Search results for "EXPRESSION"

Machine Learning Unveils Proteotypic Mimicry in Genetically Defined SCN Variants

2019

Background Novel computational algorithms for multi-omics analysis bear great potential to highlight pathomechanisms of monogenic diseases. We recently defined the in-depth proteome of primary human neutrophil granulocytes (PMID 30630937). Here, we ask the question whether proteotypic patterns differ between defined genetic subtypes associated with severe congenital neutropenia (SCN). We focus on two novel genetic variants in constituents of the signal recognition particle (SRPRA and SRP19) and previously reported SCN genotypes SRP54, HAX1, and ELANE. Methods We analyzed proteomes of highly purified neutrophil granulocytes from a total of 26 SCN patients, including 5 with homozygous splice …

Efficient High-Order Iterative Methods for Solving Nonlinear Systems and Their Application on Heat Conduction Problems

2017

[EN] For solving nonlinear systems of big size, such as those obtained by applying finite differences for approximating the solution of diffusion problem and heat conduction equations, three-step iterative methods with eighth-order local convergence are presented. The computational efficiency of the new methods is compared with those of some known ones, obtaining good conclusions, due to the particular structure of the iterative expression of the proposed methods. Numerical comparisons are made with the same existing methods, on standard nonlinear systems and a nonlinear one-dimensional heat conduction equation by transforming it in a nonlinear system by using finite differences. From these…

Unravelling the DNA sequences carried by Streptomyces coelicolor membrane vesicles

2022

AbstractMembrane vesicles (MVs) are spherical particles with nanoscale dimensions and characterized by the presence of diverse cargos, such as nucleic acids, proteins, lipids, and cellular metabolites. Many examples of (micro)organisms producing MVs are reported in literature. Among them, bacterial MVs are of particular interest because they are now considered as the fourth mechanism of horizontal gene transfer. Streptomyces bacteria are well-known for their ecological roles and ability to synthesize bioactive compounds, with Streptomyces coelicolor being the model organism. It was previously demonstrated that it can produce distinct populations of MVs characterized by different protein and…

Data set of the protein expression profiles of Luminal A, Claudin-low and overexpressing HER2+ breast cancer cell lines by iTRAQ labelling and tandem…

2015

Breast cancer is the most common and the leading cause of mortality in women worldwide. There is a dire necessity of the identification of novel molecules useful in diagnosis and prognosis. In this work we determined the differentially expression profiles of four breast cancer cell lines compared to a control cell line. We identified 1020 polypeptides labelled with iTRAQ with more than 95% in confidence. We analysed the common proteins in all breast cancer cell lines through IPA software (IPA core and Biomarkers). In addition, we selected the specific overexpressed and subexpressed proteins of the different molecular classes of breast cancer cell lines, and classified them according to prot…

2016

The perception of infant emotions is an integral part of sensitive caregiving within the mother-child relationship, a maternal ability which develops in mothers during their own attachment history. In this study we address the association between maternal attachment representation and brain activity underlying the perception of infant emotions. Event related potentials (ERPs) of 32 primiparous mothers were assessed during a three stimulus oddball task presenting negative, positive and neutral emotion expressions of infants as target, deviant or standard stimuli. Attachment representation was assessed with the Adult Attachment Interview during pregnancy. Securely attached mothers recognized …

PROX1 transcription factor controls rhabdomyosarcoma growth, stemness, myogenic properties and therapeutic targets

2022

Funding Information: ACKNOWLEDGMENTS. We would like to thank Dr. Tuomas Tammela and Dr. Monika Ehnmann for providing RMS cell lines and Dr. Jenny Högström for discussions and comments during the project. Kirsi Mattinen, Jefim Brodkin, Maxime Laird, Manon Gruchet, Ilse Paetau, Tanja Laakkonen, and Tapio Tainola are acknowledged for their excellent technical help. We also thank the Laboratory Animal Center at the University of Helsinki for expert animal care, the Biomedicum Imaging Unit for microscope support, the Biomedicum Functional Genomics Unit for the RNAseq experiments and the FIMM Technology Centre High Throughput Biomedicine for the drug sensitivity and resistance testing. Our first …

Myelin Basic Protein synthesis is regulated by small non‐coding RNA 715

2012

Oligodendroglial Myelin Basic Protein (MBP) synthesis is essential for myelin formation in the central nervous system. During oligodendrocyte differentiation, MBP mRNA is kept in a translationally silenced state while intracellularly transported, until neuron-derived signals initiate localized MBP translation. Here we identify the small non-coding RNA 715 (sncRNA715) as an inhibitor of MBP translation. SncRNA715 localizes to cytoplasmic granular structures and associates with MBP mRNA transport granule components. We also detect increased levels of sncRNA715 in demyelinated chronic human multiple sclerosis lesions, which contain MBP mRNA but lack MBP protein.

IL12A, MPHOSPH9/CDK2AP1 and RGS1 are novel multiple sclerosis susceptibility loci

2010

A recent meta-analysis identified seven single-nucleotide polymorphisms (SNPs) with suggestive evidence of association with multiple sclerosis (MS). We report an analysis of these polymorphisms in a replication study that includes 8,085 cases and 7,777 controls. A meta-analysis across the replication collections and a joint analysis with the discovery data set were performed. The possible functional consequences of the validated susceptibility loci were explored using RNA expression data. For all of the tested SNPs, the effect observed in the replication phase involved the same allele and the same direction of effect observed in the discovery phase. Three loci exceeded genome-wide significa…

UNCLES: Method for the identification of genes differentially consistently co-expressed in a specific subset of datasets

2015

Background Collective analysis of the increasingly emerging gene expression datasets are required. The recently proposed binarisation of consensus partition matrices (Bi-CoPaM) method can combine clustering results from multiple datasets to identify the subsets of genes which are consistently co-expressed in all of the provided datasets in a tuneable manner. However, results validation and parameter setting are issues that complicate the design of such methods. Moreover, although it is a common practice to test methods by application to synthetic datasets, the mathematical models used to synthesise such datasets are usually based on approximations which may not always be sufficiently repres…

Perception of emotional content in musical performances by 3–7-year- old children

2013

The emotional content expressed through musical performance has become a widely-discussed topic in music psychology during the past two decades. However, empirical evidence regarding children’s abilities in interpreting the emotional content of a musical performance is sparse. We investigated 3–7-year-old children’s abilities to interpret the emotional content expressed through performance features in music. Short musical pieces previously rated as inexpressive of emotion were recorded by three musicians with five emotional expressions (happy, sad, fearful, angry and neutral) and played to 3–7-year-old children ( N = 94), adult non-musicians ( N = 83), and adult musicians ( N = 118) who ma…