bluuebunny/crossref_metadata_2025 huggingface dataset:
Genomic Characterization of an EndemicMycobacterium tuberculosisStrain: Evolutionary and Epidemiologic Implications
Authors: Nguyen Dao , Brassard Paul , Menzies Dick , Thibert Louise , Warren Rob , Mostowy Serge , Behr Marcel
Published: June 2004

In a study of 302Mycobacterium tuberculosisclinical isolates from the low-incidence Canadian-born population of Quebec, we characterized a large endemic strain family by using genomic deletions. The DS6Quebecdeleted region (11.4 kb) defined a strain family of 143 isolates encompassing two subgroups: one characterized by pyrazinamide (PZA) susceptibility and the other marked by a PZA-monoresistant phenotype. A second deletion (8 bp) in thepncAgene was shared by all 76 isolates with the PZA resistance phenotype, whereas a third DRv0961 deletion (970 bp) defined a further subset of 15 isolates. From their deletion profiles, we derived a most parsimonious evolutionary scenario and compared multiple standard genotyping modalities (using IS6110restriction fragment length polymorphism [RFLP], spoligotyping, and mycobacterial interspersed repetitive units [MIRU]) across the deletion-based subgroups. The use of a single genotyping modality yielded an unexpectedly high proportion of clustered isolates for a high IS6110copy strain (27% by IS6110RFLP, 61% by MIRU, and 77% by spoligotyping). By combining all three modalities, only 14% were genotypically clustered overall, a result more congruent with the epidemiologic profile of reactivation tuberculosis, as suggested by the older age (mean age, 60 years), rural setting, and low proportion of epidemiologic links. These results provide insight into the evolution of genotypes in endemic strains and the potential for false clustering in molecular epidemiologic studies.
Bovine Tuberculosis (
Mycobacterium bovis
) in Wildlife in Spain
Authors: Aranaz Alicia , de Juan Lucía , Montero Natalia , Sánchez Celia , Galka Margarita , Delso Consuelo , Álvarez Julio , Romero Beatriz , Bezos Javier , Vela Ana I. , Briones Victor , Mateos Ana , Domínguez Lucas
Published: June 2004

Mycobacterium bovis
infection in wildlife and feral species is a potential source of infection for livestock and a threat to protected and endangered species. The aim of this study was to identify Spanish wild animal species infected with
M. bovis
through bacteriological culture and spacer oligonucleotide typing (spoligotyping) of isolates for epidemiological purposes. This study included samples from red deer (
Cervus elaphus
), fallow deer (
Dama dama
), wild boar (
Sus scrofa
), Iberian lynx (
Lynx pardina
), hare (
Lepus europaeus
), and cattle (
Bos taurus
). They were collected in several geographical areas that were selected for their unique ecological value and/or known relationships between wildlife and livestock. In the areas included in this survey,
M. bovis
strains with the same spoligotyping pattern were found infecting several wild species and livestock, which indicates an epidemiological link. A locally predominant spoligotype was found in these areas. Better understanding of the transmission and distribution of disease in these populations will permit more precise targeting of control measures.
Multilocus Sequence Typing Analysis of Human and Animal
Clostridium difficile
Isolates of Various Toxigenic Types
Authors: Lemee Ludovic , Dhalluin Anne , Pestel-Caron Martine , Lemeland Jean-François , Pons Jean-Louis
Published: June 2004

A multilocus sequence typing (MLST) scheme was developed to study the genetic relationships and population structure of 72
Clostridium difficile
isolates from various hosts, geographic sources, PCR ribotypes, and toxigenic types (determined by PCR targeting
tcdA
and
tcdB
genes). MLST was performed by DNA sequence analysis of seven housekeeping genes (
aroE
,
ddl
,
dutA
,
tpi
,
recA
,
gmk
, and
sodA
). The number of alleles ranged from five (
dutA
and
ddl
) to eleven (
recA
). Allelic profiles allowed the definition of 34 different sequence types (STs). These STs lacked correlation with geographic source but were well correlated to toxigenic type. The dendrogram generated from a matrix of pairwise genetic distances showed that animal isolates did not constitute a distinct lineage from human isolates and that there was no hypervirulent lineage within the population of toxigenic human isolates (isolates recovered from pseudomembranous colitis and antibiotic-associated diarrhea did not cluster in distinct lineages). However, A
−
B
+
variant isolates shared the same ST that appeared as a divergent lineage in the population studied, indicating a single evolutionary origin. The population structure was further examined by analysis of allelic polymorphism. The dendrogram generated from composite sequence-based analysis revealed a homogeneous population associated with three divergent lineages, one of which was restricted to A
−
B
+
variant isolates.
C. difficile
exhibited a clonal population structure, as revealed by the estimation of linkage disequilibrium (
Ia
) between loci. The analysis of alleles within clonal complexes estimated that point mutation generated new alleles at a frequency eightfold higher than recombinational exchange, and the congruence of the dendrograms generated from separate housekeeping loci confirmed the mutational evolution of this species.
Performance Characteristics of the Immunoglobulin G-Capture BED-Enzyme Immunoassay, an Assay To Detect Recent Human Immunodeficiency Virus Type 1 Seroconversion
Authors: Dobbs Trudy , Kennedy Susan , Pau Chou-Pong , McDougal J. Steven , Parekh Bharat S.
Published: June 2004

Recently, we developed an immunoglobulin G (IgG)-capture BED-enzyme immunoassay (BED-CEIA) to identify recent human immunodeficiency virus (HIV) type 1 (HIV-1) seroconversion for use in incidence estimates. We have established an algorithm for its use; developed quality control reagents to monitor the assay; and evaluated its performance for interrun, intrarun, and operator variability. Analysis of 144 individual plates, which involved multiple plate lots and several operators over more than a year, indicated that the coefficients of variation (CVs) were between 10 and 15% for raw optical density (OD) values in the dynamic range between 0.5 and 2.0 OD units; the CVs decreased to 5 to 10% when the OD was normalized (OD-n; OD-n = specimen OD/calibrator OD). The intrarun CVs were generally in the range of 5 to 10% for specimens with ODs <0.5 and less than 5% for specimens with ODs >0.5. The level of concordance between multiple plate lots (
n
= 6) and multiple operators (
n
= 7) was quite high (
R
2
> 0.9). Comparison of the results of the initial and the confirmatory tests with specimens with OD-n values ≤1.5 demonstrated a high degree of correlation (
R
2
= 0.92); 566 (92%) of 615 of specimens tested in the two modes retained the same classification (recent or long-term infection). The values for those specimens with changed classifications (
n
= 49) were close to the cutoff (OD-
n
= 1.0), as expected. The twofold difference in the HIV IgG contents between the controls and the calibrator reagents was exploited to monitor individual plate runs by using a control plot, which was incorporated into the spreadsheet for data entry and run monitoring. This information provides baseline data for the successful transfer of BED-CEIA to other laboratories and the use of BED-CEIA for the detection of recent HIV seroconversion and the calculation of incidence estimates worldwide.
Sensitive and Specific Monoclonal Antibody-Based Capture Enzyme Immunoassay for Detection of Nucleocapsid Antigen in Sera from Patients with Severe Acute Respiratory Syndrome
Authors: Che Xiao-yan , Qiu Li-wen , Pan Yu-xian , Wen Kun , Hao Wei , Zhang Li-ya , Wang Ya-di , Liao Zhi-yong , Hua Xu , Cheng Vincent C. C. , Yuen Kwok-yung
Published: June 2004

A rapid antigen test for the diagnosis of severe acute respiratory syndrome (SARS) is essential for control of this disease at the point of management. The nucleocapsid (N) protein of SARS-associated coronavirus (SARS-CoV) is abundantly expressed in infected-cell culture filtrate as demonstrable by Western blotting using convalescent-phase sera from patients with SARS. We used monoclonal antibodies specifically directed against N protein to establish a sensitive antigen capture sandwich enzyme-linked immunosorbent assay (ELISA) for the detection of SARS-CoV. The assay employed a mixture of three monoclonal antibodies for capture and rabbit polyclonal antibodies for detection of serum antigen in 32 cases of clinically probable SARS as defined by the World Health Organization during the epidemic in Guangzhou, China. Recombinant N protein was used as a standard to establish a detection sensitivity of approximated 50 pg/ml. The linear range of detection in clinical specimens was from 100 pg/ml to 3.2 ng/ml. Using a panel of sera collected at different points in time, the amount of circulating N antigen was found to peak 6 to 10 days after the onset of symptoms. The sensitivity of the assay was 84.6% in 13 serologically confirmed SARS patients with blood taken during the first 10 days after the onset of symptoms (11 of 13). The specificity of the assay was 98.5% in 1,272 healthy individuals (1,253 of 1,272). There was no cross-reaction with other human and animal coronaviruses in this assay. In conclusion, a sensitive and quantitative antigen capture ELISA was established for the early diagnosis and disease monitoring of SARS-CoV infection.
Generation and Infectivity Titration of an Infectious Stock of Avian Hepatitis E Virus (HEV) in Chickens and Cross-Species Infection of Turkeys with Avian HEV
Authors: Sun Z. F. , Larsen C. T. , Huang F. F. , Billam P. , Pierson F. W. , Toth T. E. , Meng X. J.
Published: June 2004

Avian hepatitis E virus (HEV), a novel virus identified from chickens with hepatitis-splenomegaly syndrome in the United States, is genetically and antigenically related to human HEV. In order to further characterize avian HEV, an infectious viral stock with a known infectious titer must be generated, as HEV cannot be propagated in vitro. Bile and feces collected from specific-pathogen-free (SPF) chickens experimentally infected with avian HEV were used to prepare an avian HEV infectious stock as a 10% suspension of positive fecal and bile samples in phosphate-buffered saline. The infectivity titer of this infectious stock was determined by inoculating 1-week-old SPF chickens intravenously with 200 μl of each of serial 10-fold dilutions (10
−2
to 10
−6
) of the avian HEV stock (two chickens were inoculated with each dilution). All chickens inoculated with the 10
−2
to 10
−4
dilutions of the infectious stock and one of the two chickens inoculated with the 10
−5
dilution, but neither of the chickens inoculated with the 10
−6
dilution, became seropositive for anti-avian HEV antibody at 4 weeks postinoculation (wpi). Two serologically negative contact control chickens housed together with chickens inoculated with the 10
−2
dilution also seroconverted at 8 wpi. Viremia and shedding of virus in feces were variable in chickens inoculated with the 10
−2
to 10
−5
dilutions but were not detectable in those inoculated with the 10
−6
dilution. The infectivity titer of the infectious avian HEV stock was determined to be 5 × 10
5
50% chicken infectious doses (CID
50
) per ml. Eight 1-week-old turkeys were intravenously inoculated with 10
5
CID
50
of avian HEV, and another group of nine turkeys were not inoculated and were used as controls. The inoculated turkeys seroconverted at 4 to 8 wpi. In the inoculated turkeys, viremia was detected at 2 to 6 wpi and shedding of virus in feces was detected at 4 to 7 wpi. A serologically negative contact control turkey housed together with the inoculated ones also became infected through direct contact. This is the first demonstration of cross-species infection by avian HEV.
Characterization of Novel Coding Sequences Specific toMycobacterium aviumsubsp.paratuberculosis: Implications for Diagnosis of Johne's Disease
Authors: Paustian Michael L. , Amonsin Alongkorn , Kapur Vivek , Bannantine John P.
Published: June 2004

Mycobacterium aviumsubsp.paratuberculosisis the causative agent of Johne's Disease, an economically important intestinal ailment of ruminants. Due to the considerable genetic and serologic cross-reactivity with closely related and ubiquitous members of theM. aviumcomplex, a species-specific method for the serological diagnosis of Johne's disease is unavailable. Computational and PCR-based analysis of the complete genome sequence ofM. aviumsubsp.paratuberculosisled to the identification of 13 open reading frames with no identifiable homologs. One of these sequences is a putative insertion element present in six copies on theM. aviumsubsp.paratuberculosisgenome. These novelM. aviumsubsp.paratuberculosisgenes were cloned intoEscherichia coliexpression vectors, and nine were successfully expressed as recombinant fusion proteins. Five of these proteins were purified in sufficient amounts to allow immunoblot analyses of their reactivity with sera from naturally infected cattle as well as mice and rabbits exposed toM. aviumsubsp.paratuberculosis. Fusion proteins representing MAP0862, MAP3732c, and MAP2963c were recognized by nearly all of the sera tested, including those from cattle in the clinical stages of disease. Notably, further analysis of the protein encoded by MAP0862 showed that it reacted with sera from additional infected cattle but not with sera from uninfected control animals. The fusion product of MAP0860c did not react with any of the sera tested, while the remaining four proteins were variably recognized by sera fromM. aviumsubsp.paratuberculosis-infected cattle. Collectively, the results of this study demonstrate the utility of genomic data to identify potential diagnostic sequences.
Prospective Comparison of the Diagnostic Potential of Real-Time PCR, Double-Sandwich Enzyme-Linked Immunosorbent Assay for Galactomannan, and a (1→3)-β-
d
-Glucan Test in Weekly Screening for Invasive Aspergillosis in Patients with Hematological Disorders
Authors: Kawazu Masahito , Kanda Yoshinobu , Nannya Yasuhito , Aoki Katsunori , Kurokawa Mineo , Chiba Shigeru , Motokura Toru , Hirai Hisamaru , Ogawa Seishi
Published: June 2004

The establishment of an optimal noninvasive method for diagnosing invasive aspergillosis (IA) is needed to improve the management of this life-threatening infection in patients with hematological disorders, and a number of noninvasive tests for IA that target different fungal components, including galactomannan, (1→3)-β-
d
-glucan (BDG), and
Aspergillus
DNA, have been developed. In this study, we prospectively evaluated the diagnostic potential of three noninvasive tests for IA that were used in a weekly screening strategy: the double-sandwich enzyme-linked immunosorbent assay (ELISA) for galactomannan (Platelia Aspergillus), a real-time PCR assay for
Aspergillus
DNA (GeniQ-Asper), and an assay for BDG (β-glucan Wako). We analyzed 149 consecutive treatment episodes in 96 patients with hematological disorders who were at high risk for IA and diagnosed 9 proven IA cases, 2 probable IA cases, and 13 possible invasive fugal infections. In a receiver-operating characteristic (ROC) analysis, the area under the ROC curve was greatest for ELISA, using two consecutive positive results (0.97;
P
= 0.036 for ELISA versus PCR,
P
= 0.055 for ELISA versus BDG). Based on the ROC curve, the cutoff for the ELISA could be reduced to an optical density index (O.D.I.) of 0.6. With the use of this cutoff for ELISA and cutoffs for PCR and BDG that give a comparable level of specificity, the sensitivity/specificity/positive predictive value/negative predictive value of the ELISA and the PCR and BDG tests were 1.00/0.93/0.55/1.00, 0.55/0.93/0.40/0.96, and 0.55/0.93/0.40/0.96, respectively. In conclusion, among these weekly screening tests for IA, the double-sandwich ELISA test was the most sensitive at predicting the diagnosis of IA in high-risk patients with hematological disorders, using a reduced cutoff of 0.6 O.D.I.
Ileocolitis Associated with
Anaerobiospirillum
in Cats
Authors: De Cock H. E. V. , Marks S. L. , Stacy B. A. , Zabka T. S. , Burkitt J. , Lu G. , Steffen D. J. , Duhamel G. E.
Published: June 2004

Ileocolitis associated with spiral bacteria identified as an
Anaerobiospirillum
sp. was found in six cats. Two cats had acute onset of gastrointestinal signs characterized by vomiting and diarrhea in one cat and vomiting in another cat, one cat had chronic diarrhea that was refractory to medical therapy; one cat had acute onset of anorexia and lethargy, and two cats had clinical signs that were not related to the gastrointestinal tract. The presence of an
Anaerobiospirillum
sp. was demonstrated on the basis of ultrastructural morphology of spiral bacteria associated with intestinal lesions and PCR amplification of a genus-specific 16S rRNA gene from affected tissues from each cat. The colons of three clinically healthy cats without lesions and one cat with mild colitis not associated with spiral bacteria were negative for
Anaerobiospirillum
spp. in the same assay. Comparative nucleotide sequence analysis of cloned PCR products from three affected cats further suggested that the spiral bacteria were closely related to
Anaerobiospirillum succiniciproducens
.
Rapid Immunochromatographic Test for Serodiagnosis of Canine Leishmaniasis
Authors: Otranto D. , Paradies P. , Sasanelli M. , Spinelli R. , Brandonisio O.
Published: June 2004

An rK39 immunochromatographic test and immunofluorescent-antibody test (IFAT) for serodiagnosis of canine leishmaniasis were evaluated. The two tests showed correlation for all but one of the sera obtained from 68 dogs confirmed as leishmaniasis cases and 40 dogs (22 healthy dogs and 18 dogs with other diseases) from areas where the disease is not endemic. Specificity was 100% for both tests, while sensitivity was 97% for the rapid test and 99% for IFAT.
Comparison of Versions 1.0 AND 1.5 of the UltraSensitive AMPLICOR HIV-1 MONITOR Test for Subjects with Low Viral Load
Authors: Jackson J. Brooks , Piwowar-Manning Estelle , Johnson-Lewis LeTanya , Bassett Roland , Demeter Lisa M. , Brambilla Donald
Published: June 2004

We compared the performance of two UltraSensitive AMPLICOR HIV-1 MONITOR kits (version 1.5 [v1.5] versus v1.0) by retesting 404 plasma samples with low viral loads (<3,000 copies/ml) with both kits. With 292 samples that initially had <50 copies/ml by the v1.0 kit, the v1.5 assay was more sensitive than the v1.0 assay for samples with human immunodeficiency virus type 1 RNA near the 50-copy/ml cutoff (
P
= 0.0146). Median numbers of copies per milliliter were similar for 112 samples with 50 to 3,000 copies/ml with no difference in sensitivity with a 200-copy/ml cutoff.
A Decline in Mupirocin Resistance in Methicillin-ResistantStaphylococcus aureusAccompanied Administrative Control of Prescriptions
Authors: Walker Elaine S. , Levy Foster , Shorman Mahmoud , David Gerard , Abdalla Jehad , Sarubbi Felix A.
Published: June 2004

Susceptibility to mupirocin was assessed in methicillin-resistantStaphylococcus aureusisolates selected from eras corresponding to differences in usage rate and prescription policies at a Veterans Affairs medical center. The eras studied encompassed from the time of introduction of the drug to its widespread use, through recommended judicious use, and finally to subsequent stringent administrative control. Prescriptions declined from 3.0 to 0.1 per 1,000 patient days. Precipitous declines first in the numbers of isolates with high-level resistance (from 31% to 4%) and then in those with low-level resistance (from 26% to 10%) accompanied prescription control.
Identification of
Campylobacter jejuni
Multilocus Sequence Type ST-21 Clonal Complex by Single-Nucleotide Polymorphism Analysis
Authors: Best E. L. , Fox A. J. , Frost J. A. , Bolton F. J.
Published: June 2004

Conserved single-nucleotide polymorphisms (SNPs) which characterize the allelic profile of the major epidemiological lineage ST-21 were identified from the alleles within the current
Campylobacter jejuni
multilocus sequence typing (MLST) database. Allelic discrimination assays were designed for the detection of SNPs, enabling rapid strain profiling for clonal complex ST-21. This method is suitable for epidemiological investigations and is complementary to full MLST.
Use of Paraffin-Embedded Tissue for Identification of
Saccharomyces cerevisiae
in a Baker's Lung Nodule by Fungal PCR and Nucleotide Sequencing
Authors: Ren Ping , Sridhar Sundara , Chaturvedi Vishnu
Published: June 2004

A 40-year-old healthy male employed in a bakery presented with a single lung nodule and underwent investigations to rule out pulmonary carcinoma. Biopsy was positive for yeast cells, which did not match common fungal pathogens. PCR assay of paraffin-embedded tissue and nucleotide sequencing with ribosomal
ITS1
-
ITS2
universal primers revealed the presence of
Saccharomyces cerevisiae
.
A Case of Epstein-Barr Virus (EBV)-Associated Thymic Carcinoid and Investigation of Existence of EBV-Infected Cells in Thymus and Thymic Tumors
Authors: Takeuchi Hiroaki , Fujita Hiroshi , Iwasaki Fumio , Takeuchi Takako , Imadome Ken-Ichi , Okumiya Toshika , Matsui Tomohiro , Takahashi Mutsuo
Published: June 2004

We describe the first case of Epstein-Barr virus (EBV)-associated thymic carcinoid tumor found by in situ hybridization (ISH) on paraffin-embedded sections. ISH revealed that both tumor cells and infiltrated lymphocytes were EBV positive, while a few EBV-infected lymphocytes were detected in 2 of 11 thymuses and 1 of 11 thymomas.
First Case Report of Catheter-Related Bacteremia Due to “
Mycobacterium lacticola
”
Authors: Kiska Deanna L. , Turenne Christine Y. , Dubansky A. Stephen , Domachowske Joseph. B.
Published: June 2004

This is the first report of infection caused by “
Mycobacterium lacticola
,” a rapidly growing, scotochromogenic mycobacterium that was isolated from the blood of an immunosuppressed child. The organism was identified by sequence analysis of >1,400 bp of the 16S rRNA gene. The clinical relevance of this isolate, coupled with its unique 16S rRNA gene sequence, should prompt further investigation to establish this organism as a valid mycobacterial species.
Hernia Repair Mesh-AssociatedMycobacterium goodiiInfection
Authors: Sohail Muhammad R. , Smilack Jerry D.
Published: June 2004

We report on a patient with an abdominal wall abscess that developed after an inguinal hernia repair that utilized synthetic mesh.Mycobacterium goodii, a recently recognized, rapidly growing mycobacterium related toM. smegmatis, was isolated both from the abdominal wall aspirate and from surgically drained material. Infection resolved following thorough debridement, mesh removal, and prolonged antimicrobial therapy. This case report extends our understanding of the spectrum ofM. goodiiinfection.
Hepatitis B Surface Antigen Variant with Multiple Mutations in the
a
Determinant in an Agammaglobulinemic Patient
Authors: Alexopoulou Alexandra , Baltayiannis Gerasimos , Jammeh Saffie , Waters Jenny , Dourakis Spyros P. , Karayiannis Peter
Published: June 2004

A patient with agammaglobulinemia developed acute hepatitis that progressed to chronic liver disease with high levels of hepatitis B virus (HBV) DNA in the absence of detectable HBsAg. Sequencing of the
a
determinant region of HBsAg revealed multiple amino acid substitutions that, unusually, also included a substitution at position 122 that defines subtype specificity. All of these mutations had a profound effect on the antigenicity of this region, which led to the complete failure of variant detection by commercially available routine diagnostic assays or laboratory-based monoclonal antibody assays.
Fatal Case of Toxic Shock-Like Syndrome Due to Group C Streptococcus Associated with Superantigen Exotoxin
Authors: Korman Tony M. , Boers Anthony , Gooding Travis M. , Curtis Nigel , Visvanathan Kumar
Published: June 2004

Group C streptococci have been reported to cause invasive disease similar to that classically associated with group A streptococcus (GAS). We describe a fatal case of toxic shock-like syndrome due to
Streptococcus equi
subsp.
zooepidemicus
. The causative organism did not possess any known GAS superantigen exotoxin genes but did show evidence of superantigen production.
Bacteremia Caused by
Gordonia bronchialis
in a Patient with Sequestrated Lung
Authors: Sng Li-Hwei , Koh T. H. , Toney S. R. , Floyd M. , Butler W. R. , Tan B. H.
Published: June 2004

Gordonia
species have been recognized as pathogens in immunocompromised and immunocompetent patients. We report the first case of bacteremia due to
Gordonia bronchialis
in a diabetic patient with a sequestrated lung. Species identification was confirmed with mycolic acid analysis by high-performance liquid chromatography and sequencing of the 16S rRNA gene.
Prosthetic Joint Infection Due to “
Helcococcus pyogenica
”
Authors: Panackal Anil A. , Houze Yolanda B. , Prentice Jennifer , Leopold Seth S. , Cookson Brad T. , Liles W. Conrad , Limaye Ajit P.
Published: June 2004

Helcococci have previously been associated with the colonization of ulcers and infections of the skin and soft tissues. We describe a case of prosthetic joint infection due to a previously undescribed organism that is genetically most closely related to
Helcococcus
.
Attenuation of the Substituent Effects Along the Aliphatic Chain
Authors: Böhm Stanislav , Exner Otto
Published: June 2004

Two series of model compounds were devised to follow the attenuation of substituent effects with an interposed methylene group: short-chain aliphatic compounds 1 and derivatives of bicyclo[2.2.2]octane 5. In all compounds, chlorine atom acts as substituent and charged oxygen atom as the functional group; the interaction of both is measured by the reaction energy of the isodesmic reaction calculated at the B3LYP/AUG-cc-pVTZ//B3LYP/6-311+G(d,p) and/or B3LYP/6-311+G(d,p) levels. Attenuation of the substituent inductive effect with the distance is less steep than observed previously in solution. It depends also markedly on the conformation but cannot be reproduced, not even approximately, by the electrostatic formula. Only for simple regular conformations, it can be described approximately by an exponential function with the transmission factor for one methylene group equal to 0.74. The behavior of isolated molecules differs in this case distinctly from the reactivity in solution. Nevertheless, the significance of the two formulas, electrostatic and exponential, is similar in the isolated molecules and in solution. These formulas represent only two different, rather crude mathematical approximations and cannot be given any physical meaning.
Synthesis and ESI-MS Alkali Metal Ion Binding Selectivities of Cone, Partial Cone, and 1,3-Alternate 1,3-Bis(α-picolyloxy)-p-tert-butylcalix[4]arene Crown-6 and 1,1'-Binaphthalene-2,2'-diyl Crown-6 Conformers
Authors: Ferguson George , Lough Alan J. , Notti Anna , Pappalardo Sebastiano , Parisi Melchiorre F. , Resnati Giuseppe
Published: June 2004

The syntheses of 1,3-bis(α-picolyloxy)-p-tert-butylcalix[4]arene crown-6 and 1,1'-binaphthalene-2,2'-diyl crown-6 title conformers have been achieved by two complementary synthetic strategies, which differ in the order in which the polyether loop and the pendant picolyl groups are introduced. The structure and conformation of all new compounds have been firmly established by NMR spectroscopy, and further proven by X-ray analysis for the intermediate p-tert-butyl-25,27-(1,1'-binaphthalene-2,2'-diyl-crown-6)-26,28-dihydroxycalix[4]arene. Within each set of conformers, the nature of the polyether chain has little or no influence on the overall conformation of the calixarene platform. The alkali metal ion binding selectivities of the two series of calixarenes have been evaluated in competitive complexation experiments by electrospray ionization mass spectrometry. In the p-tert-butylcalix[4]arene crown-6 series, partial cone and 1,3-alternate conformers show a peak selectivity for the larger Cs+ ions, while the cone one preferentially binds the smaller Na+ ions. On the other hand, the cone and 1,3-alternate binaphthyl-containing analogues show a preference for Na+ ions, the partial cone being quite unselective.
Green Chemistry for Preparation of Oligopyrrole Macrocycles Precursors: Novel Methodology for Dipyrromethanes and Tripyrromethanes Synthesis in Water
Authors: Král Vladimír , Vašek Petr , Dolensky Bohumil
Published: June 2004

A novel methodology for preparation of linear oligopyrroles is presented. Synthetic protocol uses water as a solvent for acid catalysed condensation of an aldehyde or ketone with unsubstituted pyrrole. While the most procedures for the above-mentioned compounds are performed in organic solvents, or large excess of pyrrole (used as solvent), we present here a novel, mild and efficient procedure for selective preparation of linear oligopyrroles in aqueous environment. Preparation of dipyrromethanes 3 and tripyrromethanes 4 was optimised by varying the molar ratio and concentrations of starting compounds (aldehyde to pyrrole) and acid catalyst. The high initial concentration of aldehyde and pyrrole leads to the preferential formation of 3, where the driving force for the product formation is precipitation of 3 from water solution; the reaction proceeds at room temperature within a couple of minutes in excellent yields. On the other hand, low concentration of starting compounds led to preferential formation of tripyrromethanes 4. Formation of 3 and 4 can also be controlled by the initial ratio of aldehyde and pyrrole, where generally the ratios over 1:6 gave mostly 3. Application of this synthetic protocol for ketones revealed that only 3 are formed, regardless of the ratio of starting compounds, which is interpreted as a result of lower reactivity of ketones in this particular condensation reaction.
A new stratigraphic framework for the Gaspé Belt in southern Quebec: implications for the pre-Acadian Appalachians of eastern Canada
Authors: Lavoie Denis , Asselin Esther
Published: June 2004

The post-Taconian units in the Quebec and northern New Brunswick Appalachians constitute the Gaspé Belt and geological studies have mostly focussed on its eastern Quebec segment. Biostratigraphic data indicate that the succession in southern Quebec is no older than Late Silurian and extends into the Early Devonian. Two distinct stratigraphic assemblages are present. The first assemblage (Saint-Luc, Cranbourne, and Lac Aylmer formations, and Glenbrooke Group) unconformably overlies the Humber and Dunnage zones. The units show a basal alluvial conglomerate that passes progressively to deeper marine facies upsection, which have recorded a post-Late Silurian transgressive event. The second assemblage (Saint-Francis Group and Frontenac Formation) is faulted against either Dunnage units or autochthonous post-Taconian units. It locally unconformably overlies units of the Dunnage Zone; the succession shows progressively deeper marine conditions upsection and also has recorded a post-Late Silurian transgressive event. The biostratigraphic framework suggests that some of the units that were assumed to be vertically stacked are rather laterally equivalent. Independant evidence supports the hypothesis that the Gaspé Belt in southern Quebec formed after the collapse of the Taconian orogen in Late Silurian time. This event is ascribed to the Salinian Orogeny. The framework from southern Quebec is incorporated in a regional scenario. The Gaspé Belt experienced a PridolianLochkovian sea-level rise. In Pragian time, shallower marine conditions were established in southern Quebec, whereas in the Gaspé Peninsula, the shallower conditions only occurred in early Emsian time.
Reconstruction of Taconian and Acadian paleostress regimes in the Quebec and northern New Brunswick Appalachians
Authors: Faure Stéphane , Tremblay Alain , Malo Michel
Published: June 2004

A numerical analysis of fault populations was applied in the Quebec and northern New Brunswick Appalachians to characterize paleostress fields attributed to the Taconian and Acadian orogenies. The first brittle deformation documented in the external domain of the Humber Zone is associated with the thin-skinned tectonics of the Taconian orogen. The Taconian brittle deformation, characterized by northsouth to NESW reverse conjugated brittle faults, evolved under a pure shear compressional regime (vertical σ3 axes) with σ1 axes oriented ESEWNW. The ENEWSW dextral and NW-SE sinistral faults that are observed in the St.Lawrence Lowlands are also attributed to Taconian compression. The first brittle deformation recognized in the Dunnage Zone and the Gaspé Belt is attributed to an ESEWNW compression during the Acadian Orogeny. In the Dunnage Zone of southern Quebec, the Acadian paleostress axes are similar to the directions of σ1 axes and to the pure shear compressional regime computed for the Silurian and Devonian rocks of the Gaspé Belt. In the Gaspé Peninsula, the Acadian stresses are oriented ESEWNW and are mechanically compatible with transpressional regimes. Reverse brittle faults and pure shear stress are identified along regional and secondary sets of NESW brittle faults, whereas a strike-slip stress regime is reconstructed along major eastwest faults. In the Humber Zone of the Quebec Appalachians, a second compression is identified. It is characterized by conjugate ENEWSW dextral and NWSE sinistral strike-slip faults that crosscut Taconian thrust faults. This late deformation event is attributed to a distal expression of the Acadian Orogeny.
The Red Island Road Formation: Early Devonian terrestrial fill in the Anticosti Foreland Basin, western Newfoundland
Authors: Quinn L , Bashforth A R , Burden E T , Gillespie H , Springer R K , Williams S H
Published: June 2004

More than 100 m of nearly flat-lying, fluvially derived, thick-bedded and lensoid, clast-supported conglomerate and sandstone are found on Red Island, off the coast of the Port au Port Peninsula, western Newfoundland. Formally described herein and named Red Island Road Formation, the strata represent a unique lithologic formation not exposed or known anywhere else in the region. Characteristic features include abundant, rounded, highly weathered and varnished cobbles and boulders derived from an unknown mixed volcanic and very low to low-grade metamorphic terrane. Although the unit is largely unfossiliferous, a thin sandstone bed near the top of the type section contains primitive dichotomously branched plant remains and biostratigraphically significant palynomorphs. Among more than 25 species of spores, it is the diversity of Emphanisporites, Dictyotriletes, and Dibolisporites, and in particular Dibolisporites echinaceus, Dictyotriletes canadensis, Emphanisporites annulatus, E. erraticus, and E. schultzii that indicate the Red Island Road Formation was deposited during the early and early late Emsian Emphanisporites annulatus  Camarozonotriletes sextantii Assemblage Zone. Biostratigraphy places age constraints on Acadian tectonism, local thrusting, and foreland basin development in this part of the Anticosti Basin. The suite of clasts indicates a radical shift in provenance as compared with siliciclastic units lower in the foreland basin sequence. Clearly, the source for these clasts is not local. Terranes farther afield, such as the La Poile Group in southwestern Newfoundland, should be examined as possibilities for the provenance of these rocks.
Integration and spatial analysis of high-resolution geophysical and geological data, eastern Gaspé Peninsula
Authors: St-Laurent Christine , Lebel Daniel , Lavoie Denis , Malo Michel , St-Hilaire Camille
Published: June 2004

In the vicinity of the Town of Gaspé, the relationships between the Silurian-Devonian sedimentary succession of the Gaspé Belt and the Humber and the Dunnage zones are complex. To unravel these relationships, we used high-resolution aeromagnetic data and regional gravimetric data coupled with field tectonostratigraphic information. The magnetic vertical derivative located several magnetic anomalies associated with near-surface features in the SilurianDevonian cover sequence. In particular, a conglomerate with magnetic fragments that overlies the Late Silurian Salinic Unconformity is clearly recognizable. Large ovoid anomalies of significant intensity located in the SilurianDevonian sedimentary cover area cannot be associated with any known geological feature. The interpretation of the high-pass and low-pass filtered aeromagnetic survey indicates that the ovoid anomalies originate below the SilurianDevonian cover sequence. The most significant of the ovoid anomalies is associated with a gravimetric anomaly. It is proposed that these geophysical anomalies are probably associated with ultramafic and (or) volcanic rocks correlative in the subsurface with outcrops of the CambrianOrdovician lithologies of the Lady Step Complex and (or) the Shickshock Group.
The Lower Devonian Compton Formation in southern Quebec: from delta front to pro-delta sedimentation
Authors: Lavoie Denis
Published: June 2004

The Lower Devonian Compton Formation is the uppermost unit of the St. Francis Group in the Connecticut Valley  Gaspé synclinorium of southern Quebec. The Compton Formation is composed of three informal members. Five distinct sedimentary facies have been recognized in the lower two members of the Compton Formation. High-energy, shallow-marine, and channel sands dominate the Milan member. The overlying Lac Drolet member consists of below wave base mud and silt deposits with abundant turbidite sand. The Milan member is interpreted to represent deposits of a river-dominated delta-front environment, whereas the Lac Drolet member is suggestive of below storm-wave base pro-delta deposits. The transition from the Milan member to the Lac Drolet member is correlated with the deepening event recognized in coeval succession in the Gaspé Peninsula and known as the T2 event. There, the coeval Indian Point Formation is interpreted to represent pro-delta sediments. The new paleogeographic map for the Lochkovian illustrates the development of deltaic lobes from northern Gaspé to southern Quebec. In Lochkovian, deltaic regimes were established in southern Quebec and northeastern Gaspé, whereas the intervening successions (western Gaspé Peninsula  New Brunswick) experienced significant synsedimentary tectonic collapse.
Twentieth century water quality trends in Minnesota lakes compared with presettlement variability
Authors: Ramstack Joy M , Fritz Sherilyn C , Engstrom Daniel R
Published: June 2004

A diatom-based transfer function was used to reconstruct water chemistry before European settlement in 55 Minnesota lakes. The lakes span three natural ecoregions, which differ in their history of land use, as well as in surficial geology, climate, and vegetation. Postsettlement trends were compared with water chemistry change reconstructed from two presettlement core sections (circa 1750 and 1800) as a measure of natural variability. Presettlement water quality changes were generally small and nondirectional in all three ecoregions. In contrast, half of the urban lakes showed a statistically significant increase in chloride, whereas 30% of urban and 30% of agricultural region lakes record a statistically significant increase in total phosphorus between 1800 and the present. These changes, which are attributed to road salt and nutrient runoff, are strongly correlated with the percentage of watershed area that is developed (residential or urban) in the case of chloride increases and the percentage of developed (metropolitan areas) or agricultural (agricultural areas) land in the case of nutrient increases. Water quality has changed little since 1800 for lakes in the forested regions of northeastern Minnesota. The few changes that are seen in this region are likely related to natural variations in climate or catchment soils.
Protective role of heme oxygenase in the blood vessel wall during atherogenesis
Authors: Hoekstra Kenneth A , Godin David V , Cheng Kimberly M
Published: June 2004

Several lines of evidence suggest that antioxidant processes and (or) endogenous antioxidants inhibit proatherogenic events in the blood vessel wall. Heme oxygenase (HO), which catabolizes heme to biliverdin, carbon monoxide, and catalytic iron, has been shown to have such antioxidative properties. The HO-1 isoform of heme oxygenase is ubiquitous and can be increased several fold by stimuli that induce cellular oxidative stress. Products of the HO reaction have important effects: carbon monoxide is a potent vasodilator, which is thought to play a role in modulation of vascular tone; biliverdin and its by-product bilirubin are potent antioxidants. Although HO induction results in an increase in catalytic free iron release, the enhancement of intracellular ferritin protein through HO-1 has been reported to decrease the cytotoxic effects of iron. Oxidized LDL has been shown to increase HO-1 expression in endothelial and smooth muscle cell cultures, and during atherogenesis. Further evidence of HO-1 expression associated with atherogenesis has been demonstrated in human, murine and rabbit atherosclerotic lesions. Moreover, genetic models of HO deficiency suggest that the actions of HO-1 are important in modulating the severity of atherosclerosis. Recent experiments in gene therapy using the HO gene suggest that interventions aimed at HO in the vessel wall could provide a novel therapeutic approach for the treatment or prevention of atherosclerotic disease.Key words: heme oxygenase, atherosclerosis, antioxidant enzymes, oxidized LDL, gene therapy.
Conformational change and inactivation of arginine kinase from shrimpFeneropenaeus chinensisin oxidized dithiothreitol solutions
Authors: Pan Ji-Cheng , Yu Zhen-Hang , Hui En-Fu , Zhou Hai-Meng
Published: June 2004

The effect of oxidized dithiothreitol (DTT) on the conformation and function of arginine kinase from shrimp Feneropenaeus chinensis was investigated with the methods of intrinsic fluorescence, ANS fluorescence, size exclusion chromatography (SEC), sodium dodecyl sulfate – polyacrylamide gel electrophoresis (SDS–PAGE), and activity assay. The excess molecular oxidized dithiothreitol could result in a loss of activity and conformational change of arginine kinase. The oxidized arginine kinase was characterized by monitoring the changes of fluorescence emission wavelength (excitation wavelength: 295 nm) and the intensity of 1-anilino-8-naphthalenesulfonate (ANS) binding (excitation wavelength: 380 nm) to the protein. The results of fluorescence spectra showed that the presence of oxidized DTT could result in a marked change in the enzyme tertiary structure. The conformational changes of native and oxidized arginine kinase are induced by the presence of the full set of transition state analog (TSA) components. The results of size exclusion chromatography and SDS–PAGE indicated that no disulfide bond was formed among the protein molecules in the oxidized-DTT solution.Key words: arginine kinase, oxidized dithiothreitol, conformational change, inactivation.
Maintenance of Epstein–Barr virus-derived episomal vectors in the murine Sp2/0 myeloma cell line is dependent upon exogenous expression of human EBP2
Authors: Habel Marie-Eve , Drouin Mathieu , Jung Daniel
Published: June 2004

Vectors carrying the origin of replication (oriP) and driving expression of the EBNA-1 protein from Epstein–Barr virus (EBV) replicate as extrachromosomal episomes in human cells. Whether these vectors can be maintained as episomes in murine cells is still controversial. Here we demonstrate that EBNA-1 expression alone was unable to maintain episomal expression of an EBV-based vector in the murine Sp2/0 cell line. However, we were able to obtain long-term episome maintenance in Sp2/0 cells after exogenously expressing human EBP2 by genetic engineering. Our results provide further evidence for the fundamental role of human EBP2 in episomal maintenance of EBV-based vectors. Moreover, we demonstrate that EBV-based vectors can be successfully used in cells presumably incompetent for episomal maintenance.Key words: EBV vector, EBNA-1, EBP2, episomal maintenance, mouse cell, Sp2/0 myeloma cell line.
Fifty years of partial harvesting in a mixed mesophytic forest: composition and productivity
Authors: Schuler Thomas M
Published: June 2004

Long-term silvicultural trials contribute to sustainable forest management by providing a better scientific understanding of how forest ecosystems respond to periodic timber harvesting. In this study, species composition, diversity, and net periodic growth of tree species in a mixed mesophytic forest in the central Appalachians were evaluated after about a half century of management. Three partial cutting practices on 18 research compartments and on 3 unmanaged reference compartments were evaluated (19512001) on 280 ha. Single-tree selection, diameter-limit harvesting, and timber harvesting in 0.162-ha patches were assessed on three northern red oak site index50(SI) classes: 24, 21, and 18. ShannonWeiner's diversity index (H′) declined from the first (19511959) to last (19872001) measurements and was related to both SI (P = 0.004) and treatment (P = 0.009). Sugar maple (Acer saccharum Marsh.) and red maple (Acer rubrum L.) were the two most abundant species in recent years (19872001); in contrast, in initial inventories (19511959), northern red oak (Quercus rubra L.) and chestnut oak (Quercus prinus L.) were most abundant. Net periodic annual increment (PAI) of merchantable trees (DBH ≥12.7 cm) was related to both SI (P = 0.004) and treatment (P = 0.003). Mean PAI ranged from 4.6 m3·ha1·year1for single-tree selection to 2.5 m3·ha1·year1for unmanaged reference areas across all SI classes. The decline of oak species suggests that only intensive and specific forest management focused on maintaining oak species can obtain historical levels of diversity.
Spruce budworm outbreaks in eastern Quebec over the last 450 years
Authors: Boulanger Yan , Arseneault Dominique
Published: June 2004

In this study we used dendrochronology to reconstruct the history of eastern spruce budworm (Choristoneura fumiferana (Clem.)) outbreaks over the last 450 years in the Bas-Saint-Laurent region of southeastern Quebec. In total, 260 tree cores were sampled from 204 beams in seven historic buildings and 12 trees in a virgin forest stand. Eight previously documented outbreaks (19751992, 19471958, 19141923, 18681882, 18321845, 18051812, 17521776, 17101724) and three presumed previous outbreaks (16781690, 16421648, 15771600) were identified based on periods of growth reduction. Of these 11 confirmed or presumed outbreaks, six were documented for the first time in eastern Quebec. Such data suggest that outbreak frequency has remained quite stable, with a mean interval of about 40 years between the midpoint of successive outbreaks since the mid-16th century. In addition, together with previous studies, our results indicate a strong spatial synchrony of spruce budworm outbreaks across central and eastern Quebec during the last 300 years. Consequently, our study does not support the hypothesis that spruce budworm outbreak frequency and synchrony increased during the 20th century.