bluuebunny/crossref_metadata_2025_split huggingface dataset:
New insights on the biology of swine respiratory tract mycoplasmas from a comparative genome analysis
Authors: Siqueira Franciele Maboni , Thompson Claudia Elizabeth , Virginio Veridiana Gomes , Gonchoroski Taylor , Reolon Luciano , Almeida Luiz Gonzaga , da Fonsêca Marbella Maria , de Souza Rangel , Prosdocimi Francisco , Schrank Irene Silveira , Ferreira Henrique Bunselmeyer , de Vasconcelos Ana Tereza Ribeiro , Zaha Arnaldo 
Published: March 2013

AbstractBackgroundMycoplasma hyopneumoniae,Mycoplasma flocculareandMycoplasma hyorhinislive in swine respiratory tracts.M. flocculare, a commensal bacterium, is genetically closely related toM. hyopneumoniae, the causative agent of enzootic porcine pneumonia.M. hyorhinisis also pathogenic, causing polyserositis and arthritis. In this work, we present the genome sequences ofM. flocculareandM. hyopneumoniaestrain 7422, and we compare these genomes with the genomes of otherM. hyoponeumoniaestrain and to the aM. hyorhinisgenome. These analyses were performed to identify possible characteristics that may help to explain the different behaviors of these species in swine respiratory tracts.ResultsThe overall genome organization of three species was analyzed, revealing that the ORF clusters (OCs) differ considerably and that inversions and rearrangements are common. AlthoughM. flocculareandM. hyopneumoniaedisplay a high degree of similarity with respect to the gene content, only some genomic regions display considerable synteny. Genes encoding proteins that may be involved in host-cell adhesion inM. hyopneumoniaeandM. floccularedisplay differences in genomic structure and organization. Some genes encoding adhesins of the P97 family are absent inM. flocculareand some contain sequence differences or lack of domains that are considered to be important for adhesion to host cells. The phylogenetic relationship of the three species was confirmed by a phylogenomic approach. The set of genes involved in metabolism, especially in the uptake of precursors for nucleic acids synthesis and nucleotide metabolism, display some differences in copy number and the presence/absence in the three species.ConclusionsThe comparative analyses of three mycoplasma species that inhabit the swine respiratory tract facilitated the identification of some characteristics that may be related to their different behaviors.M. hyopneumoniaeandM. floccularedisplay many differences that may help to explain why one species is pathogenic and the other is considered to be commensal. However, it was not possible to identify specific virulence determinant factors that could explain the differences in the pathogenicity of the analyzed species. TheM. hyorhinisgenome contains differences in some components involved in metabolism and evasion of the host’s immune system that may contribute to its growth aggressiveness. Several horizontal gene transfer events were identified. The phylogenomic analysis placesM. hyopneumoniae, M. flocculareandM. hyorhinisin the hyopneumoniae clade.
Deep sequencing for de novo construction of a marine fish (Sparus aurata)transcriptome database with a large coverage of protein-coding transcripts
Authors: Calduch-Giner Josep A , Bermejo-Nogales Azucena , Benedito-Palos Laura , Estensoro Itziar , Ballester-Lozano Gabriel , Sitjà-Bobadilla Ariadna , Pérez-Sánchez Jaume 
Published: March 2013

Abstract

Background
The gilthead sea bream (Sparus aurata) is the main fish species cultured in the Mediterranean area and constitutes an interesting model of research. Nevertheless, transcriptomic and genomic data are still scarce for this highly valuable species. A transcriptome database was constructed by de novo assembly of gilthead sea bream sequences derived from public repositories of mRNA and collections of expressed sequence tags together with new high-quality reads from five cDNA 454 normalized libraries of skeletal muscle (1), intestine (1), head kidney (2) and blood (1).

Results
Sequencing of the new 454 normalized libraries produced 2,945,914 high-quality reads and the de novo global assembly yielded 125,263 unique sequences with an average length of 727 nt. Blast analysis directed to protein and nucleotide databases annotated 63,880 sequences encoding for 21,384 gene descriptions, that were curated for redundancies and frameshifting at the homopolymer regions of open reading frames, and hosted at http://www.nutrigroup-iats.org/seabreamdb. Among the annotated gene descriptions, 16,177 were mapped in the Ingenuity Pathway Analysis (IPA) database, and 10,899 were eligible for functional analysis with a representation in 341 out of 372 IPA canonical pathways. The high representation of randomly selected stickleback transcripts by Blast search in the nucleotide gilthead sea bream database evidenced its high coverage of protein-coding transcripts.

Conclusions
The newly assembled gilthead sea bream transcriptome represents a progress in genomic resources for this species, as it probably contains more than 75% of actively transcribed genes, constituting a valuable tool to assist studies on functional genomics and future genome projects.
Characterization of Halomonassp. ZM3 isolated from the Zelazny Most post-flotation waste reservoir, with a special focus on its mobile DNA
Authors: Dziewit Lukasz , Pyzik Adam , Matlakowska Renata , Baj Jadwiga , Szuplewska Magdalena , Bartosik Dariusz 
Published: March 2013

Abstract

Background

Halomonas sp. ZM3 was isolated from Zelazny Most post-flotation mineral waste repository (Poland), which is highly contaminated with heavy metals and various organic compounds. Mobile DNA of the strain (i.e. plasmids and transposons) were analyzed in order to identify genetic information enabling adaptation of the bacterium to the harsh environmental conditions.

Results
The analysis revealed that ZM3 carries plasmid pZM3H1 (31,370 bp), whose replication system may be considered as an archetype of a novel subgroup of IncU-like replicons. pZM3H1 is a narrow host range, mobilizable plasmid (encodes a relaxase of the MOBV family) containing mercury resistance operon (mer) and czcD genes (mediate resistance to zinc and cobalt), which are part of a large truncated Tn3 family transposon. Further analysis demonstrated that the phenotypes determined by the pZM3H1 resistance cassette are highly dependent on the host strain. In another strand of the study, the trap plasmid pMAT1 was employed to identify functional transposable elements of Halomonas sp. ZM3. Using the sacB positive selection strategy two insertion sequences were identified: ISHsp1 - representing IS5 group of IS5 family and ISHsp2 - a distinct member of the IS630 family.

Conclusions
This study provides the first detailed description of mobile DNA in a member of the family Halomonadaceae. The identified IncU plasmid pZM3H1 confers resistance phenotypes enabling adaptation of the host strain to the Zelazny Most environment. The extended comparative analysis has shed light on the distribution of related IncU plasmids among bacteria, which, in many cases, reflects the frequency and direction of horizontal gene transfer events. Our results also identify plasmid-encoded modules, which may form the basis of novel shuttle vectors, specific for this group of halophilic bacteria.
Homo-dimerization and ligand binding by the leucine-rich repeat domain at RHG1/RFS2 underlying resistance to two soybean pathogens
Authors: Afzal Ahmed J , Srour Ali , Goil Abhishek , Vasudaven Sheeja , Liu Tianyun , Samudrala Ram , Dogra Navneet , Kohli Punit , Malakar Ayan , Lightfoot David A 
Published: March 2013

Abstract

Background
The protein encoded by GmRLK18-1 (Glyma_18_02680 on chromosome 18) was a receptor like kinase (RLK) encoded within the soybean (Glycine max L. Merr.) Rhg1/Rfs2 locus. The locus underlies resistance to the soybean cyst nematode (SCN) Heterodera glycines (I.) and causal agent of sudden death syndrome (SDS) Fusarium virguliforme (Aoki). Previously the leucine rich repeat (LRR) domain was expressed in Escherichia coli.

Results
The aims here were to evaluate the LRRs ability to; homo-dimerize; bind larger proteins; and bind to small peptides. Western analysis suggested homo-dimers could form after protein extraction from roots. The purified LRR domain, from residue 131–485, was seen to form a mixture of monomers and homo-dimers in vitro. Cross-linking experiments in vitro showed the H274N region was close (<11.1 A) to the highly conserved cysteine residue C196 on the second homo-dimer subunit. Binding constants of 20–142 nM for peptides found in plant and nematode secretions were found. Effects on plant phenotypes including wilting, stem bending and resistance to infection by SCN were observed when roots were treated with 50 pM of the peptides. Far-Western analyses followed by MS showed methionine synthase and cyclophilin bound strongly to the LRR domain. A second LRR from GmRLK08-1 (Glyma_08_g11350) did not show these strong interactions.

Conclusions
The LRR domain of the GmRLK18-1 protein formed both a monomer and a homo-dimer. The LRR domain bound avidly to 4 different CLE peptides, a cyclophilin and a methionine synthase. The CLE peptides GmTGIF, GmCLE34, GmCLE3 and HgCLE were previously reported to be involved in root growth inhibition but here GmTGIF and HgCLE were shown to alter stem morphology and resistance to SCN. One of several models from homology and ab-initio modeling was partially validated by cross-linking. The effect of the 3 amino acid replacements present among RLK allotypes, A87V, Q115K and H274N were predicted to alter domain stability and function. Therefore, the LRR domain of GmRLK18-1 might underlie both root development and disease resistance in soybean and provide an avenue to develop new variants and ligands that might promote reduced losses to SCN.
Augmentation index and aortic stiffness in bicuspid aortic valve patients with non-dilated proximal aortas
Authors: Warner Patrick J , Al-Quthami Adeeb , Brooks Erica L , Kelley-Hedgepeth Alyson , Patvardhan Eshan , Kuvin Jeffrey T , Heffernan Kevin S , Huggins Gordon S 
Published: March 2013

Abstract

Background
We compared aortic stiffness, aortic impedance and pressure from wave reflections in the setting of bicuspid aortic valve (BAV) to the tricuspid aortic valve (TAV) in the absence of proximal aortic dilation. We hypothesized BAV is associated with abnormal arterial stiffness.

Methods
Ten BAV subjects (47 ± 4 years, 6 male) and 13 TAV subjects (46 ± 4 years, 10 male) without significant aortic valve disease were prospectively recruited. Characteristic impedance (Zc) was derived from echocardiographic images and pulse wave Doppler of the left ventricular outflow tract. Applanation tonometry was performed to obtain pulse wave velocity (PWV) at several sites as measures of arterial stiffness and augmentation index (AIx) as a measure of wave reflection.

Results
There were no significant differences between BAV and TAV subjects with regard to heart rate or blood pressure. Zc was similar between BAV and TAV subjects (p=0.25) as was carotid-femoral pulse wave velocity (cf-PWV) and carotid-radial PWV (cr-PWV) between BAV and TAV subjects (p=0.99). Carotid AIx was significantly higher in BAV patients compared with TAV patients (14.3 ± 4.18% versus -3.02 ± 3.96%, p=0.007).

Conclusions
Aortic stiffness and impedance is similar between subjects with BAV and TAV with normal aortic dimensions. The significantly higher carotid AIx in BAV, a proxy of increased pressure from wave reflections, may reflect abnormal vascular function distal to the aorta.
A case–control study on the association between bladder cancer and prior bladder calculus
Authors: Chung Shiu-Dong , Tsai Ming-Chieh , Lin Ching-Chun , Lin Herng-Ching 
Published: March 2013

Abstract

Background
Bladder calculus is associated with chronic irritation and inflammation. As there is substantial documentation that inflammation can play a direct role in carcinogenesis, to date the relationship between stone formation and bladder cancer (BC) remains unclear. This study aimed to examine the association between BC and prior bladder calculus using a population-based dataset.

Methods
This case–control study included 2,086 cases who had received their first-time diagnosis of BC between 2001 and 2009 and 10,430 randomly selected controls without BC. Conditional logistic regressions were employed to explore the association between BC and having been previously diagnosed with bladder calculus.

Results
Of the sampled subjects, bladder calculus was found in 71 (3.4%) cases and 105 (1.1%) controls. Conditional logistic regression analysis revealed that the odds ratio (OR) of having been diagnosed with bladder calculus before the index date for cases was 3.42 (95% CI = 2.48-4.72) when compared with controls after adjusting for monthly income, geographic region, hypertension, diabetes, coronary heart disease, and renal disease, tobacco use disorder, obesity, alcohol abuse, and schistosomiasis, bladder outlet obstruction, and urinary tract infection. We further analyzed according to sex and found that among males, the OR of having been previously diagnosed with bladder calculus for cases was 3.45 (95% CI = 2.39-4.99) that of controls. Among females, the OR was 3.05 (95% CI = 1.53-6.08) that of controls.

Conclusions
These results add to the evidence surrounding the conflicting reports regarding the association between BC and prior bladder calculus and highlight a potential target population for bladder cancer screening.
Transcriptional effects of 1,25 dihydroxyvitamin D3physiological and supra-physiological concentrations in breast cancer organotypic culture
Authors: Milani Cintia , Katayama Maria Lucia Hirata , de Lyra Eduardo Carneiro , Welsh JoEllen , Campos Laura Tojeiro , Brentani M Mitzi , Maciel Maria do Socorro , Roela Rosimeire Aparecida , del Valle Paulo Roberto , Góes João Carlos Guedes Sampaio , Nonogaki Suely , Tamura Rodrigo Esaki , Folgueira Maria Aparecida Azevedo Koike 
Published: March 2013

Abstract

Background
Vitamin D transcriptional effects were linked to tumor growth control, however, the hormone targets were determined in cell cultures exposed to supra physiological concentrations of 1,25(OH)2D3 (50-100nM). Our aim was to evaluate the transcriptional effects of 1,25(OH)2D3 in a more physiological model of breast cancer, consisting of fresh tumor slices exposed to 1,25(OH)2D3 at concentrations that can be attained in vivo.

Methods
Tumor samples from post-menopausal breast cancer patients were sliced and cultured for 24 hours with or without 1,25(OH)2D3 0.5nM or 100nM. Gene expression was analyzed by microarray (SAM paired analysis, FDR≤0.1) or RT-qPCR (p≤0.05, Friedman/Wilcoxon test). Expression of candidate genes was then evaluated in mammary epithelial/breast cancer lineages and cancer associated fibroblasts (CAFs), exposed or not to 1,25(OH)2D3 0.5nM, using RT-qPCR, western blot or immunocytochemistry.

Results
1,25(OH)2D3 0.5nM or 100nM effects were evaluated in five tumor samples by microarray and seven and 136 genes, respectively, were up-regulated. There was an enrichment of genes containing transcription factor binding sites for the vitamin D receptor (VDR) in samples exposed to 1,25(OH)2D3 near physiological concentration. Genes up-modulated by both 1,25(OH)2D3 concentrations were CYP24A1, DPP4, CA2, EFTUD1, TKTL1, KCNK3. Expression of candidate genes was subsequently evaluated in another 16 samples by RT-qPCR and up-regulation of CYP24A1, DPP4 and CA2 by 1,25(OH)2D3 was confirmed. To evaluate whether the transcripitonal targets of 1,25(OH)2D3 0.5nM were restricted to the epithelial or stromal compartments, gene expression was examined in HB4A, C5.4, SKBR3, MDA-MB231, MCF-7 lineages and CAFs, using RT-qPCR. In epithelial cells, there was a clear induction of CYP24A1, CA2, CD14 and IL1RL1. In fibroblasts, in addition to CYP24A1 induction, there was a trend towards up-regulation of CA2, IL1RL1, and DPP4. A higher protein expression of CD14 in epithelial cells and CA2 and DPP4 in CAFs exposed to 1,25(OH)2D3 0.5nM was detected.

Conclusions
In breast cancer specimens a short period of 1,25(OH)2D3 exposure at near physiological concentration modestly activates the hormone transcriptional pathway. Induction of CYP24A1, CA2, DPP4, IL1RL1 expression appears to reflect 1,25(OH)2D3 effects in epithelial as well as stromal cells, however, induction of CD14 expression is likely restricted to the epithelial compartment.
Health and development of ART conceived young adults: a study protocol for the follow-up of a cohort
Authors: Wilson Cate , Hammarberg Karin , Bruinsma Fiona , Berg Turi , Amor David , Sanson Ann , Fisher Jane R , Halliday Jane 
Published: March 2013

AbstractBackgroundUse of assisted reproductive technologies (ART) continues to increase, yet little is known of the longer term health of ART conceived offspring. There are some adverse birth outcomes associated with ART conception but the subsequent developmental trajectory is unclear. Undertaking research in this area is challenging due the sensitive nature of the topic and the time elapsed since birth of the ART conceived young adults. The aim of this report is to describe a research protocol, including design and ethical considerations, used to compare the physical and psychosocial health outcomes of ART conceived young adults aged 18-28 years, with their spontaneously conceived peers.DesignThis is a retrospective cohort study of mothers who conceived with ART in Victoria, Australia and gave birth to a singleton child between 1982 and 1992. A current address for each mother was located and a letter of invitation to participate in the study was sent by registered mail. Participation involved completing a telephone interview about her young adult offspring’s health and development from birth to the present. Mothers were also asked for consent for the researcher to contact their son/daughter to invite them to complete a structured telephone interview about their physical and psychosocial health. A comparison group of women living in Victoria, Australia, who had given birth to a spontaneously conceived singleton child between 1982 and 1992 was recruited from the general population using random digit dialling. Data were collected from them and their young adult offspring in the same way. Regression analyses were used to evaluate relationships between ART exposure and health status, including birth defects, chronic health conditions, hospital admissions, growth and sexual development. Psychosocial wellbeing, parental relationships and educational achievement were also assessed. Factors associated with the age of disclosure of ART conception were explored with the ART group only.DiscussionThe conceptualization and development of this large project posed a number of methodological, logistical and ethical challenges which we were able to overcome. The lessons we learnt can assist others who are investigating the long-term health implications for ART conceived offspring.
Comparative analysis of the transduction efficiency of five adeno associated virus serotypes and VSV-G pseudotype lentiviral vector in lung cancer cells
Authors: Chen Chiachen , Akerstrom Victoria , Baus James , Lan Michael S , Breslin Mary B 
Published: March 2013

Abstract

Background
Lung cancer is the leading cause of cancer-related deaths in the US. Recombinant vectors based on adeno-associated virus (AAV) and lentivirus are promising delivery tools for gene therapy due to low toxicity and long term expression. The efficiency of the gene delivery system is one of the most important factors directly related to the success of gene therapy.

Methods
We infected SCLC cell lines, SHP-77, DMS 53, NCI-H82, NCI-H69, NCI-H727, NCI-H1155, and NSCLC cell lines, NCI-H23, NCI-H661, and NCI-H460 with VSV-G pseudo-typed lentivirus or 5 AAV serotypes, AAV2/1, AAV2/2, AAV2/4, AAV2/5, and AAV2/8 expressing the CMV promoter mCherry or green fluorescent protein transgene (EGFP). The transduction efficiency was analyzed by fluorescent microscopy and flow cytometry.

Results
Of all the serotypes of AAV examined, AAV2/1 was the optimal serotype in most of the lung cancer cell lines except for NCI-H69 and NCI-H82. The highest transduction rate achieved with AAV2/1 was between 30–50% at MOI 100. Compared to all AAV serotypes, lentivirus had the highest transduction efficiency of over 50% at MOI 1. Even in NCI-H69 cells resistant to all AAV serotypes, lentivirus had a 10-40% transduction rate. To date, AAV2 is the most widely-used serotype to deliver a transgene. Our results showed the transduction efficiency of AAVs tested was AAV2/1 > AA2/5 = AAV2/2> > AAV2/4 and AAV2/8.

Conclusions
This study demonstrated that VSV-G pseudotyped lentivirus and AAV2/1 can mediate expression of a transgene for lung cancer gene therapy. Overall, our results showed that lentivirus is the best candidate to deliver a transgene into lung cancer cells for treatment.
Screening for colorectal cancer with FOBT, virtual colonoscopy and optical colonoscopy: study protocol for a randomized controlled trial in the Florence district (SAVE study)
Authors: Sali Lapo , Grazzini Grazia , Carozzi Francesca , Castiglione Guido , Falchini Massimo , Mallardi Beatrice , Mantellini Paola , Ventura Leonardo , Regge Daniele , Zappa Marco , Mascalchi Mario , Milani Stefano 
Published: March 2013

Abstract

Background
Colorectal cancer (CRC) is the most frequent cancer in Europe. Randomized clinical trials demonstrated that screening with fecal occult blood test (FOBT) reduces mortality from CRC. Accordingly, the European Community currently recommends population-based screening with FOBT. Other screening tests, such as computed tomography colonography (CTC) and optical colonoscopy (OC), are highly accurate for examining the entire colon for adenomas and CRC. Acceptability represents a critical determinant of the impact of a screening program. We designed a randomized controlled trial to compare participation rate and diagnostic yield of FOBT, CTC with computer-aided diagnosis, and OC as primary tests for population-based screening.

Methods/Design
A total of 14,000 subjects aged 55 to 64 years, living in the Florence district and never screened for CRC, will be randomized in three arms: group 1 (5,000 persons) invited to undergo CTC (divided into: subgroup 1A with reduced cathartic preparation and subgroup 1B with standard bowel preparation); group 2 (8,000 persons) invited to undergo a biannual FOBT for three rounds; and group 3 (1,000 persons) invited to undergo OC. Subjects of each group will be invited by mail to undergo the selected test. All subjects with a positive FOBT or CTC test (that is, mass or at least one polyp ≥6 mm) will be invited to undergo a second-level OC. Primary objectives of the study are to compare the participation rate to FOBT, CTC and OC; to compare the detection rate for cancer or advanced adenomas of CTC versus three rounds of biannual FOBT; to evaluate referral rate for OC induced by primary CTC versus three rounds of FOBT; and to estimate costs of the three screening strategies. A secondary objective of the study is to create a biological bank of blood and stool specimens from subjects undergoing CTC and OC.

Discussion
This study will provide information about participation/acceptability, diagnostic yield and costs of screening with CTC in comparison with the recommended test (FOBT) and OC.

Trial registration
ClinicalTrials.gov Identifier: NCT01651624.