Biology subjects

Watanabe, K.

Publications and source records attributed to Watanabe, K..

At least 55 records · Page 3Linked to original sources

bioRxiv2024

APOE Genotype and Biological Age Impact Inter-Omic Associations Related to Bioenergetics

Apolipoprotein E (APOE) modifies human aging; specifically, the {varepsilon}2 and {varepsilon}4 alleles are among the strongest genetic predictors of longevity and Alzheimers disease (AD) risk, respectively. However, detailed mechanisms for their influence on aging remain unclear. Herein, we analyzed inter-omic, context-dependent association patterns across APOE genotypes, sex, and health axes in 2,229 community-dwelling individuals to test APOE genotypes for variation in metabolites and metabolite-associations tied to a previously-validated metric of biological aging (BA) based on blood biomarkers. Our analysis, supported by validation in an independent cohort, identified top APOE-associated plasma metabolites as diacylglycerols, which were increased in {varepsilon}2-carriers and trended higher in {varepsilon}4-carriers compared to {varepsilon}3-homozygotes, despite the known opposing aging effects of the allele variants. Omics association patterns of {varepsilon}2-carriers and increased biological age were also counter-intuitively similar, displaying increased associations between insulin resistance markers and energy-generating pathway metabolites. These results provide an atlas of APOE-related omic associations and support the involvement of bioenergetic pathways in mediating the impact of APOE on aging.

systems biology↗

bioRxiv2024

Maternal progesterone and adipose mPRε in pregnancy regulate the embryonic nutritional state

Sex steroid hormones such as progesterone play a pivotal role in reproductive functions and maintaining pregnancy; however, the impact of progesterone on the interaction between mother and embryo is unclear. Here, we demonstrate that the relationship between maternal progesterone and membrane progesterone receptor epsilon (mPR{varepsilon}) in adipose tissue regulates embryonic nutritional environment and growth after birth in mice. The activation of adipose mPR{varepsilon} by increased progesterone during pregnancy enhanced maternal insulin resistance through the production of prostaglandins, thereby efficiently providing glucose to embryos. The offspring of mPR{varepsilon}-deficient mothers exhibited metabolic dysfunction, whereas mPR{varepsilon}-deficient mothers with high-fat-diet-induced obesity exhibited improved insulin sensitivity. These findings establish the importance of progesterone as a nutritional regulator between mother and embryo, and suggest that mPR{varepsilon} modulators could be developed to treat pregnant glycemic control disorders such as gestational diabetes mellitus, as well as metabolic syndrome in offspring. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/609823v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@1ecd968org.highwire.dtl.DTLVardef@b5492aorg.highwire.dtl.DTLVardef@1d692ecorg.highwire.dtl.DTLVardef@47de8a_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2024

Comparative genomic analysis of multidrug-resistant clinical isolates of Mycobacterium abscessus revealed worldwide horizontal plasmid transfer

Genetic epidemiological analysis of mobile genetic elements, such as plasmids, has rarely been carried out in Mycobacterium abscessus, regardless of its usefulness in speculating the past contact between bacteria. In this study, through whole genome sequencing analysis of clinical isolates of M. abscessus sequentially collected from the same patient, we identified a single nucleotide variant that could cause antibiotic resistance, and three plasmids (pMAB625-1, pMAB625-2 and pMAB625-3) not found in the type strain. We investigated the distribution of plasmids previously identified in M. abscessus, including pMAB625 plasmids, in 462 clinical isolates worldwide in silico. pMAB625-3 was detected in the largest number of isolates. Furthermore, phylogenetic tree analysis revealed that these plasmids transferred beyond regions and subspecies and acquired unique mutations. These results indicate that transmission of plasmids increases the genomic diversity in M. abscessus, and plasmid epidemiology is useful for estimating the past contact between bacteria.

genomics↗

bioRxiv2024

Tracing Homopolymers in Oikopleura dioica's mitogenome

Oikopleura dioica is a planktonic tunicate (Appendicularia class) found extensively across the marine waters of the globe. The genome of a single male individual collected from Okinawa, Japan was sequenced using the single-molecule PacBio Hi-Fi method and assembled with NOVOLoci. The mitogenome is 39,268 bp long, featuring a large control region of around 22,000 bp. We annotated the proteins atp6, cob, cox1, cox2, cox3, nad1, nad4 and nad5, and found one more open reading frame that did not match any known gene. This study marks the first complete mitogenome assembly for an appendicularian, and reveals that A and T homopolymers cumulatively account for nearly half of its length. This reference sequence will be an asset for environmental DNA and phylogenetic studies. http://dx.doi.org/10.1364/ao.XX.XXXXXX

genomics↗

bioRxiv2024

Gaze inversion effect: Sex invariance and difference in gaze direction sensitivity

Humans are adept at distinguishing individual faces, yet inversion dramatically impairs this ability. This face inversion effect is remarkably robust across observers, but evidence is mixed as to whether inversion also impairs the perception of facial parts, particularly the eye region. Some studies have shown that featural processing is preserved or even enhanced when faces are inverted, whereas others have reported clear inversion-related impairments in feature-based judgements. These mixed findings may reflect limited statistical power, unbalanced participant sex ratios, and heterogeneous task designs. To address these issues, we examined how strongly face inversion affects sensitivity to gaze direction in a well-powered, sex-balanced sample. A total of 190 participants judged whether the eyes in briefly presented upright or inverted faces were looking directly at them or not. Inversion reliably reduced sensitivity to gaze direction, yielding a medium-to-large effect size. Females showed modestly higher overall sensitivity than males (a small-to-medium effect), whereas the inversion effect was highly similar for females and males. These findings show that brief gaze judgements are not immune to inversion, even in a task that could in principle be based largely on eye-region information. They provide quantitative constraints that models of gaze perception should accommodate, including the largely sex-invariant inversion effect.

neuroscience↗

bioRxiv2023

Can Colpoda travel across oceans? Salinity tolerance of resting cysts may enable global dispersal of the species.

Protist species are distributed worldwide. The processes that enabled this global distribution are unclear. One possible means is through the oceanic dispersal of freshwater protists, although this has not been investigated in detail to date. Here, the ability of resting cysts to tolerate saline conditions is examined as a possible mechanism that enables the oceanic dispersal of protists. Resting cysts of Colpoda cucullus, a freshwater soil protist, can tolerate saline conditions of at least 3.5% NaCl for more than one week. A transcriptome analysis showed that the relative levels of expression of genes associated with membrane function are increased in resting cysts, indicating that salinity tolerance is associated with reconstruction of the cell membrane. Additionally, the outer layer of the cyst wall, a shell-like ectocyst, includes chitin. This may function as a form of "biological armor" that protects the cell from physical stress during oceanic dispersal. Teaser: Fresh water protists may be dispersed across oceans by formation of resting cysts that can tolerate saline conditions.

zoology↗

bioRxiv2023

Diffusion of DNA on Atomically Flat 2D Material Surfaces

Accurate localization of biomolecules is pivotal for understanding biological processes. Utilizing the atomically flat surface of 2D materials offers a promising route to achieve this without the need for tethering or constraining. Here we comprehensively investigate the binding and diffusion of DNA on hexagonal boron nitride (hBN) surfaces. Our findings reveal non-specific binding of DNA to pristine hBN, with subsequent diffusion and confinement within the 2D plane. Through single-molecule experiments and computational techniques, we explore DNA dynamics, and the effects of defects, step edges and domain boundaries on the motion, which gives insights on the interactions between solid-state surfaces and biomolecules. By engineering a narrow hBN ribbon structure, we enhance confinement, demonstrating its potential in nanofluidic guiding of biomolecules. Our 2D platform serves as a proving ground for next generation high-throughput single-molecule manipulation techniques for enabling applications in biotechnology and nanotechnology.

molecular biology↗

bioRxiv2023

Rapid propagation of Ca2+ waves and electrical signals in a liverwort Marchantia polymorpha

In response to both biotic and abiotic stresses, vascular plants transmit long-distance Ca2+ and electrical signals from localized stress sites to distant tissues through their vasculature. Various models have been proposed for the mechanisms underlying the long-distance signaling, primarily centered around the presence of vascular bundles. We here demonstrate that the non-vascular liverwort Marchantia polymorpha possesses a mechanism for propagating Ca2+ waves and electrical signals in response to wounding. The propagation velocity of these signals was approximately 1-2 mm/s, equivalent to that observed in vascular plants. Both Ca2+ waves and electrical signals were inhibited by La3+ as well as tetraethylammonium chloride, suggesting crucial importance of both Ca2+ channel(s) and K+ channel(s) in wound-induced membrane depolarization as well as the subsequent long-distance signal propagation. Simultaneous recordings of Ca2+ and electrical signals indicated a tight coupling between the dynamics of these two signaling modalities. Furthermore, molecular genetic studies revealed that a GLUTAMATE RECEPTOR-LIKE (GLR) channel plays a central role in the propagation of both Ca2+ waves and electrical signals. Conversely, none of the three two-pore channels (TPCs) were implicated in either signal propagation. These findings shed light on the evolutionary conservation of rapid long-distance Ca2+ wave and electrical signal propagation involving GLRs in land plants, even in the absence of vascular tissue.

plant biology↗

bioRxiv2023

HI-FISH: WHOLE BRAIN IN SITU MAPPING OF NEURONAL ACTIVATION IN DROSOPHILA DURING SOCIAL BEHAVIORS AND OPTOGENETIC STIMULATION

Monitoring neuronal activity at single-cell resolution in freely moving Drosophila engaged in social behaviors is challenging because of their small size and lack of transparency. Extant methods, such as Flyception, are highly invasive. Whole-brain calcium imaging in head-fixed, walking flies is feasible but the animals cannot perform the consummatory phases of social behaviors like aggression or mating under these conditions. This has left open the fundamental question of whether neurons identified as functionally important for such behaviors using loss- or gain-of-function screens are actually active during the natural performance of such behaviors, and if so during which phase(s). Here we perform brain-wide mapping of active cells expressing the Immediate Early Gene hr38 using a high-sensitivity/low background FISH amplification method called HCR-3.0. Using double-labeling for hr38 mRNA and for GFP, we describe the activity of several classes of aggression-promoting neurons during courtship and aggression, including P1a cells, an intensively studied population of male-specific interneurons. Using HI-FISH in combination with optogenetic activation of aggression-promoting neurons (opto-HI-FISH) we identify candidate downstream functional targets of these cells in a brain-wide, unbiased manner. Finally we compare the activity of P1a neurons during sequential performance of courtship and aggression, using intronic vs. exonic hr38 probes to differentiate newly synthesized nuclear transcripts from cytoplasmic transcripts synthesized at an earlier time. These data provide evidence suggesting that different subsets of P1a neurons may be active during courtship vs. aggression. HI-FISH and associated methods may help to fill an important lacuna in the armamentarium of tools for neural circuit analysis in Drosophila.

neuroscience↗

bioRxiv2023

Akr1b7 functions as a master regulator in ovarian aging

At the beginning of ovarian aging, the ovulation of immature oocytes is accelerated, leading to the arrest of ovulation despite the remaining oocytes. Here, RNA expression in the ovarian aging of mice is comprehensively analyzed during the estrous cycle after ovulation stimulation. The aldo-keto reductase Akr1b7 pathway transiently activated in the ovaries of young mice disappears in those of old mice. Akr1b7--/-- mice attenuate oocyte Akt activation essential for the follicular development in primordial follicles, and enhanced ovulation in immature oocytes. The estrous cycle is extended because of the prolonged diestrous stage by a sustained progesterone level in Akr1b7--/--mice ovaries, which is caused by the decline of Cyp17a1, a major metabolic enzyme of progesterone in Akr1b7-expressed theca cell layers. In summary, the decreased Akr1b7 pathway causes ovulation of immature oocytes and a prolonged estrous cycle, typical symptoms of ovarian aging.

molecular biology↗

bioRxiv2023

Does larval ability to modulate body buoyancy explain successful colonization of freshwater environments by diadromous gobies?

Salinity is an environmental factor that strongly characterizes the habitat use patterns of aquatic organisms. However, knowledge is biased toward the effect of differences in osmotic pressure among salinity habitats; how ambient specific gravity (SG) differences determine species distribution is scarcely understood. Diadromous fish, which migrate between marine and freshwater habitats, may encounter this SG problem when they are unexpectedly landlocked in or colonize freshwater areas with low environmental SG. This is particularly serious for planktonic larval fish, which must maintain neutral buoyancy for foraging and passive locomotion, although their swimbladders are generally underdeveloped. Then, we hypothesized that the SG problem limits the establishment of freshwater resident populations in marine-originated diadromous fishes. To test this hypothesis, the SG modulation ability of newly hatched larvae was compared among three closely related diadromous goby species in Gymnogobius, one of which has freshwater resident populations. The aquarium experimental results did not support that only the species deriving freshwater residents can maintain neutral buoyancy even in freshwater conditions; that is, all three species could modulate their body SG almost equally to those of both fresh and sea waters. This suggests that the ability to maintain neutral buoyancy in freshwater had been pre-adaptively acquired prior to larval freshwater colonization. On the other hand, it is highly noteworthy that the early larvae of the target group maintained neutral buoyancy in various SG environments using swimbladders, which is the first such evidence in teleosts.

ecology↗

bioRxiv2023

Skin coat color-dependent risks and risk factors of squamous cell carcinoma and deafness of domestic cats inferred via RNA-seq data

The transcriptome data of skin cells from domestic cats with brown, orange, and white coats were analyzed using a public database to investigate the possible relationship between coat color-related gene expression and squamous cell carcinoma risk, as well as the mechanism of deafness in white cats. We found that the ratio of the expression level of genes suppressing squamous cell carcinoma to that of genes promoting squamous cell carcinoma might be considerably lower than the theoretical estimation in skin cells with orange and white coats in white-spotted cat. We also found the possibility of the frequent production of KIT lacking the first exon (d1KIT) in skin cells with white coats, and d1KIT production exhibited a substantial negative correlation with the expression of SOX10, which is essential for melanocyte formation and adjustment of hearing function. Additionally, the production of d1KIT was expected to be due to the insulating activity of the feline endogenous retrovirus 1 (FERV1) LTR in the 1st intron of KIT and its CTCF binding sequence repeat. These results contribute to basic veterinary research to understand the relationship between cat skin coat and disease risk, as well as the underlying mechanism.

zoology↗

bioRxiv2023

Engineering a highly durable adeno-associated virus receptor for analytical applications

Adeno-associated virus (AAV) is a major viral vector used in gene therapy. There are multiple AAV serotypes, and many engineered AAV serotypes with modified capsids altering tissue tropism are enthusiastically being developed. The universal AAV receptor (AAVR) is an essential receptor for multiple AAV infections. Since most AAV serotypes used in gene therapy infect cells via interaction with AAVR, the quantification of the vector-binding ability of AAV to AAVR could be an important quality check for therapeutic AAV vectors. To enable a steady evaluation of the AAV-AAVR interaction, we created an engineered AAVR through mutagenesis. Engineered AAVR showed high durability against acid while retaining its AAV-binding activity and an affinity chromatography column with engineered AAVR was also developed. This column enabled repeated binding and acid dissociation measurements of AAVR with various AAV serotypes. Our data showed that the binding affinities of AAV to AAVR were diverse among serotypes, providing insight into the relationship with the infection efficiency of AAV vectors. Thus, this affinity column can be used in process development for quality checks, quantitating capsid titers, and affinity purification of AAV vectors. Furthermore, this column may work for a useful tool of novel AAV vector capsid engineering.

bioengineering↗

bioRxiv2023

Comparison of eDNA, bulk-sample metabarcoding, and morphological approaches: A case study of riverine benthic macroinvertebrate communities

Freshwater biomonitoring is essential for aquatic biodiversity conservation. Advances in high-throughput sequencing allowed parallel sequencing of community samples containing DNA from environmental samples, i.e., metabarcoding. Two approaches of DNA-based method are widely used, bulk-sample metabarcoding the use of bulk tissues such as insects and eDNA the use of environmental samples such as air, water and soil. Despite the novelty of this approach for routine freshwater biomonitoring, questions still need to be answered about its applicability and reliability due to confounding factors, e.g., sample type, laboratory technicalities, and limitations of databases. Hence, studies on direct comparisons are essential to validate the efficiency of these molecular approaches compared to the conventional morphological approach to accurately assessed biodiversity for riverine benthic macroinvertebrate biomonitoring. This study used three approaches to estimate diversity and composition of benthic macroinvertebrates. We also evaluated the relationship between benthic macroinvertebrate communities and environmental factors. We morphologically identified 8,052 individuals from 35 families, 31 genera, and 29 species. eDNA metabarcoding identified 51 families, 84 genera, and 90 species, while 37 families, 55 genera, and 107 species were detected through bulk-sample metabarcoding. We report that bulk-sample metabarcoding showed finer taxonomic resolution than other approaches. Our study highlights the use of bulk-sample metabarcoding for macroinvertebrate biodiversity assessment.

ecology↗

bioRxiv2023

The Crucial Role of CTCF in Mitotic Progression during Early Development of Sea Urchin.

CCCTC-binding factor (CTCF), an insulator protein with 11 zinc fingers, is enriched at the boundaries of topologically associated domains (TADs) in eukaryotic genomes. In this study, we isolated and analyzed the cDNAs encoding HpCTCF, the CTCF homolog in the sea urchin Hemicentrotus pulcherrimus, to investigate its expression patterns and functions during early development of sea urchin. HpCTCF contains nine zinc fingers corresponding to fingers 2-10 of the vertebrate CTCF. The expression pattern analysis revealed that HpCTCF mRNA was detected at all developmental stages and in the entire embryo. Upon expressing the HpCTCF-GFP fusion protein in early embryos, we observed its uniform distribution within interphase nuclei. However, during mitosis, it disappeared from the chromosomes and subsequently reassembled on the chromosome during telophase. Moreover, the morpholino-mediated knockdown of HpCTCF resulted in mitotic arrest during the morula-to-blastula stage. Most of the arrested chromosomes were not phospholylated at serine 10 of histone H3, indicating that mitosis was arrested at the telophase by HpCTCF depletion. Furthermore, impaired sister chromatid segregation was observed using time-lapse imaging of HpCTCF-knockdown embryos. Thus, HpCTCF is essential for mitotic progression during the early development of sea urchins, especially during the telophase-to-interphase transition. However, the normal development of pluteus larvae in CRISPR-mediated HpCTCF knockout embryos suggests that disruption of zygotic HpCTCF expression has little effect on embryonic and larval development.

developmental biology↗

bioRxiv2023

Proteasomal regulation of ASK family kinases dictates cell fate under hyperosmotic stress

The proteasome has an essential role in proteostasis maintenance and is critical for cell survival under proteotoxic conditions including hyperosmotic stress. However, it is unknown how proteasome activity is linked to cell survival/death under hyperosmotic stress. We have previously reported that apoptosis signal-regulating kinase 3 (ASK3) contributes to cell survival through its inactivation under hyperosmotic stress. 19S regulatory particle subunits of the proteasome were enriched in the ASK3 inactivator candidates identified through our genome-wide small interfering RNA (siRNA) screen. In this study, we demonstrate that the proteasome regulates ASK3 inactivation through its proteolytic activity. Intriguingly, the proteasome inactivates ASK3 via degradation of not ASK3 per se but another ASK family member ASK1 which activates ASK3 in a kinase activity-dependent manner. Furthermore, the elevated ASK1 level under proteasome inhibition sensitizes cells to hyperosmotic stress. These findings suggest that ASK family maintenance links proteasome capacity to cell fate bifurcation under hyperosmotic stress.

molecular biology↗

bioRxiv2023

Gastrointestinal transit mathematical model in mice treated with antibiotics

High-resolution fecal pharmacokinetics are crucial for optimizing therapeutic design and evaluating gastrointestinal motility. However, empirical studies with detailed time series data remain limited. This study aims to characterize fecal pharmacokinetics through high-frequency sampling and parallelized fecal concentration quantification, establishing a simple pharmacokinetics model with physiologically interpretable parameters. We quantified vancomycin concentrations in fecal samples collected at a minimum interval of 4 hours from C57BL/6J mice following a single oral administration of either a low (1 mg/mL) or high (20 mg/mL) dose. Fecal concentrations gradually increased and exhibited an exponential decay, leading to the development of a compartmental model with an absorption phase. This simple model accurately fit the experimental data and provided physiological explanations for intra- and inter-individual pharmacokinetics variability. The results suggest that inter-individual differences in pharmacokinetics are attributable to fecal elimination capacity, which may be influenced by drug dosage via changes in gastrointestinal motility. Since the model predicts antibiotic concentrations within the gastrointestinal tract, it can be applied to fundamental studies investigating the effects of antibiotics on the gut microbiome and gastrointestinal motility.

physiology↗

bioRxiv2023

Fine-scale adaptive divergence of Aedes aegypti in heterogeneous landscapes and among climatic conditions in Metropolitan Manila, Philippines

The adaptive divergence of Aedes aegypti populations to heterogeneous environments may be a driving force behind the recent expansion of their habitat distribution and outbreaks of dengue disease in urbanized areas. In this study, we investigated the population genomics of Ae. aegypti at a regional scale in Metropolitan Manila, Philippines using double digestion restriction-site association DNA sequencing (ddRAD-Seq). Specifically, we used a Pool-Seq approach to generate a high number of single nucleotide polymorphisms (SNPs), which were used to determine local adaptation and population structure. We detected 65,473 SNPs in 217 Ae. aegypti individuals from 14 populations with 76 non-neutral SNP loci. Additionally, 57 of these non-neutral SNP loci were associated with 8 landscape variables (e.g., open space, forest, etc) and 4 climate variables (e.g., air temperature, humidity, etc). Furthermore, the percentage of the area of landscape variables, such as forest, parks and recreation, air temperature, man-made building, and open space per local population was frequently associated with non-neutral SNP loci. Most non-neutral SNP loci formed four clusters that were in linkage disequilibrium with each other in physical proximity on the chromosome and were associated with a common environmental variable. Male and female populations exhibited contrasting spatial divergence, i.e., males exhibited greater divergence, likely reflecting their different dispersal abilities. In comparative analysis of the same Ae. aegypti individuals, the pairwise FST values of 11 microsatellite markers were lower than those of neutral SNP loci, indicating that the neutral SNP loci generated via ddRAD-Seq were more sensitive in terms of detecting genetic differences between populations at fine-spatial scales. Overall, this study demonstrates the utility of ddRAD-Seq for examining genetic differences in Ae. aegypti populations, and our data on mosquito dispersal at a regional spatial scale could inform vector control programs. Author SummaryThe population expansion of dengue vector, Aedes aegypti mosquitoes is one of the factors that may promote the outbreak of the diseases. Understanding the population genomics of Ae.aegypti may contribute to better knowledge about mosquito expansion and how they can adapt to the change in environment. In this study, we used pool-based ddRAD-Seq (Double Digest Restriction site Association DNA Sequencing) to generate SNPs that occur between the Ae.aegypti populations in Metropolitan Manila, Philippines. We found that non-neutral SNP loci are frequently associated with landscape variables compared to climatic variables. Landscape variables such as forest, park and recreation, air temperature, man-made building and open space are more frequently associated with non-neutral SNPs loci. Those landscape variables may relate to the mosquitos fitness, therefore, induce the adaptive divergence within Ae.aegypti population. We also found male and female populations are exhibiting a contrast spatial divergence by using neutral SNP loci. In addition, neutral SNPs loci showed higher resolution in population structuring than microsatellite markers using the same individuals.

genomics↗