bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of clastogen-induced gene expression profiles in wild-type and DNA repair-deficient Rad54/Rad54B cells
Authors: Mahabir Anuska G , Schaap Mirjam M , Pennings Jeroen LA , van Benthem Jan , Hendriksen Coenraad FM , van Steeg Harry 
Published: January 2010

Abstract

Background
Previously we found that Rad54/Rad54B cells are more sensitive towards mitomycin C (MMC) as compared to wild-type (WT) cells. This difference in sensitivity was absent upon exposure to other clastogens like bleomycin (BLM) and γ-radiation. In order to get further insight into possible underlying mechanisms, gene expression changes in WT and Rad54/Rad54B MEFs (mouse embryonic fibroblasts) after exposure to the clastogens MMC and BLM were investigated. Exposures of these cells to mutagens (N-ac-AAF and ENU) and vehicle were taken as controls.

Results
Most exposures resulted in an induction of DNA damage signaling and apoptosis genes and a reduced expression of cell division genes in cells of both genotypes. As expected, responses to N-ac-AAF were very similar in both genotypes. ENU exposure did not lead to significant gene expression changes in cells of both genotypes, presumably due to its short half-life. Gene expression responses to clastogens, however, showed a genotype-dependent effect for BLM and MMC. MMC treated Rad54/Rad54B MEFs showed no induction of p53-signaling, DNA damage response and apoptosis as seen for all the other treatments.

Conclusion
These data support our finding that different types of clastogens exist and that responses to these types depend on the DNA repair status of the cells.
AUF1 is involved in splenic follicular B cell maintenance
Authors: Sadri Navid , Lu Jin-Yu , Badura Michelle L , Schneider Robert J 
Published: January 2010

AbstractBackgroundThe adenosine/uridine-rich element (ARE)-binding protein AUF1 functions to regulate the inflammatory response through the targeted degradation of cytokine and other mRNAs that contain specific AREs in their 3' noncoding region (3' NCR). To investigate the role of AUF1 in the immune system, we characterized the lymphoid compartments of AUF1-deficient mice.ResultsMice lacking AUF1 exhibit an altered proportion and size of splenic B cell subsets. We show prominent apoptosis in splenic B cell follicles and reduced expression of Bcl-2, A1, and Bcl-XLcorrelate with increased turnover and significant reduction in the number and proportion of splenic FO B cells in AUF1-deficient mice. In addition, AUF1-deficient mice exhibit a sharp decrease in splenic size and lymphocyte cellularity. Bone marrow transfer studies demonstrate that AUF1 deficiency induces cell-autonomous defects in mature B cell subsets but not in the overall number of splenocytes. Reconstitution of irradiated adult AUF1-deficient mice with wild-type bone marrow restores the proportion of FO and marginal zone (MZ) B cells, but does not rescue the decrease in the number of splenocytes. Functionally, AUF1-deficient mice mount an attenuated response to T cell-independent (TI) antigen, which correlates with impaired MZ B cell function.ConclusionThese data indicate that AUF1 is important in the maintenance of splenic FO B cells and adequate humoral immune responses.
Dynamics of DNA methylation and Histone H4 acetylation during floral bud differentiation in azalea
Authors: Meijón Mónica , Feito Isabel , Valledor Luis , Rodríguez Roberto , Cañal María Jesús 
Published: January 2010

AbstractBackgroundThe ability to control the timing of flowering is a key strategy for planning production in ornamental species such as azalea, however it requires a thorough understanding of floral transition. Floral transition is achieved through a complex genetic network and regulated by multiple environmental and endogenous cues. Dynamic changes between chromatin states facilitating or inhibiting DNA transcription regulate the expression of floral induction pathways in response to environmental and developmental signals. DNA methylation and histone modifications are involved in controlling the functional state of chromatin and gene expression.ResultsThe results of this work indicate that epigenetic mechanisms such as DNA methylation and histone H4 acetylation have opposite and particular dynamics during the transition from vegetative to reproductive development in the apical shoots of azalea. Global levels of DNA methylation and histone H4 acetylation as well as immunodetection of 5-mdC and acetylated H4, in addition to a morphological study have permitted the delimitation of four basic phases in the development of the azalea bud and allowed the identification of a stage of epigenetic reprogramming which showed a sharp decrease of whole DNA methylation similar to that is defined in other developmental processes in plants and in mammals.ConclusionThe epigenetic control and reorganization of chromatin seem to be decisive for coordinating floral development in azalea. DNA methylation and H4 deacetylation act simultaneously and co-ordinately, restructuring the chromatin and regulating the gene expression during soot apical meristem development and floral differentiation.
Differential gene expression in incompatible interaction between wheat and stripe rust fungus revealed by cDNA-AFLP and comparison to compatible interaction
Authors: Wang Xiaojie , Liu Wei , Chen Xianming , Tang Chunlei , Dong Yanling , Ma Jinbiao , Huang Xueling , Wei Guorong , Han Qingmei , Huang Lili , Kang Zhensheng 
Published: January 2010

Abstract

Background
Stripe rust of wheat, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most important diseases of wheat worldwide. Due to special features of hexaploid wheat with large and complex genome and difficulties for transformation, and of Pst without sexual reproduction and hard to culture on media, the use of most genetic and molecular techniques in studying genes involved in the wheat-Pst interactions has been largely limited. The objective of this study was to identify transcriptionally regulated genes during an incompatible interaction between wheat and Pst using cDNA-AFLP technique

Results
A total of 52,992 transcript derived fragments (TDFs) were generated with 64 primer pairs and 2,437 (4.6%) of them displayed altered expression patterns after inoculation with 1,787 up-regulated and 650 down-regulated. We obtained reliable sequences (>100 bp) for 255 selected TDFs, of which 113 (44.3%) had putative functions identified. A large group (17.6%) of these genes shared high homology with genes involved in metabolism and photosynthesis; 13.8% to genes with functions related to disease defense and signal transduction; and those in the remaining groups (12.9%) to genes involved in transcription, transport processes, protein metabolism, and cell structure, respectively. Through comparing TDFs identified in the present study for incompatible interaction and those identified in the previous study for compatible interactions, 161 TDFs were shared by both interactions, 94 were expressed specifically in the incompatible interaction, of which the specificity of 43 selected transcripts were determined using quantitative real-time polymerase chain reaction (qRT-PCR). Based on the analyses of homology to genes known to play a role in defense, signal transduction and protein metabolism, 20 TDFs were chosen and their expression patterns revealed by the cDNA-AFLP technique were confirmed using the qRT-PCR analysis.

Conclusion
We uncovered a number of new candidate genes possibly involved in the interactions of wheat and Pst, of which 11 TDFs expressed specifically in the incompatible interaction. Resistance to stripe rust in wheat cv. Suwon11 is executed after penetration has occurred. Moreover, we also found that plant responses in compatible and incompatible interactions are qualitatively similar but quantitatively different soon after stripe rust fungus infection.
Molecular modeling of the reductase domain to elucidate the reaction mechanism of reduction of peptidyl thioester into its corresponding alcohol in non-ribosomal peptide synthetases
Authors: Manavalan Balachandran , Murugapiran Senthil K , Lee Gwang , Choi Sangdun 
Published: January 2010

Abstract

Background
Nonribosomal peptide synthetases (NRPSs) are multienzymatic, multidomain megasynthases involved in the biosynthesis of pharmaceutically important nonribosomal peptides. The peptaibol synthetase from Trichoderma virens (TPS) is an important member of the NRPS family that exhibits antifungal properties. The majority of the NRPSs terminate peptide synthesis with the thioesterase (TE) domain, which either hydrolyzes the thioester linkage, releasing the free peptic acid, or catalyzes the intramolecular macrocyclization to produce a macrolactone product. TPS is an important NRPS that does not encompass a TE domain, but rather a reductase domain (R domain) to release the mature peptide product reductively with the aid of a NADPH cofactor. However, the catalytic mechanism of the reductase domain has not yet been elucidated.

Results
We present here a three-dimensional (3D) model of the reductase domain based on the crystal structure of vestitone reductase (VR). VR belongs to the short-chain dehydrogenase/reductase (SDR) superfamily and is responsible for the nicotinamide dinucleotide phosphate (NADPH)-dependent reduction of the substrate into its corresponding secondary alcohol product. The binding sites of the probable linear substrates, alamethicin, trichotoxin, antiamoebin I, chrysopermin C and gramicidin, were identified within the modeled R domain using multiple docking approaches. The docking results of the ligand in the active site of the R domain showed that reductase side chains have a high affinity towards ligand binding, while the thioester oxygen of each substrate forms a hydrogen bond with the OH group of Tyr176 and the thiol group of the substrate is closer to the Glu220. The modeling and docking studies revealed the reaction mechanism of reduction of thioester into a primary alcohol.

Conclusion
Peptaibol biosynthesis incorporates a single R domain, which appears to catalyze the four-electron reduction reaction of a peptidyl carrier protein (PCP)-bound peptide to its corresponding primary alcohol. Analysis of R domains present in the non-redundant (nr) database of the NCBI showed that the R domain always resides in the last NRPS module and is involved in either a two or four-electron reduction reaction.
Cost-effectiveness of human papillomavirus vaccination for prevention of cervical cancer in Taiwan
Authors: Liu Pang-Hsiang , Hu Fu-Chang , Lee Ping-Ing , Chow Song-Nan , Huang Chao-Wan , Wang Jung-Der 
Published: January 2010

Abstract

Background
Human papillomavirus (HPV) infection has been shown to be a major risk factor for cervical cancer. Vaccines against HPV-16 and HPV-18 are highly effective in preventing type-specific HPV infections and related cervical lesions. There is, however, limited data available describing the health and economic impacts of HPV vaccination in Taiwan. The objective of this study was to assess the cost-effectiveness of prophylactic HPV vaccination for the prevention of cervical cancer in Taiwan.

Methods
We developed a Markov model to compare the health and economic outcomes of vaccinating preadolescent girls (at the age of 12 years) for the prevention of cervical cancer with current practice, including cervical cytological screening. Data were synthesized from published papers or reports, and whenever possible, those specific to Taiwan were used. Sensitivity analyses were performed to account for important uncertainties and different vaccination scenarios.

Results
Under the assumption that the HPV vaccine could provide lifelong protection, the massive vaccination among preadolescent girls in Taiwan would lead to reduction in 73.3% of the total incident cervical cancer cases and would result in a life expectancy gain of 4.9 days or 8.7 quality-adjusted life days at a cost of US$324 as compared to the current practice. The incremental cost-effectiveness ratio (ICER) was US$23,939 per life year gained or US$13,674 per quality-adjusted life year (QALY) gained given the discount rate of 3%. Sensitivity analyses showed that this ICER would remain below US$30,000 per QALY under most conditions, even when vaccine efficacy was suboptimal or when vaccine-induced immunity required booster shots every 13 years.

Conclusions
Although gains in life expectancy may be modest at the individual level, the results indicate that prophylactic HPV vaccination of preadolescent girls in Taiwan would result in substantial population benefits with a favorable cost-effectiveness ratio. Nevertheless, we should not overlook the urgency to improve the compliance rate of cervical screening, particularly for older individuals.
Smoothened as a new therapeutic target for human osteosarcoma
Authors: Hirotsu Masataka , Setoguchi Takao , Sasaki Hiromi , Matsunoshita Yukihiro , Gao Hui , Nagao Hiroko , Kunigou Osamu , Komiya Setsuro 
Published: January 2010

Abstract

Background
The Hedgehog signaling pathway functions as an organizer in embryonic development. Recent studies have demonstrated constitutive activation of Hedgehog pathway in various types of malignancies. However, it remains unclear how Hedgehog pathway is involved in the pathogenesis of osteosarcoma. To explore the involvement of aberrant Hedgehog pathway in the pathogenesis of osteosarcoma, we investigated the expression and activation of Hedgehog pathway in osteosarcoma and examined the effect of SMOOTHENED (SMO) inhibition.

Results
To evaluate the expression of genes of Hedgehog pathway, we performed real-time PCR and immunohistochemistry using osteosarcoma cell lines and osteosarcoma biopsy specimens. To evaluate the effect of SMO inhibition, we did cell viability, colony formation, cell cycle in vitro and xenograft model in vivo. Real-time PCR revealed that osteosarcoma cell lines over-expressed Sonic hedgehog, Indian hedgehog, PTCH1, SMO, and GLI. Real-time PCR revealed over-expression of SMO, PTCH1, and GLI2 in osteosarcoma biopsy specimens. These findings showed that Hedgehog pathway is activated in osteosarcomas. Inhibition of SMO by cyclopamine, a specific inhibitor of SMO, slowed the growth of osteosarcoma in vitro. Cell cycle analysis revealed that cyclopamine promoted G1 arrest. Cyclopamine reduced the expression of accelerators of the cell cycle including cyclin D1, cyclin E1, SKP2, and pRb. On the other hand, p21cip1 wprotein was up-regulated by cyclopamine treatment. In addition, knockdown of SMO by SMO shRNA prevents osteosarcoma growth in vitro and in vivo.

Conclusions
These findings suggest that inactivation of SMO may be a useful approach to the treatment of patients with osteosarcoma.
A single vaccination with an inactivated bovine respiratory syncytial virus vaccine primes the cellular immune response in calves with maternal antibody
Authors: van der Sluijs Mirjam TW , Kuhn Eva M , Makoschey Birgit 
Published: January 2010

AbstractBackgroundThe efficacy of a single dose of an inactivated bovine respiratory syncytial virus (BRSV) - Parainfluenaza type 3 (PI3) -Mannheimia haemolytica(Mh) combination vaccine, in calves positive for maternal antibodies, was established in a BRSV infection study.ResultsAs expected the single vaccination did not have any effect on the decline of BRSV-specific neutralising or ELISA antibody. The cellular immune system was however primed by the vaccination. In the vaccinated group virus excretion with nasal discharge was reduced, less virus could be re-isolated from lung tissues and the lungs were less affected.ConclusionsThese results indicate that a single vaccination with an inactivated BRSV vaccine was able to break through the maternal immunity and induce partial protection in very young calves. It can be speculated that the level and duration of protection will improve after the second dose of vaccine is administered. A two-dose basic vaccination schedule is recommended under field conditions.
Neurodevelopmental effects of chronic exposure to elevated levels of pro-inflammatory cytokines in a developing visual system
Authors: Lee Ryan H , Mills Elizabeth A , Schwartz Neil , Bell Mark R , Deeg Katherine E , Ruthazer Edward S , Marsh-Armstrong Nicholas , Aizenman Carlos D 
Published: January 2010

Abstract
Background
Imbalances in the regulation of pro-inflammatory cytokines have been increasingly correlated with a number of severe and prevalent neurodevelopmental disorders, including autism spectrum disorder, schizophrenia and Down syndrome. Although several studies have shown that cytokines have potent effects on neural function, their role in neural development is still poorly understood. In this study, we investigated the link between abnormal cytokine levels and neural development using the Xenopus laevis tadpole visual system, a model frequently used to examine the anatomical and functional development of neural circuits.

Results
Using a test for a visually guided behavior that requires normal visual system development, we examined the long-term effects of prolonged developmental exposure to three pro-inflammatory cytokines with known neural functions: interleukin (IL)-1β, IL-6 and tumor necrosis factor (TNF)-α. We found that all cytokines affected the development of normal visually guided behavior. Neuroanatomical imaging of the visual projection showed that none of the cytokines caused any gross abnormalities in the anatomical organization of this projection, suggesting that they may be acting at the level of neuronal microcircuits. We further tested the effects of TNF-α on the electrophysiological properties of the retinotectal circuit and found that long-term developmental exposure to TNF-α resulted in enhanced spontaneous excitatory synaptic transmission in tectal neurons, increased AMPA/NMDA ratios of retinotectal synapses, and a decrease in the number of immature synapses containing only NMDA receptors, consistent with premature maturation and stabilization of these synapses. Local interconnectivity within the tectum also appeared to remain widespread, as shown by increased recurrent polysynaptic activity, and was similar to what is seen in more immature, less refined tectal circuits. TNF-α treatment also enhanced the overall growth of tectal cell dendrites. Finally, we found that TNF-α-reared tadpoles had increased susceptibility to pentylenetetrazol-induced seizures.

Conclusions
Taken together our data are consistent with a model in which TNF-α causes premature stabilization of developing synapses within the tectum, therefore preventing normal refinement and synapse elimination that occurs during development, leading to increased local connectivity and epilepsy. This experimental model also provides an integrative approach to understanding the effects of cytokines on the development of neural circuits and may provide novel insights into the etiology underlying some neurodevelopmental disorders.
Are acupoints specific for diseases? A systematic review of the randomized controlled trials with sham acupuncture controls
Authors: Zhang Hongwei , Bian Zhaoxiang , Lin Zhixiu 
Published: January 2010

Abstract

Background
The results of many clinical trials and experimental studies regarding acupoint specificity are contradictory. This review aims to investigate whether a difference in efficacy exists between ordinary acupuncture on specific acupoints and sham acupuncture controls on non-acupoints or on irrelevant acupoints.

Methods
Databases including Medline, Embase, AMED and Chinese Biomedical Database were searched to identify randomized controlled trials published between 1998 and 2009 that compared traditional body acupuncture on acupoints with sham acupuncture controls on irrelevant acupoints or non-acupoints with the same needling depth. The Cochrane Collaboration's tool for assessing risk of bias was employed to address the quality of the included trials.

Results
Twelve acupuncture clinical trials with sham acupuncture controls were identified and included in the review. The conditions treated varied. Half of the included trials had positive results on the primary outcomes and demonstrated acupoint specificity. However, among those six trials (total sample size: 985) with low risk of bias, five trials (sample size: 940) showed no statistically significant difference between proper and sham acupuncture treatments.

Conclusion
This review did not demonstrate the existence of acupoint specificity. Further clinical trials with larger sample sizes, optimal acupuncture treatment protocols and appropriate sham acupuncture controls are required to resolve this important issue.
Differences in the epigenetic and reprogramming properties of pluripotent and extra-embryonic stem cells implicate chromatin remodelling as an important early event in the developing mouse embryo
Authors: Santos Joana , Filipe Pereira C , Di-Gregorio Aida , Spruce Thomas , Alder Olivia , Rodriguez Tristan , Azuara Véronique , Merkenschlager Matthias , Fisher Amanda G 
Published: January 2010

Abstract

Background
During early mouse development, two extra-embryonic lineages form alongside the future embryo: the trophectoderm (TE) and the primitive endoderm (PrE). Epigenetic changes known to take place during these early stages include changes in DNA methylation and modified histones, as well as dynamic changes in gene expression.

Results
In order to understand the role and extent of chromatin-based changes for lineage commitment within the embryo, we examined the epigenetic profiles of mouse embryonic stem (ES), trophectoderm stem (TS) and extra-embryonic endoderm (XEN) stem cell lines that were derived from the inner cell mass (ICM), TE and PrE, respectively. As an initial indicator of the chromatin state, we assessed the replication timing of a cohort of genes in each cell type, based on data that expressed genes and acetylated chromatin domains, generally, replicate early in S-phase, whereas some silent genes, hypoacetylated or condensed chromatin tend to replicate later. We found that many lineage-specific genes replicate early in ES, TS and XEN cells, which was consistent with a broadly 'accessible' chromatin that was reported previously for multiple ES cell lines. Close inspection of these profiles revealed differences between ES, TS and XEN cells that were consistent with their differing lineage affiliations and developmental potential. A comparative analysis of modified histones at the promoters of individual genes showed that in TS and ES cells many lineage-specific regulator genes are co-marked with modifications associated with active (H4ac, H3K4me2, H3K9ac) and repressive (H3K27me3) chromatin. However, in XEN cells several of these genes were marked solely by repressive modifications (such as H3K27me3, H4K20me3). Consistent with TS and XEN having a restricted developmental potential, we show that these cells selectively reprogramme somatic cells to induce the de novo expression of genes associated with extraembryonic differentiation.

Conclusions
These data provide evidence that the diversification of defined embryonic and extra-embryonic lineages is accompanied by chromatin remodelling at specific loci. Stem cell lines from the ICM, TE and PrE can each dominantly reprogramme somatic cells but reset gene expression differently, reflecting their separate lineage identities and increasingly restricted developmental potentials.