bluuebunny/crossref_metadata_2025 huggingface dataset:
Inequalities and Prospects: Ethnicity and Legal Status in the Construction Labor Force After Hurricane Katrina
Authors: Vinck Patrick , Pham Phuong N. , Fletcher Laurel E. , Stover Eric
Published: December 2009

The arrival of Latino immigrant workers and the weakening of federal labor regulations after Hurricane Katrina raised concerns about labor conditions and workers’ rights. We carried out a survey of workers at 212 randomly selected addresses in the city of New Orleans, successfully interviewing 212 out of 351 workers approached (40% refusal rate). Workers were asked about their demographic, employment, and health characteristics, as well as violations of human rights they may have experienced. The survey was supplemented with in-depth qualitative interviews with Latino workers and key informants in Louisiana and Mississippi. Our study showed that Latino workers, particularly undocumented workers, experienced lower wages, more nonpayment of wages and/or overtime wages, and fewer worker protections than non-Latino workers. The poorer treatment of Latino and undocumented workers is thought to reflect employers’ perception of them as a disposable labor force. Indeed, few of the workers who arrived after Katrina, and especially low percentages of Latinos and undocumented workers, intended to settle in New Orleans.
Anterior Cingulate Volumetric Alterations in Treatment-Naïve Adults With ADHD
Authors: Makris Nikos , Seidman Larry J. , Valera Eve M. , Biederman Joseph , Monuteaux Michael C. , Kennedy David N. , Caviness Verne S. , Bush George , Crum Katherine , Brown Ariel B. , Faraone Stephen V.
Published: December 2009

Objective: We sought to examine preliminary results of brain alterations in anterior cingulate cortex (ACC) in treatment-naïve adults with ADHD. The ACC is a central brain node for the integration of cognitive control and allocation of attention, affect and drive. Thus its anatomical alteration may give rise to impulsivity, hyperactivity and inattention, which are cardinal behavioral manifestations of ADHD. Method: Segmentation and parcellation of the ACC was performed on controls ( n = 22), treated ( n = 13) and treatment-naïve adults with ADHD ( n = 13). Results: There was a 21% volume reduction in the left ACC of the treatment-naïve group relative to the control group. Also, there was a 23% volume reduction in the right ACC of the treated group relative to the control group. Conclusion: These results raise the possibility that in ADHD there are volumetric deficits persistent into adulthood, that are independent of medical treatment. (J. of Att. Dis. 2010; 13(4) 407-413)
Development of an iPod Audio Computer-Assisted Self-Interview to Increase the Representation of Low-Literacy Populations in Survey Research
Authors: Galvez Gino , Mankowski Eric S. , Braun Margaret F. , Glass Nancy
Published: December 2009

Personal electronic devices (e.g., MP3 players) have the technological capacity to administer surveys to diverse cultural and low-literacy groups. To address concerns associated with survey research and low literacy, the authors developed a novel application of the iPod® to enable self-administration of surveys. The authors provide preliminary evidence demonstrating the utility of the application from a study on intimate partner violence. Further research is needed to assess the appropriateness, functionality, and usability of the iPod and its application to survey research.
Malignant transformation of Slp65-deficient pre-B cells involves disruption of the Arf-Mdm2-p53 tumor suppressor pathway
Authors: Ta Van B. T. , de Bruijn Marjolein J. W. , ter Brugge Petra J. , van Hamburg Jan Piet , Diepstraten Hans J. A. , van Loo Pieter Fokko , Kersseboom Rogier , Hendriks Rudi W.
Published: December 2009

The adapter protein Slp65 is a key component of the precursor-B (pre-B) cell receptor. Slp65-deficient mice spontaneously develop pre-B cell leukemia, but the mechanism by which Slp65−/− pre-B cells become malignant is unknown. Loss of Btk, a Tec-family kinase that cooperates with Slp65 as a tumor suppressor, synergizes with deregulation of the c-Myc oncogene during lymphoma formation. Here, we report that the presence of the immunoglobulin heavy chain transgene VH81X prevented tumor development in Btk−/−Slp65−/− mice. This finding paralleled the reported effect of a human immunoglobulin heavy chain transgene on lymphoma development in Eμ-myc mice, expressing transgenic c-Myc. Because activation of c-Myc strongly selects for spontaneous inactivation of the p19Arf-Mdm2-p53 tumor suppressor pathway, we investigated whether disruption of this pathway is a common alteration in Slp65−/− pre-B cell tumors. We found that combined loss of Slp65 and p53 in mice transformed pre-B cells very efficiently. Aberrations in p19Arf, Mdm2, or p53 expression were found in all Slp65−/− (n = 17) and Btk−/−Slp65−/− (n = 32) pre-B cell leukemias analyzed. In addition, 9 of 10 p53−/−Slp65−/− pre-B cell leukemias manifested significant Mdm2 protein expression. These data indicate that malignant transformation of Slp65−/− pre-B cells involves disruption of the p19Arf-Mdm2-p53 tumor suppressor pathway.
STAT5 requires the N-domain for suppression of miR15/16, induction of bcl-2, and survival signaling in myeloproliferative disease
Authors: Li Geqiang , Miskimen Kristy L. , Wang Zhengqi , Xie Xiu Yan , Brenzovich Jennifer , Ryan John J. , Tse William , Moriggl Richard , Bunting Kevin D.
Published: December 2009

Phosphorylated signal transducer and activator of transcription 5 (STAT5) is a biomarker and potential molecular target for hematologic malignancies. We have shown previously that lethal myeloproliferative disease (MPD) in mice mediated by persistently activated STAT5 (STAT5aS711F) requires the N-domain, but the mechanism was not defined. We now demonstrate by retrovirally complementing STAT5abnull/null primary mast cells that relative to wild-type STAT5a, STAT5a lacking the N-domain (STAT5aΔN) ineffectively protected against cytokine withdrawal-induced cell death. Both STAT5a and STAT5aΔN bound to a site in the bcl-2 gene and both bound near the microRNA 15b/16 cluster. However, only STAT5a could effectively induce bcl-2 mRNA and reciprocally suppress miR15b/16 leading to maintained bcl-2 protein levels. After retroviral complementation of STAT5abnull/null fetal liver cells and transplantation, persistently active STAT5aS711F lacking the N-domain (STAT5aΔNS711F) was insufficient to protect c-Kit+Lin−Sca-1+ (KLS) cells from apoptosis and unable to induce bcl-2 expression, whereas STAT5aS711F caused robust KLS cell expansion, induction of bcl-2, and lethal MPD. Severe attenuation of MPD by STAT5aΔNS711F was reversed by H2k/bcl-2 transgenic expression. Overall, these studies define N-domain–dependent survival signaling as an Achilles heel of persistent STAT5 activation and highlight the potential therapeutic importance of targeting STAT5 N-domain–mediated regulation of bcl-2 family members.
DescFold: A web server for protein fold recognition
Authors: Yan Ren-Xiang , Si Jing-Na , Wang Chuan , Zhang Ziding
Published: December 2009

Background

Machine learning-based methods have been proven to be powerful in developing new fold recognition tools. In our previous work [Zhang, Kochhar and Grigorov (2005) Protein Science, 14: 431-444], a machine learning-based method called DescFold was established by using Support Vector Machines (SVMs) to combine the following four descriptors: a profile-sequence-alignment-based descriptor using Psi-blast e-values and bit scores, a sequence-profile-alignment-based descriptor using Rps-blast e-values and bit scores, a descriptor based on secondary structure element alignment (SSEA), and a descriptor based on the occurrence of PROSITE functional motifs. In this work, we focus on the improvement of DescFold by incorporating more powerful descriptors and setting up a user-friendly web server.

Results

In seeking more powerful descriptors, the profile-profile alignment score generated from the COMPASS algorithm was first considered as a new descriptor (i.e., PPA). When considering a profile-profile alignment between two proteins in the context of fold recognition, one protein is regarded as a template (i.e., its 3D structure is known). Instead of a sequence profile derived from a Psi-blast search, a structure-seeded profile for the template protein was generated by searching its structural neighbors with the assistance of the TM-align structural alignment algorithm. Moreover, the COMPASS algorithm was used again to derive a profile-structural-profile-alignment-based descriptor (i.e., PSPA). We trained and tested the new DescFold in a total of 1,835 highly diverse proteins extracted from the SCOP 1.73 version. When the PPA and PSPA descriptors were introduced, the new DescFold boosts the performance of fold recognition substantially. Using the SCOP_1.73_40% dataset as the fold library, the DescFold web server based on the trained SVM models was further constructed. To provide a large-scale test for the new DescFold, a stringent test set of 1,866 proteins were selected from the SCOP 1.75 version. At a less than 5% false positive rate control, the new DescFold is able to correctly recognize structural homologs at the fold level for nearly 46% test proteins. Additionally, we also benchmarked the DescFold method against several well-established fold recognition algorithms through the LiveBench targets and Lindahl dataset.

Conclusions

The new DescFold method was intensively benchmarked to have very competitive performance compared with some well-established fold recognition methods, suggesting that it can serve as a useful tool to assist in template-based protein structure prediction. The DescFold server is freely accessible at http://202.112.170.199/DescFold/index.html.
TransportTP: A two-phase classification approach for membrane transporter prediction and characterization
Authors: Li Haiquan , Benedito Vagner A , Udvardi Michael K , Zhao Patrick Xuechun
Published: December 2009

Background

Membrane transporters play crucial roles in living cells. Experimental characterization of transporters is costly and time-consuming. Current computational methods for transporter characterization still require extensive curation efforts, especially for eukaryotic organisms. We developed a novel genome-scale transporter prediction and characterization system called TransportTP that combined homology-based and machine learning methods in a two-phase classification approach. First, traditional homology methods were employed to predict novel transporters based on sequence similarity to known classified proteins in the Transporter Classification Database (TCDB). Second, machine learning methods were used to integrate a variety of features to refine the initial predictions. A set of rules based on transporter features was developed by machine learning using well-curated proteomes as guides.

Results

In a cross-validation using the yeast proteome for training and the proteomes of ten other organisms for testing, TransportTP achieved an equivalent recall and precision of 81.8%, based on TransportDB, a manually annotated transporter database. In an independent test using the Arabidopsis proteome for training and four recently sequenced plant proteomes for testing, it achieved a recall of 74.6% and a precision of 73.4%, according to our manual curation.

Conclusions

TransportTP is the most effective tool for eukaryotic transporter characterization up to date.
Web-based interrogation of gene expression signatures using EXALT
Authors: Wu Jun , Qiu Qingchao , Xie Lu , Fullerton Joseph , Yu Jian , Shyr Yu , George Alfred L , Yi Yajun
Published: December 2009

Background

Widespread use of high-throughput techniques such as microarrays to monitor gene expression levels has resulted in an explosive growth of data sets in public domains. Integration and exploration of these complex and heterogeneous data have become a major challenge.

Results

The EXALT (EX pression signature A naL ysis T ool) online program enables meta-analysis of gene expression profiles derived from publically accessible sources. Searches can be executed online against two large databases currently containing more than 28,000 gene expression signatures derived from GEO (Gene Expression Omnibus) and published expression profiles of human cancer. Comparisons among gene expression signatures can be performed with homology analysis and co-expression analysis. Results can be visualized instantly in a plot or a heat map. Three typical use cases are illustrated.

Conclusions

The EXALT online program is uniquely suited for discovering relationships among transcriptional profiles and searching gene expression patterns derived from diverse physiological and pathological settings. The EXALT online program is freely available for non-commercial users from http://seq.mc.vanderbilt.edu/exalt/.
The Golgi α-1,6 mannosyltransferase KlOch1p of Kluyveromyces lactis is required for Ca2+/calmodulin-based signaling and for proper mitochondrial functionality
Authors: Zanni Elena , Farina Francesca , Ricci Antonella , Mancini Patrizia , Frank Claudio , Palleschi Claudio , Uccelletti Daniela
Published: December 2009

Background

Protein N-glycosylation is a relevant metabolic pathway in eukaryotes and plays key roles in cell processes. In yeasts, outer chain branching is initiated in the Golgi apparatus by the alpha-1,6-mannosyltransferase Och1p.

Results

Here we report that, in Kluyveromyces lactis, this glycosyltransferase is also required to maintain functional mitochondria and calcium homeostasis. Cells carrying a mutation in KlOCH1 gene showed altered mitochondrial morphology, increased accumulation of ROS and reduced expression of calcium signalling genes such as calmodulin and calcineurin. Intracellular calcium concentration was also reduced in the mutant cells with respect to the wild type counterparts.

Phenotypes that occur in cells lacking the alpha-1,6-mannosyltransferase, including oxidative stress and impaired mitochondria functionality, were suppressed by increased dosage of KlCmd1p. This, in turn, acts through the action of calcineurin.

Conclusions

Proper functioning of the alpha-1,6-mannosyltransferase in the N-glycosylation pathway of K. lactis is required for maintaining normal calcium homeostasis; this is necessary for physiological mitochondria dynamics and functionality.
Mechanism of primitive duct formation in the pancreas and submandibular glands: a role for SDF-1
Authors: Hick Anne-Christine , van Eyll Jonathan M , Cordi Sabine , Forez Céline , Passante Lara , Kohara Hiroshi , Nagasawa Takashi , Vanderhaeghen Pierre , Courtoy Pierre J , Rousseau Guy G , Lemaigre Frédéric P , Pierreux Christophe E
Published: December 2009

Background

The exocrine pancreas is composed of a branched network of ducts connected to acini. They are lined by a monolayered epithelium that derives from the endoderm and is surrounded by mesoderm-derived mesenchyme. The morphogenic mechanisms by which the ductal network is established as well as the signaling pathways involved in this process are poorly understood.

Results

By morphological analyzis of wild-type and mutant mouse embryos and using cultured embryonic explants we investigated how epithelial morphogenesis takes place and is regulated by chemokine signaling. Pancreas ontogenesis displayed a sequence of two opposite epithelial transitions. During the first transition, the monolayered and polarized endodermal cells give rise to tissue buds composed of a mass of non polarized epithelial cells. During the second transition the buds reorganize into branched and polarized epithelial monolayers that further differentiate into tubulo-acinar glands. We found that the second epithelial transition is controlled by the chemokine Stromal cell-Derived Factor (SDF)-1. The latter is expressed by the mesenchyme, whereas its receptor CXCR4 is expressed by the epithelium. Reorganization of cultured pancreatic buds into monolayered epithelia was blocked in the presence of AMD3100, a SDF-1 antagonist. Analyzis of sdf1 and cxcr4 knockout embryos at the stage of the second epithelial transition revealed transient defective morphogenesis of the ventral and dorsal pancreas. Reorganization of a globular mass of epithelial cells in polarized monolayers is also observed during submandibular glands development. We found that SDF-1 and CXCR4 are expressed in this organ and that AMD3100 treatment of submandibular gland explants blocks its branching morphogenesis.

Conclusion

In conclusion, our data show that the primitive pancreatic ductal network, which is lined by a monolayered and polarized epithelium, forms by remodeling of a globular mass of non polarized epithelial cells. Our data also suggest that SDF-1 controls the branching morphogenesis of several exocrine tissues.
Transcriptional profile of Pseudomonas syringae pv. phaseolicola NPS3121 in response to tissue extracts from a susceptible Phaseolus vulgarisL. cultivar
Authors: Hernández-Morales Alejandro , De la Torre-Zavala Susana , Ibarra-Laclette Enrique , Hernández-Flores José Luis , Jofre-Garfias Alba Estela , Martínez-Antonio Agustino , Álvarez-Morales Ariel
Published: December 2009

Background

Pseudomonas syringaepv. phaseolicola is a Gram-negative plant-pathogenic bacterium that causes "halo blight" disease of beans (Phaseolus vulgarisL.). This disease affects both foliage and pods, and is a major problem in temperate areas of the world. Although several bacterial genes have been determined as participants in pathogenesis, the overall process still remains poorly understood, mainly because the identity and function of many of the genes are largely unknown. In this work, a genomic library ofP. syringaepv. phaseolicola NPS3121 was constructed and PCR amplification of individual fragments was carried out in order to print a DNA microarray. This microarray was used to identify genes that are differentially expressed when bean leaf extracts, pod extracts or apoplastic fluid were added to the growth medium.

Results

Transcription profiles show that 224 genes were differentially expressed, the majority under the effect of bean leaf extract and apoplastic fluid. Some of the induced genes were previously known to be involved in the first stages of the bacterial-plant interaction and virulence. These include genes encoding type III secretion system proteins and genes involved in cell-wall degradation, phaseolotoxin synthesis and aerobic metabolism. On the other hand, most repressed genes were found to be involved in the uptake and metabolism of iron.

Conclusion

This study furthers the understanding of the mechanisms involved, responses and the metabolic adaptation that occurs during the interaction ofP. syringaepv. phaseolicola with a susceptible host plant.
Nuclear factor I-A represses expression of the cell adhesion molecule L1
Authors: Schneegans Tanja , Borgmeyer Uwe , Hentschke Moritz , Gronostajski Richard M , Schachner Melitta , Tilling Thomas
Published: December 2009

Background

The neural cell adhesion molecule L1 plays a crucial role in development and plasticity of the nervous system. Neural cells thus require precise control of L1 expression.

Results

We identified a full binding site for nuclear factor I (NFI) transcription factors in the regulatory region of the mouse L1 gene. Electrophoretic mobility shift assay (EMSA) showed binding of nuclear factor I-A (NFI-A) to this site. Moreover, for a brain-specific isoform of NFI-A (NFI-A bs), we confirmed the interaction in vivo using chromatin immunoprecipitation (ChIP). Reporter gene assays showed that in neuroblastoma cells, overexpression of NFI-A bs repressed L1 expression threefold.

Conclusion

Our findings suggest that NFI-A, in particular its brain-specific isoform, represses L1 gene expression, and might act as a second silencer of L1 in addition to the neural restrictive silencer factor (NRSF).
Adaptive behavior of neighboring neurons during adaptation-induced plasticity of orientation tuning in V1
Authors: Nemri Abdellatif , Ghisovan Narcis , Shumikhina Svetlana , Molotchnikoff Stéphane
Published: December 2009

Background

Sensory neurons display transient changes of their response properties following prolonged exposure to an appropriate stimulus (adaptation). In adult cat primary visual cortex, orientation-selective neurons shift their preferred orientation after being adapted to a non-preferred orientation. The direction of those shifts, towards (attractive) or away (repulsive) from the adapter depends mostly on adaptation duration. How the adaptive behavior of a neuron is related to that of its neighbors remains unclear.

Results

Here we show that in most cases (75%), cells shift their preferred orientation in the same direction as their neighbors. We also found that cells shifting preferred orientation differently from their neighbors (25%) display three interesting properties: (i) larger variance of absolute shift amplitude, (ii) wider tuning bandwidth and (iii) larger range of preferred orientations among the cluster of cells. Several response properties of V1 neurons depend on their location within the cortical orientation map. Our results suggest that recording sites with both attractive and repulsive shifts following adaptation may be located in close proximity to iso-orientation domain boundaries or pinwheel centers. Indeed, those regions have a more diverse orientation distribution of local inputs that could account for the three properties above. On the other hand, sites with all cells shifting their preferred orientation in the same direction could be located within iso-orientation domains.

Conclusions

Our results suggest that the direction and amplitude of orientation preference shifts in V1 depend on location within the orientation map. This anisotropy of adaptation-induced plasticity, comparable to that of the visual cortex itself, could have important implications for our understanding of visual adaptation at the psychophysical level.
Reduced transcription of TCOF1 in adult cells of Treacher Collins syndrome patients
Authors: Masotti Cibele , Ornelas Camila C , Splendore-Gordonos Alessandra , Moura Ricardo , Félix Têmis M , Alonso Nivaldo , Camargo Anamaria A , Passos-Bueno Maria Rita
Published: December 2009

Background

Treacher Collins syndrome (TCS) is an autosomal dominant craniofacial disorder caused by frameshift deletions or duplications in theTCOF1gene. These mutations cause premature termination codons, which are predicted to lead to mRNA degradation by nonsense mediated mRNA decay (NMD). Haploinsufficiency of the gene product (treacle) during embryonic development is the proposed molecular mechanism underlying TCS. However, it is still unknown ifTCOF1expression levels are decreased in post-embryonic human cells.

Methods

We have estimatedTCOF1transcript levels through real time PCR in mRNA obtained from leucocytes and mesenchymal cells of TCS patients (n = 23) and controls (n = 18). Mutational screening and analysis of NMD were performed by direct sequencing of gDNA and cDNA, respectively.

Results

All the 23 patients had typical clinical features of the syndrome and pathogenic mutations were detected in 19 of them. We demonstrated that the expression level ofTCOF1is 18-31% lower in patients than in controls (p < 0.05), even if we exclude the patients in whom we did not detect the pathogenic mutation. We also observed that the mutant allele is usually less abundant than the wild type one in mesenchymal cells.

Conclusions

This is the first study to report decreased expression levels ofTCOF1in TCS adult human cells, but it is still unknown if this finding is associated to any phenotype in adulthood. In addition, as we demonstrated that alleles harboring the pathogenic mutations have lower expression, we herein corroborate the current hypothesis of NMD of the mutant transcript as the explanation for diminished levels ofTCOF1expression. Further, considering thatTCOF1deficiency in adult cells could be associated to pathologic clinical findings, it will be important to verify if TCS patients have an impairment in adult stem cell properties, as this can reduce the efficiency of plastic surgery results during rehabilitation of these patients.
Association between polymorphisms in DNA repair genes and survival of non-smoking female patients with lung adenocarcinoma
Authors: Yin Zhihua , Zhou Baosen , He Qincheng , Li Mingchuan , Guan Peng , Li Xuelian , Cui Zeshi , Xue Xiaoxia , Su Meng , Ma Rui , Bai Weijun , Xia Shuyue , Jiang Yanduo , Xu Shun , Lv Yi , Li Xun
Published: December 2009

Background

Excision repair cross-complementing group 1 (ERCC1) and group 2 (ERCC2), and X-ray repair cross-complementing group 1 (XRCC1) proteins play important roles in the repair of DNA damage and adducts. Single nucleotide polymorphisms (SNPs) of DNA repair genes are suspected to influence treatment effect and survival of cancer patients. This study aimed to investigate the relationship between polymorphisms in ERCC2, ERCC1 and XRCC1 genes and survival of non-smoking female patients with lung adenocarcinoma.

Methods

We used polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method to evaluate SNPs in ERCC2, ERCC1 and XRCC1 genes among 257 patients.

Results

The overall median survival time (MST) was 13.07 months. Increasing numbers of either ERCC1 118 or XRCC1 399 variant alleles were associated with shorter survival of non-smoking female lung adenocarcinoma patients (Log-rank P < 0.001). The adjusted hazard ratios (HRs) for individuals with CT or TT genotype at ERCC1 Asn118Asn were 1.48 and 2.67 compared with those with CC genotype. For polymorphism of XRCC1 399, the HRs were 1.28 and 2.68 for GA and AA genotype. When variant alleles across both polymorphisms were combined to analysis, the increasing number of variant alleles was associated with decreasing overall survival. Using the stepwise Cox regression analysis, we found that the polymorphisms in ERCC1 and XRCC1, tumor stage and chemotherapy or radiotherapy status independently predicted overall survival of non-smoking female patients with lung adenocarcinoma.

Conclusions

Genetic polymorphisms in ERCC1 and XRCC1 genes might be prognostic factors in non-smoking female patients with lung adenocarcinoma.
Paediatricians knowledge, attitudes, and practices regarding immunizations for infants in Italy
Authors: Anastasi Daniela , Di Giuseppe Gabriella , Marinelli Paolo , Angelillo Italo F
Published: December 2009

Background

The purpose of this study was to investigate whether paediatricians have appropriate knowledge, attitudes, and behaviours regarding vaccinations for infants in Italy.

Methods

A random sample of 500 paediatricians received a self-administered anonymous questionnaire covering demographic and professional characteristics; knowledge about the mandatory, recommended, and not indicated vaccinations for infants; attitudes about vaccinations for infants; behaviour regarding current administration or willingness to administer mandatory or recommended vaccinations for infants and immunization education programs of the parents.

Results

Only 42.3% paediatricians knew all recommended vaccinations for infants and this knowledge was significantly higher in females, in those who worked a higher number of hours for week, and in those who use guidelines for immunization practice. Only 10.3% had a very favourable attitude towards the utility of the recommended vaccinations for infants and this was significantly higher in those who administered recommended vaccinations for infants. A large proportion (82.7%) of paediatricians routinely informed the parents about the recommended vaccinations for infants and this appropriate behaviour was significantly higher among younger, in those with a higher number of years in practice, and in those who administered the recommended vaccinations for infants.

Conclusion

Training and educational interventions are needed in order to improve knowledge, attitudes, and behaviours regarding vaccinations for infants among paediatricians.
Characterization of the histone H2A.Z-1 and H2A.Z-2 isoforms in vertebrates
Authors: Dryhurst Deanna , Ishibashi Toyotaka , Rose Kristie L , Eirín-López José M , McDonald Darin , Silva-Moreno Begonia , Veldhoen Nik , Helbing Caren C , Hendzel Michael J , Shabanowitz Jeffrey , Hunt Donald F , Ausió Juan
Published: December 2009

Background

Within chromatin, the histone variant H2A.Z plays a role in many diverse nuclear processes including transcription, preventing the spread of heterochromatin and epigenetic transcriptional memory. The molecular mechanisms of how H2A.Z mediates its effects are not entirely understood. However, it is now known that H2A.Z has two protein isoforms in vertebrates, H2A.Z-1 and H2A.Z-2, which are encoded by separate genes and differ by 3 amino acid residues.

Results

We report that H2A.Z-1 and H2A.Z-2 are expressed across a wide range of human tissues, they are both acetylated at lysine residues within the N-terminal region and they exhibit similar, but nonidentical, distributions within chromatin. Our results suggest that H2A.Z-2 preferentially associates with H3 trimethylated at lysine 4 compared to H2A.Z-1. The phylogenetic analysis of the promoter regions of H2A.Z-1 and H2A.Z-2 indicate that they have evolved separately during vertebrate evolution.

Conclusions

Our biochemical, gene expression, and phylogenetic data suggest that the H2A.Z-1 and H2A.Z-2 variants function similarly yet they may have acquired a degree of functional independence.
Peripheral Non-Viral MIDGE Vector-Driven Delivery of β-Endorphin in Inflammatory Pain
Authors: Machelska Halina , Schroff Matthias , Oswald Detlef , Binder Waltraud , Sitte Nicolle , Mousa Shaaban A , Rittner Heike L , Brack Alexander , Labuz Dominika , Busch Melanie , Wittig Burghardt , Schäfer Michael , Stein Christoph
Published: December 2009

Background

Leukocytes infiltrating inflamed tissue produce and release opioid peptides such as β-endorphin, which activate opioid receptors on peripheral terminals of sensory nerves resulting in analgesia. Gene therapy is an attractive strategy to enhance continuous production of endogenous opioids. However, classical viral and plasmid vectors for gene delivery are hampered by immunogenicity, recombination, oncogene activation, antibacterial antibody production or changes in physiological gene expression. Non-viral, non-plasmid minimalistic, immunologically defined gene expression (MIDGE) vectors may overcome these problems as they carry only elements needed for gene transfer. Here, we investigated the effects of a nuclear localization sequence (NLS)-coupled MIDGE encoding the β-endorphin precursor proopiomelanocortin (POMC) on complete Freund's adjuvant-induced inflammatory pain in rats.

Results

POMC-MIDGE-NLS injected into inflamed paws appeared to be taken up by leukocytes resulting in higher concentrations of β-endorphin in these cells. POMC-MIDGE-NLS treatment reversed enhanced mechanical sensitivity compared with control MIDGE-NLS. However, both effects were moderate, not always statistically significant or directly correlated with each other. Also, the anti-hyperalgesic actions could not be increased by enhancing β-endorphin secretion or by modifying POMC-MIDGE-NLS to code for multiple copies of β-endorphin.

Conclusion

Although MIDGE vectors circumvent side-effects associated with classical viral and plasmid vectors, the current POMC-MIDGE-NLS did not result in reliable analgesic effectiveness in our pain model. This was possibly associated with insufficient and variable efficacy in transfection and/or β-endorphin production. Our data point at the importance of the reproducibility of gene therapy strategies for the control of chronic pain.
No difference in between-country variability in use of newly approved orphan and non- orphan medicinal products - a pilot study
Authors: Stolk Pieter , Heemstra Harald E , Leufkens Hubert GM , Bloechl-Daum Brigitte , Heerdink Eibert R
Published: December 2009

Background

Regulators and payers have to strike a balance between the needs of the patient and the optimal allocation of resources. Drugs indicated for rare diseases (orphan medicines) are a special group in this context because of their often high per unit costs. Our objective in this pilot study was to determine, for drugs used in an outpatient setting, how utilisation of centrally authorised drugs varies between countries across a selection of EU member states.

Methods

We randomly selected five orphan medicines and nine other drugs that were centrally authorised in the European Union between January 2000 and November 2006. We compared utilisation of these drugs in six European Union member states: Austria, Denmark, Finland, Portugal, The Netherlands, and Sweden. Utilisation data were expressed as Defined Daily Doses per 1000 persons per year. Variability in use across countries was determined by calculating the relative standard deviation for the utilisation rates of individual drugs across countries.

Results

No association between orphan medicine status and variability in use across countries was found (P = 0.52). Drugs with an orphan medicine status were more expensive and had a higher innovation score than drugs without an orphan medicine status.

Conclusions

The results show that the variability in use of orphan medicines in the different health care systems of the European Union appears to be comparable to the other newly authorised drugs that were included in the analysis. This means that, although strong heterogeneity in access may exist, this heterogeneity is not specific for drugs with an orphan status.
Detecting coordinated regulation of multi-protein complexes using logic analysis of gene expression
Authors: Sprinzak Einat , Cokus Shawn J , Yeates Todd O , Eisenberg David , Pellegrini Matteo
Published: December 2009

Background

Many of the functional units in cells are multi-protein complexes such as RNA polymerase, the ribosome, and the proteasome. For such units to work together, one might expect a high level of regulation to enable co-appearance or repression of sets of complexes at the required time. However, this type of coordinated regulation between whole complexes is difficult to detect by existing methods for analyzing mRNA co-expression. We propose a new methodology that is able to detect such higher order relationships.

Results

We detect coordinated regulation of multiple protein complexes using logic analysis of gene expression data. Specifically, we identify gene triplets composed of genes whose expression profiles are found to be related by various types of logic functions. In order to focus on complexes, we associate the members of a gene triplet with the distinct protein complexes to which they belong. In this way, we identify complexes related by specific kinds of regulatory relationships. For example, we may find that the transcription of complex C is increased only if the transcription of both complex A AND complex B is repressed. We identify hundreds of examples of coordinated regulation among complexes under various stress conditions. Many of these examples involve the ribosome. Some of our examples have been previously identified in the literature, while others are novel. One notable example is the relationship between the transcription of the ribosome, RNA polymerase and mannosyltransferase II, which is involved in N-linked glycan processing in the Golgi.

Conclusions

The analysis proposed here focuses on relationships among triplets of genes that are not evident when genes are examined in a pairwise fashion as in typical clustering methods. By grouping gene triplets, we are able to decipher coordinated regulation among sets of three complexes. Moreover, using all triplets that involve coordinated regulation with the ribosome, we derive a large network involving this essential cellular complex. In this network we find that all multi-protein complexes that belong to the same functional class are regulated in the same direction as a group (either induced or repressed).
Contrasting identity-by-descent estimators, association studies, and linkage analyses using the Framingham Heart Study data
Authors: Marchani Elizabeth E , Di Yanming , Choi Yoonha , Cheung Charles , Su Ming , Boehm Frederick , Thompson Elizabeth A , Wijsman Ellen M
Published: December 2009

We explored the utility of population- and pedigree-based analyses using the Framingham Heart Study genome-wide 50 k single-nucleotide polymorphism marker data provided for Genetic Analysis Workshop 16. Our aims were: 1) to compare identity-by-descent sharing estimates from variable amounts of data; 2) to apply each of these estimates to a case-control association study designed to control for relatedness among samples; and 3) to contrast these results to those obtained using model-based and model-free linkage analysis methods.
Assessing the impact of global versus local ancestry in association studies
Authors: Kang Sun Jung , Larkin Emma K , Song Yeunjoo , Barnholtz-Sloan Jill , Baechle Dan , Feng Tao , Zhu Xiaofeng
Published: December 2009

Background

To account for population stratification in association studies, principal-components analysis is often performed on single-nucleotide polymorphisms (SNPs) across the genome. Here, we use Framingham Heart Study (FHS) Genetic Analysis Workshop 16 data to compare the performance of local ancestry adjustment for population stratification based on principal components (PCs) estimated from SNPs in a local chromosomal region with global ancestry adjustment based on PCs estimated from genome-wide SNPs.

Methods

Standardized height residuals from unrelated adults from the FHS Offspring Cohort were averaged from longitudinal data. PCs of SNP genotype data were calculated to represent individual's ancestry either 1) globally using all SNPs across the genome or 2) locally using SNPs in adjacent 20-Mbp regions within each chromosome. We assessed the extent to which there were differences in association studies of height depending on whether PCs for global, local, or both global and local ancestry were included as covariates.

Results

The correlations between local and global PCs were low (r < 0.12), suggesting variability between local and global ancestry estimates. Genome-wide association tests without any ancestry adjustment demonstrated an inflated type I error rate that decreased with adjustment for local ancestry, global ancestry, or both. A known spurious association was replicated for SNPs within the lactase gene, and this false-positive association was abolished by adjustment with local or global ancestry PCs.

Conclusion

Population stratification is a potential source of bias in this seemingly homogenous FHS population. However, local and global PCs derived from SNPs appear to provide adequate information about ancestry.
Principal-component-based population structure adjustment in the North American Rheumatoid Arthritis Consortium data: impact of single-nucleotide polymorphism set and analysis method
Authors: Peloso Gina M , Timofeev Nadia , Lunetta Kathryn L
Published: December 2009

Population structure occurs when a sample is composed of individuals with different ancestries and can result in excess type I error in genome-wide association studies. Genome-wide principal-component analysis (PCA) has become a popular method for identifying and adjusting for subtle population structure in association studies. Using the Genetic Analysis Workshop 16 (GAW16) NARAC data, we explore two unresolved issues concerning the use of genome-wide PCA to account for population structure in genetic associations studies: the choice of single-nucleotide polymorphism (SNP) subset and the choice of adjustment model. We computed PCs for subsets of genome-wide SNPs with varying levels of LD. The first two PCs were similar for all subsets and the first three PCs were associated with case status for all subsets. When the PCs associated with case status were included as covariates in an association model, the reduction in genomic inflation factor was similar for all SNP sets. Several models have been proposed to account for structure using PCs, but it is not yet clear whether the different methods will result in substantively different results for association studies with individuals of European descent. We compared genome-wide association p-values and results for two positive-control SNPs previously associated with rheumatoid arthritis using four PC adjustment methods as well as no adjustment and genomic control. We found that in this sample, adjusting for the continuous PCs or adjusting for discrete clusters identified using the PCs adequately accounts for the case-control population structure, but that a recently proposed randomization test performs poorly.
Accommodating population stratification in case-control association analysis: a new test and its application to genome-wide study on rheumatoid arthritis
Authors: Zhang Yufang , Xiao Xiangjun , Wang Kai
Published: December 2009

It is well known that conventional association tests can lead to excessive false positives when there is population stratification. We propose a new test for detecting genetic association with a case-control study design. Unlike some other methods for handling population stratification, we treat the cases as a population and the controls as another one even though each of them may be a mixture of several sub-populations. A likelihood-ratio test is used to test whether the allele frequency of a testing single-nucleotide polymorphism in the case population is the same as that in the control population. This new test is applied to the Genetic Analysis Workshop 16 Problem 1 data on rheumatoid arthritis. Compared with the Pearson chi-square genotype test, the association strength of many single-nucleotide polymorphisms is decreased while the signal at the HLA region on 6p21 is maintained.
Detecting susceptibility genes for rheumatoid arthritis based on a novel sliding-window approach
Authors: Sha Qiuying , Tang Rui , Zhang Shuanglin
Published: December 2009

With the recent rapid improvements in high-throughout genotyping techniques, researchers are facing a very challenging task of large-scale genetic association analysis, especially at the whole-genome level, without an optimal solution. In this study, we propose a new approach for genetic association analysis based on a variable-sized sliding-window framework. This approach employs principal component analysis to find the optimal window size. Using the bisection algorithm in window size searching, the proposed method tackles the exhaustive computation problem. It is more efficient and effective than currently available approaches. We conduct the genome-wide association study in Genetic Analysis Workshop 16 (GAW16) Problem 1 data using the proposed method. Our method successfully identified several susceptibility genes that have been reported by other researchers and additional candidate genes for follow-up studies.
Elastic-net regularization approaches for genome-wide association studies of rheumatoid arthritis
Authors: Cho Seoae , Kim Haseong , Oh Sohee , Kim Kyunga , Park Taesung
Published: December 2009

The current trend in genome-wide association studies is to identify regions where the true disease-causing genes may lie by evaluating thousands of single-nucleotide polymorphisms (SNPs) across the whole genome. However, many challenges exist in detecting disease-causing genes among the thousands of SNPs. Examples include multicollinearity and multiple testing issues, especially when a large number of correlated SNPs are simultaneously tested. Multicollinearity can often occur when predictor variables in a multiple regression model are highly correlated, and can cause imprecise estimation of association. In this study, we propose a simple stepwise procedure that identifies disease-causing SNPs simultaneously by employing elastic-net regularization, a variable selection method that allows one to address multicollinearity. At Step 1, the single-marker association analysis was conducted to screen SNPs. At Step 2, the multiple-marker association was scanned based on the elastic-net regularization. The proposed approach was applied to the rheumatoid arthritis (RA) case-control data set of Genetic Analysis Workshop 16. While the selected SNPs at the screening step are located mostly on chromosome 6, the elastic-net approach identified putative RA-related SNPs on other chromosomes in an increased proportion. For some of those putative RA-related SNPs, we identified the interactions with sex, a well known factor affecting RA susceptibility.
Incorporating multiple-marker information to detect risk loci for rheumatoid arthritis
Authors: Wang Xuexia , Qin Huaizhen , Sha Qiuying
Published: December 2009

In genome-wide association studies, new schemes are needed to incorporate multiple-locus information. In this article, we proposed a two-stage sliding-window approach to detect associations between a disease and multiple genetic polymorphisms. In the proposed approach, we measured the genetic association between a disease and a single-nucleotide polymorphism window by the newly developed likelihood ratio test-principal components statistic, and performed a sliding-window technique to detect disease susceptibility windows. We split the whole sample into two sub-samples, each of which contained a portion of cases and controls. In the first stage, we selected the topRwindows by the statistics based on the first sub-sample, and in the second stage, we claimed significant windows by false-discovery rate correction on thep-values of the statistics based on the second sub-sample. By applying the new approach to the Genetic Analysis Workshop 16 Problem 1 data set, we detected 212 out of 531,601 windows to be responsible for rheumatoid arthritis. Except for chromosomes 4 and 18, each of the other 20 autosomes was found to harbor risk windows. Our results supported the findings of some rheumatoid arthritis susceptibility genes identified in the literature. In addition, we identified several new single-nucleotide polymorphism windows for follow-up studies.
Two-stage joint selection method to identify candidate markers from genome-wide association studies
Authors: Wu Zheyang , Aporntewan Chatchawit , Ballard David H , Lee Ji Young , Lee Joon Sang , Zhao Hongyu
Published: December 2009

The interaction among multiple genes and environmental factors can affect an individual's susceptibility to disease. Some genes may not show strong marginal associations when they affect disease risk through interactions with other genes. As a result, these genes may not be identified by single-marker methods that are widely used in genome-wide association studies. To explore this possibility in real data, we carried out a two-stage model selection procedure of joint single-nucleotide polymorphism (SNP) analysis to detect genes associated with rheumatoid arthritis (RA) using Genetic Analysis Workshop 16 genome-wide association study data. In the first stage, the genetic markers were screened through an exhaustive two-dimensional search, through which promising SNP and SNP pairs were identified. Then, LASSO was used to choose putative SNPs from the candidates identified in the first stage. We then use the RA data collected by the Wellcome Trust Case Control Consortium to validate the putative genetic factors. Balancing computational load and statistical power, this method detects joint effects that may fail to emerge from single-marker analysis. Based on our proposed approach, we not only replicated the identification of important RA risk genes, but also found novel genes and their epistatic effects on RA. To our knowledge, this is the first two-dimensional scan based analysis for a real genome-wide association study.