The Highly Conserved Codon following the Slippery Sequence Supports ?1 Frameshift Efficiency at the HIV-1 Frameshift Site

HIV-1 utilises −1 programmed ribosomal frameshifting to translate structural and enzymatic domains in a defined proportion required for replication. A slippery sequence, U UUU UUA, and a stem-loop are well-defined RNA features modulating −1 frameshifting in HIV-1. The GGG glycine codon immediately following the slippery sequence (the ‘intercodon’) contributes structurally to the start of the stem-loop but has no defined role in current models of the frameshift mechanism, as slippage is inferred to occur before the intercodon has reached the ribosomal decoding site. This GGG codon is highly conserved in natural isolates of HIV. When the natural intercodon was replaced with a stop codon two different decoding molecules—eRF1 protein or a cognate suppressor tRNA—were able to access and decode the intercodon prior to −1 frameshifting. This implies significant slippage occurs when the intercodon is in the (perhaps distorted) ribosomal A site. We accommodate the influence of the intercodon in a model of frame maintenance versus frameshifting in HIV-1.     

Alternative contingency table measures improve the power and detection of multifactor dimensionality reduction

Background  

Multifactor Dimensionality Reduction (MDR) has been introduced previously as a non-parametric statistical method for detecting gene-gene interactions. MDR performs a dimensional reduction by assigning multi-locus genotypes to either high- or low-risk groups and measuring the percentage of cases and controls incorrectly labelled by this classification – the classification error. The combination of variables that produces the lowest classification error is selected as the best or most fit model. The correctly and incorrectly labelled cases and controls can be expressed as a two-way contingency table. We sought to improve the ability of MDR to detect gene-gene interactions by replacing classification error with a different measure to score model quality.     

Ovarian Carcinoma Subtypes Are Different Diseases: Implications for Biomarker Studies

Background

Although it has long been appreciated that ovarian carcinoma subtypes (serous, clear cell, endometrioid, and mucinous) are associated with different natural histories, most ovarian carcinoma biomarker studies and current treatment protocols for women with this disease are not subtype specific. With the emergence of high-throughput molecular techniques, distinct pathogenetic pathways have been identified in these subtypes. We examined variation in biomarker expression rates between subtypes, and how this influences correlations between biomarker expression and stage at diagnosis or prognosis.

Methods and Findings

In this retrospective study we assessed the protein expression of 21 candidate tissue-based biomarkers (CA125, CRABP-II, EpCam, ER, F-Spondin, HE4, IGF2, K-Cadherin, Ki-67, KISS1, Matriptase, Mesothelin, MIF, MMP7, p21, p53, PAX8, PR, SLPI, TROP2, WT1) in a population-based cohort of 500 ovarian carcinomas that was collected over the period from 1984 to 2000. The expression of 20 of the 21 biomarkers differs significantly between subtypes, but does not vary across stage within each subtype. Survival analyses show that nine of the 21 biomarkers are prognostic indicators in the entire cohort but when analyzed by subtype only three remain prognostic indicators in the high-grade serous and none in the clear cell subtype. For example, tumor proliferation, as assessed by Ki-67 staining, varies markedly between different subtypes and is an unfavourable prognostic marker in the entire cohort (risk ratio [RR] 1.7, 95% confidence interval [CI] 1.2%–2.4%) but is not of prognostic significance within any subtype. Prognostic associations can even show an inverse correlation within the entire cohort, when compared to a specific subtype. For example, WT1 is more frequently expressed in high-grade serous carcinomas, an aggressive subtype, and is an unfavourable prognostic marker within the entire cohort of ovarian carcinomas (RR 1.7, 95% CI 1.2%–2.3%), but is a favourable prognostic marker within the high-grade serous subtype (RR 0.5, 95% CI 0.3%–0.8%).

Conclusions

The association of biomarker expression with survival varies substantially between subtypes, and can easily be overlooked in whole cohort analyses. To avoid this effect, each subtype within a cohort should be analyzed discretely. Ovarian carcinoma subtypes are different diseases, and these differences should be reflected in clinical research study design and ultimately in the management of ovarian carcinoma.     

Inducing chromosome pairing through premature condensation: analysis of wheat interspecific hybrids

At the onset of meiosis, chromosomes first decondense and then condense as the process of recognition and intimate pairing occurs between homologous chromosomes. We show here that okadaic acid, a drug known to induce chromosome condensation, can be introduced into wheat interspecific hybrids prior to meiosis to induce chromosome pairing. This pairing occurs in the presence of the Ph1 locus, which usually suppresses pairing of related chromosomes and which we show here delays condensation. Thus the timing of chromosome condensation during the onset of meiosis is an important factor in controlling chromosome pairing.     

Direct and indirect mortality in Florida during the 2004 hurricane season

Previous studies have shown that natural disasters, and hurricanes in particular, have led to more deaths than those usually documented in short post-storm surveys. Such indirect deaths, thought to be related to dietary, stress or pre-existing medical conditions, can exceed the number of direct deaths and may persist for weeks or even months beyond the event itself. In the present study, cumulative sum of deviations plots are used to quantify the number of direct and indirect deaths resulting from Hurricanes Charley, Frances, Ivan and Jeanne that made landfall in Florida in 2004. Results suggest that there was an elevated mortality for up to 2 months following each storm, resulting in a total of 624 direct and indirect deaths attributable to the storm. Trauma-related deaths that can be associated directly with the storm account for only ∼4% of the total storm-related mortality, while indirect mortality accounts for most storm-related deaths. Specifically, a large percentage of the elevated mortality was associated with heart (34%) and cancer-related deaths (19%), while diabetes (5%) and accident-related deaths (9%) account for a smaller but still significant percentage of the elevated mortality. The results further suggest that the elevated mortality was the result of additional deaths that would not have otherwise occurred within that 5 month period, and not simply a clustering of deaths that were inevitable between 1 August and 31 December 2004. The elevated mortality identified in this study is significantly greater than the official count of 31 direct and 113 indirect deaths resulting from the four hurricanes combined. This suggests a need for improved mortality counts and surveillance in order to better evaluate and identify effective prevention policies, and to identify preventable deaths.     

Biological interactions among extant and fossil clonal organisms

Biological interactions among clonal marine organisms are an important aspect of their behavior and are important in the construction of biological reefs. The interactions addressed here are among crustose and erect coralline algae, sponges, corals, and bryozoans, and may involve clones of the same species (conspecific), or different species (heterospecific). Conspecific interactions may be either between modules or clones that are produced asexually from one propagule, genetically identical, or between clones that are sexually produced from two or more propagules that may or may not be genetically identical. Juxtaposed genetically identical clones generally fuse whereas non-identical clones may or may not fuse, depending on their relatedness and histocompatibility. Most heterospecific clonal interactions are spatially competitive and result in overgrowths or stand-offs. Clone fission/fragmentation may occur as a result of biotic or abiotic processes that initially degrade but may eventually restore or even enhance ability to gain space and/or nutrients. Self-overgrowths also occur, usually over dead, diseased, or senescent parts of the same clone.     

Validation of adipose lipid content as a body condition index for polar bears

Body condition is a key indicator of individual and population health. Yet, there is little consensus as to the most appropriate condition index (CI), and most of the currently used CIs have not been thoroughly validated and are logistically challenging. Adipose samples from large datasets of capture biopsied, remote biopsied, and harvested polar bears were used to validate adipose lipid content as a CI via tests of accuracy, precision, sensitivity, biopsy depth, and storage conditions and comparisons to established CIs, to measures of health and to demographic and ecological parameters. The lipid content analyses of even very small biopsy samples were highly accurate and precise, but results were influenced by tissue depth at which the sample was taken. Lipid content of capture biopsies and samples from harvested adult females was correlated with established CIs and/or conformed to expected biological variation and ecological changes. However, lipid content of remote biopsies was lower than capture biopsies and harvested samples, possibly due to lipid loss during dart retrieval. Lipid content CI is a biologically relevant, relatively inexpensive and rapidly assessed CI and can be determined routinely for individuals and populations in order to infer large‐scale spatial and long‐term temporal trends. As it is possible to collect samples during routine harvesting or remotely using biopsy darts, monitoring and assessment of body condition can be accomplished without capture and handling procedures or noninvasively, which are methods that are preferred by local communities. However, further work is needed to apply the method to remote biopsies.     

Exercise alters fractal dimension and spatial correlation of pulmonary blood flow in the horse.

We determined the changes in fractal dimensions and spatial correlations of regional pulmonary blood flow with increasing exercise in race horses (n = 4) by using 15-microm fluorescent microspheres. Fluorescence was measured to quantitate regional blood to 1.3-cm(3) samples (n = 1,621-2,503). Perfusion distributions were characterized with fractal dimensions (a measure of spatial variability) and spatial correlations. On average, the fractal dimension decreased with exercise (trot 1.216 to gallop 1.173; P < 0. 05) despite a variable fractal dimension at rest. Spatial correlation of flow to neighboring pieces increased with exercise (trot 0.57 +/- 0.074 to gallop 0.73 +/- 0.051) and was inversely correlated with fractal dimension, indicating better spatial correlation as blood flow distribution becomes more uniform. This is the first study to document a change in fractal dimension as a result of increasing pulmonary blood flow. Spatial differences in response to vasoregulatory mediators may play a role in this phenomenon.     

The effects of provisioning and crop-raiding on the diet and foraging activities of human-commensal white-faced capuchins (Cebus capucinus)

Non-human primates are coming into increasingly frequent contact with humans and with human-modified environments. The potential for monkeys to survive in such modified landscapes is questionable, and is likely related to a species' behavioral plasticity, particularly as it relates to diet. In this study, I explore the ways in which white-faced capuchins (Cebus capucinus) adjust their diet and foraging behaviors in response to anthropogenic impact. I compare a troop of human-commensal monkeys and a similar troop of wild-feeding monkeys living within the Curú Wildlife Refuge in western Costa Rica for differences in overall diet composition and activity budgets to evaluate the impact of habitat change in this context. The commensal-living white-faced capuchins rely on raided coconut (Cocos nucifera) and oil palm (Elaeis guineensis) crops and provisioned or stolen human foods for over one-half of their total diet. Regardless of this highly anthropogenic diet, the two study troops do not significantly differ in their activity budgets, and the human-commensal troop maintains wild-foraging activities consistent with those of the wild-feeding troop. These data suggest that the white-faced capuchins at this site are responding to anthropogenic disturbance primarily through the exploitation of human food resources, but they do not yet appear to have lost the foraging skills required to survive in this modified landscape on their own. This study adds to our growing body of knowledge on primate survival in matrix habitats, and will hopefully inform primate management plans throughout the Neotropics.