Metagrowth: a new resource for the building of metabolic hypotheses in microbiology

Metagrowth is a new type of knowledge base developed to guide the experimental studies of culture conditions of obligate parasitic bacteria. We have gathered biological evidences giving possible clues to the development of the axenic (i.e. ‘cell-free’) growth of obligate parasites from various sources including published literature, genomic sequence information, metabolic databases and transporter databases. The database entries are composed of those evidences and specific hypotheses derived from them. Currently, 200 entries are available for Rickettsia prowazekii, Rickettsia conorii, Tropheryma whipplei, Treponema pallidum, Mycobacterium tuberculosis and Coxiella burnetii. The web interface of Metagrowth helps users to design new axenic culture media eventually suitable for those bacteria. Metagrowth is accessible at http://igs-server.cnrs-mrs.fr/axenic/

The Position Dependence of the SCF Screened Potential in Several Nonbenzenoid Hydrocarbons Containing a Four-Membered Ring

The bond lengths and SCF screened potentials of bicyclo- . [4.2.0]octa-1,3,5,7-tetraene (1), bicyclo[6.2.0]deca-1,3,5,7,9-pentane (2), cyclobuta[l,2:3,4]dicyclopentene (3), cyclopenta[3,4]cyclobuta[l,2]cycloheptene (4), benzo[3,4]cyclobuta[l,2]cyclooctene (5), cyclobuta[ 1,2, :3,4Jdicycloheptene (6), and cyclobuta[l,2 :3,4]dicyclooctene (7) were calculated by using the SCF screened potential MO CI method. From the bond lengths and the characteristics of the screened potentials, it is concluded that molecules 1, 2, 3, 4, 6, and 7 are polyolefinic and molecule 5 has both aromatic and polyolefinic characters

The Position Dependence of the SCF Screened Potential in Several Nonbenzenoid Hydrocarbons Containing a Four-Membered Ring

The bond lengths and SCF screened potentials of bicyclo- . [4.2.0]octa-1,3,5,7-tetraene (1), bicyclo[6.2.0]deca-1,3,5,7,9-pentane (2), cyclobuta[l,2:3,4]dicyclopentene (3), cyclopenta[3,4]cyclobuta[l,2]cycloheptene (4), benzo[3,4]cyclobuta[l,2]cyclooctene (5), cyclobuta[ 1,2, :3,4Jdicycloheptene (6), and cyclobuta[l,2 :3,4]dicyclooctene (7) were calculated by using the SCF screened potential MO CI method. From the bond lengths and the characteristics of the screened potentials, it is concluded that molecules 1, 2, 3, 4, 6, and 7 are polyolefinic and molecule 5 has both aromatic and polyolefinic characters

ICR News 2020

This Annual Report covers from 1 January to 31 December 202

Fostering Evidence-Based Education with Learning Analytics: Capturing Teaching-Learning Cases from Log Data

Evidence-based education has become more relevant in the current technology-enhanced teaching-learning era. This paper introduces how Educational BIG data has the potential to generate such evidence. As evidence-based education traditionally hooks on the meta-analysis of the literature, so there are existing platforms that support manual input of evidence as structured information. However, such platforms often focus on researchers as end-users and its design is not aligned to the practitioners’ workflow. In our work, we propose a technology-mediated process of capturing teaching-learning cases (TLCs) using a learning analytics framework. Each case is primarily a single data point regarding the result of an intervention and multiple such cases would generate an evidence of intervention effectiveness. To capture TLCs in our current context, our system automatically conducts statistical modelling of learning logs captured from Learning Management Systems (LMS) and an e-book reader. Indicators from those learning logs are evaluated by the Linear Mixed Effects model to compute whether an intervention had a positive learning effect. We present two case studies to illustrate our approach of extracting case effectiveness from two different learning contexts – one at a junior-high math class where email messages were sent as intervention and another in a blended learning context in a higher education physics class where an active learning strategy was implemented. Our novelty lies in the proposed automated approach of data aggregation, analysis, and case storing using a Learning Analytics framework for supporting evidence-based practice more accessible for practitioners

Mimivirus reveals Mre11/Rad50 fusion proteins with a sporadic distribution in eukaryotes, bacteria, viruses and plasmids

<p>Abstract</p> <p>Background</p> <p>The Mre11/Rad50 complex and the homologous SbcD/SbcC complex in bacteria play crucial roles in the metabolism of DNA double-strand breaks, including DNA repair, genome replication, homologous recombination and non-homologous end-joining in cellular life forms and viruses. Here we investigated the amino acid sequence of the Mimivirus R555 gene product, originally annotated as a Rad50 homolog, and later shown to have close homologs in marine microbial metagenomes.</p> <p>Results</p> <p>Our bioinformatics analysis revealed that R555 protein sequence is constituted from the fusion of an N-terminal Mre11-like domain with a C-terminal Rad50-like domain. A systematic database search revealed twelve additional cases of Mre11/Rad50 (or SbcD/SbcC) fusions in a wide variety of unrelated organisms including unicellular and multicellular eukaryotes, the megaplasmid of a bacterium associated to deep-sea hydrothermal vents (<it>Deferribacter desulfuricans</it>) and the plasmid of <it>Clostridium kluyveri</it>. We also showed that R555 homologs are abundant in the metagenomes from different aquatic environments and that they most likely belong to aquatic viruses. The observed phyletic distribution of these fusion proteins suggests their recurrent creation and lateral gene transfers across organisms.</p> <p>Conclusions</p> <p>The existence of the fused version of protein sequences is consistent with known functional interactions between Mre11 and Rad50, and the gene fusion probably enhanced the opportunity for lateral transfer. The abundance of the Mre11/Rad50 fusion genes in viral metagenomes and their sporadic phyletic distribution in cellular organisms suggest that viruses, plasmids and transposons played a crucial role in the formation of the fusion proteins and their propagation into cellular genomes.</p

Taxonomic distribution of large DNA viruses in the sea

Phylogenetic mapping of metagenomics data reveals the taxonomic distribution of large DNA viruses in the sea, including giant viruses of the Mimiviridae family

Horizontal gene transfer and nucleotide compositional anomaly in large DNA viruses

<p>Abstract</p> <p>Background</p> <p>DNA viruses have a wide range of genome sizes (5 kb up to 1.2 Mb, compared to 0.16 Mb to 1.5 Mb for obligate parasitic bacteria) that do not correlate with their virulence or the taxonomic distribution of their hosts. The reasons for such large variation are unclear. According to the traditional view of viruses as gifted "gene pickpockets", large viral genome sizes could originate from numerous gene acquisitions from their hosts. We investigated this hypothesis by studying 67 large DNA viruses with genome sizes larger than 150 kb, including the recently characterized giant mimivirus. Given that horizontally transferred DNA often have anomalous nucleotide compositions differing from the rest of the genome, we conducted a detailed analysis of the inter- and intra-genome compositional properties of these viruses. We then interpreted their compositional heterogeneity in terms of possible causes, including strand asymmetry, gene function/expression, and horizontal transfer.</p> <p>Results</p> <p>We first show that the global nucleotide composition and nucleotide word usage of viral genomes are species-specific and distinct from those of their hosts. Next, we identified compositionally anomalous (cA) genes in viral genomes, using a method based on Bayesian inference. The proportion of cA genes is highly variable across viruses and does not exhibit a significant correlation with genome size. The vast majority of the cA genes were of unknown function, lacking homologs in the databases. For genes with known homologs, we found a substantial enrichment of cA genes in specific functional classes for some of the viruses. No significant association was found between cA genes and compositional strand asymmetry. A possible exogenous origin for a small fraction of the cA genes could be confirmed by phylogenetic reconstruction.</p> <p>Conclusion</p> <p>At odds with the traditional dogma, our results argue against frequent genetic transfers to large DNA viruses from their modern hosts. The large genome sizes of these viruses are not simply explained by an increased propensity to acquire foreign genes. This study also confirms that the anomalous nucleotide compositions of the cA genes is sometimes linked to particular biological functions or expression patterns, possibly leading to an overestimation of recent horizontal gene transfers.</p

E-book-based learning activity during COVID-19: engagement behaviors and perceptions of Japanese junior-high school students

Recent spread of the COVID-19 forces governments around the world to temporarily close educational institutions. In this paper, we evaluated learning engagement, level of satisfaction and anxiety of e-book based remote teaching strategy on an online learning platform. The research involves 358 students at an urban junior-high school in Japan. Learning logs were analyzed to measure student engagement, whereas survey responses indicated their perception regarding the remote learning experience. Log analysis revealed that the average completion rate over 267 learning materials was 67%. We also observed a significant decrease in engagement 3 weeks after remote learning and different subjects and grades. Survey analysis showed students felt both satisfaction and anxiety about remote learning. However, there were significant differences in the level of satisfaction between different grades. The results indicated that (1) maintaining students' motivation is a challenge to remote learning in secondary schools, and (2) we need to relieve students' anxiety about their own progress in the class and their classes after the break. This study is the first to report trends in actual teaching-learning engagement, which were recorded during sessions of emergency remote teaching in Japanese schools. The results can inform the future implementation of remote learning in junior-high schools

Evidence Mining Using Course Schedule

Creating evidence from learning big data has become increasingly important as we can use eLearning infrastructure and store learning log digitally. On the other hand, we need to time and effort to create evidence because it is manual. In this paper, we proposed the method to make evidence easier. Especially, we focus on procedure to automatically select the duration of intervention and comparison data based on the course schedule information. We simulated the procedure and confirmed the making a case based on course schedule information. In the discussion part, we mentioned the points that should be further improved for practical use in the future. Through our method, we will democratize the evidence-based practice to all the teachers in schools