bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of microsatellite sequences in Vitis riparia and their applicability for genotyping of different Vitis species
Authors: Sefc Kristina M , Regner Ferdinand , Turetschek Eva , Glössl Josef , Steinkellner Herta
Published: April 2011

A Vitis riparia genomic library was screened for the presence of (GA)n simple sequence repeats (SSR) and 18 primer pairs yielding amplification products of the expected size were designed. Heterologous amplification with the primer pairs in related species (V. rupestris, V. berlandieri, V. labrusca, V. cinerea, V. aestivalis, V. vinifera, and interspecific hybrids) was successful in most primer-species combinations. Therefore, the new markers are applicable to the genotyping of a range of Vitis species. Variations in the SSR flanking sequence were detected between and within the species. The degree of polymorphism and performance of the markers were determined in up to 120 individuals of V. vinifera. Four of fifteen alleles per locus were detected and expected heterozygosity ranged between 0.37 and 0.88. Null alleles were shown to be present at two loci by a lack of heterozygous individuals and by transmission of the null alleles in a controlled cross. Regular Mendelian inheritance is indicated for all but one loci by a preliminary segregation analysis in 36 offspring. Thirteen of the markers were found suitable for the genotyping of grapevines (V. vinifera).Key words: microsatellites, simple sequence repeats, Vitis.
Isolation and characterization of polymorphic microsatellites in Cocos nucifera L.
Authors: Rivera R , Edwards K J , Barker JHA , Arnold G M , Ayad G , Hodgkin T , Karp A
Published: April 2011

Microsatellites or simple sequence repeats (SSRs) were isolated from coconut (Cocos nucifera) and tested for polymorphism on restricted germplasm. Sequencing of 197 clones from a cv. Tagnanan Tall-enriched genomic library showed that 75% contained a microsatellite, of which 64% were dinucleotide (GA/CT, CA/GT and GC/CG), 6% were trinucleotide, and 30% were compound repeats. Of 41 primer pairs tested on Tagnanan Tall genomic DNA, 38 gave the expected size product, two amplified two loci, and another gave a multilocus pattern. On 20 coconut samples, the 38 SSRs detected 198 alleles (average: 5.2 alleles per microsatellite). Genetic diversity (D = 1 - Sigma pi2) values ranged from 0.141 to 0.809. Heterozygotes were present at high frequencies among some dwarf samples. Analysis of similarity matrices based either on shared alleles at each locus (simple matching coefficient) or on allele bands across all loci (Jaccard coefficient) showed similar results. Dwarfs grouped separately from talls and showed less genetic diversity. In a wider test on 40 samples, 8 SSRs detected 64 alleles (average: eight alleles per microsatellite). These results indicate the high potential of microsatellites to detect genetic diversity in coconut germplasm.Key words: molecular markers, microsatellite, SSR, Cocos nucifera, coconut.
Nuclear DNA diversity, population differentiation, and phylogenetic relationships in the California closed-cone pines based on RAPD and allozyme markers
Authors: Wu J , Krutovskii K V , Strauss S H
Published: April 2011

We studied nuclear gene diversity and population differentiation using 91-98 randomly amplified polymorphic DNA (RAPD) loci in the California closed-cone pines knobcone (Pinus attenuata Lemm.), bishop (P. muricata D. Don), and Monterey (P. radiata D. Don) pines. A total of 384 trees from 13 populations were analyzed for RAPDs and another sample of 242 trees from 12 of these 13 populations were analyzed at 32-36 allozyme loci, using a published data set. Twenty-eight of 30 (93%) comigrating RAPD fragments tested were found to be homologous by Southern hybridization in all three species. Using an enriched mitochondrial DNA (mtDNA) preparation and a chloroplast DNA (cpDNA) library as probes, two fragments of cpDNA origin, and one of mtDNA origin present among RAPD profiles were excluded from analysis of nuclear gene diversity. RAPD markers revealed moderately higher intrapopulation gene diversity and substantially higher total genetic diversity and population differentiation than did allozyme markers for each species. We performed a simulation study using allozyme data, which showed that the dominant and biallelic nature of RAPD markers could explain the differences observed in differentiation parameters, but not in gene diversity; RAPD phenotypes appear to represent more underlying gene diversity than do allozyme phenotypes. Results of joint phylogenetic analyses of both the RAPD and allozyme markers strongly supported a common ancestor for P. radiata and P. attenuata pines, and south-to-north migration histories for all three species.Key words: allozymes, dominance, gene diversity, Pinus attenuata, Pinus muricata, Pinus radiata, phylogeny, RAPDs.
Genetic mapping of plant disease resistance gene homologues using a minimal Brassica napus L. population
Authors: Joyeux A , Fortin M G , Mayerhofer R , Good A G
Published: April 2011

Genetic mapping of plants traditionally involves the analysis of large segregating populations. However, not all individuals in a population contribute equal amounts of genetic information. It is thus possible to achieve rough mapping using a subset of the most informative individuals in the population. We have designed a minimal Brassica napus mapping population of 23 doubled-haploid plants and have tested this method using this population in the mapping of disease resistance gene homologues in B. napus. Several groups have identified such homologues in soybean and potato by amplifying sequences corresponding to conserved nucleotide-binding sites from known resistance genes. However, the sequence conservation in the leucine-rich repeat domain that is present in most of the disease resistance genes isolated has not been exploited via the polymerase chain reaction (PCR). We present the genetic mapping of Brassica napus DNA sequences amplified with primers corresponding to both the nucleotide-binding site and the leucine rich-repeat domain of the Arabidopsis thaliana RPS2 gene. We also describe a method for the quick mapping of resistance gene homologues using the polymerase chain reaction.Key words: Brassica napus, disease resistance genes, minimal mapping population, RFLP markers.
Development and identification of a complete set of Triticum aestivum - Aegilops geniculata chromosome addition lines
Authors: Friebe Bernd R , Tuleen Neal A , Gill Bikram S
Published: April 2011

The production and identification of a complete set of intact Aegilops geniculata chromosome and telosome additions to common wheat is described. All Ug and Mg genome chromosomes were tentatively assigned to their homoeologous groups based on C-banding, meiotic metaphase I pairing analyses and plant morphologies. Thirteen disomic and one monosomic wheat-Ae. geniculata chromosome additions were identified. Furthermore, two monotelosomic (MtA7UgL, MtA7MgL) and nine ditelosomic (DtA1UgS, DtA1UgL, DtA2UgS, DtA1MgL, DtA2MgL, DtA3MgS, DtA5MgS, DtA6MgL, DtA7MgS) wheat-Ae. geniculata additions were recovered. C-banding and meiotic pairing analyses revealed that all added Ug and Mg genome chromosomes are structurally unaltered compared to the Ae. geniculata parent accession. Chromosome 4Mg has a strong gametocidal gene that, when transferred to wheat, causes extensive chromosome breakage mainly in gametes lacking it. The relationships of Ae. geniculata chromosomes with those of the diploid progenitor species and derived polyploids is discussed.Key words: Triticum aestivum, Aegilops geniculata, chromosome addition lines, C-banding, genome evolution.
Patterns of puffing activity in the salivary gland polytene chromosomes of the medflyCeratitis capitata, during larval and prepupal development
Authors: Gariou-Papalexiou Angeliki , Chrysanthis George , Mintzas Anastassios C , Zacharopoulou Antigone
Published: April 2011

The patterns of puffing activity in the salivary gland polytene chromosomes have been studied during the late larval and prepupal stages of the medfly Ceratitis capitata. A total of 128 loci, with significant changes in puffing activity during this developmental period, were assigned to the five autosomes of the medfly. Two waves of puffing activity were observed, the first during the late larval stage and the second during the prepupal development. Overall puffing activity can be divided into four groups, group-IV activity being most conspicuous with 58 active loci. The major changes in puffing activity take place around jumping, a characteristic event occurring about 6 h before puparium formation, at puparium formation, and during midprepupal development. The overall puffing activity shows a positive correlation to the ecdysone titer in the hemolymph, suggesting that most of the changes in the activity of the puffs during the late larval and prepupal stages of the medfly may be regulated by ecdysone.Key words: polytene chromosomes, puffing patterns, ecdysone, Ceratitis capitata.
RFLP- and RAPD-based genetic relationships of seven diploid species ofAvenawith the A genome
Authors: Nocelli E , Giovannini T , Bioni M , Alicchio R
Published: April 2011

Relatively few molecular analyses are available for diploid oat species, which constitute the majority of the wild species of Avena and, therefore, the principal natural reservoir of variability. The present work reports an RAPD- (random amplified polymorphic DNA) and RFLP-(restriction fragment length polymorphism) based study of the intra- and interspecific variability of seven diploid A-genome oat species. Both types of markers resulted in valid tools for identifying polymorphisms both within and between species. The two statistical analyses, UPGMA (unweighted pair group method, arithmetic mean) and PCoA (principal coordinate analysis), computed on the basis of genetic similarities estimated from RAPDs and RFLPs, showed that the different accessions grouped according to species, but the similarity coefficients were consistently higher in the RFLP analysis. Furthermore, slight differences were observed in the intra- and interspecific relationships found with the two types of markers. This may support the hypothesis that the polymorphisms revealed by the two types of markers may associate with regions of the genome having different evolutionary rates. The relationships among species are not identical to those deduced from previous karyotypic and morphological studies, thus suggesting a partially different evolutionary pathway in oat speciation.Key words: RAPD and RFLP markers, genetic similarity, oat, diploids, polymorphism.
Fluorescent in situ hybridization with rDNA probes on chromosomes of Acipenser ruthenus and Acipenser naccarii (Osteichthyes Acipenseriformes)
Authors: Fontana F , Lanfredi M , Chicca M , Congiu L , Tagliavini J , Rossi R
Published: April 2011

The genes for 28S and 5S rDNA were physically mapped on the chromosomes of two sturgeon species, the sterlet (Acipenser ruthenus, 2n = 118 ± 4) and the Adriatic sturgeon (Acipenser naccarii, 2n = 248 ± 4) by fluorescent in situ hybridization. In the sterlet, the 28S rDNA was located on six chromosomes, four of which actively transcribed, while in the Adriatic sturgeon the 28S rDNA was located on a chromosome number ranging from 10 to 12, eight of which actively transcribed. The 5S rDNA was physically mapped on two chromosomes in the sterlet and on four in the Adriatic sturgeon. A more detailed characterization of the latter karyotype was obtained during this study. All these data are discussed in connection with the ploidy relationships among sturgeon species.Key words: karyotype, ploidy, FISH, 28S and 5S rDNA.
Identification and analysis of homoeologous segments of the genomes of rice andArabidopsis thaliana
Authors: Dodeweerd Anne-Marie van , Hall Caroline R , Bent Elisabeth G , Johnson Samantha J , Bevan Michael W , Bancroft Ian
Published: April 2011

Using contiguous genomic DNA sequences of Arabidopsis thaliana, we were able to identify a region of conserved structure in the genome of rice. The conserved, and presumptive homoeologous segments, are 194 kb and 219-300 kb in size in Arabidopsis and rice, respectively. They contain five homologous genes, distinguished in order by a single inversion. These represent the first homoeologous segments identified in the genomes of a dicot and a monocot, demonstrating that fine-scale conservation of genome structure exists and is detectable across this major divide in the angiosperms. The conserved framework of genes identified is interspersed with non-conserved genes, indicating that mechanisms beyond segmental inversions and translocations need to be invoked to fully explain plant genome evolution, and that the benefits of comparative genomics over such large taxonomic distances may be limited.Key words: plant genomics, comparative mapping.
Constitutive heterochromatin DNA polymorphisms in diploid Medicago sativa ssp. falcata
Authors: Bauchan G R , Hossain M A
Published: April 2011

A Giemsa C-banding technique was used to study the amount and location of constitutive heterochromatin in diploid (2n = 2x = 16) Medicago sativa ssp. falcata (L.) Arcangeli. Most accessions had the standard C-banding pattern with centromeric bands on all the chromosomes and a prominent heterochromatic band at the nucleolar organizer regions (NOR) of the satellited (SAT) chromosomes. However, we observed in various accessions that constitutive heterochromatic C-bands can exist at the telomeric ends of all the chromosomes. Interstitial bands occurred on the short arms of all chromosomes except for chromosome 3 and on the long arms of chromosomes 1, 2, 3, and 6, only. Rearranged chromosomes such as isochromosomes have been observed for the short arms of chromosomes 2 and 6. This is the first report on the existence of C-banding polymorphisms and the detection of putative isochromsomes in the chromosomes of diploid ssp. falcata which could have contributed to the variation observed in cultivated alfalfa.Key words: alfalfa, C-bands, chromosome, isochromosome.
Biotechnology and world food supply
Authors: Kasha Ken J
Published: April 2011

Biotechnology, the use of molecular and cellular tools to genetically modify and improve food supply, will play an increasing and important role in the continuing struggle to produce sufficient food for an ever increasing world population. Many of the approaches will supplement and enhance conventional breeding and also address environmental concerns and help to stabilize food production. This review provides a perspective dealing specifically with crops and three areas of biotechnology, namely, genome analysis with molecular markers, cell- and tissue-culture procedures, and the rapid and precise incorporation of genes via transformation. One must remember that biotechnology is still in its infancy, and that approaches will be greatly improved and more efficiently utilized in the future for the betterment of mankind.Key words: plants, food, hunger, genome analysis, cell culture, genetic transformation.
Development of the molecular methods for potato virus and viroid detection and prevention
Authors: Singh Rudra P
Published: April 2011

Potato is the fourth most important food crop in the world and it forms the diet of a billion consumers in developing countries, where potato production is increasing rapidly. However, potato virus diseases in developing countries are one of the major causes of lower yields. Their control requires the development of appropriate virus-detection and seed-production technologies for the region. Recent progress in developing nucleic acid based virus detection methods are reviewed. Refinements of the protocols applicable to the laboratories located in seed producing areas are discussed. Nucleic acid spot hybridization (NASH) and reverse transcription polymerase chain reaction (RT-PCR) methods are described for the detection of viruses and viroids in dormant seed tubers and insect vectors. Although the potato crop is susceptible to over 25 virus and viroid diseases, only universally economically important viruses have been dealt with here. The progress of pathogen-derived resistance for the control of potato virus diseases is elaborated, and the results of field tests indicate their feasibility in virus control.Key words: dot-blot, spot-hybridization, reverse transcription, polymerase chain reaction, transgenic plants.
Development of simple sequence repeat markers in rye (Secale cerealeL.)
Authors: Saal B , Wricke Günter
Published: April 2011

Simple sequence repeats (SSRs), also referred to as microsatellites, represent a PCR-based marker system that has been described in mammalian and plant genomes in recent years. In self-pollinating crop plants they have been shown to be superior to other DNA markers with respect to their level of polymorphism. The technical advantages compared with RFLP markers should also facilitate marker analysis in outcrossing crops like rye. In order to determine the usefulness of SSR markers in rye genetics and breeding, several genomic libraries were screened for (CT/GA)nand (GT/CA)ndinucleotide repeats. It was estimated that these motifs occur at a frequency of one per 268-519 kb. Seventy four out of 182 positive clones were sequenced, and the majority (56.8%) revealed perfect repeats, predominantly of the type (GT/CA)n(61.9%). Fifty seven primer pairs were designed and 27 (47.4%) resulted in specific SSR markers, of which 20 were genetically mapped or assigned to chromosomes or chromosome arms, respectively. The level of polymorphism of four SSR and three RFLP markers was assessed in two open-pollinated rye cultivars. On average, the SSR markers showed larger values of expected heterozygosity (0.62 vs. 0.43) and allele number (5.9 vs. 3.4) than RFLP markers in both cultivars.Key words: simple sequence repeats, microsatellites, mapping, rye, Secale cereale.
Larger genomes for molluskan land pioneers
Authors: Vinogradov Alexander E
Published: April 2011

The terrestrial pulmonate mollusks were found to have the significantly larger genomes than the aquatic pulmonates. Being shown in the independent phylogenetic branch, this phenomenon suggests that the previously observed genome enlargement in the vertebrate land pioneers (amphibians and lungfishes) was not casual. As in the vertebrates, the larger molluskan genomes are also more GC-rich. Key words: genome size, genome evolution, cytoecology, noncoding DNA, genome base composition, flow cytometry.
Physical characterization of the homoeologous Group 5 chromosomes of wheat in terms of rice linkage blocks, and physical mapping of some important genes
Authors: Sarma R N , Fish L , Gill B S , Snape J W
Published: April 2011

The wheat homoeologous Group 5 chromosomes were characterized physically in terms of rice linkage blocks using a deletion mapping approach. All three chromosomes, 5A, 5B, and 5D, were shown to have a similar structure, apart from the 4A-5A translocation on the distal end of chromosome arm 5AL. The physical mapping of rice markers on the deletion lines revealed that the whole of rice chromosome 9 is syntenous to a large block, proximal to the centromere, on the long arm. Likewise, a small segment of the distal end of the long arm showed conserved synteny with the distal one-third end of the long arm of rice chromosome 3. In between those conserved regions, there is a region on the long arm of the Group 5 chromosomes which shows broken synteny. The proximal part of the short arms of the Group 5 chromosomes showed conserved synteny with a segment of the short arm of rice chromosome 11 and the distal ends showed conserved synteny with a segment of rice chromosome 12. The physical locations of flowering time genes (Vrn and earliness per se) and the gene for grain hardness (Ha) on the Group 5 chromosomes were determined. These results indicate that comparative mapping using the deletion mapping approach is useful in the study of genome relationships, the physical location of genes, and can determine the appropriate gene cloning strategy. Key words: wheat, rice, comparative mapping, deletion lines.
Gene content and organization of a 281-kbp contig from the genome of the extremely thermophilic archaeon,Sulfolobus solfataricusP2
Authors: Charlebois Robert L , Singh Rama K , Chan-Weiher Christina C.-Y , Allard Ghislaine , Chow Cynthia , Confalonieri Fabrice , Curtis Bruce , Duguet Michel , Erauso Gael , Faguy David , Gaasterland Terry , Garrett Roger A , Gordon Paul , Jeffries Alex C , Kozera Catherine , Kushwaha Neena , Lafleur Édith , Medina Nadine , Peng Xu , Penny Susanne L , She Qunxin , St. Jean Andrew , van der Oost John , Young Felix , Zivanovic Yvan , Doolittle W Ford , Ragan Mark A , Sensen Christoph W
Published: April 2011

The sequence of a 281-kbp contig from the crenarchaeote Sulfolobus solfataricus P2 was determined and analysed. Notable features in this region include 29 ribosomal protein genes, 12 tRNA genes (four of which contain archaeal-type introns), operons encoding enzymes of histidine biosynthesis, pyrimidine biosynthesis, and arginine biosynthesis, an ATPase operon, numerous genes for enzymes of lipopolysaccharide biosynthesis, and six insertion sequences. The content and organization of this contig are compared with sequences from crenarchaeotes, euryarchaeotes, bacteria, and eukaryotes. Key words: Archaea, Sulfolobus Genome Project, comparative genomics, bioinformatics.
Linkage group alignment of sorghum RFLP maps using a RIL mapping population
Authors: Subudhi Prasanta K , Nguyen Henry T
Published: April 2011

Several molecular maps have been constructed in sorghum (Sorghum bicolor L. Moench) using a variety of probes from different grass species such as sorghum, maize, sugarcane, rice, oat, and barley. In order to enhance the utility of the existing mapping information by the sorghum research community, alignment and integration of all major molecular maps is necessary. To achieve this objective, a genetic map of 214 loci with a total map distance of 1200 cM was constructed using 98 F7sorghum recombinant inbred lines (RILs) from a cross between two inbred lines, B35 and Tx7000. Few cDNA clones of sorghum and maize related to photosynthesis and drought stress were mapped on this map for the first time. Five major restriction fragment length polymorphism (RFLP) maps independently developed in this species were used for alignment purpose. The distributions of previously mapped markers were compared with their respective sorghum maps to align each of the linkage groups. In general, consistent linear order among markers was maintained in all the linkage maps. The successful alignment of these RFLP maps will now allow selection of a large number of markers for any region of the sorghum genome with many potential applications ranging from fine mapping and marker-assisted selection to map-based cloning for the improvement of sorghum and related species.

Key words: Sorghum bicolor, linkage maps, molecular markers.
Extraordinary and extensive karyotypic variation: A 48-fold range in chromosome number in the gall-inducing scale insectApiomorpha(Hemiptera: Coccoidea: Eriococcidae)
Authors: Cook Lyn G
Published: April 2011

Chromosome number reflects strong constraints on karyotype evolution, unescaped by the majority of animal taxa. Although there is commonly chromosomal polymorphism among closely related taxa, very large differences in chromosome number are rare. This study reports one of the most extensive chromosomal ranges yet reported for an animal genus. Apiomorpha Rübsaamen (Hemiptera: Coccoidea: Eriococcidae), an endemic Australian gall-inducing scale insect genus, exhibits an extraordinary 48-fold variation in chromosome number with diploid numbers ranging from 4 to about 192. Diploid complements of all other eriococcids examined to date range only from 6 to 28. Closely related species of Apiomorpha usually have very different karyotypes, to the extent that the variation within some species- groups is as great as that across the entire genus. There is extensive chromosomal variation among populations within 17 of the morphologically defined species of Apiomorpha indicating the existence of cryptic species-complexes. The extent and pattern of karyotypic variation suggests rapid chromosomal evolution via fissions and (or) fusions. It is hypothesized that chromosomal rearrangements in Apiomorpha species may be associated with these insects' tracking the radiation of their speciose host genus, Eucalyptus.

Key words: Apiomorpha, cytogenetics, chromosomal evolution, holocentric.
Molecular cytogenetic analysis of supernumerary heterochromatic segments in Rumex acetosa
Authors: Shibata Fukashi , Hizume Masahiro , Kuroki Yuzo
Published: April 2011

The dioecious plant Rumex acetosa shows intraspecific karyotype variation, caused by supernumerary heterochromatic segments or DAPI (4',6-diamidino-2 phenylindole)-bands at the ends of the short arms of three pairs of autosomes. A DNA sequence (RAE730) specific to the supernumerary heterochromatic segments was cloned and sequenced. RAE730 was about 730 bp and AT-rich (71% AT-content). Using fluorescence in situ hybridization (FISH), RAE730 was localized in the supernumerary DAPI-positive heterochromatic segments on several mitotic chromosomes and chromocenters in interphase nuclei, but not in the DAPI-bands of Y or B chromosomes. RAE730 was tandemly arranged in the genome, and the copy number varied between plants from 40 000 to 304 000 copies per 2C, corresponding to the relative amount of supernumerary heterochromatic segments per genome. These results indicate that the karyotype variation caused by the supernumerary heterochromatic segment was generated by amplification or reduction of the tandem repeats of RAE730.

Key words: Rumex acetosa, repetitive sequence, supernumerary heterochromatic segment, intraspecific karyotype variation, DAPI-band.
Genomic in situ hybridization (GISH) reveals high chromosome pairing affinity between Lolium perenne and Festuca mairei
Authors: Cao Mingshu , Sleper David A , Dong Fenggao , Jiang Jiming
Published: April 2011

Intergeneric hybridizations have been made between species of Lolium and Festuca. It has been demonstrated, largely through conventional cytogenetic analysis, that the genomes of the two genera are related, however, much information is lacking on exactly how closely related the genomes are between the two species. We applied genomic in situ hybridization (GISH) techniques to the F1 hybrids of tetraploid Festuca mairei with a genomic constitution of M1M1M2M2 and diploid Lolium perenne with a genomic constitution of LL. It was shown in the triploid hybrids (LM1M2) that the chromosomes of M1 and M2 from F. mairei could pair with each other, and it was further discovered that L chromosomes of L. perenne paired with M1 and M2 chromosomes. Our results showed that meiocytes of Lolium-Festuca are amenable to GISH analysis, and provided direct evidence for the hypothesis that the chromosomes of Lolium and Festuca may be genetically equivalent and that reciprocal mixing of the genomes may be possible.

Key words: Lolium, Festuca, in situ hybridization, meiosis.
Molecular analyses of a repetitive DNA sequence in wheat (Triticum aestivumL.)
Authors: Ueng P P , Hang A , Tsang H , Vega J M , Wang L , Burton C S , He F T , Liu B
Published: April 2011

A repetitive sequence designated WE35 was isolated from wheat genomic DNA. This sequence consists of a 320-bp repeat unit and represents approximately 0.002% of the total wheat DNA. It is unidirectionally distributed either continuously or discretely in the genome. Ladder-like banding patterns were observed in Southern blots when the wheat genomic DNA was restricted with endonuclease enzymes EcoRI, HincII, NciI, and NdeI, which is characteristic for tandemly organized sequences. Two DNA fragments in p451 were frequently associated with the WE35 repetitive unit in a majority of λ wheat genomic clones. A 475-bp fragment homologous to the 5'-end long terminal repeat (LTR) of cereal retroelements was also found in some λ wheat genomic clones containing the repetitive unit. Physical mapping by fluorescence in situ hybridization (FISH) indicated that one pair of wheat chromosomes could be specifically detected with the WE35 positive probe p551. WE35 can be considered a chromosome-specific repetitive sequence. This repetitive unit could be used as a molecular marker for genetic, phylogenetic, and evolutionary studies in the tribe Triticeae.Key words: repetitive sequence, genomic DNA, Triticum aestivum, fluorescence in situ hybridization, long terminal repeat.
Microscopic enumeration of attached marine bacteria of seawater, marine sediment, fecal matter, and kelp blade samples following pyrophosphate and ultrasound treatments
Authors: Velji M. I. , Albright L. J.
Published: April 2011

Seawater, marine surface sediment, fecal material of the sea cucumber Parastichopus californicus, and kelp blades of Macrocystis integrifolia were treated with formaldehyde to strengthen the bacterial cells, followed by tetrasodium pyrophosphate addition and sonication to disperse these same cells. These cells were then stained with 4′,6-diamidino-2-phenylindole and counted by epifluorescent microscopy. The technique of strengthening the cells with an aldehyde and then dispersing them in a suspending medium using a deflocculent (pyrophosphate) and ultrasound caused the bacteria to be randomly distributed when filtered onto Nuclepore membranes with a lower variance within and similar variance between subsamples as compared with untreated samples. In most cases the coefficient of variation stabilized after the bacterial cells in 10 randomly chosen microscopic fields had been counted. Sediment bacterial numbers (±SE) determined by the standard technique were 5.20 (±0.36) × 1010 per gram wet weight; by this dispersion technique they were 11.30 (±0.24) × 1011 per gram, a greater than twofold increase. On young and intermediate aged kelp blades, the increased counts which resulted from this dispersion technique ranged from two- to five-fold. Bacterial cells which were epiphytic on a senescent blade and could not be counted at all by the standard technique were determined to be 3.77 (±0.14) × 106 cm−2 using this dispersion method.
Physiological effects of plasmid DNA transformation on Azotobacter vinelandii
Authors: Glick Baernard R. , Brooks Heather E. , Pasternak J. J.
Published: April 2011

Genetic transformation of Azotobacter vinelandii by the introduction of broad-host-range plasmid DNA (i.e., pRK2501, RSF1010, or pGSS15) causes a number of physiological changes. As shown here, the capacity for nitrogen fixation, mean cell size, and synthesis of siderophores are decreased, whereas the production of capsular slime is enhanced. These findings suggest that the presence of plasmid DNA imposes a "metabolic load" on Azotobacter vinelandii. Therefore, it cannot be assumed a priori that the introduction of plasmid DNA into Azotobacter vinelandii will not disrupt some normal physiological processes. The implications of these findings are discussed, specifically in the context of developing Azotobacter vinelandii as an effective bacterial fertilizer by genetic manipulation.
Comportement diélectrique du K3PO4·3H2O lors de sa déshydratation
Authors: Bottreau André-Marie , Vicq Gilbert , Forniés-Marquina Jose María , Martínez Jiménez Juan Pablo
Published: April 2011

We describe the dehydration study of the K3PO4·3H2O phosphate by thermal analysis and microwave dipolar spectroscopy at the frequencies of 3.26, 9.45, and 15.05 GHz. There are correlations between the thermodynamic parameters and their obtained results by electromagnetic characterization.
The far-infrared absorption by small metallic particles
Authors: Cao Xiaohui
Published: April 2011

In analyzing the effect of the size, coating, and shape of small metallic particles on the far-infrared absorption, we find that size and coating do not alter the far-infrared absorption noticeably, but shape has a strong influence on it. When there is a shape (or effective shape) distribution, an anomalous enhancement of the far-infrared absorption can result. PACS No.: 61.46+w, 36.40Rr
Bethe logarithms for Ps, H, and heliumlike atoms
Authors: Drake GWF , Goldman S P
Published: April 2011

A new method is presented for the calculation of the mean excitation energy (Bethe logarithm) for helium and other two-electron systems. The method requires only a single matrix diagonalization within a correlated Hylleraas basis set extended to contain a wide range of distance scales. High-precision results are obtained for the ground states of Ps and H, and all the S- and P-states of heliumlike ions up to n = 5, including finite mass corrections. The results are used to calculate revised values for the quantum electrodynamic shifts for helium, and a comparison with experiment is presented.PACS Nos.: 31.15Pf, 31.30Jv, and 32.10Hq
Gamma-induced attenuation in normal single-mode and multimode, Ge-doped and P-doped optical fibers: A fiber optic dosimeter for low dose levels
Authors: Lu Ping , Bao Xiaoyi , Brown Kellie , Kulkarni Narayan
Published: April 2011

Ge-doped, P-doped, normal single-mode (SM) and multimode (MM) optical fibers were exposed to Cobalt-60 gamma radiation at dose rates of 0.5 and 3.0 Gy/min, typical radiotherapy dose rates. A CCD-based fiber optic spectrometer was used to measure the real-time absorption spectra of these fibers in the visible region. Experimental results have shown that P-doped fiber is the most radiation-sensitive of the fibers tested. At the wavelength of 502 nm, the radiation-induced loss in P-doped fiber shows a linear relationship with the total dose with no dose-rate dependence. This indicates that dose rates have no influence on a fiber optic dosimeter operating at this wavelength. The radiation-induced losses in normal MM fibers, Ge-doped MM fibers, and Ge-doped SM fibers are shownto be dose-rate dependent. PACS No.: 42.62nBe, 42.81-i
Low-lying excitations in super-conducting bilayer systems
Authors: Grigorescu M
Published: April 2011

The ground and first excited state of two superconducting layers in interaction are studied considering two different coupling terms, one represented by the standard Josephson interaction, and one new, which is a superexchange pairing force between bilayer pairs. It is shown that a moderate to strong Josephson interaction produces a low-lying collective state, pictured as an out-of-phase oscillation of the (Bardeen-Cooper-Schreiffer) gauge angles of the two layers. This antisymmetric angular oscillation might explain the 41 meV resonance observed in neutron-scattering experiments. The bilayer pairs are formed by electrons from different layers with an antiparallel orientation of the spins, being related to the antiferromagnetic arrangement. The pair operators within the layers together with the bilayer pairs generate by commutation an so(5) algebra. It is shown that the transition between the superconducting and antiferromagnetic phases can be explained assuming the dependence on concentration of the bilayer pairing strength, with maximum at half-filling.PACS Nos.: 71.10Li, 74.50+r, 74.72-h, 03.65Fd
Two-fluid hydrodynamics of a Bose gas including damping from normal fluid transport coefficients
Authors: Nikuni T , Griffin A , Zaremba E
Published: April 2011

We extend our recent work on the two-fluid hydrodynamics of the condensate and noncondensate in a trapped Bose gas by including the dissipation associated with viscosity and thermal conduction in the thermal cloud. For purposes of illustration, we consider the hydrodynamic modes in the case of a uniform Bose gas. A finite thermal conductivity and shear viscosity give rise to a damping of the first and second sound modes, in addition to the damping found previously due to the lack of diffusive equilibrium between the condensate and noncondensate. The relaxational mode associated with this equilibration process is strongly coupled to thermal fluctuations and reduces to the usual thermal diffusion mode above the Bose-Einstein transition. In contrast to the standard Landau two-fluid hydrodynamics, we predict a damped mode centered at zero frequency, in addition to the usual second sound doublet.PACS Nos.: 03.75.Fi, 05.30Jp, 67.40.Db
Analyse de la turbulence pariétale de l'écoulement annulaire tourbillonnaire non entretenu généré par une entrée tangentielle du fluide
Authors: Legrand J , Legentilhomme P , Lefèbvre G
Published: April 2011

This work is dedicated to an experimental study of the wall shear stress in a turbulent swirling decaying flow induced by means of a tangential inlet in an annular cell. The flow pattern near both cylinders of the annulus is analyzed by means of measurements of wall velocity gradients using an electrochemical method involving micro-electrodes working in inert wall. The analysis of the axial and circumferential evolutions of the mean wall velocity gradient and of its power spectral density emphasizes the complexity and highly three-dimensional nature of the flow pattern of the annular swirling decaying flow induced by means of a single tangential inlet. Near the inner wall of the annulus, a recirculating zone, consisting of several pairs of contra-rotating cells, develops following the main helical motion of the fluid along the flow path. Near the external wall of the annular cell, high local velocities and energetic turbulent structures are detected in the vicinity of the tangential inlet. These eddies rapidly decay along the flow path because of the decrease of the swirl intensity. The setup of a recirculation bubble near the inner wall induces a quasi-axisymmetric flow behavior at the outer cylinder of the annulus. Near both walls, the power spectral densities of the velocity gradient reveal a superposition of small turbulent eddies having a low energetic level in the high-frequency domain.
Some applications of the Lambert W  function to physics
Authors: Valluri S R , Jeffrey D J , Corless R M
Published: April 2011

Two standard physics problems are solved in terms of the Lambert W  function, to show the applicability of this recently defined function to physics. Other applications of the function are cited, but not described. The problems solved concern Wien's displacement law and the fringing fields of a capacitor, the latter problem being representative of some problems solved using conformal transformations. The physical content of the solutions remains unchanged, but they gain a new elegance and convenience.

PACS No.: 41.10F
Multichannel quantum defect theory treatment of triplet gerade and ungerade d-symmetry levelsof H2 and its isotopomers
Authors: Ross S C , Jungen Ch. , Matzkin A
Published: April 2011

This work presents a systematic multichannel quantum defect theory (MQDT) analysis of the triplet d-symmetry levels of the hydrogen molecule. First, a new compilation of the best available experimental term values for these levels was prepared. Second, R-dependent quantum defect matrices for the 3Πu, 3Πg, and 3Δg states of H2 were obtained from ab initio potential-energy curves and used in an ab initio MQDT calculation of all known triplet d-symmetry rovibronic levels of H2, HD, and D2. For a few of these levels previous ab initio calculations have been reported. The agreement currently obtained is generally significantly better than that in previous work. Finally, the quantum defect matrices are used to calculate the electronic transition moments 3Πu [Formula: see text] 3Πg, 3Δg as functions of energy and internuclear distance, R, for application in a companion article. PACS Nos: 31.15Ar, 33.20Wr, 34.10+x, 34.80Kw
High-precision evaluation of the vibrational spectra of long-range molecules
Authors: Tannous C , Langlois J
Published: April 2011

Vibrational spectra of long-range molecules are determined accurately and to arbitrary accuracy with the Canonical Function Method. The energy levels of the 0g and 1u electronic states of the 23Na2 molecule are determined from the ground state up to the continuum limit. The method is validated by comparison with previous results obtained for different potentials adapted to long-range molecules. PACS Nos.: 03.65-w, 31.15Gy, 33.20.Tp
Lifetime of metastable Ne2+ ions measured at a heavy-ion storage ring
Authors: Träbert E , Wolf A , Tordoir X , Pinnington E H , Knystautas E J , Gwinner G , Calamai A G , Brooks R L
Published: April 2011

The radiative lifetime of the 2s2 2p4 1S0 level in Ne2+ ions has been measured by time-resolved observations of one of the electric-dipole forbidden decay branches, the magnetic dipole (M1) transition to the 2s2 2p4 3P1 level, on ions circulating in a heavy-ion storage ring. The result, a lifetime of 213 ± 4 ms, agrees within the mutual 2σ errors with that of a recent measurement using a radiofrequency ion trap, but is expected to suffer less from possible systematic error. It also compares very well with two calculations that have been semiempirically corrected for experimental transition energies. PACS Nos.: 32.70Cs, 39.90+d, 31.50+w, 35.80B
An exact kinetic energy operator for (HF)3 in terms of local polar and azimuthal angles
Authors: Wang X -G , Carrington Jr. T
Published: April 2011

To facilitate exploiting the symmetry of (HF)3 we propose using local polar and azimuthal angles to specify the orientation of the HF units with respect to the frame of the trimer. We present and discuss the derivation of a kinetic energy operator in local polar and azimuthal angles and PekerisJacobi coordinates. PACS No.: 31.15-P
The Ã1 A2  1 A1 system of formaldehyde, H2C=0: Reanalysis of the 110410 and 510 bands
Authors: Weber T , Bangs S , Hüttner W , Ramsay D A
Published: April 2011

A frequency-doubled dye laser was used to excite the fluorescence of formaldehyde in the region 31 09931 185 cm1. Using iodine standard lines, the wave numbers of nearly 300 lines of formaldehyde have been determined. Since these lines form only part of the overlapping 110410 and 510 bands of the Ã1A2 [Formula: see text]1A1 system, complete coverage of these bands was obtained using a Fourier-transform spectrometer. Some of the frequency-doubled lines were used as standards. Rotational analysis has been carried out and improved molecular constants obtained. The two bands show a Coriolis interaction. However, while earlier workers found an interaction proportional to Ka, we obtain a cubic dependence on this quantum number.PACS Nos.: 32.30Jc, 33.20Vq
Amplitude ratios near a Lifshitz point
Authors: Abdel-Hady A
Published: April 2011

The susceptibility amplitude ratio in the neighborhood of an m-fold Lifshitz point is calculated using the field theoretical techniques of the renormalization group, in one-loop order. A simple expression for the amplitude associated with the helical (ferromagnetic) AH (AF) branches near a Lifshitz point is also calculated. A comparison between our calculations and the available theoretical results is presented.

PACS No.: 75.40Cx
Approach to equilibrium in the micromaser
Authors: Leary D , Yau S , Carrington M , Kobes R , Kunstatter G
Published: April 2011

We examine the approach to equilibrium of the micromaser. Analytic methods are first used to show that for large times (i.e., many atoms) the convergence is governed by the next-to-leading eigenvalue of the corresponding discrete evolution matrix. The model is then studied numerically. The numerical results confirm the phase structure expected from analytic approximation methods and agree for large times with the analysis of Elmfors et al. in terms of the ``continuous master equation.'' For short times, however, we see evidence for interesting new structure not previously reported in the literature.

PACS No.: 42.55Sa
A realistic quasi-physical model of the 100 m dash
Authors: Mureika J R
Published: April 2011

A quasi-physical model (having both physical and mathematical roots) of sprint performances is presented, accounting for the influence of drag modification via wind and altitude variations.The race-time corrections for world class male sprinters are discussed, and theoretical estimates for the associated drag areas are presented. The corrections are consistent with constant-wind estimates of previous authors. At sea level, world class men's race times are adjusted by about 0.10 s for a wind speed w = 2 m s-1, while every 1000 m of altitude provides an advantage of roughly 0.030.04 s. Corrections are provided for a wide range of wind speeds (-5 to +5 m s-1) and altitudes (02500 m), as well as for variable winds whose time-averaged value does not realistically reflect the ambient conditions. A simplified algebraic expression is also presented to correct 100 m sprint times for ambient wind and altitude effects. The primary aim is to demonstrate the utility and robustness of the full model in making such predictions, after which accurate measurement of each parameter can help to fine-tune these results. As a practical example of its utility, the nullified World Record and 1988 Olympic 100 m race of Ben Johnson is studied, and compared with the present World Record of 9.79 s.

PACS Nos.: 01.80, 02.60L
Discrete quantum gravity and causal sets
Authors: Reid D D
Published: April 2011

This paper provides a thorough introduction to the physical and conceptual need for a theory of quantum gravity; some knowledge of general relativity and nonrelativistic quantum mechanics is assumed. A theory of quantum gravity would have wide-ranging implications for high-energy physics, astrophysics, and cosmology. The paper goes on to describe an important approach to quantum gravity that is not well known outside of the quantum gravity research community  causal sets. The causal-set approach falls within the framework of discrete quantum gravity, which considers the possibility that the small-scale structure of spacetime might be discrete rather than continuous. Herein, I elucidate the arguments for why a discrete causal structure might be appropriate for a theory of quantum gravity. The logical and formal development of a causal-set theory as well as a few illuminating examples are also provided. PACS Nos.: 04.60-m, 04.60Nc
Modeling optical solitons in a practical lossy fiber
Authors: Mahmood M F
Published: April 2011

An analytical investigation is presented that is based on the Lagrangian variational formulation of the interaction of two orthogonally polarized optical pulses. The pulses are governed by a pair of coupled nonlinear Schrödinger equations in a practical lossy optical fiber. PACS Nos.: 03.40Kf, 42.65Tg, 42.81Dp
Damage profile and mode observation in LiTaO3 by low-energy H+ ions
Authors: Wang K -M , Hu H , Chen F , Lu F , Zhang J -H , Liu X -D , Liu J -T , Shi B -R
Published: April 2011

LiTaO3 samples were implanted with 50, 80, 120, and 150 keV H + ions. The damage profiles in LiTaO3 induced by H+ ions were investigated using the Rutherford backscattering/channeling technique. We used TRIM (transport of ions in matter) to simulate it. It was found that the shape of the experimental damage profile was similar to one predicted by TRIM'98, but the experimental damage ratio (NDN) was higher than the calculated damage ratio based on TRIM'98. The modes in LiTaO3 were measured by a prism-coupling method for all samples. The modes were observed only for LiTaO3 implanted with 80, 120, and 150 keV H+ ions. The present result shows that optical wave guides in LiTaO3 can be formed by lower energy H+ ions.

PACS Nos.: 61.72-y, 61.82-d, 61.85+p, 78.20Ci
The motion of rapidly rotating cylinders sliding on smooth surfaces
Authors: Shegelski M R.A.
Published: April 2011

An analytical calculation is presented and used to illustrate the principal features of the motion of rapidly rotating cylinders sliding over smooth surfaces. In particular, the time dependences of the angle rotated through, the distance traveled, and the lateral deflection of the cylinder are calculated. Examples of cylinders are given for which rotation and sliding stop at different times. The theoretical results are also compared to observed motions of curling rocks sliding on "pebbled" ice.

PACS No.: 46.00