Fungal Secretome Database: Integrated platform for annotation of fungal secretomes

<p>Abstract</p> <p>Background</p> <p>Fungi secrete various proteins that have diverse functions. Prediction of secretory proteins using only one program is unsatisfactory. To enhance prediction accuracy, we constructed Fungal Secretome Database (FSD).</p> <p>Description</p> <p>A three-layer hierarchical identification rule based on nine prediction programs was used to identify putative secretory proteins in 158 fungal/oomycete genomes (208,883 proteins, 15.21% of the total proteome). The presence of putative effectors containing known host targeting signals such as RXLX [EDQ] and RXLR was investigated, presenting the degree of bias along with the species. The FSD's user-friendly interface provides summaries of prediction results and diverse web-based analysis functions through Favorite, a personalized repository.</p> <p>Conclusions</p> <p>The FSD can serve as an integrated platform supporting researches on secretory proteins in the fungal kingdom. All data and functions described in this study can be accessed on the FSD web site at <url>http://fsd.snu.ac.kr/</url>.</p

IMGD: an integrated platform supporting comparative genomics and phylogenetics of insect mitochondrial genomes

<p>Abstract</p> <p>Background</p> <p>Sequences and organization of the mitochondrial genome have been used as markers to investigate evolutionary history and relationships in many taxonomic groups. The rapidly increasing mitochondrial genome sequences from diverse insects provide ample opportunities to explore various global evolutionary questions in the superclass Hexapoda. To adequately support such questions, it is imperative to establish an informatics platform that facilitates the retrieval and utilization of available mitochondrial genome sequence data.</p> <p>Results</p> <p>The Insect Mitochondrial Genome Database (IMGD) is a new integrated platform that archives the mitochondrial genome sequences from 25,747 hexapod species, including 112 completely sequenced and 20 nearly completed genomes and 113,985 partially sequenced mitochondrial genomes. The Species-driven User Interface (SUI) of IMGD supports data retrieval and diverse analyses at multi-taxon levels. The Phyloviewer implemented in IMGD provides three methods for drawing phylogenetic trees and displays the resulting trees on the web. The SNP database incorporated to IMGD presents the distribution of SNPs and INDELs in the mitochondrial genomes of multiple isolates within eight species. A newly developed comparative SNU Genome Browser supports the graphical presentation and interactive interface for the identified SNPs/INDELs.</p> <p>Conclusion</p> <p>The IMGD provides a solid foundation for the comparative mitochondrial genomics and phylogenetics of insects. All data and functions described here are available at the web site <url>http://www.imgd.org/</url>.</p

Effect of rhBMP-2 applied with a 3D-printed titanium implant on new bone formation in rabbit calvarium

Objective: This study sought to compare the biocompatibility of a three-dimensional (3D)-printed titanium implant with a conventional machined titanium product, as well as the effect of such implant applied with recombinant human Bone Morphogenetic Protein Type 2 (rhBMP-2) for guided bone regeneration.&nbsp;Methodology: Disk-shaped titanium specimens fabricated either by the conventional machining technique or by the 3D-printing technique were compared by MC3T3-E1 cells cytotoxicity assay. New bone formation was evaluated using a rapid prototype titanium cap applied to the calvaria of 10 rabbits, which were divided into two groups: one including an atelopeptide collagen plug on one side of the cap (group I) and the other including a plug with rhBMP-2 on the other side (group II). At six and 12 weeks after euthanasia, rabbits calvaria underwent morphometric analysis through radiological and histological examination.&nbsp;Results: Through the cytotoxicity assay, we identified a significantly higher number of MC3T3-E1 cells in the 3D-printed specimen when compared to the machined specimen after 48 hours of culture. Moreover, morphometric analysis indicated significantly greater bone formation at week 12 on the side where rhBMP-2 was applied when evaluating the upper portion immediately below the ca p. Conclusion: The results suggest that 3D-printed titanium implant applied with rhBMP-2 enables new bone formation

Fungal cytochrome P450 database

<p>Abstract</p> <p>Background</p> <p>Cytochrome P450 enzymes play critical roles in fungal biology and ecology. To support studies on the roles and evolution of cytochrome P450 enzymes in fungi based on rapidly accumulating genome sequences from diverse fungal species, an efficient bioinformatics platform specialized for this super family of proteins is highly desirable.</p> <p>Results</p> <p>The Fungal Cytochrome P450 Database (FCPD) archives genes encoding P450s in the genomes of 66 fungal and 4 oomycete species (4,538 in total) and supports analyses of their sequences, chromosomal distribution pattern, and evolutionary histories and relationships. The archived P450s were classified into 16 classes based on InterPro terms and clustered into 141 groups using tribe-MCL. The proportion of P450s in the total proteome and class distribution in individual species exhibited certain taxon-specific characteristics.</p> <p>Conclusion</p> <p>The FCPD will facilitate systematic identification and multifaceted analyses of P450s at multiple taxon levels via the web. All data and functions are available at the web site <url>http://p450.riceblast.snu.ac.kr/</url>.</p

HD-Bind: Encoding of Molecular Structure with Low Precision, Hyperdimensional Binary Representations

Publicly available collections of drug-like molecules have grown to comprise 10s of billions of possibilities in recent history due to advances in chemical synthesis. Traditional methods for identifying ``hit'' molecules from a large collection of potential drug-like candidates have relied on biophysical theory to compute approximations to the Gibbs free energy of the binding interaction between the drug to its protein target. A major drawback of the approaches is that they require exceptional computing capabilities to consider for even relatively small collections of molecules. Hyperdimensional Computing (HDC) is a recently proposed learning paradigm that is able to leverage low-precision binary vector arithmetic to build efficient representations of the data that can be obtained without the need for gradient-based optimization approaches that are required in many conventional machine learning and deep learning approaches. This algorithmic simplicity allows for acceleration in hardware that has been previously demonstrated for a range of application areas. We consider existing HDC approaches for molecular property classification and introduce two novel encoding algorithms that leverage the extended connectivity fingerprint (ECFP) algorithm. We show that HDC-based inference methods are as much as 90 times more efficient than more complex representative machine learning methods and achieve an acceleration of nearly 9 orders of magnitude as compared to inference with molecular docking. We demonstrate multiple approaches for the encoding of molecular data for HDC and examine their relative performance on a range of challenging molecular property prediction and drug-protein binding classification tasks. Our work thus motivates further investigation into molecular representation learning to develop ultra-efficient pre-screening tools

Interfacial Engineering at Quantum Dot-Sensitized TiO2 Photoelectrodes for Ultrahigh Photocurrent Generation

Metal oxide semiconductor/chalcogenide quantum dot (QD) heterostructured photoanodes show photocurrent densities >30 mA/cm2 with ZnO, approaching the theoretical limits in photovoltaic (PV) cells. However, comparative performance has not been achieved with TiO2. Here, we applied a TiO2(B) surface passivation layer (SPL) on TiO2/QD (PbS and CdS) and achieved a photocurrent density of 34.59 mA/cm2 under AM 1.5G illumination for PV cells, the highest recorded to date. The SPL improves electron conductivity by increasing the density of surface states, facilitating multiple trapping/detrapping transport, and increasing the coordination number of TiO2 nanoparticles. This, along with impeded electron recombination, led to enhanced collection efficiency, which is a major factor for performance. Furthermore, SPL-treated TiO2/QD photoanodes were successfully exploited in photoelectrochemical water splitting cells, showing an excellent photocurrent density of 14.43 mA/cm2 at 0.82 V versus the Reversible Hydrogen Electrode (RHE). These results suggest a new promising strategy for the development of high-performance photoelectrochemical devices.Funding for open access charge: CRUE-Universitat Jaume IThis work was supported by the Korea Center for Artificial Photosynthesis (KCAP) of Sogang University, funded by the Ministry of Science, ICT, and Future Planning (MSIP) through a National Research Foundation of Korea (Grant no. 2009-0093883). This work also was supported by a grant from the Basic Science Research Program through the National Research Foundation (NRF) of Korea funded by the Ministry of Science and ICT (NRF-2019R1A2C1003429) and by the Ministry of Education (NRF-2018R1A6A1A03024231). Also, this work was supported by the Ministerio de Ciencia, Innovacio′n y Universidades of Spain through the project ENE2017–85087-C3-1-R. Therefore, the authors acknowledge and thank the Korean and Spanish governments for technical and financial support. S. D. G

SNUGB: a versatile genome browser supporting comparative and functional fungal genomics

<p>Abstract</p> <p>Background</p> <p>Since the full genome sequences of <it>Saccharomyces cerevisiae</it> were released in 1996, genome sequences of over 90 fungal species have become publicly available. The heterogeneous formats of genome sequences archived in different sequencing centers hampered the integration of the data for efficient and comprehensive comparative analyses. The Comparative Fungal Genomics Platform (CFGP) was developed to archive these data via a single standardized format that can support multifaceted and integrated analyses of the data. To facilitate efficient data visualization and utilization within and across species based on the architecture of CFGP and associated databases, a new genome browser was needed.</p> <p>Results</p> <p>The Seoul National University Genome Browser (SNUGB) integrates various types of genomic information derived from 98 fungal/oomycete (137 datasets) and 34 plant and animal (38 datasets) species, graphically presents germane features and properties of each genome, and supports comparison between genomes. The SNUGB provides three different forms of the data presentation interface, including diagram, table, and text, and six different display options to support visualization and utilization of the stored information. Information for individual species can be quickly accessed via a new tool named the taxonomy browser. In addition, SNUGB offers four useful data annotation/analysis functions, including 'BLAST annotation.' The modular design of SNUGB makes its adoption to support other comparative genomic platforms easy and facilitates continuous expansion.</p> <p>Conclusion</p> <p>The SNUGB serves as a powerful platform supporting comparative and functional genomics within the fungal kingdom and also across other kingdoms. All data and functions are available at the web site <url>http://genomebrowser.snu.ac.kr/</url>.</p

Broken Kramers' degeneracy in altermagnetic MnTe

Altermagnetism is a newly identified fundamental class of magnetism with vanishing net magnetization and time-reversal symmetry broken electronic structure. Probing the unusual electronic structure with nonrelativistic spin splitting would be a direct experimental verification of altermagnetic phase. By combining high-quality film growth and $in~situ$ angle-resolved photoemission spectroscopy, we report the electronic structure of an altermagnetic candidate, $\alpha$-MnTe. Temperature dependent study reveals the lifting of Kramers{\textquoteright} degeneracy accompanied by a magnetic phase transition at $T_N=267\text{ K}$ with spin splitting of up to $370\text{ meV}$, providing direct spectroscopic evidence for altermagnetism in MnTe

Systematic and searchable classification of cytochrome P450 proteins encoded by fungal and oomycete genomes

Background: Cytochrome P450 proteins (CYPs) play diverse and pivotal roles in fungal metabolism and adaptation to specific ecological niches. Fungal genomes encode extremely variableThis research has been supported by the USDA Agriculture and Food Research Initiative Competitive Grants Program (Grant no. 2010-65110-20488). The work in Lees lab has been supported by the National Research Foundation of Korea (2012–0001149 and 2012–0000141) and the NextGeneration Bio-Green 21 Program of Rural Development Administration in Korea (PJ00821201).OAIID:oai:osos.snu.ac.kr:snu2012-01/102/0000003441/6SEQ:6PERF_CD:SNU2012-01EVAL_ITEM_CD:102USER_ID:0000003441ADJUST_YN:YEMP_ID:A003535DEPT_CD:5321CITE_RATE:4.073FILENAME:첨부된 내역이 없습니다.DEPT_NM:농생명공학부EMAIL:[email protected]_YN:YCONFIRM: