bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptional Organization and Regulatory Elements of a Pseudomonas sp. Strain ADP Operon Encoding a LysR-Type Regulator and a Putative Solute Transport System
Authors: Platero Ana Isabel , García-Jaramillo Manuel , Santero Eduardo , Govantes Fernando 
Published: October 2012

ABSTRACT

The
atzS-atzT-atzU-atzV-atzW
gene cluster of the
Pseudomonas
sp. strain ADP atrazine-degradative plasmid pADP-1, which carries genes for an outer membrane protein and the components of a putative ABC-type solute transporter, is located downstream from
atzR
, which encodes the LysR-type transcriptional regulator of the cyanuric acid-degradative operon
atzDEF
. Here we describe the transcriptional organization of these genes. Our results show that all six genes are cotranscribed from the P
atzR
promoter to form the
atzRSTUVW
operon. A second, stronger promoter, P
atzT
, is found within
atzS
and directs transcription of the four distal genes. P
atzT
is σ
N
dependent, activated by NtrC in response to nitrogen limitation with the aid of IHF, and repressed by AtzR. A combination of
in vivo
mutational analysis and primer extension allowed us to locate the P
atzT
promoter and map the transcriptional start site. Similarly, we used deletion and point mutation analyses, along with
in vivo
expression studies and
in vitro
binding assays, to locate the NtrC, IHF, and AtzR binding sites and address their functionality. Our results suggest a regulatory model in which NtrC activates P
atzT
transcription via DNA looping, while AtzR acts as an antiactivator that diminishes expression by interfering with the activation process.
Genome of Enterobacteriophage Lula/phi80 and Insights into Its Ability To Spread in the Laboratory Environment
Authors: Rotman Ella , Kouzminova Elena , Plunkett Guy , Kuzminov Andrei 
Published: October 2012

ABSTRACT

The novel temperate bacteriophage Lula, contaminating laboratory
Escherichia coli
strains, turned out to be the well-known lambdoid phage phi80. Our previous studies revealed that two characteristics of Lula/phi80 facilitate its spread in the laboratory environment: cryptic lysogen productivity and stealthy infectivity. To understand the genetics/genomics behind these traits, we sequenced and annotated the Lula/phi80 genome, encountering an
E. coli
-toxic gene revealed as a gap in the sequencing contig and analyzing a few genes in more detail. Lula/phi80's genome layout copies that of lambda, yet homology with other lambdoid phages is mostly limited to the capsid genes. Lula/phi80's DNA is resistant to cutting with several restriction enzymes, suggesting DNA modification, but deletion of the phage's
damL
gene, coding for DNA adenine methylase, did not make DNA cuttable. The
damL
mutation of Lula/phi80 also did not change the phage titer in lysogen cultures, whereas the host
dam
mutation did increase it almost 100-fold. Since the high phage titer in cultures of Lula/phi80 lysogens is apparently in response to endogenous DNA damage, we deleted the only Lula/phi80 SOS-controlled gene,
dinL
. We found that
dinL
mutant lysogens release fewer phage in response to endogenous DNA damage but are unchanged in their response to external DNA damage. The toxic gene of Lula/phi80,
gamL
, encodes an inhibitor of the host ATP-dependent exonucleases, RecBCD and SbcCD. Its own antidote,
agt
, apparently encoding a modifier protein, was found nearby. Interestingly, Lula/phi80 lysogens are
recD
and
sbcCD
phenocopies, so GamL and Agt are part of lysogenic conversion.
Complete Genome Sequence of the Endophytic Enterobacter cloacae subsp. cloacae Strain ENHKU01
Authors: Liu Wing-Yee , Chung Karl Ming-Kar , Wong Chi-Fat , Jiang Jing-Wei , Hui Raymond Kin-Hi , Leung Frederick Chi-Ching 
Published: October 2012

ABSTRACT

Enterobacter cloacae
subsp.
cloacae
strain ENHKU01 is a Gram-negative endophyte isolated from a diseased pepper (
Capsicum annuum
) plant in Hong Kong. This is the first complete genome sequence report of a plant-endophytic strain of
E. cloacae
subsp.
cloacae
.
Staphylococcus aureus NorD, a Putative Efflux Pump Coregulated with the Opp1 Oligopeptide Permease, Contributes Selectively to Fitness
In Vivo
Authors: Ding Yanpeng , Fu Yingmei , Lee Jean C. , Hooper David C. 
Published: October 2012

ABSTRACT

Staphylococcus aureus
readily infects humans, causing infections from mild superficial skin infections to lethal bacteremia and endocarditis. Transporters produced by
S. aureus
allow the pathogen to adapt to a variety of settings, including survival at sites of infection and in the presence of antibiotics. The native functions of many transporters are unknown, but their potential dual contribution to fitness and antimicrobial resistance highlights their importance in staphylococcal infections. Here, we show that
S. aureus
NorD, a newly recognized efflux pump of the major facilitator superfamily, contributes to fitness in a murine subcutaneous abscess model. In community-associated methicillin-resistant
S. aureus
(CA-MRSA) strain MW2,
norD
was selectively upregulated 36-fold at the infection site relative to growth
in vitro
, and the
norD
mutant demonstrated significant fitness impairment in abscesses, with fitness 20- to 40-fold lower than that of the parent MW2 strain. Plasmid-encoded NorD could complement the fitness defect of the MW2
norD
mutant. Chromosomal
norD
expression is polycistronic with the upstream oligopeptide permease genes (
opp1ABCDF
), which encode an ABC oligopeptide transporter. Both
norD
and
opp1
were upregulated in abscesses and iron-restricted culture medium and negatively regulated by Fur, but only NorD contributed to fitness in the murine abscess model.
Genome Sequence of Staphylococcus lentus F1142, a Strain Isolated from Korean Soybean Paste
Authors: Nam Young-Do , Chung Won-Hyong , Seo Myung-Ji , Lim Seong-Il , Yi Sung-Hun 
Published: October 2012

ABSTRACT

This report describes the draft genome sequence of
Staphylococcus lentus
F1142, which was isolated from a Korean fermented soybean paste (doenjang). The draft genome sequence contained 2.79 Mbp with a G+C content of 31.8%; this is the first
S. lentus
genome to be reported.
AhpC Is Required for Optimal Production of Enterobactin by Escherichia coli
Authors: Ma Li , Payne Shelley M. 
Published: October 2012

ABSTRACT

Escherichia coli
alkyl hydroperoxide reductase subunit C (AhpC) is a peroxiredoxin that detoxifies peroxides. Here we show an additional role for AhpC in cellular iron metabolism of
E. coli
. Deletion of
ahpC
resulted in reduced growth and reduced accumulation of iron by cells grown in low-iron media. Liquid chromatography-mass spectroscopy (LC-MS) analysis of culture supernatants showed that the
ahpC
mutant secreted much less enterobactin, the siderophore that chelates and transports ferric iron under iron-limiting conditions, than wild-type
E. coli
did. The
ahpC
mutant produced less 2,3-dihydroxybenzoate, the intermediate in the enterobactin biosynthesis pathway, and providing 2,3-dihydroxybenzoate restored wild-type growth of the
ahpC
mutant. These data indicated that the defect was in an early step in enterobactin biosynthesis. Providing additional copies of
entC
, which functions in the first dedicated step of enterobactin biosynthesis, but not of other enterobactin biosynthesis genes, suppressed the mutant phenotype. Additionally, providing either shikimate or a mixture of
para
-aminobenzoate, tryptophan, tyrosine, and phenylalanine, which, like enterobactin, are synthesized from the precursor chorismate, also suppressed the mutant phenotype. These data suggested that AhpC affected the activity of EntC or the availability of the chorismate substrate.
Aquaporin AqpZ Is Involved in Cell Volume Regulation and Sensitivity to Osmotic Stress in Synechocystis sp. Strain PCC 6803
Authors: Akai Masaro , Onai Kiyoshi , Morishita Megumi , Mino Hiroyuki , Shijuku Toshiaki , Maruyama Hisataka , Arai Fumihito , Itoh Shigeru , Hazama Akihiro , Checchetto Vanessa , Szabò Ildikò , Yukutake Yoshinori , Suematsu Makoto , Yasui Masato , Ishiura Masahiro , Uozumi Nobuyuki 
Published: October 2012

ABSTRACT

The moderately halotolerant cyanobacterium
Synechocystis
sp. strain PCC 6803 contains a plasma membrane aquaporin, AqpZ. We previously reported that AqpZ plays a role in glucose metabolism under photomixotrophic growth conditions, suggesting involvement of AqpZ in cytosolic osmolarity homeostasis. To further elucidate the physiological role of AqpZ, we have studied its gene expression profile and its function in
Synechocystis
. The expression level of
aqpZ
was regulated by the circadian clock. AqpZ activity was insensitive to mercury in
Xenopus
oocytes and in
Synechocystis
, indicating that the AqpZ can be categorized as a mercury-insensitive aquaporin. Stopped-flow light-scattering spectrophotometry showed that addition of sorbitol and NaCl led to a slower decrease in cell volume of the
Synechocystis
Δ
aqpZ
strain than the wild type. The Δ
aqpZ
cells were more tolerant to hyperosmotic shock by sorbitol than the wild type. Consistent with this, recovery of oxygen evolution after a hyperosmotic shock by sorbitol was faster in the Δ
aqpZ
strain than in the wild type. In contrast, NaCl stress had only a small effect on oxygen evolution. The amount of AqpZ protein remained unchanged by the addition of sorbitol but decreased after addition of NaCl. This decrease is likely to be a mechanism to alleviate the effects of high salinity on the cells. Our results indicate that
Synechocystis
AqpZ functions as a water transport system that responds to daily oscillations of intracellular osmolarity.
Complete Genome of Transmissible Gastroenteritis Virus AYU Strain Isolated in Shanghai, China
Authors: Hou Yixuan , Yue Xiuwei , Cai Xuehui , Wang Shujie , Liu Yonggang , Yuan Congli , Cui Li , Hua Xiuguo , Yang Zhibiao 
Published: October 2012

ABSTRACT
Transmissible gastroenteritis virus strain AYU was isolated in Shanghai. The complete genome has a length of 28,582 bp and contains seven open reading frames. Sequence analysis suggested that Shanghai strain AYU and U.S. strain Purdue P115 are derived from a common ancestor, as they have 99.6% similarity at the nucleotide level.
Nine Complete Genome Sequences of Cutaneous Human Papillomavirus Genotypes Isolated from Healthy Skin of Individuals Living in Rural He Nan Province, China
Authors: Li Jingjing , Cai Hong , Xu Zhongyao , Wang Qiyan , Hang Dong , Shen Na , Liu Mengfei , Zhang Chanyuan , Abliz Amir , Ke Yang 
Published: October 2012

ABSTRACT

Nine novel human papillomavirus (HPV) types were isolated from healthy skin of individuals in rural Anyang, China. All of these isolates belong to the genus
Gammapapillomavirus
. These data will provide us with useful information for a better understanding of PV evolution and the relationship of PV with the host.
Complete Genome Sequence of Le Blanc Virus, a Third Caenorhabditis Nematode-Infecting Virus
Authors: Franz Carl J. , Zhao Guoyan , Félix Marie-Anne , Wang David 
Published: October 2012

ABSTRACT

Orsay virus and Santeuil virus, the first known viruses capable of naturally infecting the nematodes
Caenorhabditis elegans
and
Caenorhabditis briggsae
, respectively, were recently identified by high-throughput sequencing of wild
Caenorhabditis
strains. By similar analysis of another wild
C. briggsae
isolate, we have now discovered and sequenced the complete genome of a third novel virus, Le Blanc virus, that is distantly related to Orsay and Santeuil viruses. All three viruses are positive-sense RNA viruses with bipartite genomes that are most closely related to nodaviruses. Identification of a third virus capable of infecting
Caenorhabditis
nematodes enables comparative analysis of this clade of viruses and strengthens this model for investigating virus-host interactions.
Genome of a Bombyx mori Nucleopolyhedrovirus Strain Isolated from India
Authors: Fan Hai-Wei , Zhang Xue-Chao , Xu Yi-Peng , Cheng Xiao-Wen , Zhang Chuan-Xi 
Published: October 2012

ABSTRACT

Bombyx mori
nucleopolyhedrovirus (BmNPV), a member of the
Baculoviridae
, is a major pathogen of silkworm and has also been recently developed as an expression vector for heterologous gene expression in the silkworm larvae and pupae. To better understand the diversity of this important baculovirus, we sequenced the complete genome of the BmNPV strain isolated from India, where its host is available throughout the year due to its tropical climate. The genome of the Indian strain consists of 127,879 nucleotides, with a G+C content of 40.36%. There are 138 open reading frames (ORFs) encoding the predicted proteins of more than 50 amino acids. Genomic comparison of the Indian strain with 3 other reported BmNPV strains showed that the baculovirus repeat ORFs (
bro
) and homologous repeat regions (hr's) are highly variable. These results suggest that the BmNPV strain heterogeneity is mainly caused by single-nucleotide polymorphisms (SNPs) and changes in the hr's and
bro
genes.
Complete Genome Sequence of an H3N2 Avian Influenza Virus Isolated from a Live Poultry Market in Eastern China
Authors: Teng Qiaoyang , Hu Tao , Li Xuesong , Li Guoxin , Li Zejun 
Published: October 2012

ABSTRACT
Previous studies indicate that the H3 influenza virus has the ability to establish infection upon interspecies transmission and poses a threat to mammals. Therefore, it is important to enhance the surveillance of H3 avian influenza viruses (AIVs). In this study, A/duck/Shanghai/C84/2009(H3N2) (C84) was isolated from a live poultry market in Shanghai, China. Using PCR and sequencing analyses, we obtained the whole-genome sequence of this virus. The H3N2 virus proved to be a novel multiple-gene reassortant AIV whose genes were derived from H3N2, H4N6, H6N2, and H9N2. Knowledge regarding the complete genome sequence of the C84 virus will be useful for epidemiological surveillance.
Complete Genome Sequence of a Novel Human Parechovirus
Authors: Wang Chunmei , Shan Tongling , Zheng Hao , Tong Wu , Chen Fangzhou , Hu Han , He Qigai , Tong Guangzhi 
Published: October 2012

ABSTRACT

Human parechoviruses (HPeVs) belonging to the family
Picornaviridae
are widely spread pathogens among young children. We report the complete genome sequence of a novel HPeV isolated from the stool sample of a hospitalized child with diarrhea in China. The genome consists of 7,305 nucleotides, excluding the 3′ poly(A) tail, and has an open reading frame that maps between nucleotide positions 675 and 7217 and encodes a 2,180-amino-acid polyprotein. The genome sequence of the virus was sufficiently distinct from the 8 known HPeV types. Phylogenetic analysis based on the complete genome indicated that the HPeV strain represents a new genotype.
Genome of Thysanoplusia orichalcea Multiple Nucleopolyhedrovirus Lacks the Superoxide Dismutase Gene
Authors: Wang Yun-Sheng , Huang Guo-Hua , Cheng Xin-Hua , Wang Xing , Garretson Tyler A. , Dai Liang-Ying , Zhang Chuan-Xi , Cheng Xiao-Wen 
Published: October 2012

ABSTRACT

Thysanoplusia orichalcea
multiple nucleopolyhedrovirus (ThorMNPV) has high virulence to
Trichoplusia ni
and
Pseudoplusia includens
larvae, with a potential for biological control of insect pests. The genome of ThorMNPV was sequenced and found to be 132,978 bp, with a G+C content of 37.9%. There are 145 predicted open reading frames (ORFs), encoding proteins of 50 or more amino acid residues with minimal overlap. Of the 145 ORFs, 141 appeared to be homologous to those of
Autographa californica
MNPV (AcMNPV). In comparison to AcMNPV, 9 ORFs of AcMNPV were absent in ThorMNPV, including the superoxide dismutase (
sod
) gene.
DROWNING PREVENTION PROGRAMME IN NORTHERN IRAN—A CLOSER LOOK AT THE PROBLEM
Authors: Davoudi- kiakalayeh A , Mohammadi R , Yousefzade-chabok S 
Published: October 2012

BackgroundDrowning has not been well recognised as a public health problem in many developing countries including Iran.AimsThis work outlines the context of the programme; describes its design and implementation; and reviews key findings that emerged from the evaluation drowning prevention programme in northern Iran.MethodsThis article is complied based on cross-sectional study and two intervention study. Data for studies were derived from Death Registry System, Forensic Medicine, Weekly Report and household surveys. This project were located in border of Caspian Sea in northern Iran. Age group, gender, place and date of occurrence, external causes were assessed. Evaluation of the drowning prevention programme in the form of a quasiexperimental study and employed (1) pre and post interventional observations with a comparison community in a water recreational area of the Caspian Sea in northern Iran and (2) pre and post interventional observations without a comparison community in a rural area near the Caspian Sea coastline.ResultsThe risk of fatality resulting from drowning was observed to be greater during the preimplementation period than throughout the implementation period (OR=1.65). The drowning prevalence in rural areas of the Caspian Sea coastline as compared to a WHO standardised population demonstrated a continuous decrease in the age specific drowning rate among the oldest victims with a gradual decline during implementation.SignificanceThis effort suggests that the drowning prevention programme based on community based health promotion could help to both reduce the burden of drowning fatality and its related healthcare expenditure.
LEARNING FROM 20 YEAR TRENDS IN UNINTENTIONAL CHILD INJURY MORTALITY
Authors: Mytton J , Towner E , Powell J , Pilkington P , Gray S 
Published: October 2012

BackgroundThe relative significance of child injury as a cause of preventable death has increased as the ability to control infectious diseases has improved. Unintentional child injuries are now a major global cause of death and disability with the greatest burden falling on those who are most disadvantaged.Aim/Objectives/PurposeA systematic review of long term trends in child injury mortality was conducted to review progress and consider the implications for policy, practice and research.MethodsWe systematically collated and quality appraised data from publications and documents reporting unintentional child injury mortality, over periods of 20 years or more. A critical narrative synthesis explored trends by injury type and by country income group, and reported disparities in injury occurrence by age, sex, ethnicity and socio-economic group.Results/OutcomeThirty one studies meeting the inclusion criteria were identified of which 30 were included in the narrative synthesis. Only six were from middle income countries and none were from low income countries. An overall trend in falling child injury mortality masked rising road traffic injury deaths, evidence of increasing vulnerability of adolescents and widening disparities within countries when analysed by ethnic group and socioeconomic status.Significance/Contribution to the FieldWe need to adapt our knowledge of effective interventions to reduce child injury mortality for low income countries, particularly where rapid economic and social change may be increasing exposure to injury risks. Within countries, advocacy and interventions to reduce disparities in injury mortality by age, ethnicity and socioeconomic status should be prioritised.
SUCCESSFUL ROAD SAFETY INITIATIVES IN DUBAI
Authors: Adai M Bin , Banna H Al 
Published: October 2012

BackgroundDubai is one of the fastest growing cities in the world and aims to provide world class services in all sectors. The economy boom, the large increase in population and the ease of car ownership has had a direct effect on the number of traffic accidents.ObjectivesThe Roads and Transport Authority was born in 2006 with the vision of ‘safe and smooth transport for all’ is responsible for designing, constructing, maintenance of road infrastructure, safety improvement programmes. We would like to take this opportunity to shed light on the on-going and future road safety initiatives and schemes that helped to reduce road fatalities on Dubai roads.MethodsThe introduction of various traffic safety improvement projects and schemes such as a Road Safety Strategy, Pedestrian Safety and Mobility Action Plan, Road Safety Auditing, Accident Blackspots programmes, Road side improvement programmes, Work Zone improvement programmes, Speed Management programmes, Traffic Awareness Programmes, Zone wise auditing programmes, Traffic calming measures in residential and school zones and also adopting new standards and manuals which are based on best international practices.ResultsThe above systematic approach, successful road safety programmes and initiatives have contributed to reducing the rate of fatalities in Dubai from 21.9 fatality/100 k population in 2006–6.7 fatality/100 k population in 2011.SignificanceThe continuous and systematic initiatives above are certainly leading the way in the field of Traffic Safety and have managed to exceed all expectations in Dubai, the region and the world as far as traffic safety improvements are concerned.
OPTIMISING SEAT LENGTH DESIGN TO MINIMISE EXTRA PASSENGERS ON ALL-TERRAIN VEHICLES
Authors: Jennissen C , Marsico J , Steffen J , Schnell T , McGehee D , Denning G 
Published: October 2012

BackgroundThe presence of extra riders increases the likelihood of an all-terrain vehicle (ATV) crash and injury. However, many ATVs have seats long enough to accommodate passengers.Aims/Objectives/PurposeTo determine if ATV seats could be redesigned to limit use to only one rider.MethodsA convenience sampling of 14 ATV models were measured and compared, and seat dimension requirements were analysed at a 26 degree incline/decline.Results/OutcomesSeat lengths varied from 22–35 inches. The seat backs ended fairly consistently at 38–45 inches away from the handlebar attachment. Most of the seat length differences were accountable by the distance from the handlebar attachment to the front of the seat, which varied from 9–19 inches. The incline/decline study revealed that when going downhill, a rider needs to fully extend their arms and move their bottom back to the seat edge in order to move their centre of gravity behind the front tires and avoid a front rollover. When going uphill, a forward lean is sufficient to keep the operator's centre of gravity ahead of the rear tires and prevent a backward rollover.Significance/contribution to the fieldSince a rider can adequately change their centre of gravity on an uphill incline without shifting their bottom forward, the seat is not required to be as close to the handles as many manufacturers design. We suggest that a shorter seat starting further from the handlebar is the preferred ATV seat design. This should discourage multiple passenger use by reducing the space available for additional riders.