Biology subjects

Kida, I.

Publications and source records attributed to Kida, I..

6 recordsLinked to original sources

bioRxiv2024

First versatile reverse genetics system for feline coronavirus

Feline infectious peritonitis (FIP) is a fatal disease caused by feline coronavirus (FCoV). Although multiple gene mutations in FCoV likely account for FIP pathogenesis, molecular studies for FCoV have been limited due to the lack of a suitable reverse genetics system. In the present study, we established a rapid PCR-based system to generate recombinant FCoV using the circular polymerase extension reaction (CPER) method for both serotype 1 and 2 viruses. Recombinant FCoV was successfully rescued at sufficient titers to propagate the progeny viruses with high sequence accuracy. The growth kinetics of recombinant FCoV were comparable to those of the parental viruses. We successfully generated recombinants harboring spike gene from a different FCoV strain or a reporter HiBiT-tag using the CPER method. The chimeric virus demonstrated similar characteristics with the parental virus of S gene. The reporter tag stably expressed after five serial passages in the susceptible cells, and the reporter virus could be applied to evaluate the sensitivity of antiviral inhibitors using the luciferase assay system to detect HiBiT tag. Taken together, our versatile reverse genetics system for FCoV shown herein is a robust tool to characterize viral genes even without virus isolation and to investigate the molecular mechanisms of the proliferation and pathogenicity of FCoV. ImportanceFeline infectious peritonitis is a highly fatal disease in cats caused by feline coronavirus variants that can infect systemically. Because of a lack of versatile toolbox of manipulating the feline coronavirus genome, an efficient method is urgently needed for studying virus proteins responsible for the severe disease. Herein, we established a rapid reverse genetics system for the virus and demonstrated the capability of the recombinant viruses to be introduced desired modifications or reporter genes without any negative impacts on virus characteristics in cell culture. Recombinant viruses are also useful to evaluate antiviral efficacy. Overall, our system can be a promising tool to reveal the molecular mechanisms of viral life cycle of feline coronavirus and disease progression of feline infectious peritonitis.

microbiology↗

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↗

bioRxiv2019

Cerebral artery segmentation based on magnetization-prepared two rapid acquisition gradient echo multi-contrast images in 7 Tesla magnetic resonance imaging

Cerebral artery segmentation plays an important role in the direct visualization of the human brain to obtain vascular system information. At ultra-high field magnetic resonance imaging, hyperintensity of the cerebral arteries in T1 weighted (T1w) images could be segmented from brain tissues such as gray and white matter. In this study, we propose an automated method to segment the cerebral arteries using multi-contrast images including T1w images of a magnetization-prepared two rapid acquisition gradient echoes (MP2RAGE) sequence at 7 T. The proposed method employed a seed-based region-growing strategy with the following procedures. (1) Two seed regions were defined by Frangi filtering applied to T1w images and by a simple calculation from multi-contrast images, (2) the two seed regions were combined, (3) the combined seed regions were expanded using a region growing algorithm to acquire the cerebral arteries. Time-of-flight (TOF) images were obtained as a reference to evaluate the proposed method. We successfully performed vessel segmentations from T1w MP2RAGE images, which mostly overlapped with the segmentations from the TOF images. As large arteries can affect the normalization of anatomical images to the standard coordinate space in functional and structural studies, we also investigated the effect of the cerebral arteries on spatial transformation using vessel segmentation by the proposed method. As a result, the T1w image removing the cerebral arteries showed better agreement with the standard atlas compared with the T1w image containing the arteries. Thus, because the proposed method using MP2RAGE images can obtain brain tissue anatomical information as well as cerebral artery information without need for additional acquisitions such as of the TOF sequence, it is useful and time saving for medical diagnosis and functional and structural studies.

neuroscience↗

bioRxiv2018

Brain tissue segmentation based on MP2RAGE multi-contrast images in 7 T MRI

We proposed a method for segmentation of brain tissues--gray matter (GM), white matter (WM), and cerebrospinal fluid (CSF)--using multi-contrast images, including a T1 map and a uniform T1-weighted image, from a magnetization-prepared 2 rapid acquisition gradient echoes (MP2RAGE) sequence at 7 Tesla. The proposed method was evaluated with respect to the processing time and the similarity of the segmented masks of brain tissues with those obtained using FreeSurfer, FSL, and SPM12. The processing time of the proposed method (28 {+/-} 0 s) was significantly shorter than those of FSL and SPM12 (444 {+/-} 4 s and 159 {+/-} 2 s for FSL and SPM12, respectively). In the similarity assessment, the tissue mask of the brain obtained by the proposed method showed higher consistency with those obtained by FSL than with those obtained by SPM12. The proposed method misclassified the subcortical structures and large vessels since it is based on the intensities of multi-contrast images obtained using MP2RAGE, which uses a similar segmentation approach as FSL but is not based on a template image or a parcellated brain atlas, which are used for FreeSurfer and SPM12, respectively. However, the proposed method showed good segmentation in the cerebellum and WM in the medial part of the brain in comparison with the other methods. Thus, because the proposed method using different contrast images of MP2RAGE sequence showed the shortest processing time and similar segmentation ability as the other methods, it may be useful for both neuroimaging research and clinical diagnosis.

neuroscience↗

bioRxiv2018

Layer-specific ultra-high field 7T fMRI showing that threat anticipation is mediated by the pulvinar input to the superficial layers of primary visual cortex (V1)

The perceptual system gives priority to threat-relevant signals with survival value. Its mechanism may not only include the processing initiated in the presence of threat signals but also in the mere anticipation of such signals. Here, we show that the pulvinar modulates activity in the early visual cortex (V1) specifically in threat anticipation. Using ultra-high-field 7T fMRI, we examined the layer-specific interaction between V1 and the pulvinar, while taking advantage of the fact that the directionality of such interaction is anatomically constrained in specific V1 layers. Only in anticipation of a fearful face target, but not of a control happy face target, was false perception of anticipated-yet-unpresented target face accompanied by stronger activity in the V1 superficial-cortical-depth (layers 1-3), which was preceded by pre-target-onset pulvinar activity. The pulvinar may contribute to the visual processing initiated in the anticipation of threat, and play an important role in anxiety.

neuroscience↗