Molecular Phylogenetics of Perciform Fishes Using the Nuclear Recombination Activating Gene 1

The order Perciformes contains one-third of all extant fishes in twenty different suborders and over 10,000 species. Few systematic investigations have been performed on this large group of fishes at the suborder level and their evolutionary history is widely recognized as problematic. This dissertation presents three studies: a molecular phylogenetic analysis of the putative suborders of the order Perciformes, an analysis of interrelationships of the families of the perciform suborder Percoidei, and a multi-gene investigation of the percoid superfamily Sparoidea. The taxa sampled in this dissertation represent one of the most inclusive molecular datasets, to date, testing the monophyly of the Perciformes and relationships of its suborders, including the Percoidei. Analyses are performed using a 1425-1431 base fragment of exon three of the single copy, nuclear recombination activating gene 1 (RAG1). Results of these tests reject the monophyly of the Perciformes and of its largest suborder, the Percoidei. However, this study does support some previous relationships at the suborder and family level for these groups and also presents novel interpretations of many groups. A lack of nodal support is seen for mid-level clades in these analyses. Genetic bias, such as high GC content and low effective number of codons, in some taxa, is hypothesized to be one of the causes for some of the unexpected relationships found in this work. A multi-gene approach was taken to test the monophyly of the superfamily Sparoidea and its families. Analyses of RAG1, cytochrome b (cytB), and combined RAG1 + cytB datasets reject a monophyletic Sparoidea but find the Nemipteridae, Sparidae plus Centracanthidae, and Lethrinidae to be individually monophyletic. The one exception to this is in the cytB maximum likelihood phylogeny, which fails to resolve a monophyletic Lethrinidae. The phylogenetic hypotheses discussed in this dissertation are an important step toward an understanding of perciform, percoid, and sparoid relationships and deserve further testing. The high level of taxon sampling presented here should be replicated and expanded using other molecular markers to help resolve the bush at the top of the teleostean tree

Austropallene halanychi sp. nov., a new species of sea spider (Pycnogonida, Callipallenidae) from the Ross Sea, Antarctica

Here we present Austropallene halanychi sp. nov., a new species of pycnogonid within the family Callipallenidae (Pycnogonida), collected from the Ross Sea, Antarctica. While retaining key morphological features known for the genus Austropallene Hodgson, 1915a, the new species is distinguished from congeners by its much larger size, along with the combined absence of a denticle on the inner surface of the fixed finger of the chelifore claw along with the presence of small conical outgrowths where the fixed finger of the chelifore claw meets the movable finger on both the dorsal and ventral sides, and also the ability to fully close the chelifore claw. Additionally, the complete mitochondrial genome of A. halanychi is consistent with other members of the genus Austropallene in terms of gene order and directionality. A phylogenetic tree consisting of mitochondrial protein-coding gene data places A. halanychi as sister to Austropallene cornigera (Möbius, 1902). Additionally, a phylogenetic tree constructed using partial COI data from other callipallenids placed the new species in a clade containing the genus Austropallene. The combination of molecular data in addition to key morphological differences from similar species in the genus leaves no doubt that the new taxon is a new Antarctic species of Austropallene

From molecules to management: adopting DNA-based methods for monitoring biological invasions in aquatic environments

a b s t r a c t Recent technological advances have driven rapid development of DNA-based methods designed to facilitate detection and monitoring of invasive species in aquatic environments. These tools promise to improve on traditional monitoring approaches by enhancing detection sensitivity, reducing analytical turnaround times and monitoring costs, and increasing specificity of target identifications. However, despite the promise of DNA-based monitoring methods, the adoption of these tools in decision-making frameworks remains challenging. Here, rather than explore technical aspects of method development, we examine impediments to effective translation of those methods into management contexts. In addition to surveying current use of DNA-based tools for aquatic invasive species monitoring, we explore potential sources of uncertainty associated with molecular technologies and possibilities for limiting that uncertainty and effectively communicating its implications for decision-making. We pay particular attention to the recent adoption of DNA-based methods for detection of invasive Asian carp species in the United States Great Lakes region, as this example illustrates many of the challenges associated with applying molecular tools to achieve desired management outcomes. Our goal is to provide a useful assessment of the obstacles associated with integrating DNA-based methods into aquatic invasive species management, and to offer recommendations for future efforts aimed at overcoming those obstacles. Published by Elsevier Inc

Investigating diversity of pathogenic microbes in commercial bait trade water

The recreational bait trade is a potential pathway for pathogen introduction and spread when anglers dump bait shop sourced water into aquatic systems. Despite this possibility, and previous recognition of the importance of the bait trade in the spread of aquatic invasive species (AIS), to date there has been no region wide survey documenting pathogens in retail bait shops. In this study, we analyzed 96 environmental DNA samples from retail bait shops around the Great Lakes region to identify pathogens, targeting the V4 hypervariable region of the 16S rRNA gene. Additionally, we used samples from one site in Lake Michigan as a comparison to pathogen diversity and abundance in natural aquatic systems. Our results identified nine different groups of pathogens in the bait shop samples, including those that pose risks to both humans and fish species. Compared to wild sourced samples, the bait shops had higher relative abundance and greater taxonomic diversity. These findings suggest that the bait trade represents a potentially important pathway that could introduce and spread pathogens throughout the Great Lakes region. Improving pathogen screening and angler outreach should be used in combination to aid in preventing the future spread of high risk pathogens

Quantitative and Rapid DNA Detection by Laser Transmission Spectroscopy

Laser transmission spectroscopy (LTS) is a quantitative and rapid in vitro technique for measuring the size, shape, and number of nanoparticles in suspension. Here we report on the application of LTS as a novel detection method for species-specific DNA where the presence of one invasive species was differentiated from a closely related invasive sister species. The method employs carboxylated polystyrene nanoparticles functionalized with short DNA fragments that are complimentary to a specific target DNA sequence. In solution, the DNA strands containing targets bind to the tags resulting in a sizable increase in the nanoparticle diameter, which is rapidly and quantitatively measured using LTS. DNA strands that do not contain the target sequence do not bind and produce no size change of the carboxylated beads. The results show that LTS has the potential to become a quantitative and rapid DNA detection method suitable for many real-world applications

Incorporation by coordination and release of the iron chelator drug deferiprone from zinc-based metal–organic frameworks

A series of new zinc-based metal–organic framework materials has been prepared in which deferiprone is incorporated as a chelating ligand on infinite or tri-zinc secondary building units following deprotonation. Deferiprone is immediately released from the MOFs on treatments with 1 N hydrochloric acid or buffer, but slow release is observed in ethanoic acid

Extracellular vesicles from A23187-treated neutrophils cause cGAS-STING-dependent IL-6 production by macrophages

In response to several types of bacteria, as well as pharmacological agents, neutrophils produce extracellular vesicles (EVs) and release DNA in the form of neutrophil extracellular traps (NETs). However, it is unknown whether these two neutrophil products cooperate to modulate inflammation. Consistent with vital NETosis, neutrophils challenged with S. aureus, as well as those treated with A23187, released significantly more DNA relative to untreated or fMLF-treated neutrophils, with no lysis occurring for any condition. To test the hypothesis that EVs generated during NETosis caused macrophage inflammation, we isolated and characterized EVs from A23187-treated neutrophils (A23187-EVs). A23187-EVs associated with neutrophil granule proteins, histone H3, transcription factor A, mitochondrial (TFAM), and nuclear and mitochondrial DNA (mtDNA). We showed that DNA from A23187-EVs, when transfected into macrophages, led to production of IL-6 and IFN-α2, and this response was blunted by pre-treatment with the STING inhibitor H151. Next, we confirmed that A23187-EVs were engulfed by macrophages, and showed that they induced cGAS-STING-dependent IL-6 production. In contrast, neither EVs from untreated or fMLF-treated cells exhibited pro-inflammatory activity. Although detergent-mediated lysis of A23187-EVs diminished IL-6 production, removal of surface-associated DNA with DNase I treatment had no effect, and A23187-EVs did not induce IFN-α2 production. Given these unexpected results, we investigated whether macrophage mtDNA activated the cGAS-STING signaling axis. Consistent with mitochondrial outer membrane permeabilization (MOMP), a defined mechanism of mtDNA release, we observed macrophage mitochondrial membrane depolarization, a decrease in cytosolic Bax, and a decrease in mitochondrial cytochrome c, suggesting that macrophage mtDNA may initiate this EV-dependent signaling cascade. All together, these data demonstrate that A23187-EVs behave differently than transfected NET- or EV-DNA, and that neutrophil-derived EVs could be used as a model to study NF-κB-dependent STING activation

Secondary amine-functionalised metal-organic frameworks:direct syntheses versus tandem post-synthetic modifications

We compare two routes to prepare functionalised MOFs and show that direct synthesis with a functionalised dicarboxylic acid is better for zinc MOFs whereas post-synthetic modification is better for chromium MOFs.</p