Beatrice Fairfax, Tell Me What To Do!

https://digitalcommons.library.umaine.edu/mmb-vp/1079/thumbnail.jp

Evolutionary relationships in Panicoid grasses based on plastome phylogenomics (Panicoideae; Poaceae)

Background: Panicoideae are the second largest subfamily in Poaceae (grass family), with 212 genera and approximately 3316 species. Previous studies have begun to reveal relationships within the subfamily, but largely lack resolution and/or robust support for certain tribal and subtribal groups. This study aims to resolve these relationships, as well as characterize a putative mitochondrial insert in one linage. Results: 35 newly sequenced Panicoideae plastomes were combined in a phylogenomic study with 37 other species: 15 Panicoideae and 22 from outgroups. A robust Panicoideae topology largely congruent with previous studies was obtained, but with some incongruences with previously reported subtribal relationships. A mitochondrial DNA (mtDNA) to plastid DNA (ptDNA) transfer was discovered in the Paspalum lineage. Conclusions: The phylogenomic analysis returned a topology that largely supports previous studies. Five previously recognized subtribes appear on the topology to be non-monophyletic. Additionally, evidence for mtDNA to ptDNA transfer was identified in both Paspalum fimbriatum and P. dilatatum, and suggests a single rare event that took place in a common progenitor. Finally, the framework from this study can guide larger whole plastome sampling to discern the relationships in Cyperochloeae, Steyermarkochloeae, Gynerieae, and other incertae sedis taxa that are weakly supported or unresolved.Fil: Burke, Sean V.. Northern Illinois University; Estados UnidosFil: Wysocki, William P.. Northern Illinois University; Estados UnidosFil: Zuloaga, Fernando Omar. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Botánica Darwinion. Academia Nacional de Ciencias Exactas, Físicas y Naturales. Instituto de Botánica Darwinion; ArgentinaFil: Craine, Joseph M.. Jonah Ventures; Estados UnidosFil: Pires, J. Chris. University of Missouri; Estados UnidosFil: Edger, Patrick P.. Michigan State University; Estados UnidosFil: Mayfield Jones, Dustin. Donald Danforth Plant Science Center; Estados UnidosFil: Clark, Lynn G.. Iowa State University; Estados UnidosFil: Kelchner, Scot A.. University of Idaho; Estados UnidosFil: Duvall, Melvin R.. Northern Illinois University; Estados Unido

The Interannual variability of hurricane activity in the Atlantic and east pacific regions

The investigation of the interannual and interdecadal variations in hurricane activity has been an important topic of study lately, especially with regard to their implications for climate change issues. On the interannual time-scale, the El Niño and Southern Oscillation (ENSO) phase has been correlated with hurricane activity in the Atlantic and Eastern Pacific Ocean Basins. For example, various atmospheric and oceanic parameters that influence hurricane development become significantly altered during an El Niño event, leading to suppressed easterly wave development and growth in the Atlantic, but more activity in the Eastern Pacific Ocean Basin. This study examined the interannual variability of hurricane intensity (measured as wind speed and interpreted through the Saffir-Simpson Scale) from 1938 through 2007 in the Atlantic and 1970 through 2007 in the Pacific basins, respectively. These data were then compared with the occurrence of El Niño/La Niña events as defined using the Japan Meteorological Association (JMA) index. El Niño/La Niña variability superimposed on variability associated with the Pacific Decadal Oscillation (PDO) was also examined here. Not surprisingly, during an El Niño year the intensity of Atlantic hurricanes was found to be weaker than during a neutral year or a La Niña year, but these conclusions were opposite in the Eastern Pacific Ocean Basin. There were also significant differences found in hurricane intensity between El Niño and La Niña years when the PDO was in phase 1 (warm phase), rather than when the PDO was in phase 2 (cool phase). This study also examined the interannual variation in hurricane intensity by genesis region (i.e. Atlantic: the eastern and western Atlantic Ocean Basins, the Caribbean, and the Gulf of Mexico; Eastern Pacific: divided into quadrants using 20o N and 125o W as the quadrant intersection point). Finally, the utility of this information in a long-range forecast application is demonstrated

Inducible nitric oxide synthase, Nos2, does not mediate optic neuropathy and retinopathy in the DBA/2J glaucoma model

<p>Abstract</p> <p>Background</p> <p>Nitric oxide synthase 2 (NOS2) contributes to neural death in some settings, but its role in glaucoma remains controversial. NOS2 is implicated in retinal ganglion cell degeneration in a rat glaucoma model in which intraocular pressure (IOP) is experimentally elevated by blood vessel cauterization, but not in a rat glaucoma model where IOP was elevated by injection of hypertonic saline. To test the importance of NOS2 for an inherited glaucoma, in this study we both genetically and pharmacologically decreased NOS2 activity in the DBA/2J mouse glaucoma model.</p> <p>Methods</p> <p>The expression of <it>Nos2 </it>in the optic nerve head was analyzed at both the RNA and protein levels at different stages of disease pathogenesis. To test the involvement of <it>Nos2 </it>in glaucomatous neurodegeneration, a null allele of <it>Nos2 </it>was backcrossed into DBA/2J mice and the incidence and severity of glaucoma was assessed in mice of each <it>Nos2 </it>genotype. Additionally, DBA/2J mice were treated with the NOS2 inhibitor aminoguanidine and the disease compared to untreated mice.</p> <p>Results</p> <p>Optic nerve head <it>Nos2 </it>RNA levels varied and increased during moderate but decreased at early and severe stages of disease. Despite the presence of a few NOS2 positive cells in the optic nerve head, NOS2 protein was not substantially increased during the glaucoma. Genetic deficiency of <it>Nos2 </it>or aminoguanidine treatment did not alter the IOP profile of DBA/2J mice. Additionally, neither <it>Nos2 </it>deficiency nor aminoguanidine had any detectable affect on the glaucomatous optic nerve damage.</p> <p>Conclusion</p> <p>Glaucomatous neurodegeneration in DBA/2J mice does not require NOS2 activity. Further experiments involving various models are needed to assess the general importance of <it>Nos2 </it>in glaucoma.</p

Full genome sequence and sfRNA interferon antagonist activity of Zika virus from Recife, Brazil

Background: The outbreak of Zika virus (ZIKV) in the Americas has transformed a previously obscure mosquito-transmitted arbovirus of the Flaviviridae family into a major public health concern. Little is currently known about the evolution and biology of ZIKV and the factors that contribute to the associated pathogenesis. Determining genomic sequences of clinical viral isolates and characterization of elements within these are an important prerequisite to advance our understanding of viral replicative processes and virus-host interactions. Methodology/Principal findings: We obtained a ZIKV isolate from a patient who presented with classical ZIKV-associated symptoms, and used high throughput sequencing and other molecular biology approaches to determine its full genome sequence, including non-coding regions. Genome regions were characterized and compared to the sequences of other isolates where available. Furthermore, we identified a subgenomic flavivirus RNA (sfRNA) in ZIKV-infected cells that has antagonist activity against RIG-I induced type I interferon induction, with a lesser effect on MDA-5 mediated action. Conclusions/Significance: The full-length genome sequence including non-coding regions of a South American ZIKV isolate from a patient with classical symptoms will support efforts to develop genetic tools for this virus. Detection of sfRNA that counteracts interferon responses is likely to be important for further understanding of pathogenesis and virus-host interactions

A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions

The systematics of grasses has advanced through applications of plastome phylogenomics, although studies have been largely limited to subfamilies or other subgroups of Poaceae. Here we present a plastome phylogenomic analysis of 250 complete plastomes (179 genera) sampled from 44 of the 52 tribes of Poaceae. Plastome sequences were determined from high throughput sequencing libraries and the assemblies represent over 28.7 Mbases of sequence data. Phylogenetic signal was characterized in 14 partitions, including (1) complete plastomes; (2) protein coding regions; (3) noncoding regions; and (4) three loci commonly used in single and multi-gene studies of grasses. Each of the four main partitions was further refined, alternatively including or excluding positively selected codons and also the gaps introduced by the alignment. All 76 protein coding plastome loci were found to be predominantly under purifying selection, but specific codons were found to be under positive selection in 65 loci. The loci that have been widely used in multi-gene phylogenetic studies had among the highest proportions of positively selected codons, suggesting caution in the interpretation of these earlier results. Plastome phylogenomic analyses confirmed the backbone topology for Poaceae with maximum bootstrap support (BP). Among the 14 analyses, 82 clades out of 309 resolved were maximally supported in all trees. Analyses of newly sequenced plastomes were in agreement with current classifications. Five of seven partitions in which alignment gaps were removed retrieved Panicoideae as sister to the remaining PACMAD subfamilies. Alternative topologies were recovered in trees from partitions that included alignment gaps. This suggests that ambiguities in aligning these uncertain regions might introduce a false signal. Resolution of these and other critical branch points in the phylogeny of Poaceae will help to better understand the selective forces that drove the radiation of the BOP and PACMAD clades comprising more than 99.9% of grass diversity

'To live and die [for] Dixie': Irish civilians and the Confederate States of America

Around 20,000 Irishmen served in the Confederate army in the Civil War. As a result, they left behind, in various Southern towns and cities, large numbers of friends, family, and community leaders. As with native-born Confederates, Irish civilian support was crucial to Irish participation in the Confederate military effort. Also, Irish civilians served in various supporting roles: in factories and hospitals, on railroads and diplomatic missions, and as boosters for the cause. They also, however, suffered in bombardments, sieges, and the blockade. Usually poorer than their native neighbours, they could not afford to become 'refugees' and move away from the centres of conflict. This essay, based on research from manuscript collections, contemporary newspapers, British Consular records, and Federal military records, will examine the role of Irish civilians in the Confederacy, and assess the role this activity had on their integration into Southern communities. It will also look at Irish civilians in the defeat of the Confederacy, particularly when they came under Union occupation. Initial research shows that Irish civilians were not as upset as other whites in the South about Union victory. They welcomed a return to normalcy, and often 'collaborated' with Union authorities. Also, Irish desertion rates in the Confederate army were particularly high, and I will attempt to gauge whether Irish civilians played a role in this. All of the research in this paper will thus be put in the context of the Drew Gilpin Faust/Gary Gallagher debate on the influence of the Confederate homefront on military performance. By studying the Irish civilian experience one can assess how strong the Confederate national experiment was. Was it a nation without a nationalism

Landscape science: a Russian geographical tradition

The Russian geographical tradition of landscape science (landshaftovedenie) is analyzed with particular reference to its initiator, Lev Semenovich Berg (1876-1950). The differences between prevailing Russian and Western concepts of landscape in geography are discussed, and their common origins in German geographical thought in the late nineteenth and early twentieth centuries are delineated. It is argued that the principal differences are accounted for by a number of factors, of which Russia's own distinctive tradition in environmental science deriving from the work of V. V. Dokuchaev (1846-1903), the activities of certain key individuals (such as Berg and C. O. Sauer), and the very different social and political circumstances in different parts of the world appear to be the most significant. At the same time it is noted that neither in Russia nor in the West have geographers succeeded in specifying an agreed and unproblematic understanding of landscape, or more broadly in promoting a common geographical conception of human-environment relationships. In light of such uncertainties, the latter part of the article argues for closer international links between the variant landscape traditions in geography as an important contribution to the quest for sustainability