263 research outputs found
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,
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 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
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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
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