bluuebunny/crossref_metadata_2025 huggingface dataset:
Global gene expression analysis of early response to chemotherapy treatment in ovarian cancer spheroids
Authors: L'Espérance Sylvain , Bachvarova Magdalena , Tetu Bernard , Mes-Masson Anne-Marie , Bachvarov Dimcho
Published: February 2008

Background

Chemotherapy (CT) resistance in ovarian cancer (OC) is broad and encompasses diverse unrelated drugs, suggesting more than one mechanism of resistance. To better understand the molecular mechanisms controlling the immediate response of OC cells to CT exposure, we have performed gene expression profiling in spheroid cultures derived from six OC cell lines (OVCAR3, SKOV3, TOV-112, TOV-21, OV-90 and TOV-155), following treatment with 10,0 μM cisplatin, 2,5 μM paclitaxel or 5,0 μM topotecan for 72 hours.

Results

Exposure of OC spheroids to these CT drugs resulted in differential expression of genes associated with cell growth and proliferation, cellular assembly and organization, cell death, cell cycle control and cell signaling. Genes, functionally involved in DNA repair, DNA replication and cell cycle arrest were mostly overexpressed, while genes implicated in metabolism (especially lipid metabolism), signal transduction, immune and inflammatory response, transport, transcription regulation and protein biosynthesis, were commonly suppressed following all treatments. Cisplatin and topotecan treatments triggered similar alterations in gene and pathway expression patterns, while paclitaxel action was mainly associated with induction of genes and pathways linked to cellular assembly and organization (including numerous tubulin genes), cell death and protein synthesis. The microarray data were further confirmed by pathway and network analyses.

Conclusion

Most alterations in gene expression were directly related to mechanisms of the cytotoxics actions in OC spheroids. However, the induction of genes linked to mechanisms of DNA replication and repair in cisplatin- and topotecan-treated OC spheroids could be associated with immediate adaptive response to treatment. Similarly, overexpression of different tubulin genes upon exposure to paclitaxel could represent an early compensatory effect to this drug action. Finally, multicellular growth conditions that are known to alter gene expression (including cell adhesion and cytoskeleton organization), could substantially contribute in reducing the initial effectiveness of CT drugs in OC spheroids. Results described in this study underscore the potential of the microarray technology for unraveling the complex mechanisms of CT drugs actions in OC spheroids and early cellular response to treatment.
Alterations in the Notch4 pathway in cerebral endothelial cells by the HIV aspartyl protease inhibitor, nelfinavir
Authors: Grigorian Aline , Hurford Rosemary , Chao Ying , Patrick Christina , Langford T Dianne
Published: February 2008

Background

Aspartyl protease inhibitors (PIs) used to treat HIV belong to an important group of drugs that influence significantly endothelial cell functioning and angiogenic capacity, although specific mechanisms are poorly understood. Recently, PIs, particularly Nelfinavir, were reported to disrupt Notch signaling in the HIV-related endothelial cell neoplasm, Kaposi's sarcoma. Given the importance of maintaining proper cerebral endothelial cell signaling at the blood brain barrier during HIV infection, we considered potential signaling pathways such as Notch, that may be vulnerable to dysregulation during exposure to PI-based anti-retroviral regimens. Notch processing by γ-secretase results in cleavage of the notch intracellular domain that travels to the nucleus to regulate expression of genes such as vascular endothelial cell growth factor and NFκB that are critical in endothelial cell functioning. Since, the effects of HIV PIs on γ-secretase substrate pathways in cerebral endothelial cell signaling have not been addressed, we sought to determine the effects of HIV PIs on Notch and amyloid precursor protein.

Results

Exposure to reported physiological levels of Saquinavir, Indinavir, Nelfinavir and Ritonavir, significantly increased reactive oxygen species in cerebral endothelial cells, but had no effect on cell survival. Likewise, PIs decreased Notch 4-protein expression, but had no effect on Notch 1 or amyloid precursor protein expression. On the other hand, only Nelfinavir increased significantly Notch 4 processing, Notch4 intracellular domain nuclear localization and the expression of notch intracellular domain targets NFκB and matrix metalloproteinase 2. Pre-treatment with the antioxidant Vitamin E prevented PI-induced reactive oxygen species generation and partially prevented Nelfinavir-induced changes in both Notch 4 processing, and cellular localization patterns. Moreover, in support of increased expression of pro-angiogenic genes after Nelfinavir treatment, Nelfinavir did not inhibit angiogenic capacity.

Conclusion

Nelfinavir affects Notch 4 processing that results in induction of expression of the pro-angiogenic genes NFκB and matrix metalloproteinase 2 in cerebral endothelial cells.
Genetic analysis of posterior medial barrel subfield (PMBSF) size in somatosensory cortex (SI) in recombinant inbred strains of mice
Authors: Jan Taha A , Lu Lu , Li Cheng-Xiang , Williams Robert W , Waters Robert S
Published: February 2008

Background

Quantitative trait locus (QTL) mapping is an important tool for identifying potential candidate genes linked to complex traits. QTL mapping has been used to identify genes associated with cytoarchitecture, cell number, brain size, and brain volume. Previously, QTL mapping was utilized to examine variation of barrel field size in the somatosensory cortex in a limited number of recombinant inbred (RI) strains of mice. In order to further elucidate the underlying natural variation in mouse primary somatosensory cortex, we measured the size of the posterior medial barrel subfield (PMBSF), associated with the representation of the large mystacial vibrissae, in an expanded sample set that included 42 BXD RI strains, two parental strains (C57BL/6J and DBA/2J), and one F1 strain (B6D2F1). Cytochrome oxidase labeling was used to visualize barrels within the PMBSF.

Results

We observed a 33% difference between the largest and smallest BXD RI strains with continuous variation in-between. Using QTL linkage analysis from WebQTL, we generated linkage maps of raw total PMBSF and brain weight adjusted total PMBSF areas. After removing the effects of brain weight, we detected a suggestive QTL (likelihood ratio statistic [LRS]: 14.20) on the proximal arm of chromosome 4. Candidate genes under the suggestive QTL peak for PMBSF area were selected based on the number of single nucleotide polymorphisms (SNPs) present and the biological relevance of each gene. Among the candidate genes are Car8 and Rab2. More importantly, mRNA expression profiles obtained using GeneNetwork indicated a strong correlation between total PMBSF area and two genes (Adcy1 and Gap43) known to be important in mouse cortex development. GAP43 has been shown to be critical during neurodevelopment of the somatosensory cortex, while knockout Adcy1 mice have disrupted barrel field patterns.

Conclusion

We detected a novel suggestive QTL on chromosome 4 that is linked to PMBSF size. The present study is an important step towards identifying genes underlying the size and possible development of cortical structures.
Natriuretic peptide vs. clinical information for diagnosis of left ventricular systolic dysfunction in primary care
Authors: Koschack Janka , Scherer Martin , Lüers Claus , Kochen Michael M , Wetzel Dirk , Kleta Sibylle , Pouwels Claudia , Wachter Rolf , Herrmann-Lingen Christoph , Pieske Burkert , Binder Lutz
Published: February 2008

Background

Screening of primary care patients at risk for left ventricular systolic dysfunction by a simple blood-test might reduce referral rates for echocardiography. Whether or not natriuretic peptide testing is a useful and cost-effective diagnostic instrument in primary care settings, however, is still a matter of debate.

Methods

N-terminal pro-brain natriuretic peptide (NT-proBNP) levels, clinical information, and echocardiographic data of left ventricular systolic function were collected in 542 family practice patients with at least one cardiovascular risk factor. We determined the diagnostic power of the NT-proBNP assessment in ruling out left ventricular systolic dysfunction and compared it to a risk score derived from a logistic regression model of easily acquired clinical information.

Results

23 of 542 patients showed left ventricular systolic dysfunction. Both NT-proBNP and the clinical risk score consisting of dyspnea at exertion and ankle swelling, coronary artery disease and diuretic treatment showed excellent diagnostic power for ruling out left ventricular systolic dysfunction. AUC of NT-proBNP was 0.83 (95% CI, 0.75 to 0.92) with a sensitivity of 0.91 (95% CI, 0.71 to 0.98) and a specificity of 0.46 (95% CI, 0.41 to 0.50). AUC of the clinical risk score was 0.85 (95% CI, 0.79 to 0.91) with a sensitivity of 0.91 (95% CI, 0.71 to 0.98) and a specificity of 0.64 (95% CI, 0.59 to 0.67). 148 misclassifications using NT-proBNP and 55 using the clinical risk score revealed a significant difference (McNemar test; p < 0.001) that was based on the higher specificity of the clinical risk score.

Conclusion

The evaluation of clinical information is at least as effective as NT-proBNP testing in ruling out left ventricular systolic dysfunction in family practice patients at risk. If these results are confirmed in larger cohorts and in different samples, family physicians should be encouraged to rely on the diagnostic power of the clinical information from their patients.
Immunological predictors of CD4+T cell decline in antiretroviral treatment interruptions
Authors: Seoane Elena , Resino Salvador , Moreno Santiago , de Quiros Juan Carlos Lopez Bernaldo , Moreno Ana , Rubio Rafael , Gonzalez-García Juan , Arribas José Ramón , Pulido Federico , Muñoz-Fernández Ma Ángeles
Published: February 2008

Background

The common response to stopping anti-HIV treatment is an increase of HIV-RNA load and decrease in CD4+, but not all the patients have similar responses to this therapeutic strategy. The aim was to identify predictive markers of CD4+ cell count declines to < 350/μL in CD4-guided antiretroviral treatment interruptions.

Methods

27 HIV-infected patients participated in a prospective multicenter study in with a 24 month follow-up. Patients on stable highly active antiretroviral therapy (HAART), with CD4+ count > 600/μL, and HIV-RNA < 50 copies/ml for at least 6 months were offered the option to discontinue antiretroviral therapy. The main outcome was a decline in CD4+ cell count to < 350/μL.

Results

After 24 months of follow-up, 16 of 27 (59%) patients (who discontinued therapy) experienced declines in CD4+ cell count to < 350/μL. Patients with a CD4+ nadir of < 200 cells/μL had a greater risk of restarting therapy during the follow-up (RR (CI95%): 3.37 (1.07; 10.36)). Interestingly, lymphoproliferative responses to Mycobacterium tuberculosis purified protein derivative (PPD) below 10000 c.p.m. at baseline (4.77 (1.07; 21.12)), IL-4 production above 100 pg/mL at baseline (5.95 (1.76; 20.07)) in PBMC cultured with PPD, and increased IL-4 production of PBMC with p24 antigen at baseline (1.25 (1.01; 1.55)) were associated to declines in CD4+ cell count to < 350/μL.

Conclusion

Both the number (CD4+ nadir) and the functional activity of CD4+ (lymphoproliferative response to PPD) predict the CD4+ decrease associated with discontinuation of ART in patients with controlled viremia.
Characterization of novel isoforms and evaluation of SNF2L/SMARCA1 as a candidate gene for X-linked mental retardation in 12 families linked to Xq25-26
Authors: Lazzaro Maribeth A , Todd Matthew AM , Lavigne Paul , Vallee Dominic , De Maria Adriana , Picketts David J
Published: February 2008

Background

Mutations in genes whose products modify chromatin structure have been recognized as a cause of X-linked mental retardation (XLMR). These genes encode proteins that regulate DNA methylation (MeCP2), modify histones (RSK2 and JARID1C), and remodel nucleosomes through ATP hydrolysis (ATRX). Thus, genes encoding other chromatin modifying proteins should also be considered as disease candidate genes. In this work, we have characterized the SNF2L gene, encoding an ATP-dependent chromatin remodeling protein of the ISWI family, and sequenced the gene in patients from 12 XLMR families linked to Xq25-26.

Methods

We used an in silico and RT-PCR approach to fully characterize specific SNF2L isoforms. Mutation screening was performed in 12 patients from individual families with syndromic or non-syndromic XLMR. We sequenced each of the 25 exons encompassing the entire coding region, complete 5' and 3' untranslated regions, and consensus splice-sites.

Results

The SNF2L gene spans 77 kb and is encoded by 25 exons that undergo alternate splicing to generate several distinct transcripts. Specific isoforms are generated through the alternate use of exons 1 and 13, and by the use of alternate donor splice sites within exon 24. Alternate splicing within exon 24 removes a NLS sequence and alters the subcellular distribution of the SNF2L protein. We identified 3 single nucleotide polymorphisms but no mutations in our 12 patients.

Conclusion

Our results demonstrate that there are numerous splice variants of SNF2L that are expressed in multiple cell types and which alter subcellular localization and function. SNF2L mutations are not a cause of XLMR in our cohort of patients, although we cannot exclude the possibility that regulatory mutations might exist. Nonetheless, SNF2L remains a candidate for XLMR localized to Xq25-26, including the Shashi XLMR syndrome.
Design of a RCT evaluating the (cost-) effectiveness of a lifestyle intervention for male construction workers at risk for cardiovascular disease: The Health under Construction study
Authors: Groeneveld Iris F , Proper Karin I , van der Beek Allard J , van Duivenbooden Cor , van Mechelen Willem
Published: February 2008

Background

Of all workers in Dutch construction industry, 20% has an elevated risk of cardiovascular disease (CVD). A major risk factor for CVD risk is an unhealthy lifestyle. The aim of our study is to design a lifestyle intervention for construction workers with an elevated CVD risk, and to evaluate its (cost-) effectiveness.

Methods/Design

In a RCT, 692 participants will be randomised to either the control or the intervention group. The control group will receive usual care. For the intervention group, a lifestyle intervention has been designed based on interviews and current literature. The intervention will last 6 months and will comprise 3 face-to-face and 4 telephone contacts, consisting of individual counselling aimed at increasing daily physical activity (PA) and improving dietary behaviour, and/or smoking cessation. Counselling will take place at the Occupational Health Service (OHS), and will be done according to motivational interviewing (MI). Additional written information about healthy lifestyle will also be provided to those in the intervention group. At baseline, after 6 and after 12 months, measurements will take place. Primary outcome variables will be the lifestyle behaviours of concern, i.e. daily PA, dietary intake, and smoking status. Secondary outcome variables will be body mass index (BMI), systolic and diastolic blood pressure, total and HDL blood cholesterol, Hba1c and cardio-respiratory fitness (CRF). Sickness absenteeism and cost-effectiveness will be assessed as well. Multilevel analysis will be performed to compare all outcome measures between the intervention group and the control group.

Discussion

By improving lifestyle, CVD risk may be lowered, yielding benefits for both employee and employer. If proven effective, this lifestyle intervention will be implemented on a larger scale within the Occupational Health Services in construction industry.

Trial registration

Current Controlled Trials ISRCTN60545588
Double-bundle ACL reconstruction: influence of femoral tunnel orientation in knee laxity analysed with a navigation system – an in-vitro biomechanical study
Authors: Zaffagnini Stefano , Bruni Danilo , Martelli Sandra , Imakiire Naoaki , Marcacci Maurilio , Russo Alessandro
Published: February 2008

Background

This paper reports an in-vitro study for evaluating the influence of the femoral tunnel orientation in anterior cruciate ligament (ACL) double-bundle reconstructions.

Methods

This work describes the experimental protocol and results obtained for six cadaver knees using the FlashPoint optical system (Image Guided, Boulder, Colorado, USA) and a computer-assisted technique for the elaboration of anatomical and kinematic data. Each specimen was examined by the same surgeon in the following steps: (1) intact knee stability was evaluated by performing antero-posterior displacement and internal-external rotation test at 90°; (2) the ACL was resected and the knee evaluated again; (3) the ACL was reconstructed using the gracilis semi-tendinous tendon (through horizontal tunnels in femur), and the new kinematics recorded; (4) the ACL was reconstructed again with the same tendon, but with a more vertical orientation of the femoral tunnel (vertical tunnel) and kinematics was once more recorded; (5) finally the knee was dissected to digitise the anatomical structures.

Results

Off-line computer analysis of the acquired anatomical and kinematic data showed that there was a significant statistical difference (Wilcoxon test with the Montecarlo method for small samples – p = 0.035) between horizontal tunnel (HT) and vertical tunnel (VT) reconstruction both in the antero-posterior test (median antero-posterior displacement in horizontal tunnel was 0.8 mm less than in vertical tunnel reconstruction) and in the internal-external (IE) rotation test (median internal-external rotation in horizontal tunnel reconstruction was 5° less than in vertical tunnel reconstruction).

Conclusion

The analysis of graft behavior in reconstructed knees compared with normal and ACL-deficient knees suggests that the most horizontal tunnel performed better than the vertical tunnel, thus constraining optimally both antero-posterior and internal-external rotations. This finding suggests that femoral tunnel direction may be an important issue in ACL surgery.
Quantitative comparison of DNA detection by GFP-lac repressor tagging, fluorescence in situ hybridization and immunostaining
Authors: Kim Il-Han , Nagel Jens , Otten Simone , Knerr Boris , Eils Roland , Rohr Karl , Dietzel Steffen
Published: February 2008

Background

GFP-fusion proteins and immunostaining are methods broadly applied to investigate the three-dimensional organization of cells and cell nuclei, the latter often studied in addition by fluorescence in situ hybridization (FISH). Direct comparisons of these detection methods are scarce, however.

Results

We provide a quantitative comparison of all three approaches. We make use of a cell line that contains a transgene array of lac operator repeats which are detected by GFP-lac repressor fusion proteins. Thus we can detect the same structure in individual cells by GFP fluorescence, by antibodies against GFP and by FISH with a probe against the transgene array. Anti-GFP antibody detection was repeated after FISH. Our results show that while all four signals obtained from a transgene array generally showed qualitative and quantitative similarity, they also differed in details.

Conclusion

Each of the tested methods revealed particular strengths and weaknesses, which should be considered when interpreting respective experimental results. Despite the required denaturation step, FISH signals in structurally preserved cells show a surprising similarity to signals generated before denaturation.
Negative selection of chronic lymphocytic leukaemia cells using a bifunctional rosette-based antibody cocktail
Authors: Essakali Salim , Carney Dennis , Westerman David , Gambell Peter , Seymour John F , Dobrovic Alexander
Published: February 2008

Background

High purity of tumour samples is a necessity for accurate genetic and expression analysis and is usually achieved by positive selection in chronic lymphocytic leukaemia (CLL).

Results

We adapted a bifunctional rosette-based antibody cocktail for negative selection of B-cells for isolating CLL cells from peripheral blood (PB). PB samples from CLL patients were split into aliquots. One aliquot of each sample was enriched by density gradient centrifugation (DGC), while the other aliquot of each sample was incubated with an antibody cocktail for B-cell enrichment prior to DGC (RS+DGC). The purity of CLL cells after DGC averaged 74.1% (range: 15.9 – 97.4%). Using RS+DGC, the purity averaged 93.8% (range: 80.4 – 99.4%) with 23 of 29 (79%) samples showing CLL purities above 90%. RNA extracted from enriched CLL cells was of appropriately high quality for microarray analysis.

Conclusion

This study confirms the use of a bifunctional rosette-based antibody cocktail as an effective method for the purification of CLL cells from peripheral blood.
Peptides OFFGEL electrophoresis: a suitable pre-analytical step for complex eukaryotic samples fractionation compatible with quantitative iTRAQ labeling
Authors: Chenau Jérôme , Michelland Sylvie , Sidibe Jonathan , Seve Michel
Published: February 2008

Background

The proteomes of mammalian biological fluids, cells and tissues are complex and composed of proteins with a wide dynamic range. The effective way to overcome the complexity of these proteomes is to combine several fractionation steps. OFFGEL fractionation, recently developed by Agilent Technologies, provides the ability to pre-fractionate peptides into discrete liquid fractions and demonstrated high efficiency and repeatability necessary for the analysis of such complex proteomes.

Results

We evaluated OFFGEL fractionator technology to separate peptides from two complex proteomes, human secretome and human plasma, using a 24-wells device encompassing the pH range 3–10. In combination with reverse phase liquid chromatography, peptides from these two samples were separated and identified by MALDI TOF-TOF. The repartition profiles of the peptides in the different fractions were analyzed and explained by their content in charged amino acids using an algorithmic model based on the possible combinations of amino acids. We also demonstrated for the first time the compatibility of OFFGEL separation technology with the quantitative proteomic labeling technique iTRAQ allowing inclusion of this technique in complex samples comparative proteomic workflow.

Conclusion

The reported data showed that OFFGEL system provides a highly valuable tool to fractionate peptides from complex eukaryotic proteomes (plasma and secretome) and is compatible with iTRAQ labeling quantitative studies. We therefore consider peptides OFFGEL fractionation as an effective addition to our strategy and an important system for quantitative proteomics studies.
Effects of estradiol and FSH on maturation of the testis in the hypogonadal (hpg) mouse
Authors: Baines Helen , Nwagwu Margaret O , Hastie Graham R , Wiles Roman A , Mayhew Terry M , Ebling Francis JP
Published: February 2008

Background

The hypogonadal (hpg) mouse is widely used as an animal model with which to investigate the endocrine regulation of spermatogenesis. Chronic treatment of these GnRH-deficient mice with estradiol is known to induce testicular maturation and restore qualitatively normal spermatogenesis. The aim of the current studies was to investigate whether these effects of estradiol are direct effects in the testis, or indirect actions via paradoxical stimulation of FSH secretion from the pituitary gland.

Methods

Initially, Western blot and immunohistochemistry were used to analyse tissues from hpg mice to identify potential sites of action of estradiol. In the main study, hpg mice were treated for 50 days with either an estradiol implant or daily injections of recombinant human FSH, or a combination of both, to determine whether estradiol would have an additive or synergistic effect with FSH on testis development, as assessed by histological analysis and stereological quantification of Leydig, Sertoli and germ cell proliferation.

Results

Western blot analysis revealed ERα immunoreactive bands of appropriate molecular weight in extracts of testis and pituitary glands from hpg mice, and immunohistochemical studies confirmed ERα in nuclei of anterior pituitary cells and Leydig and peritubular cells in hpg mice. Histological and morphometric analyses revealed that estradiol treatment alone was as effective as FSH in promoting Sertoli cell production and proliferation of the seminiferous epithelium, resulting in the production of elongating spermatids. Combined estradiol and FSH treatment did not produce a greater effect than either treatment alone, though an increased dose of FSH significantly increased seminiferous tubule volume and testis weight and increase Sertoli cell numbers further within the same time frame. In contrast, estradiol caused substantial increases in the wet weight of the seminal vesicles, whereas FSH was without effect on this tissue, and did not augment the actions of estradiol.

Conclusion

As ERalpha receptor is abundantly expressed in the pituitary gland of hpg mice, and estradiol did not exert effects on testis development over and above those of FSH, we conclude that the action of estradiol on testis development inhpgmice is predominantly via the stimulation of pituitary FSH release.
The role of interleukin-1 in neuroinflammation and Alzheimer disease: an evolving perspective
Authors: Shaftel Solomon S , Griffin W Sue T , O'Banion M Kerry
Published: February 2008

Elevation of the proinflammatory cytokine Interleukin-1 (IL-1) is an integral part of the local tissue reaction to central nervous system (CNS) insult. The discovery of increased IL-1 levels in patients following acute injury and in chronic neurodegenerative disease laid the foundation for two decades of research that has provided important details regarding IL-1's biology and function in the CNS. IL-1 elevation is now recognized as a critical component of the brain's patterned response to insults, termed neuroinflammation, and of leukocyte recruitment to the CNS. These processes are believed to underlie IL-1's function in the setting of acute brain injury, where it has been ascribed potential roles in repair as well as in exacerbation of damage. Explorations of IL-1's role in chronic neurodegenerative disease have mainly focused on Alzheimer disease (AD), where indirect evidence has implicated it in disease pathogenesis. However, recent observations in animal models challenge earlier assumptions that IL-1 elevation and resulting neuroinflammatory processes play a purely detrimental role in AD, and prompt a need for new characterizations of IL-1 function. Potentially adaptive functions of IL-1 elevation in AD warrant further mechanistic studies, and provide evidence that enhancement of these effects may help to alleviate the pathologic burden of disease.
The first hydrophobic region of the HPV16 E5 protein determines protein cellular location and facilitates anchorage-independent growth
Authors: Lewis Caroline , Baro Marta F , Marques Margarita , Grüner Myriam , Alonso Angel , Bravo Ignacio G
Published: February 2008

The human papillomavirus type 16 E5 protein (HPV16 E5) is 83 amino acids in length and contains three well-defined hydrophobic regions. The protein is expressed at very limited amounts in transfected cells and the absence of specific antibodies has strongly hampered functional analyses. To investigate the relationship between structure and function we have synthesized a codon-adapted version of the gene (hE5) and prepared a series of N-terminal and C-terminal deletions. Immunofluorescence analyses show colocaliation of the protein with calnexin, an ER marker, EEA-1, an early endosomes marker, and Lamp-2, a lysosomal marker. No major colocalization was found between hE5 and the Golgi marker 58 K. Whereas deletions at the C-terminal end of the protein do not greatly alter the localisation pattern, deletion of the first hydrophobic region results in loss of colocalisation with the ER, early endosomes and lysosomes. Further, we show that while the complete E5 protein confers to HaCaT cells the property to grow in an anchorage-independent manner, deletion of the first hydrophobic region results in loss of growth in soft agar. We conclude that the first hydrophobic region of the E5 protein largely determines the biological properties of the viral protein.
Circuitous embolic hemorrhagic stroke: carotid pseudoaneurysm to fetal posterior cerebral artery conduit: a case report
Authors: Hoque Romy , Gonzalez-Toledo Eduardo , Minagar Alireza , Kelley Roger E
Published: February 2008

Introduction

The cervical internal carotid artery (ICA) is susceptible to injury through various mechanisms, including dissection, which can lead to pseudoaneurysm formation. Pathological processes affecting the ICA, in association with an ipsilateral fetal posterior cerebral artery (PCA), resulting in parieto-occipital strokes are rarely reported.

Case Presentation

We present a patient with a left PCA territory, presumably embolic, stroke with early hemorrhagic transformation. The identified nidus of the embolus was a carotid artery pseudoaneurysm. Manifestations included right homonymous hemianopsia with right hemiparesis and hemisensory loss.

Conclusion

Our case is unique, and of clinical interest, because it illustrates both the potential anterior-posterior circulation conduit provided by a fetal origin PCA as well as the apparent early hemorrhagic transformation of embolic infarcts that can lead to further confusion from a mechanistic standpoint.
A BAC-based integrated linkage map of the silkworm Bombyx mori
Authors: Yamamoto Kimiko , Nohata Junko , Kadono-Okuda Keiko , Narukawa Junko , Sasanuma Motoe , Sasanuma Shun-ichi , Minami Hiroshi , Shimomura Michihiko , Suetsugu Yoshitaka , Banno Yutaka , Osoegawa Kazutoyo , de Jong Pieter J , Goldsmith Marian R , Mita Kazuei
Published: February 2008

Background

In 2004, draft sequences of the model lepidopteran Bombyx mori were reported using whole-genome shotgun sequencing. Because of relatively shallow genome coverage, the silkworm genome remains fragmented, hampering annotation and comparative genome studies. For a more complete genome analysis, we developed extended scaffolds combining physical maps with improved genetic maps.

Results

We mapped 1,755 single nucleotide polymorphism (SNP) markers from bacterial artificial chromosome (BAC) end sequences onto 28 linkage groups using a recombining male backcross population, yielding an average inter-SNP distance of 0.81 cM (about 270 kilobases). We constructed 6,221 contigs by fingerprinting clones from three BAC libraries digested with different restriction enzymes, and assigned a total of 724 single copy genes to them by BLAST (basic local alignment search tool) search of the BAC end sequences and high-density BAC filter hybridization using expressed sequence tags as probes. We assigned 964 additional expressed sequence tags to linkage groups by restriction fragment length polymorphism analysis of a nonrecombining female backcross population. Altogether, 361.1 megabases of BAC contigs and singletons were integrated with a map containing 1,688 independent genes. A test of synteny using Oxford grid analysis with more than 500 silkworm genes revealed six versus 20 silkworm linkage groups containing eight or more orthologs of Apis versus Tribolium, respectively.

Conclusion

The integrated map contains approximately 10% of predicted silkworm genes and has an estimated 76% genome coverage by BACs. This provides a new resource for improved assembly of whole-genome shotgun data, gene annotation and positional cloning, and will serve as a platform for comparative genomics and gene discovery in Lepidoptera and other insects.
Visualization of pseudogenes in intracellular bacteria reveals the different tracks to gene destruction
Authors: Fuxelius Hans-Henrik , Darby Alistair C , Cho Nam-Huyk , Andersson Siv GE
Published: February 2008

Background

Pseudogenes reveal ancestral gene functions. Some obligate intracellular bacteria, such as Mycobacterium leprae and Rickettsia spp., carry substantial fractions of pseudogenes. Until recently, horizontal gene transfers were considered to be rare events in obligate host-associated bacteria.

Results

We present a visualization tool that displays the relationships and positions of degraded and partially overlapping gene sequences in multiple genomes. With this tool we explore the origin and deterioration patterns of the Rickettsia pseudogenes and find that variably present genes and pseudogenes tend to have been acquired more recently, are more divergent in sequence, and exhibit a different functional profile compared with genes conserved across all species. Overall, the origin of only one-quarter of the variable genes and pseudogenes can be traced back to the common ancestor of Rickettsia and the outgroup genera Orientia and Wolbachia. These sequences contain only a few disruptive mutations and show a broad functional distribution profile, much like the core genes. The remaining genes and pseudogenes are extensively degraded or solely present in a single species. Their functional profile was heavily biased toward the mobile gene pool and genes for components of the cell wall and the lipopolysaccharide.

Conclusion

Reductive evolution of the vertically inherited genomic core accounts for 25% of the predicted genes in the variable segments of the Rickettsia genomes, whereas 75% stems from the flux of the mobile gene pool along with genes for cell surface structures. Thus, most of the variably present genes and pseudogenes in Rickettsia have arisen from recent acquisitions.
Early and preferential induction of IL-1 receptor-associated kinase-M in THP-1 cells by LPS derived fromPorphyromonas gingivalis
Authors: Domon Hisanori , Honda Tomoyuki , Oda Taro , Yoshie Hiromasa , Yamazaki Kazuhisa
Published: February 2008

LPS of Porphyromonas gingivalis (P. gingivalis) is suggested to be a virulence factor in periodontitis, stimulating host cells to produce proinflammatory mediators. However, P. gingivalis LPS has been reported to show lower biological activity compared with Escherichia coli (E. coli) LPS. Although differences in the chemical structure of lipid A and the receptor conferring LPS signaling are thought to account for these characteristics, the precise reason is unknown. Here, we demonstrate that P. gingivalis LPS up-regulates IL-1R-associated kinase (IRAK)-M, a negative regulator of the TLR signaling pathway, in a THP-1-derived macrophage more robustly than E. coli LPS. Although down-regulation of IRAK-M by small interfering (si)RNA augmented transcription and translation of TNF-α, IL-6, and IL-12 p40 in LPS-stimulated macrophages, the effect of siRNA was more prominent in P. gingivalis LPS-stimulated cells. Degradation of IRAK-1 was more obvious in E. coli LPS-stimulated macrophages than the cells stimulated with P. gingivalis LPS, suggesting that P. gingivalis LPS-induced IRAK-M suppressed dissociation of IRAK-1 from the receptor complex, resulting in escape from subsequent degradation. This activity may be involved in the chronic infection of this bacterium in periodontal tissue by serving as an escape mechanism from immune surveillance.
Cooperation between NOD2 and Toll-like receptor 2 ligands in the up-regulation of mouse mFPR2, a G-protein-coupled Aβ42 peptide receptor, in microglial cells
Authors: Chen Keqiang , Zhang Lingzhi , Huang Jian , Gong Wanghua , Dunlop Nancy M , Wang Ji Ming
Published: February 2008

Human G-protein-coupled formyl peptide receptor-like 1 and its mouse homologue formyl peptide receptor 2 (mFPR2) mediate the chemotactic activity of a variety of pathogen and host-derived peptides, including amyloid β42, a key causative factor in Alzheimer’s disease. In mouse microglia, mFPR2 is up-regulated by pathogen-associated molecular patterns and proinflammatory cytokines, as shown, for instance, in our previous study using peptidoglycan (PGN) of Gram+ bacteria. As PGN and its components have been reported to use TLR2 and an intracellular receptor nucleotide-binding oligomerization domain 2 (NOD2), we investigated the capacity of palmitoyl-cys[(RS)-2, 3-di(palmitoyloxy)-propyl]-Ala-Gly-OH (PamCAG), a specific TLR2 ligand, and muramyl dipeptide (MDP), a NOD2 ligand, to cooperatively regulate the expression and function of mFPR2 in microglia. We found that MDP and PamCAG as well as another TLR2-specific agonist palmitoyl-3-cysteine-serine-lysine-4 (Pam3CSK4), when used alone, each increased the expression of functional mFPR2 in microglial cells, and the combination of MDP and PamCAG or Pam3CSK4 exhibited an additive effect. Mechanistic studies revealed that MDP increased the levels of TLR2 expression on the microglial cell surface and enhanced the levels of MAPKs p-38, ERK1/2, and NF-κB activated by PamCAG. Our results suggest that TLR2 and NOD2 cooperate to up-regulate the expression of mFPR2 and therefore, may actively participate in the pathogenic processes of brain inflammation and neurodegenerative diseases.
The Republican Mammy? Imagining Civic Engagement in Dred
Authors: Duquette Elizabeth
Published: February 2008

Through a sustained analysis of Harriet Beecher Stowe's second antislavery novel, Dred (1856), this essay argues for the reevaluation of Stowe's political and moral priorities and values. Focusing on the novel's examination of interest, the essay shows how Stowe challenges one of the basic tenets of American liberalism, namely that interests erode, rather than sustain, communities. The novel puts forward this critique by exploring the dangers of enthusiasm, which Stowe associates variously with alcohol, excessive religious emotion, and intellectual individualism. Despite its bleak outlook, Dred advances a positive position, represented by Millie, an older black woman who devotes the end of her life to rescuing orphaned children from poverty. Millie's commitment to and defense of principles associated with republicanism establishes her moral and political excellence, particularly in comparison with the novel's male characters, but the essay concludes by considering the larger implications of replacing the idealized figure of the Republican Mother with a figure dubbed the Republican Mammy.
The Anti-corrido of George Washington Gómez: A Narrative of Emergent Subject Formation
Authors: Sorensen Leif
Published: February 2008

This essay argues that Américo Paredes's George Washington Gómez is structured by a dynamic tension between the forms of the corrido and the bildungsroman. Drawing on recent studies of the Chicano/a literary-historical recovery and accounts of late modernism, this essay calls attention to the elements of the novel that made it unpublishable for almost fifty years. Attending closely to this tension brings forward the novel's insistent depiction of the historical impossibility of both subjectivity and literary production in the 1930s. The novel critiques and ironizes both of these totalizing narratives of subject formation, leaving the protagonist in a condition of fragmentation. In Paredes's late and peripheral version of modernism, such fragmentation is always rooted firmly in social and political contexts, suggesting that in the borderlands, totalizing scripts of identity collide and fail. The novel addresses this scandal of subject formation by dramatizing the process through which the protagonist develops a private fantasy identity informed by the corrido alongside a public “Americanized” identity by following the script of the assimilationist bildungsroman. The conclusion of Paredes's narrative satisfies the conventions of both forms even as it critiques these narratives and the subjectivities that they produce.
“A Liberal and Paternal Spirit”: Indian Agents and Native Fisheries in Canada
Authors: Schreiber Dorothee
Published: February 2008

In the 1890s native fisheries stood in the way of expanding industrial and sport fisheries in Canada. Federal regulations denied a commercial component to native fisheries, restricted harvesting to designated open seasons, and outlawed the technologically specialized and place-based fisheries on which native communities had depended for millennia. Although fisheries officers enforced these rules, Indian agents—the field workers of the Department of Indian Affairs—were the ones who oversaw day-to-day life in native villages, including the fisheries. This article examines the responses of Indian agents across Canada to an Indian Affairs circular sent in 1897, requesting information about native fisheries. The Indian agents' letters of reply suggest that it was the ordinary confrontations and administrative decisions over fishing spaces, gear, closed seasons, and licenses, rather than the official policies of the Department of Indian Affairs, that worked to redefine native fishing in accordance with settler interests. By extending so-called privileges to native fishers, Indian agents worked to conserve the resource for a settler society and assimilate native fishers into state management practices.
The UK postmortem organ retention crisis: a qualitative study of its impact on parents
Authors: Sque Magi , Long Tracy , Payne Sheila , Roche William R , Speck Peter
Published: February 2008

Objective: To explore the impact of postmortem organ retention on parents who made enquires about their babies and children when the retention of hearts and other organs removed at postmortem and stored without explicit knowledge or consent of the next-of-kin came to public attention in the UK during 1999-2004.

Design: Qualitative study conducted 2003-2004. Data were collected via semi-structured, qualitative interviews and focus groups.

Participants: 39 parents who had been affected by organ retention.

Setting: Participants were recruited via three parental peer support groups and two NHS Hospital Trusts.

Results: Transcripts of the interviews and focus groups were analysed using a thematic approach that sought patterns within the data and highlighted important similarities and differences between participants' accounts. Participants reported the distressing impact organ retention had on their lives; their need for information about the retention of their babies' or children's organs; and the difficulties in their decision making about disposal of retained body parts and tissue blocks and slides. Analysis indicated that organ retention had evoked unresolved bereavement issues and a renewal of grief as well as an opportunity for some parents to resolve ongoing bereavement concerns.

Conclusions: Parents in this study wanted NHS teams to appreciate the difficulties organ retention had caused them, deal with their enquires proactively with openness and honesty, and facilitate an environment where they felt supported and could gain the answers to their questions and concerns that were provoked by postmortem organ retention. Such issues may also have implications for the care of other parents and relatives of deceased children.
Exploiting the Structural Properties of the Underlying Markov Decision Problem in the Q-Learning Algorithm
Authors: Kunnumkal Sumit , Topaloglu Huseyin
Published: February 2008

This paper shows how to exploit the structural properties of the underlying Markov decision problem to improve the convergence behavior of the Q-learning algorithm. In particular, we consider infinite-horizon discounted-cost Markov decision problems where there is a natural ordering between the states of the system and the value function is known to be monotone in the state. We propose a new variant of the Q-learning algorithm that ensures that the value function approximations obtained during the intermediate iterations are also monotone in the state. We establish the convergence of the proposed algorithm and experimentally show that it significantly improves the convergence behavior of the standard version of the Q-learning algorithm.
Tibial Bone Geometry in Chronic Stroke Patients: Influence of Sex, Cardiovascular Health, and Muscle Mass
Authors: Pang Marco YC , Ashe Maureen C , Eng Janice J
Published: February 2008

This study aimed to examine the geometry of the tibia in chronic stroke survivors. Fifty-five ambulatory individuals with chronic stroke were included in the study. pQCT was used to obtain a cross-sectional scan of the tibia at the 30% site on both the paretic and nonparetic sides. Leg lean mass was derived from a total body scan using DXA. Each subject was also evaluated for peak oxygen consumption rate, spasticity, and functional mobility. Paired t-tests were used to compare the pQCT parameters between the two sides. Multiple linear regression analysis was used to identify the significant determinants of tibial bone strength index (BSI). In men, marrow cavity area on the paretic side was significantly greater than the nonparetic side (p = 0.011), whereas the total bone area showed no significant side-to-side difference (p = 0.252). In women, total bone area on the paretic side was significantly smaller than the nonparetic side (p = 0.003), whereas the marrow cavity area had no side-to-side difference (p = 0.367). Peak oxygen consumption (r2 = 0.739, F5,49 = 22.693, p < 0.001) and paretic leg lean mass (r2 = 0.802, F6,48 = 32.475, p < 0.001) remained independently associated with tibial BSI, after controlling for age, sex, body mass index, years since stroke onset, and physical activity level. The geometry of the tibia in stroke patients showed sex-specific side-to-side differences. The results suggested that, whereas endosteal resorption was apparent in men, periosteal resorption was more predominant in women. The results also highlight the potential importance of promoting cardiovascular health and leg muscle mass in enhancing bone geometry in chronic stroke survivors.
Physical Performance and Risk of Hip Fractures in Older Men
Authors: Cawthon Peggy Mannen , Fullman Robin L , Marshall Lynn , Mackey Dawn C , Fink Howard A , Cauley Jane A , Cummings Steven R , Orwoll Eric S , Ensrud Kristine E
Published: February 2008

The aim of these analyses was to describe the association between physical performance and risk of hip fractures in older men. Performance on five physical function exams (leg power, grip strength, usual walking pace, narrow walk balance test, and five repeated chair stands) was assessed in 5902 men ≥65 yr of age. Performance (time to complete or strength) was analyzed as quartiles, with an additional category for unable to complete the measure, in proportional hazards models. Follow-up averaged 5.3 yr; 77 incident hip fractures were confirmed by physician review of radiology reports. Poor physical performance was associated with an increased risk of hip fracture. In particular, repeated chair stand performance was strongly related to hip fracture risk. Men unable to complete this exam were much more likely to experience a hip fracture than men in the fastest quartile of this test (multivariate hazard ratio [MHR]: 8.15; 95% CI: 2.65, 25.03). Men with the worst performance (weakest/slowest quartile or unable) on at least three exams had an increased risk of hip fracture compared with men with higher functioning (MHR: 3.14, 95% CI: 1.46, 6.73). Nearly two thirds of the hip fractures (N = 49, 64%) occurred in men with poor performance on at least three exams. Poor physical function is independently associated with an increased risk of hip fracture in older men. The repeated chair stands exam should be considered in clinical settings for evaluation of hip fracture risk. Concurrent poor performance on multiple physical function exams is associated with an increased risk of hip fractures.