bluuebunny/crossref_metadata_2025 huggingface dataset:
Positive and Negative Thymocyte Selection Induced by Different Concentrations of a Single Peptide
Authors: Sebzda Eric , Wallace Valerie A. , Mayer John , Yeung Rae S. M. , Mak Tak W. , Ohashi Pamela S.
Published: October 2006

T lymphocyte maturation is dependent on interactions between the T cell receptor (TCR) expressed on the developing thymocyte and intrathymic major histocompatibility complex (MHC)-peptide ligands. The relation between the peptide-MHC complex that results in negative or positive selection has not been identified. Here, the requirements for the maturation of thymocytes expressing a defined transgenic TCR specific for a viral peptide are studied in fetal thymic organ culture. Low concentrations of the viral peptide antigen recognized by this transgenic TCR can mediate positive selection, whereas high concentrations result in thymocyte tolerance. These findings support the affinity-avidity model of thymocyte selection.
Coatomer Interaction with Di-Lysine Endoplasmic Reticulum Retention Motifs
Authors: Cosson Pierre , Letourneur François
Published: October 2006

Although signals for retention in the endoplasmic reticulum (ER) have been identified in the cytoplasmic domain of various ER-resident type I transmembrane proteins, the mechanisms responsible for ER retention are still unknown. Yeast and mammalian ER retention motifs interacted specifically in cell lysates with the coatomer, a polypeptide complex implicated in membrane traffic. Mutations that affect the ER retention capacity of the motifs also abolished binding of the coatomer. These results suggest a role for the coatomer in the retrieval of transmembrane proteins to the ER in both yeast and mammals.
High-Resolution Solution Structure of the β Chemokine hMIP-1β by Multidimensional NMR
Authors: Lodi Patricia J. , Garrett Daniel S. , Kuszewski John , Tsang Monica L.-S. , Weatherbee James A. , Leonard Warren J. , Gronenborn Angela M. , Clore G. Marius
Published: October 2006

The three-dimensional structure of a member of the β subfamily of chemokines, human macrophage inflammatory protein-1β (hMIP-1β), has been determined with the use of solution multidimensional heteronuclear magnetic resonance spectroscopy. Human MIP-1β is a symmetric homodimer with a relative molecular mass of ∼16 kilodaltons. The structure of the hMIP-1β monomer is similar to that of the related α chemokine interleukin-8 (IL-8). However, the quaternary structures of the two proteins are entirely distinct, and the dimer interface is formed by a completely different set of residues. Whereas the IL-8 dimer is globular, the hMIP-1β dimer is elongated and cylindrical. This provides a rational explanation for the absence of cross-binding and reactivity between the α and β chemokine subfamilies. Calculation of the solvation free energies of dimerization suggests that the formation and stabilization of the two different types of dimers arise from the burial of hydrophobic residues.
Direct Signaling from Astrocytes to Neurons in Cultures of Mammalian Brain Cells
Authors: Nedergaard Maiken
Published: October 2006

Although astrocytes have been considered to be supportive, rather than transmissive, in the adult nervous system, recent studies have challenged this assumption by demonstrating that astrocytes possess functional neurotransmitter receptors. Astrocytes are now shown to directly modulate the free cytosolic calcium, and hence transmission characteristics, of neighboring neurons. When a focal electric field potential was applied to single astrocytes in mixed cultures of rat forebrain astrocytes and neurons, a prompt elevation of calcium occurred in the target cell. This in turn triggered a wave of calcium increase, which propagated from astrocyte to astrocyte. Neurons resting on these astrocytes responded with large increases in their concentration of cytosolic calcium. The gap junction blocker octanol attenuated the neuronal response, which suggests that the astrocytic-neuronal signaling is mediated through intercellular connections rather than synaptically. This neuronal response to local astrocytic stimulation may mediate local intercellular communication within the brain.
Characterization of Type I Receptors for Transforming Growth Factor-β and Activin
Authors: ten Dijke Peter , Yamashita Hidetoshi , Ichijo Hidenori , Franzén Petra , Laiho Marikki , Miyazono Kohei , Heldin Carl-Henrik
Published: October 2006

Transforming growth factor-β (TGF-β) and activin exert their effects by binding to heteromeric complexes of type I and type II receptors. The type II receptors for TGF-β and activin are transmembrane serine-threonine kinases; a series of related receptors, denoted activin receptor-like kinase (ALK) 1 to 5, have recently been identified, and ALK-6 is described here. ALK-5 has been shown to be a functional TGF-β type I receptor. A systematic analysis revealed that most ALKs formed heteromeric complexes with the type II receptors for TGF-β and activin after overexpression in COS cells; however, among the six ALKs, only ALK-5 was a functional TGF-β type I receptor for activation of plasminogen activator inhibitor-1, and only ALK-2 and ALK-4 bound activin with high affinity.
Neutrophil Activation by Monomeric Interleukin-8
Authors: Rajarathnam Krishnakumar , Sykes Brian D. , Kay Cyril M. , Dewald Beatrice , Geiser Thomas , Baggiolini Marco , Clark-Lewis Ian
Published: October 2006

Interleukin-8 (IL-8), a pro-inflammatory protein, has been shown by nuclear magnetic resonance (NMR) and x-ray techniques to exist as a homodimer. An IL-8 analog was chemically synthesized, with the amide nitrogen of leucine-25 methylated to selectively block formation of hydrogen bonds between monomers and thereby prevent dimerization. This analog was shown to be a monomer, as assessed by analytical ultracentrifugation and NMR. Nevertheless, it was equivalent to IL-8 in assays of neutrophil activation, which indicates that the monomer is a functional form of IL-8.
Stat3: a STAT Family Member Activated by Tyrosine Phosphorylation in Response to Epidermal Growth Factor and Interleukin-6
Authors: Zhong Zhong , Wen Zilong , Darnell James E.
Published: October 2006

The STAT family of proteins carries out a dual function: signal transduction and activation of transcription. A new family member, Stat3, becomes activated through phosphorylation on tyrosine as a DNA binding protein in response to epidermal growth factor (EGF) and interleukin-6 (IL-6) but not interferon γ (IFN-γ). It is likely that this phosphoprotein forms homodimers as well as heterodimers with the first described member of the STAT family, Stat91 (renamed Stat1 α), which is activated by the IFNs and EGF. Differential activation of different STAT proteins in response to different ligands should help to explain specificity in nuclear signaling from the cell surface.
Binding and Suppression of the Myc Transcriptional Activation Domain by p107
Authors: Gu Wei , Bhatia Kishor , Magrath lan T. , Dang Chi V. , Dalla-Favera Riccardo
Published: October 2006

An amino-terminal transactivation domain is required for Myc to function as a transcription factor controlling cell proliferation, differentiation, and apoptosis. A complementary DNA expression library was screened with a Myc fusion protein to identify proteins interacting with this domain, and a clone encoding the Rb-related p107 protein was isolated. The p107 protein was shown to associate with Myc in vivo and to suppress the activity of the Myc transactivation domain. However, mutant forms of Myc from Burkitt lymphoma cells, which contain sequence alterations in the transactivation domain, were resistant to p107-mediated suppression. Thus, disruption of a regulatory interaction between Myc and p107 may be important in tumorigenesis.
Related Target Enhancers for Dorsal and NF-κB Signaling Pathways
Authors: González-Crespo Sergio , Levine Michael
Published: October 2006

Drosophila dorsoventral
(DV) patterning and mammalian hematopoiesis are regulated by related signaling pathways (Toll, interleukin-1) and transcription factors (dorsal, nuclear factor-κB). These factors interact with related enhancers, such as the
rhomboid
NEE and κ light chain enhancer, that contain similar arrangements of activator and repressor binding sites. It is shown that the κ enhancer can generate lateral stripes of gene expression in transgenic
Drosophila
embryos in a pattern similar to that directed by the
rhomboid
NEE.
Drosophila
DV determinants direct these stripes through the corresponding mammalian cis regulatory elements in the κ enhancer, including the κB site and κE boxes. These results suggest that enhancers can couple conserved signaling pathways to divergent gene functions.
Recombination in Adaptive Mutation
Authors: Harris Reuben S. , Longerich Simonne , Rosenberg Susan M.
Published: October 2006

The genetic requirements for adaptive mutation in
Escherichia coli
parallel those for homologous recombination in the
recB
CD pathway. Recombination-deficient
recA
and
recB
null mutant strains are deficient in adaptive reversion. A hyper-recombinagenic
recD
strain is hypermutable, and its hypermutation depends on functional
recA
and
recB
genes. Genes of subsidiary recombination systems are not required. These results indicate that the molecular mechanism by which adaptive mutation occurs includes recombination. No such association is seen for spontaneous mutation in growing cells.
Prevention of Drug Access to Bacterial Targets: Permeability Barriers and Active Efflux
Authors: Nikaido Hiroshi
Published: October 2006

Some species of bacteria have low-permeability membrane barriers and are thereby "intrinsically" resistant to many antibiotics; they are selected out in the multitude of antibiotics present in the hospital environment and thus cause many hospital-acquired infections. Some strains of originally antibiotic-susceptible species may also acquire resistance through decreases in the permeability of membrane barriers. Another mechanism for preventing access of drugs to targets is the membrane-associated energy-driven efflux, which plays a major role in drug resistance, especially in combination with the permeation barrier. Recent results indicate the existence of bacterial efflux systems of extremely broad substrate specificity, in many ways reminiscent of the multidrug resistance pump of mammalian cells. One such system seems to play a major role in the intrinsic resistance of
Pseudomonas aeruginosa
, a common opportunistic pathogen. As the pharmaceutical industry succeeds in producing agents that can overcome specific mechanisms of bacterial resistance, less specific resistance mechanisms such as permeability barriers and multidrug active efflux may become increasingly significant in the clinical setting.
A Mass Spectrometric Solution to the Address Problem of Combinatorial Libraries
Authors: Brummel Christopher L. , Lee Irene N. W. , Zhou Ying , Benkovic Stephen J. , Winograd Nicholas
Published: October 2006

The molecular weights of femtomole quantities of small peptides attached to polystyrene beads have been determined with imaging time-of-flight secondary ion mass spectrometry. The analysis is made possible by the selective clipping of the bond linking the peptide to a bead with trifluoroacetic acid vapor before the secondary ion mass spectrometry assay. The approach can be applied to large numbers of 30- to 60-micrometer polystyrene beads for the direct characterization of massive combinatorial libraries.
Structure of the Tet Repressor-tetracycline Complex and Regulation of Antibiotic Resistance
Authors: Hinrichs Winfried , Kisker Caroline , Düvel Martina , Müller Alexander , Tovar Karlheinz , Hillen Wolfgang , Saenger Wolfram
Published: October 2006

The most frequently occurring resistance of Gram-negative bacteria against tetracyclines is triggered by drug recognition of the Tet repressor. This causes dissociation of the repressor-operator DNA complex and enables expression of the resistance protein TetA, which is responsible for active efflux of tetracycline. The 2.5 angstrom resolution crystal structure of the homodimeric Tet repressor complexed with tetracycline-magnesium reveals detailed drug recognition. The orientation of the operator-binding helix-turn-helix motifs of the repressor is inverted in comparison with other DNA binding proteins. The repressor-drug complex is unable to interact with DNA because the separation of the DNA binding motifs is 5 angstroms wider than usually observed.
Diet and Health: What Should We Eat?
Authors: Willett Walter C.
Published: October 2006

Many recent studies have implicated dietary factors in the cause and prevention of important diseases, including cancer, coronary heart disease, birth defects, and cataracts. There is strong evidence that vegetables and fruits protect against these diseases; however, the active constituents are incompletely identified. Whether fat per se is a major cause of disease is a question still under debate, although saturated and partially hydrogenated fats probably increase the risk of coronary heart disease. One clear conclusion from existing epidemiologic evidence is that many individuals in the United States have suboptimal diets and that the potential for disease prevention by improved nutrition is substantial.
Bacillus subtilis
spoIIIE Protein Required for DNA Segregation During Asymmetric Cell Division
Authors: Wu Ling Juan , Errington Jeffery
Published: October 2006

Sporulation in
Bacillus subtilis
begins with an asymmetric cell division, producing a smaller prespore and a larger mother cell, both of which contain intact copies of the chromosome. The
spoIIIE
gene is required for chromosome segregation into the prespore compartment. The effects of the
spoIIIE36
mutation on σ
F
-dependent transcription are an indirect consequence of the failure of certain genes to enter the cellular compartment in which their transcription factor has become active. SpoIIIE may also be required to prevent σ
F
from becoming active in the mother cell.
Genetic Control of Programmed Cell Death in
Drosophila
Authors: White Kristin , Grether Megan E. , Abrams John M. , Young Lynn , Farrell Kim , Steller Hermann
Published: October 2006

A gene,
reaper
(
rpr
), that appears to play a central control function for the initiation of programmed cell death (apoptosis) in
Drosophila
was identified. Virtually all programmed cell death that normally occurs during
Drosophila
embryogenesis was blocked in embryos homozygous for a small deletion that includes the
reaper
gene. Mutant embryos contained many extra cells and failed to hatch, but many other aspects of development appeared quite normal. Deletions that include
reaper
also protected embryos from apoptosis caused by x-irradiation and developmental defects. However, high doses of x-rays induced some apoptosis in mutant embryos, and the resulting corpses were phagocytosed by macrophages. These data suggest that the basic cell death program is intact although it was not activated in mutant embryos. The DNA encompassed by the deletion was cloned and the
reaper
gene was identified on the basis of the ability of cloned DNA to restore apoptosis to cell death defective embryos in germ line transformation experiments. The
reaper
gene appears to encode a small peptide that shows no homology to known proteins, and
reaper
messenger RNA is expressed in cells destined to undergo apoptosis.
Involvement of Granulocyte-Macrophage Colony-Stimulating Factor in Pulmonary Homeostasis
Authors: Dranoff Glenn , Crawford Alexander D. , Sadelain Michel , Ream Beverly , Rashid Asif , Bronson Roderick T. , Dickersin G. Richard , Bachurski Cindy J. , Mark Eugene L. , Whitsett Jeffrey A. , Mulligan Richard C.
Published: October 2006

The in vivo function of murine granulocyte-macrophage colony-stimulating factor (GM-CSF) was investigated in mice, carrying a null allele of the GM-CSF gene, that were generated by gene targeting techniques in embryonic stem cells. Although steady-state hematopoiesis was unimpaired in homozygous mutant animals, all animals developed the progressive accumulation of surfactant lipids and proteins in the alveolar space, the defining characteristic of the idiopathic human disorder pulmonary alveolar proteinosis. Extensive lymphoid hyperplasia associated with lung airways and blood vessels was also found, yet no infectious agents could be detected. These results demonstrate that GM-CSF is not an essential growth factor for basal hematopoiesis and reveal an unexpected, critical role for GM-CSF in pulmonary homeostasis.
Nature's Carbonylation Catalyst: Raman Spectroscopic Evidence That Carbon Monoxide Binds to Iron, Not Nickel, in CO Dehydrogenase
Authors: Qiu Di , Kumar Manoj , Ragsdale Stephen W. , Spiro Thomas G.
Published: October 2006

Carbon monoxide dehydrogenase catalyzes the synthesis of acetyl-coenzyme A from coenzyme A, a methyl group, and carbon monoxide. The carbon monoxide binds to a mixed metal center of the enzyme, which contains nickel bridged to an iron-sulfur cluster. Resonance Raman spectroscopy has been used to identify both C-O stretching and metal-CO stretching vibrations of the carbon monoxide adduct of the enzyme. This adduct was shown by isotopic exchange to be on the pathway for acetyl-coenzyme A synthesis. The metal to which carbon monoxide is bound was established to be iron, not nickel, by preparation of enzyme from bacteria grown on iron-54 and nickel-64. The Fe-CO frequency is low, 360 wave numbers, implying a weak bond, probably because of electron donation from sulfide and thiolate ligands of the iron. A bimetallic mechanism is proposed, in which carbon monoxide binds to an iron atom and is subsequently attacked by a methyl group on a nearby nickel atom, forming an acetyl ligand, which is then transferred to coenzyme A.
Microtubule Dynamics Modulated by Guanosine Triphosphate Hydrolysis Activity of β-Tubulin
Authors: Davis Ashley , Sage Carleton R. , Dougherty Cynthia A. , Farrell Kevin W.
Published: October 2006

Microtubule dynamic instability underlies many cellular functions, including spindle morphogenesis and chromosome movement. The role of guanosine triphosphate (GTP) hydrolysis in dynamic instability was investigated by introduction of four mutations into yeast β-tubulin at amino acids 103 to 109, a site thought to participate in GTP hydrolysis. Three of the mutations increased both the assembly-dependent rate of GTP hydrolysis and the average length of steady-state microtubules over time, a measure of dynamic instability. The fourth mutation did not substantially affect the rate of GTP hydrolysis or the steady-state microtubule lengths. These results demonstrate that the rate of GTP hydrolysis can modulate microtubule length and hence dynamic instability.
A Panoramic Code for Sound Location by Cortical Neurons
Authors: Middlebrooks John C. , Clock Ann E. , Xu Li , Green David M.
Published: October 2006

By conventional spike count measures, auditory neurons in the cat's anterior ectosylvian sulcus cortical area are broadly tuned for the location of a sound source. Nevertheless, an artificial neural network was trained to classify the temporal spike patterns of single neurons according to sound location. The spike patterns of 73 percent of single neurons coded sound location with more than twice the chance level of accuracy, and spike patterns consistently carried more information than spike counts alone. In contrast to neurons that are sharply tuned for location, these neurons appear to encode sound locations throughout 360° of azimuth.
Activity-Dependent Changes in the Intrinsic Properties of Cultured Neurons
Authors: Turrigiano Gina , Abbott L. F. , Marder Eve
Published: October 2006

Learning and memory arise through activity-dependent modifications of neural circuits. Although the activity dependence of synaptic efficacy has been studied extensively, less is known about how activity shapes the intrinsic electrical properties of neurons. Lobster stomatogastric ganglion neurons fire in bursts when receiving synaptic and modulatory input but fire tonically when pharmacologically isolated. Long-term isolation in culture changed their intrinsic activity from tonic firing to burst firing. Rhythmic stimulation reversed this transition through a mechanism that was mediated by a rise in intracellular calcium concentration. These data suggest that neurons regulate their conductances to maintain stable activity patterns and that the intrinsic properties of a neuron depend on its recent history of activation.
Highly Conjugated, Acetylenyl Bridged Porphyrins: New Models for Light-Harvesting Antenna Systems
Authors: Lin Victor S.-Y. , DiMagno Stephen G. , Therien Michael J.
Published: October 2006

A new class of porphyrin-based chromophore systems has been prepared from ethyne-elaborated porphyrin synthons through the use of metal-mediated cross-coupling methodologies. These systems feature porphyrin chromophores wired together through single ethynyl linkages. This type of topological connectivity affords exceptional electronic interactions between the chromophores which are manifest in their room temperature photophysics, optical spectroscopy, and electrochemistry; these spectroscopic signatures indicate that these species model many of the essential characteristics of biological light-harvesting antenna systems.
Rules for α-Helix Termination by Glycine
Authors: Aurora Rajeev , Srinivasan Rajgopal , Rose George D.
Published: October 2006

A predictive rule for protein folding is presented that involves two recurrent glycine-based motifs that cap the carboxyl termini of α helices. In proteins, helices that terminated in glycine residues were found predominantly in one of these two motifs. These glycine structures had a characteristic pattern of polar and apolar residues. Visual inspection of known helical sequences was sufficient to distinguish the two motifs from each other and from internal glycines that fail to terminate helices. These glycine motifs—in which the local sequence selects between available structures—represent an example of a stereochemical rule for protein folding.
Short-Range DNA Looping by the
Xenopus
HMG-Box Transcription Factor, xUBF
Authors: Bazett-Jones David P. , Leblanc Benoît , Herfort Manfred , Moss Tom
Published: October 2006

Xenopus
UBF (xUBF) interacts with DNA by way of multiple HMG-box domains. When xUBF binds to the ribosomal promoter, the carboxyl-terminal acidic tail and amino-terminal HMG-box interact. Binding also leads to negative DNA supercoiling and the formation of a disk-like structure, the enhancesome. Within the enhancesome, an xUBF dimer makes a low-density protein core around which DNA is looped into a single 180-base pair turn, probably by in-phase bending. The enhancesome structure suggests a mechanism for xUBF-dependent recruitment of the TATA box-binding protein complex without direct interaction between the two factors.
Mechanism of Catalytic Oxygenation of Alkanes by Halogenated Iron Porphyrins
Authors: Grinstaff Mark W. , Hill Michael G. , Labinger Jay A. , Gray Harry B.
Published: October 2006

Halogenation of an iron porphyrin causes severe saddling of the macrocyclic structure and a large positive shift in the iron(III)/(II) redox couple. Although perhalogenated iron(II) porphyrins such as Fe(TFPPBr
8
) [H
2
TFPPBr
8
, β-octabromo-tetrakis(pentafluorophenyl)-porphyrin] are relatively resistant to autoxidation, they rapidly reduce alkyl hydroperoxides. These and related reactivity studies suggest that catalysis of alkane oxygenation by Fe(TFPPBr
8
)Cl occurs through a radical-chain mechanism in which the radicals are generated by oxidation and reduction of alkyl hydroperoxides.
Prevention of Lipopolysaccharide-Induced Lethal Toxicity by Tyrosine Kinase Inhibitors
Authors: Novogrodsky Abraham , Vanichkin Alexey , Patya Miriam , Gazit Aviv , Osherov Nir , Levitzki Alexander
Published: October 2006

Septic shock results from excessive stimulation of the host immune system, especially macrophages, by lipopolysaccharide (LPS), or endotoxin, which resides on the outer membrane of bacteria. Protein tyrosine kinase inhibitors of the tyrphostin AG 126 family protect mice against LPS-induced lethal toxicity. The protection correlates with the ability of these agents to block LPS-induced production of tumor necrosis factor α (TNF-α) and nitric oxide in macrophages as well as LPS-induced production of TNF-α in vivo. Furthermore, this inhibitory effect correlated with the potency of AG 126 to block LPS-induced tyrosine phosphorylation of a p42
MAPK
protein substrate in the murine macrophage.
Interaction of MHC Class I Molecules with the Transporter Associated with Antigen Processing
Authors: Suh Woong-Kyung , Cohen-Doyle Myrna F. , Fruh Klaus , Wang Kena , Peterson Per A. , Williams David B.
Published: October 2006

The transporter associated with antigen processing (TAP) delivers cytosolic peptides into the endoplasmic reticulum (ER) where they bind to nascent class I histocompatibility molecules. Class I-peptide complexes are then displayed at the cell surface for recognition by cytotoxic T lymphocytes. Immunoprecipitation of either TAP or class I molecules revealed an association between the transporter and diverse class I products. TAP bound preferentially to heterodimers of the class I heavy chain and β
2
-microglobulin, and the complex subsequently dissociated in parallel with transport of class I molecules from the ER to the Golgi apparatus. The TAP-class I complexes could also be dissociated in vitro by the addition of class I-binding peptides. The association of class I molecules with TAP likely promotes efficient capture of peptides before their exposure to the lumen of the ER.
Candidate Gene Associated with a Mutation Causing Recessive Polycystic Kidney Disease in Mice
Authors: Moyer Judith H. , Lee-Tischler Monica J. , Kwon Heajoon-Y. , Schrick Jeffrey J. , Avner Ellis D. , Sweeney William E. , Godfrey Virginia L. , Cacheiro Nestor L. A. , Wilkinson J. Erby , Woychik Richard P.
Published: October 2006

A line of transgenic mice was generated that contains an insertional mutation causing a phenotype similar to human autosomal recessive polycystic kidney disease. Homozygotes displayed a complex phenotype that included bilateral polycystic kidneys and an unusual liver lesion. The mutant locus was cloned and characterized through use of the transgene as a molecular marker. Additionally, a candidate polycystic kidney disease (PKD) gene was identified whose structure and expression are directly associated with the mutant locus. A complementary DNA derived from this gene predicted a peptide containing a motif that was originally identified in several genes involved in cell cycle control.
An Increased Percentage of Long Amyloid β Protein Secreted by Familial Amyloid β Protein Precursor (βApp
717
) Mutants
Authors: Suzuki Nobuhiro , Cheung Tobun T. , Cai Xiao-Dan , Odaka Asano , Otvos Laszlo , Eckman Christopher , Golde Todd E. , Younkin Steven G.
Published: October 2006

Normal processing of the amyloid β protein precursor (βAPP) results in secretion of a soluble 4-kilodalton protein essentially identical to the amyloid β protein (Aβ) that forms insoluble fibrillar deposits in Alzheimer's disease. Human neuroblastoma (M17) cells transfected with constructs expressing wild-type βAPP or the βAPP
717
mutants linked to familial Alzheimer's disease were compared by (i) isolation of metabolically labeled 4-kilodalton Aβ from conditioned medium, digestion with cyanogen bromide, and analysis of the carboxyl-terminal peptides released, or (ii) analysis of the Aβ in conditioned medium with sandwich enzyme-linked immunosorbent assays that discriminate Aβ
1-40
from the longer Aβ
1-42
. Both methods demonstrated that the 4-kilodalton Aβ released from wild-type βAPP is primarily but not exclusively Aβ
1-40
. The βAPP
717
mutations, which are located three residues carboxyl to Aβ
43
, consistently caused a 1.5- to 1.9-fold increase in the percentage of longer Aβ generated. Long Aβ (for example, Aβ
1-42
) forms insoluble amyloid fibrils more rapidly than Aβ
1-40
. Thus, the βAPP
717
mutants may cause Alzheimer's disease because they secrete increased amounts of long Aβ, thereby fostering amyloid deposition.
Structure of the Allosteric Regulatory Enzyme of Purine Biosynthesis
Authors: Smith Janet L. , Zaluzec Eugene J. , Wery Jean-Pierre , Niu Liwen , Switzer Robert L. , Zalkin Howard , Satow Yoshinori
Published: October 2006

Multiwavelength anomalous diffraction (MAD) has been used to determine the structure of the regulatory enzyme of de novo synthesis of purine nucleotides, glutamine 5-phosphoribosyl-1-pyrophosphate (PRPP) amidotransferase, fromBacillus subtilis. This allosteric enzyme, a 200-kilodalton tetramer, is subject to end product regulation by purine nucleotides. The metalloenzyme fromB. subtilisis a paradigm for the higher eukaryotic enzymes, which have been refractory to isolation in stable form. The two folding domains of the polypeptide are correlated with functional domains for glutamine binding and for transfer of ammonia to the substrate PRPP. Eight molecules of the feedback inhibitor adenosine monophosphate (AMP) are bound to the tetrameric enzyme in two types of binding sites: the PRPP catalytic site of each subunit and an unusual regulatory site that is immediately adjacent to each active site but is between subunits. An oxygen-sensitive [4Fe-4S] cluster in each subunit is proposed to regulate protein turnover in vivo and is distant from the catalytic site. Oxygen sensitivity of the cluster is diminished by AMP, which blocks a channel through the protein to the cluster. The structure is representative of both glutamine amidotransferases and phosphoribosyltransferases.
Estrogen Receptor-Associated Proteins: Possible Mediators of Hormone-Induced Transcription
Authors: Halachmi Shlomit , Marden Emily , Martin Glover , MacKay Heather , Abbondanza Ciro , Brown Myles
Published: October 2006

The estrogen receptor is a transcription factor which, when bound to estradiol, binds DNA and regulates expression of estrogen-responsive genes. A 160-kilodalton estrogen receptor-associated protein, ERAP160, was identified that exhibits estradiol-dependent binding to the receptor. Mutational analysis of the receptor shows that its ability to activate transcription parallels its ability to bind ERAP160. Antiestrogens are unable to promote ERAP160 binding and can block the estrogen-dependent interaction of the receptor and ERAP160 in a dose-dependent manner. This evidence suggests that ERAP160 may mediate estradiol-dependent transcriptional activation by the estrogen receptor. Furthermore, the ability of antiestrogens to block estrogen receptor-ERAP160 complex formation could account for their therapeutic effects in breast cancer.
The Structural Basis of Sequence-Independent Peptide Binding by OppA Protein
Authors: Tame Jeremy R. H. , Murshudov Garib N. , Dodson Eleanor J. , Neil Teresa K. , Dodson Guy G. , Higgins Christopher F. , Wilkinson Anthony J.
Published: October 2006

Specific protein-ligand interactions are critical for cellular function, and most proteins select their partners with sharp discrimination. However, the oligopeptide-binding protein of
Salmonella typhimurium
(OppA) binds peptides of two to five amino acid residues without regard to sequence. The crystal structure of OppA reveals a three-domain organization, unlike other periplasmic binding proteins. In OppA-peptide complexes, the ligands are completely enclosed in the protein interior, a mode of binding that normally imposes tight specificity. The protein fulfills the hydrogen bonding and electrostatic potential of the ligand main chain and accommodates the peptide side chains in voluminous hydrated cavities.
ZAP-70 Deficiency in an Autosomal Recessive form of Severe Combined Immunodeficiency
Authors: Chan Andrew C. , Kadlecek Theresa A. , Elder Melissa E. , Filipovich Alexandra H. , Kuo Wen-Lin , Iwashima Makio , Parslow Tristram G. , Weiss Arthur
Published: October 2006

Protein tyrosine kinases (PTKs) play an integral role in T cell activation and differentiation. Defects in the Src-family PTKs in mice and in T cell lines have resulted in variable defects in thymic development and in T cell antigen receptor (TCR) signal transduction. Here, three siblings are described with an autosomal recessive form of severe combined immunodeficiency disease (SCID) in which ZAP-70, a non-Src PTK, is absent as a result of mutations in the ZAP-70 gene. This absence is associated with defects in TCR signal transduction, suggesting an important functional role for ZAP-70.
Attenuation of Fungal Virulence by Synthetic Infectious Hypovirus Transcripts
Authors: Chen Baoshan , Choi Gil H. , Nuss Donald L.
Published: October 2006

Noninfectious, cytoplasmically transmissible viral double-stranded RNAs of the genus
Hypovirus
cause reduced virulence (hypovirulence) in the chestnut blight fungus
Cryphonectria parasitica
, providing the basis for virus-mediated biological control of a fungal disease. Synthetic transcripts corresponding to a full-length hypovirus RNA coding strand are infectious when introduced into fungal spheroplasts by electroporation. Hypovirus infections were readily established in
Cryphonectria parasitica
and in related fungal species not previously reported to harbor viruses. These results demonstrate the use of a synthetic mycovirus transcript to expand fungal host range, thereby broadening the potential application of virus-mediated hypovirulence to control fungal pathogenesis.
Silencers and Domains of Generalized Repression
Authors: Loo Stephen , Rine Jasper
Published: October 2006

Gene expression can be affected by the chromosomal position of the gene. An example of this position effect is silencing of the
HML
and
HMR
mating-type loci of
Saccharomyces cerevisiae
. An in vitro assay revealed that silencing induced a transcription-independent general occlusion of the DNA at
HMR
from sequence-specific interactions of proteins with DNA. The minimum boundaries of the silenced chromatin structure were determined, as were the contributions of the E and I silencers to the size of the silenced domain. Examination of endonuclease-sensitive sites provided evidence that neither the integrity of the chromosomal duplex nor covalent linkage of the silencers to
HMR
was important for maintenance of the silenced structure in vitro.
Built for Jumping: the Design of the Frog Muscular System
Authors: Lutz Gordon J. , Rome Lawrence C.
Published: October 2006

Frogs must generate a high level of mechanical power when they jump. The muscular system of frogs that jump is presumably designed to deliver these high powers. The length changes and activation pattern that muscles undergo during jumping were measured, and isolated muscle bundles were driven through this in vivo pattern. During jumping, muscles generated maximum power. Specifically, the muscle fibers (i) operated at optimal sarcomere lengths, (ii) operated at optimal shortening velocities, and (iii) were maximally activated during power generation. Thus, many different parameters must have evolved in concert to produce a system capable of this explosive jumping movement.
Benefit to Male Sailfin Mollies of Mating with Heterospecific Females
Authors: Schlupp Ingo , Marler Cathy , Ryan Michael J.
Published: October 2006

Female gynogens reproduce clonally but rely on sperm from heterospecific males to initiate embryogenesis. It has been assumed that males gain no benefit from such matings; thus, selection should favor males that avoid them. Here it is shown that males gain a benefit by mating with female gynogens in an asexual-sexual complex of fish. The sexual females increase their preference for males whom they observe consorting with female gynogens. Thus, gynogenetic species might persist because selection favors males to be sexually parasitized.
Regulation of MHC Class I Transport by the Molecular Chaperone, Calnexin (p88, IP90)
Authors: Jackson Michael R. , Cohen-Doyle Myrna F. , Peterson Per A. , Williams David B.
Published: October 2006

Assembled class I histocompatibility molecules, consisting of heavy chain, β
2
-microglobulin, and peptide ligand, are transported rapidly to the cell surface. In contrast, the intracellular transport of free heavy chains or peptide-deficient heavy chain-β
2
-microglobulin heterodimers is impaired. A 90-kilodalton membrane-bound chaperone of the endoplasmic reticulum (ER), termed calnexin, associates quantitatively with newly synthesized class I heavy chains, but the functions of calnexin in this interaction are unknown. Class I subunits were expressed alone or in combination with calnexin in
Drosophila melanogaster
cells. Calnexin retarded the intracellular transport of both peptide-deficient heavy chain-β
2
-microglobulin heterodimers and free heavy chains. Calnexin also impeded the rapid intracellular degradation of free heavy chains. The ability of calnexin to protect and retain class I assembly intermediates is likely to contribute to the efficient intracellular formation of class I-peptide complexes.
Retention of Unassembled Components of Integral Membrane Proteins by Calnexin
Authors: Rajagopalan Sumati , Xu Yuhui , Brenner Michael B.
Published: October 2006

Quality control mechanisms prevent the cell surface expression of incompletely assembled multisubunit receptors such as the T cell receptor (TCR). The molecular chaperone function of calnexin (IP90, p88), a 90-kilodalton protein that resides in the endoplasmic reticulum (ER), in the retention of representative chains of the TCR-CD3 complex in the ER was tested. Truncation mutants of calnexin, when transiently expressed in COS cells, were exported from the ER and either accumulated in the Golgi or progressed to the cell surface. CD3 ε chains cotransfected with the forms of calnexin that were not retained in the ER exited the ER and colocalized with calnexin. Since engineered calnexin determined the intracellular localization of the proteins associated with it, it is concluded that calnexin interacts with incompletely assembled TCR components and retains them in the ER.
Crystal Structure of the DNA Binding Domain of the Heat Shock Transcription Factor
Authors: Harrison Celia J. , Bohm A. Andrew , Nelson Hillary C. M.
Published: October 2006

The structure of the DNA binding domain, determined at 1.8 angstrom resolution, contains a three-helix bundle that is capped by a four-stranded antiparallel β sheet. This structure is a variant of the helix-turn-helix motif, typified by catabolite activator protein. In the heat shock transcription factor, the first helix of the motif (α2) has an α-helical bulge and a proline-induced kink. The angle between the two helices of the motif (α2 and α3) is about 20° smaller than the average for canonical helix-turn-helix proteins. Nevertheless, the relative positions of the first and third helices of the bundle (α1 and α3) are conserved. It is proposed here that the first helix of the three-helix bundle be considered a component of the helix-turn-helix motif.
Phase Shifting of the Circadian Clock by Induction of the
Drosophila
period
Protein
Authors: Edery Isaac , Rutila Joan E. , Rosbash Michael
Published: October 2006

Virtually all organisms manifest circadian (24-hour) rhythms, governed by an ill-defined endogenous pacemaker or clock. Several lines of evidence suggest that the
Drosophila melanogaster
period
gene product PER is a clock component. If PER were central to the time-keeping mechanism, a transient increase in its concentration would cause a stable shift in the phase of the clock. Therefore, transgenic flies bearing a heat-inducible copy of PER were subjected to temperature pulses. This treatment caused long-lasting phase shifts in the locomotor activity circadian rhythm, a result that supports the contention that PER is a bona fide clock component.
Molecular Dynamics in Liquids: Spin-Lattice Relaxation of Nitroxide Spin Labels
Authors: Robinson Bruce H. , Haas Duncan A. , Mailer Colin
Published: October 2006

Time domain pulsed saturation recovery and electron-electron double resonance spectroscopies were used to measure the spin-lattice relaxation rates of the electron and the nitrogen nucleus in nitroxide spin labels in liquids. The rotational correlation time range covered is from picoseconds to milliseconds. These rates are quantitatively explained by isotropic rotational Brownian dynamics, which modulate the interactions between the electron spin and the molecular angular momentum; the nitrogen and electron spins; and the solvent protons with both the electron and the nitrogen spins. This solves a 20-year-old problem that has limited scientific applications of nitroxides.
Maspin, a Serpin with Tumor-Suppressing Activity in Human Mammary Epithelial Cells
Authors: Zou Zhiqiang , Anisowicz Anthony , Hendrix Mary J. C. , Thor Ann , Neveu Mark , Sheng Shijie , Rafidi Kristina , Seftor Elisabeth , Sager Ruth
Published: October 2006

A gene encoding a protein related to the serpin family of protease inhibitors was identified as a candidate tumor suppressor gene that may play a role in human breast cancer. The gene product, called maspin, is expressed in normal mammary epithelial cells but not in most mammary carcinoma cell lines. Transfection of MDA-MB-435 mammary carcinoma cells with the maspin gene did not alter the cells' growth properties in vitro, but reduced the cells' ability to induce tumors and metastasize in nude mice and to invade through a basement membrane matrix in vitro. Analysis of human breast cancer specimens revealed that loss of maspin expression occurred most frequently in advanced cancers. These results support the hypothesis that maspin functions as a tumor suppressor.
Locally Distributed Synaptic Potentiation in the Hippocampus
Authors: Schuman Erin M. , Madison Daniel V.
Published: October 2006

The long-lasting increase in synaptic strength known as long-term potentiation has been advanced as a potential physiological mechanism for many forms of both developmental and adult neuronal plasticity. In many models of plasticity, intercellular communication has been proposed to account for observations in which simultaneously active neurons are strengthened together. The data presented here indicate that long-term potentiation can be communicated between synapses on neighboring neurons by means of a diffusible messenger. This distributed potentiation provides a mechanism for the cooperative strengthening of proximal synapses and may underlie a variety of plastic processes in the nervous system.
Electric Field-Induced Concentration Gradients in Lipid Monolayers
Authors: Lee Ka Yee C. , Klingler Jürgen F. , McConnell Harden M.
Published: October 2006

Externally applied electric field gradients gave rise to lateral concentration gradients in monolayers of certain binary lipid mixtures. For binary mixtures of dihydrocholesterol and dimyristoylphosphatidylcholine, the application of an electric field gradient at pressures below the critical pressure produced a liquid-liquid phase separation in a monolayer that is otherwise homogenous. At pressures slightly above the critical pressure, a field gradient produced a large concentration gradient without phase separation. The lipid concentration gradients can be described by equilibrium thermodynamic chemical potentials. The observed effects appear to be relevant to the structure and composition of biological membranes.
Mortality Rates in a Genetically Heterogeneous Population of
Caenorhabditis elegans
Authors: Brooks Anne , Lithgow Gordon J. , Johnson Thomas E.
Published: October 2006

Age-specific mortality rates in isogenic populations of the nematode
Caenorhabditis elegans
increase exponentially throughout life. In genetically heterogeneous populations, age-specific mortality increases exponentially until about 17 days and then remains constant until the last death occurs at about 60 days. This period of constant age-specific mortality results from genetic heterogeneity. Subpopulations differ in mean life-span, but they all exhibit near exponential, albeit different, rates of increase in age-specific mortality. Thus, much of the observed heterogeneity in mortality rates later in life could result from genetic heterogeneity and not from an inherent effect of aging.
Zinc Finger Phage: Affinity Selection of Fingers with New DNA-Binding Specificities
Authors: Rebar Edward J. , Pabo Carl O.
Published: October 2006

A phage display system was developed and used to select zinc finger proteins with altered DNA-binding specificities. The three zinc fingers of the Zif268 protein were expressed on the surface of filamentous phage, and a library of variants was prepared by randomizing critical amino acids in the first zinc finger. Affinity selections, using DNA sites with base changes in the region recognized by the first finger, yielded Zif268 variants that bound tightly and specifically to the new sites. This phage system provides a tool for the study of protein-DNA interactions and may offer a general method for selecting zinc finger proteins that recognize desired target sites on double-stranded DNA.
Disruption of PDGF Receptor Trafficking by Mutation of Its PI-3 Linase Binding Sites
Authors: Joly Marguerite , Kazlauskas Andrius , Fay Fredric S. , Corvera Silvia
Published: October 2006

Human platelet-derived growth factor receptors (PDGFRs) expressed in human Hep G2 cells internalized and concentrated in a juxtanuclear region near the Golgi network within 10 minutes after the cells were treated with PDGF. A PDGFR mutant (F5) that lacks high-affinity binding sites for the Src homology 2 domain-containing proteins phosphatidylinositol-3 kinase (PI-3 kinase), Ras guanosine triphosphatase activating protein, phospholipase C-γ, and a phosphotyrosine phosphatase (Syp) remained at the cell periphery. Restoration of the PI-3 kinase binding sites on F5 completely restored the ability of the receptor to concentrate intracellularly. A PDGFR mutant lacking only PI-3 kinase binding sites failed to concentrate intracellularly. Thus, PI-3 kinase binding sites appear both necessary and sufficient for the normal endocytic trafficking of the activated PDGFR.
Green Fluorescent Protein as a Marker for Gene Expression
Authors: Chalfie Martin , Tu Yuan , Euskirchen Ghia , Ward William W. , Prasher Douglas C.
Published: October 2006

A complementary DNA for the
Aequorea victoria
green fluorescent protein (GFP) produces a fluorescent product when expressed in prokaryotic (
Escherichia coli
) or eukaryotic (
Caenorhabditis elegans
) cells. Because exogenous substrates and cofactors are not required for this fluorescence, GFP expression can be used to monitor gene expression and protein localization in living organisms.
Mapping the Lectin-Like Activity of Tumor Necrosis Factor
Authors: Lucas Rudolf , Magez Stefan , De Leys Robert , Fransen Lucie , Scheerlinck Jean-Pierre , Rampelberg Murielle , Sablon Erwin , De Baetselier Patrick
Published: October 2006

Tumor necrosis factor (TNF), but not lymphotoxin (LT), is directly trypanolytic for salivarian trypanosomes. This activity was not blocked by soluble 55-kilodalton and 75-kilodalton TNF receptors, but was potently inhibited by
N,N
′-diacetylchitobiose, an oligosaccharide that binds TNF. Comparative sequence analysis of TNF and LT localized the trypanocidal region, and synthetic peptides were trypanolytic. TNF molecules in which the trypanocidal region was mutated or deleted retained tumoricidal activity. Thus, trypanosome-TNF interactions occur via a TNF domain, probably with lectin-like affinity, which is functionally and spatially distinct from the mammalian TNF receptor binding sites.