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Cell lineage tree

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https://www.readbyqxmd.com/read/27910875/an-integrated-modelling-framework-from-cells-to-organism-based-on-a-cohort-of-digital-embryos
#1
Paul Villoutreix, Julien Delile, Barbara Rizzi, Louise Duloquin, Thierry Savy, Paul Bourgine, René Doursat, Nadine Peyriéras
We conducted a quantitative comparison of developing sea urchin embryos based on the analysis of five digital specimens obtained by automatic processing of in toto 3D+ time image data. These measurements served the reconstruction of a prototypical cell lineage tree able to predict the spatiotemporal cellular organisation of a normal sea urchin blastula. The reconstruction was achieved by designing and tuning a multi-level probabilistic model that reproduced embryo-level dynamics from a small number of statistical parameters characterising cell proliferation, cell surface area and cell volume evolution along the cell lineage...
December 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27902188/sphingomonas-lutea-sp-nov-isolated-from-the-freshwater-of-artificial-reservoir
#2
Ji Hee Lee, Dae In Kim, Joo Won Kang, Chi Nam Seong
An aerobic, Gram-staining negative, gliding and yellow-pigmented bacterium, designated strain JS5T was isolated from freshwater of Juam reservoir, Republic of Korea. Cells are catalase-positive and oxidase-negative. Neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain JS5T forms an independent lineage within the genus Sphingomonas. Strain JS5T was related distantly to 'Sphingomonas parvus' GP20-2 (98.2 %, 16S rRNA gene sequence similarity), S. sediminicola Dae 20T (96.8 %) and S...
October 12, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27883891/analysis-of-cell-lineage-trees-by-exact-bayesian-inference-identifies-negative-autoregulation-of-nanog-in-mouse-embryonic-stem-cells
#3
Justin Feigelman, Stefan Ganscha, Simon Hastreiter, Michael Schwarzfischer, Adam Filipczyk, Timm Schroeder, Fabian J Theis, Carsten Marr, Manfred Claassen
Many cellular effectors of pluripotency are dynamically regulated. In principle, regulatory mechanisms can be inferred from single-cell observations of effector activity across time. However, rigorous inference techniques suitable for noisy, incomplete, and heterogeneous data are lacking. Here, we introduce stochastic inference on lineage trees (STILT), an algorithm capable of identifying stochastic models that accurately describe the quantitative behavior of cell fate markers observed using time-lapse microscopy data collected from proliferating cell populations...
November 23, 2016: Cell Systems
https://www.readbyqxmd.com/read/27883889/inferring-cell-state-transition-dynamics-from-lineage-trees-and-endpoint-single-cell-measurements
#4
Sahand Hormoz, Zakary S Singer, James M Linton, Yaron E Antebi, Boris I Shraiman, Michael B Elowitz
As they proliferate, living cells undergo transitions between specific molecularly and developmentally distinct states. Despite the functional centrality of these transitions in multicellular organisms, it has remained challenging to determine which transitions occur and at what rates without perturbations and cell engineering. Here, we introduce kin correlation analysis (KCA) and show that quantitative cell-state transition dynamics can be inferred, without direct observation, from the clustering of cell states on pedigrees (lineage trees)...
November 23, 2016: Cell Systems
https://www.readbyqxmd.com/read/27878138/measuring-process-dynamics-and-nuclear-migration-for-clones-of-neural-progenitor-cells
#5
Edgar Cardenas De La Hoz, Mark R Winter, Maria Apostolopoulou, Sally Temple, Andrew R Cohen
Neural stem and progenitor cells (NPCs) generate processes that extend from the cell body in a dynamic manner. The NPC nucleus migrates along these processes with patterns believed to be tightly coupled to mechanisms of cell cycle regulation and cell fate determination. Here, we describe a new segmentation and tracking approach that allows NPC processes and nuclei to be reliably tracked across multiple rounds of cell division in phase-contrast microscopy images. Results are presented for mouse adult and embryonic NPCs from hundreds of clones, or lineage trees, containing tens of thousands of cells and millions of segmentations...
October 2016: Computer Vision—ECCV: European Conference on Computer Vision: Proceedings
https://www.readbyqxmd.com/read/27869821/synthetic-recording-and-in-situ-readout-of-lineage-information-in-single-cells
#6
Kirsten L Frieda, James M Linton, Sahand Hormoz, Joonhyuk Choi, Ke-Huan K Chow, Zakary S Singer, Mark W Budde, Michael B Elowitz, Long Cai
Reconstructing the lineage relationships and dynamic event histories of individual cells within their native spatial context is a long-standing challenge in biology. Many biological processes of interest occur in optically opaque or physically inaccessible contexts, necessitating approaches other than direct imaging. Here, we describe a new synthetic system that enables cells to record lineage information and event histories in the genome in a format that can be subsequently read out in single cells in situ...
November 21, 2016: Nature
https://www.readbyqxmd.com/read/27863249/lineage-specific-genome-architecture-links-enhancers-and-non-coding-disease-variants-to-target-gene-promoters
#7
Biola M Javierre, Oliver S Burren, Steven P Wilder, Roman Kreuzhuber, Steven M Hill, Sven Sewitz, Jonathan Cairns, Steven W Wingett, Csilla Várnai, Michiel J Thiecke, Frances Burden, Samantha Farrow, Antony J Cutler, Karola Rehnström, Kate Downes, Luigi Grassi, Myrto Kostadima, Paula Freire-Pritchett, Fan Wang, Hendrik G Stunnenberg, John A Todd, Daniel R Zerbino, Oliver Stegle, Willem H Ouwehand, Mattia Frontini, Chris Wallace, Mikhail Spivakov, Peter Fraser
Long-range interactions between regulatory elements and gene promoters play key roles in transcriptional regulation. The vast majority of interactions are uncharted, constituting a major missing link in understanding genome control. Here, we use promoter capture Hi-C to identify interacting regions of 31,253 promoters in 17 human primary hematopoietic cell types. We show that promoter interactions are highly cell type specific and enriched for links between active promoters and epigenetically marked enhancers...
November 17, 2016: Cell
https://www.readbyqxmd.com/read/27812422/early-evolution-of-polyisoprenol-biosynthesis-and-the-origin-of-cell-walls
#8
Jonathan Lombard
After being a matter of hot debate for years, the presence of lipid membranes in the last common ancestor of extant organisms (i.e., the cenancestor) now begins to be generally accepted. By contrast, cenancestral cell walls have attracted less attention, probably owing to the large diversity of cell walls that exist in the three domains of life. Many prokaryotic cell walls, however, are synthesized using glycosylation pathways with similar polyisoprenol lipid carriers and topology (i.e., orientation across the cell membranes)...
2016: PeerJ
https://www.readbyqxmd.com/read/27774041/birth-of-archaeal-cells-molecular-phylogenetic-analyses-of-g1p-dehydrogenase-g3p-dehydrogenases-and-glycerol-kinase-suggest-derived-features-of-archaeal-membranes-having-g1p-polar-lipids
#9
Shin-Ichi Yokobori, Yoshiki Nakajima, Satoshi Akanuma, Akihiko Yamagishi
Bacteria and Eukarya have cell membranes with sn-glycerol-3-phosphate (G3P), whereas archaeal membranes contain sn-glycerol-1-phosphate (G1P). Determining the time at which cells with either G3P-lipid membranes or G1P-lipid membranes appeared is important for understanding the early evolution of terrestrial life. To clarify this issue, we reconstructed molecular phylogenetic trees of G1PDH (G1P dehydrogenase; EgsA/AraM) which is responsible for G1P synthesis and G3PDHs (G3P dehydrogenase; GpsA and GlpA/GlpD) and glycerol kinase (GlpK) which is responsible for G3P synthesis...
2016: Archaea: An International Microbiological Journal
https://www.readbyqxmd.com/read/27756227/shedding-light-on-the-expansion-and-diversification-of-the-cdc48-protein-family-during-the-rise-of-the-eukaryotic-cell
#10
Nickias Kienle, Tobias H Kloepper, Dirk Fasshauer
BACKGROUND: A defining feature of eukaryotic cells is the presence of various distinct membrane-bound compartments with different metabolic roles. Material exchange between most compartments occurs via a sophisticated vesicle trafficking system. This intricate cellular architecture of eukaryotes appears to have emerged suddenly, about 2 billion years ago, from much less complex ancestors. How the eukaryotic cell acquired its internal complexity is poorly understood, partly because no prokaryotic precursors have been found for many key factors involved in compartmentalization...
October 18, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27708645/sonar-a-high-throughput-pipeline-for-inferring-antibody-ontogenies-from-longitudinal-sequencing-of-b-cell-transcripts
#11
Chaim A Schramm, Zizhang Sheng, Zhenhai Zhang, John R Mascola, Peter D Kwong, Lawrence Shapiro
The rapid advance of massively parallel or next-generation sequencing technologies has made possible the characterization of B cell receptor repertoires in ever greater detail, and these developments have triggered a proliferation of software tools for processing and annotating these data. Of especial interest, however, is the capability to track the development of specific antibody lineages across time, which remains beyond the scope of most current programs. We have previously reported on the use of techniques such as inter- and intradonor analysis and CDR3 tracing to identify transcripts related to an antibody of interest...
2016: Frontiers in Immunology
https://www.readbyqxmd.com/read/27683060/quantification-of-the-latent-hiv-1-reservoir-using-ultra-deep-sequencing-and-primer-id-in-a-viral-outgrowth-assay
#12
Sook-Kyung Lee, Shuntai Zhou, Pedro L Baldoni, Ean Spielvogel, Nancie M Archin, Michael G Hudgens, David M Margolis, Ronald Swanstrom
BACKGROUND: In this study, we measured the latent HIV-1 reservoir harboring replication-competent HIV-1 in resting CD4+ T cells in participants on highly active antiretroviral therapy (HAART), quantitating the frequency of latent infection through the use of a Primer ID-based Ultra Deep Sequencing Assay (UDSA), in comparison to the readout of the quantitative viral outgrowth assay (QVOA). METHODS: Viral RNA derived from culture wells of QVOA that scored as HIV-1 p24 capsid (CA) antigen-positive were tagged with a specific barcode during cDNA synthesis, and the sequences within the V1-V3 region of the HIV-1 env gene were analyzed for diversity using the Primer ID-based paired-end MiSeq platform...
September 27, 2016: Journal of Acquired Immune Deficiency Syndromes: JAIDS
https://www.readbyqxmd.com/read/27649395/a-comprehensive-study-of-cyanobacterial-morphological-and-ecological-evolutionary-dynamics-through-deep-geologic-time
#13
Josef C Uyeda, Luke J Harmon, Carrine E Blank
Cyanobacteria have exerted a profound influence on the progressive oxygenation of Earth. As a complementary approach to examining the geologic record-phylogenomic and trait evolutionary analyses of extant species can lead to new insights. We constructed new phylogenomic trees and analyzed phenotypic trait data using novel phylogenetic comparative methods. We elucidated the dynamics of trait evolution in Cyanobacteria over billion-year timescales, and provide evidence that major geologic events in early Earth's history have shaped-and been shaped by-evolution in Cyanobacteria...
2016: PloS One
https://www.readbyqxmd.com/read/27649303/computational-evaluation-of-the-strict-master-and-random-template-models-of-endogenous-retrovirus-evolution
#14
Fabrícia F Nascimento, Allen G Rodrigo
Transposable elements (TEs) are DNA sequences that are able to replicate and move within and between host genomes. Their mechanism of replication is also shared with endogenous retroviruses (ERVs), which are also a type of TE that represent an ancient retroviral infection within animal genomes. Two models have been proposed to explain TE proliferation in host genomes: the strict master model (SMM), and the random template (or transposon) model (TM). In SMM only a single copy of a given TE lineage is able to replicate, and all other genomic copies of TEs are derived from that master copy...
2016: PloS One
https://www.readbyqxmd.com/read/27568212/phylogenetics-and-biogeography-of-the-dung-beetle-genus-onthophagus-inferred-from-mitochondrial-genomes
#15
Thijmen Breeschoten, Camiel Doorenweerd, Sergei Tarasov, Alfried P Vogler
Phylogenetic relationships of dung beetles in the tribe Onthophagini, including the species-rich, cosmopolitan genus Onthophagus, were inferred using whole mitochondrial genomes. Data were generated by shotgun sequencing of mixed genomic DNA from >100 individuals on 50% of an Illumina MiSeq flow cell. Genome assembly of the mixed reads produced contigs of 74 (nearly) complete mitogenomes. The final dataset included representatives of Onthophagus from all biogeographic regions, closely related genera of Onthophagini, and the related tribes Onitini and Oniticellini...
December 2016: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/27558250/a-generic-cost-effective-and-scalable-cell-lineage-analysis-platform
#16
Tamir Biezuner, Adam Spiro, Ofir Raz, Shiran Amir, Lilach Milo, Rivka Adar, Noa Chapal-Ilani, Veronika Berman, Yael Fried, Elena Ainbinder, Galit Cohen, Haim M Barr, Ruth Halaban, Ehud Shapiro
Advances in single-cell genomics enable commensurate improvements in methods for uncovering lineage relations among individual cells. Current sequencing-based methods for cell lineage analysis depend on low-resolution bulk analysis or rely on extensive single-cell sequencing, which is not scalable and could be biased by functional dependencies. Here we show an integrated biochemical-computational platform for generic single-cell lineage analysis that is retrospective, cost-effective, and scalable. It consists of a biochemical-computational pipeline that inputs individual cells, produces targeted single-cell sequencing data, and uses it to generate a lineage tree of the input cells...
November 2016: Genome Research
https://www.readbyqxmd.com/read/27557990/the-expression-of-vill-protein-is-hypoosmotic-dependent-in-the-lamellar-gill-ionocytes-of-otocephala-teleost-fish-chanos-chanos
#17
Chao-Kai Kang, Chia-Shian Lin, Yao-Chung Hu, Shu-Chuan Tsai, Tsung-Han Lee
Milkfish, a species within the primitive teleost lineage Otocephala, can survive in water conditions ranging from hypo- to hyper-saline. This study explored the effects of environmental salinity on apical morphologies of ionocytes and the expression of villin homologs in the gills of milkfish acclimated to either seawater (SW) or fresh water (FW). Scanning electron microscopy revealed that the ionocytes in the gill filaments of SW and FW milkfish, respectively, cellular apical morphologies were hole-type and squint-type...
August 21, 2016: Comparative Biochemistry and Physiology. Part A, Molecular & Integrative Physiology
https://www.readbyqxmd.com/read/27548240/quantifying-mosaic-development-towards-an-evo-devo-postmodern-synthesis-of-the-evolution-of-development-via-differentiation-trees-of-embryos
#18
Bradly Alicea, Richard Gordon
Embryonic development proceeds through a series of differentiation events. The mosaic version of this process (binary cell divisions) can be analyzed by comparing early development of Ciona intestinalis and Caenorhabditis elegans. To do this, we reorganize lineage trees into differentiation trees using the graph theory ordering of relative cell volume. Lineage and differentiation trees provide us with means to classify each cell using binary codes. Extracting data characterizing lineage tree position, cell volume, and nucleus position for each cell during early embryogenesis, we conduct several statistical analyses, both within and between taxa...
2016: Biology
https://www.readbyqxmd.com/read/27536295/expression-profiles-of-vpx-vpr-proteins-are-co-related-with-the-primate-lentiviral-lineage
#19
Yosuke Sakai, Ariko Miyake, Naoya Doi, Hikari Sasada, Yasuyuki Miyazaki, Akio Adachi, Masako Nomaguchi
Viruses of human immunodeficiency virus type 2 (HIV-2) and some simian immunodeficiency virus (SIV) lineages carry a unique accessory protein called Vpx. Vpx is essential or critical for viral replication in natural target cells such as macrophages and T lymphocytes. We have previously shown that a poly-proline motif (PPM) located at the C-terminal region of Vpx is required for its efficient expression in two strains of HIV-2 and SIVmac, and that the Vpx expression levels of the two clones are significantly different...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27536283/heterokont-predator-develorapax-marinus-gen-et-sp-nov-a-model-of-the-ochrophyte-ancestor
#20
Vladimir V Aleoshin, Alexander P Mylnikov, Gulnara S Mirzaeva, Kirill V Mikhailov, Sergey A Karpov
Heterotrophic lineages of Heterokonta (or stramenopiles), in contrast to a single monophyletic group of autotrophs, Ochrophyta, form several clades that independently branch off the heterokont stem lineage. The nearest neighbors of Ochrophyta in the phylogenetic tree appear to be almost exclusively bacterivorous, whereas the hypothesis of plastid acquisition by the ancestors of the ochrophyte lineage suggests an ability to engulf eukaryotic alga. In line with this hypothesis, the heterotrophic predator at the base of the ochrophyte lineage may be regarded as a model for the ochrophyte ancestor...
2016: Frontiers in Microbiology
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