Biology subjects

Yamaguchi, T.

Publications and source records attributed to Yamaguchi, T..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Cyanogenic millipede genome illuminates convergent evolution of cyanogenesis-related enzymes

Hydrogen cyanide (HCN) is a highly toxic biogenic compound. Unlike most natural defensive chemicals, which are typically lineage-specific, the biosynthesis and liberation of HCN, called "cyanogenesis", occur sporadically among arthropod and plant lineages. This suggests that cyanogenesis has evolved independently numerous times in the animal and plant kingdoms. Although cyanogenesis was identified in millipedes 140 years ago, the cyanogenesis-related enzymes in these arthropods remain unknown. Here, we report a complete set of cyanogenesis-related enzymes in the millipede Chamberlinius hualienensis based on an analysis combining genome sequencing and biological characterisation. The gene encoding hydroxynitrile lyase, which catalyses the liberation of HCN from (R)-mandelonitrile, and its paralogous genes were clustered, indicating sequential duplication of their coding genes, giving rise to hydroxynitrile lyase in millipedes. We discovered that (R)-mandelonitrile biosynthesis in C. hualienensis utilises a flavin-dependent monooxygenase (ChuaMOxS) for the initial aldoxime synthesis step, similar to the process in ferns, instead of cytochrome P450 (CYP) as in higher plants and insects. Furthermore, although a single CYP is responsible for converting aldoxime into cyanohydrin in plants and insects, the reaction involves two enzymes in millipedes. We found two CYPs (CYP4GL4 and CYP30008A2) that catalyse aldoxime dehydration to produce nitrile, in addition to CYP3201B1, which catalyses the formation of (R)-mandelonitrile from nitrile. The discovery of cyanogenesis-related enzymes in millipedes demonstrates that cyanogenic millipedes evolved these enzymes independently from plants and insects. Significance StatementThe biosynthesis of natural defensive chemicals is usually lineage-specific; however, cyanogenesis (hydrogen cyanide biosynthesis) occurs sporadically among animal and plant lineages. This suggests that the cyanogenesis pathway has arisen numerous times in different kingdoms; however, examples of the independent evolution of the entire pathway are rare. Based on genome sequencing analysis, we report a set of cyanogenesis-related enzymes in the millipede Chamberlinius hualienensis. Our findings demonstrate that cyanogenic millipedes evolved independently from plants and insects, providing a deeper understanding of the mechanisms underlying the evolution of metabolic pathways.

biochemistry↗

bioRxiv2025

Photoperiod decoder 1 regulates seasonal changes in energy metabolism through the growth hormone signaling pathway

Seasonal changes in metabolism are crucial for animals to adapt to annual environmental fluctuations. However, the molecular mechanisms underlying these adaptations remain poorly understood. Here, we identified a novel gene, photoperiod decoder 1 (phod1), which exhibits a unique bimodal expression pattern under long-day conditions in Japanese medaka fish (Oryzias latipes). While phod1 is conserved across many vertebrates, except for eutherians, its function remained unknown. Single-cell RNA sequencing analysis revealed that phod1 is predominantly expressed in specific pituitary cells that co-express opsin and circadian clock genes. Transcriptomic analysis using phod1 knockout fish demonstrated that phod1 is essential for photoperiodic regulation of growth hormone. Furthermore, transcriptomic and metabolomic analyses of the liver, the primary target of growth hormone, revealed significant alterations in energy metabolism. Behavioral analysis also showed that phod1 knockout fish exhibited significantly reduced locomotor activity. These findings indicate that phod1 plays a crucial role in seasonal metabolic adaptation through modulation of the growth hormone signaling pathway.

physiology↗

bioRxiv2025

Structural insights into heterohexameric assembly of epilepsy-related ligand-receptor complex LGI1-ADAM22

Leucine-rich glioma-inactivated 1 protein (LGI1) is a secreted neuronal protein consisting of the N-terminal leucine-rich repeat (LRR) and C-terminal epitempin repeat (EPTP) domains. LGI1 is linked to epilepsy, a neurological disorder that can be caused by genetic mutations of genes regulating neuronal excitability (e.g., voltage- or ligand-gated ion channels). ADAM22 is a membrane receptor that binds to LGI1 extracellularly and interacts with AMPA-type glutamate receptors via PSD-95 intracellularly to maintain normal synaptic signal transmission. Structural analysis of the LGI1-ADAM22 complex is important for understanding the molecular mechanism of epileptogenesis and developing new therapies against epilepsy. We previously reported the crystal structure of a 2:2 complex consisting of two molecules of LGI1 and two molecules of the ADAM22 ectodomain (ECD), which is suggested to bridge neurons across the synaptic cleft. On the other hand, multiangle light scattering, small-angle X-ray scattering, and cryo-EM analyses have suggested the existence of a 3:3 complex consisting of three molecules of LGI1 and three molecules of ADAM22. In the previous cryo-EM analysis, many observed particles were in a dissociated state, making it difficult to determine the three-dimensional (3D) structure of the 3:3 complex. In this study, we stabilized the 3:3 LGI1-ADAM22ECD complex using chemical crosslinking and determined the cryo-EM structures of the LGI1LRR-LGI1EPTP- ADAM22ECD and 3:3 LGI1-ADAM22ECD complexes at 2.78 [A] and 3.79 [A] resolutions, respectively. Furthermore, high-speed atomic force microscopy (HS-AFM) visualized the structural features and flexibility of the 3:3 LGI1-ADAM22ECD complex in solution. We discuss new insights into the interaction modes of the LGI1-ADAM22 higher-order complex and the structural properties of the 3:3 LGI1-ADAM22 complex. SignificanceThe neuronal secretory protein Leucine-rich glioma-inactivated 1 (LGI1) and its receptor protein ADAM22 play a critical role in maintaining normal synaptic signal transmission. Genetic mutations in LGI1 are linked to epilepsy. Structural analysis of the LGI1-ADAM22 complex is crucial for understanding the molecular mechanisms of epileptogenesis and for developing targeted treatments. In this study, we determined the cryo-EM structure of the heterohexameric LGI1-ADAM22 complex and visualized the dynamics of this complex by high-speed atomic force microscopy.

biochemistry↗

bioRxiv2024

Cnot4 heterozygosity attenuates high fat diet-induced obesity in mice and impairs PPARγ-mediated adipocyte differentiation.

Adipocyte differentiation is crucial for formation and expansion of white adipose tissue and is also associated with the pathologies of obesity. CNOT4 is an E3 ubiquitin ligase and also contains RNA binding domain. In mammals CNOT4 has been suggested to interact with CCR4-NOT complex, a major executor of mRNA poly(A) shortening. While several subunits within the CCR4-NOT complex were shown to be involved in obesity and energy metabolism, the roles of CNOT4 in obesity remain unexplored. In this study, we generated and analyzed Cnot4 knockout mice and found that Cnot4 heterozygous (Cnot4 Het) mice exhibit resistance to high fat diet-induced obesity, including significant reduction in adipose tissue mass and hepatic lipid depots. However, Cnot4 Het did not affect mRNA expression of metabolic genes as well as serum lipid levels or glucose tolerance. Mechanistically, Cnot4 Het fibroblasts significantly reduced the capability of differentiation into adipocytes and down-regulated adipogenic gene expression compared to wild type fibroblasts. Heterozygous deletion of Cnot4 down-regulated the transcriptional activity of PPAR{gamma}, thereby suppressing up-regulation of adipocyte marker gene expression in response to rosiglitazone, a PPAR{gamma} agonist. These results suggest that CNOT4 mediates adipocyte differentiation during formation and growth of adipose tissue partly through positively regulating transcriptional activity of PPAR{gamma}.

biophysics↗

bioRxiv2024

Identifying Genetic Variations in emm89 Streptococcus pyogenes Linked to Severe Invasive Infections

Streptococcus pyogenes causes mild human infections as well as life-threatening invasive diseases. Since the mutations known to enhance virulence to date account for only half of the severe invasive infections, additional mechanisms/mutations need to be identified. Here, we conducted a genome-wide association study of emm89 S. pyogenes strains to comprehensively identify pathology-related bacterial genetic factors (SNPs, indels, genes, or k-mers). Japanese (n=311) and global (n=666) cohort studies of strains isolated from invasive or non-invasive infections revealed 17 and 1,075 SNPs/indels and 2 and 169 genes, respectively, that displayed associations with invasiveness. We validated one of them, a non-invasiveness-related point mutation, fhuB T218C, by structure predictions and introducing it into a severe invasive strain and confirmed that the mutant showed slower growth in human blood. Thus, we report novel mechanisms that convert emm89 S. pyogenes to an invasive phenotype and a platform for establishing novel treatments and prevention strategies.

microbiology↗

bioRxiv2024

Comparative metagenomic analysis provides novel insights into the ecophysiology of Myxococcota in activated sludge systems

Myxobacteria, belonging to the phylum Myxococcota, are ubiquitous in soil, marine, and other environments. Recent metagenomic sequencing analysis has shown that Myxococcota are predominant in activated sludge systems; however, their ecophysiological traits remain unclear. In this study, we evaluated the potential biological functions of 46 metagenomic bins of Myxococcota reconstructed from activated sludge samples from four municipal sewage treatment plants. The results showed that most Myxococcota bins had an almost complete set of genes associated with glycolysis and the TCA cycle. Palsa-1104 and Polyangiales bins contain glycoside hydrolase GH13 and peptidase M23, which are presumably involved in the lysis of the cell wall and cellular cytoplasm, indicating that part of the Myxococcota from activated sludge can prey on other microorganisms. The previously known cell contact-dependent predatory functions of Myxococcus xanthus are conserved in the family Myxococcaceae, though not in other families. Two bins belonging to Palsa-1104 had phototrophic gene clusters, suggesting that these bins may have both heterotrophic and autotrophic metabolisms. Assessment of the social behavior of the activated sludge Myxococcota, a FruA gene, and a C-signal gene involved in the regulation of fruiting body formation were lacking in Myxococcota bins, suggesting that they are incapable of fruiting body formation. In addition, multiple bins of Myxococcota had novel secondary metabolite biosynthesis gene clusters that may be used for the predation of other bacteria in the activated sludge. Our metagenome-based analyses provide novel insights into the microbial interactions associated with Myxococcota in activated sludge ecosystems.

microbiology↗

bioRxiv2024

The interplay between peptides and RNA is critical for protoribosome compartmentalization and stability

The ribosome, owing to its exceptional conservation and biological importance, harbours a remarkable molecular fossil known as the protoribosome. It surrounds the peptidyl transferase center (PTC), responsible for peptide bond formation. While previous studies have demonstrated the PTC activity in RNA alone, our investigation reveals the intricate roles of the ribosomal protein fragments (rPeptides) within the ribosomal core. This research highlights the significance of rPeptides in stability and coacervation of two distinct protoribosomal evolutionary stages. The 617nt "big" protoribosome model which associates with rPeptides specifically, exhibits a structurally defined and rigid nature, further stabilised by the peptides. In contrast, the 136nt "small" model, previously linked to peptidyltransferase activity, displays greater structural flexibility. While this construct interacts with rPeptides with lower specificity, they induce coacervation of the "small" protoribosome across a wide concentration range, which is concomitantly dependent on the RNA sequence and structure. Moreover, these conditions protect RNA from degradation. This phenomenon suggests a significant evolutionary advantage in the RNA-protein interaction at the early stages of ribosome evolution. The distinct properties of the two protoribosomal stages suggest that rPeptides initially provided compartmentalization and prevented RNA degradation, preceding the emergence of specific RNA-protein interactions crucial for the ribosomal structural integrity. 3 keypoints- The most ancient fragments of ribosomal peptides trigger coacervation of protoribosome - The protoribosome coacervation provides protection against RNA degradation - Coacervation is more profound with a smaller and more flexible model of the protoribosome

biophysics↗

bioRxiv2023

Estrogenic control of reward prediction errors and reinforcement learning

Gonadal hormones act throughout the brain1, and neuropsychiatric disorders vary in symptom severity over the reproductive cycle, pregnancy, and perimenopause2-4. Yet how hormones influence cognitive processes is unclear. Exogenous 17{beta}-estradiol modulates dopamine signaling in the nucleus accumbens core (NAcc)5,6, which instantiates reward prediction errors (RPEs) for reinforcement learning7-16. Here we show that endogenous 17{beta}-estradiol enhances RPEs and sensitivity to previous rewards by reducing dopamine reuptake proteins in the NAcc. Rats performed a task with different reward states; they adjusted how quickly they initiated trials across states, balancing effort against expected rewards. NAcc dopamine reflected RPEs that predicted and causally influenced initiation times. Elevated endogenous 17{beta}-estradiol increased sensitivity to reward states by enhancing dopaminergic RPEs in the NAcc. Proteomics revealed reduced dopamine transporter expression. Finally, knockdown of midbrain estrogen receptors suppressed reinforcement learning. 17{beta}-estradiol therefore controls RPEs via dopamine reuptake, mechanistically revealing how hormones influence neural dynamics for motivation and learning.

neuroscience↗

bioRxiv2023

Role of Immature Choroid Plexus in the Pathology of Autism Spectrum Disorder

During gestation, the choroid plexus (ChP) produces protein-rich cerebrospinal fluid and matures prior to brain development. It is assumed that ChP dysfunction has a profound effect on developmental neuropsychiatric disorders, such as Autism Spectrum Disorder (ASD). However, the mechanisms linking immature ChP to the onset of ASD remain unclear. In this study, we found that ChP-specific CAMDI-knockout mice developed an immature ChP, alongside decreased multiciliogenesis and expression of differentiation marker genes following disruption of the cerebrospinal fluid barrier. These mice exhibited ASD-like behaviors, including impaired socialization with delayed critical period. Additionally, administration of Metformin, an FDA-approved drug, before the critical period achieved ChP maturation and restored social behaviors. Furthermore, ASD model mice and ASD patient-derived organoids developed immature ChP. These results indicate towards involvement of immature ChP in the pathogenesis of ASD and suggest the targeting of functional maturation of ChP as a therapeutic strategy for ASD.

neuroscience↗

bioRxiv2023

Heart generation via blastocyst complementation in Mesp1/2-deficient mice

Heart transplantation is the only curative option available for patients with advanced heart failure. However, donor organ shortage and graft rejection remain critical challenges in heart transplantation. Blastocyst complementation using pluripotent stem cells (PSCs) can be used to generate organs such as the pancreas and kidneys in animal models with abnormalities in essential developmental genes. Nonetheless, whether functional adult hearts can be generated with blastocyst complementation remains unclear, and it is unknown if parenchyma, blood vessels, and stroma can be generated concomitantly from PSCs using blastocyst complementation to avoid graft rejection. Here, we show the generation of functional adult hearts in acardiac Mesp1 and Mesp2 double-knockout (Mesp1/2-DKO) mice via blastocyst complementation using mouse PSCs. Our result shows that the generated hearts were structurally and functionally normal and restored embryonic lethality in Mesp1/2-DKO mice. All four cardiovascular lineages, including cardiomyocytes, vascular endothelial cells, smooth muscle cells, and cardiac fibroblasts, were virtually entirely derived from exogenous PSCs in the myocardium. Exogenous rat PSCs also generated rat-derived xenogeneic hearts in Mesp1/2-DKO mice via interspecies blastocyst complementation. Thus, blastocyst complementation is a viable technique for generating hearts derived from PSCs and may represent significant progress toward generating rejection-free hearts.

cell biology↗

bioRxiv2023

Emergence of belief-like representations through reinforcement learning

To behave adaptively, animals must learn to predict future reward, or value. To do this, animals are thought to learn reward predictions using reinforcement learning. However, in contrast to classical models, animals must learn to estimate value using only incomplete state information. Previous work suggests that animals estimate value in partially observable tasks by first forming "beliefs"--optimal Bayesian estimates of the hidden states in the task. Although this is one way to solve the problem of partial observability, it is not the only way, nor is it the most computationally scalable solution in complex, real-world environments. Here we show that a recurrent neural network (RNN) can learn to estimate value directly from observations, generating reward prediction errors that resemble those observed experimentally, without any explicit objective of estimating beliefs. We integrate statistical, functional, and dynamical systems perspectives on beliefs to show that the RNNs learned representation encodes belief information, but only when the RNNs capacity is sufficiently large. These results illustrate how animals can estimate value in tasks without explicitly estimating beliefs, yielding a representation useful for systems with limited capacity. Author SummaryNatural environments are full of uncertainty. For example, just because my fridge had food in it yesterday does not mean it will have food today. Despite such uncertainty, animals can estimate which states and actions are the most valuable. Previous work suggests that animals estimate value using a brain area called the basal ganglia, using a process resembling a reinforcement learning algorithm called TD learning. However, traditional reinforcement learning algorithms cannot accurately estimate value in environments with state uncertainty (e.g., when my fridges contents are unknown). One way around this problem is if agents form "beliefs," a probabilistic estimate of how likely each state is, given any observations so far. However, estimating beliefs is a demanding process that may not be possible for animals in more complex environments. Here we show that an artificial recurrent neural network (RNN) trained with TD learning can estimate value from observations, without explicitly estimating beliefs. The trained RNNs error signals resembled the neural activity of dopamine neurons measured during the same task. Importantly, the RNNs activity resembled beliefs, but only when the RNN had enough capacity. This work illustrates how animals could estimate value in uncertain environments without needing to first form beliefs, which may be useful in environments where computing the true beliefs is too costly.

neuroscience↗

bioRxiv2022

Exome-wide benchmark of difficult-to-sequence regions using short-read next-generation DNA sequencing

Next-generation DNA sequencing (NGS) in short-read mode has been recently used for genetic testing in various clinical settings. NGS data accuracy is crucial in clinical settings, and several reports regarding quality control of NGS data, focusing mostly on establishing NGS sequence read accuracy, have been published thus far. Variant calling is another critical source of NGS errors that remains mostly unexplored despite its established significance. In this study, we used a machine-learning-based method to establish an exome-wide benchmark of difficult-to-sequence regions using 10 genome sequence features on the basis of real-world NGS data accumulated in The Genome Aggregation Database (gnomAD) of the human reference genome sequence (GRCh38/hg38). We used the obtained metrics, designated "UNMET score," along with other lines of structural information of the human genome to identify difficult-to-sequence genomic regions using conventional NGS. Thus, the UNMET score could provide appropriate caveats to address potential sequential errors in protein-coding exons of the human reference genome sequence GRCh38/hg38 in clinical sequencing.

genomics↗

bioRxiv2022

Reconstructing cell interactions and state trajectories in pancreatic cancer stromal tumoroids

Interlineage communication within a cancer microenvironment can augment cancer cell behaviour and impact response to therapy. Patient-derived cancer organoids provide an opportunity to explore cancer cell biology, however it is a major challenge to generate a complex cancer microenvironment in vitro. Here, we established a stromal tumoroid culture system modeling pancreatic ductal adenocarcinoma (PDAC) that reconstitutes multilineage interactions between cancer, endothelial, and fibroblast cells and recapitulates several aspects of primary tumors. Whole-mount immunohistochemistry on cleared tumoroids reveals organized vessel, desmoplastic fibroblast, and glandular cancer cell phenotypes that emerge over time. Time-course scRNA-seq measurements show that tumoroid formation activates fibroblasts, altering the extracellular matrix (ECM) composition and inducing cancer cell signal-response signatures and metabolic state change. Comparison between tumoroids with normal or cancer associated fibroblasts (CAFs) reveals different ECM compositions, as well as differential effects on cancer cell behaviors and metabolism. We identify Syndecan 1 (SDC1) and Peroxisome proliferator-activated receptor gamma (PPARG) as receptor and metabolic nodes involved in cancer cell response to CAF signals, and blocking SDC1 disrupts cancer cell growth within the tumoroid. Tumoroids from multiple PDAC patients revealed co-existence of subpopulations associated with classical and basal phenotypes, and CAF-induced migration behaviors emerged in certain patient tumoroids. Comparisons between patient tumoroids revealed a multigene migration signature that develops over time reflecting a stress response mechanism that correlates with worse clinical outcome. Altogether, stromal tumoroids can be used to explore dynamic and reciprocal interactions between cancer, CAF and endothelial cell states, and our data provides new inroads into the discovery of personalized pancreatic cancer therapies.

cancer biology↗

bioRxiv2022

Simultaneous overexpression of multiple herbicide-metabolizing genes for broad-spectrum resistance in an agricultural weed Echinochloa phyllopogon

O_LIPrevious research unveiled that the overexpression of catalytically promiscuous CYP81A cytochrome P450s underlies the multiple-herbicide resistance (MHR) in a Californian population of Echinochloa phyllopogon. However, it does not fully accommodate the resistance to diverse herbicides in MHR E. phyllopogon although the genetic inheritance of MHR was suggested as under a single gene control. C_LIO_LIWe investigated the high-level resistance to diclofop-methyl in MHR E. phyllopogon. Detailed diclofop-methyl metabolism was analyzed, followed by gene expression study and functional characterization of P450 genes. The generality of the MHR mechanism was investigated using another MHR line. C_LIO_LIThe MHR line rapidly produced two distinct hydroxylated-diclofop-acid, only one of which was the major metabolite produced by CYP81A12/21. Gene expression study identified the genetically linked overexpression of a novel gene CYP709C69 with CYP81A12/21 in the MHR line. The gene conferred diclofop-methyl resistance in plants and produced another hydroxylated-diclofop-acid in yeast. The activity was observed in some CYP709C in plants. Unlike the broad substrate-specificity in CYP81As, CYP709C69 showed narrow substrate-specificity. The overexpression of the CYP81A and CYP709C69 was also observed in another MHR line. C_LIO_LIThe present findings establish a novel concept that genetically-linked simultaneous overexpression of herbicide-metabolizing genes enhances and broadens the profile of metabolic resistance in weeds. C_LI

plant biology↗

bioRxiv2021

Ambiguous Body Ownership Experience Caused by Feeling-judgement Conflict: Evidence from Subjective Measurement in Rubber Hand Illusion using Integrated Information Theory

AO_SCPLOWBSTRACTC_SCPLOWHuman body awareness is malleable and adaptive to changing contexts. The illusory sense of body-ownership has been studied since the publication of the rubber hand illusion, where ambiguous body ownership feeling, expressed as "the dummy hand is my hand even though that is not true", was first defined. Phenomenologically, the ambiguous body ownership is attributed to a conflict between feeling and judgement; in other words, it characterises a discrepancy between first-person (i.e. bottom-up) and third-person (i.e. top-down) processes. Although Bayesian inference can explain this malleability of body image sufficiently, the theory does not provide a good illustration of why we have different experiences to the same stimuli - the difficulty lies in the uncertainty regarding the concept of judgement in their theory. This study attempts to explain subjective experience during rubber hand illusions using integrated information theory (IIT). The integrated information {Phi} in IIT measures the difference between the entire system and its subsystems. This concept agrees with the phenomenological interpretation - that is, there is conflict between judgement and feeling. By analysing the seven nodes of a small body- brain system, we demonstrate that the integrity of the entire system during the illusion decreases with increasing integrity of its subsystems. These general tendencies agree well with many brain-image analyses and subjective reports; furthermore, we found that subjective ratings were associated with the {Phi}s. Our result suggests that IIT can explain the general tendency of the sense of ownership illusions and individual differences in subjective experience during the illusions.

animal behavior and cognition↗

bioRxiv2021

Empirical estimation of marine phytoplankton assemblages in coastal and offshore areas using an in situ multi-wavelength excitation fluorometer

Phytoplankton assemblages are important for understanding the quality of primary production in marine ecosystems. Here, we describe development of a methodology for monitoring marine phytoplankton assemblages using an in situ multi-wavelength excitation fluorometer (MEX) and its application for seasonal observations in coastal and offshore areas around Japan. The MEX recorded the fluorescence excited with nine light-emitting diodes, temperature, and sensor depth. We prepared reference datasets comprising temperature, MEX fluorescence, and plant-pigment-based chemotaxonomy phytoplankton assemblages. Target MEX fluorescence was decomposed by reference MEX fluorescence using a linear inverse model for calculating coefficients after the reference data were limited by temperature, followed by reconstruction of plant-pigment-based chemotaxonomy of the target MEX fluorescence using the coefficients and the chemotaxonomy assemblages of the reference data. Sensitivity analysis indicated poor estimation of the proportion and/or chlorophyll a-based abundance of chlorophytes, haptophytes, prasinophytes, and prochlorophytes; however, limiting the estimations to five chemotaxonomic groups [diatoms, dinoflagellates, cryptophytes, cyanobacteria (cyanophytes and prochlorophytes), and other eukaryotes (chlorophytes, haptophytes, and prasinophytes)] resulted in positive correlations of both the proportion and abundances, suggesting that the five taxonomic abundances were well-estimated using the MEX. Additionally, MEX observations denoted spatial and seasonal variations of phytoplankton assemblages, with high contributions from other eukaryotes in every area and season, cyanobacteria highly during the summer in surface Kuroshio and Japan Sea waters, and diatoms in the Oyashio and Oyashio-Kuroshio transition areas and the Okhotsk Sea. Furthermore, ratios of water-column-integrated chlorophyll-based abundances to those on the surface at the chemotaxonomy group level were differed among the areas and groups. These findings suggested that phytoplankton-assemblage monitoring in the vertical direction is essential for evaluation of their current biomass, and that the MEX promotes the acquisition of these observations.

ecology↗

bioRxiv2021

Expression of Spred2 in the urothelial tumorigenesis of the urinary bladder

Aberrant activation of the Ras/Raf/ERK (extracellular-signal-regulated kinase)-MAPK (mitogen-activated protein kinase) pathway is involved in the progression of cancer, including urothelial carcinoma; but the negative regulation remains unclear. In the present study, we investigated pathological expression of Spred2 (Sprouty-related EVH1 domain-containing protein 2), a negative regulator of the Ras/Raf/ERK-MAPK pathway, and the relation to ERK activation and Ki67 index in various categories of 275 urothelial tumors obtained from clinical patients. In situ hybridization demonstrated that Spred2 mRNA was highly expressed in high-grade non-invasive papillary urothelial carcinoma (HGPUC), and the expression was decreased in carcinoma in situ (CIS) and infiltrating urothelial carcinoma (IUC). Immunohistochemically, membranous Spred2 expression, important to interact with Ras/Raf, was preferentially found in HGPUC. Interestingly, membranous Spred2 expression was decreased in CIS and IUC relative to HGPUC, while ERK activation and the expression of the cell proliferation marker Ki67 index were increased. HGPUC with membranous Spred2 expression correlated significantly with lower levels of ERK activation and Ki67 index as compared to those with negative Spred2 expression. Thus, our pathological findings suggest that Spred2 negatively regulates cancer progression in non-invasive papillary carcinoma possibly through inhibiting the Ras/Raf/ERK-MAPK pathway, but this regulatory mechanism is lost in cancers with high malignancy. Spred2 appears to be a key regulator in the progression of non-invasive bladder carcinoma.

pathology↗

bioRxiv2021

In vivo KRAS G12D/V Degradation Mediated by CANDDY Using a Modified Proteasome Inhibitor

"Undruggable" proteins, such as RAS proteins, remain problematic despite efforts to discover inhibitors against them. KRAS mutants are prevalent in human cancers. Recently, the KRAS G12C inhibitor have been clinically approved, but inhibitors for KRAS G12D/V are still under development. Here, we described the development of a novel chemical knockdown strategy, termed CANDDY (Chemical knockdown with Affinity aNd Degradation DYnamics). This strategy involves a CANDDY tag modified from a proteasome inhibitor inducing direct proteasomal degradation. We constructed TUS-007 as a multispecific small molecule tethered from a KRAS interactor and CANDDY tag to target KRAS G12D/V. We confirmed that the degradation by TUS-007 was independent of target ubiquitination. This allows to solve a laborious design of matchmaker in the current ubiquitination-dependent proteolysis technology. And TUS-007 successfully suppressed tumors due to in vivo degradation of KRAS G12D/V. The CANDDY technology could represent a simple and rational strategy to degrade currently "undruggable" proteins.

pharmacology and toxicology↗