In Arabidopsis thaliana codon volatility scores reflect GC3 composition rather than selective pressure

Background: Synonymous codon usage bias has typically been correlated with, and attributed to translational efficiency. However, there are other pressures on genomic sequence composition that can affect codon usage patterns such as mutational biases. This study provides an analysis of the codon usage patterns in Arabidopsis thaliana in relation to gene expression levels, codon volatility, mutational biases and selective pressures. Results: We have performed synonymous codon usage and codon volatility analyses for all genes in the A. thaliana genome. In contrast to reports for species from other kingdoms, we find that neither codon usage nor volatility are correlated with selection pressure (as measured by dN/dS), nor with gene expression levels on a genome wide level. Our results show that codon volatility and usage are not synonymous, rather that they are correlated with the abundance of G and C at the third codon position (GC3). Conclusions: Our results indicate that while the A. thaliana genome shows evidence for synonymous codon usage bias, this is not related to the expression levels of its constituent genes. Neither codon volatility nor codon usage are correlated with expression levels or selective pressures but, because they are directly related to the composition of G and C at the third codon position, they are the result of mutational bias. Therefore, in A. thaliana codon volatility and usage do not result from selection for translation efficiency or protein functional shift as measured by positive selection

Psychosis as the sole presenting feature of hyperthyroidism: a case report

Thyroid disease is a very common entity with a wide range of presentation, We report a case of twenty six year old female presented to emergency room with frank psychosis over the course of her stay in hospital we investigated thoroughly and finally she turned out to be a case of hyperthyroidism with psychosis as the only presenting symptom and after starting her on carbimazole patient responded to the treatment remarkably

Directional wetting in anisotropic inverse opals

Porous materials display interesting transport phenomena due to the restricted motion of fluids within the nano- to micro-scale voids. Here, we investigate how liquid wetting in highly ordered inverse opals is affected by anisotropy in pore geometry. We compare samples with different degrees of pore asphericity and find different wetting patterns depending on the pore shape. Highly anisotropic structures are infiltrated more easily than their isotropic counterparts. Further, the wetting of anisotropic inverse opals is directional, with liquids filling from the side more easily. This effect is supported by percolation simulations as well as direct observations of wetting using time-resolved optical microscopy

Rational Design of Transparent Nanowire Architectures with Tunable Geometries for Preventing Marine Fouling

Marine biofouling is a sticky global problem that hinders maritime industries. Various microscale surface structures inspired by marine biological species have been explored for their anti- fouling properties. However, systematic studies of anti- marine- fouling performance on surface architectures with characteristic length- scales spanning from below 100 nm to greater than 10 µm are generally lacking. Herein, a study on the rational design and fabrication of ZnO/Al2O3 core- shell nanowire architectures with tunable geometries (length, spacing, and branching) and surface chemistry is presented. The ability of the nanowires to significantly delay or prevent marine biofouling is demonstrated. Compared to planar surfaces, hydrophilic nanowires can reduce fouling coverage by up to - 60% after 20 days. The fouling reduction mechanism is mainly due to two geometric effects: reduced effective settlement area and mechanical cell penetration. Additionally, superhydrophobic nanowires can completely prevent marine biofouling for up to 22 days. The nanowire surfaces are transparent across the visible spectrum, making them applicable to windows and oceanographic sensors. Through the rational control of surface nano- architectures, the coupled relationships between wettability, transparency, and anti- biofouling performance are identified. It is envisioned that the insights gained from the work can be used to systematically design surfaces that reduce marine biofouling in various industrial settings.Core- shell nanowire architectures with tunable geometries (length, spacing, and branching) and surface chemistry are shown to significantly delay marine biofouling. The fouling reduction mechanism is mainly due to the two effects: reduced effective settlement area and mechanical biocide. The insights gained from the work can be used to systematically design surfaces that reduce marine biofouling in various industrial settings.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/162819/3/admi202000672-sup-0001-SuppMat.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162819/2/admi202000672_am.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162819/1/admi202000672.pd

Concentrations of 137Cs^{137}Cs, 40K^{40}K radionuclides and some heavy metals in soil samples of Chochołowska Valley from Tatra National Park

This paper presents the results of determination of artificial $^{137}Cs$ and natural $^{40}K$ activity concentrations and some heavy metals in soil samples from the region of one of the main valleys of Tatra National Park (Chochołowska). Our investigation concentrated on $^{137}Cs$ and heavy metal levels in mountain soil taken from Chochołowska Valley, which revealed great variability in their concentration. The results show considerably small amounts of radionuclides $^{137}Cs$ and $^{40}K$ in the soils. Larger amounts of those elements can be found in the organic surface horizons of the soils. The evaluation of the content of those elements must be based on the bulk density analysis of the soil

The MuTHRE Model for High Quality Sub-seasonal Streamflow Forecasts

Conference theme 'Digital Water.'Sub-seasonal streamflow forecasts, with lead times up to 30 days, can provide valuable information for water management, including reservoir operation to meet environmental flow, irrigation demands, and managing flood protection storage. A key aim is to produce “seamless” probabilistic forecasts, with high quality performance across the full range of lead times (1-30 days) and time scales (daily to monthly). This paper demonstrates that the Multi-Temporal Hydrological Residual Error (MuTHRE) model can address the challenge of “seamless” sub-seasonal forecasting. The MuTHRE model is designed to capture key features of hydrological errors, namely seasonality, dynamic biases due to hydrological non-stationarity, and extreme errors poorly represented by the common Gaussian distribution. The MuTHRE model is evaluated comprehensively over 11 catchments in the MurrayDarling Basin using multiple performance metrics, across a range of lead times, months and years, and at daily and monthly time scales. It is shown to provide “high” improvements, in terms of reliability for short lead times (up to 10 days), in dry months, and dry years. Forecast performance also improved in terms of sharpness. Importantly, improvements are consistent across multiple time scales (daily and monthly). This study highlights the benefits of modelling multiple temporal characteristics of hydrological errors, and demonstrates the power of the MuTHRE model for producing seamless sub-seasonal streamflow forecasts that can be utilized for a wide range of applications.David McInerney, Mark Thyer, Dmitri Kavetski, Richard Laugesen, Narendra Tuteja, and George Kuczer

Particles at oil–air surfaces : powdered oil, liquid oil marbles, and oil foam

The type of material stabilized by four kinds of fluorinated particles (sericite and bentonite platelet clays and spherical zinc oxide) in air–oil mixtures has been investigated. It depends on the particle wettability and the degree of shear. Upon vigorous agitation, oil dispersions are formed in all the oils containing relatively large bentonite particles and in oils of relatively low surface tension (γla < 26 mN m⁻¹) like dodecane, 20 cS silicone, and cyclomethicone containing the other fluorinated particles. Particle-stabilized oil foams were obtained in oils having γla > 26 mN m⁻¹ where the advancing air–oil–solid contact angle θ lies between ca. 90° and 120°. Gentle shaking, however, gives oil-in-air liquid marbles with all the oil–particle systems except for cases where θ is <60°. For oils of tension >24 mN m⁻¹ with omniphobic zinc oxide and sericite particles for which advancing θ ≥ 90°, dry oil powders consisting of oil drops in air which do not leak oil could be made upon gentle agitation up to a critical oil:particle ratio (COPR). Above the COPR, catastrophic phase inversion of the dry oil powders to air-in-oil foams was observed. When sheared on a substrate, the dry oil powders containing at least 60 wt % of oil release the encapsulated oil, making these materials attractive formulations in the cosmetic and food industries

Paternally expressed imprinted genes under positive Darwinian selection in Arabidopsis thaliana

Genomic imprinting is an epigenetic phenomenon where autosomal genes display uniparental expression depending on whether they are maternally or paternally inherited. Genomic imprinting can arise from parental conflicts over resource allocation to the offspring, which could drive imprinted loci to evolve by positive selection. We investigate whether positive selection is associated with genomic imprinting in the inbreeding species Arabidopsis thaliana. Our analysis of 140 genes regulated by genomic imprinting in the A. thaliana seed endosperm demonstrates they are evolving more rapidly than expected. To investigate whether positive selection drives this evolutionary acceleration, we identified orthologs of each imprinted gene across 34 plant species and elucidated their evolutionary trajectories. Increased positive selection was sought by comparing its incidence among imprinted genes with non-imprinted controls. Strikingly, we find a statistically significant enrichment of imprinted paternally expressed genes (iPEGs) evolving under positive selection, 50.6% of the total, but no such enrichment for positive selection among imprinted maternally expressed genes (iMEGs). This suggests that maternally- and paternally-expressed imprinted genes are subject to different selective pressures. Almost all positively selected amino acids were fixed across 80 sequenced A. thaliana accessions, suggestive of selective sweeps in the A. thaliana lineage. The imprinted genes under positive selection are involved in processes important for seed development including auxin biosynthesis and epigenetic regulation. Our findings support a genomic imprinting model for plants where positive selection can affect paternally-expressed genes due to continued conflict with maternal sporophyte tissues, even when parental conflict is reduced in predominantly inbreeding species

Pharmacogenetic variants and risk of remdesivir-associated liver enzyme elevations in Million Veteran Program participants hospitalized with COVID-19

Remdesivir is the first US Food and Drug Administration (FDA)-approved drug for the treatment of coronavirus disease 2019 (COVID-19). We conducted a retrospective pharmacogenetic study to examine remdesivir-associated liver enzyme elevation among Million Veteran Program participants hospitalized with COVID-19 between March 15, 2020, and June 30, 2021. Pharmacogene phenotypes were assigned using Stargazer. Linear regression was performed on peak log-transformed enzyme values, stratified by population, adjusted for age, sex, baseline liver enzymes, comorbidities, and 10 population-specific principal components. Patients on remdesivir had higher peak alanine aminotransferase (ALT) values following treatment initiation compared with patients not receiving remdesivir. Remdesivir administration was associated with a 33% and 24% higher peak ALT in non-Hispanic White (NHW) and non-Hispanic Black (NHB) participants (p < 0.001), respectively. In a multivariable model, NHW CYP2C19 intermediate/poor metabolizers had a 9% increased peak ALT compared with NHW normal/rapid/ultrarapid metabolizers (p = 0.015); this association was not observed in NHB participants. In summary, remdesivir-associated ALT elevations appear to be multifactorial, and further studies are needed