bluuebunny/crossref_metadata_2025 huggingface dataset:
Marked Post-18th Century Environmental Change in High-Arctic Ecosystems
Authors: Douglas Marianne S. V. , Smol John P. , Blake Weston
Published: October 2006

Paleolimnological data from three high-arctic ponds on Cape Herschel, Ellesmere Island, Canada, show that diatom assemblages were relatively stable over the last few millennia but then experienced unparalleled changes beginning in the 19th century. The environmental factors causing these assemblage shifts may be related to recent climatic warming. Regardless of the cause, the biota of these isolated and seemingly pristine ponds have changed dramatically in the recent past and any hopes of cataloging natural assemblages may already be fruitless.
Causes of Decadal Climate Variability over the North Pacific and North America
Authors: Latif M. , Barnett T. P.
Published: October 2006

The cause of decadal climate variability over the North Pacific Ocean and North America is investigated by the analysis of data from a multidecadal integration with a state-of-the-art coupled ocean-atmosphere model and observations. About one-third of the low-frequency climate variability in the region of interest can be attributed to a cycle involving unstable air-sea interactions between the subtropical gyre circulation in the North Pacific and the Aleutian low-pressure system. The existence of this cycle provides a basis for long-range climate forecasting over the western United States at decadal time scales.
Encapsulation of Guest Molecules into a Dendritic Box
Authors: Jansen Johan F. G. A. , de Brabander-van den Berg Ellen M. M. , Meijer E. W.
Published: October 2006

Dendrimers are well-defined, highly branched macromolecules that emanate from a central core and are synthesized through a stepwise, repetitive reaction sequence. The synthesis and characterization of dendritic boxes, based on the construction of a chiral shell of protected amino acids onto poly(propyleneimine) dendrimers with 64 amine end groups, is reported here. Nuclear magnetic resonance-relaxation and optical data show that a dense shell with solid-phase character is formed. Guest molecules were captured within the internal cavities of the boxes when these boxes were constructed in the presence of guest molecules. The diffusion of guest molecules out of the boxes into solution was unmeasurably slow because of the close packing of the shell. These monomolecular dendritic containers of 5-nanometer dimensions with physically locked-in guest molecules were characterized spectroscopically.
Nondestructive Mass Selection of Small van der Waals Clusters
Authors: Schöllkopf Wieland , Toennies J. Peter
Published: October 2006

Clusters of atoms or molecules have been extensively studied by a variety of spectroscopies because of their unusual properties. Experiments with van der Waals clusters of defined sizes are not easily possible because nozzle beam expansions used in their production yield broad size distributions. Moreover, being weakly bound they readily fragment in the commonly used electron impact-ionization mass spectrometer detectors. Here it is shown that light fragile clusters of He, H
2
, and D
2
can be selected and identified nondestructively by diffraction from a transmission grating. The method is universally applicable also to heavier species and well suited for spectroscopic studies.
The Central Role of Broken Bond-Bending Constraints in Promoting Glass Formation in the Oxides
Authors: Zhang M. , Boolchand P.
Published: October 2006

A glass network of
N
atoms with
n
1
of the atoms with a coordination number of 1, and
m
2
of the atoms with a coordination number of 2 about which the bond-angle constraint is broken, will in general display a stiffness threshold (rigidity percolation threshold) when the average coordination increases to a critical value 〈
r
〉
c
= 2.4 – 0.4 (
n
1
–
m
2
)/
N
. Silica and sodium tellurate glasses provide model examples for which this general relation predicts the observed rigidity percolation threshold; this relation predicts the percolation threshold only if one includes broken bond-bending constraints due to bridging oxygen in the former network and nonbridging oxygen in the latter network. The rigidity percolation threshold in (Na
2
O)

x

(TeO
2
)

1–
x

glasses is observed to occur near
x
≃ 0.18 in tellurium-125 Lamb-Mössbauer factor measurements.
The Met Proto-Oncogene Mesenchymal to Epithelial Cell Conversion
Authors: Tsarfaty Ilan , Rong Sing , Resau James H. , Rulong Shen , da Silva Pedro Pinto , Vande Woude George F.
Published: October 2006

Coexpression of the human Met receptor and its ligand, hepatocyte growth factor/scatter factor (HGF/SF), in NIH 3T3 fibroblasts causes the cells to become tumorigenic in nude mice. The resultant tumors display lumen-like morphology, contain carcinoma-like focal areas with intercellular junctions resembling desmosomes, and coexpress epithelial (cytokeratin) and mesenchymal (vimentin) cytoskeletal markers. The tumor cells also display enhanced expression of desmosomal and tight-junction proteins. The apparent mesenchymal to epithelial conversion of the tumor cells mimics the conversion that occurs during embryonic kidney development, suggesting that Met-HGF/SF signaling plays a role in this process as well as in tumors that express both epithelial and mesenchymal markers.
Role of NO Production in NMDA Receptor-Mediated Neurotransmitter Release in Cerebral Cortex
Authors: Montague P. Read , Gancayco Carolyn D. , Winn Mark J. , Marchase Richard B. , Friedlander Michael J.
Published: October 2006

L-Glutamate and norepinephrine are examples of a major excitatory neurotransmitter and a neuromodulator in the cerebral cortex, respectively. Little is known of how chemical signaling between the anatomically distinct chemical pathways occurs. Specific activation of the
N
-methyl-D-aspartate (NMDA) class of glutamate receptor in synaptosomal preparations from guinea pig cerebral cortex caused release of both of these chemicals, and this release was blocked by agents that inhibit nitric oxide (NO) production or remove NO from the extracellular space. Furthermore, neurotransmitter release correlated with cortical NO production after NMDA receptor stimulation. These results suggest that NO production and its extracellular movement may be links in the pathway from NMDA receptor activation to changes in chemical signaling in surrounding synaptic terminals in the cerebral cortex.
Sequential Interactions of the TCR with Two Distinct Cytoplasmic Tyrosine Kinases
Authors: Iwashima Makio , Irving Bryan A. , van Oers Nicolai S. C. , Chan Andrew C. , Weiss Arthur
Published: October 2006

The T cell antigen receptor (TCR) initiates signals by interacting with cytoplasmic protein tyrosine kinases (PTKs) through a 17-residue sequence motif [called the antigen recognition activation motif (ARAM)] that is contained in the TCRζ and CD3 chains. TCR stimulation induces the tyrosine phosphorylation of several cellular substrates, including the ARAMs. Lck kinase activity is required for phosphorylation of two conserved tyrosine residues in an ARAM. This phosphorylation leads to the recruitment of a second cytoplasmic PTK, ZAP-70, through both of the ZAP-70 Src homology 2 domains and its phosphorylation. Thus, TCR signal transduction is initiated by the sequential interaction of two PTKs with TCR ARAMs.
Crystal Structure of the Principal Neutralization Site of HIV-1
Authors: Ghiara Jayant B. , Stura Enrico A. , Stanfield Robyn L. , Profy Albert T. , Wilson Ian A.
Published: October 2006

The crystal structure of a complex between a 24-amino acid peptide from the third variable (V3) loop of human immunodeficiency virus-type 1 (HIV-1) gp120 and the Fab fragment of a broadly neutralizing antibody (59.1) was determined to 3 angstrom resolution. The tip of the V3 loop containing the Gly-Pro-Gly-Arg-Ala-Phe sequence adopts a double-turn conformation, which may be the basis of its conservation in many HIV-1 isolates. A complete map of the HIV-1 principal neutralizing determinant was constructed by stitching together structures of V3 loop peptides bound to 59.1 and to an isolate-specific (MN) neutralizing antibody (50.1). Structural conservation of the overlapping epitopes suggests that this biologically relevant conformation could be of use in the design of synthetic vaccines and drugs to inhibit HIV-1 entry and virus-related cellular fusion.
Structure of the Equine Infectious Anemia Virus Tat Protein
Authors: Willbold D. , Rosin-Arbesfeld R. , Sticht H. , Frank R. , Rösch P.
Published: October 2006

Trans-activator (Tat) proteins regulate the transcription of lentiviral DNA in the host cell genome. These RNA binding proteins participate in the life cycle of all known lentiviruses, such as the human immunodeficiency viruses (HIV) or the equine infectious anemia virus (EIAV). The consensus RNA binding motifs [the trans-activation responsive element (TAR)] of HIV-1 as well as EIAV Tat proteins are well characterized. The structure of the 75-amino acid EIAV Tat protein in solution was determined by two- and three-dimensional nuclear magnetic resonance methods and molecular dynamics calculations. The protein structure exhibits a well-defined hydrophobic core of 15 amino acids that serves as a scaffold for two flexible domains corresponding to the NH
2
- and COOH-terminal regions. The core region is a strictly conserved sequence region among the known Tat proteins. The structural data can be used to explain several of the observed features of Tat proteins.
Sequestration of GPI-Anchored Proteins in Caveolae Triggered by Cross-Linking
Authors: Mayor Satyajit , Rothberg Karen G. , Maxfield Frederick R.
Published: October 2006

Glycosyl-phosphatidylinositol (GPI)-anchored proteins have been reported to reside in clusters collected over small membrane invaginations called caveolae. The detection of different GPI-anchored proteins with fluorescently labeled monoclonal antibodies showed that these proteins are not constitutively concentrated in caveolae; they enter these structures independently after cross-linking with polyclonal secondary antibodies. Analysis of the cell surface distribution of the GPI-anchored folate receptor by electron microscopy confirms these observations. Thus, multimerization of GPI-anchored proteins regulates their sequestration in caveolae, but in the absence of agents that promote clustering they are diffusely distributed over the plasma membrane.
NMR Solution Structure of a Peptide Nucleic Acid Complexed with RNA
Authors: Brown Stephen C. , Thomson Stephen A. , Veal James M. , Davis Donald G.
Published: October 2006

Peptide nucleic acids (PNA) incorporating nucleic acid bases into an achiral polyamide backbone bind to DNA in a sequence-dependent manner. The structure of a PNA-ribonucleic acid (RNA) complex was determined with nuclear magnetic resonance methods. A hexameric PNA formed a 1:1 complex with a complementary RNA that is an antiparallel, right-handed double helix with Watson-Crick base pairing similar to the "A" form structure of RNA duplexes. The achiral PNA backbone assumed a distinct conformation upon binding that differed from previously proposed models and provides a basis for further structure-based design of antisense agents.
Effects of Cerebral Ischemia in Mice Deficient in Neuronal Nitric Oxide Synthase
Authors: Huang Zhihong , Huang Paul L. , Panahian Nariman , Dalkara Turgay , Fishman Mark C. , Moskowitz Michael A.
Published: October 2006

The proposal that nitric oxide (NO) or its reactant products mediate toxicity in brain remains controversial in part because of the use of nonselective agents that block NO formation in neuronal, glial, and vascular compartments. In mutant mice deficient in neuronal NO synthase (NOS) activity, infarct volumes decreased significantly 24 and 72 hours after middle cerebral artery occlusion, and the neurological deficits were less than those in normal mice. This result could not be accounted for by differences in blood flow or vascular anatomy. However, infarct size in the mutant became larger after endothelial NOS inhibition by nitro-L-arginine administration. Hence, neuronal NO production appears to exacerbate acute ischemic injury, whereas vascular NO protects after middle cerebral artery occlusion. The data emphasize the importance of developing selective inhibitors of the neuronal isoform.
Two Binding Orientations for Peptides to the Src SH3 Domain: Development of a General Model for SH3-Ligand Interactions
Authors: Feng Sibo , Chen James K. , Yu Hongtao , Simon Julian A. , Schreiber Stuart L.
Published: October 2006

Solution structures of two Src homology 3 (SH3) domain-ligand complexes have been determined by nuclear magnetic resonance. Each complex consists of the SH3 domain and a nine-residue proline-rich peptide selected from a large library of ligands prepared by combinatorial synthesis. The bound ligands adopt a left-handed polyproline type II (PPII) helix, although the amino to carboxyl directionalities of their helices are opposite. The peptide orientation is determined by a salt bridge formed by the terminal arginine residues of the ligands and the conserved aspartate-99 of the SH3 domain. Residues at positions 3, 4, 6, and 7 of both peptides also intercalate into the ligand-binding site; however, the respective proline and nonproline residues show exchanged binding positions in the two complexes. These structural results led to a model for the interactions of SH3 domains with proline-rich peptides that can be used to predict critical residues in complexes of unknown structure. The model was used to identify correctly both the binding orientation and the contact and noncontact residues of a peptide derived from the nucleotide exchange factor Sos in association with the amino-terminal SH3 domain of the adaptor protein Grb2.
Correction of Lethal Intestinal Defect in a Mouse Model of Cystic Fibrosis by Human
CFTR
Authors: Zhou Lan , Dey Chitta R. , Wert Susan E. , DuVall Michael D. , Frizzell Raymond A. , Whitsett Jeffrey A.
Published: October 2006

Cystic fibrosis (CF) is caused by mutations in the gene encoding the cystic fibrosis transmembrane conductance regulator (
CFTR
). A potential animal model of CF, the
CFTR
-/-
mouse, has had limited utility because most mice die from intestinal obstruction during the first month of life. Human
CFTR
(h
CFTR
) was expressed in
CFTR
-/-
mice under the control of the rat intestinal fatty acid-binding protein gene promoter. The mice survived and showed functional correction of ileal goblet cell and crypt cell hyperplasia and cyclic adenosine monophosphate-stimulated chloride secretion. These results support the concept that transfer of the h
CFTR
gene may be a useful strategy for correcting physiologic defects in patients with CF.
Crystal and Molecular Structure of a Collagen-Like Peptide at 1.9 Å Resolution
Authors: Bella Jordi , Eaton Mark , Brodsky Barbara , Berman Helen M.
Published: October 2006

The structure of a protein triple helix has been determined at 1.9 angstrom resolution by x-ray crystallographic studies of a collagen-like peptide containing a single substitution of the consensus sequence. This peptide adopts a triple-helical structure that confirms the basic features determined from fiber diffraction studies on collagen: supercoiling of polyproline II helices and interchain hydrogen bonding that follows the model II of Rich and Crick. In addition, the structure provides new information concerning the nature of this protein fold. Each triple helix is surrounded by a cylinder of hydration, with an extensive hydrogen bonding network between water molecules and peptide acceptor groups. Hydroxyproline residues have a critical role in this water network. The interaxial spacing of triple helices in the crystal is similar to that in collagen fibrils, and the water networks linking adjacent triple helices in the crystal structure are likely to be present in connective tissues. The breaking of the repeating (X-Y-Gly)

n

pattern by a Gly→Ala substitution results in a subtle alteration of the conformation, with a local untwisting of the triple helix. At the substitution site, direct interchain hydrogen bonds are replaced with interstitial water bridges between the peptide groups. Similar conformational changes may occur in Gly→X mutated collagens responsible for the diseases osteogenesis imperfecta, chondrodysplasias, and Ehlers-Danlos syndrome IV.
Fatty Acylation of Two Internal Lysine Residues Required for the Toxic Activity of
Escherichia coli
Hemolysin
Authors: Stanley Peter , Packman Len C. , Koronakis Vassilis , Hughes Colin
Published: October 2006

Hemolysin of
Escherichia coli
is activated by fatty acylation of the protoxin, directed by the putative acyl transferase HlyC and by acyl carrier protein (ACP). Mass spectrometry and Edman degradation of proteolytic products from mature toxin activated in vitro with tritium-labeled acylACP revealed two fatty-acylated internal lysine residues, lysine 564 and lysine 690. Resistance of the acylation to chemical treatments suggested that fatty acid was amide linked. Substitution of the two lysines confirmed that they were the only sites of acylation and showed that although each was acylated in the absence of the other, both sites were required for in vivo toxin activity.
An All D-Amino Acid Opioid Peptide with Central Analgesic Activity from a Combinatorial Library
Authors: Dooley C. T. , Chung N. N. , Wilkes B. C. , Schiller P. W. , Bidlack J. M. , Pasternak G. W. , Houghten R. A.
Published: October 2006

A synthetic combinatorial library containing 52,128,400 D-amino acid hexapeptides was used to identify a ligand for the μ opioid receptor. The peptide, Ac-rfwink-NH
2
, bears no resemblance to any known opioid peptide. Simulations using molecular dynamics, however, showed that three amino acid moieties have the same spatial orientation as the corresponding pharmacophoric groups of the opioid peptide PLO17. Ac-rfwink-NH
2
was shown to be a potent agonist at the μ receptor and induced long-lasting analgesia in mice. Analgesia produced by intraperitoneally administered Ac-rfwink-NH
2
was blocked by intracerebroventricular administration of naloxone, demonstrating that this peptide may cross the blood-brain barrier.
Cysteine String Proteins: a Potential Link Between Synaptic Vesicles and Presynaptic Ca
2+
Channels
Authors: Mastrogiacomo Alessandro , Parsons Stanley M. , Zampighi Guido A. , Jenden Donald J. , Umbach Joy A. , Gundersen Cameron B.
Published: October 2006

Presynaptic calcium channels are key regulators of neurotransmitter release. Oocyte expression studies suggest that cysteine string proteins are essential subunits or modulators of these channels. Subcellular fractionation revealed that cysteine string proteins copurify with synaptic vesicles. An average vesicle had eight protein monomers with both the amino and carboxyl termini detected on the cytoplasmic face. Thus, docked synaptic vesicles may regulate presynaptic calcium channels and neurotransmitter release.
FGF-2: Apical Ectodermal Ridge Growth Signal for Chick Limb Development
Authors: Fallon John F. , López Airic , Ros Maria A. , Savage Mary P. , Olwin Bradley B. , Simandl B. Kay
Published: October 2006

The apical ectodermal ridge permits growth and elongation of amniote limb buds; removal causes rapid changes in mesodermal gene expression, patterned cell death, and truncation of the limb. Ectopic fibroblast growth factor (FGF)-2 supplied to the chick apical bud mesoderm after ridge removal will sustain normal gene expression and cell viability, and allow relatively normal limb development. A bioassay for FGFs demonstrated that FGF-2 was the only detectable FGF in chick limb bud extracts. By distribution and bioactivity, FGF-2 is the prime candidate for the chick limb bud apical ridge growth signal.
De Novo and Inherited Deletions of the 5q13 Region in Spinal Muscular Atrophies
Authors: Melki Judith , Lefebvre Suzie , Burglen Lydie , Burlet Philippe , Clermont Olivier , Millasseau Philippe , Reboullet Sophie , Bénichou Bernard , Zeviani Massimo , Le Paslier Denis , Cohen Daniel , Weissenbach Jean , Munnich Arnold
Published: October 2006

Spinal muscular atrophies (SMAs) represent the second most common fatal autosomal recessive disorder after cystic fibrosis. Childhood spinal muscular atrophies are divided into severe (type I) and mild forms (types II and III). By a combination of genetic and physical mapping, a yeast artificial chromosome contig of the 5q13 region spanning the disease locus was constructed that showed the presence of low copy repeats in this region. Allele segregation was analyzed at the closest genetic loci detected by markers C212 and C272 in 201 SMA families. Inherited and de novo deletions were observed in nine unrelated SMA patients. Moreover, deletions were strongly suggested in at least 18 percent of SMA type I patients by the observation of marked heterozygosity deficiency for the loci studied. These results indicate that deletion events are statistically associated with the severe form of spinal muscular atrophy.
Recovery of Visual Response of Injured Adult Rat Optic Nerves Treated with Transglutaminase
Authors: Eitan Shoshana , Solomon Arieh , Lavie Vered , Yoles Eti , Hirschberg David L. , Belkin Michael , Schwartz Michal
Published: October 2006

Failure of axons of the central nervous system in adult mammals to regenerate spontaneously after injury is attributed in part to inhibitory molecules associated with oligodendrocytes. Regeneration of central nervous system axons in fish is correlated with the presence of a transglutaminase. This enzyme dimerizes interleukin-2, and the product is cytotoxic to oligodendrocytes in vitro. Application of this nerve-derived transglutaminase to rat optic nerves, in which the injury had caused the loss of visual evoked potential response to light, promoted the recovery of that response within 6 weeks after injury. Transmission electron microscopy analysis revealed the concomitant appearance of axons in the distal stump of the optic nerve.
Convergent Pathways for Steroid Hormone- and Neurotransmitter-Induced Rat Sexual Behavior
Authors: Mani S. K. , Allen J. M. C. , Clark J. H. , Blaustein J. D. , O'Malley B. W.
Published: October 2006

Estrogen and progesterone modulate gene expression in rodents by activation of intracellular receptors in the hypothalamus, which regulate neuronal networks that control female sexual behavior. However, the neurotransmitter dopamine has been shown to activate certain steroid receptors in a ligand-independent manner. A dopamine receptor stimulant and a D
1
receptor agonist, but not a D
2
receptor agonist, mimicked the effects of progesterone in facilitating sexual behavior in female rats. The facilitatory effect of the neurotransmitter was blocked by progesterone receptor antagonists, a D
1
receptor antagonist, or antisense oligonucleotides to the progesterone receptor. The results suggest that in rodents neurotransmitters may regulate in vivo gene expression and behavior by means of cross-talk with steroid receptors in the brain.
Time-Resolved Detection of Structural Changes During the Photocycle of Spin-Labeled Bacteriorhodopsin
Authors: Steinhoff Heinz-Jürgen , Mollaaghababa Ramin , Altenbach Christian , Hideg Kálmán , Krebs Mark , Khorana H. Gobind , Hubbell Wayne L.
Published: October 2006

Bacteriorhodopsin was selectively spin labeled at residues 72, 101, or 105 after replacement of the native amino acids by cysteine. Only the electron paramagnetic resonance spectrum of the label at 101 was time-dependent during the photocycle. The spectral change rose with the decay of the M intermediate and fell with recovery of the ground state. The transient signal is interpreted as the result of movement in the C-D or E-F interhelical loop, or in both, coincident with protonation changes at the key aspartate 96 residue. These results link the optically characterized intermediates with localized conformational changes in bacteriorhodopsin during the photocycle.
Identification of the
ron
Gene Product as the Receptor for the Human Macrophage Stimulating Protein
Authors: Wang Ming-Hai , Ronsin Christophe , Gesnel Marie-Claude , Coupey Lionel , Skeel Alison , Leonard Edward J. , Breathnach Richard
Published: October 2006

Macrophage-stimulating protein (MSP) is a member of the hepatocyte growth factor-scatter factor (HGF-SF) family. Labeled MSP bound to Madin-Darby canine kidney (MDCK) cells transfected with complementary DNA encoding Ron, a cell membrane protein tyrosine kinase. Cross-linking of
125
I-labeled MSP to transfected cells (MDCK-RE7 cells) and immunoprecipitation by antibodies to Ron revealed a 220-kilodalton complex, a size consistent with that of MSP (80 kilodaltons) cross-linked to the β chain of Ron (150 kilodaltons). The binding of
125
I-labeled MSP to MDCK-RE7 cells was inhibited by unlabeled MSP, but not by HGF-SF. MSP caused phosphorylation of the β chain of Ron and induced migration of MDCK-RE7 cells. These results establish the
ron
gene product as a specific cell-surface receptor for MSP.
A Designed Peptide Ligase for Total Synthesis of Ribonuclease A with Unnatural Catalytic Residues
Authors: Jackson David Y. , Burnier John , Quan Clifford , Stanley Mark , Tom Jeffrey , Wells James A.
Published: October 2006

An engineered variant of subtilisin BPN', termed subtiligase, which efficiently ligates esterified peptides in aqueous solution, was used for the complete synthesis of ribonuclease (RNase) A that contains unnatural catalytic residues. Fully active RNase A (124 residues long) was produced in milligram quantities by stepwise ligation of six esterified peptide fragments (each 12 to 30 residues long) at yields averaging 70 percent per ligation. Variants of RNase A were produced in which the catalytic histidines at positions 12 and 119 were substituted with the unnatural amino acid 4-fluorohistidine, which has a p
K
a
of 3.5 compared to 6.8 for histidine. Large changes in the profile of the pH as it affects rate occurred for the single and double mutants with surprisingly little change in the
k
cat
for either the RNA cleavage or hydrolysis steps. The data indicate that these imidazoles function as general acids and bases, but that the proton transfer steps are not rate-limiting when the imidazoles are present in their correct protonation states. These studies indicate the potential of subtiligase for the blockwise synthesis of large proteins.
Transgenic
X. laevis
Embryos from Eggs Transplanted with Nuclei of Transfected Cultured Cells
Authors: Kroll Kristen L. , Gerhart John C.
Published: October 2006

Transgenic
Xenopus laevis
embryos were produced by transplantation of transfected cultured cell nuclei into unfertilized eggs. A
Xenopus
cell line, X-C, was stably transfected with plasmids containing a hygromycin-resistance gene and genes for either β-galactosidase with a heat shock promoter or chloramphenicol acetyltransferase (CAT) with a muscle-specific actin promoter. Nuclei transplanted from these cells into unfertilized eggs directed development of embryos containing stably integrated copies of the plasmids in each cell. Transgenic embryos showed somite-specific expression of CAT and uniform expression of β-galactosidase. Transgenic embryos produced by nuclear transplantation should be useful for testing the function of cloned genes in amphibian development.
Isolation of the Tomato
Cf-9
Gene for Resistance to
Cladosporium fulvum
by Transposon Tagging
Authors: Jones David A. , Thomas Colwyn M. , Hammond-Kosack Kim E. , Balint-Kurti Peter J. , Jones Jonathan D. G.
Published: October 2006

The tomato
Cf-9
gene confers resistance to infection by races of the fungus
Cladosporium fulvum
that carry the avirulence gene
Avr9
. The
Cf-9
gene was isolated by transposon tagging with the maize transposable element
Dissociation
. The DNA sequence of
Cf-9
encodes a putative membrane-anchored extracytoplasmic glycoprotein. The predicted protein shows homology to the receptor domain of several receptor-like protein kinases in
Arabidopsis
, to antifungal polygalacturonase-inhibiting proteins in plants, and to other members of the leucine-rich repeat family of proteins. This structure is consistent with that of a receptor that could bind Avr9 peptide and activate plant defense.
Efficient Neutralization of Primary Isolates of HIV-1 by a Recombinant Human Monoclonal Antibody
Authors: Burton Dennis R. , Pyati Jayashree , Koduri Raju , Sharp Stephen J. , Thornton George B. , Parren Paul W. H. I. , Sawyer Lynette S. W. , Hendry R. Michael , Dunlop Nancy , Nara Peter L. , Lamacchia Michael , Garratty Eileen , Stiehm E. Richard , Bryson Yvonne J. , Cao Yunzhen , Moore John P. , Ho David D. , Barbas Carlos F.
Published: October 2006

The ability of antibodies to neutralize diverse primary isolates of human immunodeficiency virus-type 1 in vitro has been questioned, with implications for the likely efficacy of vaccines. A recombinant human antibody to envelope glycoprotein gp120 was generated and used to show that primary isolates are not refractory to antibody neutralization. The recombinant antibody neutralized more than 75 percent of the primary isolates tested at concentrations that could be achieved by passive immunization, for example, to interrupt maternal-fetal transmission of virus. The broad specificity and efficacy of the antibody implies the conservation of a structural feature on gp120, which could be important in vaccine design.
Cooperative Display and Relatedness Among Males in a Lek-Mating Bird
Authors: McDonald David B. , Potts Wayne K.
Published: October 2006

Long-tailed manakins mate in leks and cooperate in multiyear male-male partnerships. An alpha male is responsible for virtually all mating, whereas a beta male assists in the courtship displays. Such altruism by the beta male poses a problem for evolutionary theory because most theoretical treatments and empirical examples of cooperative behavior involve kin selection or reciprocity. Here it is shown that alpha and beta partners are not relatives and that reciprocity is not involved. Instead, direct, though long-delayed benefits to beta males are demonstrated, which include rare copulations, ascension to alpha status, and female lek fidelity. These benefits maintain this unusual form of male-male cooperation.
Prevention of T Cell Anergy by Signaling Through the γ
c
Chain of the IL-2 Receptor
Authors: Boussiotis Vassiliki A. , Barber Dwayne L. , Nakarai Takayuki , Freeman Gordon J. , Gribben John G. , Bernstein Gregory M. , D'Andrea Alan D. , Ritz Jerome , Nadler Lee M.
Published: October 2006

When stimulated through their antigen receptor without requisite costimulation, T cells enter a state of antigen-specific unresponsiveness, termed anergy. In this study, signaling through the common γ chain of the interleukin-2 (IL-2), IL-4, and IL-7 receptors in the presence of antigen was found to be sufficient to prevent the induction of anergy. After culture with IL-2, IL-4, or IL-7, Jak3 kinase was tyrosine-phosphorylated, which correlated with the prevention of anergy. Therefore, a signal through the common γ chain may regulate the decision of T cells to either clonally expand or enter a state of anergy.
GDNF: a Potent Survival Factor for Motoneurons Present in Peripheral Nerve and Muscle
Authors: Henderson Christopher E. , Phillips Heidi S. , Pollock Richard A. , Davies Alun M. , Lemeulle Corinne , Armanini Mark , Simmons Laura , Moffet Barbara , Vandlen Richard A. , Koliatsos Vassilis E. , Rosenthal Arnon
Published: October 2006

For survival, embryonic motoneurons in vertebrates depend on as yet undefined neurotrophic factors present in the limb bud. Members of the neurotrophin family are currently the best candidates for such neurotrophic factors, but inactivation of their receptor genes leads to only partial loss of motoneurons, which suggests that other factors are involved. Glial cell line-derived neurotrophic factor (GDNF), originally identified as a trophic factor specific for dopaminergic neurons, was found to be 75-fold more potent than the neurotrophins in supporting the survival of purified embryonic rat motoneurons in culture. GDNF messenger RNA was found in the immediate vicinity of motoneurons during the period of cell death in development. In vivo, GDNF rescues and prevents the atrophy of facial motoneurons that have been deprived of target-derived survival factors by axotomy. GDNF may therefore be a physiological trophic factor for spinal motoneurons. Its potency and specificity in vitro and in vivo also make it a good candidate for treatment of motoneuron disease.
DNA Sequence from Cretaceous Period Bone Fragments
Authors: Woodward Scott R. , Weyand Nathan J. , Bunnell Mark
Published: October 2006

DNA was extracted from 80-million-year-old bone fragments found in strata of the Upper Cretaceous Blackhawk Formation in the roof of an underground coal mine in eastern Utah. This DNA was used as the template in a polymerase chain reaction that amplified and sequenced a portion of the gene encoding mitochondrial cytochrome b. These sequences differ from all other cytochrome b sequences investigated, including those in the GenBank and European Molecular Biology Laboratory databases. DNA isolated from these bone fragments and the resulting gene sequences demonstrate that small fragments of DNA may survive in bone for millions of years.
The Role of Hsp70 in Conferring Unidirectionality on Protein Translocation into Mitochondria
Authors: Ungermann Christian , Neupert Walter , Cyr Douglas M.
Published: October 2006

The entry of segments of preproteins of defined lengths into the matrix space of mitochondria was studied. The mitochondrial chaperone Hsp70 (mtHsp70) interacted with proteins emerging from the protein import channel and stabilized translocation intermediates across the membranes in an adenosine triphosphate-dependent fashion. The chaperone bound to the presequence and mature parts of preproteins. In the absence of mtHsp70 binding, preproteins with less than 30 to 40 residues in the matrix diffused out of mitochondria. Thus, protein translocation was reversible up to a late stage. The import channels in both mitochondrial membranes constitute a passive pore that interacts weakly with polypeptide chains entering the matrix.
Modulation of Epithelial Cell Growth by Intraepithelial γδ T Cells
Authors: Boismenu Richard , Havran Wendy L.
Published: October 2006

The role played in immune surveillance by γδ T cells residing in various epithelia has not been clear. It is shown here that activated γδ T cells obtained from skin and intestine express the epithelial cell mitogen keratinocyte growth factor (KGF). In contrast, intraepithelial αβ T cells, as well as all lymphoid αβ and γδ T cell populations tested, did not produce KGF or promote the growth of cultured epithelial cells. These results suggest that intraepithelial γδ T cells function in surveillance and in repair of damaged epithelial tissues.
Clonal Divergence in
Escherichia coli
as a Result of Recombination, Not Mutation
Authors: Guttman David S. , Dykhuizen Daniel E.
Published: October 2006

Nucleotide sequence analysis was performed on 12 natural isolates of
Escherichia coli
in four loci located in close proximity on the chromosome. A comparison of gene genealogies indicated that three recombination events have occurred in a subset of the strains (ECOR group A) in the time since their divergence from a common ancestor, while during the same time, no mutational divergence has occurred. The common ancestor of this subset existed no more than 2400 years ago, and recombination was shown to occur at a rate of 5.0 × 10
-9
changes per nucleotide per generation—50-fold higher than the mutation rate. Thus, recombination has been the dominant force driving the clonal divergence of the ECOR group A strains and must be considered a significant factor in structuring
E. coli
populations.
Catalytic Site Components Common to Both Splicing Steps of a Group II Intron
Authors: Chanfreau Guillaume , Jacquier Alain
Published: October 2006

The splicing of group II introns occurs in two steps involving substrates with different chemical configurations. The question of whether these two steps are catalyzed by a single or two separate active sites is a matter of debate. Here, certain bases and phosphate oxygen atoms at conserved positions in domain V of a group II self-splicing intron are shown to be required for catalysis of both splicing steps. These results show that the active sites catalyzing the two steps must, at least, share common components, ruling out the existence of two completely distinct active sites in group II introns.
Potentiated Transmission and Prevention of Further LTP by Increased CaMKII activity in Postsynaptic Hippocampal Slice Neurons
Authors: Pettit D. L. , Perlman S. , Malinow R.
Published: October 2006

Calcium-calmodulin-dependent protein kinase II (CaMKII) is a necessary component of the cellular machinery underlying learning and memory. Here, a constitutively active form of this enzyme, CaMKII(1-290), was introduced into neurons of hippocampal slices with a recombinant vaccinia virus to test the hypothesis that increased postsynaptic activity of this enzyme is sufficient to produce long-term synaptic potentiation (LTP), a prominent cellular model of learning and memory. Postsynaptic expression of CaMKII(1-290) increased CaMKII activity, enhanced synaptic transmission, and prevented more potentiation by an LTP-inducing protocol. These results, together with previous studies, suggest that postsynaptic CaMKII activity is necessary and sufficient to generate LTP.
Regulation of MHC Class II Expression by Interferon-γ Mediated by the Transactivator Gene CIITA
Authors: Steimle Viktor , Siegrist Claire-Anne , Mottet Annick , Lisowska-Grospierre Barbara , Mach Bernard
Published: October 2006

Major histocompatibility complex (MHC) class II genes are expressed constitutively in only a few cell types, but they can be induced in the majority of them, in particular by interferon-γ (IFN-γ). The MHC class II transactivator gene CIITA is defective in a form of primary MHC class II deficiency. Here it is shown that CIITA expression is controlled and induced by IFN-γ. A functional CIITA gene is necessary for class II induction, and transfection of CIITA is sufficient to activate expression of MHC class II genes in class II-negative cells in the absence of IFN-γ. CIITA is therefore a general regulator of both inducible and constitutive MHC class II expression.
Stimulation of GAL4 Derivative Binding to Nucleosomal DNA by the Yeast SWI/SNF Complex
Authors: Côté Jacques , Quinn Janet , Workman Jerry L. , Peterson Craig L.
Published: October 2006

The SWI/SNF protein complex is required for the enhancement of transcription by many transcriptional activators in yeast. Here it is shown that the purified SWI/SNF complex is composed of 10 subunits and includes the SWI1, SWI2/SNF2, SWI3, SNF5, and SNF6 gene products. The complex exhibited DNA-stimulated adenosine triphosphatase (ATPase) activity, but lacked helicase activity. The SWI/SNF complex caused a 10- to 30-fold stimulation in the binding of GAL4 derivatives to nucleosomal DNA in a reaction that required adenosine triphosphate (ATP) hydrolysis but was activation domain-independent. Stimulation of GAL4 binding by the complex was abolished by a mutant SWI2 subunit, and was increased by the presence of a histone-binding protein, nucleoplasmin. A direct ATP-dependent interaction between the SWI/SNF complex and nucleosomal DNA was detected. These observations suggest that a primary role of the SWI/SNF complex is to promote activator binding to nucleosomal DNA.
Identification of the Target of a Transcription Activator Protein by Protein-Protein Photocrosslinking
Authors: Chen Yan , Ebright Yon W. , Ebright Richard H.
Published: October 2006

Here it is shown, with the use of protein-protein photocrosslinking, that the carboxyl-terminal region of the α subunit of RNA polymerase (RNAP) is in direct physical proximity to the activating region of the catabolite gene activator protein (CAP) in the ternary complex of the
lac
promoter, RNAP, and CAP. These results strongly support the proposal that transcription activation by CAP involves protein-protein contact between the carboxyl-terminal region of the α subunit and the activating region of CAP.
Testing the Exon Theory of Genes: The Evidence from Protein Structure
Authors: Stoltzfus Arlin , Spencer David F. , Zuker Michael , Logsdon John M. , Doolittle W. Ford
Published: October 2006

A tendency for exons to correspond to discrete units of protein structure in protein-coding genes of ancient origin would provide clear evidence in favor of the exon theory of genes, which proposes that split genes arose not by insertion of introns into unsplit genes, but from combinations of primordial mini-genes (exons) separated by spacers (introns). Although putative examples of such correspondence have strongly influenced previous debate on the origin of introns, a general correspondence has not been rigorously proved. Objective methods for detecting correspondences were developed and applied to four examples that have been cited previously as evidence of the exon theory of genes. No significant correspondence between exons and units of protein structure was detected, suggesting that the putative correspondence does not exist and that the exon theory of genes is untenable.
Ability of HIV to Promote a T
H
1 to T
H
0 Shift and to Replicate Preferentially in T
H
2 and T
H
0 Cells
Authors: Maggi Enrico , Mazzetti Marcello , Ravina Adriana , Annunziato Francesco , de Carli Marco , Piccinni Marie Pierre , Manetti Roberto , Carbonari Maurizio , Pesce Anna Maria , del Prete Gianfranco , Romagnani Sergio
Published: October 2006

Both interferon γ (IFN-γ) produced by T helper 1 (T
H
1) lymphocytes and interleukin-4 (IL-4) produced by T
H
2 lymphocytes were reduced in either bulk circulating mononuclear cells or mitogen-induced CD4
+
T cell clones from the peripheral blood of individuals infected with human immunodeficiency virus (HIV). There was a preferential reduction in clones producing IL-4 and IL-5 in the advanced phases of infection. However, enhanced proportions of CD4
+
T cell clones producing both T
H
1-type and T
H
2-type cytokines (T
H
0 clones) were generated from either skin-infiltrating T cells that had been activated in vivo or peripheral blood T cells stimulated by antigen in vitro when cells were isolated from HIV-infected individuals. All T
H
2 and most T
H
0 clones supported viral replication, although viral replication was not detected in any of the T
H
1 clones infected in vitro with HIV. These results suggest that HIV (i) does not induce a definite T
H
1 to T
H
2 switch, but can favor a shift to the T
H
0 phenotype in response to recall antigens, and (ii) preferentially replicates in CD4
+
T cells producing T
H
2-type cytokines (T
H
2 and T
H
0).
The Thermal Grill Illusion: Unmasking the Burn of Cold Pain
Authors: Craig A. D. , Bushnell M. C.
Published: October 2006

In Thunberg's thermal grill illusion, first demonstrated in 1896, a sensation of strong, often painful heat is elicited by touching interlaced warm and cool bars to the skin. Neurophysiological recordings from two classes of ascending spinothalamic tract neurons that are sensitive to innocuous or noxious cold showed differential responses to the grill. On the basis of these results, a simple model of central disinhibition, or unmasking, predicted a quantitative correspondence between grill-evoked pain and cold-evoked pain, which was verified psychophysically. This integration of pain and temperature can explain the thermal grill illusion and the burning sensation of cold pain and may also provide a basis for the cold-evoked, burning pain of the classic thalamic pain syndrome.
Risking Everything? Risk Behavior, Behavior Change, and AIDS
Authors: Aggleton Peter , O'Reilly Kevin , Slutkin Gary , Davies Peter
Published: October 2006

Inquiry into the determinants of risk-related sexual behavior is important for the development of interventions to reduce the incidence of new cases of human immunodeficiency virus infection. Recent social and behavioral research has revealed much about the individual and social factors influencing risk-taking. Findings from these studies have been important in the development of new educational and community-based interventions for communities at risk in the developed and developing worlds.
Effect of the Nigrostriatal Dopamine System on Acquired Neural Responses in the Striatum of Behaving Monkeys
Authors: Aosaki Toshihiko , Graybiel Ann M. , Kimura Minoru
Published: October 2006

Dysfunction of the nigrostriatal dopamine system results in marked disorders of movement such as occur in Parkinson's disease. Functions of this dopamine-containing projection system were examined in monkeys trained in a classical conditioning task, and the effects of striatal dopamine depletion were tested. Unilateral dopamine loss substantially reduced the acquired sensory responsiveness of striatal neurons monitored electrophysiologically. This effect was ipsilateral and selective, and could be reversed by apomorphine. These results suggest that the primate nigrostriatal system modulates expression of neuronal response plasticity in the striatum during sensorimotor learning.
Autoantibodies to Glutamate Receptor GluR3 in Rasmussen's Encephalitis
Authors: Rogers Scott W. , Andrews P. Ian , Gahring Lorise C. , Whisenand Teri , Cauley Keith , Crain Barbara , Hughes Thomas E. , Heinemann Stephen F. , McNamara James O.
Published: October 2006

Rasmussen's encephalitis is a progressive childhood disease of unknown cause characterized by severe epilepsy, hemiplegia, dementia, and inflammation of the brain. During efforts to raise antibodies to recombinant glutamate receptors (GluRs), behaviors typical of seizures and histopathologic features mimicking Rasmussen's encephalitis were found in two rabbits immunized with GluR3 protein. A correlation was found between the presence of Rasmussen's encephalitis and serum antibodies to GluR3 detected by protein immunoblot analysis and by immunoreactivity to transfected cells expressing GluR3. Repeated plasma exchanges in one seriously ill child transiently reduced serum titers of GluR3 antibodies, decreased seizure frequency, and improved neurologic function. Thus, GluR3 is an autoantigen in Rasmussen's encephalitis, and an autoimmune process may underlie this disease.
Preferential Nucleosome Assembly at DNA Triplet Repeats from the Myotonic Dystrophy Gene
Authors: Wang Yuh-Hwa , Amirhaeri Sorour , Kang Seongman , Wells Robert D. , Griffith Jack D.
Published: October 2006

The expansion of CTG repeats in DNA occurs in or near genes involved in several human diseases, including myotonic dystrophy and Huntington's disease. Nucleosomes, the basic structural element of chromosomes, consist of 146 base pairs of DNA coiled about an octamer of histone proteins and mediate general transcriptional repression. Electron microscopy was used to examine in vitro the nucleosome assembly of DNA containing repeating CTG triplets. The efficiency of nucleosome formation increased with expanded triplet blocks, suggesting that such blocks may repress transcription through the creation of stable nucleosomes.
Pf1 Virus Structure: Helical Coat Protein and DNA with Paraxial Phosphates
Authors: Liu David J. , Day Loren A.
Published: October 2006

The helical path of the DNA in filamentous bacteriophage Pf1 was deduced from different kinds of existing structural information, including results from x-ray fiber diffraction. The DNA has the same pitch, 16 angstroms, as the surrounding helix of protein subunits; the rise and rotation per nucleotide are 6.1 angstroms and 132 degrees, respectively; and the phosphates are 2.5 angstroms from the axis. The DNA in Pf1 is, therefore, the most extended and twisted DNA structure known. On the basis of the DNA structure and extensive additional information about the protein, a model of the virion is proposed. In the model, the DNA bases reach out, into the protein, and the lysine and arginine side chains reach in, between the DNA bases, to stabilize the paraxial phosphate charges; the conformation of the protein subunit is a combination of α and 3
10
helices.