bluuebunny/crossref_metadata_2025 huggingface dataset:
Diversity of Potential Short Tandem Repeats in
Mycobacterium leprae
and Application for Molecular Typing
Authors: Zhang Liangfen , Budiawan Teky , Matsuoka Masanori
Published: October 2005

A recent advance in molecular typing for tracing the transmission of leprosy is the discovery of short tandem repeats (STRs) in
Mycobacterium leprae
. To substantiate polymorphic loci from STR as promising candidates for molecular typing tools in leprosy epidemiology, 44 STR loci including 33 microsatellites and 11 minisatellites were investigated among 27 laboratory strains by sequencing PCR products. Not all STRs were necessarily polymorphic. Thirty-two out of the 44 loci were polymorphic. Nine polymorphic loci were suitable for identifying genotypes according to the discriminatory capacity, stability, and reproducibility. All the strains were classified into independent genotypes by the selected nine loci. Three multicase households were subjected to molecular typing.
M. leprae
obtained from household cases showed identical copy numbers by TTC triplet alone, but the isolates from one family contact case were divided into different genotypes by adding eight other polymorphic loci. The combination of information from multiple loci allows increasing levels of discrimination and it is likely that the generation and documentation of data will result in the choice of a potential molecular typing tool for leprosy epidemiology.
Quality Control and Reference Guidelines for CLSI Broth Microdilution Susceptibility Method (M38-A Document) for Amphotericin B, Itraconazole, Posaconazole, and Voriconazole
Authors: Espinel-Ingroff A. , Fothergill A. , Ghannoum M. , Manavathu E. , Ostrosky-Zeichner L. , Pfaller M. , Rinaldi M. , Schell W. , Walsh T.
Published: October 2005

Although standard conditions are available for testing the susceptibilities of filamentous fungi to antifungal agents by the Clinical and Laboratory Standards Institute (CLSI; formerly National Committee for Clinical Laboratory Standards) broth microdilution assay, quality control (QC) MIC limits have not been established for any mold-agent combination. This multicenter (eight-center) study documented the reproducibility of tests for one isolate of
Paecilomyces variotii
ATCC MYA-3630 and 11 other mold isolates (three isolates of
Aspergillus fumigatus
; two isolates of
A. terreus
; one isolate each of
A. flavus
,
A. nidulans
,
Fusarium moniliforme
, and
F. solani
; and two isolates of
Scedosporium apiospermum
) by the CLSI reference broth microdilution method (M38-A document). Control limits (amphotericin B, 1 to 4 μg/ml; itraconazole, 0.06 to 0.5 μg/ml; posaconazole, 0.03 to 0.25 μg/ml; voriconazole, 0.015 to 0.12 μg/ml) for the selected QC
P. variotii
ATCC MYA-3630 were established by the analysis of replicate MIC results. Reference isolates and corresponding MIC ranges were also established for 6 of the 12 molds evaluated. MIC limits were not proposed for the other five molds tested due to low testing reproducibility for these isolates.
Heterogeneity of Biofilms Formed by NonmucoidPseudomonas aeruginosaIsolates from Patients with Cystic Fibrosis
Authors: Lee Baoleri , Haagensen Janus A. J. , Ciofu Oana , Andersen Jens Bo , Høiby Niels , Molin Søren
Published: October 2005

Biofilms are thought to play a key role in the occurrence of lung infections byPseudomonas aeruginosain patients with cystic fibrosis (CF). In this study, 20 nonmucoidP. aeruginosaisolates collected during different periods of chronic infection from eight CF patients were assessed with respect to phenotypic changes and in vitro biofilm formation. The physiological alterations were associated with a loss of motility (35% were nonmotile) and with decreased production of virulence factors (pyocyanin, proteases) and quorum-sensing molecules (45% of the isolates were unable to produce 3-O-C12-homoserine lactone quorum-sensing molecules). Compared with wild-type strain PAO1, mostP. aeruginosaisolates demonstrated different degrees of reduction of adherence on polystyrene surfaces. The in vitro biofilm formation of isolates was investigated in a hydrodynamic flow system. Confocal laser scanning microscope analysis showed that the biofilm structures of theP. aeruginosaisolates were highly variable in biomass and morphology. Biofilm development of six genotypically identical sequential isolates recovered from a particular patient at different time points of chronic infection (20 years) and after lung transplantation demonstrated significant changes in biofilm architectures.P. aeruginosabiofilm formation followed a trend of decreased adherence with progression of the chronic lung infection. The results suggest that the adherent characteristic of in vitro biofilm development was not essential for the longitudinal survival of nonmucoidP. aeruginosaduring chronic lung colonization.
Decay of Human Immunodeficiency Virus Type 1 Unintegrated DNA Containing Two Long Terminal Repeats in Infected Individuals after 3 to 8 Years of Sustained Control of Viremia
Authors: McDermott Jennifer L. , Martini Isabella , Ferrari Davide , Bertolotti Francesca , Giacomazzi Claudio , Murdaca Giuseppe , Puppo Francesco , Indiveri Francesco , Varnier Oliviero E.
Published: October 2005

Covert human immunodeficiency virus (HIV) replication was ongoing during the first 3 years of aviremia in 22 patients, as determined by detection of DNA containing two long terminal repeats (2LTR DNA). Although total HIV DNA was detected in 60 2LTR DNA-negative samples, the absence of 2LTR DNA in 90% of patients following 7 to 8 years of highly active antiretroviral therapy suggests suppression of cryptic viral replication.
Comparative Nucleotide Sequence Analysis of Polymorphic Variable-Number Tandem-Repeat Loci in
Mycobacterium ulcerans
Authors: Ablordey Anthony , Hilty Markus , Stragier Pieter , Swings Jean , Portaels Françoise
Published: October 2005

We analyzed a set of variable-number tandem-repeat (VNTR) loci to assess their nucleotide sequence diversity in isolates of three
Mycobacterium ulcerans
genotypes. Sequence variants in two loci resulted in intraspecies resolution of Southeast Asian and Asian genotypes in contrast to a homogenous sequence composition among African isolates. Nucleotide sequence polymorphism in repeat units can enhance discrimination of VNTR loci.
Cervical Specimen Order and Performance Measures of
Chlamydia trachomatis
Diagnostic Testing
Authors: Ghanem Khalil G. , Johnson Robert E. , Koumans Emilia H. , Marrazzo Jeanne M. , Markowitz Lauri E.
Published: October 2005

The orders of three endocervical specimens of 3,561 women for
Chlamydia trachomatis
testing were randomized to determine whether test performance measures of two nucleic acid amplification tests and a DNA probe were affected by swab order. Specimen collection order did not appear to affect the diagnostic accuracy of these tests.
Use of Stored Serum from Uganda for Development and Evaluation of a Human Immunodeficiency Virus Type 1 Testing Algorithm Involving Multiple Rapid Immunoassays
Authors: Singer Darrell E. , Kiwanuka Noah , Serwadda David , Nalugoda Fred , Hird Linda , Bulken-Hoover Jamie , Kigozi Godfrey , Malia Jennifer A. , Calero Eva K. , Sateren Warren , Robb Merlin L. , Wabwire-Mangen Fred , Wawer Maria , Gray Ronald H. , Sewankambo Nelson , Birx Deborah L. , Michael Nelson L.
Published: October 2005

We report the development and evaluation of a human immunodeficiency virus type 1 testing algorithm consisting of three rapid antibody detection tests. Stored serum samples from Uganda were utilized with a final algorithm sensitivity of 100% and a specificity of 98.9% (95% confidence interval, 98.6% to 99.3%).
Pseudomonas putida
Septicemia in a Special Care Nursery Due to Contaminated Flush Solutions Prepared in a Hospital Pharmacy
Authors: Perz Joseph F. , Craig Allen S. , Stratton Charles W. , Bodner Stanley J. , Phillips Walter E. , Schaffner William
Published: October 2005

Pseudomonas putida
bloodstream infections were reported in two preterm neonates from a special care nursery. An unopened container of preservative-free heparin flush, compounded several weeks earlier in the hospital pharmacy and from the same batch that was administered to the patients, grew
P. putida
with a pulsed-field gel electrophoresis (PFGE) pattern identical to that of the patients' isolates. Intrinsic contamination was ruled out by the absence of similar reports from other hospitals and by sterility testing of unopened stock solutions. We investigated the in vitro persistence of
P. putida
in heparinized saline: even under refrigerated conditions, inocula of 10
2
and 10
3
CFU/ml exhibited growth at 21 and 35 days, respectively. These findings highlight the need for compliance with current standards of aseptic technique and quality assurance during the preparation of compounded sterile products.
Multilocus Sequence Typing of
Escherichia coli
O26:H11 Isolates Carrying
stx
in Canada Does Not Identify Genetic Diversity
Authors: Gilmour Matthew W. , Cote Tyler , Munro Jamie , Chui Linda , Wylie John , Isaac-Renton Judith , Horsman Greg , Tracz Dobryan M. , Andrysiak Ashleigh , Ng Lai-King
Published: October 2005

Multilocus sequence typing of 31
stx
-carrying
Escherichia coli
O26:H11 strains isolated in Canada between 1999 and 2003 revealed a high degree of genetic relatedness at 10 loci, suggesting either that this is a clonal serotype (similar to O157:H7) or that additional genetic loci need to be examined.
Evaluation of Universal Probes and Primer Sets for Assessing Total Bacterial Load in Clinical Samples: General Implications and Practical Use in Endodontic Antimicrobial Therapy
Authors: Horz H. P. , Vianna M. E. , Gomes B. P. F. A. , Conrads G.
Published: October 2005

By reexamining 10 previously published “universal” PCR assays using the ARB phylogenetic software package and database with 41,000 16S rRNA gene sequences, we found that they differed considerably in their coverage of the domain
Bacteria
. We evaluated the broadest-range real-time quantitative PCR protocol for its efficacy in measuring the antimicrobial effects of endodontic treatments.
Prospective Multicenter Evaluation of a New Immunoassay and Real-Time PCR for Rapid Diagnosis of
Clostridium difficile
-Associated Diarrhea in Hospitalized Patients
Authors: van den Berg Renate J. , Bruijnesteijn van Coppenraet Lesla S. , Gerritsen Hendrik-Jan , Endtz Hubert P. , van der Vorm Eric R. , Kuijper Ed J.
Published: October 2005

In a prospective multicenter study, 367 fecal samples from 300 patients with diarrhea were tested for
Clostridium difficile
-associated diarrhea (CDAD) with a new immunochromatography assay for toxins A and B (ICTAB), a real-time PCR on the toxin B gene, and the cell cytotoxicity assay. Twenty-three (6.2%) of the 367 fecal samples were positive by the cell cytotoxicity assay. With the cell cytotoxicity assay as the “gold standard,” the sensitivity, specificity, positive predictive value, and negative predictive value for the ICTAB assay and real-time PCR were 91, 97, 70, and 99%, and 87, 96, 57 and 99%, respectively. In conclusion, both the ICTAB and the real-time PCR can be implemented as rapid screening methods for patients suspected of having CDAD.
Outbreaks in Distinct Regions Due to a Single
Klebsiella pneumoniae
Clone Carrying a
bla
VIM-1
Metallo-β-Lactamase Gene
Authors: Ikonomidis Alexandros , Tokatlidou Despina , Kristo Ioulia , Sofianou Danai , Tsakris Athanassios , Mantzana Paraskevi , Pournaras Spyros , Maniatis Antonios N.
Published: October 2005

From December 2004 to March 2005, 27
Klebsiella pneumoniae
clinical isolates that were positive by the imipenem-EDTA double-disk synergy test and that exhibited a single macrorestriction pattern were recovered in two distinct Greek hospitals. The isolates carried a transferable
bla
VIM-1
metallo-β-lactamase gene in a class 1 integron. Reverse transcriptase PCR showed that the gene was similarly expressed in low- and high-level carbapenem-resistant isolates, indicating the existence of additional resistance mechanisms. The clonal spread of VIM-1-producing
K. pneumoniae
strains in distinct regions where up to now
bla
VIM-2
and
bla
VIM-4
alleles were common is worrisome.
Comparison of Ashdown's Medium,
Burkholderia cepacia
Medium, and
Burkholderia pseudomallei
Selective Agar for Clinical Isolation of
Burkholderia pseudomallei
Authors: Peacock Sharon J. , Chieng Grace , Cheng Allen C. , Dance David A. B. , Amornchai Premjit , Wongsuvan Gumphol , Teerawattanasook Nittaya , Chierakul Wirongrong , Day Nicholas P. J. , Wuthiekanun Vanaporn
Published: October 2005

Ashdown's medium,
Burkholderia pseudomallei
selective agar (BPSA), and a commercial
Burkholderia cepacia
medium were compared for their abilities to grow
B. pseudomallei
from 155 clinical specimens that proved positive for this organism. The sensitivity of each was equivalent; the selectivity of BPSA was lower than that of Ashdown's or
B. cepacia
medium.
Development of a Nested Qualitative Real-Time PCR Assay To Detect
Aspergillus
Species DNA in Clinical Specimens
Authors: Halliday Catriona , Wu Qi Xuan , James Gregory , Sorrell Tania
Published: October 2005

We adapted a nested
Aspergillus
PCR to a nested qualitative real-time format on a LightCycler system. An evaluation using 134 clinical specimens showed that the real-time PCR assay significantly reduced the time for results to be made available without compromising sensitivity and was less labor-intensive. Its use will aid in the rapid diagnosis of invasive aspergillosis.
Use of Specific rRNA Oligonucleotide Probes for Microscopic Detection of
Mycobacterium tuberculosis
in Culture and Tissue Specimens
Authors: St. Amand Allison L. , Frank Daniel N. , De Groote Mary Ann , Basaraba Randall J. , Orme Ian M. , Pace Norman R.
Published: October 2005

Mycobacterium tuberculosis
infections are a major global health problem. Fast and accurate detection of
M. tuberculosis
is clearly needed at both the clinical level and the research level. We report a rapid and reliable in situ hybridization technique using rRNA oligonucleotide probes for the identification of
M. tuberculosis
in tissues and cultures.
Mycobacterium thermoresistibile
Infection following Knee-Replacement Surgery
Authors: LaBombardi Vincent J. , Shastry Lalita , Tischler Henry
Published: October 2005

We report a case of
Mycobacterium thermoresistibile
as a cause of infection following total knee replacement. This infection was masked by the prior isolation of a vancomycin-resistant enterococcus. The infection was resolved with long-term therapy using moxifloxacin and doxycycline.
AN ALGEBRAIC APPROACH TO A HARMONIC OSCILLATOR PLUS AN INVERSE SQUARE POTENTIAL IN TWO DIMENSIONS
Authors: DONG SHI-HAI , SUN GUO-HUA , LOZADA-CASSOU M.
Published: October 2005

The exact solutions of the Schrödinger equation with a harmonic oscillator plus an inverse square potential are obtained in two dimensions. We construct the ladder operators directly from the radial wave functions and find that these operators satisfy the commutation relations of an SU (1, 1) group. We obtain the explicit expressions of the matrix elements for some related functions ρ and [Formula: see text] with ρ = r2. We also explore another symmetry between the eigenvalues E(r) and E(ir) by substituting r→ir.
COVARIANT LINEAR PERTURBATIONS IN A CONCORDANCE MODEL
Authors: CZINNER VIKTOR , VASÚTH MÁTYÁS , LUKÁCS ÁRPÁD , PERJÉS ZOLTÁN
Published: October 2005

We present the complete solution of the first order metric and density perturbation equations in a spatially flat (K = 0), Friedmann–Robertson–Walker (FRW) universe filled with pressureless ideal fluid, in the presence of cosmological constant. We use covariant linear perturbation formalism and the comoving gauge condition to obtain the field and conservation equations. The solution contains all modes of the perturbations, i.e. scalar, vector and tensor modes, and we show that our results are in agreement with the Sachs and Wolfe metric perturbation formalism.
INVESTIGATION OF PROPERTIES OF THE CONFINED STATES IN PHOTONIC QUANTUM-WELL STRUCTURES
Authors: ZHANG YAN , GU BEN-YUAN , LIU CHUNG-PING
Published: October 2005

We present a detailed investigation of the properties of the confined states in the photonic quantum-well (PQW) structures with the use of the transfer-matrix method. The influences of various physical and geometrical parameters of the systems on the characteristics of the confined states are systematically explored. The results show that the features of the confined modes can be engineered by adjusting system parameters. It may provide a useful way to control the merits of the defect modes in order to match the requirements in photonic or microwave devices.
Thyroid hormone controls myocardial substrate metabolism through nuclear receptor-mediated and rapid posttranscriptional mechanisms
Authors: Hyyti Outi M. , Ning Xue-Han , Buroker Norman E. , Ge Ming , Portman Michael A.
Published: October 2005

Thyroid hormone regulates metabolism through transcriptional and posttranscriptional mechanisms. The integration of these mechanisms in heart is poorly understood. Therefore, we investigated control of substrate flux into the citric acid cycle (CAC) by thyroid hormone using retrogradely perfused isolated hearts ( n = 20) from control (C) and age-matched thyroidectomized rats (T). We determined substrate flux and fractional contributions (Fc) to the CAC by13C-NMR spectroscopy and isotopomer analyses in hearts perfused with [1,3-13C]acetoacetic acid (0.17 mM), l-[3-13C]lactic acid (LAC, 1.2 mM), [U-13C]long-chain mixed free fatty acids (FFA, 0.35 mM), and unlabeled glucose. Some T hearts were supplied triiodothyronine (T3, 10 nM; TT) for 60 min. Prolonged hypothyroid state reduced myocardial oxygen consumption, although T3produced no significant change. Hypothyroidism reduced overall CACfluxbut selectively altered only FFAfluxamong the individual substrates, though LACfluxtrended upward. T3rapidly decreased lactate Fc and flux.13C labeling of glutamine through glutamate was increased in T with further enhancement in TT. The glutamate-to-glutamine ratio was significantly lower in T and TT. Immunoblots detected a decrease in hypothyroid hearts for muscle carnitine palmitoyltransferase I (CPT I) and a marked increase in pyruvate dehydrogenase kinase (PDK)-2 with no changes in liver CPT I, PDK-4, or hexokinase 2. TT, but not T, displayed elevated glutamine synthetase (GS) expression. These studies showed that T3regulates cardiac metabolism through integration of several mechanisms, including changes in oxidative enzyme content and rapid modulation of individual substrates fluxes. T3also moderates forward glutamine flux, possibly by increasing the overall activity of GS.
Perinatal testosterone surge is required for normal adult bone size but not for normal bone remodeling
Authors: Sims Natalie A. , Brennan Karen , Spaliviero Jenny , Handelsman David J. , Seibel Markus J.
Published: October 2005

Although testosterone (T) has striking effects on mature skeletal size and structure, it is not clear whether this depends exclusively on adult circulating levels of T or whether additional early-life factors also play a role. We have compared the androgen-deficient hypogonadal ( hpg) mutant mouse with intact, orchidectomized, and T-treated non- hpg mice to determine relative contributions of adult and perinatal T to bone growth and development. At 3 wk of age, although trabecular and cortical bone structure was normal, bone turnover was significantly altered in hpg male mice; osteoid volume (OV/BV) and osteoblast surface (ObS/BS) were significantly lower and osteoclast surface (OcS/BS) significantly higher in hpg mice compared with age-matched non- hpg mice, pointing to a role for the perinatal T surge in determining bone turnover levels before sexual maturity. At 9 wk of age, the hpg bone phenotype mimicked closely that of age-matched non- hpg mice that had been orchidectomized at 3 wk of age, including low trabecular bone mass and high bone turnover. These bone phenotypes of hpg and orchidectomized non- hpg mice were all prevented by replacement doses of T or dihydrotestosterone (DHT), suggesting that these are determined by adult sex steroid hormones. In contrast, a short bone phenotype that could not be prevented by T or DHT treatment was observed in 9-wk-old hpg mice yet not in intact or castrated non- hpg mice. These data suggest a role for the perinatal T surge in determining adult bone length and confirms that adult circulating T determines adult bone density.
Stevioside counteracts the α-cell hypersecretion caused by long-term palmitate exposure
Authors: Hong J. , Chen L. , Jeppesen P. B. , Nordentoft I. , Hermansen K.
Published: October 2005

Long-term exposure to fatty acids impairs β-cell function in type 2 diabetes, but little is known about the chronic effects of fatty acids on α-cells. We therefore studied the prolonged impact of palmitate on α-cell function and on the expression of genes related to fuel metabolism. We also investigated whether the antihyperglycemic agent stevioside was able to counteract these effects of palmitate. Clonal α-TC1-6 cells were cultured with palmitate in the presence or absence of stevioside. After 72 h, we evaluated glucagon secretion, glucagon content, triglyceride (TG) content, and changes in gene expression. Glucagon secretion was dose-dependently increased after 72-h culture, with palmitate at concentrations ≥0.25 mM ( P < 0.05). Palmitate (0.5 mM) enhanced TG content of α-cells by 73% ( P < 0.01). Interestingly, stevioside (10−8and 10−6M) reduced palmitate-stimulated glucagon release by 22 and 45%, respectively ( P < 0.01). There was no significant change in glucagon content after 72-h culture with palmitate and/or stevioside. Palmitate increased carnitine palmitoyltransferase I (CPT I) mRNA level, whereas stevioside enhanced CPT I, peroxisome proliferator-activated receptor-γ, and stearoyl-CoA desaturase gene expressions in the presence of palmitate ( P < 0.05). In conclusion, long-term exposure to elevated fatty acids leads to a hypersecretion of glucagon and an accumulation of TG content in clonal α-TC1-6 cells. Stevioside was able to counteract the α-cell hypersecretion caused by palmitate and enhanced the expression of genes involved in fatty acid metabolism. This indicates that stevioside may be a promising antidiabetic agent in treatment of type 2 diabetes.
Differential expression of IGF system components in proliferating vs. differentiating growth plate chondrocytes: the functional role of IGFBP-5
Authors: Kiepe Daniela , Ciarmatori Sonia , Haarmann Anke , Tönshoff Burkhard
Published: October 2005

The growth plate is an important target tissue for insulin-like growth factors (IGFs), but little is known about the regulation of the IGF system during the developmental sequence of chondrocytes. We therefore examined the expression profile of IGF system components in proliferating vs. differentiating growth plate chondrocytes by use of two cell culture models of the growth cartilage. In rat growth plate chondrocytes in primary culture, IGF-I expression increased twofold during the process of differentiation. IGF-binding protein-3 (IGFBP-3) expression showed a biphasic pattern of with a twofold increase at the onset of differentiation and a downregulation in late differentiating chondrocytes to 25% of baseline levels; the expression patterns of IGFBP-2, -4 and -6 were not dependent on the developmental stage. In IGF- and IGFBP-3-deficient RCJ3.1C5.18 (RCJ) mesenchymal chondrogenic cells, IGFBP-2 and -6 synthesis declined by 50% during differentiation. IGFBP-5 expression was markedly upregulated during the process of differentiation in both cell culture models. Although IGFBP-5 overexpression did not have an IGF-independent effect on RCJ cell differentiation, it promoted IGF-I-enhanced differentiation of these cells. A potential mechanism for this effect is the specific increase of Akt phosphorylation in IGFBP-5-overexpressing cells in the presence of IGF-I, indicating an increased activity of the phosphatidylinositol (PI) 3-kinase pathway. These data suggest that the developmental stage of the chondrocyte is an important determinant of IGF and IGFBP expression and imply a functional role for IGFBP-5 for upregulating IGF action during chondrocyte differentiation in vivo.
Rat renal glucose transporter SGLT1 exhibits zonal distribution and androgen-dependent gender differences
Authors: Sabolić Ivan , Škarica Mario , Gorboulev Valentin , Ljubojević Marija , Balen Daniela , Herak-Kramberger Carol M. , Koepsell Hermann
Published: October 2005

SGLT1 (SLC5A1) mediates a part of glucose and galactose reabsorption in the mammalian proximal tubule (PT), but the detailed localization of the transporter along the tubule is still disputable. Here, we used several methods to localize rat SGLT1 (rSGLT1) in the kidneys of intact and variously treated male (M) and female (F) rats. In immunoblots of isolated cortical (C) and outer stripe (OS) brush-border membranes (BBM), a peptide-specific polyclonal antibody for rSGLT1 labeled a sharp inzone-, and gender-dependent ∼40-kDa protein and a broad ∼75-kDa band that exhibited strong zonal (OS > C) and gender differences (F > M). In tissue cryosections, the antibody strongly stained BBM of the S3 PT segments in the OS and medullary rays (F > M) and smooth muscles of the blood vessels and renal capsule (F ∼ M) and weakly stained the apical domain of other PT segments in the C (F ∼ M). The phlorizin-sensitive uptake of d-[3H]galactose in BBM vesicles, as well as the tissue abundance of rSGLT1-specific mRNA, matched the immunoblotting data related to the 75-kDa protein and the immunostaining in S3, proving zonal and gender differences in the functional transporter. Ovariectomy had no effect, castration upregulated, whereas treatment of castrated rats with testosterone, but not with estradiol or progesterone, downregulated the 75-kDa protein and the immunostaining in S3. We conclude that in the rat kidney, the expression of SGLT1 is represented by a 75-kDa protein localized largely in the PT S3 segments, where it exhibits gender differences (F > M) at both the protein and mRNA levels that are caused by androgen inhibition.
Effects of angiotensin II on the CO2dependence of HCO3−reabsorption by the rabbit S2 renal proximal tubule
Authors: Zhou Yuehan , Bouyer Patrice , Boron Walter F.
Published: October 2005

Previous authors showed that, at low doses, both basolateral and luminal ANG II increase the proximal tubule's HCO3−reabsorption rate ( JHCO3). Using out-of-equilibrium CO2/HCO3−solutions, we demonstrated that basolateral CO2increases JHCO3. Here, we examine interactions between ANG II and CO2in isolated, perfused rabbit S2 segments. We first used equilibrated 5% CO2/22 mM HCO3−/pH 7.40 in bath and lumen. At 10−11M, basolateral (BL) ANG II increased JHCO3by 41%, and luminal ANG II increased JHCO3by 35%. At 10−9M, basolateral ANG II decreased JHCO3by 43%, whereas luminal ANG II was without effect. Second, we varied [CO2]BLfrom 0 to 20% at fixed [HCO3−]BLand pHBL. Fractional stimulation produced by BL 10−11M ANG II falls when [CO2]BLexceeds 5%. Fractional inhibition produced by BL 10−9M ANG II tends to rise when [CO2]BLexceeds 5%. Regarding luminal ANG II, fractional stimulation produced by 10−11M ANG II fell monotonically as [CO2]BLrose from 0 to 20%. Fractional inhibition produced by 10−9M ANG II rose monotonically with increasing [CO2]BL. Viewed differently, ANG II at 10−11M tended to reduce stimulation by CO2, and at 10−9M, produced an even greater reduction. In conclusion, the mutual effects of 1) ANG II on the JHCO3response to basolateral CO2and 2) basolateral CO2on the JHCO3responses to ANG II suggest that the signal-transduction pathways for ANG II and basolateral CO2intersect or merge.
Inhibition of phosphatidylinositol 3-kinase stimulates activity of the small-conductance K channel in the CCD
Authors: Li Dimin , Wei Yuan , Babilonia Elisa , Wang Zhijian , Wang Wen-Hui
Published: October 2005

We used Western blotting to examine the expression of phosphatidylinositol 3-kinase (PI3K) in the renal cortex and outer medulla and employed the patch-clamp technique to study the effect of PI3K on the ROMK-like small-conductance K (SK) channels in the cortical collecting duct (CCD). Low K intake increased the expression of the 110-kDa α-subunit (p110α) of PI3K compared with rats on a normal-K diet. Because low K intake increases superoxide levels ( 2 ), the possibility that increases in superoxide anions may be responsible for the effect of low K intake on the expression of PI3K is supported by finding that addition of H2O2stimulates the expression of p110α in M1 cells. Inhibition of PI3K with either wortmannin or LY-294002 significantly increased channel activity in the CCD from rats on a K-deficient (KD) diet or on a normal-K diet. The stimulatory effect of wortmannin on ROMK channel activity cannot be mimicked by inhibition of phospholipase C with U-73122. This suggests that the effect of inhibiting PI3K was not the result of increasing the phosphatidylinositol 4,5-bisphosphate level. Moreover, application of the exogenous phosphatidylinositol 3,4,5-trisphosphate analog had no effect on channel activity in excised patches. Because low K intake has been shown to increase the activity of protein tyrosine kinase (PTK), we explored the role of the interaction between PTK and PI3K in the regulation of the SK channel activity. Inhibition of PTK increased SK channel activity in the CCD from rats on a KD diet. However, addition of wortmannin did not further increase ROMK channel activity. Also, the effect of wortmannin was abolished by treatment of CCD with phalloidin. We conclude that PI3K is involved in mediating the effect of low K intake on ROMK channel activity in the CCD and that the effect of PI3K on SK channels requires the involvement of PTK and the cytoskeleton.
Transcriptional profiling with a blood pressure QTL interval-specific oligonucleotide array
Authors: Joe Bina , Letwin Noah E. , Garrett Michael R. , Dhindaw Seema , Frank Bryan , Sultana Razvan , Verratti Kathleen , Rapp John P. , Lee Norman H.
Published: October 2005

Although the evidence for a genetic predisposition to human essential hypertension is compelling, the genetic control of blood pressure (BP) is poorly understood. The Dahl salt-sensitive (S) rat is a model for studying the genetic component of BP. Using this model, we previously reported the identification of 16 different genomic regions that contain one or more BP quantitative trait loci (QTLs). The proximal region of rat chromosome 1 contains multiple BP QTLs. Of these, we have localized the BP QTL1b region to a 13.5-cM (20.92 Mb) region. Interestingly, five additional independent studies in rats and four independent studies in humans have reported genetic linkage for BP control by regions homologous to QTL1b. To view the overall renal transcriptional topography of the positional candidate genes for this QTL, we sought a comparative gene expression profiling between a congenic strain containing QTL1b and control S rats by employing 1) a saturated QTL1b interval-specific oligonucleotide array and 2) a whole genome cDNA microarray representing 20,465 unique genes that are positioned outside the QTL. Results indicated that 17 of the 231 positional candidate genes for this QTL are differentially expressed between the two strains tested. Surprisingly, >1,500 genes outside of QTL1b were differentially expressed between the two rat strains. Integrating the results from the two approaches revealed at least one complex network of transcriptional control initiated by the positional candidate Nr2f2. This network appears to account for the majority of gene expression differences occurring outside of the QTL interval. Further substitution mapping is currently underway to test the validity of each of these differentially expressed positional candidate genes. These results demonstrate the importance of using a saturated oligonucleotide array for identifying and prioritizing differentially expressed positional candidate genes of a BP QTL.
Steinernema affine (Nematoda: Steinernematidae), a new record for North America and its distribution relative to other entomopathogenic nematodes in British Columbia
Authors: Webster John ,   Mráček, Kindlmann Pavel
Published: October 2005

Randomly selected ecosystems in the coastal Greater Vancouver, Fraser valley and southern Vancouver Island regions, and in the interior Okanagan region of British Columbia, were sampled for the presence of entomopathogenic nematodes (EPN). Of 133 soil samples, 23 contained EPN (18 with steinernematids and five with heterorhabditids). Three identified species and one unidentified species were found. Steinernema affine and S. kraussei occurred in most EPN positive locations in the coastal regions sampled. Steinernema affine was found in open habitats and S. kraussei in all types of tree habitats. Steinernema feltiae was found in only one location, White Rock, in the Greater Vancouver region, close to an ocean beach. Heterorhabditis megidis occurred in only the drier Okanagan valley region of central, southern British Columbia, which has a more extreme climate than the moist, moderate climate of the coastal region. It occurred mostly in agricultural land represented by orchards, vineyards, and secondary woodland. In field baiting and laboratory experiments S. affine appeared to be a more successful parasite than S. kraussei.
The effect of fallow on Longidorus americanus, a nematode associated with stunting of loblolly pine seedlings in Georgia, USA
Authors: Fraedrich Stephen , Cram Michelle , Zarnoch Stanley
Published: October 2005

Stunting of loblolly pine (Pinus taeda L.) seedlings, caused by Longidorus americanus, has been a problem at a Georgia (USA) nursery. Field and growth chamber studies were conducted to determine the survivability of the nematode in fallow nursery soil. The population density of L. americanus decreased rapidly in the upper 15 cm of soil in fallow field plots during the first 101 days and the nematode was not detected after 263 days. Bioassays subsequently failed to detect the nematode in the upper 30 cm of soil in fallow plots on days 263 and 365. Population densities also decreased rapidly in fallow soil during the initial 130 days of the growth chamber study and the nematode was not detected at days 334 and 427, or in subsequent bioassays. Longidorus americanus does not survive well in the upper 15-30 cm of nursery soil in the absence of a host, and the use of fallow may be an acceptable alternative to pesticides for the management of this nematode.
Variability of the ITS rDNA and identification of Nacobbus aberrans (Thorne, 1935) Thorne & Allen, 1944 (Nematoda: Pratylenchidae) by rDNA amplification
Authors: Anthoine Géraldine , Mugniéry Didier
Published: October 2005

In order to identify the false root-knot nematode, Nacobbus aberrans, a nematode of quarantine importance, investigations were undertaken at the molecular level. Study of the ITS rDNA region among six South American populations showed an extremely high polymorphism. This polymorphism is due to point mutation insertions-deletions, the importance of which is increased by the presence of a degenerate microsatellite in this region. The usefulness of the ITS rDNA is therefore questionable when designing a species-specific identification tool. A study based on partial sequences of the 18S gene was carried out. A conserved part of the 18S gene, with a low level of variation when compared to Pratylenchus spp. and Meloidogyne spp., was found in all the N. aberrans populations tested. The primer set designed for this part of the 18S gene allows the amplification of a 295 bp fragment in all the N. aberrans populations tested. No amplification was obtained with other species belonging to Pratylenchidae, Heteroderidae or Hoplolaimidae. This PCR-based identification tool is effective on all N. aberrans migratory stages. From this study it is concluded that this N. aberrans specific primer set may provide a very useful tool for the identification of South American N. aberrans populations and thereby assist diagnosticians in implementing N. aberrans quarantine regulations.
Variation in the number of Bursaphelenchus xylophilus in aliquots of stock suspensions artificially inoculated on to subject pines
Authors: Yamanobe Taro
Published: October 2005

The procedures used to estimate the number of pine wood nematodes (Bursaphelenchus xylophilus) in stock suspensions and the variation in the number of nematodes in inocula applied to subject pine trees were examined. The findings suggest that preparing dilutions using 1 ml aliquots and making two replicate dilutions and three replicate counts of each dilution (or three dilutions and two counts) results in a precision of ±15% and an elapsed time for the majority of the population estimate procedures of less than 900 seconds. Under these conditions, the variation in the number of nematodes in the inocula was estimated to range from 55 to 156% of the intended population. This variation in the number of pine wood nematodes inoculated is unavoidable; thus, researchers should account for this variation when interpreting data from trials involving the artificial inoculation of pines.
Effects of nematode infection and mulching on the yield of plantain (Musa spp., AAB-group) ratoon crops and plantation longevity in southeastern Nigeria
Authors: Auwerkerken Annemarie , Dubois Thomas , De Schutter Bart , Speijer Paul , Rotimi Omalara , De Waele Dirk , Coyne Danny , Tenkouano Abdou
Published: October 2005

The effects of nematode infection and mulching on plantain cv. Agbagba (Musa spp., AAB-group, false horn) yield and plantation longevity were examined in a field experiment at the High Rainfall Station of the International Institute of Tropical Agriculture (IITA) at Onne in southeastern Nigeria. The 2nd, 3rd and 4th crop cycles (1st, 2nd and 3rd ratoon, respectively) following the plant crop cycle (mother crop) were examined in nematode inoculated or non-inoculated and mulched or non-mulched treatments. Nematodes (Radopholus similis, Helicotylenchus multicinctus and, to a lesser extent, Helicotylenchus dihystera, Hoplolaimus pararobustus and Meloidogyne spp.) were inoculated at planting of the mother plant, but were also present in relatively high population densities in the non-inoculated treatments at harvest of the 1st crop cycle. Plants inoculated with nematodes failed to reach harvest and neither did plants in the non-inoculated non-mulched treatments in any ratoon. Only non-inoculated mulched plants reached harvest, producing 0.85, 1.22 and 0.2 Mg ha−1, respectively in the 1st, 2nd and 3rd ratoon, taking toppled, broken and dead plants into consideration. Mulched plants were larger, had more suckers, survived longer and had healthier root systems compared with non-mulched plants. Damage to roots was greater in the inoculated plants compared with the non-inoculated plants for the 1st and 2nd ratoons but not for the 3rd ratoon. Radopholus similis was most strongly associated with root damage (percentage root necrosis and dead roots), although H. multicinctus population densities were also positively correlated with percentage root necrosis. At flowering of the 1st ratoon, 71% of the inoculated non-mulched plants were dead compared with only 1% of the non-inoculated mulched plants. Helicotylenchus multicinctus remained the most abundant nematode throughout the experiment. Together with R. similis, it comprised over 95% of the plant-parasitic nematode population.
On Bulk Models of Shallow Cumulus Convection
Authors: Bellon Gilles , Stevens Bjorn
Published: October 2005

Two-layer bulk models of the cloudy boundary layer are investigated, focusing on the consistency issues between common assumptions on the turbulent mixing and the thermodynamic profiles. Simplifications of the vertical structure of the conserved variables are shown to lead to inconsistent steady states. First, linear profiles in the cloud layer are incompatible with the common parameterizations of the turbulent mixing. Second, this approximation is inconsistent with simple models of an infinitely thin inversion layer. Simple mass-flux parameterizations of the turbulence are shown to produce reasonable profiles inside the cloud layer without solving the problem of the inversion. The cloud − environment difference and the vertical gradient of the conserved variables appear as interesting test variables for such models, as well as their ability to match the free-tropospheric boundary conditions. The latter certainly requires a unified approach for the cloud and inversion layers.
Predictability and Information Theory. Part II: Imperfect Forecasts
Authors: DelSole Timothy
Published: October 2005

This paper presents a framework for quantifying predictability based on the behavior of imperfect forecasts. The critical quantity in this framework is not the forecast distribution, as used in many other predictability studies, but the conditional distribution of the state given the forecasts, called the regression forecast distribution. The average predictability of the regression forecast distribution is given by a quantity called the mutual information. Standard inequalities in information theory show that this quantity is bounded above by the average predictability of the true system and by the average predictability of the forecast system. These bounds clarify the role of potential predictability, of which many incorrect statements can be found in the literature. Mutual information has further attractive properties: it is invariant with respect to nonlinear transformations of the data, cannot be improved by manipulating the forecast, and reduces to familiar measures of correlation skill when the forecast and verification are joint normally distributed. The concept of potential predictable components is shown to define a lower-dimensional space that captures the full predictability of the regression forecast without loss of generality. The predictability of stationary, Gaussian, Markov systems is examined in detail. Some simple numerical examples suggest that imperfect forecasts are not always useful for joint normally distributed systems since greater predictability often can be obtained directly from observations. Rather, the usefulness of imperfect forecasts appears to lie in the fact that they can identify potential predictable components and capture nonstationary and/or nonlinear behavior, which are difficult to capture by low-dimensional, empirical models estimated from short historical records.
Influence of Western North Pacific Tropical Cyclones on Their Large-Scale Environment
Authors: Sobel Adam H. , Camargo Suzana J.
Published: October 2005

The authors investigate the influence of western North Pacific (WNP) tropical cyclones (TCs) on their large-scale environment by lag regressing various large-scale climate variables [atmospheric temperature, winds, relative vorticity, outgoing longwave radiation (OLR), column water vapor, and sea surface temperature (SST)] on an index of TC activity [accumulated cyclone energy (ACE)] on a weekly time scale. At all leads and lags out to several months, persistent, slowly evolving signals indicative of the El Niño–Southern Oscillation (ENSO) phenomenon are seen in all the variables, reflecting the known seasonal relationship of TCs in the WNP to ENSO. Superimposed on this are more rapidly evolving signals, at leads and lags of one or two weeks, directly associated with the TCs themselves. These include anomalies of positive low-level vorticity, negative OLR, and high column water vapor associated with anomalously positive ACE, found in the region where TCs most commonly form and develop. In the same region, lagging ACE by a week or two and so presumably reflecting the influence of TCs on the local environment, signals are found that might be expected to negatively influence the environment for later cyclogenesis. These signals include an SST reduction in the primary region of TC activity, and a reduction in column water vapor and increase in OLR that may or may not be a result of the SST reduction.

On the same short time scale, an increase in equatorial SST near and east of the date line is seen, presumably associated with equatorial surface westerly anomalies that are also found. This, combined with the correlation between ACE and ENSO indices on the seasonal time scale, suggests the possibility that TCs may play an active role in ENSO dynamics.
Equivalent-Barotropic Definition of Tropospheric Mean Temperature
Authors: Sun Che
Published: October 2005

An equivalent-barotropic (EB) description of the tropospheric temperature field is derived from the geostrophic empirical mode (GEM) in the form of a scalar function Γ(p, ϕ), where p is pressure and ϕ is 300–850-mb thickness. Baroclinic parameter ϕ plays the role of latitude at each longitudinal section. Compared with traditional Eulerian-mean methods, GEM defines a mean field in baroclinic streamfunction space with a time scale much longer than synoptic variability. It prompts an EB concept that is only based on a baroclinic field.

Monthly GEM fields are diagnosed from NCEP–NCAR reanalysis data and account for more than 90% of the tropospheric thermal variance. The circumglobal composite of GEM fields exhibits seasonal, zonal, and hemispheric asymmetries, with larger rms errors occurring in winter and in the Northern Hemisphere (NH). Zonally asymmetric features and planetary deviation from EB are seen in the NH winter GEM. Reconstruction of synoptic sections and correlation analysis reveal that the tropospheric temperature field is EB at the leading order and has a 1-day phase lag behind barotropic variations in extratropical regions.
Impact of Aerosol Intrusions on Arctic Boundary Layer Clouds. Part II: Sea Ice Melting Rates
Authors: Carrió G. G. , Jiang H. , Cotton W. R.
Published: October 2005

The potential impact of intrusions of polluted air into the Arctic basin on sea ice melting rates and the surface energy budget is examined. This paper extends a previous study to cloud-resolving simulations of the entire spring season during the 1998 Surface Heat Budget of the Arctic (SHEBA) field campaign. For that purpose, the Los Alamos National Laboratory sea ice model is implemented into the research and real-time versions of the Regional Atmospheric Modeling System at Colorado State University (RAMS@CSU). This new version of RAMS@CSU also includes a new microphysical module that considers the explicit nucleation of cloud droplets and a bimodal representation of their spectrum. Different aerosol profiles based on 4 May 1998 observations were used to characterize the polluted upper layer and the 2–3 daily SHEBA soundings were utilized to provide time-evolving boundary conditions to the model. Results indicate that entrainment of ice-forming nuclei (IFN) from above the inversion increases the sea ice melting rates when mixed-phase clouds are present. An opposite although less important effect is associated with cloud condensation nuclei (CCN) entrainment when liquid-phase clouds prevail.
Determination of an Amazon Hot Reference Target for the On-Orbit Calibration of Microwave Radiometers
Authors: Brown Shannon T. , Ruf Christopher S.
Published: October 2005

A physically based model is developed to determine hot calibration reference brightness temperatures (TBs) over depolarized regions in the Amazon rain forest. The model can be used to evaluate the end-to-end calibration of any satellite microwave radiometer operating at a frequency between 18 and 40 GHz and angle of incidence between nadir and 55°. The model is constrained by Special Sensor Microwave Imager (SSM/I) TBs measured at 19.35, 22.2, and 37.0 GHz at a 53° angle of incidence and extrapolates/interpolates those measurements to other frequencies and incidence angles. The rms uncertainty in the physically based model is estimated to be 0.57 K. For instances in which coincident SSM/I measurements are not available, an empirical formula has been fit to the physical model to provide hot reference brightness temperature as a function of frequency, incidence angle, time of day, and day of year. The empirical formula has a 0.1-K rms deviation from the physically based model for annual averaged measurements and at most a 0.6-K deviation from the model for any specific time of day or day of year.