bluuebunny/crossref_metadata_2025_split huggingface dataset:
Significant Alteration of Gene Expression in Wood Decay Fungi Postia placenta and Phanerochaete chrysosporium by Plant Species
Authors: Vanden Wymelenberg Amber , Gaskell Jill , Mozuch Michael , Splinter BonDurant Sandra , Sabat Grzegorz , Ralph John , Skyba Oleksandr , Mansfield Shawn D. , Blanchette Robert A. , Grigoriev Igor V. , Kersten Philip J. , Cullen Dan 
Published: May 2011

ABSTRACT

Identification of specific genes and enzymes involved in conversion of lignocellulosics from an expanding number of potential feedstocks is of growing interest to bioenergy process development. The basidiomycetous wood decay fungi
Phanerochaete chrysosporium
and
Postia placenta
are promising in this regard because they are able to utilize a wide range of simple and complex carbon compounds. However, systematic comparative studies with different woody substrates have not been reported. To address this issue, we examined gene expression of these fungi colonizing aspen (
Populus grandidentata
) and pine (
Pinus strobus
). Transcript levels of genes encoding extracellular glycoside hydrolases, thought to be important for hydrolytic cleavage of hemicelluloses and cellulose, showed little difference for
P. placenta
colonizing pine versus aspen as the sole carbon source. However, 164 genes exhibited significant differences in transcript accumulation for these substrates. Among these, 15 cytochrome P450s were upregulated in pine relative to aspen. Of 72
P. placenta
extracellular proteins identified unambiguously by mass spectrometry, 52 were detected while colonizing both substrates and 10 were identified in pine but not aspen cultures. Most of the 178
P. chrysosporium
glycoside hydrolase genes showed similar transcript levels on both substrates, but 13 accumulated >2-fold higher levels on aspen than on pine. Of 118 confidently identified proteins, 31 were identified in both substrates and 57 were identified in pine but not aspen cultures. Thus,
P. placenta
and
P. chrysosporium
gene expression patterns are influenced substantially by wood species. Such adaptations to the carbon source may also reflect fundamental differences in the mechanisms by which these fungi attack plant cell walls.
Validation of Heavy-Water Stable Isotope Probing for the Characterization of Rapidly Responding Soil Bacteria
Authors: Aanderud Zachary T. , Lennon Jay T. 
Published: May 2011

ABSTRACT

Rapid responses of bacteria to sudden changes in their environment can have important implications for the structure and function of microbial communities. In this study, we used heavy-water stable isotope probing (H
2
18
O-SIP) to identify bacteria that respond to soil rewetting. First, we conducted experiments to address uncertainties regarding the H
2
18
O-SIP method. Using liquid chromatography-mass spectroscopy (LC-MS), we determined that oxygen from H
2
18
O was incorporated into all structural components of DNA. Although this incorporation was uneven, we could effectively separate
18
O-labeled and unlabeled DNAs derived from laboratory cultures and environmental samples that were incubated with H
2
18
O. We found no evidence for
ex vivo
exchange of oxygen atoms between DNA and extracellular H
2
O, suggesting that
18
O incorporation into DNA is relatively stable. Furthermore, the rate of
18
O incorporation into bacterial DNA was high (within 48 to 72 h), coinciding with pulses of CO
2
generated from soil rewetting. Second, we examined shifts in the bacterial composition of grassland soils following rewetting, using H
2
18
O-SIP and bar-coded pyrosequencing of 16S rRNA genes. For some groups of soil bacteria, we observed coherent responses at a relatively course taxonomic resolution. Following rewetting, the relative recovery of
Alphaproteobacteria
,
Betaproteobacteria
, and
Gammaproteobacteria
increased, while the relative recovery of
Chloroflexi
and
Deltaproteobacteria
decreased. Together, our results suggest that H
2
18
O-SIP is effective at identifying metabolically active bacteria that influence soil carbon dynamics. Our results contribute to the ecological classification of soil bacteria while providing insight into some of the functional traits that influence the structure and function of microbial communities under dynamic soil moisture regimes.
Effect of Chemical Chaperones in Improving the Solubility of Recombinant Proteins in Escherichia coli
Authors: Prasad Shivcharan , Khadatare Prashant B. , Roy Ipsita 
Published: May 2011

ABSTRACTThe recovery of active proteins from inclusion bodies usually involves chaotrope-induced denaturation, followed by refolding of the unfolded protein. The efficiency of renaturation is low, leading to reduced yield of the final product. In this work, we report that recombinant proteins can be overexpressed in the soluble form in the host expression system by incorporating compatible solutes during protein expression. Green fluorescent protein (GFP), which was otherwise expressed as inclusion bodies, could be made to partition off into the soluble fraction when sorbitol and arginine, but not ethylene glycol, were present in the growth medium. Arginine and sorbitol increased the production of soluble protein, while ethylene glycol did not. Production of ATP increased in the presence of sorbitol and arginine, but not ethylene glycol. A control experiment with fructose addition indicated that protein solubilization was not due to a simple ATP increase. We have successfully reproduced these results with the N-terminal domain of HypF (HypF-N), a bacterial protein which forms inclusion bodies inEscherichia coli. Instead of forming inclusion bodies, HypF-N could be expressed as a soluble protein in the presence of sorbitol, arginine, and trehalose in the expression medium.
Pantethine Rescues Phosphopantothenoylcysteine Synthetase and Phosphopantothenoylcysteine Decarboxylase Deficiency in Escherichia coli but Not in Pseudomonas aeruginosa
Authors: Balibar Carl J. , Hollis-Symynkywicz Micah F. , Tao Jianshi 
Published: May 2011

ABSTRACT

Coenzyme A (CoA) plays a central and essential role in all living organisms. The pathway leading to CoA biosynthesis has been considered an attractive target for developing new antimicrobial agents with novel mechanisms of action. By using an arabinose-regulated expression system, the essentiality of
coaBC
, a single gene encoding a bifunctional protein catalyzing two consecutive steps in the CoA pathway converting 4′-phosphopantothenate to 4′-phosphopantetheine, was confirmed in
Escherichia coli
. Utilizing this regulated
coaBC
strain, it was further demonstrated that
E. coli
can effectively metabolize pantethine to bypass the requirement for
coaBC
. Interestingly, pantethine cannot be used by
Pseudomonas aeruginosa
to obviate
coaBC
. Through reciprocal complementation studies in combination with biochemical characterization, it was demonstrated that the differential characteristics of pantethine utilization in these two microorganisms are due to the different substrate specificities associated with endogenous pantothenate kinase, the first enzyme in the CoA biosynthetic pathway encoded by
coaA
in
E. coli
and
coaX
in
P. aeruginosa
.
Complete Genome Sequence of Aeromonas veronii Strain B565
Authors: Li Yanxia , Liu Yuchun , Zhou Zhemin , Huang Huoqing , Ren Yan , Zhang Yuting , Li Guannan , Zhou Zhigang , Wang Lei 
Published: May 2011

ABSTRACT

Aeromonas veronii
strain B565 was isolated from aquaculture pond sediment in China. We present here the complete genome sequence of B565 and compare it with 2 published genome sequences of pathogenic strains in the
Aeromonas
genus. The result represents an independent stepwise acquisition of virulence factors of pathogenic strains in this genus.
Identity Gene Expression in Proteus mirabilis
Authors: Gibbs Karine A. , Wenren Larissa M. , Greenberg E. Peter 
Published: May 2011

ABSTRACT

Swarming colonies of independent
Proteus mirabilis
isolates recognize each other as foreign and do not merge together, whereas apposing swarms of clonal isolates merge with each other. Swarms of mutants with deletions in the
ids
gene cluster do not merge with their parent. Thus,
ids
genes are involved in the ability of
P. mirabilis
to distinguish self from nonself. Here we have characterized expression of the
ids
genes. We show that
idsABCDEF
genes are transcribed as an operon, and we define the promoter region upstream of
idsA
by deletion analysis. Expression of the
ids
operon increased in late logarithmic and early stationary phases and appeared to be bistable. Approaching swarms of nonself populations led to increased
ids
expression and increased the abundance of
ids
-expressing cells in the bimodal population. This information on
ids
gene expression provides a foundation for further understanding the molecular details of self-nonself discrimination in
P. mirabilis
.
Genetic Transformation of the Relapsing Fever Spirochete Borrelia hermsii: Stable Integration and Expression of Green Fluorescent Protein from Linear Plasmid 200
Authors: Fine Lindy M. , Earnhart Christopher G. , Marconi Richard T. 
Published: May 2011

ABSTRACT

Tick-borne relapsing fever (TBRF) is a spirochetal disease caused by at least 15 different
Borrelia
species. It is a serious human health concern in regions of endemicity throughout the world. Transmission to humans occurs through the bites of infected
Ornithodoros
ticks. In North America, the primary
Borrelia
species associated with human disease are
B. hermsii
and
B. turicatae
. Direct demonstration of the role of putative TBRF spirochete virulence factors in the disease process has been hindered by the lack of a genetic manipulation system and complete genome sequences. Expanding on recent developments in these areas, here we demonstrate the successful generation of a clone of
B. hermsii
YOR that constitutively produces green fluorescent protein (GFP) (
B. hermsii
YOR::
kan gfp
). This strain was generated through introduction of a
kan-gfp
cassette into a noncoding region of the 200-kb
B. hermsii
linear plasmid lp200. Genetic manipulation did not affect the growth rate or trigger the loss of native plasmids.
B. hermsii
YOR::
kan gfp
retained infectivity and elicited host seroconversion. Stable production of GFP was demonstrated both
in vitro
and
in vivo
. This study represents a significant step forward in the development of tools that can be employed to study the virulence mechanisms of TBRF spirochetes.
Complete Genome Sequence of Metallosphaera cuprina, a Metal Sulfide-Oxidizing Archaeon from a Hot Spring
Authors: Liu Li-Jun , You Xiao-Yan , Zheng Huajun , Wang Shengyue , Jiang Cheng-Ying , Liu Shuang-Jiang 
Published: May 2011

ABSTRACT

The genome of the metal sulfide-oxidizing, thermoacidophilic strain
Metallosphaera cuprina
Ar-4 has been completely sequenced and annotated. Originally isolated from a sulfuric hot spring, strain Ar-4 grows optimally at 65°C and a pH of 3.5. The
M. cuprina
genome has a 1,840,348-bp circular chromosome (2,029 open reading frames [ORFs]) and is 16% smaller than the previously sequenced
Metallosphaera sedula
genome. Compared to the
M. sedula
genome, there are no counterpart genes in the
M. cuprina
genome for about 480 ORFs in the
M. sedula
genome, of which 243 ORFs are annotated as hypothetical protein genes. Still, there are 233 ORFs uniquely occurring in
M. cuprina
. Genome annotation supports that
M. cuprina
lives a facultative life on CO
2
and organics and obtains energy from oxidation of sulfidic ores and reduced inorganic sulfuric compounds.
Genome Sequence of the Clinical O4:K12 Serotype Vibrio parahaemolyticus Strain 10329
Authors: Gonzalez-Escalona N. , Strain E. A. , De Jesús A. J. , Jones J. L. , DePaola A. 
Published: May 2011

ABSTRACT

Vibrio parahaemolyticus
is the leading cause of food-borne illnesses worldwide. Here, we report a draft genome of
V. parahaemolyticus
strain 10329 of the O4:K12 serotype. It belongs to the main U.S. West Coast clonal complex of
V. parahaemolyticus
(sequence type 36 [ST36]) causing oyster-associated human illness. It contains the virulence determinants
tdh
and
trh
but appears to infect at much lower doses than
V. parahaemolyticus
strains with these same determinants from other areas, such as the U.S. Gulf and Atlantic coasts.
Genome Sequences of Listeria monocytogenes Strains J1816 and J1-220, Associated with Human Outbreaks
Authors: Chen Y. , Strain E. A. , Allard M. , Brown E. W. 
Published: May 2011

ABSTRACT

Listeria monocytogenes
has caused numerous human outbreaks. Here we report draft genomes of
L. monocytogenes
J1816 and J1-220, which belong to epidemic clones II and IV, respectively. Whole-genome sequence analysis of these strains provides a tool for studying the short-term evolution of these epidemic clones.
Draft Genome Sequence of the Marine Bacterium Streptomyces griseoaurantiacus M045, Which Produces Novel Manumycin-Type Antibiotics with a pABA Core Component
Authors: Li Fuchao , Jiang Peng , Zheng Huajun , Wang Shengyue , Zhao Guoping , Qin Song , Liu Zhaopu 
Published: May 2011

ABSTRACT

Streptomyces griseoaurantiacus
M045, isolated from marine sediment, produces manumycin and chinikomycin antibiotics. Here we present a high-quality draft genome sequence of
S. griseoaurantiacus
M045, the first marine
Streptomyces
species to be sequenced and annotated. The genome encodes several gene clusters for biosynthesis of secondary metabolites and has provided insight into genomic islands linking secondary metabolism to functional adaptation in marine
S. griseoaurantiacus
M045.
Complete Genome Sequence of the Plant Growth-Promoting Endophyte Burkholderia phytofirmans Strain PsJN
Authors: Weilharter Alexandra , Mitter Birgit , Shin Maria V. , Chain Patrick S. G. , Nowak Jerzy , Sessitsch Angela 
Published: May 2011

ABSTRACT

Burkholderia phytofirmans
PsJN
T
is able to efficiently colonize the rhizosphere, root, and above-ground plant tissues of a wide variety of genetically unrelated plants, such as potatoes, canola, maize, and grapevines. Strain PsJN shows strong plant growth-promoting effects and was reported to enhance plant vigor and resistance to biotic and abiotic stresses. Here, we report the genome sequence of this strain, which indicates the presence of multiple traits relevant for endophytic colonization and plant growth promotion.
Complete Genome Sequence of Bacillus amyloliquefaciens LL3, Which Exhibits Glutamic Acid-Independent Production of Poly-γ-Glutamic Acid
Authors: Geng Weitao , Cao Mingfeng , Song Cunjiang , Xie Hui , Liu Li , Yang Chao , Feng Jun , Zhang Wei , Jin Yinghong , Du Yang , Wang Shufang 
Published: May 2011

ABSTRACT

Bacillus amyloliquefaciens
is one of most prevalent Gram-positive aerobic spore-forming bacteria with the ability to synthesize polysaccharides and polypeptides. Here, we report the complete genome sequence of
B. amyloliquefaciens
LL3, which was isolated from fermented food and presents the glutamic acid-independent production of poly-γ-glutamic acid.
Genome Sequence of Strain TW15, a Novel Member of the Genus Ruegeria, Belonging to the Marine Roseobacter Clade
Authors: Lee Jina , Roh Seong Woon , Whon Tae Woong , Shin Na-Ri , Kim Young-Ok , Bae Jin-Woo 
Published: May 2011

ABSTRACT

Ruegeria
sp. TW15, which belongs to the family
Rhodobacteraceae
, was isolated from an ark clam in the South Sea of Korea. Here is presented the draft genome sequence of
Ruegeria
sp. TW15 (4,490,771 bp with a G+C content of 55.7%), a member of the marine
Roseobacter
clade, which comprises up to 20% of the bacterioplankton in the coastal and oceanic mixed layer.
Complete Genome of Pseudomonas mendocina NK-01, Which Synthesizes Medium-Chain-Length Polyhydroxyalkanoates and Alginate Oligosaccharides
Authors: Guo Wenbin , Wang Yuanyuan , Song Cunjiang , Yang Chao , Li Qiang , Li Baobin , Su Wenping , Sun Xiumei , Song Dongfang , Yang Xiaojuan , Wang Shufang 
Published: May 2011

ABSTRACT

Pseudomonas mendocina
NK-01 can synthesize medium-chain-length polyhydroxyalkanoate (PHA
MCL
) and alginate oligosaccharides (AO) simultaneously from glucose under conditions of limited nitrogen. Here, we report the complete sequence of the 5.4-Mbp genome of
Pseudomonas mendocina
NK-01, which was isolated from farmland soil in Tianjin, China.
Streptococcus pneumoniae Serotype 6C: an Intra- and Interclonal Complex Comparison
Authors: Thomas J. C. , Kong Y. , Sabharwal V. , Pelton S. I. , Pettigrew M. M. 
Published: May 2011

ABSTRACT

We report the annotated draft genome sequences of four serotype 6C
Streptococcus pneumoniae
isolates of differing genetic backgrounds. Serotype 6C isolates are increasing in prevalence and becoming progressively more resistant to antibiotics. As a result, these strains are likely to become more important in the near future.
Genome Sequence of Vibrio rotiferianus Strain DAT722
Authors: Chowdhury Piklu Roy , Boucher Yan , Hassan Karl A. , Paulsen Ian T. , Stokes H. W. , Labbate Maurizio 
Published: May 2011

ABSTRACT

Vibrio rotiferianus
is a marine pathogen capable of causing disease in various aquatic organisms. We announce the genome sequence of
V. rotiferianus
DAT722, which has a large chromosomal integron containing 116 gene cassettes and is a model organism for studying the role of this system in vibrio evolution.
Genome Sequence of the Ethene- and Vinyl Chloride-Oxidizing Actinomycete Nocardioides sp. Strain JS614
Authors: Coleman Nicholas V. , Wilson Neil L. , Barry Kerrie , Brettin Thomas S. , Bruce David C. , Copeland Alex , Dalin Eileen , Detter John C. , del Rio Tijana Glavina , Goodwin Lynne A. , Hammon Nancy M. , Han Shunsheng , Hauser Loren J. , Israni Sanjay , Kim Edwin , Kyrpides Nikolaos , Land Miriam L. , Lapidus Alla , Larimer Frank W. , Lucas Susan , Pitluck Sam , Richardson Paul , Schmutz Jeremy , Tapia Roxanne , Thompson Sue , Tice Hope N. , Spain Jim C. , Gossett James G. , Mattes Timothy E. 
Published: May 2011

ABSTRACT

Nocardioides
sp. strain JS614 grows on ethene and vinyl chloride (VC) as sole carbon and energy sources and is of interest for bioremediation and biocatalysis. Sequencing of the complete genome of JS614 provides insight into the genetic basis of alkene oxidation, supports ongoing research into the physiology and biochemistry of growth on ethene and VC, and provides biomarkers to facilitate detection of VC/ethene oxidizers in the environment. This is the first genome sequence from the genus
Nocardioides
and the first genome of a VC/ethene-oxidizing bacterium.
Genome Sequence of Strain IMCC3088, a Proteorhodopsin-Containing Marine Bacterium Belonging to the OM60/NOR5 Clade
Authors: Jang Yoonra , Oh Hyun-Myung , Kang Ilnam , Lee Kiyoung , Yang Seung-Jo , Cho Jang-Cheon 
Published: May 2011

ABSTRACT

Strain IMCC3088, cultivated from the Yellow Sea, is a novel isolate belonging to the OM60/NOR5 clade and is closely related to clone OM241,
Congregibacter litoralis
, and strain HTCC2080. Here, the genome sequence of strain IMCC3088 is presented, showing the absence of photosynthetic gene clusters and the presence of proteorhodopsin.
Complete Genome Sequence of Carnobacterium sp. 17-4
Authors: Voget Sonja , Klippel Barbara , Daniel Rolf , Antranikian Garabed 
Published: May 2011

ABSTRACT

Members of the carnobacteria have been extensively studied as probiotic cultures in aquacultures and protective cultures in seafood, diary, and meat. We report on the finished genome sequence of
Carnobacterium
sp. 17-4, which has been isolated from permanently cold seawater. The genetic information reveals a new circular bacteriocin biosynthesis cluster.
Complete Genome Sequence of Staphylococcus aureus T0131, an ST239-MRSA-SCC
mec
Type III Clone Isolated in China
Authors: Li Yang , Cao Boyang , Zhang Yongfu , Zhou Jiali , Yang Bin , Wang Lei 
Published: May 2011

ABSTRACT

We report here the complete genome sequence of
Staphylococcus aureus
T0131, which is a multiresistant clinical isolate recovered in China and the first sequenced epidemic ST239-MRSA-SCC
mec
type III strain obtained in Asia. Comparison with two published genomes of ST239 reveals the polymorphism among strains of this type from different continents.
Draft Genome of Phaeobacter gallaeciensis ANG1, a Dominant Member of the Accessory Nidamental Gland of Euprymna scolopes
Authors: Collins Andrew J. , Nyholm Spencer V. 
Published: May 2011

ABSTRACT

Phaeobacter gallaeciensis
strain ANG1 represents the dominant member of the bacterial consortium within the reproductive accessory nidamental gland (ANG) of the squid
Euprymna scolopes
. We present a 4.59-Mb assembly of its genome, which may provide clues as to how it benefits its host.
Genome Sequence of Gluconacetobacter sp. Strain SXCC-1, Isolated from Chinese Vinegar Fermentation Starter
Authors: Du Xin-jun , Jia Shi-ru , Yang Yue , Wang Shuo 
Published: May 2011

ABSTRACT

Gluconacetobacter
strains are prominent bacteria during traditional vinegar fermentation. Here, we report a draft genome sequence of
Gluconacetobacter
sp. strain SXCC-1. This strain was isolated from a fermentation starter (Daqu) used for commercial production of Shanxi vinegar, the best-known vinegar of China.
Perinatal or Adult Nf1 Inactivation Using Tamoxifen-Inducible PlpCre Each Cause Neurofibroma Formation
Authors: Mayes Debra A. , Rizvi Tilat A. , Cancelas Jose A. , Kolasinski Nathan T. , Ciraolo Georgianne M. , Stemmer-Rachamimov Anat O. , Ratner Nancy 
Published: May 2011

Abstract
Plexiform neurofibromas are peripheral nerve sheath tumors initiated by biallelic mutation of the NF1 tumor suppressor gene in the Schwann cell lineage. To understand whether neurofibroma formation is possible after birth, we induced Nf1 loss of function with an inducible proteolipid protein Cre allele. Perinatal loss of Nf1 resulted in the development of small plexiform neurofibromas late in life, whereas loss in adulthood caused large plexiform neurofibromas and morbidity beginning 4 months after onset of Nf1 loss. A conditional EGFP reporter allele identified cells showing recombination, including peripheral ganglia satellite cells, peripheral nerve S100β+ myelinating Schwann cells, and peripheral nerve p75+ cells. Neurofibromas contained cells with Remak bundle disruption but no recombination within GFAP+ nonmyelinating Schwann cells. Extramedullary lympho-hematopoietic expansion was also observed in PlpCre;Nf1fl/fl mice. These tumors contained EGFP+/Sca-1+ stromal cells among EGFP-negative lympho-hematopoietic cells indicating a noncell autonomous effect and unveiling a role of Nf1-deleted microenvironment on lympho-hematopoietic proliferation in vivo. Together these findings define a tumor suppressor role for Nf1 in the adult and narrow the range of potential neurofibroma-initiating cell populations. Cancer Res; 71(13); 4675–85. ©2011 AACR.