Resection of chronic expanding hematoma within the liver cyst difficult to differentiate from liver cystadenocarcinoma: A case report.

Liver cysts are common benign lesions with rare malignancy potential. Distinguishing between benign and malignant tumors within liver cysts is challenging. We present the case of a patient with a chronically expanding hematoma within a liver cyst that was resected under suspicion of liver cystadenocarcinoma. A 73-year-old female patient presented with elevated hepatobiliary enzyme levels, no viral hepatitis, elevated tumor marker levels, and preserved liver capacity (Child-Pugh grade A). Abdominal ultrasonography revealed a large cyst (>10 cm) occupying the right lobe and a 25-mm mass lesion with mixed echogenicity inside the cyst. Contrast-enhanced computed tomography showed atrophy of the parenchyma of the right lobe and dilation of the right intrahepatic bile duct due to the large cyst. Moreover, in the arterial phase, a point-like high-density area was observed inside the nodule, which increased from 25 to 35 mm over 3 months. Diffusion-weighted magnetic resonance imaging revealed a high-intensity signal within the nodule; however, positron emission tomography did not show an increased accumulation of fluorodeoxyglucose in the same area. Considering the risk of peritoneal dissemination if the cyst was punctured and found to be malignant, we performed a right hepatectomy. Pathological findings revealed a brownish fluid-filled cyst containing a dark reddish nodule diffusely filled with hematoma, confirming the absence of a malignancy. To date, the patient has not experienced recurrence. We encountered a case of a chronic, expanding hematoma originating from a liver cyst that was difficult to distinguish preoperatively from a liver cystadenocarcinoma.

Detection of Fibril Nucleation in Micrometer-Sized Protein Condensates and Suppression of Sup35NM Fibril Nucleation by Liquid-Liquid Phase Separation.

Elucidating the link between amyloid fibril formation and liquid-liquid phase separation (LLPS) is crucial in understanding the pathologies of various intractable human diseases. However, the effect of condensed protein droplets generated by LLPS on nucleation (the initial step of amyloid formation) remains unclear because of the lack of available quantitative analysis techniques. This study aimed to develop a measurement method for the amyloid droplet nucleation rate based on image analysis. We developed a method to fix micrometer-sized droplets in gel for long-term observation of protein droplets with known droplet volumes. By combining this method with image analysis, we determined the nucleation dynamics in droplets of a prion disease model protein, Sup35NM, at the single-event level. We found that the nucleation was unexpectedly suppressed by LLPS above the critical concentration (C*) and enhanced below C*. We also revealed that the lag time in the Thioflavin T assay, a semi-quantitative parameter of amyloid nucleation rate, does not necessarily reflect nucleation tendencies in droplets. Our results suggest that LLPS can suppress amyloid nucleation, contrary to the conventional hypothesis that LLPS enhances it. We believe that the proposed quantitative analytical method will provide insights into the role of LLPS from a pathological perspective.

Fluorescence Imaging of Nanoparticle Uptake into Liquid-Liquid Phase-Separated Droplets.

Liquid-liquid phase separation (LLPS) in living cells has received considerable attention in the biomedical research field. This study is the first to report nanoparticle (NP) uptake into LLPS droplets. Fluorescent dye, Nile red loaded polystyrene NPs (NR-PSt NPs) uptake into model LLPS droplets consisting of adenosine triphosphate (ATP) and poly-L-lysine (PLL) was visualized using fluorescence imaging. Fluorescence imaging showed that the LLPS droplets had a quick NP uptake behavior. Furthermore, temperature changes (4-37 °C) significantly affected the NP uptake behavior of the LLPS droplets. Moreover, the NP-incorporated droplets displayed high stability under strong ionic strength conditions (1 M NaCl). ATP measurements displayed that ATP was released from the NP-incorporated droplets, indicating that the weakly negatively charged ATP molecules and strongly negatively charged NPs were exchanged, which resulted in the high stability of the LLPS droplets. These fundamental findings will contribute to the LLPS studies using various NPs.

Phase-Separation Propensity of Non-ionic Amino Acids in Peptide-Based Complex Coacervation Systems.

Uncovering the sequence-encoded molecular grammar that governs the liquid-liquid phase separation (LLPS) of proteins is a crucial issue to understand dynamic compartmentalization in living cells and the emergence of protocells. Here, we present a model LLPS system that is induced by electrostatic interactions between anionic nucleic acids and cationic oligolysine peptides modified with 12 different non-ionic amino acids, with the aim of creating an index of "phase-separation propensity" that represents the contribution of non-ionic amino acids to LLPS. Based on turbidimetric titrations and microscopic observations, the lower critical peptide concentrations where LLPS occurs (Ccrit) were determined for each peptide. A correlation analysis between these values and known amino acid indices unexpectedly showed that eight non-ionic amino acids inhibit the generation of LLPS, whereby the extent of inhibition increases with increasing hydrophobicity of the amino acids. However, three aromatic amino acids deviate from this trend and rather markedly promote LLPS despite their high hydrophobicity. A comparison with double-stranded DNA and polyacrylic acid revealed that this is primarily due to interactions with DNA nucleobases. Our approach to quantify the contribution of non-ionic amino acids can be expected to help to provide a more accurate description and prediction of the LLPS propensity of peptides/proteins.

Validity and Reliability of Criteria for Plantar Sensation Assessment Using Semmes-Weinstein Monofilament as a Clinically Usable Index.

There is no standard clinically adaptable criterion for assessing plantar sensation for pre- and post-intervention comparisons. Studies using Semmes-Weinstein monofilaments (SWMs) to investigate intervention effects on plantar sensation vary in procedure and do not consider measurement errors. This study aimed to develop a simple criterion using SWMs to assess plantar sensation, determine the measurement error range, and identify areas of low error. Six examiners assessed 87 healthy young adults in Experiment 1, while two examiners assessed 10 participants in Experiment 2. Filaments were graded from 1 to 20 based on increasing diameter. The smallest grade that could be perceived for three sequential stimuli was used as the criterion (smallest perceivable grade, SPG). The SPG was significantly smaller at the hallux and larger at the heel than at other sites. There were no significant differences between the SPG of the repeated tests performed by the same versus different examiners. The interquartile range of the differences was <±3 at all sites. Thus, our criteria were reliable in evaluating the effects of plantar sensation interventions, especially at the heel and the middle of the metatarsal heads and could contribute to the development of more effective treatments for plantar sensations.

Quantum yield enhancement of firefly bioluminescence with biomolecular condensates.

The enzymatic luminescence reactions of fireflies are accelerated in the presence of biomolecular condensates comprising a positively charged peptide and ATP. We revealed that this acceleration is caused by the enrichment of reaction elements, local pH changes, and promotion of inhibitory intermediate dissociation, improving the bioluminescence quantum yield by approximately 10%.

Damage-free evaluation of cultured cells based on multivariate analysis with a single-polymer probe.

We present a pattern-recognition-based sensor that targets cell-derived components in culture media and evaluates cultured cells without damaging them. An array sensor made of a single-polymer probe was employed to obtain fluorescence response patterns of the analyte media, allowing successful identification of the type and state of the cells via multivariate analysis.

Polymer-based chemical-nose systems for optical-pattern recognition of gut microbiota.

Gut-microbiota analysis has been recognized as crucial in health management and disease treatment. Metagenomics, a current standard examination method for the gut microbiome, is effective but requires both expertise and significant amounts of general resources. Here, we show highly accessible sensing systems based on the so-called chemical-nose strategy to transduce the characteristics of microbiota into fluorescence patterns. The fluorescence patterns, generated by twelve block copolymers with aggregation-induced emission (AIE) units, were analyzed using pattern-recognition algorithms, which identified 16 intestinal bacterial strains in a way that correlates with their genome-based taxonomic classification. Importantly, the chemical noses classified artificial models of obesity-associated gut microbiota, and further succeeded in detecting sleep disorder in mice through comparative analysis of normal and abnormal mouse gut microbiota. Our techniques thus allow analyzing complex bacterial samples far more quickly, simply, and inexpensively than common metagenome-based methods, which offers a powerful and complementary tool for the practical analysis of the gut microbiome.

A polymer-based chemical tongue for the non-invasive monitoring of osteogenic stem-cell differentiation by pattern recognition of serum-supplemented spent media.

The development of non-invasive techniques to characterize cultured cells is invaluable not only to ensure the reproducibility of cell research, but also for quality assurance of industrial cell products for purposes such as regenerative medicine. Here, we present a polymer-based 'chemical tongue', i.e., a biosensing technique that mimics the human taste system, that is capable of non-invasively generating fluorescence response patterns that reflect the proteins secreted, and also partially consumed, by cultured cells, even from serum-supplemented media containing abundant interferants. Analysis of the spent media collected during cell culture using our chemical tongue, which consists of cationic polymers of different scaffolds appended with environmentally responsive dansyl fluorophores, led to the successful (i) identification of human-derived cell lines, (ii) monitoring of the differentiation process of stem cells, even at the stage when conventional staining was negative, and (iii) detection of cancer-cell contamination in stem cells. Since the characterization of cultured cells is usually performed via invasive methods that result in cell death, our chemical-tongue approach, which is of high practical utility, will offer a new means of addressing the growing demand for highly controlled cell production in the medical and environmental fields.

Tyrphostin AG1024 downregulates aryl hydrocarbon receptor (AhR) expression in an IGF1R and IR-independent manner.

The aryl hydrocarbon receptor (AhR) is a receptor-type transcription factor that is crucial for endocrine disruption and carcinogenesis caused by environment chemicals. Previous studies have indicated that certain intracellular signals are involved in AhR activation by their agonists, but the detailed mechanism remains unclear. In this study, we screened for important molecules for AhR activation using SCAD inhibitor kits. Among 164 kinase inhibitors listed in these kits, tyrphostin AG1024, commonly used as an inhibitor of insulin-like growth factor receptor (IGF1R) and insulin receptor (IR), was identified as a potent inhibitor of 3-methylcholanthrene (MC)-mediated AhR activation. We further investigated the mechanism by which AG1024 suppresses MC-mediated AhR activation. AG1024 decreased AhR-dependent luciferase activity, CYP1A1 gene expression, and its protein expression. However, when IGF1R siRNA and IR siRNA were used, AhR activation was slightly increased, in contrast to AG1024 treatment. In addition, AG1024 treatment downregulated the expression of AhR protein but not AhR gene, and decreased both nucleic and cytosolic AhR proteins. Therefore, AG1024 suppressed AhR activation by downregulating AhR protein expression. The molecular target of AG1024 remains unclear, and should be an important target for the regulation of AhR-dependent toxicity.

Dynamic behavior of liquid droplets with enzyme compartmentalization triggered by sequential glycolytic enzyme reactions.

Dynamic droplet formation via liquid-liquid phase separation (LLPS) is believed to be involved in the regulation of various biological processes. Here, a model LLPS system coupled with a sequential glycolytic enzymatic reaction was developed to reproduce the dynamic control of liquid droplets; (i) the droplets, which consist of poly-L-lysine and nucleotides, compartmentalize two different enzymes (hexokinase and glucose-6-phosphate dehydrogenase) individually, accelerating the overall reaction, and (ii) each enzymatic reaction triggers the formation, dissolution and long-term retention of the droplets by converting the scaffold nucleotides. This model system will offer a new aspect of enzymes associated with LLPS in living cells.

Uncharged Components of Single-Stranded DNA Modulate Liquid-Liquid Phase Separation With Cationic Linker Histone H1.

Liquid-liquid phase separation (LLPS) of proteins and DNAs has been recognized as a fundamental mechanism for the formation of intracellular biomolecular condensates. Here, we show the role of the constituent DNA components, i.e., the phosphate groups, deoxyribose sugars, and nucleobases, in LLPS with a polycationic peptide, linker histone H1, a known key regulator of chromatin condensation. A comparison of the phase behavior of mixtures of H1 and single-stranded DNA-based oligomers in which one or more of the constituent moieties of DNA were removed demonstrated that not only the electrostatic interactions between the anionic phosphate groups of the oligomers and the cationic residues of H1, but also the interactions involving nucleobases and deoxyriboses (i) promoted the generation of spherical liquid droplets via LLPS as well as (ii) increased the density of DNA and decreased its fluidity within the droplets under low-salt conditions. Furthermore, we found the formation of non-spherical assemblies with both mobile and immobile fractions at relatively higher concentrations of H1 for all the oligomers. The roles of the DNA components that promote phase separation and modulate droplet characteristics revealed in this study will facilitate our understanding of the formation processes of the various biomolecular condensates containing nucleic acids, such as chromatin organization.

Alginate-coated activated charcoal enhances fecal excretion of 2,3,7,8-tetrachlorodibenzo-p-dioxin in mice, with fewer side effects than uncoated one.

Activated charcoal (AC) is a potential candidate antidote against dioxins. However, it is difficult to take AC as a supplement on a daily basis, because its long-term ingestion causes side effects such as constipation and deficiency of fat-soluble essential nutrients and hypocholesterolemia. Alginate-coated AC, termed Health Carbon (HC), was developed to decrease the side effects of AC, but its pharmacological effects, including side effects, remains unclear. Here, we show that HC enhanced fecal excretion of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and decreased some side effects of unmodified AC, such as hypocholesterolemia, in male mice. Basal diet mixed with HC or unmodified AC at various concentrations was fed to mice for 16 days following a single intraperitoneal administration of [3H]TCDD. Both HC and unmodified AC at 3% or more significantly increased fecal excretion of [3H]TCDD in comparison with the control basal diet. Consistent with this, [3H]TCDD radioactivity in the liver-a major TCDD storage organ-was markedly decreased by HC at concentrations of 3% and 10%. In an examination of potential side effects, unmodified AC at 10% or more caused significant body weight reduction and at 20% caused significant hypocholesterolemia. In contrast, HC caused weight gain reduction only at a concentration of 20%, and there was no evidence of hypocholesterolemia at any dietary HC concentration. HC not only retains the ability of AC to enhance fecal excretion of TCDD but also reduces some of the side effects of AC.

Quadruplex Folding Promotes the Condensation of Linker Histones and DNAs via Liquid-Liquid Phase Separation.

Liquid-liquid phase separation (LLPS) of proteins and DNA has recently emerged as a possible mechanism underlying the dynamic organization of chromatin. We herein report the role of DNA quadruplex folding in liquid droplet formation via LLPS induced by interactions between DNA and linker histone H1 (H1), a key regulator of chromatin organization. Fluidity measurements inside the droplets, binding assays using G-quadruplex-selective probes, and structural analyses based on circular dichroism demonstrated that quadruplex DNA structures, such as the G-quadruplex and i-motif, promote droplet formation with H1 and decrease molecular motility within droplets. The dissolution of the droplets in the presence of additives and the LLPS of the DNA structural units indicated that, in addition to electrostatic interactions between the DNA and the intrinsically disordered region of H1, π-π stacking between quadruplex DNAs could potentially drive droplet formation, unlike in the electrostatically driven LLPS of duplex DNA and H1. According to phase diagrams of anionic molecules with various conformations, the high LLPS ability associated with quadruplex folding arises from the formation of interfaces consisting of organized planes of guanine bases and the side surfaces with a high charge density. Given that DNA quadruplex structures are well-documented in heterochromatin regions, it is imperative to understand the role of DNA quadruplex folding in the context of intranuclear LLPS.

Affinity Diversification of a Polymer Probe for Pattern-recognition-based Biosensing Using Chemical Additives.

Pattern-recognition-based sensing has attracted attention as a promising alternative to conventional sensing methods that rely on selective recognition. Here, we report on novel strategy using chemical additives with the ability to modulate probe/analyte interactions to more easily construct pattern-recognition-based sensing systems for proteins and cells. The fluorescence of dansyl-modified cationic poly-L-lysine (PLL-Dnc) is enhanced upon binding to proteins in aqueous solution, while the addition of salts, inert polymers, or alcohols modulates the protein/PLL-Dnc interactions via a variety of mechanisms. Subsequent readout of the fluorescence changes produces response patterns that reflect the characteristics of the analytes. Multivariate analysis of the response patterns allowed for accurate identification of not only eight structurally similar albumin homologues, but also four mammalian cells. This strategy, which uses inexpensive and common additives, significantly improves the accessibility of pattern-recognition-based sensing, which will offer new opportunities for the detection of various bioanalytes.

Microfluidic Sensing System with a Multichannel Surface Plasmon Resonance Chip: Damage-Free Characterization of Cells by Pattern Recognition.

The development of a versatile sensing strategy for the damage-free characterization of cultured cells is of great importance for both fundamental biological research and industrial applications. Here, we present a pattern-recognition-based cell-sensing approach using a multichannel surface plasmon resonance (SPR) chip. The chip, in which five cysteine derivatives with different structures are immobilized on Au films, is capable of generating five unique SPR sensorgrams for the cell-secreted molecules that are contained in cell culture media. An automatic statistical program was built to acquire kinetic parameters from the SPR sensorgrams and to select optimal parameters as "pattern information" for subsequent multivariate analysis. Our system rapidly (∼10 min) provides the complex information by merely depositing a small amount of cell culture media (∼25 µL) onto the chip, and the amount of information obtained is comparable to that furnished by a combination of conventional laborious biochemical assays. This noninvasive pattern-recognition-based cell-sensing approach could potentially be employed as a versatile tool for characterizing cells.

A Multichannel Pattern-Recognition-Based Protein Sensor with a Fluorophore-Conjugated Single-Stranded DNA Set.

Recently, pattern-recognition-based protein sensing has received considerable attention because it offers unique opportunities that complement more conventional antibody-based detection methods. Here, we report a multichannel pattern-recognition-based sensor using a set of fluorophore-conjugated single-stranded DNAs (ssDNAs), which can detect various proteins. Three different fluorophore-conjugated ssDNAs were placed into a single microplate well together with a target protein, and the generated optical response pattern that corresponds to each environment-sensitive fluorophore was read via multiple detection channels. Multivariate analysis of the resulting optical response patterns allowed an accurate detection of eight different proteases, indicating that fluorescence signal acquisition from a single compartment containing a mixture of ssDNAs is an effective strategy for the characterization of the target proteins. Additionally, the sensor could identify proteins, which are potential targets for disease diagnosis, in a protease and inhibitor mixture of different composition ratios. As our sensor benefits from simple construction and measurement procedures, and uses accessible materials, it offers a rapid and simple platform for the detection of proteins.

Development of Neutral pH-Responsive Microgels by Tuning Cross-Linking Conditions.

Polymer microgels that respond in a range of neutral pH can be useful for the development of molecular imaging tools and drug-delivery carriers. Here, we describe a simple approach in developing microgels that undergo volume phase transitions and substantial nuclear magnetic resonance (NMR) relaxometric changes within a narrow pH range of 6.4 to 7.4. The pH-responsive microgels were synthesized using methacrylic acid and a series of ethylene glycol dimethacrylate cross-linkers with repeating units of ethylene glycol that range from one to four. NMR relaxometry demonstrated that the transverse relaxation time (T2) of a suspension containing microgels that were cross-linked with diethylene glycol dimethacrylate sharply decreases at the pH where volume phase transition occurs. The polymer microgels cross-linked with 40 and 45 mol% of diethylene glycol dimethacrylate caused about 50% T2 reduction with decreasing pH from 6.8 to 6.4. These results demonstrated that responses of microgels to a range of neutral pH can be easily tuned by using appropriate cross-linkers with certain cross-linking degree. This approach can be useful in developing highly sensitive molecular sensors for magnetic resonance imaging (MRI) of tissue pH values.

Pattern-recognition-based Sensor Arrays for Cell Characterization: From Materials and Data Analyses to Biomedical Applications.

To capture a broader scope of complex biological phenomena, alternatives to conventional sensing based on specificity for cell detection and characterization are needed. Pattern-recognition-based sensing is an analytical method designed to mimic mammalian sensory systems for analyte identification based on the pattern recognition of multivariate data, which are generated using an array of multiple probes that cross-reactively interact with analytes. This sensing approach is significantly different from conventional specific cell sensing based on highly specific probes, including antibodies against biomarkers. Encouraged by the advantages of this technique, such as the simplicity, rapidity, and tunability of the systems without requiring a priori knowledge of biomarkers, numerous sensor arrays have been developed over the past decade and used in a variety of cell sensing applications; these include disease diagnosis, drug discovery, and fundamental research. This review summarizes recent progress in pattern-recognition-based cell sensing, with a particular focus on guidelines for designing materials and arrays, techniques for analyzing response patterns, and applications of sensor systems that are focused primarily for the biomedical field.