bluuebunny/crossref_metadata_2025 huggingface dataset:
Geophysical Monitoring of a Field‐Scale Biostimulation Pilot Project
Authors: Lane John W. , Day‐Lewis Frederick D. , Casey Clifton C.
Published: December 2005

The 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

This 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

Matrix 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

Analytic 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.
Magnetic confinement of electron and photon radiotherapy dose: A Monte Carlo simulation with a nonuniform longitudinal magnetic field
Authors: Chen Yu , Bielajew Alex F. , Litzenberg Dale W. , Moran Jean M. , Becchetti Frederick D.
Published: December 2005

It recently has been shown experimentally that the focusing provided by a longitudinal nonuniform high magnetic field can significantly improve electron beam dose profiles. This could permit precise targeting of tumors near critical areas and minimize the radiation dose to surrounding healthy tissue. The experimental results together with Monte Carlo simulations suggest that the magnetic confinement of electron radiotherapy beams may provide an alternative to proton or heavy ion radiation therapy in some cases. In the present work, the external magnetic field capability of the Monte Carlo code PENELOPE was utilized by providing a subroutine that modeled the actual field produced by the solenoid magnet used in the experimental studies. The magnetic field in our simulation covered the region from the vacuum exit window to the phantom including surrounding air. In a longitudinal nonuniform magnetic field, it is observed that the electron dose can be focused in both the transverse and longitudinal directions. The measured dose profiles of the electron beam are generally reproduced in the Monte Carlo simulations to within a few percent in the region of interest provided that the geometry and the energy of the incident electron beam are accurately known. Comparisons for the photon beam dose profiles with and without the magnetic field are also made. The experimental results are qualitatively reproduced in the simulation. Our simulation shows that the excessive dose at the beam entrance is due to the magnetic field trapping and focusing scattered secondary electrons that were produced in the air by the incident photon beam. The simulations also show that the electron dose profile can be manipulated by the appropriate control of the beam energy together with the strength and displacement of the longitudinal magnetic field.
Benchmarking analytical calculations of proton doses in heterogeneous matter
Authors: Ciangaru George , Polf Jerimy C. , Bues Martin , Smith Alfred R.
Published: December 2005

A proton dose computational algorithm, performing an analytical superposition of infinitely narrow proton beamlets (ASPB) is introduced. The algorithm uses the standard pencil beam technique of laterally distributing the central axis broad beam doses according to the Moliere scattering theory extended to slablike varying density media. The purpose of this study was to determine the accuracy of our computational tool by comparing it with experimental and Monte Carlo (MC) simulation data as benchmarks. In the tests, parallel wide beams of protons were scattered in water phantoms containing embedded air and bone materials with simple geometrical forms and spatial dimensions of a few centimeters. For homogeneous water and bone phantoms, the proton doses we calculated with the ASPB algorithm were found very comparable to experimental and MC data. For layered bone slab inhomogeneity in water, the comparison between our analytical calculation and the MC simulation showed reasonable agreement, even when the inhomogeneity was placed at the Bragg peak depth. There also was reasonable agreement for the parallelepiped bone block inhomogeneity placed at various depths, except for cases in which the bone was located in the region of the Bragg peak, when discrepancies were as large as more than 10%. When the inhomogeneity was in the form of abutting air‐bone slabs, discrepancies of as much as 8% occurred in the lateral dose profiles on the air cavity side of the phantom. Additionally, the analytical depth‐dose calculations disagreed with the MC calculations within 3% of the Bragg peak dose, at the entry and midway depths in the phantom. The distal depth‐dose 20%–80% fall‐off widths and ranges calculated with our algorithm and the MC simulation were generally within of agreement. The analytical lateral‐dose profile calculations showed smaller (by less than ) 20%–80% penumbra widths and shorter fall‐off tails than did those calculated by the MC simulations. Overall, this work validates the usefulness of our ASPB algorithm as a reasonably fast and accurate tool for quality assurance in planning wide beam proton therapy treatment of clinical sites either composed of homogeneous materials or containing laterally extended inhomogeneities that are comparable in density and located away from the Bragg peak depths.
An improved analytical model for CT dose simulation with a new look at the theory of CT dose
Authors: Dixon Robert L. , Munley Michael T. , Bayram Ersin
Published: December 2005

Gagne [Med. Phys. 16, 29–37 (1989)] has previously described a model for predicting the sensitivity and dose profiles in the slice‐widthdirection for CT scanners. The model, developed prior to the advent of multidetector CT scanners, is still widely used; however, it does not account for the effect of anode tilt on the penumbra or include the heel effect, both of which are increasingly important for the wider beams (up to) of contemporary, multidetector scanners. Additionally, it applied only on (or near) the axis of rotation, and did not incorporate the photon energy spectrum. The improved model described herein transcends all of the aforementioned limitations of the Gagne model, including extension to the peripheral phantom axes. Comparison of simulated and measured dose data provides experimental validation of the model, including verification of the superior match to the penumbra provided by the tilted‐anode model, as well as the observable effects on the cumulative dose distribution. The initial motivation for the model was to simulate the quasiperiodic dose distribution on the peripheral, phantom axes resulting from a helical scan series in order to facilitate the implementation of an improved method of CT dose measurement utilizing a short ion chamber, as proposed by Dixon [Med. Phys. 30, 1272–1280 (2003)]. A more detailed set of guidelines for implementing such measurements is also presented in this paper. In addition, some fundamental principles governing CT dose which have not previously been clearly enunciated follow from the model, and a fundamental (energy‐based) quantity dubbed “CTDI‐aperture” is introduced.
Target volume dose considerations in proton beam treatment planning for lung tumors
Authors: Engelsman Martijn , Kooy Hanne M.
Published: December 2005

We performed a treatment planning study in order to gather basic insight in the effect of setup errors and breathing motion on the cumulative proton dose to a lung tumor. We used a simplified geometry that simulates a diameter gross tumor volume (GTV) located centrally inside lung tissue. The GTV was expanded with a uniform margin into a clinical target volume (CTV) and into a variety of planning target volume (PTV's). Proton beam apertures were designed to conform the prescribed dose laterally to the PTV while the range compensator was designed to provide distal coverage of the CTV. Different smearing distances were applied to the range compensators, and the cumulative dose in the CTV was evaluated for different combinations of breathing motion and systematic setup errors. Evaluation parameters were the dose to 99% of the CTV and the equivalent uniform dose (EUD), with a surviving fraction at of . For a single proton field designed to a expansion of the CTV and without smearing applied to the range compensator, of the CTV reduced from 96% for no tumor displacement to 41% and 13% for systematic setup errors of 5 and , respectively. For a representative clinical combination, of systematic error and breathing amplitude, the EUD of the CTV was about (prescribed dose ) regardless the CTV to PTV margin, and without smearing. Smearing the range compensator increases the dose to the CTV substantially with a lateral margin and smearing distance of providing ample tumor coverage. In this latter case, of the target volume increased to 87% for a single field treatment plan. Smearing does, however, lead to an increase in dose to normal tissues distal to the clinical target volume. Next to countering geometric mismatches due to patient setup, smearing can also be used to counter the detrimental effects of breathing motion on the dose to the clinical target volume. We show that the lateral margin and smearing distance can be substantially smaller than the maximum tumor displacement due to setup errors and patient breathing, as measured by the and the EUD.
A dosimetric comparison of versus for HDR prostate brachytherapy
Authors: Lymperopoulou G. , Papagiannis P. , Sakelliou L. , Milickovic N. , Giannouli S. , Baltas D.
Published: December 2005

For the purpose of evaluating the use of for prostate High Dose Rate brachytherapy (HDR), a hypothetical source is assumed with the exact same design of the new microSelectron source replacing the active core by pure metal. Monte Carlo simulation is employed for the full dosimetric characterization of both sources and results are compared following the AAPM TG‐43 dosimetric formalism. Monte Carlo calculated dosimetry results are incorporated in a commercially available treatment planning system , which features an inverse treatment planning option based on a multiobjective dose optimization engine. The quality of prostate HDR brachytherapy using the real and hypothetical source is compared in a comprehensive analysis of different prostate implants in terms of the multiobjective dose optimization solutions as well as treatment quality indices such as Dose Volume Histograms (DVH) and the Conformal Index (COIN). Given that scattering overcompensates for absorption in intermediate photon energies and distances in the range of interest to prostate HDR brachytherapy, proves at least equivalent to irrespective of prostate volume. This has to be evaluated in view of the shielding requirements for the energies that are minimal relative to that for .
An international dosimetry exchange for boron neutron capture therapy, Part I: Absorbed dose measurements
Authors: Binns P. J. , Riley K. J. , Harling O. K. , Kiger W. S. , Munck af Rosenschöld P. M. , Giusti V. , Capala J. , Sköld K. , Auterinen I. , Serén T. , Kotiluoto P. , Uusi‐Simola J. , Marek M. , Viererbl L. , Spurny F.
Published: December 2005

An international collaboration was organized to undertake a dosimetry exchange to enable the future combination of clinical data from different centers conducting neutron capture therapy trials. As a first step (Part I) the dosimetry group from the Americas, represented by MIT, visited the clinical centers at Studsvik (Sweden), VTT Espoo (Finland), and the Nuclear Research Institute (NRI) at Rez (Czech Republic). A combined VTT/NRI group reciprocated with a visit to MIT. Each participant performed a series of dosimetry measurements under equivalent irradiation conditions using methods appropriate to their clinical protocols. This entailed in‐air measurements and dose versus depth measurements in a large water phantom. Thermal neutron flux as well as fast neutron and photon absorbed dose rates were measured. Satisfactory agreement in determining absorbed dose within the experimental uncertainties was obtained between the different groups although the measurement uncertainties are large, ranging between 3% and 30% depending upon the dose component and the depth of measurement. To improve the precision in the specification of absorbed dose amongst the participants, the individually measured dose components were normalized to the results from a single method. Assuming a boron concentration of that is typical of concentrations realized clinically with the boron delivery compound boronophenylalanine‐fructose, systematic discrepancies in the specification of the total biologically weighted dose of up to 10% were apparent between the different groups. The results from these measurements will be used in future to normalize treatment plan calculations between the different clinical dosimetry protocols as Part II of this study.
A global bioheat model with self‐tuning optimal regulation of body temperature using Hebbian feedback covariance learning
Authors: Ong M. L. , Ng E. Y. K.
Published: December 2005

In the lower brain, body temperature is continually being regulated almost flawlessly despite huge fluctuations in ambient and physiological conditions that constantly threaten the well‐being of the body. The underlying control problem defining thermal homeostasis is one of great enormity: Many systems and sub‐systems are involved in temperature regulation and physiological processes are intrinsically complex and intertwined. Thus the defining control system has to take into account the complications of nonlinearities, system uncertainties, delayed feedback loops as well as internal and external disturbances. In this paper, we propose a self‐tuning adaptive thermal controller based upon Hebbian feedback covariance learning where the system is to be regulated continually to best suit its environment. This hypothesis is supported in part by postulations of the presence of adaptive optimization behavior in biological systems of certain organisms which face limited resources vital for survival. We demonstrate the use of Hebbian feedback covariance learning as a possible self‐adaptive controller in body temperature regulation. The model postulates an important role of Hebbian covariance adaptation as a means of reinforcement learning in the thermal controller. The passive system is based on a simplified 2‐node core and shell representation of the body, where global responses are captured. Model predictions are consistent with observed thermoregulatory responses to conditions of exercise and rest, and heat and cold stress. An important implication of the model is that optimal physiological behaviors arising from self‐tuning adaptive regulation in the thermal controller may be responsible for the departure from homeostasis in abnormal states, e.g., fever. This was previously unexplained using the conventional “set‐point” control theory.
Patient specific treatment verifications for helical tomotherapy treatment plans
Authors: Thomas S. D. , Mackenzie M. , Field G. C. , Syme A. M. , Fallone B. G.
Published: December 2005

We performed two‐dimensional treatment verifications for ten patients planned and treated with helical tomotherapy. The treatment verification consisted of a film measurement as well as point dose measurements made with an ion chamber. The agreement between the calculated and the measured film dose distributions was evaluated with the gamma index calculated for three sets of criteria (2 mm and 2%, 4 mm and 3%, and 3 mm and 5%) as recommended in the literature. Good agreement was found between measured and calculated distributions without any need of normalization of the dose data but with dose map registration using reference marks. In this case, , , and passed the 2 mm and 2%, 4 mm and 3%, and 3 mm and 5% criteria, respectively. Agreement was excellent when both normalization and manual registration of the dose maps was employed. In this case , , and passed the 2 mm and 2%, 4 mm and 3%, and 3 mm and 5% criteria, respectively. The mean percent discrepancy for the point dose measurements was , , for the high dose, low dose, and critical structure point, respectively. Three criteria for a satisfactory treatment verification in the high dose regions of a plan were established. For the un‐normalized reference mark registered data 80% of pixels must pass the 3 mm and 5% criteria. For the normalized and manually registered data, 80% must pass the 2 mm and 2% criteria, and the point dose measurement must be within 2% of the calculated dose. All low dose region/critical structure point dose measurements were evaluated on a patient by patient basis. The criteria we recommend can be useful for the routine evaluation of treatment plans for tomotherapy systems.
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

Biosurfactant 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

Fungus-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

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

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

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

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

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.
Assimilation of Polysaccharides and Glucose by Major Bacterial Groups in the Delaware Estuary
Authors: Elifantz Hila , Malmstrom Rex R. , Cottrell Matthew T. , Kirchman David L.
Published: December 2005

The contribution of major bacterial groups to the assimilation of extracellular polymeric substances (EPS) and glucose in the Delaware Estuary was assessed using microautoradiography and fluorescence in situ hybridization. Bacterial groups contributed to EPS and glucose assimilation in part according to their distribution in the estuary. Abundance of the phylogenetic groups explained 35% and 55% of the variation in EPS and glucose assimilation, respectively.
Actinobacteria
contributed 70% to glucose assimilation in freshwater, while
Alphaproteobacteria
assimilated 60% of this compound in saline water. In contrast, various bacterial groups dominated the assimilation of EPS.
Actinobacteria
and
Betaproteobacteria
contributed the most in the freshwater section, whereas
Cytophaga
-like bacteria and
Alpha
- and
Gammaproteobacteria
participated in EPS assimilation in the lower part of the estuary. In addition, we examined the fraction of bacteria in each group that assimilated glucose or EPS. Overall, the fraction of bacteria in all groups that assimilated glucose was higher than the fraction that assimilated EPS (15 to 30% versus 5 to 20%, respectively). We found no correlation between the relative abundance of a group in the estuary and the fraction of bacteria actively assimilating glucose or EPS; the more active groups were often less abundant. Our results imply that the bacterial community in the Delaware Estuary is not controlled solely by “bottom-up” factors such as dissolved organic matter.
Detection and Isolation of Ultrasmall Microorganisms from a 120,000-Year-Old Greenland Glacier Ice Core
Authors: Miteva Vanya I. , Brenchley Jean E.
Published: December 2005

The abundant microbial population in a 3,043-m-deep Greenland glacier ice core was dominated by ultrasmall cells (<0.1 μm
3
) that may represent intrinsically small organisms or starved, minute forms of normal-sized microbes. In order to examine their diversity and obtain isolates, we enriched for ultrasmall psychrophiles by filtering melted ice through filters with different pore sizes, inoculating anaerobic low-nutrient liquid media, and performing successive rounds of filtrations and recultivations at 5°C. Melted ice filtrates, cultures, and isolates were analyzed by scanning electron microscopy, flow cytometry, cultivation, and molecular methods. The results confirmed that numerous cells passed through 0.4-μm, 0.2-μm, and even 0.1-μm filters. Interestingly, filtration increased cell culturability from the melted ice, yielding many isolates related to high-G+C gram-positive bacteria. Comparisons between parallel filtered and nonfiltered cultures showed that (i) the proportion of 0.2-μm-filterable cells was higher in the filtered cultures after short incubations but this difference diminished after several months, (ii) more isolates were obtained from filtered (1,290 isolates) than from nonfiltered (447 isolates) cultures, and (iii) the filtration and liquid medium cultivation increased isolate diversity (
Proteobacteria
;
Cytophaga-Flavobacteria-Bacteroides
; high-G+C gram-positive; and spore-forming, low-G+C gram-positive bacteria). Many isolates maintained their small cell sizes after recultivation and were phylogenetically novel or related to other ultramicrobacteria. Our filtration-cultivation procedure, combined with long incubations, enriched for novel ultrasmall-cell isolates, which is useful for studies of their metabolic properties and mechanisms for long-term survival under extreme conditions.
Microbial Diversity in Coastal Subsurface Sediments: a Cultivation Approach Using Various Electron Acceptors and Substrate Gradients
Authors: Köpke Beate , Wilms Reinhard , Engelen Bert , Cypionka Heribert , Sass Henrik
Published: December 2005

Microbial communities in coastal subsurface sediments are scarcely investigated and have escaped attention so far. But since they are likely to play an important role in biogeochemical cycles, knowledge of their composition and ecological adaptations is important. Microbial communities in tidal sediments were investigated along the geochemical gradients from the surface down to a depth of 5.5 m. Most-probable-number (MPN) series were prepared with a variety of different carbon substrates, each at a low concentration, in combination with different electron acceptors such as iron and manganese oxides. These achieved remarkably high cultivation efficiencies (up to 23% of the total cell counts) along the upper 200 cm. In the deeper sediment layers, MPN counts dropped significantly. Parallel to the liquid enrichment cultures in the MPN series, gradient cultures with embedded sediment subcores were prepared as an additional enrichment approach. In total, 112 pure cultures were isolated; they could be grouped into 53 different operational taxonomic units (OTU). The isolates belonged to the
Proteobacteria
, “
Bacteroidetes
,” “
Fusobacteria
,”
Actinobacteria
, and “
Firmicutes
.” Each cultivation approach yielded a specific set of isolates that in general were restricted to this single isolation procedure. Analysis of the enrichment cultures by PCR and denaturing gradient gel electrophoresis revealed an even higher diversity in the primary enrichments that was only partially reflected by the culture collection. The majority of the isolates grew well under anoxic conditions, by fermentation, or by anaerobic respiration with nitrate, sulfate, ferrihydrite, or manganese oxides as electron acceptors.
Characterization and Functional Analysis of the
MAL
and
MPH
Loci for Maltose Utilization in Some Ale and Lager Yeast Strains
Authors: Vidgren Virve , Ruohonen Laura , Londesborough John
Published: December 2005

Maltose and maltotriose are the major sugars in brewer's wort. Brewer's yeasts contain multiple genes for maltose transporters. It is not known which of these express functional transporters. We correlated maltose transport kinetics with the genotypes of some ale and lager yeasts. Maltose transport by two ale strains was strongly inhibited by other α-glucosides, suggesting the use of broad substrate specificity transporters, such as Agt1p. Maltose transport by three lager strains was weakly inhibited by other α-glucosides, suggesting the use of narrow substrate specificity transporters. Hybridization studies showed that all five strains contained complete
MAL1
,
MAL2
,
MAL3
, and
MAL4
loci, except for one ale strain, which lacked a
MAL2
locus. All five strains also contained both
AGT1
(coding a broad specificity α-glucoside transporter) and
MAL11
alleles.
MPH
genes (maltose permease homologues) were present in the lager but not in the ale strains. During growth on maltose, the lager strains expressed
AGT1
at low levels and
MALx1
genes at high levels, whereas the ale strains expressed
AGT1
at high levels and
MALx1
genes at low levels.
MPHx
expression was negligible in all strains. The
AGT1
sequences from the ale strains encoded full-length (616 amino acid) polypeptides, but those from both sequenced lager strains encoded truncated (394 amino acid) polypeptides that are unlikely to be functional transporters. Thus, despite the apparently similar genotypes of these ale and lager strains revealed by hybridization, maltose is predominantly carried by
AGT1
-encoded transporters in the ale strains and by
MALx1
-encoded transporters in the lager strains.
Microbiological Study of Lactic Acid Fermentation of Caper Berries by Molecular and Culture-Dependent Methods
Authors: Pérez Pulido Rubén , Ben Omar Nabil , Abriouel Hikmate , Lucas López Rosario , Martínez Cañamero Magdalena , Gálvez Antonio
Published: December 2005

Fermentation of capers (the fruits of
Capparis
sp.) was studied by molecular and culture-independent methods. A lactic acid fermentation occurred following immersion of caper berries in water, resulting in fast acidification and development of the organoleptic properties typical of this fermented food. A collection of 133 isolates obtained at different times of fermentation was reduced to 75 after randomly amplified polymorphic DNA (RAPD)-PCR analysis. Isolates were identified by PCR or 16S rRNA gene sequencing as
Lactobacillus plantarum
(37 isolates),
Lactobacillus paraplantarum
(1 isolate),
Lactobacillus pentosus
(5 isolates),
Lactobacillus brevis
(9 isolates),
Lactobacillus fermentum
(6 isolates),
Pediococcus pentosaceus
(14 isolates),
Pediococcus acidilactici
(1 isolate), and
Enterococcus faecium
(2 isolates). Cluster analysis of RAPD-PCR patterns revealed a high degree of diversity among lactobacilli (with four major groups and five subgroups), while pediococci clustered in two closely related groups. A culture-independent analysis of fermentation samples by temporal temperature gradient electrophoresis (TTGE) also indicated that
L. plantarum
is the predominant species in this fermentation, in agreement with culture-dependent results. The distribution of
L. brevis
and
L. fermentum
in samples was also determined by TTGE, but identification of
Pediococcus
at the species level was not possible. TTGE also allowed a more precise estimation of the distribution of
E. faecium
, and the detection of
Enterococcus casseliflavus
(which was not revealed by the culture-dependent analysis). Results from this study indicate that complementary data from molecular and culture-dependent analysis provide a more accurate determination of the microbial community dynamics during caper fermentation.
Characterization of a Thermoacidophilic
l
-Arabinose Isomerase from
Alicyclobacillus acidocaldarius
: Role of Lys-269 in pH Optimum
Authors: Lee Sang-Jae , Lee Dong-Woo , Choe Eun-Ah , Hong Young-Ho , Kim Seong-Bo , Kim Byoung-Chan , Pyun Yu-Ryang
Published: December 2005

The
araA
gene encoding
l
-arabinose isomerase (AI) from the thermoacidophilic bacterium
Alicyclobacillus acidocaldarius
was cloned, sequenced, and expressed in
Escherichia coli
. Analysis of the sequence revealed that the open reading frame of the
araA
gene consists of 1,491 bp that encodes a protein of 497 amino acid residues with a calculated molecular mass of 56,043 Da. Comparison of the deduced amino acid sequence of
A. acidocaldarius
AI (AAAI) with other AIs demonstrated that AAAI has 97% and 66% identities (99% and 83% similarities) to
Geobacillus stearothermophilus
AI (GSAI) and
Bacillus halodurans
AI (BHAI), respectively. The recombinant AAAI was purified to homogeneity by heat treatment, ion-exchange chromatography, and gel filtration. The purified enzyme showed maximal activity at pH 6.0 to 6.5 and 65°C under the assay conditions used, and it required divalent cations such as Mn
2+
, Co
2+
, and Mg
2+
for its activity. The isoelectric point (pI) of the enzyme was about 5.0 (calculated pI of 5.5). The apparent

K
m

values of the recombinant AAAI for
l
-arabinose and
d
-galactose were 48.0 mM (
V
max
, 35.5 U/mg) and 129 mM (
V
max
, 7.5 U/mg), respectively, at pH 6 and 65°C. Interestingly, although the biochemical properties of AAAI are quite similar to those of GSAI and BHAI, the three AIs from
A. acidocaldarius
(pH 6),
G. stearothermophilus
(pH 7), and
B. halodurans
(pH 8) exhibited different pH activity profiles. Based on alignment of the amino acid sequences of these homologous AIs, we propose that the Lys-269 residue of AAAI may be responsible for the ability of the enzyme to act at low pH. To verify the role of Lys-269, we prepared the mutants AAAI-K269E and BHAI-E268K by site-directed mutagenesis and compared their kinetic parameters with those of wild-type AIs at various pHs. The pH optima of both AAAI-K269E and BHAI-E268K were rendered by 1.0 units (pH 6 to 7 and 8 to 7, respectively) compared to the wild-type enzymes. In addition, the catalytic efficiency (
k
cat
/

K
m

) of each mutant at different pHs was significantly affected by an increase or decrease in
V
max
. From these results, we propose that the position corresponding to the Lys-269 residue of AAAI could play an important role in the determination of the pH optima of homologous AIs.