scholarly journals Retention of Prey Genetic Material by the Kleptoplastidic Ciliate Strombidium cf. basimorphum

2021 ◽  
Vol 12 ◽  
Author(s):  
Maira Maselli ◽  
Konstantinos Anestis ◽  
Kerstin Klemm ◽  
Per Juel Hansen ◽  
Uwe John
Keyword(s):  
Molecular Marker ◽  
Single Cell ◽  
Genetic Material ◽  
Molecular Tools ◽  
Marine Ciliate ◽  
Ciliate Species ◽  
New Findings ◽  
Nuclear Control

Many marine ciliate species retain functional chloroplasts from their photosynthetic prey. In some species, the functionality of the acquired plastids is connected to the simultaneous retention of prey nuclei. To date, this has never been documented in plastidic Strombidium species. The functionality of the sequestered chloroplasts in Strombidium species is thought to be independent from any nuclear control and only maintained via frequent replacement of chloroplasts from newly ingested prey. Chloroplasts sequestered from the cryptophyte prey Teleaulax amphioxeia have been shown to keep their functionality for several days in the ciliate Strombidium cf. basimorphum. To investigate the potential retention of prey genetic material in this ciliate, we applied a molecular marker specific for this cryptophyte prey. Here, we demonstrate that the genetic material from prey nuclei, nucleomorphs, and ribosomes is detectable inside the ciliate for at least 5 days after prey ingestion. Moreover, single-cell transcriptomics revealed the presence of transcripts of prey nuclear origin in the ciliate after 4 days of prey starvation. These new findings might lead to the reconsideration of the mechanisms regulating chloroplasts retention in Strombidium ciliates. The development and application of molecular tools appear promising to improve our understanding on chloroplasts retention in planktonic protists.

scholarly journals Single-Cell RNA Sequencing in Parkinson’s Disease

Biomedicines ◽  
2021 ◽  
Vol 9 (4) ◽  
pp. 368
Author(s):  
Shi-Xun Ma ◽  
Su Bin Lim
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Single Cell ◽  
Rna Sequencing ◽  
Rna Degradation ◽  
Postmortem Brain ◽  
Cell Type ◽  
New Findings ◽  
Postmortem Brain Tissue ◽  
Technical Challenges

Single-cell and single-nucleus RNA sequencing (sc/snRNA-seq) technologies have enhanced the understanding of the molecular pathogenesis of neurodegenerative disorders, including Parkinson’s disease (PD). Nonetheless, their application in PD has been limited due mainly to the technical challenges resulting from the scarcity of postmortem brain tissue and low quality associated with RNA degradation. Despite such challenges, recent advances in animals and human in vitro models that recapitulate features of PD along with sequencing assays have fueled studies aiming to obtain an unbiased and global view of cellular composition and phenotype of PD at the single-cell resolution. Here, we reviewed recent sc/snRNA-seq efforts that have successfully characterized diverse cell-type populations and identified cell type-specific disease associations in PD. We also examined how these studies have employed computational and analytical tools to analyze and interpret the rich information derived from sc/snRNA-seq. Finally, we highlighted important limitations and emerging technologies for addressing key technical challenges currently limiting the integration of new findings into clinical practice.

scholarly journals ETMR-05. SINGLE-CELL RNA-SEQ OF ETMR REVEALS CELL PROGRAMS OF DEVELOPMENTAL HIERARCHY AND CELLULAR DIVERSITY IN THE TUMOR MICROENVIRONMENT

2020 ◽  
Vol 22 (Supplement_3) ◽  
pp. iii323-iii323
Author(s):  
Flavia W de Faria ◽  
Marta Interlandi ◽  
Natalia Moreno ◽  
Monika Graf ◽  
Viktoria Melcher ◽  
...  
Keyword(s):  
Stem Cell ◽  
Single Cell ◽  
Molecular Mechanisms ◽  
Interaction Analysis ◽  
Cellular Heterogeneity ◽  
Receptor Interaction ◽  
Acid Oxidation ◽  
Bmp Receptors ◽  
New Findings ◽  
Developmental Hierarchy

Abstract Embryonal tumors with multilayered rosettes (ETMR) are deadly brain malignancies affecting young children. No standard treatment is available and the median survival is less than 12 months. Molecularly, the disease is characterized by the miRNA C19MC cluster amplification, with the expression of multiples miRNAs related to a stem cell program. The discoveries on the purely molecular mechanisms of the disease did not help to create a bridge for new treatment strategies so far and the cellular diversity of ETMR remains poorly understood. In this study, we used single-cell RNA sequencing of murine and human tumors to describe ETMR cellular heterogeneity. Our findings support that intra-tumoral heterogeneity is mainly characterized by 4 cellular programs defining a developmental hierarchy related to different metabolic states: 1) Early quiescent NSC-like cells supported by fatty-acid oxidation 2) Late NSC and NP-like proliferative cells fueled by glycolytic metabolism; 3) Post-mitotic neuroblast-like cells, relying on oxidative-phosphorylation; 4) NSC-like proliferative cells, with metabolic plasticity and capable of performing the three types of metabolism. Tumor-specific ligand-receptor interaction analysis revealed that ETMR exchange with microglia and vascular mural cells (MC) signals related to extracellular matrix (ECM) organization (Cxcl12-CxCr4), stem cell signaling (BMPs-BMP receptors), anti-apoptosis and survival (Ntf3-Ntrk), not seen in the control brain. In addition, the vascular MC showed a cancer-associated fibroblast (CAF) phenotype, with potential prognostic implications, as previously demonstrated for other tumors. This study provides new findings to build up a more robust understanding of ETMR biology and opens space for further studies in the field.

scholarly journals Single-cell transcriptomics allows novel insights into aging and circadian processes

2020 ◽  
Vol 19 (5-6) ◽  
pp. 343-349
Author(s):  
Sara S Fonseca Costa ◽  
Marc Robinson-Rechavi ◽  
Jürgen A Ripperger
Keyword(s):  
Single Cell ◽  
Single Cells ◽  
Cellular Level ◽  
Biological Processes ◽  
New Methods ◽  
New Findings ◽  
Single Cell Rna Sequencing ◽  
Aging And Circadian Rhythms ◽  
Insight Into ◽  
Different Time Scales

Abstract Aging and circadian rhythms are two biological processes that affect an organism, although at different time scales. Nevertheless, due to the overlap of their actions, it was speculated that both interfere or interact with each other. However, to address this question, a much deeper insight into these processes is necessary, especially at the cellular level. New methods such as single-cell RNA-sequencing (scRNA-Seq) have the potential to close this gap in our knowledge. In this review, we analyze applications of scRNA-Seq from the aging and circadian rhythm fields and highlight new findings emerging from the analysis of single cells, especially in humans or rodents. Furthermore, we judge the potential of scRNA-Seq to identify common traits of both processes. Overall, this method offers several advantages over more traditional methods analyzing gene expression and will become an important tool to unravel the link between these biological processes.

scholarly journals Single-cell RNA-Aequencing Reveals Novel Myofibroblasts with Epithelial Cell-Like Features in the Mammary Gland of Dairy Cattle

2020 ◽  
Author(s):  
Fengfei Gu ◽  
Jiajin Wu ◽  
Senlin Zhu ◽  
Teresa G. Valencak ◽  
Jian-Xin Liu ◽  
...  
Keyword(s):  
Mammary Gland ◽  
Epithelial Cell ◽  
Epithelial Cells ◽  
Dairy Cattle ◽  
Single Cell ◽  
Dairy Product ◽  
Cell Types ◽  
Marker Genes ◽  
New Findings ◽  
Luminal Cells

Abstract Background: Cow’s milk is a highly-nutritious dairy product that is widely consumed worldwide. It is secreted by the developed mammary gland (MG) of dairy cattle. However, a comprehensive understanding of cell-type diversity and cell function within bovine MG is lacking. In the current study, we used single-cell RNA sequencing to investigate the transcriptome of 24,472 high-quality MG cells isolated from newborn and adult cows. Results: Unbiased clustering analysis revealed the existence of 24 cell types, which could be divided into four categories: 9 immune, 3 epithelial, 9 fibroblast, and 3 endothelial cell types. Other cell subtypes were further identified based on re-clustering and pseudotemporal reconstruction of epithelial cells that included 3 mature luminal epithelial, 1 intermediate, and 2 progenitor cell subtypes. The individual top marker genes of these 3 mature luminal epithelial cell subtypes (L0, L1, and L5) were APOA1, STC2, and PTX3, which were further validated using immunofluorescence. Based on functional analysis, the L0, L1, and L5 cell subtypes were all involved in the upregulation of lipid metabolism, protein and hormone metabolism, and the immune response, respectively. Furthermore, we discovered a novel myofibroblast that expresses COL1A1 and CSN3, has visible epithelial-like characteristics, and shows the potential to differentiate into luminal epithelial cells, especially immune-sensing luminal cells (L5). Conclusions: We constructed the first single-cell atlas of the dairy cow MG, and our new findings of epithelial-like myofibroblast cells and their differentiation trajectories into luminal cells may provide novel insights into the development and lactogenesis in dairy cattle MGs.

Development of a novel molecular marker on the mitochondrial genome of a toxic dinoflagellate, Alexandrium spp., and its application in single-cell PCR

2007 ◽  
Vol 20 (2) ◽  
pp. 153-159 ◽  
Author(s):  
Ryoma Kamikawa ◽  
Shoko Hosoi-Tanabe ◽  
Sadaaki Yoshimatsu ◽  
Kenichi Oyama ◽  
Isao Masuda ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Molecular Marker ◽  
Single Cell ◽  
Toxic Dinoflagellate ◽  
Single Cell Pcr ◽  
Alexandrium Spp

scholarly journals Liquid biopsy: one cell at a time

2019 ◽  
Vol 3 (1) ◽  
Author(s):  
Su Bin Lim ◽  
Wen Di Lee ◽  
Jyothsna Vasudevan ◽  
Wan-Teck Lim ◽  
Chwee Teck Lim
Keyword(s):  
Single Cell ◽  
Liquid Biopsy ◽  
Temporal Dynamics ◽  
Genetic Material ◽  
Cellular Heterogeneity ◽  
Sources Of Information ◽  
Liquid Biopsies ◽  
Technological Developments ◽  
Clinically Significant ◽  
Tissue Specimens

Abstract As an alternative target to surgically resected tissue specimens, liquid biopsy has gained much attention over the past decade. Of the various circulating biomarkers, circulating tumor cells (CTCs) have particularly opened new windows into the metastatic cascade, with their functional, biochemical, and biophysical properties. Given the extreme rarity of intact CTCs and the associated technical challenges, however, analyses have been limited to bulk-cell strategies, missing out on clinically significant sources of information from cellular heterogeneity. With recent technological developments, it is now possible to probe genetic material of CTCs at the single-cell resolution to study spatial and temporal dynamics in circulation. Here, we discuss recent transcriptomic profiling efforts that enabled single-cell characterization of patient-derived CTCs spanning diverse cancer types. We further highlight how expression data of these putative biomarkers have advanced our understanding of metastatic spectrum and provided a basis for the development of CTC-based liquid biopsies to track, monitor, and predict the efficacy of therapy and any emergent resistance.

Cloning and characterisation of a new rye-specific repeated sequence

Genome ◽  
1991 ◽  
Vol 34 (1) ◽  
pp. 81-87 ◽  
Author(s):  
François Guidet ◽  
Peter Rogowsky ◽  
Christopher Taylor ◽  
Weining Song ◽  
Peter Langridge
Keyword(s):  
Molecular Marker ◽  
Dna Sequence ◽  
Repetitive Dna ◽  
Genetic Material ◽  
Repeated Sequence ◽  
Repeated Dna ◽  
New Family ◽  
Repetitive Dna Sequence ◽  
Repeated Dna Families

In this paper we describe a repetitive DNA sequence unique to the rye genome. The corresponding DNA probe (pAW173) was cloned as a 450-bp fragment and does not hybridize to wheat or barley DNA and is not related to five other repeated DNA families characterised in rye. This new family (designated the R173 family) consists of moderately repeated DNA (~ 15 000 units per genome) and is present on all seven rye chromosomes. The hybridization patterns in Southern blots indicate that it is not organised as blocks of tandem arrays and in situ hybridization shows that it is dispersed throughout the rye chromosomes. The probe has been successfully used as a molecular marker in identifying rye genetic material in a wheat background.Key words: repetitive DNA sequence, rye-specific DNA, molecular marker.

Conundrums in species concepts: the discovery of a new cryptic species segregated from Parmelina tiliacea(Ascomycota: Parmeliaceae)

2011 ◽  
Vol 43 (6) ◽  
pp. 603-616 ◽  
Author(s):  
Jano NÚÑEZ-ZAPATA ◽  
Pradeep K. DIVAKAR ◽  
Ruth DEL-PRADO ◽  
Paloma CUBAS ◽  
David L. HAWKSWORTH ◽  
...  
Keyword(s):  
Western Europe ◽  
Genetic Material ◽  
Small Region ◽  
Species Concepts ◽  
Conservation Strategies ◽  
Unexpected Result ◽  
Molecular Tools ◽  
Molecular Phylogenetic ◽  
Anatomical Characters ◽  
Genotype A

AbstractParmelina tiliacea is a common, widely distributed species in south-western Europe, easily identifiable by morphology and much used as an air pollution bioindicator in many regions. A molecular phylogenetic survey of samples from many geographical areas, using Maximum Parsimony and Bayesian inference of nuITS and mtLSU rDNA regions, revealed a group of samples geographically restricted to a small region of the Iberian Peninsula and genetically separated from the other P. tiliacea specimens studied. These samples are morphologically indistinguishable from P. tiliacea, apart from subtle anatomical characters in the ascomata (hyphae of the exciple and ascospore width), which are frequently absent. Although geographically different, the two taxa occupy similar habitats and are even sympatric in some areas, indicating that they do not exchange genetic material. This previously overlooked, and apparently endemic lineage, is described as P. cryptotiliacea sp. nov., and the name Lichen tiliaceus is epitypified by a sequenced specimen to fix the application of Parmelina tiliacea to the widespread genotype. A second unexpected result was the discovery that the morphologically distinct P. pastillifera was nested within P. tiliacea. These two cases stress the need to use molecular tools to elucidate species concepts even within widespread morphologically well-characterized macrolichens. Such investigations are necessary to improve our understanding and estimation of biodiversity, and to facilitate the development of sound biodiversity conservation strategies for lichens.

scholarly journals Concurrent processes setE. colicell division

2018 ◽  
Vol 4 (11) ◽  
pp. eaau3324 ◽  
Author(s):  
Gabriele Micali ◽  
Jacopo Grilli ◽  
Matteo Osella ◽  
Marco Cosentino Lagomarsino
Keyword(s):  
Cell Cycle ◽  
Cell Division ◽  
Single Cell ◽  
Chromosome Segregation ◽  
Genetic Material ◽  
Replication Initiation ◽  
Concurrent Processes ◽  
A Cell ◽  
Rate Limiting ◽  
Cell Data

A cell can divide only upon completion of chromosome segregation; otherwise, its daughters would lose genetic material. However, we do not know whether the partitioning of chromosomes is the key event for the decision to divide. We show how key trends in single-cell data reject the classic idea of replication-segregation as the rate-limiting process for cell division. Instead, the data agree with a model where two concurrent processes (setting replication initiation and interdivision time) set cell division on competing time scales. During each cell cycle, division is set by the slowest process (an “AND” gate). The concept of transitions between cell cycle stages as decisional processes integrating multiple inputs instead of cascading from orchestrated steps can affect the way we think of the cell cycle in general.

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