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Murata, Y.

Publications and source records attributed to Murata, Y..

At least 19 recordsLinked to original sources

SF3b inhibitors suppress proliferation of nonsmall cell lung cancer cells irrespective of EGFR mutation status

Epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) are standard care for EGFR-mutant non-small cell lung cancer (NSCLC), but acquired resistance limits their durability, and alternatives that do not depend on EGFR kinase activity are needed. We asked whether inhibitors of SF3b, a core component of the U2 small nuclear ribonucleoprotein particle, act on NSCLC cells regardless of EGFR genotype. Three lung adenocarcinoma lines were treated with pladienolide B or herboxidiene at 0.01, 0.1 and 1 uM: PC9 and HCC827, both carrying an EGFR exon 19 deletion and both inhibited by gefitinib at nanomolar concentrations, and A549, which is EGFR wild type and gefitinibin sensitive. Proliferation was followed for three days by crystal violet staining, EGFR intron 2 retention was assayed by RTPCR, and EGFR protein was measured by western blotting. Both compounds produced a concentration-dependent increase in the intron 2 retained product in all three lines, and both held proliferation at or near the day 0 cell number in all three, at concentrations down to 0.01 uM. EGFR protein was lost in PC9, reduced in A549, and only partly reduced in HCC827, where a residual band persisted in lanes whose growth was fully suppressed. Since A549 is EGFR wild-type, and published knockdown data show that removing EGFR does not suppress proliferation of wild-type lines, the growth inhibition cannot be attributed to loss of EGFR alone. We read EGFR intron 2 retention as a marker of target engagement rather than as the mechanism of the growth effect. These are the results of single experiments without replicates or statistical testing and should be read as preliminary.

molecular biology↗

Sodium butyrate inhibits the proliferation of temozolomide-resistant glioblastoma (A172) and lung adenocarcinoma (A549) cells and biphasically regulates EGFR expression

Glioblastoma carries one of the poorest prognoses of any solid tumour, and once resistance to temozolomide (TMZ) emerges there is little left to offer. Because the TMZ response is governed largely by epigenetic silencing of MGMT, histone deacetylase (HDAC) inhibitors are a rational partner for TMZ. We asked whether sodium butyrate (NaB), a short-chain fatty acid produced by the gut microbiota and a class I/IIa HDAC inhibitor, retains activity against TMZ-resistant cells. In A172 glioblastoma and A549 lung adenocarcinoma cells, NaB changed EGFR expression biphasically: EGFR exon 2-5 mRNA was induced at 0.15 mM in A172 and at 0.30 mM in A549, and was suppressed at higher concentrations, with EGFR protein following the same pattern in A172. NaB reduced proliferation of both lines from 0.31 mM in a concentration-dependent manner, more markedly in A172 than in A549. At concentrations that were inactive alone (NaB 0.30 mM, TMZ 3 {micro}M), the combination inhibited proliferation of A172 on day 3 and of A549 on days 2 and 3. TMZ-resistant sublines (A172 rTMZ, A549 rTMZ) established by stepwise exposure showed no response to TMZ 10 {micro}M alone, but NaB at 0.5 and 2.5 mM inhibited their proliferation concentration-dependently. The ratio of combination to TMZ alone was not lower in the resistant sublines than in the parental lines (A172 0.70 vs 0.86; A549 0.49 vs 0.58), indicating that the effect in resistant cells is attributable to NaB itself rather than to restored TMZ sensitivity. Millimolar exposure is the main barrier to translation.

molecular biology↗

Decoy and antisense RNA oligonucleotides targeting the EGFR exon 3 splice site suppress proliferation of A172 glioblastoma cells

Short RNA oligonucleotides directed at the 3' splice site region of EGFR exon 3 reduced the proliferation of A172 glioblastoma cells, while the same oligonucleotides had no detectable effect on A549 lung adenocarcinoma cells. Glioblastoma carries EGFR amplification in roughly a third of IDH-wildtype cases, and the A172 line harbours a tandem duplication in the EGFR tyrosine kinase domain. Because exon definition in human genes depends on RNA-binding proteins that engage exonic sequence near splice sites, we used the SpliceAid database to identify candidate RNA-binding proteins at EGFR exons 2 and 3. Y-box binding protein 1 (YB-1, encoded by YBX1), reported to drive glioblastoma growth through its RNA-binding function, scored highly immediately adjacent to the exon 3 3' splice site. We designed four 2'-modified RNA oligonucleotides carrying a nuclear localisation signal: two antisense oligonucleotides against the exon 3 region (asRNA1, spanning the splice site; asRNA2, downstream of it), a decoy complementary to the asRNA2 target (dRNA2), and a decoy carrying the YB-1 consensus binding sequence (dYB-1). In A172 cells, all four reduced EGFR protein in a single Western blot experiment, and asRNA1, asRNA2 and dRNA2 reduced proliferation relative to scrambled RNA at days 1 to 3; dYB-1 produced a comparable reduction at day 3. None of these effects was seen in A549 cells. YB-1 protein level and subcellular distribution were unchanged by the oligonucleotides, arguing against an indirect route through altered YB-1 abundance. These observations are preliminary. Every experiment reported here was performed once: the proliferation data come from single plates with three wells per group, analysed by Dunnett's test against the scrambled-RNA control, and the Western blot, RT-PCR and immunocytochemistry panels are single runs presented as representative observations. Direct binding of YB-1 to the targeted EGFR sequence has not been demonstrated. We post this work as a preprint so that the design strategy and the initial observations are available while these questions remain open.

molecular biology↗

Cube-based screening identifies a quinoa-derived synthetic microbial community that promotes plant growth and modulates root epidermal responses under salt stress

Plant-associated bacteria can improve plant performance under abiotic stress, but beneficial functions in plant microbiomes may depend on defined combinations of microorganisms rather than individual isolates alone. Here, we developed a cube-based screening strategy to identify functional synthetic microbial communities (SynComs) from 135 quinoa-associated bacterial isolates while preserving combinatorial diversity and traceability of isolate-level contributions. The isolates were divided into five 27-isolate sets, each arranged as a 3 x 3 x 3 cube in which each 3 x 3 layer was defined as a 9-isolate SynCom, generating 45 SynComs in total. Screening under 100 mM NaCl identified SynCom DY1 (SCDY1) as a candidate salt stress-mitigating consortium. SCDY1 consisted of nine taxonomically diverse isolates and exhibited a multifunctional profile, including siderophore production, phosphate solubilization, carboxymethyl cellulose degradation, indole compound production, and growth under saline conditions. In Arabidopsis thaliana, SCDY1 promoted primary root elongation and biomass accumulation in a salinity-dependent manner, with the clearest effect under 120 mM NaCl, and at least a subset of constituent bacteria was recoverable from inoculated seedlings. RNA sequencing and targeted RT-qPCR indicated that SCDY1 modulated host gene expression under moderate salinity stress, with responsive genes associated with oxidative stress, water- and oxygen-related processes, phenylpropanoid biosynthesis, glutathione metabolism, and root epidermis-related processes. Root hair phenotyping further showed that SCDY1 enhanced root hair-related traits and shifted visible root hair formation closer to the root apex. These findings identify a quinoa-derived SynCom that improves plant performance under salinity stress and provide a practical, traceable framework for discovering beneficial microbial consortia from plant-associated bacterial collections. Scope statementThis manuscript fits the Research Topic "Harnessing Plant Microbiomes for Climate Resilience: From Ecological Insight to Synthetic Community Design" in Frontiers in Plant Science because it presents a traceable strategy for discovering functional synthetic microbial communities from a stress-adapted plant-associated bacterial collection. We developed a cube-based screening strategy using 135 quinoa-associated bacterial isolates and identified a nine-isolate synthetic microbial community, SCDY1, that promotes Arabidopsis growth under moderate salinity stress. The study integrates microbiological screening, characterization of plant growth-promoting traits, bacterial re-isolation, plant growth phenotyping, RNA-seq, RT-qPCR, and root hair phenotyping. These analyses link SCDY1 treatment to salinity-dependent growth promotion, recoverable bacterial members, stress- and redox-associated transcriptional changes, phenylpropanoid-related responses, and modulation of root epidermal phenotypes. By connecting a defined SynCom with host transcriptional and root epidermal responses, this work advances understanding of beneficial plant-microbe interactions under salt stress. The cube-based design also provides a practical and traceable framework for discovering functional SynComs from large plant-associated bacterial collections, which should be of interest to researchers studying plant symbiosis, microbiome engineering, abiotic stress tolerance, and sustainable crop improvement.

plant biology↗

A quinoa-associated Pantoea isolate displays salinity-responsive auxin production and promotes plant growth under salt stress

Plant-associated bacteria can promote plant growth under saline conditions, but salinity-dependent changes in bacterial physiological traits remain insufficiently understood. Here, we isolated bacteria from seedlings of quinoa (Chenopodium quinoa Willd.) lines maintained under laboratory propagation for more than 30 years and evaluated their activity under saline conditions. A quinoa-associated Pantoea isolate, strain 6PN, promoted primary root elongation and whole-plant dry weight of Arabidopsis thaliana under salt stress, whereas no significant effect was observed under non-saline conditions. Comparative analyses with reference Pantoea agglomerans strains showed that strain 6PN exhibited salinity-responsive indole-3-acetic acid (IAA) production. Genome analysis identified a putative ipdC gene and additional genes related to stress responses, nutrient acquisition, polysaccharide biosynthesis and export, flagellar biosynthesis, and chemotaxis. Phylogenomic analysis indicated that strain 6PN was genomically distinct from representative Pantoea species examined here. In an Arabidopsis trench-plate assay, GFP-labeled strain 6PN was recovered from spatially separated plant tissues at higher levels than a GFP-labeled reference strain under saline conditions. These results identify strain 6PN as a quinoa-associated Pantoea isolate with salinity-responsive IAA production and plant growth-promoting activity under defined salt-stress conditions.

plant biology↗

A region-specific murine intestinal monolayer platform for assessing iron form-dependent transepithelial transport

Iron absorption in the small intestine has classically been described by the duodenal DMT1/FPN1 pathway for inorganic non-heme iron, yet emerging evidence suggests that chemically distinct iron forms may use region-specific routes. Nicotianamine (NA), a plant-derived metal chelator, can form NA-iron (NA-Fe) complexes and has been proposed to support intestinal iron absorption through amino acid transporter pathways. However, direct comparisons of transepithelial transfer of inorganic iron and NA-Fe across defined small intestinal regions under controlled epithelial conditions remain limited. Here, we established region-specific 2D epithelial monolayers derived from duodenal and proximal jejunal crypt organoids from male ICR mice cultured on Transwell inserts. Transcriptomic profiling indicated partial retention of regional identity, and barrier integrity was confirmed by junctional marker localization, transepithelial electrical resistance, and low paracellular permeability. We then examined expression and polarized localization of candidate transporters for inorganic iron (Dmt1/Fpn1) and NA-Fe (Pat1/Lat2). Finally, we quantified transepithelial transport using apical loading of isotope-labeled iron (55Fe) or NA-55Fe and measured radioactivity appearing in the basolateral compartment as the primary readout of transepithelial flux. Basolateral appearance of inorganic 55Fe was comparable between duodenum- and proximal jejunum-derived monolayers, whereas NA-55Fe exhibited significantly greater basolateral appearance in proximal jejunum-derived monolayers. These findings demonstrate that organoid derived, region-specific monolayers provide a tractable epithelial platform to evaluate iron form-dependent, region-specific transepithelial transfer and to enable further mechanistic dissection of NA-Fe transport. NEW & NOTEWORTHYNon-heme iron absorption may depend on iron chemical form and intestinal region, but direct epithelial comparisons are scarce. We established duodenum and proximal jejunum derived murine intestinal organoid monolayers on Transwells and quantified transepithelial flux using isotope-labeled iron. Inorganic 55Fe showed no clear regional difference, whereas NA-55Fe displayed greater basolateral appearance in proximal jejunum-derived monolayers. This platform enables mechanistic studies of NA-iron complex transport.

physiology↗

OpenCafeMol with 3SPN.2 DNA model: GPU Acceleration for Long-Time Coarse-Grained Chromatin Simulations

There is a growing demand for molecular dynamics simulations to explore longer timescale behavior of giant protein-DNA complexes such as chromatin. To address this need, we extended OpenCafeMol, a GPU-accelerated residue-level coarse-grained molecular dynamics simulator originally developed for proteins and lipids, to support 3SPN.2 and 3SPN.2C DNA models. We also implemented a hydrogen-bond-type many-body potential to model DNA-protein interactions more accurately. To further improve computational efficiency, we introduced a localized scheme for calculating base-pairing and cross-stacking interactions. Benchmark tests show that OpenCafeMol on a single GPU achieves up to 200-fold speed-up for DNA-only systems and up to 100-fold speed-up for DNA-protein complexes compared to CPU-based simulations. To demonstrate the capability of our implementation for long-timescale biological processes, we simulated an archaeal SMC-ScpA complex undergoing DNA translocation via segment capture (a proposed mechanism for DNA loop extrusion) in the presence of a DNA-bound obstacle. We observed continuous captured-loop growth accompanied by obstacle bypass within the segment capture framework.

biophysics↗

Natural variation in IBF1 disrupts its interaction with CHS1 and affects metabolism of hulls in rice

Secondary metabolites in plants have various physiological functions, including antioxidant and antibacterial activities. Previous studies have suggested genes and associated molecular mechanisms involved in the production of diverse secondary metabolites. However, much less is known about the genetic bases underlying within-species diversity in metabolite accumulation patterns, particularly in less focused tissues such as rice hulls. In this study, we aimed to identify the causal variant that affects flavonoid accumulation in rice hulls. We identified an F-box containing protein IBF1 is causal for genotypic differences in hull color through positional cloning. The variety IR64, with straw-white hulls, harbors functional IBF1 proteins that interact with a chalcone synthase, CHS1. Conversely, frame-shift mutations of IBF1 in the variety DJ123, which has pigmented hull color, resulted in a lack of a Kelch domain essential for the IBF1-CHS1 interaction. As a result, the DJ123 variant of IBF1 (IBF1DJ123) no longer interacted with CHS1, which was further supported by deep learning-based protein structural modeling. Further metabolome and transcriptome analyses using IR64 and an IR64-based chromosomal segment substitution line (CSSL) carrying IBF1DJ123 revealed an increase in the content of multiple flavonoids (such as naringenin and luteolin), while suppressing the expression of CAD involved in lignin synthesis. Metabolites in the CSSL carrying IBF1DJ123 suppressed the growth and siderophore generation activity of Pantoea species, which can act as beneficial or pathogenic endophytes. This study highlights the impact of a single gene on diverse metabolite accumulation patterns and suggests that this change may provide defense against pathogens.

plant biology↗

Mechanistic models of asymmetric hand-over-hand translocation and nucleosome navigation by CMG helicase

Faithful replication of eukaryotic chromatin requires the CMG helicase to translocate directionally along single-stranded DNA (ssDNA) while unwinding double-stranded DNA (dsDNA) and navigating nucleosomes. However, the mechanism by which CMG achieves processive translocation and deals with nucleosomal barriers remains incompletely understood. Here, using coarse-grained molecular dynamics simulations with ATP-driven conformational switching, we showed that asymmetric rotational transitions among four distinct ssDNA-binding states enable CMG to achieve directional translocation and DNA unwinding. We further demonstrated that the fork protection complex (Csm3/Tof1) and RPA enhance processivity through distinct mechanisms: Csm3/Tof1 grips the parental duplex to suppress backtracking, while RPA alleviates lagging-strand clogging. Upon nucleosome encounter, Csm3/Tof1 promoted partial unwrapping of the entry DNA, but further progression was energetically restricted near the nucleosomal dyad. The histone chaperone FACT lowered this barrier and simultaneously prevented inappropriate histone transfer to the lagging strand. Our results provide mechanistic insights into how the eukaryotic replisome coordinates helicase activity, nucleosome navigation, histone chaperon function, and histone recycling during eukaryotic DNA replication.

biophysics↗

OpenCafeMol: A GPU-accelerated coarse-grained biomoleculardynamics simulator with OpenMM library

There has been an increasing demand for longer-timescale molecular dynamics (MD) simulations of larger biomolecular systems. To meet these demands, using the C++ API of OpenMM, we developed a fast and flexible MD software, OpenCafeMol, for residue-resolution protein and lipid models that shows high performance on graphics processing unit (GPU) machines. We validated OpenCafeMol for folding small proteins, lipid membrane dynamics, and membrane protein structures. Benchmark tests of the computation times showed that OpenCafeMol with one GPU for proteins and lipid membranes can be approximately 100 and 240 times faster than the corresponding simulations on a typical CPU machine (eight cores), respectively. Taking advantage of the high speed of OpenCafeMol, we applied it to two sets of vesicle fusion simulations; one driven by force and the other coupled with conformational dynamics of a SNARE complex. In the latter, a direct MD simulation at a high temperature resulted in vesicle docking, pore formation followed by fusion, which are coupled with local folding of linkers in the SNARE complex. This opens up new avenue to study membrane-fusion mechanisms via MD simulations. The source code for OpenCafeMol is fully available.

biophysics↗

Involvement of orexin nerves in early stage of Alzheimer's disease model mice and preventive effect of orexin receptor antagonists

BackgroundMild cognitive impairment (MCI) is a condition between healthy cognition and dementia with a high probability of progression to Alzheimers disease (AD). Elevated levels of orexin (OX) have been reported in the cerebrospinal fluid of patients with MCI and AD. ObjectiveTo investigate the efficacy of dual OX receptor antagonists (suvorexant and lemborexant) in an early-stage AD mouse model (App-KI). MethodsThe expression of the OX receptor gene, the levels of suvorexant and lemborexant in the brain after a single oral dose, and their effects on locomotor activity were investigated in wild-type mice. In addition, the cognitive function of wild-type and App-KI mice was assessed using the Y-maze test after oral administration of suvorexant or lemborexant once a day for 60 d. After the behavioral test, amyloid-beta levels were quantified in the hippocampal CA1 region of App-KI mice. ResultsThe expression of the OX receptor gene was highest in the lateral hypothalamus and was also observed in other brain regions. Drug levels peaked at 20-40 min for suvorexant and 15 min for lemborexant and declined, still detectable 24 h later. Locomotor activity was reduced after suvorexant or lemborexant administration; however, 24 h after administration, locomotor activity did not differ from the control group. In particular, the Y-maze test showed that suvorexant and lemborexant prevented cognitive impairment in App-KI mice. Furthermore, suvorexant and lemborexant suppressed amyloid-beta accumulation in the hippocampal CA1 region of App-KI mice. ConclusionThe results suggest that suvorexant and lemborexant effectively suppress the early stages of AD.

animal behavior and cognition↗

CqHKT1 and CqSOS1 mediate genotype-dependent Na+ exclusion under high salt stress in quinoa

Salinity threatens crop production worldwide, and salinized areas are steadily increasing. As most crops are sensitive to salt, there is a need to improve the salt tolerance of major crops and promote the cultivation of under-utilized salt-tolerant crops. Quinoa, a pseudocereal and leafy vegetable from the Andean region of South America, is highly salt-tolerant, thrives in marginal environments, and has excellent nutritional properties. Research has often focused on epidermal bladder cells, a feature of quinoa thought to contribute to salt tolerance; however recent evidence suggests that these cells are not directly involved. The salt tolerance mechanism in quinoa remains unclear. Here, we show genotype-dependent differences in Na+ and K+ accumulation mechanisms using representative 18 lines of three genotypes by focusing on young quinoa seedlings at a stage without epidermal bladder cells. High salinity (600 mM NaCl) did not affect the early growth of all three quinoa genotypes. Under high salinity, lowland quinoa lines accumulated the most Na+ in the aerial parts, whereas southern highland lines accumulated the least. By contrast, K+ accumulation was slightly reduced in the aerial parts but significantly decreased in roots of all the genotypes. Resequencing of 18 quinoa lines supports the notion that genotype determines aboveground Na+ uptake and gene expression in response to salt stress. Using virus-induced gene silencing, we further demonstrated that CqHKT1 and CqSOS1 mediate Na+ exclusion in quinoa. These findings provide insight into salt tolerance mechanisms, serving as a basis for improving crop production under salt stress.

plant biology↗

Compromised actin dynamics underlie the orofacial cleft in Baraitser-Winter Cerebrofrontofacial Syndrome with a variant in ACTB

Craniofacial anomalies encompassing the orofacial cleft are associated with >30% of systemic congenital malformations. Baraitser-Winter Cerebrofrontofacial syndrome (BWCFF) is a rare genetic disorder attributed to variants in the actin beta (ACTB) or actin gamma genes that are correlated with a range of craniofacial abnormalities, including cleft lip and/or palate. The underlying pathological mechanism of BWCFF remains elusive, and it is necessary to investigate the etiology of orofacial clefts in BWCFF. In this study, we identified a missense variant (c.1043C>T: p.S348L) in the ACTB gene from a patient with BWCFF and concomitant cleft lip and palate. Furthermore, we performed functional assessments of this variant using various disease models such as the MDCK cell line and Xenopus laevis. These models revealed a compromised capacity of mutated ACTB to localize at the epithelial junction, consequently affecting the behavior of epithelial cells. Additionally, we made the noteworthy discovery that mutated ACTB exhibited an impaired ability to bind PROFILIN1, a critical factor in actin polymerization. This defective ability may contribute to the molecular etiology of aberrant epithelial cell adhesion and migration, resulting in orofacial cleft formation in BWCFF. Author SummaryAdvances in clinical sequencing have rapidly elucidated the genetic basis of rare diseases affecting multiple organs. In this study, we investigate the role of a variant in the ACTB gene, which is fundamental to cell structure, in causing orofacial clefts in the Baraitser-Winter Cerebrofrontofacial Syndrome (BWCFF), known for its distinctive facial anomalies. Using epithelial cell lines and frog embryo models, we investigated the effects of the ACTB gene alteration on cellular functions. Our results indicate that this genetic change disrupts the normal adhesion and movement of epithelial cells, processes that are critical for facial development. This research underscores the importance of the ACTB gene in shaping the face and suggests new directions for future research, potentially informing the diagnosis and treatment of BWCFF and related conditions.

genetics↗

Patient phenotypes and their relation to TNFα signaling and immune cell composition in critical illness and autoimmune disease

RationaleTNF inhibitors have shown promise in reducing mortality in hospitalized COVID-19 patients; one hypothesis explaining the limited clinical efficacy is patient heterogeneity in the TNF pathway. MethodsWe evaluated the effect of TNF inhibitors in a mouse model of LPS-induced acute lung injury. Using machine learning we attempted predictive enrichment of TNF signaling in patients with either ARDS or sepsis. We examined biological factors that drive heterogeneity in host responses to critical infection and their relation to clinical outcomes. ResultsIn mice, LPS induced TNF-dependent neutrophilia, alveolar permeability and endothelial injury. In humans, TNF pathway activation was significantly increased in peripheral blood of patients with critical illnesses and associated with the presence of mature neutrophils across critical illnesses and several autoimmune conditions. Machine learning using a gene signature separated patients into 5 phenotypes; one was a hyper-inflammatory, interferon-associated phenotype enriched for increased TNF pathway activation and conserved across critical illnesses and autoimmune diseases. Cell subset profiles segregated severely ill patients into neutrophil-subset-dependent groups that were enriched for disease severity, demonstrating the importance of neutrophils in the immune response in critical illness. ConclusionsTNF signaling and mature neutrophils are associated with a hyper-inflammatory phenotype of patients, shared across critical illness and autoimmune disease. This phenotyping provides a personalized medicine hypothesis to test anti-TNF therapy in severe respiratory illness. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=103 SRC="FIGDIR/small/564631v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@1e25724org.highwire.dtl.DTLVardef@c708bcorg.highwire.dtl.DTLVardef@10e7531org.highwire.dtl.DTLVardef@3014b8_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

Coordinated regulation of gene expression in Plasmodium female gametocytes by two transcription factors

Gametocytes play key roles in the Plasmodium lifecycle. They are essential for sexual reproduction as precursors of the gametes. They also play an essential role in parasite transmission to mosquitoes. Elucidation of the gene regulation at this stage is essential for understanding these two processes at the molecular level and for developing new strategies to break the parasite life cycle. We identified a novel Plasmodium transcription factor (TF), designated as a partner of AP2-FG or PFG. In this paper, we report that this TF regulates the gene expression in female gametocytes in concert with another female-specific TF AP2-FG. Upon the disruption of PFG, majority of female-specific genes were significantly downregulated, and female gametocyte lost the ability to produce ookinetes. ChIP-seq analysis showed that it was located in the same position as AP2-FG, indicating that these two TFs form a complex. ChIP-seq analysis of PFG in AP2-FG-disrupted parasites and ChIP-seq analysis of AP2-FG in PFG-disrupted parasites demonstrated that PFG mediates the binding of AP2-FG to the ten-base motif and that AP2-FG binds another motif, GCTCA, in the absence of PFG. In promoter assays, this five-base motif was identified as another female-specific cis-acting element. Genes under the control of the two forms of AP2-FG, with or without PFG, partly overlapped; however, each form had target preferences. These results suggested that combinations of these two forms generate various expression patterns among the extensive genes expressed in female gametocytes.

microbiology↗

Pooled CRISPR screening of high-content cellular phenotypes by ghost cytometry

Fast enrichment of cells based on morphological information remains a challenge, limiting genome-wide perturbation screening for diverse high-content phenotypes of cells. Here we show that multi-modal ghost cytometry-based cell sorting is applicable to fast pooled CRISPR screening for both fluorescence and label-free high-content phenotypes of millions of cells. By employing the high-content cell sorter in the fluorescence mode, we enabled the genome-wide CRISPR screening of genes that affect NF-{kappa}B nuclear translocation. Furthermore, by employing the multi-parametric, label-free mode, we performed the large-scale screening to identify a gene involved in macrophage polarization. Especially the label-free platform can enrich target phenotypes without invasive staining, preserving untouched cells for downstream assays and unlocking the potential to screen for the cellular phenotypes even when suitable markers are lacking. One-Sentence SummaryMachine vision-based cell sorter enabled genome-wide perturbation screens for high-content cell phenotypes even without labeling

cell biology↗

The stoichiometric interaction model for mesoscopic molecular dynamics simulations of liquid-liquid phase separation

Liquid-liquid phase separation (LLPS) has received considerable attention in recent years for explaining the formation of cellular biomolecular condensates. The fluidity and the complexity of their components make molecular simulation approaches indispensable for gaining structural insights. Domain-resolution mesoscopic model simulations have been explored for case in which condensates are formed by multivalent proteins with tandem domains. One problem with this approach is that interdomain pairwise interactions cannot regulate the valency of the binding domains. To overcome this problem, we propose a new potential, the stoichiometric interaction (SI) potential. First, we verified that the SI potential maintained the valency of the interacting domains for the test systems. We then examined a well-studied LLPS model system containing tandem repeats of SH3 domains and proline-rich motifs. We found that the SI potential alone cannot reproduce the phase diagram of LLPS quantitatively. We had to combine the SI and a pairwise interaction; the former and the latter represent the specific and non-specific interactions, respectively. Biomolecular condensates with the mixed SI and pairwise interaction exhibited fluidity, whereas those with the pairwise interaction alone showed no detectable diffusion. We also compared the phase diagrams of the systems containing different numbers of tandem domains with those obtained from the experiments, and found quantitative agreement in all but one case. SIGNIFICANCECells organize their interior structures as not only membrane-bound organelles but also as membrane-less organelles. Membrane-less organelles, such as stress granules, Cajal bodies, and postsynaptic density, are biomolecular condensates in which many biomolecules are gathered owing to their interactions. In some cases, biomolecular condensates are formed by tandemly connected multidomain proteins. In such cases, a mesoscopic simulation model representing each domain as a particle is effective; however, the problem with this approach is that a domain-domain pairwise interaction cannot regulate the well-defined valency. To overcome this problem, in this study, we have developed a new potential, viz. the stoichiometric interaction potential, and confirmed that this potential can reproduce the liquid-liquid phase separation of multidomain proteins, a hallmark of the membrane-less organelles.

biophysics↗

Inter-breeder differences in prepulse inhibition deficits of C57BL/6J mice in a maternal infection model for schizophrenia

Genetic and environmental factors interact with each other to influence the risk of various psychiatric diseases; however, the intensity and nature of their interactions remain to be elucidated. We used a maternal infection model using polyinosinic-polycytidylic acid (Poly(I:C)) to determine the relationship between the maternal breeding environment and behavioral changes in the offspring. We purchased pregnant C57BL/6J mice from three breeders and administered Poly(I:C) (2 mg/kg) intravenously in their tail vein on gestation day 15. The offspring were raised to 8-12 weeks old and subjected to the acoustic startle tests to measure their startle response intensity, prepulse inhibition levels, and degree of the adaptation of the startle response. No statistical interaction between Poly(I:C) administration and sex was observed for prepulse inhibition; thus, male and female mice were analyzed together. The Poly(I:C) challenge significantly decreased prepulse inhibition levels of the offspring born to the pregnant dams from Breeder A but not those from the other breeders. However, there were no significant inter-breeder differences in Poly(I:C) effects on startle response and on startle adaptation. The rearing environment of mouse dams has a prominent impact on the Poly(I:C)-induced prepulse inhibition deficits in this maternal infection model.

neuroscience↗