity of the ScFv to bind EGFRvIII. An immune phage ScFv library is successfully constructed, and the ScFv antibody fragment is capable of specific binding to EGFRvIII.

Outstanding Reference Sources: The 1994 Selection of Recent Titles.

ERIC Educational Resources Information Center

Luchsinger, Dale F.

1994-01-01

Presents an annotated bibliography of 37 outstanding reference sources published in 1993 for small to medium-sized public and academic libraries as selected by the American Library Association's Reference Services Committee. Categories include culture and civilization, biography, general, language and literature, nature, law, religion, technology,…

75 FR 42173 - Small Business Size Standards: Waiver of the Nonmanufacturer Rule

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-20

... Configured Tape Library Storage Equipment. SUMMARY: The U.S. Small Business Administration (SBA) is granting a class waiver of the Nonmanufacturer Rule for Configured Tape Library Storage Equipment, Product... Support Equipment, and PSC 7045 ADP Supplies, under the North American Industry Classification System...

SU-E-J-238: First-Order Approximation of Time-Resolved 4DMRI From Cine 2DMRI and Respiratory-Correlated 4DMRI

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

Li, G; Tyagi, N; Deasy, J

2015-06-15

Purpose: Cine 2DMRI is useful in MR-guided radiotherapy but it lacks volumetric information. We explore the feasibility of estimating timeresolved (TR) 4DMRI based on cine 2DMRI and respiratory-correlated (RC) 4DMRI though simulation. Methods: We hypothesize that a volumetric image during free breathing can be approximated by interpolation among 3DMRI image sets generated from a RC-4DMRI. Two patients’ RC-4DMRI with 4 or 5 phases were used to generate additional 3DMRI by interpolation. For each patient, six libraries were created to have total 5-to-35 3DMRI images by 0–6 equi-spaced tri-linear interpolation between adjacent and full-inhalation/full-exhalation phases. Sagittal cine 2DMRI were generated frommore » reference 3DMRIs created from separate, unique interpolations from the original RC-4DMRI. To test if accurate 3DMRI could be generated through rigid registration of the cine 2DMRI to the 3DMRI libraries, each sagittal 2DMRI was registered to sagittal cuts in the same location in the 3DMRI within each library to identify the two best matches: one with greater lung volume and one with smaller. A final interpolation between the corresponding 3DMRI was then performed to produce the first-order-approximation (FOA) 3DMRI. The quality and performance of the FOA as a function of library size was assessed using both the difference in lung volume and average voxel intensity between the FOA and the reference 3DMRI. Results: The discrepancy between the FOA and reference 3DMRI decreases as the library size increases. The 3D lung volume difference decreases from 5–15% to 1–2% as the library size increases from 5 to 35 image sets. The average difference in lung voxel intensity decreases from 7–8 to 5–6 with the lung intensity being 0–135. Conclusion: This study indicates that the quality of FOA 3DMRI improves with increasing 3DMRI library size. On-going investigations will test this approach using actual cine 2DMRI and introduce a higher order approximation for improvements. This study is in part supported by NIH (U54CA137788 and U54CA132378)« less

Linear motion device and method for inserting and withdrawing control rods

DOEpatents

Smith, Jay E.

1984-01-01

A linear motion device, more specifically a control rod drive mechanism (CRDM) for inserting and withdrawing control rods into a reactor core, is capable of independently and sequentially positioning two sets of control rods with a single motor stator and rotor. The CRDM disclosed can control more than one control rod lead screw without incurring a substantial increase in the size of the mechanism.

Use study of Excerpta Medica abstract journals: to drop or not to drop?

PubMed Central

Alligood, E C; Russo-Martin, E; Peterson, R A

1983-01-01

The directors of the Claude Moore Health Sciences Library, a medium-sized library serving the University of Virginia medical and nursing schools, were concerned over the increasing cost of periodical subscriptions and so studied the use of the printed copy of Excerpta Medica. This study had six parts: (1) availability in other campus libraries; (2) staff perceptions of in-library use; (3) results of studies performed by other libraries in the United States; (4) recorded in-library use; (5) users' opinions; and (6) personal interviews with library users and with selected departments tht corresponded with the forty-four subject areas of Excerpta Medica. The user-survey parts (4 and 5) elicited few responses, but personal interviews allowed a good look at levels of use and interest. The overall results convinced staff to drop some sections and publicize those that remained. PMID:6626797

Library-based illumination synthesis for critical CMOS patterning.

PubMed

Yu, Jue-Chin; Yu, Peichen; Chao, Hsueh-Yung

2013-07-01

In optical microlithography, the illumination source for critical complementary metal-oxide-semiconductor layers needs to be determined in the early stage of a technology node with very limited design information, leading to simple binary shapes. Recently, the availability of freeform sources permits us to increase pattern fidelity and relax mask complexities with minimal insertion risks to the current manufacturing flow. However, source optimization across many patterns is often treated as a design-of-experiments problem, which may not fully exploit the benefits of a freeform source. In this paper, a rigorous source-optimization algorithm is presented via linear superposition of optimal sources for pre-selected patterns. We show that analytical solutions are made possible by using Hopkins formulation and quadratic programming. The algorithm allows synthesized illumination to be linked with assorted pattern libraries, which has a direct impact on design rule studies for early planning and design automation for full wafer optimization.

Rapid metaphase and interphase detection of radiation-induced chromosome aberrations in human lymphocytes by chromosomal suppression in situ hybridization

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

Cremer, T.; Popp, S.; Emmerich, P.

1990-01-01

Chromosomal in situ suppression (CISS)-hybridization of biotinylated phage DNA-library inserts from sorted human chromosomes was used to decorate chromosomes 1 and 7 specifically from pter to qter and to detect structural aberrations of these chromosomes in irradiated human peripheral lymphocytes. In addition, probe pUC1.77 was used to mark the 1q12 subregion in normal and aberrant chromosomes 1. Low LET radiation (60Co-gamma-rays; 1.17 and 1.33 MeV) of lymphocyte cultures was performed with various doses (D = 0, 2, 4, 8 Gy) 5 h after stimulation with phytohaemagglutinin. Irradiated cells were cultivated for an additional 67 h before Colcemid arrested metaphase spreadsmore » were obtained. Aberrations of the specifically stained chromosomes, such as deletions, dicentrics, and rings, were readily scored after in situ hybridization with either the 1q12 specific probe or DNA-library inserts. By the latter approach, translocations of the specifically stained chromosomes could also be reliably assessed. A linear increase of the percentage of specifically stained aberrant chromosomes was observed when plotted as a function of the square of the dose D. A particular advantage of this new approach is provided by the possibility to delineate numerical and structural chromosome aberrations directly in interphase nuclei. These results indicate that cytogenetic monitoring of ionizing radiation may be considerably facilitated by CISS-hybridization.« less

Library Screen Identifies Enterococcus faecalis CcpA, the Catabolite Control Protein A, as an Effector of Ace, a Collagen Adhesion Protein Linked to Virulence

PubMed Central

Gao, Peng; Pinkston, Kenneth L.; Bourgogne, Agathe; Cruz, Melissa R.; Garsin, Danielle A.; Murray, Barbara E.

2013-01-01

The Enterococcus faecalis cell wall-anchored protein Ace is an important virulence factor involved in cell adhesion and infection. Expression of Ace on the cell surface is affected by many factors, including stage of growth, culture temperature, and environmental components, such as serum, urine, and collagen. However, the mechanisms that regulate or modulate Ace display are not well understood. With interest in identifying genes associated with Ace expression, we utilized a whole-cell enzyme-linked immunosorbent assay (ELISA)-based screening method to identify mutants from a transposon insertion mutant library which exhibited distinct Ace surface expression profiles. We identified a ccpA insertion mutant which showed significantly decreased levels of Ace surface expression at early growth phase versus those of wild-type OG1RF. Confirmation of the observation was achieved through flow cytometry and complementation analysis. Compared to the wild type, the E. faecalis ccpA mutant had an impaired ability to adhere to collagen when grown to early exponential phase, consistent with the lack of Ace expression in the early growth phase. As a key component of carbon catabolite regulation, CcpA has been previously reported to play a critical role in regulating expression of proteins involved in E. faecalis carbohydrate uptake and utilization. Our discovery is the first to associate CcpA with the production of a major E. faecalis virulence factor, providing new insights into the regulation of E. faecalis pathogenesis. PMID:23974022

A genome-wide inducible phenotypic screen identifies antisense RNA constructs silencing Escherichia coli essential genes.

PubMed

Meng, Jia; Kanzaki, Gregory; Meas, Diane; Lam, Christopher K; Crummer, Heather; Tain, Justina; Xu, H Howard

2012-04-01

Regulated antisense RNA (asRNA) expression has been employed successfully in Gram-positive bacteria for genome-wide essential gene identification and drug target determination. However, there have been no published reports describing the application of asRNA gene silencing for comprehensive analyses of essential genes in Gram-negative bacteria. In this study, we report the first genome-wide identification of asRNA constructs for essential genes in Escherichia coli. We screened 250 000 library transformants for conditional growth inhibitory recombinant clones from two shotgun genomic libraries of E. coli using a paired-termini expression vector (pHN678). After sequencing plasmid inserts of 675 confirmed inducer sensitive cell clones, we identified 152 separate asRNA constructs of which 134 inserts came from essential genes, while 18 originated from nonessential genes (but share operons with essential genes). Among the 79 individual essential genes silenced by these asRNA constructs, 61 genes (77%) engage in processes related to protein synthesis. The cell-based assays of an asRNA clone targeting fusA (encoding elongation factor G) showed that the induced cells were sensitized 12-fold to fusidic acid, a known specific inhibitor. Our results demonstrate the utility of the paired-termini expression vector and feasibility of large-scale gene silencing in E. coli using regulated asRNA expression. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Automated System Marketplace 1987: Maturity and Competition.

ERIC Educational Resources Information Center

Walton, Robert A.; Bridge, Frank R.

1988-01-01

This annual review of the library automation marketplace presents profiles of 15 major library automation firms and looks at emerging trends. Seventeen charts and tables provide data on market shares, number and size of installations, hardware availability, operating systems, and interfaces. A directory of 49 automation sources is included. (MES)

Retrospective Catalog Conversion in Mid-Sized Law Libraries: Some Practical Guidelines for Automation.

ERIC Educational Resources Information Center

Riger, Robert E.

1992-01-01

Discusses retrospective catalog conversion from the viewpoint of a law firm library. Topics discussed include reasons for retrospective conversion; preplanning; suggestions for the selection of software; conducting an inventory of the collection; sources of MARC bibliographic records; setting up an online public access catalog; and marketing…

Multiple-User Microcomputer Technology and Its Application to the Library Environment.

ERIC Educational Resources Information Center

McCarthy, Cathleen D.

1987-01-01

Demonstrates the ways in which multiuser and multitasking microcomputer systems can be used for the automation of small- to medium-sized library operations. The possibilities afforded by the IBM-PC AT microcomputer are discussed and a sample configuration with estimated cost projections is provided. (EM)

Assessing the Effectiveness of Online Library Instruction with Finance Students

ERIC Educational Resources Information Center

Friehs, Curt G.; Craig, Cindy L.

2008-01-01

Many academic librarians use online information literacy tutorials as an alternative or a supplement to in-class library instruction. Tutorials created with streaming media software such as Camtasia Studio have become increasingly popular. Librarians at a mid-sized Midwestern university have created several such tutorials demonstrating various…

75 FR 32231 - Small Business Size Standards: Waiver of the Nonmanufacturer Rule

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-07

... for configured tape library storage equipment. SUMMARY: The U.S. Small Business Administration (SBA... Storage Equipment. SBA is initiating a request that an class waiver be granted for Configured Tape Library Storage Equipment, Product Service Code (PSC) 7025 Automated Data Processing (ADP) Input/ Output and...

Delivered! A Mid-Sized Academic Library's Experience with Distance Education

ERIC Educational Resources Information Center

Bartnik, Linda

2010-01-01

Murray State University (Kentucky) has been experimenting with various means of document delivery and research instruction for its online only and satellite campuses. These include ILLiad-based document delivery, Camtasia-to-UTube tutorials, a discipline-based service called Library on Blackboard, Eluminate and other virtual instructional methods.…

Capturing Nature's Diversity

PubMed Central

Pascolutti, Mauro; Campitelli, Marc; Nguyen, Bao; Pham, Ngoc; Gorse, Alain-Dominique; Quinn, Ronald J.

2015-01-01

Natural products are universally recognized to contribute valuable chemical diversity to the design of molecular screening libraries. The analysis undertaken in this work, provides a foundation for the generation of fragment screening libraries that capture the diverse range of molecular recognition building blocks embedded within natural products. Physicochemical properties were used to select fragment-sized natural products from a database of known natural products (Dictionary of Natural Products). PCA analysis was used to illustrate the positioning of the fragment subset within the property space of the non-fragment sized natural products in the dataset. Structural diversity was analysed by three distinct methods: atom function analysis, using pharmacophore fingerprints, atom type analysis, using radial fingerprints, and scaffold analysis. Small pharmacophore triplets, representing the range of chemical features present in natural products that are capable of engaging in molecular interactions with small, contiguous areas of protein binding surfaces, were analysed. We demonstrate that fragment-sized natural products capture more than half of the small pharmacophore triplet diversity observed in non fragment-sized natural product datasets. Atom type analysis using radial fingerprints was represented by a self-organizing map. We examined the structural diversity of non-flat fragment-sized natural product scaffolds, rich in sp3 configured centres. From these results we demonstrate that 2-ring fragment-sized natural products effectively balance the opposing characteristics of minimal complexity and broad structural diversity when compared to the larger, more complex fragment-like natural products. These naturally-derived fragments could be used as the starting point for the generation of a highly diverse library with the scope for further medicinal chemistry elaboration due to their minimal structural complexity. This study highlights the possibility to capture a high proportion of the individual molecular interaction motifs embedded within natural products using a fragment screening library spanning 422 structural clusters and comprised of approximately 2800 natural products. PMID:25902039

Scaffold Library for Tissue Engineering: A Geometric Evaluation

PubMed Central

Chantarapanich, Nattapon; Puttawibul, Puttisak; Sucharitpwatskul, Sedthawatt; Jeamwatthanachai, Pongnarin; Inglam, Samroeng; Sitthiseripratip, Kriskrai

2012-01-01

Tissue engineering scaffold is a biological substitute that aims to restore, to maintain, or to improve tissue functions. Currently available manufacturing technology, that is, additive manufacturing is essentially applied to fabricate the scaffold according to the predefined computer aided design (CAD) model. To develop scaffold CAD libraries, the polyhedrons could be used in the scaffold libraries development. In this present study, one hundred and nineteen polyhedron models were evaluated according to the established criteria. The proposed criteria included considerations on geometry, manufacturing feasibility, and mechanical strength of these polyhedrons. CAD and finite element (FE) method were employed as tools in evaluation. The result of evaluation revealed that the close-cellular scaffold included truncated octahedron, rhombicuboctahedron, and rhombitruncated cuboctahedron. In addition, the suitable polyhedrons for using as open-cellular scaffold libraries included hexahedron, truncated octahedron, truncated hexahedron, cuboctahedron, rhombicuboctahedron, and rhombitruncated cuboctahedron. However, not all pore size to beam thickness ratios (PO : BT) were good for making the open-cellular scaffold. The PO : BT ratio of each library, generating the enclosed pore inside the scaffold, was excluded to avoid the impossibility of material removal after the fabrication. The close-cellular libraries presented the constant porosity which is irrespective to the different pore sizes. The relationship between PO : BT ratio and porosity of open-cellular scaffold libraries was displayed in the form of Logistic Power function. The possibility of merging two different types of libraries to produce the composite structure was geometrically evaluated in terms of the intersection index and was mechanically evaluated by means of FE analysis to observe the stress level. The couples of polyhedrons presenting low intersection index and high stress level were excluded. Good couples for producing the reinforced scaffold were hexahedron-truncated hexahedron and cuboctahedron-rhombitruncated cuboctahedron. PMID:23056147

Oxidation and metal-insertion in molybdenite surfaces: evaluation of charge-transfer mechanisms and dynamics

PubMed Central

Ramana, CV; Becker, U; Shutthanandan, V; Julien, CM

2008-01-01

Molybdenum disulfide (MoS2), a layered transition-metal dichalcogenide, has been of special importance to the research community of geochemistry, materials and environmental chemistry, and geotechnical engineering. Understanding the oxidation behavior and charge-transfer mechanisms in MoS2 is important to gain better insight into the degradation of this mineral in the environment. In addition, understanding the insertion of metals into molybdenite and evaluation of charge-transfer mechanism and dynamics is important to utilize these minerals in technological applications. Furthermore, a detailed investigation of thermal oxidation behavior and metal-insertion will provide a basis to further explore and model the mechanism of adsorption of metal ions onto geomedia. The present work was performed to understand thermal oxidation and metal-insertion processes of molybdenite surfaces. The analysis was performed using atomic force microscopy (AFM), scanning electron microscopy (SEM), transmission electron microscopy (TEM), Rutherford backscattering spectrometry (RBS), and nuclear reaction analysis (NRA). Structural studies using SEM and TEM indicate the local-disordering of the structure as a result of charge-transfer process between the inserted lithium and the molybdenite layer. Selected area electron diffraction measurements indicate the large variations in the diffusivity of lithium confirming that the charge-transfer is different along and perpendicular to the layers in molybdenite. Thermal heating of molybenite surface in air at 400°C induces surface oxidation, which is slow during the first hour of heating and then increases significantly. The SEM results indicate that the crystals formed on the molybdenite surface as a result of thermal oxidation exhibit regular thin-elongated shape. The average size and density of the crystals on the surface is dependent on the time of annealing; smaller size and high density during the first one-hour and significant increase in size associated with a decrease in density with further annealing. PMID:18534025

Oxidation and metal-insertion in molybdenite surfaces: evaluation of charge-transfer mechanisms and dynamics.

PubMed

Ramana, C V; Becker, U; Shutthanandan, V; Julien, C M

2008-06-05

Molybdenum disulfide (MoS2), a layered transition-metal dichalcogenide, has been of special importance to the research community of geochemistry, materials and environmental chemistry, and geotechnical engineering. Understanding the oxidation behavior and charge-transfer mechanisms in MoS2 is important to gain better insight into the degradation of this mineral in the environment. In addition, understanding the insertion of metals into molybdenite and evaluation of charge-transfer mechanism and dynamics is important to utilize these minerals in technological applications. Furthermore, a detailed investigation of thermal oxidation behavior and metal-insertion will provide a basis to further explore and model the mechanism of adsorption of metal ions onto geomedia.The present work was performed to understand thermal oxidation and metal-insertion processes of molybdenite surfaces. The analysis was performed using atomic force microscopy (AFM), scanning electron microscopy (SEM), transmission electron microscopy (TEM), Rutherford backscattering spectrometry (RBS), and nuclear reaction analysis (NRA).Structural studies using SEM and TEM indicate the local-disordering of the structure as a result of charge-transfer process between the inserted lithium and the molybdenite layer. Selected area electron diffraction measurements indicate the large variations in the diffusivity of lithium confirming that the charge-transfer is different along and perpendicular to the layers in molybdenite. Thermal heating of molybenite surface in air at 400 degrees C induces surface oxidation, which is slow during the first hour of heating and then increases significantly. The SEM results indicate that the crystals formed on the molybdenite surface as a result of thermal oxidation exhibit regular thin-elongated shape. The average size and density of the crystals on the surface is dependent on the time of annealing; smaller size and high density during the first one-hour and significant increase in size associated with a decrease in density with further annealing.

Identification of Genes Involved in Biofilm Formation and Respiration via Mini-Himar Transposon Mutagenesis of Geobacter sulfurreducens▿ †

PubMed Central

Rollefson, Janet B.; Levar, Caleb E.; Bond, Daniel R.

2009-01-01

Electron transfer from cells to metals and electrodes by the Fe(III)-reducing anaerobe Geobacter sulfurreducens requires proper expression of redox proteins and attachment mechanisms to interface bacteria with surfaces and neighboring cells. We hypothesized that transposon mutagenesis would complement targeted knockout studies in Geobacter spp. and identify novel genes involved in this process. Escherichia coli mating strains and plasmids were used to develop a conjugation protocol and deliver mini-Himar transposons, creating a library of over 8,000 mutants that was anaerobically arrayed and screened for a range of phenotypes, including auxotrophy for amino acids, inability to reduce Fe(III) citrate, and attachment to surfaces. Following protocol validation, mutants with strong phenotypes were further characterized in a three-electrode system to simultaneously quantify attachment, biofilm development, and respiratory parameters, revealing mutants defective in Fe(III) reduction but unaffected in electron transfer to electrodes (such as an insertion in GSU1330, a putative metal export protein) or defective in electrode reduction but demonstrating wild-type biofilm formation (due to an insertion upstream of the NHL domain protein GSU2505). An insertion in a putative ATP-dependent transporter (GSU1501) eliminated electrode colonization but not Fe(III) citrate reduction. A more complex phenotype was demonstrated by a mutant containing an insertion in a transglutaminase domain protein (GSU3361), which suddenly ceased to respire when biofilms reached approximately 50% of the wild-type levels. As most insertions were not in cytochromes but rather in transporters, two-component signaling proteins, and proteins of unknown function, this collection illustrates how biofilm formation and electron transfer are separate but complementary phenotypes, controlled by multiple loci not commonly studied in Geobacter spp. PMID:19395486

Mechanization of library procedures in a medium-sized medical library: XVI. Computer-assisted cataloging, the first decade.

PubMed Central

Bolef, D

1975-01-01

After ten years of experimentation in computer-assisted cataloging, the Washington University School of Medicine Library has decided to join the Ohio College Library Center network. The history of the library's work preceding this decision is reviewed. The data processing equipment and computers that have permitted librarians to explore different ways of presenting cataloging information are discussed. Certain cataloging processes are facilitated by computer manipulation and printouts, but the intellectual cataloging processes such as descriptive and subject cataloging are not. Networks and shared bibliographic data bases show promise of eliminating the intellectual cataloging for one book by more than one cataloger. It is in this area that future developments can be expected. PMID:1148442

Selected list of books and journals for the small medical library.

PubMed

Brandon, A N; Hill, D R

1979-04-01

This revised list of 492 books and 138 journals is intended as a selection guide for small or medium-sized hospital libraries or for the small medical library serving a specified clientele. It can also be used as a core list by small hospital library consortia. Books and journals are categorized by subject, with the books being followed by an author index and the journals by an alphabetical title listing. Items suggested for initial purchase by smaller libraries are indicated by an asterisk. To purchase the entire collection of books and to pay for annual subscriptions to all the journals would require an expenditure of about $22,500. The cost of only the asterisked items, recommended for first purchase, totals approximately $6,100.

Selected list of books and journals for the small medical library.

PubMed

Brandon, A N

1977-04-01

This revised list of 472 books and 138 journals is intended as a selection guide for small or medium-sized hospital libraries or for the small medical library serving a specified clientele. It can also be used as a core list by small hospital library consortia. Books and journals are categorized by subject, with the books being followed by an author index and the journals by an alphabetical title listing. Items suggested for initial purchase by smaller libraries are indicated by an asterisk. To purchase the entire collection of books and to pay for annual subscriptions to all the journals would require an expenditure of about $18,200. The cost of only the asterisked items recommended for first purchase totals approximately $4,500.

SU-F-T-47: MRI T2 Exclusive Based Planning Using the Endocavitary/interstitial Gynecological Benidorm Applicator: A Proposed TPS Library and Preplan Efficient Methodology

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

Richart, J; Otal, A; Rodriguez, S

Purpose: ABS and GEC-ESTRO have recommended MRI T2 for image guided brachytherapy. Recently, a new applicator (Benidorm Template, TB) has been developed in our Department (Rodriguez et al 2015). TB is fully MRI compatible because the Titanium needles and it allows the use of intrauterine tandem. Currently, TPS applicators library are not currently available for non-rigid applicators in case of interstitial component as the TB.The purpose of this work is to present the development of a library for the TB, together with its use on a pre-planning technique. Both new goals allow a very efficient and exclusive T2 MRI basedmore » planning clinical TB implementation. Methods: The developed library has been implemented in Oncentra Brachytherapy TPS, version 4.3.0 (Elekta) and now is being implemented on Sagiplan v 2.0 TPS (Eckert&Ziegler BEBIG). To model the TB, free and open software named FreeCAD and MeshLab have been used. The reconstruction process is based on three inserted A-vitamin pellets together with the data provided by the free length. The implemented preplanning procedure is as follow: 1) A MRI T2 acquisition is performed with the template in place just with the vaginal cylinder (no uterine tube nor needles). 2) The CTV is drawn and the required needles are selected using a developed Java based application and 3) A post-implant MRI T2 is performed. Results: This library procedure has been successfully applied by now in 25 patients. In this work the use of the developed library will be illustrated with clinical examples. The preplanning procedure has been applied by now in 6 patients, having significant advantages: needle depth estimation, needle positions and number are optimized a priori, time saving, etc Conclusion: TB library and pre-plan techniques are feasible and very efficient and their use will be illustrated in this work.« less

Hybrid sequencing approach applied to human fecal metagenomic clone libraries revealed clones with potential biotechnological applications.

PubMed

Džunková, Mária; D'Auria, Giuseppe; Pérez-Villarroya, David; Moya, Andrés

2012-01-01

Natural environments represent an incredible source of microbial genetic diversity. Discovery of novel biomolecules involves biotechnological methods that often require the design and implementation of biochemical assays to screen clone libraries. However, when an assay is applied to thousands of clones, one may eventually end up with very few positive clones which, in most of the cases, have to be "domesticated" for downstream characterization and application, and this makes screening both laborious and expensive. The negative clones, which are not considered by the selected assay, may also have biotechnological potential; however, unfortunately they would remain unexplored. Knowledge of the clone sequences provides important clues about potential biotechnological application of the clones in the library; however, the sequencing of clones one-by-one would be very time-consuming and expensive. In this study, we characterized the first metagenomic clone library from the feces of a healthy human volunteer, using a method based on 454 pyrosequencing coupled with a clone-by-clone Sanger end-sequencing. Instead of whole individual clone sequencing, we sequenced 358 clones in a pool. The medium-large insert (7-15 kb) cloning strategy allowed us to assemble these clones correctly, and to assign the clone ends to maintain the link between the position of a living clone in the library and the annotated contig from the 454 assembly. Finally, we found several open reading frames (ORFs) with previously described potential medical application. The proposed approach allows planning ad-hoc biochemical assays for the clones of interest, and the appropriate sub-cloning strategy for gene expression in suitable vectors/hosts.

Defining the ABC of gene essentiality in streptococci.

PubMed

Charbonneau, Amelia R L; Forman, Oliver P; Cain, Amy K; Newland, Graham; Robinson, Carl; Boursnell, Mike; Parkhill, Julian; Leigh, James A; Maskell, Duncan J; Waller, Andrew S

2017-05-31

Utilising next generation sequencing to interrogate saturated bacterial mutant libraries provides unprecedented information for the assignment of genome-wide gene essentiality. Exposure of saturated mutant libraries to specific conditions and subsequent sequencing can be exploited to uncover gene essentiality relevant to the condition. Here we present a barcoded transposon directed insertion-site sequencing (TraDIS) system to define an essential gene list for Streptococcus equi subsp. equi, the causative agent of strangles in horses, for the first time. The gene essentiality data for this group C Streptococcus was compared to that of group A and B streptococci. Six barcoded variants of pGh9:ISS1 were designed and used to generate mutant libraries containing between 33,000-66,000 unique mutants. TraDIS was performed on DNA extracted from each library and data were analysed separately and as a combined master pool. Gene essentiality determined that 19.5% of the S. equi genome was essential. Gene essentialities were compared to those of group A and group B streptococci, identifying concordances of 90.2% and 89.4%, respectively and an overall concordance of 83.7% between the three species. The use of barcoded pGh9:ISS1 to generate mutant libraries provides a highly useful tool for the assignment of gene function in S. equi and other streptococci. The shared essential gene set of group A, B and C streptococci provides further evidence of the close genetic relationships between these important pathogenic bacteria. Therefore, the ABC of gene essentiality reported here provides a solid foundation towards reporting the functional genome of streptococci.

Practice on an augmented reality/haptic simulator and library of virtual brains improves residents' ability to perform a ventriculostomy.

PubMed

Yudkowsky, Rachel; Luciano, Cristian; Banerjee, Pat; Schwartz, Alan; Alaraj, Ali; Lemole, G Michael; Charbel, Fady; Smith, Kelly; Rizzi, Silvio; Byrne, Richard; Bendok, Bernard; Frim, David

2013-02-01

Ventriculostomy is a neurosurgical procedure for providing therapeutic cerebrospinal fluid drainage. Complications may arise during repeated attempts at placing the catheter in the ventricle. We studied the impact of simulation-based practice with a library of virtual brains on neurosurgery residents' performance in simulated and live surgical ventriculostomies. Using computed tomographic scans of actual patients, we developed a library of 15 virtual brains for the ImmersiveTouch system, a head- and hand-tracked augmented reality and haptic simulator. The virtual brains represent a range of anatomies including normal, shifted, and compressed ventricles. Neurosurgery residents participated in individual simulator practice on the library of brains including visualizing the 3-dimensional location of the catheter within the brain immediately after each insertion. Performance of participants on novel brains in the simulator and during actual surgery before and after intervention was analyzed using generalized linear mixed models. Simulator cannulation success rates increased after intervention, and live procedure outcomes showed improvement in the rate of successful cannulation on the first pass. However, the incidence of deeper, contralateral (simulator) and third-ventricle (live) placements increased after intervention. Residents reported that simulations were realistic and helpful in improving procedural skills such as aiming the probe, sensing the pressure change when entering the ventricle, and estimating how far the catheter should be advanced within the ventricle. Simulator practice with a library of virtual brains representing a range of anatomies and difficulty levels may improve performance, potentially decreasing complications due to inexpert technique.

Diagnostic value of protein chips constructed by lung-cancer-associated markers selected by the T7 phage display library.

PubMed

Li, Hong-Mei; Guo, Kang; Yu, Zhuang; Feng, Rui; Xu, Ping

2015-07-01

Traditional diagnostic technology with tumor biomarkers is inefficient, expensive and requires a large number of serum samples. The purpose of this study was to construct human lung cancer protein chips with new lung cancer biomarkers screened by the T7-phage display library, and improve the early diagnosis rate of lung cancer. A T7-phage cDNA display library was constructed of fresh samples from 30 lung cancer patients. With biopanning and high-throughput screening, we gained the immunogenic phage clones from the cDNA library. The insert of selected phage was blasted at GeneBank for alignment to find the exact or the most similar known genes. Protein chips were then constructed and used to assay their expression level in lung cancer serum from 217 cases of lung cancer groups:80 cases of benign lung disease and 220 healthy controls. After four rounds of Biopanning and two rounds of enzyme-linked immunosorbent assay, 12 phage monoclonal samples were selected from 2880 phage monoclonal samples. After blasting at GeneBank, six similar genes were used to construct diagnostic protein chips. The protein chips were then used to assay expression level in lung cancer serum. The expression level of six genes in lung cancer groups was significantly higher than those in the other two groups (P < 0.05). In this study, we successfully constructed diagnostic protein chips with biomarkers selected from the lung cancer T7-phage cDNA library, which can be used for the early screening of lung cancer patients.

Occurrence of Can-SINEs and intron sequence evolution supports robust phylogeny of pinniped carnivores and their terrestrial relatives.

PubMed

Schröder, Christiane; Bleidorn, Christoph; Hartmann, Stefanie; Tiedemann, Ralph

2009-12-15

Investigating the dog genome we found 178965 introns with a moderate length of 200-1000 bp. A screening of these sequences against 23 different repeat libraries to find insertions of short interspersed elements (SINEs) detected 45276 SINEs. Virtually all of these SINEs (98%) belong to the tRNA-derived Can-SINE family. Can-SINEs arose about 55 million years ago before Carnivora split into two basal groups, the Caniformia (dog-like carnivores) and the Feliformia (cat-like carnivores). Genome comparisons of dog and cat recovered 506 putatively informative SINE loci for caniformian phylogeny. In this study we show how to use such genome information of model organisms to research the phylogeny of related non-model species of interest. Investigating a dataset including representatives of all major caniformian lineages, we analysed 24 randomly chosen loci for 22 taxa. All loci were amplifiable and revealed 17 parsimony-informative SINE insertions. The screening for informative SINE insertions yields a large amount of sequence information, in particular of introns, which contain reliable phylogenetic information as well. A phylogenetic analysis of intron- and SINE sequence data provided a statistically robust phylogeny which is congruent with the absence/presence pattern of our SINE markers. This phylogeny strongly supports a sistergroup relationship of Musteloidea and Pinnipedia. Within Pinnipedia, we see strong support from bootstrapping and the presence of a SINE insertion for a sistergroup relationship of the walrus with the Otariidae.

Genomic sequencing of Pleistocene cave bears

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

Noonan, James P.; Hofreiter, Michael; Smith, Doug

2005-04-01

Despite the information content of genomic DNA, ancient DNA studies to date have largely been limited to amplification of mitochondrial DNA due to technical hurdles such as contamination and degradation of ancient DNAs. In this study, we describe two metagenomic libraries constructed using unamplified DNA extracted from the bones of two 40,000-year-old extinct cave bears. Analysis of {approx}1 Mb of sequence from each library showed that, despite significant microbial contamination, 5.8 percent and 1.1 percent of clones in the libraries contain cave bear inserts, yielding 26,861 bp of cave bear genome sequence. Alignment of this sequence to the dog genome,more » the closest sequenced genome to cave bear in terms of evolutionary distance, revealed roughly the expected ratio of cave bear exons, repeats and conserved noncoding sequences. Only 0.04 percent of all clones sequenced were derived from contamination with modern human DNA. Comparison of cave bear with orthologous sequences from several modern bear species revealed the evolutionary relationship of these lineages. Using the metagenomic approach described here, we have recovered substantial quantities of mammalian genomic sequence more than twice as old as any previously reported, establishing the feasibility of ancient DNA genomic sequencing programs.« less

Design of redundant array of independent DVD libraries based on iSCSI

NASA Astrophysics Data System (ADS)

Chen, Yupeng; Pan, Longfa

2003-04-01

This paper presents a new approach to realize the redundant array of independent DVD libraries (RAID-LoIP) by using the iSCSI technology and traditional RAID algorithms. Our design reaches the high performance of optical storage system with following features: large storage size, highly accessing rate, random access, long distance of DVD libraries, block I/O storage, long storage life. Our RAID-LoIP system can be a good solution for broadcasting media asset storage system.

Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens.

PubMed

Saeidi, Saman; McKain, Michael R; Kellogg, Elizabeth A

2018-03-08

Herbaria are an invaluable source of plant material that can be used in a variety of biological studies. The use of herbarium specimens is associated with a number of challenges including sample preservation quality, degraded DNA, and destructive sampling of rare specimens. In order to more effectively use herbarium material in large sequencing projects, a dependable and scalable method of DNA isolation and library preparation is needed. This paper demonstrates a robust, beginning-to-end protocol for DNA isolation and high-throughput library construction from herbarium specimens that does not require modification for individual samples. This protocol is tailored for low quality dried plant material and takes advantage of existing methods by optimizing tissue grinding, modifying library size selection, and introducing an optional reamplification step for low yield libraries. Reamplification of low yield DNA libraries can rescue samples derived from irreplaceable and potentially valuable herbarium specimens, negating the need for additional destructive sampling and without introducing discernible sequencing bias for common phylogenetic applications. The protocol has been tested on hundreds of grass species, but is expected to be adaptable for use in other plant lineages after verification. This protocol can be limited by extremely degraded DNA, where fragments do not exist in the desired size range, and by secondary metabolites present in some plant material that inhibit clean DNA isolation. Overall, this protocol introduces a fast and comprehensive method that allows for DNA isolation and library preparation of 24 samples in less than 13 h, with only 8 h of active hands-on time with minimal modifications.

MSeq-CNV: accurate detection of Copy Number Variation from Sequencing of Multiple samples.

PubMed

Malekpour, Seyed Amir; Pezeshk, Hamid; Sadeghi, Mehdi

2018-03-05

Currently a few tools are capable of detecting genome-wide Copy Number Variations (CNVs) based on sequencing of multiple samples. Although aberrations in mate pair insertion sizes provide additional hints for the CNV detection based on multiple samples, the majority of the current tools rely only on the depth of coverage. Here, we propose a new algorithm (MSeq-CNV) which allows detecting common CNVs across multiple samples. MSeq-CNV applies a mixture density for modeling aberrations in depth of coverage and abnormalities in the mate pair insertion sizes. Each component in this mixture density applies a Binomial distribution for modeling the number of mate pairs with aberration in the insertion size and also a Poisson distribution for emitting the read counts, in each genomic position. MSeq-CNV is applied on simulated data and also on real data of six HapMap individuals with high-coverage sequencing, in 1000 Genomes Project. These individuals include a CEU trio of European ancestry and a YRI trio of Nigerian ethnicity. Ancestry of these individuals is studied by clustering the identified CNVs. MSeq-CNV is also applied for detecting CNVs in two samples with low-coverage sequencing in 1000 Genomes Project and six samples form the Simons Genome Diversity Project.

The measurement of acoustic properties of limited size panels by use of a parametric source

NASA Astrophysics Data System (ADS)

Humphrey, V. F.

1985-01-01

A method of measuring the acoustic properties of limited size panels immersed in water, with a truncated parametric array used as the acoustic source, is described. The insertion loss and reflection loss of thin metallic panels, typically 0·45 m square, were measured at normal incidence by using this technique. Results were obtained for a wide range of frequencies (10 to 100 kHz) and were found to be in good agreement with the theoretical predictions for plane waves. Measurements were also made of the insertion loss of aluminium, Perspex and G.R.P. panels for angles of incidence up to 50°. The broad bandwidth available from the parametric source permitted detailed measurements to be made over a wide frequency range using a single transmitting transducer. The small spot sizes obtainable with the parametric source also helped to reduce the significance of diffraction from edges of the panel under test.

Position of peripheral venous cannulae and the incidence of thrombophlebitis: an observational study.

PubMed

Cicolini, Giancarlo; Bonghi, Antonia Pollidoro; Di Labio, Luisa; Di Mascio, Rocco

2009-06-01

This paper is a report of a study conducted to investigate the most suitable location of peripheral venous cannulae to reduce the incidence of thrombophlebitis. Peripheral intravenous cannulae are used for vascular access, but the site of insertion and size of the cannula could expose patients to local and systemic infectious complications. Small cannula size is an important factor in reducing the incidence of thrombophlebitis, but cannula location has not yet been studied. Evidence-based knowledge on how to prevent these complications is needed. An observational survey carried out was carried out in 2007 with 427 patients in one Italian hospital. A structured observation protocol was used to survey the frequency of thrombophlebitis and the relationship of location and size of peripheral intravenous cannulae. The variables evaluated were age, gender, cannula size and site of cannula location. Chi-square or Student t tests were used, and the adjusted odds ratios and relative 95% confidence intervals are reported. The frequency of peripheral intravenous cannulae thrombophlebitis was higher in females (OR:1.91;CI:1.20-3.03;P < 0.006). The highest incidence was found in patients with cannulae inserted in the dorsal side of the hand veins compared to those with cannulae inserted in cubital fossa veins (OR:3.33;CI:1.37-8.07; P < 0.001). The use of cubital fossa veins rather than forearm and hand veins should be encouraged to reduce the risk of thrombophlebitis in patients with peripheral intravenous cannulae.

Strategic Planning for Library Multitype Cooperatives: Samples & Examples. ASCLA Changing Horizons Series #1.

ERIC Educational Resources Information Center

Baughman, Steven A., Ed.; Curry, Elizabeth A., Ed.

As interlibrary cooperation has proliferated in the last several decades, multitype library organizations and systems have emerged as important forces in librarianship. The need for thoughtful and organized strategic planning is an important cornerstone for the success of organizations of all sizes. Part of a project by the Interlibrary…

The Utility of Electronic Mail Follow-Ups for Library Research.

ERIC Educational Resources Information Center

Roselle, Ann; Neufeld, Steven

1998-01-01

A survey of academic librarians determined that the use of e-mail in the follow-up stage of a library research project using mailed questionnaires was as effective as postal mail in speed and size of response. Discusses additional benefits (interpersonal communication, reduced time and costs) and drawbacks (time spent identifying messages…

Recommended Reference Books for Small and Medium-Sized Libraries and Media Centers, 1998.

ERIC Educational Resources Information Center

Wynar, Bohdan S., Ed.

This annual review source is designed to assist smaller libraries in the systematic selection of suitable reference materials for their collections. Approximately 500 unabridged reviews, written by over 250 practicing librarians and subject specialists, identify and describe the most useful and affordable reference sources available for small and…

Evaluation of an Audience Response System in Library Orientations for Engineering Students

ERIC Educational Resources Information Center

Brush, Denise A.

2010-01-01

While interactive hands-on instruction is usually considered the best approach for engineering students for both their academic courses and for library instruction, the size of the engineering student population compared to the number of instructors and the available classroom space means that engineering librarians, like engineering faculty, may…

Recommended Reference Books for Small and Medium-Sized Libraries and Media Centers, 1999.

ERIC Educational Resources Information Center

Wynar, Bohdan S., Ed.

Designed to assist smaller libraries in selecting suitable reference materials for their collections, this annual review source identifies and describes 538 of the most useful and affordable reference sources available. The reviews cover reference titles published in 1998. Detailed annotations describe the nature, scope, and usability of each…

Information Technology Planning: Computers in the School Library--How Many Are Enough?

ERIC Educational Resources Information Center

Simpson, Carol

2002-01-01

Describes the development of a formula to determine the needed quantity of computers for a school library. Four types of information technology activities (administrative, personal productive, class/group productive, online public access catalog) and several variables (age levels served, campus focus, number of staff, size of student body, average…

Growing through Data

ERIC Educational Resources Information Center

Lansford, Teresa

2017-01-01

Data can be a powerful tool for self-evaluation, goal setting, and advocacy in the school library. Regardless of the grade level or the size of the student body, any school library has meaningful data to mine and learn from. Basic data such as circulation numbers can impact a myriad of areas relevant to student learning such as collection…

Health sciences library building projects: 1995 survey.

PubMed Central

Ludwig, L

1996-01-01

The Medical Library Association's fifth annual survey of recent health sciences library building projects identified twenty-five libraries planning, expanding, or constructing new library facilities. None of the fifteen new library projects are free standing structures; however, several occupy a major portion of the project space. Ten projects involve renovation of or addition to existing space. Information regarding size, cost of project, type of construction, completion date, and other factual data was provided for twelve projects. The remaining identified projects are in pre-design or early-design stages, or are awaiting funding approval. Library building projects for three hospital libraries, three academic medical libraries, and an association library are described. Each illustrates how considerations of economics and technology are changing the traditional library model from a centrally stored information depository housing a wide range of information under one roof where users come to the information, into an electronic model gradually shifting from investment in the physical presence of resources to investment in creating work space for creditible information specialists who help in-house and distanced users to obtain information electronically from any place and at any time. This new model includes a highly skilled library team to manage, filter, and package the information to users trained by these resident experts. Images PMID:8883981

Health sciences library building projects: 1995 survey.

PubMed

Ludwig, L

1996-07-01

The Medical Library Association's fifth annual survey of recent health sciences library building projects identified twenty-five libraries planning, expanding, or constructing new library facilities. None of the fifteen new library projects are free standing structures; however, several occupy a major portion of the project space. Ten projects involve renovation of or addition to existing space. Information regarding size, cost of project, type of construction, completion date, and other factual data was provided for twelve projects. The remaining identified projects are in pre-design or early-design stages, or are awaiting funding approval. Library building projects for three hospital libraries, three academic medical libraries, and an association library are described. Each illustrates how considerations of economics and technology are changing the traditional library model from a centrally stored information depository housing a wide range of information under one roof where users come to the information, into an electronic model gradually shifting from investment in the physical presence of resources to investment in creating work space for creditible information specialists who help in-house and distanced users to obtain information electronically from any place and at any time. This new model includes a highly skilled library team to manage, filter, and package the information to users trained by these resident experts.

Hospital library service and the changes in national standards.

PubMed Central

Glitz, B; Flack, V; Lovas, I M; Newell, P

1998-01-01

Two important sets of standards affecting hospital libraries were significantly revised in 1994, those of the Medical Library Association (MLA) and the Joint Commission on Accreditation of Healthcare Organizations (JCAHO). As part of its continuing efforts to monitor library services within its region, the University of California, Los Angeles Biomedical Library, Regional Medical Library for the Pacific Southwest Region of the National Network of Libraries of Medicine (NN/LM) conducted a survey in late 1994, in part to determine the effects of these revised standards on regional hospital libraries. Data from the survey were also used to provide a view of hospital libraries in the Pacific Southwest region, and to make comparisons with similar data collected in 1989. Results showed that while libraries remained stable in overall number, size, and staffing, services, especially those associated with end-user searching and interlibrary loan, increased enormously. With respect to the MLA standards, results show a high compliance level. Interesting differences were seen between the perceptions of library staff concerning their rate of compliance with the JCAHO standards and their actual compliance as measured by the MLA criteria. While some libraries appear to measure up better than their own perceptions would indicate, others may be fully aware of their actual compliance level. PMID:9549016

Insertion/Deletion Within the KDM6A Gene Is Significantly Associated With Litter Size in Goat

PubMed Central

Cui, Yang; Yan, Hailong; Wang, Ke; Xu, Han; Zhang, Xuelian; Zhu, Haijing; Liu, Jinwang; Qu, Lei; Lan, Xianyong; Pan, Chuanying

2018-01-01

A previous whole-genome association analysis identified lysine demethylase 6A (KDM6A), which encodes a type of histone demethylase, as a candidate gene associated to goat fecundity. KDM6A gene knockout mouse disrupts gametophyte development, suggesting that it has a critical role in reproduction. In this study, goat KDM6A mRNA expression profiles were determined, insertion/deletion (indel) variants in the gene identified, indel variants effect on KDM6A gene expression assessed, and their association with first-born litter size analyzed in 2326 healthy female Shaanbei white cashmere goats. KDM6A mRNA was expressed in all tissues tested (heart, liver, spleen, lung, kidney, muscle, brain, skin and testis); the expression levels in testes at different developmental stages [1-week-old (wk), 2, 3 wk, 1-month-old (mo), 1.5 and 2 mo] indicated a potential association with the mitosis-to-meiosis transition, implying that KDM6A may have an essential role in goat fertility. Meanwhile, two novel intronic indels of 16 bp and 5 bp were identified. Statistical analysis revealed that only the 16 bp indel was associated with first-born litter size (P < 0.01), and the average first-born litter size of individuals with an insertion/insertion genotype higher than that of those with the deletion/deletion genotype (P < 0.05). There was also a significant difference in genotype distributions of the 16 bp indel between mothers of single-lamb and multi-lamb litters in the studied goat population (P = 0.001). Consistently, the 16 bp indel also had a significant effect on KDM6A gene expression. Additionally, there was no significant linkage disequilibrium (LD) between these two indel loci, consistent with the association analysis results. Together, these findings suggest that the 16 bp indel in KDM6A may be useful for marker-assisted selection (MAS) of goats. PMID:29616081

Molecular Mechanisms of Cytopathogenicity of Primate Lymphotropic Retroviruses: Relevance to Treatment and Vaccine for AIDS

DTIC Science & Technology

1989-03-10

fragment of the HIV-1 genome was isolated from XBH10 and inserted into an M13 phage vector. Mutations were introduced by use of 25-mer oligonucleotides which... M13 by Eco RI and religated into the corresponding position of pHXB2gpt. The mutant AS was prepared directly from pHXB2gpt by digestion with Nde I and...detect immunocomplexes. Molecular Cloning and Sequencing of Proviral DNA A X phage library was constructed from the genomic DNA isolated from Hut78 cells

Quality control of next-generation sequencing library through an integrative digital microfluidic platform.

PubMed

Thaitrong, Numrin; Kim, Hanyoup; Renzi, Ronald F; Bartsch, Michael S; Meagher, Robert J; Patel, Kamlesh D

2012-12-01

We have developed an automated quality control (QC) platform for next-generation sequencing (NGS) library characterization by integrating a droplet-based digital microfluidic (DMF) system with a capillary-based reagent delivery unit and a quantitative CE module. Using an in-plane capillary-DMF interface, a prepared sample droplet was actuated into position between the ground electrode and the inlet of the separation capillary to complete the circuit for an electrokinetic injection. Using a DNA ladder as an internal standard, the CE module with a compact LIF detector was capable of detecting dsDNA in the range of 5-100 pg/μL, suitable for the amount of DNA required by the Illumina Genome Analyzer sequencing platform. This DMF-CE platform consumes tenfold less sample volume than the current Agilent BioAnalyzer QC technique, preserving precious sample while providing necessary sensitivity and accuracy for optimal sequencing performance. The ability of this microfluidic system to validate NGS library preparation was demonstrated by examining the effects of limited-cycle PCR amplification on the size distribution and the yield of Illumina-compatible libraries, demonstrating that as few as ten cycles of PCR bias the size distribution of the library toward undesirable larger fragments. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Correlation between extension-block K-wire insertion angle and postoperative extension loss in mallet finger fracture.

PubMed

Lee, S K; Kim, Y H; Moon, K H; Choy, W S

2018-02-01

Extension-block pinning represents a simple and reliable surgical technique. Although this procedure is commonly performed successfully, some patients develop postoperative extension loss. To date, the relationship between extension-block Kirschner wire (K-wire) insertion angle and postoperative extension loss in mallet finger fracture remains unclear. We aimed to clarify this relationship and further evaluate how various operative and non-operative factors affect postoperative extension loss after extension-block pinning for mallet finger fracture. A retrospective study was conducted to investigate a relationship between extension block K-wire insertion angle and postoperative extension loss. The inclusion criteria were: (1) a dorsal intra-articular fracture fragment involving 30% of the base of the distal phalanx with or without volar subluxation of the distal phalanx; and (2) <3 weeks delay from the injury without treatment. Extension-block K-wire insertion angle and fixation angle of the distal interphalangeal (DIP) joint were assessed using lateral radiograph at immediate postoperative time. Postoperative extension loss was assessed by using lateral radiograph at latest follow-up. Extension-block K-wire insertion angle was defined as the acute angle between extension block K-wire and longitudinal axis of middle phalangeal head. DIP joint fixation angle was defined as the acute angle between the distal phalanx and middle phalanx longitudinal axes. Seventy-five patients were included. The correlation analysis revealed that extension-block K-wire insertion angle had a negative correlation with postoperative extension loss, whereas fracture size and time to operation had a positive correlation (correlation coefficient for extension block K-wire angle: -0.66, facture size: +0.67, time to operation: +0.60). When stratifying patients in terms of negative and positive fixation angle of the DIP joint, the independent t-test showed that mean postoperative extension loss is -3.67° and +4.54° (DIP joint fixation angles of <0° and ≥0°, respectively, P=0.024). When stratifying patients in terms of extension-block K-wire insertion angle (30°, 30°-40°, >40°), ANOVA showed significantly less postoperative extension loss for higher insertion angles (>40°) than for medium insertion angles (30°-40°). Mean postoperative extension loss difference between higher insertion angle (>40°) and medium insertion angle (30°-40°) was 11° (P=0.002). Using an insertion angle of the extension-block K-wire of 40°-45° and a slightly hyperextended position of the DIP joint may help reducing postoperative extension loss. Therapeutic level III. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Artificial Leaks in Container Closure Integrity Testing: Nonlinear Finite Element Simulation of Aperture Size Originated by a Copper Wire Sandwiched between the Stopper and the Glass Vial.

PubMed

Nieto, Alejandra; Roehl, Holger; Brown, Helen; Adler, Michael; Chalus, Pascal; Mahler, Hanns-Christian

2016-01-01

Container closure integrity (CCI) testing is required by different regulatory authorities in order to provide assurance of tightness of the container closure system against possible contamination, for example, by microorganisms. Microbial ingress CCI testing is performed by incubation of the container closure system with microorganisms under specified testing conditions. Physical CCI uses surrogate endpoints, such as coloration by dye solution ingress or gas flow (helium leakage testing). In order to correlate microbial CCI and physical CCI test methods and to evaluate the methods' capability to detect a given leak, artificial leaks are being introduced into the container closure system in a variety of different ways. In our study, artificial leaks were generated using inserted copper wires between the glass vial opening and rubber stopper. However, the insertion of copper wires introduces leaks of unknown size and shape. With nonlinear finite element simulations, the aperture size between the rubber stopper and the glass vial was calculated, depending on wire diameter and capping force. The dependency of the aperture size on the copper wire diameter was quadratic. With the data obtained, we were able to calculate the leak size and model leak shape. Our results suggest that the size as well as the shape of the artificial leaks should be taken into account when evaluating critical leak sizes, as flow rate does not, independently, correlate to hole size. Capping force also affected leak size. An increase in the capping force from 30 to 70 N resulted in a reduction of the aperture (leak size) by approximately 50% for all wire diameters. From 30 to 50 N, the reduction was approximately 33%. Container closure integrity (CCI) testing is required by different regulatory authorities in order to provide assurance of tightness of the container closure system against contamination, for example, by microorganisms. Microbial ingress CCI testing is performed by incubation of the container closure system with microorganisms under specified testing conditions. Physical CCI uses surrogate endpoints, such as coloration by dye solution ingress or gas flow. In order to correlate microbial ingress CCI and physical CCI test methods and to evaluate the methods' capability to detect a given leak, artificially created defects (artificial leaks) are being introduced into the container closure system in a variety of different ways. In our study, artificial leaks were generated using inserted copper wires between the glass vial opening and rubber stopper. Up to date, the insertion of copper wires introduced leaks of unknown size and shape. With nonlinear finite element simulations, the effective aperture size between the rubber stopper and the glass vial was calculated, depending on wire diameter and capping force, and the leak shape was modelled. Our results suggest that the size as well as the shape of the artificial leaks should be taken into account when evaluating critical leak sizes, as flow rate does not, independently, correlate to the hole size. © PDA, Inc. 2016.

Morphological size evaluation of the mid-substance insertion areas and the fan-like extension fibers in the femoral ACL footprint.

PubMed

Suruga, Makoto; Horaguchi, Takashi; Iriuchishima, Takanori; Yahagi, Yoshiyuki; Iwama, Genki; Tokuhashi, Yasuaki; Aizawa, Shin

2017-08-01

The purpose of this study was to evaluate the detailed anatomy of the femoral anterior cruciate ligament (ACL) insertion site, with special attention given to the morphology of the mid-substance insertion areas and the fan-like extension fibers. Twenty-three non-paired human cadaver knees were used (7 Males, 16 Females, median age 83, range 69-96). All soft tissues around the knee were resected except the ligaments. The ACL was divided into antero-medial (AM) and postero-lateral (PL) bundles according to the difference in macroscopic tension patterns. The ACL was carefully dissected and two outlines were made of the periphery of each bundle insertion site: those which included and those which excluded the fan-like extension fibers. An accurate lateral view of the femoral condyle was photographed with a digital camera, and the images were downloaded to a personal computer. The area of each bundle, including and excluding the fan-like extension fibers, was measured with Image J software (National Institution of Health). The width and length of the mid-substance insertion sites were also evaluated using same image. The femoral ACL footprint was divided into four regions (mid-substance insertion sites of the AM and PL bundles, and fan-like extensions of the AM and PL bundles). The measured areas of the mid-substance insertion sites of the AM and PL bundles were 35.5 ± 12.5, and 32.4 ± 13.8 mm 2 , respectively. Whole width and length of the mid-substance insertion sites were 5.3 ± 1.4, and 15.5 ± 2.9 mm, respectively. The measured areas of the fan-like extensions of the AM and PL bundles were 27 ± 11.5, and 29.5 ± 12.4 mm 2 , respectively. The femoral ACL footprint was divided into quarters of approximately equal size (mid-substance insertion sites of the AM and PL bundles, and fan-like extensions of the AM and PL bundles). For clinical relevance, to perform highly reproducible anatomical ACL reconstruction, the presence of the fan-like extension fibers should be taken into consideration.

Library based x-ray scatter correction for dedicated cone beam breast CT

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

Shi, Linxi; Zhu, Lei, E-mail: leizhu@gatech.edu

Purpose: The image quality of dedicated cone beam breast CT (CBBCT) is limited by substantial scatter contamination, resulting in cupping artifacts and contrast-loss in reconstructed images. Such effects obscure the visibility of soft-tissue lesions and calcifications, which hinders breast cancer detection and diagnosis. In this work, we propose a library-based software approach to suppress scatter on CBBCT images with high efficiency, accuracy, and reliability. Methods: The authors precompute a scatter library on simplified breast models with different sizes using the GEANT4-based Monte Carlo (MC) toolkit. The breast is approximated as a semiellipsoid with homogeneous glandular/adipose tissue mixture. For scatter correctionmore » on real clinical data, the authors estimate the breast size from a first-pass breast CT reconstruction and then select the corresponding scatter distribution from the library. The selected scatter distribution from simplified breast models is spatially translated to match the projection data from the clinical scan and is subtracted from the measured projection for effective scatter correction. The method performance was evaluated using 15 sets of patient data, with a wide range of breast sizes representing about 95% of general population. Spatial nonuniformity (SNU) and contrast to signal deviation ratio (CDR) were used as metrics for evaluation. Results: Since the time-consuming MC simulation for library generation is precomputed, the authors’ method efficiently corrects for scatter with minimal processing time. Furthermore, the authors find that a scatter library on a simple breast model with only one input parameter, i.e., the breast diameter, sufficiently guarantees improvements in SNU and CDR. For the 15 clinical datasets, the authors’ method reduces the average SNU from 7.14% to 2.47% in coronal views and from 10.14% to 3.02% in sagittal views. On average, the CDR is improved by a factor of 1.49 in coronal views and 2.12 in sagittal views. Conclusions: The library-based scatter correction does not require increase in radiation dose or hardware modifications, and it improves over the existing methods on implementation simplicity and computational efficiency. As demonstrated through patient studies, the authors’ approach is effective and stable, and is therefore clinically attractive for CBBCT imaging.« less

Library based x-ray scatter correction for dedicated cone beam breast CT

PubMed Central

Shi, Linxi; Karellas, Andrew; Zhu, Lei

2016-01-01

Purpose: The image quality of dedicated cone beam breast CT (CBBCT) is limited by substantial scatter contamination, resulting in cupping artifacts and contrast-loss in reconstructed images. Such effects obscure the visibility of soft-tissue lesions and calcifications, which hinders breast cancer detection and diagnosis. In this work, we propose a library-based software approach to suppress scatter on CBBCT images with high efficiency, accuracy, and reliability. Methods: The authors precompute a scatter library on simplified breast models with different sizes using the geant4-based Monte Carlo (MC) toolkit. The breast is approximated as a semiellipsoid with homogeneous glandular/adipose tissue mixture. For scatter correction on real clinical data, the authors estimate the breast size from a first-pass breast CT reconstruction and then select the corresponding scatter distribution from the library. The selected scatter distribution from simplified breast models is spatially translated to match the projection data from the clinical scan and is subtracted from the measured projection for effective scatter correction. The method performance was evaluated using 15 sets of patient data, with a wide range of breast sizes representing about 95% of general population. Spatial nonuniformity (SNU) and contrast to signal deviation ratio (CDR) were used as metrics for evaluation. Results: Since the time-consuming MC simulation for library generation is precomputed, the authors’ method efficiently corrects for scatter with minimal processing time. Furthermore, the authors find that a scatter library on a simple breast model with only one input parameter, i.e., the breast diameter, sufficiently guarantees improvements in SNU and CDR. For the 15 clinical datasets, the authors’ method reduces the average SNU from 7.14% to 2.47% in coronal views and from 10.14% to 3.02% in sagittal views. On average, the CDR is improved by a factor of 1.49 in coronal views and 2.12 in sagittal views. Conclusions: The library-based scatter correction does not require increase in radiation dose or hardware modifications, and it improves over the existing methods on implementation simplicity and computational efficiency. As demonstrated through patient studies, the authors’ approach is effective and stable, and is therefore clinically attractive for CBBCT imaging. PMID:27487870

Image Steganography In Securing Sound File Using Arithmetic Coding Algorithm, Triple Data Encryption Standard (3DES) and Modified Least Significant Bit (MLSB)

NASA Astrophysics Data System (ADS)

Nasution, A. B.; Efendi, S.; Suwilo, S.

2018-04-01

The amount of data inserted in the form of audio samples that use 8 bits with LSB algorithm, affect the value of PSNR which resulted in changes in image quality of the insertion (fidelity). So in this research will be inserted audio samples using 5 bits with MLSB algorithm to reduce the number of data insertion where previously the audio sample will be compressed with Arithmetic Coding algorithm to reduce file size. In this research will also be encryption using Triple DES algorithm to better secure audio samples. The result of this research is the value of PSNR more than 50dB so it can be concluded that the image quality is still good because the value of PSNR has exceeded 40dB.

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

PubMed Central

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

1995-01-01

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

Scaffold diversification enhances effectiveness of a superlibrary of hyperthermophilic proteins.

PubMed

Hussain, Mahmud; Gera, Nimish; Hill, Andrew B; Rao, Balaji M

2013-01-18

The use of binding proteins from non-immunoglobulin scaffolds has become increasingly common in biotechnology and medicine. Typically, binders are isolated from a combinatorial library generated by mutating a single scaffold protein. In contrast, here we generated a "superlibrary" or "library-of-libraries" of 4 × 10(8) protein variants by mutagenesis of seven different hyperthermophilic proteins; six of the seven proteins have not been used as scaffolds prior to this study. Binding proteins for five different model targets were successfully isolated from this library. Binders obtained were derived from five out of the seven scaffolds. Strikingly, binders from this modestly sized superlibrary have affinities comparable or higher than those obtained from a library with 1000-fold higher sequence diversity but derived from a single stable scaffold. Thus scaffold diversification, i.e., randomization of multiple different scaffolds, is a powerful alternate strategy for combinatorial library construction.

The Virtual Naval Hospital: the digital library as knowledge management tool for nomadic patrons*

PubMed Central

D'Alessandro, Michael P.; D'Alessandro, Donna M.; Bakalar, Richard S.; Ashley, Denis E.; Hendrix, Mary J. C.

2005-01-01

Objective: To meet the information needs of isolated primary care providers and their patients in the US Navy, a digital health sciences library, the Virtual Naval Hospital, was created through a unique partnership between academia and government. Methods: The creation of the digital library was heavily influenced by the principles of user-centered design and made allowances for the nomadic nature of the digital library's patrons and the heterogeneous access they have to Internet bandwidth. Results: The result is a digital library that has been in operation since 1997, continues to expand in size, is heavily used, and is highly regarded by its patrons. Conclusions: The digital library is dedicated to delivering the right information at the right time to the right person so the right decision can be made, and therefore the Virtual Naval Hospital functions as a knowledge-management system for the US Navy Bureau of Medicine and Surgery. PMID:15685269

Selected list of books and journals for the small medical library.

PubMed

Brandon, A N; Hill, D R

1991-04-01

The current financial status of the health care industry is viewed both from its effect on the hospital library collection and the response of the hospital library to the financial crisis. Predecessors of this list have been intended as selection guides for a small or medium-size library in a hospital or comparable medical facility. As the prices of books and journals continue to soar, the secondary purpose as a core collection for a consortium of small hospital libraries or a network sharing library resources may eventually become its primary use. Books (607) and journals (140) are categorized by subject; the book list is followed by an author/editor index, and the subject list of journals by an alphabetical title listing. To purchase the entire collection of books and to pay for 1991 subscriptions would require about $77,700. The cost of only the asterisked items totals $29,300.

Selected list of books and journals for the small medical library.

PubMed Central

Brandon, A N; Hill, D R

1991-01-01

The current financial status of the health care industry is viewed both from its effect on the hospital library collection and the response of the hospital library to the financial crisis. Predecessors of this list have been intended as selection guides for a small or medium-size library in a hospital or comparable medical facility. As the prices of books and journals continue to soar, the secondary purpose as a core collection for a consortium of small hospital libraries or a network sharing library resources may eventually become its primary use. Books (607) and journals (140) are categorized by subject; the book list is followed by an author/editor index, and the subject list of journals by an alphabetical title listing. To purchase the entire collection of books and to pay for 1991 subscriptions would require about $77,700. The cost of only the asterisked items totals $29,300. PMID:2039906

The Virtual Naval Hospital: the digital library as knowledge management tool for nomadic patrons.

PubMed

D'Alessandro, Michael P; D'Alessandro, Donna M; Bakalar, Richard S; Ashley, Denis E; Hendrix, Mary J C

2005-01-01

To meet the information needs of isolated primary care providers and their patients in the US Navy, a digital health sciences library, the Virtual Naval Hospital, was created through a unique partnership between academia and government. The creation of the digital library was heavily influenced by the principles of user-centered design and made allowances for the nomadic nature of the digital library's patrons and the heterogeneous access they have to Internet bandwidth. The result is a digital library that has been in operation since 1997, continues to expand in size, is heavily used, and is highly regarded by its patrons. The digital library is dedicated to delivering the right information at the right time to the right person so the right decision can be made, and therefore the Virtual Naval Hospital functions as a knowledge-management system for the US Navy Bureau of Medicine and Surgery.

Visual characterization and diversity quantification of chemical libraries: 2. Analysis and selection of size-independent, subspace-specific diversity indices.

PubMed

Colliandre, Lionel; Le Guilloux, Vincent; Bourg, Stephane; Morin-Allory, Luc

2012-02-27

High Throughput Screening (HTS) is a standard technique widely used to find hit compounds in drug discovery projects. The high costs associated with such experiments have highlighted the need to carefully design screening libraries in order to avoid wasting resources. Molecular diversity is an established concept that has been used to this end for many years. In this article, a new approach to quantify the molecular diversity of screening libraries is presented. The approach is based on the Delimited Reference Chemical Subspace (DRCS) methodology, a new method that can be used to delimit the densest subspace spanned by a reference library in a reduced 2D continuous space. A total of 22 diversity indices were implemented or adapted to this methodology, which is used here to remove outliers and obtain a relevant cell-based partition of the subspace. The behavior of these indices was assessed and compared in various extreme situations and with respect to a set of theoretical rules that a diversity function should satisfy when libraries of different sizes have to be compared. Some gold standard indices are found inappropriate in such a context, while none of the tested indices behave perfectly in all cases. Five DRCS-based indices accounting for different aspects of diversity were finally selected, and a simple framework is proposed to use them effectively. Various libraries have been profiled with respect to more specific subspaces, which further illustrate the interest of the method.

Linear motion device and method for inserting and withdrawing control rods

DOEpatents

Smith, J.E.

Disclosed is a linear motion device and more specifically a control rod drive mechanism (CRDM) for inserting and withdrawing control rods into a reactor core. The CRDM and method disclosed is capable of independently and sequentially positioning two sets of control rods with a single motor stator and rotor. The CRDM disclosed can control more than one control rod lead screw without incurring a substantial increase in the size of the mechanism.

Selected list of books and journals for the small medical library.

PubMed Central

Brandon, A N

1977-01-01

This revised list of 472 books and 138 journals is intended as a selection guide for small or medium-sized hospital libraries or for the small medical library serving a specified clientele. It can also be used as a core list by small hospital library consortia. Books and journals are categorized by subject, with the books being followed by an author index and the journals by an alphabetical title listing. Items suggested for initial purchase by smaller libraries are indicated by an asterisk. To purchase the entire collection of books and to pay for annual subscriptions to all the journals would require an expenditure of about $18,200. The cost of only the asterisked items recommended for first purchase totals approximately $4,500. PMID:321057

Selected list of books and journals for the small medical library.

PubMed Central

Brandon, A N; Hill, D R

1979-01-01

This revised list of 492 books and 138 journals is intended as a selection guide for small or medium-sized hospital libraries or for the small medical library serving a specified clientele. It can also be used as a core list by small hospital library consortia. Books and journals are categorized by subject, with the books being followed by an author index and the journals by an alphabetical title listing. Items suggested for initial purchase by smaller libraries are indicated by an asterisk. To purchase the entire collection of books and to pay for annual subscriptions to all the journals would require an expenditure of about $22,500. The cost of only the asterisked items, recommended for first purchase, totals approximately $6,100. PMID:380695

Selected list of books and journals for the small medical library.

PubMed

Brandon, A N; Hill, D R

1981-04-01

This revised list of 539 books and 136 journals is intended as a selection guide for small or medium-sized hospital libraries or for small medical libraries in comparable health care facilities. It can also be used as a core list by consortia of small hospital libraries. Books and journals are categorized by subject; the book list is followed by an author index and the list of journals by an alphabetical title listing. Items suggested for initial purchase by smaller libraries, 137 books and 54 journals, are indicated by asterisks. To purchase the entire collection of books and to pay for annual subscriptions to all the journals would require an expenditure of about $30,000. The cost of only the asterisked items, which are recommended for first purchase, totals approximately $8,900.

Composing compound libraries for hit discovery--rationality-driven preselection or random choice by structural diversity?

PubMed

Weidel, Elisabeth; Negri, Matthias; Empting, Martin; Hinsberger, Stefan; Hartmann, Rolf W

2014-01-01

In order to identify new scaffolds for drug discovery, surface plasmon resonance is frequently used to screen structurally diverse libraries. Usually, hit rates are low and identification processes are time consuming. Hence, approaches which improve hit rates and, thus, reduce the library size are required. In this work, we studied three often used strategies for their applicability to identify inhibitors of PqsD. In two of them, target-specific aspects like inhibition of a homologous protein or predicted binding determined by virtual screening were used for compound preselection. Finally, a fragment library, covering a large chemical space, was screened and served as comparison. Indeed, higher hit rates were observed for methods employing preselected libraries indicating that target-oriented compound selection provides a time-effective alternative.

BESST--efficient scaffolding of large fragmented assemblies.

PubMed

Sahlin, Kristoffer; Vezzi, Francesco; Nystedt, Björn; Lundeberg, Joakim; Arvestad, Lars

2014-08-15

The use of short reads from High Throughput Sequencing (HTS) techniques is now commonplace in de novo assembly. Yet, obtaining contiguous assemblies from short reads is challenging, thus making scaffolding an important step in the assembly pipeline. Different algorithms have been proposed but many of them use the number of read pairs supporting a linking of two contigs as an indicator of reliability. This reasoning is intuitive, but fails to account for variation in link count due to contig features.We have also noted that published scaffolders are only evaluated on small datasets using output from only one assembler. Two issues arise from this. Firstly, some of the available tools are not well suited for complex genomes. Secondly, these evaluations provide little support for inferring a software's general performance. We propose a new algorithm, implemented in a tool called BESST, which can scaffold genomes of all sizes and complexities and was used to scaffold the genome of P. abies (20 Gbp). We performed a comprehensive comparison of BESST against the most popular stand-alone scaffolders on a large variety of datasets. Our results confirm that some of the popular scaffolders are not practical to run on complex datasets. Furthermore, no single stand-alone scaffolder outperforms the others on all datasets. However, BESST fares favorably to the other tested scaffolders on GAGE datasets and, moreover, outperforms the other methods when library insert size distribution is wide. We conclude from our results that information sources other than the quantity of links, as is commonly used, can provide useful information about genome structure when scaffolding.

A Library of Selenourea Precursors to PbSe Nanocrystals with Size Distributions near the Homogeneous Limit

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

Campos, Michael P.; Hendricks, Mark P.; Beecher, Alexander N.

Here, we report a tunable library of N,N,N'-trisubstituted selenourea precursors and their reaction with lead oleate at 60–150 °C to form carboxylate-terminated PbSe nanocrystals in quantitative yields. Single exponential conversion kinetics can be tailored over 4 orders of magnitude by adjusting the selenourea structure. The wide range of conversion reactivity allows the extent of nucleation ([nanocrystal] = 4.6–56.7 μM) and the size following complete precursor conversion (d = 1.7–6.6 nm) to be controlled. Narrow size distributions (σ = 0.5–2%) are obtained whose spectral line widths are dominated (73–83%) by the intrinsic single particle spectral broadening, as observed using spectral holemore » burning measurements. Here, the intrinsic broadening decreases with increasing size (fwhm = 320–65 meV, d = 1.6–4.4 nm) that derives from exciton fine structure and exciton–phonon coupling rather than broadening caused by the size distribution.« less

A Library of Selenourea Precursors to PbSe Nanocrystals with Size Distributions near the Homogeneous Limit

DOE PAGES

Campos, Michael P.; Hendricks, Mark P.; Beecher, Alexander N.; ...

2017-01-19

Here, we report a tunable library of N,N,N'-trisubstituted selenourea precursors and their reaction with lead oleate at 60–150 °C to form carboxylate-terminated PbSe nanocrystals in quantitative yields. Single exponential conversion kinetics can be tailored over 4 orders of magnitude by adjusting the selenourea structure. The wide range of conversion reactivity allows the extent of nucleation ([nanocrystal] = 4.6–56.7 μM) and the size following complete precursor conversion (d = 1.7–6.6 nm) to be controlled. Narrow size distributions (σ = 0.5–2%) are obtained whose spectral line widths are dominated (73–83%) by the intrinsic single particle spectral broadening, as observed using spectral holemore » burning measurements. Here, the intrinsic broadening decreases with increasing size (fwhm = 320–65 meV, d = 1.6–4.4 nm) that derives from exciton fine structure and exciton–phonon coupling rather than broadening caused by the size distribution.« less

Library design practices for success in lead generation with small molecule libraries.

PubMed

Goodnow, R A; Guba, W; Haap, W

2003-11-01

The generation of novel structures amenable to rapid and efficient lead optimization comprises an emerging strategy for success in modern drug discovery. Small molecule libraries of sufficient size and diversity to increase the chances of discovery of novel structures make the high throughput synthesis approach the method of choice for lead generation. Despite an industry trend for smaller, more focused libraries, the need to generate novel lead structures makes larger libraries a necessary strategy. For libraries of a several thousand or more members, solid phase synthesis approaches are the most suitable. While the technology and chemistry necessary for small molecule library synthesis continue to advance, success in lead generation requires rigorous consideration in the library design process to ensure the synthesis of molecules possessing the proper characteristics for subsequent lead optimization. Without proper selection of library templates and building blocks, solid phase synthesis methods often generate molecules which are too heavy, too lipophilic and too complex to be useful for lead optimization. The appropriate filtering of virtual library designs with multiple computational tools allows the generation of information-rich libraries within a drug-like molecular property space. An understanding of the hit-to-lead process provides a practical guide to molecular design characteristics. Examples of leads generated from library approaches also provide a benchmarking of successes as well as aspects for continued development of library design practices.

DFT Performance Prediction in FFTW

NASA Astrophysics Data System (ADS)

Gu, Liang; Li, Xiaoming

Fastest Fourier Transform in the West (FFTW) is an adaptive FFT library that generates highly efficient Discrete Fourier Transform (DFT) implementations. It is one of the fastest FFT libraries available and it outperforms many adaptive or hand-tuned DFT libraries. Its success largely relies on the huge search space spanned by several FFT algorithms and a set of compiler generated C code (called codelets) for small size DFTs. FFTW empirically finds the best algorithm by measuring the performance of different algorithm combinations. Although the empirical search works very well for FFTW, the search process does not explain why the best plan found performs best, and the search overhead grows polynomially as the DFT size increases. The opposite of empirical search is model-driven optimization. However, it is widely believed that model-driven optimization is inferior to empirical search and is particularly powerless to solve problems as complex as the optimization of DFT.

Mutation supply and the repeatability of selection for antibiotic resistance

NASA Astrophysics Data System (ADS)

van Dijk, Thomas; Hwang, Sungmin; Krug, Joachim; de Visser, J. Arjan G. M.; Zwart, Mark P.

2017-10-01

Whether evolution can be predicted is a key question in evolutionary biology. Here we set out to better understand the repeatability of evolution, which is a necessary condition for predictability. We explored experimentally the effect of mutation supply and the strength of selective pressure on the repeatability of selection from standing genetic variation. Different sizes of mutant libraries of antibiotic resistance gene TEM-1 β-lactamase in Escherichia coli, generated by error-prone PCR, were subjected to different antibiotic concentrations. We determined whether populations went extinct or survived, and sequenced the TEM gene of the surviving populations. The distribution of mutations per allele in our mutant libraries followed a Poisson distribution. Extinction patterns could be explained by a simple stochastic model that assumed the sampling of beneficial mutations was key for survival. In most surviving populations, alleles containing at least one known large-effect beneficial mutation were present. These genotype data also support a model which only invokes sampling effects to describe the occurrence of alleles containing large-effect driver mutations. Hence, evolution is largely predictable given cursory knowledge of mutational fitness effects, the mutation rate and population size. There were no clear trends in the repeatability of selected mutants when we considered all mutations present. However, when only known large-effect mutations were considered, the outcome of selection is less repeatable for large libraries, in contrast to expectations. We show experimentally that alleles carrying multiple mutations selected from large libraries confer higher resistance levels relative to alleles with only a known large-effect mutation, suggesting that the scarcity of high-resistance alleles carrying multiple mutations may contribute to the decrease in repeatability at large library sizes.

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

Sutcliffe, James, E-mail: jasutcliffe@gmail.com; Wigham, Andrew, E-mail: a.wigham@doctors.org.uk; Mceniff, Niall, E-mail: nmceniff@stjames.ie

PurposeSurgical Gastrostomy has been around since the 19th century but in 1980 the first successful percutaneous endoscopic gastrostomy was reported. A year later the first successful percutaneous gastrostomy was performed using fluoroscopic guidance. The technique for percutaneous insertion and the equipment used has been refined since then and it is now considered the gold standard for gastrostomy insertion. Here we present guidelines for image-guided enteral feeding tubes in adults.Material and MethodWe performed a review and analysis of the scientific literature, other national and international guidelines and expert opinion.ResultsStudies have shown fluoroscopic techniques have consistently higher success rates with lower ratesmore » of major complications than endoscopic techniques. However, the Achilles' heel of many fluoroscopic techniques is the requirement for smaller gastrostomy tube sizes resulting in them being more prone to blockages and thus requiring further intervention.ConclusionRadiological feeding tube insertion is a safe and effective procedure. Success rates are higher, and complication rates lower than PEG or surgical gastrostomy tube placement and innovative techniques for gastric and jejunal access mean that there are very few cases in which RIG is not possible. The principal weakness of radiologically inserted gastrostomies is the limitiation on tube size which leads to a higher rate of tube blockage. Per-oral image-guided gastrostomies have to an extent addressed this but have not been popularised. Currently many centres still consider endoscopic gastrostomies as the first line unless patients are too unwell to undergo this procedure or previous attempts have failed, in which case radioloically inserted gastrostomies are the technique of choice.« less

Immediate implant placement into fresh extraction sockets versus delayed implants into healed sockets: A systematic review and meta-analysis.

PubMed

Mello, C C; Lemos, C A A; Verri, F R; Dos Santos, D M; Goiato, M C; Pellizzer, E P

2017-09-01

The aim of this systematic review and meta-analysis was to compare the survival rate of the implants and the peri-implant tissue changes associated with implants inserted in fresh extraction sockets and those inserted in healed sockets. This review has been registered at PROSPERO under the number CRD42016043309. A systematic search was conducted by two reviewers independently in the databases PubMed/MEDLINE, Embase, and the Cochrane Library using different search terms; articles published until November 2016 were searched for. The searches identified 30 eligible studies. A total of 3,049 implants were installed in a total of 1,435 patients with a mean age of 46.68 years and a minimum of 6 months of follow-up. The survival rate of delayed implants (98.38%) was significantly greater than immediate implants (95.21%) (p=.001). For the marginal bone loss (p=.32), implant stability quotients values (p=.44), and pocket probing depth (p=.94) there was no significant difference between the analysed groups. The immediate implants placed in fresh sockets should be performed with caution because of the significantly lower survival rates than delayed implants inserted in healed sockets. Copyright © 2017 International Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.

Himar1 Transposon for Efficient Random Mutagenesis in Aggregatibacter actinomycetemcomitans

PubMed Central

Ding, Qinfeng; Tan, Kai Soo

2017-01-01

Aggregatibacter actinomycetemcomitans is the primary etiological agent of aggressive periodontal disease. Identification of novel virulence factors at the genome-wide level is hindered by lack of efficient genetic tools to perform mutagenesis in this organism. The Himar1 mariner transposon is known to yield a random distribution of insertions in an organism’s genome with requirement for only a TA dinucleotide target and is independent of host-specific factors. However, the utility of this system in A. actinomycetemcomitans is unknown. In this study, we found that Himar1 transposon mutagenesis occurs at a high frequency (×10-4), and can be universally applied to wild-type A. actinomycetemcomitans strains of serotypes a, b, and c. The Himar1 transposon inserts were stably inherited in A. actinomycetemcomitans transconjugants in the absence of antibiotics. A library of 16,000 mutant colonies of A. actinomycetemcomitans was screened for reduced biofilm formation. Mutants with transposon inserts in genes encoding pilus, putative ion transporters, multidrug resistant proteins, transcription regulators and enzymes involved in the synthesis of extracellular polymeric substance, bacterial metabolism and stress response were discovered in this screen. Our results demonstrated the utility of the Himar1 mutagenesis system as a novel genetic tool for functional genomic analysis in A. actinomycetemcomitans. PMID:29018421

The Cost of Interlibrary Loan Services in a Medium-Sized Academic Library.

ERIC Educational Resources Information Center

Naylor, Ted F.

1997-01-01

A one-year study of interlibrary loan expense was conducted at Wichita State University (KS) to identify areas of interlibrary loan expense, compare results of cost studies from large research libraries, and provide a reference point in determining how to best balance Interlibrary loans and commercial document delivery systems. Analyzes salary,…

The Role of the Systems Librarian/Administrator: A Report of the Survey.

ERIC Educational Resources Information Center

Hatcher, Karen A.

1995-01-01

A 1991 survey asked how the position of systems librarian has changed. Data from three categories of academic and research libraries was analyzed by size of library, and changes involving increasing implementation of electronic media were identified. It was found that the role of systems librarian is difficult to define while technology changes…

Supervisory Rotation: Impact on an Academic Library Reference Staff.

ERIC Educational Resources Information Center

Perdue, Bob; Piotrowski, Chris

The results of a managerial rotation program in a medium-sized academic library reference department are presented. After meeting certain minimal eligibility requirements, librarians in this department take turns on a 2-year cycle serving as head of the department. This case study is used as a model to assess both the advantages and disadvantages…

Internet Librarian '98: Proceedings of the Internet Librarian Conference (2nd, Monterey, California, November 1-5, 1998).

ERIC Educational Resources Information Center

Nixon, Carol, Comp.; Dengler, M. Heide, Comp.; McHenry, Mare L., Comp.

This proceedings contains 56 papers, presentation summaries, and/or slide presentations pertaining to the Internet, World Wide Web, intranets, and library systems. Topics include: Web databases in medium sized libraries; Dow Jones Intranet Toolkit; the future of online; Web searching and Internet basics; digital archiving; evolution of the online…

Thin Client Architecture for Networking CD-ROMs in a Medium-Sized Public Library System.

ERIC Educational Resources Information Center

Turner, Anna

1997-01-01

Describes how the Tulsa City-County Library System built a 22-branch CD-ROM-based network with the emerging thin-client/server technology, and succeeded in providing patrons with the most current research tools and information resources available. Discusses costs; networking options; the Citrix WinFrame system used; equipment and connectivity.…

Assessment of Users Information Needs and Satisfaction in Selected Seminary Libraries in Oyo State, Nigeria

ERIC Educational Resources Information Center

Adekunjo, Olalekan Abraham; Adepoju, Samuel Olusegun; Adeola, Anuoluwapo Odebunmi

2015-01-01

The study assessed users' information needs and satisfaction in selected seminary libraries in Oyo State, Nigeria. This paper employed the descriptive survey research design, whereby the expost-facto was employed with a sample size of three hundred (300) participants, selected from six seminaries located in Ibadan, Oyo and Ogbomoso, all in Oyo…

Ascending Bloom's Pyramid: Fostering Student Creativity and Innovation in Academic Library Spaces

ERIC Educational Resources Information Center

Bieraugel, Mark; Neill, Stern

2017-01-01

Our research examined the degree to which behaviors and learning associated with creativity and innovation were supported in five academic library spaces and three other spaces at a mid-sized university. Based on survey data from 226 students, we apply a number of statistical techniques to measure student perceptions of the types of learning and…

On the Solidification and Structure Formation during Casting of Large Inserts in Ferritic Nodular Cast Iron

NASA Astrophysics Data System (ADS)

Tadesse, Abel; Fredriksson, Hasse

2018-06-01

The graphite nodule count and size distributions for boiling water reactor (BWR) and pressurized water reactor (PWR) inserts were investigated by taking samples at heights of 2160 and 1150 mm, respectively. In each cross section, two locations were taken into consideration for both the microstructural and solidification modeling. The numerical solidification modeling was performed in a two-dimensional model by considering the nucleation and growth in eutectic ductile cast iron. The microstructural results reveal that the nodule size and count distribution along the cross sections are different in each location for both inserts. Finer graphite nodules appear in the thinner sections and close to the mold walls. The coarser nodules are distributed mostly in the last solidified location. The simulation result indicates that the finer nodules are related to a higher cooling rate and a lower degree of microsegregation, whereas the coarser nodules are related to a lower cooling rate and a higher degree of microsegregation. The solidification time interval and the last solidifying locations in the BWR and PWR are also different.

BAC end sequencing of Pacific white shrimp Litopenaeus vannamei: a glimpse into the genome of Penaeid shrimp

NASA Astrophysics Data System (ADS)

Zhao, Cui; Zhang, Xiaojun; Liu, Chengzhang; Huan, Pin; Li, Fuhua; Xiang, Jianhai; Huang, Chao

2012-05-01

Little is known about the genome of Pacific white shrimp ( Litopenaeus vannamei). To address this, we conducted BAC (bacterial artificial chromosome) end sequencing of L. vannamei. We selected and sequenced 7 812 BAC clones from the BAC library LvHE from the two ends of the inserts by Sanger sequencing. After trimming and quality filtering, 11 279 BAC end sequences (BESs) including 4 609 pairedends BESs were obtained. The total length of the BESs was 4 340 753 bp, representing 0.18% of the L. vannamei haploid genome. The lengths of the BESs ranged from 100 bp to 660 bp with an average length of 385 bp. Analysis of the BESs indicated that the L. vannamei genome is AT-rich and that the primary repeats patterns were simple sequence repeats (SSRs) and low complexity sequences. Dinucleotide and hexanucleotide repeats were the most common SSR types in the BESs. The most abundant transposable element was gypsy, which may contribute to the generation of the large genome size of L. vannamei. We successfully annotated 4 519 BESs by BLAST searching, including genes involved in immunity and sex determination. Our results provide an important resource for functional gene studies, map construction and integration, and complete genome assembly for this species.

Global mapping of transposon location.

PubMed

Gabriel, Abram; Dapprich, Johannes; Kunkel, Mark; Gresham, David; Pratt, Stephen C; Dunham, Maitreya J

2006-12-15

Transposable genetic elements are ubiquitous, yet their presence or absence at any given position within a genome can vary between individual cells, tissues, or strains. Transposable elements have profound impacts on host genomes by altering gene expression, assisting in genomic rearrangements, causing insertional mutations, and serving as sources of phenotypic variation. Characterizing a genome's full complement of transposons requires whole genome sequencing, precluding simple studies of the impact of transposition on interindividual variation. Here, we describe a global mapping approach for identifying transposon locations in any genome, using a combination of transposon-specific DNA extraction and microarray-based comparative hybridization analysis. We use this approach to map the repertoire of endogenous transposons in different laboratory strains of Saccharomyces cerevisiae and demonstrate that transposons are a source of extensive genomic variation. We also apply this method to mapping bacterial transposon insertion sites in a yeast genomic library. This unique whole genome view of transposon location will facilitate our exploration of transposon dynamics, as well as defining bases for individual differences and adaptive potential.

Selected list of books and journals for the small medical library.

PubMed Central

Brandon, A N

1975-01-01

This revised list of 446 books and 137 journals is intended as a selection guide for small or medium-sized hospital libraries or for the small medical library serving a specified clientele. Books and journals are categorized by subject, with the books being followed by an author index and the journals by an alphabetical title listing. Items suggested for initial purchase by smaller libraries are indicated by an asterisk. To purchase the entire collection of books and to pay for annual subscriptions to all the journals would require an expenditure for about $14,500. The cost of only the asterisked items recommended for first purchase totals approximately $4,100. PMID:1095095

Selected list of books and journals for the small medical library.

PubMed

Brandon, A N

1975-04-01

This revised list of 446 books and 137 journals is intended as a selection guide for small or medium-sized hospital libraries or for the small medical library serving a specified clientele. Books and journals are categorized by subject, with the books being followed by an author index and the journals by an alphabetical title listing. Items suggested for initial purchase by smaller libraries are indicated by an asterisk. To purchase the entire collection of books and to pay for annual subscriptions to all the journals would require an expenditure for about $14,500. The cost of only the asterisked items recommended for first purchase totals approximately $4,100.

Torso sizing ring construction for hard space suit

NASA Technical Reports Server (NTRS)

Vykukal, H. C.

1986-01-01

A hard suit for use in space or diving applications having an adjustable length torso covering that will fit a large variety of wearers is described. The torso covering comprises an upper section and a lower section which interconnect so that the covering will fit wearers with short torsos. One or more sizing rings may be inserted between the upper and lower sections to accommodate larger torso sizes as required. Since access of the astronaut to the torso covering is preferably through an opening in the back of the upper section (which is closed off by the backpack), the rings slant upward-forward from the lower edge of the opening. The lower edge of the upper covering section has a coupler which slants upward-forward from the lower edge of the back opening. The lower torso section has a similarly slanted coupler which may interfit with the upper section coupler to accommodate the smallest torso size. One or more sizing rings may be inserted between the coupler sections of the upper and lower torso sections to accommodate larger torsos. Each ring has an upper coupler which may interfit with the upper section coupler and a lower coupler which may interfit with the lower section coupler.

Compound Libraries: Recent Advances and Their Applications in Drug Discovery.

PubMed

Gong, Zhen; Hu, Guoping; Li, Qiang; Liu, Zhiguo; Wang, Fei; Zhang, Xuejin; Xiong, Jian; Li, Peng; Xu, Yan; Ma, Rujian; Chen, Shuhui; Li, Jian

2017-01-01

Hit identification is the starting point of small-molecule drug discovery and is therefore very important to the pharmaceutical industry. One of the most important approaches to identify a new hit is to screen a compound library using an in vitro assay. High-throughput screening has made great contributions to drug discovery since the 1990s but requires expensive equipment and facilities, and its success depends on the size of the compound library. Recent progress in the development of compound libraries has provided more efficient ways to identify new hits for novel drug targets, thereby helping to promote the development of the pharmaceutical industry, especially for firstin- class drugs. A multistage and systematic research of articles published between 1986 and 2017 has been performed, which was organized into 5 sections and discussed in detail. In this review, the sources and classification of compound libraries are summarized. The progress made in combinatorial libraries and DNA-encoded libraries is reviewed. Library design methods, especially for focused libraries, are introduced in detail. In the final part, the status of the compound libraries at WuXi is reported. The progress related to compound libraries, especially drug template libraries, DELs, and focused libraries, will help to identify better hits for novel drug targets and promote the development of the pharmaceutical industry. Moreover, these libraries can facilitate hit identification, which benefits most research organizations, including academics and small companies. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

A new tetracycline efflux gene, tet(40), is located in tandem with tet(O/32/O) in a human gut firmicute bacterium and in metagenomic library clones.

PubMed

Kazimierczak, Katarzyna A; Rincon, Marco T; Patterson, Andrea J; Martin, Jennifer C; Young, Pauline; Flint, Harry J; Scott, Karen P

2008-11-01

The bacterium Clostridium saccharolyticum K10, isolated from a fecal sample obtained from a healthy donor who had received long-term tetracycline therapy, was found to carry three tetracycline resistance genes: tet(W) and the mosaic tet(O/32/O), both conferring ribosome protection-type resistance, and a novel, closely linked efflux-type resistance gene designated tet(40). tet(40) encodes a predicted membrane-associated protein with 42% amino acid identity to tetA(P). Tetracycline did not accumulate in Escherichia coli cells expressing the Tet(40) efflux protein, and resistance to tetracycline was reduced when cells were incubated with an efflux pump inhibitor. E. coli cells carrying tet(40) had a 50% inhibitory concentration of tetracycline of 60 microg/ml. Analysis of a transconjugant from a mating between donor strain C. saccharolyticum K10 and the recipient human gut commensal bacterium Roseburia inulinivorans suggested that tet(O/32/O) and tet(40) were cotransferred on a mobile element. Sequence analysis of a 37-kb insert identified on the basis of tetracycline resistance from a metagenomic fosmid library again revealed a tandem arrangement of tet(O/32/O) and tet(40), flanked by regions with homology to parts of the VanG operon previously identified in Enterococcus faecalis. At least 10 of the metagenomic inserts that carried tet(O/32/O) also carried tet(40), suggesting that tet(40), although previously undetected, may be an abundant efflux gene.

From Osler's Library to the Osler Library of the History of Medicine, McGill University, Montreal: an overview.

PubMed

Lyons, Christopher

2007-01-01

The Osler Library of the History of Medicine was opened in 1929 at McGill University, Montreal, Canada. Sir William Osler (1849-1919), arguably McGill's and Canada's most famous doctor at the time, had bequeathed his magnificent library of almost 8,000 historical works in medicine and, to a lesser extent, science and literature to the university. Under the 30-year reign of its first librarian, Dr. W W. Francis, the Osler Library became famous for its rare books and for its connection with Sir William. Since the 1950s, however, the library has pursued an active collection development policy for both primary and secondary material that has taken it far beyond Osler's original gift. The library has grown in both the size and scope of its holdings and the services it offers to scholars and students of the history of medicine. These have made the Osler Library a major resource centre for studies in the history of the health sciences. This article looks at the Osler Library today in the hopes of making the range of its collections and services better known to the Canadian and international communities.

Comparison of trapezius squeeze test and jaw thrust as clinical indicators for laryngeal mask airway insertion in spontaneously breathing children

PubMed Central

Dinesh Kumar, K. K.; Bhardwaj, Neerja; Yaddanapudi, Sandhya

2017-01-01

Background and Aims: It is not known whether trapezius squeeze test (TPZ) is a better clinical test than jaw thrust (JT) to assess laryngeal mask airway (LMA) insertion conditions in children under sevoflurane anesthesia. Material and Methods: After the Institutional Ethics Committee approval and written informed parental consent, 124 American Society of Anesthesiologists I and II children of 2–8 years of age undergoing minor surgical procedures were randomized into TPZ and JT groups. The children were induced with 8% sevoflurane in oxygen at a fresh gas flow of 4 L/min. TPZ or JT was performed after 1 min of start of sevoflurane and then every 20 s till the test was negative, when end-tidal (ET) sevoflurane concentration was noted. Classic LMA of requisite size was inserted by a blinded anesthetist and conditions at the insertion of LMA, insertion time, and the number of attempts of LMA insertion were recorded. Results: The mean LMA insertion time was significantly longer (P < 0.001) for TPZ (145 ± 28.7 sec) compared to JT group (111.8 ± 31.0 sec). ET sevoflurane concentration at the time of LMA insertion was comparable in the two groups. LMA insertion conditions were similar in the two groups. There was no difference between the two groups regarding total number of attempts of LMA insertion. Heart rate (HR) decreased in both groups after LMA insertion (P < 0.001) but TPZ group had significantly lower HR compared with the JT group up to 5 min after LMA insertion (P = 0.03). Conclusion: Both JT and TPZ are equivalent clinical indicators in predicting the optimal conditions of LMA insertion in spontaneously breathing children; however, it takes a longer time to achieve a negative TPZ squeeze test. PMID:28413275

The rational for a mid-scala electrode array.

PubMed

Boyle, P J

2016-06-01

Today increasing numbers of cochlear implant candidates have residual hearing that can be aided and hence is worth trying to preserve. This means that surgical technique and electrode array design must be adapted to minimize trauma. Wide opening of the round window is often preferred to reduce drill related trauma and to avoid pressure spikes during electrode array insertion. A recent meta-analysis suggested that there is no significant correlation between hearing preservation and either insertion depth or scala position. However, a slow insertion speed of at least 30seconds was associated with better hearing preservation. An electrode design is proposed that targets the middle of the scala tympani. This minimizes frictional forces from either lateral or medial wall during insertion and imposes less static pressure on cochlear structures following insertion. The flexibility to insert via the round window requires a 0.7-mm maximum dimension at the proximal end of the array. Micro-anatomical analysis by micro-CT indicated that a 420-degree insertion depth was optimal between cochlear coverage and available space within the scala tympani. Physical measurements showed that mean insertion forces remained below 10mN during insertion. A series of 20 human temporal bone insertions found a mean insertion depth of 400 degrees with no scala dislocations. Six clinical series, in total 94 cases, found postoperative hearing in 81% of cases with a mean loss of 12dB compared to preoperative levels. Speech understanding out to one year post-fitting trended better for a mid-scala design group than for a straight electrode array group; although the differences were not statistically significant. A mid-scala array design appears able to be inserted with minimal trauma, to return a predictable insertion depth across various sizes of cochleae and to support reasonable levels of speech understanding without relying on residual hearing. Copyright © 2016. Published by Elsevier Masson SAS.

Experimental and numerical investigation on heat transfer augmentation in a circular tube under forced convection with annular differential blockages/inserts

NASA Astrophysics Data System (ADS)

Waghole, D. R.

2018-06-01

Investigation on heat transfer by generating turbulence in the fluid stream inside the circular tube is an innovative area of research for researchers. Hence, many techniques are been investigated and adopted for enhancement of heat transfer rate to reduce the size and the cost of the heat exchanger/circular tube. In the present study the effect of differential solid ring inserts /turbulators on heat transfer, friction factor of heat exchanger/circular tube was evaluated through experimentally and numerically. The experiments were conducted in range of 3000 ≤Re≤ 6500 and annular blockages 0 ≤ɸ≤50 %. The heat transfer rate was higher for differential combination of inserts as compared to tube fitted with uniform inserts. The maximum heat transfer was obtained by the use of differential metal circular ring inserts/blockages. From this study, Nusselt number, friction factor and enhancement factor are found as 2.5-3.5 times, 12% - 50.5% and 155% - 195%, respectively with water. Finally new possible correlations for predicting heat transfer and friction factor in the flow of water through the circular tube with differential blockages/inserts are proposed.

Allopatric integrations selectively change host transcriptomes, leading to varied expression efficiencies of exotic genes in Myxococcus xanthus.

PubMed

Zhu, Li-Ping; Yue, Xin-Jing; Han, Kui; Li, Zhi-Feng; Zheng, Lian-Shuai; Yi, Xiu-Nan; Wang, Hai-Long; Zhang, You-Ming; Li, Yue-Zhong

2015-07-22

Exotic genes, especially clustered multiple-genes for a complex pathway, are normally integrated into chromosome for heterologous expression. The influences of insertion sites on heterologous expression and allotropic expressions of exotic genes on host remain mostly unclear. We compared the integration and expression efficiencies of single and multiple exotic genes that were inserted into Myxococcus xanthus genome by transposition and attB-site-directed recombination. While the site-directed integration had a rather stable chloramphenicol acetyl transferase (CAT) activity, the transposition produced varied CAT enzyme activities. We attempted to integrate the 56-kb gene cluster for the biosynthesis of antitumor polyketides epothilones into M. xanthus genome by site-direction but failed, which was determined to be due to the insertion size limitation at the attB site. The transposition technique produced many recombinants with varied production capabilities of epothilones, which, however, were not paralleled to the transcriptional characteristics of the local sites where the genes were integrated. Comparative transcriptomics analysis demonstrated that the allopatric integrations caused selective changes of host transcriptomes, leading to varied expressions of epothilone genes in different mutants. With the increase of insertion fragment size, transposition is a more practicable integration method for the expression of exotic genes. Allopatric integrations selectively change host transcriptomes, which lead to varied expression efficiencies of exotic genes.

Creating stable stem regions for loop elongation in Fcabs — Insights from combining yeast surface display, in silico loop reconstruction and molecular dynamics simulations

PubMed Central

Hasenhindl, Christoph; Lai, Balder; Delgado, Javier; Traxlmayr, Michael W.; Stadlmayr, Gerhard; Rüker, Florian; Serrano, Luis; Oostenbrink, Chris; Obinger, Christian

2014-01-01

Fcabs (Fc antigen binding) are crystallizable fragments of IgG where the C-terminal structural loops of the CH3 domain are engineered for antigen binding. For the design of libraries it is beneficial to know positions that will permit loop elongation to increase the potential interaction surface with antigen. However, the insertion of additional loop residues might impair the immunoglobulin fold. In the present work we have probed whether stabilizing mutations flanking the randomized and elongated loop region improve the quality of Fcab libraries. In detail, 13 libraries were constructed having the C-terminal part of the EF loop randomized and carrying additional residues (1, 2, 3, 5 or 10, respectively) in the absence and presence of two flanking mutations. The latter have been demonstrated to increase the thermal stability of the CH3 domain of the respective solubly expressed proteins. Assessment of the stability of the libraries expressed on the surface of yeast cells by flow cytometry demonstrated that loop elongation was considerably better tolerated in the stabilized libraries. By using in silico loop reconstruction and mimicking randomization together with MD simulations the underlying molecular dynamics were investigated. In the presence of stabilizing stem residues the backbone flexibility of the engineered EF loop as well as the fluctuation between its accessible conformations were decreased. In addition the CD loop (but not the AB loop) and most of the framework regions were rigidified. The obtained data are discussed with respect to the design of Fcabs and available data on the relation between flexibility and affinity of CDR loops in Ig-like molecules. PMID:24792385

Creating stable stem regions for loop elongation in Fcabs - insights from combining yeast surface display, in silico loop reconstruction and molecular dynamics simulations.

PubMed

Hasenhindl, Christoph; Lai, Balder; Delgado, Javier; Traxlmayr, Michael W; Stadlmayr, Gerhard; Rüker, Florian; Serrano, Luis; Oostenbrink, Chris; Obinger, Christian

2014-09-01

Fcabs (Fc antigen binding) are crystallizable fragments of IgG where the C-terminal structural loops of the CH3 domain are engineered for antigen binding. For the design of libraries it is beneficial to know positions that will permit loop elongation to increase the potential interaction surface with antigen. However, the insertion of additional loop residues might impair the immunoglobulin fold. In the present work we have probed whether stabilizing mutations flanking the randomized and elongated loop region improve the quality of Fcab libraries. In detail, 13 libraries were constructed having the C-terminal part of the EF loop randomized and carrying additional residues (1, 2, 3, 5 or 10, respectively) in the absence and presence of two flanking mutations. The latter have been demonstrated to increase the thermal stability of the CH3 domain of the respective solubly expressed proteins. Assessment of the stability of the libraries expressed on the surface of yeast cells by flow cytometry demonstrated that loop elongation was considerably better tolerated in the stabilized libraries. By using in silico loop reconstruction and mimicking randomization together with MD simulations the underlying molecular dynamics were investigated. In the presence of stabilizing stem residues the backbone flexibility of the engineered EF loop as well as the fluctuation between its accessible conformations were decreased. In addition the CD loop (but not the AB loop) and most of the framework regions were rigidified. The obtained data are discussed with respect to the design of Fcabs and available data on the relation between flexibility and affinity of CDR loops in Ig-like molecules. Copyright © 2014. Published by Elsevier B.V.

WHAMII - An enumeration and insertion procedure with binomial bounds for the stochastic time-constrained traveling salesman problem

NASA Technical Reports Server (NTRS)

Dahl, Roy W.; Keating, Karen; Salamone, Daryl J.; Levy, Laurence; Nag, Barindra; Sanborn, Joan A.

1987-01-01

This paper presents an algorithm (WHAMII) designed to solve the Artificial Intelligence Design Challenge at the 1987 AIAA Guidance, Navigation and Control Conference. The problem under consideration is a stochastic generalization of the traveling salesman problem in which travel costs can incur a penalty with a given probability. The variability in travel costs leads to a probability constraint with respect to violating the budget allocation. Given the small size of the problem (eleven cities), an approach is considered that combines partial tour enumeration with a heuristic city insertion procedure. For computational efficiency during both the enumeration and insertion procedures, precalculated binomial probabilities are used to determine an upper bound on the actual probability of violating the budget constraint for each tour. The actual probability is calculated for the final best tour, and additional insertions are attempted until the actual probability exceeds the bound.

Systematic Characteristic Exploration of the Chimeras Generated in Multiple Displacement Amplification through Next Generation Sequencing Data Reanalysis

PubMed Central

Gao, Shen; Yao, Bei; Lu, Zuhong

2015-01-01

Background The chimeric sequences produced by phi29 DNA polymerase, which are named as chimeras, influence the performance of the multiple displacement amplification (MDA) and also increase the difficulty of sequence data process. Despite several articles have reported the existence of chimeric sequence, there was only one research focusing on the structure and generation mechanism of chimeras, and it was merely based on hundreds of chimeras found in the sequence data of E. coli genome. Method We finished data mining towards a series of Next Generation Sequencing (NGS) reads which were used for whole genome haplotype assembling in a primary study. We established a bioinformatics pipeline based on subsection alignment strategy to discover all the chimeras inside and achieve their structural visualization. Then, we artificially defined two statistical indexes (the chimeric distance and the overlap length), and their regular abundance distribution helped illustrate of the structural characteristics of the chimeras. Finally we analyzed the relationship between the chimera type and the average insertion size, so that illustrate a method to decrease the proportion of wasted data in the procedure of DNA library construction. Results/Conclusion 131.4 Gb pair-end (PE) sequence data was reanalyzed for the chimeras. Totally, 40,259,438 read pairs (6.19%) with chimerism were discovered among 650,430,811 read pairs. The chimeric sequences are consisted of two or more parts which locate inconsecutively but adjacently on the chromosome. The chimeric distance between the locations of adjacent parts on the chromosome followed an approximate bimodal distribution ranging from 0 to over 5,000 nt, whose peak was at about 250 to 300 nt. The overlap length of adjacent parts followed an approximate Poisson distribution and revealed a peak at 6 nt. Moreover, unmapped chimeras, which were classified as the wasted data, could be reduced by properly increasing the length of the insertion segment size through a linear correlation analysis. Significance This study exhibited the profile of the phi29MDA chimeras by tens of millions of chimeric sequences, and helped understand the amplification mechanism of the phi29 DNA polymerase. Our work also illustrated the importance of NGS data reanalysis, not only for the improvement of data utilization efficiency, but also for more potential genomic information. PMID:26440104

Designing a diverse high-quality library for crystallography-based FBDD screening.

PubMed

Tounge, Brett A; Parker, Michael H

2011-01-01

A well-chosen set of fragments is able to cover a large chemical space using a small number of compounds. The actual size and makeup of the fragment set is dependent on the screening method since each technique has its own practical limits in terms of the number of compounds that can be screened and requirements for compound solubility. In this chapter, an overview of the general requirements for a fragment library is presented for different screening platforms. In the case of the FBDD work at Johnson & Johnson Pharmaceutical Research and Development, L.L.C., our main screening technology is X-ray crystallography. Since every soaked protein crystal needs to be diffracted and a protein structure determined to delineate if a fragment binds, the size of our initial screening library cannot be a rate-limiting factor. For this reason, we have chosen 900 as the appropriate primary fragment library size. To choose the best set, we have developed our own mix of simple property ("Rule of 3") and "bad" substructure filtering. While this gets one a long way in terms of limiting the fragment pool, there are still tens of thousands of compounds to choose from after this initial step. Many of the choices left at this stage are not drug-like, so we have developed an FBDD Score to help select a 900-compound set. The details of this score and the filtering are presented. Copyright © 2011 Elsevier Inc. All rights reserved.

Using Choice as a Mechanism for Allocating Book Funds in an Academic Library.

ERIC Educational Resources Information Center

Werking, Richard Hume; Getchell, Charles M., Jr.

1981-01-01

Reiterates the need for a "literature size" approach to book fund allocations and presents a case for using reviews from "Choice" magazine as a useful means for determining literature size. References are listed. (Author/RAA)

Selected list of books and journals for the small medical library.

PubMed Central

Brandon, A N; Hill, D R

1981-01-01

This revised list of 539 books and 136 journals is intended as a selection guide for small or medium-sized hospital libraries or for small medical libraries in comparable health care facilities. It can also be used as a core list by consortia of small hospital libraries. Books and journals are categorized by subject; the book list is followed by an author index and the list of journals by an alphabetical title listing. Items suggested for initial purchase by smaller libraries, 137 books and 54 journals, are indicated by asterisks. To purchase the entire collection of books and to pay for annual subscriptions to all the journals would require an expenditure of about $30,000. The cost of only the asterisked items, which are recommended for first purchase, totals approximately $8,900. PMID:7225656

AVAL - The ASTER Volcanic Ash Library

NASA Astrophysics Data System (ADS)

Williams, D.; Ramsey, M. S.

2016-12-01

Volcanic ash is a rich data source for understanding the causal mechanisms behind volcanic eruptions. Petrologic and morphometric information can provide direct information on the characteristics of the parent magma. Understanding how erupted ash interacts with the atmosphere can help quantify the effect that explosive volcanism has on the local to regional climate, whereas a measure of the particle size distribution enables more accurate modeling of plume propagation. Remote sensing is regularly employed to monitor volcanic plumes using a suite of high temporal/low spatial resolution sensors. These methods employ radiative transfer modeling with assumptions of the transmissive properties of infrared energy through the plume to determine ash density, particle size and sulfur dioxide content. However, such approaches are limited to the optically-transparent regions, and the low spatial resolution data are only useful for large-scale trends. In a new approach, we are treating the infrared-opaque regions of the plume in a similar way to a solid emitting surface. This allows high spatial resolution orbital thermal infrared data from the dense proximal plume to be modeled using a linear deconvolution approach coupled with a spectral library to extract the particle size and petrology. The newly created ASTER Volcanic Ash Library (AVAL) provides the end member spectral suite, and is comprised of laboratory emission measurements of volcanic ash taken from a variety of different volcanic settings, to obtain a wide range of petrologies. These samples have been further subdivided into particle size fractions to account for spectral changes due to diffraction effects. Once mapped to the ASTER sensor's spectral resolution, this library is applied to image data and the plume deconvolved to estimate composition and particle size. We have analyzed eruptions at the Soufrière Hills Volcano, Montserrat, Chaitén and Puyehue-Cordón Caulle, both Chile, and Eyjafjallajökull, Iceland. These results provide particle size distributions within actively-erupting volcanic plumes for the first time in high resolution, and the petrologic information is being studied to understand the underlying eruptive processes observed.

Laparoscopic versus Open Peritoneal Dialysis Catheter Insertion: A Meta-Analysis

PubMed Central

Hagen, Sander M.; Lafranca, Jeffrey A.; Steyerberg, Ewout W.; IJzermans, Jan N. M.; Dor, Frank J. M. F.

2013-01-01

Background Peritoneal dialysis is an effective treatment for end-stage renal disease. Key to successful peritoneal dialysis is a well-functioning catheter. The different insertion techniques may be of great importance. Mostly, the standard operative approach is the open technique; however, laparoscopic insertion is increasingly popular. Catheter malfunction is reported up to 35% for the open technique and up to 13% for the laparoscopic technique. However, evidence is lacking to definitely conclude that the laparoscopic approach is to be preferred. This review and meta-analysis was carried out to investigate if one of the techniques is superior to the other. Methods Comprehensive searches were conducted in MEDLINE, Embase and CENTRAL (the Cochrane Library 2012, issue 10). Reference lists were searched manually. The methodology was in accordance with the Cochrane Handbook for interventional systematic reviews, and written based on the PRISMA-statement. Results Three randomized controlled trials and eight cohort studies were identified. Nine postoperative outcome measures were meta-analyzed; of these, seven were not different between operation techniques. Based on the meta-analysis, the proportion of migrating catheters was lower (odds ratio (OR) 0.21, confidence interval (CI) 0.07 to 0.63; P = 0.006), and the one-year catheter survival was higher in the laparoscopic group (OR 3.93, CI 1.80 to 8.57; P = 0.0006). Conclusions Based on these results there is some evidence in favour of the laparoscopic insertion technique for having a higher one-year catheter survival and less migration, which would be clinically relevant. PMID:23457554

Optimization of an RNA-Seq Differential Gene Expression Analysis Depending on Biological Replicate Number and Library Size

PubMed Central

Lamarre, Sophie; Frasse, Pierre; Zouine, Mohamed; Labourdette, Delphine; Sainderichin, Elise; Hu, Guojian; Le Berre-Anton, Véronique; Bouzayen, Mondher; Maza, Elie

2018-01-01

RNA-Seq is a widely used technology that allows an efficient genome-wide quantification of gene expressions for, for example, differential expression (DE) analysis. After a brief review of the main issues, methods and tools related to the DE analysis of RNA-Seq data, this article focuses on the impact of both the replicate number and library size in such analyses. While the main drawback of previous relevant studies is the lack of generality, we conducted both an analysis of a two-condition experiment (with eight biological replicates per condition) to compare the results with previous benchmark studies, and a meta-analysis of 17 experiments with up to 18 biological conditions, eight biological replicates and 100 million (M) reads per sample. As a global trend, we concluded that the replicate number has a larger impact than the library size on the power of the DE analysis, except for low-expressed genes, for which both parameters seem to have the same impact. Our study also provides new insights for practitioners aiming to enhance their experimental designs. For instance, by analyzing both the sensitivity and specificity of the DE analysis, we showed that the optimal threshold to control the false discovery rate (FDR) is approximately 2−r, where r is the replicate number. Furthermore, we showed that the false positive rate (FPR) is rather well controlled by all three studied R packages: DESeq, DESeq2, and edgeR. We also analyzed the impact of both the replicate number and library size on gene ontology (GO) enrichment analysis. Interestingly, we concluded that increases in the replicate number and library size tend to enhance the sensitivity and specificity, respectively, of the GO analysis. Finally, we recommend to RNA-Seq practitioners the production of a pilot data set to strictly analyze the power of their experimental design, or the use of a public data set, which should be similar to the data set they will obtain. For individuals working on tomato research, on the basis of the meta-analysis, we recommend at least four biological replicates per condition and 20 M reads per sample to be almost sure of obtaining about 1000 DE genes if they exist. PMID:29491871

Analysing and Navigating Natural Products Space for Generating Small, Diverse, But Representative Chemical Libraries.

PubMed

O'Hagan, Steve; Kell, Douglas B

2018-01-01

Armed with the digital availability of two natural products libraries, amounting to some 195 885 molecular entities, we ask the question of how we can best sample from them to maximize their "representativeness" in smaller and more usable libraries of 96, 384, 1152, and 1920 molecules. The term "representativeness" is intended to include diversity, but for numerical reasons (and the likelihood of being able to perform a QSAR) it is necessary to focus on areas of chemical space that are more highly populated. Encoding chemical structures as fingerprints using the RDKit "patterned" algorithm, we first assess the granularity of the natural products space using a simple clustering algorithm, showing that there are major regions of "denseness" but also a great many very sparsely populated areas. We then apply a "hybrid" hierarchical K-means clustering algorithm to the data to produce more statistically robust clusters from which representative and appropriate numbers of samples may be chosen. There is necessarily again a trade-off between cluster size and cluster number, but within these constraints, libraries containing 384 or 1152 molecules can be found that come from clusters that represent some 18 and 30% of the whole chemical space, with cluster sizes of, respectively, 50 and 27 or above, just about sufficient to perform a QSAR. By using the online availability of molecules via the Molport system (www.molport.com), we are also able to construct (and, for the first time, provide the contents of) a small virtual library of available molecules that provided effective coverage of the chemical space described. Consistent with this, the average molecular similarities of the contents of the libraries developed is considerably smaller than is that of the original libraries. The suggested libraries may have use in molecular or phenotypic screening, including for determining possible transporter substrates. © 2017 The Authors. Biotechnology Journal Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Determining and Meeting Personnel Training Needs

ERIC Educational Resources Information Center

Jennings, Anita

2005-01-01

The role of the library has changed significantly during the past 2 decades. Twenty years ago, it could have been considered the norm for a small to mid-sized library to have one or two computers for patron use. Staff was fortunate to have a computer connected to a printer--a tractor-feed ink jet printer--with a basic word processing application…

Statistics & Input-Output Measures for School Libraries in Colorado, 2002.

ERIC Educational Resources Information Center

Colorado State Library, Denver.

This document presents statistics and input-output measures for K-12 school libraries in Colorado for 2002. Data are presented by type and size of school, i.e., high schools (six categories ranging from 2,000 and over to under 300), junior high/middle schools (five categories ranging from 1,000-1,999 to under 300), elementary schools (four…

Ideas for Preservation Fund Raising: A Support Package for Libraries and Archives.

ERIC Educational Resources Information Center

Commission on Preservation and Access, Washington, DC.

Preservation efforts are needed immediately to save a quarter of all the volumes housed in research libraries. These books are turning to dust because alum sizing was introduced into the paper-making process in the mid-1800s. The destruction of some books can be reversed through deacidification. The content of other books can be saved only by…

EAD in the Department of Special Collections and Western Manuscripts at the Bodleian Library, United Kingdom

ERIC Educational Resources Information Center

Webb, Mike

2005-01-01

The strategy for conversion to electronic cataloguing of western manuscripts in the Bodleian Library has been to a large extent determined by circumstances--the size and variety of the manuscript collections, the existence of detailed published catalogues for the earlier collections, the availability of funds for specific purposes, and, above all,…

Searching for microbial protein over-expression in a complex matrix using automated high throughput MS-based proteomics tools.

PubMed

Akeroyd, Michiel; Olsthoorn, Maurien; Gerritsma, Jort; Gutker-Vermaas, Diana; Ekkelkamp, Laurens; van Rij, Tjeerd; Klaassen, Paul; Plugge, Wim; Smit, Ed; Strupat, Kerstin; Wenzel, Thibaut; van Tilborg, Marcel; van der Hoeven, Rob

2013-03-10

In the discovery of new enzymes genomic and cDNA expression libraries containing thousands of differential clones are generated to obtain biodiversity. These libraries need to be screened for the activity of interest. Removing so-called empty and redundant clones significantly reduces the size of these expression libraries and therefore speeds up new enzyme discovery. Here, we present a sensitive, generic workflow for high throughput screening of successful microbial protein over-expression in microtiter plates containing a complex matrix based on mass spectrometry techniques. MALDI-LTQ-Orbitrap screening followed by principal component analysis and peptide mass fingerprinting was developed to obtain a throughput of ∼12,000 samples per week. Alternatively, a UHPLC-MS(2) approach including MS(2) protein identification was developed for microorganisms with a complex protein secretome with a throughput of ∼2000 samples per week. TCA-induced protein precipitation enhanced by addition of bovine serum albumin is used for protein purification prior to MS detection. We show that this generic workflow can effectively reduce large expression libraries from fungi and bacteria to their minimal size by detection of successful protein over-expression using MS. Copyright © 2012 Elsevier B.V. All rights reserved.

Re-sequencing transgenic plants revealed rearrangements at T-DNA inserts, and integration of a short T-DNA fragment, but no increase of small mutations elsewhere.

PubMed

Schouten, Henk J; Vande Geest, Henri; Papadimitriou, Sofia; Bemer, Marian; Schaart, Jan G; Smulders, Marinus J M; Perez, Gabino Sanchez; Schijlen, Elio

2017-03-01

Transformation resulted in deletions and translocations at T-DNA inserts, but not in genome-wide small mutations. A tiny T-DNA splinter was detected that probably would remain undetected by conventional techniques. We investigated to which extent Agrobacterium tumefaciens-mediated transformation is mutagenic, on top of inserting T-DNA. To prevent mutations due to in vitro propagation, we applied floral dip transformation of Arabidopsis thaliana. We re-sequenced the genomes of five primary transformants, and compared these to genomic sequences derived from a pool of four wild-type plants. By genome-wide comparisons, we identified ten small mutations in the genomes of the five transgenic plants, not correlated to the positions or number of T-DNA inserts. This mutation frequency is within the range of spontaneous mutations occurring during seed propagation in A. thaliana, as determined earlier. In addition, we detected small as well as large deletions specifically at the T-DNA insert sites. Furthermore, we detected partial T-DNA inserts, one of these a tiny 50-bp fragment originating from a central part of the T-DNA construct used, inserted into the plant genome without flanking other T-DNA. Because of its small size, we named this fragment a T-DNA splinter. As far as we know this is the first report of such a small T-DNA fragment insert in absence of any T-DNA border sequence. Finally, we found evidence for translocations from other chromosomes, flanking T-DNA inserts. In this study, we showed that next-generation sequencing (NGS) is a highly sensitive approach to detect T-DNA inserts in transgenic plants.

Supraglottic Airway Devices: the Search for the Best Insertion Technique or the Time to Change Our Point of View?

PubMed

Sorbello, Massimiliano; Petrini, Flavia

2017-04-01

In the crowded world of supraglottic airway devices (SADs), many papers compare the easiness of insertion based on the different endpoints of an operator's satisfaction: first pass success, ventilation effectiveness, complications and morbidity. Proseal LMA ™ (Laryngeal Mask Airway, Teleflex Medical, Dublin, Ireland) has been extensively studied because on one hand it has a steeper learning curve and more complex insertion when compared with other SADs and on the other hand many alternative techniques are available to facilitate insertion. This research is part of a larger body of studies exploring the issue that some devices are more difficult to insert because of many features related to sizing, constructive material, airway conduit and cuff design, performance and last but not least experience. Nevertheless, the biggest question might be the search for a systematic categorization of insertion difficulty features and identification of criteria allowing the choice for the best device and consequently for the best insertion technique. Given that, as a result of many intrinsic characteristics of the device we are using, insertion might become the secondary issue to be considered only after we clearly identify what makes it difficult, and to be counterbalanced on the results we expect from the device, performance we can achieve and degree of airway protection it could grant. The aim of this narrative review is to consider which factors might affect or condition SAD insertion difficulty and to try identifying some criteria addressing physicians pertaining to the use of SADs in clinical practice.

Evolving artificial metalloenzymes via random mutagenesis

NASA Astrophysics Data System (ADS)

Yang, Hao; Swartz, Alan M.; Park, Hyun June; Srivastava, Poonam; Ellis-Guardiola, Ken; Upp, David M.; Lee, Gihoon; Belsare, Ketaki; Gu, Yifan; Zhang, Chen; Moellering, Raymond E.; Lewis, Jared C.

2018-03-01

Random mutagenesis has the potential to optimize the efficiency and selectivity of protein catalysts without requiring detailed knowledge of protein structure; however, introducing synthetic metal cofactors complicates the expression and screening of enzyme libraries, and activity arising from free cofactor must be eliminated. Here we report an efficient platform to create and screen libraries of artificial metalloenzymes (ArMs) via random mutagenesis, which we use to evolve highly selective dirhodium cyclopropanases. Error-prone PCR and combinatorial codon mutagenesis enabled multiplexed analysis of random mutations, including at sites distal to the putative ArM active site that are difficult to identify using targeted mutagenesis approaches. Variants that exhibited significantly improved selectivity for each of the cyclopropane product enantiomers were identified, and higher activity than previously reported ArM cyclopropanases obtained via targeted mutagenesis was also observed. This improved selectivity carried over to other dirhodium-catalysed transformations, including N-H, S-H and Si-H insertion, demonstrating that ArMs evolved for one reaction can serve as starting points to evolve catalysts for others.

Construction and functional analysis of Trichoderma harzianum mutants that modulate maize resistance to the pathogen Curvularia lunata.

PubMed

Fan, Lili; Fu, Kehe; Yu, Chuanjin; Ma, Jia; Li, Yaqian; Chen, Jie

2014-01-01

Agrobacterium tumefaciens-mediated transformation (ATMT) was used to generate an insertional mutant library of the mycelial fungus Trichoderma harzianum. From a total of 450 mutants, six mutants that showed significant influence on maize resistance to C. lunata were analyzed in detail. Maize coated with these mutants was more susceptible to C. lunata compared with those coated with a wild-type (WT) strain. Similar to other fungal ATMT libraries, all six mutants were single copy integrations, which occurred preferentially in noncoding regions (except two mutants) and were frequently accompanied by the loss of border sequences. Two mutants (T66 and T312) that were linked to resistance were characterized further. Maize seeds coated with T66 and T312 were more susceptible to C. lunata than those treated with WT. Moreover, the mutants affected the resistance of maize to C. lunata by enhancing jasmonate-responsive gene expression. T66 and T312 induced maize resistance to C. lunata infection through a jasmonic acid-dependent pathway.

Complementation of a Fanconi anemia group A cell line by UbA{sup 52}

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

Moses, R.E.; Heina, J.A.; Jakobs, P.M.

1994-09-01

Cells from patients with Fanconi anemia (FA) display chromosomal instability and increased sensitivity to mitomycin C (MMC) and diepoxybutane (DEB) relative to normal cells. Several genes act in this pathway of DNA damage processing based upon four known complementation groups in FA. We have made a cDNA expression library in a vector with a G418 selectable marker to identify FA genes other than the FA-C group. Approximately 1 x 10{sup 6} independent cDNA clones were isolated with an average cDNA size of 1.5 kb. Five cell lines resistant to MMC and DEB were isolated from 6 x 10{sup 6} G418-resistantmore » transfectants from 65 individual transfections of the FA-A fibroblast line GM6914. The isolated cell lines also showed normal chromosome stability. The same cDNA (600 bp) was recovered from three independent cell lines by PCR using flanking sequence primers. The gene has sequence identity with a known gene, the ubiquitin fusion gene, UbA{sub 52}. Interestingly, each of the cDNAs were inserted in antisense orientation relative to the cytomegalovirus (CMV) promoter as determined by sequencing and PCR using UbA{sub 52}-specific internal primers. Southern blot analysis indicated the cell lines had distinct chromosomal insertion sites. Mutation analysis by chemical cleavage showed no reading frame mutations, indicating that UbA{sub 52} is not the FA-A gene. Re-transfection with the UbA{sub 52} gene in antisense gave complementation for MMC, DEB and chromosome stability to varying degrees. Re-transfection of the antisense construct with the CMV promotor removed or with a sense construct did not alter the MMC sensitivity. We conclude that the antisense UbA{sub 52} gene has a non-specific effect, perhaps acting by altering the cell cycle or susceptibility to apoptosis.« less

Genome Analysis of the First Extensively Drug-Resistant (XDR) Mycobacterium tuberculosis in Malaysia Provides Insights into the Genetic Basis of Its Biology and Drug Resistance

PubMed Central

Kuan, Chee Sian; Chan, Chai Ling; Yew, Su Mei; Toh, Yue Fen; Khoo, Jia-Shiun; Chong, Jennifer; Lee, Kok Wei; Tan, Yung-Chie; Yee, Wai-Yan; Ngeow, Yun Fong; Ng, Kee Peng

2015-01-01

The outbreak of extensively drug-resistant tuberculosis (XDR-TB) has become an increasing problem in many TB-burdened countries. The underlying drug resistance mechanisms, including the genetic variation favored by selective pressure in the resistant population, are partially understood. Recently, the first case of XDR-TB was reported in Malaysia. However, the detailed genotype family and mechanisms of the formation of multiple drugs resistance are unknown. We sequenced the whole genome of the UM 1072388579 strain with a 2-kb insert-size library and combined with that from previously sequenced 500-bp-insert paired-end reads to produce an improved sequence with maximal sequencing coverage across the genome. In silico spoligotyping and phylogenetic analyses demonstrated that UM 1072388579 strain belongs to an ancestral-like, non-Beijing clade of East Asia lineage. This is supported by the presence of a number of lineage-specific markers, including fadD28, embA, nuoD and pks7. Polymorphism analysis showed that the drug-susceptibility profile is correlated with the pattern of resistance mutations. Mutations in drug-efflux pumps and the cell wall biogenesis pathway such as mmpL, pks and fadD genes may play an important role in survival and adaptation of this strain to its surrounding environment. In this work, fifty-seven putative promoter SNPs were identified. Among them, we identified a novel SNP located at -4 T allele of TetR/acrR promoter as an informative marker to recognize strains of East Asian lineage. Our work indicates that the UM 1072388579 harbors both classical and uncommon SNPs that allow it to escape from inhibition by many antibiotics. This study provides a strong foundation to dissect the biology and underlying resistance mechanisms of the first reported XDR M. tuberculosis in Malaysia. PMID:26110649

Large-Scale Concatenation cDNA Sequencing

PubMed Central

Yu, Wei; Andersson, Björn; Worley, Kim C.; Muzny, Donna M.; Ding, Yan; Liu, Wen; Ricafrente, Jennifer Y.; Wentland, Meredith A.; Lennon, Greg; Gibbs, Richard A.

1997-01-01

A total of 100 kb of DNA derived from 69 individual human brain cDNA clones of 0.7–2.0 kb were sequenced by concatenated cDNA sequencing (CCS), whereby multiple individual DNA fragments are sequenced simultaneously in a single shotgun library. The method yielded accurate sequences and a similar efficiency compared with other shotgun libraries constructed from single DNA fragments (>20 kb). Computer analyses were carried out on 65 cDNA clone sequences and their corresponding end sequences to examine both nucleic acid and amino acid sequence similarities in the databases. Thirty-seven clones revealed no DNA database matches, 12 clones generated exact matches (≥98% identity), and 16 clones generated nonexact matches (57%–97% identity) to either known human or other species genes. Of those 28 matched clones, 8 had corresponding end sequences that failed to identify similarities. In a protein similarity search, 27 clone sequences displayed significant matches, whereas only 20 of the end sequences had matches to known protein sequences. Our data indicate that full-length cDNA insert sequences provide significantly more nucleic acid and protein sequence similarity matches than expressed sequence tags (ESTs) for database searching. [All 65 cDNA clone sequences described in this paper have been submitted to the GenBank data library under accession nos. U79240–U79304.] PMID:9110174

Technique of laser chromosome welding for chromosome repair and artificial chromosome creation.

PubMed

Huang, Yao-Xiong; Li, Lin; Yang, Liu; Zhang, Yi

2018-04-01

Here we report a technique of laser chromosome welding that uses a violet pulse laser micro-beam for welding. The technique can integrate any size of a desired chromosome fragment into recipient chromosomes by combining with other techniques of laser chromosome manipulation such as chromosome cutting, moving, and stretching. We demonstrated that our method could perform chromosomal modifications with high precision, speed and ease of use in the absence of restriction enzymes, DNA ligases and DNA polymerases. Unlike the conventional methods such as de novo artificial chromosome synthesis, our method has no limitation on the size of the inserted chromosome fragment. The inserted DNA size can be precisely defined and the processed chromosome can retain its intrinsic structure and integrity. Therefore, our technique provides a high quality alternative approach to directed genetic recombination, and can be used for chromosomal repair, removal of defects and artificial chromosome creation. The technique may also have applicability on the manipulation and extension of large pieces of synthetic DNA.

Effect of repetitive pecking at working length for glide path preparation using G-file.

PubMed

Ha, Jung-Hong; Jeon, Hyo-Jin; Abed, Rashid El; Chang, Seok-Woo; Kim, Sung-Kyo; Kim, Hyeon-Cheol

2015-05-01

Glide path preparation is recommended to reduce torsional failure of nickel-titanium (NiTi) rotary instruments and to prevent root canal transportation. This study evaluated whether the repetitive insertions of G-files to the working length maintain the apical size as well as provide sufficient lumen as a glide path for subsequent instrumentation. The G-file system (Micro-Mega) composed of G1 and G2 files for glide path preparation was used with the J-shaped, simulated resin canals. After inserting a G1 file twice, a G2 file was inserted to the working length 1, 4, 7, or 10 times for four each experimental group, respectively (n = 10). Then the canals were cleaned by copious irrigation, and lubricated with a separating gel medium. Canal replicas were made using silicone impression material, and the diameter of the replicas was measured at working length (D0) and 1 mm level (D1) under a scanning electron microscope. Data was analysed by one-way ANOVA and post-hoc tests (p = 0.05). The diameter at D0 level did not show any significant difference between the 1, 2, 4, and 10 times of repetitive pecking insertions of G2 files at working length. However, 10 times of pecking motion with G2 file resulted in significantly larger canal diameter at D1 (p < 0.05). Under the limitations of this study, the repetitive insertion of a G2 file up to 10 times at working length created an adequate lumen for subsequent apical shaping with other rotary files bigger than International Organization for Standardization (ISO) size 20, without apical transportation at D0 level.

Investigation of imaging properties for submillimeter rectangular pinholes

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

Xia, Dan, E-mail: dxia@uchicago.edu; Moore, Stephen C., E-mail: scmoore@bwh.harvard.edu, E-mail: miaepark@bwh.harvard.edu, E-mail: mcervo@bwh.harvard.edu; Park, Mi-Ae, E-mail: scmoore@bwh.harvard.edu, E-mail: miaepark@bwh.harvard.edu, E-mail: mcervo@bwh.harvard.edu

Purpose: Recently, a multipinhole collimator with inserts that have both rectangular apertures and rectangular fields of view (FOVs) has been proposed for SPECT imaging since it can tile the projection onto the detector efficiently and the FOVs in transverse and axial directions become separable. The purpose of this study is to investigate the image properties of rectangular-aperture pinholes with submillimeter apertures sizes. Methods: In this work, the authors have conducted sensitivity and FOV experiments for 18 replicates of a prototype insert fabricated in platinum/iridium (Pt/Ir) alloy with submillimeter square-apertures. A sin{sup q}θ fit to the experimental sensitivity has been performedmore » for these inserts. For the FOV measurement, the authors have proposed a new formula to calculate the projection intensity of a flood image on the detector, taking into account the penumbra effect. By fitting this formula to the measured projection data, the authors obtained the acceptance angles. Results: The mean (standard deviation) of fitted sensitivity exponents q and effective edge lengths w{sub e} were, respectively, 10.8 (1.8) and 0.38 mm (0.02 mm), which were close to the values, 7.84 and 0.396 mm, obtained from Monte Carlo calculations using the parameters of the designed inserts. For the FOV measurement, the mean (standard deviation) of the transverse and axial acceptances were 35.0° (1.2°) and 30.5° (1.6°), which are in good agreement with the designed values (34.3° and 29.9°). Conclusions: These results showed that the physical properties of the fabricated inserts with submillimeter aperture size matched our design well.« less

Quality assurance: recommended guidelines for safe heating by capacitive-type heating technique to treat patients with metallic implants.

PubMed

Kato, Hirokazu; Kondo, Motoharu; Imada, Hajime; Kuroda, Masahiro; Kamimura, Yoshitsugu; Saito, Kazuyuki; Kuroda, Kagayaki; Ito, Koichi; Takahashi, Hideaki; Matsuki, Hidetoshi

2013-05-01

This article is a redissemination of the previous Japanese Quality Assurance Guide guidelines. Specific absorption rate and temperature distribution were investigated with respect to various aspects including metallic implant size and shape, insertion site, insertion direction, blood flow and heating power, and simulated results were compared with adverse reactions of patients treated by radio frequency capacitive-type heating. Recommended guidelines for safe heating methods for patients with metallic implants are presented based on our findings.

Temporomandibular Joint Ankylosis: "A Pediatric Difficult Airway Management".

PubMed

Sharma, Anoop; Dwivedi, Deepak; Sharma, Ram Murti

2018-01-01

Intubating a pediatric patient with temporomandibular joint ankylosis is a daunting task, and it becomes more challenging with limited mouth opening. Fiberoptic nasotracheal intubation technique is considered a gold standard. We describe an improvised technique of securing airway in the absence of appropriate-sized fiberoptic scope. The endotracheal tube inserted in the left nostril for maintaining depth of anesthesia was advanced under vision by the fiberoptic scope inserted into the right nostril, and with external laryngeal manipulation, the airway was secured with no complications.

An Investigation of the Educational Needs of Health Sciences Library Manpower: I. Definition of the Manpower Problem and Research Design*

PubMed Central

Kronick, David A.; Rees, Alan M.; Rothenberg, Lesliebeth

1970-01-01

In order to plan adequately for education in health science librarianship and to be able to project future demands and needs we need to know a great deal more about existing manpower in health science libraries. This paper, the first in a series of reports on an investigation to gather this data, discusses the research methodology and the development of an inventory of the institution-program population upon which the survey is based. An analysis in terms of geographic location, type (educational, research, etc.), administrative control, and primary cognate area of these institutions is presented, and their distribution through the various Regional Medical Library areas is noted. Preliminary estimates are made, based on a questionnaire to the libraries, on the size of the library population, their relationship to reporting programs or institutions, exclusive of the hospital population which is being covered in an independent survey. A questionnaire to library personnel is underway which will establish, along with the other questionnaires, a basis for exploring the relationships which exist between institutions or programs, libraries and manpower. PMID:5411708

DNA-Encoded Chemical Libraries: A Selection System Based on Endowing Organic Compounds with Amplifiable Information.

PubMed

Neri, Dario; Lerner, Richard A

2018-06-20

The discovery of organic ligands that bind specifically to proteins is a central problem in chemistry, biology, and the biomedical sciences. The encoding of individual organic molecules with distinctive DNA tags, serving as amplifiable identification bar codes, allows the construction and screening of combinatorial libraries of unprecedented size, thus facilitating the discovery of ligands to many different protein targets. Fundamentally, one links powers of genetics and chemical synthesis. After the initial description of DNA-encoded chemical libraries in 1992, several experimental embodiments of the technology have been reduced to practice. This review provides a historical account of important milestones in the development of DNA-encoded chemical libraries, a survey of relevant ongoing research activities, and a glimpse into the future.

42 CFR 37.203 - Autopsy specifications.

Code of Federal Regulations, 2012 CFR

2012-10-01

... under this subparagraph shall be in the metric system); (iii) Circumference of each cardiac valve when... shall be measured directly above the insertion of the anterior papillary muscle; (v) Size, number...