The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana

To take complete advantage of information on within-species polymorphism and divergence from close relatives, one needs to know the rate and the molecular spectrum of spontaneous mutations. To this end, we have searched for de novo spontaneous mutations in the complete nuclear genomes of five Arabidopsis thaliana mutation accumulation lines that had been maintained by single-seed descent for 30 generations. We identified and validated 99 base substitutions and 17 small and large insertions and deletions. Our results imply a spontaneous mutation rate of 7 × 10−9 base substitutions per site per generation, the majority of which are G:C→A:T transitions. We explain this very biased spectrum of base substitution mutations as a result of two main processes: deamination of methylated cytosines and ultraviolet light–induced mutagenesis

Mechanisms and pathways of Toxoplasma gondii transepithelial migration

Toxoplasma gondii is a ubiquitous parasite and a prevalent food-borne parasitic pathogen. Infection of the host occurs principally through oral consumption of contaminated food and water with the gastrointestinal tract being the primary route for entry into the host. To promote infection, T. gondii has evolved highly specialized strategies for rapid traversal of the single cell thick intestinal epithelial barrier. Parasite transmigration via the paracellular pathway between adjacent cells enables parasite dissemination to secondary sites of infection where chronic infection of muscle and brain tissue is established. It has recently been proposed that parasite interactions with the integral tight junction (TJ) protein occludin influences parasite transmigration of the intestinal epithelium. We review here the emerging mechanisms of T. gondii transmigration of the small intestinal epithelium alongside the developing role played in modulating the wider TJ-associated proteome to rewire host cell regulatory systems for the benefit of the parasite

Shifting Diets of Lake Trout in Northeastern Lake Michigan

Prey fish communities in Lake Michigan have been steadily changing, characterized by declines in both the quantity and quality of Alewife Alosa pseudoharengus. To evaluate concurrent changes in the diet of Lake Trout Salvelinus namaycush in northeastern Lake Michigan, we analyzed stomach contents of Lake Trout caught during gill‐net surveys and fishing tournaments from May through October 2016. We then compared the composition, on a wet‐weight basis, of 2016 diets with those previously described in a recent survey conducted in 2011. Overall, we found that Lake Trout diets in 2016 consisted mostly (94% by wet weight) of Alewives and Round Goby Neogobius melanostomus. Averaging across May through October, 61% of the Lake Trout diet consisted of Alewives. A clear seasonal shift was apparent: the diet was dominated by Round Goby (67%) during May–June, whereas Alewives dominated the diet (76%) during July–October. Seasonal dominance of Round Goby in spring Lake Trout diets has not been previously observed in northeastern Lake Michigan as Round Goby represented only 21% of the Lake Trout diet in spring of 2011. Diet composition of Lake Trout caught in gill nets did not significantly differ from diet composition of Lake Trout caught by anglers in either the May–June period or the July–October period. Although Lake Trout showed increased diet flexibility in 2016 compared with 2011, Alewives were still the predominant diet component during 2016, despite reduced Alewife biomass throughout Lake Michigan. Nonetheless, this further evidence of diet plasticity suggests that Lake Trout may be resilient to ongoing and future forage base changes.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/151367/1/nafm10318.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/151367/2/nafm10318_am.pd

Preferencias del tratamiento en pacientes con Espondiloartritis axial

Introducción: una de las premisas del Treat to Target (T2T) es la decisión conjunta del tratamiento entre el reumatólogo y el paciente. Por esta razón las preferencias del paciente juegan un rol fundamental en el éxito del tratamiento a corto y largo plazo. El objetivo de este estudio fue evaluar las preferencias de tratamiento de los pacientes con Espondiloartritis axial (EsPax) e identificar factores asociados a su elección

Graphs Cannot Be Indexed in Polynomial Time for Sub-quadratic Time String Matching, Unless SETH Fails

The string matching problem on a node-labeled graph G= (V, E) asks whether a given pattern string P has an occurrence in G, in the form of a path whose concatenation of node labels equals P. This is a basic primitive in various problems in bioinformatics, graph databases, or networks, but only recently proven to have a O(|E||P|)-time lower bound, under the Orthogonal Vectors Hypothesis (OVH). We consider here its indexed version, in which we can index the graph in order to support time-efficient string queries. We show that, under OVH, no polynomial-time indexing scheme of the graph can support querying P in time O(| P| + | E| δ| P| β), with either δ< 1 or β< 1. As a side-contribution, we introduce the notion of linear independent-components (lic) reduction, allowing for a simple proof of our result. As another illustration that hardness of indexing follows as a corollary of a lic reduction, we also translate the quadratic conditional lower bound of Backurs and Indyk (STOC 2015) for the problem of matching a query string inside a text, under edit distance. We obtain an analogous tight quadratic lower bound for its indexed version, improving the recent result of Cohen-Addad, Feuilloley and Starikovskaya (SODA 2019), but with a slightly different boundary condition.Peer reviewe

Yersinia pseudotuberculosis serotype O : 1 infection in a captive Seba's short tailed-fruit bat (Carollia perspicillata) colony in Switzerland

BackgroundBetween February and April 2016, a slight increase in mortality was observed in a colony consisting of 400 captive Seba's short-tailed bats (Carollia perspicillata). These animals cohabited with other nocturnal animal species in a dome of a private zoo in Switzerland.ResultsGross and histological analysis of two (14.3%) out of the 13 animals submitted for necropsy within this period revealed a necrosuppurative pneumonia, hepatitis, splenitis, enterocolitis, and endometritis, with abundant intralesional colonies of Gram-negative rods. Yersinia (Y.) pseudotuberculosis serotype O:1 and biotype 1 belonging to the sequence type ST90 was isolated from the affected organs in both animals. Following this diagnosis, 1/4 of the colony (99 animals) was culled and submitted for gross and histopathological analysis, and a bacterial culture selective for Yersinia spp. of lung, liver, and spleen was performed. From these 99 animals, one gravid female was tested and found to be positive for Y. pseudotuberculosis in the absence of clinical symptoms and histopathological lesions. PCR analysis of altogether three bacterial isolates for virulence factors revealed the presence of the ail gene, and one isolate was also positive for the virF and yadA plasmid genes.ConclusionsThese findings suggest that Carollia perspicillata are susceptible to lethal yersiniosis but do not represent a regular reservoir for Y. pseudotuberculosis. Culling of 1/4 of the population was sufficient to limit the spread of this infection among the colony. Moreover, no infections were detected in cohabitant nocturnal animals and caretakers, indicating that the zoonotic risk in this case was low.Peer reviewe

Methods to study splicing from high-throughput RNA Sequencing data

The development of novel high-throughput sequencing (HTS) methods for RNA (RNA-Seq) has provided a very powerful mean to study splicing under multiple conditions at unprecedented depth. However, the complexity of the information to be analyzed has turned this into a challenging task. In the last few years, a plethora of tools have been developed, allowing researchers to process RNA-Seq data to study the expression of isoforms and splicing events, and their relative changes under different conditions. We provide an overview of the methods available to study splicing from short RNA-Seq data. We group the methods according to the different questions they address: 1) Assignment of the sequencing reads to their likely gene of origin. This is addressed by methods that map reads to the genome and/or to the available gene annotations. 2) Recovering the sequence of splicing events and isoforms. This is addressed by transcript reconstruction and de novo assembly methods. 3) Quantification of events and isoforms. Either after reconstructing transcripts or using an annotation, many methods estimate the expression level or the relative usage of isoforms and/or events. 4) Providing an isoform or event view of differential splicing or expression. These include methods that compare relative event/isoform abundance or isoform expression across two or more conditions. 5) Visualizing splicing regulation. Various tools facilitate the visualization of the RNA-Seq data in the context of alternative splicing. In this review, we do not describe the specific mathematical models behind each method. Our aim is rather to provide an overview that could serve as an entry point for users who need to decide on a suitable tool for a specific analysis. We also attempt to propose a classification of the tools according to the operations they do, to facilitate the comparison and choice of methods.Comment: 31 pages, 1 figure, 9 tables. Small corrections adde

Drivers of grassland loss in Hungary during the post-socialist transformation (1987–1999)

The increase in the speed of land-cover change experienced worldwide is becoming a growing concern. Major socio-economic transitions, such as the breakdown of socialism in Europe, may lead to particularly high rates of landscape transformations. In this paper we examined the loss of semi-natural grasslands in Hungary between 1987 and 1999. We studied the relationship between 9 potential driving forces and the fate of grasslands using logistic GLMs. Grassland loss was found to be very high (1.31 % per year), which is far higher than either before or after this period. The most influential predictors of grassland loss were environmental and landscape characteristics (soil type, area of remnant grassland patches), and the socio-economic context (distance to paved road, and nearest settlement, human population density). Several processes and relationships can only be understood from a historical perspective (e.g. large extent of afforestation, strong decrease of soil water table). Grassland loss during the study period emerged as a consequence of survival strategies of individual farmers seeking adaptation to the changing environmental and socio-economic conditions, and not urbanization and agricultural intensification which are the main underlying drivers for the ongoing landscape transformations in most parts of the developed world. Though globalization increasingly influences local land use decisions , reconstructing and modelling recent landscape changes cannot be done without a proper understanding of local history and culture. Our analysis shows the importance of large-area yet high resolution landscape change research, which may reveal unexpected patterns of land cover change, undetected at coarser scales