Biology subjects

Kondo, T.

Publications and source records attributed to Kondo, T..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

Silicon Nitride Induces Osteoconduction Via Activated Mitochondrial Oxidative Phosphorylation and Neovascularization

Silicon nitride (Si3N4: SiN) is a thermodynamically stable ceramic material with excellent mechanical properties, and wear and corrosion resistance for industrial applications. SiN has been proposed for orthopedic and dental implant applications owing to its enhanced osteoconduction. However, the biological mechanisms underlying SiN-induced bone formation have not been fully elucidated. In this study, SiN significantly increased in vitro mineralization of human bone marrow mesenchymal stromal cells (BM-MSC) and in vivo peri-implant bone volume in mouse femurs compared to conventionally used titanium (Ti) implants. RNA sequencing of BM-MSC cultured on SiN disks revealed that functional gene clusters associated with mitochondrial oxidative phosphorylation were significantly elevated. SiN in an aqueous solution has been shown to release ammonium/ammonia, which may provide a source for glutamine-dependent energy production, and BM-MSC upregulated the expression of a key enzyme, glutamate-ammonia ligase under osteogenic conditions. Additionally, SiN increased the expression of functional gene clusters involved in vascular formation. The upregulation of HIF1a in vitro and increased VEGFR3-positive blanching vascular structures in vivo implied that SiN induced neovascularization. This study revealed an important mechanism through which SiN stimulated osteoconduction by unique glutamine-driven mitochondrial oxidative phosphorylation and established oxygen and nutrient supply by neovascularization, leading to stable osseointegration.

bioengineering↗

bioRxiv2024

Nuclear assembly in giant unilamellar vesicles encapsulating Xenopus egg extract

The reconstitution of a cell nucleus in a lipid bilayer-enclosed synthetic cell makes great strides in bottom-up synthetic biology. In this study, we propose a method for assembling a nucleus in giant unilamellar vesicles (GUVs). To induce reconstitution of the nucleus, we utilize interphase egg extract of African clawed frogs Xenopus laevis, known as a biochemically controllable cell-free system capable of transforming an added sperm chromatin into a nucleus in vitro. We enhanced GUV formation efficiency by the inverted emulsion method through incorporating prolonged waiting time and adding chloroform into lipid-dispersed oil, facilitating subsequent nuclear assembly reactions in the GUVs.Characterization of nucleus-like structures formed in the GUVs revealed the presence of dense DNA and accumulated GFP-NLS in the structure, indicative of functional nuclear import. Immunostaining further validated the presence of nuclear pore complexes on the surfaces of these nucleus-like structures. Our approach offers a versatile platform for constructing artificial cellular systems that closely mimic eukaryotic cells. TeaserA cell nucleus is reconstituted in lipid bilayer-enclosed confinements using egg extract from African clawed frogs.

synthetic biology↗

bioRxiv2024

Preventing CpG island hypermethylation in oocytes safeguards mouse development

In mammalian somatic and male germline cells, genomes are extensively DNA methylated (DNAme). In oocytes, however, DNAme is largely limited to transcribed regions only. Regulatory CpG-island (CGI) sequences are also devoid of repressive DNAme in somatic and germ cells of both sexes. The mechanisms restricting de novo DNAme acquisition in developing oocytes, at CGIs and globally, and the relevance thereof for regulating zygotic gene expression and embryo development after fertilization are largely unknown. Here we show that the histone H3 lysine 36 dimethyl (H3K36me2) demethylases KDM2A and KDM2B prevent genome-wide accumulation of H3K36me2, thereby impeding global DNMT3A-catalyzed de novo DNAme, including at CGI gene promoters. By recruiting variant Polycomb Repressive Complex 1 (vPRC1), they further control H2A mono-ubiquitin deposition and vPRC1-dependent gene repression. Through genetic perturbations, we demonstrate that aberrant Dnmt3a-dependent DNAme established in Kdm2a/Kdm2b double mutant oocytes represses transcription from maternal loci in two-cell embryos. The lethality of Kdm2a/Kdm2b maternally deficient pre-implantation embryos is suppressed by Dnmt3a deficiency during oogenesis. Hence, KDM2A/KDM2B are essential for confining the oocyte DNA methylome, conferring competence for early embryonic development. Our research implies that the reprogramming capacity eminent to early embryos is insufficient to erase aberrant DNAme from maternal chromatin, and that early development is vulnerable to gene dosage haplo-insufficiency effects. HIGHLIGHTSDemethylation of H3K36me2 by KDM2A and KDM2B prevents aberrant de novo DNA methylation in mouse oocytes. Sequence composition and H3K4me3 modulate the probability for aberrant H3K36me2 and DNA methylation at CpG islands. Aberrant oocyte DNA methylation is not reprogrammed in early embryos and suppresses maternal gene transcription. Aberrant oocyte DNA methylation causes embryonic lethality during pre-implantation development. GRAPHICAL SUMMARY O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=136 SRC="FIGDIR/small/595726v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@198608org.highwire.dtl.DTLVardef@1aea04dorg.highwire.dtl.DTLVardef@19e3dd7org.highwire.dtl.DTLVardef@1ee11f6_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2024

Enrichment of allelic editing outcomes by Prime Editing in iPS cells

Gene editing in human induced pluripotent stem (iPS) cells with programmable nucleases facilitates reliable disease models, but methods using double-strand break repair often produce random on-target by-products. Prime editing (PE) combines Cas9 nickase with reverse transcriptase (RT) and a prime editing guide RNA (pegRNA) encoding a repair template to reduce by-products. We implemented a GMP-compatible protocol for transfecting Cas9- or PE-2A-mCherry plasmids to track and fractionate human iPS cells based on PE expression level. We compared the editing outcomes of Cas9- and PE-based methods in a GFP-to-BFP conversion assay, at the HEK3 benchmark locus, and at the APOE Alzheimers risk locus, revealing superior precision of PE at high expression levels. Moreover, sorting cells for PE expression level influenced allelic editing outcomes at the target loci. We expect that our findings will aid in the creation of gene-edited human iPS cells with intentional heterozygous and homozygous genotypes. HighlightsO_LIDelivered large plasmids to human iPS cells under GMP-compliant conditions C_LIO_LIDeveloped a flow cytometry-based approach to enrich for PE in human iPS cells C_LIO_LIDemonstrated few on-target indels in cells regardless of PE expression C_LIO_LISorted iPS cells based on PE expression level to influence mono- or bi-allelic editing C_LI

bioengineering↗

bioRxiv2023

Bone marrow-derived CCR5-expressing macrophages promote venous thrombus resolution by up-regulating plasminogen activators and VEGF

BackgroundDeep vein thrombosis (DVT) is a common peripheral vascular disease arising from endothelial damage and can frequently result in pulmonary embolism. C-C chemokine receptor 5 (CCR5) is essentially involved in skin wound healing and pulmonary fibrosis, but the role of CCR5 still remains elusive. MethodsDeep vein thrombus was induced by the ligation of the inferior vena cava (IVC) in wild-type (WT) mice and Ccr5-/- mice, and thrombi were collected over time and various analyzes were performed. ResultsAfter ligation of the IVC in WT mice, a venous thrombus developed progressively until 5 days, and then resolved. Concomitantly, IVC ligation enhanced intrathrombotic gene and protein expression of Ccr5 and its ligand, Ccl5, and both were expressed mainly by intrathrombotic macrophages. The same treatment of Ccr5-/- mice resulted in significantly greater thrombus mass than WT mice. Moreover, the administration of a specific CCR5 inhibitor to WT mice recapitulated similar phenotypes as Ccr5-/- mice while that of CCL5 caused the opposite phenotypes. In Ccr5-/- mice, the production of intrathrombotic vascular endothelial growth factor (VEGF), tissue plasminogen activator (tPA), and urokinase-type plasminogen activator (uPA) from macrophages was significantly reduced and intrathrombotic recanalization was also suppressed compared to WT mice. Moreover, CCL5 enhanced Vegf, Plat, and Plau gene expression in WT-derived peritoneal macrophages by activating the ERK MAPK signaling pathway in vitro. ConclusionsCCR5-deficient mice exhibited reduced expression of Vegf, Plat, and Plau, with concomitant attenuated neovascularization and reduced thrombus resolution. the Thus, the augmentation of the CCL5-CCR5 axis may be effective for DVT treatment by enhancing thrombolysis.

molecular biology↗

bioRxiv2023

Collective Almost Synchronization Modeling Used for Motor Imagery EEG Classification

Classification based on feature extraction is a crucial technique to develop Brain Computer Interface (BCI) systems. The human brain can be considered as a dynamical system, and its behavior measured by EEG signals can be modeled by a group of nonlinear oscillators. Exploring the dynamical nature of EEG signals along with model based approach may improve classification accuracy in BCI. This study proposes a novel feature extraction method for the classification of Motor Imagery (MI) EEG using a dynamical network model operating in a special collective state, so called Collective Almost Synchronization (CAS). The CAS, the nonlinear oscillators set to operate in a weakly coupled regime, can be used to model an EEG. Purpose of this study is to investigate the performance of the CAS model to identify features for the classification of MI states. To achieve this goal, a linear regression method is used and linear coefficients are extracted as feature vectors. Our approach boils down to identifying patterns in the MI-EEG by associating them to the coefficients of a linear regression (or weights of an output function) constructed to model the MI-EEG signals from simulated time-series generated by a dynamical neural network. The dataset 2b from BCI Competition-IV was used to evaluate the performance of the proposed method. Results indicate that the CAS-based classification method is more robust in extracting distinguishable features from EEG signals as compared with other state-of-the-art methods. The proposed method achieved better performance on two-class MI classification. Moreover, the method developed in this study for MI classification across subjects is effective with 74.03% of the accuracy.

neuroscience↗

bioRxiv2023

Virological characteristics of the SARS-CoV-2 XBB.1.5 variant

Circulation of SARS-CoV-2 Omicron XBB has resulted in the emergence of XBB.1.5, a new Variant of Interest. Our phylogenetic analysis suggests that XBB.1.5 evolved from XBB.1 by acquiring the F486P spike (S) mutation, subsequent to the acquisition of a nonsense mutation in ORF8. Neutralization assays showed similar abilities of immune escape between XBB.1.5 and XBB.1. We determined the structural basis for the interaction between human ACE2 and the S protein of XBB.1.5, showing similar overall structures between the S proteins of XBB.1 and XBB.1.5. The intrinsic pathogenicity of XBB.1.5 in hamsters is lower than that of XBB.1. Importantly, we found that the ORF8 nonsense mutation of XBB.1.5 resulted in impairment of MHC expression. In vivo experiments using recombinant viruses revealed that the XBB.1.5 mutations are involved with reduced virulence of XBB.1.5. Together, these data suggest that the mutations in ORF8 and S could enhance spreading of XBB.1.5 in humans.

microbiology↗

bioRxiv2023

Enucleation of the C. elegans embryo revealed the mechanism of dynein-dependent spacing between microtubule asters

The centrosome is a major microtubule-organizing center in animal cells. The intracellular positioning of the centrosomes is important for proper cellular function. One of the features of centrosome positioning is the spacing between centrosomes. The spacing activity is mediated by microtubules extending from the centrosomes; however, the underlying mechanisms are not fully understood. To characterize the spacing activity in the Caenorhabditis elegans embryo, a genetic setup was developed to produce enucleated embryos. The centrosome duplicated multiple times in the enucleated embryo, which enabled us to characterize the chromosome-independent spacing activity between sister and non-sister centrosome pairs. We knocked down genes in the enucleated embryo and found that the timely spacing was dependent on cytoplasmic dynein. Based on these results, we propose a stoichiometric model of cortical and cytoplasmic pulling forces for the spacing between centrosomes. We also found a dynein-independent but non-muscle myosin II-dependent movement of the centrosomes in a later cell cycle phase. The dynein-dependent spacing mechanisms for positioning the centrosomes revealed in this study is likely functioning in the cell with nucleus and chromosomes, including the processes of centrosome separation and spindle elongation.

cell biology↗

bioRxiv2023

Combination-Based Drug Screening for Induced Oligodendrocyte Differentiation Enables Mechanistic Insight and Identifies Optimal Drug Pairs for Remyelination

Remyelination-promoting agents have significant potential utility as therapies for the treatment of demyelinating diseases, including multiple sclerosis. Clemastine and bexarotene have recently been evaluated in Phase II clinical trials to evaluate their potential in this context, with evidence for drug-induced remyelination being observed in both trials. Efficacy levels for both agents as monotherapies, as well as dose-limiting toxicities, highlight the need for more effective approaches. Additionally, questions about the relevance of M1R as the target of clemastine, and also around a mechanism involving accumulation of 8,9-unsaturated sterols, remain. Here, we have identified potent alternatives to clemastine (i.e., doxepin and orphenadrine), which are predicted to have superior tolerability and efficacy profiles and provide mechanistic insight related to M1R, and have completed pairwise drug combination screens using diverse classes of OPC differentiation-inducing agents. Vitamin D receptor agonists were found to enhance M1R antagonist-induced OL differentiation. Select compounds implicated in 8,9-unsaturated sterol accumulation synergistically enhanced the activity of bexarotene in OPCs, which resulted in insights that implicate a critical role for liver-X-receptor in the mechanisms of both sterol-dependent and bexarotene-induced remyelination.

neuroscience↗

bioRxiv2023

Microbiome ssRNA as an environmental cue to activate TLR13-dependent tissue-protective programs in CD5Lhi hepatic macrophages

Hepatic macrophages maintain liver homeostasis, but little is known about the signals that activate the hepatoprotective programs within macrophages. Here, we show that toll-like receptor 13 (TLR13), a sensor of bacterial 23S ribosomal RNA (rRNA), senses microbiome RNAs to drive tissue-protective responses in CD5Lhi hepatic macrophages. Splenomegaly and hepatomegaly developed in the absence of the endosomal RNase, RNaseT2, via TLR13-dependent macrophage proliferation. Furthermore, TLR13 in hepatic Ly6Clo macrophages activated the transcription factors LXR and MafB, leading to expression of tissue-clearance molecules, such as CD5L, C1qb, and Axl. Consequently, Rnaset2-/- mice developed resistance to acute liver injury caused by challenges with acetaminophen and lipopolysaccharide + D-galactosamine. TLR13 responses in Rnaset2-/- mice were impaired by antibiotics, suggesting that TLR13 were activated by microbiome rRNAs, which was detected in the sera and hepatic macrophages. Repeated administration of wild-type mice with the TLR13 ligand, rather than other TLR ligands, selectively increased the number of Kupffer cells, which expressed immunoregulatory and tissue-clearance genes as hepatic macrophages in Rnaset2-/- mice did. Our results suggest that microbiome ssRNA serves as an environmental cue for initiating tissue-protective TLR13 responses in hepatic macrophages. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=192 SRC="FIGDIR/small/540294v1_ufig1.gif" ALT="Figure 1"> View larger version (51K): org.highwire.dtl.DTLVardef@69614eorg.highwire.dtl.DTLVardef@737c69org.highwire.dtl.DTLVardef@1ecd9eforg.highwire.dtl.DTLVardef@d7e10d_HPS_FORMAT_FIGEXP M_FIG In the absence of an endosomal RNase, RNase T2, microbiome RNAs circulating in the vasculature activate TLR13 in hepatic macrophages to drive hepatoprotective responses through expression of immunoregulatory and tissue-clearance molecules. Consequently, mice lacking RNase T2 are resistant against acute liver injuries caused by acetaminophen and LPS + D-galactosamine. C_FIG

immunology↗

bioRxiv2023

Mouse gingival single-cell transcriptomic atlas: An activated fibroblast subpopulation guides oral barrier immunity in periodontitis

Periodontitis, one of the most common non-communicable diseases, is characterized by chronic oral inflammation and uncontrolled tooth supporting alveolar bone resorption. Its underlying mechanism to initiate aberrant oral barrier immunity has yet to be delineated. Here, we report a unique fibroblast subpopulation activated to guide oral inflammation (AG fibroblasts) identified in a single-cell RNA sequencing gingival cell atlas constructed from the mouse periodontitis models. AG fibroblasts localized beneath the gingival epithelium and in the cervical periodontal ligament responded to the ligature placement and to the discrete application of Toll-like receptor stimulants to mouse maxillary tissue. The upregulated chemokines and ligands of AG fibroblasts linked to the putative receptors of neutrophils in the early stages of periodontitis. In the established chronic inflammation, neutrophils together with AG fibroblasts appeared to induce type 3 innate lymphoid cells (ILC3s) that were the primary source of interleukin-17 cytokines. The comparative analysis of Rag2-/- and Rag2{gamma}c-/-mice suggested that ILC3 contributed to the cervical alveolar bone resorption interfacing the gingival inflammation. We propose that AG fibroblasts function as a previously unrecognized surveillant to initiate gingival inflammation leading to periodontitis through the AG fibroblast-neutrophil-ILC3 axis.

pathology↗

bioRxiv2023

Spatio-temporal remodeling of extracellular matrix orients epithelial sheet folding

Biological systems are inherently noisy; however, they produce highly stereotyped tissue morphology. Drosophila pupal wings show a highly stereotypic folding through uniform expansion and subsequent buckling of wing epithelium within a surrounding cuticle sac. The folding pattern produced by buckling is generally stochastic; it is thus unclear how buckling leads to stereotypic tissue folding of the wings. We found that the extracellular matrix (ECM) protein, Dumpy, guides the position and direction of buckling-induced folds. Dumpy anchors the wing epithelium to the overlying cuticle at specific tissue positions. Tissue-wide alterations of Dumpy deposition and degradation yielded different buckling patterns. In summary, we propose that spatio-temporal ECM remodeling shapes stereotyped tissue folding through dynamic interactions between the epithelium and its external structures. One-Sentence SummaryRemodeling of extracellular matrix protein, Dumpy, guides epithelial tissue folding during Drosophila wing development.

developmental biology↗

bioRxiv2022

Apoptotic contraction drives target cell release by cytotoxic T cells

Cytotoxic T lymphocytes (CTLs) use immune synapses to destroy infected or transformed target cells. Although the mechanisms governing synapse assembly have been studied extensively, little is known about how this interface dissociates, which is a critical step that both frees the CTL to search for additional prey and enables the phagocytosis of target corpses. Here, we applied time-lapse imaging to explore the basis for synapse dissolution and found that it occurred concomitantly with the cytoskeletal contraction of apoptotic targets. Genetic and pharmacological disruption of apoptotic contraction indicated that it was necessary for CTL dissociation. Furthermore, acute stimulation of contractile forces triggered the release of live targets, demonstrating that contraction is sufficient to drive the response. Finally, mechanically amplifying apoptotic contractility promoted faster CTL detachment and serial killing. Collectively, these results establish a biophysical basis for synapse dissolution and highlight the importance of mechanosensory feedback in the regulation of cell-cell interactions.

immunology↗

bioRxiv2022

Estimation of crossbridge-state during cardiomyocyte beating using second harmonic generation

Estimation of dynamic change of crossbridge formation in living cardiomyocytes is expected to provide crucial information for elucidating cardiomyopathy mechanisms, efficacy of an intervention, and other parameters. Here, we developed an assay system to dynamically measure second harmonic generation (SHG) polarization in pulsating cardiomyocyte and proved that the SHG anisotropy derived from myosin filaments in disease-model cardiomyocytes depended on their crossbridge status, providing an evaluation method for myosin force generation. Experiments utilizing an inheritable mutation that induces excessive myosin-actin interactions revealed that the correlation between sarcomere length and SHG anisotropy represents crossbridge formation ratio during pulsation. Furthermore, the present method found that ultraviolet irradiation induced an increased population of attached crossbridges that lost force-generating ability upon myocardial differentiation, causing acquired dysfunction. Taking an advantage of infrared two-photon excitation in SHG microscopy, myocardial dysfunction could be intravitally evaluated in a Drosophila disease model. Thus, along with the establishment of the methodology, we successfully demonstrated the applicability and effectiveness of the present method to evaluate the actomyosin activity of a drug or genetic defect on living cardiomyocytes.

biophysics↗

bioRxiv2022

Charge neutralization and β-elimination cleavage mechanism of family 42 L-rhamnose-α-1,4-D-glucuronate lyase revealed using neutron crystallography

Gum arabic (GA) is widely used as an emulsion stabilizer and edible coating, and consists of a complex carbohydrate moiety with a rhamnosyl-glucuronate group capping the non-reducing ends. Enzymes that can specifically cleave the glycosidic chains of GA and modify their properties are valuable tools for structural analysis and industrial application. Cryogenic X-ray crystal structure of GA-specific L-rhamnose--1,4-D-glucuronate lyase from Fusarium oxysporum (FoRham1), belonging to the polysaccharide lyase (PL) family 42, has been previously reported. To determine the specific reaction mechanism based on its hydrogen-containing enzyme structure, we performed joint X-ray/neutron crystallography of FoRham1. Large crystals were grown in the presence of L-rhamnose (a reaction product), and neutron and X-ray diffraction datasets were collected at room temperature up to 1.80 and 1.25 [A] resolutions, respectively. The active site contained L-rhamnose and acetate, the latter being a partial analog of glucuronate. Incomplete H/D exchange between Arg166 and acetate suggested that a strong salt-bridge interaction was maintained. Doubly deuteronated His105 and deuteronated Tyr150 supported this interaction. The unusually hydrogen-rich environment functions as a charge neutralizer for glucuronate and stabilizes the oxyanion intermediate. The NE2 atom of His85 was deprotonated and formed a hydrogen bond with the deuterated O1 hydroxy of L-rhamnose, indicating the function of His85 as the base/acid catalyst for bond cleavage via {beta}-elimination. Asp83 functions as a pivot between the two catalytic histidine residues by bridging them, and this His-His-Asp structural motif is conserved in the three PL families. Significance StatementAlthough hydrogen transfer plays an important role in enzymatic reactions, hydrogen atoms are generally invisible in macromolecular X-ray crystallography. In the reaction of polysaccharide lyases, substrate activation by negative charge stabilization of uronic acid and base/acid-catalyzed {beta}-elimination reaction have been postulated. Here, we report the neutron crystallography of polysaccharide lyase. Joint X-ray/neutron crystallography of L-rhamnose--1,4-D-glucuronate lyase from Fusarium oxysporum (FoRham1) complexed with L-rhamnose was performed, and the hydrogen and deuterium atoms were visualized at a high resolution. FoRham1 catalyzes the specific cleavage of the cap structure of gum arabic, which is useful for various applications in the food, cosmetic, and pharmaceutical industries. A detailed catalytic mechanism for FoRham1 was proposed based on the key structural features of its active site.

biophysics↗

bioRxiv2022

Comprehensive analysis of the effect of mRNA sequences on translation efficiency and accuracy

Messenger ribonucleic acid (mRNA) sequences influence the translation efficiency and accuracy. To increase our knowledge of how mRNA sequences affect ribosome translation and apply the obtained information to improve the mRNA display method, we conducted a comprehensive analysis of the effect of mRNA sequences on the translation. Translation efficiency depended strongly on the three codons following the start codon. Furthermore, the codons at the ribosomal E- and P-sites strongly influence the misreading of the A-site blank codon by near-cognate transfer RNA. The purine base after the blank codon also induced a higher misread rate than that with a pyrimidine base. Based on these findings, we demonstrated construction of highly diverse monobody and macrocyclic peptide libraries that would be useful in developing functional peptides and proteins in the future.

biochemistry↗

bioRxiv2022

Dynamic interaction of bacterial cellulose synthase subunit D (BcsD) in type I bacterial cellulose synthase

Cellulose is a promising biological material for supporting sustainable human life. This natural polymer is synthesized by cellulose synthase, a protein complex in the cell membrane. Cellulose synthase in bacteria is a hetero-subunit complex, and its subunit organization varies widely depending on the species. In the type I bacterial cellulose synthase complex, the BcsD (bacterial cellulose synthase D) protein is believed to play an important role in producing cellulose with long slender fiber morphology and high crystallinity, given the phenotype of the bcsD-deficient mutant and the specific existence of the type I operon in bacterial species synthesizing crystalline cellulose microfibrils such as Acetobacter. In this study, we successfully established a heterogeneously expressed Bcs protein in Escherichia coli as an experimental model and conducted biochemical studies for the BcsD protein and the other three major subunits of bacterial cellulose synthase, BcsA, BcsB, and BcsC. It has been shown that the BcsD protein interacts with the functionally required minimal subunits of the BcsAB complex, as well as the BcsC protein. Furthermore, it was shown that BcsD interacts with the BcsAB complex in two modes: direct protein-protein interactions and indirect interactions through the product cellulose. The former and latter modes represent the basal and active states of the type I bacterial cellulose synthase, respectively. This dynamic behavior of the BcsD protein is important for the type I bacterial cellulose synthase complex to regulate the crystallization process of cellulose.

biochemistry↗

bioRxiv2022

Lipid-correlated alterations in the transcriptome are enriched in several specific pathways in the postmortem prefrontal cortex of Japanese patients with schizophrenia

BackgroundSchizophrenia is a chronic relapsing psychiatric disorder that is characterized by many symptoms and has a high heritability. A previous study showed that specific lipid molecules belong to phosphatidylinositol (PI) and phosphatidylserine (PS) was reduced in the postmortem prefrontal cortex of patients with schizophrenia1. However, signaling pathways contributing to the lipid changes remain unknown. Here we performed two types of transcriptome analyses in patients with schizophrenia: an un-biased transcriptome analysis solely based on RNA-seq data and a correlation analysis between levels of gene expression and lipids. Methodology/Principal FindingsRNA-Seq analysis was performed in the postmortem prefrontal cortex from 10 subjects with schizophrenia and 5 controls. Correlation analysis between the transcriptome and lipidome from 9 subjects which are the same samples in the previous lipidomics study1 (Table 1). Extraction of differentially expressed genes (DEGs) and further sequence and functional group analysis revealed changes of gene expression levels in phosphoinositide 3-kinase (PI3K)-Akt signaling and the complement system. In addition, a correlation analysis clarified alterations in several signaling/metabolic pathways including lipid-correlated genes, most of which are not found as DEGs in transcriptome analysis alone. O_TBL View this table: org.highwire.dtl.DTLVardef@80d74eorg.highwire.dtl.DTLVardef@b780b7org.highwire.dtl.DTLVardef@1637f28org.highwire.dtl.DTLVardef@1315439org.highwire.dtl.DTLVardef@190a230_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 1.C_FLOATNO O_TABLECAPTIONCharacteristics of patients from whom postmortem brain samples were obtained. Abbreviations: PMI, postmortem interval, the time that has elapsed since a person has died; DOI, duration of illness, The samples used in correlation analysis are shown by black circles. C_TABLECAPTION C_TBL ConclusionsThis study provided results of the first integrated analysis of the schizophrenia-associated transcriptome and lipidome within the PFC and revealed that lipid-correlated alterations in the transcriptome are enriched in specific pathways including PI3K-Akt signaling.

pathology↗