Search results for "Sequence analysi"

Evolutionary Study of Disorder in Protein Sequences

2020

Intrinsically disordered proteins (IDPs) contain regions lacking intrinsic globular structure (intrinsically disordered regions, IDRs). IDPs are present across the tree of life, with great variability of IDR type and frequency even between closely related taxa. To investigate the function of IDRs, we evaluated and compared the distribution of disorder content in 10,695 reference proteomes, confirming its high variability and finding certain correlation along the Euteleostomi (bony vertebrates) lineage to number of cell types. We used the comparison of orthologs to study the function of disorder related to increase in cell types, observing that multiple interacting subunits of protein comple…

A New Feature Selection Methodology for K-mers Representation of DNA Sequences

2015

DNA sequence decomposition into k-mers and their frequency counting, defines a mapping of a sequence into a numerical space by a numerical feature vector of fixed length. This simple process allows to compare sequences in an alignment free way, using common similarities and distance functions on the numerical codomain of the mapping. The most common used decomposition uses all the substrings of a fixed length k making the codomain of exponential dimension. This obviously can affect the time complexity of the similarity computation, and in general of the machine learning algorithm used for the purpose of sequence analysis. Moreover, the presence of possible noisy features can also affect the…

Sustainable Working Life Patterns in a Swedish Twin Cohort : Age-Related Sequences of Sickness Absence, Disability Pension, Unemployment, and Prematu…

2022

We aimed to investigate sustainable working life via age-related sequences of sickness absence (SA), disability pension (DP), unemployment (UE), premature death, and the influence of individual characteristics, accounting for familial confounding. The sample included monozygotic (MZ) and dizygotic (DZ) same-sexed twin pairs with register data (n = 47,450) that were followed for 10 years in four age cohorts: 26–35 (n = 9892), 36–45 (n = 10,620), 46–55 (n = 12,964) and 56–65 (n = 13,974). A sequence analysis was done in a 7-element state space: 1. “Sustainable working life”: SA/DP 0–30 days and UE 0–90 days; 2. “Unemployment >90 days”: SA/DP 0–30 days and UE > 90 days; 3. “Moderate SA/DP”: SA…

Statistical analysis of life sequence data

2016

Immunoaffinity purification and characterization of mitochondrial membrane-bound D-3-hydroxybutyrate dehydrogenase from Jaculus orientalis.

2008

Abstract Background The interconversion of two important energy metabolites, 3-hydroxybutyrate and acetoacetate (the major ketone bodies), is catalyzed by D-3-hydroxybutyrate dehydrogenase (BDH1: EC 1.1.1.30), a NAD+-dependent enzyme. The eukaryotic enzyme is bound to the mitochondrial inner membrane and harbors a unique lecithin-dependent activity. Here, we report an advanced purification method of the mammalian BDH applied to the liver enzyme from jerboa (Jaculus orientalis), a hibernating rodent adapted to extreme diet and environmental conditions. Results Purifying BDH from jerboa liver overcomes its low specific activity in mitochondria for further biochemical characterization of the e…

The transcriptome analysis of Strongyloides stercoralis L3i larvae reveals targets for intervention in a neglected disease.

2012

Background: Strongyloidiasis is one of the most neglected diseases distributed worldwide with endemic areas in developed countries, where chronic infections are life threatening. Despite its impact, very little is known about the molecular biology of the parasite involved and its interplay with its hosts. Next generation sequencing technologies now provide unique opportunities to rapidly address these questions. Principal Findings: Here we present the first transcriptome of the third larval stage of S. stercoralis using 454 sequencing coupled with semi-automated bioinformatic analyses. 253,266 raw sequence reads were assembled into 11,250 contiguous sequences, most of which were novel. 8037…

Changes in gene expression during adaptation of Listeria monocytogenes to the soil environment

2011

project SEST 009; International audience; Listeria monocytogenes is a ubiquitous opportunistic pathogen responsible for listeriosis. In order to study the processes underlying its ability to adapt to the soil environment, whole-genome arrays were used to analyse transcriptome modifications 15 minutes, 30 minutes and 18 h after inoculation of L. monocytogenes EGD-e in soil extracts. Growth was observed within the first day of incubation and large numbers were still detected in soil extract and soil microcosms one year after the start of the experiment. Major transcriptional reprofiling was observed. Nutrient acquisition mechanisms (phosphoenolpyruvate-dependent phosphotransferase systems and…

Combining Sequence Analysis and Hidden Markov Models in the Analysis of Complex Life Sequence Data

2018

Life course data often consists of multiple parallel sequences, one for each life domain of interest. Multichannel sequence analysis has been used for computing pairwise dissimilarities and finding clusters in this type of multichannel (or multidimensional) sequence data. Describing and visualizing such data is, however, often challenging. We propose an approach for compressing, interpreting, and visualizing the information within multichannel sequences by finding (1) groups of similar trajectories and (2) similar phases within trajectories belonging to the same group. For these tasks we combine multichannel sequence analysis and hidden Markov modelling. We illustrate this approach with an …

Identification of markers for the selection of patients undergoing renal cell carcinoma-specific immunotherapy

2003

Renal cell carcinoma (RCC) represents the most common malignant tumor in the kidney and is resistant to conventional therapies. The diagnosis of RCC is often delayed leading to progression and metastatic spread of the disease. Thus, validated markers for the early detection of the disease as well as selection of patients undergoing specific therapy is urgently needed. Using treatment with the monoclonal antibody (mAb) G250 as a model, proteome-based strategies were implemented for the identification of markers which may allow the discrimination between responders and nonresponders prior to application of G250-mediated immunotherapy. Flow cytometry revealed G250 surface expression in approxi…

The Activation Pattern of the Antioxidant Enzymes in the Right Ventricle of Rat in Response to Pressure Overload is of Heart Failure Type

2003

In the left ventricle subjected to pressure overload activity, the antioxidant enzymes increased at the hyperfunctional stage. During the transition to heart failure, these enzymes are down-regulated, oxidative stress increases, and apoptosis progresses. Maladaptative activation of the antioxidant enzymes at an early stage may contribute to the intrinsic vulnerability of right ventricle to pressure overload. The authors studied changes in expression and activity of the enzymes manganese and copper-zinc superoxide dismutases, glutathione peroxidase, and catalase in the right ventricle of rat following induction of pulmonary hypertension by injection of monocrotaline. Increase in the manganes…