Persistence of Staphylococcus aureus as detected by polymerase chain reaction in the synovial fluid of a patient with septic arthritis

Septic arthritis commonly occurs in the rheumatoid arthritis population. The diagnosis is frequently delayed and the associated mortality is high. In this brief report, we present a patient with rheumatoid arthritis and prosthetic knee joints who developed septic arthritis and had persisting evidence of Staphylococcus aureus DNA in synovial fluid, from his knees, which was detected by polymerase chain reaction (PCR) and a gene probe. This was detected until 10 weeks of therapy despite adequate antibiotic treatment and a sterile synovial fluid. In the future, it may be found that PCR of the synovial fluid will be a valuable investigation for the diagnosis and management of septic arthritis.      

Famotidine for healing and maintenance in nonsteroidal anti- inflammatory drug-associated gastroduodenal ulceration

BACKGROUND & AIMS: Nonsteroidal anti-inflammatory drugs (NSAIDs) are strongly associated with gastroduodenal ulceration. How to manage patients with NSAID-associated ulcers is a common clinical dilemma. High-dose famotidine in the healing and maintenance of NSAID-associated gastroduodenal ulceration was therefore evaluated. METHODS: One hundred four patients with rheumatoid or osteoarthritis who had gastroduodenal ulceration received famotidine, 40 mg twice daily. Sixteen patients stopped and 88 continued their NSAID treatment. Ulcer healing was assessed endoscopically at 4 and 12 weeks. Seventy-eight NSAID users with healed ulcers were then randomized to receive 40 mg twice daily famotidine or placebo and underwent endoscopy at 4, 12, and 24 weeks. RESULTS: Cumulative ulcer healing rates at 12 weeks were 89.0% (95% confidence interval [CI], 82.3%-95.7%) for patients who continued NSAID treatment and 100% (95% CI, 82.9%-100.0%) for those who stopped. The subsequent estimated cumulative gastroduodenal ulcer relapse over 6 months for NSAID users who took placebo was 53.5% (95% CI, 36.6%- 70.3%). This was reduced to 26.0% (12.1%-39.9%) in patients taking famotidine (P = 0.011). CONCLUSIONS: High-dose famotidine is effective ulcer healing therapy in patients who stop or continue NSAID treatment and significantly reduced the cumulative incidence of gastroduodenal ulcer recurrence compared with placebo when given as maintenance therapy. (Gastroenterology 1997 Jun;112(6):1817-22)     

From a structural average to the conformational ensemble of a DNA bulge

Direct experimental measurements of conformational ensembles are critical for understanding macromolecular function, but traditional biophysical methods do not directly report the solution ensemble of a macromolecule. Small-angle X-ray scattering interferometry has the potential to overcome this limitation by providing the instantaneous distance distribution between pairs of gold-nanocrystal probes conjugated to a macromolecule in solution. Our X-ray interferometry experiments reveal an increasing bend angle of DNA duplexes with bulges of one, three, and five adenosine residues, consistent with previous FRET measurements, and further reveal an increasingly broad conformational ensemble with increasing bulge length. The distance distributions for the AAA bulge duplex (3A-DNA) with six different Au-Au pairs provide strong evidence against a simple elastic model in which fluctuations occur about a single conformational state. Instead, the measured distance distributions suggest a 3A-DNA ensemble with multiple conformational states predominantly across a region of conformational space with bend angles between 24 and 85 degrees and characteristic bend directions and helical twists and displacements. Additional X-ray interferometry experiments revealed perturbations to the ensemble from changes in ionic conditions and the bulge sequence, effects that can be understood in terms of electrostatic and stacking contributions to the ensemble and that demonstrate the sensitivity of X-ray interferometry. Combining X-ray interferometry ensemble data with molecular dynamics simulations gave atomic-level models of representative conformational states and of the molecular interactions that may shape the ensemble, and fluorescence measurements with 2-aminopurine-substituted 3A-DNA provided initial tests of these atomistic models. More generally, X-ray interferometry will provide powerful benchmarks for testing and developing computational methods.A grand challenge in biology is to understand the complex free-energy landscape of macromolecules and to decipher the resulting conformational ensembles. To perform their biological functions, macromolecules must adopt a multiplicity of conformations. Balancing and controlling different conformational states is central to biological processes including protein folding, allostery and signaling, and the stepwise assembly and function of macromolecular machines. To understand these complex molecules requires characterization of their free-energy landscapes—i.e., their equilibrium conformational ensembles. Precise measurements of conformational ensembles could allow quantitative modeling of the folding and function of biological macromolecules, would provide valuable experimental data to test current computational models and assumptions, and might facilitate the rational design of specifically acting inhibitors (1, 2).Techniques including NMR and EPR relaxation have been developed to incisively probe motions in the ensemble on different time scales, ranging from picoseconds to milliseconds (3, 4). Nonetheless, such dynamic information represents an average of the dynamics of the molecules across the conformational ensemble. In special cases, where the ensemble contains slow exchanging conformational states, these states can be separately detected [e.g., relaxation dispersion approaches can detect conformational states interconverting at tens of microseconds to hundreds of milliseconds, and single-molecule FRET (smFRET) can characterize conformational transitions at millisecond or slower time scales (5, 6)]. However, again, each of these states is an average of a more complex local conformational ensemble.To date, successes in reconstructing equilibrium ensembles have mostly relied on experimental measurement of NMR residual dipolar couplings (RDCs) (7, 8). Compared with other NMR techniques, RDCs provide long-range angular structure information that helps to generate equilibrium ensemble models (9). In combination with molecular dynamic simulations, RDCs have been used to generate ensemble models for small disordered proteins (7, 10), DNA duplexes (11), and a RNA bulge motif (12–14). In addition to RDCs, relaxation dispersion and paramagnetic relaxation enhancement have been used to detect and characterize conformational states that are in low abundance in an ensemble (5). Although powerful, these NMR-based methods, like all approaches, have limitations. For example, RDCs have difficulty distinguishing between conformations with similar angular orientations but different translational displacements (15, 16). Additional methods are needed to construct ensembles that can test and complement these current methods.To meet this challenge, we continue to develop, test, and apply the capabilities of a solution X-ray interferometry technique (17, 18). X-ray interferometry can be used to determine site-to-site distance distributions instantaneously because it relies on atomic scattering (17, 19–24). Standard small-angle X-ray scattering (SAXS) measures the sum of the scattering and scattering interference from all atoms in a macromolecule (25). As it would not be possible to decompose this sum and distinguish contributions from specific atoms or atom pairs, standard SAXS provides no site-specific information and is limited to determining the overall size and shape of macromolecules (25). X-ray interferometry overcomes this limitation through the introduction of a pair of site-specifically labeled gold nanocrystal probes and isolation of the scattering interference from this strongly scattering probe pair. This scattering interference can be directly converted into a distance distribution through a Fourier transformation, without the complications of a nonlinear mapping (26). Multiple pairs of gold nanocrystal probes, in different site-specific locations, provide matched-set distance information and increase the information content of the technique (e.g., refs. 17 and 18).Unlike standard ensemble-averaged methods such as FRET that give a single average value for the distance between each probe pair, X-ray interferometry naturally yields a distance distribution between each probe pair. Strategies measuring the time dependence of fluorescence energy transfer (27) or spin echo intensity [double electron–electron resonance (DEER)] (28) are powerful but are limited in their ability to determine an ensemble by the complex relationships between the measured values and the desired probe–probe distances. These complications amplify the uncertainty of determining an average value and introduce even greater uncertainty in determining a distance distribution and the underlying conformational ensemble.Prior results using the DNA double helix as a model experimental system (18) indicate that detailed and quantitative information about solution ensembles can be obtained. For the DNA helix, X-ray interferometry distance distributions were found to quantitatively agree with consensus elastic parameters of DNA (18). Nevertheless, the ensemble of a DNA double helix is simpler than that for most macromolecules and could be well described by broadening from a single conformation using an elastic potential. The ensembles of most biological macromolecules are likely to contain substantial anharmonicities and multiple local free-energy minima.To further test X-ray interferometry as a general method for probing macromolecule equilibrium ensembles and to determine fundamental properties of basic nucleic acid structures, we have applied X-ray interferometry to a nucleic acid helix–junction–helix (HJH) motif, the DNA bulge. DNA bulges can provide a model for the RNA bulges that are more commonly encoded in biology and can be used to engineer nanostructures (29, 30). We chose the A-bulge DNA system for this study to allow comparison with a prior smFRET study that provided models for the average structures of these DNAs (31).     

Developing a broader scientific foundation for river restoration: Columbia River food webs

Well-functioning food webs are fundamental for sustaining rivers as ecosystems and maintaining associated aquatic and terrestrial communities. The current emphasis on restoring habitat structure—without explicitly considering food webs—has been less successful than hoped in terms of enhancing the status of targeted species and often overlooks important constraints on ecologically effective restoration. We identify three priority food web-related issues that potentially impede successful river restoration: uncertainty about habitat carrying capacity, proliferation of chemicals and contaminants, and emergence of hybrid food webs containing a mixture of native and invasive species. Additionally, there is the need to place these food web considerations in a broad temporal and spatial framework by understanding the consequences of altered nutrient, organic matter (energy), water, and thermal sources and flows, reconnecting critical habitats and their food webs, and restoring for changing environments. As an illustration, we discuss how the Columbia River Basin, site of one of the largest aquatic/riparian restoration programs in the United States, would benefit from implementing a food web perspective. A food web perspective for the Columbia River would complement ongoing approaches and enhance the ability to meet the vision and legal obligations of the US Endangered Species Act, the Northwest Power Act (Fish and Wildlife Program), and federal treaties with Northwest Indian Tribes while meeting fundamental needs for improved river management.Recent years have seen substantial expenditures and sustained efforts by government agencies, indigenous people, and nongovernmental organizations to restore rivers and their declining fish stocks. These activities are under increased scrutiny to show that goals and objectives are being met (1, 2). In general, past river restoration has focused on recreating structural attributes (e.g., channel width, complexity) based on the assumption that associated ecological functions will follow (3–6). However, contemporary evidence suggests that ecosystem structure alone does not necessarily reflect how it functions in supporting life. For example, field experiments in the US Pacific Northwest have shown that trophic manipulations (e.g., nutrient additions or salmon carcass introductions) that boost the abundance of potential prey organisms also boost subsequent fish growth (7–10). In contrast, restoration of physical habitats by creating pools or adding structures yields ambiguous evidence that such efforts increase subsequent fish abundance and biomass (11–17). Although it may be premature to conclude from these studies that food availability and species interactions are more limiting to fish than the quality or quantity of the physical habitat, evidence is mounting that many habitat restoration activities are not always as effective in meeting stated goals and objectives as originally anticipated.Nationwide, river restoration practices tend to target the effects of dams, flow manipulation, and channel structure. More than $1 billion/y has been spent since 1990 on river restoration in the United States, with limited evidence of success (1). It has been argued that successful restoration should focus on restoring processes that support ecosystem services and monitoring how processes respond within an adaptive management framework (3, 18, 19). We suggest here that a balance between physical habitat restoration and an understanding of trophic processes supporting biotic communities would improve restoration effectiveness.     

Duplication of small segments within the major breakpoint cluster region in chronic myelogenous leukemia

The t(9;22) in chronic myelogenous leukemia (CML) may be reciprocal or, in a minority of cases, may result in an extensive deletion of a portion of the major breakpoint cluster region (M-bcr) of the BCR. This report provides evidence of the duplication of small segments within the M-bcr in a small group of patients with CML. Southern blots of Bgl II and Bgl II/BamHI double-digested DNA from the blood or bone marrow of 46 patients with CML were probed with a 5' 1.4-kb Taq I/HindIII M- bcr probe and a 3' 2-kb HindIII/BamHI M-bcr probe. In three patients, rearrangements were noted with both probes in Bgl II-digested DNA, but were not present in Bgl II/BamHI-digested DNA with either probe. Southern analysis of DNA samples double-digested with Bgl II and BspHI from two of these three cases showed no rearrangements with either probe; the M-bcr BspHI site is located 26 bp 3' of the BamHI site in the second intron of the M-bcr. The presence of a rearranged M-bcr with both probes in Bgl II-digested DNA and the lack of rearrangement in Bgl II/BamHI and Bgl II/BspHI double-digested DNA suggest the presence of M- bcr BamHI and BspHI sites on both 9q+ chromosome (9q+) and the Philadelphia chromosome (Ph). This implies a duplication of at least the 26-bp M-bcr BamHI/BspHI fragment in these two samples. Sequence data from one of these two cases confirmed the M-bcr breakpoints to be staggered; the Ph M-bcr breakpoint occurred 258 bp downstream from the 9q+ M-bcr breakpoint. It is concluded that a duplication of small segments within the M-bcr occurs in a small group of patients with CML, which may lead to pseudogermline patterns on Southern blot. Such a duplication may provide insight into the mechanism of some chromosomal translocations in neoplasia.     

Normalization of markers of coagulation activation with a purified protein C concentrate in adults with homozygous protein C deficiency

Homozygous or double heterozygous protein-C deficiency can present at birth with purpura fulminans or later in life with venous thrombosis. Two homozygous patients who had previously sustained thrombotic episodes were investigated at a time when they were asymptomatic and not receiving antithrombotic therapy. The plasma levels of protein-C antigen and activity in both individuals were approximately 20% of normal. We administered a highly purified plasma-derived protein C concentrate to these individuals and monitored levels of several markers of in vivo coagulation activation. Assays for protein-C activation (activated protein C and protein C activation peptide) showed a sustained increase from reduced baseline levels, whereas thrombin generation (as measured by prothrombin fragment F1 + 2) gradually decreased over about 24 hours into the normal range. These investigations provide direct evidence that protein C is converted to activated protein C in vivo, and that the protein-C anticoagulant pathway is a tonically active mechanism in the regulation of hemostatic system activation in humans.     

Antithrombin III deficiency: decreased synthesis of a biochemically normal molecule

A 29-yr-old white female has suffered from recurrent venous thromboses over the last 12 yr. Plasma antithrombin III (AT-III) levels were 48% of normal by immunoelectrophoresis and 56% by chromogenic assay. Three of four siblings and the father had similar AT-III levels without associated venous thromboses. Heparin-Sepharose chromatography demonstrated normal behavior of the patient's AT-III. Her purified AT- III could not be distinguished from AT-III purified from a normal control either by SDS polyacrylamide gel electrophoresis or by crossed immunoelectrophoresis, and the heparin cofactor activity and the progressive antithrombin activity of both AT-III samples were identical. Turnover studies were made in the patient using her own purified AT-III labeled with 131I, (*I). The results did not differ significantly from studies made with autologous *I-AT-III in two normal control women. Her fractional breakdown rate of 0.54 total plasma AT- III per day compared with 0.45 and 0.52 in the controls. These studies indicate that the patient synthesizes a normal AT-III molecule at half normal rates.     

High prevalence of a mutation in the factor V gene within the U.K. population: relationship to activated protein C resistance and familial thrombosis

Summary. Recent findings have indicated the importance of factor V (FV) in causing resistance to activated protein C (APC) in a high proportion of patients with venous thrombosis. This prompted us to investigate whether resistance could be due to defective inactivation of FVa by APC. Consequently, we amplified a 3.2 kb fragment of the FV gene sequence encoding the heavy chain APC cleavage site. DNA analysis showed a guanine to adenine transition at nucleotide 1691 in all affected members of two families with inherited APC resistance associated with thrombosis and confirmed suspected homozygosity in two individuals. The mutation, in heterozygous form, was also found in ˜3.5% of our normal population (n = 144) and correlated with low APC resistance. The high prevalence of this mutation suggests that it may be a major contributory factor in early thrombosis.     

In vitro megakaryocytopoietic and thrombopoietic activity of c-mpl ligand (TPO) on purified murine hematopoietic stem cells

Recently, the ligand for c-mpl has been identified and cloned. Initial studies of this molecule indicate that it is the platelet regulatory factor, thrombopoietin (TPO). Previous work has indicated that c-mpl is expressed in very immature hematopoietic precursors and thus raised the possibility that TPO may act directly on the hematopoietic stem cell. Therefore, in these studies, we investigate the effects of TPO on hematopoietic stem cell populations isolated from the murine fetal liver and bone marrow. Cocultivation of stem cells with fetal liver stroma give rise to multilineage expansion of the stem cells but with little or no megakaryocytopoiesis. Addition of TPO to these cocultures gives significant megakaryocyte production. This production is enhanced in combination with Kit ligand or interleukin-3. The addition of TPO to stem cell suspension cultures produces a dynamic thrombopoietic system in which stem cells undergo differentiation to produce megakaryocytes and proplatelets. These experiments show that the megakaryocytopoietic and thrombopoietic activities of TPO are initiated at the level of an early progenitor cell or upon the hematopoietic stem cell.