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https://www.readbyqxmd.com/read/29148363/hymenobacter-defluvii-sp-nov-isolated-from-wastewater-of-an-acidic-water-neutralization-facility
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
https://www.readbyqxmd.com/read/29030445/microhomology-mediated-high-throughput-gene-inactivation-strategy-for-hyperthermophilic-crenarchaeon-sulfolobus-islandicus
#9
Changyi Zhang, Rachel J Whitaker
Sulfolobus islandicus is rapidly emerging as a model system for studying the biology and evolution within the TACK lineage of the Archaeal domain. As the tree of life grows, identifying the cellular function of genes within this lineage will have significant impacts on our understanding of the evolution of Last Archaeal Eukaryote Common Ancestor (LEACA) and the differentiation of Archaea from Eukaryotes during the evolution of the modernday cell. To progress our understanding of this key Archaeal organism, we report a novel high-throughput method for targeted gene inactivation in S...
October 13, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28984217/kordia-zosterae-sp-nov-isolated-from-the-seaweed-zostera-marina
#10
Dae In Kim, Ji Hee Lee, Mi Sun Kim, Chi Nam Seong
A Gram-stain-negative, gliding and rod shaped bacterium, designated strain ZO2-23(T) was isolated from a seaweed sample collected from the West Sea, Republic of Korea. Cells are catalase-negative and oxidase-positive. Neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain ZO2-23(T) forms an independent lineage within the genus Kordia. Strain ZO2-23(T) was related to Kordia ulvae SC2(T) (98.0 %, 16S rRNA gene sequence similarity) and K. antarctica IMCC3317(T) (97.9 %). The major fatty acids of strain ZO2-23(T) were iso-C15 : 0, iso-C17 : 0 3-OH, summed feature 3 and iso-C15 : 0 3-OH...
October 6, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28968873/comparison-of-methods-for-phylogenetic-b-cell-lineage-inference-using-time-resolved-antibody-repertoire-simulations-absim
#11
Alexander Yermanos, Victor Greiff, Nike Julia Krautler, Ulrike Menzel, Andreas Dounas, Enkelejda Miho, Annette Oxenius, Tanja Stadler, Sai T Reddy
Motivation: The evolution of antibody repertoires represents a hallmark feature of adaptive B-cell immunity. Recent advancements in high-throughput sequencing have dramatically increased the resolution to which we can measure the molecular diversity of antibody repertoires, thereby offering for the first time the possibility to capture the antigen-driven evolution of B cells. However, there does not exist a repertoire simulation framework yet that enables the comparison of commonly utilized phylogenetic methods with regard to their accuracy in inferring antibody evolution...
August 31, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28958589/exposing-primary-rat-retina-cell-cultures-to-%C3%AE-rays-an-in%C3%A2-vitro-model-for-evaluating-radiation-responses
#12
Lucia Gaddini, Maria Balduzzi, Alessandro Campa, Giuseppe Esposito, Fiorella Malchiodi-Albedi, Clarice Patrono, Andrea Matteucci
Retinal tissue can receive incidental γ-rays exposure during radiotherapy either of tumors of the eye and optic nerve or of head-and-neck tumors, and during medical diagnostic procedures. Healthy retina is therefore at risk of suffering radiation-related side effects and the knowledge of pathophysiological response of retinal cells to ionizing radiations could be useful to design possible strategies of prevention and management of radiotoxicity. In this study, we have exploited an in vitro model (primary rat retinal cell culture) to study an array of biological effects induced on retinal neurons by γ-rays...
September 27, 2017: Experimental Eye Research
https://www.readbyqxmd.com/read/28933321/dokdonia-lutea-sp-nov-isolated-from-sargassum-fulvellum-seaweed
#13
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
#14
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
#15
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
#16
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
#17
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 204077(T), 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 204077(T) 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...
October 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28867205/collective-growth-in-a-small-cell-network
#18
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
#19
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
#20
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
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