bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete Genome Sequence of Strain 1860, a Crenarchaeon of the Genus Pyrobaculum Able To Grow with Various Electron Acceptors
Authors: Mardanov Andrey V. , Gumerov Vadim M. , Slobodkina Galina B. , Beletsky Alexey V. , Bonch-Osmolovskaya Elizaveta A. , Ravin Nikolai V. , Skryabin Konstantin G. 
Published: January 2012

ABSTRACT

Strain 1860, a novel member of the genus
Pyrobaculum
, is a hyperthermophilic organotrophic crenarchaeon growing anaerobically with various electron acceptors. The complete genome sequence reveals genes for several membrane-bound oxidoreductases, the Embden-Meyerhof and Entner-Doudoroff pathways for glucose metabolism, the tricarboxylic acid cycle, the glyoxylate cycle, and the dicarboxylate/4-hydroxybutyrate cycle.
Draft Genome Sequence of Plant Growth-Promoting Rhizobium Mesorhizobium amorphae, Isolated from Zinc-Lead Mine Tailings
Authors: Hao Xiuli , Lin Yanbing , Johnstone Laurel , Baltrus David A. , Miller Susan J. , Wei Gehong , Rensing Christopher 
Published: January 2012

ABSTRACT

Here, we describe the draft genome sequence of
Mesorhizobium amorphae
strain CCNWGS0123, isolated from nodules of
Robinia pseudoacacia
growing on zinc-lead mine tailings. A large number of metal(loid) resistance genes, as well as genes reported to promote plant growth, were identified, presenting a great future potential for aiding phytoremediation in metal(loid)-contaminated soil.
Genome Sequence of Corynebacterium glutamicum ATCC 14067, Which Provides Insight into Amino Acid Biosynthesis in Coryneform Bacteria
Authors: Lv Yangyong , Liao Juanjun , Wu Zhanhong , Han Shuangyan , Lin Ying , Zheng Suiping 
Published: January 2012

ABSTRACT

We report the genome sequence of
Corynebacterium glutamicum
ATCC 14067 (once named
Brevibacterium flavum
), which is useful for taxonomy research and further molecular breeding in amino acid production. Preliminary comparison with those of the reported coryneform strains revealed some notable differences that might be related to the difficulties in molecular manipulation.
Draft Genome Sequences of the Biocontrol Bacterium Mitsuaria sp. Strain H24L5A
Authors: Rong Xiaoqing , Gurel Fulya Baysal , Meulia Tea , McSpadden Gardener Brian B. 
Published: January 2012

ABSTRACT

Mitsuaria
sp. strain H24L5A is a plant-associated bacterium with proven capacities to suppress plant pathogens. Here, we report the draft genome sequences and automatic annotation of H24L5A. Comparative genomic analysis indicates H24L5A's similarity to the
Leptothrix
and
Methylibium
species, as well as several genes potentially contributing to its biocontrol activities.
Time Course of Prion Seeding Activity in Cerebrospinal Fluid of Scrapie-Infected Hamsters after Intratongue and Intracerebral Inoculations
Authors: Orrù Christina D. , Hughson Andrew G. , Race Brent , Raymond Gregory J. , Caughey Byron 
Published: January 2012

ABSTRACT

To assess prospects for early diagnosis of prion disease based on prion seeding activity in cerebrospinal fluid (CSF), we measured the activity over time in scrapie-infected hamsters by
r
eal-
t
ime
qu
aking-
i
nduced
c
onversion (RT-QuIC). After intracerebral inoculation, activity appeared in CSF within 1 day and plateaued weeks before the onset of clinical signs. However, after intratongue inoculation, activity first appeared in CSF with the onset of clinical signs, well after higher-level accumulation of seeding activity in brain.
Comparative Study Using Phenotypic, Genotypic, and Proteomics Methods for Identification of Coagulase-Negative Staphylococci
Authors: Loonen Anne J. M. , Jansz Arjan R. , Bergland Jeandery N. B. , Valkenburg Marion , Wolffs Petra F. G. , van den Brule Adriaan J. C. 
Published: January 2012

ABSTRACT

Five methods were compared to determine the most accurate method for identification of coagulase-negative staphylococci (CoNS) (
n
= 142 strains). Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) showed the best results for rapid and accurate CoNS differentiation (99.3% of strains correctly identified). An alternative to this approach could be Vitek2 combined with partial
tuf
gene sequencing (100% of strains correctly identified when both methods are performed simultaneously).
Characterization of the RNA Silencing Suppression Activity of the Ebola Virus VP35 Protein in Plants and Mammalian Cells
Authors: Zhu Yali , Cherukuri Nil Celebi , Jackel Jamie N. , Wu Zetang , Crary Monica , Buckley Kenneth J. , Bisaro David M. , Parris Deborah S. 
Published: January 2012

ABSTRACT
Ebola virus (EBOV) causes a lethal hemorrhagic fever for which there is no approved effective treatment or prevention strategy. EBOV VP35 is a virulence factor that blocks innate antiviral host responses, including the induction of and response to alpha/beta interferon. VP35 is also an RNA silencing suppressor (RSS). By inhibiting microRNA-directed silencing, mammalian virus RSSs have the capacity to alter the cellular environment to benefit replication. A reporter gene containing specific microRNA target sequences was used to demonstrate that prior expression of wild-type VP35 was able to block establishment of microRNA silencing in mammalian cells. In addition, wild-type VP35 C-terminal domain (CTD) protein fusions were shown to bind small interfering RNA (siRNA). Analysis of mutant proteins demonstrated that reporter activity in RSS assays did not correlate with their ability to antagonize double-stranded RNA (dsRNA)-activated protein kinase R (PKR) or bind siRNA. The results suggest that enhanced reporter activity in the presence of VP35 is a composite of nonspecific translational enhancement and silencing suppression. Moreover, most of the specific RSS activity in mammalian cells is RNA binding independent, consistent with VP35's proposed role in sequestering one or more silencing complex proteins. To examine RSS activity in a system without interferon, VP35 was tested in well-characterized plant silencing suppression assays. VP35 was shown to possess potent plant RSS activity, and the activities of mutant proteins correlated strongly, but not exclusively, with RNA binding ability. The results suggest the importance of VP35-protein interactions in blocking silencing in a system (mammalian) that cannot amplify dsRNA.
Beyond Anchoring: the Expanding Role of the Hendra Virus Fusion Protein Transmembrane Domain in Protein Folding, Stability, and Function
Authors: Smith Everett Clinton , Culler Megan R. , Hellman Lance M. , Fried Michael G. , Creamer Trevor P. , Dutch Rebecca Ellis 
Published: January 2012

ABSTRACTWhile work with viral fusion proteins has demonstrated that the transmembrane domain (TMD) can affect protein folding, stability, and membrane fusion promotion, the mechanism(s) remains poorly understood. TMDs could play a role in fusion promotion through direct TMD-TMD interactions, and we have recently shown that isolated TMDs from three paramyxovirus fusion (F) proteins interact as trimers using sedimentation equilibrium (SE) analysis (E. C. Smith, et al., submitted for publication). Immediately N-terminal to the TMD is heptad repeat B (HRB), which plays critical roles in fusion. Interestingly, addition of HRB decreased the stability of the trimeric TMD-TMD interactions. This result, combined with previous findings that HRB forms a trimeric coiled coil in the prefusion form of the whole protein though HRB peptides fail to stably associate in isolation, suggests that the trimeric TMD-TMD interactions work in concert with elements in the F ectodomain head to stabilize a weak HRB interaction. Thus, changes in TMD-TMD interactions could be important in regulating F triggering and refolding. Alanine insertions between the TMD and HRB demonstrated that spacing between these two regions is important for protein stability while not affecting TMD-TMD interactions. Additional mutagenesis of the C-terminal end of the TMD suggests that β-branched residues within the TMD play a role in membrane fusion, potentially through modulation of TMD-TMD interactions. Our results support a model whereby the C-terminal end of the Hendra virus F TMD is an important regulator of TMD-TMD interactions and show that these interactions help hold HRB in place prior to the triggering of membrane fusion.
Residues in the Hendra Virus Fusion Protein Transmembrane Domain Are Critical for Endocytic Recycling
Authors: Popa Andreea , Carter James R. , Smith Stacy E. , Hellman Lance , Fried Michael G. , Dutch Rebecca Ellis 
Published: January 2012

ABSTRACT
Hendra virus is a highly pathogenic paramyxovirus classified as a biosafety level four agent. The fusion (F) protein of Hendra virus is critical for promoting viral entry and cell-to-cell fusion. To be fusogenically active, Hendra virus F must undergo endocytic recycling and cleavage by the endosomal/lysosomal protease cathepsin L, but the route of Hendra virus F following internalization and the recycling signals involved are poorly understood. We examined the intracellular distribution of Hendra virus F following endocytosis and showed that it is primarily present in Rab5- and Rab4-positive endosomal compartments, suggesting that cathepsin L cleavage occurs in early endosomes. Hendra virus F transmembrane domain (TMD) residues S490 and Y498 were found to be important for correct Hendra virus F recycling, with the hydroxyl group of S490 and the aromatic ring of Y498 important for this process. In addition, changes in association of isolated Hendra virus F TMDs correlated with alterations to Hendra virus F recycling, suggesting that appropriate TMD interactions play an important role in endocytic trafficking.
Wild-Type Measles Virus with the Hemagglutinin Protein of the Edmonston Vaccine Strain Retains Wild-Type Tropism in Macaques
Authors: Takeuchi Kaoru , Nagata Noriyo , Kato Sei-ich , Ami Yasushi , Suzaki Yuriko , Suzuki Tadaki , Sato Yuko , Tsunetsugu-Yokota Yasuko , Mori Kazuyasu , Van Nguyen Nguyen , Kimura Hideki , Nagata Kyosuke 
Published: January 2012

ABSTRACT

A major difference between vaccine and wild-type strains of measles virus (MV)
in vitro
is the wider cell specificity of vaccine strains, resulting from the receptor usage of the hemagglutinin (H) protein. Wild-type H proteins recognize the signaling lymphocyte activation molecule (SLAM) (CD150), which is expressed on certain cells of the immune system, whereas vaccine H proteins recognize CD46, which is ubiquitously expressed on all nucleated human and monkey cells, in addition to SLAM. To examine the effect of the H protein on the tropism and attenuation of MV, we generated enhanced green fluorescent protein (EGFP)-expressing recombinant wild-type MV strains bearing the Edmonston vaccine H protein (MV-EdH) and compared them to EGFP-expressing wild-type MV strains.
In vitro
, MV-EdH replicated in SLAM
+
as well as CD46
+
cells, including primary cell cultures from cynomolgus monkey tissues, whereas the wild-type MV replicated only in SLAM
+
cells. However, in macaques, both wild-type MV and MV-EdH strains infected lymphoid and respiratory organs, and widespread infection of MV-EdH was not observed. Flow cytometric analysis indicated that SLAM
+
lymphocyte cells were infected preferentially with both strains. Interestingly, EGFP expression of MV-EdH in tissues and lymphocytes was significantly weaker than that of the wild-type MV. Taken together, these results indicate that the CD46-binding activity of the vaccine H protein is important for determining the cell specificity of MV
in vitro
but not the tropism
in vivo
. They also suggest that the vaccine H protein attenuates MV growth
in vivo
.
A Human Antibody Recognizing a Conserved Epitope of H5 Hemagglutinin Broadly Neutralizes Highly Pathogenic Avian Influenza H5N1 Viruses
Authors: Hu Hongxing , Voss Jarrod , Zhang Guoliang , Buchy Philippi , Zuo Teng , Wang Lulan , Wang Feng , Zhou Fan , Wang Guiqing , Tsai Cheguo , Calder Lesley , Gamblin Steve J. , Zhang Linqi , Deubel Vincent , Zhou Boping , Skehel John J. , Zhou Paul 
Published: January 2012

ABSTRACTInfluenza A virus infection is a persistent threat to public health worldwide due to its ability to evade immune surveillance through rapid genetic drift and shift. Current vaccines against influenza A virus provide immunity to viral isolates that are similar to vaccine strains. High-affinity neutralizing antibodies against conserved epitopes could provide immunity to diverse influenza virus strains and protection against future pandemic viruses. In this study, by using a highly sensitive H5N1 pseudotype-based neutralization assay to screen human monoclonal antibodies produced by memory B cells from an H5N1-infected individual and molecular cloning techniques, we developed three fully human monoclonal antibodies. Among them, antibody 65C6 exhibited potent neutralization activity against all H5 clades and subclades except for subclade 7.2 and prophylactic and therapeutic efficacy against highly pathogenic avian influenza H5N1 viruses in mice. Studies on hemagglutinin (HA)-antibody complexes by electron microscopy and epitope mapping indicate that antibody 65C6 binds to a conformational epitope comprising amino acid residues at positions 118, 121, 161, 164, and 167 (according to mature H5 numbering) on the tip of the membrane-distal globular domain of HA. Thus, we conclude that antibody 65C6 recognizes a neutralization epitope in the globular head of HA that is conserved among almost all divergent H5N1 influenza stains.
Detection of Murine Leukemia Virus in the Epstein-Barr Virus-Positive Human B-Cell Line JY, Using a Computational RNA-Seq-Based Exogenous Agent Detection Pipeline, PARSES
Authors: Lin Zhen , Puetter Adriane , Coco Joseph , Xu Guorong , Strong Michael J. , Wang Xia , Fewell Claire , Baddoo Melody , Taylor Christopher , Flemington Erik K. 
Published: January 2012

ABSTRACT
Many cell lines commonly used for biological studies have been found to harbor exogenous agents such as the human tumor viruses Epstein-Barr virus (EBV) and human papillomavirus. Nevertheless, broad-based, unbiased approaches to globally assess the presence of ectopic organisms within cell model systems have not previously been available. We reasoned that high-throughput sequencing should provide unparalleled insights into the microbiomes of tissue culture cell systems. Here we have used our RNA-seq analysis pipeline, PARSES (Pipeline for Analysis of RNA-Seq Exogenous Sequences), to investigate the presence of ectopic organisms within two EBV-positive B-cell lines commonly used by EBV researchers. Sequencing data sets from both the Akata and JY B-cell lines were found to contain reads for EBV, and the JY data set was found to also contain reads from the murine leukemia virus (MuLV). Further investigation revealed that MuLV transcription in JY cells is highly active. We also identified a number of MuLV alternative splicing events, and we uncovered evidence of APOBEC3G (apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G)-dependent DNA editing. Finally, reverse transcription-PCR analysis showed the presence of MuLV in three other human B-cell lines (DG75, Ramos, and P3HR1 Cl.13) commonly used by investigators in the Epstein-Barr virus field. We believe that a thorough examination of tissue culture microbiomes using RNA-seq/PARSES-like approaches is critical for the appropriate utilization of these systems in biological studies.
Genome Sequence of a Highly Prevalent Porcine Partetravirus in Mainland China
Authors: Li Bin , Ma Junjie , Xiao Shaobo , Wen Libin , Ni Yanxiu , Zhang Xuehan , Fang Liurong , He Kongwang 
Published: January 2012

ABSTRACT
Partetravirus is a novel defined genus of animal parvoviruses. Here, we first report the genome sequence of porcine partetravirus strain JSNJ62, which is highly prevalent in mainland China. It will help in understanding the epidemiology and molecular characteristics of the porcine partetravirus.
Impact of a high‐phosphorus diet on the sonographic and CT appearance of kidneys in degus, and possible concurrence with dental problems
Authors: Gumpenberger M. , Jeklova E. , Skoric M. , Hauptman K. , Stehlik L. , Dengg S. , Jekl V. 
Published: January 2012

The main aim of this study was to investigate the impact of pelleted diet of different mineral composition on the sonographic and CT appearance of kidneys in degus (Octodon degus). A total of 35 animals were randomly divided into five groups, fed diets containing different calcium and phosphorus contents (13.5 g/kg calcium and 6.3 g/kg phosphorus, or 9.1 g/kg calcium and 9.5 g/kg phosphorus) and given different amounts of exposure to UV light. Endoscopic examination of the oral cavity as well as renal ultrasonography and CT was performed four times at four‐month intervals throughout the study. After 14 months of feeding an experimental diet, all degus were euthanased and subsequently all kidneys were collected for histopathological examination. Animals fed a diet with high dietary phosphate and improper calcium to phosphorus ratio showed severe nephrocalcinosis. Ultrasonographic and CT kidney abnormalities presented as hyperechogenicity and hyperdensity (interpreted as nephrocalcinosis), respectively. The most striking changes were seen at the corticomedullary zone. Ultrasonography and CT correlated in all cases with histopathological findings. Dental disease developed quickly in groups fed diets with an improper calcium and phosphorus content, with obvious apical and coronal elongation of all the teeth. A possible influence of UV light access could not be proved in this study.
Pocket Proteins Suppress Head and Neck Cancer
Authors: Shin Myeong-Kyun , Pitot Henry C. , Lambert Paul F. 
Published: January 2012

Abstract
Head and neck squamous cell carcinomas (HNSCC) is a common cancer in humans long known to be caused by tobacco and alcohol use, but now an increasing percentage of HNSCC is recognized to be caused by the same human papillomaviruses (HPV) that cause cervical and other anogenital cancers. HPV-positive HNSCCs differ remarkably from HPV-negative HNSCCs in their clinical response and molecular properties. From studies in mice, we know that E7 is the dominant HPV oncoprotein in head and neck cancer. E7 is best known for its ability to inactivate pRb, the product of the retinoblastoma tumor susceptibility gene. However, loss of pRb function does not fully account for potency of E7 in causing head and neck cancer. In this study, we characterized the cancer susceptibility of mice deficient in the expression of pRb and either of two related “pocket” proteins, p107 and p130, that are also inactivated by E7. pRb/p107-deficient mice developed head and neck cancer as frequently as do HPV-16 E7 transgenic mice. The head and neck epithelia of the pRb/p107-deficient mice also displayed the same acute phenotypes and biomarker readouts as observed in the epithelia of E7 transgenic mice. Mice deficient for pRb and p130 in their head and neck epithelia showed intermediate acute and tumor phenotypes. We conclude that pRb and p107 act together to efficiently suppress head and neck cancer and are, therefore, highly relevant targets of HPV-16 E7 in its contribution to HPV-positive HNSCC. Cancer Res; 72(5); 1280–9. ©2012 AACR.
VEGF Receptor Inhibitors Block the Ability of Metronomically Dosed Cyclophosphamide to Activate Innate Immunity–Induced Tumor Regression
Authors: Doloff Joshua C. , Waxman David J. 
Published: January 2012

AbstractIn metronomic chemotherapy, frequent drug administration at lower than maximally tolerated doses can improve activity while reducing the dose-limiting toxicity of conventional dosing schedules. Although the antitumor activity produced by metronomic chemotherapy is attributed widely to antiangiogenesis, the significance of this mechanism remains somewhat unclear. In this study, we show that a 6-day repeating metronomic schedule of cyclophosphamide administration activates a potent antitumor immune response associated with brain tumor recruitment of natural killer (NK) cells, macrophages, and dendritic cells that leads to marked tumor regression. Tumor regression was blocked in nonobese diabetic/severe combined immunodeficient (NOD/SCID-γ) mice, which are deficient or dysfunctional in all these immune cell types. Furthermore, regression was blunted by NK cell depletion in immunocompetent syngeneic mice or in perforin-deficient mice, which are compromised for NK, NKT, and T-cell cytolytic functions. Unexpectedly, we found that VEGF receptor inhibitors blocked both innate immune cell recruitment and the associated tumor regression response. Cyclophosphamide administered at a maximum tolerated dose activated a transient, weak innate immune response, arguing that persistent drug-induced cytotoxic damage or associated cytokine and chemokine responses are required for effective innate immunity–based tumor regression. Together, our results reveal an innate immunity–based mechanism of tumor regression that can be activated by a traditional cytotoxic chemotherapy administered on a metronomic schedule. These findings suggest the need to carefully evaluate the clinical effects of combination chemotherapies that incorporate antiangiogenesis drugs targeting VEGF receptor. Cancer Res; 72(5); 1103–15. ©2012 AACR.
Exploiting the Mutanome for Tumor Vaccination
Authors: Castle John C. , Kreiter Sebastian , Diekmann Jan , Löwer Martin , van de Roemer Niels , de Graaf Jos , Selmi Abderraouf , Diken Mustafa , Boegel Sebastian , Paret Claudia , Koslowski Michael , Kuhn Andreas N. , Britten Cedrik M. , Huber Christoph , Türeci Özlem , Sahin Ugur 
Published: January 2012

Abstract
Multiple genetic events and subsequent clonal evolution drive carcinogenesis, making disease elimination with single-targeted drugs difficult. The multiplicity of gene mutations derived from clonal heterogeneity therefore represents an ideal setting for multiepitope tumor vaccination. Here, we used next generation sequencing exome resequencing to identify 962 nonsynonymous somatic point mutations in B16F10 murine melanoma cells, with 563 of those mutations in expressed genes. Potential driver mutations occurred in classical tumor suppressor genes and genes involved in proto-oncogenic signaling pathways that control cell proliferation, adhesion, migration, and apoptosis. Aim1 and Trrap mutations known to be altered in human melanoma were included among those found. The immunogenicity and specificity of 50 validated mutations was determined by immunizing mice with long peptides encoding the mutated epitopes. One-third of these peptides were found to be immunogenic, with 60% in this group eliciting immune responses directed preferentially against the mutated sequence as compared with the wild-type sequence. In tumor transplant models, peptide immunization conferred in vivo tumor control in protective and therapeutic settings, thereby qualifying mutated epitopes that include single amino acid substitutions as effective vaccines. Together, our findings provide a comprehensive picture of the mutanome of B16F10 melanoma which is used widely in immunotherapy studies. In addition, they offer insight into the extent of the immunogenicity of nonsynonymous base substitution mutations. Lastly, they argue that the use of deep sequencing to systematically analyze immunogenicity mutations may pave the way for individualized immunotherapy of cancer patients. Cancer Res; 72(5); 1081–91. ©2012 AACR.