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Cell lineage tree

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https://www.readbyqxmd.com/read/28424352/chromatin-module-inference-on-cellular-trajectories-identifies-key-transition-points-and-poised-epigenetic-states-in-diverse-developmental-processes
#1
Sushmita Roy, Rupa Sridharan
Changes in chromatin state play important roles in cell fate transitions. Current computational approaches to analyze chromatin modifications across multiple cell types do not model how the cell types are related on a lineage or over time. To overcome this limitation, we have developed a method called CMINT (Chromatin Module INference on Trees), a probabilistic clustering approach to systematically capture chromatin state dynamics across multiple cell types. Compared to existing approaches, CMINT can handle complex lineage topologies, capture higher quality clusters, and reliably detect chromatin transitions between cell types...
April 19, 2017: Genome Research
https://www.readbyqxmd.com/read/28399402/hematopoiesis-lineage-tree-uprooted-every-cell-is-a-rainbow
#2
Karen K Hirschi, Stefania Nicoli, Kenneth Walsh
Differentiation of hematopoietic stem cells into distinct cell types was thought to occur through a series of discrete, stable progenitor states. Work from Velten et al. (2017) now shows that hematopoietic cells differentiate via a mechanism of continuous lineage priming and thus represent a CLOUD-HSPC.
April 10, 2017: Developmental Cell
https://www.readbyqxmd.com/read/28376782/image-analysis-driven-single-cell-analytics-for-systems-microbiology
#3
Athanasios D Balomenos, Panagiotis Tsakanikas, Zafiro Aspridou, Anastasia P Tampakaki, Konstantinos P Koutsoumanis, Elias S Manolakos
BACKGROUND: Time-lapse microscopy is an essential tool for capturing and correlating bacterial morphology and gene expression dynamics at single-cell resolution. However state-of-the-art computational methods are limited in terms of the complexity of cell movies that they can analyze and lack of automation. The proposed Bacterial image analysis driven Single Cell Analytics (BaSCA) computational pipeline addresses these limitations thus enabling high throughput systems microbiology. RESULTS: BaSCA can segment and track multiple bacterial colonies and single-cells, as they grow and divide over time (cell segmentation and lineage tree construction) to give rise to dense communities with thousands of interacting cells in the field of view...
April 4, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28319093/human-haematopoietic-stem-cell-lineage-commitment-is-a-continuous-process
#4
Lars Velten, Simon F Haas, Simon Raffel, Sandra Blaszkiewicz, Saiful Islam, Bianca P Hennig, Christoph Hirche, Christoph Lutz, Eike C Buss, Daniel Nowak, Tobias Boch, Wolf-Karsten Hofmann, Anthony D Ho, Wolfgang Huber, Andreas Trumpp, Marieke A G Essers, Lars M Steinmetz
Blood formation is believed to occur through stepwise progression of haematopoietic stem cells (HSCs) following a tree-like hierarchy of oligo-, bi- and unipotent progenitors. However, this model is based on the analysis of predefined flow-sorted cell populations. Here we integrated flow cytometric, transcriptomic and functional data at single-cell resolution to quantitatively map early differentiation of human HSCs towards lineage commitment. During homeostasis, individual HSCs gradually acquire lineage biases along multiple directions without passing through discrete hierarchically organized progenitor populations...
March 20, 2017: Nature Cell Biology
https://www.readbyqxmd.com/read/28304126/transcript-profiling-of-a-novel-plant-meristem-the-monocot-cambium
#5
Matthew Zinkgraf, Suzanne Gerttula, Andrew Groover
While monocots lack the ability to produce a vascular cambium or woody growth, some monocot lineages evolved a novel lateral meristem, the monocot cambium, which supports secondary radial growth of stems. In contrast to the vascular cambium found in woody angiosperm and gymnosperm species, the monocot cambium produces secondary vascular bundles, which have an amphivasal organization of tracheids encircling a central strand of phloem. Currently there is no information concerning the molecular genetic basis of the development or evolution of the monocot cambium...
March 17, 2017: Journal of Integrative Plant Biology
https://www.readbyqxmd.com/read/28296636/discovering-sparse-transcription-factor-codes-for-cell-states-and-state-transitions-during-development
#6
Leon A Furchtgott, Samuel Melton, Vilas Menon, Sharad Ramanathan
Computational analysis of gene expression to determine both the sequence of lineage choices made by multipotent cells and to identify the genes influencing these decisions is challenging. Here we discover a pattern in the expression levels of a sparse subset of genes among cell types in B- and T-cell developmental lineages that correlates with developmental topologies. We develop a statistical framework using this pattern to simultaneously infer lineage transitions and the genes that determine these relationships...
March 15, 2017: ELife
https://www.readbyqxmd.com/read/28294138/machine-learning-applications-in-cell-image-analysis
#7
REVIEW
Andrey Kan
Machine learning refers to a set of automatic pattern recognition methods that have been successfully applied across various problem domains, including biomedical image analysis. This review focuses on machine learning applications for image analysis in light microscopy experiments with typical tasks of segmenting and tracking individual cells, and modelling of reconstructed lineage trees. After describing a typical image analysis pipeline and highlighting challenges of automatic analysis (e.g., variability in cell morphology, tracking in presence of clutters) this review gives a brief historical outlook of machine learning, followed by basic concepts and definitions required for understanding examples...
March 15, 2017: Immunology and Cell Biology
https://www.readbyqxmd.com/read/28267748/inferring-fitness-landscapes-and-selection-on-phenotypic-states-from-single-cell-genealogical-data
#8
Takashi Nozoe, Edo Kussell, Yuichi Wakamoto
Recent advances in single-cell time-lapse microscopy have revealed non-genetic heterogeneity and temporal fluctuations of cellular phenotypes. While different phenotypic traits such as abundance of growth-related proteins in single cells may have differential effects on the reproductive success of cells, rigorous experimental quantification of this process has remained elusive due to the complexity of single cell physiology within the context of a proliferating population. We introduce and apply a practical empirical method to quantify the fitness landscapes of arbitrary phenotypic traits, using genealogical data in the form of population lineage trees which can include phenotypic data of various kinds...
March 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28264564/quantitative-analysis-of-synthetic-cell-lineage-tracing-using-nuclease-barcoding
#9
Stephanie Tzouanas Schmidt, Stephanie M Zimmerman, Jianbin Wang, Stuart K Kim, Stephen R Quake
Lineage tracing by the determination and mapping of progeny arising from single cells is an important approach enabling the elucidation of mechanisms underlying diverse biological processes ranging from development to disease. We developed a dynamic sequence-based barcode system for synthetic lineage tracing and have demonstrated its performance in C. elegans, a model organism whose lineage tree is well established. The strategy we use creates lineage trees based upon the introduction of synthetically controlled mutations into cells and the propagation of these mutations to daughter cells at each cell division...
March 10, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28231507/the-phytochelatin-synthase-gene-in-date-palm-phoenix-dactylifera-l-phylogeny-evolution-and-expression
#10
Chaâbene Zayneb, Rekik Hakim Imen, Kriaa Walid, C Douglas Grubb, Khemakhem Bassem, Vandenbulcke Franck, Mejdoub Hafedh, Elleuch Amine
We studied date palm phytochelatin synthase type I (PdPCS1), which catalyzes the cytosolic synthesis of phytochelatins (PCs), a heavy metal binding protein, in plant cells. The gene encoding PdPCS1 (Pdpcs) consists of 8 exons and 7 introns and encodes a protein of 528 amino acids. PCs gene history was studied using Notung phylogeny. During evolution, gene loss from several lineages was predicted including Proteobacteria, Bilateria and Brassicaceae. In addition, eleven gene duplication events appeared toward interior nodes of the reconciled tree and four gene duplication events appeared toward the external nodes...
February 20, 2017: Ecotoxicology and Environmental Safety
https://www.readbyqxmd.com/read/28222255/stemness-signature-of-equine-marrow-derived-mesenchymal-stem-cells
#11
Morteza Zahedi, Abbas Parham, Hesam Dehghani, Hossein Kazemi Mehrjerdi
Background: Application of competent cells such as mesenchymal stem cells (MSCs) for treatment of musculoskeletal disorders in equine athletes is increasingly needed. Moreover, similarities of horse and human in size, load and types of joint injuries, make horse as a good model for MSCs therapy studies. This study was designed to isolate and characterize stemness signature of equine bone marrow-derived mesenchymal stem cells (BM-MSCs). Methods: BM of three mares was aspirated and the mononuclear cells (MNCs) were isolated using density gradient...
February 28, 2017: International Journal of Stem Cells
https://www.readbyqxmd.com/read/28207402/reconstructing-the-temporal-progression-of-biological-data-using-cluster-spanning-trees
#12
Ryan Eshleman, Rahul Singh
Identifying the temporal progression of a set of biological samples is crucial for comprehending the dynamics of the underlying molecular interactions. It is often also a basic step in data denoising and synchronization. Finally, identifying the progression order is crucial for problems like cell lineage identification, disease progression, tumor classification, and epidemiology and thus impacts the spectrum of disciplines spanning basic biology, drug discovery, and public health. Current methods that attempt solving this problem, face difficulty when it is necessary to factor-in complex relationships within the data, such as grouping, partial ordering or bifurcating or multifurcating progressions...
March 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28111289/ancient-highly-conserved-proteins-from-a-luca-with-complex-cell-biology-provide-evidence-in-support-of-the-nuclear-compartment-commonality-nucom-hypothesis
#13
REVIEW
James T Staley, John A Fuerst
The nuclear compartment commonality (NuCom) hypothesis posits a complex last common ancestor (LUCA) with membranous compartments including a nuclear membrane. Such a LUCA then evolved to produce two nucleated lineages of the tree of life: the Planctomycetes-Verrucomicrobia-Chlamydia superphylum (PVC) within the Bacteria, and the Eukarya. We propose that a group of ancient essential protokaryotic signature proteins (PSPs) originating in LUCA were incorporated into ancestors of PVC Bacteria and Eukarya. Tubulins, ubiquitin system enzymes and sterol-synthesizing enzymes are consistent with early origins of these features shared between the PVC superphylum and Eukarya...
January 19, 2017: Research in Microbiology
https://www.readbyqxmd.com/read/28094016/a-single-cell-roadmap-of-lineage-bifurcation-in-human-esc-models-of-embryonic-brain-development
#14
Zizhen Yao, John K Mich, Sherman Ku, Vilas Menon, Anne-Rachel Krostag, Refugio A Martinez, Leon Furchtgott, Heather Mulholland, Susan Bort, Margaret A Fuqua, Ben W Gregor, Rebecca D Hodge, Anu Jayabalu, Ryan C May, Samuel Melton, Angelique M Nelson, N Kiet Ngo, Nadiya V Shapovalova, Soraya I Shehata, Michael W Smith, Leah J Tait, Carol L Thompson, Elliot R Thomsen, Chaoyang Ye, Ian A Glass, Ajamete Kaykas, Shuyuan Yao, John W Phillips, Joshua S Grimley, Boaz P Levi, Yanling Wang, Sharad Ramanathan
During human brain development, multiple signaling pathways generate diverse cell types with varied regional identities. Here, we integrate single-cell RNA sequencing and clonal analyses to reveal lineage trees and molecular signals underlying early forebrain and mid/hindbrain cell differentiation from human embryonic stem cells (hESCs). Clustering single-cell transcriptomic data identified 41 distinct populations of progenitor, neuronal, and non-neural cells across our differentiation time course. Comparisons with primary mouse and human gene expression data demonstrated rostral and caudal progenitor and neuronal identities from early brain development...
January 5, 2017: Cell Stem Cell
https://www.readbyqxmd.com/read/28065919/force-of-habit-shrubs-trees-and-contingent-evolution-of-wood-anatomical-diversity-using-croton-euphorbiaceae-as-a-model-system
#15
Rafael Arévalo, Benjamin W van Ee, Ricarda Riina, Paul E Berry, Alex C Wiedenhoeft
Background and Aims: Wood is a major innovation of land plants, and is usually a central component of the body plan for two major plant habits: shrubs and trees. Wood anatomical syndromes vary between shrubs and trees, but no prior work has explicitly evaluated the contingent evolution of wood anatomical diversity in the context of these plant habits. Methods: Phylogenetic comparative methods were used to test for contingent evolution of habit, habitat and wood anatomy in the mega-diverse genus Croton (Euphorbiaceae), across the largest and most complete molecular phylogeny of the genus to date...
March 1, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28043631/the-first-population-structure-and-comparative-genomics-analysis-of-mycobacterium-africanum-strains-from-ghana-reveals-higher-diversity-of-lineage-5
#16
Isaac D Otchere, Simon R Harris, Sanches L Busso, Adwoa Asante-Poku, Stephen Osei-Wusu, Kwadwo Koram, Julian Parkhill, Sebastien Gagneux, Dorothy Yeboah-Manu
OBJECTIVE/BACKGROUND: Mycobacterium africanum (MAF) remains an important TB causing pathogen in West Africa; however, little is known about its population structure and actual diversity which may have implications for diagnostics and vaccines. We carried out comparative genomics analysis of candidate Mycobacterium tuberculosis (MTB) and MAF using whole genome sequencing. METHODS: Clinical MTB complex strains (n=187) comprising L4 (n=22), L5 (n=126), and L6 (n=39) isolated over 8years from Ghana were whole genome sequenced...
December 2016: International Journal of Mycobacteriology
https://www.readbyqxmd.com/read/28032601/characterization-and-phylogenetic-analysis-of-kr%C3%A3-ppel-like-transcription-factor-klf-gene-family-in-tree-shrews-tupaia-belangeri-chinensis
#17
Ming Shao, Guang-Zhe Ge, Wen-Jing Liu, Ji Xiao, Hou-Jun Xia, Yu Fan, Feng Zhao, Bao-Li He, Ceshi Chen
Krüppel-like factors (KLFs) are a family of zinc finger transcription factors regulating embryonic development and diseases. The phylogenetics of KLFs has not been studied in tree shrews, an animal lineage with a closer relationship to primates than rodents. Here, we identified 17 KLFs from Chinese tree shrew (Tupaia belangeri chinensis). KLF proteins are highly conserved among humans, monkeys, rats, mice and tree shrews compared to zebrafish and chickens. The CtBP binding site, Sin3A binding site and nuclear localization signals are largely conserved between tree shrews and human beings...
March 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28009262/cell-lineage-trees-bear-fruit
#18
Jordi Garcia-Ojalvo
Two inference approaches harness the information present in cell lineage trees to better understand the dynamic transitions between cell states.
December 21, 2016: Cell Systems
https://www.readbyqxmd.com/read/27935595/identification-of-the-fitness-determinants-of-budding-yeast-on-a-natural-substrate
#19
Marie Filteau, Guillaume Charron, Christian R Landry
The budding yeasts are prime models in genomics and cell biology, but the ecological factors that determine their success in non-human-associated habitats is poorly understood. In North America Saccharomyces yeasts are present on the bark of deciduous trees, where they feed on bark and sap exudates. In the North East, Saccharomyces paradoxus is found on maples, which makes maple sap a natural substrate for this species. We measured growth rates of S. paradoxus natural isolates on maple sap and found variation along a geographical gradient not explained by the inherent variation observed under optimal laboratory conditions...
April 2017: ISME Journal
https://www.readbyqxmd.com/read/27910875/an-integrated-modelling-framework-from-cells-to-organism-based-on-a-cohort-of-digital-embryos
#20
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
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