bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison of Self-Collected and Physician-Collected Vaginal Swabs for Microbiome Analysis
Authors: Forney Larry J. , Gajer Pawel , Williams Christopher J. , Schneider G. Maria , Koenig Sara S. K. , McCulle Stacey L. , Karlebach Shara , Brotman Rebecca M. , Davis Catherine C. , Ault Kevin , Ravel Jacques
Published: March 2010

To our knowledge, no data are available on whether the microbial species composition and abundance sampled with self-collected vaginal swabs are comparable to those of swabs collected by clinicians. Twenty healthy women were recruited to the study during a routine gynecological visit. Eligible women were between 18 and 40 years old with regular menstrual cycles. Participants self-collected a vaginal swab using a standardized protocol and then were examined by a physician, who collected an additional five swabs from the lateral wall of the mid-vagina. In this study, the self-collected and three physician-obtained swabs were analyzed and compared using terminal restriction fragment length polymorphism and sequence analyses of the 16S rRNA genes. Vaginal microbial community comparative statistical analyses of both T-RFLP and 16S rRNA gene sequence datasets revealed that self-collected vaginal swabs sampled the same microbial diversity as physician collected swabs of the mid-vagina. These findings enable large-scale, field-based studies of the vaginal microbiome.
Replacing Reverse Line Blot Hybridization Spoligotyping of the
Mycobacterium tuberculosis
Complex
Authors: Honisch Christiane , Mosko Michael , Arnold Catherine , Gharbia Saheer E. , Diel Roland , Niemann Stefan
Published: March 2010

Spoligotyping is a tool for the molecular characterization/typing of
Mycobacterium tuberculosis
complex (MTBC) strains based on target sequences (spacers) in the direct repeat (DR) region (14). The standard spoligotyping assay involves the hybridization of amplified sample DNA to nylon membrane-immobilized oligonucleotides whose sequences are representative of 43 spacer regions. Variations in the number of spacers as a result of deletions of adjacent blocks of repetitive units allow the differentiation of clinical isolates. In the present study, we developed a new multiplexed primer extension-based spoligotyping assay using automated matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) that improves the classical reverse line blot hybridization assay with respect to reproducibility, throughput, process flow, ease of use, and data analysis. Validation of the MALDI-TOF MS-based spoligotyping assay with two sample sets with a total of 326 samples resulted in 96.6% concordance (315/326) when the full spoligotype patterns were compared with the results of standard spoligotyping and 99.9% concordance when the results were compared with those of individual primer extension assays. Ten strains (including two
Mycobacterium canettii
strains) showed discordant results with one or two spacer differences from the membrane-based spoligotyping result. Most discordant samples were identified to be the result of ambiguities in the interpretation of weak hybridization signals in the reverse line blot assay and sequence variations in the spacer regions. We established a new automated primer extension assay and successfully validated it for use for the routine typing of MTBC strains in the research and public health laboratory environments. The present multiplex levels of up to 30 are extendable and allow the additional incorporation of controls and antibiotic resistance markers.
The
De Novo
Methyltransferases DNMT3a and DNMT3b Target the Murine Gammaherpesvirus Immediate-Early Gene 50 Promoter during Establishment of Latency
Authors: Gray Kathleen S. , Forrest J. Craig , Speck Samuel H.
Published: March 2010

The role of epigenetic modifications in the regulation of gammaherpesvirus latency has been a subject of active study for more than 20 years. DNA methylation, associated with transcriptional silencing in mammalian genomes, has been shown to be an important mechanism in the transcriptional control of several key gammaherpesvirus genes. In particular, DNA methylation of the functionally conserved immediate-early replication and transcription activator (RTA) has been shown to regulate Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus Rta expression. Here we demonstrate that the murine gammaherpesvirus (MHV68) homolog, encoded by gene 50, is also subject to direct repression by DNA methylation, both
in vitro
and
in vivo
. We observed that the treatment of latently MHV68-infected B-cell lines with a methyltransferase inhibitor induced virus reactivation. In addition, we show that the methylation of the recently characterized distal gene 50 promoter represses activity in a murine macrophage cell line. To evaluate the role of
de novo
methyltransferases (DNMTs) in the establishment of these methylation marks, we infected mice in which conditional DNMT3a and DNMT3b alleles were selectively deleted in B lymphocytes. DNMT3a/DNMT3b-deficient B cells were phenotypically normal, displaying no obvious compromise in cell surface marker expression or antibody production either in naïve mice or in the context of nonviral and viral immunogens. However, mice lacking functional DNMT3a and DNMT3b in B cells exhibited hallmarks of deregulated MHV68 lytic replication, including increased splenomegaly and the presence of infectious virus in the spleen at day 18 following infection. In addition, total gene 50 transcript levels were elevated in the spleens of these mice at day 18, which correlated with the hypomethylation of the distal gene 50 promoter. However, by day 42 postinfection, aberrant virus replication was resolved, and we observed wild-type frequencies of viral genome-positive splenocytes in mice lacking functional DNMT3a and DNMT3b in B lymphocytes. The latter correlated with increased CpG methylation in the distal gene 50 promoter, which was restored to levels similar to those of littermate controls harboring functional DNMT3a and DNMT3b alleles in B lymphocytes, suggesting the existence of an alternative mechanism for the
de novo
methylation of the MHV68 genome. Importantly, this DNMT3a/DNMT3b-independent methylation appeared to be targeted specifically to the gene 50 promoter, as we observed that the promoters for MHV68 gene 72 (v-cyclin) and M11 (v-bcl2) remained hypomethylated at day 42 postinfection. Taken together, these data provide the first evidence of the importance of DNA methylation in regulating gammaherpesvirus RTA/gene 50 transcription during virus infection
in vivo
and provide insight into the hierarchy of host machinery required to establish this modification.
Human Cytomegalovirus IE2 86 and IE2 40 Proteins Differentially Regulate UL84 Protein Expression Posttranscriptionally in the Absence of Other Viral Gene Products
Authors: Sanders Rebecca L. , Spector Deborah H.
Published: March 2010

It has previously been demonstrated that, during human cytomegalovirus infection, the viral IE2 86 and IE2 40 proteins are both important for the expression of an early-late viral protein, UL84. Here, we show that expression of the UL84 protein is enhanced upon cotransfection with either IE2 86 or IE2 40, although IE2 40 appears to play a more important role. The UL84 protein levels are tightly linked to the amount of IE2 40 present, but this does not appear to be true for IE2 86. RNA remains constant for all corresponding proteins, indicating posttranscriptional regulation of UL84. The first 105 amino acids of UL84 are necessary and sufficient for this phenotype, and this region is also required for an interaction with IE2 86 and IE2 40. Treatment with proteasome inhibitors shows that UL84 exhibits some proteasome-dependent degradation, and UL84 is not protected against this degradation when coexpressed with IE2 86 or IE2 40. UL84 also exhibits an inhibitory effect on IE2 86 and IE2 40 protein levels in these cotransfection assays. Further, we show that the amino acid sequence of UL84 is important for the enhancement governed by IE2 40. These results indicate that IE2 86, IE2 40, and UL84 serve to regulate protein expression in a posttranscriptional fashion and that this regulation is independent of other viral proteins.
Phenotypic and Functional Profile of HIV-Inhibitory CD8 T Cells Elicited by Natural Infection and Heterologous Prime/Boost Vaccination
Authors: Freel Stephanie A. , Lamoreaux Laurie , Chattopadhyay Pratip K. , Saunders Kevin , Zarkowsky David , Overman R. Glenn , Ochsenbauer Christina , Edmonds Tara G. , Kappes John C. , Cunningham Coleen K. , Denny Thomas N. , Weinhold Kent J. , Ferrari Guido , Haynes Barton F. , Koup Richard A. , Graham Barney S. , Roederer Mario , Tomaras Georgia D.
Published: March 2010

Control of HIV-1 replication following nonsterilizing HIV-1 vaccination could be achieved by vaccine-elicited CD8
+
T-cell-mediated antiviral activity. To date, neither the functional nor the phenotypic profiles of CD8
+
T cells capable of this activity are clearly understood; consequently, little is known regarding the ability of vaccine strategies to elicit them. We used multiparameter flow cytometry and viable cell sorts from phenotypically defined CD8
+
T-cell subsets in combination with a highly standardized virus inhibition assay to evaluate CD8
+
T-cell-mediated inhibition of viral replication. Here we show that vaccination against HIV-1 Env and Gag-Pol by DNA priming followed by recombinant adenovirus type 5 (rAd5) boosting elicited CD8
+
T-cell-mediated antiviral activity against several viruses with either lab-adapted or transmitted virus envelopes. As it did for chronically infected virus controllers, this activity correlated with HIV-1-specific CD107a or macrophage inflammatory protein 1β (MIP-1β) expression from HIV-1-specific T cells. Moreover, for vaccinees or virus controllers, purified memory CD8
+
T cells from a wide range of differentiation stages were capable of significantly inhibiting virus replication. Our data define attributes of an antiviral CD8
+
T-cell response that may be optimized in the search for an efficacious HIV-1 vaccine.
Acceleration of Hepatitis C Virus Envelope Evolution in Humans Is Consistent with Progressive Humoral Immune Selection during the Transition from Acute to Chronic Infection
Authors: Liu Lin , Fisher Brian E. , Dowd Kimberly A. , Astemborski Jacquie , Cox Andrea L. , Ray Stuart C.
Published: March 2010

During the transition from acute to chronic infection in individuals persistently infected with hepatitis C virus (HCV), cellular responses initiate within the first 6 months of primary infection and collapse thereafter, whereas humoral responses activate later during the chronic phase. Whether and how this deviation of immune responses specifically influences HCV evolution are unknown. To determine the pattern of HCV evolution during this critical period, we conducted extensive sequence analysis on annual clonal hemigenomic sequences for up to 3 years in six well-characterized subjects, using statistical methods that accounted for repeated measures. Significantly different evolutionary rates were observed in envelope versus nonenvelope genes, with an increasing rate of nonsynonymous change (
dN
) in envelope genes and a stable
dN
in nonenvelope genes (
P
= 0.006). The ratio of the envelope to nonenvelope nonsynonymous rate increased from 2 in year 1 to 5 in years 2 and 3. Centripetal changes (reversions toward matching of the worldwide subtype 1a consensus sequence) were frequently observed during the 3-year transition from acute infection to chronicity, even in the presence of neutralizing antibody (NAb) pressure. Remarkably, sequences of hypervariable region 1 (HVR1) remained stable for up to 21 months in the absence of NAb pressure in one subject, followed by rapid changes that were temporally associated with the detection of NAb responses, which strongly suggests that HVR1 evolution is shaped by NAb pressure. These data provide the first systematic estimates of HCV evolutionary rates in multiple genes during early infection
in vivo
and provide additional evidence for deterministic, rather than random, evolution of HCV.
A Role for the C Terminus of Mopeia Virus Nucleoprotein in Its Incorporation into Z Protein-Induced Virus-Like Particles
Authors: Shtanko Olena , Imai Masaki , Goto Hideo , Lukashevich Igor S. , Neumann Gabriele , Watanabe Tokiko , Kawaoka Yoshihiro
Published: March 2010

Arenaviruses are enveloped, negative-strand RNA viruses. For several arenaviruses, virus-like particle (VLP) formation requires the viral matrix Z protein. However, the mechanism by which viral ribonucleoprotein complexes are incorporated into virions is poorly understood. Here, we show that the expression of the Z protein and nucleoprotein (NP) of Mopeia virus, a close relative of the pathogenic Lassa virus, resulted in the highly selective incorporation of the NP protein into Z protein-induced VLPs. Moreover, the Z protein promoted the association of NP with cellular membranes, suggesting that the association of NP, Z, and the cellular membranes may facilitate the efficient incorporation of NP into VLPs. By employing a series of NP deletion constructs and testing their VLP incorporation, we further demonstrated an important role for the C-terminal half of NP in its incorporation into VLPs.
Influenza H1N1 A/Solomon Island/3/06 Virus Receptor Binding Specificity Correlates with Virus Pathogenicity, Antigenicity, and Immunogenicity in Ferrets
Authors: Xu Qi , Wang Weijia , Cheng Xing , Zengel James , Jin Hong
Published: March 2010

Influenza viruses attach to cells via a sialic acid moiety (sialic acid receptor) that is α2-3 linked or α2-6 linked to galactose (α2-3SAL or α2-6SAL); sialic acid acts as a receptor for the virus. Using lectin staining, we demonstrated that the α2-6SAL configuration is predominant in the respiratory tract of ferrets, including trachea, bronchus, and lung alveolus tissues. Recombinant wild-type (rWT) influenza A/Solomon Island/3/06 (SI06) (H1N1) viruses were constructed to assess the impact of the hemagglutinin (HA) variations (amino acids 190 or 226) identified in natural variants on virus replication in the upper and lower respiratory tract of ferrets, as well as virus antigenicity and immunogenicity. A single amino acid change at residue 226 (from Gln to Arg) in the HA of SI06 resulted in the complete loss of binding to α2-6SAL and a concomitant loss of the virus's ability to replicate in the lower respiratory tract of ferrets. In contrast, the virus with Gln226 in the HA protein has a receptor binding preference for α2-6SAL and replicates efficiently in the lungs. There was a good correlation between viral replication in the lungs of ferrets and disease symptoms. In addition, we also showed that the 190 and 226 residues affected viral antigenicity and immunogenicity. Our data emphasize the necessity of thoroughly assessing wild-type influenza viruses for their suitability as reference strains and for carefully selecting the HA antigen for vaccine production during annual influenza vaccine evaluation processes.
Measles Virus-Induced Immunosuppression in SLAM Knock-In Mice
Authors: Koga Ritsuko , Ohno Shinji , Ikegame Satoshi , Yanagi Yusuke
Published: March 2010

Measles virus (MV) causes transient severe immunosuppression in patients, which may lead to secondary viral and bacterial infections, largely accounting for measles-related morbidity and mortality. MV is known to infect immune cells by using the human signaling lymphocyte activation molecule (SLAM; also called CD150) as a cellular receptor, but the mechanism by which MV causes immunosuppression is not well understood. We show that MV infection of SLAM knock-in mice, in which the V domain of mouse SLAM was replaced by the V domain of human SLAM, crossed with alpha/beta-interferon receptor knockout mice, reproduced many immunological alterations observed in human patients. These included lymphopenia, inhibition of T-cell proliferation and antibody production, increased production of the Th2 cytokine interleukin-4 (IL-4) and the immunosuppressive cytokine IL-10, and suppression of contact hypersensitivity. Gross redistribution of lymphocytes among lymphoid tissues was not apparent in infected mice, nor was an increase of regulatory T cells. The numbers of lymphocytes in lymph nodes remained almost unchanged after MV infection, despite enhanced apoptosis, suggesting that lymph nodes were replenished with lymphocytes from the peripheral blood, which may have contributed to the observed lymphopenia in the spleen. Blocking of IL-10 by use of an anti-IL-10 receptor antibody ameliorated suppression of contact hypersensitivity in infected mice. These results indicate that SLAM knock-in mice lacking the expression of the alpha/beta-interferon receptor serve as a useful small animal model with which to elucidate MV-induced immunosuppression.
Gene Expression Profiling Indicates the Roles of Host Oxidative Stress, Apoptosis, Lipid Metabolism, and Intracellular Transport Genes in the Replication of Hepatitis C Virus
Authors: Blackham Samantha , Baillie Andrew , Al-Hababi Fadel , Remlinger Katja , You Shihyun , Hamatake Robert , McGarvey Michael J.
Published: March 2010

Hepatitis C virus (HCV) is a leading cause of chronic liver disease. The identification and characterization of key host cellular factors that play a role in the HCV replication cycle are important for the understanding of disease pathogenesis and the identification of novel antiviral therapeutic targets. Gene expression profiling of JFH-1-infected Huh7 cells by microarray analysis was performed to identify host cellular genes that are transcriptionally regulated by infection. The expression of host genes involved in cellular defense mechanisms (apoptosis, proliferation, and antioxidant responses), cellular metabolism (lipid and protein metabolism), and intracellular transport (vesicle trafficking and cytoskeleton regulation) was significantly altered by HCV infection. The gene expression patterns identified provide insight into the potential mechanisms that contribute to HCV-associated pathogenesis. These include an increase in proinflammatory and proapoptotic signaling and a decrease in the antioxidant response pathways of the infected cell. To investigate whether any of the host genes regulated by infection were required by HCV during replication, small interfering RNA (siRNA) silencing of host gene expression in HCV-infected cells was performed. Decreasing the expression of host genes involved in lipid metabolism (TXNIP and CYP1A1 genes) and intracellular transport (RAB33b and ABLIM3 genes) reduced the replication and secretion of HCV, indicating that they may be important factors for the virus replication cycle. These results show that major changes in the expression of many different genes in target cells may be crucial in determining the outcome of HCV infection.
Analysis of Apoptosis of Memory T Cells and Dendritic Cells during the Early Stages of Viral Infection or Exposure to Toll-Like Receptor Agonists
Authors: Bahl Kapil , Hüebner Anette , Davis Roger J. , Welsh Raymond M.
Published: March 2010

Profound type I interferon (IFN-I)-dependent attrition of memory CD8 and CD4 T cells occurs early during many infections. It is dramatic at 2 to 4 days following lymphocytic choriomeningitis virus (LCMV) infection of mice and can be elicited by the IFN-inducing Toll receptor agonist poly(I:C). We show that this attrition occurs in many organs, indicating that it is due to T cell loss rather than redistribution. This loss correlated with elevated intracellular staining of T cellsex vivofor activated caspases but with only low levels ofex vivostaining with annexin V, probably due to the rapid clearance of apoptotic cellsin vivo. Instead, a high frequency of annexin V-reactive CD8α+dendritic cells (DCs), which are known to be highly phagocytic, accumulated in the spleen as the memory T cell populations disappeared. After shortin vitroincubation, memory phenotype T cells isolated from LCMV-infected mice (day 3) or mice treated with poly(I:C) (12 h) displayed substantial DNA fragmentation, as detected by terminal deoxynucleotidyltransferase-mediated dUTP-biotin nick end labeling (TUNEL) assay, compared to T cells isolated from uninfected mice, indicating a role for apoptosis in the memory T cell attrition. This apoptosis of memory CD8 T cells early during LCMV infection was reduced in mice lacking the proapoptotic molecule Bim. Evidence is presented showing that high levels of T cell attrition, as found in young mice, correlate with reduced immunodomination by cross-reactive memory cells.
Novel Infectious cDNA Clones of Hepatitis C Virus Genotype 3a (Strain S52) and 4a (Strain ED43): Genetic Analyses and
In Vivo
Pathogenesis Studies
Authors: Gottwein Judith M. , Scheel Troels K. H. , Callendret Benoit , Li Yi-Ping , Eccleston Heather B. , Engle Ronald E. , Govindarajan Sugantha , Satterfield William , Purcell Robert H. , Walker Christopher M. , Bukh Jens
Published: March 2010

Previously, RNA transcripts of cDNA clones of hepatitis C virus (HCV) genotypes 1a (strains H77, HCV-1, and HC-TN), 1b (HC-J4, Con1, and HCV-N), and 2a (HC-J6 and JFH1) were found to be infectious in chimpanzees. However, only JFH1 was infectious in human hepatoma Huh7 cells. We performed genetic analysis of HCV genotype 3a (strain S52) and 4a (strain ED43) prototype strains and generated full-length consensus cDNA clones (pS52 and pED43). Transfection of Huh7.5 cells with RNA transcripts of these clones did not yield cells expressing HCV Core. However, intrahepatic transfection of chimpanzees resulted in robust infection with peak HCV RNA titers of ∼5.5 log
10
international units (IU)/ml. Genomic consensus sequences recovered from serum at the times of peak viral titers were identical to the sequences of the parental plasmids. Both chimpanzees developed acute hepatitis with elevated liver enzymes and significant necroinflammatory liver changes coinciding with detection of gamma interferon-secreting, intrahepatic T cells. However, the onset and broadness of intrahepatic T-cell responses varied greatly in the two animals, with an early (week 4) multispecific response in the ED43-infected animal (3 weeks before the first evidence of viral control) and a late (week 11) response with limited breadth in the S52-infected animal (without evidence of viral control). Autologous serum neutralizing antibodies were not detected during the acute infection in either animal. Both animals became persistently infected. In conclusion, we generated fully functional infectious cDNA clones of HCV genotypes 3a and 4a. Proof of functionality of all genes might further the development of recombinant cell culture systems for these important genotypes.
In utero drugs of abuse exposure testing for newborn twins
Authors: Wang Ping , Molina Claudia P , Maldonado Joyce E , Bernard David W
Published: March 2010

This report describes testing of a case of in utero drugs of abuse exposure in which discordant results were seen between urine and meconium, and between twin meconium samples. The discordance between urine and meconium could be explained by the differences in detection window, threshold concentration and screening technology, and the discordance between dizygotic twin meconium samples could be explained by the differences in drug diffusion and placental and fetal biotransformation of drugs. The meconium sample of one twin screened negative for benzodiazepines was reported positive in the confirmation assay with higher sensitivity and a lower cut-off concentration. Negative screening results of drugs of abuse should be interpreted with caution, taking into account matrix type, reactivity of drugs in the assay and cut-off concentration. If screening results are inconsistent with each other or with the clinical scenario, confirmation testing using more sensitive and specific methods with lower cut-offs is warranted.
Does rituximab aggravate pre-existing hypogammaglobulinaemia?: Table 1
Authors: Diwakar Lavanya , Gorrie Sheryl , Richter Alex , Chapman Oliver , Dhillon Paul , Al-Ghanmi Fayza , Noorani Sadia , Krishna Mamidipudi T , Huissoon Aarnoud
Published: March 2010

Rituximab, an anti-CD20 chimeric antibody, is the first monoclonal agent to be used in the therapy of cancer. It has been hailed as one of the most important therapeutic developments of the decade. While transient peripheral B cell depletion is common after rituximab therapy, immunoglobulin levels are generally not affected. This is because CD20 is expressed on pre-B and mature B lymphocytes but not on stem cells or plasma cells. Two adult patients with pre-existing primary antibody deficiency who presented with recurrent infections immediately following rituximab use for the treatment of refractory idiopathic thrombocytopenic purpura (ITP) are described. Both were previously treated with various immunosuppressive agents without any notable infective problems. However, a few weeks after treatment with rituximab, these patients presented with clinically significant immunodeficiency requiring intravenous immunoglobulin replacement therapy. This striking temporal relationship between rituximab administration and onset of infections suggests that rituximab has accelerated the presentation of immune deficiency in these patients. Increased vigilance around the use of newer immunomodulatory agents such as rituximab is recommended.
Enterococcus raffinosussinusitis post-Aspergillus flavusparanasal infection, in a patient with myelodysplastic syndrome: report of a case and concise review of pertinent literature
Authors: Savini Vincenzo , Catavitello Chiara , Favaro Marco , Masciarelli Gioviana , Astolfi Daniela , Balbinot Andrea , Bianco Azaira , Mauti Alessandro , Dianetti Janet , Fontana Carla , D'Amario Claudio , D'Antonio Domenico
Published: March 2010

A case ofEnterococcus raffinosusnosocomial sinusitis which appeared to complicate a previousAspergillus flavusparanasal infection is presented. This uncommon enterococcal species is rarely responsible for human diseases, and has never previously been associated with sinusitis.
Adenoid cystic carcinomas of the breast and salivary glands (or ‘The strange case of Dr Jekyll and Mr Hyde’ of exocrine gland carcinomas)
Authors: Marchiò Caterina , Weigelt Britta , Reis-Filho Jorge S
Published: March 2010

Adenoid cystic carcinoma (AdCC) is a tumour with myoepithelial differentiation and characterised by the presence of a dual population of basaloid and luminal cells arranged in specific growth patterns. These tumours, regardless of the anatomical site, are characterised by expression of the proto-oncogene and therapeutic target c-KIT, and seem to harbour a specific chromosomal translocation t(6;9) leading to the fusion geneMYB-NFIBand overexpression of the oncogeneMYB. However, the clinical behaviour of salivary gland and breast AdCC differs; while salivary gland lesions have a relatively high proclivity to metastasise, patients with breast AdCCs have an excellent outcome. Here the clinical, morphological and molecular features, and potential therapeutic targets of salivary gland and breast AdCCs are reviewed.
Lymphatics and D2-40/podoplanin expression in gastrointestinal stromal tumours of the stomach with and without lymph node metastasis: an immunohistochemical study with special reference to the Carney triad
Authors: Agaimy Abbas , Carney J Aidan
Published: March 2010

Background

Lymph node metastasis of gastric gastrointestinal stromal tumours (GISTs) in children and young adults, especially those with the Carney triad, is common (∼29%) and contrasts with that of sporadic gastric GISTs (≤2%). The mechanism responsible for this difference in tumour behaviour is not understood. In previous studies, expression of the lymphatic endothelial marker D2-40/podoplanin in carcinoma cells and the presence of intratumoural/peritumoural lymphatics have been correlated with tumour invasiveness and nodal metastasis.

Methods

This study investigated the presence of intratumoural and peritumoural lymphatics, and expression of D2-40/podoplanin, in 16 patients with syndromic/paediatric gastric GISTs (11 patients had Carney triad, two had Carney–Stratakis syndrome and three had paediatric GISTs suspicious for the Carney triad) with histologically verified metastasis to regional lymph nodes. The results were compared with those found in 35 sporadic gastric GISTs lacking nodal spread using the antibody D2-40/podoplanin.

Results

The mean ages at GIST diagnosis in the patients with syndromic/paediatric GISTs and those with sporadic GISTs were 18 years and 67 years, respectively. Intratumoural lymphatics were detected with comparable frequency in the two tumour sets (25% and 17%, respectively; p=0.705). Peritumoural lymphatics were equally present in the tumours from both of the groups. Moderate/strong cytoplasmic/membranous staining for D2-40/podoplanin was frequent in the neoplastic cells of syndromic/paediatric GISTs (87%), and infrequent in sporadic GISTs (3%) (p<0.001).

Conclusion

The results indicate that intratumoural lymphangiogenesis is probably not involved in lymphatic spread in syndromic/paediatric GISTs. The biological significance of D2-40/podoplanin expression in tumour cells of syndromic/paediatric GISTs and its possible role in lymphatic tumour spread remain to be further investigated.
Novel epitheliomesenchymal biphasic stomach tumour (gastroblastoma) in a 9-year-old: morphological, usltrastructural and immunohistochemical findings
Authors: Shin Dong Hoon , Lee Jung Hee , Kang Hyun Jeong , Choi Kyung Un , Kim Jee Yeon , Park Do Youn , Lee Chang Hun , Sol Mee Young , Park Jae Hong , Kim Hae Young , Montgomery Elizabeth
Published: March 2010

Gastroblastoma is a rare gastric epitheliomesenchymal biphasic tumour composed of spindle and epithelial cells, reported by Miettinenet alin a series of three cases in 2009. All those cases arose in stomachs of young adults. Neither the epithelial nor the mesenchymal component displayed sufficient atypia to diagnose a carcinosarcoma or other malignancy. On immunohistochemistry, the epithelial component expressed cytokeratin, and the mesenchymal component was positive for vimentin and CD10. Miettinenet aldesignated these neoplasms as gastroblastomas based on their similarities with other childhood blastomas such as pleuropulmonary blastoma and nephroblastoma. This report describes a probable fourth case of this unique type of neoplasm. The present case arose in the gastric antrum of a 9-year-old boy. While similarities were evident with the other cases, there were some differences. The epithelial component was more predominant and showed more mature morphology. Immunohistochemically, the epithelial component showed immunolabelling for c-KIT and CD56. The mesenchymal component was only focally positive for CD10. Ultrastructually, desmosomes and microvilli were found supporting a truly epithelial lesion.
A comparison of two DNA barcode markers for species discrimination in the red algal family Kallymeniaceae (Gigartinales, Florideophyceae), with a description of Euthora timburtonii sp. nov.
Authors: Clarkston Bridgette E. , Saunders Gary W.
Published: March 2010

Accurate identification of many red algae to the species level using only morphological characters can be difficult. The emerging field of “molecular-assisted alpha taxonomy” can greatly alleviate this issue. In this approach, a large number of specimens are sequenced for a standard DNA marker as a first step to genetic species assignment, followed by detailed morphological observations. Regions of both the mitochondrial cytochrome c oxidase I gene (COI-5P) and the plastid 23S rRNA gene (UPA) have been proposed as DNA barcode markers to accomplish this task. We compared the utility of each marker as a species identification tool using members of the marine red algal family Kallymeniaceae from British Columbia, Canada. Our results indicate that COI-5P is a more sensitive marker for delimiting species, but that it can be difficult to acquire clean amplification products for many isolates of Kallymeniaceae, owing to biological contamination. This problem can be overcome by using specific primers. UPA, on the other hand, has universal primers that work in diverse lineages (e.g., red, brown, and green algae), but lower interspecific sequence variation, which has the potential to underestimate species diversity, although this was not observed in our study. During our survey, we uncovered a new species of the Kallymeniaceae, Euthora timburtonii Clarkston et G.W. Saunders sp. nov., which we describe here.
Exploring the role of root anatomy in P-mediated control of colonization by arbuscular mycorrhizal fungi
Authors: Sharda J. N. , Koide R. T.
Published: March 2010

Alterations of root anatomy have been largely ignored as potential mechanisms for phosphorus-mediated control of arbuscular mycorrhizal colonization. However, at least three anatomical traits including the proportion of root length with a suberized hypodermis, the distribution of hypodermal passage cells, and the proportion of root volume as intercellular air space may influence the degree of colonization. In the present study, we determined whether these traits could be altered by variation in plant phosphorus (P) status. We grew 15 angiosperm species from 13 families, each at two P availabilities, and determined how P status influenced the three root traits. Of the three traits, only the distribution of passage cells was significantly affected by phosphorus status; high P plants possessed a reduced proportion of root length with passage cells. Therefore, in species with passage cells, change in the proportion of root length with passage cells may represent one mechanism for phosphorus-mediated control of mycorrhizal colonization. However, individual species responses to P treatment varied widely, and no single anatomical mechanism appeared to be responsible for the control of mycorrhizal colonization in all species.
Sex ratio variation in gynodioecious species ofEchiumendemic to the Canary Islands
Authors: Dorken Marcel E.
Published: March 2010

Species of Echium from the Canary Islands represent an adaptive radiation of plants involving evolutionary changes in habitat and life form. Alongside these changes, evolutionary transitions of the sexual system have occurred: approximately one quarter of Echium species from the Canary Islands are dimorphic for gender, paralleling other adaptive radiations of plants on oceanic islands, such as Schiedea in Hawaii. Here, I report on the variation in the frequency of female plants among eight gynodioecious populations representing four species of Echium on the island of Tenerife, and provide preliminary estimates of the seed fertility of females and hermaphrodites, which is an important determinant of the sex ratio for gynodioecious species. Across populations, female frequencies ranged between 6% and 54%, a much wider range than had previously been reported for gynodioecious species of Echium on the Canary Islands. Substantial frequencies of female plants occurred, even though no differences in the seed fertility of females and hermaphrodites were detected.
Floral nectary structure, nectar production, and carbohydrate composition in theLiliumAsiatic hybrid ‘Trésor’
Authors: Stolar Jessica , Davis Arthur R.
Published: March 2010

Floral nectary structure, nectar production, and carbohydrate composition were compared from petals (“inner tepals”) and sepals (“outer tepals”) of Lilium Asiatic hybrid ‘Trésor’ (Liliaceae). The six nectaries each occupied a narrow furrow bordered by two convergent ridges extending adaxially from the petal and sepal base. Each sepal nectary furrow was shorter and more concealed. In both nectary types, many vascular bundles comprising xylem and phloem supplied 5.5–8 layers of nectariferous parenchyma cells below the epidermis, which lacked stomata. Transmission electron microscopy of sepal nectaries demonstrated that parts of the outer epidermal wall adhered to an intact but uplifted cuticle in nectar-secreting flowers. Both apoplastic and symplastic routes were continuous from the vascular bundles to the nectary epidermis. Starch breakdown from amyloplasts throughout the nectary likely augmented nectar production. Nectar solute concentration from another Asiatic hybrid, ‘Orange Pixie’, was also significantly higher in petals. In ‘Trésor’, significantly more nectar was available from sepals, possibly reflecting reduced evaporation from multiple nectar droplets within the covered nectary furrow. However, for both hybrids, the same quantity of nectar sugar was produced by petals and sepals. Nectar composition from petals and sepals also was alike, in ‘Orange Pixie’ averaging 67/19/14 (= sucrose/fructose/glucose) and 59/25/17, respectively, and in ‘Trésor’ averaging 68/23/10 and 62/27/12, respectively.
Nitrogen use efficiency: re-consideration of the bioengineering approach
Authors: Brauer Elizabeth K. , Shelp Barry J.
Published: March 2010

There is considerable confusion about N use efficiency (NUE) in the plant literature. We would like to propose the simple and ubiquitous definitions described by Good et al. (2004) as a starting point for studies of NUE. Based on this terminology, there is evidence from breeding programs for variation in both uptake efficiency (UpE) and utilization efficiency (UtE). Molecular physiology studies typically address mechanisms for improving NUE, but often do not calculate NUE or even acquire appropriate data for calculating NUE. Herein, we report in detail on recent studies involving molecular approaches for improving NUE, and calculate changes in NUE where possible. The evidence suggests that there is potential for improving usage index and UpE in dicots and UpE and UtE in monocots by overexpressing enzymes for N assimilation, specifically glutamine synthetase 1, glutamate synthase, and alanine aminotransferase. If decreased fertilizer-N input and improved NUE are truly goals of the plant biology community, researchers are encouraged to (i) consider the use of both wild type and azygous controls, (ii) compare general NUE (on the basis of grain or biomass yield per unit of applied N) of overexpression mutants and controls at both limiting and non-limiting N levels, (iii) select an appropriate type of specific NUE for assessing the physiological mechanisms involved (uptake versus internal utilization), and (iv) confirm promising results under field conditions.
Structure of the Betts Cove Ophiolite Complex beneath the western margin of Notre Dame Bay, Newfoundland
Authors: Spicer B. , Morris B. , Ugalde H. , Slavinski H. , Skulski T.
Published: March 2010

Ophiolitic rocks emplaced following closure of the Ordovician Iapetus Ocean outcrop around the western margins of Notre Dame Bay in western Newfoundland. Previous geological and geophysical models have interpreted the Betts Cove Ophiolite Complex (BCO) as a series of imbricate thrust slices. A new three-dimensional (3-D) model indicates that locally the BCO has the form of a northeast-trending doubly plunging syncline that was later segmented by a series of normal and high-angle reverse faults. This segmentation is interpreted in terms of a Carboniferous graben structure that is responsible for the current morphology of the Notre Dame Bay. The 3-D model incorporates new high-resolution aeromagnetic, marine magnetic, and topographic imagery. In addition, newly available structural information is used to both constrain the geometry of the geological contacts in the near surface and to map contacts in the subsurface. Calibration of the computed geophysical models was achieved using newly acquired magnetic susceptibility data. The resulting 3-D model, which is compatible with all aspects of the geological and geophysical data, provides an explanation for the distribution of Ordovician ophiolites around Notre Dame Bay.
Diagenesis to metamorphism transition in an episutural basin: the late Paleozoic St. Mary’s Basin, Nova Scotia, Canada
Authors: Abad Isabel , Murphy J. Brendan , Nieto Fernando , Gutiérrez-Alonso Gabriel
Published: March 2010

The Late Devonian – Early Carboniferous St. Mary’s Basin in the Canadian Appalachians consists of Horton Group fluviatile and lacustrine clastic rocks. The basin occurs along the boundary between the Avalon and Meguma terranes and developed during coeval dextral shear along that boundary. X-ray diffraction reveals that the rocks contain ubiquitous quartz, K-white mica, and albite; illite–smectite mixed layers and chlorite are very common and Na–K mica, kaolinite, chlorite–smectite mixed layers, K-feldspar, berthierine, and rutile occur in some samples. Crystal-chemical parameters of white mica indicate the pressure and temperature of mineral growth and discriminate between diagenetic, anchizone, and low-grade metamorphic processes. Kübler index values measured in the 5 Å peak and the presence of chlorite–mica stacks are indicative of high-anchizone–epizone grades, with a crystallinity (crystal size and number of defects) that increases towards the Chedabucto Fault, which defines the northern margin of the basin. Kübler index values measured in the 10 Å peak indicate that a late fluid-rich event could have produced the observed illite–smectite mixed layers. The overall clay-mineral content and the b-cell dimension of the K-white micas are typical of postdepositional evolution in extensional sedimentary basins with high heat flow (>35 °C/km). Taken together, our data record two superposed events related to deformation along the basin margins and coeval regional fluid flow, in which retrograde reactions at temperature T < 200 °C were superimposed on a pre-existing prograde assemblage typical of high-anchizone – lower greenschist-facies conditions (T > 300 °C). Regional syntheses indicate that this fluid flow may have occurred during episodes of Late Carboniferous dextral shear along the Avalon–Meguma terrane boundary.
Tidal movements and residency of subyearling Chinook salmon (Oncorhynchus tshawytscha) in an Oregon salt marsh channel
Authors: Hering David K. , Bottom Daniel L. , Prentice Earl F. , Jones Kim K. , Fleming Ian A.
Published: March 2010

A novel application of full-duplex passive integrated transponder (PIT) tag technology was used to investigate movements of individual subyearling Chinook salmon ( Oncorhynchus tshawytscha ; fork length ≥ 60 mm) into and out of tidally flooded salt marsh habitat in the Salmon River estuary, Oregon, USA. PIT interrogation was effective, with mean tag detection ≥ 92%. Salmon movement peaked late during both flood and ebb tide periods, indicating that salmon did not drift passively. Most movements were in the direction of tidal currents, but 20% of individuals entered the channel against the ebbing tide. Individuals occupied the intertidal channel for a median 4.9 h and as long as 8.9 h per tidal cycle, and few were detected moving when water depth was <0.4 m. Some individuals used the channel on multiple successive tidal cycles, and others entered intermittently over periods of up to 109 days. Using an individual-based approach, we characterized diversity of juvenile Chinook salmon behavior within a marsh channel, providing insight into the value of such habitats for conservation and restoration of salmon populations.
Experimental assessment of the bioenergetic and behavioural differences between two morphologically distinct populations of Arctic char (Salvelinus alpinus)
Authors: Guénard Guillaume , Boisclair Daniel , Ugedal Ola , Forseth Torbjørn , Jonsson Bror , Fleming Ian A.
Published: March 2010

A common environment experiment was conducted to assess the magnitude of the difference in growth, consumption, activity rate, and spatial and temporal patterns of habitat use between morphologically different populations of Arctic char ( Salvelinus alpinus ) originating from two Norwegian lakes. These two lakes contrasted sharply in terms of surface area, depth, elevation, length of the winter period, and fish community structure (presence–absence of brown trout, Salmo trutta ). The experimental framework encompassed four littoral enclosures (average volume, 146 m3) stocked with char from either of the two populations with duplicated treatments. Char morphology was quantified with numerical image analysis, food consumption was estimated using caesium analysis (133Cs), and activity cost and patterns were determined using video cameras. Char populations were morphologically distinct and reacted differently in growth (1.9-fold difference between populations), food consumption (3-fold difference), and spatial activity patterns (20-fold difference) to the conditions prevailing in the enclosures. The results highlight that functional differences between morphologically distinct char may drive important differences in their bioenergetic and behavioural responses when exposed to similar environmental conditions. Such functional differences should be incorporated when developing habitat or trophic cascade models.
The fire pulse: wildfire stimulates flux of aquatic prey to terrestrial habitats driving increases in riparian consumers
Authors: Malison Rachel L. , Baxter Colden V.
Published: March 2010

We investigated the midterm effects of wildfire (in this case, five years after the fire) of varying severity on periphyton, benthic invertebrates, emerging adult aquatic insects, spiders, and bats by comparing unburned sites with those exposed to low severity (riparian vegetation burned but canopy intact) and high severity (canopy completely removed) wildfire. We observed no difference in periphyton chlorophyll a or ash-free dry mass among different burn categories but did observe significantly greater biomass of benthic invertebrates in both high severity burned and unburned reaches versus low severity burned reaches. Moreover, a significantly greater flux of adult aquatic insect emergence occurred at sites that experienced high severity fire versus low severity burned and unburned sites. The greatest number of spiders and bat echolocation calls were also observed at sites of high severity fire. Our results suggest that fires of different severity may have very different affects on stream-riparian food webs and that high severity wildfire may lead to an extended “fire pulse” that stimulates aquatic productivity and flux of prey to terrestrial habitats, driving local increases in riparian consumers.
Design, synthesis, and properties of benzobisthiadiazole-based donor–π–acceptor–π–donor type of low-band-gap chromophores and polymers
Authors: Qian Gang , Wang Zhi Yuan
Published: March 2010

A novel low-band-gap chromophore (5, 0.86 eV) having fluorene as a donor, benzobisthiadiazole (BBTD) as an acceptor, and pyrrole as a π-spacer was successfully designed and synthesized, to probe the effect of π-spacer on the band-gap level of the donor–π–acceptor–π–donor type of chromophores. Compared with the thiophene spacer analogue (in compound 3), the intramolecular hydrogen bonding between the pyrrole and the neighboring BBTD unit pushes the absorption maximum and fluorescence emission of chromophore 5 into the near-infrared spectral region with a red shift of 172 and 158 nm, respectively. The same red-shift phenomenon can also be realized by addition of Lewis acid (e.g., BF3) to the BBTD-containing chromophores with other spacers. Attempt of using low-band-gap chromophore 5 in bulk heterojunction (BHJ) solar cells was made, showing a non-optimized photovoltaic device with the power conversion efficiency of 0.01%. A precursor approach to introduction of the alkaline-labile BBTD acceptor into the polymer backbone has been demonstrated by successful synthesis of low-band-gap polymer P2. The same strategy can be in principle applied to the synthesis of a series of low-band-gap chromophores or polymers with strong acceptors.