Biology subjects

Miyamoto, S.

Publications and source records attributed to Miyamoto, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Individual leadership in cattle persists when collective movement is induced by robotic herding

In social species, some individuals consistently lead collective movements while others follow, but whether these roles persist when movement is externally induced remains unknown. Robotic herding offers a way to address this: animals are displaced by an approaching device, yet retain the option to stay, to move or to follow a conspecific that has moved. We recorded spontaneous group departures in a herd of 18 Japanese Black cows on three days, then recorded which individuals initiated movement away from a quadruped robot, which followed and which remained, across an eight-day herding trial. Cows that frequently initiated spontaneous departures and attracted followers also initiated movement away from the robot more often and drew more followers, whereas habitual followers tended to be less effective initiators. Follower frequency during herding was unrelated to any characteristic measured. Individual leadership therefore persists when movement is induced by a robot. Behavioural roles may thus be expressed under moderate external constraint, provided animals retain some freedom of choice. Identifying leaders from spontaneous departures offers a practical route to more efficient robotic herding.

animal behavior and cognition↗

bioRxiv2026

Constitutive PI3K-AKT activation promotes steatohepatitis through de novo lipogenesis despite enhanced mitochondrial β-oxidation, essential fatty acid depletion and reduced lipid peroxidation

Background. Activation of de novo lipogenesis (DNL) is a major hallmark of steatotic liver disease (SLD), a highly prevalent group of diseases ranging from a harmless steatosis to more severe steatohepatitis, cirrhosis, and hepatocellular carcinoma. We interrogated herein the early alterations in liver proteome, transcriptome, lipidome, inflammation, fibrosis, and oxidative status in a mouse model of progressive SLD induced by constitutive activation of PI3K-AKT signaling, the major inducer of DNL. Methods. Male, 8 weeks-old mice bearing phosphatase and tensin homolog (Pten) deletion and therefore constitutive activation of PI3K-AKT in hepatocytes (albumin-Cre) and littermate controls were evaluated for liver steatosis, injury, lipid peroxidation, metabolism, proteome, lipidome and transcriptome either upon feeding with a chow or high-fat diets supplemented or not with linoleic acid or after treatment with vehicle or acetyl-CoA carboxylase (ACC) inhibitor (ND-630, 20 mg/kg/day, i.p.) Results. Mice bearing Pten deletion and therefore constitutive activation of PI3K-AKT in hepatocytes display steatohepatitis characterized by enhanced DNL, severe steatosis, hepatocyte ballooning, inflammation, fibrosis and hepatomegaly, which, unexpectedly, was associated with reduced lipid peroxidation, increased GSH content and enhanced rates of triacylglycerol turnover, fatty acid {beta}-oxidation, tricarboxylic acid cycle flux, and mitochondrial respiration, altogether promoting a robust lipidome remodeling mainly defined by enrichment of DNL-derived fatty acids in detriment of a broad depletion of essential fatty acids (linoleic and -linolenic acids) and cardiolipins. Dietary restoration of liver linoleic acid content mildly attenuated liver inflammation, without however affecting lipid peroxidation and improving steatosis and fibrosis, whereas pharmacological acetyl-CoA carboxylase (ACC) and DNL inhibition markedly reduced steatosis, inflammation and fibrosis, despite further lowering hepatic linoleic acid content. Conclusions. Collectively, these findings support a harmful role of essential fatty acids depletion fomenting liver inflammation and identify DNL as a major culprit of steatohepatitis induced by constitutive PI3K-AKT activation.

biochemistry↗

bioRxiv2026

Animal-robot interaction in the field: stronger responses and slower habituation of grazing cattle to a quadruped robot than to a drone

Robotic herding offers a promising off-animal approach to controlling the spatial distribution of grazing livestock. Nevertheless, the habituation of cattle to herding stimuli remains a critical obstacle to its practical use. This study presents the first field investigation of behavioral responses of grazing cattle to herding by a quadruped robot. We compared the herding efficacy of a drone and a quadruped robot, and tracked daily changes in responsiveness during continuous herding. Trials were conducted in a 1.1-ha pasture with Japanese Black breeding cows from June to October 2023. The quadruped robot elicited stronger avoidance responses with shorter latencies than the drone, and herding was more successful with the robot. During consecutive daily herding with the robot, behavioral responsiveness declined progressively over the initial 5 days, at a markedly slower rate than previously reported for drone herding. Following a 24-day interruption, responsiveness partially increased, but declined rapidly again over the subsequent two days. These results indicate that the quadruped robot constitutes a more persistent aversive stimulus than a drone for grazing cattle, although habituation management strategies (such as diversifying stimuli or combining sensory modalities) will be necessary for sustained control of grazing distribution.

animal behavior and cognition↗

bioRxiv2025

Oxysterol Alterations in SOD1G93A ALS Rats: 25-Hydroxycholesterol and LPS-Binding Protein in Disease Progression

BackgroundDisruptions in cholesterol and oxysterol metabolism, along with neuroinflammation, are linked to amyotrophic lateral sclerosis (ALS), though the underlying mechanisms remain unclear. Given evidence of increased intestinal permeability in ALS, we investigated its link to neuroinflammation and oxysterol alterations in SOD1G93A rats. MethodsOxysterols were quantified in plasma and spinal cord from presymptomatic and symptomatic SOD1G93A rats and age-matched controls via ultra-high performance liquid chromatography coupled with high-resolution mass spectrometry. Circulating LBP, a marker of intestinal permeability, was quantified via ELISA. ResultsOxysterols involved in bile acid biosynthesis - 7-hydroxycholesterol, 27-hydroxycholesterol (27-OH), and 3{beta}-hydroxycholestenoic acid - were increased in the plasma of symptomatic rats. The neuronal oxysterol 24(S)-hydroxycholesterol (24(S)-OH) decreased in the spinal cord but increased in the plasma. In contrast, 27-OH and 25-hydroxycholesterol (25-OH) levels were elevated in both plasma and spinal cord, with 25-OH rising during the presymptomatic stage. Presymptomatic animals also exhibited elevated LBP levels, which strongly correlated with spinal cord 25-OH levels, suggesting a link between systemic inflammation and neuroinflammation in ALS. ConclusionOxysterol alterations in plasma and spinal cord suggest compromised blood-spinal cord barrier integrity and early neuroinflammation. Elevated LBP levels indicate increased intestinal permeability and circulating LPS as contributors to neuroinflammation and neurodegeneration. These findings highlight 25-OH and LBP as markers and mediators of gut-brain axis interactions in ALS pathogenesis, particularly in the presymptomatic phase.

neuroscience↗

bioRxiv2025

Longitudinal analysis of antibody titers after primary and booster mRNA COVID-19 vaccination can identify individuals at risk for breakthrough infection

A key issue in the post-COVID-19 era is the ongoing administration of COVID-19 vaccines. Repeated vaccination is essential for preparing against currently circulating and newly emerging SARS-CoV-2 variants while enabling people to continue with daily life. Optimizing vaccination strategies is crucial to efficiently manage medical resources and establish an effective vaccination framework. Therefore, it is important to quantitatively understand vaccine-induced immunity dynamics and to be able to identify poor responders with lower sustained antibody titers as potential priorities for revaccination. We investigated longitudinal antibody titer data in a cohort of 2,526 people in Fukushima, Japan, from April 2021 to November 2022 for whom basic demographic and health information was available. Using mathematical modeling and machine learning, we stratified the time-course patterns of antibody titers after 2 primary doses and 1 booster dose of mRNA COVID-19 vaccines. We identified 3 notable populations, which we refer to as the durable, the vulnerable, and the rapid-decliner populations, approximately half of which remained in the same population after the booster dose. Notably, the rapid-decliner population experienced earlier infections than the others. Furthermore, when comparing IgG(S) titers, IgA(S) titers, and T-spot counts between participants who experienced breakthrough infections after booster vaccination and those who did not, we found that IgA(S) titers were significantly lower in breakthrough infected participants during the early stage after booster vaccination. Our computational approach is adaptable to various types of vaccinations. This flexibility can inform policy decisions on vaccine distribution to enhance immunity both in future pandemics and in the post-COVID-19 era.

immunology↗

bioRxiv2024

Comparative study of Ergosterol and 7-dehydrocholesterol and their Endoperoxides: Generation, Identification and Impact in Phospholipid Membranes and Melanoma Cells

Melanoma is an aggressive cancer that has attracted attention in recent years due to its high mortality rate of 80%. Damage caused by oxidative stress generated by radical (type I reaction) and singlet oxygen, 1O2 (type II reaction) oxidative reactions may induce cancer. Thus, studies that aim to unveil the mechanism that drives these oxidative damage processes become relevant. Ergosterol, an analogue of 7-dehydrocholesterol, important in the structure of cell membranes, is widely explored in cancer treatment. However, to date little is known about the impact of different oxidative reactions on these sterols in melanoma treatment, and conflicting results about their effectiveness complicates the understanding of their role in oxidative damage. Our results highlight differences among ergosterol, 7-dehydrocholesterol (7-DHC) and cholesterol in membrane properties when subjected to distinct oxidative reactions. Furthermore, we conducted a comparative study exploring the mechanisms of cell damage by photodynamic treatment in A375 melanoma. Notably, endoperoxides from ergosterol and 7-DHC generated by 1O2 showed superior efficacy in reducing the viability of A375 cells compared to their precursor molecules. We also describe a step-by-step process to produce and identify endoperoxides derived from ergosterol and 7-DHC. While further studies are needed, this work provides new insights for understanding cancer cell death induced by different oxidative reactions in the presence of biologically relevant sterols.

biochemistry↗

bioRxiv2024

Genome-directed study uncovers a family of phospholipases and highlights the diversity of Salmonella T6SS effectors.

Bacterial warfare is a common and ancient phenomenon in nature, where bacterial species use strategies to inhibit the growth or kill competitors. This involves the production and deployment of antibacterial toxins that disrupt essential cellular processes in target cells. The continuous arms race in which bacteria acquire new toxin and immunity proteins to promote increased adaptation to their environment is responsible for the diversification of this toxin repertoire. Here, we deployed in-silico strategies to analyze 10,000 genomes and identify effectors secreted via the type VI secretion system of Salmonella. We identified 128 candidates, which are widespread in a vast array of Salmonella serovars and other bacterial species. Tox-Act1 is among the most frequent candidates and was selected for in-depth characterization. Tox-Act1 contains a permuted NlpC/P60 papain-like catalytic core characteristic of lipid-targeting members rather than the typical peptidases or amidases. Evolutionary analysis revealed the relationship of Tox-Act1 with acyltransferases. Biochemical assays with purified toxin and lipidomics of intoxicated cells showed that Tox-Act1 exhibits phospholipase activity, cleaving off acyl groups from phosphatidylglycerol and phosphatidylethanolamine. In addition, we demonstrate that Tox-Act1 is secreted in a T6SS-dependent manner and provide a competitive advantage during colonization of the gut of infected mice. This work broadens our understanding of toxin domains and provides the first direct characterization of a lipid-targeting NlpC/P60 domain in biological conflicts.

microbiology↗

bioRxiv2024

Identification of novel human 15-lipoxygenase-2 (h15-LOX-2) inhibitors using a virtual screening approach

The human 15-lipoxygenase-2 (h15-LOX-2) is a non-heme iron-containing enzyme that catalyzes the regio- and stereospecific oxygenation of polyunsaturated fatty acids, mainly arachidonic acid, and is implicated in the biosynthesis of pro- and anti-inflammatory lipid mediators. The biological roles of h15-LOX-2 have not been completely unveiled, but it has been suggested that high expression levels of h15-LOX-2 are related to the pathogenesis of atherosclerosis and of some types of cancer. Inhibitors of h15-LOX-2 might be helpful for a deeper understanding of its roles in physiological and pathophysiological processes, in addition to representing potential drug candidates for treating human diseases. Nevertheless, only a few h15-LOX-2 inhibitors have been reported in the literature to date. Here, aiming to search for novel h15-LOX-2 inhibitors, we used a virtual screening (VS) approach, consisting of four consecutive filters (shape-based matching, 2D structural "dissimilarity", docking, and careful visual inspection), which were applied to a "curated" version of the ZINC database, pre-filtered for potential drug-like compounds. Six novel h15- LOX-2 inhibitors, with inhibitory potencies in the micromolar range, were identified. Ki values were determined for two inhibitors, compounds 10 [Ki = (16.4 {+/-} 8.1) M] and 13 [Ki = (15.1 {+/-} 7.6) M], which showed a mixed-type mechanism of inhibition. According to docking predictions, the identified inhibitors occupy the more solvent-exposed arm of the U-shaped h15-LOX-2 active sites cavity, possibly blocking the access of the substrate to the active site. The identified inhibitors are structurally different from the few h15-LOX-2 inhibitors reported in the literature, in addition to fulfilling drug-like criteria. Overall, our results provide a valuable contribution to the search for novel inhibitors of h15-LOX-2, a so-far underexploited target enzyme.

biochemistry↗

bioRxiv2024

PRDX6 contributes to selenocysteine metabolism and ferroptosis resistance

Selenocysteine (Sec) metabolism is crucial for cellular function and ferroptosis prevention and has traditionally been thought to begin with the uptake of the Sec carrier selenoprotein P (SELENOP). Following uptake, Sec released from SELENOP undergoes metabolisation via selenocysteine lyase (SCLY), producing selenide, a substrate used by selenophosphate synthetase 2 (SEPHS2), which provides the essential selenium donor - selenophosphate - for the biosynthesis of the selenocysteine tRNA. Here, we report the discovery of an alternative pathway mediating Sec metabolisation that is independent of SCLY and mediated by peroxiredoxin 6 (PRDX6). Mechanistically, we demonstrate that PRDX6 can readily react with selenide and interact with SEPHS2, potentially acting as a selenium delivery system. Moreover, we demonstrate the presence and functional significance of this alternative route in cancer cells where we reveal a notable association between elevated expression of PRDX6 with a highly aggressive neuroblastoma subtype. Altogether, our study sheds light on a previously unrecognized aspect of Sec metabolism and its implications in ferroptosis, offering new avenues for therapeutic exploitation.

cell biology↗

bioRxiv2024

Influenza A virus circumvents the innate immune response through the sequestration of double-stranded RNA

Double-stranded RNA (dsRNA), which induces an innate immune response against viral infections, is rarely detected in influenza A virus (IAV)-infected cells. Nevertheless, we previously reported that the IAV ribonucleoprotein complex (vRNP) generates looped dsRNAs during RNA synthesis in vitro. This finding suggests that IAV possesses a specific mechanism for sequestering dsRNA within infected cells, thereby enabling viral evasion of the innate immune response. Here, we found that dsRNAs were produced in infected cells lacking the expression of viral non-structural protein 1 (NS1) and nuclear export protein (NEP), both encoded by the same RNA segment. Interestingly, NS1 molecules masked the entire looped dsRNA generated by vRNP, implying a potential role for NS1 in segregating viral dsRNA from cytoplasmic dsRNA sensors, including retinoic acid inducible gene-I (RIG-I). Furthermore, dsRNAs were sequestered within the nucleus of infected cells due to the absence of NEP, while their translocation to the cytoplasm occurred only upon NEP expression. Notably, the cytoplasmic translocation of dsRNA triggered the innate immune response in an RIG-I-dependent manner. These findings highlight IAVs distinctive strategy for circumventing innate immunity by sequestration of dsRNAs. Author summaryIt is widely recognized that double-stranded RNA (dsRNA) produced during viral infection triggers an innate immune response. However, the influenza A virus (IAV) has been thought to rarely produce dsRNA within infected cells. Here, we confirmed the limited dsRNA production in the nucleus of IAV-infected cells and found that the cells lacked expressions of viral non-structural protein 1 (NS1) and nuclear export protein (NEP), both derived from a single RNA segment. High-speed atomic force microscopy demonstrated that NS1 entirely concealed dsRNA produced by the viral ribonucleoprotein complexes, thereby segregating it from cytoplasmic dsRNA sensors that trigger the innate immune response. Interestingly, NEP expression caused cytoplasmic translocation of dsRNA, resulting in the nuclear translocation of interferon regulatory factor 3, which initiates an innate immune response. Collectively, our findings suggest that IAV employs a sophisticated strategy to circumvent the innate immune system, wherein the expressions of NS1 and NEP exert considerable influence.

microbiology↗

bioRxiv2024

Plasmalogen oxidation induces the generation of excited molecules and electrophilic lipid species

Plasmalogens are glycerophospholipids with a vinyl-ether linkage at the sn-1 position of the glycerol backbone. Despite being suggested as antioxidants due to the high reactivity of their vinyl ether groups with reactive oxygen species (ROS), our study reveals the generation reactive oxygen and electrophilic lipid species from oxidized plasmalogen intermediates. By conducting a comprehensive analysis of the oxidation products by liquid chromatography coupled to high-resolution mass spectrometry (LC-MS) we demonstrate that singlet molecular oxygen [O2 (1{Delta}g)] reacts with the vinyl ether bond, producing hydroperoxyl acetal as major primary product (97%) together with minor quantities of dioxetane (3%). Furthermore, we show that these primary oxidized intermediates lead to the formation of excited triplet carbonyls, O2 (1{Delta}g), and electrophilic phospholipid and fatty aldehyde species, as secondary reactive products. The generation of excited triplet carbonyls from dioxetane thermal decomposition was confirmed by light emission measurements in the visible region using dibromoantracene as a triplet enhancer. Moreover, O2 (1{Delta}g) generation from dioxetane and hydroperoxyacetal was evidenced by detection of near-infrared light emission at 1270 nm and chemical trapping experiments. Additionally, we have thoroughly characterized alpha-beta unsaturated phopspholipid and fatty aldehydes by LC-MS analysis using two probes that specifically reacts with aldehydes and alpha-beta unsaturated carbonyls. Overall, our findings demonstrate the generation of excited molecules and electrophilic lipid species from oxidized plasmalogen species unveiling the potential prooxidant nature of plasmalogen oxidized products. Significance StatementPlasmalogens, the most abundant subclass of ether lipids in mammalian cells, have traditionally been regarded as antioxidants. However, our study reveals a new perspective, shedding light on the generation of chemiexcited and reactive lipid species during plasmalogen photooxidation. We provide direct evidence revealing the production of excited triplet carbonyls and singlet molecular oxygen as secondary reactive products originating from dioxetane and hydroperoxyacetal intermediates. Importantly, we also demonstrate the generation of electrophilic alpha-beta unsaturated phospholipids and fatty aldehydes through plasmalogen oxidation. These findings highlight the production of excited states and reactive lipid species resulting from plasmalogen oxidation, which can potentially induce oxidative modifications in biological systems.

biochemistry↗

bioRxiv2023

Plasma Oxylipin Profiling by High Resolution Mass Spectrometry Reveal Signatures of Inflammation and Hypermetabolism in Amyotrophic Lateral Sclerosis

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized not only by progressive loss of motor neurons, but also linked to systemic hypermetabolism, oxidative stress, and inflammation. In this context, oxylipins have been investigated as signaling molecules linked to neurodegeneration. However, the nature and role of major oxylipins involved in ALS disease progression remain unclear. Importantly, most methods focused on oxylipin analysis are based on low resolution mass spectrometry (LRMS), which usually confers high sensitivity, but not great accuracy for lipid identification, as provided by high-resolution MS (HRMS). Here, we established an ultra-high performance liquid chromatography coupled HRMS (LC-HRMS) method for simultaneous analysis of 126 oxylipins in plasma, including lipid hydroxides, ketones, epoxides, prostaglandins, leukotrienes, and others in a 15-minute run. Intra- and inter-day method validation showed high sensitivity (0.3 - 25 pg), accuracy and precision for more than 90 % of quality controls. This method was applied for the analysis of oxylipins in plasma of ALS rats overexpressing the mutant human Cu/Zn-superoxide dismutase gene (SOD1-G93A) at asymptomatic (ALS 70 days old) and symptomatic stages (ALS 120 days old), and their respective age-matched wild type controls (WT 70 days old and WT 120 days old). From the 56 oxylipins identified in plasma, 17 species were significantly altered. Remarkably, most of oxylipins linked to inflammation and oxidative stress derived from arachidonic acid, such as, prostaglandins, lipoxins, mono-hydroxides, and isoprostane, were increased in ALS 120d rats. In contrast, the linoleic acid diols involved in fatty acid uptake and {beta}-oxidation, 9(10)-DiHOME and 12(13)-DiHOME, were strongly decreased in the ALS 120d. In summary, we developed and validated a high-throughput LC-HRMS method for oxylipin analysis and provided a comprehensive overview of plasma oxylipins involved in ALS disease progression. Noteworthy, the oxylipins altered in plasma of ALS 120d rats have potential to be investigated and used as biomarkers for inflammation and hypermetabolism in ALS. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=136 SRC="FIGDIR/small/547101v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@937099org.highwire.dtl.DTLVardef@1c5847forg.highwire.dtl.DTLVardef@7dd09borg.highwire.dtl.DTLVardef@a9f8d_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2022

Representational similarity learning reveals a graded multi-dimensional semantic space in the human anterior temporal cortex

Neurocognitive models of semantic memory have proposed that the ventral anterior temporal lobes (vATLs) encode a graded and multidimensional semantic space--yet neuroimaging studies seeking brain regions that encode semantic structure rarely identify these areas. In simulations we show that this discrepancy may arise from a crucial mismatch between theory and analysis approach. Utilizing an analysis recently formulated to investigate graded multidimensional representations, representational similarity learning (RSL), we decoded semantic structure from ECoG data collected from the vATL cortical surface while participants named line drawings of common items. The results reveal a graded, multidimensional semantic space encoded in neural activity across the vATL, which evolves over time and simultaneously expresses both broad and finer-grained semantic structure amongst animate and inanimate concepts. The work resolves the apparent discrepancy within the semantic cognition literature and, more importantly, suggests a new approach to discovering representational structure in neural data more generally. Conflict of interestThe Department of Epilepsy, Movement Disorders, and Physiology, Kyoto University Graduate School of Medicine conducts Industry-Academia Collaboration Courses, supported by Eisai Co., Ltd, Nihon Kohden Corporation, Otsuka Pharmaceutical Co., and UCB Japan Co., Ltd.

neuroscience↗

bioRxiv2022

Intranasal vaccination induced cross-protective secretory IgA antibodies against SARS-CoV-2 variants with reducing the potential risk of lung eosinophilic immunopathology

To control the coronavirus disease 2019 (COVID-19) pandemic, there is a need to develop vaccines to prevent infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. One candidate is a nasal vaccine capable of inducing secretory IgA antibodies in the mucosa of the upper respiratory tract, the initial site of infection. However, regarding the development of COVID-19 vaccines, there is concern about the potential risk of inducing lung eosinophilic immunopathology as a vaccine-associated enhanced respiratory disease as a result of the T helper 2 (Th2)-dominant adaptive immune response. In this study, we investigated the protective effect against virus infection induced by intranasal vaccination of recombinant trimeric spike protein derived from SARS-CoV-2 adjuvanted with CpG oligonucleotides, ODN2006, in mouse model. The intranasal vaccine combined with ODN2006 successfully induced not only systemic spike-specific IgG antibodies, but also secretory IgA antibodies in the nasal mucosa. Secretory IgA antibodies showed high protective ability against SARS-CoV-2 variants (Alpha, Beta and Gamma variants) compared to IgG antibodies in the serum. The nasal vaccine of this formulation induced a high number of IFN-{gamma}-secreting cells in the draining cervical lymph nodes and a lower spike-specific IgG1/IgG2a ratio compared to that of subcutaneous vaccination with alum as a typical Th2 adjuvant. These features are consistent with the induction of the Th1 adaptive immune response. In addition, mice intranasally vaccinated with ODN2006 showed less lung eosinophilic immunopathology after viral challenge than mice subcutaneously vaccinated with alum adjuvant. Our findings indicate that intranasal vaccine adjuvanted with ODN2006 could be a candidate that can prevent the infection of antigenically different variant viruses, reducing the risk of vaccine-associated enhanced respiratory disease.

microbiology↗

bioRxiv2021

Timelapse viability assay to detect division and death of primary multiple myeloma cells in response to drug treatments with single cell resolution

Heterogeneity among cancer cells and in the tumor microenvironment (TME) is thought to be a significant contributor to the heterogeneity of clinical therapy response observed between patients and can evolve over time. A primary example of this is multiple myeloma (MM), a generally incurable cancer where such heterogeneity contributes to the persistent evolution of drug resistance. However, there is a paucity of functional assays for studying this heterogeneity in patient samples or for assessing the influence of the patient TME on therapy response. Indeed, the population-averaged data provided by traditional drug response assays and the large number of cells required for screening remain significant hurdles to advancement. To address these hurdles, we developed a suite of accessible technologies for quantifying functional drug response to a panel of therapies in ex vivo three-dimensional culture using small quantities of a patients own cancer and TME components. This suite includes tools for label-free single-cell identification and quantification of both cell division and death events with a standard brightfield microscope, an open-source software package for objective image analysis and feasible data management of multi-day timelapse experiments, and a new approach to fluorescent detection of cell death that is compatible with long-term imaging of primary cells. These new tools and capabilities are used to enable sensitive, objective, functional characterization of primary MM cell therapy response in the presence of TME components, laying the foundation for future studies and efforts to enable predictive assessment drug efficacy for individual patients. Insight BoxThe new tools and capabilities described here allow new insights into functional primary cell therapy response by (i) enabling more drugs to be tested on precious and limited numbers of patient cells ex vivo (ii) providing the ability to discriminate both cell division and death events over multiple days with single-cell resolution, and (iii) by incorporating the influences of a patients own cancer cells and TME components on drug response.

bioengineering↗

bioRxiv2021

Calorie Restriction Maintains Mitochondrial Function and Redox Balance Avoiding Lipidomic Reprogramming during Isoproterenol-Induced Cardiac Hypertrophy

Cardiac hypertrophy induces a metabolic shift, leading to a preferential consumption of glucose (over fatty acids) to support the high energetic demand. Typically, health cardiac tissue utilizes more fat than any other organ. Calorie restriction is a dietary procedure that induces health benefits and lifespan extension in many organisms. Given the beneficial effects of calorie restriction and the metabolic dysregulation seen during cardiac hypertrophy, we hypothesized that calorie restriction prevents cardiac hypertrophy, lipid, mitochondrial, and redox dysregulations. Strikingly, calorie restriction reversed isoproterenol-induced cardiac hypertrophy, lowered succinate driven mitochondrial H2O2 production, improved mitochondrial function (indicated as a higher Respiratory Control Ratio - RCR) and avoided mitochondrial superoxide dismutase (MnSOD) and glutathione peroxidase (GPX) repression. To gain insight into how calorie restriction could interfere with the metabolic changes induced by cardiac hypertrophy, we performed lipidomic profiling. Calorie restriction protected against the consumption of several triglycerides (TG) linked to unsaturated fatty acids, and the accumulation of TGs containing saturated fatty acids observed in hypertrophic samples. Cardiac hypertrophy induced an increase in ceramides, phosphoethanolamines and acylcarnitines (12:0, 14:0, 16:0 and 18:0) that were also reversed by calorie restriction. Altogether, our data demonstrate that hypertrophy changes the cardiac lipidome, causes mitochondrial disturbances and oxidative stress. All these changes are prevented by calorie restriction intervention in vivo. This study uncovers calorie restriction as a resource protect cardiac tissue and prevent cardiac hypertrophy-induced lipidomic remodeling.

biochemistry↗

bioRxiv2021

Resource sharing by outer membrane vesicles from a citrus pathogen

The causative agent of citrus canker disease, Xanthomonas citri pv. citri, was found to produce copious amounts of outer membrane vesicles (OMVs), frequently forming long membranous tubes under different culture conditions. Lipidomic analysis revealed significant differences in lipid composition between purified vesicles in relation to whole cells. The results suggest an enrichment in saturated cardiolipins and a decrease in unsaturated lipids in the OMV samples, possibly granting them a more rigid structure while allowing their high degree of curvature caused by their small diameters. The vesicles proteome was found to be significantly enriched in TonB-dependent receptors related to the acquisition of different nutrients. These proteins are known to transport siderophores, which were evidenced to be present in purified X. citri OMVs, along with essential metals including iron, zinc, and manganese quantified by elemental analysis. The availability of vesicle-associated nutrients to be incorporated by cells was demonstrated by the use of OMVs as the sole carbon source for bacterial growth. At last, the vesicles also presented esterase and protease activities, which have been associated with virulence in phytopathogens. These evidences point that X. citri cells can use OMVs to share resources within microbial communities, which has potential implications for microbial interactions and plant colonization, affecting their survival and persistence on the host and in the environment. ImportanceThe shedding of outer membrane vesicles appears to be universal in Gram-negative bacteria and effectively constitutes a unique secretion pathway for diverse molecules and proteins. To study their possible functions in the citrus pathogen Xanthomonas citri, purified vesicles from this bacterium were studied by omics and functional approaches. Nutrient transporters were found associated to these structures, which were evidenced to contain siderophores and essential metals. The availability of these nutrients to be incorporated by cells was then demonstrated by showing that purified vesicles can be used as sole carbon sources for microbial growth. Additionally, the samples also presented esterase and protease activities which can contribute to the release of substrates from plant host tissues. These observations help to establish the developing idea of vesicles as shared bacterial resources which can participate in shaping host-associated microbial communities in contrast to other interactions such as bacterial competition.

microbiology↗

bioRxiv2021

Influenza virus ribonucleoprotein complex formation occurs in the nucleolus

Influenza A virus double-helical ribonucleoprotein complex (vRNP) performs transcription and replication of viral genomic RNA (vRNA). Unlike most RNA viruses, vRNP formation accompanied by vRNA replication is carried out in the nucleus of virus-infected cell. However, the precise subnuclear site remains unknown. Here, we report the subnuclear site of vRNP formation in influenza virus. We found that all vRNP components were colocalized in the nucleolus of virus-infected cells at early stage of infection. Mutational analysis showed that nucleolar localization of viral nucleoprotein, a major vRNP component, is critical for functional double-helical vRNP formation. Furthermore, nucleolar disruption of virus-infected cells inhibited vRNP component assembly into double-helical vRNPs, resulting in decreased vRNA transcription and replication. Collectively, our findings demonstrate that the vRNA replication-coupled vRNP formation occurs in the nucleolus, demonstrating the importance of the nucleolus for influenza virus life cycle.

microbiology↗