Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus

<p>Abstract</p> <p>Background</p> <p>The number of completely sequenced plastid genomes available is growing rapidly. This array of sequences presents new opportunities to perform comparative analyses. In comparative studies, it is often useful to compare across wide phylogenetic spans and, within angiosperms, to include representatives from basally diverging lineages such as the genomes reported here: <it>Nuphar advena </it>(from a basal-most lineage) and <it>Ranunculus macranthus </it>(a basal eudicot). We report these two new plastid genome sequences and make comparisons (within angiosperms, seed plants, or all photosynthetic lineages) to evaluate features such as the status of <it>ycf15 </it>and <it>ycf68 </it>as protein coding genes, the distribution of simple sequence repeats (SSRs) and longer dispersed repeats (SDR), and patterns of nucleotide composition.</p> <p>Results</p> <p>The <it>Nuphar </it>[GenBank:<ext-link ext-link-type="gen" ext-link-id="NC_008788">NC_008788</ext-link>] and <it>Ranunculus </it>[GenBank:<ext-link ext-link-type="gen" ext-link-id="NC_008796">NC_008796</ext-link>] plastid genomes share characteristics of gene content and organization with many other chloroplast genomes. Like other plastid genomes, these genomes are A+T-rich, except for rRNA and tRNA genes. Detailed comparisons of <it>Nuphar </it>with <it>Nymphaea</it>, another Nymphaeaceae, show that more than two-thirds of these genomes exhibit at least 95% sequence identity and that most SSRs are shared. In broader comparisons, SSRs vary among genomes in terms of abundance and length and most contain repeat motifs based on A and T nucleotides.</p> <p>Conclusion</p> <p>SSR and SDR abundance varies by genome and, for SSRs, is proportional to genome size. Long SDRs are rare in the genomes assessed. SSRs occur less frequently than predicted and, although the majority of the repeat motifs do include A and T nucleotides, the A+T bias in SSRs is less than that predicted from the underlying genomic nucleotide composition. In codon usage third positions show an A+T bias, however variation in codon usage does not correlate with differences in A+T-richness. Thus, although plastome nucleotide composition shows "A+T richness", an A+T bias is not apparent upon more in-depth analysis, at least in these aspects. The pattern of evolution in the sequences identified as <it>ycf15 </it>and <it>ycf68 </it>is not consistent with them being protein-coding genes. In fact, these regions show no evidence of sequence conservation beyond what is normal for non-coding regions of the IR.</p

Pulmonary Effects of Indoor- and Outdoor-Generated Particles in Children with Asthma

Most particulate matter (PM) health effects studies use outdoor (ambient) PM as a surrogate for personal exposure. However, people spend most of their time indoors exposed to a combination of indoor-generated particles and ambient particles that have infiltrated. Thus, it is important to investigate the differential health effects of indoor- and ambient-generated particles. We combined our recently adapted recursive model and a predictive model for estimating infiltration efficiency to separate personal exposure (E) to PM(2.5) (PM with aerodynamic diameter ≤2.5 μm) into its indoor-generated (E(ig)) and ambient-generated (E(ag)) components for 19 children with asthma. We then compared E(ig) and E(ag) to changes in exhaled nitric oxide (eNO), a marker of airway inflammation. Based on the recursive model with a sample size of eight children, E(ag) was marginally associated with increases in eNO [5.6 ppb per 10-μg/m(3) increase in PM(2.5); 95% confidence interval (CI), −0.6 to 11.9; p = 0.08]. E(ig) was not associated with eNO (−0.19 ppb change per 10μg/m(3)). Our predictive model allowed us to estimate E(ag) and E(ig) for all 19 children. For those combined estimates, only E(ag) was significantly associated with an increase in eNO (E(ag): 5.0 ppb per 10-μg/m(3) increase in PM(2.5;) 95% CI, 0.3 to 9.7; p = 0.04; E(ig): 3.3 ppb per 10-μg/m(3) increase in PM(2.5); 95% CI, −1.1 to 7.7; p = 0.15). Effects were seen only in children who were not using corticosteroid therapy. We conclude that the ambient-generated component of PM(2.5) exposure is consistently associated with increases in eNO and the indoor-generated component is less strongly associated with eNO

Integrating evolutionary theory and social-ecological systems research to address the sustainability challenges of the Anthropocene

The rapid, human-induced changes in the Earth system during the Anthropocene present humanity with critical sustainability challenges. Social-ecological systems (SES) research provides multiple approaches for understanding the complex interactions between humans, social systems, and environments and how we might direct them towards healthier and more resilient futures. However, general theories of SES change have yet to be fully developed. Formal evolutionary theory has been applied as a dynamic theory of change of complex phenomena in biology and the social sciences, but rarely in SES research. In this paper, we explore the connections between both fields, hoping to foster collaboration. After sketching out the distinct intellectual traditions of SES research and evolutionary theory, we map some of their terminological and theoretical connections. We then provide examples of how evolutionary theory might be incorporated into SES research through the use of systems mapping to identify evolutionary processes in SES, the application of concepts from evolutionary developmental biology to understand the connections between systems changes and evolutionary changes, and how evolutionary thinking may help design interventions for beneficial change. Integrating evolutionary theory and SES research can lead to a better understanding of SES changes and positive interventions for a more sustainable Anthropocene. This article is part of the theme issue 'Evolution and sustainability: gathering the strands for an Anthropocene synthesis'

Associations between Health Effects and Particulate Matter and Black Carbon in Subjects with Respiratory Disease

We measured fractional exhaled nitric oxide (FE(NO)), spirometry, blood pressure, oxygen saturation of the blood (SaO(2)), and pulse rate in 16 older subjects with asthma or chronic obstructive pulmonary disease (COPD) in Seattle, Washington. Data were collected daily for 12 days. We simultaneously collected PM(10) and PM(2.5) (particulate matter ≤10 μm or ≤2.5 μm, respectively) filter samples at a central outdoor site, as well as outside and inside the subjects’ homes. Personal PM(10) filter samples were also collected. All filters were analyzed for mass and light absorbance. We analyzed within-subject associations between health outcomes and air pollution metrics using a linear mixed-effects model with random intercept, controlling for age, ambient relative humidity, and ambient temperature. For the 7 subjects with asthma, a 10 μg/m(3) increase in 24-hr average outdoor PM(10) and PM(2.5) was associated with a 5.9 [95% confidence interval (CI), 2.9–8.9] and 4.2 ppb (95% CI, 1.3–7.1) increase in FE(NO), respectively. A 1 μg/m(3) increase in outdoor, indoor, and personal black carbon (BC) was associated with increases in FE(NO) of 2.3 ppb (95% CI, 1.1–3.6), 4.0 ppb (95% CI, 2.0–5.9), and 1.2 ppb (95% CI, 0.2–2.2), respectively. No significant association was found between PM or BC measures and changes in spirometry, blood pressure, pulse rate, or SaO(2) in these subjects. Results from this study indicate that FE(NO) may be a more sensitive marker of PM exposure than traditional health outcomes and that particle-associated BC is useful for examining associations between primary combustion constituents of PM and health outcomes

Methods for Obtaining and Analyzing Whole Chloroplast Genome Sequences

During the past decade there has been a rapid increase in our understanding of plastid genome organization and evolution due to the availability of many new completely sequenced genomes. Currently there are 43 complete genomes published and ongoing projects are likely to increase this sampling to nearly 200 genomes during the next five years. Several groups of researchers including ours have been developing new techniques for gathering and analyzing entire plastid genome sequences and details of these developments are summarized in this chapter. The most important recent developments that enhance our ability to generate whole chloroplast genome sequences involve the generation of pure fractions of chloroplast genomes by whole genome amplification using rolling circular amplification, cloning genomes into Fosmid or BAC vectors, and the development of an organellar annotation program (DOGMA). In addition to providing details of these methods, we provide an overview of methods for analyzing complete plastid genome sequences for repeats and gene content, as well as approaches for using gene order and sequence data for phylogeny reconstruction. This explosive increase in the number of sequenced plastid genomes and improved computational tools will provide many insights into the evolution of these genomes and much new data for assessing relationships at deep nodes in plants and other photosynthetic organisms

Multiplicative interaction of functional inflammasome genetic variants in determining the risk of gout

Introduction: The acute gout flare results from a localised self-limiting innate immune response to monosodium urate (MSU) crystals deposited in joints in hyperuricaemic individuals. Activation of the caspase recruitment domain-containing protein 8 (CARD8) NOD-like receptor pyrin-containing 3 (NLRP3) inflammasome by MSU crystals and production of mature interleukin-1 beta (IL-1 beta) is central to acute gouty arthritis. However very little is known about genetic control of the innate immune response involved in acute gouty arthritis. Therefore our aim was to test functional single nucleotide polymorphism (SNP) variants in the toll-like receptor (TLR)-inflammasome-IL-1 beta axis for association with gout. Methods: 1,494 gout cases of European and 863 gout cases of New Zealand (NZ) Polynesian (Maori and Pacific Island) ancestry were included. Gout was diagnosed by the 1977 ARA gout classification criteria. There were 1,030 Polynesian controls and 10,942 European controls including from the publicly-available Atherosclerosis Risk in Communities (ARIC) and Framingham Heart (FHS) studies. The ten SNPs were either genotyped by Sequenom MassArray or by Affymetrix SNP array or imputed in the ARIC and FHS datasets. Allelic association was done by logistic regression adjusting by age and sex with European and Polynesian data combined by meta-analysis. Sample sets were pooled for multiplicative interaction analysis, which was also adjusted by sample set. Results: Eleven SNPs were tested in the TLR2, CD14, IL1B, CARD8, NLRP3, MYD88, P2RX7, DAPK1 and TNXIP genes. Nominally significant (P <0.05) associations with gout were detected at CARD8 rs2043211 (OR = 1.12, P = 0.007), IL1B rs1143623 (OR = 1.10, P = 0.020) and CD14 rs2569190 (OR = 1.08; P = 0.036). There was significant multiplicative interaction between CARD8 and IL1B (P = 0.005), with the IL1B risk genotype amplifying the risk effect of CARD8. Conclusion: There is evidence for association of gout with functional variants in CARD8, IL1B and CD14. The gout-associated allele of IL1B increases expression of IL-1 beta-the multiplicative interaction with CARD8 would be consistent with a synergy of greater inflammasome activity (resulting from reduced CARD8) combined with higher levels of pre-IL-1 beta expression leading to increased production of mature IL-1 beta in gout

Analysis of 81 Genes From 64 Plastid Genomes Resolves Relationships in Angiosperms and Identifies Genome-Scale Evolutionary Patterns

Angiosperms are the largest and most successful clade of land plants with \u3e250,000 species distributed in nearly every terrestrial habitat. Many phylogenetic studies have been based on DNA sequences of one to several genes, but, despite decades of intensive efforts, relationships among early diverging lineages and several of the major clades remain either incompletely resolved or weakly supported. We performed phylogenetic analyses of 81 plastid genes in 64 sequenced genomes, including 13 new genomes, to estimate relationships among the major angiosperm clades, and the resulting trees are used to examine the evolution of gene and intron content. Phylogenetic trees from multiple methods, including model-based approaches, provide strong support for the position of Amborella as the earliest diverging lineage of flowering plants, followed by Nymphaeales and Austrobaileyales. The plastid genome trees also provide strong support for a sister relationship between eudicots and monocots, and this group is sister to a clade that includes Chloranthales and magnoliids. Resolution of relationships among the major clades of angiosperms provides the necessary framework for addressing numerous evolutionary questions regarding the rapid diversification of angiosperms. Gene and intron content are highly conserved among the early diverging angiosperms and basal eudicots, but 62 independent gene and intron losses are limited to the more derived monocot and eudicot clades. Moreover, a lineage-specific correlation was detected between rates of nucleotide substitutions, indels, and genomic rearrangements

The stem cell organisation, and the proliferative and gene expression profile of Barrett's epithelium, replicates pyloric-type gastric glands

Objective: Barrett's oesophagus shows appearances described as ‘intestinal metaplasia’, in structures called ‘crypts’ but do not typically display crypt architecture. Here, we investigate their relationship to gastric glands. Methods: Cell proliferation and migration within Barrett's glands was assessed by Ki67 and iododeoxyuridine (IdU) labelling. Expression of mucin core proteins (MUC), trefoil family factor (TFF) peptides and LGR5 mRNA was determined by immunohistochemistry or by in situ hybridisation, and clonality was elucidated using mitochondrial DNA (mtDNA) mutations combined with mucin histochemistry. Results: Proliferation predominantly occurs in the middle of Barrett's glands, diminishing towards the surface and the base: IdU dynamics demonstrate bidirectional migration, similar to gastric glands. Distribution of MUC5AC, TFF1, MUC6 and TFF2 in Barrett's mirrors pyloric glands and is preserved in Barrett's dysplasia. MUC2-positive goblet cells are localised above the neck in Barrett's glands, and TFF3 is concentrated in the same region. LGR5 mRNA is detected in the middle of Barrett's glands suggesting a stem cell niche in this locale, similar to that in the gastric pylorus, and distinct from gastric intestinal metaplasia. Gastric and intestinal cell lineages within Barrett's glands are clonal, indicating derivation from a single stem cell. Conclusions: Barrett's shows the proliferative and stem cell architecture, and pattern of gene expression of pyloric gastric glands, maintained by stem cells showing gastric and intestinal differentiation: neutral drift may suggest that intestinal differentiation advances with time, a concept critical for the understanding of the origin and development of Barrett's oesophagus

Are JWST/NIRCam Color Gradients in the Lensed z = 2.3 Dusty Star-forming Galaxy El Anzuelo Due to Central Dust Attenuation or Inside-out Galaxy Growth?

Gradients in the mass-to-light ratio of distant galaxies impede our ability to characterize their size and compactness. The long-wavelength filters of JWST?s NIRCam offer a significant step forward. For galaxies at Cosmic Noon (z ? 2), this regime corresponds to the rest-frame near-infrared, which is less biased toward young stars and captures emission from the bulk of a galaxy?s stellar population. We present an initial analysis of an extraordinary lensed dusty star-forming galaxy at z = 2.3 behind the El Gordo cluster (z = 0.87), named El Anzuelo (?The Fishhook?) after its partial Einstein-ring morphology. The far-UV to near-IR spectral energy distribution suggests an intrinsic star formation rate of 81 yr 2 7 M 1 - ?+ - and dust attenuation AV ? 1.6, in line with other DSFGs on the star-forming main sequence. We develop a parametric lens model to reconstruct the source plane structure of dust imaged by the Atacama Large Millimeter/submillimeter Array, far-UV to optical light from Hubble, and near-IR imaging with 8 filters of JWST/NIRCam, as part of the Prime Extragalactic Areas for Reionization and Lensing Science program. The source-plane half-light radius is remarkably consistent from ?1 to 4.5 ?m, despite a clear color gradient where the inferred galaxy center is redder than the outskirts. We interpret this to be the result of both a radially decreasing gradient in attenuation and substantial spatial offsets between UV- and IR-emitting components. A spatial decomposition of the SED reveals modestly suppressed star formation in the inner kiloparsec, which suggests that we are witnessing the early stages of inside-out quenching