bluuebunny/crossref_metadata_2025 huggingface dataset:
Multicenter Performance Evaluation of a New TaqMan PCR Assay for Monitoring Human Immunodeficiency Virus RNA Load
Authors: Perrin L. , Pawlotsky J. M. , Bouvier-Alias M. , Sarrazin C. , Zeuzem S. , Colucci G.
Published: December 2006

A TaqMan real-time PCR assay, the COBAS TaqMan human immunodeficiency virus (HIV) (HPS-CTMHIV) PCR assay, recently developed for the quantification of HIV type 1 RNA in plasma, was evaluated in comparison with the licensed COBAS AMPLICOR HIV-1 MONITOR (CAHIM) assay. In this study, we have analyzed the tests' sensitivities, precisions, and linearities using multiple replicates of a standard panel of HIV RNA covering a 7-logarithm range of concentrations, as well as serial threefold dilutions of high-titer clinical samples. The subtype inclusivity was also investigated, using a panel of subtypes A to H, while a collection of 160 clinical samples was analyzed to assess the tests' specificities and the systems' similarities. The results of these experiments showed that the HPS-CTMHIV assay has a sensitivity of 53 copies/ml (95% hit rate), 100% specificity, and good intra- and interassay precision. The results of the HPS-CTMHIV assay were linear in the 50- to 10
7
-copies/ml range, with a correlation coefficient (
R
) for expected versus observed results of 0.98. Compared to the CAHIM assay, the HPS-CTMHIV assay showed a high correlation (
R
= 0.99) across the dynamic range of RNA concentrations that, for the CAHIM assay, requires two different sample preparations. Equivalent performances were also observed for the two systems in the detection and quantification of HIV subtypes A to H. These data indicate that the HPS-CTMHIV assay may be one of the tests of choice for monitoring viral load throughout the course of HIV infection and during highly active antiretroviral therapy.
Interlaboratory Study of Quality Control Isolates for a Broth Microdilution Method (Modified CLSI M38-A) for Testing Susceptibilities of Dermatophytes to Antifungals
Authors: Ghannoum M. A. , Arthington-Skaggs B. , Chaturvedi V. , Espinel-Ingroff A. , Pfaller M. A. , Rennie R. , Rinaldi M. G. , Walsh T. J.
Published: December 2006

The Clinical and Laboratory Standards Institute (CLSI; formerly National Committee for Clinical Laboratory Standards, or NCCLS) M38-A standard for the susceptibility testing of filamentous fungi does not specifically address the testing of dermatophytes. In 2003, a multicenter study investigated the reproducibility of the microdilution method developed at the Center for Medical Mycology, Cleveland, Ohio, for testing the susceptibility of dermatophytes. Data from that study supported the introduction of this method for testing dermatophytes in the future version of the CLSI M38-A standard. In order for the method to be accepted by CLSI, appropriate quality control isolates needed to be identified. To that end, an interlaboratory study, involving the original six laboratories plus two additional sites, was conducted to evaluate potential candidates for quality control isolates. These candidate strains included five
Trichophyton rubrum
strains known to have elevated MICs to terbinafine and five
Trichophyton mentagrophytes
strains. Antifungal agents tested included ciclopirox, fluconazole, griseofulvin, itraconazole, posaconazole, terbinafine, and voriconazole. Based on the data generated, two quality control isolates, one
T. rubrum
isolate and one
T. mentagrophytes
isolate, were identified and submitted to the American Type Culture Collection (ATCC) for inclusion as reference strains. Ranges encompassing 95.2 to 97.9% of all data points for all seven drugs were established.
Borrelia burgdorferi
Genetic Markers and Disseminated Disease in Patients with Early Lyme Disease
Authors: Jones Kathryn L. , Glickstein Lisa J. , Damle Nitin , Sikand Vijay K. , McHugh Gail , Steere Allen C.
Published: December 2006

Three genetic markers of
Borrelia burgdorferi
have been associated with disseminated disease: the OspC type, the 16S-23S rRNA intergenic spacer type (RST), and
vlsE
. Here, we modified previous methods so as to identify the three markers by PCR and restriction fragment length polymorphism in parallel, analyzed
B. burgdorferi
isolates from erythema migrans (EM) skin lesions in 91 patients, and correlated the results with evidence of dissemination. OspC type A was found approximately twice as frequently in patients with disseminated disease, whereas type K was identified approximately twice as often in those without evidence of dissemination, but these trends were not statistically significant. The remaining seven types identified were found nearly equally in patients with or without evidence of dissemination. RST 1 strains were significantly associated with dissemination (
P
= 0.03), whereas RST 2 and RST 3 strains tended to have an inverse association with this outcome. The
vlsE
gene was identified in all 91 cases, using primer sets specific for an N-terminal sequence of
B. burgdorferi
strain B31 (
vlsE
B31
) or strain 297 (
vlsE
297
), but neither marker was associated with dissemination. Specific combinations of the three genetic markers usually occurred together. OspC type A was always found with RST 1 and
vlsE
B31
, type K was always identified with RST 2 and more often with
vlsE
297
, and types E and I were almost always found with RST 3 and equally often with
vlsE
B31
and
vlsE
297
. We conclude that
B. burgdorferi
strains vary in their capacity to disseminate, but almost all strains isolated from EM lesions sometimes caused disseminated disease.
Quantification of Genital Human Immunodeficiency Virus Type 1 (HIV-1) DNA in Specimens from Women with Low Plasma HIV-1 RNA Levels Typical of HIV-1 Nontransmitters
Authors: Benki Sarah , McClelland R. Scott , Emery Sandra , Baeten Jared M. , Richardson Barbra A. , Lavreys Ludo , Mandaliya Kishorchandra , Overbaugh Julie
Published: December 2006

Studies of human immunodeficiency virus type 1 (HIV-1) transmission suggest that genital HIV-1 RNA and DNA may both be determinants of HIV-1 infectivity. Despite its potential role in HIV-1 transmission, there are limited quantitative data on genital HIV-1 DNA. Here we validated an in-house real-time PCR method for quantification of HIV-1 DNA in genital specimens. In reactions with 100 genomes to 1 genome isolated from a cell line containing one HIV-1 provirus/cell, this real-time PCR assay is linear and agrees closely with a commercially available real-time PCR assay specific for a cellular housekeeping gene. In mock genital samples spiked with low numbers of HIV-1-infected cells such that the expected HIV-1 DNA copy number/reaction was 100, 10, or 5, the average copy number/reaction was 80.2 (standard deviation [SD], 28.3), 9.1 (SD, 5.4), or 3.1 (SD, 2.1), respectively. We used this method to examine genital HIV-1 DNA levels in specimens from women whose low plasma HIV-1 RNA levels are typical of HIV-1 nontransmitters. The median HIV-1 DNA copy number in endocervical secretions from these women (1.8 HIV-1 DNA copies/10,000 cells) was lower than that for women with higher plasma HIV-1 RNA levels (16.6 HIV-1 DNA copies/10,000 cells) (P= 0.04), as was the median HIV-1 DNA copy number in vaginal secretions (undetectable versus 1.0 HIV-1 DNA copies/10,000 cells). These data suggest that women with low plasma HIV-1 RNA and thus a predicted low risk of HIV-1 transmission have low levels of genital HIV-1 cell-associated virus. The assay described here can be utilized in future efforts to examine the role of cell-associated HIV-1 in transmission.
Presence of the
exoU
Gene of
Pseudomonas aeruginosa
Is Correlated with Cytotoxicity in MDCK Cells but Not with Colonization in BALB/c Mice
Authors: Lin Hsi-Hsun , Huang Shiao-ping , Teng Hsiu-Chen , Ji Dar-Der , Chen Yao-Shen , Chen Ya-Lei
Published: December 2006

A total of 141 independent strains of
Pseudomonas aeruginosa
with different heterogeneities in the
exo
gene (
exoS
,
exoT
,
exoU
, and
exoY
) background were examined for their pathogenic roles. Results indicated that the
exoU
gene is the major contributor to cytotoxicity in Madin-Darby canine kidney cells but is not related to bacterial colonization in mice.
Antimicrobial Susceptibility Patterns and Staphylococcal Cassette Chromosome
mec
Types of, as Well as Panton-Valentine Leukocidin Occurrence among, Methicillin-Resistant
Staphylococcus aureus
Isolates from Children and Adults in Middle Tennessee
Authors: Kilic Abdullah , Li Haijing , Stratton Charles W. , Tang Yi-Wei
Published: December 2006

Antimicrobial susceptibility patterns, Panton-Valentine leukocidin (PVL) occurrence, and staphylococcal cassette chromosome
mec
(SCC
mec
) types in methicillin-resistant
Staphylococcus aureus
(MRSA) strains isolated from children and adults at Vanderbilt University Medical Center during a 12-month period were evaluated. A total of 1,315 MRSA isolates were collected, of which 748 (36.7%) were recovered from children. Among all isolates, 448 (34.1%) were SCC
mec
-II, and 847 (64.4%) were SCC
mec
-IV. More SCC
mec
-IV isolates were recovered from children than SCC
mec
-II isolates (424 [50.1%] versus 50 [11.2%]; odds ration [OR] = 7.98;
P
< 0.000001). The PVL gene was detected in 93.6% of SCC
mec
-IV isolates, in contrast to 0.2% in SCC
mec
-II isolates. Within SCC
mec
-IV isolates, a statistically higher PVL occurrence was noticed in children (98.1%) than in adults (89.1%) (OR = 6.34;
P
< 0.000001). Overall, SCC
mec
-II strains showed greater resistance than SCC
mec
-IV strains to clindamycin, erythromycin, levofloxacin, gentamicin, rifampin, minocycline, and trimethoprim-sulfamethoxazole. Both SCC
mec
-II and SCC
mec
-IV strains recovered from adults were more resistant to these antibiotics than those recovered from children. SCC
mec
-II strains were predominantly recovered from the respiratory tract, whereas SCC
mec
-IV strains were predominantly recovered from skin, soft tissue, abscesses, and surgical wounds. These data indicate that SCC
mec
-IV MRSA isolates frequently infect children in middle Tennessee and are likely to harbor the PVL gene.
Determination of MICs of Aminocandin for
Candida
spp. and Filamentous Fungi
Authors: Isham N. , Ghannoum M. A.
Published: December 2006

Candida
and As
pergillus
spp., as well as other filamentous molds, have increasingly been reported as the causes of severe invasive fungal infections. We evaluated the new echinocandin aminocandin (AMN) for its antifungal activities against a range of fungal pathogens by determination of the MICs for the organisms. The MICs of the comparator drugs amphotericin B, caspofungin, micafungin, and voriconazole were also determined. The MICs of AMN for 25 strains each of non-
Candida albicans Candida
spp. (including
Candida parapsilosis
,
Candida krusei
,
Candida guilliermondii
, and
Candida tropicalis
),
Aspergillus fumigatus
,
Scedosporium
spp.,
Fusarium
spp., and zygomycetes (including
Absidia
,
Mucor
, and
Rhizopus
spp.) were determined by using the Clinical and Laboratory Standards Institute M27-A2 and M38-A methodologies for yeasts and filamentous molds, respectively. The MIC ranges of AMN for all yeasts were similar (0.03 to 4.0 μg/ml), while the MIC ranges of AMN for filamentous fungi were species specific. AMN demonstrated potent antifungal activity against
A. fumigatus
, limited activity against
Scedosporium
spp., and no activity against zygomycetes or
Fusarium
spp. Our data showed that AMN demonstrated potent antifungal activities against all of the yeasts and
Aspergillus
isolates tested, suggesting that AMN could be an important addition to our arsenal of antifungals for the treatment of invasive fungal disease.
A Protein Encoded by the Bovine Herpesvirus 1 Latency-Related Gene Interacts with Specific Cellular Regulatory Proteins, Including CCAAT Enhancer Binding Protein Alpha
Authors: Meyer Florencia , Perez Sandra , Geiser Vicki , Sintek Mark , Inman Melissa , Jones Clinton
Published: December 2006

Following acute infection, bovine herpesvirus 1 establishes latency in sensory neurons of trigeminal ganglia (TG). Reactivation from latency occurs periodically, resulting in the shedding of infectious virus. The latency-related (LR) RNA is abundantly expressed in TG of latently infected calves, and the expression of LR proteins is necessary for dexamethasone-induced reactivation from latency. Previously published studies also identified an alternatively spliced LR transcript which is abundantly expressed in TG at 7 days after infection and has the potential to encode a novel LR fusion protein. Seven days after infection is when extensive viral gene expression is extinguished in TG and latency is established, suggesting that LR gene products influence the establishment of latency. In this study, we used a bacterial two-hybrid assay to identify cellular proteins that interact with the novel LR fusion protein. The LR fusion protein interacts with two proteins that can induce apoptosis (Bid and Cdc42) and with CCAAT enhancer binding protein alpha (C/EBP-α). Additional studies confirmed that the LR fusion protein interacts with human or insect C/EBP-α. C/EBP-α protein expression is induced in TG neurons of infected calves and after dexamethasone-induced reactivation from latency. Wild-type C/EBP-α, but not a DNA binding mutant of C/EBP-α, enhances plaque formation in bovine cells. We hypothesize that interactions between the LR fusion protein and C/EBP-α promote the establishment of latency.
Rapid Reversion of Sequence Polymorphisms Dominates Early Human Immunodeficiency Virus Type 1 Evolution
Authors: Li Bin , Gladden Adrianne D. , Altfeld Marcus , Kaldor John M. , Cooper David A. , Kelleher Anthony D. , Allen Todd M.
Published: December 2006

The error-prone replication of human immunodeficiency virus type 1 (HIV-1) enables it to continuously evade host CD8
+
T-cell responses. The observed transmission, and potential accumulation, of CD8
+
T-cell escape mutations in the population may suggest a gradual adaptation of HIV-1 to immune pressures. Recent reports, however, have highlighted the propensity of some escape mutations to revert upon transmission to a new host in order to restore efficient replication capacity. To more specifically address the role of reversions in early HIV-1 evolution, we examined sequence polymorphisms arising across the HIV-1 genome in seven subjects followed longitudinally 1 year from primary infection. As expected, numerous nonsynonymous mutations were associated with described CD8
+
T-cell epitopes, supporting a prominent role for cellular immune responses in driving early HIV-1 evolution. Strikingly, however, a substantial proportion of substitutions (42%) reverted toward the clade B consensus sequence, with nearly one-quarter of them located within defined CD8 epitopes not restricted by the contemporary host's HLA. More importantly, these reversions arose significantly faster than forward mutations, with the most rapidly reverting mutations preferentially arising within structurally conserved residues. These data suggest that many transmitted mutations likely incur a fitness cost that is recovered through retrieval of an optimal, or ancestral, form of the virus. The propensity of mutations to revert may limit the accumulation of immune pressure-driven mutations in the population, thus preserving critical CD8
+
T-cell epitopes as vaccine targets, and argue against an unremitting adaptation of HIV-1 to host immune pressures.
Examination of a Fusogenic Hexameric Core from Human Metapneumovirus and Identification of a Potent Synthetic Peptide Inhibitor from the Heptad Repeat 1 Region
Authors: Miller Scott A. , Tollefson Sharon , Crowe James E. , Williams John V. , Wright David W.
Published: December 2006

Paramyxoviruses are a leading cause of childhood illness worldwide. A recently discovered paramyxovirus, human metapneumovirus (hMPV), has been studied by our group in order to determine the structural relevance of its fusion (F) protein to other well-characterized viruses utilizing type I integral membrane proteins as fusion aids. Sequence analysis and homology models suggested the presence of requisite heptad repeat (HR) regions. Synthetic peptides from HR regions 1 and 2 (HR-1 and -2, respectively) were induced to form a thermostable (melting temperature, ∼90°C) helical structure consistent in mass with a hexameric coiled coil. Inhibitory studies of hMPV HR-1 and -2 indicated that the synthetic HR-1 peptide was a significant fusion inhibitor with a 50% inhibitory concentration and a 50% effective concentration of ∼50 nM. Many viral fusion proteins are type I integral membrane proteins utilizing the formation of a hexameric coiled coil of HR peptides as a major driving force for fusion. Our studies provide evidence that hMPV also uses a coiled-coil structure as a major player in the fusion process. Additionally, viral HR-1 peptide sequences may need further investigation as potent fusion inhibitors.
Contributions of Two Nuclear Localization Signals of Influenza A Virus Nucleoprotein to Viral Replication
Authors: Ozawa Makoto , Fujii Ken , Muramoto Yukiko , Yamada Shinya , Yamayoshi Seiya , Takada Ayato , Goto Hideo , Horimoto Taisuke , Kawaoka Yoshihiro
Published: December 2006

The RNA genome of influenza A virus, which forms viral ribonucleoprotein complexes (vRNPs) with viral polymerase subunit proteins (PA, PB1, and PB2) and nucleoprotein (NP), is transcribed and replicated in the nucleus. NP, the major component of vRNPs, has at least two amino acid sequences that serve as nuclear localization signals (NLSs): an unconventional NLS (residues 3 to 13; NLS1) and a bipartite NLS (residues 198 to 216; NLS2). Although both NLSs are known to play a role in nuclear transport, their relative contributions to viral replication are poorly understood. We therefore investigated their contributions to NP subcellular/subnuclear localization, viral RNA (vRNA) transcription, and viral replication. Abolishing the unconventional NLS caused NP to localize predominantly to the cytoplasm and affected its activity in vRNA transcription. However, we were able to create a virus whose NP contained amino acid substitutions in NLS1 known to abolish its nuclear localization function, although this virus was highly attenuated. These results indicate that while the unconventional NLS is not essential for viral replication, it is necessary for efficient viral mRNA synthesis. On the other hand, the bipartite NLS, whose contribution to the nuclear transport of NP is limited, was essential for vRNA transcription and NP's nucleolar accumulation. A virus with nonfunctional NLS2 could not be generated. Thus, the bipartite NLS, but not the unconventional NLS, of NP is essential for influenza A virus replication.
Impact of Natural Polymorphism within the gp41 Cytoplasmic Tail of Human Immunodeficiency Virus Type 1 on the Intracellular Distribution of Envelope Glycoproteins and Viral Assembly
Authors: Lambelé Marie , Labrosse Béatrice , Roch Emmanuelle , Moreau Alain , Verrier Bernard , Barin Francis , Roingeard Philippe , Mammano Fabrizio , Brand Denys
Published: December 2006

The motifs involved in the various functions of the human immunodeficiency virus type 1 (HIV-1) gp41 cytoplasmic tail (CT), particularly those related to the intracellular trafficking and assembly of envelope glycoproteins (Env) onto core particles, have generally been assessed with a restricted panel of T-cell laboratory-adapted virus strains. Here, we investigated gp41 CT sequences derived from individuals infected with HIV-1 viruses of various subtypes. We identified four patients harboring HIV variants with a natural polymorphism in the membrane-proximal tyrosine-based signal Y712SPL or the Y802W803diaromatic motif, which are two major determinants of Env intracellular trafficking. Confocal microscopy showed that the intracellular distribution of Env with a mutation in the tyrosine or diaromatic motif differed from that of Env with no mutation in these motifs. Surprisingly, the gp41 CTs of the primary viruses also had differential effects on the intracellular distribution of Env, independently of mutations in the tyrosine or diaromatic motifs, suggesting the involvement of additional determinants. Furthermore, analyses of virus replication kinetics indicated that the effects of mutations in the tyrosine or diaromatic motifs on viral replication depended on the gp41 CT context. These effects were at least partly due to differences in the efficiency of Env incorporation into virions. Thus, polymorphisms in primary HIV-1 gp41 CTs at the quasispecies or subtype level can influence the intracellular distribution of Env, its incorporation into virions, and viral replication capacity.
A review of bioconcentration factor (BCF) and bioaccumulation factor (BAF) assessments for organic chemicals in aquatic organisms
Authors: Arnot Jon A , Gobas Frank APC
Published: December 2006

Bioaccumulation assessment is important in the scientific evaluation of risks that chemicals may pose to humans and the environment and is a current focus of regulatory effort. The status of bioaccumulation evaluations for organic chemicals in aquatic systems is reviewed to reduce uncertainty in bioaccumulation measurement, to provide quality data for assessment, and to assist in model development. A review of 392 scientific literature and database sources includes 5317 bioconcentration factor (BCF) and 1656 bioaccumulation factor (BAF) values measured for 842 organic chemicals in 219 aquatic species. A data quality assessment finds that 45% of BCF values are subject to at least one major source of uncertainty and that measurement errors generally result in an underestimation of actual BCF values. A case study of organic chemicals on the Canadian Domestic Substances List indicates that empirical data are available for less than 4% of the chemicals that require evaluation and of these chemicals, 76% have less than three acceptable quality BCF or BAF values. Field BAFs tend to be greater than laboratory BCFs emphasizing the importance of environmental measurement for reliable assessment; however, only 0.2% of current use organic chemicals have BAF measurements. Key parameters influencing uncertainty and variability in BCF and BAF data are discussed using reviewed data and models. A critical evaluation of representative BCF and BAF models in relation to existing measurements and regulatory criteria in Canada indicate the probability of Type II errors, i.e., false negatives or ``misses'', using BCF models for bioaccumulation assessment may be as high as 70.6% depending on the model. Recommendations for the selection of measured and modelled values used in bioaccumulation assessment are provided, and improvements for the science and regulatory criteria are proposed.Key words: bioconcentration, bioconcentration factor, bioaccumulation, bioaccumulation factor, octanol–water partition coefficient, fish.
Phosphatidylcholine catabolism in the MCF-7 cell cycle
Authors: Lin Weiyang , Arthur Gilbert
Published: December 2006

The catabolism of phosphatidylcholine (PtdCho) appears to play a key role in regulating the net accumulation of the lipid in the cell cycle. Current protocols for measuring the degradation of PtdCho at specific cell-cycle phases require prolonged periods of incubation with radiolabelled choline. To measure the degradation of PtdCho at the S and G2 phases in the MCF-7 cell cycle, protocols were developed with radiolabelled lysophosphatidylcholine (lysoPtdCho), which reduces the labelling period and minimizes the recycling of labelled components. Although most of the incubated lysoPtdCho was hydrolyzed to glycerophosphocholine (GroPCho) in the medium, the kinetics of the incorporation of label into PtdCho suggests that the labelled GroPCho did not contribute significantly to cellular PtdCho formation. A protocol which involved exposing the cells twice to hydroxyurea, was also developed to produce highly synchronized MCF-7 cells with a profile of G1:S:G2/M of 90:5:5. An analysis of PtdCho catabolism in the synchronized cells following labelling with lysoPtdCho revealed that there was increased degradation of PtdCho in early to mid-S phase, which was attenuated in the G2/M phase. The results suggest that the net accumulation of PtdCho in MCF-7 cells may occur in the G2 phase of the cell cycle.
Distinct functional contributions of 2 GABP–NRF-2 recognition sites within the context of the human TOMM70 promoter
Authors: Blesa José R. , Hernández-Yago José
Published: December 2006

TOMM70 is a subunit of the outer mitochondrial membrane translocase that plays a major role as a receptor of hydrophobic preproteins targeted to mitochondria. We have previously reported 2 binding sites for the transcription factor GABP–NRF-2 in the promoter region of the human TOMM70 gene that are important in activating transcription. To assess the functionality and actual role of these sites, chromatin immunoprecipitation, site-directed mutagenesis, and electrophoretic mobility shift assays were carried out. We conclude that GABP–NRF-2 binds in vivo to the TOMM70 promoter, and that the 2 GABP–NRF-2 binding sites of the promoter have different functional contributions in promoting TOMM70 expression. Evidence is provided that they work in an additive manner as single sites.
The Wilms tumour suppressor protein WT1 (+KTS isoform) binds alpha-actinin 1 mRNA via its zinc-finger domain
Authors: Morrison A.A. , Venables J.P. , Dellaire G. , Ladomery M.R.
Published: December 2006

Mutations in WT1 are associated with developmental syndromes that affect the urogenital system and neoplasms, including Wilms tumour, acute myeloid leukemia, and breast and prostate cancers. The WT1 protein belongs to the early growth response family of zinc-finger transcription factors. Uniquely to WT1, an evolutionarily conserved alternative splice event inserts the tripeptide KTS, between zinc fingers 3 and 4. Whereas –KTS isoforms bind DNA and activate or repress transcription, +KTS isoforms bind DNA less efficiently and interact with splice factors and RNA in vitro and in vivo. Although candidate DNA targets have been found, physiological mRNA targets are yet to be defined. We examined the distribution of WT1 in ribonucleoprotein (RNP) complexes in nuclear extract prepared from M15 cells, a mouse mesonephric fetal kidney cell line. WT1 cofractionated with the splice factor PSF in large RNP particles ≥2 MDa. We also found that PSF co-immunoprecipitated with WT1, suggesting a functional interaction between these 2 multifunctional proteins. Using yeast three-hybrid library constructed from the co-immunoprecipitated RNA we found that WT1 (+KTS) binds close to or at the start codon of alpha-actinin 1 (ACTN1) mRNA. A band shift assay confirmed the ability of the WT1 zinc-finger domain (+KTS) to bind this sequence in vitro. ACTN1 is the first likely physiological mRNA target of WT1.
Effects of streptozotocin-induced diabetes mellitus on some bone turnover markers in the vertebrae of ovary-intact and ovariectomized adult rats
Authors: Gopalakrishnan V. , Arunakaran J. , Aruldhas M. M. , Srinivasan N.
Published: December 2006

Diabetes mellitus and estrogen deficit are known causes of osteopenia in animal models as well as in humans. In the present work, the combined effect of ovariectomy and diabetes was investigated. Diabetes was induced in ovary-intact and ovariectomized female Wistar rats with a single injection (50 mg/kg body weight, i.p.) of streptozotocin. The rats were administered insulin (I) daily or 17-β estradiol (E2) on alternate days for a period of 35 days and sacrificed. Serum calcium (Ca2+), phosphorus (P), alkaline phosphatase (ALP), tartrate-resistant acid phosphatase (TRAP), vertebral ALP, collagen, and glycosaminoglycans were estimated. The levels of serum Ca2+and P increased in diabetic rats, but decreased after I or E2treatments. Serum ALP and TRAP activity increased in the ovary-intact and ovariectomized diabetic rats. Vertebral ALP activity increased in ovariectomized diabetic rats, but decreased in diabetic rats, which were treated with I or E2. In the vertebrae, TRAP activity was elevated as a result of diabetes, but this was prevented by insulin or estradiol. Diabetes induced a decrease in total collagen in the vertebrae, while I or E2treatment induced an increase. The levels of chondroitin sulphate and heparan sulphate decreased significantly in the vertebrae of both ovary-intact and ovariectomized diabetic rats, while hyaluronic acid increased. In conclusion, diabetes and ovariectomy each seem to affect the process of matrix formation and mineralization in the bone, and this is aggravated by the combination of diabetes and ovariectomy. The effects of I and E2were similar, and both hormones reversed the changes brought about by diabetes.
Corticosterone impairs the mRNA expression and activity of 3β- and 17β-hydroxysteroid dehydrogenases in adult rat Leydig cells
Authors: Badrinarayanan R. , Rengarajan S. , Nithya P. , Balasubramanian K.
Published: December 2006

Clinical and experimental studies, including our own observations, have shown the adverse effects of excess glucocorticoids on testicular steroid hormone production. The present study was designed to gain insight into the molecular mechanisms by which excess corticosterone impairs Leydig cell steroidogenesis. To achieve this, adult rats were administered with corticosterone-21-acetate (2 mg/100 g body weight) twice daily for 15 days. After the treatment period, rats were killed by decapitation. The testes were removed, decapsulated aseptically and used for the isolation of Leydig cells. Purified Leydig cells were used for assessing the activity of 3β- and 17β-hydroxysteroid dehydrogenases (HSDs) and total RNA isolation. For in vitro studies, purified Leydig cells (7.5 × 106cells) of control rats were plated in culture flasks and exposed to different concentrations (50, 100, 200, 400, and 800 nmol/L) of corticosterone for 24 h. At the end of incubation, total RNA was isolated from cultured Leydig cells, and the mRNA of 3β- and 17β-HSDs was quantified by RT–PCR. A significant reduction in the activities and levels of 3β-HSD type-I and 17β-HSD type-III mRNAs in Leydig cells were observed. In vitro studies demonstrated a dose-dependent significant impairment in both the activity and mRNA expression of these enzymes. These results suggest that corticosterone might have a direct effect on the transcription of the genes of 3β- and 17β-HSD. It is inferred from the present in vivo and in vitro studies that one of the molecular mechanisms by which excess corticosterone decreases the steroidogenic potency of Leydig cells is by suppressing the mRNA expression of 3β-HSD type-I and 17β-HSD type-III enzymes.
Aminonaphthoquinone induces oxidative stress inStaphylococcus aureus
Authors: Medina L.F.C. , Hertz P.F. , Stefani V. , Henriques J.A.P. , Zanotto-Filho A. , Brandelli A.
Published: December 2006

The biological activity of 5-amino-8-hydroxy-1,4-naphthoquinone (ANQ) on Staphylococcus aureus was investigated in comparison with the unsubstituted 1,4-naphthoquinone (NQ). Complete inhibition of microbial growth was observed with ANQ and NQ at 50 and 10 µg/mL, respectively. The antibacterial effect of naphthoquinones decreased in the presence of sodium ascorbate, but the superoxide scavenger 4,5-dihydroxy-1,3-benzene-disulfonic acid (Tiron) was able to protect S. aureus only from the harmful effect of ANQ. Naphthoquinones blocked oxygen uptake and induced cyanide-insensitive oxygen consumption. When combining rotenone or salicylhydroxamic acid with ANQ or NQ, a slight decrease in respiratory activity was observed. Assays in the presence of naphthoquinones induced an increase of lipid peroxidation in S. aureus, as determined by thiobarbituric acid reactive substances. These results showed that 1,4-naphthoquinones effectively act as electron acceptors and induce an increase in reactive oxygen species that are toxic to S. aureus cells.
The functional response of U937 macrophage-like cells is modulated by extracellular matrix proteins and mechanical strain
Authors: Matheson Loren A. , Maksym Geoffrey N. , Santerre J. Paul , Labow Rosalind S.
Published: December 2006

Extracellular matrix proteins (ECMs) play a significant role in the transfer of mechanical strain to monocyte-derived macrophages (MDMs) affecting morphological changes in a foreign body reaction. This study investigated how the functional responses of U937 macrophage-like cells differed when subjected to 2 dynamic strain types (nonuniform biaxial or uniform uniaxial strain) while cultured on siloxane membranes coated with either collagen type I or RGD peptide repeats (ProNectin®). Biaxial strain caused an increase in intracellular esterase and acid phosphatase (AP) activities, as well as monocyte-specific esterase (MSE) protein levels in cells that were seeded on either uncoated surfaces (shown previously) or collagen, but not ProNectin®. Released AP activity, but not released esterase activity, was increased on all surfaces. Biaxial strain increased IL-6, but not IL-8 on all surfaces. When cells were subjected to uniaxial strain, intracellular esterase increased on coated surfaces only, whereas intracellular AP activity was unaffected. Both esterase and AP released activities increased on all surfaces. Uniaxial strain increased the release of IL-6 on all surfaces, but IL-8 on coated surfaces only. This study demonstrated for the first time that ECM proteins could specifically modulate cellular responses to different types of strain. Using this approach with an in vitro cell system may help to unravel the complex function of MDMs in the foreign-body reaction.
A SIMPLE ALPHABET-INDEPENDENT FM-INDEX
Authors: GRABOWSKI SZYMON , NAVARRO GONZALO , PRZYWARSKI RAFAŁ , SALINGER ALEJANDRO , MÄKINEN VELI
Published: December 2006

We design a succinct full-text index based on the idea of Huffman-compressing the text and then applying the Burrows-Wheeler transform over it. The resulting structure can be searched as an FM-index, with the benefit of removing the sharp dependence on the alphabet size, σ, present in that structure. On a text of length n with zero-order entropy H0, our index needs O(n(H0 + 1)) bits of space, without any significant dependence on σ. The average search time for a pattern of length m is O(m(H0 + 1)), under reasonable assumptions. Each position of a text occurrence can be located in worst case time O((H0 + 1) log n), while any text substring of length L can be retrieved in O((H0 + 1)L) average time in addition to the previous worst case time. Our index provides a relevant space/time tradeoff between existing succinct data structures, with the additional interest of being easy to implement. We also explore other coding variants alternative to Huffman and exploit their synchronization properties. Our experimental results on various types of texts show that our indexes are highly competitive in the space/time tradeoff map.
INTERACTING BUSINESS CYCLE FLUCTUATIONS: A TWO-COUNTRY MODEL
Authors: CHIARELLA CARL , FLASCHEL PETER , HUNG HING
Published: December 2006

In this paper, we develop a model of business cycle fluctuations between two interacting open economies within the disequilibrium or non-market clearing paradigm. We analyze the main feedback mechanisms (Keynes, Mundell, Rose and Dornbusch) driving the dynamics and the conflict between their stabilizing and destabilizing tendencies and how these depend on certain key speeds of adjustment in the real and foreign exchange sectors. We explore numerically a variety of situations of interacting price cycles in the two countries, where the steady state is locally repelling, but where the overall dynamics are bounded in an economically meaningful domain by assuming downward money wage rigidity.
THE STATE-AND-SPEED OF THE ECONOMIES IN ASEAN-5: A GEOMETRY ANALYSIS
Authors: KWEK KIAN-TENG , CHO CHO-WAI
Published: December 2006

The many unique findings on economic growth studies by the flying geese analysis (Kwan, 1994), the convergence-catching-up analysis (Lim and McAleer, 2003), and competitive index rankings by the World Economic Forum (WEF) and the International Institute for Management Development (IMD), all provide country rankings and comparisons only on one plane, i.e., to determine which country is doing best, better or worst. But we introduce a new measurement based on geometric planes that enables us to measure the "state and speed of the economy", to determine the actual "economic size" due to policy actions, and to evaluate macroeconomic policies' effectiveness and coherence in producing real economic growth.
A NOTE ON THE CORRELATION RELATIONSHIP AMONG SINGAPORE, HONG KONG AND THE US CAPITAL MARKETS SINCE THE HONG KONG HANDOVER: IMPLICATION FOR INTERNATIONAL PORTFOLIO MANAGEMENT
Authors: CHAN LEO H.
Published: December 2006

In this note, I document the change in correlation between Hong Kong, Singapore and the US financial market indexes using Geweke Measures after the handover of Hong Kong to China. The results show that these relationships have changed significantly. While the feedback relationship between Hong Kong, Singapore and the US markets increase after the handover of Hong Kong, the increases in feedback relationship between Singapore and the US markets is relatively higher compared to the change between Hong Kong and the US markets.
Current Status of the Myriapod Class Diplopoda (Millipedes): Taxonomic Diversity and Phylogeny
Authors: Sierwald Petra , Bond Jason E.
Published: December 2006

The arthropod class Diplopoda, the millipedes, ranks among the most diverse groups of terrestrial organisms, with over 12,000 species described. Although they play an important ecological role in most terrestrial ecosystems, little is known about the group's diversity, morphology, and phylogeny compared with other arthropod groups. We review diplopod natural history and discuss the historical and current literature pertaining to millipede morphology, ecology, chemical defenses, and the paleontological record of the group's ancient history. Diplopod systematics, past and present, are reviewed with a focus on taxonomy, collections, and biogeography. The phylogenetics of the class is reviewed, with particular attention on diplopod placement within the Myriapoda and emphasis on recent advances using molecular approaches to phylogenetic reconstruction. We present (a) the first combined morphological and molecular analysis of the millipede orders, and (b) a list of critically evaluated characteristics of nominal clades identifying putative apomorphies.
Sexual dimorphism of ornithine decarboxylase in the mouse adrenal: influence of polyamine deprivation on catecholamine and corticoid levels
Authors: Bastida Carmen M. , Cremades Asunción , Castells Maria T. , López-Contreras Andrés J. , López-García Carlos , Sánchez-Mas Jesús , Peñafiel Rafael
Published: December 2006

Adrenal sexual dimorphism is thought to be important in explaining sex-related differences regarding prevalent diseases and the responses to stress and drugs. We report here that in CD1 mice there is marked sexual dimorphism affecting not only gland size and corticoid hormone secretion but also adrenal ornithine decarboxylase (ODC), polyamine, and catecholamine levels in which testosterone appears to be a major determinant. Our results show that adrenal weight, ODC activity, and corticosterone and aldosterone secretion were higher in female than in male mice and that orchidectomy brought these male parameters closer to the values found in females. mRNA levels of steroidogenic proteins SF-1, Dax-1, steroid 21-hydroxylase, and aldosterone synthase appeared to be slightly higher in female than in male adrenals. Immunocytochemical analysis of adrenal ODC revealed that immunoreactivity was higher in females than in males and was located mainly in the cortical cells, and especially in zona glomerulosa, whereas no sex differences in ODC mRNA levels were observed. These results suggest that sex-associated differences in the expression of ODC in the mouse adrenal gland appear to be related mainly to posttranscriptional mechanisms. Combination treatment of mice with α-difluoromethylornithine (a suicide inhibitor of ODC) and a polyamine-deficient diet produced a marked decrease in adrenal polyamine and catecholamine levels and a significant reduction in plasma corticosterone and aldosterone concentrations that were not associated with a decrease in the mRNA levels of steroidogenic proteins. All of these data suggest a relevant role for testosterone, ODC, and polyamines in the mouse adrenal function.
Progesterone-induced sphingosine kinase-1 expression in the rat uterus during pregnancy and signaling consequences
Authors: Jeng Yow-Jiun , Suarez Victor R. , Izban Michael G. , Wang Hui-Qun , Soloff Melvyn S.
Published: December 2006

Sphingosine 1-phosphate (Sph-1- P), a product of sphingomyelin metabolism, can act via a family of cognate G protein-coupled receptors or as an intracellular second messenger for agonists acting through their membrane receptors. In view of the general growth promoting and developmental effects of Sph-1- P on target cells, we hypothesized that it plays a role in adaptation of the uterus to pregnancy. We analyzed its potential role and that of the related lysophospholipid lysophosphatidic acid in the pregnant rat uterus by examining changes in mRNA levels of cognate receptors and enzymes involved in their turnover. Of these, only sphingosine kinase-1 (SphK1) was markedly changed (∼30-fold increase), being localized in the glandular epithelium, vasculature, and the myometrium. Uterine SphK1 mRNA and protein levels paralleled those of serum progesterone, and treatment with progesterone or an antagonist elevated or reduced SphK1 mRNA expression, respectively. Progesterone also increased SphK1 mRNA steady-state levels in a rat myometrial/leiomyoma cell line (ELT3). Overexpressing human SphK1 in these cells resulted in increased levels of the cell cycle regulator cyclin D1 and increased myosin light-chain phosphorylation. Ectopic expression of SphK1 also resulted in increased proliferation rates, possibly in conjunction with increased cyclin D1 expression. These studies suggest that the uterine expression of SphK1 mediates processes involved in growth and differentiation of uterine tissues during pregnancy.
PPARα activation reverses adverse effects induced by high-saturated-fat feeding on pancreatic β-cell function in late pregnancy
Authors: Holness Mark J. , Smith Nicholas D. , Greenwood Gemma K. , Sugden Mary C.
Published: December 2006

We examined whether the additional demand for insulin secretion imposed by dietary saturated fat-induced insulin resistance during pregnancy is accommodated at late pregnancy, already characterized by insulin resistance. We also assessed whether effects of dietary saturated fat are influenced by PPARα activation or substitution of 7% of dietary fatty acids (FAs) with long-chain ω-3 FA, manipulations that improve insulin action in the nonpregnant state. Glucose tolerance at day 19 of pregnancy in the rat was impaired by high-saturated-fat feeding throughout pregnancy. Despite modestly enhanced glucose-stimulated insulin secretion (GSIS) in vivo, islet perifusions revealed an increased glucose threshold and decreased glucose responsiveness of GSIS in the saturated-fat-fed pregnant group. Thus, insulin resistance evoked by dietary saturated fat is partially countered by augmented insulin secretion, but compensation is compromised by impaired islet function. Substitution of 7% of saturated FA with long-chain ω-3 FA suppressed GSIS in vivo but did not modify the effect of saturated-fat feeding to impair GSIS by perifused islets. PPARα activation (24 h) rescued impaired islet function that was identified using perifused islets, but GSIS in vivo was suppressed such that glucose tolerance was not improved, suggesting modification of the feedback loop between insulin action and secretion.
(−)-Catechin suppresses expression of Kruppel-like factor 7 and increases expression and secretion of adiponectin protein in 3T3-L1 cells
Authors: Cho Si Young , Park Pil Joon , Shin Hyun Jung , Kim Young-Kyung , Shin Dong Wook , Shin Eui Seok , Lee Hyoung Ho , Lee Byeong Gon , Baik Joo-Hyun , Lee Tae Ryong
Published: December 2006

Adiponectin is an adipocyte-specific secretory hormone that can increase insulin sensitivity and promote adipocyte differentiation. Administration of adiponectin to obese or diabetic mice reduces plasma glucose and free fatty acid levels. Green tea polyphenols possess many pharmacological activities such as antioxidant, anti-inflammatory, antiobesity, and antidiabetic activities. To investigate whether green tea polyphenols have an effect on the regulation of adiponectin, we measured expression and secretion levels of adiponectin protein after treatment of each green tea polyphenols in 3T3-L1 adipocytes. We found that (−)-catechin enhanced the expression and secretion of adiponectin protein in a dose- and time-dependent manner. Furthermore, treatment of (−)-catechin increased insulin-dependent glucose uptake in differentiated adipocytes and augmented the expression of adipogenic marker genes, including PPARγ, CEBPα, FAS, and SCD-1, when (−)-catechin was treated during adipocyte differentiation. In search of the molecular mechanism responsible for inducible effect of (−)-catechin on adiponectin expression, we found that (−)-catechin markedly suppresses the expression of Kruppel-like factor 7 (KLF7) protein, which has recently been reported to inhibit the expression of adiponectin and other adipogenesis related genes, including leptin, PPARγ, C/EBPα, and aP2 in adipocytes. KLF7 is a transcription factor in adipocyte and plays an important role in the pathogenesis of type 2 diabetes. Taken together, these data suggest that the upregulation of adiponectin protein by (−)-catechin may involve, at least in part, suppression of KLF7 in 3T3-L1 cells.
Aging results in paradoxical susceptibility of fat cell progenitors to lipotoxicity
Authors: Guo Wen , Pirtskhalava Tamar , Tchkonia Tamara , Xie Weisheng , Thomou Thomas , Han Jianrong , Wang Tong , Wong Siu , Cartwright Andrew , Hegardt Fausto G. , Corkey Barbara E. , Kirkland James L.
Published: December 2006

Aging is associated with metabolic syndrome, tissue damage by cytotoxic lipids, and altered fatty acid handling. Fat tissue dysfunction may contribute to these processes. This could result, in part, from age-related changes in preadipocytes, since they give rise to new fat cells throughout life. To test this hypothesis, preadipocytes cultured from rats of different ages were exposed to oleic acid, the most abundant fatty acyl moiety in fat tissue and the diet. At fatty acid concentrations at which preadipocytes from young animals remained viable, cells from old animals accumulated lipid in multiple small lipid droplets and died, with increased apoptotic index, caspase activity, BAX, and p53. Rather than inducing apoptosis, oleic acid promoted adipogenesis in preadipocytes from young animals, with appearance of large lipid droplets. CCAAT/enhancer-binding protein-α (C/EBPα) and peroxisome proliferator-activated receptor-γ (PPARγ) increased to a greater extent in cells from young than old animals after oleate exposure. Oleic acid, but not glucose, oxidation was impaired in preadipocytes and fat cells from old animals. Expression of carnitine palmitoyltransferase (CPT)-1, which catalyzes the rate-limiting step in fatty acid β-oxidation, was not reduced in preadipocytes from old animals. At lower fatty acid levels, constitutively active CPT I expression enhanced β-oxidation. At higher levels, CPT I was not as effective in enhancing β-oxidation in preadipocytes from old as young animals, suggesting that mitochondrial dysfunction may contribute. Consistent with this, medium-chain acyl-CoA dehydrogenase expression was reduced in preadipocytes from old animals. Thus preadipocyte fatty acid handling changes with aging, with increased susceptibly to lipotoxicity and impaired fatty acid-induced adipogenesis and β-oxidation.