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Background The advancement of hybrid sequencing technologies is increasingly expanding genome assemblies that are often annotated using hybrid sequencing transcriptomics, leading to improved genome characterization and the identification of novel genes and isoforms in a wide variety of organisms. Results We developed an easy-to-use genome-guided transcriptome annotation pipeline that uses assembled transcripts from hybrid sequencing data as input and distinguishes between coding and long non-coding RNAs by integration of several bioinformatic approaches, including gene reconciliation with previous annotations in GTF format. We demonstrated the efficiency of this approach by correctly assembling and annotating all exons from the chicken SCO-spondin gene (containing more than 105 exons), including the identification of missing genes in the chicken reference annotations by homology assignments. Conclusions Our method helps to improve the current transcriptome annotation of the chicken brain. Our pipeline, implemented on Anaconda/Nextflow and Docker is an easy-to-use package that can be applied to a broad range of species, tissues, and research areas helping to improve and reconcile current annotations. The code and datasets are publicly available at https://github.com/cfarkas/annotate_my_genomes

A density functional theory study was performed to analyse the interaction of COCl2 onto A-doped graphene nanosheets (AG, where A: Al, Si, Ti, Cr, Mn, Fe). Adsorption configurations, adsorption energies, electronic properties, and the interaction in a co-adsorption regime were characterised in detail for all the adsorbent-adsorbate complexes. The results show that these materials are excellent COCl2 adsorbents, with adsorption energies of up to 1.1 eV/molecule and remarkable changes in the electronic properties. The changes in the adsorption stability in a co-adsorption regime indicates that TiG and CrG are efficient adsorbents at low and high relative COCl2 concentrations; while, AlG, MnG and FeG will be efficient only at low relative COCl2 concentrations, where the adsorption stability per COCl2 molecule significantly decreases with respect to the single adsorption. Otherwise, the COCl2 adsorption and electronic response in aerobic environments was found to be suitable only for CrG and MnG, where the electronic response is based on the recognition of the [COCl2]δ+–dopant–[O2]δ− intermediate. This work allows to propose new graphene-based materials for the adsorption, filtration, and/or collection of toxic COCl2.

BackgroundWe aimed to further characterize and analyze in depth intra-host variation and founder variants of SARS-CoV-2 worldwide up until August 2020, by examining in excess of 94,000 SARS-CoV-2 viral sequences in order to understand SARS-CoV-2 variant evolution, how these variants arose and identify any increased mortality associated with these variants.Methods and FindingsWe combined worldwide sequencing data from GISAID and Sequence Read Archive (SRA) repositories and discovered SARS-CoV-2 hypermutation occurring in less than 2% of COVID19 patients, likely caused by host mechanisms involved APOBEC3G complexes and intra-host microdiversity. Most of this intra-host variation occurring in SARS-CoV-2 are predicted to change viral proteins with defined variant signatures, demonstrating that SARS-CoV-2 can be actively shaped by the host immune system to varying degrees. At the global population level, several SARS-CoV-2 proteins such as Nsp2, 3C-like proteinase, ORF3a and ORF8 are under active evolution, as evidenced by their increased πN/ πS ratios per geographical region. Importantly, two emergent variants: V1176F in co-occurrence with D614G mutation in the viral Spike protein, and S477N, located in the Receptor Binding Domain (RBD) of the Spike protein, are associated with high fatality rates and are increasingly spreading throughout the world. The S477N variant arose quickly in Australia and experimental data support that this variant increases Spike protein fitness and its binding to ACE2.ConclusionsSARS-CoV-2 is evolving non-randomly, and human hosts shape emergent variants with positive fitness that can easily spread into the population. We propose that V1776F and S477N variants occurring in the Spike protein are two novel mutations occurring in SARS-CoV-2 and may pose significant public health concerns in the future.Author SummaryWe have developed an efficient bioinformatics pipeline that has allowed us obtain the most complete picture to date of how the SARS-CoV-2 virus has changed during the last eight month global pandemic and will continue to change in the near future. We characterized the importance of the host immune response in shaping viral variants at different degrees, evidenced by hypermutation responses on SARS-CoV-2 in less than 2% of infections and positive selection of several viral proteins by geographical region. We underscore how human hosts are shaping emergent variants with positive fitness that can easily spread into the population, evidenced by variants V1176F and S477N, located in the stalk and receptor binding domains of the Spike protein, respectively. Variant V1176 is associated with increased mortality rates in Brazil and variant S477N is associated with increased mortality rates over the world. In addition, it has been experimentally demonstrated that S477N variant increase fitness of Spike protein and its binding with ACE2, thus predicting to increase virulence of SARS-CoV-2. This limits the concept of ‘herd immunity’ proposals and re-emphasize the need to limit the spread of the virus to avoid emergence of more virulent forms of SARS-CoV-2 that can spread worldwide.

Quaternary alkyl 2-phenylpyridinium and 2-(2,4-difluorophenyl)pyridinium amines with iodide, hexafluorophosphate and bis(trifluoromethylsulfonyl)imide anions have been fully characterized by 1H NMR, FT-IR and MALDI mass spectroscopic methods and studied by quantum chemistry calculations. The compounds with bis(trifluoromethylsulfonyl)imide anion can be classified as ionic liquids, because they melt at room temperature. The quaternary amines with iodide and hexafluorophosphate anions are solid at 25 °C. The X-ray diffraction characterization of the 2-(2,4-difluorophenyl)-1-methylphenylpyridinium hexafluorophosphate and 1-ethyl-2-(2,4-difluorophenyl)phenylpyridinium hexafluorophosphate show an extensive series of C H⋯F, C F⋯π and P F⋯π intermolecular interactions, which give rise to a supramolecular network. The relationship between the solid-state structures and the melting points is discussed by the evaluation of the thermal behavior based on experimental data from Differential Scanning Calorimetry (DSC) studies, and also using the analysis of the ion pairs binding energies. These new compounds based on phenylpyridine allow us to grow the diversity of ionic liquids and their crystalline salts, increasing the knowledge about the chemical and physical properties of these ionic species.

We provide a systematic ab initio study on the adsorption of 2-thiophene curcuminoid (2-thphCCM) molecules on a Au(111) surface. In this work we present the determination of the optimal configuration of a single molecule on the surface as well as a detailed study of the energetics of the different arrangements of two molecules considering their intermolecular interactions. We simulate the STM measurements associated with the optimal configuration and compare it with the experimental data.

Different polymorphs of Nb2O5 can be obtained depending on the pressure and temperature of calcination leading to different catalytic properties. Two polymorphs of niobia, T-Nb2O5 and B-Nb2O5, have been investigated by means of density functional/plane waves method. The equation of state predicted that B-Nb2O5 phase is more stable than the T-Nb2O5 at low temperature; however at high pressure both phases are stable. These results are in good agreement with the available experimental data. The calculated cohesive energies of 6.63 and 6.59 eV·atom–1 for the B-Nb2O5 and T-Nb2O5, respectively, also corroborate this conclusion, and it can be compared to the experimental value of 9.56 eV atom–1 estimated for the most thermodynamically stable phase. The topological analyses based on quantum theory of atoms in molecules (QTAIM) and electron localization function (ELF) were applied and reveal bonds with large ionic character for both phases. The B-Nb2O5 presented larger stiffness than T-Nb2O5, and the oxygen sites ...

Following a thermodynamics point of view, we analyzed a set of photosensitization mechanisms (energy transfer, electron transfer) given by seven reactions applied to porphyrin–ruthenium(II) complexes ( 1 – 6 ) and their fragments (ruthenium complexes: 7 – 12 ; porphyrin: 13 ) at the B3LYP/6–31G(d,p)/LANL2DZ level of theory in condensed phase (aqueous solution). We found that whereas for the fragments ( 7 – 13 ) an energy-transfer process between their first triplet excited state (T 1 ) and molecular oxygen ( 3 O 2 ) to yield singlet oxygen ( 1 O 2 ) is favored, the privileged channels for the photosensitizers ( 1 – 6 ) correspond to production of a superoxide anion radical (O 2 − ) by electron transfer between 3 O 2 and the photosensitizers (P) either in their P(T 1 ) excited state or as a radical anion P − . The reaction channels involving P − are more exergonic by 13–17 kcal/mol with respect to the process involving P(T 1 ). These results suggest that the anionic photosensitizer would likely acquire more importance for the photodamage in the cell.

The immobilization and removal of trivalent arsenic [As(III)] onto A-doped graphene (AG: AC93H24) nanoadsorbents with first-row transition metals (A: Sc Zn) was characterized by means of theoretical computations in the gas phase and in an explicit/implicit solvent media. In the gas phase, AG adsorbents have a high affinity toward As(III), with adsorption energies in the range of 1.2–2.0 eV, where the chemical acid-base interaction takes place mainly by bidentate surface complexation like in mineral surfaces. Moreover, the adsorption stability is improved at least 229% compared to the adsorption onto intrinsic graphene. The different binding abilities emerge from the interplay and balance between intermolecular electrostatic interactions and repulsive steric terms due to Pauli repulsion; the best adsorbents show high intermolecular electrostatic energies Eels (−0.4 eV), and low contributions of the repulsive steric terms as a result of the decrease in the number of 3d electrons. The analysis of the stability in the water model indicates that all the adsorbents (excepting ScG and ZnG) could be considered as remarkable potential adsorbents of trivalent arsenicals from aqueous sources at neutral pH, and mainly without the competition of water molecules by the adsorption active sites. The bidentate surface complexation is not affected underwater, and the chemisorption remains as the main adsorption mechanism whereby As(III) is immobilized. Therefore, doped graphene with first-row transition metals could be considered as a new class of remarkable nanoadsorbents for wastewater treatment and water purification, where in terms of energy saving, a pre-oxidation process to convert As(III) to As(V) is not required.