bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic Diversity of Coxsackievirus A16 Associated with Hand, Foot, and Mouth Disease Epidemics in Japan from 1983 to 2003
Authors: Hosoya Mitsuaki , Kawasaki Yukihiko , Sato Masatoki , Honzumi Ken , Hayashi Akio , Hiroshima Toyomasa , Ishiko Hiroaki , Kato Kazuo , Suzuki Hitoshi
Published: November 2006

To
clarify the chronologic genetic diversity of coxsackievirus A16
(CV-A16) strains associated with hand, foot, and mouth disease (HFMD)
epidemics in a restricted area and their genetic relation with those
isolated in other areas, we investigated the genetic diversity of the
129 CV-A16 strains associated with HFMD epidemics in Fukushima, Japan,
from 1983 to 2003, and compared their genetic relation to 49 CV-A16
strains isolated in other areas of Japan and in China by using
phylogenetic analysis based on the VP4 sequences. Phylogenetic
reconstruction of the CV-A16 strains isolated in Fukushima from 1983 to
2003 demonstrated three distinct genetically divergent clusters related
to HFMD epidemics that occurred from 1984 to 1994 (including the 1985
and 1991 outbreaks), HFMD epidemics from 1987 to 1998 (including the
1988 and 1998 outbreaks), and HFMD epidemics from 1995 to 2003
(including the 1995 and 2002 outbreaks). CV-A16 strains isolated during
each period in Fukushima formed a single cluster with those isolated
during essentially the same time period in other areas of Japan and in
China. Our results demonstrated that prevalent CV-A16 strains causing
HFMD in Fukushima, Japan, genetically changed twice during 21
epidemics, and changes were also observed in the CV-A16 strains causing
HFMD epidemics in other areas. We concluded that repeated outbreaks of
CV-A16-related HFMD in Japan were caused, in part, by the introduction
of genetically changed CV-A16 strains, which might be transmitted
overseas.
Association of Putative Enteroaggregative
Escherichia coli
Virulence Genes and Biofilm Production in Isolates from Travelers to Developing Countries
Authors: Mohamed Jamal A. , Huang David B. , Jiang Zhi-Dong , DuPont Herbert L. , Nataro James P. , Belkind-Gerson Jaime , Okhuysen Pablo C.
Published: November 2006

Enteroaggregative
Escherichia coli
(EAEC) is an emerging enteric pathogen that causes acute and chronic diarrhea among children, human immunodeficiency virus-infected patients, and travelers to developing regions of the world. The pathogenesis of EAEC strains involves the production of biofilm. In this study, we determined the association between presence of putative EAEC virulence genes and biofilm formation in 57 EAEC isolates (as defined by HEp-2 adherence) from travelers with diarrhea and in 18 EAEC isolates from travelers without diarrhea. Twelve nondiarrheagenic
E. coli
isolates from healthy travelers were used as controls. Biofilm formation was measured by using a microtiter plate assay with the crystal violet staining method, and the presence of the putative EAEC virulence genes
aap
,
aatA
,
aggR
,
astA
,
irp2
,
pet
,
set1A
, and
shf
was determined by PCR. EAEC isolates were more likely to produce biofilm than nondiarrheagenic
E. coli
isolates (
P
= 0.027), and the production of biofilm was associated with the virulence genes
aggR
,
set1A
,
aatA
, and
irp2
, which were found in 16 (40%), 17 (43%), 10 (25%), and 27 (68%) of the biofilm producers versus only 4 (11%), 6 (6%), 2 (6%), and 15 (43%) in non-biofilm producers (
P
= 0.008 for
aggR
,
P
= 0.0004 for
set1A
,
P
= 0.029 for
aatA
, and
P
= 0.04 for
irp2
). Although the proportion of EAEC isolates producing biofilm in patients with diarrhea (51%) was similar to that in patients without diarrhea (61%), biofilm production was related to the carriage of
aggR
(
P
= 0.015),
set1A
(
P
= 0.001), and
aatA
(
P
= 0.025). Since
aggR
is a master regulator of EAEC, the presence of
aap
(
P
= 0.004),
astA
(
P
= 0.001),
irp2
(
P
= 0.0006),
pet
(
P
= 0.002), and
set1A
(
P
= 0.014) in an
aggR
versus an
aggR
-lacking background was investigated and was also found to be associated with biofilm production. This study suggests that biofilm formation is a common phenomenon among EAEC isolates derived from travelers with or without diarrhea and that multiple genes associated with biofilm formation are regulated by
aggR
.
Rapid Multiplex PCR Assay for Identification of USA300 Community-Associated Methicillin-Resistant
Staphylococcus aureus
Isolates
Authors: Bonnstetter Kristin K. , Wolter Daniel J. , Tenover Fred C. , McDougal Linda K. , Goering Richard V.
Published: November 2006

Recent reports have noted a discernible increase in the number of community-associated methicillin-resistant
Staphylococcus aureus
(CA-MRSA) infections in patients without traditional risk factors. In the United States, the most prominent CA-MRSA strain encodes Panton-Valentine leukocidin (PVL) cytotoxin genes, belongs to pulsed field gel electrophoresis type USA300 and multilocus sequence type 8, and carries staphylococcal cassette chromosome
mec
(SCC
mec
) type IV. At present, molecular characterization of MRSA strains, such as USA300, can be time-consuming and is often beyond the technical capability of many clinical laboratories, making routine identification difficult. We analyzed the chromosomal regions flanking the SCC
mec
element in 44 USA300 MRSA isolates and identified a signature “AT repeat” sequence within the conserved hypothetical gene SACOL0058 located 1.4 kb downstream of the 3′ end of the J1-SCC
mec
chromosomal junction. Only USA300 isolates tested contained a sequence of ≥6 AT repeats in combination with PVL (e.g., related USA500 or Iberian strains had ≥6 AT repeats but were PVL negative). Using a locked nucleic acid primer specific for ≥6 AT repeats in combination with primers to detect PVL, we developed a multiplex PCR assay specific for the identification of USA300 strains. Multiplex results were 100% concordant with DNA sequencing, suggesting that the method has promise as a means of rapidly identifying USA300 isolates.
Strain-Specific Single-Nucleotide Polymorphism Assays for the
Bacillus anthracis
Ames Strain
Authors: Van Ert Matthew N. , Easterday W. Ryan , Simonson Tatum S. , U'Ren Jana M. , Pearson Talima , Kenefic Leo J. , Busch Joseph D. , Huynh Lynn Y. , Dukerich Megan , Trim Carla B. , Beaudry Jodi , Welty-Bernard Amy , Read Timothy , Fraser Claire M. , Ravel Jacques , Keim Paul
Published: November 2006

Highly precise diagnostics and forensic assays can be developed through a combination of evolutionary analysis and the exhaustive examination of genomic sequences. In
Bacillus anthracis
, whole-genome sequencing efforts revealed ca. 3,500 single-nucleotide polymorphisms (SNPs) among eight different strains and evolutionary analysis provides the identification of canonical SNPs. We have previously shown that SNPs are highly evolutionarily stable, and the clonal nature of
B. anthracis
makes them ideal signatures for subtyping this pathogen. Here we identified SNPs that define the lineage of
B. anthracis
that contains the Ames strain, the strain used in the 2001 bioterrorist attacks in the United States. Sequencing and real-time PCR were used to validate these SNPs across
B. anthracis
strains, including (i) 88 globally and genetically diverse isolates; (ii) isolates that were shown to be genetic relatives of the Ames strain by multiple-locus variable number tandem repeat analysis (MLVA); and (iii) several different lab stocks of the Ames strain, including a clinical isolate from the 2001 letter attack. Six SNPs were found to be highly specific for the Ames strain; four on the chromosome, one on the pX01 plasmid, and one on the pX02 plasmid. All six SNPs differentiated the
B. anthracis
Ames strain from the 88 unique
B. anthracis
strains, while five of the six separated Ames from its close genetic relatives. The use of these SNPs coupled with real-time PCR allows specific and sensitive (<100 fg of template DNA) identification of the Ames strain. This evolutionary and genomics-based approach provides an effective means for the discovery of strain-specific SNPs in
B. anthracis
.
Evaluation of Commercial Rubella Immunoglobulin G Avidity Assays
Authors: Mubareka Samira , Richards Hannah , Gray Michael , Tipples Graham A.
Published: November 2006

We compared the performances of five commercial rubella virus immunoglobulin G (IgG) avidity assays. The Adaltis (kappa = 0.28) and Diesse (kappa = 0.33) assays showed poor correlation, the Behring assay (kappa = 0.68) showed good correlation, and the Euroimmun (kappa = 0.95) and Radim (kappa = 0.94) assays showed excellent correlation with a well-established in-house rubella virus IgG avidity assay. The Euroimmun and Radim assays were statistically significantly better than the other commercial assays (
P
< 0.01).
Nosocomial Liver Abscess Caused by Extended-Spectrum Beta-Lactamase-ProducingKlebsiella pneumoniae
Authors: Lin Jung-Chung , Siu L. K. , Fung Chang-Phone , Yeh Kao-Ming , Chang Feng-Yee
Published: November 2006

A nosocomial pyogenic liver abscess caused by an extended-spectrum beta-lactamase-producingKlebsiella pneumoniaeisolate presented in a man with adenocarcinoma of the stomach. TheK. pneumoniaestrain isolated from blood and liver aspirate cultures after antibiotic therapy for recurrent bacteremia was resistant to all extended-spectrum beta-lactams except imipenem and differed fromK. pneumoniaestrains causing community-acquired liver abscesses.
Isolation of
Bartonella quintana
from a Woman and a Cat following Putative Bite Transmission
Authors: Breitschwerdt Edward B. , Maggi Ricardo G. , Sigmon Betsy , Nicholson William L.
Published: November 2006

We report here the detection of
Bartonella quintana
, after putative bite transmission, in pre-enrichment blood cultures from a woman and from two feral barn cats. Prospective molecular epidemiological studies are necessary to characterize the risk of human
Bartonella quintana
infection following cat bites.
Double-Locus Sequence Typing Using
clfB
and
spa
, a Fast and Simple Method for Epidemiological Typing of Methicillin-Resistant
Staphylococcus aureus
Authors: Kuhn G. , Francioli P. , Blanc D. S.
Published: November 2006

Sequence-based epidemiological typing of methicillin-resistant
Staphylococcus aureus
(MRSA) has recently been promoted because it results in unambiguous data sets that can be organized in local and global databases. The replacement of previous typing methods, such as the highly discriminatory pulsed-field gel electrophoresis (PFGE), has been attempted with various markers and typing schemes, including
spa
typing and multilocus sequence typing. However, despite a number of advantages, none of these methods showed convincing evidence for performance in epidemiological typing comparable to that of PFGE. By using three sets of 48 MRSA strains comprising isolates that were (i) genetically highly diverse, (ii) genetically related, and (iii) obtained from long-term carriers, we analyzed the performance of the four highly polymorphic
S. aureus
markers:
clfA
,
clfB
,
fnbA
, and
spa
. Typeability, discriminatory power, in vivo stability, and evolution of these markers were compared to those of PFGE. Clearly, none of the markers alone could match the discriminatory power of PFGE (63 genotypes; index of discrimination of 0.96). Instead, this could be achieved by combining markers in pairs. We showed that by using only 3′ partial sequences of approximately 500 bp, the majority of each marker's discriminatory power was displayed, and using the partial sequences, the best performance was obtained with the combination of
clfB
and
spa
(57 genotypes; index of discrimination of 0.94). Genetic changes were not observed for any of the sequence markers over a period of 3 years and in the case of partial sequences for a period of more than 4 years. This is in contrast to PFGE where changes occurred after several months. The genetic differences found between isolate pairs of long-term carriers and among highly related isolates indicated clonal evolution. A typing scheme based on 500-bp 3′ partial sequences of
clfB
and
spa
is proposed.
Newly Developed Primers for Comprehensive Amplification of the
rpoB
Gene and Detection of Rifampin Resistance in
Mycobacterium tuberculosis
Authors: Rigouts Leen , Nolasco Oscar , de Rijk Pim , Nduwamahoro Elie , Van Deun Armand , Ramsay Andy , Arevalo Jorge , Portaels Françoise
Published: November 2006

New
rpoB
gene primers for detecting Rif
r
in
Mycobacterium tuberculosis
complex bacteria achieved 100% specificity and 88% (fresh sputa) and 92% (ethanol-preserved sputa) diagnostic sensitivity and detected up to 4 CFU/sample. Of the 99 Rif
r
isolates examined, 97% had mutations within cluster I, 2% at codon 176, and 1% at codon 497.
Identification ofVibrioIsolates by a Multiplex PCR Assay andrpoBSequence Determination
Authors: Tarr Cheryl L. , Patel Jayna S. , Puhr Nancy D. , Sowers Evangeline G. , Bopp Cheryl A. , Strockbine Nancy A.
Published: November 2006

Vibrio, a diverse genus of aquatic bacteria, currently includes 72 species, 12 of which occur in human clinical samples. Of these 12, three species—Vibrio cholerae,Vibrio parahaemolyticus, andVibrio vulnificus—account for the majority ofVibrioinfections in humans. Rapid and accurate identification ofVibriospecies has been problematic because phenotypic characteristics are variable within species and biochemical identification requires 2 or more days to complete. To facilitate the identification of human-pathogenic species, we developed a multiplex PCR that uses species-specific primers to amplify gene regions in four species (V. cholerae,V. parahaemolyticus,V. vulnificus, andV. mimicus). The assay was tested on a sample of 309Vibrioisolates representing 26 named species (including 12 human pathogens) that had been characterized by biochemical methods. A total of 190 isolates that had been identified as one of the four target species all yielded results consistent with the previous classification. The assay identified an additional fourV. parahaemolyticusisolates among the other 119 isolates. Sequence analysis based onrpoBwas used to validate the multiplex results for these four isolates, and all clustered with otherV. parahaemolyticussequences. TherpoBsequences for 12 of 15 previously unidentified isolates clustered with otherVibriospecies in a phylogenetic analysis, and three isolates appeared to represent unnamedVibriospecies. The PCR assay provides a simple, rapid, and reliable tool for identification of the majorVibriopathogens in clinical samples, andrpoBsequencing provides an additional identification tool for other species in the genusVibrio.
Multicenter Studies of Tigecycline Disk Diffusion Susceptibility Results for
Acinetobacter
spp
Authors: Jones Ronald N. , Ferraro Mary Jane , Reller L. Barth , Schreckenberger Paul C. , Swenson Jana M. , Sader Helio S.
Published: November 2006

Acinetobacter
sp. isolates having multidrug resistance (MDR) patterns have become common in many medical centers worldwide, limiting therapeutic options. A five-center study tested 103 contemporary clinical
Acinetobacter
spp., including MDR strains, by reference broth microdilution and disk diffusion (15-μg disk content) methods against tigecycline. Applying U.S. Food and Drug Administration tigecycline breakpoint criteria for
Enterobacteriaceae
(susceptibility at ≤2 μg/ml [≤1 μg/ml by the European Committee on Antimicrobial Susceptibility Testing]; disk diffusion breakpoints at ≥19 mm and ≤14 mm) to
Acinetobacter
spp. led to an unacceptable error rate (23.3%). However, an adjustment of tigecycline disk diffusion breakpoints (susceptible/resistant) to ≥16/≤12 mm reduced intermethod errors to an acceptable level (only 9.7%, all minor).
Age-Related Urinary Excretion of BK Polyomavirus by Nonimmunocompromised Individuals
Authors: Zhong Shan , Zheng Huai-Ying , Suzuki Motofumi , Chen Qin , Ikegaya Hiroshi , Aoki Naoto , Usuku Shuzo , Kobayashi Nobuyoshi , Nukuzuma Souichi , Yasuda Yukiharu , Kuniyoshi Noboru , Yogo Yoshiaki , Kitamura Tadaichi
Published: November 2006

Two polyomaviruses, BK virus (BKV) and JC virus (JCV), are ubiquitous in the human population, generally infecting children asymptomatically and then persisting in renal tissue. It is generally thought that reactivation leads to productive infection for both viruses, with progeny shed in the urine. Several studies have shown that the rate of JC viruria increases with the age of the host, but a systematic approach to examine the shedding of BKV has not been developed. To elucidate the relationship between BK viruria and host age, we obtained urine from donors (healthy volunteers or nonimmunocompromised patients) who were divided into nine age groups, each containing 50 members. A high-sensitivity PCR was used to detect BKV and JCV DNA from urinary samples, and the specificity of amplification was confirmed by sequencing or restriction analysis of the amplified fragments. The rate of BK viruria was relatively low in subjects aged <30 years but gradually increased with age in subjects aged ≥30 years. However, BK viruria was less frequent than JC viruria in adults. The detected BKV isolates were classified into subtypes, and detection rates for individual subtypes were compared among age groups; this analysis showed that viruria of subtypes I (the most prevalent subtype) and IV (the second most prevalent subtype) occurred more frequently in older subjects. Therefore, our results reveal new aspects of BK viruria in nonimmunocompromised individuals.
Prevalence and Antibacterial Susceptibility of
mef
(A)-Positive Macrolide-Resistant
Streptococcus pneumoniae
over 4 Years (2000 to 2004) of the PROTEKT US Study
Authors: Farrell David J. , File Thomas M. , Jenkins Stephen G.
Published: November 2006

In the United States, approximately 30% of
Streptococcus pneumoniae
isolates are macrolide (erythromycin [ERY]) resistant (ERSP), most commonly due to expression of the
mef
(A) gene previously associated with lower-level ERY resistance (ERY
r
; MIC = 1 to 4 μg/ml). The data from the PROTEKT US surveillance study were analyzed to evaluate the prevalence and antibacterial susceptibility of
mef
(A)-positive ERSP. In all, 26,634 isolates of
S. pneumoniae
were collected in the United States between 2000 and 2004 from centers common to all years. ERY
r
was stable at approximately 29% over the 4 years, but the proportion of ERSP isolates positive for
mef
(A) alone decreased (year 1 [2000 to 2001], 69.0%; year 4 [2003 to 2004], 60.7%), with the sharpest declines seen in isolates from patients from 0 to 2 years of age. Conversely, the proportion isolates positive for both
erm
(B) and
mef
(A) increased over the duration of the present study (year 1, 9.3%; year 4, 19.1%), a change that was again most marked in patients aged ≤2 years. The majority of ERSP isolates expressing
mef
(A) alone exhibited higher than previously reported levels of ERY
r
(MIC
90
= 16 μg/ml). However, the ketolide antibacterial telithromycin consistently demonstrated in vitro activity against these isolates over the 4 years of the study (MIC
90
= 0.5 to 1 μg/ml).
Clonal Structure of
Enterococcus faecalis
Isolated from Polish Hospitals: Characterization of Epidemic Clones
Authors: Kawalec Magdalena , Pietras Zbigniew , Daniłowicz Emilia , Jakubczak Aleksandra , Gniadkowski Marek , Hryniewicz Waleria , Willems Rob J. L.
Published: November 2006

To study the population structure of
Enterococcus faecalis
from Polish hospitals, 291 isolates were typed by pulsed-field gel electrophoresis and a novel multilocus sequence typing scheme (P. Ruiz-Garbajosa et al., J. Clin. Microbiol. 44:2220-2228, 2006). The isolates originated from geographically widespread medical institutions and were recovered during a 10-year period (1996 to 2005) from different clinical sources. The analysis grouped the isolates into five epidemic and 71 sporadic clones. The importance of the previously identified global clonal complexes CC2 and CC9 was corroborated by our findings that two of the Polish epidemic clones, A and J, were classified into these clonal complexes (CCs). However, the two most predominant clones, C (ST40) and F (CC87), did not cluster in the aforementioned CCs and may represent novel epidemic CCs. These clones may have emerged in Central Europe. Clone F, carrying glycopeptide resistance determinants of VanA or VanB phenotypes, caused several outbreaks in hematology units and appeared to be the most prevalent clone in recent years in Poland. Antimicrobial susceptibility testing and additional tests for pathogenicity-related phenotypes (hemolysin and gelatinase production) and genes (
asa1
and
esp
) were performed to further characterize these epidemic clones. Multidrug resistance, glycopeptide resistance, presence of
asa1
, and production of hemolysin appeared to be statistically significant features related to epidemicity. Production of gelatinase was significant for two of the epidemic clones, whereas presence of the
esp
gene was not specific for the epidemic clones.
Statistical Analyses of Correlation between Fluconazole MICs for
Candida
spp. Assessed by Standard Methods Set Forth by the European Committee on Antimicrobial Susceptibility Testing (E.Dis. 7.1) and CLSI (M27-A2)
Authors: Rodriguez-Tudela Juan Luis , Donnelly J. Peter , Pfaller Michael A. , Chryssantou Erja , Warn Peter , Denning David W. , Espinel-Ingroff Ana , Barchiesi Francesco , Cuenca-Estrella Manuel
Published: November 2006

The European Committee on Antimicrobial Susceptibility Testing (EUCAST) Subcommittee on Antifungal Susceptibility Testing recently published a standard for determining the susceptibility of fermentative yeasts to antifungals. From the beginning, the EUCAST and its North American counterpart, the CLSI, decided to work together in order to establish common standards. As part of this exercise, the susceptibility of a set of 475 yeast isolates was tested by both standards. The intraclass correlation coefficient and the equations defining the linear regression between both methods were estimated. Both methods produced very similar results, with an intraclass correlation coefficient of 0.954 (0.945 to 0.962), although linear regression analysis shows that the EUCAST standard resulted in slightly lower MICs. There were only eight isolates showing at least four twofold dilution MIC differences between both standards. After 24 h of incubation, the MICs obtained by the CLSI method were equivalent to those obtained by the EUCAST standard. In summary, both methods produce very similar MICs, indicating that methodology does not pose any obstacle to obtaining uniform standards for antifungal susceptibility testing of yeasts.
The Adenovirus L4 33-Kilodalton Protein Binds to Intragenic Sequences of the Major Late Promoter Required for Late Phase-Specific Stimulation of Transcription
Authors: Ali Humayra , LeRoy Gary , Bridge Gemma , Flint S. J.
Published: November 2006

The adenovirus late IVa
2
protein is required for maximally efficient transcription from the viral major late (ML) promoter, and hence, the synthesis of the majority of viral late proteins. This protein is a sequence-specific DNA-binding protein that also promotes the assembly of progeny virus particles. Previous studies have established that a IVa
2
protein dimer (DEF-B) binds specifically to an intragenic ML promoter sequence necessary for late phase-specific stimulation of ML transcription. However, activation of transcription from the ML promoter correlates with binding of at least one additional infected-cell-specific protein, termed DEF-A, to the promoter. Using an assay for the DNA-binding activity of DEF-A, we identified the unknown protein by using conventional purification methods, purification of FLAG-tagged IVa
2
-protein-containing complexes, and transient synthesis of viral late proteins. The results of these experiments established that the viral L4 33-kDa protein is the only component of DEF-A: the IVa
2
and L4 33-kDa proteins are necessary and sufficient for formation of all previously described complexes in the intragenic control region of the ML promoter. Furthermore, the L4 33-kDa protein binds to the promoter with the specificity characteristic of DEF-A and stimulates transcription from the ML promoter in transient-expression assays.
Loss of Naïve Cells Accompanies Memory CD4
+
T-Cell Depletion during Long-Term Progression to AIDS in Simian Immunodeficiency Virus-Infected Macaques
Authors: Nishimura Yoshiaki , Igarashi Tatsuhiko , Buckler-White Alicia , Buckler Charles , Imamichi Hiromi , Goeken Robert M. , Lee Wendy R. , Lafont Bernard A. P. , Byrum Russ , Lane H. Clifford , Hirsch Vanessa M. , Martin Malcolm A.
Published: November 2006

Human immunodeficiency virus and simian immunodeficiency virus (SIV) induce a slow progressive disease, characterized by the massive loss of memory CD4
+
T cells during the acute infection followed by a recovery phase in which virus replication is partially controlled. However, because the initial injury is so severe and virus production persists, the immune system eventually collapses and a symptomatic fatal disease invariably occurs. We have assessed CD4
+
T-cell dynamics and disease progression in 12 SIV-infected rhesus monkeys for nearly 2 years. Three macaques exhibiting a rapid progressor phenotype experienced rapid and irreversible loss of memory, but not naïve, CD4
+
T lymphocytes from peripheral blood and secondary lymphoid tissues and died within the first 6 months of virus inoculation. In contrast, SIV-infected conventional progressor animals sustained marked but incomplete depletions of memory CD4
+
T cells and continuous activation/proliferation of this T-lymphocyte subset. This was associated with a profound loss of naïve CD4
+
T cells from peripheral blood and secondary lymphoid tissues, which declined at rates that correlated with disease progression. These data suggest that the persistent loss of memory CD4
+
T cells, which are being eliminated by direct virus killing and activation-induced cell death, requires the continuous differentiation of naïve into memory CD4
+
T cells. This unrelenting replenishment process eventually leads to the exhaustion of the naïve CD4
+
T-cell pool and the development of disease.
Identification of the FHL2 Transcriptional Coactivator as a New Functional Target of the E7 Oncoprotein of Human Papillomavirus Type 16
Authors: Campo-Fernández Beatriz , Morandell Dieter , Santer Frédéric R. , Zwerschke Werner , Jansen-Dürr Pidder
Published: November 2006

We identified the transcriptional coactivator FHL2 as a novel target of the human papillomavirus type 16 (HPV-16) E7 oncoprotein, which plays a major role in cell transformation. The interaction with FHL2 is abolished by mutations in conserved regions 1 and 2 and in the C-terminal zinc finger domain of E7, all required for its transforming potential. We found that E7 impairs the coactivator function of FHL2 on both β-catenin/LCF-dependent and AP-1-dependent promoters. Thus, the interaction with HPV-16 E7 leads to a promoter-specific impairment of FHL2 function and this may contribute to cell transformation.
Role of the Amphipathic Peptide of Semliki Forest Virus Replicase Protein nsP1 in Membrane Association and Virus Replication
Authors: Spuul Pirjo , Salonen Anne , Merits Andres , Jokitalo Eija , Kääriäinen Leevi , Ahola Tero
Published: November 2006

Semliki Forest virus RNA replication takes place in association with specific cytoplasmic vacuoles, derived from the endosomal apparatus. Of the four virus-encoded replicase proteins, nsP1 serves as the membrane anchor of the replication complex. An amphipathic peptide segment, G
245
STLYTESRKLLRSWHLPSV
264
, has been implicated in the membrane binding of nsP1. nsP1 variants with changes within the peptide were studied after protein expression and in the context of virus infection. Proteins with mutations R253E and W259A accumulated in the cytoplasm and were very poorly palmitoylated. The same mutations also drastically affected the localization of the precursor polyprotein P123, and they were lethal when introduced into the virus genome. Mutations R253A and L255A+L256A partially changed the localization of nsP1, and the respective viruses acquired compensatory changes. L255A+L256A only yielded virus encoding L255A+L256V, indicating the importance of a hydrophobic residue in the central 256 position. When fused to green fluorescent protein, the peptide was required in at least two tandem copies to effect a change in localization, but even then the fusion protein was associated with membranes in a nonspecific manner. Thus, the amphipathic peptide is a crucial element for the membrane association of nsP1 and the replication complex. It provides essential affinity for membranes, and other regions of nsP1 also appear to contribute to the localization of the protein.
Lysis of Human Immunodeficiency Virus Type 1 by a Specific Secreted Human Phospholipase A2
Authors: Kim Jae-Ouk , Chakrabarti Bimal K. , Guha-Niyogi Anuradha , Louder Mark K. , Mascola John R. , Ganesh Lakshmanan , Nabel Gary J.
Published: November 2006

Phospholipase A2(PLA2) proteins affect cellular activation, signal transduction, and possibly innate immunity. A specific secretory PLA2, sPLA2-X, is shown here to neutralize human immunodeficiency virus type 1 (HIV-1) through degradation of the viral membrane. Catalytic function was required for antiviral activity, and the target cells of infection were unaffected. sPLA2-X potently reduced gene transfer of HIV-1 Env-pseudotyped lentivirus vectors and inhibited the replication of both CCR5- and CXCR4-tropic HIV-1 in human CD4+T cells. Virions resistant to damage by antibody and complement were sensitive to lysis by sPLA2-X, suggesting a novel mechanism of antiviral surveillance independent of the acquired immune system.
Packaging of the Virion Host Shutoff (Vhs) Protein of Herpes Simplex Virus: Two Forms of the Vhs Polypeptide Are Associated with Intranuclear B and C Capsids, but Only One Is Associated with Enveloped Virions
Authors: Read G. Sullivan , Patterson Mary
Published: November 2006

The virion host shutoff (Vhs) protein (UL41) is a minor component of herpes
simplex virus virions which, following penetration, accelerates
turnover of host and viral mRNAs. Infected cells contain 58-kDa and
59.5-kDa forms of Vhs, which differ in the extent of phosphorylation,
yet only a 58-kDa polypeptide is incorporated into virions. In
pulse-chase experiments, the primary Vhs translation product comigrated
in sodium dodecyl sulfate-polyacrylamide gel electrophoresis with the
58-kDa virion polypeptide, and could be chased to 59.5 kDa. While both
59.5-kDa and 58-kDa forms were found in nuclear and cytoplasmic
fractions, the 59.5-kDa form was significantly enriched in the nucleus.
Both forms were associated with intranuclear B and C capsids, yet only
the 58-kDa polypeptide was found in enveloped cytoplasmic virions. A
58-kDa form, but not the 59.5-kDa form, was found in L particles,
noninfectious particles that contain an envelope and tegument but no
capsid. The data suggest that virions contain two populations of Vhs
that are packaged by different pathways. In the first pathway, the
primary translation product is processed to 59.5 kDa, is transported to
the nucleus, binds intranuclear capsids, and is converted to 58 kDa at
some stage prior to final envelopment. The second pathway
does not involve the 59.5-kDa form or interactions between Vhs and
capsids. Instead, the primary translation product is phosphorylated to
the 58-kDa virion form and packaged through interactions with other
tegument proteins in the cytoplasm or viral envelope proteins at the
site of final
envelopment.
Forward backward studies of 22Ne(28Si)-emulsion interactions at (4.1-4.5) AGeV/c
Authors: Abdel-Aziz S S
Published: November 2006

The characteristics of nucleus–nucleus collisions at high energies are investigated for the interaction of 22Ne and 28Si with emulsion nuclei . The multiplicity and correlations of the forward (θ < 90°) and backward (θ ≥ 90°) secondary particles emitted are calculated according to the modified cascade and modified Fritiof models. The predictions of the two models are compared with experimental data at an incident momentum of (4.1–4.5) GeV/c per nucleon. Both models depend on the Monte Carlo techniques where the modified cascade model implies the superposition of nucleon–nucleon interactions, and the modified Fritiof model utilizes the Regge theory for the description of the cascading process. Comparison with data shows no clear preference of one model over the other. However, the modified Fritiof model seems to be nearer to the experimental data than the modified cascade model.PACS No.: 13.85.–t
Effect of vegetation control on the survival and growth of Scots pine and Norway spruce planted on former agricultural land
Authors: Jylhä Paula , Hytönen Jyrki
Published: November 2006

The effects of competing vegetation and various weed control methods (fibreboard mulch, cover crop of clover, and various herbicides) on the survival and growth of Scots pine (Pinus sylvestris L.) and Norway spruce (Picea abies (L.) Karst.) seedlings were compared based on 6- to 11-year data from a field experiment established as a randomized block design with three replications in southern Finland. The most effective herbicides significantly reduced the weed cover for 2 or 3 years. The mortality, basal diameter, height, and volume of Scots pine significantly correlated with percent cover of the ground vegetation. In the case of Norway spruce, only the stem diameter correlated significantly with percent cover of the competing vegetation. This was probably due to the severe frost damage that occurred in the third growing season. The mortality of pine began to increase only when the vegetation cover had exceeded 60%. After 11 years, the stand volume on the pine plots treated with terbuthylazine was almost double that of the untreated plots (32 vs. 17 m3·ha–1), but this difference was not statistically significant. Mulch and cover crop did not significantly affect pine growth or mortality. Recurrent frost damage may explain why none of the studied treatments significantly affected the mortality and volume growth of Norway spruce.
Interactions between influences of genotype and grass competition on growth and wood stiffness of juvenile radiata pine in a summer-dry environment
Authors: Mason Euan G
Published: November 2006

Clones of radiata pine (Pinus radiata D. Don) were established in two experiments on two contrasting pasture sites in Canterbury, New Zealand, with four levels of competition from grass as main plots within each experiment. Control was extended over the first 5 years at one site, whereas grass at the other site was controlled by a single herbicidal spray immediately after planting. At the latter site, 1 m diameter spots cleared with herbicide were compared with the same size spot created using a woven mat. Grass competition added up to 3 years to a rotation, and the gain from control was correlated with spot size. Competition control was most critical during the first year after planting. Trees grown within spots cleared by mats grew more slowly than those in weed-free spots cleared with herbicide. Green dynamic modulus of elasticity was related to genotype and increased with both slenderness and higher levels of pruning. Significant interactions between genotype and level of competition were observed for growth, indicating that choice of genotype can be a useful way of coping with pasture competition if managers wish to reduce the use of herbicides.
The influence of irrigation and fertilization on heartwood and sapwood contents in 18-year-old Eucalyptus globulus trees
Authors: Miranda Isabel , Gominho Jorge , Lourenço Ana , Pereira Helena
Published: November 2006

The quality of wood from 18-year-old Tasmanian bluegum (Eucalyptus globulus Labill.) trees was assessed in relation to heartwood content, accumulation of extractives, and pulp yield using two growth conditions: control (C) and growth optimized by irrigation and fertilization in the first 6 years of growth (IL). Within the tree, heartwood content decreased from the base upwards, representing, on average, 77.7% and 67.6% at the base and 7.0% and 4.8% at 29.3 m height for IL and C trees, respectively. Heartwood volume represented 65.6% and 55.6% of total tree volume for IL and C trees, respectively. Heartwood content was positively correlated with tree growth, while sapwood content remained rather constant, with a radial width of approximately 2 cm. Heartwood contained more extractives than sapwood (5.3% vs. 4.0%) and pulp yield was lower from heartwood than from sapwood (58.0% vs. 56.0%). Pulp yield was negatively correlated with content of extractives. No difference in extractives or pulp yield was found between IL and C trees. The presence of heartwood decreases the quality of raw material for pulping and should be regarded as a stem-quality variable in eucalypt forestry.
Use of growth curve derivatives to illustrate acceleration and deceleration of growth in young plantations under variable competition
Authors: Newton Michael , Cole Elizabeth C
Published: November 2006

Deceleration of growth rates can give an indication of competition and the need for thinning in early years but can be difficult to detect. We computed the first and second derivatives of the von Bertalanffy – Richards equation to assess impacts of density and vegetation control in young plantations in western Oregon. The first derivative describes the response in growth and the second derivative describes the change in growth over time. Three sets of density experiments were used: (i) pure Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco), (ii) mixed Douglas-fir and grand fir (Abies grandis (Dougl. ex D. Don) Lindl.), and (iii) mixed western hemlock (Tsuga heterophylla (Raf.) Sarg.) and red alder (Alnus rubra Bong.). Original planting densities ranged from 475 to 85 470 trees·ha–1 (4.6 m × 4.6 m to 0.34 m × 0.34 m spacing); western hemlock and red alder plots were weeded and unweeded. For the highest densities, the second derivative was rarely above zero for any of the time periods, indicating that the planting densities were too high for tree growth to enter an exponential phase. As expected, the lower the density, the greater and later the peak in growth for both the first and second derivatives. Weeding increased the growth peaks, and peaks were reached earlier in weeded than in unweeded plots. Calculations of this sort may help modelers identify when modifiers for competition and density are needed in growth equations. Specific applications help define onset of competition, precise determining of timing of peak growth, period of acceleration of growth, and interaction of spacing and age in determination of peaks of increment or acceleration or deceleration.
Five-year growth responses of Douglas-fir, western hemlock, and western redcedar seedlings to manipulated levels of overstory and understory competition
Authors: Harrington Timothy B
Published: November 2006

Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco), western hemlock (Tsuga heterophylla (Raf.) Sarg.), and western redcedar (Thuja plicata Donn ex D. Don) seedlings were planted in March 2001 within three clearcut-harvested, shelterwood, or thinned stands of mature Douglas-fir near Olympia, Washington. From 2002 to 2005, areas of vegetation control of 0, 4.5, or 9 m2were maintained with herbicides around a total 162 seedlings per species. Photosynthetically active radiation (PAR) was 34%, 62%, and 100% of full sunlight in thinned stands, shelterwoods, and clearcuts, respectively. Effects of overstory level and vegetation control on seedling growth and resource availability generally were additive. Seedling stem volume index in clearcuts averaged four to eight times that observed in thinned stands, and with vegetation control, it averaged two to four times that observed without it. In thinned stands, relative growth rate of seedling stem volume index had a positive linear relationship with PAR (R2 = 0.38). Foliar nitrogen content of Douglas-fir explained 71% of the variation in relative growth rate. Factors explaining the most variation in foliar nitrogen content differed between thinned stands (PAR, R2 = 0.34) and clearcuts or shelterwoods (midday water potential, R2 = 0.63), suggesting that light and root competition, respectively, were the primary growth-limiting factors for these overstory levels.
Fates of live trees retained in forest cutting units, western Cascade Range, Oregon
Authors: Busby Posy E , Adler Peter , Warren Timothy L , Swanson Frederick J
Published: November 2006

Live trees, standing dead trees, and downed logs have been retained in some forest harvest sites in the Pacific Northwest to fulfill various ecological objectives. To assess the fates of retained trees following partial cutting of mature forests in the central western Cascade Range in Oregon, we inventoried standing live and dead trees and toppled trees in 21 cutting units in 1993 and 2001. In 1993, 1–10 years after cutting, an average of 65% of the initially retained trees (average of counts for all sites) were alive and standing, 12% had been toppled or topped by wind, 13% had become snags by natural processes, and 10% were converted to snags by management action, including cutting, blasting, girdling, and inoculation with fungi. By 2001, when cutting-unit ages ranged from 9 to 18 years, 54% of the retained trees were alive and standing, 10%–21% had been toppled or topped by wind, 11%–22% had become snags by natural processes, and 14% had been converted to snags by management action. The highest levels of mortality occurred at sites with abundant intentional snag creation and (or) prescribed fire following harvest. The rate of mortality due to windthrow declined over time, possibly because the remaining trees were more windfirm.
Relationships between root form and growth, stability, and mortality in planted versus naturally regenerated lodgepole pine in north-central British Columbia
Authors: Robert Jeanne A , Lindgren B Staffan
Published: November 2006

The roots of container-grown and manually planted lodgepole pine, Pinus contorta Dougl. ex Loud. var. latifolia Engelm., are often deformed, potentially impacting their health relative to that of naturally regenerated trees. We evaluated 12 root characteristics to elucidate the type and severity of root deformities in planted pine aged 3–10 years, as well as to determine the impact of root form on their growth and stability. Results showed that root deformity is widespread: 95.0% of planted trees versus 50.9% of naturally regenerated trees had either moderate or severe root deformities. A logistic regression using the 12 root characteristics strongly distinguished between planted and naturally regenerated trees. Aboveground growth form was affected in that planted trees had a lower height-to-diameter ratio than naturally regenerated trees. In young planted trees with low or moderate root deformities, but not in trees with severely deformed roots (65.0% of all planted trees in our study), both height- and diameter-growth rates were higher than in naturally regenerated trees. Growth differences may be attributed to differential resource allocation resulting from translocation inhibition caused by root deformation. In spite of very different root systems, there was no difference in the horizontal stability of planted versus naturally regenerated trees. However, planted trees have a significantly lower root cross-sectional area and may therefore be at a higher risk of mortality, primarily from attack by the Warren root collar weevil, Hylobius warreni Wood.
Impact of root-rot pathogens on forest succession in unmanaged Pinus mugo stands in the Central Alps
Authors: Bendel M , Kienast F , Rigling D , Bugmann H
Published: November 2006

In the mountain pine (Pinus mugo subsp. uncinata (DC.) Domin) forests of the Swiss National Park in the Central Alps, disease centers associated with the root-rot fungi Heterobasidion annosum (Fr.) Bref. and Armillaria spp. are characteristic elements. We assessed the impact of these pathogens on forest dynamics by studying transects running across disease centers into the adjacent forest. Overall, mountain pine was the most abundant regenerating tree species and accounted for 84% of all seedlings (<20 cm high) and 93% of all saplings (20–130 cm high), whereas Swiss stone pine (Pinus cembra L.) was less frequent (15% seedlings : 7% saplings). The density of mountain pine seedlings did not differ significantly between the disease centers and the adjacent forest, whereas mountain pine saplings were more frequent within the disease centers, indicating that growth from the seedling to the sapling stage was favoured in disease centers. There was significantly more dead wood and a greater diversity of plant species in the disease centers than in the adjacent forest. The results suggest that root-rot fungi slow down succession towards stands with a higher proportion of P. cembra by causing premature mortality of mountain pines and creating disease centers with dense mountain pine regeneration.
Trade-offs between competition and facilitation: a case study of vegetation management in the interior cedar–hemlock forests of southern British Columbia
Authors: Simard Suzanne , Vyse Alan
Published: November 2006

Vegetation-management practices are applied in temperate-zone forests on the assumption that changing the competitive environment between conifers and unwanted vegetation will improve conifer productivity. We review this assumption using research examining interactions between paper birch (Betula papyrifera Marsh.) and conifers in the highly productive Interior Cedar Hemlock zone of British Columbia. We have found that both competition and facilitation are important in young plantations, where paper birch competes for light, reducing growth of shade-intolerant conifers, but having a facilitative effect on shade-tolerant conifers. This facilitative effect may result from greater ectomycorrhizal diversity, population sizes of Armillaria ostoyae (Romagn.) Herink antagonistic bacteria, and associative nitrogen fixation in plantations where interior Douglas-fir (Pseudotsuga menziesii var. glauca (Beissn.) Franco) is mixed with paper birch. Where paper birch is manually cut or girdled, conifers grow faster in diameter, but more die as a result of A. ostoyae root disease, and these responses increase with increasing weeding intensity. The weeding treatments do not affect plant community species richness but reduce paper birch dominants and increase understory structural diversity. British Columbia forest policy has been slow to respond to these findings, and we suggest that as a result, the forested landscape incurs substantial risk. We propose additional pathways for managing Interior Cedar Hemlock mixtures to ensure that the natural mix of forest types in the landscape is maintained.
Assessment of temporal changes in aboveground forest tree biomass using aerial photographs and allometric equations
Authors: Massada Avi Bar , Carmel Yohay , Tzur Gilad Even , Grünzweig José M , Yakir Dan
Published: November 2006

Studies of forest biomass dynamics typically use long-term forest inventory data, available in only a few places around the world. We present a method that uses photogrammetric measurements from aerial photographs as an alternative to time-series field measurements. We used photogrammetric methods to measure tree height and crown diameter, using four aerial photographs of Yatir Forest, a semi-arid forest in southern Israel, taken between 1978 and 2003. Height and crown-diameter measurements were transformed to biomass using an allometric equation generated from 28 harvested Aleppo pine (Pinus halepensis Mill.) trees. Mean tree biomass increased from 6.37 kg in 1978 to 97.01 kg in 2003. Mean plot biomass in 2003 was 2.48 kg/m2 and aboveground primary productivity over the study period ranged between 0.14 and 0.21 kg/m2 per year. There was systematic overestimation of tree height and systematic underestimation of crown diameter, which was corrected for at all time points between 1978 and 2003. The estimated biomass was significantly related to field-measured biomass, with an R2 value of 0.78. This method may serve as an alternative to field sampling for studies of forest biomass dynamics, assuming that there is sufficient spatial and temporal coverage of the investigated area using high-quality aerial photography, and that the tree tops are distinguishable in the photographs.