Search results for "Quotation"

Gut microbiota and aging-A focus on centenarians.

2020

Gut microbiota (GM) is a dynamic organ throughout the lifespan. Aging is a complex process that comprises a plethora of mechanisms such as senescence, immunosenescence and inflammaging, representing important pathways of age-related diseases. GM structure could both influence and be influenced by aging occurring changes within the host. A unique category of long living individuals exists, namely centenarians that have the outstanding capacity to adapt to various challenges. Longevity seems to be associated with certain GM which, among other factors, might render individuals more resistant to age-related diseases and subsequently to long living. Diet, prebiotics, probiotics and synbiotics ma…

Innate and Adaptive Immunity in Aging and Longevity: The Foundation of Resilience

2020

The interrelation of the processes of immunity and senescence now receives an unprecedented emphasis during the COVID-19 pandemic, which brings to the fore the critical need to combat immunosenescence and improve the immune function and resilience of older persons. Here we review the historical origins and the current state of the science of innate and adaptive immunity in aging and longevity. From the modern point of view, innate and adaptive immunity are not only affected by aging but also are important parts of its underlying mechanisms. Excessive levels or activity of antimicrobial peptides, C-reactive protein, complement system, TLR/NF-κB, cGAS/STING/IFN 1,3 and AGEs/RAGE pathways, mye…

2018

Sex differences in lifespan are ubiquitous, but the underlying causal factors remain poorly understood. Inter- and intrasexual social interactions are well known to influence lifespan in many taxa, but it has proved challenging to separate the role of sex-specific behaviours from wider physiological differences between the sexes. To address this problem, we genetically manipulated the sexual identity of the nervous system—and hence sexual behaviour—in Drosophila melanogaster , and measured lifespan under varying social conditions. Consistent with previous studies, masculinization of the nervous system in females induced male-specific courtship behaviour and aggression, while nervous system…

PCSK9-D374Y mediated LDL-R degradation can be functionally inhibited by EGF-A and truncated EGF-A peptides: An in vitro study.

2019

Abstract Background and aims Proprotein convertase subtilisin/kexin type 9 (PCSK9) binds to low density lipoprotein receptor (LDLR) through the LDLR epidermal growth factor-like repeat A (EGF-A) domain and induces receptor internalization and degradation. PCSK9 has emerged as a novel therapeutic target for hypercholesterolemia. Clinical studies with PCSK9 inhibiting antibodies have demonstrated strong LDL-c lowering effects, but other therapeutic approaches using small molecule inhibitors for targeting PCSK9 functions may offer supplementary therapeutic options. The aim of our study was to evaluate the effect of synthetic EGF-A analogs on mutated (D374Y) PCSK9-D374Y mediated LDLR degradatio…

parSRA: A framework for the parallel execution of short read aligners on compute clusters

2018

The growth of next generation sequencing datasets poses as a challenge to the alignment of reads to reference genomes in terms of both accuracy and speed. In this work we present parSRA, a parallel framework to accelerate the execution of existing short read aligners on distributed-memory systems. parSRA can be used to parallelize a variety of short read alignment tools installed in the system without any modification to their source code. We show that our framework provides good scalability on a compute cluster for accelerating the popular BWA-MEM and Bowtie2 aligners. On average, it is able to accelerate sequence alignments on 16 64-core nodes (in total, 1024 cores) with speedup of 10.48 …

ParDRe: faster parallel duplicated reads removal tool for sequencing studies

2016

This is a pre-copyedited, author-produced version of an article accepted for publication in Bioinformatics following peer review. The version of record [insert complete citation information here] is available online at: https://doi.org/10.1093/bioinformatics/btw038 [Abstract] Summary: Current next generation sequencing technologies often generate duplicated or near-duplicated reads that (depending on the application scenario) do not provide any interesting biological information but can increase memory requirements and computational time of downstream analysis. In this work we present ParDRe , a de novo parallel tool to remove duplicated and near-duplicated reads through the clustering of S…

Reference genome assessment from a population scale perspective: an accurate profile of variability and noise.

2017

Abstract Motivation Current plant and animal genomic studies are often based on newly assembled genomes that have not been properly consolidated. In this scenario, misassembled regions can easily lead to false-positive findings. Despite quality control scores are included within genotyping protocols, they are usually employed to evaluate individual sample quality rather than reference sequence reliability. We propose a statistical model that combines quality control scores across samples in order to detect incongruent patterns at every genomic region. Our model is inherently robust since common artifact signals are expected to be shared between independent samples over misassembled regions …

MSAProbs-MPI: parallel multiple sequence aligner for distributed-memory systems

2016

This is a pre-copyedited, author-produced version of an article accepted for publication in Bioinformatics following peer review. The version of recordJorge González-Domínguez, Yongchao Liu, Juan Touriño, Bertil Schmidt; MSAProbs-MPI: parallel multiple sequence aligner for distributed-memory systems, Bioinformatics, Volume 32, Issue 24, 15 December 2016, Pages 3826–3828, https://doi.org/10.1093/bioinformatics/btw558is available online at: https://doi.org/10.1093/bioinformatics/btw558 [Abstracts] MSAProbs is a state-of-the-art protein multiple sequence alignment tool based on hidden Markov models. It can achieve high alignment accuracy at the expense of relatively long runtimes for large-sca…

Simulation-based estimation of branching models for LTR retrotransposons

2017

Abstract Motivation LTR retrotransposons are mobile elements that are able, like retroviruses, to copy and move inside eukaryotic genomes. In the present work, we propose a branching model for studying the propagation of LTR retrotransposons in these genomes. This model allows us to take into account both the positions and the degradation level of LTR retrotransposons copies. In our model, the duplication rate is also allowed to vary with the degradation level. Results Various functions have been implemented in order to simulate their spread and visualization tools are proposed. Based on these simulation tools, we have developed a first method to evaluate the parameters of this propagation …

Competing species system as a qualitative model of radiation therapy

2016

To examine complex features of tumor dynamics we analyze a competing-species lattice model that takes into account the competition for nutrients or space as well as interaction with therapeutic factors such as drugs or radiation. Our model might be interpreted as a certain prey–predator system having three trophic layers: (i) the basal species that might be interpreted as nutrients; (ii) normal and tumor cells that consume nutrients, and (iii) therapeutic factors that might kill either nutrient, normal or tumor cells. Using a wide spectrum of parameters we examined survival of our species and tried to identify the corresponding dynamical regimes. It was found that the radiotherapy influence…