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Diagenesis of dinosaur eggshell from the Gobi Desert, Mongolia
Graf, John,Tabor, Neil J.,Ferguson, Kurt,Winkler, Dale A.,Lee, Yuong-Nam,May, Steven,Jacobs, Louis L. Elsevier 2018 Palaeogeography, palaeoclimatology, palaeoecology Vol.494 No.-
<P><B>Abstract</B></P> <P>In order to test for paleoenvironmental and paleoecological parameters important in dinosaur evolution, thirty-four fragments of dinosaur eggshell, paleosol carbonates from six localities, and calcite crystals from inside a dinosaur femur were collected from the Campanian to Maastrichtian Baruungoyot and Nemegt formations, Gobi Desert, Mongolia. The samples were examined for diagenesis using light microscopy, SEM, and cathodoluminescence, and each was analyzed for δ<SUP>13</SUP>C and δ<SUP>18</SUP>O values. Eggshell isotope values plot along two trends of enrichment, with paleosol carbonate nodule values plotting along locality specific trends. Convergence of the trends suggests similar initial conditions among localities. Permian-age detrital zircons in the fossiliferous sediment suggest that enriched eggshell and paleosol carbonate nodule δ<SUP>13</SUP>C values may have been caused by phreatic zone diagenetic alteration by waters with an aqueous bicarbonate component derived from interaction and dissolution of Permian calcareous marine host rocks. Our hypothetical model for eggshell diagenesis assumes a stable carbon- and oxygen-isotope domain space delimited by three end members: (1) apparently unaltered eggshell with primary microstructure, (2) non-luminescent eggshell with no preserved microstructure, and (3) luminescent eggshell with no preserved microstructure. The two end members showing no preservation of microstructure indicate different phases of diagenetic alteration in the presence of vadose and phreatic waters. None of the samples analyzed can be shown to be sufficiently unaltered for analysis using standard techniques. Biologically, eggshell is porous to facilitate the movement of gases while an embryo is developing within the egg. Geologically, that same property allows the flow of diagenetic ground waters, which modifies the primary isotopic signature of eggshell.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Stable isotopes in dinosaur eggshell are used to infer paleobiology and paleoenvironment. </LI> <LI> However, porosity that facilitates movement of gases, makes fossil eggshells prone to diagenesis. </LI> <LI> δ<SUP>13</SUP>C and δ<SUP>18</SUP>O in Mongolian Cretaceous eggshell from the Gobi Desert indicate rampant diagenesis. </LI> <LI> Eggshell was subjected to shallow-burial, vadose and phreatic zone diagenesis. </LI> </UL> </P>
A novice’s guide to analyzing NGS-derived organelle and metagenome data
송해중,이준모,Louis Graf,노미나,Huan Qiu,Debashish Bhattacharya,윤환수 한국조류학회I 2016 ALGAE Vol.31 No.2
Next generation sequencing (NGS) technologies have revolutionized many areas of biological research due to thesharp reduction in costs that has led to the generation of massive amounts of sequence information. Analysis of large genomedata sets is however still a challenging task because it often requires significant computer resources andknowledge of bioinformatics. Here, we provide a guide for an uninitiated who wish to analyze high-throughput NGSdata. We focus specifically on the analysis of organelle genome and metagenome data and describe the currentbioinformatic pipelines suited for this purpose.
Andersen, Robert A.,Graf, Louis,Malakhov, Yuriy,Yoon, Hwan Su Informa UK (TaylorFrancis) 2017 Phycologia Vol.56 No.6
<P>Ochromonas triangulata, the type species for a genus with over 125 taxa, was collected for only the second time, again from the type locality. Cell morphology, cell division, palmelloid stage and cyst structure generally agreed with the original description. Molecular phylogenetic analysis based on the 18S rRNA gene revealed 13 clades of Ochromonas-like flagellates as well as the clade represented by our O. triangulata strain and the nearly identical strain RCC-21/AC025. We also conducted a concatenated analysis using the 18S rRNA and the rbcL genes, and we recovered the same 14 clades. One clade, containing strains CCAP 933/27 and CCMP1861, previously named Ochromonas tuberculata, was re-identified as Chrysastrella paradoxa and Chrysastrella breviappendiculata, respectively. One clade included the Poterioochromonas strains but we were unable to convincingly connect species names to the strains because authentic strains were unknown or not examined. Organisms in the clade that included the well-known Ochromonas danica were assigned to Chlorochromonas. The generic name Melkoniania gen. nov. was proposed for one distinct clade of marine flagellates. These changes addressed some of the issues associated with the polyphyletic Ochromonas sensu lato but many problems remained.</P>
Kelps in Korea: from population structure to aquaculture to potential carbon sequestration
Hwang, Eun Kyoung,Boo, Ga Hun,Graf, Louis,Yarish, Charles,Yoon, Hwan Su,Kim, Jang Kyun The Korean Society of Phycology 2022 ALGAE Vol.37 No.2
Korea is one of the most advanced countries in kelp aquaculture. The brown algae, Undaria pinnatifida and Saccharina japonica are major aquaculture species and have been principally utilized for human food and abalone feed in Korea. This review discusses the diversity, population structure and genomics of kelps. In addition, we have introduced new cultivar development efforts considering climate change, and potential carbon sequestration of kelp aquaculture in Korea. U. pinnatifida showed high diversity within the natural populations but reduced genetic diversity in cultivars. However, very few studies of S. japonica have been conducted in terms of population structure. Since studies on cultivar development began in early 2000s, five U. pinnatifida and one S. japonica varieties have been registered to the International Union for the Protection of New Varieties of Plants (UPOV). To meet the demands for seaweed biomass in various industries, more cultivars should be developed with specific traits to meet application demands. Additionally, cultivation technologies should be diversified, such as integrated multi-trophic aquaculture (IMTA) and offshore aquaculture, to achieve environmental and economic sustainability. These kelps are anticipated to be important sources of blue carbon in Korea.
A novice’s guide to analyzing NGS-derived organelle and metagenome data
Song, Hae Jung,Lee, JunMo,Graf, Louis,Rho, Mina,Qiu, Huan,Bhattacharya, Debashish,Yoon, Hwan Su The Korean Society of Phycology 2016 ALGAE Vol.31 No.2
Next generation sequencing (NGS) technologies have revolutionized many areas of biological research due to the sharp reduction in costs that has led to the generation of massive amounts of sequence information. Analysis of large genome data sets is however still a challenging task because it often requires significant computer resources and knowledge of bioinformatics. Here, we provide a guide for an uninitiated who wish to analyze high-throughput NGS data. We focus specifically on the analysis of organelle genome and metagenome data and describe the current bioinformatic pipelines suited for this purpose.