Shotgun metagenomic analysis of microbial communities from the Loxahatchee nature preserve in the Florida Everglades.

BackgroundCurrently, much is unknown about the taxonomic diversity and the mechanisms of methane metabolism in the Florida Everglades ecosystem. The Loxahatchee National Wildlife Refuge is a section of the Florida Everglades that is almost entirely unstudied in regard to taxonomic profiling. This short report analyzes the metagenome of soil samples from this Refuge to investigate the predominant taxa, as well as the abundance of genes involved in environmentally significant metabolic pathways related to methane production (nitrogen fixation and dissimilatory sulfite reduction).MethodsShotgun metagenomic sequencing using the Illumina platform was performed on 17 soil samples from four different sites within the Loxahatchee National Wildlife Refuge, and underwent quality control, assembly, and annotation. The soil from each sample was tested for water content and concentrations of organic carbon and nitrogen.ResultsThe three most common phyla of bacteria for every site were Actinobacteria, Acidobacteria, and Proteobacteria; however, there was variation in relative phylum composition. The most common phylum of Archaea was Euryarchaeota for all sites. Alpha and beta diversity analyses indicated significant congruity in taxonomic diversity in most samples from Sites 1, 3, and 4 and negligible congruity between Site 2 and the other sites. Shotgun metagenomic sequencing revealed the presence of biogeochemical biomarkers of particular interest (e.g., mrcA, nifH, and dsrB) within the samples. The normalized abundances of mcrA, nifH, and dsrB exhibited a positive correlation with nitrogen concentration and water content, and a negative correlation with organic carbon concentration.ConclusionThis Everglades soil metagenomic study allowed examination of wetlands biological processes and showed expected correlations between measured organic constituents and prokaryotic gene frequency. Additionally, the taxonomic profile generated gives a basis for the diversity of prokaryotic microbial life throughout the Everglades

Seasonal calibration of the end-cretaceous Chicxulub impact event

The end-Cretaceous Chicxulub impact triggered Earth’s last mass-extinction, extinguishing ~ 75% of species diversity and facilitating a global ecological shift to mammal-dominated biomes. Temporal details of the impact event on a fine scale (hour-to-day), important to understanding the early trajectory of mass-extinction, have largely eluded previous studies. This study employs histological and histo-isotopic analyses of fossil fish that were coeval with a unique impact-triggered mass-death assemblage from the Cretaceous-Paleogene (KPg) boundary in North Dakota (USA). Patterns of growth history, including periodicity of ẟ18O and ẟ13C and growth band morphology, plus corroborating data from fish ontogeny and seasonal insect behavior, reveal that the impact occurred during boreal Spring/Summer, shortly after the spawning season for fish and most continental taxa. The severity and taxonomic symmetry of response to global natural hazards are influenced by the season during which they occur, suggesting that post-impact perturbations could have exerted a selective force that was exacerbated by seasonal timing. Data from this study can also provide vital hindsight into patterns of extant biotic response to global-scale hazards that are relevant to both current and future biomes

Seasonal calibration of the end-cretaceous Chicxulub impact event

From Springer Nature via Jisc Publications RouterHistory: received 2021-08-29, accepted 2021-11-29, collection 2021-12, registration 2021-12-01, pub-electronic 2021-12-08, online 2021-12-08Publication status: PublishedAbstract: The end-Cretaceous Chicxulub impact triggered Earth’s last mass-extinction, extinguishing ~ 75% of species diversity and facilitating a global ecological shift to mammal-dominated biomes. Temporal details of the impact event on a fine scale (hour-to-day), important to understanding the early trajectory of mass-extinction, have largely eluded previous studies. This study employs histological and histo-isotopic analyses of fossil fish that were coeval with a unique impact-triggered mass-death assemblage from the Cretaceous-Paleogene (KPg) boundary in North Dakota (USA). Patterns of growth history, including periodicity of ẟ18O and ẟ13C and growth band morphology, plus corroborating data from fish ontogeny and seasonal insect behavior, reveal that the impact occurred during boreal Spring/Summer, shortly after the spawning season for fish and most continental taxa. The severity and taxonomic symmetry of response to global natural hazards are influenced by the season during which they occur, suggesting that post-impact perturbations could have exerted a selective force that was exacerbated by seasonal timing. Data from this study can also provide vital hindsight into patterns of extant biotic response to global-scale hazards that are relevant to both current and future biomes

A Functional Genomics Approach Identifies Candidate Effectors from the Aphid Species Myzus persicae (Green Peach Aphid)

Aphids are amongst the most devastating sap-feeding insects of plants. Like most plant parasites, aphids require intimate associations with their host plants to gain access to nutrients. Aphid feeding induces responses such as clogging of phloem sieve elements and callose formation, which are suppressed by unknown molecules, probably proteins, in aphid saliva. Therefore, it is likely that aphids, like plant pathogens, deliver proteins (effectors) inside their hosts to modulate host cell processes, suppress plant defenses, and promote infestation. We exploited publicly available aphid salivary gland expressed sequence tags (ESTs) to apply a functional genomics approach for identification of candidate effectors from Myzus persicae (green peach aphid), based on common features of plant pathogen effectors. A total of 48 effector candidates were identified, cloned, and subjected to transient overexpression in Nicotiana benthamiana to assay for elicitation of a phenotype, suppression of the Pathogen-Associated Molecular Pattern (PAMP)–mediated oxidative burst, and effects on aphid reproductive performance. We identified one candidate effector, Mp10, which specifically induced chlorosis and local cell death in N. benthamiana and conferred avirulence to recombinant Potato virus X (PVX) expressing Mp10, PVX-Mp10, in N. tabacum, indicating that this protein may trigger plant defenses. The ubiquitin-ligase associated protein SGT1 was required for the Mp10-mediated chlorosis response in N. benthamiana. Mp10 also suppressed the oxidative burst induced by flg22, but not by chitin. Aphid fecundity assays revealed that in planta overexpression of Mp10 and Mp42 reduced aphid fecundity, whereas another effector candidate, MpC002, enhanced aphid fecundity. Thus, these results suggest that, although Mp10 suppresses flg22-triggered immunity, it triggers a defense response, resulting in an overall decrease in aphid performance in the fecundity assays. Overall, we identified aphid salivary proteins that share features with plant pathogen effectors and therefore may function as aphid effectors by perturbing host cellular processes

Temporal Compounding: A Novel Implementation and Its Impact on Quality and Diagnostic Value in Echocardiography

AbstractTemporal compounding can be used to suppress acoustic noise in transthoracic cardiac ultrasound by spatially averaging partially decorrelated images acquired over consecutive cardiac cycles. However, the reliable spatial and temporal alignment of the corresponding frames in consecutive cardiac cycles is vital for effective implementation of temporal compounding. This study introduces a novel, efficient, accurate and robust technique for the spatiotemporal alignment of consecutive cardiac cycles with variable temporal characteristics. Furthermore, optimal acquisition parameters, such as the number of consecutive cardiac cycles used, are derived. The effect of the proposed implementation of temporal compounding on cardiac ultrasound images is quantitatively assessed (32 clinical data sets providing a representative range of image qualities and diagnostic values) using measures such as tissue signal-to-noise ratio, chamber signal-to-noise ratio, tissue/chamber contrast and detectability index, as well as a range of clinical measurements, such as chamber diameter and wall thickness, performed during routine echocardiographic examinations. Temporal compounding (as implemented) consistently improved the image quality and diagnostic value of the processed images, when compared with the original data by: (i) increasing tissue and cavity signal-to-noise ratios as well as tissue/cavity detectability index, (ii) improving the corresponding clinical measurement repeatability and inter-operator measurement agreement, while (iii) reducing the number of omitted measurements caused by data corruption

Optimization of the synthesis protocol to study long non-coding RNAs by NMR

Die Entdeckung nicht-codierender RNAs hat ein breites Forschungsfeld innerhalb der Wissenschaftsgemeinde eröffnet. Diese RNAs werden mit zahlreichen Prozessen in allen Organismen in Verbindung gebracht. Um ihre Funktion und deren zu Grunde liegenden Prinzipien zu verstehen, sind die Kenntnis von Struktur und Dynamik dieser RNAs entscheidend. NMR Spektroskopie ist eine leistungsfähige Methode für solche Untersuchungen. Da spektrale Überlappung die Untersuchung längerer RNAs ansonsten behindern würde, werden Isotopenmarkierungen eingeführt. Die Synthese solcher spezifisch markierten RNA Sequenzen wird durch Festphasensynthese ermöglicht. Da für NMR Spektroskopie größere Probenmengen erforderlich sind als für andere verbreitete Methoden, ist ein effizientes Syntheseprotokoll entscheidend für den Forschungserfolg. In dieser Arbeit wurde das Syntheseprotokoll für RNA Oligonucleotide auf mehreren Ebenen optimiert: Zunächst wurde die Festphasensynthese, im Speziellen der basische Entschützungsschritt, verbessert und potentielle Nebenreaktionen mit LC-ESI-MS Untersuchungen der Syntheserohprodukte analysiert. Des Weiteren wurde die RNA Synthese mittels biochemischer Ligation verbessert, in dem die Ansatzgröße erhöht wurde, um den Arbeitsaufwand für die Produktion ausreichender Probenmengen zu reduzieren. Im dritten Teil wurden drei Uridin- bzw. Dihydrouridinphosphoramiditbausteine mit isotopenmarkierten Riboseeinheiten synthetisiert. Diese besitzen großes Potential für zukünftige NMR Untersuchungen von dynamischen Prozessen im D-Arm von tRNAs.Non-coding RNAs represent a field of research of great interest within the scientific community. Ever since their discovery, non-coding RNAs have been successfully tied to a multitude of different processes in all organisms. Elucidation of structure and dynamics of these RNAs is the key to understanding their function and the principles involved in that function. NMR spectroscopy has emerged as a powerful tool for this research. However, site-specific isotope labeling is crucial to overcome spectral overlap when studying longer RNAs by NMR spectroscopy. Solid-phase synthesis enables the production of such specifically labeled RNAs. As larger amounts of RNA are needed for NMR studies compared to other methods, efficient synthesis of oligonucleotides is essential. In this work, synthesis of oligonucleotides was optimized on different levels. First, the solid-phase synthesis and particularly the following alkaline deprotection process was improved and possible side-reactions evaluated by LC-ESI-MS studies of the crude synthesis products. Second, the upscaling of RNA ligation was undertaken, which significantly reduces the work-time necessary to produce a sufficient amount of RNA for NMR studies by this approach. Finally, three different stable-isotope labeled uridine and dihydrouridine phosphoramidite building blocks were synthesized. These possess high potential as NMR targets for the study of the dynamic processes found in the D-arm of tRNAs.submitted by David Klingler, BScKurzbeschreibung in deutscher SpracheUniversität Innsbruck, Masterarbeit, 2019(VLID)442811

Metal---metal multiple bonds : IV. The chemistry of bis(cyclopentadienyldicarbonyl-molybdenum) (Mo[triple bond]Mo)

The synthesis and chemistry of Cp2Mo2(CO)4 (I) a coplex containing a reaction Mo[triple bond]Mo triple bond, are described. The formation of I in refluxing xylene is shown to occur via odd-electron intermediates from homolysis of the Mo---Mo bond in the Cp2Mo2(CO)6 precursor. Numerous soft nucleophiles add to I to give complexes, e.g., trans-(CpMo(CO)2L)2 (L = Ph3P, P(OMe)3), ([mu]-RC2R')Cp2Mo2(CO)4, and ([mu]-SR)2Cp2Mo2(CO)4. (Et4N)(Cp2Mo2(CO)4CN) may be isolated from the reaction of cyanide ion with I. Iodine and hydrogen chloride react to give Cp2Mo2(CO)4I2 and ([mu]-H)([mu]-Cl)Cp2Mo2(CO)4, respectively. Silver and mercuric ions are reduced to the metal by I, but Ph2Hg gives (CpMo(CO)3)2Hg in addition to metallic mercury. With tetracyanoethylene, I forms [CpMo(CO)4]+[TCNE]-. Complex I mimics the reaction of acetylenes with L4Pt (L = Ph3P) and forms the triangulo-cluster, ([mu]-L2Pt)Cp2Mo2(CO)4. With Na2Fe(CO)4, Cp2Mo2(CO)4I2 forms the analogous cluster, ([mu]-Fe(CO)4)Cp2Mo2(CO)4. By electron counting rules, these clusters should contain Mo=Mo double bonds. Evidence is presented which indicates I and Co2(CO)8 form an unstable tetrahedrane cluster. At 100[deg]C in toluene, I may reversibly dimerize to give a tetrahedrane Mo4-cluster, as shown by scrambling experiments. Complex I reacts slowly with Mn2(CO)10 to give CpMo(CO)3Mn(CO)5 as the only isolable mixed-metal product.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/22488/1/0000029.pd

Three papers on Internet centered activism: governance, mobilization, and lobbying

Thesis (Ph. D.)--University of Rochester. Department of Political Science, 2013.Digital media have dramatically lowered the costs of interest group communication with their members, altering the definition of what it means to be a member of an organization. Though organizations have a new ability to inexpensively maintain and mobilize large lists of non-paying members, the implications of this ability for interest group decision-making, mobilization and lobbying have not been explored. This project examines the circumstances under which presidents can use personal grassroots lobbying organizations to make targeted appeals to their partisan supporters, and finds that these appeals are only effective when there is unified government and the president takes relatively extreme policy positions. This project also uses survey data from a large non-profit advocacy organization to break down the membership experience and analyze how various media forms update individual beliefs about the expected utility of membership, finding that one-way messages like email and mailers influence goal beliefs and direct experience influences efficacy beliefs, but social media is not influential. Finally, this project also introduces a leadership model of interest group policy determination that allows separate provision of club and private goods to members, allowing some so-called members to affiliate but not pay dues, but choose a third option where they remove themselves from no-cost membership. I find that, when the preferred policies of individuals with financial resources differ from those of voters as a whole, groups which can cheaply provide valuable material incentives to contributors choose policies closer to those preferred by the financially well-endowed, while decreasing the costs of affiliation-only, or ersatz, membership causes leaders to choose policies closer to that of the mean voter