bluuebunny/crossref_metadata_2025_split huggingface dataset:
Contributions of Atmospheric CO and Hydrogen Uptake to Microbial Dynamics on Recent Hawaiian Volcanic Deposits
Authors: King Gary M. 
Published: July 2003

ABSTRACT

A series of sites were established on Hawaiian volcanic deposits ranging from about 18 to 300 years old. Three sites occurred in areas that supported tropical rain forests; the remaining sites were in areas that supported little or no plant growth. Sites >26 years old consumed atmospheric CO and hydrogen at rates ranging from about 0.2 to 5 mg of CO m
−2
day
−1
and 0.1 to 4 mg of H
2
m
−2
day
−1
, respectively. Respiration, measured as CO
2
production, for a subset of the sites ranged from about 40 to >1,400 mg of CO
2
m
−2
day
−1
. CO and H
2
accounted for about 13 to 25% of reducing equivalent flow for all but a forested site, where neither substrate appeared significant. Based on responses to chloroform fumigation, hydrogen utilization appeared largely due to microbial uptake. In contrast to results for CO and hydrogen, methane uptake occurred consistently only at the forest site. Increasing deposit age was generally accompanied by increasing concentrations of organic matter and microbial biomass, measured as phospholipid phosphate. Exoenzymatic activities (acid and alkaline phosphatases and α- and β-glucosidases) were positively correlated with deposit age in spite of considerable variability within sites. The diversity of substrates utilized in Biolog Ecoplate assays also increased with deposit age, possibly reflecting changes in microbial community complexity.
Identification of a New Ribosomal Protection Type of Tetracycline Resistance Gene,
tet
(36), from Swine Manure Pits
Authors: Whittle Gabrielle , Whitehead Terence R. , Hamburger Nathan , Shoemaker Nadja B. , Cotta Michael A. , Salyers Abigail A. 
Published: July 2003

ABSTRACT

Previously, only one ribosome protection type of a tetracycline resistance gene,
tetQ
, had been identified in
Bacteroides
spp. During an investigation of anaerobic bacteria present in swine feces and manure storage pits, a tetracycline-resistant
Bacteroides
strain was isolated. Subsequent analysis showed that this new
Bacteroides
strain,
Bacteroides
sp. strain 139, did not contain
tetQ
but contained a previously unidentified tetracycline resistance gene. Sequence analysis showed that the tetracycline resistance gene from
Bacteroides
sp. strain 139 encoded a protein (designated Tet 36) that defines a new class of ribosome protection types of tetracycline resistance. Tet 36 has 60% amino acid identity over 640 aa to TetQ and between 31 and 49% amino acid identity to the nine other ribosome protection types of tetracycline resistance genes. The
tet
(36) region was not observed to transfer from
Bacteroides
sp. strain 139 to another
Bacteroides
sp. under laboratory conditions. Yet
tet
(36) was found in other genera of bacteria isolated from the same swine manure pits and from swine feces. Phylogenetic analysis of the
tet
(36)-containing isolates indicated that
tet
(36) was present not only in the
Cytophaga-Flavobacter-Bacteroides
group to which
Bacteroides
sp. strain 139 belongs but also in gram-positive genera and gram-negative proteobacteria, indicating that horizontal transfer of
tet
(36) is occurring between these divergent phylogenetic groups in the farm environment.
Saprotrophic and Mycoparasitic Components of Aggressiveness of
Trichoderma harzianum
Groups toward the Commercial Mushroom
Agaricus bisporus
Authors: Williams Josie , Clarkson John M. , Mills Peter R. , Cooper Richard M. 
Published: July 2003

ABSTRACT

We examined the mycoparasitic and saprotrophic behavior of isolates representing groups of
Trichoderma harzianum
to establish a mechanism for the aggressiveness towards
Agaricus bisporus
in infested commercial compost. Mycoparasitic structures were infrequently observed in interaction zones on various media, including compost, with cryoscanning electron microscopy.
T. harzianum
grows prolifically in compost in the absence or presence of
A. bisporus
, and the aggressive European (Th2) and North American (Th4) isolates produced significantly higher biomasses (6.8- and 7.5-fold, respectively) in compost than did nonaggressive, group 1 isolates. All groups secreted depolymerases that could attack the cell walls of
A. bisporus
and of wheat straw, and some were linked to aggressiveness. Growth on mushroom cell walls in vitro resulted in rapid production of chymoelastase and trypsin-like proteases by only the Th2 and Th4 isolates. These isolates also produced a dominant protease isoform (pI 6.22) and additional chitinase isoforms. On wheat straw, Th4 produced distinct isoforms of cellulase and laminarinase, but there was no consistent association between levels or isoforms of depolymerases and aggressiveness. Th3's distinctive profiles confirmed its reclassification as
Trichoderma atroviride.
Proteases and glycanases were detected for the first time in sterilized compost colonized by
T. harzianum
. Xylanase dominated, and some isoforms were unique to compost, as were some laminarinases. We hypothesize that aggressiveness results from competition, antagonism, or parasitism but only as a component of, or following, extensive saprotrophic growth involving degradation of wheat straw cell walls.
Quantum Dots as Strain- and Metabolism-Specific Microbiological Labels
Authors: Kloepfer J. A. , Mielke R. E. , Wong M. S. , Nealson K. H. , Stucky G. , Nadeau J. L. 
Published: July 2003

ABSTRACT
Biologically conjugated quantum dots (QDs) have shown great promise as multiwavelength fluorescent labels for on-chip bioassays and eukaryotic cells. However, use of these photoluminescent nanocrystals in bacteria has not previously been reported, and their large size (3 to 10 nm) makes it unclear whether they inhibit bacterial recognition of attached molecules and whether they are able to pass through bacterial cell walls. Here we describe the use of conjugated CdSe QDs for strain- and metabolism-specific microbial labeling in a wide variety of bacteria and fungi, and our analysis was geared toward using receptors for a conjugated biomolecule that are present and active on the organism's surface. While cell surface molecules, such as glycoproteins, make excellent targets for conjugated QDs, internal labeling is inconsistent and leads to large spectral shifts compared with the original fluorescence, suggesting that there is breakup or dissolution of the QDs. Transmission electron microscopy of whole mounts and thin sections confirmed that bacteria are able to extract Cd and Se from QDs in a fashion dependent upon the QD surface conjugate.
Temperature-Regulated Bleaching and Lysis of the Coral
Pocillopora damicornis
by the Novel Pathogen
Vibrio coralliilyticus
Authors: Ben-Haim Yael , Zicherman-Keren Maya , Rosenberg Eugene 
Published: July 2003

ABSTRACT

Coral bleaching is the disruption of symbioses between coral animals and their photosynthetic microalgal endosymbionts (zooxanthellae). It has been suggested that large-scale bleaching episodes are linked to global warming. The data presented here demonstrate that
Vibrio coralliilyticus
is an etiological agent of bleaching of the coral
Pocillopora damicornis
. This bacterium was present at high levels in bleached
P. damicornis
but absent from healthy corals. The bacterium was isolated in pure culture, characterized microbiologically, and shown to cause bleaching when it was inoculated onto healthy corals at 25°C. The pathogen was reisolated from the diseased tissues of the infected corals. The zooxanthella concentration in the bacterium-bleached corals was less than 12% of the zooxanthella concentration in healthy corals. When
P. damicornis
was infected with
V. coralliilyticus
at higher temperatures (27 and 29°C), the corals lysed within 2 weeks, indicating that the seawater temperature is a critical environmental parameter in determining the outcome of infection. A large increase in the level of the extracellular protease activity of
V. coralliilyticus
occurred at the same temperature range (24 to 28°C) as the transition from bleaching to lysis of the corals. We suggest that bleaching of
P. damicornis
results from an attack on the algae, whereas bacterium-induced lysis and death are promoted by bacterial extracellular proteases. The data presented here support the bacterial hypothesis of coral bleaching.
In Situ Identification of Intracellular Bacteria Related to
Paenibacillus
spp. in the Mycelium of the Ectomycorrhizal Fungus
Laccaria bicolor
S238N
Authors: Bertaux J. , Schmid M. , Prevost-Boure N. Chemidlin , Churin J. L. , Hartmann A. , Garbaye J. , Frey-Klett P. 
Published: July 2003

ABSTRACT

Bacterial proliferations have recurrently been observed for the past 15 years in fermentor cultures of the ectomycorrhizal fungus
Laccaria bicolor
S238N, suggesting the presence of cryptic bacteria in the collection culture of this fungus. In this study, intracellular bacteria were detected by fluorescence in situ hybridization in combination with confocal laser scanning microscopy in several collection subcultures of
L. bicolor
S238N. They were small (0.5 μm in diameter), rare, and heterogeneously distributed in the mycelium and were identified as
Paenibacillus
spp. by using a 16S rRNA-directed oligonucleotide probe initially designed for bacteria isolated from a fermentor culture of
L. bicolor
S238N.
Development of Antibiotic-Overproducing Strains by Site-Directed Mutagenesis of the
rpsL
Gene in
Streptomyces lividans
Authors: Okamoto-Hosoya Yoshiko , Okamoto Susumu , Ochi Kozo 
Published: July 2003

ABSTRACT

Certain
rpsL
(which encodes the ribosomal protein S12) mutations that confer resistance to streptomycin markedly activate the production of antibiotics in
Streptomyces
spp. These
rpsL
mutations are known to be located in the two conserved regions within the S12 protein. To understand the roles of these two regions in the activation of silent genes, we used site-directed mutagenesis to generate eight novel mutations in addition to an already known (K88E) mutation that is capable of activating antibiotic production in
Streptomyces lividans
. Of these mutants, two (L90K and R94G) activated antibiotic production much more than the K88E mutant. Neither the L90K nor the R94G mutation conferred an increase in the level of resistance to streptomycin and paromomycin. Our results demonstrate the efficacy of the site-directed mutagenesis technique for strain improvement.
Visualization of an Endophytic
Streptomyces
Species in Wheat Seed
Authors: Coombs Justin T. , Franco Christopher M. M. 
Published: July 2003

ABSTRACT

Endophytic filamentous actinobacteria were isolated from surface-sterilized roots of wheat plants. Endophytic colonization of germinating wheat seed was examined using one of these endophytes,
Streptomyces
sp. strain EN27, tagged with the
egfp
gene. Endophytic colonization was observed from a very early stage of plant development with colonization of the embryo, endosperm, and emerging radicle.
Complement Resistance Is Essential for Colonization of the Digestive Tract of
Hirudo medicinalis
by
Aeromonas
Strains
Authors: Braschler Thomas R. , Merino Susana , Tomás Juan M. , Graf Joerg 
Published: July 2003

ABSTRACT

From the crop of the medicinal leech,
Hirudo medicinalis
, only
Aeromonas veronii
bv. sobria can be cultured consistently. Serum-sensitive
A. veronii
mutants were unable to colonize
H. medicinalis
, indicating the importance of the mammalian complement system for this unusual simplicity. Complementation of one selected mutant restored its ability to colonize. Serum-sensitive mutants are the first mutant class with a colonization defect for this symbiosis.
Rapid Staining and Enumeration of Small Numbers of Total Bacteria in Water by Solid-Phase Laser Cytometry
Authors: Broadaway Susan C. , Barton Stephanie A. , Pyle Barry H. 
Published: July 2003

ABSTRACT
The nucleic acid stain SYBR Green I was evaluated for use with solid-phase laser cytometry to obtain total bacterial cell counts from several water sources with small bacterial numbers. Results were obtained within 30 min and exceeded or equaled counts on R2A agar plates incubated for 14 days at room temperature.
Improved Adaptation to Cold-Shock, Stationary-Phase, and Freezing Stresses in
Lactobacillus plantarum
Overproducing Cold-Shock Proteins
Authors: Derzelle Sylviane , Hallet Bernard , Ferain Thierry , Delcour Jean , Hols Pascal 
Published: July 2003

ABSTRACT

We have investigated the effect of overproducing each of the three cold shock proteins (CspL, CspP, and CspC) in the mesophilic lactic acid bacterium
Lactobacillus plantarum
NC8. CspL overproduction transiently alleviated the reduction in growth rate triggered by exposing exponentially growing cells to cold shock (8°C), suggesting that CspL is involved in cold adaptation. The strain overproducing CspC resumed growth more rapidly when stationary-phase cultures were diluted into fresh medium, indicating a role in the adaptation and recovery of nutritionally deprived cells. Overproduction of CspP led to an enhanced capacity to survive freezing.
Identification and Tracing of
Bifidobacterium
Species by Use of Enterobacterial Repetitive Intergenic Consensus Sequences
Authors: Ventura Marco , Meylan Valerie , Zink Ralf 
Published: July 2003

ABSTRACT

Eighty-nine
Bifidobacterium
strains from 26 species were identified and classified to the species level with an enterobacterial repetitive intergenic consensus (ERIC)-PCR approach. We demonstrated that ERIC-PCR is useful for a phylogenetic and taxonomical analysis but as well as for a species composition analysis of mixed bifidobacterial cultures isolated from dairy products and other environments.
Use of Root Organ Cultures To Investigate the Interaction between
Glomus intraradices
and
Pratylenchus coffeae
Authors: Elsen Annemie , Declerck Stephane , De Waele Dirk 
Published: July 2003

ABSTRACT

The interaction between
Glomus intraradices
and
Pratylenchus coffeae
on transformed carrot roots was studied in root organ culture.
G. intraradices
provided the roots with increased protection against
P. coffeae
by suppressing nematode reproduction in the roots. The internal and external mycorrhizal development was not influenced by the presence of the nematodes.
Nontyphoidal Salmonellae in United Kingdom Badgers: Prevalence and Spatial Distribution
Authors: Wilson J. Sian , Hazel Sarah M. , Williams Nicola J. , Phiri Amos , French Nigel P. , Hart C. Anthony 
Published: July 2003

ABSTRACT

Eighteen (72%) of 25 badger social groups were found to excrete
Salmonella enterica
serovar Ried,
S. enterica
serovar Binza,
S. enterica
serovar Agama, or
S. enterica
serovar Lomita. Each serovar was susceptible to a panel of antimicrobials. Based on results of pulsed-field gel electrophoresis, the
S. enterica
serovar Agama and
S. enterica
serovar Binza isolates were very similar, but two clones each of
S. enterica
serovar Lomita and
S. enterica
serovar Ried were found. Badgers excreting
S. enterica
serovar Agama were spatially clustered.
Oligonucleotide Probes That Detect Quantitatively Significant Groups of Butyrate-Producing Bacteria in Human Feces
Authors: Hold Georgina L. , Schwiertz Andreas , Aminov Rustam I. , Blaut Michael , Flint Harry J. 
Published: July 2003

ABSTRACT16S rRNA-targeted oligonucleotide probes were designed for butyrate-producing bacteria from human feces. Three new cluster-specific probes detected bacteria related toRoseburia intestinalis,Faecalibacterium prausnitzii, andEubacterium halliiat mean populations of 2.3, 3.8, and 0.6%, respectively, in samples from 10 individuals. Additional species-level probes accounted for no more than 1%, with a mean of 7.7%, of the total human fecal microbiota identified as butyrate producers in this study. Bacteria related toE. halliiand the generaRoseburiaandFaecalibacteriumare therefore among the most abundant known butyrate-producing bacteria in human feces.
Inactivation of Vegetative Cells, but Not Spores, of
Bacillus anthracis
,
B. cereus
, and
B. subtilis
on Stainless Steel Surfaces Coated with an Antimicrobial Silver- and Zinc-Containing Zeolite Formulation
Authors: Galeano Belinda , Korff Emily , Nicholson Wayne L. 
Published: July 2003

ABSTRACT

Stainless steel surfaces coated with paints containing a silver- and zinc-containing zeolite (AgION antimicrobial) were assayed in comparison to uncoated stainless steel for antimicrobial activity against vegetative cells and spores of three
Bacillus
species, namely,
B. anthracis
Sterne,
B. cereus
T, and
B. subtilis
168. Under the test conditions (25°C and 80% relative humidity), the zeolite coating produced approximately 3 log
10
inactivation of vegetative cells within a 5- to 24-h period, but viability of spores of the three species was not significantly affected.
Sir Edward Mellanby, G.B.E., K.C.B., M.D., F.R.C.P., F.R.S. (1884-1955): The Man, Research Worker, and Statesman
Authors: Platt B. S. 
Published: July 2003

Sir Edward MelIanby had accepted a cordial invitation from the Editorial Committee of the Annual Review of Biochemistry to contribute this Prefatory Chapter. Unhappily, before he had completed his seventy-first year, he died suddenly on Sunday, January 30, 1955, about mid-day, after he had spent the morning at his research. His draft of the introduction to his contribution to this volume is printed below in the section“ to British Biochemistry.” For nearly six years after retiring from the post of Secretary of the Medical Research Council, he continued to engage in research work and in many scientific affairs. He was, for example, active in the Royal Society, of which he had been a Fellow for 30 years, and he was one of its Vice-Presidents. Sir Henry Dale has recently completed an Obituary Notice of Mellanby for the Royal Society (1955); this tribute is of such grandeur as perhaps only a man of Sir Henry's eminence could contribute, and I shall quote from this to give the weight of wisdom, experience, and knowledge to this chapter.
HOW TO GET PAID FOR HAVING FUN
Authors: Koshland Daniel E. 
Published: July 2003

When writing a prefatory chapter for Annual Reviews a scientist is confronted with the question of what in his or her life might be interesting to others. In my case I was appalled at the absence of material that generates good novels: no broken homes, no misunderstood childhood, no criminal youth gangs, no disastrous liaisons. A landscape of boredom from sea to shining sea. If there is one overlying theme it is that I got paid for doing what I enjoyed all my life. I wish I could say I had cleverly plotted to achieve this nirvana by a series of Machiavellian measures. The truth, however, is closer to the course of the Lord High Executioner in the Mikado: I was “...wafted by a favoring gale as one sometimes is in trances.” As I look back, each new chapter in my life seems to have been a mutation of Pasteur’s phrase “chance to the prepared mind.” Once I had decided to be a scientist, the events seemed to flow as if by accident. However, in retrospect I see that the experience of each phase of my life presaged the next “accidental happening.” But I was surprised at the “random walk” nature of my life.
Asia-Wide Emissions of Greenhouse Gases
Authors: Siddiqi Toufiq A. 
Published: July 2003

Emissions of principal greenhouse gases (GHGs) from Asia are increasing faster than those from any other continent. This is a result of rapid economic growth, as well as the fact that almost half of the world's population lives in Asian countries. In this paper, we provide estimates of emissions of the two principal greenhouse gases, carbon dioxide (C02) and methane (CH4), from individual countries and areas. Recent literature has been reviewed for emission estimates for individual sources, such as carbon dioxide from cement manufacture, and methane from rice fields. There are very large uncertainties in many of these estimates, so several estimates are provided, where available. The largest anthropogenic source of CO2 emissions is the use of fossil fuels. Energy consumption data from 1992 have been used to calculate estimated emissions of CO2 from this source. In view of the ongoing negotiations to limit future greenhouse gas emissions, estimates of projected CO2 emissions from the developing countries of Asia are also provided. These are likely to be 3 times their 1986 levels by 2010, under “business as usual” scenarios. Even with the implementation of energy efficiency measures and fuel switching where feasible, the emissions of CO2 are likely to double within the same time period.
Semiochemical Parsimony in the Arthropoda
Authors: Blum Murray S. 
Published: July 2003

A wide variety of arthropods have adapted their own semiochemicals to subserve multiple functions in diverse contexts. Semiochemicals, the pheromones and allomones, have been detected in arthropod species in six orders, and it has been clearly established that these compounds are used with great parsimony. The versatility of these invertebrates in using these natural products for an incredible diversity of functions emphasizes the significance of semiochemicals in the evolutionary biology of the Arthropoda. Multifunctional pheromones have proved to be especially characteristic of the queens of eusocial species. Compounds such as the queen substance of the honey bee, Apis mellifera, possess unrelated primer and releaser functions for the workers and act as a sex attractant for drones. Females of other hymenopterous species exploit the secretions of sting-associated glands as sex pheromones, whereas a variety of nonhymenopterous species have adapted components in diverse defensive secretions to function as sex pheromones. The alarm pheromones of many arthropods are also used as defensive allomones, activity inhibitors, cryptic alarm pheromones, aggregative attractants, robbing agents, digging agents, trail pheromones, and antimicrobial agents. Defensive allomones also possess some of these parsimonious roles; in addition, however, some of these compounds possess highly distinctive roles, such as functioning as lethal attractants for prey or, in the aquatic milieu, cuticular wetting agents. Clearly, the availability of a variety of pheromones and allomones has enabled arthropods to evolve an elegant semiochemical parsimony with which to exploit the biological milieu.
Etiology of Type I Diabetes Mellitus: Heterogeneity and Immunological Events Leading to Clinical Onset
Authors: Doniach D. , Bottazzo G. F. , Path M. R. C. , Cudworth A. G. 
Published: July 2003

Type I diabetes is a heterogeneous disorder and the causes of pancreatic beta-cell destruction are unknown. In 1-2% of all cases, viruses (e.g. coxsackie, rubella, mumps, or beta-cell poisons) have been implicated. Twin studies suggest at most 50% of genetic predisposition. In this review we describe the autoimmune components which, in association with inheritance of HLA-haplotypes in susceptible families, allow the future selection of predisposed sibs for possible preventive therapy to retard loss of insulin secretion. The known association of the endocrine autoimmune organ-specific disorders in 10% of Type I diabetics is the extreme expression of the other main genetic ingredient in the development of insulitis in this disease, irrespective of the triggering environmental components. In this “polyendocrine” subgroup and in the “juvenile-onset” cases there is a prolonged latency period during which pancreatic autoimmunity markers are present before clinical expression of the disease.