bluuebunny/crossref_metadata_2025_split huggingface dataset:
Formation of Nanoscale Elemental Silver Particles via Enzymatic Reduction by
Geobacter sulfurreducens
Authors: Law Nicholas , Ansari Saadia , Livens Francis R. , Renshaw Joanna C. , Lloyd Jonathan R. 
Published: August 2008

ABSTRACT

Geobacter sulfurreducens
reduced Ag(I) (as insoluble AgCl or Ag
+
ions), via a mechanism involving
c
-type cytochromes, precipitating extracellular nanoscale Ag(0). These results extend the range of metals known to be reduced by
Geobacter
species and offer a method for recovering silver from contaminated water as potentially useful silver nanoparticles.
Biodegradation of 2-Ethylhexyl Nitrate by
Mycobacterium austroafricanum
IFP 2173
Authors: Nicolau Elodie , Kerhoas Lucien , Lettere Martine , Jouanneau Yves , Marchal Rémy 
Published: August 2008

ABSTRACT

2-Ethyhexyl nitrate (2-EHN) is a major additive of fuel that is used to increase the cetane number of diesel. Because of its wide use and possible accidental release, 2-EHN is a potential pollutant of the environment. In this study,
Mycobacterium austroafricanum
IFP 2173 was selected from among several strains as the best 2-EHN degrader. The 2-EHN biodegradation rate was increased in biphasic cultures where the hydrocarbon was dissolved in an inert non-aqueous-phase liquid, suggesting that the transfer of the hydrophobic substrate to the cells was a growth-limiting factor. Carbon balance calculation, as well as organic-carbon measurement, indicated a release of metabolites in the culture medium. Further analysis by gas chromatography revealed that a single metabolite accumulated during growth. This metabolite had a molecular mass of 114 Da as determined by gas chromatography/mass spectrometry and was provisionally identified as 4-ethyldihydrofuran-2(3H)-one by liquid chromatography-tandem mass spectrometry analysis. Identification was confirmed by analysis of the chemically synthesized lactone. Based on these results, a plausible catabolic pathway is proposed whereby 2-EHN is converted to 4-ethyldihydrofuran-2(3H)-one, which cannot be metabolized further by strain IFP 2173. This putative pathway provides an explanation for the low energetic efficiency of 2-EHN degradation and its poor biodegradability.
Characterization and Deposition of Respirable Large- and Small-Particle Bioaerosols
Authors: Thomas Richard J. , Webber Daniel , Sellors William , Collinge Aaron , Frost Andrew , Stagg Anthony J. , Bailey Stephen C. , Jayasekera Pramukh N. , Taylor Rosa R. , Eley Steve , Titball Richard W. 
Published: August 2008

ABSTRACT

The deposition patterns of large-particle microbiological aerosols within the respiratory tract are not well characterized. A novel system (the flow-focusing aerosol generator [FFAG]) which enables the generation of large (>10-μm) aerosol particles containing microorganisms under laboratory conditions was characterized to permit determination of deposition profiles within the murine respiratory tract. Unlike other systems for generating large aerosol particles, the FFAG is compatible with microbiological containment and the inhalational challenge of animals. By use of entrapped
Escherichia coli
cells,
Bacillus atrophaeus
spores, or FluoSphere beads, the properties of aerosols generated by the FFAG were compared with the properties of aerosols generated using the commonly available Collison nebulizer, which preferentially generates small (1- to 3-μm) aerosol particles. More entrapped particulates (15.9- to 19.2-fold) were incorporated into 9- to 17-μm particles generated by the FFAG than by the Collison nebulizer. The 1- to 3-μm particles generated by the Collison nebulizer were more likely to contain a particulate than those generated by the FFAG.
E. coli
cells aerosolized using the FFAG survived better than those aerosolized using the Collison nebulizer. Aerosols generated by the Collison nebulizer and the FFAG preferentially deposited in the lungs and nasal passages of the murine respiratory tract, respectively. However, significant deposition of material also occurred in the gastrointestinal tract after inhalation of both the small (89.7%)- and large (61.5%)-particle aerosols. The aerosols generated by the Collison nebulizer and the FFAG differ with respect to mass distribution, distribution of the entrapped particulates, bacterial survival, and deposition within the murine respiratory tract.
Development of a Transposon Mutagenesis System in the Oral Spirochete
Treponema denticola
Authors: Yang Yu , Stewart Philip E. , Shi Xiaoguang , Li Chunhao 
Published: August 2008

ABSTRACT

Here, we report successful transposon mutagenesis in the oral spirochete
Treponema denticola
. A modified
Himar1
transposon, including a new antibiotic selection cassette for
T. denticola
, generated mutations affecting cell division, transport, and chemotaxis, among other processes. This random mutagenesis system should facilitate research on the biology and pathogenesis of this spirochete, which is associated with human periodontal diseases.
Crenarchaeota
and Their Role in the Nitrogen Cycle in a Subsurface Radioactive Thermal Spring in the Austrian Central Alps
Authors: Weidler Gerhard W. , Gerbl Friedrich W. , Stan-Lotter Helga 
Published: August 2008

ABSTRACT

Previous results from a 16S rRNA gene library analysis showed high diversity within the prokaryotic community of a subterranean radioactive thermal spring, the “Franz-Josef-Quelle” (FJQ) in Bad Gastein, Austria, as well as evidence for ammonia oxidation by crenarchaeota. This study reports further characterization of the community by denaturing gradient gel electrophoresis (DGGE) analysis, fluorescence in situ hybridization (FISH), and semiquantitative nitrification measurements. DGGE bands from three types of samples (filtered water, biofilms on glass slides, and naturally grown biofilms), including samples collected at two distinct times (January 2005 and July 2006), were analyzed. The archaeal community consisted mainly of
Crenarchaeota
of the soil-subsurface-freshwater group (group 1.1b) and showed a higher diversity than in the previous 16S rRNA gene library analysis, as was also found for crenarchaeal
amoA
genes. No bacterial
amoA
genes were detected. FISH analysis of biofilms indicated the presence of archaeal cells with an abundance of 5.3% (±4.5%) in the total 4′,6-diamidino-2-phenylindole (DAPI)-stained community. Microcosm experiments of several weeks in duration showed a decline of ammonium that correlated with an increase of nitrite, the presence of crenarchaeal
amoA
genes, and the absence of bacterial
amoA
genes. The data suggested that only ammonia-oxidizing archaea (AOA) perform the first step of nitrification in this 45°C environment. The crenarchaeal
amoA
gene sequences grouped within a novel cluster of
amoA
sequences from the database, originating from geothermally influenced environments, for which we propose the designation “thermal spring” cluster and which may be older than most AOA from soils on earth.
Identification of Lacto-N-Biose I Phosphorylase fromVibrio vulnificusCMCP6
Authors: Nakajima Masahiro , Kitaoka Motomitsu 
Published: August 2008

ABSTRACTA β-1,3-galactosyl-N-acetylhexosamine phosphorylase (GalGlyNAcP) homolog gene was cloned fromVibrio vulnificusCMCP6. In synthetic reactions, the recombinant enzyme acted only with GlcNAc and GalNAc as acceptors in the presence of α-d-galactose-1-phosphate as a donor to form lacto-N-biose I (LNB) (Galβ1 → 3GlcNAc) and galacto-N-biose (GNB) (Galβ1 → 3GalNAc), respectively. GlcNAc was a much better acceptor than GalNAc. The enzyme also phosphorolysed LNB faster than it phosphorolysed GNB, and thekcat/Kmfor LNB was approximately 60 times higher than thekcat/Kmfor GNB. This result indicated that the enzyme was remarkably different from GalGlyNAcP fromBifidobacterium longum, which has similar activities with LNB and GNB, and GalGlyNAcP fromClostridium perfringens, which is a GNB-specific enzyme. The enzyme is the first LNB-specific enzyme that has been found and was designated lacto-N-biose I phosphorylase. The discovery of an LNB-specific GalGlyNAcP resulted in recategorization of bifidobacterial GalGlyNAcPs as galacto-N-biose/lacto-N-biose I phosphorylases.
C-Terminal Signals Regulate Targeting of Glycosylphosphatidylinositol-Anchored Proteins to the Cell Wall or Plasma Membrane in
Candida albicans
Authors: Mao Yuxin , Zhang Zimei , Gast Charles , Wong Brian 
Published: August 2008

ABSTRACT

Fungal glycosylphosphatidylinositol (GPI)-anchored proteins localize to the plasma membrane (PM), cell wall (CW), or both. To study signals that regulate PM versus CW targeting in
Candida albicans
, we (i) fused the N and/or C termini of the GPI CW protein Hwp1p and the GPI PM protein Ecm331p to green fluorescent protein (GFP) and (ii) expressed and localized the resulting fusions. Forty-seven amino acids from the C terminus of Hwp1p were sufficient to target GFP to the CW, and 66 amino acids from the C terminus of Ecm331p were sufficient to target GFP to the PM. Truncation and mutagenesis studies showed that G390 was the ω cleavage site in Ecm331p. Domain exchange and mutagenesis studies showed that (i) the 5 amino acids immediately N-terminal to the ω sites (the ω − 5 to ω − 1 amino acids) played key roles in targeting to the PM or CW; (ii) KK and FE residues at positions ω − 1 and ω − 2, respectively, targeted to the PM and CW; and (iii) a loss of I at position ω − 5 increased PM retention. Small fluorescent reporters can be used to study the peptide signals that regulate PM versus CW targeting of GPI proteins and may be useful for identifying proteins that interact with key targeting signals.
Assembly of the
Trypanosoma brucei
60S Ribosomal Subunit Nuclear Export Complex Requires Trypanosome-Specific Proteins P34 and P37
Authors: Prohaska Kimberly , Williams Noreen 
Published: August 2008

ABSTRACT

We previously identified two
Trypanosoma brucei
RNA binding proteins, P34 and P37, and determined that they are essential for proper ribosomal assembly in this organism. Loss of these proteins via RNA interference is lethal and causes a decrease in both 5S rRNA levels and formation of 80S ribosomes, concomitant with a decrease in total cellular protein synthesis. These data suggest that these proteins are involved at some point in the ribosomal biogenesis pathway. In the current study, we have performed subcellular fractionation in conjunction with immune capture experiments specific for 60S ribosomal proteins and accessory factors in order to determine when and where P34 and P37 are involved in the ribosomal biogenesis pathway. These studies demonstrate that P34 and P37 associate with the 60S ribosomal subunit at the stage of the nucleolar 90S particle and remain associated subsequent to nuclear export. In addition, P34 and P37 associate with conserved 60S ribosomal subunit nuclear export factors exportin 1 and Nmd3, suggesting that they are components of the 60S ribosomal subunit nuclear export complex in
T. brucei
. Most significantly, the pre-60S complex does not associate with exportin 1 or Nmd3 in the absence of P34 and P37. These results demonstrate that, although
T. brucei
60S ribosomal subunits utilize a nuclear export complex similar to that described for other organisms, trypanosome-specific factors are essential to the process.
Transitions in Sexuality: Recapitulation of an Ancestral Tri- and Tetrapolar Mating System in
Cryptococcus neoformans
Authors: Hsueh Yen-Ping , Fraser James A. , Heitman Joseph 
Published: August 2008

ABSTRACT

Sex is orchestrated by the mating-type locus (
MAT
) in fungi and by sex chromosomes in plants and animals. In fungi, two patterns of sexuality occur: bipolar with a single, typically biallelic sex determinant that promotes inbreeding, and tetrapolar with two unlinked, often multiallelic sex determinants that restrict inbreeding. Multiallelism in either bipolar or tetrapolar mating systems promotes outcrossing.
Cryptococcus neoformans
is a pathogenic bipolar yeast with two unusually large
MAT
alleles (
a/
α) spanning >100 kb, ∼100-fold larger than many other fungal
MAT
loci. Based on comparative genomic analysis, this unusual
MAT
locus is hypothesized to have evolved from an ancestral tetrapolar system. In this model, the unlinked homeodomain (HD) transcription factor and pheromone/receptor tetrapolar loci acquired additional sex-related genes and then fused via chromosomal translocation, forming an intermediate transitional mating system (which we term tripolar), which then underwent recombination and gene conversion to fashion the extant bipolar
MAT
alleles. To experimentally validate this model,
C. neoformans
was engineered to have a tetrapolar mating system by relocating the
MAT SXI1
α and
SXI2
a
HD genes to an unlinked genomic locale. Genetic and molecular analyses revealed that this modified organism could complete a tetrapolar sexual cycle. Analysis of progeny generated from bipolar, tripolar, and tetrapolar crosses provides direct experimental evidence that the tripolar state confers decreased fertility and therefore may represent an unstable evolutionary intermediate. These findings illustrate how transitions between outcrossing and inbreeding preference occur by involving sex determinant linkage and collapse from multiallelic to biallelic sex determination, providing insights into both fungal sex evolution and early steps in sex chromosome evolution.
Functional Studies of Multiple Thioredoxins from
Mycobacterium tuberculosis
Authors: Akif Mohd , Khare Garima , Tyagi Anil K. , Mande Shekhar C. , Sardesai Abhijit A. 
Published: August 2008

ABSTRACT

Cytoplasmic protein reduction via generalized thiol/disulfide exchange reactions and maintenance of cellular redox homeostasis is mediated by the thioredoxin superfamily of proteins. Here, we describe the characterization of the thioredoxin system from
Mycobacterium tuberculosis
, whose genome bears the potential to encode three putative thioredoxins from the open reading frames designated

trxA
Mtb

,

trxB
Mtb

, and

trxC
Mtb

. We show that all three thioredoxins, overproduced in
Escherichia coli
, are able to reduce insulin, a model substrate, in the presence of dithiothreitol. However, we observe that thioredoxin reductase is not capable of reducing TrxA

Mtb

in an NADPH-dependent manner, indicating that only TrxB

Mtb

and TrxC

Mtb

are the biologically active disulfide reductases. The absence of detectable mRNA transcripts of

trxA
Mtb

observed when
M. tuberculosis
strain H37Rv was cultivated under different growth conditions suggests that

trxA
Mtb

expression may be cryptic. The measured redox potentials of TrxB

Mtb

and TrxC

Mtb

(−262 ± 2 mV and −269 ± 2 mV, respectively) render these proteins somewhat more oxidizing than
E. coli
thioredoxin 1 (TrxA). In
E. coli
strains lacking components of cytoplasmic protein reduction pathways, heterologous expression of the mycobacterial thioredoxins was able to effectively substitute for their function.
In Vivo Inactivation of the Mycobacterial Integral Membrane Stearoyl Coenzyme A Desaturase DesA3 by a C-Terminus-Specific Degradation Process
Authors: Chang Yong , Wesenberg Gary E. , Bingman Craig A. , Fox Brian G. 
Published: August 2008

ABSTRACT

DesA3 (Rv3229c) from
Mycobacterium tuberculosis
is a membrane-bound stearoyl coenzyme A Δ
9
desaturase that reacts with the oxidoreductase Rv3230c to produce oleic acid. This work provides evidence for a mechanism used by mycobacteria to regulate this essential enzyme activity. DesA3 expressed as a fusion with either a C-terminal His
6
or c-myc tag had consistently higher activity and stability than native DesA3 having the native C-terminal sequence of LAA, which apparently serves as a binding determinant for a mycobacterial protease/degradation system directed at DesA3. Fusion of only the last 12 residues of native DesA3 to the C terminus of green fluorescent protein (GFP) was sufficient to make GFP unstable. Furthermore, the comparable C-terminal sequence from the
Mycobacterium smegmatis
DesA3 homolog Msmeg_1886 also conferred instability to the GFP fusion. Systematic examination revealed that residues with charged side chains, large nonpolar side chains, or no side chain at the last two positions were most important for stabilizing the construct, while lesser effects were observed at the third-from-last position. Using these rules, a combinational substitution of the last three residues of DesA3 showed that either DKD or LEA gave the best enhancement of stability for the modified GFP in
M. smegmatis
. Moreover, upon mutagenesis of LAA at the C terminus in native DesA3 to either of these tripeptides, the modified enzyme had enhanced catalytic activity and stability. Since many proteases are conserved within bacterial families, it is reasonable that
M. tuberculosis
will use a similar C-terminal degradation system to posttranslationally regulate the activity of DesA3 and other proteins. Application of these rules to the
M. tuberculosis
genome revealed that ∼10% the proteins encoded by essential genes may be susceptible to C-terminal proteolysis. Among these, an annotation is known for less than half, underscoring a general lack of understanding of proteins that have only temporal existence in a cell.
The Transcriptional Factors MurR and Catabolite Activator Protein Regulate
N
-Acetylmuramic Acid Catabolism in
Escherichia coli
Authors: Jaeger Tina , Mayer Christoph 
Published: August 2008

ABSTRACT

The MurNAc etherase MurQ of
Escherichia coli
is essential for the catabolism of the bacterial cell wall sugar
N
-acetylmuramic acid (MurNAc) obtained either from the environment or from the endogenous cell wall (i.e., recycling). High-level expression of
murQ
is required for growth on MurNAc as the sole source of carbon and energy, whereas constitutive low-level expression of
murQ
is sufficient for the recycling of peptidoglycan fragments continuously released from the cell wall during growth of the bacteria. Here we characterize for the first time the expression of
murQ
and its regulation by MurR, a member of the poorly characterized RpiR/AlsR family of transcriptional regulators. Deleting
murR
abolished the extensive lag phase observed for
E. coli
grown on MurNAc and enhanced
murQ
transcription some 20-fold. MurR forms a stable multimer (most likely a tetramer) and binds to two adjacent inverted repeats within an operator region. In this way MurR represses transcription from the
murQ
promoter and also interferes with its own transcription. MurNAc-6-phosphate, the substrate of MurQ, was identified as a specific inducer that weakens binding of MurR to the operator. Moreover,
murQ
transcription depends on the activation by cyclic AMP (cAMP)-catabolite activator protein (CAP) bound to a class I site upstream of the
murQ
promoter.
murR
and
murQ
are divergently orientated and expressed from nonoverlapping face-to-face (convergent) promoters, yielding transcripts that are complementary at their 5′ ends. As a consequence of this unusual promoter arrangement, cAMP-CAP also affects
murR
transcription, presumably by acting as a roadblock for RNA polymerase.
Chemotaxis as an Emergent Property of a Swarm
Authors: Taylor Rion G. , Welch Roy D. 
Published: August 2008

ABSTRACT

We have characterized and quantified a form of bacterial chemotaxis that manifests only as an emergent property by measuring symmetry breaking in a swarm of
Myxococcus xanthus
exposed to a two-dimensional nutrient gradient from within an agar substrate.
M. xanthus
chemotaxis requires cell-cell contact and coordinated motility, as individual motile cells exhibit only nonvectorial movement in the presence of a nutrient gradient. Genes that specifically affect
M. xanthus
chemotaxis include at least 10 of the 53 that express enhancer binding proteins of the NtrC-like class, an indication that this behavior is controlled through transcription, most likely by a complex signal transduction network.
The
Anabaena
sp. Strain PCC 7120 Gene all2874 Encodes a Diguanylate Cyclase and Is Required for Normal Heterocyst Development under High-Light Growth Conditions
Authors: Neunuebel M. Ramona , Golden James W. 
Published: August 2008

ABSTRACT

The genome of the heterocyst-forming cyanobacterium
Anabaena
sp. strain PCC 7120 harbors 14 genes containing a GGDEF diguanylate cyclase domain. We found that inactivation of one of these genes, all2874, caused abnormal heterocyst development. The all2874 mutant showed a pronounced reduction in heterocyst frequency during diazotrophic growth and reduced vegetative cell size compared to the wild type. The severity of the mutant phenotype varied with light intensity; at high light intensity, the mutant phenotype was accentuated, whereas at low light intensity the phenotype was similar to wild type. Under high-light growth conditions, the initial heterocyst frequency and pattern for the all2874 mutant were normal, but within 4 days following nitrogen step-down, many intervals between heterocysts increased to as many as 200 vegetative cells, whereas in the wild type the intervals were less than 25 vegetative cells. Filaments containing these unusually long vegetative cell intervals between heterocysts also contained intervals of normal length. An all2874 mutant strain carrying a P

patS

-
gfp
transcriptional reporter fusion failed to show normal upregulation of the reporter, which indicates that the decrease in heterocyst frequency is due to an early block in differentiation before induction of the
patS
gene, which in the wild type takes place 8 h after nitrogen step-down. Genetic epistasis experiments suggest that All2874 acts upstream of the master regulator HetR in differentiating cells. We also showed that purified All2874 functions as a diguanylate cyclase in vitro. We hypothesize that All2874 is required for the normal regulation of heterocyst frequency under high-light growth conditions.
σ32-Mediated Negative Regulation ofSalmonellaPathogenicity Island 1 Expression
Authors: Matsui Mari , Takaya Akiko , Yamamoto Tomoko 
Published: August 2008

ABSTRACTSalmonellapathogenicity island 1 (SPI1) enables infecting salmonellae to invade the intestinal epithelium and induce a proinflammatory response and macrophage cell death. SPI1 expression is controlled by a complex cascade with several transcriptional regulators within the island and global regulators outside it. Previously, we reported that DnaK-depleted salmonellae could neither invade epithelial cells nor secrete SPI1-encoded proteins, suggesting that DnaK is involved in the expression of SPI1. Here, we found that DnaK is involved in SPI1 expression through inhibition of σ32protein, which directs the transcription of a group of genes in response to various global stresses. Overproduction of σ32resulted in decreased levels of the SPI1-specific transcriptional regulators HilD and HilA. Further analysis demonstrated that the σ32-mediated system negatively regulates HilD and HilA at the posttranslational and transcriptional levels, respectively. The executioner of this negative regulation was shown to be a σ32-induced protein ATP-dependent Lon protease, which specifically degrades HilD. Since HilD can activatehilAtranscription, is at the top of the hierarchical SPI1 regulatory loop, and has a dominant role, the posttranslational control of HilD by Lon is critically important for precise expression of SPI1. Consequently, we suggest that SPI1 expression is controlled by the feedback regulatory loop in which σ32induces Lon to control turnover of HilD, and DnaK, which inhibits σ32function, leading to the modulation oflonexpression. This regulation in response to a specific combination of environmental signals would ensure that SPI1 expression is restricted to a few specific locations in the host.