bluuebunny/crossref_metadata_2025 huggingface dataset:
Requirement for GD3 Ganglioside in CD95- and Ceramide-Induced Apoptosis
Authors: De Maria Ruggero , Lenti Luisa , Malisan Florence , d'Agostino Federica , Tomassini Barbara , Zeuner Ann , Rippo Maria Rita , Testi Roberto
Published: July 2002

Gangliosides participate in development and tissue differentiation. Cross-linking of the apoptosis-inducing CD95 protein (also called Fas or APO-1) in lymphoid and myeloid tumor cells triggered GD3 ganglioside synthesis and transient accumulation. CD95-induced GD3 accumulation depended on integral receptor “death domains” and on activation of a family of cysteine proteases called caspases. Cell-permeating ceramides, which are potent inducers of apoptosis, also triggered GD3 synthesis. GD3 disrupted mitochondrial transmembrane potential (ΔΨ
m
), and induced apoptosis, in a caspase-independent fashion. Transient overexpression of the GD3 synthase gene directly triggered apoptosis. Pharmacological inhibition of GD3 synthesis and exposure to GD3 synthase antisense oligodeoxynucleotides prevented CD95-induced apoptosis. Thus, GD3 ganglioside mediates the propagation of CD95-generated apoptotic signals in hematopoietic cells.
An Area Specialized for Spatial Working Memory in Human Frontal Cortex
Authors: Courtney Susan M. , Petit Laurent , Maisog José Ma. , Ungerleider Leslie G. , Haxby James V.
Published: July 2002

Working memory is the process of maintaining an active representation of information so that it is available for use. In monkeys, a prefrontal cortical region important for spatial working memory lies in and around the principal sulcus, but in humans the location, and even the existence, of a region for spatial working memory is in dispute. By using functional magnetic resonance imaging in humans, an area in the superior frontal sulcus was identified that is specialized for spatial working memory. This area is located more superiorly and posteriorly in the human than in the monkey brain, which may explain why it was not recognized previously.
Siliceous Tablets in the Larval Shells of Apatitic Discinid Brachiopods
Authors: Williams Alwyn , Cusack Maggie , Buckman James O. , Stachel Thomas
Published: July 2002

The marine bivalved Brachiopoda are abundant throughout the geological record and have apatitic (CaPO
4
-rich) or calcitic (CaCO
3
-rich) shells. Vesicles covering the larval valves of living apatitic-shelled discinids contain tablets of silica. The tablets are cemented into close-packed mosaics by spherular apatite in glycosaminoglycans. They are usually lost as vesicles degrade but leave imprints on the underlying apatitic shell. Similar imprints ornament larval surfaces of some of the earliest Paleozoic apatitic-shelled brachiopods and may also be indicators of siliceous biomineralization.
Ribosome-Catalyzed Peptide-Bond Formation with an A-Site Substrate Covalently Linked to 23
S
Ribosomal RNA
Authors: Green Rachel , Switzer Christopher , Noller Harry F.
Published: July 2002

In the ribosome, the aminoacyl–transfer RNA (tRNA) analog 4-thio-dT-p-C-p-puromycin crosslinks photochemically with G2553 of 23
S
ribosomal RNA (rRNA). This covalently linked substrate reacts with a peptidyl-tRNA analog to form a peptide bond in a peptidyl transferase–catalyzed reaction. This result places the conserved 2555 loop of 23
S
rRNA at the peptidyl transferase A site and suggests that peptide bond formation can occur uncoupled from movement of the A-site tRNA. Crosslink formation depends on occupancy of the P site by a tRNA carrying an intact CCA acceptor end, indicating that peptidyl-tRNA, directly or indirectly, helps to create the peptidyl transferase A site.
A Marine Natural Product Inhibitor of Kinesin Motors
Authors: Sakowicz Roman , Berdelis Michael S. , Ray Krishanu , Blackburn Christine L. , Hopmann Cordula , Faulkner D. John , Goldstein Lawrence S. B.
Published: July 2002

Members of the kinesin superfamily of motor proteins are essential for mitotic and meiotic spindle organization, chromosome segregation, organelle and vesicle transport, and many other processes that require microtubule-based transport. A compound, adociasulfate-2, was isolated from a marine sponge,
Haliclona
(also known as
Adocia
) species, that inhibited kinesin activity by targeting its motor domain and mimicking the activity of the microtubule. Thus, the kinesin-microtubule interaction site could be a useful target for small molecule modulators, and adociasulfate-2 should serve as an archetype for specific inhibitors of kinesin functions.
Ultrathin Films of a Polyelectrolyte with Layered Architecture
Authors: Esker A. R. , Mengel C. , Wegner G.
Published: July 2002

Posttransfer modification of preformed Langmuir-Blodgett films of poly(
tert
-butyl methacrylate) and poly(
tert
-butyl acrylate) by gaseous hydrochloric acid yields films with layered architecture of poly(methacrylic acid) and poly(acrylic acid), respectively. X-ray reflectivity and infrared spectroscopy confirm monolayer by monolayer transfer of the source polymers and their transformation to acid multilayer assemblies with retention of low surface roughnesses. The incorporation of cross-linking groups into the system offers the possibility for further chemical modification to produce ultrathin films of model networks desirable for bioadsorption studies and as hydrophilic spacing layers for tethered membranes.
Structure of the
Escherichia coli
RNA Polymerase α Subunit Amino-Terminal Domain
Authors: Zhang Gongyi , Darst Seth A.
Published: July 2002

The 2.5 angstrom resolution x-ray crystal structure of the
Escherichia coli
RNA polymerase (RNAP) α subunit amino-terminal domain (αNTD), which is necessary and sufficient to dimerize and assemble the other RNAP subunits into a transcriptionally active enzyme and contains all of the sequence elements conserved among eukaryotic α homologs, has been determined. The αNTD monomer comprises two distinct, flexibly linked domains, only one of which participates in the dimer interface. In the αNTD dimer, a pair of helices from one monomer interact with the cognate helices of the other to form an extensive hydrophobic core. All of the determinants for interactions with the other RNAP subunits lie on one face of the αNTD dimer. Sequence alignments, combined with secondary-structure predictions, support proposals that a heterodimer of the eukaryotic RNAP subunits related to
Saccharomyces cerevisiae
Rpb3 and Rpb11 plays the role of the αNTD dimer in prokaryotic RNAP.
Multi-Atom Resonant Photoemission: A Method for Determining Near-Neighbor Atomic Identities and Bonding
Authors: Kay A. , Arenholz E. , Mun S. , Garcı́a de Abajo F. J. , Fadley C. S. , Denecke R. , Hussain Z. , Van Hove M. A.
Published: July 2002

Measurements and theoretical calculations are reported for an interatomic multi-atom resonant photoemission (MARPE) effect that permits direct determination of near-neighbor atomic identities (atomic numbers). MARPE occurs when the photon energy is tuned to a core-level absorption edge of an atom neighboring the emitting atom, with the emitting level having a lower binding energy than the resonant level. Large peak-intensity enhancements of 33 to 105 percent and energy-integrated effects of 11 to 29 percent were seen in three metal oxides. MARPE should also be sensitive to bond distance, bonding type, and magnetic order, and be observable via the secondary processes of x-ray fluorescence and Auger decay.
Impaired Spatial Learning after Saturation of Long-Term Potentiation
Authors: Moser Edvard I. , Krobert Kurt A. , Moser May-Britt , Morris Richard G. M.
Published: July 2002

If information is stored as activity-driven increases in synaptic weights in the hippocampal formation, saturation of hippocampal long-term potentiation (LTP) should impair learning. Here, rats in which one hippocampus had been lesioned were implanted with a multielectrode stimulating array across and into the angular bundle afferent to the other hippocampus. Repeated cross-bundle tetanization caused cumulative potentiation. Residual synaptic plasticity was assessed by tetanizing a naı̈ve test electrode in the center of the bundle. Spatial learning was disrupted in animals with no residual LTP (<10 percent) but not in animals that were capable of further potentiation. Thus, saturation of hippocampal LTP impairs spatial learning.
Requirement for IL-13 Independently of IL-4 in Experimental Asthma
Authors: Grünig Gabriele , Warnock Martha , Wakil Adil E. , Venkayya Rajeev , Brombacher Frank , Rennick Donna M. , Sheppard Dean , Mohrs Markus , Donaldson Debra D. , Locksley Richard M. , Corry David B.
Published: July 2002

The pathogenesis of asthma reflects, in part, the activity of T cell cytokines. Murine models support participation of interleukin-4 (IL-4) and the IL-4 receptor in asthma. Selective neutralization of IL-13, a cytokine related to IL-4 that also binds to the α chain of the IL-4 receptor, ameliorated the asthma phenotype, including airway hyperresponsiveness, eosinophil recruitment, and mucus overproduction. Administration of either IL-13 or IL-4 conferred an asthma-like phenotype to nonimmunized T cell–deficient mice by an IL-4 receptor α chain–dependent pathway. This pathway may underlie the genetic associations of asthma with both the human 5q31 locus and the IL-4 receptor.
T Lymphocyte Costimulation Mediated by Reorganization of Membrane Microdomains
Authors: Viola Antonella , Schroeder Susanne , Sakakibara Yoichi , Lanzavecchia Antonio
Published: July 2002

Although dispensable, costimulation through CD28 facilitates activation of naı̈ve T lymphocytes. CD28 engagement led to the redistribution and clustering of membrane and intracellular kinase-rich raft microdomains at the site of T cell receptor (TCR) engagements. Although not affecting TCR down-regulation, this process led to higher and more stable tyrosine phosphorylation of several substrates and higher consumption of Lck. These results may provide a general mechanism for amplifying receptor signaling by reorganization of membrane microdomains.
Horizontal Propagation of Visual Activity in the Synaptic Integration Field of Area 17 Neurons
Authors: Bringuier Vincent , Chavane Frédéric , Glaeser Larry , Frégnac Yves
Published: July 2002

The receptive field of a visual neuron is classically defined as the region of space (or retina) where a visual stimulus evokes a change in its firing activity. At the cortical level, a challenging issue concerns the roles of feedforward, local recurrent, intracortical, and cortico-cortical feedback connectivity in receptive field properties. Intracellular recordings in cat area 17 showed that the visually evoked synaptic integration field extends over a much larger area than that established on the basis of spike activity. Synaptic depolarizing responses to stimuli flashed at increasing distances from the center of the receptive field decreased in strength, whereas their onset latency increased. These findings suggest that subthreshold responses in the unresponsive region surrounding the classical discharge field result from the integration of visual activation waves spread by slowly conducting horizontal axons within primary visual cortex.
Crystallographic Evidence for Preformed Dimers of Erythropoietin Receptor Before Ligand Activation
Authors: Livnah Oded , Stura Enrico A. , Middleton Steven A. , Johnson Dana L. , Jolliffe Linda K. , Wilson Ian A.
Published: July 2002

Erythropoietin receptor (EPOR) is thought to be activated by ligand-induced homodimerization. However, structures of agonist and antagonist peptide complexes of EPOR, as well as an EPO-EPOR complex, have shown that the actual dimer configuration is critical for the biological response and signal efficiency. The crystal structure of the extracellular domain of EPOR in its unliganded form at 2.4 angstrom resolution has revealed a dimer in which the individual membrane-spanning and intracellular domains would be too far apart to permit phosphorylation by JAK2. This unliganded EPOR dimer is formed from self-association of the same key binding site residues that interact with EPO-mimetic peptide and EPO ligands. This model for a preformed dimer on the cell surface provides insights into the organization, activation, and plasticity of recognition of hematopoietic cell surface receptors.
Phenotypic Change Caused by Transcriptional Bypass of Uracil in Nondividing Cells
Authors: Viswanathan Anand , You Ho Jin , Doetsch Paul W.
Published: July 2002

Cytosine deamination to uracil occurs frequently in cellular DNA. In vitro, RNA polymerase efficiently inserts adenine opposite to uracil, resulting in G to A base substitutions. In vivo, uracil could potentially alter transcriptional fidelity, resulting in production of mutant proteins. This study demonstrates that in nondividing
Escherichia coli
cells, a DNA template base replaced with uracil in a stop codon in the firefly luciferase gene results in conversion of inactive to active luciferase. The level of transcriptional base substitution is dependent on the capacity to repair uracil. These results provide evidence for a DNA damage–dependent, transcription-driven pathway for generating mutant proteins in nondividing cells.
Structure of the
Escherichia coli
Fumarate Reductase Respiratory Complex
Authors: Iverson Tina M. , Luna-Chavez César , Cecchini Gary , Rees Douglas C.
Published: July 2002

The integral membrane protein fumarate reductase catalyzes the final step of anaerobic respiration when fumarate is the terminal electron acceptor. The homologous enzyme succinate dehydrogenase also plays a prominent role in cellular energetics as a member of the Krebs cycle and as complex II of the aerobic respiratory chain. Fumarate reductase consists of four subunits that contain a covalently linked flavin adenine dinucleotide, three different iron-sulfur clusters, and at least two quinones. The crystal structure of intact fumarate reductase has been solved at 3.3 angstrom resolution and demonstrates that the cofactors are arranged in a nearly linear manner from the membrane-bound quinone to the active site flavin. Although fumarate reductase is not associated with any proton-pumping function, the two quinones are positioned on opposite sides of the membrane in an arrangement similar to that of the Q-cycle organization observed for cytochrome bc
1
.
Staphylococcus aureus
Sortase, an Enzyme that Anchors Surface Proteins to the Cell Wall
Authors: Mazmanian Sarkis K. , Liu Gwen , Ton-That Hung , Schneewind Olaf
Published: July 2002

Surface proteins of Gram-positive bacteria are linked to the bacterial cell wall by a mechanism that involves cleavage of a conserved Leu-Pro-X-Thr-Gly (LPXTG) motif and that occurs during assembly of the peptidoglycan cell wall. A
Staphylococcus aureus
mutant defective in the anchoring of surface proteins was isolated and shown to carry a mutation in the
srtA
gene. Overexpression of
srtA
increased the rate of surface protein anchoring, and homologs of
srtA
were found in other pathogenic Gram-positive bacteria. The protein specified by
srtA
, sortase, may be a useful target for the development of new antimicrobial drugs.
Energetic Iron(VI) Chemistry: The Super-Iron Battery
Authors: Licht Stuart , Wang Baohui , Ghosh Susanta
Published: July 2002

Higher capacity batteries based on an unusual stabilized iron(VI) chemistry are presented. The storage capacities of alkaline and metal hydride batteries are largely cathode limited, and both use a potassium hydroxide electrolyte. The new batteries are compatible with the alkaline and metal hydride battery anodes but have higher cathode capacity and are based on available, benign materials. Iron(VI/III) cathodes can use low-solubility K
2
FeO
4
and BaFeO
4
salts with respective capacities of 406 and 313 milliampere-hours per gram. Super-iron batteries have a 50 percent energy advantage compared to conventional alkaline batteries. A cell with an iron(VI) cathode and a metal hydride anode is significantly (75 percent) rechargeable.
Onset of Fermi Degeneracy in a Trapped Atomic Gas
Authors: DeMarco B. , Jin D. S.
Published: July 2002

An evaporative cooling strategy that uses a two-component Fermi gas was employed to cool a magnetically trapped gas of 7 × 10
5
40
K atoms to 0.5 of the Fermi temperature
T
F
. In this temperature regime, where the state occupation at the lowest energies has increased from essentially zero at high temperatures to nearly 60 percent, quantum degeneracy was observed as a barrier to evaporative cooling and as a modification of the thermodynamics. Measurements of the momentum distribution and the total energy of the confined Fermi gas directly revealed the quantum statistics.
Ultrasonic Deposition of High-Selectivity Nanoporous Carbon Membranes
Authors: Shiflett Mark B. , Foley Henry C.
Published: July 2002

Ultrasonic deposition creates a thin film of polymer on a tubular, macroporous, stainless steel support. Using polyfurfuryl alcohol as the nanoporous carbon precursor and a pyrolysis temperature of 723 kelvin, a membrane was prepared with the following permeances, measured in moles per square meter per Pascal per second: nitrogen, 1.8 × 10
−12
; oxygen, 5.6 × 10
−11
; helium, 3.3 × 10
−10
; and hydrogen, 6.1 × 10
−10
. The ideal separation factors as compared to that for nitrogen are 30:1, 178:1, and 331:1 for oxygen, helium, and hydrogen, respectively.
Aging-Dependent Large Accumulation of Point Mutations in the Human mtDNA Control Region for Replication
Authors: Michikawa Yuichi , Mazzucchelli Franca , Bresolin Nereo , Scarlato Guglielmo , Attardi Giuseppe
Published: July 2002

Progressive damage to mitochondrial DNA (mtDNA) during life is thought to contribute to aging processes. However, this idea has been difficult to reconcile with the small fraction of mtDNA so far found to be altered. Here, examination of mtDNA revealed high copy point mutations at specific positions in the control region for replication of human fibroblast mtDNA from normal old, but not young, individuals. Furthermore, in longitudinal studies, one or more mutations appeared in an individual only at an advanced age. Some mutations appeared in more than one individual. Most strikingly, a T414G transversion was found, in a generally high proportion (up to 50 percent) of mtDNA molecules, in 8 of 14 individuals above 65 years of age (57 percent) but was absent in 13 younger individuals.
Mirror-Image Confusion in Single Neurons of the Macaque Inferotemporal Cortex
Authors: Rollenhagen J. E. , Olson C. R.
Published: July 2002

Humans and animals confuse lateral mirror images, such as the letters “b” and “d,” more often than vertical mirror images, such as the letters “b” and “p.” Experiments were performed to find a neural correlate of this phenomenon. Visually responsive pattern-selective neurons in the inferotemporal cortex of macaque monkeys responded more similarly to members of a lateral mirror-image pair than to members of a vertical mirror-image pair. The phenomenon developed within 20 milliseconds of the onset of the visual response and persisted to its end. It occurred during presentation of stimuli both at the fovea and in the periphery.
Rapid Progression to AIDS in HIV
+
Individuals with a Structural Variant of the Chemokine Receptor CX
3
CR1
Authors: Faure Sophie , Meyer Laurence , Costagliola Dominique , Vaneensberghe Céline , Genin Emmanuelle , Autran Brigitte , ALT French , Groups IMMUNOCO Study , Delfraissy Jean-François , Group SEROCO Study , McDermott David H. , Murphy Philip M. , Debré Patrice , Théodorou Ioannis , Combadière Christophe
Published: July 2002

Human immunodeficiency virus (HIV) enters cells in vitro via CD4 and a coreceptor. Which of 15 known coreceptors are important in vivo is poorly defined but may be inferred from disease-modifying mutations, as for CCR5. Here two single nucleotide polymorphisms are described in Caucasians in CX
3
CR1, an HIV coreceptor and leukocyte chemotactic/adhesion receptor for the chemokine fractalkine. HIV-infected patients homozygous for CX
3
CR1-I249 M280, a variant haplotype affecting two amino acids (isoleucine-249 and methionine-280), progressed to AIDS more rapidly than those with other haplotypes. Functional CX
3
CR1 analysis showed that fractalkine binding is reduced among patients homozygous for this particular haplotype. Thus, CX
3
CR1-I249 M280 is a recessive genetic risk factor in HIV/AIDS.
The Outcome of Acute Hepatitis C Predicted by the Evolution of the Viral Quasispecies
Authors: Farci Patrizia , Shimoda Atsushi , Coiana Alessandra , Diaz Giacomo , Peddis Giovanna , Melpolder Jacqueline C. , Strazzera Antonello , Chien David Y. , Munoz Santiago J. , Balestrieri Angelo , Purcell Robert H. , Alter Harvey J.
Published: July 2002

The mechanisms by which hepatitis C virus (HCV) induces chronic infection in the vast majority of infected individuals are unknown. Sequences within the HCV
E1
and
E2
envelope genes were analyzed during the acute phase of hepatitis C in 12 patients with different clinical outcomes. Acute resolving hepatitis was associated with relative evolutionary stasis of the heterogeneous viral population (quasispecies), whereas progressing hepatitis correlated with genetic evolution of HCV. Consistent with the hypothesis of selective pressure by the host immune system, the sequence changes occurred almost exclusively within the hypervariable region 1 of the
E2
gene and were temporally correlated with antibody seroconversion. These data indicate that the evolutionary dynamics of the HCV quasispecies during the acute phase of hepatitis C predict whether the infection will resolve or become chronic.
Transport of Peptide-MHC Class II Complexes in Developing Dendritic Cells
Authors: Turley Shannon J. , Inaba Kayo , Garrett Wendy S. , Ebersold Melanie , Unternaehrer Julia , Steinman Ralph M. , Mellman Ira
Published: July 2002

Major histocompatibility complex class II (MHC II) molecules capture peptides within the endocytic pathway to generate T cell receptor (TCR) ligands. Immature dendritic cells (DCs) sequester intact antigens in lysosomes, processing and converting antigens into peptide–MHC II complexes upon induction of DC maturation. The complexes then accumulate in distinctive, nonlysosomal MHC II
+
vesicles that appear to migrate to the cell surface. Although the vesicles exclude soluble lysosomal contents and antigen-processing machinery, many contain MHC I and B7 costimulatory molecules. After arrival at the cell surface, the MHC and costimulatory molecules remain clustered. Thus, transport of peptide–MHC II complexes by DCs not only accomplishes transfer from late endocytic compartments to the plasma membrane, but does so in a manner that selectively concentrates TCR ligands and costimulatory molecules for T cell contact.
Mechanism of ATP-Dependent Promoter Melting by Transcription Factor IIH
Authors: Kim Tae-Kyung , Ebright Richard H. , Reinberg Danny
Published: July 2002

We show that transcription factor IIH ERCC3 subunit, the DNA helicase responsible for adenosine triphosphate (ATP)–dependent promoter melting during transcription initiation, does not interact with the promoter region that undergoes melting but instead interacts with DNA downstream of this region. We show further that promoter melting does not change protein-DNA interactions upstream of the region that undergoes melting but does change interactions within and downstream of this region. Our results rule out the proposal that IIH functions in promoter melting through a conventional DNA-helicase mechanism. We propose that IIH functions as a molecular wrench: rotating downstream DNA relative to fixed upstream protein-DNA interactions, thereby generating torque on, and melting, the intervening DNA.
Electrochemical Micromachining
Authors: Schuster Rolf , Kirchner Viola , Allongue Philippe , Ertl Gerhard
Published: July 2002

The application of ultrashort voltage pulses between a tool electrode and a workpiece in an electrochemical environment allows the three-dimensional machining of conducting materials with submicrometer precision. The principle is based on the finite time constant for double-layer charging, which varies linearly with the local separation between the electrodes. During nanosecond pulses, the electrochemical reactions are confined to electrode regions in close proximity. This technique was used for local etching of copper and silicon as well as for local copper deposition.
Subatomic Features on the Silicon (111)-(7×7) Surface Observed by Atomic Force Microscopy
Authors: Giessibl Franz J. , Hembacher S. , Bielefeldt H. , Mannhart J.
Published: July 2002

The atomic force microscope images surfaces by sensing the forces between a sharp tip and a sample. If the tip-sample interaction is dominated by short-range forces due to the formation of covalent bonds, the image of an individual atom should reflect the angular symmetry of the interaction. Here, we report on a distinct substructure in the images of individual adatoms on silicon (111)-(7×7), two crescents with a spherical envelope. The crescents are interpreted as images of two atomic orbitals of the front atom of the tip. Key for the observation of these subatomic features is a force-detection scheme with superior noise performance and enhanced sensitivity to short-range forces.
Inflammation Dampened by Gelatinase A Cleavage of Monocyte Chemoattractant Protein-3
Authors: McQuibban G. Angus , Gong Jiang-Hong , Tam Eric M. , McCulloch Christopher A. G. , Clark-Lewis Ian , Overall Christopher M.
Published: July 2002

Tissue degradation by the matrix metalloproteinase gelatinase A is pivotal to inflammation and metastases. Recognizing the catalytic importance of substrate-binding exosites outside the catalytic domain, we screened for extracellular substrates using the gelatinase A hemopexin domain as bait in the yeast two-hybrid system. Monocyte chemoattractant protein–3 (MCP-3) was identified as a physiological substrate of gelatinase A. Cleaved MCP-3 binds to CC-chemokine receptors–1, –2, and –3, but no longer induces calcium fluxes or promotes chemotaxis, and instead acts as a general chemokine antagonist that dampens inflammation. This suggests that matrix metalloproteinases are both effectors and regulators of the inflammatory response.
Resonant Electron Scattering by Defects in Single-Walled Carbon Nanotubes
Authors: Bockrath Marc , Liang Wenjie , Bozovic Dolores , Hafner Jason H. , Lieber Charles M. , Tinkham M. , Park Hongkun
Published: July 2002

We report the characterization of defects in individual metallic single-walled carbon nanotubes by transport measurements and scanned gate microscopy. A sizable fraction of metallic nanotubes grown by chemical vapor deposition exhibits strongly gate voltage–dependent resistance at room temperature. Scanned gate measurements reveal that this behavior originates from resonant electron scattering by defects in the nanotube as the Fermi level is varied by the gate voltage. The reflection coefficient at the peak of a scattering resonance was determined to be about 0.5 at room temperature. An intratube quantum dot device formed by two defects is demonstrated by low-temperature transport measurements.
Glycolipid Antigen Processing for Presentation by CD1d Molecules
Authors: Prigozy Theodore I. , Naidenko Olga , Qasba Pankaj , Elewaut Dirk , Brossay Laurent , Khurana Archana , Natori Takenori , Koezuka Yasuhiko , Kulkarni Ashok , Kronenberg Mitchell
Published: July 2002

The requirement for processing glycolipid antigens in T cell recognition was examined with mouse CD1d-mediated responses to glycosphingolipids (GSLs). Although some disaccharide GSL antigens can be recognized without processing, the responses to three other antigens, including the disaccharide GSL Gal(α1→2)GalCer (Gal, galactose; GalCer, galactosylceramide), required removal of the terminal sugars to permit interaction with the T cell receptor. A lysosomal enzyme, α-galactosidase A, was responsible for the processing of Gal(α1→2)GalCer to generate the antigenic monosaccharide epitope. These data demonstrate a carbohydrate antigen processing system analogous to that used for peptides and an ability of T cells to recognize processed fragments of complex glycolipids.
Induction of Direct Antimicrobial Activity Through Mammalian Toll-Like Receptors
Authors: Thoma-Uszynski Sybille , Stenger Steffen , Takeuchi Osamu , Ochoa Maria Teresa , Engele Matthias , Sieling Peter A. , Barnes Peter F. , Röllinghoff Martin , Bölcskei Pal L. , Wagner Manfred , Akira Shizuo , Norgard Michael V. , Belisle John T. , Godowski Paul J. , Bloom Barry R. , Modlin Robert L.
Published: July 2002

The mammalian innate immune system retains from
Drosophila
a family of homologous Toll-like receptors (TLRs) that mediate responses to microbial ligands. Here, we show that TLR2 activation leads to killing of intracellular
Mycobacterium tuberculosis
in both mouse and human macrophages, through distinct mechanisms. In mouse macrophages, bacterial lipoprotein activation of TLR2 leads to a nitric oxide–dependent killing of intracellular tubercle bacilli, but in human monocytes and alveolar macrophages, this pathway was nitric oxide–independent. Thus, mammalian TLRs respond (as
Drosophila
Toll receptors do) to microbial ligands and also have the ability to activate antimicrobial effector pathways at the site of infection.
Genealogical and Evolutionary Inference with the Human Y Chromosome
Authors: Stumpf Michael P. H. , Goldstein David B.
Published: July 2002

Population genetics has emerged as a powerful tool for unraveling human history. In addition to the study of mitochondrial and autosomal DNA, attention has recently focused on Y-chromosome variation. Ambiguities and inaccuracies in data analysis, however, pose an important obstacle to further development of the field. Here we review the methods available for genealogical inference using Y-chromosome data. Approaches can be divided into those that do and those that do not use an explicit population model in genealogical inference. We describe the strengths and weaknesses of these model-based and model-free approaches, as well as difficulties associated with the mutation process that affect both methods. In the case of genealogical inference using microsatellite loci, we use coalescent simulations to show that relatively simple generalizations of the mutation process can greatly increase the accuracy of genealogical inference. Because model-free and model-based approaches have different biases and limitations, we conclude that there is considerable benefit in the continued use of both types of approaches.
Molecular Characterization of Integrons in
Acinetobacter baumannii
: Description of a Hybrid Class 2 Integron
Authors: Ploy Marie-Cécile , Denis François , Courvalin Patrice , Lambert Thierry
Published: July 2002

Twenty
Acinetobacter baumannii
strains resistant to various antibiotics were analyzed for integron content and sequences of the amplification products. Sixteen clinical isolates had a class 1 integron, 2 contained an additional class 1 or class 2 integron, but no class 3 integron was detected. Thirteen strains had integrons with a single cassette:
aac
(
3
)-
Ia
(9 strains),
ant
(
2
")-
Ia
(2 strains), or
aac
(
6
′)-
Ib
(2 strains); 1 had
aac
(
6
′)-
Ib
and
oxa20
cassettes and an unknown gene; and 1 had an integron containing
ant
(
2
")-
Ia
and an
oxa3
cassette truncated by IS
6100
. The remaining strains harbored class 1 integrons with gene cassettes previously found in
Enterobacteriaceae
. One integron had a hybrid structure composed of
intI2
and the 3′ conserved segment of class 1 integrons. These data indicate that integrons play a major role in multidrug resistance in
Acinetobacter
.
PMS-601, a New Platelet-Activating Factor Receptor Antagonist That Inhibits Human Immunodeficiency Virus Replication and Potentiates Zidovudine Activity in Macrophages
Authors: Martin M. , Serradji N. , Dereuddre-Bosquet N. , Le Pavec G. , Fichet G. , Lamouri A. , Heymans F. , Godfroid J. J. , Clayette P. , Dormont D.
Published: July 2002

We assessed the anti-human immunodeficiency virus (anti-HIV) activity in vitro of new platelet-activating factor (PAF) receptor antagonists, as PAF and viral replication are thought to be involved in HIV neuropathogenesis. We found that PMS-601 inhibited proinflammatory cytokine synthesis and HIV replication in macrophages and potentiated the antiretroviral activity of zidovudine. These results suggest that PMS-601 is of potential value as an adjuvant treatment for HIV infection.
Pharmacokinetics of Ciprofloxacin in the Human Eye: a Clinical Study and Population Pharmacokinetic Analysis
Authors: Morlet Nigel , Graham Garry G. , Gatus Barrie , McLachlan Andrew J. , Salonikas Chris , Naidoo Daya , Goldberg Ivan , Lam Chi Man
Published: July 2002

Ciprofloxacin, a fluoroquinolone antibiotic active against a wide variety of bacteria, is one of a few antibiotics which enters the human eye after oral administration. However, little is known about its pharmacokinetics in the human eye. One or two oral doses of 750 mg of ciprofloxacin (at a 12-h interval) were administered to 48 patients at various times prior to ocular surgery. Clotted blood, aqueous, and vitreous were collected at surgery, and the concentrations of ciprofloxacin were assayed by high-performance liquid chromatography. Our data were combined with those of others, and a population pharmacokinetic analysis was conducted. The concentrations of ciprofloxacin in both aqueous and vitreous were lower than those in serum and peaked at a later time. The pharmacokinetics of ciprofloxacin in aqueous and vitreous were fitted to a compartmental model in which the antibiotic was transferred into and out of the two compartments (aqueous and vitreous) by first-order processes. Population pharmacokinetic software, P-Pharm, was used to calculate the mean half-lives of the loss of ciprofloxacin from aqueous and vitreous, which were 3.5 and 5.3 h, respectively. At steady state, the mean ratios of then concentrations in aqueous and vitreous to the concentrations in serum were 23 and 17%, respectively. After the administration of one or two doses of 750 mg of ciprofloxacin, the concentrations in both aqueous and vitreous in a number of patients were lower than the MICs at which 90% of isolates are inhibited (0.5 mg/liter) for common intraocular bacterial pathogens. Simulations of concentrations in the eye after the administration of higher doses (1,500 mg of ciprofloxacin as a single dose, two doses of 750 mg 2 h apart, and 750 mg every 6 h) indicated that in approximately 20% of patients the concentrations would still be below 0.5 mg/liter. Although oral ciprofloxacin may be a beneficial adjunctive therapy, the use of oral ciprofloxacin alone may not be adequate for perioperative prophylaxis or for treatment of bacterial endophthalmitis.
Pharmacokinetic Profile and Tolerability of Indinavir-Ritonavir Combinations in Healthy Volunteers
Authors: Saah Alfred J. , Winchell Gregory A. , Nessly Michael L. , Seniuk Melissa A. , Rhodes Rand R. , Deutsch Paul J.
Published: July 2002

This was a randomized, double-blind, placebo-controlled parallel study in human immunodeficiency virus type 1 (HIV-1)-uninfected healthy subjects to investigate the pharmacokinetic interaction between indinavir (IDV) and ritonavir (RTV). Subjects were allocated to treatment groups of IDV given with RTV in the following milligram doses twice daily: 800 mg of IDV-100 mg of RTV (800-100 mg), 800-200, 800-400, and 400-400 mg, placebo of IDV with RTV doses of 100, 200, and 400 mg, and placebo of both IDV and RTV. Doses of both drugs were administered for 14 days with a low-fat meal and one dose on day 15 with a high-fat meal. Blood was obtained for drug concentration measurements on days 14 and 15. Seventy-three volunteers enrolled in the study: 29 men and 44 women. Fifty-three volunteers completed the study. When compared to standard historical data for 800 mg of IDV every 8 h (q8h), the IDV area under the concentration-time curve for 24 h (AUC
24
) of IDV-RTV regimens 400-400, 800-100, and 800-200 mg were at least 1.4, 2.3, and 3.3 times higher, respectively, regardless of meal. The concentrations at the end of the dosing interval were 10 to 25 times higher than that observed in the standard regimen of 800 mg of IDV q8h for IDV-RTV 800-100 and 800-200 mg regimens, respectively. RTV at 200 mg maximally enhanced the IDV profile. Improved tolerability was associated with IDV-RTV 800-100 mg versus IDV-RTV 800-200, 800-400, and 400-400 mg q12h. The advantages of IDV-RTV twice daily over 800 mg of IDV q8h include no food restrictions and twice-daily dosing. Also, the regimens achieve levels of IDV that may be helpful in suppressing strains of HIV-1 that have reduced susceptibility to IDV or other protease inhibitors.
Effects of Miltefosine and Other Alkylphosphocholines on Human Intestinal Parasite
Entamoeba histolytica
Authors: Seifert Karin , Duchêne Michael , Wernsdorfer Walther H. , Kollaritsch Herwig , Scheiner Otto , Wiedermann Gerhard , Hottkowitz Thomas , Eibl Hansjörg
Published: July 2002

The protozoan parasite
Entamoeba histolytica
is the cause of amoebic dysentery and liver abscess. It is therefore responsible for significant morbidity and mortality in a number of countries. Infections with
E. histolytica
are treated with nitroimidazoles, primarily with metronidazole. At this time, there is a lack of useful alternative classes of substances for the treatment of invasive amoebiasis. Alkylphosphocholines (alkyl-PCs) such as hexadecyl-PC (miltefosine) were originally developed as antitumor agents, but recently they have been successfully used for the treatment of visceral leishmaniasis in humans. We examined hexadecyl-PC and several other alkyl-PCs with longer alkyl chains, with and without double bond(s), for their activity against two strains of
E. histolytica
. The compounds with the highest activity were oleyl-PC, octadecyl-PC, and nonadecenyl-PC, with 50% effective concentrations for 48 h of treatment between 15 and 21 μM for strain SFL-3 and between 73 and 98 μM for strain HM-1:IMSS. We also tested liposomal formulations of these alkyl-PCs and miltefosine. The alkyl-PC liposomes showed slightly lower activity, but are expected to be well tolerated. Liposomal formulations of oleyl-PC or closely related alkyl-PCs could be promising candidates for testing as broad-spectrum antiprotozoal and antitumor agents in humans.
Inhibitory Activities of Lansoprazole against Respiration in
Helicobacter pylori
Authors: Nagata Kumiko , Sone Nobuhito , Tamura Toshihide
Published: July 2002

Lansoprazole and its derivative AG-1789 dose-dependently inhibited cellular respiration by an endogenous substrate and decreased the ATP level in
Helicobacter pylori
cells. The inhibitory action of lansoprazole and AG-1789 against respiration was specific to substrates such as pyruvate and α-ketoglutarate and similar to the inhibitory action of rotenone, which is an inhibitor for the mitochondrial respiratory chain. Growth inhibition by lansoprazole and AG-1789 as well as by rotenone was augmented at high oxygen concentrations under atmospheric conditions. Since the 50% inhibitory concentrations of these compounds for the respiration were close to their MICs for
H. pylori
growth, the growth inhibition might be due to respiratory inhibition by these compounds.
Activities of Polymyxin B and Cecropin A-Melittin Peptide CA(1-8)M(1-18) against a Multiresistant Strain of
Acinetobacter baumannii
Authors: Saugar José María , Alarcón Teresa , López-Hernández Susana , López-Brea Manuel , Andreu David , Rivas Luis
Published: July 2002

Polymyxin B (PXB) and the cecropin A-melittin hybrid CA(1-8)M(1-18) (KWKLFKKIGIGAVLKVLTTGLPALIS-NH
2
) were compared for antibiotic activity on reference and multiresistant
Acinetobacter baumannii
strains. Significant differences for both peptides were observed on their inner membrane interaction and inhibition by environmental factors, supporting the use of CA(1-8)M(1-18) as a potential alternative to PXB against
Acinetobacter
.
Application of 5′-Nuclease PCR for Quantitative Detection of
Listeria monocytogenes
in Pure Cultures, Water, Skim Milk, and Unpasteurized Whole Milk
Authors: Nogva Hege Karin , Rudi Knut , Naterstad Kristine , Holck Askild , Lillehaug Dag
Published: July 2002

PCR techniques have significantly improved the detection and identification of bacterial pathogens. Countless adaptations and applications have been described, including quantitative PCR and the latest innovation, real-time PCR. In real-time PCR, e.g., the 5′-nuclease chemistry renders the automated and direct detection and quantification of PCR products possible (P. M. Holland et al., Proc. Natl. Acad. Sci. USA 88:7276–7280, 1991). We present an assay for the quantitative detection of
Listeria monocytogenes
based on the 5′-nuclease PCR using a 113-bp amplicon from the listeriolysin O gene (
hlyA
) as the target. The assay was positive for all isolates of
L. monocytogenes
tested (65 isolates including the type strain) and negative for all other
Listeria
strains (16 isolates from five species tested) and several other bacteria (18 species tested). The application of 5′-nuclease PCR in diagnostics requires a quantitative sample preparation step. Several magnetic bead-based strategies were evaluated, since these systems are simple and relatively easy to automate. The combination of nonspecific binding of bacteria to paramagnetic beads, with subsequent DNA purification by use of the same beads, gave the most satisfactory result. The detection limit was approximately 6 to 60 CFU, quantification was linear over at least 7 log units, and the method could be completed within 3 h. In conclusion, a complete quantitative method for
L. monocytogenes
in water and in skimmed and raw milk was developed.
Simultaneous Enhancement of Thermostability and Catalytic Activity of Phospholipase A
1
by Evolutionary Molecular Engineering
Authors: Song Jae Kwang , Rhee Joon Shick
Published: July 2002

The thermal stability and catalytic activity of phospholipase A
1
from
Serratia
sp. strain MK1 were improved by evolutionary molecular engineering. Two thermostable mutants were isolated after sequential rounds of error-prone PCR performed to introduce random mutations and filter-based screening of the resultant mutant library; we determined that these mutants had six (mutant TA3) and seven (mutant TA13) amino acid substitutions. Different types of substitutions were found in the two mutants, and these substitutions resulted in an increase in nonploar residues (mutant TA3) or in differences between side chains for polar or charged residues (mutant TA13). The wild-type and mutant enzymes were purified, and the effect of temperature on the stability and catalytic activity of the enzymes was investigated. The melting temperatures of the TA3 and TA13 enzymes were increased by 7 and 11°C, respectively, compared with the melting temperature of the wild-type enzyme. Thus, we found that evolutionary molecular engineering was an effective and efficient approach for increasing thermostability without compromising enzyme activity.
Inactivation of Isocitrate Lyase Leads to Increased Production of Medium-Chain-Length Poly(3-Hydroxyalkanoates) in
Pseudomonas putida
Authors: Klinke Stefan , Dauner Michael , Scott George , Kessler Birgit , Witholt Bernard
Published: July 2002

Medium-chain-length (mcl) poly(3-hydroxyalkanoates) (PHAs) are storage polymers that are produced from various substrates and accumulate in
Pseudomonas
strains belonging to rRNA homology group I. In experiments aimed at increasing PHA production in
Pseudomonas
strains, we generated an mcl PHA-overproducing mutant of
Pseudomonas putida
KT2442 by transposon mutagenesis, in which the
aceA
gene was knocked out. This mutation inactivated the glyoxylate shunt and reduced the in vitro activity of isocitrate dehydrogenase, a rate-limiting enzyme of the citric acid cycle. The genotype of the mutant was confirmed by DNA sequencing, and the phenotype was confirmed by biochemical experiments. The
aceA
mutant was not able to grow on acetate as a sole carbon source due to disruption of the glyoxylate bypass and exhibited two- to fivefold lower isocitrate dehydrogenase activity than the wild type. During growth on gluconate, the difference between the mean PHA accumulation in the mutant and the mean PHA accumulation in the wild-type strain was 52%, which resulted in a significant increase in the amount of mcl PHA at the end of the exponential phase in the mutant
P. putida
KT217. On the basis of a stoichiometric flux analysis we predicted that knockout of the glyoxylate pathway in addition to reduced flux through isocitrate dehydrogenase should lead to increased flux into the fatty acid synthesis pathway. Therefore, enhanced carbon flow towards the fatty acid synthesis pathway increased the amount of mcl PHA that could be accumulated by the mutant.
A Spore Counting Method and Cell Culture Model for Chlorine Disinfection Studies of
Encephalitozoon
syn.
Septata intestinalis
Authors: Wolk D. M. , Johnson C. H. , Rice E. W. , Marshall M. M. , Grahn K. F. , Plummer C. B. , Sterling C. R.
Published: July 2002

The microsporidia have recently been recognized as a group of pathogens that have potential for waterborne transmission; however, little is known about the effects of routine disinfection on microsporidian spore viability. In this study, in vitro growth of
Encephalitozoon
syn.
Septata intestinalis
, a microsporidium found in the human gut, was used as a model to assess the effect of chlorine on the infectivity and viability of microsporidian spores. Spore inoculum concentrations were determined by using spectrophotometric measurements (percent transmittance at 625 nm) and by traditional hemacytometer counting. To determine quantitative dose-response data for spore infectivity, we optimized a rabbit kidney cell culture system in 24-well plates, which facilitated calculation of a 50% tissue culture infective dose (TCID
50
) and a minimal infective dose (MID) for
E. intestinalis
. The TCID
50
is a quantitative measure of infectivity and growth and is the number of organisms that must be present to infect 50% of the cell culture wells tested. The MID is as a measure of a system's permissiveness to infection and a measure of spore infectivity. A standardized MID and a standardized TCID
50
have not been reported previously for any microsporidian species. Both types of doses are reported in this paper, and the values were used to evaluate the effects of chlorine disinfection on the in vitro growth of microsporidia. Spores were treated with chlorine at concentrations of 0, 1, 2, 5, and 10 mg/liter. The exposure times ranged from 0 to 80 min at 25°C and pH 7. MID data for
E. intestinalis
were compared before and after chlorine disinfection. A 3-log reduction (99.9% inhibition) in the
E. intestinalis
MID was observed at a chlorine concentration of 2 mg/liter after a minimum exposure time of 16 min. The log
10
reduction results based on percent transmittance-derived spore counts were equivalent to the results based on hemacytometer-derived spore counts. Our data suggest that chlorine treatment may be an effective water treatment for
E. intestinalis
and that spectrophotometric methods may be substituted for labor-intensive hemacytometer methods when spores are counted in laboratory-based chlorine disinfection studies.