bluuebunny/crossref_metadata_2025_split huggingface dataset:
Separation of the bacterial species, Escherichia coli, from mixed-species microbial communities for transcriptome analysis
Authors: Dai Dongjuan , Holder Diane , Raskin Lutgarde , Xi Chuanwu 
Published: March 2011

Abstract

Background
The study of bacterial species interactions in a mixed-species community can be facilitated by transcriptome analysis of one species in the community using cDNA microarray technology. However, current applications of microarrays are mostly limited to single species studies. The purpose of this study is to develop a method to separate one species, Escherichia coli as an example, from mixed-species communities for transcriptome analysis.

Results

E. coli cells were separated from a dual-species (E. coli and Stenotrophomonas maltophilia) community using immuno-magnetic separation (IMS). High recovery rates of E. coli were achieved. The purity of E. coli cells was as high as 95.0% separated from suspended mixtures consisting of 1.1 - 71.3% E. coli, and as high as 96.0% separated from biofilms with 8.1% E. coli cells. Biofilms were pre-dispersed into single-cell suspensions. The reagent RNAlater (Ambion, Austin, TX) was used during biofilm dispersion and IMS to preserve the transcriptome of E. coli. A microarray study and quantitative PCR confirmed that very few E. coli genes (only about eight out of 4,289 ORFs) exhibited a significant change in expression during dispersion and separation, indicating that transcriptional profiles of E. coli were well preserved.

Conclusions
A method based on immuno-magnetic separation (IMS) and application of RNAlater was developed to separate a bacterial species, E. coli as an example, from mixed-species communities while preserving its transcriptome. The method combined with cDNA microarray analysis should be very useful to study species interactions in mixed-species communities.
The role of Endobronchial ultrasound guided transbronchial needle aspiration (EBUS-TBNA) for qualitative diagnosis of mediastinal and hilar lymphadenopathy: a prospective analysis
Authors: Ye Ting , Hu Hong , Luo Xiaoyang , Chen Haiquan 
Published: March 2011

Abstract

Background
Recently EBUS-TBNA, which has a sensitivity of 94.6%, specificity of 100% and diagnostic accuracy rate of 96.3% as previously reported, has been widely used for patients with mediastinal and hilar lymphadenopathy or suspected lung cancer to get accurate diagnosis. The purpose of the current study was to evaluate the usefulness of EBUS-TBNA in obtaining cytological and histological diagnosis of mediastinal and hilar lymph nodes compared to the results obtained with conventional mediastinoscopy as previously reported, and to assess the relationship of diagnostic accuracy and number of passes and size of lymph nodes.

Methods
101 patients with mediastinal and hilar lymphadenopathy or suspected lung cancer in our institution were included in this prospective study. EBUS-TBNA was performed in all cases. The final diagnosis was confirmed by cytology, surgical results, and/or clinical follow-up for at least 6 months. Sensitivity, specificity, accuracy, and positive and negative predictive values were calculated using standard formulas.

Results
In 101 patients, EBUS-TBNA was successfully performed to obtain samples from 225 lymph nodes, 7 lung masses, 1 mediastinal mass and 2 esophageal masses. 63 malignant tumors and 38 benign diseases were confirmed. Epidermal growth factor receptor mutation was detected in 10 biopsy samples, and epidermal growth factor receptor mutation was detected in 4 cases. With respect to the correct diagnosis of mediastinal and hilar lymphadenopathy, EBUS-TBNA had a sensitivity of 95.08%, specificity of 100%, positive predictive value of 100%, negative predictive value of 93.02%, and overall accuracy of 97.02%. The relationship of diagnostic accuracy and number of lymph node passes or size of lymph nodes was both insignificant (p = 0.27; p = 0.23). The procedure was uneventful without complications.

Conclusions
EBUS-TBNA is an accurate and safe tool in diagnosis of mediastinal and hilar lymphadenopathy. It cannot completely replace mediastinoscopy, it may indeed reduce the number of mediastinoscopy procedures. In some cases, it can necessarily be the first-line procedure before mediastinoscopy.
Correlation of SHOX2 Gene Amplification and DNA Methylation in Lung Cancer Tumors
Authors: Schneider Katja U , Dietrich Dimo , Fleischhacker Michael , Leschber Gunda , Merk Johannes , Schäper Frank , Stapert Henk R , Vossenaar Erik R , Weickmann Sabine , Liebenberg Volker , Kneip Christoph , Seegebarth Anke , Erdogan Fikret , Rappold Gudrun , Schmidt Bernd 
Published: March 2011

Abstract

Background
DNA methylation in the SHOX2 locus was previously used to reliably detect lung cancer in a group of critical controls, including 'cytologically negative' samples with no visible tumor cell content, at a high specificity based on the analysis of bronchial lavage samples. This study aimed to investigate, if the methylation correlates with SHOX2 gene expression and/or copy number alterations. An amplification of the SHOX2 gene locus together with the observed tumor-specific hypermethylation might explain the good performance of this marker in bronchial lavage samples.

Methods

SHOX2 expression, gene copy number and DNA methylation were determined in lung tumor tissues and matched morphologically normal adjacent tissues (NAT) from 55 lung cancer patients. Quantitative HeavyMethyl (HM) real-time PCR was used to detect SHOX2 DNA methylation levels. SHOX2 expression was assayed with quantitative real-time PCR, and copy numbers alterations were measured with conventional real-time PCR and array CGH.

Results
A hypermethylation of the SHOX2 locus in tumor tissue as compared to the matched NAT from the same patient was detected in 96% of tumors from a group of 55 lung cancer patients. This correlated highly significantly with the frequent occurrence of copy number amplification (p < 0.0001), while the expression of the SHOX2 gene showed no difference.

Conclusions
Frequent gene amplification correlated with hypermethylation of the SHOX2 gene locus. This concerted effect qualifies SHOX2 DNA methylation as a biomarker for lung cancer diagnosis, especially when sensitive detection is needed, i.e. in bronchial lavage or blood samples.
Antifoam addition to shake flask cultures of recombinant Pichia pastoris increases yield
Authors: Routledge Sarah J , Hewitt Christopher J , Bora Nagamani , Bill Roslyn M 
Published: March 2011

AbstractBackgroundPichia pastorisis a widely-used host for recombinant protein production. Initial screening for both suitable clones and optimum culture conditions is typically carried out in multi-well plates. This is followed by up-scaling either to shake-flasks or continuously stirred tank bioreactors. A particular problem in these formats is foaming, which is commonly prevented by the addition of chemical antifoaming agents. Intriguingly, antifoams are often added without prior consideration of their effect on the yeast cells, the protein product or the influence on downstream processes such as protein purification. In this study we characterised, for the first time, the effects of five commonly-used antifoaming agents on the total amount of recombinant green fluorescent protein (GFP) secreted from shake-flask cultures of this industrially-relevant yeast.ResultsAddition of defined concentrations of Antifoam A (Sigma), Antifoam C (Sigma), J673A (Struktol), P2000 (Fluka) or SB2121 (Struktol) to shake-flask cultures ofP. pastorisincreased the total amount of recombinant GFP in the culture medium (the total yield) and in the case of P2000, SB2121 and J673A almost doubled it. When normalized to the culture density, the GFP specific yield (μg OD595-1) was only increased for Antifoam A, Antifoam C and J673A. Whilst none of the antifoams affected the growth rate of the cells, addition of P2000 or SB2121 was found to increase culture density. There was no correlation between total yield, specific yield or specific growth rate and the volumetric oxygen mass transfer coefficient (kLa) in the presence of antifoam. Moreover, the antifoams did not affect the dissolved oxygen concentration of the cultures. A comparison of the amount of GFP retained in the cell by flow cytometry with that in the culture medium by fluorimetry suggested that addition of Antifoam A, Antifoam C or J673A increased the specific yield of GFP by increasing the proportion secreted into the medium.ConclusionsWe show that addition of a range of antifoaming agents to shake flask cultures ofP. pastorisincreases the total yield of the recombinant protein being produced. This is not only a simple method to increase the amount of protein in the culture, but our study also provides insight into how antifoams interact with microbial cell factories. Two mechanisms are apparent: one group of antifoams (Antifoam A, Antifoam C and J673A) increases the specific yield of GFP by increasing the total amount of protein produced and secreted per cell, whilst the second (P2000 or SB2121) increases the total yield by increasing the density of the culture.
The duration of diarrhea and fever is associated with growth faltering in rural Malawian children aged 6-18 months
Authors: Weisz Ariana , Meuli Gus , Thakwalakwa Chrissie , Trehan Indi , Maleta Kenneth , Manary Mark 
Published: March 2011

Abstract
Nutrition support programs that only focus upon better complementary feeding remain an insufficient means of limiting growth faltering in vulnerable populations of children. To determine if symptoms of acute infections correlate with the incidence of growth faltering in rural Malawian children, the associations between fever, diarrhea, and cough with anthropometric measures of stunting, wasting, and underweight were investigated. Data were analyzed from a trial where 209 children were provided with adequate complementary food and followed fortnightly from 6-18 months of age. Linear mixed model analysis was used to test for associations. Diarrheal disease was inversely associated with changes in height-for-age Z-score (HAZ), mid-upper arm circumference Z-score (MUACZ), and weight-for-age Z-score (WAZ). Fever was also inversely associated with changes in MUACZ and WAZ. These results suggest that initiatives to reduce febrile and diarrheal diseases are needed in conjunction with improved complementary feeding to limit growth faltering in rural Malawi.
Kriged and modeled ambient air levels of benzene in an urban environment: an exposure assessment study
Authors: Whitworth Kristina W , Symanski Elaine , Lai Dejian , Coker Ann L 
Published: March 2011

Abstract

Background
There is increasing concern regarding the potential adverse health effects of air pollution, particularly hazardous air pollutants (HAPs). However, quantifying exposure to these pollutants is problematic.

Objective
Our goal was to explore the utility of kriging, a spatial interpolation method, for exposure assessment in epidemiologic studies of HAPs. We used benzene as an example and compared census tract-level kriged predictions to estimates obtained from the 1999 U.S. EPA National Air Toxics Assessment (NATA), Assessment System for Population Exposure Nationwide (ASPEN) model.

Methods
Kriged predictions were generated for 649 census tracts in Harris County, Texas using estimates of annual benzene air concentrations from 17 monitoring sites operating in Harris and surrounding counties from 1998 to 2000. Year 1999 ASPEN modeled estimates were also obtained for each census tract. Spearman rank correlation analyses were performed on the modeled and kriged benzene levels. Weighted kappa statistics were computed to assess agreement between discretized kriged and modeled estimates of ambient air levels of benzene.

Results
There was modest correlation between the predicted and modeled values across census tracts. Overall, 56.2%, 40.7%, 31.5% and 28.2% of census tracts were classified as having 'low', 'medium-low', 'medium-high' and 'high' ambient air levels of benzene, respectively, comparing predicted and modeled benzene levels. The weighted kappa statistic was 0.26 (95% confidence interval (CI) = 0.20, 0.31), indicating poor agreement between the two methods.

Conclusions
There was a lack of concordance between predicted and modeled ambient air levels of benzene. Applying methods of spatial interpolation for assessing exposure to ambient air pollutants in health effect studies is hindered by the placement and number of existing stationary monitors collecting HAP data. Routine monitoring needs to be expanded if we are to use these data to better assess environmental health risks in the future.
Generation of novel cationic antimicrobial peptides from natural non-antimicrobial sequences by acid-amide substitution
Authors: Ueno Satoshi , Minaba Masaomi , Nishiuchi Yuji , Taichi Misako , Tamada Yasushi , Yamazaki Toshimasa , Kato Yusuke 
Published: March 2011

Abstract

Background
Cationic antimicrobial peptides (CAMPs) are well recognized to be promising as novel antimicrobial and antitumor agents. To obtain novel skeletons of CAMPs, we propose a simple strategy using acid-amide substitution (i.e. Glu→Gln, Asp→Asn) to confer net positive charge to natural non-antimicrobial sequences that have structures distinct from known CAMPs. The potential of this strategy was verified by a trial study.

Methods
The pro-regions of nematode cecropin P1-P3 (P1P-P3P) were selected as parent sequences. P1P-P3P and their acid-amide-substituted mutants (NP1P-NP3P) were chemically synthesized. Bactericidal and membrane-disruptive activities of these peptides were evaluated. Conformational changes were estimated from far-ultraviolet circular dichroism (CD) spectra.

Results
NP1P-NP3P acquired potent bactericidal activities via membrane-disruption although P1P-P3P were not antimicrobial. Far-ultraviolet CD spectra of NP1P-NP3P were similar to those of their parent peptides P1P-P3P, suggesting that NP1P-NP3P acquire microbicidal activity without remarkable conformational changes. NP1P-NP3P killed bacteria in almost parallel fashion with their membrane-disruptive activities, suggesting that the mode of action of those peptides was membrane-disruption. Interestingly, membrane-disruptive activity of NP1P-NP3P were highly diversified against acidic liposomes, indicating that the acid-amide-substituted nematode cecropin pro-region was expected to be a unique and promising skeleton for novel synthetic CAMPs with diversified membrane-discriminative properties.

Conclusions
The acid-amide substitution successfully generated some novel CAMPs in our trial study. These novel CAMPs were derived from natural non-antimicrobial sequences, and their sequences were completely distinct from any categories of known CAMPs, suggesting that such mutated natural sequences could be a promising source of novel skeletons of CAMPs.
Post - prandial rise of microvesicles in peripheral blood of healthy human donors
Authors: Šuštar Vid , Bedina-Zavec Apolonija , Štukelj Roman , Frank Mojca , Ogorevc Eva , Janša Rado , Mam Keriya , Veranič Peter , Kralj-Iglič Veronika 
Published: March 2011

Abstract

Background
Microvesicles isolated from body fluids are membrane - enclosed fragments of cell interior which carry information on the status of the organism. It is yet unclear how metabolism affects the number and composition of microvesicles in isolates from the peripheral blood.

Aim
To study the post - prandial effect on microvesicles in isolates from the peripheral blood of 21 healthy donors, in relation to blood cholesterol and blood glucose concentrations.

Results
The average number of microvesicles in the isolates increased 5 hours post - prandially by 52%; the increase was statistically significant (p = 0.01) with the power P = 0.68, while the average total blood cholesterol concentration, average low density lipoprotein cholesterol concentration (LDL-C) and average high density lipoprotein cholesterol concentration (HDL-C) all remained within 2% of their fasting values. We found an 11% increase in triglycerides (p = 0.12) and a 6% decrease in blood glucose (p < 0.01, P = 0.74). The post - prandial number of microvesicles negatively correlated with the post - fasting total cholesterol concentration (r = - 0.46, p = 0.035) while the difference in the number of microvesicles in the isolates between post - prandial and post - fasting states negatively correlated with the respective difference in blood glucose concentration (r = - 0.39, p = 0.05).

Conclusions
In a population of healthy human subjects the number of microvesicles in isolates from peripheral blood increased in the post - prandial state. The increase in the number of microvesicles was affected by the fasting concentration of cholesterol and correlated with the decrease in blood glucose.
Proteomics: a subcellular look at spermatozoa
Authors: du Plessis Stefan S , Kashou Anthony H , Benjamin David J , Yadav Satya P , Agarwal Ashok 
Published: March 2011

Abstract

Background
Male-factor infertility presents a vexing problem for many reproductively active couples. Many studies have focused on abnormal sperm parameters. Recent advances in proteomic techniques, especially in mass spectrometry, have aided in the study of sperm and more specifically, sperm proteins. The aim of this study was to review the current literature on the various proteomic techniques, and their usefulness in diagnosing sperm dysfunction and potential applications in the clinical setting.

Methods
Review of PubMed database. Key words: spermatozoa, proteomics, protein, proteome, 2D-PAGE, mass spectrometry.

Results
Recently employed proteomic methods, such as two-dimensional polyacrylamide gel electrophoresis, mass spectrometry, and differential in gel electrophoresis, have identified numerous sperm-specific proteins. They also have provided a further understanding of protein function involved in sperm processes and for the differentiation between normal and abnormal states. In addition, studies on the sperm proteome have demonstrated the importance of post-translational modifications, and their ability to bring about physiological changes in sperm function. No longer do researchers believe that in order for them to elucidate the biochemical functions of genes, mere knowledge of the human genome sequence is sufficient. Moreover, a greater understanding of the physiological function of every protein in the tissue-specific proteome is essential in order to unravel the biological display of the human genome.

Conclusion
Recent advances in proteomic techniques have provided insight into sperm function and dysfunction. Several multidimensional separation techniques can be utilized to identify and characterize spermatozoa. Future developments in bioinformatics can further assist researchers in understanding the vast amount of data collected in proteomic studies. Moreover, such advances in proteomics may help to decipher metabolites which can act as biomarkers in the detection of sperm impairments and to potentially develop treatment for infertile couples.
Further comprehensive studies on sperm-specific proteome, mechanisms of protein function and its proteolytic regulation, biomarkers and functional pathways, such as oxidative-stress induced mechanisms, will provide better insight into physiological functions of the spermatozoa. Large-scale proteomic studies using purified protein assays will eventually lead to the development of novel biomarkers that may allow for detection of disease states, genetic abnormalities, and risk factors for male infertility. Ultimately, these biomarkers will allow for a better diagnosis of sperm dysfunction and aid in drug development.
Double suicide genes driven by kinase domain insert containing receptor promoter selectively kill human lung cancer cells
Authors: Ma Junrong , Li Mi , Mei Longyong , Zhou Qinghua , Liu Lunxu , Yu Xijie , Che Guowei 
Published: March 2011

Abstract

Background
To investigate the selective killing efficacy of the double suicide genes driven by KDR promoter.

Materials and methods
A double suicide gene system with the KDR promoter, pcDNA3-KDRp-CDglyTK, was constructed and transfected into lung cancer cell lines L9981 and NL9980, and human hepatocellular carcinoma cell line HepG2. The efficiency and specificity of the double suicide gene system were assayed by in vitro cellular proliferation and apoptosis, as well as in vivo xenograft studies.

Results
The transgenic CD and TK genes were only expressed in L9981 and NL9980 but not in HepG2 cells. Pre-treating transfected cells with 5-Fc and GCV significantly reduced proliferation, enhanced apoptosis in L9981 and NL9980 but not in HepG2 cells. The tumor formed by L9981 and NL9980 cells with the double suicide gene system was much smaller in vivo.

Conclusion
Tumor targeted expression of CDglyTK gene driven by KDR promotor represents a novel strategy for effective gene therapy of tumor with intrinsic KDR.
MiRNA-205 modulates cellular invasion and migration via regulating zinc finger E-box binding homeobox 2 expression in esophageal squamous cell carcinoma cells
Authors: Matsushima Kayoko , Isomoto Hajime , Yamaguchi Naoyuki , Inoue Naoki , Machida Haruhisa , Nakayama Toshiyuki , Hayashi Tomayoshi , Kunizaki Masaki , Hidaka Shigekazu , Nagayasu Takeshi , Nakashima Masahiro , Ujifuku Kenta , Mitsutake Norisato , Ohtsuru Akira , Yamashita Shunichi , Korpal Manav , Kang Yibin , Gregory Philip A , Goodall Gregory J , Kohno Shigeru , Nakao Kazuhiko 
Published: March 2011

Abstract

Background
Esophageal squamous cell carcinoma (ESCC) is often diagnosed at later stages until they are incurable. MicroRNA (miR) is a small, non-coding RNA that negatively regulates gene expression mainly via translational repression. Accumulating evidence indicates that deregulation of miR is associated with human malignancies including ESCC. The aim of this study was to identify miR that could be specifically expressed and exert distinct biological actions in ESCC.

Methods
Total RNA was extracted from ESCC cell lines, OE21 and TE10, and a non-malignant human esophageal squamous cell line, Het-1A, and subjected to microarray analysis. Expression levels of miR that showed significant differences between the 2 ESCC and Het-1A cells based on the comprehensive analysis were analyzed by the quantitative reverse transcriptase (RT)-PCR method. Then, functional analyses, including cellular proliferation, apoptosis and Matrigel invasion and the wound healing assay, for the specific miR were conducted. Using ESCC tumor samples and paired surrounding non-cancerous tissue obtained endoscopically, the association with histopathological differentiation was examined with quantitative RT-PCR.

Results
Based on the miR microarray analysis, there were 14 miRs that showed significant differences (more than 2-fold) in expression between the 2 ESCC cells and non-malignant Het-1A. Among the significantly altered miRs, miR-205 expression levels were exclusively higher in 5 ESCC cell lines examined than any other types of malignant cell lines and Het-1A. Thus, miR-205 could be a specific miR in ESCC. Modulation of miR-205 expression by transfection with its precursor or anti-miR-205 inhibitor did not affect ESCC cell proliferation and apoptosis, but miR-205 was found to be involved in cell invasion and migration. Western blot revealed that knockdown of miR-205 expression in ESCC cells substantially enhanced expression of zinc finger E-box binding homeobox 2, accompanied by reduction of E-cadherin, a regulator of epithelial mesenchymal transition. The miR-205 expression levels were not associated with histological differentiation of human ESCC.

Conclusions
These results imply that miR-205 is an ESCC-specific miR that exerts tumor-suppressive activities with EMT inhibition by targeting ZEB2.