A comparison of software packages that assess linkage using a variance components approach

We report single-point and multipoint results from three statistical genetics software packages using a variance components approach for quantitative traits. When possible, we have shown the effects of covariates. Results from GENEHUNTER, SOLAR, and ACT software packages are compared for the quantitative trait immunoglobulin E (IgE) using chromosome 5 asthma familial data from Oxfordshire (England), Perth (Australia), and Freiburg (Germany), and using the genome-wide German data. Although few differences among variance components results for GENEHUNTER, SOLAR, and ACT were detected on a limited region of chromosome 5, these packages showed larger disagreement in the German data for chromosomes 1, 9, and 14.

Quantitative studies on the peroxidation of human low-density lipoprotein initiated by superoxide and by charged and neutral alkylperoxyl radicals

Rates of peroxidation of human LDL and rates of consumption of the LDL's alpha-tocopherol (TocH) have been measured at 37 degrees C. Peroxidation was initiated by radicals generated in the aerated aqueous phase at known rates by thermal decomposition of appropriate precursors: superoxide (O2(*-)/HOO(*)) from a hyponitrite and alkylperoxyls (ROO(*), two positively charged, one negatively charged and one neutral) from azo compounds. The efficiencies of escape from the solvent cage of the geminate pair of neutral carbon-centered radicals was found to be 0.1, but it was 0.5 for the three charged radicals, a result attributed to radical/radical Coulombic repulsion within the cage. All four alkylperoxyls initiated and terminated tocopherol-mediated peroxidation (TMP) with about equal efficiency and essentially all of these radicals that were generated were consumed in these two reactions. TMP is a radical chain process, and when initiated by the alkylperoxyls, the rate of LDL peroxidation was faster in the early stages while TocH was present than later, after all of this "antioxidant" had been consumed. In contrast, only about 3-4% of the generated superoxide radicals reacted in any measurable fashion with TocH-containing LDL at pH's from 7.6 to 6.5 and peroxidation was much slower than with a similar rate of generation of alkylperoxyls. After all the TocH had been consumed, LDL peroxidation was negligible at pH 7.6 and 7.4, but at pH 6.8 and 6.5, the peroxidation rates showed a large increase over the rates while the TocH had been present. That is, endogenous TocH behaves as an antioxidant in LDL subjected to attack by the physiologically relevant superoxide radical, whereas TocH behaves as a prooxidant in LDL subjected to attack by the probably far less physiologically important alkylperoxyls. Rates of LDL peroxidation initiated by superoxide increased as the pH was decreased, and the results are consistent with the initiation of peroxidation of fresh LDL occurring via H-atom abstraction from TocH by HOO(*) to form the Toc(*) radical and termination by reaction of O2(*-) with Toc(*), a process that occurs partly by addition leading to TocH consumption and partly by electron plus proton transfer leading to the regeneration of TocH.

Aptiganel hydrochloride in acute ischemic stroke: a randomized controlled trial

CONTEXT

Tissue plasminogen activator is the only thrombolytic agent approved in the United States for treatment of acute ischemic stroke, and has limitations. Aptiganel hydrochloride is a novel and selective ligand for the ion-channel site of the N-methyl-D-aspartate receptor-channel complex and a promising neuroprotective agent in animal models of focal brain ischemia.

OBJECTIVE

To determine whether aptiganel improves the clinical outcome for acute ischemic stroke patients.

DESIGN

Nested phase 2/phase 3 randomized controlled trial conducted between July 1996 and September 1997.

SETTING

One hundred fifty-six medical centers in the United States, Canada, Australia, South Africa, England, and Scotland.

PARTICIPANTS

A total of 628 patients with hemispheric ischemic stroke (50.3% male; mean age, 71.5 years).

INTERVENTIONS

Patients were randomly assigned within 6 hours of stroke to receive 1 of 3 treatment regimens: high-dose aptiganel (5-mg bolus followed by 0.75 mg/h for 12 hours; n = 214); low-dose aptiganel (3-mg bolus followed by 0.5 mg/h for 12 hours; n = 200); or placebo (n = 214).

MAIN OUTCOME MEASURES

The primary efficacy end point was the Modified Rankin Scale score at 90 days after stroke onset. Secondary end points included mortality and change in National Institutes of Health (NIH) Stroke Scale score at 7 days after stroke.

RESULTS

The trial was suspended by the sponsor and the independent data and safety monitoring board because of both a lack of efficacy and a potential imbalance in mortality. There was no improvement in outcome for either aptiganel (low-dose or high-dose) group compared with the placebo group at 90 days (median Modified Rankin Scale score for all 3 treatment groups = 3; P =.31). At 7 days, placebo-treated patients exhibited slightly greater neurological improvement on the NIH Stroke Scale than high-dose aptiganel patients (mean improvement for placebo group, -0.8 points vs for high-dose aptiganel, 0.9 points; P =.04). The mortality rate at 120 days in patients treated with high-dose aptiganel was higher than that in patients who received placebo (26.3% vs 19.2%; P =.06). Mortality in the low-dose aptiganel group was 22.5% (P =.39 vs placebo).

CONCLUSIONS

Aptiganel was not efficacious in patients with acute ischemic stroke at either of the tested doses, and m ay be harmful. The larger proportion of patients with favorable outcomes and lower mortality rate in the placebo group suggest that glutamate blockade with aptiganel may have detrimental effects in an undifferentiated population of stroke patients.

Arterial strokes associated with factor V Leiden mutation

A 41-year-old Caucasian woman was admitted with right hemiparesis and blurred vision. There was no history of hypertension, diabetes, ischaemic heart disease, previous stroke, oral contraceptive use or miscarriages nor any family history of stroke. She was a non-smoker. Clinical examination confirmed the presence of right-sided weakness. There were no carotid bruits and her fundi were normal. Computed tomography scan of the brain confirmed the presence of a large infarct in the right middle cerebral artery territory (Figure 1). Full blood count, urea, creatinine, glucose and cholesterol levels were normal. Autoimmune profile, including antinuclear antibody, antineutrophil cytoplasmic antibody and anticardiolipin antibody, were negative. Other thrombophilia tests, including lupus anticoagulant, antithrombin III, plasminogen and protein S levels, were normal. Her electrocardiogram, chest X-ray, echocardiogram and a carotid Doppler study were unremarkable. A thrombophilia screen revealed markedly decreased activated protein C activity at 1.32 (normal ratio 2.25—2.63) when tested with factor V deficient plasma suggestive of factor V Leiden mutation.

Controversies in heart failure. Are beneficial effects of angiotensin-converting enzyme inhibitors attenuated by aspirin in patients with heart failure?

To whatever extent the improvement in symptoms and survival rendered by treatment with ACE inhibitors is attributable to their effects on the circulation and the kidneys, this benefit can be rescinded by concomitant administration of aspirin. Although some useful prostaglandin-independent actions may persist, shutting down the entire prostaglandin system and trading off a substantial portion of the potential risk reduction with forfeit of salutary hemodynamic and renal effects is a high price to pay just to suppress production of TXA2. In patients requiring treatment for heart failure, if possible, aspirin should be avoided and the integrity of prostaglandin metabolism respected; the severer the heart failure the more compelling. There are other ways to inhibit platelet aggregation, some equally effective or even better than aspirin. Orally active platelet glycoprotein IIb/IIIa receptor antagonists, which may be more efficient than aspirin, have been developed and are now in clinical testing. Ticlopidine and clopidogrel, although more expensive than aspirin, are as easy to use and at least as effective as aspirin. Finally, because patients with severer heart failure are likely to be those with very low ejection fractions, these patients are good candidates for oral anticoagulation even though this treatment requires additional monitoring.

Global analysis of protein activities using proteome chips

To facilitate studies of the yeast proteome, we cloned 5800 open reading frames and overexpressed and purified their corresponding proteins. The proteins were printed onto slides at high spatial density to form a yeast proteome microarray and screened for their ability to interact with proteins and phospholipids. We identified many new calmodulin- and phospholipid-interacting proteins; a common potential binding motif was identified for many of the calmodulin-binding proteins. Thus, microarrays of an entire eukaryotic proteome can be prepared and screened for diverse biochemical activities. The microarrays can also be used to screen protein-drug interactions and to detect posttranslational modifications.

Dioxygen-dependent metabolism of nitric oxide in mammalian cells

Steady-state gradients of NO within tissues and cells are controlled by rates of NO synthesis, diffusion, and decomposition. Mammalian cells and tissues actively decompose NO. Of several cell lines examined, the human colon CaCo-2 cell produces the most robust NO consumption activity. Cellular NO metabolism is mostly O2-dependent, produces near stoichiometric NO3-, and is inhibited by the heme poisons CN-, CO (K(I) approximately 3 microM), phenylhydrazine, and NO and the flavoenzyme inhibitor diphenylene iodonium. NO consumption is saturable by O2 and NO and shows apparent K(M) values for O2 and NO of 17 and 0.2 microM, respectively. Mitochondrial respiration, O2*-, and H2O2 are neither sufficient nor necessary for O2-dependent NO metabolism by cells. The existence of an efficient mammalian heme and flavin-dependent NO dioxygenase is suggested. NO dioxygenation protects the NO-sensitive aconitases, cytochrome c oxidase, and cellular respiration from inhibition, and may serve a dual function in cells by limiting NO toxicity and by spatially coupling NO and O2 gradients.

Development of drug resistance in patients receiving combinations of zidovudine, didanosine and nevirapine

OBJECTIVE

To evaluate the development of phenotypic and genotypic resistance to zidovudine, didanosine and nevirapine as a function of the virologic response to therapy in a group of drug-naive individuals receiving various combinations of these agents.

DESIGN

All patients were enrolled in a double-blind controlled randomized trial (the INCAS study) and were selected for detailed resistance studies based on specimen availability and virologic response.

METHODS

Within the three study groups (zidovudine/nevirapine, zidovudine/didanosine or zidovudine/nevirapine/didanosine), 16, 19 and 24 patients, respectively, had evaluable baseline isolates and remained in the study > 24 weeks. Phenotypic resistance to all three drugs was evaluated using the VIRCO recombinant virus assay. Genotypic sequencing was done on selected specimens from patients receiving zidovudine/nevirapine/didanosine.

RESULTS

After 24 weeks, all available isolates taken from patients receiving nevirapine were resistant to this agent, while 18/21 (86%) patients receiving triple therapy carried such isolates at 30--60 weeks. At 24 weeks, zidovudine resistance developed in 4/40 isolates but was more frequent after 30--60 weeks, especially in patients on two drugs. The degree of zidovudine resistance (rise in concentration required for 50% inhibition) appeared lower in the triple therapy group compared with zidovudine/didanosine (P = 0.0004). All nevirapine-resistant isolates that were sequenced carried at least one mutation associated with resistance, most often K103N and/or Y181C.

CONCLUSION

The use of highly active drug therapies may be associated with a beneficial effect on the development of antiretroviral drug resistance. The characteristics of virologic suppression that must be maintained to avoid resistance are currently being studied in hypothesis-driven clinical trials.

High exposure to nevirapine in plasma is associated with an improved virological response in HIV-1-infected individuals

OBJECTIVE

To explore relationships between exposure to nevirapine and the virological response in HIV-1-infected individuals participating in the INCAS trial.

METHODS

The elimination rate constant of plasma HIV-1 RNA (k) was calculated during the first 2 weeks of treatment with nevirapine, zidovudine and didanosine in 51 antiretroviral-naive HIV-1-infected patients. The relationships between the value of k, the time to reach an undetectable HIV-1 RNA concentration in plasma (< 20 copies/ml) and the success of therapy after 52 weeks of treatment as dependent variables and the exposure to nevirapine, baseline HIV-1 RNA and baseline CD4 cell count as independent variables, were explored using linear regression analyses, proportional hazard models and logistic analyses, respectively.

RESULTS

The value of k for HIV-1 RNA in plasma was positively and significantly associated with the mean plasma nevirapine concentration during the first 2 weeks of therapy (P = 0.011) and the baseline HIV-1 RNA (P = 0.008). Patients with a higher exposure to nevirapine reached undetectable levels of HIV-1 RNA in plasma more rapidly (P = 0.03). From 12 weeks on, the median nevirapine plasma concentration was significantly correlated with success of therapy after 52 weeks (P < 0.02).

CONCLUSIONS

A high exposure to nevirapine (in a twice daily regimen) is significantly associated with improved virological response in the short as well as in the long term. These findings suggest that optimization of nevirapine concentration might be used as a tool to improve virological outcome in (antiretroviral-naive) patients treated with nevirapine.

Physical mapping with automatic capture of hybridization data

MOTIVATION

Contig maps are a type of physical map that show the native order of a set of overlapping genomic clones. Overlaps between clones can be detected by finding common sequences using a number of experimental protocols including hybridization of probes. All current mapping algorithms of which we are aware require that hybridizations be scored using a fixed number of discrete values (typically 0/1 or high/medium/low). When hybridization data is captured automatically using digital equipment, this provides the opportunity for hybridization intensities to be used in map construction. More fine-grained distinctions in the levels of hybridization may be exploited by algorithms to generate more accurate physical maps.

RESULTS

We describe an approach to creating contig maps that uses measured hybridization intensities instead of data scored with a fixed number of discrete values. We describe and compare four algorithms for creating physical maps with hybridization intensities. Simulations using measured intensities sampled from actual data on Aspergillus nidulans indicate that using hybridization intensities rather than data that is automatically scored with respect to threshold values may yield more accurate physical maps.

ODS2: a multiplatform software application for creating integrated physical and genetic maps

A contig map is a physical map that shows the native order of a library of overlapping genomic clones. One common method for creating such maps involves using hybridization to detect clone overlaps. False- positive and false-negative hybridization errors, the presence of chimeric clones, and gaps in library coverage lead to ambiguity and error in the clone order. Genomes with good genetic maps, such as Neurospora crassa, provide a means for reducing ambiguities and errors when constructing contig maps if clones can be anchored with genetic markers to the genetic map. A software application called ODS2 for creating contig maps based on clone-clone hybridization data is presented. This application is also designed to exploit partial ordering information provided by anchorage of clones to a genetic map. This information, along with clone-clone hybridization data, is used by a clone ordering algorithm and is represented graphically, allowing users to interactively align physical and genetic maps. ODS2 has a graphical user interface and is implemented entirely in Java, so it runs on multiple platforms. Other features include the flexibility of storing data in a local file or relational database and the ability to create full or minimum tiling contig maps.

Hepatitis B virus X protein activates transcription by bypassing CREB phosphorylation, not by stabilizing bZIP-DNA complexes

Although previous work has shown that the hepatitis B virus X protein (pX) stabilizes complexes between basic region leucine zipper (bZIP) proteins and target DNA, the relationship between enhanced binding and transcriptional activation has not been established. Here we show that interactions between CREB and pX, which coincidentally enhance DNA affinity, are necessary but not sufficient for increased transcriptional potency. Further, we show that transcriptional activation by pX requires a form of CREB in which Ser-133 is not phosphorylated. By stimulating the transcriptional potency of unphosphorylated CREB, pX can up-regulate the expression of cAMP-responsive genes implicated in hepatocyte proliferation, leading ultimately to the development of liver cancer after viral infection.