bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of Quantitative Trait Loci Across Recombinant Inbred Lines and Testcross Populations for Traits of Agronomic Importance in Rice
Authors: You Aiqing , Lu Xinggui , Jin Huajun , Ren Xiang , Liu Kai , Yang Guocai , Yang Haiyuan , Zhu Lili , He Guangcun 
Published: December 2005

Abstract
This study was conducted to determine whether quantitative trait loci (QTL) controlling traits of agronomic importance detected in recombinant inbred lines (RILs) are also expressed in testcross (TC) hybrids of rice. A genetic map was constructed using an RIL population derived from a cross between B5 and Minghui 63, a parent of the most widely grown hybrid rice cultivar in China. Four TC hybrid populations were produced by crossing the RILs with three maintaining lines for the widely used cytoplasmic male-sterile (CMS) lines and the genic male-sterile line Peiai64s. The mean values of the RILs for the seven traits investigated were significantly correlated to those of the F1 hybrids in the four TC populations. Twenty-seven main-effect QTL were identified in the RILs. Of these, the QTL that had the strongest effect on each of the seven traits in the RILs was detected in two or more of the TC populations, and six other QTL were detected in one TC population. Epistatic analysis revealed that the effect of epistatic QTL was relatively weak and cross combination specific. Searching publicly available QTL data in rice revealed the positional convergence of the QTL with the strongest effect in a wide range of populations and under different environments. Since the main-effect QTL is expressed across different testers, and in different genetic backgrounds and environments, it is a valuable target for gene manipulation and for further application in rice breeding. When a restorer line that expresses main-effect QTL is bred, it could be used in a number of cross combinations.
Optimal Haplotype Structure for Linkage Disequilibrium-Based Fine Mapping of Quantitative Trait Loci Using Identity by Descent
Authors: Grapes L , Firat M Z , Dekkers J C M , Rothschild M F , Fernando R L 
Published: December 2005

Abstract
A linkage disequilibrium-based method for fine mapping quantitative trait loci (QTL) has been described that uses similarity between individuals' marker haplotypes to determine if QTL alleles are identical by descent (IBD) to model covariances among individuals' QTL alleles for a mixed linear model. Mapping accuracy with this method was found to be sensitive to the number of linked markers that was included in the haplotype when fitting the model at a putative position of the QTL. The objective of this study was to determine the optimal haplotype structure for this IBD-based method for fine mapping a QTL in a previously identified QTL region. Haplotypes consisting of 1, 2, 4, 6, or all 10 available markers were fit as a “sliding window” across the QTL region under ideal and nonideal simulated population conditions. It was found that using haplotypes of 4 or 6 markers as a sliding “window” resulted in the greatest mapping accuracy under nearly all conditions, although the true IBD state at a putative QTL position was most accurately predicted by IBD probabilities obtained using all markers. Using 4 or 6 markers resulted in greater discrimination of IBD probabilities between positions while maintaining sufficient accuracy of IBD probabilities to detect the QTL. Fitting IBD probabilities on the basis of a single marker resulted in the worst mapping accuracy under all conditions because it resulted in poor accuracy of IBD probabilities. In conclusion, for fine mapping using IBD methods, marker information must be used in a manner that results in sensitivity of IBD probabilities to the putative position of the QTL while maintaining sufficient accuracy of IBD probabilities to detect the QTL. Contrary to expectation, use of haplotypes of 4–6 markers to derive IBD probabilities, rather than all available markers, best fits these criteria. Thus for populations similar to those simulated here, optimal mapping accuracy for this IBD-based fine-mapping method is obtained with a haplotype structure including a subset of all available markers.
After the Duplication: Gene Loss and Adaptation in Saccharomyces Genomes
Authors: Cliften Paul F , Fulton Robert S , Wilson Richard K , Johnston Mark 
Published: December 2005

Abstract
The ancient duplication of the Saccharomyces cerevisiae genome and subsequent massive loss of duplicated genes is apparent when it is compared to the genomes of related species that diverged before the duplication event. To learn more about the evolutionary effects of the duplication event, we compared the S. cerevisiae genome to other Saccharomyces genomes. We demonstrate that the whole genome duplication occurred before S. castellii diverged from S. cerevisiae. In addition to more accurately dating the duplication event, this finding allowed us to study the effects of the duplication on two separate lineages. Analyses of the duplication regions of the genomes indicate that most of the duplicated genes (∼85%) were lost before the speciation. Only a small amount of paralogous gene loss (4–6%) occurred after speciation. On the other hand, S. castellii appears to have lost several hundred genes that were not retained as duplicated paralogs. These losses could be related to genomic rearrangements that reduced the number of chromosomes from 16 to 9. In addition to S. castellii, other Saccharomyces sensu lato species likely diverged from S. cerevisiae after the duplication. A thorough analysis of these species will likely reveal other important outcomes of the whole genome duplication.
Evidence for Recombination of Mitochondrial DNA in Triploid Crucian Carp
Authors: Guo Xinhong , Liu Shaojun , Liu Yun 
Published: December 2005

Abstract
In this study, we report the complete mitochondrial DNA (mtDNA) sequences of the allotetraploid and triploid crucian carp and compare the complete mtDNA sequences between the triploid crucian carp and its female parent Japanese crucian carp and between the triploid crucian carp and its male parent allotetraploid. Our results indicate that the complete mtDNA nucleotide identity (98%) between the triploid crucian carp and its male parent allotetraploid was higher than that (93%) between the triploid crucian carp and its female parent Japanese crucian carp. Moreover, the presence of a pattern of identity and difference at synonymous sites of mitochondrial genomes between the triploid crucian carp and its parents provides direct evidence that triploid crucian carp possessed the recombination mtDNA fragment (12,759 bp) derived from the paternal fish. These results suggest that mtDNA recombination was derived from the fusion of the maternal and paternal mtDNAs. Compared with the haploid egg with one set of genome from the Japanese crucian carp, the diploid sperm with two sets of genomes from the allotetraploid could more easily make its mtDNA fuse with the mtDNA of the haploid egg. In addition, the triple hybrid nature of the triploid crucian carp probably allowed its better mtDNA recombination. In summary, our results provide the first evidence of mtDNA combination in polyploid fish.
Transcriptional Reprogramming and Backup Between Duplicate Genes: Is It a Genomewide Phenomenon?
Authors: He Xionglei , Zhang Jianzhi 
Published: December 2005

Abstract
Deleting a duplicate gene often results in a less severe phenotype than deleting a singleton gene, a phenomenon commonly attributed to functional compensation among duplicates. However, duplicate genes rapidly diverge in expression patterns after duplication, making functional compensation less probable for ancient duplicates. Case studies suggested that a gene may provide compensation by altering its expression upon removal of its duplicate copy. On the basis of this observation and a genomic analysis, it was recently proposed that transcriptional reprogramming and backup among duplicates is a genomewide phenomenon in the yeast Saccharomyces cerevisiae. Here we reanalyze the yeast data and show that the high dispensability of duplicate genes with low expression similarity is a consequence of expression similarity and gene dispensability, each being correlated with a third factor, the number of protein interactions per gene. There is little evidence supporting widespread functional compensation of divergently expressed duplicate genes by transcriptional reprogramming.
Transcriptome Analysis and Physical Mapping of Barley Genes in Wheat–Barley Chromosome Addition Lines
Authors: Cho Seungho , Garvin David F , Muehlbauer Gary J 
Published: December 2005

Abstract
Wheat–barley chromosome addition lines are useful genetic resources for a variety of studies. In this study, transcript accumulation patterns in Betzes barley, Chinese Spring wheat, and Chinese Spring–Betzes chromosome addition lines were examined with the Barley1 Affymetrix GeneChip probe array. Of the 4014 transcripts detected in Betzes but not in Chinese Spring, 365, 271, 265, 323, 194, and 369 were detected in wheat–barley disomic chromosome addition lines 2(2H), 3(3H), 4(4H), 7(5H), 6(6H), and 1(7H), respectively. Thus, 1787 barley transcripts were detected in a wheat genetic background and, by virtue of the addition line in which they were detected, were physically mapped to barley chromosomes. We validated and extended our approach to physically map barley genes to the long and short arms of chromosome 6(6H). Our physical map data exhibited a high level of synteny with homologous sequences on the wheat and/or rice syntenous chromosomes, indicating that our barley physical maps are robust. Our results show that barley transcript detection in wheat–barley chromosome addition lines is an efficient approach for large-scale physical mapping of genes.
Genetic and Molecular Characterization of the I Locus of Phaseolus vulgaris
Authors: Vallejos C Eduardo , Astua-Monge Gustavo , Jones Valerie , Plyler Tammy R , Sakiyama Ney S , Mackenzie Sally A 
Published: December 2005

Abstract
The I locus of the common bean, Phaseolus vulgaris, controls the development of four different phenotypes in response to inoculation with Bean common mosaic virus, Bean common mosaic necrosis virus, several other related potyviruses, and one comovirus. We have generated a high-resolution linkage map around this locus and have aligned it with a physical map constructed with BAC clones. These clones were obtained from a library of the cultivar “Sprite,” which carries the dominant allele at the I locus. We have identified a large cluster of TIR–NBS–LRR sequences associated within this locus, which extends over a distance &gt;425 kb. Bean cultivars from the Andean or Mesoamerican gene pool that contain the dominant allele share the same haplotypes as revealed by gel blot hybridizations with a TIR probe. In contrast, beans with a recessive allele display simpler and variable haplotypes. A survey of wild accessions from Argentina to Mexico showed that this multigene family has expanded significantly during evolution and domestication. RNA gel blot analysis indicated that the TIR family of genes plays a role in the response to inoculations with BCMV or BCMNV.
zds1, a Novel Gene Encoding an Ortholog of Zds1 and Zds2, Controls Sexual Differentiation, Cell Wall Integrity and Cell Morphology in Fission Yeast
Authors: Yakura Miyo , Ozoe Fumiyo , Ishida Hideki , Nakagawa Tsuyoshi , Tanaka Katsunori , Matsuda Hideyuki , Kawamukai Makoto 
Published: December 2005

Abstract
While screening for genes that reverse the sporulation-deficient phenotype of the ras1Δ diploid Schizosaccharomyces pombe strain, we identified zds1. This gene shares sequence homology with the ZDS1 and ZDS2 genes from Saccharomyces cerevisiae, which appear to be involved in multiple cellular events. Expression of Zds1 in ras1Δ diploid cells elevated their sporulation rate from 0.3 to 11.2%. Expression of the Zds1 C-terminal region increased the sporulation rate further (to 21.9%) while introduction of the Zds1 N-terminal region had no effect. zds1 expression did not induce sporulation in strains with mutations in genes participating in the downstream MAP kinase cascade. The zds1-disrupted strain is sensitive to CaCl2, and this effect is suppressed by the C-terminal region of Zds1. The growth of the zds1Δ strain is markedly inhibited by cold temperatures, while its viability decreased in the stationary phase. Moreover, the zds1Δ strain is round in shape and very sensitive to zymolyase, and its cell wall becomes thicker than that of wild type. Thus, zds1 must be required to maintain cell wall integrity. The Zds1–GFP fusion protein localized to the cytosol, the septum, and the cell cortex. Its localization in the septum was dependent on its C-terminal region. Overexpression of the C-terminal region of Zds1 induced multi-septa and abnormal zygotes. We propose that the C-terminal region is the functional domain of Zds1 while the N-terminal region is a negative regulatory region. Thus, Zds1 is involved in multiple cellular events in fission yeast, including sexual differentiation, Ca2+ tolerance, cell wall integrity, viability in the stationary phase, and cell morphology.
Patterns of Nucleotide Diversity in Wild and Cultivated Sunflower
Authors: Liu Aizhong , Burke John M 
Published: December 2005

Abstract
Interest in the level and organization of nucleotide diversity in domesticated plant lineages has recently been motivated by the potential for using association-based mapping techniques as a means for identifying the genes underlying complex traits. To date, however, such data have been available only for a relatively small number of well-characterized plant taxa. Here we provide the first detailed description of patterns of nucleotide polymorphism in wild and cultivated sunflower (Helianthus annuus), using sequence data from nine nuclear genes. The resuflts of this study indicate that wild sunflower harbors at least as much nucleotide diversity as has been reported in other wild plant taxa, with randomly selected sequence pairs being expected to differ at 1 of every 70 bp. In contrast, cultivated sunflower has retained only 40–50% of the diversity present in the wild. Consistent with this dramatic reduction in polymorphism, a phylogenetic analysis of our data revealed that the cultivars form a monophyletic clade, adding to the growing body of evidence that sunflower is the product of a single domestication. Eight of the nine loci surveyed appeared to be evolving primarily under purifying selection, while the remaining locus may have been the subject of positive selection. Linkage disequilibrium (LD) decayed very rapidly in the self-incompatible wild sunflower, with the expected LD falling to negligible levels within 200 bp. The cultivars, on the other hand, exhibited somewhat higher levels of LD, with nonrandom associations persisting up to ∼1100 bp. Taken together, these results suggest that association-based approaches will provide a high degree of resolution for the mapping of functional variation in sunflower.
Patterns of Diversity and Linkage Disequilibrium Within the Cosmopolitan Inversion In(3R)Payne in Drosophila melanogaster Are Indicative of Coadaptation
Authors: Kennington W Jason , Partridge Linda , Hoffmann Ary A 
Published: December 2005

Abstract
The cosmopolitan inversion In(3R)Payne in Drosophila melanogaster decreases in frequency with increasing distance from the equator on three continents, indicating it is subject to strong natural selection. We investigated patterns of genetic variation and linkage disequilibrium (LD) in 24 molecular markers located within and near In(3R)Payne to determine if different parts of the inversion responded to selection the same way. We found reduced variation in the markers we used compared to others distributed throughout the genome, consistent with the inversion having a relatively recent origin (&lt;Ne generations). LD between markers and In(3R)Payne varied significantly among markers within the inversion, with regions of high association interspersed by regions of low association. Several factors indicate that these patterns were not due to demographic factors such as admixture and bottlenecks associated with colonization, but instead reflected strong epistatic selection. Furthermore, we found that nonadjacent regions with high association to the inversion contained markers with the strongest clinal patterns in allele frequency; in most cases, the level of clinal variation was beyond what could be explained by hitchhiking with In(3R)Payne, indicating that genes within these regions are targets of selection. Our results provide some support for the hypothesis that inversions persist in natural populations because they hold together favorable combinations of alleles that act together to facilitate adaptive shifts.
Mothers’ Reflections on Raising a Child with a Craniofacial Anomaly
Authors: Klein Tovah , Pope Alice W. , Getahun Eskedar , Thompson Jill 
Published: December 2005

Objective: To conduct a qualitative evaluation of parenting among families with school-aged and young adolescent children with craniofacial anomalies (CFAs). Methods: Interview responses were obtained from nine mothers of children ages 9 to 14 years old with CFAs. Mothers were asked to describe their perceptions of their children, their children's special needs because of CFAs, and their parenting strategies. Narratives were coded into categories, including maternal concerns and worries, children's strengths, proactive maternal behaviors, and role of CFAs in the families’ lives. Results and Conclusions: Mothers’ responses indicated concern and protectiveness because of the challenges of having a CFA, as well as parenting strategies intended to promote autonomy and positive social and emotional adjustment.
Immunophenotype of Human Adipose-Derived Cells: Temporal Changes in Stromal-Associated and Stem Cell–Associated Markers
Authors: Mitchell James B. , McIntosh Kevin , Zvonic Sanjin , Garrett Sara , Floyd Z. Elizabeth , Kloster Amy , Di Halvorsen Yuan , Storms Robert W. , Goh Brian , Kilroy Gail , Wu Xiying , Gimble Jeffrey M. 
Published: December 2005

Abstract
Adipose tissue represents an abundant and accessible source of multipotent adult stem cells and is used by many investigators for tissue engineering applications; however, not all laboratories use cells at equivalent stages of isolation and passage. We have compared the immunophenotype of freshly isolated human adipose tissue-derived stromal vascular fraction (SVF) cells relative to serial-passaged adipose-derived stem cells (ASCs). The initial SVF cells contained colony-forming unit fibroblasts at a frequency of 1:32. Colony-forming unit adipocytes and osteoblasts were present in the SVF cells at comparable frequencies (1:28 and 1:16, respectively). The immunophenotype of the adipose-derived cells based on flow cytometry changed progressively with adherence and passage. Stromal cell–associated markers (CD13, CD29, CD44, CD63, CD73, CD90, CD166) were initially low on SVF cells and increased significantly with successive passages. The stem cell–associated marker CD34 was at peak levels in the SVF cells and/or early-passage ASCs and remained present, although at reduced levels, throughout the culture period. Aldehyde dehydrogenase and the multidrug-resistance transport protein (ABCG2), both of which have been used to identify and characterize hematopoietic stem cells, are expressed by SVF cells and ASCs at detectable levels. Endothelial cell–associated markers (CD31, CD144 or VE-cadherin, vascular endothelial growth factor receptor 2, von Willebrand factor) were expressed on SVF cells and did not change significantly with serial passage. Thus, the adherence to plastic and subsequent expansion of human adipose-derived cells in fetal bovine serum-supplemented medium selects for a relatively homogeneous cell population, enriching for cells expressing a stromal immunophenotype, compared with the heterogeneity of the crude SVF.
Popular Health Education and Propaganda in Times of Peace and War in Mexico City, 1890s–1920s
Authors: Agostoni Claudia 
Published: December 2005

Health education and propaganda acquired importance during the late 19th and early 20th centuries in Mexico City, as physicians, hygienists, and schoolteachers attempted to teach the principles of public health to a culturally and socially heterogeneous urban population. I explore the organization of the Popular Hygiene Exhibition of 1910 and the importance of health education before and after the armed phase of the Mexican Revolution, and why children and the indigenous populations became the main recipients of health education programs.
Outcomes of Recognizing Depressed Chinese American Patients in Primary Care
Authors: Yeung Albert , Kung Winnie W. , Murakami Jessica L. , Mischoulon David , Alpert Jonathan E. , Nierenberg Andrew A. , Fava Maurizio 
Published: December 2005

Purpose: This study aims to examine the effect of identifying Chinese American patients as having major depressive disorder (MDD) to their primary care physicians (PCPs) on the latter's attention given to the treatment of depression. Methodology: Forty Chinese American patients from a primary care clinic were identified as having major depressive disorder (MDD), and their primary care physicians (PCPs) were notified of the diagnosis by letter. Three months later, medical records of subjects in the study were reviewed to see if their PCPs had intervened through referral and/or initiated treatment of depression. Results: PCPs documented intervention in 19 patients (47%) regarding their depression. Two of these patients (11%) were started on an antidepressant. Four (21%) accepted and 13 (68%) declined referral to mental health services. No intervention was recorded for 21 (53%) patients. Conclusion: We conclude that recognition alone of MDD among Chinese Americans in the community primary care setting does not lead to adequate initiation of treatment for depression by PCPs.
Written Emotional Expression and Religion: Effects on PTSD Symptoms
Authors: Chen Yung Y. 
Published: December 2005

Objective: Previous research has found an association between writing about traumatic events and well-being. This study examined the effects of taking a religious perspective during a trauma-writing exercise. Method: Participants included 177 college students who were assigned randomly to either a conventional trauma writing or a religious trauma writing condition. Participants in the conventional writing condition were instructed to write about a traumatic experience, while participants in the religious writing condition were instructed to write about the trauma from a religious/spiritual perspective. Well-being was assessed by symptoms of PTSD at one-month follow-up. Results: Writing condition was found to interact with trauma severity and gender to affect PTSD symptoms at follow-up. Conventional writing was more effective (in reducing PTSD symptoms) for participants reporting lower trauma severity than for those who reported higher trauma severity. Effects of religious writing on PTSD symptoms were not influenced by trauma severity. Also, women benefited more from religious writing than men did with regard to reductions in PTSD symptoms. Conclusion: It appears possible to adapt the conventional written emotional expression procedure in a way that encourages individuals to take a religious perspective, thereby augmenting effects on distress. These findings support further investigation of integrating religion into trauma interventions, particularly for individuals exposed to highly traumatic events.