A Blog Around The Clock

New and Exciting in PLoS this week

Friday is the day when four of our journals publish new articles. Let’s take a look at those I find most interesting (and ‘bloggable’). 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:

Interspecific Hybridization as a Tool to Understand Vocal Divergence: The Example of Crowing in Quail (Genus Coturnix):

Understanding the mechanisms that lead organisms to be separated into distinct species remains a challenge in evolutionary biology. Interspecific hybridization, which results from incomplete reproductive isolation, is a useful tool to investigate such mechanisms. In birds, interspecific hybridization is relatively frequent, despite the fact that closed species exhibit morphological and behavioural differences. Evolution of behaviour is difficult to investigate on a large timescale since it does not ‘fossilize’. Here I propose that calls of hybrid non-songbirds that develop without the influence of learning may help in understanding the gradual process that leads to vocal divergence during speciation. I recorded crows produced by the European quail (Coturnix c. coturnix), the domestic Japanese quail (Coturnix c. japonica) and their hybrids (F1, F2 and backcrosses). Most crowing patterns were intermediate to those of the parental species; some were similar to one or the other parental species, or not present in either parental species. I also observed vocal changes in hybrid crows during the breeding season and from one year to the other. This vocal variability resembles those observed during the ontogeny of the crow in quails. It is likely that similar mechanisms involved in vocal changes during ontogeny might have driven vocal divergence in the species of Palearctic quails. I suggest that hybrid crows might have resembled those produced by intermediary forms of quails during speciation.

Differential Associations of Early- and Late-Night Sleep with Functional Brain States Promoting Insight to Abstract Task Regularity:

Solving a task with insight has been associated with occipital and right-hemisphere activations. The present study tested the hypothesis if sleep-related alterations in functional activation states modulate the probability of insight into a hidden abstract regularity of a task. State-dependent functional activation was measured by beta and alpha electroencephalographic (EEG) activity and spatial synchronization. Task-dependent functional activation was assessed by slow cortical potentials (SPs). EEG parameters during the performance of the Number Reduction Task (NRT) were compared between before sleep and after sleep sessions. In two different groups, the relevant sleep occurred either in the first or in the second half of the night, dominated by slow wave sleep (SWS) or by rapid eye movement (REM) sleep. Changes in EEG parameters only occurred in the early-night group, not in the late-night group and indicated occipital and right-hemisphere functional alterations. These changes were associated with off-line consolidation of implicit task representations and with the amount of SWS but they did not predict subsequent insight. The gain of insight was, however, independently associated with changes of spectral beta and alpha measures only in those subjects from the two sleep groups who would subsequently comprehend the hidden regularity of the task. Insight-related enhancement of right frontal asymmetry after sleep did not depend on sleep stages. It is concluded that off-line restructuring of implicit information during sleep is accompanied by alterations of functional activation states after sleep. This mechanism is promoted by SWS but not by REM sleep and may contribute to attaining insight after sleep. Original neurophysiologic evidence is provided for alterations of the functional activation brain states after sleep. These alterations are associated with a decrease in controlled processing within the visual system and with an increase in the functional connectivity of the right hemisphere, and are supported by SWS in the first half of the night.

Ten Simple Rules for Organizing a Virtual Conference–Anywhere:

Unlike conventional conferences, virtual conferencing permits the involvement of a greater number of participants who would otherwise be unable to participate in events of this breadth owing to (1) limited travel fellowships, if any; (2) lack of time to travel to distant conference locations; and (3) insufficient accommodation and subsistence funds. These factors apply in general to the post-/undergraduate student community and especially to the target audiences that reside in developing countries. Minimizing the requirement to travel also means that the availability of invited speakers is greatly increased, improving the chances of attracting highly relevant and high-impact presenters.

Through the use of video conferencing software, virtual conferences are able to provide an accessible and cost-effective alternative to real time conferences while retaining the key benefits presented by an on-site conference, such as learning opportunities, sharing of ideas, and networking. The use of inexpensive “commodity off-the-shelf” (COTS) technologies permit anyone with an Internet connection, Web cam, and headset to give and/or attend a presentation. According to Andrew Sage, Cisco Systems’ vice president for marketing, virtual conferences “can live on long after the physical booths have been torn down,” while content continues to be viewed in a dedicated virtual environment by many people, even after the conclusion of the event [5].

A Primer on Metagenomics:

Metagenomics is a discipline that enables the genomic study of uncultured microorganisms. Faster, cheaper sequencing technologies and the ability to sequence uncultured microbes sampled directly from their habitats are expanding and transforming our view of the microbial world. Distilling meaningful information from the millions of new genomic sequences presents a serious challenge to bioinformaticians. In cultured microbes, the genomic data come from a single clone, making sequence assembly and annotation tractable. In metagenomics, the data come from heterogeneous microbial communities, sometimes containing more than 10,000 species, with the sequence data being noisy and partial. From sampling, to assembly, to gene calling and function prediction, bioinformatics faces new demands in interpreting voluminous, noisy, and often partial sequence data. Although metagenomics is a relative newcomer to science, the past few years have seen an explosion in computational methods applied to metagenomic-based research. It is therefore not within the scope of this article to provide an exhaustive review. Rather, we provide here a concise yet comprehensive introduction to the current computational requirements presented by metagenomics, and review the recent progress made. We also note whether there is software that implements any of the methods presented here, and briefly review its utility. Nevertheless, it would be useful if readers of this article would avail themselves of the comment section provided by this journal, and relate their own experiences. Finally, the last section of this article provides a few representative studies illustrating different facets of recent scientific discoveries made using metagenomics.

Five Questions about Viruses and MicroRNAs:

MicroRNAs (miRNAs) are ~22-nt regulatory RNAs expressed by all multicellular eukaryotes [1]. Humans encode >700 miRNAs and similar numbers are likely to exist in other mammalian species. Almost all cellular miRNAs are initially transcribed by RNA polymerase II (Pol II) as part of a long, capped, polyadenylated primary miRNA (pri-miRNA) precursor. The miRNA forms part of one arm of an RNA stem-loop that consists of an ~32-bp imperfect stem flanked by unstructured RNA sequences. This stem-loop is recognized by the nuclear RNase III enzyme Drosha, which cleaves the stem to liberate an ~60-nt pre-miRNA hairpin. The pre-miRNA is then transported to the cytoplasm where it is cleaved by a second RNase III enzyme, called Dicer, which removes the terminal loop to generate the miRNA duplex intermediate. One strand of this duplex is incorporated into the RNA-induced silencing complex (RISC), where it acts as a guide RNA to direct RISC to complementary mRNA species [1]. Depending on the level of complementarity, RISC can either cleave bound mRNAs and/or inhibit their translation. Inhibition of mRNA translation generally requires full complementarity of the mRNA to nucleotides 2 through 7 or 8 from the miRNA 5′ end–the miRNA seed region. The primary, and possibly sole, function of mammalian miRNAs is therefore to act as specific post-transcriptional inhibitors of mRNA function.

Will Widgets and Semantic Tagging Change Computational Biology?:

We argue here, through the use of several examples from our work in support of structural biology, that the answer to the question posed by the title of this Perspective is a resounding yes. The discussion that follows is aimed primarily at those of the journal’s readers who are biological resource developers and Web page developers interested in developing the richest possible Web pages. However, those of you who simply use biological resources might find this a helpful discussion in understanding what is on the horizon. Whatever your interest, please let us hear your opinion on the question posed by this Perspective through the associated comment feature.

The Shifting Demographic Landscape of Pandemic Influenza:

As Pandemic (H1N1) 2009 influenza spreads around the globe, it strikes school-age children more often than adults. Although there is some evidence of pre-existing immunity among older adults, this alone may not explain the significant gap in age-specific infection rates. Based on a retrospective analysis of pandemic strains of influenza from the last century, we show that school-age children typically experience the highest attack rates in primarily naive populations, with the burden shifting to adults during the subsequent season. Using a parsimonious network-based mathematical model which incorporates the changing distribution of contacts in the susceptible population, we demonstrate that new pandemic strains of influenza are expected to shift the epidemiological landscape in exactly this way. Our analysis provides a simple demographic explanation for the age bias observed for H1N1/09 attack rates, and suggests that this bias may shift in coming months. These results have significant implications for the allocation of public health resources for H1N1/09 and future influenza pandemics.