Gene expression profiles of Japanese precious coral Corallium japonicum during gametogenesis.

Background: Corallium japonicum, a prized resource in Japan, plays a vital role in traditional arts and fishing industries. Because of diminished stock due to overexploitation, ongoing efforts are focused on restoration through transplantation. This study aimed to enhance our understanding of the reproductive biology of these valuable corals and find more efficient methods for sex determination, which may significantly contribute to conservation initiatives. Methods: We used 12 three-month aquarium reared C. japonicum colony fragments, conducted histological analysis for maturity and sex verification, and performed transcriptome analysis via de novo assembly and mapping using the C. rubrum transcriptome to explore gene expression differences between female and male C. japonicum. Results: Our histological observations enabled sex identification in 33% of incompletely mature samples. However, the sex of the remaining 67% of samples, classified as immature, could not be identified. RNA-seq yielded approximately 21-31 million short reads from 12 samples. De novo assembly yielded 404,439 highly expressed transcripts. Among them, 855 showed significant differential expression, with 786 differentially expressed transcripts between females and males. Heatmap analysis highlighted 283 female-specific and 525 male-specific upregulated transcripts. Transcriptome assembly mapped to C. rubrum yielded 28,092 contigs, leading to the identification of 190 highly differentially expressed genes, with 113 upregulated exclusively in females and 70 upregulated exclusively in males. Blastp analysis provided putative protein annotations for 83 female and 72 male transcripts. Annotation analysis revealed that female biological processes were related to oocyte proliferation and reproduction, whereas those in males were associated with cell adhesion. Discussion: Transcriptome analysis revealed sex-specific gene upregulation in incompletely mature C. japonicum and shared transcripts with C. rubrum, providing insight into its gene expression patterns. This study highlights the importance of using both de novo and reference-based assembly methods. Functional enrichment analysis showed that females exhibited enrichment in cell proliferation and reproduction pathways, while males exhibited enrichment in cell adhesion pathways. To the best of our knowledge, this is the first report on the gene expressions of each sex during the spawning season. Our findings offer valuable insights into the physiological ecology of incompletely mature red Japanese precious corals and suggest a method for identifying sex using various genes expressed in female and male individuals. In the future, techniques such as transplantation, artificial fertilization, and larval rearing may involve sex determination methods based on differences in gene expression to help conserve precious coral resources and ecosystems.

Rare Coexistence of Aldosterone-producing Adrenocortical Adenoma Confirmed by an Immunohistochemical Analysis of Steroidogenic Enzymes with Adrenal Ectopic Thyroid Tissue: A Case Report and Literature Review.

A 56-year-old man presented with a history of hypertension; clinically, the patient had primary aldosteronism (PA) and a 4-cm left adrenal tumor. The left adrenal glands, resected by adrenalectomy, also contained ectopic thyroid tissue (ETT). An immunohistochemical analysis of steroid-converting enzymes revealed an aldosterone-producing adenoma (APA). Among 19 previously reported cases of adrenal ETT, 4 had adrenal hormonal abnormalities, all of which were PA. This is the first case of adrenal ETT coexisting with APA, confirmed by steroid-converting enzyme expression. Further analyses using cumulative case data are required to clarify the correlation between adrenal ETT and APA.

Clonal Origin and Lineage Ambiguity in Mixed Neuroendocrine Carcinoma of the Uterine Cervix.

Small-cell neuroendocrine carcinoma (SCNEC) of the cervix is a rare disease characterized by a high incidence of mixed tumors with other types of cancer. The mechanism underlying this mixed phenotype is not well understood. This study established a panel of organoid lines from patients with SCNEC of the cervix and ultimately focused on one line, which retained a mixed tumor phenotype, both in vitro and in vivo. Histologically, both organoids and xenograft tumors showed distinct differentiation into either SCNEC or adenocarcinoma in some regions and ambiguous differentiation in others. Tracking single cells indicated the existence of cells with bipotential differentiation toward SCNEC and adenocarcinomas. Single-cell transcriptional analysis identified three distinct clusters: SCNEC-like, adenocarcinoma-like, and a cluster lacking specific differentiation markers. The expression of neuroendocrine markers was enriched in the SCNEC-like cluster but not exclusively. Human papillomavirus 18 E6 was enriched in the SCNEC-like cluster, which showed higher proliferation and lower levels of the p53 pathway. After treatment with anticancer drugs, the expression of adenocarcinoma markers increased, whereas that of SCNEC decreased. Using a reporter system for keratin 19 expression, changes in the differentiation of each cell were shown to be associated with the shift in differentiation induced by drug treatment. These data suggest that mixed SCNEC/cervical tumors have a clonal origin and are characterized by an ambiguous and flexible differentiation state.

Positive Regulation of S-Adenosylmethionine on Chondrocytic Differentiation via Stimulation of Polyamine Production and the Gene Expression of Chondrogenic Differentiation Factors.

S-adenosylmethionine (SAM) is considered to be a useful therapeutic agent for degenerative cartilage diseases, although its mechanism is not clear. We previously found that polyamines stimulate the expression of differentiated phenotype of chondrocytes. We also found that the cellular communication network factor 2 (CCN2) played a huge role in the proliferation and differentiation of chondrocytes. Therefore, we hypothesized that polyamines and CCN2 could be involved in the chondroprotective action of SAM. In this study, we initially found that exogenous SAM enhanced proteoglycan production but not cell proliferation in human chondrocyte-like cell line-2/8 (HCS-2/8) cells. Moreover, SAM enhanced gene expression of cartilage-specific matrix (aggrecan and type II collagen), Sry-Box transcription factor 9 (SOX9), CCN2, and chondroitin sulfate biosynthetic enzymes. The blockade of the methionine adenosyltransferase 2A (MAT2A) enzyme catalyzing intracellular SAM biosynthesis restrained the effect of SAM on chondrocytes. The polyamine level in chondrocytes was higher in SAM-treated culture than control culture. Additionally, Alcian blue staining and RT-qPCR indicated that the effects of SAM on the production and gene expression of aggrecan were reduced by the inhibition of polyamine synthesis. These results suggest that the stimulation of polyamine synthesis and gene expression of chondrogenic differentiation factors, such as CCN2, account for the mechanism underlying the action of SAM on chondrocytes.

Effect of carnosine synthesis precursors in the diet on jejunal metabolomic profiling and biochemical compounds in slow-growing Korat chicken.

The slow-growing Korat chicken (KR) has been developed to provide an alternative breed for smallholder farmers in Thailand. Carnosine enrichment in the meat can distinguish KR from other chicken breeds. Therefore, our aim was to investigate the effect of enriched carnosine synthesis, obtained by the ß-alanine and L-histidine precursor supplementation in the diet, on changes to metabolomic profiles and biochemical compounds in slow-growing KR jejunum tissue. Four hundred 21-day-old female KR chickens were divided into 4 experimental groups: a group with a basal diet, a group with a basal diet supplemented with 1.0% ß-alanine, 0.5% L-histidine, and a mix of 1.0% ß-alanine and 0.5% L-histidine. The feeding trial lasted 70 d. Ten randomly selected chickens from each group were slaughtered. Metabolic profiles were analyzed using proton nuclear magnetic resonance spectroscopy. In total, 28 metabolites were identified. Significant changes in the concentrations of these metabolites were detected between the groups. Partial least squares discriminant analysis was used to distinguish the metabolites between the experimental groups. Based on the discovered metabolites, 34 potential metabolic pathways showed differentiation between groups, and 8 pathways (with impact values higher than 0.05, P < 0.05, and FDR < 0.05) were affected by metabolite content. In addition, biochemical changes were monitored using synchrotron radiation-based Fourier transform infrared microspectroscopy. Supplementation of ß-alanine alone in the diet increased the ß-sheets and decreased the α-helix content in the amide I region, and supplementation of L-histidine alone in the diet also increased the ß-sheets. Furthermore, the relationship between metabolite contents and biochemical compounds were confirmed using principal component analysis (PCA). Results from the PCA indicated that ß-alanine and L-histidine precursor group was highly positively correlated with amide I, amide II, creatine, tyrosine, valine, isoleucine, and aspartate. These findings can help to understand the relationships and patterns between the spectral and metabolic processes related to carnosine synthesis.

Localized Amyloid A amyloidsis of ureter: A case report.

Amyloidosis of the ureter is a rare disease, distinguishing it from a neoplasm is difficult. A 64-year-old Japanese woman suffered from macrohematuria and left side hydronephrosis with ultrasound in 2014. Retrograde pyelography revealed no ureter tumor at that time. The patient had macrohematuria, left side hydronephrosis, and ureteral stenosis in the left ureter on retrograde pyelography. She was suspected of having a ureter tumor when she was 71 years old in 2021. The patient underwent ureteroscopy with biopsy. Pathological specimens contained the amyloid A component, based on immunohistochemistry staining. We diagnosed the patient with amyloid A amyloidosis of the ureter.

Expression and function of CCN2-derived circRNAs in chondrocytes.

Cellular communication network factor 2 (CCN2) molecules promote endochondral ossification and articular cartilage regeneration, and circular RNAs (circRNAs), which arise from various genes and regulate gene expression by adsorbing miRNAs, are known to be synthesized from CCN2 in human vascular endothelial cells and other types of cells. However, in chondrocytes, not only the function but also the presence of CCN2-derived circRNA remains completely unknown. In the present study, we investigated the expression and function of CCN2-derived circRNAs in chondrocytes. Amplicons smaller than those from known CCN2-derived circRNAs were observed using RT-PCR analysis that could specifically amplify CCN2-derived circRNAs in human chondrocytic HCS-2/8 cells. The nucleotide sequences of the PCR products indicated novel circRNAs in the HCS-2/8 cells that were different from known CCN2-derived circRNAs. Moreover, the expression of several Ccn2-derived circRNAs in murine chondroblastic ATDC5 cells was confirmed and observed to change alongside chondrocytic differentiation. Next, one of these circRNAs was knocked down in HCS-2/8 cells to investigate the function of the human CCN2-derived circRNA. As a result, CCN2-derived circRNA knockdown significantly reduced the expression of aggrecan mRNA and proteoglycan synthesis. Our data suggest that CCN2-derived circRNAs are expressed in chondrocytes and play a role in chondrogenic differentiation. Production and role of CCN2-derived RNAs in chondrocytes.

Potential application of Staphylococcus species detection in the specific identification of saliva.

When found at crime scenes, saliva constitutes forensically relevant evidence. Although several tests have been developed to effectively identify saliva in such circumstances, most cannot discriminate between saliva and nasal secretion. Recently, studies have developed saliva tests involving oral bacteria as salivary markers. Although the specificity of such tests has been evaluated on most biological specimens, their specificity for nasal secretion samples remains to be tested. Herein, to improve the specificity of the saliva detection tests for nasal secretion samples, we reanalyzed a public microbiome dataset and conducted inhouse 16S rRNA sequencing to identify a new marker to distinguish between saliva and nasal secretions. The sequencing data indicated the existence of oral bacteria such as Streptococcus in nasal secretion samples, which may be responsible for the false positives in the saliva tests. Furthermore, we found that including the 16S rRNA gene of the genus Staphylococcus as a nasal secretion marker may improve the specificity of PCR-based saliva tests for nasal secretion samples. In addition, we assessed the specificity of previously developed salivary bacteria detection tests for nasal secretion samples and oral bacterial markers were detected in two of eight nasal secretion samples, which led to the false positive results for saliva detection. Thus, the specificity of such tests can be improved by adding Staphylococcus as a nasal marker, as revealed by our sequencing analysis.

Dual roles of cellular communication network factor 6 (CCN6) in the invasion and metastasis of oral cancer cells to bone via binding to BMP2 and RANKL.

The acquisition of motility via epithelial-mesenchymal transition (EMT) and osteoclast induction are essential for the invasion and metastasis of oral squamous cell carcinoma (OSCC) to bone. However, the molecule suppressing both EMT and osteoclastogenesis is still unknown. In this study, we found that cellular communication network factor 6 (CCN6) was less produced in a human OSCC cell line, HSC-3 with mesenchymal phenotype, than in HSC-2 cells without it. Notably, CCN6 interacted with bone morphogenetic protein 2 (BMP2) and suppressed the cell migration of HSC-3 cells stimulated by BMP2. Moreover, knockdown of CCN6 in HSC-2 cells led to the promotion of EMT and enhanced the effect of transforming growth factor-ß (TGF-ß) on the promotion of EMT. Furthermore, CCN6 combined with BMP2 suppressed EMT. These results suggest that CCN6 strongly suppresses EMT in cooperation with BMP2 and TGF-ß. Interestingly, CCN6 combined with BMP2 increased the gene expression of receptor activator of nuclear factor-κB ligand (RANKL) in HSC-2 and HSC-3 cells. Additionally, CCN6 interacted with RANKL, and CCN6 combined with RANKL suppressed RANKL-induced osteoclast formation. In metastatic lesions, increasing BMP2 due to the bone destruction led to interference with binding of CCN6 to RANKL, which results in the promotion of bone metastasis of OSCC cells due to continuous osteoclastogenesis. These findings suggest that CCN6 plays dual roles in the suppression of EMT and in the promotion of bone destruction of OSCC in primary and metastatic lesions, respectively, through cooperation with BMP2 and interference with RANKL.

Omega-3 meat enrichment and L-FABP, PPARA, and LPL genes expression are modified by the level and period of tuna oil supplementation in slow-growing chickens.

This study proposes a strategy to manipulate the fatty acid (FA) content in slow-growing Korat chicken (KRC) meat using tuna oil (TO). To determine the optimal level and feeding period of TO supplementation, we conducted a study investigating the effects of dietary TO levels and feeding periods on meat quality, omega-3 polyunsaturated fatty acid (n-3 PUFA) composition, and gene expression related to FA metabolism in KRC breast meat. At 3 wk of age, 700 mixed-sex KRC were assigned to seven augmented factorial treatments with a completely randomized design, each consisting of four replicate pens containing 25 chickens per pen. The control group received a corn-soybean-based diet with 4.5% rice bran oil (RBO), while varying amounts of TO (1.5%, 3.0%, or 4.5%) replaced a portion of the RBO content in the experimental diets. The chickens were fed these diets for 3 and 6 wk, respectively, before being slaughtered at 9 wk. Our results indicated no significant interactions between TO levels and feeding periods on the growth performance or meat quality of KRC (P > 0.05). However, the liver fatty acid-binding protein gene (L-FABP, also known as FABP1), responsible for FA transport and accumulation, showed significantly higher expression in the chickens supplemented with 4.5% TO (P < 0.05). The chickens supplemented with 4.5% TO for a longer period (3 to 9 wk of age) exhibited the lowest levels of n-6 PUFA and n-6 to n-3 ratio, along with the highest levels of eicosapentaenoic acid, docosahexaenoic acid, and n-3 PUFA in the breast meat (P < 0.05). However, even a short period of supplementation with 4.5% TO (6 to 9 wk of age) was adequate to enrich slow-growing chicken meat with high levels of n-3 PUFA, as recommended previously. Our findings indicated that even a short period of tuna oil supplementation could lead to desirable levels of omega-3 enrichment in slow-growing chicken meat. This finding has practical implications for the poultry industry, providing insights into optimal supplementation strategies for achieving desired FA profiles without adversely affecting growth performance or meat quality.

This study investigated the effect of different levels and feeding periods of tuna oil (TO), a source of omega-3 polyunsaturated fatty acids (n-3 PUFA), was used to modify the fatty acid (FA) profile in slow-growing Korat chicken (KRC) meat. The interaction between TO supplementation levels and feeding periods did not influence growth performance or meat quality in KRC. However, higher level of TO supplementation led to increased expression of the liver fatty acid-binding protein gene, which is involved in FA transport and accumulation. The highest levels of eicosapentaenoic acid, docosahexaenoic acid, and n-3 PUFA were detected in the chickens that were fed 4.5% TO supplementation for a long period (3 to 9 wk of age). These chickens also had the lowest amounts of omega-6 polyunsaturated fatty acids (n-6 PUFA) and n-6 to n-3 ratio. Interestingly, even a short period of 4.5% TO supplementation (6 to 9 wk of age) in slow-growing chickens was sufficient to enrich the KRC meat with n-3 PUFA. These findings highlight the potential for improving the nutritional profile of chicken meat by regulating TO supplementation in the diet.

Transcriptome analysis of the uterovaginal junction containing sperm storage tubules in heat-stressed breeder hens.

Sperm storage tubules (SSTs) in the uterovaginal junction (UVJ) of the oviduct are major sites of sperm storage after artificial insemination or mating. Female birds may regulate sperm motility in the UVJ. Heat stress can decrease the reproductive ability of broiler breeder hens. However, its effects on UVJ remain unclear. Changes in gene expression aid in understanding heat stress-affected molecular mechanisms. Herein, we wanted to conduct a comparative transcriptomic analysis to identify the differentially expressed genes (DEGs) in the UVJ of breeder hens under thermoneutral (23°C) and heat stress (36°C for 6 h) conditions. The results indicated that cloacal temperatures and respiratory rates were significantly increased in heat-stressed breeder hens (P < 0.05). Total RNA was extracted from the hen UVJ tissues containing SSTs after heat exposure. Transcriptome analysis identified 561 DEGs, including 181 upregulated DEGs containing heat shock protein (HSP) transcripts and 380 downregulated DEGs containing immune-related genes, such as interleukin 4-induced 1, radical S-adenosyl methionine domain containing 2, and 2'-5'-oligoadenylate synthetase like, in heat-stressed hens. Gene Ontology analysis revealed the significantly enriched terms involving HSPs. Kyoto Encyclopedia of Genes and Genomes analysis identified 9 significant pathways, including the protein processing in endoplasmic reticulum (11 genes including HSPs), neuroactive ligand-receptor interaction (13 genes including luteinizing hormone/choriogonadotropin receptor), biosynthesis of amino acids (4 genes including tyrosine aminotransferase), ferroptosis (3 genes including heme oxygenase 1), and nitrogen metabolism (carbonic anhydrase [CA]-12 and CA6) pathways. Protein-protein interaction network analysis of DEGs revealed 2 large networks, one containing upregulated HSPs and the other containing downregulated interferon-stimulating genes. Overall, heat stress inhibits innate immunity in the UVJ tissues of broiler chickens, and heat-stressed chickens protect their cells by increasing the expression levels of HSPs. The identified genes are potential candidates for further exploration of the UVJ in heat-stressed hens. The identified molecular pathways and networks increase our understanding of the sperm storage reservoirs (UVJ containing SSTs) within the reproductive tract and may be used to prevent heat stress-induced fertility loss in breeder hens.

Cytogenetic evidence and dmrt linkage indicate male heterogamety in a non-bilaterian animal.

The diversity of sex determination systems in animals suggests that sex chromosomes evolve independently across different lineages. However, the present data on these systems is largely limited and represented mainly by bilaterian animals. Sex chromosomes and sex determination system based on cytogenetic evidence remain a mystery among non-bilaterians, the most basal animals. Here, we investigated the sex determination system of a non-bilaterian (Goniopora djiboutiensis) based on karyotypic analysis and identification of locus of dmrt1, a known master sex-determining gene in many animals. Results showed that among the three isolated dmrt genes, GddmrtC was sperm-linked. Fluorescence in situ hybridization revealed that 47% of the observed metaphase cells contained the GddmrtC locus on the shorter chromosome of the heteromorphic pair, whereas the other 53% contained no GddmrtC locus and pairing of the longer chromosome of the heteromorphic pair was observed. These findings provided the cytogenetic evidence for the existence of the Y sex chromosome in a non-bilaterian animal and supports male heterogamety as previously reported in other non-bilaterian species using RAD sequencing. The Y chromosome-specific GddmrtC sequence was most homologous to the vertebrate dmrt1, which is known for its role in male sex determination and differentiation. Our result on identification of putative sex chromosomes for G. djiboutiensis may contribute into understanding of the possible genetic sex determination systems in non-bilaterian animals.

Thigh muscle metabolic response is linked to feed efficiency and meat characteristics in slow-growing chicken.

The Korat chicken (KR) is a slow-growing Thai chicken breed with relatively poor feed efficiency (FE) but very tasty meat with high protein and low fat contents, and a unique texture. To enhance the competitiveness of KR, its FE should be improved. However, selecting for FE has an unknown effect on meat characteristics. Thus, understanding the genetic basis underlying FE traits and meat characteristics is needed. In this study, 75 male KR birds were raised up to 10 wk of age. For each bird, the feed conversion ratio (FCR), residual feed intake (RFI), and physicochemical properties, flavor precursors, and biological compounds in the thigh meat were evaluated. At 10 wk of age, thigh muscle samples from 6 birds (3 with high FCR and 3 with low FCR values) were selected, and their proteomes were investigated using a label-free proteomic method. Weighted gene coexpression network analysis (WGCNA) was used to screen the key protein modules and pathways. The WGCNA results revealed that FE and meat characteristics significantly correlated with the same protein module. However, the correlation was unfavorable; improving FE may result in a decrease in meat quality through the alteration in biological processes including glycolysis/gluconeogenesis, metabolic pathway, carbon metabolism, biosynthesis of amino acids, pyruvate metabolism, and protein processing in the endoplasmic reticulum. The hub proteins of the significant module (TNNT1, TNNT3, TNNI2, TNNC2, MYLPF, MYH10, GADPH, PGK1, LDHA, and GPI) were also identified to be associated with energy metabolism, and muscle growth and development. Given that the same proteins and pathways are present in FE and meat characteristics but in opposite directions, selection practices for KR should simultaneously consider both trait groups to maintain the high meat quality of KR while improving FE.

Do not overwork: cellular communication network factor 3 for life in cartilage.

Cellular communication network factor (CCN) 3, which is one of the founding members of the CCN family, displays diverse functions. However, this protein generally represses the proliferation of a variety of cells. Along with skeletal development, CCN3 is produced in cartilaginous anlagen, growth plate cartilage and epiphysial cartilage. Interestingly, CCN3 is drastically induced in the growth plates of mice lacking CCN2, which promotes endochondral ossification. Notably, chondrocytes in these mutant mice with elevated CCN3 production also suffer from impaired glycolysis and energy metabolism, suggesting a critical role of CCN3 in cartilage metabolism. Recently, CCN3 was found to be strongly induced by impaired glycolysis, and in our study, we located an enhancer that mediated CCN3 regulation via starvation. Subsequent investigations specified regulatory factor binding to the X-box 1 (RFX1) as a transcription factor mediating this CCN3 regulation. Impaired glycolysis is a serious problem, resulting in an energy shortage in cartilage without vasculature. CCN3 produced under such starved conditions restricts energy consumption by repressing cell proliferation, leading chondrocytes to quiescence and survival. This CCN3 regulatory system is indicated to play an important role in articular cartilage maintenance, as well as in skeletal development. Furthermore, CCN3 continues to regulate cartilage metabolism even during the aging process, probably utilizing this regulatory system. Altogether, CCN3 seems to prevent "overwork" by chondrocytes to ensure their sustainable life in cartilage by sensing energy metabolism. Similar roles are suspected to exist in relation to systemic metabolism, since CCN3 is found in the bloodstream.

Cellular Fluorescence Imaging for the Evaluation of Bioactivity of CCN Family Proteins.

The method of labeling proteins of interest with fluorescent dyes that can specifically stain organelles in living cells provides a tool for investigating various cellular processes under a microscope. Visualization (imaging) of the cells using fluorescence has many advantages, including the ability to stain multiple cell organelles and intracellular proteins simultaneously and discriminately, and is used in many research fields. In this chapter, we describe the observation of cell organelles using fluorescence staining to analyze the functions of CCN family proteins involved in various cellular events.

Protocols for Screening Peptides Binding to CCN Family Proteins and Their Extended Utility.

The function of CCN family proteins is determined by their interactions with multiple cofactors that are present in the microenvironment. Therefore, determining these cofactors is critically important in understanding the molecular function of CCN family members. For this objective, a bacteriophage random peptide display library is a suitable tool. In this library, each filamentous bacteriophage is designed to display an oligopeptide of 7-20 random amino acid residues on its surface. Bacteriophage clones that possess peptides that bind to a CCN family protein are selected through several cycles of a process called biopanning or affinity selection. By determining the nucleotide sequence of the DNA that encodes the displayed peptide, the oligopeptides that specifically bind to the CCN family member can be specified. The obtained peptide sequences can be utilized to design peptide aptamers for CCN family proteins, or as a key sequence to determine new CCN family cofactor candidates in silico. Instead of a random peptide cDNA library, an antibody cDNA library from naïve lymphocytes or from B cells immunized by a CCN family protein can be used in order to obtain a highly specific CCN family detection or functional modulation tool.

Analyses of the Posttranscriptional Regulation of CCN Genes: Approach to Multiple Steps of CCN2 Gene Expression.

Cells generally control the concentration of mRNA via transcriptional and posttranscriptional regulation, so the separate contributions of synthesis and degradation (decay) cannot be discriminated by the quantification of mRNA. To elucidate the contribution of posttranscriptional regulation, all experimental procedures for the analysis of the total transcript level, transcriptional induction, degradation of the target mRNA, and inhibition of mRNA translation are performed either individually or in combination. From our experience, measurement of the steady-state levels of mRNA using quantitative real-time polymerase chain reaction is an essential first step in quantifying the ccn2 gene expression. Subsequently, the effect of transcription rates should be assessed by reporter assays of the ccn2 promoter and nuclear run-on assays. The stability of ccn2 mRNAs is then evaluated in the presence of a metabolic inhibitor actinomycin D, followed by mRNA degradation assays in vitro. Finally, repression of ccn2 mRNA translation can be estimated by comparing the expression of mRNA and protein changes. We herein report the strategic methods used in a series of analyses to elucidate the possible involvement of the posttranscriptional regulatory mechanism of the ccn2 gene and show how this approach can, in theory, be used to elucidate the posttranscriptional regulation of other genes belonging to the CCN family.

Utilizing Public Molecular Biological Databases for CCN Family Research.

Classically, scientific research has been driven by hypotheses based on personal inspiration and intuition against the background of personal knowledge. In contrast, scientists have recently proposed that scientific research should basically be driven by data, meaning big data yielded by preliminary omic analyses in this context. A genuine hypothesis-driven strategy is usually exciting but occasionally ends up with negative conclusions, whereas a data-driven approach is less exciting and cost-consuming but produces significant outcomes in most cases. Here, we should be aware that a number of bioscientific resources provide a variety of big data free of charge. Therefore, one of the most effective research strategies is to construct a research question based on comprehensive knowledge derived not only from inside information, but also from the analysis of data available to everybody. However, a classical scientist without a sufficient bioinformatic background may hesitate in dealing with information supplied through the Internet. This chapter is aimed at CCN family researchers who do not possess specific bioinformatic knowledge and/or huge grants-in-aid, in order to assist them in developing their research by taking advantage of the scientific treasury open to the public.

Novel Cell Biological Assays for Measuring Bone Remodeling Activities of CCN Proteins.

Although two-dimensional (2D) cultures from bone lineage cells are often used, it is well-known that this culture system is completely different from the in vivo bone matrix environment. In this paper, we describe a 3D culture method using both the mouse osteocytic cell line, MLO-Y4, and an osteocyte-enriched population of the cells isolated from mice. These cells are embedded in collagen gel with recombinant cellular communication network (CCN) factor proteins; then, osteoblasts or osteoclasts are inoculated and cultured on the collagen gel. Because this method mimics the in vitro bone matrix environment, it is useful for understanding the detailed mechanism of actions of CCN proteins in the bone matrix.

Gene Expression Analysis of CCNs Along with Odontoblastic Differentiation In Vivo.

Dental pulp cells (DPCs) differentiate into odontoblasts. To observe odontoblastic differentiation, the detection of dentinogenesis-specific molecules such as dentin sialophosphoprotein (DSPP) and the measurement of alkaline phosphatase (ALP) activity are reliable approaches. CCN family member 2 (CCN2) has been proposed as a marker for dentinogenesis. Our recent study revealed that the expression levels of Ccn4, Ccn5, and Ccn6 were changed in accordance with odontoblastic differentiation. Therefore, Ccn4, Ccn5, and Ccn6, as well as Ccn2, could serve as a comprehensive set of markers for dentinogenesis. Here, we describe a method of measuring the Ccns expression levels in differentiating rat DPCs.