bluuebunny/crossref_metadata_2025_split huggingface dataset:
THE EFFECTS OF VEGETATION AND SOIL TYPE ON STREAMBANK EROSION, SOUTHWESTERN VIRGINIA, USA1
Authors: Wynn Theresa , Mostaghimi Saied 
Published: June 2007

ABSTRACT:The goal of this research was to evaluate the relative effects of root density, freeze/thaw cycling, and soil properties on the erodibility and critical shear stress of streambanks. The erodibility and critical shear stress of rooted bank soils were measured in situ at 25 field sites using a submerged jet test device; several soil, vegetation, and stream chemistry characteristics shown to influence soil erosion were also assessed. Multiple linear regression analysis was conducted to determine those factors that most influenced streambank erodibility and the relative impact of riparian vegetation. Study results indicated that soil erosion is a complex phenomenon that depends primarily on soil bulk density. Freeze/thaw cycling, soil antecedent moisture content, the density of roots with diameters of 2 to 20 mm, soil texture, and the interaction of soil pore water and stream water had a significant impact on soil erodibility and critical shear stress, depending on soil type. Riparian vegetation had multiple significant effects on soil erodibility. In addition to reducing soil erodibility through root reinforcement, the streamside vegetation affected soil moisture and altered the local microclimate, which in turn affected freeze/thaw cycling (FTC). This study represents the first in situ testing of the erodibility of vegetated streambanks and provides a quantitative analysis on the effects of vegetation on streambank erosion, relative to other soil physical and chemical parameters.
RIPARIAN LAND USES AND PRECIPITATION INFLUENCES ON STREAM BANK EROSION IN CENTRAL IOWA1
Authors: Zaimes George N. , Schultz Richard C. , Isenhart Thomas M. 
Published: June 2007

ABSTRACT:Human alterations to the Iowa landscape, such as elimination of native vegetation for row crop agriculture and grazing, channelization of streams, and tile and ditch drainage, have led to deeply incised channels with accelerated streambank erosion. The magnitude of streambank erosion and soil loss were compared along Bear Creek in central Iowa. The subreaches are bordered by differing land uses, including reestablished riparian forest buffers, row crop fields, and continuously grazed riparian pastures. Erosion pins were measured from June 1998 to July 2002 to estimate the magnitude of streambank erosion. Total streambank soil loss was estimated by using magnitude of bank erosion, soil bulk density, and severely eroded bank area. Significant seasonal and yearly differences in magnitude of bank erosion and total soil loss were partially attributed to differences in precipitation and associated discharges. Riparian forest buffers had significantly lower magnitude of streambank erosion and total soil loss than the other two riparian land uses. Establishment of riparian forest buffers along all of the nonbuffered subreaches would have reduced stream‐bank soil loss by an estimated 77 to 97 percent, significantly decreasing sediment in the stream, a major water quality problem in Iowa.
BLACK WILLOW CUTTING SURVIVAL IN STREAMBANK PLANTINGS, SOUTHEASTERN UNITED STATES1
Authors: Pezeshki S. Reza. , Shields F. Douglas. 
Published: June 2007

ABSTRACT:Field studies were conducted on black willow (Salix nigra) cuttings planted for riparian zone restoration along Harland Creek, Twentymile Creek, and Little Topashaw Creek in Mississippi, USA. Planted cuttings were 2.5 to 3 m long and had base diameters of 2.5 to 7.5 cm. Streams were unstable, deeply incised sand bed channels with eroding banks 1 to 6 m high. Soil texture, redox potential (Eh), depth to water table, and willow survival were monitored for two to three years after planting. While many factors influence willow cuttings at restoration sites, soil texture and moisture are key to plant success. In these studies, plant survival and growth were best for cuttings planted in soils with less than 40 percent silt‐clay content and a water table 0.5 m to 1.0 m below the soil surface during the growing season. These conditions produced soil Eh greater than approximately 200 mV and were most often observed 1 to 2 m higher than the bank toe. These findings suggest criteria useful for preplanting site evaluations. Additional evidence suggests that preplanting soaking enhances performance of black willow cuttings. Additional factors (channel erosion, herbivory by beaver, and competition from exotics) may control performance over periods longer than two to three years.
Teaching High School Students and College Freshmen Product
Development by Deterministic Design With PREP
Authors: Graham M. , Slocum A. , Sánchez R. Moreno 
Published: June 2007

Abstract
This paper describes an effective method for teaching design in a deterministic manner that is especially effective for under-represented students (e.g., culture, race, gender, physical disability, personality, etc.). Ten years ago we postulated that students can learn a deterministic design process not only to learn about design, but to better study math and science with peers through the use of an ordered peer-review process. The foundation of Deterministic Design is that everything happens for a reason (science, e.g., physics) and a systematic approach should be used first by individuals in a team to ask and answer questions. To ensure participation and to check that items have not been overlooked, work by individuals is followed by a Peer-Review Evaluation Process (PREP) and then the team brainstorms. Deterministic Design has designers describing what is to be done (functional requirements), how it can be done (design parameters), why it will work (analysis), who else has done similar work (references), and what are the risks and possible countermeasures. PREP is especially useful for diverse teams of designers with members from various backgrounds and personalities. It is also especially useful for enabling introverted team members to fully contribute to the development of designs.
Involvement of a Quorum-Sensing-Regulated Lipase Secreted by a Clinical Isolate of
Burkholderia glumae
in Severe Disease Symptoms in Rice
Authors: Devescovi Giulia , Bigirimana Joseph , Degrassi Giuliano , Cabrio Laura , LiPuma John J. , Kim Jinwoo , Hwang Ingyu , Venturi Vittorio 
Published: June 2007

ABSTRACT

Burkholderia glumae
is an emerging rice pathogen in several areas around the world. Closely related
Burkholderia
species are important opportunistic human pathogens for specific groups of patients, such as patients with cystic fibrosis and patients with chronic granulomatous disease. Here we report that the first clinical isolate of
B. glumae
, strain AU6208, has retained its capability to be very pathogenic to rice. As previously reported for rice isolate
B. glumae
BGR1 (and also for the clinical isolate AU6208), TofI or TofR acyl homoserine lactone (AHL) quorum sensing played a pivotal role in rice virulence. We report that AHL quorum sensing in
B. glumae
AU6208 regulates secreted LipA lipase and toxoflavin, the phytotoxin produced by
B. glumae. B. glumae
AU6208
lipA
mutants were no longer pathogenic to rice, indicating that the lipase is an important virulence factor. It was also established that type strain
B. glumae
ATCC 33617 did not produce toxoflavin and lipase and was nonpathogenic to rice. It was determined that in strain ATCC 33617 the LuxR family quorum-sensing sensor/regulator TofR was inactive. Introducing the
tofR
gene of
B. glumae
AU6208 in strain ATCC 33617 restored its ability to produce toxoflavin and the LipA lipase. This study extends the role of AHL quorum sensing in rice pathogenicity through the regulation of a lipase which was demonstrated to be a virulence factor. It is the first report of a clinical
B. glumae
isolate retaining strong rice pathogenicity and finally determined that
B. glumae
can undergo phenotypic conversion through a spontaneous mutation in the
tofR
regulator.
Mycobacterium parascrofulaceum
in Acidic Hot Springs in Yellowstone National Park
Authors: Santos Ricardo , Fernandes João , Fernandes Nuno , Oliveira Fernanda , Cadete Manuela 
Published: June 2007

ABSTRACT

Mycobacterium parascrofulaceum
was found in Norris Geyser Basin, Yellowstone National Park, in a system composed of two acidic (pH 3.0) springs with temperatures between 56°C at the source and 40°C at the confluence of both springs. Growth and survival assays at 56°C for 60 days were performed, confirming the origin of the strain.
Molecular Characterization and Evolution of Arthropod-Pathogenic
Rickettsiella
Bacteria
Authors: Cordaux Richard , Paces-Fessy Mélanie , Raimond Maryline , Michel-Salzat Alice , Zimmer Martin , Bouchon Didier 
Published: June 2007

ABSTRACT

We determined the 16S rRNA gene sequences of three crustacean “
Rickettsiella armadillidii
” strains.
Rickettsiella
bacteria overall appear to form a monophyletic group that diverged from
Coxiella
bacteria ∼350 million years ago. Therefore, the genus
Rickettsiella
as a whole (not just
Rickettsiella grylli
) should be classified among the
Gammaproteobacteria
instead of the
Alphaproteobacteria
.
Parvibaculum lavamentivorans
DS-1
T
Degrades Centrally Substituted Congeners of Commercial Linear Alkylbenzenesulfonate to Sulfophenyl Carboxylates and Sulfophenyl Dicarboxylates
Authors: Schleheck David , Knepper Thomas P. , Eichhorn Peter , Cook Alasdair M. 
Published: June 2007

ABSTRACT

Commercial linear alkylbenzenesulfonate (LAS) contains 20 congeners of linear alkanes (C
10
to C
13
) substituted subterminally with the 4-sulfophenyl moiety in any position from lateral to central.
Parvibaculum lavamentivorans
DS-1
T
degrades each of eight laterally substituted congeners [e.g., 2-(4-sulfophenyl)decane (2-C10-LAS); herein, compounds are named systematically by chain length (e.g., C
10
) and by the position of the substituent on the chain (e.g., position 2)] to a major sulfophenyl carboxylate [SPC; here 3-(4-sulfophenyl)butyrate (3-C4-SPC)] and two minor products, namely, the α,β-unsaturated SPC (SPC-2H, here 3-C4-SPC-2H) and the SPC+2C (here 5-C6-SPC) species (D. Schleheck, T. P. Knepper, K. Fischer, and A. M. Cook, Appl. Environ. Microbiol. 70:4053-4063). The degradation of centrally substituted congeners by strain DS-1 was examined in this work. 5-C10-LAS yielded not only the predicted 4-C8-SPC, 4-C8-SPC-2H, and 6-C10-SPC (about 70% of products) but also sulfophenyl dicarboxylates (SPdC), i.e., C6-, C8-, and C10-SPdC. These were identified by electrospray ionization-mass spectrometry (ESI-MS) after separation by high-pressure liquid chromatography (HPLC). ESI ion-trap MS and ESI-time of flight-MS were used to confirm the identities of key intermediates. Different mixtures of congeners obtained by separation of commercial LAS by HPLC were degraded, and the degradative products were compared. If a congener carried the sulfophenyl substituent on the 5, 6, or 7 position, SPdCs were formed as well as SPC, SPC-2H, and SPC+2C, whereas the substituent on the 2, 3, or 4 position yielded only SPC, SPC-2H, and SPC+2C. Some 50 products were generated from the 20 LAS congeners: 11 major SPCs, each with an SPC-2H and an SPC+2C (i.e., 33 SPC and SPC-2H species), and about 17 SPdC species. A large array of compounds, many in low quantities, is thus generated by
P. lavamentivorans
DS-1 during the degradation of commercial LAS.
Identification of Human-Pathogenic Strains of Shiga Toxin-Producing
Escherichia coli
from Food by a Combination of Serotyping and Molecular Typing of Shiga Toxin Genes
Authors: Beutin Lothar , Miko Angelika , Krause Gladys , Pries Karin , Haby Sabine , Steege Katja , Albrecht Nadine 
Published: June 2007

ABSTRACT

We examined 219 Shiga toxin-producing
Escherichia coli
(STEC) strains from meat, milk, and cheese samples collected in Germany between 2005 and 2006. All strains were investigated for their serotypes and for genetic variants of Shiga toxins 1 and 2 (Stx1 and Stx2).
stx
1
or variant genes were detected in 88 (40.2%) strains and
stx
2
and variants in 177 (80.8%) strains. Typing of
stx
genes was performed by
stx
-specific PCRs and by analysis of restriction fragment length polymorphisms (RFLP) of PCR products. Major genotypes of the Stx1 (
stx
1
,
stx
1c
, and
stx
1d
) and the Stx2 (
stx
2
,
stx
2d
,
stx
2-O118
,
stx
2e
, and
stx
2g
) families were detected, and multiple types of
stx
genes coexisted frequently in STEC strains. Only 1.8% of the STEC strains from food belonged to the classical enterohemorrhagic
E. coli
(EHEC) types O26:H11, O103:H2, and O157:H7, and only 5.0% of the STEC strains from food were positive for the
eae
gene, which is a virulence trait of classical EHEC. In contrast, 95 (43.4%) of the food-borne STEC strains carried
stx
2
and/or mucus-activatable
stx
2d
genes, an indicator for potential high virulence of STEC for humans. Most of these strains belonged to serotypes associated with severe illness in humans, such as O22:H8, O91:H21, O113:H21, O174:H2, and O174:H21.
stx
2
and
stx
2d
STEC strains were found frequently in milk and beef products. Other
stx
types were associated more frequently with pork (
stx
2e
), lamb, and wildlife meat (
stx
1c
). The combination of serotyping and
stx
genotyping was found useful for identification and for assignment of food-borne STEC to groups with potential lower and higher levels of virulence for humans.
Metal Ions May Suppress or Enhance Cellular Differentiation in
Candida albicans
and
Candida tropicalis
Biofilms
Authors: Harrison Joe J. , Ceri Howard , Yerly Jerome , Rabiei Maryam , Hu Yaoping , Martinuzzi Robert , Turner Raymond J. 
Published: June 2007

ABSTRACT

Candida albicans
and
Candida tropicalis
are polymorphic fungi that develop antimicrobial-resistant biofilm communities that are characterized by multiple cell morphotypes. This study investigated cell type interconversion and drug and metal resistance as well as community organization in biofilms of these microorganisms that were exposed to metal ions. To study this,
Candida
biofilms were grown either in microtiter plates containing gradient arrays of metal ions or in the Calgary Biofilm Device for high-throughput susceptibility testing. Biofilm formation and antifungal resistance were evaluated by viable cell counts, tetrazolium salt reduction, light microscopy, and confocal laser scanning microscopy in conjunction with three-dimensional visualization. We discovered that subinhibitory concentrations of certain metal ions (CrO
4
2−
, Co
2+
, Cu
2+
, Ag
+
, Zn
2+
, Cd
2+
, Hg
2+
, Pb
2+
, AsO
2
−
, and SeO
3
2−
) caused changes in biofilm structure by blocking or eliciting the transition between yeast and hyphal cell types. Four distinct biofilm community structure types were discerned from these data, which were designated “domed,” “layer cake,” “flat,” and “mycelial.” This study suggests that
Candida
biofilm populations may respond to metal ions to form cell-cell and solid-surface-attached assemblages with distinct patterns of cellular differentiation.
Real-Time Reverse Transcription-PCR for Transcriptional Expression Analysis of Virulence and Housekeeping Genes in Viable but NonculturableVibrio parahaemolyticusafter Recovery of Culturability
Authors: Coutard François , Lozach Solen , Pommepuy Monique , Hervio-Heath Dominique 
Published: June 2007

ABSTRACTA real-time reverse transcription-PCR method was developed to determine whether the recovery of culturability of viable but nonculturable (VBNC)Vibrio parahaemolyticusinduced the expression of virulence genes coding for the thermostable direct hemolysin and for type III secretion system 2 (TTSS2). The culturability of clinical strain Vp5 ofV. parahaemolyticusin artificial seawater at 4°C was monitored, and the VBNC state was obtained. One day after entry into the VBNC state, temperature upshifts to 20 and 37°C allowed the recovery of culturability. Standard curves for the relative quantification of expression of the housekeeping genesrpoS,pvsA,fur, andpvuA; thetdh2gene; and the TTSS2 genes (VPA1354, VPA1346, and VPA1342) were established. The levels of expression of thepvsAandpvuAgenes were stable and were used to normalize the levels of expression of the other genes. No transcriptional induction of the selected virulence genes under the temperature conditions used to recover the culturability of the VBNC bacteria was observed. The study results demonstrate that the recovery of culturability of VBNC cells of pathogenicV. parahaemolyticusis restricted to regrowth, without correlation with the induction of virulence gene expression. Disease induction would depend mainly on host-pathogen interactions that allow the expression of the virulence genes. This is the first time that the use of mRNA to detect viable cells was evaluated by computing the half-lives of multiple mRNA species under conditions inducing the VBNC state.
Phylogeography of the Thermophilic CyanobacteriumMastigocladus laminosus
Authors: Miller Scott R. , Castenholz Richard W. , Pedersen Deana 
Published: June 2007

ABSTRACTWe have taken a phylogeographic approach to investigate the demographic and evolutionary processes that have shaped the geographic patterns of genetic diversity for a sample of isolates of the cosmopolitan thermophilic cyanobacterialMastigocladus laminosusmorphotype collected from throughout most of its range. AlthoughM. laminosusis found in thermal areas throughout the world, our observation that populations are typically genetically differentiated on local geographic scales suggests the existence of dispersal barriers, a conclusion corroborated by evidence for genetic isolation by distance. Genealogies inferred using nitrogen metabolism gene sequence data suggest that a significant amount of the extant global diversity ofM. laminosuscan be traced back to a common ancestor associated with the western North American hot spot currently located below Yellowstone National Park. Estimated intragenic recombination rates are comparable to those of pathogenic bacteria known for their capacity to exchange DNA, indicating that genetic exchange has played an important role in generating novel variation duringM. laminosusdiversification. Selection has constrained protein changes at loci involved in the assimilation of both dinitrogen and nitrate, suggesting the historic use of both nitrogen sources in this heterocystous cyanobacterium. Lineage-specific differences in thermal performance were also observed.
Quorum Sensing in
Escherichia coli
Is Signaled by AI-2/LsrR: Effects on Small RNA and Biofilm Architecture
Authors: Li Jun , Attila Can , Wang Liang , Wood Thomas K. , Valdes James J. , Bentley William E. 
Published: June 2007

ABSTRACT

The regulatory network for the uptake of
Escherichia coli
autoinducer 2 (AI-2) is comprised of a transporter complex, LsrABCD; its repressor, LsrR; and a cognate signal kinase, LsrK. This network is an integral part of the AI-2 quorum-sensing (QS) system. Because LsrR and LsrK directly regulate AI-2 uptake, we hypothesized that they might play a wider role in regulating other QS-related cellular functions. In this study, we characterized physiological changes due to the genomic deletion of
lsrR
and
lsrK
. We discovered that many genes were coregulated by
lsrK
and
lsrR
but in a distinctly different manner than that for the
lsr
operon (where LsrR serves as a repressor that is derepressed by the binding of phospho-AI-2 to the LsrR protein). An extended model for AI-2 signaling that is consistent with all current data on AI-2, LuxS, and the LuxS regulon is proposed. Additionally, we found that both the quantity and architecture of biofilms were regulated by this distinct mechanism, as
lsrK
and
lsrR
knockouts behaved identically. Similar biofilm architectures probably resulted from the concerted response of a set of genes including
flu
and
wza
, the expression of which is influenced by
lsrRK
. We also found for the first time that the generation of several small RNAs (including DsrA, which was previously linked to QS systems in
Vibrio harveyi
) was affected by LsrR. Our results suggest that AI-2 is indeed a QS signal in
E. coli
, especially when it acts through the transcriptional regulator LsrR.
A Genomic View of Sugar Transport inMycobacterium smegmatisandMycobacterium tuberculosis
Authors: Titgemeyer Fritz , Amon Johannes , Parche Stephan , Mahfoud Maysa , Bail Johannes , Schlicht Maximilian , Rehm Nadine , Hillmann Dietmar , Stephan Joachim , Walter Britta , Burkovski Andreas , Niederweis Michael 
Published: June 2007

ABSTRACTWe present a comprehensive analysis of carbohydrate uptake systems of the soil bacteriumMycobacterium smegmatisand the human pathogenMycobacterium tuberculosis. Our results show thatM. smegmatishas 28 putative carbohydrate transporters. The majority of sugar transport systems (19/28) inM. smegmatisbelong to the ATP-binding cassette (ABC) transporter family. In contrast to previous reports, we identified genes encoding all components of the phosphotransferase system (PTS), including permeases for fructose, glucose, and dihydroxyacetone, inM. smegmatis. It is anticipated that the PTS ofM. smegmatisplays an important role in the global control of carbon metabolism similar to those of other bacteria.M. smegmatisfurther possesses one putative glycerol facilitator of the major intrinsic protein family, four sugar permeases of the major facilitator superfamily, one of which was assigned as a glucose transporter, and one galactose permease of the sodium solute superfamily. Our predictions were validated by gene expression, growth, and sugar transport analyses. Strikingly, we detected only five sugar permeases in the slow-growing speciesM. tuberculosis, two of which occur inM. smegmatis. Genes for a PTS are missing inM. tuberculosis. Our analysis thus brings the diversity of carbohydrate uptake systems of fast- and a slow-growing mycobacteria to light, which reflects the lifestyles ofM. smegmatisandM. tuberculosisin their natural habitats, the soil and the human body, respectively.
Escherichia coliMalic Enzymes: Two Isoforms with Substantial Differences in Kinetic Properties, Metabolic Regulation, and Structure
Authors: Bologna Federico P. , Andreo Carlos S. , Drincovich María F. 
Published: June 2007

ABSTRACTMalic enzymes (MEs) catalyze the oxidative decarboxylation of malate in the presence of a divalent metal ion. In eukaryotes, well-conserved cytoplasmic, mitochondrial, and plastidic MEs have been characterized. On the other hand, distinct groups can be detected among prokaryotic MEs, which are more diverse in structure and less well characterized than their eukaryotic counterparts. InEscherichia coli, two genes with a high degree of homology to ME can be detected:sfcAandmaeB. MaeB possesses a multimodular structure: the N-terminal extension shows homology to ME, while the C-terminal extension shows homology to phosphotransacetylases (PTAs). In the present work, a detailed characterization of the products ofE. colisfcAandmaeBwas performed. The results indicate that the two MEs exhibit relevant kinetic, regulatory, and structural differences. SfcA is a NAD(P) ME, while MaeB is a NADP-specific ME highly regulated by key metabolites. Characterization of truncated versions of MaeB indicated that the PTA domain is not essential for the ME reaction. Nevertheless, truncated MaeB without the PTA domain loses most of its metabolic ME modulation and its native oligomeric state. Thus, the association of the two structural domains in MaeB seems to facilitate metabolic control of the enzyme. Although the PTA domain in MaeB is highly similar to the domains of proteins with PTA activity, MaeB and its PTA domain do not exhibit PTA activity. Determination of the distinct properties of recombinant products ofsfcAandmaeBperformed in the present work will help to clarify the roles of MEs in prokaryotic metabolism.