bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bacterial Reductive Dissolution of Crystalline Fe(III) Oxide in Continuous-Flow Column Reactors
Authors: Roden Eric E. , Urrutia Matilde M. , Mann Carroll J. 
Published: July 2002

ABSTRACT
Bacterial reductive dissolution of synthetic crystalline Fe(III) oxide-coated sand was studied in continuous-flow column reactors in comparison with parallel batch cultures. The cumulative amount of aqueous Fe(II) exported from the columns over a 6-month incubation period corresponded to (95.0 ± 3.7)% (n = 3) of their original Fe(III) content. Wet-chemical analysis revealed that only (6.5 ± 3.2)% of the initial Fe(III) content remained in the columns at the end of the experiment. The near-quantitative removal of Fe was visibly evidenced by extensive bleaching of color from the sand in the columns. In contrast to the column reactors, Fe(II) production quickly reached an asymptote in batch cultures, and only (13.0 ± 2.2)% (n = 3) of the Fe(III) oxide content was reduced. Sustained bacterial-cell growth occurred in the column reactors, leading to the production and export of a quantity of cells 100-fold greater than that added during inoculation. Indirect estimates of cell growth, based on the quantity of Fe(III) reduced, suggest that only an approximate doubling of initial cell abundance was likely to have occurred in the batch cultures. Our results indicate that removal of biogenic Fe(II) via aqueous-phase transport in the column reactors decreased the passivating influence of surface-bound Fe(II) on oxide reduction activity, thereby allowing a dramatic increase in the extent of Fe(III) oxide reduction and associated bacterial growth. These findings have important implications for understanding the fate of organic and inorganic contaminants whose geochemical behavior is linked to Fe(III) oxide reduction.
Prokaryotic Diversity in
Zostera noltii
-Colonized Marine Sediments
Authors: Cifuentes Ana , Antón Josefa , Benlloch Susana , Donnelly Andrew , Herbert Rodney A. , Rodríguez-Valera Francisco 
Published: July 2002

ABSTRACT

The diversity of microorganisms present in a sediment colonized by the phanerogam
Zostera noltii
has been analyzed. Microbial DNA was extracted and used for constructing two 16S rDNA clone libraries for
Bacteria
and
Archaea
. Bacterial diversity was very high in these samples, since 57 different sequences were found among the 60 clones analyzed. Eight major lineages of the Domain
Bacteria
were represented in the library. The most frequently retrieved bacterial group (36% of the clones) was δ-
Proteobacteria
related to sulfate-reducing bacteria. The second most abundant group (27%) was γ-
Proteobacteria
, including five clones closely related to S-oxidizing endosymbionts. The archaeal clone library included members of
Crenarchaeota
and
Euryarchaeota
, with nine different sequences among the 15 analyzed clones, indicating less diversity when compared to the
Bacteria
organisms. None of these sequences was closely related to cultured
Archaea
organisms.
Viral Density and Virus-to-Bacterium Ratio in Deep-Sea Sediments of the Eastern Mediterranean
Authors: Danovaro Roberto , Serresi Michela 
Published: July 2002

ABSTRACT

Viruses are now recognized as a key component in pelagic systems, but their role in marine sediment has yet to be assessed. In this study bacterial and viral densities were determined at nine deep-sea stations selected from three main sites (i.e., the Sporades Basin, the Cretan Sea, and the Ierapetra Trench at depths of 1,232, 1,840, and 4,235 m, respectively) of the Eastern Mediterranean. The three areas were characterized by different phytopigment and biopolymeric carbon concentrations and by changes in the protein and carbohydrate pools. A gradient of increasing trophic conditions was observed from the Sporades Basin (North Aegean) to the Ierapetra Trench (South Aegean). Viral densities (ranging from 1 × 10
9
to 2 × 10
9
viruses ml of sediment
−1
) were significantly correlated to bacterial densities (
n
= 9,
r
2
= 0.647) and reached values up to 3 orders of magnitude higher than those generally reported for the water column. However, the virus-to-bacterium density ratio in deep-sea sediments was about 1 order of magnitude lower (range of 2 to 5, with a modal value of 2.6) than in pelagic environments. Virus density decreased vertically with depth in sediment cores at all stations and was below detection limits at the 10-cm depth of the abyssal sediments of the Ierapetra Trench. Virus density in the sediment apparently reflected a gradient of particle fluxes and trophic conditions, displaying the highest values in the Sporades Basin. The low virus-to-bacterium ratios and their inverse relationship with station depth suggest that the role played by viruses in controlling deep-sea benthic bacterial assemblages and biogeochemical cycles is less relevant than in pelagic systems.
Horizontal Heterogeneity of Denitrifying Bacterial Communities in Marine Sediments by Terminal Restriction Fragment Length Polymorphism Analysis
Authors: Scala David J. , Kerkhof Lee J. 
Published: July 2002

ABSTRACT

Although it is widely believed that horizontal patchiness exists in microbial sediment communities, determining the extent of variability or the particular members of the bacterial community which account for the observed differences among sites at various scales has not been routinely demonstrated. In this study, horizontal heterogeneity was examined in time and space for denitrifying bacteria in continental shelf sediments off Tuckerton, N.J., at the Rutgers University Long-Term Ecosystem Observatory (LEO-15). Characterization of the denitrifying community was done using PCR amplification of the nitrous oxide reductase (
nosZ
) gene combined with terminal restriction fragment length polymorphism analysis. Spatial scales from centimeters to kilometers were examined, while temporal variation was assayed over the course of 1995 to 1996. Sorenson's indices (pairwise similarity values) were calculated to permit comparison between samples. The similarities of benthic denitrifiers ranged from 0.80 to 0.85 for centimeter scale comparisons, from 0.52 to 0.79 for meter level comparisons, and from 0.23 to 0.53 for kilometer scale comparisons. Sorenson's indices for temporal comparisons varied from 0.12 to 0.74. A cluster analysis of the similarity values indicated that the composition of the denitrifier assemblages varied most significantly at the kilometer scale and between seasons at individual stations. Specific
nosZ
genes were identified which varied at centimeter, meter, or kilometer scales and may be associated with variability in meio- or macrofaunal abundance (centimeter scale), bottom topography (meter scale), or sediment characteristics (kilometer scale).
Parallel Processing of Substrate Correlates with Greater Functional Stability in Methanogenic Bioreactor Communities Perturbed by Glucose
Authors: Hashsham Syed A. , Fernandez Ana S. , Dollhopf Sherry L. , Dazzo Frank B. , Hickey Robert F. , Tiedje James M. , Criddle Craig S. 
Published: July 2002

ABSTRACT
Parallel processing is more stable than serial processing in many areas that employ interconnected activities. This hypothesis was tested for microbial community function using two quadruplicate sets of methanogenic communities, each set having substantially different populations. The two communities were maintained at a mean cell residence time of 16 days and a mean glucose loading rate of 0.34 g/liter-day in variable-volume reactors. To test stability to perturbation, they were subjected to an instantaneous glucose pulse that resulted in a 6.8-g/liter reactor concentration. The pattern of accumulated products in response to the perturbation was analyzed for various measures of functional stability, including resistance, resilience, and reactivity for each product. A new stability parameter, “moment of amplification envelope,” was used to compare the soluble compound stability. These parameters indicated that the communities with predominantly parallel substrate processing were functionally more stable in response to the perturbation than the communities with predominantly serial substrate processing. The data also indicated that there was good replication of function under perturbed conditions; the degrees of replication were 0.79 and 0.83 for the two test communities.
Molecular Studies on the Ecology of
Listeria monocytogenes
in the Smoked Fish Processing Industry
Authors: Norton Dawn M. , McCamey Meghan A. , Gall Kenneth L. , Scarlett Janet M. , Boor Kathryn J. , Wiedmann Martin 
Published: July 2002

ABSTRACT

We have applied molecular approaches, including PCR-based detection strategies and DNA fingerprinting methods, to study the ecology of
Listeria monocytogenes
in food processing environments. A total of 531 samples, including raw fish, fish during the cold-smoking process, finished product, and environmental samples, were collected from three smoked fish processing facilities during five visits to each facility. A total of 95 (17.9%) of the samples tested positive for
L. monocytogenes
using a commercial PCR system (BAX for Screening/
Listeria monocytogenes
), including 57 (27.7%) environmental samples (
n
= 206), 8 (7.8%) raw material samples (
n
= 102), 23 (18.1%) samples from fish in various stages of processing(
n
= 127), and 7 (7.3%) finished product samples (
n
= 96).
L. monocytogenes
was isolated from 85 samples (16.0%) using culture methods. Used in conjunction with a 48-h enrichment in
Listeria
Enrichment Broth, the PCR system had a sensitivity of 91.8% and a specificity of 96.2%. To track the origin and spread of
L. monocytogenes
, isolates were fingerprinted by automated ribotyping. Fifteen different ribotypes were identified among 85 isolates tested. Ribotyping data established possible contamination patterns, implicating raw materials and the processing environment as potential sources of finished product contamination. Analysis of the distribution of ribotypes revealed that each processing facility had a unique contamination pattern and that specific ribotypes persisted in the environments of two facilities over time (
P
≤ 0.0006). We conclude that application of molecular approaches can provide critical information on the ecology of different
L. monocytogenes
strains in food processing environments. This information can be used to develop practical recommendations for improved control of this important food-borne pathogen in the food industry.
Percent G+C Profiling Accurately Reveals Diet-Related Differences in the Gastrointestinal Microbial Community of Broiler Chickens
Authors: Apajalahti Juha H. A. , Kettunen Anu , Bedford Michael R. , Holben William E. 
Published: July 2002

ABSTRACT

Broiler chickens from eight commercial farms in Southern Finland were analyzed for the structure of their gastrointestinal microbial community by a nonselective DNA-based method, percent G+C-based profiling. The bacteriological impact of the feed source and in-farm whole-wheat amendment of the diet was assessed by percent G+C profiling. Also, a phylogenetic 16S rRNA gene (rDNA)-based study was carried out to aid in interpretation of the percent G+C profiles. This survey showed that most of the 16S rDNA sequences found could not be assigned to any previously known bacterial genus or they represented an unknown species of one of the taxonomically heterogeneous genera, such as
Ruminococcus
or
Clostridium
. The data from bacterial community profiling were analyzed by
t
-test, multiple linear regression, and principal-component statistical approaches. The percent G+C profiling method with appropriate statistical analyses detected microbial community differences smaller than 10% within each 5% increment of the percent G+C profiles. Diet turned out to be the strongest determinant of the cecal bacterial community structure. Both the source of feed and local feed amendment changed the bacteriological profile significantly, whereas profiles of individual farms with identical feed regimens hardly differed from each other. This suggests that the management of typical Finnish farms is relatively uniform or that hygiene on the farm, in fact, has little impact on the structure of the cecal bacterial community. Therefore, feed compounders should have a significant role in the modulation of gut microflora and consequently in prevention of gastrointestinal disorders in farm animals.
Biotransformations of Paralytic Shellfish Toxins by Bacteria Isolated from Bivalve Molluscs
Authors: Smith Elizabeth A. , Grant Faye , Ferguson Carolyn M. J. , Gallacher Susan 
Published: July 2002

ABSTRACT
Due to the possibility that bacteria could be involved in the clearance of paralytic shellfish toxins (PST) from bivalve molluscs, investigations into which, if any, bacteria were able to grow at the expense of PST focused on several common shellfish species. These species were blue mussels, oysters, razor fish, cockles, and queen and king scallops. Bacteria associated with these shellfish were isolated on marine agar 2216 and characterized by their carbon utilization profiles (BIOLOG). Selected isolates from groups demonstrating 90% similarity were screened for their ability to metabolize a range of PST (gonyautoxins 1 and 4 [GTX 1/4], GTX 2/3, GTX 5, saxitoxin, and neosaxitoxin) using a novel screening method and confirming its results by high-performance liquid chromatography. Results suggest that molluscan bacteria have different capacities to utilize and transform PST analogues. For example, isolates M12 and R65 were able to reductively transform GTX 1/4 with concomitant production of GTX 2/3, while isolate Q5 apparently degraded GTX 1/4 without the appearance of other GTXs. Other observed possible mechanisms of PST transformations include decarbamoylation by isolate M12 and sulfation of GTXs by isolates Q5, R65, M12, and C3. These findings raise questions as to the possible role of bacteria resident in the shellfish food transport system. Some researchers have suggested that the microflora play a role in supplying nutritional requirements of the host. This study demonstrates that bacteria may also be involved in PST transformation and elimination in molluscan species.
Application of the 5′ Fluorogenic Exonuclease Assay (TaqMan) for Quantitative Ribosomal DNA and rRNA Analysis in Sediments
Authors: Stults Jennie R. , Snoeyenbos-West Oona , Methe Barbara , Lovley Derek R. , Chandler Darrell P. 
Published: July 2002

ABSTRACT

In this study, we report on the development of quantitative PCR and reverse transcriptase PCR assays for the 16S rRNA of
Geobacter
spp. and identify key issues related to fluorogenic reporter systems for nucleic acid analyses of sediments. The lower detection limit of each assay was 5 to 50 fg of genomic DNA or ≤2 pg of 16S rRNA. TaqMan PCR spectral traces from uncontaminated, amended aquifer sediments were significantly lower (
P
< 0.0002) than traces for the external standard curve. We also observed a similar, significant decrease in mean quencher emissions for undiluted extracts relative to those for diluted extracts (
P
< 0.0001). If PCR enumerations were based solely upon the undiluted sample eluant, the TaqMan assay generated an inaccurate result even though the threshold cycle (
C

t

) measurements were precise and reproducible in the sediment extracts. Assay accuracy was significantly improved by employing a system of replicate dilutions and replicate analyses for both DNA and rRNA quantitation. Our results clearly demonstrate that fluorescence quenching and autofluorescence can significantly affect TaqMan PCR enumeration accuracy, with subsequent implications for the design and implementation of TaqMan PCR to sediments and related environmental samples.
Bile Salt Hydrolase Activity and Resistance to Toxicity of Conjugated Bile Salts Are Unrelated Properties in Lactobacilli
Authors: Moser Scott A. , Savage Dwayne C. 
Published: July 2002

ABSTRACT

Bacteria of numerous species isolated from the human gastrointestinal tract express bile salt hydrolase (BSH) activity. How this activity contributes to functions of the microorganisms in the gastrointestinal tract is not known. We tested the hypothesis that a BSH protects the cells that produce it from the toxicity of conjugated bile salts. Forty-nine strains of numerous
Lactobacillus
spp. were assayed to determine their capacities to express BSH activities (taurodeoxycholic acid [TDCA] hydrolase and taurocholic acid [TCA] hydrolase activities) and their capacities to resist the toxicity of a conjugated bile acid (TDCA). Thirty of these strains had been isolated from the human intestine, 15 had been recovered from dairy products, and 4 had originated from other sources. Twenty-six of the strains expressed both TDCA hydrolase and TCA hydrolase activities. One strain that expressed TDCA hydrolase activity did not express TCA hydrolase activity. Conversely, in one strain for which the assay for TDCA hydrolase activity gave a negative result there was evidence of TCA hydrolase activity. Twenty-five of the strains were found to resist the toxicity of TDCA. Fourteen of these strains were of human origin, nine were from dairy products, and two were from other sources. Of the 26 strains expressing both TDCA hydrolase and TCA hydrolase activities, 15 were resistant to TDCA toxicity, 6 were susceptible, and 5 gave inconclusive results. Of the 17 strains that gave negative results for either of the enzymes, 7 were resistant to the toxicity, 9 were susceptible, and 1 gave inconclusive results. These findings do not support the hypothesis tested. They suggest, however, that BSH activity is important at some level for lactobacillus colonization of the human intestine.
Metabolic Engineering of the Morphology of
Aspergillus oryzae
by Altering Chitin Synthesis
Authors: Müller Christian , McIntyre Mhairi , Hansen Kim , Nielsen Jens 
Published: July 2002

ABSTRACT

Morphology and α-amylase production during submerged cultivation were examined in a wild-type strain (A1560) and in strains of
Aspergillus oryzae
in which chitin synthase B (
chsB
) and chitin synthesis myosin A (
csmA
) have been disrupted (ChsB/G and CM101). In a flowthrough cell, the growth of submerged hyphal elements was studied online, making it possible to examine the growth kinetics of the three strains. The average tip extension rates of the CM101 and ChsB/G strains were 25 and 88% lower, respectively, than that of the wild type. The branching intensity in the CM101 strain was 25% lower than that in the wild type, whereas that in the ChsB/G strain was 188% higher. During batch cultivation, inseparable clumps were formed in the wild-type strain, while no or fewer large inseparable clumps existed in the cultivations of the ChsB/G and CM101 strains. The α-amylase productivity was not significantly different in the three strains. A strain in which the transcription of
chsB
could be controlled by the nitrogen source-regulated promoter
niiA
(NiiA1) was examined during chemostat cultivation, and it was found that the branching intensity could be regulated by regulating the promoter, signifying an important role for
chsB
in branching. However, the pattern of branching responded very slowly to the change in transcription, and increased branching did not affect α-amylase productivity. α-Amylase residing in the cell wall was stained by immunofluorescence, and the relationship between tip number and enzyme secretion is discussed.
Flow Cytometric Microsphere-Based Immunoassay: Analysis of Secreted Cytokines in Whole-Blood Samples from Asthmatics
Authors: Camilla Christophe , Mély Laurent , Magnan Antoine , Casano Brice , Prato Sabine , Debono Stephane , Montero Felix , Defoort Jean-Philippe , Martin Marie , Fert Vincent 
Published: July 2002

ABSTRACT

The ability of flow cytometry to resolve multiple parameters was used in a microsphere-based flow cytometric assay for the simultaneous determination of several cytokines in a sample. The flow cytometer microsphere-based assay (FMBA) for cytokines consists of reagents and dedicated software, specifically designed for the quantitative determination of cytokines. We have made several improvements in the multiplex assay: (i) dedicated software specific for the quantitative multiplex assay that processes data automatically, (ii) a stored master calibration curve with a two-point recalibration to adjust the stored curve periodically, and (iii) an internal standard to normalize the detection step in each sample. Overall analytical performance, including sensitivity, reproducibility, and dynamic range, was investigated for interleukin-4 (IL-4), IL-6, IL-10, IL-12, gamma interferon (IFN-γ), and tumor necrosis factor alpha. These assays were found to be reproducible and accurate, with a sensitivity in the picograms-per-milliliter range. Results obtained with FMBA correlate well with commercial enzyme-linked immunosorbent assay data (
r
> 0.98) for all cytokines assayed. This multiplex assay was applied to the determination of cytokine profiles in whole blood from atopic and nonatopic patients. Our results show that atopic subjects' blood produces more IL-4 (
P
= 0.003) and less IFN-γ (
P
= 0.04) than the blood of nonatopic subjects. However, atopic asthmatic subjects' blood produces significantly more IFN-γ than that of atopic nonasthmatic subjects (
P
= 0.03). The results obtained indicate that the FMBA technology constitutes a powerful system for the quantitative, simultaneous determination of secreted cytokines in immune diseases.
Dengue Virus Replicative Intermediate RNA Detection by Reverse Transcription-PCR
Authors: Vaughan Gilberto , Olivera Hiram , Santos-Argumedo Leopoldo , Landa Abraham , Briseño Baltasar , Escobar-Gutiérrez Alejandro 
Published: July 2002

ABSTRACT
Dengue virus replication involves synthesis of a replicative intermediate RNA (RI-RNA), whose presence reveals an actual infection. We report on a simple and rapid reverse transcription-PCR for the detection of viral RI-RNA in infected cells. The product is demonstrated at 20 min postinfection. This method is useful for the study of virus-cell tropism.
Identification of Group B Streptococcal Sip Protein, Which Elicits Cross-Protective Immunity
Authors: Brodeur Bernard R. , Boyer Martine , Charlebois Isabelle , Hamel Josée , Couture France , Rioux Clément R. , Martin Denis 
Published: July 2002

ABSTRACT

A protein of group B streptococci (GBS), named Sip for surface immunogenic protein, which is distinct from previously described surface proteins, was identified after immunological screening of a genomic library. Immunoblots using a Sip-specific monoclonal antibody indicated that a protein band with an approximate molecular mass of 53 kDa which did not vary in size was present in every GBS strain tested. Representatives of all nine GBS serotypes were included in the panel of strains. Cloning and sequencing of the
sip
gene revealed an open reading frame of 1,305 nucleotides coding for a polypeptide of 434 amino acid residues, with a calculated pI of 6.84 and molecular mass of 45.5 kDa. Comparison of the nucleotide sequences from six different strains confirmed with 98% identity that the
sip
gene is highly conserved among GBS isolates. N-terminal amino acid sequencing also indicated the presence of a 25-amino-acid signal peptide which is cleaved in the mature protein. More importantly, immunization with the recombinant Sip protein efficiently protected CD-1 mice against deadly challenges with six GBS strains of serotypes Ia/c, Ib, II/R, III, V, and VI. The data presented in this study suggest that this highly conserved protein induces cross-protective immunity against GBS infections and emphasize its potential as a universal vaccine candidate.