bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Characterization of an NADPH-Dependent Acetoin Reductase/2,3-Butanediol Dehydrogenase from
Clostridium beijerinckii
NCIMB 8052
Authors: Raedts John , Siemerink Marco A. J. , Levisson Mark , van der Oost John , Kengen Servé W. M. 
Published: January 2014

ABSTRACT

Acetoin reductase is an important enzyme for the fermentative production of 2,3-butanediol, a chemical compound with a very broad industrial use. Here, we report on the discovery and characterization of an acetoin reductase from
Clostridium beijerinckii
NCIMB 8052. An
in silico
screen of the
C. beijerinckii
genome revealed eight potential acetoin reductases. One of them (
CBEI_1464
) showed substantial acetoin reductase activity after expression in
Escherichia coli
. The purified enzyme (
C. beijerinckii
acetoin reductase [Cb-ACR]) was found to exist predominantly as a homodimer. In addition to acetoin (or 2,3-butanediol), other secondary alcohols and corresponding ketones were converted as well, provided that another electronegative group was attached to the adjacent C-3 carbon. Optimal activity was at pH 6.5 (reduction) and 9.5 (oxidation) and around 68°C. Cb-ACR accepts both NADH and NADPH as electron donors; however, unlike closely related enzymes, NADPH is preferred (

K
m

, 32 μM). Cb-ACR was compared to characterized close homologs, all belonging to the “threonine dehydrogenase and related Zn-dependent dehydrogenases” (COG1063). Metal analysis confirmed the presence of 2 Zn
2+
atoms. To gain insight into the substrate and cofactor specificity, a structural model was constructed. The catalytic zinc atom is likely coordinated by Cys
37
, His
70
, and Glu
71
, while the structural zinc site is probably composed of Cys
100
, Cys
103
, Cys
106
, and Cys
114
. Residues determining NADP specificity were predicted as well. The physiological role of Cb-ACR in
C. beijerinckii
is discussed.
Duplex PCR Methods for the Molecular Detection of
Escherichia fergusonii
Isolates from Broiler Chickens
Authors: Simmons Karen , Rempel Heidi , Block Glenn , Forgetta Vincenzo , Vaillancourt Rolland , Malouin François , Topp Edward , Delaquis Pascal , Diarra Moussa S. 
Published: January 2014

ABSTRACT

Escherichia fergusonii
is an emerging pathogen that has been isolated from a wide range of infections in animals and humans. Primers targeting specific genes, including
yliE
(encoding a conserved hypothetical protein of the cellulose synthase and regulator of cellulose synthase island),
EFER
_
1569
(encoding a hypothetical protein, putative transcriptional activator for multiple antibiotic resistance), and
EFER
_
3126
(encoding a putative triphosphoribosyl-dephospho-coenzyme A [CoA]), were designed for the detection of
E. fergusonii
by conventional and real-time PCR methods. Primers were screened by
in silico
PCR against 489 bacterial genomic sequences and by both PCR methods on 55 reference and field strains. Both methods were specific and sensitive for
E. fergusonii
, showing amplification only for this bacterium. Conventional PCR required a minimum bacterial concentration of approximately 10
2
CFU/ml, while real-time PCR required a minimum of 0.3 pg of DNA for consistent detection. Standard curves showed an efficiency of 98.5%, with an
R
2
value of 0.99 for the real-time PCR assay. Cecal and cloacal contents from 580 chickens were sampled from broiler farms located in the Fraser Valley (British Columbia, Canada). Presumptive
E. fergusonii
isolates were recovered by enrichment and plating on differential and selective media. Of 301 total presumptive isolates, 140 (46.5%) were identified as
E. fergusonii
by biochemical profiling with the API 20E system and 268 (89.0%) using PCR methods.
E. fergusonii
detection directly from cecal and cloacal samples without preenrichment was achieved with both PCR methods. Hence, the PCR methods developed in this work significantly improve the detection of
E. fergusonii
.
pH Signaling in Human Fungal Pathogens: a New Target for Antifungal Strategies
Authors: Cornet Muriel , Gaillardin Claude 
Published: January 2014

ABSTRACT

Fungi are exposed to broadly fluctuating environmental conditions, to which adaptation is crucial for their survival. An ability to respond to a wide pH range, in particular, allows them to cope with rapid changes in their extracellular settings. PacC/Rim signaling elicits the primary pH response in both model and pathogenic fungi and has been studied in multiple fungal species. In the predominant human pathogenic fungi, namely,
Candida albicans
,
Aspergillus fumigatus
, and
Cryptococcus neoformans
, this pathway is required for many functions associated with pathogenesis and virulence. Aspects of this pathway are fungus specific and do not exist in mammalian cells. In this review, we highlight recent advances in our understanding of PacC/Rim-mediated functions and discuss the growing interest in this cascade and its factors as potential drug targets for antifungal strategies. We focus on both conserved and distinctive features in model and pathogenic fungi, highlighting the specificities of PacC/Rim signaling in
C. albicans
,
A. fumigatus
, and
C. neoformans
. We consider the role of this pathway in fungal virulence, including modulation of the host immune response. Finally, as now recognized for other signaling cascades, we highlight the role of pH in adaptation to antifungal drug pressure. By acting on the PacC/Rim pathway, it may therefore be possible (i) to ensure fungal specificity and to limit the side effects of drugs, (ii) to ensure broad-spectrum efficacy, (iii) to attenuate fungal virulence, (iv) to obtain additive or synergistic effects with existing antifungal drugs through tolerance inhibition, and (v) to slow the emergence of resistant mutants.
A Genomewide Overexpression Screen Identifies Genes Involved in the Phosphatidylinositol 3-Kinase Pathway in the Human Protozoan Parasite Entamoeba histolytica
Authors: Koushik Amrita B. , Welter Brenda H. , Rock Michelle L. , Temesvari Lesly A. 
Published: January 2014

ABSTRACT

Entamoeba histolytica
is a protozoan parasite that causes amoebic dysentery and liver abscess.
E. histolytica
relies on motility, phagocytosis, host cell adhesion, and proteolysis of extracellular matrix for virulence. In eukaryotic cells, these processes are mediated in part by phosphatidylinositol 3-kinase (PI3K) signaling. Thus, PI3K may be critical for virulence. We utilized a functional genomics approach to identify genes whose products may operate in the PI3K pathway in
E. histolytica
. We treated a population of trophozoites that were overexpressing genes from a cDNA library with a near-lethal dose of the PI3K inhibitor wortmannin. This screen was based on the rationale that survivors would be overexpressing gene products that directly or indirectly function in the PI3K pathway. We sequenced the overexpressed genes in survivors and identified a cDNA encoding a Rap GTPase, a protein previously shown to participate in the PI3K pathway. This supports the validity of our approach. Genes encoding a coactosin-like protein, EhCoactosin, and a serine-rich
E. histolytica
protein (SREHP) were also identified. Cells overexpressing EhCoactosin or SREHP were also less sensitive to a second PI3K inhibitor, LY294002. This corroborates the link between these proteins and PI3K. Finally, a mutant cell line with an increased level of phosphatidylinositol (3,4,5)-triphosphate, the product of PI3K activity, exhibited increased expression of SREHP and EhCoactosin. This further supports the functional connection between these proteins and PI3K in
E. histolytica
. To our knowledge, this is the first forward-genetics screen adapted to reveal genes participating in a signal transduction pathway in this pathogen.
Population of Endogenous Pararetrovirus Genomes in Carrizo Citrange
Authors: Roy Avijit , Shao Jonathan , Schneider William L. , Hartung John S. , Brlansky Ronald H. 
Published: January 2014

ABSTRACT
The complete genome sequences of three related endogenous pararetroviruses (EPRVs) were obtained by 454 sequencing of nucleic acid extracts from Carrizo citrange, used as a citrus rootstock. Numerous homologous sequences have been found in the sweet orange genome. The new EPRVs are most closely related to petunia vein-clearing virus.
Whole-Genome Sequences of Streptococcus thermophilus Strains TH1435 and TH1436, Isolated from Raw Goat Milk
Authors: Treu Laura , Vendramin Veronica , Bovo Barbara , Campanaro Stefano , Corich Viviana , Giacomini Alessio 
Published: January 2014

ABSTRACT

We report the genome sequences of two
Streptococcus thermophilus
strains, TH1435 and TH1436, isolated from raw goat milk devoted to the production of artisanal cheese in the Friuli-Venezia Giulia region in Italy. The genome sequences of these two quickly acidifying strains are the first available genome sequences of
S. thermophilus
strains isolated in Italy.
Complete Genome Sequence of Cronobacter sakazakii Strain CMCC 45402
Authors: Zhao Zhijing , Wang Lei , Wang Bin , Liang Haoyu , Ye Qiang , Zeng Ming 
Published: January 2014

ABSTRACT

Cronobacter sakazakii
is considered to be an important pathogen involved in life-threatening neonatal infections. Here, we report the annotated complete genome sequence of
C. sakazakii
strain CMCC 45402, obtained from a milk sample in China. The major findings from the genomic analysis provide a better understanding of the isolates from China.
Draft Genome Sequences of 11 Staphylococcus epidermidis Strains Isolated from Wild Mouse Species
Authors: Wang Jun , Kuenzel Sven , Baines John F. 
Published: January 2014

ABSTRACT

We report here the draft genome sequences of 11 strains of
Staphylococcus epidermidis
, a common bacterium inhabiting the skin of humans and other animals. These isolates, obtained from five mouse species, provide valuable information on the native
Staphylococcus
spp. of this important model organism and form a basis for studying host-bacterial interactions in their natural environment.
The Genome of the Predominant Equine
Lactobacillus
Species, Lactobacillus equi, Is Reflective of Its Lifestyle Adaptations to an Herbivorous Host
Authors: O'Donnell Michelle M. , Harris Hugh M. B. , O'Toole Paul W. , Ross R. Paul 
Published: January 2014

ABSTRACT

We report the draft genome sequence of
Lactobacillus equi
strain DPC6820, isolated from equine feces.
L. equi
is a predominant
Lactobacillus
species in the horse hindgut microbiota. An examination of the genome identified genes and enzymes highlighting
L. equi
adaptations to the herbivorous gastrointestinal tract of the horse, including fructan hydrolases. This genome sequence may help us further understand the microbial ecology of the equine hindgut and the influence lactobacilli have on it.
Draft Genome Sequence of Kurthia huakuii LAM0618
T
, an Organic-Pollutant-Degrading Strain Isolated from Biogas Slurry
Authors: Ruan Zhiyong , Wang Yanwei , Song Jinlong , Zhai Yi , Zhang Chi , Chen Chao , Li Yanting , Zhao Bingqiang , Zhao Bin 
Published: January 2014

ABSTRACT

Kurthia huakuii
LAM0618
T
is a facultative anaerobic pollutant-degrading bacterium isolated from biogas slurry. An analysis of the draft genome sequence of LAM0618
T
reveals a genome size of 3,585,165 bp, with a mean G+C content of 39.1%. The genome contains 3,560 coding sequences and 112 tRNA and 33 rRNA genes.
Draft Genome Sequence of Saccharomyces cerevisiae IR-2, a Useful Industrial Strain for Highly Efficient Production of Bioethanol
Authors: Sahara Takehiko , Fujimori Kazuhiro E. , Nezuo Maiko , Tsukahara Masatoshi , Tochigi Yuki , Ohgiya Satoru , Kamagata Yoichi 
Published: January 2014

ABSTRACT

We sequenced the genome of
Saccharomyces cerevisiae
IR-2, which is a diploid industrial strain with flocculation activity and the ability to efficiently produce bioethanol. The approximately 11.4-Mb draft genome information provides useful insights into metabolic engineering for the production of bioethanol from biomass.
Complete Genome Sequence of
Hyphomicrobium nitrativorans
Strain NL23, a Denitrifying Bacterium Isolated from Biofilm of a Methanol-Fed Denitrification System Treating Seawater at the Montreal Biodome
Authors: Martineau Christine , Villeneuve Céline , Mauffrey Florian , Villemur Richard 
Published: January 2014

ABSTRACT

Hyphomicrobium nitrativorans
strain NL23 has been isolated from the biofilm of a denitrification system treating seawater. This strain has the capacity to denitrify using methanol as a carbon source. Here, we report the complete genome sequence of this strain in an effort to increase understanding of the function of this bacterium within the biofilm.
Genome Sequence of
Martelella
sp. Strain AD-3, a Moderately Halophilic Polycyclic Aromatic Hydrocarbon-Degrading Bacterium
Authors: Cui Changzheng , Li Pengpeng , Liu Gao , Tang Hongzhi , Lin Kuangfei , Luo Qishi , Liu Shanshan , Xu Ping , Liu Yongdi 
Published: January 2014

ABSTRACT

Martelella
sp. strain AD-3, enriched from a petroleum-contaminated site with high salinity, can efficiently degrade polycyclic aromatic hydrocarbons. Here, we report the 4.75-Mb genome sequence of strain AD-3 with its genetic feature of helping to remediate environmental organic pollutants.
Genome Sequence Analysis of the Biogenic Amine-Degrading Strain Lactobacillus casei 5b
Authors: Ladero Victor , Herrero-Fresno Ana , Martinez Noelia , del Río Beatriz , Linares Daniel M. , Fernández María , Martín María Cruz , Alvarez Miguel A. 
Published: January 2014

ABSTRACT

We here report a 3.02-Mbp annotated draft assembly of the
Lactobacillus casei
5b genome. The sequence of this biogenic amine-degrading dairy isolate may help identify the mechanisms involved in the catabolism of biogenic amines and perhaps shed light on ways to reduce the presence of these toxic compounds in food.
Draft Genome Sequence of
Blastomonas
sp. Strain CACIA 14H2, a Heterotrophic Bacterium Associated with Cyanobacteria
Authors: Lima Alex Ranieri Jerônimo , Siqueira Andrei Santos , dos Santos Bruno Garcia Simões , da Silva Fábio Daniel Florêncio , Lima Clayton Pereira , Cardoso Jedson Ferreira , Vianez-Júnior João Lídio S. G. , Nunes Márcio Roberto Teixeira , Gonçalves Evonnildo Costa 
Published: January 2014

ABSTRACT

With the new methods for assembling sequence data from metagenomic samples, the genomic study of heterotrophic bacterium-cyanobacterium associations can now be improved. In this work, the draft genome sequence of
Blastomonas
sp. strain CACIA 14H2, obtained from a nonaxenic culture of a
Cyanobium
sp., is presented.
Parallel Pathways for Nitrite Reduction during Anaerobic Growth in Thermus thermophilus
Authors: Alvarez Laura , Bricio Carlos , Hidalgo Aurelio , Berenguer José 
Published: January 2014

ABSTRACT

Respiratory reduction of nitrate and nitrite is encoded in
Thermus thermophilus
by the respective transferable gene clusters. Nitrate is reduced by a heterotetrameric nitrate reductase (Nar) encoded along transporters and regulatory signal transduction systems within the nitrate respiration conjugative element (NCE). The nitrite respiration cluster (
nic
) encodes homologues of nitrite reductase (Nir) and nitric oxide reductase (Nor). The expression and role of the
nirSJM
genes in nitrite respiration were analyzed. The three genes are expressed from two promoters, one (
nirSp
) producing a tricistronic mRNA under aerobic and anaerobic conditions and the other (
nirJp
) producing a bicistronic mRNA only under conditions of anoxia plus a nitrogen oxide. As for its nitrite reductase homologues, NirS is expressed in the periplasm, has a covalently bound heme
c
, and conserves the heme
d
1
binding pocket. NirJ is a cytoplasmic protein likely required for heme
d
1
synthesis and NirS maturation. NirM is a soluble periplasmic homologue of cytochrome
c
552
. Mutants defective in
nirS
show normal anaerobic growth with nitrite and nitrate, supporting the existence of an alternative Nir in the cells. Gene knockout analysis of different candidate genes did not allow us to identify this alternative Nir protein but revealed the requirement for Nar in NirS-dependent and NirS-independent nitrite reduction. As the likely role for Nar in the process is in electron transport through its additional cytochrome
c
periplasmic subunit (NarC), we concluded all the Nir activity takes place in the periplasm by parallel pathways.
Expression and Targeting of Secreted Proteins from Chlamydia trachomatis
Authors: Bauler Laura D. , Hackstadt Ted 
Published: January 2014

ABSTRACT

Chlamydia trachomatis
is an obligate intracellular pathogen that replicates in a vacuole termed the inclusion. Many of the interactions of chlamydiae with the host cell are dependent upon bacterial protein synthesis and presumably exposure of these proteins to the cytosol. Because of the dearth of genetic tools for chlamydiae, previous studies examining secreted proteins required the use of heterologous bacterial systems. Recent advances in genetic manipulation of chlamydia now allow for transformation of the bacteria with plasmids. We describe here a shuttle vector system, pBOMB4, that permits expression of recombinant proteins under constitutive or conditional promoter control. We show that the inclusion membrane protein IncD is secreted in a type III-dependent manner from
Yersinia pseudotuberculosis
and also secreted from
C. trachomatis
in infected cells where it localizes appropriately to the inclusion membrane. IncD truncated of the first 30 amino acids containing the secretion signal is no longer secreted and is retained by the bacteria. Cytosolic exposure of secreted proteins can be confirmed by using CyaA, GSK, or microinjection assays. A protein predicted to be retained within the bacteria, NrdB is indeed localized to the chlamydia. In addition, we have shown that the chlamydial effector protein, CPAF, which is secreted into the host cell cytosol by a Sec-dependent pathway, also accesses the cytosol when expressed from this system. These assays should prove useful to assess the secretion of other chlamydial proteins that are potentially exposed to the cytosol of the host cell.
A Signaling Pathway Involving the Diguanylate Cyclase CelR and the Response Regulator DivK Controls Cellulose Synthesis in Agrobacterium tumefaciens
Authors: Barnhart D. Michael , Su Shengchang , Farrand Stephen K. 
Published: January 2014

ABSTRACTThe production of cellulose fibrils is involved in the attachment ofAgrobacterium tumefaciensto its plant host. Consistent with previous studies, we reported recently that a putative diguanylate cyclase,celR, is required for synthesis of this polymer inA. tumefaciens. In this study, the effects ofcelRand other components of the regulatory pathway of cellulose production were explored. Mutational analysis ofcelRdemonstrated that the cyclase requires the catalytic GGEEF motif, as well as the conserved aspartate residue of a CheY-like receiver domain, for stimulating cellulose production. Moreover, a site-directed mutation within the PilZ domain of CelA, the catalytic subunit of the cellulose synthase complex, greatly reduced cellulose production. In addition, deletion ofdivK, the first gene of thedivK-celRoperon, also reduced cellulose production. This requirement fordivKwas alleviated by expression of a constitutively active form of CelR, suggesting that DivK acts upstream of CelR activation. Based on bacterial two-hybrid assays, CelR homodimerizes but does not interact with DivK. The mutation indivKadditionally affected cell morphology, and this effect was complementable by a wild-type copy of the gene, but not by the constitutively active allele ofcelR. These results support the hypothesis that CelR is a bona fide c-di-GMP synthase and that the nucleotide signal produced by this enzyme activates CelA via the PilZ domain. Our studies also suggest that the DivK/CelR signaling pathway inAgrobacteriumregulates cellulose production independent of cell cycle checkpoint systems that are controlled bydivK.
Social supply of alcohol to Korean high school students: a cross-sectional International Alcohol Control Study
Authors: Asante Lydia S , Chun Sungsoo , Yun Mieun , Newell Maxine 
Published: January 2014

PurposeUnderage drinking is strictly prohibited by law, nevertheless, adolescents report having access through social supply from family, friends and other members of the society. The aim of this study was to determine the primary suppliers of alcohol to Korean teenagers.DesignCross-sectional study.SettingData were collected from 21 high schools in geographically diverse regions in South Korea from June to July 2012 as part of the International Alcohol Control Study.ParticipantsData were analysed from 247 high schoolers aged 16–18 years old as part of the International Alcohol Control Study.Primary and secondary outcome measuresSocial supply to high school students.ResultsMore than 56% of high schoolers who participated in the International Alcohol Control Survey had been supplied alcohol at least once. Of this number, approximately 59% were males. Parents (especially fathers) and friends were the main suppliers, with friends contributing greater volumes (205 g) of alcohol. Of the number of students provided by mothers, 52% of them were females while 73% of respondents provided by friends were males. The most significant place for alcohol supply was at special events. Males were at higher odds for risky drinking.ConclusionsThese results support previous findings about the role of parents and friends in underage drinking in South Korean high school drinkers.
Lean thinking in hospitals: is there a cure for the absence of evidence? A systematic review of reviews
Authors: Andersen Hege , Røvik Kjell Arne , Ingebrigtsen Tor 
Published: January 2014

ObjectiveLean interventions aim to improve quality of healthcare by reducing waste and facilitate flow in work processes. There is conflicting evidence on the outcomes of lean thinking, with quantitative and qualitative studies often contradicting each other. We suggest that reviewing the literature within the approach of a new contextual framework can deepen our understanding of lean as a quality-improvement method. This article theorises the concept of context by establishing a two-dimensional conceptual framework acknowledging lean as complex social interventions, deployed in different organisational dimensions and domains. The specific aim of the study was to identify factors facilitating intended outcomes from lean interventions, and to understand when and how different facilitators contribute.DesignA two-dimensional conceptual framework was developed by combining Shortell'sDimensions of capabilitywith Walshes’Domains of an intervention. We then conducted a systematic review of lean review articles concerning hospitals, published in the period 2000–2012. The identified lean facilitators were categorised according to the intervention domains and dimensions of capability provided by the framework.ResultsWe provide a framework emphasising context by relating facilitators to domains and dimensions of capability. 23 factors enabling a successful lean intervention in hospitals were identified in the systematic review, where management and a supportive culture, training, accurate data, physicians and team involvement were most frequent.ConclusionsIn the absence of evidence, the two-dimensional framework, incorporating the context, may prove useful for future research on variation in outcomes from lean interventions. Findings from the review suggest that characteristics and local application of lean, in addition to strategic and cultural capability, should be given further attention in healthcare quality improvement.