Learning mutational graphs of individual tumour evolution from single-cell and multi-region sequencing data

Background. A large number of algorithms is being developed to reconstruct evolutionary models of individual tumours from genome sequencing data. Most methods can analyze multiple samples collected either through bulk multi-region sequencing experiments or the sequencing of individual cancer cells. However, rarely the same method can support both data types. Results. We introduce TRaIT, a computational framework to infer mutational graphs that model the accumulation of multiple types of somatic alterations driving tumour evolution. Compared to other tools, TRaIT supports multi-region and single-cell sequencing data within the same statistical framework, and delivers expressive models that capture many complex evolutionary phenomena. TRaIT improves accuracy, robustness to data-specific errors and computational complexity compared to competing methods. Conclusions. We show that the application of TRaIT to single-cell and multi-region cancer datasets can produce accurate and reliable models of single-tumour evolution, quantify the extent of intra-tumour heterogeneity and generate new testable experimental hypotheses

International Coordination of Long-Term Ocean Biology Time Series Derived from Satellite Ocean Color Data

[ABSTRACT] In this paper, we will describe plans to coordinate the initial development of long-term ocean biology time series derived from global ocean color observations acquired by the United States, Japan and Europe, Specifically, we have been commissioned by the International Ocean Color Coordinating Group (IOCCG) to coordinate the development of merged products derived from the OCTS, SeaWiFS, MODIS, MERIS and GLI imagers. Each of these missions will have been launched by the year 2002 and will have produced global ocean color data products. Our goal is to develop and document the procedures to be used by each space agency (NASA, NASDA, and ESA) to merge chlorophyll, primary productivity, and other products from these missions. This coordination is required to initiate the production of long-term ocean biology time series which will be continued operationally beyond 2002. The purpose of the time series is to monitor interannual to decadal-scale variability in oceanic primary productivity and to study the effects of environmental change on upper ocean biogeochemical processes

List of identified proteins from GeLC-MS/MS analysis of size exclusion chromatography fraction 2.

a<p>UniprotKB accession number.</p>b<p>Bands in which the protein was identified.</p>c<p>Percentage content according to label free quantitation approach.</p

Summary of the ELISA results obtained with the Ag5 enriched antigen test and four commercial kits.

<p>Summary of the ELISA results obtained with the Ag5 enriched antigen test and four commercial kits.</p

Immunoreactive bands subjected to mass spectrometry analysis.

<p>HCF was separated by SDS-PAGE and the resulting gel was cut in two parts, one of them subjected to western blot experiment with serum 1, the other part stained and further processed for protein identification Left: Immunoreactive profile observed by western immunoblotting on non-reduced (N) and reduced (R) HCF samples. Right: reactive bands excised from the SDS-PAGE gel and subjected to LC-MS/MS identification. M: molecular weight markers.</p

SDS-PAGE and relative protein abundance of fraction 2 from size exclusion chromatography of sheep HCF.

<p>A: Laemmli buffer with (R) or without 400 mM DTT (N) was added to aliquots of 500 ng (lanes 1N-1R), 1 µg (lanes 2N-2R) and 2 µg (lanes 3N-3R) of size exclusion chromatography fraction 2, and subjected to SDS-PAGE on 4–10% acrylamide gel. Lane M: molecular weight markers. Gel was silver stained and then analyzed by GeLC-MS/MS, by cutting lanes 3N and 3R in 7 bands (a–g) each. B: pie chart representing the relative protein abundance of fraction 2 from GeLC-MS/MS analysis of lane 3R. According to label free quantitation, Ag5 represents the most abundant component of the fraction, reaching about 63% of the total content.</p

SDS-PAGE separation of sheep HCF.

<p>Two lung (lanes 1–2, 5–6) and two liver (lanes 3–4, 7–8) HCF samples were separated under non-reducing (N, lanes 1–4) and reducing conditions (R, lanes 5–8) by SDS-PAGE on 15% acrylamide gels. Each sample was loaded after concentration and desalting by ultrafiltration. Due to the different starting protein concentrations, different volumes of each sample, ranging from 7.5 µL to 17.5 µL, where used to reach loads of 20 µg/lane. Coomassie Blue staining was performed. Lane M: molecular weight markers.</p

Comparative evaluation of Ag5 and commercial ELISA kits.

<p>Boxplots summarizing the absorbance values obtained with the Ag5 preparation and commercial ELISA kits on CE patients and control subjects. Patient and control sera are plotted according to the clinical status. The dashed and dotted lines indicate the upper and lower cutoff values, respectively. ABS: absorbance at the wavelength required for each assay. Differences in absorbance between the patient and control groups were statistically significant for all the assays (P<0.001).</p

List of identified proteins from selected SDS-PAGE bands of Figure 1.

a<p>UniprotKB accession number.</p

Western immunoblotting of human sera against Ag5 enriched preparation.

<p>Fraction 2 from size exclusion chromatography of HCF was used as antigen in western blotting experiments under non-reducing conditions. Sera from CE patients (1–13) and control subjects (14–24) were tested against a total of 300 ng of protein sample loaded in each single-well gel; this amount corresponds approximately to about 10 ng of proteins per multiscreen slot. All CE patients sera react against the Ag5 protein band, although with a variable intensity probably depending on the antibody titer of each serum. Moreover, control sera do not give any non-specific response. All sera were tested in at least three separate experiments. The molecular weight region of Ag5 (60 kDa) is indicated on the left.</p