Biology subjects

Uchida, K.

Publications and source records attributed to Uchida, K..

30 records · Page 2Linked to original sources

bioRxiv2024

Genetic diversity and differentiation of a mycoheterotrophic orchid (Cymbidium macrorhizon) under urbanization

Urbanization exerts substantial pressures on genetic diversity of plant species. However, depending on species-specific life history, the direction/magnitude of urbanization impacts can vary. To elucidate relationships between life history and urbanization effects, there are needs to accumulate the knowledge on genetic diversity/differentiation along urban-rural gradients for species with unique traits. We examined these facets based on genome-wide single nucleotide polymorphisms of a mycoheterotrophic and vegetative-dormant orchid, Cymbidium macrorhizon, for eleven populations in remnant forests along an urban gradient within the Tokyo metropolitan area, Japan. The reduced inbreeding coefficient and increased genetic differentiation were observed with increased proportion of surrounding urban land-use 50 years ago rather than in recent years. This pattern might reflect lowest heterozygosity under intensive urbanization due to population bottleneck and genetic drift due to habitat shrinkage and fragmentation. The significant impacts of past landscape on the indices might indicate time lags of genetic erosion, namely intra-specific extinction debt, due to longevity and dormancy. Therefore, 30% increase of urban land-use since 1970s has not yet affected genetic erosion, resulting in its progression in the future. We emphasize the importance not only to assess genetic diversity but also to connect the assessments with life history and spatiotemporal urbanization impacts.

ecology↗

bioRxiv2024

Regional differences in cell characteristics in electric eel electric organs indicate electrocyte development with ventral to dorsal migration.

Electric eels (Electrophorus) are renowned for their ability to generate electric discharge, which is used for prey capture and defense. Their electric organs (EOs) are located along the lateral-ventral region of the tail and contain electrocytes, which are multinucleated syncytium cells. The developmental origin of the electrocyte is mesodermal lineage cells observed in the ventral part of the myotome. However, it is unclear whether these precursor cells are also maintained in later stages and contribute to electric organ growth in adulthood. In this study, we report regional differences in cell morphology within the main EO (mEO) and identify a candidate cell population for electrocyte progenitors at the juvenile stages of Electrophorus. The cell morphology and distribution from the ventral terminal to the dorsal region of the mEO suggest the segregation of progenitors from the ventral cluster and their gradual transformation into mature multinucleated electrocytes via cell fusion and layering along the dorsal axis. Immunohistochemistry revealed strong expression of sodium-potassium adenosine triphosphatase (Na+/K+-ATPase), a key component in generating electric discharge in the mEO, across most mEO regions, except in the ventral cluster cells. Based on these observations, we propose that electrocyte progenitors develop from ventral cluster cells in the mEO and differentiate into mature multinucleated cells as they migrate dorsally. This is the first report to approach the developmental process of Electrophorus electrocytes from cell morphology and genetic profiles. Our findings represent a breakthrough in understanding the differentiation of electrocytes during the growth stages of Electrophorus.

developmental biology↗

bioRxiv2024

Generation of humanized mouse models to support therapeutic development for SYNGAP1 and STXBP1 disorders

Heterozygous variants in SYNGAP1 and STXBP1 cause distinct neurodevelopmental disorders due to haploinsufficiency of essential synaptic proteins. As gene targeted approaches to correct these disorders often target non-conserved genomic regions, thus limiting their clinical translation, we generated humanized mouse models wherein the entire Syngap1 or Stxbp1 loci were replaced with their human counterparts. Stxbp1 humanized mice exhibited impaired viability, while Stxbp1 hybrid mice (Stxbp1Hu/+) were viable and suitable for evaluating target engagement of human-specific therapeutics. Syngap1 humanized mice were viable and successfully crossed with Syngap1 heterozygous mice to produce a Syngap1 humanized-haploinsufficient model (Syngap1Hu/-). Syngap1Hu/- mice displayed haploinsufficient levels of human SYNGAP1, disease-relevant behaviors, and EEG abnormalities including epileptiform activity and generalized slowing. Importantly, parallel analysis in a cohort of patients with SYNGAP1-disorder revealed similar electrophysiological signatures. Finally, we showed that human gene-targeted antisense oligonucleotides modulate human SYNGAP1 expression in Syngap1Hu/- neurons. Together, we describe new models to support pre-clinical therapeutic development for SYNGAP1 and STXBP1 disorders and identify translational biomarkers of SYNGAP1-disorder in mice and humans to benchmark therapeutic testing.

neuroscience↗

bioRxiv2024

Microtubule forces drive nuclear damage in LMNA cardiomyopathy

Nuclear homeostasis requires a balance of forces between the cytoskeleton and nucleus. Mutations in the LMNA gene, which encodes the nuclear envelope proteins lamin A/C, disrupt this balance by weakening the nuclear lamina. This results in nuclear damage in contractile tissues and ultimately muscle disease. Intriguingly, disrupting the LINC complex that connects the cytoskeleton to the nucleus has emerged as a promising strategy to ameliorate LMNA-associated cardiomyopathy. Yet how LINC complex disruption protects the cardiomyocyte nucleus remains unclear. To address this question, we developed an assay to quantify the coupling of cardiomyocyte contraction to nuclear deformation and interrogated its dependence on the nuclear lamina and LINC complex. We found that, surprisingly, the LINC complex was mostly dispensable for transferring contractile strain to the nucleus, and that increased nuclear strain in lamin A/C-deficient cardiomyocytes was not rescued by LINC complex disruption. Instead, LINC complex disruption eliminated the cage of microtubules encircling the nucleus. Disrupting microtubules was sufficient to prevent nuclear damage and rescue cardiac function induced by lamin A/C deficiency. We computationally simulated the stress fields surrounding cardiomyocyte nuclei and show how microtubule forces generate local vulnerabilities that damage lamin A/C-deficient nuclei. Our work pinpoints localized, microtubule-dependent force transmission to the nucleus as a pathological driver and therapeutic target for LMNA- cardiomyopathy. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=131 SRC="FIGDIR/small/579774v5_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@1443daeorg.highwire.dtl.DTLVardef@12d7a8borg.highwire.dtl.DTLVardef@c85900org.highwire.dtl.DTLVardef@14b3c89_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2023

Membrane molecule bouncer enables follicle fertilization in a viviparous teleost: Poecilia reticulata (guppy)

Fertilization is a fundamental mechanism of sexual reproduction. Generally, oocytes are ovulated from the ovarian follicles and contact the sperm outside the ovarian medulla. Unlike this, follicle fertilization which means the egg contact with sperm in the ovarian medulla without ovulation is known in the viviparous teleost species belonging to the Poeciliidae. In this study, we focused on a viviparous teleost species, Poecilia reticulata (guppy). Our sperm tracking assay indicated that the sperm reached the immature oocytes with a germinal vesicle, and the fertilized immature oocytes were presumed to contribute to littermates. The binding between immature oocytes and sperm is a specific trait in the guppy, which was not observed in Danio rerio (zebrafish) or Oryzias latipes (medaka). The loss- and gain-of-function assays indicated that bouncer plays a critical role in immature oocyte-to-sperm binding. This fertilization trait in immature oocytes may provide certain advantages for females with respect to nutrition or other gestation costs. Our findings shed light on the unique reproductive strategies of guppy and contribute to our understanding of the diverse reproductive mechanisms in vertebrates. Summary statementUnlike general vertebrates, guppys oocyte fertilizes with sperm in the ovarian medulla at the immature stages. The distinctive trait depends on the Ly6/uPAR protein bouncer.

developmental biology↗

bioRxiv2023

Machine learning-assisted medium optimization revealed the discriminated strategies for improved production of the foreign and native metabolites

The medium composition was crucial for achieving the best performance of synthetic construction. What and how medium components determined the production of the synthetic construction remained poorly investigated. To address the questions, a comparative survey with two genetically engineered Escherichia coli strains was performed. As a case study, the strains carried the synthetic pathways for producing the aromatic compounds of 4APhe or Tyr, which were common in the upstream but differentiated in the downstream metabolism. Bacterial growth and compound production were examined in hundreds of medium combinations that comprised 48 pure chemicals. The resultant data sets linking the medium composition to bacterial growth and production were subjected to machine learning for improved production. Intriguingly, the primary medium components determining the production of 4PheA and Tyr were differentiated, which were the initial resource (glucose) of the synthetic pathway and the inducer (IPTG) of the synthetic construction, respectively. Fine-tuning of the primary component significantly increased the yields of 4APhe and Tyr, indicating that a single component could be crucial for the performance of synthetic construction. Transcriptome analysis observed the local and global changes in gene expression for improved production of 4APhe and Tyr, respectively, revealing divergent metabolic strategies for producing the foreign and native metabolites. The study demonstrated that ML-assisted medium optimization could provide a novel point of view on how to make the synthetic construction meet the original design.

systems biology↗

bioRxiv2022

Negative legacy effects of past forest use on plant diversity in semi-natural grasslands on ski slopes

Over the past century, grassland and forest ecosystems globally have been heavily influenced by land use changes driven by diverse socioeconomic activities. Ski resorts are a modern land-use type associated with biodiversity loss in mountain ecosystems worldwide. Below the treeline, by contrast, some ski slopes have been shown to provide suboptimal semi-natural habitats for native grassland plants and animals, depending on specific construction and management practices. We compared environmental factors and grassland vegetation between two types of ski slopes in central Japan with different land-use histories: slopes constructed on old pastures (pasture slopes) and slopes constructed by clearing secondary forests or Larix kaempferi plantations established on abandoned pastures during the 1940s-1990s (forest slopes). We examined the effects of land use history and machine grading as well as other environmental factors on ski slope vegetation, including total species richness and the richness of native, endangered, and exotic plants, using a total of 108 plots of 2 m x 10 m. Compared to pasture slopes, forest slopes exhibited significantly lower richness of total plants and native grassland species, including endangered species. Forest slopes were more graded than pasture slopes, resulting in lower native and higher exotic grassland species richness. A significantly lower duration of direct sunlight on forest slopes than on pasture slopes possibly decreased endangered species diversity. The lower species richness on forest slopes may be partly caused by seed dispersal limitations. Our findings demonstrate that ski slopes have good potential to support numerous native grassland plant species, including endangered species, but this potential is significantly and negatively affected by forest use history and concomitant environmental changes. The conservation of semi-natural conditions on pasture slopes as habitats for native grassland species can be promoted through the maintenance of annual mowing practices, avoidance of machine grading, and wider ski courses. NomenclatureYonekura & Kajita (2003) BG Plants: index of Japanese names and scientific names (YList; http://ylist.info/index.html)

plant biology↗

bioRxiv2022

'Ripple effects' of urban environmental characteristics on cognitive processes in Eurasian red squirrels.

O_LIUrban areas are expanding exponentially, leading more wildlife species to reside and settle in this environment. Urban environmental characteristics, such as human disturbance or green coverage, have been shown to affect some cognitive abilities such as innovative problem-solving performance of wildlife species. However, an untested hypothesis is that due to the shared underlying cognitive mechanisms, these affected performances may induce a ripple effect, and continue to affect other related cognitive processes (the ripple effect hypothesis). C_LIO_LIWe tested this hypothesis by targeting two cognitive abilities, generalisation and memory, that overlap the cognitive mechanisms (learning and memory) of the original problem solving task in urban Eurasian red squirrels. These squirrels reside in 11 urban areas where they had previously repeatedly solved the original task (the innovators), and that their solving performance in the original task was affected by the selected urban environmental characteristics. We presented two established food-extraction tasks to the innovators to measure their performance in applying the learned successful solutions when solving a similar but novel problem (i.e., generalisation process) and recalling the learned solution of the original problem when solving the same task after an extended period of time (i.e., memory). C_LIO_LIOur results provide more detailed information to refine the hypothesis; the initial effects of urban environmental characteristics on the performance of the original task affect performance at individual level but not at population level. These affected performance includes individuals generalisation solving latency across successes as well as their first solving latency in the memory task. C_LIO_LIUrban environmental characteristics affect solving performance at both population and individual levels. Some environmental characteristics such as direct and indirect human disturbance affect the success of solving the generalisation task and the memory task at site level whereas other environmental characteristics such as green coverage affect the individuals solving latency in both tasks. C_LIO_LIOverall, our results support the ripple effect hypothesis, indicating that urban environmental characteristics have a more global impact on shaping cognitive performance than previously has shown, and thus provide a better understanding of the mechanism that supports wildlife in adapting to urban environments. C_LI

animal behavior and cognition↗

bioRxiv2022

Transcriptional, post-transcriptional, and post-translational mechanisms rewrite the tubulin code during cardiac hypertrophy and failure

A proliferated and post-translationally modified microtubule network underlies cellular growth in cardiac hypertrophy and contributes to contractile dysfunction in heart failure. Yet how the heart achieves this modified network is poorly understood. Determining how the "tubulin code" - the permutations of tubulin isoforms and post-translational modifications - is rewritten upon cardiac stress may provide new targets to modulate cardiac remodeling. Further, while tubulin can autoregulate its own expression, it is unknown if autoregulation is operant in the heart or tuned in response to stress. Here we use heart failure patient samples and murine models of cardiac remodeling to interrogate transcriptional, autoregulatory, and post-translational mechanisms that contribute to microtubule network remodeling at different stages of heart disease. We find that autoregulation is operant across tubulin isoforms in the heart and leads to an apparent disconnect in tubulin mRNA and protein levels in heart failure. We also find that within 4 hours of a hypertrophic stimulus and prior to cardiac growth, microtubule detyrosination is rapidly induced to help stabilize the network. This occurs concomitant with rapid transcriptional and autoregulatory activation of specific tubulin isoforms and microtubule motors. Upon continued hypertrophic stimulation, there is an increase in post-translationally modified microtubule tracks and anterograde motors to support cardiac growth, while total tubulin content increases through progressive transcriptional and autoregulatory induction of tubulin isoforms. Our work provides a new model for how the tubulin code is rapidly rewritten to establish a proliferated, stable microtubule network that drives cardiac remodeling, and provides the first evidence of tunable tubulin autoregulation during pathological progression.

molecular biology↗

bioRxiv2021

Identification of bacterial drug-resistant cells by the convolutional neural network in transmission electron microscope images

The emergence of bacteria that are resistant to antibiotics is common in areas where antibiotics are used widely. The current standard procedure for detecting bacterial drug resistance is based on bacterial growth under antibiotic treatments. Here we describe the morphological changes in enoxacin-resistant Escherichia coli cells and the computational method used to identify these resistant cells in transmission electron microscopy (TEM) images without using antibiotics. Our approach was to create patches from TEM images of enoxacin-sensitive and enoxacin-resistant E. coli strains, use a convolutional neural network for patch classification, and identify the strains on the basis of the classification results. The proposed method was highly accurate in classifying cells, achieving an accuracy rate of 0.94. Using a gradient-weighted class activation mapping to visualize the region of interest, enoxacin-resistant and enoxacin-sensitive cells were characterized by comparing differences in the envelope. Moreover, Pearsons correlation coefficients suggested that four genes, including lpp, the gene encoding the major outer membrane lipoprotein, were strongly associated with the image features of enoxacin-resistant cells.

systems biology↗

bioRxiv2021

An ancestral function of strigolactones as symbiotic rhizosphere signals

In flowering plants, carotenoid-derived strigolactones (SLs) have dual functions as hormones that regulate growth and development, and as rhizosphere signaling molecules that induce symbiosis with arbuscular mycorrhizal (AM) fungi. Here, we report the identification of bryosymbiol (BSB), a previously unidentified SL from the bryophyte Marchantia paleacea. BSB is also found in vascular plants, indicating that it is ancestral in land plants. BSB synthesis is enhanced at AM symbiosis permissive conditions and BSB deficient mutants are impaired in AM symbiosis. In contrast, the absence of BSB synthesis has little effect on the growth and gene expression. We show that the introduction of the SL receptor of Arabidopsis renders M. paleacea cells BSB-responsive. These results suggest that BSB is not perceived by M. paleacea cells due to the lack of cognate SL receptors. We propose that SLs originated as AM symbiosis-inducing rhizosphere signaling molecules and were later recruited as plant hormone.

plant biology↗

bioRxiv2020

Genetic characterization of Streptococcus pyogenes emm 89 strains isolated in Japan from 2011 to 2019

Streptococcal toxic shock syndrome (STSS) caused by Streptococcus pyogenes emm89 strains has been increasing in several countries and reported to be linked with a recently emerged clade of emm89 strains, designated clade 3. In Japan, epidemiological and genetic information for emm89 strains remains elusive. In this study, we utilized emm89 strains isolated from both STSS (89 isolates) and non-STSS (72 isolates) infections in Japan from 2011 to 2019, and conducted whole-genome sequencing and comparative analysis, which resulted in classification of a large majority into clade 3 regardless of disease severity. In addition, STSS-associated genes and SNPs were found in clade 3 strains, including mutations of streptokinase (Ska), control of virulence sensor (CovS), serum opacity factor (SOF), sortase (SrtB), and fibronectin-binding protein F1 (PrtF1), and absence of the hylP1 gene encoding hyaluronidase. These findings provide insights into notable genetic features of emm89 strains.

microbiology↗