bluuebunny/crossref_metadata_2025_split huggingface dataset:
transAlign: using amino acids to facilitate the multiple alignment of protein-coding DNA sequences
Authors: Bininda-Emonds Olaf RP 
Published: June 2005

Abstract
Background
Alignments of homologous DNA sequences are crucial for comparative genomics and phylogenetic analysis. However, multiple alignment represents a computationally difficult problem. For protein-coding DNA sequences, it is more advantageous in terms of both speed and accuracy to align the amino-acid sequences specified by the DNA sequences rather than the DNA sequences themselves. Many implementations making use of this concept of "translated alignments" are incomplete in the sense that they require the user to manually translate the DNA sequences and to perform the amino-acid alignment. As such, they are not well suited to large-scale automated alignments of large and/or numerous DNA data sets.

Results
transAlign is an open-source Perl script that aligns protein-coding DNA sequences via their amino-acid translations to take advantage of the superior multiple-alignment capabilities and speed of an amino-acid alignment. It operates by translating each DNA sequence into its corresponding amino-acid sequence, passing the entire matrix to ClustalW for alignment, and then back-translating the resulting amino-acid alignment to derive the aligned DNA sequences. In the translation step, transAlign determines the optimal orientation and reading frame for each DNA sequence according to the desired genetic code. It also checks for apparent frame shifts in the DNA sequences and can handle frame-shifted sequences in one of three ways (delete, align as amino acids regardless, or profile align as DNA). As a set of comparative benchmarks derived from six protein-coding genes for mammals shows, the strategy implemented in transAlign always improves the speed and usually the apparent accuracy of the alignment of protein-coding DNA sequences.

Conclusion
transAlign represents one of few full and cross-platform implementations of the concept of translated alignments. Both the advantages accruing from performing a translated alignment and the suite of user-definable options available in the program mean that transAlign is ideally suited for large-scale automated alignments of very large and/or very numerous protein-coding DNA data sets. However, the good performance offered by the program also translates to the alignment of any set of protein-coding sequences. transAlign, including the source code, is freely available at http://www.tierzucht.tum.de/Bininda-Emonds/ (under "Programs").
FGF10/FGFR2b signaling plays essential roles during in vivo embryonic submandibular salivary gland morphogenesis
Authors: Jaskoll Tina , Abichaker George , Witcher Daniel , Sala Frederic G , Bellusci Saverio , Hajihosseini Mohammad K , Melnick Michael 
Published: June 2005

AbstractBackgroundAnalyses ofFgf10andFgfr2bmutant mice, as well as human studies, suggest that FGF10/FGFR2b signaling may play an essential, nonredundant role during embryonic SMG development. To address this question, we have analyzed the SMG phenotype inFgf10andFgfr2bheterozygous and null mutant mice. In addition, although previous studies suggest that the FGF10/FGFR2b and FGF8/FGFR2c signaling pathways are functionally interrelated, little is known about the functional relationship between these two pathways during SMG development. We have designedin vivoandin vitroexperiments to address this question.ResultsWe analyzedFgf10andFgfr2bheterozygous mutant and null mice and demonstrate dose-dependent SMG phenotypic differences. Hypoplastic SMGs are seen inFgf10andFgfr2bheterozygotes whereas SMG aplasia is seen inFgf10andFgfr2bnull embryos. Complementaryin vitrostudies further indicate that FGF10/FGFR2b signaling regulates SMG epithelial branching and cell proliferation. To delineate the functional relationship between the FGF10/FGFR2b and FGF8/FGFR2c pathways, we compared the SMG phenotype inFgfr2c+/Δ/Fgf10+/-double heterozygous mice to that seen in wildtype,Fgf10+/-(Fgfr2c+/+/Fgf10+/-) andFgfr2c+/Δ(Fgfr2c+/Δ/Fgf10+/+) single heterozygous mutant littermates and demonstrate genotype-specific SMG phenotypes. In addition, exogenous FGF8 was able to rescue the abnormal SMG phenotype associated with abrogated FGFR2b signalingin vitroand restore branching to normal levels.ConclusionOur data indicates that FGF10/FGFR2b signaling is essential for the SMG epithelial branching and histodifferentiation, but not earliest initial bud formation. The functional presence of other endogenous signaling pathways could not prevent complete death of embryonic SMG cells inFgf10andFgfr2bnull mice. Though we were able to rescue the abnormal phenotype associated with reducedin vitroFGF10/FGFR2b signaling with exogenous FGF8 supplementation, our results indicate that the FGF10/FGFR2b and FGF8/FGFR2c are nonredundant signaling pathways essential forin vivoembryonic SMG development. What remains to be determined is thein vivofunctional relationship between the FGF10/FGFR2b signal transduction pathway and other key signaling pathways, and how these pathways are integrated during embryonic SMG development to compose the functional epigenome.
E-cadherin and β-catenin expression in early stage cervical carcinoma: a tissue microarray study of 147 cases
Authors: Fadare Oluwole , Reddy Harini , Wang Jun , Hileeto Denise , Schwartz Peter E , Zheng Wenxin 
Published: June 2005

Abstract

Background
The disruption of intercellular adhesions is an important component of the acquisition of invasive properties in epithelial malignancies. Alterations in the cell-cell adhesion complex, E-Cadherin/β-Catenin, have been implicated in the oncogenesis of carcinomas arising from various anatomic sites and have been correlated with adverse clinico-pathologic parameters. In this study, the authors investigated the immunohistochemical expression of E-Cadherin and β-Catenin in a cohort of early stage cervical cancers to determine its prognostic significance and to investigate differences between the three major histological subtypes.

Patients and methods
A tissue microarray of 147 cases of FIGO stage 1A and 1B cervical carcinomas [96 squamous cell carcinomas (SCC), 35 adenocarcinomas (AC), 12 adenosquamous carcinomas (ASQ), 4 miscellaneous types] was constructed from our archived surgical pathology files and stained with monoclonal antibodies to E-Cadherin and β-Catenin. Cases were scored by multiplying the intensity of staining (1 to 3 scale) by the percentage of cells stained (0–100%) for a potential maximum score of 300. For both markers, "preserved" expression was defined as bright membranous staining with a score of 200 or above. "Impaired" expression included any of the following: negative staining, a score less than 200, or exclusively cytoplasmic or nuclear delocalization.

Results
Impaired expression of β-Catenin was found in 85.7%, 66.7%, & 58.3% of AC, SCC & ASQ respectively. Impaired expression of E-Cadherin was found in 94.3%, 86.5% & 100% of cases of AC, SCC, & ASQ respectively. The differences between the histologic subtypes were not significant. For the whole cohort, a comparsion of cases showing impaired versus preserved of E-Cadherin and β-Catenin expression showed no significant differences with respect to recurrence free survival, overall survival, patient age, histologic grade, and frequency of lymphovascular invasion or lymph node involvement. There was no correlation between the status of both markers for all three histological subtypes (overall spearman correlation co-efficient r = 0.12, p = 0.14)

Conclusion
Impairment of E-Cadherin and β-Catenin expression is very frequent in early stage cervical cancers, and alterations in the E-Cadherin/β-Catenin cell adhesion complex are therefore likely involved in the pathogenesis of cervical carcinomas even at their earliest stages. None of the three major histological subtypes of cervical carcinoma (SCC, ADCA, ADSQ) is significantly more likely than the others to show impairment in E-Cadherin and β-Catenin expression. Overall, the expression of both markers does not significantly correlate with clinico-pathological parameters of prognostic significance.
Results after 24 years of prophylactic surgery for rheumatoid atlantoaxial subluxation
Authors: Tanaka N. , Sakahashi H. , Hirose K. , Ishima T. , Takahashi H. , Ishii S. 
Published: June 2005

We evaluated the use of surgical stabilisation for atlantoaxial subluxation after a follow-up of 24 years in 50 rheumatoid patients who had some degree of pain but no major neurological deficit. The mortality of patients treated by atlantoaxial fusion was significantly lower than for those who received conservative treatment. The deaths resulted from infection or comorbid conditions. The significantly high relative risks of mortality from conservative treatment compared with surgical treatment were mutilating disease and susceptible factors on both of the HLA-DRB1 alleles. Relief from pain and neurological and functional recovery were better, and the radiological degree of atlantoaxial translocation was less in those who were surgically treated compared with those who were not. Two patients had superficial local infections after surgery. We conclude that prophylactic atlantoaxial fusion is better than conservative treatment in these patients.
Prenatal ultrasound diagnosis of club foot
Authors: Bar-On E. , Mashiach R. , Inbar O. , Weigl D. , Katz K. , Meizner I. 
Published: June 2005

Club foot was diagnosed by ultrasonography in 91 feet (52 fetuses) at a mean gestational age of 22.1 weeks (14 to 35.6). Outcome was obtained by chart review in 26 women or telephone interview in 26. Feet were classified as normal, positional deformity, isolated club foot or complex club foot. At initial diagnosis, 69 feet (40 fetuses) were classified as isolated club foot and 22 feet (12 fetuses) as complex club foot. The diagnosis was changed after follow-up ultrasound scan in 13 fetuses (25%), and the final ultrasound diagnosis was normal in one fetus, isolated club foot in 31 fetuses, and complex club foot in 20 fetuses. At birth, club foot was found in 79 feet in 43 infants for a positive predictive value of 83%. Accuracy of the specific diagnosis of isolated club foot or complex club foot was lower; 63% at the initial ultrasound scan and 73% at the final scan. The difference in diagnostic accuracy between isolated and complex club foot was not statistically significant. In no case was postnatal complex club foot undiagnosed on fetal ultrasound and all inaccuracies were overdiagnoses. Karyotyping was performed in 25 cases. Abnormalities were noted in three fetuses, all with complex club foot and with additional findings on ultrasound.
Health-related quality of life in patients before and after surgery for a herniated lumbar disc
Authors: Jansson K.-å. , Németh G. , Granath F. , Jönsson B. , Blomqvist P. 
Published: June 2005

We investigated the pre-operative and one-year post-operative health-related quality of life (HRQOL) outcome by using a Euroqol (EQ-5D) questionnaire in 263 patients who had undergone surgery for herniation of a lumbar disc. Data from the National Swedish Register for lumbar spinal surgery between 2001 and 2002 were used and, in addition, a comparison between our cohort and a Swedish EQ-5D population survey was performed. We analysed the pre- and post-operative quality of life data, age, gender, smoking habits, pain and walking capacity. The mean age of the patients was 42 years (20 to 66); 155 (59%) were men and 69 (26%) smoked. Pre-operatively, 72 (17%) could walk at least 1 km compared with 200 (76%) postoperatively. The mean EQ-5D score improved from 0.29 to 0.70, and the HRQOL improved in 195 (74%) of the patients. The pre-operative score did not influence the post-operative score. In most patients, all five EQ-5D dimensions improved, but did not reach the level reported by an age- and gender-matched population sample (mean difference 0.17). Predictors for poor outcome were smoking, a short pre-operative walking distance, and a long history of back pain.
Defining the Female "I" in the Public Domain: The Narrators of Lilika Nakou's Î Î±ÏÎ±ÏÏÏÎ±ÏÎ·Î¼Î­Î½Î¿Î¹ and Margarita Liberaki's Î¤Î± ÏÎ¬Î¸Î¹Î½Î± ÎºÎ±ÏÎ­Î»Î±
Authors: Camatsos Efrosini 
Published: June 2005

Abstract: Lilika Nakou's Gone Astray /Î Î±ÏÎ±ÏÏÏÎ±ÏÎ·Î¼Î­Î½Î¿Î¹ (1935) and Margarita Liberaki's The Straw Hats /Î¤Î± ÏÎ¬Î¸Î¹Î½Î± ÎºÎ±ÏÎ­Î»Î± (1946) were written during periods of political turmoil. However, neither novel explicitly deals with political or national issues; instead, both of them focus on the personal experiences of their protagonists. This suggests that the female authors remain within the traditionally female private sphere in accordance with the male/ female and public/private oppositions. Nonetheless, the two novels are narrated by a female character, placing the female "I" in the public domain. An interesting phenomenon occurs in both narratives when the "I" disappears. This shift in perspective is subversive and political because it reveals women's struggle to enter and establish an identity of the female "I" in the public domain.
A Segmental Deletion Series Generated by Sister-Chromatid Transposition of Ac Transposable Elements in Maize
Authors: Zhang Jianbo , Peterson Thomas 
Published: June 2005

Abstract
Certain configurations of maize Ac/Ds transposon termini can undergo alternative transposition reactions leading to chromosome breakage and various types of stable chromosome rearrangements. Here, we show that a particular allele of the maize p1 gene containing an intact Ac element and a nearby terminally deleted Ac element (fAc) can undergo sister-chromatid transposition (SCT) reactions that generate large flanking deletions. Among 35 deletions characterized, all begin at the Ac termini in the p1 gene and extend to various flanking sites proximal to p1. The deletions range in size from the smallest of 12,567 bp to the largest of &gt;4.6 cM; &gt;80% of the deletions removed the p2 gene, a paralog of p1 located ∼60 kb from p1 in the p1-vv allele and its derivatives. Sequencing of representative cases shows that the deletions have precise junctions between the transposon termini and the flanking genomic sequences. These results show that SCT events can efficiently generate interstitial deletions that are useful for in vivo dissection of local genome regions and for the rapid correlation of genetic and physical maps. Finally, we discuss evidence suggesting that deletions induced by alternative transposition reactions can occur at other genomic loci, indicating that this mechanism may have had a significant impact on genome evolution.
A Genetic Screen for Maternal-Effect Suppressors of decapentaplegic Identifies the eukaryotic translation initiation factor 4A in Drosophila
Authors: Li Jinghong , Li Willis X , Gelbart William M 
Published: June 2005

Abstract
The Dpp signaling pathway is essential for many developmental processes in Drosophila and its activity is tightly regulated. To identify additional regulators of Dpp signaling, we conducted a genetic screen for maternal-effect suppressors of dpp haplo-insufficiency. We screened ∼7000 EMS-mutagenized genomes and isolated and mapped seven independent dominant suppressors of dpp, Su(dpp), which were recovered as second-site mutations that resulted in viable flies in trans-heterozygous with dppH46, a dpp null allele. Most of the Su(dpp) mutants exhibited increased cell numbers of the amnioserosa, a cell type specified by the Dpp pathway, suggesting that these mutations may augment Dpp signaling activity. Here we report the unexpected identification of one of the Su(dpp) mutations as an allele of the eukaryotic translation initiation factor 4A (eIF4A). We show that Su(dpp)YE9 maps to eIF4A and that this allele is associated with a substitution, arginine 321 to histidine, at a well-conserved amino acid and behaves genetically as a dominant-negative mutation. This result provides an intriguing link between a component of the translation machinery and Dpp signaling.
Genetic Consequences of Selection During the Evolution of Cultivated Sunflower
Authors: Burke John M , Knapp Steven J , Rieseberg Loren H 
Published: June 2005

AbstractWe mapped quantitative trait loci (QTL) controlling differences in seed oil content and composition between cultivated and wild sunflower and used the results, along with those of a previous study of domestication-related QTL, to guide a genome-wide analysis of genetic variation for evidence of past selection. The effects of the seed oil QTL were almost exclusively in the expected direction with respect to the parental phenotypes. A major, oil-related QTL cluster mapped near a cluster of domestication-related QTL on linkage group six (LG06), the majority of which have previously been shown to have effects that are inconsistent with the parental phenotypes. To test the hypothesis that this region was the target of a past selective sweep, perhaps resulting in the fixation of the antagonistic domestication-related QTL, we analyzed simple sequence repeat (SSR) diversity from 102 markers dispersed throughout the sunflower genome. Our results indicate that LG06 was most likely the target of multiple selective sweeps during the postdomestication era. Strong directional selection in concert with genetic hitchhiking therefore offers a possible explanation for the occurrence of numerous domestication-related QTL with apparently maladaptive phenotypic effects.
Functional Mapping of Quantitative Trait Loci That Interact With thehgMutation to Regulate Growth Trajectories in Mice
Authors: Wu Rongling , Ma Chang-Xing , Hou Wei , Corva Pablo , Medrano Juan F 
Published: June 2005

AbstractThe high growth (hg) mutation increases body size in mice by 30–50%. Given the complexity of the genetic regulation of animal growth, it is likely that the effect of this major locus is mediated by other quantitative trait loci (QTL) with smaller effects within a web of gene interactions. In this article, we extend our functional mapping model to characterize modifier QTL that interact with the hg locus during ontogenetic growth. Our model is derived within the maximum-likelihood context, incorporated by mathematical aspects of growth laws and implemented with the EM algorithm. In an F2 population founded by a congenic high growth (HG) line and non-HG line, a highly additive effect due to the hg gene was detected on growth trajectories. Three QTL located on chromosomes 2 and X were identified to trigger significant additive and/or dominant effects on the process of growth. The most significant finding made from our model is that these QTL interact with the hg locus to affect the shapes of the growth process. Our model provides a powerful means for understanding the genetic architecture and regulation of growth rate and body size in mammals.
Concerted Evolution in the Repeats of an Immunomodulating Cell Surface Protein, SOWgp, of the Human Pathogenic Fungi Coccidioides immitis and C. posadasii
Authors: Johannesson Hanna , Townsend Jeffrey P , Hung Chiung-Yu , Cole Garry T , Taylor John W 
Published: June 2005

Abstract
Genome dynamics that allow pathogens to escape host immune responses are fundamental to our understanding of host-pathogen interactions. Here we present the first population-based study of the process of concerted evolution in the repetitive domain of a protein-coding gene. This gene, SOWgp, encodes the immunodominant protein in the parasitic phase of the human pathogenic fungi Coccidioides immitis and C. posadasii. We sequenced the entire gene from strains representing the geographic ranges of the two Coccidioides species. By using phylogenetic and genetic distance analyses we discovered that the repetitive part of SOWgp evolves by concerted evolution, predominantly by the mechanism of unequal crossing over. We implemented a mathematical model originally developed for multigene families to estimate the rate of homogenization and recombination of the repetitive array, and the results indicate that the pattern of concerted evolution is a result of homogenization of repeat units proceeding at a rate close to the nucleotide point mutation rate. The release of the SOWgp molecules by the pathogen during proliferation may mislead the host: we speculate that the pathogen benefits from concerted evolution of repeated domains in SOWgp by an enhanced ability to misdirect the host's immune system.
Maximum-Likelihood Methods for Detecting Recent Positive Selection and Localizing the Selected Site in the Genome
Authors: Li Haipeng , Stephan Wolfgang 
Published: June 2005

Abstract
Two maximum-likelihood methods are proposed for detecting recent, strongly positive selection and for localizing the target of selection along a recombining chromosome. The methods utilize the compact mutation frequency spectrum at multiple neutral loci that are partially linked to the selected site. Using simulated data, we show that the power of the tests lies between 80 and 98% in most cases, and the false positive rate could be as low as ∼10% when the number of sampled marker loci is sufficiently large (≥20). The confidence interval around the estimated position of selection is reasonably narrow. The methods are applied to X chromosome data of Drosophila melanogaster from a European and an African population. Evidence of selection was found for both populations (including a selective sweep that was shared between both populations).
RESISTANCE TO FUSARIUM OXYSPORUM 1, a Dominant Arabidopsis Disease-Resistance Gene, Is Not Race Specific
Authors: Diener Andrew C , Ausubel Frederick M 
Published: June 2005

Abstract
Arabidopsis thaliana ecotypes differ in their susceptibility to Fusarium wilt diseases. Ecotype Taynuilt-0 (Ty-0) is susceptible to Fusarium oxysporum forma specialis (f.) matthioli whereas Columbia-0 (Col-0) is resistant. Segregation analysis of a cross between Ty-0 and Col-0 revealed six dominant RESISTANCE TO FUSARIUM OXYSPORUM (RFO) loci that significantly contribute to f. matthioli resistance in Col-0 relative to Ty-0. We refer to the locus with the strongest effect as RFO1. Ty-0 plants in which only the Col-0 allele of RFO1 (RFO1Col-0) was introduced were resistant to f. matthioli. Surprisingly, RFO1Col-0 also conferred resistance to f. raphani, demonstrating that RFO1-mediated resistance is not race specific. Expression of resistance by RFO2, RFO4, or RFO6 was dependent on RFO1Col-0. Map-based cloning of RFO1Col-0 showed that RFO1 is identical to the previously named Arabidopsis gene WAKL22 (WALL-ASSOCIATED KINASE-LIKE KINASE 22), which encodes a receptor-like kinase that does not contain an extracellular leucine-rich repeat domain. Consistent with these results, a Col-0 rfo1 loss-of-function mutant was more susceptible to f. matthioli, f. conglutinans, and f. raphani. Thus, RFO1 encodes a novel type of dominant disease-resistance protein that confers resistance to a broad spectrum of Fusarium races.
Genetic Instability Induced by Overexpression of DNA Ligase I in Budding Yeast
Authors: Subramanian Jaichandar , Vijayakumar Sangeetha , Tomkinson Alan E , Arnheim Norman 
Published: June 2005

Abstract
Recombination and microsatellite mutation in humans contribute to disorders including cancer and trinucleotide repeat (TNR) disease. TNR expansions in wild-type yeast may arise by flap ligation during lagging-strand replication. Here we show that overexpression of DNA ligase I (CDC9) increases the rates of TNR expansion, of TNR contraction, and of mitotic recombination. Surprisingly, this effect is observed with catalytically inactive forms of Cdc9p protein, but only if they possess a functional PCNA-binding site. Furthermore, in vitro analysis indicates that the interaction of PCNA with Cdc9p and Rad27p (Fen1) is mutually exclusive. Together our genetic and biochemical analysis suggests that, although DNA ligase I seals DNA nicks during replication, repair, and recombination, higher than normal levels can yield genetic instability by disrupting the normal interplay of PCNA with other proteins such as Fen1.