Table_1_SCDevDB: A Database for Insights Into Single-Cell Gene Expression Profiles During Human Developmental Processes.xlsx

Single-cell RNA-seq studies profile thousands of cells in developmental processes. Current databases for human single-cell expression atlas only provide search and visualize functions for a selected gene in specific cell types or subpopulations. These databases are limited to technical properties or visualization of single-cell RNA-seq data without considering the biological relations of their collected cell groups. Here, we developed a database to investigate single-cell gene expression profiling during different developmental pathways (SCDevDB). In this database, we collected 10 human single-cell RNA-seq datasets, split these datasets into 176 developmental cell groups, and constructed 24 different developmental pathways. SCDevDB allows users to search the expression profiles of the interested genes across different developmental pathways. It also provides lists of differentially expressed genes during each developmental pathway, T-distributed stochastic neighbor embedding maps showing the relationships between developmental stages based on these differentially expressed genes, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes analysis results of these differentially expressed genes. This database is freely available at https://scdevdb.deepomics.org</p

MOESM1 of SpliceFinder: ab initio prediction of splice sites using convolutional neural network

Additional file 1 Figure S1 The performance of models with different number of layers

MOESM4 of SpliceFinder: ab initio prediction of splice sites using convolutional neural network

Additional file 4 Figure S4 The performance of models trained with data of other species

MOESM3 of SpliceFinder: ab initio prediction of splice sites using convolutional neural network

Additional file 3 Figure S3 The splice site prediction accuracy of different methods for other species

MOESM2 of SpliceFinder: ab initio prediction of splice sites using convolutional neural network

Additional file 2 Figure S2 Evaluation of different methods with various metrics

MOESM1 of MIRIA: a webserver for statistical, visual and meta-analysis of RNA editing data in mammals

Additional file 1: Table S1. The data source from NCBI

Cyanamide as a Highly Efficient Organocatalyst for the Glycolysis Recycling of PET

Due to the antibiodegradable properties, numerous plastics have been accumulated in the ecosystem and aggravate ecological pollution. Poly (ethylene terephthalate) (PET) is among the most used plastics. Glycolysis of PET is a useful approach to solve the waste PET pollution and obtain bis­(2-hydroxyethyl) terephthalate (BHET). In this paper, waste PET was efficiently depolymerized through glycolysis catalyzed by cyanamide. In particular, compared with the previously reported catalyst, cyanamide is more readily available and can be used directly in catalysis without a complex preparation process. Under optimal conditions, PET was completely depolymerized with up to nearly 100% BHET yield. Even at a temperature as low as 150 °C, a good BHET yield can be obtained. The application potential of this glycolysis procedure was demonstrated by its excellent performance in the glycolysis of various real PET wastes like transparent and opaque PET samples and polyester foam and by the high quality of the obtained BHET products. The mechanism was studied by 1H NMR analysis, and DFT calculations showed that the higher activity of cyanamide than its trimer, melamine, is due to the stronger hydrogen bonds formed between cyanamide and PET or ethylene glycol

Visible-Light-Driven Enhanced Biohydrogen Production by Photo-Biohybrid System Based on Photoelectron Transfer between Intracellular Photosensitizer Gold Nanoparticles and Clostridium butyricum

Biohydrogen is a clean and renewable energy, but the low yield caused by the lack of reducing power in cells greatly restricts the industrialization of biohydrogen production. Photo-biohybrid systems (PBSs) can integrate the high light energy utilization efficiency of photocatalysts with the excellent catalytic performance of microorganisms. Here, gold nanoparticles were targeted into Clostridium butyricum as intracellular photosensitizers to construct a PBS that could efficiently produce biohydrogen under visible light, with the apparent quantum yield as high as 19.31%. Compared with the dark-fermented C. butyricum, the biohydrogen production of PBS increased by 88.74%. The mechanism of photoelectrons from Au NPs to C. butyricum was elucidated by the transcriptome. Compared with the dark-fermented biohybrids, the expressions of biohydrogen generation-related enzymes, such as hydrogenase and pyruvate formate lyase genes, in the PBS were all upregulated more than 2 times. Furthermore, the genes of riboflavin synthase, electron transfer flavoprotein (ETF), and FAD-dependent oxidoreductase, which are closely related to electron transformation, were all significantly upregulated. The photoelectrons were transferred to the hydrogenase via ETF and FAD2+ to enhance biohydrogen production, independent of pyruvate decomposition. This PBS provides theoretical guidance for constructing an efficient light-driven microbial manufacturing system

Plasmonic Catalysis on Au–Pd Nanoalloy for Self-Hydrogen Transfer Hydrogenolysis of Lignin β‑O‑4 Models under Visible Light

In the present study, we combined plasmonic Au and catalytically active Pd to develop a new photocatalyst of Au–Pd nanoalloy supported on ZrO2 nanopowder. Plasmonic catalysis was conducted on Au–Pd nanoalloy using visible light to cleave the C–O ether bond of lignin β-O-4 linkage. The generated hot electrons decreased the apparent activation energy of this reaction and enabled it to proceed at mild conditions. A β-O-4 dimer model, 2-phenoxy-1-phenylethanol, was effectively cleaved (98% conversion) to acetophenone (95% yield) and phenol (92% yield) under visible light at 80 °C for 24 h. This reaction occurred through a self-hydrogen transfer hydrogenolysis pathway. The dehydrogenation at the Cα position generated a “hydrogen pool” on Au–Pd, which will insert into the β-O-4 linkage to cleave the C–O ether bond. The photocatalyst could well maintain its activity after recycling. This study provides a new photocatalytic procedure for solar energy utilization and lignin valorization

The expression of muscle-related miRNAs during the skeletal muscle development of Tongcheng pigs was detected using real-time PCR.

<p>The miRNAs obtained from the longissimus dorsi of the Tongcheng pigs between E90 and D100 were evaluated. At least 3 animals were used for each time point, and the expression of the miRNAs was normalized to that of U6.</p