bluuebunny/crossref_metadata_2025_split huggingface dataset:
Root-Specific Reduction of Cytokinin Causes Enhanced Root Growth, Drought Tolerance, and Leaf Mineral Enrichment inArabidopsisand Tobacco
Authors: Werner Tomáš , Nehnevajova Erika , Köllmer Ireen , Novák Ondřej , Strnad Miroslav , Krämer Ute , Schmülling Thomas 
Published: December 2010

AbstractOptimizing root system architecture can overcome yield limitations in crop plants caused by water or nutrient shortages. Classic breeding approaches are difficult because the trait is governed by many genes and is difficult to score. We generated transgenic Arabidopsis thaliana and tobacco (Nicotiana tabacum) plants with enhanced root-specific degradation of the hormone cytokinin, a negative regulator of root growth. These transgenic plants form a larger root system, whereas growth and development of the shoot are similar. Elongation of the primary root, root branching, and root biomass formation were increased by up to 60% in transgenic lines, increasing the root-to-shoot ratio. We thus demonstrated that a single dominant gene could regulate a complex trait, root growth. Moreover, we showed that cytokinin regulates root growth in a largely organ-autonomous fashion that is consistent with its dual role as a hormone with both paracrine and long-distance activities. Transgenic plants had a higher survival rate after severe drought treatment. The accumulation of several elements, including S, P, Mn, Mg, Zn, as well as Cd from a contaminated soil, was significantly increased in shoots. Under conditions of sulfur or magnesium deficiency, leaf chlorophyll content was less affected in transgenic plants, demonstrating the physiological relevance of shoot element accumulation. Our approach might contribute to improve drought tolerance, nutrient efficiency, and nutrient content of crop plants.
Among Developmental Regulators, StuA but Not BrlA Is Essential for Penicillin V Production in
Penicillium chrysogenum
Authors: Sigl Claudia , Haas Hubertus , Specht Thomas , Pfaller Kristian , Kürnsteiner Hubert , Zadra Ivo 
Published: December 2010

ABSTRACT

In filamentous fungi, secondary metabolism is often linked with developmental processes such as conidiation. In this study we analyzed the link between secondary metabolism and conidiation in the main industrial producer of the β-lactam antibiotic penicillin, the ascomycete
Penicillium chrysogenum
. Therefore, we generated mutants defective in two central regulators of conidiation, the transcription factors BrlA and StuA. Inactivation of either
brlA
or
stuA
blocked conidiation and altered hyphal morphology during growth on solid media, as shown by light and scanning electron microscopy, but did not affect biomass production during liquid-submerged growth. Genome-wide transcriptional profiling identified a complex StuA- and BrlA-dependent regulatory network, including genes previously shown to be involved in development and secondary metabolism. Remarkably, inactivation of
stuA
, but not
brlA
, drastically downregulated expression of the penicillin biosynthetic gene cluster during solid and liquid-submerged growth. In agreement, penicillin V production was wild-type-like in
brlA
-deficient strains but 99% decreased in
stuA
-deficient strains during liquid-submerged growth, as shown by high-performance liquid chromatography (HPLC) analysis. Thus, among identified regulators of penicillin V production StuA has the most severe influence. Overexpression of
stuA
increased the transcript levels of
brlA
and
abaA
(another developmental regulator) and derepressed conidiation during liquid-submerged growth but did not affect penicillin V productivity. Taken together, these data demonstrate an intimate but not exclusive link between regulation of development and secondary metabolism in
P. chrysogenum.
Bacterial Killing by Dry Metallic Copper Surfaces
Authors: Santo Christophe Espírito , Lam Ee Wen , Elowsky Christian G. , Quaranta Davide , Domaille Dylan W. , Chang Christopher J. , Grass Gregor 
Published: December 2010

ABSTRACT
Metallic copper surfaces rapidly and efficiently kill bacteria. Cells exposed to copper surfaces accumulated large amounts of copper ions, and this copper uptake was faster from dry copper than from moist copper. Cells suffered extensive membrane damage within minutes of exposure to dry copper. Further, cells removed from copper showed loss of cell integrity. Acute contact with metallic copper surfaces did not result in increased mutation rates or DNA lesions. These findings are important first steps for revealing the molecular sensitive targets in cells lethally challenged by exposure to copper surfaces and provide a scientific explanation for the use of copper surfaces as antimicrobial agents for supporting public hygiene.
Linking Low-Level Stable Isotope Fractionation to Expression of the Cytochrome P450 Monooxygenase-Encoding
ethB
Gene for Elucidation of Methyl
tert
-Butyl Ether Biodegradation in Aerated Treatment Pond Systems
Authors: Jechalke Sven , Rosell Mònica , Martínez-Lavanchy Paula M. , Pérez-Leiva Paola , Rohwerder Thore , Vogt Carsten , Richnow Hans H. 
Published: December 2010

ABSTRACT

Multidimensional compound-specific stable isotope analysis (CSIA) was applied in combination with RNA-based molecular tools to characterize methyl tertiary (
tert
-) butyl ether (MTBE) degradation mechanisms occurring in biofilms in an aerated treatment pond used for remediation of MTBE-contaminated groundwater. The main pathway for MTBE oxidation was elucidated by linking the low-level stable isotope fractionation (mean carbon isotopic enrichment factor [ε
C
] of −0.37‰ ± 0.05‰ and no significant hydrogen isotopic enrichment factor [ε
H
]) observed in microcosm experiments to expression of the
ethB
gene encoding a cytochrome P450 monooxygenase able to catalyze the oxidation of MTBE in biofilm samples both from the microcosms and directly from the ponds. 16S rRNA-specific primers revealed the presence of a sequence 100% identical to that of
Methylibium petroleiphilum
PM1, a well-characterized MTBE degrader. However, neither expression of the
mdpA
genes encoding the alkane hydroxylase-like enzyme responsible for MTBE oxidation in this strain nor the related MTBE isotope fractionation pattern produced by PM1 could be detected, suggesting that this enzyme was not active in this system. Additionally, observed low inverse fractionation of carbon (ε
C
of +0.11‰ ± 0.03‰) and low fractionation of hydrogen (ε
H
of −5‰ ± 1‰) in laboratory experiments simulating MTBE stripping from an open surface water body suggest that the application of CSIA in field investigations to detect biodegradation may lead to false-negative results when volatilization effects coincide with the activity of low-fractionating enzymes. As shown in this study, complementary examination of expression of specific catabolic genes can be used as additional direct evidence for microbial degradation activity and may overcome this problem.
Quantification and Genotyping of Human Sapoviruses in the Llobregat River Catchment, Spain
Authors: Sano Daisuke , Pérez-Sautu Unai , Guix Susana , Pintó Rosa Maria , Miura Takayuki , Okabe Satoshi , Bosch Albert 
Published: December 2010

ABSTRACTHuman sapoviruses (SaVs) were quantified and characterized in an 18-month survey conducted along the Llobregat river catchment area in Spain. Sample types included freshwater, untreated and treated wastewater, and drinking water. All genogroups were recovered, and a seasonal distribution was observed. This is the first report of SaV quantification and genotyping in the environment outside Japan.
Wide Host Range and Strong Lytic Activity ofStaphylococcusaureusLytic Phage Stau2
Authors: Hsieh Sue-Er , Lo Hsueh-Hsia , Chen Shui-Tu , Lee Mong-Chuan , Tseng Yi-Hsiung 
Published: December 2010

ABSTRACTIn searching for an alternative antibacterial agent against multidrug-resistantStaphylococcusaureus, we have isolated and characterized a lytic staphylophage, Stau2. It possesses a double-stranded DNA genome estimated to be about 134.5 kb and a morphology resembling that of members of the familyMyoviridae. With an estimated latency period of 25 min and a burst size of 100 PFU/infected cell, propagation of Stau2 in liquid culture gave a lysate of ca. 6 × 1010PFU/ml. It was stable at pH 5 to 13 in normal saline at room temperature for at least 4 weeks and at −85°C for more than 2 years, while 1 × 109out of 2 × 1012PFU/ml retained infectivity after 36 months at 4°C. Stau2 could lyse 80% of theS.aureusisolates (164/205) obtained from hospitals in Taiwan, with complete lysis of most of the isolates tested within 3 h; however, it was anS.aureus-specific phage because no lytic infection could be found in the coagulase-negative staphylococci tested. Its host range amongS.aureusisolates was wider than that of polyvalent phage K (47%), which can also lyse many other staphylococcal species. Experiments with mice demonstrated that Stau2 could provide 100% protection from lethal infection when a multiplicity of infection of 10 was administered immediately after a challenge withS.aureusS23. Considering these results, Stau2 could be considered at least as a candidate for topical phage therapy or an additive in the food industry.
New Anaerobic, Ammonium-Oxidizing Community Enriched from Peat Soil
Authors: Hu Bao-lan , Rush Darci , van der Biezen Erwin , Zheng Ping , van Mullekom Mark , Schouten Stefan , Sinninghe Damsté Jaap S. , Smolders Alfons J. P. , Jetten Mike S. M. , Kartal Boran 
Published: December 2010

ABSTRACT

Anaerobic ammonium-oxidizing (anammox) bacteria have been recognized as an important sink for fixed nitrogen and are detected in many natural environments. However, their presence in terrestrial ecosystems has long been overlooked, and their contribution to the nitrogen cycling in natural and agricultural soils is currently unknown. Here we describe the enrichment and characterization of anammox bacteria from a nitrogen-loaded peat soil. After 8 months of incubation with the natural surface water of the sampling site and increasing ammonium and nitrite concentrations, anammox cells constituted 40 to 50% of the enrichment culture. The two dominant anammox phylotypes were affiliated with “
Candidatus
Jettenia asiatica” and “
Candidatus
Brocadia fulgida.” The enrichment culture converted NH
4
+
and NO
2
−
to N
2
with the previously reported stoichiometry (1:1.27) and had a maximum specific anaerobic ammonium oxidation rate of 0.94 mmol NH
4
+
·g (dry weight)
−1
·h
−1
at pH 7.1 and 32°C. The diagnostic anammox-specific lipids were detected at a concentration of 650 ng·g (dry weight)
−1
, and pentyl-[3]-ladderane was the most abundant ladderane lipid.
Using the Systematic Review Methodology To Evaluate Factors That Influence the Persistence of Influenza Virus in Environmental Matrices
Authors: Irwin C. K. , Yoon K. J. , Wang C. , Hoff S. J. , Zimmerman J. J. , Denagamage T. , O'Connor A. M. 
Published: December 2010

ABSTRACTUnderstanding factors that influence persistence of influenza virus in an environment without host animals is critical to appropriate decision-making for issues such as quarantine downtimes, setback distances, and eradication programs in livestock production systems. This systematic review identifies literature describing persistence of influenza virus in environmental samples, i.e., air, water, soil, feces, and fomites. An electronic search of PubMed, CAB, AGRICOLA, Biosis, and Compendex was performed, and citation relevance was determined according to the aim of the review. Quality assessment of relevant studies was performed using criteria from experts in virology, disease ecology, and environmental science. A total of 9,760 abstracts were evaluated, and 40 appeared to report the persistence of influenza virus in environmental samples. Evaluation of full texts revealed that 19 of the 40 studies were suitable for review, as they described virus concentration measured at multiple sampling times, with viruses detectable at least twice. Seven studies reported persistence in air (six published before 1970), seven in water (five published after 1990), two in feces, and three on surfaces. All three fomite and five air studies addressed human influenza virus, and all water and feces studies pertained to avian influenza virus. Outcome measurements were transformed to half-lives, and resultant multivariate mixed linear regression models identified influenza virus surviving longer in water than in air. Temperature was a significant predictor of persistence over all matrices. Salinity and pH were significant predictors of persistence in water conditions. An assessment of the methodological quality review of the included studies revealed significant gaps in reporting critical aspects of study design.
Functional and Phylogenetic Analysis of
ureD
in Shiga Toxin-Producing
Escherichia coli
Authors: Steyert Susan R. , Rasko David A. , Kaper James B. 
Published: December 2010

ABSTRACT

Enterohemorrhagic
Escherichia coli
(EHEC) is a food-borne pathogen that can cause severe health complications and utilizes a much lower infectious dose than other
E. coli
pathotypes. Despite having an intact
ure
locus,
ureDABCEFG
, the majority of EHEC strains are phenotypically urease negative under tested conditions. Urease activity potentially assists with survival fitness by enhancing acid tolerance during passage through the stomach or by aiding with colonization in either human or animal reservoirs. Previously, in the EHEC O157:H7 Sakai strain, a point mutation in
ureD
, encoding a urease chaperone protein, was identified, resulting in a substitution of an amber stop codon for glutamine. This single nucleotide polymorphism (SNP) is observed in the majority of EHEC O157:H7 isolates and correlates with a negative urease phenotype
in vitro
. We demonstrate that the lack of urease activity
in vitro
is not solely due to the amber codon in
ureD.
Our analysis has identified two additional SNPs in
ureD
affecting amino acid positions 38 and 205, in both cases determining whether the encoded amino acid is leucine or proline. Phylogenetic analysis based on Ure protein sequences from a variety of urease-encoding bacteria demonstrates that the proline at position 38 is highly conserved among Gram-negative bacteria. Experiments reveal that the L38P substitution enhances urease enzyme activity; however, the L205P substitution does not. Multilocus sequence typing analysis for a variety of Shiga toxin-producing
E. coli
isolates combined with the
ureD
sequence reveals that except for a subset of the O157:H7 strains, neither the
in vitro
urease-positive phenotype nor the
ureD
sequence is phylogenetically restricted.
Three
motAB
Stator Gene Products in
Bdellovibrio bacteriovorus
Contribute to Motility of a Single Flagellum during Predatory and Prey-Independent Growth
Authors: Morehouse Karen A. , Hobley Laura , Capeness Michael , Sockett R. Elizabeth 
Published: December 2010

ABSTRACT

The predatory bacterium
Bdellovibrio bacteriovorus
uses flagellar motility to locate regions rich in Gram-negative prey bacteria, colliding and attaching to prey and then ceasing flagellar motility. Prey are then invaded to form a “bdelloplast” in a type IV pilus-dependent process, and prey contents are digested, allowing
Bdellovibrio
growth and septation. After septation,
Bdellovibrio
flagellar motility resumes inside the prey bdelloplast prior to its lysis and escape of
Bdellovibrio
progeny.
Bdellovibrio
can also grow slowly outside prey as long flagellate host-independent (HI) cells, cultured on peptone-rich media. The
B. bacteriovorus
HD100 genome encodes three pairs of MotAB flagellar motor proteins, each of which could potentially form an inner membrane ion channel, interact with the FliG flagellar rotor ring, and produce flagellar rotation. In 2004, Flannagan and coworkers (R. S. Flannagan, M. A. Valvano, and S. F. Koval, Microbiology 150:649-656, 2004) used antisense RNA and green fluorescent protein (GFP) expression to downregulate a single
Bdellovibrio motA
gene and reported slowed release from the bdelloplast and altered motility of the progeny. Here we inactivated each pair of
motAB
genes and found that each pair contributes to motility, both predatorily, inside the bdelloplast and during HI growth; however, each pair was dispensable, and deletion of no pair abolished motility totally. Driving-ion studies with phenamil, carbonyl cyanide
m
-chlorophenylhydrazone (CCCP), and different pH and sodium conditions indicated that all Mot pairs are proton driven, although the sequence similarities of each Mot pair suggests that some may originate from halophilic species. Thus,
Bdellovibrio
is a “dedicated motorist,” retaining and expressing three pairs of
mot
genes.
The Recombinase IntA Is Required for Excision of
esp
-Containing ICE
Efm1
in
Enterococcus faecium
Authors: Top Janetta , Sinnige Jan C. , Majoor Eline A. M. , Bonten Marc J. M. , Willems Rob J. L. , van Schaik Willem 
Published: December 2010

ABSTRACT

Comparative genome analysis of
Enterococcus faecium
recently revealed that a genomic island containing the
esp
gene, referred to as the
esp
-containing pathogenicity island (
esp
PAI), can be transferred by conjugation and contains a partial Tn
916
-like element and an integrase gene,
intA
. Here, we characterize the role of
intA
in the excision of the
esp
PAI. An
intA
insertion-deletion mutant in
E. faecium
E1162 (E1162Δ
intA
) was constructed and in
trans
complemented with wild-type
intA
(E1162Δ
intA
::pEF30). Circular intermediates (CI) of excised
esp
PAI were determined using inverse PCR analysis on purified chromosomal DNA from strains E1162, E1162Δ
esp
, E1162Δ
intA
, and E1162Δ
intA
::pEF30. In E1162 and E1162Δ
esp
, CI of the
esp
PAI were detected. No CI were detected in E1162Δ
intA
, while in the complemented strain E1162Δ
intA
::pEF30 CI formation was restored, indicating that
intA
is essential for excision and subsequent mobilization of the
esp
-containing genomic island in
E. faecium.
Based on the fact that this island can be mobilized and is self-transmissible, we propose to change the name of the
esp
PAI to ICE
Efm1
.
Mapping Functional Domains of Colicin M
Authors: Helbig Stephanie , Braun Volkmar 
Published: December 2010

ABSTRACT

Colicin M (Cma) lyses
Escherichia coli
cells by inhibiting murein biosynthesis through hydrolysis of the phosphate ester between C
55
-polyisoprenol and
N
-acetylmuramyl (MurNAc)-pentapeptide-GlcNAc in the periplasm. To identify Cma functional domains, we isolated 54 point mutants and small deletion mutants and examined their cytotoxicity levels. Activity and uptake mutants were distinguished by osmotic shock, which transfers Cma into the periplasm independent of the specific FhuA receptor and the Ton system. Deletion of the hydrophobic helix α1, which extends from the compact Cma structure, abolished interference with the antibiotic albomycin, which is transported across the outer membrane by the same system as Cma, thereby identifying α1 as the Cma site that binds to FhuA. Deletion of the C-terminal Lys-Arg strongly reduced Cma translocation across the outer membrane after binding to FhuA. Conversion of Asp226 to Glu, Asn, or Ala inactivated Cma. Asp226 is exposed at the Cma surface and is surrounded by Asp225, Asp229, His235, Tyr228, and Arg236; replacement of each with alanine inactivated Cma. We propose that Asp226 directly participates in phosphate ester hydrolysis and that the surrounding residues contribute to the active site. These residues are strongly conserved in Cma-like proteins of other species. Replacement of other conserved residues with alanine inactivated Cma; these mutations probably altered the Cma structure, as particularly apparent for mutants in the unique open β-barrel of Cma, which were isolated in lower yields. Our results identify regions in Cma responsible for uptake and activity and support the concept of a three-domain arrangement of Cma.
Genome Sequence of
Lactobacillus coryniformis
subsp.
coryniformis
KCTC 3167
Authors: Nam Seong-Hyeuk , Choi Sang-Haeng , Kang Aram , Kim Dong-Wook , Kim Dae-Soo , Kim Ryong Nam , Kim Aeri , Park Hong-Seog 
Published: December 2010

ABSTRACT

Lactobacillus coryniformis
subsp.
coryniformis
is known to be present during the manufacturing process of kimchi, the best-known traditional Korean dish. Here, we present the draft genome sequence of
Lactobacillus coryniformis
subsp.
coryniformis
type strain KCTC 3167 (2,964,752 bp, with a G+C content of 42.8%), which consists of 55 scaffolds.
Complete Genome Sequence of the Bacterium
Methylovorus
sp. Strain MP688, a High-Level Producer of Pyrroloquinolone Quinone
Authors: Xiong Xiang-hua , Zhi Jing-Juan , Yang Lu , Wang Jian-hua , Zhao Yan , Wang Xin , Cui Yan-Jiu , Dong Fang , Li Miao-Xin , Yang Yan-Xin , Wei Na , An Jia-jia , Du Bao-Hua , Liang Long , Zhang Jing-Sheng , Zhou Wei , Cheng Shao-Feng , He Tao , Wang Li , Chen Hui-Peng , Liu Dang-Sheng , Zhang Wei-cai 
Published: December 2010

ABSTRACT

Methylotrophic bacteria are widespread microbes which can use one carbon compound as their only carbon and energy sources. Here we report the finished, annotated genome sequence of the methylotrophic bacterium
Methylovorus
sp. strain MP688, which was isolated from soil for high-level production of pyrroloquinolone quinone (PQQ) in our lab.
The Minor Pilin Subunit Sgp2 Is Necessary for Assembly of the Pilus Encoded by thesrtGCluster ofStreptococcus suis
Authors: Okura Masatoshi , Osaki Makoto , Fittipaldi Nahuel , Gottschalk Marcelo , Sekizaki Tsutomu , Takamatsu Daisuke 
Published: December 2010

ABSTRACTGram-positive pili are composed of covalently bound pilin subunits whose assembly is mediated via a pilus-specific sortase(s). Major subunits constitute the pilus backbone and are therefore essential for pilus formation. Minor subunits are also incorporated into the pilus, but they are considered to be dispensable for backbone formation. ThesrtGcluster is one of the putative pilus gene clusters identified in the major swine pathogenStreptococcus suis. It consists of one sortase gene (srtG) and two putative pilin subunit genes (sgp1andsgp2). In this study, by constructing mutants for each of the genes in the cluster and by both immunoblotting and immunogold electron microscopic analysis with antibodies against Sgp1 and Sgp2, we found that thesrtGcluster mediates the expression of pilus-like structures inS. suisstrain 89/1591. In this pilus, Sgp1 forms the backbone, whereas Sgp2 is incorporated as the minor subunit. In accordance with the current model of pilus assembly by Gram-positive organisms, the major subunit Sgp1 was indispensable for backbone formation and the cognate sortase SrtG mediated the polymerization of both subunits. However, unlike other well-characterized Gram-positive bacterial pili, the minor subunit Sgp2 was required for polymerization of the major subunit Sgp1. Because Sgp2 homologues are encoded in several other Gram-positive bacterial pilus gene clusters, in some types of pili, minor pilin subunits may contribute to backbone formation by a novel mechanism.