BioMed Roundup

This month in Bio-Med Roundup:

Klein and Ferré-D’Amaré and Salehi-Ashtiani et al . provided insights into the evolution and mechanism of action of self-cleaving ribozymes.
Tuskan et al . presented the genome sequence of the black cottonwood tree, Populus trichocarpa .
Sturm et al . showed that the malaria parasite moves from liver to blood in membranous vesicles that cannot be detected by the immune system.
Fukata et al. identified a pairing of proteins in neurons that may be relevant to the pathogenesis of human epilepsy.
Warren et al . showed that the proteasome can splice together and reorder peptides to increase the diversity of the antigenic repertoire.

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Genetics
Neuroscience
Biochemistry/Structural Biology
Microbiology
Cell/Developmental Biology
Psychology
Medicine
Immunology
Plant Science

This month’s Bio-Med Roundup is sponsored by Polyplus-transfection
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GENETICS

Phytophthora Genome Sequences Uncover Evolutionary Origins and Mechanisms of Pathogenesis ( 1 September 2006 )
B. M. Tyler, S. Tripathy, X. Zhang, P. Dehal, R. H. Y. Jiang, A. Aerts, F. D. Arredondo, L. Baxter, D. Bensasson, J. L. Beynon et al.
The enigmatic parasite that causes sudden oak death carries the genetic signature of an ancestral photosynthetic symbiont that suggests a recent expansion of pathogenic protein families.
http://www.sciencemag.org/cgi/content/abstract/313/5791/1261

Human Lineage–Specific Amplification, Selection, and Neuronal Expression of DUF1220 Domains ( 1 September 2006 )
M. C. Popesco, E. J. MacLaren, J. Hopkins, L. Dumas, M. Cox, L. Meltesen, L. McGavran, G. J. Wyckoff, J. M. Sikela
A comparison of human and four great-ape genomes reveals that a class of neural genes appears to have been dramatically amplified in the human lineage.
http://www.sciencemag.org/cgi/content/abstract/313/5791/1304

Gene Transposition as a Cause of Hybrid Sterility in Drosophila ( 8 September 2006 )
J. P. Masly, C. D. Jones, M. A. F. Noor, J. Locke, H. A. Orr
Movement of an essential sperm motility gene to a different chromosome in Drosophila can result in sterile hybrids and, potentially, speciation without sequence evolution.
http://www.sciencemag.org/cgi/content/abstract/313/5792/1448

The Genome of Black Cottonwood , Populus trichocarpa (Torr. & Gray) ( 15 September 2006 )
G. A. Tuskan, S. DiFazio, S. Jansson, J. Bohlmann, I. Grigoriev, U. Hellsten, N. Putnam, S. Ralph, S. Rombauts, A. Salamov et al.
The poplar genome was duplicated 60 to 65 million years ago, marking the emergence of this tree family, but overall has evolved more slowly than that of Arabidopsis .
http://www.sciencemag.org/cgi/content/abstract/313/5793/1596

SUMO1 Haploinsufficiency Leads to Cleft Lip and Palate ( 22 September 2006 )
F. S. Alkuraya, I. Saadi, J. J. Lund, A. Turbe-Doan, C. C. Morton, R. L. Maas
A protein modification is important during development to promote appropriate palate formation.
http://www.sciencemag.org/cgi/content/abstract/313/5794/1751

Global Genetic Change Tracks Global Climate Warming in Drosophila subobscura ( 22 September 2006 )
J. Balanyá, J. M. Oller, R. B. Huey, G. W. Gilchrist, L. Serra
On three continents, a low-latitude, natural genetic variant of the fruit fly is increasingly found at higher latitudes, paralleling climate warming over the past 25 years.
http://www.sciencemag.org/cgi/content/abstract/313/5794/1773

A Genomewide Search for Ribozymes Reveals an HDV-Like Sequence in the Human CPEB3 Gene ( 22 September 2006 )
K. Salehi-Ashtiani, A. Lupták, A. Litovchick, J. W. Szostak
Excision of a self-cleaving RNA in the human genome may have formed the similar hepatitis delta virus.
http://www.sciencemag.org/cgi/content/abstract/313/5794/1788
See related Perspective at http://www.sciencemag.org/cgi/content/summary/313/5794/1745

The Connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes, and Disease ( 29 September 2006 )
J. Lamb, E. D. Crawford, D. Peck, J. W. Modell, I. C. Blat, M. J. Wrobel, J. Lerner, J.-P. Brunet, A. Subramanian, K. N. Ross et al.
Comparison of mRNAs evoked by small molecules in human cells to mRNA expressed in diseases and in response to drugs suggests new therapeutic approaches.
http://www.sciencemag.org/cgi/content/abstract/313/5795/1929

Dok-7 Mutations Underlie a Neuromuscular Junction Synaptopathy ( 29 September 2006 )
D. Beeson, O. Higuchi, J. Palace, J. Cossins, H. Spearman, S. Maxwell, J. Newsom-Davis, G. Burke, P. Fawcett, M. Motomura et al.
An inherited muscle disease in which certain muscles are weak is caused by mutations in a protein needed for proper formation of the neuromuscular junction.
http://www.sciencemag.org/cgi/content/abstract/313/5795/1975

NEUROSCIENCE

A Role for the Macaque Anterior Cingulate Gyrus in Social Valuation ( 1 September 2006 )
P. H. Rudebeck, M. J. Buckley, M. E. Walton, M. F. S. Rushworth
Monkeys rely on the anterior cingulate cortex in processing socially potent information, such as another monkey staring at them.
http://www.sciencemag.org/cgi/content/abstract/313/5791/1310

Hoxa2- and Rhombomere-Dependent Development of the Mouse Facial Somatosensory Map ( 8 September 2006 )
F. Oury, Y. Murakami, J.-S. Renaud, M. Pasqualetti, P. Charnay, S.-Y. Ren, F. M. Rijli
The genes that define general brain structure in the early embryo are also responsible for the organization of the neural circuit that processes sensory information.
http://www.sciencemag.org/cgi/content/abstract/313/5792/1408

Temporal and Spatial Enumeration Processes in the Primate Parietal Cortex ( 8 September 2006 )
A. Nieder, I. Diester, O. Tudusciuc
One brain area performs elementary math tasks but has separate subregions for counting in time and space, which both connect to a single region that represents the abstract number.
http://www.sciencemag.org/cgi/content/abstract/313/5792/1431

High Gamma Power Is Phase-Locked to Theta Oscillations in Human Neocortex ( 15 September 2006 )
R. T. Canolty, E. Edwards, S. S. Dalal, M. Soltani, S. S. Nagarajan, H. E. Kirsch, M. S. Berger, N. M. Barbaro, R. T. Knight
A characteristic, low-frequency brain wave modulates ultrahigh-frequency oscillations, thereby allowing communication among areas of the cortex that support behavior.
http://www.sciencemag.org/cgi/content/abstract/313/5793/1626

Waking Experience Affects Sleep Need in Drosophila ( 22 September 2006 )
I. Ganguly-Fitzgerald, J. Donlea, P. J. Shaw
Drosophila sleep is disrupted by intense social interaction during the previous 5 days, a process that involves a number of learning and memory genes.
http://www.sciencemag.org/cgi/content/abstract/313/5794/1775

PirB Restricts Ocular-Dominance Plasticity in Visual Cortex ( 22 September 2006 )
J. Syken, T. GrandPre, P. O. Kanold, C. J. Shatz
A molecule that is usually thought of as a hallmark of the immune system interacts with a receptor in the brain to limit the plasticity of the visual system during development.
http://www.sciencemag.org/cgi/content/abstract/313/5794/1795

Epilepsy-Related Ligand/Receptor Complex LGI1 and ADAM22 Regulate Synaptic Transmission ( 22 September 2006 )
Y. Fukata, H. Adesnik, T. Iwanaga, D. S. Bredt, R. A. Nicoll, M. Fukata
A complex of proteins that are linked to epilepsy syndromes functions at brain synapses and could provide a therapeutic target.
http://www.sciencemag.org/cgi/content/abstract/313/5794/1792
See related Perspective at http://www.sciencemag.org/cgi/content/summary/313/5794/1744

BIOCHEMISTRY/STRUCTURAL BIOLOGY

Exploiting the Reversibility of Natural Product Glycosyltransferase-Catalyzed Reactions ( 1 September 2006 )
C. Zhang, B. R. Griffith, Q. Fu, C. Albermann, X. Fu, I.-K. Lee, L. Li, J. S. Thorson
In addition to adding sugar residues, glycosyltransferases can also remove them, making these enzymes valuable for modifying natural products to make new drugs.
http://www.sciencemag.org/cgi/content/abstract/313/5791/1291

Structural Asymmetry of AcrB Trimer Suggests a Peristaltic Pump Mechanism ( 1 September 2006 )
M. A. Seeger, A. Schiefner, T. Eicher, F. Verrey, K. Diederichs, K. M. Pos
A drug efflux pump extrudes molecules such as bile salts, detergents, and antibiotics from cells through a constricted pore in a process that mimics peristalsis.
http://www.sciencemag.org/cgi/content/abstract/313/5791/1295

The Dynamic Energy Landscape of Dihydrofolate Reductase Catalysis ( 15 September 2006 )
D. D. Boehr, D. McElheny, H. J. Dyson, P. E. Wright
An enzyme progresses through its reaction cycle by fluctuating between the ground state and the higher-energy states of each kinetic intermediate.
http://www.sciencemag.org/cgi/content/abstract/313/5793/1638
See related Perspective at http://www.sciencemag.org/cgi/content/summary/313/5793/1586

Structural Basis of glmS Ribozyme Activation by Glucosamine-6-Phosphate (22 September 2006)
D. J. Klein and A. R. Ferré-D’Amaré
A small-molecule coenzyme activates a ribozyme by binding to a preformed site where it participates in catalysis, not by allosteric regulation.
http://www.sciencemag.org/cgi/content/abstract/313/5794/1752
See related Perspective at http://www.sciencemag.org/cgi/content/summary/313/5794/1745

Structure of the 70 S Ribosome Complexed with mRNA and tRNA (29 September 2006)
M. Selmer, C. M. Dunham, F. V. Murphy, IV, A. Weixlbaumer, S. Petry, A. C. Kelley, J. R. Weir, V. Ramakrishnan
The structure of the bacterial ribosome complexed with mRNA and tRNA at 2.8 angstrom resolution shows the detailed interaction of the ribosome with its substrates and metal ions.
http://www.sciencemag.org/cgi/content/abstract/313/5795/1935

Structure of the Exon Junction Core Complex with a Trapped DEAD-Box ATPase Bound to RNA ( 29 September 2006 )
C. B. F. Andersen, L. Ballut, J. S. Johansen, H. Chamieh, K. H. Nielsen, C. L. P. Oliveira, J. Skov Pedersen, B. Séraphin, H. Le Hir, G. Rom Andersen
A structure of a complex that binds to new mRNA reveals how two proteins inhibit the ATPase activity of an RNA helicase to ensure tight binding.
http://www.sciencemag.org/cgi/content/abstract/313/5795/1968

MICROBIOLOGY

Manipulation of Host Hepatocytes by the Malaria Parasite for Delivery into Liver Sinusoids (1 September 2006)
A. Sturm, R. Amino, C. van de Sand, T. Regen, S. Retzlaff, A. Rennenberg, A. Krueger, J.-M. Pollok, R. Menard, V. T. Heussler
The malaria parasite moves from liver to blood by inducing liver cells to die and, in the process, to bud off parasite-containing vesicles that cannot be detected by the immune system.
http://www.sciencemag.org/cgi/content/abstract/313/5791/1287
See related Perspective at http://www.sciencemag.org/cgi/content/summary/313/5791/1245

Humanization of Yeast to Produce Complex Terminally Sialylated Glycoproteins ( 8 September 2006 )
S. R. Hamilton, R. C. Davidson, N. Sethuraman, J. H. Nett, Y. Jiang, S. Rios, P. Bobrowicz, T. A. Stadheim, H. Li, B.-K. Choi,
Yeast strains engineered to glycosylate proteins in a characteristically human pattern can make synthetic erythropoietin that functions properly in humans.
http://www.sciencemag.org/cgi/content/abstract/313/5792/1441

C-Terminal Signal Sequence Promotes Virulence Factor Secretion in Mycobacterium tuberculosis ( 15 September 2006 )
P. A. DiGiuseppe Champion, S. A. Stanley, M. M. Champion, E. J. Brown, J. S. Cox
The pathogen that causes tuberculosis tags proteins for processing by its unusual secretory system with an unstructured carboxyl terminal sequence.
http://www.sciencemag.org/cgi/content/abstract/313/5793/1632
See related Perspective at http://www.sciencemag.org/cgi/content/summary/313/5793/1583

An Alternative Bactericidal Mechanism of Action for Lantibiotic Peptides That Target Lipid II ( 15 September 2006 )
H. E. Hasper, N. E. Kramer, J. L. Smith, J. D. Hillman, C. Zachariah, O. P. Kuipers, B. de Kruijff, E. Breukink
A new class of antibiotics has an unusual target—a molecule needed for bacterial cell wall synthesis—and may be especially useful against resistant microbes.
http://www.sciencemag.org/cgi/content/abstract/313/5793/1636

CELL/DEVELOPMENTAL BIOLOGY

CYK-4/GAP Provides a Localized Cue to Initiate Anteroposterior Polarity upon Fertilization ( 1 September 2006 )
N. Jenkins, J. R. Saam, S. E. Mango
The polarity of the one-cell nematode embryo, which eventually establishes the anterior and posterior ends of the adult, arises from the local injection of a sperm factor.
http://www.sciencemag.org/cgi/content/abstract/313/5791/1298

The Mevalonate Pathway Controls Heart Formation in Drosophila by Isoprenylation of G γ1 (1 September 2006)
P. Yi, Z. Han, X. Li, E. N. Olson
A genetic screen for heart mutants reveals that the pathway for isoprenoid biosynthesis functions in heart development.
http://www.sciencemag.org/cgi/content/abstract/313/5791/1301

Isolated Chloroplast Division Machinery Can Actively Constrict After Stretching (8 September 2006)
Y. Yoshida, H. Kuroiwa, O. Misumi, K. Nishida, F. Yagisawa, T. Fujiwara, H. Nanamiya, F. Kawamura, T. Kuroiwa
A molecular motor called dynamin provides the force needed to contract the filamentous ring that pinches and divides choloroplasts during cell division.
http://www.sciencemag.org/cgi/content/abstract/313/5792/1435

Human IRGM Induces Autophagy to Eliminate Intracellular Mycobacteria (8 September 2006)
S. B. Singh, A. S. Davis, G. A. Taylor, V. Deretic
A small GTP binding protein, associated with innate immunity, is required for cells to use large membrane-bound organelles to sequester and eliminate bacteria that have invaded their cytoplasm.
http://www.sciencemag.org/cgi/content/abstract/313/5792/1438

Opposing Activities Protect Against Age-Onset Proteotoxicity ( 15 September 2006 )
E. Cohen, J. Biesch ke, R. M. Perciavalle, J. W. Kelly, A. Dillin
The insulin/insulin-like receptor pathway can detoxify protein aggregates in worms engineered to express excess protein in their muscles, perhaps partly explaining its role in aging.
http://www.sciencemag.org/cgi/content/abstract/313/5793/1604

Caveolin-1 Is Essential for Liver Regeneration ( 15 September 2006 )
M. A. Fernández, C. Albor, M. Ingelmo-Torres, S. J. Nixon, C. Ferguson, T. Kurzchalia, F. Tebar, C. Enrich, R. G. Parton, A. Pol
Mice lacking a protein that helps cells internalize other proteins and signaling molecules seem to be normal, but their livers cannot regenerate after being damaged.
http://www.sciencemag.org/cgi/content/abstract/313/5793/1628
See related Perspective at http://www.sciencemag.org/cgi/content/summary/313/5793/1581

Imaging Intracellular Fluorescent Proteins at Nanometer Resolution ( 15 September 2006 )
E. Betzig, G. H. Patterson, R. Sougrat, O. Wolf Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, H. F. Hess
Proteins of interest can be labeled with fluorescent tags and located by photoactivated localization microscopy (PALM) in thin sections and fixed cells at near-molecular resolution.
http://www.sciencemag.org/cgi/content/abstract/313/5793/1642

PSYCHOLOGY

Reducing the Racial Achievement Gap: A Social-Psychological Intervention (1 September 2006)
G. L. Cohen, J. Garcia, N. Apfel, A. Master
A writing assignment that affirmed seventh-grade students’ positive self-image reduced the subsequent difference in grades between African and European Americans.
http://www.sciencemag.org/cgi/content/abstract/313/5791/1305
See related Perspective at http://www.sciencemag.org/cgi/content/summary/313/5791/1251

Detecting Awareness in the Vegetative State (8 September 2006)
A. M. Owen, M. R. Coleman, M. Boly, M. H. Davis, S. Laureys, J. D. Pickard
Brain imaging reveals that an unconscious, unresponsive patient can imagine moving around her home, as assessed by activity in spatial navigation regions of the brain.
http://www.sciencemag.org/cgi/content/abstract/313/5792/1402
See related Perspective at http://www.sciencemag.org/cgi/content/summary/313/5792/1395

Washing Away Your Sins: Threatened Morality and Physical Cleansing (8 September 2006)
C.-B. Zhong and K. Liljenquist
Lab experiments reveal unexpected parallels between feelings of moral purity and physical cleanliness, perhaps explaining the ubiquity of religious cleansing rituals.
http://www.sciencemag.org/cgi/content/abstract/313/5792/1451

MEDICINE

Exogenous Induction of Cerebral beta-Amyloidogenesis Is Governed by Agent and Host (22 September 2006)
M. Meyer-Luehmann, J. Coomaraswamy, T. Bolmont, S. Kaeser, C. Schaefer, E. Kilger, A. Neuenschwander, D. Abramowski, P. Frey, A. L. Jaton et al.
Injecting transgenic mice with amyloid deposits from patients with Alzheimer’s disease can induce similar deposits and pathology in their brains.
http://www.sciencemag.org/cgi/content/abstract/313/5794/1781

Therapy-Induced Acute Recruitment of Circulating Endothelial Progenitor Cells to Tumors (22 September 2006)
Y. Shaked, A. Ciarrocchi, M. Franco, C. R. Lee, S. Man, A. M. Cheung, D. J. Hicklin, D. Chaplin, F. S. Foster, R. Benezra, R. S. Kerbel
Adding an antiangiogenic agent to certain anticancer drugs reduces their tendency to promote the formation of new blood vessels in tumors, improving their efficacy.
http://www.sciencemag.org/cgi/content/abstract/313/5794/1785

Type, Density, and Location of Immune Cells Within Human Colorectal Tumors Predict Clinical Outcome ( 29 September 2006 )
J. Galon, A. Costes, F. Sanchez-Cabo, A. Kirilovsky, B. Mlecnik, C. Lagorce-Pagès, M. Tosolini, M. Camus, A. Berger, P. Wind et al.
The progress of colorectal cancer in patients can be predicted from the characteristics of the immune cells found in their tumors.
http://www.sciencemag.org/cgi/content/abstract/313/5795/1960

IMMUNOLOGY

An Antigen Produced by Splicing of Noncontiguous Peptides in the Reverse Order ( 8 September 2006 )
E. H. Warren, N. J. Vigneron, M. A. Gavin, P. G. Coulie, V. Stroobant, A. Dalet, S. S. Tykodi, S. M. Xuereb, J. K. Mito, S. R. Riddell, B. J. Van den Eynde
The proteasome can splice together and reorder peptides to increase the diversity of the antigenic repertoire.
http://www.sciencemag.org/cgi/content/abstract/313/5792/1444
See related Perspective at http://www.sciencemag.org/cgi/content/summary/313/5792/1398

Reversal of the TCR Stop Signal by CTLA-4 ( 29 September 2006 )
H. Schneider, J. Downey, A. Smith, B. H. Zinselmeyer, C. Rush, J. M. Brewer, B. Wei, N. Hogg, P. Garside, C. E. Rudd
A protein responsible for preventing unwanted immune responses discourages extended liaisons between activated immune cells.
http://www.sciencemag.org/cgi/content/abstract/313/5795/1972
See related Perspective at http://www.sciencemag.org/cgi/content/summary/313/5795/1902

PLANT SCIENCE

Volatile Chemical Cues Guide Host Location and Host Selection by Parasitic Plants ( 29 September 2006 )
J. B. Runyon, M. C. Mescher, C. M. De Moraes
A parasitic plant locates a preferred host by detecting its released odors; disrupting this process could help control parasites of crop plants.
http://www.sciencemag.org/cgi/content/abstract/313/5795/1964