bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of β-Lactamase in Antibiotic-Resistant
Bacillus cereus
Spores
Authors: Fenselau Catherine , Havey Crystal , Teerakulkittipong Nuttinee , Swatkoski Stephen , Laine Olli , Edwards Nathan 
Published: December 2007

ABSTRACT

β-Lactamase type I is reported for the first time to occur in the sporulated form in a penicillin-resistant
Bacillus
species. The enzyme was readily characterized from the
B. cereus
5/B line (ATCC 13061) by mass spectrometry and two-dimensional gel electrophoresis.
Molecular Detection and Characterization of Gastroenteritis Viruses Occurring Naturally in the Stream Waters of Manaus, Central Amazônia, Brazil
Authors: Miagostovich Marize P. , Ferreira Fabiana F. M. , Guimarães Flávia R. , Fumian Túlio M. , Diniz-Mendes Leonardo , Luz Sérgio Luiz B. , Silva Luciete A. , Leite José Paulo G. 
Published: December 2007

ABSTRACT
To assess the presence of the four main viruses responsible for human acute gastroenteritis in a hydrographic network impacted by a disordered urbanization process, a 1-year study was performed involving water sample collection from streams in the hydrographic basin surrounding the city of Manaus, Amazonas, Brazil. Thirteen surface water sample collection sites, including different areas of human settlement characterized as urban, rural, and primary forest, located in the Tarumã-Açu, São Raimundo, Educandos, and Puraquequara microbasins, were defined with a global positioning system. At least one virus was detected in 59.6% (31/52) of the water samples analyzed, and rotavirus was the most frequent (44.2%), followed by human adenovirus (30.8%), human astrovirus (15.4%), and norovirus (5.8%). The viral contamination observed mainly in the urban streams reflected the presence of a local high-density population and indicated the gastroenteritis burden from pathogenic viruses in the water, principally due to recreational activities such as bathing. The presence of viral genomes in areas where fecal contamination was not demonstrated by bacterial indicators suggests prolonged virus persistence in aquatic environments and emphasizes the enteric virus group as the most reliable for environmental monitoring.
Root Infection and Systemic Colonization of Maize byColletotrichum graminicola
Authors: Sukno Serenella A. , García Verónica M. , Shaw Brian D. , Thon Michael R. 
Published: December 2007

ABSTRACTColletotrichum graminicolais a filamentous ascomycete that causes anthracnose disease of maize. While the fungus can cause devastating foliar leaf blight and stalk rot diseases, little is known about its ability to infect roots. Previously published reports suggest thatC. graminicolamay infect maize roots and that root infections may contribute to the colonization of aboveground plant tissues, leading to disease. To determine whetherC. graminicolacan infect maize roots and whether root infections can result in the colonization of aboveground plant tissues, we developed a green fluorescent protein-tagged strain and used it to study the plant root colonization and infection process in vivo. We observed structures produced by other root pathogenic fungi, including runner hyphae, hyphopodia, and microsclerotia. A mosaic pattern of infection resulted from specific epidermal and cortical cells becoming infected by intercellular hyphae while surrounding cells were uninfected, a pattern that is distinctly different from that described for leaves. Interestingly, falcate conidia, normally restricted to acervuli, were also found filling epidermal cells and root hairs. Twenty-eight percent of plants challenged with soilborne inoculum became infected in aboveground plant parts (stem and/or leaves), indicating that root infection can lead to asymptomatic systemic colonization of the plants. Many of the traits observed forC. graminicolahave been previously reported for other root-pathogenic fungi, suggesting that these traits are evolutionally conserved in multiple fungal lineages. These observations suggest that root infection may be an important component of the maize anthracnose disease cycle.
Secretion of Flavins byShewanellaSpecies and Their Role in Extracellular Electron Transfer
Authors: von Canstein Harald , Ogawa Jun , Shimizu Sakayu , Lloyd Jonathan R. 
Published: December 2007

ABSTRACTFe(III)-respiring bacteria such asShewanellaspecies play an important role in the global cycle of iron, manganese, and trace metals and are useful for many biotechnological applications, including microbial fuel cells and the bioremediation of waters and sediments contaminated with organics, metals, and radionuclides. Several alternative electron transfer pathways have been postulated for the reduction of insoluble extracellular subsurface minerals, such as Fe(III) oxides, byShewanellaspecies. One such potential mechanism involves the secretion of an electron shuttle. Here we identify for the first time flavin mononucleotide (FMN) and riboflavin as the extracellular electron shuttles produced by a range ofShewanellaspecies. FMN secretion was strongly correlated with growth and exceeded riboflavin secretion, which was not exclusively growth associated but was maximal in the stationary phase of batch cultures. Flavin adenine dinucleotide was the predominant intracellular flavin but was not released by live cells. The flavin yields were similar under both aerobic and anaerobic conditions, with total flavin concentrations of 2.9 and 2.1 μmol per gram of cellular protein, respectively, after 24 h and were similar under dissimilatory Fe(III)-reducing conditions and when fumarate was supplied as the sole electron acceptor. The flavins were shown to act as electron shuttles and to promote anoxic growth coupled to the accelerated reduction of poorly crystalline Fe(III) oxides. The implications of flavin secretion byShewanellacells living at redox boundaries, where these mineral phases can be significant electron acceptors for growth, are discussed.
Low Temperature Decreases the Phylogenetic Diversity of Ammonia-Oxidizing Archaea and Bacteria in Aquarium Biofiltration Systems
Authors: Urakawa Hidetoshi , Tajima Yoshiyuki , Numata Yoshiyuki , Tsuneda Satoshi 
Published: December 2007

ABSTRACT
The phylogenetic diversity and species richness of ammonia-oxidizing archaea (AOA) and bacteria (AOB) were examined with aquarium biofiltration systems. Species richness, deduced from rarefaction analysis, and diversity indices indicated that the phylogenetic diversity and species richness of AOA are greater than those of AOB; the diversity of AOA and of AOB is minimized in cold-water aquaria. This finding implies that temperature is a key factor influencing the population structure and diversity of AOA and AOB in aquarium biofiltration systems.
Determination of the Shear Force at the Balance between Bacterial Attachment and Detachment in Weak-Adherence Systems, Using a Flow Displacement Chamber
Authors: Nejadnik M. Reza , van der Mei Henny C. , Busscher Henk J. , Norde Willem 
Published: December 2007

ABSTRACT
We introduce a procedure for determining shear forces at the balance between attachment and detachment of bacteria under flow. This procedure can be applied to derive adhesion forces in weak-adherence systems, such as polymer brush coatings, which are currently at the center of attention for their control of bacterial adhesion and biofilm formation.
Role of
galK
and
galM
in Galactose Metabolism by
Streptococcus thermophilus
Authors: Vaillancourt Katy , Bédard Nathalie , Bart Christian , Tessier Mélanie , Robitaille Gilles , Turgeon Nathalie , Frenette Michel , Moineau Sylvain , Vadeboncoeur Christian 
Published: December 2007

ABSTRACT

Streptococcus thermophilus
is unable to metabolize the galactose moiety of lactose. In this paper, we show that a transformant of
S. thermophilus
SMQ-301 expressing
Streptococcus salivarius galK
and
galM
was able to grow on galactose and expelled at least twofold less galactose into the medium during growth on lactose.
Aerosolization of Particulate (1→3)-β-
d
-Glucan from Moldy Materials
Authors: Seo Sung-Chul , Reponen Tiina , Levin Linda , Borchelt Tiffany , Grinshpun Sergey A. 
Published: December 2007

ABSTRACT

Mold-damaged building materials may contain biologically active agents, such as (1→3)-β-
d
-glucan, allergens, and mycotoxins, which have been associated with adverse health effects. The release of these components from contaminated surfaces into the air is not well understood. The purpose of this study was to characterize the release of particulate (1→3)-β-
d
-glucan from the surface of artificially mold-contaminated materials.
Aspergillus versicolor
and
Stachybotrys chartarum
were grown on malt extract agar (MEA), white ceiling tiles, and a wall-papered gypsum board for 1 and 6 months. The (1→3)-β-
d
-glucan on the surfaces of moldy materials and in air samples collected from these materials was analyzed by the
Limulus
amebocyte lysate assay. The aerosolization ratio was defined as the amount of (1→3)-β-
d
-glucan in the air divided by the amount on the surface. The results showed that the aerosolization of particulate (1→3)-β-
d
-glucan was influenced mainly by the type of material and the fungal species. For
A. versicolor
, the aerosolization ratios of particulate (1→3)-β-
d
-glucan released from the three types of material were not significantly different. However, the ratios for
S. chartarum
released from ceiling tiles and gypsum board were significantly higher than the ratios for this organism released from MEA (
P
< 0.001) and were comparable to those for
A. versicolor
. These findings indicate that the use of MEA in aerosolization experiments is likely to underestimate the release of
S. chartarum
particles from building materials. These results provide important background information for design of future laboratory or animal experiments, as well as for interpretation of field measurement data.
Characterization of the Gene Cluster Responsible for Cylindrospermopsin Biosynthesis
Authors: Mihali Troco Kaan , Kellmann Ralf , Muenchhoff Julia , Barrow Kevin D. , Neilan Brett A. 
Published: December 2007

ABSTRACTToxic cyanobacterial blooms cause economic losses and pose significant public health threats on a global scale. Characterization of the gene cluster for the biosynthesis of the cyanobacterial toxin cylindrospermopsin (cyr) inCylindrospermopsis raciborskiiAWT205 is described, and the complete biosynthetic pathway is proposed. Thecyrgene cluster spans 43 kb and is comprised of 15 open reading frames containing genes required for the biosynthesis, regulation, and export of the toxin. Biosynthesis is initiated via an amidinotransfer onto glycine followed by five polyketide extensions and subsequent reductions, and rings are formed via Michael additions in a stepwise manner. The uracil ring is formed by a novel pyrimidine biosynthesis mechanism and tailoring reactions, including sulfation and hydroxylation that complete biosynthesis. These findings enable the design of toxic strain-specific probes and allow the future study of the regulation and biological role of cylindrospermopsin.
Bacteriophage Prevalence in the Genus
Azospirillum
and Analysis of the First Genome Sequence of an
Azospirillum brasilense
Integrative Phage
Authors: Boyer Mickaël , Haurat Jacqueline , Samain Sylvie , Segurens Béatrice , Gavory Frédérick , González Víctor , Mavingui Patrick , Rohr René , Bally René , Wisniewski-Dyé Florence 
Published: December 2007

ABSTRACT

The prevalence of bacteriophages was investigated in 24 strains of four species of plant growth-promoting rhizobacteria belonging to the genus
Azospirillum
. Upon induction by mitomycin C, the release of phage particles was observed in 11 strains from three species. Transmission electron microscopy revealed two distinct sizes of particles, depending on the identity of the
Azospirillum
species, typical of the
Siphoviridae
family. Pulsed-field gel electrophoresis and hybridization experiments carried out on phage-encapsidated DNAs revealed that all phages isolated from
A. lipoferum
and
A. doebereinerae
strains had a size of about 10 kb whereas all phages isolated from
A. brasilense
strains displayed genome sizes ranging from 62 to 65 kb. Strong DNA hybridizing signals were shown for most phages hosted by the same species whereas no homology was found between phages harbored by different species. Moreover, the complete sequence of the
A. brasilense
Cd bacteriophage (ΦAb-Cd) genome was determined as a double-stranded DNA circular molecule of 62,337 pb that encodes 95 predicted proteins. Only 14 of the predicted proteins could be assigned functions, some of which were involved in DNA processing, phage morphogenesis, and bacterial lysis. In addition, the ΦAb-Cd complete genome was mapped as a prophage on a 570-kb replicon of strain
A. brasilense
Cd, and a region of 27.3 kb of ΦAb-Cd was found to be duplicated on the 130-kb pRhico plasmid previously sequenced from
A. brasilense
Sp7, the parental strain of
A. brasilense
Cd.
RNA Silencing Gene Truncation in the Filamentous Fungus
Aspergillus nidulans
Authors: Hammond T. M. , Bok J. W. , Andrewski M. D. , Reyes-Domínguez Y. , Scazzocchio C. , Keller N. P. 
Published: December 2007

ABSTRACT

The genus
Aspergillus
is ideally suited for the investigation of RNA silencing evolution because it includes species that have experienced a variety of RNA silencing gene changes. Our work on this subject begins here with the model species
Aspergillus nidulans
. Filamentous ascomycete fungi generally each encode two of the core RNA silencing proteins, Dicer and Argonaute, but
A. nidulans
appears to have lost one of each to gene truncation events. Although a role in growth, development, or RNA silencing was not detected for the truncated genes, they do produce spliced and poly(A)-tailed transcripts, suggesting that they may have an undetermined biological function. Population analysis demonstrates that the truncated genes are fixed at the species level and that their full-length orthologs in a closely related species are also unstable. With these gene truncation events,
A. nidulans
encodes only a single intact Dicer and Argonaute. Their deletion results in morphologically and reproductively normal strains that are incapable of experimental RNA silencing. Thus, our results suggest that the remaining
A. nidulans
RNA silencing genes have a “nonhousekeeping” function, such as defense against viruses and transposons.
Fission Yeast Mitogen-Activated Protein Kinase Sty1 Interacts with Translation Factors
Authors: Asp Eva , Nilsson Daniel , Sunnerhagen Per 
Published: December 2007

ABSTRACT

Signaling by stress-activated mitogen-activated protein kinase (MAPK) pathways influences translation efficiency in mammalian cells and budding yeast. We have investigated the stress-activated MAPK from fission yeast, Sty1, and its downstream protein kinase, Mkp1/Srk1, for physically associated proteins using tandem affinity purification tagging. We find Sty1, but not Mkp1, to bind to the translation elongation factor eukaryotic elongation factor 2 (eEF2) and the translation initiation factor eukaryotic initiation factor 3a (eIF3a). The Sty1-eIF3a interaction is weakened under oxidative or hyperosmotic stress, whereas the Sty1-eEF2 interaction is stable. Nitrogen deprivation causes a transient strengthening of both the Sty1-eEF2 and the Sty1-Mkp1 interactions, overlapping with the time of maximal Sty1 activation. Analysis of polysome profiles from cells under oxidative stress, or after hyperosmotic shock or nitrogen deprivation, shows that translation in
sty1
mutant cells recovers considerably less efficiently than that in the wild type. Cells lacking the Sty1-regulated transcription factor Atf1 are deficient in maintaining and recovering translational activity after hyperosmotic shock but not during oxidative stress or nitrogen starvation. In cells lacking Sty1, eIF3a levels are decreased, and phosphorylation of eIF3a is reduced. Taken together, our data point to a central role in translational adaptation for the stress-activated MAPK pathway in fission yeast similar to that in other investigated eukaryotes, with the exception that fission yeast MAPK-activated protein kinases seem not to be directly involved in this process.
PhoP-PhoP Interaction at Adjacent PhoP Binding Sites Is Influenced by Protein Phosphorylation
Authors: Sinha Akesh , Gupta Sankalp , Bhutani Shweta , Pathak Anuj , Sarkar Dibyendu 
Published: December 2007

ABSTRACT

Mycobacterium tuberculosis
PhoP regulates the expression of unknown virulence determinants and the biosynthesis of complex lipids. PhoP, like other members of the OmpR family, comprises a phosphorylation domain at the amino-terminal half and a DNA-binding domain at the carboxy-terminal half of the protein. To explore structural effect of protein phosphorylation and to examine effect of phosphorylation on DNA binding, purified PhoP was phosphorylated by acetyl phosphate in a reaction that was dependent on Mg
2+
and Asp-71. Protein phosphorylation was not required for DNA binding; however, phosphorylation enhanced in vitro DNA binding through protein-protein interaction(s). Evidence is presented here that the protein-protein interface is different in the unphosphorylated and phosphorylated forms of PhoP and that specific DNA binding plays a critical role in changing the nature of the protein-protein interface. We show that phosphorylation switches the transactivation domain to a different conformation, which specifies additional protein-protein contacts between PhoP protomers bound to adjacent cognate sites. Together, our observations raise the possibility that PhoP, in the unphosphorylated and phosphorylated forms, may be capable of adopting different orientations as it binds to a vast array of genes to activate or repress transcription.
A Transposase-Independent Mechanism Gives Rise to Precise Excision of IS256from Insertion Sites inStaphylococcus epidermidis
Authors: Hennig Susanne , Ziebuhr Wilma 
Published: December 2007

ABSTRACTThe mobile element IS256causes phase variation of biofilm formation inStaphylococcus epidermidisby insertion and precise excision from theicaADBCoperon. Precise excision, i.e., removal of the target site duplications (TSDs) and restoration of the original DNA sequence, occurs rarely but independently of functional transposase. Instead, the integrity of the TSDs is crucial for precise excision. Excision increased significantly when the TSDs were brought into closer spatial proximity, suggesting that excision is a host-driven process that might involve most likely illegitimate recombination.
Phage Response to CRISPR-Encoded Resistance in
Streptococcus thermophilus
Authors: Deveau Hélène , Barrangou Rodolphe , Garneau Josiane E. , Labonté Jessica , Fremaux Christophe , Boyaval Patrick , Romero Dennis A. , Horvath Philippe , Moineau Sylvain 
Published: December 2007

ABSTRACT

Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated genes are linked to a mechanism of acquired resistance against bacteriophages. Bacteria can integrate short stretches of phage-derived sequences (spacers) within CRISPR loci to become phage resistant. In this study, we further characterized the efficiency of CRISPR1 as a phage resistance mechanism in
Streptococcus thermophilus
. First, we show that CRISPR1 is distinct from previously known phage defense systems and is effective against the two main groups of
S. thermophilus
phages. Analyses of 30 bacteriophage-insensitive mutants of
S. thermophilus
indicate that the addition of one new spacer in CRISPR1 is the most frequent outcome of a phage challenge and that the iterative addition of spacers increases the overall phage resistance of the host. The added new spacers have a size of between 29 to 31 nucleotides, with 30 being by far the most frequent. Comparative analysis of 39 newly acquired spacers with the complete genomic sequences of the wild-type phages 2972, 858, and DT1 demonstrated that the newly added spacer must be identical to a region (named proto-spacer) in the phage genome to confer a phage resistance phenotype. Moreover, we found a CRISPR1-specific sequence (NNAGAAW) located downstream of the proto-spacer region that is important for the phage resistance phenotype. Finally, we show through the analyses of 20 mutant phages that virulent phages are rapidly evolving through single nucleotide mutations as well as deletions, in response to CRISPR1.
Diversity, Activity, and Evolution of CRISPR Loci in
Streptococcus thermophilus
Authors: Horvath Philippe , Romero Dennis A. , Coûté-Monvoisin Anne-Claire , Richards Melissa , Deveau Hélène , Moineau Sylvain , Boyaval Patrick , Fremaux Christophe , Barrangou Rodolphe 
Published: December 2007

ABSTRACT

Clustered regularly interspaced short palindromic repeats (CRISPR) are hypervariable loci widely distributed in prokaryotes that provide acquired immunity against foreign genetic elements. Here, we characterize a novel
Streptococcus thermophilus
locus, CRISPR3, and experimentally demonstrate its ability to integrate novel spacers in response to bacteriophage. Also, we analyze CRISPR diversity and activity across three distinct CRISPR loci in several
S. thermophilus
strains. We show that both CRISPR repeats and
cas
genes are locus specific and functionally coupled. A total of 124 strains were studied, and 109 unique spacer arrangements were observed across the three CRISPR loci. Overall, 3,626 spacers were analyzed, including 2,829 for CRISPR1 (782 unique), 173 for CRISPR2 (16 unique), and 624 for CRISPR3 (154 unique). Sequence analysis of the spacers revealed homology and identity to phage sequences (77%), plasmid sequences (16%), and
S. thermophilus
chromosomal sequences (7%). Polymorphisms were observed for the CRISPR repeats, CRISPR spacers,
cas
genes, CRISPR motif, locus architecture, and specific sequence content. Interestingly, CRISPR loci evolved both via polarized addition of novel spacers after exposure to foreign genetic elements and via internal deletion of spacers. We hypothesize that the level of diversity is correlated with relative CRISPR activity and propose that the activity is highest for CRISPR1, followed by CRISPR3, while CRISPR2 may be degenerate. Globally, the dynamic nature of CRISPR loci might prove valuable for typing and comparative analyses of strains and microbial populations. Also, CRISPRs provide critical insights into the relationships between prokaryotes and their environments, notably the coevolution of host and viral genomes.
CotC-CotU Heterodimerization during Assembly of the
Bacillus subtilis
Spore Coat
Authors: Isticato Rachele , Pelosi Assunta , Zilhão Rita , Baccigalupi Loredana , Henriques Adriano O. , De Felice Maurilio , Ricca Ezio 
Published: December 2007

ABSTRACT

We report evidence that CotC and CotU, two previously identified components of the
Bacillus subtilis
spore coat, are produced concurrently in the mother cell chamber of the sporulating cell under the control of σ
K
and GerE and immediately assembled around the forming spore. In the coat, the two proteins interact to form a coat component of 23 kDa. The CotU-CotC interaction was not detected in two heterologous hosts, suggesting that it occurs only in
B. subtilis
. Monomeric forms of both CotU and CotC failed to be assembled at the surface of the developing spore and accumulated in the mother cell compartment of cells mutant for
cotE
. In contrast, neither CotU nor CotC accumulated in the mother cell compartment of cells mutant for
cotH
. These results suggest that CotH is required to protect both CotU and CotC in the mother cell compartment of the sporangium and that CotE is needed to allow their assembly and subsequent interaction at the spore surface.