bluuebunny/crossref_metadata_2025 huggingface dataset:
Inhibition of Transcription Elongation by the VHL Tumor Suppressor Protein
Authors: Duan D. Roxanne , Pause Arnim , Burgess Wilson H. , Aso Teijiro , Chen David Y. T. , Garrett Karla P. , Conaway Ronald C. , Conaway Joan W. , Linehan W. Marston , Klausner Richard D.
Published: October 2006

Germline mutations in the von Hippel-Lindau tumor suppressor gene (
VHL
) predispose individuals to a variety of tumors, including renal carcinoma, hemangioblastoma of the central nervous system, and pheochromocytoma. Here, a cellular transcription factor, Elongin (SIII), is identified as a functional target of the VHL protein. Elongin (SIII) is a heterotrimer consisting of a transcriptionally active subunit (A) and two regulatory subunits (B and C) that activate transcription elongation by RNA polymerase II. The VHL protein was shown to bind tightly and specifically to the Elongin B and C subunits and to inhibit Elongin (SIII) transcriptional activity in vitro. These findings reveal a potentially important transcriptional regulatory network in which the VHL protein may play a key role.
A Simple Genetic Basis for a Complex Psychological Trait in Laboratory Mice
Authors: Flint Jonathan , Corley Robin , DeFries John C. , Fulker David W. , Gray Jeffrey A. , Miller Stacey , Collins Allan C.
Published: October 2006

Psychological traits are commonly inferred from covariation in sets of behavioral measures that otherwise appear to have little in common. Emotionality in mice is such a trait, defined here by covariation in activity and defecation in a novel environment and emergence into the open arms of an elevated plus maze. Behavioral and quantitative trait analyses were conducted on four measures obtained from 879 mice from an F
2
intercross. Three loci, on murine chromosomes 1, 12, and 15, were mapped that influence emotionality. This trait, inferred from studies of strain, sex, and individual differences in rodents, may be related to human susceptibility to anxiety or neuroticism.
Decreased Muscarinic Receptor Binding in the Arcuate Nucleus in Sudden Infant Death Syndrome
Authors: Kinney Hannah C. , Filiano James J. , Sleeper Lynn A. , Mandell Frederick , Valdes-Dapena Marie , White W. Frost
Published: October 2006

Muscarinic cholinergic activity in the human arcuate nucleus at the ventral medullary surface is postulated to be involved in cardiopulmonary control. A significant decrease in [
3
H]quinuclidinyl benzilate binding to muscarinic receptors in the arcuate nucleus is now shown to occur in sudden infant death syndrome (SIDS) infants, compared to infants dying acutely of known causes. In infants with chronic oxygenation abnormalities, binding is low in other nuclei, as well as in the arcuate nucleus. The binding deficit in the arcuate nucleus of SIDS infants might contribute to a failure of responses to cardiopulmonary challenges during sleep.
Association of the Yeast Pheromone Response G Protein βγ Subunits with the Map Kinase Scaffold Ste5p
Authors: Whiteway Malcolm S. , Wu Cunle , Leeuw Thomas , Clark Karen , Fourest-Lieuvin Anne , Thomas David Y. , Leberer Ekkehard
Published: October 2006

The mating response pathway of the yeast
Saccharomyces cerevisiae
includes a heterotrimeric guanine nucleotide-binding protein (G protein) that activates a mitogen-activated protein (MAP) kinase cascade by an unknown mechanism. An amino-terminal fragment of the MAP kinase scaffold protein Ste5p that interfered with pheromone-induced cell cycle arrest was identified. A haploid-specific interaction between the amino terminus of Ste5p and the G protein β subunit Ste4p was also detected in a two-hybrid assay, and the product of a signaling-defective allele of
STE4
was defective in this interaction. In cells with a constitutively activated pheromone response pathway, epitope-tagged Ste4p was coimmunoprecipitated with Ste5p. Thus, association of the G protein and the MAP kinase cassette via the scaffolding protein Ste5p may transmit the G protein signal.
CDC25 Phosphatases as Potential Human Oncogenes
Authors: Galaktionov Konstantin , Lee Arthur K. , Eckstein Jens , Draetta Giulio , Meckler Jason , Loda Massimo , Beach David
Published: October 2006

Cyclin-dependent kinases (CDKs) are activated by CDC25 phosphatases, which remove inhibitory phosphate from tyrosine and threonine residues. In human cells, CDC25 proteins are encoded by a multigene family, consisting of
CDC25A
,
CDC25B
, and
CDC25C
. In rodent cells, human CDC25A or CDC25B but not CDC25C phosphatases cooperate with either Ha-

RAS
G12V

or loss of
RB1
in oncogenic focus formation. Such transformants were highly aneuploid, grew in soft agar, and formed high-grade tumors in nude mice. Overexpression of CDC25B was detected in 32 percent of human primary breast cancers tested. The CDC25 phosphatases may contribute to the development of human cancer.
Switching Recognition of Two tRNA Synthetases with an Amino Acid Swap in a Designed Peptide
Authors: Auld Douglas S. , Schimmel Paul
Published: October 2006

The genetic code is based on specific interactions between transfer RNA (tRNA) synthetases and their cognate tRNAs. The anticodons for methionine and isoleucine tRNAs differ by a single nucleotide, and changing this nucleotide in an isoleucine tRNA is sufficient to change aminoacylation specificity to methionine. Results of combinatorial mutagenesis of an anticodon-binding-helix loop peptide were used to design a hybrid sequence composed of amino acid residues from methionyl- and isoleucyl-tRNA synthetases. When the hybrid sequence was transplanted into isoleucyl-tRNA synthetase, active enzyme was generated in vivo and in vitro. The transplanted peptide did not confer function to methionyl-tRNA synthetase, but the substitution of a single amino acid within the transplanted peptide conferred methionylation and prevented isoleucylation. Thus, the swap of a single amino acid in the transplanted peptide switches specificity between anticodons that differ by one nucleotide.
Requirement for Phosphatidylinositol-3 Kinase in the Prevention of Apoptosis by Nerve Growth Factor
Authors: Yao Ryoji , Cooper Geoffrey M.
Published: October 2006

Nerve growth factor (NGF) induces both differentiation and survival of neurons by binding to the Trk receptor protein tyrosine kinase. Although Ras is required for differentiation, it was not required for NGF-mediated survival of rat pheochromocytoma PC-12 cells in serum-free medium. However, the ability of NGF to prevent apoptosis (programmed cell death) was inhibited by wortmannin or LY294002, two specific inhibitors of phosphatidylinositol (PI)-3 kinase. Moreover, platelet-derived growth factor (PDGF) prevented apoptosis of PC-12 cells expressing the wild-type PDGF receptor, but not of cells expressing a mutant receptor that failed to activate PI-3 kinase. Cell survival thus appears to be mediated by a PI-3 kinase signaling pathway distinct from the pathway that mediates differentiation.
Ras-Dependent Induction of Cellular Responses by Constitutively Active Phosphatidylinositol-3 Kinase
Authors: Hu Qianjin , Klippel Anke , Muslin Anthony J. , Fantl Wendy J. , Williams Lewis T.
Published: October 2006

Phosphatidylinositol (Pl)-3 kinase is one of many enzymes stimulated by growth factors. A constitutively activated mutant, p110*, that functions independently of growth factor stimulation was constructed to determine the specific responses regulated by Pl-3 kinase. The p110* protein exhibited high specific activity as a Pl-3 kinase and as a protein kinase. Expression of p110* in NIH 3T3 cells induced transcription from the
fos
promoter. Co-expression of dominant negative Ras blocked this response. When expressed in
Xenopus laevis
oocytes, p110* increased the amount of guanosine 5′-triphosphate-bound Ras, caused activation of the Ras effector Raf-1, and induced Ras-dependent oocyte maturation. These findings show that Pl-3 kinase can stimulate diverse Ras-dependent cellular processes, including oocyte maturation and
fos
transcription.
E5531, a Pure Endotoxin Antagonist of High Potency
Authors: Christ William J. , Asano Osamu , Robidoux Andrea L. C. , Perez Michel , Wang Yuan , Dubuc Gloria R. , Gavin Wendy E. , Hawkins Lynn D. , McGuinness Pamela D. , Mullarkey Maureen A. , Lewis Michael D. , Kishi Yoshito , Kawata Tsutomu , Bristol John R. , Rose Jeffrey R. , Rossignol Daniel P. , Kobayashi Seiichi , Hishinuma leharu , Kimura Akifumi , Asakawa Naoki , Katayama Kouichi , Yamatsu lsao
Published: October 2006

Shock due to Gram-negative bacterial sepsis is a consequence of acute inflammatory response to lipopolysaccharide (LPS) or endotoxin released from bacteria. LPS is a major constituent of the outer membrane of Gram-negative bacteria, and its terminal disaccharide phospholipid (lipid A) portion contains the key structural features responsible for toxic activity. Based on the proposed structure of nontoxicRhodobacter capsulatuslipid A, a fully stabilized endotoxin antagonist E5531 has been synthesized. In vitro, E5531 demonstrated potent antagonism of LPS-mediated cellular activation in a variety of systems. In vivo, E5531 protected mice from LPS-induced lethality and, in cooperation with an antibiotic, protected mice from a lethal infection of viableEscherichia coli.
Stretching of a Single Tethered Polymer in a Uniform Flow
Authors: Perkins Thomas T. , Smith Douglas E. , Larson Ronald G. , Chu Steven
Published: October 2006

The stretching of single, tethered DNA molecules by a flow was directly visualized with fluorescence microscopy. Molecules ranging in length (
L
) from 22 to 84 micrometers were held stationary against the flow by the optical trapping of a latex microsphere attached to one end. The fractional extension
x
/
L
is a universal function of η
v
L
0.54 ± 0.05
, where η and
v
are the viscosity and velocity of the flow, respectively. This relation shows that the DNA is not "free-draining" (that is, hydrodynamic coupling within the chain is not negligible) even near full extension (∼80 percent). This function has the same form over a long range as the fractional extension versus force applied at the ends of a worm-like chain. For small deformations (< 30 percent of full extension), the extension increases with velocity as
x
∼
v
0.70 ± 0.08
. The relative size of fluctuations in extension decreases as σ

x

/
x
≅ 0.42 exp(-4.9
x
/
L
). Video images of the fluctuating chain have a cone-like envelope and show a sharp increase in intensity at the free end.
Protein Lipidation in Cell Signaling
Authors: Casey Patrick J.
Published: October 2006

The ability of cells to communicate with and respond to their external environment is critical for their continued existence. A universal feature of this communication is that the external signal must in some way penetrate the lipid bilayer surrounding the cell. In most cases of such signal acquisition, the signaling entity itself does not directly enter the cell but rather transmits its information to specific proteins present on the surface of the cell membrane. These proteins then communicate with additional proteins associated with the intracellular face of the membrane. Membrane localization and function of many of these proteins are dependent on their covalent modification by specific lipids, and it is the processes involved that form the focus of this article.
Integrins and Signal Transduction Pathways: the Road Taken
Authors: Clark Edwin A. , Brugge Joan S.
Published: October 2006

Adhesive interactions play critical roles in directing the migration, proliferation, and differentiation of cells; aberrations in such interactions can lead to pathological disorders. These adhesive interactions, mediated by cell surface receptors that bind to ligands on adjacent cells or in the extracellular matrix, also regulate intracellular signal transduction pathways that control adhesion-induced changes in cell physiology. Though the extracellular molecular interactions involving many adhesion receptors have been well characterized, the adhesion-dependent intracellular signaling events that regulate these physiological alterations have only begun to be elucidated. This article will focus on recent advances in our understanding of intracellular signal transduction pathways regulated by the integrin family of adhesion receptors.
Localization of Protein Kinases by Anchoring Proteins: a Theme in Signal Transduction
Authors: Mochly-Rosen Daria
Published: October 2006

A fundamental question in signal transduction is how stimulation of a specific protein kinase leads to phosphorylation of particular protein substrates throughout the cell. Recent studies indicate that specific anchoring proteins located at various sites in the cell compartmentalize the kinases to their sites of action. Inhibitors of the interactions between kinases and their anchoring proteins inhibit the functions mediated by the kinases. These data indicate that the location of these anchoring proteins provides some of the specificity of the responses mediated by each kinase and suggest that inhibitors of the interaction between the kinases and their anchoring proteins may be useful as therapeutic agents.
Identification of a Dual Specificity Kinase That Activates the Jun Kinases and p38-Mpk2
Authors: Lin Anning , Minden Audrey , Martinetto Horacio , Claret Francois-Xavier , Lange-Carter Carol , Mercurio Frank , Johnson Gary L. , Karin Michael
Published: October 2006

One Ras-dependent protein kinase cascade leading from growth factor receptors to the ERK (extracellular signal-regulated kinases) subgroup of mitogen-activated protein kinases (MAPKs) is dependent on the protein kinase Raf-1, which activates the MEK (MAPK or ERK kinase) dual specificity kinases. A second protein kinase cascade leading to activation of the Jun kinases (JNKs) is dependent on MEKK (MEK kinase). A dual-specificity kinase that activates JNK, named JNKK, was identified that functions between MEKK and JNK. JNKK activated the JNKs but did not activate the ERKs and was unresponsive to Raf-1 in transfected HeLa cells. JNKK also activated another MAPK, p38 (Mpk2; the mammalian homolog of HOG1 from yeast), whose activity is regulated similarly to that of the JNKs.
Crystal Structure of the Mammalian Grb2 Adaptor
Authors: Maignan Sébastien , Guilloteau Jean-Pierre , Fromage Nadine , Arnoux Bernadette , Becquart Jérôme , Ducruix Arnaud
Published: October 2006

The mammalian growth factor receptor-binding protein Grb2 is an adaptor that mediates activation of guanine nucleotide exchange on Ras. Grb2 binds to the receptor through its SH2 domain and to the carboxyl-terminal domain of Son of sevenless through its two SH3 domains. It is thus a key element in the signal transduction pathway. The crystal structure of Grb2 was determined to 3.1 angstrom resolution. The asymmetric unit is composed of an embedded dimer. The interlaced junctions between the SH2 and SH3 domains bring the two adjacent faces of the SH3 domains in van der Waals contact but leave room for the binding of proline-rich peptides.
Revealing the Architecture of a K
+
Channel Pore Through Mutant Cycles with a Peptide Inhibitor
Authors: Hidalgo Patricia , MacKinnon Roderick
Published: October 2006

Thermodynamic mutant cycles provide a formalism for studying energetic coupling between amino acids on the interaction surface in a protein-protein complex. This approach was applied to the Shaker potassium channel and to a high-affinity peptide inhibitor (scorpion toxin) that binds to its pore entryway. The assignment of pairwise interactions defined the spatial arrangement of channel amino acids with respect to the known inhibitor structure. A strong constraint was placed on the Shaker channel pore-forming region by requiring its amino-terminal border to be 12 to 15 angstroms from the central axis. This method is directly applicable to sodium, calcium, and other ion channels where inhibitor or modulatory proteins bind with high affinity.
Cloning of Immunoglobulin-Superfamily Members Associated with HLA-C and HLA-B Recognition by Human Natural Killer Cells
Authors: Colonna Marco , Samaridis Jacqueline
Published: October 2006

Cytotoxicity by natural killer (NK) cells is inhibited by major histocompatibility complex (MHC) class I molecules on target cells. This inhibition may be mediated by NK receptors with different MHC specificities. A family of four NK-specific complementary DNAs (cDNAs), designated NKATs (NK-associated transcripts), was identified that encoded related transmembrane proteins, characterized by an extracellular region with two or three immunoglobulin-superfamily domains and by a cytoplasmic domain with an unusual antigen receptor activation motif (ARAM). The distribution of these cDNAs was clonotypic and correlated with NK cell inhibition by particular class I alleles. Thus, NKAT cDNAs may encode receptors for class I molecules on NK cells.
The Role of Igβ in Precursor B Cell Transition and Allelic Exclusion
Authors: Papavasiliou Fotini , Misulovin Ziva , Suh Heikyung , Nussenzweig Michel C.
Published: October 2006

Lymphocytes express multicomponent receptor complexes that mediate diverse antigen-dependent and antigen-independent responses. Despite the central role of antigen-independent events in B cell development, little is known about the mechanisms by which they are initiated. The association between the membrane immunoglobulin (Ig) M heavy chain (mμ) and the Igα-Igβ heterodimer is now shown to be essential in inducing both the transition from progenitor to precursor B cells and subsequent allelic exclusion in transgenic mice. The cytoplasmic domain of Igβ is sufficient to induce these early antigen-independent events by a mechanism that requires conserved tyrosine residues in this protein.
Mutations in the Sulfonylurea Receptor Gene in Familial Persistent Hyperinsulinemic Hypoglycemia of Infancy
Authors: Thomas Pamela M. , Cote Gilbert J. , Wohllk Nelson , Haddad Bassem , Mathew P. M. , Rabl Wolfgang , Aguilar-Bryan Lydia , Gagel Robert F. , Bryan Joseph
Published: October 2006

Familial persistent hyperinsulinemic hypoglycemia of infancy (PHHI), an autosomal recessive disorder characterized by unregulated insulin secretion, is linked to chromosome 11p14-15.1. The newly cloned high-affinity sulfonylurea receptor (
SUR
) gene, a regulator of insulin secretion, was mapped to 11p15.1 by means of fluorescence in situ hybridization. Two separate
SUR
gene splice site mutations, which segregated with disease phenotype, were identified in affected individuals from nine different families. Both mutations resulted in aberrant processing of the RNA sequence and disruption of the putative second nucleotide binding domain of the SUR protein. Abnormal insulin secretion in PHHI appears to be caused by mutations in the
SUR
gene.
Induction of Apoptosis in Uninfected Lymphocytes by HIV-1 Tat Protein
Authors: Li Chiang J. , Friedman David J. , Wang Chuanlin , Metelev Valeri , Pardee Arthur B.
Published: October 2006

Infection by human immunodeficiency virus-type 1 (HIV-1) is typified by the progressive depletion of CD4 T lymphocytes and deterioration of immune function in most patients. A central unresolved issue in acquired immunodeficiency syndrome (AIDS) pathogenesis is the mechanism underlying this T cell depletion. HIV-1 Tat protein was shown to induce cell death by apoptosis in a T cell line and in cultured peripheral blood mononuclear cells from uninfected donors. This Tat-induced apoptosis was inhibitable by growth factors and was associated with enhanced activation of cyclin-dependent kinases.
Expression Cloning of a Protective
Leishmania
Antigen
Authors: Mougneau Evelyne , Altare Frédéric , Wakil Adil E. , Zheng Shichun , Coppola Thierry , Wang Zhi-En , Waldmann Rainer , Locksley Richard M. , Glaichenhaus Nicolas
Published: October 2006

Parasite-specific CD4
+
T cells have been shown to transfer protection against
Leishmania major
in susceptible BALB/c mice. An epitope-tagged expression library was used to identify the antigen recognized by a protective CD4
+
T cell clone. The expression library allowed recombinant proteins made in bacteria to be captured by macrophages for presentation to T cells restricted to major histocompatibility complex class II. A conserved 36-kilodalton member of the tryptophan-aspartic acid repeat family of proteins was identified that was expressed in both stages of the parasite life cycle. A 24-kilodalton portion of this antigen protected susceptible mice when administered as a vaccine with interleukin-12 before infection.
Molecular Genetics of Plant Disease Resistance
Authors: Staskawicz Brian J. , Ausubel Frederick M. , Baker Barbara J. , Ellis Jeffrey G. , Jones Jonathan D. G.
Published: October 2006

Plant breeders have used disease resistance genes (
R
genes) to control plant disease since the turn of the century. Molecular cloning of
R
genes that enable plants to resist a diverse range of pathogens has revealed that the proteins encoded by these genes have several features in common. These findings suggest that plants may have evolved common signal transduction mechanisms for the expression of resistance to a wide range of unrelated pathogens. Characterization of the molecular signals involved in pathogen recognition and of the molecular events that specify the expression of resistance may lead to novel strategies for plant disease control.
The Ethylene Signal Transduction Pathway in Plants
Authors: Ecker Joseph R.
Published: October 2006

Ethylene (C
2
H
4
), the chemically simplest plant hormone, is among the best-characterized plant growth regulators. It participates in a variety of stress responses and developmental processes. Genetic studies in
Arabidopsis
have defined a number of genes in the ethylene signal transduction pathway. Isolation of two of these genes has revealed that plants sense this gas through a combination of proteins that resemble both prokaryotic and eukaryotic signaling proteins. Ethylene signaling components are likely conserved for responses as diverse as cell elongation, cell fate patterning in the root epidermis, and fruit ripening. Genetic manipulation of these genes will provide agriculture with new tools to prevent or modify ethylene responses in a variety of plants.
Prebiotic Synthesis of 5-Substituted Uracils: A Bridge Between the RNA World and the DNA-Protein World
Authors: Robertson Michael P. , Miller Stanley L.
Published: October 2006

Under prebiotic conditions, formaldehyde adds to uracil at the C-5 position to produce 5-hydroxymethyluracil with favorable rates and equilibria. Hydroxymethyluracil adds a variety of nucleophiles, such as ammonia, glycine, guanidine, hydrogen sulfide, hydrogen cyanide, imidazole, indole, and phenol, to give 5-substituted uracils with the side chains of most of the 20 amino acids in proteins. These reactions are sufficiently robust that, if uracil had been present on the primitive Earth, then these substituted uracils would also have been present. The ribozymes of the RNA world would have included many of the functional groups found in proteins today, and their catalytic activities may have been considerably greater than presently assumed.
Oral Immunization with a Recombinant Bacterial Antigen Produced in Transgenic Plants
Authors: Haq Tariq A. , Mason Hugh S. , Clements John D. , Arntzen Charles J.
Published: October 2006

The binding subunit of
Escherichia coli
heat-labile enterotoxin (LT-B) is a highly active oral immunogen. Transgenic tobacco and potato plants were made with the use of genes encoding LT-B or an LT-B fusion protein with a microsomal retention sequence. The plants expressed the foreign peptides, both of which formed oligomers that bound the natural ligand. Mice immunized by gavage produced serum and gut mucosal anti-LT-B immunoglobulins that neutralized the enterotoxin in cell protection assays. Feeding mice fresh transgenic potato tubers also caused oral immunization.
Immune System Impairment and Hepatic Fibrosis in Mice Lacking the Dioxin-Binding Ah Receptor
Authors: Fernandez-Salguero Pedro , Pineau Thie , Hilbert David M. , McPhail Timothy , Lee Susanna S. T. , Kimura Shioko , Nebert Daniel W. , Rudikoff Stuart , Ward Jerrold M. , Gonzalez Frank J.
Published: October 2006

The aryl hydrocarbon (Ah) receptor (AHR) mediates many carcinogenic and teratogenic effects of environmentally toxic chemicals such as dioxin. An AHR-deficient (Ahr
-/-
) mouse line was constructed by homologous recombination in embryonic stem cells. Almost half of the mice died shortly after birth, whereas survivors reached maturity and were fertile. The Ahr
-/-
mice showed decreased accumulation of lymphocytes in the spleen and lymph nodes, but not in the thymus. The livers of Ahr
-/-
mice were reduced in size by 50 percent and showed bile duct fibrosis. Ahr
-/-
mice were also nonresponsive with regard to dioxin-mediated induction of genes encoding enzymes that catalyze the metabolism of foreign compounds. Thus, the AHR plays an important role in the development of the liver and the immune system.
Identification and Characterization of a Prostaglandin Transporter
Authors: Kanai Naoaki , Lu Run , Satriano Joseph A. , Bao Yi , Wolkoff Allan W. , Schuster Victor L.
Published: October 2006

Carrier-mediated prostaglandin transport has been postulated to occur in many tissues. On the basis of sequence homology, the protein of unknown function encoded by the rat matrin F/G complementary DNA was predicted to be an organic anion transporter. Expression of the matrin F/G complementary DNA in HeLa cells or
Xenopus
oocytes conferred the property of specific transport of prostaglandins. The tissue distribution of matrin F/G messenger RNA and the sensitivity of matrin F/G-induced prostaglandin transport to inhibitors were similar to those of endogenous prostaglandin transport. The protein encoded by the matrin F/G complementary DNA is thus preferably called PGT because it is likely to function as a prostaglandin transporter.
Control of Proton Sensitivity of the NMDA Receptor by RNA Splicing and Polyamines
Authors: Traynelis Stephen F. , Hartley Melissa , Heinemann Stephen F.
Published: October 2006

The function of the
N
-methyl-D-aspartate (NMDA)-preferring glutamate receptor can be regulated by extracellular pH, a process that may be important during ischemia in the brain or during seizures. Protons inhibit NMDA receptor function by 50 percent at pH 7.3 through interactions with the NR1 subunit, and both polyamines and NR1 exon 5 potentiate receptor function through relief of the tonic proton inhibition present at physiological pH. A single amino acid (lysine 211) was identified that mediates the effects of exon 5 in the rat brain. Electroneutral substitutions at this position restored pH sensitivity and, consequently, polyamine relief of tonic inhibition. This effect, together with the structural similarities between polyamines and the surface loop encoded by exon 5, suggest that exon 5 may act as a tethered pH-sensitive constitutive modulator of NMDA receptor function.
KAI1
, a Metastasis Suppressor Gene for Prostate Cancer on Human Chromosome 11p11.2
Authors: Dong Jin-Tang , Lamb Pattie W. , Rinker-Schaeffer Carrie W. , Vukanovic Jasminka , Ichikawa Tomohiko , Isaacs John T. , Barrett J. Carl
Published: October 2006

A gene from human chromosome 11p11.2 was isolated and was shown to suppress metastasis when introduced into rat AT6.1 prostate cancer cells. Expression of this gene, designated
KAI1
, was reduced in human cell lines derived from metastatic prostate tumors.
KAI1
specifies a protein of 267 amino acids, with four hydrophobic and presumably transmembrane domains and one large extracellular hydrophilic domain with three potential N-glycosylation sites.
KAI1
is evolutionarily conserved, is expressed in many human tissues, and encodes a member of a structurally distinct family of leukocyte surface glycoproteins. Decreased expression of this gene may be involved in the malignant progression of prostate and other cancers.
The "Wake-Sleep" Algorithm for Unsupervised Neural Networks
Authors: Hinton Geoffrey E. , Dayan Peter , Frey Brendan J. , Neal Radford M.
Published: October 2006

An unsupervised learning algorithm for a multilayer network of stochastic neurons is described. Bottom-up "recognition" connections convert the input into representations in successive hidden layers, and top-down "generative" connections reconstruct the representation in one layer from the representation in the layer above. In the "wake" phase, neurons are driven by recognition connections, and generative connections are adapted to increase the probability that they would reconstruct the correct activity vector in the layer below. In the "sleep" phase, neurons are driven by generative connections, and recognition connections are adapted to increase the probability that they would produce the correct activity vector in the layer above.
T Helper Cell Subsets in Insulin-Dependent Diabetes
Authors: Katz Jonathan D. , Benoist Christophe , Mathis Diane
Published: October 2006

It has been proposed that the development of insulin-dependent diabetes is controlled by the T helper 1 (T
H
1) versus T
H
2 phenotype of autoreactive T
H
cells: T
H
1 cells would promote diabetes, whereas T
H
2 cells would actually protect from disease. This proposition was tested by establishing cultures of TH1 and TH2 cells that express an identical diabetogenic T cell receptor and comparing their ability to initiate disease in neonatal nonobese diabetic mice. T
H
1-like cells actively promoted diabetes; T
H
2-like cells invaded the islets but did not provoke disease—neither did they provide substantial protection.
Deregulated T Cell Activation and Autoimmunity in Mice Lacking Interleukin-2 Receptor β
Authors: Suzuki Haruhiko , Kündig Thomas M. , Furlonger Caren , Wakeham Andrew , Timms Emma , Matsuyama Toshifumi , Schmits Rudolf , Simard John J. L. , Ohashi Pamela S. , Griesser Henrik , Taniguchi Tadatsugu , Paige Christopher J. , Mak Tak W.
Published: October 2006

In mice lacking the interleukin-2 receptor β chain (IL-2Rβ), T cells were shown to be spontaneously activated, resulting in exhaustive differentiation of B cells into plasma cells and the appearance of high serum concentrations of immunoglobulins G1 and E as well as autoantibodies that cause hemolytic anemia. Marked infiltrative granulocytopoiesis was also apparent, and the animals died after about 12 weeks. Depletion of CD4
+
T cells in mutant mice rescued B cells without reversion of granulocyte abnormalities. T cells did not proliferate in response to polyclonal activators, nor could antigen-specific immune responses be elicited. Thus, IL-2Rβ is required to keep the activation programs of T cells under control, to maintain homeostasis, and to prevent autoimmunity.
Repositioning of a Domain in a Modular Polyketide Synthase to Promote Specific Chain Cleavage
Authors: Cortes Jesus , Wiesmann Kirsten E. H. , Roberts Gareth A. , Brown Murray J. B. , Staunton James , Leadlay Peter F.
Published: October 2006

Macrocyclic polyketides exhibit an impressive range of medically useful activities, and there is great interest in manipulating the genes that govern their synthesis. The 6-deoxyerythronolide B synthase (DEBS) of
Saccharopolyspora erythraea
, which synthesizes the aglycone core of the antibiotic erythromycin A, has been modified by repositioning of a chain-terminating cyclase domain to the carboxyl-terminus of DEBS1, the multienzyme that catalyzes the first two rounds of polyketide chain extension. The resulting mutant markedly accelerates formation of the predicted triketide lactone, compared to a control in which the repositioned domain is inactive. Repositioning of the cyclase should be generally useful for redirecting polyketide synthesis to obtain polyketides of specified chain lengths.
Multiple Origins of Lichen Symbioses in Fungi Suggested by SSU rDNA Phylogeny
Authors: Gargas Andrea , DePriest Paula T. , Grube Martin , Tehler Anders
Published: October 2006

Phylogenetic hypotheses provide a context for examining the evolution of heterotrophic lifestyles. The lichen lifestyle, which is the symbiotic association of fungi with algae, is found in various representatives of Dicaryomycotina, both Ascomycetes and Basidiomycetes. A highly resolved parsimony analysis of small subunit ribosomal DNA (SSU rDNA) sequences suggests at least five independent origins of the lichen habit in disparate groups of Ascomycetes and Basidiomycetes. Because lichen associations arose from parasitic, mycorrhizal, or free-living saprobic fungi, neither mutualism nor parasitism should be construed as endpoints in symbiont evolution.
Reliability of Spike Timing in Neocortical Neurons
Authors: Mainen Zachary F. , Sejnowski Terrence J.
Published: October 2006

It is not known whether the variability of neural activity in the cerebral cortex carries information or reflects noisy underlying mechanisms. In an examination of the reliability of spike generation using recordings from neurons in rat neocortical slices, the precision of spike timing was found to depend on stimulus transients. Constant stimuli led to imprecise spike trains, whereas stimuli with fluctuations resembling synaptic activity produced spike trains with timing reproducible to less than 1 millisecond. These data suggest a low intrinsic noise level in spike generation, which could allow cortical neurons to accurately transform synaptic input into spike sequences, supporting a possible role for spike timing in the processing of cortical information by the neocortex.
Linked Regularities in the Development and Evolution of Mammalian Brains
Authors: Finlay Barbara L. , Darlington Richard B.
Published: October 2006

Analysis of data collected on 131 species of primates, bats, and insectivores showed that the sizes of brain components, from medulla to forebrain, are highly predictable from absolute brain size by a nonlinear function. The order of neurogenesis was found to be highly conserved across a wide range of mammals and to correlate with the relative enlargement of structures as brain size increases, with disproportionately large growth occurring in late-generated structures. Because the order of neurogenesis is conserved, the most likely brain alteration resulting from selection for any behavioral ability may be a coordinated enlargement of the entire nonolfactory brain.
A Nuclear-Encoded Form II RuBisCO in Dinoflagellates
Authors: Morse David , Salois Patrick , Markovic Paul , Hastings J. Woodland
Published: October 2006

The chloroplasts of most dinoflagellates are unusual in that they are surrounded by three membranes and contain the carotenoid peridinin. The ribulose-1,5-bisphosphate carboxylase-oxygenase (RuBisCO) in dinoflagellate chloroplasts was found here to also be unusual. Unlike other eukaryotes, dinoflagellates containing peridinin use a form of RuBisCO (form II) previously found only in some species of proteobacteria. Furthermore, this RuBisCO is not encoded in the chloroplast DNA, as is the case in other organisms, but is encoded by the nuclear DNA. The unusual nature of this enzyme and location of its gene support the idea that dinoflagellate chloroplasts may have had a distinctive evolutionary origin.
Crystal Structure of
Pseudomonas mevalonii
HMG-CoA Reductase at 3.0 Angstrom Resolution
Authors: Lawrence C. Martin , Rodwell Victor W. , Stauffacher Cynthia V.
Published: October 2006

The rate-limiting step in cholesterol biosynthesis in mammals is catalyzed by 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase, a four-electron oxidoreductase that converts HMG-CoA to mevalonate. The crystal structure of HMG-CoA reductase from
Pseudomonas mevalonii
was determined at 3.0 angstrom resolution by multiple isomorphous replacement. The structure reveals a tightly bound dimer that brings together at the subunit interface the conserved residues implicated in substrate binding and catalysis. These dimers are packed about a threefold crystallographic axis, forming a hexamer with 23 point group symmetry. Difference Fourier studies reveal the binding sites for the substrates HMG-CoA and reduced or oxidized nicotinamide adenine dinucleotide [NAD(H)] and demonstrate that the active sites are at the dimer interfaces. The HMG-CoA is bound by a domain with an unusual fold, consisting of a central α helix surrounded by a triangular set of walls of β sheets and α helices. The NAD(H) is bound by a domain characterized by an antiparallel β structure that defines a class of dinucleotide-binding domains.
Construction of a Soluble Adenylyl Cyclase Activated by G
s
α and Forskolin
Authors: Tang Wei-Jen , Gilman Alfred G.
Published: October 2006

A soluble adenylyl cyclase was constructed by linkage of portions of the cytosolic domains of the mammalian type I and type II enzymes. The soluble enzyme was stimulated by both forskolin and the α subunit of the heterotrimeric guanine nucleotide-binding protein (G protein) G
s
(G
s
α). Expression of the construct complemented the catabolic defect in a strain of
Escherichia coli
that is deficient in adenylyl cyclase activity. The active, approximately 60-kilodalton enzyme accumulated in the cytoplasmic fraction of
E. coli
to yield activities in excess of 1 nanomole per minute per milligram of protein. The two sets of transmembrane helices of mammalian adenylyl cyclases are thus not necessary for the catalytic or the most characteristic regulatory activities of the enzyme. This system may be useful for both genetic and biochemical analysis of G protein-regulated adenylyl cyclases.
Experimental Tests of the Roles of Adaptation, Chance, and History in Evolution
Authors: Travisano Michael , Mongold Judith A. , Bennett Albert F. , Lenski Richard E.
Published: October 2006

The contributions of adaptation, chance, and history to the evolution of fitness and cell size were measured in two separate experiments using bacteria. In both experiments, populations propagated in identical environments achieved similar fitnesses, regardless of prior history or subsequent chance events. In contrast, the evolution of cell size, a trait weakly correlated with fitness, was more strongly influenced by history and chance.
Structure-Based Design of Transcription Factors
Authors: Pomerantz Joel L. , Sharp Phillip A. , Pabo Carl O.
Published: October 2006

Computer modeling suggested that transcription factors with novel sequence specificities could be designed by combining known DNA binding domains. This structure-based strategy was tested by construction of a fusion protein, ZFHD1, that contained zinc fingers 1 and 2 from Zif268, a short polypeptide linker, and the homeodomain from Oct-1. The fusion protein bound optimally to a sequence containing adjacent homeodomain (TAATTA) and zinc finger (NGGGNG) subsites. When fused to an activation domain, ZFHD1 regulated promoter activity in vivo in a sequence-specific manner. Analysis of known protein-DNA complexes suggests that many other DNA binding proteins could be designed in a similar fashion.
Cleavage of an Amide Bond by a Ribozyme
Authors: Dai Xiaochang , De Mesmaeker Alain , Joyce Gerald F.
Published: October 2006

A variant form of a group I ribozyme, optimized by in vitro evolution for its ability to catalyze magnesium-dependent phosphoester transfer reactions involving DNA substrates, also catalyzes the cleavage of an unactivated alkyl amide when that linkage is presented in the context of an oligodeoxynucleotide analog. Substrates containing an amide bond that joins either two DNA oligos, or a DNA oligo and a short peptide, are cleaved in a magnesium-dependent fashion to generate the expected products. The first-order rate constant, k
cat
, is 0.1 × 10
-5
min
-1
to 1 × 10
-5
min
-1
for the DNA-flanked substrates, which corresponds to a rate acceleration of more than 10
3
as compared with the uncatalyzed reaction.
A Phagosome-to-Cytosol Pathway for Exogenous Antigens Presented on MHC Class I Molecules
Authors: Kovacsovics-Bankowski M. , Rock K. L.
Published: October 2006

Peptides from endogenous proteins are presented by major histocompatibility complex class I molecules, but antigens (Ags) in the extracellular fluids are generally not. However, pathogens or particulate Ags that are internalized into phagosomes of macrophages (MØs) stimulate CD8 T cells. The presentation of these Ags is resistant to chloroquine but is blocked by inhibitors of the proteasome, a mutation in the TAP1-TAP2 transporter, and brefeldin A. Moreover, phagocytosis of a ribosomal-inactivating protein inhibited MØ protein synthesis. These results demonstrate that MØs transfer Ags from phagosomes into the cytosol and that endogenous and exogenous Ags use a final common pathway for class I presentation.
Inhibition of Ras-Induced Proliferation and Cellular Transformation by p16
INK4
Authors: Serrano Manuel , Gómez-Lahoz Enrique , DePinho Ronald A. , Beach David , Bar-Sagi Dafna
Published: October 2006

The cyclin-dependent kinase 4 (CDK4) regulates progression through the G
1
phase of the cell cycle. The activity of CDK4 is controlled by the opposing effects of the D-type cyclin, an activating subunit, and p16
INK4
, an inhibitory subunit. Ectopic expression of p16
INK4
blocked entry into S phase of the cell cycle induced by oncogenic Ha-Ras, and this block was relieved by coexpression of a catalytically inactive CDK4 mutant. Expression of p16
INK4
suppressed cellular transformation of primary rat embryo fibroblasts by oncogenic Ha-Ras and Myc, but not by Ha-Ras and E1a. Together, these observations provide direct evidence that p16
INK4
can inhibit cell growth.
Mechanisms of Rhodopsin Inactivation in Vivo as Revealed by a COOH-Terminal Truncation Mutant
Authors: Chen Jeannie , Makino Clint L. , Peachey Neal S. , Baylor Denis A. , Simon Melvin I.
Published: October 2006

Although biochemical experiments suggest that rhodopsin and other receptors coupled to heterotrimeric guanosine triphosphate-binding proteins (G proteins) are inactivated by phosphorylation near the carboxyl (COOH)-terminus and the subsequent binding of a capping protein, little is known about the quenching process in vivo. Flash responses were recorded from rods of transgenic mice in which a fraction of the rhodopsin molecules lacked the COOH-terminal phosphorylation sites. In the single photon regime, abnormally prolonged responses, attributed to activation of individual truncated rhodopsins, occurred interspersed with normal responses. The occurrence of the prolonged responses suggests that phosphorylation is required for normal shutoff. Comparison of normal and prolonged single photon responses indicated that rhodopsin begins to be quenched before the peak of the electrical response and that quenching limits the response amplitude.
Structural Basis for Sugar Translocation Through Maltoporin Channels at 3.1 Å Resolution
Authors: Schirmer Tilman , Keller Thomas A. , Wang Yan-Fei , Rosenbusch Jurg P.
Published: October 2006

Trimeric maltoporin (LamB protein) facilitates the diffusion of maltodextrins across the outer membrane of Gram-negative bacteria. The crystal structure of maltoporin from
Escherichia coli
, determined to a resolution of 3.1 angstroms, reveals an 18-stranded, antiparallel β-barrel that forms the framework of the channel. Three inwardly folded loops contribute to a constriction about halfway through the channel. Six contingent aromatic residues line the channel and form a path from the vestibule to the periplasmic outlet. Soaking of a crystal with maltotriose revealed binding of the sugar to this hydrophobic track across the constriction, which suggests that maltose and linear oligosaccharides may be translocated across the membrane by guided diffusion along this path.
Mutations of Keratinocyte Transglutaminase in Lamellar Ichthyosis
Authors: Huber Marcel , Rettler Irmingard , Bernasconi Katja , Frenk Edgar , Lavrijsen Sjan P. M. , Ponec Maria , Bon Anita , Lautenschlager Stefan , Schorderet Daniel F. , Hohl Daniel
Published: October 2006

Lamellar ichthyosis is a severe congenital skin disorder characterized by generalized large scales and variable redness. Affected individuals in three families exhibited drastically reduced keratinocyte transglutaminase (TGK) activity. In two of these families, expression of
TGK
transcripts was diminished or abnormal and no TGK protein was detected. Homozygous or compound heterozygous mutations of the
TGK
gene were identified in all families. These data suggest that defects in TGK cause lamellar ichthyosis and that intact cross-linkage of cornified cell envelopes is required for epidermal tissue homeostasis.
Imaging with Intermolecular Multiple-Quantum Coherences in Solution Nuclear Magnetic Resonance
Authors: Richter Wolfgang , Lee Sanghyuk , Warren Warren S. , He Qiuhong
Published: October 2006

A magnetic resonance imaging technique based on intermolecular multiple-quantum coherences in solution (the correlated spectroscopy revamped by asymmetric
z
gradient echo detection or CRAZED experiment) is described here. Correlations between spins in different molecules were detected by magnetic-field gradient pulses. In order for a correlation to yield an observable signal, the separation between the two spins must be within a narrow band that depends on the area of the gradient pulses. The separation can be tuned from less than 10 micrometers to more than 1 millimeter, a convenient range for many applications.
Neutron Reflection Study of Bovine β-Casein Adsorbed on OTS Self-Assembled Monolayers
Authors: Fragneto Giovanna , Thomas Robert K. , Rennie Adrian R. , Penfold Jeffrey
Published: October 2006

Specular neutron reflection has been used to determine the structure and composition of bovine β-casein adsorbed on a solid surface from an aqueous phosphate-buffered solution at pH 7. The protein was adsorbed on a hydrophobic monolayer self-assembled from deuterated octadecyltrichlorosilane solution on a silicon (111) surface. A two-layer structure formed consisting of one dense layer of thickness 23 ± 1 angstroms and a surface coverage of 1.9 milligrams per square meter adjacent to the surface and an external layer protruding into the solution of thickness 35 ± 1 angstroms and 12 percent protein volume fraction. The structure of the (β-casein) layer is explained in terms of the charge distribution in the protein.
Minor Groove Recognition of the Conserved G⋅U Pair at the
Tetrahymena ribozyme
Reaction Site
Authors: Strobel Scott A. , Cech Thomas R.
Published: October 2006

The guanine-uracil (G⋅U) base pair that helps to define the 5′-splice site of group I introns is phylogenetically highly conserved. In such a wobble base pair, G makes two hydrogen bonds with U in a geometry shifted from that of a canonical Watson-Crick pair. The contribution made by individual functional groups of the G⋅U pair in the context of the
Tetrahymena
ribozyme was examined by replacement of the G⋅U pair with synthetic base pairs that maintain a wobble configuration, but that systematically alter functional groups in the major and minor grooves of the duplex. The substitutions demonstrate that the exocyclic amine of G, when presented on the minor groove surface by the wobble base pair conformation, contributes substantially (2 kilocalories⋅mole
-1
) to binding by making a tertiary interaction with the ribozyme active site. It contributes additionally to transition state stabilization. The ribozyme active site also makes tertiary contacts with a tripod of 2′-hydroxyls on the minor groove surface of the splice site helix. This suggests that the ribozyme binds the duplex primarily in the minor groove. The alanyl aminoacyl transfer RNA (tRNA) synthetase recognizes the exocyclic amine of an invariant G⋅U pair and contacts a similar array of 2′-hydroxyls when binding the tRNA
Ala
acceptor stem, providing an unanticipated parallel between protein-RNA and RNA-RNA interactions.