Papers To Watch
Papers to watch
The Scientist Staff | Dec 1, 2007
Credit: © James Cavallini / Photo Researchers, Inc." /> Credit: © James Cavallini / Photo Researchers, Inc. J.C. Hermann et al., "Structure-based activity prediction for an enzyme of unknown function," Nature, 448:775-9, Aug. 16, 2007. The X-ray crystallographic structure of the gene product Tm0936 from the amidohydrolase superfamily, deposited by a structural genomics consortium, was used to dock, score, and sort a library of 22,500 high-energy intermediates
Unleashing neurogenesis
The Scientist Staff | Dec 1, 2007
While looking for regulators of neurogenesis, Hongjun Song at Johns Hopkins University School of Medicine and colleagues found that inhibiting the function of the gene disrupted-in-schizophrenia 1 (DISC1) promoted neurogenic behavior.1 The gene is known as a susceptibility gene for mood disorders and schizophrenia, though this was not the focus of Song et al.'s research. They were interested in a previous observation that DISC1 is highly expressed in two areas of the adult brain that
Solving AMPK
The Scientist Staff | Dec 1, 2007
The enzyme AMP-activated protein kinase (AMPK) has been shown to be central to regulating several metabolic systems such as glucose uptake, oxidation of fatty acids, and insulin sensitivity, but the crystal structure of the mammalian enzyme remained elusive. Bing Xiao and others from the United Kingdom's National Institute for Medical Research used X-ray crystallography to map the structure of AMPK when bound to AMP and ATP, which the enzyme binds competitively,1 illuminating AMPK regul
Papers to Watch
The Scientist Staff | Oct 1, 2007
N. Stern-Ginossar, et al., "Host immune system gene targeting by a viral miRNA." Science, 317:376-81, July 20, 2007. Upon infection of its host, human cytomegalovirus (HCMV) expresses a miRNA that directly down-regulates expression of an immunorelated gene, MICB. Thus, it appears that HCMV has developed two distinct mechanisms to down-regulate expression of the same immunorelated gene, with the RNA-based strategy presumably being more ancient. -
Model variation
The Scientist Staff | Oct 1, 2007
Credit: © Dr. Jeremy Burgess / Photo Researchers, Inc." /> Credit: © Dr. Jeremy Burgess / Photo Researchers, Inc. To better understand how evolutionary pressures have helped shape genetic variation in Arabidopsis thaliana, Detlef Weigel from the Salk Institute for Biological Studies in La Jolla, Calif., and colleagues used high-density oligonucleotide arrays to look at single nucleotide polymorphisms of 20 diverse strains of the plant.1 The group found that, since 2000, abo
Group migration
The Scientist Staff | Oct 1, 2007
While the internal mechanisms that guide cell migration have been described for individual cells, Pernille Rørth at the European Molecular Biology Laboratory in Heidelberg, Germany, and colleagues examined signaling activation in Drosophila border cells to uncover how groups of cells migrate collectively. They found that in the later phase of migration, leading cells have more mitogen-activated protein (MAP) kinase activation than trailing cells.1 "What's setting direction
Papers to Watch
The Scientist Staff | Sep 1, 2007
S. Ge et al.,"A critical period for enhanced synaptic plasticity in newly generated neurons of the adult brain," Neuron, 54:559-66, May 24, 2007. "By following GFP-labeled newly-born adult dentate granule cells, a critical period of 1-1.5 months was identified, and the increased plasticity depended on developmentally regulated synaptic expression of NR2B-containing NMDA [N-methyl d-aspartate] receptors. This critical period may be important for mediating e
Lifespan Controls Fail
The Scientist Staff | Sep 1, 2007
Credit: Courtesy of wikimedia" /> Credit: Courtesy of wikimedia Scientists had previously found that mutations in the Indy (I'm not dead yet) gene in male Drosophila from a particular genetic background result in flies with doubled lifespan. Linda Partridge at University College London and her colleagues aimed to use Indy mutant flies as positive controls for studies on how single genes affect longevity, but instead, they found that the mutants didn't live as long as previous work ha
Transvascular siRNA Delivery
The Scientist Staff | Sep 1, 2007
The tight network of endothelial cells of brain capillaries have, until now, kept therapeutic molecules, such as small interfering RNAs (siRNAs), from crossing from the blood into the brain. Such molecules could potentially silence targeted genes expressed in neurologic disorders. N. Manjunath Swamy from Harvard University Medical School and colleagues synthesized a peptide derived from rabies virus glycoprotein (RVG) and showed that the 29-amino-acid peptide bound specifically to acety
HIV: from chimps to humans
The Scientist Staff | Aug 1, 2007
HIV-1 strains in humans arose from three independent ape-to-human transmissions in the early 20th century, but the viral adaptation in humans remained unknown until now. Paul Sharp and colleagues from the University of Nottingham Queens Medical Centre in England compared full-length genome sequences of chimpanzee HIV strains with inferred ancestral sequences for three different phylogenetic HIV-1 groups in humans: M, N and O. They found that cross-species transmission in all three gr
Inflammation pathways
The Scientist Staff | Aug 1, 2007
Credit: David M. Phillips / Photo Researchers, Inc" /> Credit: David M. Phillips / Photo Researchers, Inc To uncover the inflammatory pathways involved in cell injury and death, Kenneth Rock at the University of Massachusetts and colleagues injected necrotic cells into mice deficient in various toll-like receptors and found that neutrophilic inflammatory response was not significantly reduced.1 Using the same strategy in interleukin-1 (IL-1) receptor-deficient mice, along with mice
Papers to Watch
The Scientist Staff | Aug 1, 2007
T.Y. James et al., "Reconstructing the early evolution of Fungi using a six-gene phylogeny," Nature 443:818-22, Oct. 19, 2007. This paper presents a broad molecular phylogeny of the fungi and highlights the basal nature of the chytrids. This six-gene phylogeny is a major advance for understanding the evolution of fungal traits. Joe Heitman Duke University Medical Center, USA
Papers to Watch
The Scientist Staff | Jul 1, 2007
Y. Zhou et al., "The mammalian Golgi regulates numb signaling in asymmetric cell division by releasing ACBD3 during mitosis," Cell, 129:163-78, Apr. 6, 2007. This excellent paper reports a novel means of coupling cell-cycle progression with cell fate decisions. The authors show that the fragmentation of the Golgi complex, which precedes mitosis of neural progenitor cells, releases a Numb binding protein, thereby modulating cell fate decisions fol
Profiling Human Histones
The Scientist Staff | Jul 1, 2007
Some patterns of histone methylation are linked to human gene activation, and other patterns are linked to gene repression. By combining chromatin immunoprecipitation with new Solexa 1G sequencing technology, Artem Barski at the National Institutes of Health and colleagues from the University of California, Los Angeles, generated genome-wide maps for histone methylations and correlated methylation events with different levels of gene expression.1 The researchers saw differences in methy
Butterfly Eyes
The Scientist Staff | Jul 1, 2007
Credit: © Gary Boisvert" /> Credit: © Gary Boisvert Butterflies and some mammals rely on color vision for survival. Francesca Frentiu, from the University of California, Irvine, and colleagues used epimicrospectrophotometry and gene sequencing to show that the photopigment opsin gene in the butterfly genus Limenitis has evolved similarly to the opsin gene in primates.1 The researchers measured light wavelengths reflected off the butterflies' tapetum lucidum and found a spec
The Congenic Footprint
The Scientist Staff | Jun 1, 2007
Backcrossing knockout alleles into inbred mouse strains is common procedure, but unintended consequences can occur. Leonard C. Schalkwyk of the Institute of Psychiatry at Kings College London and collaborators at the University of Tartu in Estonia backcrossed cholecystokynin 2 knockouts with C57BL/6 mice and demonstrated a "congenic footprint," a remaining fragment of the flanking stem cell-derived chromosome that causes differences in gene expression.1 "What you have here is
Tailing Lateralization
The Scientist Staff | Jun 1, 2007
A dog's tail reveals unambiguous messages about its mood. Now, a study on tail wagging may lend credence to the contested theory that nonhuman vertebrates have asymmetric brain function. Angelo Quaranta and colleagues from the University of Bari and the University of Trieste in Italy trained video cameras on the posteriors of 30 dogs while exposing them to four separate visual stimuli: the dog's owner, an unfamiliar person, a dominant unfamiliar dog, and a cat. Familiar and nonth
Papers to watch
The Scientist Staff | Jun 1, 2007
G. Cumming et al., "Error bars in experimental biology," J Cell Biol, 177: 7-11, April 9, 2007. Different kinds of error bars can mean very different things. The authors suggest eight simple rules to assist with effective use and interpretation of error bars. This paper is a must read for every scientist who thinks that triplicate plates from a single experiment counts as n=3! Andy Gro
Papers to watch
The Scientist Staff | May 1, 2007
Credit: Courtesy of The International Union of Crystallography" /> Credit: Courtesy of The International Union of Crystallography S.N. Willis et al., ?Apoptosis initiated when BH3 ligands engage multiple Bcl-2 homologs, not Bax or Bak,? Science, 315:856?9, Feb. 9, 2007. The authors leverage knockout mice lacking BH3-only ?activators? to examine how the Bcl2 protein family cont
Crystal structure made easy
The Scientist Staff | May 1, 2007
Credit: Courtesy of the International Union of Crystallography" /> Credit: Courtesy of the International Union of Crystallography Crystallizing proteins is a daunting task. Last year Alexander McPherson of the University of California, Irvine, and colleagues proposed a novel strategy to develop crystals quickly by including high concentrations of small molecules to the so-called mother liquors. They analyzed data on the crystallization of 81 different protein cultur