bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptional regulation of the operon encoding stress-responsive ECF sigma factor SigH and its anti-sigma factor RshA, and control of its regulatory network in Corynebacterium glutamicum
Authors: Busche Tobias , Šilar Radoslav , Pičmanová Martina , Pátek Miroslav , Kalinowski Jörn 
Published: September 2012

Abstract

Background
The expression of genes in Corynebacterium glutamicum, a Gram-positive non-pathogenic bacterium used mainly for the industrial production of amino acids, is regulated by seven different sigma factors of RNA polymerase, including the stress-responsive ECF-sigma factor SigH. The sigH gene is located in a gene cluster together with the rshA gene, putatively encoding an anti-sigma factor. The aim of this study was to analyze the transcriptional regulation of the sigH and rshA gene cluster and the effects of RshA on the SigH regulon, in order to refine the model describing the role of SigH and RshA during stress response.

Results
Transcription analyses revealed that the sigH gene and rshA gene are cotranscribed from four sigH housekeeping promoters in C. glutamicum. In addition, a SigH-controlled rshA promoter was found to only drive the transcription of the rshA gene. To test the role of the putative anti-sigma factor gene rshA under normal growth conditions, a C. glutamicum rshA deletion strain was constructed and used for genome-wide transcription profiling with DNA microarrays. In total, 83 genes organized in 61 putative transcriptional units, including those previously detected using sigH mutant strains, exhibited increased transcript levels in the rshA deletion mutant compared to its parental strain. The genes encoding proteins related to disulphide stress response, heat stress proteins, components of the SOS-response to DNA damage and proteasome components were the most markedly upregulated gene groups. Altogether six SigH-dependent promoters upstream of the identified genes were determined by primer extension and a refined consensus promoter consisting of 45 original promoter sequences was constructed.

Conclusions
The rshA gene codes for an anti-sigma factor controlling the function of the stress-responsive sigma factor SigH in C. glutamicum. Transcription of rshA from a SigH-dependent promoter may serve to quickly shutdown the SigH-dependent stress response after the cells have overcome the stress condition. Here we propose a model of the regulation of oxidative and heat stress response including redox homeostasis by SigH, RshA and the thioredoxin system.
Evolution of selenoproteins in the metazoan
Authors: Jiang Liang , Ni Jiazuan , Liu Qiong 
Published: September 2012

Abstract

Background
The selenocysteine (Sec) containing proteins, selenoproteins, are an important group of proteins present throughout all 3 kingdoms of life. With the rapid progression of selenoprotein research in the post-genomic era, application of bioinformatics methods to the identification of selenoproteins in newly sequenced species has become increasingly important. Although selenoproteins in human and other vertebrates have been investigated, studies of primitive invertebrate selenoproteomes are rarely reported outside of insects and nematodes.

Result
A more integrated view of selenoprotein evolution was constructed using several representative species from different evolutionary eras. Using a SelGenAmic-based selenoprotein identification method, 178 selenoprotein genes were identified in 6 invertebrates: Amphimedon queenslandica, Trichoplax adhaerens, Nematostella vectensis, Lottia gigantean, Capitella teleta, and Branchiostoma floridae. Amphioxus was found to have the most abundant and variant selenoproteins of any animal currently characterized, including a special selenoprotein P (SelP) possessing 3 repeated Trx-like domains and Sec residues in the N-terminal and 2 Sec residues in the C-terminal. This gene structure suggests the existence of two different strategies for extension of Sec numbers in SelP for the preservation and transportation of selenium. In addition, novel eukaryotic AphC-like selenoproteins were identified in sponges.

Conclusion
Comparison of various animal species suggests that even the most primitive animals possess a selenoproteome range and variety similar to humans. During evolutionary history, only a few new selenoproteins have emerged and few were lost. Furthermore, the massive loss of selenoproteins in nematodes and insects likely occurred independently in isolated partial evolutionary branches.
A proteomic investigation of Fusobacterium nucleatum alkaline-induced biofilms
Authors: Chew Jactty , Zilm Peter S , Fuss Janet M , Gully Neville J 
Published: September 2012

AbstractBackgroundThe Gram negative anaerobeFusobacterium nucleatumhas been implicated in the aetiology of periodontal diseases. Although frequently isolated from healthy dental plaque, its numbers and proportion increase in plaque associated with disease. One of the significant physico-chemical changes in the diseased gingival sulcus is increased environmental pH. When grown under controlled conditions in our laboratory,F. nucleatumsubspeciespolymorphumformed mono-culture biofilms when cultured at pH 8.2. Biofilm formation is a survival strategy for bacteria, often associated with altered physiology and increased virulence. A proteomic approach was used to understand the phenotypic changes inF. nucleatumcells associated with alkaline induced biofilms. The proteomic based identification of significantly altered proteins was verified where possible using additional methods including quantitative real-time PCR (qRT-PCR), enzyme assay, acidic end-product analysis, intracellular polyglucose assay and Western blotting.ResultsOf 421 proteins detected on two-dimensional electrophoresis gels, spot densities of 54 proteins varied significantly (p < 0.05) inF. nucleatumcultured at pH 8.2 compared to growth at pH 7.4. Proteins that were differentially produced in biofilm cells were associated with the functional classes; metabolic enzymes, transport, stress response and hypothetical proteins. Our results suggest that biofilm cells were more metabolically efficient than planktonic cells as changes to amino acid and glucose metabolism generated additional energy needed for survival in a sub-optimal environment. The intracellular concentration of stress response proteins including heat shock protein GroEL and recombinational protein RecA increased markedly in the alkaline environment. A significant finding was the increased abundance of an adhesin, Fusobacterial outer membrane protein A (FomA). This surface protein is known for its capacity to bind to a vast number of bacterial species and human epithelial cells and its increased abundance was associated with biofilm formation.ConclusionThis investigation identified a number of proteins that were significantly altered byF. nucleatumin response to alkaline conditions similar to those reported in diseased periodontal pockets. The results provide insight into the adaptive mechanisms used byF. nucleatumbiofilms in response to pH increase in the host environment.
The effect of environmental conditions on expression of Bacteroides fragilis and Bacteroides thetaiotaomicron C10 protease genes
Authors: Thornton Roibeard F , Murphy Elizabeth C , Kagawa Todd F , O’Toole Paul W , Cooney Jakki C 
Published: September 2012

Abstract

Background

Bacteroides fragilis and Bacteroides thetaiotaomicron are members of the normal human intestinal microbiota. However, both organisms are capable of causing opportunistic infections, during which the environmental conditions to which the bacteria are exposed change dramatically. To further explore their potential for contributing to infection, we have characterized the expression in B. thetaiotaomicron of four homologues of the gene encoding the C10 cysteine protease SpeB, a potent extracellular virulence factor produced by Streptococcus pyogenes.

Results
We identified a paralogous set of genes (btp genes) in the B. thetaiotaomicron genome, that were related to C10 protease genes we recently identified in B. fragilis. Similar to C10 proteases found in B. fragilis, three of the B. thetaiotaomicron homologues were transcriptionally coupled to genes encoding small proteins that are similar in structural architecture to Staphostatins, protease inhibitors associated with Staphopains in Staphylococcus aureus. The expression of genes for these C10 proteases in both B. fragilis and B. thetaiotaomicron was found to be regulated by environmental stimuli, in particular by exposure to oxygen, which may be important for their contribution to the development of opportunistic infections.

Conclusions
Genes encoding C10 proteases are increasingly identified in operons which also contain genes encoding proteins homologous to protease inhibitors. The Bacteroides C10 protease gene expression levels are responsive to different environmental stimuli suggesting they may have distinct roles in the bacterial-host interaction.
Postoperative complications following colectomy for ulcerative colitis: A validation study
Authors: Ma Christopher , Crespin Marcelo , Proulx Marie-Claude , DeSilva Shanika , Hubbard James , Prusinkiewicz Martin , Nguyen Geoffrey C , Panaccione Remo , Ghosh Subrata , Myers Robert P , Quan Hude , Kaplan Gilaad G 
Published: September 2012

Abstract

Background
Ulcerative colitis (UC) patients failing medical management require colectomy. This study compares risk estimates for predictors of postoperative complication derived from administrative data against that of chart review and evaluates the accuracy of administrative coding for this population.

Methods
Hospital administrative databases were used to identify adults with UC undergoing colectomy from 1996–2007. Medical charts were reviewed and regression analyses comparing chart versus administrative data were performed to assess the effect of age, emergent operation, and Charlson comorbidities on the occurrence of postoperative complications. Sensitivity, specificity, and positive/negative predictive values of administrative coding for identifying the study population, Charlson comorbidities, and postoperative complications were assessed.

Results
Compared to chart review, administrative data estimated a higher magnitude of effect for emergent admission (OR 2.52 [95% CI: 1.80–3.52] versus 1.49 [1.06–2.09]) and Charlson comorbidities (OR 2.91 [1.86–4.56] versus 1.50 [1.05–2.15]) as predictors of postoperative complications. Administrative data correctly identified UC and colectomy in 85.9% of cases. The administrative database was 37% sensitive in identifying patients with ≥ 1Charlson comorbidity. Restricting analysis to active comorbidities increased the sensitivity to 63%. The sensitivity of identifying patients with at least one postoperative complication was 68%; restricting analysis to more severe complications improved the sensitivity to 84%.

Conclusions
Administrative data identified the same risk factors for postoperative complications as chart review, but overestimated the magnitude of risk. This discrepancy may be explained by coding inaccuracies that selectively identifying the most serious complications and comorbidities.
Peripheral artery disease in peritoneal dialysis and hemodialysis patients: single-center retrospective study in Taiwan
Authors: Lee Chun-Chuan , Wu Chih-Jen , Chou Li-Hua , Shen Su-Mei , Chiang Sheng-Fang , Jen Pi-Chu , Yeh Mei-Ching , Pan Chi-Feng 
Published: September 2012

Abstract

Background
Peripheral artery disease (PAD) is a condition characterized by restricted blood flow to the extremities, and is especially common in the elderly. PAD increases the risk for mortality and morbidity in patients with end-stage renal disease (ESRD), especially those on hemodialysis (HD).

Methods
The records of 484 patients with end-stage renal disease who were on HD or peritoneal dialysis (PD) were reviewed. PAD was diagnosed based on the ankle-brachial pressure index (ABI). Demographic and clinical characteristics were analyzed.

Results
PAD had an overall prevalence of 18.2% and was significantly more common in HD patients (21.8%) than in PD patients (4.8%). Advanced age, diabetes mellitus, smoking, low parathyroid hormone level, elevated serum ferritin, elevated serum glucose, and low serum creatinine levels increased the risk for PAD. PAD was independently associated with advanced age, diabetes mellitus, duration of dialysis, low serum creatinine, and hyperlipidemia. PD patients had a significantly lower prevalence of PAD than HD patients, maybe due to their younger age and lower prevalence of diabetes mellitus in this present study.

Conclusions
The prevalence of PAD was greater in the HD group than the PD group. Most of the risk factors for PAD were specific to HD, and no analyzed factor was significantly associated with PAD in PD patients.
Prevalence and risk factors of childbirth-related post-traumatic stress symptoms
Authors: Modarres Maryam , Afrasiabi Sedigheh , Rahnama Parvin , Montazeri Ali 
Published: September 2012

AbstractBackgroundThere is evidence that traumatic birth experiences are associated with psychological impairments. This study aimed to estimate the prevalence of childbirth-related post-traumatic stress symptoms and its obstetric and perinatal risk factors among a sample of Iranian women.MethodsThis was a cross-sectional study carried out in Bushehr, Iran during a 3-months period from July to September 2009. Data were collected from all women attending eleven healthcare centers for postnatal care 6 to 8 weeks after childbirth. Those who had a traumatic delivery were identified and entered into the study. In order to assess childbirth-related post-traumatic stress, the Post-traumatic Symptom Scale-Interview (PSS-I) was administered. Data on demographic, obstetric and perinatal characteristics also were collected. Multivariate logistic regression was performed to examine the association between childbirth-related post-traumatic stress and demographic and obstetric and perinatal variables.ResultsIn all, 400 women were initially evaluated. Of these, 218 women (54.5%) had a traumatic delivery and overall, 80 women (20%) were found to be suffering from post-partum post-traumatic stress disorder (PTSD). Multiple logistic regression analysis revealed that post-partum PTSD was associated with educational level, gestational age at delivery, number of prenatal care visits, pregnancy complications, pregnancy intervals, labor duration, and mode of delivery.ConclusionsThe findings indicated that the prevalence of traumatic birth experiences and post-partum PTSD were relatively high among Iranian women. The findings also indicated that obstetric and perinatal variables were independently the most significant contributing factors to women’s post-partum PTSD. It seems that a better perinatal care and supportive childbirth might help to reduce the burden of post-partum PTSD among this population.
Urinary levels of Hepatocarcinoma-intestine-pancreas/Pancreatitis-associated protein as a diagnostic biomarker in patients with bladder cancer
Authors: Nitta Yujiro , Konishi Hiroyuki , Makino Tetsuya , Tanaka Tomoaki , Kawashima Hidenori , Iovanna Juan L , Nakatani Tatsuya , Kiyama Hiroshi 
Published: September 2012

Abstract

Background
To assess the possibility of hepatocarcinoma-intestine-pancreas/pancreatitis-associated protein (HIP/PAP) as a biological marker for detecting Bladder cancer (BCa), we examined the expression of HIP/PAP in both BCa specimens and BCa cell lines and measured HIP/PAP levels in urine from patients with BCa.

Methods
HIP/PAP expression in BCa samples was evaluated by western blot analysis, and urinary levels of HIP/PAP in patients with BCa were measured by enzyme-linked immunosorbent assay. Urine samples were collected from 10 healthy volunteers and 109 with benign urological disorders as controls, and from 101 patients who were diagnosed with BCa.

Results
HIP/PAP was highly expressed in BCa samples as compared with control bladder. Urinary HIP/PAP concentrations were significantly higher in BCa patients than in controls (median value; 3.184 pg/mL vs. 55.200 pg/mL, P <0.0001, by Mann–Whitney U test). Urinary HIP/PAP levels in BCa patients correlated positively with pathological T stages and progression-risk groups among non-muscle invasive BCa (P = 0.0008, by Kruskal-Wallis test). Regarding the recurrence-risk classifications of non-muscle invasive BCa, the urinary levels of HIP/PAP were significantly higher in the intermediate than in the low risk group (P = 0.0002, by Mann–Whitney U test). Based on a cut-off of 8.5 pg/mL, the ability of urinary HIP/PAP levels to detect BCa had a sensitivity of 80.2%, specificity of 78.2%, positive predictive value (PPV) of 75.7%, and negative predictive value (NPV) of 82.3%.

Conclusions
HIP/PAP was abundantly expressed in BCa, and the urinary levels of HIP/PAP could be a novel and potent biomarker for detection of BCa, and also for predicting the risks of recurrence- and progression-risk of non-muscle invasive BCa. A large scale study will be needed to establish the usefulness of this biomarker.
Quality assessment and anti-obesity activity of Stellaria media (Linn.) Vill
Authors: Rani Neerja , Vasudeva Neeru , Sharma Surendra Kumar 
Published: September 2012

AbstractBackgroundObesity is recognized as a social problem, associated with serious health risks and increased mortality. Numerous trials have been conducted to find and develop new anti-obesity drugs through herbal sources to minimize side effects associated with the present anti-obesity drugs. The present study was designed to evaluate the quality control parameters, quantitative phytochemical analysis (total phenolic, total flavonoids and total saponin content), and the anti-obesity effect of lyophilized juice (LJ) ofStellaria media(Linn.) Vill. by employingin vitroandin vivomodels.MethodsIn vitrostudies were performed to evaluate the inhibitory activity of LJ on pancreatic amylase and lipase. Thein vivopancreatic lipase activity was evaluated by measurement of plasma triacylglycerol levels after oral administration of lipid emulsion to swiss albino mice. Furthermore, the anti-obesity effect of LJ was assessed at two doses, 400 mg/kg and 900 mg/kg body weight in mice fed a high-fat-diet with or without LJ for 6 weeks.ResultsThe LJ inhibited pancreatic amylase and lipase activityin vitroand elevated plasma triacylglycerol level in mice. LJ suppressed the increase in body weight, retroperitoneal adipose tissue, liver weights and serum parametersviz.,total cholesterol, total triglyceride, LDL-cholesterol level at the dose of 900 mg/kg body weight of the mice fed with high fat diet. The total phenolic, flavonoid and saponin contents were found to be 0.26 mg/g, 1.4 mg/g and 1.19 μg/g respectively of LJ.ConclusionThe anti-obesity effects of LJ in high-fat-diet fed mice may be partly mediated through delaying the intestinal absorption of dietary fat and carbohydrate by inhibiting digestive enzymes.
Assessing cardiovascular risk in regional areas: the Healthy Hearts – Beyond City Limits program
Authors: Carrington Melinda J , Jennings Garry L , Clark Robyn A , Stewart Simon 
Published: September 2012

Abstract

Background
Cardiovascular disease (CVD) is more prevalent in regional and remote Australia compared to metropolitan areas. The aim of Healthy Hearts was to determine age and sex specific CVD risk factor levels and the potential value of national risk clinics.

Methods
Healthy Hearts was an observational research study conducted in four purposefully selected higher risk communities in regional Victoria, Australia. The main outcome measures were the proportion of participants with CVD risk factors with group comparisons to determine the adjusted likelihood of elevated risk factor levels. Trained personnel used a standardized protocol over four weeks per community to measure CVD risk factor levels, estimate absolute CVD risk and provide feedback and advice.

Results
A total of 2125 self-selected participants were assessed (mean age 58 ± 15 years, 57% women). Overall, CVD risk factors were highly prevalent. More men than women had ≥ 2 modifiable CVD risk factors (76% vs. 68%, p < .001), pre-existing CVD (20 vs. 15%, p < .01) and a major ECG abnormality requiring follow-up (15% vs. 7%, p < .001) . Less men reported depressive symptoms compared to women (28% vs. 22%, p < .01). A higher proportion of women were obese (adjusted OR 1.36, 95% CI 1.13 to 1.63), and physically inactive (adjusted OR 1.32, 95% CI 1.07 to 1.63).

Conclusions
High CVD risk factor levels were confirmed for regional Victoria. Close engagement with individuals and communities provides scope for the application of regional risk management clinics to reduce the burden of CVD risk in regional Australia.
Changes in the expression of proteins associated with aerobic glycolysis and cell migration are involved in tumorigenic ability of two glioma cell lines
Authors: Ramão Anelisa , Gimenez Marcela , Laure Helen Julie , Izumi Clarice , Vida Rodrigo Cesar dos Santos , Oba-Shinjo Sueli , Marie Suely Kazue Nagahashi , Rosa Jose Cesar 
Published: September 2012

AbstractBackgroundThe most frequent and malignant brain cancer is glioblastoma multiforme (GBM). In gliomas, tumor progression and poor prognosis are associated with the tumorigenic ability of the cells. U87MG cells (wild-type p53) are known to be tumorigenic in nude mice, but T98G cells (mutant p53) are not tumorigenic. We investigated the proteomic profiling of these two cell lines in order to gain new insights into the mechanisms that may be involved in tumorigenesis.ResultsWe found 24 differentially expressed proteins between T98G and U87MG cells. Gene Ontology supports the notion that over-representation of differentially expressed proteins is involved in glycolysis, cell migration and stress oxidative response. Among those associated with the glycolysis pathway, TPIS and LDHB are up-regulated in U87MG cells. Measurement of glucose consumption and lactate production suggests that glycolysis is more effective in U87MG cells. On the other hand, G6PD expression was 3-fold higher in T98G cells and this may indicate a shift to the pentose-phosphate pathway. Moreover, GRP78 expression was also three-fold higher in T98G than in U87MG cells. Under thapsigargin treatment both cell lines showed increased GRP78 expression and the effect of this agent was inversely correlated to cell migration. Quantitative RT-PCR and immunohistochemistry of GRP78 in patient samples indicated a higher level of expression of GRP78 in grade IV tumors compared to grade I and non-neoplastic tissues, respectively.ConclusionsTaken together, these results suggest an important role of proteins involved in key functions such as glycolysis and cell migration that may explain the difference in tumorigenic ability between these two glioma cell lines and that may be extrapolated to the differential aggressiveness of glioma tumors.
Successful treatment with the mTOR inhibitor everolimus in a patient with Perivascular epithelioid cell tumor
Authors: Gennatas Constantine , Michalaki Vasiliki , Vasilatou Kairi Paraskevi , Kondi-Paphiti Agathi , Voros Dionysios 
Published: September 2012

Abstract
Perivascular epithelioid cell tumor (PEComa) is an extremely rare neoplasm that appears to arise most commonly at visceral (especially gastrointestinal and uterine), retroperitoneal, and abdominopelvic sites. Malignant PEComas exist but are very rare. These tumors represent a family of mesenchymal neoplasms, mechanistically linked through activation of the mTOR signaling pathway. Metastatic PEComa is a rare form of sarcoma for which no effective therapy has been described previously and that has a uniformly fatal outcome. Although there is no known effective therapy, the molecular pathophysiology of aberrant mTOR signaling provides a scientific rationale to target this pathway therapeutically. The difficulty in determining optimal therapy, owing to the sparse literature available, led us to present this case. On this basis, we report a case of metastatic retroperitoneal PEComa treated with an oral mTOR inhibitor, with everolimus achieving significant clinical response.