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July 11, 2023

Ribosome expert Kamena Kostova transitions to Staff Scientist role at Carnegie

Abstract
A group of diseases have been shown to correlate with a phenomenon called microbiome dysbiosis, where the bacterial species composition of the gut becomes abnormal. The gut microbiome of an animal is influenced by many factors including diet, exposures to bacteria during post-gestational growth, lifestyle, and disease status. Studies also show that host genetics can affect microbiome composition. We sought to test whether host genetic background is associated with gut microbiome composition in the Norwegian Lundehund dog, a highly inbred breed with an effective population size of 13 individuals. The Lundehund has a high rate of a protein-losing enteropathy in the small intestine that is often reported as Lundehund syndrome, which negatively affects longevity and life-quality. An outcrossing project with the Buhund, Norrbottenspets, and Icelandic sheepdog was recently established to reintroduce genetic diversity to the Lundehund and improve its health. To assess whether there was an association between host genetic diversity and the microbiome composition, we sampled the fecal microbiomes of 75 dogs of the parental (Lundehund), F1 (Lundehund x Buhund), and F2 (F1 x Lundehund) generations. We found significant variation in microbiome composition from the parental Lundehund generation compared to the outcross progeny. The variation observed in purebred Lundehunds corresponded to dysbiosis as seen by a highly variable microbiome composition with an elevated Firmicutes to Bacteroidetes ratio and an increase in the prevalence of Streptococcus bovis/Streptococcus equinus complex, a known pathobiont that can cause several diseases. We tracked several other environmental factors including diet, the presence of a cat in the household, living in a farm and the use of probiotics, but we did not find evidence of an effect of these on microbiome composition and alpha diversity. In conclusion, we found an association between host genetics and gut microbiome composition, which in turn may be associated with the high incidence of Lundehund syndrome in the purebred parental dogs.
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Abstract
We present the discovery of two exoplanets transiting TOI-836 (TIC 440887364) using data from TESS Sector 11 and Sector 38. TOI-836 is a bright (T = 8.5 mag), high proper motion (similar to 200 mas yr(-1)), low metallicity ([Fe/H]asymptotic to-0.28) K-dwarf with a mass of 0.68 +/- 0.05 M-? and a radius of 0.67 +/- 0.01 R-?. We obtain photometric follow-up observations with a variety of facilities, and we use these data sets to determine that the inner planet, TOI-836 b, is a 1.70 +/- 0.07 R-circle plus super-Earth in a 3.82-d orbit, placing it directly within the so-called "radius valley'. The outer planet, TOI-836 c, is a 2.59 +/- 0.09 R-circle plus mini-Neptune in an 8.60-d orbit. Radial velocity measurements reveal that TOI-836 b has a mass of 4.5 +/- 0.9 M-circle plus, while TOI-836 c has a mass of 9.6 +/- 2.6 M-circle plus. Photometric observations show Transit Timing Variations (TTVs) on the order of 20 min for TOI-836 c, although there are no detectable TTVs for TOI-836 b. The TTVs of planet TOI-836 c may be caused by an undetected exterior planet
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Abstract
Both volcano-tectonic (VTs) and deep long-period earthquakes (DLPs) have been documented at Akutan Volcano, Alaska and may reflect different active processes helpful for eruption forecasting. In this study, we perform high-resolution earthquake detection, classification, and relocation using seismic data from 2005 to 2017 to investigate their relationship with underlying magmatic processes. We find that the 2,787 VTs and 787 DLPs are concentrated above and below the inferred magma reservoir respectively. They both are clustered as swarms and occur preferentially during inflation episodes with no spatial migrations. However, moment release rates of DLP swarms show a stronger correlation with inflation and their low-frequency content is likely a source instead of a path effect. Therefore, we infer that DLPs are directly related to unsteady magma movement through a complex pathway. In comparison, repeating events are observed in VTs. Thus, we conclude that they represent fault rupture triggered by magma/fluid movement or larger earthquakes.
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Abstract
Elucidating biological processes has relied on the establishment of model organisms, many of which offer advantageous features such as rapid axenic growth, extensive knowledge of their physiological features and gene content, and the ease with which they can be genetically manipulated. The unicellular green alga Chlamydomonas reinhardtii has been an exemplary model that has enabled many scientific breakthroughs over the decades, especially in the fields of photosynthesis, cilia function and biogenesis, and the acclimation of photosynthetic organisms to their environment. Here, we discuss recent molecular/technological advances that have been applied to C. reinhardtii and how they have further fostered its development as a "flagship" algal system. We also explore the future promise of this alga in leveraging advances in the fields of genomics, proteomics, imaging, and synthetic biology for addressing critical future biological issues.
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Peter Gao
July 07, 2023
Awards

Peter Gao awarded Scialog grant for biosignature research

Abstract
Rock fragments of the Cb-type asteroid Ryugu returned to Earth by the JAXA Hayabusa2 mission share mineralogical, chemical, and isotopic properties with the Ivuna-type (CI) carbonaceous chondrites. Similar to CI chondrites, these fragments underwent extensive aqueous alteration and consist predominantly of hydrous minerals likely formed in the presence of liquid water on the Ryugu parent asteroid. Here we present an in situ analytical survey performed by secondary ion mass spectrometry from which we have estimated the D/H ratio of Ryugu's hydrous minerals, D/H-Ryugu, to be [165 +/- 19] x 10(-6), which corresponds to delta D-Ryugu = +59 +/- 121 parts per thousand (2 sigma). The hydrous mineral D/H-Ryugu's values for the two sampling sites on Ryugu are similar; they are also similar to the estimated D/H ratio of hydrous minerals in the CI chondrites Orgueil and Alais. This result reinforces a link between Ryugu and CI chondrites and an inference that Ryugu's samples, which avoided terrestrial contamination, are our best proxy to estimate the composition of water at the origin of hydrous minerals in CI-like material. Based on this data and recent literature studies, the contribution of CI chondrites to the hydrogen of Earth's surficial reservoirs is evaluated to be similar to 3%. We conclude that the water responsible for the alteration of Ryugu's rocks was derived from water ice precursors inherited from the interstellar medium; the ice partially re-equilibrated its hydrogen with the nebular H-2 before being accreted on the Ryugu's parent asteroid.
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Abstract
We have studied the high-pressure vibrational and structural behavior of bulk graphite and graphene nanoplatelets at room temperature by means of high-pressure Raman spectroscopic and x-ray diffraction probes. We have detected a clear pressure-induced structural transition in both materials, evidenced by the appearance of new Bragg peaks and Raman features, deviating from the starting hexagonal graphitic structure. The high-pressure phase is identified as a partially disordered orthorhombic structure, consisting of mixed sp2- and sp3-type bonding. Our experimental findings serve as direct evidence for the existence of a metastable transient modification in cold compressed carbon, lying between the sp2-type graphite and sp3-type diamond allotropes.
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Abstract
The local structure and density of ternary Fe-C-S liquid alloys have been studied using a combination of in situ X-ray diffraction and absorption experiments between 1 and 5 GPa and 1600-1900 K. The addition of up to 12 at% of carbon (C) to Fe-S liquid alloys does not significantly modify the structure, which is largely controlled by the perturbation to the Fe-Fe network induced by S atoms. The liquid density determined from diffraction and/or absorption techniques allows us to build a non-ideal ternary mixing model as a function of pressure, temperature, and composition in terms of the content of alloying light elements. The composition of the Moon's core is addressed based on this thermodynamic model. Under the assumption of a homogeneous liquid core proposed by two recent Moon models, the sulfur content would be 27-36 wt% or 12-23 wt%, respectively, while the carbon content is mainly limited by the Fe-C-S miscibility gap, with an upper bound of 4.3 wt%. On the other hand, if the core is partially molten, the core temperature is necessarily lower than 1850 K estimated in the text, and the composition of both the inner and outer core would be controlled by aspects of the Fe-C-S phase diagram not yet sufficiently constrained.
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Abstract
Transposable elements (TE) are mobile DNA sequences whose excessive proliferation endangers the host. Although animals have evolved robust TE-targeting defenses, including Piwi-interacting (pi)RNAs, retrotransposon LINE-1 (L1) still thrives in humans and mice. To gain insights into L1 endurance, we characterized L1 Bodies (LBs) and ORF1p complexes in germ cells of piRNA-deficient Maelstrom null mice. We report that ORF1p interacts with TE RNAs, genic mRNAs, and stress granule proteins, consistent with earlier studies. We also show that ORF1p associates with the CCR4-NOT deadenylation complex and PRKRA, a Protein Kinase R factor. Despite ORF1p interactions with these negative regulators of RNA expression, the stability and translation of LB-localized mRNAs remain unchanged. To scrutinize these findings, we studied the effects of PRKRA on L1 in cultured cells and showed that it elevates ORF1p levels and L1 retrotransposition. These results suggest that ORF1p-driven condensates promote L1 propagation, without affecting the metabolism of endogenous RNAs.
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