bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diversity, Evolution, and Functionality of Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) Regions in the Fire Blight Pathogen Erwinia amylovora
Authors: Rezzonico Fabio , Smits Theo H. M. , Duffy Brion 
Published: April 2011

ABSTRACTThe clustered regularly interspaced short palindromic repeat (CRISPR)/Cas system confers acquired heritable immunity against mobile nucleic acid elements in prokaryotes, limiting phage infection and horizontal gene transfer of plasmids. In CRISPR arrays, characteristic repeats are interspersed with similarly sized nonrepetitive spacers derived from transmissible genetic elements and acquired when the cell is challenged with foreign DNA. New spacers are added sequentially and the number and type of CRISPR units can differ among strains, providing a record of phage/plasmid exposure within a species and giving a valuable typing tool. The aim of this work was to investigate CRISPR diversity in the highly homogeneous speciesErwinia amylovora, the causal agent of fire blight. A total of 18 CRISPR genotypes were defined within a collection of 37 cosmopolitan strains. Strains from Spiraeoideae plants clustered in three major groups: groups II and III were composed exclusively of bacteria originating from the United States, whereas group I generally contained strains of more recent dissemination obtained in Europe, New Zealand, and the Middle East. Strains from Rosoideae and Indian hawthorn (Rhaphiolepis indica) clustered separately and displayed a higher intrinsic diversity than that of isolates from Spiraeoideae plants. Reciprocal exclusion was generally observed between plasmid content and cognate spacer sequences, supporting the role of the CRISPR/Cas system in protecting against foreign DNA elements. However, in several group III strains, retention of plasmid pEU30 is inconsistent with a functional CRISPR/Cas system.
Bifidobacterial Diversity and the Development of New Microbial Source Tracking Indicators
Authors: Ballesté Elisenda , Blanch Anicet R. 
Published: April 2011

ABSTRACT

Many studies suggest a close relationship between species of
Bifidobacterium
and their hosts. Thus, species such as
B. adolescentis
and
B. thermacidophilum
subsp.
porcinum
have been proposed as potential indicators of human and porcine fecal pollution. The diversity of bifidobacteria in wastewaters (human and animal) and slurries is analyzed using nested PCR followed by denaturant gradient gel electrophoresis (DGGE). The sewage samples showed similar DGGE patterns. The predominant bands were recognized as
B. adolescentis
,
B. longum
, and two unidentified species related to
B. adolescentis
. A single band detected in poultry samples was identified as
B. saeculare
. Bifidobacterial diversity was higher within porcine and bovine samples. The main bands in porcine samples were identified as
B. minimum
, an unknown species, and
B. thermophilum/B. thermacidophilum
subsp.
porcinum
. The latter species was also identified among the main bands in bovine samples together with
B. pseudolongum
and
B. ruminantium
. We then attempted to isolate the host-specific strains. DGGE bands were examined to develop specific probes to screen environmental samples by colony hybridization and further isolation of strains from positively hybridized colonies. Bifidobacterial strains that are host associated by DGGE bands to human and pig were successfully isolated from the environment:
B. adolescentis
from human sewage samples and the unidentified species related to pig from slurries and slaughterhouse wastewater. Neither the poultry-associated
B. saeculare
nor the ruminant-associated
B. pseudolongum
could be isolated with the current methodology, suggesting either a low prevalence in the samples or failure of the culture to grow in the media used.
Influence of Season and Geography on Campylobacter jejuni and C. coli Subtypes in Housed Broiler Flocks Reared in Great Britain
Authors: Jorgensen F. , Ellis-Iversen J. , Rushton S. , Bull S. A. , Harris S. A. , Bryan S. J. , Gonzalez A. , Humphrey T. J. 
Published: April 2011

ABSTRACT

Geographical and seasonal variation in the incidence and prevalence of
Campylobacter jejuni
and
C. coli
in housed broiler flocks reared in Great Britain in 2004 to 2006 was investigated in this study. Ceca (30) from 797 flocks, not subject to prior partial depopulation and reared on 211 farms, were examined individually for the presence of
Campylobacter
spp. The best-fitting climatic factors explained approximately 46% of the prevalence of
Campylobacter
-colonized flocks at slaughter and consisted of a combination of temperature at slaughter, number of sunshine hours in placement month, and millimeters of rainfall in placement month. Positive flocks were more likely to be slaughtered between June and November than during the rest of the year and to be reared in northern Great Britain than in central or southern Great Britain.
C. jejuni
was identified in approximately 90% of flocks, and
C. coli
was present in 10% of flocks. The most common clonal complexes identified in 226 isolates typed by multilocus sequence typing (MLST) were ST-45, ST-21, ST-574, ST-443, and ST-828. Flocks slaughtered at the same time were more likely to have similar complexes, and ST-45 had a seasonal pattern, with the highest prevalence in June, and was also more likely to be present in flocks reared in northern Great Britain.
Glutathione Facilitates Antibiotic Resistance and Photosystem I Stability during Exposure to Gentamicin in Cyanobacteria
Authors: Cameron Jeffrey C. , Pakrasi Himadri B. 
Published: April 2011

ABSTRACT

Understanding mechanisms of antibiotic resistance is important to the fields of biology and medicine. We find that glutathione contributes to antibiotic resistance in the cyanobacterium
Synechocystis
sp. PCC 6803. Our results also suggest that glutathione protects photosystem I from oxidative damage resulting from growth in the presence of gentamicin.
Quantification of Propionibacterium acidipropionici P169 Bacteria in Environmental Samples by Use of Strain-Specific Primers Derived by Suppressive Subtractive Hybridization
Authors: Peng Min , Smith Alexandra H. , Rehberger Thomas G. 
Published: April 2011

ABSTRACT

A quantitative PCR (qPCR) assay targeting a gene identified by suppressive subtractive hybridization (SSH) was developed to detect
Propionibacterium acidipropionici
P169, with a threshold of 10
4
CFU/U of dairy feed or rumen fluid. The report is the first using a molecular marker generated by SSH to quantify a bacterial strain in environmental samples.
Microbes in High Arctic Snow and Implications for the Cold Biosphere
Authors: Harding Tommy , Jungblut Anne D. , Lovejoy Connie , Vincent Warwick F. 
Published: April 2011

ABSTRACT

We applied molecular, microscopic, and culture techniques to characterize the microbial communities in snow and air at remote sites in the Canadian High Arctic (Ward Hunt Island, Ellesmere Island, and Cornwallis Island, latitudes 74 to 83
o
N). Members of the
Bacteria
and
Eukarya
were prevalent in the snow, and their small subunit (SSU) rRNA gene signatures indicated strong local aerial transport within the region over the preceding 8 months of winter snowpack accumulation. Many of the operational taxonomic units (OTUs) were similar to previously reported SSU rRNA gene sequences from the Arctic Ocean, suggesting the importance of local aerial transport processes for marine microbiota. More than 47% of the cyanobacterial OTUs in the snow have been previously found in microbial mats in the region, indicating that this group was also substantially derived from local sources. Viable cyanobacteria isolated from the snow indicated free exchange between the snow and adjacent mat communities. Other sequences were most similar to those found outside the Canadian Arctic but were from snow, lake and sea ice, glaciers and permafrost, alpine regions, Antarctica, and other regions of the Arctic, supporting the concept of global distribution of microbial ecotypes throughout the cold biosphere.
Acetogens and Acetoclastic Methanosarcinales Govern Methane Formation in Abandoned Coal Mines
Authors: Beckmann Sabrina , Lueders Tillmann , Krüger Martin , von Netzer Frederick , Engelen Bert , Cypionka Heribert 
Published: April 2011

ABSTRACT

In abandoned coal mines, methanogenic archaea are responsible for the production of substantial amounts of methane. The present study aimed to directly unravel the active methanogens mediating methane release as well as active bacteria potentially involved in the trophic network. Therefore, the stable-isotope-labeled precursors of methane, [
13
C]acetate and H
2
-
13
CO
2
, were fed to liquid cultures from hard coal and mine timber from a coal mine in Germany. Guided by methane production rates, samples for DNA stable-isotope probing (SIP) with subsequent quantitative PCR and denaturing gradient gel electrophoretic (DGGE) analyses were taken over 6 months. Surprisingly, the formation of [
13
C]methane was linked to acetoclastic methanogenesis in both the [
13
C]acetate- and the H
2
-
13
CO
2
-amended cultures of coal and timber. H
2
-
13
CO
2
was used mainly by acetogens related to
Pelobacter acetylenicus
and
Clostridium
species. Active methanogens, closely affiliated with
Methanosarcina barkeri
, utilized the readily available acetate rather than the thermodynamically more favorable hydrogen. Thus, the methanogenic microbial community appears to be highly adapted to the low-H
2
conditions found in coal mines.
Overestimation of the Abundance of Sulfate-Reducing Bacteria in Human Feces by Quantitative PCR Targeting the Desulfovibrio 16S rRNA Gene
Authors: Christophersen C. T. , Morrison M. , Conlon M. A. 
Published: April 2011

ABSTRACT

The dominant genus of sulfate-reducing bacteria (SRB) in humans is
Desulfovibrio
, and quantitative PCR (QPCR) targeting the 16S rRNA gene is often used in assays. We show that the 16S rRNA gene assay overestimated SRB abundance in feces from 24 adults compared to QPCR assays using primers targeting two genes involved in SRB energy metabolism.
pmoA
Primers for Detection of Anaerobic Methanotrophs
Authors: Luesken Francisca A. , Zhu Baoli , van Alen Theo A. , Butler Margaret K. , Diaz Marina Rodriguez , Song Bongkeun , Op den Camp Huub J. M. , Jetten Mike S. M. , Ettwig Katharina F. 
Published: April 2011

ABSTRACT

Published
pmoA
primers do not match the
pmoA
sequence of “
Candidatus
Methylomirabilis oxyfera,” a bacterium that performs nitrite-dependent anaerobic methane oxidation. Therefore, new
pmoA
primers for the detection of “
Ca
. Methylomirabilis oxyfera”-like methanotrophs were developed and successfully tested on freshwater samples from different habitats. These primers expand existing molecular tools for the study of methanotrophs in the environment.
Use of
1
H Nuclear Magnetic Resonance To Measure Intracellular Metabolite Levels during Growth and Asexual Sporulation in Neurospora crassa
Authors: Kim James D. , Kaiser Kayla , Larive Cynthia K. , Borkovich Katherine A. 
Published: April 2011

ABSTRACT

Conidiation is an asexual sporulation pathway that is a response to adverse conditions and is the main mode of dispersal utilized by filamentous fungal pathogens for reestablishment in a more favorable environment. Heterotrimeric G proteins (consisting of α, β, and γ subunits) have been shown to regulate conidiation in diverse fungi. Previous work has demonstrated that all three of the Gα subunits in the filamentous fungus
Neurospora crassa
affect the accumulation of mass on poor carbon sources and that loss of
gna-3
leads to the most dramatic effects on conidiation. In this study, we used
1
H nuclear magnetic resonance (NMR) to profile the metabolome of
N. crassa
in extracts isolated from vegetative hyphae and conidia from cultures grown under conditions of high or low sucrose. We compared wild-type and Δ
gna-3
strains to determine whether lack of
gna-3
causes a significant difference in the global metabolite profile. The results demonstrate that the global metabolome of wild-type hyphae is influenced by carbon availability. The metabolome of the Δ
gna-3
strain cultured on both high and low sucrose is similar to that of the wild type grown on high sucrose, suggesting an overall defect in nutrient sensing in the mutant. However, analysis of individual metabolites revealed differences in wild-type and Δ
gna-3
strains cultured under conditions of low and high sucrose.
Regulation of Pathogenic Spore Germination by CgRac1 in the Fungal Plant Pathogen Colletotrichum gloeosporioides
Authors: Nesher Iris , Minz Anna , Kokkelink Leonie , Tudzynski Paul , Sharon Amir 
Published: April 2011

ABSTRACTColletotrichum gloeosporioidesis a facultative plant pathogen: it can live as a saprophyte on dead organic matter or as a pathogen on a host plant. Different patterns of conidial germination have been recognized under saprophytic and pathogenic conditions, which also determine later development. Here we describe the role of CgRac1 in regulating pathogenic germination. The hallmark of pathogenic germination is unilateral formation of a single germ tube following the first cell division. However, transgenic strains expressing a constitutively active CgRac1 (CA-CgRac1) displayed simultaneous formation of two germ tubes, with nuclei continuing to divide in both cells after the first cell division. CA-CgRac1 also caused various other abnormalities, including difficulties in establishing and maintaining cell polarity, reduced conidial and hyphal adhesion, and formation of immature appressoria. Consequently, CA-CgRac1 isolates were completely nonpathogenic. Localization studies with cyan fluorescent protein (CFP)-CgRac1 fusion protein showed that the CgRac1 protein is abundant in conidia and in hyphal tips. Although the CFP signal was equally distributed in both cells of a germinating conidium, reactive oxygen species accumulated only in the cell that produced a germ tube, indicating that CgRac1 was active only in the germinating cell. Collectively, our results show that CgRac1 is a major regulator of asymmetric development and that it is involved in the regulation of both morphogenesis and nuclear division. Modification of CgRac1 activity disrupts the morphogenetic program and prevents fungal infection.
Genome Sequence of Strain TW25, a Novel Member of the Genus Ornithinibacillus in the Family Bacillaceae
Authors: Whon Tae Woong , Roh Seong Woon , Shin Na-Ri , Kim Min-Soo , Kim Young-Ok , Bae Jin-Woo 
Published: April 2011

ABSTRACT

Ornithinibacillus
sp. strain TW25, belonging to the family
Bacillaceae
, was isolated from a dead ark clam during a mass mortality event. Here, the draft genome sequence of strain TW25 (3,843,870 bp, with a G+C content of 36.7%) is reported. This is the first
Ornithinibacillus
genome to be sequenced.
Genome Sequences of Mycoplasma alligatoris A21JP2
T
and Mycoplasma crocodyli MP145
T
Authors: Brown D. R. , Farmerie W. G. , May M. , Benders G. A. , Durkin A. S. , Hlavinka K. , Hostetler J. , Jackson J. , Johnson J. , Miller R. H. , Paralanov V. , Radune D. , Szczypinski B. , Glass J. I. 
Published: April 2011

ABSTRACT

Mycoplasma alligatoris
and
Mycoplasma crocodyli
are closely related siblings, one being highly virulent and the other relatively attenuated. We compared their genomes to better understand the mechanisms and origins of
M. alligatoris
' remarkable virulence amid a clade of harmless or much less virulent species. Although its chromosome was refractory to closure,
M. alligatoris
differed most notably by its complement of sialidases and other genes of the
N
-acetylneuraminate scavenging and catabolism pathway.
Complete Genome Sequence of the Cellulolytic Thermophile Clostridium thermocellum DSM1313
Authors: Feinberg Lawrence , Foden Justine , Barrett Trisha , Davenport Karen Walston , Bruce David , Detter Chris , Tapia Roxanne , Han Cliff , Lapidus Alla , Lucas Susan , Cheng Jan-Fang , Pitluck Samuel , Woyke Tanja , Ivanova Natalia , Mikhailova Natalia , Land Miriam , Hauser Loren , Argyros D. Aaron , Goodwin Lynne , Hogsett David , Caiazza Nicky 
Published: April 2011

ABSTRACT

Clostridium thermocellum
DSM1313 is a thermophilic, anaerobic bacterium with some of the highest rates of cellulose hydrolysis reported. The complete genome sequence reveals a suite of carbohydrate-active enzymes and demonstrates a level of diversity at the species level distinguishing it from the type strain ATCC 27405.
Genome Sequence of Streptomyces griseus Strain XylebKG-1, an Ambrosia Beetle-Associated Actinomycete
Authors: Grubbs Kirk J. , Biedermann Peter H. W. , Suen Garret , Adams Sandra M. , Moeller Joseph A. , Klassen Jonathan L. , Goodwin Lynne A. , Woyke Tanja , Munk A. Christine , Bruce David , Detter Chris , Tapia Roxanne , Han Cliff S. , Currie Cameron R. 
Published: April 2011

ABSTRACT

Streptomyces griseus
strain XylebKG-1 is an insect-associated strain of the well-studied actinobacterial species
S. griseus
. Here, we present the genome of XylebKG-1 and discuss its similarity to the genome of
S. griseus
subsp. griseus NBRC13350. XylebKG-1 was isolated from the fungus-cultivating
Xyleborinus saxesenii
system. Given its similarity to free-living
S. griseus
subsp. griseus NBRC13350, comparative genomics will elucidate critical components of bacterial interactions with insects.
Complete Genome Sequence of Lactococcus lactis subsp.
lactis
CV56, a Probiotic Strain Isolated from the Vaginas of Healthy Women
Authors: Gao Yong , Lu Ying , Teng Kun-Ling , Chen Mei-Ling , Zheng Hua-Jun , Zhu Yong-Qiang , Zhong Jin 
Published: April 2011

ABSTRACT

Lactic acid bacteria that exist in the urinogenital system play an important role in maintaining the health of the host. Here, we report the finished and annotated genome of a
Lactococcus
strain that was isolated from the vaginas of healthy women and shows probiotic properties, including nisin A production and adhesion to vaginal epithelial cells.
Genome-Wide Identification of Transcription Start Sites Yields a Novel Thermosensing RNA and New Cyclic AMP Receptor Protein-Regulated Genes in Escherichia coli
Authors: Raghavan Rahul , Sage Alan , Ochman Howard 
Published: April 2011

ABSTRACT

Intergenic regions often contain regulatory elements that control the expression of flanking genes. Using a deep-sequencing approach, we identified numerous new transcription start sites in
Escherichia coli
, yielding a new thermosensing regulatory RNA and seven genes previously unknown to be under the control of the global regulator CRP.
Role of Rbp1 in the Acquired Chill-Light Tolerance of Cyanobacteria
Authors: Tan Xiaoming , Zhu Tao , Shen Si , Yin Chuntao , Gao Hong , Xu Xudong 
Published: April 2011

ABSTRACT

Synechocystis
sp. strain PCC 6803 cultured at 30°C losses viability quickly under chill (5°C)-light stress but becomes highly tolerant to the stress after conditioning at 15°C (Y. Yang, C. Yin, W. Li, and X. Xu, J. Bacteriol.
190:
1554–1560, 2008). Hypothetically, certain factors induced during preconditioning are involved in acquisition of chill-light tolerance. In this study, Rbp1 (RNA-binding protein 1) rather than Rbp2 was found to be accumulated during preconditioning, and the accumulation of Rbp1 was correlated with the increase of chill-light tolerance. Inactivation of its encoding gene
rbp1
led to a great reduction in the acquired chill-light tolerance, while ectopic expression of
rbp1
enabled the cyanobacterium to survive the chill-light stress without preconditioning. Microarray analyses suggested that the Rbp1-dependent chill-light tolerance may not be based on its influence on mRNA abundance of certain genes. Similarly to that in
Synechocystis
, the Rbp1 homologue(s) can be accumulated in
Microcystis
cells collected from a subtropic lake in low-temperature seasons. Rbp1 is the first factor shown to be both accumulated early during preconditioning and directly involved in development of chill-light tolerance in
Synechocystis
. Its accumulation may greatly enhance the overwintering capability in certain groups of cyanobacteria.
The health paradox of occupational and leisure-time physical activity
Authors: Holtermann A , Hansen J V , Burr H , Søgaard K , Sjøgaard G 
Published: April 2011

BackgroundOccupational and leisure-time physical activity are considered to provide similar health benefits. The authors tested this hypothesis.MethodsA representative sample of Danish employees (n=7144, 52% females) reported levels of occupational and leisure-time physical activity in 2005. Long-term sickness absence (LTSA) spells of ≥3 consecutive weeks were retrieved from a social-transfer payment register from 2005 to 2007.Results341 men and 620 females experienced a spell of LTSA during the period. Cox analyses adjusted for age, gender, smoking, alcohol, body mass index, chronic disease, social support from immediate superior, emotional demands, social class and occupational or leisure-time physical activity showed a decreased risk for LTSA among workers with moderate (HR 0.85, CI 0.72 to 1.01) and high (HR 0.77, CI 0.62 to 0.95) leisure-time physical activity in reference to those with low leisure-time physical activity. In contrast, an increased risk for LTSA was shown among workers with moderate (HR 1.59, CI 1.35 to 1.88) and high (HR 1.84, CI 1.55 to 2.18) occupational physical activity referencing those with low occupational physical activity.ConclusionThe hypothesis was rejected. In a dose–response manner, occupational physical activity increased the risk for LTSA, while leisure-time physical activity decreased the risk for LTSA. The findings indicate opposing effects of occupational and leisure-time physical activity on global health.
Use of abbreviations by healthcare professionals: what is the way forward?
Authors: Sinha S , McDermott F , Srinivas G , Houghton P W J 
Published: April 2011

ABSTRACT

Objective
To assess the understanding of commonly used abbreviations in the medical records among healthcare professionals.

Methods
A selection of abbreviations from surgical inpatient admissions (gathered over a 10 day period in October 2008), in the form of a standard questionnaire, was shown to different members of a multidisciplinary team to examine interpretation and knowledge.

Results
209 questionnaires were analysed. The average correct response was 43%. Foundation Year 1 (F1) doctors scored the highest with 57% correct responses, whereas dieticians fared worst (20% correct). Among different abbreviations, NAD (91%) and SCBU (93%) were most often correctly answered, whereas CIC (3%) and STS (0.5%) were the most incorrectly answered. Certain abbreviations which are mostly used by nurses (eg, OTT) achieved a 75% correct response by them compared to only 11% by F1 and 10% by F2 doctors (p&lt;0.001). Similarly, abbreviations such as COBH (p=0.025) and LUTS (p&lt;0.001), although mostly correctly answered by junior doctors, were very poorly answered by nurses.

Conclusion
The majority of healthcare professionals have a very poor knowledge of commonly used abbreviations. Use of unambiguous and approved list of abbreviations is suggested in order to ensure good communication in patient care.