Biology subjects

Namikawa, M.

Publications and source records attributed to Namikawa, M..

2 recordsLinked to original sources

bioRxiv2026

A bone fragment-based protocol for molecular analysis of osteocyte-associated transcripts in human bone specimens

Osteocytes play a central role in bone remodeling, mineral metabolism, and skeletal homeostasis, but direct molecular analysis of human osteocytes remains technically challenging because they are embedded within the mineralized bone matrix. Surgically obtained human bone specimens provide valuable material for studying human bone biology; however, surface-associated cells, marrow-derived cells, and adherent soft tissues can confound downstream transcript analysis. Here, we describe a bone fragment-based protocol for preparing surgically obtained human bone specimens for molecular analysis of osteocyte-associated transcripts. The protocol consists of mechanical trimming, mincing into small bone fragments, repeated washing, and five sequential rounds of collagenase digestion to reduce non-osteocytic cellular components associated with the bone surface and marrow spaces. The remaining mineralized bone fragments are then frozen in liquid nitrogen, cryogenically pulverized, and lysed in TRIzol reagent for total RNA extraction. Histological validation using residual maxillary bone specimens showed that sequential collagenase digestion markedly reduced adherent soft tissue and extra-matrix nuclei while preserving osteocyte lacunar occupancy. This protocol provides a practical workflow for bone fragment-based RNA analysis focused on osteocyte-associated transcripts in human bone specimens. Specifications table O_TBL View this table: org.highwire.dtl.DTLVardef@1cec618org.highwire.dtl.DTLVardef@2f746forg.highwire.dtl.DTLVardef@1854247org.highwire.dtl.DTLVardef@1c26c1aorg.highwire.dtl.DTLVardef@1473a88_HPS_FORMAT_FIGEXP M_TBL C_TBL

cell biology↗

bioRxiv2022

Nitrogen uptake pattern of dry direct-seeding rice and its contribution to yield in a cool temperate climate

Dry direct-seeding rice (DDSR) cultivation is expected to reduce production costs compared with transplanted rice (TPR); however, its low nitrogen (N) use efficiency (NUE) has hindered cost reduction. Additionally, polymer-coated urea application in rice cultivation is reduced for plastic pollution regulation. The split application of urea can be an alternative, but it has not been used in northeastern Japan, hence needs to be investigated. We conducted DDSR and TPR field experiments for three years using two cultivars and three or two N regimes to determine factors limiting yield and NUE using a standard cultivar ( Akitakomachi) and a high-yielding cultivar ( Yumiazusa) grown under different N regimes. The yield, yield components, and N uptake of DDSR were analyzed, and examined the contribution of N uptake until panicle initiation and heading for spikelet number by multiple regression compared to that of TPR. Additionally, we investigated the detailed N uptake pattern on DDSR until PI using the two parameters, which were calculated by exponential regression of N uptake during the vegetative period. DDSR yield was lower than that of TPR by 11% and revealed that both fertilizer recovery rate and crop NUE (yield per unit N uptake) contributed to the lower yield. N uptake until the fifth leaf age significantly influenced the N uptake until panicle initiation. DDSR yield with normal urea in this study proportion was not significantly different compared to coated urea application, indicating the possibility to be an alternative N application method.

plant biology↗