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You searched for: Publication year rev 7994-2006 Remove constraint Publication year rev: 7994-2006 Subject clones Remove constraint Subject: clones
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1. AFLP Analysis of the Phenetic Organization and Genetic Diversity in the Sugarcane Complex, Saccharum and Erianthus

Author:
A. Selvi; N. V. Nair; J. L. Noyer; N. K. Singh; N. Balasundaram; K. C. Bansal; K. R. Koundal; T. Mohapatra
Source:
Genetic resources and crop evolution 2006 v.53 no.4 pp. 831-842
ISSN:
0925-9864
Subject:
Saccharum; amplified fragment length polymorphism; breeding programs; clones; cluster analysis; genetic markers; genetic similarity; genetic variation; hybrids; phylogeny; random amplified polymorphic DNA technique; restriction fragment length polymorphism; sugarcane; taxonomy
Abstract:
... Amplified fragment length polymorphism (AFLP) markers were evaluated for determining the phylogenetic relationships, and the diversity in the Saccharum complex using 30 clones belonging to S. officinarum, S. robustum, S. spontaneum, S. barberi, S. sinense and the related genus Erianthus. The phenetic tree of the species clones based on AFLP data was consistent with the known taxonomical relationsh ...
DOI:
10.1007/s10722-004-6376-6

2. Abundance and Population Structure of Ammonia-Oxidizing Bacteria That Inhabit Canal Sediments Receiving Effluents from Municipal Wastewater Treatment Plants

Author:
Urakawa, Hidetoshi; Maki, Hideaki; Kawabata, Sumiko; Fujiwara, Taketomo; Ando, Haruo; Kawai, Toshio; Hiwatari, Takehiko; Kohata, Kunio; Watanabe, Masataka
Source:
Applied and environmental microbiology 2006 v.72 no.10 pp. 6845-6850
ISSN:
0099-2240
Subject:
Nitrosomonas; bacteria; clones; effluents; fluorescent antibody technique; polymerase chain reaction; population structure; restriction mapping; sediments; wastewater; wastewater treatment
Abstract:
... A polyphasic, culture-independent study was conducted to investigate the abundance and population structure of ammonia-oxidizing bacteria (AOB) in canal sediments receiving wastewater discharge. The abundance of AOB ranged from 0.2 to 1.9% and 1.6 to 5.7% of the total bacterial fraction by real-time PCR and immunofluorescence staining, respectively. Clone analysis and restriction endonuclease anal ...
DOI:
10.1128/AEM.00807-06
PubMed:
17021242
PubMed Central:
PMC1610321

3. Advanced resources for plant genomics: a BAC library specific for the short arm of wheat chromosome 1B

Author:
Janda, Jaroslav; Šafář, Jan; Kubaláková, Marie; Bartoš, Jan; Kovářová, Pavlína; Suchánková, Pavla; Pateyron, Stephanie; Číhalíková, Jarmila; Sourdille, Pierre; Šimková, Hana; Faivre-Rampant, Patricia; Hřibová, Eva; Bernard, Michel; Lukaszewski, Adam; Doležel, Jaroslav; Chalhoub, Boulos
Source:
plant journal 2006 v.47 no.6 pp. 977-986
ISSN:
0960-7412
Subject:
DNA; Triticum aestivum; bacterial artificial chromosomes; clones; crops; genome; genomics; molecular cloning; probability; sorting; wheat
Abstract:
... Common wheat (Triticum aestivum L., 2n = 6x = 42) is a polyploid species possessing one of the largest genomes among the cultivated crops (1C is approximately 17 000 Mb). The presence of three homoeologous genomes (A, B and D), and the prevalence of repetitive DNA make sequencing the wheat genome a daunting task. We have developed a novel 'chromosome arm-based' strategy for wheat genome sequencing ...
DOI:
10.1111/j.1365-313X.2006.02840.x
PubMed:
16911585

4. Advantage of Using Inosine at the 3' Termini of 16S rRNA Gene Universal Primers for the Study of Microbial Diversity

Author:
Ben-Dov, Eitan; Shapiro, Orr H.; Siboni, Nachshon; Kushmaro, Ariel
Source:
Applied and environmental microbiology 2006 v.72 no.11 pp. 6902-6906
ISSN:
0099-2240
Subject:
Firmicutes; Proteobacteria; annealing; clones; genes; microbial communities; polymerase chain reaction; ribosomal RNA; temperature
Abstract:
... To overcome the shortcomings of universal 16S rRNA gene primers 8F and 907R when studying the diversity of complex microbial communities, the 3' termini of both primers were replaced with inosine. A comparison of the clone libraries derived using both primer sets showed seven bacterial phyla amplified by the altered primer set (8F-I/907R-I) whereas the original set amplified sequences belonging al ...
DOI:
10.1128/AEM.00849-06
PubMed:
16950904
PubMed Central:
PMC1636166

5. Age-Related Shifts in Leaf Chemistry of Clonal Aspen (Populus tremuloides)

Author:
Donaldson, J.R.; Stevens, M.T.; Barnhill, H.R.; Lindroth, R.L.
Source:
Journal of chemical ecology 2006 v.32 no.7 pp. 1415-1429
ISSN:
0098-0331
Subject:
proanthocyanidins; developmental stages; plant-insect relations; herbivores; clones; plant age
Abstract:
... Developmental changes in plant structure and function can influence both mammalian and arthropod feeding preferences for many woody plant species. This study documents age-related changes that occur in the leaf chemistry of trembling aspen (Populus tremuloides Michx., Salicaceae) and discusses implications for the herbivore community and ecosystem processes. We collected leaves from replicate rame ...
DOI:
10.1007/s10886-006-9059-2
PubMed:
16724272

6. Allelic Size Standards and Reference Genotypes to Unify International Cocoa (Theobroma cacao L.) Microsatellite Data

Author:
Cryer, N. C.; Fenn, M. G. E.; Turnbull, C. J.; Wilkinson, M. J.
Source:
Genetic resources and crop evolution 2006 v.53 no.8 pp. 1643-1652
ISSN:
0925-9864
Subject:
germplasm; microsatellite repeats; alleles; Theobroma cacao; clones; genotype; gene banks; DNA fingerprinting; cultivar identification; genetic markers
Abstract:
... Standardisation of microsatellite allele profiles between laboratories is of fundamental importance to the transferability of genetic fingerprint data and the identification of clonal individuals held at multiple sites. Here we describe two methods of standardisation applied to the microsatellite fingerprinting of 429 Theobroma cacao L. trees representing 345 accessions held in the worlds largest ...
DOI:
10.1007/s10722-005-1286-9

7. Analysis of ESTs from Lutzomyia longipalpis sand flies and their contribution toward understanding the insect-parasite relationship

Author:
Dillon, R.J.; Ivens, A.C.; Churcher, C.; Holroyd, N.; Quail, M.A.; Rogers, M.E.; Soares, M.B.; Bonaldo, M.F.; Casavant, T.L.; Lehane, M.J.
Source:
Genomics 2006 v.88 no.6 pp. 831-840
ISSN:
0888-7543
Subject:
Lutzomyia longipalpis; midgut; expressed sequence tags; clones; digestion; insect physiology; cDNA libraries; immune response
DOI:
10.1016/j.ygeno.2006.06.011
PubMed:
16887324
PubMed Central:
PMC2675706

8. Analysis of Expressed Sequence Tags from the Harmful Alga, Prymnesium parvum (Prymnesiophyceae, Haptophyta)

Author:
John W. La Claire II
Source:
Marine biotechnology 2006 v.8 no.5 pp. 534-546
ISSN:
1436-2228
Subject:
Prymnesium; biochemical pathways; cDNA libraries; clones; complementary DNA; databases; expressed sequence tags; phosphates; photosynthesis; protein synthesis; proteins; secretion; toxicity; toxins; unigenes
Abstract:
... A cDNA library was constructed from late log-phase cultures of the ichthyotoxin-producing haptophyte, Prymnesium parvum. Approximately 6,300 single-pass 5′ nucleotide sequences (out of nearly 8,000 randomly isolated clones) achieved length and quality criteria for incorporation into an expressed sequence tag (EST) database. Collectively, 3,415 unique genes (tentative unigenes [TUGs]) were assemble ...
DOI:
10.1007/s10126-005-5182-2

9. Analysis of expressed sequence tags from Cryptomeria japonica pollen reveals novel pollen-specific transcripts

Author:
Futamura, N.; Ujino-Ihara, T.; Nishiguchi, M.; Kanamori, H.; Yoshimura, K.; Sakaguchi, M.; Shinohara, K.
Source:
Tree physiology 2006 v.26 no.12 pp. 1517-1528
ISSN:
0829-318X
Subject:
messenger RNA; protein synthesis; forest trees; complementary DNA; Cryptomeria japonica; allergens; clones; gene expression; expressed sequence tags; transcription (genetics); transcriptome; amino acid sequences; pollen; poisonous plants; Japan
Abstract:
... Cryptomeria japonica D. Don is one of the most important forest trees in Japan, but more than 10% of the Japanese population is allergic to its pollen. We constructed a cDNA library derived from pollen grains of C. japonica and performed an analysis of expressed sequence tags (ESTs). We obtained partial sequences from 1929 clones, which represented 1365 unique transcripts. Among the unique transcr ...
DOI:
10.1093/treephys/26.12.1517
PubMed:
17169891

10. Anchoring of a large set of markers onto a BAC library for the development of a draft physical map of the grapevine genome

Author:
Lamoureux, D.; Bernole, A.; Le Clainche, I.; Tual, S.; Thareau, V.; Paillard, S.; Legeai, F.; Dossat, C.; Wincker, P.; Oswald, M.
Source:
Theoretical and applied genetics 2006 v.113 no.2 pp. 344-356
ISSN:
0040-5752
Subject:
microsatellite repeats; DNA libraries; bacterial artificial chromosomes; wine grapes; polymerase chain reaction; expressed sequence tags; clones; Vitis vinifera; wine cultivars; physical chromosome mapping; genetic markers
Abstract:
... Five hundred and six EST-derived markers, 313 SSR markers and 26 BAC end-derived or SCAR markers were anchored by PCR on a subset of a Cabernet Sauvignon BAC library representing six genome equivalents pooled in three dimensions. In parallel, the 12,351 EST clusters of the grapevine UniGene set (build #11) from NCBI were used to design 12,125 primers pairs and perform electronic PCR on 67,543 nonr ...
DOI:
10.1007/s00122-006-0301-7
PubMed:
16791700

11. Antigenic Variation of TprK V Regions Abrogates Specific Antibody Binding in Syphilis

Author:
LaFond, Rebecca E.; Molini, Barbara J.; Van Voorhis, Wesley C.; Lukehart, Sheila A.
Source:
Infection and immunity 2006 v.74 no.11 pp. 6244-6251
ISSN:
0019-9567
Subject:
Treponema pallidum; antibodies; antigenic variation; clones; cross reaction; genes; immunoassays; rabbits; synthetic peptides
Abstract:
... The tprK gene in the syphilis spirochete, Treponema pallidum subsp. pallidum, undergoes antigenic variation in seven variable (V) regions. tprK is highly variable within T. pallidum strains, and a method has been developed to derive clones of T. pallidum that express a single, unique tprK sequence. Rabbits were infected with three different T. pallidum clones or the parent strain from which the cl ...
DOI:
10.1128/IAI.00827-06
PubMed:
16923793
PubMed Central:
PMC1695500

12. Antioxidant capacity of crude extracts from clones of banana and plane species

Author:
Perez-Perez, E.M.; Rodriguez-Malaver, A.J.; Padilla, N.; Medina-Ramirez, G.; Davila, J.
Source:
Journal of medicinal food 2006 v.9 no.4 pp. 517-523
ISSN:
1096-620X
Subject:
hybrids; plantains (fruit); uric acid; free radicals; lipid peroxidation; plant extracts; hydroperoxides; clones; Musa acuminata; Musa balbisiana; oxidation; interspecific hybridization; superoxide anion; antioxidant activity; ultraviolet radiation; bananas
DOI:
10.1089/jmf.2006.9.517
PubMed:
17201639

13. Artificial induction of flowering in sugarcane under sub-tropical conditions — A successful approach

Author:
R. P. Srivastava; S. P. Singh; PRATAP Singh; S. B. Singh
Source:
Sugar tech 2006 v.8 no.2-3 pp. 184-186
ISSN:
0972-1525
Subject:
Saccharum spontaneum; adverse effects; clones; crossing; flowering; flowers; genotype; pollen; solar radiation; subtropics; sugarcane; temperature
Abstract:
... Four hours extra dark treatment in artificially made photoperiodic chamber induced early flowering in flowering clones i.e. S. 55/99, S. 187/91,S. 301/86, S. 116/2K.S. 73/89 after 12to 14th weeks. Maximum and minimum temperature ranged from 31.0 and 21.4°C respectively. Control plants of respective genotypes flowered generally after one month of the treated plants. Flowered genotypes in photoperio ...
DOI:
10.1007/BF02943658

14. Bacteria Associated with Mucus and Tissues of the Coral Oculina patagonica in Summer and Winter

Author:
Koren, Omry; Rosenberg, Eugene
Source:
Applied and environmental microbiology 2006 v.72 no.8 pp. 5254-5259
ISSN:
0099-2240
Subject:
DNA; Pseudomonas; Vibrio splendidus; agar; bacteria; bacterial communities; centrifugation; clones; corals; databases; genes; gold; mucus; nucleotide sequences; ribosomal RNA; summer; winter
Abstract:
... The relative abundance of bacteria in the mucus and crushed tissue of the Mediterranean coral Oculina patagonica was determined by analyses of the 16S rRNA genes of isolated colonies and from a 16S rRNA clone library of extracted DNA. By SYBR gold staining, the numbers of bacteria in mucus and tissue samples were 6.2 x 10⁷ and 8.3 x 10⁸/cm² of coral surface, respectively, 99.8% of which failed to ...
DOI:
10.1128/AEM.00554-06
PubMed:
16885273
PubMed Central:
PMC1538755

15. Biogeography and Landscape-Scale Diversity of the Dominant Crenarchaeota of Soil

Author:
Oline, David K.; Schmidt, Steven K.; Grant, Michael C.
Source:
Microbial ecology 2006 v.52 no.3 pp. 480-490
ISSN:
0095-3628
Subject:
Crenarchaeota; alpine tundra; biogeography; clones; nucleotide sequences; polymerase chain reaction; ribosomal DNA; soil; soil sampling; soil surveys; Rocky Mountain region
Abstract:
... We surveyed the diversity of soil Archaea across a large scale elevational gradient of ecosystem types, from foothills forest to alpine tundra in the Front Range of the Rocky Mountains. We used a dilution technique to sequence the single most abundant archaeal 16S rDNA sequence in each of the 40 soil cores distributed across the gradient to compare our results to those of typical 16S clone library ...
DOI:
10.1007/s00248-006-9101-5
PubMed:
16909343

16. Carbon Isotope Discrimination, Gas Exchange and Stem Growth of Four Euramerican Hybrid Poplars under Different Watering Regimes

Author:
Voltas, J.; Serrano, L.; Hernandez, M.; Peman, J.
Source:
New forests 2006 v.31 no.3 pp. 435-451
ISSN:
0169-4286
Subject:
gas exchange; drought; carbon; seasonal variation; carbon dioxide; hybrids; stomatal conductance; stems; isotopes; dry matter accumulation; clones; water stress; photosynthesis; Populus; forest trees; net assimilation rate; tree growth; water use efficiency; flood irrigation; genetic variation; Spain
Abstract:
... Seasonal changes in carbon isotope discrimination (Δ) and gas exchange traits were assessed in four Populusxeuramericana clones differing in growth potential. Measurements were made during the second year after establishment in the field under two watering regimes, which were defined by the time-span between flood irrigations, hence resulting in different dry-down cycles: high irrigation (conserva ...
DOI:
10.1007/s11056-005-0879-7

17. Carotenoid Cleavage Dioxygenase (CmCCD4a) Contributes to White Color Formation in Chrysanthemum Petals

Author:
Ohmiya, Akemi; Kishimoto, Sanae; Aida, Ryutaro; Yoshioka, Satoshi; Sumitomo, Katsuhiko
Source:
Plant physiology 2006 v.142 no.3 pp. 1193-1201
ISSN:
0032-0889
Subject:
Chrysanthemum morifolium; RNA interference; amino acid sequences; carotenoids; clones; color; corolla; cultivars; gene expression; leaves; roots; sequence homology; stems
Abstract:
... The white petals of chrysanthemum (Chrysanthemum morifolium Ramat.) are believed to contain a factor that inhibits the accumulation of carotenoids. To find this factor, we performed polymerase chain reaction-Select subtraction screening and obtained a clone expressed differentially in white and yellow petals. The deduced amino acid sequence of the protein (designated CmCCD4a) encoded by the clone ...
DOI:
10.1104/pp.106.087130
PubMed:
16980560
PubMed Central:
PMC1630759

18. Characterization of Monoclonal Antibodies Against Fowl Adenovirus Serotype 1 (FAV1) Isolated from Gizzard Erosion

Author:
Taharaguchi, S.; Ito, H.; Ohta, H.; Takase, K.
Source:
Avian diseases 2006 v.50 no.3 pp. 331-335
ISSN:
0005-2086
Subject:
Fowl aviadenovirus A; chickens; hybridomas; disease detection; lesions (animal); gizzard; serodiagnosis; viral diseases of animals and humans; serotypes; poultry diseases; tissue analysis; clones; pathogen identification; enzyme-linked immunosorbent assay; monoclonal antibodies; viral proteins
Abstract:
... Six clones of monoclonal antibodies (Mabs) to fowl adenovirus (FAV) serotype 1 were produced. All Mabs reacted positively by enzyme-linked immunosorbent assay. Three Mabs recognized the putative 100-kD hexon protein and reacted to serotype 1 specifically by western blot analysis but did not react to other FAV serotypes (2, 3, 4, 5, 6, 7, and 8a). These Mabs will be useful for immunodiagnosis of FA ...
DOI:
10.1637/7460-102605R.1
PubMed:
17039830

19. Characterization, Distribution, and Expression of Novel Genes among Eight Clinical Isolates of Streptococcus pneumoniae

Author:
Shen, Kai; Gladitz, John; Antalis, Patricia; Dice, Bethany; Janto, Benjamin; Keefe, Randy; Hayes, Jay; Ahmed, Azad; Dopico, Richard; Ehrlich, Nathan; Jocz, Jennifer; Kropp, Laura; Yu, Shujun; Nistico, Laura; Greenberg, David P.; Barbadora, Karen; Preston, Robert A.; Post, J. Christopher; Ehrlich, Garth D.; Hu, Fen Z.
Source:
Infection and immunity 2006 v.74 no.1 pp. 321-330
ISSN:
0019-9567
Subject:
RNA-directed DNA polymerase; Streptococcus pneumoniae; clones; genes; genomics; open reading frames; polymerase chain reaction; proteins; serotypes; virulence
Abstract:
... Eightlow-passage-number Streptococcus pneumoniae clinical isolates,each of a different serotype and a different multilocus sequence type,were obtained from pediatric participants in a pneumococcal vaccinetrial. Comparative genomic analyses were performed with these strainsand two S. pneumoniae reference strains. Individual genomiclibraries were constructed for each of the eight clinical isolates,w ...
DOI:
10.1128/IAI.74.1.321-330.2006
PubMed:
16368987
PubMed Central:
PMC1346598

20. Chromosome-shuffling technique for selected chromosomal segments in Saccharomyces cerevisiae

Author:
Minetaka Sugiyama; Eishi Yamamoto; Yukio Mukai; Yoshinobu Kaneko; Masafumi Nishizawa; Satoshi Harashima
Source:
Applied microbiology and biotechnology 2006 v.72 no.5 pp. 947-952
ISSN:
0175-7598
Subject:
Saccharomyces cerevisiae; Southern blotting; chromosomes; clones; diploidy; engineering; gene dosage; hybrids; prediction; quantitative analysis
Abstract:
... We describe a novel chromosome engineering technique for shuffling selected regions of chromosomes from two strains in Saccharomyces cerevisiae: The technique starts with the construction of MATa and MATα strains in which a particular chromosome is split at exactly the same site in both strains such that the split chromosomes generated are marked with different markers. The two strains are then cr ...
DOI:
10.1007/s00253-006-0342-5
PubMed:
16505990

21. Clonal Adaptive Radiation in a Constant Environment

Author:
Maharjan, Ram; Seeto, Shona; Notley-McRobb, Lucinda; Ferenci, Thomas
Source:
Science 2006 v.313 no.5786 pp. 514-517
ISSN:
0036-8075
Subject:
Escherichia coli; adaptive radiation; biodiversity; clones; ecological competition; ecotypes; ingredients; new combination; permeability; phenotype
Abstract:
... The evolution of new combinations of bacterial properties contributes to biodiversity and the emergence of new diseases. We investigated the capacity for bacterial divergence with a chemostat culture of Escherichia coli. A clonal population radiated into more than five phenotypic clusters within 26 days, with multiple variations in global regulation, metabolic strategies, surface properties, and n ...
DOI:
10.1126/science.1129865

22. Clonal Dissemination of Escherichia coli O157:H7 Subtypes among Dairy Farms in Northeast Ohio

Author:
Wetzel, Amy N.; LeJeune, Jeffrey T.
Source:
Applied and environmental microbiology 2006 v.72 no.4 pp. 2621-2626
ISSN:
0099-2240
Subject:
water pollution; cattle diseases; litter (bedding); restriction mapping; epidemiology; geographical variation; dairy cattle; feces; clones; wild birds; dairy farming; water troughs; Escherichia coli O157; drinking water; Escherichia infections; Ohio
Abstract:
... To ascertain the extent to which indistinguishable strains of Escherichia coli O157:H7 are shared between farms, molecular characterization was performed on E. coli O157:H7 isolates recovered during a longitudinal study of 20 dairy farms in northeast Ohio. Of the 20 dairy farms sampled, 16 were located in a primary area and 4 were located in two other distant geographical areas. A total of 92 E. c ...
DOI:
10.1128/AEM.72.4.2621-2626.2006
PubMed:
16597966
PubMed Central:
PMC1449053

23. Clonal cultures of Histomonas meleagridis, Tetratrichomonas gallinarum and a Blastocystis sp. established through micromanipulation

Author:
Hess, M.; Kolbe, T.; Grabensteiner, E.; Prosl, H.
Source:
Parasitology 2006 v.133 no.5 pp. 547-554
ISSN:
0031-1820
Subject:
cell culture; turkeys; Histomonas meleagridis; cecum; ribosomal DNA; Blastocystis; clones; pathogen identification; protozoal infections; nucleotide sequences; Tetratrichomonas; ultrastructure
DOI:
10.1017/S0031182006000758

24. Clonal propagation of an important medicinal tree Crataeva nurvala through enhanced axillary branching

Author:
Shirin, F.; Maravi, S.
Source:
Journal of herbs, spices & medicinal plants 2006 v.12 no.1-2 pp. 165-174
ISSN:
1049-6475
Subject:
Capparaceae; medicinal plants; clones; vegetative propagation; branching; callus culture; Ayurvedic medicine; trees; explants; stem nodes; benzyladenine; culture media; kinetin; callus formation; plantlets; shoots
DOI:
10.1300/J044v12n01_15

25. Clonal structure of invasive hoary cress (Lepidium draba) infestations

Author:
Gaskin John F.
Source:
Weed science 2006 v.54 no.3 pp. 428-434
ISSN:
0043-1745
Subject:
Lepidium draba; broadleaf weeds; perennials; invasive species; population genetics; spatial distribution; seedlings; rhizomes; genetic markers; amplified fragment length polymorphism; clones; vegetative propagation; biological control; seed productivity; Utah; South Dakota
Abstract:
... Hoary cress is a perennial herbaceous weed that has invaded agricultural and natural areas of western North America. Invasions are often composed of dense patches, and it is unclear whether clonal growth via lateral rhizomes or seedling recruitment is the dominant method of patch expansion. To study the clonal structure of this invasive, six patches from three USA populations (194 ramets) were ana ...
Handle:
10113/43424
DOI:
10.1614/WS-05-138R.1

26. Clonal variation in stomatal characteristics related to biomass production of 12 poplar (Populus) clones in a short rotation coppice culture

Author:
Al Afas, N.; Marron, N.; Ceulemans, R.
Source:
Environmental and experimental botany 2006 v.58 no.1-3 pp. 279-286
ISSN:
0098-8472
Subject:
interspecific variation; hybrids; forest trees; canopy; coppicing; interspecific hybridization; genetic variation; dry matter accumulation; clones; plant density; length; forest plantations; Populus; stomata
Abstract:
... Twelve poplar (Populus) clones, belonging to different species and interspecific hybrids, were studied during the third growing season of the second rotation of a high density coppice culture. Stomatal characteristics, as stomatal density and stomatal length, were examined for fully expanded leaves from all clones and at two canopy positions (upper and lower canopy). Above-ground biomass productio ...
DOI:
10.1016/j.envexpbot.2005.09.003

27. Cloning, Expression, and Characterization of Aminopeptidase P from the Hyperthermophilic Archaeon Thermococcus sp. Strain NA1

Author:
Lee, Hyun Sook; Kim, Yun Jae; Bae, Seung Seob; Jeon, Jeong Ho; Lim, Jae Kyu; Jeong, Byeong Chul; Kang, Sung Gyun; Lee, Jung-Hyun
Source:
Applied and environmental microbiology 2006 v.72 no.3 pp. 1886-1890
ISSN:
0099-2240
Subject:
Escherichia coli; Nematoda; Thermococcus; amino acids; catalytic activity; clones; enzymes; genomics; half life; metals; molecular weight; open reading frames; pH; proteins; sequence analysis; temperature
Abstract:
... Genomic analysis of a hyperthermophilic archaeon, Thermococcus sp. strain NA1, revealed the presence of a 1,068-bp open reading frame encoding a protein consisting of 356 amino acids with a calculated molecular mass of 39,714 Da (GenBank accession no. DQ144132). Sequence analysis showed that it was similar to the putative aminopeptidase P (APP) of Thermococcus kodakaraensis KOD1. Amino acid residu ...
DOI:
10.1128/AEM.72.3.1886-1890.2006
PubMed:
16517635
PubMed Central:
PMC1393192

28. Cloning, characterization and localization of three novel class III peroxidases in lignifying xylem of Norway spruce (Picea abies)

Author:
Marjamaa, K.; Hilden, K.; Kukkola, E.; Lehtonen, M.; Holkeri, H.; Haapaniemi, P.; Koutaniemi, S.; Teeri, T.H.; Fagerstedt, K.; Lundell, T.
Source:
Plant molecular biology 2006 v.61 no.4-5 pp. 719-732
ISSN:
0167-4412
Subject:
secretion; seedlings; phylogeny; lignification; trees; genes; roots; endoplasmic reticulum; tracheids; cell walls; Picea abies; clones; amino acids; signal peptide; peroxidase; in situ hybridization; messenger RNA; complementary DNA; lignin; tobacco; protoplasts; green fluorescent protein; Catharanthus roseus; growth rings
Abstract:
... Plant class III peroxidases (POXs) take part in the formation of lignin and maturation of plant cell walls. However, only a few examples of such peroxidases from gymnosperm tree species with highly lignified xylem tracheids have been implicated so far. We report here cDNA cloning of three xylem-expressed class III peroxidase encoding genes from Norway spruce (Picea abies). The translated proteins, ...
DOI:
10.1007/s11103-006-0043-6

29. Cloning, genetic and physical mapping of resistance gene analogs in barley (Hordeum vulgare L.)

Author:
Mammadov, J.A.; Liu, Z.; Biyashev, R.M.; Muehlbauer, G.J.; Saghai Maroof, M.A.
Source:
Plant breeding 2006 v.125 no.1 pp. 32-42
ISSN:
0179-9541
Subject:
restriction fragment length polymorphism; barley; bacterial artificial chromosomes; Hordeum vulgare; genomic libraries; polymerase chain reaction; expressed sequence tags; clones; disease resistance; physical chromosome mapping; genetic markers; plant proteins
Abstract:
... The majority of verified plant disease resistance genes isolated to date belong to the NBS-LRR class, encoding proteins with a predicted nucleotide binding site (NBS) and a leucine-rich repeat (LRR) region. Using degenerate primers, designed from the conserved motifs of the NBS region in tobacco N and Arabidopsis RPS2 genes, we isolated 190 resistance gene analogs (RGA) clones from barley genomic ...
DOI:
10.1111/j.1439-0523.2006.01166.x

30. Combining ability for disease resistance, yield, and horticultural traits of cacao (Theobroma cacao L.) clones

Author:
Cervantes-Martinez, C.; Brown, J.S.; Schnell, R.J.; Phillips-Mora, W.; Takrama, J.F.; Motamayor, J.C.
Source:
Journal of the American Society for Horticultural Science 2006 v.131 no.2 pp. 231-241
ISSN:
0003-1062
Subject:
quantitative trait loci; marker-assisted selection; fungal diseases of plants; hybridization; Theobroma cacao; clones; agronomic traits; plant rots; Phytophthora palmivora; crop yield; disease resistance; pods; general combining ability; specific combining ability; cultivar identification; Moniliophthora roreri; Costa Rica
Abstract:
... Knowledge of genetic differences among commonly cultivated cacao clones, as well as the type of gene action involved for disease resistance, yield, quality, and horticultural traits, are essential for cacao breeders to select parental clones efficiently and effectively. This information is also critical for quantitative geneticists in designing and improving quantitative trait loci (QTL) localizat ...
Handle:
10113/21524

31. Community structure and function in a H2-based membrane biofilm reactor capable of bioreduction of selenate and chromate

Author:
Jinwook Chung; Hodon Ryu; Morteza Abbaszadegan; Bruce E. Rittmann
Source:
Applied microbiology and biotechnology 2006 v.72 no.6 pp. 1330-1339
ISSN:
0175-7598
Subject:
Dechloromonas; bacteria; biofilm; chromium; clones; community structure; energy-dispersive X-ray analysis; functional diversity; pollutants; scanning electron microscopy; selenium
Abstract:
... Two different H₂-based, denitrifying membrane-biofilm reactors (MBfRs) initially reduced Se(VI) or Cr(VI) stably to Se⁰ or Cr(III). When the oxidized contaminants in the influent were switched, each new oxidized contaminant was reduced immediately, and its reduction soon was approximately the same or greater than it had been in its original MBfR. The precipitation of reduced selenium and chromium ...
DOI:
10.1007/s00253-006-0439-x

32. Comparative genomic analysis links karyotypic evolution with genomic evolution in the Indian Muntjac (Muntiacus muntjak vaginalis)

Author:
Zhou, Qi; Huang, Ling; Zhang, Jianguo; Zhao, Xiangyi; Zhang, Qingpeng; Song, Fei; Chi, Jianxiang; Yang, Fengtang; Wang, Wen
Source:
Chromosoma 2006 v.115 no.6 pp. 427-436
ISSN:
0009-5915
Subject:
sequence analysis; karyotyping; bacterial artificial chromosomes; humans; evolution; dogs; clones; mice; genomics; introns; Muntiacus
Abstract:
... The karyotype of Indian muntjacs (Muntiacus muntjak vaginalis) has been greatly shaped by chromosomal fusion, which leads to its lowest diploid number among the extant known mammals. We present, here, comparative results based on draft sequences of 37 bacterial artificial clones (BAC) clones selected by chromosome painting for this special muntjac species. Sequence comparison on these BAC clones u ...
DOI:
10.1007/s00412-006-0066-4
PubMed:
16791631

33. Comparison of the chicken and zebra finch Z chromosomes shows evolutionary rearrangements

Author:
Itoh, Yuichiro; Kampf, Kathy; Arnold, Arthur P.
Source:
Chromosome research 2006 v.14 no.8 pp. 805-815
ISSN:
0967-3849
Subject:
DNA; Taeniopygia guttata; W chromosome; Z chromosome; bacterial artificial chromosomes; chickens; clones; fluorescence in situ hybridization; genes; repetitive sequences
Abstract:
... Using fluorescent in-situ hybridization (FISH) of zebra finch (Taeniopygia guttata) bacterial artificial chromosome (BAC) clones, we determined the chromosomal localizations of 14 zebra finch genes that are Z-linked in chickens: ATP5A1, CHD1, NR2F1, DMRT1, PAM, GHR, HSD17B4, NIPBL, ACO1, HINT1, SMAD2, SPIN, NTRK2 and UBE2R2. All 14 genes also map to the zebra finch Z chromosome, indicating substan ...
DOI:
10.1007/s10577-006-1082-1
PubMed:
17139532

34. Complete assignment of the chromosomes of Gossypium hirsutum L. by translocation and fluorescence in situ hybridization mapping

Author:
Wang, K.; Song, X.; Han, Z.; Guo, W.; Yu, J.Z.; Sun, J.; Pan, J.; Kohel, R.J.; Zhang, T.
Source:
Theoretical and applied genetics 2006 v.113 no.1 pp. 73-80
ISSN:
0040-5752
Subject:
cotton; fluorescence in situ hybridization; DNA libraries; bacterial artificial chromosomes; Gossypium hirsutum; linkage groups; DNA probes; clones; chromosome translocation; physical chromosome mapping
Abstract:
... Significant progress has been made in the construction of genetic maps in the tetraploid cotton Gossypium hirsutum. However, six linkage groups (LGs) have still not been assigned to specific chromosomes, which is a hindrance for integrated genetic map construction. In the present research, specific bacterial artificial chromosome (BAC) clones constructed in G. hirsutum acc. TM-1 for these six LGs ...
Handle:
10113/5999
DOI:
10.1007/s00122-006-0273-7
PubMed:
16609860

35. Conservation ofSaccharum spontaneum as defuzzed true seed

Author:
N. Rajendra Prasad; N. Balasundaram
Source:
Sugar tech 2006 v.8 no.2-3 pp. 112-115
ISSN:
0972-1525
Subject:
breeding programs; clones; cold; cold storage; germination; germplasm; storage temperature; sugarcane; true seeds; viability
Abstract:
... Storing true seed (fluff) of sugarcane germplasm at low temperatures for preserving its germinability was highlighted as an alternative or complementary method for their maintenance and further utilisation in a Sugarcane Breeding Programme. The viability of defuzzed true seed collected from 50Saccharum spontaneum clones stored at -20°C temperature for five years was investigated .The germination p ...
DOI:
10.1007/BF02943643

36. Construction of BAC and BIBAC libraries from sunflower and identification of linkage group-specific clones by overgo hybridization

Author:
Feng, J.; Vick, B.A.; Lee, M.K.; Zhang, H.B.; Jan, C.C.
Source:
Theoretical and applied genetics 2006 v.113 no.1 pp. 23-32
ISSN:
0040-5752
Subject:
Helianthus annuus; DNA libraries; bacterial artificial chromosomes; linkage groups; clones; nucleic acid hybridization; genetic markers; restriction fragment length polymorphism
Abstract:
... Complementary BAC and BIBAC libraries were constructed from nuclear DNA of sunflower cultivar HA 89. The BAC library, constructed with BamHI in the pECBAC1 vector, contains 107,136 clones and has an average insert size of 140 kb. The BIBAC library was constructed with HindIII in the plant-transformation-competent binary vector pCLD04541 and contains 84,864 clones, with an average insert size of 13 ...
Handle:
10113/5997
DOI:
10.1007/s00122-006-0265-7
PubMed:
16612648

37. Construction of a highly enriched marsupial Y chromosome-specific BAC sub-library using isolated Y chromosomes

Author:
N. Sankovic; M. L. Delbridge; F. Grützner; M. A. Ferguson-Smith; P. C. M. O’Brien; J. A. Marshall Graves
Source:
Chromosome research 2006 v.14 no.6 pp. 657-664
ISSN:
0967-3849
Subject:
DNA; Macropus eugenii; Pan troglodytes; Y chromosome; bacterial artificial chromosomes; clones; genome; humans
Abstract:
... The Y chromosome is perhaps the most interesting element of the mammalian genome but comparative analysis of the Y chromosome has been impeded by the difficulty of assembling a shotgun sequence of the Y. BAC-based sequencing has been successful for the human and chimpanzee Y but is difficult to do efficiently for an atypical mammalian model species (Skaletsky et al. 2003, Kuroki et al. 2006). We s ...
DOI:
10.1007/s10577-006-1076-z
PubMed:
16964572

38. Construction of a large phage display antibody library by in vitro package and in vivo recombination

Author:
Xiaodong Cen; Qun Bi; Shenggeng Zhu
Source:
Applied microbiology and biotechnology 2006 v.71 no.5 pp. 767-772
ISSN:
0175-7598
Subject:
DNA; antibodies; clones; peptide libraries; phages; recombinases; sequence diversity; virus assembly
Abstract:
... Capacity and diversity are extremely important to the quality of various phage display libraries. In this work, λ phage-based in vitro package was applied to construct a filamentous phage display antibody library so as to enlarge its capacity and introduce more sequence diversity in the final library. In vivo recombination via Cre recombinase/lox sites was also exploited to create VH/VL combinatio ...
DOI:
10.1007/s00253-006-0334-5

39. Construction of an infectious cDNA clone of Ribgrass mosaic virus Shanghai isolate and its modification to express an epitope of Mycobacterium tuberculosis

Author:
Zhu, H. Q.; Chen, J. P.; Yu, S. Q.
Source:
Archives of virology 2006 v.151 no.9 pp. 1853-1861
ISSN:
0304-8608
Subject:
Mycobacterium tuberculosis; Nicotiana glutinosa; Ribgrass mosaic virus; Western blotting; clones; complementary DNA; electron microscopes; genes; messenger RNA; polymerase chain reaction
Abstract:
... Infectious cDNA clones of the Shanghai isolate of Ribgrass mosaic virus (RMV) were produced by joining four overlapping cDNA fragments and also in a single step by long template PCR. After inoculation of Nicotiana glutinosa with either RNA transcripts or the cDNA under the control of the CaMV 35S promoter, plants developed typical symptoms, and viral coat protein could be detected in them by Weste ...
DOI:
10.1007/s00705-006-0740-0
PubMed:
16596330

40. Correlation between clonal means and open-pollinated seedling progeny means and its implications for radiata pine breeding strategy

Author:
Kumar, S.
Source:
Canadian journal of forest research = 2006 v.36 no.8 pp. 1968-1975
ISSN:
0045-5067
Subject:
tree breeding; Pinus radiata; genetic improvement; open pollination; genetic correlation; recurrent selection; clones; genotype; progeny testing; heritability; New Zealand
Abstract:
... Open-pollinated (OP) offspring of individual genotypes are commonly used for estimating their breeding values in recurrent selection programmes. Alternatively, vegetative propagules of individual genotypes could also be used to evaluate their relative performance. However, the mean for the vegetative propagules of a genotype represents an estimate of its total genotypic value, and it may or may no ...
DOI:
10.1139/x06-082

41. Culture Isolation and Culture-Independent Clone Libraries Reveal New Marine Synechococcus Ecotypes with Distinctive Light and N Physiologies

Author:
Ahlgren, Nathan A.; Rocap, Gabrielle
Source:
Applied and environmental microbiology 2006 v.72 no.11 pp. 7193-7204
ISSN:
0099-2240
Subject:
ribosomal RNA; microbial communities; ecotypes; nitrogen; physiology; nitrate nitrogen; clones; nitrates; Prochlorococcus; nitrites; Synechococcus; Sargasso Sea
Abstract:
... Marine microbial communities often contain multiple closely related phylogenetic clades, but in many cases, it is still unclear what physiological traits differentiate these putative ecotypes. The numerically abundant marine cyanobacterium Synechococcus can be divided into at least 14 clades. In order to better understand ecotype differentiation in this genus, we assessed the diversity of a Synech ...
DOI:
10.1128/AEM.00358-06
PubMed:
16936060
PubMed Central:
PMC1636174

42. Cytological and Other Aspects of Pathogenesis-related Gene Expression in Tomato Plants Grown on a Suppressive Compost

Author:
KAVROULAKIS, NEKTARIOS; PAPADOPOULOU, KALLIOPE K.; NTOUGIAS, SPYRIDON; ZERVAKIS, GEORGIOS I.; EHALIOTIS, CONSTANTINOS
Source:
Annals of botany 2006 v.98 no.3 pp. 555-564
ISSN:
0305-7364
Subject:
Solanum lycopersicum; clones; complementary DNA; composts; gene expression; gene expression regulation; genes; in situ hybridization; pathogens; peat; phloem; proteins; root systems; roots; stele; stems; systemic acquired resistance; tomatoes
Abstract:
... BACKGROUND: and Aims Recent studies have shown that certain composts may trigger indirect defence mechanisms by sensitizing the plant to create an increased state of resistance, similar to systemic acquired resistance. In this study, the capacity of a disease-suppressive compost to alter the expression pattern of certain pathogenesis-related (PR) genes in the root system of tomato plants (Solanum ...
DOI:
10.1093/aob/mcl149
PubMed:
16877456
PubMed Central:
PMC2803568

43. DAXX interacts with phage ΦC31 integrase and inhibits recombination

Author:
Chen, Jin-zhong; Ji, Chao-neng; Xu, Guan-lan; Pang, Rong-yan; Yao, Ji-hua; Zhu, Huan-zhang; Xue, Jing-lun; Jia, William
Source:
Nucleic acids research 2006 v.34 no.21 pp. 6298-6304
ISSN:
0305-1048
Subject:
RNA; bacteriophages; baits; brain; cDNA libraries; clones; complementary DNA; genes; humans; hybridization; precipitin tests; proteins
Abstract:
... Phage ΦC31 integrase has potential as a means of inserting therapeutic genes into specific sites in the human genome. However, the possible interactions between ΦC31 integrase and cellular proteins have never been investigated. Using pLexA-ΦC31 integrase as bait, we screened a pB42AD-human fetal brain cDNA library for potential interacting cellular proteins. Among 61 positives isolated from 10⁶ in ...
DOI:
10.1093/nar/gkl890
PubMed:
17098929
PubMed Central:
PMC1669754

44. DBTSS: DataBase of Human Transcription Start Sites, progress report 2006

Author:
Yamashita, Riu; Suzuki, Yutaka; Wakaguri, Hiroyuki; Tsuritani, Katsuki; Nakai, Kenta; Sugano, Sumio
Source:
Nucleic acids research 2006 v.34 pp. D86
ISSN:
0305-1048
Subject:
Danio rerio; Rhodophyta; clones; databases; genes; humans; malaria; mice; models; nucleic acids; sequence analysis
Abstract:
... DBTSS was first constructed in 2002 based on precise, experimentally determined 5' end clones. Several major updates and additions have been made since the last report. First, the number of human clones has drastically increased, going from 190 964 to 1 359 000. Second, information about potential alternative promoters is presented because the number of 5' end clones is now sufficient to determine ...

45. Detection and distribution of probiotic Escherichia coli Nissle 1917 clones in swine herds in Germany

Author:
Kleta, S.; Steinrück, H.; Breves, G.; Duncker, S.; Laturnus, C.; Wieler, L.H.; Schierack, P.
Source:
Journal of applied microbiology 2006 v.101 no.6 pp. 1357-1366
ISSN:
1364-5072
Subject:
intestinal microorganisms; herds; epithelial cells; Salmonella Typhimurium; bacterial adhesion; farms; models; clones; polymerase chain reaction; probiotics; pulsed-field gel electrophoresis; wild boars; screening; piglets; Escherichia coli; Germany
Abstract:
... To verify the presence of Escherichia coli Nissle 1917 as a natural isolate in swine and to characterize in vitro probiotic properties as well as in vivo persistence in a feeding experiment. During studies on the intestinal microflora of pigs, we isolated E. coli Nissle 1917 sporadically from a pig population over a period of 1 year. The identity of the isolates as E. coli Nissle 1917 was verified ...
DOI:
10.1111/j.1365-2672.2006.03019.x

46. Determination of genetic stability in long-term somatic embryogenic cultures and derived plantlets of cork oak using microsatellite markers

Author:
Lopes, T.; Pinto, G.; Loureiro, J.; Costa, A.; Santos, C.
Source:
Tree physiology 2006 v.26 no.9 pp. 1145-1152
ISSN:
0829-318X
Subject:
micropropagation; DNA fingerprinting; 2,4-D; callus; genetic markers; microsatellite repeats; dose response; explants; clones; Quercus suber; in vitro regeneration; leaves; somatic embryos; forest trees; culture media; zeatin; genetic stability; somatic embryogenesis; genetic variation; Portugal
Abstract:
... Microsatellites were used to test genetic stability in somatic embryos (SE) of Quercus suber L. The SE were obtained by a simple somatic embryogenesis protocol: leaf explants from two adult plants (QsG0, QsG5) and from two juvenile plants (QsGM1, QsGM2) were inoculated on Murashige and Skoog (MS) medium with 2,4-dichlorophenoxyacetic acid and zeatin. Calluses with primary embryogenic structures we ...
DOI:
10.1093/treephys/26.9.1145
PubMed:
16740490

47. Development and Characterization of Stable Sediment-Free Anaerobic Bacterial Enrichment Cultures That Dechlorinate Aroclor 1260

Author:
Bedard, Donna L.; Bailey, Jessica J.; Reiss, Brandon L.; Van Slyke Jerzak, Greta
Source:
Applied and environmental microbiology 2006 v.72 no.4 pp. 2460-2470
ISSN:
0099-2240
Subject:
delta-Proteobacteria; acetates; gases; ribosomal RNA; polychlorinated biphenyls; beta-Proteobacteria; major genes; sediments; DNA; clones; remediation; dechlorination; Clostridiales; restriction fragment length polymorphism; butyrates; chlorine; detectors; enrichment culture; Pseudomonas; rivers; Dehalococcoidales; slurries
Abstract:
... We have developed sediment-free anaerobic enrichment cultures that dechlorinate a broad spectrum of highly chlorinated polychlorinated biphenyls (PCBs). The cultures were developed from Aroclor 1260-contaminated sediment from the Housatonic River in Lenox, MA. Sediment slurries were primed with 2,6-dibromobiphenyl to stimulate Process N dechlorination (primarily meta dechlorination), and sediment ...
DOI:
10.1128/AEM.72.4.2460-2470.2006
PubMed:
16597944
PubMed Central:
PMC1448987

48. Development of SSR markers located in the G1 linkage group of apricot (Prunus armeniaca L.) using a bacterial artificial chromosome library

Author:
VILANOVA, S.; SORIANO, J.M.; LALLI, D.A.; ROMERO, C.; ABBOTT, A.G.; LLÁCER, G.; BADENES, M.L.
Source:
Molecular ecology notes 2006 v.6 no.3 pp. 789-791
ISSN:
1471-8278
Subject:
Prunus armeniaca; apricots; bacterial artificial chromosomes; clones; genome; linkage groups; microsatellite repeats; restriction fragment length polymorphism
Abstract:
... Sixteen simple sequence repeats (SSRs) of apricot (Prunus armeniaca L.) were isolated from a bacterial artificial chromosome (BAC) library. Twelve restriction fragment length polymorphism (RFLP) probes mapped on LG1 of the Prunus general map were hybridized to the BAC library in order to select clones belonging to G1 linkage group of apricot. Selected BACs were digested, subcloned and hybridized w ...
DOI:
10.1111/j.1471-8286.2006.01346.x

49. Development of a Dinoflagellate-Oriented PCR Primer Set Leads to Detection of Picoplanktonic Dinoflagellates from Long Island Sound

Author:
Lin, Senjie; Zhang, Huan; Hou, Yubo; Miranda, Lilibeth; Bhattacharya, Debashish
Source:
Applied and environmental microbiology 2006 v.72 no.8 pp. 5626-5630
ISSN:
0099-2240
Subject:
DNA; DNA primers; Dinophyceae; clones; ecosystems; genes; islands; polymerase chain reaction; ribosomal RNA
Abstract:
... We developed dinoflagellate-specific 18S rRNA gene primers. PCR amplification using these oligonucleotides for a picoplanktonic DNA sample from Long Island Sound yielded 24 clones, and all but one of these clones were dinoflagellates primarily belonging to undescribed and Amoebophrya-like lineages. These results highlight the need for a systematic investigation of picodinoflagellate diversity in b ...
DOI:
10.1128/AEM.00586-06
PubMed:
16885319
PubMed Central:
PMC1538694

50. Development of a rapid strain differentiation method for methicillin-resistant Staphylococcus aureus isolated in Japan by detecting phage-derived open-reading frames

Author:
Suzuki, M.; Tawada, Y.; Kato, M.; Hori, H.; Mamiya, N.; Hayashi, Y.; Nakano, M.; Fukushima, R.; Katai, A.; Tanaka, T.; Hata, M.; Matsumoto, M.; Takahashi, M.; Sakae, K.
Source:
Journal of applied microbiology 2006 v.101 no.4 pp. 938-947
ISSN:
1364-5072
Subject:
Staphylococcus aureus; antibiotic resistance; bacteriophages; chromosomes; clones; genomic islands; genotyping; hospitals; methicillin; open reading frames; pandemic; pulsed-field gel electrophoresis; Japan
Abstract:
... To develop a rapid genotyping method for investigating outbreaks of methicillin-resistant strains of Staphylococcus aureus (MRSA) isolated in Japan. Isolates were genotyped by detecting the keeping pattern of 16 open-reading frames (ORFs), a process we call phage ORF typing (POT). Thirteen of the ORFs were selected from phage genomes and one from a genomic island SaGIm in the genome of strain Mu50 ...
DOI:
10.1111/j.1365-2672.2006.02932.x