Parsimony accelerated maximum likelihood searches

Phylogenetic search is a key tool used in a variety of biological research endeavours. However, this search problem is known to be computationally difficult, due to the astronomically large search space, making the use of heuristic methods necessary. The performance of heuristic methods for finding Maximum Likelihood (ML) trees can be improved by using parsimony as an initial estimator for ML. The time spent in performing the parsimony search to boost performance is insignificant compared to the time spent in the ML search, leading to an overall gain in search time. These parsimony boosted ML searches lead to topologies with scores statistically similar to the unboosted searches, but in less time.

DNA reference alignment benchmarks based on tertiary structure of encoded proteins

MOTIVATION

Multiple sequence alignments (MSAs) are at the heart of bioinformatics analysis. Recently, a number of multiple protein sequence alignment benchmarks (i.e. BAliBASE, OXBench, PREFAB and SMART) have been released to evaluate new and existing MSA applications. These databases have been well received by researchers and help to quantitatively evaluate MSA programs on protein sequences. Unfortunately, analogous DNA benchmarks are not available, making evaluation of MSA programs difficult for DNA sequences.

RESULTS

This work presents the first known multiple DNA sequence alignment benchmarks that are (1) comprised of protein-coding portions of DNA (2) based on biological features such as the tertiary structure of encoded proteins. These reference DNA databases contain a total of 3545 alignments, comprising of 68 581 sequences. Two versions of the database are available: mdsa_100s and mdsa_all. The mdsa_100s version contains the alignments of the data sets that TBLASTN found 100% sequence identity for each sequence. The mdsa_all version includes all hits with an E-value score above the threshold of 0.001. A primary use of these databases is to benchmark the performance of MSA applications on DNA data sets. The first such case study is included in the Supplementary Material.

Soy protein and isoflavones influence adiposity and development of metabolic syndrome in the obese male ZDF rat

BACKGROUND/AIMS

Previously, we demonstrated that soy protein ameliorates the diabetic phenotype in several rodent models of obesity and metabolic syndrome (MS). This study was designed to further elucidate factors related to adiposity, glycemic control, and renal function in male Zucker Diabetic Fatty (ZDF/Lepr(fa)) rats.

METHODS

Animals were randomly assigned to one of four diets: control, casein (C); low isoflavone (LIS) soy protein; high isoflavone (HIS) soy protein, or casein + rosiglitazone (CR) for 11 weeks. At sacrifice, physiological, biochemical, and molecular parameters were determined.

RESULTS

Body weight and total adiposity were higher in LIS and CR diet groups despite lower food intake. Additionally, these animals exhibited differential regulation of adipose-specific proteins (PPAR-gamma and GLUT4) and enzyme activity (FAS and GPDH). HIS-fed animals had reduced total and liver adiposity. Glycemic control was prolonged in both soy-based and rosiglitazone (RGZ) groups. Renal dysfunction was significantly reduced in soy-fed and RGZ-treated rodents as demonstrated by lower levels of proteinuria and dilated tubules with proteinaceous casts.

CONCLUSION

Collectively, these data provide evidence that soy protein with low or high isoflavone content may have therapeutic significance in reducing severity of diabetes, MS, and renal disease as demonstrated in this preclinical model.

Development of enzymatic probes of oxidative and nitrosative DNA damage caused by reactive nitrogen species

Chronic inflammation is associated with a variety of human diseases, including cancer, with one possible mechanistic link involving over-production of nitric oxide (NO*) by activated macrophages. Subsequent reaction of NO* with superoxide in the presence of carbon dioxide yields nitrosoperoxycarbonate (ONOOCO2-), a strong oxidant that reacts with guanine in DNA to form a variety of oxidation and nitration products, such 2'-deoxy-8-oxoguanosine. Alternatively, the reaction of NO and O2 leads to the formation of N2O3, a nitrosating agent that causes nucleobase deamination to form 2'-deoxyxanthosine (dX) and 2'-deoxyoxanosine (dO) from dG; 2'-deoxyinosine (dI) from dA; and 2'-deoxyuridine (dU) from dC, in addition to abasic sites and dG-dG cross-links. The presence of both ONOOCO2- and N2O3 at sites of inflammation necessitates definition of the relative roles of oxidative and nitrosative DNA damage in the genetic toxicology of inflammation. To this end, we sought to develop enzymatic probes for oxidative and nitrosative DNA lesions as a means to quantify the two types of DNA damage in in vitro DNA damage assays, such as the comet assay and as a means to differentially map the lesions in genomic DNA by the technique of ligation-mediated PCR. On the basis of fragmentary reports in the literature, we first systematically assessed the recognition of dX and dI by a battery of DNA repair enzymes. Members of the alkylpurine DNA glycosylase family (E. coli AlkA, murine Aag, and human MPG) all showed repair activity with dX (k(cat)/Km 29 x 10(-6), 21 x 10(-6), and 7.8 x 10(-6) nM(-1) min(-1), respectively), though the activity was considerably lower than that of EndoV (8 x 10(-3) nM(-1) min(-1)). Based on these results and other published studies, we focused the development of enzymatic probes on two groups of enzymes, one with activity against oxidative damage (formamidopyrimidine-DNA glycosylase (Fpg); endonuclease III (EndoIII)) and the other with activity against nucleobase deamination products (uracil DNA glycosylase (Udg); AlkA). These combinations were assessed for recognition of DNA damage caused by N2O3 (generated with a NO*/O2 delivery system) or ONOOCO2- using a plasmid nicking assay and by LC-MS analysis. Collectively, the results indicate that a combination of AlkA and Udg react selectively with DNA containing only nitrosative damage, while Fpg and EndoIII react selectively with DNA containing oxidative base lesions caused by ONOOCO2-. The results suggest that these enzyme combinations can be used as probes to define the location and quantity of the oxidative and nitrosative DNA lesions produced by chemical mediators of inflammation in systems, such as the comet assay, ligation-mediated polymerase chain reaction, and other assays of DNA damage and repair.

Hepatitis A vaccination--a prison-based solution for a community-based outbreak?

In December 2001, an increase in cases of hepatitis A was observed in South Yorkshire. Cases were predominantly young males who reported injecting drug use. A community-based vaccination programme was introduced in November 2002, but new cases continued to occur. In March 2003, a vaccination campaign was implemented in the local prison for a four-week period. One thousand two hundred and thirty-six (91%) prisoners were vaccinated. Two thirds (895/1,363) of the prisoners came from the area affected by the outbreak and 52% (465/895) reported injecting drugs. The median age of injectors was 25 years. Notifications of cases of hepatitis A from South Yorkshire ceased in August 2003. Although on this occasion the prison vaccination campaign was probably implemented too late to have had a significant impact on the local outbreak, a large number of young male injectors from the local area were successfully vaccinated. This suggests that a prison-based intervention offers a potentially effective way of immunising the IDU population and interrupting a community-based outbreak.

Registered nurses' experiences with an evidence-based home care pathway for myocardial infarction clients

OBJECTIVES

To obtain home health nurses' comments on an evidence-based care pathway for post myocardial infarction.

DESIGN

A qualitative design was used.

SETTING

Culturally diverse, lower income area of a large city.

PARTICIPANTS

All home health nurses from one nursing agency who participated in a comparative study on the impact of the evidence-based care pathway.

RESULTS

The largest number of comments made by the nurses were related to the beneficial impact of the pathway on the provision of quality nursing care and on increased job satisfaction. The home health nurses reported that the pathway increased clients' knowledge of medications and diet. In addition, they commented that they were able to use the pathway effectively because of the training they received from the inpatient cardiac nurses.

CONCLUSIONS

This qualitative study demonstrates the benefits of investing in the implementation of best practice guidelines by home health nurses. However, nursing associations, such as the Canadian Community Health Nurses Initiatives Group, will need to continue to champion for additional funds to support the additional expenses incurred.

Serum alpha-fetoprotein screening for hepatoblastoma in children with Beckwith-Wiedemann syndrome or isolated hemihyperplasia

An elevated risk of hepatoblastoma for children with Beckwith-Wiedemann syndrome or isolated hemihyperplasia is well established. We describe five children with Beckwith-Wiedemann syndrome or isolated hemihyperplasia for whom serial serum alpha-fetoprotein screening, usually in combination with abdominal ultrasound, led to early detection of hepatoblastoma.

Migrating mesoderm establish a uniform distribution of laminin in the developing grasshopper embryo

The basal lamina is composed of molecules which physically interact to form a network that serves as a migrational scaffold for many cell types. In the developing peripheral nervous system of the grasshopper, neuronal growth cones are intimately associated with the basal lamina as they migrate. Laminin is a major component of the basal lamina and is a potent promoter of neurite outgrowth in vitro. However, it is unclear what the source of laminin is or how the distribution of laminin within the basal lamina is established. To address this question, grasshopper laminin subunit genes were cloned. As expected, laminin was found within the basal lamina throughout the embryo, in particular in the limb bud, where its expression is coincident with the outgrowth and guidance of the Tibial (Til) pioneer neurons. Surprisingly, the synthesis of beta and gamma chains of laminin was restricted to migratory mesodermal cells, while in other nonmigratory tissues, such as epithelium and presumptive muscle, beta and gamma chains of laminin were not detected. In spite of this, laminin immunoreactivity in the basal lamina appears uniform and is available as a substrate for axonal outgrowth.

Intrathymic kidney cells delay the onset of lupus nephritis in MRL-lpr/lpr mice

Introduction of antigens to maturing T cells in the neonatal thymus is an effective means of inducing tolerance; however, it is uncertain whether developing, pathogenic, autoreactive T cells can be selectively modulated during systemic autoimmunity. To address this issue, syngeneic cells, derived from the kidneys of pre-diseased, lupus-prone, MRL-lpr/lpr mice were administered intrathymically to either neonatal or young MRL-lpr/lpr mice. For comparison, littermates were injected with splenocytes, islet cells or saline. Kidney cells administered to neonatal mice resulted in attenuation of nephritis, despite elevated serum autoantibody levels, IgG deposits and lymphadenopathy. This effect was not observed with administration of either the renal cell preparations to older mice or islet cells to younger mice, although splenocytes provided some benefit in younger mice. The results indicate that a subset of autoreactive T cells, distinct from those that augment autoantibody production and lymphadenopathy, are necessary for the expression of severe nephritis in MRL-lpr/lpr mice, and they provide further support for a renal antigen-specific component to the phenotype,