ALBERT

Description: The optimal combination of particle and tube size for simulation of a single tube of a wall-cooled multitubular Fischer-Tropsch (FT) reactor with cobalt as catalyst was determined. The maximum size of the tubes, realized without temperature runaway, enhances with increasing particle size until an optimal value is reached, thereby improving the production rate of liquid fuels per tube. Reasons for this are that heat transfer to the cooled tube wall for a given tube size is considerably enhanced by increasing the particle size and that the influence of pore diffusion on the effective rate of FT synthesis gets stronger with rising particle size, which reduces the temperature sensitivity of the reactor and decreases the danger of a temperature runaway. The simulations indicate that the use of FT eggshell catalysts is not an option for fixed-bed reactors. The temperature sensitivity of the reactor is strongly enhanced, which decreases the maximum tube size and with that the productivity per tube. All these effects are valid in general for wall-cooled fixed-bed reactors. Respective criteria are presented. With cobalt as catalyst, the optimal combination of particle size and tube size for simulation of a single tube of a wall-cooled multitubular Fischer-Tropsch reactor was established. The maximum size of the tubes, realized without temperature runaway, is improved with increasing particle size until an optimal value is reached, thereby improving the production rate of liquid fuels per tube.

Description: Simulation of a single tube of a wall-cooled multitubular Fischer-Tropsch (FT) reactor with a cobalt catalyst indicates that the reactor performance is improved by enlarging the catalyst particle diameter. This aspect is studied for variation of the particle size for a fixed tube diameter and vice versa. For a syngas conversion per pass of about 30 % as target and a typical industrially used single-tube diameter of 40 mm, a particle size of 〉 3 mm is appropriate with regard to a high production rate of higher hydrocarbons. For a particle diameter of 〈 3 mm, a temperature runaway can only be avoided by rather low cooling temperatures, and the target conversion cannot be reached. In addition, the pressure drop then gets rather high. The reasons for this behavior are: (i) the heat transfer to the cooled tube wall for a given tube size is considerably enhanced by increasing the particle size; (ii) the influence of pore diffusion on the effective rate gets stronger with rising particle size which decreases the danger of temperature runaway. Detailed simulation of the influence of the catalyst particle size on the behavior of a multitubular Fischer-Tropsch reactor with regard to syngas conversion and production rate of hydrocarbons per tube in a wall-cooled single tube with cobalt as catalyst indicates that the reactor performance is improved by enlarging the catalyst particle diameter. Reasons for this unexpected behavior are evaluated.

Description: To provide context for the diversification of archosaurs--the group that includes crocodilians, dinosaurs, and birds--we generated draft genomes of three crocodilians: Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the comparatively rapid evolution is derived in birds. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs, thereby providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4386873/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4386873/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Green, Richard E -- Braun, Edward L -- Armstrong, Joel -- Earl, Dent -- Nguyen, Ngan -- Hickey, Glenn -- Vandewege, Michael W -- St John, John A -- Capella-Gutierrez, Salvador -- Castoe, Todd A -- Kern, Colin -- Fujita, Matthew K -- Opazo, Juan C -- Jurka, Jerzy -- Kojima, Kenji K -- Caballero, Juan -- Hubley, Robert M -- Smit, Arian F -- Platt, Roy N -- Lavoie, Christine A -- Ramakodi, Meganathan P -- Finger, John W Jr -- Suh, Alexander -- Isberg, Sally R -- Miles, Lee -- Chong, Amanda Y -- Jaratlerdsiri, Weerachai -- Gongora, Jaime -- Moran, Christopher -- Iriarte, Andres -- McCormack, John -- Burgess, Shane C -- Edwards, Scott V -- Lyons, Eric -- Williams, Christina -- Breen, Matthew -- Howard, Jason T -- Gresham, Cathy R -- Peterson, Daniel G -- Schmitz, Jurgen -- Pollock, David D -- Haussler, David -- Triplett, Eric W -- Zhang, Guojie -- Irie, Naoki -- Jarvis, Erich D -- Brochu, Christopher A -- Schmidt, Carl J -- McCarthy, Fiona M -- Faircloth, Brant C -- Hoffmann, Federico G -- Glenn, Travis C -- Gabaldon, Toni -- Paten, Benedict -- Ray, David A -- 1U41HG006992-2/HG/NHGRI NIH HHS/ -- 1U41HG007234-01/HG/NHGRI NIH HHS/ -- 5U01HG004695/HG/NHGRI NIH HHS/ -- R01 HG002939/HG/NHGRI NIH HHS/ -- U41 HG006992/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2014 Dec 12;346(6215):1254449. doi: 10.1126/science.1254449. Epub 2014 Dec 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA. ed@soe.ucsc.edu david.a.ray@ttu.edu. ; Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611, USA. ; Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA. Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA. ; Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. ; Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA. ; Bioinformatics and Genomics Programme, Centre for Genomic Regulation, 08003 Barcelona, Spain. Universitat Pompeu Fabra, 08003 Barcelona, Spain. ; Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA. Department of Biology, University of Texas, Arlington, TX 76019, USA. ; Department of Computer and Information Sciences, University of Delaware, Newark, DE 19717, USA. ; Department of Biology, University of Texas, Arlington, TX 76019, USA. ; Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile. ; Genetic Information Research Institute, Mountain View, CA 94043, USA. ; Institute for Systems Biology, Seattle, WA 98109, USA. ; Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA. ; Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA. ; Institute of Experimental Pathology (ZMBE), University of Munster, D-48149 Munster, Germany. Department of Evolutionary Biology (EBC), Uppsala University, SE-752 36 Uppsala, Sweden. ; Porosus Pty. Ltd., Palmerston, NT 0831, Australia. Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia. Centre for Crocodile Research, Noonamah, NT 0837, Australia. ; Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia. ; Departamento de Desarrollo Biotecnologico, Instituto de Higiene, Facultad de Medicina, Universidad de la Republica, Montevideo, Uruguay. ; Moore Laboratory of Zoology, Occidental College, Los Angeles, CA 90041, USA. ; College of Agriculture and Life Sciences, University of Arizona, Tucson, AZ 85721, USA. ; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. ; School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA. ; Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC 27607, USA. ; Howard Hughes Medical Institute, Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA. ; Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA. ; Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA. Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, MS 39762, USA. ; Institute of Experimental Pathology (ZMBE), University of Munster, D-48149 Munster, Germany. ; Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA. ; Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA. Howard Hughes Medical Institute, Bethesda, MD 20814, USA. ; Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA. ; China National GeneBank, BGI-Shenzhen, Shenzhen, China. Center for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark. ; Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan. ; Department of Earth and Environmental Sciences, University of Iowa, Iowa City, IA 52242, USA. ; Department of Animal and Food Sciences, University of Delaware, Newark, DE 19717, USA. ; School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ 85721, USA. ; Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90019, USA. Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA. ; Bioinformatics and Genomics Programme, Centre for Genomic Regulation, 08003 Barcelona, Spain. Universitat Pompeu Fabra, 08003 Barcelona, Spain. Institucio Catalana de Recerca i Estudis Avancats, 08010 Barcelona, Spain. ; Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA. ; Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA. Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA. ed@soe.ucsc.edu david.a.ray@ttu.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25504731" target="_blank"〉PubMed〈/a〉

Description: Vesper bats (family Vespertilionidae) experienced a rapid adaptive radiation beginning around 36 Ma that resulted in the second most species-rich mammalian family (〉400 species). Coincident with that radiation was an initial burst of DNA transposon activity that has continued into the present in some species. Such extensive and recent DNA transposon activity has not been seen in any other extant mammal. Indeed, retrotransposon activity is much more common in all other sequenced mammal genomes. Deep sequencing of the small RNA fraction from a vespertilionid bat, Eptesicus fuscus , as well as a dog and horse revealed large numbers of 17–24 bp putative miRNAs (p/miRNAs). Although the origination rate of p/miRNAs is similar in all three taxa, 61.1% of postdivergence p/miRNAs in Eptesicus are derived from transposable elements (TEs) compared with only 23.9% and 16.5% in the dog and horse, respectively. Not surprisingly, given the retrotransposon bias of dog and horse, the majority of TE-derived p/miRNAs are associated with retrotransposons. In Eptesicus , however, 58.7% of the TE-derived and 35.9% of the total p/miRNAs arose not from retrotransposons but from bat-specific DNA transposons. Notably, we observe that the timing of the DNA transposon expansion and the resulting introduction of novel p/miRNAs coincide with the rapid diversification of the family Vespertilionidae. Furthermore, potential targets of the DNA transposon-derived p/miRNAs are identifiable and enriched for genes that are important for regulation of transcription. We propose that lineage-specific DNA transposon activity lead to the rapid and repeated introduction of novel p/miRNAs. Some of these p/miRNAs are likely functional miRNAs and potentially influenced the diversification of Vespertilionidae. Our observations suggest a mechanism for introducing functional genomic variation rapidly through the expansion of DNA transposons that fits within the TE-thrust hypothesis.

Description: Aims The Gap Partitioning Hypothesis (GPH) posits that gaps create heterogeneity in resources crucial for tree regeneration in closed-canopy forests, allowing trees with contrasting strategies to coexist along resource gradients. Few studies have examined gap partitioning of temperate, ground-layer vascular plants. We used a ground-layer plant community of a temperate deciduous forest in northern Wisconsin, USA, as a model system to test whether the GPH extends to the relatively species-rich ground layer. Methods We used a well-replicated experimental approach that included a gap opening gradient (five gap sizes, 6, 10, 20, 30 and 46 m diameter, and undisturbed reference areas), a within-gap location gradient (gap edge to center), and a temporal gradient (0, 2, 6 and 13 years after gap creation). The data were observations of ground-layer plant abundance, published plant traits, and a modeled index of understory light environments. We ordinated the plant abundance data and evaluated the relationships of composition, traits and light environment by gap size, location along the forest-gap transect and time, with several approaches such as correlations, descriptivestatistics, non-parametric tests of group differences and indicator species importance values. Important Findings Ground-layer plant composition and traits differed across gap sizes, within-gap locations and over time. Gaps of all sizes differed in composition from undisturbed areas, and all pair-wise combinations of gap size also differed in composition, except the 6 m from the 10-m gaps. Large gaps (46 m) also displayed within-gap compositional gradients from gap edge to center locations. Compositional differences in gap size were evident 2 years after gap creation and, contrary to our hypotheses, remained different over the 13-year period, even in gaps with crown closure. In contrast to the neutral theory, species functional traits and microenvironmental conditions were related to variation in ground-layer composition. Species with smaller seeds, lower shade tolerance, later bloom times, shorter stature and longer leaves were associated with higher light, more central gap locations, larger gap sizes and greater time since gap creation. The correlation between gap size and ground-layer plant composition and traits provides evidence for gap partitioning by the diverse ground-layer community in this temperate deciduous forest community.

Description: We present an analysis of SO2 column densities derived from GOME-2 satellite measurements for the Kīlauea volcano (Hawai`i) for 2007–2012. During a period of enhanced degassing activity in March–November 2008, monthly mean SO2 emission rates and effective SO2 lifetimes are determined simultaneously from the observed downwind plume evolution and meteorological wind fields, without further model input. Kīlauea is particularly suited for quantitative investigations from satellite observations owing to the absence of interfering sources, the clearly defined downwind plumes caused by steady trade winds, and generally low cloud fractions. For March–November 2008, the effective SO2 lifetime is 1–2 days, and Kīlauea SO2 emission rates are 9–21 kt day−1, which is about 3 times higher than initially reported from ground-based monitoring systems.

Description: Active long-path differential optical absorption spectroscopy (LP-DOAS) has been an effective tool for measuring atmospheric trace gases for several decades. However, instruments were large, heavy and power-inefficient, making their application to remote environments extremely challenging. Recent developments in fibre-coupling telescope technology and the availability of ultraviolet light emitting diodes (UV-LEDS) have now allowed us to design and construct a lightweight, portable, low-power LP-DOAS instrument for use at remote locations and specifically for measuring degassing from active volcanic systems. The LP-DOAS was used to measure sulfur dioxide (SO2) emissions from La Fossa crater, Vulcano, Italy, where column densities of up to 1.2 × 1018 molec cm−2 (~ 500 ppmm) were detected along open paths of up to 400 m in total length. The instrument's SO2 detection limit was determined to be 2 × 1016 molec cm−2 (~ 8 ppmm), thereby making quantitative detection of even trace amounts of SO2 possible. The instrument is capable of measuring other volcanic volatile species as well. Though the spectral evaluation of the recorded data showed that chlorine monoxide (ClO) and carbon disulfide (CS2) were both below the instrument's detection limits during the experiment, the upper limits for the X / SO2 ratio (X = ClO, CS2) could be derived, and yielded 2 × 10−3 and 0.1, respectively. The robust design and versatility of the instrument make it a promising tool for monitoring of volcanic degassing and understanding processes in a range of volcanic systems.