Search results for "Recombination"

Mitochondrial introgression suggests extensive ancestral hybridization events among Saccharomyces species.

2017

Horizontal gene transfer (HGT) in eukaryotic plastids and mitochondrial genomes is common, and plays an important role in organism evolution. In yeasts, recent mitochondrial HGT has been suggested between S. cerevisiae and S. paradoxus. However, few strains have been explored given the lack of accurate mitochondrial genome annotations. Mitochondrial genome sequences are important to understand how frequent these introgressions occur, and their role in cytonuclear incompatibilities and fitness. Indeed, most of the Bateson-Dobzhansky-Muller genetic incompatibilities described in yeasts are driven by cytonuclear incompatibilities. We herein explored the mitochondrial inheritance of several wor…

Mechanisms of viral mutation

2016

The remarkable capacity of some viruses to adapt to new hosts and environments is highly dependent on their ability to generate de novo diversity in a short period of time. Rates of spontaneous mutation vary amply among viruses. RNA viruses mutate faster than DNA viruses, single-stranded viruses mutate faster than double-strand virus, and genome size appears to correlate negatively with mutation rate. Viral mutation rates are modulated at different levels, including polymerase fidelity, sequence context, template secondary structure, cellular microenvironment, replication mechanisms, proofreading, and access to post-replicative repair. Additionally, massive numbers of mutations can be intro…

Inherited variants in XRCC2 and the risk of breast cancer

2019

Background XRCC2 participates in homologous recombination and in DNA repair. XRCC2 has been reported to be a breast cancer susceptibility gene and is now included in several breast cancer susceptibility gene panels. Methods We sequenced XRCC2 in 617 Polish women with familial breast cancer and found a founder mutation. We then genotyped 12,617 women with breast cancer and 4599 controls for the XRCC2 founder mutation. Results We identified a recurrent truncating mutation of XRCC2 (c.96delT, p.Phe32fs) in 3 of 617 patients with familial breast cancer who were sequenced. The c.96delT mutation was then detected in 29 of 12,617 unselected breast cancer cases (0.23%) compared to 11 of 4599 cancer…

New Insights into the Genome Organization of Yeast Killer Viruses Based on “Atypical” Killer Strains Characterized by High-Throughput Sequencing

2017

Viral M-dsRNAs encoding yeast killer toxins share similar genomic organization, but no overall sequence identity. The dsRNA full-length sequences of several known M-viruses either have yet to be completed, or they were shorter than estimated by agarose gel electrophoresis. High-throughput sequencing was used to analyze some M-dsRNAs previously sequenced by traditional techniques, and new dsRNAs from atypical killer strains of Saccharomyces cerevisiae and Torulaspora delbrueckii. All dsRNAs expected to be present in a given yeast strain were reliably detected and sequenced, and the previously-known sequences were confirmed. The few discrepancies between viral variants were mostly located aro…

Telomere Length Determines TERRA and R-Loop Regulation through the Cell Cycle

2017

Maintenance of a minimal telomere length is essential to prevent cellular senescence. When critically short telomeres arise in the absence of telomerase, they can be repaired by homology-directed repair (HDR) to prevent premature senescence onset. It is unclear why specifically the shortest telomeres are targeted for HDR. We demonstrate that the non-coding RNA TERRA accumulates as HDR-promoting RNA-DNA hybrids (R-loops) preferentially at very short telomeres. The increased level of TERRA and R-loops, exclusively at short telomeres, is due to a local defect in RNA degradation by the Rat1 and RNase H2 nucleases, respectively. Consequently, the coordination of TERRA degradation with telomere r…

Conditional Gene-Targeting in Mice: Problems and Solutions.

2018

Comparison of CRISPR and marker based methods for the engineering of phage T7

2020

With the recent rise in interest in using lytic bacteriophages as therapeutic agents, there is an urgent requirement to understand their fundamental biology to enable the engineering of their genomes. Current methods of phage engineering rely on homologous recombination, followed by a system of selection to identify recombinant phages. For bacteriophage T7, the host genescmkortrxhave been used as a selection mechanism along with both type I and II CRISPR systems to select against wild-type phage and enrich for the desired mutant. Here we systematically compare all three systems; we show that the use of marker-based selection is the most efficient method and we use this to generate multiple …

2020

Telomeres have the ability to adopt a lariat conformation and hence, engage in long and short distance intra-chromosome interactions. Budding yeast telomeres were proposed to fold back into subtelomeric regions, but a robust assay to quantitatively characterize this structure has been lacking. Therefore, it is not well understood how the interactions between telomeres and non-telomeric regions are established and regulated. We employ a telomere chromosome conformation capture (Telo-3C) approach to directly analyze telomere folding and its maintenance inS.cerevisiae. We identify the histone modifiers Sir2, Sin3 and Set2 as critical regulators for telomere folding, which suggests that a disti…

Measurement of spin-orbital angular momentum interactions in relativistic heavy-ion collisions

2020

The first evidence of spin alignment of vector mesons ($K^{*0}$ and $\phi$) in heavy-ion collisions at the Large Hadron Collider (LHC) is reported. The spin density matrix element $\rho_{00}$ is measured at midrapidity ($|y| <$ 0.5) in Pb-Pb collisions at a center-of-mass energy ($\sqrt{s_{\rm NN}}$) of 2.76 TeV with the ALICE detector. $\rho_{00}$ values are found to be less than 1/3 (1/3 implies no spin alignment) at low transverse momentum ($p_{\rm T} <$ 2 GeV/$c$) for $K^{*0}$ and $\phi$ at a level of 3$\sigma$ and 2$\sigma$, respectively. No significant spin alignment is observed for the $K^0_S$ meson (spin = 0) in Pb-Pb collisions and for the vector mesons in $pp$ collisions. The meas…

Incorporation of Li dopant into Cu2ZnSnSe4 photovoltaic absorber: hybrid-functional calculations

2015

We have studied the formation of Li extrinsic defects in CuZnSnSe by first-principles hybrid functional calculations. Li atoms in the Cu site (Li) and Li atoms in the Se site (Li) are the most and the least stable point defect, respectively. The formation energies of two Li interstitial defects with different numbers of nearest neighbors are the same. These interstitial point defects act as a donor but do not create gap states. Formation of the acceptor point defects (Li and Li) is less likely in p-type CuZnSnSe compared with n-type CuZnSnSe. In contrast to Li which does not create gap states, the formation of Li creates two charge transition levels in the middle of the bandgap which might …