Astragalus robbinsii var. fernaldii (Fernald's Milkvetch) is a federally listed taxon of "special concern" due for re-assessment by COSEWIC. Restricted to the Strait of Belle Isle region of Atlantic Canada, its taxonomy in respect to two co-occurring congeners, Astragalus eucosmus and Astragalus robbinsii var. minor, has been questioned due to the variable states of the varieties' diagnostic characters. To clarify phylogenetic relationships within this species complex we studied variation in chloroplast DNA, AFLPs and morphology. Chloroplast DNA sequence data distinguished A. r. var. minor from A. eucosmus and most A. r. var. fernaldii. Three A. r. var. fernaldii populations possessed the A. r. var. minor haplotype, and AFLPs revealed no population structure, indicative of gene flow between taxa and populations. Morphometric analysis indicates that A. r. var. fernaldii is closer to A. eucosmus than A. r. var. minor. Based on these results taxonomic recognition of A. r. var. fernaldii is unwarranted, and we recommend that the taxon be merged into A. eucosmus.

A Thesis submitted to The University of Arizona College of Medicine - Phoenix in partial fulfillment of the requirements for the Degree of Doctor of Medicine. / Severe acute malnutrition (SAM) affects 13 million children under the age of 5 worldwide, and contributes to 1‐2 million preventable deaths each year. Malnutrition is a significant factor in approximately one third of the nearly 8 million deaths in children who are under 5 years of age worldwide. There have been many revolutions in treatment of SAM over time; however, the exact etiology of this preventable condition is not well understood. This review serves to identify the most common risk factors for the development of SAM in children and to identify the most effective treatment for the disease. There are many factors that contribute to developing and surviving SAM as a child, and this systematic review serves to highlight the most common variables that lead to this cause of mortality. An exhaustive review of PubMed was conducted to complete this review. The literature review demonstrates that the most common risk factor for the development of SAM is low maternal literacy.

The modern study of the origins and evolution of the group Cetacea (whales and porpoises) began with a key work published in 1966 which named an archaic group of ungulates, the Mesonychids, as the ancestors of Cetacea. Since that time, the use of both morphological and molecular techniques have split systematists into two camps. Morphological and molecular data have led workers to believe that the closest extant relatives of Cetacea are Artiodactyla, the even-toed ungulates, although a few morphologists believe that it is the Perissodactyla, the odd-toed ungulates. Later molecular studies indicate that Cetaceans are not only closely related to Artiodactyla, but may be members of that group and further, that their closest relative may be the Hippopotamus. Although the Hippopotamus hypothesis is controversial, the evidence supporting it is compelling. The idea merits serious consideration, and it may be that the morphological evidence needs to be re-evaluated.

<p> SEM observations have revealed unknown and previously undetected stages of the bloom-forming dinoflagellate Prorocentrum growing inside calcium carbonate-encrusted perithallial cells of the rhodolith-forming Lithothamnion sp. (Hapalidiaceae, Hapalidiales, Rhodophyta) in the NW Gulf of Mexico. Roundish structures inside the coralline cells were clustered together, surrounded by a thin membrane. Organized blebs, projections of the cytoplasm into the plasma membrane, as well as a suite of varying extracellular ornamentation patterns, were observed. Openings on the surface of some of the structures looked like characteristic thecal pores found in thecal plates of some dinoflagellates. DNA was extracted from inside the rhodolith and sequenced using dinoflagellate-specific cob1-primers. When blasting the resulting DNA sequences, it proved to be an exact match for Prorocentrum lima. Cells were isolated from inside the rhodoliths and cultured, revealing the presence of another set of endolithic life stages identified as Haptophyta (Prymnesiophyta), confirmed by single cell 18S rDNA sequencing. This research illustrates and illuminates newly found benthic life history stages of two ecologically important taxa of primary producers that also cause harmful algal blooms, such as the formation of red tides, fish kills, or shellfish poisoning events in the Gulf of Mexico. </p>

<p> Several new discoveries in <i>Euphorbia</i> L. subg. <i> Chamaesyce</i> Raf. sect. <i>Anisophyllum</i> Roeper for the Trans-Pecos region of Texas are documented. These include <i>E. ophthalmica </i> Pers., a species new to the Trans-Pecos from Marfa, Presidio County; <i> E. abramsiana</i> L.C. Wheeler new to Texas from Brewster and Presidio Counties; <i>E. vermiculata</i> Raf., new to Texas from Alpine, Brewster County; <i>E. cryptorubra</i> N.C. Taylor &amp; M. Terry, a newly described species from southern Hudspeth County and northern Chihuahua, Mexico; notes on <i>E. golondrina</i> L.C. Wheeler including two potential novelties; and notes on <i>E. fendleri</i> Torr. &amp; A. Gray, a problematic species complex. The sections concerning <i>E. abramsiana</i> and <i>E. cryptorubra</i> have been published Taylor and Terry (2016) in Phytoneuron and the Journal of the Botanical Institute of Texas respectively. Within <i>E. golondrina</i> and <i> E. fendleri,</i> there is much room for study, and directions for future investigations are indicated. Provided at the end is a key to all species now known for the Trans-Pecos region of Texas.</p>

<p> The brachyuran superfamily Palicoidea &Scaron;tev&ccaron;i&cacute;, 2005, commonly referred to as stilt-crabs, currently includes the families Crossotonotidae Moosa and Ser&eacute;ne, 1981 and Palicidae Bouvier, 1898, consisting of two and nine genera, respectively. Both genus and species level relationships remain largely enigmatic and are based primarily upon highly variable morphological characters. Molecular phylogenetic analyses, based on COI and 16S mitochondrial gene sequences, are used to clarify relationships among primarily western Atlantic species and to independently validate diagnostic morphological characters. The resultant molecular phylogenetic tree resolves three major clades: one grouping <i>Palicus affinis, Palicus alternatus,</i> and <i> Palicus bahamensis;</i> a second grouping <i>Palicus faxoni</i> and <i>Palicus obesus;</i> and the third grouping <i>Crossotonotus </i> sp., <i>Pseudopalicus</i> sp., <i>Palicus cristatipes, </i> and <i>Palicus sica.</i> Putative specimens of <i> P. floridanus</i> were positioned as sister species to other groups. Molecular phylogenetic evidence infers intrageneric evolutionary history of <i> Palicus</i> Philippi, 1838, concordant with relationships suggested by gonopod morphology of congeners. Gonopod morphology was found to be highly conserved within species, moderately conserved among species sharing a common clade, and divergent among species in different well-separated clades. Conversely, many morphological characters that have historically been applied to describe and identify palicids were found to be highly variable within species, inconsistently variable among species, and in some cases relatively conserved across divergent clades. On the basis of present molecular phylogenetic analyses, separation of the families Crossotonotidae and Palicidae may be supported only if further revisions to membership of the family Palicidae were to be undertaken. These revisions are deferred pending more robust genetic analyses.</p>

Proof of concept lidar research has, to date, examined wall-to-wall models of forest ecosystems. While these studies have been important for verifying lidars efficacy for forest surveys, complete coverage is likely not the most cost effective means of using lidar as auxiliary data for operational surveys; sampling of some sort being the better alternative. This study examines the effectiveness of sampling with high point-density scanning lidar data and shows that systematic sampling is a better alternative to simple random sampling. It examines the bias and mean squared error of various estimators, and concludes that a linear-trend-based and especially an autocorrelation-assisted variance estimator perform better than the commonly used simple random sampling based-estimator when sampling is systematic.

<p> The integration of advances in computing technology with major innovations in sequence data collection and phylogenetic inference has revolutionized evolutionary biology in the 21^st century. In particular, the continual development of both theory and software that allow for more flexibility in utilizing molecular clock methods has radically transformed our understanding of the mode and tempo of diversification across the Tree of Life. Over the course of five chapters, this dissertation explores methodological challenges to phylogenetic inference with the aim of better understanding the evolutionary history of the Holocentridae (squirrelfishes and soldierfishes). </p><p> Chapter 1 begins by focusing on the problem of accommodating clade specific rate heterogeneity in molecular clock analyses. While various nucleotide substitution models have been developed to accommodate among lineage rate heterogeneity, recently developed "uncorrelated relaxed clock" and "random local clock" models are predicted to perform better in the presence of lineage specific rate heterogeneity as these models relax assumptions of inheritance of nucleotide substitution rates between descendant lineages. Using simulations and two cetacean (whale and dolphin) datasets as a case study, we demonstrate abrupt changes in rate isolated to one or a few lineages in the phylogeny can mislead rate and age estimation, even when the node of interest is calibrated; and provide suggestions for diagnosing extreme clade specific rate heterogeneity.</p><p> Homoplasy is another important, yet often overlooked, source of error in phylogenetic studies. Chapters 2 and 3 utilize phylogenetic informative approaches to screen nucleotide sequence data for homoplasious site patterns. Using phylogenetic informativeness profiles, chapter 2 reconciles two competing hypotheses of ray-finned fish divergence times by highlighting that mitogenomic based Jurassic and Triassic divergence time estimates for most major lineages of spiny-rayed (acanthomorph) fishes were an artifact of tree extension. Evolutionary relationships of early diverging acanthomorph fishes are also contentious, with molecular data supporting either holocentrids or a clade comprised of holocentrids and primarily deep-sea fishes as the sister lineage to the species-rich percomorpha. Chapter 3 reveals this conflict to also be largely driven by homoplasy and reconciles results based on previously published data with a 132 gene next-generation sequence dataset to identify the sister lineage of percomorph and the phylogenetic placement of holocentrid fishes.</p><p> Chapter 4 continues to explore holocentrid evolutionary relationships. Using a multi-locus dataset that includes all but one holocentrid genus, this chapter provides the first molecular phylogeny of the group. The systematics of holocentrid fishes has unstable for over 100 years. We demonstrate several of the key synapomorphies for holocentrid genera are in fact homoplasious. Likewise, several genera of holocentrine (squirrelfish) are rendered consistently paraphyletic by a series of maximum-likelihood and Bayesian analyses and we propose taxonomic revisions to reflect shared ancestry.</p><p> Chapter 5 further investigates the temporal history of holocentrid evolution. Contemporary holocentrid species richness is concentrated in the Indo-Australian Archipelago (IAA), yet these fishes also represent some of the most numerous fossil taxa in deposits of the Eocene West Tethyan biodiversity hotspot. Using likelihood-based methods integrated with a molecular timetree that incorporates fossils as tip taxa, we reconstruct the history of range evolution for these fishes. Following the collapse of the West Tethys, holocentrids exhibit a signature of increased range fragmentation, becoming isolated between the Atlantic and Indo-Pacific Ocean basins. However, rather than originating within the emerging IAA hotspot, the IAA appears to have acted as a reservoir for holocentrid diversity that originated in adjacent regions over deep evolutionary timescales. By integrating extinct lineages, these results provide a necessary historic perspective on the formation and maintenance of global marine biodiversity. </p>

<p> Viral infection and the subsequent immune responses such as the expression of interferon beta (<i>ifnb1</i>) show extreme levels of cell to cell variability. A fraction of cells get infected and a fraction of infected cells induce an <i>ifnb1</i> response. These responding cells then signal to coordinate appropriate immune responses required to clear infection. The mechanism of propagation of this response at the single cell level is critical to generate an appropriate defense against the virus, yet is incompletely understood. </p><p> Interesting work on cell to cell variability has been done using transfected <i>ifnb1</i> reporter constructs. However, this approach has several limitations. The reporter systems introduce multiple copies of the reporter construct in each cell, which does not reflect the conditions in the intact cells where only two of the interferon promoter and gene are present. This alters the <i>ifnb1</i> enhanceosome stoichiometry from the one present in a normal physiological environment, and potentially distorts the patterns of single cell responses observed. In addition, reporter constructs integrate the response that occur over many hours, which makes it difficult to measure the expression dynamics that occur early after exposure to infection. Such measurements in the intact cells would be helpful for understanding the mechanisms underlying the propagation of this immune response. </p><p> In order to obtain sensitive and accurate measurements of changes in gene expression in infected single cells, we used single-cell single-molecule mRNA imaging to directly and simultaneously count the transcripts of <i> ifnb1</i> and that of a virus (Newcastle disease virus) gene Hemagglutinin-neuraminidase hn . This experimental approach enabled us to measure the single-cell responses from the very early stages of infection, in primary immune cells. Simultaneous measurement of <i>ifnb1</i> and the viral gene hn high lighted the variation in responses across cells, the temporal evolution of the expression of the two genes and their single cell correlation following infection. </p><p> We find that the single cell <i>ifnb1</i> response to virus infection shows a temporally dispersed (asynchronous) pattern. A small fraction of infected cells respond very early and more <i>ifnb1</i> expressing cells are recruited at later time after infection. In contrast, the single <i> ifnb1</i> response to the toll like receptor stimulant LPS, follows a highly synchronous pattern, where in a large number of cells showed an <i> ifnb1</i> response around the same time after treatment. These results suggest that the temporal evolution of single cell <i>ifnb1</i> responses was likely dependent on the type of the inducing stimuli. Furthermore we observed that extracellular signaling plays an important role in introducing cell-to-cell variability in <i>ifnb1</i>gene induction in response to virus infection. Inhibition of extracellular signaling converted the response to virus infection into an early synchronous LPS-like response. Thus extracellular signaling shapes the temporally dispersed pattern of single cell <i> ifnb1</i> response to viral infection. </p><p> The pattern of <i>ifnb1</i> responses to virus infection involves an increase in the amplitude of the response per cell as well as an increase in the number of responding cells over time of infection. These properties may enable cells to fine tune the <i>ifnb1</i> responses gradually. This strategy of mounting an antiviral cytokine response may be useful in calibrating the immune response such that an appropriate antiviral response is generated and cellular toxicity resulting from excessive cytokine expression is usually avoided.</p>

Thesis (Ph.D.)--University of California, San Francisco, 2009. / Source: Dissertation Abstracts International, Volume: 71-02, Section: B, page: . Adviser: Chao Tang. Includes supplementary digital materials.