bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Diversity of the Q Fever Agent,Coxiella burnetii, Assessed by Microarray-Based Whole-Genome Comparisons
Authors: Beare Paul A. , Samuel James E. , Howe Dale , Virtaneva Kimmo , Porcella Stephen F. , Heinzen Robert A. 
Published: March 2006

ABSTRACTCoxiella burnetii, a gram-negative obligate intracellular bacterium, causes human Q fever and is considered a potential agent of bioterrorism. Distinct genomic groups ofC. burnetiiare revealed by restriction fragment-length polymorphisms (RFLP). Here we comprehensively define the genetic diversity ofC. burnetiiby hybridizing the genomes of 20 RFLP-grouped and four ungrouped isolates from disparate sources to a high-density custom Affymetrix GeneChip containing all open reading frames (ORFs) of the Nine Mile phase I (NMI) reference isolate. We confirmed the relatedness of RFLP-grouped isolates and showed that two ungrouped isolates represent distinct genomic groups. Isolates contained up to 20 genomic polymorphisms consisting of 1 to 18 ORFs each. These were mostly complete ORF deletions, although partial deletions, point mutations, and insertions were also identified. A total of 139 chromosomal and plasmid ORFs were polymorphic among allC. burnetiiisolates, representing ca. 7% of the NMI coding capacity. Approximately 67% of all deleted ORFs were hypothetical, while 9% were annotated in NMI as nonfunctional (e.g., frameshifted). The remaining deleted ORFs were associated with diverse cellular functions. The only deletions associated with isogenic NMI variants of attenuated virulence were previously described large deletions containing genes involved in lipopolysaccharide (LPS) biosynthesis, suggesting that these polymorphisms alone are responsible for the lower virulence of these variants. Interestingly, a variant of the Australia QD isolate producing truncated LPS had no detectable deletions, indicating LPS truncation can occur via small genetic changes. Our results provide new insight into the genetic diversity and virulence potential ofCoxiellaspecies.
Cross-Linked Peptidoglycan Mediates Lysostaphin Binding to the Cell Wall Envelope ofStaphylococcus aureus
Authors: Gründling Angelika , Schneewind Olaf 
Published: March 2006

ABSTRACTStaphylococcus simulansbv. staphylolyticus secretes lysostaphin, a bacteriocin that cleaves pentaglycine cross bridges in the cell wall ofStaphylococcus aureus. The C-terminal cell wall-targeting domain (CWT) of lysostaphin is required for selective binding of this bacteriocin toS. aureuscells; however, the molecular target for this was unknown. We used purified green fluorescent protein fused to CWT (GFP-CWT) to reveal species-specific association of the reporter with staphylococci. GFP-CWT boundS. aureuscells as well as purified peptidoglycan sacculi. The addition of cross-linked murein, disaccharides linked to interconnected wall peptides, blocked GFP-CWT binding to staphylococci, whereas murein monomers or lysostaphin-solubilized cell wall fragments did not.S. aureusstrain Newman variants lacking the capacity for synthesizing polysaccharide capsule (capFO), poly-N-acetylglucosamine (icaAC), lipoprotein (lgt), cell wall-anchored proteins (srtA), or the glycolipid anchor of lipoteichoic acid (ypfP) bound GFP-CWT similar to wild-type staphylococci. AtagOmutant strain, defective in the synthesis of polyribitol wall teichoic acid attached to the cell wall envelope, displayed increased GFP-CWT binding. In contrast, afemABmutation, reducing both the amount and the length of peptidoglycan cross-linking (monoglycine cross bridges), showed a dramatic reduction in GFP-CWT binding. Thus, the CWT domain of lysostaphin directs the bacteriocin to cross-linked peptidoglycan, which also serves as the substrate for its glycyl-glycine endopeptidase domain.
Mutations in DivL and CckA Rescue a
divJ
Null Mutant of
Caulobacter crescentus
by Reducing the Activity of CtrA
Authors: Pierce Deanne L. , O'Donnol Danielle S. , Allen Rebecca C. , Javens June W. , Quardokus Ellen M. , Brun Yves V. 
Published: March 2006

ABSTRACT

Polar development and cell division in
Caulobacter crescentus
are controlled and coordinated by multiple signal transduction proteins.
divJ
encodes a histidine kinase. A null mutation in
divJ
results in a reduced growth rate, cell filamentation, and mislocalized stalks. Suppressor analysis of
divJ
identified mutations in genes encoding the tyrosine kinase (
divL
) and the histidine kinase (
cckA
). The
divL
and
cckA
suppressor alleles all have single amino acid substitutions, some of which confer a temperature-sensitive phenotype, particularly in a wild-type background. Analysis of transcription levels from several positively regulated CtrA-dependent promoters reveals high expression in the
divJ
mutant, suggesting that DivJ normally serves to reduce CtrA activity. The
divL
and
cckA
suppressors reduce the amount of transcription from promoters positively regulated by CtrA, indicating that the mutations in
divL
and
cckA
are suppressing the defects of the
divJ
mutant by reducing the abnormally high level of CtrA activity. Immunoblotting showed no major perturbations in the CtrA protein level in any of these strains, suggesting that the high amount of CtrA activity seen in the
divJ
mutant and the reduced amount of activity in the suppressors are regulated at the level of activation and not transcription, translation, or degradation. In vivo phosphorylation assays confirmed that
divJ
mutants have elevated levels of CtrA phosphorylation and that this level is reduced in the suppressors with mutations in
divL
.
Coenzyme B12 Controls Transcription of the
Streptomyces
Class Ia Ribonucleotide Reductase
nrdABS
Operon via a Riboswitch Mechanism
Authors: Borovok Ilya , Gorovitz Batia , Schreiber Rachel , Aharonowitz Yair , Cohen Gerald 
Published: March 2006

ABSTRACT

Ribonucleotide reductases (RNRs) catalyze the conversion of ribonucleotides to deoxyribonucleotides and are essential for de novo DNA synthesis and repair. Streptomycetes contain genes coding for two RNRs. The class Ia RNR is oxygen dependent, and the class II RNR is oxygen independent and requires coenzyme B12. Either RNR is sufficient for vegetative growth. We show here that the
Streptomyces coelicolor
M145
nrdABS
genes encoding the class Ia RNR are regulated by coenzyme B12. The 5′-untranslated region of
nrdABS
contains a 123-nucleotide B12 riboswitch. Similar B12 riboswitches are present in the corresponding regions of eight other
S. coelicolor
genes. The effect of B12 on growth and
nrdABS
transcription was examined in a mutant in which the
nrdJ
gene, encoding the class II RNR, was deleted. B12 concentrations of just 1 μg/liter completely inhibited growth of the NrdJ mutant strain. Likewise, B12 significantly reduced
nrdABS
transcription. To further explore the mechanism of B12 repression, we isolated in the
nrdJ
deletion strain mutants that are insensitive to B12 inhibition of growth. Two classes of mutations were found to map to the B12 riboswitch. Both conferred resistance to B12 inhibition of
nrdABS
transcription and are likely to affect B12 binding. These results establish that B12 regulates overall RNR expression in reciprocal ways, by riboswitch regulation of the class Ia RNR
nrdABS
genes and by serving as a cofactor for the class II RNR.
Analysis of
Escherichia coli
Global Gene Expression Profiles in Response to Overexpression and Deletion of CspC and CspE
Authors: Phadtare Sangita , Tadigotla Vasisht , Shin Weon-Hye , Sengupta Anirvan , Severinov Konstantin 
Published: March 2006

ABSTRACT

The
Escherichia coli
cold shock protein CspA family consists of nine proteins (CspA to CspI), of which two, CspE and CspC, are constitutively produced at 37°C and are involved in regulation of expression of genes encoding stress response proteins but can also perform an essential function during cold acclimation. In this study, we analyzed global transcript profiles of cells lacking
cspE
and
cspC
as well as cells individually overexpressing these proteins or a CspE mutant that is unable to melt nucleic acids and is defective in cold acclimation. The analysis reveals sets of genes whose expression (i) is regulated by CspC and CspE at physiological temperature or cold shock conditions and (ii) depends on the nucleic acid melting function of CspE. Bioinformatic analysis of the latter group reveals that many of those genes contain promoter-proximal sequences that can block transcript elongation and may be targeted by the nucleic acid melting function of CspE.
Identification of RamA, a Novel LuxR-Type Transcriptional Regulator of Genes Involved in Acetate Metabolism of
Corynebacterium glutamicum
Authors: Cramer Annette , Gerstmeir Robert , Schaffer Steffen , Bott Michael , Eikmanns Bernhard J. 
Published: March 2006

ABSTRACT

In
Corynebacterium glutamicum
, the acetate-activating enzymes phosphotransacetylase and acetate kinase and the glyoxylate cycle enzymes isocitrate lyase and malate synthase are coordinately up-regulated in the presence of acetate in the growth medium. This regulation is due to transcriptional control of the respective
pta-ack
operon and the
aceA
and
aceB
genes, brought about at least partly by the action of the negative transcriptional regulator RamB. Using cell extracts of
C. glutamicum
and employing DNA affinity chromatography, mass spectrometry, and peptide mass fingerprinting, we identified a LuxR-type transcriptional regulator, designated RamA, which binds to the
pta-ack
and
aceA/aceB
promoter regions. Inactivation of the
ramA
gene in the genome of
C. glutamicum
resulted in mutant RG2. This mutant was unable to grow on acetate as the sole carbon and energy source and, in comparison to the wild type of
C. glutamicum
, showed very low specific activities of phosphotransacetylase, acetate kinase, isocitrate lyase, and malate synthase, irrespective of the presence of acetate in the medium. Comparative transcriptional
cat
fusion experiments revealed that this deregulation takes place at the level of transcription. By electrophoretic mobility shift analysis, purified His-tagged RamA protein was shown to bind specifically to the
pta-ack
and the
aceA/aceB
promoter regions, and deletion and mutation studies revealed in both regions two binding motifs each consisting of tandem A/C/TG
4-6
T/C or AC
4-5
A/G/T stretches separated by four or five arbitrary nucleotides. Our data indicate that RamA represents a novel LuxR-type transcriptional activator of genes involved in acetate metabolism of
C. glutamicum
.
Product Repression of Alkane Monooxygenase Expression in
Pseudomonas butanovora
Authors: Doughty D. M. , Sayavedra-Soto L. A. , Arp D. J. , Bottomley P. J. 
Published: March 2006

ABSTRACT

Physiological and regulatory mechanisms that allow the alkane-oxidizing bacterium
Pseudomonas butanovora
to consume C
2
to C
8
alkane substrates via butane monooxygenase (BMO) were examined. Striking differences were observed in response to even- versus odd-chain-length alkanes. Propionate, the downstream product of propane oxidation and of the oxidation of other odd-chain-length alkanes following β-oxidation, was a potent repressor of BMO expression. The transcriptional activity of the BMO promoter was reduced with as little as 10 μM propionate, even in the presence of appropriate inducers. Propionate accumulated stoichiometrically when 1-propanol and propionaldehyde were added to butane- and ethane-grown cells, indicating that propionate catabolism was inactive during growth on even-chain-length alkanes. In contrast, propionate consumption was induced (about 80 nmol propionate consumed · min
−1
· mg protein
−1
) following growth on the odd-chain-length alkanes, propane and pentane. The induction of propionate consumption could be brought on by the addition of propionate or pentanoate to the growth medium. In a reporter strain of
P. butanovora
in which the BMO promoter controls β-galactosidase expression, only even-chain-length alcohols (C
2
to C
8
) induced β-galactosidase following growth on acetate or butyrate. In contrast, both even- and odd-chain-length alcohols (C
3
to C
7
) were able to induce β-galactosidase following the induction of propionate consumption by propionate or pentanoate.
Molecular and Physiological Effects of Mycobacterial
oxyR
Inactivation
Authors: Pagán-Ramos Eileen , Master Sharon S. , Pritchett Christopher L. , Reimschuessel Renate , Trucksis Michele , Timmins Graham S. , Deretic Vojo 
Published: March 2006

ABSTRACT

The majority of slow-growing mycobacteria have a functional
oxyR
, the central regulator of the bacterial oxidative stress response. In contrast, this gene has been inactivated during the evolution of
Mycobacterium tuberculosis
. Here we inactivated the
oxyR
gene in
Mycobacterium marinum
, an organism used to model
M. tuberculosis
pathogenesis. Inactivation of
oxyR
abrogated induction of
ahpC
, a gene encoding alkylhydroperoxide reductase, normally activated upon peroxide challenge. The absence of
oxyR
also resulted in increased sensitivity to the front-line antituberculosis drug isoniazid. Inactivation of
oxyR
in
M. marinum
did not affect either virulence in a fish infection model or survival in human macrophages. Our findings demonstrate, at the genetic and molecular levels, a direct role for OxyR in
ahpC
regulation in response to oxidative stress. Our study also indicates that
oxyR
is not critical for virulence in
M. marinum
. However,
oxyR
inactivation confers increased sensitivity to isonicotinic acid hydrazide, suggesting that the natural loss of
oxyR
in the tubercle bacillus contributes to the unusually high sensitivity of
M. tuberculosis
to isoniazid.
Pharmacogenetics and Regulation of Human CytochromeP450 1B1: Implications in Hormone-Mediated Tumor Metabolism and a Novel Target for Therapeutic Intervention
Authors: Sissung Tristan M. , Price Douglas K. , Sparreboom Alex , Figg William D. 
Published: March 2006

AbstractSeveral of the hormone-mediated cancers (breast, endometrial, ovarian, and prostate) represent major cancers in both incidence and mortality rates. The etiology of these cancers is in large part modulated by the hormones estrogen and testosterone. As advanced disease develops, the common treatment for these cancers is chemotherapy. Thus, genes that can alter tissue response to hormones and alter clinical response to chemotherapy are of major interest. The cytochrome P450 1B1 (CYP1B1) may be involved in disease progression and modulate the treatment in the above hormone-mediated cancers. This review will focus on the pharmacogenetics of CYP1B1 in relation to hormone-mediated cancers and provide an assessment of cancer risk based on CYP1B1 polymorphisms and expression. In addition, it will provide a summary of CYP1B1 gene regulation and expression in normal and neoplastic tissue. (Mol Cancer Res 2006;4(3):1–16)
12/15 Lipoxygenase Mediates Monocyte Adhesion to Aortic Endothelium in Apolipoprotein E–Deficient Mice Through Activation of RhoA and NF-κB
Authors: Bolick David T. , Srinivasan Suseela , Whetzel Angela , Fuller Lauren C. , Hedrick Catherine C. 
Published: March 2006

Objectives—12/15 lipoxygenase (12/15LO) has been implicated as a mediator of inflammation and atherosclerosis. In the current study, we identified mechanisms through which 12/15LO mediates monocyte:endothelial interactions in vivo in apolipoprotein E-deficient mice (apoEKO), a well-characterized mouse model of atherosclerosis.Methods and Results—In apoEKO mice that are also deficient in 12/15LO (doubleKO), monocyte adhesion to aorta in vivo was reduced by 95% in doubleKO mice compared with apoEKO mice. Inhibition of 12/15LO in apoEKO mice in vivo using CDC (Cinnamyl-3,4-Dihydroxy-a-Cyanocinnamate) prevented monocyte adhesion to aortic endothelium in apoEKO mice. Aortic endothelium of apoEKO mice had significant activation of rhoA compared with doubleKO aortic endothelium. Further, apoEKO aorta displayed significant activation of NF-κB. DoubleKO aorta displayed little nuclear localization of NF-κB. Finally, we found significant upregulation of intercellular adhesion molecule-1 (ICAM-1) on apoEKO aortic endothelium compared with doubleKO endothelium. Inhibition of rhoA and PKCα significantly reduced NF-κB activation, ICAM-1 induction, and monocyte adhesion to aorta.Conclusions—We conclude that 12/15LO products activate endothelial rhoA and PKCα. Activation of rhoA and PKCα cause activation and translocation of NF-κB to the nucleus, which, in turn, results in induction of ICAM-1. Induction of ICAM-1 on aortic endothelium stimulates monocyte:endothelial adhesion in vivo in apoEKO mice.
Petrology of forearc peridotite from the Hahajima Seamount, the Izu-Bonin arc, with special reference to chemical characteristics of chromian spinel
Authors: Okamura H. , Arai S. , Kim Y.-U. 
Published: March 2006

AbstractForearc peridotite is generally characterized by low Mg# (= Mg/[Mg + Fe2+] atomic ratio) at a given Cr# (= Cr/[Cr + Al] atomic ratio) of chromian spinel compared to common abyssal peridotite. This may be due to (1) smaller modal abundance of spinel and/or (2) lower equilibrium temperature, for the forearc peridotite. Forearc peridotite has the same amount of spinel as abyssal peridotite, eliminating the first possibility. Spinel in harzburgite and dunite from the Hahajima Seamount at the Izu-Bonin forearc, has a large Cr#, >0.57, and the Mg# is slightly variable towards low values at a given Cr#. The Mg# of spinel cores decreases strongly with a decrease in size. This is due to cooling along with hydration, which gave rise to a compositional variation of Ca-amphibole, from edenitic hornblende (high-temperature) to tremolite (low-temperature) in the Hahajima peridotite. The average two- pyroxene temperature of the Hahajima peridotite, 921°C, is less than that of the abyssal peridotite (1138°C), which is not consistent with a size-dependent Mg# of spinel for the latter. Forearc peridotite has been cooled effectively by H2O released from the subducted slab, causing a small Mg# of their spinels.
Detrital chrome-spinel grains in heavy-mineral sand deposits from southeast Africa
Authors: Pownceby M. , Bourne P. 
Published: March 2006

AbstractDetrital chrome-spinels are contaminant grains within ilmenite concentrates produced from heavy-mineral deposits along the coast of southeast Africa. The presence of even minor levels of chromia in the predominantly ilmenite-rich concentrates, downgrades their market value as potential feedstocks for the production of titania pigment. An understanding of their composition can assist in their removal from the ilmenite concentrates.Compositions from a database of close to 900 chrome-spinel analyses shows the major element components and their ranges (in wt.%) are: Cr: 0.4-45.3, Al: 0.0-31.0, Fe: 8.5-69.6 and Mg: 0.0-12.2. Minor components include Ti: 0.1-11.4 and Zn: 0.0-13.7.The chrome-spinel data fall into two compositionally distinct groups. The first group of spinels is dominated by a strong trend reflecting the mutual substitution between Al3+ and Cr3+ in the spinel structure. The second group of spinels is characterized by compositions containing abundant Fe3O4magnetite component. The clear division between chrome-spinel compositional types indicates the grains are derived from at least two chemically dissimilar provenances.The compositional differences between the chrome-spinel groups has a positive impact on subsequent ilmenite upgrading treatments as the spinels which contain the highest magnetite component are easily removed via low-intensity magnetic separation procedures.
Platinum-group mineral assemblages in the Platreef at the Sandsloot Mine, northern Bushveld Complex, South Africa
Authors: Holwell D. A. , McDonald I. , Armitage P. E. B. 
Published: March 2006

AbstractPlatinum group mineral (PGM) assemblages in the Platreef at Sandsloot, northern Bushveld Complex, in a variety of lithologies reveal a complex multi-stage mineralization history. During crystallization of the Platreef pyroxenites, platinum group elements (PGE) and base-metal sulphides (BMS) were distributed thoughout the interstitial liquid forming a telluride-dominant assemblage devoid of PGE sulphides. Redistribution of PGE into the metamorphic footwall by hydrothermal fluids has formed arsenide-, alloy- and antimonide-dominant assemblages, indicating a significant volatile influence during crystallization. Serpentinization of the footwall has produced an antimonide-dominant PGM assemblage. Parts of the igneous reef were subjected to alteration by a late-stage, Fe-rich fluid, producing ultramafic zones where the telluride-dominant assemblage has been recrystallized to an alloy-dominant one, particularly rich in Pt-Fe and Pd-Pb alloys. A thin, small-volume zone of PGE-BMS mineralization along the base of the hangingwall contains a primary PGM assemblage that is locally altered to one dominated by Pt/Pd germanides. This is thought to have formed when the new pulse of Main Zone magma entered the chamber, and scavenged PGE from the underlying Platreef pyroxenites. That each major rock type at Sandsloot contains a distinctive PGM assemblage reflects the importance of syn- and post-emplacement fluid and magmatic processes on the development of Platreef mineralization.
Paratooite-(La), a new lanthanum-dominant rare-earth copper carbonate from Paratoo, South Australia
Authors: Pring A. , Wallwork K. , Brugger J. , U. Kolitsch  
Published: March 2006

AbstractParatooite-(La) is a new lanthanum-dominant rare-earth copper carbonate from the Paratoo copper mine, near Yunta, Olary district, South Australia. Paratooite-(La) occurs as sheaves and radiating sprays of blade-like to tabular pale blue crystals in thin fissures in a slaty country rock. Individual crystals are typically 50–200 μm in maximum dimension but <5 μm thick. Associated minerals include donnayite-(Y), kamphaugite-(Y), and bastnäsite-(La). Electron microprobe and CHN analyses gave: La2O3 26.47; Pr2O3 7.74; Nd2O3 8.15; Sm2O3 0.66; Gd2O3 0.85; Y2O3 0.72; CaO 7.57; SrO 3.15; Na2O 3.3; CuO 5.77; F 0.24; CO2 32.05; NO2 1.12; -O=F -0.10; sum 100.03, yielding an empirical formula of (La3.54Ca2.94Na2.32Nd1.05Pr1.03Sr0.66Y0.14Gd0.10Sm0.08)Σ11.86Cu1.58(C15.84N0.53)O47.76F0.24. The simplified formula is (REE ,Ca,Na,Sr)6Cu(CO3)8 or possibly REE3(Ca,Sr)2NaCu(CO3)8. The mineral is pale turquoise-blue to pale blue in colour, transparent, with a pearly to vitreous lustre and a pale blue streak. No cleavage was observed but the morphology and TEM studies indicate a cleavage parallel to ﹛100﹜. The Mohs hardness is estimated to be 4. The strongest lines in the X-ray powder pattern are [dobs (Iobs) (hkl )]: 5.047 (53) (200); 4.786 (49) (021); 3.957 (43) (220); 3.468 (43) (012, 221); 2.927 (100) (202); 2.530 (52) (241); 2.344 (22) (420,103); 2.232 (20) (421). A synchrotron powder diffraction pattern was indexed on a primitive orthorhombic cell with a = 10.0862(5), b = 12.8088(6), c = 7.2360(4) Å, V= 934.8(1) Å3 and Z = 2. The crystal structure of the new mineral could not be determined but powder diffraction data indicate the space group is probably P 222, Pmmm , P 2221 or Pmm2. The measured density is 3.68(3) g/cm3 and the calculated density is 3.78 g/cm3. Paratooite-(La) is biaxial negative with α = 1.605(3), β = 1.696(3) and γ = 1.752(2); pleochroism is medium strong; X very pale bluish, Y and Z bluish (with greenish tint) with absorption Z ≈ Y >> X. Paratooite-(La) is a supergene mineral which precipitated from mildly basic carbonated groundwaters. The mineral is named for the type locality.