bluuebunny/crossref_metadata_2025_split huggingface dataset:
Discrete ultrahigh‐pressure domains in the Western Gneiss Region, Norway: implications for formation and exhumation
Authors: ROOT D. B. , HACKER B. R. , GANS P. B. , DUCEA M. N. , EIDE E. A. , MOSENFELDER J. L. 
Published: February 2005

AbstractNew eclogite localities and new 40Ar/39Ar ages within the Western Gneiss Region of Norway define three discrete ultrahigh‐pressure (UHP) domains that are separated by distinctly lower pressure, eclogite facies rocks. The sizes of the UHP domains range from c. 2500 to 100 km2; if the UHP culminations are part of a continuous sheet at depth, the Western Gneiss Region UHP terrane has minimum dimensions of c. 165 × 50 × 5 km. 40Ar/39Ar mica and K‐feldspar ages show that this outcrop pattern is the result of gentle regional‐scale folding younger than 380 Ma, and possibly 335 Ma. The UHP and intervening high‐pressure (HP) domains are composed of eclogite‐bearing orthogneiss basement overlain by eclogite‐bearing allochthons. The allochthons are dominated by garnet amphibolite and pelitic schist with minor quartzite, carbonate, calc‐silicate, peridotite, and eclogite. Sm/Nd core and rim ages of 992 and 894 Ma from a 15‐cm garnet indicate local preservation of Precambrian metamorphism within the allochthons. Metapelites within the allochthons indicate near‐isothermal decompression following (U)HP metamorphism: they record upper amphibolite facies recrystallization at 12–17 kbar and c. 750 °C during exhumation from mantle depths, followed by a low‐pressure sillimanite + cordierite overprint at c. 5 kbar and c. 750 °C. New 40Ar/39Ar hornblende ages of 402 Ma document that this decompression from eclogite‐facies conditions at 410–405 Ma to mid‐crustal depths occurred in a few million years. The short timescale and consistently high temperatures imply adiabatic exhumation of a UHP body with minimum dimensions of 20–30 km. 40Ar/39Ar muscovite ages of 397–380 Ma show that this extreme heat advection was followed by rapid cooling (c. 30 °C Myr−1), perhaps because of continued tectonic unroofing.
Thrombotic microangiopathy after combined autografting–allografting for multiple myeloma – report of three cases
Authors: Kornacker M. , Luft T. , Ho A. D. , Schaefer H.‐J. 
Published: February 2005

Abstract:Thrombotic microangiopathy (TMA) has been described as a complication of bone marrow or stem cell transplantation. It is usually associated with high dose therapy for autologous transplantation or myeloablative conditioning in the allogeneic setting. Here we report three cases of TMA after reduced intensity conditioning and allogeneic peripheral blood stem cell transplantation. All three patients had high dose Melphalan therapy with autologous stem cell support preceding the allogeneic transplantation for several weeks, which may have contributed to endothelial damage and subsequent development of TMA.
Beringian Paleoecology Inferred from Permafrost-Preserved Fungal DNA
Authors: Lydolph Magnus C. , Jacobsen Jonas , Arctander Peter , Gilbert M. Thomas P. , Gilichinsky David A. , Hansen Anders J. , Willerslev Eske , Lange Lene 
Published: February 2005

ABSTRACT
The diversity of fungi in permanently frozen soil from northeastern Siberia was studied by culture-independent PCR amplification of diverse environmental 18S rRNA genes. Elaborate protocols to avoid contamination during drilling, sampling, and amplification were used. A broad diversity of eukaryotic DNA sequences that were 510 bp long, including sequences of various fungi, plants, and invertebrates, could be obtained reproducibly from samples that were up to 300,000 to 400,000 years old. The sequences revealed that ancient fungal communities included a diversity of cold-adapted yeasts, dark-pigmented fungi, plant-parasitic fungi, and lichen mycobionts. DNA traces of tree-associated macrofungi in a modern tundra sample indicated that there was a shift in fungal diversity following the last ice age and supported recent results showing that there was a severe change in the plant composition in northeastern Siberia during this period. Interestingly, DNA sequences with high homology to sequences of coprophilic and keratinophilic fungi indicated that feces, hair, skin, and nails could have been sources of ancient megafauna DNA recently reported to be present in small amounts of Siberian permafrost sediments.
Utilization of Fluorescent Microspheres and a Green Fluorescent Protein-Marked Strain for Assessment of Microbiological Contamination of Permafrost and Ground Ice Core Samples from the Canadian High Arctic
Authors: Juck D. F. , Whissell G. , Steven B. , Pollard W. , McKay C. P. , Greer C. W. , Whyte L. G. 
Published: February 2005

ABSTRACT

Fluorescent microspheres were applied in a novel fashion during subsurface drilling of permafrost and ground ice in the Canadian High Arctic to monitor the exogenous microbiological contamination of core samples obtained during the drilling process. Prior to each drill run, a concentrated fluorescent microsphere (0.5-μm diameter) solution was applied to the interior surfaces of the drill bit, core catcher, and core tube and allowed to dry. Macroscopic examination in the field demonstrated reliable transfer of the microspheres to core samples, while detailed microscopic examination revealed penetration levels of less than 1 cm from the core exterior. To monitor for microbial contamination during downstream processing of the permafrost and ground ice cores, a
Pseudomonas
strain expressing the green fluorescent protein (GFP) was painted on the core exterior prior to processing. Contamination of the processed core interiors with the GFP-expressing strain was not detected by culturing the samples or by PCR to detect the
gfp
marker gene. These methodologies were quick, were easy to apply, and should help to monitor the exogenous microbiological contamination of pristine permafrost and ground ice samples for downstream culture-dependent and culture-independent microbial analyses.
Nine-Year Study of the Occurrence of Culturable Viruses in Source Water for Two Drinking Water Treatment Plants and the Influent and Effluent of a Wastewater Treatment Plant in Milwaukee, Wisconsin (August 1994 through July 2003)
Authors: Sedmak Gerald , Bina David , MacDonald Jeffrey , Couillard Lon 
Published: February 2005

ABSTRACT
Reoviruses, enteroviruses, and adenoviruses were quantified by culture for various ambient waters in the Milwaukee area. From August 1994 through July 2003, the influent and effluent of a local wastewater treatment plant (WWTP) were tested monthly by a modified U.S. Environmental Protection Agency Information Collection Rule (ICR) organic flocculation cell culture procedure for the detection of culturable viruses. Modification of the ICR procedure included using Caco-2, RD, and HEp-2 cells in addition to BGM cells. Lake Michigan source water for two local drinking water treatment plants (DWTPs) was also tested monthly for culturable viruses by passing 200 liters of source water through a filter and culturing a concentrate representing 100 liters of source water. Reoviruses, enteroviruses, and adenoviruses were detected frequently (105 of 107 samples) and, at times, in high concentration in WWTP influent but were detected less frequently (32 of 107 samples) in plant effluent and at much lower concentrations. Eighteen of 204 samples (8.8%) of source waters for the two DWTPs were positive for virus and exclusively positive for reoviruses at relatively low titers. Both enteroviruses and reoviruses were detected in WWTP influent, most frequently during the second half of the year.
Isolation and Characterization of Temperate Bacteriophages of
Clostridium difficile
Authors: Goh Shan , Riley Thomas V. , Chang Barbara J. 
Published: February 2005

ABSTRACT

The lack of information on bacteriophages of
Clostridium difficile
prompted this study. Three of 56 clinical
C. difficile
isolates yielded double-stranded DNA phages φC2, φC5, φC6, and φC8 upon induction. Superinfection and DNA analyses revealed relatedness between the phages, while partial sequencing of φC2 showed nucleotide homology to the sequenced
C. difficile
strain CD630.
Surface Plasmon Resonance Imaging-Based Protein Array Chip System for Monitoring a Hexahistidine-Tagged Protein during Expression and Purification
Authors: Ro Hyeon-Su , Jung Sun Ok , Kho Byung Hoon , Hong Hyung Pyo , Lee Jae Sung , Shin Yong-Beom , Kim Min Gon , Chung Bong Hyun 
Published: February 2005

ABSTRACT

A surface plasmon resonance imaging-based Ni
2+
-iminodiacetic acid-coated gold chip system was developed to enable specific detection of a hexahistidine-tagged recombinant protein in crude extracts or in column chromatography fractions. This system is especially advantageous for high-throughput analysis of multiple proteins.
Genetic Diversity ofCylindrospermopsisStrains (Cyanobacteria) Isolated from Four Continents
Authors: Gugger Muriel , Molica Renato , Le Berre Brigitte , Dufour Philippe , Bernard Cécile , Humbert Jean-François 
Published: February 2005

ABSTRACTThe genetic diversity ofCylindrospermopsisstrains (cyanobacteria) was examined using mainly the 16S-23S internally transcribed spacer (ITS1) sequences. Strains were grouped in three clusters: (i) America, (ii) Europe, and (iii) Africa and Australia. These results suggested a recent spread ofCylindrospermopsisacross the American and European continents from restricted warm refuge areas instead of exchanges between continents. On the other hand, they also suggested a recent colonization of Australia by African strains.
High-Level Acetaldehyde Production in
Lactococcus lactis
by Metabolic Engineering
Authors: Bongers Roger S. , Hoefnagel Marcel H. N. , Kleerebezem Michiel 
Published: February 2005

ABSTRACT

Efficient conversion of glucose to acetaldehyde is achieved by nisin-controlled overexpression of
Zymomonas mobilis
pyruvate decarboxylase (
pdc
) and
Lactococcus lactis
NADH oxidase (
nox
) in
L. lactis
. In resting cells, almost 50% of the glucose consumed could be redirected towards acetaldehyde by combined overexpression of
pdc
and
nox
under anaerobic conditions.
Efficacy of Removal of Sucrose-Supplemented Interproximal Plaque by Electric Toothbrushes in an In Vitro Model
Authors: Hope C. K. , Petrie A. , Wilson M. 
Published: February 2005

ABSTRACT
Electric toothbrushes were evaluated using a model of plaque removal by fluid shear forces. Sucrose supplementation during plaque development did not affect the removal of bacteria from biofilm exposed to low-energy shear but did increase their resistance to high-energy shear. The toothbrush supplying high-energy shear forces removed significantly more viable bacteria.
Rapid and Simple Quantification of Bacterial Cells by Using a Microfluidic Device
Authors: Sakamoto Chieko , Yamaguchi Nobuyasu , Nasu Masao 
Published: February 2005

ABSTRACT
This study investigated a microfluidic chip-based system (on-chip flow cytometry) for quantification of bacteria both in culture and in environmental samples. Bacterial numbers determined by this technique were similar to those obtained by direct microscopic count. The time required for this on-chip flow cytometry was only 30 min per 6 samples.
Variation in 16S-23S rRNA Intergenic Spacer Regions in
Photobacterium damselae
: a Mosaic-Like Structure
Authors: Osorio Carlos R. , Collins Matthew D. , Romalde Jesús L. , Toranzo Alicia E. 
Published: February 2005

ABSTRACT

Phenotypically,
Photobacterium damselae
subsp.
piscicida
and
P. damselae
subsp.
damselae
are easily distinguished. However, their 16S rRNA gene sequences are identical, and attempts to discriminate these two subspecies by molecular tools are hampered by their high level of DNA-DNA similarity. The 16S-23S rRNA internal transcribed spacers (ITS) were sequenced in two strains of
Photobacterium damselae
subsp.
piscicida
and two strains of
P. damselae
subsp.
damselae
to determine the level of molecular diversity in this DNA region. A total of 17 different ITS variants, ranging from 803 to 296 bp were found, some of which were subspecies or strain specific. The largest ITS contained four tRNA genes (tDNAs) coding for tRNA
Glu(UUC)
, tRNA
Lys(UUU)
, tRNA
Val(UAC)
, and tRNA
Ala(GGC)
. Five amplicons contained tRNA
Glu(UUC)
combined with two additional tRNA genes, including tRNA
Lys(UUU)
, tRNA
Val(UAC)
, or tRNA
Ala(UGC)
. Five amplicons contained tRNA
Ile(GAU)
and tRNA
Ala(UGC)
. Two amplicons contained tRNA
Glu(UUC)
and tRNA
Ala(UGC)
. Two different isoacceptor tRNA
Ala
genes (GGC and UGC anticodons) were found. The five smallest amplicons contained no tRNA genes. The tRNA-gene combinations tRNA
Glu(UUC)
-tRNA
Val(UAC)
-tRNA
Ala(UGC)
and tRNA
Glu(UUC)
-tRNA
Ala(UGC)
have not been previously reported in bacterial ITS regions. The number of copies of the ribosomal operon (
rrn
) in the
P. damselae
chromosome ranged from at least 9 to 12. For ITS variants coexisting in two strains of different subspecies or in strains of the same subspecies, nucleotide substitution percentages ranged from 0 to 2%. The main source of variation between ITS variants was due to different combinations of DNA sequence blocks, constituting a mosaic-like structure.
Isotope Labeling and Microautoradiography of Active Heterotrophic Bacteria on the Basis of Assimilation of
14
CO
2
Authors: Hesselsoe Martin , Nielsen Jeppe Lund , Roslev Peter , Nielsen Per Halkjær 
Published: February 2005

ABSTRACT

Most heterotrophic bacteria assimilate CO
2
in various carboxylation reactions during biosynthesis. In this study, assimilation of
14
CO
2
by heterotrophic bacteria was used for isotope labeling of active microorganisms in pure cultures and environmental samples. Labeled cells were visualized by microautoradiography (MAR) combined with fluorescence in situ hybridization (FISH) to obtain simultaneous information about activity and identity. Cultures of
Escherichia coli
and
Pseudomonas putida
assimilated sufficient
14
CO
2
during growth on various organic substrates to obtain positive MAR signals. The MAR signals were comparable with the traditional MAR approach based on uptake of
14
C-labeled organic substrates. Experiments with
E. coli
showed that
14
CO
2
was assimilated during both fermentation and aerobic and anaerobic respiration. The new MAR approach, HetCO
2
-MAR, was evaluated by targeting metabolic active filamentous bacteria, including “
Candidatus
Microthrix parvicella” in activated sludge. “
Ca.
Microthrix parvicella” was able to take up oleic acid under anaerobic conditions, as shown by the traditional MAR approach with [
14
C]oleic acid. However, the new HetCO
2
-MAR approach indicated that “
Ca.
Microthrix parvicella,” did not significantly grow on oleic acid under anaerobic conditions with or without addition of NO
2
−
, whereas the addition of O
2
or NO
3
−
initiated growth, as indicated by detectable
14
CO
2
assimilation. This is a metabolic feature that has not been described previously for filamentous bacteria. Such information could not have been derived by using the traditional MAR procedure, whereas the new HetCO
2
-MAR approach differentiates better between substrate uptake and substrate metabolism that result in growth. The HetCO
2
-MAR results were supported by stable isotope analysis of
13
C-labeled phospholipid fatty acids from activated sludge incubated under aerobic and anaerobic conditions in the presence of
13
CO
2
. In conclusion, the novel HetCO
2
-MAR approach expands the possibility for studies of the ecophysiology of uncultivated microorganisms.
Metabolically Independent and Accurately AdjustableAspergillussp. Expression System
Authors: Pachlinger Robert , Mitterbauer Rudolf , Adam Gerhard , Strauss Joseph 
Published: February 2005

ABSTRACTFilamentous fungi are well-established expression hosts often used to produce extracellular proteins of use in the food and pharmaceutical industries. The expression systems presently used inAspergillusspecies rely on either strong constitutive promoters, e.g., that for glyceraldehyde-3-phosphate dehydrogenase, or inducible systems derived from metabolic pathways, e.g.,glaA(glucoamylase) oralc(alcohol dehydrogenase). We describe forAspergillus nidulansandAspergillus nigera novel expression system that utilizes the transcriptional activation of the human estrogen receptor by estrogenic substances. The system functions independently from metabolic signals and therefore can be used with low-cost, complex media. A combination of positive and negative regulatory elements in the promoter drives the expression of a reporter gene, yielding a linear dose response to the inducer. The off status is completely tight, yet the system responds within minutes to induction and reaches a level of expression of up to 15% of total cell protein after 8 h. BothAspergillusspecies are very sensitive to estrogenic substances, and low-cost inducers function in the picomolar concentration range, at which estrogenic substances also can be found in the environment. Given this high sensitivity to estrogens,Aspergilluscells carrying estrogen-responsive units could be used to detect xenoestrogens in food or in the environment.
Regulation of Resistance to Copper in
Xanthomonas axonopodis
pv. vesicatoria
Authors: Voloudakis Andreas E. , Reignier Therese M. , Cooksey Donald A. 
Published: February 2005

ABSTRACT

Copper-resistant strains of
Xanthomonas axonopodis
pv. vesicatoria were previously shown to carry plasmid-borne copper resistance genes related to the
cop
and
pco
operons of
Pseudomonas syringae
and
Escherichia coli
, respectively. However, instead of the two-component (
copRS
and
pcoRS
) systems determining copper-inducible expression of the operons in
P. syringae
and
E. coli
, a novel open reading frame,
copL
, was found to be required for copper-inducible expression of the downstream multicopper oxidase
copA
in
X. axonopodis. copL
encodes a predicted protein product of 122 amino acids that is rich in histidine and cysteine residues, suggesting a possible direct interaction with copper. Deletions or frameshift mutations within
copL
, as well as an amino acid substitution generated at the putative start codon of
copL
, caused a loss of copper-inducible transcriptional activation of
copA
. A nonpolar insertion of a kanamycin resistance gene in
copL
resulted in copper sensitivity in the wild-type strain. However, repeated attempts to complement
copL
mutations in
trans
failed. Analysis of the genomic sequence databases shows that there are
copL
homologs upstream of
copAB
genes in
X. axonopodis
pv. citri,
X. campestris
pv. campestris, and
Xylella fastidiosa
. The cloned promoter area upstream of
cop
A in
X. axonopodis
pv. vesicatoria did not function in
Pseudomonas syringae
or in
E. coli
, nor did the
P. syringae cop
promoter function in
Xanthomonas
. However, a transcriptional fusion of the
Xanthomonas cop
promoter with the
Pseudomonas copABCDRS
was able to confer resistance to copper in
Xanthomonas
, showing divergence in the mechanisms of regulation of the resistance to copper in phytopathogenic bacteria.
Thio Wax Ester Biosynthesis Utilizing the Unspecific Bifunctional Wax Ester Synthase/Acyl Coenzyme A:Diacylglycerol Acyltransferase of
Acinetobacter
sp. Strain ADP1
Authors: Uthoff Stefan , Stöveken Tim , Weber Nikolaus , Vosmann Klaus , Klein Erika , Kalscheuer Rainer , Steinbüchel Alexander 
Published: February 2005

ABSTRACT

The bifunctional wax ester synthase/acyl coenzyme A (acyl-CoA):diacylglycerol acyltransferase (WS/DGAT) from
Acinetobacter
sp. strain ADP1 (formerly
Acinetobacter calcoaceticus
ADP1) mediating the biosyntheses of wax esters and triacylglycerols was used for the in vivo and in vitro biosynthesis of thio wax esters and dithio wax esters. For in vitro biosynthesis, 5′His
6
WS/DGAT comprising an N-terminal His
6
tag was purified from the soluble protein fraction of
Escherichia coli
Rosetta(DE3)pLysS (pET23a::

5′His
6

atf
). By employing SP-Sepharose high-pressure and Ni-nitrilotriacetic acid fast-protein liquid chromatographies, a 19-fold enrichment with a final specific activity of 165.2 nmol mg of protein
−1
min
−1
was achieved by using 1-hexadecanol and palmitoyl-CoA as substrates. Incubation of purified 5′His
6
WS/DGAT with 1-hexadecanethiol and palmitoyl-CoA as substrates resulted in the formation of palmitic acid hexadecyl thio ester (10.4% relative specific activity of a 1-hexadecanol control). Utilization of 1,8-octanedithiol and palmitoyl-CoA as substrates led to the formation of 1-
S
-monopalmitoyloctanedithiol and minor amounts of 1,8-
S
-dipalmitoyloctanedithiol (59.3% relative specific activity of a 1-hexadecanol control). The latter dithio wax ester was efficiently produced when 1-
S
-monopalmitoyloctanedithiol and palmitoyl-CoA were used as substrates (13.4% specific activity relative to that of a 1-hexadecanol control). For the in vivo biosynthesis of thio wax esters, the knockout mutant
Acinetobacter
sp. strain ADP1
acr1
ΩKm, which is unable to produce fatty alcohols, was used. Cultivation of
Acinetobacter
sp. strain ADP1
acr1
ΩKm in the presence of gluconate, 1-hexadecanethiol, and oleic acid in nitrogen-limited mineral salts medium resulted in the accumulation of unusual thio wax esters that accounted for around 1.19% (wt/wt) of the cellular dry weight and consisted mainly of oleic acid hexadecyl thioester as revealed by gas chromatography-mass spectrometry.
Effects of Growth Medium, Inoculum Size, and Incubation Time on Culturability and Isolation of Soil Bacteria
Authors: Davis Kathryn E. R. , Joseph Shayne J. , Janssen Peter H. 
Published: February 2005

ABSTRACT

Soils are inhabited by many bacteria from phylogenetic groups that are poorly studied because representatives are rarely isolated in cultivation studies. Part of the reason for the failure to cultivate these bacteria is the low frequency with which bacterial cells in soil form visible colonies when inoculated onto standard microbiological media, resulting in low viable counts. We investigated the effects of three factors on viable counts, assessed as numbers of CFU on solid media, and on the phylogenetic groups to which the isolated colony-forming bacteria belong. These factors were inoculum size, growth medium, and incubation time. Decreasing the inoculum size resulted in significant increases in the viable count but did not appear to affect colony formation by members of rarely isolated groups. Some media that are traditionally used for soil microbiological studies returned low viable counts and did not result in the isolation of members of rarely isolated groups. Newly developed media, in contrast, resulted in high viable counts and in the isolation of many members of rarely isolated groups, regardless of the inoculum size. Increased incubation times of up to 3 months allowed the development of visible colonies of members of rarely isolated groups in conjunction with the use of appropriate media. Once isolated, pure cultures of members of rarely isolated groups took longer to form visible colonies than did members of commonly isolated groups. Using these new media and extended incubation times, we were able to isolate many members of the phyla
Acidobacteria
(subdivisions 1, 2, 3, and 4),
Gemmatimonadetes
,
Chloroflexi
, and
Planctomycetes
(including representatives of the previously uncultured WPS-1 lineage) as well as members of the subclasses
Rubrobacteridae
and
Acidimicrobidae
of the phylum
Actinobacteria
.