Search results for "Sequencing"

Suppression of oncogenic lethality by reintegration oflethal (2) giant larvae DNA sequence into thedrosophila genome

1986

Putative Breast Cancer Driver Mutations in TBX3 Cause Impaired Transcriptional Repression

2015

The closely related T-box transcription factors TBX2 and TBX3 are frequently overexpressed in melanoma and various types of human cancers, in particular, breast cancer. The overexpression of TBX2 and TBX3 can have several cellular effects, among them suppression of senescence, promotion of epithelial–mesenchymal transition, and invasive cell motility. In contrast, loss of function of TBX3 and most other human T-box genes causes developmental haploinsufficiency syndromes. Stephens and colleagues (1), by exome sequencing of breast tumor samples, identified five different mutations in TBX3, all affecting the DNA-binding T-domain. One in-frame deletion of a single amino acid, p.N212delN, was ob…

A high-throughput genome-wide siRNA screen for ciliogenesis identifies new ciliary functional components and ciliopathy genes.

2015

Defects in primary cilium biogenesis underlie the ciliopathies, a growing group of genetic disorders. We describe the first whole genome siRNA-based reverse genetics screen for defects in biogenesis and/or maintenance of the primary cilium, obtaining a global resource for investigation and interventions into the processes that are critical for the ciliary system. In total, we identified 83 candidate ciliogenesis and ciliopathy genes, including 15 components of the ubiquitin-proteasome system. The validated hits also include 12 encoding G-protein-coupled receptors, and three encoding pre-mRNA processing factors (PRPF6, PRPF8 and PRPF31) mutated in autosomal dominant retinitis pigmentosa. Com…

Evolution of small prokaryotic genomes

2015

As revealed by genome sequencing, the biology of prokaryotes with reduced genomes is strikingly diverse. These include free-living prokaryotes with ∼800 genes as well as endosymbiotic bacteria with as few as ∼140 genes. Comparative genomics is revealing the evolutionary mechanisms that led to these small genomes. In the case of free-living prokaryotes, natural selection directly favored genome reduction, while in the case of endosymbiotic prokaryotes neutral processes played a more prominent role. However, new experimental data suggest that selective processes may be at operation as well for endosymbiotic prokaryotes at least during the first stages of genome reduction. Endosymbiotic prokar…

SARS-CoV-2 genome surveillance in Mainz, Germany, reveals convergent origin of the N501Y spike mutation in a hospital setting

2021

AbstractWhile establishing a regional SARS-Cov-2 variant surveillance by genome sequencing, we have identified three infected individuals in a clinical setting (two long-term hospitalized patients and a nurse) that shared the spike N501Y mutation within a genotype background distinct from the current viral variants of concern. We suggest that the adaptive N501Y mutation, known to increase SARS-CoV-2 transmissibility, arose by convergent evolution around December in Mainz, Germany. Hospitalized patients with a compromised immune system may be a potential source of novel viral variants, which calls for monitoring viral evolution by genome sequencing in clinical settings.

2004

Background As an alternative to direct DNA sequencing of PCR products, random PCR-RFLP is an efficient technique to discriminate between species. The PCR-RFLP-method is an inexpensive tool in forensic science, even if the template is degraded or contains only traces of DNA from various species.

The impact of next-generation sequencing technology on preimplantation genetic diagnosis and screening.

2013

Largely because of efforts required to complete the Human Genome Project, DNA sequencing has undergone a steady transformation with still-ongoing developments of high-throughput sequencing machines for which the cost per reaction is falling drastically. Similarly, the fast-changing landscape of reproductive technologies has been improved by genetic approaches. Preimplantation genetic diagnosis and screening were established more than two decades ago for selecting genetically normal embryos to avoid inherited diseases and to give the highest potential to achieve stable pregnancies. Most recent additions to the IVF practices (blastocyst/trophectoderm biopsy, embryo vitrification) and adoption…

Adaptive response to wine selective pressures shapes the genome of a Saccharomyces interspecies hybrid

2021

During industrial processes, yeasts are exposed to harsh conditions, which eventually lead to adaptation of the strains. In the laboratory, it is possible to use experimental evolution to link the evolutionary biology response to these adaptation pressures for the industrial improvement of a specific yeast strain. In this work, we aimed to study the adaptation of a wine industrial yeast in stress conditions of the high ethanol concentrations present in stopped fermentations and secondary fermentations in the processes of champagne production. We used a commercial Saccharomyces cerevisiae × S. uvarum hybrid and assessed its adaptation in a modified synthetic must (M-SM) containing high ethan…

A sensitive issue: Pyrosequencing as a valuable forensic SNP typing platform

2006

Analysing minute amounts of DNA is a routine challenge in forensics in part due to the poor sensitivity of an instrument and its inability to detect results from forensic samples. In this study, the sensitivity of the Pyrosequencing method is investigated using varying concentrations of DNA and five autosomal single nucleotide polymorphisms in singleplex on both available instrument models; the PSQ™ 96MA and PSQ™ HS 96A. A detailed comparison of the two models was completed while establishing a lower limit of detection on both instruments to give results supporting the use of Pyrosequencing as a valuable forensic SNP typing platform. © 2005 Elsevier B.V. All rights reserved.

Amplified fragment length polymorphisms and sequence data in the phylogenetic analysis of polyploids: multiple origins of Veronica cymbalaria (Planta…

2007

Summary • The origin of polyploid Veronica cymbalaria (Plantaginaceae) was investigated using DNA sequence data and amplified fragment length polymorphism (AFLP) fingerprints to reveal the parentage of this taxon. The use of AFLP fingerprints in phylogenetic analysis is problematic and various methods have therefore been compared. • DNA sequence data (for the internal transcribed spacer (ITS) region and the plastid trnL-F region (trnL intron, 3’exon, and trnL-F spacer)) and polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) analysis of the ITS region suggested a reliable hypothesis for the evolution of the V. cymbalaria complex. This hypothesis allowed evaluation …