bluuebunny/crossref_metadata_2025 huggingface dataset:
Microscale Nutrient Patches in Planktonic Habitats Shown by Chemotactic Bacteria
Authors: Blackburn Nicholas , Fenchel Tom , Mitchell Jim
Published: July 2002

Are nutrients available to microbial communities in micropatches long enough to influence growth and competition? And what are the sources of such patches? To answer these questions, the swimming behavior of chemotactic bacteria in seawater samples was examined. Clusters of bacteria formed in conjunction with cell lysis and excretion by protozoa. These point sources of nutrients spread into spherical patches a few millimeters in diameter and sustained swarms of bacteria for about 10 minutes. Within that time, a large proportion of the nutrients was encountered by bacteria, chemotactic and nonchemotactic alike. Chemotaxis is advantageous for bacteria using patches over a certain size.
Plant Paralog to Viral Movement Protein That Potentiates Transport of mRNA into the Phloem
Authors: Xoconostle-Cázares Beatriz , Xiang Yu , Ruiz-Medrano Roberto , Wang Hong-Li , Monzer Jan , Yoo Byung-Chun , McFarland K. C. , Franceschi Vincent R. , Lucas William J.
Published: July 2002

CmPP16 from
Cucurbita maxima
was cloned and the protein was shown to possess properties similar to those of viral movement proteins.
CmPP16
messenger RNA (mRNA) is present in phloem tissue, whereas protein appears confined to sieve elements (SE). Microinjection and grafting studies revealed that CmPP16 moves from cell to cell, mediates the transport of sense and antisense RNA, and moves together with its mRNA into the SE of scion tissue. CmPP16 possesses the characteristics that are likely required to mediate RNA delivery into the long-distance translocation stream. Thus, RNA may move within the phloem as a component of a plant information superhighway.
Silencing of Genes Flanking the P1 Plasmid Centromere
Authors: Rodionov Oleg , Łobocka Małgorzata , Yarmolinsky Michael
Published: July 2002

Partition modules stabilize bacterial plasmids and chromosomes by actively promoting their segregation into daughter cells. The partition module of plasmid P1 is typical and consists of a centromere site,
parS
, and genes that encode proteins ParA and ParB. We show that ParB can silence genes flanking
parS
(to which ParB binds), apparently by polymerizing along the DNA from a nucleation site at
parS
. Wild-type ParB contacts an extensive region of P1 DNA; silencing-defective ParB proteins, which were found to be partition-defective, are less able to spread. Hence, the silenced structure appears to function in partitioning.
Widespread Iron Limitation of Phytoplankton in the South Pacific Ocean
Authors: Behrenfeld Michael J. , Kolber Zbigniew S.
Published: July 2002

Diel fluorescence patterns were discovered in phytoplankton sampled over 7000 kilometers of the South Pacific Ocean that appear indicative of iron-limiting growth conditions. These patterns were rapidly lost after in situ iron enrichment and were not observed during a 15,000-kilometer transect in the Atlantic Ocean where iron concentrations are relatively high. Laboratory studies of marine
Synechococcus
sp. indicated that the patterns in the South Pacific are a unique manifestation of iron limitation on the fluorescence signature of state transitions. Results suggest that primary productivity is iron limited not only throughout the equatorial Pacific but also over much of the vast South Pacific gyre.
Dependence of Human Stem Cell Engraftment and Repopulation of NOD/SCID Mice on CXCR4
Authors: Peled Amnon , Petit Isabelle , Kollet Orit , Magid Michal , Ponomaryov Tanya , Byk Tamara , Nagler Arnon , Ben-Hur Herzl , Many Ariel , Shultz Leonard , Lider Ofer , Alon Ronen , Zipori Dov , Lapidot Tsvee
Published: July 2002

Stem cell homing and repopulation are not well understood. The chemokine stromal cell–derived factor-1 (SDF-1) and its receptor CXCR4 were found to be critical for murine bone marrow engraftment by human severe combined immunodeficient (SCID) repopulating stem cells. Treatment of human cells with antibodies to CXCR4 prevented engraftment. In vitro CXCR4-dependent migration to SDF-1 of CD34
+
CD38
−/low
cells correlated with in vivo engraftment and stem cell function. Stem cell factor and interleukin-6 induced CXCR4 expression on CD34
+
cells, which potentiated migration to SDF-1 and engraftment in primary and secondary transplanted mice. Thus, up-regulation of CXCR4 expression may be useful for improving engraftment of repopulating stem cells in clinical transplantation.
Facilitation of Signal Onset and Termination by Adenylyl Cyclase
Authors: Scholich Klaus , Mullenix Jason B. , Wittpoth Claus , Poppleton Helen M. , Pierre Sandra C. , Lindorfer Margaret A. , Garrison James C. , Patel Tarun B.
Published: July 2002

The α subunit (G
sα
) of the stimulatory heterotrimeric guanosine triphosphate binding protein (G protein) G
s
activates all isoforms of mammalian adenylyl cyclase. Adenylyl cyclase (Type V) and its subdomains, which interact with G
sα
, promoted inactivation of the G protein by increasing its guanosine triphosphatase (GTPase) activity. Adenylyl cyclase and its subdomains also augmented the receptor-mediated activation of heterotrimeric G
s
and thereby facilitated the rapid onset of signaling. These findings demonstrate that adenylyl cyclase functions as a GTPase activating protein (GAP) for the monomeric G
sα
and enhances the GTP/GDP exchange factor (GEF) activity of receptors.
Mitochondrial Diseases in Man and Mouse
Authors: Wallace Douglas C.
Published: July 2002

Over the past 10 years, mitochondrial defects have been implicated in a wide variety of degenerative diseases, aging, and cancer. Studies on patients with these diseases have revealed much about the complexities of mitochondrial genetics, which involves an interplay between mutations in the mitochondrial and nuclear genomes. However, the pathophysiology of mitochondrial diseases has remained perplexing. The essential role of mitochondrial oxidative phosphorylation in cellular energy production, the generation of reactive oxygen species, and the initiation of apoptosis has suggested a number of novel mechanisms for mitochondrial pathology. The importance and interrelationship of these functions are now being studied in mouse models of mitochondrial disease.
Simple Lessons from Complexity
Authors: Goldenfeld Nigel , Kadanoff Leo P.
Published: July 2002

The complexity of the world is contrasted with the simplicity of the basic laws of physics. In recent years, considerable study has been devoted to systems that exhibit complex outcomes. This experience has not given us any new laws of physics, but has instead given us a set of lessons about appropriate ways of approaching complex systems.
Control of mRNA Decay by Heat Shock-Ubiquitin-Proteasome Pathway
Authors: Laroia Gaurav , Cuesta Rafael , Brewer Gary , Schneider Robert J.
Published: July 2002

Cytokine and proto-oncogene messenger RNAs (mRNAs) are rapidly degraded through AU-rich elements in the 3′ untranslated region. Rapid decay involves AU-rich binding protein AUF1, which complexes with heat shock proteins hsc70-hsp70, translation initiation factor eIF4G, and poly(A) binding protein. AU-rich mRNA decay is associated with displacement of eIF4G from AUF1, ubiquitination of AUF1, and degradation of AUF1 by proteasomes. Induction of hsp70 by heat shock, down-regulation of the ubiquitin-proteasome network, or inactivation of ubiquitinating enzyme E1 all result in hsp70 sequestration of AUF1 in the perinucleus-nucleus, and all three processes block decay of AU-rich mRNAs and AUF1 protein. These results link the rapid degradation of cytokine mRNAs to the ubiquitin-proteasome pathway.
The Seductive Melody of the Strings
Authors: Perkowitz Sidney
Published: July 2002

The Elegant Universe
Superstrings, Hidden Dimensions, and the Quest for the Ultimate Theory. Brian Greene. Norton, New York, 1999. 464 pp. $27.95. ISBN 0-393-04688-5.

Writing for a general audience, physicist Greene presents an account of recent theoretical developments and argues that string theory appears to be a promising route toward an ultimate theory of everything.
Toward Benign Ends
Authors: Leitner Walter
Published: July 2002

Green chemistry aims to reduce or eliminate "the use or generation of hazardous substances in the design, manufacture, and application of chemical products." These two volumes offer a succinct introduction to the field and highlight a wide range of current activities within it, including research on catalysis, solvents, and supercritical fluids.
Different Trajectories of Parallel Evolution During Viral Adaptation
Authors: Wichman H. A. , Badgett M. R. , Scott L. A. , Boulianne C. M. , Bull J. J.
Published: July 2002

The molecular basis of adaptation is a major focus of evolutionary biology, yet the dynamic process of adaptation has been explored only piecemeal. Experimental evolution of two bacteriophage lines under strong selection led to over a dozen nucleotide changes genomewide in each replicate. At least 96 percent of the amino acid substitutions appeared to be adaptive, and half the changes in one line also occurred in the other. However, the order of these changes differed between replicates, and parallel substitutions did not reflect the changes with the largest beneficial effects or indicate a common trajectory of adaptation.
Fault Slip Rates at Depth from Recurrence Intervals of Repeating Microearthquakes
Authors: Nadeau Robert M. , McEvilly Thomas V.
Published: July 2002

Unique attributes in sequences of recurring, similar microearthquakes at Parkfield, California, provide a means for inferring slip rate at depth throughout the active fault surface from the time intervals between sequence events. Application of the method using an 11-year microseismicity record revealed systematic spatial and temporal changes in the slip rate that were synchronous with earthquake activity and other independent measures of fault-zone slip. If this phenomenon is found to be generally common behavior in active faults, it forms the basis for a method to monitor the changing strain field throughout a seismogenic fault zone.
Archean Molecular Fossils and the Early Rise of Eukaryotes
Authors: Brocks Jochen J. , Logan Graham A. , Buick Roger , Summons Roger E.
Published: July 2002

Molecular fossils of biological lipids are preserved in 2700-million-year-old shales from the Pilbara Craton, Australia. Sequential extraction of adjacent samples shows that these hydrocarbon biomarkers are indigenous and syngenetic to the Archean shales, greatly extending the known geological range of such molecules. The presence of abundant 2α-methylhopanes, which are characteristic of cyanobacteria, indicates that oxygenic photosynthesis evolved well before the atmosphere became oxidizing. The presence of steranes, particularly cholestane and its 28- to 30-carbon analogs, provides persuasive evidence for the existence of eukaryotes 500 million to 1 billion years before the extant fossil record indicates that the lineage arose.
Common Dynamic Structure of Canada Lynx Populations Within Three Climatic Regions
Authors: Stenseth Nils Chr. , Chan Kung-Sik , Tong Howell , Boonstra Rudy , Boutin Stan , Krebs Charles J. , Post Eric , O'Donoghue Mark , Yoccoz Nigel G. , Forchhammer Mads C. , Hurrell James W.
Published: July 2002

Across the boreal forest of Canada, lynx populations undergo regular density cycles. Analysis of 21 time series from 1821 onward demonstrated structural similarity in these cycles within large regions of Canada. The observed population dynamics are consistent with a regional structure caused by climatic features, resulting in a grouping of lynx population dynamics into three types (corresponding to three climatic-based geographic regions): Pacific-maritime, Continental, and Atlantic-maritime. A possible link with the North Atlantic Oscillation is suggested.
Search for Cross-Species Transmission of Porcine Endogenous Retrovirus in Patients Treated with Living Pig Tissue
Authors: Paradis Khazal , Langford Gillian , Long Zhifeng , Heneine Walid , Sandstrom Paul , Switzer William M. , Chapman Louisa E. , Lockey Chris , Onions David ,   The XEN 111 Study Group, Otto Edward
Published: July 2002

Pig organs may offer a solution to the shortage of human donor organs for transplantation, but concerns remain about possible cross-species transmission of porcine endogenous retrovirus (PERV). Samples were collected from 160 patients who had been treated with various living pig tissues up to 12 years earlier. Reverse transcription–polymerase chain reaction (RT-PCR) and protein immunoblot analyses were performed on serum from all 160 patients. No viremia was detected in any patient. Peripheral blood mononuclear cells from 159 of the patients were analyzed by PCR using PERV-specific primers. No PERV infection was detected in any of the patients from whom sufficient DNA was extracted to allow complete PCR analysis (97 percent of the patients). Persistent microchimerism (presence of donor cells in the recipient) was observed in 23 patients for up to 8.5 years.
Light-Independent Role of CRY1 and CRY2 in the Mammalian Circadian Clock
Authors: Griffin Edmund A. , Staknis David , Weitz Charles J.
Published: July 2002

Cryptochrome (CRY), a photoreceptor for the circadian clock in
Drosophila
, binds to the clock component TIM in a light-dependent fashion and blocks its function. In mammals, genetic evidence suggests a role for CRYs within the clock, distinct from hypothetical photoreceptor functions. Mammalian CRY1 and CRY2 are here shown to act as light-independent inhibitors of CLOCK-BMAL1, the activator driving
Per1
transcription. CRY1 or CRY2 (or both) showed light-independent interactions with CLOCK and BMAL1, as well as with PER1, PER2, and TIM. Thus, mammalian CRYs act as light-independent components of the circadian clock and probably regulate
Per1
transcriptional cycling by contacting both the activator and its feedback inhibitors.
Implication of Tubby Proteins as Transcription Factors by Structure-Based Functional Analysis
Authors: Boggon Titus J. , Shan Wei-Song , Santagata Sandro , Myers Samuel C. , Shapiro Lawrence
Published: July 2002

Tubby-like proteins (TULPs) are found in a broad range of multicellular organisms. In mammals, genetic mutation of tubby or other TULPs can result in one or more of three disease phenotypes: obesity (from which the name “tubby” is derived), retinal degeneration, and hearing loss. These disease phenotypes indicate a vital role for tubby proteins; however, no biochemical function has yet been ascribed to any member of this protein family. A structure-directed approach was employed to investigate the biological function of these proteins. The crystal structure of the core domain from mouse tubby was determined at a resolution of 1.9 angstroms. From primarily structural clues, experiments were devised, the results of which suggest that TULPs are a unique family of bipartite transcription factors.
Isolation of West Nile Virus from Mosquitoes, Crows, and a Cooper's Hawk in Connecticut
Authors: Anderson John F. , Andreadis Theodore G. , Vossbrinck Charles R. , Tirrell Shirley , Wakem Edward M. , French Richard A. , Garmendia Antonio E. , Van Kruiningen Herbert J.
Published: July 2002

West Nile (WN) virus, a mosquito-transmitted virus native to Africa, Asia, and Europe, was isolated from two species of mosquitoes,
Culex pipiens
and
Aedes vexans
, and from brain tissues of 28 American crows,
Corvus brachyrhynchos
, and one Cooper's hawk,
Accipiter cooperii
, in Connecticut. A portion of the genome of virus isolates from four different hosts was sequenced and analyzed by comparative phylogenetic analysis. Our isolates from Connecticut were similar to one another and most closely related to two WN isolates from Romania (2.8 and 3.6 percent difference). If established in North America, WN virus will likely have severe effects on human health and on the health of populations of birds.
Posttranscriptional Gene Silencing in
Neurospora
by a RecQ DNA Helicase
Authors: Cogoni Carlo , Macino Giuseppe
Published: July 2002

The phenomenon of posttranscriptional gene silencing (PTGS), which occurs when a transgene is introduced into a cell, is poorly understood. Here, the
qde-3
gene, which is required for the activation and maintenance of gene silencing in the fungus
Neurospora crassa
, was isolated. Sequence analysis revealed that the
qde-3
gene belongs to the RecQ DNA helicase family. The QDE3 protein may function in the DNA-DNA interaction between introduced transgenes or with an endogenous gene required for gene-silencing activation. In animals, genes that are homologous to RecQ protein, such as the human genes for Bloom's syndrome and Werner's syndrome, may also function in PTGS.
A Mammalian H
+
Channel Generated Through Alternative Splicing of the NADPH Oxidase Homolog
NOH-1
Authors: Bánfi Botond , Maturana Andrés , Jaconi Stefano , Arnaudeau Serge , Laforge Terese , Sinha Bhanu , Ligeti Erzsébet , Demaurex Nicolas , Krause Karl-Heinz
Published: July 2002

Voltage-gated proton (H
+
) channels are found in many human and animal tissues and play an important role in cellular defense against acidic stress. However, a molecular identification of these unique ion conductances has so far not been achieved. A 191–amino acid protein is described that, upon heterologous expression, has properties indistinguishable from those of native H
+
channels. This protein is generated through alternative splicing of messenger RNA derived from the gene
NOH-1
(NADPH oxidase homolog 1, where NADPH is the reduced form of nicotinamide adenine dinucleotide phosphate).
Physics of Iron at Earth's Core Conditions
Authors: Laio A. , Bernard S. , Chiarotti G. L. , Scandolo S. , Tosatti E.
Published: July 2002

The bulk properties of iron at the pressure and temperature conditions of Earth's core were determined by a method that combines first-principles and classical molecular dynamic simulations. The theory indicates that (i) the iron melting temperature at inner-core boundary (ICB) pressure (330 gigapascals) is 5400 (±400) kelvin; (ii) liquid iron at ICB conditions is about 6% denser than Earth's outer core; and (iii) the shear modulus of solid iron close to its melting line is 140 gigapascals, consistent with the seismic value for the inner core. These results reconcile melting temperature estimates based on sound velocity shock wave data with those based on diamond anvil cell experiments.
Sparse Coding and Decorrelation in Primary Visual Cortex During Natural Vision
Authors: Vinje William E. , Gallant Jack L.
Published: July 2002

Theoretical studies suggest that primary visual cortex (area V1) uses a sparse code to efficiently represent natural scenes. This issue was investigated by recording from V1 neurons in awake behaving macaques during both free viewing of natural scenes and conditions simulating natural vision. Stimulation of the nonclassical receptive field increases the selectivity and sparseness of individual V1 neurons, increases the sparseness of the population response distribution, and strongly decorrelates the responses of neuron pairs. These effects are due to both excitatory and suppressive modulation of the classical receptive field by the nonclassical receptive field and do not depend critically on the spatiotemporal structure of the stimuli. During natural vision, the classical and nonclassical receptive fields function together to form a sparse representation of the visual world. This sparse code may be computationally efficient for both early vision and higher visual processing.
A Domain in TNF Receptors That Mediates Ligand-Independent Receptor Assembly and Signaling
Authors: Chan Francis Ka-Ming , Chun Hyung J. , Zheng Lixin , Siegel Richard M. , Bui Kimmie L. , Lenardo Michael J.
Published: July 2002

A conserved domain in the extracellular region of the 60- and 80-kilodalton tumor necrosis factor receptors (TNFRs) was identified that mediates specific ligand-independent assembly of receptor trimers. This pre–ligand-binding assembly domain (PLAD) is physically distinct from the domain that forms the major contacts with ligand, but is necessary and sufficient for the assembly of TNFR complexes that bind TNF-α and mediate signaling. Other members of the TNFR superfamily, including TRAIL receptor 1 and CD40, show similar homotypic association. Thus, TNFRs and related receptors appear to function as preformed complexes rather than as individual receptor subunits that oligomerize after ligand binding.
Evidence for Superfluidity in Para-Hydrogen Clusters Inside Helium-4 Droplets at 0.15 Kelvin
Authors: Grebenev Slava , Sartakov Boris , Toennies J. Peter , Vilesov Andrei F.
Published: July 2002

A linear carbonyl sulfide (OCS) molecule surrounded by 14 to 16 para-hydrogen (pH
2
) molecules, or similar numbers of ortho-deuterium (oD
2
) molecules, within large helium-4 (
4
He) droplets and inside mixed
4
He/
3
He droplets was investigated by infrared spectroscopy. In the pure
4
He droplets (0.38 kelvin), both systems exhibited spectral features that indicate the excitation of angular momentum around the OCS axis. In the colder
4
He/
3
He droplets (0.15 kelvin), these features remained in the oD
2
cluster spectra but disappeared in the pH
2
spectra, indicating that the angular momentum is no longer excited. These results are consistent with the onset of superfluidity, thereby providing the first evidence for superfluidity in a liquid other than helium.
Patterning of the Zebrafish Retina by a Wave of Sonic Hedgehog Activity
Authors: Neumann Carl J. , Nuesslein-Volhard Christiane
Published: July 2002

The
Drosophila
retina is patterned by a morphogenetic wave driven by the Hedgehog signaling protein. Hedgehog, secreted by the first neurons, induces neuronal differentiation and
hedgehog
expression in nearby uncommitted cells, thereby propagating the wave. Evidence is presented here that the zebrafish Hedgehog homolog, Sonic Hedgehog, is also expressed in the first retinal neurons, and that Sonic Hedgehog drives a wave of neurogenesis across the retina, strikingly similar to the wave in
Drosophila
. The conservation of this patterning mechanism is unexpected, given the highly divergent structures of vertebrate and invertebrate eyes, and supports a common evolutionary origin of the animal visual system.
Discovery of Young, Isolated Planetary Mass Objects in the σ Orionis Star Cluster
Authors: Zapatero Osorio M. R. , Béjar V. J. S. , Martı́n E. L. , Rebolo R. , Navascués D. Barrado y , Bailer-Jones C. A. L. , Mundt R.
Published: July 2002

We present the discovery by optical and near-infrared imaging of an extremely red, low-luminosity population of isolated objects in the young, nearby stellar cluster around the multiple, massive star σ Orionis. The proximity (352 parsecs), youth (1 million to 5 million years), and low internal extinction make this cluster an ideal site to explore the substellar domain from the hydrogen mass limit down to a few Jupiter masses. Optical and near-infrared low-resolution spectroscopy of three of these objects confirms the very cool spectral energy distribution (atmospheric effective temperatures of 1700 to 2200 kelvin) expected for cluster members with masses in the range 5 to 15 times that of Jupiter. Like the planets of the solar system, these objects are unable to sustain stable nuclear burning in their interiors, but in contrast they are not bound to stars. This new kind of isolated giant planet, which apparently forms on time scales of less than a few million years, offers a challenge to our understanding of the formation processes of planetary mass objects.
Actin-Based Plasticity in Dendritic Spines
Authors: Matus Andrew
Published: July 2002

The central nervous system functions primarily to convert patterns of activity in sensory receptors into patterns of muscle activity that constitute appropriate behavior. At the anatomical level this requires two complementary processes: a set of genetically encoded rules for building the basic network of connections, and a mechanism for subsequently fine tuning these connections on the basis of experience. Identifying the locus and mechanism of these structural changes has long been among neurobiology's major objectives. Evidence has accumulated implicating a particular class of contacts, excitatory synapses made onto dendritic spines, as the sites where connective plasticity occurs. New developments in light microscopy allow changes in spine morphology to be directly visualized in living neurons and suggest that a common mechanism, based on dynamic actin filaments, is involved in both the formation of dendritic spines during development and their structural plasticity at mature synapses.
Nota Bene: Seven Scientists Up Close
Authors: Voss David
Published: July 2002

Me & Isaac Newton
. Michael Apted, Director. First Look Pictures, Los Angeles, 2000. See:
http://www.clearblueskyfilms.com/documentaries/main/

In this film by Michael Apted (director of the acclaimed Seven Up series), seven scientists comment on their lives, their research, and the place of science in society.
Development of CD8α-Positive Dendritic Cells from a Common Myeloid Progenitor
Authors: Traver David , Akashi Koichi , Manz Markus , Merad Miriam , Miyamoto Toshihiro , Engleman Edgar G. , Weissman Irving L.
Published: July 2002

Dendritic cells (DCs) are critical in both initiating adaptive immune responses and maintaining tolerance to self antigens. These apparently contradictory roles have been suggested to depend on different subsets of DCs that arise from either myeloid or lymphoid hematopoietic origins, respectively. Although DC expression of CD8α is attributed to a lymphoid origin, here we show that both CD8α
+
and CD8α
−
DCs can arise from clonogenic common myeloid progenitors in both thymus and spleen. Thus, expression of CD8α is not indicative of a lymphoid origin, and phenotypic and functional differences among DC subsets are likely to reflect maturation status rather than ontogeny.
The Role of Br
2
and BrCl in Surface Ozone Destruction at Polar Sunrise
Authors: Foster Krishna L. , Plastridge Robert A. , Bottenheim Jan W. , Shepson Paul B. , Finlayson-Pitts Barbara J. , Spicer Chester W.
Published: July 2002

Bromine atoms are believed to play a central role in the depletion of surface-level ozone in the Arctic at polar sunrise. Br
2
, BrCl, and HOBr have been hypothesized as bromine atom precursors, and there is evidence for chlorine atom precursors as well, but these species have not been measured directly. We report here measurements of Br
2
, BrCl, and Cl
2
made using atmospheric pressure chemical ionization–mass spectrometry at Alert, Nunavut, Canada. In addition to Br
2
at mixing ratios up to ∼25 parts per trillion, BrCl was found at levels as high as ∼35 parts per trillion. Molecular chlorine was not observed, implying that BrCl is the dominant source of chlorine atoms during polar sunrise, consistent with recent modeling studies. Similar formation of bromine compounds and tropospheric ozone destruction may also occur at mid-latitudes but may not be as apparent owing to more efficient mixing in the boundary layer.
Intracellular Functions of N-Linked Glycans
Authors: Helenius Ari , Aebi and Markus
Published: July 2002

N-linked oligosaccharides arise when blocks of 14 sugars are added cotranslationally to newly synthesized polypeptides in the endoplasmic reticulum (ER). These glycans are then subjected to extensive modification as the glycoproteins mature and move through the ER via the Golgi complex to their final destinations inside and outside the cell. In the ER and in the early secretory pathway, where the repertoire of oligosaccharide structures is still rather small, the glycans play a pivotal role in protein folding, oligomerization, quality control, sorting, and transport. They are used as universal “tags” that allow specific lectins and modifying enzymes to establish order among the diversity of maturing glycoproteins. In the Golgi complex, the glycans acquire more complex structures and a new set of functions. The division of synthesis and processing between the ER and the Golgi complex represents an evolutionary adaptation that allows efficient exploitation of the potential of oligosaccharides.
In Vitro Activities of the Ketolides Telithromycin (HMR 3647) and HMR 3004 Compared to Those of Clarithromycin against Slowly Growing Mycobacteria at pHs 6.8 and 7.4
Authors: Rastogi Nalin , Goh Khye Seng , Berchel Mylene , Bryskier André
Published: July 2002

The in vitro activities of HMR 3647 (telithromycin) and HMR 3004, two novel semisynthetic ketolides, were investigated and compared with that of the reference macrolide drug, clarithromycin, against 34 strains of slowly growing mycobacteria at pHs 6.8 and 7.4, as determined radiometrically. The MICs at pH 7.4 were about 1 to 2 dilutions lower than those observed at pH 6.8. In terms of the highest to the lowest activity, the three antibiotics could be classified as follows: clarithromycin > HMR 3004 > HMR 3647. Among the species tested,
Mycobacterium bovis
BCG,
M. ulcerans
,
M. avium
, and
M. paratuberculosis
were moderately susceptible to HMR 3004 and HMR 3647 (MICs at pH 7.4, ≤5.0 and ≤20.0 μg/ml, respectively, versus ≤1.25 μg/ml for clarithromycin), whereas
M. tuberculosis
,
M. africanum
,
M. bovis
, and
M. simiae
were resistant (MICs, ≥10.0 and ≥40.0 μg/ml, respectively, at pH 7.4). Although not more active than clarithromycin in vitro, the high level of intracellular accumulation of the two ketolides inside phagocytes warrants further screening in experimental animal models.
Undecylenic Acid Inhibits Morphogenesis of
Candida albicans
Authors: McLain Nealoo , Ascanio Rhoda , Baker Carol , Strohaver Robert A. , Dolan Joseph W.
Published: July 2002

Resilient liners are frequently used to treat denture stomatitis, a condition often associated with
Candida albicans
infections. Of 10 liners tested, 2 were found to inhibit the switch from the yeast form to hyphae and a third was found to stimulate this switch. The inhibitor was determined to be undecylenic acid.
Identification of the Coumermycin A
1
Biosynthetic Gene Cluster of
Streptomyces rishiriensis
DSM 40489
Authors: Wang Zhao-Xin , Li Shu-Ming , Heide Lutz
Published: July 2002

The biosynthetic gene cluster of the aminocoumarin antibiotic coumermycin A
1
was cloned by screening of a cosmid library of
Streptomyces rishiriensis
DSM 40489 with heterologous probes from a dTDP-glucose 4,6-dehydratase gene, involved in deoxysugar biosynthesis, and from the aminocoumarin resistance gyrase gene
gyrB
r
. Sequence analysis of a 30.8-kb region upstream of
gyrB
r
revealed the presence of 28 complete open reading frames (ORFs). Fifteen of the identified ORFs showed, on average, 84% identity to corresponding ORFs in the biosynthetic gene cluster of novobiocin, another aminocoumarin antibiotic. Possible functions of 17 ORFs in the biosynthesis of coumermycin A
1
could be assigned by comparison with sequences in GenBank. Experimental proof for the function of the identified gene cluster was provided by an insertional gene inactivation experiment, which resulted in an abolishment of coumermycin A
1
production.
In Vitro Susceptibility Tests for Cationic Peptides: Comparison of Broth Microdilution Methods for Bacteria That Grow Aerobically
Authors: Giacometti A. , Cirioni O. , Barchiesi F. , Del Prete M. S. , Fortuna M. , Caselli F. , Scalise G.
Published: July 2002

The in vitro susceptibilities of 90 clinical isolates of gram-positive and gram-negative aerobic bacteria to six cationic peptides, buforin II, cecropin P1, indolicidin, magainin II, nisin, and ranalexin, were evaluated by two broth microdilution methods. The first method was performed according to the procedures outlined by the National Committee for Clinical Laboratory Standards for bacteria that grow aerobically, while the second was performed according to the procedures recently proposed by the R. E. W. Hancock laboratory for testing antimicrobial peptides. Overall, the first method produced MICs two- and fourfold higher than the second method.
Stenotrophomonas maltophiliaD457R Contains a Cluster of Genes from Gram-Positive Bacteria Involved in Antibiotic and Heavy Metal Resistance
Authors: Alonso Ana , Sanchez Patricia , Martínez José L.
Published: July 2002

A cluster of genes involved in antibiotic and heavy metal resistance has been characterized from a clinical isolate of the gram-negative bacteriumStenotrophomonas maltophilia. These genes include a macrolide phosphotransferase (mphBM) and a cadmium efflux determinant (cadA), together with the genecadCcoding for its transcriptional regulator. ThecadC cadAregion is flanked by a truncated IS257sequence and a region coding for abin3invertase. Despite their presence in a gram-negative bacterium, these genetic elements share a common gram-positive origin. The possible origin of these determinants as a remnant composite transposon as well as the role of gene transfer between gram-positive and gram-negative bacteria for the acquisition of antibiotic resistance determinants in chronic, mixed infections is discussed.
Antimicrobial Resistance and Spread of Class 1 Integrons among
Salmonella
Serotypes
Authors: Guerra Beatriz , Soto Sara , Cal Santiago , Mendoza M. Carmen
Published: July 2002

The resistance profiles, for 15 antimicrobial agents, of 333
Salmonella
strains representing the most frequent nontyphoidal serotypes, isolated between 1989 and 1998 in a Spanish region, and 9 reference strains were analyzed. All strains were susceptible to amikacin, ceftazidime, ciprofloxacin, and imipenem, and 31% were susceptible to all antimicrobials tested. The most frequent types of resistance were to sulfadiazine, tetracycline, streptomycin, spectinomycin, ampicillin, and chloramphenicol (ranging from 46 to 22%); 13% were resistant to these six drugs. This multidrug resistance pattern was found alone or together with other resistance types within serotypes Typhimurium (45%), Panama (23%), and Virchow (4%). Each isolate was also screened for the presence of class 1 integrons and selected resistance genes therein; seven variable regions which carried one (
aadA1a
,
aadA2
, or
pse-1
) or two (
dfrA14-aadA1a
,
dfrA1-aadA1a
,
oxa1-aadA1a
, or
sat1-aadA1a
) resistance genes were found in integrons.
Mutation in 23S rRNA Responsible for Resistance to 16-Membered Macrolides and Streptogramins in
Streptococcus pneumoniae
Authors: Depardieu Florence , Courvalin Patrice
Published: July 2002

Streptococcus pneumoniae
clinical isolate BM4455 was resistant to 16-membered macrolides and to streptogramins. This unusual resistance phenotype was due to an A
2062
C (
Escherichia coli
numbering) mutation in domain V of the four copies of 23S rRNA.
Emergence of Reduced Susceptibility and Resistance to Fluoroquinolones in
Escherichia coli
in Taiwan and Contributions of Distinct Selective Pressures
Authors: McDonald L. Clifford , Chen Feng-Jui , Lo Hsiu-Jung , Yin Hsiao-Chuan , Lu Po-Liang , Huang Cheng-Hua , Chen Pei , Lauderdale Tsai-Ling , Ho Monto
Published: July 2002

A survey of 1,203
Escherichia coli
isolates from 44 hospitals in Taiwan revealed that 136 (11.3%) isolates were resistant to fluoroquinolones and that another 261 (21.7%) isolates had reduced susceptibility. Resistance was more common in isolates responsible for hospital-acquired (mostly in intensive care units) infections (17.5%) than in other adult inpatient (11.4%;
P
= 0.08) and outpatient isolates (11.9%;
P
> 0.1). Similarly, reduced susceptibility was more common in isolates responsible for hospital-acquired infections (30.9%) than in other adult inpatient (21.0%;
P
= 0.04) and outpatient (21.4%;
P
= 0.06) isolates. Isolates from pediatric patients were less likely to be resistant (1.3 versus 12.0%;
P
< 0.01) but were nearly as likely to have reduced susceptibility (17.7 versus 21.9%;
P
> 0.1) as nonpediatric isolates. There was an inverse relationship in the proportion of isolates that were resistant versus the proportion that had reduced susceptibility among isolates from individual hospitals (
R
= 0.031; P < 0.05). In an analysis of isolates from two hospitals, all 9 resistant strains possessed double point mutations in
gyrA
and all 19 strains with reduced susceptibility strains had single point mutations; no mutations were found among fully susceptible strains. Risk factors for resistance included underlying cancer (odds ratio [OR], 83; 95% confidence interval [CI
95
], 7.3 to 2,241;
P
< 0.001), exposure to a quinolone (OR, undefined;
P
= 0.02), and exposure to a nonquinolone antibiotic (OR, 20; CI
95
, 2.2 to 482;
P
< 0.001); underlying cancer was the only independent risk factor (OR, 83; CI
95
, 8.6 to 807;
P
< 0.001). There were no significant associations between any of these factors and reduced susceptibility. Whereas acute and chronic quinolone use in cancer patients is a major selective pressure for resistance, other undetermined but distinct selective pressures appear to be more responsible for reduced susceptibility to fluoroquinolones in
E. coli
.
Cross-Resistance between Triclosan and Antibiotics in
Pseudomonas aeruginosa
Is Mediated by Multidrug Efflux Pumps: Exposure of a Susceptible Mutant Strain to Triclosan Selects
nfxB
Mutants Overexpressing MexCD-OprJ
Authors: Chuanchuen Rungtip , Beinlich Kerry , Hoang Tung T. , Becher Anna , Karkhoff-Schweizer RoxAnn R. , Schweizer Herbert P.
Published: July 2002

Triclosan is an antiseptic frequently added to items as diverse as soaps, lotions, toothpaste, and many commonly used household fabrics and plastics. Although wild-type
Pseudomonas aeruginosa
expresses the triclosan target enoyl-acyl carrier protein reductase, it is triclosan resistant due to expression of the MexAB-OprM efflux system. Exposure of a susceptible Δ(
mexAB-oprM
) strain to triclosan selected multidrug-resistant bacteria at high frequencies. These bacteria hyperexpressed the MexCD-OprJ efflux system due to mutations in its regulatory gene,
nfxB
. The MICs of several drugs for these mutants were increased up to 500-fold, including the MIC of ciprofloxacin, which was increased 94-fold. Whereas the MexEF-OprN efflux system also participated in triclosan efflux, this antimicrobial was not a substrate for MexXY-OprM.
Therapeutic Potential of Human Neutrophil Peptide 1 against Experimental Tuberculosis
Authors: Sharma Sudhir , Verma Indu , Khuller G. K.
Published: July 2002

The therapeutic efficacy of human neutrophil peptide 1 (HNP-1) against experimental tuberculosis in mice on the basis of numbers of CFU has been examined. Mice infected with 1.5 × 104CFU ofMycobacterium tuberculosisH37Rv and treated with different doses of HNP-1 injected subcutaneously exhibited significant clearance of bacilli from lungs, livers, and spleens. There were time- and dose-dependent decreases in the bacillary load in lungs, livers, and spleens of the HNP-1-treated animals compared to that in controls (untreated animals). These observations strongly suggest the therapeutic activity of HNP-1 against tuberculosis.
In Vitro Activities of the Novel Ketolide Telithromycin (HMR 3647) against Erythromycin-Resistant
Streptococcus
Species
Authors: Jalava Jari , Kataja Janne , Seppälä Helena , Huovinen Pentti
Published: July 2002

The in vitro susceptibilities of 184 erythromycin-resistant streptococci to a novel ketolide, telithromycin (HMR 3647), were tested. These clinical isolates included 111
Streptococcus pyogenes
, 18 group C streptococcus, 18 group G streptococcus, and 37
Streptococcus pneumoniae
strains. The MICs for all but eight
S. pyogenes
strains were ≤0.5 μg/ml, indicating that telithromycin is active in vitro against erythromycin-resistant
Streptococcus
strains. All strains for which MICs were ≥1 μg/ml had an
erm
(B) resistance gene and six strains for which MICs were ≥4 μg/ml had a constitutive
erm
(B) gene (MIC range, 4 to 64 μg/ml). Interestingly, for
S. pneumoniae
strains with a constitutive
erm
(B) gene, MICs were ≤0.25 μg/ml (MIC range, ≤0.008 to 0.25 μg/ml). Our in vitro data show that for
S. pyogenes
strains which constitutively express the
erm
(B) methylase gene, MICs are so high that the strains might be clinically resistant to telithromycin.
Identification of Genes Induced by a Macrophage Activator, S-28463, Using Gene Expression Array Analysis
Authors: Buates Sureemas , Matlashewski Greg
Published: July 2002

S-28463 and imiquimod are imidazoquinoline compounds which stimulate microbicidal activity by inducing a local immune response at the site of application. Imiquimod-containing cream is an effective clinical treatment against cervical warts caused by human papillomavirus infection. Imiquimod also induces leishmanicidal activity both in vitro in macrophages and in vivo in a mouse model for cutaneous leishmaniasis. The major target cells of S-28463 and imiquimod are macrophages. To explore the molecular basis in which imidazoquinolines generate macrophage microbicidal activity, a cDNA gene array analysis was undertaken to identify genes induced by S-28463. Out of 588 genes screened in this assay, only 13 genes were significantly induced by S-28463. Remarkably, virtually all of the induced genes are involved in macrophage activation and inflammatory response. This experimental approach defines the mechanism of action of this clinically relevant compound in the induction of microbicidal activity in macrophages and also potentially identifies novel genes associated with microbicidal activity in this cell type.
N-Terminal Fatty Acid Substitution Increases the Leishmanicidal Activity of CA(1-7)M(2-9), a Cecropin-Melittin Hybrid Peptide
Authors: Chicharro Cristina , Granata Cesare , Lozano Rosario , Andreu David , Rivas Luis
Published: July 2002

In order to improve the leishmanicidal activity of the synthetic cecropin A-melittin hybrid peptide CA(1-7)M(2-9) (KWKLFKKIGAVLKVL-NH
2
), a systematic study of its acylation with saturated linear fatty acids was carried out. Acylation of the N
ɛ
-7 lysine residue led to a drastic decrease in leishmanicidal activity, whereas acylation at lysine 1, in either the α or the ɛ NH
2
group, increased up to 3 times the activity of the peptide against promastigotes and increased up to 15 times the activity of the peptide against amastigotes. Leishmanicidal activity increased with the length of the fatty acid chain, reaching a maximum for the lauroyl analogue (12 carbons). According to the fast kinetics, dissipation of membrane potential, and parasite membrane permeability to the nucleic acid binding probe SYTOX green, the lethal mechanism was directly related to plasma membrane permeabilization.
SHV-16, a β-Lactamase with a Pentapeptide Duplication in the Omega Loop
Authors: Arpin Corinne , Labia Roger , Andre Catherine , Frigo Cécile , El Harrif Zoubida , Quentin Claudine
Published: July 2002

A clinical isolate ofKlebsiella pneumoniaewas found to be resistant to ampicillin (MIC of 128 μg/ml), ticarcillin (MIC of 512 μg/ml), and ceftazidime (MIC of 128 μg/ml) and susceptible to all other β-lactams; a synergistic effect between clavulanate and ceftazidime suggested the presence of an extended-spectrum β-lactamase (ESBL). Transconjugants inEscherichia coliwere obtained at low levels (10−7per donor cell) and exhibited a similar β-lactam resistance pattern (resistant to ampicillin, ticarcillin, and ceftazidime at 64 μg/ml). The ESBL, pI 7.6, was encoded by a large plasmid (>100 kb) which did not carry any other resistance determinant. The ESBL-encoding gene was amplified by PCR usingblaSHV-specific primers and was sequenced. The deduced amino acid sequence of the SHV-16 ESBL showed that it differed from SHV-1 by only a pentapeptide insertion (163DRWET167) corresponding to a tandem duplication in the omega loop. The implication of the 163a-DRWET163b-DRWET sequence in ceftazidime resistance was confirmed by cloning eitherblaSHV-1orblaSHV-16in the same vector, subsequently introduced in the sameE. colistrain. Under these isogenic conditions, SHV-16 conferred a 32-fold increase in ceftazidime MIC compared to that with SHV-1. Furthermore, site-directed mutagenesis experiments modifying either E166aA or E166bA revealed that the functional glutamic residue was that located in the first copy of the duplicated sequence. But surprisingly, the second E166b also conferred a low-level resistance to ceftazidime. This work is the first description of a class A enzyme exhibiting an extended substrate specificity due to an insertion instead of a nucleotide substitution(s) in a clinical isolate.
Expression of Ubiquitin Gene in
Microsporum canis
and
Trichophyton mentagrophytes
Cultured with Fluconazole
Authors: Kano Rui , Okabayashi Ken , Nakamura Yuka , Watanabe Shinichi , Hasegawa Atsuhiko
Published: July 2002

The expression of the ubiquitin (Ub) gene in dermatophytes was examined for its relation to resistance against the antifungal drug fluconazole. The nucleotide sequences and the deduced amino acid sequences of the Ub gene in
Microsporum canis
were proven to be 99% similar to those of the Ub gene in
Trichophyton mentagrophytes
. Expression of mRNA of Ub in
M. canis
and
T. mentagrophytes
was enhanced when the fungi were cultured with fluconazole. The antifungal activity of fluconazole against these dermatophytes was increased in the presence of Ub proteasome inhibitor.
Diversity of Ribosomal Mutations Conferring Resistance to Macrolides, Clindamycin, Streptogramin, and Telithromycin in
Streptococcus pneumoniae
Authors: Canu Annie , Malbruny Brigitte , Coquemont Maëlle , Davies Todd A. , Appelbaum Peter C. , Leclercq Roland
Published: July 2002

Mechanisms of resistance were studied in 22 macrolide-resistant mutants selected in vitro from 5 parental strains of macrolide-susceptible
Streptococcus pneumoniae
by serial passage in various macrolides (T. A. Davies, B. E. Dewasse, M. R. Jacobs, and P. C. Appelbaum, Antimicrob. Agents Chemother., 44:414–417, 2000). Portions of genes encoding ribosomal proteins L22 and L4 and 23S rRNA (domains II and V) were amplified by PCR and analyzed by single-strand conformational polymorphism analysis to screen for mutations. The DNA sequences of amplicons from mutants that differed from those of parental strains by their electrophoretic migration profiles were determined. In six mutants, point mutations were detected in the L22 gene (G95D, P99Q, A93E, P91S, and G83E). The only mutant selected by telithromycin (for which the MIC increased from 0.008 to 0.25 μg/ml) contained a combination of three mutations in the L22 gene (A93E, P91S, and G83E). L22 mutations were combined with an L4 mutation (G71R) in one strain and with a 23S rRNA mutation (C2611A) in another strain. Nine other strains selected by various macrolides had A2058G (
n
= 1), A2058U (
n
= 2), A2059G (
n
= 1), C2610U (
n
= 1), and C2611U (
n
= 4) mutations (
Escherichia coli
numbering) in domain V of 23S rRNA. One mutant selected by clarithromycin and resistant to all macrolides tested (MIC, >32 μg/ml) and telithromycin (MIC, 4 μg/ml) had a single base deletion (A752) in domain II. In six remaining mutants, no mutations in L22, L4, or 23S rRNA could be detected.
Efficacy of Monoclonal Antibodies against Defined Antigens for Passive Immunotherapy of Chronic Gastrointestinal Cryptosporidiosis
Authors: Riggs Michael W. , Schaefer Deborah A. , Kapil Sushila J. , Barley-Maloney Lise , Perryman Lance E.
Published: July 2002

Cryptosporidium parvumis an important cause of diarrhea in humans and calves and can persistently infect immunocompromised hosts. Presently, there are no consistently effective parasite-specific drugs for cryptosporidiosis. We hypothesized that neutralizing monoclonal antibodies (MAbs) targeting the apical complex and surface antigens CSL, GP25-200, and P23 could passively immunize against cryptosporidiosis. We recently reported that a formulation of MAbs 3E2 (anti-CSL), 3H2 (anti-GP25-200), and 1E10 (anti-P23) provided significant additive prophylactic efficacy over that of the individual MAbs in neonatal ICR mice. In the present study, these MAbs were evaluated for therapeutic efficacy against persistent infection in adult gamma interferon-depleted SCID mice. 3E2 demonstrated the most significant and consistent therapeutic effect, reducing intestinal infection in two experiments. In one experiment, 3E2 plus 3H2 and 3E2 plus 3H2 plus 1E10 also significantly reduced infection; however, no significant increase in efficacy over 3E2 alone was apparent. The results indicate that anti-CSL MAb 3E2 has highly significant efficacy in reducing, but not eliminating, persistentC. parvuminfection.