Biology subjects

Abe, H.

Publications and source records attributed to Abe, H..

31 records · Page 2Linked to original sources

bioRxiv2022

Group A Streptococcus Induces Lysosomal Dysfunction in THP-1 Macrophages

The human-specific bacterial pathogen Group A Streptococcus (GAS) is a significant cause of morbidity and mortality. Macrophages are important to control GAS infection, but previous data indicate that GAS can persist in macrophages. In this study, we detail the molecular mechanisms by which GAS survives in THP-1 macrophages. Our fluorescence microscopy studies demonstrate that GAS are readily phagocytosed by macrophages, but persist within phagolysosomes. These phagolysosomes are not acidified, which is in agreement with our findings that GAS cannot survive in low pH environments. We find that the secreted pore-forming toxin Streptolysin O (SLO) perforates the phagolysosomal membrane, allowing leakage of not only protons, but large proteins including the lysosomal protease cathepsin B. Additionally, GAS blocks the activity of vacuolar ATPase (v-ATPase) to prevent acidification of the phagolysosome. Thus, while GAS does not inhibit fusion of the lysosome with the phagosome, it has multiple mechanisms to prevent proper phagolysosome function, allowing for persistence of the bacteria within the macrophage. This has important implications for not only the initial response but the overall functionality of the macrophages, which may lead to the resulting pathologies in GAS infection. Our data suggests that therapies aimed at improving macrophage function may positively impact patient outcomes in GAS infection.

microbiology↗

bioRxiv2022

Single-Cell Transcriptome Analyses Reveal the Cell Diversity and Developmental Features of Human Gastric and Metaplastic Mucosa

The stomach is an important digestive organ with a variety of biological functions. However, due to the complexity of its cellular and glandular composition, the precise cellular biology has yet to be elucidated. In this study, we conducted single-cell RNA sequence analysis of the human stomach and constructed a 137,610-cell dataset, the largest cell atlas reported to date. By integrating this single-cell analysis with spatial cellular distribution analysis, we were able to clarify novel aspects of the developmental and tissue homeostatic ecosystems in the human stomach. We identified LEFTY1+ as a potential stem cell marker in both gastric and intestinal metaplastic glands. We also revealed skewed distribution patterns for PDGFRA+BMP4+WNT5A+ fibroblasts that play pivotal roles in, or even precede, the phenotypic changes from gastric to metaplastic mucosa. Our extensive dataset will function as a fundamental resource in investigations of the stomach, including studies on development, aging, and carcinogenesis.

genomics↗

bioRxiv2022

Extremely low level of genetic diversity in Gentiana yakushimensis, an endangered species in Yakushima Island, Japan

Rare or endangered species largely contributing to global biodiversity are essential components of ecosystems. Because genetic diversity depends not only on apparent population size but also demographic processes, the conservation priority of endangered species based on population genetics needs to be assessed by comparison with common congeners and demographic events. In this study, we performed population genetic analysis for Gentiana yakushimensis Makino, a rare and endangered plant species with an isolated distribution on Yakushima Island, Japan. We performed comparison of genetic diversity with the congener (Gentiana triflora Pall. var. japonica (Kusn.) H.Hara), demographic inference, and bottleneck test based on genome-wide single nucleotide polymorphisms. The result was that G. yakushimensis had an extremely low genetic diversity level and a high inbreeding coefficient level compared to those of the congener. The population of G. yakushimensis was estimated to experience an expansion during the Last Glacial Maximum and a recent bottleneck by the demographic inference and the bottleneck test. Therefore, the low level of genetic diversity of this species might have resulted from the impact of the recent bottleneck and the long-term maintenance of a small population size. Due to the long lifespan of the genus Gentiana, the current level of genetic diversity probably does not reflect a large part of recent demographic events, which requires long-term monitoring of changes in genetic diversity to identify the time lag between the reduction in apparent population size and genetic diversity as a future outlook.

genetics↗

bioRxiv2022

Clonal spreading of tumor-infiltrating T cells underlies the robust antitumor immune responses

The repertoire of tumor-infiltrating T cells is an emerging perspective for characterizing effective antitumor T-cell responses. Oligoclonal expansion of tumor T-cell repertoire has been evaluated; however, their association with antitumor effects is unclear. We demonstrated that the polyclonal fraction of the tumor-reactive T-cell repertoire consisting of relatively minor clones increased in tumor-bearing mice treated with anti-PD-L1 or anti-CD4 monoclonal antibody, which was correlated with antitumor effect. Meanwhile, the size of the oligoclonal fraction consisting of major clones remained unchanged. Moreover, the polyclonal fraction was enriched in progenitor exhausted T cells, which are essential for a durable antitumor response, and was more dependent on CCR7+ migratory dendritic cells, which are responsible for priming tumor-reactive T cells in the tumor-draining lymph nodes. These results suggest that the expansion of diverse tumor-reactive clones ("clonal spreading") is an important mechanism by which anti-PD-L1 and anti-CD4 treatments induce robust and durable antitumor T-cell responses.

immunology↗

bioRxiv2022

Novel orthonairovirus in rodents and shrews, Gabon

Small mammals harbor various zoonotic viruses and are natural reservoirs for emerging viruses. Here, we identified a novel orthonairovirus, which is genetically close to the virus suggested the association with human neural diseases. The virus was found in 24.6% of the small mammals captured in Gabon, Central Africa.

microbiology↗

bioRxiv2022

Connectional architecture of the prefrontal cortex in the marmoset brain

Prefrontal cortex (PFC) has dramatically expanded in primates, but its organization and interactions with other brain regions are only partially understood. We performed high-resolution connectomic mapping of marmoset PFC and found two contrasting corticocortical and corticostriatal projection patterns: "patchy" projections that formed many columns of submillimeter scale in nearby and distant regions and "diffuse" projections that spread widely across the cortex and striatum. Parcellation-free analyses revealed representations of PFC gradients in these projections local and global distribution patterns. We also demonstrated column-scale precision of reciprocal cortico-cortical connectivity, suggesting that PFC contains a mosaic of discrete columns. Diffuse projections showed considerable diversity in the laminar patterns of axonal spread. In mice, columnar projections were much less conspicuous, underscoring the importance of the primate model. Altogether, these fine-grained analyses reveal important principles of local and long-distance PFC circuits in marmosets and provide insights into the functional organization of the primate brain.

neuroscience↗

bioRxiv2021

Green spotted puffer can detect an almost nontoxic TTX analog odor using crypt olfactory sensory neurons

Tetrodotoxin (TTX) is a well-known neurotoxin that functions as a defense substance for toxic puffers. Several behavioral studies reported that TTX attracts toxic puffers belonging to the genus Takifugu. Although our electrophysiological and behavioral studies showed that a TTX analog, 5,6,11-trideoxyTTX, acts as an olfactory chemoattractant for grass puffers (T. alboplumbeus), it is unclear whether toxic puffers are commonly attracted to 5,6,11-trideoxyTTX, and which types of olfactory sensory neurons (OSNs) detect 5,6,11-trideoxyTTX. Here we investigated whether the green spotted puffer (Dichotomyctere nigroviridis), a phylogenetically different species from the grass puffer, is attracted to 5,6,11-trideoxyTTX. Administration of 5,6,11-trideoxyTTX attracted green spotted puffers, but TTX or vehicle did not. Furthermore, immunohistochemistry of the olfactory epithelium exposed to 5,6,11-trideoxyTTX with an antibody against phosphorylated ribosomal protein S6 (pS6), a neuronal activity marker, labeled oval cells with apical invagination. These oval cells were also labeled by the antibody against S100, a specific marker of crypt OSNs. Thus, our results suggest that 5,6,11-trideoxyTTX acts as an olfactory chemoattractant that is detected by crypt-type OSNs in the olfactory epithelium of green spotted puffers. Toxic puffers may use 5,6,11-trideoxyTTX as an olfactory chemoattractant involved in reproduction and parental care or as an olfactory cue of TTX-bearing organisms for effective toxification. Summary statementBehavioral and immunohistochemical experiments suggest that an almost nontoxic TTX analog, 5,6,11-trideoxyTTX, acts as an olfactory chemoattractant for green spotted puffers, and crypt-type olfactory sensory neurons detect it.

zoology↗

bioRxiv2021

Almost nontoxic tetrodotoxin analog, 5,6,11-trideoxytetrodotoxin, as an olfactory chemoattractant for the grass puffer

Toxic puffers contain the potent neurotoxin, tetrodotoxin (TTX). Although TTX is considered to serve as a defense substance, previous behavioral studies have demonstrated that TTX acts as an attractive pheromone for some toxic puffers. To elucidate the physiological mechanism of putative pheromonal action of TTX, we examined whether grass puffers Takifugu alboplumbeus can detect TTX. Electroolfactogram (EOG) results suggest that the olfactory epithelium (OE) of grass puffers responded to a type of TTX analog (5,6,11-trideoxyTTX), although it did not respond to TTX. We also examined the attractive action of 5,6,11-trideoxyTTX on grass puffers by recording their swimming behavior under dark conditions. Grass puffers preferred to stay on the side of the aquarium where 5,6,11-trideoxyTTX was administered, and their swimming speed decreased. Additionally, odorant-induced labeling of olfactory sensory neurons by immunohistochemistry against neural activity marker (phosphorylated extracellular signal regulated kinase; pERK) revealed that labeled olfactory sensory neurons were localized in the region surrounding "islets" where there was considered as nonsensory epithelium. 5,6,11-trideoxyTTX has been known to accumulate in grass puffers, but its toxicity is much lower (almost nontoxic) than TTX. Our results suggest that toxic puffers may positively use this TTX analog, which has been present in their body with TTX but whose function was unknown, as an odorant for chemical communication or effective TTX accumulation.

zoology↗

bioRxiv2021

Fine-tuning of β-catenin in thymic epithelial cells is required for postnatal T cell development

In the thymus, the thymic epithelium provides a microenvironment essential for the development of functionally competent and self-tolerant T cells. Previous findings showed that modulation of Wnt/{beta}-catenin signaling in thymic epithelial cells (TECs) disrupts embryonic thymus organogenesis. However, the role of {beta}-catenin in TECs for postnatal T cell development remains to be elucidated. Here, we analyzed gain-of-function (GOF) and loss-of-function (LOF) of {beta}-catenin highly specific in TECs. We found that GOF of {beta}-catenin in TECs results in severe thymic dysplasia and T cell deficiency beginning from the embryonic period. By contrast, LOF of {beta}-catenin in TECs reduces the number of cortical TECs and thymocytes modestly and only postnatally. These results indicate that fine-tuning of {beta}-catenin expression within a permissive range is required for TECs to generate an optimal microenvironment to support postnatal T cell development.

immunology↗

bioRxiv2020

RNF8 is not required for histone-to-protamine exchange in spermiogenesis

A member of the PIWI family of proteins, MIWI, binds to Piwi-interacting RNA (piRNA) and is essential in mouse spermiogenesis. A recent study demonstrated that MIWI is an essential regulator of the histone-to-protamine exchange in spermiogenesis and that this function is mediated by its binding to an ubiquitin ligase, RNF8. However, here we confirm that RNF8 is not required for histone-to-protamine exchange in spermiogenesis. We show that histone-to-protamine exchange takes place in Rnf8-deficient mice, while RNF8 mediates ubiquitination of H2A on the sex chromosomes in meiosis, the prior stage of spermatogenesis. Therefore, the infertile phenotype of MIWI mutant mice cannot be explained by a RNF8-mediated mechanism in spermiogenesis.

developmental biology↗

bioRxiv2020

Native cyclase-associated protein and actin from Xenopus laevis oocytes form a 4:4 complex with a tripartite structure

Cyclase-associated protein (CAP) is a conserved actin-binding protein that regulates multiple aspects of actin filament dynamics, including polymerization, depolymerization, filament severing, and nucleotide exchange. Intriguingly, CAP has been isolated from different cells and tissues as an equimolar complex with actin, and previous studies have shown that a CAP-actin complex contains six molecules each of CAP and actin. Here, we successfully isolated a complex of Xenopus cyclase-associated protein 1 (XCAP1) and actin from oocyte extracts and demonstrated that the complex contained four molecules each of XCAP1 and actin. The XCAP1-actin complex remained stable as a single population of 340 kDa in hydrodynamic analysis using gel filtration or analytical ultracentrifugation. Examination of the XCAP1-actin complex by high-speed atomic force microscopy revealed a tripartite structure: a middle globular domain and two globular arms. The two arms were connected with the middle globular domain by a flexible linker and observed in two states with different heights, presumably representing the presence or absence of G-actin. We hypothesize that the middle globular domain corresponds to a tetramer of the N-terminal helical-folded domain of XCAP1, and that each arm in the high state corresponds to a hetero-tetramer containing a dimer of the C-terminal CARP domain of XCAP1 and two G-actin molecules. This novel configuration of a CAP-actin complex may represent a functionally important aspect of this complex.

cell biology↗

bioRxiv2019

The NanoZoomer Connectomics Pipeline for Tracer Injection Studies of the Marmoset Brain

We describe our connectomics pipeline for processing tracer injection data for the brain of the common marmoset (Callithrix jacchus). Brain sections were imaged using a batch slide scanner (NanoZoomer 2.0-HT) and we used artificial intelligence to precisely segment the anterograde tracer signal from the background in the fluorescence images. The shape of each brain was reconstructed by reference to a block-face and all data was mapped into a common 3D brain space with atlas and 2D cortical flat map. To overcome the effect of using a single template atlas to specify cortical boundaries, each brain was cytoarchitectonically annotated and used for making an individual 3D atlas. Registration between the individual and common brain cortical boundaries in the flat map space was done to absorb the variation of each brain and precisely map all tracer injection data into one cortical brain space. We describe the methodology of our pipeline and analyze tracer segmentation and brain registration accuracy. Results show our pipeline can successfully process and normalize tracer injection experiments into a common space, making it suitable for large-scale connectomics studies with a focus on the cerebral cortex.

neuroscience↗

bioRxiv2018

Nearest-neighbor parameter for inosine-cytosine pairs through a combined experimental and computational approach

In RNA secondary structure prediction, nearest-neighbor parameters are used to determine the stability of a given structure. We derived the nearest-neighbor parameters for RNAs containing inosine-cytosine pairs. For parameter derivation, we developed a method that combines UV adsorption measurement experiments with free-energy calculations using molecular dynamics simulations. The method provides fast drop-in parameters for modified bases. Derived parameters were compared and found to be consistent with existing parameters for canonical RNAs. A duplex with an internal inosine-cytosine pair is 0.9 kcal/mol more unstable than the same duplex with an internal guanine-cytosine pair, and is as stable as the one with an internal adenine-uracil pair (only 0.1 kcal/mol more stable) on average.

bioinformatics↗