bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of a Universal Microarray Based on the Ligation Detection Reaction and 16S rRNA Gene Polymorphism To Target Diversity of Cyanobacteria
Authors: Castiglioni Bianca , Rizzi Ermanno , Frosini Andrea , Sivonen Kaarina , Rajaniemi Pirjo , Rantala Anne , Mugnai Maria Angela , Ventura Stefano , Wilmotte Annick , Boutte Christophe , Grubisic Stana , Balthasart Pierre , Consolandi Clarissa , Bordoni Roberta , Mezzelani Alessandra , Battaglia Cristina , De Bellis Gianluca 
Published: December 2004

ABSTRACT

The cyanobacteria are photosynthetic prokaryotes of significant ecological and biotechnological interest, since they strongly contribute to primary production and are a rich source of bioactive compounds. In eutrophic fresh and brackish waters, their mass occurrences (water blooms) are often toxic and constitute a high potential risk for human health. Therefore, rapid and reliable identification of cyanobacterial species in complex environmental samples is important. Here we describe the development and validation of a microarray for the identification of cyanobacteria in aquatic environments. Our approach is based on the use of a ligation detection reaction coupled to a universal array. Probes were designed for detecting 19 cyanobacterial groups including
Anabaena
/
Aphanizomenon
,
Calothrix
,
Cylindrospermopsis
,
Cylindrospermum
,
Gloeothece
, halotolerants,
Leptolyngbya
, Palau
Lyngbya
,
Microcystis
,
Nodularia
,
Nostoc
,
Planktothrix
, Antarctic
Phormidium
,
Prochlorococcus
,
Spirulina
,
Synechococcus
,
Synechocystis
,
Trichodesmium
, and
Woronichinia
. These groups were identified based on an alignment of over 300 cyanobacterial 16S rRNA sequences. For validation of the microarrays, 95 samples (24 axenic strains from culture collections, 27 isolated strains, and 44 cloned fragments recovered from environmental samples) were tested. The results demonstrated a high discriminative power and sensitivity to 1 fmol of the PCR-amplified 16S rRNA gene. Accurate identification of target strains was also achieved with unbalanced mixes of PCR amplicons from different cyanobacteria and an environmental sample. Our universal array method shows great potential for rapid and reliable identification of cyanobacteria. It can be easily adapted to future development and could thus be applied both in research and environmental monitoring.
Prevalence and Characterization of Shiga Toxin-Producing
Escherichia coli
in Swine Feces Recovered in the National Animal Health Monitoring System's Swine 2000 Study
Authors: Fratamico Pina M. , Bagi Lori K. , Bush Eric J. , Solow Barbara T. 
Published: December 2004

ABSTRACT

A study was conducted to determine the prevalence of Shiga toxin-producing
Escherichia coli
(STEC) in swine feces in the United States as part of the National Animal Health Monitoring System's Swine 2000 study. Fecal samples collected from swine operations from 13 of the top 17 swine-producing states were tested for the presence of STEC. After enrichment of swine fecal samples in tryptic soy broth, the samples were tested for the presence of
stx
1
and
stx
2
by use of the TaqMan
E. coli
STX1 and STX2 PCR assays. Enrichments of samples positive for
stx
1
and/or
stx
2
were plated, and colony hybridization was performed using digoxigenin-labeled probes complementary to the
stx
1
and
stx
2
genes. Positive colonies were picked and confirmed by PCR for the presence of the
stx
1
,
stx
2
, or
stx
2e
genes, and the isolates were serotyped. Out of 687 fecal samples tested using the TaqMan assays, 70% (484 of 687) were positive for Shiga toxin genes, and 54% (370 of 687), 64% (436 of 687), and 38% (261 of 687) were positive for
stx
1
,
stx
2
, and both toxin genes, respectively. Out of 219 isolates that were characterized, 29 (13%) produced
stx
1
, 14 (6%) produced
stx
2
, and 176 (80%) produced
stx
2e
. Twenty-three fecal samples contained at least two STEC strains that had different serotypes but that had the same toxin genes or included a strain that possessed
stx
1
in addition to a strain that possessed
stx
2
or
stx
2e
. The STEC isolates belonged to various serogroups, including O2, O5, O7, O8, O9, OX10, O11, O15, OX18, O20, O57, O65, O68, O69, O78, O91, O96, O100, O101, O120, O121, O152, O159, O160, O163, and O untypeable. It is noteworthy that no isolates of serogroup O157 were recovered. Results of this study indicate that swine in the United States harbor STEC that can potentially cause human illness.
Prevalence and Seasonal Variations of Six Bee Viruses in
Apis mellifera
L. and
Varroa destructor
Mite Populations in France
Authors: Tentcheva Diana , Gauthier Laurent , Zappulla Nathalie , Dainat Benjamin , Cousserans François , Colin Marc Edouard , Bergoin Max 
Published: December 2004

ABSTRACT

A survey of six bee viruses on a large geographic scale was undertaken by using seemingly healthy bee colonies and the PCR technique. Samples of adult bees and pupae were collected from 36 apiaries in the spring, summer, and autumn during 2002.
Varroa destructor
samples were collected at the end of summer following acaricide treatment. In adult bees, during the year deformed wing virus (DWV) was found at least once in 97% of the apiaries, sacbrood virus (SBV) was found in 86% of the apiaries, chronic bee paralysis virus (CBPV) was found in 28% of the apiaries, acute bee paralysis virus (ABPV) was found in 58% of the apiaries, black queen cell virus (BQCV) was found in 86% of the apiaries, and Kashmir bee virus (KBV) was found in 17% of the apiaries. For pupae, the following frequencies were obtained: DWV, 94% of the apiaries; SBV, 80% of the apiaries; CBPV, none of the apiaries; ABPV, 23% of the apiaries; BQCV, 23% of the apiaries; and KBV, 6% of the apiaries. In
Varroa
samples, the following four viruses were identified: DWV (100% of the apiaries), SBV (45% of the apiaries), ABPV (36% of the apiaries), and KBV (5% of the apiaries). The latter findings support the putative role of mites in transmitting these viruses. Taken together, these data indicate that bee virus infections occur persistently in bee populations despite the lack of clinical signs, suggesting that colony disease outbreaks might result from environmental factors that lead to activation of viral replication in bees.
Differentiation of the Gene Clusters Encoding Botulinum Neurotoxin Type A Complexes in
Clostridium botulinum
Type A, Ab, and A(B) Strains
Authors: Franciosa Giovanna , Floridi Francesca , Maugliani Antonella , Aureli Paolo 
Published: December 2004

ABSTRACT

We describe a strategy to identify the clusters of genes encoding components of the botulinum toxin type A (boNT/A) complexes in 57 strains of
Clostridium botulinum
types A, Ab, and A(B) isolated in Italy and in the United States from different sources. Specifically, we combined the results of PCR for detecting the
ha33
and/or
p47
genes with those of
boNT/A
PCR-restriction fragment length polymorphism analysis. Three different type A toxin gene clusters were revealed; type A1 was predominant among the strains from the United States, whereas type A2 predominated among the Italian strains, suggesting a geographic distinction between strains. By contrast, no relationship between the toxin gene clusters and the clinical or food source of strains was evident. In two
C. botulinum
type A isolates from the United States, we recognized a third type A toxin gene cluster (designated type A3) which was similar to that previously described only for
C. botulinum
type A(B) and Ab strains. Total genomic DNA from the strains was subjected to pulsed-filed gel electrophoresis and randomly amplified polymorphic DNA analyses, and the results were consistent with the
boNT/A
gene clusters obtained.
Occurrence of Microbial Indicators and
Clostridium perfringens
in Wastewater, Water Column Samples, Sediments, Drinking Water, and Weddell Seal Feces Collected at McMurdo Station, Antarctica
Authors: Lisle John T. , Smith James J. , Edwards Diane D. , McFeters Gordon A. 
Published: December 2004

ABSTRACT

McMurdo Station, Antarctica, has discharged untreated sewage into McMurdo Sound for decades. Previous studies delineated the impacted area, which included the drinking water intake, by using total coliform and
Clostridium perfringens
concentrations. The estimation of risk to humans in contact with the impacted and potable waters may be greater than presumed, as these microbial indicators may not be the most appropriate for this environment. To address these concerns, concentrations of these and additional indicators (fecal coliforms,
Escherichia coli
, enterococci, coliphage, and enteroviruses) in the untreated wastewater, water column, and sediments of the impacted area and drinking water treatment facility and distribution system at McMurdo Station were determined. Fecal samples from Weddell seals in this area were also collected and analyzed for indicators. All drinking water samples were negative for indicators except for a single total coliform-positive sample. Total coliforms were present in water column samples at higher concentrations than other indicators. Fecal coliform and enterococcus concentrations were similar to each other and greater than those of other indicators in sediment samples closer to the discharge site.
C. perfringens
concentrations were higher in sediments at greater distances from the discharge site. Seal fecal samples contained concentrations of fecal coliforms,
E. coli
, enterococci, and
C. perfringens
similar to those found in untreated sewage. All samples were negative for enteroviruses. A wastewater treatment facility at McMurdo Station has started operation, and these data provide a baseline data set for monitoring the recovery of the impacted area. The contribution of seal feces to indicator concentrations in this area should be considered.
Molecular Characterization of a Dechlorinating Community Resulting from In Situ Biostimulation in a Trichloroethene-Contaminated Deep, Fractured Basalt Aquifer and Comparison to a Derivative Laboratory Culture
Authors: Macbeth Tamzen W. , Cummings David E. , Spring Stefan , Petzke Lynn M. , Sorenson Kent S. 
Published: December 2004

ABSTRACTSodium lactate additions to a trichloroethene (TCE) residual source area in deep, fractured basalt at a U.S. Department of Energy site have resulted in the enrichment of the indigenous microbial community, the complete dechlorination of nearly all aqueous-phase TCE to ethene, and the continued depletion of the residual source since 1999. The bacterial and archaeal consortia in groundwater obtained from the residual source were assessed by using PCR-amplified 16S rRNA genes. A clone library of bacterial amplicons was predominated by those from members of the classClostridia(57 of 93 clones), of which a phylotype most similar to that of the homoacetogenAcetobacteriumsp. strain HAAP-1 was most abundant (32 of 93 clones). The remainingBacteriaconsisted of phylotypes affiliated withSphingobacteria,Bacteroides,Spirochaetes,Mollicutes, andProteobacteriaand candidate divisions OP11 and OP3. The two proteobacterial phylotypes were most similar to those of the known dechlorinatorsTrichlorobacter thiogenesandSulfurospirillum multivorans. Although not represented by the bacterial clones generated with broad-specificity bacterial primers, aDehalococcoides-like phylotype was identified with genus-specific primers. Only four distinct phylotypes were detected in the groundwater archaeal library, including predominantly a clone affiliated with the strictly acetoclastic methanogenMethanosaeta concilii(24 of 43 clones). A mixed culture that completely dechlorinates TCE to ethene was enriched from this groundwater, and both communities were characterized by terminal restriction fragment length polymorphism (T-RFLP). According to T-RFLP, the laboratory enrichment community was less diverse overall than the groundwater community, with 22 unique phylotypes as opposed to 43 and a higher percentage ofClostridia, including theAcetobacteriumpopulation. Bioreactor archaeal structure was very similar to that of the groundwater community, suggesting that methane is generated primarily via the acetoclastic pathway, using acetate generated by lactate fermentation and acetogenesis in both systems.
Complete Nucleotide Sequence of the Conjugative Tetracycline Resistance Plasmid pFBAOT6, a Member of a Group of IncU Plasmids with Global Ubiquity
Authors: Rhodes Glenn , Parkhill Julian , Bird Christine , Ambrose Kerrie , Jones Matthew C. , Huys Geert , Swings Jean , Pickup Roger W. 
Published: December 2004

ABSTRACT

This study presents the first complete sequence of an IncU plasmid, pFBAOT6. This plasmid was originally isolated from a strain of
Aeromonas caviae
from hospital effluent (Westmorland General Hospital, Kendal, United Kingdom) in September 1997 (G. Rhodes, G. Huys, J. Swings, P. McGann, M. Hiney, P. Smith, and R. W. Pickup, Appl. Environ. Microbiol.
66:
3883-3890, 2000) and belongs to a group of related plasmids with global ubiquity. pFBAOT6 is 84,748 bp long and has 94 predicted coding sequences, only 12 of which do not have a possible function that has been attributed. Putative replication, maintenance, and transfer functions have been identified and are located in a region in the first 31 kb of the plasmid. The replication region is poorly understood but exhibits some identity at the protein level with replication proteins from the gram-positive bacteria
Bacillus
and
Clostridium
. The mating pair formation system is a
virB
homologue, type IV secretory pathway that is similar in its structural organization to the mating pair formation systems of the related broad-host-range (BHR) environmental plasmids pIPO2, pXF51, and pSB102 from plant-associated bacteria. Partitioning and maintenance genes are homologues of genes in IncP plasmids. The DNA transfer genes and the putative
oriT
site also exhibit high levels of similarity with those of plasmids pIPO2, pXF51, and pSB102. The genetic load region encompasses 54 kb, comprises the resistance genes, and includes a class I integron, an IS
630
relative, and other transposable elements in a 43-kb region that may be a novel Tn
1721
-flanked composite transposon. This region also contains 24 genes that exhibit the highest levels of identity to chromosomal genes of several plant-associated bacteria. The features of the backbone of pFBAOT6 that are shared with this newly defined group of environmental BHR plasmids suggest that pFBAOT6 may be a relative of this group, but a relative that was isolated from a clinical bacterial environment rather than a plant-associated bacterial environment.
Flow Cytometry-Assisted Cloning of Specific Sequence Motifs from Complex 16S rRNA Gene Libraries
Authors: Nielsen Jeppe L. , Schramm Andreas , Bernhard Anne E. , van den Engh Gerrit J. , Stahl David A. 
Published: December 2004

ABSTRACT

A flow cytometry method was developed for rapid screening and recovery of cloned DNA containing common sequence motifs. This approach, termed fluorescence-activated cell sorting-assisted cloning, was used to recover sequences affiliated with a unique lineage within the
Bacteroidetes
not abundant in a clone library of environmental 16S rRNA genes.
Reproductive and therapeutic cloning, germline therapy, and purchase of gametes and embryos: comments on Canadian legislation governing reproduction technologies
Authors: Bernier L , Grégoire D 
Published: December 2004

In Canada, the Assisted Human Reproduction Act received royal assent on 29 March 2004. The approach proposed by the federal government responds to Canadians’ strong desire for an enforceable legislative framework in the field of reproduction technologies through criminal law. As a result of the widening gap between the rapid pace of technological change and governing legislation, a distinct need was perceived to create a regulatory framework to guide decisions regarding reproductive technologies.In this article the three main topics covered in the new legislation are commented on: cloning, germline therapy, and purchase of gametes and embryos. Some important issues also covered in the new legislation, such as privacy and access to information, data protection, identity of donors, and inspection, will not be addressed.
Obtaining explicit consent for the use of archival tissue samples: practical issues
Authors: Furness P N , Nicholson M L 
Published: December 2004

Background::Over the past few years, research ethics committees have increasingly demanded explicit consent before archival tissue samples can be used in research projects. Current UK guidance in this area requires an assessment of whether it is “practical” to obtain explicit consent. Ethics committees have little experience or evidence to help them to judge what is “practical” in this context.Methods::We attempted to obtain general consent for research use of surplus tissue from renal transplant biopsies from the entire patient population of the renal transplant unit in Leicester. The nature of this patient population would be expected to facilitate this task.Results::A total of 495 letters were sent. Attempts were made to contact non-responders when they attended the outpatient clinic. One year after the initiation of the project, the opinions of 26% of the patients had still not been ascertained.Conclusions::The results confirm that the vast majority of patients are happy for “surplus” biopsy material to be used for research; the situation does not parallel the use of autopsy tissue. A requirement to obtain explicit consent for the study of archival tissue is likely, however, to block or at least seriously delay research, which is contrary to the public interest and specifically may harm the interests of the patients concerned. In the UK, the problem of tissue being used against the wishes of the donor has now been largely replaced by the problem ofprohibitionof tissue use against the wishes of the donor.
BEAMLAB AND REPRODUCIBLE RESEARCH
Authors: DONOHO DAVID L. , HUO XIAOMING 
Published: December 2004

In the first 'Wavelets and Statistics' conference proceedings1, our group published 'Wavelab and Reproducible Research', in which we advocated using the internet for publication of software and data so that research results could be duplicated by others. Much has happened in the last decade that bears on the notion of reproducibility, and we will review our experience. We will also describe a new software package BEAMLAB containing routines for multiscale geometric analysis, and describe some of its capabilities.BEAMLAB makes available, in one package, all the code to reproduce all the figures in our recently published articles on beamlets, curvelets and ridgelets. The interested reader can inspect the source code to see what algorithms were used, and how parameters were set to produce the figures, and will then be able to modify the source codes to produce variations of our results.Some new examples of numerical studies based on BEAMLAB are provided here.
Dexamethasone resistance in B-cell precursor childhood acute lymphoblastic leukemia occurs downstream of ligand-induced nuclear translocation of the glucocorticoid receptor
Authors: Bachmann Petra S. , Gorman Rosemary , MacKenzie Karen L. , Lutze-Mann Louise , Lock Richard B. 
Published: December 2004

AbstractGlucocorticoids are among the most effective agents used in the treatment of childhood acute lymphoblastic leukemia (ALL), and patient response to treatment is an important determinant of long-term outcome. Despite its clinical significance, the molecular basis of glucocorticoid resistance in lymphoid malignancies is still poorly understood. We have recently developed a highly clinically relevant experimental model of childhood ALL, in which primary childhood ALL biopsies were established as xenografts in nonobese diabetic/severe combined immunodeficient (NOD/SCID) mice. The in vivo and in vitro responses of a panel of these xenografts to the glucocorticoid, dexamethasone, reflected the outcome of the patients from whom they were derived. In this report we show that glucocorticoid resistance in B-cell precursor (BCP) ALL xenografts was not due to down-regulation of the glucocorticoid receptor (GR) nor to defective ligand binding of the GR. Moreover, dexamethasone-induced GR translocation from the cytoplasm to the nucleus was comparable in all xenografts. However, glucocorticoid resistance was associated with profoundly attenuated induction of the BH3-only proapoptotic protein, Bim, when xenograft cells were exposed to dexamethasone. These results show that dexamethasone resistance in BCP ALL xenografts occurs downstream of ligand-induced nuclear translocation of the GR, but upstream of Bim induction.
Inhibiting primary effusion lymphoma by lentiviral vectors encoding short hairpin RNA
Authors: Godfrey Andrew , Anderson John , Papanastasiou Antigoni , Takeuchi Yasu , Boshoff Chris 
Published: December 2004

AbstractWe use lentiviral-delivered RNA interference (RNAi) to inhibit the growth of a model of primary effusion lymphoma (PEL) in vitro and in vivo. RNAi is a phenomenon allowing the sequence-specific targeting and silencing of exogenous and endogenous gene expression and is being applied to inhibit viral replication both in vitro and in vivo. We show that silencing of genes believed to be essential for the Kaposi sarcoma-associated herpesvirus (KSHV) latent life cycle (the oncogenic cluster) has a varied effect in PEL cell lines cultured in vitro, however, concomitant silencing of the viral cyclin (vcyclin) and viral FLICE (Fas-associating protein with death domain-like interleukin-1β-converting enzyme) inhibitory protein (vFLIP) caused efficient apoptosis in all PEL lines tested. We demonstrate that in a murine model of PEL, lentiviral-mediated RNA interference both inhibits development of ascites and can act as a treatment for established ascites. We also show that the administered lentiviral vectors are essentially limited to the peritoneal cavity, which has advantages for safety and dosage in a therapeutic setting. This shows the use of lentiviral-mediated RNA interference in vivo as a potential therapeutic against a virally driven human cancer.
Hematopoietic cells regulate the angiogenic switch during tumorigenesis
Authors: Okamoto Rika , Ueno Masaya , Yamada Yoshihiro , Takahashi Naoko , Sano Hideto , Suda Toshio , Takakura Nobuyuki 
Published: December 2004

Abstract
Hematopoietic cells (HCs) promote blood vessel formation by producing various proangiogenic cytokines and chemokines and matrix metalloproteinases. We injected mouse colon26 colon cancer cells or human PC3 prostate adenocarcinoma cells into mice and studied the localization of HCs during tumor development. HCs were distributed in the inner tumor mass in all of the tumor tissues examined; however, the localization of HCs in the tumor tissue differed depending on the tumor cell type. In the case of colon26 tumors, as the tumor grew, many mature HCs migrated into the tumor mass before fine capillary formation was observed. On the other hand, although very few HCs migrated into PC3 tumor tissue, c-Kit+ hematopoietic stem/progenitor cells accumulated around the edge of the tumor. Bone marrow suppression induced by injection of anti–c-Kit neutralizing antibody suppressed tumor angiogenesis by different mechanisms according to the tumor cell type: bone marrow suppression inhibited the initiation of sprouting angiogenesis in colon26 tumors, while it suppressed an increase in the caliber of newly developed blood vessels at the tumor edge in PC3 tumors. Our findings suggest that HCs are involved in tumor angiogenesis and regulate the angiogenic switch during tumorigenesis.
Observation of Gas-to-Particle Conversion at Low Concentration of SO2 by Using a Flow-type Reactor
Authors: Kobara Hitomi , Yamauchi Hideaki , Takeuchi Koji , Ibusuki Takashi 
Published: December 2004

Abstract
Particle generation by SO2 gas-to-particle conversion in a flow-type reactor was examined. The reactor can minimize losses of reactants and products due to adsorption onto the wall surface, and a material balance between consumed SO2 and sulfate in generated particles was in very good agreement as compared with previous studies.