bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete Genome Sequence of the Sugar Cane Endophyte Pseudomonas aurantiaca PB-St2, a Disease-Suppressive Bacterium with Antifungal Activity toward the Plant Pathogen
Colletotrichum falcatum
Authors: Mehnaz Samina , Bauer Judith S. , Gross Harald 
Published: January 2014

ABSTRACT

The endophytic bacterium
Pseudomonas aurantiaca
PB-St2 exhibits antifungal activity and represents a biocontrol agent to suppress red rot disease of sugar cane. Here, we report the completely sequenced 6.6-Mb genome of
P. aurantiaca
PB-St2. The sequence contains a repertoire of biosynthetic genes for secondary metabolites that putatively contribute to its antagonistic activity and its plant-microbe interactions.
Draft Genome Sequence of Saccharomyces cerevisiae NAM34-4C, a Lactic Acid-Assimilating Industrial Yeast Strain
Authors: Sahara Takehiko , Fujimori Kazuhiro E. , Nezuo Maiko , Tsukahara Masatoshi , Tochigi Yuki , Ohgiya Satoru , Tang Yue-Qin , Kida Kenji , Taguchi Hisataka , Akamatsu Takashi , Kamagata Yoichi 
Published: January 2014

ABSTRACT

We determined the genome sequence of industrial
Saccharomyces cerevisiae
strain NAM34-4C, which would be useful for bioethanol production. The approximately 11.5-Mb draft genome sequence of NAM34-4C will provide remarkable insights into metabolic engineering for effective production of bioethanol from biomass.
Revised Genome Sequence of Staphylococcus aureus Bacteriophage K
Authors: Gill Jason J. 
Published: January 2014

ABSTRACT

Bacteriophage K is a member of the virulent Twort-like group of myophages infecting
Staphylococcus aureus
. The revised sequence presented here includes 12,436 bp of additional sequence not present in the previously available phage K genome (GenBank accession no. NC_005880) and updated annotations, and has been reopened at the predicted terminal repeat boundary.
Draft Genome Sequence of
Sclerotinia borealis
, a Psychrophilic Plant Pathogenic Fungus
Authors: Mardanov Andrey V. , Beletsky Alexey V. , Kadnikov Vitaly V. , Ignatov Alexander N. , Ravin Nikolai V. 
Published: January 2014

ABSTRACT

Sclerotinia borealis
is a necrotrophic phytopathogenic fungus notable for its wide host range and environmental persistence. It grows at low temperatures, causing snow mold disease of crop plants. To understand the molecular mechanisms of its pathogenesis and adaptation to the psychrophilic lifestyle, we determined the 39.3-Mb draft genome sequence of
S. borealis
F-4128.
Draft Genome Sequence of a Human-Associated Isolate of
Methanobrevibacter arboriphilicus
, the Lowest-G+C-Content Archaeon
Authors: Khelaifia Saber , Garibal Marc , Robert Catherine , Raoult Didier , Drancourt Michel 
Published: January 2014

ABSTRACT

We report the draft genome sequence of
Methanobrevibacter arboriphilicus
strain ANOR1, isolated from the human gut. Its 2.21-Mb genome exhibits a 25.46% G+C content, the lowest value among archaea. The genome of
M. arboriphilicus
contains a total of 2,111 open reading frames and three clusters of regularly interspaced short palindromic repeat (CRISPR) loci with associated Cas proteins.
Metagenomic Sequencing of Two Salton Sea Microbiomes
Authors: Hawley Erik R. , Schackwitz Wendy , Hess Matthias 
Published: January 2014

ABSTRACT
The Salton Sea is the largest inland body of water in California, with salinities ranging from brackish freshwater to hypersaline. The lake experiences high nutrient input, and its surface water is exposed to temperatures up to 40°C. Here, we report the community profiles associated with surface water from the Salton Sea.
Complete Genome Sequence of Paenibacillus polymyxa CR1, a Plant Growth-Promoting Bacterium Isolated from the Corn Rhizosphere Exhibiting Potential for Biocontrol, Biomass Degradation, and Biofuel Production
Authors: Eastman Alexander W. , Weselowski Brian , Nathoo Naeem , Yuan Ze-Chun 
Published: January 2014

ABSTRACT

Here we report the complete genome sequence of the bacterium
Paenibacillus polymyxa
CR1 (accession no. CP006941), which consists of one circular chromosome of 6,024,666 bp with 5,283 coding sequences (CDS), 87 tRNAs, and 12 rRNA operons. Data presented will allow for further insights into the mechanisms underpinning agriculturally and industrially relevant processes.
Complete Genome Sequence of Salmonella enterica Serovar Agona Pulsed-Field Type SAGOXB.0066, Cause of a 2008 Pan-European Outbreak
Authors: McCusker Matthew P. , Hokamp Karsten , Buckley James F. , Wall Patrick G. , Martins Marta , Fanning Séamus 
Published: January 2014

ABSTRACT

Salmonella enterica
serovar Agona is in the top 10 most common nontyphoidal serovars reported in humans in the European Union. Here we report the complete genome sequence of an
S. enterica
serovar Agona isolate, designated 24249, that was the cause of a pan-European outbreak in 2008 with 163 confirmed cases reported.
Draft Genome Sequence of
Williamsia
sp. Strain D3, Isolated From the Darwin Mountains, Antarctica
Authors: Guerrero Leandro D. , Makhalanyane Thulani P. , Aislabie Jackie M. , Cowan Don A. 
Published: January 2014

ABSTRACT

Actinobacteria are the dominant taxa in Antarctic desert soils. Here, we describe the first draft genome of a member of the genus
Williamsia
(strain D3) isolated from Antarctic soil. The genome of this psychrotolerant bacterium may help to elucidate crucial survival mechanisms for organisms inhabiting cold desert soil systems.
Evaluation of the Bruker MALDI Biotyper for Identification of Gram-Positive Rods: Development of a Diagnostic Algorithm for the Clinical Laboratory
Authors: Schulthess Bettina , Bloemberg Guido V. , Zbinden Reinhard , Böttger Erik C. , Hombach Michael 
Published: January 2014

ABSTRACT

Reported matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) identification rates of Gram-positive rods (GPR) are low compared to identification rates of Gram-positive cocci. In this study, three sample preparation methods were compared for MALDI-TOF MS identification of 190 well-characterized GPR strains: direct transfer, direct transfer-formic acid preparation, and ethanol-formic acid extraction. Using the interpretation criteria recommended by the manufacturer, identification rates were significantly higher for direct transfer-formic acid preparation and ethanol-formic acid extraction than for direct transfer. Reducing the species cutoff from 2.0 to 1.7 significantly increased species identification rates. In a subsequent prospective study, 215 clinical GPR isolates were analyzed by MALDI-TOF MS, and the results were compared to those for identification using conventional methods, with discrepancies being resolved by 16S rRNA and
rpoB
gene analysis. Using the direct transfer-formic acid preparation and a species cutoff of 1.7, congruencies on the genus and species levels of 87.4% and 79.1%, respectively, were achieved. In addition, the rate of nonidentified isolates dropped from 12.1% to 5.6% when using an extended database, i.e., the Bruker database amended by reference spectra of the 190 GPR of the retrospective study. Our data demonstrate three ways to improve GPR identification by the Bruker MALDI Biotyper, (i) optimize sample preparation using formic acid, (ii) reduce cutoff scores for species identification, and (iii) expand the database. Based on our results, we suggest an identification algorithm for the clinical laboratory combining MALDI-TOF MS with nucleic acid sequencing.
Performance of Phenotypic Tests for Detection of Penicillinase in Staphylococcus aureus Isolates from Australia
Authors: Papanicolas Lito E. , Bell Jan M. , Bastian Ivan 
Published: January 2014

ABSTRACT

Recent studies have shown that chromogenic cephalosporin tests are inferior to disc zone edge tests in detecting penicillinase in
Staphylococcus aureus
isolates, resulting in a change to CLSI and EUCAST guidelines in 2012. We sought to confirm these findings using Australian isolates and compare the performance of the CLSI and EUCAST methods, which use different disc strengths, penicillin at 10 units (P10) and 1 unit (P1), respectively. Using
blaZ
PCR as the reference standard, the sensitivities of the tests for detection of penicillinase production were as follows: Cefinase disc test, 24/38 isolates (63%); P10 disc zone edge test, 34/38 isolates (89%); P10 disc diameter test, 25/38 isolates (66%); P1 disc zone edge test, 38/38 isolates (100%); and P1 disc diameter test, 38/38 isolates (100%). We also found that the P10 disc zone edge test reading was interpreted differently by the clinical laboratory and the study investigators in 11% of instances. Our findings support those of previous studies showing that chromogenic cephalosporin-based β-lactamase tests are inferior to disc methods in detecting
S. aureus
penicillinase. We also conclude that the EUCAST method using the P1 disc has the best performance, particularly because the P1 disc zone diameter reading closely correlated with penicillinase production and reading of the disc zone diameter is less subjective than reading of the zone edge.
Simultaneous Detection and Discrimination of Virulent and Benign Dichelobacter nodosus in Sheep of Flocks Affected by Foot Rot and in Clinically Healthy Flocks by Competitive Real-Time PCR
Authors: Stäuble Anna , Steiner Adrian , Frey Joachim , Kuhnert Peter 
Published: January 2014

ABSTRACT

Ovine foot rot caused by
Dichelobacter nodosus
is affecting sheep worldwide. The current diagnostic methods are difficult and cumbersome. Here, we present a competitive real-time PCR based on allelic discrimination of the protease genes
aprV2
and
aprB2
. This method allows direct detection and differentiation of virulent and benign
D. nodosus
from interdigital skin swabs in a single test. Clinically affected sheep harbored high loads of only virulent strains, whereas healthy sheep had lower loads of predominantly benign strains.
Divergent H7 Immunogens Offer Protection from H7N9 Virus Challenge
Authors: Krammer Florian , Albrecht Randy A. , Tan Gene S. , Margine Irina , Hai Rong , Schmolke Mirco , Runstadler Jonathan , Andrews Sarah F. , Wilson Patrick C. , Cox Rebecca J. , Treanor John J. , García-Sastre Adolfo , Palese Peter 
Published: January 2014

ABSTRACT
The emergence of avian H7N9 viruses in humans in China has renewed concerns about influenza pandemics emerging from Asia. Vaccines are still the best countermeasure against emerging influenza virus infections, but the process from the identification of vaccine seed strains to the distribution of the final product can take several months. In the case of the 2009 H1N1 pandemic, a vaccine was not available before the first pandemic wave hit and therefore came too late to reduce influenza morbidity. H7 vaccines based on divergent isolates of the Eurasian and North American lineages have been tested in clinical trials, and seed strains and reagents are already available and can potentially be used initially to curtail influenza-induced disease until a more appropriately matched H7N9 vaccine is ready. In a challenge experiment in the mouse model, we assessed the efficacy of both inactivated virus and recombinant hemagglutinin vaccines made from seed strains that are divergent from H7N9 from each of the two major H7 lineages. Furthermore, we analyzed the cross-reactive responses of sera from human subjects vaccinated with heterologous North American and Eurasian lineage H7 vaccines to H7N9. Vaccinations with inactivated virus and recombinant hemagglutinin protein preparations from both lineages raised hemagglutination-inhibiting antibodies against H7N9 viruses and protected mice from stringent viral challenges. Similar cross-reactivity was observed in sera of human subjects from a clinical trial with a divergent H7 vaccine. Existing H7 vaccine candidates based on divergent strains could be used as a first line of defense against an H7N9 pandemic. In addition, this also suggests that H7N9 vaccines that are currently under development might be stockpiled and used for divergent avian H7 strains that emerge in the future.

IMPORTANCE
Sporadic human infections with H7N9 viruses started being reported in China in the early spring of 2013. Despite a significant drop in the number of infections during the summer months of 2013, an increased number of cases has already been reported for the 2013-2014 winter season. The high case fatality rate, the ability to bind to receptors in the human upper respiratory tract in combination with several family clusters, and the emergence of neuraminidase inhibitor-resistant variants that show no loss of pathogenicity and the ability to transmit in animal models have raised concerns about a potential pandemic and have spurred efforts to produce vaccine candidates. Here we show that antigen preparations from divergent H7 strains are able to induce protective immunity against H7N9 infection.
Rock-magnetic evidence for the low-temperature emplacement of the Habushiura pyroclastic density current, Niijima Island, Japan
Authors: Nakaoka Reina , Suzuki-Kamata Keiko 
Published: January 2014

Abstract
The emplacement temperatures of accidental and juvenile fragments in the Habushiura pyroclastic density current (PDC) deposit were estimated using analysis of rock magnetism. The Habushiura PDC was generated in a costal or shallow offshore area during the early stage of the AD 886 phreatomagmatic eruption on Niijima Island, Japan. We collected 160 samples from 11 beds, which include three lithofacies types: a massive lapilli tuff (Facies A); a graded and/or diffusely stratified lapilli tuff (Facies B); and a swarm of large pumice (Facies C). Juvenile specimens from Facies A and C show a wide range of emplacement temperatures, from less than 150 °C up to 300 °C, in contrast with the emplacement temperatures lower than 150 °C of Facies B. Morphological features of the ash components and random changes in palaeomagnetic direction by stepwise thermal demagnetization indicate that low-temperature emplacement occurred by phreatomagmatic eruptions and ingestion of ambient air by the turbulent current. The emplacement temperatures of accidental fragments were up to 380 °C, which is higher than juvenile fragments. They are thought to have cooled more slowly than juvenile fragments due to the smaller surface area with respect to their volume.
Genetic Validation of the Protein Arginine Methyltransferase PRMT5 as a Candidate Therapeutic Target in Glioblastoma
Authors: Yan Fengting , Alinari Lapo , Lustberg Mark E. , Katherine Martin Ludmila , Cordero-Nieves Hector M. , Banasavadi-Siddegowda Yeshavanth , Virk Selene , Barnholtz-Sloan Jill , Bell Erica Hlavin , Wojton Jeffrey , Jacob Naduparambil K. , Chakravarti Arnab , Nowicki Michal O. , Wu Xin , Lapalombella Rosa , Datta Jharna , Yu Bo , Gordon Kate , Haseley Amy , Patton John T. , Smith Porsha L. , Ryu John , Zhang Xiaoli , Mo Xiaokui , Marcucci Guido , Nuovo Gerard , Kwon Chang-Hyuk , Byrd John C. , Chiocca E. Antonio , Li Chenglong , Sif Said , Jacob Samson , Lawler Sean , Kaur Balveen , Baiocchi Robert A. 
Published: January 2014

AbstractGlioblastoma is the most common and aggressive histologic subtype of brain cancer with poor outcomes and limited treatment options. Here, we report the selective overexpression of the protein arginine methyltransferase PRMT5 as a novel candidate theranostic target in this disease. PRMT5 silences the transcription of regulatory genes by catalyzing symmetric dimethylation of arginine residues on histone tails. PRMT5 overexpression in patient-derived primary tumors and cell lines correlated with cell line growth rate and inversely with overall patient survival. Genetic attenuation of PRMT5 led to cell-cycle arrest, apoptosis, and loss of cell migratory activity. Cell death was p53-independent but caspase-dependent and enhanced with temozolomide, a chemotherapeutic agent used as a present standard of care. Global gene profiling and chromatin immunoprecipitation identified the tumor suppressor ST7 as a key gene silenced by PRMT5. Diminished ST7 expression was associated with reduced patient survival. PRMT5 attenuation limited PRMT5 recruitment to the ST7 promoter, led to restored expression of ST7 and cell growth inhibition. Finally, PRMT5 attenuation enhanced glioblastoma cell survival in a mouse xenograft model of aggressive glioblastoma. Together, our findings defined PRMT5 as a candidate prognostic factor and therapeutic target in glioblastoma, offering a preclinical justification for targeting PRMT5-driven oncogenic pathways in this deadly disease. Cancer Res; 74(6); 1752–65. ©2014 AACR.
Activated ERBB2/HER2 Licenses Sensitivity to Apoptosis upon Endoplasmic Reticulum Stress through a PERK-Dependent Pathway
Authors: Martín-Pérez Rosa , Palacios Carmen , Yerbes Rosario , Cano-González Ana , Iglesias-Serret Daniel , Gil Joan , Reginato Mauricio J. , López-Rivas Abelardo 
Published: January 2014

Abstract
HER2/Neu/ERBB2 is a receptor tyrosine kinase overexpressed in approximately 20% of human breast tumors. Truncated or mutant isoforms that show increased oncogenicity compared with the wild-type receptor are found in many breast tumors. Here, we report that constitutively active ERBB2 sensitizes human breast epithelial cells to agents that induce endoplasmic reticulum stress, altering the unfolded protein response (UPR) of these cells. Deregulation of the ERK, AKT, and mTOR activities elicited by mutant ERBB2 was involved in mediating this differential UPR response, elevating the response to endoplasmic reticulum stress, and apoptotic cell death. Mechanistic investigations revealed that the increased sensitivity of mutant ERBB2-expressing cells to endoplasmic reticulum stress relied upon a UPR effector signaling involving the PERK–ATF4–CHOP pathway, upregulation of the proapoptotic cell surface receptor TRAIL-R2, and activation of proapoptotic caspase-8. Collectively, our results offer a rationale for the therapeutic exploration of treatments inducing endoplasmic reticulum stress against mutant ERBB2-expressing breast tumor cells. Cancer Res; 74(6); 1766–77. ©2014 AACR.
The Structural Basis of PI3K Cancer Mutations: From Mechanism to Therapy
Authors: Liu Shujuan , Knapp Stefan , Ahmed Ahmed Ashour 
Published: January 2014

Abstract
While genetic alteration in the p85α-p110α (PI3K) complex represents one of the most frequent driver mutations in cancer, the wild-type complex is also required for driving cancer progression through mutations in related pathways. Understanding the mechanistic basis of the function of the phosphoinositide 3-kinase (PI3K) is essential for designing optimal therapeutic targeting strategies. Recent structural data of the p85α/p110α complex unraveled key insights into the molecular mechanisms of the activation of the complex and provided plausible explanations for the well-established biochemical data on p85/p110 dimer regulation. A wealth of biochemical and biologic information supported by recent genetic findings provides a strong basis for additional p110-independent function of p85α in the regulation of cell survival. In this article, we review the structural, biochemical, and biologic mechanisms through which p85α regulates the cancer cell life cycle with an emphasis on the recently discovered genetic alterations in cancer. As cancer progression is dependent on multiple biologic processes, targeting key drivers such as the PI3K may be required for efficacious therapy of heterogeneous tumors typically present in patients with late-stage disease. Cancer Res; 74(3); 641–6. ©2014 AACR.
Haemophilia A mutations in patients with non-severe phenotype associated with a discrepancy between one-stage and chromogenic factor VIII activity assays
Authors: Pavlova Anna , Delev Daniel , Pezeshkpoor Behnaz , Müller Jens , Oldenburg Johannes 
Published: January 2014

SummaryAbout one-third of patients with non-severe haemophilia A (HA) show a discrepancy of factor (F)VIII activity (FVIII:C) measured by one-stage (FVIII:C1st), two-stage assays or the chromogenic method (FVIII:Cchr). The aim of the study was to characterise the mutation profile in patients with FVIII:C assay discrepancies. FVIII:C discrepancy was considered significant if the calculated ratio between FVIII:C1st and FVIII:Cchr was ≤ 0.6. In 16 patients FVIII:C1st was higher than FVIII:Cchr. The reverse phenomenon was observed in 83 patients. Genetic analysis revealed 23 different missense mutations of which 17 were novel. Most mutations, exhibiting a higher FVIII:C1st were localised in the A1-A2-A3 interface. The majority of mutations associated with FVIII:Cchr>FVIII:C1st discrepancy were located close to or within the thrombin cleavage sites, FIX or vWF binding sites. Our data show a correlation between FVIII:C and thrombin generation testing with a clear differentiation between patients with haemophilia and normal controls. However, in the subgroup of FVIII:C1st>FVIII:Cchr discrepancy, the endogenous thrombin potential and peak thrombin parameters were similar to non-discrepant haemophilia patients, while in the inverse discrepancy FVIII:Cchr>FVIII:C1st, these variables showed values close to that of the normal control group. Certain hereditary F8 mis-sense mutations cause discrepancy in FVIII:C as measured with different assays. This can lead to failure in diagnosing HA or incorrectly classifying the severity of the disease. Therefore, we recommend that initial diagnosis of non-severe HA phenotypes should be based on results of both FVIII:C1st and FVIII:Cchr assays.