Mechanical Properties and Histological Evaluation of Bone Grafting Materials Containing Different Ratios of Calcium Phosphate Cement and Porous β-tricalcium Phosphate Granules

Article信州医学雑誌 66(2): 139-150(2018)journal articl

Organelle DNA degradation contributes to the efficient use of phosphate in seed plants

Mitochondria and chloroplasts (plastids) both harbour extranuclear DNA that originates from the ancestral endosymbiotic bacteria. These organelle DNAs (orgDNAs) encode limited genetic information but are highly abundant, with multiple copies in vegetative tissues, such as mature leaves. Abundant orgDNA constitutes a substantial pool of organic phosphate along with RNA in chloroplasts, which could potentially contribute to phosphate recycling when it is degraded and relocated. However, whether orgDNA is degraded nucleolytically in leaves remains unclear. In this study, we revealed the prevailing mechanism in which organelle exonuclease DPD1 degrades abundant orgDNA during leaf senescence. The DPD1 degradation system is conserved in seed plants and, more remarkably, we found that it was correlated with the efficient use of phosphate when plants were exposed to nutrient-deficient conditions. The loss of DPD1 compromised both the relocation of phosphorus to upper tissues and the response to phosphate starvation, resulting in reduced plant fitness. Our findings highlighted that DNA is also an internal phosphate-rich reservoir retained in organelles since their endosymbiotic origin

Large-scale clustering of CAGE tag expression data

Background: Recent analyses have suggested that many genes possess multiple transcription start sites (TSSs) that are differentially utilized in different tissues and cell lines. We have identified a huge number of TSSs mapped onto the mouse genome using the cap analysis of gene expression (CAGE) method. The standard hierarchical clustering algorithm, which gives us easily understandable graphical tree images, has difficulties in processing such huge amounts of TSS data and a better method to calculate and display the results is needed. Results: We use a combination of hierarchical and non-hierarchical clustering to cluster expression profiles of TSSs based on a large amount of CAGE data to profit from the best of both methods. We processed the genome-wide expression data, including 159,075 TSSs derived from 127 RNA samples of various organs of mouse, and succeeded in categorizing them into 70-100 clusters. The clusters exhibited intriguing biological features: a cluster supergroup with a ubiquitous expression profile, tissue-specific patterns, a distinct distribution of non-coding RNA and functional TSS groups. Conclusion: Our approach succeeded in greatly reducing the calculation cost, and is an appropriate solution for analyzing large-scale TSS usage data

Identification of Dipeptidyl-Peptidase (DPP)5 and DPP7 in Porphyromonas endodontalis, Distinct from Those in Porphyromonas gingivalis

Dipeptidyl peptidases (DPPs) that liberate dipeptides from the N-terminal end of oligopeptides are crucial for the growth of Porphyromonas species, anaerobic asaccharolytic gram negative rods that utilize amino acids as energy sources. Porphyromonas endodontalis is a causative agent of periapical lesions with acute symptoms and Asp/Glu-specific DPP11 has been solely characterized in this organism. In this study, we identified and characterized two P. endodontalis DPPs, DPP5 and DPP7. Cell-associated DPP activity toward Lys-Ala-4-methylcoumaryl-7- amide (MCA) was prominent in P. endodontalis ATCC 35406 as compared with the Porphyromonas gingivalis strains ATCC 33277, 16-1, HW24D1, ATCC 49417, W83, W50, and HNA99. The level of hydrolysis of Leu-Asp-MCA by DPP11, Gly- Pro-MCA by DPP4, and Met-Leu-MCA was also higher than in the P. gingivalis strains. MER236725 and MER278904 are P. endodontalis proteins belong to the S9- and S46-family peptidases, respectively. Recombinant MER236725 exhibited enzymatic properties including substrate specificity, and salt- and pH-dependence similar to P. gingivalis DPP5 belonging to the S9 family. However, the kcat/Km figure (194 mM21?sec21) for the most potent substrate (Lys-Ala-MCA) was 18.4-fold higher as compared to the P. gingivalis entity (10.5 mM21?sec21). In addition, P. endodontalis DPP5 mRNA and protein contents were increased several fold as compared with those in P. gingivalis. Recombinant MER278904 preferentially hydrolyzed Met-Leu-MCA and exhibited a substrate specificity similar to P. gingivalis DPP7 belonging to the S46 family. In accord with the deduced molecular mass of 818 amino acids, a 105-kDa band was immunologically detected, indicating that P. endodontalis DPP7 is an exceptionally large molecule in the DPP7/DPP11/S46 peptidase family. The enhancement of four DPP activities was conclusively demonstrated in P. endodontalis, and remarkable Lys-Ala-MCAhydrolysis was achieved by qualitative and quantitative potentiation of the DPP5 molecule

Effect of dormancy on the development of phloem fiber clusters

The development of phloem fibers was investigated in poplars grown under artificially fixed conditions and under an artificially shortened annual cycle system that includes a dormancy phase. The phloem tissues in these trees formed two- or three-layer fiber clusters; however, clusters in trees that underwent periodic dormancy were larger than those in trees that did not. Individual fibers were also larger in the former than in the latter, as assessed on transverse sections. Differences were most pronounced in the radial diameter of fibers in the layer nearest the cambium. These results suggest that dormancy affects both the size of fiber clusters and the diameter of individual fibers. Furthermore, these results imply that dormancy affects the development of phloem fibers, and that the shortened annual cycle system is a useful model for investigating phloem development caused by dormancy repetition

Experimental Study of Intra-Ring Anatomical Variation in <i>Populus alba</i> L. with Respect to Changes in Temperature and Day-Length Conditions

There are various studies on annual ring structural variations in plants grown in the field under varying meteorological statistics. However, related experimental approach is limited, hitherto. In this study, complete artificial conditions with growth chambers were adopted to evaluate the influence of day length and temperature on intra-ring structure formation. The basic artificial growing conditions have been previously reported as “shortened annual cycle system”, which consisted of the following three stages mimicking seasons approximately: Stage 1, spring/summer; Stage 2, autumn; and Stage 3, winter. This system shortens an annual cycle of Populus alba to 5 months. In this study, Stage 2 was modified in two ways: one was a condition in which the temperature was fixed and the day length was gradually shortened, and the other was a condition with a fixed day length and gradually lowered temperature. In the former condition, the cell wall of fibers thickened from the middle of the ring, and the vessel diameter became smaller from the same position. The wood in the latter condition appeared more natural in terms of wall thickness and vessel shape; however, the thickness of the wall reduced in the starting position of Stage 2. It may have been caused by the shortage of material for cell production under a high temperature but a short day length

<Note>Architectural morphogenesis of poplar grown in a shortened annual cycle system

Tree architecture is an important feature of plant environmental adaptation and affects many aspects of forestry, as well as both timber and orchard fruit production. However, studying tree architecture indoors in standard lab environments is challenging due to the large size and long growth cycles of trees. Here, we developed miniaturized poplar trees with branching architecture similar to field-grown trees by using a shortened annual cycle system. Control poplars grown under typical fixed conditions in a growth room had no branches and formed simple shapes consisting of a single stem and leaves. We observed simultaneous breaking of dormancy of several buds resulting in such architectural complexity. Our results suggest that apical dominance is lost in the shortened annual system as dormancy is broken. In contrast, apical dominance persisted in control trees grown under typical fixed conditions