Next Generation Gene Synthesis by targeted retrieval of bead-immobilized, sequence verified DNA clones from a high throughput pyrosequencing device

The setup of synthetic biological systems involving millions of bases is still limited by the required high quality of synthetic DNA. Important drivers to further open up the field are the accuracy and scale of chemical DNA synthesis and the downstream processing of longer DNA assembled from short fragments. We developed a new, highly parallel and miniaturized method for the preparation of high quality DNA termed “Megacloning” by using Next Generation Sequencing (NGS) technology in a preparative way. We demonstrate our method by processing both conventional and microarray-derived DNA oligonucleotides in combination with a bead-based high throughput pyrosequencing platform, gaining a 500-fold error reduction for microarray oligonucleotides in a first embodiment. We also show the assembly of synthetic genes as part of the Megacloning process. In principle, up to millions of DNA fragments can be sequenced, characterized and sorted in a single Megacloner run, enabling many new applications

Instantaneous band gap collapse in photoexcited monoclinic VO2_2 due to photocarrier doping

Using femtosecond time-resolved photoelectron spectroscopy we demonstrate that photoexcitation transforms monoclinic VO$_2$ quasi-instantaneously into a metal. Thereby, we exclude an 80 femtosecond structural bottleneck for the photoinduced electronic phase transition of VO$_2$. First-principles many-body perturbation theory calculations reveal a high sensitivity of the VO$_2$ bandgap to variations of the dynamically screened Coulomb interaction, supporting a fully electronically driven isostructral insulator-to-metal transition. We thus conclude that the ultrafast band structure renormalization is caused by photoexcitation of carriers from localized V 3d valence states, strongly changing the screening \emph{before} significant hot-carrier relaxation or ionic motion has occurred

Deciphering the porcine intestinal microRNA transcriptome

<p>Abstract</p> <p>Background</p> <p>While more than 700 microRNAs (miRNAs) are known in human, a comparably low number has been identified in swine. Because of the close phylogenetic distance to humans, pigs serve as a suitable model for studying e.g. intestinal development or disease. Recent studies indicate that miRNAs are key regulators of intestinal development and their aberrant expression leads to intestinal malignancy.</p> <p>Results</p> <p>Here, we present the identification of hundreds of apparently novel miRNAs in the porcine intestine. MiRNAs were first identified by means of deep sequencing followed by miRNA precursor prediction using the miRDeep algorithm as well as searching for conserved miRNAs. Second, the porcine miRNAome along the entire intestine (duodenum, proximal and distal jejunum, ileum, ascending and transverse colon) was unraveled using customized miRNA microarrays based on the identified sequences as well as known porcine and human ones. In total, the expression of 332 intestinal miRNAs was discovered, of which 201 represented assumed novel porcine miRNAs. The identified hairpin forming precursors were in part organized in genomic clusters, and most of the precursors were located on chromosomes 3 and 1, respectively. Hierarchical clustering of the expression data revealed subsets of miRNAs that are specific to distinct parts of the intestine pointing to their impact on cellular signaling networks.</p> <p>Conclusions</p> <p>In this study, we have applied a straight forward approach to decipher the porcine intestinal miRNAome for the first time in mammals using a piglet model. The high number of identified novel miRNAs in the porcine intestine points out their crucial role in intestinal function as shown by pathway analysis. On the other hand, the reported miRNAs may share orthologs in other mammals such as human still to be discovered.</p

Lineshape Asymmetry for joint CPT and three photon N resonances

We show that a characteristic two photon lineshape asymmetry arises in coherent population trapping (CPT) and three photon (N) resonances because both resonances are simultaneously induced by modulation sidebands in the interrogating laser light. The N resonance is a three-photon resonance in which a two-photon Raman excitation is combined with a resonant optical pumping field. This joint CPT and N resonance can be the dominant source of lineshape distortion, with direct relevance for the operation of miniaturized atomic frequency standards. We present the results of both an experimental study and theoretical treatment of the asymmetry of the joint CPT and N resonance under conditions typical to the operation of an N resonance clock.Comment: Accepted for publication in Optics Letters, 5 page

Vollenzymatische Triglyceridbestimmung im Continuous Flow System am 12-Kanal-Analysator

Peer Reviewe

A blood based 12-miRNA signature of Alzheimer disease patients

Background: Alzheimer disease (AD) is the most common form of dementia but the identification of reliable, early and non-invasive biomarkers remains a major challenge. We present a novel miRNA-based signature for detecting AD from blood samples. Results: We apply next-generation sequencing to miRNAs from blood samples of 48 AD patients and 22 unaffected controls, yielding a total of 140 unique mature miRNAs with significantly changed expression levels. Of these, 82 have higher and 58 have lower abundance in AD patient samples. We selected a panel of 12 miRNAs for an RT-qPCR analysis on a larger cohort of 202 samples, comprising not only AD patients and healthy controls but also patients with other CNS illnesses. These included mild cognitive impairment, which is assumed to represent a transitional period before the development of AD, as well as multiple sclerosis, Parkinson disease, major depression, bipolar disorder and schizophrenia. miRNA target enrichment analysis of the selected 12 miRNAs indicates an involvement of miRNAs in nervous system development, neuron projection, neuron projection development and neuron projection morphogenesis. Using this 12-miRNA signature, we differentiate between AD and controls with an accuracy of 93%, a specificity of 95% and a sensitivity of 92%. The differentiation of AD from other neurological diseases is possible with accuracies between 74% and 78%. The differentiation of the other CNS disorders from controls yields even higher accuracies. Conclusions: The data indicate that deregulated miRNAs in blood might be used as biomarkers in the diagnosis of AD or other neurological diseases

Rare earth contributions to the X-ray magnetic circular dichroism at the Co K edge in rare earth-cobalt compounds investigated by multiple-scattering calculations

The X-ray magnetic circular dichroism (XMCD) has been measured at the Co K edge in Co-hcp and R-Co compounds (R=La, Tb, Dy). The structure of the experimental XMCD spectra in the near-edge region has been observed to be highly sensitive to the magnetic environment of the absorbing site. Calculations of the XMCD have been carried out at the Co K edge in Co metal, LaCo$_5$ and TbCo$_5$ within the multiple-scattering framework including the spin-orbit coupling. In the three systems, the XMCD spectra in the near-edge region are well reproduced. The possibility to separate and quantitatively estimate the local effects from those due to the neighboring atoms in the XMCD cross section makes possible a more physical understanding of the spectra. The present results emphasize the major role played by the $d$ states of the Tb ions in the XMCD spectrum at the Co K edge in the TbCo$_5$ compound.Comment: 34 pages, revtex, 10 eps figures included with epsf, after referee revie

Seasonal Variations of Seismic Activity on Mars?

We analyze the sequence of seismic events of different types as recorded by the SEIS instrument of the InSight mission. After several weeks without any detection, event counts started to increase at the end of May 2019. The majority of recorded events belongs to the class of 2.4 Hz events, which prominently excite a continuously observed natural resonance frequency. Comparison with expected event counts from a constant-rate Poisson process shows a repeated, step wise increase of the event rate with time. At the same time, event amplitudes, and hence magnitudes, are found to increase as well