Biology subjects

Min, B.

Publications and source records attributed to Min, B..

22 records · Page 2Linked to original sources

bioRxiv2021

Evolutionary innovations through gain and loss of genes in the ectomycorrhizal Boletales

O_LIIn this study, we aim to identify genomic traits of the transitions to the ectomycorrhizal ecology within the Boletales, one of the most diverse lineages of symbiotrophic fungi. C_LIO_LIWe sequenced the genomes and compared the gene repertoires of symbiotrophic Boletales species to their saprotrophic brown-rot relatives. We also reconstructed gene duplication/loss histories along a time-calibrated phylogeny. C_LIO_LIWe showed that the rate of gene duplication is constant along the backbone of Boletales phylogeny with large loss events in lineages leading to several families. The rate of gene family expansion sharply increased in the late Miocene and mostly took place in Boletaceae. C_LIO_LIMost of the ectomycorrhizal Boletales are characterized by a large genome size due to transposable element (TE) expansions and a reduction in the diversity of plant cell wall degrading enzymes (PCWDEs) compared to their brown-rot relatives. However, several species in the Boletaceae, Paxillaceae and Boletinellaceae have kept a substantial set of endoglucanases and LPMOs acting on cellulose/hemicellulose and fungal polysaccharides suggesting that they may partly decompose organic matter by a combined activity of oxidative and hydrolytic enzymes. C_LIO_LIThe present study provides novel insights on our understanding of the mechanisms that influence the evolutionary diversification of boletes and symbiosis evolution. C_LI

genomics↗

bioRxiv2020

BATF3-dependent induction of IL-27 by B cells bridges the innate and adaptive stages of the antibody response

B cells are exposed to innate and T cell stimuli during the antibody response, although whether and how they functionally integrate such signals are unclear. Here we have identified IL-27 as the cytokine specifically produced by murine B cells upon sequential stimulation by TLR ligands and then CD154 and IL-21, the hallmark factors of T follicular helper cells, and during the T-dependent antibody response to a conjugated hapten or virus infection. B-cell Il27p28 transcription is concomitant with increased locus accessibility and depends on newly induced BATF3 transcription factor. IL-27-producing B cells are inefficient in antibody secretion, but cooperate with IFN{gamma} to promote proliferation, survival, class-switching and plasma cell differentiation of CD40-activated B cells, leading to optimal IgG2a and IgG1 responses. Overall, IL-27-producing B cells function as "helper" B cells that integrate the innate and adaptive stages of the antibody response. One-sentence summaryB cells integrate innate TLR and adaptive CD40 signals to induce BATF3 transcription factor for production of IL-27, which together with INFg optimizes antibody responses.

immunology↗

bioRxiv2020

A neural circuit mechanism of categorical perception: top-down signaling in the primate cortex

In contrast to feedforward architecture commonly used in deep networks at the core of todays AI revolution, the biological cortex is endowed with an abundance of feedback projections. Feedback signaling is often difficult to differentially identify, and its computational roles remain poorly understood. Here, we investigated a cognitive phenomenon, called categorical perception (CP), that reveals the influences of high-level category learning on low-level feature-based perception, as a putative signature of top-down signaling. By examining behavioral data from a visual motion delayed matching experiment in non-human primates, we found that, after categorization training, motion directions closer to (respectively, away from) a category center became more (less) difficult to discriminate. This distance-dependent discrimination performance change along the dimension relevant to the learned categories provides direct evidence for the CP phenomenon. To explain this experimental finding, we developed a neural circuit model that incorporated key neurophysiological findings in visual categorization, working memory and decision making. Our model accounts for the behavioral data indicative of CP, pinpoints its circuit basis, suggests novel experimentally testable predictions and provides a functional explanation for its existence. Our work shows that delayed matching paradigms in non-human primates combined with biologically-based modeling can serve as a promising model system for elucidating the neural mechanisms of CP, as a manifestation of top-down signaling in the cortex. Significant StatementCategorical perception is a cognitive phenomenon revealing the influences of high-level category learning on low-level feature-based perception. However, its underlying neural mechanisms are largely unknown. Here, we found behavioral evidence for this phenomenon from a visual motion delayed matching experiment in non-human primates. We developed a neural circuit model that can account for this behavioral data, pinpoints its circuit basis, suggests novel experimentally testable predictions and provides a functional explanation for its existence. Our work shows that delayed matching paradigms in non-human primates combined with biologically-based modeling can serve as a promising model system for elucidating the neural mechanisms of categorical perception, as a manifestation of top-down signaling in the cortex.

neuroscience↗

bioRxiv2019

Unusual genome expansion and transcription suppression in ectomycorrhizal Tricholoma matsutake by repetitive insertions of transposable elements

Genome sequence of Tricholoma matsutake was revealed as the one of the large fungal genomes published up to date at 189.0 Mbp with 15,305 predicted genes. The unusual size of this fungal genome contained frequent colonization of transposable elements (TEs) occupying more than half of the entire genome. We identified that 702 genes were surrounded by TEs and 83.2% of those genes were never transcribed at any development stage. This observation corroborated that the insertion of transposable elements alters the transcription of the genes neighboring TEs.\n\nRepeat-induced point mutation such as C to T hypermutation with a bias over CpG dinucleotides was also recognized in this genome, representing a typical defense mechanism against TEs during evolution. Many transcription factor genes were activated in both primordia and fruiting body, which indicates that many regulatory processes are shared during developmental stages. Small secreted protein genes (<300 aa) were dominantly transcribed in hyphae, where symbiotic interactions occur with hosts. Comparative analysis with 37 Agaricomycetes genomes revealed that IstB-like domain (PF01695) was conserved in taxonomically diverse mycorrhizal genomes, where the T. matsutake genome contained four copies of this domain. Three of the IstB-like genes were overexpressed in hyphae. In the CAZyme analysis, reduced CAZyme genes were found as other ectomycorrhizal genomes including a lot of loss of glycoside hydrolase genes. Also, auxiliary activity genes were dominantly transcribed in primordia. The T. matsutake genome sequence provides insight into the large genome size and clues to understand unusual fungal genome expansion.

genomics↗