bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reversal of Flagellar Rotation Is Important in Initial Attachment of
Escherichia coli
to Glass in a Dynamic System with High- and Low-Ionic-Strength Buffers
Authors: McClaine Jennifer W. , Ford Roseanne M. 
Published: July 2002

ABSTRACT

The attachment rates of wild-type, smooth-swimming, tumbly, and paralyzed
Escherichia coli
to glass was measured at fluid velocities of 0.0044 and 0.044 cms
−1
(corresponding to shear rates of 0.34 and 3.4 s
−1
, respectively), in 0.02 and 0.2 M buffer solutions. At the highest ionic strength, we did not observe a significant difference in the attachment rate of wild-type and paralyzed cells at either fluid velocity. However, when the ionic strength was reduced, paralyzed bacteria attached at rates 4 and 10 times lower than that of the wild type under fluid velocities of 0.0044 and 0.044 cms
−1
, respectively. This suggested that the rotation of the flagella assisted in attachment. We then compared the attachment rates of smooth-swimming (counterclockwise rotation only) and tumbly (clockwise rotation only) cells to the wild type to determine whether the direction of rotation was important to cell attachment. At 0.0044 cms
−1
, the smooth-swimming cells attached at rates similar to that of the wild type in both buffer solutions but significantly less at the higher fluid velocity. Tumbly cells attached at much lower rates under all conditions. Thus, the combination of clockwise and counterclockwise flagellar rotation and their coupling appeared to be important in cell attachment. We considered a number of hypotheses to interpret these observations, including a residence time analysis and a comparison of traditional Derjaguin-Landau-Verwey-Overbeek (DLVO) theory to soft-particle theory.
Response of Endophytic Bacterial Communities in Potato Plants to Infection with
Erwinia carotovora
subsp.
atroseptica
Authors: Reiter Birgit , Pfeifer Ulrike , Schwab Helmut , Sessitsch Angela 
Published: July 2002

ABSTRACT

The term endophyte refers to interior colonization of plants by microorganisms that do not have pathogenic effects on their hosts, and various endophytes have been found to play important roles in plant vitality. In this study, cultivation-independent terminal restriction fragment length polymorphism analysis of 16S ribosomal DNA directly amplified from plant tissue DNA was used in combination with molecular characterization of isolates to examine the influence of plant stress, achieved by infection with the blackleg pathogen
Erwinia carotovora
subsp.
atroseptica
, on the endophytic population in two different potato varieties. Community analysis clearly demonstrated increased bacterial diversity in infected plants compared to that in control plants. The results also indicated that the pathogen stress had a greater impact on the bacteria population than the plant genotype had. Partial sequencing of the 16S rRNA genes of isolated endophytes revealed a broad phylogenetic spectrum of bacteria, including members of the α, β, and γ subgroups of the
Proteobacteria
, high- and low-G+C-content gram-positive organisms, and microbes belonging to the
Flexibacter-Cytophaga-Bacteroides
group. Screening of the isolates for antagonistic activity against
E. carotovora
subsp.
atroseptica
revealed that 38% of the endophytes protected tissue culture plants from blackleg disease.
Extensive Profiling of a Complex Microbial Community by High-Throughput Sequencing
Authors: Hill Janet E. , Seipp Robyn P. , Betts Martin , Hawkins Lindsay , Van Kessel Andrew G. , Crosby William L. , Hemmingsen Sean M. 
Published: July 2002

ABSTRACT

Complex microbial communities remain poorly characterized despite their ubiquity and importance to human and animal health, agriculture, and industry. Attempts to describe microbial communities by either traditional microbiological methods or molecular methods have been limited in both scale and precision. The availability of genomics technologies offers an unprecedented opportunity to conduct more comprehensive characterizations of microbial communities. Here we describe the application of an established molecular diagnostic method based on the chaperonin-60 sequence, in combination with high-throughput sequencing, to the profiling of a microbial community: the pig intestinal microbial community. Four libraries of cloned
cpn60
sequences were generated by two genomic DNA extraction procedures in combination with two PCR protocols. A total of 1,125 cloned
cpn60
sequences from the four libraries were sequenced. Among the 1,125 cloned
cpn60
sequences, we identified 398 different nucleotide sequences encoding 280 unique peptide sequences. Pairwise comparisons of the 398 unique nucleotide sequences revealed a high degree of sequence diversity within the library. Identification of the likely taxonomic origins of cloned sequences ranged from imprecise, with clones assigned to a taxonomic subclass, to precise, for cloned sequences with 100% DNA sequence identity with a species in our reference database. The compositions of the four libraries were compared and differences related to library construction parameters were observed. Our results indicate that this method is an alternative to 16S rRNA sequence-based studies which can be scaled up for the purpose of performing a potentially comprehensive assessment of a given microbial community or for comparative studies.
Preservation of Lymphocyte Immunophenotype and Proliferative Responses in Cryopreserved Peripheral Blood Mononuclear Cells from Human Immunodeficiency Virus Type 1-Infected Donors: Implications for Multicenter Clinical Trials
Authors: Reimann Keith A. , Chernoff Miriam , Wilkening Cynthia L. , Nickerson Christine E. , Landay Alan L. ,   The ACTG Immunology Advanced Technology Laboratories
Published: July 2002

ABSTRACT

Human immunodeficiency virus type 1 (HIV-1) infection results in impaired immune function that can be measured by changes in immunophenotypically defined lymphocyte subsets and other in vitro functional assays. These in vitro assays may also serve as early indicators of efficacy when new therapeutic strategies for HIV-1 infection are being evaluated. However, the use of in vitro assays of immune function in multicenter clinical trials has been hindered by their need to be performed on fresh specimens. We assessed the feasibility of using cryopreserved peripheral blood mononuclear cells (PBMC) for lymphocyte immunophenotyping and for lymphocyte proliferation at nine laboratories. In HIV-1-infected patients with moderate CD4
+
lymphocyte loss, the procedures of density gradient isolation, cryopreservation, and thawing of PBMC resulted in significant loss of CD19
+
B cells but no measurable loss of total T cells or CD4
+
or CD8
+
T cells. No significant changes were seen in CD28
−
CD95
+
lymphocytes after cell isolation and cryopreservation. However, small decreases in HLA-DR
+
CD38
+
lymphocytes and of CD45RA
+
CD62L
+
were observed within both the CD4
+
and CD8
+
subsets. Fewer than 10% of those specimens that showed positive PBMC proliferative responses to mitogens or microbial antigens lost their responsiveness after cryopreservation. These results support the feasibility of cryopreserving PBMC for immunophenotyping and functional testing in multicenter AIDS clinical trials. However, small changes in selected lymphocyte subsets that may occur after PBMC isolation and cryopreservation will need to be assessed and considered in the design of each clinical trial.
Development of the Antinuclear and Anticytoplasmic Antibody Consensus Panel by the Association of Medical Laboratory Immunologists
Authors: James Karen , Carpenter A. Betts , Cook Linda , Marchand Richard , Nakamura Robert M. 
Published: July 2002

ABSTRACT
The Association of Medical Laboratory Immunologists (AMLI) have developed a panel of antinuclear and anticytoplasmic antibody consensus sera that can be useful for enzyme immunoassay (EIA), Ouchterlony, and immunofluorescence assay methods. It was developed to assist in the evaluation of newly available EIA methods for the detection of autoantibodies. The panel of sera was evaluated in several clinical laboratories and a large number of laboratories owned by manufacturers of clinical autoantibody testing kits. The majority of sera performed well for the EIAs in both the clinical laboratories and the manufacturers' laboratories, but some samples had discrepant results. A major source of discrepancy is the current inability of the EIA results to be directly compared in a quantitative way as no standardization exists. The evaluation demonstrated lower sensitivity of detection by the Ouchterlony method. The limited evaluation of the sera with immunoblotting and Western blotting did not show good agreement with other methods. Further work must be done to standardize blotting methods prior to their use in routine clinical testing. The sera are now available to vendors and clinical laboratories for use in the detection of SS-A, SS-B, Sm, U1-RNP, Scl-70, Jo-1, double-stranded DNA, and centromere antibodies. The availability of the consensus sera will help evaluate and improve the EIA methods currently being used.
Comparison of Commercial Latex Agglutination and Sandwich Enzyme Immunoassays with a Competitive Binding Inhibition Enzyme Immunoassay for Detection of Antigenemia and Antigenuria in a Rabbit Model of Invasive Aspergillosis
Authors: Hurst Steven F. , Reyes Guadalupe H. , McLaughlin David W. , Reiss Errol , Morrison Christine J. 
Published: July 2002

ABSTRACT

A commercial latex agglutination assay (LA) and a sandwich enzyme immunoassay (SEIA) (Sanofi Diagnostics Pasteur, Marnes-la-Coquette, France) were compared with a competitive binding inhibition assay (enzyme immunoassay [EIA]) to determine the potential uses and limitations of these antigen detection tests for the sensitive, specific, and rapid diagnosis of invasive aspergillosis (IA). Toward this end, well-characterized serum and urine specimens were obtained by using a rabbit model of IA. Serially collected serum or urine specimens were obtained daily from control rabbits or from rabbits immunosuppressed and infected systemically with
Aspergillus fumigatus
. By 4 days after infection, EIA, LA, and SEIA detected antigen in the sera of 93, 93, and 100% of
A. fumigatus
-infected rabbits, respectively, whereas antigen was detected in the urine of 93, 100, and 100% of the rabbits, respectively. False-positive results for non-
A. fumigatus
-infected rabbits for EIA, LA, and SEIA were as follows: for serum, 14, 11, and 23%, respectively; for urine, 14, 84, and 90%, respectively. Therefore, although the sensitivities of all three tests were similar, the specificity was generally greater for EIA than for LA or SEIA. Infection was also detected earlier by EIA, by which the serum of 53% of
A. fumigatus
-infected rabbits was positive as early as 1 day after infection, whereas the serum of only 27% of the rabbits tested by LA was positive. Although the serum of 92% of
A. fumigatus
-infected rabbits was positive by SEIA as early as 1 day after infection, the serum of a high percentage (50%) was false positive before infection. The urine of 21% of
A. fumigatus
-infected rabbits was positive by EIA as early as 1 day after infection, and the urine of none of the rabbits was false positive before infection. When EIA results for urine specimens were combined with those for serum, sensitivity was improved (i.e., 67% of rabbits were positive by 1 day after infection and only one rabbit gave a false-positive result). A total of 93% of
A. fumigatus
-infected rabbits were positive for antigen in urine as early as 1 day after infection and the urine of 100% of the rabbits was positive by SEIA. However, before infection, 79% of
A. fumigatus
-infected rabbits were false positive for antigen in urine by LA and 90% were false positive for antigen in urine by SEIA. These data indicate that the EIA has the potential to be used to diagnose IA with both serum and urine specimens and to detect a greater number of infections earlier with greater specificity than the specificities achieved with the commercial tests.
Differentiation of
Bartonella
Species by a Microimmunofluorescence Assay, Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis, and Western Immunoblotting
Authors: Liang Zhongxing , Raoult Didier 
Published: July 2002

ABSTRACT

Bartonella
species can be differentiated by microimmunofluorescence assay, sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), and immunoblotting with murine polyclonal antisera to
Bartonella henselae
,
B. quintana
,
B. elizabethae
, and
B. bacilliformis
. A pairwise comparison on the basis of SDS-PAGE protein profiles demonstrated similarity values for proteins of different
Bartonella
species ranging from 28.6 to 86.4%. Antigenic relationships revealed by immunoblotting with murine antisera were equivalent to those of proteins observed by SDS-PAGE. A dendrogram obtained on the basis of protein bands of SDS-polyacrylamide gels showed that
Bartonella
species could be divided into three groups.
B. bacilliformis
was distinct from all other
Bartonella
species;
B. grahamii
,
B. taylorii
,
B. doshiae
, and
B. vinsonii
formed a cluster, as did
B. henselae
,
B. quintana
,
B. elizabethae
, and
B. clarridgeiae
. These relationships were consistent with those revealed by parsimony trees derived from 16S rRNA and
gltA
gene sequencing. SDS-PAGE analysis showed that 120-, 104-, 85-, 71-, 54-, 47-, 40-, 33-, 30-, and 19-kDa proteins were present in all species, with the 54-kDa protein being the most dominant. Proteins with a molecular mass of less than 54 kDa allow the differentiation of species and are a possible target for future species-specific antibodies and antigens.
Identifying Diagnostic Peptides for Lyme Disease through Epitope Discovery
Authors: Kouzmitcheva Galina A. , Petrenko Valery A. , Smith George P. 
Published: July 2002

ABSTRACTSerum antibodies from patients with Lyme disease (LD) were used to affinity select peptide epitopes from 12 large random peptide libraries in phage display format. The selected peptides were surveyed for reactivity with a panel of positive sera (from LD patients) and negative sera (from subjects without LD), thus identifying 17 peptides with a diagnostically useful binding pattern: reactivity with at least three positive sera and no reactivity with any of the negative sera. The peptides define eight sequence motifs, none of which can be matched convincingly with segments of proteins fromBorrelia burgdorferi, the LD pathogen; evidently, then, they are “mimotopes,” mimicking natural pathogen epitopes without matching contiguous amino acids of pathogen proteins. Peptides like these could be the basis of a new diagnostic enzyme-linked immunosorbent assay for LD, with sufficient specificity and sensitivity to replace expensive immunoblotting tests that are currently required for definitive serological diagnosis. Moreover, the method used to discover these peptides did not require any knowledge of the pathogen and involved generic procedures that are applicable to almost any infectious disease, including emerging diseases for which no pathogen has yet been identified.
Lateral-Flow Assay for Rapid Serodiagnosis of Human Leptospirosis
Authors: Smits Henk L. , Eapen C. K. , Sugathan Sheela , Kuriakose Mariamma , Gasem M. Hussein , Yersin Claude , Sasaki David , Pujianto Bambang , Vestering Marc , Abdoel Theresia H. , Gussenhoven George C. 
Published: July 2002

ABSTRACT

An assay device for the rapid detection of
Leptospira
-specific immunoglobulin M (IgM) antibodies in human sera is presented. The sensitivity (85.8%) and specificity (93.6%) of the assay compared well (91.9% agreement) with those of an IgM enzyme-linked immunosorbent assay routinely used in the serodiagnosis of leptospirosis. The sensitivity of the assay varied with the stage of the disease. The assay uses stabilized components and is simply performed by the addition of serum and sample fluid to the sample well of the assay device. The assay is read after 10 min, and a positive result is obtained when staining of the test line is observed.
Early Diagnosis of Scrub Typhus with a Rapid Flow Assay Using Recombinant Major Outer Membrane Protein Antigen (r56) of
Orientia tsutsugamushi
Authors: Ching W.-M. , Rowland D. , Zhang Z. , Bourgeois A. L. , Kelly D. , Dasch G. A. , Devine P. L. 
Published: July 2002

ABSTRACT

The variable 56-kDa major outer membrane protein of
Orientia tsutsugamushi
is the immunodominant antigen in human scrub typhus infections. We developed a rapid immunochromatographic flow assay (RFA) for the detection of immunoglobulin M (IgM) and IgG antibodies to
O. tsutsugamushi
. The RFA employs a truncated recombinant 56-kDa protein from the Karp strain as the antigen. The performance of the RFA was evaluated with a panel of 321 sera (serial bleedings of 85 individuals suspected of scrub typhus) which were collected in the Pescadore Islands, Taiwan, from 1976 to 1977. Among these 85 individuals, IgM tests were negative for 7 cases by both RFA and indirect fluorescence assay (IFA) using Karp whole-cell antigen. In 29 cases specific responses were detected by the RFA earlier than by IFA, 44 cases had the same detection time, and 5 cases were detected earlier by IFA than by RFA. For IgG responses, 4 individuals were negative with both methods, 37 cases exhibited earlier detection by RFA than IFA, 42 cases were detected at the same time, and 2 cases were detected earlier by IFA than by RFA. The sensitivities of RFA detection of antibody in sera from confirmed cases were 74 and 86% for IgM and IgG, respectively. When IgM and IgG results were combined, the sensitivity was 89%. A panel of 78 individual sera collected from patients with no evidence of scrub typhus was used to evaluate the specificity of the RFA. The specificities of the RFA were 99% for IgM and 97% for IgG. The sensitivities of IFA were 53 and 73% for IgM and IgG, respectively, and were 78% when the results of IgM and IgG were combined. The RFA test was significantly better than the IFA test for the early detection of antibody to scrub typhus in primary infections, while both tests were equally sensitive with reinfected individuals.
Posttreatment Follow-Up of
Helicobacter pylori
Infection Using a Stool Antigen Immunoassay
Authors: Roth Daniel E. , Taylor David N. , Gilman Robert H. , Meza Rina , Katz Uriel , Bautista Christian , Cabrera Lilia , Velapatiño Billie , Lebron Carlos , Razúri Manuel , Watanabe J. , Monath T. ,   The Gastrointestinal Physiology Working Group
Published: July 2002

ABSTRACT

The
Helicobacter pylori
stool antigen enzyme immunoassay (HpSA) was evaluated during posttreatment follow-up of patients in a country with a very high prevalence of
H. pylori
infection. From among 273 dyspeptic individuals (18 to 55 years) initially recruited from a shantytown in Lima, Peru, 238 participants who met the inclusion criteria and were suspected to be
H. pylori
positive based on
14
C urea breath test (UBT) results underwent endoscopy. Participants with endoscopy-proven infections received standard eradication therapy and were monitored by UBT and HpSA at 1 month following treatment and at 3-month intervals for 9 months posttreatment. A second endoscopy was performed if UBT results showed evidence of treatment failure or
H. pylori
recurrence. Biopsy results were considered the “gold standard” in all analyses. Among patients who underwent endoscopy, HpSA had a pretreatment sensitivity of 93%. Two-hundred thirty patients completed the treatment regimen, of whom 201 (93%) were considered to have had successful treatment outcomes based on a negative follow-up UBT. Thirty-two patients with UBT-defined treatment failures or
H. pylori
recurrences at any point during the 9-month follow-up underwent a second endoscopy. In the posttreatment setting, HpSA had an overall sensitivity of 73% and a specificity of 67%. Agreement between UBT and HpSA diminished throughout the follow-up. Among 14 participants in whom HpSA remained positive at 1 month following treatment despite UBT evidence of treatment success, 12 (86%) became HpSA negative within 3 months posttreatment. Although this study confirmed the validity of the HpSA in the initial assessment of dyspeptic patients, the test demonstrated a reduced overall accuracy in the detection of treatment failures and
H. pylori
recurrences during 9 months of posttreatment follow-up. Furthermore, in some patients it may take up to 3 months after successful eradication for antigen shedding to diminish to levels within the negative HpSA range.
Expression of Natural Peptide Antibiotics in Human Articular Cartilage and Synovial Membrane
Authors: Paulsen Friedrich , Pufe Thomas , Petersen Wolf , Tillmann Bernhard 
Published: July 2002

ABSTRACT
In view of frequent present use of invasive procedures on limb joints, it is astonishing that articular joint inflammation is a rare event. We questioned whether antimicrobial peptides play a role in protecting human articular cartilage and synovial membrane against inflammatory agents. Our results implicate defensins in the protection of human articular joints against pathogens.
Quantification of Substance P mRNA in Human Immune Cells by Real-Time Reverse Transcriptase PCR Assay
Authors: Lai Jian-Ping , Douglas Steven D. , Shaheen Farida , Pleasure David E. , Ho Wen-Zhe 
Published: July 2002

ABSTRACTWe have applied a newly developed real-time reverse transcriptase (RT) PCR (RT-PCR) assay for quantification of substance P (SP) mRNA expression (the SP real-time RT-PCR assay) in human blood monocyte-derived macrophages, peripheral blood lymphocytes, and microglia isolated from fetal brain. The SP real-time RT-PCR assay had a sensitivity of 60 mRNA copies, with a dynamic range of detection between 60 and 600,000 copies of the SP gene transcript per reaction mixture. The coefficient of variation of the threshold cycle number between the SP real-time RT-PCR assays was less than 1.16%. This assay with an SP-specific primer pair efficiently recognizes all four isoforms of preprotachykinin A (the SP precursor) gene transcripts. In order to use this assay to measure the levels of SP mRNA in the human immune cells quantitatively, we designed a specific probe (molecular beacon) derived from exon 3 of the SP gene. We demonstrated that the real-time RT-PCR quantitatively detected SP mRNA in the human immune cells, among which the microglia isolated from fetal brain had the highest levels of SP mRNA. The SP real-time PCR assay yielded reproducible data, as the intra-assay variation was less than 1%. Thus, it is feasible to apply the real-time RT-PCR assay for quantification of SP mRNA levels in human immune cells, as well as in other nonneuronal cells. Since SP is a major modulator of neuroimmunoregulation, this assay has the potential for widespread application for basic and clinical investigations.