bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of Sea‐Level Rise on Ground Water Flow in a Coastal Aquifer System
Authors: Masterson John P. , Garabedian Stephen P. 
Published: January 2007

AbstractThe effects of sea‐level rise on the depth to the fresh water/salt water interface were simulated by using a density‐dependent, three‐dimensional numerical ground water flow model for a simplified hypothetical fresh water lens that is similar to shallow, coastal aquifers found along the Atlantic coast of the United States. Simulations of sea‐level rise of 2.65 mm/year from 1929 to 2050 resulted in an increase in water levels relative to a fixed datum, yet a net decrease in water levels relative to the increased sea‐level position. The net decrease in water levels was much greater near a gaining stream than farther from the stream. The difference in the change in water levels is attributed to the dampening effect of the stream on water level changes in response to sea‐level rise. In response to the decreased water level altitudes relative to local sea level, the depth to the fresh water/salt water interface decreased. This reduction in the thickness of the fresh water lens varied throughout the aquifer and was greatly affected by proximity to a ground water fed stream and whether the stream was tidally influenced. Away from the stream, the thickness of the fresh water lens decreased by about 2% from 1929 to 2050, whereas the fresh water lens thickness decreased by about 22% to 31% for the same period near the stream, depending on whether the stream was tidally influenced. The difference in the change in the fresh water/salt water interface position is controlled by the difference in the net decline in water levels relative to local sea level.
On the Use and Error of Approximation in the Domenico (1987) Solution
Authors: West Michael R. , Kueper Bernard H. , Ungs Michael J. 
Published: January 2007

AbstractA mathematical solution for solute transport in a three‐dimensional porous medium with a patch source under steady‐state, uniform ground water flow conditions was developed by Domenico (1987). The solution derivation strategy used an approximate approach to solve the boundary value problem, resulting in a nonexact solution. Variations of the Domenico (1987) solution are incorporated into the software programs BIOSCREEN and BIOCHLOR, which are frequently used to evaluate subsurface contaminant transport problems. This article mathematically elucidates the error in the approximation and presents simulations that compare different versions of the Domenico (1987) solution to an exact analytical solution to demonstrate the potential error inherent in the approximate expressions. Results suggest that the accuracy of the approximate solutions is highly variable and dependent on the selection of input parameters. For solute transport in a medium‐grained sand aquifer, the Domenico (1987) solution underpredicts solute concentrations along the centerline of the plume by as much as 80% depending on the case of interest. Increasing the dispersivity, time, or dimensionality of the system leads to increased error. Because more accurate exact analytical solutions exist, we suggest that the Domenico (1987) solution, and its predecessor and successor approximate solutions, need not be employed as the basis for screening tools at contaminated sites.
Domenico Solution—Is It Valid?
Authors: Srinivasan V. , Clement T.P. , Lee K.K. 
Published: January 2007

AbstractThe Domenico solution is widely used in several analytical models for simulating ground water contaminant transport scenarios. Unfortunately, many textbook as well as journal article treatments of this approximate solution are full of empirical statements that are developed without mathematical rigor. For this reason, a rigorous analysis of this solution is warranted. In this article, we present a mathematical method to derive the Domenico solution and explore its limits. Our analysis shows that the Domenico solution is a true analytical solution when the value of longitudinal dispersivity is zero. For nonzero longitudinal dispersivity values, the Domenico solution will introduce a finite amount of error. We use an example problem to quantify the nature of this error and suggest some general guidelines for the appropriate use of this solution.
Improved Fluorescent In Situ Hybridization Method for Detection of Bacteria from Activated Sludge and River Water by Using DNA Molecular Beacons and Flow Cytometry
Authors: Lenaerts Jeremy , Lappin-Scott Hilary M. , Porter Jonathan 
Published: February 2007

ABSTRACT

Fluorescent in situ hybridization (FISH) remains a key technique in microbial ecology. Molecular beacons (MBs) are self-reporting probes that have potential advantages over linear probes for FISH. MB-FISH strategies have been described using both DNA-based and peptide nucleic acid (PNA)-based approaches. Although recent reports have suggested that PNA MBs are superior, DNA MBs have some advantages, most notably cost. The data presented here demonstrate that DNA MBs are suitable for at least some FISH applications in complex samples, providing superior discriminatory power compared to that of corresponding linear DNA-FISH probes. The use of DNA MBs for flow cytometric detection of
Pseudomonas putida
resulted in approximately double the signal-to-noise ratio of standard linear DNA probes when using laboratory-grown cultures and yielded improved discrimination of target cells in spiked environmental samples, without a need for separate washing steps. DNA MBs were also effective for the detection and cell sorting of both spiked and indigenous
P. putida
from activated sludge and river water samples. The use of DNA MB-FISH presents another increase in sensitivity, allowing the detection of bacteria in environmental samples without the expense of PNA MBs or multilaser flow cytometry.
Spatial and Temporal Population Dynamics of a Naturally Occurring Two-Species Microbial Community inside the Digestive Tract of the Medicinal Leech
Authors: Kikuchi Yoshitomo , Graf Joerg 
Published: February 2007

ABSTRACT

The medicinal leech,
Hirudo verbana
, is one of the simplest naturally occurring models for digestive-tract symbioses, where only two bacterial species,
Aeromonas veronii
bv. sobria (γ-
Proteobacteria
) and a
Rikenella
-like bacterium (
Bacteroidetes
), colonize the crop, the largest compartment of the leech digestive tract. In this study, we investigated spatial and temporal changes of the localization and microcolony structure of the native symbionts in the crop, after ingestion of a sterile blood meal, by fluorescence in situ hybridization. The population dynamics differed between the two symbiotic bacteria.
A. veronii
was detected mainly as individual cells inside the intraluminal fluid (ILF) during 14 days after feeding (daf) unless it was found in association with
Rikenella
microcolonies. The
Rikenella
-like bacteria were observed not only inside the ILF but also in association with the luminal surface of the crop epithelium. The sizes of
Rikenella
microcolonies changed dynamically through the 14-day period. From 3 daf onward, mixed microcolonies containing both species were frequently observed, with cells of both species tightly associating with each other. The sizes of the mixed microcolonies were consistently larger than the size of either single-species microcolony, suggesting a synergistic interaction of the symbionts. Lectin staining with succinylated wheat germ agglutinin revealed that the planktonic microcolonies present in the ILF were embedded in a polysaccharide matrix containing
N
-acetylglucosamine. The simplicity, symbiont-symbiont interaction, and mixed microcolonies of this naturally occurring, digestive-tract symbiosis lay the foundation for understanding the more complex communities residing in most animals.
Multiplex PCR Assay for Detection of
Vibrio vulnificus
Biotype 2 and Simultaneous Discrimination of Serovar E Strains
Authors: Sanjuán Eva , Amaro Carmen 
Published: February 2007

ABSTRACT

In the present work we develop a multiplex PCR assay for the detection and identification of the fish pathogen
Vibrio vulnificus
biotype 2 with discriminating potential for zoonotic strains (serovar E). The PCR assay allowed the identification of two new biotype 2 serovar E human isolates from culture collections. Finally, the multiplex was successfully applied to both diagnosis and carrier detection in field samples.
Universal Sample Preparation Method for Characterization of Bacteria by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry
Authors: Liu Haihong , Du Zongmin , Wang Jin , Yang Ruifu 
Published: February 2007

ABSTRACT

Mass spectrometry has been a very useful method to rapidly identify microorganisms associated with infectious diseases, detect bioterrorism threats, and discriminate among different subtypes of a pathogen. In this study, we developed a universal method for bacterial identification by matrix-assisted laser desorption ionization-time of flight mass spectrometry. The effects on the mass spectrum of different experimental conditions, including the amount of bacterial cells used and treatment procedures with different solutions, matrix species, and solvents, were examined, and an optimized protocol was developed. Several different bacterial species, including
Yersinia pestis
,
Escherichia coli
,
Burkholderia cepacia
,
Bacillus anthracis
, and
Staphylococcus aureus
, which covered the gram-negative and -positive species and spore-producing and non-spore-producing species, were analyzed to evaluate the utility of the protocol. The results showed that five different species and different strains of the same species (9 strains of
S. aureus
and 10 strains of
E. coli
) could be discriminated clearly by their peak profiles in a mass range of 1,000 to 20,000 Da. This protocol is simple, rapid, and easy to perform; has excellent reproducibility; and is suitable for the construction of a mass spectrum fingerprinting database, which helps in fast bacterial identification via database searching.
Transposon Mutagenesis To Improve the Growth of Recombinant
Saccharomyces cerevisiae
on
d
-Xylose
Authors: Ni Haiying , Laplaza José M. , Jeffries Thomas W. 
Published: February 2007

ABSTRACT

Saccharomyces cerevisiae
L2612 transformed with genes for xylose reductase and xylitol dehydrogenase (
XYL1
and
XYL2
) grows well on glucose but very poorly on
d
-xylose. When a gene for
d
-xylulokinase (
XYL3
or
XKS1
) is overexpressed, growth on glucose is unaffected, but growth on xylose is blocked. Spontaneous or chemically induced mutants of this engineered yeast that would grow on xylose could, however, be obtained. We therefore used insertional transposon mutagenesis to identify two loci that can relieve this xylose-specific growth inhibition. One is within the open reading frame (ORF) of
PHO13
, and the other is approximately 500 bp upstream from the
TAL1
ORF. Deletion of
PHO13
or overexpression of
TAL1
resulted in a phenotype similar to the insertional mutation events. Quantitative PCR showed that deletion of
PHO13
increased transcripts for
TAL1
, indicating that the growth inhibition imposed by the overexpression of
XYL3
on xylose can be relieved by an overexpression of transcripts for downstream enzymes. These results may be useful in constructing better xylose-fermenting
S. cerevisiae
strains.
Characterization of an
Escherichia coli
O157:H7 Plasmid O157 Deletion Mutant and Its Survival and Persistence in Cattle
Authors: Lim Ji Youn , Sheng Haiqing , Seo Keun Seok , Park Yong Ho , Hovde Carolyn J. 
Published: February 2007

ABSTRACT

Escherichia coli
O157:H7 causes hemorrhagic colitis and hemolytic-uremic syndrome in humans, and its major reservoir is healthy cattle. An F-like 92-kb plasmid, pO157, is found in most
E. coli
O157:H7 clinical isolates, and pO157 shares sequence similarities with plasmids present in other enterohemorrhagic
E. coli
serotypes. We compared wild-type (WT)
E. coli
O157:H7 and an isogenic ΔpO157 mutant for (i) growth rates and antibiotic susceptibilities, (ii) survival in environments with various acidity, salt, or heat conditions, (iii) protein expression, and (iv) survival and persistence in cattle following oral challenge. Growth, metabolic reactions, and antibiotic resistance of the ΔpO157 mutant were indistinguishable from those of its complement and the WT. However, in cell competition assays, the WT was more abundant than the ΔpO157 mutant. The ΔpO157 mutant was more resistant to acidic synthetic bovine gastric fluid and bile than the WT. In vivo, the ΔpO157 mutant survived passage through the bovine gastrointestinal tract better than the WT but, interestingly, did not colonize the bovine rectoanal junction mucosa as well as the WT. Many proteins were differentially expressed between the ΔpO157 mutant and the WT. Proteins from whole-cell lysates and membrane fractions of cell lysates were separated using sodium dodecyl sulfate-polyacrylamide gel electrophoresis and two-dimensional gel electrophoresis. Ten differentially expressed ∼50-kDa proteins were identified by quadrupole-time of flight mass spectrometry and sequence matching with the peptide fragment database. Most of these proteins, including tryptophanase and glutamate decarboxylase isozymes, were related to survival under salvage conditions, and expression was increased by the deletion of pO157. This suggested that the genes on pO157 regulate some chromosomal genes.
Consumption of Methane and CO
2
by Methanotrophic Microbial Mats from Gas Seeps of the Anoxic Black Sea
Authors: Treude Tina , Orphan Victoria , Knittel Katrin , Gieseke Armin , House Christopher H. , Boetius Antje 
Published: February 2007

ABSTRACT

The deep anoxic shelf of the northwestern Black Sea has numerous gas seeps, which are populated by methanotrophic microbial mats in and above the seafloor. Above the seafloor, the mats can form tall reef-like structures composed of porous carbonate and microbial biomass. Here, we investigated the spatial patterns of CH
4
and CO
2
assimilation in relation to the distribution of ANME groups and their associated bacteria in mat samples obtained from the surface of a large reef structure. A combination of different methods, including radiotracer incubation, beta microimaging, secondary ion mass spectrometry, and catalyzed reporter deposition fluorescence in situ hybridization, was applied to sections of mat obtained from the large reef structure to locate hot spots of methanotrophy and to identify the responsible microbial consortia. In addition, CO
2
reduction to methane was investigated in the presence or absence of methane, sulfate, and hydrogen. The mat had an average δ
13
C carbon isotopic signature of −67.1‰, indicating that methane was the main carbon source. Regions dominated by ANME-1 had isotope signatures that were significantly heavier (−66.4‰ ± 3.9 ‰ [mean ± standard deviation;
n
= 7]) than those of the more central regions dominated by ANME-2 (−72.9‰ ± 2.2 ‰;
n
= 7). Incorporation of
14
C from radiolabeled CH
4
or CO
2
revealed one hot spot for methanotrophy and CO
2
fixation close to the surface of the mat and a low assimilation efficiency (1 to 2% of methane oxidized). Replicate incubations of the mat with
14
CH
4
or
14
CO
2
revealed that there was interconversion of CH
4
and CO
2.
The level of CO
2
reduction was about 10% of the level of anaerobic oxidation of methane. However, since considerable methane formation was observed only in the presence of methane and sulfate, the process appeared to be a rereaction of anaerobic oxidation of methane rather than net methanogenesis.
Selective Phylogenetic Analysis Targeting 16S rRNA Genes of Hyperthermophilic Archaea in the Deep-Subsurface Hot Biosphere
Authors: Kimura Hiroyuki , Ishibashi Jun-Ichiro , Masuda Harue , Kato Kenji , Hanada Satoshi 
Published: February 2007

ABSTRACTInternational drilling projects for the study of microbial communities in the deep-subsurface hot biosphere have been expanded. Core samples obtained by deep drilling are commonly contaminated with mesophilic microorganisms in the drilling fluid, making it difficult to examine the microbial community by 16S rRNA gene clone library analysis. To eliminate mesophilic organism contamination, we previously developed a new method (selective phylogenetic analysis [SePA]) based on the strong correlation between the guanine-plus-cytosine (G+C) contents of the 16S rRNA genes and the optimal growth temperatures of prokaryotes, and we verified the method's effectiveness (H. Kimura, M. Sugihara, K. Kato, and S. Hanada, Appl. Environ. Microbiol.72:21-27, 2006). In the present study we ascertained SePA's ability to eliminate contamination by archaeal rRNA genes, using deep-sea hydrothermal fluid (117°C) and surface seawater (29.9°C) as substitutes for deep-subsurface geothermal samples and drilling fluid, respectively. Archaeal 16S rRNA gene fragments, PCR amplified from the surface seawater, were denatured at 82°C and completely digested with exonuclease I (Exo I), while gene fragments from the deep-sea hydrothermal fluid remained intact after denaturation at 84°C because of their high G+C contents. An examination using mixtures of DNAs from the two environmental samples showed that denaturation at 84°C and digestion with Exo I completely eliminated archaeal 16S rRNA genes from the surface seawater. Our method was quite useful for culture-independent community analysis of hyperthermophilic archaea in core samples recovered from deep-subsurface geothermal environments.
Efficient Synthesis of Simvastatin by Use of Whole-Cell Biocatalysis
Authors: Xie Xinkai , Tang Yi 
Published: February 2007

ABSTRACT

Simvastatin is a semisynthetic derivative of the fungal polyketide lovastatin and is an important drug for lowering cholesterol levels in adults. We have developed a one-step, whole-cell biocatalytic process for the synthesis of simvastatin from monacolin J. By using an
Escherichia coli
strain overexpressing the previously discovered acyltransferase LovD (X. Xie, K. Watanabe, W. A. Wojcicki, C. C. Wang, and Y. Tang, Chem. Biol. 13:1161-1169, 2006), we were able to achieve >99% conversion of monacolin J to simvastatin without the use of any chemical protection steps. The key finding was a membrane-permeable substrate, α-dimethylbutyryl-
S
-methyl-mercaptopropionate, that was efficiently utilized by LovD as the acyl donor. The process was scaled up for gram-scale synthesis of simvastatin. We also demonstrated that simvastatin synthesized via this method can be readily purified from the fermentation broth with >90% recovery and >98% purity as determined by high-performance liquid chromatography. Bioconversion using high-cell-density, fed-batch fermentation was also examined. The whole-cell biocatalysis can therefore be an attractive alternative to currently used multistep semisynthetic transformations.
Effect of Lignocellulose-Derived Inhibitors on Growth of and Ethanol Production by Growth-Arrested
Corynebacterium glutamicum
R
Authors: Sakai Shinsuke , Tsuchida Yoshiki , Okino Shohei , Ichihashi Osamu , Kawaguchi Hideo , Watanabe Takashi , Inui Masayuki , Yukawa Hideaki 
Published: February 2007

ABSTRACT

In cellulosic ethanol production, pretreatment of a biomass to facilitate enzymatic hydrolysis inevitably yields fermentation inhibitors such as organic acids, furans, and phenols. With representative inhibitors included in the medium at various concentrations, individually or in various combinations, ethanol production by
Corynebacterium glutamicum
R under growth-arrested conditions was investigated. In the presence of various inhibitors, the 62 to 100% ethanol productivity retained by the
C. glutamicum
R-dependent method far exceeded that retained by previously reported methods.
Localized Tufts of Fibrils onStaphylococcus epidermidisNCTC 11047 Are Comprised of the Accumulation-Associated Protein
Authors: Banner Miriam A. , Cunniffe John G. , Macintosh Robin L. , Foster Timothy J. , Rohde Holger , Mack Dietrich , Hoyes Emmy , Derrick Jeremy , Upton Mathew , Handley Pauline S. 
Published: February 2007

ABSTRACTStaphylococcus epidermidisis both a human skin commensal and an opportunistic pathogen, causing infections linked to implanted medical devices. This paper describes localized tufts of fibrillar appendages on a subpopulation (25%) of wild-type (WT)S. epidermidisNCTC 11047 cells. The fibrils (122.2 ± 10.8 nm long) are usually in a lateral position on the cells. Fibrillar (Fib+) and nonfibrillar (Fib−) subpopulations were separated (enriched) by 34 sequential partitions of WT cells between a buffer phase and a hexadecane phase. Following enrichment, hydrophobic cells from the hexadecane phase comprised 70% Fib+cells and the less hydrophobic cells from the buffer phase entirely comprised Fib−cells. The Fib+and Fib−subpopulations did not revert on subculture (34 times) on solid medium. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of cell surface proteins from WT, Fib+, and Fib−cells revealed two high-molecular-mass proteins (280 kDa and 230 kDa) on the WT and Fib+cells that were absent from the Fib−cells. Amino acid sequencing revealed that fragments of both the 280- and 230-kDa proteins had 100% identity to theaccumulation-associatedprotein (Aap). Aap is known to cause biofilm formation if it is truncated by loss of the terminal A domain. Immunogold staining with anti-Aap antibodies labeled tuft fibrils of the WT and Fib+cells but not the cell surface of Fib−cells. The tufts were labeled with N-terminally directed antibodies (anti-A domain), showing that the fibrillar Aap was not truncated on the cell surface. Thus, the presence of full-length Aap correlated with the low biofilm-forming abilities of both WT and Fib+S. epidermidisNCTC 11047 populations. Reverse transcription-PCR showed thataapwas transcribed in both Fib+and Fib−cells. We therefore propose that full-length Aap is expressed on cells ofS. epidermidisNCTC 11047 as tufts of short fibrils and that fibril expression is regulated at a posttranscriptional level.
Translocation of α-Synuclein Expressed in
Escherichia coli
Authors: Ren Guoping , Wang Xi , Hao Shufeng , Hu Hongyu , Wang Chih-chen 
Published: February 2007

ABSTRACT

α-Synuclein is a major component of Lewy bodies in Parkinson's disease. Although no signal sequence is apparent, α-synuclein expressed in
Escherichia coli
is mostly located in the periplasm. The possibilities that α-synuclein translocated into the periplasm across the inner membrane by the SecA or the Tat targeting route identified in bacteria and that α-synuclein was released through MscL were excluded. The signal recognition particle-dependent pathway is involved in the translocation of α-synuclein. The C-terminal 99-to-140 portion of the α-synuclein molecule plays a signal-like role for its translocation into the periplasm, cooperating with the central 61-to-95 section. The N-terminal 1-to-60 region is not required for this translocation.