bluuebunny/crossref_metadata_2025_split huggingface dataset:
Host gene response to endosymbiont and pathogen in the cereal weevil Sitophilus oryzae
Authors: Vigneron Aurélien , Charif Delphine , Vincent-Monégat Carole , Vallier Agnès , Gavory Frédérick , Wincker Patrick , Heddi Abdelaziz 
Published: January 2012

AbstractBackgroundInsects thriving on nutritionally poor habitats have integrated mutualistic intracellular symbiotic bacteria (endosymbionts) in a bacteria-bearing tissue (the bacteriome) that isolates the endosymbionts and protects them against a host systemic immune response. Whilst the metabolic and physiological features of long-term insect associations have been investigated in detail over the past decades, cellular and immune regulations that determine the host response to endosymbionts and pathogens have attracted interest more recently.ResultsTo investigate bacteriome cellular specificities and weevil immune responses to bacteria, we have constructed and sequenced 7 cDNA libraries fromSitophilus oryzaewhole larvae and bacteriomes. Bioinformatic analysis of 26,886 ESTs led to the generation of 8,941 weevil unigenes. Based onin silicoanalysis and on the examination of genes involved in the cellular pathways of potential interest to intracellular symbiosis (i.e.cell growth and apoptosis, autophagy, immunity), we have selected and analyzed 29 genes using qRT-PCR, taking into consideration bacteriome specificity and symbiosis impact on the host response to pathogens. We show that the bacteriome tissue accumulates transcripts from genes involved in cellular development and survival, such as the apoptotic inhibitorsiap2andiap3, and endosomal fusion and trafficking, such asRab7,Hrs, andSNARE. As regards our investigation into immunity, we first strengthen the bacteriome immunomodulation previously reported inS. zeamais.We show that the sarcotoxin, the c-type lysozyme, and thewpgrp2genes are downregulated in theS. oryzaebacteriome, when compared to aposymbiotic insects and insects challenged withE. coli. Secondly, transcript level comparison between symbiotic and aposymbiotic larvae provides evidence that the immune systemic response to pathogens is decreased in symbiotic insects, as shown by the relatively high expression ofwpgrp2,wpgrp3, coleoptericin-B, diptericin, and sarcotoxin genes in aposymbiotic insects.ConclusionsLibrary sequencing significantly increased the number of unigenes, allowing for improved functional and genetic investigations in the cereal weevilS. oryzae. Transcriptomic analyses support selective and local immune gene expression in the bacteriome tissue and uncover cellular pathways that are of potential interest to bacteriocyte survival and homeostasis. Bacterial challenge experiments have revealed that the systemic immune response would be less induced in a symbiotic insect, thus highlighting new perspectives on host immunity in long-term invertebrate co-evolutionary associations.
Metabolic stasis in an ancient symbiosis: genome-scale metabolic networks from two Blattabacterium cuenoti strains, primary endosymbionts of cockroaches
Authors: González-Domenech Carmen Maria , Belda Eugeni , Patiño-Navarrete Rafael , Moya Andrés , Peretó Juli , Latorre Amparo 
Published: January 2012

Abstract

Background
Cockroaches are terrestrial insects that strikingly eliminate waste nitrogen as ammonia instead of uric acid. Blattabacterium cuenoti (Mercier 1906) strains Bge and Pam are the obligate primary endosymbionts of the cockroaches Blattella germanica and Periplaneta americana, respectively. The genomes of both bacterial endosymbionts have recently been sequenced, making possible a genome-scale constraint-based reconstruction of their metabolic networks. The mathematical expression of a metabolic network and the subsequent quantitative studies of phenotypic features by Flux Balance Analysis (FBA) represent an efficient functional approach to these uncultivable bacteria.

Results
We report the metabolic models of Blattabacterium strains Bge (iCG238) and Pam (iCG230), comprising 296 and 289 biochemical reactions, associated with 238 and 230 genes, and 364 and 358 metabolites, respectively. Both models reflect both the striking similarities and the singularities of these microorganisms. FBA was used to analyze the properties, potential and limits of the models, assuming some environmental constraints such as aerobic conditions and the net production of ammonia from these bacterial systems, as has been experimentally observed. In addition, in silico simulations with the iCG238 model have enabled a set of carbon and nitrogen sources to be defined, which would also support a viable phenotype in terms of biomass production in the strain Pam, which lacks the first three steps of the tricarboxylic acid cycle. FBA reveals a metabolic condition that renders these enzymatic steps dispensable, thus offering a possible evolutionary explanation for their elimination. We also confirm, by computational simulations, the fragility of the metabolic networks and their host dependence.

Conclusions
The minimized Blattabacterium metabolic networks are surprisingly similar in strains Bge and Pam, after 140 million years of evolution of these endosymbionts in separate cockroach lineages. FBA performed on the reconstructed networks from the two bacteria helps to refine the functional analysis of the genomes enabling us to postulate how slightly different host metabolic contexts drove their parallel evolution.
Microbial community of predatory bugs of the genus Macrolophus(Hemiptera: Miridae)
Authors: Machtelinckx Thijs , Van Leeuwen Thomas , Van De Wiele Tom , Boon Nico , De Vos Winnok H , Sanchez Juan-Antonio , Nannini Mauro , Gheysen Godelieve , De Clercq Patrick 
Published: January 2012

Abstract

Background
The predatory mirids of the genus Macrolophus are key natural enemies of various economically important agricultural pests. Both M. caliginosus and M. pygmaeus are commercially available for the augmentative biological control of arthropod pests in European greenhouses. The latter species is known to be infected with Wolbachia -inducing cytoplasmic incompatibility in its host- but the presence of other endosymbionts has not been demonstrated. In the present study, the microbial diversity was examined in various populations of M. caliginosus and M. pygmaeus by 16S rRNA sequencing and denaturing gradient gel electrophoresis.

Results
Besides Wolbachia, a co-infection of 2 Rickettsia species was detected in all M. pygmaeus populations. Based on a concatenated alignment of the 16S rRNA gene, the gltA gene and the coxA gene, the first is phylogenetically related to Rickettsia bellii, whereas the other is closely related to Rickettsia limoniae. All M. caliginosus populations were infected with the same Wolbachia and limoniae-like Rickettsia strain as M. pygmaeus, but did not harbour the bellii-like Rickettsia strain. Interestingly, individuals with a single infection were not found. A PCR assay on the ovaries of M. pygmaeus and M. caliginosus indicated that all endosymbionts are vertically transmitted. The presence of Wolbachia and Rickettsia in oocytes was confirmed by a fluorescence in situ hybridisation. A bio-assay comparing an infected and an uninfected M. pygmaeus population suggested that the endosymbionts had minor effects on nymphal development of their insect host and did not influence its fecundity.

Conclusion
Two species of the palaearctic mirid genus Macrolophus are infected with multiple endosymbionts, including Wolbachia and Rickettsia. Independent of the origin, all tested populations of both M. pygmaeus and M. caliginosus were infected with three and two endosymbionts, respectively. There was no indication that infection with endosymbiotic bacteria had a fitness cost in terms of development and fecundity of the predators.
Integration of gene-based markers in a pearl millet genetic map for identification of candidate genes underlying drought tolerance quantitative trait loci
Authors: Sehgal Deepmala , Rajaram Vengaldas , Armstead Ian Peter , Vadez Vincent , Yadav Yash Pal , Hash Charles Thomas , Yadav Rattan Singh 
Published: January 2012

Abstract

Background
Identification of genes underlying drought tolerance (DT) quantitative trait loci (QTLs) will facilitate understanding of molecular mechanisms of drought tolerance, and also will accelerate genetic improvement of pearl millet through marker-assisted selection. We report a map based on genes with assigned functional roles in plant adaptation to drought and other abiotic stresses and demonstrate its use in identifying candidate genes underlying a major DT-QTL.

Results
Seventy five single nucleotide polymorphism (SNP) and conserved intron spanning primer (CISP) markers were developed from available expressed sequence tags (ESTs) using four genotypes, H 77/833-2, PRLT 2/89-33, ICMR 01029 and ICMR 01004, representing parents of two mapping populations. A total of 228 SNPs were obtained from 30.5 kb sequenced region resulting in a SNP frequency of 1/134 bp. The positions of major pearl millet linkage group (LG) 2 DT-QTLs (reported from crosses H 77/833-2 × PRLT 2/89-33 and 841B × 863B) were added to the present consensus function map which identified 18 genes, coding for PSI reaction center subunit III, PHYC, actin, alanine glyoxylate aminotransferase, uridylate kinase, acyl-CoA oxidase, dipeptidyl peptidase IV, MADS-box, serine/threonine protein kinase, ubiquitin conjugating enzyme, zinc finger C- × 8-C × 5-C × 3-H type, Hd3, acetyl CoA carboxylase, chlorophyll a/b binding protein, photolyase, protein phosphatase1 regulatory subunit SDS22 and two hypothetical proteins, co-mapping in this DT-QTL interval. Many of these candidate genes were found to have significant association with QTLs of grain yield, flowering time and leaf rolling under drought stress conditions.

Conclusions
We have exploited available pearl millet EST sequences to generate a mapped resource of seventy five new gene-based markers for pearl millet and demonstrated its use in identifying candidate genes underlying a major DT-QTL in this species. The reported gene-based markers represent an important resource for identification of candidate genes for other mapped abiotic stress QTLs in pearl millet. They also provide a resource for initiating association studies using candidate genes and also for comparing the structure and function of distantly related plant genomes such as other Poaceae members.
Household secondhand smoke exposure of elementary schoolchildren in Southern Taiwan and factors associated with their confidence in avoiding exposure: a cross-sectional study
Authors: Huang Hsiao-Ling , Yen Yea-Yin , Lin Pi-Li , Chiu Chin-Hsuan , Hsu Chih-Cheng , Chen Ted , Hu Chih-Yang , Lin Ya-Ying , Lee Chien-Hung , Chen Fu-Li 
Published: January 2012

Abstract

Background
Exposure to household Secondhand Smoke (SHS) poses a major health threat to children after an indoor smoking ban was imposed in Taiwan. This study aimed to assess the household SHS exposure in elementary school children in southern Taiwan and the factors associated with their avoidance of SHS exposure before and after the implementation of Taiwan's new Tobacco Hazards Prevention Act in 2009.

Methods
In this cross-sectional school-based study, data on household SHS exposure, avoidance of SHS and related variables was obtained from the 2008 and 2009 Control of School-aged Children Smoking Study Survey. A random sample of 52 elementary schools was included. A total of 4450 3-6 graders (aged 8-13) completed the questionnaire. Regression models analyzed factors of children's self-confidence to avoid household SHS exposure.

Results
Over 50% of children were found to have lived with a family member who smoked in front of them after the new law enacted, and 35% of them were exposed to household SHS more than 4 days a week. Having a positive attitude toward smoking (β = -0.05 to -0.06) and high household SHS exposure (β = -0.34 to -0.47) were significantly associated with a lower avoidance of SHS exposure. Comparing to girls, boys had lower scores in their knowledge of tobacco hazards; and this factor was significantly related to their SHS avoidance (β = 0.13-0.14).

Conclusions
The intervention program should enhance school children do actively avoid exposure to SHS in home settings, and more importantly, provide tobacco hazard knowledge to male students to avoid exposure to household SHS for themselves. The results also provide further evidence that Tobacco Hazards Prevention Act should perhaps be extended to the family environment in order to protect children from the hazards of household SHS exposure.
Timing of surgery for hip fracture and in-hospital mortality: a retrospective population-based cohort study in the Spanish National Health System
Authors: Librero Julián , Peiró Salvador , Leutscher Edith , Merlo Juan , Bernal-Delgado Enrique , Ridao Manuel , Martínez-Lizaga Natalia , Sanfélix-Gimeno Gabriel 
Published: January 2012

AbstractBackgroundWhile the benefits or otherwise of early hip fracture repair is a long-running controversy with studies showing contradictory results, this practice is being adopted as a quality indicator in several health care organizations. The aim of this study is to analyze the association between early hip fracture repair and in-hospital mortality in elderly people attending public hospitals in the Spanish National Health System and, additionally, to explore factors associated with the decision to perform early hip fracture repair.MethodsA cohort of 56,500 patients of 60-years-old and over, hospitalized for hip fracture during the period 2002 to 2005 in all the public hospitals in 8 Spanish regions, were followed up using administrative databases to identify the time to surgical repair and in-hospital mortality. We used a multivariate logistic regression model to analyze the relationship between the timing of surgery (< 2 days from admission) and in-hospital mortality, controlling for several confounding factors.ResultsEarly surgery was performed on 25% of the patients. In the unadjusted analysis early surgery showed an absolute difference in risk of mortality of 0.57 (from 4.42% to 3.85%). However, patients undergoing delayed surgery were older and had higher comorbidity and severity of illness. Timeliness for surgery was not found to be related to in-hospital mortality once confounding factors such as age, sex, chronic comorbidities as well as the severity of illness were controlled for in the multivariate analysis.ConclusionsOlder age, male gender, higher chronic comorbidity and higher severity measured by the Risk Mortality Index were associated with higher mortality, but the time to surgery was not.
5-alpha-reductase type I (SRD5A1) is up-regulated in non-small cell lung cancer but does not impact proliferation, cell cycle distribution or apoptosis
Authors: Kapp Friedrich G , Sommer Anette , Kiefer Thomas , Dölken Gottfried , Haendler Bernard 
Published: January 2012

AbstractBackgroundNon-small cell lung cancer (NSCLC) is one of the most frequent malignancies and has a high mortality rate due to late detection and lack of efficient treatments. Identifying novel drug targets for this indication may open the way for new treatment strategies. Comparison of gene expression profiles of NSCLC and normal adjacent tissue (NAT) allowed to determine that 5-alpha-reductase type I (SRD5A1) was up-regulated in NSCLC compared to NAT. This raised the question whether SRD5A1 was involved in sustained proliferation and survival of NSCLC.MethodssiRNA-mediated silencing of SRD5A1 was performed in A549 and NCI-H460 lung cancer cell lines in order to determine the impact on proliferation, on distribution during the different phases of the cell cycle, and on apoptosis/necrosis. In addition, lung cancer cell lines were treated with 4-azasteroids, which specifically inhibit SRD5A1 activity, and the effects on proliferation were measured. Statistical analyses using ANOVA and post-hoc Tamhane-T2-test were performed. In the case of non-parametric data, the Kruskal-Wallis test and the post-hoc Mann-Whitney-U-test were used.ResultsThe knock-down of SRDA51 expression was very efficient with the SRD5A1 transcripts being reduced to 10% of control levels. Knock-down efficiency was furthermore confirmed at the protein level. However, no effect of SRD5A1 silencing was observed in the proliferation assay, the cell cycle analysis, and the apoptosis/necrosis assay. Treatment of lung cancer cell lines with 4-azasteroids did not significantly inhibit proliferation.ConclusionsIn summary, the results suggest that SRD5A1 is not a crucial enzyme for the sustained proliferation of NSCLC cell lines.
Optical sensing nanostructures for porous silicon rugate filters
Authors: Li Sha , Hu Dehong , Huang Jianfeng , Cai Lintao 
Published: January 2012

Abstract
Porous silicon rugate filters [PSRFs] and combination PSRFs [C-PSRFs] are emerging as interesting sensing materials due to their specific nanostructures and superior optical properties. In this work, we present a systematic study of the PSRF fabrication and its nanostructure/optical characterization. Various PSRF chips were produced with resonance peaks that are adjustable from visible region to near-infrared region by simply increasing the periods of sine currents in a programmed electrochemical etching method. A regression analysis revealed a perfect linear correlation between the resonant peak wavelength and the period of etching current. By coupling the sine currents with several different periods, C-PSRFs were produced with defined multiple resonance peaks located at desired positions. A scanning electron microscope and a microfiber spectrophotometer were employed to analyze their physical structure and feature spectra, respectively. The sensing properties of C-PSRFs were investigated in an ethanol vapor, where the red shifts of the C-PSRF peaks had a good linear relationship with a certain concentration of ethanol vapor. As the concentration increased, the slope of the regression line also increased. The C-PSRF sensors indicated the high sensitivity, quick response, perfect durability, reproducibility, and versatility in other organic gas sensing.
A low-grade chondrosarcoma presenting as an unusual cervical mass in the hyoid bone: a case report
Authors: Tachino Hirohiko , Fushiki Hiroaki , Ishida Masayuki , Watanabe Yukio 
Published: January 2012

Abstract

Introduction
A chondrosarcoma originating from the hyoid bone is very rare. Here, we describe a case of low-grade chondrosarcoma of hyoid origin and discuss its preoperative imaging features, including those on positron emission tomography-computed tomography, and its recurrence rate.

Case presentation
A 42-year-old Japanese man noticed a mass in the right submandibular region of his neck. A hard 3.0 × 2.8 cm tumor was noted on the right side of his hyoid bone. The mass was immobile and moved with deglutition.

Conclusion
Even though radiographic studies, including positron emission tomography-computed tomography, were inconclusive, the cartilaginous tumor was surgically removed en bloc, and the tumor was diagnosed based on the results of pathological investigations. Close follow-up is recommended in such cases due to the potential for recurrences, because local recurrence occurred in 50% of the reported cases of grade one chondrosarcomas.
Primary follicular lymphoma of the epididymis positive for t(14;18)(q32;q21)/IGH- BCL2 and negative for BCL2 protein expression: a case report
Authors: Tralongo Vincenzo , Becchina Gaspare , Nagar Claudia , Ottoveggio Gabriella , Mason Silvia , Seno Barbara , Sessa Francesca , Frattini Milo , Genovese Francesco 
Published: January 2012

Abstract

Introduction
Non-Hodgkin lymphoma (NHL) can involve the paratesticular organs as the primary disease, as primary testicular lymphoma that secondarily involves the paratesticular structures, as the initial site of presentation of occult nodal disease or as the result of disease dissemination. Primary follicular lymphoma of the epididymis in an adult is extremely rare. Little is known about primary adult paratesticular/epididimal lymphomas.

Case presentation
We report a rare case of primary follicular non-Hodgkin lymphoma of the epididymis in a 90-year-old Caucasian man who presented with a left scrotal mass. Bone marrow biopsy was negative and computed tomography of the total body revealed no evidence of extratesticular involvement. Macroscopically, the epididymis was replaced completely by a uniform mass. Histologic studies revealed a dense lymphoid infiltrate predominantly composed of centrocytes with admixed centroblasts. Immunohistochemical analyses demonstrated that neoplastic cells strongly expressed CD45RB, CD20, CD79a, bcl-6 and CD10; bcl-2 immunostaining was negative. Molecular studies showed the presence of the monoclonal IgH gene rearrangement and the IgH/BCL2 rearrangement. The lymphoma was classified as follicular lymphoma, low grade, grade 1-2. The patient subsequently underwent radical orchiectomy, did not receive chemotherapy and post-operative follow-up showed absence of disease recurrence.

Conclusions
The case of primary follicular lymphoma of epididymis, reported here, is considered a very rare event. It is characterized by clinically indolent localized disease, a good clinical outcome, lack of expression of BCL2 protein and the presence of the t(14;18)(q32;q21)/IGH-BCL2. Even if it is a single case, the primary follicular lymphoma epididymis with t(14;18) could represent either a variant of the previously reported t(14;18)-negative primary paratesticular follicular lymphoma or a distinct biological entity. To report additional cases in the future would be helpful in resolving this question.
The association of Toll-like receptor 4 gene polymorphisms with the development of emphysema in Japanese subjects: a case control study
Authors: Ito Michiko , Hanaoka Masayuki , Droma Yunden , Kobayashi Nobumitsu , Yasuo Masanori , Kitaguchi Yoshiaki , Horiuchi Toshimichi , Ikegawa Kayoko , Katsuyama Yoshihiko , Kubo Keishi , Ota Masao 
Published: January 2012

Abstract

Background
The principal role of Toll-like receptor 4 (TLR4) is the induction of immune responses to lipopolysaccharides. Previously, mice deficient in the TLR4 gene exhibited up-regulation of the NADPH oxidase system in the lungs. This resulted in increased oxidant generation and elastolytic activity, which led to pulmonary emphysema. It was suggested that TLR4 might maintain constitutive lung integrity by modulating oxidant generation. We investigated whether single nucleotide polymorphisms (SNPs) in the TLR4 gene were associated with the emphysema phenotype in Japanese subjects with chronic obstructive pulmonary disease (COPD).

Results
Seven SNPs in the TLR4 gene (rs10759930, rs1927914, rs12377632, rs2149356, rs11536889, rs7037117, and rs7045953) were genotyped with allelic discrimination assays. The frequencies of SNPs were compared between 106 patients with the emphysema phenotype of COPD and 137 healthy smokers. We found that the positivity of the individuals with the major G allele of rs11536889 was significantly less in the emphysema group than the control group (p = 0.019). The frequencies of the minor C allele and the distribution of the CC genotype as well as the frequency of the major haplotype that carried the minor C allele of rs11536889 were all significantly higher in the emphysema group than the control group (p = 0.0083, 0.019, and 0.004, respectively). Furthermore, the strength of the association of the CC genotype with the emphysema phenotype was in an odds ratio of 2.60 with 95% confidence intervals from 1.17 to 5.78. However, these significances were not apparent after adjust for age and smoking history by logistic regression. No associations were observed between the rs11536889 and the low attenuation area score, the forced expiratory volume, and the carbon monoxide diffusion capacity in the emphysema group.

Conclusions
The minor C allele of the rs11536889 SNP in the TLR4 gene is likely associated with the risk of developing emphysema in the Japanese population.