bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular evidence for the identity of the Magenta petrel
Authors: LAWRENCE HAYLEY A. , MILLAR CRAIG D. , IMBER MICHAEL J. , CROCKETT DAVID E. , ROBINS JUDITH H. , SCOFIELD R. PAUL. , TAYLOR GRAEME A. , LAMBERT DAVID M. 
Published: January 2009

AbstractA lone petrel was shot from the decks of an Italian warship (the ‘Magenta’) while it was sailing the South Pacific Ocean in 1867, far from land. The species, unknown to science, was named the ‘Magenta petrel’ (Procellariiformes, Procellariidae, Pterodroma magentae). No other specimens of this bird were collected and the species it represented remained a complete enigma for over 100 years. We compared DNA sequence of the mitochondrial cytochrome b gene from the Magenta petrel to that of other petrels using phylogenetic methods and ancient DNA techniques. Our results strongly suggest that the Magenta petrel specimen is a Chatham Island taiko. Furthermore, given the collection location of the Magenta petrel, our finding indicates that the Chatham Island taiko forages far into the Pacific Ocean (near South America). This has implications for the conservation of the taiko, one of the world's rarest seabirds.
Isolation and characterization of nuclear microsatellite loci from Ceratopetalum apetalum (Cunoniaceae)
Authors: HESLEWOOD MARGARET M. , PORTER CAROLYN , AVINO MARIANO , ROSSETTO MAURIZIO 
Published: January 2009

AbstractWe identified 16 polymorphic nuclear microsatellite loci from an AG‐enriched library of Ceratopetalum apetalum. These loci were tested across two populations of C. apetalum, a single population of C. gummiferum and representatives of four other congeneric taxa. Fourteen loci were identified as polymorphic in at least one other species. These microsatellites will be used to look at population dynamics of species with varying distributions and presumed low dispersal capabilities within the genus Ceratopetalum.
Selecting barcoding loci for plants: evaluation of seven candidate loci with species‐level sampling in three divergent groups of land plants
Authors: HOLLINGSWORTH MICHELLE L. , ANDRA CLARK ALEX , FORREST LAURA L. , RICHARDSON JAMES , PENNINGTON R. TOBY , LONG DAVID G. , COWAN ROBYN , CHASE MARK W. , GAUDEUL MYRIAM , HOLLINGSWORTH PETER M. 
Published: January 2009

AbstractThere has been considerable debate, but little consensus regarding locus choice for DNA barcoding land plants. This is partly attributable to a shortage of comparable data from all proposed candidate loci on a common set of samples. In this study, we evaluated the seven main candidate plastid regions (rpoC1, rpoB, rbcL, matK, trnH‐psbA, atpF‐atpH, psbK‐psbI) in three divergent groups of land plants [Inga (angiosperm); Araucaria (gymnosperm); Asterella s.l. (liverwort)]. Across these groups, no single locus showed high levels of universality and resolvability. Interspecific sharing of sequences from individual loci was common. However, when multiple loci were combined, fewer barcodes were shared among species. Evaluation of the performance of previously published suggestions of particular multilocus barcode combinations showed broadly equivalent performance. Minor improvements on these were obtained by various new three‐locus combinations involving rpoC1, rbcL, matK and trnH‐psbA, but no single combination clearly outperformed all others. In terms of absolute discriminatory power, promising results occurred in liverworts (e.g. c. 90% species discrimination based on rbcL alone). However, Inga (rapid radiation) and Araucaria (slow rates of substitution) represent challenging groups for DNA barcoding, and their corresponding levels of species discrimination reflect this (upper estimate of species discrimination = 69% in Inga and only 32% in Araucaria; mean = 60% averaging all three groups).
Isolation and characterization of microsatellite loci in Merluccius australis and cross‐species amplification
Authors: MACHADO‐SCHIAFFINO G. , GARCIA‐VAZQUEZ E. 
Published: January 2009

AbstractEight novel and two heterologous microsatellite pairs of primers are presented for the Austral hake (Merluccius australis), representing the first microsatellite markers available for this species. Loci were characterized for 50 individuals from two populations in South America (Argentinean and Chilean coasts). All loci were polymorphic within M. australis (5 to 30 alleles per locus; observed heterozygosity between 0.320 and 0.840), and therefore useful for population genetic studies within the species. Cross‐species transferability was tested for 100 individuals from four additional species within the Merluccius genus (M. albidus, M. bilinearis, M. gayi and M. hubbsi), and results indicate that most of these primers pairs will likely be useful for population genetic studies on Merluccius species.
Development of simple sequence repeat markers for Japanese isolates of Magnaporthe grisea
Authors: SUZUKI F. , SUGA H. , TOMIMURA K. , FUJI S. , ARAI M. , KOBA A. , NAKAJIMA T. 
Published: January 2009

AbstractWe developed nine simple sequence repeat (SSR) markers useful for differentiating Japanese isolates of Magnaporthe grisea through a bioinformatic approach. Repeat sequences in the genome of M. grisea were identified by a Tandem Repeat Finding program. Length polymorphisms at 28 loci were examined, nine of which were selected on the basis of detected polymorphisms. These nine SSR markers showed a Nei's gene diversity ranging from 0.23 to 0.91 among 48 field isolates of two natural populations. These SSR markers are well suited for M. grisea epidemiology and population genetics.
Isolation and characterization of microsatellite markers from the great hornbill, Buceros bicornis
Authors: CHAMUTPONG SIRIPHATR , SAITO DAICHI S. , VISESHAKUL NAREERAT , NISHIUMI ISAO , POONSWAD PILAI , PONGLIKITMONGKOL MATHUROSE 
Published: January 2009

AbstractThirteen polymorphic microsatellite markers were isolated and characterized from the great hornbill, Buceros bicornis. In analyses of 20 individuals, the numbers of alleles per locus varied from two to 11. The expected and observed heterozygosities ranged from 0.22 to 0.88 and from 0.20 to 1.00, respectively. The mean polymorphic information content was 0.62. Among these, three loci deviated from the Hardy–Weinberg equilibrium. However, no significant genotypic disequilibrium was detected between any pair of loci. These microsatellite markers are useful for the population genetic study of the great hornbill.
Isolation and characterization of microsatellite markers in tree lizards (Urosaurus ornatus)
Authors: HAENEL GREGORY J. 
Published: January 2009

AbstractTree lizards (Urosaurus ornatus) are a highly accessible species useful in testing theories of life‐history evolution and behavioural ecology. A polymerase chain reaction‐based method was used to isolate nine polymorphic tetranucleotide microsatellite loci from the genome of these lizards. The isolated loci displayed 5 to 9 alleles in the populations screened. Observed heterozygosity ranged from 0.333 to 0.900. Results indicate these loci now provide a basis to study mate choice, parentage, and population genetic structure within this species.
Novel microsatellite loci in the grass snake (Natrix natrix) and cross‐amplification in the dice snake (Natrix tessellata)
Authors: MEISTER B. , ARMBRUSTER G. F. J. , FRAUENFELDER N. , BAUR B. 
Published: January 2009

AbstractSix novel polymorphic microsatellite loci are presented for the grass snake (Natrix natrix), a species with declining populations in many regions. The number of alleles per locus ranged from two to seven. Four dice snake (Natrix tessellata) microsatellites were polymorphic in the grass snake with three to four alleles. At two loci, the expected heterozygosity differed significantly from observed heterozygosity. Cross‐amplification of the grass snake markers in the dice snake showed two polymorphic microsatellites with two and four alleles.
Microsatellite markers for the endemic New Zealand long‐tailed bat (Chalinolobus tuberculatus)
Authors: DEKROUT ANDREA , CURSONS RAYMOND T. , WILKINS RICHARD J. 
Published: January 2009

AbstractThe New Zealand long‐tailed bat (Chalinolobus tuberculatus) is an endangered species which is now absent from many habitats where they were previously observed. However, population genetics studies have been hampered by the lack of reliable genetic markers. We have developed 13 microsatellite markers, and at least eight of these are suitable for population studies. Nine of these markers also cross‐react with the closely related Australian species C. gouldii. These markers may prove of general utility in the genus Chalinolobus.
Microsatellite loci for Ponto‐Caspian gobies: markers for assessing exotic invasions
Authors: FELDHEIM KEVIN A. , WILLINK PHILLIP , BROWN JOSHUA E. , MURPHY DOUGLAS J. , NEILSON MATTHEW E. , STEPIEN CAROL A. 
Published: January 2009

AbstractWe developed and tested eight polymorphic microsatellite loci for Ponto‐Caspian ‘neogobiin’ gobies, many of which are invasive in Eurasia and North America, whose study will aid understanding of the population genetics underlying their success. We tested samples from one to two locations from 12 taxa in the recently revised genera Babka, Benthophilus, Mesogobius, Neogobius = Apollonia, Ponticola and Proterorhinus; including the bighead, Caspian, knout, monkey, racer, round, tadpole and tubenose gobies; and taxa from introduced vs. native populations, those diverging between fresh and marine waters, and those differentiated between the Black and Caspian Seas. Populations conformed to Hardy–Weinberg equilibrium expectations, averaging five to 15 alleles per locus and 0.11 to 0.67 mean heterozygosity. Allelic variation significantly differentiated among all taxa and populations.
Effect of bromfenac ophthalmic solution on ocular inflammation following cataract surgery
Authors: Miyanaga Masaru , Miyai Takashi , Nejima Ryohei , Maruyama Yoko , Miyata Kazunori , Kato Satoshi 
Published: January 2009

Abstract.Purpose:  This study compared the post‐cataract surgery anti‐inflammatory effects of topical treatment with 0.1% bromfenac, 0.1% betamethasone or both on postoperative anterior chamber inflammation and corneal swelling.Methods:  Seventy‐two patients with no eye disease other than cataract were enrolled in a prospective, randomized study to undergo phacoemulsification combined with intraocular lens implantation. After cataract surgery, patients were randomized to treatment with bromfenac, betamethasone or both agents. Twenty‐five eyes were assigned to bromfenac, 23 to betamethasone and 24 to the combined treatment group. Inflammatory reactions in the anterior chamber were measured with laser flare photometry preoperatively and at 1 and 3 days, 1 and 2 weeks, and 1 and 2 months postoperatively. Intraocular pressure (IOP) and corneal thickness were measured at the same time‐points. Best corrected visual acuity (BCVA) was measured preoperatively and at 2 days, 1 and 2 weeks, and 1 and 2 months postoperatively. Specular microscope endothelial photography of the central region of the cornea was performed preoperatively and at 3 months after surgery.Results:  There were no significant differences among the bromfenac, betamethasone and combined treatment groups in BCVA, IOP, aqueous flare or corneal thickness. Cystoid macular oedema was present in one eye treated with betamethasone.Conclusions:  There were no significant differences in anti‐inflammatory effects among the three treatments. These findings suggest that bromfenac is as effective as betamethasone in minimizing inflammatory reactions after cataract surgery.
Autosomal dominant pericentral retinal dystrophy caused by a novel missense mutation in the TOPORS gene
Authors: Selmer Kaja Kristine , Grøndahl Jan , Riise Ruth , Brandal Kristin , Braaten Øivind , Bragadottir Ragnheidur , Undlien Dag Erik 
Published: January 2009

Abstract.Purpose:  This study aimed to identify the genetic cause of autosomal dominant pericentral retinal dystrophy (adPRD) in a large Norwegian family with 35 affected members.Methods:  The family was characterized by clinical ophthalmological examination along with fundus photography, dark adaptometry and electroretinography. We performed a genome‐wide linkage analysis followed by sequencing of a candidate gene to identify the mutation causing the disease.Results:  The ophthalmological examinations revealed an atypical form of retinitis pigmentosa (RP), which we prefer to call adPRD. Compared with classical RP, this phenotype has a favourable prognosis. Linkage analysis showed a linkage peak covering the most recently reported adRP gene TOPORS. This gene was sequenced in 19 family members and a novel missense mutation, c.1205a>c, resulting in an amino acid substitution p.Q402P, was detected in all affected members. The mutation showed complete co‐segregation with the disease in this family, with a LOD score of 7.3. It is located in a highly conserved region and alignment with the appropriate DNA sequence from other species shows complete conservation of this amino acid. The mutation was not detected in 207 healthy, unrelated controls of Norwegian origin.Conclusions:  We present a novel mutation in the TOPORS gene co‐segregating with a distinct phenotype of adPRD in a large Norwegian family.
Dynamics of Polyphosphate-Accumulating Bacteria in Wastewater Treatment Plant Microbial Communities Detected via DAPI (4′,6′-Diamidino-2-Phenylindole) and Tetracycline Labeling
Authors: Günther S. , Trutnau M. , Kleinsteuber S. , Hause G. , Bley T. , Röske I. , Harms H. , Müller S. 
Published: January 2009

ABSTRACT

Wastewater treatment plants with enhanced biological phosphorus removal represent a state-of-the-art technology. Nevertheless, the process of phosphate removal is prone to occasional failure. One reason is the lack of knowledge about the structure and function of the bacterial communities involved. Most of the bacteria are still not cultivable, and their functions during the wastewater treatment process are therefore unknown or subject of speculation. Here, flow cytometry was used to identify bacteria capable of polyphosphate accumulation within highly diverse communities. A novel fluorescent staining technique for the quantitative detection of polyphosphate granules on the cellular level was developed. It uses the bright green fluorescence of the antibiotic tetracycline when it complexes the divalent cations acting as a countercharge in polyphosphate granules. The dynamics of cellular DNA contents and cell sizes as growth indicators were determined in parallel to detect the most active polyphosphate-accumulating individuals/subcommunities and to determine their phylogenetic affiliation upon cell sorting. Phylotypes known as polyphosphate-accumulating organisms, such as a “
Candidatus
Accumulibacter”-like phylotype, were found, as well as members of the genera
Pseudomonas
and
Tetrasphaera
. The new method allows fast and convenient monitoring of the growth and polyphosphate accumulation dynamics of not-yet-cultivated bacteria in wastewater bacterial communities.
Improved Fermentation Performance of a Lager Yeast after Repair of Its
AGT1
Maltose and Maltotriose Transporter Genes
Authors: Vidgren Virve , Huuskonen Anne , Virtanen Hannele , Ruohonen Laura , Londesborough John 
Published: January 2009

ABSTRACT

The use of more concentrated, so-called high-gravity and very-high-gravity (VHG) brewer's worts for the manufacture of beer has economic and environmental advantages. However, many current strains of brewer's yeasts ferment VHG worts slowly and incompletely, leaving undesirably large amounts of maltose and especially maltotriose in the final beers. α-Glucosides are transported into
Saccharomyces
yeasts by several transporters, including Agt1, which is a good carrier of both maltose and maltotriose. The
AGT1
genes of brewer's ale yeast strains encode functional transporters, but the
AGT1
genes of the lager strains studied contain a premature stop codon and do not encode functional transporters. In the present work, one or more copies of the
AGT1
gene of a lager strain were repaired with DNA sequence from an ale strain and put under the control of a constitutive promoter. Compared to the untransformed strain, the transformants with repaired
AGT1
had higher maltose transport activity, especially after growth on glucose (which represses endogenous α-glucoside transporter genes) and higher ratios of maltotriose transport activity to maltose transport activity. They fermented VHG (24° Plato) wort faster and more completely, producing beers containing more ethanol and less residual maltose and maltotriose. The growth and sedimentation behaviors of the transformants were similar to those of the untransformed strain, as were the profiles of yeast-derived volatile aroma compounds in the beers.
Stress- and Growth Rate-Related Differences between Plate Count and Real-Time PCR Data during Growth of
Listeria monocytogenes
Authors: Reichert-Schwillinsky Franziska , Pin Carmen , Dzieciol Monika , Wagner Martin , Hein Ingeborg 
Published: January 2009

ABSTRACT

To assess the overestimation of bacterial cell counts in real-time PCR in relation to stress and growth phase, four different strains of
L. monocytogenes
were exposed to combinations of osmotic stress (0.5 to 8% [vol/vol] NaCl) and acid stress (pH 5 to 7) in a culture model at a growth temperature of 10°C or were grown under optimal conditions. Growth curves obtained from real-time PCR, optical density, and viable count data were compared. As expected, optical density data revealed entirely different growth curves. Good to moderate growth conditions yielded good correlation of real-time PCR data and plate count data (
r
2
= 0.96 and 0.99) with similar cell counts. When growth conditions became worse, the numbers of CFU decreased during the stationary phase, whereas real-time-PCR-derived bacterial cell equivalents differed in this regard; the correlation worsened (
r
2
= 0.84). However, fitted growth curves revealed that maximum growth rates calculated from real-time PCR data were not significantly different from those derived from plate count data. The overestimation of bacterial cell counts by real-time PCR observed in the stationary phase under higher-stress conditions might be explained by the accumulation of viable but nonculturable bacteria or dead bacteria and extracellular DNA. Considering these results, real-time PCR data collected from naturally contaminated samples should be viewed with caution.
Construction of Disarmed Ti Plasmids Transferable between
Escherichia coli
and
Agrobacterium
Species
Authors: Kiyokawa Kazuya , Yamamoto Shinji , Sakuma Kei , Tanaka Katsuyuki , Moriguchi Kazuki , Suzuki Katsunori 
Published: January 2009

ABSTRACT

Agrobacterium
-mediated plant transformation has been used widely, but there are plants that are recalcitrant to this type of transformation. This transformation method uses bacterial strains harboring a modified tumor-inducing (Ti) plasmid that lacks the transfer DNA (T-DNA) region (disarmed Ti plasmid). It is desirable to develop strains that can broaden the host range. A large number of
Agrobacterium
strains have not been tested yet to determine whether they can be used in transformation. In order to improve the disarming method and to obtain strains disarmed and ready for the plant transformation test, we developed a simple scheme to make certain Ti plasmids disarmed and simultaneously maintainable in
Escherichia coli
and mobilizable between
E. coli
and
Agrobacterium
. To establish the scheme in nopaline-type Ti plasmids, a neighboring segment to the left of the left border sequence, a neighboring segment to the right of the right border sequence of pTi-SAKURA, a cassette harboring the pSC101 replication gene between these two segments, the broad-host-range IncP-type
oriT
, and the gentamicin resistance gene were inserted into a suicide-type
sacB
-containing vector. Replacement of T-DNA with the cassette in pTiC58 and pTi-SAKURA occurred at a high frequency and with high accuracy when the tool plasmid was used. We confirmed that there was stable maintenance of the modified Ti plasmids in
E. coli
strain S17-1λpir and conjugal transfer from
E. coli
to Ti-less
Agrobacterium
strains and that the reconstituted
Agrobacterium
strains were competent to transfer DNA into plant cells. As the modified plasmid delivery system was simple and efficient, conversion of strains to the disarmed type was easy and should be applicable in studies to screen for useful strains.
Evolutionary History of the
phl
Gene Cluster in the Plant-Associated Bacterium
Pseudomonas fluorescens
Authors: Moynihan Jennifer A. , Morrissey John P. , Coppoolse Eric R. , Stiekema Willem J. , O'Gara Fergal , Boyd E. Fidelma 
Published: January 2009

ABSTRACT

Pseudomonas fluorescens
is of agricultural and economic importance as a biological control agent largely because of its plant association and production of secondary metabolites, in particular 2,4-diacetylphloroglucinol (2,4-DAPG). This polyketide, which is encoded by the eight-gene
phl
cluster, has antimicrobial effects on phytopathogens, promotes amino acid exudation from plant roots, and induces systemic resistance in plants. Despite its importance, 2,4-DAPG production is limited to a subset of
P. fluorescens
strains. Determination of the evolution of the
phl
cluster and understanding the selective pressures promoting its retention or loss in lineages of
P. fluorescens
will help in the development of
P. fluorescens
as a viable and effective inoculant for application in agriculture. In this study, genomic and sequence-based approaches were integrated to reconstruct the phylogeny of
P. fluorescens
and the
phl
cluster. It was determined that 2,4-DAPG production is an ancestral trait in the species
P. fluorescens
but that most lineages have lost this capacity through evolution. Furthermore, intragenomic recombination has relocated the
phl
cluster within the
P. fluorescens
genome at least three times, but the integrity of the cluster has always been maintained. The possible evolutionary and functional implications for retention of the
phl
cluster and 2,4-DAPG production in some lineages of
P. fluorescens
are discussed.
Codon-Optimized Fluorescent Proteins Designed for Expression in Low-GC Gram-Positive Bacteria
Authors: Sastalla Inka , Chim Kannie , Cheung Gordon Y. C. , Pomerantsev Andrei P. , Leppla Stephen H. 
Published: January 2009

ABSTRACT

Fluorescent proteins have wide applications in biology. However, not all of these proteins are properly expressed in bacteria, especially if the codon usage and genomic GC content of the host organism are not ideal for high expression. In this study, we analyzed the DNA sequences of multiple fluorescent protein genes with respect to codons and GC content and compared them to a low-GC gram-positive bacterium,
Bacillus anthracis
. We found high discrepancies for cyan fluorescent protein (CFP), yellow fluorescent protein (YFP), and the photoactivatable green fluorescent protein (PAGFP), but not GFP, with regard to GC content and codon usage. Concomitantly, when the proteins were expressed in
B. anthracis
, CFP- and YFP-derived fluorescence was undetectable microscopically, a phenomenon caused not by lack of gene transcription or degradation of the proteins but by lack of protein expression. To improve expression in bacteria with low genomic GC contents, we synthesized a codon-optimized
gfp
and constructed optimized photoactivatable
pagfp
,
cfp
, and
yfp
, which were in contrast to nonoptimized genes highly expressed in
B. anthracis
and in another low-GC gram-positive bacterium,
Staphylococcus aureus.
Using optimized GFP as a reporter, we were able to monitor the activity of the protective antigen promoter of
B. anthracis
and confirm its dependence on bicarbonate and regulators present on virulence plasmid pXO1.