Dynamical evolution of second-generation circumstellar/protoplanetary disks in evolved wide binary systems

In mass-transferring wide binary stellar systems, the companion star can capture some of the mass released in wind by the primary evolved star, and form an accretion disk. Such accretion disks could evolve to form disks of comparable properties to protoplanetary disks and may enable the formation of new planets and/or the interactions, re-growth, and re-migration of pre-existing planets in the newly formed disks. We study the formation and the dynamical evolution of such "second generation" (SG) protoplanetary disks in evolved wide binary systems, with primaries in the mass range of 1-8 Solar mass. We follow their evolution from the asymptotic giant branch (AGB) phase of the red giant stellar donor until its evolution to become a white dwarf. We perform 1D semi-analytical numerical simulations for several binary systems varying the mass of the evolved stellar donor and the initial orbital distance, taking into account the changing mass-loss rates and the binary orbital expansion due to mass-loss. We calculate the radial density profile of the formed SG accretion disk and its temperature profile, considering a non-stationary viscosity profile which depends on the radial temperature profile. We find that SG circumstellar disks evolve to form a long-lived stable structure over the lifetime of the donor star, and we show that we can consistently produce the observed conditions and accretion rate inferred for the Mira evolved wide-binary system. The quasi-steady state radial surface density profiles are comparable with the typical range of masses and densities of observed (regular "first-generation") protoplanetary disks. This suggests that realistic SG disks can give rise to a second phase of planet formation and dynamics in old wide binary systems

Dynamical evolution of a young planetary system: stellar flybys in co-planar orbital configuration

Stellar flybys in star clusters may perturb the evolution of young planetary systems in terms of disk truncation, planetary migration and planetary mass accretion. We investigate the feedback of a young planetary system during a single close stellar encounter in a typical open young stellar cluster. We consider 5 masses for the stellar perturbers: 0.5, 0.8, 1, 3 and 8 M$_{Sun}$, in coplanar, prograde and retrograde orbits respect to the planetary disk, varying the pertruber-host star orbital periastron from 100 AU to 500 AU. We have made 3D modelizations with the smooth particle hydrodynamics code GaSPH of a system composed by a solar type star surrounded by a low density disk where a giant planet is embedded in. We focus on the dynamical evolution of global parameters characterizing the disk and the planet, like the Lagrangian radius containing the $63.2\%$ of the mass of the disk, the distance of the planet to its host star, the planet orbital eccentricity and the planetary mass accretion. We find that the most part of the simulated systems show a significant disk truncation after a single close encounter, a final orbital distance of the Jovian, from the central star, lower than the unperturbed case and, finally, the perturbed systems show a final mass accretion of the Jovian planet larger than the non-perturbed case. Therefore, stellar flybys significantly perturb the dynamics of a young planetary system, regardless the orbital configuration of the stellar perturber. In such experiments, the final disk radius and the orbital parameters of the Jovian planet are considerably affected by the stellar close encounter

Preliminary Findings: Relationship Between IgG-Based Food Elimination and Whole-Body Inflammation

High levels of whole-body inflammation are associated with increased risk of poor health outcomes and chronic disease. Inflammatory symptoms (e.g., digestive, psychological, and whole-body irritation) are commonly addressed via food elimination diets, yet individual differences may exist for persons with unique immunoglobulin-G (IgG) mediated food sensitivities. Few studies have examined IgG food sensitivities using an understood biomarker of inflammation, high-sensitivity C-Reactive Protein (hsCRP). Identification of IgG mediated food sensitivities may be a feasible means for targeted-food elimination seeking to address inflammatory symptoms. PURPOSE: To assess measurable changes in primary outcomes, hsCRP and inflammatory symptomology, within subjects following an IgG targeted-food elimination diet compared to standard diet. METHODS: From 2021-2023, 20 subjects (male: n=20, Age=26 ± 7.6, Wt (kg)=88.43 ± 20.74, LBM (kg)=67.44 ± 10.15) underwent both a 4-week standard diet and 4-week IgG-targeted elimination diet, in a cross-over design ordered by random assignment. Body composition (InBody 570, BIA), inflammation (hsCRP blood draw), and symptomology (Inflammatory Symptom Screening Questionnaire) were assessed at baseline. Participants completed hsCRP and symptom screeners at the following appointments: start and end of baseline (days 1, 8), after week one and week four of first (days 15, 36) and second diet assignment (days 43, 64). Food logging was done throughout the duration of the study. Correlations and ANOVAs were run to assess relationships between demographics and hsCRP and symptom screener scores, as well as any interaction between diet condition, time point, or diet order. Data are reported as mean ± standard error. RESULTS: No meaningful correlations were found between InBody assessments and primary outcomes. No differences were found in hsCRP measurements between any of the time points in the standard and elimination diet conditions (p=.810). On the contrary, differences in inflammatory symptom scores were dependent on diet condition (p\u3c.001). During their standard diet, participants reported increased symptom frequency at week one (20.40) and week four (20.33). Greater differences in inflammatory symptomology were found the longer participants eliminated food; after one week of elimination (15.20) compared to one week of standard diet (-5.20, p=.001) and four weeks of standard diet (-5.13, p=.003). Differences were magnified by the fourth week of elimination (10.67) compared to week one (-9.73, p\u3c.001) and week four of standard diet (-9.667, p\u3c.001). CONCLUSION: This study suggests targeted IgG-based food elimination diets significantly reduce inflammatory symptoms despite finding no detectable changes in whole body inflammation via hsCRP. The results presented here influenced a subsequent study examining the effect of plant versus animal protein on athletic performance in individuals with and without whey IgG sensitivities

A Comprehensive GC–MS Sub-Microscale Assay for Fatty Acids and its Applications

Fatty acid analysis is essential to a broad range of applications including those associated with the nascent algal biofuel and algal bioproduct industries. Current fatty acid profiling methods require lengthy, sequential extraction and transesterification steps necessitating significant quantities of analyte. We report the development of a rapid, microscale, single-step, in situ protocol for GC–MS lipid analysis that requires only 250 μg dry mass per sample. We furthermore demonstrate the broad applications of this technique by profiling the fatty acids of several algal species, small aquatic organisms, insects and terrestrial plant material. When combined with fluorescent techniques utilizing the BODIPY dye family and flow cytometry, this micro-assay serves as a powerful tool for analyzing fatty acids in laboratory and field collected samples, for high-throughput screening, and for crop assessment. Additionally, the high sensitivity of the technique allows for population analyses across a wide variety of taxa

Chloroplast genome sequencing analysis of Heterosigma akashiwo CCMP452 (West Atlantic) and NIES293 (West Pacific) strains

Background: Heterokont algae form a monophyletic group within the stramenopile branch of the tree of life. These organisms display wide morphological diversity, ranging from minute unicells to massive, bladed forms. Surprisingly, chloroplast genome sequences are available only for diatoms, representing two (Coscinodiscophyceae and Bacillariophyceae) of approximately 18 classes of algae that comprise this taxonomic cluster. A universal challenge to chloroplast genome sequencing studies is the retrieval of highly purified DNA in quantities sufficient for analytical processing. To circumvent this problem, we have developed a simplified method for sequencing chloroplast genomes, using fosmids selected from a total cellular DNA library. The technique has been used to sequence chloroplast DNA of two Heterosigma akashiwo strains. This raphidophyte has served as a model system for studies of stramenopile chloroplast biogenesis and evolution. Results: H. akashiwo strain CCMP452 (West Atlantic) chloroplast DNA is 160,149 bp in size with a 21,822-bp inverted repeat, whereas NIES293 (West Pacific) chloroplast DNA is 159,370 bp in size and has an inverted repeat of 21,665 bp. The fosmid cloning technique reveals that both strains contain an isomeric chloroplast DNA population resulting from an inversion of their single copy domains. Both strains contain multiple small inverted and tandem repeats, non-randomly distributed within the genomes. Although both CCMP452 and NIES293 chloroplast DNAs contains 197 genes, multiple nucleotide polymorphisms are present in both coding and intergenic regions. Several protein-coding genes contain large, in-frame inserts relative to orthologous genes in other plastids. These inserts are maintained in mRNA products. Two genes of interest in H. akashiwo, not previously reported in any chloroplast genome, include tyrC, a tyrosine recombinase, which we hypothesize may be a result of a lateral gene transfer event, and an unidentified 456 amino acid protein, which we hypothesize serves as a G-protein-coupled receptor. The H. akashiwo chloroplast genomes share little synteny with other algal chloroplast genomes sequenced to date. Conclusion: The fosmid cloning technique eliminates chloroplast isolation, does not require chloroplast DNA purification, and reduces sequencing processing time. Application of this method has provided new insights into chloroplast genome architecture, gene content and evolution within the stramenopile cluster

Review of the algal biology program within the National Alliance for Advanced Biofuels and Bioproducts

In 2010, when the National Alliance for Advanced Biofuels and Bioproducts (NAABB) consortium began, little was known about the molecular basis of algal biomass or oil production. Very few algal genome sequences were available and efforts to identify the best-producing wild species through bioprospecting approaches had largely stalled after the U.S. Department of Energy's Aquatic Species Program. This lack of knowledge included how reduced carbon was partitioned into storage products like triglycerides or starch and the role played by metabolite remodeling in the accumulation of energy-dense storage products. Furthermore, genetic transformation and metabolic engineering approaches to improve algal biomass and oil yields were in their infancy. Genome sequencing and transcriptional profiling were becoming less expensive, however; and the tools to annotate gene expression profiles under various growth and engineered conditions were just starting to be developed for algae. It was in this context that an integrated algal biology program was introduced in the NAABB to address the greatest constraints limiting algal biomass yield. This review describes the NAABB algal biology program, including hypotheses, research objectives, and strategies to move algal biology research into the twenty-first century and to realize the greatest potential of algae biomass systems to produce biofuels

Complete genome sequence of the entomopathogenic and metabolically versatile soil bacterium Pseudomonas entomophila

Pseudomonas entomophila is an entomopathogenic bacterium that, upon ingestion, kills Drosophila melanogaster as well as insects from different orders. The complete sequence of the 5.9-Mb genome was determined and compared to the sequenced genomes of four Pseudomonas species. P. entomophila possesses most of the catabolic genes of the closely related strain P. putida KT2440, revealing its metabolically versatile properties and its soil lifestyle. Several features that probably contribute to its entomopathogenic properties were disclosed. Unexpectedly for an animal pathogen, P. entomophila is devoid of a type III secretion system and associated toxins but rather relies on a number of potential virulence factors such as insecticidal toxins, proteases, putative hemolysins, hydrogen cyanide and novel secondary metabolites to infect and kill insects. Genome-wide random mutagenesis revealed the major role of the two-component system GacS/GacA that regulates most of the potential virulence factors identified

A Gene in the Process of Endosymbiotic Transfer

BACKGROUND: The endosymbiotic birth of organelles is accompanied by massive transfer of endosymbiont genes to the eukaryotic host nucleus. In the centric diatom Thalassiosira pseudonana the Psb28 protein is encoded in the plastid genome while a second version is nuclear-encoded and possesses a bipartite N-terminal presequence necessary to target the protein into the diatom complex plastid. Thus it can represent a gene captured during endosymbiotic gene transfer. METHODOLOGY/PRINCIPAL FINDINGS: To specify the origin of nuclear- and plastid-encoded Psb28 in T. pseudonana we have performed extensive phylogenetic analyses of both mentioned genes. We have also experimentally tested the intracellular location of the nuclear-encoded Psb28 protein (nuPsb28) through transformation of the diatom Phaeodactylum tricornutum with the gene in question fused to EYFP. CONCLUSIONS/SIGNIFICANCE: We show here that both versions of the psb28 gene in T. pseudonana are transcribed. We also provide experimental evidence for successful targeting of the nuPsb28 fused with EYFP to the diatom complex plastid. Extensive phylogenetic analyses demonstrate that nucleotide composition of the analyzed genes deeply influences the tree topology and that appropriate methods designed to deal with a compositional bias of the sequences and the long branch attraction artefact (LBA) need to be used to overcome this obstacle. We propose that nuclear psb28 in T. pseudonana is a duplicate of a plastid localized version, and that it has been transferred from its endosymbiont

The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing.

Microbial ecology is plagued by problems of an abstract nature. Cell sizes are so small and population sizes so large that both are virtually incomprehensible. Niches are so far from our everyday experience as to make their very definition elusive. Organisms that may be abundant and critical to our survival are little understood, seldom described and/or cultured, and sometimes yet to be even seen. One way to confront these problems is to use data of an even more abstract nature: molecular sequence data. Massive environmental nucleic acid sequencing, such as metagenomics or metatranscriptomics, promises functional analysis of microbial communities as a whole, without prior knowledge of which organisms are in the environment or exactly how they are interacting. But sequence-based ecological studies nearly always use a comparative approach, and that requires relevant reference sequences, which are an extremely limited resource when it comes to microbial eukaryotes. In practice, this means sequence databases need to be populated with enormous quantities of data for which we have some certainties about the source. Most important is the taxonomic identity of the organism from which a sequence is derived and as much functional identification of the encoded proteins as possible. In an ideal world, such information would be available as a large set of complete, well curated, and annotated genomes for all the major organisms from the environment in question. Reality substantially diverges from this ideal, but at least for bacterial molecular ecology, there is a database consisting of thousands of complete genomes from a wide range of taxa, supplemented by a phylogeny-driven approach to diversifying genomics [2]. For eukaryotes, the number of available genomes is far, far fewer, and we have relied much more heavily on random growth of sequence databases, raising the question as to whether this is fit for purpose

The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing

International audienceCurrent sampling of genomic sequence data from eukaryotes is relatively poor, biased, and inadequate to address important questions about their biology, evolution, and ecology; this Community Page describes a resource of 700 transcriptomes from marine microbial eukaryotes to help understand their role in the world's oceans