bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vegetation Change and Soil Nutrient Distribution along an Oasis‐Desert Transitional Zone in Northwestern China
Authors: Chen Bao‐Ming , Wang Gen‐Xuan , Cheng Dong‐Liang , Deng Jian‐Min , Peng Shao‐Lin , An Fu‐Bo 
Published: October 2007

Abstract Many studies have focused on soil nutrient heterogeneity and islands of fertility in arid ecosystems. However, few have been conducted on an oasis‐desert transitional zone where there is a vegetation pattern changing from shrubs to annual herbs. The goal of the present study was to understand vegetation and soil nutrient heterogenity along an oasis‐desert transitional zone in northwestern China. Three replicated sampling belts were selected at 200 m intervals along the transitional zone. Twenty‐one quadrats (10 × 10 m) at 50 m intervals were located along each sampling belt. The vegetation cover was estimated through the quadrats, where both the soil under the canopy and the open soil were sampled simultaneously. The dominated shrub was Haloxylon ammodendron in the areas close to the oasis and Nitraria tangutorum dominated the areas close to the desert. In general, along the transitional zone the vegetation cover decreased within 660 m, increased above 660 m and decreased again above 1 020 m (close to the desert). The soil nutrients (organic matter, total N, NO3− and NH4+) showed significant differences along the zone. The soil nutrients except the soil NH4+ under the canopy were higher than those in open soil, confirming “islands of fertility” or nutrient enrichment. Only a slight downward trend of the level of “islands of fertility” for soil organic matter appeared in the area within 900 m. Soil organic matter both under canopy and in interspace showed a positive correlation with the total vegetation cover, however, there was no significant correlation between the other soil nutrients and the total vegetation cover. We also analyzed the relationship between the shrubs and annuals and the soil nutrients along the zone. Similarly, there was no significant correlation between them, except soil organic matter with the annuals. The results implied that annual plants played an important role in soil nutrient enrichment in arid ecosystem.
Mass Production of Intergeneric Chromosomal Translocations through Pollen Irradiation of Triticum durum‐Haynaldia villosa Amphiploid
Authors: Bie Tong‐De , Cao Ya‐Ping , Chen Pei‐Du 
Published: October 2007

Abstract
Haynaldia villosa possesses a lot of important agronomic traits and has been a powerful gene resource for wheat improvement. However, only several wheat–H. villosa translocation lines have been reported so far. In this study, we attempted to develop an efficient method for inducing wheat–H. villosa chromosomal translocations. Triticum durum‐Haynaldia villosa amphiploid pollen treated with 1 200 rad 60Co‐γ‐rays was pollinated to Triticum aestivum cv. ‘Chinese Spring’. Ninety‐eight intergeneric translocated chromosomes between T. durum and H. villosa were detected by genomic in situ hybridization in 44 of 61 M1 plants, indicating a translocation occurrence frequency of 72.1%; much higher than ever reported. There were 26, 62 and 10 translocated chromosomes involving whole arm translocations, terminal translocations, and intercarlary translocations, respectively. Of the total 108 breakage‐fusion events, 79 involved interstitial regions and 29 involved centric regions. The ratio of small segment terminal translocations (W·W‐V) was much higher than that of large segment terminal translocations (W‐V·V). All of the M1 plants were self‐sterile, and their backcross progeny was all obtained with ‘Chinese Spring’ as pollen donors. Transmission analysis showed that most of the translocations were transmittable. This study provides a new strategy for rapid mass production of wheat‐alien chromosomal translocations, especially terminal translocations that will be more significant for wheat improvement.
Use of Sera from Humans and Dolphins with Lacaziosis and Sera from Experimentally Infected Mice for Western Blot Analyses of
Lacazia loboi
Antigens
Authors: Mendoza Leonel , Belone Andréa F. F. , Vilela Raquel , Rehtanz Manuela , Bossart Gregory D. , Reif John S. , Fair Patricia A. , Durden Wendy N. , St. Leger Judy , Travassos Luiz R. , Rosa Patricia S. 
Published: October 2007

ABSTRACT

Antibodies in the sera of patients with lacaziosis recognized an ∼193-kDa antigen and other
Lacazia loboi
antigens.
Paracoccidioides brasiliensis
gp43 antigen was detected by all evaluated sera, but they failed to detect a protein with the same molecular mass in
L. loboi
extracts. This study is the first to examine the humoral response to
L. loboi
antigens by using multiple host sera.
Serologic Evidence for Reactivation of Cryptococcosis in Solid-Organ Transplant Recipients
Authors: Saha D. C. , Goldman D. L. , Shao X. , Casadevall A. , Husain S. , Limaye A. P. , Lyon M. , Somani J. , Pursell K. , Pruett T. L. , Singh N. 
Published: October 2007

ABSTRACT

Cryptococcosis is a significant infection with a high mortality in solid-organ transplant recipients. Nonetheless, the pathogenesis of this disease is poorly understood. It has been hypothesized that cryptococcosis may result from either primary infection or reactivation of a latent infection. Sera were obtained from transplant recipients prior to transplantation and at the time they developed cryptococcosis. Control sera were obtained before and after transplant from patients who did not develop cryptococcosis. Sera were tested for antibodies against
Cryptococcus neoformans
by using an immunoblot assay. Antibody responses were also compared with those observed in sera from rats with experimental pulmonary cryptococcosis. In all, 52% of the transplant recipients who developed cryptococcosis exhibited serologic evidence of cryptococcal infection before transplantation. These patients developed cryptococcosis significantly earlier after transplant than patients without preexisting reactivity did (5.6 ± 3.4 months compared to 40.6 ± 63.8 months, respectively [
P
= 0.0011]). The results from our study suggest that a substantial proportion of transplant-associated cryptococcosis cases result from the reactivation of a latent infection. These findings also highlight the potential utility of serologic studies in identifying patients at risk for the development of cryptococcosis after transplantation.
Western Blot Assay Using Recombinant p26 Antigen for Detection of Equine Infectious Anemia Virus-Specific Antibodies
Authors: Alvarez I. , Gutierrez G. , Ostlund E. , Barrandeguy M. , Trono K. 
Published: October 2007

ABSTRACTWe analyzed the performance of a single-band Western blot (WB) test using recombinant p26 (rp26) capsid protein of equine infectious anemia virus. According to the results obtained, the rp26 WB test is a reliable confirmatory diagnostic tool to be used as a complementary test after an enzyme-linked immunosorbent assay or agar gel immunodiffusion test yielding doubtful results.
Evaluation of a Novel PCR-Based Assay for Detection and Identification of
Chlamydia trachomatis
Serovars in Cervical Specimens
Authors: Quint Koen , Porras Carolina , Safaeian Mahboobeh , González Paula , Hildesheim Allan , Quint Wim , van Doorn Leen-Jan , Silva Sandra , Melchers Willem , Schiffman Mark , Rodríguez Ana Cecilia , Wacholder Sholom , Freer Enrique , Cortes Bernal , Herrero Rolando 
Published: October 2007

ABSTRACT

The aims of this study were to compare a novel PCR-based
Chlamydia trachomatis
detection and genotyping (Ct-DT) assay with the FDA-approved, commercially available
C. trachomatis
detection Hybrid Capture 2 (HC2) assay and to investigate the
C. trachomatis
serovar distribution among young women in a rural Costa Rican study population. A total of 5,828 sexually active women participating in a community-based trial in Costa Rica were tested for
C. trachomatis
by HC2. A sample of 1,229 specimens consisting of 100% HC2
C. trachomatis
-positive specimens (
n
= 827) and a random sample of 8% HC2
C. trachomatis
-negative specimens (
n
= 402) were tested with the Ct-DT assay. Agreement between the two assays was determined by the unweighted kappa statistic. Discrepant specimens were tested with a second commercially available test (COBAS TaqMan). The Ct-DT-positive specimens were further analyzed with the Ct-DT genotyping step to investigate the distribution of 14 different
C. trachomatis
serovars (A, B/Ba, C, D/Da, E, F, G/Ga, H, I/Ia, J, K, L1, L2/L2a, and L3). After accounting for the sampling fraction selected for Ct-DT testing, crude agreement with the HC2 assay was 98% and the kappa was 0.92 (95% confidence interval [CI], 0.89 to 0.97). The 33 discordant samples that were further analyzed with the COBAS TaqMan test showed better agreement with the Ct-DT assay (31/33,
P
< 0.001). Among the 806 Ct-DT-positive samples, serovar E was the most common serovar (31%), followed by serovars F and D (both 21%) and serovar I (15%). In conclusion, the novel Ct-DT assay permits reliable detection and identification of
C. trachomatis
serovars.
Novel Light-Upon-Extension Real-Time PCR Assays for Detection and Quantification of Genogroup I and II Noroviruses in Clinical Specimens
Authors: Nordgren Johan , Bucardo Filemón , Dienus Olaf , Svensson Lennart , Lindgren Per-Eric 
Published: October 2007

ABSTRACT

Norovirus is now recognized as the leading cause of nonbacterial acute gastroenteritis in adults, causing numerous outbreaks worldwide. We have developed two novel light-upon-extension (LUX) real-time PCR assays for detection and quantification of norovirus genogroups I and II. The LUX system uses a fluorophore attached to one primer having a self-quenching hairpin structure, making it cost-effective and specific. The assays were evaluated against clinical stool specimens (
n
= 103) from Sweden and Nicaragua and compared to established methods. The norovirus assay detected more positive stool specimens (47/103) than conventional PCR (39/103) and corresponded to a TaqMan real-time PCR, with the exception of one specimen. Furthermore, the assays correctly identified all (
n
= 11) coded control specimens in a reference panel containing various genogroups and genotypes. Both LUX real-time PCR assays had a wide dynamic range, detecting from ≤10
1
to 10
7
genes per reaction, resulting in a theoretical lower limit of ≤∼20 000 viruses per gram of stool. No cross-reactivity was noticed with specimens containing other enteric viruses, and by using melting curve analysis we could differentiate between norovirus genogroups I and II.
Comparison between Quantitative Nucleic Acid Sequence-Based Amplification, Real-Time Reverse Transcriptase PCR, and Real-Time PCR for Quantification ofLeishmaniaParasites
Authors: van der Meide Wendy , Guerra Jorge , Schoone Gerard , Farenhorst Marit , Coelho Leíla , Faber William , Peekel Inge , Schallig Henk 
Published: October 2007

ABSTRACTDNA or RNA amplification methods for detection ofLeishmaniaparasites have advantages regarding sensitivity and potential quantitative characteristics in comparison with conventional diagnostic methods but are often still not routinely applied. However, the use and application of molecular assays are increasing, but comparative studies on the performance of these different assays are lacking. The aim of this study was to compare three molecular assays for detection and quantification ofLeishmaniaparasites in serial dilutions of parasites and in skin biopsies collected from cutaneous leishmaniasis (CL) patients in Manaus, Brazil. A serial dilution of promastigotes spiked in blood was tested in triplicate in three different runs by quantitative nucleic acid sequence-based amplification (QT-NASBA), quantitative real-time reverse transcriptase PCR (qRT-PCR), and quantitative real-time PCR (qPCR). In addition, the costs, durations, and numbers of handling steps were compared, and 84 skin biopsies from patients with suspected CL were tested. Both QT-NASBA and qRT-PCR had a detection limit of 100 parasites/ml of blood, while qPCR detected 1,000 parasites/ml. QT-NASBA had the lowest range of intra-assay variation (coefficients of variation [CV], 0.5% to 3.3%), while qPCR had the lowest range of interassay variation (CV, 0.4% to 5.3%). Furthermore, qRT-PCR had higherr2values and amplification efficiencies than qPCR, and qPCR and qRT-PCR had faster procedures than QT-NASBA. All assays performed equally well with patient samples, with significant correlations between parasite counts. Overall, qRT-PCR is preferred over QT-NASBA and qPCR as the most optimal diagnostic assay for quantification ofLeishmaniaparasites, since it was highly sensitive and reproducible and the procedure was relatively fast.
Molecular Epidemiology of
Escherichia coli
Producing Extended-Spectrum β-Lactamases Isolated in Rome, Italy
Authors: Carattoli Alessandra , García-Fernández Aurora , Varesi Paola , Fortini Daniela , Gerardi Serena , Penni Adriano , Mancini Carlo , Giordano Alessandra 
Published: October 2007

ABSTRACT

Escherichia coli
strains producing extended-spectrum β-lactamases (ESBLs) are a major problem in many different hospitals worldwide, causing outbreaks as well as sporadic infections. The prevalence of
Escherichia coli
ESBL producers was analyzed in a surveillance study performed on the population attending the Policlinico Umberto I, the largest university hospital in Rome, Italy. We also investigated genotypes, pathogenicity islands, and plasmids in the ESBL-positive
E. coli
isolates as further markers that are useful in describing the epidemiology of the infections. In this survey, 163 nonreplicate isolates of
Escherichia coli
were isolated from patients from 86 different wards, and 28 were confirmed as ESBL producers. A high prevalence (26/28) of CTX-M-15 producers was observed within the bacterial population circulating in this hospital, and the dissemination of this genetic trait was associated with the spread of related strains; however, these do not have the characteristics of a single epidemic clone spreading. The dissemination was also linked to horizontal transfer among the prevalent
E. coli
genotypes of multireplicon plasmids showing FIA, FIB, and FII replicons in various combinations, which are well adapted to the
E. coli
species. The analysis of related bacteria suggests a probable interpatient transmission occurring in several wards, causing small outbreaks.
Evaluation of the Vitek 2 System with a Variety of
Staphylococcus
Species
Authors: Delmas Julien , Chacornac Jean Paul , Robin Frédéric , Giammarinaro Philippe , Talon Régine , Bonnet Richard 
Published: October 2007

ABSTRACT

The Vitek 2 gram-positive (GP) card was compared with an oligonucleotide array approach for the identification of 190
Staphylococcus
strains, including 35 species, isolated from clinical and environmental specimens. The GP card provided a rapid and reliable identification of most species, whatever their origin.
Mycobacterium bovis
BCG Vertebral Osteomyelitis after Intravesical BCG Therapy, Diagnosed by PCR-Based Genomic Deletion Analysis
Authors: Nikaido Takuya , Ishibashi Kei , Otani Koji , Yabuki Shoji , Konno Shinichi , Mori Shuichi , Ohashi Kazutaka , Ishida Takashi , Nakano Michiko , Yamaguchi Osamu , Suzutani Tatsuo , Kikuchi Shinichi 
Published: October 2007

ABSTRACT

We report a case of
Mycobacterium bovis
BCG vertebral osteomyelitis 1.8 years after intravesical BCG therapy for bladder cancer. We differentiated BCG from other
Mycobacterium tuberculosis
complex members by PCR analysis of deletion regions and started an appropriate chemotherapy regimen resulting in the remission of symptoms within 1 month.
Influence of Type of Culture Medium on Characterization ofMycobacterium aviumsubsp.paratuberculosisSubtypes
Authors: Cernicchiaro N. , Wells S. J. , Janagama H. , Sreevatsan S. 
Published: October 2007

ABSTRACTWe evaluated the effects of culture and/or enrichment methods on the selection ofMycobacterium aviumsubsp.paratuberculosissubtypes.M. aviumsubsp.paratuberculosisisolates from bovine fecal samples processed using a centrifugation protocol were investigated in both liquid (MGIT ParaTb tubes) and solid (Herrold's egg yolk medium) culture media. For this evaluation,M. aviumsubsp.paratuberculosissubtyping was based on the sequence variation in two of the most discriminatory short sequence repeat loci, i.e., mononucleotide G and trinucleotide GGT, in isolates from liquid and solid cultures. This study identified the existence of one major predominating fingerprint (>13G-5GGT) in bovine fecal samples, regardless of the type of medium used for isolation. Matched-pair analysis of subtypes showed that 69% of samples presented unique subtypes in the two culture media used, while 31% shared the same G-GGT allele. Furthermore, the liquid culture method appeared to select for a more genotypically diverse subtype population than the solid culture method. The variety of subtypes observed between liquid and solid cultures obtained from the same fecal samples suggests that the culture method could provide a “microbiological” bias and lead to a discrepancy in the growth ofM. aviumsubsp.paratuberculosisstrains. In conclusion, this study identified that these two types of culture media determined differential growth ofM. aviumsubsp.paratuberculosisstrains and that this should be considered in evaluating detection capabilities of diagnostic tests or interpreting data from molecular epidemiological studies performed using conventional solid fecal culture or automated liquid medium culture methods.
Lodderomyces elongisporus
Masquerading as
Candida parapsilosis
as a Cause of Bloodstream Infections
Authors: Lockhart Shawn R. , Messer Shawn A. , Pfaller Michael A. , Diekema Daniel J. 
Published: October 2007

ABSTRACT

Ten yeast bloodstream isolates identified as
Candida parapsilosis
by conventional methods grew as turquoise blue colonies on Chromagar media. Subsequent sequence analysis showed that these isolates were the species
Lodderomyces elongisporus
. To our knowledge, this is the first published report of
L. elongisporus
as a cause of human disease.
The Antiapoptotic Herpes Simplex Virus Glycoprotein J Localizes to Multiple Cellular Organelles and Induces Reactive Oxygen Species Formation
Authors: Aubert Martine , Chen Zheng , Lang Robin , Dang Chung H. , Fowler Carla , Sloan Derek D. , Jerome Keith R. 
Published: October 2007

ABSTRACT

The
Us5
gene of herpes simplex virus (HSV) encodes glycoprotein J (gJ). The only previously reported function of gJ was its ability to inhibit apoptosis. However, the mechanism by which gJ prevents apoptosis is not understood, and it is not known whether gJ mediates additional cellular effects. In this study, we evaluated the expression, localization, and cellular effects of
Us5
/gJ.
Us5
was first expressed 4 h after infection. gJ was detectable at 6 h and was expressed in glycosylated and unglycosylated forms.
Us5
was regulated as a late gene, with partial dependency on DNA replication for expression.
Us5
expression was delayed in the absence of ICP22; furthermore, expression of
Us5
in
trans
protected cells from apoptosis induced by an HSV mutant with deletion of ICP27, suggesting that the antiapoptotic effects of ICP22 and ICP27 are mediated in part through effects on gJ expression. Within HSV-infected or
Us5
-transfected cells, gJ was distributed widely, especially to the endoplasmic reticulum,
trans
-Golgi network, and early endosomes. gJ interacted with F
o
F
1
ATP synthase subunit 6 by a yeast two-hybrid screen and had strong antiapoptotic effects, which were mediated by protein rather than mRNA. Antiapoptotic activity required the extracellular and transmembrane domains of gJ, but not the intracellular domain. Consistent with inhibition of F
o
F
1
ATP synthase function,
Us5
was required for HSV-induced reactive oxygen species (ROS) formation, and gJ was sufficient to induce ROS in
Us5
-transfected cells. Thus, HSV gJ is a multifunctional protein, modulating other cellular processes in addition to inhibition of apoptosis.
The Tyrosine Kinase sf-Stk and Its Downstream Signals Are Required for Maintenance of Friend Spleen Focus-Forming Virus-Induced Fibroblast Transformation
Authors: Jelacic Tanya M. , Thompson Delores , Hanson Charlotte , Cmarik Joan L. , Nishigaki Kazuo , Ruscetti Sandra 
Published: October 2007

ABSTRACT
Infection of erythroid progenitor cells by Friend spleen focus-forming virus (SFFV) leads to acute erythroid hyperplasia and eventually to erythroleukemia in susceptible strains of mice. The viral envelope protein, SFFV gp55, forms a complex with the erythropoietin receptor (EpoR) and a short form of the receptor tyrosine kinase Stk (sf-Stk), activating both and inducing Epo-independent proliferation. Recently, we discovered that coexpression of SFFV gp55 and sf-Stk is sufficient to transform NIH 3T3 and primary fibroblasts. In the current study, we demonstrate that sf-Stk and its downstream effectors are critical to this transformation. Unlike SFFV-derived erythroleukemia cells, which depend on PU.1 expression for maintenance of the transformed phenotype, SFFV gp55-sf-Stk-transformed fibroblasts are negative for PU.1. Underscoring the importance of sf-Stk to fibroblast transformation, knockdown of sf-Stk abolished the ability of these cells to form anchorage-independent colonies. Like SFFV-infected erythroid cells, SFFV gp55-sf-Stk-transformed fibroblasts express high levels of phosphorylated MEK, ERK, phosphatidylinositol 3-kinase (PI3K), Gab1/2, Akt, Jun kinase (JNK), and STAT3, but unlike virus-infected erythroid cells they fail to express phosphorylated STATs 1 and 5, which may require involvement of the EpoR. In addition, the p38 mitogen-activated protein kinase (MAPK) stress response is suppressed in the transformed fibroblasts. Inhibition of either JNK or the PI3K pathway decreases both monolayer proliferation and anchorage-independent growth of the transformed fibroblasts as does the putative kinase inhibitor luteolin, but inhibition of p38 MAPK has no effect. Our results indicate that sf-Stk is a molecular endpoint of transformation that could be targeted directly or with agents against its downstream effectors.
Rous Sarcoma Virus (RSV) Integration In Vivo: a CA Dinucleotide Is Not Required in U3, and RSV Linear DNA Does Not Autointegrate
Authors: Oh Jangsuk , Chang Kevin W. , Wierzchoslawski Rafal , Alvord W. Gregory , Hughes Stephen H. 
Published: October 2007

ABSTRACT
The sequences required for integration of retroviral DNA have been analyzed in vitro. However, the in vitro experiments do not agree on which sequences are required for integration: for example, whether or not the conserved CA dinucleotide in the 3′ end of the viral DNA is required for normal integration. At least a portion of the problem is due to differences in the experimental conditions used in the in vitro assays. To avoid the issue of what experimental conditions to use, we took an in vivo approach. We made mutations in the 5′ end of the U3 sequence of the Rous sarcoma virus (RSV)-derived vector RSVP(A)Z. We present evidence that, in RSV, the CA dinucleotide in the 5′ end of U3 is not essential for appropriate integration. This result differs from the results seen with mutations in the U5 end, where the CA appears to be essential for proper integration in vivo. In addition, based on the structure of circular viral DNAs smaller than the full-length viral genome, our results suggest that there is little, if any, integrase-mediated autointegration of RSV linear DNA in vivo.