bluuebunny/crossref_metadata_2025_split huggingface dataset:
WATERSHED AND LAKE WATER QUALITY ASSESSMENT: AN INTEGRATED MODELING APPROACH1
Authors: Mankin K R. , Koelliker J. K. , Kalita P. K. 
Published: June 2007

ABSTRACTWatershed planning groups and action agencies seek to understand how lake water quality responds to changes in watershed management. This study developed and demonstrated the applicability of an integrated modeling approach for providing this information. An integrated model linking watershed conditions to water‐quality of the receiving lake incorporated the following components: (1) an event‐based AGNPS model to estimate watershed pollutant losses; (2) annualization of AGNPS results to produce annual lake pollutant loadings; (3) a base flow separation package, SAM, to estimate base flow; (4) estimates of nutrients in base flow and point sources; and (5) linkage of watershed loadings directly to EUTROMOD lake water quality algorithms. Results are presented for Melvern Lake, a 28‐km2 multipurpose reservoir with a 900‐km2 agricultural watershed in east central Kansas. Reasonable estimates of current lake quality were attained using an average phosphorus availability factor of 31 percent to calibrate model results to measured in‐lake phosphorus. Comparison of a range of possible scenarios, including all cropland changed to no‐till (best case) and all CRP and good‐condition grasslands changed to cropland (worst case), indicated only a (4 percent change for in‐lake phosphorus and a (2 percent change for chlorophyll a. These results indicated that this watershed is not sensitive to projected changes in land use and management.
WALNUT CREEK WATERSHED MONITORING PROJECT, IOWA MONITORING WATER QUALITY IN RESPONSE TO PRAIRIE RESTORATION1
Authors: Schilling Keith E. , Thompson Carol A. 
Published: June 2007

ABSTRACT: Land use and surface water data for nitrogen and pesticides (1995 to 1997) are reported for the Walnut Creek Watershed Monitoring Project, Jasper County Iowa. The Walnut Creek project was established in 1995 as a nonpoint source monitoring program in relation to watershed habitat restoration and agricultural management changes implemented at the Neal Smith National Wildlife Refuge by the U.S. Fish and Wildlife Service. The monitoring project utilizes a paired‐watershed approach (Walnut and Squaw creeks) as well as upstream/downstream comparisons on Walnut for analysis and tracking of trends. From 1992 to 1997, 13.4 percent of the watershed was converted from row crop to native prairie in the Walnut Creek watershed. Including another 6 percent of watershed farmed on a cash‐rent basis, land use changes have been implemented on 19.4 percent of the watershed by the USFWS. Nitrogen and pesticide applications were reduced an estimated 18 percent and 28 percent in the watershed from land use changes.Atrazine was detected most often in surface water with frequencies of detection ranging from 76–86 percent. No significant differences were noted in atrazine concentrations between Walnut and Squaw Creek. Nitrate‐N concentrations measured in both watersheds were similar; both basins showed a similar pattern of detection and an overall reduction in nitrate‐N concentrations from upstream to downstream monitoring sites. Water quality improvements are suggested by nitrate‐N and chloride ratios less than one in the Walnut Creek watershed and low nitrate‐N concentrations measured in the subbasin of Walnut Creek containing the greatest amount of land use changes. Atrazine and nitrate‐N concentrations from the lower portion of the Walnut Creek watershed (including the prairie restoration area) may be decreasing in relation to the upstream untreated component of the watershed. The frequencies of pesticide detections and mean nitrate‐N concentrations appear related to the percentage of row crop in the basins and subbasins.Although some results are encouraging, definitive water quality improvements have not been observed during the first three years of monitoring. Possible reasons include: (1) more time is needed to adequately detect changes; (2) the size of the watershed is too large to detect improvements; (3) land use changes are not located in the area of the watershed where they would have greatest effect; or (4) water quality improvements have occurred but have been missed by the project monitoring design. Longer‐term monitoring will allow better evaluation of the impact of restoration activities on water quality.
DISCHARGE AND SUSPENDED SEDIMENT PATTERNS OF AN INTERMITTENT COLD DESERT STREAM1
Authors: Ellison Christopher A. , Skinner Quentin D. , Ready Katta J. 
Published: June 2007

ABSTRACT:Sage Creek in south‐central Wyoming is listed as impaired by the U.S. Environmental Protection Agency (USEPA) due to its sediment contribution to the North Platte River. Despite the magnitude of sediment impacts on streams, little research has been conducted to characterize patterns of sediment transport or to model suspended sediment concentration in many arid western U.S. streams. This study examined the relationship between stream discharge and suspended sediment concentration near the Sage Creek and North Platte River confluence from 1998 through 2003. The objectives were to determine patterns of stream discharge and suspended sediment concentration, produce a sediment prediction model, and compare sediment concentrations for the six‐year period. Stream discharge and suspended sediment transport responded rapidly to convective storms and spring runoff events. During the study period, events exceeding 0.23 m3/s accounted for 92 percent of the sediment load, which is believed to originate from erodible headwater uplands. Further analysis of these data indicates that time series modeling is superior to simple linear regression in predicting sediment concentration. Significant increases in suspended sediment concentration occurred in all years except 2003. This analysis suggests that a six‐year monitoring record was insufficient to factor out impacts from climate, geology, and historical sediment storage.
Identification and Isolation of a
Castellaniella
Species Important during Biostimulation of an Acidic Nitrate- and Uranium-Contaminated Aquifer
Authors: Spain Anne M. , Peacock Aaron D. , Istok Jonathan D. , Elshahed Mostafa S. , Najar Fares Z. , Roe Bruce A. , White David C. , Krumholz Lee R. 
Published: June 2007

ABSTRACT

Immobilization of uranium in groundwater can be achieved through microbial reduction of U(VI) to U(IV) upon electron donor addition. Microbial community structure was analyzed in ethanol-biostimulated and control sediments from a high-nitrate (>130 mM), low-pH, uranium-contaminated site in Oak Ridge, TN. Analysis of small subunit (SSU) rRNA gene clone libraries and polar lipid fatty acids from sediments revealed that biostimulation resulted in a general decrease in bacterial diversity. Specifically, biostimulation resulted in an increase in the proportion of
Betaproteobacteria
(10% of total clones in the control sediment versus 50 and 79% in biostimulated sediments) and a decrease in the proportion of
Gammaproteobacteria
and
Acidobacteria
. Clone libraries derived from dissimilatory nitrite reductase genes (
nirK
and
nirS
) were also dominated by clones related to
Betaproteobacteria
(98% and 85% of total
nirK
and
nirS
clones, respectively). Within the
nirK
libraries, one clone sequence made up 59 and 76% of sequences from biostimulated sediments but only made up 10% of the control
nirK
library. Phylogenetic analysis of SSU rRNA and
nirK
gene sequences from denitrifying pure cultures isolated from the site indicate that all belong to a
Castellaniella
species; nearly identical sequences also constituted the majority of biostimulated SSU rRNA and
nirK
clone libraries. Thus, by combining culture-independent with culture-dependent techniques, we were able to link SSU rRNA clone library information with
nirK
sequence data and conclude that a potentially novel
Castellaniella
species is important for in situ nitrate removal at this site.
Responses of Wild-Type and Resistant Strains of the Hyperthermophilic BacteriumThermotoga maritimato Chloramphenicol Challenge
Authors: Montero Clemente I. , Johnson Matthew R. , Chou Chung-Jung , Conners Shannon B. , Geouge Sarah G. , Tachdjian Sabrina , Nichols Jason D. , Kelly Robert M. 
Published: June 2007

ABSTRACTTranscriptomes and growth physiologies of the hyperthermophileThermotoga maritimaand an antibiotic-resistant spontaneous mutant were compared prior to and following exposure to chloramphenicol. While the wild-type response was similar to that of mesophilic bacteria, reduced susceptibility of the mutant was attributed to five mutations in 23S rRNA and phenotypic preconditioning to chloramphenicol.
Production of Recombinant β-Hexosaminidase A, a Potential Enzyme for Replacement Therapy for Tay-Sachs and Sandhoff Diseases, in the Methylotrophic Yeast
Ogataea minuta
Authors: Akeboshi Hiromi , Chiba Yasunori , Kasahara Yoshiko , Takashiba Minako , Takaoka Yuki , Ohsawa Mai , Tajima Youichi , Kawashima Ikuo , Tsuji Daisuke , Itoh Kohji , Sakuraba Hitoshi , Jigami Yoshifumi 
Published: June 2007

ABSTRACT

Human β-hexosaminidase A (HexA) is a heterodimeric glycoprotein composed of α- and β-subunits that degrades GM2 gangliosides in lysosomes. GM2 gangliosidosis is a lysosomal storage disease in which an inherited deficiency of HexA causes the accumulation of GM2 gangliosides. In order to prepare a large amount of HexA for a treatment based on enzyme replacement therapy (ERT), recombinant HexA was produced in the methylotrophic yeast
Ogataea minuta
instead of in mammalian cells, which are commonly used to produce recombinant enzymes for ERT. The problem of antigenicity due to differences in N-glycan structures between mammalian and yeast glycoproteins was potentially resolved by using α-1,6-mannosyltransferase-deficient (
och1
Δ) yeast as the host. Genes encoding the α- and β-subunits of HexA were integrated into the yeast cell, and the heterodimer was expressed together with its isozymes HexS (αα) and HexB (ββ). A total of 57 mg of β-hexosaminidase isozymes, of which 13 mg was HexA (αβ), was produced per liter of medium. HexA was purified with immobilized metal affinity column for the His tag attached to the β-subunit. The purified HexA was treated with α-mannosidase to expose mannose-6-phosphate (M6P) residues on the N-glycans. The specific activities of HexA and M6P-exposed HexA (M6PHexA) for the artificial substrate 4MU-GlcNAc were 1.2 ± 0.1 and 1.7 ± 0.3 mmol/h/mg, respectively. The sodium dodecyl sulfate-polyacrylamide gel electrophoresis pattern suggested a C-terminal truncation in the β-subunit of the recombinant protein. M6PHexA was incorporated dose dependently into GM2 gangliosidosis patient-derived fibroblasts via M6P receptors on the cell surface, and degradation of accumulated GM2 ganglioside was observed.
Development of a Novel Genetic System To Create Markerless Deletion Mutants of
Bdellovibrio bacteriovorus
Authors: Steyert Susan R. , Pineiro Silvia A. 
Published: June 2007

ABSTRACT

Bdellovibrio bacteriovorus
is a species of unique obligate predatory bacteria that utilize gram-negative bacteria as prey. Their life cycle alternates between a motile extracellular phase and a growth phase within the prey cell periplasm. The mechanism of prey cell invasion and the genetic networks and regulation during the life cycle have not been elucidated. The obligate predatory nature of the
B. bacteriovorus
life cycle suggests the use of this bacterium in potential applications involving pathogen control but adds complexity to the development of practical genetic systems that can be used to determine gene function. This work reports the development of a genetic technique for allelic exchange or gene inactivation by construction of in-frame markerless deletion mutants including the use of a counterselectable marker in
B. bacteriovorus
. A suicide plasmid carrying the
sacB
gene for counterselection was used to inactivate the
strB
gene in
B. bacteriovorus
HD100 by an in-frame deletion. Despite the inactivation of the
strB
gene,
B. bacteriovorus
was found to retain resistance to high concentrations of streptomycin. The stability of a plasmid for use in complementation experiments was also investigated, and it was determined that pMMB206 replicates autonomously in
B. bacteriovorus
. Development of this practical genetic system now facilitates the study of
B. bacteriovorus
at the molecular level and will aid in understanding the regulatory networks and gene function in this fascinating predatory bacterium.
Overexpression of the Calcineurin Target
CRZ1
Provides Freeze Tolerance and Enhances the Fermentative Capacity of Baker's Yeast
Authors: Panadero Joaquín , Hernández-López Maria José , Prieto José Antonio , Randez-Gil Francisca 
Published: June 2007

ABSTRACT

Recent years have shown a huge growth in the market of industrial baker's yeasts (
Saccharomyces cerevisiae
), with the need for strains affording better performance in prefrozen dough. Evidence suggests that during the freezing process, cells can suffer biochemical damage caused by osmotic stress. Nevertheless, the involvement of ion-responsive transcriptional factors and pathways in conferring freeze resistance has not yet been examined. Here, we have investigated the role of the salt-responsive calcineurin-Crz1p pathway in mediating tolerance to freezing by industrial baker's yeast. Overexpression of
CRZ1
in the industrial HS13 strain increased both salt and freeze tolerance and improved the leavening ability of baker's yeast in high-sugar dough. Moreover, engineered cells were able to produce more gas during fermentation of prefrozen dough than the parental strain. Similar effects were observed for overexpression of Td
CRZ1
, the homologue to
CRZ1
in
Torulaspora delbrueckii
, suggesting that expression of calcineurin-Crz1p target genes can alleviate the harmful effects of ionic stress during freezing. However, overexpression of
STZ
and
FTZ
, two unrelated
Arabidopsis thaliana
genes encoding Cys
2
/His
2
-type zinc finger proteins, also conferred freeze resistance in yeast. Furthermore, experiments with Δ
cnb1
and Δ
crz1
mutants failed to show a freeze-sensitive phenotype, even in cells pretreated with NaCl. Overall, our results demonstrate that overexpression of
CRZ1
has the potential to be a useful tool for increasing freeze tolerance and fermentative capacity in industrial strains. However, these effects do not appear to be mediated through activation of known salt-responding pathways.
Characterization of a Novel Gene for Strain Typing Reveals Substructuring of
Aspergillus fumigatus
across North America
Authors: Balajee S. Arunmozhi , Tay Sun T. , Lasker Brent A. , Hurst Steve F. , Rooney Alejandro P. 
Published: June 2007

ABSTRACT

Fifty-five epidemiologically linked
Aspergillus fumigatus
isolates obtained from six nosocomial outbreaks of invasive aspergillosis were subtyped by sequencing the polymorphic region of the gene encoding a putative cell surface protein, Afu3g08990 (denoted as CSP). Comparative sequence analysis showed that genetic diversity was generated in the coding region of this gene by both tandem repeats and point mutations. Each unique sequence in an outbreak cluster was assigned an arbitrary number or CSP sequence type. The CSP typing method was able to identify “clonal” and genotypically distinct
A. fumigatus
isolates, and the results of this method were concordant with those of another discriminatory genotyping technique, the
Afut1
restriction fragment length polymorphism typing method. The novel single-locus sequence typing (CSP typing) strategy appears to be a simple, rapid, discriminatory tool that can be readily shared across laboratories. In addition, we found that
A. fumigatus
isolates substructured into multiple clades; interestingly, one clade consisted of isolates predominantly representing invasive clinical isolates recovered from cardiac transplant patients from two different outbreak situations. We also found that the
A. fumigatus
isolate Af293, whose genome has been sequenced, possesses a CSP gene structure that is substantially different from those of the other
A. fumigatus
strains studied here, highlighting the need for further taxonomic study.
Coding Tandem Repeats Generate Diversity in
Aspergillus fumigatus
Genes
Authors: Levdansky Emma , Romano Jacob , Shadkchan Yona , Sharon Haim , Verstrepen Kevin J. , Fink Gerald R. , Osherov Nir 
Published: June 2007

ABSTRACT

Genes containing multiple coding mini- and microsatellite repeats are highly dynamic components of genomes. Frequent recombination events within these tandem repeats lead to changes in repeat numbers, which in turn alters the amino acid sequence of the corresponding protein. In bacteria and yeasts, the expansion of such coding repeats in cell wall proteins is associated with alterations in immunogenicity, adhesion, and pathogenesis. We hypothesized that identification of repeat-containing putative cell wall proteins in the human pathogen
Aspergillus fumigatus
may reveal novel pathogenesis-related elements. Here, we report that the genome of
A. fumigatus
contains as many as 292 genes with internal repeats. Fourteen of 30 selected genes showed size variation of their repeat-containing regions among 11 clinical
A. fumigatus
isolates. Four of these genes, Afu3g08990, Afu2g05150 (
MP
-
2
), Afu4g09600, and Afu6g14090, encode putative cell wall proteins containing a leader sequence and a glycosylphosphatidylinositol anchor motif. All four genes are expressed and produce variable-size mRNA encoding a discrete number of repeat amino acid units. Their expression was altered during development and in response to cell wall-disrupting agents. Deletion of one of these genes, Afu3g08990, resulted in a phenotype characterized by rapid conidial germination and reduced adherence to extracellular matrix suggestive of an alteration in cell wall characteristics. The Afu3g08990 protein was localized to the cell walls of dormant and germinating conidia. Our findings suggest that a subset of the
A. fumigatus
cell surface proteins may be hypervariable due to recombination events in their internal tandem repeats. This variation may provide the functional diversity in cell surface antigens which allows rapid adaptation to the environment and/or elusion of the host immune system.
Binding of Human Plasminogen toBifidobacterium
Authors: Candela Marco , Bergmann Simone , Vici Manuela , Vitali Beatrice , Turroni Silvia , Eikmanns Bernhard J. , Hammerschmidt Sven , Brigidi Patrizia 
Published: June 2007

ABSTRACTBifidobacteria constitute up to 3% of the total microbiota and represent one of the most important health-promoting bacterial groups of the human intestinal microflora. The presence ofBifidobacteriumin the human gastrointestinal tract has been directly related to several health-promoting activities; however, to date, no information about the specific mechanisms of interaction with the host is available. In order to provide some insight into the molecular mechanisms involved in the interaction with the host, we investigated whetherBifidobacteriumwas able to capture human plasminogen on the cell surface. By using flow cytometry, we demonstrated a dose-dependent human plasminogen-binding activity for four strains belonging to three bifidobacterial species:Bifidobacterium lactis,B. bifidum, andB. longum. The binding of human plasminogen toBifidobacteriumwas dependent on lysine residues of surface protein receptors. By using a proteomic approach, we identified five putative plasminogen-binding proteins in the cell wall fraction of the model strainB. lactisBI07. The data suggest that plasminogen binding toB. lactisis due to the concerted action of a number of proteins located on the bacterial cell surface, some of which are highly conserved cytoplasmic proteins which have other essential cellular functions. Our findings represent a step forward in understanding the mechanisms involved in theBifidobacterium-host interaction.
Mutations of the Quorum Sensing-Dependent Regulator VjbR Lead to Drastic Surface Modifications inBrucella melitensis
Authors: Uzureau Sophie , Godefroid Marie , Deschamps Chantal , Lemaire Julien , De Bolle Xavier , Letesson Jean-Jacques 
Published: June 2007

ABSTRACTSuccessful establishment of infection by bacterial pathogens requires fine-tuning of virulence-related genes. Quorum sensing (QS) is a global regulation process based on the synthesis of, detection of, and response to small diffusible molecules, calledN-acyl-homoserine lactones (AHL), in gram-negative bacteria. In numerous species, QS has been shown to regulate genes involved in the establishment of pathogenic interactions with the host.Brucella melitensisproducesN-dodecanoyl homoserine lactones (C12-HSL), which down regulate the expression of flagellar genes and of thevirBoperon (encoding a type IV secretion system), both of which encode surface virulence factors. A QS-related regulator, called VjbR, was identified as a transcriptional activator of these genes. We hypothesized that VjbR mediates the C12-HSL effects described above.vjbRalleles mutated in the region coding for the AHL binding domain were constructed to test this hypothesis. These alleles expressed intransin a ΔvjbRbackground behave as constitutive regulators both in vitro and in a cellular model of infection. Interestingly, the resultingB. melitensisstrains, unable to respond to AHLs, aggregate spontaneously in liquid culture. Preliminary characterization of these strains showed altered expression of some outer membrane proteins and overproduction of a matrix-forming exopolysaccharide, suggesting for the first time thatB. melitensiscould form biofilms. Together, these results indicate that QS through VjbR is a major regulatory system of important cell surface structures ofBrucellaand as such plays a key role in host-pathogen interactions.
Complementation Analysis of the Cold-Sensitive Phenotype of the
Escherichia coli csdA
Deletion Strain
Authors: Awano Naoki , Xu Chunying , Ke Haiping , Inoue Koichi , Inouye Masayori , Phadtare Sangita 
Published: June 2007

ABSTRACT

The cold shock response of
Escherichia coli
is elicited by downshift of temperature from 37°C to 15°C and is characterized by induction of several cold shock proteins, including CsdA, during the acclimation phase. CsdA, a DEAD-box protein, has been proposed to participate in a variety of processes, such as ribosome biogenesis, mRNA decay, translation initiation, and gene regulation. It is not clear which of the functions of CsdA play a role in its essential cold shock function or whether all do, and so far no protein has been shown to complement its function in vivo. Our screening of an
E. coli
genomic library for an in vivo counterpart of CsdA that can compensate for its absence at low temperature revealed only one protein, RhlE, another DEAD-box RNA helicase. We also observed that although not detected in our genetic screening, two cold shock-inducible proteins, namely, CspA, an RNA chaperone, and RNase R, an exonuclease, can also complement the cold shock function of CsdA. Interestingly, the absence of CsdA and RNase R leads to increased sensitivity of the cells to even moderate temperature downshifts. The correlation between the helicase activity of CsdA and the stability of mRNAs of cold-inducible genes was shown using
cspA
mRNA, which was significantly stabilized in the Δ
csdA
cells, an effect counteracted by overexpression of wild-type CsdA or RNase R but not by that of the helicase-deficient mutant of CsdA. These results suggest that the primary role of CsdA in cold acclimation of cells is in mRNA decay and that its helicase activity is pivotal for promoting degradation of mRNAs stabilized at low temperature.