Population Genetics And Mixed Stock Analysis Of Chum Salmon (Oncorhynchus Keta) With Molecular Genetics

Thesis (Ph.D.) University of Alaska Fairbanks, 2012Chum salmon (Oncorhynchus keta) are important for subsistence and commercial harvest in Alaska. Variability of returns to western Alaskan drainages that caused economic hardship for stakeholders has led to speculation about reasons, which may include both anthropogenic and environmental causes in the marine environment. Mixed stock analysis (MSA) compares genetic information from an individual caught at sea to a reference baseline of genotypes to assign it to its population of origin. Application of genetic baselines requires several complex steps that can introduce bias. The bias may reduce the accuracy of MSA and result in overly-optimistic evaluations of baselines. Moreover, some applications that minimize bias cannot use informative haploid mitochondrial variation. Costs of baseline development are species-specific and difficult to predict. Finally, because populations of western Alaskan chum salmon demonstrate weak genetic divergence, samples from mixtures cannot be accurately assigned to a population of origin. The chapters of this thesis address three challenges. The first chapter describes technical aspects of genetic marker development. The second chapter describes a method to evaluate the precision and accuracy of a genetic baseline that accepts any type of data and reduces bias that may have been introduced during baseline development. This chapter also includes a method that places a cost on baseline development by predicting the number of markers needed to achieve a given accuracy. The final chapter explores the reasons for the weak genetic structure of western Alaskan chum salmon populations. The results of those analyses and both geological and archaeological data suggest that recent environmental and geological processes may be involved. The methods and analyses in this thesis can be applied to any species and may be particularly useful for other western Alaskan species

Does the act of surgery provoke activation of "latent" metastases in early breast cancer?

This paper is written in support of the challenging article by Retsky and colleagues in this issue of Breast Cancer Research, and develops on the idea that the act of surgery can provoke the outgrowth of dormant micrometastases, which often leads to the failure of screening to deliver its promise. The therapeutic consequence of this idea involves the use of antiangiogenic drugs before surgery

Potentially adaptive mitochondrial haplotypes as a tool to identify divergent nuclear loci

1. Genetic tools are commonly used for conservation and management of at-risk species. Individuals are often sampled from mixtures that are composed of many populations, which creates a need to assign individuals to their source. This can be problematic when the genetic divergence among source populations is weak but can be improved using adaptive genetic loci, which should show stronger levels of divergence. 2. We previously reported a signature of positive selection in the mitochondrial-encoded ND5 subunit of complex I in diverse taxa. The respiratory machinery of the mitochondria in salmonids is composed of more than 80 nuclear genes and there is substantial interaction between nuclear and mitochondrial expressed gene products. Recent studies report adaptive variation in mitochondrial function as well as co-evolution between mitochondrial and nuclear genomes. We used potentially adaptive ND5-based mitochondrial haplotypes to identify nuclear loci that would display increased levels of genetic divergence compared to neutral nuclear loci in chum salmon (Oncorhynchus keta). Populations in a geographic area the size of France have previously demonstrated weak genetic divergence even after substantial discovery efforts by multiple laboratories for allozymes, microsatellites and SNPs over the last two decades. 3. We used RAD-based next-generation sequencing and identified a nuclear-encoded subunit of mitochondrial complex I that was a significant FST outlier and 14 other divergent nuclear markers that improve genetic assignment of individuals to their population of origin relative to assignments based on neutral markers alone. 4. This work demonstrates how a known adaptive marker can be leveraged to increase the probability of identifying divergent markers for applied genetics tools that may be biologically linked to it

Techno–ecological synergies of solar energy for global sustainability

The strategic engineering of solar energy technologies—from individual rooftop modules to large solar energy power plants—can confer significant synergistic outcomes across industrial and ecological boundaries. Here, we propose techno–ecological synergy (TES), a framework for engineering mutually beneficial relationships between technological and ecological systems, as an approach to augment the sustainability of solar energy across a diverse suite of recipient environments, including land, food, water, and built-up systems. We provide a conceptual model and framework to describe 16 TESs of solar energy and characterize 20 potential techno–ecological synergistic outcomes of their use. For each solar energy TES, we also introduce metrics and illustrative assessments to demonstrate techno–ecological potential across multiple dimensions. The numerous applications of TES to solar energy technologies are unique among energy systems and represent a powerful frontier in sustainable engineering to minimize unintended consequences on nature associated with a rapid energy transition

The Best and Worst of Contracts Decisions: An Anthology

Five hundred years ago, the common law of contract was without substance. It was form-procedure. Plaintiffs picked a form of action, and common law judges made sure someone besides themselves answered all the hard questions; the parties, a jury, or a ritual determined the winner and the remedy. Judges ran a switch on a conflicts-resolution railway. Thomas More, when Chancellor of England (1529-33), urged judges to lay tracks and control the trains. The problem, he said, was that the judges, by the verdict of the jury[,] cast off all quarrels from themselves. The judges soon assumed greater authority, taking responsibility for the law\u27s substance. The consideration requirement was in place by 1539, and judges afterwards imposed doctrine upon doctrine. Over centuries, they created the common law of contract. That law is now mature, more or less, meaning that judges have tools to fix what they want to fix, and feel free to do so. The law they created-the common law of contract-is a remarkable intellectual and political achievement

Chromosomal-level assembly of the Asian Seabass genome using long sequence reads and multi-layered scaffolding

We report here the ~670 Mb genome assembly of the Asian seabass (Lates calcarifer), a tropical marine teleost. We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish species to derive a chromosome-level assembly with a contig N50 size over 1 Mb and scaffold N50 size over 25 Mb that span ~90% of the genome. The population structure of L. calcarifer species complex was analyzed by re-sequencing 61 individuals representing various regions across the species' native range. SNP analyses identified high levels of genetic diversity and confirmed earlier indications of a population stratification comprising three clades with signs of admixture apparent in the South-East Asian population. The quality of the Asian seabass genome assembly far exceeds that of any other fish species, and will serve as a new standard for fish genomics

The Use of Preoperative Epoetin-α in Revision Hip Arthroplasty

PURPOSE: To evaluate the efficacy of preoperative epoetin-α on the revision hip arthroplasty patient. We hypothesized that epoetin-α will reduce blood transfusion. A pertinent review of the literature is provided. METHODS: Forty-six patients were retrospectively reviewed. Sixteen patients received epoetin-α. Patients were case matched by age, preoperative hemoglobin, surgery, gender, and BMI. The clinical triggers for blood transfusion during or after the procedure were determined based on peri- and postoperative hemoglobin levels, ASA score, and/or clinical symptoms consistent with anemia. Blood salvage was not used. RESULTS: Blood transfusion and length of stay were decreased in the epoetin-α group. Hemoglobin in the intervention group increased from 12.0 to 14.5, preoperatively. Patients who received epoetin-α were 0.78 (RR=0.225) times as likely to receive a transfusion. Number Needed to Treat (NNT) to avoid one allogeneic transfusion was 1.84. Age, Gender, BMI, ASA, total and hidden blood loss, preoperative Iron supplements, preop Hct, preop PLT, PT, PTT, and INR were similar. One (6.0%) patient developed an uncomplicated deep venous thrombosis in the intervention group. CONCLUSIONS: The mildly anemic revision hip arthroplasty patient is at increased risk for transfusion. Epoetin-α increased preoperative hemoglobin counts and reduced transfusions in this study; it also decreased patient length of hospital stay likely allowing for an earlier readiness to resume normal activities and/or meet short-term milestones. A randomized study to evaluate the direct and indirect costs of such a treatment methodology in the mildly anemic revision patient may be warranted