Trade and Management: Exclusive Economic Zones and the Changing Japanese Surimi Market

The United States' increasing competitive advantage in international seafood trade in Alaska walleye pollock. Theragra chalcogramma, has contributed to higher prices for surimi-based goods and structural changes in seafood production and trade in Japan. The objectives of this analytical investigation include: 1) Evaluation of the role reversal of Japan and the United States in international seafood trade and 2) quantification of the impact of rising prices of frozen surimi on household consumption of surimi-based foods in Japan. This study documents Japan's regression from "seafood self-sufficiency" to increasing dependence on imported products and raw materials. In particular, Japan's growing dependence on American fishermen and seafood producers is described. Surimi production by the United States, and its emerging dominance over Japanese sources of supply, are especially significant. Results of the analysis suggest that Japanese consumer demand for surimi-based food stuffs correlates directly with "competitive" food prices, e.g., pork, chicken, and beef, and inversely with personal income. Also revealed is how rising household income and relative price shifts among competing animal protein sources in the Japanese diet have contributed to declining household consumption of surimi-based foods, specifically, and a shift away from seafoods in favor of beef, in general. The linkages between, for example. Japanese domestic seafood production and consumption, international trade in marine products, and resource management decisions in the U.S. EEZ present a picture of a changing global marketplace. Increasingly, actions in one arena will have perhaps profound implications in the others

Delimiting Species in the Mountaintops : New Trails for Studying Genomic Architecture and Sequencing Historical Specimens Uncover Hidden Diversity within the breve Species Group of Bembidion (Coleoptera : Carabidae)

Species are one of the foundational units upon which entire fields of scientific inquiry are built. Discovering and documenting the planet’s biodiversity remains one of the grand challenges of science. A proper conceptualization of species provides a critical framework for diverse fields such as biophysics, biochemistry, agriculture and pharmacology, and for all of comparative biology. The need to advance the knowledge of biodiversity, and improve the methods used to study that diversity is the central aim of this dissertation. The work presented herein centers on investigating patterns of diversity in the Bembidion breve species group, a group of small ground beetles (Coleoptera: Carabidae) found at high elevations in the mountains of western North America. In undertaking to discover and document cryptic species present in this group, a set of challenges and opportunities led to research projects that develop the breve group as an ideal system for developing innovative approaches for conducting molecular studies in diverse non-model groups. In addressing challenges associated with the identification of a 100-year-old type specimens in the breve group, Chapter 2 presents a methodological study designed to optimize sample preparation protocols for next-generation of small-bodied specimens with degraded DNA. Compare the library preparation success of several library preparation protocols on low DNA input from several old specimens, including type specimens, ranging from 58–159 years in age. I also test the effect of enzymatic repair on library success and use several metrics of sequencing success to evaluate the effect of the various treatments. I demonstrate that excellent library preparation and sequencing success can be obtained using as little as 1 ng of degraded input DNA. I recommend simple library preparation protocol modifications that can be used to optimize sample preparation success of challenging museum specimens, and make recommendations for preserving valuable DNA of rare or unique specimens. In Chapter 3, the I present the species delimitation and taxonomic revision of breve species group. In a group that has consisted of two recognized species for the last several decades, the I use molecular, morphological, and geographic data as evidence that at least nine species are present in the group and provides identification tools and species distribution data. I present a novel, sequence-based approach to identifying a 100-year-old type specimen that used evidence of copy number variation within the ribosomal DNA (rDNA) cistron (the rDNA region that encodes for 18S and 18S ribosomal RNA genes) to confirm the identity the type specimen of Bembidion lividulum, a specimen for which degradation evident in DNA sequence data prevented unambiguous identification using analysis of gene trees. In Chapter 4, I further investigate interesting patterns of copy number variation within the rDNA cistron first reported in Chapter 3. I describe a simple method detecting signatures of genomic architecture using copy number variation profiles of the rDNA cistron to produce “rDNA profiles”. I investigate the pattern of signatures in rDNA profiles among and within species of the breve group. I show that rDNA profiles hold excellent signal at the species level in a challenging species group, and is variable across a broader taxonomic group in the Bembidion subgenus Plataphus. I demonstrate that this approach is compatible with phylogenomic data generation workflows, and use fluorescence in situ hybridization (FISH) to corroborate patterns seen in rDNA profiles. These results highlight the potential value of methods that incorporate signal of genomic architecture and in species delimitation/phylogenetics, and how the patterns observed in those studies provide natural synergy with studies on genome evolution

Climate oscillations, glacial refugia, and dispersal ability: factors influencing the genetic structure of the least salmonfly, Pteronarcella badia (Plecoptera), in Western North America

Background: Phylogeographic studies of aquatic insects provide valuable insights into mechanisms that shape the genetic structure of communities, yet studies that include broad geographic areas are uncommon for this group. We conducted a broad scale phylogeographic analysis of the least salmonfly Pteronarcella badia (Plecoptera) across western North America. We tested hypotheses related to mode of dispersal and the influence of historic climate oscillations on population genetic structure. In order to generate a larger mitochondrial data set, we used 454 sequencing to reconstruct the complete mitochondrial genome in the early stages of the project. Results: Our analysis revealed high levels of population structure with several deeply divergent clades present across the sample area. Evidence from five mitochondrial genes and one nuclear locus identified a potentially cryptic lineage in the Pacific Northwest. Gene flow estimates and geographic clade distributions suggest that overland flight during the winged adult stage is an important dispersal mechanism for this taxon. We found evidence of multiple glacial refugia across the species distribution and signs of secondary contact within and among major clades. Conclusions: This study provides a basis for future studies of aquatic insect phylogeography at the inter-basin scale in western North America. Our findings add to an understanding of the role of historical climate isolations in shaping assemblages of aquatic insects in this region. We identified several geographic areas that may have historical importance for other aquatic organisms with similar distributions and dispersal strategies as P. badia. This work adds to the ever-growing list of studies that highlight the potential of next-generation DNA sequencing in a phylogenetic context to improve molecular data sets from understudied groups

New Tricks (2015)

As above, so below, as within, so without, as the universe, so the soul. Hermes Trismegistus I am but a humbly painted vessel of the Almighty Artist, here to share in this uniquely significant piece of the great mural. They say that art imitates life and that through the creation of art we become one with the divine painter of the universe. That is why the calling of the artist is the most noble of pursuits, for the artist is the truest reflection of the source of things. Yet art is not finite and cannot be nailed down. Like the artist, art channels itself through many different vessels and media. It is elusive, but when encountered there is a definite understanding the that Almighty Artist is present in the work. In this, our collective effort at paying homage to our inner artist, we have collected together reflections of life as channeled through the talented artists of Dakota State University. Mirroring the Master Creation, New Tricks has become a perfectly reflected world of its own. Each piece of art inside the magazine has been given life and granted power to interact with the rest of creation, namely you. So it is with great honor that we present to you the many mirrors of our souls, so that they may act as portals for you to venture deep and greet the eternal inside of us

Відгук офіційного опонента доктора філологічних наук, професора Кузьменка В.І. на дисертацію Галича А.О. за темою Жанрові модифікації портретного дискурсу в документалістиці ХХ – ХХІ ст

У дисертації вперше в українському літературознавстві здійснено комплексне дослідження особливостей портретування в документальній літературі, осмислено його специфіку у творах різних жанрів, простежено складники портретних характеристик, визначено домінантні підходи до створення портретів. Удосконалено системну класифікацію портретів в українській документалістиці згідно з новітніми досягненнями літературознавства. Уточнено структуру, семіотику й семантику портрета в різних жанрах мемуарної, біографічної (автобіографічної) літератури. Набули подальшого розвитку модифікації портретів у документальних творах. Розширено й уточнено формулювання низки теоретичних понять, зокрема таких, як портрет, концентрований портрет, деконцентрований портрет, автопортрет, парний портрет, колективний портрет, оніричний портрет, некропортрет. Залучено до аналізу тексти, зокрема останніх літ, які досі не були предметом наукових студій, а також маловідомі архівні матеріали.У дисертації вперше в українському літературознавстві здійснено комплексне дослідження особливостей портретування в документальній літературі, осмислено його специфіку у творах різних жанрів, простежено складники портретних характеристик, визначено домінантні підходи до створення портретів. Удосконалено системну класифікацію портретів в українській документалістиці згідно з новітніми досягненнями літературознавства. Уточнено структуру, семіотику й семантику портрета в різних жанрах мемуарної, біографічної (автобіографічної) літератури. Набули подальшого розвитку модифікації портретів у документальних творах. Розширено й уточнено формулювання низки теоретичних понять, зокрема таких, як портрет, концентрований портрет, деконцентрований портрет, автопортрет, парний портрет, колективний портрет, оніричний портрет, некропортрет. Залучено до аналізу тексти, зокрема останніх літ, які досі не були предметом наукових студій, а також маловідомі архівні матеріали.У дисертації вперше в українському літературознавстві здійснено комплексне дослідження особливостей портретування в документальній літературі, осмислено його специфіку у творах різних жанрів, простежено складники портретних характеристик, визначено домінантні підходи до створення портретів. Удосконалено системну класифікацію портретів в українській документалістиці згідно з новітніми досягненнями літературознавства. Уточнено структуру, семіотику й семантику портрета в різних жанрах мемуарної, біографічної (автобіографічної) літератури. Набули подальшого розвитку модифікації портретів у документальних творах. Розширено й уточнено формулювання низки теоретичних понять, зокрема таких, як портрет, концентрований портрет, деконцентрований портрет, автопортрет, парний портрет, колективний портрет, оніричний портрет, некропортрет. Залучено до аналізу тексти, зокрема останніх літ, які досі не були предметом наукових студій, а також маловідомі архівні матеріали

New Tricks (2014)

It is an exclusive secret if one knows a muse and it is an even more exclusive ability if said person is able to channel her beauty. For most people, seducing a muse is no easy task. It takes a special kind of creative mind to attract the personification of art. Frequently, the rigorous process of invoking one of the muses often involves a set of rituals that resemble courtship displays. Muses demand undying attention and affection from their vessel before they will allow themselves to flow through a mortal instrument and onto a medium of art. In those rare moments, a beautiful process of creation happens and a little piece of the divine is brought down to the Earth in the form of a painting, poem, or epic tale. It is considered one thing to channel the muses and create art, but it is considered a whole other thing to gather the individual musings of creative minds in an attempt to create a collection of inspired works. With the help of many talented people, that is exactly what has been accomplished in this publication. From collecting and reviewing the submissions to all the technical work behind the scenes, the New Tricks team had to call upon their own muses to produce this wonderful collection of artwork, poems, and short stories. It is with much pride and admiration that I prsent you the 2014 issue of New Tricks. Enjoy

Length of the weaning period affects postweaning growth, health, and carcass merit of ranch-direct beef calves weaned during the fall

Bovine respiratory disease (BRD) is the most economically devastating feedlot disease. Risk factors associated with incidence of BRD include (1) stress associated with maternal separation, (2) stress associated with introduction to an unfamiliar environment, (3) poor intake associated with introduction of novel feedstuffs into the animal\u27s diet, (4) exposure to novel pathogens upon transport to a feeding facility and commingling with unfamiliar cattle, (5) inappropriately administered respiratory disease vaccination programs, and (6) poor response to respiratory disease vaccination programs. Management practices that are collectively referred to as preconditioning are thought to minimize damage to the beef carcass from the BRD complex. Preconditioning management reduces the aforementioned risk factors for respiratory disease by (1) using a relatively long ranch-of-origin weaning period following maternal separation, (2) exposing calves to concentrate-type feedstuffs, and (3) producing heightened resistance to respiratory disease-causing organisms through a preweaning vaccination program. The effectiveness of such programs for preserving animal performance is highly touted by certain segments of the beef industry. Ranch-of-origin weaning periods of up to 60 days are suggested for preconditioning beef calves prior to sale; however, optimal length of the ranch-of-origin weaning period has not been determined experimentally. The objective of this study was to test the validity of beef industry assumptions about appropriate length of ranch-of-origin weaning periods for calves aged 160 to 220 days and weaned during the fall

The Freshman, vol. 4, no. 1

The Freshman was a weekly, student newsletter issued on Mondays throughout the academic year. The newsletter included calendar notices, coverage of campus social events, lectures, and athletic teams. The intent of the publication was to create unity, a sense of community, and class spirit among first year students. The Class of 1937 run of The Freshman featured original cover art by sketch artist Jack Frost (John Edward Frost, 1915-1997), who was born in Eastport, Maine. He attended the University of Maine for only a single academic year before moving to Massachusetts to work for the Boston Herald. Frost later became a columnist and illustrator for the Boston Post

Diverse interventions that extend mouse lifespan suppress shared age-associated epigenetic changes at critical gene regulatory regions

Background: Age-associated epigenetic changes are implicated in aging. Notably, age-associated DNA methylation changes comprise a so-called aging “clock”, a robust biomarker of aging. However, while genetic, dietary and drug interventions can extend lifespan, their impact on the epigenome is uncharacterised. To fill this knowledge gap, we defined age-associated DNA methylation changes at the whole-genome, single-nucleotide level in mouse liver and tested the impact of longevity-promoting interventions, specifically the Ames dwarf Prop1 df/df mutation, calorie restriction and rapamycin. Results: In wild-type mice fed an unsupplemented ad libitum diet, age-associated hypomethylation was enriched at super-enhancers in highly expressed genes critical for liver function. Genes harbouring hypomethylated enhancers were enriched for genes that change expression with age. Hypermethylation was enriched at CpG islands marked with bivalent activating and repressing histone modifications and resembled hypermethylation in liver cancer. Age-associated methylation changes are suppressed in Ames dwarf and calorie restricted mice and more selectively and less specifically in rapamycin treated mice. Conclusions: Age-associated hypo- and hypermethylation events occur at distinct regulatory features of the genome. Distinct longevity-promoting interventions, specifically genetic, dietary and drug interventions, suppress some age-associated methylation changes, consistent with the idea that these interventions exert their beneficial effects, in part, by modulation of the epigenome. This study is a foundation to understand the epigenetic contribution to healthy aging and longevity and the molecular basis of the DNA methylation clock

Successful Recovery of Nuclear Protein-Coding Genes from Small Insects in Museums Using Illumina Sequencing

Correction: 7 Mar 2016: The PLOS ONE Staff (2016) Correction: Successful Recovery of Nuclear Protein-Coding Genes from Small Insects in Museums Using Illumina Sequencing. PLOS ONE 11(3): e0151124. https://doi.org/10.1371/journal.pone.0151124In this paper we explore high-throughput Illumina sequencing of nuclear protein-coding, ribosomal, and mitochondrial genes in small, dried insects stored in natural history collections. We sequenced one tenebrionid beetle and 12 carabid beetles ranging in size from 3.7 to 9.7 mm in length that have been stored in various museums for 4 to 84 years. Although we chose a number of old, small specimens for which we expected low sequence recovery, we successfully recovered at least some low-copy nuclear protein-coding genes from all specimens. For example, in one 56-year-old beetle, 4.4 mm in length, our de novo assembly recovered about 63% of approximately 41,900 nucleotides in a target suite of 67 nuclear protein-coding gene fragments, and 70% using a reference-based assembly. Even in the least successfully sequenced carabid specimen, reference-based assembly yielded fragments that were at least 50% of the target length for 34 of 67 nuclear protein-coding gene fragments. Exploration of alternative references for reference-based assembly revealed few signs of bias created by the reference. For all specimens we recovered almost complete copies of ribosomal and mitochondrial genes. We verified the general accuracy of the sequences through comparisons with sequences obtained from PCR and Sanger sequencing, including of conspecific, fresh specimens, and through phylogenetic analysis that tested the placement of sequences in predicted regions. A few possible inaccuracies in the sequences were detected, but these rarely affected the phylogenetic placement of the samples. Although our sample sizes are low, an exploratory regression study suggests that the dominant factor in predicting success at recovering nuclear protein-coding genes is a high number of Illumina reads, with success at PCR of COI and killing by immersion in ethanol being secondary factors; in analyses of only high-read samples, the primary significant explanatory variable was body length, with small beetles being more successfully sequenced.Data Availability Statement: Raw reads for all museum and reference specimens are submitted to NCBI Sequence Read Archive (accessions SRR2939013– SRR2939027). Focal gene fragments recovered from the de novo assembly of Lagriinae n. gen. and those that were newly sequenced for the phylogeny of Lagriinae are deposited in GenBank (accessions KU233685-KU234083). Focal gene fragments from PCR/Sanger sequencing and the IlluminaMerged sequences of carabids are also deposited in GenBank (accessions KU233685- KU234083). The Tribolium castaneum and Bembidion sp. nr transversale query sequences used to probe our museum specimens for the 67 nuclear protein-coding gene fragments and all alignments used in phylogenetic analyses (including the DeNovo, FarRef, and NearRef sequences), as well as trees from the phylogenetic tests, are deposited in Dryad (data available from the Dryad Digital Repository: http://doi.org/xx)