bluuebunny/crossref_metadata_2025_split huggingface dataset:
Type‐Curve Interpretation of Multirate Single‐Hole Pneumatic Injection Tests in Unsaturated Fractured Rock
Authors: Illman Walter A. , Neuman Shlomo P. 
Published: August 2005

AbstractMore than 270 multirate single‐hole pneumatic injection tests were conducted by Guzman et al. (1996) within six shallow vertical and inclined boreholes in unsaturated fractured tuff at the Apache Leap Research Site (ALRS) near Superor, Arizona. The authors used steady‐state formulae to obtain air permeability values for the rock based solely on late pressure data from each test. We developed pressure and pressure‐derivative type‐curves for the interpretation of transient data from these tests, which account for storage in the test interval due to air compressibility and skin effect due to damage to the surrounding rock. We applied our type‐curves to pressure data from more than 40 of the tests to obtain information about air permeability, skin factor, phenomenology, and dimensionality of the flow regime on a nominal scale of 1 m in the immediate vicinity of each test interval. Our air permeabilities agreed well with those determined previously by means of steady‐ state formulae but correlated poorly with fracture density data. Nonlinear effects due to air compressibility were pronounced, but skin effect was generally small or nonexistent. Nonlinear two‐phase flow and inertia were evident but did not have a significant impact on type‐curve interpretation of the test data. Most of these data fit a continuum model of spherical airflow around the test interval, but a few fit a continuum model of radial flow or suggest the dominance of a single fracture. We take this to imply that fractures at the site are pneumatically well connected and can, for the most part, be treated as a porous continuum when analyzing airflow on scales of 1 m or more. This is supported by the finding that 1 m scale air permeability data from single‐hole tests at the ALRS are amenable to geostatistical analysis (Chen et al. 2000), which views them as a sample from a random field defined over a continuum. That the same holds true on larger scale is indicated by our ability to interpret cross‐hole pneumatic injection tests at the site by means of type‐curves and inverse methods (Illman et al. 1998), which treat the entire rock mass as a porous continuum.
Metabolism of the Aliphatic Nitramine 4-Nitro-2,4-Diazabutanal by
Methylobacterium
sp. Strain JS178
Authors: Fournier Diane , Trott Sandra , Hawari Jalal , Spain Jim 
Published: August 2005

ABSTRACT

The aliphatic nitramine 4-nitro-2,4-diazabutanal (NDAB; C
2
H
5
N
3
O
3
) is a ring cleavage metabolite that accumulates during the aerobic degradation of the energetic compound hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) by various
Rhodococcus
spp. NDAB is also produced during the alkaline hydrolysis of either RDX or octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) and during the photolysis of RDX. Traces of NDAB were observed in a soil sampled from an ammunition-manufacturing facility contaminated with both HMX and RDX, suggesting natural attenuation. In this study, we report the isolation of a soil bacterium that is able to degrade NDAB under aerobic conditions. The isolate is a pink-pigmented facultative methylotroph affiliated with the genus
Methylobacterium
. The strain, named
Methylobacterium
sp. strain JS178, degrades NDAB as a sole nitrogen source, with concomitant growth and formation of 1 molar equivalent of nitrous oxide (N
2
O). Comparison of the growth yield of strain JS178 grown on NDAB, nitrite (NO
2
−
), or ammonium (NH
4
+
) as a nitrogen source revealed that 1 N equivalent is assimilated from each mole of NDAB, which completes the nitrogen mass balance. In radiotracer experiments, strain JS178 mineralized 1 C of the [
14
C]NDAB produced in situ from [
14
C]RDX by
Rhodococcus
sp. strain DN22. Studies on the regulation of NDAB degradation indicated that allantoin, an intermediate in the purine catabolic pathway and a central molecule in the storage and transport of nitrogen in plants, up-regulated the enzyme(s) involved in the degradation of the nitramine. The results reveal the potential for the sequential participation of rhodococci and methylobacteria to effect the complete degradation of RDX.
Impact of Plant Species and Site on Rhizosphere-Associated Fungi Antagonistic to
Verticillium dahliae
Kleb
Authors: Berg Gabriele , Zachow Christin , Lottmann Jana , Götz Monika , Costa Rodrigo , Smalla Kornelia 
Published: August 2005

ABSTRACT

Fungi with antagonistic activity toward plant pathogens play an essential role in plant growth and health. To analyze the effects of the plant species and the site on the abundance and composition of fungi with antagonistic activity toward
Verticillium dahliae
, fungi were isolated from oilseed rape and strawberry rhizosphere and bulk soil from three different locations in Germany over two growing seasons. A total of 4,320 microfungi screened for in vitro antagonism toward
Verticillium
resulted in 911 active isolates. This high proportion of fungi antagonistic toward the pathogen
V. dahliae
was found for bulk and rhizosphere soil at all sites. A plant- and site-dependent specificity of the composition of antagonistic morphotypes and their genotypic diversity was found. The strawberry rhizosphere was characterized by preferential occurrence of
Penicillium
and
Paecilomyces
isolates and low numbers of morphotypes (
n
= 31) and species (
n
= 13), while
Monographella
isolates were most frequently obtained from the rhizosphere of oilseed rape, for which higher numbers of morphotypes (n = 41) and species (n = 17) were found.
Trichoderma
strains displayed high diversity in all soils, but a high degree of plant specificity was shown by BOX-PCR fingerprints. The diversity of rhizosphere-associated antagonists was lower than that of antagonists in bulk soil, suggesting that some fungi were specifically enriched in each rhizosphere. A broad spectrum of new
Verticillium
antagonists was identified, and the implications of the data for biocontrol applications are discussed.
Functional Importance of Deletion Mutant Genotypes in an Insect Nucleopolyhedrovirus Population
Authors: Simón Oihane , Williams Trevor , López-Ferber Miguel , Caballero Primitivo 
Published: August 2005

ABSTRACT

A Nicaraguan isolate of a nucleopolyhedrovirus (SfNIC) that attacks the fall armyworm,
Spodoptera frugiperda
, survives as a mixture of nine genotypes (SfNIC A to I) that all present genomic deletions, except variant B (complete genotype). Sequencing of cloned restriction fragments revealed that genotypic variants lack between 5 and 16 of the open reading frames present in a contiguous sequence of 18 kb of the SfNIC genome. The absence of oral infectivity of SfNIC-C and -D variants is related to the deletion of the
pif
and/or
pif-2
gene, while that of SfNIC-G remains unexplained. The presence of open reading frame 10, homolog of Se030, also appeared to influence pathogenicity in certain variants. Previous studies demonstrated a significant positive interaction between genotypes B and C. We compared the median lethal concentration of single genotypes (A, B, C, D, and F) and co-occluded genotype mixtures (B+A, B+D, B+F, A+C, and F+C in a 3:1 ratio). Mixtures B+A and B+D showed increased pathogenicity, although only B+D restored the activity of the mixture to that of the natural population. Mixtures of two deletion variants (A+C and F+C) did not show interactions in pathogenicity. We conclude that minority genotypes have an important influence on the overall pathogenicity of the population. These results clearly demonstrate the value of retaining genotypic diversity in virus-based bioinsecticides.
Simultaneous Display of Multiple Foreign Peptides in the FliD Capping and FliC Filament Proteins of the
Escherichia coli
Flagellum
Authors: Majander Katariina , Korhonen Timo K. , Westerlund-Wikström Benita 
Published: August 2005

ABSTRACT

The bacterial flagellum is composed of more than 20 different proteins. The filament, which constitutes the major extracellular part of the flagellum, is built up of approximately 20,000 FliC molecules that assemble at the growing distal end of the filament. A capping structure composed of five FliD molecules located at the tip of the filament promotes polymerization of FliC. Lack of FliD leads to release of the subunits into the growth medium. We show here that FliD can be successfully used in bacterial surface display. We tested various insertion sites in the capping protein, and the optimal region for display was at the variable region in FliD. Deletion and/or insertion at other sites resulted in decreased formation of flagella. We further developed the technique into a multihybrid display system in which three foreign peptides are simultaneously expressed within the same flagellum, i.e., D repeats of FnBPA from
Staphylococcus aureus
at the tip and fragments of YadA from
Yersinia enterocolitica
as well as SlpA from
Lactobacillus crispatus
along the filament. This technology can have biotechnological applications, e.g., in simultaneous delivery of several effector molecules.
Correlation of Biological Activity and Reactor Performance in Biofiltration of Toluene with the Fungus
Paecilomyces variotii
CBS115145
Authors: García-Peña Inés , Hernández Sergio , Auria Richard , Revah Sergio 
Published: August 2005

ABSTRACT

A biofiltration system inoculated with the mold
Paecilomyces variotii
CBS115145 showed a toluene elimination capacity (EC) of around 250 g/m
3
of biofilter/h, which was higher than the values usually reported for bacteria.
P. variotii
assimilated
m
- and
p
-cresols but not the
o
isomer. Initial toluene hydroxylation occurred both on the methyl group and through the
p
-cresol pathway. These results were corroborated by detecting benzyl alcohol, benzaldehyde, and
p
-cresol as volatile intermediates. In liquid cultures with toluene as a substrate, the activity of toluene oxygenase (TO) was 5.6 nmol of O
2
/min/mg of biomass, and that of benzyl alcohol dehydrogenase was 16.2 nmol of NADH/min/mg of protein. Toluene biodegradation determined from the TO activity in the biofilter depended on the biomass distribution and the substrate concentration. The specific enzymatic activity decreased from 6.3 to 1.9 nmol of O
2
/min/mg of biomass along the reactor. Good agreement was found between the EC calculated from the TO activity and the EC measured on the biofilter. The results were confirmed by short-time biofiltration experiments. Average EC measured in different biofiltration experiments and EC calculated from the TO activity showed a linear relation, suggesting that in the biofilters, EC was limited by biological reaction. As the enzymatic activities of
P. variotii
were similar to those reported for bacteria, the high performance of the fungal biofilters can possibly be explained by the increased transfer of the hydrophobic compounds, including oxygen, from the gas phase to the mycelia, overcoming the transfer problems associated with the flat bacterial biofilms.
In Vitro Study of Lipid Biosynthesis in an Anaerobically Methane-Oxidizing Microbial Mat
Authors: Blumenberg Martin , Seifert Richard , Nauhaus Katja , Pape Thomas , Michaelis Walter 
Published: August 2005

ABSTRACT

The anaerobic oxidation of methane (AOM) is a key process in the global methane cycle, and the majority of methane formed in marine sediments is oxidized in this way. Here we present results of an in vitro
13
CH
4
labeling study (δ
13
CH
4
, ∼5,400‰) in which microorganisms that perform AOM in a microbial mat from the Black Sea were used. During 316 days of incubation, the
13
C uptake into the mat biomass increased steadily, and there were remarkable differences for individual bacterial and archaeal lipid compounds. The greatest shifts were observed for bacterial fatty acids (e.g., hexadec-11-enoic acid [16:1Δ11]; difference between the δ
13
C at the start and the end of the experiment [Δδ
13
C
start-end
], ∼160‰). In contrast, bacterial glycerol diethers exhibited only slight changes in δ
13
C (Δδ
13
C
start-end
, ∼10‰). Differences were also found for individual archaeal lipids. Relatively high uptake of methane-derived carbon was observed for archaeol (Δδ
13
C
start-end
, ∼25‰), a monounsaturated archaeol, and biphytanes, whereas for
sn
-2-hydroxyarchaeol there was considerably less change in the δ
13
C (Δδ
13
C
start-end
, ∼2‰). Moreover, an increase in the uptake of
13
C for compounds with a higher number of double bonds within a suite of polyunsaturated 2,6,10,15,19-pentamethyleicosenes indicated that in methanotrophic archaea there is a biosynthetic pathway similar to that proposed for methanogenic archaea. The presence of group-specific biomarkers (for ANME-1 and ANME-2 associations) and the observation that there were differences in
13
C uptake into specific lipid compounds confirmed that multiple phylogenetically distinct microorganisms participate to various extents in biomass formation linked to AOM. However, the greater
13
C uptake into the lipids of the sulfate-reducing bacteria (SRB) than into the lipids of archaea supports the hypothesis that there is autotrophic growth of SRB on small methane-derived carbon compounds supplied by the methane oxidizers.
Secretion of Human Serum Albumin by
Kluyveromyces lactis
Overexpressing
KlPDI1
and
KlERO1
Authors: Lodi Tiziana , Neglia Barbara , Donnini Claudia 
Published: August 2005

ABSTRACT

The control of protein conformation during translocation through the endoplasmic reticulum is often a bottleneck for heterologous protein production. The core pathway of the oxidative folding machinery includes two conserved proteins: Pdi1p and Ero1p. We increased the dosage of the genes encoding these proteins in the yeast
Kluyveromyces lactis
and evaluated the secretion of heterologous proteins.
KlERO1
, an orthologue of
Saccharomyces cerevisiae ERO1
, was cloned by functional complementation of the
ts
phenotype of an
Scero1
mutant. The expression of
KlERO1
was induced by treatment of the cells with dithiothreitol and by overexpression of human serum albumin (HSA), a disulfide bond-rich protein. Duplication of either
PDI1
or
ERO1
led to a similar increase in HSA yield. Duplication of both genes accelerated the secretion of HSA and improved cell growth rate and yield. Increasing the dosage of
KlERO1
did not affect the production of human interleukin 1β, a protein that has no disulfide bridges. The results confirm that the
ERO1
genes of
S. cerevisiae
and
K. lactis
are functionally similar even though portions of their coding sequence are quite different and the phenotypes of mutants overexpressing the genes differ. The marked effects of
KlERO1
copy number on the expression of heterologous proteins with a high number of disulfide bridges suggests that control of
KlERO1
and
KlPDI1
is important for the production of high levels of heterologous proteins of this type.
Chemobiosynthesis of Novel 6-Deoxyerythronolide B Analogues by Mutation of the Loading Module of 6-Deoxyerythronolide B Synthase 1
Authors: Murli Sumati , MacMillan Karen S. , Hu Zhihao , Ashley Gary W. , Dong Steven D. , Kealey James T. , Reeves Christopher D. , Kennedy Jonathan 
Published: August 2005

ABSTRACT

Chemobiosynthesis (J. R. Jacobsen, C. R. Hutchinson, D. E. Cane, and C. Khosla, Science 277:367-369, 1997) is an important route for the production of polyketide analogues and has been used extensively for the production of analogues of 6-deoxyerythronolide B (6-dEB). Here we describe a new route for chemobiosynthesis using a version of 6-deoxyerythronolide B synthase (DEBS) that lacks the loading module. When the engineered DEBS was expressed in both
Escherichia coli
and
Streptomyces coelicolor
and fed a variety of acyl-thioesters, several novel 15-
R
-6-dEB analogues were produced. The simpler “monoketide” acyl-thioester substrates required for this route of 15-
R
-6-dEB chemobiosynthesis allow greater flexibility and provide a cost-effective alternative to diketide-thioester feeding to DEBS KS1
o
for the production of 15-
R
-6-dEB analogues. Moreover, the facile synthesis of the monoketide acyl-thioesters allowed investigation of alternative thioester carriers. Several alternatives to
N
-acetyl cysteamine were found to work efficiently, and one of these, methyl thioglycolate, was verified as a productive thioester carrier for mono- and diketide feeding in both
E. coli
and
S. coelicolor
.
Rapid Detection of Enteroviruses in Small Volumes of Natural Waters by Real-Time Quantitative Reverse Transcriptase PCR
Authors: Fuhrman Jed A. , Liang Xiaolin , Noble Rachel T. 
Published: August 2005

ABSTRACT

Despite viral contamination of recreational waters, only bacterial, not viral, indicators are monitored routinely, due to a lack of rapid and cost-effective assays. We used negatively charged filters to capture enteroviruses from seawater and freshwater. Viral RNA was extracted using a commercial kit, and the viruses were quantified by real-time quantitative reverse transcriptase PCR (qRT-PCR). Poliovirus (6.6 to 330,000 virus particles/ml) was added to samples from watersheds in Los Angeles, California, and analysis showed that with 50-ml samples, a cellulose acetate/nitrate (HA) filter yielded final recovery of 51% (
r
2
= 0.99) in fresh water and 23% (
r
2
= 0.90) in seawater. However, for additions of low levels of virus (more likely to represent field samples; <10
4
enterovirus particles/ml), the recovery was lower and more variable, with HA being best in freshwater (17%,
r
2
= 0.97) and the type GF/F glass filter having higher average recovery in seawater (GF/F, 17%;
r
2
= 0.93; HA 12%,
r
2
= 0.87). The optimized method was used with 1-liter field samples from two very different freshwater “creeks” that drain into Santa Monica Bay, California: Topanga Creek (TC), a relatively pristine mountain creek, and Ballona Creek (BC), a concrete-lined urban storm drain. One TC site out of 10 and 2 BC sites out of 7 tested significantly positive for enteroviruses, with higher enterovirus concentrations in BC than in TC (ca. 10 to 25 versus 1 equivalent enterovirus particle/ml). The presented filtration-qRT-PCR approach is fast (<8 h from sampling to results), sensitive, and cost efficient and is promising for monitoring viral contamination in environmental water samples.
Analysis of the
hupSL
Operon of the Nonheterocystous Cyanobacterium
Lyngbya majuscula
CCAP 1446/4: Regulation of Transcription and Expression under a Light-Dark Regimen
Authors: Leitão Elsa , Oxelfelt Fredrik , Oliveira Paulo , Moradas-Ferreira Pedro , Tamagnini Paula 
Published: August 2005

ABSTRACT

This work presents the characterization of an uptake hydrogenase from a marine filamentous nonheterocystous cyanobacterium,
Lyngbya majuscula
CCAP 1446/4. The structural genes encoding the uptake hydrogenase (
hupSL
) were isolated and characterized, and regulatory sequences were identified upstream of
hupS
. In silico analysis highlighted various sets of long repetitive sequences within the
hupSL
intergenic region and downstream of
hupL
. The transcriptional regulator that operates global nitrogen control in cyanobacteria (NtcA) was shown to bind to the promoter region, indicating its involvement in the transcriptional regulation of
hupSL
. Under N
2
-fixing conditions and a 12-h light/12-h dark regime, H
2
uptake activity was shown to follow a daily pattern with a clear maximum towards the end of the dark period, preceded by an increase in the transcript levels initiated in the end of the light phase. Novel antibodies directed against HupL of
Lyngbya majuscula
CCAP 1446/4 were used to monitor the protein levels throughout the 24-h period. The results suggest that protein turnover occurs, with degradation taking place during the light phase and de novo synthesis occurring during the dark phase, coinciding with the pattern of H
2
uptake. Taking into account our results and the established correlation between the uptake hydrogenase activity and N
2
fixation in cyanobacteria, it seems probable that both processes are confined to the dark period in aerobically grown cells of
Lyngbya majuscula
CCAP 1446/4.
Culturability and Coexistence of Colony-Forming and Single-Cell Marine Bacterioplankton
Authors: Simu Karin , Holmfeldt Karin , Zweifel Ulla Li , Hagström Åke 
Published: August 2005

ABSTRACT
Culturability and coexistence of bacterioplankton exhibiting different life strategies were investigated in the Baltic Sea and Skagerrak Sea. Bacterial numbers were estimated using a dilution-to-extinction culturing assay (DCA) and calculated as the most probable number, based on six different methods to detect bacterial growth in the DCA. Irrespective of the method used to detect growth, the fraction of multiplying cells never exceeded 10%, using the total count of 4′,6′-diamidino-2-phenylindole (DAPI)-stainable cells as a reference. Furthermore, the data also showed that non-colony-forming bacteria made up the majority of the viable cells, confirming molecular results showing dominance of non-colony-forming bacteria in clone libraries. The results obtained are in agreement with previous observations, indicating that bacterial assemblages in seawater are dominated by small, active subpopulations coexisting with a large group of inactive cells. The ratio of colony-forming to non-colony-forming bacteria was approximately 10 to 20 times higher in the brackish Baltic Sea than in the Skagerrak Sea. These two sea areas differ in (for example) their levels of bacterial production, dissolved organic carbon, and salinity. We suggest that the relative importance of colony-forming versus non-colony-forming bacterioplankton may be linked to environmental characteristics.
Insights into the Biosynthesis of the Benzoquinone Ansamycins Geldanamycin and Herbimycin, Obtained by Gene Sequencing and Disruption
Authors: Rascher Andreas , Hu Zhihao , Buchanan Greg O. , Reid Ralph , Hutchinson C. Richard 
Published: August 2005

ABSTRACT

Geldanamycin and the closely related herbimycins A, B, and C were the first benzoquinone ansamycins to be extensively studied for their antitumor properties as small-molecule inhibitors of the Hsp90 protein chaperone complex. These compounds are produced by two different
Streptomyces hygroscopicus
strains and have the same modular polyketide synthase (PKS)-derived carbon skeleton but different substitution patterns at C-11, C-15, and C-17. To set the stage for structural modification by genetic engineering, we previously identified the gene cluster responsible for geldanamycin biosynthesis. We have now cloned and sequenced a 115-kb segment of the herbimycin biosynthetic gene cluster from
S. hygroscopicus
AM 3672, including the genes for the PKS and most of the post-PKS tailoring enzymes. The similarities and differences between the gene clusters and biosynthetic pathways for these closely related ansamycins are interpreted with support from the results of gene inactivation experiments. In addition, the organization and functions of genes involved in the biosynthesis of the 3-amino-5-hydroxybenzoic acid (AHBA) starter unit and the post-PKS modifications of progeldanamycin were assessed by inactivating the subclusters of AHBA biosynthetic genes and two oxygenase genes (
gdmM
and
gdmL
) that were proposed to be involved in formation of the geldanamycin benzoquinoid system. A resulting novel geldanamycin analog, KOS-1806, was isolated and characterized.
Presence and Characterization of a Mosaic Genomic Island Which Distinguishes Sorbitol-Fermenting Enterohemorrhagic
Escherichia coli
O157:H
−
from
E. coli
O157:H7
Authors: Janka Andreas , Becker Georg , Sonntag Anne-Katharina , Bielaszewska Martina , Dobrindt Ulrich , Karch Helge 
Published: August 2005

ABSTRACT

A mosaic genomic island comprising
Shigella
resistance locus (SRL) sequences flanked by segments of
Escherichia coli
O157:H7 strain EDL933 O islands 43, 81, and 82 was identified in sorbitol-fermenting (SF) enterohemorrhagic
Escherichia coli
(EHEC) O157:H
−
strain 493/89. This mosaic island is absent from strain EDL933. PCR targeting the SRL-related sequence is a useful tool to distinguish SF EHEC O157:H
−
from EHEC O157:H7.