bluuebunny/crossref_metadata_2025_split huggingface dataset:
Isolation of a
Nodulisporium
Species from a Case of Cerebral Phaeohyphomycosis
Authors: Umabala P. , Lakshmi V. , Murthy A. R. , Prasad V. S. S. V. , Sundaram C. , Beguin H. 
Published: July 2002

ABSTRACT

A fungal infection of the brain of a 55-year-old male patient is reported. The lesion and involved fungus were located exclusively in the right medial temporo-parietal region. The patient was successfully treated with surgical resection of the lesion and antifungal chemotherapy. Few pathogenic dematiaceous fungi exhibit neurotropism and can cause primary infection in the central nervous system (CNS). The etiological agent is described as a
Nodulisporium
species. To date
Nodulisporium
has never been reported as an agent of CNS infection in humans.
Genetic Diversity of
Mycobacterium tuberculosis
in Sicily Based on Spoligotyping and Variable Number of Tandem DNA Repeats and Comparison with a Spoligotyping Database for Population-Based Analysis
Authors: Sola Christophe , Ferdinand Severine , Mammina Caterina , Nastasi Antonino , Rastogi Nalin 
Published: July 2002

ABSTRACT

In a previous study, we proposed to associate spoligotyping and typing with the variable number of tandem DNA repeats (VNTR) as an alternative strategy to IS
6110
-restriction fragment length polymorphism (RFLP) for molecular epidemiological studies on tuberculosis. The aim of the present study was to further evaluate this PCR-based typing strategy and to describe the population structure of
Mycobacterium tuberculosis
in another insular setting, Sicily. A collection of 106 DNA samples from
M. tuberculosis
patient isolates was characterized by spoligotyping and VNTR typing. All isolates were independently genotyped by the standard IS
6110
-RFLP method, and clustering results between the three methods were compared. The totals for the clustered isolates were, respectively, 15, 60, and 82% by IS
6110
-RFLP, spoligotyping, and VNTR typing. The most frequent spoligotype included type 42 that missed spacers 21 to 24 and spacers 33 to 36 and derived types 33, 213, and 273 that, together represented as much as 26% of all isolates, whereas the Haarlem clade of strains (types 47 and 50, VNTR allele 32333) accounted for 9% of the total strains. The combination of spoligotyping and VNTR typing results reduced the number of clusters to 43% but remained superior to the level of IS
6110
-RFLP clustering (ca. 15%). All but one IS
6110
-defined cluster were identified by the combination of spoligotyping and VNTR clustering results, whereas 9 of 15 spoligotyping-defined clusters could be further subdivided by IS
6110
-RFLP. Reinterpretation of previous IS
6110
-RFLP results in the light of spoligotyping-VNTR typing results allowed us to detect an additional cluster that was previously missed. Although less discriminative than IS
6110
-RFLP, our results suggest that the use of the combination of spoligotyping and VNTR typing is a good screening strategy for detecting epidemiological links for the study of tuberculosis epidemiology at the molecular level.
Rotavirus G and P Genotypes in Rural Ghana
Authors: Asmah Richard H. , Green Jon , Armah George E. , Gallimore Chris I. , Gray Jim J. , Iturriza-Gómara Mirren , Anto Francis , Oduro Abraham , Binka Fred N. , Brown David W. G. , Cutts Felicity 
Published: July 2002

ABSTRACT
An epidemiological study of rotavirus infection was conducted on specimens collected from patients with gastroenteritis and domiciled in the rural Upper Eastern Region of Ghana during 1998. Fifty isolates, randomly selected from 165 human group A rotavirus-positive samples, were G and P characterized by a reverse transcription (RT)-PCR assay using a seminested multiplex method. Rotaviruses of the G3 genotype were found to be the predominant strain (78%), followed by G2 (14%) and G1 (2%). Mixed infections, as shown by combinations of G3 and G2 (4%) and G3 and G1 (2%), were also observed. P typing showed P[4] (72.34%) to be the prevalent strain, followed by P[6] (21.3%), P[8] (2.13%), and a combination of P[4] and P[6] (4.3%).
Comparison of the BacT/Alert PF Pediatric FAN Blood Culture Bottle with the Standard Pediatric Blood Culture Bottle, the Pedi-BacT
Authors: Krisher Karen K. , Gibb Patrick , Corbett Sandra , Church Deidre 
Published: July 2002

ABSTRACT

The performance of the BacT/Alert PF (Organon-Teknika Corp., Durham, N.C.), a new nonvented pediatric FAN blood culture bottle, was compared to that of the original pediatric bottle, the Pedi-BacT, with matched aerobic cultures obtained from two separate facilities. A total of 244 clinically significant isolates were recovered from 4,015 compliant pairs. Among the positive cultures, 170 (70%) isolates were detected in both the BacT/Alert PF and the Pedi-BacT bottles, while 47 (19%) isolates were recovered in the BacT/Alert PF bottle only and 27 (11%) isolates were recovered in the Pedi-BacT bottle only. Although isolation of specific microorganisms was comparable for the two bottles, the total number of organisms recovered by the BacT/Alert PF was greater than that by the Pedi-BacT (
P
= 0.0272). In addition, more organisms were recovered by the BacT/Alert PF bottle from the blood of patients receiving antimicrobial therapy (
P
= 0.0180). Overall time to detection was similar for the two bottles; however, a significantly decreased mean time to detection was recorded for yeast from the BacT/Alert PF bottle (22.9 h;
P
= 0.0001) and staphylococci from the Pedi-BacT bottle (22.5 h;
P
= 0.0056). One false-negative culture and five false-positive cultures occurred with the Pedi-BacT bottle, compared to one false-positive culture with the BacT/Alert PF bottle. The BacT/Alert PF bottle is a reliable blood culture bottle for pediatric blood culture specimens and may offer improved recovery of microbes from patients on antimicrobial therapy. The use of the nonvented bottle will both facilitate bottle processing and decrease expenditures for materials due to the elimination of the venting needles required for the original vented bottles.
Determination of
Enterococcus faecalis groESL
Full-Length Sequence and Application for Species Identification
Authors: Teng Lee-Jene , Hsueh Po-Ren , Wang Yi-Hui , Lin Hsiao-Mann , Luh Kwen-Tay , Ho Shen-Wu 
Published: July 2002

ABSTRACT

Amplification of the partial Cpn60 (or GroEL) gene segment has been used for identification of many bacteria, including
Enterococcus
species. To obtain more sequence data from
groESL
genes of
Enterococcus faecalis
, the full-length sequence of the
E. faecalis groESL
genes containing
groES
(285 bp), spacer (57 bp), and
groEL
(1,626 bp) was determined. A database search of GenBank revealed that the deduced
E. faecalis
GroES and GroEL proteins show significant homology to the GroES and GroEL proteins of other bacteria. The GroEL (
groEL
) of
E. faecalis
had the highest identity with
Streptococcus pneumoniae
(81.8% amino acid sequence identity and 73.0% nucleotide sequence identity), followed by
Lactococcus zeae
, while GroES (
groES
) had 60.2% (64.6%) identity with
Lactobacillus zeae
and 58.5% (66.2%) identity with
Lactococcus lactis
, followed by 57.0% (65.5%) identity with
Bacillus subtilis.
Based on the
groES
sequence, an
E. faecalis
-specific PCR assay was developed, and this PCR assay was positive for all the
E. faecalis
strains tested. Dot blot hybridization using either
groES
or
groEL
as the probe distinguished
E. faecalis
clearly from other species, indicating that both genes can be used as suitable targets for
E. faecalis
identification. Moreover, broad-range PCR-restriction fragment length polymorphism of
groESL
was designed to differentiate eight commonly encountered
Enterococcus
species. The
Enterococcus
species of reference strains could be easily differentiated on the basis of restriction patterns produced by
Hae
III and
Rsa
I. The DNA-based assays developed in this study provide an alternative to currently used methods of identification for clinically important enterococcal species.
Isolation and Characterization of a Species-Specific DNA Fragment for Identification of
Candida
(
Torulopsis
)
glabrata
by PCR
Authors: Becker Karsten , Badehorn Dörte , Keller Birgit , Schulte Martina , Böhm Karl Heinz , Peters Georg , Fegeler Wolfgang 
Published: July 2002

ABSTRACT

A PCR specific for
Candida glabrata
that amplifies a mitochondrial rRNA gene fragment was developed by analysis of
C. glabrata
-specific agarose gel bands, which were generated by arbitrarily primed PCR. The expected PCR product was successfully amplified with genomic DNA from 95
C. glabrata
isolates but not from a number of other fungal isolates.
A Stem-Loop Motif Formed by the Immediate 5′ Terminus of the Bovine Viral Diarrhea Virus Genome Modulates Translation as well as Replication of the Viral RNA
Authors: Yu Haiying , Isken Olaf , Grassmann Claus W. , Behrens Sven-Erik 
Published: July 2002

ABSTRACT

Bovine viral diarrhea virus
(BVDV), a
Pestivirus
member of the
Flaviviridae
family, has a positive-stranded RNA genome which consists of a single open reading frame (ORF) and untranslated regions (UTRs) at the 5′ and 3′ ends. The 5′ UTR harbors extensive RNA structure motifs; most of them were shown to contribute to an internal ribosomal entry site (IRES), which mediates cap-independent translation of the ORF. The extreme 5′-terminal region of the BVDV genome had so far been believed not to be required for IRES function. By structure probing techniques, we initially verified the existence of a computer-predicted stem-loop motif at the 5′ end of the viral genome (hairpin Ia) as well as at the 3′ end of the complementary negative-strand replication intermediate [termed hairpin Ia (−)]. While the stem of this structure is mainly constituted of nucleotides that are conserved among pestiviruses, the loop region is predominantly composed of variable residues. Taking a reverse genetics approach to a subgenomic BVDV replicon RNA (DI9c) which could be equally employed in a translation as well as replication assay system based on BHK-21 cells, we obtained the following results. (i) Proper folding of the Ia stem was found to be crucial for efficient translation. Thus, in the context of an authentic replication-competent viral RNA, the 5′-terminal motif operates apparently as an integral functional part of the ribosome entry. (ii) An intact loop structure and a stretch of nucleotide residues that constitute a portion of the stem of the Ia or the Ia (−) motif, respectively, were defined to represent important determinants of the RNA replication pathway. (iii) Formation of the stem structure of the Ia (−) motif was determined to be not critical for RNA replication. In summary, our findings affirmed that the 5′-terminal region of the BVDV genome encodes a bifunctional secondary structure motif which may enable the viral RNA to switch from the translation to the replicative cycle and vice versa.
Functional Implications of the Human T-Lymphotropic Virus Type 1 Transmembrane Glycoprotein Helical Hairpin Structure
Authors: Maerz Anne L. , Center Rob J. , Kemp Bruce E. , Kobe Bostjan , Poumbourios Pantelis 
Published: July 2002

ABSTRACT
Retrovirus entry into cells follows receptor binding by the surface-exposed envelope glycoprotein (Env) subunit (SU), which triggers the membrane fusion activity of the transmembrane (TM) protein. TM protein fragments expressed in the absence of SU adopt helical hairpin structures comprising a central coiled coil, a region of chain reversal containing a disulfide-bonded loop, and a C-terminal segment that packs onto the exterior of the coiled coil in an antiparallel manner. Here we used in vitro mutagenesis to test the functional role of structural elements observed in a model helical hairpin, gp21 of human T-lymphotropic virus type 1. Membrane fusion activity requires the stabilization of the N and C termini of the central coiled coil by a hydrophobic N cap and a small hydrophobic core, respectively. A conserved Gly-Gly hinge motif preceding the disulfide-bonded loop, a salt bridge that stabilizes the chain reversal region, and interactions between the C-terminal segment and the coiled coil are also critical for fusion activity. Our data support a model whereby the chain reversal region transmits a conformational signal from receptor-bound SU to induce the fusion-activated helical hairpin conformation of the TM protein.
Cooperation of Multiple CCR5 Coreceptors Is Required for Infections by Human Immunodeficiency Virus Type 1
Authors: Kuhmann Shawn E. , Platt Emily J. , Kozak Susan L. , Kabat David 
Published: July 2002

ABSTRACT
In addition to the primary cell surface receptor CD4, CCR5 or another coreceptor is necessary for infections by human immunodeficiency virus type 1 (HIV-1), yet the mechanisms of coreceptor function and their stoichiometries in the infection pathway remain substantially unknown. To address these issues, we studied the effects of CCR5 concentrations on HIV-1 infections using wild-type CCR5 and two attenuated mutant CCR5s, one with the mutation Y14N at a critical tyrosine sulfation site in the amino terminus and one with the mutation G163R in extracellular loop 2. The Y14N mutation converted a YYT sequence at positions 14 to 16 to an NYT consensus site for N-linked glycosylation, and the mutant protein was shown to be glycosylated at that position. The relationships between HIV-1 infectivity values and CCR5 concentrations took the form of sigmoidal (S-shaped) curves, which were dramatically altered in different ways by these mutations. Both mutations shifted the curves by factors of approximately 30- to 150-fold along the CCR5 concentration axis, consistent with evidence that they reduce affinities of virus for the coreceptor. In addition, the Y14N mutation specifically reduced the maximum efficiencies of infection that could be obtained at saturating CCR5 concentrations. The sigmoidal curves for all R5 HIV-1 isolates were quantitatively consistent with a simple mathematical model, implying that CCR5s reversibly associate with cell surface HIV-1 in a concentration-dependent manner, that approximately four to six CCR5s assemble around the virus to form a complex needed for infection, and that both mutations inhibit assembly of this complex but only the Y14N mutation also significantly reduces its ability to successfully mediate HIV-1 infections. Although several alternative models would be compatible with our data, a common feature of these alternatives is the cooperation of multiple CCR5s in the HIV-1 infection pathway. This cooperativity will need to be considered in future studies to address in detail the mechanism of CCR5-mediated HIV-1 membrane fusion.
Intracellular Cre-Mediated Deletion of the Unique Packaging Signal Carried by a Herpes Simplex Virus Type 1 Recombinant and Its Relationship to the Cleavage-Packaging Process
Authors: Logvinoff Carine , Epstein Alberto L. 
Published: July 2002

ABSTRACT

To gain further insight on the function of the herpes simplex virus type 1 (HSV-1) packaging signal (
a
sequence), we constructed a recombinant virus containing a unique
a
sequence, which was flanked by two loxP sites in parallel orientation. The phenotype of this recombinant, named HSV-1 LaL, was studied in cell lines which either express or do not express Cre recombinase. Although LaL virus multiplication was only slightly reduced in standard cell lines, its growth was strongly inhibited in Cre-expressing cells. In these cells,
a
sequences were detected mostly in low-molecular-weight DNA circles, indicating that they had been excised from virus DNA by site-specific recombination. Deletion of the
a
sequences from the viral genome resulted in the accumulation of uncleaved replication intermediates, as observed by pulsed-field gel electrophoresis. B-type capsids also accumulated in these cells, as shown both by electron microscopy and by sucrose gradient sedimentation. Further examination of the status of
a
sequences in Cre-expressing cells indicated that high-level amplification of this sequence can occur in the absence of the cleavage-packaging process. Moreover, the amplified
a
signals in small circular DNA molecules remained uncleaved, indicating that these molecules were not able to efficiently interact with the cleavage-packaging machinery. The cleavage-packaging machinery and the structural proteins required to assemble virions were, however, functional in HSV-1 LaL-infected Cre-expressing cells, since this system could be used to package plasmid DNA harboring an origin of virus replication and one normal
a
signal. This is the first study in which accumulation both of uncleaved replication intermediates and of B capsids has been obtained in the presence of the full set of proteins required to package virus DNA.
Intracellular Localization of Vaccinia Virus Extracellular Enveloped Virus Envelope Proteins Individually Expressed Using a Semliki Forest Virus Replicon
Authors: Lorenzo María M. , Galindo Inmaculada , Griffiths Gareth , Blasco Rafael 
Published: July 2002

ABSTRACT
The extracellular enveloped virus (EEV) form of vaccinia virus is bound by an envelope which is acquired by wrapping of intracellular virus particles with cytoplasmic vesicles containing trans-Golgi network markers. Six virus-encoded proteins have been reported as components of the EEV envelope. Of these, four proteins (A33R, A34R, A56R, and B5R) are glycoproteins, one (A36R) is a nonglycosylated transmembrane protein, and one (F13L) is a palmitylated peripheral membrane protein. During infection, these proteins localize to the Golgi complex, where they are incorporated into infectious virus that is then transported and released into the extracellular medium. We have investigated the fates of these proteins after expressing them individually in the absence of vaccinia infection, using a Semliki Forest virus expression system. Significant amounts of proteins A33R and A56R efficiently reached the cell surface, suggesting that they do not contain retention signals for intracellular compartments. In contrast, proteins A34R and F13L were retained intracellularly but showed distributions different from that of the normal infection. Protein A36R was partially retained intracellularly, decorating both the Golgi complex and structures associated with actin fibers. A36R was also transported to the plasma membrane, where it accumulated at the tips of cell projections. Protein B5R was efficiently targeted to the Golgi region. A green fluorescent protein fusion with the last 42 C-terminal amino acids of B5R was sufficient to target the chimeric protein to the Golgi region. However, B5R-deficient vaccinia virus showed a normal localization pattern for other EEV envelope proteins. These results point to the transmembrane or cytosolic domain of B5R protein as one, but not the only, determinant of the retention of EEV proteins in the wrapping compartment.
The Rice Tungro Bacilliform Virus Gene II Product Interacts with the Coat Protein Domain of the Viral Gene III Polyprotein
Authors: Herzog Etienne , Guerra-Peraza Orlene , Hohn Thomas 
Published: July 2002

ABSTRACT

Rice tungro bacilliform virus
(RTBV) is a plant pararetrovirus whose DNA genome contains four genes encoding three proteins and a large polyprotein. The function of most of the viral proteins is still unknown. To investigate the role of the gene II product (P2), we searched for interactions between this protein and other RTBV proteins. P2 was shown to interact with the coat protein (CP) domain of the viral gene III polyprotein (P3) both in the yeast two-hybrid system and in vitro. Domains involved in the P2-CP association have been identified and mapped on both proteins. To determine the importance of this interaction for viral multiplication, the infectivity of RTBV gene II mutants was investigated by agroinoculation of rice plants. The results showed that virus viability correlates with the ability of P2 to interact with the CP domain of P3. This study suggests that P2 could participate in RTBV capsid assembly.
Regulation of Adenovirus Membrane Penetration by the Cytoplasmic Tail of Integrin β5
Authors: Wang Kena , Guan Tinglu , Cheresh David A. , Nemerow Glen R. 
Published: July 2002

ABSTRACTAdenovirus (Ad) cell entry involves sequential interactions with host cell receptors that mediate attachment (CAR), internalization (αvβ3 and αvβ5), and penetration (αvβ5) of the endosomal membrane. These events allow the virus to deliver its genome to the nucleus. While integrins αvβ3 and αvβ5 both promote Ad internalization into cells, integrin αvβ5 selectively facilitates Ad-mediated membrane permeabilization and endosome rupture. In the experiments reported herein, we demonstrate that the intracellular domain of the integrin β5 subunit specifically regulates Ad-mediated membrane permeabilization and gene delivery. CS-1 melanoma cells expressing a truncated integrin β5 or a chimeric (β5-β3) cytoplasmic tail (CT) supported normal levels of Ad endocytosis but had reduced Ad-mediated gene delivery and membrane permeabilization relative to cells expressing a wild-type integrin β5. Thin-section electron microscopy revealed that virion particles were capable of being endocytosed into cells expressing a truncated β5CT, but they failed to escape cytoplasmic vesicles and translocate to the nucleus. Site-specific mutagenesis studies suggest that a C-terminal TVD motif in the β5CT plays a major role in Ad membrane penetration.
cis
- and
trans
-Acting Elements in Flavivirus RNA Replication
Authors: Khromykh Alexander A. , Sedlak Petra L. , Westaway Edwin G. 
Published: July 2002

ABSTRACT

Most of the seven flavivirus nonstructural proteins (NS1 to NS5) encoded in the distal two-thirds of the RNA positive-sense genome are believed to be essential components of RNA replication complexes. To explore the functional relationships of these components in RNA replication, we used
trans
-complementation analysis of full-length infectious RNAs of Kunjin (KUN) virus with a range of lethal in-frame deletions in the nonstructural coding region, using as helper a repBHK cell line stably producing functional replication complexes from KUN replicon RNA. Recently we showed that replication of KUN RNAs with large carboxy-terminal deletions including the entire RNA polymerase region in the NS5 gene, representing 34 to 75% of the NS5 coding content, could be complemented after transfection into repBHK cells. In this study we have demonstrated that KUN RNAs with deletions of 84 to 97% of the NS1 gene, or of 13 to 63% of the NS3 gene including the entire helicase region, were also complemented in repBHK cells with variable efficiencies. In contrast, KUN RNAs with deletions in any of the other four nonstructural genes NS2A, NS2B, NS4A, and NS4B were not complemented. We have also demonstrated successful
trans
complementation of KUN RNAs containing either combined double deletions in the NS1 and NS5 genes or triple deletions in the NS1, NS3, and NS5 genes comprising as much as 38% of the entire nonstructural coding content. Based on these and our previous complementation results, we have generated a map of
cis
- and
trans
-acting elements in RNA replication for the nonstructural coding region of the flavivirus genome. These results are discussed in the context of our model on formation and composition of the flavivirus replication complex, and we suggest molecular mechanisms by which functions of some defective components of the replication complex can be complemented by their wild-type counterparts expressed from another (helper) RNA molecule.