keyword
MENU ▼
Read by QxMD icon Read
search

Cell lineage tree

keyword
https://www.readbyqxmd.com/read/28222255/stemness-signature-of-equine-marrow-derived-mesenchymal-stem-cells
#1
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
#2
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...
February 9, 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
#3
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
#4
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
#5
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...
January 8, 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
#6
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
#7
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...
December 10, 2016: Oncotarget
https://www.readbyqxmd.com/read/28009262/cell-lineage-trees-bear-fruit
#8
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
#9
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...
December 9, 2016: ISME Journal
https://www.readbyqxmd.com/read/27910875/an-integrated-modelling-framework-from-cells-to-organism-based-on-a-cohort-of-digital-embryos
#10
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-freshwater-of-an-artificial-reservoir
#11
Ji Hee Lee, Dae In Kim, Joo Won Kang, Chi Nam Seong
An aerobic, Gram-stain-negative, gliding and yellow-pigmented bacterium, designated strain JS5T, was isolated from freshwater of Juam reservoir, Republic of Korea. Cells were catalase-positive and oxidase-negative. The 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), Sphingomonas sediminicola Dae 20T (96...
December 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
#12
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
#13
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
#14
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
#15
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 synthetic system that enables cells to record lineage information and event histories in the genome in a format that can be subsequently read out of single cells in situ. This system, termed memory by engineered mutagenesis with optical in situ readout (MEMOIR), is based on a set of barcoded recording elements termed scratchpads...
January 5, 2017: Nature
https://www.readbyqxmd.com/read/27863249/lineage-specific-genome-architecture-links-enhancers-and-non-coding-disease-variants-to-target-gene-promoters
#16
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
#17
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
#18
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
#19
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
#20
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
keyword
keyword
37160
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"