bluuebunny/crossref_metadata_2025_split huggingface dataset:
The hydrogenosomes of Psalteriomonas lanterna
Authors: de Graaf Rob M , Duarte Isabel , van Alen Theo A , Kuiper Jan WP , Schotanus Klaas , Rosenberg Jörg , Huynen Martijn A , Hackstein Johannes HP 
Published: December 2009

Abstract

Background
Hydrogenosomes are organelles that produce molecular hydrogen and ATP. The broad phylogenetic distribution of their hosts suggests that the hydrogenosomes of these organisms evolved several times independently from the mitochondria of aerobic progenitors. Morphology and 18S rRNA phylogeny suggest that the microaerophilic amoeboflagellate Psalteriomonas lanterna, which possesses hydrogenosomes and elusive "modified mitochondria", belongs to the Heterolobosea, a taxon that consists predominantly of aerobic, mitochondriate organisms. This taxon is rather unrelated to taxa with hitherto studied hydrogenosomes.

Results
Electron microscopy of P. lanterna flagellates reveals a large globule in the centre of the cell that is build up from stacks of some 20 individual hydrogenosomes. The individual hydrogenosomes are surrounded by a double membrane that encloses a homogeneous, dark staining matrix lacking cristae. The "modified mitochondria" are found in the cytoplasm of the cell and are surrounded by 1-2 cisterns of rough endoplasmatic reticulum, just as the mitochondria of certain related aerobic Heterolobosea. The ultrastructure of the "modified mitochondria" and hydrogenosomes is very similar, and they have the same size distribution as the hydrogenosomes that form the central stack.
The phylogenetic analysis of selected EST sequences (Hsp60, Propionyl-CoA carboxylase) supports the phylogenetic position of P. lanterna close to aerobic Heterolobosea (Naegleria gruberi). Moreover, this analysis also confirms the identity of several mitochondrial or hydrogenosomal key-genes encoding proteins such as a Hsp60, a pyruvate:ferredoxin oxidoreductase, a putative ADP/ATP carrier, a mitochondrial complex I subunit (51 KDa), and a [FeFe] hydrogenase.

Conclusion
Comparison of the ultrastructure of the "modified mitochondria" and hydrogenosomes strongly suggests that both organelles are just two morphs of the same organelle. The EST studies suggest that the hydrogenosomes of P. lanterna are physiologically similar to the hydrogenosomes of Trichomonas vaginalis and Trimastix pyriformis. Phylogenetic analysis of the ESTs confirms the relationship of P. lanterna with its aerobic relative, the heterolobosean amoeboflagellate Naegleria gruberi, corroborating the evolution of hydrogenosomes from a common, mitochondriate ancestor.
Genome-based polymorphic microsatellite development and validation in the mosquito Aedes aegypti and application to population genetics in Haiti
Authors: Lovin Diane D , Washington Katie O , deBruyn Becky , Hemme Ryan R , Mori Akio , Epstein Sarah R , Harker Brent W , Streit Thomas G , Severson David W 
Published: December 2009

Abstract

Background
Microsatellite markers have proven useful in genetic studies in many organisms, yet microsatellite-based studies of the dengue and yellow fever vector mosquito Aedes aegypti have been limited by the number of assayable and polymorphic loci available, despite multiple independent efforts to identify them. Here we present strategies for efficient identification and development of useful microsatellites with broad coverage across the Aedes aegypti genome, development of multiplex-ready PCR groups of microsatellite loci, and validation of their utility for population analysis with field collections from Haiti.

Results
From 79 putative microsatellite loci representing 31 motifs identified in 42 whole genome sequence supercontig assemblies in the Aedes aegypti genome, 33 microsatellites providing genome-wide coverage amplified as single copy sequences in four lab strains, with a range of 2-6 alleles per locus. The tri-nucleotide motifs represented the majority (51%) of the polymorphic single copy loci, and none of these was located within a putative open reading frame. Seven groups of 4-5 microsatellite loci each were developed for multiplex-ready PCR. Four multiplex-ready groups were used to investigate population genetics of Aedes aegypti populations sampled in Haiti. Of the 23 loci represented in these groups, 20 were polymorphic with a range of 3-24 alleles per locus (mean = 8.75). Allelic polymorphic information content varied from 0.171 to 0.867 (mean = 0.545). Most loci met Hardy-Weinberg expectations across populations and pairwise FST comparisons identified significant genetic differentiation between some populations. No evidence for genetic isolation by distance was observed.

Conclusion
Despite limited success in previous reports, we demonstrate that the Aedes aegypti genome is well-populated with single copy, polymorphic microsatellite loci that can be uncovered using the strategy developed here for rapid and efficient screening of genome supercontig assemblies. These loci are suitable for genetic and population studies using multiplex-PCR.
A recent duplication revisited: phylogenetic analysis reveals an ancestral duplication highly-conserved throughout the Oryza genus and beyond
Authors: Jacquemin Julie , Laudié Michèle , Cooke Richard 
Published: December 2009

AbstractBackgroundThe role of gene duplication in the structural and functional evolution of genomes has been well documented. Analysis of complete rice (Oryza sativa) genome sequences suggested an ancient whole genome duplication, common to all the grasses, some 50-70 million years ago and a more conserved segmental duplication between the distal regions of the short arms of chromosomes 11 and 12, whose evolutionary history is controversial.ResultsWe have carried out a comparative analysis of this duplication within the wild species of the genusOryza, using a phylogenetic approach to specify its origin and evolutionary dynamics. Paralogous pairs were isolated for nine genes selected throughout the region in allOryzagenome types, as well as in two outgroup species,Leersia perrieriandPotamophila parviflora. AllOryzaspecies display the same global evolutionary dynamics but some lineage-specific features appear towards the proximal end of the duplicated region. The same level of conservation is observed between the redundant copies of the tetraploid speciesOryza minuta. The presence of orthologous duplicated blocks in the genome of the more distantly-related species,Brachypodium distachyon, strongly suggests that this duplication between chromosomes 11 and 12 was formed as part of the whole genome duplication common to all Poaceae.ConclusionOur observations suggest that recurrent but heterogeneous concerted evolution throughout theOryzagenus and in related species has led specifically to the extremely high sequence conservation occurring in this region of more than 2 Mbp.
Evaluation of prescribing patterns in a German network of CAM physicians for the treatment of patients with hypertension: a prospective observational study
Authors: Jeschke Elke , Ostermann Thomas , Vollmar Horst C , Kröz Matthias , Bockelbrink Angelina , Witt Claudia M , Willich Stefan N , Matthes Harald 
Published: December 2009

Abstract

Background
The management of hypertension is a key challenge in modern health systems. This study aimed to investigate hypertension treatment strategies among physicians specialized in complementary and alternative medicine (CAM) in Germany by analysing prescribing patterns and comparing these to the current treatment guidelines issued by the German Hypertension Society.

Methods
In this prospective, multicentre observational study, which included 25 primary care physicians specialized in CAM treatment, prescriptions and diagnoses were analysed for each consecutive hypertensive patient using routine electronic data. Data analysis was performed using univariate statistical tests (Chi square test, Cochran-Armitage trend test). Multiple logistic regression was used to determine factors associated with antihypertensive medication.

Results
In the year 2005, 1320 patients with 3278 prescriptions were included (mean age = 64.2 years (SD = 14.5), 63.5% women). Most patients were treated with conventional antihypertensive monotherapies (n = 838, 63.5%). Beta-blockers were the most commonly prescribed monotherapy (30.7%), followed by ACE inhibitors (24.0%). Combination treatment usually consisted of two antihypertensive drugs administered either as separate agents or as a coformulation. The most common combination was a diuretic plus an ACE inhibitor (31.2% of dual therapies). Patient gender, age, and comorbidities significantly influenced which treatment was prescribed. 187 patients (14.2%) received one or more CAM remedies, most of which were administered in addition to classic monotherapies (n = 104). Men (OR = 0.66; 95% CI: 0.54-0.80) and patients with diabetes (OR = 0.55; 95% CI: 0.42-0.0.73), hypercholesterolaemia (OR = 0.59; 95% CI: 0.47-0.75), obesity (OR = 0.74; 95% CI: 0.57-0.97), stroke (OR = 0.54; 95% CI: 0.40-0.74), or prior myocardial infarction (OR = 0.37; 95% CI: 0.17-0.81) were less likely to receive CAM treatment.

Conclusions
The large majority of antihypertensive treatments prescribed by CAM physicians in the present study complied with the current German Hypertension Society treatment guidelines. Deviations from the guidelines were observed in one of every seven patients receiving some form of CAM treatment.
Cadmium burden and the risk and phenotype of prostate cancer
Authors: Chen Yi-Chun , Pu Yeong S , Wu Hsi-Chin , Wu Tony T , Lai Ming Kuen , Yang Chun Y , Sung Fung-Chang 
Published: December 2009

Abstract

Background
Studies on the association between prostate cancer and cadmium exposure have yielded conflicting results. This study explored cadmium burden on the risk and phenotype of prostate cancer in men with no evident environmental exposure.

Methods
Hospital-based 261 prostate cancer cases and 267 controls with benign diseases were recruited from four hospitals in Taiwan. Demographic, dietary and lifestyle data were collected by standardized questionnaires. Blood cadmium (BCd) and creatinine-adjusted urine cadmium (CAUCd) levels were measured for each participant. Statistical analyses measured the prostate cancer risk associated with BCd and CAUCd separately, controlling for age, smoking and institution. BCd and CAUCd levels within cases were compared in relation to the disease stage and the Gleason score.

Results
High family income, low beef intake, low dairy product consumption and positive family history were independently associated with the prostate carcinogenesis. There was no difference in BCd levels between cases and controls (median, 0.88 versus 0.87 μg/l, p = 0.45). Cases had lower CAUCd levels than controls (median, 0.94 versus 1.40 μg/g creatinine, p = 0.001). However, cases with higher BCd and CAUCd levels tended to be at more advanced stages and to have higher Gleason scores. The prostate cancer cases with Gleason scores of ≥ 8 had an odds ratio of 2.89 (95% confidence interval 1.25-6.70), compared with patients with scores of 2-6.

Conclusion
Higher CAUCd and BCd levels may be associated with advanced cancer phenotypes, but there was only a tenuous association between cadmium and prostate cancer.
Overexpression of inhibitor of DNA-binding (ID)-1 protein related to angiogenesis in tumor advancement of ovarian cancers
Authors: Maw Min Khine , Fujimoto Jiro , Tamaya Teruhiko 
Published: December 2009

Abstract

Background
The inhibitor of DNA-binding (ID) has been involved in cell cycle regulation, apoptosis and angiogenesis. This prompted us to study ID functions in tumor advancement of ovarian cancers.

Methods
Sixty patients underwent surgery for ovarian cancers. In ovarian cancers, the levels of ID-1, ID-2 and ID-3 mRNAs were determined by real-time reverse transcription-polymerase chain reaction. The histoscore with the localization of ID-1 was determined by immunohistochemistry. Patient prognosis was analyzed with a 36-month survival rate. Microvessel counts were determined by immunohistochemistry for CD34 and factor VIII-related antigen.

Results
ID-1 histoscores and mRNA levels both significantly (p < 0.001) increased in ovarian cancers according to clinical stage, regardless of histopathological type. Furthermore, 30 patients with high ID-1 expression had a lower survival rate (53%) compared to patients with low ID-1 expression (80%). ID-1 histoscores and mRNA levels significantly (p < 0.0001) correlated with microvessel counts in ovarian cancers.

Conclusion
ID-1 increased in ovarian cancer cells during tumor progression. Moreover, ID-1 expression levels correlated with microvessel counts. Therefore, ID-1 might work on tumor advancement via angiogenesis and is considered to be a candidate for a prognostic indicator in ovarian cancers.
IL4 gene polymorphism and previous malaria experiences manipulate anti-Plasmodium falciparum antibody isotype profiles in complicated and uncomplicated malaria
Authors: Tangteerawatana Piyatida , Perlmann Hedvig , Hayano Masashi , Kalambaheti Thareerat , Troye-Blomberg Marita , Khusmith Srisin 
Published: December 2009

AbstractBackgroundTheIL4-590 gene polymorphism has been shown to be associated with elevated levels of anti-Plasmodium falciparumIgG antibodies and parasite intensity in the malaria protected Fulani of West Africa. This study aimed to investigate the possible impact ofIL4-590C/T polymorphism on anti-P. falciparumIgG subclasses and IgE antibodies levels and the alteration of malaria severity in complicated and uncomplicated malaria patients with or without previous malaria experiences.MethodsAnti-P.falciparumIgG subclasses and IgE antibodies in plasma of complicated and uncomplicated malaria patients with or without previous malaria experiences were analysed using ELISA.IL4-590 polymorphisms were genotyped using RFLP-PCR. Statistical analyses of the IgG subclass levels were done by Oneway ANOVA. Genotype differences were tested by Chi-squared test.ResultsTheIL4-590T allele was significantly associated with anti-P. falciparumIgG3 antibody levels in patients with complicated (P= 0.031), but not with uncomplicated malaria (P= 0.622). Complicated malaria patients with previous malaria experiences carryingIL4-590TT genotype had significantly lower levels of anti-P. falciparumIgG3 (P= 0.0156), while uncomplicated malaria patients with previous malaria experiences carrying the same genotype had significantly higher levels(P= 0.0206) compared to theirIL4-590 counterparts. The different anti-P. falciparumIgG1 and IgG3 levels among IL4 genotypes were observed. Complicated malaria patients with previous malaria experiences tended to have lower IgG3 levels in individuals carrying TT when compared to CT genotypes (P= 0.075). In contrast, complicated malaria patients without previous malaria experiences carrying CC genotype had significantly higher anti-P. falciparumIgG1 than those carrying either CT or TT genotypes (P= 0.004,P= 0.002, respectively).ConclusionThe results suggest thatIL4-590C or T alleles participated differently in the regulation of anti-malarial antibody isotype profiles in primary and secondary malaria infection and, therefore, could play an important role in alteration of malaria severity.
A replication study of the association between the IL12B promoter allele CTCTAA and susceptibility to cerebral malaria in Thai population
Authors: Naka Izumi , Patarapotikul Jintana , Tokunaga Katsushi , Hananantachai Hathairad , Tsuchiya Naoyuki , Ohashi Jun 
Published: December 2009

Abstract

Background
Interleukin-12 (IL-12), a heterodimeric cytokine composed of p35 and p40 subunits, has been thought to play an important role in the pathogenesis of malaria. The IL-12p40 subunit is encoded by the IL12B gene. An IL12B promoter allele, CTCTAA, at rs17860508 has been reported to be associated with susceptibility to cerebral malaria in African populations. However, this association has not so far been replicated in non-African populations.

Methods
To examine whether the CTCTAA allele is associated with susceptibility to cerebral malaria in Asian populations, 303 Thai patients with Plasmodium falciparum malaria (109 cerebral malaria and 194 mild malaria patients) were genotyped for rs17860508 by PCR-direct sequencing.

Results
The CTCTAA allele showed a significant association with susceptibility to cerebral malaria in the Thai population (allelic OR = 1.37; one sided P-value = 0.030).

Conclusions
The existence of a significant association between the CTCTAA allele and susceptibility to cerebral malaria was confirmed in Southeast Asian population, which was previously reported in African populations.
Intein-mediated site-specific conjugation of Quantum Dots to proteins in vivo
Authors: Charalambous Anna , Andreou Maria , Skourides Paris A 
Published: December 2009

Abstract
We describe an intein based method to site-specifically conjugate Quantum Dots (QDs) to target proteins in vivo. This approach allows the covalent conjugation of any nanostructure and/or nanodevice to any protein and thus the targeting of such material to any intracellular compartment or signalling complex within the cells of the developing embryo. We genetically fused a pleckstrin-homology (PH) domain with the N-terminus half of a split intein (IN). The C-terminus half (IC) of the intein was conjugated to QDs in vitro. IC-QD's and RNA encoding PH-IN were microinjected into Xenopus embryos. In vivo intein-splicing resulted in fully functional QD-PH conjugates that could be monitored in real time within live embryos. Use of Near Infra Red (NIR)-emitting QDs allowed monitoring of QD-conjugates within the embryo at depths where EGFP is undetectable demonstrating the advantages of QD's for this type of experiment. In conclusion, we have developed a novel in vivo methodology for the site-specific conjugation of QD's and other artificial structures to target proteins in different intracellular compartments and signaling complexes.
Adolescent body satisfaction: the role of perceived parental encouragement for physical activity
Authors: Savage Jennifer S , DiNallo Jennifer M , Downs Danielle Symons 
Published: December 2009

Abstract

Background
Parents play an important role in the development of children's health behaviors, but less is known about the role of parental encouragement for physical activity (PA) on youth PA behavior and body image satisfaction. The purposes of this study were to: (1) longitudinally assess whether adolescent PA at age 15 mediates the effect of perceived parental encouragement for PA at age 15 for predicting adolescent body satisfaction at age 16, while controlling for body mass index (BMI), and (2) examine the extent to which adolescent sex moderates this association.

Methods
Participants were 379 boys and girls assessed at 15 and 16 years of age, who completed surveys as part of a larger longitudinal study in their health/physical education classes in a school district in Central Pennsylvania. Participants completed measures of their perception of parental encouragement for PA, PA behavior, body satisfaction, and height and weight to calculate BMI at age 15 and 16 (i.e., 10th and 11th grades). Pearson correlations were used to examine the association among the study variables and hierarchical regression analyses were used to predict body satisfaction at age 16.

Results
Perceived encouragement for PA from fathers, but not mothers, at age 15, was significantly associated with adolescent PA at age 15 and body satisfaction scores at age 16. Adolescents reporting higher PA behavior and perceived encouragement for PA from fathers at age 15 had higher body satisfaction scores at age 16. Moreover, adolescent PA at age 15 mediated the association between perceived fathers' encouragement for PA at age 15 and adolescent body satisfaction at age 16, when controlling for BMI. Examining the moderating effect of adolescent sex on this association revealed that adolescent PA no longer mediated the association between perceived encouragement for PA from fathers and adolescent body satisfaction, and sex moderated this association.

Discussion
These findings suggest that, regardless of adolescent BMI, fathers may play an instrumental role in adolescents' body image satisfaction by positively influencing PA behavior. However, the influence of perceived encouragement for PA from fathers on adolescent body satisfaction and PA behavior may differ for boys and girls.
Increased immunogenicity of surviving tumor cells enables cooperation between liposomal doxorubicin and IL-18
Authors: Alagkiozidis Ioannis , Facciabene Andrea , Carpenito Carmine , Benencia Fabian , Jonak Zdenka , Adams Sarah , Carroll Richard G , Gimotty Phyllis A , Hammond Rachel , Danet-Desnoyers Gwen-äel , June Carl H , Powell Daniel J , Coukos George 
Published: December 2009

Abstract

Background
Liposomal doxorubicin (Doxil) is a cytotoxic chemotherapy drug with a favorable hematologic toxicity profile. Its active drug, doxorubicin, has interesting immunomodulatory properties. Here, the effects of Doxil on surviving tumor cell immunophenotype were investigated.

Methods
Using ID8 murine ovarian cancer cells, the immunomodulatory effects of Doxil were studied by measuring its impact on ovarian cancer cell expression of MHC class-I and Fas, and susceptibility to immune attack in vitro. To evaluate the ability of Doxil to cooperate with cancer immunotherapy, the interaction between Doxil and Interleukin 18 (IL-18), a pleiotropic immunostimulatory cytokine, was investigated in vivo in mice bearing ID8-Vegf tumors.

Results
While Doxil killed ID8 tumor cells in a dose-dependent manner, tumor cells escaping Doxil-induced apoptosis upregulated surface expression of MHC-I and Fas, and were sensitized to CTL killing and Fas-mediated death in vitro. We therefore tested the hypothesis that the combination of immunotherapy with Doxil provides positive interactions. Combination IL-18 and Doxil significantly suppressed tumor growth compared with either monotherapy in vivo and uniquely resulted in complete tumor regression and long term antitumor protection in a significant proportion of mice.

Conclusion
These data demonstrate that Doxil favorably changes the immunophenotype of a large fraction of the tumor that escapes direct killing thus creating an opportunity to expand tumor killing by immunotherapy, which can be capitalized through addition of IL-18 in vivo.
Computer aided data acquisition tool for high-throughput phenotyping of plant populations
Authors: Vankadavath Raju Naik , Hussain Appibhai Jakir , Bodanapu Reddaiah , Kharshiing Eros , Basha Pinjari Osman , Gupta Soni , Sreelakshmi Yellamaraju , Sharma Rameshwar 
Published: December 2009

Abstract

Background
The data generated during a course of a biological experiment/study can be sometimes be massive and its management becomes quite critical for the success of the investigation undertaken. The accumulation and analysis of such large datasets often becomes tedious for biologists and lab technicians. Most of the current phenotype data acquisition management systems do not cater to the specialized needs of large-scale data analysis. The successful application of genomic tools/strategies to introduce desired traits in plants requires extensive and precise phenotyping of plant populations or gene bank material, thus necessitating an efficient data acquisition system.

Results
Here we describe newly developed software "PHENOME" for high-throughput phenotyping, which allows researchers to accumulate, categorize, and manage large volume of phenotypic data. In this study, a large number of individual tomato plants were phenotyped with the "PHENOME" application using a Personal Digital Assistant (PDA) with built-in barcode scanner in concert with customized database specific for handling large populations.

Conclusion
The phenotyping of large population of plants both in the laboratory and in the field is very efficiently managed using PDA. The data is transferred to a specialized database(s) where it can be further analyzed and catalogued. The "PHENOME" aids collection and analysis of data obtained in large-scale mutagenesis, assessing quantitative trait loci (QTLs), raising mapping population, sampling of several individuals in one or more ecological niches etc.