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

freeIbis: An efficient basecaller with calibrated quality scores for Illumina sequencers

Motivation: The conversion of the raw intensities obtained from next-generation sequencing platforms into nucleotide sequences with well-calibrated quality scores is a critical step in the generation of good sequence data. While recent model-based approaches can yield highly accurate calls, they require a substantial amount of processing time and/or computational resources. We previously introduced Ibis, a fast and accurate basecaller for the Illumina platform. We have continued active development of Ibis to take into account developments in the Illumina technology, as well as to make Ibis fully open source. Results: We introduce here freeIbis, which offers significant improvements in sequence accuracy owing to the use of a novel multiclass support vector machine (SVM) algorithm. Sequence quality scores are now calibrated based on empirically observed scores, thus providing a high correlation to their respective error rates. These improvements result in downstream advantages including improved genotyping accuracy. Availability and implementation: FreeIbis is freely available for use under the GPL (http://bioinf.eva.mpg.de/freeibis/). It requires a Python interpreter and a C++ compiler. Tailored versions of LIBOCAS and LIBLINEAR are distributed along with the package. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online

The Rewarding Nature of Social Interactions

The objective of this short review is to highlight rewarding aspects of social interactions for humans and discuss their neural basis. Thereby we report recent research findings to illustrate how social stimuli in general are processed in the reward system and highlight the role of Theory of Mind as one mediating process for experiencing social reward during social interactions. In conclusion we discuss clinical implications for psychiatry and psychotherapy

Risk Assessment Plan for Petroleum Underground Storage Tanks in Kentucky

This study addresses the development of guidelines for corrective actions to be applied to petroleum underground storage tanks (USTs) within the Commonwealth of Kentucky. The report presents findings and recommendations for gasoline, diesel fuel, heating oil, kerosene, jet fuel, and waste oil

Борьба с биообрастанием природных и сточных вод с использованием энергетических воздействий

Данная работа посвящена анализу методов очистки воды для борьбы с биологическим обрастанием технологического оборудования. Рассмотрены различные способы борьбы с биологическим обрастанием, в том числе: реагентные, безреагентные и электрические. Сформирована концепция применения способа борьбы с биологическим обрастанием технологического оборудования путем электрической обработки теплоносителя. Приведена схема установки, таблица результатов и диаграмма.This work is devoted to the analysis of methods of water purification for fight against biological fouling of processing equipment. Various ways of fight against biological fouling are considered, including: reagent, reagentless and electric. The concept of application of a way of fight against biological fouling of processing equipment by electric processing of the heat carrier is created. The scheme of installation, the table of results and the chart is provided

Proximity effect in granular superconductor-normal metal structures

We fabricated three-dimensional disordered Pb-Cu granular structures, with various metal compositions. The typical grain size of both metals is smaller than the superconductor and normal metal coherence lengths, thus satisfying the Cooper limit. The critical temperature of the samples was measured and compared with the critical temperature of bilayers. We show how the proximity effect theories, developed for bilayers, can be modified for random mixtures and we demonstrate that our experimental data fit well the de Gennes weak coupling limit theory in the Cooper limit. Our results indicate that, in granular structures, the Cooper limit can be satisfied over a wide range of concentrations.Comment: 15 pages, 4 figure