bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficacy of Zidovudine Compared to Stavudine, Both in Combination with Lamivudine and Indinavir, in Human Immunodeficiency Virus-Infected Nucleoside-Experienced Patients with No Prior Exposure to Lamivudine, Stavudine, or Protease Inhibitors (Novavir Trial)
Authors: Joly Véronique , Flandre Philippe , Meiffredy Vincent , Brun-Vezinet Françoise , Gastaut Jean-Albert , Goujard Cécile , Remy Gérard , Descamps Diane , Ruffault Annick , Certain Agnès , Aboulker Jean-Pierre , Yeni for the Novavir Study Group Patrick 
Published: July 2002

ABSTRACTWe compared the efficacy and the toxicity of zidovudine (AZT) versus stavudine (d4T), in combination with lamivudine (3TC) and indinavir, in AZT-, dideoxyinosine (ddI)-, and/or dideoxycytosine (ddC)-experienced patients in a randomized comparative multicenter trial. One hundred seventy human immunodeficiency virus type 1 (HIV-1)-infected patients, who had received AZT, ddI, and/or ddC for at least 6 months but were naive for d4T, 3TC, and protease inhibitors, were randomized to AZT at 250 to 300 mg twice daily, 3TC at 150 mg twice daily, and indinavir at 800 mg every 8 h or to d4T at 40 mg twice daily, 3TC at 150 mg twice daily, and indinavir at 800 mg every 8 h. The primary endpoint was time to virological failure, defined as plasma HIV-1 RNA levels of >5,000 copies/ml after at least 8 weeks of antiretroviral therapy. Additional endpoints were change from baseline in CD4 cell counts, AIDS-defining events and adverse events, and proportion of patients with HIV-1 RNA levels of <500 copies/ml and HIV-1 RNA levels of <50 copies/ml. At week 80, 15 patients in the AZT arm and 14 patients in the d4T arm had reached the primary endpoint, and time to virological failure did not differ between the two arms (P= 0.98). In the d4T and in the AZT arms, 67 and 73% of patients, respectively, had HIV-1 RNA levels of <500 copies/ml (P= 0.50). The median change from baseline in CD4 cell count was 195 × 106and 175 × 106/liter for the d4T- and AZT-containing arms, respectively. The proportions of patients with HIV-1 RNA levels of <50 copies/ml at weeks 8, 16, and 24 were similar in the two arms. The occurrence of serious adverse events was not significantly different between arms. In conclusion, in these patients heavily pretreated with AZT, switching from AZT to d4T when initiating indinavir and 3TC did not bring any additional benefit compared to maintaining AZT.
Effects of Soil and Water Content on Methyl Bromide Oxidation by the Ammonia-Oxidizing Bacterium
Nitrosomonas europaea
Authors: Duddleston Khrystyne N. , Bottomley Peter J. , Porter Angela , Arp Daniel J. 
Published: July 2002

ABSTRACT

Little information exists on the potential of NH
3
-oxidizing bacteria to cooxidize halogenated hydrocarbons in soil. A study was conducted to examine the cooxidation of methyl bromide (MeBr) by an NH
3
-oxidizing bacterium,
Nitrosomonas europaea
, under soil conditions. Soil and its water content modified the availability of NH
4
+
and MeBr and influenced the relative rates of substrate (NH
3
) and cosubstrate (MeBr) oxidations. These observations highlight the complexity associated with characterizing soil cooxidative activities when soil and water interact to differentially affect substrate and cosubstrate availabilities.
Effect of Model Sorptive Phases on Phenanthrene Biodegradation: Different Enrichment Conditions Influence Bioavailability and Selection of Phenanthrene-Degrading Isolates
Authors: Grosser Robert J. , Friedrich Michael , Ward David M. , Inskeep William P. 
Published: July 2002

ABSTRACT

The sorption of organic contaminants by natural organic matter (NOM) often limits substrate bioavailability and is an important factor affecting microbial degradation rates in soils and sediments. We hypothesized that reduced substrate bioavailability might influence which microbial assemblages are responsible for contaminant degradation under enrichment culture conditions. Our primary goal was to characterize enrichments in which different model organic solid phases were used to establish a range of phenanthrene bioavailabilities for soil microorganisms. Phenanthrene sorption coefficients (expressed as log

K
D

values) ranged from 3.0 liters kg
−1
for Amberlite carboxylic acid cation-exchange resin (AMB) to 3.5 liters kg
−1
for Biobeads polyacrylic resin (SM7) and 4.2 liters kg
−1
for Biobeads divinyl benzene resin (SM2). Enrichment cultures were established for control (no sorptive phase), sand, AMB, SM7, and SM2 treatments by using two contaminated soils (from Dover, Ohio, and Libby, Mont.) as the initial inocula. The effects of sorption by model phases on the degradation of phenanthrene were evaluated for numerous transfers in order to obtain stable microbial assemblages representative of sorptive and nonsorptive enrichment cultures and to eliminate the effects of the NOM present in the initial inoculum. Phenanthrene degradation rates were similar for each soil inoculum and ranged from 4 to 5 μmol day
−1
for control and sand treatments to approximately 0.4 μmol day
−1
in the presence of the SM7 sorptive phase. The rates of phenanthrene degradation in the highly sorptive SM2 enrichment culture were insignificant; consequently, stable microbial populations could not be obtained. Bacterial isolates obtained from serial dilutions of enrichment culture samples exhibited significant differences in rates of phenanthrene degradation performed in the presence of SM7, suggesting that enrichments performed in the presence of a sorptive phase selected for different microbial assemblages than control treatments containing solid phase phenanthrene.
Genotyping
Cryptosporidium parvum
with an
hsp70
Single-Nucleotide Polymorphism Microarray
Authors: Straub Timothy M. , Daly Don S. , Wunshel Sharon , Rochelle Paul A. , DeLeon Ricardo , Chandler Darrell P. 
Published: July 2002

ABSTRACT

We investigated the application of an oligonucleotide microarray to (i) specifically detect
Cryptosporidium
spp., (ii) differentiate between closely related
C. parvum
isolates and
Cryptosporidium
species, and (iii) differentiate between principle genotypes known to infect humans. A microarray of 68 capture probes targeting seven single-nucleotide polymorphisms (SNPs) within a 190-bp region of the
hsp70
gene of
Cryptosporidium parvum
was constructed. Labeled
hsp70
targets were generated by PCR with biotin- or Cy3-labeled primers. Hybridization conditions were optimized for hybridization time, temperature, and salt concentration. Two genotype I
C. parvum
isolates (TU502 and UG502), two
C. parvum
genotype II isolates (Iowa and GCH1), and DNAs from 22 non-
Cryptosporidium
sp. organisms were used to test method specificity. Only DNAs from
C. parvum
isolates produced labeled amplicons that could be hybridized to and detected on the array. Hybridization patterns between genotypes were visually distinct, but identification of SNPs required statistical analysis of the signal intensity data. The results indicated that correct mismatch discrimination could be achieved for all seven SNPs for the UG502 isolate, five of seven SNPs for the TU502 isolate, and six of seven SNPs for both the Iowa and GCH1 isolates. Even without perfect mismatch discrimination, the microarray method unambiguously distinguished between genotype I and genotype II isolates and demonstrated the potential to differentiate between other isolates and species on a single microarray. This method may provide a powerful new tool for water utilities and public health officials for assessing point and nonpoint source contamination of water supplies.
Use of Formalin-Fixed, Propidium Iodide-Stained Human Leukocytes as a Standard for Enumerating CD4
+
T Lymphocytes in a Single-Platform Assay
Authors: Harrison G. M. , Bennett A. J. , Moody M. , Read G. F. , Williams P. E. 
Published: July 2002

ABSTRACT
A new, inexpensive method is described that enables lymphocytes to be enumerated very precisely. Normal leukocytes were simultaneously stained and fixed with a propidium iodide-paraformaldehyde solution. The preparation obtained (CellBeads) was used as an internal standard for cell enumeration by flow cytometry and was stable at 4°C for at least 60 days. Unlike synthetic beads, the CellBeads behaved similarly to normal cells during red blood cell lysis and cell washing procedures. When known numbers of CellBeads were added to whole-blood samples and the numbers of CellBeads and lymphocytes were determined, highly reproducible and accurate enumerations were obtained—far more so than when synthetic beads were used. This inexpensive method is suitable for routine use.
Cell-Mediated Immune Response during PrimaryChlamydia pneumoniaeInfection
Authors: Halme S. , Latvala J. , Karttunen R. , Palatsi I. , Saikku P. , Surcel H.-M. 
Published: July 2002

ABSTRACTThe development ofChlamydia pneumoniae-specific cell-mediated immunity was studied during a primaryC. pneumoniaeinfection. The immune response was detected as positive lymphocyte proliferation and secretion of interferon gamma.C. pneumoniae-induced activation of both CD4+and CD8+T cells was detected in the early phase of infection, but activation of only CD4+T cells was detected in the later stage.
Antigen Specificity in Experimental Bovine Tuberculosis
Authors: Rhodes S. G. , Gavier-Widen D. , Buddle B. M. , Whelan A. O. , Singh M. , Hewinson R. G. , Vordermeier H. M. 
Published: July 2002

ABSTRACT

This report describes the kinetics of T-cell responses to a panel of mycobacterial antigens (PPD-M, PPD-A, ESAT-6, Ag85, 38kD, MPB64, MPB70, MPB83, hsp16.1, hsp65, and hsp70) following experimental infection of cattle with
Mycobacterium bovis
. Increased antigen-specific lymphocyte proliferation, gamma interferon, and interleukin-2 responses were observed in all calves following infection. Positive lymphocyte proliferation and cytokine responses to PPD-M and ESAT-6 were observed throughout the infection period studied. In contrast, responses to all other antigens were more variable and were not constantly present, suggesting that antigen cocktails rather than individual antigens should be used for immunodiagnosis. The detection of cytokine responses in the absence of lymphocyte proliferation, particularly during the early stages of infection, suggests a role for antigen-specific cytokine readout systems in the early identification of
M. bovis
infection in cattle.
Activity and Cross-Reactivity of Antibodies Induced in Mice by Immunization with a Group B Meningococcal Conjugate
Authors: Coquillat D. , Bruge J. , Danve B. , Latour M. , Hurpin C. , Schulz D. , Durbec P. , Rougon G. 
Published: July 2002

ABSTRACTThe capsular polysaccharide of group BNeisseriameningitidisis composed of a linear homopolymer of α(2-8)N-acetyl neuraminic acid or polysialic acid (PSA) that is also carried by isoforms of the mammalian neural cell adhesion molecule (NCAM), which is especially expressed on brain cells during development. Here we analyzed the ability of antibodies induced by the candidate vaccineN-propionyl polysaccharide tetanus toxoid conjugate to recognize PSA-NCAM. We hyperimmunized mice to produce a pool of antisera and a series of immunoglobulin G monoclonal antibodies and evaluated their self-reactivity profile by using a battery of tests (immunoprecipitation, immunoblotting, and immunofluorescence detection on live cells and human tissue sections) chosen for their sensitivity and specificity to detect PSA-NCAM in various environments. We also searched for the effects of the vaccine-induced antibodies in two functional assays involving cell lysis or cell migration. Although they were highly bactericidal, all the antibodies tested showed very low or no recognition of PSA-NCAM, in contrast to PSA-specific monoclonal antibodies used as controls. Different patterns of cross-reactions were revealed by the tests used, likely due to affinity and specificity differences among the populations of induced antibodies. Furthermore, neither cell lysis nor perturbation of migration was observed in the presence of the tested antibodies. Importantly, we showed that whereas enzymatic removal of PSA groups from the surfaces of live cells perturbed their migration, blocking them with PSA-specific antibodies was not functionally detrimental. Taken together, our data indicated that this candidate vaccine induced antibodies that could not demonstrate an immunopathologic effect.
Oral Administration of Formaldehyde-Killed Recombinant Bacteria Expressing a Mimic of the Shiga Toxin Receptor Protects Mice from Fatal Challenge with Shiga-Toxigenic
Escherichia coli
Authors: Paton James C. , Rogers Trisha J. , Morona Renato , Paton Adrienne W. 
Published: July 2002

ABSTRACT

Gastrointestinal disease caused by Shiga toxin-producing
Escherichia coli
(STEC) is frequently complicated by life-threatening toxin-induced systemic sequelae, including the hemolytic uremic syndrome. We previously constructed a recombinant bacterium displaying a Shiga toxin receptor mimic on its surface which neutralized Shiga toxins with very high efficiency. Moreover, oral administration of the live bacterium completely protected mice from challenge with virulent STEC. In this study, we investigated the protective capacity of formaldehyde-killed receptor mimic bacteria, as these are likely to be safer for administration to humans. The killed bacteria completely protected STEC-challenged mice when administered three times daily; incomplete protection was achieved using two doses per day. Commencement of therapy could be delayed for up to 48 h after challenge without diminishing protection, depending on the virulence of the challenge strain. Thus, administration of this agent early in the course of human STEC disease may prevent progression to life-threatening complications.
Functional Opsonic Activity of Human Serum Antibodies to Inner Core Lipopolysaccharide (galE) of Serogroup B Meningococci Measured by Flow Cytometry
Authors: Plested Joyce S. , Ferry Berne L. , Coull Philip A. , Makepeace Katherine , Lehmann Anne K. , MacKinnon Fiona G. , Griffiths Helen G. , Herbert Mark A. , Richards James C. , Moxon E. Richard 
Published: July 2002

ABSTRACTA recently described flow cytometric opsonophagocytic assay (OPA) was adapted to quantify the functional activity of serum antibodies specifically directed against serogroup B inner core lipopolysaccharide (LPS) ofNeisseria meningitidis. The percentage of human peripheral polymorphonuclear leukocytes and monocytes (PMNms) ingesting fluorescently labeled, ethanol-fixedN. meningitidisorganisms (phagocytic activity) in the presence of human sera was measured to reflect the serum opsonic activity against the bacterium. The contribution to opsonophagocytic activity of antibodies to inner core LPS was estimated by comparing the opsonic activities of adult and infant sera before and after adsorbing anti-LPS antibodies from the sera using purified LPS extracted from an LPS mutant (galE) ofN. meningitidisstrain MC58 (B:15:P1.7,16:L3). The specificity of the assay was further investigated using monoclonal antibody (MAb) B5, which binds to an inner core LPS epitope ofN. meningitidis. A dose-dependent decrease in phagocytic activity was observed when MAb B5 was incubated with LPS from an inner core LPS (galE) mutant. Similarly, the number of PMNms ingesting fluorescently labeled polystyrene beads coated with inner core (galE) LPS decreased in a dose-dependent fashion when MAb B5 was incubated with various concentrations of the homologous inner core LPS. Strong correlations were found between the concentration of serum antibodies to inner core LPS (galE) versus the phagocytic activity using healthy adult sera (r2= 0.89). There was a correlation between phagocytic ingestion and initiation of intracellular oxidative burst (r2= 0.99) using polystyrene beads coated with inner core LPS and opsonized with the same sera using the oxidative burst indicator system dihydrorhodamine123/rhodamine 123. OPA results were also found to correlate closely with the results of the serum bactericidal assay using MAb B5 against theN. meningitidisMC58galEmutant in the presence of human complement (r2= 0.994,P= 0.003, two-tailed test). These studies demonstrate that functional antibodies are produced in humans against meningococcal inner core LPS and that the OPA is a useful approach to study the opsonic activity of antibodies to inner core LPS in health and disease.
Magnesium Uptake by CorA Is Essential for Viability of the Gastric Pathogen
Helicobacter pylori
Authors: Pfeiffer Jens , Guhl Johannes , Waidner Barbara , Kist Manfred , Bereswill Stefan 
Published: July 2002

ABSTRACT

We show here that Mg
2+
acquisition by CorA is essential for
Helicobacter pylori
in vitro, as
corA
mutants did not grow in media without Mg
2+
supplementation. Complementation analysis performed with an
Escherichia coli corA
mutant revealed that
H. pylori
CorA transports nickel and cobalt in addition to Mg
2+
. However, Mg
2+
is the dominant CorA substrate, as the
corA
mutation affected neither cobalt and nickel resistance nor nickel induction of urease in
H. pylori
. The drastic Mg
2+
requirement (20 mM) of
H. pylori corA
mutants indicates that CorA plays a key role in the adaptation to the low-Mg
2+
conditions predominant in the gastric environment.
The TRAP-Like SplA Protein Is a
trans
-Acting Negative Regulator of Spore Photoproduct Lyase Synthesis during
Bacillus subtilis
Sporulation
Authors: Fajardo-Cavazos Patricia , Nicholson Wayne L. 
Published: July 2002

ABSTRACT

UV resistance of bacterial endospores derives from a unique DNA photochemistry in which the major UV photoproduct is the thymine dimer 5-thyminyl-5,6-dihydrothymine (spore photoproduct [SP]) instead of cyclobutane pyrimidine dimers. Repair of SP during spore germination is due in large part to the activity of the enzyme SP lyase encoded by
splB
, the second cistron of the
splAB
operon. Expression of the
splAB
operon in
Bacillus subtilis
is transcriptionally activated by the Eς
G
form of RNA polymerase during morphological stage III in the developing forespore compartment, and SP lyase is packaged into the dormant spore. In addition to temporal and compartmental control of
splAB
expression, a second regulatory circuit which modulates the level of expression of
splB-lacZ
fusions without altering their developmental timing or compartmentalization is reported here. This second regulatory circuit involves the negative action of the
splA
gene product, a 79-amino-acid protein with approximately 50% similarity and 17% identity to TRAP, the tryptophan RNA-binding attenuation protein from
B. subtilis
and
Bacillus pumilus
.
Control of
asgE
Expression during Growth and Development of
Myxococcus xanthus
Authors: Garza Anthony G. , Harris Baruch Z. , Greenberg Brandon M. , Singer Mitchell 
Published: July 2002

ABSTRACT

One of the earliest events in the
Myxococcus xanthus
developmental cycle is production of an extracellular cell density signal called A-signal (or A-factor). Previously, we showed that cells carrying an insertion in the
asgE
gene fail to produce normal levels of this cell-cell signal. In this study we found that expression of
asgE
is growth phase regulated and developmentally regulated. Several lines of evidence indicate that
asgE
is cotranscribed with an upstream gene during development. Using primer extension analyses, we identified two 5′ ends for this developmental transcript. The DNA sequence upstream of one 5′ end has similarity to the promoter regions of several genes that are A-signal dependent, whereas sequences located upstream of the second 5′ end show similarity to promoter elements identified for genes that are C-signal dependent. Consistent with this result is our finding that mutants failing to produce A-signal or C-signal are defective for developmental expression of
asgE
. In contrast to developing cells, the large majority of the
asgE
transcript found in vegetative cells appears to be monocistronic. This finding suggests that
asgE
uses different promoters for expression during vegetative growth and development. Growth phase regulation of
asgE
is abolished in a
relA
mutant, indicating that this vegetative promoter is induced by starvation. The data presented here, in combination with our previous results, indicate that the level of AsgE in vegetative cells is sufficient for this protein to carry out its function during development.
sal
Genes Determining the Catabolism of Salicylate Esters Are Part of a Supraoperonic Cluster of Catabolic Genes in
Acinetobacter
sp. Strain ADP1
Authors: Jones Rheinallt M. , Pagmantidis Vassilis , Williams Peter A. 
Published: July 2002

ABSTRACT

A 5-kbp region upstream of the
are-ben-cat
genes was cloned from
Acinetobacter
sp. strain ADP1, extending the supraoperonic cluster of catabolic genes to 30 kbp. Four open reading frames,
salA
,
salR
,
salE
, and
salD
, were identified from the nucleotide sequence. Reverse transcription-PCR studies suggested that these open reading frames are organized into two convergent transcription units,
salAR
and
salDE
. The
salE
gene, encoding a protein of 239 residues, was ligated into expression vector pET5a. Its product, SalE, was shown to have esterase activity against short-chain alkyl esters of 4-nitrophenol but was also able to hydrolyze ethyl salicylate to ethanol and salicylic acid. A mutant of ADP1 with a Km
r
cassette introduced into
salE
had lost the ability to utilize only ethyl and methyl salicylates of the esters tested as sole carbon sources, and no esterase activity against ethyl salicylate could be detected in cell extracts. SalE was induced during growth on ethyl salicylate but not during growth on salicylate itself.
salD
encoded a protein of undetermined function with homologies to the
Escherichia coli
FadL membrane protein, which is involved in facilitating fatty acid transport, and a number of other proteins detected during aromatic catabolism, which may also function in hydrocarbon transport or uptake processes. A Km
r
cassette insertion in
salD
deleteriously affected cell growth and viability. The
salA
and
salR
gene products closely resemble two
Pseudomonas
proteins, NahG and NahR, respectively encoding salicylate hydroxylase and the LysR family regulator of both salicylate and naphthalene catabolism.
salA
was cloned into pUC18 together with
salR
and
salE
, and its gene product showed salicylate-inducible hydroxylase activity against a range of substituted salicylates, with the same relative specific activities as found in wild-type ADP1 grown on salicylate. Mutations involving insertion of Km
r
cassettes into
salA
and
salR
eliminated expression of salicylate hydroxylase activity and the ability to grow on either salicylate or ethyl salicylate. Studies of mutants with disruptions of genes of the β-ketoadipate pathway with or without an additional
salE
mutation confirmed that ethyl salicylate and salicylate were channeled into the β-ketoadipate pathway at the level of catechol and thence dissimilated by the
cat
gene products. SalR appeared to regulate expression of
salA
but not
salE
.