bluuebunny/crossref_metadata_2025 huggingface dataset:
Use of an Oligonucleotide Array for Laboratory Diagnosis of Bacteria Responsible for Acute Upper Respiratory Infections
Authors: Roth Stina B. , Jalava Jari , Ruuskanen Olli , Ruohola Aino , Nikkari Simo
Published: September 2004

We developed a diagnostic array of oligonucleotide probes targeting species-specific variable regions of the genes encoding topoisomerases GyrB and ParE of respiratory bacterial pathogens. Suitable broad-range primer sequences were designed based on alignment of
gyrB/parE
sequences from nine different bacterial species. These species included
Corynebacterium diphtheriae
,
Fusobacterium necrophorum
,
Haemophilus influenzae
,
Legionella pneumophila
,
Moraxella catarrhalis
,
Mycoplasma pneumoniae
,
Staphylococcus aureus
,
Streptococcus pneumoniae
, and
Streptococcus pyogenes
. Specific probe sequences were selected by comparative analysis against the European Bioinformatics Database, as well as
gyrB/parE
sequences generated for this study. To verify specificity, at least six initial oligonucleotide probe sequences per bacterial species were tested by hybridization on a solid glass support using culture collection strains as templates. Finally, three oligonucleotide probes per bacterial species were utilized to examine 65 middle ear fluid and 29 throat swab samples. The sensitivities of the developed assay compared to classic culture from middle ear fluid samples for
H. influenzae
,
M. catarrhalis
, and
S. pneumoniae
were 96 (93 for culture), 73 (93 for culture), and 100% (78% for culture), respectively. No cross-reactivity with bacterial species belonging to the normal oral flora was observed when the 29 throat swab samples were studied. The sensitivity of the assay to detect
S. pyogenes
from these samples was 93% (80% for culture). These results provide a proof of concept for the diagnostic use of microarray technology based on broad-range topoisomerase gene amplification, followed by hybridization and specific detection of bacterial species.
Rapid and Specific Detection of
tdh
,
trh
1, and
trh
2 mRNA of
Vibrio parahaemolyticus
by Transcription-Reverse Transcription Concerted Reaction with an Automated System
Authors: Nakaguchi Yoshitsugu , Ishizuka Tetsuya , Ohnaka Satoru , Hayashi Toshinori , Yasukawa Kiyoshi , Ishiguro Takahiko , Nishibuchi Mitsuaki
Published: September 2004

Vibrio parahaemolyticus
strains carrying the thermostable direct hemolysin (TDH)
tdh
gene, the TDH-related hemolysin (
trh
) gene, or both genes are considered virulent strains. We previously demonstrated that the transcription-reverse transcription concerted (TRC) method could be used to quantify the amount of mRNA transcribed from the
tdh
gene by using an automated detection system. In this study, we devised two TRC-based assays to quantify the mRNAs transcribed from the
trh
1 and
trh
2 genes, the two representative
trh
genes. The TRC-based detection assays for the
tdh
,
trh
1, and
trh
2 transcripts could specifically and quantitatively detect 10
3
to 10
7
copies of the corresponding calibrator RNAs. We examined by the three TRC assays the total RNA preparations extracted from 103 strains of
Vibrio parahaemolyticus
carrying the
tdh
,
trh
1, or
trh
2 gene in various combinations. The
tdh
,
trh
1, and
trh
2 mRNAs in the total RNA preparations were specifically quantified, and the time needed for detection ranged from 9 to 19 min, from 14 to 18 min, and from 9 to 12 min, respectively. The results showed that this automated TRC assays could detect the
tdh
,
trh
1, and
trh
2 mRNAs specifically, quantitatively, and rapidly. The relative levels of TDH determined by the immunological method and that of
tdh
mRNA determined by the TRC assays for most
tdh
-positive strains correlated. Interestingly, the levels of TDH produced from the strains carrying both
tdh
and
trh
genes were lower than those carrying only the
tdh
gene, whereas the levels of mRNA did not significantly differ between the two groups.
Simple Chemical Extraction Method for DNA Isolation from
Aspergillus fumigatus
and Other
Aspergillus
Species
Authors: Jin J. , Lee Y.-K. , Wickes B. L.
Published: September 2004

DNA was successfully isolated from numerous
Aspergillus
spp. by use of a commercial kit. DNA that was easily digested and yielded PCR products up to 8.5 kb in size was recovered from broth or agar cultures. The ease and speed of this protocol provide an alternative to physical methods of DNA isolation.
Surveillance Study (2000 to 2001) of G- and P-Type Human Rotaviruses Circulating in South Korea
Authors: Min Bok Soon , Noh Yoon Ju , Shin Jin Ho , Baek Sun Young , Kim Jae Ok , Min Kyung Il , Ryu Seung Rel , Kim Byoug Guk , Kim Do Keun , Lee Seok Ho , Min Hong Ki , Ahn Byung Yoon , Park Sue Nie
Published: September 2004

Human
rotavirus VP4 and VP7 gene sequences were amplified by reverse
transcription-PCR from 53% (322 of 607) of fecal specimens
collected from children with severe diarrhea who visited hospitals in
six urban areas of South Korea in 2000 and 2001. G2 was the most
frequently found G type (constituted 50.6%), followed by G1
(30.1%) and G4 (13.0%). Although the P types of high
incidence were P[4] (53.1%) and P[8]
(21.4%), a significant incidence of P[6]
(20.2%) was also noticeable. The commonest G- and P-type
combination found in this study was G2P[4], rather than
G1P[8], the most prevalent type known
worldwide.
Usefulness of the GenoType MTBC Assay for Differentiating Species of the
Mycobacterium tuberculosis
Complex in Cultures Obtained from Clinical Specimens
Authors: Richter Elvira , Weizenegger Michael , Fahr Anne-Marie , Rüsch-Gerdes Sabine
Published: September 2004

A novel DNA strip assay, GenoType MTBC, was evaluated for differentiation of
Mycobacterium tuberculosis
complex species from 77 positive liquid cultures in clinical practice. Species identification (
M. tuberculosis
[71 strains],
Mycobacterium bovis
subsp.
bovis
[5 strains], and
Mycobacterium africanum
subtype I [1 strain]) results were identical to conventional results. The sensitivity was slightly higher for this test than for the AccuProbe assay.
Comparison of the Real-Time PCR Method and the Gen-Probe Amplified
Mycobacterium tuberculosis
Direct Test for Detection of
Mycobacterium tuberculosis
in Pulmonary and Nonpulmonary Specimens
Authors: Lemaître Nadine , Armand Sylvie , Vachée Anne , Capilliez Odile , Dumoulin Christine , Courcol René J.
Published: September 2004

Real-time PCR was compared to Amplified
Mycobacterium tuberculosis
Direct Test (AMTDII) for 100 clinical specimens. The overall sensitivities of the real-time PCR method and AMTDII were similar for respiratory and nonrespiratory specimens. However, real-time PCR seemed to be less susceptible to amplification inhibitors than AMTDII.
Fosfomycin and Rifampin Disk Diffusion Tests for Detection of
Escherichia coli
Mutator Strains
Authors: Galán Juan-Carlos , Tato Marta , Baquero María-Rosario , Turrientes Carmen , Baquero Fernando , Martinez José-Luis
Published: September 2004

A simple method, using commercial disks to detect
Escherichia coli
mutator strains, is proposed. The breakpoint for detecting strains with a mutation frequency ≥5 × 10
−7
was established at ≥70 and ≥20 colonies in the inhibition zone of fosfomycin and rifampin disks, respectively, after seeding 100 μl of an overnight culture. Strains with <30 and <10 colonies in fosfomycin and rifampin inhibition zones are presumptively non-mutators.
Community-Acquired
Clostridium difficile
Diarrhea Caused by Binary Toxin, Toxin A, and Toxin B Gene-Positive Isolates in Hungary
Authors: Terhes Gabriella , Urbán Edit , Sóki József , Hamid Kanjo Abdul , Nagy Elisabeth
Published: September 2004

The aim of this work was to study the toxin types of
Clostridium difficile
isolates originating from different parts of Hungary. A PCR method was used for amplification of the two major toxin genes and the binary toxin gene and to detect the deletion or insertion in the 3′ end of the toxin A gene. The findings were compared with the results of cytotoxicity assays on the HeLa cell line. One hundred twelve isolates were tested; the toxin A and toxin B genes were detected in 79 strains by the PCR method. All of the isolates that were positive by the PCR method were also positive by the cytotoxicity assay. All of the other strains (
n
= 33) were negative for the toxin A and toxin B genes; in these cases, cytopathic effects on the cell line were not observed. No
tcdA
-negative and
tcdB
-positive isolates were found by the PCR method. In two cases, the presence of a binary toxin gene was observed by PCR; both isolates that were isolated from diarrheal feces carried the
tcdA
and
tcdB
genes. No prior hospitalization had occurred in either case.
In Vitro Susceptibilities of Isolates of
Sporothrix schenckii
to Itraconazole and Terbinafine
Authors: Kohler Lidiane Meire , Monteiro Paulo César Fialho , Hahn Rosane Christine , Hamdan Júnia Soares
Published: September 2004

Thirty isolates of the yeast form of
Sporothrix schenckii
were evaluated for in vitro susceptibility to itraconazole and terbinafine by the recommended NCCLS modified technique (M27-A2). The MICs of itraconazole obtained oscillated between 0.062 and 4.0 μg/ml, and those of terbinafine oscillated between 0.007 and 0.50 μg/ml; therefore, terbinafine showed greater in vitro activity.
Prevalence of Hepatitis C Virus Infection among Hemodialysis Patients at a Tertiary-Care Hospital in Mexico City, Mexico
Authors: Méndez-Sánchez Nahum , Motola-Kuba Daniel , Chavez-Tapia Norberto C. , Bahena Jesús , Correa-Rotter Ricardo , Uribe Misael
Published: September 2004

We determined the prevalence of hepatitis C virus (HCV) in hemodialysis patients by antibody testing and HCV RNA determination by PCR. A total of 149 patients with kidney failure with replacement therapy were tested. The prevalence of anti-HCV was 6.7% (10 of 149 patients), and viremia was detectable in 8 of 149 (5%) patients. Three of 149 patients (2%) were anti-HCV negative with detectable HCV RNA.
Antimicrobial Susceptibilities of Invasive Pediatric
Abiotrophia
and
Granulicatella
Isolates
Authors: Zheng Xiaotian , Freeman Alexandra F. , Villafranca Jay , Shortridge Dee , Beyer Jill , Kabat William , Dembkowski Karen , Shulman Stanford T.
Published: September 2004

Abiotrophia
and
Granulicatella
species have been associated with various infections. Antimicrobial susceptibility data for these nutritionally variant streptococcus-like organisms, especially for pediatric isolates, are very limited. Little is known about the genetic bases of their resistance mechanisms. We report the results of identification to bacterial species level, antimicrobial susceptibility testing, macrolide resistance testing, and detection of genes encoding that resistance for a collection of 15 pediatric clinical isolates from normally sterile sites. Our results indicate that the prevalence of beta-lactam and macrolide resistance is high and that both
erm
and
mef
are found in these isolates.
Evaluation of Conventional Castaneda and Lysis Centrifugation Blood Culture Techniques for Diagnosis of Human Brucellosis
Authors: Mantur Basappa G. , Mangalgi Smita S.
Published: September 2004

We investigated the role of the lysis centrifugation blood culture technique over the conventional Castaneda technique for the diagnosis of human brucellosis. The lysis centrifugation technique has been found to be more sensitive in both acute (20% higher sensitivity;
P
< 0.00001) and chronic (40% higher sensitivity;
P
= 0.087) forms of brucellosis. The major advantage of lysis centrifugation was in the mean detection time, which was only 2.4 days in acute and 2.7 days in chronic cases, with 103 out of 110 (93.6%) and 17 out of 20 (85%) cultures from acute and chronic brucellosis, respectively, detected before the conventional culture was positive. Our results confirmed the potential usefulness of the lysis technique in diagnosis and institution of appropriate antibiotic therapy.
Detection of Hepatitis A Virus RNA in Saliva
Authors: Mackiewicz Vincent , Dussaix Elisabeth , Le Petitcorps Marie-France , Roque-Afonso Anne Marie
Published: September 2004

Hepatitis A virus (HAV) is shed in feces but also in saliva. HAV RNA was detected in saliva in five out of six acutely infected patients with HAV viremia. Serum and saliva sequences were identical. The simplicity of obtaining material allows the recommendation of the use of saliva for investigation of outbreaks.
Multicenter Validation of the
cppB
Gene as a PCR Target for Detection of
Neisseria gonorrhoeae
Authors: Bruisten S. M. , Noordhoek G. T. , van den Brule A. J. C. , Duim B. , Boel C. H. E. , El-Faouzi K. , du Maine R. , Mulder S. , Luijt D. , Schirm J.
Published: September 2004

The
cppB
gene is often used as a target for detection of
Neisseria gonorrhoeae
by PCR. Using a coded panel of 500 DNA samples, we determined that the
cppB
gene is missing in 5.8% of
N. gonorrhoeae
strains, and therefore we consider the
cppB
gene to be an unsuitable target.
Variability of Germinative Potential among Pathogenic Species of
Aspergillus
Authors: Araujo Ricardo , Rodrigues Acacio Gonçalves
Published: September 2004

The objective of our study was to evaluate parameters influencing the germination of
Aspergillus
conidia. Inoculum concentration and age significantly influenced germination. Different incubation temperatures revealed significant differences among
Aspergillus
species. The internal human milieu provides the ideal conditions for the development of invasive disease by
Aspergillus fumigatus
but restricts invasion by
Aspergillus flavus
and
Aspergillus niger
.
Sequencing and Phylogenetic Analysis of Human Genotype P[6] Rotavirus Strains Detected in Hungary Provides Evidence for Genetic Heterogeneity within the P[6] VP4 Gene
Authors: Bányai Krisztián , Martella Vito , Jakab Ferenc , Melegh Béla , Szücs György
Published: September 2004

Although rotavirus genotype P[6] is one of the three most common VP4 specificities associated with human infection, the relatively few sequence data available in public databases suggest that the genetic variability within P[6] might be presently unexplored. Thus far, two human P[6] lineages (M37-like and AU19-like) and a single porcine P[6] lineage (Gottfried-like) have been identified by phylogenetic analysis. Serologic studies demonstrated that these three lineages are antigenically distinct from each other, a finding based on which they were classified into three subtypes, P2A[6] (M37-like), P2B[6] (Gottfried-like), and P2C[6] (AU19-like). To study heterogeneity within this genotype, we selected for molecular characterization a total of six P[6] strains detected during an ongoing surveillance in Hungary. The variable region of the VP4 gene was subjected to sequencing and phylogenetic analysis. Our data indicated that these six strains fell into two phylogenetic lineages distinguishable from the human lineages M37-like and AU19-like and from the porcine lineage Gottfried-like. Further studies are needed to understand whether these two novel lineages are genuine human strains or might have originated from animal strains and to evaluate the antigenic relationship of the novel Hungarian P[6] strains to the three established subtypes.
Characterization of Avian H3N3 and H1N1 Influenza A Viruses Isolated from Pigs in Canada
Authors: Karasin Alexander I. , West Keith , Carman Suzanne , Olsen Christopher W.
Published: September 2004

H3N3 and H1N1 influenza A viruses were isolated from Canadian pigs in 2001 and 2002. These viruses are phylogenetically related to waterfowl viruses and antigenically distinct from reference swine influenza viruses. The isolation of these viruses reemphasizes the potential for interspecies transmission of influenza viruses from waterfowl to pigs in North America.
Pneumolysin Is a Key Factor in Misidentification of Macrolide-Resistant
Streptococcus pneumoniae
and Is a Putative Virulence Factor of
S. mitis
and Other Streptococci
Authors: Neeleman Chris , Klaassen Corné H. W. , Klomberg Debbie M. , de Valk Hanneke A. , Mouton Johan W.
Published: September 2004

We evaluated the applicability of
ply
PCR for confirmation of the identification of
Streptococcus pneumoniae. lytA
PCR, 16S rRNA sequencing, and amplified-fragment length polymorphism were used as reference methods. In contrast to the
lytA
gene, the
ply
gene proved to be not specific for
S. pneumoniae
. The presence of the
ply
gene in other streptococci, in particular
Streptococcus mitis
, suggests that pneumolysin plays a pathogenic role.
Comparison of the Sensititre YeastOne Colorimetric Antifungal Panel with a Modified NCCLS M38-A Method To Determine the Activity of Voriconazole against Clinical Isolates of
Aspergillus
spp
Authors: Castro Carmen , Serrano M. Carmen , Flores Bernardo , Espinel-Ingroff Ana , Martín-Mazuelos Estrella
Published: September 2004

The
susceptibilities of 63 isolates of
Aspergillus
spp. to
voriconazole were evaluated by a modified NCCLS M38-A method and the
Sensititre YeastOne method. The overall agreement was 82.5%,
ranging from 100% for
Aspergillus niger
and
Aspergillus terreus
to 62.5% for
Aspergillus
flavus
. Discrepancies between the methods were due to higher
Sensititre MICs. The Sensititre YeastOne method could have potential
value for susceptibility testing of
Aspergillus
spp. to
voriconazole.
Development of a Real-Time PCR Assay Using SYBR Green I for Provirus Load Quantification in a Murine Model of AIDS
Authors: Casabianca Anna , Orlandi Chiara , Fraternale Alessandra , Magnani Mauro
Published: September 2004

A real-time PCR assay using SYBR Green I for quantification of provirus load in a murine model of AIDS (i.e., LP-BM5 infection) was developed and validated. In this method, data are normalized against the 18S rRNA gene. The method has a dynamic range of 8 logs and a sensitivity of one copy.
Differing Patterns of Liver Disease Progression and Hepatitis C Virus (HCV) Quasispecies Evolution in Children Vertically Coinfected with HCV and Human Immunodeficiency Virus Type 1
Authors: Canobio Sophie , Guilbert Cynthia M. , Troesch Myriam , Samson Johanne , Lemay Mireille , Pelletier Veronique Anne , Bernard-Bonnin Anne-Claude , Kozielski Rafal , Lapointe Normand , Martin Steven R. , Soudeyns Hugo
Published: September 2004

Hepatitis C virus (HCV) quasispeciation was studied in two children vertically coinfected with HCV and human immunodeficiency virus type 1 (HIV-1). HCV quasispecies diversification and liver injury were more significant in patient C1, who was immunocompetent with anti-HIV therapy, than in patient C2, who was immunosuppressed, in consistency with modulation of HCV quasispeciation and liver injury by immunocompetence in coinfected children.
Pathogenic Differences between North American and Latin American Strains of
Histoplasma capsulatum
var.
capsulatum
in Experimentally Infected Mice
Authors: Durkin Michelle M. , Connolly Patricia A. , Karimi Kian , Wheat Emerson , Schnizlein-Bick Carol , Allen Stephen D. , Alves Katia , Tewari Ram P. , Keath Elizabeth
Published: September 2004

Clinical differences in histoplasmosis between North America and Brazil prompted investigation of experimental infection with representative strains. Mortality was higher with Latin American strains, and lung pathology showed large necrotizing granuloma with prominent neutrophilic infiltration. Chronic disease was unique to the North American strain.
Cladophialophora bantiana
Brain Abscess in a Solid-Organ Transplant Recipient: Case Report and Review of the Literature
Authors: Levin Todd P. , Baty Darric E. , Fekete Thomas , Truant Allan L. , Suh Byungse
Published: September 2004

Cerebral phaeohyphomycosis caused by
Cladophialophora bantiana
is a rare disease. We describe a heart and bilateral lung transplant recipient who was unsuccessfully treated for a
C. bantiana
brain abscess. This report compares the present case to those of other solid-organ transplant recipients with the same infection and to those of patients who did not receive transplants.
NeonatalCandida albicansSeptic Thrombosis of the Portal Vein followed by Cavernous Transformation of the Vessel
Authors: Pacifico Lucia , Panero Alessandra , Colarizi Patrizia , Matrunola Marco , Simonetti Antonella F. , Chiesa Claudio
Published: September 2004

We report two premature neonates withCandida albicansseptic thrombosis of the portal vein who developed, in very early childhood, the sonographic appearance of cavernous transformation of the vessel and/or clinical signs of extrahepatic portal hypertension.
Pyelonephritis and Urosepsis Caused by
Streptococcus pneumoniae
Authors: Dufke Severin , Kunze-Kronawitter Heike , Schubert Sören
Published: September 2004

This report presents the case of a patient with a massive pyelonephritis and a urosepsis caused by
Streptococcus pneumoniae
. This case is unusual as the focus was distant from the respiratory tract, the usual primary site of infection caused by this organism. No other primary site of infection was documented.
Mycobacterium heckeshornense
Infection in an Immunocompetent Patient and Identification by 16S rRNA Sequence Analysis of Culture Material and a Histopathology Tissue Specimen
Authors: van Hest Rob , van der Zanden Adri , Boeree Martin , Kremer Kristin , Dessens Mirjam , Westenend Pieter , Maraha Boulos , van Uffelen René , Schütte Ronald , de Lange Wiel
Published: September 2004

Mycobacterium heckeshornense
is a rare isolate in clinical specimens. We performed simultaneous 16S rRNA sequence analysis of a mycobacterium culture and a histopathology specimen to determine the relevance of
M. heckeshornense
infection in an immunocompetent patient initially presenting with pneumothorax.
Bacteremia Caused by
Clostridium symbiosum
Authors: Elsayed Sameer , Zhang Kunyan
Published: September 2004

We describe a fatal case of
Clostridium symbiosum
bacteremia in a 70-year-old man with metastatic colon cancer. Our report is the first, in the world literature, of human infection caused by this microorganism.
Bacteremic Infection with
Pantoea ananatis
Authors: De Baere Thierry , Verhelst Rita , Labit Caroline , Verschraegen Gerda , Wauters Georges , Claeys Geert , Vaneechoutte Mario
Published: September 2004

A 73-year-old man was hospitalized for dyspnea and bilateral ankle edema. During his hospital stay he presented anal hemorrhage and developed a high fever after colonoscopy. A set of aerobic and anaerobic blood culture bottles yielded a pure culture of gram-negative rods, susceptible to all antibiotics tested. The API20E code was 1005133, resulting in a very good identification as
Pantoea
sp. Subsequent sequencing of the 16S rRNA gene revealed a final identification as
Pantoea ananatis.
The patient was given intravenous and oral therapy with piperacillin-tazobactam and ofloxacin and recovered completely from his infection.
Streptococcus porcinus
as a Cause of Spontaneous Preterm Human Stillbirth
Authors: Martin Christian , Fermeaux Véronique , Eyraud Jean-Luc , Aubard Yves
Published: September 2004

We report, to our knowledge, on the first case of a woman suffering stillbirth due to
Streptococcus porcinus
on the basis of microbiologic and histologic data.
Continuous Ambulatory Peritoneal Dialysis-Related Peritonitis Associated with Lancefield Group G Beta-Hemolytic Streptococcus: Report of Two Cases Requiring Tenckhoff Catheter Removal
Authors: Woo Patrick C. Y. , Wong Samson S. Y. , Lau Susanna K. P. , Yuen Kwok-yung
Published: September 2004

We describe the first two cases of continuous ambulatory peritoneal dialysis-related peritonitis associated with Lancefield group G beta-hemolytic streptococci in the literature. Both patients presented with abdominal pain and turbid dialysis effluent with or without fever. Both had concomitant gastrointestinal tract disturbance. Both did not respond to intraperitoneal cefazolin and tobramycin and required removal of the Tenckhoff catheters.
Rapid Identification of
Mycobacterium genavense
with a New Commercially Available Molecular Test, INNO-LiPA MYCOBACTERIA v2
Authors: Trueba François , Fabre Michel , Saint-Blancard Patrick
Published: September 2004

We report a rare mesenteric localized
Mycobacterium genavense
infection in a severely immunocompromised human immunodeficiency virus-infected patient. An INNO-LiPA MYCOBACTERIA v2 test was performed directly on biopsy samples. This new molecular tool could be used for simultaneous identification of mycobacterium species from human specimens, but other studies are needed to validate our first results.
Campylobacter fetus
of Reptile Origin as a Human Pathogen
Authors: Tu Zheng-Chao , Zeitlin Gary , Gagner Jean-Pierre , Keo Thormika , Hanna Bruce A. , Blaser Martin J.
Published: September 2004

A
Campylobacter
species was isolated from blood from a febrile patient with precursor T-cell acute lymphoblastic leukemia, and after antibiotic treatment, a similar bacterium was isolated from blood 37 days later. Although phenotypic testing did not definitively identify the organisms, molecular analysis indicated that they were the same strain of
Campylobacter fetus
subsp.
fetus
and were of reptile origin.
Cost-Effective Method for Identification of Dimorphic Fungi
Authors: Hughes Alice D. , Lorusso Giovanni D. , Greer Donald L.
Published: September 2004

Traditional methods to identify dimorphic fungi dictate that the mold be converted to the yeast phase at 35 to 37°C. We present a time- and cost-saving method of confirming the identification of a dimorph by using special stains to demonstrate the yeast phase directly growing in the original clinical specimens.
Regulatory mechanisms during the plant  arbuscular mycorrhizal fungus interaction
Authors: Vierheilig Horst
Published: September 2004

Abundant data are available on some aspects of the arbuscular mycorrhizal symbiosis, for example, plant nutrition, but because of difficulties immanent to arbuscular mycorrhizal fungi, such as the inability to culture them axenically, the relatively long time it takes to achieve root colonization, and the simultaneous presence of different morphologic stages of the fungus in the root, less information is accumulated on other aspects such as the regulation of mycorrhization. Regulatory processes in the plant  arbuscular mycorrhizal fungus interaction start before root colonization by the fungus and even before a direct physical contact between the host and the fungal symbiont. Some of the signals exchanged are still a matter of debate and will be discussed further on. After the penetration of the root by the fungus, depending on the developmental stage of the arbuscular mycorrhizal association (e.g., early or mature), a range of plant responses is activated. The possible function of several plant responses in the regulation of mycorrhization is discussed.Key words: arbuscular mycorrhiza, Glomales, autoregulation, flavonoid, recognition, root exudates.
Evolutionary studies of ectomycorrhizal fungi: recent advances and future directions
Authors: Bruns Thomas D , Shefferson Richard P
Published: September 2004

The three biggest advances in fungal molecular phylogenetics in the last few years have been (1) the huge expansion in data sets, (2) the development of nonribosomal loci for phylogenetic analysis, and (3) the use of increasingly sophisticated types of analyses. In addition, advances in parallel computing hold great promise for dramatic increases in speed of analysis. These changes have had, or will have, a direct impact on mycorrhizal ecology through the use of sequence-based identification and an indirect impact through the conclusions drawn from such studies. One problem in the field has been the accidental addition of erroneous sequences to the public databases through a variety of means, including polymerase change reaction contamination. We discuss several examples, suggest ways to identify errors, and argue the case for third-party annotations of sequences. Multiple studies have produced compelling evidence that the ectomycorrhizal habit has developed convergently in multiple lineages of fungi and plants. We reexamine the case for loss of the ectomycorrhizal habit in fungi and show that the results are model dependent.Key words: internal transcribed spacer (ITS) region, peroxidase genes, likelihood models, erroneous data, ectomycorrhizal habit.
Global environmental change and the biology of arbuscular mycorrhizas: gaps and challenges
Authors: Fitter A H , Heinemeyer A , Husband R , Olsen E , Ridgway K P , Staddon P L
Published: September 2004

Our ability to make predictions about the impact of global environmental change on arbuscular mycorrhizal (AM) fungi and on their role in regulating biotic response to such change is seriously hampered by our lack of knowledge of the basic biology of these ubiquitous organisms. Current information suggests that responses to elevated atmospheric CO2 will be largely controlled by host-plant responses, but that AM fungi will respond directly to elevated soil temperature. Field studies, however, suggest that changes in vegetation in response to environmental change may play the largest role in determining the structure of the AM fungal community. Nevertheless, the direct response of AM fungi to temperature may have large implications for rates of C cycling. New evidence shows that AM fungal hyphae may be very short lived, potentially acting as a rapid route by which C may cycle back to the atmospohere; we need, therefore, to measure the impact of soil temperature on hyphal turnover. There is also an urgent need to discover the extent to which AM fungal species are differentially adapted to abiotic environmental factors, as they apparently are to plant hosts. If they do show such an adaptation, and if the number of species is much greater than the number currently described (150), as seems almost certain, then there is the potential for several new fields of study, including community ecology and biogeography of AM fungi, and these will give us new insights into the impacts of global environmental change on AM fungi in moderating the impacts of global environmental change on ecosystems.Key words: arbuscular mycorrhiza, temperature, diversity, community structure, ecosystem, carbon cycle.
cDNA arrays as a tool to identify mycorrhiza-regulated genes: identification of mycorrhiza-induced genes that encode or generate signaling molecules implicated in the control of root growth
Authors: Liu Jinyuan , Blaylock Laura A , Harrison Maria J
Published: September 2004

Arbuscular mycorrhizas (AM) are symbiotic associations formed by fungi from the Glomeromycota and most angiosperms. Despite the widespread occurrence of the association, its ecological significance, and its potential importance in agriculture, relatively little is known at the molecular level about the development, functioning, and regulation of the symbiosis. We have selected Medicago truncatula Gaertn. 'Jemalong' and an AM fungus, Glomus versiforme (Karsten) Berch, for molecular genetic analyses of the AM symbiosis. Here we used macroarrays as a screening tool to enable the rapid identification of genes that show differential expression in mycorrhizal roots. Forty-three genes showing increased transcript levels and 18 genes showing decreased transcripts in mycorrhizal roots were identified. This set contained several genes predicted to encode regulatory proteins including an alpha-fucosidase implicated in the generation of signaling molecules that modulate plant growth and a gene encoding a putative peptide also implicated in the control of plant growth.Key words: legume, symbiosis, arbuscular mycorrhizal fungi.
The dynamics of symbiosis: an historical overview
Authors: Sapp Jan
Published: September 2004

Two facets of symbiosis theory are discussed: the role of symbiosis in evolution and the evolution and ecology of symbiosis. Research on symbiosis developed in virtual conflict with the aims and doctrines of the major biological disciplines for most of the 20th century. To gain a better understanding of this aspect of biology, I briefly sketch some of the phenomena and issues that have shaped discourse over its scope and significance. Diverse explanations for the various relations exhibited by symbiosis have been proposed from the 19th century to the present. The usefulness of the word itself has been debated, and its anthropomorphisms have been discussed. Research on mycorrhizas has been paradigmatic for revealing the dynamic nature of symbiosis and the inherent complexities of costbenefit accounting across the parasitismmutualism continuum.Key words: ecology, evolution, parasitism, mutualism, mycorrhizas, symbiosis.
The evolutionary implications of exploitation in mycorrhizas
Authors: Egger Keith N , Hibbett David S
Published: September 2004

Some views of mutualism, where the fitness of two symbiotic partners is higher in association than when apart, assume that they necessarily evolve towards greater benefit for the partners. Most mutualisms, however, seem prone to conflicts of interest that destabilize the partnership. These conflicts arise in part because mutualistic outcomes are conditional, depending upon complex interactions between environmental, developmental, and genotypic factors. Mutualisms are also subject to exploitation or cheating. Although various compensating mechanisms have been proposed to explain how mutualism can be maintained in the presence of exploiters, none of these mechanisms can eliminate exploitation. In this paper we explore various compensating mechanisms in mycorrhizas, examine the evidence for exploitation in mycorrhizas, and conclude that mycorrhizal mutualisms exhibit characteristics that are more consistent with a concept of reciprocal parasitism. We propose that researchers should not assume mycorrhizas are mutualistic based upon structural characteristics or limited functional studies showing bilateral exchange and should view mycorrhizas as occupying a wider range on the symbiotic continuum, including commensalism and antagonism. We recommend that comparative studies of mycorrhizas incorporate other types of root associations that have traditionally been considered antagonistic.Key words: mycorrhizas, mutualism, exploiters, compensating mechanisms, symbiotic continuum.
Networks of power and influence: the role of mycorrhizal mycelium in controlling plant communities and agroecosystem functioning
Authors: Leake Jonathan , Johnson David , Donnelly Damian , Muckle Gemma , Boddy Lynne , Read David
Published: September 2004

Extraradical mycelia of mycorrhizal fungi are normally the hidden half of the symbiosis, but they are powerful underground influences upon biogeochemical cycling, the composition of plant communities, and agroecosystem functioning. Mycorrhizal mycelial networks are the most dynamic and functionally diverse components of the symbiosis, and recent estimates suggest they are empowered by receiving as much as 10% or more of the net photosynthate of their host plants. They often constitute 20%30% of total soil microbial biomass yet are undetected by standard measures of biomass used by soil scientists and agromomists. Mycorrhizal mycelia provide extensive pathways for carbon and nutrient fluxes through soil, often exceeding tens of metres per gram of soil. We consider the amounts of photosynthate power allocated to these mycelial networks and how this is used in fungal respiration, biomass, and growth and in influencing soil, plant, and ecosystem processes. The costs and functional benefits to plants linking to these networks are fungal specific and, because of variations in physiology and host specificity, are not shared equally; some plants even depend exclusively on these networks for carbon. We briefly assess the potential contribution of extraradical mycorrhizal mycelium to sustainable agriculture and maintenance of biodiversity and highlight technologies that promise new vistas and improved fine-scale resolution of the dynamic spatial and temporal functioning of these networks in soil.Key words: arbuscular mycorrhiza, ectomycorrhiza, extraradical mycelium, hyphal networks.
Exploring structural definitions of mycorrhizas, with emphasis on nutrient-exchange interfaces
Authors: Peterson R. Larry , Massicotte Hugues B
Published: September 2004

The roots or other subterranean organs of most plants develop symbioses, mycorrhizas, with fungal symbionts. Historically, mycorrhizas have been placed into seven categories based primarily on structural characteristics. A new category has been proposed for symbiotic associations of some leafy liverworts. An important feature of mycorrhizas is the interface involved in nutrient exchange between the symbionts. With the exception of ectomycorrhizas, in which fungal hyphae remain external to plant cell walls, all mycorrhizas are characterized by fungal hyphae breaching cell walls but remaining separated from the cell cytoplasm by a plant-derived membrane and an interfacial matrix that forms an apoplastic compartment. The chemical composition of the interfacial matrix varies in complexity. In arbuscular mycorrhizas (both Arum-type and Paris-type), molecules typical of plant primary cell walls (i.e., cellulose, pectins, β-1,3-glucans, hydroxyproline-rich glycoproteins) are present. In ericoid mycorrhizas, only rhamnogalacturonans occur in the interfacial matrix surrounding intracellular hyphal complexes. The matrix around intracellular hyphal complexes in orchid mycorrhizas lacks plant cell wall compounds until hyphae begin to senesce, then molecules similar to those found in primary cell walls are deposited. The interfacial matrix has not been studied in arbutoid mycorrhizas and ectendomycorrhizas. In ectomycorrhizas, the apoplastic interface consists of plant cell wall and fungal cell wall; alterations in these may enhance nutrient transfer. In all mycorrhizas, nutrients must pass into the symplast of both partners at some point, and therefore current research is exploring the nature of the opposing membranes, particularly in relation to phosphorus and sugar transporters.Key words: interface, apoplastic compartment, Hartig net, arbuscule, intracellular complex, nutrient exchange.
Inoculum of arbuscular mycorrhizal fungi for production systems: science meets business
Authors: Gianinazzi Silvio , Vosátka Miroslav
Published: September 2004

The development of an industrial activity producing microbial inocula is a complex procedure that involves for companies not only the development of the necessary biotechnological know-how, but also the ability to respond to the specifically related legal, ethical, educational, and commercial requirements. At present, commercial arbuscular mycorrhizal (AM) inocula are produced in nursery plots, containers with different substrates and plants, aeroponic systems, or, more recently, in vitro. Different formulated products are available on the market, which creates the need for the establishment of standards for widely accepted quality control. Progress should be made towards registration procedures that stimulate the development of the mycorrhizal industry. Biotechnology science linked to this industrial activity needs to be reinforced, particularly with regards to (i) the development of molecular probes for monitoring arbuscular mycorrhizal inocula in the field, (ii) increasing knowledge on the ecophysiology of AM fungi in anthropogenically disturbed ecosystems and on the interactions of AM fungi with other rhizosphere microbes, and (iii) selection of new plant varieties with enhanced mycorrhizal traits and of AM fungi with new symbiotic traits. However, one of the main tasks for both producers and researchers is to raise awareness in the public about potentials of mycorrhizal technology for sustainable plant production and soil conservation.Key words: Glomeromycota, biotechnology, quality control, legal aspects, commercial aspects.
Prospects and limitations for mycorrhizas in biocontrol of root pathogens
Authors: Whipps John M
Published: September 2004

More than 80 disease biocontrol products are on the market worldwide, but none of these contain mycor rhizal fungi. This is despite ample evidence that both arbuscular mycorrhizal fungi and ectomycorrhizal fungi can control a number of plant diseases. A procedure for successful development of disease biocontrol agents in general is used as a background to examine the potential for achieving commercial mycorrhizal biocontrol agents. This includes (i) selection and screening; (ii) characterization involving identification, studies of modes of action and ecophysiology, as well as inoculum production, formulation, application and shelf life; (iii) registration. The last stage is problematic for mycorrhizal fungi, as currently they can be sold as plant growth promoters without any form of costly registration, even though in some instances they may actually function to some extent through biocontrol activity. The significance of this approach is discussed, and some possible ways of enhancing biocontrol by mycorrhizas are considered.Key words: arbuscular mycorrhizas, ectomycorrhizas, biological disease control, soilborne pathogens, modes of action, ecology.
Partner communication in the arbuscular mycorrhizal interaction
Authors: Bécard G , Kosuta S , Tamasloukht M , Séjalon-Delmas N , Roux C
Published: September 2004

During 400 million years of genomegenome interaction, plants and arbuscular mycorrhizal (AM) fungi have become highly interdependent, both ecologically and physiologically. As a result, the differentiation of a functional mycorrhiza is a multistep process requiring the active participation of both partners. During the presymbiotic stage of the AM interaction, some active molecules present in root exudates rapidly induce several fungal genes, in addition to stimulating important cellular and metabolic functions in the fungus, such as mitochondrial biogenesis and respiration. As a result of this activation, the fungus can use its lipidic reserves and reach further developmental stages. Subsequently, the fungus produces factors that induce new gene expression in roots. The fact that the partners of the AM symbiosis exchange such "pheromonal" active molecules during the presymbiotic stage of their interaction suggests the existence of other cross-signaling molecules during the symbiotic stage. These later signals might be involved in activating fungal fatty acid synthesis and sugar uptake or be responsible for specific plant gene induction. Now the challenge is to characterize the chemical nature and the exact role of these fungal and plant regulators in the AM symbiosis.Key words: arbuscular mycorrhizal symbiosis, signaling, root exudates, Myc factor, respiration, lipid metabolism.
Intraspecific genetic variation in arbuscular mycorrhizal fungi and its consequences for molecular biology, ecology, and development of inoculum
Authors: Sanders Ian R
Published: September 2004

It has been known for some time that different arbuscular mycorrhizal fungal (AMF) taxa confer differences in plant growth. Although genetic variation within AMF species has been given less attention, it could potentially be an ecologically important source of variation. Ongoing studies on variability in AMF genes within Glomus intraradices indicate that at least for some genes, such as the BiP gene, sequence variability can be high, even in coding regions. This suggests that genetic variation within an AMF may not be selectively neutral. This clearly needs to be investigated in more detail for other coding regions of AMF genomes. Similarly, studies on AMF population genetics indicate high genetic variation in AMF populations, and a considerable amount of variation seen in phenotypes in the population can be attributed to genetic differences among the fungi. The existence of high within-species genetic variation could have important consequences for how investigations on AMF gene expression and function are conducted. Furthermore, studies of within-species genetic variability and how it affects variation in plant growth will help to identify at what level of precision ecological studies should be conducted to identify AMF in plant roots in the field. A population genetic approach to studying AMF genetic variability can also be useful for inoculum development. By knowing the amount of genetic variability in an AMF population, the maximum and minimum numbers of spores that will contain a given amount of genetic diversity can be estimated. This could be particularly useful for developing inoculum with high adaptability to different environments.Key words: arbuscular mycorrhizas, symbiosis, genomics, genetic diversity, population genetics, evolutionary ecology.
Functional genomics of arbuscular mycorrhiza: decoding the symbiotic cell programme
Authors: Gianinazzi-Pearson Vivienne , Brechenmacher Laurent
Published: September 2004

More extensive insight into plant genes involved in the symbiotic programme of arbuscular mycorrhiza is presently being achieved by global approaches that aim to discover novel genes or subsets of genes that are essential to cell programmes in the different steps of plantfungal interactions. The strategy of functional genomics based on large-scale differential RNA expression analyses (differential-display reverse transcriptase - PCR), electronic Northerns, suppressive subtractive hybridization, DNA chips) is presented, with a focus on arbuscular mycorrhiza in Pisum sativum and Medicago truncatula. The most recent knowledge about gene networks that are modulated in roots during arbuscular establishment and functioning is discussed.Key words: arbuscular mycorrhiza, symbiotic programme, gene expression, pea, annual alfalfa.
Exploring functional definitions of mycorrhizas: Are mycorrhizas always mutualisms?
Authors: Jones Melanie D , Smith Sally E
Published: September 2004

Mycorrhizas are considered to be classic mutualisms. Here, we define mutualism as a reciprocal increase in fitness of the symbionts, and we review the evidence for mycorrhizal mutualism at the community, whole-plant, and cellular scales. It is difficult to use results of most mycorrhizal studies because (i) fungal contribution to nutrient uptake is not accurately estimated, (ii) increased growth is not necessarily correlated with increased plant fecundity or survival, especially in communities, and (iii) benefits that occur only at certain times of year, or under specific extreme conditions, may not be detected. To produce the nonmycorrhizal controls required to study mutualism in the field, soil microflora and fauna must be severely perturbed; therefore, it is virtually impossible to evaluate effects of mycorrhizas on plant fitness under realistic conditions. Using the evidence available, we conclude that mycorrhizas can occupy various positions along the continuum from parasitism to mutualism, depending on the specific plant and fungal genotypes and their abiotic and biotic environments. Although we discuss the possibility of defining mycorrhizas by some physiological characteristic, we conclude that mycorrhizas should be defined on a structural or developmental basis and that any requirement to demonstrate mutualism be eliminated.Key words: mycorrhiza, mutualism, parasitism, physiology, fitness, community.