Catalogue Search | MBRL
Are you sure you want to remove the book from the shelf?
{{itemTitle}}
44,392
result(s) for
"Lopez, M"
Sort by:
ChromoMap: an R package for interactive visualization of multi-omics data and annotation of chromosomes
Background
The recent advancements in high-throughput sequencing have resulted in the availability of annotated genomes, as well as of multi-omics data for many living organisms. This has increased the need for graphic tools that allow the concurrent visualization of genomes and feature-associated multi-omics data on single publication-ready plots.
Results
We present chromoMap, an R package, developed for the construction of interactive visualizations of chromosomes/chromosomal regions, mapping of any chromosomal feature with known coordinates (i.e., protein coding genes, transposable elements, non-coding RNAs, microsatellites, etc.), and chromosomal regional characteristics (i.e. genomic feature density, gene expression, DNA methylation, chromatin modifications, etc.) of organisms with a genome assembly. ChromoMap can also integrate multi-omics data (genomics, transcriptomics and epigenomics) in relation to their occurrence across chromosomes. ChromoMap takes tab-delimited files (BED like) or alternatively R objects to specify the genomic co-ordinates of the chromosomes and elements to annotate. Rendered chromosomes are composed of continuous windows of a given range, which, on hover, display detailed information about the elements annotated within that range. By adjusting parameters of a single function, users can generate a variety of plots that can either be saved as static image or as HTML documents.
Conclusions
ChromoMap’s flexibility allows for concurrent visualization of genomic data in each strand of a given chromosome, or of more than one homologous chromosome; allowing the comparison of multi-omic data between genotypes (e.g. species, varieties, etc.) or between homologous chromosomes of phased diploid/polyploid genomes. chromoMap is an extensive tool that can be potentially used in various bioinformatics analysis pipelines for genomic visualization of multi-omics data.
Journal Article
Cospeciation vs host-shift speciation: methods for testing, evidence from natural associations and relation to coevolution
Hosts and their symbionts are involved in intimate physiological and ecological interactions. The impact of these interactions on the evolution of each partner depends on the time-scale considered. Short-term dynamics – ‘coevolution’ in the narrow sense – has been reviewed elsewhere. We focus here on the long-term evolutionary dynamics of cospeciation and speciation following host shifts. Whether hosts and their symbionts speciate in parallel, by cospeciation, or through host shifts, is a key issue in host–symbiont evolution. In this review, we first outline approaches to compare divergence between pairwise associated groups of species, their advantages and pitfalls. We then consider recent insights into the long-term evolution of host–parasite and host–mutualist associations by critically reviewing the literature. We show that convincing cases of cospeciation are rare (7%) and that cophylogenetic methods overestimate the occurrence of such events. Finally, we examine the relationships between short-term coevolutionary dynamics and long-term patterns of diversification in host–symbiont associations. We review theoretical and experimental studies showing that short-term dynamics can foster parasite specialization, but that these events can occur following host shifts and do not necessarily involve cospeciation. Overall, there is now substantial evidence to suggest that coevolutionary dynamics of hosts and parasites do not favor long-term cospeciation.
Journal Article
Superman : President Luthor
His fame bolstered after helping to rebuild Gotham City after an earthquake, billionaire Lex Luthor decides to run for the highest office in the land, the American presidency.
Book
Nutritive Value of Wheat Bran Diets Supplemented With Fresh Carrots and Wet Brewers’ Grains in Yellow Mealworm
Abstract
We evaluated the effect of supplementation of a wheat bran (WB) diet with fresh carrots (FC) or wet brewer’s grains (WBG) on the growth performance and chemical composition of Tenebrio molitor larvae. Additionally, a digestibility trial was performed to determine the nutritional value of the raw materials used. The control diet was based on WB-only. Two other diets were formulated in which WB was supplemented with FC (FC diet) or with WBG (WBG diet). The experiment was conducted in trays (12 per treatment) and lasted 90 d. Larval weight, feed intake, and excreted feces were controlled in each tray the experiment. The digestibility trial was performed from 48 to 62 d post-hatch. Results showed digestibility coefficients of ashes, crude protein, and gross energy were significantly higher in FC diet compared with the other diets. Consequently, both digestible energy (DE) and digestible protein (DP) contents of FC were also significantly higher than those obtained for WB and WBG diets (on av. +1.12 megajoule [MJ] DE and +9.15 g DP per kg dry matter [DM]; P < 0.003). Mealworms fed FC diet showed significantly higher final weight and average daily gain than those fed the WBG diet (+12.4%), being higher in WBG than in WB diet (+3.5%). Dietary treatment did not affect DM, ashes, ether extract, and crude protein content of mealworms obtained. Some dietary effects on amino acid and fatty acid composition were observed. This study provides novel data and a unique experimental approach to assess the nutritional value of raw materials in mealworms.
Journal Article
Influence of COVID-19 confinement on students’ performance in higher education
This study analyzes the effects of COVID-19 confinement on the autonomous learning performance of students in higher education. Using a field experiment with 458 students from three different subjects at Universidad Autónoma de Madrid (Spain), we study the differences in assessments by dividing students into two groups. The first group (control) corresponds to academic years 2017/2018 and 2018/2019. The second group (experimental) corresponds to students from 2019/2020, which is the group of students that had their face-to-face activities interrupted because of the confinement. The results show that there is a significant positive effect of the COVID-19 confinement on students' performance. This effect is also significant in activities that did not change their format when performed after the confinement. We find that this effect is significant both in subjects that increased the number of assessment activities and subjects that did not change the student workload. Additionally, an analysis of students' learning strategies before confinement shows that students did not study on a continuous basis. Based on these results, we conclude that COVID-19 confinement changed students' learning strategies to a more continuous habit, improving their efficiency. For these reasons, better scores in students' assessment are expected due to COVID-19 confinement that can be explained by an improvement in their learning performance.
Journal Article
Seasonal phosphorus and nitrogen cycling in four Japanese cool-temperate forest species
Purpose
In plant-soil systems, phosphorus partitioning during the annual cycle related to nitrogen partitioning remains largely unknown. The present study aims at assessing the soil-plant P allocation patterns of four tree species along four phenological stages and its relationship with tissues and soil N concentrations.
Methods
Cryptomeria japonica, Larix kaempferi, Fagus crenata
and
Robinia pseudoacacia
trees were selected to sample coarse roots, sapwood, foliage, litter and soil during four phenological stages where total and Olsen extractable P and nitrogen content were measured respectively.
Results
Intra- and inter plant tissue nitrogen correlated well with phosphorus during the four phenological stages, especially root nitrogen.
Fagus
and
Robinia
were phosphorus limited,
Larix
was nitrogen limited and
Cryptomeria
co-limited. All species reabsorbed phosphorus and nitrogen from foliage prior to leaf abscission and stored nitrogen in roots and sapwood. Phosphorus storage was solely found in sapwood of
Robinia
. Soil dissolved ammonium correlated positively with nitrogen reabsorption efficiency during the green leaf stage, while single soil nutrient variables did not correlate with phosphorus reabsorption efficiency.
Conclusions
Plant tissues nitrogen partitioning correlated well with their respective phosphorus partitioning and the increase of soil NH
4
+
correlated positively with nitrogen reabsorption efficiency, regardless of tree species during the green leaf stage. The results of this study show the intricate relationship that exists between nitrogen and phosphorus in the soil-plant continuum as well as the tree species specific internal cycling of these nutrients.
Journal Article
Patterns, dynamics and consequences of microplastic ingestion by the temperate coral, Astrangia poculata
Microplastics (less than 5 mm) are a recognized threat to aquatic food webs because they are ingested at multiple trophic levels and may bioaccumulate. In urban coastal environments, high densities of microplastics may disrupt nutritional intake. However, behavioural dynamics and consequences of microparticle ingestion are still poorly understood. As filter or suspension feeders, benthic marine invertebrates are vulnerable to microplastic ingestion. We explored microplastic ingestion by the temperate coral Astrangia poculata . We detected an average of over 100 microplastic particles per polyp in wild-captured colonies from Rhode Island. In the laboratory, corals were fed microbeads to characterize ingestion preference and retention of microplastics and consequences on feeding behaviour. Corals were fed biofilmed microplastics to test whether plastics serve as vectors for microbes. Ingested microplastics were apparent within the mesenterial tissues of the gastrovascular cavity. Corals preferred microplastic beads and declined subsequent offerings of brine shrimp eggs of the same diameter, suggesting that microplastic ingestion can inhibit food intake. The corals co-ingested Escherichia coli cells with microbeads. These findings detail specific mechanisms by which microplastics threaten corals, but also hint that the coral A. poculata , which has a large coastal range, may serve as a useful bioindicator and monitoring tool for microplastic pollution.
Journal Article
Association Between Bacteremia Due to Streptococcus gallolyticus subsp. gallolyticus (Streptococcus bovis I) and Colorectal Neoplasia: A Case-Control Study
Background. The association between bacteremia by Streptococcus gallolyticus subsp. gallolyticus (SGG) and colorectal neoplasia (CRN) is well established but the frequency of the association varies widely in different studies. We conducted a case-control study to assess the association between SGG bacteremia and CRN. Methods. An analysis of all SGG bacteremias was performed during the period 1988-2011. The frequency of CRN in patients with SGG bacteremia was compared with the frequency of CRN in a symptomatic control group of patients matched at a 1:2 ratio for gender and age (±3 years) without S. bovis bacteremia and personal history of CRN and with increased risk of CRN (by the presence of symptoms, signs, or test suspicious of colonic pathology or by family history of CRN). Results. One hundred nine cases of SGG bacteremia were detected (mean age, 66 years; 87% male). Colonoscopy was performed in 98 cases, diagnosing 69 cases of CRN: 57 adenomas (39 advanced adenomas) and 12 invasive carcinomas. Only 4 cases had suspected CRN before the blood culture. The prevalence of CRN was higher in patients with SGG bacteremia than in the 196 control patients (70% vs 32%; odds ratio [OR], 5.1; 95% confidence interval [CI], 3.0-8.6). This difference was not significant when comparing nonadvanced adenomas (19% vs 12%), but we found significant differences in advanced adenomas (40% vs 16%; OR, 3.5; 95% CI, 2.0-6.1) and invasive carcinomas (12% vs 5%; OR, 2.9; 95% CI, 1.2-6.9). Conclusions. The frequency of CRN among SGG infected patients is significantly increased compared with symptomatic age-matched controls, indicating that SGG infection is a strong indicator for underlying occult malignancy.
Journal Article