bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptional Regulation of the
pdt
Gene Cluster of
Pseudomonas stutzeri
KC Involves an AraC/XylS Family Transcriptional Activator (PdtC) and the Cognate Siderophore Pyridine-2,6-Bis(Thiocarboxylic Acid)
Authors: Morales Sergio E. , Lewis Thomas A. 
Published: November 2006

ABSTRACT

In order to gain an understanding of the molecular mechanisms dictating production of the siderophore and dechlorination agent pyridine-2,6-bis(thiocarboxylic acid) (PDTC), we have begun characterization of a gene found in the
pdt
gene cluster of
Pseudomonas stutzeri
KC predicted to have a regulatory role. That gene product is an AraC family transcriptional activator, PdtC. Quantitative reverse transcription-PCR and expression of transcriptional reporter fusions were used to assess a role for
pdtC
in the transcription of
pdt
genes. PdtC and an upstream, promoter-proximal DNA segment were required for wild-type levels of expression from the promoter of a predicted biosynthesis operon (P

pdt
F

). At least two other transcriptional units within the
pdt
cluster were also dependent upon
pdtC
for expression at wild-type levels. The use of a heterologous,
Pseudomonas putida
host demonstrated that
pdtC
and an exogenously added siderophore were necessary and sufficient for expression from the
pdtF
promoter, i.e., none of the PDTC utilization genes within the
pdt
cluster were required for transcriptional signaling. Tests using the promoter of the
pdtC
gene in transcriptional reporter fusions indicated siderophore-dependent negative autoregulation similar to that seen with other AraC-type regulators of siderophore biosynthesis and utilization genes. The data increase the repertoire of siderophore systems known to be regulated by this type of transcriptional activator and have implications for PDTC signaling.
Fermentation of High Concentrations of Maltose by
Saccharomyces cerevisiae
Is Limited by the COMPASS Methylation Complex
Authors: Houghton-Larsen Jens , Brandt Anders 
Published: November 2006

ABSTRACT

In
Saccharomyces cerevisiae
, genes encoding maltose permeases and maltases are located in the telomeric regions of different chromosomes. The COMPASS methylation complex, which methylates lysine 4 on histone H3, controls the silencing of telomeric regions. Yeast strains deleted for
SWD1
,
SWD3
,
SDC1
,
SET1
,
BRE2
, or
SPP1
, encoding components of the COMPASS complex, fermented a medium containing 22% maltose with noticeably higher attenuation than did the wild type, resulting in production of up to 29% more ethanol. The least effective strain was
spp1
. Absence of COMPASS components had no effect on the fermentation of media with 20% glucose, 20% sucrose, or 16% maltose. Deletion of
SWD3
resulted in larger amounts of
MAL12
transcript, encoding maltase, at the late stages of fermentation of 22% maltose. A similar effect on maltase activity and maltose uptake capability was seen. The lysine 4 residue of histone H3 was trimethylated in wild-type cells at the late stages, while only small amounts of the dimethylated form were detected. Trimethylation and dimethylation of this residue were not detected in strains deleted for
SWD1
,
SWD3
,
SET1
,
BRE2
, or
SDC1
. Trimethylated lysine 4 was apparent only at the early stages (48 and 96 h) of fermentation in an
spp1
strain. This work indicates that the COMPASS complex represses the expression of maltose utilization genes during the late stages of fermentation of a high concentration of maltose.
Molecular Characterization of
Cryptosporidium
spp. from Children in Kolkata, India
Authors: Das Pradeep , Roy Seuli Saha , MitraDhar Kakali , Dutta Phalguni , Bhattacharya Mihir K. , Sen Abhik , Ganguly Sandipan , Bhattacharya Sujit K. , Lal Altaf A. , Xiao Lihua 
Published: November 2006

ABSTRACT

The intracellular parasite
Cryptosporidium
is responsible for severe diarrhea in immunocompromised persons in developing countries. Few studies on the characterization of the parasite in India are available. In this study, molecular characterization of the parasite from diarrheic children was carried out by PCR-restriction fragment length polymorphism analysis. At least three genotypes were identified. Out of 40 positive samples, 35 were positive for
C. hominis
, 4 were positive for
C. parvum
, and 1 was positive for
C. felis
. This study clearly suggests that cryptosporidiosis in this region is caused largely by anthroponotic transmission.
High Prevalence of Human Enterovirus A Infections in Natural Circulation of Human Enteroviruses
Authors: Witsø Elisabet , Palacios Gustavo , Cinek Ondrej , Stene Lars C. , Grinde Bjørn , Janowitz Diana , Lipkin W. Ian , Rønningen Kjersti S. 
Published: November 2006

ABSTRACT
Human enterovirus (HEV) infections can be asymptomatic or cause only mild illness; recent evidence may implicate HEV infection in type 1 diabetes mellitus and myocarditis. Here, we report the molecular characterization of HEV obtained in serial monthly collections from healthy Norwegian infants. A total of 1,255 fecal samples were collected from 113 healthy infants beginning at age 3 months and continuing to 28 months. The samples were analyzed for HEV nucleic acid by real-time PCR. Fifty-eight children (51.3%) had HEV infections. One hundred forty-five positive samples were typed directly by nucleotide sequencing of the VP1 region. HEV-A was detected most frequently, with an overall prevalence of 6.8%. HEV-B was present in 4.8% of the samples and HEV-C in only 0.2% of the samples. No poliovirus or HEV-D group viruses were detected. Twenty-two different serotypes were detected in the study period: the most common were EV71 (14.5%), CAV6 (10.5%), CAV4 (8.9%), E18 (8.9%), and CBV3 (7.3%). These findings suggest that the prevalence of HEV infections in general, and HEV-A infections in particular, has been underestimated in epidemiological studies based on virus culture.
Comparison of a PCR-Restriction Fragment Length Polymorphism (PCR-RFLP) Assay to Pulsed-Field Gel Electrophoresis To Determine the Effect of Repeated Subculture and Prolonged Storage on RFLP Patterns of Shiga Toxin-Producing
Escherichia coli
O157:H7
Authors: Shima Kensuke , Wu Yuluo , Sugimoto Norihiko , Asakura Masahiro , Nishimura Kazuhiko , Yamasaki Shinji 
Published: November 2006

ABSTRACT

In this study, we compared a recently developed PCR-restriction fragment length polymorphism (PCR-RFLP) assay with pulsed-field gel electrophoresis (PFGE) using three different Shiga toxin-producing
Escherichia coli
(STEC) strains to understand whether repeated subculture in vitro and prolonged storage at room temperature affect the RFLP patterns of STEC. The PFGE profiles of the STEC strains changed by 1 to 8 fragments after repeated subculture and prolonged storage; one strain was no longer clonal after repeated subculture compared to the original isolate according to the Tenover criteria. In contrast, RFLP patterns obtained by PCR-RFLP were identical after repeated subculture and prolonged storage. These data clearly indicate that the PCR-RFLP assay which is based on the diversity of region V, a regulatory region of Stx-phage, was not affected by repeated subculture and prolonged storage and is a more practical and reliable method for molecular typing of STEC strains.
Effects of
Bifidobacterium lactis
Bb12 Supplementation on Intestinal Microbiota of Preterm Infants: a Double-Blind, Placebo-Controlled, Randomized Study
Authors: Mohan Ruchika , Koebnick Corinna , Schildt Janko , Schmidt Sabine , Mueller Manfred , Possner Mike , Radke Michael , Blaut Michael 
Published: November 2006

ABSTRACT

The gastrointestinal microbiota of preterm infants in a neonatal intensive care unit differs from that of term infants. In particular, the colonization of preterm infants by bifidobacteria is delayed. A double-blind, placebo-controlled, randomized clinical study was performed on 69 preterm infants to investigate the role of
Bifidobacterium lactis
Bb12 supplementation in modifying the gut microbiota. Both culture-dependent and culture-independent approaches were used to study the gut microbiota. Bifidobacterial numbers, determined by fluorescence in situ hybridization, were significantly higher in the probiotic than in the placebo group (log
10
values per g of fecal wet weight: probiotic, 8.18 + 0.54 [standard error of the mean]; placebo, 4.82 + 0.51;
P
< 0.001). A similar trend for bifidobacterial numbers was also obtained with the culture-dependent method. The infants supplemented with Bb12 also had lower viable counts of
Enterobacteriaceae
(log
10
values of CFU per g of fecal wet weight: probiotic, 7.80 + 0.34; placebo, 9.03 + 0.35;
P
= 0.015) and
Clostridium
spp. (probiotic, 4.89 + 0.30; placebo, 5.99 + 0.32;
P
= 0.014) than the infants in the placebo group. Supplementation of
B. lactis
Bb12 did not reduce the colonization by antibiotic-resistant organisms in the study population. However, the probiotic supplementation increased the cell counts of bifidobacteria and reduced the cell counts of enterobacteria and clostridia.
In Vitro Antifungal-Drug Susceptibilities of Mycelial and Yeast Forms of
Penicillium marneffei
Isolates in Cambodia
Authors: Sar Borann , Boy Sambo , Keo Chantary , Ngeth Chan Chhaya , Prak Narom , Vann Mich , Monchy Didier , Sarthou Jean Louis 
Published: November 2006

ABSTRACT

Penicillium marneffei
infection is an important disease among human immunodeficiency virus patients in Southeast Asia. The in vitro antifungal-drug susceptibilities of 29 clinical isolates and 5 isolates from bamboo rats collected from 2002 to 2004 were determined. The
P. marneffei
yeast form is more susceptible than the mycelial form to amphotericin B and ketoconazole, while the mycelial and yeast forms displayed similar susceptibilities to flucytosine and itraconazole. The MICs of fluconazole were higher for both mycelial and yeast forms.
Detection of Rare G3P[19] Porcine Rotavirus Strains in Chiang Mai, Thailand, Provides Evidence for Origin of the VP4 Genes of Mc323 and Mc345 Human Rotaviruses
Authors: Maneekarn Niwat , Khamrin Pattara , Chan-it Wisoot , Peerakome Supatra , Sukchai Sujin , Pringprao Kidsadagon , Ushijima Hiroshi 
Published: November 2006

ABSTRACT
Among 175 fecal specimens collected from diarrheic piglets during a surveillance of porcine rotavirus (PoRV) strains in Chiang Mai, Thailand, 39 (22.3%) were positive for group A rotaviruses. Of these, 33.3% (13 of 39) belonged to G3P[19], which was a rare P genotype seldom reported. Interestingly, their VP4 nucleotide sequences were most closely related to human P[19] strains (Mc323 and Mc345) isolated in 1989 from the same geographical area where these PoRV strains were isolated. These P[19] PoRV strains were also closely related to another human P[19] strain (RMC321), isolated from India in 1990. The VP4 sequence identities with human P[19] were 95.4% to 97.4%, while those to a porcine P[19] strain (4F) were only 87.6 to 89.1%. Phylogenetic analysis of the VP4 gene revealed that PoRV P[19] strains clustered with human P[19] strains in a monophyletic branch separated from strain 4F. Analysis of the VP7 gene confirmed that these strains belonged to the G3 genotype and shared 97.7% to 98.3% nucleotide identities with other G3 PoRV strains circulating in the regions. This close genetic relationship was also reflected in the phylogenetic analysis of their VP7 genes. Altogether, the findings provided peculiar evidence that supported the porcine origin of VP4 genes of Mc323 and Mc345 human rotaviruses.
Genotyping Hepatitis C Viruses from Southeast Asia by a Novel Line Probe Assay That Simultaneously Detects Core and 5′ Untranslated Regions
Authors: Noppornpanth Suwanna , Sablon Erwin , De Nys Kathy , Lien Truong Xuan , Brouwer Jan , Van Brussel Marianne , Smits Saskia L. , Poovorawan Yong , Osterhaus Albert D. M. E. , Haagmans Bart L. 
Published: November 2006

ABSTRACT
Hepatitis C viruses (HCVs) display a high level of sequence diversity and are currently divided into six genotypes. A line probe assay (LiPA), which targets the 5′ untranslated region (5′UTR) of the HCV genome, is widely used for genotyping. However, this assay cannot distinguish many genotype 6 subtypes from genotype 1 due to high sequence similarity in the 5′UTR. We investigated the accuracy of a new generation LiPA (VERSANT HCV genotype 2.0 assay), in which genotyping is based on 5′UTR and core sequences, by testing 75 selected HCV RNA-positive sera from Southeast Asia (Vietnam and Thailand). For comparison, sera were tested on the 5′UTR based VERSANT HCV genotype assay and processed for sequence analysis of the 5′UTR-to-core and NS5b regions as well. Phylogenetic analysis of both regions revealed the presence of genotype 1, 2, 3, and 6 viruses. Using the new LiPA assay, genotypes 6c to 6l and 1a/b samples were more accurately genotyped than with the previous test only targeting the 5′UTR (96% versus 71%, respectively). These results indicate that the VERSANT HCV genotype 2.0 assay is able to discriminate genotypes 6c to 6l from genotype 1 and allows a more accurate identification of genotype 1a from 1b by using the genotype-specific core information.
Pyrosequencing, a High-Throughput Method for Detecting Single Nucleotide Polymorphisms in the Dihydrofolate Reductase and Dihydropteroate Synthetase Genes of
Plasmodium falciparum
Authors: Zhou Zhiyong , Poe Amanda C. , Limor Josef , Grady Katharine K. , Goldman Ira , McCollum Andrea M. , Escalante Ananias A. , Barnwell John W. , Udhayakumar Venkatachalam 
Published: November 2006

ABSTRACT

A pyrosequencing protocol was developed as a rapid and reliable method to identify the mutations of the
dhfr
and
dhps
genes of
Plasmodium falciparum
that are associated with antifolate resistance. The accuracy and specificity of this method were tested using six laboratory-cultured
P. falciparum
isolates harboring known single nucleotide polymorphisms (SNPs) in the genes
dhfr
(codons 50, 51, 59, 108, and 164) and
dhps
(codons 436, 437, 540, 581, and 613). The lowest threshold for detection of all the SNPs tested by pyrosequencing was the equivalent of two to four parasite genomes. Also, this method was highly specific for
P. falciparum
, as it did not amplify any DNA products from the other species of human malaria parasites. We also mixed wild-type and mutant-type parasite DNAs in various proportions to determine how pyrosequencing, restriction fragment length polymorphism (RFLP), and direct conventional sequencing (for
dhfr
) compared with each other in detecting different SNPs in the mixture. In general, pyrosequencing and RFLP showed comparable sensitivities in detecting most of the SNPs in
dhfr
except for the 164L mutation, which required at least twice the amount of DNA for pyroseqencing as for RFLP. For detecting SNPs in
dhps
, pyrosequencing was slightly more sensitive than RFLP and direct sequencing. Overall, pyrosequencing was faster and less expensive than either RFLP or direct sequencing. Thus, pyrosequencing is a practical alternative method that can be used in a high-throughput format for molecular surveillance of antimalarial-drug resistance.
MultiCode-RTx Real-Time PCR System for Detection of Subpopulations of K65R Human Immunodeficiency Virus Type 1 Reverse Transcriptase Mutant Viruses in Clinical Samples
Authors: Svarovskaia Evguenia S. , Moser Michael J. , Bae Andrew S. , Prudent James R. , Miller Michael D. , Borroto-Esoda Katyna 
Published: November 2006

ABSTRACTWe report a real-time PCR assay capable of detecting drug-resistant human immunodeficiency virus type 1 reverse transcriptase K65R mutant virus at a level of 0.5% in polymorphic patient plasma specimens. Fifty-three treatment-naïve and 20 treatment-experienced specimens were successfully genotyped with the new method. Results were in agreement with population sequencing and the labor-intensive single-genome sequencing method.
Diametrically contractive maps and fixed points
Authors: Baronti Marco , Casini Emanuele , Papini Pier Luigi 
Published: November 2006

AbstractContractive maps have nice properties concerning fixed points; a big amount of literature has been devoted to fixed points of nonexpansive maps. The class of shrinking (or strictly contractive) maps is slightly less popular: few specific results on them (not applicable to all nonexpansive maps) appear in the literature and some interesting problems remain open. As an attempt to fill this gap, a condition half way between shrinking and contractive maps has been studied recently. Here we continue the study of the latter notion, solving some open problems concerning these maps.
Strong convergence theorems for asymptotically nonexpansive mappings and asymptotically nonexpansive semigroups
Authors: Su Yongfu , Qin Xiaolong 
Published: November 2006

AbstractStrong convergence theorems are obtained from modified Halpern iterative scheme for asymptotically nonexpansive mappings and asymptotically nonexpansive semigroups, respectively. Our results extend and improve the recent ones announced by Nakajo, Takahashi, Kim, Xu, and some others.
Coevolution of Down-Valley Flow and the Nocturnal Boundary Layer in Complex Terrain
Authors: Pinto J. O. , Parsons D. B. , Brown W. O. J. , Cohn S. , Chamberlain N. , Morley B. 
Published: November 2006

AbstractAn enhanced National Center for Atmospheric Research (NCAR) integrated sounding system (ISS) was deployed as part of the Vertical Transport and Mixing (VTMX) field experiment, which took place in October of 2000. The enhanced ISS was set up at the southern terminus of the Great Salt Lake Valley just north of a gap in the Traverse Range (TR), which separates the Great Salt Lake and Utah Lake basins. This location was chosen to sample the dynamic and thermodynamic properties of the flow as it passes over the TR separating the two basins. The enhanced ISS allowed for near-continuous sampling of the nocturnal boundary layer (NBL) and low-level winds associated with drainage flow through the gap in the TR. Diurnally varying winds were observed at the NCAR site on days characterized by weak synoptic forcing and limited cloud cover. A down-valley jet (DVJ) was observed on about 50% of the nights during VTMX, with the maximum winds usually occurring within 150 m of the surface. The DVJ was associated with abrupt warming at low levels as a result of downward mixing and vertical transport of warm air from the inversion layer above. Several processes were observed to contribute to vertical transport and mixing at the NCAR site. Pulses in the strength of the DVJ contributed to vertical transport by creating localized areas of low-level convergence. Gravity waves and Kelvin–Helmholtz waves, which facilitated vertical mixing near the surface and atop the DVJ, were observed with a sodar and an aerosol backscatter lidar that were deployed as part of the enhanced ISS. The nonlocal nature of the processes responsible for generating turbulence in strongly stratified surface layers in complex terrain confounds surface flux parameterizations typically used in mesoscale models that rely on Monin–Obukhov similarity theory. This finding has major implications for modeling NBL structure and drainage flows in regions of complex terrain.
Characterization of T-cell population in children with prolonged fetal exposure to dexamethasone for anti-Ro/SS-A antibodies associated congenital heart block
Authors: Airó P , Scarsi M , Brucato A , Benicchi T , Malacarne F , Cavazzana I , Danieli E , LiDestri M , Motta M , Caimi L , Tincani A , Imberti L 
Published: November 2006

The objectives of the study were to characterize the production, function and survival of T lymphocytes of children with prolonged fetal exposure to dexamethasone for anti-Ro/SS-A antibodies associated congenital complete heart block. The analysis of thymic function, studied by measuring the level of T-cell receptor excision circles, was performed by real time PCR, the composition of T-cell subpopulation was evaluated by flow cytometry and the T-cell diversity was assayed by heteroduplex analysis. T-cell competence was gauged at two functional levels by determining the proliferation and the number of T-cell divisions and by measuring γ-interferon production after mitogenic stimulation. We observed that the thymic output, distribution of T-cell subsets, thymidine incorporation, number of T-cell divisions, and γ-interferon production were comparable to those of age-matched control. On the contrary, heteroduplex analysis demonstrated the presence of both polyclonal and oligoclonal peripheral T-cell repertoires. In conclusion, the analysis of the T-cell compartment in children with prolonged intrauterine exposure to high dose dexamethasone did not disclose any relevant abnormality, except a restriction of T-cell receptor diversity in some patients.
Outcome of pregnancies complicated by systemic sclerosis and mixed connective tissue disease
Authors: Chung L , Flyckt R LR , Colón I , Shah A A , Druzin M , Chakravarty E F 
Published: November 2006

Systemic sclerosis (SSc) and mixed connective tissue disease (MCTD) are rare autoimmune diseases which share the common feature of non-inflammatory vasculopathy. Studies evaluating pregnancy outcomes in these patients have yielded conflicting results. We sought to describe the outcomes of pregnancies associated with SSc and MCTD followed at our center utilizing a retrospective review of all pregnant women with SSc and MCTD followed at Stanford University from 1993 to 2003. We identified 20 pregnancies occurring in 13 women with SSc or MCTD. Twelve pregnancies occurred in seven women with SSc and eight pregnancies occurred in six women with MCTD. The overall preterm delivery rate was 39% and small for gestational age infants occurred in 50% and 63% of pregnancies associated with SSc and MCTD, respectively. Fetal loss complicated two pregnancies in women with severe diffuse SSc and the antiphospholipid antibody syndrome. There were no cases of congenital heartblock among infants, and only one case of pre-eclampsia was observed. Maternal flares of disease during pregnancy were generally mild. Most pregnancies in women with SSc and MCTD in this cohort were uncomplicated. The high rates of prematurity and small for gestational age infants underscore the risk for growth restriction consistent with the vasculopathy associated with these diseases.
Fatigue in cancer patients treated with cytotoxic drugs
Authors: Hartvig Per , Aulin Johan , Hugerth Matilda , Wallenberg Sofia , Wagenius Gunnar 
Published: November 2006

Study objectives. Cancer-related fatigue is a significant and distressing problem for the cancer patient, affecting their physical and psychosocial function negatively, and reducing their quality of life. The aims of this study were to assess frequency, severity, and the consequence of fatigue in cancer outpatients receiving cytotoxic drugs, using an existing international fatigue scale applied for Swedish use. Methods. The study used a non-randomized, prospective design to evaluate fatigue and its impact on quality of life in outpatients receiving cytotoxic drugs. Once a week, 147 cancer patients, in an outpatient ward for cytotoxic drug administration, filled out questionnaires containing 13 items from the Fatigue Symptom Inventory (FSI), and five additional questions. Results. Prevalence of fatigue was 92% in the week after all patients had received cytotoxic drugs, and patients were statistically significantly more fatigued during than before treatment. The degree of fatigue was highest the week after treatment, and declined over the following week. Other symptoms, especially depressed mood, showed a strong correlation with cancer and cytotoxic-induced fatigue. Lung and breast cancer patients experienced the highest degree of fatigue. Some cytotoxic drug regimens were, apart from the underlying disease, associated with high fatigue scores, eg, those with cyclophosphamide or gemcitabine. Patients not receiving first line treatment scored significantly higher fatigue with more influence on daily living. Conclusion. The study verified that fatigue is a common side effect, and affects quality of life negatively, even for outpatients receiving cytotoxic drugs. The clinical oncology pharmacist must inform patients that a severe tiredness, fatigue, may follow cytotoxic drug administration.