Biology subjects

Yamamoto, Y.

Publications and source records attributed to Yamamoto, Y..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

Evolution of invertebrate Cdk4/6-Cdkn2 system

The cell cycle is driven by cyclin-dependent kinases (Cdks). The decision whether the cell cycle proceeds is made during G1 phase, when Cdk4/6 functions. Cyclin-dependent kinase inhibitor 2 (Cdkn2) is a specific inhibitor of Cdk4/6, and their interaction depends on D84 in Cdkn2 and R24/31 in Cdk4/6. This knowledge is based mainly on studies in mammalian cells. Here, we comprehensively analyzed Cdk4/6 and Cdkn2 in invertebrates and found that Cdk4/6 was present in most of the investigated phyla, but the distribution of Cdkn2 was rather uneven among and within the phyla. The positive charge of R24/R31 in Cdk4/6 was conserved in all analyzed species in phyla with Cdkn2. The presence of Cdkn2 and the conservation of the positive charge were statistically correlated. We also found that Cdkn2 has been tightly linked to Fas associated factor 1 (Faf1) during evolution. We discuss potential interactions between Cdkn2 and Cdk4/6 in evolution and the possible cause of the strong conservation of the microsynteny.

evolutionary biology↗

bioRxiv2024

Label-free imaging of cellular organization in living mammalian cells via external apodization phase-contrast microscopy

Developing techniques to visualize intracellular structures, which influence the spatiotemporal functionality of biomolecules, is essential for elucidating mechanisms governing cellular behavior. In this study, we demonstrate that label-free external apodization phase-contrast (ExAPC) microscopy serves as a valuable tool for the simultaneous observation of various intracellular structures with high spatiotemporal resolution, while successfully mitigating halo artifacts. Additionally, through quantitative analysis of images obtained by combining ExAPC microscopy with fluorescence microscopy, we identified distinct heterogeneities in biomolecular condensates, lipid droplets, and mitochondria. Our findings highlight the potential of ExAPC microscopy to provide detailed insights into alterations in intracellular structures associated with diverse cellular processes, corroborating the existing knowledge and potentially contributing to the discovery of novel cellular mechanisms.

cell biology↗

bioRxiv2023

How to control unpredictable others in court-net sports

Competition in sports does not involve a single solution because individuals aim to behave unpredictably, thereby preventing others from predicting their actions. This study determined how individuals in court net sports tried to control others unpredictable behavior, thereby addressing the gap of the lack of clarity about strategies employed by individuals in competitive situations. We employed a switching hybrid dynamics model, considering external inputs when analyzing individual behaviors. The study shows that skilled individuals, unlike intermediate players, exhibit greater regularity in their behavior, lead others to anticipate this regularity, and employ strategies to disrupt these expectations. This strategy exploits the principles of active human inference, implying that competition involves cooperation. We revealed this by analyzing both human decision-making and behavior in actual matches as discrete and continuous dynamical systems. This strategy helps policymakers adopt a new policy targeting cooperation with competitors, which would increase competitiveness in our daily lives.

biophysics↗

bioRxiv2023

Overcoming antibody-resistant SARS-CoV-2 variants with bispecific antibodies constructed using non-neutralizing antibodies

A current challenge is the emergence of SARS-CoV-2 variants, such as BQ.1.1 and XBB.1.5, that can evade immune defenses, thereby limiting antibody drug effectiveness. Emergency-use antibody drugs, including the widely effective bebtelovimab, are losing their benefits. One potential approach to address this issue are bispecific antibodies which combine the targeting abilities of two antibodies with distinct epitopes. We engineered neutralizing bispecific antibodies in the IgG-scFv format from two initially non-neutralizing antibodies, CvMab-6 (which binds to the receptor-binding domain [RBD]) and CvMab-62 (targeting a spike protein S2 subunit epitope adjacent to the known anti-S2 antibody epitope). Furthermore, we created a bispecific antibody by incorporating the scFv of bebtelovimab with our anti-S2 antibody, demonstrating significant restoration of effectiveness against bebtelovimab-resistant BQ.1.1 variants. This study highlights the potential of neutralizing bispecific antibodies, which combine existing less effective anti-RBD antibodies with anti-S2 antibodies, to revive the effectiveness of antibody therapeutics compromised by immune-evading variants.

microbiology↗

bioRxiv2023

Virological characteristics of the SARS-CoV-2 Omicron EG.5.1 variant

In middle-late 2023, a sublineage of SARS-CoV-2 Omicron XBB, EG.5.1 (a progeny of XBB.1.9.2), is spreading rapidly around the world. Here, we performed multiscale investigations to reveal virological features of newly emerging EG.5.1 variant. Our phylogenetic-epidemic dynamics modeling suggested that two hallmark substitutions of EG.5.1, S:F456L and ORF9b:I5T, are critical to the increased viral fitness. Experimental investigations addressing the growth kinetics, sensitivity to clinically available antivirals, fusogenicity and pathogenicity of EG.5.1 suggested that the virological features of EG.5.1 is comparable to that of XBB.1.5. However, the cryo-electron microscopy reveals the structural difference between the spike proteins of EG.5.1 and XBB.1.5. We further assessed the impact of ORF9b:I5T on viral features, but it was almost negligible at least in our experimental setup. Our multiscale investigations provide the knowledge for understanding of the evolution trait of newly emerging pathogenic viruses in the human population.

microbiology↗

bioRxiv2023

Visuomotor activity associated with conditioned hand movements in premotor cortex of blindsight macaques

Some patients with damage to the primary visual cortex (V1) can respond to visual stimuli in their affected visual field, even though they report loss of visual awareness. This phenomenon is termed blindsight. To clarify the visuomotor transformation for hand movement control in the blindsight condition, we conducted multichannel electrocorticographical recordings from the ipsilesional frontal cortex including the frontal eye field, premotor, primary motor, and somatosensory areas during a delayed conditioned two-alternative forced choice manual response task with arbitrary assignment of push-pull manual responses in relation to the visual target cue locations before and after unilateral V1 lesioning in macaque monkeys. Before lesioning, the activity in the dorsal premotor cortex (PMd) showed short latency task-related {theta} ~ band responses that were significantly higher in the successful trials than in the error/miss trials at approximately 200 ms after target cue onset. At 2-3 months after lesioning, the monkeys regained a >80% success rate in response to appearance of the target cue in the lesion-affected visual field. At this stage, similar task-related {theta} ~ band target cue responses were observed in the PMd. Further, Granger causality from the PMd to the primary motor cortex was enhanced in the {theta} ~ , {gamma}, and high-{gamma} bands during the delay period of the task. These results suggested that the PMd plays a crucial role in mediating the visual signals for execution of hand movements in blindsight monkeys. Significant StatementBlindsight is a curious phenomenon in which the patients with damage to the primary visual cortex can still respond to visual stimulus in their blinded visual field despite loss of awareness. Previously we clarified the critical circuits for visually guided saccadic eye movements in blindsight macaques, however, those for the control of hand movements are still unclear. Here, we have recorded the multichannel electrocorticography in the frontal cortices during the conditioned manual response task and found that the dorsal premotor cortex exhibits task-related {theta} ~ band target cue responses at approximately 200 ms after the visual cue onset, similarly to the intact state. This is the first report of electrophysiological recordings in the frontal lobe of the blindsight subjects.

neuroscience↗

bioRxiv2022

Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants

In late 2022, the SARS-CoV-2 Omicron subvariants have highly diversified, and XBB is spreading rapidly around the world. Our phylogenetic analyses suggested that XBB emerged by recombination of two co-circulating BA.2 lineages, BJ.1 and BM.1.1.1 (a progeny of BA.2.75), during the summer of 2022 around India. In vitro experiments revealed that XBB is the most profoundly resistant variant to BA.2/5 breakthrough infection sera ever and is more fusogenic than BA.2.75. Notably, the recombination breakpoint is located in the receptor-binding domain of spike, and each region of recombined spike conferred immune evasion and augmented fusogenicity to the XBB spike. Finally, the intrinsic pathogenicity of XBB in hamsters is comparable to or even lower than that of BA.2.75. Our multiscale investigation provided evidence suggesting that XBB is the first documented SARS-CoV-2 variant increasing its fitness through recombination rather than single mutations.

microbiology↗

bioRxiv2022

Convergent evolution of the SARS-CoV-2 Omicron subvariants leading to the emergence of BQ.1.1 variant

In late 2022, although the SARS-CoV-2 Omicron subvariants have highly diversified, some lineages have convergently acquired amino acid substitutions at five critical residues in the spike protein. Here, we illuminated the evolutionary rules underlying the convergent evolution of Omicron subvariants and the properties of one of the latest lineages of concern, BQ.1.1. Our phylogenetic and epidemic dynamics analyses suggest that Omicron subvariants independently increased their viral fitness by acquiring the convergent substitutions. Particularly, BQ.1.1, which harbors all five convergent substitutions, shows the highest fitness among the viruses investigated. Neutralization assays show that BQ.1.1 is more resistant to breakthrough BA.2/5 infection sera than BA.5. The BQ.1.1 spike exhibits enhanced binding affinity to human ACE2 receptor and greater fusogenicity than the BA.5 spike. However, the pathogenicity of BQ.1.1 in hamsters is comparable to or even lower than that of BA.5. Our multiscale investigations provide insights into the evolutionary trajectory of Omicron subvariants.

microbiology↗

bioRxiv2022

SARS-CoV-2 Omicron BA.2.75 variant may be much more infective than preexisting variants

ObjectivesIn our previous research, we developed a mathematical model via molecular simulation analysis to predict the infectivity of seven SARS-CoV-2 variants. In this report, we aimed to predict the relative risk of the recent new variants of SARS-CoV-2 as based on our previous research. MethodsWe subjected Omicron BA.4/5 and BA.2.75 variants of SARS-CoV-2 to the analysis to determine the absolute evolutionary distance of the spike protein gene (S gene) of the variants from the Wuhan variant so as to appreciate the changes in the spike protein. We performed the molecular docking simulation analyses of the spike proteins with human angiotensin-converting enzyme 2 (ACE2) to understand the docking affinities of these variants. We then compared the evolutionary distances and the docking affinities of these variants with those of the seven variants that we had analyzed in our previous research. ResultsThe evolutionary distances of the S gene in BA.4/5 and BA.2.75 from the Wuhan variant were longer than those of the other variants. BA.2.75 had the highest docking affinity of the spike protein with ACE2 (ratio per Wuhan variant). ConclusionThe important results from this analysis are the following: BA.2.75 has both the highest docking affinity and the longest evolutionary distance of the S gene. These results suggest that BA.2.75 infection can spread farther than can infections of preexisting variants.

bioinformatics↗

bioRxiv2022

Virological characteristics of the SARS-CoV-2 Omicron BA.2.75

SARS-CoV-2 Omicron BA.2.75 emerged in May 2022. BA.2.75 is a BA.2 descendant but is phylogenetically different from BA.5, the currently predominant BA.2 descendant. Here, we showed that the effective reproduction number of BA.2.75 is greater than that of BA.5. While the sensitivity of BA.2.75 to vaccination- and BA.1/2 breakthrough infection-induced humoral immunity was comparable to that of BA.2, the immunogenicity of BA.2.75 was different from that of BA.2 and BA.5. Three clinically-available antiviral drugs were effective against BA.2.75. BA.2.75 spike exhibited a profound higher affinity to human ACE2 than BA.2 and BA.5 spikes. The fusogenicity, growth efficiency in human alveolar epithelial cells, and intrinsic pathogenicity in hamsters of BA.2.75 were comparable to those of BA.5 but were greater than those of BA.2. Our multiscale investigations suggest that BA.2.75 acquired virological properties independently of BA.5, and the potential risk of BA.2.75 to global health is greater than that of BA.5.

microbiology↗

bioRxiv2022

Comparative pathogenicity of SARS-CoV-2 Omicron subvariants including BA.1, BA.2, and BA.5

Unremitting emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants imposes us to continuous control measurement. Given the rapid spread, new Omicron subvariant named BA.5 is urgently required for characterization. Here we analyzed BA.5 with the other Omicron variants BA.1, BA.2, and ancestral B.1.1 comprehensively. Although in vitro growth kinetics of BA.5 is comparable among the Omicron subvariants, BA.5 become much more fusogenic than BA.1 and BA.2. The airway-on-a-chip analysis showed that the ability of BA.5 to disrupt the respiratory epithelial and endothelial barriers is enhanced among Omicron subvariants. Furthermore, in our hamster model, in vivo replication of BA.5 is comparable with that of the other Omicrons and less than that of the ancestral B.1.1. Importantly, inflammatory response against BA.5 is strong compared with BA.1 and BA.2. Our data suggest that BA.5 is still low pathogenic compared to ancestral strain but evolved to induce enhanced inflammation when compared to prior Omicron subvariants.

microbiology↗

bioRxiv2022

Virological characteristics of the novel SARS-CoV-2 Omicron variants including BA.2.12.1, BA.4 and BA.5

After the global spread of SARS-CoV-2 Omicron BA.2 lineage, some BA.2-related variants that acquire mutations in the L452 residue of spike protein, such as BA.2.9.1 and BA.2.13 (L452M), BA.2.12.1 (L452Q), and BA.2.11, BA.4 and BA.5 (L452R), emerged in multiple countries. Our statistical analysis showed that the effective reproduction numbers of these L452R/M/Q-bearing BA.2-related Omicron variants are greater than that of the original BA.2. Neutralization experiments revealed that the immunity induced by BA.1 and BA.2 infections is less effective against BA.4/5. Cell culture experiments showed that BA.2.12.1 and BA.4/5 replicate more efficiently in human alveolar epithelial cells than BA.2, and particularly, BA.4/5 is more fusogenic than BA.2. Furthermore, infection experiments using hamsters indicated that BA.4/5 is more pathogenic than BA.2. Altogether, our multiscale investigations suggest that the risk of L452R/M/Q-bearing BA.2-related Omicron variants, particularly BA.4 and BA.5, to global health is potentially greater than that of original BA.2. HighlightsO_LISpike L452R/Q/M mutations increase the effective reproduction number of BA.2 C_LIO_LIBA.4/5 is resistant to the immunity induced by BA.1 and BA.2 infections C_LIO_LIBA.2.12.1 and BA.4/5 more efficiently spread in human lung cells than BA.2 C_LIO_LIBA.4/5 is more pathogenic than BA.2 in hamsters C_LI

microbiology↗

bioRxiv2022

The gradient-based parameter optimization to determine membrane ionic current composition of human induced pluripotent stem cell-derived cardiomyocytes

1.Premature cardiac myocytes derived from human-induced pluripotent stem cells (hiPSC-CMs) show heterogeneous action potentials (APs), most probably because of different expression patterns of membrane ionic currents. We aim to develop a method of determining expression patterns of functional channels in terms of the whole-cell ionic conductances (Gx) using individual spontaneous AP configurations. However, it has been suggested that apparently identical AP configurations were obtained by different sets of ionic currents in a mathematical model of cardiac membrane excitation. If so, the inverse problem of Gx estimation might not be solved. We computationally tested the feasibility of the gradient-based optimization method. For realistic examination, conventional cell-specific models were prepared by superimposing the model output of AP on each experimental AP record by the conventional manual adjustment of Gxs of the baseline model. Then, Gxs of 4 ~ 6 major ionic currents of the cell-specific models were randomized within a range of {+/-}5 ~ 15% and were used as initial parameter sets for the gradient-based automatic Gxs recovery by decreasing the mean square error (MSE) between the target and model output. When plotted all data points of MSE - Gx relation during the optimization, we found that the randomized population of Gxs progressively converged to the original value of the cell-specific model with decreasing MSE. To confirm the absence of any other local minimum in the global search space, we mapped the MSE by randomizing Gxs over a range of 0.1 ~ 10 times the control. No additional local minimum of MSE was obvious in the whole parameter space besides the global minimum of MSE at the default model parameter.

physiology↗

bioRxiv2022

Aberrant regulation of serine metabolite drives extracellular vesicle release and cancer progression

Cancer cells secrete extracellular vesicles (EVs) to regulate cells in the tumor microenvironment to benefit their own growth and survive in the patients body. Although emerging evidence has demonstrated the molecular mechanisms of EV release, regulating cancer-specific EV secretion remains challenging. In this study, we applied a microRNA library to reveal the universal mechanisms of EV secretion from cancer cells. Here, we identified miR-891b and its direct target gene, phosphoserine aminotransferase 1 (PSAT1), which promotes EV secretion through the serine-ceramide synthesis pathway. Inhibition of PSAT1 affected EV secretion in multiple types of cancer, suggesting that the miR-891b/PSAT1 axis shares a common mechanism of EV secretion from cancer cells. Interestingly, aberrant PSAT1 expression also regulated cancer metastasis via EV secretion. Our data link between the PSAT1-controlled EV secretion mechanism and cancer metastasis and show the potential of this mechanism as a therapeutic target in multiple types of cancer.

cancer biology↗

bioRxiv2022

Development of transformation for genome editing of an emerging model organism

With the advances in genomic sequencing, many organisms with novel biological properties are ripe for use as emerging model organisms. However, to make full use of them, transformation methods need to be developed to permit genome editing. Here, we present development of transformation for the fungus fly Sciara (Bradysia) coprophila; this may serve as a paradigm for development of transformation for other emerging systems, especially insects. Sciara has a variety of unique biological features including locus-specific developmentally-regulated DNA amplification; chromosome imprinting; a monopolar spindle in male meiosis I; non-disjunction of the X chromosome in male meiosis II; X chromosome elimination in early embryogenesis; germ line limited (L) chromosomes; high resistance to radiation. Mining the unique biology of Sciara requires a transformation system to test mutations of DNA sequences that may play roles for these features. We describe a Sciara transformation system using a modified piggyBac transformation vector and detailed protocols we have developed to accommodate Sciara-specific requirements. This advance will provide a platform for us and others in the growing Sciara community to take advantage of this unique biological system. In addition, the versatile piggyBac vectors described here and transformation methods will be useful for other emerging model systems. Author BiographiesSusan A. Gerbi (Ph.D. with Joseph Gall at Yale University 1970) is the George Eggleston, Professor of Biochemistry at Brown University. Her research includes chromosomes, DNA replication and ribosomal RNA. She was President and is a Fellow of ASCB, a Fellow of AAAS and received the RI Governors Award for Scientific Achievement. Other honors include RNA Society/CSHL Press Distinguished Research Mentor award; GSA George Beadle award; ASCB Senior Leadership/ Mentoring Award. She is a national leader in graduate education, including member of the National Academy of Sciences Panel on Bridges to Independence that led to the NIH K99 program, Chair of the AAMC Graduate Research Education Training Group; Chair of the FASEB Consensus Conference on Graduate Education. Yutaka Yamamoto (M.D. Kansai Medical University 1990; Ph.D. with Walter Gehring at Biozentrum - Basel 1995; postdoc with David Glover at Dundee University and University of Cambridge) is a research associate at Brown University. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=65 SRC="FIGDIR/small/488772v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@17fce9aorg.highwire.dtl.DTLVardef@1d4e96forg.highwire.dtl.DTLVardef@129a689org.highwire.dtl.DTLVardef@1748fd8_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2022

Screening of the optimal CpG-oligodeoxynucleotide for anti-inflammatory responses in avian macrophage cell line HD11

CpG-oligodeoxynucleotides (CpG-ODN) has been shown to possess immunostimulatory features in both mammals and birds. However, compared to its pro-inflammatory effects, little is known about the anti-inflammatory responses triggered by CpG-ODN in avian cells. Hence, in this study, we aimed to characterize the anti-inflammatory response in the chick macrophage cell line HD11 under the stimulation of five kinds of CpG-ODN: CpG-A1585, CpG-AD35, CpG-B1555, CpG-BK3, and CpG-C2395. Single-stimulus CpG-B1555, CpG-BK3, and CpG-C2395 induced the interleukin (IL)-10 expression without causing cellular injury. The effects of pretreatment with each CpG-ODN before subsequent lipopolysaccharide stimulation were also evaluated. Interestingly, only CpG-C2395 maintained a high expression level in this situation. Finally, expression analysis of inflammation-related genes, such as the tumor necrosis factor-, IL-1{beta}, IL-6, and Toll-like receptor 4, was conducted, and pretreatment with CpG-C2395 significantly reduced their expression. Overall, our results shed light on the anti-inflammatory responses triggered by CpG-C2395 stimulation using a comparative analysis of three major classes of CpG-ODN in chick macrophages.

immunology↗

bioRxiv2021

Astroglial CD38 regulates social memory and synapse formation through SPARCL1 in the medial prefrontal cortex

Social behavior is essential for the health, survival and reproduction of animals, yet the role of astrocytes in social behavior is largely unknown. CD38 is critical for social behaviors by regulating oxytocin release from hypothalamic neurons. On the other hand, CD38 is most abundantly expressed in astrocytes especially in the postnatal cortex, and is important for astroglial development. Here, we demonstrate that astroglial CD38 plays a pivotal role in the social behavior. Selective deletion of CD38 in postnatal astrocytes, but not in adult astrocytes, specifically impaired social memory without any other behavioral abnormalities. Morphological analysis revealed reductions in spine numbers, mature spines and excitatory synapse numbers in the pyramidal neurons of the medial prefrontal cortex (mPFC) due to deletion of astroglial CD38 in the postnatal brain. Astrocyte-conditioned medium (ACM) of CD38 KO astrocytes reduced synaptogenesis of cortical neurons by reducing extracellular SPARCL1, a synaptogenic protein. Finally, the release of SPARCL1 from astrocytes is regulated by CD38/cADPR/calcium signaling. Our data indicate that astroglial CD38 developmentally regulates social memory and neural circuit formation in the developing brain by promoting synaptogenesis through SPARCL1.

neuroscience↗

bioRxiv2021

Single-cell meta-analysis of cigarette smoking lung atlas

Single-cell RNA-seq (scRNA-seq) technologies have been broadly utilized to reveal molecular mechanisms of respiratory pathology and physiology at single-cell resolution. Here, we established single-cell meta-analysis (scMeta-analysis) by integrating data from 8 public datasets, including 104 lung scRNA-seq samples with clinicopathological information and designated a cigarette smoking lung atlas. The atlas revealed early carcinogenesis events and defined the alterations of single-cell transcriptomics, cell population, and fundamental properties of biological pathways induced by smoking. In addition, we developed two novel scMeta-analysis methods: VARIED (Visualized Algorithms of Relationships In Expressional Diversity) and AGED (Aging-related Gene Expressional Differences). VARIED analysis revealed expressional diversity associated with smoking carcinogenesis. AGED analysis revealed differences in gene expression related to both aging and smoking states. The scMeta-analysis pave the way to utilize publicly -available scRNA-seq data and provide new insights into the effects of smoking and into cellular diversity in human lungs, at single-cell resolution.

cancer biology↗