bluuebunny/crossref_metadata_2025_split huggingface dataset:
Next‐generation mapping of Arabidopsis genes
Authors: Austin Ryan S. , Vidaurre Danielle , Stamatiou George , Breit Robert , Provart Nicholas J. , Bonetta Dario , Zhang Jianfeng , Fung Pauline , Gong Yunchen , Wang Pauline W. , McCourt Peter , Guttman David S. 
Published: April 2011

SummaryNext‐generation genomic sequencing technologies have made it possible to directly map mutations responsible for phenotypes of interest via direct sequencing. However, most mapping strategies proposed to date require some prior genetic analysis, which can be very time‐consuming even in genetically tractable organisms. Here we present a de novo method for rapidly and robustly mapping the physical location of EMS mutations by sequencing a small pooled F2 population. This method, called Next Generation Mapping (NGM), uses a chastity statistic to quantify the relative contribution of the parental mutant and mapping lines to each SNP in the pooled F2 population. It then uses this information to objectively localize the candidate mutation based on its exclusive segregation with the mutant parental line. A user‐friendly, web‐based tool for performing NGM analysis is available at http://bar.utoronto.ca/NGM. We used NGM to identify three genes involved in cell‐wall biology in Arabidopsis thaliana, and, in a power analysis, demonstrate success in test mappings using as few as ten F2 lines and a single channel of Illumina Genome Analyzer data. This strategy can easily be applied to other model organisms, and we expect that it will also have utility in crops and any other eukaryote with a completed genome sequence.
Effect of Dietary Fibre on Reproductive Performance of Sows During the First Two Parities
Authors: Che L , Feng D , Wu D , Fang Z , Lin Y , Yan T 
Published: April 2011

ContentsThe aim of this study was to investigate the effect of dietary fibre on reproductive performance during the first two parities. Gilts were randomly allocated to receive three fibrous diets from days 1–90 of gestation, including low fibre [low fiber (LF), 10.8% neutral detergent fiber (NDF), n = 132], middle fibre [middle fiber (MF), 15.8% NDF, n = 132] and high fibre diet (HF, 20.8% NDF, n = 135), until completion of the second parity. Response criteria included backfat measurements, litter size and pig weight at parturition and day 22 of lactation, weaning‐oestrus‐interval, oestrus rate, sow farrowing and culling rate, uniformity of newborns and relative organ weights. The results showed sows fed LF diet in parity 1 gained more backfat (p < 0.05) during gestation but lost more (p < 0.05) during lactation than sows fed HF diet. Furthermore, sows fed LF diet farrowed more pigs (+0.7–1.1 pigs, p < 0.05) and pigs born alive (+1.0 pigs, p < 0.05) relative to sows fed HF diet. Likewise, sows fed LF and MF diets had greater litter weights at parturition (both p = 0.06) and day 22 after lactation (both p < 0.05). In parity 2, yet, it was MF diet to increase both total pigs born and pigs born alive (+0.9–1.1 pigs, p < 0.05) and litter weight (p = 0.05) relative to other diets. After 22 d of lactation, intriguingly, sows fed HF diet had most pigs alive (p < 0.01–0.07) and heavier litter weight (p = 0.07 or 0.2). Feeding HF diet also increased internal organs weight of newborns (p < 0.05). Collectively, feeding LF and MF diets had beneficial effects on litter weight at parturition and day 22 of lactation in parity 1, and feeding MF diet until parity 2 was able to improve litter size and weight at parturition, but this positive effect disappeared after 22 days of lactation, instead feeding HF diet showed the optimal litter performance.
Comparison of the Effects of Environmental Parameters on Growth Rates of Vibrio vulnificus Biotypes I, II, and III by Culture and Quantitative PCR Analysis
Authors: Chase Eva , Harwood Valerie J. 
Published: April 2011

ABSTRACT

Vibrio vulnificus
is a natural inhabitant of estuarine waters. The three known biotypes include (i) most human pathogens, (ii) primarily eel pathogens, and (iii) pathogens associated with fish and with human wound infections in Israel. Despite the frequently lethal consequences of
V. vulnificus
infections, the growth rates of the various biotypes and their response to environmental changes are not well characterized. We compared the specific growth rates (μ) of a representative of each biotype by culture and quantitative PCR (qPCR) analysis in a defined medium under varied pH, temperature, and salinity. Growth rates based on culturable concentrations were always higher than those based on qPCR estimates; however, both enumeration methods yielded comparable results on the influence of environmental factors on growth rates. Temperature (25°C, 30°C, 37°C), pH (7.0, 8.0), and salinity (5 to 40‰) all had significant effects on the μ of each biotype. Temperature had the greatest effect on the μ of biotype 1 (CMCP6), whereas salinity had the greatest effect on the μ of biotypes 2 (ATCC 33147) and 3 (302/99). The biotypes' growth rates varied significantly; biotype 1 grew most rapidly, while biotype 3 grew most slowly. The highest growth rates were achieved at 37°C, pH 7.0, and salinities of 15 to 30‰ (μ = 4.0, 2.9, and 2.4 generations h
−1
for biotypes 1, 2, and 3, respectively). Other strains of the biotypes yielded comparable results, suggesting that the physiological responses of the biotypes are differentially affected by parameters that are highly variable both in estuarine environments and between the free-living and pathogen states of
V. vulnificus
.
Differing Growth Responses of Major Phylogenetic Groups of Marine Bacteria to Natural Phytoplankton Blooms in the Western North Pacific Ocean
Authors: Tada Yuya , Taniguchi Akito , Nagao Ippei , Miki Takeshi , Uematsu Mitsuo , Tsuda Atsushi , Hamasaki Koji 
Published: April 2011

ABSTRACT

Growth and productivity of phytoplankton substantially change organic matter characteristics, which affect bacterial abundance, productivity, and community structure in aquatic ecosystems. We analyzed bacterial community structures and measured activities inside and outside phytoplankton blooms in the western North Pacific Ocean by using bromodeoxyuridine immunocytochemistry and fluorescence
in situ
hybridization (BIC-FISH).
Roseobacter/Rhodobacter
, SAR11,
Betaproteobacteria
,
Alteromonas
, SAR86, and
Bacteroidetes
responded differently to changes in organic matter supply.
Roseobacter/Rhodobacter
bacteria remained widespread, active, and proliferating despite large fluctuations in organic matter and chlorophyll
a
(Chl-
a
) concentrations. The relative contribution of
Bacteroidetes
to total bacterial production was consistently high. Furthermore, we documented the unexpectedly large contribution of
Alteromonas
to total bacterial production in the bloom. Bacterial abundance, productivity, and growth potential (the proportion of growing cells in a population) were significantly correlated with Chl-
a
and particulate organic carbon concentrations. Canonical correspondence analysis showed that organic matter supply was critical for determining bacterial community structures. The growth potential of each bacterial group as a function of Chl-
a
concentration showed a bell-shaped distribution, indicating an optimal organic matter concentration to promote growth. The growth of
Alteromonas
and
Betaproteobacteria
was especially strongly correlated with organic matter supply. These data elucidate the distinctive ecological role of major bacterial taxa in organic matter cycling during open ocean phytoplankton blooms.
Complete Genome Sequence of Bacillus amyloliquefaciens TA208, a Strain for Industrial Production of Guanosine and Ribavirin
Authors: Zhang Guoqiang , Deng Aihua , Xu Qingyang , Liang Yong , Chen Ning , Wen Tingyi 
Published: April 2011

ABSTRACT

Here, we report the complete genome sequence of
Bacillus amyloliquefaciens
TA208, a strain for industrial production of guanosine and synthesis of ribavirin by assimilation of formamide. Comparison of its genome sequence with those of strains DSM7 and FZB42 revealed horizontal gene transfer represented by unique prophages and restriction-modification systems and indicated significant accumulation of guanosine.
The Sensor Kinase KinB Regulates Virulence in Acute Pseudomonas aeruginosa Infection
Authors: Chand Nikhilesh S. , Lee Jenny See-Wai , Clatworthy Anne E. , Golas Aaron J. , Smith Roger S. , Hung Deborah T. 
Published: April 2011

ABSTRACT

Two-component sensors are widely used by bacteria to sense and respond to the environment.
Pseudomonas aeruginosa
has one of the largest sets of two-component sensors known in bacteria, which likely contributes to its unique ability to adapt to multiple environments, including the human host. Several of these two-component sensors, such as GacS and RetS, have been shown to play roles in virulence in rodent infection models. However, the role and function of the majority of these two-component sensors remain unknown.
Danio rerio
is a recently characterized model host for pathogenesis-related studies that is amenable to higher-throughput analysis than mammalian models. Using zebrafish embryos as a model host, we have systematically tested the role of 60 two-component sensors and identified 6 sensors that are required for
P. aeruginosa
virulence. We found that KinB is required for acute infection in zebrafish embryos and regulates a number of virulence-associated phenotypes, including quorum sensing, biofilm formation, and motility. Its regulation of these phenotypes is independent of its kinase activity and its known response regulator AlgB, suggesting that it does not fit the canonical two-component sensor-response regulator model.
The use of CellaVision competency software for external quality assessment and continuing professional development
Authors: Horiuchi Yuki , Tabe Yoko , Idei Mayumi , Bengtsson Hans-Inge , Ishii Kiyoshi , Horii Takashi , Miyake Kazunori , Satoh Naotake , Miida Takashi , Ohsaka Akimichi 
Published: April 2011

AimsQuality assessment of blood cell morphological testing, such as white blood cell (WBC) differential and its interpretation, is one of the most important and difficult assignments in haematology laboratories. A monthly survey was performed to assess the possible role of the proficiency testing program produced by CellaVision competency software (CCS) in external quality assessment (EQA) of the clinical laboratories of affiliated university hospitals and the effective utilisation of this program in continuing professional development (CPD).MethodsFour monthly proficiency surveys were conducted in collaboration with four clinical laboratories affiliated with the teaching hospitals of Juntendo University of Medicine in Japan.ResultsEQA results by the CCS proficiency testing program revealed a difference of performance levels of WBC differential and morphological interpretation and a discrepancy in the WBC differential criteria among laboratories. With regard to the utilisation of this proficiency program as a tool for CPD, this program successfully improved the performance of the low-scoring laboratories and less experienced individuals.ConclusionsThe CCS proficiency testing program was useful for the quality assessment of laboratory performance, for education, and for the storage and distribution of cell images to be utilised for further standardisation and education.
Intraspecific variation in sex heterochromatin of species B of the Anopheles dirus complex in Thailand
Authors: Baimai V. , Traipakvasin A. 
Published: April 2011

Cytological examination of F1 larval mitotic chromosomes from a total of 126 families of Anopheles dirus species B from southern Thailand populations has revealed a pronounced quantitative variation of constitutive heterochromatin in the two sex chromosomes. Five types of X chromosomes and four types of Y chromosomes have been identified in this study. Such gross variation in sex chromosomes is most likely due to a gradual acquisition of extra heterochromatin. Key words: Anopheles, heterochromatin variation, coevolution, sex chromosomes.
A separate control for frequency and within-bivalent distribution of chiasmata in rye (Secale cereale L.)
Authors: Lein V. , Lelley T. 
Published: April 2011

Six genetically different inbred genotypes of spring-type rye Secale cereale with differences in the average number and in the positional distribution of chiasmata were used in this study. The line with the lowest chiasma frequency was chosen as the female parent and crossed with the other five lines. Parental, F1, and F2 data were collected on chiasma number and on chiasma distribution between and within bivalents. Evidence for a polygenic control of both phenomena was found. Chiasma distribution between bivalents within pollen mother cells obviously follows a binomial distribution. This is effected by a mechanism that prevents the formation of a second chiasma on a chromosome arm as long as chromosome arms without chiasma remain; i.e., with 14 chiasmata seven ring bivalents will generally be formed. This mechanism causes a very strong negative correlation between frequency and between-cell variance of chiasmata. The number of chiasmata is independent of their position within the bivalents. A very close correlation between the number of pollen mother cells without univalents and the number of fertile pollen grains was found. Key words: inbred rye, genetic control, chiasma frequency, chiasma distribution, heterosis.
The effect of gamma radiation on recombination frequency in Caenorhabditis elegans
Authors: Kim J. S. , Rose A. M. 
Published: April 2011

We have studied the effect of gamma radiation on recombination frequency for intervals across the cluster of linkage group I in Caenorhabditis elegans. Recombination frequency increased approximately twofold across the dpy-5–unc-13 interval after treatment with 2000 rads (1 rad = 10 mGy) of cobalt 60 gamma radiation. Several factors affecting the magnitude of the increase have been characterized. Recombination frequency increased more with higher doses of radiation. However, the increase in recombination frequency with increasing dose was accompanied by a reduced average number of progeny from radiation-treated individuals. The amount of the increase was affected by meiotic stage, age at the time of treatment (premeiotic), and radiation dose. The increase in recombination was detectable in the B brood and remained elevated for the remainder of egg production. X-chromosome nondisjunction was also increased by radiation treatment. A high frequency of the recombinant progeny produced with radiation treatment were sterile unlike their nonrecombinant siblings. When parameters affecting recombination frequency are held constant during treatment, chromosomal regions of high gene density on the meiotic map increased more (fourfold) than an adjacent region of low gene density (no increase). The greatest increase was across the dpy-14–unc-13 interval near the center of the gene cluster. These results may suggest that the physical length of DNA per map unit is greater within the cluster than outside. Key words: recombination, radiation, nondisjunction, map expansion, genetic map.
Chromosome location and linkage of a new gene (Lr33) for reaction to Puccinia recondita in common wheat
Authors: Dyck P. L. , Kerber E. R. , Lukow O. M. 
Published: April 2011

A gene for resistance to Puccinia recondita, originally detected in wheat (Triticum aestivum L.) accessions PI58548, PI268454, and PI268316, has been located on the long arm of chromosome 1B, 3.1 ± 1.2 crossover units from the centromere. In a cross between the backcross line RL6057 containing this new gene, now designated Lr33, and the backcross line RL6078 containing gene Lr26, gene Lr33 is closely linked to gene Lr26 (or the translocation breakpoint) with an estimated 2.6 ± 0.8 recombination value. RL6057 and RL6078 differ in gliadin bands that are controlled by genes on the short arm of chromosome 1B or 1R. The banding difference was completely associated with the presence or absence of Lr26. Key words: Triticum, Puccinia, linkage.
Inheritance and expression of tissue-specific catalase activity during development and aging in mice
Authors: Schisler N. J. , Singh S. M. 
Published: April 2011

The catalase activity in the liver, kidney, lung, and blood hemolysate was measured in newborn, 21-, 70-, 175-, and >400-day-old mice from the strains BALB/c, Csb, C3H/HeSnJ, C3H/S, C57BL/6J, SW, and 129/ReJ. Catalase activity was found to be highest in the liver (~0.33 U/mg protein) followed by the kidney (~0.13 U/mg protein), lung (~0.05 U/mg protein), and blood hemolysate (~0.03 U/mg protein). ANOVA analysis indicated significant differences in enzyme activity among strains and age groups studied. The developmental profiles of enzyme activity were tissue and strain specific. Catalase activity in the blood, for example, was generally higher at birth and at old age, whereas the kidney catalase activity was low at birth and increased substantially with age. Strains could be classified as normal (129/ReJ, BALB/c, C3H/HeSnJ, C3H/S), hypocatalasemic (C57BL/6J, SW), and acatalasemic (Csb) with respect to enzyme activity and it was on this basis that the inheritance of the catalase phenotype was studied using appropriate crosses. The enzyme activity level in each tissue appears to be governed by a unique set of genetic regulators/modifiers that interact with a single structural gene (Cs) or its product to produce the catalase phenotype. Some of these (e.g., Ce-1 and Ce-2) have been previously described but based on the results of various crosses reported here, more must exist that remain still uncharacterized at the molecular level. Models proposed for the inheritance of the catalase phenotype vary in complexity from single allelic differences between strains (e.g., BALB/c × Csb; blood) to a system of multiple interacting genetic determinants (e.g., BALB/c × Csb; liver) each having dominant (e.g., C57BL/6J over BALB/c; liver) and recessive components (e.g., gene(s) conferring the acatalasemic phenotype in BALB/c × Csb; blood and kidney). Such results are important and offer an interesting model to further characterize aspects of eukaryotic gene regulation. Key words: catalase, inbred mice, tissue specificity, developmental profile, inheritance.
Among- and within-population variability for forage yield and Fusarium resistance in birdsfoot-trefoil
Authors: Hill Jr. R. R. , Zeiders K. E. 
Published: April 2011

Polycross families of birdsfoot-trefoil, Lotus corniculatus L., were evaluated in the greenhouse for number of live plants 120 days after inoculation with Fusarium oxysporum (Schlecht) Snyd. & Hans, and in the field for forage yield and stand scores. The parents of the polycross progenies came from 11 different birdsfoot-trefoil cultivars. The objective of the experiment was to determine relative importance of source population and parents within source population as sources of variability for reaction for F. oxysporum, forage yield, and stand score. Expected values for means of polycross families within source populations and for source populations were expressed in terms of parameters from a previously developed autotetraploid genetic model. All genetic effects were present in the equations, but variation among source populations would be important only if the source populations differed in gene frequencies. Source populations were the only significant source of variation for the number of live plants 120 days after inoculation with F. oxysporum and the stand score. A significant year by source population interaction was observed for total season yield. The correlation between number of live plants in the greenhouse and the stand score was significant. We concluded (i) selection of source population was important when breeding for resistance to F. oxysporum or improved stand but not for total season yield, and (ii) successful breeding for resistance to F. oxysporum would contribute to improved persistence in birdsfoot-trefoil. Key words: Lotus corniculatus L., Fusarium oxysporum, polycross progeny, selection.
Inheritance and linkage relationships of 6-phosphogluconate dehydrogenase isozymes in soybean
Authors: Chiang Y. C. , Kiang Y. T. 
Published: April 2011

The inheritance of 6-phosphogluconate dehydrogenase (6-PGD) in dry seeds of cultivated and wild soybean was studied electrophoretically. There are four 6-PGD anodal bands that are controlled by three loci. Bands 1 and 3 are homodimers, whereas band 2 is the interlocus heterodimer of bands 1 and 3, which are products of the Pgd1 and Pgd2 loci, respectively. Both Pgd1 and Pgd2 loci have three codominant alleles (Pgd1-a, Pgd1-b, Pgd1-c and Pgd2-a, Pgd2-b, Pgd2-c) and each of the alleles specifies an isozyme band. The two variants of the fourth band are the result of two codominant alleles (Pgd3-a and Pgd3-b) of the Pgd3 locus. The Pgd3-a allele is found only in PI486.220, a Glycine soja accession from Japan. The Pgd2 is linked to Ap, Ti, and Lap1 in the order of Ap–Ti–Lap1–Pgd2 and belongs to linkage group 9. Key words: soybean isozymes linkage, genetics of Pgd loci.
Metaphase association of mammalian chromosomes
Authors: Mayr-Wohlfart U. , Adolph S. , Klett Ch. , Hameister H. 
Published: April 2011

The association behavior of chromosomes bearing nucleolar organizer region (NOR) and (or) C-heterochromatin in metaphase plates was analyzed. Different species with an informative chromosomal localization of NOR and C-heterochromatin were evaluated. Several examples indicate that the well-known metaphase association is not due to NORs or NOR activity per se. Other mechanisms such as ectopic pairing are responsible for the association. These types of pairing seem to be enhanced by the chromatin-decondensing effect of nearby NOR activity. Key words: NOR, C-heterochromatin, metaphase association.
The cytogenetic relationship between Cicer judaicum Boiss. and Cicer chorassanicum (Bge.) M. Pop.
Authors: Ahmad F. , Slinkard A. E. , Scoles G. J. 
Published: April 2011

A single plant was produced of the interspecific hybrid Cicer judaicum Boiss. (2n = 16) × Cicer chorassanicum (Bge.) M. Pop. (2n = 16), but none was produced from the reciprocal cross. The hybrid plant was intermediate in morphology between the parental species with the dominant purple flower color of C. judaicum. The hybrid plant had a diploid somatic chromosome number of 2n = 16 and was characterized cytologically. The hybrid had a low chiasmata frequency (5.4 ± 1.2 vs. 12.1 and 11.4 in the parental species) per cell and was highly sterile. The flowers were abnormal in that the stigma and style grew out of the keel, while the anthers remained inside. Sterility and abnormal floral structure may play important roles in maintenance of species identity. Key words: interspecific hybrid.