Quantitative analysis of Nipah virus proteins released as virus-like particles reveals central role for the matrix protein

BACKGROUND: Nipah virus (NiV) is an emerging paramyxovirus distinguished by its ability to cause fatal disease in both animal and human hosts. Together with Hendra virus (HeV), they comprise the genus Henipavirus in the Paramyxoviridae family. NiV and HeV are also restricted to Biosafety Level-4 containment and this has hampered progress towards examining details of their replication and morphogenesis. Here, we have established recombinant expression systems to study NiV particle assembly and budding through the formation of virus-like particles (VLPs). RESULTS: When expressed by recombinant Modified Vaccinia virus Ankara (rMVA) or plasmid transfection, individual NiV matrix (M), fusion (F) and attachment (G) proteins were all released into culture supernatants in a membrane-associated state as determined by sucrose density gradient flotation and immunoprecipitation. However, co-expression of F and G along with M revealed a shift in their distribution across the gradient, indicating association with M in VLPs. Protein release was also altered depending on the context of viral proteins being expressed, with F, G and nucleocapsid (N) protein reducing M release, and N release dependent on the co-expression of M. Immunoelectron microscopy and density analysis revealed VLPs that were similar to authentic virus. Differences in the budding dynamics of NiV proteins were also noted between rMVA and plasmid based strategies, suggesting that over-expression by poxvirus may not be appropriate for studying the details of recombinant virus particle assembly and release. CONCLUSION: Taken together, the results indicate that NiV M, F, and G each possess some ability to bud from expressing cells, and that co-expression of these viral proteins results in a more organized budding process with M playing a central role. These findings will aid our understanding of paramyxovirus particle assembly in general and could help facilitate the development of a novel vaccine approach for henipaviruses

Measurement of the neutrino component of an anti-neutrino beam observed by a non-magnetized detector

Two independent methods are employed to measure the neutrino flux of the anti-neutrino-mode beam observed by the MiniBooNE detector. The first method compares data to simulated event rates in a high purity \numu induced charged-current single \pip (CC1\pip) sample while the second exploits the difference between the angular distributions of muons created in \numu and \numub charged-current quasi-elastic (CCQE) interactions. The results from both analyses indicate the prediction of the neutrino flux component of the pre-dominately anti-neutrino beam is over-estimated - the CC1\pip analysis indicates the predicted \numu flux should be scaled by $0.76 \pm 0.11$, while the CCQE angular fit yields $0.65 \pm 0.23$. The energy spectrum of the flux prediction is checked by repeating the analyses in bins of reconstructed neutrino energy, and the results show that the spectral shape is well modeled. These analyses are a demonstration of techniques for measuring the neutrino contamination of anti-neutrino beams observed by future non-magnetized detectors.Comment: 15 pages, 7 figures, published in Physical Review D, latest version reflects changes from referee comment

Genomic catastrophes frequently arise in esophageal adenocarcinoma and drive tumorigenesis

Oesophageal adenocarcinoma (EAC) incidence is rapidly increasing in Western countries. A better understanding of EAC underpins efforts to improve early detection and treatment outcomes. While large EAC exome sequencing efforts to date have found recurrent loss-offunction mutations, oncogenic driving events have been underrepresented. Here we use a combination of whole-genome sequencing (WGS) and single-nucleotide polymorphism-array profiling to show that genomic catastrophes are frequent in EAC, with almost a third (32%, n¼40/123) undergoing chromothriptic events. WGS of 22 EAC cases show that catastrophes may lead to oncogene amplification through chromothripsis-derived double-minute chromosome formation (MYC and MDM2) or breakage-fusion-bridge (KRAS, MDM2 and RFC3). Telomere shortening is more prominent in EACs bearing localized complex rearrangements. Mutational signature analysis also confirms that extreme genomic instability in EAC can be driven by somatic BRCA2 mutations. These findings suggest that genomic catastrophes have a significant role in the malignant transformation of EAC

An empirical algorithm for light absorption by ocean water based on color

Empirical algorithms for the total absorption coefficient and absorption coefficient by pigments for surface waters at 440 nm were developed by applying a quadratic formula that combines two spectral ratios of remote-sensing reflectance. For total absorption coefficients ranging from 0.02 to 2.0 m⁻¹, a goodness of fit was achieved between the measured and modeled data with a root-mean-squared difference between the measured and modeled values for log10 scale(RMSDₗₒ₁₀) of 0.062 (15.3% for linear scale, number of samples N = 63), while RMSDₗₒ₁₀ is 0.111 ( 29.1% for linear scale, N = 126) for pigment absorption (ranging from 0.01 to 1.0 m⁻¹). As alternatives to pigment concentration algorithms, the absorption algorithms developed can be applied to the coastal zone color scanner and sea-viewing wide-field-of-view sensor data to derive inherent optical properties of the ocean. For the same data sets, we also directly related the chlorophyll a concentrations to the spectral ratios and obtained an RMSDₗₒ₁₀ value of 0.218 (65.2% for linear scale, N = 120) for concentrations ranging from 0.06 to 50.0 mg m⁻³. These results indicate that it is more accurate to estimate the absorption coefficients than the pigment concentrations from remotely sensed data. This is likely due to the fact that for the broad range of waters studied the pigment-specific absorption coefficient at 440nm ranged from 0.02 to 0.2 m² (mg chl)⁻¹. As an indirect test of the algorithms developed, the chlorophyll a concentration algorithm is applied to an independent global dataset and an RMSDₗₒ₁₀ of 0.191( 55.2% for linear scale, N = 919) is obtained. There is no independent global absorption data set available as yet to test the absorption algorithms

First Measurements of Inclusive Muon Neutrino Charged Current Differential Cross Sections on Argon

The ArgoNeuT collaboration presents the first measurements of inclusive muon neutrino charged current differential cross sections on argon. Obtained in the NuMI neutrino beamline at Fermilab, the results are reported in terms of outgoing muon angle and momentum. The data are consistent with the Monte Carlo expectation across the full range of kinematics sampled, $0^\circ$$<\theta_\mu$$<36^\circ$ and 0$<P_\mu$$<25$ GeV/c. Along with confirming the viability of liquid argon time projection chamber technology for neutrino detection, the measurements allow tests of low energy neutrino scattering models important for interpreting results from long baseline neutrino oscillation experiments designed to investigate CP violation and the orientation of the neutrino mass hierarchy.Comment: 5 pages, 3 figure

Cre recombinase expression cooperates with homozygous FLT3 internal tandem duplication knockin mouse model to induce acute myeloid leukemia

Murine models offer a valuable tool to recapitulate genetically defined subtypes of AML, and to assess the potential of compound mutations and clonal evolution during disease progression. This is of particular importance for difficult to treat leukemias such as FLT3 internal tandem duplication (ITD) positive AML. While conditional gene targeting by Cre recombinase is a powerful technology that has revolutionized biomedical research, consequences of Cre expression such as lack of fidelity, toxicity or off-target effects need to be taken into consideration. We report on a transgenic murine model of FLT3-ITD induced disease, where Cre recombinase expression alone, and in the absence of a conditional allele, gives rise to an aggressive leukemia phenotype. Here, expression of various Cre recombinases leads to polyclonal expansion of FLT3(ITD/ITD) progenitor cells, induction of a differentiation block and activation of Myc-dependent gene expression programs. Our report is intended to alert the scientific community of potential risks associated with using this specific mouse model and of unexpected effects of Cre expression when investigating cooperative oncogenic mutations in murine models of cancer

When TADs go bad: chromatin structure and nuclear organisation in human disease

Chromatin in the interphase nucleus is organised as a hierarchical series of structural domains, including self-interacting domains called topologically associating domains (TADs). This arrangement is thought to bring enhancers into closer physical proximity with their target genes, which often are located hundreds of kilobases away in linear genomic distance. TADs are demarcated by boundary regions bound by architectural proteins, such as CTCF and cohesin, although much remains to be discovered about the structure and function of these domains. Recent studies of TAD boundaries disrupted in engineered mouse models show that boundary mutations can recapitulate human developmental disorders as a result of aberrant promoter-enhancer interactions in the affected TADs. Similar boundary disruptions in certain cancers can result in oncogene overexpression, and CTCF binding sites at boundaries appear to be hyper-mutated across cancers. Further insights into chromatin organisation, in parallel with accumulating whole genome sequence data for disease cohorts, are likely to yield additional valuable insights into the roles of noncoding sequence variation in human disease

Safety and utility of image-guided research biopsies in relapsed high-grade serous ovarian carcinoma-experience of the BriTROC consortium.

BACKGROUND: Investigating tumour evolution and acquired chemotherapy resistance requires analysis of sequential tumour material. We describe the feasibility of obtaining research biopsies in women with relapsed ovarian high-grade serous carcinoma (HGSC). METHODS: Women with relapsed ovarian HGSC underwent either image-guided biopsy or intra-operative biopsy during secondary debulking, and samples were fixed in methanol-based fixative. Tagged-amplicon sequencing was performed on biopsy DNA. RESULTS: We screened 519 patients in order to enrol 220. Two hundred and two patients underwent successful biopsy, 118 of which were image-guided. There were 22 study-related adverse events (AE) in the image-guided biopsies, all grades 1 and 2; pain was the commonest AE. There were pre-specified significant AE in 3/118 biopsies (2.5%). 87% biopsies were fit-for-purpose for genomic analyses. Median DNA yield was 2.87 μg, and was higher in biopsies utilising 14 G or 16 G needles compared to 18 G. TP53 mutations were identified in 94.4% patients. CONCLUSIONS: Obtaining tumour biopsies for research in relapsed HGSC is safe and feasible. Adverse events are rare. The large majority of biopsies yield sufficient DNA for genomic analyses-we recommend use of larger gauge needles and methanol fixation for such biopsies, as DNA yields are higher but with no increase in AEs

Author Correction: Nuclear-mitochondrial DNA segments resemble paternally inherited mitochondrial DNA in humans

An amendment to this paper has been published and can be accessed via a link at the top of the paper

Somatic point mutation calling in low cellularity tumors

Somatic mutation calling from next-generation sequencing data remains a challenge due to the difficulties of distinguishing true somatic events from artifacts arising from PCR, sequencing errors or mis-mapping. Tumor cellularity or purity, sub-clonality and copy number changes also confound the identification of true somatic events against a background of germline variants. We have developed a heuristic strategy and software (http://www.qcmg.org/bioinformatics/qsnp/) for somatic mutation calling in samples with low tumor content and we show the superior sensitivity and precision of our approach using a previously sequenced cell line, a series of tumor/normal admixtures, and 3,253 putative somatic SNVs verified on an orthogonal platform.Karin S. Kassahn, Oliver Holmes, Katia Nones, Ann-Marie Patch, David K. Miller, Angelika N. Christ, Ivon Harliwong, Timothy J. Bruxner, Qinying Xu, Matthew Anderson, Scott Wood, Conrad Leonard, Darrin Taylor, Felicity Newell, Sarah Song, Senel Idrisoglu, Craig Nourse, Ehsan Nourbakhsh, Suzanne Manning, Shivangi Wani, Anita Steptoe, Marina Pajic, Mark J. Cowley, Mark Pinese, David K. Chang, Anthony J. Gill, Amber L. Johns, Jianmin Wu, Peter J. Wilson, Lynn Fink, Andrew V. Biankin, Nicola Waddell, Sean M. Grimmond, John V. Pearso