Just in case you missed them, there were other papers published in seven PLoS Journals this week besides Ida 😉
Here are my own picks for the week – you go and look for your own favourites. As always, and for the first time this applies to all seven journals, 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.
Effects of Nocturnal Light on (Clock) Gene Expression in Peripheral Organs: A Role for the Autonomic Innervation of the Liver:
The biological clock, located in the hypothalamic suprachiasmatic nucleus (SCN), controls the daily rhythms in physiology and behavior. Early studies demonstrated that light exposure not only affects the phase of the SCN but also the functional activity of peripheral organs. More recently it was shown that the same light stimulus induces immediate changes in clock gene expression in the pineal and adrenal, suggesting a role of peripheral clocks in the organ-specific output. In the present study, we further investigated the immediate effect of nocturnal light exposure on clock genes and metabolism-related genes in different organs of the rat. In addition, we investigated the role of the autonomic nervous system as a possible output pathway of the SCN to modify the activity of the liver after light exposure. First, we demonstrated that light, applied at different circadian times, affects clock gene expression in a different manner, depending on the time of day and the organ. However, the changes in clock gene expression did not correlate in a consistent manner with those of the output genes (i.e., genes involved in the functional output of an organ). Then, by selectively removing the autonomic innervation to the liver, we demonstrated that light affects liver gene expression not only via the hormonal pathway but also via the autonomic input. Nocturnal light immediately affects peripheral clock gene expression but without a clear correlation with organ-specific output genes, raising the question whether the peripheral clock plays a “decisive” role in the immediate (functional) response of an organ to nocturnal light exposure. Interestingly, the autonomic innervation of the liver is essential to transmit the light information from the SCN, indicating that the autonomic nervous system is an important gateway for the SCN to cause an immediate resetting of peripheral physiology after phase-shift inducing light exposures.
The history of modern science is punctuated by moments when the fruits of science captivate the public imagination. Traces of these impressions can be found in works of art; for instance, one sees the influence of 17th century astronomy on poetry in Paradise Lost, as when Satan stops by the sun to ask for directions to the earth, Milton alludes to Galileo’s discovery of sunspots: “There lands the Fiend, a spot like which perhaps/Astronomer in the Sun’s lucent Orbe/Through his glaz’d Optic Tube yet never saw” and in the sudden emergence of the ellipse in baroque architecture . More recently, scholars have argued for the influence of relativity theory on the development of cubist painting  and of both relativity and quantum mechanics on the poetry of T.S. Eliot . (“What might have been is an abstraction/Remaining a perpetual possibility/Only in a world of speculation.”)
Numerous endemic mammals, including dwarf elephants, goats, hippos and deers, evolved in isolation in the Mediterranean islands during the Pliocene and Pleistocene. Most of them subsequently became extinct during the Holocene. Recently developed high-throughput sequencing technologies could provide a unique tool for retrieving genomic data from these extinct species, making it possible to study their evolutionary history and the genetic bases underlying their particular, sometimes unique, adaptations. A DNA extraction of a ~6,000 year-old bone sample from an extinct caprine (Myotragus balearicus) from the Balearic Islands in the Western Mediterranean, has been subjected to shotgun sequencing with the GS FLX 454 platform. Only 0.27% of the resulting sequences, identified from alignments with the cow genome and comprising 15,832 nucleotides, with an average length of 60 nucleotides, proved to be endogenous. A phylogenetic tree generated with Myotragus sequences and those from other artiodactyls displays an identical topology to that generated from mitochondrial DNA data. Despite being in an unfavourable thermal environment, which explains the low yield of endogenous sequences, our study demonstrates that it is possible to obtain genomic data from extinct species from temperate regions.
Data annotation (manual data curation) tasks are at the very heart of modern biology. Experts performing curation obviously differ in their efficiency, attitude, and precision, but directly measuring their performance is not easy. We propose an experimental design schema and associated mathematical models with which to estimate annotator-specific correctness in large multi-annotator efforts. With these, we can compute confidence in every annotation, facilitating the effective use of all annotated data, even when annotations are conflicting. Our approach retains all annotations with computed confidence values, and provides more comprehensive training data for machine learning algorithms than approaches where only perfect-agreement annotations are used. We provide results of independent testing that demonstrate that our methodology works. We believe these models can be applied to and improve upon a wide variety of annotation tasks that involve multiple annotators.
Meiosis is a sequence of two specialized cell divisions during which haploid gametes are generated. During meiotic prophase, homologous chromosomes pair and recombine to allow proper separation of chromosomes during the first meiotic division. The pairing mechanism is challenged by the presence of the largely nonhomologous sex chromosomes in spermatocytes of male mammals, since X and Y pair only in the short regions of homology. The unpaired nonhomologous regions are recognized and transcriptionally silenced, which leads to the formation of the so-called XY body. In mammalian females, which carry two homologous X chromosomes, no such structure is formed and the sex chromosomes are both active in oocytes. We asked whether meiotic silencing of sex chromosomes also occurs during gametogenesis in chickens. In this species, males carry two Z chromosomes, and females are ZW. We show that Z and W fully pair in oocytes, despite the overall lack of sequence homology. Surprisingly, the ZW pair is transcriptionally silenced during meiotic prophase and remains inactive until the two chromosomes have largely separated. Reactivation of Z at this stage may be necessary to allow expression of genes that are required for further oocyte development. These data show that meiotic sex chromosome silencing occurs also in species with female heterogamety.
The sex chromosomes are among the most rapidly evolving and most diverse genetic systems in all of biology. Students of model organisms may, however, have the false impression that there is only one chromosomal mechanism of specifying sex. Among the best-studied metazoans, the XY system is indeed the rule, with inheritance of two X’s determining the female sex (XX), and inheritance of an X and a Y specifying the male sex (XY) . In this system, females produce only one type of oocyte (X), whereas males produce two types of sperm (X and Y). However, sex is not always determined this way. Throughout evolution, the XY system has co-existed alongside the lesser known ZW system, a scheme exemplified by members of the avian clade who diverged from Mammalia 300 million years ago (Figure 1) ,. In birds, females are the heterogametic sex, as females have one Z and one W chromosome (ZW) and can therefore produce two types of gametes (Z or W oocytes). By contrast, males are ZZ and can produce only one type of gamete (homogametic)–the Z-bearing sperm. In XY and ZW systems, the homologous sex chromosomes are genetically unequal due to suppression of homologous recombination and accumulation of deleterious mutations on one chromosome of the heterogametic sex . In the XY system, it is the Y that genetically degenerates; in the ZW system, it is the W. Today, the mammalian X carries over three times more genes than the Y does, whereas the chicken Z carries over ten times more than the W.
As the Obama administration moves to enact meaningful and comprehensive health care reform in the United States, tobacco control must be elevated as a public health priority . Though tobacco control efforts have been recognized as a top public health achievement of the 20th century , tobacco use continues to be the leading preventable cause of death in the US . As Box 1 shows, the US bears a heavy burden from the health and fiscal effects of smoking. Thus, continued progress in preventing tobacco use and promoting smoking cessation must be a leading priority for health care reform under the new administration. This policy paper gives the current status of tobacco control policies, initiatives, and legislative action at the time of going to press.