Non-excitable fluorescent protein orthologs found in ctenophores

Background: Fluorescent proteins are optically active proteins found across many clades in metazoans. A fluorescent protein was recently identified in a ctenophore, but this has been suggested to derive from a cnidarian, raising again the question of origins of this group of proteins. Results: Through analysis of transcriptome data from 30 ctenophores, we identified a member of an orthologous group of proteins similar to fluorescent proteins in each of them, as well as in the genome of Mnemiopsis leidyi. These orthologs lack canonical residues involved in chromophore formation, suggesting another function. Conclusions: The phylogenetic position of the ctenophore protein family among fluorescent proteins suggests that this gene was present in the common ancestor of all ctenophores and that the fluorescent protein previously found in a ctenophore actually derives from a siphonophore

A comparison across non-model animals suggests an optimal sequencing depth for de novo transcriptome assembly

Background: The lack of genomic resources can present challenges for studies of non-model organisms. Transcriptome sequencing offers an attractive method to gather information about genes and gene expression without the need for a reference genome. However, it is unclear what sequencing depth is adequate to assemble the transcriptome de novo for these purposes. Results: We assembled transcriptomes of animals from six different phyla (Annelids, Arthropods, Chordates, Cnidarians, Ctenophores, and Molluscs) at regular increments of reads using Velvet/Oases and Trinity to determine how read count affects the assembly. This included an assembly of mouse heart reads because we could compare those against the reference genome that is available. We found qualitative differences in the assemblies of whole-animals versus tissues. With increasing reads, whole-animal assemblies show rapid increase of transcripts and discovery of conserved genes, while single-tissue assemblies show a slower discovery of conserved genes though the assembled transcripts were often longer. A deeper examination of the mouse assemblies shows that with more reads, assembly errors become more frequent but such errors can be mitigated with more stringent assembly parameters. Conclusions: These assembly trends suggest that representative assemblies are generated with as few as 20 million reads for tissue samples and 30 million reads for whole-animals for RNA-level coverage. These depths provide a good balance between coverage and noise. Beyond 60 million reads, the discovery of new genes is low and sequencing errors of highly-expressed genes are likely to accumulate. Finally, siphonophores (polymorphic Cnidarians) are an exception and possibly require alternate assembly strategies

Design of synthetic bacterial communities for predictable plant phenotypes

Specific members of complex microbiota can influence host phenotypes, depending on both the abiotic environment and the presence of other microorganisms. Therefore, it is challenging to define bacterial combinations that have predictable host phenotypic outputs. We demonstrate that plant-bacterium binary-association assays inform the design of small synthetic communities with predictable phenotypes in the host. Specifically, we constructed synthetic communities that modified phosphate accumulation in the shoot and induced phosphate starvation-responsive genes in a predictable fashion. We found that bacterial colonization of the plant is not a predictor of the plant phenotypes we analyzed. Finally, we demonstrated that characterizing a subset of all possible bacterial synthetic communities is sufficient to predict the outcome of untested bacterial consortia. Our results demonstrate that it is possible to infer causal relationships between microbiota membership and host phenotypes and to use these inferences to rationally design novel communitie

Changes in reflectin protein phosphorylation are associated with dynamic iridescence in squid

Author Posting. © The Author(s), 2009. This is the author's version of the work. It is posted here by permission of The Royal Society for personal use, not for redistribution. The definitive version was published in Journal of The Royal Society Interface 6 (2010): 549-560, doi:10.1098/rsif.2009.0299.Many cephalopods exhibit remarkable dermal iridescence, a component of their complex, dynamic camouflage and communication. In the species Euprymna scolopes, the light-organ iridescence is static and is due to reflectin protein-based platelets assembled into lamellar thin-film reflectors called iridosomes, contained within iridescent cells called iridocytes. Squid in the family Loliginidae appear to be unique in that the dermis possesses a dynamic iridescent component, with reflective, colored structures that are assembled and disassembled under the control of the muscarinic cholinergic system and the associated neurotransmitter acetylcholine (Mathger et al. 2004). Here we present the sequences and characterization of three new members of the reflectin family associated with the dynamically changeable iridescence in Loligo and not found in static Euprymna iridophores. In addition, we show that application of genistein, a protein tyrosine kinase inhibitor, suppresses acetylcholine- and calcium-induced iridescence in Loligo. We further demonstrate that two of these novel reflectins are extensively phosphorylated in concert with the activation of iridescence by exogenous acetylcholine. This phosphorylation and the correlated iridescence can be blocked with genistein. Our results suggest that tyrosine phosphorylation of reflectin proteins is involved in the regulation of dynamic iridescence in Loligo.We gratefully acknowledge support from Anteon contract F33615-03-D-5408 to the Marine Biological Laboratory, Woods Hole, MA and grant # W911NF-06-1-0285 from the Army Research Office to D.E.M

The effects of theaflavin-enriched black tea extract on muscle soreness, oxidative stress, inflammation, and endocrine responses to acute anaerobic interval training: a randomized, double-blind, crossover study

<p>Abstract</p> <p>Background</p> <p>Muscle soreness and decreased performance often follow a bout of high-intensity exercise. By reducing these effects, an athlete can train more frequently and increase long-term performance. The purpose of this study is to examine whether a high-potency, black tea extract (BTE) alters the delayed onset muscle soreness (DOMS), oxidative stress, inflammation, and cortisol (CORT) responses to high-intensity anaerobic exercise.</p> <p>Methods</p> <p>College-age males (N = 18) with 1+ yrs of weight training experience completed a double-blind, placebo-controlled, crossover study. Subjects consumed the BTE (1,760 mg BTE·d^-1) or placebo (PLA) for 9 days. Each subject completed two testing sessions (T1 & T2), which occurred on day 7 of the intervention. T1 & T2 consisted of a 30 s Wingate Test plus eight 10 s intervals. Blood samples were obtained before, 0, 30 & 60 min following the interval sessions and were used to analyze the total to oxidized glutathione ratio (GSH:GSSG), 8-isoprostane (8-iso), CORT, and interleukin 6 (IL-6) secretion. DOMS was recorded at 24 & 48 h post-test using a visual analog scale while BTE or PLA continued to be administered. Significance was set at <it>P < 0.05</it>.</p> <p>Results</p> <p>Compared to PLA, BTE produced significantly higher average peak power (<it>P = 0.013</it>) and higher average mean power (<it>P = 0.067</it>) across nine WAnT intervals. BTE produced significantly lower DOMS compared to PLA at 24 h post test (<it>P < 0.001</it>) and 48 h post test (<it>P < 0.001</it>). Compared to PLA, BTE had a slightly higher GSH:GSSG ratio at baseline which became significantly higher at 30 and 60 min post test (<it>P < 0.002</it>). AUC analysis revealed BTE to elicit significantly lower GSSG secretion (<it>P = 0.009</it>), significantly higher GSH:GSSG ratio (<it>P = 0.001</it>), and lower CORT secretion (<it>P = 0.078</it>) than PLA. AUC analysis did not reveal a significant difference in total IL-6 response (<it>P = 0.145</it>) between conditions.</p> <p>Conclusions</p> <p>Consumption of theaflavin-enriched black tea extract led to improved recovery and a reduction in oxidative stress and DOMS responses to acute anaerobic intervals. An improved rate of recovery can benefit all individuals engaging in high intensity, anaerobic exercise as it facilitates increased frequency of exercise.</p

Occurrence of Isopenicillin-N-Synthase Homologs in Bioluminescent Ctenophores and Implications for Coelenterazine Biosynthesis

<div><p>The biosynthesis of the luciferin coelenterazine has remained a mystery for decades. While not all organisms that use coelenterazine appear to make it themselves, it is thought that ctenophores are a likely producer. Here we analyze the transcriptome data of 24 species of ctenophores, two of which have published genomes. The natural precursors of coelenterazine have been shown to be the amino acids L-tyrosine and L-phenylalanine, with the most likely biosynthetic pathway involving cyclization and further modification of the tripeptide Phe-Tyr-Tyr (“FYY”). Therefore, we searched the ctenophore transcriptome data for genes with the short peptide “FYY” as part of their coding sequence. We recovered a group of candidate genes for coelenterazine biosynthesis in the luminous species which encode a set of highly conserved non-heme iron oxidases similar to isopenicillin-N-synthase. These genes were absent in the transcriptomes and genome of the two non-luminous species. Pairwise identities and substitution rates reveal an unusually high degree of identity even between the most unrelated species. Additionally, two related groups of non-heme iron oxidases were found across all ctenophores, including those which are non-luminous, arguing against the involvement of these two gene groups in luminescence. Important residues for iron-binding are conserved across all proteins in the three groups, suggesting this function is still present. Given the known functions of other members of this protein superfamily are involved in heterocycle formation, we consider these genes to be top candidates for laboratory characterization or gene knockouts in the investigation of coelenterazine biosynthesis.</p></div

Base substitution ratios for <i>Mnemiopsis</i> genes.

<p>Base substitution ratios for <i>Mnemiopsis</i> genes.</p

Percent Identity Matrix of <i>Mnemiopsis</i> genes and proteins.

<p>Percent Identity Matrix of <i>Mnemiopsis</i> genes and proteins.</p

Top BLAST hits for FYY proteins in Swissprot.

<p>Top BLAST hits for FYY proteins in Swissprot.</p

Percent Identity Matrix of all 2-oxoglutarate Fe-Group 2 proteins.

<p>Percent Identity Matrix of all 2-oxoglutarate Fe-Group 2 proteins.</p