bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inhibition of vascular smooth muscle cell migration by serum from rats treated orally with Saiko-ka-Ryukotsu-Borei-To, a traditional Chinese formulation
Authors: Chung Hwa-Jin , Maruyama Ikuro , Tani Tadato 
Published: September 2004

Abstract
Oral administration of Saiko-ka-Ryukotsu-Borei-To (SRB), a traditional Chinese formulation, has been found to prevent intimal thickening of the carotid artery after balloon endothelial denudation in cholesterol-fed rats. To clarify the mechanism of this effect, the present study investigated if SRB inhibits vascular smooth muscle cell (VSMC) migration, which plays an important role in the development of intimal thickening after endothelial injury. The serum (SRB serum) sampled from cholesterol-fed rats treated orally with SRB for 3 days before and 4 days after the injury dose-dependently inhibited the migration of cultured VSMCs. When added directly to cultured VSMCs, the SRB extract did not inhibit VSMC migration. It is remarkable that SRB serum, which may contain a much lower concentration of SRB ingredients compared with the SRB extract, inhibited cultured VSMC migration. The present testing system using serum obtained from animals treated orally with traditional Chinese formulations may be useful for clarifying the pharmacological efficacy of such drugs, including many non-absorbable components. Furthermore, it may be useful in the search for new active compounds in serum after oral administration of traditional Chinese formulations, the active metabolites of which have not been identified.
Hyperici herba extract interaction with artificial lipid bilayers
Authors: Neagoe Ioana , Macri Beatrice M , Flonta Maria Luisa 
Published: September 2004

Abstract
Hyperici herba (Hyp) is the aerial part collected during the flowering period from the well-known herb, Hypericum perforatum. Black lipid membrane experiments were performed to investigate the effect of the ethanolic Hyp extract on the electrical properties (capacitance and conductance) of artificial lipid bilayers. Hyp extract (1–10 μg mL−1) induced a concentration-dependent increase of both specific transmembrane capacitance and conductance in phosphatidylcholine (PC) membranes. The effect on conductance was enhanced when the Hyp extract (3 μg mL−1) was present on both sides of the membrane (Gm = 77.89 ± 8.81 nS cm−2, n = 5) compared with single-sided application (Gm = 36.48 ± 2.41 nS cm−2, n = 5). In bilayers containing PC and phosphatidylserine (PS), PC:PS, the Hyp extract effect was greater than on pure PC bilayers, although the surface charge was not the determining factor of this enhanced activity. Adding cholesterol to the PC:PS mixture reverted the conductance increase induced by the Hyp extract in a dose-dependent manner. The specific pattern of the Hyp extract interaction with lipid bilayers has possible consequences concerning its absorption and bioavailability, as well as its pharmacodynamic effects on neuronal excitability.
Developing indicators: issues in the use of quantitative data about poverty
Authors: Spicker Paul 
Published: September 2004

English
Indicators are often confused with measures. This article argues that precise measurement is often inappropriate in relation to complex, multidimensional issues such as poverty. A good indicator should be understood as a pointer, not a measure. It should be accessible, robust and reinforced by other pointers. By treating indicators as quantities, summary indices conceal key issues, hide the values and concepts implicit in the exercise, and are vulnerable to mathematical accident. Using multiple indicators is sounder in principle, in methodological terms, and in practical application.
Rough sleeping in rural England: challenging a problem denied
Authors: Robinson David 
Published: September 2004

English
Rough sleeping in rural England is a social problem denied. This neglect reflects the more general noncoupling of homelessness and rurality, with idyll-ised notions of rural England informing interpretations of social problems in rural spaces. This article contends that this non-coupling also stems from the inappropriate application of traditional methods for estimating rough sleeping in rural locations. The particular geography of problem recognition that has driven the policy response to rough sleeping is revealed and the insights provided by and challenges raised through the application of an alternative method of counting rough sleeping sensitive to the rural context are exposed.
Fyn kinase–tubulin interaction during meiosis of rat eggs
Authors: Talmor-Cohen A , Tomashov-Matar R , Tsai W B , Kinsey W H , Shalgi R 
Published: September 2004

Prior to fertilization, the spindle of vertebrate eggs must remain stable and well organized during the second meiotic meta-phase arrest (MII). In a previous study we have determined that the completion of meiosis is a Src family kinase (SFK)-dependent event. In the current study we have used the SFK inhibitors, SU6656 and PP2, and demonstrated that inhibition of SFKs caused the formation of a disorganized spindle. The observation that proper organization of an MII spindle is an SFK-dependent process, combined with our previous finding that Fyn kinase is localized at the microtubules (MTs), prompted us to examine the potential role of Fyn in MT signaling. Our results show an association between Fyn and tubulin, the ability of Fyn to phosphorylate tubulinin vitroand stimulation of meiosis completion by injection of a constitutively active form of Fyn (CAF).We suggested that SFKs mediate significant functions during the organization of the MII spindle. In view of CAF injection experiments, and of the pronounced concentration of Fyn kinase at the spindle, we propose that Fyn may play an important role in some aspects of the spindle functions, possibly those involving the MTs.
A Microsatellite Genetic Linkage Map for XiphophorusSequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession nos. AY258640, AY258896.
Authors: Walter R B , Rains J D , Russell J E , Guerra T M , Daniels C , Johnston Dennis A , Kumar Jay , Wheeler A , Kelnar K , Khanolkar V A , Williams E L , Hornecker J L , Hollek L , Mamerow M M , Pedroza A , Kazianis S 
Published: September 2004

Abstract
Interspecies hybrids between distinct species of the genus Xiphophorus are often used in varied research investigations to identify genomic regions associated with the inheritance of complex traits. There are 24 described Xiphophorus species and a greater number of pedigreed strains; thus, the number of potential interspecies hybrid cross combinations is quite large. Previously, select Xiphophorus experimental crosses have been shown to exhibit differing characteristics between parental species and among the hybrid fishes derived from crossing them, such as widely differing susceptibilities to chemical or physical agents. For instance, genomic regions harboring tumor suppressor and oncogenes have been identified via linkage association of these loci with a small set of established genetic markers. The power of this experimental strategy is related to the number of genetic markers available in the Xiphophorus interspecies cross of interest. Thus, we have undertaken the task of expanding the suite of easily scored markers by characterization of Xiphophorus microsatellite sequences. Using a cross between Xiphophorus maculatus and X. andersi, we report a linkage map predominantly composed of microsatellite markers. All 24 acrocentric chromosome sets of Xiphophorus are represented in the assembled linkage map with an average intergenomic distance of 7.5 cM. Since both male and female F1 hybrids were used to produce backcross progeny, these recombination rates were compared between “male” and “female” maps. Although several genomic regions exhibit differences in map length, male- and female-derived maps are similar. Thus Xiphophorus, in contrast to zebrafish, Danio rerio, and several other vertebrate species, does not show sex-specific differences in recombination. The microsatellite markers we report can be easily adapted to any Xiphophorus interspecies and some intraspecies crosses, and thus provide a means to directly compare results derived from independent experiments.
Radiation Hybrid Mapping of the Species Cytoplasm-Specific (scsae) Gene in Wheat
Authors: Hossain Khwaja G , Riera-Lizarazu Oscar , Kalavacharla Venugopal , Vales M Isabel , Maan Schivcharan S , Kianian Shahryar F 
Published: September 2004

Abstract
Radiation hybrid (RH) mapping is based on radiation-induced chromosome breakage and analysis of chromosome segment retention or loss using molecular markers. In durum wheat (Triticum turgidum L., AABB), an alloplasmic durum line [(lo) durum] has been identified with chromosome 1D of T. aestivum L. (AABBDD) carrying the species cytoplasm-specific (scsae) gene. The chromosome 1D of this line segregates as a whole without recombination, precluding the use of conventional genome mapping. A radiation hybrid mapping population was developed from a hemizygous (lo) scsae− line using 35 krad gamma rays. The analysis of 87 individuals of this population with 39 molecular markers mapped on chromosome 1D revealed 88 radiation-induced breaks in this chromosome. This number of chromosome 1D breaks is eight times higher than the number of previously identified breaks and should result in a 10-fold increase in mapping resolution compared to what was previously possible. The analysis of molecular marker retention in our radiation hybrid mapping panel allowed the localization of scsae and 8 linked markers on the long arm of chromosome 1D. This constitutes the first report of using RH mapping to localize a gene in wheat and illustrates that this approach is feasible in a species with a large complex genome.
Population Genetic Evidence for Rapid Changes in Intraspecific Diversity and Allelic Cycling of a Specialist Defense Gene in ZeaSequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession nos. AY320258–320280, AY52550, AY52551, AY52552, AY52553, AY52554, AY52555, AY52556, AY52557, AY52558, AY52559, and AY549598, AY549599, AY549600, AY549601, AY549602, AY549603, AY549604, AY549605, AY549606, AY549607, AY549608, AY549609, AY549610, AY549611, AY549612, AY549613, AY549614, AY549615, AY549616, AY549617, AY549618, AY549619, AY549620, AY549621, AY549622, AY549623, AY549624, AY549625, AY549626, AY549627, AY549628, AY549629, AY549630, AY549631, AY549632, AY549633, AY549634, AY549635, AY549636, AY549637, AY549638.
Authors: Tiffin Peter , Hacker Robert , Gaut Brandon S 
Published: September 2004

Abstract
Two patterns of plant defense gene evolution are emerging from molecular population genetic surveys. One is that specialist defenses experience stronger selection than generalist defenses. The second is that specialist defenses are more likely to be subject to balancing selection, i.e., evolve in a manner consistent with balanced-polymorphism or trench-warfare models of host-parasite coevolution. Because most of the data of specialist defenses come from Arabidopsis thaliana, we examined the genetic diversity and evolutionary history of three defense genes in two outcrossing species, the autotetraploid Zea perennis and its most closely related extant relative the diploid Z. diploperennis. Intraspecific diversity at two generalist defenses, the protease inhibitors wip1 and mpi, were consistent with a neutral model. Like previously studied genes in these taxa, wip1 and mpi harbored similar levels of diversity in Z. diploperennis and Z. perennis. In contrast, the specialist defense hm2 showed strong although distinctly different departures from a neutral model in the two species. Z. diploperennis appears to have experienced a strong and recent selective sweep. Using a rejection-sampling coalescent method, we estimate the strength of selection on Z. diploperennis hm2 to be ∼3.0%, which is approximately equal to the strength of selection on tb1 during maize domestication. Z. perennis hm2 harbors three highly diverged alleles, two of which are found at high frequency. The distinctly different patterns of diversity may be due to differences in the phase of host-parasite coevolutionary cycles, although higher hm2 diversity in Z. perennis may also reflect reduced efficacy of selection in the autotetraploid relative to its diploid relative.
Quantitative Trait Loci Affecting Life Span in Replicated Populations of Drosophila melanogaster. I. Composite Interval Mapping
Authors: Forbes Scott N , Valenzuela Robert K , Keim Paul , Service Philip M 
Published: September 2004

Abstract
Composite interval mapping was used to identify life-span QTL in F2 progeny of three crosses between different pairs of inbred lines. Each inbred line was derived from a different outbred population that had undergone long-term selection for either long or short life span. Microsatellite loci were used as genetic markers, and confidence intervals for QTL location were estimated by bootstrapping. A minimum of 10 QTL were detected, nine of which were located on the two major autosomes. Five QTL were present in at least two crosses and five were present in both sexes. Observation of the same QTL in more than one cross was consistent with the hypothesis that genetic variation for life span is maintained by balancing selection. For all QTL except one, allelic effects were in the direction predicted on the basis of outbred source population. Alleles that conferred longer life were always at least partially dominant.
Estimating the Degree of Saturation in Mutant Screens
Authors: Pollock David D , Larkin John C 
Published: September 2004

Abstract
Large-scale screens for loss-of-function mutants have played a significant role in recent advances in developmental biology and other fields. In such mutant screens, it is desirable to estimate the degree of “saturation” of the screen (i.e., what fraction of the possible target genes has been identified). We applied Bayesian and maximum-likelihood methods for estimating the number of loci remaining undetected in large-scale screens and produced credibility intervals to assess the uncertainty of these estimates. Since different loci may mutate to alleles with detectable phenotypes at different rates, we also incorporated variation in the degree of mutability among genes, using either gamma-distributed mutation rates or multiple discrete mutation rate classes. We examined eight published data sets from large-scale mutant screens and found that credibility intervals are much broader than implied by previous assumptions about the degree of saturation of screens. The likelihood methods presented here are a significantly better fit to data from published experiments than estimates based on the Poisson distribution, which implicitly assumes a single mutation rate for all loci. The results are reasonably robust to different models of variation in the mutability of genes. We tested our methods against mutant allele data from a region of the Drosophila melanogaster genome for which there is an independent genomics-based estimate of the number of undetected loci and found that the number of such loci falls within the predicted credibility interval for our models. The methods we have developed may also be useful for estimating the degree of saturation in other types of genetic screens in addition to classical screens for simple loss-of-function mutants, including genetic modifier screens and screens for protein-protein interactions using the yeast two-hybrid method.
A Genetic Screen for Dominant Modifiers of a cyclin E Hypomorphic Mutation Identifies Novel Regulators of S-Phase Entry in Drosophila
Authors: Brumby Anthony , Secombe Julie , Horsfield Julie , Coombe Michelle , Amin Nancy , Coates Deborah , Saint Robert , Richardson Helena 
Published: September 2004

Abstract
Cyclin E together with its kinase partner Cdk2 is a critical regulator of entry into S phase. To identify novel genes that regulate the G1- to S-phase transition within a whole animal we made use of a hypomorphic cyclin E mutation, DmcycEJP, which results in a rough eye phenotype. We screened the X and third chromosome deficiencies, tested candidate genes, and carried out a genetic screen of 55,000 EMS or X-ray-mutagenized flies for second or third chromosome mutations that dominantly modified the DmcycEJP rough eye phenotype. We have focused on the DmcycEJP suppressors, S(DmcycEJP), to identify novel negative regulators of S-phase entry. There are 18 suppressor gene groups with more than one allele and several genes that are represented by only a single allele. All S(DmcycEJP) tested suppress the DmcycEJP rough eye phenotype by increasing the number of S phases in the postmorphogenetic furrow S-phase band. By testing candidates we have identified several modifier genes from the mutagenic screen as well as from the deficiency screen. DmcycEJP suppressor genes fall into the classes of: (1) chromatin remodeling or transcription factors; (2) signaling pathways; and (3) cytoskeletal, (4) cell adhesion, and (5) cytoarchitectural tumor suppressors. The cytoarchitectural tumor suppressors include scribble, lethal-2-giant-larvae (lgl), and discs-large (dlg), loss of function of which leads to neoplastic tumors and disruption of apical-basal cell polarity. We further explored the genetic interactions of scribble with S(DmcycEJP) genes and show that hypomorphic scribble mutants exhibit genetic interactions with lgl, scab (αPS3-integrin—cell adhesion), phyllopod (signaling), dEB1 (microtubule-binding protein—cytoskeletal), and moira (chromatin remodeling). These interactions of the cytoarchitectural suppressor gene, scribble, with cell adhesion, signaling, cytoskeletal, and chromatin remodeling genes, suggest that these genes may act in a common pathway to negatively regulate cyclin E or S-phase entry.
Linkage Maps of Microsatellite DNA Markers for the Pacific Oyster Crassostrea gigasWe dedicate this study to the memory of Will Borgenson, who reared and cared for the parents of the mapping families.
Authors: Hubert Sophie , Hedgecock Dennis 
Published: September 2004

Abstract
We constructed male and female consensus linkage maps for the Pacific oyster Crassostrea gigas, using a total of 102 microsatellite DNA markers typed in 11-day-old larvae from three families. We identified 11 and 12 linkage groups in the male and female consensus maps, respectively. Alignment of these separate maps, however, suggests 10 linkage groups, which agrees with the haploid chromosome number. The male linkage map comprises 88 loci and spans 616.1 cM, while the female map comprises 86 loci and spans 770.5 cM. The male and the female maps share 74 loci; 2 markers remain unlinked. The estimated coverages for the consensus linkage maps are 79% for the male and 70–75% for the female, on the basis of two estimates of genome length. Ninety-five percent of the genome is expected to lie within 16 and 21 cM of markers on the male and female maps, respectively, while 95% of simulated minimum distances to the male and female maps are within 10.1 and 13.6 cM, respectively. Females have significantly more recombination than males, across 118 pairs of linked markers in common to the parents of the three families. Significant differences in recombination and orders of markers are also evident among same-sex parents of different families as well as sibling parents of opposite sex. These observations suggest that polymorphism for chromosomal rearrangements may exist in natural populations, which could have profound implications for interpreting the evolutionary genetics of the oyster. These are the first linkage maps for a bivalve mollusc that use microsatellite DNA markers, which should enable them to be transferred to other families and to be useful for further genetic analyses such as QTL mapping.
Gene Conversion and Crossing Over Along the 405-kb Left Arm of Saccharomyces cerevisiae Chromosome VII
Authors: Malkova Anna , Swanson Johanna , German Miriam , McCusker John H , Housworth Elizabeth A , Stahl Franklin W , Haber James E 
Published: September 2004

Abstract
Gene conversions and crossing over were analyzed along 10 intervals in a 405-kb region comprising nearly all of the left arm of chromosome VII in Saccharomyces cerevisiae. Crossover interference was detected in all intervals as measured by a reduced number of nonparental ditypes. We have evaluated interference between crossovers in adjacent intervals by methods that retain the information contained in tetrads as opposed to single segregants. Interference was seen between intervals when the distance in the region adjacent to a crossover was &lt;∼35 cM (90 kb). At the met13 locus, which exhibits ∼9% gene conversions, those gene conversions accompanied by crossing over exerted interference in exchanges in an adjacent interval, whereas met13 gene conversions without an accompanying exchange did not show interference. The pattern of exchanges along this chromosome arm can be represented by a counting model in which there are three nonexchange events between adjacent exchanges; however, maximum-likelihood analysis suggests that ∼8–12% of the crossovers on chromosome VII arise by a separate, noninterfering mechanism.
Comparative Mapping in the Pinaceae
Authors: Krutovsky Konstantin V , Troggio Michela , Brown Garth R , Jermstad Kathleen D , Neale David B 
Published: September 2004

Abstract
A comparative genetic map was constructed between two important genera of the family Pinaceae. Ten homologous linkage groups in loblolly pine (Pinus taeda L.) and Douglas fir (Pseudotsuga menziesii [Mirb.] Franco) were identified using orthologous expressed sequence tag polymorphism (ESTP) and restriction fragment length polymorphism (RFLP) markers. The comparative mapping revealed extensive synteny and colinearity between genomes of the Pinaceae, consistent with the hypothesis of conservative chromosomal evolution in this important plant family. This study reports the first comparative map in forest trees at the family taxonomic level and establishes a framework for comparative genomics in Pinaceae.
Stress and Survival of Aging Escherichia coli rpoS Colonies
Authors: Saint-Ruf Claude , Taddei François , Matic Ivan 
Published: September 2004

Abstract
In Escherichia coli, the expression of the RpoS regulon is known to be crucial for survival in liquid cultures during stationary phase. By measuring cell viability and by transcriptome analysis, here we show that rpoS cells as well as wild-type cells survive when they form colonies on solid media.
Analysis of Deinococcus radiodurans's Transcriptional Response to Ionizing Radiation and Desiccation Reveals Novel Proteins That Contribute to Extreme Radioresistance
Authors: Tanaka Masashi , Earl Ashlee M , Howell Heather A , Park Mie-Jung , Eisen Jonathan A , Peterson Scott N , Battista John R 
Published: September 2004

Abstract
During the first hour after a sublethal dose of ionizing radiation, 72 genes were upregulated threefold or higher in D. radiodurans R1. Thirty-three of these loci were also among a set of 73 genes expressed in R1 cultures recovering from desiccation. The five transcripts most highly induced in response to each stress are the same and encode proteins of unknown function. The genes (ddrA, ddrB, ddrC, ddrD, and pprA) corresponding to these transcripts were deleted, both alone and in all possible two-way combinations. Characterization of the mutant strains defines three epistasis groups that reflect different cellular responses to ionizing radiation-induced damage. The ddrA and ddrB gene products have complementary activities and inactivating both loci generates a strain that is more sensitive to ionizing radiation than strains in which either single gene has been deleted. These proteins appear to mediate efficient RecA-independent processes connected to ionizing radiation resistance. The pprA gene product is not necessary for homologous recombination during natural transformation, but nevertheless may participate in a RecA-dependent process during recovery from radiation damage. These characterizations clearly demonstrate that novel mechanisms significantly contribute to the ionizing radiation resistance in D. radiodurans.