Editors' Choice

Science  01 Mar 2013:
Vol. 339, Issue 6123, pp. 1012
  1. Evolution

    Darwinian Genomics

    1. Laura M. Zahn
    CREDIT: PUTNEYMARK/FLICKR

    The finches of the Galapagos archipelago helped Darwin articulate the theory of evolution by natural selection as he identified differences in bird phenotypes, especially size and beak shape, across the island chain. Rands et al. provide a draft sequence of the genome of the large ground finch and compared it to other previously sequenced genomes, including its closest sequenced relative—the zebra finch. Comparative genomics was used to establish a gene set from the sequences and identified selective constraint in both of the genomes. Analyses of positive selection identified genes, including those that likely have a role in reproduction, that are under selection in both zebra finches and large ground finches. In addition, genes specific to the ground finch were identified, including those that have demonstrated effects on beak phenotypes. This study lays the groundwork for further analysis of the genomic changes that accompany speciation and adaptation.

    BMC Genomics 14, 95 (2013).

  2. Cell Biology

    HIF Puts on the Brakes

    1. L. Bryan Ray

    The ability of most cells to respond appropriately to availability or absence of oxygen is a fundamental requirement for survival. Much of the physiological response of a cell or organism to hypoxia, from angiogenesis and metabolic changes to control of cell division, is coordinated by the transcription factor hypoxia-inducible factor-1 (HIF-1). Hubbi et al. report that the HIF-1α subunit also has a nontranscriptional role in promoting arrest of the cell division cycle when cells sense hypoxia. In cells deprived of oxygen, HIF-1α accumulated and bound to the prereplication complex, a set of proteins that mark origins of DNA replication, thus rapidly blocking DNA replication and cell division. The transcriptonal transactivation domain of HIF-1α was not required for this effect. HIF-1α appears to be a balancing point for the cell's response to oxygen: Growth-promoting signals oppose the actions of HIF-1α and promote its binding to another protein at replication origins, the helicase MCM (minichromosome maintenance), which enhances degradation of HIF-1α.

    Sci. Signal. 6, ra10 (2013).

  3. Cell Biology

    It Takes Teamwork

    1. Stella M. Hurtley

    Cells contain molecular motors, including dynein and kinesin, that move a variety of cargoes along microtubules. Dyneins are often used by cells to generate large forces during, for example, nuclear migration, mitotic spindle orientation, and reorientation of the cytoskeleton during wound healing. Individual motors, however, are limited in the amount of force they can generate on their own. How are large forces generated and sustained inside cells? Rai et al. developed methods to use optical tweezers for precise, quantitative force measurement inside cells. The results show, paradoxically, that dyneins, which are weak and erratic at the single-motor level, show excellent teamwork to generate large and persistent forces inside cells. Kinesins, on the other hand, which are strong and persistent at a single-motor level, fail to generate force collectively. The forces upon moving phagosomes loaded with latex beads increased linearly with dynein number. Hendricks et al. also found that transport of phagosomes was driven by multiple dynein motors. Thus a force of certain magnitude can be generated simply by changing the number of dynein motors depending on the specific requirement in the cell.

    Cell 152, 172 (2013); Proc. Natl. Acad. Sci. U.S.A. 109, 18447 (2012).

  4. Behavior

    Too Busy to Pick Up the Phone

    1. Gilbert Chin

    One version of an adage attributed by some to Yogi Berra is that the difference between theory and practice is greater in practice than in theory. One arena where the existence of such a difference is intuitively plausible is when researchers ask questions of a sample of humans in the general population. Despite extensive prior work in many disciplines, not only on survey design but also on adjusting for the relatively high contemporary rates of nonresponse, Heffetz and Rabin have succeeded in identifying a new and intriguing source of potential bias that affects whether inferences drawn from the sample can be applied more widely. They look at the relation between the number of phone calls required to reach a respondent and the answer to a yes/no question about happiness across a handful of demographic dimensions. Splitting the respondents into above versus below median income, they find that almost 9 out of 10 of the richer people are happy versus about 4 out of 5 of the poorer folk—and that there is no difference between busier (i.e., harder to reach) and not-so-busy respondents. On the other hand, women who are easy to reach are happier than similar men, whereas the opposite is true when comparing men and women who are harder to reach. One final point is that inferences about the population would be very much affected by whether people who could not be reached at all would be assumed to be similar to the average respondent or to the busier ones.

    Am. Econ. Rev., in press (2013; http://ssrn.com/abstract=2101097).

  5. Microbiology

    Bacterial Growth at −15°C

    1. Nicholas S. Wigginton

    Life as a bacterium in the permafrost is not easy. Not only are subzero temperatures the norm, but the liquid water that is available is quite salty. Therefore, for bacteria to survive in these conditions, they need to be well adapted to cold and high-salinity environments. Isolated from Arctic permafrost, the aerobic heterotroph Planococcus halocryophilus is an example of one such species that is up to the task. Through a series of batch and microcosm growth experiments, Mykytczuk et al. show that P. halocryophilus grew—albeit at the slow generation time of 50 days—and had an active carbon metabolism at −15°C. Genomic analyses suggest that this organism has a diverse set of traits to help it survive in addition to those related to cold and osmotic adaptation, including several modifications to the cell envelope and increased tolerance to oxidative stress. Indeed, transcriptomic profiles from cells grown at a range of temperatures and salinities down to −15°C and 18% NaCl show specific parallel responses to mitigate cold and salty conditions. Because a large portion of the world's soil is in permafrost regions, increased activity of these microbial communities may result from warmer temperatures or greater temperature fluctuations.

    CREDIT: N. C. S. MYKYTCZUK ET AL., THE ISME JOURNAL (7 FEBRUARY 2013) © NATURE PUBLISHING GROUP

    ISME J. 10.1038/ismej.2013.8 (2013).

  6. Biochemistry

    Mimicking a Membrane

    1. Valda Vinson

    A challenge in membrane structure determination is selecting membrane-mimicking media that facilitate proper protein folding and function. Detergent micelles are commonly used for structural studies; however, these are often not optimal for protein stability and function. Phospholipid nanodiscs are a promising membrane mimetic; however, the large molecular weight of nanodiscs has hampered their use in structural determination by multidimensional nuclear magnetic resonance (NMR) spectroscopy. Nanodiscs are formed by two copies of a membrane scaffold protein wrapping around a patch of phospholipid bilayer. Hagn et al. engineered a set of shorter variants of the scaffold protein ApoA-I that formed a range of smaller nanodiscs. Using membrane proteins embedded in these smaller nanodiscs together with high deuteration levels of proteins and lipids and advanced NMR methods allowed NMR resonance assignment and high-resolution structure determination of membrane proteins. The set of scaffold proteins could be screened for optimal NMR spectra of small to medium-sized membrane proteins. This method allowed the authors to obtain good-quality spectra for bacteriorhodopsin and to determine the structure of OmpX, a bacterial outer-membrane protein.

    CREDIT: F. HAGN ET AL., JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 135, 1919 (1 FEBRUARY 2013) © 2013 AMERICAN CHEMICAL SOCIETY

    JACS 135, 1919 (2013).

  7. Planetary Science

    The Moon's Indigenous Water

    1. Maria Cruz

    Until 5 years ago, the Moon was thought to be essentially bone dry. Analysis of the samples brought back by the Apollo and Luna missions had not revealed any hydrous components. Recent studies, however, using improved analytical techniques, reported the detection of water in some lunar rocks, and observations from orbiting spacecraft showed that water is present in the lunar surface. Some of this water is thought to have been delivered by meteorites and through solar-wind implantation of hydrogen; another part is thought be indigenous. Using Fourier transform infrared spectroscopy, Hui et al. have detected water in two Apollo samples representative of the Moon's primary crust, crystallized from the lunar magma ocean that is thought to have once covered the Moon. Water in these samples is indigenous—with solar-wind implantation ruled out by the use of grains that came from the interior of the individual Apollo rocks—and it was present at very early times, before the crust solidified. The authors estimate that the initial water content of the lunar magma ocean was around 320 parts per million. This water could have prolonged the crystallization of the magma ocean.

    Nat. Geosci. 10.1038/ngeo1735 (2013).

Log in to view full text

Via your Institution

Log in through your institution

Log in through your institution