1. High throughput single-cell genome sequencing gives insights into ...
Here, we applied and validated a high throughput single-cell genome sequencing method to study for the first time the extent and dynamics of whole karyotype ...
Leishmania, a unicellular eukaryotic parasite, is a unique model for aneuploidy and cellular heterogeneity, along with their potential role in adaptation to environmental stresses. Somy variation within clonal populations was previously explored in a small subset of chromosomes using fluorescence hybridization methods. This phenomenon, termed mosaic aneuploidy (MA), might have important evolutionary and functional implications but remains under-explored due to technological limitations. Here, we applied and validated a high throughput single-cell genome sequencing method to study for the first time the extent and dynamics of whole karyotype heterogeneity in two clonal populations of Leishmania promastigotes representing different stages of MA evolution in vitro. We found that drastic changes in karyotypes quickly emerge in a population stemming from an almost euploid founder cell. This possibly involves polyploidization/hybridization at an early stage of population expansion, followed by assorted ploidy reduction. During further stages of expansion, MA increases by moderate and gradual karyotypic alterations, affecting a defined subset of chromosomes. Our data provide the first complete characterization of MA in Leishmania and pave the way for further functional studies.
2. High throughput single-cell genome sequencing gives insights into the ...
25 mei 2021 · ... Hideo Imamura ... donovani strains which was used as control for high levels of mosaicism in aneuploidy and for estimation of doublets.
Leishmania , a unicellular eukaryotic parasite, is a unique model for aneuploidy and cellular heterogeneity, along with their potential role in adaptation to environmental stresses. Somy variation within clonal populations was previously explored in a small subset of chromosomes using fluorescence hybridization methods. This phenomenon, termed mosaic aneuploidy (MA), might have important evolutionary and functional implications but remains under-explored due to technological limitations. Here, we applied and validated a high throughput single-cell genome sequencing method to study for the first time the extent and dynamics of whole karyotype heterogeneity in two Leishmania clonal populations representing different stages of MA evolution in vitro. We found that drastic changes in karyotypes quickly emerge in a population stemming from an almost euploid founder cell. This possibly involves polyploidization/hybridization at an early stage of population expansion, followed by assorted ploidy reduction. During further stages of expansion, MA increases by moderate and gradual karyotypic alterations. MA usually affected a defined subset of chromosomes, of which some display an enrichment in snoRNA genes which could represent an adaptative benefit to the amplification of these chromosomes. Our data provide the first complete characterization of MA in Leishmania and pave the way for further functional studies. Note to the BioRxiv community The present preprint is a revision of an old...
3. High throughput single-cell genome sequencing gives insights into the ...
10 dec 2021 · We applied and validated a high throughput single-cell genome sequencing method to study for the first time the extent and dynamics of whole karyotype ...
Leishmania, a unicellular eukaryotic parasite, is a unique model for aneuploidy and cellular heterogeneity, along with their potential role in adaptation to environmental stresses. Somy variation within clonal populations was previously explored in ...
4. Exploring the evolution and adaptive role of mosaic aneuploidy in a ...
26 mei 2021 · Exploring the evolution and adaptive role of mosaic aneuploidy in a clonal Leishmania donovani population using high throughput single cell ...
Maintenance of stable ploidy over continuous mitotic events is a paradigm for most higher eukaryotes. Defects in chromosome segregation and/or replication can lead to aneuploidy, a condition often considered deleterious. However, in Leishmania , a Protozoan parasite, aneuploidy is a constitutive feature, where variations of somies represent a mechanism of gene expression adaptation, possibly impacting phenotypes. Strikingly, clonal Leishmania populations display cell-to-cell somy variation, a phenomenon named mosaic aneuploidy (MA). However, until recently, no method was available for the determination of the complete karyotype of single Leishmania parasites. To overcome this limitation, we used here for the first time a high-throughput single-cell genomic sequencing (SCGS) method to estimate individual karyotypes of 1560 promastigote cells in a clonal population of Leishmania donovani . We identified 128 different karyotypes, of which 4 were dominant. A network analysis revealed that most karyotypes are linked to each other by changes in copy number of a single chromosome and allowed us to propose a hypothesis of MA evolution. Moreover, aneuploidy patterns that were previously described by Bulk Genome Sequencing as emerging during first contact of promastigotes populations with different drugs are already pre-existing in single karyotypes in the SCGS data, suggesting a (pre-)adaptive role of MA. Additionally, the degree of somy variation was chromosome-specific. The SCGS als...
5. Refining wet lab experiments with in silico searches: A rational quest for ...
Hideo Imamura, ... BackgroundThe search for diagnostic biomarkers has been profiting from a growing number of high quality sequenced genomes and freely available ...
BackgroundThe search for diagnostic biomarkers has been profiting from a growing number of high quality sequenced genomes and freely available bioinformatic...
6. Aneuploidy and mosaicism: a strategy for early adaptation todrug pressure ...
Imamura, Hideo (Researcher); Van den Broeck, Frederik (Researcher) ... Using single cell genomics and high-resolution tracking of parasite lineages ...
Project Details
7. A high-throughput, selective method for RNA-seq in Trypanosomatids
16 jun 2017 · ... high-resolution and high-throughput fashion. We first analyzed ... Domagalska, Géraldine de Muylder, Manu Vanaerschot, Hideo Imamura, Franck ...
High throughput sequencing techniques are poorly adapted for in vivo studies of parasites, which require prior in vitro culturing and purification. Trypanosomatids, a group of kinetoplastid protozoans, possess a distinctive feature in their transcriptional mechanism whereby a specific Spliced Leader (SL) sequence is added to the 5′end of each mRNA by trans-splicing. This allows to discriminate Trypansomatid RNA from mammalian RNA and forms the basis of our new multiplexed protocol for high-throughput, selective RNA-sequencing called SL-seq. We provided a proof-of-concept of SL-seq in Leishmania donovani, the main causative agent of visceral leishmaniasis in humans, and successfully applied the method to sequence Leishmania mRNA directly from infected macrophages and from highly diluted mixes with human RNA. mRNA profiles obtained with SL-seq corresponded largely to those obtained from conventional poly-A tail purification methods, indicating both enumerate the same mRNA pool. However, SL-seq offers additional advantages, including lower sequencing depth requirements, fast and simple library prep and high resolution splice site detection. SL-seq is therefore ideal for fast and massive parallel sequencing of parasite transcriptomes directly from host tissues. Since SLs are also present in Nematodes, Cnidaria and primitive chordates, this method could also have high potential for transcriptomics studies in other organisms.
8. Diversity and within-host evolution of parasites from VL and VL/HIV ...
6 apr 2021 · The largest focus of VL in Ethiopia is driven by high prevalence in migrant agricultural workers and associated with a high rate of co-infection ...
Visceral leishmaniasis (VL) is a fatal disease and a growing public health problem in East Africa, where Ethiopia has one of the highest VL burdens. The largest focus of VL in Ethiopia is driven by high prevalence in migrant agricultural workers and associated with a high rate of co-infection with HIV. This co-infection makes VL more difficult to treat successfully, and is associated with a high rate of relapse, with VL/HIV patients frequently experiencing many relapses of VL before succumbing to this infection. We present genome-wide data on Leishmania donovani isolates from a longitudinal study of cohorts of VL and VL/HIV patients reporting to a single clinic in Ethiopia. Extensive clinical data allows us to investigate the influence of co-infection and relapse on the populations of parasites infecting these patients. We find that the same parasite population is responsible for both VL and VL/HIV infections, and that in most cases, disease relapse is caused by recrudescence of the population of parasites that caused primary VL. Complex, multi-clonal infections are present in both primary and relapse cases, but the infrapopulation of parasites within a patient loses genetic diversity between primary disease presentation and subsequent relapses, presumably due to a population bottleneck induced by treatment. These data suggest that VL/HIV relapses are not caused by genetically distinct parasite infections, nor by re-infection. Treatment of VL does not lead to sterile cure, an...
9. A rational quest for diagnostic peptides in visceral leishmaniasis
... high accessibility to B-cells. Selected candidates had their linear epitopes ... AU - Imamura, Hideo. AU - Dujardin, Jean-Claude. AU - El-Safi, Sayda. AU ...
See AlsoEleanor Henry SpousesBACKGROUND: The search for diagnostic biomarkers has been profiting from a growing number of high quality sequenced genomes and freely available bioinformatic tools. These can be combined with wet lab experiments for a rational search. Improved, point-of-care diagnostic tests for visceral leishmaniasis (VL), early case detection and surveillance are required. Previous investigations demonstrated the potential of IgG1 as a biomarker for monitoring clinical status in rapid diagnostic tests (RDTs), although using a crude lysate antigen (CLA) as capturing antigen. Replacing the CLA by specific antigens would lead to more robust RDTs.
10. A rational quest for diagnostic peptides in visceral leishmaniasis
6 mei 2019 · Hideo Imamura. Affiliation: Department of Biomedical Sciences ... high accessibility to B-cells. Selected candidates had their linear ...
Author summary Visceral leishmaniasis (VL) is a neglected tropical disease caused by protozoan parasites of the Leishmania donovani complex. Without treatment, VL is fatal. Although diagnostic techniques, mainly based on the detection of anti-Leishmania antibodies are available, invasive procedures such as microscopy from spleen or bone marrow aspirates are still required for the diagnosis of seronegative VL suspects, for the detection of recurrent cases and to confirm cure after successful treatment. Previous investigations showed the potential of IgG1 as a biomarker of post-chemotherapeutic relapse for VL in rapid diagnostic tests (RDTs) sensitised with crude lysate antigen (CLA). Here we employed in silico tools to search for desired protein features in a large number of L. donovani antigens detected by human IgG1 in western blots. We then employed prediction algorithms to profile epitopes from the shortlisted proteins. We screened a panel of high-scoring peptides in a high-throughput manner using arrays, with low reagent consumption. The most reactive peptide was adapted to RDTs, showing promising results of both sensitivity and specificity. This peptide has the potential of replacing the CLAs in IgG1 RDTs. Thus we believe that in silico tools can be used to optimise wet lab experiments for a rational search of biomarkers.
11. IMAMURA Kosuke - Directory of Researchers at Kanazawa University
15 mrt 2024 · High Efficiency Image Coding Using Matching Pursuits. A video coding ... Imamura, Hideo Hashimoto 35 5 653-662 2005/09. Conference ...
last modified：2024/03/15
12. High throughput single-cell genome sequencing gives insights into the ...
High throughput single-cell genome sequencing gives insights into the generation and evolution of mosaic aneuploidy inLeishmania donovani.
AbstractLeishmania, a unicellular eukaryotic parasite, is a unique model for aneuploidy and cellular heterogeneity, along with their potential role in adaptation to environmental stresses. Somy variation within clonal populations was previously explored in a small subset of chromosomes using fluorescence hybridization methods. This phenomenon, termed mosaic aneuploidy (MA), might have important evolutionary and functional implications but remains under-explored due to technological limitations. Here, we ap…
13. Exploring the evolution and adaptive role of mosaic aneuploidy in a ...
26 mei 2021 · Negreira , Pieter Monsieurs , Hideo Imamura , Ilse Maes , Nada Kuk ... To overcome this limitation, we used here for the first time a high ...
Maintenance of stable ploidy over continuous mitotic events is a paradigm for most higher eukaryotes. Defects in chromosome segregation and/or replication can lead to aneuploidy, a condition often considered deleterious. However, in Leishmania, a Protozoan parasite, aneuploidy is a constitutive feature, where variations of somies represent a mechanism of gene expression adaptation, possibly impacting phenotypes. Strikingly, clonal Leishmania populations display cell-to-cell somy variation, a phe
14. High Electron Mobility Silicon Films Grown on Sapphire at High Growth ...
High Electron Mobility Silicon Films Grown on Sapphire at High Growth Rate, Yoshihiro Imamura, Katsuhiko Daido, Kazushige Mimegishi, Hideo Nakanishi.
High Electron Mobility Silicon Films Grown on Sapphire at High Growth Rate, Imamura, Yoshihiro, Daido, Katsuhiko, Mimegishi, Kazushige, Nakanishi, Hideo
15. A High-Speed Closest Codeword Search Algorithm for Vector ...
書誌. 論文. A High-Speed Closest Codeword Search Algorithm for Vector Quantization Using the Pyramid Structure of Codewords. Ahmed SWILEM, Kousuke IMAMURA, ...
Vector quantization (VQ) for image compression requires expensive time to find the closest codeword in both encoding and codebook design. In this pape …
16. Our Professionals | About Us | ABeam Consulting
High Technology · Food · Supply Chain Management. Yoichiro ... Tatsuya Imamura. Principal. LinkedIn · DX · Supply Chain Management · Engineering ...
ABeam Consulting strives to be the No. 1 global consulting firm originating from Japan and Asia, providing services tailored to each country and region through professionals in each industry, sector, and service and alliance partners around the world. We are a comprehensive management consulting firm that provides services tailored to each country and region. We introduce our professionals who contribute to the transformation of organizations, companies, and society as transformation partners who create value together with our clients.
