bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microviridae
, a Family Divided: Isolation, Characterization, and Genome Sequence of φMH2K, a Bacteriophage of the Obligate Intracellular Parasitic Bacterium
Bdellovibrio bacteriovorus
Authors: Brentlinger Karie L. , Hafenstein Susan , Novak Christopher R. , Fane Bentley A. , Borgon Robert , McKenna Robert , Agbandje-McKenna Mavis 
Published: July 2002

ABSTRACT

A novel single-stranded DNA phage, φMH2K, of
Bdellovibrio bacteriovorus
was isolated, characterized, and sequenced. This phage is a member of the
Microviridae
, a family typified by bacteriophage φX174. Although
B. bacteriovorus
and
Escherichia coli
are both classified as proteobacteria, φMH2K is only distantly related to φX174. Instead, φMH2K exhibits an extremely close relationship to the
Microviridae
of
Chlamydia
in both genome organization and encoded proteins. Unlike the double-stranded DNA bacteriophages, for which a wide spectrum of diversity has been observed, the single-stranded icosahedral bacteriophages appear to fall into two distinct subfamilies. These observations suggest that the mechanisms driving single-stranded DNA bacteriophage evolution are inherently different from those driving the evolution of the double-stranded bacteriophages.
Pseudomonas aeruginosa
Displays Multiple Phenotypes during Development as a Biofilm
Authors: Sauer Karin , Camper Anne K. , Ehrlich Garth D. , Costerton J. William , Davies David G. 
Published: July 2002

ABSTRACT

Complementary approaches were employed to characterize transitional episodes in
Pseudomonas aeruginosa
biofilm development using direct observation and whole-cell protein analysis. Microscopy and in situ reporter gene analysis were used to directly observe changes in biofilm physiology and to act as signposts to standardize protein collection for two-dimensional electrophoretic analysis and protein identification in chemostat and continuous-culture biofilm-grown populations. Using these approaches, we characterized five stages of biofilm development: (i) reversible attachment, (ii) irreversible attachment, (iii) maturation-1, (iv) maturation-2, and (v) dispersion. Biofilm cells were shown to change regulation of motility, alginate production, and quorum sensing during the process of development. The average difference in detectable protein regulation between each of the five stages of development was 35% (approximately 525 proteins). When planktonic cells were compared with maturation-2 stage biofilm cells, more than 800 proteins were shown to have a sixfold or greater change in expression level (over 50% of the proteome). This difference was higher than when planktonic
P. aeruginosa
were compared with planktonic cultures of
Pseudomonas putida
. Las quorum sensing was shown to play no role in early biofilm development but was important in later stages. Biofilm cells in the dispersion stage were more similar to planktonic bacteria than to maturation-2 stage bacteria. These results demonstrate that
P. aeruginosa
displays multiple phenotypes during biofilm development and that knowledge of stage-specific physiology may be important in detecting and controlling biofilm growth.
Salicylate 5-Hydroxylase from
Ralstonia
sp. Strain U2: a Monooxygenase with Close Relationships to and Shared Electron Transport Proteins with Naphthalene Dioxygenase
Authors: Zhou Ning-Yi , Al-Dulayymi Jumáa , Baird Mark S. , Williams Peter A. 
Published: July 2002

ABSTRACT

The genes from the oxygenase cluster
nagAaGHAbAcAd
of naphthalene-degrading
Ralstonia
sp. strain U2 were cloned and overexpressed. Salicylate 5-hydroxylase (S5H) activity, converting salicylate to gentisate, was present in vitro only in the single extract of cells with overexpressed
nagAaGHAb
or in a mixture of three cell extracts containing, respectively, NagGH (the oxygenase components), NagAa (ferredoxin reductase), and NagAb (ferredoxin). Each of the three extracts required for S5H activity was rate limiting in the presence of excess of the others but, when in excess, did not affect the rate of catalysis. S5H catalyzed the 5-hydroxylation of the aromatic rings of 3- and 4-substituted salicylates. However, the methyl group of 5-methylsalicylate was hydroxylated to produce the 5-hydroxymethyl derivative and the 6-position on the ring of 5-chlorosalicylate was hydroxylated, producing 5-chloro-2,6-dihydroxybenzoate. In an assay for the
nag
naphthalene dioxygenase (NDO) based on the indole-linked oxidation of NADH, three extracts were essential for activity (NagAcAd, NagAa, and NagAb). NDO and S5H were assayed in the presence of all possible combinations of the
nag
proteins and the corresponding
nah
NDO proteins from the “classical” naphthalene degrader
P. putida
NCIMB9816. All three oxygenase components functioned with mixed combinations of the electron transport proteins from either strain. The S5H from strain U2 is a unique monooxygenase which shares sequence similarity with dioxygenases such as NDO but is also sufficiently similar in structure to interact with the same electron transport chain and probably does so in vivo during naphthalene catabolism in strain U2.
nblS, a Gene Involved in Controlling Photosynthesis-Related Gene Expression during High Light and Nutrient Stress inSynechococcus elongatusPCC 7942
Authors: van Waasbergen Lorraine G. , Dolganov Nadia , Grossman Arthur R. 
Published: July 2002

ABSTRACTThe HliA protein of the cyanobacteriumSynechococcus elongatusPCC 7942 is a small, thylakoid-associated protein that appears to play a role in photoprotection; its transcript rapidly accumulates in response to high-intensity light (HL) and thehligene family is required for survival of cells in high light. In order to discover regulatory factors involved in HL acclimation in cyanobacteria, a screen was performed for chemically generated mutants unable to properly control expression of thehliAgene in response to HL. One such mutant was identified, and complementation analysis led to the identification of the affected gene, designatednblS. Based on its deduced protein sequence, NblS appears to be a membrane-bound, PAS-domain-bearing, sensor histidine kinase of two-component regulatory systems in bacteria. ThenblSmutant was unable to properly control light intensity-mediated expression of several other photosynthesis-related genes, including all threepsbAgenes and thecpcBAgenes. The mutant was also unable to control expression of thehliAandpsbAgenes in response to low-intensity blue/UV-A light, a response that may be related to the HL-mediated regulation of the genes. Additionally, in response to nutrient deprivation, thenblSmutant was unable to properly control accumulation of thenblAtranscript and associated degradation of the light-harvesting phycobilisomes. ThenblSmutant dies more rapidly than wild-type cells following exposure to HL or nutrient deprivation, likely due to its inability to properly acclimate to these stress conditions. Thus, the NblS protein is involved in the control of a number of processes critical for altering the photosynthetic apparatus in response to both HL and nutrient stress conditions.
Detection and Differentiation of Old World Orthopoxviruses: Restriction Fragment Length Polymorphism of the
crmB
Gene Region
Authors: Loparev Vladimir N. , Massung Robert F. , Esposito Joseph J. , Meyer Hermann 
Published: July 2002

ABSTRACT

A restriction fragment length polymorphism (RFLP) assay was developed to identify and differentiate Old World, African-Eurasian orthopoxviruses (OPV): variola, vaccinia, cowpox, monkeypox, camelpox, ectromelia, and taterapox viruses. The test uses amplicons produced from virus genome DNA by PCR with a consensus primer pair designed from sequences determined for the cytokine response modifier B (
crmB
) gene of 43 different OPV strains of known taxonomic origin. The primer pair amplified a single specific product from each of the 115 OPV samples tested. Size-specific amplicons identified and differentiated ectromelia and vaccinia virus strains, which contain a truncated
crmB
gene, and enabled their differentiation from other OPV species. Restriction digests of amplified products allowed the identification and differentiation of variola, monkeypox, camelpox, vaccinia, and cowpox virus species and strains.
Performance of Applied Biosystems ViroSeq HIV-1 Genotyping System for Sequence-Based Analysis of Non-Subtype B Human Immunodeficiency Virus Type 1 from Uganda
Authors: Mracna Martin , Becker-Pergola Graziella , Dileanis Joann , Guay Laura A. , Cunningham Shawn , Jackson J. Brooks , Eshleman Susan H. 
Published: July 2002

ABSTRACT
The Applied Biosystems ViroSeq HIV-1 Genotyping System is a commercially available, integrated system for sequence-based analysis of drug resistance mutations in human immunodeficiency virus type 1 (HIV-1) protease and reverse transcriptase (RT). We evaluated the performance of this system for analysis of non-subtype B HIV-1 by analyzing plasma samples from Ugandan women and infants. Plasma samples were obtained from 105 women and 25 infants enrolled in a Ugandan clinical trial. HIV-1 analysis was performed with the ViroSeq system according to the manufacturer's instructions, except that the volume of plasma used for analysis was less than the recommended 0.5 ml for some samples. Viral loads ranged from 2,313 to 2,336,400 copies/ml. PCR products suitable for sequencing were amplified from all samples tested. Complete sequences for protease (amino acids 1 to 99) and RT (amino acids 1 to 320) were obtained for 102 of 105 (97%) of the maternal samples tested and all 25 of the infant samples tested. Complete double-stranded sequences were obtained for 90 of 105 (86%) of the maternal samples tested and 22 of 25 (88%) of the infant samples tested. The sequences obtained with this system were used for HIV-1 subtyping. The subtypes identified were A, C, D, and A/D recombinant HIV-1. The performances of the seven sequencing primers were similar for the subtypes examined. The ViroSeq system performs well for analysis of Ugandan plasma samples with subtypes A, C, D, and A/D recombinant HIV-1. The availability of this genotyping system should facilitate studies of HIV-1 drug resistance in countries where these subtypes are prevalent.
Prevalence of
Leishmania infantum
Infection in Dogs Living in an Area of Canine Leishmaniasis Endemicity Using PCR on Several Tissues and Serology
Authors: Solano-Gallego Laia , Morell Pere , Arboix Margarita , Alberola Jordi , Ferrer Lluis 
Published: July 2002

ABSTRACT

We studied and compared the prevalence of
Leishmania
infection and the seroprevalence and the prevalence of canine leishmaniasis in an area where canine leishmaniasis is endemic. One hundred dogs living on the island of Mallorca (Spain) were studied. In this study, we clinically examined each dog for the presence of symptoms compatible with leishmaniasis, determined the titer of anti-
Leishmania
antibodies, and investigated the presence of
Leishmania
DNA by PCR in skin, conjunctiva, and bone marrow samples of each dog. The prevalence of the disease and the seroprevalence were 13 and 26%, respectively. In 63% of the dogs,
Leishmania
DNA could be detected by PCR in at least one of the tissues studied. The results of positive PCR in the bone marrow, the conjunctiva, and the skin were 17.8, 32, and 51%, respectively. The prevalence of the infection, 67%, was calculated using all animals that were seropositive and/or positive by PCR with any tissue. The results showed that the majority of dogs living in an area where canine leishmaniasis is endemic are infected by
Leishmania
and that the prevalence of infection is much greater than the prevalence of overt
Leishmania
-related disease.
Nocardia africana
sp. nov., a New Pathogen Isolated from Patients with Pulmonary Infections
Authors: Hamid Mohamed E. , Maldonado Luis , Sharaf Eldin Ghada S. , Mohamed Maha F. , Saeed Nageeb S. , Goodfellow Michael 
Published: July 2002

ABSTRACT

Eight actinomycete strains, isolated from 8 out of 400 sputum samples examined, taken from patients with pulmonary diseases at the Chest Unit of Khartoum Teaching Hospital in the Sudan, were provisionally assigned to the genus
Nocardia
according to morphological criteria. These isolates were studied further in order to establish their taxonomic status. They were found to have morphological and chemical properties typical of nocardiae and formed a monophyletic clade in the 16S ribosomal DNA tree together with
Nocardia vaccinii
. The strains showed a unique pattern of phenotypic properties that distinguished them from representatives of recognized
Nocardia
species, including
Nocardia vaccinii
. The strains were considered to merit species status and were designated
Nocardia africana
sp. nov. The findings of the present study are consistent with the view that pulmonary nocardiosis may occur in a substantial proportion of patients who exhibit chronic lung diseases in African countries. It is important, therefore, that clinicians in such countries consider this condition, especially when patients with respiratory infections fail to respond to antitubercular therapy.
Identification of Canine Coronavirus Strains from Feces by S Gene Nested PCR and Molecular Characterization of a New Australian Isolate
Authors: Naylor Matthew J. , Harrison Gavan A. , Monckton Robert P. , McOrist Steven , Lehrbach Philip R. , Deane Elizabeth M. 
Published: July 2002

ABSTRACT
A nested PCR (nPCR) assay for the detection of canine coronavirus (CCV) in fecal samples is described. The target sequence for the assay was a 514-bp fragment within the spike (S) glycoprotein gene. The sensitivity of the assay is extremely high, detecting as little as 25 50% tissue culture infective doses per g of unprocessed feces. A clinical trial using dogs challenged orally with CCV SA4 and CCV NVSL was used to compare viral isolation and the nPCR assay as detection techniques over a 2-week period of infection. Virus isolation detected CCV shedding from day 4 to 9 postchallenge, while the nPCR assay detected CCV shedding from day 4 to 13 postchallenge. Cloning and sequencing of the nPCR assay product enabled investigation of the evolutionary relationships between strains within the S gene. The simple and rapid procedure described here makes this assay an ideal alternative technique to electron microscopy and viral isolation in cell culture for detection of CCV shedding in feces. The described assay also provides a method of identifying new strains of CCV without the complicated and time-consuming practice of raising antibodies to individual strains. This is illustrated by the identification, for the first time, of an Australian isolate of CCV (UWSMN-1).
Diversity within Reference Strains of
Corynebacterium matruchotii
Includes
Corynebacterium durum
and a Novel Organism
Authors: Barrett Sara L. Rassoulian , Cookson Brad T. , Carlson LaDonna C. , Bernard Kathryn A. , Coyle Marie B. 
Published: July 2002

ABSTRACT

Corynebacterium matruchotii
has been the subject of numerous dental pathogenesis studies. The purpose of the present study was to resolve concerns about diversity within the reference strains of
C. matruchotii
through analysis of seven strains procured from the American Type Culture Collection (ATCC). Analysis of whole-cell fatty acid profiles with the library generation software of Microbial ID Inc. revealed that three types of organisms have been deposited in the ATCC as
C. matruchotii
. These three groups of organisms were also distinguishable by DNA-DNA dot blot hybridization, by sequences of two hypervariable regions of the 16S rRNA gene, and by the pyrrolidonyl arylamidase test. These studies indicate that two
C. matruchotii
reference strains, ATCC 33449 and ATCC 33822, are members of the recently proposed species,
Corynebacterium durum
. The colonial morphology and biochemical reactions of the
C. durum
strains are more diverse than originally reported. Strain ATCC 43833 is unique and represents a novel species. In addition to the type strain, ATCC 14266, true members of the species
C. matruchotii
include ATCC strains 14265, 33806, and 43832 plus two reference strains, L2 and Richardson 13, which comprise the vast majority of strains used in dental pathogenesis research with this species.
16S Ribosomal DNA Sequence Analysis Distinguishes Biotypes of
Streptococcus bovis
:
Streptococcus bovis
Biotype II/2 Is a Separate Genospecies and the Predominant Clinical Isolate in Adult Males
Authors: Clarridge Jill E. , Attorri Silvia M. , Zhang Qing , Bartell John 
Published: July 2002

ABSTRACT

We characterized 22 human clinical strains of
Streptococcus bovis
by genotypic (16S rRNA gene sequence analysis [MicroSeq]; Applied Biosystems, Foster City, Calif.) and phenotypic (API 20 Strep and Rapid ID32 Strep systems (bioMerieux Vitek, Hazelton, Mo.) methods. The strains, isolated from blood, cerebrospinal fluid (CSF), and urine, formed two distinct 16S ribosomal DNA sequence clusters. Three strains which were associated with endocarditis urinary tract infection (UTI), and sepsis clustered with the
S. bovis
type strain ATCC 33317 (cluster 1); other closely related type strains were
S. equinus
and
S. infantarius
. Nineteen strains clustered at a distance of about 2.5% dissimilarity to the
S. bovis
type strain (cluster 2) and were associated with central nervous system (CNS) disease in addition to endocarditis, UTI, and sepsis. All strains were distinct from
S. gallolyticus
. Within cluster 2, a single strain grouped with ATCC strain 43143 (cluster 2a) and may be phenotypically distinct. All the other strains formed a second subgroup (cluster 2b) that was biochemically similar to
S. bovis
biotype II/2 (mannitol negative and beta galactosidase, alpha galactosidase, beta glucuronidase, and trehalose positive). The API 20 Strep system identified isolates of cluster 2b as
S. bovis
biotype II/2, those of cluster 1 as
S. bovis
biotype II/1, and that of cluster 2a as
S. bovis
biotype I. There was an excellent correlation of biotype and genotype:
S. bovis
biotype II/2 isolates form a separate genospecies distinct from the
S. bovis, S. gallolyticus
, and
S. infantarius
type strains and are the most common isolates in adult males.
Myxobolus
sp., Another Opportunistic Parasite in Immunosuppressed Patients?
Authors: Moncada Ligia I. , López Myriam C. , Murcia Martha I. , Nicholls Santiago , León Frecia , Guı́o Olga Lucia , Corredor Augusto 
Published: July 2002

ABSTRACT

During a study of intestinal parasitic infections in human immunodeficiency virus-positive patients, a parasite belonging to the phylum
Myxozoa
, recently described from human samples, was identified in one sample. When this parasite was stained by the modified Ziehl-Neelsen staining method, the features of the spores were identified: they were pyriform in shape, had thick walls, and had one suture and two polar capsules, with each one having four or five coils. The suture and two polar capsules were observed with the chromotrope-modified stain. The number of stools passed was more than 30 per day, but oocysts of
Isospora belli
were also found. Upon reexamination of some formalin- or merthiolate-iodine-formaldehyde-preserved samples an identical parasite was found in another sample from a patient presenting with diarrhea.
Strongyloides stercoralis
larvae and eggs of
Hymenolepis nana
and
Ascaris lumbricoides
were also found in this sample. Given that both patients were also infected with other pathogens that cause diarrhea, the possible pathogenic role of this parasite could not be established. The probable route of infection also could not be established.
Simple and Efficient Method for Measuring Anti-Toxoplasma Immunoglobulin Antibodies in Human Sera Using Complement-Mediated Lysis of Transgenic Tachyzoites Expressing β-Galactosidase
Authors: Dando Caroline , Gabriel Katie E. , Remington Jack S. , Parmley Stephen F. 
Published: July 2002

ABSTRACT

A simple and efficient method using transgenic
Toxoplasma gondii
tachyzoites expressing β-galactosidase was developed for detection of specific antibodies against the parasite in sera of patients. The titers obtained with the new test were similar to those obtained with the Sabin-Feldman dye test run in parallel. Although significant changes in endpoint titers were not observed when sera drawn sequentially at 2- to 3-week intervals were tested with both procedures, apparent differences in antibody affinity were observed with the new test which were not perceptible with the Sabin-Feldman dye test. Like the Sabin-Feldman dye test, the new test is based on complement lysis of tachyzoites, but it is much easier to perform and the reaction is read colorimetrically instead of visually.
Citrate Synthase Gene Sequence: a New Tool for Phylogenetic Analysis and Identification of
Ehrlichia
Authors: Inokuma Hisashi , Brouqui Philippe , Drancourt Michel , Raoult Didier 
Published: July 2002

ABSTRACT

The sequence of the citrate synthase gene (
gltA
) of 13 ehrlichial species (
Ehrlichia chaffeensis
,
Ehrlichia canis
,
Ehrlichia muris
, an
Ehrlichia
species recently detected from
Ixodes ovatus
,
Cowdria ruminantium
,
Ehrlichia phagocytophila
,
Ehrlichia equi
, the human granulocytic ehrlichiosis [HGE] agent,
Anaplasma marginale
,
Anaplasma centrale
,
Ehrlichia sennetsu
,
Ehrlichia risticii
, and
Neorickettsia helminthoeca
) have been determined by degenerate PCR and the Genome Walker method. The ehrlichial
gltA
genes are 1,197 bp (
E. sennetsu
and
E. risticii
) to 1,254 bp (
A. marginale
and
A. centrale
) long, and GC contents of the gene vary from 30.5% (
Ehrlichia
sp. detected from
I. ovatus
) to 51.0% (
A. centrale
). The percent identities of the
gltA
nucleotide sequences among ehrlichial species were 49.7% (
E. risticii
versus
A. centrale
) to 99.8% (HGE agent versus
E. equi
). The percent identities of deduced amino acid sequences were 44.4% (
E. sennetsu
versus
E. muris
) to 99.5% (HGE agent versus
E. equi
), whereas the homology range of 16S rRNA genes was 83.5% (
E. risticii
versus the
Ehrlichia
sp. detected from
I. ovatus
) to 99.9% (HGE agent,
E. equi
, and
E. phagocytophila
). The architecture of the phylogenetic trees constructed by
gltA
nucleotide sequences or amino acid sequences was similar to that derived from the 16S rRNA gene sequences but showed more-significant bootstrap values. Based upon the alignment analysis of the ehrlichial
gltA
sequences, two sets of primers were designed to amplify tick-borne
Ehrlichia
and
Neorickettsia
genogroup
Ehrlichia
(
N. helminthoeca
,
E. sennetsu
, and
E. risticii
), respectively. Tick-borne
Ehrlichia
species were specifically identified by restriction fragment length polymorphism (RFLP) patterns of
Acs
I and
Xho
I with the exception of
E. muris
and the very closely related ehrlichia derived from
I. ovatus
for which sequence analysis of the PCR product is needed. Similarly,
Neorickettsia
genogroup
Ehrlichia
species were specifically identified by RFLP patterns of
Rca
I digestion. If confirmed this technique will be useful in rapidly identifying
Ehrlichia
spp.
Diversity of
Babesia
Infecting European Sheep Ticks (
Ixodes ricinus
)
Authors: Duh Darja , Petrovec Miroslav , Avsic-Zupanc Tatjana 
Published: July 2002

ABSTRACT

Questing
Ixodes ricinus
(Acari: Ixodidae) adult and nymphal ticks collected in various parts of Slovenia were tested for the presence of babesial parasites with a PCR assay based on the nuclear small subunit rRNA gene (nss-ribosomal DNA [rDNA]). Thirteen of 135 ticks were found to contain babesial DNA. Sequence determination and analysis of amplified portions of nss-rDNA revealed their identity with
Babesia microti
and a high degree of homology with
Babesia odocoilei
and
Babesia divergens
. The results of this study represent the first genetic evidence of
B. microti
and
B. divergens
-like parasites in
I. ricinus
ticks in Europe.