Waveform Memory for Real-Time FPGA Test of Fiber-Optic Receiver DSPs

Verification of advanced circuit implementations poses many challenges. For complex digital signal processing (DSP) circuits, logic simulations may be prohibitively slow when non-stationary scenarios are considered. A real-time emulation technique like the Fiber-on-Chip (FoC) approach can significantly speed up DSP logic verification. However, a potential weakness with this type of emulation is that it does not use data obtained from experiments, but synthetically creates test data. We introduce a waveform memory, which can be integrated with FoC systems and similar emulators, and which allows measured waveforms to be stored and fed to DSP circuits under test. We perform real-time FPGA experiments where we evaluate a carrier-phase recovery (CPR) module that is tested using either waveform data or synthetic data. Our results for the two different data sets show that the CPR module behaves similarly, both qualitatively and quantitatively, which indicates that the synthetic phase-noise model is a valid replacement of measured data

Optical absorption spectra of metal oxides from time-dependent density functional theory and many-body perturbation theory based on optimally-tuned hybrid functionals

Using both time-dependent density functional theory (TDDFT) and the ``single-shot" $GW$ plus Bethe-Salpeter equation ($GW$-BSE) approach, we compute optical band gaps and optical absorption spectra from first principles for eight common binary and ternary closed-shell metal oxides (MgO, Al$_2$O$_3$, CaO, TiO$_2$, Cu$_2$O, ZnO, BaSnO$_3$, and BiVO$_4$), based on the non-empirical Wannier-localized optimally-tuned screened range-separated hybrid functional. Overall, we find excellent agreement between our TDDFT and $GW$-BSE results and experiment, with a mean absolute error less than 0.4 eV, including for Cu$_2$O and ZnO, traditionally considered to be challenging for both methods

Uso de marcadores SSR para identificaci\uf3n de germoplasma de papa en el programa de mejoramiento de INIA de Chile

Molecular markers based on Simple Sequence Repeats (SSR) are a very efficient tool for potato ( Solanum tuberosum L. ) genotype identification and can be very useful for germplasm conservation and management. With the purpose of incorporate this technology into the potato breeding program of the National Institute of Agricultural Research (INIA) Chile, a set of 26 SSR markers was evaluated on a sample of 71 potato genotypes. Each marker was characterized for number and combinations of alleles, scoring quality, polymorphic information content (PIC) and discrimination power (D). From the total, only 21 SSR markers showed up scoreable products and the allele number ranged between 2 and 17. The observed allelic combinations among the different potato genotypes ranged from 2 to 47; however, unique genotypes detected by each SSR marker ranged from 0 to 38. The observed (Do) and expected (Dj) discriminatory power ranged from 0.23 to 0.98 and from 0.43 to 0.92, respectively. The seven SSR markers which showed the highest Do scores were STM1009 (0.98), STM1020 (0.97), STM0031 (0.97), STM2013 (0.96), STM1008 (0.94), STM1052 (0.93) and STM0019 (0.91). The STM1009, STM1020 and STM1008 markers are multi-loci SSR, where each one amplifies more than one locus of the potato genome. The utilization of the multi-loci type of marker, or combinations of several SSR markers in either PCR-multiplex or pseudo-multiplex reactions, are good options to increase the speed and reduce the cost of SSR markers application.Los marcadores moleculares basados en Secuencias Simples Repetidas (SSR) constituyen una herramienta altamente eficaz para la identificaci\uf3n de genotipos de papa ( Solanum tuberosum L. ) y pueden ser de gran utilidad en la conservaci\uf3n y manejo de germoplasma. Con el prop\uf3sito de incorporar esta tecnolog\ueda al Programa de Mejoramiento de Papa del Instituto de Investigaciones Agropecuarias (INIA) de Chile, se evalu\uf3 un grupo de 26 marcadores SSR sobre una muestra de 71 genotipos de papa. Cada marcador se caracteriz\uf3 seg\ufan su n\ufamero de alelos y sus respectivas combinaciones, calidad de lectura, contenido de informaci\uf3n polim\uf3rfica (PIC) y poder discriminatorio (D). Del total s\uf3lo 21 marcadores SSR mostraron productos legibles con un n\ufamero de alelos que vari\uf3 entre 2 y 17. Las combinaciones al\ue9licas observadas variaron desde 2 a 47; sin embargo, los genotipos \ufanicos detectados por cada marcador fueron desde 0 a 38. El poder discriminatorio observado (Do) y esperado (Dj) estuvo entre 0,23 a 0,98 y entre 0,43 a 0,92, respectivamente. Los siete marcadores que presentaron mayor Do fueron STM1009 (0,98), STM1020 (0.97), STM0031 (0,97), STM2013 (0,96), STM1008 (0,94), STM1052 (0,93) y STM0019 (0,91). Los marcadores STM1009, STM1020 y STM1008 corresponden a SSR multi-loci, donde cada uno amplifica m\ue1s de un locus desde distintas regiones del genoma de la papa. La utilizaci\uf3n de este tipo de marcadores multi-loci, o de combinaciones de varios SSR en reacciones de PCR-m\ufaltiplex o pseudos-m\ufaltiplex son una buena alternativa para aumentar rapidez y disminuir costo en la aplicaci\uf3n de marcadores SSR

Design of Novel Relaxase Substrates Based on Rolling Circle Replicases for Bioconjugation to DNA Nanostructures

During bacterial conjugation and rolling circle replication, HUH endonucleases, respectively known as relaxases and replicases, form a covalent bond with ssDNA when they cleave their target sequence (nic site). Both protein families show structural similarity but limited amino acid identity. Moreover, the organization of the inverted repeat (IR) and the loop that shape the nic site differs in both proteins. Arguably, replicases cleave their target site more efficiently, while relaxases exert more biochemical control over the process. Here we show that engineering a relaxase target by mimicking the replicase target, results in enhanced formation of protein-DNA covalent complexes. Three widely different relaxases, which belong to MOBF, MOBQ and MOBP families, can properly cleave DNA sequences with permuted target sequences. Collaterally, the secondary structure that the permuted targets acquired within a supercoiled plasmid DNA resulted in poor conjugation frequencies underlying the importance of relaxase accessory proteins in conjugative DNA processing. Our results reveal that relaxase and replicase targets can be interchangeable in vitro. The new Rep substrates provide new bioconjugation tools for the design of sophisticated DNA-protein nanostructures.This work was financed by grants BFU2014-55534-C2-1-P from the Spanish Ministry of Economy and Competitiveness and 612146/FP7-ICT- 2013 and 282004/FP7-HEALTH.2011.2.3.1-2 from the European Union Seventh Framework Programme to FC and grant BFU2014-55534-C2-2-P from the Spanish Ministry of Economy and Competitiveness to GM. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Sequencing the Potato Genome: Outline and First Results to Come from the Elucidation of the Sequence of the World’s Third Most Important Food Crop

Potato is a member of the Solanaceae, a plant family that includes several other economically important species, such as tomato, eggplant, petunia, tobacco and pepper. The Potato Genome Sequencing Consortium (PGSC) aims to elucidate the complete genome sequence of potato, the third most important food crop in the world. The PGSC is a collaboration between 13 research groups from China, India, Poland, Russia, the Netherlands, Ireland, Argentina, Brazil, Chile, Peru, USA, New Zealand and the UK. The potato genome consists of 12 chromosomes and has a (haploid) length of approximately 840 million base pairs, making it a medium-sized plant genome. The sequencing project builds on a diploid potato genomic bacterial artificial chromosome (BAC) clone library of 78000 clones, which has been fingerprinted and aligned into ~7000 physical map contigs. In addition, the BAC-ends have been sequenced and are publicly available. Approximately 30000 BACs are anchored to the Ultra High Density genetic map of potato, composed of 10000 unique AFLPTM markers. From this integrated genetic-physical map, between 50 to 150 seed BACs have currently been identified for every chromosome. Fluorescent in situ hybridization experiments on selected BAC clones confirm these anchor points. The seed clones provide the starting point for a BAC-by-BAC sequencing strategy. This strategy is being complemented by whole genome shotgun sequencing approaches using both 454 GS FLX and Illumina GA2 instruments. Assembly and annotation of the sequence data will be performed using publicly available and tailor-made tools. The availability of the annotated data will help to characterize germplasm collections based on allelic variance and to assist potato breeders to more fully exploit the genetic potential of potat