The temporal protein signature analyses of developing human deciduous molar tooth germ.

The tooth serves as an exemplary model for developmental studies, encompassing epithelial-mesenchymal transition and cell differentiation. The essential factors and pathways identified in tooth development will help understand the natural development process and the malformations of mineralized tissues such as skeleton. The time-dependent proteomic changes were investigated through the proteomics of healthy human molars during embryonic stages, ranging from the cap-to-early bell stage. A comprehensive analysis revealed 713 differentially expressed proteins (DEPs) exhibiting five distinct temporal expression patterns. Through the application of weighted gene co-expression network analysis (WGCNA), 24 potential driver proteins of tooth development were screened, including CHID1, RAP1GDS1, HAPLN3, AKAP12, WLS, GSS, DDAH1, CLSTN1, AFM, RBP1, AGO1, SET, HMGB2, HMGB1, ANP32A, SPON1, FREM1, C8B, PRPS2, FCHO2, PPP1R12A, GPALPP1, U2AF2, and RCC2. Then, the proteomics and transcriptomics expression patterns of these proteins were further compared, complemented by single-cell RNA-sequencing (scRNA-seq). In summary, this study not only offers a wealth of information regarding the molecular intricacies of human embryonic epithelial and mesenchymal cell differentiation but also serves as an invaluable resource for future mechanistic inquiries into tooth development.

Expression pattern of NLRC5 in the postnatal mouse brain.

Nucleotide oligomerization domain-like receptors (NLRs), belonging to a large family of pattern recognition receptors, participate in the host's first line of defense against invading pathogens. Caspase recruitment domain containing 5 (NLRC5), the largest member in the NLR family, is demonstrated to be involved in the innate immune response and inflammatory diseases far and wide. Recent studies report that NLRC5 is associated with some central nervous system (CNS) diseases. Besides, NLRC5 is a mastery regulator for the expression of MHC class I both in the immune system and the CNS, while MHC class I is expressed and exerts its function in the brain. Therefore, it is necessary to investigate the expression pattern of NLRC5 in the developing and adult CNS. In our study, postnatal brain sections of C57BL/6 J mice are analyzed for the expression of NLRC5 protein by immunofluorescence. In the postnatal stages of developing telencephalon, NLRC5 exhibits a spatial and temporal expression pattern. NLRC5 is time-specifically expressed in subfields of hippocampus and different layers of prefrontal cortex. Moreover, it is shown that NLRC5 is highly cell type specific. It can be expressed in large quantities by neurons and microglia, but rarely expressed by astrocytes. Taken together, our research is important for further understanding the biological characteristics of NLRC5 and its function in the CNS.

[Cloning,subcellular localization and spatio-temporal expression analysis of a flavonoid 3-O-glucosyltransferase gene( SmUF3GT) in Salvia miltiorrhiza].

The family of flavonoid 3-O-glucosyltransferase catalyzes the modification of anthocyanin from unstable-structure to stable-structure. In this study,based on homology cloning and transcriptome library,we isolated the full-length c DNA of UDP-glucose: flavonoid 3-O-glucosyltransferase( named SmUF3GT) from the flower tissues of S. miltiorrhiza. This gene was consisted of 1 353 bp open reading frames( ORF) encoding 450 amino acids. And the SmUF3GT protein was performed for the bioinformatic analysis. Our results showed that the protein was preliminary localized in the Golgi and peroxisome of cytosol,as well as plasma membrane and cell nuclear.QRT-PCR analyses indicated that SmUF3GT expressed differently in all tissues and organs but roots of S. miltiorrhiza and S. miltiorrhiza f.alba. During floral development,the expression of SmUF3GT showed a trend of rising fist and then down in purple-flower Danshen,whereas decreasing sharply fist and then slowly in white-flower Danshen. The present study provides basic information for further research on the network of synthesis and accumulation of flavonoids in S.miltiorrhiza.

Cloning,subcellular localization and spatio-temporal expression analysis of a flavonoid 3-O-glucosyltransferase gene( SmUF3GT) in Salvia miltiorrhiza / 中国中药杂志

The family of flavonoid 3-O-glucosyltransferase catalyzes the modification of anthocyanin from unstable-structure to stable-structure. In this study,based on homology cloning and transcriptome library,we isolated the full-length c DNA of UDP-glucose: flavonoid 3-O-glucosyltransferase( named SmUF3GT) from the flower tissues of S. miltiorrhiza. This gene was consisted of 1 353 bp open reading frames( ORF) encoding 450 amino acids. And the SmUF3GT protein was performed for the bioinformatic analysis. Our results showed that the protein was preliminary localized in the Golgi and peroxisome of cytosol,as well as plasma membrane and cell nuclear.QRT-PCR analyses indicated that SmUF3GT expressed differently in all tissues and organs but roots of S. miltiorrhiza and S. miltiorrhiza f.alba. During floral development,the expression of SmUF3GT showed a trend of rising fist and then down in purple-flower Danshen,whereas decreasing sharply fist and then slowly in white-flower Danshen. The present study provides basic information for further research on the network of synthesis and accumulation of flavonoids in S.miltiorrhiza.

Systems-level analysis of risk genes reveals the modular nature of schizophrenia.

Schizophrenia (SCZ) is a complex mental disorder with high heritability. Genetic studies (especially recent genome-wide association studies) have identified many risk genes for schizophrenia. However, the physical interactions among the proteins encoded by schizophrenia risk genes remain elusive and it is not known whether the identified risk genes converge on common molecular networks or pathways. Here we systematically investigated the network characteristics of schizophrenia risk genes using the high-confidence protein-protein interactions (PPI) from the human interactome. We found that schizophrenia risk genes encode a densely interconnected PPI network (P = 4.15 × 10-31). Compared with the background genes, the schizophrenia risk genes in the interactome have significantly higher degree (P = 5.39 × 10-11), closeness centrality (P = 7.56 × 10-11), betweeness centrality (P = 1.29 × 10-11), clustering coefficient (P = 2.22 × 10-2), and shorter average shortest path length (P = 7.56 × 10-11). Based on the densely interconnected PPI network, we identified 48 hub genes and 4 modules formed by highly interconnected schizophrenia genes. We showed that the proteins encoded by schizophrenia hub genes have significantly more direct physical interactions. Gene ontology (GO) analysis revealed that cell adhesion, cell cycle, immune system response, and GABR-receptor complex categories were enriched in the modules formed by highly interconnected schizophrenia risk genes. Our study reveals that schizophrenia risk genes encode a densely interconnected molecular network and demonstrates the modular nature of schizophrenia.

Transcriptomic insights into temporal expression pattern of autophagy genes during monocytic and granulocytic differentiation.

Macroautophagy/autophagy plays an essential role in hematopoietic stem cell (HSC) differentiation. However, the role of autophagy during monocytic and granulocytic differentiation remains poorly understood. Hence, we first represented global transcriptomic analysis for temporal expression of autophagy genes during monocytic and granulocytic differentiation by combining RNA-Seq data with monocytic and granulocytic induction in CD34+ hematopoietic stem and progenitor cells. According to a self-organizing map (SOM) algorithm, our results show temporal expression patterns of autophagy genes during monocytic and granulocytic differentiation. More importantly, 22 autophagy genes present significantly divergent roles during monocytic and granulocytic differentiation, indicating these autophagy genes could be important factors involved in the differentiation of myeloid progenitors into monocytes and granulocytes.

Repertoire of bone morphogenetic proteins and growth/differentiation factors in ovary of the Indian wall lizard (Hemidactylus flaviviridis) with emphasis on differential expression and gonadotropic regulation of bmp15 and gdf9.

Analysis of ovarian transcriptome of Indian wall lizard demonstrates the existence of several bone morphogenetic proteins (bmp1, 2, 3, 3b, 7, 8, 15) and growth/differentiation factors (gdf5, 9) for the first time in reptilian ovary. The characterization of putative full-length/partial protein sequences of BMPs (BMP2, 3, 3b, 7, 15) and GDF9 showed high homology of their TGF-ß domain with that of other vertebrates while BMP1 bore homology to zinc-dependent metalloprotease. Phylogenetic analyses showed clustering of BMPs and GDF9 from wall lizards with that of squamates lying in close proximity to chelonia, crocodilia and aves. This study also correlates the expression of ovarian bmp15 and gdf9 with folliculogenesis. Level of bmp15 dramatically increased with the onset of follicular growth in early recrudescence and attained peak during late recrudescence whereas gdf9 sharply decreased during recrudescence as compared to regression. Nonetheless, expression of these growth factors decreased appreciably with the formation of vitellogenic follicle during breeding phase. Ovarian expression of bmp15 and gdf9 appeared to be regulated by gonadotropin as bmp15 considerably increased while gdf9 decreased in parallel to follicular development after administration of 3 injections of FSH. Expression of both the growth factors declined with the prolongation of treatment that led to formation of early/late vitellogenic follicle. Our in vitro study revealed stimulatory effect of FSH on expression of bmp15 and gdf9 in early growing, previtellogenic and early vitellogenic follicles. In light of in vitro results, FSH-induced in vivo decline in gene expression seems to be due to some other FSH-induced factor.

Identification and Characterization of 30 K Protein Genes Found in Bombyx mori (Lepidoptera: Bombycidae) Transcriptome.

The 30 K proteins, the major group of hemolymph proteins in the silkworm, Bombyx mori (Lepidoptera: Bombycidae), are structurally related with molecular masses of ∼30 kDa and are involved in various physiological processes, e.g., energy storage, embryonic development, and immune responses. For this report, known 30 K protein gene sequences were used as Blastn queries against sequences in the B. mori transcriptome (SilkTransDB). Twenty-nine cDNAs (Bm30K-1-29) were retrieved, including four being previously unidentified in the Lipoprotein_11 family. The genomic structures of the 29 genes were analyzed and they were mapped to their corresponding chromosomes. Furthermore, phylogenetic analysis revealed that the 29 genes encode three types of 30 K proteins. The members increased in each type is mainly a result of gene duplication with the appearance of each type preceding the differentiation of each species included in the tree. Real-Time Quantitative Polymerase Chain Reaction (Q-PCR) confirmed that the genes could be expressed, and that the three types have different temporal expression patterns. Proteins from the hemolymph was separated by SDS-PAGE, and those with molecular mass of ∼30 kDa were isolated and identified by mass spectrometry sequencing in combination with searches of various databases containing B. mori 30K protein sequences. Of the 34 proteins identified, 13 are members of the 30 K protein family, with one that had not been found in the SilkTransDB, although it had been found in the B. mori genome. Taken together, our results indicate that the 30 K protein family contains many members with various functions. Other methods will be required to find more members of the family.