bluuebunny/crossref_metadata_2025_split huggingface dataset:
A population genetic signature of human releases in an invasive ladybeetle
Authors: Kajita Yukie , O'Neill Eric M. , Zheng Yanbing , Obrycki John J. , Weisrock David W. 
Published: October 2012

AbstractBiological invasions have been accelerated by a variety of human activities. Propagule pressure, the number of introduced individuals and independent introductions, is probably to be influenced by these human activities and may be an important factor for successful range expansion in new environments. We tested whether the current distribution of the predatory ladybeetle Coccinella septempunctata in the introduced range (USA) is the result of multiple historical human introductions or natural range expansion from the first established populations in the USA. To test this hypothesis, we compared historical records of propagule size, propagule number, specific introduction locations and the date of each introduction, with estimates of genetic variation in mitochondrial DNA (cytochrome oxidase I). Our results indicated that genetic diversity in the introduced range was positively correlated with historical records of propagule size and number and negatively correlated with distance to nearest introduction point, suggesting that multiple human releases were successful. Higher genetic diversity in populations found near introduction points suggest that initial founder effects were limited, but lower genetic diversity found farther from introduction points is probably the result of serial founder effects during secondary range expansion. These results suggest that the current distribution of C. septempunctata in the introduced range is the result of a combination of human releases and short‐range expansion from multiple established populations in the introduced range.
The ribosome binding site of a mini‐ORF protects a T3SS mRNA from degradation by RNase E
Authors: Lodato Patricia B. , Hsieh Ping‐Kun , Belasco Joel G. , Kaper James B. 
Published: October 2012

SummaryEnterohaemorrhagic Escherichia coli harbours a pathogenicity island encoding a type 3 secretion system used to translocate effector proteins into the cytosol of intestinal epithelial cells and subvert their function. The structural proteins of the translocon are encoded in a major espADB mRNA processed from a precursor. The translocon mRNA should be highly susceptible to RNase E cleavage because of its AU‐rich leader region and monophosphorylated 5′‐terminus, yet it manages to avoid rapid degradation. Here, we report that the espADB leader region contains a strong Shine–Dalgarno element (SD2) and a translatable mini‐ORF of six codons. Disruption of SD2 so as to weaken ribosome binding significantly reduces the concentration and stability of esp mRNA, whereas codon substitutions that impair translation of the mini‐ORF have no such effect. These findings suggest that occupancy of SD2 by ribosomes, but not mini‐ORF translation, helps to protect espADB mRNA from degradation, likely by hindering RNase E access to the AU‐rich leader region.
Escherichia coliDNA polymerase III is responsible for the high level of spontaneous mutations in mutT strains
Authors: Yamada Masami , Shimizu Masatomi , Katafuchi Atsushi , Grúz Petr , Fujii Shingo , Usui Yukio , Fuchs Robert P. , Nohmi Takehiko 
Published: October 2012

SummaryReactive oxygen species induce oxidative damage in DNA precursors, i.e. dNTPs, leading to point mutations upon incorporation. Escherichia coli mutT strains, deficient in the activity hydrolysing 8‐oxo‐7,8‐dihydro‐2′‐deoxyguanosine 5′‐triphosphate (8‐oxo‐dGTP), display more than a 100‐fold higher spontaneous mutation frequency over the wild‐type strain. 8‐oxo‐dGTP induces A to C transversions when misincorporated opposite template A. Here, we report that DNA pol III incorporates 8‐oxo‐dGTP ≈ 20 times more efficiently opposite template A compared with template C. Single, double or triple deletions of pol I, pol II, pol IV or pol V had modest effects on the mutT mutator phenotype. Only the deletion of all four polymerases led to a 70% reduction of the mutator phenotype. While pol III may account for nearly all 8‐oxo‐dGTP incorporation opposite template A, it only extends ≈ 30% of them, the remaining 70% being extended by the combined action of pol I, pol II, pol IV or pol V. The unique property of pol III, a C‐family DNA polymerase present only in eubacteria, to preferentially incorporate 8‐oxo‐dGTP opposite template A during replication might explain the high spontaneous mutation frequency in E. coli mutT compared with the mammalian counterparts lacking the 8‐oxo‐dGTP hydrolysing activities.
Optimization of K‐edge imaging with spectral CT
Authors: He Peng , Wei Biao , Cong Wenxiang , Wang Ge 
Published: October 2012

Purpose:Spectral/multienergy CT has the potential to distinguish different materials by K‐edge characteristics. K‐edge imaging involves the two energy bins on both sides of a K‐edge. The authors propose a K‐edge imaging optimization model to determine these two energy bins.Methods:K‐edge image contrast with spectral CT depends on the specifications of the two energy bins on both sides of a K‐edge in the attenuation profile of a relatively high atomic number material. The wider the energy bin width is, the lower the noise level is, and the poorer the reconstructed image contrast is. Here the authors introduce the signal difference to noise ratio (SDNR) criterion to optimize the energy bin widths on both sides of the K‐edge for the maximum SDNR.Results:The authors study K‐edge imaging with spectral CT, analyze the effect of K‐edge energy bins on the resultant image quality, and establish guidelines for the optimization of energy thresholds. In simulation, the authors demonstrate that our K‐edge imaging optimization approach maximizes SDNR in reconstructed images.Conclusions:This proposed approach can be readily generalized to deal with more general settings and determine the best energy bins for K‐edge imaging.
The cerebral vasomotor response in varying CO2 concentrations, as evaluated using cine phase contrast MRI: Flow, volume, and cerebrovascular resistance indices
Authors: Liu Yi‐Jui , Huang Teng‐Yi , Lee Yi‐Hsiung , Juan Chun‐Jung 
Published: October 2012

Purpose:Previous studies have identified that impaired cerebral vasomotor reactivity (VMR) is associated with a higher risk of stroke and transient ischemic attack. This study aims to evaluate VMR by measuring the blood flow waveforms of the supplying arteries and dural sinuses using cine phase contrast MRI (PC MRI) and hypercapnic challenge.Methods:PC MRI flow quantification was performed on an oblique slice approximately perpendicular to the target vessels to include the left (LICA) and right internal carotid artery (RICA), basilar artery (BA), sinus rectus (SR), and superior sagittal sinus (SSS). A total of four PC MRI scans were performed at different CO2 concentrations (room air and 3%, 5%, and 7% CO2).Results:The analyses obtained the flow parameters and cerebrovascular resistance parameters for all five vessels. Results indicated that the vascular resistance indices decreased with increasing CO2 concentration in four vessels (LICA, RICA, BA, and SR). The obtained VMR parameters demonstrated exponential increases with increasing CO2 concentration.Conclusions:Using entire blood flow waveforms, this study applied separate flow dynamics during systolic and diastolic periods to obtain cerebrovascular resistance parameters and extensive flow‐related information. It is the first to investigate the cerebrovascular resistance parameters under hypercapnic challenge using cine MRI. This technique could provide a useful tool for clinical application in cerebrovascular disease.
Genome Sequence of Pectobacterium sp. Strain SCC3193
Authors: Koskinen J. Patrik , Laine Pia , Niemi Outi , Nykyri Johanna , Harjunpää Heidi , Auvinen Petri , Paulin Lars , Pirhonen Minna , Palva Tapio , Holm Liisa 
Published: October 2012

ABSTRACT

We report the complete and annotated genome sequence of the plant-pathogenic enterobacterium
Pectobacterium
sp. strain SCC3193, a model strain isolated from potato in Finland. The
Pectobacterium
sp. SCC3193 genome consists of a 516,411-bp chromosome, with no plasmids.
Twenty-One Genome Sequences from Pseudomonas Species and 19 Genome Sequences from Diverse Bacteria Isolated from the Rhizosphere and Endosphere of Populus deltoides
Authors: Brown Steven D. , Utturkar Sagar M. , Klingeman Dawn M. , Johnson Courtney M. , Martin Stanton L. , Land Miriam L. , Lu Tse-Yuan S. , Schadt Christopher W. , Doktycz Mitchel J. , Pelletier Dale A. 
Published: October 2012

ABSTRACT

To aid in the investigation of the
Populus deltoides
microbiome, we generated draft genome sequences for 21
Pseudomonas
strains and 19 other diverse bacteria isolated from
Populus deltoides
roots. Genome sequences for isolates similar to
Acidovorax
,
Bradyrhizobium
,
Brevibacillus
,
Caulobacter
,
Chryseobacterium
,
Flavobacterium
,
Herbaspirillum
,
Novosphingobium
,
Pantoea
,
Phyllobacterium
,
Polaromonas
,
Rhizobium
,
Sphingobium
, and
Variovorax
were generated.
Genome Sequence of the Lantibiotic Bacteriocin Producer Streptococcus salivarius Strain K12
Authors: Barretto Caroline , Alvarez-Martin Pablo , Foata Francis , Renault Pierre , Berger Bernard 
Published: October 2012

ABSTRACT

Streptococcus salivarius
is a prevalent commensal species of the oropharyngeal tract.
S. salivarius
strain K12 is an isolate from the saliva of a healthy child, used as an oral probiotic. Here, we report its genome sequence, i.e., the full sequence of the 190-kb megaplasmid pSsal-K12 and a high-quality draft 2.2-Gb chromosomal sequence.
Draft Genome Sequences of 21 Salmonella enterica Serovar Enteritidis Strains
Authors: Timme Ruth E. , Allard Marc W. , Luo Yan , Strain Errol , Pettengill James , Wang Charles , Li Cong , Keys Christine E. , Zheng Jie , Stones Robert , Wilson Mark R. , Musser Steven M. , Brown Eric W. 
Published: October 2012

ABSTRACT

Salmonella enterica
subsp.
enterica
serovar Enteritidis is a common food-borne pathogen, often associated with shell eggs and poultry. Here, we report draft genomes of 21
S.
Enteritidis strains associated with or related to the U.S.-wide 2010 shell egg recall. Eleven of these genomes were from environmental isolates associated with the egg outbreak, and 10 were reference isolates from previous years, unrelated to the outbreak. The whole-genome sequence data for these 21 human pathogen strains are being released in conjunction with the newly formed 100K Genome Project.
Genome Sequence of Kocuria atrinae C3-8, Isolated from Jeotgal, a Traditional Korean Fermented Seafood
Authors: Nam Young-Do , Seo Myung-Ji , Lim Seong-Il , Park So-lim 
Published: October 2012

ABSTRACT

Kocuria
is a Gram-positive coccus, catalase-positive, coagulase-negative, strictly aerobic bacterial genus in the family
Micrococcaceae
.
Kocuria atrinae
C3-8 was isolated from a traditional Korean fermented seafood. This study describes the first genome sequence of
K. atrinae
strain C3-8, which has a 3.19-Mbp genome and a G+C content of 63.8%.
Next-Generation Sequencing and
De Novo
Assembly, Genome Organization, and Comparative Genomic Analyses of the Genomes of Two Helicobacter pylori Isolates from Duodenal Ulcer Patients in India
Authors: Kumar Narender , Mukhopadhyay Asish K. , Patra Rajashree , De Ronita , Baddam Ramani , Shaik Sabiha , Alam Jawed , Tiruvayipati Suma , Ahmed Niyaz 
Published: October 2012

ABSTRACT

The prevalence of different
H. pylori
genotypes in various geographical regions indicates region-specific adaptations during the course of evolution. Complete genomes of
H. pylori
from countries with high infection burdens, such as India, have not yet been described. Herein we present genome sequences of two
H. pylori
strains, NAB47 and NAD1, from India. In this report, we briefly mention the sequencing and finishing approaches, genome assembly with downstream statistics, and important features of the two draft genomes, including their phylogenetic status. We believe that these genome sequences and the comparative genomics emanating thereupon will help us to clearly understand the ancestry and biology of the Indian
H. pylori
genotypes, and this will be helpful in solving the so-called Indian enigma, by which high infection rates do not corroborate the minuscule number of serious outcomes observed, including gastric cancer.
Whole-Genome Shotgun Sequencing of a Colonizing Multilocus Sequence Type 17 Streptococcus agalactiae Strain
Authors: Singh Pallavi , Springman A. Cody , Davies H. Dele , Manning Shannon D. 
Published: October 2012

ABSTRACT

This report highlights the whole-genome shotgun draft sequence for a
Streptococcus agalactiae
strain representing multilocus sequence type (ST) 17, isolated from a colonized woman at 8 weeks postpartum. This sequence represents an important addition to the published genomes and will promote comparative genomic studies of
S. agalactiae
recovered from diverse sources.
Complete Genome Sequence of the Ethanol-Producing Zymomonas mobilis subsp. mobilis Centrotype ATCC 29191
Authors: Desiniotis Andreas , Kouvelis Vassili N. , Davenport Karen , Bruce David , Detter Chris , Tapia Roxanne , Han Cliff , Goodwin Lynne A. , Woyke Tanja , Kyrpides Nikos C. , Typas Milton A. , Pappas Katherine M. 
Published: October 2012

ABSTRACT

Zymomonas mobilis
is an ethanologenic bacterium that has been studied for use in biofuel production. Of the sequenced
Zymomonas
strains, ATCC 29191 has been described as the phenotypic centrotype of
Zymomonas mobilis
subsp.
mobilis
, the taxon that harbors the highest ethanol-producing
Z. mobilis
strains. ATCC 29191 was isolated in Kinshasa, Congo, from palm wine fermentations. This strain is reported to be a robust levan producer, while in recent years it has been employed in studies addressing
Z. mobilis
respiration. Here we announce the finishing and annotation of the ATCC 29191 genome, which comprises one chromosome and three plasmids.
Draft Genome Sequence of Turicella otitidis ATCC 51513, Isolated from Middle Ear Fluid from a Child with Otitis Media
Authors: Brinkrolf Karina , Schneider Jessica , Knecht Marina , Rückert Christian , Tauch Andreas 
Published: October 2012

ABSTRACT

Turicella otitidis
is an unusual corynebacterium with a controversial role in otitis media in children. Metabolic capabilities deduced from the draft genome indicate its adaptation to habitats on the human skin and in the intestine. The lack of candidate virulence factors implies that
T. otitidis
has a low pathogenic potential.
Genome Sequence and Comparative Pathogenomics Analysis of a Salmonella enterica Serovar Typhi Strain Associated with a Typhoid Carrier in Malaysia
Authors: Yap Kien-Pong , Gan Han Ming , Teh Cindy Shuan Ju , Baddam Ramani , Chai Lay-Ching , Kumar Narender , Tiruvayipati Suma Avasthi , Ahmed Niyaz , Thong Kwai-Lin 
Published: October 2012

ABSTRACT

Salmonella enterica
serovar Typhi is a human pathogen that causes typhoid fever predominantly in developing countries. In this article, we describe the whole genome sequence of the
S. Typhi
strain CR0044 isolated from a typhoid fever carrier in Kelantan, Malaysia. These data will further enhance the understanding of its host persistence and adaptive mechanism.
Draft Genome Sequence of the Quality Control Strain Enterococcus faecalis ATCC 29212
Authors: Kim Eun Bae , Kopit Lauren M. , Harris Linda J. , Marco Maria L. 
Published: October 2012

ABSTRACT

Enterococcus faecalis
ATCC 29212, a vancomycin-sensitive strain, has been extensively used as a representative control strain for clinical and laboratory experiments. Here we report the draft genome and annotation of this strain, containing 3,027,060 bp, with a G+C content of 37.2% in 126 contigs (≥500 bp).
Draft Genome Sequence of Lactobacillus gigeriorum CRBIP 24.85
T
, Isolated from a Chicken Crop
Authors: Cousin Sylvie , Ma Laurence , Creno Sophie , Clermont Dominique , Loux Valentin , Bizet Chantal , Bouchier Christiane 
Published: October 2012

ABSTRACT

We report the draft genome of the strain
Lactobacillus gigeriorum
CRBIP 24.85
T
, isolated from a chicken crop. The total length of the 60 scaffolds is about 1.9 Mb, with a GC content of 38% and 2,062 protein-coding sequences (CDS).
Complete Genome Sequence of the Thermophilic, Piezophilic, Heterotrophic Bacterium Marinitoga piezophila KA3
Authors: Lucas Susan , Han James , Lapidus Alla , Cheng Jan-Fang , Goodwin Lynne A. , Pitluck Sam , Peters Lin , Mikhailova Natalia , Teshima Hazuki , Detter John C. , Han Cliff , Tapia Roxanne , Land Miriam , Hauser Loren , Kyrpides Nikos C. , Ivanova Natalia , Pagani Ioanna , Vannier Pauline , Oger Phil , Bartlett Douglas H. , Noll Kenneth M. , Woyke Tanja , Jebbar Mohamed 
Published: October 2012

ABSTRACT

Marinitoga piezophila
KA3 is a thermophilic, anaerobic, chemoorganotrophic, sulfur-reducing bacterium isolated from the Grandbonum deep-sea hydrothermal vent site at the East Pacific Rise (13°N, 2,630-m depth). The genome of
M. piezophila
KA3 comprises a 2,231,407-bp circular chromosome and a 13,386-bp circular plasmid. This genome was sequenced within Department of Energy Joint Genome Institute CSP 2010.
Genome Sequence of an OXA23-Producing, Carbapenem-Resistant Acinetobacter baumannii Strain of Sequence Type ST75
Authors: Liu Shiwei , Wang Yufei , Xu Jie , Li Yan , Guo Jie , Ke Yuehua , Yuan Xitong , Wang Lili , Du Xinying , Wang Zhoujia , Huang Liuyu , Zhang Ning , Chen Zeliang 
Published: October 2012

ABSTRACT

The increase of
Acinetobacter baumannii
resistance to carbapenems is of great concern. OXA23 is one of the most prevalent carbapenemases of
A. baumannii
that causes outbreaks. Here, we announce the genome sequence of an OXA23-producing
A. baumannii
strain assigned ST75, a newly emerged sequence type harboring carbapenemase.
Genome Sequence of Pseudomonas aeruginosa Strain AH16, Isolated from a Patient with Chronic Pneumonia in China
Authors: Wu Da-Qiang , Cheng Huijuan , Wang Changzhong , Zhang Changfeng , Wang Yan , Shao Jing , Duan Qiangjun 
Published: October 2012

ABSTRACT

Pseudomonas aeruginosa
AH16 is a virulent strain isolated from a patient with chronic pneumonia in China. Here, we present a 6.8-Mb (G+C content, 66.13%) assembly of its genome with 6,332 putative coding sequences, which may provide insights into the genomic basis of activity of the clinical
P. aeruginosa
strain in China.
Genomic Analysis of Mycobacterium abscessus Strain M139, Which Has an Ambiguous Subspecies Taxonomic Position
Authors: Ngeow Yun Fong , Wee Wei Yee , Wong Yan Ling , Tan Joon Liang , Ongi Chia Su , Ng Kee Peng , Choo Siew Woh 
Published: October 2012

ABSTRACT

Mycobacterium abscessus
is a ubiquitous, rapidly growing species of nontuberculous mycobacteria that colonizes organic surfaces and is frequently associated with opportunistic infections in humans. We report here the draft genome sequence of
Mycobacterium abscessus
strain M139, which shows genomic features reported to be characteristic of both
Mycobacterium abscessus
subsp.
abscessus
and
Mycobacterium abscessus
subsp.
massiliense
.
Genome Sequence of Acinetobacter baumannii AC12, a Polymyxin-Resistant Strain Isolated from Terengganu, Malaysia
Authors: Gan Han Ming , Lean Soo-Sum , Suhaili Zarizal , Thong Kwai-Lin , Yeo Chew Chieng 
Published: October 2012

ABSTRACT

Acinetobacter baumannii
is a major cause of nosocomial infection worldwide. We report the draft genome sequence of
A. baumannii
AC12, a multidrug-resistant nosocomial strain with additional resistance to carbapenems and polymyxin. The genome data will provide insights into the genetic basis of antimicrobial resistance and its adaptive mechanism.
Whole-Genome Sequence of Enterobacter sp. Strain SST3, an Endophyte Isolated from Jamaican Sugarcane (Saccharum sp.) Stalk Tissue
Authors: Gan Han Ming , McGroty Sean E. , Chew Teong Han , Chan Kok Gan , Buckley Larry J. , Savka Michael A. , Hudson André O. 
Published: October 2012

ABSTRACT

Enterobacter
sp. strain SST3 is an endophytic bacterium isolated from
Saccharum
spp. Here we present its annotated draft genome that may shed light on its role as a bacterial endophyte of sugarcane. To our knowledge, this is the first genome announcement of a sugarcane-associated bacterium from the genus
Enterobacter
.
Draft Genome Sequences of Four Axenic Mycoplasma genitalium Strains Isolated from Denmark, Japan, and Australia
Authors: McGowin Chris L. , Ma Liang , Jensen Jørgen S. , Mancuso Miriam M. , Hamasuna Ryoichi , Adegboye David , Martin David H. 
Published: October 2012

ABSTRACT

The DNA genome of
Mycoplasma genitalium
currently represents the smallest of all known human bacterial pathogens. Despite their clinical importance in sexually transmitted infection and relevance as model bacterial pathogens, genomic diversity among
M. genitalium
strains worldwide is unknown. Herein we present the complete draft genome sequences of four geographically diverse strains of
M. genitalium
.
Genome Sequence of Pseudomonas putida S12, a Potential Platform Strain for Industrial Production of Valuable Chemicals
Authors: Tao Fei , Shen Yaling , Fan Ziqi , Tang Hongzhi , Xu Ping 
Published: October 2012

ABSTRACT

Pseudomonas putida
strain S12, a well-studied solvent-tolerant bacterium, is considered a platform strain for the production of many chemicals. Here, we present a 6.28-Mb assembly of its genome sequence. We have annotated 32 coding sequences (CDSs) encoding efflux systems of organic compounds and 195 CDSs responsible for the metabolism of aromatic compounds.
Genome Sequences of Three Live Attenuated Vaccine Strains of Brucella Species and Implications for Pathogenesis and Differential Diagnosis
Authors: Wang Yufei , Ke Yuehua , Wang Zhoujia , Yuan Xitong , Qiu Yefeng , Zhen Qing , Xu Jie , Li Tiefeng , Wang Dali , Huang Liuyu , Chen Zeliang 
Published: October 2012

ABSTRACT

Live attenuated vaccines play essential roles in the prevention of brucellosis. Here, we report the draft genome sequences of three vaccine strains,
Brucella melitensis
M5-10,
B. suis
S2-30, and
B. abortus
104M. Primary genome sequence analysis identified mutations, deletions, and insertions which have implications for attenuation and signatures for differential diagnosis.
Genome Sequence of Lysinibacillus boronitolerans F1182, Isolated from a Traditional Korean Fermented Soybean Product
Authors: Nam Young-Do , Seo Myung-Ji , Lim Seong-Il , Lee So-Young 
Published: October 2012

ABSTRACT

Lysinibacillus
is a Gram-positive, rod-shaped, and round-spore-forming bacterial genus of the family
Bacillaceae
. We analyzed the genome sequence of
Lysinibacillus boronitolerans
F1182, isolated from a traditional Korean fermented soybean product. The genome sequence contained 4.46 Mbp with a G+C content of 37.5%. This is the first report of an
L. boronitolerans
genome.
Genome Sequence of the Welan Gum-Producing Strain Sphingomonas sp. ATCC 31555
Authors: Wang Xiaoyu , Tao Fei , Gai Zhonghui , Tang Hongzhi , Xu Ping 
Published: October 2012

ABSTRACT

Sphingomonas
sp. strain ATCC 31555 can produce an anionic heteropolysaccharide, welan gum, which shows excellent stability and viscosity retention even at high temperatures. Here we present a 4.0-Mb assembly of its genome sequence. We have annotated 10 coding sequences (CDSs) responsible for the welan gum biosynthesis and 55 CDSs related to monosaccharide metabolism.
Genome Sequence of the Plant Growth-Promoting Rhizobacterium Pseudomonas putida S11
Authors: Ponraj Paramasivan , Shankar Manoharan , Ilakkiam Devaraj , Rajendhran Jeyaprakash , Gunasekaran Paramasamy 
Published: October 2012

ABSTRACT

Here we report the genome sequence of a plant growth-promoting rhizobacterium,
Pseudomonas putida
S11. The length of the draft genome sequence is approximately 5,970,799 bp, with a G+C content of 62.4%. The genome contains 6,076 protein-coding sequences.