bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Broad-Spectrum Blast Resistance Gene Pi9 Encodes a Nucleotide-Binding Site–Leucine-Rich Repeat Protein and Is a Member of a Multigene Family in Rice
Authors: Qu Shaohong , Liu Guifu , Zhou Bo , Bellizzi Maria , Zeng Lirong , Dai Liangying , Han Bin , Wang Guo-Liang 
Published: December 2005

Abstract
The broad-spectrum rice blast resistance gene Pi9 was cloned using a map-based cloning strategy. Sequencing of a 76-kb bacterial artificial chromosome (BAC) contig spanning the Pi9 locus led to identification of six tandemly arranged resistance-like genes with a nucleotide-binding site (NBS) and leucine-rich repeats (LRRs) (Nbs1-Pi9–Nbs6-Pi9). Analysis of selected Pi9 deletion mutants and transformation of a 45-kb fragment from the BAC contig into the susceptible rice cultivar TP309 narrowed down Pi9 to the candidate genes Nbs2-Pi9 and Nbs3-Pi9. Disease evaluation of the transgenic lines carrying the individual candidate genes confirmed that Nbs2-Pi9 is the Pi9 gene. Sequence comparison analysis revealed that the six paralogs at the Pi9 locus belong to four classes and gene duplication might be one of the major evolutionary forces contributing to the formation of the NBS–LRR gene cluster. Semiquantitative reverse transcriptase (RT)–PCR analysis showed that Pi9 was constitutively expressed in the Pi9-resistant plants and was not induced by blast infection. The cloned Pi9 gene provides a starting point to elucidate the molecular basis of the broad-spectrum disease resistance and the evolutionary mechanisms of blast resistance gene clusters in rice.
Pheromones and Pheromone Receptors Are Required for Proper Sexual Development in the Homothallic Ascomycete Sordaria macrospora
Authors: Mayrhofer Severine , Weber Jan M , Pöggeler Stefanie 
Published: December 2005

Abstract
The homothallic, filamentous ascomycete Sordaria macrospora is self-fertile and produces sexual fruiting bodies (perithecia) without a mating partner. Even so, S. macrospora transcriptionally expresses two pheromone-precursor genes (ppg1 and ppg2) and two pheromone-receptor genes (pre1 and pre2). The proteins encoded by these genes are similar to α-factor-like and a-factor-like pheromones and to G-protein-coupled pheromone receptors of the yeast Saccharomyces cerevisiae. It has been suggested that in S. macrospora, PPG1/PRE2 and PPG2/PRE1 form two cognate pheromone–receptor pairs. To investigate their function, we deleted (Δ) pheromone-precursor genes (Δppg1, Δppg2) and receptor genes (Δpre1, Δpre2) and generated single- as well as double-knockout strains. No effect on vegetative growth, fruiting-body, and ascospore development was seen in the single pheromone-mutant and receptor-mutant strains, respectively. However, double-knockout strains lacking any compatible pheromone-receptor pair (Δpre2/Δppg2, Δpre1/Δppg1) and the double-pheromone mutant (Δppg1/Δppg2) displayed a drastically reduced number of perithecia and sexual spores, whereas deletion of both receptor genes (Δpre1/Δpre2) completely eliminated fruiting-body and ascospore formation. The results suggest that pheromones and pheromone receptors are required for optimal sexual reproduction of the homothallic S. macrospora.
Cytogenetic and Molecular Evaluation of Centromere-Associated DNA Sequences From a Marsupial (Macropodidae:Macropus rufogriseus) X Chromosome
Authors: Bulazel Kira , Metcalfe Cushla , Ferreri Gianni C , Yu Jingwei , Eldridge Mark D B , O'Neill Rachel J 
Published: December 2005

AbstractThe constitution of the centromeric portions of the sex chromosomes of the red-necked wallaby, Macropus rufogriseus (family Macropodidae, subfamily Macropodinae), was investigated to develop an overview of the sequence composition of centromeres in a marsupial genome that harbors large amounts of centric and pericentric heterochromatin. The large, C-band-positive centromeric region of the X chromosome was microdissected and the isolated DNA was microcloned. Further sequence and cytogenetic analyses of three representative clones show that all chromosomes in this species carry a 178-bp satellite sequence containing a CENP-B DNA binding domain (CENP-B box) shown herein to selectively bind marsupial CENP-B protein. Two other repeats isolated in this study localize specifically to the sex chromosomes yet differ in copy number and intrachromosomal distribution. Immunocytohistochemistry assays with anti-CENP-E, anti-CREST, anti-CENP-B, and anti-trimethyl-H3K9 antibodies defined a restricted point localization of the outer kinetochore at the functional centromere within an enlarged pericentric and heterochromatic region. The distribution of these repeated sequences within the karyotype of this species, coupled with the apparent high copy number of these sequences, indicates a capacity for retention of large amounts of centromere-associated DNA in the genome of M. rufogriseus.
How Are Humans Related to Other Primates?: A Guided Inquiry Laboratory for Undergraduate Students
Authors: Kalinowski Steven T , Taper Mark L , Metz Anneke M 
Published: December 2005

Abstract
Understanding that phylogenies depict the evolutionary history of species is a critical concept for undergraduate biology students. We present an inquiry-based laboratory exercise exploring this concept in the context of the human phylogeny. This activity reinforces several important biological concepts and skills. Bolstered concepts include that evolution is descent with modification, that evolution is a genetic process, and that humans are closely related to apes. In terms of thinking skills, the lab gives students practice with hypothetical-deductive thinking, quantifying patterns from complex data, and evaluating evidence.
Quantitative Trait Locus Analysis of Atherosclerosis in an Intercross Between C57BL/6 and C3H Mice Carrying the Mutant Apolipoprotein E Gene
Authors: Su Zhiguang , Li Yuhua , James Jessica C , McDuffie Marcia , Matsumoto Alan H , Helm Gregory A , Weber James L , Lusis Aldons J , Shi Weibin 
Published: December 2005

Abstract
Inbred mouse strains C57BL/6J (B6) and C3H/HeJ (C3H) differ significantly in atherosclerosis susceptibility and plasma lipid levels on the apolipoprotein E-deficient (apoE−/−) background when fed a Western diet. To determine genetic factors contributing to the variations in these phenotypes, we performed quantitative trait locus (QTL) analysis using an intercross between the two strains carrying the apoE−/− gene. Atherosclerotic lesions at the aortic root and plasma lipid levels of 234 female F2 mice were analyzed after being fed a Western diet for 12 weeks. QTL analysis revealed one significant QTL, named Ath22 (42 cM, LOD 4.1), on chromosome 9 and a suggestive QTL near D11mit236 (20 cM, LOD 2.4) on chromosome 11 that influenced atherosclerotic lesion size. One significant QTL on distal chromosome 1, which accounted for major variations in plasma LDL/VLDL cholesterol and triglyceride levels, coincided with a QTL having strong effects on body weight. Plasma LDL/VLDL cholesterol or triglyceride levels of F2 mice were significantly correlated with body weight, but they were not correlated with atherosclerotic lesion sizes. These data indicate that atherosclerosis susceptibility and plasma cholesterol levels are controlled by separate genetic factors in the B6 and C3H mouse model and that genetic linkages exist between body weight and lipoprotein metabolism.
Regulation of the Oxidative Stress Response Through Slt2p-Dependent Destruction of Cyclin C in Saccharomyces cerevisiae
Authors: Krasley Elizabeth , Cooper Katrina F , Mallory Michael J , Dunbrack Roland , Strich Randy 
Published: December 2005

Abstract
The Saccharomyces cerevisiae C-type cyclin and its cyclin-dependent kinase (Cdk8p) repress the transcription of several stress response genes. To relieve this repression, cyclin C is destroyed in cells exposed to reactive oxygen species (ROS). This report describes the requirement of cyclin C destruction for the cellular response to ROS. Compared to wild type, deleting cyclin C makes cells more resistant to ROS while its stabilization reduces viability. The Slt2p MAP kinase cascade mediates cyclin C destruction in response to ROS treatment but not heat shock. This destruction pathway is important as deleting cyclin C suppresses the hypersensitivity of slt2 mutants to oxidative damage. The ROS hypersensitivity of an slt2 mutant correlates with elevated programmed cell death as determined by TUNEL assays. Consistent with the viability studies, the elevated TUNEL signal is reversed in cyclin C mutants. Finally, two results suggest that cyclin C regulates programmed cell death independently of its function as a transcriptional repressor. First, deleting its corepressor CDK8 does not suppress the slt2 hypersensitivity phenotype. Second, the human cyclin C, which does not repress transcription in yeast, does regulate ROS sensitivity. These findings demonstrate a new role for the Slt2p MAP kinase cascade in protecting the cell from programmed cell death through cyclin C destruction.
The in Vivo Characterization of Translesion Synthesis Across UV-Induced Lesions in Saccharomyces cerevisiae: Insights Into Polζ- and Polη-Dependent Frameshift Mutagenesis
Authors: Abdulovic Amy L , Jinks-Robertson Sue 
Published: December 2005

Abstract
UV irradiation, a known carcinogen, induces the formation of dipyrimidine dimers with the predominant lesions being cyclobutane pyrimidine dimers (CPDs) and pyrimidine (6-4) pyrimidone adducts (6-4PPs). The relative roles of the yeast translesion synthesis DNA polymerases Polζ and Polη in UV survival and mutagenesis were examined using strains deficient in one or both polymerases. In addition, photoreactivation was used to specifically remove CPDs, thus allowing an estimate to be made of the relative contributions of CPDs vs. 6-4PPs to overall survival and mutagenesis. In terms of UV-induced mutagenesis, we focused on the +1 frameshift mutations detected by reversion of the lys2ΔA746 allele, as Polζ produces a distinct mutational signature in this assay. Results suggest that CPDs are responsible for most of the UV-associated toxicity as well as for the majority of UV-induced frameshift mutations in yeast. Although the presence of Polη generally suppresses UV-induced mutagenesis, our data suggest a role for this polymerase in generating some classes of +1 frameshifts. Finally, the examination of frameshift reversion spectra indicates a hierarchy between Polη and Polζ with respect to the bypass of UV-induced lesions.
A Versatile and Efficient Gene-Targeting System for Aspergillus nidulans
Authors: Nayak Tania , Szewczyk Edyta , Oakley C Elizabeth , Osmani Aysha , Ukil Leena , Murray Sandra L , Hynes Michael J , Osmani Stephen A , Oakley Berl R 
Published: December 2005

Abstract
Aspergillus nidulans is an important experimental organism, and it is a model organism for the genus Aspergillus that includes serious pathogens as well as commercially important organisms. Gene targeting by homologous recombination during transformation is possible in A. nidulans, but the frequency of correct gene targeting is variable and often low. We have identified the A. nidulans homolog (nkuA) of the human KU70 gene that is essential for nonhomologous end joining of DNA in double-strand break repair. Deletion of nkuA (nkuAΔ) greatly reduces the frequency of nonhomologous integration of transforming DNA fragments, leading to dramatically improved gene targeting. We have also developed heterologous markers that are selectable in A. nidulans but do not direct integration at any site in the A. nidulans genome. In combination, nkuAΔ and the heterologous selectable markers make up a very efficient gene-targeting system. In experiments involving scores of genes, 90% or more of the transformants carried a single insertion of the transforming DNA at the correct site. The system works with linear and circular transforming molecules and it works for tagging genes with fluorescent moieties, replacing genes, and replacing promoters. This system is efficient enough to make genomewide gene-targeting projects feasible.
Transposition of Regulatory Elements by P-Element-Mediated Rearrangements in Drosophila melanogaster
Authors: Pomerantseva Ekaterina , Biryukova Inna , Silicheva Rita , Savitskaya Ekaterina , Golovnin Anton , Georgiev Pavel 
Published: December 2005

Abstract
Previously we described highly unstable mutations in the yellow locus, induced by the chimeric element and consisting of sequences from a distally located 1A unique genomic region, flanked by identical copies of an internally deleted 1.2-kb P element. Here we show that a sequence, which is part of the yellow 1A region, can be transmitted to the AS-C by successive inversion and reinversion generated by yellow- and AS-C-located P elements. The chimeric element contains a regulatory element from the 1A region that specifically blocks yellow wing and body enhancers and simultaneously stimulates yellow expression in bristles. These results suggest that P-element-generated chimeric elements may play a certain role in rapid changes of regulatory regions of genes during evolution.
Association between Growth and Pan I* Genotype within Atlantic Cod Full‐Sibling Families
Authors: Case Richard A. J. , Hutchinson William F. , Hauser Lorenz , Buehler Vivian , Clemmesen Catriona , Dahle Geir , Kjesbu Olav S. , Moksness Erlend , Otterå Håkon , Paulsen Helge , Svåsand Terje , Thorsen Anders , Carvalho Gary R. 
Published: January 2006

AbstractStudies of the pantophysin (Pan I*) locus in Atlantic cod Gadus morhua and other marine gadoids indicate that the locus is under positive selection; in Atlantic cod, genotypic variation at this locus has been linked to differences in growth. Here, we present preliminary data comparing the growth and condition of different Atlantic cod Pan I* genotypes within families held under seminatural mesocosm conditions. Larvae from three full‐sibling families carrying Pan I*bb or Pan I*ab genotypes were reared for 10 weeks in two mesocosms. Multivariate analysis of variance indicated that larvae carrying the Pan I*ab genotype exhibited significantly higher standard length, dry weight, and RNA: DNA ratio (condition factor) than did larvae that carried the Pan I*bb genotype, potentially indicating selection. The influence of linked loci cannot be excluded; indeed, the absence of a significant correlation between genotype and growth in one family may substantiate this. The lack of differences in survival among genotypes indicates that moderate selective effects are acting primarily through size‐specific mortality and fecundity. The proposed putative fitness effects, together with documented marked geographic differentiation in the wild, have implications for Atlantic cod population structure, effective migration rates, recruitment, and local adaptation, which are of particular relevance in a species threatened by continuing exploitation and rising sea temperatures.
Epigenetic Information and Estrogen Receptor Alpha Expression in Breast Cancer
Authors: Giacinti Laura , Claudio Pier Paolo , Lopez Massimo , Giordano Antonio 
Published: January 2006

Learning ObjectivesAfter completing this course, the reader will be able to: Describe the role of epigenetic information in the regulation of gene expression and in the development of cancer.Explain the important role of estrogen receptor expression in breast cancer as a prognostic marker and predictive factor of response to endocrine therapy.Evaluate the current and potential role that the comprehension of the molecular biology of a tumor may have in finding a new therapeutic approach in cancer treatment.Access and take the CME test online and receive 1 AMA PRA category 1 credit at CME.TheOncologist.com
How Do U.S. Medical Oncologists Learn and Apply New Clinical Trials Information from Press Releases in Nonmedical Media? A Case Study Based on ECOG 4599
Authors: Dornbusch Daniel , Allegra Carmen , Willey Joanne , Andrews Michele , Leff Richard , Epstein James , Jones James , Lokey Lee , Green Mark R. 
Published: January 2006

Learning Objectives
After completing this course, the reader will be able to: Discuss new vehicles for the initial release of practice-relevant phase III clinical trial data.Describe the limited educational impact of such information transfer vehicles on the medical oncology community.Explain the potential risks to medical oncologists and their patients because of underinformed or non–evidence-based therapeutic recommendations involving new indications for commercially available agents.Discuss the development of new strategies for effective knowledge transfer of preliminary, practice-relevant, clinical trial data.
Access and take the CME test online and receive 1 AMA PRA category 1 credit at CME.TheOncologist.com
Lung Cancer Highlights from ASCO 2005
Authors: Belvedere Ornella , Grossi Francesco 
Published: January 2006

Learning Objectives
After completing this course, the reader will be able to: Discuss the results of recent trials on the addition of a molecularly targeted agent to standard first-line chemotherapy in NSCLC.Explain the role of surgery in the treatment of stage III NSCLC.Discuss the current status of adjuvant chemotherapy in NSCLC.
Access and take the CME test online and receive 1 AMA PRA category 1 credit at CME.TheOncologist.com
Quarks, Leptons, Fermions, and Bosons—The Subatomic World of Radiation Therapy
Authors: Welsh James S. 
Published: January 2006

Learning Objectives
After completing this course, the reader will be able to: Describe where the commonly prescribed forms of radiation such as photons, electrons, and protons fit into the grander scheme of subatomic particles.Discuss the categories of subatomic particles prescribed in radiation oncology such as bosons, fermions, leptons, quarks, baryons, hadrons, and mesons.Categorize fundamental particles as fermions or bosons based on their spin.Categorize particles as leptons or quarks based on their types of interactions.Categorize hadrons as baryons or mesons based on their quark composition.
Access and take the CME test online and receive 1 AMA PRA category 1 credit at CME.TheOncologist.com
Patients Previously Transfused or Treated with Epoetin Alfa at Low Baseline Hemoglobin Are at Higher Risk for Subsequent Transfusion: An Integrated Analysis of the Canadian Experience
Authors: Quirt Ian , Kovacs Michael , Couture Félix , Turner A. Robert , Noble Michael , Burkes Ronald , Dolan Sean , Plante Richard K. , Lau Catherine Y. , Chang José , Camacho Fernando 
Published: January 2006

Learning Objectives
After completing this course, the reader will be able to: Identify chemotherapy patients at risk of transfusion by carefully monitoring hemoglobin levels and prior incidence of transfusion.Define the optimal Hb target at which epoetin alfa treatment should be initiated to minimize subsequent transfusion need.Understand that more than 85% of units transfused occurred in patients receiving epoetin alfa with baseline Hb &lt;10g/dl and evaluate the clinical impact of early treatment initiation.
Access and take the CME test online and receive 1 AMA PRA category 1 credit at CME.TheOncologist.com
Anionische Übergangsmetallkomplexe mit terminalen Carbid‐, Nitrid‐ und Phosphidliganden als Synthesebausteine für niederkoordinierte Phosphorverbindungen
Authors: Cummins Christopher C. 
Published: December 2005

AbstractAnionische Komplexe mit terminalen einatomigen Nitrid‐, Phosphid‐ und Carbidliganden sind ausgezeichnete Ausgangsmaterialien für die Synthese von Liganden mit niederkoordinierten Phosphorzentren in der schützenden Koordinationssphäre eines Metallkomplexes. Salzeliminierungsreaktionen mit Chlorphosphanen führen zu Phosphaisocyanid‐, Iminophosphinimid‐ und Diorganophosphanylphosphiniden‐Komplexen, in denen die ungewöhnlichen Phosphorliganden durch Koordination stabilisiert sind. Röntgenstrukturanalysen und Dichtefunktionalrechnungen erhellen die Bindungsverhältnisse in diesen Verbindungen.
Terminal, Anionic Carbide, Nitride, and Phosphide Transition‐Metal Complexes as Synthetic Entries to Low‐Coordinate Phosphorus Derivatives
Authors: Cummins Christopher C. 
Published: December 2005

AbstractAnionic terminal one‐atom nitride, phosphide, and carbide complexes are excellent starting materials for the synthesis of ligands containing low‐coordinate phosphorus centers in the protecting coordination sphere of the metal complex. Salt‐elimination reactions with chlorophosphanes lead to phosphaisocyanide, iminophosphinimide, and diorganophosphanylphosphinidene complexes in which the unusual phosphorus ligands are stabilized by coordination. X‐ray structure analyses and density‐functional calculations illuminate the bonding in these compounds.
Collagen and proteoglycan turnover in focally damaged human ankle cartilage: Evidence for a generalized response and active matrix remodeling across the entire joint surface
Authors: Aurich Matthias , Mwale Fackson , Reiner Agnes , Mollenhauer Juergen A. , Anders Jens O. , Fuhrmann Reneé A. , Kuettner Klaus E. , Poole A. Robin , Cole Ada A. 
Published: December 2005

AbstractObjectiveAlthough cartilage lesions occur in the ankles, osteoarthritis rarely develops in the ankles, suggesting that ankle cartilage can up‐regulate mechanisms to repair the damaged matrix. To define these processes, we compared cartilage samples obtained from normal tali and from lesional sites of damaged tali.MethodsCartilage samples were obtained from the tali of normal ankles and from 3 sites on tali with lesions (the lesion, adjacent to the lesion, and far removed from the lesion). Cartilage was analyzed for type II collagen (CII) messenger RNA, C‐terminal type II procollagen propeptide (CPII), the collagenase cleavage neoepitope (Col2‐3/4Cshort), and the denaturation epitope (Col2‐3/4m). For the assessment of type IX collagen, the COL2 and NC4 domains were evaluated. The cartilage samples were also assayed for glycosaminoglycans, epitope 846 of aggrecan, and DNA.ResultsThe DNA content, epitope 846, COL2(IX), and the denaturation epitope were significantly increased in lesional cartilage. Although there was a tendency toward an increase in CII content and CPII, the increase did not reach significance. Neither the NC4(IX) domain nor Col2‐3/4C was elevated. Surprisingly, changes in cartilage both adjacent to and remote from the lesion were similar to those in the lesion.ConclusionThe changes observed in cartilage obtained from the lesion and from sites adjacent to the lesion were not surprising; however, the changes in cartilage obtained from sites remote from the lesion were unexpected. This up‐regulation of matrix turnover in ankles with degenerative lesions may indicate a physiologic response of the entire articular surface to repair the damaged matrix, which is not restricted to the lesion site. This suggests that there may be some mechanism of communication across the cartilage. The response by ankle cartilage obtained from a site remote from the lesion has not been observed in the knee.