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Cell lineage tree

Simon Mitchell, Koushik Roy, Thomas A Zangle, Alexander Hoffmann
Rapid antibody production in response to invading pathogens requires the dramatic expansion of pathogen-derived antigen-specific B lymphocyte populations. Whether B cell population dynamics are based on stochastic competition between competing cell fates, as in the development of competence by the bacterium Bacillus subtilis , or on deterministic cell fate decisions that execute a predictable program, as during the development of the worm Caenorhabditis elegans , remains unclear. Here, we developed long-term live-cell microscopy of B cell population expansion and multiscale mechanistic computational modeling to characterize the role of molecular noise in determining phenotype heterogeneity...
March 7, 2018: Proceedings of the National Academy of Sciences of the United States of America
Anne Müsch
The vertebrate liver presents a fascinating case study for how cell form is optimized for function. To execute its duties the liver assembles two distinct lumen-forming epithelial phenotypes: Firstly, cords with a branched, capillary-like luminal network formed between hepatocytes (bile canaliculi); and secondly, tubular ducts formed by biliary epithelial cells arranged around a central cavity and connected to the bile canaliculi. How these remarkably different epithelial polarity phenotypes are generated and joined into a contiguous luminal network are major unresolved questions...
March 2, 2018: Current Opinion in Cell Biology
Orsolya Kapuy, P K Vinod, Gábor Bánhegyi, Béla Novák
Ostreococcus tauri is the smallest free-living unicellular organism with one copy of each core cell cycle genes in its genome. There is a growing interest in this green algae due to its evolutionary origin. Since O. tauri is diverged early in the green lineage, relatively close to the ancestral eukaryotic cell, it might hold a key phylogenetic position in the eukaryotic tree of life. In this study, we focus on the regulatory network of its cell division cycle. We propose a mathematical modelling framework to integrate the existing knowledge of cell cycle network of O...
February 19, 2018: Plant Physiology and Biochemistry: PPB
Christopher Maximilian Arends, Joel Galan-Sousa, Kaja Hoyer, Willy Chan, Marten Jäger, Kenichi Yoshida, Ricarda Seemann, Daniel Noerenberg, Nils Waldhueter, Helga Fleischer-Notter, Friederike Christen, Clemens A Schmitt, Bernd Dörken, Uwe Pelzer, Marianne Sinn, Tomasz Zemojtel, Seishi Ogawa, Sven Märdian, Adrian Schreiber, Annegret Kunitz, Ulrike Krüger, Lars Bullinger, Elena Mylonas, Mareike Frick, Frederik Damm
Clonal hematopoiesis of indeterminate potential (CHIP) occurs in an age-related manner and associates with an increased risk of hematologic cancer, atherosclerotic disease, and shorter overall survival. Little is known about the cell of origin, repartition patterns of clonal mutations within the hematopoietic differentiation tree, and its dynamics under evolutionary pressure. Using targeted sequencing, CHIP was identified in 121 out of 437 elderly individuals (27.7%). Variant allele frequencies (VAFs) of 91 mutations were studied in six peripheral blood cell fractions...
March 1, 2018: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
William S DeWitt, Luka Mesin, Gabriel D Victora, Vladimir N Minin, Frederick A Matsen
Modern biological techniques enable very dense genetic sampling of unfolding evolutionary histories, and thus frequently sample some genotypes multiple times. This motivates strategies to incorporate genotype abundance information in phylogenetic inference. In this paper, we synthesize a stochastic process model with standard sequence-based phylogenetic optimality, and show that tree estimation is substantially improved by doing so. Our method is validated with extensive simulations and an experimental single-cell lineage tracing study of germinal center B cell receptor affinity maturation...
February 20, 2018: Molecular Biology and Evolution
Seon Choi, Joo Won Kang, Jung-Hoon Yoon, Chi Nam Seong
A non-motile, proteorhodopsin-containing, yellow and rod-shaped bacterial strain, designated ZODW10T , was isolated from the seaweed Zostera marina collected from the West Sea, Republic of Korea. Cells were Gram-stain-negative, aerobic and non-motile. The isolate required sea salts for growth. A carotenoid pigment was produced. A phylogenetic tree based on 16S rRNA gene sequences showed that strain ZODW10T forms an evolutionary lineage within the radiation enclosing members of the genus Dokdonia with Dokdoniadiaphoros CIP 108745T (96...
February 1, 2018: International Journal of Systematic and Evolutionary Microbiology
Sarah Marburger, Markos A Alexandrou, John B Taggart, Simon Creer, Gary Carvalho, Claudio Oliveira, Martin I Taylor
Genome size varies significantly across eukaryotic taxa and the largest changes are typically driven by macro-mutations such as whole genome duplications (WGDs) and proliferation of repetitive elements. These two processes may affect the evolutionary potential of lineages by increasing genetic variation and changing gene expression. Here, we elucidate the evolutionary history and mechanisms underpinning genome size variation in a species-rich group of Neotropical catfishes (Corydoradinae) with extreme variation in genome size-0...
February 14, 2018: Proceedings. Biological Sciences
Yuan-Dong Hu, Qiong Zhao, Xue-Rong Zhang, Liu-Lin Xiong, Zi-Bin Zhang, Piao Zhang, Rong-Ping Zhang, Ting-Hua Wang
Neural stem cells (NSCs) are characterized by the ability of self‑renewal and capacity to proliferate and produce new nervous tissue. NSCs are capable of differentiating to three lineages of neural cells, including neurons, oligodendrocytes and astrocytes. Furthermore, hippocampal NSCs transplantation can improve the neurological deficits associated with expression of cytokines. Therefore, to compare the properties of NSCs of tree shrews and rats in vitro, NSCs from tree shrews (tsNSCs) and rats f(rNSCs) were isolated...
February 12, 2018: Molecular Medicine Reports
Takashi Komori, Yoshihiro Muragaki, Mikhail F Chernov
Current World Health Organization (WHO) classification of the neuroepithelial tumors is cell lineage-oriented and based on a presumed developmental tree of the central nervous system (CNS). It defines three main groups of gliomas, namely astrocytomas, oligodendrogliomas, and ependymomas, and additionally presumes their 4-tiered histopathological grading (WHO grades I to IV). Nevertheless, the impact of tumor pathology on clinically related parameters may be frequently much better predicted by genetics, than by histological appearance of the lesion...
2018: Progress in Neurological Surgery
R Ariel Gomez, Maria Luisa S Sequeira-Lopez
An accumulating body of evidence suggests that renin-expressing cells have developed throughout evolution as a mechanism to preserve blood pressure and fluid volume homeostasis as well as to counteract a number of homeostatic and immunological threats. In the developing embryo, renin precursor cells emerge in multiple tissues, where they differentiate into a variety of cell types. The function of those precursors and their progeny is beginning to be unravelled. In the developing kidney, renin-expressing cells control the morphogenesis and branching of the renal arterial tree...
January 30, 2018: Nature Reviews. Nephrology
Maria Consiglia Bragazzi, Lorenzo Ridola, Samira Safarikia, Sabina Di Matteo, Daniele Costantini, Lorenzo Nevi, Vincenzo Cardinale
Cholangiocarcinoma (CCA) is a heterogeneous group of malignancies that may develop at any level of the biliary tree. CCA is currently classified into intrahepatic (iCCA), perihilar (pCCA) and distal (dCCA) on the basis of its anatomical location. Notably, although these three CCA subtypes have common features, they also have important inter- and intra-tumor differences that can affect their pathogenesis and outcome. A unique feature of CCA is that it manifests in the hepatic parenchyma or large intrahepatic and extrahepatic bile ducts, furnished by two distinct stem cell niches: the canals of Hering and the peribiliary glands, respectively...
January 2018: Annals of Gastroenterology: Quarterly Publication of the Hellenic Society of Gastroenterology
Alejo E Rodriguez-Fraticelli, Samuel L Wolock, Caleb S Weinreb, Riccardo Panero, Sachin H Patel, Maja Jankovic, Jianlong Sun, Raffaele A Calogero, Allon M Klein, Fernando D Camargo
Haematopoiesis, the process of mature blood and immune cell production, is functionally organized as a hierarchy, with self-renewing haematopoietic stem cells and multipotent progenitor cells sitting at the very top. Multiple models have been proposed as to what the earliest lineage choices are in these primitive haematopoietic compartments, the cellular intermediates, and the resulting lineage trees that emerge from them. Given that the bulk of studies addressing lineage outcomes have been performed in the context of haematopoietic transplantation, current models of lineage branching are more likely to represent roadmaps of lineage potential than native fate...
January 11, 2018: Nature
Xyrus X Maurer-Alcalá, Rob Knight, Laura A Katz
Separate germline and somatic genomes are found in numerous lineages across the eukaryotic tree of life, often separated into distinct tissues (e.g., in plants, animals, and fungi) or distinct nuclei sharing a common cytoplasm (e.g., in ciliates and some foraminifera). In ciliates, germline-limited (i.e., micronuclear-specific) DNA is eliminated during the development of a new somatic (i.e., macronuclear) genome in a process that is tightly linked to large-scale genome rearrangements, such as deletions and reordering of protein-coding sequences...
January 9, 2018: MBio
Joana Carrelha, Yiran Meng, Laura M Kettyle, Tiago C Luis, Ruggiero Norfo, Verónica Alcolea, Francesca Grasso, Adriana Gambardella, Amit Grover, Kari Högstrand, Allegra M Lord, Alejandra Sanjuan-Pla, Petter S Woll, Claus Nerlov, Jacobsen Sten Eirik W
Rare multipotent hematopoietic stem cells (HSCs) in adult bone marrow (BM) with extensive self-renewal potential possess the ability to efficiently replenish all myeloid and lymphoid blood cells1, securing long-term multilineage reconstitution following physiological and clinical challenges, including chemotherapy and hematopoietic transplantations2-4. HSC transplantation remains the only curative treatment for many hematological malignancies, but inefficient blood-lineage replenishment remains a major cause of morbidity and mortality5-6...
January 3, 2018: Nature
Alexandra M Gehring, Travis J Sanders, Thomas J Santangelo
The advent of single cell genomics and the continued use of metagenomic profiling in diverse environments has exponentially increased the known diversity of life. The recovered and assembled genomes predict physiology, consortium interactions and gene function, but experimental validation of metabolisms and molecular pathways requires more directed approaches. Gene function-and the correlation between phenotype and genotype is most obviously studied with genetics, and it is therefore critical to develop techniques permitting rapid and facile strain construction...
November 20, 2017: Bio-protocol
Emmanouil I Athanasiadis, Jan G Botthof, Helena Andres, Lauren Ferreira, Pietro Lio, Ana Cvejic
The success of marker-based approaches for dissecting haematopoiesis in mouse and human is reliant on the presence of well-defined cell surface markers specific for diverse progenitor populations. An inherent problem with this approach is that the presence of specific cell surface markers does not directly reflect the transcriptional state of a cell. Here, we used a marker-free approach to computationally reconstruct the blood lineage tree in zebrafish and order cells along their differentiation trajectory, based on their global transcriptional differences...
December 11, 2017: Nature Communications
Ram Hari Dahal, Jaisoo Kim
Two isolates of bacterial strains A15T and A17 were isolated from stream bank soil in Kyonggi University. Cells were aerobic, Gram-stain-negative, oxidase- and catalase-positive, motile, non-spore-forming, rod-shaped, opaque, and cream coloured. Both strains hydrolysed CM-cellulose. Strains were able to grow at 20-42 °C, pH 5.5-10.0 and at 1.5 % NaCl concentration (w/v). Indole test was positive. Analyses of phylogenetic trees based on its 16S rRNA gene sequences indicated that strain A15T formed a lineage within the family Rhodospirillaceae of the phylum Proteobacteria which was distinct from Ferrovibrio denitrificans S3T (98...
January 2018: International Journal of Systematic and Evolutionary Microbiology
Tanja Stadler, Stavroula Skylaki, Konstantinos D Kokkaliaris, Timm Schroeder
Stem cells play a central role in the regeneration and repair of multicellular organisms. However, it remains far from trivial to reliably identify them. Despite decades of work, current techniques to isolate hematopoietic stem cells (HSCs) based on cell-surface markers only result in 50% purity, i.e. half of the sorted cells are not stem cells when functionally tested. Modern microscopy techniques allow us to follow single cells and their progeny for up to weeks in vitro, while recording the cell fates and lifetime of each individual cell...
February 14, 2018: Journal of Theoretical Biology
Nathan J Kenny, Jasper M de Goeij, Didier M de Bakker, Casey G Whalen, Eugene Berezikov, Ana Riesgo
Regeneration is an essential process for all multicellular organisms, allowing them to recover effectively from internal and external injury. This process has been studied extensively in a medical context in vertebrates, with pathways often investigated mechanistically, both to derive increased understanding and as potential drug targets for therapy. Several species from other parts of the metazoan tree of life, including Hydra, planarians and echinoderms, noted for their regenerative capabilities, have previously been targeted for study...
November 29, 2017: Marine Genomics
Charles Dussiau, Michaela Fontenay
Myelodysplastic syndromes (MDS) are hematopoietic stem cell (HSC) disorders in which recurrent chromosome abnormalities and gene mutations define a clonal hematopoiesis. The MDS-initiating cell is a rare HSC which transmits the genetic abnormalities to its myeloid and lymphoid progeny. The heterogeneity of MDS phenotypes could be linked to the diversity of genetic events involving epigenetic regulators, chromatin modifiers, splicing factors, transcription factors and signaling adaptors, the various combinations and order of mutations in cooperating genes, and the variegation of clonal hematopoietic hierarchy...
February 2018: Experimental Hematology
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