Improved Visualization of DNA in Aqueous Buffer with the Atomic Force Microscope

An improved method has been developed for imaging deoxyribonucleic acid (DNA) in aqueous buffer with the atomic force microscope (AFM). DNA on untreated mica can be imaged in aqueous buffer with the AFM if the DNA is deposited onto the mica in a buffer with HEPES and MgCl2, if the sample is rinsed thoroughly with high water pressure, and if the imaging is done with an electron beam-deposited (EBD) tip that has been deposited in the scanning electron microscope (SEM). The water rinse removes DNA that is otherwise easily scraped off the substrate. There is evidence that sharper tips may be more damaging to DNA when imaged in aqueous buffer especially when the DNA is bound tightly to the mica. The ability to image DNA in nearly biological conditions has potential applications for imaging biomolecular processes with the AFM

Estudio médico-legal de los marcadores genéticos empleados en investigación de paternidad y criminalística : tesis doctoral

Índice. Tesis inédita de la Universidad Complutense de Madrid, Facultad de Medicina, Departamento de Toxicología y Legislación sanitaria.Depto. de Farmacología y ToxicologíaFac. de MedicinaTRUEProQuestpu

Direct measurement of the mechanical work during translocation by the ribosome.

A detailed understanding of tRNA/mRNA translocation requires measurement of the forces generated by the ribosome during this movement. Such measurements have so far remained elusive and, thus, little is known about the relation between force and translocation and how this reflects on its mechanism and regulation. Here, we address these questions using optical tweezers to follow translation by individual ribosomes along single mRNA molecules, against an applied force. We find that translocation rates depend exponentially on the force, with a characteristic distance close to the one-codon step, ruling out the existence of sub-steps and showing that the ribosome likely functions as a Brownian ratchet. We show that the ribosome generates ∼13 pN of force, barely sufficient to unwind the most stable structures in mRNAs, thus providing a basis for their regulatory role. Our assay opens the way to characterizing the ribosomes full mechano-chemical cycle

Genetic recombination is targeted towards gene promoter regions in dogs

The identification of the H3K4 trimethylase, PRDM9, as the gene responsible for recombination hotspot localization has provided considerable insight into the mechanisms by which recombination is initiated in mammals. However, uniquely amongst mammals, canids appear to lack a functional version of PRDM9 and may therefore provide a model for understanding recombination that occurs in the absence of PRDM9, and thus how PRDM9 functions to shape the recombination landscape. We have constructed a fine-scale genetic map from patterns of linkage disequilibrium assessed using high-throughput sequence data from 51 free-ranging dogs, Canis lupus familiaris. While broad-scale properties of recombination appear similar to other mammalian species, our fine-scale estimates indicate that canine highly elevated recombination rates are observed in the vicinity of CpG rich regions including gene promoter regions, but show little association with H3K4 trimethylation marks identified in spermatocytes. By comparison to genomic data from the Andean fox, Lycalopex culpaeus, we show that biased gene conversion is a plausible mechanism by which the high CpG content of the dog genome could have occurred.Comment: Updated version, with significant revision

Patterns of genomic and phenomic diversity in wine and table grapes.

Grapes are one of the most economically and culturally important crops worldwide, and they have been bred for both winemaking and fresh consumption. Here we evaluate patterns of diversity across 33 phenotypes collected over a 17-year period from 580 table and wine grape accessions that belong to one of the world's largest grape gene banks, the grape germplasm collection of the United States Department of Agriculture. We find that phenological events throughout the growing season are correlated, and quantify the marked difference in size between table and wine grapes. By pairing publicly available historical phenotype data with genome-wide polymorphism data, we identify large effect loci controlling traits that have been targeted during domestication and breeding, including hermaphroditism, lighter skin pigmentation and muscat aroma. Breeding for larger berries in table grapes was traditionally concentrated in geographic regions where Islam predominates and alcohol was prohibited, whereas wine grapes retained the ancestral smaller size that is more desirable for winemaking in predominantly Christian regions. We uncover a novel locus with a suggestive association with berry size that harbors a signature of positive selection for larger berries. Our results suggest that religious rules concerning alcohol consumption have had a marked impact on patterns of phenomic and genomic diversity in grapes

Hyperspectral Sensors as a Management Tool to Prevent the Invasion of the Exotic Cordgrass Spartina densiflora in the Doñana Wetlands

We test the use of hyperspectral sensors for the early detection of the invasive dense-flowered cordgrass (Spartina densiflora Brongn.) in the Guadalquivir River marshes, Southwestern Spain. We flew in tandem a CASI-1500 (368–1052 nm) and an AHS (430–13,000 nm) airborne sensors in an area with presence of S. densiflora. We simplified the processing of hyperspectral data (no atmospheric correction and no data-reduction techniques) to test if these treatments were necessary for accurate S. densiflora detection in the area. We tested several statistical signal detection algorithms implemented in ENVI software as spectral target detection techniques (matched filtering, constrained energy minimization, orthogonal subspace projection, target-constrained interference minimized filter, and adaptive coherence estimator) and compared them to the well-known spectral angle mapper, using spectra extracted from ground-truth locations in the images. The target S. densiflora was easy to detect in the marshes by all algorithms in images of both sensors. The best methods (adaptive coherence estimator and target-constrained interference minimized filter) on the best sensor (AHS) produced 100% discrimination (Kappa = 1, AUC = 1) at the study site and only some decline in performance when extrapolated to a new nearby area. AHS outperformed CASI in spite of having a coarser spatial resolution (4-m vs. 1-m) and lower spectral resolution in the visible and near-infrared range, but had a better signal to noise ratio. The larger spectral range of AHS in the short-wave and thermal infrared was of no particular advantage. Our conclusions are that it is possible to use hyperspectral sensors to map the early spread S. densiflora in the Guadalquivir River marshes. AHS is the most suitable airborne hyperspectral sensor for this task and the signal processing techniques target-constrained interference minimized filter (TCIMF) and adaptive coherence estimator (ACE) are the best performing target detection techniques that can be employed operationally with a simplified processing of hyperspectral images.This study has been funded by the Spanish Ministry of Science and Innovation through the research projects HYDRA (No. CGL2006-02247/BOS) and HYDRA2 (CGL2009-09801/BOS), by the National Parks Authority (Organismo Autonomo de Parques Nacionales) of the Spanish Ministry of Environment to project OAPN 042/2007, and by funding from the European Union (EU) Horizon 2020 research and innovation program under grant agreement No. 641762 to ECOPOTENTIAL project. The Espacio Natural de Doñana provided permits for field work in protected areas with restricted access. We are grateful to the Instituto Nacional de Técnica Aeroespacial (INTA), Spain, for performing the airborne campaign and the geometric correction of the images. J.B. has to acknowledge a sabbatical stay at Pye Laboratory of the Commonwealth Scientific and Research Organization (CSIRO) Marine and Atmospheric Sciences, Australia, and at the Climate Change Cluster (C3) of the University of Technology Sydney, Australia, funded by the Spanish Ministry of Education, during data analysis and writing of this paper. This publication is a contribution from CEIMAR and also a contribution from CEICAMBIO. We acknowledge support by the CSIC Open Access Publication Initiative through its Unit of Information Resources for Research (URICI

Patterns of Positive Selection in Six Mammalian Genomes

Genome-wide scans for positively selected genes (PSGs) in mammals have provided insight into the dynamics of genome evolution, the genetic basis of differences between species, and the functions of individual genes. However, previous scans have been limited in power and accuracy owing to small numbers of available genomes. Here we present the most comprehensive examination of mammalian PSGs to date, using the six high-coverage genome assemblies now available for eutherian mammals. The increased phylogenetic depth of this dataset results in substantially improved statistical power, and permits several new lineage- and clade-specific tests to be applied. Of ∼16,500 human genes with high-confidence orthologs in at least two other species, 400 genes showed significant evidence of positive selection (FDR<0.05), according to a standard likelihood ratio test. An additional 144 genes showed evidence of positive selection on particular lineages or clades. As in previous studies, the identified PSGs were enriched for roles in defense/immunity, chemosensory perception, and reproduction, but enrichments were also evident for more specific functions, such as complement-mediated immunity and taste perception. Several pathways were strongly enriched for PSGs, suggesting possible co-evolution of interacting genes. A novel Bayesian analysis of the possible “selection histories” of each gene indicated that most PSGs have switched multiple times between positive selection and nonselection, suggesting that positive selection is often episodic. A detailed analysis of Affymetrix exon array data indicated that PSGs are expressed at significantly lower levels, and in a more tissue-specific manner, than non-PSGs. Genes that are specifically expressed in the spleen, testes, liver, and breast are significantly enriched for PSGs, but no evidence was found for an enrichment for PSGs among brain-specific genes. This study provides additional evidence for widespread positive selection in mammalian evolution and new genome-wide insights into the functional implications of positive selection.</p