bluuebunny/crossref_metadata_2025_split huggingface dataset:
Land‐use History Affects the Distribution of the Saprophytic Orchid Wullschlaegelia calcarata in Puerto Rico's Tabonuco Forest1
Authors: Bergman Erin , Ackerman James D. , Thompson Jill , Zimmerman Jess K. 
Published: May 2006

ABSTRACTHuman activities such as logging and agriculture can severely damage forest ecosystems by changing forest structure, ecosystem function, and biodiversity. These changes may have long‐lasting consequences, which influence forest recovery. We investigated the effect of past human disturbance on the current distribution of an understory, achlorophyllous orchid, Wullschlaegelia calcarata in Puerto Rico's tropical rain forest after 70 yr of recovery. Our study site was the 16‐ha Luquillo Forest Dynamics Plot located in the Luquillo Experimental Forest, which has four areas with differing intensity of land use that have been distinguished from variation in canopy cover seen in aerial photographs taken in 1936. We recorded orchids in six 10‐m‐wide, 500‐m‐long transects across four different areas of land‐use history. We found that the orchid was not present in an area of the plot which had <20 percent canopy cover in 1936, and was most abundant in the area with >80 percent canopy cover, which had been minimally impacted by human activity. Tree species composition varied among land‐use history areas, and our observations suggested that this variation might be influencing the local distribution of W. calcarata. We also measured leaf litter biomass and identified the leaves of litter in areas with and without the orchid. Litter with a high proportion of Buchenavia tetraphylla leaves had more orchids. Even though human disturbance ceased in 1932, land‐use history in the Luquillo Forest still casts a shadow over the distribution of W. calcarata.
Nutrient Limitation in a Fire‐derived, Nitrogen‐rich Hawaiian Grassland1
Authors: D'Antonio Carla M. , Mack Michelle C. 
Published: May 2006

ABSTRACTGrasslands created by grass invasions into shrublands or woodlands followed by fire are now a dominant feature of many seasonally dry environments. In Hawaii Volcanoes National Park, introduced perennial grasses dominate grasslands created by fire in grass‐invaded woodlands. In a previous study, we found that net primary production in these grasslands is substantially lower than in unburned woodlands. Yet, our estimates of annual net nitrogen (N) mineralization showed higher rates in these savannas than in the unburned woodlands, rates that appear to greatly exceed annual N demand by the vegetation. We therefore hypothesized that N should not be limited to the plants growing in these sites. We tested this hypothesis with a 2‐yr fertilization experiment. At peak biomass, we found a 30 percent increase in live biomass in plots with N added and no increase in production with only phosphorus (P) added. N and P together were synergistic, suggesting that co‐limitation or P limitation becomes important when N is more available. Plants responded to added N by increasing individual leaf area and shoot length by over 50 percent. Tissue N was higher with added N; hence, biomass N was substantially higher. Tissue P concentrations declined with N addition but were elevated by P addition despite lack of a growth response to P alone. Overall, N limitation exists despite high annual rates of net N mineralization, and co‐limitation of production by P may occur when N is abundant. Here, asynchrony between plant nutrient demand and N availability may contribute to N limitation.
Resolution of MRS Applied to the Characterization of Hard‐Rock Aquifers
Authors: Legchenko Anatoly , Descloitres Marc , Bost Adelphe , Ruiz Laurent , Reddy Mohan , Girard Jean‐François , Sekhar Muddu , Mohan Kumar M.S. , Braun Jean‐Jacques 
Published: May 2006

AbstractThe performance of the Magnetic Resonance Sounding (MRS) method applied to the investigation of heterogeneous hard‐rock aquifers was studied. It was shown using both numerical modeling and field measurements that MRS could be applied to the investigation of the weathered part of hard‐rock aquifers when the product of the free water content multiplied by the thickness of the aquifer is >0.2 (for example, 10‐m‐thick layer with a 2% water content). Using a currently available one‐dimensional MRS system, the method allows the characterization of two‐dimensional subsurface structures with acceptable accuracy when the size of the subsurface anomaly is equal to or greater than the MRS loop. However, the fractured part of hard‐rock aquifers characterized by low effective porosity (<0.5%) cannot be resolved using currently available MRS equipment. It was found that shallow water in the weathered part of the aquifer may screen MRS signals from deeper water‐saturated layers, thus further reducing the possibility of investigating deeper fractured aquifers. A field study using the NUMISplus MRS system developed by IRIS Instruments was carried out on an experimental watershed in southern India. A heterogeneous unconfined aquifer in a gneissic formation was successfully localized, and MRS results were confirmed by drilling shortly after the geophysical study. The top of the aquifer revealed by MRS was found to be in a good agreement with observed static water level measurements in boreholes.
The Influence of Well Hydraulics on the Spatial Distribution of Well Incrustations
Authors: Houben Georg J. 
Published: May 2006

AbstractIn many cases, the operation of wells is hampered by the formation of mineral incrustations. From field studies, it is known that the distribution of incrustations in wells is quite inhomogeneous. Flow models were calculated to assess the hydraulic background of this phenomenon. For horizontal flow, the screen section facing the natural flow direction receives the majority of the total inflow. This phenomenon increases with increasing natural gradients of flow. The vertical distribution of water intake is also quite inhomogeneous. In partially penetrating wells, the uppermost part of the screen receives much more inflow than the deeper screen sections. These flow inhomogenities involve elevated flow velocities and may cause increased influx of shallow, oxygenated water, all conditions favorable for incrustation growth. Field investigations on incrusting wells clearly show that the identified screen areas of elevated flow are indeed much more prone to incrustation deposition. Such sections require more attention during rehabilitations. A suction flow control device can help to homogenize the inflow but can cause elevated entrance loss when affected by incrustation buildup itself.
Spatial Localizations of Mam22 and Mam12 in the Magnetosomes of
Magnetospirillum magnetotacticum
Authors: Taoka Azuma , Asada Ryuji , Sasaki Hideaki , Anzawa Kazushi , Wu Long-Fei , Fukumori Yoshihiro 
Published: May 2006

ABSTRACT

Magnetospirillum magnetotacticum
possesses intracellular magnetite particles with a chain-like structure, termed magnetosomes. The bacterium expresses 22-kDa and 12-kDa magnetosome-associated proteins, termed Mam22 (MamA) and Mam12 (MamC), respectively. In this study, we investigated the structure of the purified magnetosomes with transmission electron microscopic techniques and found that the magnetosomes consisted of four compartments, i.e., magnetite crystal, magnetosomal membrane, interparticle connection, and magnetosomal matrix. Furthermore, we determined the precise localizations of Mam22 and Mam12 using immunogold staining of the purified magnetosomes and ultrathin sections of the bacterial cells. Interestingly, most Mam22 existed in the magnetosomal matrix, whereas Mam12 was strictly localized in the magnetosomal membrane. Moreover, the recombinant Mam22 was attached to the magnetosomal matrix of the Mam22-deficient magnetosomes prepared by alkaline treatment, such as 0.1 M Caps-NaOH buffer (pH 11.0). The spatial localization of the magnetosome-associated proteins in the magnetosomal chain provides useful information to elucidate the functional roles of these proteins.
Characterization of the Siderophore ofFrancisella tularensisand Role offslAin Siderophore Production
Authors: Sullivan Jonathan Tabb , Jeffery Erin Field , Shannon John D. , Ramakrishnan Girija 
Published: May 2006

ABSTRACTWe determined that LVS and Schu S4 strains of the human pathogenFrancisella tularensisexpress a siderophore when grown under iron-limiting conditions. We purified this siderophore by conventional column chromatography and high-pressure liquid chromatography and used mass spectrometric analysis to demonstrate that it is structurally similar to the polycarboxylate siderophore rhizoferrin. The siderophore promoted the growth of LVS and Schu S4 strains in iron-limiting media. We identified a potential siderophore biosynthetic gene cluster encoded byfslABCDin theF. tularensisgenome. The first gene in the cluster,fslA, encodes a member of the superfamily of nonribosomal peptide synthetase-independent siderophore synthetases (NIS synthetases) characterized by the aerobactin synthetases IucA and IucC. We determined thatfslAis transcribed as part of an operon with downstream genefslBand that the expression of the locus is induced by iron starvation. A targeted in-frame nonpolar deletion offslAin LVS resulted in the loss of siderophore expression and in a reduced ability ofF. tularensisto grow under conditions of iron limitation. Siderophore activity and the ability to grow under iron limitation could be regained by introducing thefslA+gene on a complementing plasmid. Our results suggest that thefslA-dependent siderophore is important for survival ofF. tularensisin an iron-deficient environment.
Isolation and Characterization of VceC Gain-of-Function Mutants That Can Function with the AcrAB Multiple-Drug-Resistant Efflux Pump of
Escherichia coli
Authors: Vediyappan Govindsamy , Borisova Tatyana , Fralick Joe A. 
Published: May 2006

ABSTRACT

VceC is the outer membrane component of the major facilitator (MF) VceAB-VceC multiple-drug-resistant (MDR) efflux pump of
Vibrio cholerae
. TolC is the outer membrane component of the resistance-nodulation-division AcrAB-TolC efflux pump of
Escherichia coli
. Although these proteins share little amino acid sequence identity, their crystal structures can be readily superimposed upon one another. In this study, we have asked if TolC and VceC are interchangeable for the functioning of the AcrAB and VceAB pumps. We have found that TolC can replace VceC to form a functional VceAB-TolC MDR pump, but VceC cannot replace TolC to form a functional AcrAB-VceC pump. However, we have been able to isolate gain-of-function (gof) VceC mutants which can functionally interface with AcrAB. These mutations map to four different amino acids located at the periplasmic tip of VceC. Chemical cross-linkage experiments indicate that both wild-type and gof mutant VceC can physically interact with the AcrAB complex, suggesting that these gof mutations are not affecting the recruitment of VceC to the AcrAB complex but rather its ability to functionally interface with the AcrAB pump.
Structural and Functional Characterization of Three Polyketide Synthase Gene Clusters in
Bacillus amyloliquefaciens
FZB 42
Authors: Chen Xiao-Hua , Vater Joachim , Piel Jörn , Franke Peter , Scholz Romy , Schneider Kathrin , Koumoutsi Alexandra , Hitzeroth Gabriele , Grammel Nicolas , Strittmatter Axel W. , Gottschalk Gerhard , Süssmuth Roderich D. , Borriss Rainer 
Published: May 2006

ABSTRACT

Although bacterial polyketides are of considerable biomedical interest, the molecular biology of polyketide biosynthesis in
Bacillus
spp., one of the richest bacterial sources of bioactive natural products, remains largely unexplored. Here we assign for the first time complete polyketide synthase (PKS) gene clusters to
Bacillus
antibiotics. Three giant modular PKS systems of the
trans
-acyltransferase type were identified in
Bacillus amyloliquefaciens
FZB 42. One of them,
pks1
, is an ortholog of the
pksX
operon with a previously unknown function in the sequenced model strain
Bacillus subtilis
168, while the
pks2
and
pks3
clusters are novel gene clusters. Cassette mutagenesis combined with advanced mass spectrometric techniques such as matrix-assisted laser desorption ionization-time of flight mass spectrometry and liquid chromatography-electrospray ionization mass spectrometry revealed that the
pks1
(
bae
) and
pks3
(
dif
) gene clusters encode the biosynthesis of the polyene antibiotics bacillaene and difficidin or oxydifficidin, respectively. In addition,
B. subtilis
OKB105 (
pheA sfp
0
), a transformant of the
B. subtilis
168 derivative JH642, was shown to produce bacillaene, demonstrating that the
pksX
gene cluster directs the synthesis of that polyketide.
A New Integrative Conjugative Element Occurs in
Mycoplasma agalactiae
as Chromosomal and Free Circular Forms
Authors: Marenda Marc , Barbe Valérie , Gourgues Géraldine , Mangenot Sophie , Sagne Evelyne , Citti Christine 
Published: May 2006

ABSTRACT

An integrative conjugative element, ICEA, was characterized in
Mycoplasma agalactiae
strain 5632, in which it occurs as multiple chromosomal copies and as a free circular form. The distribution of ICEA sequences in
M. agalactiae
strains and their occurrence in
Mycoplasma bovis
suggest the spreading of the element within or between species.
Mutationally Altered Signal Output in the Nart (NarX-Tar) Hybrid Chemoreceptor
Authors: Ward Scott M. , Bormans Arjan F. , Manson Michael D. 
Published: May 2006

ABSTRACT
Signal-transducing proteins that span the cytoplasmic membrane transmit information about the environment to the interior of the cell. In bacteria, these signal transducers include sensor kinases, which typically control gene expression via response regulators, and methyl-accepting chemoreceptor proteins, which control flagellar rotation via the CheA kinase and CheY response regulator. We previously reported that a chimeric protein (Nart) that joins the ligand-binding, transmembrane, and linker regions of the NarX sensor kinase to the signaling and adaptation domains of the Tar chemoreceptor elicits a repellent response to nitrate and nitrite. As with NarX, nitrate evokes a stronger response than nitrite. Here we show that mutations targeting a highly conserved sequence (the P box) in the periplasmic domain alter chemoreception by Nart and signaling by NarX similarly. In particular, the G51R substitution converts Nart from a repellent receptor into an attractant receptor for nitrate. Our results underscore the conclusion that the fundamental mechanism of transmembrane signaling is conserved between homodimeric sensor kinases and chemoreceptors. They also highlight the plasticity of the coupling between ligand binding and signal output in these systems.
The
ectD
Gene, Which Is Involved in the Synthesis of the Compatible Solute Hydroxyectoine, Is Essential for Thermoprotection of the Halophilic Bacterium
Chromohalobacter salexigens
Authors: García-Estepa Raúl , Argandoña Montserrat , Reina-Bueno Mercedes , Capote Nieves , Iglesias-Guerra Fernando , Nieto Joaquín J. , Vargas Carmen 
Published: May 2006

ABSTRACT

The halophilic bacterium
Chromohalobacter salexigens
synthesizes and accumulates compatible solutes in response to salt and temperature stress.
13
C-nuclear magnetic resonance analysis of cells grown in minimal medium at the limiting temperature of 45°C revealed the presence of hydroxyectoine, ectoine, glutamate, trehalose (not present in cells grown at 37°C), and the ectoine precursor,
N
γ-acetyldiaminobutyric acid. High-performance liquid chromatography analyses showed that the levels of ectoine and hydroxyectoine were maximal during the stationary phase of growth. Accumulation of hydroxyectoine was up-regulated by salinity and temperature, whereas accumulation of ectoine was up-regulated by salinity and down-regulated by temperature. The
ectD
gene, which is involved in the conversion of ectoine to hydroxyectoine, was isolated as part of a DNA region that also contains a gene whose product belongs to the AraC-XylS family of transcriptional activators. Orthologs of
ectD
were found within the sequenced genomes of members of the proteobacteria, firmicutes, and actinobacteria, and their products were grouped into the ectoine hydroxylase subfamily, which was shown to belong to the superfamily of Fe(II)- and 2-oxoglutarate-dependent oxygenases. Analysis of the ectoine and hydroxyectoine contents of an
ectABC ectD
mutant strain fed with 1 mM ectoine or hydroxyectoine demonstrated that
ectD
is required for the main ectoine hydroxylase activity in
C. salexigens
. Although in minimal medium at 37°C the wild-type strain grew with 0.5 to 3.0 M NaCl, with optimal growth at 1.5 M NaCl, at 45°C it could not cope with the lowest (0.75 M NaCl) or the highest (3.0 M NaCl) salinity, and it grew optimally at 2.5 M NaCl. The
ectD
mutation caused a growth defect at 45°C in minimal medium with 1.5 to 2.5 M NaCl, but it did not affect growth at 37°C at any salinity tested. With 2.5 M NaCl, the
ectD
mutant synthesized 38% (at 37°C) and 15% (at 45°C) of the hydroxyectoine produced by the wild-type strain. All of these data reveal that hydroxyectoine synthesis mediated by the
ectD
gene is thermoregulated and essential for thermoprotection of
C. salexigens
.
Different Roles of EIIAB
Man
and EII
Glc
in Regulation of Energy Metabolism, Biofilm Development, and Competence in
Streptococcus mutans
Authors: Abranches Jacqueline , Candella Melissa M. , Wen Zezhang T. , Baker Henry V. , Burne Robert A. 
Published: May 2006

ABSTRACT

The phosphoenolpyruvate:sugar phosphotransferase system (PTS) is the major carbohydrate transport system in oral streptococci. The mannose-PTS of
Streptococcus mutans
, which transports mannose and glucose, is involved in carbon catabolite repression (CCR) and regulates the expression of known virulence genes. In this study, we investigated the role of EII
Glc
and EIIAB
Man
in sugar metabolism, gene regulation, biofilm formation, and competence. The results demonstrate that the inactivation of
ptsG
, encoding a putative EII
Glc
, did not lead to major changes in sugar metabolism or affect the phenotypes of interest. However, the loss of EII
Glc
was shown to have a significant impact on the proteome and to affect the expression of a known virulence factor, fructan hydrolase (
fruA
). JAM1, a mutant strain lacking EIIAB
Man
, had an impaired capacity to form biofilms in the presence of glucose and displayed a decreased ability to be transformed with exogenous DNA. Also, the lactose- and cellobiose-PTSs were positively and negatively regulated by EIIAB
Man
, respectively. Microarrays were used to investigate the profound phenotypic changes displayed by JAM1, revealing that EIIAB
Man
of
S. mutans
has a key regulatory role in energy metabolism, possibly by sensing the energy levels of the cells or the carbohydrate availability and, in response, regulating the activity of transcription factors and carbohydrate transporters.
Utilization of the Methoxymalonyl-Acyl Carrier Protein Biosynthesis Locus for Cloning the Oxazolomycin Biosynthetic Gene Cluster from
Streptomyces albus
JA3453
Authors: Zhao Chunhua , Ju Jianhua , Christenson Steven D. , Smith Wyatt C. , Song Danfeng , Zhou Xiufen , Shen Ben , Deng Zixin 
Published: May 2006

ABSTRACT

Oxazolomycin (OZM), a hybrid peptide-polyketide antibiotic, exhibits potent antitumor and antiviral activities. Using degenerate primers to clone genes encoding methoxymalonyl-acyl carrier protein (ACP) biosynthesis as probes, a 135-kb DNA region from
Streptomyces albus
JA3453 was cloned and found to cover the entire OZM biosynthetic gene cluster. The involvement of the cloned genes in OZM biosynthesis was confirmed by deletion of a 12-kb DNA fragment containing six genes for methoxymalonyl-ACP biosynthesis from the specific region of the chromosome, as well as deletion of the
ozmC
gene within this region, to generate OZM-nonproducing mutants.
Albomycin Uptake via a Ferric Hydroxamate Transport System ofStreptococcus pneumoniaeR6
Authors: Pramanik Avijit , Braun Volkmar 
Published: May 2006

ABSTRACTThe antibiotic albomycin is highly effective againstStreptococcus pneumoniae, with an MIC of 10 ng/ml. The reason for the high efficacy was studied by measuring the uptake of albomycin intoS. pneumoniae. Albomycin was transported via the system that transports the ferric hydroxamates ferrichrome and ferrioxamine B. These two ferric hydroxamates antagonized the growth inhibition by albomycin and salmycin. Cross-inhibition of the structurally different ferric hydroxamates to both antibiotics can be explained by the similar iron coordination centers of the four compounds. [55Fe3+]ferrichrome and [55Fe3+]ferrioxamine B were taken up by the same transport system intoS. pneumoniae. Mutants in the adjacentfhuD,fhuB, andfhuGgenes were transport inactive and resistant to the antibiotics. Albomycin, ferrichrome, ferrioxamine B, and salmycin bound to the isolated FhuD protein and prevented degradation by proteinase K. Thefhulocus consisting of thefhuD,fhuB,fhuG, andfhuCgenes determines a predicted ABC transporter composed of the FhuD binding lipoprotein, the FhuB and FhuG transport proteins, and the FhuC ATPase. It is concluded that active transport of albomycin mediates the high antibiotic efficacy inS. pneumoniae.
The Superoxide Dismutases of
Bacillus anthracis
Do Not Cooperatively Protect against Endogenous Superoxide Stress
Authors: Passalacqua Karla D. , Bergman Nicholas H. , Herring-Palmer Amy , Hanna Philip 
Published: May 2006

ABSTRACT

The
Bacillus anthracis
chromosome encodes four unique, putative superoxide dismutase (
sod
) genes. During exponential growth and sporulation,
sodA1
,
sodA2
, and
sodC
are transcribed constitutively throughout the growth cycle as individual genes. In contrast, the transcription of
sod15
occurs mainly during late exponential and sporulation phases as part of a four-gene operon that may be involved in spore formation. Vegetative cell and spore lysates of wild-type Sterne and superoxide dismutase deletion (
Δsod
) mutants show detectable SOD activity for SODA1 and SODA2, and protein analysis suggests that these two proteins form active homodimers and heterodimers. A comparison of the growth of parental versus Δ
sod
mutants under various chemical oxidative stresses indicates that Δ
sodA1
mutants are particularly sensitive to endogenously produced superoxide, whereas Δ
sodA2
, Δ
sod15
, and Δ
sodC
mutants remain as resistant to this stress as the parental strain. In addition, in mouse survival assays, Δ
sod15
and Δ
sodA1
were responsible for less end-point death, but the level of decreased virulence does not fall within a statistically significant range. Collectively, these data show that
sodA1
acts as a major protectant from intracellular superoxide stress, that
sod15
is transcribed as part of an operon that may play a role in cell morphology, and that
sodA2
and
sodC
may have minor roles that are not apparent in the conditions tested here.
Transcription of the
Bacillus subtilis gerK
Operon, Which Encodes a Spore Germinant Receptor, and Comparison with That of Operons Encoding Other Germinant Receptors
Authors: Igarashi Takao , Setlow Peter 
Published: May 2006

ABSTRACT

The
gerA
,
gerB
, and
gerK
operons, which encode germinant receptors in spores of
Bacillus subtilis
, were transcribed only in sporulation, and their mRNA levels peaked initially ∼3 h before the initiation of accumulation of the spore's dipicolinic acid. After a rapid fall, levels of these mRNAs peaked again ∼5 h later. In one wild-type strain (PS832),
gerA
mRNA was the most abundant, with levels of
gerB
and
gerK
mRNAs ∼50% of that of
gerA
mRNA, whereas
gerB
mRNA was the most abundant in another wild-type strain (PY79). The synthesis of
gerK
mRNA in sporulation was abolished by loss of the forespore-specific RNA polymerase sigma factor, σ
G
, and induction of σ
G
synthesis in vegetative cells led to synthesis of
gerK
mRNA. SpoVT, a regulator of σ
G
-dependent gene expression, repressed
gerK
expression. The
gerK
promoter showed sequence similarities to σ
G
-dependent promoters, and deletion of elements of this putative promoter abolished
gerK
expression in sporulation.