bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative trait loci underlying domestication- and yield-related traits in anOryza sativa ×Oryza rufipogonadvanced backcross population
Authors: Tan Lubin , Zhang Peijiang , Liu Fengxia , Wang Guijuan , Ye Sheng , Zhu Zuofeng , Fu Yongcai , Cai Hongwei , Sun Chuanqing 
Published: September 2008

To understand the genetic characteristics of the traits related to differentiation between cultivated rice and its wild progenitor, genetic factors controlling domestication- and yield-related traits were identified using a BC3F2population derived from an accession of common wild rice (donor, Oryza rufipogon Griff.) collected from Yuanjiang, Yunnan province, China, and an indica cultivar, Teqing (recipient, Oryza sativa L.). A genetic linkage map consisting of 125 simple sequence repeat (SSR) markers was constructed. Based on the phenotypes of the 383 BC3F2families evaluated in two environments, two domestication-related morphological traits, panicle shape and growth habit, were found to be controlled by single Mendelian factors. This implies that the recessive mutations of single genes controlling some morphological traits could have been easily selected during early domestication. By single-point analysis and interval mapping, 59 putative quantitative trait loci (QTLs) that influence 11 quantitative traits were detected at two sites, and 37.5% of the QTL alleles originating from O. rufipogon had a beneficial effect for yield-related traits in the Teqing background. Regions with significant QTLs for domestication- and yield-related traits were detected on chromosomes 1, 4, 5, 7, 8, and 12. Fine mapping and cloning of these domestication-related genes and QTLs will be useful in elucidating the origin and differentiation of Asian cultivated rice in the future.
The Pic19 NBS-LRR gene family members are closely linked toScmv1, but not involved in maize resistance to sugarcane mosaic virus
Authors: Jiang Lu , Ingvardsen Christina Rønn , Lübberstedt Thomas , Xu Mingliang 
Published: September 2008

Sugarcane mosaic virus (SCMV) is the causal pathogen for a severe mosaic virus disease of maize worldwide. In our previous research, the maize resistance gene analog (RGA) Pic19 and its three cognate BAC contigs were mapped to the same region as the SCMV resistance gene Scmv1. Here we report the isolation and characterization of the Pic19R gene family members from the inbred line FAP1360A, which shows complete resistance to SCMV. Two primer pairs were designed based on the conserved regions among the known Pic19 paralogs and used for rapid amplification of cDNA ends of FAP1360A. Six full-length cDNAs, corresponding to the Pic19R-1 to -6 paralogs, were obtained. Three of them (Pic19R-1 to -3) had uninterrupted coding sequences and were, therefore, regarded as candidates for the Scmv1 gene. A total of 18 positive BAC clones harboring the Pic19R-2 to -5 paralogs were obtained from the FAP1360A BAC library and assembled into two BAC contigs. Two markers, tagging Pic19R-2 and -3 and Pic19R-4, were developed and used to genotype a high-resolution mapping population segregating solely for the Scmv1 locus. Although closely linked, none of these three Pic19R paralogs co-segregated with the Scmv1 locus. Analysis of the Pic19R family indicated that the Pic19R-1 paralog is identical to the known Rxo1 gene conferring resistance to rice bacterial streak disease and none of the other Pic19R paralogs seems to be involved in resistance to SCMV.
Phylogenetic analysis of Carthamus species based on the nucleotide sequence of the nuclear SACPD gene and chloroplast trnL–trnF IGS region
Authors: Sasanuma Tsuneo , Sehgal Deepmala , Sasakuma Tetsuo , Raina Soom Nath 
Published: September 2008

To clarify the phylogenetic relationships of Carthamus species, we performed sequence analysis of the nuclear stearoyl acyl carrier protein desaturase (SACPD) gene and the chloroplast intergenic spacer region between leucine and phenylalanine tRNA genes (trnL–trnF IGS) in 13 taxa of Carthamus. The previous division of the genus into 4 taxonomic sections and allocation of particular genomes to various taxa on the basis of morphological, cytogenetic, and biosystematic analyses is not supported by the present study. Our results provide evidence of the occurrence of 5 nuclear genomes (A, B, C, X, and Y) and 3 cytoplasm types (A, B, and C) in the genus Carthamus. The cultivated safflower, C. tinctorius (2n = 24), has the B genome and type B cytoplasm. Both of these are not present in the polyploid taxa. This contradicts the earlier view that one of the genomes involved in the origin of the polyploid taxa of Carthamus is the B genome. Comparison with an outgroup species ( Cirsium japonicum ) indicated that C. arborescens is the most primitive species in the genus. Carthamus palaestinus is genetically closest to the cultivated safflower.
Y-specific sequences and polymorphisms in rainbow trout and Chinook salmon
Authors: Brunelli Joseph P. , Wertzler Kelsey J. , Sundin Kyle , Thorgaard Gary H. 
Published: September 2008

Improved methods for genetically sexing salmonids and for characterization of Y-chromosome homologies between species can contribute to understanding the evolution of sex chromosomes and sex-determining mechanisms. In this study we have explored 12.5 kb of Y-chromosome-specific sequence flanking the previously described OtY2 locus in Chinook salmon ( Oncorhynchus tshawytscha ) and 21 kb of homologous rainbow trout ( Oncorhynchus mykiss ) Y-chromosome-specific sequence. This is the first confirmed Y-specific sequence for rainbow trout. New Y-specific markers are described for Chinook salmon (OtY3) and rainbow trout (OmyY1), which are readily detected by PCR assays and are advantageous because they also produce autosomal control amplification products. Additionally, AFLP analysis of Chinook salmon yielded another potential Y-chromosome marker. These descriptions will facilitate genotypic sexing and should be useful for population studies of Y-chromosome polymorphisms and for future studies to characterize what appears to be a common sex-determining mechanism between these species.
Décontamination de sols pollués par les hydrocarbures aromatiques polycycliques par biodégradation en présence de substrats organiques supplémentaires
Authors: Siméon Nathalie , Mercier Guy , Blais Jean-François , Ouvrard Stéphanie , Cébron Aurélie , Leyval Corinne , Goergen Jean-Louis , Guedon Emmanuel 
Published: September 2008

Les hydrocarbures aromatiques polycycliques (HAP) sont connus pour être cancérigènes et mutagènes. Cette étude a porté sur la biodégradation de HAP (les 16 HAP de la liste prioritaire établie par l’Agence américaine de protection de l’environnement) présents dans un sol industriel en ajoutant des substrats organiques comme du lisier de porc, du compost de crevettes ou des boues d’épuration. Les boues municipales et le lisier de porc ont été utilisés comme inoculum pour améliorer la biodégradation des HAP. Les résultats ont montré une biodégradation de 60 % de la somme des 16 HAP en 16 semaines à 30 °C. Cette dégradation a été obtenue dans le cas d’une biopile composée de 75 % de sol pollué, 10 % d’inoculum (boues acclimatées), 10 % de boues brutes et 3 % de paille (pour améliorer le niveau d’aération). Pour cette condition, le ratio sol–amendements était de 1,0:0,3 et le rapport C/N de 30. Lors de cet essai, le GC-MS montre un taux de 68 % ± 16 % de dégradation des HAP de cinq à six cycles. La quantification de la HAP-dioxygénase par « polymerase chain reaction » en temps réel montre que la majorité des bactéries dégradantes provenant du sol contaminé et de l’inoculum sont des Gram+, alors que l’inoculum fait à partir des boues favorise le développement des bactéries dégradantes Gram–.
Differences in nitric oxide steady states between arginine, hypoxanthine, uracil auxotrophs (AHU) and non-AHU strains ofNeisseria gonorrhoeaeduring anaerobic respiration in the presence of nitrite
Authors: Barth Kenneth , Clark Virginia L. 
Published: September 2008

Neisseria gonorrhoeae can grow by anaerobic respiration using nitrite as an alternative electron acceptor. Under these growth conditions, N. gonorrhoeae produces and degrades nitric oxide (NO), an important host defense molecule. Laboratory strain F62 has been shown to establish and maintain a NO steady-state level that is a function of the nitrite reductase/NO reductase ratio and is independent of cell number. The nitrite reductase activities (122–197 nmol NO2reduced·min–1·OD600–1) and NO reductase activities (88–155 nmol NO reduced·min–1·OD600–1) in a variety of gonococcal clinical isolates were similar to the specific activities seen in F62 (241 nmol NO2reduced·min–1·OD600–1and 88 nmol NO reduced·min–1·OD600–1, respectively). In seven gonococcal strains, the NO steady-state levels established in the presence of nitrite were similar to that of F62 (801–2121 nmol·L–1NO), while six of the strains, identified as arginine, hypoxanthine, and uracil auxotrophs (AHU), that cause asymptomatic infection in men had either two- to threefold (373–579 nmol·L–1NO) or about 100-fold (13–24 nmol·L–1NO) lower NO steady-state concentrations. All tested strains in the presence of a NO donor, 2,2′-(hydroxynitrosohydrazono)bis-ethanimine/NO, quickly lowered and maintained NO levels in the noninflammatory range of NO (<300 nmol·L–1). The generation of a NO steady-state concentration was directly affected by alterations in respiratory control in both F62 and an AHU strain, although differences in membrane function are suspected to be responsible for NO steady-state level differences in AHU strains.
Phenotypic and genotypic analysis of Flavobacterium psychrophilum isolates from Ontario salmonids with bacterial coldwater disease
Authors: Hesami Shohreh , Allen Katie J. , Metcalf Devon , Ostland Vaughn E. , MacInnes Janet I. , Lumsden John S. 
Published: September 2008

Flavobacterium psychrophilum is the causative agent of bacterial coldwater disease (BCWD) and rainbow trout fry syndrome. BCWD has a considerable economic impact on aquaculture operations in Ontario, Canada, and our limited understanding of the population structure and epidemiology of F. psychrophilum isolates is an impediment to the development of improved management strategies. Seventy-five 16S rRNA gene and gyr polymerase chain reaction positive isolates of F. psychrophilum that had been collected over a 16-year period from farmed salmonids with tail rot, necrotic myositis, and osteochondrosis were characterized morphologically, biochemically, and genotypically. Although the isolates were homogeneous by preliminary biochemical and phenotypic characterization, two distinct biovars were found by API ZYM testing. As well, four restriction pattern types were detected by 16S rRNA polymerase chain reaction – restriction fragment length polymorphism analysis and there was a significant (P < 0.001) correlation between biovar I and digestion with MaeIII and between biovar II and digestion with MnlI or no site (P < 0.05). Further heterogenity was detected by sequence analysis of a 194 bp stem loop 3 region of rRNA. Nine sequence types were identified; 40/46 biovar I isolates were sequence type “a”, while 21/32 biovar II isolates belonged to either sequence type “c” or “d”. More than one biovar and genotype was identified among the strains recovered from separate fish sampled from three groups of rainbow trout ( Oncorhynchus mykiss ) experiencing BCWD mortality events. No association was found between genotype or biovar and type of disease. Taken together, these data suggest that F. psychrophilum from Ontario can be grouped into two major lineages based on biovar and 16S rRNA polymorphisms, and although three major strain types were most frequently isolated in this study, it appears that the population of F. psychrophilum with pathogenic potential is quite heterogeneous.
Prevalence of rectal carriage of extended-spectrum β-lactamase-producingEscherichia coliamong elderly people in community settings in China
Authors: Tian Su Fei , Chen Bai Yi , Chu Yun Zhuo , Wang Shuang 
Published: September 2008

The importance of community-acquired infections due to extended-spectrum β-lactamase-producing (ESBL) Escherichia coli has been increasingly recognized in recent years. No comprehensive data are available on the prevalence, risk factors, and genotypes of ESBL production in community residents in China. Rectal samples from 270 elderly people were collected in four communities in Shenyang (China). Colonies were screened by double-disk synergy test for ESBL production and then, ESBLs were characterized by PCR and sequencing. The clonal relatedness of all ESBL-producing isolates was determined by pulsed-field gel electrophoresis. Potential risk factors for rectal carriage of ESBL producers were examined by multivariate analysis. The prevalence of rectal carriage of ESBL-producing E. coli was 7.0%. All 19 ESBL-producing isolates produced CTX-M-type ESBLs, including CTX-M-14 (11 strains), CTX-M-22 (3 strains), CTX-M-79 (3 strains), CTX-M-24 (1 strain), and CTX-M-24 and CTX-M-79 together (1 strain). CTX-M-79 ESBL was first detected worldwide. ESBL-producing strains were clonally unrelated. Appearance of ESBL producers is strongly associated with the use of antibiotics in the past 3 months (odds ratio 3.2, 95% CI 1.1–9.0, P = 0.03). Our results show the importance of the intestinal tract as a reservoir for ESBL-producing isolates in community settings in China and that the use of antibiotics in the past 3 months is clearly linked to rectal carriage of ESBL producers.
Construction ofBacillus thuringiensiswild-type S76 and Cry–derivatives expressing a green fluorescent protein: two potential marker organisms to study bacteria–plant interactions
Authors: Parente Ana Flávia , Silva-Pereira Ildinete , Baldani José Ivo , Tibúrcio Victor Hugo da Silva , Báo Sônia Nair , De-Souza Marlene T. 
Published: September 2008

Collectively, the species Bacillus thuringiensis , Bacillus cereus , and Bacillus anthracis represent microorganisms of high economic, medical, and biodefense importance. Although the genetic correlation and pathogenic characteristics have been extensively dissected, the ecological properties of these three species in their natural environments remain poorly understood. Thus, a tractable marker for detecting these bacteria under specific environmental and physiological conditions is a valuable tool. With this purpose, a plasmid (pAD43-25) carrying a functional gfp gene sequence (gfpmut3A) was introduced into the wild-type strain Bacillus thuringiensis subsp. kurstaki S76, which bears approximately 11 plasmids, allowing constitutive synthesis of green fluorescent protein (GFP) during vegetative growth (strain S76GFP+). Additionally, this vector was transferred to a plasmid-cured (Cry–) B. thuringiensis host. Bright green cells were detected by fluorescence microscopy in both recombinants by 2 h after inoculation in liquid medium and could be seen throughout the remaining cultivation time until complete sporulation was accomplished. For strain S76GFP+protein profile and plasmid DNA analyses indicate, respectively, that this recombinant maintained Cry proteins expression and resident plasmid outline. Thus, in addition to the potential of strain S76GFP+as a marker organism in bacteria–plant interaction studies, the production and stability of active GFPmut3a make this unique expression system a useful experimental model to study adaptive changes of host–plasmid as well as plasmid–plasmid relationships in a population of cells stressed by the production of a recombinant protein.
An intracellular symbiont and other microbiota associated with field-collected populations of sawflies (Hymenoptera: Symphyta)
Authors: Graham Robert I. , Zahner Viviane , Lucarotti Christopher J. 
Published: September 2008

Six species of sawfly (Hymenoptera: Symphyta) from four taxonomic families (Agridae, Diprionidae, Pamphiliidae, and Tenthredinidae) were collected from locations across Canada and surveyed for their associated microbiota. Total DNA was extracted from individual insects, and polymerase chain reaction (PCR) was used to amplify the conserved 16S rRNA gene from microbiota. Denaturing gradient gel electrophoresis (DGGE) and restriction fragment length polymorphism (RFLP) were undertaken to separate bacterial clones associated with the host insect. Sequencing of the PCR–DGGE and PCR–RFLP products revealed a dominance of α- and γ-Proteobacteria, with most sequences showing high similarity to bacteria previously identified from other insect species and environmental samples. Additionally, a strain of the bacterial endosymbiont Wolbachia and a Wolbachia bacteriophage were identified from the mountain ash sawfly ( Pristiphora geniculata ).
The carbon and oxygen stable isotopic composition of cultured benthic foraminifera
Authors: McCorkle Daniel C. , Bernhard Joan M. , Hintz Christopher J. , Blanks Jessica K. , Chandler G. Thomas , Shaw Timothy J. 
Published: September 2008

Abstract

Laboratory cultures of several species of benthic foraminifera were grown under controlled physical and chemical conditions during months-long experiments carried out at the University of South Carolina in 2001 and 2002. A dozen experimental culture chambers contained a
c
. 1–3 mm layer of trace-metal free silica substrate, and were continuously flushed with water from a large (1600 L) seawater reservoir with known, constant temperature and composition (δ
18
O(water), carbonate system chemistry, and trace element concentrations). Each year, in most of the culture chambers, one or more species reproduced, producing hundreds of juveniles which grew into size classes ranging from 100 to 500 microns.
Bulimina aculeata
was the most successful species in the 2001 cultures, and both
B. aculeata
and
Rosalina vilardeboana
were abundant in 2002.

We determined the shell C and O isotopic composition of the cultured foraminifera, and compared these isotopic values with the water chemistry of the culture chambers, and also with the shell chemistry of field specimens collected from sites on the North Carolina and South Carolina (USA) continental margin. The cultured foraminifera showed substantial offsets from the δ
13
C of system water dissolved inorganic carbon (−0.5 to −2.5‰, depending on species) and smaller offsets (0 to −0.5‰) from the predicted δ
18
O of calcite in equilibrium with the culture system water at the growth temperature. These offsets reflect at least three factors: species-dependent vital effects; ontogenetic variations in shell chemistry; and the aqueous carbonate chemistry ([CO
3
−
] or pH) of the experimental system.
Seasonal dynamics of coastal water masses in a Scottish fjord and their potential influence on benthic foraminiferal shell geochemistry
Authors: Cage Alix G. , Austin William E. N. 
Published: September 2008

Abstract

Pronounced seasonal heating of middle and high latitude shelf seas results in large temporal changes in seawater temperature that have the potential to be recorded by benthic foraminifera. Predicted oxygen isotope composition for calcite precipitating in equilibrium conditions with seawater suggest that pronounced ‘seasonal isotope effects’ may be encountered in the growth history of benthic foraminifera. Such ‘seasonal’ effects can be difficult to distinguish from so-called ‘vital effects’, where shell and equilibrium calcite values are offset by a constant difference in oxygen isotope values. Preliminary findings suggest that benthic foraminifera may have more than one phase of growth, for example
Ammonia becarii
calcifies in spring and late summer, potentially introducing apparent intra-annual and inter-annual temperature variations of >1°C into palaeoclimatic reconstructions when mixed-season populations are sampled. We highlight the need to select species-specific palaeotemperature equations to establish reliable isotopic disequilibria and illustrate the importance of understanding the ‘seasonal isotope effect’ when considering disequilibrium effects in foraminifera which have grown in seasonally-changing environments.
Isotopic variability in the intertidal acorn barnacle
Semibalanus balanoides
: a potentially novel sea-level proxy indicator
Authors: Craven K. F. , Bird M. I. , Austin W. E. N. , Wynn J. 
Published: September 2008

Abstract

We report variations in the δ
13
C and δ
18
O values of barnacle skeletal carbonate as well as the δ
13
C and δ
15
N value of tissue from specimens of the acorn barnacle
S. balanoides
, as a function of elevation within its living range on the Isle of May, Scotland. Individuals were sampled over a 3.50 m range at 0.25 m intervals (1.00–4.50 m above ordnance datum). Carbonate δ
18
O values (2.44±0.13‰ [1σ], n=45) and tissue δ
15
N values (8.17±0.42‰, n=15) do not vary systematically with elevation. The δ
13
C value of shell carbonate increases with elevation by
c.
1‰ (total range: −0.77‰ to +0.63‰), but the variability between samples at the same elevation suggests that this relationship will be of limited use in constraining palaeo-elevation. By contrast, tissue δ
13
C values show systematic variation with elevation, increasing by
c
. 8‰ (total range: −19.36‰ to −8.77‰) with increasing elevation.

These results suggest that there is potential to use the tissue δ
13
C values to determine the elevation of a Fixed Biological Indicator (FBI) such as
S. balanoides
within its living range. If this is also true of the organic matrix of the carbonate skeleton, and if this organic matrix is preserved in Holocene FBIs, then the potential exists to use carbon isotopes to more precisely constrain the palaeo-elevation of FBIs within their living range and hence palaeo sea-level. The small range of carbonate δ
18
O values suggests that oxygen isotopes in FBIs can be used to constrain water δ
18
O values if an independent estimate of temperature is available, or temperature if an independent estimate of salinity is available.
Biogeochemical controls on palaeoceanographic environmental proxies: a review
Authors: James Rachael H. , Austin William E. N. 
Published: September 2008

Abstract
Scientific observations of our oceans and climate go back no more than a couple of hundred years. Most of our information about the evolution of Earth's ocean-climate system relies instead on proxies – primarily measurements of sediment components that respond to changes in environmental parameters. This paper provides an overview of some of the most important biological and geochemical proxies and outlines their contribution to our understanding of the ocean-climate system. We also discuss some of the challenges that need to be overcome to obtain accurate records. These include: better understanding of the controls on the mechanisms of biomineralization; the impacts of post-depositional dissolution and diagenesis on primary proxy relationships; proxy validation; and analytical considerations.
Some fundamental features of biomineralization
Authors: Williams R. J. P. 
Published: September 2008

Abstract
This contribution summarizes the considerations that are of major importance in inorganic mineral formation before we look at specific biological minerals. Some factors which have to be taken into account (other than those that are well-known from inorganic (abiological) precipitations) are: the nature of the biological organic matrix; the restricted volume, outside or inside the cytoplasm, which can cause differences in impurity content (Mg); crystal morphology; and isotopic fractionation. Cases such as those of corals, foraminifera and coccoliths are taken as examples.