bluuebunny/crossref_metadata_2025_split huggingface dataset:
Population Structure and Abundance of Arsenite-Oxidizing Bacteria along an Arsenic Pollution Gradient in Waters of the Upper Isle River Basin, France
Authors: Quéméneur Marianne , Cébron Aurélie , Billard Patrick , Battaglia-Brunet Fabienne , Garrido Francis , Leyval Corinne , Joulian Catherine 
Published: May 2010

ABSTRACT

Denaturing gradient gel electrophoresis (DGGE) and quantitative real-time PCR (qPCR) were successfully developed to monitor functional
aoxB
genes as markers of aerobic arsenite oxidizers. DGGE profiles showed a shift in the structure of the
aoxB
-carrying bacterial population, composed of members of the
Alpha
-,
Beta
- and
Gammaproteobacteria
, depending on arsenic (As) and E
h
levels in Upper Isle River Basin waters. The highest
aoxB
gene densities were found in the most As-polluted oxic surface waters but without any significant correlation with environmental factors. Arsenite oxidizers seem to play a key role in As mobility in As-impacted waters.
Regrowth of Potential Opportunistic Pathogens and Algae in Reclaimed-Water Distribution Systems
Authors: Jjemba Patrick K. , Weinrich Lauren A. , Cheng Wei , Giraldo Eugenio , LeChevallier Mark W. 
Published: May 2010

ABSTRACT

A study of the quality of reclaimed water in treated effluent, after storage, and at three points in the distribution system of four plants in California, Florida, Massachusetts, and New York was conducted for 1 year. The plants had different treatment processes (conventional versus membrane bioreactor), production capacities, and methods for storage of the water, and the intended end uses of the water were different. The analysis focused on the occurrence of indicator bacteria (heterotrophic bacteria, coliforms,
Escherichia coli
, and enterococci) and opportunistic pathogens (
Aeromonas
spp., enteropathogenic
E. coli
O157:H7,
Legionella
spp.,
Mycobacterium
spp., and
Pseudomonas
spp.), as well as algae. Using immunological methods,
E. coli
O157:H7 was detected in the effluent of only one system, but it was not detected at the sampling points, suggesting that its survival in the system was poor. Although all of the treatment systems effectively reduced the levels of bacteria in the effluent, bacteria regrew in the reservoir and distribution systems because of the loss of residual disinfectant and high assimilable organic carbon levels. In the systems with open reservoirs, algal growth reduced the water quality by increasing the turbidity and accumulating at the end of the distribution system. Opportunistic pathogens, notably
Aeromonas
,
Legionella
,
Mycobacterium
, and
Pseudomonas
, occurred more frequently than indicator bacteria (enterococci, coliforms, and
E. coli
). The
Mycobacterium
spp. were very diverse and occurred most frequently in membrane bioreactor systems, and
Mycobacterium cookii
was identified more often than the other species. The public health risk associated with these opportunistic pathogens in reclaimed water is unknown. Collectively, our results show the need to develop best management practices for reclaimed water to control bacterial regrowth and degradation of water before it is utilized at the point of use.
Aspergillus fumigatus Catalytic Glucokinase and Hexokinase: Expression Analysis and Importance for Germination, Growth, and Conidiation
Authors: Fleck Christian B. , Brock Matthias 
Published: May 2010

ABSTRACT

Fungi contain several hexokinases, which are involved either in sugar phosphorylation or in carbon source sensing. Glucose and fructose phosphorylations appear to rely exclusively on glucokinase and hexokinase. Here, we characterized the catalytic glucokinase and hexokinase from the opportunistic human pathogen
Aspergillus fumigatus
and showed that both enzymes display different biochemical properties and play different roles during growth and development. Glucokinase efficiently activates glucose and mannose but activates fructose only to a minor extent. Hexokinase showed a high efficiency for fructose activation but also activated glucose and mannose. Transcript and activity determinations revealed high levels of glucokinase in resting conidia, whereas hexokinase was associated mainly with the mycelium. Consequentially, a glucokinase mutant showed delayed germination at low glucose concentrations, whereas colony growth was not overly affected. The deletion of hexokinase had only a minor impact on germination but reduced colony growth, especially on sugar-containing media. Transcript determinations from infected mouse lungs revealed the expression of both genes, indicating a contribution to virulence. Interestingly, a double-deletion mutant showed impaired growth not only on sugars but also on nonfermentable nutrients, and growth on gluconeogenic carbon sources was strongly suppressed in the presence of glucose. Furthermore, the
glkA hxkA
deletion affected cell wall integrity, implying that both enzymes contribute to the cell wall composition. Additionally, the absence of either enzyme deregulated carbon catabolite repression since mutants displayed an induction of isocitrate lyase activity during growth on glucose-ethanol medium. Therefore, both enzymes seem to be required for balancing carbon flux in
A. fumigatus
and are indispensable for growth under all nutritional conditions.
A
-Mating-Type Gene Expression Can Drive Clamp Formation in the Bipolar Mushroom Pholiota microspora (Pholiota nameko)
Authors: Yi Ruirong , Mukaiyama Hiroyuki , Tachikawa Takashi , Shimomura Norihiro , Aimi Tadanori 
Published: May 2010

ABSTRACT

In the bipolar basidiomycete
Pholiota microspora
, a pair of homeodomain protein genes located at the
A
-mating-type locus regulates mating compatibility. In the present study, we used a DNA-mediated transformation system in
P. microspora
to investigate the homeodomain proteins that control the clamp formation. When a single homeodomain protein gene (
A3-hox1
or
A3-hox2
) from the
A3
monokaryon strain was transformed into the
A4
monokaryon strain, the transformants produced many pseudoclamps but very few clamps. When two homeodomain protein genes (
A3-hox1
and
A3-hox2
) were transformed either separately or together into the
A4
monokaryon, the ratio of clamps to the clamplike cells in the transformants was significantly increased to ca. 50%. We therefore concluded that the gene dosage of homeodomain protein genes is important for clamp formation. When the
sip
promoter was connected to the coding region of
A3-hox1
and
A3-hox2
and the fused fragments were introduced into NGW19-6 (
A4
), the transformants achieved more than 85% clamp formation and exhibited two nuclei per cell, similar to the dikaryon (NGW12-163 × NGW19-6). The results of real-time reverse transcription-PCR confirmed that
sip
promoter activity is greater than that of the native promoter of homeodomain protein genes in
P. microspora.
Thus, we concluded that nearly 100% clamp formation requires high expression levels of homeodomain protein genes and that altered expression of the
A
-mating-type genes alone is sufficient to drive true clamp formation.
Genome Analysis of
Moraxella catarrhalis
Strain RH4, a Human Respiratory Tract Pathogen
Authors: de Vries Stefan P. W. , van Hijum Sacha A. F. T. , Schueler Wolfgang , Riesbeck Kristian , Hays John P. , Hermans Peter W. M. , Bootsma Hester J. 
Published: May 2010

ABSTRACT

Moraxella catarrhalis
is an emerging human-restricted respiratory tract pathogen that is a common cause of childhood otitis media and exacerbations of chronic obstructive pulmonary disease in adults. Here, we report the first completely assembled and annotated genome sequence of an isolate of
M. catarrhalis
, strain RH4, which originally was isolated from blood of an infected patient. The RH4 genome consists of 1,863,286 nucleotides that form 1,886 protein-encoding genes. Comparison of the RH4 genome to the ATCC 43617 contigs demonstrated that the gene content of both strains is highly conserved.
In silico
phylogenetic analyses based on both 16S rRNA and multilocus sequence typing revealed that RH4 belongs to the seroresistant lineage. We were able to identify almost the entire repertoire of known
M. catarrhalis
virulence factors and mapped the members of the biosynthetic pathways for lipooligosaccharide, peptidoglycan, and type IV pili. Reconstruction of the central metabolic pathways suggested that RH4 relies on fatty acid and acetate metabolism, as the genes encoding the enzymes required for the glyoxylate pathway, the tricarboxylic acid cycle, the gluconeogenic pathway, the nonoxidative branch of the pentose phosphate pathway, the beta-oxidation pathway of fatty acids, and acetate metabolism were present. Moreover, pathways important for survival under challenging
in vivo
conditions, such as the iron-acquisition pathways, nitrogen metabolism, and oxidative stress responses, were identified. Finally, we showed by microarray expression profiling that ∼88% of the predicted coding sequences are transcribed under
in vitro
conditions. Overall, these results provide a foundation for future research into the mechanisms of
M. catarrhalis
pathogenesis and vaccine development.
ExsA Recruits RNA Polymerase to an Extended −10 Promoter by Contacting Region 4.2 of Sigma-70
Authors: Vakulskas Christopher A. , Brutinel Evan D. , Yahr Timothy L. 
Published: May 2010

ABSTRACT

ExsA is a member of the AraC family of transcriptional activators and is required for expression of the
Pseudomonas aeruginosa
type III secretion system (T3SS). ExsA-dependent promoters consist of two binding sites for monomeric ExsA located approximately 50 bp upstream of the transcription start sites. Binding to both sites is required for recruitment of σ
70
-RNA polymerase (RNAP) to the promoter. ExsA-dependent promoters also contain putative −35 hexamers that closely match the σ
70
consensus but are atypically spaced 21 or 22 bp from the −10 hexamer. Because several nucleotides located within the putative −35 region are required for ExsA binding, it is unclear whether the putative −35 region makes an additional contribution to transcription initiation. In the present study we demonstrate that the putative −35 hexamer is dispensable for ExsA-independent transcription from the P

exsC

promoter and that deletion of σ
70
region 4.2, which contacts the −35 hexamer, has no effect on ExsA-independent transcription from P

exsC

. Region 4.2 of σ
70
, however, is required for ExsA-dependent activation of the P

exsC

and P

exsD

promoters. Genetic data suggest that ExsA directly contacts region 4.2 of σ
70
, and several amino acids were found to contribute to the interaction.
In vitro
transcription assays demonstrate that an extended −10 element located in the P

exsC

promoter is important for overall promoter activity. Our collective data suggest a model in which ExsA compensates for the lack of a −35 hexamer by interacting with region 4.2 of σ
70
to recruit RNAP to the promoter.
The Cyclic Dipeptide Cyclo(Phe-Pro) Inhibits Cholera Toxin and Toxin-Coregulated Pilus Production in O1 El Tor
Vibrio cholerae
Authors: Bina Xiaowen R. , Bina James E. 
Published: May 2010

ABSTRACT

Cyclo(Phe-Pro) is a cyclic dipeptide produced by multiple
Vibrio
species. In this work, we present evidence that cyclo(Phe-Pro) inhibits the production of the virulence factors cholera toxin (CT) and toxin-coregulated pilus (TCP) in O1 El Tor
Vibrio cholerae
strain N16961 during growth under virulence gene-inducing conditions. The cyclo(Phe-Pro) inhibition of CT and TCP production correlated with reduced transcription of the virulence regulator
tcpPH
and was alleviated by overexpression of
tcpPH
.
Mutations in the
Bacillus subtilis
β Clamp That Separate Its Roles in DNA Replication from Mismatch Repair
Authors: Dupes Nicole M. , Walsh Brian W. , Klocko Andrew D. , Lenhart Justin S. , Peterson Heather L. , Gessert David A. , Pavlick Cassie E. , Simmons Lyle A. 
Published: May 2010

ABSTRACT

The β clamp is an essential replication sliding clamp required for processive DNA synthesis. The β clamp is also critical for several additional aspects of DNA metabolism, including DNA mismatch repair (MMR). The
dnaN5
allele of
Bacillus subtilis
encodes a mutant form of β clamp containing the G73R substitution. Cells with the
dnaN5
allele are temperature sensitive for growth due to a defect in DNA replication at 49°C, and they show an increase in mutation frequency caused by a partial defect in MMR at permissive temperatures. We selected for intragenic suppressors of
dnaN5
that rescued viability at 49°C to determine if the DNA replication defect could be separated from the MMR defect. We isolated three intragenic suppressors of
dnaN5
that restored growth at the nonpermissive temperature while maintaining an increase in mutation frequency. All three
dnaN
alleles encoded the G73R substitution along with one of three novel missense mutations. The missense mutations isolated were S22P, S181G, and E346K. Of these, S181G and E346K are located near the hydrophobic cleft of the β clamp, a common site occupied by proteins that bind the β clamp. Using several methods, we show that the increase in mutation frequency resulting from each
dnaN
allele is linked to a defect in MMR. Moreover, we found that S181G and E346K allowed growth at elevated temperatures and did not have an appreciable effect on mutation frequency when separated from G73R. Thus, we found that specific residue changes in the
B. subtilis
β clamp separate the role of the β clamp in DNA replication from its role in MMR.
Identification of Multiple Substrates of the StkP Ser/Thr Protein Kinase in
Streptococcus pneumoniae
Authors: Nováková Linda , Bezoušková Silvia , Pompach Petr , Špidlová Petra , Sasková Lenka , Weiser Jaroslav , Branny Pavel 
Published: May 2010

ABSTRACT

Monitoring the external environment and responding to its changes are essential for the survival of all living organisms. The transmission of extracellular signals in prokaryotes is mediated mainly by two-component systems. In addition, genomic analyses have revealed that many bacteria contain eukaryotic-type Ser/Thr protein kinases. The human pathogen
Streptococcus pneumoniae
encodes 13 two-component systems and has a single copy of a eukaryotic-like Ser/Thr protein kinase gene designated
stkP
. Previous studies demonstrated the pleiotropic role of the transmembrane protein kinase StkP in pneumococcal physiology. StkP regulates virulence, competence, and stress resistance and plays a role in the regulation of gene expression. To determine the intracellular signaling pathways controlled by StkP, we used a proteomic approach for identification of its substrates. We detected six proteins phosphorylated on threonine by StkP continuously during growth. We identified three new substrates of StkP: the Mn-dependent inorganic pyrophosphatase PpaC, the hypothetical protein spr0334, and the cell division protein DivIVA. Contrary to the results of a previous study, we did not confirm that the α-subunit of RNA polymerase is a target of StkP. We showed that StkP activation and substrate recognition depend on the presence of a peptidoglycan-binding domain comprising four extracellular penicillin-binding protein- and Ser/Thr kinase-associated domain (PASTA domain) repeats. We found that StkP is regulated in a growth-dependent manner and likely senses intracellular peptidoglycan subunits present in the cell division septa. In addition,
stkP
inactivation results in cell division defects. Thus, the data presented here suggest that StkP plays an important role in the regulation of cell division in pneumococcus.
Enrichment and characterization of MTBE-degrading cultures under iron and sulfate reducing conditions
Authors: Raynal M. , Crimi B. , Pruden A. 
Published: May 2010

The aim of this study was to enrich cultures capable of anaerobic methyl tert-butyl ether (MTBE) biodegradation and to determine their compositions using biomolecular tools. MTBE biodegradation as the sole carbon source was observed under Fe(III) and SO42–reducing conditions and with both electron acceptors present together. The estimated MTBE biodegradation rates ranged from 3.80 to 9.20 mg·L–1·d–1when Fe(III) was the sole electron acceptor, from 1.46 to 1.70 mg·L–1·d–1when Fe(III) and SO42–were present together, and from 1.13 to 1.71 mg·L–1·d–1when SO42–was the sole electron acceptor. Five to eight members were identified in the three consortia, and their characteristics were congruent with the electron acceptor conditions. A clone 99% similar to a recently described MTBE degrader, Ochrobactrum cytisi, was detected in both cultures containing Fe(III). Other 16S rRNA gene sequences detected were highly similar at the species or genus level to additional known MTBE degraders, including Pseudomonas spp. (cometabolic), Sphinogomonas, Achromobacter, and Rhodococcus. Results suggest that the buildup of intermediates and (or) the presence of sulfides had an inhibitory effect on biodegradation. Anaerobic MTBE biodegradation remains poorly understood, and degrading strains still have not been identified to date. This work represents the first detailed 16S rRNA gene profiling of highly enriched iron- and sulfate-reducing MTBE-degrading consortia. These results may provide useful biomarkers to support current efforts for confirming anaerobic MTBE biodegradation in the field.
Effect of co-contaminants on the dechlorination of polychlorinated biphenylsPaper submitted to the Journal of Environmental Engineering and Science.
Authors: Kone Macoura , Chang Yanjun , Achari Gopal , Langford Cooper H. 
Published: May 2010

A promising photolysis based technology to dechlorinate polychlorinated biphenyls (PCBs), extracted from soils, in alkaline isopropanol (IPA) as reaction medium has been proposed. To be marketable the impact of co-contaminants extracted along with the PCBs, on the photodechlorination process needs investigation. In this paper the effectiveness of the photodeclorination process on PCBs extracted from samples of a representative soil containing co-contaminants is reported. The photodechlorination of PCBs extracted from weathered soils showed promising results of more than 76% dechlorination within the first hour of UV irradiation. Nearly complete dechlorination (96%) was achieved after 2 h of UV irradiation. To provide quantitative controlled appraisal of the effect of co-contaminants and explanation of the effects, dechlorination of neat Aroclor 1254 in the presence of the common co-contaminant, transformer oil, was evaluated. Further, the effect of transformer oil on some of the individual PCB congeners in the Aroclor mixture was also studied. The difference in the maximum percentage dechlorination of PCBs with and without transformer oil is 15%.
Residue patterning in helix interiorsThis paper is one of a selection of papers published in this special issue entitled “Canadian Society of Biochemistry, Molecular & Cellular Biology 52nd Annual Meeting — Protein Folding: Principles and Diseases” and has undergone the Journal's usual peer review process.
Authors: Wathen Brent , Jia Zongchao 
Published: May 2010

The α-helix remains a focus of research because of its importance to protein folding and structure. Nevertheless, despite numerous empirical, computational, and theoretical studies, the fundamental structural properties governing their formation and stability are still unclear. We have examined the statistical occurrence of polar and apolar residue patterning in helical interiors in a large, non-redundant dataset, and compared these patterns with those found in other structural environments. While the familiar amphipathic distributions for both polar and apolar residues are evident, our analysis also finds significant differences between these distributions. Non-amphipathic signals can also be discerned within both distributions. Most interestingly, among various positional patterning, an analysis of immediate (i,i + 1) helical neighbours found: (i) clear neighbouring preferences, with high (low) occurrences of hydrophobics (hydrophilics) next to Gly, Pro, and short polar residues; (ii) high negative (positive) correlation between residue helical propensities and the degree of neighbouring hydrophobicity (hydrophilicity); and (iii) a preferred ordering among neighbours, implying an inherent helix directionality. Because (i,i + 1) helical pairs have limited side chain – side chain interactions, thermodynamic considerations cannot readily explain these observations, nor can evolutionary pressures that enhance tertiary interactions via amphipathicity, as this particular spacing does not segregate residues onto either the same or opposing helical faces. We suggest that the mechanism of helix formation may be partly responsible for these observations. In particular, the high negative correlation between residue helical propensities and neighbouring hydrophobicity suggests that hydrophobicity may play a more important role in helix formation than currently recognized.
Bacterial–protozoal interactions in a microbial community of rumen ciliateEntodinium caudatumculture under mercury stress
Authors: Kišidayová S. , Houserová P. , Váradyová Z. , Mihaliková K. , Pristaš P. , Javorský P. 
Published: May 2010

We examined the role of rumen ciliates, using Entodinium caudatum as a model organism, in the detoxification of soluble mercury(II) in vitro under conditions with enhanced or reduced diversity of a co-culture bacterial population as well as the effects of long-term mercury(II) stress on in vitro fermentation parameters and major mercury detoxification products. The E. caudatum growth depended on the capability of the co-culture bacterial population to develop resistance to mercury(II) chloride and on culture conditions. The production of fermentation gas was reduced (P < 0.01) in contrast to methane production. Proportions of volatile fatty acids were affected; however, the total concentration of volatile fatty acids was not influenced. No organic mercury species were detected after long-term application (>1 month) of mercury(II) chloride. The major mercury species was inorganic mercury(II) with substantial accumulation in the bacterial fraction (70%) and less in black sediment (21%) and ciliate fraction (9%) at the 25 µmol/L mercury(II) dose. The data indicate that free-living bacteria protect the ciliate cells by transforming mercury(II) into its insoluble forms.
Production and properties of α-amylase fromBacillussp. BKL20
Authors: Kubrak Olha I. , Storey Janet M. , Storey Kenneth B. , Lushchak Volodymyr I. 
Published: May 2010

As a result of screening Bacillus sp. strains isolated from different natural substrates, strain BKL20 was identified as a producer of a thermostable alkaline α-amylase. Maximum production of this α-amylase was achieved by optimizing culture conditions. Production of α-amylase seemed to be independent of the presence of starch in the culture medium and was stimulated by the presence of peptone (0.3%, m/v) and yeast extract (0.2%, m/v). The enzyme was thermostable and retained amylolytic activity after 30 min of incubation at 60 and 70 °C. High activity was maintained over a broad pH range, from 6.0 to 11.0, and the enzyme remained active after alkaline incubation for 24 h. Bacillus sp. BKL20 α-amylase was not stimulated by Ca2+or other bivalent metal cations and was not inhibited by EGTA or EDTA at 1–10 mmol/L, suggesting that this α-amylase is a Ca2+-independent enzyme. It also showed good resistance to both oxidizing (H2O2) and denaturating (urea) agents.