Road blocks on paleogenomes - polymerase extension profiling reveals the frequency of blocking lesions in ancient DNA

Although the last few years have seen great progress in DNA sequence retrieval from fossil specimens, some of the characteristics of ancient DNA remain poorly understood. This is particularly true for blocking lesions, i.e. chemical alterations that cannot be bypassed by DNA polymerases and thus prevent amplification and subsequent sequencing of affected molecules. Some studies have concluded that the vast majority of ancient DNA molecules carry blocking lesions, suggesting that the removal, repair or bypass of blocking lesions might dramatically increase both the time depth and geographical range of specimens available for ancient DNA analysis. However, previous studies used very indirect detection methods that did not provide conclusive estimates on the frequency of blocking lesions in endogenous ancient DNA. We developed a new method, polymerase extension profiling (PEP), that directly reveals occurrences of polymerase stalling on DNA templates. By sequencing thousands of single primer extension products using PEP methodology, we have for the first time directly identified blocking lesions in ancient DNA on a single molecule level. Although we found clear evidence for blocking lesions in three out of four ancient samples, no more than 40% of the molecules were affected in any of the samples, indicating that such modifications are far less frequent in ancient DNA than previously thought

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Single-dot Spectroscopy of GaAs Quantum Dots Fabricated by Filling of Self-assembled Nanoholes

We study the optical emission of single GaAs quantum dots (QDs). The QDs are fabricated by filling of nanoholes in AlGaAs and AlAs which are generated in a self-assembled fashion by local droplet etching with Al droplets. Using suitable process parameters, we create either uniform QDs in partially filled deep holes or QDs with very broad size distribution in completely filled shallow holes. Micro photoluminescence measurements of single QDs of both types establish sharp excitonic peaks. We measure a fine-structure splitting in the range of 22–40μeV and no dependence on QD size. Furthermore, we find a decrease in exciton–biexciton splitting with increasing QD size

Time-Resolved Studies of a Rolled-Up Semiconductor Microtube Laser

We report on lasing in rolled-up microtube resonators. Time-resolved studies on these semiconductor lasers containing GaAs quantum wells as optical gain material reveal particularly fast turn-on-times and short pulse emissions above the threshold. We observe a strong red-shift of the laser mode during the pulse emission which is compared to the time evolution of the charge-carrier density calculated by rate equations

Optical Properties of GaAs Quantum Dots Fabricated by Filling of Self-Assembled Nanoholes

Experimental results of the local droplet etching technique for the self-assembled formation of nanoholes and quantum rings on semiconductor surfaces are discussed. Dependent on the sample design and the process parameters, filling of nanoholes in AlGaAs generates strain-free GaAs quantum dots with either broadband optical emission or sharp photoluminescence (PL) lines. Broadband emission is found for samples with completely filled flat holes, which have a very broad depth distribution. On the other hand, partly filling of deep holes yield highly uniform quantum dots with very sharp PL lines

Three-Dimensionally Confined Optical Modes in Quantum Well Microtube Ring Resonators

We report on microtube ring resonators with quantum wells embedded as an optically active material. Optical modes are observed over a broad energy range. Their properties strongly depend on the exact geometry of the microtube along its axis. In particular we observe (i) preferential emission of light on the inside edge of the microtube and (ii) confinement of light also in direction of the tube axis by an axially varying geometry which is explained in an expanded waveguide model.Comment: 5 pages, 4 figure

8x14Gb/s ring WDM modulator array with integrated tungsten heaters and Ge monitor photodetectors

An 8x14Gb/s wavelength-division multiplexed Si ring modulator array is presented with uniform channel performance. Tungsten heaters and Ge monitor photodetectors at the ring modulator drop ports are co-integrated to track and control the modulation quality