The Mechanisms of Codon Reassignments in Mitochondrial Genetic Codes

Many cases of non-standard genetic codes are known in mitochondrial genomes. We carry out analysis of phylogeny and codon usage of organisms for which the complete mitochondrial genome is available, and we determine the most likely mechanism for codon reassignment in each case. Reassignment events can be classified according to the gain-loss framework. The gain represents the appearance of a new tRNA for the reassigned codon or the change of an existing tRNA such that it gains the ability to pair with the codon. The loss represents the deletion of a tRNA or the change in a tRNA so that it no longer translates the codon. One possible mechanism is Codon Disappearance, where the codon disappears from the genome prior to the gain and loss events. In the alternative mechanisms the codon does not disappear. In the Unassigned Codon mechanism, the loss occurs first, whereas in the Ambiguous Intermediate mechanism, the gain occurs first. Codon usage analysis gives clear evidence of cases where the codon disappeared at the point of the reassignment and also cases where it did not disappear. Codon disappearance is the probable explanation for stop to sense reassignments and a small number of reassignments of sense codons. However, the majority of sense to sense reassignments cannot be explained by codon disappearance. In the latter cases, by analysis of the presence or absence of tRNAs in the genome and of the changes in tRNA sequences, it is sometimes possible to distinguish between the Unassigned Codon and Ambiguous Intermediate mechanisms. We emphasize that not all reassignments follow the same scenario and that it is necessary to consider the details of each case carefully.Comment: 53 pages (45 pages, including 4 figures + 8 pages of supplementary information). To appear in J.Mol.Evo

Structural chirality of polar skyrmions probed by resonant elastic x-ray scattering

An escalating challenge in condensed-matter research is the characterization of emergent order-parameter nanostructures such as ferroelectric and ferromagnetic skyrmions. Their small length scales coupled with complex, three-dimensional polarization or spin structures makes them demanding to trace out fully. Resonant elastic x-ray scattering (REXS) has emerged as a technique to study chirality in spin textures such as skyrmions and domain walls. It has, however, been used to a considerably lesser extent to study analogous features in ferroelectrics. Here, we present a framework for modeling REXS from an arbitrary arrangement of charge quadrupole moments, which can be applied to nanostructures in materials such as ferroelectrics. With this, we demonstrate how extended reciprocal space scans using REXS with circularly polarized x rays can probe the three-dimensional structure and chirality of polar skyrmions. Measurements, bolstered by quantitative scattering calculations, show that polar skyrmions of mixed chirality coexist, and that REXS allows valuation of relative fractions of right- and left-handed skyrmions. Our quantitative analysis of the structure and chirality of polar skyrmions highlights the capability of REXS for establishing complex topological structures toward future application exploits.M. R. M. and R. R. were supported by the Quantum Materials program from the Office of Basic Energy Sciences, U.S. Department of Energy (DE-AC02-05CH11231). V. A. S., J. W. F., and L. W. M. acknowledge the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Award No. DE-SC-0012375 for support to study complex-oxide heterostructure with x-ray scattering. L. W. M. and R. R. acknowledge partial support from the Army Research Office under the ETHOS MURI via cooperative agreement W911NF-21-2-0162. J. Í. acknowledge financial support from the Luxembourg National Research Fund through project FNR/C18/MS/12705883/REFOX. Diamond Light Source, UK, is acknowledged for beam time on beam line I10 under proposal NT24797. K. T. K., S. Y. P., and D. R. L. acknowledge support from the National Research Foundation of Korea, under Grant No. NRF-2020R1A2C1009597, NRF-2019K1A3A7A09033387, and NRF-2021R1C1C1009494. M. A. P. G. acknowledges support by the Czech Science Foundation (Project No. 19-28594X). This research used resources of the Advanced Light Source, a U.S. DOE Office of Science User Facility under Contract No. DE-AC02-05CH11231. This research used resources of the Advanced Photon Source, a U.S. Department of Energy (DOE) Office of Science User Facility at Argonne National Laboratory and is based on research supported by the U.S. DOE Office of Science-Basic Energy Sciences, under Contract No. DE-AC02-06CH11357. S. D. gratefully acknowledges a start-up grant from Indian Institute of Science, Bangalore, India. F. G.-O., P. G.-F., and J. J. acknowledge financial support from Grant No. PGC2018-096955-B-C41 funded by MCIN/AEI/10.13039/501100011033 and by ERDF “A way of making Europe,” by the European Union. F. G.-O. acknowledges financial support from Grant No. FPU18/04661 funded by MCIN/AEI/10.13039/50110001103

Polarons and confinement of electronic motion to two dimensions in a layered transition metal oxide

A very remarkable feature of the layered transition metal oxides (TMOs), whose most famous members are the high-temperature superconductors (HTSs), is that even though they are prepared as bulk three-dimensional single crystals, they display hugely anisotropic electrical and optical properties, seeming to be insulating perpendicular to the layers and metallic within them. This is the phenomenon of confinement, a concept at odds with the conventional theory of solids and recognized as due to magnetic and electron-lattice interactions in the layers which must be overcome at a substantial energy cost if electrons are to be transferred between layers. The associated energy gap or 'pseudogap' is particularly obvious in experiments where charge is moved perpendicular to the planes, most notably scanning tunneling microscopy (STM) and polarized infrared spectroscopy. Here, using the same experimental tools, we show that there is a second family of TMOs - the layered manganites La2-2xSr1+2xMn2O7 (LSMO) - with even more extreme confinement and pseudogap effects. The data, which are the first to resolve atoms in any metallic manganite, demonstrate quantitatively that because they are attached to polarons - lattice and spin textures within the planes -, it is equally difficult to remove carriers from the planes via vacuum tunneling into a conventional metallic tip, as it is for them to move between Mn-rich layers within the material itself

Dispersal and population structure at different spatial scales in the subterranean rodent Ctenomys australis

<p>Abstract</p> <p><b>Background</b></p> <p>The population genetic structure of subterranean rodent species is strongly affected by demographic (e.g. rates of dispersal and social structure) and stochastic factors (e.g. random genetic drift among subpopulations and habitat fragmentation). In particular, gene flow estimates at different spatial scales are essential to understand genetic differentiation among populations of a species living in a highly fragmented landscape. <it>Ctenomys australis </it>(the sand dune tuco-tuco) is a territorial subterranean rodent that inhabits a relatively secure, permanently sealed burrow system, occurring in sand dune habitats on the coastal landscape in the south-east of Buenos Aires province, Argentina. Currently, this habitat is threatened by urban development and forestry and, therefore, the survival of this endemic species is at risk. Here, we assess population genetic structure and patterns of dispersal among individuals of this species at different spatial scales using 8 polymorphic microsatellite loci. Furthermore, we evaluate the relative importance of sex and habitat configuration in modulating the dispersal patterns at these geographical scales.</p> <p>Results</p> <p>Our results show that dispersal in <it>C. australis </it>is not restricted at regional spatial scales (~ 4 km). Assignment tests revealed significant population substructure within the study area, providing support for the presence of two subpopulations from three original sampling sites. Finally, male-biased dispersal was found in the Western side of our study area, but in the Eastern side no apparent philopatric pattern was found, suggesting that in a more continuous habitat males might move longer distances than females.</p> <p>Conclusions</p> <p>Overall, the assignment-based approaches were able to detect population substructure at fine geographical scales. Additionally, the maintenance of a significant genetic structure at regional (~ 4 km) and small (less than 1 km) spatial scales despite apparently moderate to high levels of gene flow between local sampling sites could not be explained simply by the linear distance among them. On the whole, our results support the hypothesis that males disperse more frequently than females; however they do not provide support for strict philopatry within females.</p

Patterns of genetic diversity in southern and southeastern Araucaria angustifolia (Bert.) O. Kuntze relict populations

Habitat fragmentation and a decrease in population size may lead to a loss in population genetic diversity. For the first time, the reduction in genetic diversity in the northernmost limit of natural occurence (southeastern Brazil) of Araucaria angustifolia in comparison with populations in the main area of the species continuous natural distribution (southern Brazil), was tested. The 673 AFLPs markers revealed a high level of genetic diversity for the species (Ht = 0.27), despite anthropogenic influence throughout the last century, and a decrease of H in isolated populations of southeastern Brazil (H = 0.16), thereby indicating the tendency for higher genetic diversity in remnant populations of continuous forests in southern Brazil, when compared to natural isolated populations in the southeastern region. A strong differentiation among southern and southeastern populations was detected (AMOVA variance ranged from 10%-15%). From Bayesian analysis, it is suggested that the nine populations tested form five “genetic clusters” (K = 5). Five of these populations, located in the northernmost limit of distribution of the species, represent three “genetic clusters”. These results are in agreement with the pattern of geographic distribution of the studied populations

Assessment of the Food Habits of the Moroccan Dorcas Gazelle in M’Sabih Talaa, West Central Morocco, Using the trnL Approach

Food habits of the Moroccan dorcas gazelle, Gazella dorcas massaesyla, previously investigated in the 1980s using microhistological fecal analysis, in the M’Sabih Talaa Reserve, west central Morocco, were re-evaluated over three seasons (spring, summer and autumn 2009) using the trnL approach to determine the diet composition and its seasonal variation from fecal samples. Taxonomic identification was carried out using the identification originating from the database built from EMBL and the list of plant species within the reserve. The total taxonomic richness in the reserve was 130 instead of 171 species in the 1980s. The diet composition revealed to be much more diversified (71 plant taxa belonging to 57 genus and 29 families) than it was 22 years ago (29 identified taxa). Thirty-four taxa were newly identified in the diet while 13 reported in 1986–87 were not found. Moroccan dorcas gazelle showed a high preference to Acacia gummifera, Anagallis arvensis, Glebionis coronaria, Cladanthus arabicus, Diplotaxis tenuisiliqua, Erodium salzmannii, Limonium thouini, Lotus arenarius and Zizyphus lotus. Seasonal variations occurred in both number (40–41 taxa in spring-summer and 49 taxa in autumn vs. respectively 23–22 and 26 in 1986–1987) and taxonomic type of eaten plant taxa. This dietary diversification could be attributed either to the difference in methods of analysis, trnL approach having a higher taxonomic resolution, or a potential change in nutritional quality of plants over time

Short- and long-term outcomes of uvulopalatopharyngoplasty for snoring.

Uvulopalatopharyngoplasty is a well established and highly successful operation in the treatment of snoring. However, most published data are based on relatively short-term follow-up results. Anecdotal cases of late recurrence of snoring after an initially successful surgical result have been reported but few formal studies have been performed to determine the true magnitude of this problem. We compared the short-term and long-term results on our patients and found the late recurrence rate after a minimum follow-up period of 12 months (range: 12-84 months, mean 31.3 months) to be in the region of 13%. The risk of recurrence was directly related to the body mass index

Investigation of cardiac function in children with suspected obstructive sleep apnea.

OBJECTIVE: To assess the prevalence of cardiac failure in a group of children with suspected obstructive sleep apnea (OSA) and to assess the need for preoperative electrocardiograms (ECGs) and chest radiographs (CXRs) in children with OSA. DESIGN: Case record review of 271 children having (adeno)tonsillectomy for symptoms of OSA. METHOD: Preoperative ECGs and CXRs were assessed for signs of right atrial or ventricular hypertrophy or failure. Case records were assessed for evidence of cardiac failure during anaesthesia. RESULTS: One child with congenital heart disease had signs of cardiac failure preoperatively. No other cases of atrial or ventricular hypertrophy or failure were found. CONCLUSIONS: Cardiac failure appears to be uncommon in children with symptoms of OSA. Preoperative ECG and CXR are essential in only selected cases