Search results for "genomics"

Pharmacogenomic identification of small molecules for lineage specific manipulation of subventricular zone germinal activity

2017

Strategies for promoting neural regeneration are hindered by the difficulty of manipulating desired neural fates in the brain without complex genetic methods. The subventricular zone (SVZ) is the largest germinal zone of the forebrain and is responsible for the lifelong generation of interneuron subtypes and oligodendrocytes. Here, we have performed a bioinformatics analysis of the transcriptome of dorsal and lateral SVZ in early postnatal mice, including neural stem cells (NSCs) and their immediate progenies, which generate distinct neural lineages. We identified multiple signaling pathways that trigger distinct downstream transcriptional networks to regulate the diversity of neural cells …

Nutrigenetics, nutrigenomics and phenotypic outcomes of dietary low-dose alcohol consumption in the suppression and induction of cancer development: …

2020

It is known that the intake of alcoholic beverages may impair genetic and epigenetic regulatory events with consequent crucial effects on cell phenotypes and that its association with selected genotypes can lead to a different risk of cancer in the population. The aim of this review is to pick up selected studies on this topic and recapitulate some of the biochemical and nutrigenetic/nutrigenomic aspects involved in the impact of dietary low-dose alcohol consumption on the switching-on or -off of tumorigenic pathways. These include i) the existence of predisposing or protective human genotypes and the relationship between dietary compounds and alcohol in the promotion or inhibition of carci…

Letter to the Editor: Solution structure of hypothetical protein TA1414 from Thermoplasma acidophilum

2004

Microarray-Based Determination of Response of Tumor Cells to Cycloshikonin

2011

Metagenomic Analysis of Milk of Healthy and Mastitis-Suffering Women.

2015

Background: Some studies have been conducted to assess the composition of the bacterial communities inhabiting human milk, but they did not evaluate the presence of other microorganisms, such as fungi, archaea, protozoa, or viruses. Objective: This study aimed to compare the metagenome of human milk samples provided by healthy and mastitis-suffering women. Methods: DNA was isolated from human milk samples collected from 10 healthy women and 10 women with symptoms of lactational mastitis. Shotgun libraries from total extracted DNA were constructed and the libraries were sequenced by 454 pyrosequencing. Results: The amount of human DNA sequences was ≥ 90% in all the samples. Among the bacteri…

Whole-Genome Analyses

2014

Abstract Average nucleotide identity (ANI) was proposed almost 10 years ago as a means to compare genetic relatedness among prokaryotic strains. It was found that values around 95% corresponded to the 70% DNA–DNA hybridization cut-off value that is widely used to delineate archaeal and bacterial species. ANI calculations are one of the many aspects and approaches that can be derived from comparative genomic data and used for taxonomic purposes. Here, an overview about the impact and current usage of ANI values is given together with details of the existing user-friendly package tool, the biology-oriented software package JSpecies, which can be used to generate two types of ANI calculations …

On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data

2021

AbstractBackgroundDuring the Neolithic expansion, cattle accompanied humans and spread from their domestication centres to colonize the ancient world. In addition, European cattle occasionally intermingled with both indicine cattle and local aurochs resulting in an exclusive pattern of genetic diversity. Among the most ancient European cattle are breeds that belong to the so-called Podolian trunk, the history of which is still not well established. Here, we used genome-wide single nucleotide polymorphism (SNP) data on 806 individuals belonging to 36 breeds to reconstruct the origin and diversification of Podolian cattle and to provide a reliable scenario of the European colonization, throug…

Potential of ‘Omics’ Technologies for Implementation in Research on Phytotherapeutical Toxicology

2012

Abstract High toxicity is the most common reason why new agents drop out of drug development in the pharmaceutical industry. There is hope that toxicogenomics facilitates the early detection of toxic effects and their molecular mechanisms of action during preclinical studies to remove potentially toxic substances from the development. Herbal remedies consist of mixtures of different herbs, which represent a considerable source of heterogeneity and toxicity. They may be caused by botanical misidentification, contamination with pesticides, heavy metals, organic solvents, microbials and radioactivity. Intentional faked herbal products may contain chemical drugs or hormones. Approaches to apply…

Spectrum of novel mutations found in Waardenburg syndrome types 1 and 2: implications for molecular genetic diagnostics

2013

Objectives Till date, mutations in the genes PAX3 and MITF have been described in Waardenburg syndrome (WS), which is clinically characterised by congenital hearing loss and pigmentation anomalies. Our study intended to determine the frequency of mutations and deletions in these genes, to assess the clinical phenotype in detail and to identify rational priorities for molecular genetic diagnostics procedures. Design Prospective analysis. Patients 19 Caucasian patients with typical features of WS underwent stepwise investigation of PAX3 and MITF . When point mutations and small insertions/deletions were excluded by direct sequencing, copy number analysis by multiplex ligation-dependent probe …

Mapping of 7-methylguanosine (m7G), 3-methylcytidine (m3C), dihydrouridine (D) and 5-hydroxycytidine (ho5C) RNA modifications by AlkAniline-Seq

2021

Precise and reliable mapping of modified nucleotides in RNA is a challenging task in epitranscriptomics analysis. Only deep sequencing-based methods are able to provide both, a single-nucleotide resolution and sufficient selectivity and sensitivity. A number of protocols employing specific chemical reagents to distinguish modified RNA nucleotides from canonical parental residues have already proven their performance. We developed a deep-sequencing analytical pipeline for simultaneous detection of several modified nucleotides of different nature (methylation, hydroxylation, reduction) in RNA. The AlkAniline-Seq protocol uses intrinsic fragility of the N-glycosidic bond present in certain mod…