Genome-wide tracking of unmethylated DNA Alu repeats in normal and cancer cells

Methylation of the cytosine is the most frequent epigenetic modification of DNA in mammalian cells. In humans, most of the methylated cytosines are found in CpG-rich sequences within tandem and interspersed repeats that make up to 45% of the human genome, being Alu repeats the most common family. Demethylation of Alu elements occurs in aging and cancer processes and has been associated with gene reactivation and genomic instability. By targeting the unmethylated SmaI site within the Alu sequence as a surrogate marker, we have quantified and identified unmethylated Alu elements on the genomic scale. Normal colon epithelial cells contain in average 25 486 ± 10 157 unmethylated Alu's per haploid genome, while in tumor cells this figure is 41 995 ± 17 187 (P = 0.004). There is an inverse relationship in Alu families with respect to their age and methylation status: the youngest elements exhibit the highest prevalence of the SmaI site (AluY: 42%; AluS: 18%, AluJ: 5%) but the lower rates of unmethylation (AluY: 1.65%; AluS: 3.1%, AluJ: 12%). Data are consistent with a stronger silencing pressure on the youngest repetitive elements, which are closer to genes. Further insights into the functional implications of atypical unmethylation states in Alu elements will surely contribute to decipher genomic organization and gene regulation in complex organisms

Redesign of LAOBP to bind novel L amino acid ligands

Computational protein design is still a challenge for advancing structure-function relationships. While recent advances in this field are promising, more information for genuine predictions is needed. Here, we discuss different approaches applied to install novel glutamine (Gln) binding into the Lysine/Arginine/Ornithine binding protein (LAOBP) from Salmonella typhimurium. We studied the ligand binding behavior of two mutants: a binding pocket grafting design based on a structural superposition of LAOBP to the Gln binding protein QBP from Escherichia coli and a design based on statistical coupled positions. The latter showed the ability to bind Gln even though the protein was not very stable. Comparison of both approaches highlighted a nonconservative shared point mutation between LAOBP_graft and LAOBP_sca. This context dependent L117K mutation in LAOBP turned out to be sufficient for introducing Gln binding, as confirmed by different experimental techniques. Moreover, the crystal structure of LAOBP_L117K in complex with its ligand is reported

Haplotypic characterization of the olive ridley turtle (Lepidochelys olivacea) in northwest Mexico: the northernmost limit of its distribution

Caracterización haplotípica de la tortuga golfina (Lepidochelys olivacea) en el noroeste de México: el límite septentrional de su distribución La tortuga golfina (L. olivacea) tiene una distribución pantropical. En el Pacífico oriental, los límites oficiales de su zona de reproducción son la península de Baja California y el sur de Sinaloa, en México. La playa de Ceuta en Elota, Sinaloa, México ha servido de sitio de protección para L. olivacea durante más de tres decenios. En este estudio, se caracterizó genéticamente la población de L. olivacea de la playa de Ceuta. Concretamente, se amplificó un fragmento de 712 pb de la región de control del ADNmt de 32 tortugas golfinas. Se identificaron ocho haplotipos (siete tras reducir a ~468 pb) y se incluyeron dos haplotipos nuevos (Lo–T7 y Lo–T8) y cinco haplotipos que se habían identificado anteriormente en otras playas de anidación. El haplotipo Lo–T2 era dominante (~60 %) en las muestras: h = 0,6048 (± 0,0974) y π = 0,002212 (± 0,001504). Si bien este estudio se realizó en el límite septentrional de la zona de anidación de la tortuga golfina en el Pacífico oriental, el grupo estudiado presenta una diversidad genética moderada y pertenece a una población que, en la escala evolutiva, ha pasado recientemente por una expansión demográfica. Debido a que la tortuga golfina del Pacífico oriental se considera resiliente a la variación ambiental, es necesario estudiar las zonas de anidación en el noroeste de México.The olive ridley sea turtle (L. olivacea) has a pantropical distribution. In the Eastern Pacific, the official limits of its reproduction area are south of the Baja California peninsula and south of Sinaloa, Mexico. Ceuta beach in Elota, Sinaloa, Mexico, has served as a protection site for L. olivacea for over three decades. In this study, the L. olivacea population from Ceuta beach was genetically characterized. Specifically, a 712–bp fragment from the control region of mtDNA was amplified from 32 olive ridley turtles. Eight haplotypes (seven after cutting to ~468 bp) were identified, and these included two novel haplotypes (Lo–T7 and Lo–T8) and five haplotypes that were previously identified in other nesting beaches. The Lo–T2 haplotype was dominant (~60 %) in the samples: h = 0.6048 (± 0.0974) and π = 0.002212 (± 0.001504). Although this study was conducted in the northernmost limit of the olive ridley turtle nesting distribution in the eastern Pacific, the sampled group presents moderate genetic diversity and belongs to a population that, on an evolutionary scale, only recently underwent demographic expansion. Because the olive ridley turtle in the eastern Pacific is considered resilient to environmental variation, nesting area studies in northwest Mexico are necessary.Caracterización haplotípica de la tortuga golfina (Lepidochelys olivacea) en el noroeste de México: el límite septentrional de su distribución La tortuga golfina (L. olivacea) tiene una distribución pantropical. En el Pacífico oriental, los límites oficiales de su zona de reproducción son la península de Baja California y el sur de Sinaloa, en México. La playa de Ceuta en Elota, Sinaloa, México ha servido de sitio de protección para L. olivacea durante más de tres decenios. En este estudio, se caracterizó genéticamente la población de L. olivacea de la playa de Ceuta. Concretamente, se amplificó un fragmento de 712 pb de la región de control del ADNmt de 32 tortugas golfinas. Se identificaron ocho haplotipos (siete tras reducir a ~468 pb) y se incluyeron dos haplotipos nuevos (Lo–T7 y Lo–T8) y cinco haplotipos que se habían identificado anteriormente en otras playas de anidación. El haplotipo Lo–T2 era dominante (~60 %) en las muestras: h = 0,6048 (± 0,0974) y π = 0,002212 (± 0,001504). Si bien este estudio se realizó en el límite septentrional de la zona de anidación de la tortuga golfina en el Pacífico oriental, el grupo estudiado presenta una diversidad genética moderada y pertenece a una población que, en la escala evolutiva, ha pasado recientemente por una expansión demográfica. Debido a que la tortuga golfina del Pacífico oriental se considera resiliente a la variación ambiental, es necesario estudiar las zonas de anidación en el noroeste de México

Shrub encroachment of Iberian dehesas: implications on total forage productivity

The Iberian dehesa, a grazed Mediterranean open woodland, is an outstanding example of a silvopastoral system. Shrub encroachment has been proposed as an effective method to facilitate natural tree regeneration and ensure the sustainability of silvopastoral systems. At the same time, shrubs can affect both pasture understory and tree overstory production. The effects of varying intensities of shrub encroachment on the productivity of four forage components of this system—pasture, acorns, shrub browse and tree browse—were tested and the overall metabolisable energy (ME) under different scenarios of vegetation structure was calculated. Two common shrub species with contrasting plant architectures and ecological functions were studied as models: Cistus ladanifer and Retama sphaerocarpa. Cistus negatively affected acorn, tree browse and pasture production, whereas Retama positively affected pasture and browse production and was neutral for acorn production. The highest ME values were found when tree cover was ca. 70 % and C. ladanifer cover was low or R. sphaerocarpa cover was medium. The authors recommend conserving and promoting patched three-layered plots in Iberian dehesas and similar extensive silvopastoral systems where certain shrub species could simultaneously encourage the sustainability of these systems and reinforce (with R. sphaerocarpa) or maintain (with C. ladanifer) their productivity.Spanish Ministry of Science and Innovation (AGL2006-09435/FOR) and the Regional Government of Extremadura (PRI07C044).http://link.springer.com/journal/104572016-08-31hb201