Biology subjects

Makita, N.

Publications and source records attributed to Makita, N..

4 recordsLinked to original sources

bioRxiv2023

Genetic and transcriptomic dissection of nitrate-independent function of Arabidopsis NRT1.1/NPF6.3/CHL1 under high ammonium condition

The Arabidopsis nitrate transceptor NRT1.1/NPF6.3/CHL1 regulates physiological responses to nitrate. Several studies have reported that Arabidopsis plants lacking NRT1.1 show enhanced shoot growth under toxic levels of ammonium without nitrate, suggesting a nitrate-independent function for NRT1.1. To further investigate this nitrate-independent function and its impact on ammonium tolerance, we conducted genetic analysis, tissue-specific expression analysis, and transcriptome analysis using various NRT1.1-related lines. Transgenic plants expressing either nonphosphomimic or phosphomimic mutants of NRT1.1 exhibited similar ammonium tolerance to the wild-type. The chl1-9 mutant, in which NRT1.1 with the P492L substitution is localized intracellularly rather than at the plasma membrane and fails to transport nitrate, showed significantly improved ammonium tolerance. Confocal imaging revealed that the NRT1.1-GFP signal was detected in the plasma membrane of various tissues, including cotyledon pavement cells, hypocotyl epidermal cells, mesophyll cells, root cap cells, and epidermal cells near root tips. In early seedlings, the absence of functional NRT1.1 altered the expression of genes associated with aliphatic glucosinolate biosynthesis, ethylene signaling, and low pH stress. Genes predicted to encode products localized to the extracellular space were enriched among those differentially expressed due to NRT1.1 deficiency. Our data suggest that in the absence of nitrate, plasma membrane-targeted NRT1.1 reduces ammonium tolerance irrespective of its phosphorylation state with alterations of gene expression associated with stress and senescence.

plant biology↗

bioRxiv2023

Atf3 controls transitioning in female mitochondrial cardiomyopathy as identified by single-cell transcriptomics

Oxidative phosphorylation defects results in mitochondrial diseases, with cardiac involvement markedly impacting prognosis. However, the mechanisms underlying the transition from compensation to dysfunction in response to metabolic deficiency remain unclear, impeding the development of effective treatments. Here, we employed single-nucleus RNA sequencing (snRNA-seq) on hearts from mitochondrial cardiomyopathy (MCM) mice with cardiac-specific Ndufs6 knockdown (FS6KD). Pseudotime trajectory analysis of cardiomyocytes from early stage of female FS6KD hearts revealed dynamic cellular state transitioning from compensation to severe compromise, coincided with transient upregulation of a critical transcription factor, activating transcription factor 3 (Atf3). Genetic ablation or adeno-associated virus-mediated Atf3 knockdown in FS6KD mice effectively delayed cardiomyopathy progression in a female-specific manner. Notably, human MCM snRNA-seq revealed a similar transition, including the dynamic expression of ATF3. In conclusion, our findings highlight a fate-determining role of Atf3 in female MCM progression, providing a promising therapeutic candidate for the currently intractable disease.

cell biology↗

bioRxiv2022

Poly(2-oxazoline)-based polyplexes as a PEG-free plasmid DNA delivery platform

The present study expands the versatility of cationic poly(2-oxazoline) (POx) copolymers as a PEG-free platform for gene delivery to immune cells, such as monocytes and macrophages. Several block copolymers are developed by varying non-ionic hydrophilic blocks (poly(2-methyl-2-oxazoline) (pMeOx) or poly(2-ethyl-2-oxazoline) (pEtOx), cationic blocks, and an optional hydrophobic block (poly(2-isopropyl-2-oxazoline) (iPrOx). The cationic blocks are produced by side chain modification of 2-methoxy-carboxyethyl-2-oxazoline (MestOx) block precursor with diethylenetriamine (DET) or tris(2-aminoethyl)amine (TREN). For the attachment of a targeting ligand, mannose, we employed azide-alkyne cycloaddition click chemistry methods. Of the two cationic side chains, polyplexes made with DET-containing copolymers transfect macrophages significantly better than those made with TREN-based copolymer. Likewise, non-targeted pEtOx-based diblock copolymer is more active in cell transfection than pMeOx-based copolymer. The triblock copolymer with hydrophobic block iPrOx performs poorly compared to the diblock copolymer which lacks this additional block. Surprisingly, attachment of a mannose ligand to either of these copolymers is inhibitory for transfection. Despite similarities in size and design, mannosylated polyplexes result in lower cell internalization compared to non-mannosylated polyplexes. Thus, PEG-free, non-targeted DET- and pEtOx-based diblock copolymer outperforms other studied structures in the transfection of macrophages and displays transfection levels comparable to GeneJuice, a commercial non-lipid transfection reagent.

bioengineering↗

bioRxiv2022

Spring dynamics and regional variation in two different root developmental types in seedlings of a boreal evergreen conifer species

Premise of researchIn boreal forests with various snow cover conditions, local adaptation can be expected in spring root exploration due to soil freezing or competition for the fundamental niche. However, few studies have investigated the adaptive strategies for acquiring soil space and resources after snow thawing. To get insights for the eco-evolutional significance of root growth dynamics in boreal regions, this study evaluated the intraspecific variation of morphology and structures in pioneer roots and fibrous roots. MethodologyValidation model specie was Abies sachalinensis, a representative boreal conifer species with local adaptation. Five-year-old seedlings derived from an eastern provenance with low snow cover and a northern provenance with high snow cover were grown for two years in a common garden of high snow cover region. To predict spring growth patterns of roots, seedlings were dug up in early spring just after snow thawing and late spring after one month has passed. Pioneer roots exploring soil space and fibrous roots acquiring soil resource were respectively collected, and their functions were evaluated by morphology and structures indicating its construction costs and maturity. Pivotal resultsIn pioneer roots, morphological and structural difference between sampling months were significant only in northern provenance, and high construction cost and well-developed structure were observed in early spring. This represents the intraspecific variation in reaction norms of pioneer roots to spring soil environment, indicating the soil space exploration in northern provenance may start in early spring or earlier. In fibrous roots, differences of specific root length and area between sampling months were significant only in eastern provenance, and low construction cost were observed in early spring. This may reflect the plastic responses of fibrous roots to the condition of high snow cover region. ConclusionsThis study indicated that local adaptation to contrasting snow cover condition may lead to the differentiation of spring root growth dynamics for the competitive or conservative strategies. Our results address better understandings of the mechanisms of niche acquisition in evergreen conifer.

ecology↗