Urinary biomarkers to assess exposure of cats to environmental tobacco smoke.

Objective: To evaluate the use of urinary biomarkers to assess exposure of cats to environmental tobacco smoke (ETS).

Animals: 61 healthy client-owned cats (19 from households in which smoking was reported and 42 from households in which there was no smoking).

Procedures: Urine samples were obtained from each cat and assayed for total nicotine (nicotine plus nicotine glucuronide) and total cotinine (cotinine plus cotinine glucuronide) content by use of gas chromatography-mass spectrometry.

Early PLDalpha-mediated events in response to progressive drought stress in Arabidopsis: a transcriptome analysis.

Phospholipase D (PLD) has been implicated in a variety of stresses including osmotic stress and wounding. PLDalpha1-derived phosphatidic acid interacts with ABI1 phosphatase 2C and promotes abscisic acid signalling. It has also been shown to regulate proline biosynthesis negatively.

Effects of chronic ozone exposure on gene expression in Arabidopsis thaliana ecotypes and in Thellungiella halophila.

Arabidopsis thaliana (At) ecotypes Columbia-0 (Col-0), Wassilewskija (WS), Cape Verde Islands (Cvi-0) and a relative, Thellungiella halophila (Th), were exposed to 20-25% over ambient ozone [O3] in a free air concentration enrichment (FACE) experiment (http://www.soyFACE. uiuc.

Assessing the potential of bacterial DNA profiling for forensic soil comparisons.

A pilot study was undertaken to evaluate DNA profiling of the bacterial community in soil as an alternative to geological methods for forensic soil comparisons. Soil samples from three different ecosystems were compared, and the variation within and between ecologically different sites was determined by using terminal restriction fragment (TRF) analysis of 16S ribosomal DNA. Comparison of TRF profiles revealed that samples from within a specific ecosystem (e.

Recombination patterns in aphthoviruses mirror those found in other picornaviruses.

Foot-and-mouth disease virus (FMDV) is thought to evolve largely through genetic drift driven by the inherently error-prone nature of its RNA polymerase. There is, however, increasing evidence that recombination is an important mechanism in the evolution of these and other related picornoviruses. Here, we use an extensive set of recombination detection methods to identify 86 unique potential recombination events among 125 publicly available FMDV complete genome sequences.

Response diversity of Arabidopsis thaliana ecotypes in elevated [CO2] in the field.

Free Air [CO(2)] Enrichment (FACE) allows for plant growth under fully open-air conditions of elevated [CO(2)] at concentrations expected to be reached by mid-century. We used Arabidopsis thaliana ecotypes Col-0, Cvi-0, and WS to analyze changes in gene expression and metabolite profiles of plants grown in "SoyFACE" (http://www.soyface.

Worker exposure and a risk assessment of malathion and fenthion used in the control of Mediterranean fruit fly in South Australia.

In 2001, an outbreak of Mediterranean fruit fly in Adelaide was controlled by South Australian Government workers applying organophosphorus insecticides (OPs) to domestic gardens. Residents made claims of adverse effects associated with allegations that worker application practices were poor and led to contamination of homes, residents and pets. The concerns led to a Parliamentary enquiry, the suspension of OP applications for fruit fly control, and the investigation of alternative methods of combating fruit fly in metropolitan Adelaide.

Evidence of ancient papillomavirus recombination.

An open question amongst papillomavirus taxonomists is whether recombination has featured in the evolutionary history of these viruses. Since the onset of the global AIDS epidemic, the question is somewhat less academic, because immune-compromised human immunodeficiency virus patients are often co-infected with extraordinarily diverse mixtures of human papillomavirus (HPV) types. It is expected that these conditions may facilitate the emergence of HPV recombinants, some of which might have novel pathogenic properties.

Land use change effects on forest carbon cycling throughout the southern United States.

We modeled the effects of afforestation and deforestation on carbon cycling in forest floor and soil from 1900 to 2050 throughout 13 states in the southern United States. The model uses historical data on gross (two-way) transitions between forest, pasture, plowed agriculture, and urban lands along with equations describing changes in carbon over many decades for each type of land use change. Use of gross rather than net land use transition data is important because afforestation causes a gradual gain in carbon stocks for many decades, while deforestation causes a much more rapid loss in carbon stocks.

The capsid protein of beak and feather disease virus binds to the viral DNA and is responsible for transporting the replication-associated protein into the nucleus.

Circoviruses lack an autonomous DNA polymerase and are dependent on the replication machinery of the host cell for de novo DNA synthesis. Accordingly, the viral DNA needs to cross both the plasma membrane and the nuclear envelope before replication can occur. Here we report on the subcellular distribution of the beak and feather disease virus (BFDV) capsid protein (CP) and replication-associated protein (Rep) expressed via recombinant baculoviruses in an insect cell system and test the hypothesis that the CP is responsible for transporting the viral genome, as well as Rep, across the nuclear envelope.

Preferences for follow-up after treatment for lung cancer: assessing the nurse-led option.

Pressure on lung cancer clinics is increasing with the "2-week wait" initiative. This initiative is one of the key targets set out in the National Health Service (NHS) Cancer Plan for the United Kingdom, whereby all patients presenting with symptoms which may be indicative of a cancer diagnosis will be seen by a consultant within 2 weeks of initial presentation at their primary care provider. This has resulted in busy clinics, with the potential for extended clinic waiting times and unmet needs for information and psychosocial support on the part of patients and families.

XcisClique: analysis of regulatory bicliques.

Background: Modeling of cis-elements or regulatory motifs in promoter (upstream) regions of genes is a challenging computational problem. In this work, set of regulatory motifs simultaneously present in the promoters of a set of genes is modeled as a biclique in a suitably defined bipartite graph. A biologically meaningful co-occurrence of multiple cis-elements in a gene promoter is assessed by the combined analysis of genomic and gene expression data.

The statistics of identifying differentially expressed genes in Expresso and TM4: a comparison.

Background: Analysis of DNA microarray data takes as input spot intensity measurements from scanner software and returns differential expression of genes between two conditions, together with a statistical significance assessment. This process typically consists of two steps: data normalization and identification of differentially expressed genes through statistical analysis. The Expresso microarray experiment management system implements these steps with a two-stage, log-linear ANOVA mixed model technique, tailored to individual experimental designs.

Minimization of genetic distances by the consensus, ancestral, and center-of-tree (COT) sequences for HIV-1 variants within an infected individual and the design of reagents to test immune reactivity.

Eliciting maximal immune responses to highly divergent viruses is a challenge and a focus in AIDS vaccine development. Another challenge is to identify the immune correlates of protective immunity. Recent AIDS vaccine design approaches attempt to use reconstructed centralized viral sequences that minimize genetic differences to circulating viruses.

Human immunodeficiency virus type 1 env evolves toward ancestral states upon transmission to a new host.

Selecting human immunodeficiency virus (HIV) sequences for inclusion within vaccines has been a difficult problem, as circulating HIV strains evolve relentlessly and become increasingly divergent over time. We report an assessment of this divergence from three perspectives: (i) across different hosts as a function of time of infection, (ii) between donors and recipients in known transmission pairs, and (iii) within individual hosts over time in relation to the initially replicating virus and to the deduced ancestral sequence of the intrahost viral population. Surprisingly, we consistently found less divergence between viruses from different individuals sampled in primary infection than in individuals sampled at more advanced stages of illness.

Sources of variation in ancestral sequence reconstruction for HIV-1 envelope genes.

We characterized the variation in the reconstructed ancestor of 118 HIV-1 envelope gene sequences arising from the methods used for (a) estimating and (b) rooting the phylogenetic tree, and (c) reconstructing the ancestor on that tree, from (d) the sequence format, and from (e) the number of input sequences. The method of rooting the tree was responsible for most of the sequence variation both among the reconstructed ancestral sequences and between the ancestral and observed sequences. Variation in predicted 3-D structural properties of the ancestors mirrored their sequence variation.

Plasmid-specified FemABX-like immunity factor in Staphylococcus sciuri DD 4747.

A plasmid from Staphylococcus sciuri DD 4747 had three open reading frames: a replication gene, an N-acetylmuramyl-l-alanine amidase-like gene, and a gene similar to the lysostaphin endopeptidase resistance gene (epr/lif). The epr-like gene was introduced into S. aureus RN4220; the recombinant strain was more resistant to lysostaphin endopeptidase and its cell wall peptidoglycan contained more serines and fewer glycines than the parental strain with the shuttle vector alone.

H++: a server for estimating pKas and adding missing hydrogens to macromolecules.

The structure and function of macromolecules depend critically on the ionization (protonation) states of their acidic and basic groups. A number of existing practical methods predict protonation equilibrium pK constants of macromolecules based upon their atomic resolution Protein Data Bank (PDB) structures; the calculations are often performed within the framework of the continuum electrostatics model. Unfortunately, these methodologies are complex, involve multiple steps and require considerable investment of effort.

Carbon stocks and projections on public forestlands in the United States, 1952-2040.

Approximately 37% of forestlands in the conterminous United States are publicly owned; they represent a substantial area of potential carbon sequestration in US forests and in forest products. However, large areas of public forestlands traditionally have been less intensively inventoried than privately owned forests. Thus, less information is available about their role as carbon sinks.

Evidence of unique genotypes of beak and feather disease virus in southern Africa.

Psittacine beak and feather disease (PBFD), caused by Beak and feather disease virus (BFDV), is the most significant infectious disease in psittacines. PBFD is thought to have originated in Australia but is now found worldwide; in Africa, it threatens the survival of the indigenous endangered Cape parrot and the vulnerable black-cheeked lovebird. We investigated the genetic diversity of putative BFDVs from southern Africa.

Immunogen sequence: the fourth tier of AIDS vaccine design.

While worldwide efforts to develop an effective HIV-1 vaccine are underway, the virus continues to spread, particularly in developing countries where the delivery of antiviral therapies presents formidable challenges. Vaccine research has largely focused on three general aspects: vectors, adjuvants, and immunization schedules. Our group favor the use of computational methods to design potential immunogens that capture the genetic and biological features of circulating viruses.

Compartmentalization of human immunodeficiency virus type 1 between blood monocytes and CD4+ T cells during infection.

Distinct sequences of human immunodeficiency virus type 1 (HIV-1) have been found between different tissue compartments or subcompartments within a given tissue. Whether such compartmentalization of HIV-1 occurs between different cell populations is still unknown. Here we address this issue by comparing HIV-1 sequences in the second constant region through the fifth hypervariable region (C2 to V5) of the surface envelope glycoprotein (Env) between viruses in purified blood CD14(+) monocytes and CD4(+) T cells obtained longitudinally from five infected patients over a time period ranging from 117 to 3,409 days postseroconversion.

The streptococcolytic enzyme zoocin A is a penicillin-binding protein.

Zoocin A is a streptococcolytic enzyme produced by Streptococcus equi subsp. zooepidemicus 4881 that has an unknown site of action on the peptidoglycans of susceptible organisms. Analysis of a mutant strain in which the genes for zoocin A and resistance to zoocin A were inactivated revealed that this strain was more susceptible to beta-lactam antibiotics than the parental organism.

Differences in the expressed HLA class I alleles effect the differential clustering of HIV type 1-specific T cell responses in infected Chinese and caucasians.

China is a region of the world with a rapidly spreading HIV-1 epidemic. Studies providing insights into HIV-1 pathogenesis in infected Chinese are urgently needed to support the design and testing of an effective HIV-1 vaccine for this population. HIV-1-specific T cell responses were characterized in 32 HIV-1-infected individuals of Chinese origin and compared to 34 infected caucasians using 410 overlapping peptides spanning the entire HIV-1 clade B consensus sequence in an IFN-gamma ELISpot assay.

Toxicity of environmental lead and the influence of intestinal absorption in children.

Exposure to metals, particularly lead, remains a widespread issue that is associated with historical and current industrial practices. Whereas the toxic properties of metals are well described, exposure to metals per se is only one of many factors contributing to elevated blood metal concentrations and their consequent health effects in humans. The absorbed dose of metal is affected by geochemical, biochemical, and physiological parameters that influence the rate and extent of absorption.