bluuebunny/crossref_metadata_2025 huggingface dataset:
The IGS-ETS in Bacillus(Insecta Phasmida): molecular characterization and the relevance of sex in ribosomal DNA evolution
Authors: Ricci Andrea , Scali Valerio , Passamonti Marco
Published: November 2008

Background

DNA encoding for ribosomal RNA (rDNA) is arranged in tandemly-repeated subunits, each containing ribosomal genes and non-coding spacers. Because tandemly-repeated, rDNA evolves under a balanced influence of selection and "concerted evolution", which homogenizes rDNA variants over the genome (through genomic turnover mechanisms) and the population (through sexuality).

Results

In this paper we analyzed the IGS-ETS of the automictic parthenogen Bacillus atticus and the bisexual B. grandii, two closely related stick-insect species. Both species share the same IGS-ETS structure and sequence, including a peculiar head-to-tail array of putative transcription enhancers, here named Bag530. Sequence variability of both IGS-ETS and Bag530 evidenced a neat geographic and subspecific clustering in B. grandii, while B. atticus shows a little but evident geographic structure. This was an unexpected result, since the parthenogen B. atticus should lack sequence fixation through sexuality. In B. atticus a new variant might spread in a given geographic area through colonization by an all-female clone, but we cannot discard the hypothesis that B. atticus was actually a bisexual taxon in that area at the time the new variant appeared. Moreover, a gene conversion event between two Bag530 variants of B. grandii benazzii and B. grandii maretimi suggested that rRNA might evolve according to the so-called "library hypothesis" model, through differential amplification of rDNA variants in different taxa.

Conclusion

On the whole, Bacillus rDNA evolution appears to be under a complex array of interacting mechanisms: homogenization may be achieved through genomic turnover that stabilizes DNA-binding protein interactions but, simultaneously, new sequence variants can be adopted, either by direct appearance of newly mutated repeats, or by competition among repeats, so that both DNA-binding proteins and repeat variants drive each other's evolution. All this, coupled with chromosome reshuffling due to sexuality (when present), might drive a quick fixation of new rDNA variants in the populations.
Genome-wide transcriptional response of an avian pathogenic Escherichia coli (APEC) pst mutant
Authors: Crépin Sébastien , Lamarche Martin G , Garneau Philippe , Séguin Julie , Proulx Julie , Dozois Charles M , Harel Josée
Published: November 2008

Background

Avian pathogenic E. coli (APEC) are associated with extraintestinal diseases in poultry. The pstSCAB-phoU operon belongs to the Pho regulon and encodes the phosphate specific transport (Pst) system. A functional Pst system is required for full virulence in APEC and other bacteria and contributes to resistance of APEC to serum, to cationic antimicrobial peptides and acid shock. The global mechanisms contributing to the attenuation and decreased resistance of the APEC pst mutant to environmental stresses have not been investigated at the transcriptional level. To determine the global effect of a pst mutation on gene expression, we compared the transcriptomes of APEC strain χ7122 and its isogenic pst mutant (K3) grown in phosphate-rich medium.

Results

Overall, 470 genes were differentially expressed by at least 1.5-fold. Interestingly, the pst mutant not only induced systems involved in phosphate acquisition and metabolism, despite phosphate availability, but also modulated stress response mechanisms. Indeed, transcriptional changes in genes associated with the general stress responses, including the oxidative stress response were among the major differences observed. Accordingly, the K3 strain was less resistant to reactive oxygen species (ROS) than the wild-type strain. In addition, the pst mutant demonstrated reduced expression of genes involved in lipopolysaccharide modifications and coding for cell surface components such as type 1 and F9 fimbriae. Phenotypic tests also established that the pst mutant was impaired in its capacity to produce type 1 fimbriae, as demonstrated by western blotting and agglutination of yeast cells, when compared to wild-type APEC strain χ7122.

Conclusion

Overall, our data elucidated the effects of a pst mutation on the transcriptional response, and further support the role of the Pho regulon as part of a complex network contributing to phosphate homeostasis, adaptive stress responses, and E. coli virulence.
A novel custom high density-comparative genomic hybridization array detects common rearrangements as well as deep intronic mutations in dystrophinopathies
Authors: Bovolenta Matteo , Neri Marcella , Fini Sergio , Fabris Marina , Trabanelli Cecilia , Venturoli Anna , Martoni Elena , Bassi Elena , Spitali Pietro , Brioschi Simona , Falzarano Maria S , Rimessi Paola , Ciccone Roberto , Ashton Emma , McCauley Joanne , Yau Shu , Abbs Stephen , Muntoni Francesco , Merlini Luciano , Gualandi Francesca , Ferlini Alessandra
Published: November 2008

Background

The commonest pathogenic DMD changes are intragenic deletions/duplications which make up to 78% of all cases and point mutations (roughly 20%) detectable through direct sequencing. The remaining mutations (about 2%) are thought to be pure intronic rearrangements/mutations or 5'-3' UTR changes. In order to screen the huge DMD gene for all types of copy number variation mutations we designed a novel custom high density comparative genomic hybridisation array which contains the full genomic region of the DMD gene and spans from 100 kb upstream to 100 kb downstream of the 2.2 Mb DMD gene.

Results

We studied 12 DMD/BMD patients who either had no detectable mutations or carried previously identified quantitative pathogenic changes in the DMD gene. We validated the array on patients with previously known mutations as well as unaffected controls, we identified three novel pure intronic rearrangements and we defined all the mutation breakpoints both in the introns and in the 3' UTR region. We also detected a novel polymorphic intron 2 deletion/duplication variation. Despite the high resolution of this approach, RNA studies were required to confirm the functional significance of the intronic mutations identified by CGH. In addition, RNA analysis identified three intronic pathogenic variations affecting splicing which had not been detected by the CGH analysis.

Conclusion

This novel technology represents an effective high throughput tool to identify both common and rarer DMD rearrangements. RNA studies are required in order to validate the significance of the CGH array findings. The combination of these tools will fully cover the identification of causative DMD rearrangements in both coding and non-coding regions, particularly in patients in whom standard although extensive techniques are unable to detect a mutation.
The expression and antigenicity of a truncated spike-nucleocapsid fusion protein of severe acute respiratory syndrome-associated coronavirus
Authors: Mu Feng , Niu Dongsheng , Mu Jingsong , He Bo , Han Weiguo , Fan Baoxing , Huang Shengyong , Qiu Yan , You Bo , Chen Weijun
Published: November 2008

Background

In the absence of effective drugs, controlling SARS relies on the rapid identification of cases and appropriate management of the close contacts, or effective vaccines for SARS. Therefore, developing specific and sensitive laboratory tests for SARS as well as effective vaccines are necessary for national authorities.

Results

Genes encoding truncated nucleocapsid (N) and spike (S) proteins ofSARSCoVwere cloned into the expression vectorpQE30and fusionally expressed inEscherichia coliM15. The fusion protein was analyzed for reactivity with SARS patients' sera and with anti-sera against the two human coronavirusesHCoV229E andHCoVOC43 by ELISA, IFA and immunoblot assays. Furthermore, to evaluate the antigen-specific humoral antibody and T-cell responses in mice, the fusion protein was injected into 6-week-old BALB/c mice and a neutralization test as well as a T-cell analysis was performed. To evaluate the antiviral efficacy of immunization, BALB/c mice were challenged intranasally withSARSCoVat day 33 post injection and viral loads were determined by fluorescent quantitative RT-PCR. Serological results showed that the diagnostic sensitivity and specificity of the truncated S-N fusion protein derived the SARS virus were > 99% (457/460) and 100.00% (650/650), respectively. Furthermore there was no cross-reactivity with other two human coronaviruses. High titers of antibodies toSRASCoVappeared in the immunized mice and the neutralization test showed that antibodies to the fusion protein could inhibitSARSCoV. The T cell proliferation showed that the fusion protein could induce an antigen-specific T-cell response. Fluorescent quantitative RT-PCR showed that BALB/c mice challenged intranasally withSARSCoVat day 33 post injection were completely protected from virus replication.

Conclusion

The truncated S-N fusion protein is a suitable immunodiagnostic antigen and vaccine candidate.
The MYST histone acetyltransferases are essential for gametophyte development in Arabidopsis
Authors: Latrasse David , Benhamed Moussa , Henry Yves , Domenichini Séverine , Kim Wanhui , Zhou Dao-Xiu , Delarue Marianne
Published: November 2008

Background

Histone acetyltransferases (HATs) play critical roles in the regulation of chromatin structure and gene expression. Arabidopsis genome contains 12 HAT genes, but the biological functions of many of them are still unknown. In this work, we studied the evolutionary relationship and cellular functions of the two Arabidopsis HAT genes homologous to the MYST family members.

Results

An extensive phylogenetic analysis of 105 MYST proteins revealed that they can be divided into 5 classes, each of which contains a specific combination of protein modules. The two Arabidopsis MYST proteins, HAM1 and HAM2, belong to a "green clade", clearly separated from other families of HATs. Using a reverse genetic approach, we show that HAM1 and HAM2 are a functionally redundant pair of genes, as single Arabidopsis ham1 and ham2 mutants displayed a wild-type phenotype, while no double mutant seedling could be recovered. Genetic analysis and cytological study revealed that ham1ham2 double mutation induced severe defects in the formation of male and female gametophyte, resulting in an arrest of mitotic cell cycle at early stages of gametogenesis. RT-PCR experiments and the analysis of transgenic plants expressing the GUS reporter gene under the HAM1 or the HAM2 promoter showed that both genes displayed an overlapping expression pattern, mainly in growing organs such as shoots and flower buds.

Conclusion

The work presented here reveals novel properties for MYST HATs in Arabidopsis. In addition to providing an evolutionary relationship of this large protein family, we show the evidence of a link between MYST and gamete formation as previously suggested in mammalian cells. A possible function of the Arabidopsis MYST protein-mediated histone acetylation during cell division is suggested.
Human genetic selection on the MTHFR 677C>T polymorphism
Authors: Mayor-Olea Álvaro , Callejón Gonzalo , Palomares Arturo R , Jiménez Ana J , Gaitán María Jesús , Rodríguez Alfonso , Ruiz Maximiliano , Reyes-Engel Armando
Published: November 2008

Background

The prevalence of genotypes of the 677C>T polymorphism for the MTHFR gene varies among humans. In previous studies, we found changes in the genotypic frequencies of this polymorphism in populations of different ages, suggesting that this could be caused by an increase in the intake of folate and multivitamins by women during the periconceptional period. The aim was to analyze changes in the allelic frequencies of this polymorphism in a Spanish population, including samples from spontaneous abortions (SA).

Methods

A total of 1305 subjects born in the 20th century were genotyped for the 677C>T polymorphism using allele specific real-time PCR with Taqman® probes. A section of our population (n = 276) born in 1980–1989 was compared with fetal samples (n = 344) from SA of unknown etiology from the same period.

Results

An increase in the frequency of the T allele (0.38 vs 0.47; p < 0.001) and of the TT genotype (0.14 vs 0.24; p < 0.001) in subjects born in the last quarter of the century was observed. In the 1980–1989 period, the results show that the frequency of the wild type genotype (CC) is about tenfold lower in the SA samples than in the controls (0.03 vs 0.33; p < 0.001) and that the frequency of the TT genotype increases in the controls (0.19 to 0.27) and in the SA samples (0.20 to 0.33 (p < 0.01)); r = 0.98.

Conclusion

Selection in favor of the T allele has been detected. This selection could be due to the increased fetal viability in early stages of embryonic development, as is deduced by the increase of mutants in both living and SA populations.
Availability of healthier options in traditional and nontraditional rural fast-food outlets
Authors: Creel Jennifer S , Sharkey Joseph R , McIntosh Alex , Anding Jenna , Huber J Charles
Published: November 2008

Background

Food prepared away from home has become increasingly popular to U.S. families, and may contribute to obesity. Sales have been dominated by fast food outlets, where meals are purchased for dining away from home or in the home. Although national chain affiliated fast-food outlets are considered the main source for fast food, fast foods are increasingly available in convenience stores and supermarkets/grocery stores. In rural areas, these nontraditional fast-food outlets may provide most of the opportunities for procurement of fast foods.

Methods

Using all traditional and nontraditio nal fast-food outlets identified in six counties in rural Texas, the type and number of regular and healthiermenu options were surveyed using on-site observation in all food venues that were primarily fast food, supermarket/grocery store, and convenience store and compared with 2005 Dietary Guidelines.

Results

Traditional fast-food outlets represented 84 (41%) of the 205 opportunities for procurement of fast food; 109 (53.2%) were convenience stores and 12 (5.8%) supermarkets/grocery stores. Although a s imilar variety of regular breakfast and lunch/dinner entrées were available in traditional fast-food outlets and convenience stores, the variety of healthier breakfast and lunch/dinner entrées was significantly greater in fast food outlets. Compared with convenience stores, supermarkets/grocery stores provided a greater variety of regular and healthier entrées and lunch/dinner side dishes.

Conclusion

Convenience stores and supermarkets/grocery stores more than double the potential access to fast foods in this rural area than traditional fast-food outlets alone; however, traditional fast food outlets offer greater opportunity for healthier fast food options than convenience stores. A complete picture of fast food environment and the availability of healthier fast food options are essential to understand environmental influences on diet and health outcomes, and identify potential targets for intervention.
Enhanced production of nitric oxide, reactive oxygen species, and pro-inflammatory cytokines in very long chain saturated fatty acid-accumulated macrophages
Authors: Yanagisawa Naotake , Shimada Kazunori , Miyazaki Tetsuro , Kume Atsumi , Kitamura Yohei , Sumiyoshi Katsuhiko , Kiyanagi Takashi , Iesaki Takafumi , Inoue Nao , Daida Hiroyuki
Published: November 2008

Background

Deterioration of peroxisomal β-oxidation activity causes an accumulation of very long chain saturated fatty acids (VLCSFA) in various organs. We have recently reported that the levels of VLCSFA in the plasma and/or membranes of blood cells were significantly higher in patients with metabolic syndrome and in patients with coronary artery disease than the controls. The aim of the present study is to investigate the effect of VLCSFA accumulation on inflammatory and oxidative responses in VLCSFA-accumulated macrophages derived from X-linked adrenoleukodystrophy (X-ALD) protein (ALDP)-deficient mice.

Results

Elevated levels of VLCSFA were confirmed in macrophages from ALDP-deficient mice. The levels of nitric oxide (NO) production stimulated by lipopolysaccharide (LPS) and interferon-γ (IFN-γ), intracellular reactive oxygen species (ROS), and pro-inflammatory cytokines, including tumor necrosis factor-α (TNF-α), interluekin-6 (IL-6), and interleukin-12p70 (IL-12p70), were significantly higher in macrophages from ALDP-deficient mice than in those from wild-type mice. The inducible NO synthase (iNOS) mRNA expression also showed an increase in macrophages from ALDP-deficient mice.

Conclusion

These results suggested that VLCSFA accumulation in macrophages may contribute to the pathogenesis of inflammatory diseases through the enhancement of inflammatory and oxidative responses.
Drug/diet synergy for managing malignant astrocytoma in mice: 2-deoxy-D-glucose and the restricted ketogenic diet
Authors: Marsh Jeremy , Mukherjee Purna , Seyfried Thomas N
Published: November 2008

Background

Astrocytomas are largely dependent on glycolysis to satisfy their bioenergetic requirements for growth and survival. Therapies that target glycolysis can potentially manage astrocytoma growth and progression. Dietary restriction of the high fat/low carbohydrate ketogenic diet (KD-R) reduces glycolysis and is effective in managing experimental mouse and human astrocytomas. The non-metabolizable glucose analogue, 2-deoxy-D-glucose (2-DG), is a potent glycolytic inhibitor that can mimic effects of energy restriction both in vitro and in vivo, but can also produce adverse effects when administered at doses greater than 200 mg/kg. The goal here was to determine if low doses of 2-DG could act synergistically with the KD-R to better manage growth of the CT-2A malignant mouse astrocytoma.

Methods

The therapeutic effect of a KD-R supplemented with a low dose of 2-DG (25 mg/kg) was examined in adult C57BL/6J mice bearing the syngeneic CT-2A malignant astrocytoma grown orthotopically. Mice were fed the standard unrestricted diet for the first 3 days after tumor implantation prior to their separation into one of four diet groups fed either a standard rodent diet in unrestricted amounts (SD-UR) or a KD-R with or without 2-DG for 10 days. The KD-R was restricted to reduce body weight by about 20%. 2-DG was initiated 6 days after tumor implantation and was continued for 7 days. Brain tumors were excised and weighed.

Results

Energy intake, body weights, and CT-2A tumor weights were similar in the SD-UR and the SD-UR+2-2DG mouse groups over the dietary treatment period (days 3–13). Tumor weights were about 48% and 80% lower in the KD-R and in the KD-R+2-DG groups, respectively, than in the SD-UR group. Mouse health and vitality was better in the KD-R group than in the KD-R+2-DG group.

Conclusion

Astrocytoma growth was reduced more in the KD-R mouse group supplemented with 2-DG than in the mouse groups receiving either dietary restriction or 2-DG alone, indicating a synergistic interaction between the drug and the diet. The results suggest that management of malignant astrocytoma with restricted ketogenic diets could be enhanced when combined with drugs that inhibit glycolysis.
Conditional associative learning examined in a paralyzed patient with amyotrophic lateral sclerosis using brain-computer interface technology
Authors: Iversen IH , Ghanayim N , Kübler A , Neumann N , Birbaumer N , Kaiser J
Published: November 2008

Background

Brain-computer interface methodology based on self-regulation of slow-cortical potentials (SCPs) of the EEG (electroencephalogram) was used to assess conditional associative learning in one severely paralyzed, late-stage ALS patient. After having been taught arbitrary stimulus relations, he was evaluated for formation of equivalence classes among the trained stimuli.

Methods

A monitor presented visual information in two targets. The method of teaching was matching to sample. Three types of stimuli were presented: signs (A), colored disks (B), and geometrical shapes (C). The sample was one type, and the choice was between two stimuli from another type. The patient used his SCP to steer a cursor to one of the targets. A smiley was presented as a reward when he hit the correct target. The patient was taught A-B and B-C (sample – comparison) matching with three stimuli of each type. Tests for stimulus equivalence involved the untaught B-A, C-B, A-C, and C-A relations. An additional test was discrimination between all three stimuli of one equivalence class presented together versus three unrelated stimuli. The patient also had sessions with identity matching using the same stimuli.

Results

The patient showed high accuracy, close to 100%, on identity matching and could therefore discriminate the stimuli and control the cursor correctly. Acquisition of A-B matching took 11 sessions (of 70 trials each) and had to be broken into simpler units before he could learn it. Acquisition of B-C matching took two sessions. The patient passed all equivalence class tests at 90% or higher.

Conclusion

The patient may have had a deficit in acquisition of the first conditional association of signs and colored disks. In contrast, the patient showed clear evidence that A-B and B-C training had resulted in formation of equivalence classes. The brain-computer interface technology combined with the matching to sample method is a useful way to assess various cognitive abilities of severely paralyzed patients, who are without reliable motor control.
Antimicrobial and antioxidant activities of Cortex Magnoliae Officinalis and some other medicinal plants commonly used in South-East Asia
Authors: Chan Lai Wah , Cheah Emily LC , Saw Constance LL , Weng Wanyu , Heng Paul WS
Published: November 2008

Background

Eight medicinal plants were tested for their antimicrobial and antioxidant activities. Different extraction methods were also tested for their effects on the bioactivities of the medicinal plants.

Methods

Eight plants, namely Herba Polygonis Hydropiperis (Laliaocao), Folium Murraya Koenigii (Jialiye), Rhizoma Arachis Hypogea (Huashenggen), Herba Houttuyniae (Yuxingcao), Epipremnum pinnatum (Pashulong), Rhizoma Typhonium Flagelliforme (Laoshuyu), Cortex Magnoliae Officinalis (Houpo) and Rhizoma Imperatae (Baimaogen) were investigated for their potential antimicrobial and antioxidant properties.

Results

Extracts of Cortex Magnoliae Officinalis had the strongest activities against M. Smegmatis, C. albicans, B. subtilis and S. aureus. Boiled extracts of Cortex Magnoliae Officinalis, Folium Murraya Koenigii, Herba Polygonis Hydropiperis and Herba Houttuyniae demonstrated greater antioxidant activities than other tested medicinal plants.

Conclusion

Among the eight tested medicinal plants, Cortex Magnoliae Officinalis showed the highest antimicrobial and antioxidant activities. Different methods of extraction yield different spectra of bioactivities.
Arena3D: visualization of biological networks in 3D
Authors: Pavlopoulos Georgios A , O'Donoghue Seán I , Satagopam Venkata P , Soldatos Theodoros G , Pafilis Evangelos , Schneider Reinhard
Published: November 2008

Background

Complexity is a key problem when visualizing biological networks; as the number of entities increases, most graphical views become incomprehensible. Our goal is to enable many thousands of entities to be visualized meaningfully and with high performance.

Results

We present a new visualization tool, Arena3D, which introduces a new concept of staggered layers in 3D space. Related data – such as proteins, chemicals, or pathways – can be grouped onto separate layers and arranged via layout algorithms, such as Fruchterman-Reingold, distance geometry, and a novel hierarchical layout. Data on a layer can be clustered via k-means, affinity propagation, Markov clustering, neighbor joining, tree clustering, or UPGMA ('unweighted pair-group method with arithmetic mean'). A simple input format defines the name and URL for each node, and defines connections or similarity scores between pairs of nodes. The use of Arena3D is illustrated with datasets related to Huntington's disease.

Conclusion

Arena3D is a user friendly visualization tool that is able to visualize biological or any other network in 3D space. It is free for academic use and runs on any platform. It can be downloaded or lunched directly from http://arena3d.org. Java3D library and Java 1.5 need to be pre-installed for the software to run.
Carboplatin-induced gene expression changes in vitroare prognostic of survival in epithelial ovarian cancer
Authors: Konstantinopoulos Panagiotis A , Fountzilas Elena , Pillay Kamana , Zerbini Luiz F , Libermann Towia A , Cannistra Stephen A , Spentzos Dimitrios
Published: November 2008

Background

We performed a time-course microarray experiment to define the transcriptional response to carboplatin in vitro, and to correlate this with clinical outcome in epithelial ovarian cancer (EOC). RNA was isolated from carboplatin and control-treated 36M2 ovarian cancer cells at several time points, followed by oligonucleotide microarray hybridization. Carboplatin induced changes in gene expression were assessed at the single gene as well as at the pathway level. Clinical validation was performed in publicly available microarray datasets using disease free and overall survival endpoints.

Results

Time-course and pathway analyses identified 317 genes and 40 pathways (designated time-course and pathway signatures) deregulated following carboplatin exposure. Both types of signatures were validated in two separate platinum-treated ovarian and NSCLC cell lines using published microarray data. Expression of time-course and pathway signature genes distinguished between patients with unfavorable and favorable survival in two independent ovarian cancer datasets. Among the pathways most highly induced by carboplatin in vitro, the NRF2, NF-kB, and cytokine and inflammatory response pathways were also found to be upregulated prior to chemotherapy exposure in poor prognosis tumors.

Conclusion

Dynamic assessment of gene expression following carboplatin exposure in vitro can identify both genes and pathways that are correlated with clinical outcome. The functional relevance of this observation for better understanding the mechanisms of drug resistance in EOC will require further evaluation.
Sensitization of ovarian cancer cells to cisplatin by genistein: the role of NF-kappaB
Authors: Solomon Leigh A , Ali Shadan , Banerjee Sanjeev , Munkarah Adnan R , Morris Robert T , Sarkar Fazlul H
Published: November 2008

Background

Platinum-resistance (PR) continues to be a major problem in the management of epithelial ovarian cancer (EOC). Response to various chemotherapeutic agents is poor in patients deemed PR. Genistein, a soy isoflavone has been shown to enhance the effect of chemotherapy in prostate and pancreatic cancer cells in vitro and in vivo by reversing chemo-resistance phenotype. The goal of this study was to investigate the effects of combination therapy with genistein and cisplatin as well as other cytotoxic conventional chemotherapeutic agents in platinum-sensitive (PS) and resistant EOC cells.

Methods

The PS human ovarian cancer cell line A2780 and its PR clone C200 cells were pretreated with genistein, followed by the combination of genistein and either cisplatin, taxotere or gemcitabine. Cell survival and apoptosis was assessed by MTT and histone-DNA ELISA. Electrophoretic mobility shift assay (EMSA) was used to evaluate NF-κB DNA binding activity. Western blot analysis was performed with antibodies to Bcl-2, Bcl-xL, survivin, c-IAP and PARP.

Results

Reduction in cell viability, and corresponding induction of apoptosis was observed with genistein pretreatment followed by combination treatment with each of the drugs in both cell lines. The PS cell line was pretreated for 24 hours; in contrast, the PR cell line required 48 hours pretreatment to achieve a response. The anti-apoptotic genes c-IAP1, Bcl-2, Bcl-xL, survivin and NF-κB DNA binding activity were all found to be down-regulated in the combination groups.

Conclusion

This study convincingly demonstrated that the current strategy can be translated in a pre-clinical animal model, and thus it should stimulate future clinical trial for the treatment of drug-resistant ovarian cancer.
Genome adaptation to chemical stress: clues from comparative transcriptomics in Saccharomyces cerevisiae and Candida glabrata
Authors: Lelandais Gaëlle , Tanty Véronique , Geneix Colette , Etchebest Catherine , Jacq Claude , Devaux Frédéric
Published: November 2008

Background

Recent technical and methodological advances have placed microbial models at the forefront of evolutionary and environmental genomics. To better understand the logic of genetic network evolution, we combined comparative transcriptomics, a differential clustering algorithm and promoter analyses in a study of the evolution of transcriptional networks responding to an antifungal agent in two yeast species: the free-living model organism Saccharomyces cerevisiae and the human pathogen Candida glabrata.

Results

We found that although the gene expression patterns characterizing the response to drugs were remarkably conserved between the two species, part of the underlying regulatory networks differed. In particular, the roles of the oxidative stress response transcription factors ScYap1p (in S. cerevisiae) and Cgap1p (in C. glabrata) had diverged. The sets of genes whose benomyl response depends on these factors are significantly different. Also, the DNA motifs targeted by ScYap1p and Cgap1p are differently represented in the promoters of these genes, suggesting that the DNA binding properties of the two proteins are slightly different. Experimental assays of ScYap1p and Cgap1p activities in vivo were in accordance with this last observation.

Conclusions

Based on these results and recently published data, we suggest that the robustness of environmental stress responses among related species contrasts with the rapid evolution of regulatory sequences, and depends on both the coevolution of transcription factor binding properties and the versatility of regulatory associations within transcriptional networks.
Whole genome transcriptome polymorphisms in Arabidopsis thaliana
Authors: Zhang Xu , Byrnes Jake K , Gal Thomas S , Li Wen-Hsiung , Borevitz Justin O
Published: November 2008

Whole genome tiling arrays are a key tool for profiling global genetic and expression variation. In this study we present our methods for detecting transcript level variation, splicing variation and allele specific expression in Arabidopsis thaliana. We also developed a generalized hidden Markov model for profiling transcribed fragment variation de novo. Our study demonstrates that whole genome tiling arrays are a powerful platform for dissecting natural transcriptome variation at multi-dimension and high resolution.
Chromatin Central: towards the comparative proteome by accurate mapping of the yeast proteomic environment
Authors: Shevchenko Anna , Roguev Assen , Schaft Daniel , Buchanan Luke , Habermann Bianca , Sakalar Cagri , Thomas Henrik , Krogan Nevan J , Shevchenko Andrej , Stewart A Francis
Published: November 2008

Background

Understanding the design logic of living systems requires the understanding and comparison of proteomes. Proteomes define the commonalities between organisms more precisely than genomic sequences. Because uncertainties remain regarding the accuracy of proteomic data, several issues need to be resolved before comparative proteomics can be fruitful.

Results

The Saccharomyces cerevisiae proteome presents the highest quality proteomic data available. To evaluate the accuracy of these data, we intensively mapped a proteomic environment, termed 'Chromatin Central', which encompasses eight protein complexes, including the major histone acetyltransferases and deacetylases, interconnected by twelve proteomic hyperlinks. Using sequential tagging and a new method to eliminate background, we confirmed existing data but also uncovered new subunits and three new complexes, including ASTRA, which we suggest is a widely conserved aspect of telomeric maintenance, and two new variations of Rpd3 histone deacetylase complexes. We also examined the same environment in fission yeast and found a very similar architecture based on a scaffold of orthologues comprising about two-thirds of all proteins involved, whereas the remaining one-third is less constrained. Notably, most of the divergent hyperlinks were found to be due to gene duplications, hence providing a mechanism for the fixation of gene duplications in evolution.

Conclusions

We define several prerequisites for comparative proteomics and apply them to examine a proteomic environment in unprecedented detail. We suggest that high resolution mapping of proteomic environments will deliver the highest quality data for comparative proteomics.
A Class Act
Authors: Krahulik Karen C.
Published: November 2008

In “A Class Act,” Karen C. Krahulik returns to the scene of her community history of Provincetown, Massachusetts, but uses a different methodology to assess the relationship between gentrification and transgression. Remaining within, but not confined by, the fields of history and oral history, Krahulik turns also to queer theory and performance studies to examine how artistic expression can be disruptive of Provincetown's seemingly facile slide toward homonormativity. In one section Krahulik assesses how the star of her essay, Ryan Landry, converted an underprivileged childhood into a successful form of “white trash” performance called, “booger drag.” In another section she analyzes not only the subversive content, but also the timing of Landry's performances in a town that once was, but is no longer, necessarily queer. Analyzing Provincetown's history in the context of Landry's vexed iterations, allows Krahulik to provide a much more nuanced analysis of change over time in one of this country's most renowned gay resort meccas.
“Queen of the Picket Line”: Beauty Contests in the Post–world War II Canadian Labor Movement, 1945–1970
Authors: Sangster Joan
Published: November 2008

This article examines the proliferation of beauty contests sponsored by the union movement after World War II, as a means of exploring the contradictions of the Fordist accord for women workers, and also feminist scholarship on beauty and the body. Beauty contests were articulations of labor pride and identity; they reflected the popular culture of the post-war period, labor's search for respectability, and labor's attempts to entice women into the movement by appealing to women's culture. A few contests even offered more subversive meanings of beauty by celebrating the `queen of the picket line.' However, most labor beauty contests promoted competitive individualism, consumption, and images of passive femininity that kept women marginalized on the sidelines of the labor movements. Le Bal des Midinettes, sponsored by the ILGWU, was an excellent example of these contradictions, espousing both faith in the Cinderella myth and a sense of French Canadian working-class pride. While theories stressing identity, agency, and subjectivity offer some insights into beauty contests, feminist-materialist analyses of commodification, exploitation, and ideology remain essential to our understanding of their meaning for, and impact on women workers in this period.
Phenotypic differences in terrestrial frog embryos: effect of water potential and phase
Authors: Andrewartha Sarah J. , Mitchell Nicola J. , Frappell Peter B.
Published: November 2008

The terrestrial embryos of many amphibians obtain water in two ways; in a liquid phase from the substrate on which eggs are deposited, and in a vapour phase from the surrounding atmosphere. We tested whether the mode of water flux (liquid or vapour) affected the morphology and metabolic traits of the terrestrial Victorian smooth froglet (Geocrinia victoriana) embryos by incubating eggs both with a liquid water source and at a range of vapour water potentials. We found that embryos incubated with a liquid water source(ψπ=0 kPa) were better hydrated than embryos incubated with a vapour water source (ψv=0 kPa), and grew to a larger size. Eggs incubated in atmospheres with lower ψv values showed significant declines in mass and in the thickness of the jelly capsule, while embryos primarily showed reductions in dry mass, total length, tail length and fin height. The most significant deviations from control (ψv=0 kPa) values were observed when the ψv of the incubation media was less than the osmotic water potential (ψπ) of the embryonic interstitial fluid (approximately –425 kPa). Despite the caveat that a ψv of 0 kPa is probably difficult to achieve under our experimental conditions, the findings indicate the importance for eggs under natural conditions of contacting liquid water in the nesting substrate to allow swelling of the capsule.
Haemoglobin as a buoyancy regulator and oxygen supply in the backswimmer(Notonectidae, Anisops)
Authors: Matthews Philip G. D. , Seymour Roger S.
Published: November 2008

Unlike all other diving insects, backswimmers of the genus Anisopscan exploit the pelagic zone by temporarily achieving near-neutral buoyancy during the course of a dive. They begin a dive positively buoyant due to the large volume of air carried in their ventral air-stores, but rapidly enter a protracted period of near-neutral buoyancy before becoming negatively buoyant. This dive profile is due to haemoglobin found in large tracheated cells in the abdomen. Fibre optic oxygen probes placed in the air-stores of submerged bugs revealed that oxygen partial pressure (PO2)dropped in a sigmoid curve, where a linear decline preceded a plateau between 5.1 and 2.0 kPa, before a final drop. Buoyancy measurements made by attaching backswimmers to a sensitive electronic balance showed the same three phases. Inactivating the haemoglobin by fumigating backswimmers with 15% CO eliminated both buoyancy and PO2 plateaus. Oxygen unloaded from the haemoglobin stabilises the air-store during the neutrally buoyant phase after a decrease in volume of between 16% and 19%. Using measurements of air-store PO2 and volume, it was calculated that during a dive the haemoglobin and air-store contribute 0.25 and 0.26μl of oxygen, respectively.
Hypotaurine and sulfhydryl-containing antioxidants reduce H2S toxicity in erythrocytes from a marine invertebrate
Authors: Ortega J. A. , Ortega J. M. , Julian D.
Published: November 2008

Hypotaurine (HT) has been proposed to reduce sulfide toxicity in some deep-sea invertebrates by scavenging free radicals produced from sulfide oxidation or by scavenging sulfide via the reaction of HT with sulfide, forming thiotaurine (ThT). We tested whether HT or several antioxidants could reduce the total dissolved sulfide concentration in buffered seawater exposed to H2S, and whether HT, ThT or antioxidants could increase the viability of Glycera dibranchiataerythrocytes exposed to H2S in vitro. We found that 5 and 50 mmol l–1 HT reduced the dissolved sulfide in cell-free buffer exposed to H2S by up to 80% whereas the antioxidants glutathione ethyl ester (GEE), N-acetylcysteine (NAC), l-ascorbic acid (ASC), Tempol and Trolox had no consistent effect. Exposure of erythrocytes to 0.10%–3.2% H2S (producing 0.18–4.8 mmol l–1 sulfide) decreased the fraction of viable cells, as evidenced by loss of plasma membrane integrity, with virtually no cells remaining viable at 1.0% or more H2S. Addition of HT (0.5–50 mmol l–1) significantly increased the fraction of viable cells (e.g. from 0.01 to 0.84 at 0.32% H2S) whereas ThT (0.5 and 5 mmol l–1) decreased cell viability. GEE (0.03–3 mmol l–1) and NAC (0.001–1 mmol l–1), which contain sulfhydryl groups, increased cell viability during H2S exposure but to a lesser extent than HT whereas ASC, Tempol and Trolox, which do not contain sulfhydryl groups, decreased viability or had no effect. These data show that HT can protect cells from sulfide in vitro and suggest that sulfide scavenging, rather than free radical scavenging, is the most important mechanism of protection.
Low-temperature CO Oxidation over Coprecipitated Co–Ce–Mn Oxides
Authors: Guo Qiang , Tang Zhao , Liu Yuan
Published: November 2008

Co3O4–CeO2–MnOx catalysts prepared by coprecipitation are very active for CO oxidation at low temperature, and 100% CO conversion is obtained at −70 °C over the best catalyst; Adding a small mount of MnOx in CoOx–CeO2 can improve the dispersion of cobalt oxide and ceria effectively, which leads to high CO oxidation activity.
Catalytic Conjugate Addition of Indoles to 4-Aryl-4-oxobut-2-enoates by FeCl3
Authors: Wang Xiaoxia , Zhang Yaohong , Xiao Xiaohui , Li Xinsheng
Published: November 2008

The conjugate addition of indoles to 4-aryl-4-oxobut-2-enoates was achieved with FeCl3 as a catalyst under mild conditions. The reaction was highly regioselective and afforded a variety of new 3-substituted indoles in good to excellent yields.
The horofunction boundary of the Hilbert geometry
Authors: Walsh Cormac
Published: November 2008

We investigate the horofunction boundary of the Hilbert geometry defined on an arbitrary finite-dimensional bounded convex domainD. We determine its set of Busemann points, which are those points that are the limits of “almost-geodesics”. In addition, we show that any sequence of points converging to a point in the horofunction boundary also converges in the usual sense to a point in the Euclidean boundary ofD. We prove that all horofunctions are Busemann points if and only if the set of extreme sets of the polar ofDis closed in the Painlevé–Kuratowski topology.
Totally non-real divisors in linear systems on smooth real curves
Authors: Coppens Marc
Published: November 2008

Let X be a smooth real curve of genus g ≥ 1 having some real point. Define M(X) as being the smallest integer m such that each line bundle L on X of even degree at least 2m having restrictions of even degree to each connected component of X(ℝ) contains a totally non-real divisor inside |L| (hence a divisor containing no real point of X). In this paper we prove that M(X) = g.
Recent progress in research on the cutting processes of wood. A review COST Action E35 2004–2008: Wood machining – micromechanics and fracture
Authors: Orlowski Kazimierz A. , Palubicki Bartosz
Published: November 2008

Recent progress in research on the cutting processes of wood is presented, particularly in regard to new methods of accomplishing an increase in volume recovery by sawmills. The suitability of modern fracture mechanics was demonstrated for the estimation of the cutting power for saws in which kerfs are different from saws used in cutting tests, and whereby the data of sawn material – such as the specific work of surface formation (toughness) and the shear yield stress – were determined. Cutting tests were carried out on the modern frame sawing machine (sash gang saw) for narrow-kerf sawing with the hybrid dynamically balanced driving system and elliptical teeth trajectory movement.
Sicherheitsbewertung von Fahrstrategien kognitiver Automobile Safety Assessment of Driving Strategies of Cognitive Cars
Authors: Althoff Matthias , Stursberg Olaf , Buss Martin
Published: November 2008

Von (kognitiven) autonomen Fahrzeugen geplante Fahrtrajektorien können in statischen Umgebungen durch Kollisionsabfragen mit den zu umfahrenden Hindernissen abgesichert werden. In den meisten Straßenverkehrsszenarien genügt dieses Vorgehen nicht, da zusätzlich die Dynamik anderer Verkehrsteilnehmer berücksichtigt werden muss. Dazu werden in dieser Arbeit die erreichbaren Straßenbereiche und die Wahrscheinlichkeitsverteilung der Positionen anderer Verkehrsteilnehmer (unter Berücksichtigung von Interaktion) bestimmt. Dies erlaubt die Bestimmung der Kollisionswahrscheinlichkeiten des autonomen Fahrzeugs mit anderen Verkehrsteilnehmern, so dass geplante Fahrtrajektorien des kognitiven Fahrzeugs hinsichtlich ihrer Sicherheit bewertet werden können.
Regelung von drehzahlvariablen Windenergieanlagen Control of Variable Speed Wind Turbines
Authors: Geyler Martin , Caselitz Peter
Published: November 2008

Im vorliegenden Übersichtsbeitrag soll der Stand der Technik bei der Regelung großer drehzahlvariabler Windenergieanlagen mit Blattwinkelverstellung dargestellt werden. Ausgehend von den grundlegenden aerodynamischen Prinzipen wird detailliert auf die regelungstechnischen Problemstellungen bei diesem Anlagenkonzept eingegangen. Ein Ausblick auf zukünftig zu erwartende Entwicklungen wird gegeben.
Der Löwe von Tadmor. Palmyra und der unwahrscheinliche Aufstieg des Septimius OdaenathusThe Lion of Tadmor. Palmyra and the Improbable Ascension of Septimius Odaenathus
Authors: Sommer Michael
Published: November 2008

Für ein Dutzend Jahre, von der Niederlage Valerians bei Karrhai (260 n. Chr.) bis zur Einnahme der Stadt durch Kaiser Aurelian (272 n. Chr.) war Palmyra ein Brennpunkt römischer Reichspolitik. Als Roms Herrschaft über seine orientalischen Provinzen unter dem kombinierten Druck sasanidischer Offensiven und der Einbrüche wandernder Stämme an den nördlichen Reichsgrenzen zusammenzubrechen drohte und selbst Großstädte wie Antiocheia dem Feind ihre Tore öffneten, schlug die Stunde des Septimius Odaenathus, des Exarchen von Palmyra, den das zeitgenössische 13. Sibyllinische Orakel zum sonnengesandten Löwen, zur quasi-messianischen Rettergestalt verklärte. Unter Führung des Palmyreners gingen die Reste der geschlagenen Legionen, verstärkt um das Aufgebot der Oasenstadt, in die Offensive und standen wenig später vor den Toren der persischen Hauptstadt Ktesiphon. Odaenathus starb 167 oder 168 n. Chr. unter ungeklärten Umständen; die Nachfolge traten seine Witwe Zenobia und der gemeinsame, noch unmündige Sohn Vaballathus an. Während beide sich als legitime Erben des mit weitreichenden Sondervollmachten ausgestatteten Odaenathus betrachteten, konnten Roms Kaiser den einzigartigen Autonomiestatus Palmyras nicht länger akzeptieren. Ein Krieg war unvermeidlich; ihn konnte Palmyra gegen das wieder erstarkte Rom nur verlieren. Wie ist der kometenhafte Aufstieg des Septimius Odaenathus zu erklären? Was waren die Voraussetzungen dafür, daß Palmyra  im römischen Reichsverband  zu einer autonom agierenden politischen Größe heranreifte? Und wo lagen die Gründe für das Zerwürfnis zwischen Odaenaths Erben und den Kaisern in Rom? Der Beitrag versucht sich in der Beantwortung dieser gerade auch für das Verständnis der römischen Herrschaft insgesamt elementaren Fragen.