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https://www.readbyqxmd.com/read/28933321/dokdonia-lutea-sp-nov-isolated-from-sargassum-fulvellum-seaweed
#1
Seon Choi, Joo Won Kang, Ji Hee Lee, Chi Nam Seong
A non-motile, yellow-coloured and rod-shaped bacterium, designated strain SFD34T, was isolated from seaweed collected from the South Sea, Republic of Korea. Cells were Gram-stain-negative, aerobic, catalase-positive and oxidase-negative. The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G. Strain SFD34T contained MK-6 and phosphatidylethanolamine as the only isoprenoid quinone and major polar lipid, respectively. The DNA G+C content was 35 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain SFD34T formed evolutionary lineage within the radiation enclosing the members of the genus Dokdonia with Dokdoniapacifica SW230T (96...
September 21, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28928963/recent-advances-in-understanding-the-roles-of-whole-genome-duplications-in-evolution
#2
REVIEW
Carol MacKintosh, David E K Ferrier
Ancient whole-genome duplications (WGDs)- paleopolyploidy events-are key to solving Darwin's 'abominable mystery' of how flowering plants evolved and radiated into a rich variety of species. The vertebrates also emerged from their invertebrate ancestors via two WGDs, and genomes of diverse gymnosperm trees, unicellular eukaryotes, invertebrates, fishes, amphibians and even a rodent carry evidence of lineage-specific WGDs. Modern polyploidy is common in eukaryotes, and it can be induced, enabling mechanisms and short-term cost-benefit assessments of polyploidy to be studied experimentally...
2017: F1000Research
https://www.readbyqxmd.com/read/28927434/sifit-inferring-tumor-trees-from-single-cell-sequencing-data-under-finite-sites-models
#3
Hamim Zafar, Anthony Tzen, Nicholas Navin, Ken Chen, Luay Nakhleh
Single-cell sequencing enables the inference of tumor phylogenies that provide insights on intra-tumor heterogeneity and evolutionary trajectories. Recently introduced methods perform this task under the infinite-sites assumption, violations of which, due to chromosomal deletions and loss of heterozygosity, necessitate the development of inference methods that utilize finite-sites models. We propose a statistical inference method for tumor phylogenies from noisy single-cell sequencing data under a finite-sites model...
September 19, 2017: Genome Biology
https://www.readbyqxmd.com/read/28922872/ancient-occasional-host-switching-of-maternally-transmitted-bacterial-symbionts-of-chemosynthetic-vesicomyid-clams
#4
Genki Ozawa, Shigeru Shimamura, Yoshihiro Takaki, Kiyotaka Takishita, Tetsuro Ikuta, James P Barry, Tadashi Maruyama, Katsunori Fujikura, Takao Yoshida
Vesicomyid clams in deep-sea chemosynthetic ecosystems harbor sulfur-oxidizing bacteria in their gill epithelial cells. These symbionts, which are vertically transmitted, are species-specific and thought to have cospeciated with their hosts. However, recent studies indicate incongruent phylogenies between some vesicomyid clams and their symbionts, suggesting that symbionts are horizontally transmitted. To more precisely understand the evolution of vesicomyid clams and their symbionts, we compared the evolution of vesicomyid clams and their symbionts through phylogenetic analyses using multi-gene data sets...
September 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28920829/allobranchiibius-huperziae-gen-nov-sp-nov-a-member-of-dermacoccaceae-isolated-from-the-root-of-a-medicinal-plant-huperzia-serrata-thunb
#5
Meng-Jie Ai, Ye Sun, Hong-Min Sun, Hong-Yu Liu, Li-Yan Yu, Yu-Qin Zhang
A Gram-stain-positive, non-spore-forming actinobacterial strain, designated CPCC 204077T, was isolated from the surface-sterilized root of a medicinal plant Huperzia serrata (Thunb.) collected from Sichuan Province, south-west China. The peptidoglycan type of strain CPCC 204077T was detected as A4α with an l-Lys-l-Ser-d-Asp interpeptide bridge. Galactose, glucose, rhamnose and ribose were the sugar compositions in the whole-cell hydrolysates. MK-8(H4) was the only menaquinone. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, one unidentified phospholipid and one unidentified glycolipid...
September 18, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28867205/collective-growth-in-a-small-cell-network
#6
Jasmin Imran Alsous, Paul Villoutreix, Alexander M Berezhkovskii, Stanislav Y Shvartsman
Theoretical studies suggest that many of the emergent properties associated with multicellular systems arise already in small networks [1, 2]. However, the number of experimental models that can be used to explore collective dynamics in well-defined cell networks is still very limited. Here we focus on collective cell behavior in the female germline cyst in Drosophila melanogaster, a stereotypically wired network of 16 cells that grows by ∼4 orders of magnitude with unequal distribution of volume among its constituents...
September 11, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28866993/winogradskyella-flava-sp-nov-isolated-from-the-brown-alga-sargassum-fulvellum
#7
Ji Hee Lee, Joo Won Kang, Soon Bum Shin, Chi Nam Seong
An aerobic, gliding and yellow-pigmented bacterium, designated strain SFD31T, was isolated from brown alga collected from the South Sea, Republic of Korea. Cells were Gram-stain-negative, and catalase- and oxidase-positive. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain SFD31T forms an independent lineage within the genus Winogradskyella. Strain SFD31T was related distantly to Winogradskyella echinorum KMM 6211T (97.9 %, 16S rRNA gene sequence similarity), Winogradskyellalitoriviva KMM 6491T (97...
September 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28854597/evolutionary-dynamics-of-cryptophyte-plastid-genomes
#8
Jong Im Kim, Christa E Moore, John M Archibald, Debashish Bhattacharya, Gangman Yi, Hwan Su Yoon, Woongghi Shin
Cryptophytes are an ecologically important group of largely photosynthetic unicellular eukaryotes. This lineage is of great interest to evolutionary biologists because their plastids are of red algal secondary endosymbiotic origin and the host cell retains four different genomes (host nuclear, mitochondrial, plastid, and red algal nucleomorph). Here, we report a comparative analysis of plastid genomes from six representative cryptophyte genera. Four newly sequenced cryptophyte plastid genomes of Chroomonas mesostigmatica, Ch...
July 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28820093/sphingomonas-limnosediminicola-sp-nov-and-sphingomonas-palustris-sp-nov-isolated-from-freshwater-environments
#9
Ji Hee Lee, Dae In Kim, Han Na Choe, Soon Dong Lee, Chi Nam Seong
Two aerobic, Gram-stain-negative, gliding and yellow-pigmented bacteria, designated strains 03SUJ6T and WM95T were isolated from freshwater sediment of Juam reservoir and freshwater of Woopo wetland, Republic of Korea, respectively. Cells of the two strains are motile by gliding and catalase- and oxidase-positive. The 16S rRNA gene sequence similarity between 03SUJ6T and WM95T was 97.7 %, but their DNA-DNA relatedness was 55.1 %. A maximum-likelihood phylogenetic tree based on 16S rRNA gene sequences showed that 03SUJ6T and WM95T each form independent lineages within the genus Sphingomonas...
August 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28813413/polylox-barcoding-reveals-haematopoietic-stem-cell-fates-realized-in-vivo
#10
Weike Pei, Thorsten B Feyerabend, Jens Rössler, Xi Wang, Daniel Postrach, Katrin Busch, Immanuel Rode, Kay Klapproth, Nikolaus Dietlein, Claudia Quedenau, Wei Chen, Sascha Sauer, Stephan Wolf, Thomas Höfer, Hans-Reimer Rodewald
Developmental deconvolution of complex organs and tissues at the level of individual cells remains challenging. Non-invasive genetic fate mapping has been widely used, but the low number of distinct fluorescent marker proteins limits its resolution. Much higher numbers of cell markers have been generated using viral integration sites, viral barcodes, and strategies based on transposons and CRISPR-Cas9 genome editing; however, temporal and tissue-specific induction of barcodes in situ has not been achieved. Here we report the development of an artificial DNA recombination locus (termed Polylox) that enables broadly applicable endogenous barcoding based on the Cre-loxP recombination system...
August 24, 2017: Nature
https://www.readbyqxmd.com/read/28813177/how-single-cell-genomics-is-changing-evolutionary-and-developmental-biology
#11
John C Marioni, Detlev Arendt
The recent flood of single-cell data not only boosts our knowledge of cells and cell types, but also provides new insight into development and evolution from a cellular perspective. For example, assaying the genomes of multiple cells during development reveals developmental lineage trees-the kinship lineage-whereas cellular transcriptomes inform us about the regulatory state of cells and their gradual restriction in potency-the Waddington lineage. Beyond that, the comparison of single-cell data across species allows evolutionary changes to be tracked at all stages of development from the zygote, via different kinds of stem cells, to the differentiating cells...
August 16, 2017: Annual Review of Cell and Developmental Biology
https://www.readbyqxmd.com/read/28798101/genomic-exploration-of-the-diversity-ecology-and-evolution-of-the-archaeal-domain-of-life
#12
REVIEW
Anja Spang, Eva F Caceres, Thijs J G Ettema
About 40 years ago, Archaea were recognized as a major prokaryotic domain of life besides Bacteria. Recently, cultivation-independent sequencing methods have produced a wealth of genomic data for previously unidentified archaeal lineages, several of which appear to represent newly revealed branches in the tree of life. Analyses of some recently obtained genomes have uncovered previously unknown metabolic traits and provided insights into the evolution of archaea and their relationship to eukaryotes. On the basis of our current understanding, much archaeal diversity still defies genomic exploration...
August 11, 2017: Science
https://www.readbyqxmd.com/read/28780931/multiregional-tumor-trees-are-not-phylogenies
#13
João M Alves, Tamara Prieto, David Posada
Tumor samples most often comprise a mixture of different cell lineages. Multiregional trees built from bulk mutational profiles do not consider this heterogeneity and can potentially lead to erroneous evolutionary inferences, including biased timing of somatic mutations, spurious parallel mutation events, and/or incorrect chronological ordering of metastatic events.
August 2017: Trends in Cancer
https://www.readbyqxmd.com/read/28780147/stem-cells-in-pulmonary-disease-and-regeneration
#14
REVIEW
Rohan R Nadkarni, Soumeya Abed, Jonathan S Draper
The epithelial cells lining the mammalian lung are subjected to constant interaction with the external environment, necessitating robust regeneration strategies to deal with cell loss due to natural turnover or damage arising from inhaled agents or disease. Since lung epithelial function extends beyond respiratory gas exchange to include roles such as immune defense and mucociliary clearance, a diverse complement of epithelial cell types exists that are regionally distributed along the respiratory tree and extensive surface area of the alveolar interface...
August 2, 2017: Chest
https://www.readbyqxmd.com/read/28774266/evolution-of-the-p53-mdm2-pathway
#15
Emma Åberg, Fulvio Saccoccia, Manfred Grabherr, Wai Ying Josefin Ore, Per Jemth, Greta Hultqvist
BACKGROUND: The p53 signalling pathway, which controls cell fate, has been extensively studied due to its prominent role in tumor development. The pathway includes the tumor supressor protein p53, its vertebrate paralogs p63 and p73, and their negative regulators MDM2 and MDM4. The p53/p63/p73-MDM system is ancient and can be traced in all extant animal phyla. Despite this, correct phylogenetic trees including both vertebrate and invertebrate species of the p53/p63/p73 and MDM families have not been published...
August 3, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28754286/mitochondria-are-not-captive-bacteria
#16
Ajith Harish, Charles G Kurland
Lynn Sagan's conjecture (1967) that three of the fundamental organelles observed in eukaryote cells, specifically mitochondria, plastids and flagella were once free-living primitive (prokaryotic) cells was accepted after considerable opposition. Even though the idea was swiftly refuted for the specific case of origins of flagella in eukaryotes, the symbiosis model in general was accepted for decades as a realistic hypothesis to describe the endosymbiotic origins of eukaryotes. However, a systematic analysis of the origins of the mitochondrial proteome based on empirical genome evolution models now indicates that 97% of modern mitochondrial protein domains as well their homologues in bacteria and archaea were present in the universal common ancestor (UCA) of the modern tree of life (ToL)...
July 25, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28715148/lineage-specific-epitope-profiles-for-hpai-h5-pre-pandemic-vaccine-selection-and-evaluation
#17
Xueting Qiu, Venkata R Duvvuri, Jonathan B Gubbay, Richard J Webby, Ghazi Kayali, Justin Bahl
BACKGROUND: Multiple highly pathogenic avian influenza (HPAI) H5 viruses continue to co-circulate. This has complicated pandemic preparedness and confounded effective vaccine candidate selection and evaluation. OBJECTIVES: In this study, we aimed to predict and map the diversity of CD8+ T-cell epitopes among H5 hemagglutinin (HA) gene lineages to estimate CD8+ T-cell immunity in humans induced by vaccine candidates. METHODS: A dataset consisting of 1125 H5 HA sequences collected between 1996 and 2017 from avian and humans was assembled for phylogenetic and lineage-specific epitope analyses...
July 17, 2017: Influenza and Other Respiratory Viruses
https://www.readbyqxmd.com/read/28693426/evolution-gene-expression-profiling-and-3d-modeling-of-csld-proteins-in-cotton
#18
Yanpeng Li, Tiegang Yang, Dandan Dai, Ying Hu, Xiaoyang Guo, Hongxia Guo
BACKGROUND: Among CESA-like gene superfamily, the cellulose synthase-like D (CSLD) genes are most similar to cellulose synthase genes and have been reported to be involved in tip-growing cell and stem development. However, there has been no genome-wide characterization of this gene subfamily in cotton. We thus sought to analyze the evolution and functional characterization of CSLD proteins in cotton based on fully sequenced cotton genomes. RESULTS: A total of 23 full-length CSLD proteins were identified in Gossypium raimondii, Gossypium arboreum and Gossypium hirsutum...
July 10, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28691666/hymenobacter-tenuis-sp-nov-isolated-from-wastewater-of-an-acidic-water-neutralization-facility
#19
Joo Won Kang, Ji Hee Lee, Han Na Choe, Chi Nam Seong
A non-motile, red-pink-coloured, rod-shaped bacterium, designated strain POB6T, was isolated from a wastewater treatment facility, Republic of Korea. Cells were Gram-stain-negative, aerobic, catalase-positive and oxidase-negative. The major fatty acids were iso-C15 : 0, C16 : 1ω5c, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B). The strain contained menaquinone MK-7 as the only isoprenoid quinone, phosphatidylethanolamine as the major polar lipid and sym-homospermidine as the major polyamine...
July 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28690608/phylogenetic-tracings-of-proteome-size-support-the-gradual-accretion-of-protein-structural-domains-and-the-early-origin-of-viruses-from-primordial-cells
#20
Arshan Nasir, Kyung Mo Kim, Gustavo Caetano-Anollés
Untangling the origin and evolution of viruses remains a challenging proposition. We recently studied the global distribution of protein domain structures in thousands of completely sequenced viral and cellular proteomes with comparative genomics, phylogenomics, and multidimensional scaling methods. A tree of life describing the evolution of proteomes revealed viruses emerging from the base of the tree as a fourth supergroup of life. A tree of domains indicated an early origin of modern viral lineages from ancient cells that co-existed with the cellular ancestors...
2017: Frontiers in Microbiology
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