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1. The β Pictoris b Hill sphere transit campaign: II. Searching for the signatures of the β Pictoris exoplanets through time delay analysis of the δ Scuti pulsations

   https://doi.org/10.1051/0004-6361/202347754  

   Zieba, Sebastian; Zwintz, Konstanze; Kenworthy, Matthew; Hey, Daniel; Murphy, Simon J; Kuschnig, Rainer; Abe, Lyu; Agabi, Abdelkrim; Mekarnia, Djamel; Guillot, Tristan; et al (July 2024, Astronomy & Astrophysics)

   TheβPictoris system is the closest known stellar system with directly detected gas giant planets, an edge-on circumstellar disc, and evidence of falling sublimating bodies and transiting exocomets. The inner planet,βPictoris c, has also been indirectly detected with radial velocity (RV) measurements. The star is a knownδScuti pulsator, and the long-term stability of these pulsations opens up the possibility of indirectly detecting the gas giant planets through time delays of the pulsations due to a varying light travel time. We search for phase shifts in theδScuti pulsations consistent with the known planetsβPictoris b and c and carry out an analysis of the stellar pulsations ofβPictoris over a multi-year timescale. We used photometric data collected by the BRITE-Constellation, bRing, ASTEP, and TESS to derive a list of the strongest and most significantδScuti pulsations. We carried out an analysis with the open-source python package maelstrom to study the stability of the pulsation modes ofβPictoris in order to determine the long-term trends in the observed pulsations. We did not detect the expected signal forβPictoris b orβPictoris c. The expected time delay is 6 s forβPictoris c and 24 s forβPictoris b. With simulations, we determined that the photometric noise in all the combined data sets cannot reach the sensitivity needed to detect the expected timing drifts. An analysis of the pulsational modes ofβPictoris using maelstrom showed that the modes themselves drift on the timescale of a year, fundamentally limiting our ability to detect exoplanets aroundβPictoris via pulsation timing. 

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2. The phenotypic spectrum of PTCD3 deficiency

   https://doi.org/10.1002/jmd2.12424  

   Lace, Baiba; Faqeih, Eissa; Kaya, Namik; Krumina, Zita; Mayr, Johannes_A; Micule, Ieva; Wright, Nathan_Thompson; Achleitner, Melanie_T; AlQudairy, Hanan; Pajusalu, Sander; et al (May 2024, JIMD Reports)

   Abstract ThePTCD3gene product (protein PTCD3 or MRPS39) forms the entry channel of the mitochondrial small ribosomal subunit and binds to single‐stranded mRNA. Here, we expand on the clinical manifestations ofPTCD3pathogenic variants by describing an early‐onset patient with Leigh‐like syndrome and two patients with milder form of disease, with combined oxidative phosphorylation deficiency. A 34‐year‐old male and his 33‐year‐old sister both have horizontal nystagmus, pronounced rough tremor, truncal ataxia, dysmetria, spasticity and hyperreflexia. The basal respiration rate decreased significantly for the male patient and his mother (p < 0.0001) compared to the controls. The whole genome sequencing analysis revealed two heterozygous variants in thePTCD3: c.1182T>A, p.(Tyr394Ter) and c.805C>T, p.(His269Tyr). Tyr394Ter variant ablates the C‐terminal half of the protein, including a significant portion of the central fold. In silico modelling for the variant His269Tyr shows that the inclusion of the slightly larger tyrosine sidechain is well tolerated, with no significant change in either the position or the movement of the surrounding area. The third case is a 9‐year‐old boy, who has a global developmental delay, central hypotonia, hyperreflexia and abnormal MRI.PTCD3pathogenic variant c.538+4A>G was identified by whole exome sequencing. To test the variant's effect on splicing, an RT‐PCR experiment was performed, which revealed skipping of an out‐of‐frame exon 7. 

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3. Phosphate enrichment induces increased dominance of the parasite Aquarickettsia in the coral Acropora cervicornis

   https://doi.org/10.1093/femsec/fiac013  

   Klinges, J Grace; Patel, Shalvi H; Duke, William C; Muller, Erinn M; Vega Thurber, Rebecca L (February 2022, FEMS Microbiology Ecology)

   Abstract Nutrient pollution is linked to coral disease susceptibility and severity, but the mechanism behind this effect remains underexplored. A recently identified bacterial species, ‘Ca. Aquarickettsia rohweri,’ is hypothesized to parasitize the Caribbean staghorn coral, Acropora cervicornis, leading to reduced coral growth and increased disease susceptibility. Aquarickettsia rohweri is hypothesized to assimilate host metabolites and ATP and was previously demonstrated to be highly nutrient-responsive. As nutrient enrichment is a pervasive issue in the Caribbean, this study examined the effects of common nutrient pollutants (nitrate, ammonium, and phosphate) on a disease-susceptible genotype of A. cervicornis. Microbial diversity was found to decline over the course of the experiment in phosphate-, nitrate-, and combined-treated samples, and quantitative PCR indicated that Aquarickettsia abundance increased significantly across all treatments. Only treatments amended with phosphate, however, exhibited a significant shift in Aquarickettsia abundance relative to other taxa. Furthermore, corals exposed to phosphate had significantly lower linear extension than untreated or nitrate-treated corals after 3 weeks of nutrient exposure. Together these data suggest that while experimental tank conditions, with an elevated nutrient regime associated with coastal waters, increased total bacterial abundance, only the addition of phosphate significantly altered the ratios of Aquarickettsia compared to other members of the microbiome. 

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4. The Complex Landscape of Structural Divergence Between the Drosophila pseudoobscura and D. persimilis Genomes

   https://doi.org/10.1093/gbe/evae047  

   Carpinteyro-Ponce, Javier; Machado, Carlos A (March 2024, Genome Biology and Evolution)

   Vieira, Cristina (Ed.)

   Abstract Structural genomic variants are key drivers of phenotypic evolution. They can span hundreds to millions of base pairs and can thus affect large numbers of genetic elements. Although structural variation is quite common within and between species, its characterization depends upon the quality of genome assemblies and the proportion of repetitive elements. Using new high-quality genome assemblies, we report a complex and previously hidden landscape of structural divergence between the genomes of Drosophila persimilis and D. pseudoobscura, two classic species in speciation research, and study the relationships among structural variants, transposable elements, and gene expression divergence. The new assemblies confirm the already known fixed inversion differences between these species. Consistent with previous studies showing higher levels of nucleotide divergence between fixed inversions relative to collinear regions of the genome, we also find a significant overrepresentation of INDELs inside the inversions. We find that transposable elements accumulate in regions with low levels of recombination, and spatial correlation analyses reveal a strong association between transposable elements and structural variants. We also report a strong association between differentially expressed (DE) genes and structural variants and an overrepresentation of DE genes inside the fixed chromosomal inversions that separate this species pair. Interestingly, species-specific structural variants are overrepresented in DE genes involved in neural development, spermatogenesis, and oocyte-to-embryo transition. Overall, our results highlight the association of transposable elements with structural variants and their importance in driving evolutionary divergence. 

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5. The long and short of the S ‐locus in Turnera (Passifloraceae)

   https://doi.org/10.1111/nph.15970  

   Shore, Joel S.; Hamam, Hasan J.; Chafe, Paul D. J.; Labonne, Jonathan D. J.; Henning, Paige M.; McCubbin, Andrew G. (July 2019, New Phytologist)

   Summary Distyly is an intriguing floral adaptation that increases pollen transfer precision and restricts inbreeding. It has been a model system in evolutionary biology since Darwin. Although theS‐locus determines the long‐ and short‐styled morphs, the genes were unknown inTurnera. We have now identified these genes.We used deletion mapping to identify, and then sequence,BACclones and genome scaffolds to constructS/shaplotypes. We investigated candidate gene expression, hemizygosity, and used mutants, to explore gene function.Thes‐haplotype possessed 21 genes collinear with a region of chromosome 7 of grape. TheS‐haplotype possessed three additional genes and two inversions.TsSPH1was expressed in filaments and anthers,TsYUC6in anthers andTsBAHDin pistils. Long‐homostyle mutants did not possessTsBAHDand a short‐homostyle mutant did not expressTsSPH1.Three hemizygous genes appear to determine S‐morph characteristics inT. subulata. Hemizygosity is common to all distylous species investigated, yet the genes differ. The pistil candidate gene,TsBAHD, differs from that ofPrimula, but both may inactivate brassinosteroids causing short styles.TsYUC6is involved in auxin synthesis and likely determines pollen characteristics.TsSPH1is likely involved in filament elongation. We propose an incompatibility mechanism involvingTsYUC6andTsBAHD. 

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