Inteins, introns, and homing endonucleases: recent revelations about the life cycle of parasitic genetic elements

Self splicing introns and inteins that rely on a homing endonuclease for propagation are parasitic genetic elements. Their life-cycle and evolutionary fate has been described through the homing cycle. According to this model the homing endonuclease is selected for function only during the spreading phase of the parasite. This phase ends when the parasitic element is fixed in the population. Upon fixation the homing endonuclease is no longer under selection, and its activity is lost through random processes. Recent analyses of these parasitic elements with functional homing endonucleases suggest that this model in its most simple form is not always applicable. Apparently, functioning homing endonuclease can persist over long evolutionary times in populations and species that are thought to be asexual or nearly asexual. Here we review these recent findings and discuss their implications. Reasons for the long-term persistence of a functional homing endonuclease include: More recombination (sexual and as a result of gene transfer) than previously assumed for these organisms; complex population structures that prevent the element from being fixed; a balance between active spreading of the homing endonuclease and a decrease in fitness caused by the parasite in the host organism; or a function of the homing endonuclease that increases the fitness of the host organism and results in purifying selection for the homing endonuclease activity, even after fixation in a local population. In the future, more detailed studies of the population dynamics of the activity and regulation of homing endonucleases are needed to decide between these possibilities, and to determine their relative contributions to the long term survival of parasitic genes within a population. Two outstanding publications on the amoeba Naegleria group I intron (Wikmark et al. BMC Evol Biol 2006, 6:39) and the PRP8 inteins in ascomycetes (Butler et al.BMC Evol Biol 2006, 6:42) provide important stepping stones towards integrated studies on how these parasitic elements evolve through time together with, or despite, their hosts

The intein of the Thermoplasma A-ATPase A subunit: Structure, evolution and expression in E. coli

BACKGROUND: Inteins are selfish genetic elements that excise themselves from the host protein during post translational processing, and religate the host protein with a peptide bond. In addition to this splicing activity, most reported inteins also contain an endonuclease domain that is important in intein propagation. RESULTS: The gene encoding the Thermoplasma acidophilum A-ATPase catalytic subunit A is the only one in the entire T. acidophilum genome that has been identified to contain an intein. This intein is inserted in the same position as the inteins found in the ATPase A-subunits encoding gene in Pyrococcus abyssi, P. furiosus and P. horikoshii and is found 20 amino acids upstream of the intein in the homologous vma-1 gene in Saccharomyces cerevisiae. In contrast to the other inteins in catalytic ATPase subunits, the T. acidophilum intein does not contain an endonuclease domain. T. acidophilum has different codon usage frequencies as compared to Escherichia coli. Initially, the low abundance of rare tRNAs prevented expression of the T. acidophilum A-ATPase A subunit in E. coli. Using a strain of E. coli that expresses additional tRNAs for rare codons, the T. acidophilum A-ATPase A subunit was successfully expressed in E. coli. CONCLUSIONS: Despite differences in pH and temperature between the E. coli and the T. acidophilum cytoplasms, the T. acidophilum intein retains efficient self-splicing activity when expressed in E. coli. The small intein in the Thermoplasma A-ATPase is closely related to the endonuclease containing intein in the Pyrococcus A-ATPase. Phylogenetic analyses suggest that this intein was horizontally transferred between Pyrococcus and Thermoplasma, and that the small intein has persisted in Thermoplasma apparently without homing

Non-uniform target illumination in deflagration regime : thermal smoothing

Thermal smoothing in the plasma ablated from a laser target under weakly nonuniform irradiation is analyzed, assuming absorption at nc and a deflagration regime (conduction restricted to a thin quasisteady layer next to the target). Magnetic generation effects are included and found to be weak. Differences from results available in the literature are explained; the importance of the character of the underdense flow at uniform irradiation is emphasized

Factorizing LambdaMART for cold start recommendations

Recommendation systems often rely on point-wise loss metrics such as the mean squared error. However, in real recommendation settings only few items are presented to a user. This observation has recently encouraged the use of rank-based metrics. LambdaMART is the state-of-the-art algorithm in learning to rank which relies on such a metric. Despite its success it does not have a principled regularization mechanism relying in empirical approaches to control model complexity leaving it thus prone to overfitting. Motivated by the fact that very often the users' and items' descriptions as well as the preference behavior can be well summarized by a small number of hidden factors, we propose a novel algorithm, LambdaMART Matrix Factorization (LambdaMART-MF), that learns a low rank latent representation of users and items using gradient boosted trees. The algorithm factorizes lambdaMART by defining relevance scores as the inner product of the learned representations of the users and items. The low rank is essentially a model complexity controller; on top of it we propose additional regularizers to constraint the learned latent representations that reflect the user and item manifolds as these are defined by their original feature based descriptors and the preference behavior. Finally we also propose to use a weighted variant of NDCG to reduce the penalty for similar items with large rating discrepancy. We experiment on two very different recommendation datasets, meta-mining and movies-users, and evaluate the performance of LambdaMART-MF, with and without regularization, in the cold start setting as well as in the simpler matrix completion setting. In both cases it outperforms in a significant manner current state of the art algorithms

El hombre de Laramie (The man from Laramie; Anthony Mann, 1955)

Rodríguez, HJ. (2006). El hombre de Laramie (The man from Laramie; Anthony Mann, 1955). Nosferatu. Revista de cine. (53):160-161. http://hdl.handle.net/10251/41490.Importación Masiva1601615

Vivir la muerte

Rodríguez, HJ. (1998). Vivir la muerte. Banda aparte. (12):42-45. http://hdl.handle.net/10251/42285.Importación Masiva42451

Daydream Mechanics

Rodríguez, HJ. (2001). Daydream Mechanics. Banda aparte. (20):76-77. http://hdl.handle.net/10251/42500.Importación Masiva76772

Biostratigraphic study with planktic foraminifera of the Santonian-Campanian in the Deba-Zumaia section (Gipuzkoa): New biozonation with heterohelicids

A biostratigraphic study with Santonian and Campanian planktic foraminifera was carried out in the turbiditic facies of the coastline between Deba and Zumaia (Gipuzkoa), which comprises the Itziar and Aguinaga formations. Due to the low abundance of planktic foraminifera, particularly in globotruncanids, the biostratigraphic study was based on species belonging to the group of heterohelicids. We have identified 7 biozones, one of which (Sigalia rugocostata Zone) has been defined in this work. The position of the Santonian/Campanian boundary has been recognized for the first time in the Basque Coast Geopark through the use of this new biozonation with heterohelicidsSe ha realizado un estudio bioestratigráfico con foraminíferos planctónicos del Santoniense y Campaniense en las facies turbidíticas del tramo litoral entre Deba y Zumaia (Guipúzcoa), el cual comprende las formaciones Itziar y Aguinaga. Debido a la escasez de foraminíferos planctónicos del grupo de globotruncánidos, el estudio bioestratigráfico se ha basado en especies pertenecientes al grupo de los heterohelícidos. Se han identificado 7 biozonas, una de las cuales (Zona de Sigalia rugocostata) ha sido definida en este trabajo. Esta nueva biozonación ha permitido reconocer por primera vez la posición del límite Santoniense/Campaniense en el Geoparque de la Costa Vasc

Carl T. Dreyer

Rodríguez, HJ. (2000). Carl T. Dreyer. Banda aparte. (19):87-88. http://hdl.handle.net/10251/42475.Importación Masiva87881