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Fujiwara, K.

Publications and source records attributed to Fujiwara, K..

At least 19 recordsLinked to original sources

The LudP arrest peptide stalls translation by remodeling the ribosomal A-site

Bacterial ribosome arrest peptides couple translation to secretion and membrane homeostasis, providing an intracellular regulatory feedback system. Although several Sec/YidC-associated arrest peptides have been characterized, how evolutionarily diverse peptides converge on equivalent physiological outcomes remains unclear. Here we identify LudP (Lacrimispora upstream of secDF peptide), a previously unrecognized arrest peptide conserved in the genus Lacrimispora and encoded immediately upstream of secDF. In vitro and in vivo assays show that LudP induces robust Gram-positive-specific translation arrest that is released in a Sec signal-dependent manner. Using systematic mutagenesis and deep mutational scanning, we define a compact 15-residue C-terminal arrest element that governs arrest stability and A-site residue selectivity. Cryo-electron microscopy reveals that a LudP nascent-chain -helix in the exit tunnel remodels the peptidyltransferase center, with Asp133-dependent conformational rearrangements of 23S rRNA, notably U2506, sterically and energetically destabilizing productive A-site aminoacyl-tRNA accommodation. These findings support functional convergent evolution of secretion-coupled arrest peptides across bacterial lineages.

molecular biology↗

Convergent evolution of extreme snout elongation in deep-sea fishes reveals constrained trajectories

Phenotypic extremes are scattered across the Tree of Life, suggesting that evolutionary constraints often limit their emergence. Yet striking departures from standard body plans, such as elongate snouts, have evolved convergently across deep time. We investigate extreme morphologies in two distantly related deep-sea fish clades: spikefishes (pufferfish relatives) and snipefishes (seahorse relatives). Using spikefishes as a study system, including all 24 living and fossil species, we integrated genome-wide phylogenomic data with a fossil and extant morphological character matrix, skull shape and dentition analyses from 64 CT scans, phenotypic and divergence matrices from >200 X-rays, functional manipulations of freshly collected and cleared-and-stained specimens, and formal convergence test across 300 percomorph species. We show that snout elongation evolved independently twice within spikefishes, reaching intermediate and extreme conditions along one predictable, ordered trajectory of additive skeletal rearrangements. Snout bones form a highly integrated, semi-autonomous module that channels evolutionary change along intrinsic lines of least resistance, coinciding with accelerated cranial evolution and expanded morphospaces in a clade with enhanced cranial mobility. Snipefishes converge on the same body plan through largely non-homologous elements and distinct linkage mechanics, except for near-identical vomer convergence. Extreme morphologies can emerge when phenotypic integration aligns with functional innovation, guiding evolution along repeatable trajectories.

evolutionary biology↗

Nanoscale Core-Rim Compartmentalization of Histamine and GABA within Individual Synaptic Vesicles

Classical synaptic transmission assumes that amino acid neurotransmitters and monoamines are stored in distinct vesicle populations. Here, we provide structural evidence for a dual-transmitter organization in which histamine and GABA are spatially partitioned into a core and rim within individual synaptic vesicles. Using an engineered glutaraldehyde-NaBH4; immuno-electron microscopy platform, quantitative analysis of 2,195 vesicles revealed a previously unrecognized nanoscale architecture, with histamine-associated signal concentrated within the vesicular core (95.1%), while GABA is organized toward the peripheral rim. Light microscopy further demonstrated extensive histamine-GABA correspondence across central and peripheral tissues, including sympathetic ganglia and adrenal medulla. This intravesicular segregation challenges the conventional separation of amino acid and monoamine storage into distinct vesicle classes and reveals that chemically distinct transmitters can occupy organized domains within a single vesicular lumen. This architecture may provide a structural basis for the distinct physiological modes of GABAergic and histaminergic signaling, linking nanoscale vesicular organization to their established differences in temporal action.

cell biology↗

A Polarized Histamine-GABA Core-Rim Architecture within Synaptic Vesicles

Neuroscience traditionally assumes that amino acid transmitters occupy clear synaptic vesicles, whereas monoamines reside in dense-core vesicles. Using a glutaraldehyde-NaBH epitope-engineering platform enabling ultrastructural detection of small amines, we identify a polarized histamine-GABA vesicular organization within conventional GABAergic vesicles. Quantitative electron microscopy demonstrates histamine condensed into a dense intraluminal core, while complementary GABA immunolabeling supports the localization of GABA toward the vesicle periphery, consistent with a membrane-proximal rim. This conserved architecture across central, autonomic, and endocrine GABAergic systems provides a structural framework for temporally differentiated inhibitory signaling, challenges the clear-versus-dense-core vesicle paradigm, and establishes a unified principle for dual-transmitter architecture. One-sentence summaryUsing glutaraldehyde-NaBH4-based ultrastructural analysis, we identified a novel "core histamine-rim GABA" vesicular architecture within GABAergic neurons, fundamentally redefining traditional models of dual-transmitter co-packaging and release dynamics.

neuroscience↗

Analysis of publicly available genomic data

Ethambutol (EMB) is a vital drug for treating Mycobacterium avium-intracellulare (MAI) infections; however, the genomic mutations underlying EMB resistance in MAI remain unclear. Herein, we evaluated eight sets of MAI clinical isolates, each containing at least two serial isolates collected from the same patient who received EMB in Japan. In four sets, the isolates independently increased EMB MIC by 4-fold, coinciding with mutations in the upstream region of embA or those corresponding to Mycobacterium tuberculosis (Mtb) embB Met306Val and Gln497Arg. Based on the increased EMB MIC values, we defined normal and elevated EMB MICs as [≤]8 {micro}g/mL and [≥]16 {micro}g/mL, respectively. In the other four sets, all of the isolates had elevated EMB MICs. In silico promoter prediction and expression analysis indicated that the upstream region of embA corresponds to the embA-embB promoter region, and mutations in this region increased the transcription of embA and embB, increasing EMB MICs. Furthermore, the analysis of 60 epidemiologically unrelated strains revealed that isolates with mutations in the embA-embB promoter and at embB codons 306/497 exhibited significantly higher EMB MICs compared with those without mutations. Publicly available genomic data demonstrate the worldwide occurrence of these mutations in clinical isolates. These results establish an association between elevated EMB MICs and mutations at embB codons 306/497 and the embA-embB promoter and are expected to predict EMB resistance.

microbiology↗

Dynamical Biomarkers of Creative Cognition Across Divergent and Convergent Problem-Solving

Creativity fluctuates markedly from moment to moment, even within the same individual, yet the neural dynamics that determines whether a given attempt produces a highly creative idea remains poorly understood. Prior studies have identified static EEG correlates of creative thinking, but these do not explain how brain activity is dynamically organized before and during successful idea generation. Here, we model creative cognition as trajectories through a neural state space using energy landscape analysis (ELA) of EEG recorded during two complementary problem-solving paradigms: the divergent Alternative Uses Test (AUT) and the convergent, goal-directed Fusion Innovation Test (FIT). Across both tasks, creative success was associated with dissociable dynamical signatures in the resting and ideation stages. Before ideation, greater diversity of resting-state patterns of activity, corresponding to possible attractors, indexed a preparatory substrate of creative potential, showing weak trial-level effects but robust subject-level coupling with performance. During ideation, higher creativity was predicted by how the brain traversed its accessible state space: successful trials were characterized by traversal biased toward sustained exploration within stable attractor basins rather than frequent switching between basins of attraction ({beta} = 0.104, p = 0.004, trial-level). These findings identify a task-invariant, biologically grounded dynamical mechanism of creative cognition and show that creative performance depends not only on which neural states are available, but also on how neural activity traverses that state space.

neuroscience↗

Constitutive sporulation in wild fission yeast enhances insect-mediated survival

Sexual reproduction in yeast typically occurs under nutrient-limited conditions, producing stress-resistant spores that promote survival. However, wild Schizosaccharomyces japonicus strains isolated from fruit flies exhibit constitutive sporulation even under nutrient-rich conditions. Here we demonstrate that this nutrient-independent sporulation enhances survival by enabling spores to resist digestion by Drosophila melanogaster, and that although such strains are disadvantageous under nutrient-rich conditions, they are positively selected during insect predation. Genetic analyses reveal that multiple mutations in six meiotic regulatory genes, acting via epistasis, underlie this phenotype. This trait is widely distributed across natural populations throughout Japan. These findings suggest that constitutive sexual reproduction functions as an adaptive strategy facilitating insect-mediated dispersal, reflecting an ecological context where sexual reproduction is maintained despite its costs. This work provides new insights into yeast-insect symbiosis, evolutionary dynamics of sexual adaptation, and potential applications in yeast breeding.

evolutionary biology↗

Deciphering the evolution of sex determination across the termite tree of life using high-quality genome assemblies

Most termites exhibit a unique sex-determining system, featuring multiple X and Y chromosomes that fuse into large complexes during male meiosis. The evolutionary origins of such complexes remain largely unknown. Using the genomes of 45 termites and two cockroaches, we investigated the evolution of sex determination systems in an entire insect lineage. We found that termite sex chromosomes are largely undifferentiated, likely reflecting extensive ongoing recombination. Evolving from the X0 system of cockroaches, most early-diverging termites exhibit a Y chromosome bearing the sex-determining gene doublesex, whereas doublesex is autosomal in most other termites. In contrast, other species exhibit multiple sex chromosomes that have undergone frequent turnover, except for Termitidae, which harbor conserved sex chromosomes. Our findings reveal important reworkings of the ancestral transformer-doublesex pathway in termites and suggest a potential role of doublesex in the formation of meiotic chromosomal complexes and caste differentiation.

evolutionary biology↗

Geometric inference of cross-species transcriptome correspondence using Gromov-Wasserstein optimal transport

Sequence homology reveals evolutionary gene correspondences, but identifying functionally corresponding genes within specific cell types or during cell fate specification remains non-trivial. Here, frameworks that translate insights from model organisms into other species would accelerate wet-lab studies, so we develop Species-OT, a cross-species transcriptome analysis framework using Gromov-Wasserstein optimal transport, which quantitatively compares the geometry of transcriptome distributions. Given a pair of bulk or single-cell RNA-sequencing datasets, Species-OT returns a gene-to-gene correspondence capturing probabilistic alignments of regulatory roles, and a transcriptomic distance quantifying overall divergence. Applied pairwise, Species-OT yields a transcriptomic discrepancy array and a hierarchical clustering tree analogous to a phylogenetic tree. We validate Species-OT using bulk RNA-seq data for cell fate specification from pluripotent stem cells in mice, monkeys, and humans and scRNA-seq data from pluripotent stem cells of six mammalian species. Species-OT identifies gene correspondences within cell fate specification, while transcriptomic discrepancies recapitulate expected species relationships.

bioinformatics↗

Population genomic scan of endogenous retrovirus insertions revealed cryptic drivers of selective sweep in wild house mouse genomes

Endogenous retroviruses (ERVs) represent a major source of structural variation in mammalian genomes, yet their diversity in wild populations remains poorly understood. Here, we conduct a comprehensive genome-wide survey of non-reference ERV insertions in wild house mice (Mus musculus) to characterize their distribution and evolutionary dynamics. Using a newly developed bioinformatics pipeline, we detected and annotated over 100,000 non-reference ERV insertions from short-read sequencing data across 163 wild mouse genomes. Our analyses revealed marked differences in ERV insertion patterns among subspecies and populations, including variation in genomic localization and population-specific polymorphisms. These heterogeneous patterns suggest distinct evolutionary histories and host-retrovirus interactions across populations. For instance, we describe the distribution of the ERV-derived Fv4 locus, which shows subspecies-restricted occurrence and confers resistance to murine leukemia viruses (MLVs). Several lines of evidence showed that the spread of Fv4 insertions in Korean population has been driven by adaptive introgression from neighboring populations. Our study provides the first large-scale population genomic scan of ERV diversity in wild house mice. By cataloguing extensive polymorphism in non-reference ERV insertions, our results highlight the role of ERVs as dynamic genomic elements that contribute to structural variation and adaptive evolution. Article SummaryEndogenous retroviruses (ERVs) are viral sequences embedded in animal genomes that can create structural genetic variation. In this study, we conducted a genome-wide survey of non-reference ERV insertions in 163 wild house mice using short-read sequencing data and a newly developed computational pipeline. We identified more than 100,000 polymorphic ERV insertions and found substantial differences among subspecies and geographic populations. One example, the ERV-derived Fv4 locus, illustrates how ERV variation can influence the genetic pattern of polymorphisms in the species. These results demonstrate that ERVs are dynamic genomic elements that contribute to population divergence and adaptive evolution.

evolutionary biology↗

Chromosome-scale genomes of two wild flowering cherrys (Cerasus itosakura and C. jamasakura) provide insights into structural evolution in Prunus

Flowering cherries (genus Cerasus) are iconic trees in Japan, celebrated for their cultural and ecological significance. Despite their prominence, high-quality genomic resources for wild Cerasus species have been limited. Here, we report chromosome-level genome assemblies of two representative Japanese cherries: Cerasus itosakura, a progenitor of the widely cultivated C. xyedoensis Somei-yoshino, and Cerasus jamasakura, a traditional popular wild species endemic to Japan. Using deep PacBio long-read and Illumina short-read sequencing, combined with reference-guided scaffolding based on near-complete C. speciosa genome, we generated assemblies of 259.1 Mbp (C. itosakura) and 312.6 Mbp (C. jamasakura), with both >98% BUSCO completeness. Consistent with their natural histories, C. itosakura showed low heterozygosity, while C. jamasakura displayed high genomic diversity. Comparative genomic analyses revealed structural variations, including large chromosomal inversions. Notably, the availability of both the previously published C. speciosa genome and our new C. itosakura genome enabled the reconstruction of proxy haplotypes for both parental lineages of Somei-yoshino. Comparison with the phased genome of Somei-yoshino revealed genomic discrepancies, suggesting that the cultivar may have arisen from genetically distinct or admixed individuals, and may also reflect intraspecific diversity. Our results offer genomic foundations for evolutionary and breeding studies in Cerasus and Prunus.

genomics↗

Highly selective SGLT2 inhibitors suppress glucose uptake in alpha-TC1 cells, while glucagon secretion is not affected.

The existence of sodium-glucose cotransporter 2 (SGLT2) in pancreatic alpha cells and its potential roles in glucagon secretion remain controversial, despite its well-established function in renal glucose reabsorption. While some studies suggest SGLT2 presence and its involvement in glucagon regulation, others deny its expression in alpha cells. To clarify this dispute, we investigated the functional effects of highly selective SGLT2 inhibitors, dapagliflozin and empagliflozin, on glucose uptake, intracellular ATP levels, and glucagon secretion in alpha-TC1 cells, a widely used model for glucagon-secreting cells in culture. The SGLT2 inhibitors significantly suppressed basal glucose uptake in alpha-TC1 cells, indicating functional SGLT2 presence. However, the inhibitors did not affect glucagon secretion. Neither the SGLT2 inhibitors nor the more potent glucose transport inhibitor, cytochalasin B, altered intracellular ATP levels or glucagon secretion. In contrast, pharmacological inhibition of K/ATP channels increased glucagon secretion without affecting glucose uptake or ATP levels. These results suggest that while SGLT2 is functionally present at low levels and mediates basal glucose uptake in alpha-TC1 cells, its inhibition has insufficient influence on intracellular ATP levels, and therefore glucagon secretion remains stable. Furthermore, our observations support predominant involvement of K/ATP channels in regulating glucagon secretion. Further studies in human purified pancreatic alpha cells in addition to islets are warranted to fully elucidate SGLT2s role in alpha-cell physiology.

pharmacology and toxicology↗

Downregulation of LATS1/2 Drives Endothelial Senescence-Associated Stemness (SAS) and Atherothrombotic Lesion Formation

BackgroundAtherothrombosis, the main event leading to acute coronary syndrome (ACS), is strongly linked to disturbed blood flow (d-flow) regions. Although the involvement of the Hippo pathway and its kinases Large Tumor Suppressor Kinase 1and 2 (LATS 1 and 2) in mechanical stress responses is known, the mechanisms by which d-flow simultaneously induces senescence, proliferation, and atherothrombosis remain unclear. MethodsThe role of endothelial cells (EC)-specific LATS1/2 was examined using EC specific knock-out (EKO) mice in a partial left carotid ligation (PLCL) model. Plaque spatial multi-omics analysis was performed by integrating imaging mass cytometry, sequential immunofluorescence (COMET), and spatial metabolomics at the single-cell level in human and mouse atherosclerotic plaques. ResultsIn tamoxifen-inducible Lats1homo(-/-) /Lats2 homo(-/-) EC-specific knockout (EKO) mice, deletion of LATS1/2 induced by tamoxifen led to fatal outcomes, characterized by severe systemic edema and markedly increased vascular permeability. In contrast, Lats1het(+/-)/Lats2 homo(-/-)-EKO mice survived and developed atherothrombotic plaques exhibiting neovascularization even without further additional dietary or genetic intervention. Spatial proteomics analysis revealed that LATS1/2 depletion in ECs triggered a senescence-associated stemness (SAS) phenotype, primarily driven by CD38 upregulation. Complementary spatial metabolomics profiling demonstrated a significant increase in sulfite and taurine within LATS1/2-deficient plaques, indicating lowered sulfite oxidase (SUOX) activity. Mechanistically, CD38 upregulation was found to suppress SUOX expression, induce the reverse mode of mitochondrial complex V, and increase succinate dehydrogenase (SDH) activity along with ATP consumption. Paradoxically, despite ATP depletion, this metabolic disturbance enhanced glutamate metabolism and the tricarboxylic acid (TCA) cycle, sustaining EC proliferation under energetically stressed conditions. The combined effect of LATS1/2 deletion and CD38 activation established a unique EC phenotype defined by increased SAS, leading to proliferation, senescence, and eventual cell death. These pathological processes culminated in the formation of atherothrombotic plaques, which were attenuated by inhibition of CD38. Notably, a similar phenotype--marked by metabolically active ECs--was observed in human atherothrombotic plaques, suggesting translational relevance. ConclusionLoss of LATS1/2 in ECs induces SAS state that promotes excessive EC proliferation, senescent cell accumulation, and the development of structurally fragile, leaky neo vessels--hallmarks of atherothrombotic lesions. CD38-mediated SUOX deficiency further amplifies this pathological process by inducing mitochondrial dysfunction, depleting ATP, and triggering compensatory upregulation of glutamate and TCA cycle metabolism. These findings identify a novel LATS1/2-CD38-SUOX axis in ECs that orchestrates SAS-driven atherothrombosis. Targeting CD38 may represent a promising therapeutic strategy to mitigate vascular dysfunction and plaque instability in high-risk ACS patients. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=191 HEIGHT=200 SRC="FIGDIR/small/660635v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@149d313org.highwire.dtl.DTLVardef@1c0988borg.highwire.dtl.DTLVardef@15efec9org.highwire.dtl.DTLVardef@1a96e03_HPS_FORMAT_FIGEXP M_FIG C_FIG Under normal physiological conditions, LATS1/2 and Lamin A work together to suppress CD38 expression. Lamin A binds directly to the CD38 promoter to repress transcription, and LATS1/2 interact with Lamin A to reinforce this suppression. This collaboration helps maintain low CD38 activity and preserves cellular NAD levels. However, under disturbed flow (d-flow), both LATS1/2 and Lamin A are downregulated. The loss of this dual repression leads to increased CD38 NADase expression. Elevated CD38 accelerates NAD consumption, causing NAD depletion--a hallmark of cellular senescence. Reduced NAD disrupts key metabolic and stress-response pathways, contributing to the onset of the senescent state. At the same time, CD38 suppresses sulfite oxidase (SUOX), leading to sulfite accumulation and mitochondrial redox imbalance. This shift activates the reverse mode of mitochondrial Complex V, which decreases ATP production and increases mitochondrial ROS, intensifying metabolic and oxidative stress in endothelial cells (ECs). In response, ECs compensate by upregulating succinate dehydrogenase (SDH), enhancing TCA cycle activity and glutamate metabolism. This metabolic adaptation provides the biosynthetic building blocks needed for cell growth and proliferation. As a result, ECs adopt a paradoxical phenotype: they show classical features of stress-induced senescence (such as NAD depletion, oxidative stress, and cell cycle arrest signals), while simultaneously undergoing metabolic activation and proliferation, also mediated by YAP. This defines a non-canonical endothelial program known as senescence-associated stemness (SAS), characterized by the formation of abnormal, proliferative, yet fragile neovessels. These dysfunctional vessels contribute to atherothrombosis, setting this process apart from the more stable lesions typical of conventional atherosclerosis.

molecular biology↗

Cell Morphology and Biophysical Mechanisms-Informed Traction Force Microscopy Using Machine Learning

AO_SCPLOWBSTRACTC_SCPLOWQuantitative evaluation of cell motility is essential for understanding biological functions. Traction force microscopy (TFM) is a method for quantifying cellular traction forces. By performing inverse mathematical analysis of substrate deformations induced by cellular forces, it is possible to estimate the underlying traction forces. Among various approaches for detecting substrate deformations, the most widely used is to track the displacement of fluorescent beads randomly embedded in the substrate. However, it is well known that the accuracy of force estimation deteriorates when the observation density is low. Furthermore, standardized datasets have not been established, as validation settings--such as random force distributions on the substrate, cell size, and bead density--vary across studies. To enable quantitative evaluation, we constructed a dataset based on the biophysical mechanism by which cellular traction forces are transmitted to the substrate through stress fibers, clutch proteins, and focal adhesions. In addition, we proposed a novel machine learning model that incorporates cell shape information obtained from observations, and we designed a loss function that accounts for both force magnitude and direction. As a result, our method enables highly accurate force estimation even under sparse observation conditions.

biophysics↗

Membrane-enhanced repulsive interactions regulate protein diffusion in cell-size space

Intracellular molecular organization is often explained by attractive interactions driving clustering and phase separation. Although consideration of repulsive forces is essential in physics, their roles remain unclear in cellular contexts. Here, we demonstrated the fundamental role of repulsion in regulating protein diffusion within cell-size space. By analyzing negatively charged protein diffusion in bulk solutions and in cell-size spaces with membranes, we revealed that membrane-enhanced repulsion inhibited protein diffusion in cell-size spaces. This was due to the amplified electrostatic interactions among proteins because of the large membrane area-to-volume ratio. Notably, ATP, a cellular central energy source, further inhibited protein diffusion in cell-size spaces, whereas protein wave propagation on the membrane counteracted this inhibition. These findings suggest an active regulatory mechanism restoring molecular mobility by dynamically adjusting membrane-enhanced repulsive forces. Our study challenges the traditional emphasis on attractive interactions, highlighting repulsion as a critical tunable factor governing molecular transport and spatial organization in cells. TeaserProtein diffusion within crowded cell-size spaces is tuned by membrane-enhanced repulsion and its active regulation.

biophysics↗

Artificial soil systems: A tool for investigating microbial life strategy effects on substrate mineralization

Soil microbes play a critical role in carbon (C) cycling, however, the influence of microbial life strategies and their interactions on C mineralization remains poorly understood. This study aimed to investigate how r- and K-strategist bacteria influence glucose mineralization using an artificial soil system, focusing on Bacillus subtilis and Streptomyces cinnamoneus. Through a 14-day incubation experiment, we found that B. subtilis exhibited rapid and high respiration rates, while S. cinnamoneus showed slower, delayed respiration rates, supporting their respective r/K classification. In co-culture treatments, cumulative glucose mineralization converged with B. subtilis monoculture levels and positively correlated with its relative abundance. These findings demonstrate that artificial soil systems effectively reveal how microbial interactions drive C dynamics, offering a controlled approach to elucidate mechanisms underlying soil C cycling.

microbiology↗

Bulk sample testing by real-time PCR for detecting Diaporthe destruens-infected seedlings of sweet potatoes

Foot rot disease of sweet potato is a fungal disease that causes serious damage to sweet potato production. It is especially important to check the health of seedlings as there is a risk that if the seed tubers or stem seedlings infected with foot rot pathogen are introduced into the production fields, it will rapidly spread throughout the fields. We have already developed a real-time PCR method to diagnose sweet potatoes contaminated with foot rot pathogen. In this study, to apply this method to the bulk sample testing, we provided examples on estimating the "probability of detection (POD)" for detecting bulk samples, and determining the number of subgroups and the number of samples in each subgroup for the bulk sample testing. Our results indicate that, for tubers, when testing between 100 and 1200 fragments per bulk sample, the lowest detection rate was approximately 81% at 800 fragments. For stems, when testing between 100 and 600 fragments, the lowest detection rate was approximately 83% at 500 fragments. Based on the estimated POD, the required sample size for bulk testing was calculated as follows: for the impermissible threshold proportion of contamination of infected plants (p) of 1%, between 390 and 624 samples are needed, while for p of 0.1%, between 3,840 and 6,228 samples are required. The bulk sample testing method using real-time PCR demonstrated in this study will become a powerful quality testing method for checking the health of sweet potato seedlings, and will make a significant contribution to sweet potato production.

plant biology↗

Evaluation of real-time PCR performance for detecting Diaporthe destruens in sweet potatoes

Sweet potato foot rot disease caused by Diaporthe destruens is a major threat to sweet potato production. Rapid and accurate detection in advance is essential to secure healthy plants or to implement effective control. In this study, we evaluated the detection performance of a real-time PCR method previously developed by our research group. The evaluation was conducted using sweet potato samples collected in the field, including those naturally infected with D. destruens. Based on the real-time PCR results and the actual occurrence of the disease, a receiver operating characteristic (ROC) curve was generated, and the area under the curve (AUC) was calculated. The AUC values ranged from 0.7041571 to 0.9204286, confirming that this real-time PCR method is a well-balanced detection method for both tubers and stems. Furthermore, to minimize the occurrence of false negatives, the cycle threshold (Ct) cutoff was set at 35, and detection performance (sensitivity, specificity, accuracy, etc.) was analyzed. Then, by considering abnormal melting temperature (Tm) values as negative, high accuracy was achieved, with values of 0.871212 for tubers and 0.715447 for stems. This study not only evaluated the detection performance of the real-time PCR for foot rot pathogens but also contributes to providing information on the methodology and significance of performance evaluation in various real-time PCR genetic detection methods.

plant biology↗