bluuebunny/crossref_metadata_2025 huggingface dataset:
Comprehensive and high‐resolution typing of swine leukocyte antigen DQA from genomic DNA and determination of 25 new SLA class II haplotypes
Authors: Le M. T. , Choi H. , Choi M.‐K. , Nguyen D. T. , Kim J.‐H. , Seo H. G. , Cha S.‐Y. , Seo K. , Chun T. , Schook L. B. , Park C.
Published: November 2012

We previously reported the development of genomic‐DNA‐based high‐resolution genotyping methods for SLA‐DQB1 and DRB1. Here, we report the successful typing of SLA‐DQA using similar methodological principles. We designed a method for comprehensive genotyping of SLA‐DQA using intronic sequence information of SLA‐DQA exon 2 that we had obtained from 12 animals with different SLA‐DQB1 genotypes. We expanded our typing to 76 selected animals with diverse DQB1 and DRB1 genotypes, 140 random animals from 7 pig breeds, and 3 wild boars. This resulted in the identification of 17 DQA alleles with 49 genotypes. Two new alleles were identified from wild boars. Combine with SLA‐DQB1, and DRB1 typing results, we identified 34 SLA class II haplotypes including 25 that were previously unreported.
Characterization of three novel HLA alleles with silent nucleotide substitutions
Authors: Endres R. O. , Hoffman A. D. , Palmer P. , Scott I. , Souza S.
Published: November 2012

Characterization of the novel HLA alleles B*35:11:03, B*42:01:03, and B*51:01:35 is described.
Identification of a new allele HLA‐B*40:213 by polymerase chain reaction sequence based typing in a Chinese patient suffering from chloroma
Authors: Liu Y.
Published: November 2012

This new HLA‐B allele differs from the closest allele B*40:01:01 by two nucleotide changes at codons 102 and 267.
TNFA promoter alleles – frequencies and linkage with classical HLA genes in a South German Caucasian population
Authors: Fürst D. , Zollikofer Ch. , Schrezenmeier H. , Mytilineos J.
Published: November 2012

The tumor necrosis factor alpha (TNFA) promoter region exhibits several polymorphisms, which have been hypothesized to influence gene expression, thereby associating positively or negatively with inflammatory conditions. Many studies have focused on single nucleotide polymorphisms (SNPs) taking not into account additive or inverse effects between different SNPs. We typed 1,021 healthy Caucasian volunteer stem cell donors for their TNFA promoter as well as their HLA‐A,‐C,‐B,‐DRB1 loci. Using statistical methods, we reconstructed TNFA promoter alleles and analyzed their frequency and linkage with HLA genes. We show that the number of TNFA promoter alleles frequent enough to be analyzed in clinical studies is limited and that a strong linkage with classical HLA genes is present, especially for the extended HLA‐haplotype HLA‐A*01:01/HLA‐C*07:01/HLA‐B*08:01/TNFA promoter allele 3/HLA*DRB1*03:01. Taking into account SNP frequency information, it is possible to quite accurately deduce TNFA promoter alleles by generic Sanger sequencing, obviating the need for elaborating allele‐specific sequencing. This information may enable investigators to consider the complete TNFA regulatory region in a phase‐separated manner in contrast to previous approaches examining only one or few isolated SNPs.
Phylogenetic relationships in three species of canine Demodex mite based on partial sequences of mitochondrial 16S rDNA
Authors: Sastre Natalia , Ravera Ivan , Villanueva Sergio , Altet Laura , Bardagí Mar , Sánchez Armand , Francino Olga , Ferrer Lluís
Published: November 2012

Background –  The historical classification of Demodex mites has been based on their hosts and morphological features. Genome sequencing has proved to be a very effective taxonomic tool in phylogenetic studies and has been applied in the classification of Demodex. Mitochondrial 16S rDNA has been demonstrated to be an especially useful marker to establish phylogenetic relationships.

Hypothesis/Objectives –  To amplify and sequence a segment of the mitochondrial 16S rDNA from Demodex canis and Demodex injai, as well as from the short‐bodied mite called, unofficially, D. cornei and to determine their genetic proximity.

Methods –  Demodex mites were examined microscopically and classified as Demodex folliculorum (one sample), D. canis (four samples), D. injai (two samples) or the short‐bodied species D. cornei (three samples). DNA was extracted, and a 338 bp fragment of the 16S rDNA was amplified and sequenced.

Results –  The sequences of the four D. canis mites were identical and shared 99.6 and 97.3% identity with two D. canis sequences available at GenBank. The sequences of the D. cornei isolates were identical and showed 97.8, 98.2 and 99.6% identity with the D. canis isolates. The sequences of the two D. injai isolates were also identical and showed 76.6% identity with the D. canis sequence.

Conclusion –  Demodex canis and D. injai are two different species, with a genetic distance of 23.3%. It would seem that the short‐bodied Demodex mite D. cornei is a morphological variant of D. canis.
Charge trapping analysis of Al2O3 films deposited by atomic layer deposition using H2O or O3 as oxidant
Authors: González Mireia Bargalló , Rafí Joan Marc , Beldarrain Oihane , Zabala Miguel , Campabadal Francesca
Published: November 2012

In this work, the authors focus on the charge trapping behavior of Al2O3 layers deposited by atomic layer deposition. The goal is to give an insight into the effects of the oxidant source (H2O or O3) and the postdeposition anneal on the charging phenomena and the generation of new defects during electrical stress. For this purpose, current–voltage, capacitance–voltage, and conductance–voltage characteristics of Al/Al2O3/p-Si capacitors are analyzed before and after constant voltage stress and several phenomena such as the generation of neutral traps in the bulk dielectric, slow states, interface states, and charge trapping related degradation during the electrical stress are investigated. Finally, the impact of the oxidant source on the Al2O3 layer reliability is discussed.
Robust Photogeneration of H
2
in Water Using Semiconductor Nanocrystals and a Nickel Catalyst
Authors: Han Zhiji , Qiu Fen , Eisenberg Richard , Holland Patrick L. , Krauss Todd D.
Published: November 2012

Robust Reduction

A major challenge in the design of artificial photosynthesis catalysts has been their instability under the reaction conditions—a problem that plants and other autotrophs address by perpetually reproducing their biochemical machinery.

Han
et al.

(p.
1321
, published online 8 November) now demonstrate a system for photoreductive hydrogen generation in water that manifests undiminished activity for weeks at a time. Semiconductor nanoparticles for light absorption were combined with a soluble nickel complex for the catalytic chemistry. The system currently requires a sacrificial electron donor, but its robustness shows promise for future pairing with an integrated oxidation catalyst.
Acute Inflammation Initiates the Regenerative Response in the Adult Zebrafish Brain
Authors: Kyritsis Nikos , Kizil Caghan , Zocher Sara , Kroehne Volker , Kaslin Jan , Freudenreich Dorian , Iltzsche Anne , Brand Michael
Published: November 2012

The Good Side of Inflammation

The zebrafish brain is much more adept than the human brain at recovering after traumatic injury.

Kyritsis
et al.

(p.
1353
, published online 8 November; see the Perspective by

Stella

) investigated the cellular events that support regeneration in the zebrafish brain. Although inflammation is part of the response in both settings, the zebrafish brain goes on to initiate proliferation of replacement neurons. By inciting inflammation without neuronal damage, radial glial cells could be pushed into neurogenesis.
Draft Genome Sequence of Lactobacillus casei W56
Authors: Hochwind Kerstin , Weinmaier Thomas , Schmid Michael , van Hemert Saskia , Hartmann Anton , Rattei Thomas , Rothballer Michael
Published: November 2012

We announce the draft genome sequence of
Lactobacillus casei
W56 in one contig. This strain shows immunomodulatory and probiotic properties. The strain is also an ingredient of commercially available probiotic products.
Genome Sequence of the Biocontrol Agent Microbacterium barkeri Strain 2011-R4
Authors: Liu Jian , Zhou Qing , Ibrahim Muhammad , Liu He , Jin Gulei , Zhu Bo , Xie Guanlin
Published: November 2012

Microbacterium barkeri
strain 2011-R4 is a Gram-positive epiphyte which has been confirmed as a biocontrol agent against several plant pathogens in our previous studies. Here, we present the draft genome sequence of this strain, which was isolated from the rice rhizosphere in Tonglu city, Zhejiang province, China.
Draft Genome Sequence of Paenisporosarcina sp. Strain TG-20, a Psychrophilic Bacterium Isolated from the Basal Ice of Taylor Glacier
Authors: Lee Jun Hyuck , Koh Hye Yeon , Lee Sung Gu , Doyle Shawn , Christner Brent C. , Kim Hak Jun
Published: November 2012

We report the draft genome sequence of
Paenisporosarcina
sp. strain TG-20, which is 4.12 Mb in size and consists of 4,071 protein-coding genes and 76 RNA genes. The genome sequence of
Paenisporosarcina
sp. TG-20 may provide useful information about molecular adaptations that enhance survival in icy subsurface environments.
First Genome Sequence of a Burkholderia pseudomallei Isolate in China, Strain BPC006, Obtained from a Melioidosis Patient in Hainan
Authors: Fang Yao , Huang Yong , Li Qian , Chen Hai , Yao Zhen , Pan Jin , Gu Jiang , Tang Bin , Wang Hai-guang , Yu Bo , Tong Yi-gang , Zou Quan-ming , Mao Xu-hu
Published: November 2012

Melioidosis, caused by
Burkholderia pseudomallei
, is considered to be endemic to Northern Australia and Southeast Asia, with high mortality and relapse rates, regardless of powerful antibiotic therapy. Here we report the first genome sequence of
Burkholderia pseudomallei
strain BPC006, obtained from a melioidosis patient in Hainan, China. The genome sizes of the 2 chromosomes were determined to be 4,001,777 bp and 3,153,284 bp.
Genome Sequence of the Corynebacterium pseudotuberculosis Cp316 Strain, Isolated from the Abscess of a Californian Horse
Authors: Ramos Rommel Thiago Jucá , Silva Artur , Carneiro Adriana Ribeiro , Pinto Anne Cybelle , Soares Siomar de Castro , Santos Anderson Rodrigues , Almeida Sintia Silva , Guimarães Luis Carlos , Aburjaile Flávia Figueira , Barbosa Eudes Guilherme Vieira , Dorella Fernanda Alves , Rocha Flávia Souza , Cerdeira Louise Teixeira , Barbosa Maria Silvanira , Tauch Andreas , Edman Judy , Spier Sharon , Miyoshi Anderson , Schneider Maria Paula Cruz , Azevedo Vasco
Published: November 2012

The bacterium
Corynebacterium pseudotuberculosis
is of major veterinary importance because it affects livestock, particularly sheep, goats, and horses, in several countries, including Australia, Brazil, the United States, and Canada, resulting in significant economic losses. In the present study, we describe the complete genome of the
Corynebacterium pseudotuberculosis
Cp316 strain, biovar equi, isolated from the abscess of a North American horse.
Complete Genome Sequence of Actinobacillus suis H91-0380, a Virulent Serotype O2 Strain
Authors: MacInnes Janet I. , Mackinnon Joanne , Bujold Adina R. , Ziebell Kim , Kropinski Andrew M. , Nash John H. E.
Published: November 2012

Here, we report the first complete genome sequence of
Actinobacillus suis
, an important opportunistic pathogen of swine. By comparing the genome sequence of
A. suis
with those of other members of the family
Pasteurellaceae
, we hope to better understand the role of these organisms in health and disease in swine.
Draft Genome Sequence of Marine-Derived Streptomyces sp. Strain AA0539, Isolated from the Yellow Sea, China
Authors: Xiong Zhi-Qiang , Wang Yong
Published: November 2012

Here, we report the draft genome sequence of
Streptomyces
sp. strain AA0539, isolated from marine sediment of the Yellow Sea, China. Its small genome (∼5.8 Mb) contains large, unique genes and gene clusters for diverse secondary metabolites, suggesting great potential as a source for the discovery of novel natural products.
Draft Genome Sequence of Bacillus isronensis Strain B3W22, Isolated from the Upper Atmosphere
Authors: Shivaji S. , Ara Sreenivas , Singh Sanjay Kumar , Bandi Sunil , Singh Aditya , Pinnaka Anil Kumar
Published: November 2012

We report the 4.0-Mb genome sequence of
Bacillus isronensis
strain B3W22 isolated from air collected at an altitude ranging from 27 to 30 km above the city of Hyderabad, in India. This genome sequence will contribute to the objective of determining the microbial diversity of the upper atmosphere.
Genome Sequence of Pedobacter arcticus sp. nov., a Sea Ice Bacterium Isolated from Tundra Soil
Authors: Yin Ye , Yue Guidong , Gao Qiang , Wang Zhiyong , Peng Fang , Fang Chengxiang , Yang Xu , Pan Li
Published: November 2012

Pedobacter arcticus
sp. nov. was originally isolated from tundra soil collected from Ny-Ålesund, in the Arctic region of Norway. It is a Gram-negative bacterium which shows bleb-shaped appendages on the cell surface. Here, we report the draft annotated genome sequence of
Pedobacter arcticus
sp. nov., which belongs to the genus
Pedobacter
.
Draft Genome Sequence of the Methane-Oxidizing Bacterium Methylococcus capsulatus (Texas)
Authors: Kleiveland Charlotte R. , Hult Lene T. Olsen , Kuczkowska Katarzyna , Jacobsen Morten , Lea Tor , Pope Phillip B.
Published: November 2012

Methanotrophic bacteria perform major roles in global carbon cycles via their unique enzymatic activities that enable the oxidation of one-carbon compounds, most notably methane. Here we describe the annotated draft genome sequence of the aerobic methanotroph
Methylococcus capsulatus
(Texas), a type strain originally isolated from sewer sludge.
Whole-Genome Sequence of Livestock-Associated ST398 Methicillin-Resistant Staphylococcus aureus Isolated from Humans in Canada
Authors: Golding George R. , Bryden Louis , Levett Paul N. , McDonald Ryan R. , Wong Alice , Graham Morag R. , Tyler Shaun , Van Domselaar Gary , Mabon Philip , Kent Heather , Butaye Patrick , Smith Tara C. , Kadlec Kristina , Schwarz Stefan , Weese Scott J. , Mulvey Michael R.
Published: November 2012

Despite reports of high colonization rates of ST398 livestock-associated methicillin-resistantStaphylococcus aureus(LA-MRSA) among pigs and pig farmers, the incidence of LA-MRSA infection in the general population in Canada appears to be rare in comparison to that in some European countries. In this study, the complete genome sequence of a Canadian representative LA-MRSA isolate (08BA02176) from a human postoperative surgical site infection was acquired and compared to the sequenced genome of an LA-MRSA isolate (S0385) from Europe to identify genetic traits that may explain differences in the success of these particular strains in some locales.
Draft Genome Sequence of Bacillus pumilus BA06, a Producer of Alkaline Serine Protease with Leather-Dehairing Function
Authors: Zhao Chuan-Wu , Wang Hai-Yan , Zhang Yi-Zheng , Feng Hong
Published: November 2012

Bacillus pumilus
BA06 was isolated from the proteinaceous soil and produced an extracellular alkaline protease with leather-dehairing function. The genome of BA06 was sequenced. The comparative genome analysis indicated that strain BA06 is different in genome from the other
B. pumilus
strains, with limited insertions, deletions, and rearrangements.
Genome Sequence of Leuconostoc pseudomesenteroides Strain 4882, Isolated from a Dairy Starter Culture
Authors: Meslier Victoria , Loux Valentin , Renault Pierre
Published: November 2012

The nonstarter lactic acid bacterium
Leuconostoc pseudomesenteroides
is a species widely found in the dairy industry and plays a key role in the formation of aromatic compounds. Here, we report the first genome sequence of a dairy strain of
Leuconostoc pseudomesenteroides
, which is 2 Mb.
Draft Genome Sequences of Actinomyces timonensis Strain 7400942
T
and Its Prophage
Authors: Gorlas Aurore , Gimenez Grégory , Raoult Didier , Roux Véronique
Published: November 2012

A draft genome sequence of
Actinomyces timonensis
, an anaerobic bacterium isolated from a human clinical osteoarticular sample, is described here. CRISPR-associated proteins, insertion sequence, and toxin-antitoxin loci were found on the genome. A new virus or provirus, AT-1, was characterized.
Draft Genome Sequence of Strain P7-3-5, a New Flavobacteriaceae Bacterium Isolated from Intertidal Sand
Authors: Zhang Xi-Ying , Xie Bin-Bin , Qin Qi-Long , Liu Ang , Chen Xiu-Lan , Zhou Bai-Cheng , Zhang Yu-Zhong
Published: November 2012

The
Flavobacteriaceae
bacterium strain P7-3-5 was isolated from intertidal sand of the Yellow Sea, China. Analysis of the 16S rRNA gene sequences showed that strain P7-3-5 formed a distinct phylogenetic lineage within the family
Flavobacteriaceae.
The genome of strain P7-3-5 was sequenced to facilitate the physiological, ecological, and evolutionary studies of the bacteria within the family
Flavobacteriaceae
.
Draft Genome Sequence of Escherichia coli AI27, a Porcine Isolate Belonging to Phylogenetic Group B1
Authors: Lee Kihyun , Yi Hana , Cho Yong-Joon , Jang Jeonghwan , Hur Hor-Gil , Chun Jongsik
Published: November 2012

Escherichia coli
AI27 is a putatively commensal strain isolated from feces of a pig. Here we report the draft genome sequence of
E. coli
AI27. This is the first porcine strain in the phylogenetic group B1 whose genome sequence has been determined.
Draft Genome Sequence of the Fish Pathogen Vibrio harveyi Strain ZJ0603
Authors: Huang Yucong , Jian Jichang , Lu Yishan , Cai Shuanghu , Wang Bei , Tang Jufen , Pang Huanying , Ding Yu , Wu Zaohe
Published: November 2012

Vibrio harveyi
is an important pathogen that causes vibriosis in various aquatic organisms. Here, we announce the draft genome sequence of
V. harveyi
strain ZJ0603, which was isolated from diseased Orange-spotted grouper (
Epinephelus coioides
) in Guangdong, China.
Draft Genome Sequence of Rahnella aquatilis Strain HX2, a Plant Growth-Promoting Rhizobacterium Isolated from Vineyard Soil in Beijing, China
Authors: Guo Yanbin , Jiao Ziwei , Li Lei , Wu Di , Crowley David E. , Wang Yongjun , Wu Wenliang
Published: November 2012

Rahnella aquatilis
strain HX2 is a plant growth-promoting, disease-suppressive rhizobacterium that was isolated from a vineyard soil in Beijing, China. Here, we report the genome sequence of this strain, which provides a valuable resource for future research examining the mechanisms of traits associated with plant growth promotion and biocontrol.
Genome Sequence of Rhizobium grahamii CCGE502, a Broad-Host-Range Symbiont with Low Nodulation Competitiveness in Phaseolus vulgaris
Authors: Althabegoiti M. Julia , Lozano Luis , Torres-Tejerizo Gonzalo , Ormeño-Orrillo Ernesto , Rogel Marco A. , González Víctor , Martínez-Romero Esperanza
Published: November 2012

Here we present the genome sequence of
Rhizobium grahamii
CCGE502.
R. grahamii
groups with other newly described broad-host-range species, which are not very efficient
Phaseolus vulgaris
symbionts, with a wide geographic distribution and which constitutes a novel
Rhizobium
clade.
Genome Sequence of Exiguobacterium antarcticum B7, Isolated from a Biofilm in Ginger Lake, King George Island, Antarctica
Authors: Carneiro Adriana Ribeiro , Ramos Rommel Thiago Jucá , Dall'Agnol Hivana , Pinto Anne Cybelle , de Castro Soares Siomar , Santos Anderson Rodrigues , Guimarães Luis Carlos , Almeida Sintia Silva , Baraúna Rafael Azevedo , das Graças Diego Assis , Franco Luciano Chaves , Ali Amjad , Hassan Syed Shah , Nunes Catarina Isabel P. , Barbosa Maria Silvanira , Fiaux Karina Kelly , Aburjaile Flávia Figueira , Barbosa Eudes Guilherme Vieira , Bakhtiar Syeda Marriam , Vilela Daniella , Nóbrega Felipe , dos Santos Adriana Lopes , Carepo Marta Sofia P. , Azevedo Vasco , Schneider Maria Paula Cruz , Pellizari Vivian Helena , Silva Artur
Published: November 2012

Exiguobacterium antarcticum
is a psychotropic bacterium isolated for the first time from microbial mats of Lake Fryxell in Antarctica. Many organisms of the genus
Exiguobacterium
are extremophiles and have properties of biotechnological interest, e.g., the capacity to adapt to cold, which make this genus a target for discovering new enzymes, such as lipases and proteases, in addition to improving our understanding of the mechanisms of adaptation and survival at low temperatures. This study presents the genome of
E. antarcticum
B7, isolated from a biofilm sample of Ginger Lake on King George Island, Antarctic peninsula.
Draft Genome Sequence of Paenisporosarcina sp. Strain TG-14, a Psychrophilic Bacterium Isolated from Sediment-Laden Stratified Basal Ice from Taylor Glacier, McMurdo Dry Valleys, Antarctica
Authors: Koh Hye Yeon , Lee Sung Gu , Lee Jun Hyuck , Doyle Shawn , Christner Brent C. , Kim Hak Jun
Published: November 2012

The psychrophilic bacterium
Paenisporosarcina
sp. TG-14 was isolated from sediment-laden stratified basal ice from Taylor Glacier, McMurdo Dry Valleys, Antarctica. Here we report the draft genome sequence of this strain, which may provide useful information on the cold adaptation mechanism in extremely variable environments.
Genome Sequence of Multidrug-Resistant Escherichia coli EC302/04, Isolated from a Human Tracheal Aspirate
Authors: Ho Wing-Sze , Gan Han-Ming , Yap Kien-Pong , Balan Ganeswrie , Yeo Chew Chieng , Thong Kwai-Lin
Published: November 2012

Escherichia coli
is an important etiologic agent of lower respiratory tract infections (LRTI). Multidrug-resistant
E. coli
EC302/04 was isolated from a tracheal aspirate, and its genome sequence is expected to provide insights into antimicrobial resistance as well as adaptive and virulence mechanisms of
E. coli
involved in LRTI.
Complete Genome Sequence of Leuconostoc carnosum Strain JB16, Isolated from Kimchi
Authors: Jung Ji Young , Lee Se Hee , Jeon Che Ok
Published: November 2012

Leuconostoc carnosum
strain JB16 was isolated from kimchi, the traditional Korean fermented food. Here, we report the complete genome sequence of
L. carnosum
strain JB16, consisting of a 1,645,096-bp circular chromosome with a G+C content of 37.24% and four plasmids.
Complete Genome Sequence of Leuconostoc gelidum Strain JB7, Isolated from Kimchi
Authors: Jung Ji Young , Lee Se Hee , Jeon Che Ok
Published: November 2012

A strain of
Leuconostoc gelidum
, designated strain JB7, was isolated from kimchi, the representative Korean traditional fermented food. Here we announce the complete genome sequence of
L. gelidum
strain JB7, consisting of a 1,893,499-bp circular chromosome with a G+C content of 36.68%, and provide a description of its annotation.
Draft Genome Sequence of High-Melanin-Yielding Aeromonas media Strain WS
Authors: Chai Baozhong , Wang He , Chen Xiangdong
Published: November 2012

We sequenced the genome of the high-melanin-yielding
Aeromonas media
strain WS and then analyzed genes potentially involved in melanin formation. The 4.2-Mb draft genome carries multiple genes responsible for pyomelanin synthesis and other candidate genes identified in our separate study, which have no homolog in other strains of
Aeromonas
species.
Complete Genome Sequence of Brucella canis BCB018, a Strain Isolated from a Human Patient
Authors: Wang Yufei , Ke Yuehua , Zhen Qing , Yuan Xitong , Xu Jie , Qiu Yefeng , Wang Zhoujia , Li Tiefeng , Wang Dali , Huang Liuyu , Chen Zeliang
Published: November 2012

Brucella canisis considered a rare cause of human brucellosis because of difficulties in presumptive diagnosis and underestimation of the incidence. Here, we report the draft genome sequence of aBrucella canisisolate, BCB018, isolated from a human patient, providing precious resources for comparative genomics analysis ofBrucellafield strains.
Complete Genome Sequence of Alcanivorax dieselolei Type Strain B5
Authors: Lai Qiliang , Li Weiwei , Shao Zongze
Published: November 2012

Alcanivorax dieselolei
B5
T
was isolated from oil-contaminated surface water of the Bohai Sea of China and characterized by the efficient degradation of alkane (C
5
-C
36
). Here we report the complete genome of B5
T
and genes associated with alkane degradation.
Draft Genome Sequence of the Extremely Halophilic Archaeon Halogranum salarium B-1
T
Authors: Kim Kwang Kyu , Lee Keun Chul , Lee Jung-Sook
Published: November 2012

Halogranum salarium
is an extremely halophilic archaeon isolated from evaporitic salt crystals and belongs to the family
Halobacteriaceae
. Here, we present the 4.5-Mb draft genome sequence of the type strain (B-1
T
) of
H. salarium
. This is the first report of the draft genome sequence of a haloarchaeon in the genus
Halogranum
.
Complete Genome Sequence of the Pyrene-Degrading Bacterium Cycloclasticus sp. Strain P1
Authors: Lai Qiliang , Li Weiwei , Wang Baojiang , Yu Zhiwei , Shao Zongze
Published: November 2012

Cycloclasticus
sp. strain P1 was isolated from deep-sea sediments of the Pacific Ocean and characterized as a unique bacterium in the degradation of pyrene, a four-ring polycyclic aromatic hydrocarbon (PAH). Here we report the complete genome of P1 and genes associated with PAH degradation.
Genome Sequence of Borrelia garinii Strain NMJW1, Isolated from China
Authors: Jiang Baogui , Yao Hongwu , Tong Yigang , Yang Xiaofeng , Huang Yong , Jiang Jiafu , Cao Wuchun
Published: November 2012

We announce the draft genome sequence of
Borrelia garinii
strain NMJW1, isolated from
Ixodes persulcatus
in northeastern China. The 902,789-bp linear chromosome (28.4% GC content) contains 813 open reading frames, 33 tRNAs, and 4 complete rRNAs.
Genome Sequence of Mycobacterium abscessus Strain M152
Authors: Ngeow Yun Fong , Wong Yan Ling , Tan Joon Liang , Ong Chia Sui , Ng Kee Peng , Choo Siew Woh
Published: November 2012

Mycobacterium abscessus
is an environmental bacterium with increasing clinical relevance. Here, we report the annotated whole-genome sequence of
M. abscessus
strain M152.
Genome Sequence of Roseomonas sp. Strain B5, a Quorum-Quenching
N
-Acylhomoserine Lactone-Degrading Bacterium Isolated from Malaysian Tropical Soil
Authors: Chen Jian-Woon , Gan Han Ming , Yin Wai-Fong , Chan Kok-Gan
Published: November 2012

Roseomonas
sp. strain B5 was isolated from Malaysian tropical soil that showed
N
-acylhomoserine lactone degradation. This is the first genome announcement of a member from the genus of
Roseomonas
and the first report on the quorum-quenching activity of
Roseomonas
spp.
Draft Genome Sequence of Oceaniovalibus guishaninsula JLT2003
T
Authors: Tang Kai , Liu Kesao , Jiao Nianzhi
Published: November 2012

Oceaniovalibus
guishaninsula
, as a representative of a new genus within the family
Rhodobacteraceae
, was isolated from surface seawater that was sulfidic. Here, we present the draft genome sequence of the type strain, JLT2003
T
.
Bilateral paraganglioma
Authors: Trivedi Rushikesh Yogesh , Leong Samuel C
Published: November 2012

A 41-year-old man presented with bilateral, painless, non-pulsatile left-sided neck swelling. This was noticed incidentally on a routine medical check-up. He had no significant medical history and did not take any regular medications. Urinary catecholamines and routine blood tests were all normal, and when he had been examined he was normotensive. The MRI scan revealed an enhancing lesion on the left side of the neck as seen in figure 1; it measured 4 cm×3 cm and had a ‘salt and pepper’ appearance causing splaying of the internal and external carotid arteries at the level of the bulb. There was a similar enhancing lesion on the right side, measuring 2.6 cm×2 cm at the level of the carotid bifurcation and 5 cm× 2.6 cm at the jugular bulb, this is seen in figure 1. A diagnosis of bilateral paraganglioma was made.
Mai infection simulating metastatic breast cancer
Authors: Mohamad Bashar , Iqbal Muhammad Nouman , Gopal K V , Arshad Saaima , Daw Hamed A
Published: November 2012

We represent a case of an asymptomatic female who was found to have a mass in the right breast which confirmed an invasive ductal carcinoma by core biopsy. After 3 months of completion of chemo-radiotherapy, the patient remained totally asymptomatic. However, positron emission tomography scan showed four hypermetabolic lesions in the left lung thought to be consistent with metastatic disease. Standard uptake value ranged between 3.86 and 6; the results were consistent with metastatic breast cancer, so wedge resection was performed. Caseating granulomatous inflammation with necrosis was reported. Ultimately culture revealedMycobacterium aviumintracellulare infection. The lesions resolved completely after a course of antibiotics.
A rareCFTRintronic mutation related to a mild CF disease in a 12-year-old girl
Authors: Nathan Nadia , Girodon Emmanuelle , Clement Annick , Corvol Harriet
Published: November 2012

We report the case of a 12-year-old girl with an allergic bronchopulmonary aspergillosis (ABPA), intermediate sweat chloride tests and one cystic fibrosis (CF)-causing mutation, p.Phe508del. After extensive screening of the CF transmembrane regulator (CFTR) gene, she finally was found to carry a rare deep intronic mutation (c.872-1110_1113delGAAT), which confirmed the atypical mild CF disease. Although a classical steroid treatment did not allow the healing of the ABPA, an omalizumab therapy led to a long-term recovery. This case emphasises the need to search for rareCFTRgene mutations as far as possible when a CF disease is evocated. Moreover, it also highlights that although omalizumab is not yet recognised as a classical ABPA treatment in CF, it should be considered as an alternative therapy in steroid-resistant patients.
Interventional treatment for acute ischaemic stroke in an 86-year-old
Authors: Lavan Amanda Hanora , Brennan Paul , Donegan Ciaran F , Williams David J P
Published: November 2012

An 86-year-old lady presented to the accident and emergency department with a 90 min history of receptive and expressive dysphasia. There were no motor symptoms or visual symptoms reported. A partial anterior circulation stroke was diagnosed. On examination, she had a National Institutes of Health Stroke Scale of 6. CT angiography showed an occlusive thrombus within the left internal carotid artery extending into the left M1 segment of the middle cerebral artery and the proximal A1 segment of the anterior cerebral artery. Intra-arterial thrombectomy was preformed. Full recovery was achieved.
Efficacy and cost of micronutrient treatment of childhood psychosis
Authors: Rodway Megan , Vance Annette , Watters Amany , Lee Helen , Bos Elske , Kaplan Bonnie J
Published: November 2012

Psychosis is difficult to treat effectively with conventional pharmaceuticals, many of which have adverse long-term health consequences. In contrast, there are promising reports from several research groups of micronutrient treatment (vitamins, minerals, amino acids and essential fatty acids) of mood, anxiety and psychosis symptoms using a complex formula that appears to be safe and tolerable. We review previous studies using this formula to treat mental symptoms, and present an 11-year-old boy with a 3-year history of mental illness whose parents chose to transition him from medication to micronutrients. Symptom severity was monitored in three clusters: anxiety, obsessive compulsive disorder and psychosis. Complete remission of psychosis occurred, and severity of anxiety and obsessional symptoms decreased significantly (p<0.001); the improvements are sustained at 4-year follow-up. A cost comparison revealed that micronutrient treatment was <1% of his inpatient mental healthcare. Additional research on broad-spectrum micronutrient treatment is warranted.
Hypoglycaemia associated with co-trimoxazole use in a 56-year-old Caucasian woman with renal impairment
Authors: Forde Donall G , Aberdein Jody , Tunbridge Anne , Stone Ben
Published: November 2012

Here we present a case of refractory hypoglycaemia associated with use of the antibiotic trimethoprim-sulfamethoxazole (TMP-SMX). This was used to treatPneumocystis jiroveciipneumonia (PCP) infection. The patient had significant pre-existing renal impairment with a kidney transplant in situ. Refractory hypoglycaemia occurred 5 days after starting the antibiotic and persisted for 36 h after its cessation. SMX contains the same sulphanilamide structural group as the oral hypoglycaemic agents called sulphonureas. SMX could therefore act as an insulin secretagogue. The inappropriately raised insulin and c-peptide levels seen in our patient support this theory. The 5-day asymptomatic period would allow sufficient time for the drug to accumulate and the extended period seen after its cessation would be seen in a dose-dependent side effect. Following 3 days of observation and continuous glycaemic support on the High Dependency Unit she was discharged back to the ward, with no further occurrence of hypoglycaemia.
Neurocardiogenic syncope: a rare presentation of pharyngeal lymphoma
Authors: Li Anthony , Bandali Alykhan , Ghani Saqib , Reid Colin
Published: November 2012

Syncope is a common symptom of patients attending emergency departments, yet presents significant diagnostic and therapeutic challenges. We present a rare cause of recurrent vasovagal syncope with predominant cardioinhibitory response due to lymphoma surrounding and compressing the carotid artery treated successfully with radiotherapy.
Comparison of clinical outcomes between intermittent and continuous monitoring of central venous oxygen saturation (ScvO2) in patients with severe sepsis and septic shock: a pilot study
Authors: Huh Jin Won , Oh Bum Jin , Lim Chae-Man , Hong Sang-Bum , Koh Younsuck
Published: November 2012

Background

The Surviving Sepsis Campaign (SSC) to improve patient outcomes in severe sepsis and septic shock contains recommendations for protocolised resuscitation including early goal-directed therapy (EGDT) resuscitation. In EGDT, central venous oxygen saturation (ScvO2) is measured as the target monitoring value. The objective of this study was to determine whether intermittent measurement of ScvO2is as clinically effective as continuous monitoring in EGDT implementation.

Methods

This prospective, observational, pilot study was performed at an emergency room and general ward in ASAN Medical Centre, a 2680-bed teaching hospital. One hundred and six patients with severe sepsis or septic shock were enrolled and assigned to an intermittent monitoring group (n=53) or continuous monitoring group (n=53).

Results

Within 6 h of the EGDT, interventions by the treating physicians were assessed, including intravenous fluid administration, use of vasopressors and compliance with SSC bundles. After 6 h of the EGDT, 41.5% of all goals (primary outcome) were achieved in the intermittent group and 35.8% in the continuous group (p=0.550). Intensive Care Unit (ICU) mortality, hospital mortality and length of ICU stay did not differ between groups.

Conclusions

During EGDT, intermittent ScvO2monitoring was not inferior to continuous ScvO2monitoring when delivered within the first 6 h of intervention.
Patients’ and ambulance service clinicians’ experiences of prehospital care for acute myocardial infarction and stroke: a qualitative study
Authors: Togher Fiona Jayne , Davy Zowie , Siriwardena Aloysius Niroshan
Published: November 2012

Background

Patients with suspected acute myocardial infarction (AMI) and stroke commonly present first to the ambulance service. Little is known about experiences of prehospital care which are important for measuring the quality of services for patients with AMI or stroke.

Aim

We explored experiences of patients, who had accessed the ambulance service for AMI or stroke, and clinicians regularly treating patients for these conditions in the prehospital setting.

Method

A qualitative research design was employed to obtain rich and detailed data to explore and compare participants’ experiences of emergency prehospital care for AMI and stroke.

Results

We conducted 33 semistructured interviews with service users and clinicians and one focus group with five clinicians. Four main themes emerged: communication, professionalism, treatment of condition and the transition from home to hospital. Patients focused on both personal and technical skills. Technical knowledge and relational skills together contributed to a perception of professionalism in ambulance personnel. Patients’ experience was enhanced when physical, emotional and social needs were attended to and they emphasised effective communication within the clinician–patient relationship to be the key. However, we found a discrepancy between paramedics’ perceptions of patients’ expectations and patients’ lack of knowledge of the paramedic role.

Conclusions

Factors that contribute to better patient experience are not necessarily understood in the same way by patients and clinicians. Our findings can contribute to the development of patient experience measures for prehospital care.
Identifying older people at high risk of future falls: development and validation of a screening tool for use in emergency departments
Authors: Tiedemann Anne , Sherrington Catherine , Orr Teresa , Hallen Jamie , Lewis Donna , Kelly Ann , Vogler Constance , Lord Stephen R , Close Jacqueline C T
Published: November 2012

Background

Hospital emergency departments (EDs) treat a high proportion of older people, many as a direct consequence of falling.

Objective

To develop and externally validate a fall risk screening tool for use in hospital EDs and to compare the tool's predictive ability to existing screening tools.

Methods

This prospective cohort study involved two hospital EDs in Sydney, Australia. Potential participants were people aged 70+ years who presented to the ED after falling or with a history of 2+ falls in the previous year and were subsequently discharged. 219 people participated in the tool development study and 178 people participated in the external validation study. Study measures included number of fallers during the 6-month follow-up period, and physical status, medical history, fall history and community service use.

Results

31% and 35% of participants fell in the development and external validation samples, respectively. The developed two-item screening tool included: 2+ falls in the past year (OR 4.18, 95% CI 2.61 to 6.68) and taking 6+ medications (OR 1.89, CI 1.18 to 3.04). The area under the receiver operating characteristic curve (AUC) was 0.70 (0.64–0.76). This represents significantly better predictive ability than the measure of 2+ previous falls alone (AUC 0.67, 0.62–0.72, p=0.02) and similar predictive ability to the FROP-Com (AUC 0.73, 0.67–0.79, p=0.25) and PROFET screens (AUC 0.70, 0.62–0.78, p=0.5).

Conclusions

A simple, two-item screening tool demonstrated good external validity and accurately discriminated between fallers and non-fallers. This tool could identify high risk individuals who may benefit from onward referral or intervention after ED discharge.
CT coronary angiography: new risks for low-risk chest pain
Authors: Radecki Ryan Patrick
Published: November 2012

Widespread conservative management of low-risk chest pain has motivated the development of a rapid triage strategy based on CT coronary angiography (CTCA) in the Emergency Department (ED). Recently, three prominent trials using this technology in the ED setting have presented results in support of its routine use. However, these studies fail to show the incremental prognostic value of CTCA over clinical and biomarker-based risk-stratification strategies, demonstrate additional downstream costs and interventions, and result in multiple harms associated with radio-contrast and radiation exposure. Observing the widespread overdiagnosis of pulmonary embolism following availability of CT pulmonary angiogram as a practice pattern parallel, CTCA use for low-risk chest pain in the ED should be advanced only with caution.
Effect of paralytic type on time to post-intubation sedative use in the emergency department
Authors: Watt John M , Amini Albert , Traylor Brittany R , Amini Richard , Sakles John C , Patanwala Asad E
Published: November 2012

Objective

To determine the difference between rocuronium and succinylcholine with regard to post-intubation sedative initiation in the emergency department.

Methds

This was a retrospective cohort study conducted in a tertiary care emergency department (ED) in the USA. Consecutive adult patients intubated in the ED using succinylcholine or rocuronium for paralysis were included. Data collected included patient demographics, vital signs, medications used post-intubation and times of drug administration. Patients were divided into two groups based on the type of paralytic used for rapid sequence intubation: (1) rocuronium or (2) succinylcholine. All patients received etomidate for induction of sedation. Time between intubation and post-intubation sedative use was compared between the two groups using an unpaired Student's t test.

Main results

A total of 200 patients were included in the final analyses (100 patients in each group). There were no significant differences between the groups with regard to patient demographics, vital signs or other baseline characteristics. After intubation, 77.5% (n=155) of patients were initiated on a sedative infusion of propofol (n=148) or midazolam (n=7). The remaining patients received sedation as bolus doses only. Mean time between intubation and post-intubation sedative use was significantly greater in the rocuronium group compared with the succinylcholine group (27 min vs 15 min, respectively; p<0.001).

Conclusions

Patients intubated with rocuronium had greater delays in post-intubation sedative initiation compared with succinylcholine.
The influence of vigorous running and cycling exercise on hunger perceptions and plasma acylated ghrelin concentrations in lean young men
Authors: Wasse Lucy K. , Sunderland Caroline , King James A. , Miyashita Masashi , Stensel David J.
Published: November 2012

Vigorous running suppresses plasma acylated ghrelin concentrations but the limited literature on cycling suggests that acylated ghrelin is unchanged, perhaps because body mass is supported during cycling. It is important from a research and applied perspective to determine whether acylated ghrelin and hunger responses are exercise-mode specific. This study sought to examine this. Eleven recreationally active males fasted overnight and completed three 4-h trials: control, running, and cycling, in a random order. Participants rested throughout the control trial and ran or cycled at 70% of mode-specific maximal oxygen uptake for the first hour during exercise trials, resting thereafter. Hunger was measured every 0.5 h using visual analogue scales. Eight venous blood samples were collected to determine acylated ghrelin concentrations and a standardised meal was consumed at 3 h. Compared with the control trial, acylated ghrelin concentrations were suppressed to a similar extent at 0.5 and 1 h during the running (p < 0.005) and cycling (p < 0.001) trials. Area under the curve values for ghrelin concentration over time were lower during exercise trials versus control (Control: 606 ± 379; Running: 455 ± 356; Cycling: 448 ± 315 pg·mL−1·4 h−1; mean ± SD, p < 0.05). Hunger values did not differ significantly between trials but an interaction effect (p < 0.05) indicated a tendency for hunger to be suppressed during exercise. Thus, at similar relative exercise intensities, plasma acylated ghrelin concentrations are suppressed to a similar extent during running and cycling.
Physiological aspects of the subcellular localization of glycogen in skeletal muscle
Authors: Nielsen Joachim , Ørtenblad Niels
Published: November 2012

Glucose is stored in skeletal muscle fibers as glycogen, a branched-chain polymer observed in electron microscopy images as roughly spherical particles (known as β-particles of 10–45 nm in diameter), which are distributed in distinct localizations within the myofibers and are physically associated with metabolic and scaffolding proteins. Although the subcellular localization of glycogen has been recognized for more than 40 years, the physiological role of the distinct localizations has received sparse attention. Recently, however, studies involving stereological, unbiased, quantitative methods have investigated the role and regulation of these distinct deposits of glycogen. In this report, we review the available literature regarding the subcellular localization of glycogen in skeletal muscle as investigated by electron microscopy studies and put this into perspective in terms of the architectural, topological, and dynamic organization of skeletal muscle fibers. In summary, the distribution of glycogen within skeletal muscle fibers has been shown to depend on the fiber phenotype, individual training status, short-term immobilization, and exercise and to influence both muscle contractility and fatigability. Based on all these data, the available literature strongly indicates that the subcellular localization of glycogen has to be taken into consideration to fully understand and appreciate the role and regulation of glycogen metabolism and signaling in skeletal muscle. A full understanding of these phenomena may prove vital in elucidating the mechanisms that integrate basic cellular events with changing glycogen content.
Effects of juices enriched with xanthan and β-glucan on the glycemic response and satiety of healthy men
Authors: Paquin Julie , Bédard Alexandra , Lemieux Simone , Tajchakavit Sasithorn , Turgeon Sylvie L.
Published: November 2012

This study compared the effects of 3 palatable juices enriched with different polysaccharides with a control nonenriched juice on glucose and insulin responses as well as on appetite sensations and determined whether the polysaccharide-induced viscosity contributed to the effects of enriched juices on these variables. Using a randomized crossover design, 14 healthy male subjects consumed 4 juices: 3 juices were enriched with either xanthan gum, β-glucan, or a mix of xanthan gum and β-glucan, and the control juice had no added polysaccharides. Viscosity was measured at a shear rate of 30 s−1, which represented an approximation of the viscosity in the gastrointestinal tract. One-sided tests were used in this study. Compared with the control juice, the juice supplemented with the mix of xanthan gum and β-glucan and the juice enriched with β-glucan alone led to a significant attenuation of the incremental peak of glucose (–0.8 mmol·L−1, p = 0.001; and –0.5 mmol·L−1, p = 0.03; respectively). However, no difference between juices was found for the incremental area under the curve for glucose, insulin, and appetite sensations. At 30 s−1, only juices enriched with either the β-glucan/xanthan mixture or β-glucan alone yielded viscosity values higher than 0.1 Pa·s. These results highlight that the consumption of a palatable juice enriched with β-glucan alone or in mixture with xanthan gum reduces the glucose peak response compared with a juice with no added polysaccharides. The viscosity at a shear rate of 30 s−1 seems to be linked to this effect.