bluuebunny/crossref_metadata_2025 huggingface dataset:
Search for past life on Mars: Physical and chemical characterization of minerals of biotic and abiotic origin: 2. Aragonite
Authors: Stalport F. , Coll P. , Szopa C. , Person A. , Navarro‐González R. , Cabane M. , Ausset P. , Vaulay M. J.
Published: December 2007

One of the major objectives of the future Martian surface probes will be to reveal a past or present biological activity. We propose that biominerals could have recorded such an activity at Mars, and thus could be interesting targets for these missions. Therefore, we try to find a method capable to discriminate biominerals from their geochemical counterparts. With this aim, various terrestrial aragonites of biotic and abiotic origins were studied as reference minerals, because they could have also been produced at Mars. Their thermal properties were studied with differential thermal analysis, and then compared. The results show that biotic aragonites thermally decompose at temperatures at least 20°C lower than the temperatures of decomposition of abiotic aragonites. Therefore, the temperatures of thermal degradation of such biominerals could be a relevant parameter to find a past biological activity at Mars, and differential thermal analysis could be useful for situ astrobiological exploration of Mars.
Expression and analysis of thymosin α1 concatemer in Escherichia coli
Authors: Chen Yuhui , Zhao Lingxia , Shen Guoan , Cui Lijie , Ren Weiwei , Zhang Hui , Qian Hongmei , Tang Kexuan
Published: December 2007

Tα1 (thymosin α 1) is important in treating immunodeficiency and other diseases. In order to study the feasibility of expressing Tα1 in plants, as the first attempt, we designed and synthesized the Tα1 gene according to the plant codon usage preference and constructed the 4×Tα1 concatemer (four copies of a DNA sequence arranged end‐to‐end in tandem). The latter was inserted into Escherichia coli expression vector pQE30, resulting in a recombinant plasmid that was subsequently transformed into E. coli M15. The 4×Tα1 concatemer protein was successfully expressed in E. coli in a soluble form. The expressed protein was purified and its bioactivity was analysed by MTT [3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyl‐2H‐tetrazolium bromide] assay. Preliminary results showed that the 4×Tα1 concatemer protein could stimulate the mice spleen lymphocyte proliferation. This is the first report on the expression of 4×Tα1 concatemer that was synthesized according to plant codon usage preference in an E. coli expression system. The present study provides the basis for expressing the synthesized active Tα1 gene in plants in the future.
Evoked brain responses are generated by feedback loops
Authors: Garrido Marta I. , Kilner James M. , Kiebel Stefan J. , Friston Karl J.
Published: December 2007

Neuronal responses to stimuli, measured electrophysiologically, unfold over several hundred milliseconds. Typically, they show characteristic waveforms with early and late components. It is thought that early or exogenous components reflect a perturbation of neuronal dynamics by sensory input bottom-up processing. Conversely, later, endogenous components have been ascribed to recurrent dynamics among hierarchically disposed cortical processing levels, top-down effects. Here, we show that evoked brain responses are generated by recurrent dynamics in cortical networks, and late components of event-related responses are mediated by backward connections. This evidence is furnished by dynamic causal modeling of mismatch responses, elicited in an oddball paradigm. We used the evidence for models with and without backward connections to assess their likelihood as a function of peristimulus time and show that backward connections are necessary to explain late components. Furthermore, we were able to quantify the contribution of backward connections to evoked responses and to source activity, again as a function of peristimulus time. These results link a generic feature of brain responses to changes in the sensorium and a key architectural component of functional anatomy; namely, backward connections are necessary for recurrent interactions among levels of cortical hierarchies. This is the theoretical cornerstone of most modern theories of perceptual inference and learning.
Son of Notch, a Winged‐helix Gene Involved in Boundary Formation in the Drosophila Wing
Authors: Park Eungsik , Suh Hyunsuk , Kim Changsoo , Park Seungwoo , Dorsett Dale , Yim Jeongbin
Published: December 2007

A P element enhancer trap screen was conducted to identify genes involved in dorsal‐ventral boundary formation in Drosophila. The son of Notch (son) gene was identified by the son2205 enhancer trap insertion, which is a partial loss‐of‐function mutation. Based on son2205 mutant phenotypes and genetic interactions with Notch and wingless mutations, we conclude that son participates in wing development, and functions in the Notch signaling pathway at the dorsal‐ventral boundary in the wing. Notch signaling pathway components activate son enhancer trap expression in wing cells. son enhancer trap expression is regulated positively by wingless, and negatively by cut in boundary cells. Ectopic Son protein induces wingless and cut expression in wing discs. We hypothesize that there is positive feedback regulation of son by wingless, and negative regulation by cut at the dorsal‐ventral boundary during wing development.
Role of the MRP1/ABCC1 Multidrug Transporter Protein in Cancer
Authors: Munoz Marcia , Henderson Michelle , Haber Michelle , Norris Murray
Published: December 2007

Multidrug resistance is a major obstacle to cancer treatment and leads to poor prognosis for the patient. Multidrug resistance‐associated protein 1 (MRP1) transports a wide range of therapeutic agents as well as diverse physiological substrates and may play a role in the development of drug resistance in several cancers including those of the lung, breast and prostate, as well as childhood neuroblastoma. The majority of patients with neuroblastoma present with widely disseminated disease at diagnosis and despite intensive treatment, the prognosis for such patients is dismal. There is increasing evidence that MRP1 is a MYCN target gene involved in the development of multidrug resistance in neuroblastoma. Given the importance of MRP1 overexpression in neuroblastoma, MRP1 inhibition may be a clinically relevant approach to improving patient outcome in this disease.
affyGG: computational protocols for genetical genomics with Affymetrix arrays
Authors: Alberts Rudi , Vera Gonzalo , Jansen Ritsert C.
Published: December 2007

Motivation: Affymetrix arrays use multiple probes per gene to measure mRNA abundances. Standard software takes averages over probes. Important information may be lost if polymorphisms in the mRNA affect the hybridization of individual probes.

Results: We present custom software to analyze genetical genomics experiments in human, mouse and other organisms: (i) an R package providing functions for QTL analysis at the individual probe level and (ii) Perl scripts providing custom tracks in the UCSC Genome Browser to check for sequence polymorphisms in probe regions.

Availability:  http://gbic.biol.rug.nl/supplementary

Contact:  r.c.jansen@rug.nl
A new algorithm for cluster analysis of genomic methylation: the Helicobacter pylori case
Authors: Vale F.F. , Encarnação P. , Vítor J. M. B.
Published: December 2007

Motivation: The genomic methylation analysis is useful to type bacteria that have a high number of expressed type II methyltransferases. Methyltransferases are usually committed to Restriction and Modification (R-M) systems, in which the restriction endonuclease imposes high pressure on the expression of the cognate methyltransferase that hinder R-M system loss. Conventional cluster methods do not reflect this tendency. An algorithm was developed for dendrogram construction reflecting the propensity for conservation of R-M Type II systems.

Results: The new algorithm was applied to 52 Helicobacter pylori strains from different geographical regions and compared with conventional clustering methods. The algorithm works by first grouping strains that share a common minimum set of R-M systems and gradually adds strains according to the number of the R-M systems acquired. Dendrograms revealed a cluster of African strains, which suggest that R-M systems are present in H.pylori genome since its human host migrates from Africa.

Availability: The software files are available at http://www.ff.ul.pt/paginas/jvitor/Bioinformatics/MCRM_algorithm.zip

Contact:  filipavale@fe.ucp.pt

Supplementary information: Supplementary data are available at Bioinformatics online.
Reactivity pattern of 92 monoclonal antibodies with 15 human papillomavirus types
Authors: Rizk Raeda Z. , Christensen Neil D. , Michael Kristina M. , Müller Martin , Sehr Peter , Waterboer Tim , Pawlita Michael
Published: December 2007

Most anti-human papillomavirus (HPV) capsid antibody assays are based on virus-like particles (VLP). We evaluated glutathione S-transferase (GST)–L1 fusion proteins as ELISA antigens for determining type specificity and cross-reactivity of 92 VLP-specific monoclonal antibodies (mAb) generated against nine mucosal alpha papillomavirus types of species 7, 9 and 10. The antibody panel included 25 new mAb, and 24 previously published mAb are further characterized. We determined the cross-reactivity patterns with 15 different HPV types representing 6 species (alpha1, 2, 4, 7, 9 and 10) and neutralization and cross-neutralization properties with HPV types 6, 11, 16, 18 and 45. Eighty-nine (97 %) of the antibodies including 34, 71 and 14 recognizing neutralizing, conformational and linear epitopes, respectively, reacted with the GST–L1 protein of the HPV type used as immunogen, with log titres ranging from 2.0 to 7.3. Of these 89 antibodies, 52 % were monotypic, 20 % showed intra-species and 28 % inter-species cross-reactivity. Log neutralization titres to the immunogen HPV ranged from 1.7 to 5.6. A single cross-neutralizing mAb (H6.L12) was found. ELISA titres were always higher than neutralization titres. All neutralizing epitopes were conformational and mostly type-specific. Our data show that bacterially expressed, affinity-purified GST–L1 fusion proteins display a broad variety of epitopes and thus are well suited for detection of HPV antibodies. Cross-reactivity is associated with linear as well as conformational epitopes. Distantly related mucosal and skin alpha papillomaviruses share some conformational epitopes and the phylogenetic L1-based species definition may not define a serological unit since no species-specific epitope was found.
Histone modifications associated with herpes simplex virus type 1 genomes during quiescence and following ICP0-mediated de-repression
Authors: Coleman Heather M. , Connor Viv , Cheng Zara S. C. , Grey Finn , Preston Chris M. , Efstathiou Stacey
Published: December 2007

In the current study, it was shown that repressed virus genomes in quiescently infected MRC5 cells adopt a repressed histone-associated structure marked by the enrichment of deacetylated histones at a wide variety of herpes simplex virus type 1 (HSV-1) promoters. In addition, it was shown that genome de-repression, mediated by HSV-2 superinfection or delivery of ICP0 using a recombinant adenovirus vector, resulted in the enrichment of acetylated histones on HSV DNA. These data indicate that ICP0-mediated genome de-repression is intimately linked to enrichment of acetylated histones at virus promoters. The fold change in association of pan-acetylated histone H3 following Ad.TRE.ICP0-mediated de-repression consistently revealed promoter-specific variation, with the highest fold changes (>50-fold) being observed at the latency-associated transcript promoter and enhancer regions. Chromatin immunoprecipitation analyses using an antibody specific to the C terminus of histone H3 as a surrogate measure of nucleosome occupancy revealed little variability in the total loading of histone H3 at the various HSV promoters. This observation suggests that acetylation of histone H3 in response to ICP0 expression is not uniformly targeted across the HSV-1 genome during ICP0-mediated de-repression.
Induction of L1 and L2 β-Lactamases of
Stenotrophomonas maltophilia
Authors: Hu Rouh-Mei , Huang Kuang-Jay , Wu Lii-Tzu , Hsiao Ying-Ju , Yang Tsuey-Ching
Published: December 2007

Isogenic L1 and L2 gene knockout mutants of
Stenotrophomonas maltophilia
KJ (KJΔL1 and KJΔL2, respectively) were constructed by
xylE
gene replacement. Induction kinetics of the L1 and L2 genes were evaluated by testing catechol 2,3-dioxygenase activity in the mutants. The results suggested that the induction of the L1 and L2 genes was differentially regulated.
Adsorption of Amikacin, a Significant Mechanism of Elimination by Hemofiltration
Authors: Tian Qi , Gomersall Charles D. , Ip Margaret , Tan Perpetua E. , Joynt Gavin M. , Choi Gordon Y. S.
Published: December 2007

We used an in vitro model of continuous venovenous hemofiltration (CVVH) to characterize amikacin adsorption by polyacrylonitrile (PAN) and polyamide filters. A blood-crystalloid mixture dosed with amikacin was pumped from a reservoir through a hemofiltration circuit and back to the reservoir. All ultrafiltrate was also returned to the reservoir. The level of adsorption was calculated from the fall in the amikacin concentration. The dose and the initial concentration of amikacin were varied, as were the pH, the type of hemofilter, and the hemofilter surface area. The reversibility of adsorption and the effect of repeated dosing were also studied. The level of adsorption by 0.6-m
2
PAN filters was significantly greater than that by 0.6-m
2
polyamide filters. Adsorption was increased by increasing the dose of amikacin even when the initial concentration was unchanged. It was unaffected by the pH (pH 6.8 or 7.4) or the hemofilter surface area (0.6 m
2
or 0.9 m
2
). Repeated doses of amikacin resulted in further adsorption. In a saturation experiment, the maximum adsorptive capacity of 0.6-m
2
PAN hemofilters was at least 546.9 mg (range, 427.6 to 577.5 mg). The adsorption of amikacin by hemofilters is irreversible and was associated with the dose and the hemofilter material but not the hemofilter surface area. Close monitoring of peak amikacin levels should be considered for patients receiving CVVH with PAN hemofilters.
Relative Replication Capacity and Selective Advantage Profiles of Protease Inhibitor-Resistant Hepatitis C Virus (HCV) NS3 Protease Mutants in the HCV Genotype 1b Replicon System
Authors: He Yupeng , King Martin S. , Kempf Dale J. , Lu Liangjun , Lim Hock Ben , Krishnan Preethi , Kati Warren , Middleton Timothy , Molla Akhteruzzaman
Published: December 2007

We characterized the selective advantage profiles of a panel of hepatitis C virus (HCV) NS3 protease mutants with three HCV protease inhibitors (PIs), BILN-2061, ITMN-191, and VX-950, using a genotype 1b HCV replicon system. Selective advantage curves were generated by a novel mathematical method that factors in the degree of drug susceptibility provided by the mutation, the base-level replication capacity of the mutant in the absence of drugs, and the overall viral replication levels as a function of drug concentration. Most of the mutants showed significantly increased selective advantages over the wild-type species upon drug treatment. Each drug is associated with unique selective advantage profiles that reflect its antiviral activity and mutant susceptibility. Five mutants (R155K/Q, A156T, and D168A/V) showed significant levels of selective advantage after treatment with >10 nM (∼7 times the wild-type 50% effective concentration [EC50]) of BILN-2061. R155K displayed dominant levels of selective advantage over the other mutants upon treatment with ITMN-191 over a broad range of concentrations. Upon VX-950 treatment, various mutants (A156T, A156S, R155K, T54A, V170A, V36M/R155K, and R155Q) exhibited high levels of selective advantage in different drug concentration ranges, with A156T and A156S being the dominant mutants at >3 μM (∼10 times the wild-type EC50) of VX-950. This method provides more accurate estimates of the behavior of various mutants under drug pressure than replication capacity analysis. We noted that the R155K mutant shows reduced susceptibility to all three PIs and significant selective advantage, raising concern over the potential emergence of R155K as a multidrug-resistant, highly fit mutant in HCV patients treated with PIs.
In Vitro Capability of Faropenem To Select for Resistant Mutants of
Streptococcus pneumoniae
and
Haemophilus influenzae
Authors: Kosowska-Shick Klaudia , Clark Catherine , Credito Kim , Dewasse Bonifacio , Beachel Linda , Ednie Lois , Appelbaum Peter C.
Published: December 2007

When tested against nine strains of pneumococci and six of
Haemophilus influenzae
of various resistotypes, faropenem failed to select for resistant mutants after 50 days of consecutive subculture in subinhibitory concentrations. Faropenem also yielded low rates of spontaneous mutations against all organisms of both species. By comparison, resistant clones were obtained with macrolides, ketolides, and quinolones.
Antigen Delivered by Anthrax Lethal Toxin Induces the Development of Memory CD8
+
T Cells That Can Be Rapidly Boosted and Display Effector Functions
Authors: Shaw Christine A. , Starnbach Michael N.
Published: December 2007

Memory CD8
+
T cells are essential for protective immunity against many intracellular pathogens; therefore, stimulation of this population of cells is an important goal of vaccination. We have previously shown that a detoxified derivative of
Bacillus anthracis
anthrax lethal toxin (LT) can deliver heterologous CD8
+
T-cell epitopes to the major histocompatibility complex class I processing and presentation pathway of murine host cells and that immunization of mice with these LT-antigen fusion proteins leads to the induction of antigen-specific CD8
+
T cells. In this report we extend these findings to include a detailed characterization of the phenotypic and functional properties of the T cells stimulated by the LT-based system. We found that after an initial period of expansion and contraction, antigen-specific CD8
+
T cells differentiated into a pool of memory cells that produced gamma interferon and displayed in vivo cytotoxic activity. The transition to memory cells appeared to be quite rapid based on an analysis of the phenotypic marker CD127 and the effectiveness of a booster immunization administered early after the initial immunization. We also investigated the composition of the memory T-cell pool induced by this system and found that while one immunization induced a mixture of effector memory T cells (CD62L
low
) and central memory T cells (CD62L
high
), a second immunization preferentially elevated the effector memory T-cell frequency. Finally, we demonstrated that mice that received prime-boost immunizations of LT-antigen proteins were more protected in a
Listeria monocytogenes
challenge model than mice that received only one immunization.
Intracellular Interleukin-1α Mediates Interleukin-8 Production Induced byChlamydia trachomatisInfection via a Mechanism Independent of Type I Interleukin-1 Receptor
Authors: Cheng Wen , Shivshankar Pooja , Zhong Youmin , Chen Ding , Li Zhongyu , Zhong Guangming
Published: December 2007

Chlamydia trachomatisinfection induces a wide array of inflammatory cytokines and chemokines, which may contribute to chlamydia-induced pathologies. However, the precise mechanisms by whichChlamydiainduces cytokines remain unclear. Here we demonstrate that the proinflammatory cytokine interleukin-1α (IL-1α) plays an essential role in chlamydial induction of the chemokine IL-8. Cells deficient in IL-1α expression or IL-1α-competent cells treated with IL-1α-specific small interfering RNA failed to produce IL-8 in response to chlamydial infection. However, neutralization of extracellular IL-1α or blockade of or deficiency in type I IL-1 receptor (IL-1RI) signaling did not affect chlamydial induction of IL-8 in cells capable of producing IL-1α. These results suggest that IL-1α can mediate the chlamydial induction of IL-8 via an intracellular mechanism independent of IL-1RI, especially during the early stage of the infection cycle. This conclusion is further supported by the observations that expression of a transgene-encoded full-length IL-1α fusion protein in the nuclei enhanced IL-8 production and that nuclear localization of chlamydia-induced precursor IL-1α correlated with chlamydial induction of IL-8. Thus, we have identified a novel mechanism for chlamydial induction of the chemokine IL-8.
Characterization of Two Putative Cytochrome
c
Peroxidases of
Campylobacter jejuni
Involved in Promoting Commensal Colonization of Poultry
Authors: Bingham-Ramos Lacey K. , Hendrixson David R.
Published: December 2007

Campylobacter jejuni
is a leading cause of bacterial gastroenteritis in humans throughout the world, but infection of animals, especially poultry, results in a commensal colonization of the intestines. We previously found that a mutant lacking
docA
, which encodes a putative cytochrome
c
peroxidase (CCP), demonstrates up to a 10
5
-fold reduction in colonization of the chick cecum compared to wild-type
C. jejuni
strain 81-176. Predictions from genomic sequences identified CJJ0382 as a second locus in
C. jejuni
encoding a CCP, making the bacterium unusual in having two putative CCPs. To understand what advantages are imparted by having two putative CCPs, we compared the colonization requirements of
C. jejuni
mutants lacking DocA or Cjj0382. Unlike the Δ
docA
mutant, a ΔCJJ0382 mutant demonstrates a maximal 50-fold colonization defect that is dependent on the inoculum dose. The colonization differences of mutants lacking DocA or Cjj0382 suggest that the two predicted CCPs are unlikely to perform redundant functions during in vivo growth. In the characterizations of DocA and Cjj0382, we found that they are stable periplasmic proteins with an apparent heme-dependent peroxidase activity, which are characteristics of bacterial CCPs. However, the peroxidase activities of the proteins do not appear to contribute to resistance to hydrogen peroxide. Instead, we found that resistance to hydrogen peroxide in
C. jejuni
is mostly attributed to the cytoplasmic catalase KatA. Our data suggest that DocA and Cjj0382 have characteristics of CCPs but likely perform different physiological functions for the bacterium in colonization that are not related to resisting oxidative stress.
Job adjustment and absence from work in mid-pregnancy in the Norwegian Mother and Child Cohort Study (MoBa)
Authors: Kristensen P , Nordhagen R , Wergeland E , Bjerkedal T
Published: December 2007

Background:

Pregnant women at work have special needs, and sick leave is common. However, job adjustment in pregnancy is addressed in European legislation. Our main objective was to examine if job adjustment was associated with reduced absence.

Methods:

This study is based on the Norwegian Mother and Child Cohort Study (MoBa) conducted by the Norwegian Institute of Public Health. 28 611 employed women filled in questionnaires in weeks 17 and 30 in pregnancy. The risk of absence for more than 2 weeks was studied among those who were not absent in week 17 (n = 22 932), and the probability of return to work in week 30 among those who were absent in week 17 (n = 5679). Data were based on self-report. The influence of job adjustment (three categories: not needed, needed but not obtained, needed and obtained) was analysed in additive models in multivariable binomial regression. Associations with other job characteristics and work environment factors were also analysed.

Results:

The risk of absence for more than 2 weeks was 0.308 and the probability of return to work was 0.137. Compared with women who needed but did not achieve job adjustment, obtained job adjustment was associated with a 0.107 decreased risk of absence (95% confidence interval 0.090 to 0.125) in a model including other job characteristics and work environment factors. Job adjustment was correspondingly associated with a 0.041 (0.023 to 0.059) increased probability of return to work. Absence was associated with adverse work environment, whereas the opposite pattern was found for return to work among those who started off being absent.

Conclusions:

Job adjustment was associated with reduced absence from work in pregnancy. Results should be interpreted cautiously because of low participation in MoBa and potential information bias from self-reported data.
ON LATTICES EMBEDDABLE INTO LATTICES OF ORDER-CONVEX SETS: CASE OF TREES
Authors: SEMENOVA MARINA V. , ZAMOJSKA-DZIENIO ANNA
Published: December 2007

We find a syntactic characterization of the class of lattices embeddable into convexity lattices of posets which are trees. The characterization implies that this class forms a finitely based variety.
ENCODING VIDEO SEQUENCES IN FRACTAL-BASED COMPRESSION
Authors: SANKARAGOMATHI B. , GANESAN L. , ARUMUGAM S.
Published: December 2007

With the rapid increase in the use of computers and the Internet, the demand for higher transmission and better storage is increasing as well. This paper describes the different techniques for data (image-video) compression in general and, in particular, the new compression technique called fractal image compression. Fractal image compression is based on self-similarity, where one part of an image is similar to the other part of the same image. Low bit rate color image sequence coding is very important for video transmission and storage applications. The most significant aspect of this work is the development of color images using fractal-based color image compression, since little work has been done previously in this area. The results obtained show that the fractal-based compression works for the color images works as well as for the gray-scale images. Nevertheless, the encoding of the color images takes more time than the gray-scale images.

Color images are usually compressed in a luminance-chrominance coordinate space, with the compression performed independently for each coordinate by applying the monochrome image processing techniques. For image sequence compression, the design of an accurate and efficient algorithm for computing motion to exploit the temporal redundancy has been one of the most active research areas in computer vision and image compression. Pixel-based motion estimation algorithms address pixel correspondence directly by identifying a set of local features and computing a match between these features across the frames. These direct techniques share the common pitfall of high computation complexity resulting from the dense vector fields produced. For block matching motion estimation algorithms, the quad-tree data structure is frequently used in image coding to recursively decompose an image plane into four non-overlapping rectangular blocks.
Mapping for high pressure gas pipelines in South Wales
Authors: Birch G. P.
Published: December 2007

Objectives

In order to mitigate against environmental impact, to satisfy the design criteria and to ensure the long-term integrity of the construction, the Transmission Department of Wales Gas sought geotechnical advice on the routing and design of a major gas transmission system. This system was being built to reinforce the gas supplies to the industrial valleys of South Wales. The opportunity was taken to apply geomorphological mapping at an early stage in route planning so as to avoid abortive design work on alignments which might subsequently prove unsuitable or too costly to engineer (Fig. 1). Pipeline engineers welcomed the approach, which commenced by obtaining an understanding of the client’s objectives and industry design guidance. Working as part of the project team, engineering geomorphologists provided guidance from initial routing studies through detailed design to construction, which was completed without contractual conflict arising out of unforeseen ground conditions.

The Project

Gas supplies to the industrial valleys of South Wales developed in piecemeal fashion outwards from the individual coking plants set up by collieries in the valley floors. The introduction of natural gas from the North Sea in the 1970s provided the opportunity to invest in a new transmission system emanating from the new high-pressure grid on the north edge of the Coal Field basin.

The ‘backbone’ of the project is a 30 km north-south, high-pressure, welded steel transmission/storage pipeline (oversized up to 1200 mm diameter to permit storage by pressure-packing) linking the North Sea feeder main at Dowlais, near Methyr Tydfil, with the Cardiff feeder main at Nantgarw, near Caerphilly (Fig. 2).
The Rest of the Solar System
Authors: Kivelson Margaret Galland
Published: December 2007

Should one call it serendipity to have stumbled into a career in space plasma physics within the first decade of the era of satellite exploration? The author had the good fortune to have done so. In early years, she repeatedly was told that she did not look like a physicist, but it was physics that provided her a rewarding opportunity to elucidate the characteristics of the space plasmas of terrestrial and planetary magnetospheres and to discover unexpected properties of the Galilean moons of Jupiter. Here, she describes some of her scientific contributions and introduces family members, colleagues, students, and friends who helped her along her trajectory and participated in her scientific investigations.
Functional Diversity of Human Protection of Telomeres 1 Isoforms in Telomere Protection and Cellular Senescence
Authors: Yang Qin , Zhang Ran , Horikawa Izumi , Fujita Kaori , Afshar Yalda , Kokko Antti , Laiho Päivi , Aaltonen Lauri A. , Harris Curtis C.
Published: December 2007

Protection of telomeres 1 (POT1) proteins in various organisms bind telomeres and regulate their structure and function. In contrast to mice carrying two distinct POT1 genes encoding two POT1 proteins (POT1a and POT1b), humans have the single POT1 gene. In addition to full-length POT1 protein (variant v1), the human POT1 gene encodes four other variants due to alternative RNA splicing (variants v2, v3, v4, and v5), whose functions are poorly understood. The functional analyses of the NH2-terminally and COOH-terminally truncated POT1 variants in this study showed that neither the single-stranded telomere-binding ability of the NH2-terminal oligonucleotide-binding (OB) folds nor the telomerase-dependent telomere elongation activity mediated by the COOH-terminal TPP1-interacting domain was telomere protective by itself. Importantly, a COOH-terminally truncated variant (v5), which consists of the NH2-terminal OB folds and the central region of unknown function, was found to protect telomeres and prevent cellular senescence as efficiently as v1. Our data revealed mechanistic and functional differences between v1 and v5: (a) v1, but not v5, functions through the maintenance of telomeric 3′ overhangs; (b) p53 is indispensable to v5 knockdown-induced senescence; and (c) v5 functions at only a fraction of telomeres to prevent DNA damage signaling. Furthermore, v5 was preferentially expressed in mismatch repair (MMR)-deficient cells and tumor tissues, suggesting its role in chromosome stability associated with MMR deficiency. This study highlights a human-specific complexity in telomere protection and damage signaling conferred by functionally distinct isoforms from the single POT1 gene. [Cancer Res 2007;67(24):11677–86]
Betulinic Acid, a Catalytic Inhibitor of Topoisomerase I, Inhibits Reactive Oxygen Species–Mediated Apoptotic Topoisomerase I–DNA Cleavable Complex Formation in Prostate Cancer Cells but Does Not Affect the Process of Cell Death
Authors: Ganguly Agneyo , Das Benubrata , Roy Amit , Sen Nilkantha , Dasgupta Somdeb Bose , Mukhopadhayay Sibabrata , Majumder Hemanta K.
Published: December 2007

The ubiquitious enzyme topoisomerase I can be targeted by drugs which turn these enzymes into cellular poisons and subsequently induce cell death. Drugs like staurosporine, which do not target topoisomerase I directly, can also lead to stabilization of topoisomerase I–DNA cleavable complexes by an indirect process of reactive oxygen species (ROS) generation and subsequent oxidative DNA damage. In this study, we show that betulinic acid, a catalytic inhibitor of topoisomerases, inhibits the formation of apoptotic topoisomerase I–DNA cleavable complexes in prostate cancer cells induced by drugs like camptothecin, staurosporine, and etoposide. Although events like ROS generation, oxidative DNA damage, and DNA fragmentation were observed after betulinic acid treatment, there is no topoisomerase I–DNA cleavable complex formation, which is a key step in ROS-induced apoptotic processes. We have shown that betulinic acid interacts with cellular topoisomerase I and prohibits its interaction with the oxidatively damaged DNA. Using oligonucleotide containing 8-oxoguanosine modification, we have shown that betulinic acid inhibits its cleavage by topoisomerase I in vitro. Whereas silencing of topoisomerase I gene by small interfering RNA reduces cell death in the case of staurosporine and camptothecin, it cannot substantially reduce betulinic acid–induced cell death. Thus, our study provides evidence that betulinic acid inhibits formation of apoptotic topoisomerase I–DNA complexes and prevents the cellular topoisomerase I from directly participating in the apoptotic process. [Cancer Res 2007;67(24):11848–58]
Proapoptotic BH3-Only BCL-2 Family Protein BIM Connects Death Signaling from Epidermal Growth Factor Receptor Inhibition to the Mitochondrion
Authors: Deng Jing , Shimamura Takeshi , Perera Samanthi , Carlson Nicole E. , Cai Dongpo , Shapiro Geoffrey I. , Wong Kwok-Kin , Letai Anthony
Published: December 2007

A subset of lung cancers expresses mutant forms of epidermal growth factor receptor (EGFR) that are constitutively activated. Cancers bearing activated EGFR can be effectively targeted with EGFR inhibitors such as erlotinib. However, the death-signaling pathways engaged after EGFR inhibition are poorly understood. Here, we show that death after inhibition of EGFR uses the mitochondrial, or intrinsic, pathway of cell death controlled by the BCL-2 family of proteins. BCL-2 inhibits cell death induced by erlotinib, but BCL-2–protected cells are thus rendered BCL-2–dependent and sensitive to the BCL-2 antagonist ABT-737. BH3 profiling reveals that mitochondrial BCL-2 is primed by death signals after EGFR inhibition in these cells. As this result implies, key death-signaling proteins of the BCL-2 family, including BIM, were found to be up-regulated after erlotinib treatment and intercepted by overexpressed BCL-2. BIM is induced by lung cancer cell lines that are sensitive to erlotinib but not by those resistant. Reduction of BIM by siRNA induces resistance to erlotinib. We show that EGFR activity is inhibited by erlotinib in H1650, a lung cancer cell line that bears a sensitizing EGFR mutation, but that H1650 is not killed. We identify the block in apoptosis in this cell line, and show that a novel form of erlotinib resistance is present, a block in BIM up-regulation downstream of EGFR inhibition. This finding has clear implications for overcoming resistance to erlotinib. Resistance to EGFR inhibition can be modulated by alterations in the intrinsic apoptotic pathway controlled by the BCL-2 family of proteins. [Cancer Res 2007;67(24):11867–75]
SNAI1 Is Required for Tumor Growth and Lymph Node Metastasis of Human Breast Carcinoma MDA-MB-231 Cells
Authors: Olmeda David , Moreno-Bueno Gema , Flores Juana M. , Fabra Angels , Portillo Francisco , Cano Amparo
Published: December 2007

The transcription factor, SNAI1 (Snail), has recently been proposed as an important mediator of tumor invasion because of its role in E-cadherin down-regulation and induction of epithelial-mesenchymal transition. In human breast cancer, the expression of SNAI1 and/or the homologous SNAI2 (Slug) has been associated with E-cadherin repression, local or distant metastasis, tumor recurrence, or poor prognosis in different tumor series. However, the specific contribution of either factor to breast tumor progression is still unclear. We have analyzed the role of SNAI1 in human breast cancer by loss of function studies and provide evidence of a major role for SNAI1 in both primary tumor growth and metastasis of human breast carcinoma MDA-MB-231 cells. Specific silencing of SNAI1 by short hairpin RNA induces a decrease in mesenchymal and proinvasive markers (MMP9, ID1, SPARC) in MDA-MB-231 cells, concomitant with reduced in vitro invasive behavior. More importantly, stable SNAI1 silencing in MDA-MB-231 cells leads to a dramatic reduction of in vivo tumor incidence and growth rate. Tumors induced by MDA-MB-231-SNAI1–silenced cells show extensive necrotic regions and a significant decrease in invasive and angiogenic markers. Moreover, SNAI1 silencing increases the sensitivity of MDA-MB-231 cells to chemotherapeutics relevant in breast cancer treatments, gemcitabine and docetaxel. Remarkably, analysis of cell lines derived from lymph node metastasis indicates that SNAI1 expression is required for metastatic dissemination. [Cancer Res 2007;67(24):11721–31]
Identification of 14-3-3𝛉 as an Antigen that Induces a Humoral Response in Lung Cancer
Authors: Pereira-Faca Sandra R. , Kuick Rork , Puravs Eric , Zhang Qing , Krasnoselsky Alexei L. , Phanstiel Douglas , Qiu Ji , Misek David E. , Hinderer Robert , Tammemagi Martin , Landi Maria Teresa , Caporaso Neil , Pfeiffer Ruth , Edelstein Cim , Goodman Gary , Barnett Matt , Thornquist Mark , Brenner Dean , Hanash Samir M.
Published: December 2007

We have implemented a strategy to identify tumor antigens that induce a humoral immune response in lung cancer based on the analysis of tumor cell proteins. Chromatographically fractionated protein extracts from three lung cancer cell lines were subjected to Western blotting and hybridization with individual sera to determine serum antibody binding. Two sets of sera were initially investigated. One set consisted of sera from 19 newly diagnosed subjects with lung adenocarcinoma and 19 matched controls. A second independent set consisted of sera from 26 newly diagnosed subjects with lung adenocarcinoma and 24 controls matched for age, gender, and smoking history. One protein that exhibited significant reactivity with both sets of cancer sera (P = 0.0008) was confidently identified by mass spectrometry as 14-3-3𝛉. Remarkably, significant autoantibody reactivity against 14-3-3𝛉 was also observed in an analysis of a third set consisting of 18 prediagnostic lung cancer sera collected as part of the Beta-Carotene and Retinol Efficacy Trial cohort study, relative to 19 matched controls (P = 0.0042). A receiver operating characteristic curve constructed with a panel of three proteins consisting of 14-3-3𝛉 identified in this study, plus annexin 1 and protein gene product 9.5 proteins previously identified as associated with autoantibodies in lung cancer, gave a sensitivity of 55% at 95% specificity (area under the curve, 0.838) in discriminating lung cancer at the preclinical stage from matched controls. [Cancer Res 2007;67(24):12000–6]
Role of Rb-Dependent and Rb-Independent Functions of Papillomavirus E7 Oncogene in Head and Neck Cancer
Authors: Strati Katerina , Lambert Paul F.
Published: December 2007

Infection with high-risk human papillomaviruses (HPV) and in particular the expression of the viral proteins E6 and E7 have been associated with the etiology of a subset of head and neck squamous cell cancer (HNSCC). However, the individual consequences of E6 and E7 expression in an in vivo model have not been examined in these tissues. We have used transgenes that direct expression of the HPV16 E6 and E7 proteins to the head and neck tissues of mice to dissect the contribution of these proteins to head and neck carcinogenesis. We report here that E7 is the major transforming oncogene in HPV-associated HNSCC, whereas E6 is more likely to play a secondary role in contributing to later stages of carcinogenesis. Furthermore, a conditional deletion of Rb, a prominent target for E7, in the same tissues did not recapitulate all E7-mediated phenotypes. Although our results do not preclude an important role for the E7-pRb interaction, they highlight the importance of pRb-independent functions of E7 in head and neck carcinogenesis. [Cancer Res 2007;67(24):11585–93]
Different S/M Checkpoint Responses of Tumor and Non–Tumor Cell Lines to DNA Replication Inhibition
Authors: Rodríguez-Bravo Verónica , Guaita-Esteruelas Sandra , Salvador Noelia , Bachs Oriol , Agell Neus
Published: December 2007

Cell cycle checkpoint abrogation, especially the inhibition of Chk1 in combination with DNA-damaging treatments, has been proposed as a promising way of sensitizing cancer cells. However, less is known about the possibility to selectively affect tumor cells when they are treated with agents that block DNA synthesis in combination with replication checkpoint inhibitors. Here, we present clear insights in the different responses of tumor and non-transformed cells to the inhibition of DNA replication with hydroxyurea in combination with checkpoint abrogation via inhibition of Ataxia telangiectasia–mutated– (ATM) and Rad3-related/ATM (ATR/ATM) and Chk1 kinases. Interestingly, we find that non-transformed cell lines activate ATR/ATM- and Chk1-independent pathways in response to replication inhibition to prevent mitotic entry with unreplicated DNA. In contrast, tumor cell lines such as HCT116 and HeLa cells rely entirely on Chk1 activity for a proper response to replication inhibitors. Our results show that p38 is activated in response to hydroxyurea treatment and collaborates with Chk1 to prevent mitotic entry in non-transformed cell lines by maintaining cyclin B1/Cdk1 complexes inactive. Furthermore, DNA replication arrest down-regulates cyclin B1 promoter activity in non-transformed cells, but not in tumor cells in a Chk1- and p38-independent way. Thus, our data show that non-transformed cells present a more robust DNA replication checkpoint response compared with tumor cells that involves activation of the p38 pathway. We show that some of these responses to replication block can be lost in tumor cells, causing a defective checkpoint and providing a rationale for tumor-selective effects of combined therapies. [Cancer Res 2007;67(24):11648–56]
ERK-Dependent MKP-1–Mediated Cisplatin Resistance in Human Ovarian Cancer Cells
Authors: Wang Juan , Zhou Jun-Ying , Wu Gen Sheng
Published: December 2007

Mitogen-activated protein kinase (MAPK) phosphatase-1 (MKP-1) is the MAPK phosphatase family member that negatively regulates MAPK signaling. Our previous study showed that MKP-1 is involved in cisplatin resistance, but the mechanism underlying its resistance is not understood. Here, we show that ERK2-mediated MKP-1 expression is critical for cisplatin resistance. Specifically, we showed that in the human ovarian cancer cell lines, cisplatin induces MKP-1 through phosphorylation. We also showed that inhibition of ERK2 activity by the MEK1/2 inhibitor U0126 or by small interfering RNA silencing decreases MKP-1 induction, leading to an increase in cisplatin-induced cell death, which mimicked the results obtained with cells in which MKP-1 is down-regulated. Importantly, down-regulation of ERK2 decreased cisplatin-induced MKP-1 phosphorylation, suggesting that MKP-1 phosphorylation depends on ERK2 activity. Furthermore, down-regulation of ERK2 or MKP-1 enhanced cisplatin-induced apoptosis. In addition, we showed that down-regulation of ERK2 or MKP-1 decreases the basal level of Bcl-2 protein and that inhibition of Bcl-2 activity sensitizes ovarian cancer cells to cisplatin. Collectively, our results indicate that induction of MKP-1 by cisplatin is through phosphorylation involving ERK signaling and that MKP-1 plays a critical role in ERK-mediated cisplatin resistance. Thus, our results suggest that targeting ERK-MKP-1 signaling could overcome cisplatin resistance in human ovarian cancer. [Cancer Res 2007;67(24):11933–41]
TRA-8 anti-DR5 monoclonal antibody and gemcitabine induce apoptosis and inhibit radiologically validated orthotopic pancreatic tumor growth
Authors: DeRosier Leo Christopher , Vickers Selwyn M. , Zinn Kurt R. , Huang Zhi , Wang Wenquan , Grizzle William E. , Sellers Jeffrey , Stockard Cecil R. , Zhou Tong , Oliver Patsy G. , Arnoletti Pablo , LoBuglio Albert F. , Buchsbaum Donald J.
Published: December 2007

Purpose: To evaluate agonistic TRA-8 monoclonal antibody to human death receptor 5 (DR5) and gemcitabine in vitro and in an orthotopic pancreatic cancer model. Experimental Design: Pancreatic cancer cell lines were screened for DR5 expression, cytotoxicity, and apoptosis induced by TRA-8, gemcitabine, or gemcitabine and TRA-8. An orthotopic model of pancreatic cancer was established in severe combined immunodeficient mice. Mice were treated with TRA-8, gemcitabine, or a combination for one or two cycles of therapy. Tumor growth (ultrasound) and survival were analyzed. Results: All five pancreatic cancer cell lines showed DR5 protein expression and varying sensitivity to TRA-8–mediated cytotoxicity. MIA PaCa-2 cells were very sensitive to TRA-8, moderately resistant to gemcitabine, with additive cytotoxicity to the combination. S2-VP10 cells were resistant to TRA-8 and sensitive to gemcitabine with synergistic sensitivity to the combination. Combination treatment in vitro produced enhanced caspase-3 and caspase-8 activation. A single cycle of therapy produced comparable efficacy for single-agent TRA-8 and the combination of TRA-8 and gemcitabine, with significant reduction in tumor size and prolonged survival compared with gemcitabine alone or control animals. With two cycles of therapy, TRA-8 and combination therapy produced enhanced inhibition of tumor growth compared with single-agent gemcitabine or untreated animals. However, the combination regimen showed enhanced survival as compared with single-agent TRA-8. Conclusions: Pancreatic cancer cell lines express varying levels of DR5 and differ in their sensitivity to TRA-8 and gemcitabine-induced cytotoxicity. TRA-8 with two cycles of gemcitabine therapy produced the best overall survival. [Mol Cancer Ther 2007;6(12):3198–207]
Evidence for dual mode of action of a thiosemicarbazone, NSC73306: a potent substrate of the multidrug resistance–linked ABCG2 transporter
Authors: Wu Chung-Pu , Shukla Suneet , Calcagno Anna Maria , Hall Matthew D. , Gottesman Michael M. , Ambudkar Suresh V.
Published: December 2007

Multidrug resistance due to reduced drug accumulation is a phenomenon predominantly caused by the overexpression of members of the ATP-binding cassette (ABC) transporters, including ABCB1 (P-glycoprotein), ABCG2, and several ABCC family members [multidrug resistance–associated protein (MRP)]. We previously reported that a thiosemicarbazone derivative, NSC73306, is cytotoxic to carcinoma cells that overexpress functional P-glycoprotein, and it resensitizes these cells to chemotherapeutics. In this study, we investigated the effect of NSC73306 on cells overexpressing other ABC drug transporters, including ABCG2, MRP1, MRP4, and MRP5. Our findings showed that NSC73306 is not more toxic to cells that overexpress these transporters compared with their respective parental cells, and these transporters do not confer resistance to NSC73306 either. In spite of this, we observed that NSC73306 is a transport substrate for ABCG2 that can effectively inhibit ABCG2-mediated drug transport and reverse resistance to both mitoxantrone and topotecan in ABCG2-expressing cells. Interactions between NSC73306 and the ABCG2 drug-binding site(s) were confirmed by its stimulatory effect on ATPase activity (140–150 nmol/L concentration required for 50% stimulation) and by inhibition of [125I]iodoarylazidoprazosin photolabeling (50% inhibition at 250–400 nmol/L) of the substrate-binding site(s). Overall, NSC73306 seems to be a potent modulator of ABCG2 that does not interact with MRP1, MRP4, or MRP5. Collectively, these data suggest that NSC73306 can potentially be used, due to its dual mode of action, as an effective agent to overcome drug resistance by eliminating P-glycoprotein–overexpressing cells and by acting as a potent modulator that resensitizes ABCG2-expressing cancer cells to chemotherapeutics. [Mol Cancer Ther 2007;6(12):3287–96]