bluuebunny/crossref_metadata_2025 huggingface dataset:
Computational analysis of LexA regulons in Cyanobacteria
Authors: Li Shan , Xu Minli , Su Zhengchang
Published: September 2010

Background

The transcription factor LexA plays an important role in the SOS response inEscherichia coliand many other bacterial species studied. Although thelexAgene is encoded in almost every bacterial group with a wide range of evolutionary distances, its precise functions in each group/species are largely unknown. More recently, it has been shown thatlexAgenes in two cyanobacterial genomesNostoc sp. PCC 7120 andSynechocystis sp. PCC 6803 might have distinct functions other than the regulation of the SOS response. To gain a general understanding of the functions of LexA and its evolution in cyanobacteria, we conducted the current study.

Results

Our analysis indicates that six of 33 sequenced cyanobacterial genomes do not harbor alexAgene although they all encode the key SOS response genes, suggesting that LexA is not an indispensable transcription factor in these cyanobacteria, and that their SOS responses might be regulated by different mechanisms. Our phylogenetic analysis suggests thatlexAwas lost during the course of evolution in these six cyanobacterial genomes. For the 26 cyanobacterial genomes that encode alexAgene, we have predicted their LexA-binding sites and regulons using an efficient binding site/regulon prediction algorithm that we developed previously. Our results show that LexA in most of these 26 genomes might still function as the transcriptional regulator of the SOS response genes as seen inE. coliand other organisms. Interestingly, putative LexA-binding sites were also found in some genomes for some key genes involved in a variety of other biological processes including photosynthesis, drug resistance, etc., suggesting that there is crosstalk between the SOS response and these biological processes. In particular, LexA in bothSynechocystis sp.PCC6803 andGloeobacter violaceusPCC7421 has largely diverged from those in other cyanobacteria in the sequence level. It is likely that LexA is no longer a regulator of the SOS response inSynechocystis sp. PCC6803.

Conclusions

In most cyanobacterial genomes that we analyzed, LexA appears to function as the transcriptional regulator of the key SOS response genes. There are possible couplings between the SOS response and other biological processes. In some cyanobacteria, LexA has adapted distinct functions, and might no longer be a regulator of the SOS response system. In some other cyanobacteria,lexAappears to have been lost during the course of evolution. The loss oflexAin these genomes might lead to the degradation of its binding sites.
Identification of Burkholderia mallei and Burkholderia pseudomallei adhesins for human respiratory epithelial cells
Authors: Balder Rachel , Lipski Serena , Lazarus John J , Grose William , Wooten Ronald M , Hogan Robert J , Woods Donald E , Lafontaine Eric R
Published: September 2010

Background

Burkholderia pseudomalleiandBurkholderia malleicause the diseases melioidosis and glanders, respectively. A well-studied aspect of pathogenesis by these closely-related bacteria is their ability to invade and multiply within eukaryotic cells. In contrast, the means by whichB. pseudomalleiandB. malleiadhere to cells are poorly defined. The purpose of this study was to identify adherence factors expressed by these organisms.

Results

Comparative sequence analyses identified a gene product in the published genome ofB. malleistrain ATCC23344 (locus # BMAA0649) that resembles the well-characterizedYersinia enterocoliticaautotransporter adhesin YadA. The gene encoding thisB. malleiprotein, designatedboaA, was expressed inEscherichia coliand shown to significantly increase adherence to human epithelial cell lines, specifically HEp2 (laryngeal cells) and A549 (type II pneumocytes), as well as to cultures of normal human bronchial epithelium (NHBE). Consistent with these findings, disruption of theboaAgene inB. malleiATCC23344 reduced adherence to all three cell types by ~50%. The genomes of theB. pseudomalleistrains K96243 and DD503 were also found to containboaAand inactivation of the gene in DD503 considerably decreased binding to monolayers of HEp2 and A549 cells and to NHBE cultures.

A second YadA-like gene product highly similar to BoaA (65% identity) was identified in the published genomic sequence ofB. pseudomalleistrain K96243 (locus # BPSL1705). The gene specifying this protein, termedboaB, appears to beB. pseudomallei-specific. Quantitative attachment assays demonstrated that recombinantE. coliexpressing BoaB displayed greater binding to A549 pneumocytes, HEp2 cells and NHBE cultures. Moreover, aboaBmutant ofB. pseudomalleiDD503 showed decreased adherence to these respiratory cells. Additionally, aB. pseudomalleistrain lacking expression of bothboaAandboaBwas impaired in its ability to thrive inside J774A.1 murine macrophages, suggesting a possible role for these proteins in survival within professional phagocytic cells.

Conclusions

TheboaAandboaBgenes specify adhesins that mediate adherence to epithelial cells of the human respiratory tract. TheboaAgene product is shared byB. pseudomalleiandB. malleiwhereas BoaB appears to be aB. pseudomallei-specific adherence factor.
Treatment with the C5a receptor antagonist ADC-1004 reduces myocardial infarction in a porcine ischemia-reperfusion model
Authors: van der Pals Jesper , Koul Sasha , Andersson Patrik , Götberg Matthias , Ubachs Joey FA , Kanski Mikael , Arheden Håkan , Olivecrona Göran K , Larsson Bengt , Erlinge David
Published: September 2010

Background

Polymorphonuclear neutrophils, stimulated by the activated complement factor C5a, have been implicated in cardiac ischemia/reperfusion injury. ADC-1004 is a competitive C5a receptor antagonist that has been shown to inhibit complement related neutrophil activation. ADC-1004 shields the neutrophils from C5a activation before they enter the reperfused area, which could be a mechanistic advantage compared to previous C5a directed reperfusion therapies. We investigated if treatment with ADC-1004, according to a clinically applicable protocol, would reduce infarct size and microvascular obstruction in a large animal myocardial infarct model.

Methods

In anesthetized pigs (42-53 kg), a percutaneous coronary intervention balloon was inflated in the left anterior descending artery for 40 minutes, followed by 4 hours of reperfusion. Twenty minutes after balloon inflation the pigs were randomized to an intravenous bolus administration of ADC-1004 (175 mg, n = 8) or saline (9 mg/ml, n = 8). Area at risk (AAR) was evaluated by ex vivo SPECT. Infarct size and microvascular obstruction were evaluated by ex vivo MRI. The observers were blinded to the treatment at randomization and analysis.

Results

ADC-1004 treatment reduced infarct size by 21% (ADC-1004: 58.3 ± 3.4 vs control: 74.1 ± 2.9%AAR, p = 0.007). Microvascular obstruction was similar between the groups (ADC-1004: 2.2 ± 1.2 vs control: 5.3 ± 2.5%AAR, p = 0.23). The mean plasma concentration of ADC-1004 was 83 ± 8 nM at sacrifice. There were no significant differences between the groups with respect to heart rate, mean arterial pressure, cardiac output and blood-gas data.

Conclusions

ADC-1004 treatment reduces myocardial ischemia-reperfusion injury and represents a novel treatment strategy of myocardial infarct with potential clinical applicability.
Periodic assessment of plasma sFlt-1 and PlGF concentrations and its association with placental morphometry in gestational hypertension (GH) - a prospective follow-up study
Authors: Jeevaratnam Kamalan , Nadarajah Vishna Devi , Judson John Paul , Nalliah Sivalingam , Abdullah Mohd Farouk
Published: September 2010

Background

Hypertensive disorders in pregnancy contributes to about 12% of maternal deaths in Malaysia and similarly worldwide. Early detection and adequate management are preventable strategies. Biochemical markers of abnormal angiogenesis would be more specific in early detection than routine blood pressure and proteinuria measurements. The aim of this study was to estimate maternal plasma PlGF and sFlt-1 levels in pregnant women with gestational hypertension at three intervals of pregnancy and correlate these biomarker levels with placental morphometry.

Methods

Venous blood samples (antepartum, intrapartum and post partum periods) were drawn to estimate for sFlt-1 and PlGF levels while placental tissue samples were examined for placental morphometry.

Results

PlGF levels were lower in gestational hypertension (GH) compared to normotensive during antepartum and intrapartum period, whereas sFlt-1 levels were elevated in GH at antepartum, intrapartum and postpartum intervals during pregnancy. An inverse relationship between these two biomarkers was observed through correlation analysis. PlGF levels were inversely correlated with total villous surface area of the placental periphery (TCsa-C) and villous capillarization (VC-C) of the placental periphery.

Conclusion

We established periodic values of for sFlt-1 and PlGF levels for the first time in an ethnically diverse Malaysian setting. We suggest the development of GH in women is related to defective capillarization. In demonstrating periodic changes, this study suggest the possibility of developing GH and other long term health complications as a result of prolonged exposure to sFlt-1. The correlation between PlGF levels and morphometric findings also support possible capillarization defect.
Thrombospondin-4 is a putative tumour-suppressor gene in colorectal cancer that exhibits age-related methylation
Authors: Greco Sonia A , Chia June , Inglis Kelly J , Cozzi Sarah-Jane , Ramsnes Ingunn , Buttenshaw Ronald L , Spring Kevin J , Boyle Glen M , Worthley Daniel L , Leggett Barbara A , Whitehall Vicki LJ
Published: September 2010

Background

Thrombospondin-4 (THBS4) is a member of the extracellular calcium-binding protein family and is involved in cell adhesion and migration. The aim of this study was to evaluate the potential role of deregulation of THBS4 expression in colorectal carcinogenesis. Of particular interest was the possible silencing of expression by methylation of the CpG island in the gene promoter.

Methods

Fifty-five sporadic colorectal tumours stratified for the CpG Island Methylator Phenotype (CIMP) were studied. Immunohistochemical staining of THBS4 protein was assessed in normal and tumour specimens. Relative levels of THBS4 transcript expression in matched tumours and normal mucosa were also determined by quantitative RT-PCR. Colony forming ability was examined in 8 cell lines made to overexpress THBS4. Aberrant promoter hypermethylation was investigated as a possible mechanism of gene disruption using MethyLight. Methylation was also assessed in the normal colonic tissue of 99 patients, with samples biopsied from four regions along the length of the colon.

Results

THBS4 expression was significantly lower in tumour tissue than in matched normal tissue. Immunohistochemical examination demonstrated that THBS4 protein was generally absent from normal epithelial cells and tumours, but was occasionally expressed at low levels in the cytoplasm towards the luminal surface in vesicular structures. Forced THBS4 over-expression caused a 50-60% repression of tumour colony growth in all eight cell lines examined compared to control cell lines. Tumours exhibited significantly higher levels of methylation than matched normal mucosa, and THBS4 methylation correlated with the CpG island methylator phenotype. There was a trend towards decreased gene expression in tumours exhibiting high THBS4 methylation, but the correlation was not significant. THBS4 methylation was detectable in normal mucosal biopsies where it correlated with increasing patient age and negatively with the occurrence of adenomas elsewhere in the colon.

Conclusions

THBS4 shows increased methylation in colorectal cancer, but this is not strongly associated with altered gene expression, either because methylation has not always reached a critical level or because other factors influence THBS4 expression. THBS4 may act as a tumour suppressor gene, demonstrated by its suppression of tumour colony formation in vitro. THBS4 methylation is detectable in normal colonic mucosa and its level may be a biomarker for the occurrence of adenomas and carcinoma.
FLT3mutation incidence and timing of origin in a population case series of pediatric leukemia
Authors: Chang Patrick , Kang Michelle , Xiao Anny , Chang Jeffrey , Feusner James , Buffler Patricia , Wiemels Joseph
Published: September 2010

Background

Mutations in FLT3 result in activated tyrosine kinase activity, cell growth stimulation, and a poor prognosis among various subtypes of leukemia. The causes and timing of the mutations are not currently known. We evaluated the prevalence and timing of origin of FLT3 mutations in a population series of childhood leukemia patients from Northern California.

Methods

We screened and sequenced FLT3 mutations (point mutations and internal tandem duplications, ITDs) among 517 childhood leukemia patients, and assessed whether these mutations occurred before or after birth using sensitive "backtracking" methods.

Results

We determined a mutation prevalence of 9 of 73 acute myeloid leukemias (AMLs, 12%) and 9 of 441 acute lymphocytic leukemias (ALLs, 2%). Among AMLs, FLT3 mutations were more common in older patients, and among ALLs, FLT3 mutations were more common in patients with high hyperdiploidy (3.7%) than those without this cytogenetic feature (1.4%). Five FLT3 ITDs, one deletion mutation, and 3 point mutations were assessed for their presence in neonatal Guthrie spots using sensitive real-time PCR techniques, and no patients were found to harbor FLT3 mutations at birth.

Conclusions

FLT3 mutations were not common in our population-based patient series in California, and patients who harbor FLT3 mutations most likely acquire them after they are born.
Antitumour activity of a potent MEK inhibitor RDEA119/BAY 869766 combined with rapamycin in human orthotopic primary pancreatic cancer xenografts
Authors: Chang Qing , Chapman Mark S , Miner Jeffrey N , Hedley David W
Published: September 2010

Background

Combining MEK inhibitors with other signalling pathway inhibitors or conventional cytotoxic drugs represents a promising new strategy against cancer. RDEA119/BAY 869766 is a highly potent and selective MEK1/2 inhibitor undergoing phase I human clinical trials. The effects of RDEA119/BAY 869766 as a single agent and in combination with rapamycin were studied in 3 early passage primary pancreatic cancer xenografts, OCIP19, 21, and 23, grown orthotopically.

Methods

Anti-cancer effects were determined in separate groups following chronic drug exposure. Effects on cell cycle and downstream signalling were examined by flow cytometry and western blot, respectively. Plasma RDEA119 concentrations were measured to monitor the drug accumulation in vivo.

Results

RDEA119/BAY 869766 alone or in combination with rapamycin showed significant growth inhibition in all the 3 models, with a significant decrease in the percentage of cells in S-phase, accompanied by a large decrease in bromodeoxyuridine labelling and cell cycle arrest predominantly in G1. The S6 ribosomal protein was inhibited to a greater extent with combination treatment in all the three models. Blood plasma pharmacokinetic analyses indicated that RDEA119 levels achieved in vivo are similar to those that produce target inhibition and cell cycle arrest in vitro.

Conclusions

Agents targeting the ERK and mTOR pathway have anticancer activity in primary xenografts, and these results support testing this combination in pancreatic cancer patients.
Sexual knowledge, attitudes and activity of men conscripted into the military
Authors: Chao Jiankang , Lin Yenchin , Ma Michia , Ku Yanchiou , Tsai Chinghong , Shi Mingder
Published: September 2010

Background

Military conscripts may experience a change in their attitude towards sex at times when sexual urges are at their peak during their physical growth. This study examines the experience, understanding, knowledge and attitudes regarding sexual activity of the military conscripts.

Methods

Data was obtained from a cross-sectional survey of 1127 young adult military conscripts, and were evaluated in Southern Taiwan from January to July 2009, their demographic data, sexual knowledge, attitudes and activities were assessed.

Results

Nearly 43% of the participants had performed penetrative vaginal intercourse at least once; 34% of the participants performed heterosexual oral sex at least once; almost 7% of participants had had homosexual intercourse, and 7.5% of participants had experienced homosexual oral sex in the past year. The mean sexual knowledge score based on 30 questions was 23.2 ± 4.0. The higher the educational level of the participants, the greater sexual knowledge they had obtained.

Conclusion

This study found that 43% of unmarried young recruits had experienced premarital sexual activity. However, their sexual knowledge was insufficient and should be strengthened by sex education from an earlier age. College aged and adult learners also have sex education needs, especially with regard to integrating sexuality and life, being able to relate responsibly as sexual beings to others, the use of contraception, and about sexually transmitted disease.

Keywords

Young recruits, Sexual behavior, Sexual knowledge, Sex education
Myositis autoantibodies in Korean patients with inflammatory myositis: Anti-140-kDa polypeptide antibody is primarily associated with rapidly progressive interstitial lung disease independent of clinically amyopathic dermatomyositis
Authors: Kang Eun Ha , Nakashima Ran , Mimori Tsuneyo , Kim Jinhyun , Lee Yun Jong , Lee Eun Bong , Song Yeong Wook
Published: September 2010

Background

To investigate the association between myositis autoantibodies and clinical subsets of inflammatory myositis in Korean patients.

Methods

Immunoprecipitation was performed using the sera of classic polymyositis (PM) (n = 11) and dermatomyositis (DM) (n = 38) patients who met the Bohan and Peter criteria for definite inflammatory myositis. A panel of defined myositis autoantibodies was surveyed to investigate the association between each autoantibody and clinical subsets of inflammatory myositis.

Results

Either MSAs, anti-p140, or anti-p155/140 antibodies were found in 63.3% (31/49) of the study subjects. Anti-140-kDa-polypeptide (anti-p140) (18.4%, 9/49) and anti-155/140-kDa polypeptide (anti-p155/140) (16.3%, 8/49) antibodies were the most common, followed by anti-Mi2 (14.3%, 7/49), anti-ARS (12.2%, 6/49) and anti-SRP (2.0%, 1/49) antibodies. All MSAs and anti-p140 and anti-p155/140 antibodies were mutually exclusive. Anti-p140 (23.7%, 9/38), anti-p155/140 (21.1%, 8/38), and anti-Mi2 (18.4%, 3/38) antibodies were found exclusively in DM patients. Anti-p140 antibody was associated with rapidly progressive interstitial lung disease (ILD) (p = 0.001), with a sensitivity of 100.0% (4/4) and a specificity of 85.3% (29/34) in DM patients. Anti-p155/140 antibody was associated with cancer-associated DM (p = 0.009), with a sensitivity of 55.6% (5/9) and a specificity of 89.7% (26/29). Cancer-associated survival was significantly worse when anti-p155/140 antibody was present (19.2 ± 7.6 vs. 65.0 ± 3.5 months, p = 0.032). Finally, anti-ARS antibodies were associated with stable or slowly progressive ILD in PM and DM patients (p = 0.005).

Conclusions

Anti-p140 and anti-p155/140 antibodies were commonly found autoantibodies in Korean patients with inflammatory myositis. Despite the lack of clinically amyopathic DM patients in the study subjects, a strong association was observed between anti-p140 antibody and rapidly progressive ILD. Anti-p155/140 antibody was associated with cancer-associated myositis and poor survival.
Frequent epigenetic inactivation of RASSF2 in thyroid cancer and functional consequences
Authors: Schagdarsurengin Undraga , Richter Antje M , Hornung Juliane , Lange Cornelia , Steinmann Katrin , Dammann Reinhard H
Published: September 2010

Background

The Ras association domain family (RASSF) encodes for distinct tumor suppressors and several members are frequently silenced in human cancer. In our study, we analyzed the role of RASSF2, RASSF3, RASSF4, RASSF5A, RASSF5C and RASSF6 and the effectors MST1, MST2 and WW45 in thyroid carcinogenesis.

Results

Frequent methylation of the RASSF2 and RASSF5A CpG island promoters in thyroid tumors was observed. RASSF2 was methylated in 88% of thyroid cancer cell lines and in 63% of primary thyroid carcinomas. RASSF2 methylation was significantly increased in primary thyroid carcinoma compared to normal thyroid, goiter and follicular adenoma (0%, 17% and 0%, respectively; p < 0.05). Patients which were older than 60 years were significantly hypermethylated for RASSF2 in their primary thyroid tumors compared to those younger than 40 years (90% vs. 38%; p < 0.05). RASSF2 promoter hypermethylation correlated with its reduced expression and treatment with a DNA methylation inhibitor reactivated RASSF2 transcription. Over-expression of RASSF2 reduced colony formation of thyroid cancer cells. Functionally our data show that RASSF2 interacts with the proapoptotic kinases MST1 and MST2 and induces apoptosis in thyroid cancer cell lines. Deletion of the MST interaction domain of RASSF2 reduced apoptosis significantly (p < 0.05).

Conclusion

These results suggest that RASSF2 encodes a novel epigenetically inactivated candidate tumor suppressor gene in thyroid carcinogenesis.
Factors affecting the relationship between psychological status and quality of life in COPD patients
Authors: Balcells Eva , Gea Joaquim , Ferrer Jaume , Serra Ignasi , Orozco-Levi Mauricio , de Batlle Jordi , Rodriguez Esther , Benet Marta , Donaire-González David , Antó Josep M , Garcia-Aymerich Judith ,   the PAC-COPD Study Group
Published: September 2010

Background

This study aims to (i) evaluate the association between anxiety and depressive symptoms and health-related quality of life (HRQoL); and (ii) identify the effect modifiers of this relationship in patients with chronic obstructive pulmonary disease (COPD).

Methods

A total of 337 clinically stable COPD patients answered the St. George's Respiratory Questionnaire (SGRQ) (assessing HRQoL) and the Hospital Anxiety and Depression Scale (HADS). Socio-demographic information, lung function, and other clinical data were collected.

Results

Most patients (93%) were male; they had a mean (SD) age of 68 (9) years and mild to very severe COPD (post-bronchodilator FEV1 52 (16)% predicted). Multivariate analyses showed that anxiety, depression, or both conditions were associated with poor HRQoL (for all SGRQ domains). The association between anxiety and total HRQoL score was 6.7 points higher (indicating a worse HRQoL) in current workers than in retired individuals. Estimates for patients with "both anxiety and depression" were 5.8 points lower in stage I-II than in stage III-IV COPD, and 10.2 points higher in patients with other comorbidities than in those with only COPD.

Conclusions

This study shows a significant association between anxiety, depression, or both conditions and impaired HRQoL. Clinically relevant factors affecting the magnitude of this association include work status, COPD severity, and the presence of comorbidities.
Association between -238 but not -308 polymorphism of Tumor necrosis factor alpha (TNF-alpha)v and unexplained recurrent spontaneous abortion (URSA) in Chinese population
Authors: Liu Chunmei , Wang Jing , Zhou Sirui , Wang Binbin , Ma Xu
Published: September 2010

Objectives

TNF-alpha is a critical cytokine produced by Th1 cells while altered T helper 1 (Th1)-Th2 balance is found crucial for a successful pregnancy.

Study Design

A cohort of 132 Southern Chinese Han RSA patients and 152 controls constituted the subjects of this study. Two functional polymorphisms -308 and -238 of TNF-alpha were studied by association analysis.

Results

lack of association was found in TNF-alpha -308 SNP yet a significant difference was discovered in -238 polymorphism.

Conclusion

This study suggested that TNF-alpha may be a risk factor in Chinese RSA patients. However the ethnic differences may also contribute to the results.
Quantitative phosphoproteomic analysis of prion-infected neuronal cells
Authors: Wagner Wibke , Ajuh Paul , Löwer Johannes , Wessler Silja
Published: September 2010

Prion diseases or transmissible spongiform encephalopathies (TSEs) are fatal diseases associated with the conversion of the cellular prion protein (PrPC) to the abnormal prion protein (PrPSc). Since the molecular mechanisms in pathogenesis are widely unclear, we analyzed the global phospho-proteome and detected a differential pattern of tyrosine- and threonine phosphorylated proteins in PrPSc-replicating and pentosan polysulfate (PPS)-rescued N2a cells in two-dimensional gel electrophoresis. To quantify phosphorylated proteins, we performed a SILAC (stable isotope labeling by amino acids in cell culture) analysis and identified 105 proteins, which showed a regulated phosphorylation upon PrPSc infection. Among those proteins, we validated the dephosphorylation of stathmin and Cdc2 and the induced phosphorylation of cofilin in PrPSc-infected N2a cells in Western blot analyses. Our analysis showed for the first time a differentially regulated phospho-proteome in PrPSc infection, which could contribute to the establishment of novel protein markers and to the development of novel therapeutic intervention strategies in targeting prion-associated disease.
Three-day dendritic cells for vaccine development: Antigen uptake, processing and presentation
Authors: Bürdek Maja , Spranger Stefani , Wilde Susanne , Frankenberger Bernhard , Schendel Dolores J , Geiger Christiane
Published: September 2010

Background

Antigen-loaded dendritic cells (DC) are capable of priming naïve T cells and therefore represent an attractive adjuvant for vaccine development in anti-tumor immunotherapy. Numerous protocols have been described to date using different maturation cocktails and time periods for the induction of mature DC (mDC) in vitro. For clinical application, the use of mDC that can be generated in only three days saves on the costs of cytokines needed for large scale vaccine cell production and provides a method to produce cells within a standard work-week schedule in a GMP facility.

Methods

In this study, we addressed the properties of antigen uptake, processing and presentation by monocyte-derived DC prepared in three days (3d mDC) compared with conventional DC prepared in seven days (7d mDC), which represent the most common form of DC used for vaccines to date.

Results

Although they showed a reduced capacity for spontaneous antigen uptake, 3d mDC displayed higher capacity for stimulation of T cells after loading with an extended synthetic peptide that requires processing for MHC binding, indicating they were more efficient at antigen processing than 7d DC. We found, however, that 3d DC were less efficient at expressing protein after introduction of in vitro transcribed (ivt)RNA by electroporation, based on published procedures. This deficit was overcome by altering electroporation parameters, which led to improved protein expression and capacity for T cell stimulation using low amounts of ivt RNA.

Conclusions

This new procedure allows 3d mDC to replace 7d mDC for use in DC-based vaccines that utilize long peptides, proteins or ivt RNA as sources of specific antigen.
The inverse association of serum HBV DNA level with HDL and adiponectin in chronic hepatitis B infection
Authors: Mohamadkhani Ashraf , Sayemiri Kourosh , Ghanbari Reza , Elahi Elham , Poustchi Hossein , Montazeri Ghodratollah
Published: September 2010

BACKGROUND

The natural history of hepatitis B virus (HBV) is complex and influenced by the level of viral replication and host factors. The hepatoprotective role of high density lipoproteins (HDL) and adiponectin as host factors on HBV persistence is less well understood.

METHODS

To investigate correlation between HBV DNA level with clinical parameters in patients with chronic hepatitis B, 92 male subjects with HBV infection without any risk factors for diabetes were enrolled in this study. Age and BMI of the study population were matched and HBV DNA, ALT, tumor necrosis factor alpha (TNF-α), adiponectin and lipid levels was measured.

RESULTS

Serum HBV DNA correlated inversely with serum HDL level (r = -0.23; P = 0.014). The median of log copies/ml for HBV DNA (3.67) was considered as cut off point. Patients with HBV DNA level higher than cut off point had lower adiponectin (8.7 ± 5.3 vs 10.7 ± 4.9 μg/ml p = 0.05). Also, adiponectin had a negative correlation with TNF-α (r = -0.21, P = 0.04) and positive correlations with HDL (r = 0.18, P = 0.043).Multivariate regression models show that serum HDL level is an independed factor to predict serum HBV DNA.

CONCLUSION

Our findings showed that higher HBV DNA levels are associated with lower HDL and adiponectin but induced TNF-alpha values.
Molecular characterization, structural analysis and determination of host range of a novel bacteriophage LSB-1
Authors: Chai Yaming , Xiong Hongyan , Ma Xiangyu , Cheng Liqing , Huang Guorong , Zhang Zhonglin Lin Lin
Published: September 2010

Background

Bacteriophages (phages) are widespread in the environment and play a crucial role in the evolution of their bacterial hosts and the emergence of new pathogens.

Results

LSB-1, a reference coliphage strain, was classified as a member of the Podoviridae family with a cystic form (50 ± 5 nm diameter) and short tail (60 ± 5 nm long). The double stranded DNA was about 30 kilobase pairs in length. We identified its host range and determined the gp17 sequences and protein structure using shotgun analysis and bioinformatics technology.

Conclusions

Coliphage LSB-1 possesses a tailspike protein with endosialidase activity which is probably responsible for its specific enteroinvasive E.coli host range within the laboratory.
In vivo Whole-Cell Patch-Clamp Recording of Sensory Synaptic Responses of Cingulate Pyramidal Neurons to Noxious Mechanical Stimuli in Adult Mice
Authors: Koga Kohei , Li Xiangyao , Chen Tao , Steenland Hendrik W , Descalzi Giannina , Zhuo Min
Published: September 2010

The anterior cingulate cortex (ACC) plays important roles in emotion, learning, memory and persistent pain. Our previous in vitro studies have demonstrated that pyramidal neurons in layer II/III of the adult mouse ACC can be characterized into three types: regular spiking (RS), intermediate (IM) and intrinsic bursting (IB) cells, according to their action potential (AP) firing patterns. However, no in vivo information is available for the intrinsic properties and sensory responses of ACC neurons of adult mice. Here, we performed in vivo whole-cell patch-clamp recordings from pyramidal neurons in adult mice ACC under urethane anesthetized conditions. First, we classified the intrinsic properties and analyzed their slow oscillations. The population ratios of RS, IM and IB cells were 10, 62 and 28%, respectively. The mean spontaneous APs frequency of IB cells was significantly greater than those of RS and IM cells, while the slow oscillations were similar among ACC neurons. Peripheral noxious pinch stimuli induced evoked spike responses in all three types of ACC neurons. Interestingly, IB cells showed significantly greater firing frequencies than RS and IM cells. In contrast, non-noxious brush did not induce any significant response. Our studies provide the first in vivo characterization of ACC neurons in adult mice, and demonstrate that ACC neurons are indeed nociceptive. These findings support the critical roles of ACC in nociception, from mice to humans.
ATHENA: A knowledge-based hybrid backpropagation-grammatical evolution neural network algorithm for discovering epistasis among quantitative trait Loci
Authors: Turner Stephen D , Dudek Scott M , Ritchie Marylyn D
Published: September 2010

Background

Growing interest and burgeoning technology for discovering genetic mechanisms that influence disease processes have ushered in a flood of genetic association studies over the last decade, yet little heritability in highly studied complex traits has been explained by genetic variation. Non-additive gene-gene interactions, which are not often explored, are thought to be one source of this "missing" heritability.

Methods

Stochastic methods employing evolutionary algorithms have demonstrated promise in being able to detect and model gene-gene and gene-environment interactions that influence human traits. Here we demonstrate modifications to a neural network algorithm in ATHENA (the Analysis Tool for Heritable and Environmental Network Associations) resulting in clear performance improvements for discovering gene-gene interactions that influence human traits. We employed an alternative tree-based crossover, backpropagation for locally fitting neural network weights, and incorporation of domain knowledge obtainable from publicly accessible biological databases for initializing the search for gene-gene interactions. We tested these modificationsin silicousing simulated datasets.

Results

We show that the alternative tree-based crossover modification resulted in a modest increase in the sensitivity of the ATHENA algorithm for discovering gene-gene interactions. The performance increase was highly statistically significant when backpropagation was used to locally fit NN weights. We also demonstrate that using domain knowledge to initialize the search for gene-gene interactions results in a large performance increase, especially when the search space is larger than the search coverage.

Conclusions

We show that a hybrid optimization procedure, alternative crossover strategies, and incorporation of domain knowledge from publicly available biological databases can result in marked increases in sensitivity and performance of the ATHENA algorithm for detecting and modelling gene-gene interactions that influence a complex human trait.
Radiographic correlates of hallux valgus severity in older people
Authors: D'Arcangelo Paul R , Landorf Karl B , Munteanu Shannon E , Zammit Gerard V , Menz Hylton B
Published: September 2010

Background

The severity of hallux valgus is easily appreciated by its clinical appearance, however x‐ray measurements are also frequently used to evaluate the condition, particularly if surgery is being considered. There have been few large studies that have assessed the validity of these x‐ray observations across a wide spectrum of the deformity. In addition, no studies have specifically focused on older people where the progression of the disorder has largely ceased. Therefore, this study aimed to explore relationships between relevant x‐ray observations with respect to hallux valgus severity in older people.

Methods

This study utilised 402 x‐rays of 201 participants (74 men and 127 women) aged 65 to 94 years. All participants were graded using the Manchester Scale ‐ a simple, validated system to grade the severity of hallux valgus ‐ prior to radiographic assessment. A total of 19 hallux valgus‐related x‐ray observations were performed on each set of x‐rays. These measurements were then correlated with the Manchester Scale scores.

Results

Strong, positive correlations were identified between the severity of hallux valgus and the hallux abductus angle, the proximal articular set angle, the sesamoid position and congruency of the first metatarsophalangeal joint. As hallux valgus severity increased, so did the frequency of radiographic osteoarthritis of the first metatarsophalangeal joint and a round first metatarsal head. A strong linear relationship between increased relative length of the first metatarsal and increased severity of hallux valgus was also observed.

Conclusions

Strong associations are evident between the clinical appearance of hallux valgus and a number of hallux valgus‐related x‐ray observations indicative of structural deformity and joint degeneration. As it is unlikely that metatarsal length increases as a result of hallux valgus deformity, increased length of the first metatarsal relative to the second metatarsal may be a contributing factor to the development and/or progression of hallux valgus.
Development of a practical guide for the early recognition for malignant melanoma of the foot and nail unit
Authors: Bristow Ivan R , de Berker David AR
Published: September 2010

Background

Malignant melanoma is a rare but potentially lethal form of cancer which may arise on the foot. Evidence suggests that due to misdiagnosis and later recognition, foot melanoma has a poorer prognosis than cutaneous melanoma elsewhere.

Methods

A panel of experts representing podiatry and dermatologists with a special interest in skin oncology was assembled to review the literature and clinical evidence to develop a clinical guide for the early recognition of plantar and nail unit melanoma.

Results

A systematic review of the literature revealed little high quality data to inform the guide. However a significant number of case reports and series were available for analysis. From these, the salient features were collated and summarised into the guide. Based on these features a new acronym “CUBED” for foot melanoma was drafted and incorporated in the guide.

Conclusions

The use of this guide may help clinicians in their assessment of suspicious lesions on the foot (including the nail unit). Earlier detection of suspicious pedal lesions may facilitate earlier referral for expert assessment and definitive diagnosis. The guide is currently being field tested amongst practitioners.
Heritability patterns in hand osteoarthritis: the role of osteophytes
Authors: Ishimori Mariko L , Altman Roy D , Cohen Myles J , Cui Jinrui , Guo Xiuqing , Rotter Jerome I , Weisman Michael H
Published: September 2010

Introduction

The objective of the present study was to assess heritability of clinical and radiographic features of hand osteoarthritis (OA) in affected patients and their siblings.

Methods

A convenience sample of patients with clinical and radiographic hand OA and their siblings were evaluated by examination and radiography. Radiographs were scored for hand OA features by radiographic atlas. The heritability of hand OA phenotypes was assessed for clinical and radiographic measures based on anatomic locations and radiographic characteristics. Phenotypic data were transformed to reduce non-normality, if necessary. A variance components approach was used to calculate heritability.

Results

One hundred and thirty-six probands with hand OA and their sibling(s) were enrolled. By anatomic location, the highest heritability was seen with involvement of the first interphalangeal joint (h2 = 0.63, P = 0.00004), the first carpometacarpal joint (h2 = 0.38, P = 0.01), the distal interphalangeal joints (h2 = 0.36, P = 0.02), and the proximal interphalangeal joints (h2 = 0.30, P = 0.03) with osteophytes. The number and severity of joints with osteophyte involvement was heritable overall (h2 = 0.38, P = 0.008 for number and h2 = 0.35, P = 0.01 for severity) and for all interphalangeal joints (h2 = 0.42, P = 0.004 and h2 = 0.33, P = 0.02). The severity of carpometacarpal joint involvement was also heritable (h2 = 0.53, P = 0.0006). Similar results were obtained when the analysis was limited to the Caucasian sample.

Conclusions

In a population with clinical and radiographic hand OA and their siblings, the presence of osteophytes was the most sensitive biomarker for hand OA heritability. Significant heritability was detected for anatomic phenotypes by joint location, severity of joint involvement with osteophytes as well as for overall number and degree of hand OA involvement. These findings are in agreement with the strong genetic predisposition for hand OA reported by others. The results support phenotyping based on severity of osteophytes and a joint-specific approach. More specific phenotypes may hold greater promise in the study of genetics in hand OA.
Refeeding syndrome influences outcome of anorexia nervosa patients in intensive care unit: an observational study
Authors: Vignaud Marie , Constantin Jean-Michel , Ruivard Marc , Villemeyre-Plane Michele , Futier Emmanuel , Bazin Jean-Etienne , Annane Djillali ,   AZUREA group (AnorexieRea Study Group)
Published: September 2010

Introduction

Data on the epidemiology and management of anorexia nervosa (AN) in the intensive care unit (ICU) are scarce. The aim of this study was to evaluate the prevalence and associated morbidity and mortality of AN in French ICUs.

Methods

We randomly selected 30 ICUs throughout France. Thereafter, we retrospectively analyzed all patients with AN admitted to any of these 30 ICUs between May 2006 and May 2008. We considered demographic data, diagnosis at admission and complications occurring during the stay, focusing on refeeding syndrome and management of refeeding.

Results

Eleven of the 30 ICUs participated in the retrospective study, featuring 68 patients, including 62 women. Average body mass index at the admission was 12 ± 3 kg/m2. Twenty one were mechanically ventilated, mainly for neurological reasons. The reported average calorie intake was 22.3 ± 13 kcal/kg/24 h. Major diagnoses at admission were metabolic problems, refeeding survey and voluntary drug intoxication and infection. The most common complications were metabolic, hematological, hepatic, and infectious events, of which 10% occurred during refeeding. Seven patients developed refeeding syndrome. At day one, the average calorie intake was higher for patients who developed refeeding syndrome (23.2 ± 5 Kcal/kg/j; n = 7) versus patients without refeeding syndrome (14.1 ± 3 Kcal/kg/j; n = 61) P = 0.02. Seven patients died, two from acute respiratory distress syndrome and five from multiorgan-failure associated with major hydroelectrolytic problems.

Conclusions

The frequency of AN in ICU patients is very low and the crude mortality in this group is about 10%. Prevention and early-detection of refeeding syndrome is the key point.
Prognostic value of continuous EEG monitoring during therapeutic hypothermia after cardiac arrest
Authors: Rossetti Andrea O , Urbano Luis A , Delodder Frederik , Kaplan Peter W , Oddo Mauro
Published: September 2010

Introduction

Continuous EEG (cEEG) is increasingly used to monitor brain function in neuro-ICU patients. However, its value in patients with coma after cardiac arrest (CA), particularly in the setting of therapeutic hypothermia (TH), is only beginning to be elucidated. The aim of this study was to examine whether cEEG performed during TH may predict outcome.

Methods

From April 2009 to April 2010, we prospectively studied 34 consecutive comatose patients treated with TH after CA who were monitored with cEEG, initiated during hypothermia and maintained after rewarming. EEG background reactivity to painful stimulation was tested. We analyzed the association between cEEG findings and neurologic outcome, assessed at 2 months with the Glasgow-Pittsburgh Cerebral Performance Categories (CPC).

Results

Continuous EEG recording was started 12 ± 6 hours after CA and lasted 30 ± 11 hours. Nonreactive cEEG background (12 of 15 (75%) among nonsurvivors versus none of 19 (0) survivors; P < 0.001) and prolonged discontinuous "burst-suppression" activity (11 of 15 (73%) versus none of 19; P < 0.001) were significantly associated with mortality. EEG seizures with absent background reactivity also differed significantly (seven of 15 (47%) versus none of 12 (0); P = 0.001). In patients with nonreactive background or seizures/epileptiform discharges on cEEG, no improvement was seen after TH. Nonreactive cEEG background during TH had a positive predictive value of 100% (95% confidence interval (CI), 74 to 100%) and a false-positive rate of 0 (95% CI, 0 to 18%) for mortality. All survivors had cEEG background reactivity, and the majority of them (14 (74%) of 19) had a favorable outcome (CPC 1 or 2).

Conclusions

Continuous EEG monitoring showing a nonreactive or discontinuous background during TH is strongly associated with unfavorable outcome in patients with coma after CA. These data warrant larger studies to confirm the value of continuous EEG monitoring in predicting prognosis after CA and TH.
Sequence and structure of Brassica rapachromosome A3
Authors: Mun Jeong-Hwan , Kwon Soo-Jin , Seol Young-Joo , Kim Jin A , Jin Mina , Kim Jung Sun , Lim Myung-Ho , Lee Soo-In , Hong Joon Ki , Park Tae-Ho , Lee Sang-Choon , Kim Beom-Jin , Seo Mi-Suk , Baek Seunghoon , Lee Min-Jee , Shin Ja Young , Hahn Jang-Ho , Hwang Yoon-Jung , Lim Ki-Byung , Park Jee Young , Lee Jonghoon , Yang Tae-Jin , Yu Hee-Ju , Choi Ik-Young , Choi Beom-Soon , Choi Su Ryun , Ramchiary Nirala , Lim Yong Pyo , Fraser Fiona , Drou Nizar , Soumpourou Eleni , Trick Martin , Bancroft Ian , Sharpe Andrew G , Parkin Isobel AP , Batley Jacqueline , Edwards Dave , Park Beom-Seok
Published: September 2010

Background

The species Brassica rapa includes important vegetable and oil crops. It also serves as an excellent model system to study polyploidy-related genome evolution because of its paleohexaploid ancestry and its close evolutionary relationships with Arabidopsis thaliana and other Brassica species with larger genomes. Therefore, its genome sequence will be used to accelerate both basic research on genome evolution and applied research across the cultivated Brassica species.

Results

We have determined and analyzed the sequence of B. rapa chromosome A3. We obtained 31.9 Mb of sequences, organized into nine contigs, which incorporated 348 overlapping BAC clones. Annotation revealed 7,058 protein-coding genes, with an average gene density of 4.6 kb per gene. Analysis of chromosome collinearity with the A. thaliana genome identified conserved synteny blocks encompassing the whole of the B. rapa chromosome A3 and sections of four A. thaliana chromosomes. The frequency of tandem duplication of genes differed between the conserved genome segments in B. rapa and A. thaliana, indicating differential rates of occurrence/retention of such duplicate copies of genes. Analysis of 'ancestral karyotype' genome building blocks enabled the development of a hypothetical model for the derivation of the B. rapa chromosome A3.

Conclusions

We report the near-complete chromosome sequence from a dicotyledonous crop species. This provides an example of the complexity of genome evolution following polyploidy. The high degree of contiguity afforded by the clone-by-clone approach provides a benchmark for the performance of whole genome shotgun approaches presently being applied in B. rapa and other species with complex genomes.
Novel venom gene discovery in the platypus
Authors: Whittington Camilla M , Papenfuss Anthony T , Locke Devin P , Mardis Elaine R , Wilson Richard K , Abubucker Sahar , Mitreva Makedonka , Wong Emily SW , Hsu Arthur L , Kuchel Philip W , Belov Katherine , Warren Wesley C
Published: September 2010

Background

To date, few peptides in the complex mixture of platypus venom have been identified and sequenced, in part due to the limited amounts of platypus venom available to study. We have constructed and sequenced a cDNA library from an active platypus venom gland to identify the remaining components.

Results

We identified 83 novel putative platypus venom genes from 13 toxin families, which are homologous to known toxins from a wide range of vertebrates (fish, reptiles, insectivores) and invertebrates (spiders, sea anemones, starfish). A number of these are expressed in tissues other than the venom gland, and at least three of these families (those with homology to toxins from distant invertebrates) may play non-toxin roles. Thus, further functional testing is required to confirm venom activity. However, the presence of similar putative toxins in such widely divergent species provides further evidence for the hypothesis that there are certain protein families that are selected preferentially during evolution to become venom peptides. We have also used homology with known proteins to speculate on the contributions of each venom component to the symptoms of platypus envenomation.

Conclusions

This study represents a step towards fully characterizing the first mammal venom transcriptome. We have found similarities between putative platypus toxins and those of a number of unrelated species, providing insight into the evolution of mammalian venom.