Still getting used to the new publication schedule. Yup, new papers just got published in four out of seven PLoS journals. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week - you go and look for your own favourites:
Environmental Change Enhances Cognitive Abilities in Fish:
Animals with higher cognitive abilities should be better capable of producing new, modified, or innovative behaviors as this ability could allow them to cope better with unpredictable environmental changes. Changing environments may hence select for higher cognitive abilities. Similarly, changing conditions during ontogeny can cause plastic responses, helping individuals to adapt to their current environment. In this study, we have used the cichlid fish Simochromis pleurospilus to show experimentally that individuals subjected to a change in food ration early in life (i.e., low to high or vice versa) outperform fish kept on constant rations in a learning task later in life. Remarkably, this result was independent of the direction of the implemented change or the average amount of food each fish received, and the results in the juvenile stage did not change in adulthood. Our results suggest that a single environmental change early in life might enhance cognitive abilities in animals.
A Study of the Influence of Sex on Genome Wide Methylation:
Sex differences in methylation status have been observed in specific gene-disease studies and healthy methylation variation studies, but little work has been done to study the impact of sex on methylation at the genome wide locus-to-locus level or to determine methods for accounting for sex in genomic association studies. In this study we investigate the genomic sex effect on saliva DNA methylation of 197 subjects (54 females) using 20,493 CpG sites. Three methods, two-sample T-test, principle component analysis and independent component analysis, all successfully identify sex influences. The results show that sex not only influences the methylation of genes in the X chromosome but also in autosomes. 580 autosomal sites show strong differences between males and females. They are found to be highly involved in eight functional groups, including DNA transcription, RNA splicing, membrane, etc. Equally important is that we identify some methylation sites associated with not only sex, but also other phenotypes (age, smoking and drinking level, and cancer). Verification was done through an independent blood cell DNA methylation data (1298 CpG sites from a cancer panel array). The same genomic site-specific influence pattern and potential confounding effects with cancer were observed. The overlapping rate of identified sex affected genes between saliva and blood cell is 81% for X chromosome, and 8% for autosomes. Therefore, correction for sex is necessary. We propose a simple correction method based on independent component analysis, which is a data driven method and accommodates sample differences. Comparison before and after the correction suggests that the method is able to effectively remove the potentially confounding effects of sex, and leave other phenotypes untouched. As such, our method is able to disentangle the sex influence on a genome wide level, and paves the way to achieve more accurate association analyses in genome wide methylation studies.
As the novel pandemic influenza A (H1N1) (pH1N1) virus spread around the world in late spring 2009 with a well-matched pandemic vaccine not immediately available, the question of partial protection afforded by seasonal influenza vaccine arose. Coverage of the seasonal influenza vaccine had reached 30%-40% in the general population in 2008-09 in the US and Canada, following recent expansion of vaccine recommendations.
Serology studies demonstrated a lack of cross-reactive antibody to the novel virus in vaccinated and unvaccinated people under 60 years of age, suggesting that there would be no protection against pandemic influenza from natural immunity or seasonal vaccination [1]. By contrast, about one third of seniors over 60 y had cross-reactive antibodies [1], perhaps due to childhood exposure to antigenically similar A/H1N1 viruses. As a result, the mean age of pandemic cases and deaths was younger than that of interpandemic seasons [2], a signature age shift also experienced in three historical influenza pandemics [3].
A Synthetic Uric Acid Analog Accelerates Cutaneous Wound Healing in Mice:
Wound healing is a complex process involving intrinsic dermal and epidermal cells, and infiltrating macrophages and leukocytes. Excessive oxidative stress and associated inflammatory processes can impair wound healing, and antioxidants have been reported to improve wound healing in animal models and human subjects. Uric acid (UA) is an efficient free radical scavenger, but has a very low solubility and poor tissue penetrability. We recently developed novel UA analogs with increased solubility and excellent free radical-scavenging properties and demonstrated their ability to protect neural cells against oxidative damage. Here we show that the uric acid analog (6, 8 dithio-UA, but not equimolar concentrations of UA or 1, 7 dimethyl-UA) modified the behaviors of cultured vascular endothelial cells, keratinocytes and fibroblasts in ways consistent with enhancement of the wound healing functions of all three cell types. We further show that 6, 8 dithio-UA significantly accelerates the wound healing process when applied topically (once daily) to full-thickness wounds in mice. Levels of Cu/Zn superoxide dismutase were increased in wound tissue from mice treated with 6, 8 dithio-UA compared to vehicle-treated mice, suggesting that the UA analog enhances endogenous cellular antioxidant defenses. These results support an adverse role for oxidative stress in wound healing and tissue repair, and provide a rationale for the development of UA analogs in the treatment of wounds and for modulation of angiogenesis in other pathological conditions.
The MAHB, the Culture Gap, and Some Really Inconvenient Truths by Paul R. Ehrlich:
The human predicament--climate disruption, loss of biodiversity and ecosystem services, toxification of the planet, the potential impacts of nuclear war, and social and economic inequities that impede solutions to escalating environmental problems--has been amply described [1]. Although the steps needed to solve the predicament are clear, few have been taken--even as the situation steadily declines. The trend in greenhouse gas emissions has continued rapidly upward. The extermination of biodiversity and loss of natural services has proceeded unabated. The number of hungry people has hit an all-time high, which means that so has the number of immune-compromised individuals. That, combined with continued rapid population growth, increases the probabilities of vast epidemics [2]. In Asia, melting of the Himalayan water tower [3] and rising temperatures threaten the food supply of 1.6 billion people [4] whose countries are armed with nuclear weapons [5]. There also have been increasing signs of great toxic peril for humanity and its life-support systems, with a growing threat from the release of hormone-disrupting chemicals that could even be shifting the human sex ratio [6] and reducing sperm counts.
Recently, metagenomic studies have identified viable Pepper mild mottle virus (PMMoV), a plant virus, in the stool of healthy subjects. However, its source and role as pathogen have not been determined. 21 commercialized food products containing peppers, 357 stool samples from 304 adults and 208 stool samples from 137 children were tested for PMMoV using real-time PCR, sequencing, and electron microscopy. Anti-PMMoV IgM antibody testing was concurrently performed. A case-control study tested the association of biological and clinical symptoms with the presence of PMMoV in the stool. Twelve (57%) food products were positive for PMMoV RNA sequencing. Stool samples from twenty-two (7.2%) adults and one child (0.7%) were positive for PMMoV by real-time PCR. Positive cases were significantly more likely to have been sampled in Dermatology Units (p<10â6), to be seropositive for anti-PMMoV IgM antibodies (p = 0.026) and to be patients who exhibited fever, abdominal pains, and pruritus (p = 0.045, 0.038 and 0.046, respectively). Our study identified a local source of PMMoV and linked the presence of PMMoV RNA in stool with a specific immune response and clinical symptoms. Although clinical symptoms may be imputable to another cofactor, including spicy food, our data suggest the possibility of a direct or indirect pathogenic role of plant viruses in humans.
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