bluuebunny/crossref_metadata_2025 huggingface dataset:
Parental Care and Clutch Sizes in North and South American Birds
Authors: Martin Thomas E. , Martin P. R. , Olson C. R. , Heidinger B. J. , Fontaine J. J.
Published: July 2002

The evolutionary causes of small clutch sizes in tropical and Southern Hemisphere regions are poorly understood. Alexander Skutch proposed 50 years ago that higher nest predation in the south constrains the rate at which parent birds can deliver food to young and thereby constrains clutch size by limiting the number of young that parents can feed. This hypothesis for explaining differences in clutch size and parental behaviors between latitudes has remained untested. Here, a detailed study of bird species in Arizona and Argentina shows that Skutch's hypothesis explains clutch size variation within North and South America. However, neither Skutch's hypothesis nor two major alternatives explain differences between latitudes.
Drug Discovery: A Historical Perspective
Authors: Drews Jürgen
Published: July 2002

Driven by chemistry but increasingly guided by pharmacology and the clinical sciences, drug research has contributed more to the progress of medicine during the past century than any other scientific factor. The advent of molecular biology and, in particular, of genomic sciences is having a deep impact on drug discovery. Recombinant proteins and monoclonal antibodies have greatly enriched our therapeutic armamentarium. Genome sciences, combined with bioinformatic tools, allow us to dissect the genetic basis of multifactorial diseases and to determine the most suitable points of attack for future medicines, thereby increasing the number of treatment options. The dramatic increase in the complexity of drug research is enforcing changes in the institutional basis of this interdisciplinary endeavor. The biotech industry is establishing itself as the discovery arm of the pharmaceutical industry. In bridging the gap between academia and large pharmaceutical companies, the biotech firms have been effective instruments of technology transfer.
Mitotic Misregulation and Human Aging
Authors: Ly Danith H. , Lockhart David J. , Lerner Richard A. , Schultz Peter G.
Published: July 2002

Messenger RNA levels were measured in actively dividing fibroblasts isolated from young, middle-age, and old-age humans and humans with progeria, a rare genetic disorder characterized by accelerated aging. Genes whose expression is associated with age-related phenotypes and diseases were identified. The data also suggest that an underlying mechanism of the aging process involves increasing errors in the mitotic machinery of dividing cells in the postreproductive stage of life. We propose that this dysfunction leads to chromosomal pathologies that result in misregulation of genes involved in the aging process.
Positional Syntenic Cloning and Functional Characterization of the Mammalian Circadian Mutation
tau
Authors: Lowrey Phillip L. , Shimomura Kazuhiro , Antoch Marina P. , Yamazaki Shin , Zemenides Peter D. , Ralph Martin R. , Menaker Michael , Takahashi Joseph S.
Published: July 2002

The
tau
mutation is a semidominant autosomal allele that dramatically shortens period length of circadian rhythms in Syrian hamsters. We report the molecular identification of the
tau
locus using genetically directed representational difference analysis to define a region of conserved synteny in hamsters with both the mouse and human genomes. The
tau
locus is encoded by casein kinase I epsilon (CKIɛ), a homolog of the
Drosophila
circadian gene
double-time
. In vitro expression and functional studies of wild-type and
tau
mutant CKIɛ enzyme reveal that the mutant enzyme has a markedly reduced maximal velocity and autophosphorylation state. In addition, in vitro CKIɛ can interact with mammalian PERIOD proteins, and the mutant enzyme is deficient in its ability to phosphorylate PERIOD. We conclude that
tau
is an allele of hamster CKIɛ and propose a mechanism by which the mutation leads to the observed aberrant circadian phenotype in mutant animals.
Architecture of RNA Polymerase II and Implications for the Transcription Mechanism
Authors: Cramer Patrick , Bushnell David A. , Fu Jianhua , Gnatt Averell L. , Maier-Davis Barbara , Thompson Nancy E. , Burgess Richard R. , Edwards Aled M. , David Peter R. , Kornberg Roger D.
Published: July 2002

A backbone model of a 10-subunit yeast RNA polymerase II has been derived from x-ray diffraction data extending to 3 angstroms resolution. All 10 subunits exhibit a high degree of identity with the corresponding human proteins, and 9 of the 10 subunits are conserved among the three eukaryotic RNA polymerases I, II, and III. Notable features of the model include a pair of jaws, formed by subunits Rpb1, Rpb5, and Rpb9, that appear to grip DNA downstream of the active center. A clamp on the DNA nearer the active center, formed by Rpb1, Rpb2, and Rpb6, may be locked in the closed position by RNA, accounting for the great stability of transcribing complexes. A pore in the protein complex beneath the active center may allow entry of substrates for polymerization and exit of the transcript during proofreading and passage through pause sites in the DNA.
Evolutionary Exploitation of Design Options by the First Animals with Hard Skeletons
Authors: Thomas R. D. K. , Shearman Rebecca M. , Stewart Graham W.
Published: July 2002

The set of viable design elements available for animals to use in building skeletons has been fully exploited. Analysis of animal skeletons in relation to the multivariate, theoretical “Skeleton Space” has shown that a large proportion of these options are used in each phylum. Here, we show that structural elements deployed in the skeletons of Burgess Shale animals (Middle Cambrian) incorporate 146 of 182 character pairs defined in this morphospace. Within 15 million years of the appearance of crown groups of phyla with substantial hard parts, at least 80 percent of skeletal design elements recognized among living and extinct marine metazoans were exploited.
Assessment of Oceanic Productivity with the Triple-Isotope Composition of Dissolved Oxygen
Authors: Luz Boaz , Barkan Eugeni
Published: July 2002

Plant production in the sea is a primary mechanism of global oxygen formation and carbon fixation. For this reason, and also because the ocean is a major sink for fossil fuel carbon dioxide, much attention has been given to estimating marine primary production. Here, we describe an approach for estimating production of photosynthetic oxygen, based on the isotopic composition of dissolved oxygen of seawater. This method allows the estimation of integrated oceanic productivity on a time scale of weeks.
Rab1 Recruitment of p115 into a cis-SNARE Complex: Programming Budding COPII Vesicles for Fusion
Authors: Allan Bernard B. , Moyer Bryan D. , Balch William E.
Published: July 2002

The guanosine triphosphatase Rab1 regulates the transport of newly synthesized proteins from the endoplasmic reticulum to the Golgi apparatus through interaction with effector molecules, but the molecular mechanisms by which this occurs are unknown. Here, the tethering factor p115 was shown to be a Rab1 effector that binds directly to activated Rab1. Rab1 recruited p115 to coat protein complex II (COPII) vesicles during budding from the endoplasmic reticulum, where it interacted with a select set of COPII vesicle–associated SNAREs (soluble
N
-ethylmaleimide–sensitive factor attachment protein receptors) to form a cis-SNARE complex that promotes targeting to the Golgi apparatus. We propose that Rab1-regulated assembly of functional effector-SNARE complexes defines a conserved molecular mechanism to coordinate recognition between subcellular compartments.
Atmospheric Influence of Earth's Earliest Sulfur Cycle
Authors: Farquhar James , Bao Huiming , Thiemens Mark
Published: July 2002

Mass-independent isotopic signatures for δ33S, δ34S, and δ36S from sulfide and sulfate in Precambrian rocks indicate that a change occurred in the sulfur cycle between 2090 and 2450 million years ago (Ma). Before 2450 Ma, the cycle was influenced by gas-phase atmospheric reactions. These atmospheric reactions also played a role in determining the oxidation state of sulfur, implying that atmospheric oxygen partial pressures were low and that the roles of oxidative weathering and of microbial oxidation and reduction of sulfur were minimal. Atmospheric fractionation processes should be considered in the use of sulfur isotopes to study the onset and consequences of microbial fractionation processes in Earth's early history.
Uptake of Glutamate into Synaptic Vesicles by an Inorganic Phosphate Transporter
Authors: Bellocchio Elizabeth E. , Reimer Richard J. , Fremeau Robert T. , Edwards Robert H.
Published: July 2002

Previous work has identified two families of proteins that transport classical neurotransmitters into synaptic vesicles, but the protein responsible for vesicular transport of the principal excitatory transmitter glutamate has remained unknown. We demonstrate that a protein that is unrelated to any known neurotransmitter transporters and that was previously suggested to mediate the Na
+
-dependent uptake of inorganic phosphate across the plasma membrane transports glutamate into synaptic vesicles. In addition, we show that this vesicular glutamate transporter, VGLUT1, exhibits a conductance for chloride that is blocked by glutamate.
Formation, Stability, and Breakup of Nanojets
Authors: Moseler Michael , Landman Uzi
Published: July 2002

Atomistic molecular dynamics simulations reveal the formation of nanojets with velocities up to 400 meters per second, created by pressurized injection of fluid propane through nanoscale convergent gold nozzles with heating or coating of the nozzle exterior surface to prevent formation of thick blocking films. The atomistic description is related to continuum hydrodynamic modeling through the derivation of a stochastic lubrication equation that includes thermally triggered fluctuations whose influence on the dynamical evolution increases as the jet dimensions become smaller. Emergence of double-cone neck shapes is predicted when the jet approaches nanoscale molecular dimensions, deviating from the long-thread universal similarity solution obtained in the absence of such fluctuations.
Incorporation of Short-Lived
10
Be in a Calcium-Aluminum-Rich Inclusion from the Allende Meteorite
Authors: McKeegan Kevin D. , Chaussidon Marc , Robert François
Published: July 2002

Enrichments in boron-10/boron-11 in a calcium-aluminum–rich inclusion from the Allende carbonaceous chondrite are correlated with beryllium/boron in a manner indicative of the in situ decay of short-lived beryllium-10. Because this radionuclide is produced only by nuclear spallation reactions, its existence in early solar system materials attests to intense irradiation processes in the solar nebula. The particle fluence inferred from the initial beryllium-10/beryllium-9 is sufficient to produce other short-lived nuclides, calcium-41 and manganese-53, found in meteorites, but the high canonical abundance of aluminum-26 may still require seeding of the solar system by radioactive stellar debris.
Whistle Matching in Wild Bottlenose Dolphins (
Tursiops truncatus
)
Authors: Janik Vincent M.
Published: July 2002

Dolphin communication is suspected to be complex, on the basis of their call repertoires, cognitive abilities, and ability to modify signals through vocal learning. Because of the difficulties involved in observing and recording individual cetaceans, very little is known about how they use their calls. This report shows that wild, unrestrained bottlenose dolphins use their learned whistles in matching interactions, in which an individual responds to a whistle of a conspecific by emitting the same whistle type. Vocal matching occurred over distances of up to 580 meters and is indicative of animals addressing each other individually.
Altered River Morphology in South Africa Related to the Permian-Triassic Extinction
Authors: Ward Peter D. , Montgomery David R. , Smith Roger
Published: July 2002

The Permian-Triassic transition in the Karoo Basin of South Africa was characterized by a rapid and apparently basin-wide change from meandering to braided river systems, as evidenced by preserved sedimentary facies. This radical changeover in river morphology is consistent with geomorphic consequences stemming from a rapid and major die-off of rooted plant life in the basin. Evidence from correlative nonmarine strata elsewhere in the world containing fluvial Permian-Triassic boundary sections suggests that a catastrophic terrestrial die-off of vegetation was a global event, producing a marked increase in sediment yield as well as contributing to the global δ
13
C excursion across the Permian-Triassic boundary.
A Niche Maintaining Germ Line Stem Cells in the
Drosophila
Ovary
Authors: Xie Ting , Spradling Allan C.
Published: July 2002

Stromal cells are thought to generate specific regulatory microenviroments or “niches” that control stem cell behavior. Characterizing stem cell niches in vivo remains an important goal that has been difficult to achieve. The individual ovarioles of the
Drosophila
ovary each contain about two germ line stem cells that maintain oocyte production. Here we show that anterior ovariolar somatic cells comprising three cell types act as a germ line stem cell niche. Germ line stem cells lost by normal or induced differentiation are efficiently replaced, and the ability to repopulate the niche increases the functional lifetime of ovarioles in vivo. Our studies implicate one of the somatic cell types, the cap cells, as a key niche component.
A Quantum Dot Single-Photon Turnstile Device
Authors: Michler P. , Kiraz A. , Becher C. , Schoenfeld W. V. , Petroff P. M. , Zhang Lidong , Hu E. , Imamoglu A.
Published: July 2002

Quantum communication relies on the availability of light pulses with strong quantum correlations among photons. An example of such an optical source is a single-photon pulse with a vanishing probability for detecting two or more photons. Using pulsed laser excitation of a single quantum dot, a single-photon turnstile device that generates a train of single-photon pulses was demonstrated. For a spectrally isolated quantum dot, nearly 100% of the excitation pulses lead to emission of a single photon, yielding an ideal single-photon source.
In Vitro Antihepadnaviral Activities of Combinations of Penciclovir, Lamivudine, and Adefovir
Authors: Colledge Danni , Civitico Gilda , Locarnini Stephen , Shaw Tim
Published: July 2002

Penciclovir {9-[2-hydroxy-1-(hydroxymethyl)-ethoxymethyl]guanine [PCV]}, lamivudine ([−]-β-l-2′,3′-dideoxy-3′-thiacytidine [3TC]), and adefovir (9-[2-phosphonylmethoxyethyl]-adenine [PMEA]) are potent inhibitors of hepatitis B virus (HBV) replication. Lamivudine has recently received approval for clinical use against chronic human HBV infection, and both PCV and PMEA have undergone clinical trials against HBV in their respective prodrug forms {famciclovir and adefovir dipivoxil [bis-(POM)-PMEA]}. Since multidrug combinations are likely to be used to control HBV infection, investigation of potential interactions between PCV, 3TC, and PMEA is important. Primary duck hepatocyte cultures which were either acutely or congenitally infected with the duck hepatitis B virus (DHBV) were used to investigate in vitro interactions between PCV, 3TC, and PMEA. Here we show that the anti-DHBV effects of all the combinations containing PCV, 3TC, and PMEA are greater than that of each of the individual components and that their combined activities are approximately additive or synergistic. These results may underestimate the potential in vivo usefulness of PMEA-containing combinations, since there is evidence that PMEA has immunomodulatory activity and, at least in the duck model of chronic HBV infection, is capable of inhibiting DHBV replication in cells other than hepatocytes, the latter being unaffected by treatment with either PCV or 3TC. Further investigation of the antiviral activities of these drug combinations is therefore required, particularly since each of the component drugs is already in clinical use.
Mutations in
Plasmodium falciparum
Cytochrome
b
That Are Associated with Atovaquone Resistance Are Located at a Putative Drug-Binding Site
Authors: Korsinczky Michael , Chen Nanhua , Kotecka Barbara , Saul Allan , Rieckmann Karl , Cheng Qin
Published: July 2002

Atovaquone is the major active component of the new antimalarial drug Malarone. Considerable evidence suggests that malaria parasites become resistant to atovaquone quickly if atovaquone is used as a sole agent. The mechanism by which the parasite develops resistance to atovaquone is not yet fully understood. Atovaquone has been shown to inhibit the cytochrome
bc
1
(CYT
bc
1
) complex of the electron transport chain of malaria parasites. Here we report point mutations in
Plasmodium falciparum
CYT
b
that are associated with atovaquone resistance. Single or double amino acid mutations were detected from parasites that originated from a cloned line and survived various concentrations of atovaquone in vitro. A single amino acid mutation was detected in parasites isolated from a recrudescent patient following atovaquone treatment. These mutations are associated with a 25- to 9,354-fold range reduction in parasite susceptibility to atovaquone. Molecular modeling showed that amino acid mutations associated with atovaquone resistance are clustered around a putative atovaquone-binding site. Mutations in these positions are consistent with a reduced binding affinity of atovaquone for malaria parasite CYT
b
.
The Ovine Cathelicidin SMAP29 Kills Ovine Respiratory Pathogens In Vitro and in an Ovine Model of Pulmonary Infection
Authors: Brogden K. A. , Kalfa V. C. , Ackermann M. R. , Palmquist D. E. , McCray P. B. , Tack B. F.
Published: July 2002

Cathelicidins are antimicrobial peptides from sheep (SMAP29 and SMAP34), rabbits (CAP11 and CAP18), rodents (CRAMP), and humans (FALL39, LL37, and h/CAP18). In a broth microdilution assay against nine ovine pathogens, SMAP29, SMAP34, mouse CRAMP, CAP18, CAP18
31
, CAP18
28
, CAP18
22
, and CAP18
21a
were the most active, with MICs as low as 0.6 μg/ml. Other cathelicidins were less active. In lambs with pneumonia, 0.5 mg of SMAP29 reduced the concentration of bacteria in both bronchoalveolar lavage fluid and consolidated pulmonary tissues. Hence, the antimicrobial activity of SMAP29 suggests that it has applications in the treatment of respiratory tract infections.
In Vitro Killing of
Candida albicans
by Fatty Acids and Monoglycerides
Authors: Bergsson Gudmundur , Arnfinnsson Jóhann , Steingrı́msson Ólafur , Thormar Halldor
Published: July 2002

The susceptibility of
Candida albicans
to several fatty acids and their 1-monoglycerides was tested with a short inactivation time, and ultrathin sections were studied by transmission electron microscopy (TEM) after treatment with capric acid. The results show that capric acid, a 10-carbon saturated fatty acid, causes the fastest and most effective killing of all three strains of
C. albicans
tested, leaving the cytoplasm disorganized and shrunken because of a disrupted or disintegrated plasma membrane. Lauric acid, a 12-carbon saturated fatty acid, was the most active at lower concentrations and after a longer incubation time.
Multidrug Resistance Is Mediated by Large Plasmids Carrying a Class 1 Integron in the Emergent
Salmonella enterica
Serotype [4,5,12:i:−]
Authors: Guerra Beatriz , Soto Sara M. , Argüelles Jose M. , Mendoza M. Carmen
Published: July 2002

A multidrug-resistant
Salmonella enterica
serotype [4,5,12:i:−] clone carried a class 1 integron harboring
dfrA12
and
aadA2
gene cassettes and
bla
TEM-1
,
aac(3)-IV
,
cmlA1
, and
tetA
genes located in large plasmids of about 140 kb (carrying
spv
) or 120 kb (lacking
spv
). Several segregants, lacking multidrug resistance, contained a plasmid smaller than the parental one and no longer hybridized with probes for the lost resistances. The genes mediating resistance to ampicillin, chloramphenicol, and tetracycline in the [4,5,12:i:−] clone are different from those found in the pentadrug-resistant serotype Typhimurium DT104 clone.
Single- and Multiple-Dose Pharmacokinetics of Caspofungin in Healthy Men
Authors: Stone Julie A. , Holland Sherry D. , Wickersham Peter J. , Sterrett Andrew , Schwartz Michael , Bonfiglio Cynthia , Hesney Michael , Winchell Gregory A. , Deutsch Paul J. , Greenberg Howard , Hunt Thomas L. , Waldman Scott A.
Published: July 2002

Caspofungin, a glucan synthesis inhibitor, is being developed as a parenteral antifungal agent. The pharmacokinetics of caspofungin following 1-h intravenous infusions in healthy men was investigated in four phase I studies. In an alternating two-panel (six men each), rising-single-dose study, plasma drug concentrations increased proportionally with the dose following infusions of 5 to 100 mg. The β-phase half-life was 9 to 10 h. The plasma drug clearance rate averaged 10 to 12 ml/min. Renal clearance of unchanged drug was a minor pathway of elimination (∼2% of the dose). Multiple-dose pharmacokinetics were investigated in a 2-week, serial-panel (5 or 6 men per panel) study of doses of 15, 35, and 70 mg administered daily; a 3-week, single-panel (10 men) study of a dose of 70 mg administered daily; and a parallel panel study (8 men) of a dose of 50 mg administered daily with or without a 70-mg loading dose on day 1. Moderate accumulation was observed with daily dosing. The degree of drug accumulation and the time to steady state were somewhat dose dependent. Accumulation averaged 24% at 15 mg daily and ∼50% at 50 and 70 mg daily. Mean plasma drug concentrations were maintained above 1.0 μg/ml, a target selected to exceed the MIC at which 90% of the isolates of the most clinically relevant species of
Candida
were inhibited, throughout therapy with daily treatments of 70 or 50 mg plus the loading dose, while they fell below the target for the first 2 days of a daily treatment of 50 mg without the loading dose. Caspofungin infused intravenously as a single dose or as multiple doses was generally well tolerated. In conclusion, the pharmacokinetics of caspofungin supports the clinical evaluation of once-daily dosing regimens for efficacy against fungal infections.
Characterization of Wild-Type and Cidofovir-Resistant Strains of Camelpox, Cowpox, Monkeypox, and Vaccinia Viruses
Authors: Smee Donald F. , Sidwell Robert W. , Kefauver Debbie , Bray Mike , Huggins John W.
Published: July 2002

Cidofovir {[(S)-1-(3-hydroxy-2-phosphonylmethoxypropyl)cytosine] [HPMPC]}-resistant forms of camelpox, cowpox, monkeypox, and vaccinia viruses were developed by prolonged passage in Vero 76 cells in the presence of drug. Eight- to 27-fold-higher concentrations of cidofovir were required to inhibit the resistant viruses than were needed to inhibit the wild-type (WT) viruses. Resistant viruses were characterized by determining their cross-resistance to other antiviral compounds, examining their different replication abilities in two cell lines, studying the biochemical basis of their drug resistance, and assessing the degrees of their virulence in mice. These viruses were cross resistant to cyclic HPMPC and, with the exception of vaccinia virus, to (S)-1-(3-hydroxy-2-phosphonylmethoxypropyl)adenine. Three of the four resistant cowpox and monkeypox viruses exhibited reduced abilities to infect and replicate in 3T3 cells compared to their abilities in Vero 76 cells. Compared to the WT virus polymers the resistant cowpox virus DNA polymerase was 8.5-fold less sensitive to inhibition by cidofovir diphosphate, the active form of the drug. Intracellular phosphorylation of [3H]cidofovir was not stimulated or inhibited by infection with resistant cowpox virus. In intranasally infected BALB/c mice, WT cowpox virus was 80-fold more virulent than the resistant virus. Cidofovir treatment (100 mg/kg of body weight, given one time only as early as 5 min after virus challenge) of a resistant cowpox virus infection could not protect mice from mortality. However, the drug prevented mortality in 80 to 100% of the mice treated with a single 100-mg/kg dose at 1, 2, 3, or 4 days after WT virus challenge. By application of these results to human orthopoxvirus infections, it is anticipated that resistant viruses may be untreatable with cidofovir but their virulence may be attenuated. Studies will need to be conducted with cidofovir-resistant monkeypox virus in monkeys to further support these hypotheses.
Development of 16S rRNA-Based Probes for the
Coriobacterium
Group and the
Atopobium
Cluster and Their Application for Enumeration of
Coriobacteriaceae
in Human Feces from Volunteers of Different Age Groups
Authors: Harmsen Hermie J. M. , Wildeboer-Veloo Alida C. M. , Grijpstra Jan , Knol Jan , Degener John E. , Welling Gjalt W.
Published: July 2002

Two 16S rRNA-targeted probes were developed: one for the
Coriobacterium
group and the other for the
Atopobium
cluster (which comprises most of the
Coriobacteriaceae
species, including the
Coriobacterium
group). The new probes were based on sequences of three new
Coriobacteriaceae
strains isolated from human feces and clinical material and sequences from databases. Application of the probes to fecal samples showed that formula-fed infants had higher numbers of
Coriobacterium
group cells in their feces than breast-fed infants. In addition, based on the presented results, it is hypothesized that with the increasing age of a person, the diversity of
Atopobium
cluster species present in the feces increases.
Microscale Diversity of the GenusNitrobacterin Soil on the Basis of Analysis of Genes Encoding rRNA
Authors: Grundmann G. L. , Normand P.
Published: July 2002

We looked at the diversity of NO2−oxidizers at field scale by examining isolates at clump scale and in microsamples of soil (diameter, 50 μm). The genetic distances (as determined by amplified ribosomal DNA restriction analysis performed withNitrobacter-specific primers) in a small clump of soil were as large as those between reference strains from large geographical areas. Diversity in individual microsamples was shown by serotyping.
Isolation and Characterization of aHelicobactersp. from the Gastric Mucosa of Dolphins,Lagenorhynchus acutusandDelphinus delphis
Authors: Harper Claudia M. G. , Dangler Charles A. , Xu Shilu , Feng Yan , Shen Zeli , Sheppard Barbara , Stamper Andrew , Dewhirst Floyd E. , Paster Bruce J. , Fox James G.
Published: July 2002

Gastric ulcerations in dolphins have been reported for decades. Some of these lesions were associated with parasitic infections. However, cases of nonparasitic gastric ulcers with no clearly defined etiology also have been reported in wild and captive dolphins. Considerable speculation exists as to whether dolphins haveHelicobacter-associated gastritis and peptic ulcer disease. The stomachs of seven stranded Atlantic white-sided dolphins,Lagenorhynchus acutus, and 1 common dolphin,Delphinus delphis, were assessed for the presence ofHelicobacterspecies. NovelHelicobacterspecies were identified by culture in the gastric mucosa of two of the eight dolphins studied and by PCR in seven of the eight dolphins. The gram-negative organisms were urease, catalase, and oxidase positive. Spiral to fusiform bacteria were detected in gastric mucosa by Warthin Starry staining. Histopathology revealed mild to moderate diffuse lymphoplasmacytic gastritis within the superficial mucosa of the main stomach. The pyloric stomach was less inflamed, and bacteria did not extend deep into the glands. The lesions parallel those observed inHelicobacter pylori-infected humans. Bacteria from two dolphins classified by 16S rRNA analysis clustered with gastric helicobacters and represent a novelHelicobactersp. most closely related toH. pylori. These findings suggest that a novelHelicobactersp. may play a role in the etiopathogenesis of gastritis and gastric ulcers in dolphins. To our knowledge this represents the first isolation and characterization of a novelHelicobactersp. from a marine mammal and emphasizes the wide host distribution and pathogenic potential of this increasingly important genus.
Characterization and Chromosomal Mapping of Antimicrobial Resistance Genes inSalmonella entericaSerotype Typhimurium
Authors: Daly M. , Fanning S.
Published: July 2002

Two hundred and twenty-sixSalmonella entericaserotype Typhimurium isolates were examined for the presence of integron-associated gene cassettes. All but two of the non-DT104 isolates, together with DT104 isolates, contained gene cassettes. Amplicons of 1.5 kbp each were found in two non-DT104 isolates, encoding adhfrIgene (trimethoprim resistance) linked to anaadAgene (streptomycin and spectinomycin resistance), by site-specific recombination. DT104 isolates of resistance (R) type ACSSuT possessed the recently described 1.0- and 1.2-kbp gene cassettes. Macrorestriction analysis withXbaI and DNA probing mappedant(3")-1a,blaPSE-1, anddhfrIgenes to large multiresistant gene clusters in a DT170a isolate and a DT193 isolate. In contrast, all DT104 isolates (R-type ACSSuT) possessed a conserved 10-kbpXba1DNA fragment. Our study highlights the occurrence of integrons (and antimicrobial resistance determinants) among serotype Typhimurium isolates other than DT104. Larger and previously unrecognized multiresistance gene clusters were identified in these isolates by DNA probing.
Variation in Tolerance and Virulence in the Chestnut Blight Fungus-Hypovirus Interaction
Authors: Peever Tobin L. , Liu Yir-Chung , Cortesi Paolo , Milgroom Michael G.
Published: July 2002

Chestnut blight, caused by the fungusCryphonectria parasitica, has been effectively controlled with double-stranded RNA hypoviruses in Europe for over 40 years. The marked reduction in the virulence ofC. parasiticaby hypoviruses is a phenomenon known as hypovirulence. This virus-fungus pathosystem has become a model system for the study of biological control of fungi with viruses. We studied variation in tolerance to hypoviruses in fungal hosts and variation in virulence among virus isolates from a local population in Italy. Tolerance is defined as the relative fitness of a fungal individual when infected with hypoviruses (compared to being uninfected); virulence is defined for each hypovirus as the reduction in fitness of fungal hosts relative to virus-free hosts. Six hypovirus-infected isolates ofC. parasiticawere sampled from the population, and each hypovirus was transferred into six hypovirus-free recipient isolates. The resulting 36 hypovirus-fungus combinations were used to estimate genetic variation in tolerance to hypoviruses, in hypovirus virulence, and in virus-fungus interactions. Four phenotypes were evaluated for each virus-fungus combination to estimate relative fitness: (i) sporulation, i.e., the number of asexual spores (conidia) produced; (ii) canker area on field-inoculated chestnut trees, (iii) vertical transmission of hypoviruses into conidia, and (iv) conidial germination. Two-way analysis of variance (ANOVA) revealed significant interactions (P< 0.001) between viruses and fungal isolates for sporulation and canker area but not for conidial germination or transmission. One-way ANOVA among hypoviruses (within each fungal isolate) and among fungal isolates (within each hypovirus) revealed significant genetic variation (P< 0.01) in hypovirus virulence and fungal tolerance within several fungal isolates, and hypoviruses, respectively. These interactions and the significant genetic variation in several fitness characters indicate the potential for future evolution of these characters. However, biological control is unlikely to break down due to evolution of tolerance to hypoviruses in the fungus because the magnitudes of tolerance and interactions were relatively small.
Ectomycorrhizal Specificity Patterns in a Mixed
Pinus contorta
and
Picea engelmannii
Forest in Yellowstone National Park
Authors: Cullings Kenneth W. , Vogler Detlev R. , Parker Virgil T. , Finley Sara Katherine
Published: July 2002

We used molecular genetic methods to test two hypotheses, (i) that host plant specificity among ectomycorrhizal fungi would be common in a closed-canopy, mixed
Pinus contorta-Picea engelmannii
forest in Yellowstone National Park and (ii) that specificity would be more common in the early successional tree species,
P. contorta
, than in the invader,
P. engelmannii
. We identified 28 ectomycorrhizal fungal species collected from 27 soil cores. The proportion of
P. engelmannii
to
P. contorta
ectomycorrhizae was nearly equal (52 and 48%, respectively). Of the 28 fungal species, 18 composed greater than 95% of the fungal community. No species was associated exclusively with
P. contorta
, but four species, each found in only one core, and one species found in two cores were associated exclusively with
P. engelmannii
. These fungi composed less than 5% of the total ectomycorrhizae. Thus, neither hypothesis was supported, and hypothesized benefits of ectomycorrhizal specificity to both trees and fungi probably do not exist in this system.
Fatty Acid Competition as a Mechanism by Which
Enterobacter cloacae
Suppresses
Pythium ultimum
Sporangium Germination and Damping-Off
Authors: van Dijk Karin , Nelson Eric B.
Published: July 2002

Interactions between plant-associated microorganisms play important roles in suppressing plant diseases and enhancing plant growth and development. While competition between plant-associated bacteria and plant pathogens has long been thought to be an important means of suppressing plant diseases microbiologically, unequivocal evidence supporting such a mechanism has been lacking. We present evidence here that competition for plant-derived unsaturated long-chain fatty acids between the biological control bacterium
Enterobacter cloacae
and the seed-rotting oomycete,
Pythium ultimum
, results in disease suppression. Since fatty acids from seeds and roots are required to elicit germination responses of
P. ultimum
, we generated mutants of
E. cloacae
to evaluate the role of
E. cloacae
fatty acid metabolism on the suppression of
Pythium
sporangium germination and subsequent plant infection. Two mutants of
E. cloacae
EcCT-501R3, Ec31 (
fadB
) and EcL1 (
fadL
), were reduced in β-oxidation and fatty acid uptake, respectively. Both strains failed to metabolize linoleic acid, to inactivate the germination-stimulating activity of cottonseed exudate and linoleic acid, and to suppress
Pythium
seed rot in cotton seedling bioassays. Subclones containing
fadBA
or
fadL
complemented each of these phenotypes in Ec31 and EcL1, respectively. These data provide strong evidence for a competitive exclusion mechanism for the biological control of
P. ultimum
-incited seed infections by
E. cloacae
where
E. cloacae
prevents the germination of
P. ultimum
sporangia by the efficient metabolism of fatty acid components of seed exudate and thus prevents seed infections.
Diacetyl and α-Acetolactate Overproduction by
Lactococcus lactis
subsp.
lactis
Biovar Diacetylactis Mutants That Are Deficient in α-Acetolactate Decarboxylase and Have a Low Lactate Dehydrogenase Activity
Authors: Monnet Christophe , Aymes Frédéric , Corrieu Georges
Published: July 2002

Lactococcus lactis
subsp.
lactis
biovar diacetylactis strains are utilized in several industrial processes for producing the flavoring compound diacetyl or its precursor α-acetolactate. Using random mutagenesis with nitrosoguanidine, we selected mutants that were deficient in α-acetolactate decarboxylase and had low lactate dehydrogenase activity. The mutants produced large amounts of α-acetolactate in anaerobic milk cultures but not in aerobic cultures, except when the medium was supplemented with catalase, yeast extract, or hemoglobin.
Effect of Increased Yeast Alcohol Acetyltransferase Activity on Flavor Profiles of Wine and Distillates
Authors: Lilly M. , Lambrechts M. G. , Pretorius I. S.
Published: July 2002

The distinctive flavor of wine, brandy, and other grape-derived alcoholic beverages is affected by many compounds, including esters produced during alcoholic fermentation. The characteristic fruity odors of the fermentation bouquet are primarily due to a mixture of hexyl acetate, ethyl caproate (apple-like aroma), iso-amyl acetate (banana-like aroma), ethyl caprylate (apple-like aroma), and 2-phenylethyl acetate (fruity, flowery flavor with a honey note). The objective of this study was to investigate the feasibility of improving the aroma of wine and distillates by overexpressing one of the endogenous yeast genes that controls acetate ester production during fermentation. The synthesis of acetate esters by the wine yeastSaccharomyces cerevisiaeduring fermentation is ascribed to at least three acetyltransferase activities, namely, alcohol acetyltransferase (AAT), ethanol acetyltransferase, and iso-amyl AAT. To investigate the effect of increased AAT activity on the sensory quality of Chenin blanc wines and distillates from Colombar base wines, we have overexpressed the alcohol acetyltransferase gene (ATF1) ofS. cerevisiae. TheATF1gene, located on chromosome XV, was cloned from a widely used commercial wine yeast strain ofS. cerevisiae, VIN13, and placed under the control of the constitutive yeast phosphoglycerate kinase gene (PGK1) promoter and terminator. Chromoblot analysis confirmed the integration of the modified copy ofATF1into the genome of three commercial wine yeast strains (VIN7, VIN13, and WE228). Northern blot analysis indicated constitutive expression ofATF1at high levels in these yeast transformants. The levels of ethyl acetate, iso-amyl acetate, and 2-phenylethyl acetate increased 3- to 10-fold, 3.8- to 12-fold, and 2- to 10-fold, respectively, depending on the fermentation temperature, cultivar, and yeast strain used. The concentrations of ethyl caprate, ethyl caprylate, and hexyl acetate only showed minor changes, whereas the acetic acid concentration decreased by more than half. These changes in the wine and distillate composition had a pronounced effect on the solvent or chemical aroma (associated with ethyl acetate and iso-amyl acetate) and the herbaceous and heads-associated aromas of the final distillate and the solvent or chemical and fruity or flowery characters of the Chenin blanc wines. This study establishes the concept that the overexpression of acetyltransferase genes such asATF1could profoundly affect the flavor profiles of wines and distillates deficient in aroma, thereby paving the way for the production of products maintaining a fruitier character for longer periods after bottling.
Quantitative Use of Fluorescent In Situ Hybridization To Examine Relationships between Mycolic Acid-Containing Actinomycetes and Foaming in Activated Sludge Plants
Authors: Davenport Russell J. , Curtis Thomas P. , Goodfellow Michael , Stainsby Fiona M. , Bingley Marc
Published: July 2002

The formation of viscous foams on aeration basins and secondary clarifiers of activated sludge plants is a common and widespread problem. Foam formation is often attributed to the presence of mycolic acid-containing actinomycetes (mycolata). In order to examine the relationship between the number of mycolata and foam, we developed a group-specific probe targeting the 16S rRNA of the mycolata, a protocol to permeabilize mycolata, and a statistically robust quantification method. Statistical analyses showed that a lipase-based permeabilization method was quantitatively superior to previously described methods (P<< 0.05). When mixed liquor and foam samples were examined, most of the mycolata present were rods or cocci, although filamentous mycolata were also observed. A nested analysis of variance showed that virtually all of the measured variance occurred between fields of view and not between samples. On this basis we determined that as few as five fields of view could be used to give a statistically meaningful sample. Quantitative fluorescent in situ hybridization (FISH) was used to examine the relationship between foaming and the concentration of mycolata in a 20-m3completely mixed activated sludge plant. Foaming occurred when the number of mycolata exceeded a certain threshold value. Baffling of the plant affected foaming without affecting the number of mycolata. We tentatively estimated that the threshold foaming concentration of mycolata was about 2 × 106cells ml−1or 4 × 1012cells m−2. We concluded that quantitative use of FISH is feasible and that quantification is a prerequisite for rational investigation of foaming in activated sludge.
Contribution of
dps
to Acid Stress Tolerance and Oxidative Stress Tolerance in
Escherichia coli
O157:H7
Authors: Choi Sang Ho , Baumler David J. , Kaspar Charles W.
Published: July 2002

An
Escherichia coli
O157:H7
dps
::
nptI
mutant (FRIK 47991) was generated, and its survival was compared to that of the parent in HCl (synthetic gastric fluid, pH 1.8) and hydrogen peroxide (15 mM) challenges. The survival of the mutant in log phase (5-h culture) was significantly impaired (4-log
10
-CFU/ml reduction) compared to that of the parent strain (ca. 1.0-log
10
-CFU/ml reduction) after a standard 3-h acid challenge. Early-stationary-phase cells (12-h culture) of the mutant decreased by ca. 4 log
10
CFU/ml while the parent strain decreased by approximately 2 log
10
CFU/ml. No significant differences in the survival of late-stationary-phase cells (24-h culture) between the parent strain and the mutant were observed, although numbers of the parent strain declined less in the initial 1 h of acid challenge. FRIK 47991 was more sensitive to hydrogen peroxide challenge than was the parent strain, although survival improved in stationary phase. Complementation of the mutant with a functional
dps
gene restored acid and hydrogen peroxide tolerance to levels equal to or greater than those exhibited by the parent strain. These results demonstrate that decreases in survival were from the absence of Dps or a protein regulated by Dps. The results from this study establish that Dps contributes to acid tolerance in
E. coli
O157:H7 and confirm the importance of Dps in oxidative stress protection.
Axial Differences in Community Structure of
Crenarchaeota
and
Euryarchaeota
in the Highly Compartmentalized Gut of the Soil-Feeding Termite
Cubitermes orthognathus
Authors: Friedrich Michael W. , Schmitt-Wagner Dirk , Lueders Tillmann , Brune Andreas
Published: July 2002

Methanogenesis represents an important electron sink reaction in the hindgut of soil-feeding termites. This is the first comprehensive analysis of the archaeal community structure within the highly compartmentalized intestinal tract of a humivorous insect, combining clonal analysis and terminal restriction fragment (T-RF) length polymorphism (T-RFLP) fingerprinting of the archaeal communities in the different gut compartments of
Cubitermes orthognathus
. We found that the morphological and physicochemical heterogeneity of the gut is reflected in a large phylogenetic diversity and pronounced axial differences in the composition of the archaeal gut microbiota, notably among those clones or ribotypes that could be assigned to methanogenic taxa. Comparative analysis of the relative frequencies of different archaeal lineages among the small-subunit rRNA gene (SSU rDNA) clones and their corresponding T-RF indicated that the archaeal community in the anterior, extremely alkaline hindgut compartment (P1) consists mainly of members of the
Methanosarcinaceae
, whereas
Methanobacteriaceae
and
Methanomicrobiales
predominate in the subsequent, more posterior compartments (P3/4a and P4b). The relative abundance of
Thermoplasmales
increased towards the rectum (P5). SSU rDNA sequences representing
Crenarchaeota
, which have not yet been reported to occur in the intestinal tracts of arthropods, were detected in all gut sections. We discuss how the spatial distribution of methanogenic populations may be linked to axial heterogeneity in the physicochemical gut conditions and to functional adaptations to their respective ecological niches.
Vancomycin-ResistantEnterococcusspp. Isolated from Wastewater and Chicken Feces in the United States
Authors: Harwood Valerie J. , Brownell Miriam , Perusek William , Whitlock John E.
Published: July 2002

Vancomycin-resistantEnterococcusspp. (VRE) were isolated from sewage and chicken feces but not from other animal fecal sources (dog, cow, and pig) or from surface waters tested. VRE from hospital wastewater were resistant to ≥20 μg of vancomycin/ml and possessed thevanAgene. VRE from residential wastewater and chicken feces were resistant to 3 to 5 μg of vancomycin/ml and possessed thevanCgene.
Determination of Oligopeptide Diversity within a Natural Population ofMicrocystisspp. (Cyanobacteria) by Typing Single Colonies by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry
Authors: Fastner Jutta , Erhard Marcel , von Döhren Hans
Published: July 2002

Besides the most prominent peptide toxin, microcystin, the cyanobacteriaMicrocystisspp. have been shown to produce a large variety of other bioactive oligopeptides. We investigated for the first time the oligopeptide diversity within a naturalMicrocystispopulation by analyzing single colonies directly with matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS). The results demonstrate a high diversity of known cyanobacterial peptides such as microcystins, anabaenopeptins, microginins, aeruginosins, and cyanopeptolins, but also many unknown substances in theMicrocystiscolonies. Oligopeptide patterns were mostly related to specificMicrocystistaxa.Microcystis aeruginosa(Kütz.) Kütz. colonies contained mainly microcystins, occasionally accompanied by aeruginosins. In contrast, microcystins were not detected inMicrocystis ichthyoblabeKütz.; instead, colonies of this species contained anabaenopeptins and/or microginins or unknown peptides. Within a third group,Microcystis wesenbergii(Kom.) Kom. in Kondr., chiefly a cyanopeptolin and an unknown peptide were found. Similar patterns, however, were also found in colonies which could not be identified to species level. The significance of oligopeptides as a chemotaxonomic tool within the genusMicrocystisis discussed. It could be demonstrated that the typing of single colonies by MALDI-TOF MS may be a valuable tool for ecological studies of the genusMicrocystisas well as in early warning of toxic cyanobacterial blooms.
Deletion of the
GRE3
Aldose Reductase Gene and Its Influence on Xylose Metabolism in Recombinant Strains of
Saccharomyces cerevisiae
Expressing the
xylA
and
XKS1
Genes
Authors: Träff K. L. , Otero Cordero R. R. , van Zyl W. H. , Hahn-Hägerdal B.
Published: July 2002

Saccharomyces cerevisiae
ferments hexoses efficiently but is unable to ferment xylose. When the bacterial enzyme xylose isomerase (XI) from
Thermus thermophilus
was produced in
S
.
cerevisiae,
xylose utilization and ethanol formation were demonstrated. In addition, xylitol and acetate were formed. An unspecific aldose reductase (AR) capable of reducing xylose to xylitol has been identified in
S
.
cerevisiae
. The
GRE3
gene, encoding the AR enzyme, was deleted in
S
.
cerevisiae
CEN.PK2-1C, yielding YUSM1009a. XI from
T
.
thermophilus
was produced, and endogenous xylulokinase from
S
.
cerevisiae
was overproduced in
S
.
cerevisiae
CEN.PK2-1C and YUSM1009a. In recombinant strains from which the
GRE3
gene was deleted, xylitol formation decreased twofold. Deletion of the
GRE3
gene combined with expression of the
xylA
gene from
T
.
thermophilus
on a replicative plasmid generated recombinant xylose utilizing
S
.
cerevisiae
strain TMB3102, which produced ethanol from xylose with a yield of 0.28 mmol of C from ethanol/mmol of C from xylose. None of the recombinant strains grew on xylose.