A computational approach for identifying pathogenicity islands in prokaryotic genomes

BACKGROUND: Pathogenicity islands (PAIs), distinct genomic segments of pathogens encoding virulence factors, represent a subgroup of genomic islands (GIs) that have been acquired by horizontal gene transfer event. Up to now, computational approaches for identifying PAIs have been focused on the detection of genomic regions which only differ from the rest of the genome in their base composition and codon usage. These approaches often lead to the identification of genomic islands, rather than PAIs. RESULTS: We present a computational method for detecting potential PAIs in complete prokaryotic genomes by combining sequence similarities and abnormalities in genomic composition. We first collected 207 GenBank accessions containing either part or all of the reported PAI loci. In sequenced genomes, strips of PAI-homologs were defined based on the proximity of the homologs of genes in the same PAI accession. An algorithm reminiscent of sequence-assembly procedure was then devised to merge overlapping or adjacent genomic strips into a large genomic region. Among the defined genomic regions, PAI-like regions were identified by the presence of homolog(s) of virulence genes. Also, GIs were postulated by calculating G+C content anomalies and codon usage bias. Of 148 prokaryotic genomes examined, 23 pathogenic and 6 non-pathogenic bacteria contained 77 candidate PAIs that partly or entirely overlap GIs. CONCLUSION: Supporting the validity of our method, included in the list of candidate PAIs were thirty four PAIs previously identified from genome sequencing papers. Furthermore, in some instances, our method was able to detect entire PAIs for those only partial sequences are available. Our method was proven to be an efficient method for demarcating the potential PAIs in our study. Also, the function(s) and origin(s) of a candidate PAI can be inferred by investigating the PAI queries comprising it. Identification and analysis of potential PAIs in prokaryotic genomes will broaden our knowledge on the structure and properties of PAIs and the evolution of bacterial pathogenesis

Eficacia antiincrustante de una formulación de pintura de reducción controlada con acetofenona

Biofouling is an inevitable problem that occurs continually on marine fishing vessels and other small crafts. The nature of the antifouling (AF) coatings used to prevent biofouling on these small vessels is of great environmental concern. Therefore, the efficacy of a non-toxic AF candidate, acetophenone, was evaluated in preliminary laboratory assays using marine bacteria, diatom and Ulva spores. At a low concentration of 100 μg cm–2 of acetophenone, spore attachment of a green fouling alga was significantly reduced (p < 0.01). Similarly, 40% acetophenone coatings significantly inhibited diatom attachment. This new non-toxic AF agent was incorporated into controlled depletion paint (CDP). Fouling coverage (%), biomass, and fouling resistance (%) were estimated. On CDP coatings made with acetophenone (40%), a significant decrease in fouling biomass was estimated (p < 0.01).El biofouling es un problema inevitable que ocurre continuamente en los buques de pesca marina y en las pequeñas embarcaciones. La naturaleza de los recubrimientos antiincrustantes (AF) usados para prevenir el bioincrustado en estos pequeños buques tiene gran preocupación ambiental. Por lo tanto, la eficacia de un candidato AF no tóxico, la acetofenona, se evaluó en ensayos preliminares de laboratorio usando bacterias marinas, diatomeas y esporas de Ulva. A una concentración baja de 100 μg cm–2 de acetofenona, la adherencia de esporas de una alga incrustante verde se redujo significativamente (p < 0.01). Del mismo modo, el revestimiento de acetofenona a un nivel del 40% inhibieró significativamente la adherencia de diatomeas. Además, esta nueva acetofenona AF no tóxica se incorporó a la pintura de reducción controlada (CDP). La cobertura de las incrustaciones (%), la biomasa y la resistencia a la incrustación (%) fueron estimadas. En recubrimientos de CDP donde se incorporó la acetofenona (40%), se estimó una disminución significativa de la biomasa incrustante (p < 0.01)

Towards pathogenomics: a web-based resource for pathogenicity islands

Pathogenicity islands (PAIs) are genetic elements whose products are essential to the process of disease development. They have been horizontally (laterally) transferred from other microbes and are important in evolution of pathogenesis. In this study, a comprehensive database and search engines specialized for PAIs were established. The pathogenicity island database (PAIDB) is a comprehensive relational database of all the reported PAIs and potential PAI regions which were predicted by a method that combines feature-based analysis and similarity-based analysis. Also, using the PAI Finder search application, a multi-sequence query can be analyzed onsite for the presence of potential PAIs. As of April 2006, PAIDB contains 112 types of PAIs and 889 GenBank accessions containing either partial or all PAI loci previously reported in the literature, which are present in 497 strains of pathogenic bacteria. The database also offers 310 candidate PAIs predicted from 118 sequenced prokaryotic genomes. With the increasing number of prokaryotic genomes without functional inference and sequenced genetic regions of suspected involvement in diseases, this web-based, user-friendly resource has the potential to be of significant use in pathogenomics. PAIDB is freely accessible at

Sound-Guided Semantic Video Generation

The recent success in StyleGAN demonstrates that pre-trained StyleGAN latent space is useful for realistic video generation. However, the generated motion in the video is usually not semantically meaningful due to the difficulty of determining the direction and magnitude in the StyleGAN latent space. In this paper, we propose a framework to generate realistic videos by leveraging multimodal (sound-image-text) embedding space. As sound provides the temporal contexts of the scene, our framework learns to generate a video that is semantically consistent with sound. First, our sound inversion module maps the audio directly into the StyleGAN latent space. We then incorporate the CLIP-based multimodal embedding space to further provide the audio-visual relationships. Finally, the proposed frame generator learns to find the trajectory in the latent space which is coherent with the corresponding sound and generates a video in a hierarchical manner. We provide the new high-resolution landscape video dataset (audio-visual pair) for the sound-guided video generation task. The experiments show that our model outperforms the state-of-the-art methods in terms of video quality. We further show several applications including image and video editing to verify the effectiveness of our method

Evolution of ribosomal DNA-derived satellite repeat in tomato genome

<p>Abstract</p> <p>Background</p> <p>Tandemly repeated DNA, also called as satellite DNA, is a common feature of eukaryotic genomes. Satellite repeats can expand and contract dramatically, which may cause genome size variation among genetically-related species. However, the origin and expansion mechanism are not clear yet and needed to be elucidated.</p> <p>Results</p> <p>FISH analysis revealed that the satellite repeat showing homology with intergenic spacer (IGS) of rDNA present in the tomato genome. By comparing the sequences representing distinct stages in the divergence of rDNA repeat with those of canonical rDNA arrays, the molecular mechanism of the evolution of satellite repeat is described. Comprehensive sequence analysis and phylogenetic analysis demonstrated that a long terminal repeat retrotransposon was interrupted into each copy of the 18S rDNA and polymerized by recombination rather than transposition via an RNA intermediate. The repeat was expanded through doubling the number of IGS into the 25S rRNA gene, and also greatly increasing the copy number of type I subrepeat in the IGS of 25-18S rDNA by segmental duplication. Homogenization to a single type of subrepeat in the satellite repeat was achieved as the result of amplifying copy number of the type I subrepeat but eliminating neighboring sequences including the type II subrepeat and rRNA coding sequence from the array. FISH analysis revealed that the satellite repeats are commonly present in closely-related <it>Solanum </it>species, but vary in their distribution and abundance among species.</p> <p>Conclusion</p> <p>These results represent that the dynamic satellite repeats were originated from intergenic spacer of rDNA unit in the tomato genome. This result could serve as an example towards understanding the initiation and the expansion of the satellite repeats in complex eukaryotic genome.</p

Cellular and Tissue Selectivity of AAV Serotypes for Gene Delivery to Chondrocytes and Cartilage

Background: Despite several studies on the effect of adeno-associated virus (AAV)-based therapeutics on osteoarthritis (OA), information on the transduction efficiency and applicable profiles of different AAV serotypes to chondrocytes in hard cartilage tissue is still limited. Moreover, the recent discovery of additional AAV serotypes makes it necessary to screen for more suitable AAV serotypes for specific tissues. Here, we compared the transduction efficiencies of 14 conventional AAV serotypes in human chondrocytes, mouse OA models, and human cartilage explants obtained from OA patients. Methods: To compare the transduction efficiency of individual AAV serotypes, green fluorescent protein (GFP) expression was detected by fluorescence microscopy or western blotting. Likewise, to compare the transduction efficiencies of individual AAV serotypes in cartilage tissues, GFP expression was determined using fluorescence microscopy or immunohistochemistry, and GFP-positive cells were counted. Results: Only AAV2, 5, 6, and 6.2 exhibited substantial transduction efficiencies in both normal and OA chondrocytes. All AAV serotypes except AAV6 and rh43 could effectively transduce human bone marrow mesenchymal stem cells. In human and mouse OA cartilage tissues, AAV2, AAV5, AAV6.2, AAV8, and AAV rh39 showed excellent tissue specificity based on transduction efficiency. These results indicate the differences in transduction efficiencies of AAV serotypes between cellular and tissue models. Conclusions: Our findings indicate that AAV2 and AAV6.2 may be the best choices for AAV-mediated gene delivery into intra-articular cartilage tissue. These AAV vectors hold the potential to be of use in clinical applications to prevent OA progression if appropriate therapeutic genes are inserted into the vector

WATCHFUL OBSERVATION VERSUS EARLY AORTIC VALVE REPLACEMENT FOR SYMPTOMATIC PATIENTS WITH LOW-GRADIENT SEVERE AORTIC STENOSIS AND PRESERVED EJECTION FRACTION

Brief Communications Arising: arising from X. Dong, B. Milholland & J. Vijg Nature 538, 257–259 (2016); doi:10.1038/nature19793. Comments by: Beer, J.A.A. de, Bardoutsos, A. & Janssen, F. (2017)

Children\u27s exposure to food advertising on free-to-air television: an Asia-Pacific perspective

There is an established link between food promotions and children\u27s food purchase and consumption. Children in developing countries may be more vulnerable to food promotions given the relative novelty of advertising in these markets. This study aimed to determine the scope of television food advertising to children across the Asia-Pacific to inform policies to restrict this marketing. Six sites were sampled, including from China, Indonesia, Malaysia and South Korea. At each site, 192 h of television were recorded (4 days, 16 h/day, three channels) from May to October 2012. Advertised foods were categorized as core/healthy, non-core/unhealthy or miscellaneous, and by product type. Twenty-seven percent of advertisements were for food/beverages, and the most frequently advertised product was sugar-sweetened drinks. Rates of non-core food advertising were highest during viewing times most popular with children, when between 3 (South Korea) and 15 (Indonesia) non-core food advertisements were broadcast each hour. Children in the Asia-Pacific are exposed to high volumes of unhealthy food/beverage television advertising. Different policy arrangements for food advertising are likely to contribute to regional variations in advertising patterns. Cities with the lowest advertising rates can be identified as exemplars of good policy practice

Unlocking the hidden chemical space in cubic-phase garnet solid electrolyte for efficient quasi-all-solid-state lithium batteries

Garnet-type Li7La3Zr2O12 (LLZO) solid electrolytes (SE) demonstrates appealing ionic conductivity properties for all-solid-state lithium metal battery applications. However, LLZO (electro)chemical stability in contact with the lithium metal electrode is not satisfactory for developing practical batteries. To circumvent this issue, we report the preparation of various doped cubic-phase LLZO SEs without vacancy formation (i.e., Li = 7.0 such as Li7La3Zr0.5Hf0.5Sc0.5Nb0.5O12 and Li7La3Zr0.4Hf0.4Sn0.4Sc0.4Ta0.4O12). The entropy-driven synthetic approach allows access to hidden chemical space in cubic-phase garnet and enables lower solid-state synthesis temperature as the cubic-phase nucleation decreases from 750 to 400 ??C. We demonstrate that the SEs with Li = 7.0 show better reduction stability against lithium metal compared to SE with low lithium contents and identical atomic species (i.e., Li = 6.6 such as Li6.6La3Zr0.4Hf0.4Sn0.4Sc0.2Ta0.6O12). Moreover, when a Li7La3Zr0.4Hf0.4Sn0.4Sc0.4Ta0.4O12 pellet is tested at 60 ??C in coin cell configuration with a Li metal negative electrode, a LiNi1/3Co1/3Mn1/3O2-based positive electrode and an ionic liquid-based electrolyte at the cathode|SE interface, discharge capacity retention of about 92% is delivered after 700 cycles at 0.8 mA/cm2 and 60 ??C