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Detection of GPI-anchored protein-deficient cells in patients with aplastic anaemia and evidence for clonal expansion during the clinical course.

The incidence of patients with aplastic anaemia (AA) who show a deficiency of glycosylphosphatidylinositol (GPI)-anchored proteins on their peripheral blood (PB) or bone marrow (BM) cells is higher than that previously reported. We analysed the expression of CD55 or CD59 on PB and BM cells and those of colonies and bursts formed in cultures with marrow cells from AA patients. 4/21 (19%) AA cases later developed paroxysmal nocturnal haemoglobinuria (PNH). 7/17 (41. 2%) AA cases showed a subpopulation without GPI-anchored proteins. The defect characteristic for PNH was observed only on the colonies/bursts but not on the PB or BM cells in three cases. We found the affected colonies/bursts in cultures using thawed marrow cells which had been cryopreserved at the diagnosis of aplasia in one patient who developed PNH 3 years later. Two different mutations of the PIG-A gene were found in the colonies/bursts at the time of AA. The nucleotide sequences were identical between the colonies/bursts at the time of AA and those after the transition to PNH. However, one of the mutations was detected only at the haemopoietic progenitor level but not in PB granulocytes. There may be latent subclones with PNH abnormalities which could expand to the level of clinical detection, or which do not progress and remain indolent for a relatively long time, implying the different extents of clonal expansion among the affected progenitors.

Adolescent↗

Drug resistance mutations in HIV-1-infected subjects during protease inhibitor-containing highly active antiretroviral therapy with nelfinavir or indinavir.

OBJECTIVES: The aim of this retrospective study was to evaluate treatment outcome and characterize the pattern of genotype mutations in subjects with treatment failure on highly active antiretroviral therapy (HAART) containing nelfinavir or indinavir. STUDY DESIGN AND METHODS: The database of the Swiss HIV Cohort Study was screened for all subjects naive to protease inhibitor (PI) treatment who started HAART with nelfinavir or indinavir, responded initially (HIV-RNA <400 copies/ml) and received >24 weeks of treatment. Responders with subsequent treatment failure (HIV-RNA >1000 copies/ml, bordered by HIV-RNA >400 copies/ml) were selected for genotypic analysis. RESULTS: Initial treatment response, maintenance of response and subsequent virological failure were observed at a comparable frequency in 1143 nelfinavir and 1555 indinavir subjects. Of the treatment-naive patients, 13% who took nelfinavir and 16% who took indinavir had HIV-RNA >1000 copies/ml at least once. These values increased to 24 and 27%, respectively, for reverse transcriptase inhibitor-experienced subjects. Genotypic analysis in a subset of subjects with virological failure identified 30N as the only primary mutation in the nelfinavir subjects (8 out of 21, 38%) whereas isolated or combined 82A/T and 461/L mutations were detected in the indinavir subjects (9 out of 20, 45%). CONCLUSIONS: In this population of previously PI-naive subjects, the rate of virological failure and the frequency of resistance mutations at the time of virological failure were comparable in subjects receiving nelfinavir- or indinavir-containing HAART. In nelfinavir subjects, 30N was the only primary mutation whereas isolated or combined 82A/T and 461/L mutations were detected in indinavir subjects.

Acquired Immunodeficiency Syndrome↗

[The detection and study of the dynamics of the count of nonculturable forms of Yersinia pseudotuberculosis in the environment by using the polymerase chain reaction].

On the basis of the polymerase chain reaction (PCR) a test system permitting the detection of Y.pseudotuberculosis in different environmental objects was developed. On a model approximating natural conditions the dynamics of the amount of these bacteria in sterile soil extract were studied. The comparison of the amount of Y.pseudotuberculosis, determined in terms of colony forming units and by the detection of their DNA marker fragment with the use of PCR, showed the possibility of the transition of Y.pseudotuberculosis cells into the noncultivated state during their persistence in the aqueous soil extract.

Bacteriological Techniques↗

CD34-deficient mice have reduced eosinophil accumulation after allergen exposure and show a novel crossreactive 90-kD protein.

CD34 is expressed on the surface of hematopoietic stem/progenitor cells, stromal cells, and on the surface of high-endothelial venules (HEV). CD34 binds L-selectin, an adhesion molecule important for leukocyte rolling on venules and lymphocyte homing to peripheral lymph nodes (PLN). We generated CD34-deficient mutant animals through the use of homologous recombination. Wild-type and mutant animals showed no differences in lymphocyte binding to PLN HEV, in leukocyte rolling on venules or homing to PLN, in neutrophil extravasation into peritoneum in response to inflammatory stimulus, nor in delayed type hypersensitivity. Anti-L-selectin monoclonal antibody (MEL-14) also inhibited these immune responses similarly in both CD34-deficient and wild-type mice. However, eosinophil accumulation in the lung after inhalation of a model allergen, ovalbumin, is several-fold lower in mutant mice. We found no abnormalities in hematopoiesis in adult mice and interactions between mutant progenitor cells and a stromal cell line in vitro were normal. No differences existed in the recovery of progenitor cells after 5-fluorouracil treatment, nor in the mobilization of progenitor cells after granulocyte colony-stimulating factor treatment compared with wild-type animals. Surprisingly, although CD34 was not expressed in these mice, a portion of its 90-kD band crossreactive with MECA79 remained after Western blot. Thus, we have identified an additional molecule(s) that might be involved in leukocyte trafficking. These results indicate that CD34 plays an important role in eosinophil trafficking into the lung.

Allergens↗

Rapid measurement of regional cerebral blood flow in the baboon using 15O-labelled water and dynamic positron emission tomography.

The sensitivity and reproducibility of rapid measurements of regional cerebral flow (rCBF) using a bolus injection of H2 15O and dynamic positron emission tomography (PET) were investigated in anaesthetised baboons. The cerebrovascular reactivity to changes in arterial pCO2 was used as an experimental support. PET data were acquired over 4 min following a single bolus intravenous injection of H2 15O, while arterial blood was withdrawn for continuous activity counting. Images were reconstructed with a dynamic sequence of 45 x 2s + 15 x 10s, including a correction for decay. Regional values of CBF were derived from non-linear least-squares fits of the time activity curves using a four-parameter two-compartment model. The results obtained with a four-parameter fitting method were compared with those obtained with two other rapid estimation methods, first fitting two parameters only, CBF and partition coefficient (p), and secondly autoradiography (with p fixed at 0.95 ml brain ml blood-1). Twelve regions of interest were analysed. The values for the basal CBF obtained from 13 measurements in two baboons were close to published values obtained with other techniques. Reproducibility checks showed a mean variation of 9.7 per cent. The CBF measurements performed in hypercapnic conditions gave results similar to published data in other animal species, showing a 4.5 +/- 0.9 per cent increase in CBF per mm Hg paCO2. The results obtained with the three estimation techniques were closely correlated. The dynamic bolus H2 15O method appeared to be suitable for high blood flow measurements.

Animals↗

Protective role of phosphorylation in turnover of glial fibrillary acidic protein in mice.

Glial fibrillary acidic protein (GFAP), the principal intermediate filament (IF) protein of mature astrocytes in the CNS, plays specific roles in astrocyte functions. GFAP has multiple phosphorylation sites at its N-terminal head domain. To examine the role of phosphorylation at these sites, we generated a series of substitution mutant mice in which phosphorylation sites (Ser/Thr) were replaced by Ala, in different combinations. Gfap(hm3/hm3) mice carrying substitutions at all five phosphorylation sites showed extensive decrease in both filament formation and amounts of GFAP. Gfap(hm1/hm1) and Gfap(hm2/hm2) mice, which carry substitutions at three of five sites and in different combinations, showed differential phenotypes. Although Gfap(hm3/hm3) mice retained GFAP filaments in Bergmann glia in the cerebellum, the (Gfap(hm3/hm3):Vim(-/-)) mice lacked GFAP filaments. Pulse-chase experiments of cultured astrocytes indicated that the Hm3-GFAP encoded by Gfap(hm3) was unstable particularly in the absence of vimentin, another IF protein. These results revealed the role of phosphorylation in turnover of GFAP and a synergistic role of GFAP and vimentin in the dynamics of glial filaments. The data further suggest that each of the phosphorylated sites has a distinct impact on the dynamics of GFAP.

Animals↗

Divergence of HIV-1 quasispecies in an epidemiologic cluster.

BACKGROUND: During treatment with blood components prepared from an HIV-infected donation, two recipients became infected in 1985. One recipient infected her sexual partner. OBJECTIVE: To evaluate the evolution of the originally-shared HIV-1 quasispecies in different human hosts over time, sequence data were obtained from serum from the actual donation sample of blood, and from plasma samples collected from the four members of the epidemiologic cluster over a period extending from 1986 to 1993. METHODS: The V3 hypervariable region of env and the gag p17 gene were analysed. CD4 and CD8 counts, as well as HIV RNA burden data, were collected. RESULTS: One patient died from AIDS during the study. This patient showed a greater degree of diversity in the V3 region, with a higher positive charge over time, than the other individuals. Phylogenetic analysis revealed that the V3 sequences from each of the four individuals occupied separate branches of a phylogenetic reconstruction (tree). Two distinct subgroups evolved in the donor, one with GPGR and the other with GSGR/GSGK at the tip of the V3 loop. This latter group was not detected in the other individuals. The sequences in the sexual partner were no more related to those in the infecting transfusion recipient than to sequences from the other members of the cluster, consistent with sexual transmission having occurred at a time shortly after the recipient was infected. CONCLUSION: The shared HIV-1 quasispecies in this epidemiologic cluster diverged in an individual-specific manner.

Amino Acid Sequence↗

Combining sequence and time series expression data to learn transcriptional modules.

Our goal is to cluster genes into transcriptional modules--sets of genes where similarity in expression is explained by common regulatory mechanisms at the transcriptional level. We want to learn modules from both time series gene expression data and genome-wide motif data that are now readily available for organisms such as S. cereviseae as a result of prior computational studies or experimental results. We present a generative probabilistic model for combining regulatory sequence and time series expression data to cluster genes into coherent transcriptional modules. Starting with a set of motifs representing known or putative regulatory elements (transcription factor binding sites) and the counts of occurrences of these motifs in each gene's promoter region, together with a time series expression profile for each gene, the learning algorithm uses expectation maximization to learn module assignments based on both types of data. We also present a technique based on the Jensen-Shannon entropy contributions of motifs in the learned model for associating the most significant motifs to each module. Thus, the algorithm gives a global approach for associating sets of regulatory elements to "modules" of genes with similar time series expression profiles. The model for expression data exploits our prior belief of smooth dependence on time by using statistical splines and is suitable for typical time course data sets with relatively few experiments. Moreover, the model is sufficiently interpretable that we can understand how both sequence data and expression data contribute to the cluster assignments, and how to interpolate between the two data sources. We present experimental results on the yeast cell cycle to validate our method and find that our combined expression and motif clustering algorithm discovers modules with both coherent expression and similar motif patterns, including binding motifs associated to known cell cycle transcription factors.

Algorithms↗

Capillary zone electrophoresis of biological substances with fused silica capillaries having zero or constant electroosmotic flow.

A series of capillary surface modifications entailing multilayered coatings were introduced and evaluated in capillary zone electrophoresis of biological substances, e.g., proteins, peptides, oligosaccharides and nucleotides. In one set of surface modifications, large molecular weight hydroxypropyl cellulose afforded "zero" flow capillaries, which were used as precursors for developing anodal flow capillaries. When "zero" flow capillaries were further functionalized with a charge polyethyleneimine layer to which a top polyether layer was covalently attached, the resulting anodal electroosmotic flow was relatively weak due to the high viscosity of the coated wall imparted by the hydroxypropyl cellulose layer. Capillaries with relatively strong and constant anodal electroosmotic flow were best achieved when the inner capillary surface was first chemically derivatized with methylated (i.e., quaternarized) polyethyleneimine hydroxyethylated. This hydroxylated and permanently charged polymeric coating yielded constant anodal flow regardless of electrolyte pH. The hydroxyl groups of the charged polymeric coating permitted the covalent attachment of polyether chains, which minimized electrostatic interaction between the positive charges of the polymeric layer and oppositely charged biopolymers. Under these conditions, rapid transport of acidic biopolymers past the detection point in the separation capillary could be achieved, and relatively high plate counts were obtained.

Amino Acid Sequence↗

The stability of tropomyosin, a two-stranded coiled-coil protein, is primarily a function of the hydrophobicity of residues at the helix-helix interface.

The sequences of coiled coils are characterized by a repeating heptad of amino acids, abcdefg, in which the a and d residues are generally hydrophobic and form the interface between the two alpha-helices. In this study, rat and chicken alpha-tropomyosins (alpha-TMs) have been used as models to determine whether the effects of mutations on the stability of two-stranded coiled coils can be predicted by a simple algorithm. The thermal stabilities of three wild-type muscle alpha-TMs and nine chimeras, in which the second and/or sixth or ninth coding exons of one alpha-TM cDNA were replaced with exons from other alpha-TM cDNAs, with a sequence encoding the GCN4 leucine zipper or a random coil sequence, have been obtained using circular dichroism spectroscopy. Tropomyosin is almost completely helical along its entire length, but there is no correlation of the thermal stability of the alpha-TMs with the helical propensity of their component amino acids. The stability can be predicted (P = 0.90), however, by assigning a weight to every amino acid residue in each sequence, depending on its frequency of occurrence at the abcdef or g position in a data base of coiled-coil fibrous proteins, and summing all the weights. The correlation improves if only the residues at the a and d interface are counted (P = 0.94). The major factor modulating the thermal stability appears to be the hydrophobicity of the residues at the coiled-coil interface, since there is a high correlation (P = 0.91) of the TM values with the sum of the hydrophobic moments of the residues found at the a and d positions.

Algorithms↗

Fundamental and distinct roles of P-selectin and LFA-1 in ischemia/reperfusion-induced leukocyte-endothelium interactions in the mouse colon.

OBJECTIVE: To study the adhesive mechanisms underlying ischemia/reperfusion (I/R)-induced leukocyte-endothelium interactions in the colon. SUMMARY BACKGROUND DATA: Leukocyte recruitment is a key feature in I/R-induced tissue injury, but the mechanisms regulating leukocyte rolling and adhesion in the colon are not known. The authors recently developed a new model to study the molecular mechanisms of I/R-provoked leukocyte-endothelium interactions in the colon microcirculation using inverted intravital fluorescence microscopy. METHODS: The superior mesenteric artery was occluded for 30 minutes and leukocyte responses were analyzed after 120 minutes of reperfusion in colonic venules in mice. The adhesive mechanisms underlying I/R-induced leukocyte rolling and adhesion were investigated using monoclonal antibodies against L-, E- and P-selectin, and CD11a gene-targeted mice were used to examine the role of lymphocyte function antigen-1 (LFA-1, CD11a/CD18). RESULTS: Reperfusion provoked a clear-cut increase in leukocyte rolling and adhesion in colonic venules compared to negative controls. Both P- and E-selectin mRNA were expressed in the colon after this I/R insult. Pretreatment with an anti-P-selectin antibody reduced leukocyte rolling and adhesion by 88% and 85%, respectively, whereas antibodies against L- and E-selectin had no effect. Moreover, I/R-induced leukocyte adhesion in LFA-1-deficient mice was reduced by more than 95%. CONCLUSIONS: This study provides evidence that leukocyte rolling is exclusively and nonredundantly mediated by P-selectin and that firm adhesion is supported by LFA-1 in I/R-induced leukocyte recruitment in the colon. Taken together, both P-selectin and LFA-1 may be important targets to control pathologic inflammation in I/R-induced tissue injury in the colon.

Analysis of Variance↗

Genomic structure of an attenuated quasi species of HIV-1 from a blood transfusion donor and recipients.

A blood donor infected with human immunodeficiency virus-type 1 (HIV-1) and a cohort of six blood or blood product recipients infected from this donor remain free of HIV-1-related disease with stable and normal CD4 lymphocyte counts 10 to 14 years after infection. HIV-1 sequences from either virus isolates or patient peripheral blood mononuclear cells had similar deletions in the nef gene and in the region of overlap of nef and the U3 region of the long terminal repeat (LTR). Full-length sequencing of one isolate genome and amplification of selected HIV-1 genome regions from other cohort members revealed no other abnormalities of obvious functional significance. These data show that survival after HIV infection can be determined by the HIV genome and support the importance of nef or the U3 region of the LTR in determining the pathogenicity of HIV-1.

Adult↗

Development of a LightCycler PCR assay for detection and quantification of Aspergillus fumigatus DNA in clinical samples from neutropenic patients.

The increasing incidence of invasive aspergillosis, a life-threatening infection in immunocompromised patients, emphasizes the need to improve the diagnostic tools for this disease. We established a LightCycler-based real-time PCR assay to detect and quantify rapidly, specifically, and sensitively Aspergillus fumigatus DNA in both bronchoalveolar lavage (BAL) and blood samples from high-risk patients. The primers and hybridization probes were derived from an A. fumigatus-specific sequence of the mitochondrial cytochrome b gene. The assay is linear in the range between 13.2 fg and 1.3 ng of A. fumigatus DNA, corresponding to 3 to 300,000 CFU per ml of BAL fluid or blood. No cross-amplification was observed with human DNA or with the DNA of fungal or bacterial pathogens. For clinical evaluation we investigated 10 BAL samples from nine neutropenic patients with malignant hematological diseases and 12 blood samples from seven neutropenic patients with malignant hematological diseases. Additionally, we tested one blood sample and one BAL sample from each of two neutropenic patients. In order to characterize the validity of the novel PCR assay, only samples that had shown positive results by a previously described sensitive and specific nested PCR assay were tested. Twelve of 12 BAL samples and 6 of 14 blood samples gave positive results by the LightCycler PCR assay. Eight of 14 blood samples gave negative results by the novel method. The LightCycler PCR-mediated quantification of the fungal burden showed 15 to 269,018 CFU per ml of BAL sample and 298 to 104,114 CFU per ml of blood sample. Twenty of 20 BAL samples and 50 of 50 blood samples from subjects without evidence of invasive pulmonary aspergillosis (IPA) were PCR negative. Compared to a previously described nested PCR assay, these preliminary data for the novel real-time PCR assay indicate a less sensitive rate of detection of IPA in high-risk patients, but the assay may be valuable for quantification of the fungal burden in individual clinical samples.

Aspergillosis↗

Hepatitis C virus (HCV) diversity in HIV-HCV-coinfected subjects initiating highly active antiretroviral therapy.

Because of increased mortality and reduced treatment response rates in subjects coinfected with human immunodeficiency virus (HIV) and hepatitis C virus (HCV), understanding the selection pressures underlying the evolution of HCV is important for the development of strategies to control both viruses. We therefore investigated diversity of HCV in 11 HIV-HCV-coinfected subjects initiating highly active antiretroviral therapy (HAART). Distinct categories of HCV virologic response to suppression of HIV were identified. The diversity of quasi species at several genomic regions was characterized over the course of a 48-week period. Consensus data suggested a shift in the virus population at all loci except the 5' untranslated region (UTR) after initiation of HAART. Intrasubject genetic distance and entropy were highest in hypervariable region (HVR)-1. In contrast, variation in the 5' UTR was limited. Positive immune selection pressure directed against HVR-1, but not other protein-coding regions, was also detected. These data suggest that there are several mechanisms by which suppression of HIV replication and a reconstituted immune system influence diversity of HCV in HIV-HCV-coinfected subjects.

Adult↗

Increases in alpha oscillatory power reflect an active retinotopic mechanism for distracter suppression during sustained visuospatial attention.

Human electrophysiological (EEG) studies have demonstrated the involvement of alpha band (8- to 14-Hz) oscillations in the anticipatory biasing of attention. In the context of visual spatial attention within bilateral stimulus arrays, alpha has exhibited greater amplitude over parietooccipital cortex contralateral to the hemifield required to be ignored, relative to that measured when the same hemifield is to be attended. Whether this differential effect arises solely from alpha desynchronization (decreases) over the "attending" hemisphere, from synchronization (increases) over the "ignoring" hemisphere, or both, has not been fully resolved. This is because of the confounding effect of externally evoked desynchronization that occurs involuntarily in response to visual cues. Here, bilateral flickering stimuli were presented simultaneously and continuously over entire trial blocks, such that externally evoked alpha desynchronization is equated in precue baseline and postcue intervals. Equivalent random letter sequences were superimposed on the left and right flicker stimuli. Subjects were required to count the presentations of the target letter "X" at the cued hemifield over an 8-s period and ignore the sequence in the opposite hemifield. The data showed significant increases in alpha power over the ignoring hemisphere relative to the precue baseline, observable for both cue directions. A strong attentional bias necessitated by the subjective difficulty in gating the distracting letter sequence is reflected in a large effect size of 2.1 (eta2 = 0.82), measured from the attention x hemisphere interaction. This strongly suggests that alpha synchronization reflects an active attentional suppression mechanism, rather than a passive one reflecting "idling" circuits.

Adult↗

Toward a census of bacteria in soil.

For more than a century, microbiologists have sought to determine the species richness of bacteria in soil, but the extreme complexity and unknown structure of soil microbial communities have obscured the answer. We developed a statistical model that makes the problem of estimating richness statistically accessible by evaluating the characteristics of samples drawn from simulated communities with parametric community distributions. We identified simulated communities with rank-abundance distributions that followed a truncated lognormal distribution whose samples resembled the structure of 16S rRNA gene sequence collections made using Alaskan and Minnesotan soils. The simulated communities constructed based on the distribution of 16S rRNA gene sequences sampled from the Alaskan and Minnesotan soils had a richness of 5,000 and 2,000 operational taxonomic units (OTUs), respectively, where an OTU represents a collection of sequences not more than 3% distant from each other. To sample each of these OTUs in the Alaskan 16S rRNA gene library at least twice, 480,000 sequences would be required; however, to estimate the richness of the simulated communities using nonparametric richness estimators would require only 18,000 sequences. Quantifying the richness of complex environments such as soil is an important step in building an ecological framework. We have shown that generating sufficient sequence data to do so requires less sequencing effort than completely sequencing a bacterial genome.

Alaska↗

Analysis of the fluctuating microbial counts in commercial raw milk--a case study.

Microbial counts of raw milk from eight commercial dairy farms recorded over a period of about 2 years were obtained from a processing plant. All the counts formed irregular fluctuating series whose statistical properties were examined. In all eight cases the autocorrelation function indicated that the counts were random and had no underlying periodicity. This suggested that the fluctuations, at least to some extent, reflected the combined effect of numerous factors, some unknown, and that these factors operate randomly and independently. In five out of the eight cases the fluctuating pattern of the record could be described by a probabilistic model based on the assumption that the counts have a lognormal distribution. The validity of the model was confirmed by comparing the calculated frequencies of counts exceeding preselected levels with those actually observed in fresh data. The model enabled ranking the five sources on the basis of anticipated frequencies of excessive counts rather than on the basis of mean performance. Two sequences had clearly identified regions with different statistical characteristics. They were interpreted as a reflection of changes in the sanitary conditions at the corresponding farms. In one case, both the overall magnitudes and the fluctuation amplitude of the counts progressively decreased, a situation for which the described model as formulated was inapplicable.

Animals↗

Diagnosing influenza: the value of clinical clues and laboratory tests.

OBJECTIVE: Our goal was to determine the utility of clinical clues, white blood cell (WBC) and differential counts, and a rapid antigen test for differentiating influenza from coexistent infectious diseases during influenza epidemics. STUDY DESIGN: Data were collected during 3 consecutive influenza outbreaks over a 2-year period. The information collected included date of onset, symptoms, vaccine status, WBC and differential counts, ZstatFlu test (ZymeTx, Oklahoma City, Ok), and influenza culture. Using culture positivity as the criterion for influenza diagnosis, we compared cases with noncases on each variable independently and by logistic regression. Receiver operating characteristic curves were plotted for WBC count, ZstatFlu, and their combination in an effort to determine the most useful diagnostic strategy. POPULATION: We included consecutive patients presenting to a family practice office with fever, cough, sore throat, myalgia, and/or headache during flu season. OUTCOMES MEASURED: The outcomes were sensitivity, specificity, and other measures of test accuracy. RESULTS: Culture-positive cases could not be reliably distinguished from those that were culture negative using symptoms or vaccination status. Both WBC count and ZstatFlu results discriminated fairly well, and their combination did somewhat better. Differential counts were not helpful. WBC counts above 8000 were associated with a low probability of influenza. The sensitivity and specificity of the ZstatFlu were 65% and 83%, respectively. CONCLUSIONS: Our data suggest that symptoms and vaccine status do not reliably identify patients with influenza. Use of WBC counts and the ZstatFlu test can be helpful. The sequence, combination, and criteria for use of these tests depend on tradeoffs between undertreatment of influenza cases and the overtreatment of noninfluenza cases, and the cost and benefit projections for individual patients.

Adult↗