Construction of a high-resolution genetic linkage map and comparative genome analysis for the reef-building coral Acropora millepora

Section of Integrative Biology, School of Biological Sciences, University of Texas at Austin, 1 University Station C0930, Austin, TX 78712, USABackground: Worldwide, coral reefs are in decline due to a range of anthropogenic disturbances, and are now also under threat from global climate change. Virtually nothing is currently known about the genetic factors that might determine whether corals adapt to the changing climate or continue to decline. Quantitative genetics studies aiming to identify the adaptively important genomic loci will require a high-resolution genetic linkage map. The phylogenetic position of corals also suggests important applications for a coral genetic map in studies of ancestral metazoan genome architecture. Results: We constructed a high-resolution genetic linkage map for the reef-building coral Acropora millepora, the first genetic map reported for any coral, or any non-Bilaterian animal. More than 500 single nucleotide polymorphism (SNP) markers were developed, most of which are transferable in populations from Orpheus Island and Great Keppel Island. The map contains 429 markers (393 gene-based SNPs and 36 microsatellites) distributed in 14 linkage groups, and spans 1,493 cM with an average marker interval of 3.4 cM. Sex differences in recombination were observed in a few linkage groups, which may be caused by haploid selection. Comparison of the coral map with other metazoan genomes (human, nematode, fly, anemone and placozoan) revealed synteny regions. Conclusions: Our study develops a framework that will be essential for future studies of adaptation in coral and it also provides an important resource for future genome sequence assembly and for comparative genomics studies on the evolution of metazoan genome structure.Integrative [email protected]

A Fuzzy Mining Algorithm for Association-Rule Knowledge Discovery

Due to increasing use of very large database and data warehouses, discovering useful knowledge from transactions is becoming an important research area. On the other hand, using fuzzy classification in data mining has been developed in recent years. Hong and Lee proposed a general learning method that automatically derives fuzzy if-then rules and membership functions from a set of given training examples using a decision table. But it is complex if there are many attributes or if the predefined unit is small. Hong and Chen improve it by first selecting relevant attributes and building appropriate initial membership functions. Based on Hong’s heuristic algorithm of membership functions and Apriori approach, we propose a fuzzy mining algorithm to explore association rules from given quantitative transactions. Experimental results on Iris data show that the proposed algorithm effectively induces more association rules

Understanding the Effect of Social Media Overload on Academic Performance: A Stressor-Strain-Outcome Perspective

Social media has deeply penetrated into university students’ daily lives, inducing excessive usage that can result in social media overload. However, only few studies have explored the adverse consequences of social media use from a pedagogical perspective. This paper aims to investigate the effects of overload on students’ academic performance and the underlying mechanism. Based on the stressor-strain-outcome model, we propose that information, communication, and social overloads influence technostress and exhaustion of students, which in turn impair their academic performance. Results from a study of 249 Chinese social media users in universities reveal that all three types of overload enhance technostress, but only information overload significantly affect exhaustion. Both technostress and exhaustion have negative effects on academic performance. This study enriches social media literature by identifying a more comprehensive classification of social media-related overload among university students and investigating the exact mechanism of excessive social media use in educational environment

Segmental Spatiotemporal CNNs for Fine-grained Action Segmentation

Joint segmentation and classification of fine-grained actions is important for applications of human-robot interaction, video surveillance, and human skill evaluation. However, despite substantial recent progress in large-scale action classification, the performance of state-of-the-art fine-grained action recognition approaches remains low. We propose a model for action segmentation which combines low-level spatiotemporal features with a high-level segmental classifier. Our spatiotemporal CNN is comprised of a spatial component that uses convolutional filters to capture information about objects and their relationships, and a temporal component that uses large 1D convolutional filters to capture information about how object relationships change across time. These features are used in tandem with a semi-Markov model that models transitions from one action to another. We introduce an efficient constrained segmental inference algorithm for this model that is orders of magnitude faster than the current approach. We highlight the effectiveness of our Segmental Spatiotemporal CNN on cooking and surgical action datasets for which we observe substantially improved performance relative to recent baseline methods.Comment: Updated from the ECCV 2016 version. We fixed an important mathematical error and made the section on segmental inference cleare

Genome-wide analysis of transposable elements and tandem repeats in the compact placozoan genome

<p>Abstract</p> <p/> <p>The placozoan <it>Trichoplax adhaerens </it>has a compact genome with many primitive eumetazoan characteristics. In order to gain a better understanding of its genome architecture, we conducted a detailed analysis of repeat content in this genome. The transposable element (TE) content is lower than that of other metazoans, and the few TEs present in the genome appear to be inactive. A new phylogenetic clade of the <it>gypsy</it>-like LTR retrotransposons was identified, which includes the majority of <it>gypsy</it>-like elements in <it>Trichoplax</it>. A particular microsatellite motif (ACAGT) exhibits unexpectedly high abundance, and also has strong association with its nearby genes.</p> <p>Reviewers</p> <p>This article was reviewed by Dr. Jerzy Jurka and Dr. I. King Jordan.</p

Flux of Root-Derived Carbon into the Nematode Micro-Food Web: A Comparison of Grassland and Agroforest

Carbon (C) cycling is crucial to agroecosystem functioning. Important determinants for the belowground C flow are soil food webs, with microorganisms and microfaunal grazers, i.e., nematodes, as key biota. The present study investigates the incorporation of plant-derived C into the nematode micro-food web under two different cropping systems, grassland (ryegrass (Lolium perenne L.) and white clover (Trifolium repens L.)) and agroforest (willow (Salix schwerinii Wolf and Salix viminalis L)). To quantify the C flux from the plant into the soil micro-food web, grass and willow were pulse-labeled with 13CO2 and the incorporation of 13C into the nematode trophic groups was monitored 3, 7, 14 and 28 days after labeling. The natural stable isotope signals (13C/12C, 15N/14N) were analyzed to determine the structure of the nematode micro-food web. The natural isotopic δ15N signal revealed different trophic levels for omnivores and predators in grassland and agroforest soils. The incorporation of plant C into nematode tissue was detectable three days after 13CO2 labeling with the highest and fastest C allocation in plant feeders in grassland, and in fungal feeders in agroforest soil. C flux dynamics between the aboveground vegetation and belowground micro-food web varied with cropping system. This demonstrates that crop-specific translocation of C affects the multitrophic interactions in the root environment, which in turn can alter soil nutrient cycling.Peer Reviewe

Personalized Financial News Recommendation Algorithm Based on Ontology

AbstractTo deal with the challenge of information overload, in this paper, we propose a financial news recommendation algorithm which help users find the articles that are interesting to read. To settle the ambiguity problem, a new presented OF-IDF method is employed to represent the unstructured text data in the form of key concepts, synonyms and synsets which are all stored in the domain ontology. For users, the recommendation algorithm build the profiles based on their behaviors to detect the genuine interests and predict current interests automatically and in real time by applying the thinking of relevance feedback. Finally, the experiment conducted on a financial news dataset demonstrates that the proposed algorithm significantly outperforms the performance of a traditional recommender

Molecular and cellular evidence for biased mitotic gene conversion in hybrid scallop

<p>Abstract</p> <p>Background</p> <p>Concerted evolution has been believed to account for homogenization of genes within multigene families. However, the exact mechanisms involved in the homogenization have been under debate. Use of interspecific hybrid system allows detection of greater level of sequence variation, and therefore, provide advantage for tracing the sequence changes. In this work, we have used an interspecific hybrid system of scallop to study the sequence homogenization processes of rRNA genes.</p> <p>Results</p> <p>Through the use of a hybrid scallop system (<it>Chlamys farreri </it>♀ × <it>Argopecten irradians </it>♂), here we provide solid molecular and cellular evidence for homogenization of the rDNA sequences into maternal genotypes. The ITS regions of the rDNA of the two scallop species exhibit distinct sequences and thereby restriction fragment length polymorphism (RFLP) patterns, and such a difference was exploited to follow the parental ITS contributions in the F1 hybrid during early development using PCR-RFLP. The representation of the paternal ITS decreased gradually in the hybrid during the development of the hybrid, and almost diminished at the 14th day after fertilization while the representation of the maternal ITS gradually increased. Chromosomal-specific fluorescence <it>in situ </it>hybridization (FISH) analysis in the hybrid revealed the presence of maternal ITS sequences on the paternal ITS-bearing chromosomes, but not vice versa. Sequence analysis of the ITS region in the hybrid not only confirmed the maternally biased conversion, but also allowed the detection of six recombinant variants in the hybrid involving short recombination regions, suggesting that site-specific recombination may be involved in the maternally biased gene conversion.</p> <p>Conclusion</p> <p>Taken together, these molecular and cellular evidences support rapid concerted gene evolution via maternally biased gene conversion. As such a process would lead to the expression of only one parental genotype, and have the opportunities to generate recombinant intermediates; this work may also have implications in novel hybrid zone alleles and genetic imprinting, as well as in concerted gene evolution. In the course of evolution, many species may have evolved involving some levels of hybridization, intra- or interspecific, the sex-biased sequence homogenization could have led to a greater role of one sex than the other in some species.</p