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Cell lineage tree

Zackary J Jay, Jacob P Beam, Mensur Dlakić, Douglas B Rusch, Mark A Kozubal, William P Inskeep
The discovery of archaeal lineages is critical to our understanding of the universal tree of life and evolutionary history of the Earth. Geochemically diverse thermal environments in Yellowstone National Park provide unprecedented opportunities for studying archaea in habitats that may represent analogues of early Earth. Here, we report the discovery and characterization of a phylum-level archaeal lineage proposed and herein referred to as the 'Marsarchaeota', after the red planet. The Marsarchaeota contains at least two major subgroups prevalent in acidic, microaerobic geothermal Fe(III) oxide microbial mats across a temperature range from ~50-80 °C...
May 14, 2018: Nature Microbiology
Thao Anh Tran, Luca Gentile
In planarians, pluripotency can be studied in vivo in the adult animal, making these animals a unique model system where pluripotency-based regeneration (PBR) -and its therapeutic potential- can be investigated. This review focuses on recent findings to build a cloud model of fate restriction likelihood for planarian stem and progenitor cells. Recently, a computational approach based on functional and molecular profiling at the single cell level was proposed for human hematopoietic stem cells. Based on data generated both in vivo and ex vivo, we hypothesized that planarian stem cells could acquire multiple direction lineage biases, following a "badlands" landscape...
May 1, 2018: Seminars in Cell & Developmental Biology
Juemin Xi, Junying Chen, Miaoling Xu, Hongying Yang, Songjiao Wen, Yue Pan, Xiaodan Wang, Chao Ye, Lijuan Qiu, Qiangming Sun
BACKGROUD: Variations in HPV LCR/E6/E7 have been shown to be associated with the viral persistence and cervical cancer development. So far, there are few reports about the polymorphisms of the HPV-58 LCR/E6/E7 sequences in Southwest China. This study aims to characterize the gene polymorphisms of the HPV-58 LCR/E6/E7 sequences in women of Southwest China, and assess the effects of variations on the immune recognition of viral E6 and E7 antigens. METHODS: Twelve LCR/E6/E7 of the HPV-58 isolates were amplified and sequenced...
April 25, 2018: Virology Journal
Mireya Plass, Jordi Solana, F Alexander Wolf, Salah Ayoub, Aristotelis Misios, Petar Glažar, Benedikt Obermayer, Fabian J Theis, Christine Kocks, Nikolaus Rajewsky
Flatworms of the species Schmidtea mediterranea are immortal-adult animals contain a large pool of pluripotent stem cells that continuously differentiate to all adult cell types. Therefore, single-cell transcriptome profiling of adult animals should reveal mature and progenitor cells. By combining perturbation experiments, gene expression analysis, a computational method that predicts future cell states from the transcriptional changes, and a lineage reconstruction method, we placed all major cell types onto a single lineage tree that connects all cells to a single stem cell compartment...
April 19, 2018: Science
Kazuhiko Tsuboi, Hiroyuki D Sakai, Naswandi Nur, Kenneth M Stedman, Norio Kurosawa, Antonius Suwanto
A novel hyperthermophilic, acidophilic and facultatively anaerobic archaeon, strain KD-1T , was isolated from an acidic hot spring in Indonesia and characterized with the phylogenetically related species Sulfurisphaera ohwakuensis Kurosawa et al. 1998, Sulfolobus tokodaii Suzuki et al., 2002 and Sulfolobus yangmingensis Jan et al. 1999. Cells of KD-1T were irregular cocci with diameters of 0.9-1.3 µm. The strain grew at 60-90 °C (optimum 80-85 °C), pH 2.5-6.0 (optimum pH 3.5-4.0) and 0-1.0 % (w/v) NaCl concentration...
April 19, 2018: International Journal of Systematic and Evolutionary Microbiology
Annie Visser, Marieke E Doorenspleet, Niek de Vries, Fred K L Spijkervet, Arjan Vissink, Richard J Bende, Hendrika Bootsma, Frans G M Kroese, Nicolaas A Bos
Previous studies revealed high incidence of acquired N-glycosylation sites acquired N-glycosylation sites in RNA transcripts encoding immunoglobulin heavy variable region (IGHV) 3 genes from parotid glands of primary Sjögren's syndrome (pSS) patients. In this study, next generation sequencing was used to study the extent of ac-Nglycs among clonally expanded cells from all IGVH families in the salivary glands of pSS patients. RNA was isolated from parotid gland biopsies of five pSS patients and five non-pSS sicca controls...
2018: Frontiers in Immunology
Bastiaan Spanjaard, Bo Hu, Nina Mitic, Pedro Olivares-Chauvet, Sharan Janjuha, Nikolay Ninov, Jan Philipp Junker
A key goal of developmental biology is to understand how a single cell is transformed into a full-grown organism comprising many different cell types. Single-cell RNA-sequencing (scRNA-seq) is commonly used to identify cell types in a tissue or organ. However, organizing the resulting taxonomy of cell types into lineage trees to understand the developmental origin of cells remains challenging. Here we present LINNAEUS (lineage tracing by nuclease-activated editing of ubiquitous sequences)-a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells...
April 9, 2018: Nature Biotechnology
Teofil Nakov, Jeremy M Beaulieu, Andrew J Alverson
Patterns of species richness are commonly linked to life history strategies. In diatoms, an exceptionally diverse lineage of photosynthetic heterokonts important for global photosynthesis and burial of atmospheric carbon, lineages with different locomotory and reproductive traits differ dramatically in species richness, but any potential association between life history strategy and diversification has not been tested in a phylogenetic framework. We constructed a time-calibrated, 11-gene, 1151-taxon phylogeny of diatoms - the most inclusive diatom species tree to date...
April 6, 2018: New Phytologist
Bushra Raj, Daniel E Wagner, Aaron McKenna, Shristi Pandey, Allon M Klein, Jay Shendure, James A Gagnon, Alexander F Schier
The lineage relationships among the hundreds of cell types generated during development are difficult to reconstruct. A recent method, GESTALT, used CRISPR-Cas9 barcode editing for large-scale lineage tracing, but was restricted to early development and did not identify cell types. Here we present scGESTALT, which combines the lineage recording capabilities of GESTALT with cell-type identification by single-cell RNA sequencing. The method relies on an inducible system that enables barcodes to be edited at multiple time points, capturing lineage information from later stages of development...
March 28, 2018: Nature Biotechnology
Sagar, Josip Stefan Herman, John Andrew Pospisilik, Dominic Grün
Understanding biological systems at a single cell resolution may reveal several novel insights which remain masked by the conventional population-based techniques providing an average readout of the behavior of cells. Single-cell transcriptome sequencing holds the potential to identify novel cell types and characterize the cellular composition of any organ or tissue in health and disease. Here, we describe a customized high-throughput protocol for single-cell RNA-sequencing (scRNA-seq) combining flow cytometry and a nanoliter-scale robotic system...
2018: Methods in Molecular Biology
Nan-Nan Wang, Chang-Ming Li, Ying-Xiu Li, Zong-Jun Du
An orange-coloured, slender rod-shaped, gliding bacterium, designated NS08T , was isolated from coastal water of Xiaoshi Island, Weihai, China (37° 31' 36'' N 122° 00' 58'' E). Cells were Gram-stain-negative, non-spore-forming, non-flagellated, aerobic, catalase-positive and oxidase-negative. Growth occurred at 10-37 °C (optimum 30 °C), in the presence of 1.0-5.0 % (w/v) NaCl (optimum 2.0-3.0 %) and at pH 6.5-9.0 (optimum pH 7.0-7.5). Carotenoid pigments were produced but flexirubin-type pigments were not...
March 26, 2018: International Journal of Systematic and Evolutionary Microbiology
Xiao-Xia Luo, Guang-Bin Gao, Zhan-Feng Xia, Zheng-Jun Chen, Chuan-Xing Wan, Li-Li Zhang
The taxonomic position of a novel actinomycete, strain TRM 41337T , isolated from sediment of a salt lake, Xiaoerkule Lake, Xinjiang, China, was determined by a polyphasic approach. Strain TRM 41337T grew optimally at 28 °C and in the presence of 1 % (w/v) NaCl. It grew at up to pH 12. The whole-cell sugars of strain TRM 41337T were ribose and xylose. The diagnostic diamino acid contained ll-diaminopimelic acid. The polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositolmannoside and two other unidentified phospholipids...
March 26, 2018: International Journal of Systematic and Evolutionary Microbiology
Seon Choi, Joo Won Kang, Mi Sun Kim, Jung-Hoon Yoon, Chi Nam Seong
A non-motile, orange-coloured and rod-shaped bacterial strain, designated strain ZOW29T , was isolated from a seaweed sample collected from the South Sea, Republic of Korea. Cells were Gram-stain-negative, aerobic and non-motile. The isolate required sea salts for growth. Carotenoid pigment was produced. A phylogenetic tree based on 16S rRNA gene sequences showed that strain ZOW29T forms an evolutionary lineage within the radiation enclosing the members of the genus Dokdonia with Dokdonia diaphoros MSKK-32T , Dokdonia eikasta PMA-26T and Dokdonia donghaensis DSW-1T (97...
March 23, 2018: International Journal of Systematic and Evolutionary Microbiology
Calvin K Lee, Jaime de Anda, Amy E Baker, Rachel R Bennett, Yun Luo, Ernest Y Lee, Joshua A Keefe, Joshua S Helali, Jie Ma, Kun Zhao, Ramin Golestanian, George A O'Toole, Gerard C L Wong
Using multigenerational, single-cell tracking we explore the earliest events of biofilm formation by Pseudomonas aeruginosa During initial stages of surface engagement (≤20 h), the surface cell population of this microbe comprises overwhelmingly cells that attach poorly (∼95% stay <30 s, well below the ∼1-h division time) with little increase in surface population. If we harvest cells previously exposed to a surface and direct them to a virgin surface, we find that these surface-exposed cells and their descendants attach strongly and then rapidly increase the surface cell population...
March 20, 2018: Proceedings of the National Academy of Sciences of the United States of America
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 20, 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...
May 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 article, 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...
May 1, 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...
March 2018: International Journal of Systematic and Evolutionary Microbiology
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