bluuebunny/crossref_metadata_2025 huggingface dataset:
FAP-1: A Protein Tyrosine Phosphatase That Associates with Fas
Authors: Sato Takaaki , Irie Shinji , Kitada Shinichi , Reed John C.
Published: October 2006

Fas is a cell surface receptor that controls a poorly understood signal transduction pathway that leads to cell death by means of apoptosis. A protein tyrosine phosphatase, FAP-1, capable of interacting with the cytosolic domain of Fas, was identified. The carboxyl terminal 15 amino acids of Fas are necessary and sufficient for interaction with FAP-1. FAP-1 expression is highest in tissues and cell lines that are relatively resistant to Fas-mediated cytotoxicity. Gene transfer-mediated elevations in FAP-1 partially abolished Fas-induced apoptosis in a T cell line. These findings are consistent with an inhibitory effect of FAP-1 on Fas signal transduction.
FGF Binding and FGF Receptor Activation by Synthetic Heparan-Derived Di- and Trisaccharides
Authors: Ornitz David M. , Herr Andrew B. , Nilsson Marianne , Westman Jacob , Svahn Carl-Magnus , Waksman Gabriel
Published: October 2006

Fibroblast growth factors (FGFs) require a polysaccharide cofactor, heparin or heparan sulfate (HS), for receptor binding and activation. To probe the molecular mechanism by which heparin or HS (heparin/HS) activates FGF, small nonsulfated oligosaccharides found within heparin/HS were assayed for activity. These synthetic and isomerically pure compounds can activate the FGF signaling pathway. The crystal structures of complexes between FGF and these heparin/HS oligosaccharides reveal several binding sites on FGF and constrain possible mechanisms by which heparin/HS can activate the FGF receptor. These studies establish a framework for the molecular design of compounds capable of modulating FGF activity.
Role of B61, the Ligand for the Eck Receptor Tyrosine Kinase, in TNF-α-Induced Angiogenesis
Authors: Pandey Akhilesh , Shao Haining , Marks Rory M. , Polverini Peter J. , Dixit Vishva M.
Published: October 2006

B61, a cytokine-inducible endothelial gene product, is the ligand for the Eck receptor protein tyrosine kinase (RPTK). Expression of a B61-immunoglobulin chimera showed that B61 could act as an angiogenic factor in vivo and a chemoattractant for endothelial cells in vitro. The Eck RPTK was activated by tumor necrosis factor-α (TNF-α) through induction of B61, and an antibody to B61 attenuated angiogenesis induced by TNF-α but not by basic fibroblast growth factor. This finding suggests the existence of an autocrine or paracrine loop involving activation of the Eck RPTK by its inducible ligand B61 after an inflammatory stimulus, the net effect of which would be to promote angiogenesis, a hallmark of chronic inflammation.
CD1 Recognition by Mouse NK1
+
T Lymphocytes
Authors: Bendelac Albert , Lantz Olivier , Quimby Mary E. , Yewdell Jonathan W. , Bennink Jack R. , Brutkiewicz Randy R.
Published: October 2006

Rare major histocompatibility complex (MHC) class I-like CD1-specific T cells have been isolated from human blood, but it has not been determined whether these clones are part of a defined subset of CD1-specific T cells selected during T cell development, or whether their recognition of CD1 is a fortuitous cross-reaction. In mice, an entire subset of αβ thymocytes with a unique phenotype was found to be CD1-specific. This particular subset, and its human counterpart, provide evidence that CD1 has a general role in selecting and interacting with specialized αβ T cells.
Receptor Endocytosis and Dendrite Reshaping in Spinal Neurons After Somatosensory Stimulation
Authors: Mantyh Patrick W. , DeMaster Eric , Malhotra Amit , Ghilardi  , Rogers Scott D. , Mantyh Christopher R. , Liu Hantao , Basbaum Allan I. , Vigna  , Maggio John E. , Simone Donald A.
Published: October 2006

In vivo somatosensory stimuli evoked the release of substance P from primary afferent neurons that terminate in the spinal cord and stimulated endocytosis of substance P receptors in rat spinal cord neurons. The distal dendrites that showed substance P receptor internalization underwent morphological reorganization, changing from a tubular structure to one characterized by swollen varicosities connected by thin segments. This internalization and dendritic structural reorganization provided a specific image of neurons activated by substance P. Thus receptor internalization can drive reversible structural changes in central nervous system neurons in vivo. Both of these processes may be involved in neuronal plasticity.
The Culture of Credit
Authors: Cohen Jon
Published: October 2006

Scientific ideals call for collaboration and sharing. But in today's competitive scientific enterprise, a tremendous premium is placed on individual credit, setting the stage for conflict.
Structural Basis for Phosphotyrosine Peptide Recognition by Protein Tyrosine Phosphatase 1B
Authors: Jia Zongchao , Barford David , Flint Andrew J. , Tonks Nicholas K.
Published: October 2006

The crystal structures of a cysteine-215→serine mutant of protein tyrosine phosphatase 1B complexed with high-affinity peptide substrates corresponding to an autophosphorylation site of the epidermal growth factor receptor were determined. Peptide binding to the protein phosphatase was accompanied by a conformational change of a surface loop that created a phosphotyrosine recognition pocket and induced a catalytically competent form of the enzyme. The phosphotyrosine side chain is buried within the protein and anchors the peptide substrate to its binding site. Hydrogen bonds between peptide main-chain atoms and the protein contribute to binding affinity, and specific interactions of acidic residues of the peptide with basic residues on the surface of the enzyme confer sequence specificity.
Requirement for TNF-α and IL-1α in Fetal Thymocyte Commitment and Differentiation
Authors: Zúñiga-Pflücker Juan Carlos , Jiang Di , Lenardo Michael J.
Published: October 2006

CD25 expression occurs early in thymocyte differentiation. The mechanism of induction of CD25 before T cell receptor rearrangement and the importance of this mechanism for T cell development are unknown. In a thymus reconstitution assay, tumor necrosis factor α (TNF-α) and interleukin-1α (IL-1α), two cytokines produced within the thymic microenvironment, induced CD25 expression on early immature thymocytes. Either TNF-α or IL-1α was necessary for further thymocyte maturation and CD4
+
CD8
+
differentiation. In irradiated mice reconstituted with CD117
+
CD25
+
thymocytes, commitment to the T cell lineage was marked by the loss of precursor multipotency.
Peptide Binding and Presentation by Mouse CD1
Authors: Castaño A. Raúl , Tangri Shabnam , Miller Jeffrey E. W. , Holcombe Hilda R. , Jackson Michael R. , Huse William D. , Kronenberg Mitchell , Peterson Per A.
Published: October 2006

CD1 molecules are distantly related to the major histocompatibility complex (MHC) class I proteins. They are of unknown function. Screening random peptide phage display libraries with soluble empty mouse CD1 (mCD1) identified a peptide binding motif. It consists of three anchor positions occupied by aromatic or bulky hydrophobic amino acids. Equilibrium binding studies demonstrated that mCD1 binds peptides containing the appropriate motif with relatively high affinity. However, in contrast to classical MHC class I molecules, strong binding to mCD1 required relatively long peptides. Peptide-specific, mCD1-restricted T cell responses can be raised, which suggests that the findings are of immunological significance.
Whole-Genome Random Sequencing and Assembly of
Haemophilus influenzae
Rd
Authors: Fleischmann Robert D. , Adams Mark D. , White Owen , Clayton Rebecca A. , Kirkness Ewen F. , Kerlavage Anthony R. , Bult Carol J. , Tomb Jean-Francois , Dougherty Brian A. , Merrick Joseph M. , McKenney Keith , Sutton Granger , FitzHugh, Will , Fields Chris , Gocayne Jeannine D. , Scott John , Shirley Robert , Liu Li-lng , Glodek Anna , Kelley Jenny M. , Weidman Janice F. , Phillips Cheryl A. , Spriggs Tracy , Hedblom Eva , Cotton Matthew D. , Utterback Teresa R. , Hanna Michael C. , Nguyen David T. , Saudek Deborah M. , Brandon Rhonda C. , Fine Leah D. , Fritchman Janice L. , Fuhrmann Joyce L. , Geoghagen N. S. M. , Gnehm Cheryl L. , McDonald Lisa A. , Small Keith V. , Fraser Claire M. , Smith Hamilton O. , Venter J. Craig
Published: October 2006

An approach for genome analysis based on sequencing and assembly of unselected pieces of DNA from the whole chromosome has been applied to obtain the complete nucleotide sequence (1,830,137 base pairs) of the genome from the bacterium
Haemophilus influenzae
Rd. This approach eliminates the need for initial mapping efforts and is therefore applicable to the vast array of microbial species for which genome maps are unavailable. The
H. influenzae
Rd genome sequence (Genome Sequence DataBase accession number L42023) represents the only complete genome sequence from a free-living organism.
Frequency and Distribution of DNA Uptake Signal Sequences in the
Haemophilus influenzae
Rd Genome
Authors: Smith Hamilton O. , Tomb Jean-Francois , Dougherty Brian A. , Fleischmann Robert D. , Venter J. Craig
Published: October 2006

The naturally transformable, Gram-negative bacterium
Haemophilus influenzae
Rd preferentially takes up DNA of its own species by recognizing a 9-base pair sequence, 5′-AAGTGCGGT, carried in multiple copies in its chromosome. With the availability of the complete genome sequence, 1465 copies of the 9-base pair uptake site have been identified. Alignment of these sites unexpectedly reveals an extended consensus region of 29 base pairs containing the core 9-base pair region and two downstream 6-base pair A/T-rich regions, each spaced about one helix turn apart. Seventeen percent of the sites are in inverted repeat pairs, many of which are located downstream to gene termini and are capable of forming stem-loop structures in messenger RNA that might function as signals for transcription termination.
Potential Mechanism for Sustained Antiretroviral Efficacy of AZT-3TC Combination Therapy
Authors: Larder Brendan A. , Kemp Sharon D. , Harrigan P. Richard
Published: October 2006

Combinations of antiretroviral drugs that prevent or delay the appearance of drug-resistant human immunodeficiency virus-type 1 (HIV-1) mutants are urgently required. Mutants resistant to 3′-azidothymidine (AZT, zidovudine) became phenotypically sensitive in vitro by mutation of residue 184 of viral reverse transcriptase to valine, which also induced resistance to (-)2′-deoxy-3′-thiacytidine (3TC). Furthermore, AZT-3TC coresistance was not observed during extensive in vitro selection with both drugs. In vivo AZT-3TC combination therapy resulted in a markedly greater decrease in serum HIV-1 RNA concentrations than treatment with AZT alone, even though valine-184 mutants rapidly emerged. Most samples assessed from the combination group remained AZT sensitive at 24 weeks of therapy, consistent with in vitro mutation studies.
A Mechanism for the Specific Immunogenicity of Heat Shock Protein-Chaperoned Peptides
Authors: Suto Ryuichiro , Srivastava Pramod K.
Published: October 2006

Endogenously synthesized antigenic determinants are generally presented on major histocompatibility complex (MHC) class I molecules, whereas exogenous determinants are presented by MHC class II molecules. Here, it is shown that exogenous antigens chaperoned by a heat shock protein can be channeled into the endogenous pathway, presented by MHC class I molecules, and recognized by CD8
+
T lymphocytes. This pathway is functional only in a subset of macrophages among the cell types tested. These observations provide a basis for the tumor-specific and virus-specific immunogenicity of cognate heat shock protein preparations and offer a mechanism for the classical phenomenon of cross-priming.
Nicotine Enhancement of Fast Excitatory Synaptic Transmission in CNS by Presynaptic Receptors
Authors: McGehee Daniel S. , Heath Mark J. S. , Gelber Shari , Devay Piroska , Role Lorna W.
Published: October 2006

The behavioral and cognitive effects of nicotine suggest that nicotinic acetylcholine receptors (nAChRs) participate in central nervous system (CNS) function. Although nAChR subunit messenger RNA (mRNA) and nicotine binding sites are common in the brain, there is little evidence for synapses mediated by nAChRs in the CNS. To test whether CNS nAChRs might modify rather than mediate transmission, the regulation of excitatory synaptic transmission by these receptors was examined. Nanomolar concentrations of nicotine enhanced both glutamatergic and cholinergic synaptic transmission by activation of presynaptic nAChRs that increased presynaptic [Ca
2+
]
i
. Pharmacological and subunit deletion experiments reveal that these presynaptic nAChRs include the α7 subunit. These findings reveal that CNS nAChRs enhance fast excitatory transmission, providing a likely mechanism for the complex behavioral effects of nicotine.
Activation of Dual T Cell Signaling Pathways by the Chemokine RANTES
Authors: Bacon Kevin B. , Premack Brett A. , Gardner Phyllis , Schall Thomas J.
Published: October 2006

The chemokine RANTES induced biphasic mobilization of Ca
2+
in T cells. The initial peak, a transient increase in cytosolic Ca
2+
mediated by a heterotrimeric guanine nucleotide-binding protein (G protein)-coupled pathway, was associated predominantly with chemotaxis. The second peak, Ca
2+
release and sustained influx dependent on protein tyrosine kinases, was associated with a spectrum of cellular responses—Ca
2+
channel opening, interleukin-2 receptor expression, cytokine release, and T cell proliferation—characteristic of T cell receptor activation. Other chemokines did not produce these responses. Thus, in addition to inducing chemotaxis, RANTES can act as an antigen-independent activator of T cells in vitro.
Regulated Subcellular Distribution of the NR1 Subunit of the NMDA Receptor
Authors: Ehlers Michael D. , Tingley Whittemore G. , Huganir Richard L.
Published: October 2006

NMDA (
N
-methyl -D-aspartate) receptors are selectively localized at the postsynaptic membrane of excitatory synapses in the mammalian brain. The molecular mechanisms underlying this localization were investigated by expressing the NR1 subunit of the NMDA receptor in fibroblasts. NR1 splice variants containing the first COOH-terminal exon cassette (NR1A and NR1D) were located in discrete, receptor-rich domains associated with the plasma membrane. NR1 splice variants lacking this exon cassette (NR1C and NR1E) were distributed throughout the cell, with large amounts of NR1 protein present in the cell interior. Insertion of this exon cassette into the COOH-terminus of the GluR1 AMPA (α-amino-3-hydroxy-5-methyl-4-isoxazole propionate) receptor was sufficient to cause GluR1 to be localized to discrete, receptor-rich domains. Furthermore, protein kinase C phosphorylation of specific serines within this exon disrupted the receptor-rich domains. These results demonstrate that amino acid sequences contained within the NR1 molecule serve to localize this receptor subunit to discrete membrane domains in a manner that is regulated by alternative splicing and protein phosphorylation.
Domain Interaction Between NMDA Receptor Subunits and the Postsynaptic Density Protein PSD-95
Authors: Kornau Hans-Christian , Schenker Leslie T. , Kennedy Mary B. , Seeburg Peter H.
Published: October 2006

The
N
-methyl-D-aspartate (NMDA) receptor subserves synaptic glutamate-induced transmission and plasticity in central neurons. The yeast two-hybrid system was used to show that the cytoplasmic tails of NMDA receptor subunits interact with a prominent postsynaptic density protein PSD-95. The second PDZ domain in PSD-95 binds to the seven-amino acid, COOH-terminal domain containing the terminal
t
SXV motif (where S is serine, X is any amino acid, and V is valine) common to NR2 subunits and certain NR1 splice forms. Transcripts encoding PSD-95 are expressed in a pattern similar to that of NMDA receptors, and the NR2B subunit co-localizes with PSD-95 in cultured rat hippocampal neurons. The interaction of these proteins may affect the plasticity of excitatory synapses.
Understanding C-H Bond Oxidations: H⋅ and H
-
Transfer in the Oxidation of Toluene by Permanganate
Authors: Gardner Kimberly A. , Mayer James M.
Published: October 2006

The oxidation of toluene by permanganate has been studied as a model for the oxidation of C-H bonds by metal reagents, metalloenzymes, and metal oxide surfaces. In water, the reaction proceeds by hydride (H
-
) transfer from toluene to a permanganate oxygen, whereas in toluene solution, permanganate abstracts a hydrogen atom (H⋅). The ability of permanganate to abstract a hydrogen atom is rationalized on the basis of the strong O-H bond formed on H⋅ addition to permanganate. This approach allows understanding and prediction of the rates of hydrogen atom transfer from substrates to metal active sites.
A Specialized Pathway Affecting Virulence Glycoconjugates of
Leishmania
Authors: Descoteaux Albert , Luo Ya , Turco Salvatore J. , Beverley Stephen M.
Published: October 2006

For virulence and transmission, the protozoan parasite
Leishmania
must assemble a complex glycolipid on the cell surface, the lipophosphoglycan (LPG). Functional complementation identified the gene
LPG2
, which encodes an integral Golgi membrane protein implicated in intracellular compartmentalization of LPG biosynthesis.
Ipg2
-
mutants lack only characteristic disaccharide-phosphate repeats, normally present on both LPG and other surface or secreted molecules considered critical for infectivity. In contrast, a related yeast gene,
VAN2/VRG4
, is essential and required for general Golgi function. These results suggest that
LPG2
participates in a specialized virulence pathway, which may offer an attractive target for chemotherapy.
Common Virulence Factors for Bacterial Pathogenicity in Plants and Animals
Authors: Rahme Laurence G. , Stevens Emily J. , Wolfort Sean F. , Shao Jing , Tompkins Ronald G. , Ausubel Frederick M.
Published: October 2006

A
Pseudomonas aeruginosa
strain (UCBPP-PA14) is infectious both in an Arabidopsis thaliana leaf infiltration model and in a mouse full-thickness skin burn model. UCBPP-PA14 exhibits ecotype specificity for
Arabidopsis
, causing a range of symptoms from none to severe in four different ecotypes. In the mouse model, UCBPP-PA14 is as lethal as other well-studied
P. aeruginosa
strains. Mutations in the UCBPP-PA14
toxA
,
plcS
, and
gacA
genes resulted in a significant reduction in pathogenicity in both hosts, indicating that these genes encode virulence factors required for the full expression of pathogenicity in both plants and animals.
Sex Differences in Mental Test Scores, Variability, and Numbers of High-Scoring Individuals
Authors: Hedges Larry V. , Nowell Amy
Published: October 2006

Sex differences in central tendency, variability, and numbers of high scores on mental tests have been extensively studied. Research has not always seemed to yield consistent results, partly because most studies have not used representative samples of national populations. An analysis of mental test scores from six studies that used national probability samples provided evidence that although average sex differences have been generally small and stable over time, the test scores of males consistently have larger variance. Except in tests of reading comprehension, perceptual speed, and associative memory, males typically outnumber females substantially among high-scoring individuals.
Liquid to Hexatic to Crystalline Order in Langmuir-Blodgett Films
Authors: Viswanathan Ravishankar , Madsen Lars L. , Zasadzinski Joseph A. , Schwartz Daniel K.
Published: October 2006

Atomic force microscope images of zinc arachidate (ZnA
2
) Langmuir-Blodgett films show that three- and five-layer films are "hexatic," with long-range bond-orientational order and short-range positional correlations of three to five lattice repeats. The monolayer in contact with the substrate is disordered. Films of seven or more layers of ZnA
2
are crystalline. A population of dislocations, most likely originating at the substrate, disrupts the positional but not the orientational order of the lattice, leading to hexatic layers intermediate between crystal and liquid. The influence of the substrate propagates farther into ZnA
2
films than into cadmium arachidate films because the molecular cohesion is much weaker in ZnA
2
than in cadmium arachidate, as evidenced by a less dense molecular packing.
Rational Design of Peptide Antibiotics by Targeted Replacement of Bacterial and Fungal Domains
Authors: Stachelhaus Torsten , Schneider Axel , Marahiel Mohamed A.
Published: October 2006

Peptide synthetases involved in the nonribosomal synthesis of peptide secondary metabolites possess a highly conserved domain structure. The arrangement of these domains within the multifunctional enzymes determines the number and order of the amino acid constituents of the peptide product. A general approach has been developed for targeted substitution of amino acid-activating domains within the
srfA
operon, which encodes the protein templates for the synthesis of the lipopeptide antibiotic surfactin in
Bacillus subtilis
. Exchange of domain-coding regions of bacterial and fungal origin led to the construction of hybrid genes that encoded peptide synthetases with altered amino acid specificities and the production of peptides with modified amino acid sequences.
Conversion of Bacteriorhodopsin into a Chloride Ion Pump
Authors: Sasaki Jun , Brown Leonid S. , Chon Young-Shin , Kandori Hideki , Maeda Akio , Needleman Richard , Lanyi Janos K.
Published: October 2006

In the light-driven proton pump bacteriorhodopsin, proton transfer from the retinal Schiff base to aspartate-85 is the crucial reaction of the transport cycle. In halorhodopsin, a light-driven chloride ion pump, the equivalent of residue 85 is threonine. When aspartate-85 was replaced with threonine, the mutated bacteriorhodopsin became a chloride ion pump when expressed in
Halobacterium salinarium
and, like halorhodopsin, actively transported chloride ions in the direction opposite from the proton pump. Chloride was bound to it, as revealed by large shifts of the absorption maximum of the chromophore, and its photointermediates included a red-shifted state in the millisecond time domain, with its amplitude and decay rate dependent on chloride concentration. Bacteriorhodopsin and halorhodopsin thus share a common transport mechanism, and the interaction of residue 85 with the retinal Schiff base determines the ionic specificity.
The TBP-TFIIA Interaction in the Response to Acidic Activators in Vivo
Authors: Stargell Laurie A. , Struhl Kevin
Published: October 2006

A yeast TBP mutant (N2-1) is described here that is defective specifically in responding to acidic activators in vivo. N2-1 does not support activation by Gal4, Ace1, and Gcn4, but appears unaffected for constitutive transcription, repression by the Cyc8-Tup1 and Not complexes, and transcription by polymerase I (Pol) and Pol III. In vitro, N2-1 fails to interact with TFIIA, but it associates normally with a TATA element, an acidic activation domain, and TFIIB. Fusion of the small subunit of TFIIA to N2-1 restores activation function in vivo. Thus, an efficient interaction between TBP and TFIIA is required for transcriptional activation in vivo.
Tissue- and Species-Specific Expression of sp56, a Mouse Sperm Fertilization Protein
Authors: Bookbinder L. H. , Cheng A. , Bleil J. D.
Published: October 2006

Mouse sperm recognize and bind to ZP3, one of three glycoproteins in the egg's zona pellucida. A mouse sperm protein, sp56, was identified that has the characteristics expected of the sperm protein responsible for recognition of ZP3. The complementary DNA encoding sp56 was isolated, and its primary sequence indicates that sp56 is a member of a superfamily of protein receptors. It was shown that sp56 expression is restricted to mouse spermatids and that the presence or absence of sp56 on sperm from different species accounts for species specificity of sperm-egg recognition in mice.
HERG, a Human Inward Rectifier in the Voltage-Gated Potassium Channel Family
Authors: Trudeau Matthew C. , Warmke Jeffrey W. , Ganetzky Barry , Robertson Gail A.
Published: October 2006

In contrast to other members of the Eag family of voltage-gated, outwardly rectifying potassium channels, the human
eag
-related gene (
HERG
) has now been shown to encode an inwardly rectifying potassium channel. The properties of HERG channels are consistent with the gating properties of Eag-related and other outwardly rectifying, S4-containing potassium channels, but with the addition of an inactivation mechanism that attenuates potassium efflux during depolarization. Because mutations in HERG cause a form of long-QT syndrome, these properties of HERG channel function may be critical to the maintenance of normal cardiac rhythmicity.
Regulation of Human Leukocyte p21-Activated Kinases Through G Protein—Coupled Receptors
Authors: Knaus Ulla G. , Morris Sharron , Dong Hui-Jia , Chernoff Jonathan , Bokoch Gary M.
Published: October 2006

The Rac guanosine 5′-triphosphate (GTP)-binding proteins regulate oxidant production by phagocytic leukocytes. Two Ste20-related p21-activated kinases (PAKs) were identified as targets of Rac in human neutrophils. Activity of the ∼65- and ∼68-kilodalton PAKs was rapidly stimulated by chemoattractants acting through pertussis toxin-sensitive heterotrimeric GTP-binding proteins (G proteins). Native and recombinant PAKs phosphorylated the p47
phox
reduced nicotinamide adenine dinucleotide phosphate (NADPH) oxidase component in a Rac-GTP-dependent manner. The action of PAKs during phagocyte activation by G protein-coupled pathways may contribute to regulation of NADPH oxidase activity.
Targeted Disruption of Mouse EGF receptor: Effect of Genetic Background on Mutant Phenotype
Authors: Threadgill David W. , Dlugosz Andrzej A. , Hansen Laura A. , Tennenbaum Tamar , Lichti Ulrike , Yee Della , LaMantia Christian , Mourton Tracy , Herrup Karl , Harris Raymond C. , Barnard John A. , Yuspa Stuart H. , Coffey Robert J. , Magnuson Terry
Published: October 2006

Gene targeting was used to create a null allele at the epidermal growth factor receptor locus (
Egfr
). The phenotype was dependent on genetic background. EGFR deficiency on a CF-1 background resulted in peri-implantation death due to degeneration of the inner cell mass. On a 129/Sv background, homozygous mutants died at mid-gestation due to placental defects; on a CD-1 background, the mutants lived for up to 3 weeks and showed abnormalities in skin, kidney, brain, liver, and gastrointestinal tract. The multiple abnormalities associated with EGFR deficiency indicate that the receptor is involved in a wide range of cellular activities.
Strain-Dependent Epithelial Defects in Mice Lacking the EGF Receptor
Authors: Sibilia Maria , Wagner Erwin F.
Published: October 2006

Mice and cells lacking the epidermal growth factor receptor (EGFR) were generated to examine its physiological role in vivo. Mutant fetuses are retarded in growth and die at mid-gestation in a 129/Sv genetic background, whereas in a 129/Sv × C57BL/6 cross some survive until birth and even to postnatal day 20 in a 129/Sv × C57BL/6 × MF1 background. Death in utero probably results from a defect in the spongiotrophoblast layer of the placenta. Newborn mutant mice have open eyes, rudimentary whiskers, immature lungs, and defects in the epidermis, correlating with the expression pattern of the EGFR as monitored by β-galactosidase activity. These defects are probably cell-autonomous because chimeric mice generated with EGFR
-/-
embryonic stem cells contribute small amounts of mutant cells to some organs. These results indicate that the EGFR regulates epithelial proliferation and differentiation and that the genetic background influences the resulting phenotype.
Requirement of the Yeast
RTH1
5′ to 3′ Exonuclease for the Stability of Simple Repetitive DNA
Authors: Johnson Robert E. , Kovvali Gopala K. , Prakash Louise , Prakash Satya
Published: October 2006

Simple repetitive DNA sequences are unstable in human colorectal cancers and a variety of other cancers. Mutations in the DNA mismatch repair genes
MSH2
,
MLH1
, and
PMS1
result in elevated rates of spontaneous mutation and cause a marked increase in the instability of simple repeats. Compared with the wild type, a null mutation in the yeast
RTH1
gene, which encodes a 5′ to 3′ exonuclease, was shown to increase the rate of instability of simple repetitive DNA by as much as 280 times and to increase the spontaneous mutation rate by 30 times. Epistasis analyses were consistent with the hypothesis that this
RTH1
-encoded nuclease has a role in the
MSH2-MLH-1-PMS1
mismatch repair pathway.
A Role in B Cell Activation for CD22 and the Protein Tyrosine Phosphatase SHP
Authors: Doody Gina M. , Justement Louis B. , Delibrias Catherine C. , Matthews R. James , Lin Jiejian , Thomas Matthew L. , Fearon Douglas T.
Published: October 2006

CD22 is a membrane immunoglobulin (mIg)-associated protein of B cells. CD22 is tyrosine-phosphorylated when mIg is ligated. Tyrosine-phosphorylated CD22 binds and activates SHP, a protein tyrosine phosphatase known to negatively regulate signaling through mIg. Ligation of CD22 to prevent its coaggregation with mIg lowers the threshold at which mIg activates the B cell by a factor of 100. In secondary lymphoid organs, CD22 may be sequestered away from mIg through interactions with counterreceptors on T cells. Thus, CD22 is a molecular switch for SHP that may bias mIg signaling to anatomic sites rich in T cells.
Lack of Interferon γ Receptor β Chain and the Prevention of Interferon γ Signaling in T
H
1 Cells
Authors: Pernis Alessandra , Gupta Sanjay , Gollob Kenneth J. , Garfein Evan , Coffman Robert L. , Schindler Chris , Rothman Paul
Published: October 2006

The ability of interferon γ (IFN-γ) to inhibit the proliferation of type 2 T helper cells (T
H
2), but not that of type 1 (T
H
1) cells, suggests that helper cell subsets might differ in their activation of the IFN-γ signaling pathway. The IFN-γ-inducible signal transducing factor (STF-IFNγ) was activated in murine T
H
2 but not in T
H
1 cell clones, because in the latter the second chain of the IFN-γ receptor (accessory factor 1 or IFN-γRβ) was absent. Thus, T
H
1 cells use receptor modification to prevent the activation of STF-IFNγ and achieve an IFN-γ-resistant state.
Structurally Complex and Highly Active RNA Ligases Derived from Random RNA Sequences
Authors: Ekland Eric H. , Szostak Jack W. , Bartel David P.
Published: October 2006

Seven families of RNA ligases, previously isolated from random RNA sequences, fall into three classes on the basis of secondary structure and regiospecificity of ligation. Two of the three classes of ribozymes have been engineered to act as true enzymes, catalyzing the multiple-turnover transformation of substrates into products. The most complex of these ribozymes has a minimal catalytic domain of 93 nucleotides. An optimized version of this ribozyme has a
k
cat
exceeding one per second, a value far greater than that of most natural RNA catalysts and approaching that of comparable protein enzymes. The fact that such a large and complex ligase emerged from a very limited sampling of sequence space implies the existence of a large number of distinct RNA structures of equivalent complexity and activity.
Telomerase in Yeast
Authors: Cohn Marita , Blackburn Elizabeth H.
Published: October 2006

The ribonucleoprotein enzyme telomerase synthesizes telomeric DNA by copying an internal RNA template sequence. The telomerase activities of the yeasts
Saccharomyces castellii
and
Saccharomyces cerevisiae
—with regular and irregular telomeric sequences, respectively—have now been identified and characterized. The
S. cerevisiae
activity required the telomerase RNA gene
TLC1
but not the
EST1
gene, both of which are required for normal telomere maintenance in vivo. This activity exhibited low processivity and produced no regularly repeated products. An inherently high stalling frequency of the
S. cerevisiae
telomerase may account for its in vitro properties and for the irregular telomeric sequences of this yeast.
Simultaneous Identification of Bacterial Virulence Genes by Negative Selection
Authors: Hensel Michael , Shea Jacqueline E. , Gleeson Colin , Jones Michael D. , Dalton Emma , Holden David W.
Published: October 2006

An insertional mutagenesis system that uses transposons carrying unique DNA sequence tags was developed for the isolation of bacterial virulence genes. The tags from a mixed population of bacterial mutants representing the inoculum and bacteria recovered from infected hosts were detected by amplification, radiolabeling, and hybridization analysis. When applied to a murine model of typhoid fever caused by
Salmonella typhimurium
, mutants with attenuated virulence were revealed by use of tags that were present in the inoculum but not in bacteria recovered from infected mice. This approach resulted in the identification of new virulence genes, some of which are related to, but functionally distinct from, the
inv/spa
family of
S. typhimurium
.
Permeation Selectivity by Competition in a Delayed Rectifier Potassium Channel
Authors: Korn Stephen J. , Ikeda Stephen R.
Published: October 2006

Permeation selectivity was studied in two human potassium channels, Kv2.1 and Kv1.5, expressed in a mouse cell line. With normal concentrations of potassium and sodium, both channels were highly selective for potassium. On removal of potassium, Kv2.1 displayed a large sodium conductance that was inhibited by low concentrations of potassium. The channel showed a competition mechanism of selectivity similar to that of calcium channels. In contrast, Kv1.5 displayed a negligible sodium conductance on removal of potassium. The observation that structurally similar potassium channels show different abilities to conduct sodium provides a basis for understanding the structural determinants of potassium channel selectivity.
Interaction of Papillomavirus E6 Oncoproteins with a Putative Calcium-Binding Protein
Authors: Chen Jason J. , Reid Carl E. , Band Vimla , Androphy Elliot J.
Published: October 2006

Human papillomaviruses (HPVs) are associated with the majority of cervical cancers and encode a transforming protein, E6, that interacts with the tumor suppressor protein p53. Because E6 has p53-independent transforming activity, the yeast two-hybrid system was used to search for other E6-binding proteins. One such protein, E6BP, interacted with cancer-associated HPV E6 and with bovine papillomavirus type 1 (BPV-1) E6. The transforming activity of BPV-1 E6 mutants correlated with their E6BP-binding ability. E6BP is identical to a putative calcium-binding protein, ERC-55, that appears to be localized in the endoplasmic reticulum.
Effects of the
obese
Gene Product on Body Weight Regulation in
ob
/
ob
Mice
Authors: Pelleymounter Mary Ann , Cullen Mary Jane , Baker Mary Beth , Hecht Randy , Winters Dwight , Boone Thomas , Collins Frank
Published: October 2006

C57BL/6J mice with a mutation in the
obese
(
ob
)gene are obese, diabetic, and exhibit reduced activity, metabolism, and body temperature. Daily intraperitoneal injection of these mice with recombinant OB protein lowered their body weight, percent body fat, food intake, and serum concentrations of glucose and insulin. In addition, metabolic rate, body temperature, and activity levels were increased by this treatment. None of these parameters was altered beyond the level observed in lean controls, suggesting that the OB protein normalized the metabolic status of the
ob
/
ob
mice. Lean animals injected with OB protein maintained a smaller weight loss throughout the 28-day study and showed no changes in any of the metabolic parameters. These data suggest that the OB protein regulates body weight and fat deposition through effects on metabolism and appetite.
Induction of MHC Class I Genes in Neurons
Authors: Neumann Harald , Cavalié Adolfo , Jenne Dieter E. , Wekerle Hartmut
Published: October 2006

Whether neurons express major histocompatibility complex (MHC) class I genes has not been firmly established. The techniques of confocal laser microscopy, patch clamp electrophysiology, and reverse transcriptase-polymerase chain reaction were combined here to directly examine the inducibility of MHC class I genes in individual cultured rat hippocampal neurons. Transcription of MHC class I genes was very rare in neurons with spontaneous action potentials. In electrically silent neurons, transcription was noted, with expression of β
2
-microglobulin under tighter control than in class I heavy chain molecules. Surface expression of class I molecules occurred only in electrically silent neurons treated with interferon γ. Immunosurveillance by cytotoxic T cells may be focused on functionally impaired neurons.
Circuit Simulation of Genetic Networks
Authors: McAdams Harley H. , Shapiro Lucy
Published: October 2006

Genetic networks with tens to hundreds of genes are difficult to analyze with currently available techniques. Because of the many parallels in the function of these biochemically based genetic circuits and electrical circuits, a hybrid modeling approach is proposed that integrates conventional biochemical kinetic modeling within the framework of a circuit simulation. The circuit diagram of the bacteriophage lambda lysis-lysogeny decision circuit represents connectivity in signal paths of the biochemical components. A key feature of the lambda genetic circuit is that operons function as active integrated logic components and introduce signal time delays essential for the in vivo behavior of phage lambda.
Structure of Bam HI Endonuclease Bound to DNA: Partial Folding and Unfolding on DNA Binding
Authors: Newman Matthew , Strzelecka Teresa , Dorner Lydia F. , Schildkraut Ira , Aggarwal Aneel K.
Published: October 2006

The crystal structure of restriction endonuclease Bam HI complexed to DNA has been determined at 2.2 angstrom resolution. The DNA binds in the cleft and retains a B-DNA type of conformation. The enzyme, however, undergoes a series of conformational changes, including rotation of subunits and folding of disordered regions. The most striking conformational change is the unraveling of carboxyl-terminal α helices to form partially disordered "arms." The arm from one subunit fits into the minor groove while the arm from the symmetry related subunit follows the DNA sugar-phosphate backbone. Recognition of DNA base pairs occurs primarily in the major groove, with a few interactions occurring in the minor groove. Tightly bound water molecules play an equally important role as side chain and main chain atoms in the recognition of base pairs. The complex also provides new insights into the mechanism by which the enzyme catalyzes the hydrolysis of DNA phosphodiester groups.
Fabrication of Submicrometer Features on Curved Substrates by Microcontact Printing
Authors: Jackman Rebecca J. , Wilbur James L. , Whitesides George M.
Published: October 2006

Microcontact printing (μCP) has been used to produce patterned self-assembled monolayers (SAMs) with submicrometer features on curved substrates with radii of curvature as small as 25 micrometers. Wet-chemical etching that uses the patterned SAMs as resists transfers the patterns formed by μCP into gold. At present, there is no comparable method for microfabrication on curved surfaces.
Detection of Creatinine by a Designed Receptor
Authors: Bell T. W. , Hou Z. , Luo Y. , Drew M. G. B. , Chapoteau E. , Czech B. P. , Kumar A.
Published: October 2006

An artificial receptor has been designed to bind creatinine with a color change (chromogenic response) caused by proton transfer from one end of the receptor to the other. The receptor was synthesized and found to extract creatinine from water into chlorocarbon solvents. The color change in the organic layer is specific for creatinine relative to other organic solutes, and it is selective for creatinine relative to sodium, potassium, and ammonium ions. The chromogenic mechanism is revealed by x-ray crystal structures of creatinine, the free receptor, and the complex, showing "induced fit" binding resulting from electronic complementarity between host and guest.
Rescue of the
En-1
Mutant Phenotype by Replacement of
En-1
with
En-2
Authors: Hanks Mark , Wurst Wolfgang , Anson-Cartwright Lynn , Auerbach Anna B. , Joyner Alexandra L.
Published: October 2006

The related mouse
Engrailed
genes
En-1
and
En-2
are expressed from the one- and approximately five-somite stages, respectively, in a similar presumptive mid-hindbrain domain. However, mutations in
En-1
and
En-2
produce different phenotypes.
En-1
mutant mice die at birth with a large mid-hindbrain deletion, whereas
En-2
mutants are viable, with cerebellar defects. To determine whether these contrasting phenotypes reflect differences in temporal expression or biochemical activity of the En proteins,
En-1
coding sequences were replaced with
En-2
sequences by gene targeting. This rescued all
En-1
mutant defects, demonstrating that the difference between
En-1
and
En-2
stems from their divergent expression patterns.
A Gene Outside the Human MHC Related to Classical HLA Class I Genes
Authors: Hashimoto Keiichiro , Hirai Momoki , Kurosawa Yoshikazu
Published: October 2006

By presenting antigenic peptides to T lymphocytes, major histocompatibility complex (MHC) class I molecules play important roles in the human immune system. Knowledge is limited on the evolutionary history of human MHC class I-related molecules. An expressed class I gene,
MR1
, has now been identified on human chromosome 1q25, outside the MHC. In contrast to other known human divergent class I genes,
MR1
encodes peptide-binding domains similar to those encoded by human leukocyte antigen (HLA) class I genes on chromosome 6 and by nonmammalian classical MHC class I genes. This gene may thus contribute to understanding the evolution of the MHC.
Excision of Deoxyribose Phosphate Residues by DNA Polymerase β During DNA Repair
Authors: Matsumoto Yoshihiro , Kim Kyung
Published: October 2006

Eukaryotic DNA polymerase β (pol β) can catalyze DNA synthesis during base excision DNA repair. It is shown here that pol β also catalyzes release of 5′-terminal deoxyribose phosphate (dRP) residues from incised apurinic-apyrimidinic sites, which are common intermediate products in base excision repair. The catalytic domain for this activity resides within an amino-terminal 8-kilodalton fragment of pol β, which comprises a distinct structural domain of the enzyme. Magnesium is required for the release of dRP from double-stranded DNA but not from a single-stranded oligonucleotide. Analysis of the released products indicates that the excision reaction occurs by β-elimination rather than hydrolysis.
Resonance Light Scattering: A New Technique for Studying Chromophore Aggregation
Authors: Pasternack Robert F. , Collings Peter J.
Published: October 2006

Light scattering experiments are usually performed at wavelengths away from absorption bands, but for species that aggregate, enhancements in light scattering of several orders of magnitude can be observed at wavelengths characteristic of these species. Resonance light scattering is shown to be a sensitive and selective method for studying electronically coupled chromophore arrays. The approach is illustrated with several examples drawn from porphyrin and chlorin chemistry. The physical principles underlying resonance light scattering are discussed, and the advantages and limitations of the technique are reviewed.
Protein Reaction Kinetics in a Room-Temperature Glass
Authors: Hagen Stephen J. , Hofrichter James , Eaton William A.
Published: October 2006

Protein reaction kinetics in aqueous solution at room temperature are often simplified by the thermal averaging of conformational substates. These substates exhibit widely varying reaction rates that are usually exposed by trapping in a glass at low temperature. Here, it is shown that the solvent viscosity, rather than the low temperature, is primarily responsible for the trapping. This was demonstrated by placement of myoglobin in a glass at room temperature and subsequent observation of inhomogeneous reaction kinetics. The high solvent viscosity slowed the rate of crossing the energy barriers that separated the substates and also suppressed any change in the average protein conformation after ligand dissociation.
Object-Centered Direction Selectivity in the Macaque Supplementary Eye Field
Authors: Olson C. R. , Gettner S. N.
Published: October 2006

Object-centered spatial awareness—awareness of the location, relative to an object, of its parts—plays an important role in many aspects of perception, imagination, and action. One possible basis for this capability is the existence in the brain of neurons with sensory receptive fields or motor action fields that are defined relative to an object-centered frame. In experiments described here, neuronal activity was monitored in the supplementary eye field of macaque monkeys making eye movements to the right or left end of a horizontal bar. Neurons were found to fire differentially as a function of the end of the bar to which an eye movement was made. This is direct evidence for the existence of neurons sensitive to the object-centered direction of movements.
Photodeposition of Micrometer-Scale Polymer Patterns on Optical Imaging Fibers
Authors: Healey Brian G. , Foran Stacy E. , Walt David R.
Published: October 2006

Microstructures were fabricated on optical imaging fibers with a photopolymerization technique. Monodisperse polymeric microarrays were produced containing spots of 2.5 micrometers in diameter spaced 4.5 micrometers apart. Polymer microarrays were also deposited on other substrates by using imaging fibers for light delivery. The technique allows micrometer-scale photopatterning with masks larger than the desired dimensions.
Impaired Energy Homeostasis in C/EBPα Knockout Mice
Authors: Wang Nai-dy , Finegold Milton J. , Bradley Allan , Ou Ching N. , Abdelsayed Sandy V. , Wilde Margaret D. , Taylor L. Ranee , Wilson Deborah R. , Darlington Gretchen J.
Published: October 2006

Mice homozygous for the targeted deletion of the
c/ebp
α gene, which expresses the CCAAT/enhancer-binding protein α (C/EBPα), did not store hepatic glycogen and died from hypoglycemia within 8 hours after birth. In these mutant mice, the amounts of glycogen synthase messenger RNA were 50 to 70 percent of normal and the transcriptional induction of the genes for two gluconeogenic enzymes, phosphoenolpyruvate carboxykinase and glucose-6-phosphatase, was delayed. The hepatocytes and adipocytes of the mutant mice failed to accumulate lipid and the expression of the gene for uncoupling protein, the defining marker of brown adipose tissue, was reduced. This study demonstrates that C/EBPα is critical for the establishment and maintenance of energy homeostasis in neonates.
Complex Cooperative Strategies in Group-Territorial African Lions
Authors: Heinsohn Robert , Packer Craig
Published: October 2006

Female lions (
Panthera leo
) showed persistent individual differences in the extent to which they participated in group-territorial conflict. When intergroup encounters were simulated by playback of aggressive vocalizations, some individuals consistently led the approach to the recorded intruder, whereas others lagged behind and avoided the risks of fighting. The lead females recognized that certain companions were laggards but failed to punish them, which suggests that cooperation is not maintained by reciprocity. Modification of the "odds" in these encounters revealed that some females joined the group response when they were most needed, whereas other lagged even farther behind. The complexity of these responses emphasizes the great diversity of individual behavior in this species and the inadequacy of current theory to explain cooperation in large groups.