bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractThe 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.
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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACTDespite 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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACTBrucella 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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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
.