bluuebunny/crossref_metadata_2025 huggingface dataset:
Isolation of Soil Bacteria Adapted To Degrade Humic Acid-Sorbed Phenanthrene
Authors: Vacca D. J. , Bleam W. F. , Hickey W. J.
Published: July 2005

The goal of these studies was to determine how sorption by humic acids affected the bioavailability of polynuclear aromatic hydrocarbons (PAHs) to PAH-degrading microbes. Micellar solutions of humic acid were used as sorbents, and phenanthrene was used as a model PAH. Enrichments from PAH-contaminated soils established with nonsorbed phenanthrene yielded a total of 25 different isolates representing a diversity of bacterial phylotypes. In contrast, only three strains ofBurkholderiaspp. and one strain each ofDelftiasp. andSphingomonassp. were isolated from enrichments with humic acid-sorbed phenanthrene (HASP). Using [14C]phenanthrene as a radiotracer, we verified that only HASP isolates were capable of mineralizing HASP, a phenotype hence termed “competence.” Competence was an all-or-nothing phenotype: noncompetent strains showed no detectable phenanthrene mineralization in HASP cultures, but levels of phenanthrene mineralization effected by competent strains in HASP and NSP cultures were not significantly different. Levels and rates of phenanthrene mineralization exceeded those predicted to be supported solely by the metabolism of phenanthrene in the aqueous phase of HASP cultures. Thus, competent strains were able to directly access phenanthrene sorbed by the humic acids and did not rely on desorption for substrate uptake. To the best of our knowledge, this is the first report of (i) a selective interaction between aerobic bacteria and humic acid molecules and (ii) differential bioavailability to bacteria of PAHs sorbed to a natural biogeopolymer.
Purification, Characterization, and Crystallization of the Components of the Nitrobenzene and 2-Nitrotoluene Dioxygenase Enzyme Systems
Authors: Parales R. E. , Huang R. , Yu C.-L. , Parales J. V. , Lee F. K. N. , Lessner D. J. , Ivkovic-Jensen M. M. , Liu W. , Friemann R. , Ramaswamy S. , Gibson D. T.
Published: July 2005

The protein components of the 2-nitrotoluene (2NT) and nitrobenzene dioxygenase enzyme systems from
Acidovorax
sp. strain JS42 and
Comamonas
sp. strain JS765, respectively, were purified and characterized. These enzymes catalyze the initial step in the degradation of 2-nitrotoluene and nitrobenzene. The identical shared reductase and ferredoxin components were monomers of 35 and 11.5 kDa, respectively. The reductase component contained 1.86 g-atoms iron, 2.01 g-atoms sulfur, and one molecule of flavin adenine dinucleotide per monomer. Spectral properties of the reductase indicated the presence of a plant-type [2Fe-2S] center and a flavin. The reductase catalyzed the reduction of cytochrome
c
, ferricyanide, and 2,6-dichlorophenol indophenol. The ferredoxin contained 2.20 g-atoms iron and 1.99 g-atoms sulfur per monomer and had spectral properties indicative of a Rieske [2Fe-2S] center. The ferredoxin component could be effectively replaced by the ferredoxin from the
Pseudomonas
sp. strain NCIB 9816-4 naphthalene dioxygenase system but not by that from the
Burkholderia
sp. strain LB400 biphenyl or
Pseudomonas putida
F1 toluene dioxygenase system. The oxygenases from the 2-nitrotoluene and nitrobenzene dioxygenase systems each had spectral properties indicating the presence of a Rieske [2Fe-2S] center, and the subunit composition of each oxygenase was an α
3
β
3
hexamer. The apparent

K
m

of 2-nitrotoluene dioxygenase for 2NT was 20 μM, and that for naphthalene was 121 μM. The specificity constants were 7.0 μM
−1
min
−1
for 2NT and 1.2 μM
−1
min
−1
for naphthalene, indicating that the enzyme is more efficient with 2NT as a substrate. Diffraction-quality crystals of the two oxygenases were obtained.
A Multigene Phylogenetic Study of Clonal Diversity and Divergence in North American Strains of the Plant Pathogen
Xylella fastidiosa
Authors: Schuenzel Erin L. , Scally Mark , Stouthamer Richard , Nunney Leonard
Published: July 2005

Xylella fastidiosa
is a pathogen that causes leaf scorch and related diseases in over 100 plant species, including Pierce's disease in grapevines (PD), phony peach disease (PP), plum leaf scald (PLS), and leaf scorch in almond (ALS), oak (OAK), and oleander (OLS). We used a high-resolution DNA sequence approach to investigate the evolutionary relationships, geographic variation, and divergence times among the
X. fastidiosa
isolates causing these diseases in North America. Using a large data set of 10 coding loci and 26 isolates, the phylogeny of
X. fastidiosa
defined three major clades. Two of these clades correspond to the recently identified
X. fastidiosa
subspecies
piercei
(PD and some ALS isolates) and
X. fastidiosa
subsp.
multiplex
(OAK, PP, PLS, and some ALS isolates). The third clade grouped all of the OLS isolates into a genetically distinct group, named
X. fastidiosa
subsp.
sandyi
. These well-differentiated clades indicate that, historically,
X. fastidiosa
has been a clonal organism. Based on their synonymous-site divergence (∼3%), these three clades probably originated more than 15,000 years ago, long before the introduction of the nonnative plants that characterize most infections. The sister clades of
X. fastidiosa
subsp.
sandyi
and
X. fastidiosa
subsp.
piercei
have synonymous-site evolutionary rates 2.9 times faster than
X. fastidiosa
subsp.
multiplex
, possibly due to generation time differences. Within
X. fastidiosa
subsp.
multiplex
, a low level (∼0.1%) of genetic differentiation indicates the recent divergence of ALS isolates from the PP, PLS, and OAK isolates due to host plant adaptation and/or allopatry. The low level of variation within the
X. fastidiosa
subsp.
piercei
and
X. fastidiosa
subsp.
sandyi
clades, despite their antiquity, suggests strong selection, possibly driven by host plant adaptation.
Role for Glycine Betaine Transport in
Vibrio cholerae
Osmoadaptation and Biofilm Formation within Microbial Communities
Authors: Kapfhammer Dagmar , Karatan Ece , Pflughoeft Kathryn J. , Watnick Paula I.
Published: July 2005

Vibrio cholerae
is a halophilic facultative human pathogen found in marine and estuarine environments. Accumulation of compatible solutes is important for growth of
V. cholerae
at NaCl concentrations greater than 250 mM. We have identified and characterized two compatible solute transporters, OpuD and PutP, that are involved in uptake of glycine betaine and proline by
V. cholerae. V. cholerae
does not, however, possess the
bet
genes, suggesting that it is unable to synthesize glycine betaine. In contrast, many
Vibrio
species are able to synthesize glycine betaine from choline. It has been shown that many bacteria not only synthesize but also secrete glycine betaine. We hypothesized that sharing of compatible solutes might be a mechanism for cooperativity in microbial communities. In fact, we have demonstrated that, in high-osmolarity medium,
V. cholerae
growth and biofilm development are enhanced by supplementation with either glycine betaine or spent media from other bacterial species. Thus, we propose that compatible solutes provided by other microorganisms may contribute to survival of
V. cholerae
in the marine environment through facilitation of osmoadaptation and biofilm development.
Improved and Versatile Transformation System Allowing Multiple Genetic Manipulations of the Hyperthermophilic Archaeon
Thermococcus kodakaraensis
Authors: Sato Takaaki , Fukui Toshiaki , Atomi Haruyuki , Imanaka Tadayuki
Published: July 2005

We have recently developed a gene disruption system for the hyperthermophilic archaeon
Thermococcus kodakaraensis
by utilizing a
pyrF
-deficient mutant, KU25, as a host strain and the
pyrF
gene as a selectable marker. To achieve multiple genetic manipulations for more advanced functional analyses of genes in vivo, it is necessary to establish multiple host-marker systems or to develop a system in which repeated utilization of one marker gene is possible. In this study, we first constructed a new host strain, KU216 (Δ
pyrF
), by specific and almost complete deletion of endogenous
pyrF
through homologous recombination. In this refined host, there is no need to consider unknown mutations caused by random mutagenesis, and unlike in the previous host, KU25, there is little, if any, possibility that unintended recombination between the marker gene and the chromosomal allele occurs. Furthermore, a new host-marker combination of a
trpE
deletant, KW128 (Δ
pyrF
Δ
trpE
::
pyrF
), and the
trpE
gene was developed. This system made it possible to isolate transformants through a more simple selection procedure as well as to deduce the transformation efficiency, overcoming practical disadvantages of the first system. The effects of the transformation conditions were also investigated using this system. Finally, we have also established a system in which repeated utilization of the counterselectable
pyrF
marker is possible through its excision by pop-out recombination. Both endogenous and exogenous sequences could be applied as tandem repeats flanking the marker
pyrF
for pop-out recombination. A double deletion mutant, KUW1 (Δ
pyrF
Δ
trpE
), constructed with the pop-out strategy, was demonstrated to be a useful host for the dual markers
pyrF
and
trpE
. Likewise, a triple deletion mutant, KUWH1 (Δ
pyrF
Δ
trpE
Δ
hisD
), could also be constructed. The transformation systems developed here now provide the means for extensive genetic studies in this hyperthermophilic archaeon.
Development of a
recA
Gene-Based Identification Approach for the Entire
Burkholderia
Genus
Authors: Payne George W. , Vandamme Peter , Morgan Sara H. , LiPuma John J. , Coenye Tom , Weightman Andrew J. , Jones T. Hefin , Mahenthiralingam Eshwar
Published: July 2005

Burkholderia
is an important bacterial genus containing species of ecological, biotechnological, and pathogenic interest. With their taxonomy undergoing constant revision and the phenotypic similarity of several species, correct identification of
Burkholderia
is difficult. A genetic scheme based on the
recA
gene has greatly enhanced the identification of
Burkholderia cepacia
complex species. However, the PCR developed for the latter approach was limited by its specificity for the complex. By alignment of existing and novel
Burkholderia recA
sequences, we designed new PCR primers and evaluated their specificity by testing a representative panel of
Burkholderia
strains. PCR followed by restriction fragment length polymorphism analysis of an 869-bp portion of the
Burkholderia recA
gene was not sufficiently discriminatory. Nucleotide sequencing followed by phylogenetic analysis of this
recA
fragment differentiated both putative and known
Burkholderia
species and all members of the
B. cepacia
complex. In addition, it enabled the design of a
Burkholderia
genus-specific
recA
PCR that produced a 385-bp amplicon, the sequence of which was also able to discriminate all species examined. Phylogenetic analysis of 188 novel
recA
genes enabled clarification of the taxonomic position of several important
Burkholderia
strains and revealed the presence of four novel
B. cepacia
complex
recA
lineages. Although the
recA
phylogeny could not be used as a means to differentiate
B. cepacia
complex strains recovered from clinical infection versus the natural environment, it did facilitate the identification of clonal strain types of
B. cepacia
,
B. stabilis
, and
B. ambifaria
capable of residing in both niches.
Location of theBombyx moriAminopeptidase N Type 1 Binding Site onBacillus thuringiensisCry1Aa Toxin
Authors: Atsumi Shogo , Mizuno Eri , Hara Hirotaka , Nakanishi Kazuko , Kitami Madoka , Miura Nami , Tabunoki Hiroko , Watanabe Ayako , Sato Ryoichi
Published: July 2005

We analyzed the binding site on Cry1Aa toxin for the Cry1Aa receptor inBombyx mori, 115-kDa aminopeptidase N type 1 (BmAPN1) (K. Nakanishi, K. Yaoi, Y. Nagino, H. Hara, M. Kitami, S. Atsumi, N. Miura, and R. Sato, FEBS Lett.519:215-220, 2002), by using monoclonal antibodies (MAbs) that block binding between the binding site and the receptor. First, we produced a series of MAbs against Cry1Aa and obtained two MAbs, MAbs 2C2 and 1B10, that were capable of blocking the binding between Cry1Aa and BmAPN1 (blocking MAbs). The epitope of the Fab fragments of MAb 2C2 overlapped the BmAPN1 binding site, whereas the epitope of the Fab fragments of MAb 1B10 did not overlap but was located close to the binding site. Using three approaches for epitope mapping, we identified two candidate epitopes for the blocking MAbs on Cry1Aa. We constructed two Cry1Aa toxin mutants by substituting a cysteine on the toxin surface at each of the two candidate epitopes, and the small blocking moleculeN-(9-acridinyl)maleimide (NAM) was introduced at each cysteine substitution to determine the true epitope. The Cry1Aa mutant with NAM bound to Cys582 did not bind either of the two blocking MAbs, suggesting that the true epitope for each of the blocking MAbs was located at the site containing Val582, which also consisted of508STLRVN513and582VFTLSAHV589. These results indicated that the BmAPN1 binding site overlapped part of the region blocked by MAb 2C2 that was close to but excluded the actual epitope of MAb 2C2 on domain III of Cry1Aa toxin. We also discuss another area on Cry1Aa toxin as a new candidate site for BmAPN1 binding.
Diel Variations in Carbon Metabolism by Green Nonsulfur-Like Bacteria in Alkaline Siliceous Hot Spring Microbial Mats from Yellowstone National Park
Authors: van der Meer Marcel T. J. , Schouten Stefan , Bateson Mary M. , Nübel Ulrich , Wieland Andrea , Kühl Michael , de Leeuw Jan W. , Sinninghe Damsté Jaap S. , Ward David M.
Published: July 2005

Green nonsulfur-like bacteria (GNSLB) in hot spring microbial mats are thought to be mainly photoheterotrophic, using cyanobacterial metabolites as carbon sources. However, the stable carbon isotopic composition of typical
Chloroflexus
and
Roseiflexus
lipids suggests photoautotrophic metabolism of GNSLB. One possible explanation for this apparent discrepancy might be that GNSLB fix inorganic carbon only during certain times of the day. In order to study temporal variability in carbon metabolism by GNSLB, labeling experiments with [
13
C]bicarbonate, [
14
C]bicarbonate, and [
13
C]acetate were performed during different times of the day. [
14
C]bicarbonate labeling indicated that during the morning, incorporation of label was light dependent and that both cyanobacteria and GNSLB were involved in bicarbonate uptake.
13
C-labeling experiments indicated that during the morning, GNSLB incorporated labeled bicarbonate at least to the same degree as cyanobacteria. The incorporation of [
13
C]bicarbonate into specific lipids could be stimulated by the addition of sulfide or hydrogen, which both were present in the morning photic zone. The results suggest that GNSLB have the potential for photoautotrophic metabolism during low-light periods. In high-light periods, inorganic carbon was incorporated primarily into
Cyanobacteria
-specific lipids. The results of a pulse-labeling experiment were consistent with overnight transfer of label to GNSLB, which could be interrupted by the addition of unlabeled acetate and glycolate. In addition, we observed direct incorporation of [
13
C]acetate into GNSLB lipids in the morning. This suggests that GNSLB also have a potential for photoheterotrophy in situ.
Identity and Ecophysiology of Uncultured Actinobacterial Polyphosphate-Accumulating Organisms in Full-Scale Enhanced Biological Phosphorus Removal Plants
Authors: Kong Yunhong , Nielsen Jeppe Lund , Nielsen Per Halkjær
Published: July 2005

Microautoradiography combined with fluorescence in situ hybridization (MAR-FISH) was used to screen for potential polyphosphate-accumulating organisms (PAO) in a full-scale enhanced biological phosphorus removal (EBPR) plant. The results showed that, in addition to unculturedRhodocyclus-related PAO, two morphotypes hybridizing with gene probes for the gram-positiveActinobacteriawere also actively involved in uptake of orthophosphate (Pi). Clone library analysis and further investigations by MAR-FISH using two new oligonucleotide probes revealed that both morphotypes, cocci in clusters of tetrads and short rods in clumps, were relatively closely related to the genusTetrasphaerawithin the familyIntrasporangiaceaeof theActinobacteria(93 to 98% similarity in their 16S rRNA genes). FISH analysis of the community biomass in the treatment plant investigated showed that the short rods (targeted by probe Actino-658) were the most abundant (12% of allBacteriahybridizing with general bacterial probes), while the cocci in tetrads (targeted by probe Actino-221) made up 7%. Both morphotypes took up Piaerobically only if, in a previous anaerobic phase, they had taken up organic matter from wastewater or a mixture of amino acids. They could not take up short-chain fatty acids (e.g., acetate), glucose, or ethanol under anaerobic or aerobic conditions. The storage compound produced during the anaerobic period was not polyhydroxyalkanoates, as forRhodocyclus-related PAO, and its identity is still unknown. Growth and uptake of Pitook place in the presence of oxygen and nitrate but not nitrite, indicating a lack of denitrifying ability. A survey of the occurrence of these actinobacterial PAO in 10 full-scale EBPR plants revealed that both morphotypes were widely present, and in several plants more abundant than theRhodocyclus-related PAO, thus playing a very important role in the EBPR process.
Multiple-Mutation Reaction: a Method for Simultaneous Introduction of Multiple Mutations into theglpKGene ofMycoplasma pneumoniae
Authors: Hames Claudine , Halbedel Sven , Schilling Oliver , Stülke Jörg
Published: July 2005

InMycoplasma pneumoniae, the UGA opal codon specifies tryptophan rather than a translation stop site. This often makes it difficult to expressMycoplasmaproteins inE. coliisolates. In this work, we developed a strategy for the one-step introduction of several mutations. This method, the multiple-mutation reaction, is used to simultaneously replace nine opal codons in theM. pneumoniae glpKgene.
Prevalence and Antimicrobial Resistance of
Campylobacter
spp. and
Salmonella
Serovars in Organic Chickens from Maryland Retail Stores
Authors: Cui Shenghui , Ge Beilei , Zheng Jie , Meng Jianghong
Published: July 2005

Retail organic (
n
= 198) and conventional (
n
= 61) chickens were analyzed. Most organic (76%) and conventional (74%) chickens were contaminated with campylobacters. Salmonellae were recovered from 61% of organic and 44% of conventional chickens. All
Salmonella enterica
serovar Typhimurium isolates from conventional chickens were resistant to five or more antimicrobials, whereas most
S. enterica
serovar Typhimurium isolates (79%) from organic chickens were susceptible to 17 antimicrobials tested.
16S rRNA Phylogeny of Sponge-Associated Cyanobacteria
Authors: Steindler Laura , Huchon Dorothée , Avni Adi , Ilan Micha
Published: July 2005

Phylogenetic analyses of 16S rRNA sequences of sponge-associated cyanobacteria showed them to be polyphyletic, implying that they derived from multiple independent symbiotic events. Most of the symbiont sequences were affiliated to a group of
Synechococcus
and
Prochlorococcus
species. However, other symbionts were related to different groups, such as the
Oscillatoriales
.
Effect of an Artificial RNA Marker on Gene Expression in
Escherichia coli
Authors: Tucker Don L. , Karouia Fathi , Wang Jim , Luo Yi , Li Tong-Bin , Willson Richard C. , Fofanov Yuriy , Fox George E.
Published: July 2005

Transcriptional analysis was used to examine the effect of a genomically encoded artificial RNA on
Escherichia coli
in rich and minimal media. Only the expression of a single gene,
deoC
, was unequivocally affected under both conditions.
E. coli
marker strains of this type may be useful in monitoring the fate and transport of bacteria in various applications.
Clinical and Immunological Features of 65 Iranian Patients with Common Variable Immunodeficiency
Authors: Aghamohammadi Asghar , Farhoudi Abolhasan , Moin Mostafa , Rezaei Nima , Kouhi Ali , Pourpak Zahra , Yaseri Nima , Movahedi Masoud , Gharagozlou Mohammad , Zandieh Fariborz , Yazadni Fereshteh , Arshi Saba , MohammadZadeh Iraj , Ghazi Bahram MirSaeid , Mahmoudi Maryam , Tahaei SeyedAmir , Isaeian Anna
Published: July 2005

Common variable immunodeficiency (CVID) is a primary immunodeficiency disease characterized by hypogammaglobulinemia and recurrent bacterial infections. The records of 65 patients with CVID (37 males and 28 females) in the age range of 24 to 537 months were reviewed. By the year 2003, 11 patients had died and seven patients could not be located. The total follow-up period was 221 patient-years. The median diagnostic delay (time between onset and diagnosis) in our patient group was 60 months. At the time of diagnosis, the baseline serum immunoglobulin G (IgG), IgM, and IgA levels were below the level normal for the patients' age; the medians for this group were 120, 10, and 0 mg/dl, respectively. All of the patients presented with infectious diseases at the time of onset, the most common of which were otitis media, diarrhea, pneumonia, and sinusitis. Acute and recurrent infections were also found in almost all of the patients, particularly involving respiratory and gastrointestinal systems. The most common infections, before diagnosis and during follow-up, were pneumonia, acute diarrhea, acute sinusitis, and otitis media. CVID should be considered in any patient with a history of recurrent infections and decreased levels of all serum immunoglobulin isotypes.
Proteomic but Not Enzyme-Linked Immunosorbent Assay Technology Detects Amniotic Fluid Monomeric Calgranulins from Their Complexed Calprotectin Form
Authors: Buhimschi Irina A. , Buhimschi Catalin S. , Weiner Carl P. , Kimura Tatsuji , Hamar Benjamin D. , Sfakianaki Anna K. , Norwitz Errol R. , Funai Edmund F. , Ratner Elena
Published: July 2005

Four proteomic biomarkers (human neutrophil peptide 1 [HNP1], HNP2 [defensins], calgranulin C [Cal-C], and Cal-A) characterize the fingerprint of intra-amniotic inflammation (IAI). We compared proteomic technology using surfaced-enhanced laser desorption-ionization-time of flight (SELDI-TOF) mass spectrometry to enzyme-linked immunosorbent assay (ELISA) for detection of these biomarkers. Amniocentesis was performed on 48 women enrolled in two groups: those with intact membranes (
n
= 27; gestational age [GA], 26.0 ± 0.8 weeks) and those with preterm premature rupture of the membranes (PPROM;
n
= 21; GA, 28.4 ± 0.9 weeks). Paired abdominal amniotic fluids (aAFs)-vaginal AFs (vAFs) were analyzed in PPROM women. Quantitative aspects of HNP1-3, Cal-C, Cal-A, and calprotectin (a complex of Cal-A with Cal-B) were assessed by ELISA. SELDI-TOF mass spectrometry tracings from 16/48 (33.3%) aAFs and 13/17 (88.2%) vAFs were consistent with IAI (three or four biomarkers present). IAI (by SELDI-TOF mass spectrometry) was associated with increased HNP1-3 and Cal-C measured by ELISA. However, immunoassays detected Cal-A in only 4 of the AFs even though its specific SELDI-TOF mass spectrometry peak was identified in 19/48 AFs. Calprotectin immunoreactivity was decreased in AFs retrieved from women with IAI (
P
= 0.01). In conclusion, IAI is associated with increased HNP1-3 levels. In the absence of isoform-specific ELISAs, mass spectrometry remains the only way to discriminate the HNP biomarker isoforms. Monomeric Cal-A is not reliably estimated by specific ELISA as it binds to Cal-B to form the calprotectin complex. Cal-C was reliably measured by SELDI-TOF mass spectrometry or specific ELISA.
Evaluation of Rapid Prenatal Human Immunodeficiency Virus Testing in Rural Cameroon
Authors: Granade Timothy C. , Parekh Bharat S. , Tih Pius M. , Welty Thomas , Welty Edith , Bulterys Marc , Ndikintum George , Nkuoh Godlove , Tancho Samuel
Published: July 2005

Pregnant women (
n
= 859) in rural Cameroonian prenatal clinics were screened by two rapid human immunodeficiency virus (HIV) antibody tests (rapid tests [RT]) (Determine and Hema-Strip) using either whole blood or plasma. One additional RT (Capillus, HIV-CHEK, or Sero-Card) was used to resolve discordant results. RT results were compared with HIV-1 enzyme immunoassay (EIA) and Western blot (WB) results of matched dried blood spots (DBS) to assess the accuracy of HIV RTs. DBS EIA/WB identified 83 HIV antibody-reactive, 763 HIV antibody-nonreactive, and 13 indeterminate specimens. RT results were evaluated in serial (two consecutive tests) or parallel (two simultaneous tests) testing algorithms. A serial algorithm using Determine and Hema-Strip yielded sensitivity and specificity results of 97.6% and 99.7%, respectively, whereas a parallel RT algorithm using Determine plus a second RT produced a sensitivity and specificity of 100% and 99.7%, respectively. HIV RTs provide excellent alternatives for identifying HIV infection, and their field performance could be monitored using DBS testing strategies.
Characterization of Acute-Phase Humoral Immunity to Monkeypox: Use of Immunoglobulin M Enzyme-Linked Immunosorbent Assay for Detection of Monkeypox Infection during the 2003 North American Outbreak
Authors: Karem Kevin L. , Reynolds Mary , Braden Zach , Lou Gin , Bernard Nikeva , Patton Joanne , Damon Inger K.
Published: July 2005

A monkeypox outbreak occurred in the United States in 2003. Patient's sera were sent to the Centers for Disease Control and Prevention as a part of outbreak response measures. Clinical and epidemiologic information was abstracted from the case investigation forms. Serum samples from patients were tested by using an immunoglobulin M (IgM)-capture and an IgG enzyme-linked immunosorbent assay ELISA against
Orthopoxvirus
antigen. The detection of antiviral IgG and IgM antibodies and the kinetics of the antiviral IgG and IgM antibody responses were evaluated. Patients were classified as confirmed, probable, or suspect cases or were excluded as cases based on laboratory test results and epidemiologic and clinical criteria. A total of 37 confirmed case patients with monkeypox were identified, and 116 patients were excluded as case patients based on molecular testing or insufficient epidemiology and clinical data to warrant classification as a suspect or probable case. Of 37 confirmed case patients, 36 had a known history (presence or absence) of smallpox vaccination. Of those, 29 of the 36 either had or developed an IgG response, while 34 of the 36 developed an IgM response, regardless of vaccination status. Serum collected ≥5 days for IgM detection or serum collected ≥8 days after rash onset for IgG detection was most efficient for the detection of monkeypox virus infection. IgM ELISA detects recent infection with orthopoxviruses and, in this case, recent infection with monkeypox virus. In addition, analysis of paired sera for IgG and IgM detected seroconversion, another indicator of recent infection. The ELISA results correlated with the virologic PCR and viral culture results, indicating its diagnostic capabilities for monkeypox and potentially other orthopoxvirus infections due to zoonotic transmission or bioterrorism events.
Immunoglobulin M Enzyme-Linked Immunosorbent Assay Using Recombinant Polypeptides for Diagnosis of Dengue
Authors: Videa Elsa , Coloma Maria Josefina , dos Santos Flavia Barreto , Balmaseda Angel , Harris Eva
Published: July 2005

We demonstrate that a mixture of four recombinant dengue virus E polypeptides corresponding to the N-terminal region of the envelope protein from all serotypes substitutes for standard antigens in two immunoglobulin M enzyme-linked immunosorbent assay formats with 100% concordance, making these polypeptides a useful and accessible reagent for serological diagnosis of dengue in endemic countries.
Development of Rapid Immunochromatographic Test with Recombinant NcSAG1 for Detection of Antibodies toNeospora caninumin Cattle
Authors: Liao Min , Zhang Shoufa , Xuan Xuenan , Zhang Guohong , Huang Xiaohong , Igarashi Ikuo , Fujisaki Kozo
Published: July 2005

An immunochromatographic test (ICT) with recombinant surface antigen 1 ofNeospora caninum(NcSAG1) was developed for the rapid detection of antibodies toN. caninumin cattle. The ICT was used to clearly discriminate between immunofluorescent-antibody test (IFAT)-positive bovine sera and IFAT-negative bovine sera. Serum samples collected from cattle in Yanbian, China, were examined by the ICT. Of the 96 serum samples, 23 (24.0%) were positive by the ICT, and 19 (19.8%) samples were positive by a previously developed enzyme-linked immunosorbent assay (ELISA). Eighteen of 19 ELISA-positive samples were positive according to the ICT. A good agreement was found between the results of the ICT and the ELISA. The results presented here suggest that the ICT with recombinant truncated NcSAG1 fused to glutathioneS-transferase is a useful and reliable method for the detection of antibodies toN. caninumin cattle.
Cell Cycle Dynamics and Quorum Sensing inCandida albicansChlamydospores Are Distinct from Budding and Hyphal Growth
Authors: Martin Stephen W. , Douglas Lois M. , Konopka James B.
Published: July 2005

The regulation of morphogenesis in the human fungal pathogenCandida albicansis under investigation to better understand how the switch between budding and hyphal growth is linked to virulence. Therefore, in this study we examined the ability ofC. albicansto undergo a distinct type of morphogenesis to form large thick-walled chlamydospores whose role in infection is unclear, but they act as a resting form in other species. During chlamydospore morphogenesis, cells switch to filamentous growth and then develop elongated suspensor cells that give rise to chlamydospores. These filamentous cells were distinct from true hyphae in that they were wider and were not inhibited by the quorum-sensing factor farnesol. Instead, farnesol increased chlamydospore production, indicating that quorum sensing can also have a positive role. Nuclear division did not occur across the necks of chlamydospores, as it does in budding. Interestingly, nuclei divided within the suspensor cells, and then one daughter nucleus subsequently migrated into the chlamydospore. Septins were not detected near mitotic nuclei but were localized at chlamydospore necks. At later stages, septins localized throughout the chlamydospore plasma membrane and appeared to form long filamentous structures. Deletion of theCDC10orCDC11septins caused greater curvature of cells growing in a filamentous manner and morphological defects in suspensor cells and chlamydospores. These studies identify aspects of chlamydospore morphogenesis that are distinct from bud and hyphal morphogenesis.
A CDC42 Homologue in
Claviceps purpurea
Is Involved in Vegetative Differentiation and Is Essential for Pathogenicity
Authors: Scheffer Jan , Chen Changbin , Heidrich Patrick , Dickman Martin B. , Tudzynski Paul
Published: July 2005

Claviceps purpurea
, a biotrophic pathogen of cereals, has developed a unique pathogenic strategy including an extended period of unbranched directed growth in the host's style and ovarian tissue to tap the vascular system. Since the small GTPase Cdc42 has been shown to be involved in cytoskeleton organization and polarity in other fungi, we investigated the role of Cdc42 in the development and pathogenicity of
C. purpurea
. Expression of heterologous dominant-active (DA) and dominant-negative (DN) alleles of
Colletotrichum trifolii
in a wild strain of
C. purpurea
had significant impact on vegetative differentiation: whereas DA Ct
cdc42
resulted in loss of conidiation and in aberrant cell shape, expression of DN Ct
cdc42
stimulated branching and conidiation. Deletion of the endogenous Cp
cdc42
gene was not lethal but led to a phenotype comparable to that of DN Ct
cdc42
transformants. ΔCp
cdc42
mutants were nonpathogenic; i.e., they induced no disease symptoms. Cytological analysis (light microscopy and electron microscopy) revealed that the mutants can penetrate and invade the stylar tissue. However, invasive growth was arrested in an early stage, presumably induced by plant defense reactions (necrosis or increased production of reactive oxygen species), which were never observed in wild-type infection. The data show a significant impact of Cp
cdc42
on vegetative differentiation and pathogenicity in
C. purpurea
.
Centrin Scaffold in
Chlamydomonas reinhardtii
Revealed by Immunoelectron Microscopy
Authors: Geimer Stefan , Melkonian Michael
Published: July 2005

In the flagellate green alga
Chlamydomonas reinhardtii
the Ca
2+
-binding EF-hand protein centrin is encoded by a single-copy gene. Previous studies have localized the protein to four distinct structures in the flagellar apparatus: the nucleus-basal body connector, the distal connecting fiber, the flagellar transitional region, and the axoneme. To explain the disjunctive distribution of centrin, the interaction of centrin with as yet unknown specific centrin-binding proteins has been implied. Here, we demonstrate using serial section postembedding immunoelectron microscopy of isolated cytoskeletons that centrin is located in additional structures (transitional fibers and basal body lumen) and that the centrin-containing structures of the basal apparatus are likely part of a continuous filamentous scaffold that extends from the nucleus to the flagellar bases. In addition, we show that centrin is located in the distal lumen of the basal body in a rotationally asymmetric structure, the V-shaped filament system. This novel centrin-containing structure has also been detected near the distal end of the probasal bodies. Taken together, these results suggest a role for a rotationally asymmetric centrin “seed” in the growth and development of the centrin scaffold following replication of the basal apparatus.
Hyphal Guidance and Invasive Growth in
Candida albicans
Require the Ras-Like GTPase Rsr1p and Its GTPase-Activating Protein Bud2p
Authors: Hausauer Danielle L. , Gerami-Nejad Maryam , Kistler-Anderson Cassandra , Gale Cheryl A.
Published: July 2005

Candida albicans
, the most prevalent fungal pathogen of humans, causes superficial mycoses, invasive mucosal infections, and disseminated systemic disease. Many studies have shown an intriguing association between
C. albicans
morphogenesis and the pathogenesis process. For example, hyphal cells have been observed to penetrate host epithelial cells at sites of wounds and between cell junctions. Ras- and Rho-type GTPases regulate many morphogenetic processes in eukaryotes, including polarity establishment, cell proliferation, and directed growth in response to extracellular stimuli. We found that the
C. albicans
Ras-like GTPase Rsr1p and its predicted GTPase-activating protein Bud2p localized to the cell cortex, at sites of incipient daughter cell growth, and provided landmarks for the positioning of daughter yeast cells and hyphal cell branches, similar to the paradigm in the model yeast
Saccharomyces cerevisiae
. However, in contrast to
S. cerevisiae
, CaRsr1p and CaBud2p were important for morphogenesis:
C. albicans
strains lacking Rsr1p or Bud2p had abnormal yeast and hyphal cell shapes and frequent bends and promiscuous branching along the hypha and were unable to invade agar. These defects were associated with abnormal actin patch polarization, unstable polarisome localization at hyphal tips, and mislocalized septin rings, consistent with the idea that GTP cycling of Rsr1p stabilizes the axis of polarity primarily to a single focus, thus ensuring normal cell shape and a focused direction of polarized growth. We conclude that the Rsr1p GTPase functions as a polarity landmark for hyphal guidance and may be an important mediator of extracellular signals during processes such as host invasion.
Galactomannoproteins of
Aspergillus fumigatus
Authors: Morelle W. , Bernard M. , Debeaupuis J.-P. , Buitrago M. , Tabouret M. , Latgé J.-P.
Published: July 2005

Galactofuranose-containing molecules have been repeatedly shown to be important antigens among human fungal pathogens, including
Aspergillus fumigatus
. Immunogenic galactofuran determinants have been poorly characterized chemically, however. We reported here the characterization of two glycoproteins of
A. fumigatus
with an N-glycan containing galactofuranose. These proteins are a phospholipase C and a phytase. Chemical characterization of the N-glycan indicates that it is a mixture of Hex
5-13
HexNAc
2
oligosaccharides, the major molecular species corresponding to Hex
6-8
HexNAc
2
. The N-glycan contained one galactofuranose unit that was in a terminal nonreducing position attached to the 2 position of Man. This single terminal nonreducing galactofuranose is essential for the immunoreactivity of the N-glycans assessed either with a monoclonal antibody that recognizes a tetra-β-1,5-galactofuran chain of galactomannan or with
Aspergillus
-infected patient sera.
Systematic Characterization of the ADP-Ribose Pyrophosphatase Family in the Cyanobacterium
Synechocystis
sp. Strain PCC 6803
Authors: Okuda Kenji , Hayashi Hidenori , Nishiyama Yoshitaka
Published: July 2005

We have characterized four putative ADP-ribose pyrophosphatases Sll1054, Slr0920, Slr1134, and Slr1690 in the cyanobacterium
Synechocystis
sp. strain PCC 6803. Each of the recombinant proteins was overexpressed in
Escherichia coli
and purified. Sll1054 and Slr0920 hydrolyzed ADP-ribose specifically, while Slr1134 hydrolyzed not only ADP-ribose but also NADH and flavin adenine dinucleotide. By contrast, Slr1690 showed very low activity for ADP-ribose and had four substitutions of amino acids in the Nudix motif, indicating that Slr1690 is not an active ADP-ribose pyrophosphatase. However, the quadruple mutation of Slr1690, T73G/I88E/K92E/A94G, which replaced the mutated amino acids with those conserved in the Nudix motif, resulted in a significant (6.1 × 10
2
-fold) increase in the
k
cat
value. These results suggest that Slr1690 might have evolved from an active ADP-ribose pyrophosphatase. Functional and clustering analyses suggested that Sll1054 is a bacterial type, while the other three and Slr0787, which was characterized previously (Raffaelli et al., FEBS Lett. 444:222-226, 1999), are phylogenetically diverse types that originated from an archaeal Nudix protein via molecular evolutionary mechanisms, such as domain fusion and amino acid substitution.
EXTENSION OF THE STRUCTURE THEOREM OF BORCHERS AND ITS APPLICATION TO HALF-SIDED MODULAR INCLUSIONS
Authors: ARAKI HUZIHIRO , ZSIDÓ LÁSZLÓ
Published: July 2005

A result of H.-W. Wiesbrock is extended from the case of a common cyclic and separating vector for the half-sided modular inclusion N ⊂ M of von Neumann algebras to the case of a common faithful normal semi-finite weight and at the same time a gap in Wiesbrock's proof is filled in.
QUANTUM ENERGY INEQUALITIES IN TWO-DIMENSIONAL CONFORMAL FIELD THEORY
Authors: FEWSTER CHRISTOPHER J. , HOLLANDS STEFAN
Published: July 2005

Quantum energy inequalities (QEIs) are state-independent lower bounds on weighted averages of the stress-energy tensor, and have been established for several free quantum field models. We present rigorous QEI bounds for a class of interacting quantum fields, namely the unitary, positive energy conformal field theories (with stress-energy tensor) on two-dimensional Minkowski space. The QEI bound depends on the weight used to average the stress-energy tensor and the central charge(s) of the theory, but not on the quantum state. We give bounds for various situations: averaging along timelike, null and spacelike curves, as well as over a space-time volume. In addition, we consider boundary conformal field theories and more general "moving mirror" models.

Our results hold for all theories obeying a minimal set of axioms which — as we show — are satisfied by all models built from unitary highest-weight representations of the Virasoro algebra. In particular, this includes all (unitary, positive energy) minimal models and rational conformal field theories. Our discussion of this issue collects together (and, in places, corrects) various results from the literature which do not appear to have been assembled in this form elsewhere.
STATIC EINSTEIN'S UNIVERSE AS A QUANTUM SOLUTION OF CAUSAL QUANTUM GRAVITY
Authors: SHOJAI ALI , SHOJAI FATIMAH , DADHICH NARESH
Published: July 2005

We shall in the framework of Bohmian quantum gravity show that it is possible to find a pure quantum state which leads to the static Einstein universe whose classical counterpart is flat space–time. We obtain the solution in the long-wavelength approximation. At the end an exact solution is found.
QUANTITATIVE CHARACTERIZATION OF THE COMPLEXITY OF MULTICHANNEL HUMAN EEGS
Authors: RAPP P. E. , CELLUCCI C. J. , WATANABE T. A. A. , ALBANO A. M.
Published: July 2005

In this contribution, eleven different measures of the complexity of multichannel EEGs are described, and their effectiveness in discriminating between two behavioral conditions (eyes open resting versus eyes closed resting) is compared. Ten of the methods were variants of the algorithmic complexity and the covariance complexity. The eleventh measure was a multivariate complexity measure proposed by Tononi and Edelman. The most significant between-condition change was observed with Tononi–Edelman complexity which decreased in the eyes open condition. Of the algorithmic complexity measures tested, the binary Lempel–Ziv complexity and the binary Lempel–Ziv redundancy of the first principal component following mean normalization and normalization against the standard deviation gave the most significant between-group discrimination. A time-dependent generalization of the covariance complexity that can be applied to nonstationary multichannel signals is also described.
ON ENTROPY OF CHUA'S CIRCUITS
Authors: YANG XIAO-SONG , LI QINGDU
Published: July 2005

In this paper we revisit the well-known Chua's circuit and give a discussion on entropy of this circuit. We present a formula for the topological entropy of a Chua's circuit in terms of the Poincaré map derived from the ordinary differential equations of this Chua's circuit by computer simulation arguments.
FOURTH-ORDER NEARLY-SYMMETRIC CNNS EXHIBITING COMPLEX DYNAMICS
Authors: DI MARCO M. , FORTI M. , GRAZZINI M. , PANCIONI L.
Published: July 2005

In this paper, the possible presence of complex dynamics in nearly-symmetric standard Cellular Neural Networks (CNNs), is investigated. A one-parameter family of fourth-order CNNs is presented, which exhibits a cascade of period-doubling bifurcations leading to the birth of a complex attractor, close to some nominal symmetric CNN. Different from previous work on this topic, the bifurcations and complex dynamics are obtained for small relative errors with respect to the nominal interconnections. The fourth-order CNNs have negative (inhibitory) interconnections between distinct neurons, and are designed by a variant of a technique proposed by Smale to embed a given dynamical system within a competitive dynamical system of larger order.
A DOUBLE-SCROLL ROSSLER SYSTEM
Authors: ALVAREZ-RAMIREZ JOSE , CERVANTES ILSE , ESPINOSA-PAREDES GILBERTO
Published: July 2005

This letter uses a singular perturbation method to introduce a double-scroll version of the Rossler system. Its generation and basic dynamic behavior are briefly described.
Novel Distributed Fiber-Optic Strain Sensor by Localizing Dynamic Grating in Polarization-Maintaining Erbium-Doped Fiber: Proposal and Theoretical Analysis
Authors: Fan Xinyu , He Zuyuan , Hotate Kazuo
Published: July 2005

A novel scheme of distributed fiber-optic strain sensor by localizing a dynamic grating in a polarization-maintaining erbium-doped fiber is proposed. The dynamic grating, which is introduced by launching two counterpropagating coherent light beams into a pumped erbium-doped fiber per gain saturation, is examined. A theoretical model of the dynamic grating is given and used to perform simulations of the reflectivity of the dynamic grating localized by synthesizing the optical coherence function. Theoretical analysis and numerical simulation of the novel sensor scheme show that the Bragg frequency of the dynamic grating will shift according by 0.426 MHz/µε to strain in a typical polarization-maintaining erbium-doped fiber.
High-Quality 2'' Bulk-Like Free-Standing GaN Grown by HydrideVapour Phase Epitaxy on a Si-doped Metal Organic Vapour Phase Epitaxial GaN Template with an Ultra Low Dislocation Density
Authors: Gogova Daniela , Larsson Henrik , Kasic Alexander , Yazdi Gholam Reza , Ivanov Ivan , Yakimova Rositza , Monemar Bo , Aujol Eric , Frayssinet Eric , Faurie Jean-Pierre , Beaumont Bernard , Gibart Pierre
Published: July 2005

High-quality 2'' crack-free free-standing GaN has been attained by hydride vapour phase epitaxial growth on a Si-doped MOVPE GaN template with a low dislocation density and subsequent laser-induced lift-off process. A low value of dislocation density of ∼2.0×107 cm-2 on the Ga-polar face was determined from cathodoluminescence images. X-ray diffraction (XRD) and low-temperature photoluminescence (PL) were exploited to investigate the structural and optical properties of the GaN material. The full width at half maximum value of XRD ω-scan of the free-standing GaN is 248 arcsec for the (1 0 1 4) reflection. The XRD and low-temperature PL mapping measurements consistently proved the high crystalline quality as well as the lateral homogeneity and the small residual stress of the material. Hence, the bulk-like free-standing GaN studied here is highly advantageous for being used as a lattice-constant and thermal-expansion-coefficient matched substrate for additional strain-free homoepitaxy of III–nitrides-based device heterostructures. The strain-free homoepitaxy will significantly reduce the defect density and thus, an improvement of the device performance and lifetime could be achieved.
Modeling and Simulation of Hydrogenated Amorphous Silicon Thin-Film Transistors
Authors: Hafdi Zoubeida , Aida Mohamed Salah
Published: July 2005

A simple analytical dc model for hydrogenated amorphous silicon thin-film transistors including an accumulation region is developed. The model describes the device properties and physical phenomena of hydrogenated amorphous silicon. Current–voltage characteristics are related to basic material and device parameters. In the blocking state, drain leakage current is modeled using previously reported results. In the lower and upper threshold regimes, both deep and tail states are taken into account. The density of states in band gap is modeled by assuming an exponential distribution of the deep and tail states. The results show that the generated current–voltage characteristics show good agreement with previously reported data. The study of apparent threshold voltage, field effect mobility and ON–OFF current ratio shows that in the lower threshold regime, parameter behavior is governed by the deep states in the middle of an amorphous silicon gap while the tail state distribution controls the upper-threshold-regime behavior. The model is simplified analytically to lessen the cost of and complexity in fabricating large-area displays and optimizing their performance.
Effects of Temperature and Humidity on Electrical Properties of Organic Semiconductor Orange Dye Films Deposited from Solution
Authors: Moiz Syed A. , Ahmed Mansoor M. , Karimov Khasan S.
Published: July 2005

In this study the effects of temperature and humidity on electrical properties of organic semiconductor orange dye (OD) have been examined. Thin films of OD were deposited from 10 wt.% aqueous solution on Au and SnO2 substrates at room temperature under normal gravity conditions, i.e., 1 g and also by using a spin coater at an angular speed of 1000 RPM. Two different types of structures: surface OD/Au and sandwich Al/OD/SnO2, Al/OD/Au were fabricated and their DC and low frequency AC characteristics were evaluated for the temperature range 30–70°C at ambient humidity of 50–80%. It was observed that the Schottky characteristics exhibited by these devices are temperature and humidity dependent. It was further observed that devices with Al electrodes act as a primary battery and the zero biased current (I
zo) increases by increasing the device temperature which is explained on the basis of temperature assisted electrochemical reaction due to the correction of Al electrode. It was found that certain sandwich structures are more sensitive to humidity than others and the observed resistance to humidity ratio for OD/Au was 5.4 whereas for Ga/OD/Au samples it was 5.0.