bluuebunny/crossref_metadata_2025_split huggingface dataset:
Construction and characterization of two BAC libraries fromBrachypodium distachyon, a new model for grass genomics
Authors: Huo Naxin , Gu Yong Q. , Lazo Gerard R. , Vogel John P. , Coleman-Derr Devin , Luo Ming-Cheng , Thilmony Roger , Garvin David F. , Anderson Olin D. 
Published: November 2006

Brachypodium is well suited as a model system for temperate grasses because of its compact genome and a range of biological features. In an effort to develop resources for genome research in this emerging model species, we constructed 2 bacterial artificial chromosome (BAC) libraries from an inbred diploid Brachypodium distachyon line, Bd21, using restriction enzymes HindIII and BamHI. A total of 73 728 clones (36 864 per BAC library) were picked and arrayed in 192 384-well plates. The average insert size for the BamHI and HindIII libraries is estimated to be 100 and 105 kb, respectively, and inserts of chloroplast origin account for 4.4% and 2.4%, respectively. The libraries individually represent 9.4- and 9.9-fold haploid genome equivalents with combined 19.3-fold genome coverage, based on a genome size of 355 Mb reported for the diploid Brachypodium, implying a 99.99% probability that any given specific sequence will be present in each library. Hybridization of the libraries with 8 starch biosynthesis genes was used to empirically evaluate this theoretical genome coverage; the frequency at which these genes were present in the library clones gave an estimated coverage of 11.6- and 19.6-fold genome equivalents. To obtain a first view of the sequence composition of the Brachypodium genome, 2185 BAC end sequences (BES) representing 1.3 Mb of random genomic sequence were compared with the NCBI GenBank database and the GIRI repeat database. Using a cutoff expectation value of E < 10−10, only 3.3% of the BESs showed similarity to repetitive sequences in the existing database, whereas 40.0% had matches to the sequences in the EST database, suggesting that a considerable portion of the Brachypodium genome is likely transcribed. When the BESs were compared with individual EST databases, more matches hit wheat than maize, although their EST collections are of a similar size, further supporting the close relationship between Brachypodium and the Triticeae. Moreover, 122 BESs have significant matches to wheat ESTs mapped to individual chromosome bin positions. These BACs represent colinear regions containing the mapped wheat ESTs and would be useful in identifying additional markers for specific wheat chromosome regions.
Chronic exposure to stretch–shortening contractions results in skeletal muscle adaptation in young rats and maladaptation in old rats
Authors: Cutlip Robert G. , Baker Brent A. , Geronilla Kenneth B. , Mercer Robert R. , Kashon Michael L. , Miller Gerald R. , Murlasits Zsolt , Alway Stephen E. 
Published: November 2006

The objective of this research was to investigate skeletal muscle response to a chronic administration of stretch–shortening cycles (SSCs) in young and old rats. Dorsiflexor muscles of old (30 months, n = 5) and young (12 weeks, n = 6) rats were exposed 3 times/week for 4.5 weeks to a protocol of 80 maximal SSCs per exposure in vivo. Skeletal muscle response was characterized by isometric and dynamic performance, as well as by muscle wet mass and quantitative morphological analyses following the exposure period. The performance of the young and old groups was not statistically different at the start of the exposure. By the end of the exposure, however, a statistical difference was noted, as performance increased significantly in the young animals and decreased significantly in the old animals. Muscle wet mass of the left tibialis anterior (TA) in the treated limb was significantly greater in the youngthan in the old animals (p < 0.001), whereas there was no difference in the contra-lateral TA. No degenerative myofibers or changes in non-cellular interstitium were noted in either age group, but a significant increase was observed in the volume of the cellular interstitium in the exposed limb of the old animals (p = 0.01), which is indicative of an inflammatory response. Thus, a chronic exposure of SSCs results in significant performance increase and muscle hypertrophy in young animals, and a significant performance decrease and an increased cellular interstitial response in old animals. These findings suggest that age may impair the ability of skeletal muscle to adapt to repetitive mechanical loading, even in the absence of degeneration.
Habitat requirements of the Yellow-bellied Sapsucker,Sphyrapicus varius, in boreal mixedwood forests of northwestern Canada
Authors: Savignac C. , Machtans C.S. 
Published: November 2006

Despite its role as a keystone species, few studies have investigated the habitat requirements of the Yellow-bellied Sapsucker ( Sphyrapicus varius (L., 1766)) in the northwestern part of its range, where the current forest harvesting rotation schedule and targets for reducing the prevalence of old and mixedwood stands may reduce the optimal habitat for this species. We studied nesting and foraging habitat requirements of nesting sapsuckers in a boreal mixedwood forest of northwestern Canada by collecting data on nesting sites and foraging substrates on twenty-four 16- to 56-ha plots distributed among four habitat types in 1998 and 2002. Nests (n = 68) were generally found in large (≥22 cm diameter at breast height) trembling aspen ( Populus tremuloides Michx) that were alive but declining and that showed high incidence (81.1%) of heartwood rot infection ( Phellinus tremulae (Bondarzev) Bondarzev & Borisov in Bondarzev). Nest-site use by sapsuckers was predicted mainly by the presence of external fungal conks and tree diameter. Among tree species used as foraging substrates, paper birch ( Betula papyrifera Marsh.) (65.6%) and green alder ( Alnus viridis (Vill.) Lam. & DC.) (21.3%) were used most frequently. The use of birch was strongly correlated with its availability. Mature forests had higher densities of nesting sites and foraging substrates than immature aspen stands. In addition to reconfirming the importance of mature mixedwood forests for Yellow-bellied Sapsuckers, our study also indicates that forest harvest rotations in northwestern Canada should exceed 90 years to promote the keystone role of this species.
Female mating frequency increases with temperature in two cricket species, Gryllodes sigillatus and Acheta domesticus (Orthoptera: Gryllidae)
Authors: Kindle Tashika K. , Johnson Kristen M. , Ivy Tracie M. , Weddle Carie B. , Sakaluk Scott K. 
Published: November 2006

Although the effect of temperature on calling song of male crickets has been widely studied, its influence on female mating behaviour remains largely unexplored. We examined the effect of varying temperature on female mating frequency in two cricket species ( Gryllodes sigillatus (F. Walker, 1869) (= Gryllodes supplicans (F. Walker, 1859)) and Acheta domesticus L., 1758) by providing females with multiple mating partners and recording the number of matings over 72 h intervals using time-lapse video recording. Female mating frequency increased with temperature in both species, but increased more steeply in A. domesticus than in G. sigillatus. Temperature accounted for approximately 50% of the variation in female mating frequency. These results suggest that the threshold for mating in females is temperature dependent, such that at lower temperatures only certain males are able to elicit the female mounting response required for successful mating. If temperature affects female selectivity, then male mating success in different seasons may vary, with a wider range of males gaining the opportunity to copulate at warmer times of the year. Consequently, the intensity of sexual selection may vary seasonally.
A new composite implicit iterative process for a finite family of nonexpansive mappings in Banach spaces
Authors: Gu Feng , Lu Jing 
Published: November 2006

AbstractThe purpose of this paper is to study the weak and strong convergence of implicit iteration process with errors to a common fixed point for a finite family of nonexpansive mappings in Banach spaces. The results presented in this paper extend and improve the corresponding results of Chang and Cho (2003), Xu and Ori (2001), and Zhou and Chang (2002).
Imaging Mitogen-Activated Protein Kinase Function in Xenograft Models of Prostate Cancer
Authors: Ilagan Romyla , Pottratz Jill , Le Kim , Zhang Liqun , Wong Steven G. , Ayala Raul , Iyer Meera , Wu Lily , Gambhir Sanjiv S. , Carey Michael 
Published: November 2006

Abstract
Mitogen-activated protein kinases (MAPK) play important roles in malignancy. The ability to detect and quantitate MAPKs in live animal models of cancer will facilitate an understanding of disease progression. We have developed a gene expression-based imaging system that detects and quantifies MAPK activity in prostate cancer tumors implanted into severe combined immunodeficient mice. The imaging technology uses a modified version of two-step transcriptional amplification (TSTA). The tissue specificity of gene expression is imparted by an enhanced version of the prostate-specific antigen regulatory region that expresses GAL4-ELK1. GAL4-ELK1 confers MAPK specificity by activating a firefly luciferase (FLuc) reporter gene when the Ets-like transcription factor (ELK) 1 activation domain is phosphorylated by MAPK. FLuc activity in live animals was detected using the Xenogen In vivo Imaging System. We validated the TSTA-ELK1 system by analyzing its response to epidermal growth factor treatment in transfected tissue culture cells and in adenovirus (AdTSTA-ELK1)–injected prostate cancer xenograft tumors. We measured MAPK activity in two well-characterized xenograft models, CWR22 and LAPC9. Although no significant differences in MAPK levels were detected between androgen-dependent and androgen-independent xenografts, the CWR22 models display significantly higher levels of AdTSTA-ELK1 activity versus LAPC9. Western blots of tumor extracts showed that the elevated imaging signal in CWR22 xenografts correlated with elevated levels of phosphorylated extracellular signal-regulated kinase 1/2 but not p38 or c-Jun NH2-terminal kinase. We conclude that a gene expression-based optical imaging system can accurately detect and quantify MAPK activity in live animals. (Cancer Res 2006; 66(22): 10778-85)
Inhibition of Prostate Tumor Growth and Bone Remodeling by the Vascular Targeting Agent VEGF121/rGel
Authors: Mohamedali Khalid A. , Poblenz Ann T. , Sikes Charles R. , Navone Nora M. , Thorpe Philip E. , Darnay Bryant G. , Rosenblum Michael G. 
Published: November 2006

Abstract
The pathophysiology of tumor growth following skeletal metastases and the poor response of this type of lesion to therapeutic intervention remains incompletely understood. Vascular endothelial growth factor (VEGF)-A and its receptors play a role in both osteoclastogenesis and tumor growth. Systemic (i.v.) treatment of nude mice bearing intrafemoral prostate (PC-3) tumors with the vascular ablative agent VEGF121/recombinant gelonin (rGel) strongly inhibited tumor growth. Fifty percent of treated animals had complete regression of bone tumors with no development of lytic bone lesions. Immunohistochemical analysis showed that VEGF121/rGel treatment suppressed tumor-mediated osteoclastogenesis in vivo. In vitro treatment of murine osteoclast precursors, both cell line (RAW264.7) and bone marrow–derived monocytes (BMM), revealed that VEGF121/rGel was selectively cytotoxic to osteoclast precursor cells rather than mature osteoclasts. VEGF121/rGel cytotoxicity was mediated by Flt-1, which was down-regulated during osteoclast differentiation. Analysis by flow cytometry and reverse transcription-PCR showed that both BMM and RAW264.7 cells display high levels of Flt-1 but low levels of Flk-1. Internalization of VEGF121/rGel into osteoclast precursor cells was suppressed by pretreatment with an Flt-1 neutralizing antibody or by placenta growth factor but not with an Flk-1 neutralizing antibody. Thus, VEGF121/rGel inhibits osteoclast maturation in vivo and it seems that this process is important in the resulting suppression of skeletal osteolytic lesions. This is a novel and unique mechanism of action for this class of agents and suggests a potentially new approach for treatment or prevention of tumor growth in bone. (Cancer Res 2006; 66(22): 10919-28)
Decreased NKX3.1 Protein Expression in Focal Prostatic Atrophy, Prostatic Intraepithelial Neoplasia, and Adenocarcinoma: Association with Gleason Score and Chromosome 8p Deletion
Authors: Bethel Carlise R. , Faith Dennis , Li Xiang , Guan Bin , Hicks Jessica L. , Lan Fusheng , Jenkins Robert B. , Bieberich Charles J. , De Marzo Angelo M. 
Published: November 2006

Abstract
NKX3.1 is a homeobox gene located at chromosome 8p21.2, and one copy is frequently deleted in prostate carcinoma. Prior studies of NKX3.1 mRNA and protein in human prostate cancer and prostatic intraepithelial neoplasia (PIN) have been conflicting, and expression in focal prostate atrophy lesions has not been investigated. Immunohistochemical staining for NKX3.1 on human tissue microarrays was decreased in most focal atrophy and PIN lesions. In carcinoma, staining was inversely correlated with Gleason grade. Fluorescence in situ hybridization showed that no cases of atrophy had loss or gain of 8p, 8 centromere, or 8q24 (C-MYC) and only 12% of high-grade PIN lesions harbored loss of 8p. By contrast, NKX3.1 staining in carcinoma was correlated with 8p loss and allelic loss was inversely related to Gleason pattern. Quantitative reverse transcription-PCR for NKX3.1 mRNA using microdissected atrophy revealed a concordance with protein in five of seven cases. In carcinoma, mRNA levels were decreased in 6 of 12 cases but mRNA levels correlated with protein levels in only 4 of 12 cases, indicating translational or post-translational control. In summary, NKX3.1 protein is reduced in focal atrophy and PIN but is not related to 8p allelic loss in these lesions. Therefore, whereas genetic disruption of NKX3.1 in mice leads to PIN, nongenetic mechanisms reduce NKX3.1 protein levels early in human prostate carcinogenesis, which may facilitate both proliferation and DNA damage in atrophic and PIN cells. Monoallelic deletions on chromosome 8p are associated with more advanced invasive and aggressive disease. (Cancer Res 2006; 66(22): 10683-90)
Improved Tumor Control through Circadian Clock Induction by Seliciclib, a Cyclin-Dependent Kinase Inhibitor
Authors: Iurisci Ida , Filipski Elisabeth , Reinhardt Jens , Bach Stéphane , Gianella-Borradori Athos , Iacobelli Stefano , Meijer Laurent , Lévi Francis 
Published: November 2006

Abstract
The circadian timing system and the cell division cycle are frequently deregulated in cancer. The therapeutic relevance of the reciprocal interactions between both biological rhythms was investigated using Seliciclib, a cyclin-dependent kinase (CDK) inhibitor (CDKI). Mice bearing Glasgow osteosarcoma received Seliciclib (300 mg/kg/d orally) or vehicle for 5 days at Zeitgeber time (ZT) 3, 11, or 19. On day 6, tumor mRNA 24-hour expression patterns were determined for clock genes (Per2, Rev-erbα, and Bmal1) and clock-controlled cell cycle genes (c-Myc, Wee1, cyclin B1, and CDK1) with quantitative reverse transcription-PCR. Affinity chromatography on immobilized Seliciclib identified CDK1/CDK2 and extracellular signal-regulated kinase (ERK) 1/ERK2, CDK7/CDK9, and casein kinase CK1ε as Seliciclib targets, which respectively regulate cell cycle, transcription, and circadian clock in Glasgow osteosarcoma. Seliciclib reduced tumor growth by 55% following dosing at ZT3 or ZT11 and by 35% at ZT19 compared with controls (P &lt; 0.001). Tolerability was also best at ZT3. Mean transcriptional activity of Rev-erbα, Per2, and Bmal1 was arrhythmic in the tumors of untreated mice. Seliciclib induced rhythmic clock gene expression patterns with physiologic phase relations only after ZT3 dosing. c-Myc and Wee1 mRNAs displayed synchronous circadian rhythms in the tumors of control mice receiving vehicle only but not in those of mice given the drug. Seliciclib further enhanced Wee1 expression irrespective of dosing time, an effect that reinforced G2-M gating. Seliciclib also inhibited CK1ε, which determines circadian period length. The coordination of clock gene expression patterns in tumor cells was associated with best antitumor activity of Seliciclib. The circadian clock and its upstream regulators represent relevant targets for CDKIs. (Cancer Res 2006; 66(22): 10720-8)
Gonadotropin-Releasing Hormone Promotes Ovarian Cancer Cell Invasiveness through c-Jun NH2-Terminal Kinase–Mediated Activation of Matrix Metalloproteinase (MMP)-2 and MMP-9
Authors: Cheung Lydia W.T. , Leung Peter C.K. , Wong Alice S.T. 
Published: November 2006

Abstract
Gonadotropin-releasing hormone (GnRH) receptor is present in 80% of ovarian cancer, and numerous studies have provided evidence for a role of GnRH in cell proliferation. In this study, the effect of GnRH on the invasion potential of ovarian cancer cells was investigated. In vitro migration and cell invasion assays with the ovarian cancer cell lines Caov-3 and OVCAR-3 revealed the biphasic nature of GnRH; low concentrations of GnRH agonist (GnRHa) increased the cell motility and invasiveness of these cells, but at increased concentrations, the stimulatory effect was insignificant. Reverse transcription-PCR, Western blot, and gelatin zymography showed that the expression of metastasis-related proteinases, matrix metalloproteinase (MMP)-2 and MMP-9, was up-regulated and activated by GnRHa. Moreover, we observed that GnRHa was able to transactivate the MMP-2 and MMP-9 promoters. The invasive/migratory phenotype activated by GnRHa can be blocked by specific inhibitors or neutralizing antibodies to MMP-2 and MMP-9. Knockdown of the GnRH receptor using small interfering RNA significantly inhibited the GnRH-induced MMP activation, invasion, and migration. In addition, we showed that the c-Jun NH2-terminal kinase, but not extracellular signal-regulated kinase 1/2 or p38 mitogen-activated protein kinase, signaling pathway was critical for GnRH-mediated up-regulation of MMP, cell invasion, and motility. These results indicate for the first time an expanded role for GnRH in other aspects of ovarian tumor progression, such as metastasis, via activation of MMP and the subsequent increase in cell migration and invasion. (Cancer Res 2006; 66(22): 10902-10)
Up-regulation of Expression of the Ubiquitin Carboxyl-Terminal Hydrolase L1 Gene in Human Airway Epithelium of Cigarette Smokers
Authors: Carolan Brendan J. , Heguy Adriana , Harvey Ben-Gary , Leopold Philip L. , Ferris Barbara , Crystal Ronald G. 
Published: November 2006

Abstract
Neuroendocrine differentiation is a common feature of lung cancer and increased numbers of neuroendocrine cells and their peptides have been described in chronic smokers. To understand the effects of cigarette smoking on the gene expression profile of neuroendocrine cells, microarray analysis with TaqMan confirmation was used to assess airway epithelial samples obtained by fiberoptic bronchoscopy from 81 individuals [normal nonsmokers, normal smokers, smokers with early chronic obstructive lung disease (COPD), and smokers with established COPD]. Of 11 genes considered to be neuroendocrine cell specific, only ubiquitin carboxyl-terminal hydrolase L1 (UCHL1), a member of the ubiquitin proteasome pathway, was consistently up-regulated in smokers compared with nonsmokers. Up-regulation of UCHL1 at the protein level was observed with immunohistochemical analysis of bronchial biopsies of smokers compared with nonsmokers. UCHL1 expression was evident only in neuroendocrine cells of the airway epithelium in nonsmokers; however, UCHL1 was also expressed in ciliated epithelial cells in smokers. This observation may add further weight to recent observations that ciliated cells are capable of transdifferentiating to other airway epithelial cells. In the context that UCHL1 is involved in the degradation of unwanted, misfolded, or damaged proteins within the cell and is overexpressed in &gt;50% of lung cancers, its overexpression in chronic smokers may represent an early event in the complex transformation from normal epithelium to overt malignancy. (Cancer Res 2006; 66(22): 10729-40)
Germ-Line Genetic Variation in the Key Androgen-Regulating Genes Androgen Receptor, Cytochrome P450, and Steroid-5-α-Reductase Type 2 Is Important for Prostate Cancer Development
Authors: Lindström Sara , Wiklund Fredrik , Adami Hans-Olov , Bälter Katarina Augustsson , Adolfsson Jan , Grönberg Henrik 
Published: November 2006

Abstract
Prostate cancer risk may be influenced by single genetic variants in the hormone-regulating genes androgen receptor (AR), cytochrome P450 (CYP17), and steroid-5-α-reductase type 2 (SRD5A2). In this study, we comprehensively investigated polymorphisms in these three loci and their joint effect in a large population-based study. We selected 23 haplotype-tagging single-nucleotide polymorphisms (htSNP) that could uniquely describe &gt;95% of the haplotypes (6 in AR, 6 in CYP17, and 11 in SRD5A2). These htSNPs were then genotyped in the Cancer Prostate in Sweden population (2,826 case subjects and 1,705 controls). We observed significant association for several SNPs in the AR gene (P = 0.004-0.02) and CYP17 (P = 0.009-0.05) and one SNP in SRD5A2 (P = 0.02). Carriers of the most common AR haplotype had a significant excess risk to develop prostate cancer [odds ratio (OR), 1.25; 95% confidence interval (95% CI), 1.1-1.5; P = 0.002], yielding an estimated population attributable risk of 16% (95% CI, 0.06-0.25). Combining risk alleles from these genes yielded a 12% risk increase for each additional high-risk allele carried (95% CI, 1.1-1.2; P for trend = 9.2 × 10−5), with an overall OR of 1.87 (95% CI, 1.0-3.4) for carriers of all five included risk alleles, an OR of 2.13 (P for trend = 8 × 10−4) for advanced disease, and an OR of 4.35 (P for trend = 7 × 10−5) for disease onset before age 65 years. Genetic variation in key genes in the androgen pathway is important for development of prostate cancer and may account for a considerable proportion of all prostate cancers. Carriers of five high-risk alleles in the AR, CYP17, and SRD5A2 genes are at ∼2-fold excess risk to develop prostate cancer. (Cancer Res 2006; 66(22): 11077-83)
Les smectites latées du domaine Atlantique depuis le Jurassique superieur: gisement et signification
Authors: Holtzapffel T. , Chamley H. 
Published: November 2006

ResumeL'étude concerne 225 échantillons d'âge Jurassique à actuel de l'Océan Atlantique. La comparaison de l'abondance des smectites lattées, estimée sur micrographies électroniques, et de divers paramètres des sédiments, apporte des informations nouvelles sur la genèse et la signification de ces minéraux dans des sédiments non volcanoclastiques et non remainés. L'élaboration des smectites lattées par recristallisation diagénétique de smectites détritiques est favorisée lorsque la microperméabilité du sédiment est réduite (argiles fibreuses et particules calcaires, surtout les foraminifères, peu abondantes); lorsque les échanges chimiques à bilan constant avec le milieu interstitiel sont facilités (smectites abondantes) et lorsque la vitesse de dépôt est faible à moyenne. Dans les autres cas, la recristallisation de smectites lattées est très réduite ou absente. L'identification de ces minéraux dans les sédiments permet de préciser les conditions paléogéographiques de dépôt. La rareté des smectites lattées au Plio—Quaternaire pourrait être liée à l'extension des grands refroidissements mondiaux du climat.