bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fetal programming of fat and collagen in porcine skeletal muscles
Authors: Karunaratne J. F. , Ashton C. J. , Stickland N. C. 
Published: December 2005

AbstractConnective tissue plays a key role in the scaffolding and development of skeletal muscle. Pilot studies carried out in our laboratory have shown that the smallest porcine littermate has a higher content of connective tissue within skeletal muscle compared with its largest littermate. The present study investigated the prenatal development of intralitter variation in terms of collagen content within connective tissue and intramuscular fat of the M. semitendinosus. Twenty‐three pairs of porcine fetuses from a Large White–Landrace origin were used aged from 36 to 86 days of gestation. The largest and smallest littermates were chosen by weight and the M. semitendinosus was removed from each. Complete transverse muscle sections were stained with Oil Red O (detection of lipids) and immunocytochemistry was performed using an antibody to collagen I. Slides were analysed and paired t‐Tests revealed the smallest littermate contained a significantly higher proportion of fat deposits and collagen I content compared with the largest littermate. Recent postnatal studies showing elevated levels of intramuscular lipids and low scores for meat tenderness in the smallest littermate corroborate our investigations. It can be concluded that the differences seen in connective tissue elements have a fetal origin that may continue postnatally.
Overweight, obesity and the food service industry
Authors: Edwards John S. A. , Engström Katja , Hartwell Heather J. 
Published: December 2005

AbstractIn many countries people are eating out more often and the food service industry has encouraged/reacted to this with business activities such as ‘super‐sizing’, product bundling and ‘all you can eat buffets’. At the same time, the incidence of overweight and obesity has increased throughout the world and the food service industry has been implicated if not blamed entirely for this situation. However, is the food service industry rightly condemned as the obesity villain? This article considers some of the factors in the obesity debate and concludes that it is not a ‘one‐way street’ and both the food service industry and consumer alike bear responsibility for the current situation.
The lifetime of grand design
Authors: Merrifield M. R. , Rand R. J. , Meidt S. E. 
Published: December 2005

Abstract
The lifetime of the structure in grand design spiral galaxies is observationally ill-determined, but is essentially set by how accurately the rotation of the pattern can be characterized by a single angular pattern speed. This paper derives a generalized version of the Tremaine–Weinberg method for observationally determining pattern speeds, in which the pattern speed is allowed to vary arbitrarily with radius. The departures of the derived pattern speed from a constant then provide a simple metric of the lifetime of the spiral structure. Application of this method to CO observations of NGC 1068 reveals that the pattern speed of the spiral structure in this galaxy varies rapidly with radius, and that the lifetime of the spiral structure is correspondingly very short. If this result turns out to be common in grand-design spiral galaxies, then these features will have to be viewed as highly transient phenomena.
Geophysical Monitoring of a Field‐Scale Biostimulation Pilot Project
Authors: Lane John W. , Day‐Lewis Frederick D. , Casey Clifton C. 
Published: December 2005

AbstractThe USGS conducted a geophysical investigation in support of a U.S. Naval Facilities Engineering Command, Southern Division field‐scale biostimulation pilot project at Anoka County Riverfront Park (ACP), downgradient of the Naval Industrial Reserve Ordnance Plant, Fridley, Minnesota. The goal of the pilot project is to evaluate subsurface injection of vegetable oil emulsion (VOE) to stimulate microbial degradation of chlorinated hydrocarbons. To monitor the emplacement and movement of the VOE and changes in water chemistry resulting from VOE dissolution and/or enhanced biological activity, the USGS acquired cross‐hole radar zero‐offset profiles, traveltime tomograms, and borehole geophysical logs during five site visits over 1.5 years. Analysis of pre‐ and postinjection data sets using petrophysical models developed to estimate VOE saturation and changes in total dissolved solids provides insights into the spatial and temporal distribution of VOE and ground water with altered chemistry. Radar slowness‐difference tomograms and zero‐offset slowness profiles indicate that the VOE remained close to the injection wells, whereas radar attenuation profiles and electromagnetic induction logs indicate that bulk electrical conductivity increased downgradient of the injection zone, diagnostic of changing water chemistry. Geophysical logs indicate that some screened intervals were located above or below zones of elevated dissolved solids; hence, the geophysical data provide a broader context for interpretation of water samples and evaluation of the biostimulation effort. Our results include (1) demonstration of field and data analysis methods for geophysical monitoring of VOE biostimulation and (2) site‐specific insights into the spatial and temporal distributions of VOE at the ACP.
MODFLOW/MT3DMS–Based Simulation of Variable‐Density Ground Water Flow and Transport
Authors: Langevin Christian D. , Guo Weixing 
Published: December 2005

AbstractThis paper presents an approach for coupling MODFLOW and MT3DMS for the simulation of variable‐density ground water flow. MODFLOW routines were modified to solve a variable‐density form of the ground water flow equation in which the density terms are calculated using an equation of state and the simulated MT3DMS solute concentrations. Changes to the MODFLOW and MT3DMS input files were kept to a minimum, and thus existing data files and data files created with most pre‐ and postprocessors can be used directly with the SEAWAT code. The approach was tested by simulating the Henry problem and two of the saltpool laboratory experiments (low‐ and high‐density cases). For the Henry problem, the simulated results compared well with the steady‐state semianalytic solution and also the transient isochlor movement as simulated by a finite‐element model. For the saltpool problem, the simulated breakthrough curves compared better with the laboratory measurements for the low‐density case than for the high‐density case but showed good agreement with the measured salinity isosurfaces for both cases. Results from the test cases presented here indicate that the MODFLOW/MT3DMS approach provides accurate solutions for problems involving variable‐density ground water flow and solute transport.
Springflow Hydrographs: Eogenetic vs. Telogenetic Karst
Authors: Florea Lee J. , Vacher H.L. 
Published: December 2005

AbstractMatrix permeability in the range of 10−11 to 10−14 m2 characterizes eogenetic karst, where limestones have not been deeply buried. In contrast, limestones of postburial, telogenetic karst have matrix permeabilities on the order of 10−15 to 10−20 m2. Is this difference in matrix permeability paralleled by a difference in the behavior of springs draining eogenetic and telogenetic karst? Log Q/Qmin flow duration curves from 11 eogenetic‐karst springs in Florida and 12 telogenetic‐karst springs in Missouri, Kentucky, and Switzerland, plot in different fields because of the disparate slopes of the curves. The substantially lower flow variability in eogenetic‐karst springs, which results in the steeper slopes of their flow duration curves, also makes for a strong contrast in patterns (e.g., “flashiness”) between the eogenetic‐karst and telogenetic‐karst spring hydrographs. With respect to both spring hydrographs and the flow duration curves derived from them, the eogenetic‐karst springs of Florida are more like basalt springs of Idaho than the telogenetic‐karst springs of the study. From time‐series analyses on discharge records for 31 springs and published time‐series results for 28 additional sites spanning 11 countries, we conclude that (1) the ratio of maximum to mean (Qmax/Qmean) discharge is less in springs of eogenetic karst than springs of telogenetic karst; (2) aquifer inertia (system memory) is larger in eogenetic karst; (3) eogenetic‐karst aquifers take longer to respond to input signals; and (4) high‐frequency events affect discharge less in eogenetic karst. All four of these results are consistent with the hypothesis that accessible storage is larger in eogenetic‐karst aquifers than in telogenetic‐karst aquifers.
Building Pit Dewatering: Application of Transient Analytic Elements
Authors: Zaadnoordijk Willem J. 
Published: December 2005

AbstractAnalytic elements are well suited for the design of building pit dewatering. Wells and drains can be modeled accurately by analytic elements, both nearby to determine the pumping level and at some distance to verify the targeted drawdown at the building site and to estimate the consequences in the vicinity. The ability to shift locations of wells or drains easily makes the design process very flexible. The temporary pumping has transient effects, for which transient analytic elements may be used. This is illustrated using the free, open‐source, object‐oriented analytic element simulator TimSL for the design of a building pit dewatering near a canal. Steady calculations are complemented with transient calculations. Finally, the bandwidths of the results are estimated using linear variance analysis.
Importance of 3-Hydroxy Fatty Acid Composition of Lipopeptides for Biosurfactant Activity
Authors: Youssef Noha H. , Duncan Kathleen E. , McInerney Michael J. 
Published: December 2005

ABSTRACTBiosurfactant production may be an economic approach to improving oil recovery. To obtain candidates most suitable for oil recovery, 207 strains, mostly belonging to the genusBacillus, were tested for growth and biosurfactant production in medium with 5% NaCl under aerobic and anaerobic conditions. All strains grew aerobically with 5% NaCl, and 147 strains produced a biosurfactant. Thirty-five strains grew anaerobically with 5% NaCl, and two produced a biosurfactant. In order to relate structural differences to activity, eight lipopeptide biosurfactants with different specific activities produced by variousBacillusspecies were purified by a new protocol. The amino acid compositions of the eight lipopeptides were the same (Glu/Gln:Asp/Asn:Val:Leu, 1:1:1:4), but the fatty acid compositions differed. Multiple regression analysis showed that the specific biosurfactant activity depended on the ratios of bothisoto normal even-numbered fatty acids andanteisotoisoodd-numbered fatty acids. A multiple regression model accurately predicted the specific biosurfactant activities of four newly purified biosurfactants (r2= 0.91). The fatty acid composition of the biosurfactant produced byBacillus subtilissubsp.subtilisstrain T89-42 was altered by the addition of branched-chain amino acids to the growth medium. The specific activities of biosurfactants produced in cultures with different amino acid additions were accurately predicted by the multiple regression model derived from the fatty acid compositions (r2= 0.95). Our work shows that many strains ofBacillus mojavensisandBacillus subtilisproduce biosurfactants and that the fatty acid composition is important for biosurfactant activity.
Symbiotic Fungi Produce Laccases Potentially Involved in Phenol Degradation in Fungus Combs of Fungus-Growing Termites in Thailand
Authors: Taprab Yaovapa , Johjima Toru , Maeda Yoshimasa , Moriya Shigeharu , Trakulnaleamsai Savitr , Noparatnaraporn Napavarn , Ohkuma Moriya , Kudo Toshiaki 
Published: December 2005

ABSTRACTFungus-growing termites efficiently decompose plant litter through their symbiotic relationship with basidiomycete fungi of the genusTermitomyces. Here, we investigated phenol-oxidizing enzymes in symbiotic fungi and fungus combs (a substrate used to cultivate symbiotic fungi) from termites belonging to the generaMacrotermes,Odontotermes, andMicrotermesin Thailand, because these enzymes are potentially involved in the degradation of phenolic compounds during fungus comb aging. Laccase activity was detected in all the fungus combs examined as well as in the culture supernatants of isolated symbiotic fungi. Conversely, no peroxidase activity was detected in any of the fungus combs or the symbiotic fungal cultures. The laccase cDNA fragments were amplified directly from RNA extracted from fungus combs of five termite species and a fungal isolate using degenerate primers targeting conserved copper binding domains of basidiomycete laccases, resulting in a total of 13 putative laccase cDNA sequences being identified. The full-length sequences of the laccase cDNA and the corresponding gene,lcc1-2, were identified from the fungus comb ofMacrotermes gilvusand aTermitomycesstrain isolated from the same fungus comb, respectively. Partial purification of laccase from the fungus comb showed that thelcc1-2gene product was a dominant laccase in the fungus comb. These findings indicate that the symbiotic fungus secretes laccase to the fungus comb. In addition to laccase, we report novel genes that showed a significant similarity with fungal laccases, but the gene product lacked laccase activity. Interestingly, these genes were highly expressed in symbiotic fungi of all the termite hosts examined.
Isolation and Characterization of
o
-Xylene Oxygenase Genes from
Rhodococcus opacus
TKN14
Authors: Maruyama Takahiro , Ishikura Masaharu , Taki Hironori , Shindo Kazutoshi , Kasai Hiroaki , Haga Miyuki , Inomata Yukie , Misawa Norihiko 
Published: December 2005

ABSTRACT

o
-Xylene is one of the most difficult-to-degrade environmental pollutants. We report here
Rhodococcus
genes mediating oxygenation in the first step of
o
-xylene degradation.
Rhodococcus opacus
TKN14, isolated from soil contaminated with
o
-xylene, was able to utilize
o
-xylene as the sole carbon source and to metabolize it to
o
-methylbenzoic acid. A cosmid library from the genome of this strain was constructed in
Escherichia coli
. A bioconversion analysis revealed that a cosmid clone incorporating a 15-kb NotI fragment had the ability to convert
o
-xylene into
o
-methylbenzyl alcohol. The sequence analysis of this 15-kb region indicated the presence of a gene cluster significantly homologous to the naphthalene-inducible dioxygenase gene clusters (
nidABCD
) that had been isolated from
Rhodococcus
sp. strain I24. Complementation studies, using
E. coli
expressing various combinations of individual open reading frames, revealed that a gene (named
nidE
) for rubredoxin (Rd) and a novel gene (named
nidF
) encoding an auxiliary protein, which had no overall homology with any other proteins, were indispensable for the methyl oxidation reaction of
o
-xylene, in addition to the dioxygenase iron-sulfur protein genes (
nidAB
). Regardless of the presence of NidF, the enzyme composed of NidABE was found to function as a typical naphthalene dioxygenase for converting naphthalene and various (di)methylnaphthalenes into their corresponding
cis
-dihydrodiols. All the
nidABEF
genes were transcriptionally induced in
R. opacus
TKN14 by the addition of
o
-xylene to a mineral salt medium. It is very likely that these genes are involved in the degradation pathways of a wide range of aromatic hydrocarbons by
Rhodococcus
species as the first key enzyme.
At Least 1 in 20 16S rRNA Sequence Records Currently Held in Public Repositories Is Estimated To Contain Substantial Anomalies
Authors: Ashelford Kevin E. , Chuzhanova Nadia A. , Fry John C. , Jones Antonia J. , Weightman Andrew J. 
Published: December 2005

ABSTRACT

A new method for detecting chimeras and other anomalies within 16S rRNA sequence records is presented. Using this method, we screened 1,399 sequences from 19 phyla, as defined by the Ribosomal Database Project, release 9, update 22, and found 5.0% to harbor substantial errors. Of these, 64.3% were obvious chimeras, 14.3% were unidentified sequencing errors, and 21.4% were highly degenerate. In all, 11 phyla contained obvious chimeras, accounting for 0.8 to 11% of the records for these phyla. Many chimeras (43.1%) were formed from parental sequences belonging to different phyla. While most comprised two fragments, 13.7% were composed of at least three fragments, often from three different sources. A separate analysis of the
Bacteroidetes
phylum (2,739 sequences) also revealed 5.8% records to be anomalous, of which 65.4% were apparently chimeric. Overall, we conclude that, as a conservative estimate, 1 in every 20 public database records is likely to be corrupt. Our results support concerns recently expressed over the quality of the public repositories. With 16S rRNA sequence data increasingly playing a dominant role in bacterial systematics and environmental biodiversity studies, it is vital that steps be taken to improve screening of sequences prior to submission. To this end, we have implemented our method as a program with a simple-to-use graphic user interface that is capable of running on a range of computer platforms. The program is called Pintail, is released under the terms of the GNU General Public License open source license, and is freely available from our website at
http://www.cardiff.ac.uk/biosi/research/biosoft/
.
Activity and Phylogenetic Diversity of Bacterial Cells with High and Low Nucleic Acid Content and Electron Transport System Activity in an Upwelling Ecosystem
Authors: Longnecker K. , Sherr B. F. , Sherr E. B. 
Published: December 2005

ABSTRACT

We evaluated whether bacteria with higher cell-specific nucleic acid content (HNA) or an active electron transport system, i.e., positive for reduction of 5-cyano-2,3-ditolyl tetrazolium chloride (CTC), were responsible for the bulk of bacterioplankton metabolic activity. We also examined whether the phylogenetic diversity of HNA and CTC-positive cells differed from the diversity of
Bacteria
with low nucleic acid content (LNA). Bacterial assemblages were sampled both in eutrophic shelf waters and in mesotrophic offshore waters in the Oregon coastal upwelling region. Cytometrically sorted HNA, LNA, and CTC-positive cells were assayed for their cell-specific [
3
H]leucine incorporation rates. Phylogenetic diversity in sorted non-radioactively labeled samples was assayed using denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA genes. Cell-specific rates of leucine incorporation of HNA and CTC-positive cells were on average only slightly greater than the cell-specific rates of LNA cells. HNA cells accounted for most bacterioplankton substrate incorporation due to high abundances, while the low abundances of CTC-positive cells resulted in only a small contribution by these cells to total bacterial activity. The proportion of the total bacterial leucine incorporation attributable to LNA cells was higher in offshore regions than in shelf waters. Sequence data obtained from DGGE bands showed broadly similar phylogenetic diversity across HNA, LNA, and CTC-positive cells, with between-sample and between-region variability in the distribution of phylotypes. Our results suggest that LNA bacteria are not substantially different from HNA bacteria in either cell-specific rates of substrate incorporation or phylogenetic composition and that they can be significant contributors to bacterial metabolism in the sea.
Effect of Elevated Tropospheric Ozone on the Structure of Bacterial Communities Inhabiting the Rhizosphere of Herbaceous Plants Native to Germany
Authors: Dohrmann Anja B. , Tebbe Christoph C. 
Published: December 2005

ABSTRACT

Current elevated concentrations of ozone in the atmosphere, as they are observed during summer seasons, can cause severe effects on plant vegetation. This study was initiated to analyze whether ozone-stressed plants also transfer signals below ground and thereby alter the bacterial community composition in their rhizospheres. Herbaceous plants, native to Germany, with tolerance (
Anthoxanthum odoratum
,
Achillea millefolium
,
Poa pratensis
,
Rumex acetosa
, and
Veronica chamaedrys
) and sensitivity (
Matricaria chamomilla
,
Sonchus asper
, and
Tanacetum vulgare
) to ozone, raised in the greenhouse, were exposed in open-top chambers to two different ozone regimes, i.e., “summer stress” and a normal ozone background. DNA of bacterial cells from the rhizospheres was directly extracted, and partial sequences of the 16S rRNA genes were PCR amplified with primers targeting the following phylogenetic groups:
Bacteria
, α-
Proteobacteria
,
Actinobacteria
, and
Pseudomonas
, respectively. The diversity of the amplified products was analyzed by genetic profiling based on single-strand conformation polymorphism (SSCP). Neither the tolerant nor the sensitive plants, the latter with visible above-ground damage, showed ozone-induced differences in any of the SSCP profiles, with the single exception of
Actinobacteria
-targeted profiles from
S. asper
. To increase the stress,
S. asper
was germinated and raised in the continuous presence of an elevated level of ozone. SSCP profiles with
Bacteria
-specific primers combined with gene probe hybridizations indicated an ozone-related increase in a
Xanthomonas
-related 16S rRNA gene and a decrease in the respective gene from the plant plastids. The fact that only this latter unrealistic scenario caused a detectable effect demonstrated that ozone stress has a surprisingly small effect on the structural diversity of the bacterial community in rhizospheres.
Planktonic-Cell Yield of a Pseudomonad Biofilm
Authors: Bester Elanna , Wolfaardt Gideon , Joubert Lydia , Garny Kerstin , Saftic Sanja 
Published: December 2005

ABSTRACT

Biofilm cells differ phenotypically from their free-floating counterparts. Differential growth rates in biofilms are often referred to, particularly in response to limited diffusion of oxygen and nutrients. We observed growth rates of attached
Pseudomonas
sp. strain CT07 cells that were notably higher than the maximum specific growth rate measured in batch culture. Despite dilution rates in continuous flow cells that exceeded the maximum planktonic specific growth rate by 58 times, sampling of the effluent revealed >10
9
cells ml
−1
, suggesting that biofilms function as a source of planktonic cells through high cell yield and detachment. Further investigation demonstrated considerable planktonic cell yield from biofilms as young as 6 h, indicating that detachment is not limited to established biofilms. These biofilm-detached cells were more sensitive to a commercial biocide than associated biofilm- and chemostat-cultivated populations, implying that detached biofilm cells exhibit a character that is distinct from that of attached and planktonic cell populations.