Dynamic Genomes of Eukaryotes and the Maintenance of Genomic Integrity

Many biologists assume that eukaryotic genomes are transmitted stably between generations with only minor variations. Yet, this presumed constancy is at odds with data indicating that eukaryotic genomes are dynamic, varying extensively in content among many different lineages. Thus, rather than being constant, genomes vary considerably within individuals during their lifetimes

Genome Dynamics are Influenced by Food Source in \u3ci\u3eAllogromia laticollaris\u3c/i\u3e Strain CSH (Foraminifera)

Across the eukaryotic tree of life, genomes vary within populations and within individuals during their life cycle. Understanding intraspecific genome variation in diverse eukaryotes is key to elucidating the factors that underlie this variation. Here, we characterize genome dynamics during the life cycle of Allogromia laticollaris strain CSH, a member of the Foraminifera, using fluorescence microscopy and reveal extensive variation in nuclear size and DNA content. Both nuclear size and DNA content are tightly correlated across a 700-fold range in cell volume. In contrast to models in yeast where nuclear size is determined solely by cell size, the relationship in A. laticollaris CSH differs according to both life cycle stage and food source. Feeding A. laticollaris CSH a diet that includes algae results in a 2-fold increase in DNA content in reproductive cells compared with a diet of bacteria alone. This difference in DNA content likely corresponds to increased fecundity, as reproduction occurs through segregation of the polyploid nucleus into numerous daughter nuclei. Environmentally mediated variation in DNA content may be a widespread phenomenon, as it has been previously reported in the plant flax and the flagellate Euglena. We hypothesize that DNA content is influenced by food in other single-celled eukaryotes with ploidy cycles and that this genome flexibility may enable these eukaryotes to maximize fitness across changing environmental conditions

Development of a Consensus Statement for the Definition, Diagnosis, and Treatment of Acute Exacerbations of Idiopathic Pulmonary Fibrosis Using the Delphi Technique.

© 2015, The Author(s).Introduction: There is a lack of agreed and established guidelines for the treatment of acute exacerbations of idiopathic pulmonary fibrosis (AE-IPF). This reflects, in part, the limited evidence-base underpinning the management of AE-IPF. In the absence of high-quality evidence, the aim of this research was to develop a clinician-led consensus statement for the definition, diagnosis and treatment of AE-IPF. Methods: A literature review was conducted to obtain published material on the definition and treatment of AE-IPF. The results of this review were circulated to an online panel of clinicians for review. Statements were then shared with ten expert respiratory clinicians who regularly treat patients with IPF. A Delphi technique was then used to develop a consensus statement for the definition, diagnosis and treatment of AE-IPF. During the first round of review, clinicians rated the clarity of each statement, the extent to which the statement should be included and provided comments. In two subsequent rounds of review, clinicians were provided with the group median inclusion rating for each statement, and any revised wording of statements to aid clarity. Clinicians were asked to repeat the clarity and inclusion ratings for the revised statements. Results: The literature review, online panel discussion, and face-to-face meeting generated 65 statements covering the definition, diagnosis, and management of AE-IPF. Following three rounds of blind review, 90% of clinicians agreed 39 final statements. These final statements included a definition of AE-IPF, approach to diagnosis, and treatment options, specifically: supportive measures, use of anti-microbials, immunosuppressants, anti-coagulants, anti-fibrotic therapy, escalation, transplant management, and long-term management including discharge planning. Conclusion: This clinician-led consensus statement establishes the ‘best practice’ for the management and treatment of AE-IPF based on current knowledge, evidence, and available treatments. Funding: Boehringer Ingelheim Ltd., Bracknell, West Berkshire, UK

The Dynamic Nature of Eukaryotic Genomes

Analyses of diverse eukaryotes reveal that genomes are dynamic, sometimes dramatically so. In numerous lineages across the eukaryotic tree of life, DNA content varies within individuals throughout life cycles and among individuals within species. Discovery of examples of genome dynamism is accelerating as genome sequences are completed from diverse eukaryotes. Though much is known about genomes in animals, fungi, and plants, these lineages represent only 3 of the 60-200 lineages of eukaryotes. Here, we discuss diverse genomic strategies in exemplar eukaryotic lineages, including numerous microbial eukaryotes, to reveal dramatic variation that challenges established views of genome evolution. For example, in the life cycle of some members of the radiolaria, ploidy increases from haploid (N) to approximately 1,000N, whereas intrapopulation variability of the enteric parasite Entamoeba ranges from 4N to 40N. Variation has also been found within our own species, with substantial differences in both gene content and chromosome lengths between individuals. Data on the dynamic nature of genomes shift the perception of the genome from being fixed and characteristic of a species (typological) to plastic due to variation within and between species

The Origin of Solar Activity in the Tachocline

Solar active regions, produced by the emergence of tubes of strong magnetic field in the photosphere, are restricted to within 35 degrees of the solar equator. The nature of the dynamo processes that create and renew these fields, and are therefore responsible for solar magnetic phenomena, are not well understood. We analyze the magneto-rotational stability of the solar tachocline for general field geometry. This thin region of strong radial and latitudinal differential rotation, between the radiative and convective zones, is unstable at latitudes above 37 degrees, yet is stable closer to the equator. We propose that small-scale magneto-rotational turbulence prevents coherent magnetic dynamo action in the tachocline except in the vicinity of the equator, thus explaining the latitudinal restriction of active regions. Tying the magnetic dynamo to the tachocline elucidates the physical conditions and processes relevant to solar magnetism.Comment: 10 pages, 1 figure, accepted for publication in ApJ

Molecular Data are Transforming Hypotheses on the Origin and Diversification of Eukaryotes

The explosion of molecular data has transformed hypotheses on both the origin of eukaryotes and the structure of the eukaryotic tree of life. Early ideas about the evolution of eukaryotes arose through analyses of morphology by light microscopy and, later, electron microscopy. Though such studies have proven powerful at resolving more recent events, theories on origins and diversification of eukaryotic life have been substantially revised in light of analyses of molecular data including gene and, increasingly, whole-genome sequences. By combining these approaches, progress has been made in elucidating the origin and diversification of eukaryotes. Yet many aspects of the evolution of eukaryotic life remain to be illuminated

What do we really know about the appropriateness of radiation emitting imaging for low back pain in primary and emergency care? A systematic review and meta-analysis of medical record reviews

Background Since 2000, guidelines have been consistent in recommending when diagnostic imaging for low back pain should be obtained to ensure patient safety and reduce unnecessary tests. This systematic review and meta-analysis was conducted to determine the pooled proportion of CT and x-ray imaging of the lumbar spine that were considered appropriate in primary and emergency care. Methods Pubmed, CINAHL, The Cochrane Database of Systematic Reviews and Embase were searched for synonyms of “low back pain”, “guidelines”, and “adherence” that were published after 2000. Titles, abstracts, and full texts were reviewed for inclusion with forward and backward tracking on included studies. Included studies had data extracted and synthesized. Risk of bias was performed on all studies, and GRADE was performed on included studies that provided data on CT and x-ray separately. A random effect, single proportion meta-analysis model was used. Results Six studies were included in the descriptive synthesis, and 5 studies included in the meta-analysis. Five of the 6 studies assessed appropriateness of x-rays; two of the six studies assessed appropriateness of CTs. The pooled estimate for appropriateness of x-rays was 43% (95% CI: 30%, 56%) and the pooled estimate for appropriateness of CTs was 54% (95% CI: 51%, 58%). Studies did not report adequate information to fulfill the RECORD checklist (reporting guidelines for research using observational data). Risk of bias was high in 4 studies, moderate in one, and low in one. GRADE for x-ray appropriateness was low-quality and for CT appropriateness was very-low-quality. Conclusion While this study determined a pooled proportion of appropriateness for both x-ray and CT imaging for low back pain, there is limited confidence in these numbers due to the downgrading of the evidence using GRADE. Further research on this topic is needed to inform our understanding of x-ray and CT appropriateness in order to improve healthcare systems and decrease patient harms

Turning the Crown Upside Down: Gene Tree Parsimony Roots the Eukaryotic Tree of Life

The first analyses of gene sequence data indicated that the eukaryotic tree of life consisted of a long stem of microbial groups topped by a crown-containing plants, animals, and fungi and their microbial relatives. Although more recent multigene concatenated analyses have refined the relationships among the many branches of eukaryotes, the root of the eukaryotic tree of life has remained elusive. Inferring the root of extant eukaryotes is challenging because of the age of the group (∼1.7-2.1 billion years old), tremendous heterogeneity in rates of evolution among lineages, and lack of obvious outgroups for many genes. Here, we reconstruct a rooted phylogeny of extant eukaryotes based on minimizing the number of duplications and losses among a collection of gene trees. This approach does not require outgroup sequences or assumptions of orthology among sequences. We also explore the impact of taxon and gene sampling and assess support for alternative hypotheses for the root. Using 20 gene trees from 84 diverse eukaryotic lineages, this approach recovers robust eukaryotic clades and reveals evidence for a eukaryotic root that lies between the Opisthokonta (animals, fungi and their microbial relatives) and all remaining eukaryotes