Phylogenomics and plastome evolution of Lithospermeae (Boraginaceae).

BACKGROUND: Lithospermeae is the largest tribe within Boraginaceae. The tribe has been the focus of multiple phylogenetic studies over the last 15 years, with most focused on one genus or a few genera. In the present study, we newly sequenced 69 species of Lithospermeae and relatives to analyze the phylogenomic relationships among its members as well as the evolution of the plastid genome. RESULTS: The phylogeny of Lithospermeae resolved from the plastid genome and nrDNA cistron is generally congruent with prior studies, but is better resolved and supported. Increasing character sampling across the plastid genome results in gradually more similar trees to that from the entire plastid genome. Overall, plastid genome structure was quite consistent across Lithospermeae. Codon Usage Bias (CUB) analyses demonstrate that across Lithospermeae plastid genomes were rich in AT and poor in GC. Mutation may play a greater role than selection across the plastid genome of Lithospermeae. The present study is the first to highlight the CUB characteristics of Lithospermeae species, which can help elucidate the mechanisms underlying patterns of molecular evolution and improve the expression levels of exogenous genes by codon optimization. CONCLUSIONS: This study provides a comprehensive phylogenomic analysis of Lithospermeae, significantly enhancing our understanding of the phylogenetic relationships and plastid genome evolution within this largest tribe of Boraginaceae. By utilizing an expanded genomic sampling approach, we have achieved increased resolution and support among the evolutionary relationships of the tribe, in line with but improving upon previous studies. The analyses of plastid genome structure revealed consistency across Lithospermeae, with a notable CUB. This study marks the first investigation into the CUB of Lithospermeae species and sets the stage for further research on the molecular evolution of plastid genomes across Boraginaceae.

Phylogenomics, floral evolution, and biogeography of Lithospermum L. (Boraginaceae).

Lithospermum (Boraginaceae), a geographically cosmopolitan medium-sized genus, includes diverse floral morphology, with variation in corolla size and shape and in breeding system. Over the past decade, multiple studies have examined the evolutionary history of Lithospermum, with most utilizing DNA regions from the plastid genome and/or the nuclear ribosomal internal transcribed spacer. These studies have, in general, not resulted in well-resolved and well-supported phylogenies. In the present study, 298 nuclear DNA regions, amplified via target sequence capture, were utilized for phylogenetic reconstruction for Lithospermum and relatives in Boraginaceae, and patterns of floral evolution, species diversification, and biogeography were examined. Based on multiple phylogenetic methods, Lithospermum is resolved as monophyletic, and the New World species of the genus are also monophyletic. While minimal phylogenetic incongruence is resolved within the nuclear genome, incongruence between the nuclear and plastid genomes is recovered. This is likely due to incomplete lineage sorting during early diversification of the genus in the Americas approximately 7.8 million years ago. At least four shifts to longer corollas are identified throughout Lithospermum, and this may be due to selection for hummingbird-pollinated flowers, particularly for species in Mexico and the southwestern United States. In the New World, one clade of species of the genus diversified primarily across the United States and Canada, and another radiated throughout the mountains of Mexico.

Parsing a plethora of pollen: the role of pollen size and shape in the evolution of Boraginaceae.

Pollen, the microgametophyte of seed plants, has an important role in plant reproduction and, therefore, evolution. Pollen is variable in, for example, size, shape, aperture number; these features are particularly diverse in some plant taxa and can be diagnostic. In one family, Boraginaceae, the range of pollen diversity suggests the potential utility of this family as a model for integrative studies of pollen development, evolution and molecular biology. In the present study, a comprehensive survey of the diversity and evolution of pollen from 538 species belonging to 72 genera was made using data from the literature and additional scanning electron microscopy examination. Shifts in diversification rates and the evolution of various quantitative characters were detected, and the results revealed remarkable differences in size, shape and number of apertures. The pollen of one subfamily, Boraginoideae, is larger than that in Cynoglossoideae. The diversity of pollen shapes and aperture numbers in one tribe, Lithospermeae, is greater than that in the other tribes. Ancestral pollen for the family was resolved as small, prolate grains that bear three apertures and are iso-aperturate. Of all the tribes, the greatest number of changes in pollen size and aperture number were observed in Lithospermeae and Boragineae, and the number of apertures was found to be stable throughout all tribes of Cynoglossoideae. In addition, the present study showed that diversification of Boraginaceae cannot be assigned to a single factor, such as pollen size, and the increased rate of diversification for species-rich groups (e.g. Cynoglossum) is not correlated with pollen size or shape evolution. The palynological data and patterns of character evolution presented in the study provide better resolution of the roles of geographical and ecological factors in the diversity and evolution of pollen grains of Boraginaceae, and provide suggestions for future palynological research across the family.

Insights into the individual evolutionary origins of Yersinia virulence factor effector proteins.

Pathogenic Yersinia bacteria, including Y. pseudotubuclosis Y. enterocolitica, and Y. pestis, contain the mosaic plasmid pYV that encodes for, among other things, a number of proteinaceous virulence factors. While the evolutionary histories of many of the biovars and strains of pathogenic Yersinia species are well documented, the origins of many of the individual virulence factors have not been comprehensively examined. Here, the evolutionary origins of the genes coding for a set of Yersinia outer protein (Yop) virulence factors were investigated through phylogenetic reconstruction and subsequence analysis. It was found that many of these genes had only a few sequenced homologs and none of the resolved phylogenies recovered the same relationships as was resolved from chromosomal analyses. Many of the evolutionary relationships differ greatly among genes on the plasmid, and variation is also found across different domains of the same gene, which provides evidence of the mosaic nature of the plasmid as well as multiple genes on the plasmid. This mosaic aspect also relates to patterns of selection, which vary among the studied domains.

How to build distylous flowers: comparative floral development and evolution of distylous species across the angiosperms.

PREMISE: Distyly, a plant breeding system characterized by two floral morphs that have reciprocal positioning of anthers and stigmas, is known from at least 27 angiosperm families, making it an excellent example of convergent evolution. The various manners in which patterns of floral development produce the distinct anther and stigma heights in each morph remain largely unexplored from developmental and evolutionary perspectives. METHODS: In 15 species representing at least 12 origins of distyly, heights and lengths of floral organs in each morph throughout development were examined using light microscopy. Patterns of floral organ development were determined and compared among species. Family-level phylogenies of distylous species and relatives were reconstructed, and patterns of ancestral herkogamy were resolved. RESULTS: Differences in floral development between morphs resulted in 12 patterns leading to the anther and stigma positions characterizing distyly. Distylous species evolved from ancestors with different types of herkogamy, with approach herkogamy and lack of herkogamy resolved most frequently. CONCLUSIONS: Seven of the 12 patterns of floral development are known from only one species, with three other patterns described among pairs of close relatives. The most common pattern of floral development, described from at least seven genera, involves for anther heights, distinct intermorph growth rates and for stigma heights, growth rates that differ between morphs only during later development. This pattern is common among subclass Lamiidae, suggesting canalized development within the taxon. Among distylous species, the same type of ancestral herkogamy can give rise to different patterns of floral development.

A phylogenetic analysis of morphological and molecular characters of Boraginaceae: evolutionary relationships, taxonomy, and patterns of character evolution.

The angiosperm family Boraginaceae includes ca. 1600 species distributed among ca. 110 genera. Some floral features are constant within the family, but many vegetative, floral, pollen, and nutlet traits vary. Utilizing 224 species of Boraginaceae and related taxa, five matrices were constructed with various combinations of morphological characters, three chloroplast DNA regions, and one nuclear ribosomal DNA region. Phylogenetic analyses were conducted for these matrices, and patterns of character evolution were examined. Boraginaceae is resolved as monophyletic, with Wellstedia as its sister. Codon is sister to Boraginaceae + Wellstedia. Although most of the investigated morphological characters have a low consistency index, particular character states are synapomorphies for large clades in each of the tribes of the family. In Boraginaceae, the breeding system heterostyly evolved at least 12 times, which is the largest number of origins resolved in any family; therefore Boraginaceae can serve as a model for the evolution and development of heterostyly. Nutlet ornamentation is most diverse in Cynoglosseae and Trichodesmeae, while pollen and floral features are most variable in Boragineae and Lithospermeae. Phylogenetic relationships and patterns of character evolution identified in the present study set the stage for future work creating an updated taxonomic system of Boraginaceae.

Introduction to the Special Issue of Plants on "Advances in Plant Reproductive Ecology and Conservation Biology".

Plant reproductive ecology explores aspects of the biology and ecology of plants ranging from breeding systems, plant-pollinator interactions, seed germination, floral traits, and much more [...].

Subjective and objective parameters of the adult female voice after cricotracheal resection and dilation.

OBJECTIVES: We compared the voice outcomes after cricotracheal resection (CTR) and airway dilation in adult women. METHODS: We performed long-term comprehensive voice assessments in 23 adult women treated for laryngotracheal stenosis, including acoustic and perceptual measurements of voice, videostroboscopy, the Voice Handicap Index, and an open-ended subjective questionnaire. RESULTS: Voice measures were abnormal in both groups. Objective pitch and loudness measurements were significantly more impaired after CTR than after dilation. Perceptual ratings of voice were worse after CTR than after dilation, particularly with regard to breathiness, pitch, and loudness. The CTR group was more likely to report a voice disorder, reported significantly more voice symptoms, and had higher voice handicap scores. Videostroboscopy was frequently abnormal in both groups, with more evidence of vocal hyperfunction after CTR. Self-ratings of breathing and swallowing were generally high in both groups, but voice satisfaction was rated lower after CTR. CONCLUSIONS: Voice was more significantly negatively impacted by CTR than by dilation. Surprisingly, many individuals in both groups reported improvements--a finding that possibly highlights the impact of laryngotracheal stenosis on airflow and vocal function before surgery. The importance of patient selection and preoperative counseling is emphasized, along with the potential need for voice therapy.

The Conservation Genetics of Iris lacustris (Dwarf Lake Iris), a Great Lakes Endemic.

Iris lacustris, a northern Great Lakes endemic, is a rare species known from 165 occurrences across Lakes Michigan and Huron in the United States and Canada. Due to multiple factors, including habitat loss, lack of seed dispersal, patterns of reproduction, and forest succession, the species is threatened. Early population genetic studies using isozymes and allozymes recovered no to limited genetic variation within the species. To better explore genetic variation across the geographic range of I. lacustris and to identify units for conservation, we used tunable Genotyping-by-Sequencing (tGBS) with 171 individuals across 24 populations from Michigan and Wisconsin, and because the species is polyploid, we filtered the single nucleotide polymorphism (SNP) matrices using polyRAD to recognize diploid and tetraploid loci. Based on multiple population genetic approaches, we resolved three to four population clusters that are geographically structured across the range of the species. The species migrated from west to east across its geographic range, and minimal genetic exchange has occurred among populations. Four units for conservation are recognized, but nine adaptive units were identified, providing evidence for local adaptation across the geographic range of the species. Population genetic analyses with all, diploid, and tetraploid loci recovered similar results, which suggests that methods may be robust to variation in ploidy level.

Comparative floral development in Lithospermum (Boraginaceae) and implications for the evolution and development of heterostyly.

PREMISE OF THE STUDY: The evolution and development of floral developmental patterns were investigated in three heterostylous and three homostylous species of Lithospermum to determine whether species that independently acquired the same floral form follow the same pattern of development or different patterns. METHODS: Using light and scanning electron microscopy, we observed developmental patterns in flowers at different stages of maturity. These patterns were compared within individual species, between heterostylous morphs, and among heterostylous and homostylous species. KEY RESULTS: Although heterostyly has been determined by phylogenetic analysis to have originated independently in each of the heterostylous species, flowers of the long-style morph of each species follow similar patterns of gross development, as do those of the short-style morph. In addition, the flowers of each morph develop in a manner similar to those of their respective homostylous, herkogamous relatives. However, the developmental patterns of the stylar epidermal cells differ among these species and between heterostylous and homostylous species. CONCLUSIONS: Floral developmental patterns in homostylous species provide evidence that modification of specific traits, such as patterns of stylar growth, can lead to the evolution of heterostyly. The developmental changes that affect the positions of the stigmas and anthers in each morph likely involve either temporal or spatial modifications of gene function. The floral developmental patterns described here and the occurrence of multiple types of herkogamy within some species of Lithospermum provide evidence that heterostylous species in the genus have originated via distinct evolutionary developmental pathways.

A phylogenetic analysis of morphological and molecular characters of Lithospermum L. (Boraginaceae) and related taxa: evolutionary relationships and character evolution.

Lithospermum (Boraginaceae) includes ca. 60 species and exhibits a wide range of floral, palynological, and vegetative diversity. Phylogenetic analyses based on 10 chloroplast DNA regions and 22 morphological characters were conducted in order to (i) examine evolutionary relationships within Lithospermum and among related genera of Boraginaceae, and (ii) investigate patterns of morphological evolution. Several morphological features, such as long-funnelform corollas, faucal appendages, reciprocal herkogamy, and evident secondary leaf venation, have evolved multiple times within the genus. In contrast, other morphological features, including the presence of glands and the position and number of pollen pores, are less plastic and tend to characterize larger clades. Some features, including the presence of glands, are interpreted as symplesiomorphic for Lithospermum, while others, such as evident secondary leaf venation, appear to have originated repeatedly. The range of structural diversity that occurs among the species of Lithospermum suggests the potential utility of this genus as a model for integrative studies of evolution, development, and molecular biology.© The Willi Hennig Society 2011.

Extended transcervical video-assisted thymectomy.

This article describes surgery using a transcervical approach with thoracoscopic visualization. The video-assisted extended approach is well suited for patients undergoing thymectomy for myasthenia gravis, thymic cysts, small thymoma, or mediastinal parathyroid adenoma. It incorporates the minimally invasive nature of the transcervical method with the extensive anterior mediastinal dissection, while allowing for complete removal of the thymus and anterior mediastinal fat and avoiding the morbidity of a sternotomy.

Contrast-enhanced MDCT characteristics of parathyroid adenomas.

OBJECTIVE: Minimally invasive directed parathyroidectomy has replaced conventional surgical techniques aimed at exploring all four glands in the bilateral neck. These changes have created the need for better preoperative imaging localization techniques. In this article, we describe the CT imaging characteristics of surgically confirmed adenomas and review anatomy and embryology to aid the radiologist in successfully identifying adenomas using contrast-enhanced CT. CONCLUSION: Knowledge of normal CT appearance, contrast enhancement, and expected location are critical to correct interpretation of parathyroid adenoma at CT.

Morphological Analysis of Size and Shape (MASS): An integrative software program for morphometric analyses of leaves.

PREMISE: Morphometric analysis is a common approach for comparing and categorizing botanical samples; however, completing a suite of analyses using existing tools may require a multi-stage, multi-program process. To facilitate streamlined analysis within a single program, Morphological Analysis of Size and Shape (MASS) for leaves was developed. Its utility is demonstrated using exemplar leaf samples from Acer saccharum, Malus domestica, and Lithospermum. METHODS: Exemplar samples were obtained from across a single tree (Acer saccharum), three trees in the same species (Malus domestica), and online, digitized herbarium specimens (Lithospermum). MASS was used to complete simple geometric measurements of samples, such as length and area, as well as geometric morphological analyses including elliptical Fourier and Procrustes analyses. Principal component analysis (PCA) of data was also completed within the same program. RESULTS: MASS is capable of making desired measurements and analyzing traditional morphometric data as well as landmark and outline data. DISCUSSION: Using MASS, differences were observed among leaves of the three studied taxa, but only in Malus domestica were differences statistically significant or correlated with other morphological features. In the future, MASS could be applied for analysis of other two-dimensional organs and structures. MASS is available for download at https://github.com/gillianlynnryan/MASS.

Do medical students studying in the United Kingdom have an adequate factual knowledge of basic life support?

BACKGROUND: Healthcare professionals have a duty to maintain basic life support (BLS) skills. This study aims to evaluate medical students' factual knowledge of BLS and the training they receive. METHODS: A cross-sectional, closed-response questionnaire was distributed to the first- and fourth-year students studying at institutions in the United Kingdom. The paper questionnaire sought to quantify respondent's previous BLS training, factual knowledge of the BLS algorithm using five multiple choice questions (MCQs), and valuate their desire for further BLS training. Students received 1 point for each correctly identified answer to the 5 MCQ's. RESULTS: A total of 3,732 complete responses were received from 21 medical schools. Eighty percent (n=2,999) of students completed a BLS course as part of their undergraduate medical studies. There was a significant difference (P<0.001) in the percentage of the fourth-year students selecting the correct answer in all the MCQ's compared to the first-year students except in identifying the correct depth of compressions required during CPR (P=0.095). Overall 10.3% (95% CI 9.9% to 10.7%) of respondents correctly identified the answer to 5 MCQ's on BLS 9% of the first-year students (n=194) and 12% of the fourth-year students (n=190). On an institutional level the proportion of students answering all MCQ's correctly ranged from 2% to 54% at different universities. Eighty-one percent of students (n=3,031) wished for more BLS training in their curriculum. CONCLUSION: Factual knowledge of BLS is poor among medical students in the UK. There is a disparity in standards of knowledge across institutions and respondents indicating that they would like more training.

Integrity of developing spinal motor columns is regulated by neural crest derivatives at motor exit points.

Spinal motor neurons must extend their axons into the periphery through motor exit points (MEPs), but their cell bodies remain within spinal motor columns. It is not known how this partitioning is established in development. We show here that motor neuron somata are confined to the CNS by interactions with a neural crest subpopulation, boundary cap (BC) cells that prefigure the sites of spinal MEPs. Elimination of BC cells by surgical or targeted genetic ablation does not perturb motor axon outgrowth but results in motor neuron somata migrating out of the spinal cord by translocating along their axons. Heterologous neural crest grafts in crest-ablated embryos stop motor neuron emigration. Thus, before the formation of a mature transitional zone at the MEP, BC cells maintain a cell-tight boundary that allows motor axons to cross but blocks neuron migration.

Efficacy of nodal dissection for treatment of persistent/recurrent papillary thyroid cancer.

CONTEXT: Although commonly performed, data are lacking regarding efficacy and safety of lymph node dissection (LND) for recurrent/persistent papillary thyroid cancer (PTC). OBJECTIVE: Evaluate the efficacy and morbidity of LND in recurrent/persistent PTC. DESIGN: Retrospective review of central or lateral LND performed for persistent/recurrent PTC between January 2004 and March 2006. SETTING: Multidisciplinary thyroid cancer clinic with a single surgeon at an academic medical center. PARTICIPANTS: Seventy-five patients who underwent 79 LND for persistent/residual PTC. Safety analysis included all 79 resections. Exclusion criteria for the efficacy analysis were factors prohibiting evaluation of thyroglobulin (Tg) response. Forty-one resections were included in the efficacy analysis. INTERVENTION: Selective LND per standard of care. MAIN OUTCOME MEASURE: Primary outcome was the Tg response to LND. Secondary outcomes were surgical complications. RESULTS: Thirty-nine of the 41 evaluable resections also had Tg data allowing classification of Tg response. Of 39 classifiable resections, 16 (41%) resulted in undetectable postoperative stimulated Tg levels. An additional 12 resections resulted in significant (> or =50%) reductions in suppressed or stimulated Tg levels for an overall improvement rate of 72%. Of all 79 resections, 25 (32%) resulted in minor and 7 (9%) resulted in major complications. CONCLUSIONS: LND for persistent/recurrent PTC is a relatively safe procedure in experienced hands. It can lead to an undetectable Tg in 41% of cases and produce a major Tg reduction in an additional 31%. Its efficacy in short-term follow-up is comparable with that reported for I-131, and it should be considered in the management of persistent/recurrent PTC.

Neural crest boundary cap cells constitute a source of neuronal and glial cells of the PNS.

Boundary cap (BC) cells are neural crest derivatives that form clusters at the surface of the neural tube, at entry and exit points of peripheral nerve roots. Using various knock-in alleles of the mouse gene Egr2 (also known as Krox20), the expression of which, in trunk regions, is initially restricted to BC cells, we were able to trace BC cell progeny during development and analyze their fate. Trunk BC-derived cells migrated along peripheral axons and colonized spinal nerve roots and dorsal root ganglia (DRG). All Schwann cell precursors occupying the dorsal roots were derived from BC cells. In the DRG, BC-derived cells were the progenitors of both neurons, mainly nociceptive afferents, and satellite cells. These data indicate that BC cells constitute a source of peripheral nervous system (PNS) components that, after the major neural crest ventrolateral migratory stream, feeds a secondary wave of migration to the PNS.

The homeodomain transcription factor drg11 is expressed in primary sensory neurons and their putative CNS targets during embryonic development of the zebrafish.

The drg11 gene is a member of the vertebrate aristaless-related gene family and encodes a paired homeodomain transcription factor. Its expression is largely restricted to PNS neurons subserving somatosensory functions and their CNS targets in rodents. The phenotype of drg11 null mice suggests that it is crucial for the proper development in the embryo of nociceptive circuits. To allow functional studies in the zebrafish, a simple vertebrate model organism, we have cloned the homologous gene and studied its expression throughout embryonic development. drg11 transcripts are first detected at neurula stage in the developing trigeminal ganglion, where it persists throughout development. This is followed by transient expression in spinal cord mechanosensory Rohon-Beard neurons shortly before axogenesis. Expression is later evident in neuronal populations of the dorsal spinal cord and in the dorsal root ganglia. In the developing brain, drg11 expression is mainly restricted to sensory neuron populations of the midbrain and hindbrain, in cranial sensory ganglia and in the habenula. Unlike rodents, however, trochlear motor neurons transiently express drg11. Our results suggest that drg11 expression in the developing zebrafish is, in common with its mammalian homologous gene, predominantly localised to neurons in sensory processing areas of the embryonic nervous system and is both spatially and temporally regulated.