bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluation of the established non-MHC multiple sclerosis loci in an Indian population
Authors: Pandit Lekha , Ban Maria , Sawcer Stephen , Singhal Bhim , Nair Shyam , Radhakrishnan Kurupath , Shetty Rajesh , Misri Z , Hegde Suresh , Bhat Irruvathur Gopalakrishna
Published: October 2010

Background: Multiple sclerosis (MS) is a chronic demyelinating neurodegenerative disorder with a strong genetic component.

Objective: The prevalence of MS in India is low compared with white populations of Northern European descent.

Methods: In order to ascertain whether disease susceptibility genes are the same across different populations, we completed the first investigation in the Indian MS population of 15 MS loci outside of the major histocompatibility (MHC) region that were previously identified and validated with MS susceptibility through genome-wide association and replication studies in white populations.

Results: In total, 197 Indian patients and 197 unrelated controls were analyzed. The most associated single nucleotide polymorphism (SNP) within this study was rs6897932 in the IL7R gene, which showed a strong protective effect in this data set (rs 6897932, OR = 0.5543, 95% CI = 0.37–0.78, p = 0.0009727). Two other SNPs were nominally associated with MS in this dataset, namely CLEC16A rs 12708716 (p = 0.0082, OR = 1.478, 95% CI = 1.106–1.975) and CD226 rs763361 ( p = 0.03971, OR = 1.353, CI = 1.014–1.805). For the majority of the remaining SNPs (7/14), the trend for association was in the same direction as in previous studies in the white population.

Conclusions: Although the power of this study was limited, our preliminary data suggest that disease susceptibility genes in MS in the Indian population may be similar to those of western populations.
“We’re mad as hell and we’re not going to take it anymore”: Anger self-stereotyping and collective action
Authors: Leonard Diana J. , Moons Wesley G. , Mackie Diane M. , Smith Eliot R.
Published: October 2010

What can motivate members of disadvantaged groups to take action on behalf of their group? This research assessed a model in which measured perceptions of (study 1) and manipulated information about (study 2) other women’s anger influenced female participants’ group-based anger, their subsequent appraisals of instances of possible discrimination, and finally their collective action tendencies. Consistent with Intergroup Emotions Theory, the results suggested that emotional self-stereotyping is one mechanism by which group members can become motivated to respond to possible discrimination, a process supported by group-based anger-driven appraisals about specific discrimination events.
Interactions in Black and White: Racial differences and similarities in response to interracial interactions
Authors: Doerr Celeste , Ashby Plant E. , Kunstman Jonathan W. , Buck David
Published: October 2010

The current work examined Black and White people’s expectancies for interracial interactions. Across two studies, we found that Black people, compared to White people, had more positive past interracial contact, which statistically explained Black compared to White people’s greater self-efficacy for interracial interactions. This self-efficacy, in turn, contributed to less of a desire to avoid future interracial interactions (Study 2) and partially accounted for race differences in actual amounts of subsequent interracial contact (Study 1). However, Black participants also had heightened concerns about being the target of bias in interracial interactions, which contributed to responses to imagined future interactions. These findings suggest that cultural experiences affect individuals’ expectancies for interracial interactions and that these expectancies, in turn, have consequences for the quality and quantity of interracial contact.
Functional Isolation Within the Cerebral Cortex in the Vegetative State
Authors: Sarà Marco , Pistoia Francesca , Pasqualetti Patrizio , Sebastiano Fabio , Onorati Paolo , Rossini Paolo M.
Published: October 2010

Background. Establishing prognosis in patients in a persistent vegetative state (VS) is still challenging. Neural networks underlying consciousness may be regarded as complex systems whose outputs show a degree of unpredictability experimentally quantifiable by means of nonlinear parameters such as approximate entropy (ApEn). Objective. The authors propose that the VS might be the result of derangement of the above neural networks, with an ensuing decrease in complexity and mutual interconnectivity: this might lead to a functional isolation within the cerebral cortex and to a reduction in the chaotic behavior of its outputs, with monotony taking the place of unpredictability. To test this hypothesis, the authors investigated whether nonlinear dynamics methods applied to electroencephalography (EEG) recordings may be able to predict outcomes. Methods. A total of 38 vegetative patients and 40 matched healthy controls were investigated. At admission, all patients were assessed by means of the Extended Glasgow Outcomes Coma Scale (E-GOS) and the Coma Recovery Scale–Revised (CRS-R). At the same time an EEG recording was performed and used for time series analysis and ApEn computation. Patients were clinically reassessed at 6 months from the first evaluation. Results. Mean ApEn values (0.73, standard deviation [SD] = 0.12 vs 0.97, SD = 0.02; P < .001) were lower in patients than in controls. Patients with the lowest ApEn values either died (n = 14) or remained in a VS (n = 12), whereas patients with the highest ApEn values became minimally conscious (n = 5) or showed partial (n = 4) or full recovery (n = 3). Conclusions. These findings suggest that dynamic correlates of neural residual complexity might help in predicting outcomes in vegetative patients.
Posterolateral Surface Electrical Stimulation of Abdominal Expiratory Muscles to Enhance Cough in Spinal Cord Injury
Authors: Butler Jane E. , Lim Julianne , Gorman Robert B. , Boswell-Ruys Claire , Saboisky Julian P. , Lee Bonsan B. , Gandevia Simon C.
Published: October 2010

Background. Spinal cord injury (SCI) patients have respiratory complications because of abdominal muscle weakness and paralysis, which impair the ability to cough. Objective. This study aims to enhance cough in high-level SCI subjects (n = 11, SCI at or above T6) using surface electrical stimulation of the abdominal muscles via 2 pairs of posterolaterally placed electrodes. Methods. From total lung capacity, subjects performed maximum expiratory pressure (MEP) efforts against a closed airway and voluntary cough efforts. Both efforts were performed with and without superimposed trains of electrical stimulation (50 Hz, 1 second) at a submaximal intensity set to evoke a gastric pressure ( Pga) of 40 cm H2O at functional residual capacity. Results. In the MEP effort, stimulation increased the maximal Pga (from 21.4 ± 7.0 to 59.0 ± 5.7 cm H2O) and esophageal pressure ( Pes; 47.2 ± 11.7 to 65.6 ± 13.6 cm H2O). During the cough efforts, stimulation increased Pga (19.5 ± 6.0 to 57.9 ± 7.0 cm H2O) and Pes (31.2 ± 8.7 to 56.6 ± 10.5 cm H2O). The increased expiratory pressures during cough efforts with stimulation increased peak expiratory flow (PEF, by 36% ± 5%), mean expiratory flow (by 80% ± 8%), and expired lung volume (by 41% ± 16%). In every subject, superimposed electrical stimulation improved peak expiratory flow during cough efforts (by 0.99 ± 0.12 L/s; range, 0.41-1.80 L/s). Wearing an abdominal binder did not improve stimulated cough flows or pressures. Conclusions. The increases in Pga and PEF with electrical stimulation using the novel posterolateral electrode placement are 2 to 3 times greater than improvements reported in other studies. This suggests that posterolateral electrical stimulation of abdominal muscles is a simple noninvasive way to enhance cough in individuals with SCI.
Effects on Locomotion, Muscle, Bone, and Blood Induced by a Combination Therapy Eliciting Weight-Bearing Stepping in Nonassisted Spinal Cord–Transected Mice
Authors: Guertin Pierre A. , Ung Roth-Visal , Rouleau Pascal , Steuer Inge
Published: October 2010

Background. The health benefits associated with physical activity–based rehabilitation in patients with no lower-extremity motor function after a spinal cord injury (SCI) is uncertain. Methods. The authors assessed signs of efficacy, safety, and utility associated with a novel pharmacological combination therapy to activate central pattern generator (CPG) activity and corresponding locomotor activity in complete thoracic Th9/10-transected mice. Results. Subcutaneous administration 4 times per week for 1 month of 1.5 mg/kg buspirone, 1.5 mg/kg apomorphine, 12.5 mg/kg benserazide, and 50 mg/kg L-DOPA induced episodes of weight-bearing stepping on a treadmill in nonassisted paraplegic mice for 45-minute sessions. Hindlimb muscle cross-sectional area and fiber area values as well as several blood cell constituent levels assessed at 30 days postinjury were positively affected by the combination therapy, as compared with controls. Episodes of locomotion remained effective on each treatment. Femoral bone mineral density loss was not prevented by triple therapy. Conclusion. Although translation of these findings needs further experimentation, similar pharmacological activation of the CPG offers a novel therapeutic target to provide some health benefits in motor-complete SCI patients.
The pathogenesis of idiopathic pulmonary fibrosis
Authors: Coward William R. , Saini Gauri , Jenkins Gisli
Published: October 2010

Idiopathic pulmonary fibrosis (IPF) is a progressive fibrotic lung disease with an appalling prognosis. The failure of anti-inflammatory therapies coupled with the observation that deranged epithelium overlies proliferative myofibroblasts to form the fibroblastic focus has lead to the emerging concept that IPF is a disease of deregulated epithelial-mesenchymal crosstalk. IPF is triggered by an as yet unidentified alveolar injury that leads to activation of transforming growth factor-β (TGF-β) and alveolar basement membrane disruption. In the presence of persisting injurious pathways, or disrupted repair pathways, activated TGF-β can lead to enhanced epithelial apoptosis and epithelial-to-mesenchymal transition (EMT) as well as fibroblast, and fibrocyte, transformation into myofibroblasts which are resistant to apoptosis. The resulting deposition of excess disrupted matrix by these myofibroblasts leads to the development of IPF.
Metallurgical analysis of Al/Cu friction stir spot welding
Authors: Heideman R. , Johnson C. , Kou S.
Published: October 2010

Friction stir spot welding between a 1·5 mm 6061 Al-T6 sheet and a 1·5 mm Cu sheet was conducted. The effects of the following parameters on the lap shear weld strength were investigated: tool pin length, shoulder plunge depth, weld time and tool rotation speed. With rotation speeds of 2000 rev min−1 and a 2·60 mm tool pin length, weld strengths just over 2000 N were produced. Welds made at 1000 rev min−1 with 1·83 or 2·60 mm tool pin lengths produced weak welds, with strengths below 900 N. Stronger welds had a Cu ring extruded upward from the lower Cu sheet into the upper Al sheet, which promoted bonding and interlocking between the sheets. The interface between this Cu ring and the surrounding aluminium was free of Al/Cu intermetallics. The weld strength appeared driven by the aluminium layer thickness between the tip of the Cu ring and the keyhole with the strength increasing by 2833 N mm−1 of aluminium layer thickness.
AC–GTAW of aluminium – new perspective for evaluation of role of positive polarity time
Authors: Dutra J. Carlos , Cirino L. Machado , Gonçalves e Silva R. Henrique
Published: October 2010

Experiments were carried out to determine the effect of the positive polarity time on cathodic cleaning, arc voltage, arc power and weld bead geometry on AC–GTAW of aluminium. Welding current was kept constant in both positive (EP) and negative polarity. During the experiments current and voltage monitoring was performed to further analysis of arc voltage and arc power. There was an increase in the weld depth and fusion areas when longer EP times were used. This behaviour differs from the traditional literature relating to welding processes with non-consumable electrodes. However, this increase occurs from a certain point, when the EP time is >4·0 ms over a total period of 20·0 ms. The use of a minimum EP time was found to be sufficient to perform the oxide removal, yielding weld beads with satisfactory fusion characteristics and minimum wear of the tungsten electrode.
Spot weldability of δ-TRIP steel containing 0·4 wt-%C
Authors: Yi H. L. , Lee K. Y. , Lim J. H. , Bhadeshia H. K. D. H.
Published: October 2010

Strong steels are usually difficult to resistance spot weld because of the tendency to form hard phases. This applies particularly to the transformation induced plasticity (TRIP) assisted steels with relatively high carbon equivalents. A new development in this context is the δ-TRIP steel, designed to retain δ-ferrite as a stable phase at all temperatures below melting. Fully martensitic regions are therefore avoided, making it possible to weld in spite of the high carbon concentration. The authors present here the first spot welding tests on the novel alloy system.
Opposing roles for HIF-1α and HIF-2α in the regulation of angiogenesis by mononuclear phagocytes
Authors: Eubank Tim D. , Roda Julie M. , Liu Haowen , O'Neil Todd , Marsh Clay B.
Published: October 2010

Macrophages contribute to tumor growth through the secretion of the proangiogenic molecule vascular endothelial growth factor (VEGF). We previously observed that monocytes treated with the cytokine granulocyte-macrophage colony-stimulating factor (GM-CSF) produce a soluble form of the VEGF receptor-1 (sVEGFR-1), which neutralizes VEGF biologic activity. The VEGF and VEGFR-1 promoters both contain a hypoxia regulatory element, which binds the hypoxia-inducible factor (HIF) transcription factors under hypoxic conditions. Based on this observation, we examined VEGF and sVEGFR-1 production from monocytes cultured at various O2 concentrations. The amount of sVEGFR-1 production observed from GM-CSF-treated monocytes increased with decreasing levels of O2. This sVEGFR-1 was biologically active and sequestered VEGF. To evaluate the role of the HIFs in sVEGFR-1 production, we used macrophages with a genetic deletion of HIF-1α. HIF-1α−/− macrophages cultured with GM-CSF at hypoxia secreted diminished amounts of VEGF compared with HIF-1α+/+ macrophages, whereas sVEGFR-1 secretion was unaffected. In contrast, siRNA-mediated knockdown of HIF-2α inhibited the production of sVEGFR-1 in response to GM-CSF and low O2, whereas VEGF production was unaffected. These studies suggest that hypoxia, generally thought to promote angiogenesis, can induce antiangiogenic behavior from macrophages within a GM-CSF–rich environment. Furthermore, these results suggest specific and independent roles for HIF-1α and HIF-2α in hypoxic macrophages.
AKAP9 regulation of microtubule dynamics promotes Epac1-induced endothelial barrier properties
Authors: Sehrawat Seema , Ernandez Thomas , Cullere Xavier , Takahashi Mikiko , Ono Yoshitaka , Komarova Yulia , Mayadas Tanya N.
Published: October 2010

Adhesive forces at endothelial cell-cell borders maintain vascular integrity. cAMP enhances barrier properties and controls cellular processes through protein kinase A bound to A-kinase anchoring proteins (AKAPs). It also activates exchange protein directly activated by cAMP (Epac1), an exchange factor for Ras-related protein 1 (Rap1) GTPases that promotes cadherin- and integrin-mediated adhesion through effects on the actin cytoskeleton. We demonstrate that AKAP9 facilitates the microtubule polymerization rate in endothelial cells, interacts with Epac1, and is required for Epac1-stimulated microtubule growth. AKAP9 is not required for maintaining barrier properties under steady-state conditions. Rather, it is essential when the cell is challenged to make new adhesive contacts, as is the case when Epac activation enhances barrier function through a mechanism that, surprisingly, requires integrin adhesion at cell-cell contacts. In the present study, defects in Epac-induced responses in AKAP9-silenced cells were evident despite an intact Epac-induced increase in Rap activation, cortical actin, and vascular endothelial-cadherin adhesion. We describe a pathway that integrates Epac-mediated signals with AKAP9-dependent microtubule dynamics to coordinate integrins at lateral borders.
The prolyl isomerase Pin1 acts as a novel molecular switch for TNF-α–induced priming of the NADPH oxidase in human neutrophils
Authors: Boussetta Tarek , Gougerot-Pocidalo Marie-Anne , Hayem Gilles , Ciappelloni Silvia , Raad Houssam , Arabi Derkawi Riad , Bournier Odile , Kroviarski Yolande , Zhou Xiao Zhen , Malter James S. , Lu Ping K. , Bartegi Aghleb , Dang Pham My-Chan , El-Benna Jamel
Published: October 2010

Neutrophils play a key role in host defense by releasing reactive oxygen species (ROS). However, excessive ROS production by neutrophil nicotinamide adenine dinucleotide phosphate (NADPH) oxidase can damage bystander tissues, thereby contributing to inflammatory diseases. Tumor necrosis factor-α (TNF-α), a major mediator of inflammation, does not activate NADPH oxidase but induces a state of hyperresponsiveness to subsequent stimuli, an action known as priming. The molecular mechanisms by which TNF-α primes the NADPH oxidase are unknown. Here we show that Pin1, a unique cis-trans prolyl isomerase, is a previously unrecognized regulator of TNF-α–induced NADPH oxidase hyperactivation. We first showed that Pin1 is expressed in neutrophil cytosol and that its activity is markedly enhanced by TNF-α. Inhibition of Pin1 activity with juglone or with a specific peptide inhibitor abrogated TNF-α–induced priming of neutrophil ROS production induced by N-formyl-methionyl-leucyl-phenylalanine peptide (fMLF). TNF-α enhanced fMLF-induced Pin1 and p47phox translocation to the membranes and juglone inhibited this process. Pin1 binds to p47phox via phosphorylated Ser345, thereby inducing conformational changes that facilitate p47phox phosphorylation on other sites by protein kinase C. These findings indicate that Pin1 is critical for TNF-α–induced priming of NADPH oxidase and for excessive ROS production. Pin1 inhibition could potentially represent a novel anti-inflammatory strategy.
Histone deacetylase inhibitors impair innate immune responses to Toll-like receptor agonists and to infection
Authors: Roger Thierry , Lugrin Jérôme , Le Roy Didier , Goy Geneviève , Mombelli Matteo , Koessler Thibaud , Ding Xavier C. , Chanson Anne-Laure , Reymond Marlies Knaup , Miconnet Isabelle , Schrenzel Jacques , François Patrice , Calandra Thierry
Published: October 2010

Regulated by histone acetyltransferases and deacetylases (HDACs), histone acetylation is a key epigenetic mechanism controlling chromatin structure, DNA accessibility, and gene expression. HDAC inhibitors induce growth arrest, differentiation, and apoptosis of tumor cells and are used as anticancer agents. Here we describe the effects of HDAC inhibitors on microbial sensing by macrophages and dendritic cells in vitro and host defenses against infection in vivo. HDAC inhibitors down-regulated the expression of numerous host defense genes, including pattern recognition receptors, kinases, transcription regulators, cytokines, chemokines, growth factors, and costimulatory molecules as assessed by genome-wide microarray analyses or innate immune responses of macrophages and dendritic cells stimulated with Toll-like receptor agonists. HDAC inhibitors induced the expression of Mi-2β and enhanced the DNA-binding activity of the Mi-2/NuRD complex that acts as a transcriptional repressor of macrophage cytokine production. In vivo, HDAC inhibitors increased the susceptibility to bacterial and fungal infections but conferred protection against toxic and septic shock. Thus, these data identify an essential role for HDAC inhibitors in the regulation of the expression of innate immune genes and host defenses against microbial pathogens.
Hypoxia inhibits senescence and maintains mesenchymal stem cell properties through down-regulation of E2A-p21 by HIF-TWIST
Authors: Tsai Chih-Chien , Chen Yann-Jang , Yew Tu-Lai , Chen Ling-Lan , Wang Jir-You , Chiu Chao-Hua , Hung Shih-Chieh
Published: October 2010

Although low-density culture provides an efficient method for rapid expansion of human mesenchymal stem cells (MSCs), MSCs enriched by this method undergo senescence and lose their stem cell properties, which could be preserved by combining low-density and hypoxic culture. The mechanism was mediated through direct down-regulation of E2A-p21 by the hypoxia-inducible factor–1α (HIF-1α)–TWIST axis. Expansion under normoxia induced E2A and p21 expression, which were abrogated by overexpression of TWIST, whereas siRNA against TWIST up-regulated E2A and p21 in hypoxic cells. Furthermore, siRNA against p21 in normoxic cells enhanced proliferation and increased differentiation potential, whereas overexpression of p21 in hypoxic cells induced a decrease in proliferation and a loss of differentiation capacity. More importantly, MSCs expanded under hypoxic conditions by up to 100 population doublings, exhibited telomerase activity with maintained telomere length, normal karyotyping, and intact genetic integrity, and did not form tumors. These results support low-density hypoxic culture as a method for efficiently expanding MSCs without losing stem cell properties or increasing tumorigenicity.
Infusion of ex vivo expanded T regulatory cells in adults transplanted with umbilical cord blood: safety profile and detection kinetics
Authors: Brunstein Claudio G. , Miller Jeffrey S. , Cao Qing , McKenna David H. , Hippen Keli L. , Curtsinger Julie , DeFor Todd , Levine Bruce L. , June Carl H. , Rubinstein Pablo , McGlave Philip B. , Blazar Bruce R. , Wagner John E.
Published: October 2010

Acute graft-versus-host disease (aGVHD) is associated with high risk of morbidity and mortality and is a common complication after double umbilical cord blood (UCB) transplantation. To reduce these risks, we established a method of CD4+CD25+FoxP3+ T regulatory cell (Treg) enrichment from cryopreserved UCB followed by a 18 + 1-day expansion culture including anti-CD3/anti-CD28 antibody-coated beads and recombinant human interleukin-2. In a “first-in-human” clinical trial, we evaluated the safety profile of UCB Treg in 23 patients. Patients received a dose of 0.1-30 × 105UCB Treg/kg after double UCB transplantation. The targeted Treg dose was achieved in 74% of cultures, with all products being suppressive in vitro (median 86% suppression at a 1:4 ratio). No infusional toxicities were observed. After infusion, UCB Treg could be detected for 14 days, with the greatest proportion of circulating CD4+CD127−FoxP3+ cells observed on day +2. Compared with identically treated 108 historical controls without Treg, there was a reduced incidence of grade II-IV aGVHD (43% vs 61%, P = .05) with no deleterious effect on risks of infection, relapse, or early mortality. These results set the stage for a definitive study of UCB Treg to determine its potency in preventing allogeneic aGVHD. This study is registered at http://www.clinicaltrials.gov as NCT00602693.
Cytokine polymorphisms in Th1/Th2 pathway genes, body mass index, and risk of non-Hodgkin lymphoma
Authors: Chen Yingtai , Zheng Tongzhang , Lan Qing , Foss Francine , Kim Christopher , Chen Xuezhong , Dai Min , Li Yumin , Holford Theodore , Leaderer Brian , Boyle Peter , Chanock Stephen J. , Rothman Nathaniel , Zhang Yawei
Published: October 2010

We conducted a population-based, case-control study in Connecticut women to test the hypothesis that genetic variations in Th1 and Th2 cytokine genes modify the relationship between body mass index (BMI) and risk of non-Hodgkin lymphoma (NHL). Compared with those with BMI less than 25 kg/m2, women with BMI more than or equal to 25 kg/m2 had 50% to 90% increased risk of NHL among women who carried IFNGR2 (rs9808753) AA, IL5 (rs2069812) CT/TT, IL7R (rs1494555) AA, and TNF (rs1799724) CC genotypes, but no increased risk among women with IFNGR2 AG/GG, IL5 CC, IL7R AG/GG, and TNF CT/TT genotypes. A significant interaction with BMI was only observed for IFNGR2 (rs9808753 Pforinteraction = .034) and IL7R (rs1494555 Pforinteraction = .016) for NHL overall; IL7R (rs1494555 Pforinteraction = .016) and TNF (1799724 Pforinteraction = .031) for B-cell lymphoma; and IL5 (rs2069812 Pforinteraction = .034) for T-cell lymphoma. After stratification by common B-cell lymphoma subtypes, a significant interaction was observed for IFNGR2 (rs9808753 Pforinteraction = .006), IL13 (rs20541 Pforinteraction = .019), and IL7R (rs1494555 Pforinteraction = .012) for marginal zone B-cell lymphoma; IL7R (rs1494555 Pforinteraction = .017) for small lymphocytic lymphoma/chronic lymphocytic leukemia; and IL12A (rs568408 Pforinteraction = .013) and TNF (1799724 Pforinteraction = .04) for follicular lymphoma. The results suggest that common genetic variation in Th1/Th2 pathway genes may modify the association between BMI and NHL risk.
A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study
Authors: Durand Jérôme , Bodénès Catherine , Chancerel Emilie , Frigerio Jean-Marc , Vendramin Giovanni , Sebastiani Federico , Buonamici Anna , Gailing Oliver , Koelewijn Hans-Peter , Villani Fiorella , Mattioni Claudia , Cherubini Marcello , Goicoechea Pablo G , Herrán Ana , Ikaran Ziortza , Cabané Cyril , Ueno Saneyoshi , Alberto Florian , Dumoulin Pierre-Yves , Guichoux Erwan , de Daruvar Antoine , Kremer Antoine , Plomion Christophe
Published: October 2010

Background

Expressed Sequence Tags (ESTs) are a source of simple sequence repeats (SSRs) that can be used to develop molecular markers for genetic studies. The availability of ESTs for Quercus robur and Quercus petraea provided a unique opportunity to develop microsatellite markers to accelerate research aimed at studying adaptation of these long-lived species to their environment. As a first step toward the construction of a SSR-based linkage map of oak for quantitative trait locus (QTL) mapping, we describe the mining and survey of EST-SSRs as well as a fast and cost-effective approach (bin mapping) to assign these markers to an approximate map position. We also compared the level of polymorphism between genomic and EST-derived SSRs and address the transferability of EST-SSRs in Castanea sativa (chestnut).

Results

A catalogue of 103,000 Sanger ESTs was assembled into 28,024 unigenes from which 18.6% presented one or more SSR motifs. More than 42% of these SSRs corresponded to trinucleotides. Primer pairs were designed for 748 putative unigenes. Overall 37.7% (283) were found to amplify a single polymorphic locus in a reference full-sib pedigree of Quercus robur. The usefulness of these loci for establishing a genetic map was assessed using a bin mapping approach. Bin maps were constructed for the male and female parental tree for which framework linkage maps based on AFLP markers were available. The bin set consisting of 14 highly informative offspring selected based on the number and position of crossover sites. The female and male maps comprised 44 and 37 bins, with an average bin length of 16.5 cM and 20.99 cM, respectively. A total of 256 EST-SSRs were assigned to bins and their map position was further validated by linkage mapping. EST-SSRs were found to be less polymorphic than genomic SSRs, but their transferability rate to chestnut, a phylogenetically related species to oak, was higher.

Conclusion

We have generated a bin map for oak comprising 256 EST-SSRs. This resource constitutes a first step toward the establishment of a gene-based map for this genus that will facilitate the dissection of QTLs affecting complex traits of ecological importance.
Identification of expression QTL (eQTL) of genes expressed in porcine M. longissimus dorsi and associated with meat quality traits
Authors: Ponsuksili Siriluck , Murani Eduard , Schwerin Manfred , Schellander Karl , Wimmers Klaus
Published: October 2010

Background

Genetic analysis of transcriptional profiles is a promising approach for identifying and dissecting the genetics of complex traits like meat performance. Accordingly, expression levels obtained by microarray analysis were taken as phenotypes in a linkage analysis to map eQTL. Moreover, expression levels were correlated with traits related to meat quality and principle components with high loadings of these traits. By using an up-to-date annotation and localization of the respective probe-sets, the integration of eQTL mapping data and information of trait correlated expression finally served to point to candidate genes for meat quality traits.

Results

Genome-wide transcriptional profiles of M. longissimus dorsi RNAs samples of 74 F2 animals of a pig resource population revealed 11,457 probe-sets representing genes expressed in the muscle. Linkage analysis of expression levels of these probe-sets provided 9,180 eQTL at the suggestive significance threshold of LOD > 2. We mapped 653 eQTL on the same chromosome as the corresponding gene and these were designated as 'putative cis- eQTL'. In order to link eQTL to the traits of interest, probe-sets were addressed with relative transcript abundances that showed correlation with meat quality traits at p ≤ 0.05. Out of the 653 'putative cis- eQTL', 262 transcripts were correlated with at least one meat quality trait. Furthermore, association of expression levels with composite traits with high loadings for meat quality traits generated by principle component analysis were taken into account leading to a list of 85 genes exhibiting cis- eQTL and trait dependent expression.

Conclusion

Holistic expression profiling was integrated with QTL analysis for meat quality traits. Correlations between transcript abundance and meat quality traits, combined with genetic positional information of eQTL allowed us to prioritise candidate genes for further study.
Quantitative trait loci mapping reveals candidate pathways regulating cell cycle duration in Plasmodium falciparum
Authors: Reilly Ayala Heather B , Wacker Mark A , Siwo Geoffrey , Ferdig Michael T
Published: October 2010

Background

Elevated parasite biomass in the human red blood cells can lead to increased malaria morbidity. The genes and mechanisms regulating growth and development of Plasmodium
falciparum through its erythrocytic cycle are not well understood. We previously showed that strains HB3 and Dd2 diverge in their proliferation rates, and here use quantitative trait loci mapping in 34 progeny from a cross between these parent clones along with integrative bioinformatics to identify genetic loci and candidate genes that control divergences in cell cycle duration.

Results

Genetic mapping of cell cycle duration revealed a four-locus genetic model, including a major genetic effect on chromosome 12, which accounts for 75% of the inherited phenotype variation. These QTL span 165 genes, the majority of which have no predicted function based on homology. We present a method to systematically prioritize candidate genes using the extensive sequence and transcriptional information available for the parent lines. Putative functions were assigned to the prioritized genes based on protein interaction networks and expression eQTL from our earlier study. DNA metabolism or antigenic variation functional categories were enriched among our prioritized candidate genes. Genes were then analyzed to determine if they interact with cyclins or other proteins known to be involved in the regulation of cell cycle.

Conclusions

We show that the divergent proliferation rate between a drug resistant and drug sensitive parent clone is under genetic regulation and is segregating as a complex trait in 34 progeny. We map a major locus along with additional secondary effects, and use the wealth of genome data to identify key candidate genes. Of particular interest are a nucleosome assembly protein (PFL0185c), a Zinc finger transcription factor (PFL0465c) both on chromosome 12 and a ribosomal protein L7Ae-related on chromosome 4 (PFD0960c).
Genome-wide inference of regulatory networks in Streptomyces coelicolor
Authors: Castro-Melchor Marlene , Charaniya Salim , Karypis George , Takano Eriko , Hu Wei-Shou
Published: October 2010

Background

The onset of antibiotics production in Streptomyces species is co-ordinated with differentiation events. An understanding of the genetic circuits that regulate these coupled biological phenomena is essential to discover and engineer the pharmacologically important natural products made by these species. The availability of genomic tools and access to a large warehouse of transcriptome data for the model organism, Streptomyces coelicolor, provides incentive to decipher the intricacies of the regulatory cascades and develop biologically meaningful hypotheses.

Results

In this study, more than 500 samples of genome-wide temporal transcriptome data, comprising wild-type and more than 25 regulatory gene mutants of Streptomyces coelicolor probed across multiple stress and medium conditions, were investigated. Information based on transcript and functional similarity was used to update a previously-predicted whole-genome operon map and further applied to predict transcriptional networks constituting modules enriched in diverse functions such as secondary metabolism, and sigma factor. The predicted network displays a scale-free architecture with a small-world property observed in many biological networks. The networks were further investigated to identify functionally-relevant modules that exhibit functional coherence and a consensus motif in the promoter elements indicative of DNA-binding elements.

Conclusions

Despite the enormous experimental as well as computational challenges, a systems approach for integrating diverse genome-scale datasets to elucidate complex regulatory networks is beginning to emerge. We present an integrated analysis of transcriptome data and genomic features to refine a whole-genome operon map and to construct regulatory networks at the cistron level in Streptomyces coelicolor. The functionally-relevant modules identified in this study pose as potential targets for further studies and verification.
Transcriptome analysis of parallel-evolved Escherichia coli strains under ethanol stress
Authors: Horinouchi Takaaki , Tamaoka Kuniyasu , Furusawa Chikara , Ono Naoaki , Suzuki Shingo , Hirasawa Takashi , Yomo Tetsuya , Shimizu Hiroshi
Published: October 2010

Background

Understanding ethanol tolerance in microorganisms is important for the improvement of bioethanol production. Hence, we performed parallel-evolution experiments using Escherichia coli cells under ethanol stress to determine the phenotypic changes necessary for ethanol tolerance.

Results

After cultivation of 1,000 generations under 5% ethanol stress, we obtained 6 ethanol-tolerant strains that showed an approximately 2-fold increase in their specific growth rate in comparison with their ancestor. Expression analysis using microarrays revealed that common expression changes occurred during the adaptive evolution to the ethanol stress environment. Biosynthetic pathways of amino acids, including tryptophan, histidine, and branched-chain amino acids, were commonly up-regulated in the tolerant strains, suggesting that activating these pathways is involved in the development of ethanol tolerance. In support of this hypothesis, supplementation of isoleucine, tryptophan, and histidine to the culture medium increased the specific growth rate under ethanol stress. Furthermore, genes related to iron ion metabolism were commonly up-regulated in the tolerant strains, which suggests the change in intracellular redox state during adaptive evolution.

Conclusions

The common phenotypic changes in the ethanol-tolerant strains we identified could provide a fundamental basis for designing ethanol-tolerant strains for industrial purposes.
Interleukin-33 contributes to both M1 and M2 chemokine marker expression in human macrophages
Authors: Joshi Amrita D , Oak Sameer R , Hartigan Adam J , Finn William G , Kunkel Steven L , Duffy Karen E , Das Anuk , Hogaboam Cory M
Published: October 2010

Background

Interleukin-33 is a member of the IL-1 cytokine family whose functions are mediated and modulated by the ST2 receptor. IL-33-ST2 expression and interactions have been explored in mouse macrophages but little is known about the effect of IL-33 on human macrophages. The expression of ST2 transcript and protein levels, and IL-33-mediated effects on M1 (i.e. classical activation) and M2 (i.e. alternative activation) chemokine marker expression in human bone marrow-derived macrophages were examined.

Results

Human macrophages constitutively expressed the membrane-associated (i.e. ST2L) and the soluble (i.e. sST2) ST2 receptors. M2 (IL-4 + IL-13) skewing stimuli markedly increased the expression of ST2L, but neither polarizing cytokine treatment promoted the release of sST2 from these cells. When added to naïve macrophages alone, IL-33 directly enhanced the expression of CCL3. In combination with LPS, IL-33 blocked the expression of the M2 chemokine marker CCL18, but did not alter CCL3 expression in these naive cells. The addition of IL-33 to M1 macrophages markedly increased the expression of CCL18 above that detected in untreated M1 macrophages. Similarly, alternatively activated human macrophages treated with IL-33 exhibited enhanced expression of CCL18 and the M2 marker mannose receptor above that detected in M2 macrophages alone.

Conclusions

Together, these data suggest that primary responses to IL-33 in bone marrow derived human macrophages favors M1 chemokine generation while its addition to polarized human macrophages promotes or amplifies M2 chemokine expression.
Fragile X astrocytes induce developmental delays in dendrite maturation and synaptic protein expression
Authors: Jacobs Shelley , Nathwani Meera , Doering Laurie C
Published: October 2010

Background

Fragile X syndrome is the most common inherited form of mental impairment characterized by cognitive impairment, attention deficit and autistic behaviours. The mouse model of Fragile X is used to study the underlying neurobiology associated with behavioral deficiencies. The effect of Fragile X glial cells on the development of neurons has not been studied. We used a co-culture technique in combination with morphometrics on immunostained neurons to investigate the role of astrocytes in the development delays associated with hippocampal neuron development.

Results

We found that hippocampal neurons grown on Fragile X astrocytes exhibited a significant difference from the neurons grown with normal astrocytes after 7 days in vitro for many parameters including increases in dendritic branching and in area of the cell body. However, after 21 days in culture, the neurons grown on Fragile X astrocytes exhibited morphological characteristics that did not differ significantly from the neurons grown on normal astrocytes. With antibodies to the pre-synaptic protein, synapsin, and to the excitatory post-synaptic protein, PSD-95, we quantified the number of developing excitatory synapses on the dendrites. In addition to the delays in dendritic patterning, the development of excitatory synapses was also delayed in the hippocampal neurons.

Conclusions

These experiments are the first to establish a role for astrocytes in the delayed growth characteristics and abnormal morphological features in dendrites and synapses that characterize the Fragile X syndrome.
Exploratory factor analysis of self-reported symptoms in a large, population-based military cohort
Authors: Kelton Molly L , LeardMann Cynthia A , Smith Besa , Boyko Edward J , Hooper Tomoko I , Gackstetter Gary D , Bliese Paul D , Hoge Charles W , Smith Tyler C ,   the Millennium Cohort Study Team
Published: October 2010

Background

US military engagements have consistently raised concern over the array of health outcomes experienced by service members postdeployment. Exploratory factor analysis has been used in studies of 1991 Gulf War-related illnesses, and may increase understanding of symptoms and health outcomes associated with current military conflicts in Iraq and Afghanistan. The objective of this study was to use exploratory factor analysis to describe the correlations among numerous physical and psychological symptoms in terms of a smaller number of unobserved variables or factors.

Methods

The Millennium Cohort Study collects extensive self-reported health data from a large, population-based military cohort, providing a unique opportunity to investigate the interrelationships of numerous physical and psychological symptoms among US military personnel. This study used data from the Millennium Cohort Study, a large, population-based military cohort. Exploratory factor analysis was used to examine the covariance structure of symptoms reported by approximately 50,000 cohort members during 2004-2006. Analyses incorporated 89 symptoms, including responses to several validated instruments embedded in the questionnaire. Techniques accommodated the categorical and sometimes incomplete nature of the survey data.

Results

A 14-factor model accounted for 60 percent of the total variance in symptoms data and included factors related to several physical, psychological, and behavioral constructs. A notable finding was that many factors appeared to load in accordance with symptom co-location within the survey instrument, highlighting the difficulty in disassociating the effects of question content, location, and response format on factor structure.

Conclusions

This study demonstrates the potential strengths and weaknesses of exploratory factor analysis to heighten understanding of the complex associations among symptoms. Further research is needed to investigate the relationship between factor analytic results and survey structure, as well as to assess the relationship between factor scores and key exposure variables.
Serial interferon-gamma release assays during treatment of active tuberculosis in young adults
Authors: Lee Sei Won , Lee Choon-Taek , Yim Jae-Joon
Published: October 2010

Background

The role of interferon-γ release assay (IGRA) in monitoring responses to anti-tuberculosis (TB) treatment is not clear. We evaluated the results of the QuantiFERON-TB Gold In-tube (QFT-GIT) assay over time during the anti-TB treatment of adults with no underlying disease.

Methods

We enrolled soldiers who were newly diagnosed with active TB and admitted to the central referral military hospital in South Korea between May 1, 2008 and September 30, 2009. For each participant, we preformed QFT-GIT assay before treatment (baseline) and at 1, 3, and 6 months after initiating anti-TB medication.

Results

Of 67 eligible patients, 59 (88.1%) completed the study protocol. All participants were males who were human immunodeficiency virus (HIV)-negative and had no chronic diseases. Their median age was 21 years (range, 20-48). Initially, 57 (96.6%) patients had positive QFT-GIT results, and 53 (89.8%), 42 (71.2%), and 39 (66.1%) had positive QFT-GIT results at 1, 3, and 6 months, respectively. The IFN-γ level at baseline was 5.31 ± 5.34 IU/ml, and the levels at 1, 3, and 6 months were 3.95 ± 4.30, 1.82 ± 2.14, and 1.50 ± 2.12 IU/ml, respectively. All patients had clinical and radiologic improvements after treatment and were cured. A lower IFN-γ level, C-reactive protein ≥ 3 mg/dl, and the presence of fever (≥ 38.3°C) at diagnosis were associated with negative reversion of the QFT-GIT assay.

Conclusion

Although the IFN-γ level measured by QFT-GIT assay decreased after successful anti-TB treatment in most participants, less than half of them exhibited QFT-GIT reversion. Thus, the reversion to negativity of the QFT-GIT assay may not be a good surrogate for treatment response in otherwise healthy young patients with TB.
Anemia and chronic kidney disease are potential risk factors for mortality in stroke patients: a historic cohort study
Authors: Del Fabbro Patrizia , Luthi Jean-Christophe , Carrera Emmanuel , Michel Patrik , Burnier Michel , Burnand Bernard
Published: October 2010

Background

Chronic kidney disease (CKD) is associated to a higher stroke risk. Anemia is a common consequence of CKD, and is also a possible risk factor for cerebrovascular diseases. The purpose of this study was to examine if anemia and CKD are independent risk factors for mortality after stroke.

Methods

This historic cohort study was based on a stroke registry and included patients treated for a first clinical stroke in the stroke unit of one academic hospital over a three-year period. Mortality predictors comprised demographic characteristics, CKD, glomerular filtration rate (GFR), anemia and other stroke risk factors. GFR was estimated by means of the simplified Modification of Diet in Renal Disease formula. Renal function was assessed according to the Kidney Disease Outcomes Quality Initiative (K/DOQI)-CKD classification in five groups. A value of hemoglobin < 120 g/L in women and < 130 g/L in men on admission defined anemia. Kaplan-Meier survival curves and Cox models were used to describe and analyze one-year survival.

Results

Among 890 adult stroke patients, the mean (Standard Deviation) calculated GFR was 64.3 (17.8) ml/min/1.73 m2 and 17% had anemia. Eighty-two (10%) patients died during the first year after discharge. Among those, 50 (61%) had K/DOQI CKD stages 3 to 5 and 32 (39%) stages 1 or 2 (p < 0.001). Anemia was associated with an increased risk of death one year after discharge (p < 0.001). After adjustment for other factors, a higher hemoglobin level was independently associated with decreased mortality one year after discharge [hazard ratio (95% CI) 0.98 (0.97-1.00)].

Conclusions

Both CKD and anemia are frequent among stroke patients and are potential risk factors for decreased one-year survival. The inclusion of patients with a first-ever clinical stroke only and the determination of anemia based on one single measure, on admission, constitute limitations to the external validity. We should investigate if an early detection and management of both CKD and anemia could improve survival in stroke patients.
Ras-association domain family 1C protein promotes breast cancer cell migration and attenuates apoptosis
Authors: Reeves Mark E , Baldwin Scott W , Baldwin Melissa L , Chen Shin-Tai , Moretz Jeremy M , Aragon Robert J , Li Xinmin , Strong Donna D , Mohan Subburaman , Amaar Yousef G
Published: October 2010

Background

The Ras association domain family 1 (RASSF1) gene is a Ras effector encoding two major mRNA forms, RASSF1A and RASSF1C, derived by alternative promoter selection and alternative mRNA splicing. RASSF1A is a tumor suppressor gene. However, very little is known about the function of RASSF1C both in normal and transformed cells.

Methods

Gene silencing and over-expression techniques were used to modulate RASSF1C expression in human breast cancer cells. Affymetrix-microarray analysis was performed using T47D cells over-expressing RASSF1C to identify RASSF1C target genes. RT-PCR and western blot techniques were used to validate target gene expression. Cell invasion and apoptosis assays were also performed.

Results

In this article, we report the effects of altering RASSF1C expression in human breast cancer cells. We found that silencing RASSF1C mRNA in breast cancer cell lines (MDA-MB231 and T47D) caused a small but significant decrease in cell proliferation. Conversely, inducible over-expression of RASSF1C in breast cancer cells (MDA-MB231 and T47D) resulted in a small increase in cell proliferation. We also report on the identification of novel RASSF1C target genes. RASSF1C down-regulates several pro-apoptotic and tumor suppressor genes and up-regulates several growth promoting genes in breast cancer cells. We further show that down-regulation of caspase 3 via overexpression of RASSF1C reduces breast cancer cells' sensitivity to the apoptosis inducing agent, etoposide. Furthermore, we found that RASSF1C over-expression enhances T47D cell invasion/migrationin vitro.

Conclusion

Together, our findings suggest that RASSF1C, unlike RASSF1A, is not a tumor suppressor, but instead may play a role in stimulating metastasis and survival in breast cancer cells.