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Background: With the development of single-cell technology, many cell traits can be measured. Furthermore, the multi-omics profiling technology could jointly measure two or more traits in a single cell simultaneously. In order to process the various data accumulated rapidly, computational methods for multimodal data integration are needed. Results: Here, we present inClust+, a deep generative framework for the multi-omics. It's built on previous inClust that is specific for transcriptome data, and augmented with two mask modules designed for multimodal data processing: an input-mask module in front of the encoder and an output-mask module behind the decoder. InClust+ was first used to integrate scRNA-seq and MERFISH data from similar cell populations, and to impute MERFISH data based on scRNA-seq data. Then, inClust+ was shown to have the capability to integrate the multimodal data (e.g. tri-modal data with gene expression, chromatin accessibility and protein abundance) with batch effect. Finally, inClust+ was used to integrate an unlabeled monomodal scRNA-seq dataset and two labeled multimodal CITE-seq datasets, transfer labels from CITE-seq datasets to scRNA-seq dataset, and generate the missing modality of protein abundance in monomodal scRNA-seq data. In the above examples, the performance of inClust+ is better than or comparable to the most recent tools in the corresponding task. Conclusions: The inClust+ is a suitable framework for handling multimodal data. Meanwhile, the successful implementation of mask in inClust+ means that it can be applied to other deep learning methods with similar encoder-decoder architecture to broaden the application scope of these models. [ABSTRACT FROM AUTHOR]

Summary: The brown planthopper (BPH) is the most destructive pest of rice. The MYB transcription factors are vital for rice immunity, but most are activators. Although MYB22 positively regulates rice resistance to BPH and has an EAR motif associated with active repression, it remains unclear whether it is a transcriptional repressor affecting rice–BPH interaction.Genetic analyses revealed that MYB22 regulates rice resistance to BPH via its EAR motif. Several biochemical experiments (e.g. transient transcription assay, Y2H, LCA, and BiFC) indicated that MYB22 is a transcriptional repressor that interacts with the corepressor TOPLESS via its EAR motif and recruits HDAC1 to form a tripartite complex.Flavonoid‐3′‐hydroxylase (F3′H) is a flavonoid biosynthesis pathway‐related gene that negatively regulates rice resistance to BPH. Based on a bioinformatics analysis and the results of EMSA and transient transcription assays, MYB22 can bind directly to the F3′H promoter and repress gene expression along with TOPLESS and HDAC1.We revealed a transcriptional regulatory mechanism influencing the rice–BPH interaction that differs from previously reported mechanisms. Specifically, MYB22–TOPLESS–HDAC1 is a novel transcriptional repressor complex with components that synergistically and positively regulate rice resistance to BPH through the transcriptional repression of F3′H. [ABSTRACT FROM AUTHOR]

Brown planthopper (BPH) is the most destructive insect pest to rice that causes tremendous yield loss each year in rice planting Asia and South-East Asia areas. Compared with traditional chemical-based treatment, utilization of plant endogenous resistance is a more effective and environmental-friendly way for BPH control. Accordingly, quite a few quantitative trait loci (QTLs) for BPH resistance were cloned using forward genetics. However, BPH is apt to change quickly into new biotypes to overcome plant resistance, therefore, new resistance resources and genes are continuously needed. miRNAs are important regulators in both plant development and physiological regulation including immunity, and might be used as effective supplements for BPH resistance QTLs. miR159 is an ancient and conserved miRNA. In this study, we found that each OsMIR159 gene in rice responded to BPH feeding very obviously, and genetic function assay proved them to negatively regulate BPH resistance, with STTM159 showing resistance to BPH, and over expression of OsmiR159d susceptible to BPH. One target genes of OsmiR159, OsGAMYBL2, positively regulated BPH resistance. Further biochemical studies revealed that OsGAMYBL2 could directly bind to the promoter of G-protein γ subunit encoding GS3 gene and repress its expression. And genetically, GS3 responded to BPH feeding promptly and negatively regulated BPH resistance, GS3 over expression plants were susceptible to BPH, while GS3 knock-out plants were resistant to BPH. Thus, we identified new function of OsmiR159–OsGAMYBL2 in mediating BPH response, and revealed a new OsmiR159–G protein pathway that mediates BPH resistance in rice. [ABSTRACT FROM AUTHOR]

Abstract: The silkworm Bombyx mori is one of the most economically important insects and serves as a model for Lepidoptera insects. We used serial analysis of gene expression (SAGE) to derive profiles of expressed genes during the developmental life cycle of the silkworm and to create a reference for understanding silkworm metamorphosis. We generated four SAGE libraries, one from each of the four developmental stages of the silkworm. In total we obtained 257,964 SAGE tags, of which 39,485 were unique tags. Sorted by copy number, 14.1% of the unique tags were detected at a median to high level (five or more copies), 24.2% at lower levels (two to four copies), and 61.7% as single copies. Using a basic local alignment search tool on the EST database, 35% of the tags matched known silkworm expressed sequence tags. SAGE demonstrated that a number of the genes were up- or down-regulated during the four developmental phases of the egg, larva, pupa, and adult. Furthermore, we found that the generation of longer cDNA fragments from SAGE tags constituted the most efficient method of gene identification, which facilitated the analysis of a large number of unknown genes. [Copyright &y& Elsevier]

Abstract: The green alga Haematococcus pluvialis can produce large amounts of pink carotenoid astaxanthin which is a high value ketocarotenoid. In our study, transcriptional expression patterns of eight carotenoid genes in H. pluvialis in response to SA were measured using qRT-PCR. Results indicated that both 25 and 50mg/L salicylic acid (SA) could increase astaxanthin productivity and enhance transcriptional expression of eight carotenoid genes in H. pluvialis. But these genes exhibited different expression profiles. Moreover, SA25 (25mg/L SA) induction had a greater effect on the transcriptional expression of ipi-1, psy, pds, crtR-B and lyc (more than 6-fold up-regulation) than on ipi-2, bkt and crtO, but SA50 (50mg/L SA) treatment had a greater impact on the transcriptional expression of ipi-1, ipi-2, pds, crtR-B and lyc than on psy, bkt and crtO. Furthermore, astaxanthin biosynthesis under SA was up-regulated mainly by ipi-1, ipi-2, psy, crtR-B, bkt and crtO at transcriptional level, lyc at post-transcriptional level and pds at both levels. Summarily, these results suggest that SA constitute molecular signals in the network of astaxanthin biosynthesis. Induction of astaxanthin accumulation by SA without any other stimuli presents an attractive application potential in astaxanthin production with H. pluvialis. [Copyright &y& Elsevier]

Abstract: Many genes act together during the complex process of insect larval and pupal development. 20-Hydroxyecdysone interacts with juvenile hormone to control insect growth and development and then activates several transcription factors, i.e., Broad, E74, and E75, and, subsequently, the late target genes. To investigate this phenomenon, we used serial analysis of gene expression (SAGE) tag-based cDNA microarray analysis to monitor the global gene expression profile during larval development and larva–pupa metamorphosis of the silkworm Bombyx mori. Of the 330 clones that were dotted to the chip, 267 were obtained by generating longer cDNA fragments from SAGE tags for gene identification, and the others were obtained from SAGE tag-matched genes or expressed sequence tags from public databases. According to the gene expression profile, the genes were classified into 12 clusters using a self-organizing map analysis. The results were partially confirmed using real-time reverse transcription–polymerase chain reaction. We obtained 22 full-length cDNAs using rapid amplification of 5′ cDNA ends, of which eight genes were novel in the silkworm. Our results indicated that use of a cDNA microarray based on SAGE tags is effective for identifying and examining some low-expression genes associated with insect development. [Copyright &y& Elsevier]