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At least 541 records · Page 30Linked to original sources
PubMed2001

Vaccination with attenuated simian immunodeficiency virus by DNA inoculation.

Delivering attenuated lentivirus vaccines as proviral DNA would be simple and inexpensive. Inoculation of macaques with wild-type simian immunodeficiency virus strain mac239 (SIV(mac239)) DNA or SIV(mac239) DNA containing a single deletion in the 3' nef-long terminal repeat overlap region (nef/LTR) led to sustained SIV infections and AIDS. Injection of SIV(mac239) DNA containing identical deletions in both the 5' LTR and 3' nef/LTR resulted in attenuated SIV infections and substantial protection against subsequent mucosal SIV(mac251) challenge.

Amino Acid Sequence↗
PubMed2003

Influence of high salinities on the degradation of diesel fuel by bacterial consortia.

Microbial communities from three Argentinean saline soils were extracted and tested for their ability to degrade diesel fuel in liquid culture at salinities between 0% and 25%. In each case, the degradation process was continuously monitored by measuring oxygen consumption. Two communities (CR1 and CR2) showed nearly equal degrees of degradation across a salinity range of 0%-10% (the former degrading about 63% of the diesel fuel and the latter about 70% after 53 and 80 d, respectively). Furthermore, the degree of degradation was not significantly lower in the presence of 17.5% salt (58% and 65% degraded, respectively). A third community (El Zorro) showed a maximum turnover at 5% salt (79% diesel fuel degraded) and significant degradation (66%) at a salinity of 10%. However, the degree of degradation by this community clearly dropped at 0% and 15% salt. None of the communities were able to degrade diesel fuel in the presence of 25% salt, but the living cell counts showed that components of the microbial population survived the long-term exposure. The surviving portion is obviously sufficient to allow substantial restoration of the original community, as verified by the BIOLOG method. Isolates of the CR1 community were identified as members of the genera Cellulomonas, Bacillus, Dietzia, and Halomonas. In light of our investigations, the bioremediation of contaminated saline soils should be quite possible if the salinity of the soil water is lower than 15% or if it is reduced below this limit by the addition of water.

Agriculture↗
PubMed2006

Design and evaluation of 16S rRNA sequence based oligonucleotide probes for the detection and quantification of Comamonas testosteroni in mixed microbial communities.

BACKGROUND: The beta-proteobacterial species Comamonas testosteroni is capable of biotransformation and also biodegradation of a range of chemical compounds and thus potentially useful in chemical manufacturing and bioremediation. The ability to detect and quantify members of this species in mixed microbial communities thus may be desirable. RESULTS: We have designed an oligonucleotide probe for use in fluorescent in situ hybridization (FISH) and two pairs of PCR primers targeting a C. testosteroni subgroup. The FISH probe and one of the PCR primer pairs are suitable for quantification of C. testosteroni in mixed microbial communities using FISH followed by quantitative image analysis or real-time quantitative PCR, respectively. This has been shown by analysis of samples from an enrichment of activated sludge on testosterone resulting in an increase in abundance and finally isolation of C. testosteroni. Additionally, we have successfully used quantitative PCR to follow the C. testosteroni abundance during a laboratory scale wastewater bioaugmentation experiment. CONCLUSION: The oligonucleotides presented here provide a useful tool to study C. testosteroni population dynamics in mixed microbial communities.

Colony Count, Microbial↗
PubMed2000

Humoral immune responses in Cr2-/- mice: enhanced affinity maturation but impaired antibody persistence.

Deficiency in CD21/CD35 by disruption of the Cr2 loci leads to impaired humoral immune responses. In this study, we detail the role of CD21/CD35 on Ab responses to the hapten (4-hydroxy-3-nitrophenyl)acetyl conjugated to chicken gamma-globulin. Surprisingly, Cr2-/- mice generate significant Ab responses and germinal center (GC) reactions to low doses of this Ag in alum, although the magnitude of their responses is much reduced in comparison with those of Cr2+/- and C57BL/6 controls. Increasing Ag dose partially corrected this deficit. In situ study of the somatic genetics of GC B cells demonstrated that VDJ hypermutation does not require CD21/CD35, and Cr2-/- mice exhibited enhanced affinity maturation of serum Ab in the post-GC phase of the primary response. On the other hand, Cr2-/- mice displayed accelerated loss of serum Ab and long-lived Ab-forming cells. These observations suggest that B cell activation/survival signals mediated by CD21 and/or the retention of Ag by CD21/CD35 play important roles in the generation, quality, and maintenance of serum Ab.

Amino Acid Sequence↗
PubMed2006

Selection of anti-double-stranded DNA B cells in autoimmune MRL-lpr/lpr mice.

Abs to DNA and nucleoproteins are expressed in systemic autoimmune diseases, whereas B cells producing such Abs are edited, deleted, or inactivated in healthy individuals. Why autoimmune individuals fail to regulate is not well understood. In this study, we investigate the sources of anti-dsDNA B cells in autoimmune transgenic MRL-lpr/lpr mice. These mice are particularly susceptible to lupus because they carry a site-directed transgene, H76R that codes for an anti-DNA H chain. Over 90% of the B cells are eliminated in the bone marrow of these mice, and the few surviving B cells are associated with one of two Vkappa editors, Vkappa38c and Vkappa21D. Thus, it appears that negative selection by deletion and editing are intact in MRL-lpr/lpr mice. However, a population of splenic B cells in the H76R MRL-lpr/lpr mice produces IgG anti-nuclear Abs, and these mice have severe autoimmune organ damage. These IgG Abs are not associated with editors but instead use a unique Vkappa gene, Vkappa23. The H76R/Vkappa23 combination has a relatively high affinity for dsDNA and an anti-nuclear Ab pattern characteristic of lupus. Therefore, this Vkappa gene may confer a selective advantage to anti-DNA Abs in diseased mice.

Amino Acid Sequence↗
PubMed2004

PCR method based on the ogdH gene for the detection of Salmonella spp. from chicken meat samples.

In a previous paper, the ogdH gene that encodes 2-oxoglutarate dehydrogenase was isolated from Salmonella typhimurium. The catalytic N-terminal region in the enzyme was found to be very specific for the Salmonella species. Therefore, the aim of the present study was to detect S. typhimurium in food sources using primers designed for OGDH-1 and OGDH-2 which were based on the salmonella-specific region of the ogdH gene. A simple polymerase chain reaction (PCR) detection method was developed to detect low numbers of S. typhimurium in a chicken meat microbial consortium. Using the ogdH-specific primers under stringent amplification conditions and for gene probe analysis, fewer than 100 colony-forming units (CFUs) were detectable when pure cultures were employed. When the PCR assay was run on S. typhimurium-contaminated meat contents, only the positive meat samples containing as few as 200 CFUs reacted to the assay. The method employed for sample processing is simple and it was determined to provide a sensitive means of detecting trace amounts of S. typhimurium-specific sequences in the presence of mixed meat microbial populations. When compared with six representative intestinal gram-negative bacterial strains in foods, including Vibrio parahaemolyticus, V. vulnificus, Enterobacter cloacae, E. coli O157:H7, Pseudomonas aeruginosa, and Proteus sp., S. typhimurium had a unique and distinct PCR product (796 bp). In conclusion, the two OGDH primers were found to be rapid and sensitive detectors of Salmonella spp for the PCR method.

Animals↗
PubMed1995

Intermittent shedding of human immunodeficiency virus in semen: implications for sexual transmission.

PURPOSE: We attempt to increase our understanding of human immunodeficiency virus (HIV) shedding in semen. MATERIALS AND METHODS: We followed 16 seropositive men for up to 27 months by HIV cocultivation, with a subset evaluated using the polymerase chain reaction. RESULTS: The proportion with at least 1 HIV positive semen culture increased from 3 of 16 subjects (19%) at visit 1 to 10 (63%) by visit 5. Overall, HIV was cultured from 25 of 114 specimens (22%). Shedding was intermittent for each of the 10 men with at least 1 positive culture and seminal shedding patterns were highly variable. CONCLUSIONS: By culture and polymerase chain reaction, HIV is shed intermittently in the semen. If cultures are performed often enough most seropositive men shed HIV in the semen.

Base Sequence↗
PubMed2003

HIV-1 in genital tract and plasma of women: compartmentalization of viral sequences, coreceptor usage, and glycosylation.

Worldwide, 90% of HIV-1 infections are transmitted heterosexually. Because the genital mucosa are the sites of initial contact with HIV-1 for most exposed individuals, study of the virus from the genital tract is critical for the development of vaccines and therapeutics. Previous analyses of HIV-1 in various tissues have documented compartmentalization of viral genomes. Whether compartmentalization was associated with viral phenotypic differences or immune status, however, was not well understood. We compared HIV-1 gp120 env sequences from the genital tract and plasma of 12 women. Eight women displayed compartmentalized HIV-1 RNA genomes, with viral sequences from each site that were clearly discrete, yet phylogenetically related. The remaining four exhibited env sequences that were intermingled between the two sites. Women with compartmentalized HIV-1 genomes had higher CD4+ cell counts than those displaying intermingled strains (P = 0.02). Intrapatient HIV-1 recombinants comprising sequences that were characteristic of both sites were identified. We next compared viral phenotypes in each compartment. HIV-1 coreceptor usage was often compartmentalized (P 0.01). The number of N-linked glycosylation sites, associated with neutralization resistance, also differed between compartments (P < 0.01). Furthermore, disparities between the density of gp120 glycosylations in each compartment correlated with higher CD4+ counts (P = 0.03). These data demonstrate that the genital tract and plasma can harbor populations of replicating HIV-1 with different phenotypes. The association of higher CD4+ cell counts with compartmentalization of viral genomes and density of gp120 glycosylations suggests that the immune response influences the development of viral genotypes in each compartment. These findings are relevant to the prevention and control of HIV-1 infection.

Adult↗
PubMed1994

Quantitation of follicular non-Hodgkin's lymphoma cells carrying t(14;18) in a patient before and after allogeneic bone marrow transplantation.

BACKGROUND: A competitive PCR method was developed, enabling accurate quantitation of residual lymphoma cells carrying the t(14;18) in blood and bone marrow samples of follicular non-Hodgkin's lymphoma (NHL) patients during treatment. PATIENTS AND METHODS: A patient with residual lymphoma cells received an allogeneic bone marrow transplantation (BMT). Since BMT, the patient has been in continuing clinical complete remission. RESULTS: Using the competitive PCR and two-step PCR method, we were able to demonstrate a gradual decline in the number of lymphoma cells within consecutive patient blood and bone marrow samples after BMT. CONCLUSIONS: The competitive PCR is a suitable method for the detection of minimal residual disease. Further research might reveal the clinical relevance of data obtained by this method.

Adult↗
PubMed1999

Comparative phylogenetic assignment of environmental sequences of genes encoding 16S rRNA and numerically abundant culturable bacteria from an anoxic rice paddy soil.

We used both cultivation and direct recovery of bacterial 16S rRNA gene (rDNA) sequences to investigate the structure of the bacterial community in anoxic rice paddy soil. Isolation and phenotypic characterization of 19 saccharolytic and cellulolytic strains are described in the accompanying paper (K.-J. Chin, D. Hahn, U. Hengstmann, W. Liesack, and P. H. Janssen, Appl. Environ. Microbiol. 65:5042-5049, 1999). Here we describe the phylogenetic positions of these strains in relation to 57 environmental 16S rDNA clone sequences. Close matches between the two data sets were obtained for isolates from the culturable populations determined by the most-probable-number counting method to be large (3 x 10(7) to 2.5 x 10(8) cells per g [dry weight] of soil). This included matches with 16S rDNA similarity values greater than 98% within distinct lineages of the division Verrucomicrobia (strain PB90-1) and the Cytophaga-Flavobacterium-Bacteroides group (strains XB45 and PB90-2), as well as matches with similarity values greater than 95% within distinct lines of descent of clostridial cluster XIVa (strain XB90) and the family Bacillaceae (strain SB45). In addition, close matches with similarity values greater than 95% were obtained for cloned 16S rDNA sequences and bacteria (strains DR1/8 and RPec1) isolated from the same type of rice paddy soil during previous investigations. The correspondence between culture methods and direct recovery of environmental 16S rDNA suggests that the isolates obtained are representative geno- and phenotypes of predominant bacterial groups which account for 5 to 52% of the total cells in the anoxic rice paddy soil. Furthermore, our findings clearly indicate that a dual approach results in a more objective view of the structural and functional composition of a soil bacterial community than either cultivation or direct recovery of 16S rDNA sequences alone.

Anaerobiosis↗
PubMed2004

Quantitative image quality evaluation of pixel-binning in a flat-panel detector for x-ray fluoroscopy.

X-ray fluoroscopy places stringent design requirements on new flat-panel (FP) detectors, requiring both low-noise electronics and high data transfer rates. Pixel-binning, wherein data from more that one detector pixel are collected simultaneously, not only lowers the data transfer rate but also increases x-ray counts and pixel signal-to-noise ratio (SNR). In this study, we quantitatively assessed image quality of image sequences from four acquisition methods; no-binning and three types of binning; in synthetic images using a clinically relevant task of detecting an extended guidewire in a four-alternative forced-choice paradigm. Binning methods were conventional data-line (D) and gate-line (G) binning, and a novel method in which alternate frames in an image sequence used D and G binning. Two detector orientations placed the data lines either parallel or perpendicular to the guide wire. At a low exposure of 0.6 microR (1.548 x 10(-10) C/kg) per frame, irrespective of detector orientation, D binning with its reduced electronic noise was significantly (p<0.1) better than the other acquisition methods. On average, alternate binning performed better than G binning. At a higher exposure of 4.0 microR (10.32 x 10(-10) C/kg) per frame, with data lines parallel to the guidewire, detection with D binning was significantly (p<0.1) better than G binning. However, with data lines perpendicular to the guidewire, G binning was significantly (p<0.1) better than D binning because the partial area effect was reduced. Alternate binning was the best binning method when results were averaged over both orientations, and it was as good as the best binning method at either orientation. In addition, at low and high exposures, alternate binning gave a temporally fused image with a smooth guidewire, an important image quality feature not assessed in a detection experiment. While at high exposure, detection with no binning was as good, or better, than the best binning method, it might be impractical at fluoroscopy imaging rates. A computational observer model based on signal detection theory successfully fit data and was used to predict effects of similar acquisition methods. Results from this study suggest the use of exposure-dependent detector binning in fluoroscopy that switches between D binning and alternate binning at low and high exposures, respectively.

Fluoroscopy↗
PubMed2025

Beyond Blacklists: A Critical Assessment of Exclusion Set Generation Strategies and Alternative Approaches.

Short-read sequencing data can be affected by alignment artifacts in certain genomic regions. Removing reads overlapping these exclusion regions, previously known as Blacklists, help to potentially improve biological signal. Tools like the widely used Blacklist software facilitate this process, but their algorithmic details and parameter choices are not always clearly documented, affecting reproducibility and biological relevance. We examined the Blacklist software and found that pre-generated exclusion sets were difficult to reproduce due to variability in input data, aligner choice, and read length. We also identified and addressed a coding issue that led to over-annotation of high-signal regions. We further explored the use of "sponge" sequences-unassembled genomic regions such as satellite DNA, ribosomal DNA, and mitochondrial DNA-as an alternative approach. Aligning reads to a genome that includes sponge sequences reduced signal correlation in ChIP-seq data comparably to Blacklist-derived exclusion sets while preserving biological signal. Sponge-based alignment also had minimal impact on RNA-seq gene counts, suggesting broader applicability beyond chromatin profiling. These results highlight the limitations of fixed exclusion sets and suggest that sponge sequences offer a flexible, alignment-guided strategy for reducing artifacts and improving functional genomics analyses.

Journal Article↗
PubMed1998

Activity of protegrins against yeast-phase Candida albicans.

We used a two-stage radial diffusion assay to perform a structure-activity study of the antifungal effects of protegrin-1 (PG-1) on yeast-phase Candida albicans. While doing so, we computed MICs from the radial diffusion assay data by three methods and compared the respective values with results from colony count and broth microdilution assays. This allowed us to identify several technical modifications that improved the sensitivity and accuracy of radial diffusion assays. We found that both PG-1 and enantiomeric PG-1 (composed exclusively of D-amino acids) were potently fungicidal for yeast-phase C. albicans. The protegrins PG-2, -3, and -5, but not PG-4, were as effective as PG-1. At least one intramolecular disulfide bond was required to retain optimal candidacidal activity at physiological NaCl concentrations. Truncated variants of PG-1 that lacked its first four residues showed decreased candidacidal activity, although their activity against bacteria was substantially intact. Altering the beta-turn region (residues 9 to 12) of PG-1 or its variants further decreased candidacidal activity. These studies suggest that only 12 residues are needed to endow protegrin molecules with strong antibacterial activity and that at least 4 additional residues are needed to add potent antifungal properties. Thus, the 16-residue protegrin PG-2 likely represents the minimal structure needed for broad-spectrum antimicrobial activity encompassing bacteria and fungi.

Amino Acid Sequence↗
PubMed2006

Dynamic path analysis-a new approach to analyzing time-dependent covariates.

In this article we introduce a general approach to dynamic path analysis. This is an extension of classical path analysis to the situation where variables may be time-dependent and where the outcome of main interest is a stochastic process. In particular we will focus on the survival and event history analysis setting where the main outcome is a counting process. Our approach will be especially fruitful for analyzing event history data with internal time-dependent covariates, where an ordinary regression analysis may fail. The approach enables us to describe how the effect of a fixed covariate partly is working directly and partly indirectly through internal time-dependent covariates. For the sequence of times of event, we define a sequence of path analysis models. At each time of an event, ordinary linear regression is used to estimate the relation between the covariates, while the additive hazard model is used for the regression of the counting process on the covariates. The methodology is illustrated using data from a randomized trial on survival for patients with liver cirrhosis.

Aged↗
PubMed1981

Attention switching and patterns of sound locations in counting clicks.

The present study investigates the process of auditory attention switching by means of experiments in which observers counted the number of monaurally and interaurally presented clicks. Several studies have reported that the number of interaurally presented events was underestimated relative to monaurally presented ones. Ten Hoopen and Vos, however, could not replicate this phenomenon. The data from Experiment 1 demonstrate that such a discrepancy is caused by the different orders in which the monaural and interaural sequences were presented. With blocked presentation, interaural sequences were counted less well than monaural sequences, whereas there was no difference when all sequence types were randomized. An attention-switching mechanism was proposed to account for performance on interaural sequences during blocked presentation. In the random case observers presumably did not switch their attention to and fro, but "multiplexed" the channels. Experiment 2 investigated whether observers can deliberately suppress the process of attention switching when confronted with blocked interaural sequences. The results show that they cannot, which suggests that attention switching is an automatic process.

Adult↗
PubMed1996

BAL in children: a controlled study of differential cytology and cytokine expression profiles by alveolar cells in pediatric sarcoidosis.

STUDY OBJECTIVE: The development of BAL in children for both research and clinical purposes has been limited so far by the difficulty in establishing reference values. The aim of the study was (1) to define composition of BAL cellular components in control children and to evaluate the ability of these cells to express various cytokines, and (2) to study modifications of differential cytology and BAL cell cytokine responses in children with interstitial lung disorders. POPULATIONS AND METHODS: Two groups were investigated: a control group of 16 children who were concluded to be free of parenchymal lung disease after complete pulmonary investigation, and a group of 11 children with pulmonary sarcoidosis. Differential cytology was evaluated by standard techniques. BAL cell cytokine expression was studied at the level of messenger RNA (mRNA) by reverse transcription-polymerase chain reaction (RT-PCR) methods. RESULTS: In the control group, differential cell counts appeared to be similar to values reported in adult populations with normal distribution of the data and no influence of age. In this group, no transcripts for interleukin-1beta (IL-1beta), tumor necrosis factor-alpha (TNF-alpha), IL-6, and transforming (correction of tranforming) growth factor-beta (TGF-beta) could be detected. In children with sarcoidosis, different profiles of IL-1beta, TNF-alpha, IL-6, and TGF-beta expression were individualized which seemed to be related to the activity and/or severity of the disease, IL-6 and TGF-beta mRNA being observed only in the more severe forms. CONCLUSION: These data provide information on BAL cell number and function in children. Characterization of BAL cytokine expression patterns during the course of interstitial lung diseases in children may be of great interest for evaluation of disease activity and/or severity and therefore for planning of therapy.

Actins↗
PubMedDate not supplied

Time series for modelling counts from a relapsing-remitting disease: application to modelling disease activity in multiple sclerosis.

Many chronic diseases are relapsing-remitting diseases, in which subjects alternate between periods with increasing and decreasing disease activity; relapsing-remitting multiple sclerosis is an example. This paper proposes two classes of models for sequences of counts observed from a relapsing-remitting disease. In the first, the relapsing-remitting nature of the data is modelled by a Poisson time series with a periodic trend in the mean. In this approach, the mean is expressed as a function of a sinusoidal trend and past observations of the time series. An algorithm that uses GLIM is developed, and it results in maximum-likelihood estimation for the amplitude, frequency and autoregressive effects. In the second class of models, the relapsing-remitting behaviour is described by a Poisson time series in which changes in the mean follow a latent Markov chain. An EM algorithm is developed for maximum-likelihood estimation for this model. The two models are illustrated and compared with data from a study evaluating the use of serial magnetic resonance imaging as a measure of disease activity in relapsing-remitting multiple sclerosis.

Algorithms↗
PubMed2001

The cerebrocortical areas in normal brain aging and in Alzheimer's disease: noticeable differences in the lipid peroxidation level and in antioxidant defense.

The markers of oxidative stress were measured in four cerebrocortical regions of Alzheimer's disease (AD) and age-matched control brains. In controls the levels of diene conjugates (DC) and lipid peroxides (LOOH) were significantly higher in the sensory postcentral and occipital primary cortex than in the temporal inferior or frontal inferior cortex. The antioxidant capacity (AOC) was highest in the temporal, and GSH in the frontal inferior cortex. The highest activity of superoxide dismutase (SOD) and catalase (CAT) was found in the occipital primary cortex. Compared with controls, significantly higher level of DC and LOOH and attenuated AOC were evident in AD temporal inferior cortex. In AD frontal inferior cortex moderate increase in LOOH was associated with positive correlation between SOD activity and counts of senile plaques. Our data suggest that in AD cerebral cortex, the oxidative stress is expressed in the reducing sequence: temporal inferior cortex > frontal inferior cortex > sensory postcentral cortex approximately = occipital primary cortex, corresponding to the histopathological spreading of AD from the associative to primary cortical areas.

Aging↗