Biology subjects

Matsumoto, T.

Publications and source records attributed to Matsumoto, T..

32 records · Page 2Linked to original sources

bioRxiv2023

Improvement of cell growth in green algae Chlamydomonas reinhardtii through co-cultivation with yeast Saccharomyces cerevisiae

Biological fixation methods have attracted considerable attention because they can be applied for the fixation of dilute CO2 in the atmosphere. Co-cultivation of certain microalgae with heterotrophic microorganisms can increase the growth potential of microalgae under dilute CO2 conditions. The objective of this study was to determine the culture conditions under which the growth potential of green algae Chlamydomonas reinhardtii is enhanced by co-culturing with the yeast Saccharomyces cerevisiae, and to identify the cause of the enhanced growth potential using transcriptome analysis. When C. reinhardtii and S. cerevisiae were co-cultured with an initial green algae to yeast inoculum ratio of 1:3, the cell concentration of C. reinhardtii reached 133 x 105 cells/mL on day 18 of culture, which was 1.5 times higher than that of the monoculture. Transcriptome analysis revealed that the expression levels of 363 green algae and 815 yeast genes were altered through co-cultivation. These include genes responsible for ammonium transport and CO2 enrichment mechanism in green algae and the genes responsible for glycolysis and stress responses in yeast. In conclusion, we identified the culture condition suitable for the co-cultivation of C. reinhardtii and S. cerevisiae. In addition, we discuss the cause of the increased growth potential of C. reinhardtii based on transcriptome analysis data. Although further studies are needed to elucidate the full impact of microbial interactions in C. reinhardtii and S. cerevisiae co-cultures, the findings of this study represent an important first step toward achieving this goal.

bioengineering↗

bioRxiv2023

Synergistic effects of PARP inhibitors by Schlafen 11 and BRCA2-deficiency through accumulation of single-strand DNA gaps behind a fork

Poly (ADP-ribose) polymerase (PARP) inhibitors (PARPis) induce synthetic lethality in breast cancer gene (BRCA)-deficient tumors. Besides the original model proposed by accumulation of double-strand DNA breaks due to the impaired homologous recombination, accumulation of single-strand DNA (ssDNA) gaps due to impaired BRCA-mediated Okazaki fragment processing has emerged as an alternative mechanism of synthetic lethality. Accordingly, PARPis induce ssDNA gaps behind a replication fork in BRCA-deficient cells. Schlafen 11 (SLFN11), a member of the SLFN family, binds replication protein A (RPA)-coated ssDNA gaps and sensitizes cancer cells to DNA-damaging anticancer agents. These facts motivated us to examine the combinational effects of SLFN11 and BRCA-deficiency on PARPis sensitivity. Here, we show that SLFN11 and BRCA2-deficiency synergistically increased sensitivity to PARPis (talazoparib, niraparib, olaparib, and veliparib) at specific concentrations, where SLFN11 alone showed marginal effects. Using chromatin-bound proteins and alkaline BrdU comet assays in human cancer cells, we revealed that ssDNA gaps induced by PARPis were increased by SLFN11 or BRCA2-deficiency and that the combination of the two had the greatest effect. SLFN11 was recruited to and colocalized with chromatin-bound RPA2 under PARPis. SLFN11 recruited around a fork under DNA damage blocked replication, whereas SLFN11 recruited behind a fork under PARPis did not. Chromatin recruitment of SLFN11 and RPA2 was attenuated by the MRE11 inhibitor mirin. Hence, our studies showed that BRCA2-deficiency increased ssDNA gaps behind a fork under PARPis treatment, where SLFN11 bound and further increased the gaps. Our findings provide a mechanistic understanding of favorable responses to PARPis in SLFN11-proficient and BRCA-deficient tumors. SignificanceThis study reveals how SLFN11 enhances the antitumor effects of PARP inhibitors in BRCA2-deficient cancer cells and highlights the importance of analyzing SLFN11 expression in addition to BRCA analysis in clinical practice.

cancer biology↗

bioRxiv2023

Cdc48 and its co-factor Ufd1 segregate CENP-A from centromeric chromatin and can induce chromosome elimination in the fission yeast Schizosaccharomyces pombe.

CENP-A, a variant of histone H3, determines the identity of the centromere, a chromosome locus at which a microtubule attachment site termed kinetochore is assembled. Because the position and size of the centromere and its number per chromosome must be maintained for the faithful segregation of chromosomes, the distribution of CENP-A is strictly regulated. In this study, we have aimed to understand mechanisms to regulate the distribution of CENP-A by a genetic approach in the fission yeast Schizosaccharomyces pombe. A mutant of the ufd1+ gene (ufd1-73) encoding a cofactor of Cdc48 ATPase is sensitive to CENP-A expressed at a high level and allows mislocalization of CENP-A. ChIP analysis has revealed that the level of CENP-A in centromeric chromatin is increased in the ufd1-73 mutant even when CENP-A is expressed at a normal level. A preexisting mutant of the cdc48+ gene (cdc48-353) phenocopies the ufd1-73 mutant. We have also shown that Cdc48 and Ufd1 proteins physically interact with centromeric chromatin. Finally, Cdc48 ATPase with Ufd1 artificially recruited to the centromere of a mini-chromosome (Ch16) induce a loss of CENP-A from Ch16, resulting in an increased rate of chromosome loss. It appears that Cdc48 ATPase, together with its cofactor Ufd1 segregates excess CENP-A from chromatin, likely in a direct manner, to maintain proper distribution of CENP-A. This mechanism may play an important role in centromere disassembly, a process to eliminate CENP-A massively to inactivate the kinetochore function during development, differentiation, and stress response in other organisms. Significance statementMaintaining the proper distribution of CENP-A is crucial for centromere identity. This process involves accurate positioning of CENP-A and removal of excess CENP-A from chromatin. The Cdc48-Ufd1 complex is essential for this regulation as it acts as a segregase that directly eliminates surplus CENP-A from chromatin. These findings have therapeutic significance as targeting the Cdc48 complex can potentially correct abnormal karyotypes in disomic embryos and prevent trisomic disorders like Down syndrome. This research advances our understanding of centromeric chromatin regulation and its potential therapeutic applications.

molecular biology↗

bioRxiv2023

Meat without vegetables: An ancient ecotype of Helicobacter pylori found in Indigenous populations and animal adapted lineages.

The colonization of our stomachs by Helicobacter pylori is believed to predate the oldest splits between extant human populations. We identify a "Hardy" ecospecies of H. pylori associated with indigenous groups, isolated from people in Siberia, Canada, USA and Chile. The ecospecies shares the ancestry of "Ubiquitous" H. pylori from the same geographical region in most of the genome but has nearly fixed SNP differences in 100 genes, many of which encode outer membrane proteins and host interaction factors. For these parts of the genome, the ecospecies has a separate, independently evolving gene pool with a distinct evolutionary history. H. acinonychis, found in big cats, and a newly identified primate-associated lineage both belong to the Hardy ecospecies and both represent human to animal host jumps. Most strains from the ecospecies encode an additional iron-dependent urease that is shared by Helicobacter from carnivorous hosts, as well as a tandem duplication of vacA, encoding the vacuolating toxin. We conclude that H. pylori split into two highly distinct ecospecies in Africa and that both dispersed around the globe with humans, but the Hardy ecospecies has gone extinct in most parts of the world. Our analysis also pushes back the likely length of the association between H. pylori and humans.

microbiology↗

bioRxiv2023

Arabidopsis thaliana subclass I ACTIN DEPOLYMERIZING FACTORs regulate nuclear organization and gene expression

ACTIN DEPOLYMERIZING FACTOR (ADF) is a conserved protein that regulates the organization and dynamics of actin microfilaments. Eleven ADFs in the Arabidopsis thaliana genome are grouped into four subclasses, and subclass I ADFs, ADF1-4, are all expressed throughout the plant. Previously, we showed that subclass I ADFs function in the regulation of the response against powdery mildew fungus as well as in the regulation of cell size and endoreplication. Here, we report a new role of subclass I ADFs in the regulation of nuclear organization and gene expression. Through a microscopic observation of epidermal cells in mature leaves, we found that the size of chromocenters in both adf4 and transgenic lines where expression of subclass I ADFs are downregulated (ADF1-4Ri) was reduced compared with that of wild-type Col-0. A. thaliana possesses eight ACTIN genes, among which ACT2, -7, and -8 are expressed in vegetative organs. The chromocenter size in act7, but not in the act2/8 double mutant, was enlarged compared with that in Col-0. Microarray analysis revealed that 1,818 genes were differentially expressed in adf4 and ADF1-4Ri. In particular, expression of 22 nucleotide-binding leucine-rich repeat (NLR) genes, which are involved in effector-triggered plant immunity, was reduced in adf4 and ADF1-4Ri. qRT-PCR confirmed the altered expressions shown with microarray analysis. Overall, these results suggest that ADF regulates various aspects of plant physiology through its role in regulation of nuclear organization and gene expression. The mechanism how ADF and ACTIN regulate nuclear organization and gene expression is discussed.

cell biology↗

bioRxiv2022

Fc-modified SARS-CoV-2 neutralizing antibodies with therapeutic effects in two animal models.

The use of therapeutic neutralizing antibodies against SARS-CoV-2 infection has been highly effective. However, there remain few practical antibodies against viruses that are acquiring mutations. In this study, we created 494 monoclonal antibodies from COVID-19-convalescent patients, and identified antibodies that exhibited comparable neutralizing ability to clinically used antibodies in the neutralization assay using pseudovirus and authentic virus including variants of concerns. These antibodies have different profiles against various mutations, which were confirmed by cell-based assay and cryo-electron microscopy. To prevent antibody-dependent enhancement, N297A modification was introduced, and showed a reduction of lung viral RNAs by therapeutic administration in a hamster model. In addition, an antibody cocktail consisting of three antibodies was also administered therapeutically to a macaque model, which resulted in reduced viral titers of swabs and lungs and reduced lung tissue damage scores. These results showed that our antibodies have sufficient antiviral activity as therapeutic candidates.

microbiology↗

bioRxiv2021

Microscopic characterization of local strain field in healing tissue in the central third defect of mouse patellar tendon at early-phase of healing

Tendons exhibit a hierarchical collagen structure, wherein higher-level components, such as collagen fibres and fascicles, are elongated, slid, and rotated during macroscopic stretching. These mechanical behaviours of collagen fibres play important roles in stimulating tenocytes, imposing stretching, compression, and shear deformation. It was hypothesised that a lack of local fibre behaviours in healing tendon tissue may result in a limited application of mechanical stimuli to cells within the tissue, leading to incomplete recovery of tissue structure and functions in regenerated tendons. Therefore, the present study aimed to measure the microscopic strain field in the healing tendon tissue. A central third defect was created in the patellar tendon of mice, and the regenerated tissue in the defect was examined by tensile testing, collagen fibre analysis, and local strain measurement using confocal microscopy at 3 and 6 weeks after surgery. Healing tissue at 3 weeks exhibited a significantly lower strength and disorganised collagen fibre structure compared with the normal tendon. These characteristics at 6 weeks remained significantly different from those of the normal tendon. Moreover, the magnitude of local shear strain in the healing tissue under 4% tissue strain was significantly smaller than that in the normal tendon. Differences in the local strain field may be reflected in the cell nuclear shape and possibly the amount of mechanical stimuli applied to the cells during tendon deformation. Accordingly, restoration of a normal local mechanical environment in the healing tissue may be key to a better healing outcome of tendon injury.

bioengineering↗

bioRxiv2021

Genome-wide association study of gastric cancer- and duodenal ulcer-derived Helicobacter pylori strains reveals discriminatory amino acid differences and novel oncoprotein candidates

Genome-wide association studies (GWASs) can reveal genetic variations associated with a phenotype in the absence of any hypothesis of candidate genes. The problem of false-positive sites linked with the responsible site might be bypassed in bacteria with a high homologous recombination rate, such as Helicobacter pylori, which causes gastric cancer (GC). We conducted a GWAS followed by regression-based prediction of GC and duodenal ulcer H. pylori strains. We identified 14 single nucleotide polymorphisms (11 amino acid changes) that, combined, allowed effective disease discrimination. They were often informative of the underlying molecular mechanisms, such as electric charge alteration at the ligand-binding pocket, alteration in subunit interaction, and mode-switching of DNA methylation. We also identified three novel virulence factors/oncoprotein candidates. These results provide both defined targets for further informatic and experimental analyses to gain insights into GC pathogenesis and a basis for identifying a set of biomarkers for application in clinical settings.

physiology↗

bioRxiv2021

Optimal transport analysis reveals trajectories in steady-state systems

Understanding how cells change their identity and behaviour in living systems is an important question in many fields of biology. The problem of inferring cell trajectories from single-cell measurements has been a major topic in the single-cell analysis community, with different methods developed for equilibrium and non-equilibrium systems (e.g. haematopoeisis vs. embryonic development). We show that optimal transport analysis, a technique originally designed for analysing time-courses, may also be applied to infer cellular trajectories from a single snapshot of a population in equilibrium. Therefore optimal transport provides a unified approach to inferring trajectories, applicable to both stationary and non-stationary systems. Our method, StationaryOT, is mathematically motivated in a natural way from the hypothesis of a Waddingtons epigenetic landscape. We implemented StationaryOT as a software package and demonstrate its efficacy when applied to simulated data as well as single-cell data from Arabidopsis thaliana root development.

bioinformatics↗

bioRxiv2020

Reconstruction of the urinary tract at the appropriate time reduces fibrosis of the metanephros in rats as judged by imaging

Chronic kidney disease leads to high morbidity rates among humans. It is a serious disease that requires curative treatments other than kidney transplantation. Recently, we successfully established the iPS-derived generated kidney, which might produce urine. The urine can be directed to the native bladder with a stepwise peristaltic ureter system, followed by anastomosis with the recipient ureter for reconstruction of the urinary tract. However, the growth of the regenerated kidney varies significantly, whereas the time window of the anastomosis is quite narrow. Therefore, this study was conducted to evaluate the growth of transplanted metanephros with bladder periodically and noninvasively using computed tomography and ultrasonography. Ultrasonographic findings showed high correlations with computed tomographic findings and clearly evaluated metanephros with bladder. We found that the degree of growth of the metanephros with bladder after the transplantation differed in each individual. However, most of them reached the appropriate period for urinary tract reconstruction within 3 weeks after transplantation. Optimizing the stepwise peristaltic ureter system anastomosis by ultrasonography reduced long-term tubular dilation of the metanephros, thereby decreasing fibrosis caused by transforming growth factor-{beta}. This may be significantly related to long-term maturation of fetal grafts. These results provide new insights into transplanting regenerated kidneys in higher animals. We are one step closer to the first human trial of kidney generation.

developmental biology↗

bioRxiv2019

APOBEC3B reporter myeloma cell lines identify DNA damage response pathways leading to APOBEC3B expression

Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC) DNA cytosine deaminase 3B (A3B) is a DNA editing enzyme which induces genomic DNA mutations in multiple myeloma and various other cancers. APOBEC family proteins are highly homologous so it is especially difficult to investigate the biology of A3B alone in cancer cells. To investigate A3B function in myeloma cells easily and comprehensively, we used CRISPR/Cas9 to generate A3B reporter cells that contain 3xFLAG tag and IRES-EGFP sequences integrated at the end of the A3B gene. These reporter cells stably express 3xFLAG tagged A3B and the reporter EGFP and this expression is enhanced under known stimuli, such as PMA. Conversely, shRNA knockdown of A3B decreased EGFP fluorescence and 3xFLAG tagged A3B protein levels. We screened a series of anticancer treatments using these cell lines and identified that most conventional therapies, such as antimetabolites or radiation, exacerbated endogenous A3B expression, but recent molecular targeting drugs, including bortezomib, lenalidomide and elotuzumab, did not. Furthermore, chemical inhibition of ATM, ATR and DNA-PK suppressed the EGFP expression upon treatment with antimetabolites. These results suggest that DNA damage response triggers A3B expression through ATM, ATR and DNA-PK signaling.

cancer biology↗

bioRxiv2019

Evaluation of the impact of seasonal variations in photoperiod on the hepatic metabolism of medaka (Oryzias latipes)

Organisms living in temperate regions are sensitive to seasonal variations in the environment; they are known to accumulate energy as fat in their livers during the winter when days are shorter, temperatures are lower, and food is scarce. However, the impact of variations in photoperiod alone on hepatic lipid metabolism has not been well-studied. Therefore, in this study, we analyzed lipid metabolism in the liver of medaka, Oryzias latipes, while varying the length of days at constant temperature. Larger amounts of fatty acids accumulated in the liver after 14 days under short-day conditions than under long-day conditions. Metabolome analysis showed no accumulation of the long-chain unsaturated fatty acids required at low temperatures, but showed a significant accumulation of long-chain saturated fatty acids. Short-day conditions induced decreased levels of succinate, fumarate, and malate in the tricarboxylic acid cycle, decreased expression of PPAR, and decreased accumulation of acylcarnitine, which suggested inhibition of lipolysis. In addition, when a high-fat diet was administered to transparent medaka under short-day conditions, larger amounts of fat accumulated and medaka with fatty liver were efficiently produced. Detailed analysis of the relationship between seasonal changes and hepatic steatosis will be important in the future as hepatic diseases become more prevalent in modern society; the findings obtained in our study will be useful for research studies pertaining to the relationship between photoperiod and disorders such as hepatic steatosis and non-alcoholic steatohepatitis.

physiology↗

bioRxiv2019

Modeling the Human Segmentation Clock with Pluripotent Stem Cells

Pluripotent stem cells (PSCs) have increasingly been used to model different aspects of embryogenesis and organ formation1. Despite recent advances in the in vitro induction of major mesodermal lineages and mesoderm-derived cell types2,3, experimental model systems that can recapitulate more complex biological features of human mesoderm development and patterning are largely missing. Here, we utilized induced pluripotent stem cells (iPSCs) for the stepwise in vitro induction of presomitic mesoderm (PSM) and its derivatives to model distinct aspects of human somitogenesis. We focused initially on modeling the human segmentation clock, a major biological concept believed to underlie the rhythmic and controlled emergence of somites, which give rise to the segmental pattern of the vertebrate axial skeleton. We succeeded to observe oscillatory expression of core segmentation clock genes, including HES7 and DKK1, and identified novel oscillatory genes in human iPSC-derived PSM. We furthermore determined the period of the human segmentation clock to be around five hours and showed the presence of dynamic traveling wave-like gene expression within in vitro induced human PSM. Utilizing CRISPR/Cas9-based genome editing technology, we then targeted genes, for which mutations in patients with abnormal axial skeletal development such as spondylocostal dysostosis (SCD) (HES7, LFNG and DLL3) or spondylothoracic dysostosis (STD) (MESP2) have been reported. Subsequent analysis of patient-like iPSC knock-out lines as well as patient-derived iPSCs together with their genetically corrected isogenic controls revealed gene-specific alterations in oscillation, synchronization or differentiation properties, validating the overall utility of our model system, to recapitulate not only key features of human somitogenesis but also to provide novel insights into diseases associated with the formation and patterning of the human axial skeleton.

developmental biology↗

bioRxiv2017

Frequent Non-random Shifts in the Temporal Sequence of Developmental Landmark Events during Fish Evolutionary Diversification

Morphological transformations can be generated by evolutionary changes in the sequence of developmental events. In this study, we examined the evolutionary dynamics of the developmental sequence on a macroevolutionary scale using the teleost. Using the information from previous reports describing the development of 31 species, we extracted the developmental sequences of 19 landmark events involving the formation of phylogenetically conserved body parts; we then inferred ancestral developmental sequences by two different parsimony-based methods--event-pairing (Jeffery, Bininda-Emonds, Coates & Richardson, 2002a) and continuous analysis (Germain & Laurin, 2009). The phylogenetic comparisons of these sequences revealed event-dependent heterogeneity in the frequency of sequence changes. Most of the sequence changes occurred as exchanges of temporally neighboring events. The phylogenetic analyses suggested that the ancestral species had experienced frequent changes in developmental sequences. Although the analyses showed that these heterochronic changes accumulated along phylogenic time, the precise distribution of the changes over the teleost phylogeny remains unclear due to technical limitations. Finally, this first comprehensive analysis of teleost developmental sequences will provide solid ground on which to elucidate the significance of developmental timing in animal morphological diversification.

evolutionary biology↗