Whole genome experimental maps of DNA G-quadruplexes in multiple species

Genomic maps of DNA G-quadruplexes (G4s) can help elucidate the roles that these secondary structures play in various organisms. Herein, we employ an improved version of a G-quadruplex sequencing method (G4-seq) to generate whole genome G4 maps for 12 species that include widely studied model organisms and also pathogens of clinical relevance. We identify G4 structures that form under physiological K+ conditions and also G4s that are stabilized by the G4-targeting small molecule pyridostatin (PDS). We discuss the various structural features of the experimentally observed G-quadruplexes (OQs), highlighting differences in their prevalence and enrichment across species. Our study describes diversity in sequence composition and genomic location for the OQs in the different species and reveals that the enrichment of OQs in gene promoters is particular to mammals such as mouse and human, among the species studied. The multi-species maps have been made publicly available as a resource to the research community. The maps can serve as blueprints for biological experiments in those model organisms, where G4 structures may play a role.

Prevalence of small-scale jets from the networks of the solar transition region and chromosphere

As the interface between the Sun's photosphere and corona, the chromosphere and transition region play a key role in the formation and acceleration of the solar wind. Observations from the Interface Region Imaging Spectrograph reveal the prevalence of intermittent small-scale jets with speeds of 80 to 250 kilometers per second from the narrow bright network lanes of this interface region. These jets have lifetimes of 20 to 80 seconds and widths of ≤300 kilometers. They originate from small-scale bright regions, often preceded by footpoint brightenings and accompanied by transverse waves with amplitudes of ~20 kilometers per second. Many jets reach temperatures of at least ~10(5) kelvin and constitute an important element of the transition region structures. They are likely an intermittent but persistent source of mass and energy for the solar wind.

Energy release in the solar corona from spatially resolved magnetic braids

It is now apparent that there are at least two heating mechanisms in the Sun's outer atmosphere, or corona. Wave heating may be the prevalent mechanism in quiet solar periods and may contribute to heating the corona to 1,500,000 K (refs 1-3). The active corona needs additional heating to reach 2,000,000-4,000,000 K; this heat has been theoretically proposed to come from the reconnection and unravelling of magnetic 'braids'. Evidence favouring that process has been inferred, but has not been generally accepted because observations are sparse and, in general, the braided magnetic strands that are thought to have an angular width of about 0.2 arc seconds have not been resolved. Fine-scale braiding has been seen in the chromosphere but not, until now, in the corona. Here we report observations, at a resolution of 0.2 arc seconds, of magnetic braids in a coronal active region that are reconnecting, relaxing and dissipating sufficient energy to heat the structures to about 4,000,000 K. Although our 5-minute observations cannot unambiguously identify the field reconnection and subsequent relaxation as the dominant heating mechanism throughout active regions, the energy available from the observed field relaxation in our example is ample for the observed heating.

Challenges in biodegradation of trace organic contaminants--gasoline oxygenates and sex hormones

Advances in analytical methods have led to the identification of several classes of organic chemicals that are associated with adverse environmental effects. Two such classes of organic chemicals, gasoline oxygenates and sex hormones, are used to illustrate challenges associated with the biodegradation of trace organic contaminants. Gasoline oxygenates can be present in groundwater, alone, or commingled with xylene, at appreciable concentrations. However, target-treated water standards dictate that gasoline oxygenates be reduced to the microgram-per-liter concentration range before consumption. Sex hormones, on the other hand, are present in wastewater matrixes in the part-per-trillion concentration range, and the biggest challenge that must be met, before optimizing their removal, is facilitating their detection.

A novel cell-based scintillation proximity assay for studying protein function and activity in vitro using membrane-soluble scintillants

Here we describe for the first time a cell-based scintillation proximity assay using membrane soluble scintillants (MSS). MSS have a scintillant "head" group (2,5-diphenyloxazole) attached to a lipophilic "tail." MSS do not scintillate in an aqueous environment in the presence of a radioactive source: however, in a non-aqueous environment, such as a lipid bilayer (e.g., liposome or cell membrane), scintillation does occur. MSS can be incorporated into liposomes. When these MSS-containing liposomes are fused with the plasma membranes of cells in culture the MSS are incorporated into the cell membrane. Radiolabelled molecules in close proximity to the cell membrane will then elicit a scintillation signal. This system has been used to successfully monitor [(14)C]methionine uptake in HeLa cells and may be used in radiochemical and radioligand binding assays either in vivo or on microsomal preparations obtained from tissues. This new scintillation proximity technology could be readily adapted for high-throughput screening.

Interaction of dystrophin fragments with model membranes

The interaction with membrane lipids of recombinant fragments of human dystrophin, corresponding to a single structural repeating unit of the rod domain, was examined. Surface plasmon resonance, constant-pressure isotherms in a Langmuir surface film balance, and interfacial rheology were used to observe binding of the polypeptides and its effects on the properties of the lipid film. Modification of the monolayer properties was found to depend on the presence of phosphatidylserine in the lipid mixture and on the native tertiary fold of the polypeptide; thus a fragment with the minimum chain length required for folding (117 residues) or longer caused a contraction of the surface area at constant pressure, whereas fragments of 116 residues or less had no effect. The full extent of contraction was reached at a surface concentration of lipid corresponding to an average area of about 42 A2 per lipid molecule. A dystrophin fragment with the native, folded conformation induced a large increase in surface shear viscosity of the lipid film, whereas an unfolded fragment had no effect. Within a wide range of applied shear, the shear viscosity remained Newtonian. Binding of liposomes to immobilized dystrophin fragments could be observed by surface plasmon resonance and was again related to the conformational state of the polypeptide and the presence of phosphatidylserine in the liposomes. Our results render it likely that intact dystrophin interacts directly and strongly with the sarcolemmal lipid bilayer and grossly modifies its material properties.

Cloning of a disintegrin metalloproteinase that processes precursor tumour-necrosis factor-alpha

Tumour-necrosis factor-alpha (TNF-alpha) is a cytokine that contributes to a variety of inflammatory disease states. The protein exists as a membrane-bound precursor of relative molecular mass 26K which can be processed by a TNF-alpha-converting enzyme (TACE), to generate secreted 17K mature TNF-alpha. We have purified TACE and cloned its complementary DNA. TACE is a membrane-bound disintegrin metalloproteinase. Structural comparisons with other disintegrin-containing enzymes indicate that TACE is unique, with noteable sequence identity to MADM, an enzyme implicated in myelin degradation, and to KUZ, a Drosophila homologue of MADM important for neuronal development. The expression of recombinant TACE (rTACE) results in the production of functional enzyme that correctly processes precursor TNF-alpha to the mature form. The rTACE provides a readily available source of enzyme to help in the search for new anti-inflammatory agents that target the final processing stage of TNF-alpha production.

Non-ICU care of hemodynamically stable mechanically ventilated patients

OBJECTIVE

To analyze a 4 1/2-year experience caring for hemodynamically stable mechanically ventilated patients on a nonmonitored respiratory care floor (RCF) for therapeutic outcome, utilization, and costs.

DESIGN

A retrospective medical records review.

SETTING

ICUs and an RCF of a university-affiliated tertiary care center.

PARTICIPANTS

Two hundred twenty-four patients requiring more than 24 h of mechanical ventilation cared for on the RCF.

RESULTS

The mean age of patients was 67 +/- 17 years. Of the admissions, 58% were from the medical ICU, 28% were from surgical ICUs, and 9.4% were from general medical floors. Patients spent 50 +/- 66 days mechanically ventilated on the RCF. Overall survival was 50.4% with 93.8% of surviving patients successfully weaned from mechanical ventilation. Survival by diagnostic group demonstrated highest probability of survival in patients with trauma and lowest in patients with multisystem failure. Of the survivors, 39% were discharged home, 34% to a rehabilitation unit, and 24% to a skilled nursing facility. Savings based on differential of costs between the ICU and RCF, primarily from reduced staffing requirements, were estimated at $4.1 million.

CONCLUSION

Use of a nonmonitored RCF for the care of hemodynamically stable mechanically ventilated patients yields acceptable therapeutic outcomes while providing the institution with increased flexibility in critical care bed management and significant financial savings.

Relationship of drinking water disinfectants to plasma cholesterol and thyroid hormone levels in experimental studies

The effects of drinking water containing 2 or 15 ppm chlorine (pH 6.5 and 8.5), chlorine dioxide, and monochloramine on thyroid function and plasma cholesterol were studied because previous investigators have reported cardiovascular abnormalities in experimental animals exposed to chlorinated water. Plasma thyroxine (T4) levels, as compared to controls, were significantly decreased in pigeons fed a normal or high-cholesterol diet and drinking water containing these drinking water disinfectants at a concentration of 15 ppm (the exception was chlorine at pH 6.5) for 3 months. In most of the treatment groups, T4 levels were significantly lower following the exposure to drinking water containing the 2 ppm dose. Increases in plasma cholesterol were frequently observed in the groups with lower T4 levels. This association was most evident in pigeons fed the high-cholesterol diet and exposed to these disinfectants at a dose of 15 ppm. For example, after 3 months of exposure to deionized water or water containing 15 ppm monochloramine, plasma cholesterol was 1266 +/- 172 and 2049 +/- 212 mg/dl, respectively, a difference of 783 mg/dl. The factor(s) associated with the effect of these disinfectants on plasma T4 and cholesterol is not known. We suggest however that these effects are probably mediated by products formed when these disinfectants react with organic matter in the upper gastrointestinal tract.