bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Genomic Landscape of Short Insertion and Deletion Polymorphisms in the Chicken (Gallus gallus) Genome: A High Frequency of Deletions in Tandem Duplicates
Authors: Brandström Mikael , Ellegren Hans 
Published: May 2007

Abstract
It is increasingly recognized that insertions and deletions (indels) are an important source of genetic as well as phenotypic divergence and diversity. We analyzed length polymorphisms identified through partial (0.25×) shotgun sequencing of three breeds of domestic chicken made by the International Chicken Polymorphism Map Consortium. A data set of 140,484 short indel polymorphisms in unique DNA was identified after filtering for microsatellite structures. There was a significant excess of tandem duplicates at indel sites, with deletions of a duplicate motif outnumbering the generation of duplicates through insertion. Indel density was lower in microchromosomes than in macrochromosomes, in the Z chromosome than in autosomes, and in 100 bp of upstream sequence, 5′-UTR, and first introns than in intergenic DNA and in other introns. Indel density was highly correlated with single nucleotide polymorphism (SNP) density. The mean density of indels in pairwise sequence comparisons was 1.9 × 10−4 indel events/bp, ∼5% the density of SNPs segregating in the chicken genome. The great majority of indels involved a limited number of nucleotides (median 1 bp), with A-rich motifs being overrepresented at indel sites. The overrepresentation of deletions at tandem duplicates indicates that replication slippage in duplicate sequences is a common mechanism behind indel mutation. The correlation between indel and SNP density indicates common effects of mutation and/or selection on the occurrence of indels and point mutations.
Bayesian Mapping of Genomewide Interacting Quantitative Trait Loci for Ordinal Traits
Authors: Yi Nengjun , Banerjee Samprit , Pomp Daniel , Yandell Brian S 
Published: May 2007

Abstract
Development of statistical methods and software for mapping interacting QTL has been the focus of much recent research. We previously developed a Bayesian model selection framework, based on the composite model space approach, for mapping multiple epistatic QTL affecting continuous traits. In this study we extend the composite model space approach to complex ordinal traits in experimental crosses. We jointly model main and epistatic effects of QTL and environmental factors on the basis of the ordinal probit model (also called threshold model) that assumes a latent continuous trait underlies the generation of the ordinal phenotypes through a set of unknown thresholds. A data augmentation approach is developed to jointly generate the latent data and the thresholds. The proposed ordinal probit model, combined with the composite model space framework for continuous traits, offers a convenient way for genomewide interacting QTL analysis of ordinal traits. We illustrate the proposed method by detecting new QTL and epistatic effects for an ordinal trait, dead fetuses, in a F2 intercross of mice. Utility and flexibility of the method are also demonstrated using a simulated data set. Our method has been implemented in the freely available package R/qtlbim, which greatly facilitates the general usage of the Bayesian methodology for genomewide interacting QTL analysis for continuous, binary, and ordinal traits in experimental crosses.
Patterns of Molecular Variation and Evolution in Drosophila americana and Its Relatives
Authors: Maside Xulio , Charlesworth Brian 
Published: May 2007

Abstract
We present the results of a survey of DNA sequence variability at X-linked and autosomal loci in Drosophila americana and of patterns of DNA sequence evolution among D. americana and four other related species in the virilis group of Drosophila. D. americana shows a typical level of silent polymorphism for a Drosophila species, but has an unusually low ratio of nonsynonymous to silent variation. Both D. virilis and D. americana also show a low ratio of nonsynonymous to synonymous substitutions along their respective lineages since the split from their common ancestor. The proportion of amino acid substitutions between D. americana and its relatives that are caused by positive selection, as estimated by extensions of the McDonald–Kreitman test, appears to be unusually high. We cannot, however, exclude the possibility that this reflects a recent increase in the intensity of selection on nonsynonymous mutations in D. americana and D. virilis. We also find that base composition at neutral sites appears to be in overall equilibrium among these species, but there is evidence for departure from equilibrium for codon usage in some lineages.
The Formation of the Polyploid Hybrids From Different Subfamily Fish Crossings and Its Evolutionary Significance
Authors: Liu Shaojun , Qin Qinbo , Xiao Jun , Lu Wenting , Shen Jiamin , Li Wei , Liu Jifang , Duan Wei , Zhang Chun , Tao Min , Zhao Rurong , Yan Jinpeng , Liu Yun 
Published: May 2007

Abstract
This study provides genetic evidences at the chromosome, DNA content, DNA fragment and sequence, and morphological levels to support the successful establishment of the polyploid hybrids of red crucian carp × blunt snout bream, which belonged to a different subfamily of fish (Cyprininae subfamily and Cultrinae subfamily) in the catalog. We successfully obtained the sterile triploid hybrids and bisexual fertile tetraploid hybrids of red crucian carp (RCC) (♀) × blunt snout bream (BSB) (♂) as well as their pentaploid hybrids. The triploid hybrids possessed 124 chromosomes with two sets from RCC and one set from BSB; the tetraploid hybrids had 148 chromosomes with two sets from RCC and two sets from BSB. The females of tetraploid hybrids produced unreduced tetraploid eggs that were fertilized with the haploid sperm of BSB to generate pentaploid hybrids with 172 chromosomes with three sets from BSB and two sets from RCC. The ploidy levels of triploid, tetraploid, and pentaploid hybrids were confirmed by counting chromosomal number, forming chromosomal karyotype, and measuring DNA content and erythrocyte nuclear volume. The similar and different DNA fragments were PCR amplified and sequenced in triploid, tetraploid hybrids, and their parents, indicating their molecular genetic relationship and genetic markers. In addition, this study also presents results about the phenotypes and feeding habits of polyploid hybrids and discusses the formation mechanism of the polyploid hybrids. It is the first report on the formation of the triploid, tetraploid, and pentaploid hybrids by crossing parents with a different chromosome number in vertebrates. The formation of the polyploid hybrids is potentially interesting in both evolution and fish genetic breeding.
A Rho-Binding Protein Kinase C-Like Activity Is Required for the Function of Protein Kinase N in Drosophila Development
Authors: Betson Martha , Settleman Jeffrey 
Published: May 2007

Abstract
The Rho GTPases interact with multiple downstream effectors to exert their biological functions, which include important roles in tissue morphogenesis during the development of multicellular organisms. Among the Rho effectors are the protein kinase N (PKN) proteins, which are protein kinase C (PKC)-like kinases that bind activated Rho GTPases. The PKN proteins are well conserved evolutionarily, but their biological role in any organism is poorly understood. We previously determined that the single Drosophila ortholog of mammalian PKN proteins, Pkn, is a Rho/Rac-binding kinase essential for Drosophila development. By performing “rescue” studies with various Pkn mutant constructs, we have defined the domains of Pkn required for its role during Drosophila development. These studies suggested that Rho, but not Rac binding is important for Pkn function in development. In addition, we determined that the kinase domain of PKC53E, a PKC family kinase, can functionally substitute for the kinase domain of Pkn during development, thereby exemplifying the evolutionary strategy of “combining” functional domains to produce proteins with distinct biological activities. Interestingly, we also identified a requirement for Pkn in wing morphogenesis, thereby revealing the first postembryonic function for Pkn.
Ure2p Function Is Enhanced by Its Prion Domain in Saccharomyces cerevisiae
Authors: Shewmaker Frank , Mull Lori , Nakayashiki Toru , Masison Daniel C , Wickner Reed B 
Published: May 2007

Abstract
The Ure2 protein of Saccharomyces cerevisiae can become a prion (infectious protein). At very low frequencies Ure2p forms an insoluble, infectious amyloid known as [URE3], which is efficiently transmitted to progeny cells or mating partners that consequently lose the normal Ure2p nitrogen regulatory function. The [URE3] prion causes yeast cells to grow slowly, has never been identified in the wild, and confers no obvious phenotypic advantage. An N-terminal asparagine-rich domain determines Ure2p prion-forming ability. Since ure2Δ strains are complemented by plasmids that overexpress truncated forms of Ure2p lacking the prion domain, the existence of the [URE3] prion and the evolutionary conservation of an N-terminal extension have remained mysteries. We find that Ure2p function is actually compromised in vivo by truncation of the prion domain. Moreover, Ure2p stability is diminished without the full-length prion domain. Mca1p, like Ure2p, has an N-terminal Q/N-rich domain whose deletion reduces its steady-state levels. Finally, we demonstrate that the prion domain may affect the interaction of Ure2p with other components of the nitrogen regulation system, specifically the negative regulator of nitrogen catabolic genes, Gzf3p.
The in Silico Map-Based Cloning of Pi36, a Rice Coiled-Coil–Nucleotide-Binding Site–Leucine-Rich Repeat Gene That Confers Race-Specific Resistance to the Blast Fungus
Authors: Liu Xinqiong , Lin Fei , Wang Ling , Pan Qinghua 
Published: May 2007

Abstract
The indica rice variety Kasalath carries Pi36, a gene that determines resistance to Chinese isolates of rice blast and that has been located to a 17-kb interval on chromosome 8. The genomic sequence of the reference japonica variety Nipponbare was used for an in silico prediction of the resistance (R) gene content of the interval and hence for the identification of candidate gene(s) for Pi36. Three such sequences, which all had both a nucleotide-binding site and a leucine-rich repeat motif, were present. The three candidate genes were amplified from the genomic DNA of a number of varieties by long-range PCR, and the resulting amplicons were inserted into pCAMBIA1300 and/or pYLTAC27 vectors to determine sequence polymorphisms correlated to the resistance phenotype and to perform transgenic complementation tests. Constructs containing each candidate gene were transformed into the blast-susceptible variety Q1063, which allowed the identification of Pi36-3 as the functional gene, with the other two candidates being probable pseudogenes. The Pi36-encoded protein is composed of 1056 amino acids, with a single substitution event (Asp to Ser) at residue 590 associated with the resistant phenotype. Pi36 is a single-copy gene in rice and is more closely related to the barley powdery mildew resistance genes Mla1 and Mla6 than to the rice blast R genes Pita, Pib, Pi9, and Piz-t. An RT–PCR analysis showed that Pi36 is constitutively expressed in Kasalath.
Littoral Fish Community Response to Smallmouth Bass Removal from an Adirondack Lake
Authors: Weidel Brian C. , Josephson Daniel C. , Kraft Clifford E. 
Published: May 2007

AbstractLarge‐scale observational studies in eastern Canada and the northeastern USA have concluded that introduced littoral predators are responsible for reductions in native fish diversity and abundance. To determine whether nonnative predator removal could increase native littoral fish abundance, we removed 47,682 smallmouth bass Micropterus dolomieu from a 271‐ha Adirondack lake during a 6‐year period. Two years after removal began, habitat‐stratified snorkel surveys indicated a greater than 90% reduction in smallmouth bass abundance. The relative abundances of six native littoral species increased (4‐90 times preremoval abundances) within 2 years of smallmouth bass removal. Decreased relative predation risk during the experiment reflected the reduction in littoral predators and identified seasonal differences in nearshore predation risk. The smallmouth bass population was resilient to removal, producing strong year‐classes throughout the experiment. Mechanical removal was successful at decreasing smallmouth bass abundance and increasing native fish abundance, but removal must be conducted on a yearly basis to maintain low smallmouth bass population abundance. Our results provide experimental evidence regarding the need to prevent littoral predator introductions in Adirondack waters and offer support for nonnative control wherever native fish species conservation is a management priority.
Mesenchymal Stem Cells Inhibit the Differentiation of Dendritic Cells Through an Interleukin-6-Dependent Mechanism
Authors: Djouad Farida , Charbonnier Louis-Marie , Bouffi Carine , Louis-Plence Pascale , Bony Claire , Apparailly Florence , Cantos Céline , Jorgensen Christian , Noël Danièle 
Published: May 2007

Abstract
Mesenchymal stem cells (MSC) are of particular interest for their potential clinical use in tissue engineering as well as for their capacity to reduce the incidence and severity of graft-versus-host disease in allogeneic transplantation. We have previously shown that MSC-mediated immune suppression acts via the secretion of soluble factor(s) induced upon stimulation. The aim of this study was to identify the molecule(s) involved and the underlying mechanism(s). We show that murine MSC secrete high levels of interleukin (IL)-6 and vascular endothelial growth factor, which are directly correlated to the inhibition of T-cell proliferation. The T-cell activation is partially restored upon addition of a neutralizing anti-IL-6 antibody or the prostaglandin E2 inhibitor indomethacin. Interestingly, no indoleamine 2,3-dioxygenase activity was detected in our conditions. Instead, we show that MSC reduce the expression of major histocompatibility complex class II, CD40, and CD86 costimulatory molecules on mature dendritic cells (DC), which was responsible for a decrease in T-cell proliferation. Moreover, we show that the differentiation of bone marrow progenitors into DC cultured with conditioned supernatants from MSC was partly inhibited through the secretion of IL-6. Altogether, these data suggest that IL-6 is involved in the immunoregulatory mechanism mediated by MSC through a partial inhibition of DC differentiation but is probably not the main mechanism.
Disclosure of potential conflicts of interest is found at the end of this article.
Concise Review: Telomere Biology in Normal and Leukemic Hematopoietic Stem Cells
Authors: Drummond Mark W. , Balabanov Stefan , Holyoake Tessa L. , Brummendorf Tim H. 
Published: May 2007

Abstract
The measurement of telomere length can give an insight into the replicative history of the cells in question. Much of the observed telomere loss occurs at the stem and progenitor cell level, even though these populations express the enzyme telomerase. Telomerase-transfected hematopoietic stem cells (HSC), although able to maintain telomere length, are still limited in terms of ability to undergo sequential transplantation, and other factors require to be addressed to achieve optimal levels of stem cell expansion. Unchecked telomere loss by HSC, meanwhile, would appear to play a significant role in the pathogenesis of bone marrow failure, as observed in the condition dyskeratosis congenita. This heterogeneous inherited condition appears to exhibit telomerase dysfunction as a common final pathogenic mechanism. Although less well-established for acquired marrow failure syndromes, mutations in key telomerase components have been described. The identification of the leukemic stem cell (LSC), along with the desire to target this population with anti-leukemia therapy, demands that telomerase biology be fully understood in this cell compartment. Future studies using primary selected LSC-rich samples are required. A better understanding of telomerase regulation in this population may allow effective targeting of the telomerase enzyme complex using small molecule inhibitors or additional novel approaches.
Disclosure of potential conflicts of interest is found at the end of this article.
Über das Drehspulengalvanometer
Authors: Jaeger W. 
Published: May 2007

AbstractEinleitung. Empfindlichkeit des Nadelgalvanometers. Drehspulengalvanometer: a) Bewegung eines schwingenden Systems im aperiodischen Grenzfall; b) Bedingungen für die Empfindlichkeit des Drehspulengalvanometers; c) Einfluß der Dämpfung im offenen Stromkreis und des Klemmenwiderstandes auf die Empfindlichkeit; Formeln zur Berechnung der Galvanometerkonstanten; e) Anwendung der Drehspulengalvanometer; f) Ballistische Galvanometer; g) Vergleichung der Empfindlichkeiten des Nadel‐ und Drehspulengalvanometers. Zusammenstellung.
Über die Lichtemission der Kanalstrahlen in Wasserstoff
Authors: Stark J. 
Published: May 2007

Abstract
Teil Träger der Linienspektra. ‐ § 1. Einleitung. § 2. Methoden der Untersuchung. § 3. Aussehen des Doppler‐Effektes. § 4. Konstanz des Doppler‐Effektes innerhalb einer Serie. § 5. Elektrische Ladung des Trägers der Wasserstoffserie. § 6. Elektrische Ladung der Träger von Duplet‐ und Tripletserien, Komplexität des Linienspektrums eines Elementes. § 7. Folgerungen über die Ionisierung und die Lichtemission der chemischen Elemente. § 8. Verbreiterung der Spektrallinien durch Erhöhung der Dichte. § 9. Reflexion und Zerstreuung der Kanalstrahlen. § 10. Die Linie 4688 und das Bandenspektrum in den Kanalstrahlen.
Teil. Translationsgeschwindigkeit und Strahlungsintensität. ‐ § 11. Ionisierung hinter der Kathode, Ursprung der Intensität des Bandenspektrums und der ruhenden Intensität des Linienspektrums. § 12. Parallelismus zwischen Translationsgeschwindigkeit und Temperatur, Vergleich der ruhenden und der bewegten Intensität. § 13. Internsitätsverteilung im Doppler‐Effekt. § 14. Das Intensitätsminimum im Doppler‐Effekt, Forderung für das Auftreten des effektes. § 15. Intensitätsverteilung in einem Serienglied. § 16. Intensitätsverteilung in einer Serie. § 17. Verbreiterung in einer Linienserie durch den Doppler‐Effekt.
Teil. Translationsgeschwindigkeit und Wellenlänge. ‐ § 18. Einleitung, Fehlerquellen. § 19. Verbreiterung der Linien bei normaler Stellung der Beobachtungs‐ und der Translationsrichtung. § 20. Verschiebung der Linienmitte nach Rot. § 21. Verschiebung von Serienlinien durch Erhöhung der Temperatur.
Weitere Mitteilungen über das Saitengalvanometer. Analyse der saitengalvanometrischen Kurven. Masse und Spannung des Quarzfadens und Widerstand gegen die Fadenbewegung
Authors: Einthoven W. 
Published: May 2007

Abstract1. Einleitung. ‐ 2. Die Grundsätze der befolgten Methode. ‐ 3. die masse der Saite. ‐ 4. Der Widerstand gegen die Saitenbewegung. ‐ 5. Die Beschleunigung.
Oszillatorische Entladung polarisierter Zellen
Authors: Krüger F. 
Published: May 2007

AbstractI. Einleitung. ‐ II. Theorie. A. Diffusionskapazität. B. Doppelschichten‐ oder Oberflächendichtigkeitskapazität. C. Gleichzeitiges Vorhandensein von Diffusions‐ und Doppelschichtenkapazität. D. Kapazität der Ionenreaktionsgeschwindigkeit. E. Abhängigkeit von der Stromintensität. ‐ III. Versuchsanordnung. ‐ IV. Versuchsergebnisse. A. Quecksilberelektroden. B. Platinelektroden. C. Palladiumelektroden. ‐ V. Schluß. ‐ IV. Zusammenfassung.
Die Präzisionsmessung starker magnetischer Felder; Étalons der magnetischen Feldstärke
Authors: Gans R. , Gmelin P. 
Published: May 2007

Abstract§ 1. Einleitung. Skizzierung der Methoden. – § 2. Das magnetische Grundétalon. a) Die Inhomogenität des Étalonfeldes. b) Der Proportionalitätsbereich des Grundétalons. – § 3. Die erste Meßmethode. a) Die Eichung der Paschenschen Normalspulen mit der Tangentenbussole. b) Die Inhomogenität des Feldes in den Normalspulen. c) Die absolute Messung der Feldstärke des Grundétalons. – § 4. Die zweite Meßmethode. a) Das wechselseitige Induktionsnormal des Tübinger physikalischen Instituts. b) Die ballistische Induktionsspule. c) Die absolute Messung der Feldstärke des Grundétalons. – § 5. Die Eichung eines Étalons der magnetischen Feldstärke. – Anhang. § 6. Das Normal der Selbstinduktion des Tübinger physikalischen Instituts. – § 7. Die Vergleichung von Siemens & Halskeschen Normalien der wechselseitigen Induktion mit dem Tübinger Normal.
Spektralanalytische Beobachtungen an Kanalstrahlen mit Hilfe großer Dispersion
Authors: Stark J. , Steubing W. 
Published: May 2007

Abstract§ 1. Methoden. § 2. Fehlerquellen. § 3. Der erste Schwellenwert der Geschwindigkeit für das Auftreten bewegter Intensität. § 4. Die Verteilung der bewegten Intensität im Geschwindigkeitsspektrum der Kanalstrahlen. § 5. Bemerkungen zu Angaben anderer Autoren. § 6. Der zweite Schwellenwert der Geschwindigkeit in der Verteilungskurve der bewegten Intensität. § 7. Relation zwischen der maximalen kinetischen Energie von Kanalstrahlen und der maximalen sie erzeugenden elektrischen Arbeit. § 8. Messungen an dem Doppler‐Effekt reflektierter Kanalstrahlen.
Die Theorie des starren Elektrons in der Kinematik des Relativitätsprinzips
Authors: Born Max 
Published: May 2007

AbstractEinleitung p. 1. ‐ Erstes Kapitel. Die Kinematik des starren Körpers. § 1. Der starre Körper der alten Mechanik p. 6. § 2. Die Differentialbedingungen der Starrheit p. 11. § 3. Die Kontinuitätsgleichung und die inkompressible Strömung p. 16. § 4. Die geradlinige Translation des starren Körpers p. 19. § 5. Die Hyperbelbewegung p. 25. ‐ Zweites Kapitel. Das Feld des starren Elektrons bei der Hyperbelbewegung. § 6. Retardierte Potentiale und Feldstärken p. 27. § 7. Vergleich der Ausdrücke für die retardierten Potentiale p. 29. § 8. Berechnung der Potentiale bei der Hyperbelbewegung p. 34. § 9. Die Feldstärken bei der Hyperbelbewegung p. 37. § 10. Transformation der Wellengleichung, der Potentiale und Feldstärrken auf ein mitbewegtes Koordinatensystem p. 39. ‐ Drittes Kapitel. Die Dynamik des starren Elektrons bei der Hyperbelbewegung. § 11. Die resultierenden Kräfte und die Bewegungsgleichungen p. 45. § 12. Die resultierenden inneren Kräfte bei der Hyperbelbewegung p. 49. § 13. Die elektrodynamische Ruhmasse p. 54.
Experimentelle und theoretische Grundlagen des elastischen und mechanischen Stoßes
Authors: Ramsauer Carl 
Published: May 2007

AbstractEinleitung. Entwickelung der beiden Stoßtheorien und bisherige Versuche p. 417. ‐ I. Teil. Der elastische Stoß p. 420. 1. Kap. Theorie des elastischen Stoßes p. 420. § 1. Zylinder von gleichem Material und gleichem Querschnitt p. 420. § 2. Zylinder von beliebigem Material und Querschnitt p. 425. 2. Kap. Versuchsanordnung und Methoden p. 429. § 1. Material der Zylinder p. 429. § 2. Anordnungen zur Hervorbringung eines einwandfreien Longitudinalstoßes p. 431. § 3. Die Spiegelmethode zur Untersuchung des Stoßvorganges im einzelnen p. 434. § 4. Die Schattenmethode zur Messung der Geschwindigkeiten nach dem Stoß p. 443. § 5. Die elektrische Methode zur Messung der Stoßzeiten p. 445. 3. Kap. Versuchsergebnisse p. 446. § 1. Versuche zur Prüfung der Spiegelmethode p. 446. § 2. Versuche an Stahlspiralen p. 451. § 3. Versuche an Kautschukzylindern von gleichem Querschnitt p. 459. § 4. Versuche an Kautschukzylindern von ungleichem Querschnitt p. 470. § 5. Versuche an Zylindern von ungleichem Material p. 473. Zusammenfassung des ersten Teiles p. 477. ‐ II. Teil. Der mechanische Stoß p. 478. 1. Kap. Untersuchung des Idealfalles p. 478. 2. Kap. Die elastischen Vorgänge beim Stoß „starrer”︁ Körper p. 482. 3. Kap. Der Stoß zwischen Kautschukzylindern mit halbkugelförmigem Kopf p. 487. Zusammenfassung des zweiten Teiles p. 493.