Biology subjects

Kato, H.

Publications and source records attributed to Kato, H..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Whole-genome sequencing reveals the molecular basis of sex determination in the dioecious wild yam Dioscorea tokoro

Dioecious plants, which have distinct male and female individuals, constitute [~]5% of angiosperm species and have emerged frequently and independently from hermaphroditic ancestors. Although recent molecular studies of sex determination have started to reveal the diversity of the genetic systems underlying dioecy, research on the evolution of dioecy is limited, especially in monocots. Here, we describe the molecular basis of sex determination in the monocot Dioscorea tokoro, a dioecious wild yam endemic to East Asia. Chromosome-scale and haplotype-resolved genome assemblies and linkage analysis suggested that this plant has a male heterogametic sex determination (XY) system, with sex determination regions located on chromosome 3. Sequence read coverage analysis of the sex chromosomes revealed X- and Y-specific regions in putative pericentromeric chromosome regions. Within the Y-specific region, we identified two candidate genes that are likely involved in sex determination: BLH9, encoding a homeobox protein, and HSP90, encoding a molecular chaperone. BLH9 has similar functions to AtBLH9 in Arabidopsis thaliana. BLH9 is thought to suppress female organ development, whereas HSP90 might be required for pollen development. These results shed light on the complex evolution of dioecy in plants. Author summarySexual reproduction is a nearly universal, indispensable feature of evolution in eukaryotes. The molecular mechanisms underlying sex determination vary depending on the taxon. However, most information about this process was derived from studies of model organisms and/or domesticated species. To elucidate the diversity and evolution of sex determination, we need to expand the taxonomic breadth of these investigations. Here, we focused on the monocot genus Dioscorea, which contains species with multiple sex-determination systems, suggesting that frequent evolutionary transitions occur between the different sex-determination systems. We investigated the genetics of sex determination in Dioscorea tokoro, a dioecious wild yam endemic to East Asia. Whole-genome assembly and genetic analysis, along with transcriptome analysis, suggested that this species employs a male heterogametic sex determination (XY) system, with two Y-chromosome-specific genes that might be involved in male and female differentiation. These findings enhance our understanding of the complex evolution of dioecy.

plant biology↗

bioRxiv2025

Analysis of Treacher Collins syndrome 4-associated mutations in Schizosaccharomyces pombe

Treacher Collins syndrome (TCS) is a rare congenital disorder characterized by craniofacial deformities. Although mutations in several genes involved in ribosome biogenesis have been identified in patients with TCS, the molecular mechanisms by which these mutations exert their effects remain poorly understood. In this study, we established Schizosaccharomyces pombe models for TCS type 4 (TCS4) by introducing specific mutations in the rpa2 gene, which encodes Rpa2, the second largest subunit of RNA polymerase I (Pol I). TCS4-associated rpa2R1022C and rpa2R1022S mutations impaired cell growth without altering Rpa2 protein levels. These mutants were defective in 35S pre-rRNA biogenesis and were sensitive to the Pol I inhibitor BMH-21. These findings underscore the essential role of Rpa2 residues associated with TCS4 in rRNA transcription and cell growth.

molecular biology↗

bioRxiv2025

Modular architecture confers robustness to damage and facilitates recovery in spiking neural networks modeling in vitro neurons

Impaired brain function is restored following injury through dynamic processes that involve synaptic plasticity. This restoration is supported by the brains inherent modular organization, which promotes functional separation and redundancy. However, it remains unclear how the modular structure interacts with synaptic plasticity, most notably in the form of spike-timing-dependent plasticity (STDP), to define the damage response and recovery efficiency. In this work, we numerically modeled the response and recovery to damage of a neuronal network in vitro bearing a modular structure. Consistent with the in vitro observations, the in silico numerical model effectively captured the decline and subsequent recovery of spontaneous activity following the injury. We revealed that the modular structure confers robustness to injury, minimizes the decrease in neuronal activity, and promotes recovery via STDP. Finally, using the reservoir computing framework, we show that information representation in the neuronal network improves with the recovery of synchronous activity. Our work provides an experimental-numerical platform for predicting recovery in damaged neuronal networks and may help developing effective models for brain injury.

neuroscience↗

bioRxiv2025

Defining epithelial stem cell heterogeneity through undulating structures of the skin and oral mucosa

Epithelial stem cells exhibit heterogeneity, with distinct stem cell populations occupying specific tissue regions. The human skin displays a characteristic undulating structure at the epidermal-dermal junction, which supports mechanical strength and influences the spatial organization of epithelial stem cells. Unlike human skin, mouse skin lacks these undulations, complicating studies into the effects of tissue architecture on stem cell distribution. Here, we leverage the mouse oral mucosa, which possesses an undulating structure similar to human skin, to characterize stem cell division dynamics and long-term fate in vivo. Using a combination of H2B-GFP pulse-chase analysis and lineage tracing with Dlx1-CreER and Slc1a3-CreER models, we demonstrate that slow-and fast-cycling stem cells localize to distinct anatomical regions relative to the undulating structure and maintain their respective compartments during tissue homeostasis. A three-dimensional culture model using micropatterned collagen scaffolds that recapitulate the undulating structures in vitro reveals that the mechanical environment generated by the undulating structures partially induces proliferative heterogeneity in epithelial stem cells. This study proposes tissue undulating surface structure as a common principle as a niche component that defines the localization of compartmentalized stem cell populations across different epithelial tissues. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=123 SRC="FIGDIR/small/634195v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@b3046aorg.highwire.dtl.DTLVardef@e6cd8forg.highwire.dtl.DTLVardef@c169ccorg.highwire.dtl.DTLVardef@8f772_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2025

Single-cell genomics of single soil aggregates: methodological assessment and potential implications with a focus on nitrogen metabolism

Soil particles in plant rooting zone are largely clustered to form complex porous structural unit called aggregates where highly diverse microbes coexist and drive biogeochemical cycling. The complete extraction of microbial cells and DNA from soil is a substantial task as certain microbes exhibit strong adhesion to soil surfaces and/or inhabit deep within aggregates. Yet, the degree of aggregate dispersion and the efficacy of extraction have rarely been examined, and thus adequate cell extraction method from soil remain unclear. We aimed to develop an optimal method of cell extraction for single-cell genomics (SCG) analysis of single soil aggregates by focusing on water-stable macroaggregates (diameter: 5.6-8.2 mm) isolated from a topsoil of cultivated Acrisol. Using the same six individual aggregates, we performed both SCG sequencing and amplicon analysis. While both bead-vortexing and sonication dispersion methods improved the extractability of bacterial cells compared to previous studies, the latter yielded higher number and more diverse microbes compared to the former. The analyses of nitrogen-cycling and exopolysaccharides-related genes suggested that the sonication-assisted extraction led to greater recovery of microbes strongly attached to soil particles and/or inhabited the aggregate subunits that were more physically stable (e.g., aggregate core). Further SCG analysis revealed that all six aggregates held intact microbes having the genes (i.e., potentials) to convert nitrate into all possible nitrogen forms while some low-abundance genes showed inter-aggregate heterogeneity. In addition, all six aggregates studied showed overall similarity in pore characteristics, phylum-level composition, and the microbial functional redundancy. Together, these results suggest that water-stable macroaggregates may act as a functional unit in soil and show potential as a useful experimental unit in soil microbial ecology. Our study also suggest that conventional methods employed for the extraction of cell and DNA may not be optimal. The current findings underscore the necessity to advance extraction methodologies, thereby facilitating a more comprehensive understanding of the microbial diversity and functioning within soil environments.

microbiology↗

bioRxiv2024

Mixed DAMP/MAMP oligosaccharides promote both growth and defense against fungal pathogens of cucumber

Plants recognize a variety of environmental molecules, thereby triggering appropriate responses to biotic or abiotic stresses. Substances containing microbes-associated molecular patterns (MAMPs) and damage-associated molecular patterns (DAMPs) are representative inducers of pathogen resistance and damage repair, thus treatment of healthy plants with such substances can pre-activate plant immunity and cell repair functions. In this study, the effects of DAMP/MAMP oligosaccharides mixture (Oligo-Mix) derived from plant cell wall (cello-oligosaccharide and xylo-oligosaccharide), and fungal cell wall (chitin-oligosaccharide) were examined in cucumber. Treatment of cucumber with Oligo-Mix promoted root germination and plant growth, along with increased chlorophyll contents in the leaves. Oligo-Mix treatment also induced typical defense responses such as MAP kinase activation and callose deposition in leaves. Pretreatment of Oligo-Mix enhanced disease resistance of cucumber leaves against pathogenic fungi Podosphaera xanthii (powdery mildew) and Colletotrichum orbiculare (anthracnose). Oligo-Mix treatment increased the induction of hypersensitive cell death around the infection site of pathogens, which inhibited further infection and the conidial formation of pathogens on the cucumber leaves. RNA-seq analysis revealed that Oligo-Mix treatment upregulated genes associated with plant structural reinforcement, responses to abiotic stresses and plant defense. These results suggested that Oligo-Mix has beneficial effects on growth and disease resistance in cucumber, making it a promising biostimulant for agricultural application.

plant biology↗

bioRxiv2024

Neutralizing antibody evasion of SARS-CoV-2 JN.1 derivatives KP.3, KP.3.1.1, LB.1, and XEC

The emergence of SARS-CoV-2 variants poses ongoing challenges to vaccine efficacy. We evaluated neutralizing antibody responses against JN.1 and its derivatives (KP.3, KP.3.1.1, LB.1, and XEC) in healthcare workers who received seven doses of BNT162b2, including XBB.1.5 monovalent vaccine. In COVID-19-naive individuals, KP.3.1.1 and LB.1 showed substantial immune escape, while previously infected individuals maintained neutralization activity against all variants. We also demonstrated that JN.1-based immunization induces robust cross-neutralizing activity against emerging variants. A single amino acid deletion at position 31 in the spike protein significantly impacted immune evasion. These findings support the potential effectiveness of JN.1-based vaccines while highlighting the need for continued surveillance and vaccine optimization.

immunology↗

bioRxiv2024

Chemical genetics reveals cross-activation of plant developmental signaling by the immune peptide-receptor pathway

Cells sense and integrate multiple signals to coordinate development and defence. A receptor-kinase signaling pathway for plant stomatal development shares components with the immunity pathway. The mechanism ensuring their signal specificities remains unclear. Using chemical genetics, here we report the identification of a small molecule, kC9, that triggers excessive stomatal differentiation by inhibiting the canonical ERECTA receptor-kinase pathway. kC9 binds to and inhibits the downstream MAP kinase MPK6, perturbing its substrate interaction. Strikingly, activation of immune signaling by a bacterial flagellin peptide nullified kC9s effects on stomatal development. This cross-activation of stomatal development by immune signaling depends on the immune receptor FLS2 and occurs even in the absence of kC9 if the ERECTA-family receptor population becomes suboptimal. Furthermore, proliferating stomatal-lineage cells are vulnerable to the immune signal penetration. Our findings suggest that the signal specificity between development and immunity can be ensured by MAP Kinase homeostasis reflecting the availability of upstream receptors, thereby providing a novel view on signal specificity.

plant biology↗

bioRxiv2024

Generation of a biliary tract cancer cell line atlas reveals molecular subtypes and therapeutic targets

Biliary tract cancers (BTCs) are a group of deadly malignancies encompassing intrahepatic and extrahepatic cholangiocarcinoma, gallbladder carcinoma, and ampullary carcinoma. Here, we present the integrative analysis of 63 BTC cell lines via multi-omics clustering and genome- scale CRISPR screens, providing a platform to illuminate BTC biology and inform therapeutic development. We identify dependencies broadly enriched in BTC compared to other cancers as well as dependencies selective to the anatomic subtypes. Notably, cholangiocarcinoma cell lines are stratified into distinct lineage subtypes based on biliary or dual biliary/hepatocyte marker signatures, associated with dependency on specific lineage survival factors. Transcriptional analysis of patient specimens demonstrates the prognostic significance of these lineage subtypes. Additionally, we delineate strategies to enhance targeted therapies or to overcome resistance in cell lines with key driver gene mutations. Furthermore, clustering based on dependencies and proteomics data elucidates unexpected functional relationships, including a BTC subgroup with partial squamous differentiation. Thus, this cell line atlas reveals potential therapeutic targets in molecularly defined BTCs, unveils biologically distinct disease subtypes, and offers a vital resource for BTC research.

cancer biology↗

bioRxiv2024

Regulation of ROP GTPase cycling between active/inactive states is essential for vegetative organogenesis in Marchantia polymorpha

Rho/Rac of plant (ROP) GTPases are a plant-specific subfamily of Rho small GTP-binding proteins that function as molecular switches by being converted to the active state by guanine nucleotide exchange factors (GEFs) and to the inactive state by GTPase-activating proteins (GAPs). The bryophyte Marchantia polymorpha contains single-copy genes encoding ROP (MpROP), two types of GEFs (ROPGEF and SPIKE (SPK)), and two types of GAPs (ROPGAP and ROP enhancer (REN)). MpROP regulates the development of various organs, including the air chambers, rhizoids, and clonal propagule gemmae. While the sole PRONE-type ROPGEF, KARAPPO (MpKAR), plays an essential role in gemma initiation, little is known about the in-planta functions of other ROP regulatory factors in M. polymorpha. In this study, we focused on the functions of two types of GAPs: MpROPGAP and MpREN. Loss-of-function Mprenge single mutants showed pleiotropic defects in thallus growth, air chamber formation, rhizoid tip growth, and gemma development, whereas MpROPGAP mutants showed no detectable abnormalities. Despite the distinctive domain structures of MpROPGAP and MpREN, MpropgapgeMprenge double mutants showed more severe phenotypes than the Mprenge single mutants, suggesting redundant functions of MpROPGAP and MpREN in gametophyte organogenesis. Interestingly, overexpression of MpROPGAP, MpREN, and dominant-negative MpROP (MpROPDN) resulted in similar air chamber defects, as well as loss-of-function of MpREN and MpROPGAP and overexpression of constitutively active MpROP (MpROPCA), suggesting importance of activation/inactivation cycling (or balancing) of MpROP. Furthermore, we proved the contributions of the sole DOCK family GEF, MpSPK, to MpROP-regulated air chamber formation. In summary, our results demonstrate a significant role of the two GAPs in the development of various organs and that the two GEFs are responsible for organogenesis through the control of the MpROP active/inactive cycle in the vegetative growth of M. polymorpha.

plant biology↗

bioRxiv2023

Chemical inhibition of stomatal differentiation by perturbation of the master-regulatory bHLH heterodimer via an ACT-Like domain

Selective perturbation of protein interactions with chemical compounds enables dissection and control of developmental processes. Differentiation of stomata, cellular valves vital for plant growth and survival, is specified by the basic-helix-loop-helix (bHLH) heterodimers. Harnessing a new amination reaction, we here report a synthesis, derivatization, target identification, and mode of action of an atypical doubly-sulfonylated imidazolone, Stomidazolone, which triggers stomatal stem cell arrest. Our forward chemical genetics followed by biophysical analyses elucidated that Stomidazolone directly binds to the C-terminal ACT-Like (ACTL) domain of MUTE, a master regulator of stomatal differentiation, and perturbs its heterodimerization with a partner bHLH, SCREAM in vitro and in plant cells. On the other hand, Stomidazolone analogs that are biologically inactive did not bind to MUTE or disrupt the SCREAM-MUTE heterodimers. Guided by structural docking modeling, we rationally designed MUTE with reduced Stomidazolone binding. These engineered MUTE proteins are fully functional and confer Stomidazolone resistance in vivo. Our study identifies doubly-sulfonylated imidazolone as a direct inhibitor of the stomatal master regulator, further expanding the chemical space for perturbing bHLH-ACTL proteins to manipulate plant development.

plant biology↗

bioRxiv2023

Control of cell fate specification and patterning by an ancestral microRNA

The formation of an organized body requires the establishment and maintenance of cells with structural and functional distinctive characteristics. A central question in developmental biology is how changes in the regulation of genes drive cell specification and patterning1. microRNAs (miRNAs) are small non-coding RNAs that regulate development through mRNA cleavage and/or translational repression2. In plants, miRNAs regulate key aspects including growth, development, stem cell maintenance, vegetative phase change, leaf morphogenesis, floral organ formation and flowering time3. Biogenesis of plant miRNAs depends on the activity of DICER-LIKE 1 (DCL1), an RNase type III endonuclease that processes double stranded RNA to give rise to mature miRNAs 4. The genomes of todays flora contain at least one bona fide copy of DCL1 5,6. Using Marchantia polymorpha -a model bryophyte that allows comparative approaches to infer characteristics of the ancestral land plant-, we demonstrate that MpDCL1a is required for the biogenesis of miRNAs and uncovered a central role for miR166/Homeodomain Zipper Class III-regulated auxin synthesis in the specification of cell identity, patterning, meristem function, laminar expansion and the development of the body in the last common ancestor of extant land plants.

plant biology↗

bioRxiv2023

Characterization of an EG.5.1 clinical isolate in vitro and in vivo

EG.5.1 is a subvariant of the SARS-CoV-2 Omicron XBB variant that is rapidly increasing in prevalence worldwide. EG.5.1 has additional substitutions in its spike protein (namely, Q52H and F456L) compared with XBB.1.5. However, the pathogenicity, transmissibility, and immune evasion properties of clinical isolates of EG.5.1 are largely unknown. In this study, we used wild-type Syrian hamsters to investigate the replicative ability, pathogenicity, and transmissibility of a clinical EG.5.1 isolate. Our data show that there are no obvious differences in growth ability and pathogenicity between EG.5.1 and XBB.1.5, and both EG.5.1 and XBB.1.5 are attenuated compared to a Delta variant isolate. We also found that EG.5.1 is transmitted more efficiently between hamsters compared with XBB.1.5. In addition, unlike XBB.1.5, we detected EG.5.1 virus in the lungs of four of six exposed hamsters, suggesting that the virus tropism of EG.5.1 is different from that of XBB.1.5 after airborne transmission. Finally, we assessed the neutralizing ability of plasma from convalescent individuals and found that the neutralizing activity against EG.5.1 was slightly, but significantly, lower than that against XBB.1.5 or XBB.1.9.2. This suggests that EG.5.1 effectively evades humoral immunity and that the amino acid differences in the S protein of EG.5.1 compared with that of XBB.1.5 or XBB.1.9.2 (i.e., Q52H, R158G, and F456L) alter the antigenicity of EG.5.1. Our data suggest that the increased transmissibility and altered antigenicity of EG.5.1 may be driving its increasing prevalence over XBB.1.5 in the human population.

microbiology↗

bioRxiv2023

Induction of plant disease resistance by mixed oligosaccharide elicitors prepared from plant cell wall and crustacean shells

Basal plant immune responses are activated by the recognition of the conserved pathogen-associated molecular patterns (PAMPs), or breakdown molecules released from plants after damage by pathogen infection, so-called danger-associated molecular patterns (DAMPs). While chitin-oligosaccharide (CHOS), a primary component of the fungal cell wall, is most known as PAMP, plant cell wall-derived oligosaccharides, cello-oligosaccharides (COS) from cellulose and xylo-oligosaccharide (XOS) from hemicellulose, are representative DAMPs, which activate signaling steps similar to PAMP-induced immunity to elicit defenses and provide protection against pathogens. In this study, elicitor activities of COS prepared from cotton linters, XOS prepared from corn cobs as well as chitin-oligosaccharide (CHOS) from crustacean shells were comparatively investigated. In Arabidopsis, treatment of COS, XOS or CHOS triggered typical defense responses such as reactive oxygen species (ROS) production, activation of MAP kinases phosphorylation, callose depositions, and activation of the promoter for defense-related transcription factor WRKY33. When COS, XOS and CHOS were used at concentrations with similar activity in inducing ROS production and callose depositions, CHOS was particularly highly potent in activating the MAPK kinases and WRKY33 promoters. Among the COS and XOS with different degrees of polymerization (DP), cellotriose (DP3) and xylotetraose (DP4) showed the highest activity for the activation of WRKY33 promoter. Simultaneous treatment of COS, XOS and CHOS leads to a strong transcriptional change for defense-related genes, and gene ontology (GO) enrichment analysis of RNAseq data revealed that a mixture of three oligosaccharide (oligo-mix) effectively activate the plants disease resistance. In practice, treatment of the oligo-mix enhanced the resistance of tomato to powdery mildew, but plant growth was not inhibited but rather tended to be promoted, providing evidence that mixed oligosaccharides have beneficial effects on improving disease resistance in plants, making them a promising class of compounds for practical application.

plant biology↗

bioRxiv2023

hnRNPM and ELAVL1 control type I interferon induction by promoting IRF3 phosphorylation downstream of both cGAS and RIG-I

RIG-I and cGAS are crucial sensors of viral nucleic acids and induce type I IFNs via TBK1/IKK and IRF3. Here, we have identified hnRNPM as a novel positive regulator of IRF3 phosphorylation and type I IFN induction downstream of both cGAS and RIG-I. Combining interactome analysis and genome editing, we further identified ELAVL1 as an immune-relevant interactor of hnRNPM. Depletion of hnRNPM or ELAVL1 impaired type I IFN induction by HSV-1 and SeV. In addition, we found that hnRNPM and ELAVL1 interact with TBK1 and NF-kB p65. Confocal microscopy revealed cytosolic and perinuclear interactions between hnRNPM, ELAVL1, and TBK1. To our knowledge, hnRNPM and ELAVL1 represent the first non-redundant signaling components merging the cGAS-STING and RIG-I-MAVS pathways, thus representing a novel platform that fuels antiviral defense.

immunology↗

bioRxiv2023

Ketone-loading as A Novel Sports Nutrition Strategy: Chronic Ketone Supplementation Elicits Further Favorable Metabolic Changes in Keto-adapted Mice

BackgroundA ketogenic diet (KD) induces nutritional ketosis (NS), benefits fatty acid oxidation (FAO), and favors moderate-intensity exercise capacity. The status that the body accommodates to produce and utilize ketone bodies (KB) and fatty acids as primary fuel sources is termed keto-adaptation. However, keto-adaptation requires time, while long-term KD also involves unfavored adverse effects. Exogenous ketone body (EKBs) administration has been introduced to elicit the advantages of NS. However, the direct use of EKBs fails to bring desired outcomes. We hypothesized that EKBs might only be effective during keto-adaptation. MethodsMale C57BL/6J mice (n = 24) were divided into three groups: a control diet (Con, n = 8), a ketogenic diet (KD, n = 8), and a KD plus a ketone body (DL-{beta}-Hydroxybutyric acid sodium salt, BHB) administration (KD+BHB, n = 8). After six weeks of KD administration, mice in the KD+BHB group receive BHB added into water bottles for another six weeks. Blood KB concentration is monitored throughout the experiment, while liver, gastrocnemius, and soleus mRNA are analyzed using RT-PCR. ResultsBoth KD and KD+BHB induced and sustained NS and enhanced hepatic and muscular key genes regulating FAO. In addition, BHB administration upon keto-adaptation further increased circulating KB concentration and enhanced expressional levels of FAO-mediating genes (ACO, HADH, ACADM, and MLYCD in the gastrocnemius muscle; ACO, HADH, and MLYCD in the soleus muscle), and energy-regulating genes (PPARA and PPARG) in the liver and skeletal muscle compared to a KD. ConclusionCompared to KD alone, chronic administration of KBs upon keto-adaptation increased the expression of key genes that favor FAO or maintain energy homeostasis in the liver and skeletal muscle. Instead of directly using EKBs in non-keto-adapted individuals, it is encouraged to use EKBs upon keto-adaptation status to elicit their energy-utilizing effects. HighlightsThis is the first report to evaluate the metabolic effects using exogenous ketone bodies on keto-adapted individuals. Administration of exogenous ketone body upon keto-adaptation furtherly increased circulating ketone bodies. Administration of exogenous ketone body upon keto-adaptation individuals enhanced expression of genes related to fatty acid oxidation and energy hemostasis.

biochemistry↗

bioRxiv2023

Asymmetric patterns of nucleosome positioning sequences in protein-coding regions

Although nucleosome positioning is key to epigenetic regulation, how the DNA sequence contributes to positioning remains elusive, especially in the context of transcription direction. Analysis of nucleotide bases with respect to the nucleosomal DNA coordinates requires precise nucleosomal mapping information on the genome. However, currently available base-pair-resolution nucleosome maps based on cysteine-mediated chemical cleavage do not fully satisfy the requirement due to method-specific cleavage biases. Here, we generated a chimeric nucleosomal DNA model to achieve less-biased prediction. The model revealed that yeast protein-coding sequences have higher affinity for the promoter-proximal half of nucleosomes than for the distal half. Strikingly, peaks of calculated affinity scores for the promoter-proximal half periodically matched the first few nucleosome positions. Detailed analysis of nucleotide bases revealed that the AA dinucleotide in the left side of the top strand contributes to nucleosome detection frequency in intergenic regions, while the complementary dinucleotide TT is preferred in the other side. In contrast, the sense strand is AA-rich throughout the nucleosome coordinate in protein-coding regions, which is consistent with asymmetric affinity. These data suggest that eukaryotes have evolved DNA sequences with asymmetric affinity for nucleosome formation to maintain epigenetic integrity of protein-coding regions.

genomics↗

bioRxiv2022

Inflammatory response induced in pulmonary embolic lung: Evaluation usinga reproducible murine pulmonary embolism model.

BackgroundSince previously established models of pulmonary embolism showed a large variability in the degree of ischemia, it is difficult to assess the pathophysiological response in the lung after embolization. Here, we established a model of pulmonary embolism by certain amount of relatively small thrombi, in which the degree of ischemia was reproducible. MethodsThrombi with a maximum diameter of 100 m or 500 m were administered intravenously under anesthesia, and the survival ratio at 4 hours was evaluated. The location of thrombi in the lung was visualized by administration of fluorescent-labeled thrombus, and the hemodynamics of the lung after administration of thrombi was evaluated. CT angiography was also performed to evaluate the ratio of the embolized vessels. In addition, cytokine mRNAs was quantified 4 hours in embolized lung. Immunohistochemical analysis for interleukin (IL)-6 and CD68 as a marker of macrophages were also performed. ResultsIt was found that mice with 100 m clots, but not with 500 m clots, showed a dose-dependence of survival between 2.3 L/g and 3.0 L/g at 4 hours from embolization induction. In mice treated with 2.5 L/g of 100 m thrombus, thrombi were located in the peripheral region of the lung, which was consistent with the disruption of blood circulation the peripheral region. In addition, about 60% of the vessels with a diameter of less than 100 m were occluded in these mice. In the lungs after 4 hours of embolization, IL-6 mRNA and tumor necrosis factor (TNF)- mRNA were significantly higher and lower than control lungs. IL-6 was expressed in CD68-positive macrophages in both embolized and control lungs after 4 hours of embolization, and the number of each positive cells were comparable in both embolized and control lungs. ConclusionsThese results show that the pulmonary embolization model induced by a certain amount of small thrombus is useful for evaluating the pathological responses in the embolized lung. Furthermore, it was found that IL-6 expression was increased in macrophages in the embolized lung, indicating that inflammatory responses may contribute to the pathogenesis of pulmonary embolism.

pathology↗