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https://www.readbyqxmd.com/read/29333066/new-insights-into-cholangiocarcinoma-multiple-stems-and-related-cell-lineages-of-origin
#1
REVIEW
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
https://www.readbyqxmd.com/read/29323290/clonal-analysis-of-lineage-fate-in-native-haematopoiesis
#2
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
https://www.readbyqxmd.com/read/29317511/exploration-of-the-germline-genome-of-the-ciliate-chilodonella-uncinata-through-single-cell-omics-transcriptomics-and-genomics
#3
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
https://www.readbyqxmd.com/read/29298288/hierarchically-related-lineage-restricted-fates-of-multipotent-haematopoietic-stem-cells
#4
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
https://www.readbyqxmd.com/read/29276725/markerless-gene-editing-in-the-hyperthermophilic-archaeon-thermococcus-kodakarensis
#5
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
https://www.readbyqxmd.com/read/29229905/single-cell-rna-sequencing-uncovers-transcriptional-states-and-fate-decisions-in-haematopoiesis
#6
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
https://www.readbyqxmd.com/read/29219808/ferrovibrio-soli-sp-nov-a-novel-cellulolytic-bacterium-isolated-from-stream-bank-soil
#7
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...
December 8, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29208470/on-the-statistical-analysis-of-single-cell-lineage-trees
#8
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...
December 2, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29198427/towards-the-identification-of-ancestrally-shared-regenerative-mechanisms-across-the-metazoa-a-transcriptomic-case-study-in-the-demosponge-halisarca-caerulea
#9
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
https://www.readbyqxmd.com/read/29175473/mechanisms-underlying-the-heterogeneity-of-myelodysplastic-syndromes
#10
REVIEW
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...
November 22, 2017: Experimental Hematology
https://www.readbyqxmd.com/read/29174886/a-new-lineage-of-eukaryotes-illuminates-early-mitochondrial-genome-reduction
#11
Jan Janouškovec, Denis V Tikhonenkov, Fabien Burki, Alexis T Howe, Forest L Rohwer, Alexander P Mylnikov, Patrick J Keeling
The origin of eukaryotic cells represents a key transition in cellular evolution and is closely tied to outstanding questions about mitochondrial endosymbiosis [1, 2]. For example, gene-rich mitochondrial genomes are thought to be indicative of an ancient divergence, but this relies on unexamined assumptions about endosymbiont-to-host gene transfer [3-5]. Here, we characterize Ancoracysta twista, a new predatory flagellate that is not closely related to any known lineage in 201-protein phylogenomic trees and has a unique morphology, including a novel type of extrusome (ancoracyst)...
December 4, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/29169316/coevolution-of-siglec-11-and-siglec-16-via-gene-conversion-in-primates
#12
Toshiyuki Hayakawa, Zahra Khedri, Flavio Schwarz, Corinna Landig, Suh-Yuen Liang, Hai Yu, Xi Chen, Naoko T Fujito, Yoko Satta, Ajit Varki, Takashi Angata
BACKGROUND: Siglecs-11 and -16 are members of the sialic acid recognizing Ig-like lectin family, and expressed in same cells. Siglec-11 functions as an inhibitory receptor, whereas Siglec-16 exhibits activating properties. In humans, SIGLEC11 and SIGLEC16 gene sequences are extremely similar in the region encoding the extracellular domain due to gene conversions. Human SIGLEC11 was converted by the nonfunctional SIGLEC16P allele, and the converted SIGLEC11 allele became fixed in humans, possibly because it provides novel neuroprotective functions in brain microglia...
November 23, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29148363/hymenobacter-defluvii-sp-nov-isolated-from-wastewater-of-an-acidic-water-neutralization-facility
#13
Joo Won Kang, Seon Choi, Han Na Choe, Chi Nam Seong
A non-motile, pink-coloured and rod-shaped bacterium, designated strain POA9(T), was isolated from a wastewater treatment facility, Republic of Korea. Cells were Gram-reaction-negative, aerobic, catalase-positive and oxidase-negative. The major fatty acids were C16 : 1ω5c, iso-C15 : 0, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and anteiso-C15 : 0. The strain contained MK-7 as the only isoprenoid quinone, phosphatidylethanolamine as the major polar lipid and sym-homospermidine as the major polyamine...
November 17, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29145476/an-immunohistochemical-identification-key-for-cell-types-in-adult-mouse-prostatic-and-urethral-tissue-sections
#14
Kyle A Wegner, Mark T Cadena, Ryan Trevena, Anne E Turco, Adam Gottschalk, Richard B Halberg, Jinjin Guo, Jill A McMahon, Andrew P McMahon, Chad M Vezina
Though many methods can be used to identify cell types contained in complex tissues, most require cell disaggregation and destroy information about where cells reside in relation to their microenvironment. Here, we describe a polytomous key for cell type identification in intact sections of adult mouse prostate and prostatic urethra. The key is organized as a decision tree and initiates with one round of immunostaining for nerve, epithelial, fibromuscular/hematolymphoid, or vascular associated cells. Cell identities are recursively eliminated by subsequent staining events until the remaining pool of potential cell types can be distinguished by direct comparison to other cells...
2017: PloS One
https://www.readbyqxmd.com/read/29138289/the-evolution-of-cortical-development-the-synapsid-diapsid-divergence
#15
REVIEW
Andre M Goffinet
The cerebral cortex covers the rostral part of the brain and, in higher mammals and particularly humans, plays a key role in cognition and consciousness. It is populated with neuronal cell bodies distributed in radially organized layers. Understanding the common and lineage-specific molecular mechanisms that orchestrate cortical development and evolution are key issues in neurobiology. During evolution, the cortex appeared in stem amniotes and evolved divergently in two main branches of the phylogenetic tree: the synapsids (which led to present day mammals) and the diapsids (reptiles and birds)...
November 15, 2017: Development
https://www.readbyqxmd.com/read/29123225/archaea-and-the-origin-of-eukaryotes
#16
REVIEW
Laura Eme, Anja Spang, Jonathan Lombard, Courtney W Stairs, Thijs J G Ettema
Woese and Fox's 1977 paper on the discovery of the Archaea triggered a revolution in the field of evolutionary biology by showing that life was divided into not only prokaryotes and eukaryotes. Rather, they revealed that prokaryotes comprise two distinct types of organisms, the Bacteria and the Archaea. In subsequent years, molecular phylogenetic analyses indicated that eukaryotes and the Archaea represent sister groups in the tree of life. During the genomic era, it became evident that eukaryotic cells possess a mixture of archaeal and bacterial features in addition to eukaryotic-specific features...
November 10, 2017: Nature Reviews. Microbiology
https://www.readbyqxmd.com/read/29112874/the-origin-and-diversification-of-mitochondria
#17
REVIEW
Andrew J Roger, Sergio A Muñoz-Gómez, Ryoma Kamikawa
Mitochondria are best known for their role in the generation of ATP by aerobic respiration. Yet, research in the past half century has shown that they perform a much larger suite of functions and that these functions can vary substantially among diverse eukaryotic lineages. Despite this diversity, all mitochondria derive from a common ancestral organelle that originated from the integration of an endosymbiotic alphaproteobacterium into a host cell related to Asgard Archaea. The transition from endosymbiotic bacterium to permanent organelle entailed a massive number of evolutionary changes including the origins of hundreds of new genes and a protein import system, insertion of membrane transporters, integration of metabolism and reproduction, genome reduction, endosymbiotic gene transfer, lateral gene transfer and the retargeting of proteins...
November 6, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/29079176/t-complex-associated-testis-expressed-3-tcte3-is-a-novel-marker-for-pancreatobiliary-carcinomas
#18
Chaohui Lisa Zhao, Yiang Hui, Li Juan Wang, Kara Lombardo, Dongfang Yang, Shamlal Mangray, Evgeny Yakirevich, Ali Amin, Chiung-Kuei Huang, Shaolei Lu
Several markers of pancreatobiliary lineage have been described in the literature. However, none have demonstrated sufficient specificity and sensitivity to warrant diagnostic use. We evaluated the utility of T-complex-associated-testis-expressed 3 (TCTE3) as a pancreatobiliary marker. A set of 247 adenocarcinomas from the gastrointestinal (GI) tract was identified including 18 from the gastroesophageal junction (GEJ), 29 stomach, 17 ampullary, 62 pancreatic, and 16 common bile duct and gallbladder (CBD/GB), 13 non-ampullary small intestine, 32 colon, and 24 rectum...
October 24, 2017: Human Pathology
https://www.readbyqxmd.com/read/29073352/antigen-driven-lymphoproliferations-in-sj%C3%A3-gren-s-syndrome-patients-accumulate-in-complement-receptor-2-cd21-low-b-cells
#19
Salomé Glauzy, Marco Boccitto, Jason M Bannock, Fabien R Delmotte, David Saadoun, Patrice Cacoub, John A Ice, Kathy L Sivils, Judith A James, Sandra L Wolin, Eric Meffre
OBJECTIVE: Sjögren's Syndrome (SS) patients are prone to develop malignant lymphomas and a correlation has been established between lymphoproliferations and the presence in patients' blood of an unusual B cell population that downregulated complement receptor 2/CD21. We sought to determine from which B cell compartment lymphoproliferations in SS patients emerge and what are the mechanisms that promote these clonal B cell expansions. METHODS: Using a PCR-based approach that allows us to clone and express, in vitro, recombinant antibodies produced by single B cells, we tested the reactivity of antibodies expressed by CD19(+) CD10(-) CD27(-) IgM(+) CD21(-/low) cells from SS patients...
October 26, 2017: Arthritis & Rheumatology
https://www.readbyqxmd.com/read/29061890/phylogenetic-tests-for-evolutionary-innovation-the-problematic-link-between-key-innovations-and-exceptional-diversification
#20
REVIEW
Daniel L Rabosky
Evolutionary innovation contributes to the spectacular diversity of species and phenotypes across the tree of life. 'Key innovations' are widely operationalized within evolutionary biology as traits that facilitate increased diversification rates, such that lineages bearing the traits ultimately contain more species than closely related lineages lacking the focal trait. In this article, I briefly review the inference, analysis and interpretation of evolutionary innovation on phylogenetic trees. I argue that differential rates of lineage diversification should not be used as the basis for key innovation tests, despite the statistical tractability of such approaches...
December 5, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
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