bluuebunny/crossref_metadata_2025 huggingface dataset:
Recontextualization of the Corporate Values of a Danish MNC in a Subsidiary in Bangalore
Authors: Gertsen Martine Cardel , Zølner Mette
Published: January 2012

The authors analyze the recontextualization of the corporate values of a multinational company (MNC) in one of its subsidiaries. The authors draw upon qualitative material from a case study of a company of Danish origin and its endeavors to implement its corporate values in an Indian subsidiary in Bangalore. The authors show how these values take on new meanings when interpreted by local employees. On the one hand, their understandings are shaped by the prevailing meaning system, including leadership ideals, and on the other hand, by their resources and strategies. To further their understanding of the recontextualization, the authors point to a need to go beyond the system of signification shared within a national culture and include social agency, of which they conceive in Bourdieusian terms.
Dropping shock response of corrugated paperboard cushioning packaging system
Authors: Wang Jun , Wang Zhi-Wei , Duan Fang , Lu Li-Xin , Gao De , Chen An-jun
Published: January 2012

In this paper, a dynamic model was proposed for a corrugated paperboard cushioning packaging system. The variational iteration method was applied and the multiplier was identified. The approximate solution for the nonlinear equations was obtained and compared with the numerical simulation results with ordinary differential equation solver in MATLAB, showing good agreement. Then resonance conditions were obtained, which should be avoided in the cushioning packaging design.
No proinflammatory signature in CD34+ hematopoietic progenitor cells in multiple sclerosis patients
Authors: Lutterotti A , Jelčić I , Schulze C , Schippling S , Breiden P , Mazzanti B , Reinhardt S , DiGioia M , Repice A , Massacesi L , Sputtek A , Salinas-Riester G , Kroeger N , Sospedra M , Saccardi R , Zander A , Martin R
Published: January 2012

Autologous hematopoietic stem cell transplantation (aHSCT) has been used as a therapeutic approach in multiple sclerosis (MS). However, it is still unclear if the immune system that emerges from autologous CD34+ hematopoietic progenitor cells (HPC) of MS patients is pre-conditioned to re-develop the proinflammatory phenotype. The objective of this article is to compare the whole genome gene and microRNA expression signature in CD34+ HPC of MS patients and healthy donors (HD). CD34+ HPC were isolated from peripheral blood of eight MS patients and five HD and analyzed by whole genome gene expression and microRNA expression microarray. Among the differentially expressed genes (DEGs) only TNNT1 reached statistical significance (logFC=3.1, p<0.01). The microRNA expression was not significantly different between MS patients and HD. We did not find significant alterations of gene expression or microRNA profiles in CD34+ HPCs of MS patients. Our results support the use of aHSCT for treatment of MS.
The role of context stability and behavioural stability in the mere measurement effect: An examination across six behaviours
Authors: Lawrence Claire , Ferguson Eamonn
Published: January 2012

Asking about intentions and behaviour may alter future reports of health behaviours due to the stability of the behaviours (behavioural stability hypothesis), or changes in performance context (context stability hypothesis). Two studies ( Ns = 116, 177) confirmed the distinction between stable and unstable behaviours and explored context stability for six health-related behaviours. Study 3 used a longitudinal intervention design in which the intervention group ( N time 1 = 292, N time 2 = 149) reported their intentions and past-behaviours at time 1 while the non-intervention group ( N = 118) did not. The context stability hypothesis was supported.
The romantic experiences of adolescents with a visible difference: Exploring concerns, protective factors and support needs
Authors: Griffiths Catrin , Williamson Heidi , Rumsey Nichola
Published: January 2012

Injuries or conditions that affect appearance can increase adolescents’ risk of psychosocial and interpersonal difficulties and may also impact on romantic relationships – an important aspect of adolescent development. A mixed method online approach explored the romantic experiences of 40 adolescents with a variety of visible differences. Young people identified appearance-related romantic concerns that cause distress, and impede the development and enjoyment of romantic relations. In contrast, some shared positive experiences and evidence of attitudes and behaviours that appear to protect against these concerns. Adolescents requested online peer support specific to their appearance-related needs. These findings can inform intervention development.
Grammaticality judgment of Chinese and English sentences by native speakers of alphasyllabary: A reaction time study
Authors: Leong Che Kan , Tsung Linda T.H. , Tse Shek Kam , Shum Mark Shui Kee , Ki Wing Wah
Published: January 2012

A group of 118 sixteen-year-old students of ethnic Indian and Pakistani origin, learning school Chinese, judged on-line the grammaticality of 18 pairs of sentences in Chinese and English. We hypothesized: (a) The students might not perform worse in simple Chinese sentence processing as compared with equivalent English sentences. (b) There would be an overall school effect as proxy for learning experience. (c) Grammatically correct sentences would be processed more efficiently than anomalous ones. MANCOVA (age as covariate) and efficiency indices, by taking into account both accuracy and reaction time, support the hypotheses. The results are discussed in learning form and meaning of school Chinese.
Complement C3 is a novel plasma clot component with anti-fibrinolytic properties
Authors: Howes Joanna-Marie , Richardson Victoria R , Smith Kerrie A , Schroeder Verena , Somani Riyaz , Shore Anna , Hess Katharina , Ajjan Ramzi , Pease Richard J , Keen Jeffrey N , Standeven Kristina F , Carter Angela M
Published: January 2012

Background and method:

Increased plasma clot density and prolonged lysis times are associated with cardiovascular disease. In this study, we employed a functional proteomics approach to identify novel clot components which may influence clot phenotypes.

Results:

Analysis of perfused, solubilised plasma clots identified inflammatory proteins, including complement C3, as novel clot components. Analysis of paired plasma and serum samples confirmed concentration-dependent incorporation of C3 into clots. Surface plasmon resonance indicated high-affinity binding interactions between C3 and fibrinogen and fibrin. Turbidimetric clotting and lysis assays indicated C3 impaired fibrinolysis in a concentration-dependent manner, both in vitro and ex vivo.

Conclusion:

These data indicate functional interactions between complement C3 and fibrin leading to prolonged fibrinolysis. These interactions are physiologically relevant in the context of protection following injury and suggest a mechanistic link between increased plasma C3 concentration and acute cardiovascular thrombotic events.
Inhibition of Pyk2 blocks lung inflammation and injury in a mouse model of acute lung injury
Authors: Duan Yingli , Learoyd Jonathan , Meliton Angelo Y , Leff Alan R , Zhu Xiangdong
Published: January 2012

Background

Proline-rich tyrosine kinase 2 (Pyk2) is essential in neutrophil degranulation and chemotaxis in vitro. However, its effect on the process of lung inflammation and edema formation during LPS induced acute lung injury (ALI) remains unknown. The goal of the present study was to determine the effect of inhibiting Pyk2 on LPS-induced acute lung inflammation and injury in vivo.

Methods

C57BL6 mice were given either 10 mg/kg LPS or saline intratracheally. Inhibition of Pyk2 was effected by intraperitoneal administration TAT-Pyk2-CT 1 h before challenge. Bronchoalveolar lavage analysis of cell counts, lung histology and protein concentration in BAL were analyzed at 18 h after LPS treatment. KC and MIP-2 concentrations in BAL were measured by a mouse cytokine multiplex kit. The static lung compliance was determined by pressure-volume curve using a computer-controlled small animal ventilator. The extravasated Evans blue concentration in lung homogenate was determined spectrophotometrically.

Results

Intratracheal instillation of LPS induced significant neutrophil infiltration into the lung interstitium and alveolar space, which was attenuated by pre-treatment with TAT-Pyk2-CT. TAT-Pyk2-CT pretreatment also attenuated 1) myeloperoxidase content in lung tissues, 2) vascular leakage as measured by Evans blue dye extravasation in the lungs and the increase in protein concentration in bronchoalveolar lavage, and 3) the decrease in lung compliance. In each paradigm, treatment with control protein TAT-GFP had no blocking effect. By contrast, production of neutrophil chemokines MIP-2 and keratinocyte-derived chemokine in the bronchoalveolar lavage was not reduced by TAT-Pyk2-CT. Western blot analysis confirmed that tyrosine phosphorylation of Pyk2 in LPS-challenged lungs was reduced to control levels by TAT-Pyk2-CT pretreatment.

Conclusions

These results suggest that Pyk2 plays an important role in the development of acute lung injury in mice and that pharmacological inhibition of Pyk2 might provide a potential therapeutic strategy in the pretreatment for patients at imminent risk of developing acute lung injury.
Depletion of the actin bundling protein SM22/transgelin increases actin dynamics and enhances the tumourigenic phenotypes of cells
Authors: Thompson Oliver , Moghraby Jeelan S , Ayscough Kathryn R , Winder Steve J
Published: January 2012

Background

SM22 has long been studied as an actin-associated protein. Interestingly, levels of SM22 are often reduced in tumour cell lines, while they are increased during senescence possibly indicating a role for SM22 in cell fate decisions via its interaction with actin. In this study we aimed to determine whether reducing levels of SM22 could actively contribute to a tumourigenic phenotype.

Results

We demonstrate that in REF52 fibroblasts, decreased levels of SM22 disrupt normal actin organization leading to changes in the motile behaviour of cells. Interestingly, SM22 depletion also led to an increase in the capacity of cells to spontaneously form podosomes with a concomitant increase in the ability to invade Matrigel. In PC3 prostate epithelial cancer cells by contrast, where SM22 is undetectable, re-expression of SM22 reduced the ability to invade Matrigel. Furthermore SM22 depleted cells also had reduced levels of reactive oxygen species when under serum starvation stress.

Conclusions

These findings suggest that depletion of SM22 could contribute to tumourigenic properties of cells. Reduction in SM22 levels would tend to promote cell survival when cells are under stress, such as in a hypoxic tumour environment, and may also contribute to increases in actin dynamics that favour metastatic potential.
Estimation of linkage disequilibrium in four US pig breeds
Authors: Badke Yvonne M , Bates Ronald O , Ernst Catherine W , Schwab Clint , Steibel Juan P
Published: January 2012

Background

The success of marker assisted selection depends on the amount of linkage disequilibrium (LD) across the genome. To implement marker assisted selection in the swine breeding industry, information about extent and degree of LD is essential. The objective of this study is to estimate LD in four US breeds of pigs (Duroc, Hampshire, Landrace, and Yorkshire) and subsequently calculate persistence of phase among them using a 60 k SNP panel. In addition, we report LD when using only a fraction of the available markers, to estimate persistence of LD over distance.

Results

Average r

2
between adjacent SNP across all chromosomes was 0.36 for Landrace, 0.39 for Yorkshire, 0.44 for Hampshire and 0.46 for Duroc. For markers 1 Mb apart, r

2
ranged from 0.15 for Landrace to 0.20 for Hampshire. Reducing the marker panel to 10% of its original density, average r

2
ranged between 0.20 for Landrace to 0.25 for Duroc. We also estimated persistence of phase as a measure of prediction reliability of markers in one breed by those in another and found that markers less than 10 kb apart could be predicted with a maximal accuracy of 0.92 for Landrace with Yorkshire.

Conclusions

Our estimates of LD, although in good agreement with previous reports, are more comprehensive and based on a larger panel of markers. Our estimates also confirmed earlier findings reporting higher LD in pigs than in American Holstein cattle, especially at increasing marker distances (> 1 Mb). High average LD (r

2
> 0.4) between adjacent SNP found in this study is an important precursor for the implementation of marker assisted selection within a livestock species.

Results of this study are relevant to the US purebred pig industry and critical for the design of programs of whole genome marker assisted evaluation and selection. In addition, results indicate that a more cost efficient implementation of marker assisted selection using low density panels with genotype imputation, would be feasible for these breeds.
Postmortem cardiac tissue maintains gene expression profile even after late harvesting
Authors: Gupta Simone , Halushka Marc K , Hilton Gina M , Arking Dan E
Published: January 2012

Background

Gene expression studies can be used to help identify disease-associated genes by comparing the levels of expressed transcripts between cases and controls, and to identify functional genetic variants (expression quantitative loci or eQTLs) by comparing expression levels between individuals with different genotypes. While many of these studies are performed in blood or lymphoblastoid cell lines due to tissue accessibility, the relevance of expression differences in tissues that are not the primary site of disease is unclear. Further, many eQTLs are tissue specific. Thus, there is a clear and compelling need to conduct gene expression studies in tissues that are specifically relevant to the disease of interest. One major technical concern about using autopsy-derived tissue is how representative it is of physiologic conditions, given the effect of postmortem interval on tissue degradation.

Results

In this study, we monitored the gene expression of 13 tissue samples harvested from a rapid autopsy heart (non-failed heart) and 7 from a cardiac explant (failed heart) through 24 hours of autolysis. The 24 hour autopsy simulation was designed to reflect a typical autopsy scenario where a body may begin cooling to ambient temperature for ~12 hours, before transportation and storage in a refrigerated room in a morgue. In addition, we also simulated a scenario wherein the body was left at room temperature for up to 24 hours before being found. A small fraction (< 2.5%) of genes showed fluctuations in expression over the 24 hr period and largely belong to immune and signal response and energy metabolism-related processes. Global expression analysis suggests that RNA expression is reproducible over 24 hours of autolysis with 95% genes showing < 1.2 fold change. Comparing the rapid autopsy to the failed heart identified 480 differentially expressed genes, including several types of collagens, lumican (LUM), natriuretic peptide A (NPPA) and connective tissue growth factor (CTGF), which allows for the clear separation between failing and non-failing heart based on gene expression profiles.

Conclusions

Our results demonstrate that RNA from autopsy-derived tissue, even up to 24 hours of autolysis, can be used to identify biologically relevant expression pattern differences, thus serving as a practical source for gene expression experiments.
Increased sensitivity of next generation sequencing-based expression profiling after globin reduction in human blood RNA
Authors: Mastrokolias Anastasios , den Dunnen Johan T , van Ommen GertJan B , 't Hoen Peter AC , van Roon-Mom Willeke MC
Published: January 2012

Background

Transcriptome analysis is of great interest in clinical research, where significant differences between individuals can be translated into biomarkers of disease. Although next generation sequencing provides robust, comparable and highly informative expression profiling data, with several million of tags per blood sample, reticulocyte globin transcripts can constitute up to 76% of total mRNA compromising the detection of low abundant transcripts. We have removed globin transcripts from 6 human whole blood RNA samples with a human globin reduction kit and compared them with the same non-reduced samples using deep Serial Analysis of Gene Expression.

Results

Globin tags comprised 52-76% of total tags in our samples. Out of 21,633 genes only 87 genes were detected at significantly lower levels in the globin reduced samples. In contrast, 11,338 genes were detected at significantly higher levels in the globin reduced samples. Removing globin transcripts allowed us to also identify 2112 genes that could not be detected in the non-globin reduced samples, with roles in cell surface receptor signal transduction, G-protein coupled receptor protein signalling pathways and neurological processes.

Conclusions

The reduction of globin transcripts in whole blood samples constitutes a reproducible and reliable method that can enrich data obtained from next generation sequencing-based expression profiling.
Microarray analysis on germfree mice elucidates the primary target of a traditional Japanese medicine juzentaihoto: acceleration of IFN-α response via affecting the ISGF3-IRF7 signaling cascade
Authors: Munakata Kaori , Takashima Kiyoe , Nishiyama Mitsue , Asano Naoko , Mase Akihito , Hioki Kyoji , Ohnishi Yasuyuki , Yamamoto Masahiro , Watanabe Kenji
Published: January 2012

Background

The traditional Japanese medicine juzentaihoto (JTX) is a pharmaceutical grade multi-herbal medicine widely used for the prevention of cancer metastasis and infection in immuno-compromized patients in Japan. The effect of JTX has been supposed to be intimately affected by the immunological properties of host and enteric microflora. The influence of JTX on the gene expression profile in the large and small intestines was investigated by microarray analyses using mice of different strains with or without enteric microflora.

Results

In all types of mice, including germfree (GF) animals, the genes most affected by two-week oral JTX treatment were the type 1 interferon (IFN)-related genes including Stat1, Isgf3g and Irf7, which play a critical role in the feedback loop of IFN-α production cascade. In IQI specific pathogen free (SPF) mice JTX increased the steady state level of the expression of IFN-related genes, but had the opposite effect in IQI GF and BALB/c SPF mice. Promoter analysis suggests that tandem repeated $IRFF (the promoter sequences for interferon regulatory factors) may be a primary target for JTX action. Pre-treatment of JTX accelerated the effects of an oral IFN "inducer" 2-amino-5-bromo-6-methyl-4-pyrimidinol (ABMP) (up-regulation of IFN-α production in IQI strain and down-regulation in BALB/c mice), which is in good accordance with the effect of JTX on gene expression of type 1 IFN-related genes.

Conclusions

Microarray analysis revealed that the target of JTX might be the transcription machinery regulating the steady-state level of genes involved in the ISGF3-IRF7 cascade, whose effect is bi-directional in a strain- and microbiota-dependent manner.
Improving ChIP-seq peak-calling for functional co-regulator binding by integrating multiple sources of biological information
Authors: Osmanbeyoglu Hatice Ulku , Hartmaier Ryan J , Oesterreich Steffi , Lu Xinghua
Published: January 2012

Background

Chromatin immunoprecipitation coupled with massively parallel sequencing (ChIP-seq) is increasingly being applied to study genome-wide binding sites of transcription factors. There is an increasing interest in understanding the mechanism of action of co-regulator proteins, which do not bind DNA directly, but exert their effects by binding to transcription factors such as the estrogen receptor (ER). However, due to the nature of detecting indirect protein-DNA interaction, ChIP-seq signals from co-regulators can be relatively weak and thus biologically meaningful interactions remain difficult to identify.

Results

In this study, we investigated and compared different statistical and machine learning approaches including unsupervised, supervised, and semi-supervised classification (self-training) approaches to integrate multiple types of genomic and transcriptomic information derived from our experiments and public database to overcome difficulty of identifying functional DNA binding sites of the co-regulator SRC-1 in the context of estrogen response. Our results indicate that supervised learning with naïve Bayes algorithm significantly enhances peak calling of weak ChIP-seq signals and outperforms other machine learning algorithms. Our integrative approach revealed many potential ERα/SRC-1 DNA binding sites that would otherwise be missed by conventional peak calling algorithms with default settings.

Conclusions

Our results indicate that a supervised classification approach enables one to utilize limited amounts of prior knowledge together with multiple types of biological data to enhance the sensitivity and specificity of the identification of DNA binding sites from co-regulator proteins.
Soybean Knowledge Base (SoyKB): a web resource for soybean translational genomics
Authors: Joshi Trupti , Patil Kapil , Fitzpatrick Michael R , Franklin Levi D , Yao Qiuming , Cook Jeffrey R , Wang Zheng , Libault Marc , Brechenmacher Laurent , Valliyodan Babu , Wu Xiaolei , Cheng Jianlin , Stacey Gary , Nguyen Henry T , Xu Dong
Published: January 2012

Background

Soybean Knowledge Base (SoyKB) is a comprehensive all-inclusive web resource for soybean translational genomics. SoyKB is designed to handle the management and integration of soybean genomics, transcriptomics, proteomics and metabolomics data along with annotation of gene function and biological pathway. It contains information on four entities, namely genes, microRNAs, metabolites and single nucleotide polymorphisms (SNPs).

Methods

SoyKB has many useful tools such as Affymetrix probe ID search, gene family search, multiple gene/metabolite search supporting co-expression analysis, and protein 3D structure viewer as well as download and upload capacity for experimental data and annotations. It has four tiers of registration, which control different levels of access to public and private data. It allows users of certain levels to share their expertise by adding comments to the data. It has a user-friendly web interface together with genome browser and pathway viewer, which display data in an intuitive manner to the soybean researchers, producers and consumers.

Conclusions

SoyKB addresses the increasing need of the soybean research community to have a one-stop-shop functional and translational omics web resource for information retrieval and analysis in a user-friendly way. SoyKB can be publicly accessed at http://soykb.org/.
Construction and analysis of a plant non-specific lipid transfer protein database (nsLTPDB)
Authors: Wang Nai-Jyuan , Lee Chi-Ching , Cheng Chao-Sheng , Lo Wei-Cheng , Yang Ya-Fen , Chen Ming-Nan , Lyu Ping-Chiang
Published: January 2012

Background

Plant n on-s pecific l ipid t ransfer p roteins (nsLTPs) are small and basic proteins. Recently, nsLTPs have been reported involved in many physiological functions such as mediating phospholipid transfer, participating in plant defence activity against bacterial and fungal pathogens, and enhancing cell wall extension in tobacco. However, the lipid transfer mechanism of nsLTPs is still unclear, and comprehensive information of nsLTPs is difficult to obtain.

Methods

In this study, we identified 595 nsLTPs from 121 different species and constructed an nsLTPs database -- nsLTPDB -- which comprises the sequence information, structures, relevant literatures, and biological data of all plant nsLTPs http://nsltpdb.life.nthu.edu.tw/.

Results

Meanwhile, bioinformatics and statistics methods were implemented to develop a classification method for nsLTPs based on the patterns of the eight highly-conserved cysteine residues, and to suggest strict Prosite-styled patterns for Type I and Type II nsLTPs. The pattern of Type I is C X2 V X5-7 C [V, L, I] × Y [L, A, V] X8-13 CC × G X12 D × [Q, K, R] X2 CXC X16-21 P X2 C X13-15C, and that of Type II is C X4 L X2 C X9-11 P [S, T] X2 CC X5 Q X2-4 C[L, F]C X2 [A, L, I] × [D, N] P X10-12 [K, R] X4-5 C X3-4 P X0-2 C. Moreover, we referred the Prosite-styled patterns to the experimental mutagenesis data that previously established by our group, and found that the residues with higher conservation played an important role in the structural stability or lipid binding ability of nsLTPs.

Conclusions

Taken together, this research has suggested potential residues that might be essential to modulate the structural and functional properties of plant nsLTPs. Finally, we proposed some biologically important sites of the nsLTPs, which are described by using a new Prosite-styled pattern that we defined.
Immunoproteomics based identification of thioredoxin reductase GliT and novel Aspergillus fumigatus antigens for serologic diagnosis of invasive aspergillosis
Authors: Shi Li-ning , Li Fang-qiu , Huang Mei , Lu Jing-fen , Kong Xiao-xiang , Wang Shi-qin , Shao Hai-feng
Published: January 2012

Background

There has been a rising incidence of invasive aspergillosis (IA) in critically ill patients, even in the absence of an apparent predisposing immunodeficiency. The diagnosis of IA is difficult because clinical signs are not sensitive and specific, and serum galactomannan has relatively low sensitivity in this group of patients. Therefore, more prompt and accurate disease markers for early diagnosis are needed. To establish disease markers demands a thorough knowledge of fungal antigens which may be detected in the serum or other body fluids of patients. Herein we report novel immunodominant antigens identified from extracellular proteins of Aspergillus fumigatus.

Results

Extracellular proteins of A. fumigatus were separated by two-dimensional electrophoresis (2-DE) and probed with the sera from critically ill patients with proven IA. The immunoreactive protein spots were identified by MALDI-TOF mass spectrometry (MALDI-TOF -MS). Forty spots from 2DE gels were detected and 17 different proteins were identified as immunogenic in humans. Function annotation revealed that most of these proteins were metabolic enzymes involved in carbohydrate, fatty acid, amino acid, and energy metabolism. One of the proteins, thioredoxin reductase GliT (TR), which showed the best immunoactivity, was analyzed further for secretory signals, protein localization, and homology. The results indicated that TR is a secretory protein with a signal sequence exhibiting a high probability for secretion. Furthermore, TR did not match any human proteins, and had low homology with most other fungi. The recombinant TR was recognized by the sera of all proven IA patients with different underlying diseases in this study.

Conclusions

The immunoreactive proteins identified in this study may be helpful for the diagnosis of IA in critically ill patients. Our results indicate that TR and other immunodominant antigens have potential as biomarkers for the serologic diagnosis of invasive aspergillosis.
Feminizing Wolbachia: a transcriptomics approach with insights on the immune response genes in Armadillidium vulgare
Authors: Chevalier Frédéric , Herbinière-Gaboreau Juline , Charif Delphine , Mitta Guillaume , Gavory Frédéric , Wincker Patrick , Grève Pierre , Braquart-Varnier Christine , Bouchon Didier
Published: January 2012

Background

Wolbachia are vertically transmitted bacteria known to be the most widespread endosymbiont in arthropods. They induce various alterations of the reproduction of their host, including feminization of genetic males in isopod crustaceans. In the pill bug Armadillidium vulgare, the presence of Wolbachia is also associated with detrimental effects on host fertility and lifespan. Deleterious effects have been demonstrated on hemocyte density, phenoloxidase activity, and natural hemolymph septicemia, suggesting that infected individuals could have defective immune capacities. Since nothing is known about the molecular mechanisms involved in Wolbachia-A. vulgare interactions and its secondary immunocompetence modulation, we developed a transcriptomics strategy and compared A. vulgare gene expression between Wolbachia-infected animals (i.e., “symbiotic” animals) and uninfected ones (i.e., “asymbiotic” animals) as well as between animals challenged or not challenged by a pathogenic bacteria.

Results

Since very little genetic data is available on A. vulgare, we produced several EST libraries and generated a total of 28 606 ESTs. Analyses of these ESTs revealed that immune processes were over-represented in most experimental conditions (responses to a symbiont and to a pathogen). Considering canonical crustacean immune pathways, these genes encode antimicrobial peptides or are involved in pathogen recognition, detoxification, and autophagy. By RT-qPCR, we demonstrated a general trend towards gene under-expression in symbiotic whole animals and ovaries whereas the same gene set tends to be over-expressed in symbiotic immune tissues.

Conclusion

This study allowed us to generate the first reference transcriptome ever obtained in the Isopoda group and to identify genes involved in the major known crustacean immune pathways encompassing cellular and humoral responses. Expression of immune-related genes revealed a modulation of host immunity when females are infected by Wolbachia, including in ovaries, the crucial tissue for the Wolbachia route of transmission.
Wolbachia surface protein induces innate immune responses in mosquito cells
Authors: Pinto Sofia B , Mariconti Mara , Bazzocchi Chiara , Bandi Claudio , Sinkins Steven P
Published: January 2012

Background

Wolbachiaendosymbiotic bacteria are capable of inducing chronic upregulation of insect immune genes in some situations and this phenotype may influence the transmission of important insect-borne pathogens. However the molecules involved in these interactions have not been characterized.

Results

Here we show that recombinant Wolbachia Surface Protein (WSP) stimulates increased transcription of immune genes in mosquito cells derived from the mosquito Anopheles gambiae, which is naturally uninfected with Wolbachia; at least two of the upregulated genes, TEP1 and APL1, are known to be important in Plasmodium killing in this species. When cells from Aedes albopictus, which is naturally Wolbachia-infected, were challenged with WSP lower levels of upregulation were observed than for the An. gambiaecells.

Conclusions

We have found that WSP is a strong immune elicitor in a naturally Wolbachia-uninfected mosquito species (Anopheles gambiae) while a milder elicitor in a naturally-infected species (Aedes albopictus). Since the WSP of a mosquito non-native (nematode) Wolbachia strain was used, these data suggest that there is a generalized tolerance to WSP in Ae. albopictus.
Tandem repeat markers as novel diagnostic tools for high resolution fingerprinting of Wolbachia
Authors: Riegler Markus , Iturbe-Ormaetxe Iñaki , Woolfit Megan , Miller Wolfgang J , O’Neill Scott L
Published: January 2012

Background

Strains of the endosymbiotic bacteriumWolbachia pipientisare extremely diverse both genotypically and in terms of their induced phenotypes in invertebrate hosts. Despite extensive molecular characterisation ofWolbachiadiversity, little is known about the actual genomic diversity within or between closely related strains that group tightly on the basis of existing gene marker systems, including Multiple Locus Sequence Typing (MLST). There is an urgent need for higher resolution fingerprinting markers ofWolbachiafor studies of population genetics, horizontal transmission and experimental evolution.

Results

The genome of thewMelWolbachiastrain that infectsDrosophila melanogastercontains inter- and intragenic tandem repeats that may evolve through expansion or contraction. We identified hypervariable regions inwMel, including intergenic Variable Number Tandem Repeats (VNTRs), and genes encoding ankyrin (ANK) repeat domains. We amplified these markers from 14 relatedWolbachiastrains belonging to supergroup A and were successful in differentiating size polymorphic alleles. Because of their tandemly repeated structure and length polymorphism, the markers can be used in a PCR-diagnostic multilocus typing approach, analogous to the Multiple Locus VNTR Analysis (MLVA) established for many other bacteria and organisms. The isolated markers are highly specific for supergroup A and not informative for other supergroups. However,in silicoanalysis of completed genomes from other supergroups revealed the presence of tandem repeats that are variable and could therefore be useful for typing target strains.

Conclusions

Wolbachiagenomes contain inter- and intragenic tandem repeats that evolve through expansion or contraction. A selection of polymorphic tandem repeats is a novel and useful PCR diagnostic extension to the existing MLST typing system ofWolbachia, as it allows rapid and inexpensive high-throughput fingerprinting of closely related strains for which polymorphic markers were previously lacking.
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

Background

Insects 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.

Results

To 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.

Conclusions

Library 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

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

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

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

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

Background

While 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.

Methods

A 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.

Results

Early 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.

Conclusions

Older 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.