Genomic and signalling pathway characterization of the NZM panel of melanoma cell lines: A valuable model for studying the impact of genetic diversity in melanoma

Melanoma is a disease associated with a very high mutation burden and thus the possibility of a diverse range of oncogenic mechanisms that allow it to evade therapeutic interventions and the immune system. Here, we describe the characterization of a panel of 102 cell lines from metastatic melanomas (the NZM lines), including using whole‐exome and RNA sequencing to analyse genetic variants and gene expression changes in a subset of this panel. Lines possessing all major melanoma genotypes were identified, and hierarchical clustering of gene expression profiles revealed four broad subgroups of cell lines. Immunogenotyping identified a range of HLA haplotypes as well as expression of neoantigens and cancer–testis antigens in the lines. Together, these characteristics make the NZM panel a valuable resource for cell‐based, immunological and xenograft studies to better understand the diversity of melanoma biology and the responses of melanoma to therapeutic interventions.     

Empirical Mode Decomposition and Wavelet Transform Based ECG Data Compression Scheme

ObjectiveIn health-care systems, compression is an essential tool to solve the storage and transmission problems. In this regard, this paper reports a new electrocardiogram (ECG) data compression scheme which employs sifting function based empirical mode decomposition (EMD) and discrete wavelet transform.MethodEMD based on sifting function is utilized to get the first intrinsic mode function (IMF). After EMD, the first IMF and four significant sifting functions are combined together. This combination is free from many irrelevant components of the signal. Discrete wavelet transform (DWT) with mother wavelet ‘bior4.4’ is applied to this combination. The transform coefficients obtained after DWT are passed through dead-zone quantization. It discards small transform coefficients lying around zero. Further, integer conversion of coefficients and run-length encoding are utilized to achieve a compressed form of ECG data.ResultsCompression performance of the proposed scheme is evaluated using 48 ECG records of the MIT-BIH arrhythmia database. In the comparison of compression results, it is observed that the proposed method exhibits better performance than many recent ECG compressors. A mean opinion score test is also conducted to evaluate the true quality of the reconstructed ECG signals.ConclusionThe proposed scheme offers better compression performance with preserving the key features of the signal very well.     

Discovery of pyrazolo[1,5-a]pyridines as p110α-selective PI3 kinase inhibitors

We have made a novel series of pyrazolo[1,5-a]pyridines as PI3 kinase inhibitors, and demonstrated their selectivity for the p110α isoform over the other Class Ia PI3 kinases. We investigated the SAR around the pyrazolo[1,5-a]pyridine ring system, and found compound 5x to be a particularly potent example (p110α IC(50) 0.9nM). This compound inhibits cell proliferation and phosphorylation of Akt/PKB, a downstream marker of PI3 kinase activity, and showed in vivo activity in an HCT-116 human xenograft model.     

RV-Typer: A Web Server for Typing of Rhinoviruses Using Alignment-Free Approach

Rhinoviruses (RV) are increasingly being reported to cause mild to severe infections of respiratory tract in humans. RV are antigenically the most diverse species of the genus Enterovirus and family Picornaviridae. There are three species of RV (RV-A, -B and -C), with 80, 32 and 55 serotypes/types, respectively. Antigenic variation is the main limiting factor for development of a cross-protective vaccine against RV.Serotyping of Rhinoviruses is carried out using cross-neutralization assays in cell culture. However, these assays become laborious and time-consuming for the large number of strains. Alternatively, serotyping of RV is carried out by alignment-based phylogeny of both protein and nucleotide sequences of VP1. However, serotyping of RV based on alignment-based phylogeny is a multi-step process, which needs to be repeated every time a new isolate is sequenced. In view of the growing need for serotyping of RV, an alignment-free method based on “return time distribution” (RTD) of amino acid residues in VP1 protein has been developed and implemented in the form of a web server titled RV-Typer. RV-Typer accepts nucleotide or protein sequences as an input and computes return times of di-peptides (k = 2) to assign serotypes. The RV-Typer performs with 100% sensitivity and specificity. It is significantly faster than alignment-based methods. The web server is available at http://bioinfo.net.in/RV-Typer/home.html.     

Effect of various aqueous extracting agents on fluorescence properties of waste tea residue derived carbon dots (WTR-CDs): Comparative spectroscopic analysis

Fluorescent carbon dots (CDs) are one of the important carbonaceous nanomaterials in the area of nanoscience and nanotechnology because of their interesting physical as well as chemical properties. Herein we studied the effect of various aqueous extracting agents on fluorescence properties of waste tea residue-based carbon dots (WTR-CDs). WTR-CDs are firstly synthesized by utilizing kitchen waste-based carbonaceous biomass. To check the role of various aqueous media during the course of WTR-CDs synthesis from carbonized carbon powder, extraction of WTR-CDs was carried out in various kinds of aqueous media viz., only aqueous (100% water, WT), aqueous-alcoholic (10% ethanol, ET), aqueous-acidic (10% acetic acid, AA), and aqueous-basic (10% ammonia, AM). The consequences of extracting agents on the photophysical properties of final WTR-CDs-WT, WTR-CDs-ET, WTR-CDs-AA and WTR-CDs-AM were also discussed in detail. We have observed interesting blue shift fluorescence spectra in acidic medium for WTR-CDs-AA and polar protic solvents compared to polar aprotic medium. The solvatochromic behaviour of WTR-CDs-WT in model polar and non-polar solvent was also studied. The effect of cationic, anionic and non-anionic surfactants on the fluorescence of WTR-CDs-WT was also evaluated. The proposed findings may help researchers in the near future to obtain fast, easy and direct synthesize CDs from a variety of biomass-based precursors under different aqueous conditions.     

Remusatia vivipara lectin and Sclerotium rolfsii lectin interfere with the development and gall formation activity of Meloidogyne incognita in transgenic tomato

Transgenic Research - Root knot nematodes are serious threats to growth and yield of solaneous crops including tomato. In this study, a binary vector carrying Remusatia vivipara...     

Pegasys: software for executing and integrating analyses of biological sequences

Background  

We present Pegasys – a flexible, modular and customizable software system that facilitates the execution and data integration from heterogeneous biological sequence analysis tools.     

A Phenazine based colorimetric and fluorescent chemosensor for sequential detection of Ag+ and I− in aqueous media

A new colorimetric and fluorescent probe MNTPZ based on 1H‐imidazo[4,5‐b]phenazine derivative has been designed and synthesized for successive detection of Ag⁺ and I^?. The probe MNTPZ shows selective colorimetric response by a change in color from yellow to orange and “turn‐off” fluorometric response upon binding with Ag⁺ in DMSO: Water (pH = 7, 1:1, v/v) over other cations. The binding mode of probe MNTPZ to Ag⁺ was studied by Job's plot, ¹H NMR studies, FT‐IR spectroscopy and DFT calculations. Moreover, the situ generated probe MNTPZ + Ag⁺ complex acted as an efficient fluorometric “turn‐on” probe for I^? via Ag⁺ displacement approach. The detection limit of probe MNTPZ for Ag⁺ and the resultant complex probe MNTPZ + Ag⁺ for I^? were determined to be 1.36 μmol/L and 1.03 μmol/L respectively. Notably, the developed probe was successfully used for quantitative determination of I^? in real samples with satisfactory results.     

A drug targeting only p110α can block phosphoinositide 3-kinase signalling and tumour growth in certain cell types

Genetic alterations in PI3K (phosphoinositide 3-kinase) signalling are common in cancer and include deletions in PTEN (phosphatase and tensin homologue deleted on chromosome 10), amplifications of PIK3CA and mutations in two distinct regions of the PIK3CA gene. This suggests drugs targeting PI3K, and p110α in particular, might be useful in treating cancers. Broad-spectrum inhibition of PI3K is effective in preventing growth factor signalling and tumour growth, but suitable inhibitors of p110α have not been available to study the effects of inhibiting this isoform alone. In the present study we characterize a novel small molecule, A66, showing the S-enantiomer to be a highly specific and selective p110α inhibitor. Using molecular modelling and biochemical studies, we explain the basis of this selectivity. Using a panel of isoform-selective inhibitors, we show that insulin signalling to Akt/PKB (protein kinase B) is attenuated by the additive effects of inhibiting p110α/p110β/p110δ in all cell lines tested. However, inhibition of p110α alone was sufficient to block insulin signalling to Akt/PKB in certain cell lines. The responsive cell lines all harboured H1047R mutations in PIK3CA and have high levels of p110α and class-Ia PI3K activity. This may explain the increased sensitivity of these cells to p110α inhibitors. We assessed the activation of Akt/PKB and tumour growth in xenograft models and found that tumours derived from two of the responsive cell lines were also responsive to A66 in vivo. These results show that inhibition of p110α alone has the potential to block growth factor signalling and reduce growth in a subset of tumours.