In situ proliferation and differentiation of macrophages in dental pulp

The presence of macrophages in dental pulp is well known. However, whether these macrophages proliferate and differentiate in the dental pulp in situ, or whether they constantly migrate from the blood stream into the dental pulp remains unknown. We have examined and compared the development of dental pulp macrophages in an organ culture system with in vivo tooth organs to clarify the developmental mechanism of these macrophages. The first mandibular molar tooth organs from ICR mice aged between 16 days of gestation (E16) to 5 days postnatally were used for in vivo experiments. Those from E16 were cultured for up to 14 days with or without 10% fetal bovine serum. Dental pulp tissues were analyzed with immunohistochemistry to detect the macrophages and with reverse transcription and the polymerase chain reaction (RT-PCR) for the detection of factors related to macrophage development. The growth curves for the in vivo and in vitro cultured cells revealed similar numbers of F4/80-positive macrophages in the dental pulp. RT-PCR analysis indicated the constant expression of myeloid colony-stimulating factor (M-CSF) in both in-vivo- and in-vitro-cultured dental pulp tissues. Anti-M-CSF antibodies significantly inhibited the increase in the number of macrophages in the dental pulp. These results suggest that (1) most of the dental pulp macrophages proliferate and differentiate in the dental pulp without a supply of precursor cells from the blood stream, (2) M-CSF might be a candidate molecule for dental pulp macrophage development, and (3) serum factors might not directly affect the development of macrophages

Circadian oscillator proteins across the kingdoms of life : Structural aspects 06 Biological Sciences 0601 Biochemistry and Cell Biology

Circadian oscillators are networks of biochemical feedback loops that generate 24-hour rhythms and control numerous biological processes in a range of organisms. These periodic rhythms are the result of a complex interplay of interactions among clock components. These components are specific to the organism but share molecular mechanisms that are similar across kingdoms. The elucidation of clock mechanisms in different kingdoms has recently started to attain the level of structural interpretation. A full understanding of these molecular processes requires detailed knowledge, not only of the biochemical and biophysical properties of clock proteins and their interactions, but also the three-dimensional structure of clockwork components. Posttranslational modifications (such as phosphorylation) and protein-protein interactions, have become a central focus of recent research, in particular the complex interactions mediated by the phosphorylation of clock proteins and the formation of multimeric protein complexes that regulate clock genes at transcriptional and translational levels. The three-dimensional structures for the cyanobacterial clock components are well understood, and progress is underway to comprehend the mechanistic details. However, structural recognition of the eukaryotic clock has just begun. This review serves as a primer as the clock communities move towards the exciting realm of structural biology

Genome-scale embryonic developmental profile of gene expression in the common house spider Parasteatoda tepidariorum

We performed RNA sequencing (RNA-Seq) at ten successive developmental stages in embryos of the common house spider Parasteatoda tepidariorum. Two independent datasets from two pairs of parents represent the normalized coverage of mapped RNA-Seq reads along scaffolds of the P. tepidariorum genome assembly. Transcript abundance was calculated against existing AUGUSTUS gene models. The datasets have been deposited in the Gene Expression Omnibus (GEO) Database at the National Center for Biotechnology Information (NCBI) under the accession number GSE112712

Additional file 2 of Lineage-specific, fast-evolving GATA-like gene regulates zygotic gene activation to promote endoderm specification and pattern formation in the Theridiidae spider

Additional file 2: Table S1. List of DEG candidates identified by comparative transcriptome analysis of c versus i/p cells from stage-3 embryo (comparison I). Table S2. List of DEG candidates identified by comparative transcriptome analysis of p versus c/i cells from stage-3 embryo (comparison II). Table S3. List of DEG candidates identified by comparative transcriptome analysis of i versus c/p cells from stage-3 embryo (comparison III). Table S4. List of DEG candidates indentified by comparative transcriptome analysis of c versus p cells from stage-4 embryo. Table S5. List of DEG candidates identified by comparative transcriptome analysis of c versus p cells from early stage-5 embryo

Additional file 7 of Lineage-specific, fast-evolving GATA-like gene regulates zygotic gene activation to promote endoderm specification and pattern formation in the Theridiidae spider

Additional file 7: Table S7. List of bioinformatic resources used for phylogenetic characterization of Fuchi and other GATA family members in spiders. Table S8. Amino acid sequence alignment and classification of GATA family members from spiders and other metazoans

Additional file 5 of Lineage-specific, fast-evolving GATA-like gene regulates zygotic gene activation to promote endoderm specification and pattern formation in the Theridiidae spider

Additional file 5: Movie S2. Time-lapse video showing phenotypes gfp, g26874, g7720, and g4238 pRNAi embryos. Time after egg laying (AEL) and time after start of recording are indicated. Movie starts are adjusted by the timing of blastoderm formation. Some of the embryos are the same as those shown in Fig. 3A. Scale bar, 100 µm

Additional file 11 of Lineage-specific, fast-evolving GATA-like gene regulates zygotic gene activation to promote endoderm specification and pattern formation in the Theridiidae spider

Additional file 11: Table S14. Data from comparative analysis of read counts in extracted ATAC-seq peaks between Pt-hh pRNAi and wild-type embryos at stage 3 using edgeR. Table S15. List of differential ATAC-seq peaks between Pt-hh pRNAi and wild-type embryos at stage 3 (FDR < 0.05)

Additional file 14 of Lineage-specific, fast-evolving GATA-like gene regulates zygotic gene activation to promote endoderm specification and pattern formation in the Theridiidae spider

Additional file 14. Multi-fasta format file of 118 sequences (75 amino acid sites) used for the first ML analysis

Additional file 4 of Lineage-specific, fast-evolving GATA-like gene regulates zygotic gene activation to promote endoderm specification and pattern formation in the Theridiidae spider

Additional file 4: Table S6. Summary of a pilot pRNAi screen of 19 selected genes