Landscape and inchannel factors affecting the distribution and abundance of riverine smallmouth bass in Missouri

The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file.Title from title screen of research.pdf file (viewed on July 22, 2009)Thesis (Ph. D.) University of Missouri-Columbia 2008.I developed a series of spatially-nested research objectives to identify habitat elements related to the distribution and abundance of riverine smallmouth bass Micropterus dolomieu in Missouri. The range of smallmouth bass was identified using a few natural-occurring landscape variables: coarse-textured soils within the watershed, watershed relief, and soil permeability. Relative abundance could be predicted within this range using natural landscape and stream segment variables: soil permeability, channel gradient, stream size, spring-flow volume, and local slope. Densities of smallmouth bass in stream segments depended on interactions between land use and particularly important natural-occurring features (coarse-textured soils and soil permeability). Higher relative abundances based on natural features related to higher densities in pasture watersheds whereas urban watersheds generally had the lowest densities of fish regardless of natural conditions. Densities of young of year were higher in stream segments with high spring flows compared to low spring flows but not for other age classes. Young of year used warmer microhabitats than adults regardless of spring-flow influence. Velocity was the most significant variable identifying microhabitats used by young of year whereas depth was important in small streams and stream segments classified by pasture land use.Includes bibliographical reference

Passive Integrated Transponder Tags: Review of Studies on Warmwater Fishes With Notes on Additional Species

Although numerous studies have assessed retention and survival of passive integrated transponder (PIT) tags, data are scattered and information gaps remain for many diminutive fishes. Our study objectives were to 1) systematically review PIT tag studies and summarize retention, growth, and survival data for warmwater fishes; and 2) conduct a laboratory study to evaluate the retention, survival, and growth effects of intracoelomic-placed, half duplex PIT tags on six small-bodied species common to warmwater streams. Our systematic review suggested small sample sizes were common within PIT tag retention and survival studies (39% with n ≤ 20) and that many experiments (15%, 14 of 97) failed to use control fish as part of their evaluations. Studies focused primarily on short-term changes (15 d to 2 y) in tag retention and survival. Tag retention was equal to or greater than 90% in 85% of the experiments reviewed and median survival was 92%. Growth was reported by fishes in the majority of reviewed studies. We found similar results after PIT tagging (peritoneum tagging using 12- or 23-mm half duplex tags) adult Cardinal Shiner Luxilus cardinalis, Central Stoneroller Campostoma annomalum, Greenside Darter Etheostoma blennioides, Orangethroat Darter Etheostoma spectabile, Slender Madtom Noturus exilis, and juvenile Smallmouth Bass Micropterus dolomieu. Tag retention for all species was high, with only one tag loss recorded after 60 d. Survival was also high (≥88%) for all of our species with the exception of Orangethroat Darter (56% survival). No significant difference in mean growth between treatment and control groups was found. Both our results and the findings of the literature review suggested generally high tag retention and low mortality in tagged fishes (across 31 species reviewed). However, within our study (e.g., Orangethroat Darter) and from the literature, examples of negative effects of PIT tagging on fishes were apparent, suggesting methodological testing is necessary before using PIT tags in field studies. We suggest future studies would benefit from addressing the behavioral implications that may be associated with tagging and examination of longer-term tag retention. Furthermore, standard reporting (i.e., sample sizes) in PIT tag studies would be beneficial, and use of control subjects or groups for statistical comparisons is needed

Paradigm versus paradox on the prairie: testing competing stream fish movement frameworks using an imperiled Great Plains minnow

Background: Movement information can improve conservation of imperiled species, yet movement is not quantified for many organisms in need of conservation. Prairie chub (Macrhybopsis australis) is a regionally endemic freshwater fish with unquantified movement ecology and currently considered for listing under the Endangered Species Act. The purpose of this study was to test competing ecological theories for prairie chub movement, including the colonization cycle hypothesis (CCH) that posits adults must make upstream movements to compensate for downstream drift at early life stages, and the restricted movement paradigm (RMP) that describes populations as heterogeneous mixes of mostly stationary and few mobile fish. Methods: We tagged prairie chub with visible implant elastomer during the summer (May–August) of 2019 and 2020 to estimate net distance moved (m) and movement rate (m/d). We tested the hypotheses that observed prairie chub movement would be greater than expected under the RMP and that prairie chub movement would be biased in an upstream direction as predicted by the CCH. Results: We tagged 5771 prairie chub and recaptured 213 individuals across 2019 and 2020. The stationary and mobile components of the prairie chub population moved an order of magnitude further and faster than expected under the RMP during both years. However, we found only limited evidence of upstream bias in adult prairie chub movement as would be expected under the CCH. Conclusions: Our findings are partly inconsistent with the RMP and the CCH, and instead closely follow the drift paradox (DP), in which upstream populations persist despite presumed downstream drift during early life stages and in the apparent absence of upstream bias in recolonization. Previous mathematical solutions to the DP suggest organisms that experience drift maintain upstream populations through either minimization of drift periods such that small amounts of upstream movement are needed to counter the effects of advection or increasing dispersal regardless of directionality. We conclude that the resolution to the DP for prairie chub is an increase in total dispersal and our results provide insight into the spatial scales at which prairie chub conservation and management may need to operate to maintain broad-scale habitat connectivity

A Hierarchical Approach to Fish Conservation in Semiarid Landscapes: A Need to Understand Multiscale Environmental Relationships

A multiscale perspective is essential for conservation planning of riverine fishes. Coarse-scale habitat (e.g., basis) can influence both finer-scale habitat characteristics (e.g., reaches and microhabitat) and associated species distributions. Finer-scale management and habitat rehabilitation efforts can fail without the consideration of coarser-scale constraints. We provide a conceptual hierarchical framework for multiscale fish conservation strategies in the semiarid Great Plains. The Great Plains stream network is highly fragmented due to dam construction, water withdrawals, and increased drought severity. Our framework uses relationships with basin-scale connectivity and streamflow and reach-scale physicochemical characteristics in the context of aiding species reintroduction and stream habitat improvements

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Sympathetic cooling and detection of molecular ions in a Penning trap

Published versio

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN