Polymorph Selection Research Articles

A mixture model for determining SARS-Cov-2 variant composition in pooled samples.

Despite of the fast development of highly effective vaccines to control the current COVID-19 pandemics, the unequal distribution and availability of these vaccines worldwide and the number of people infected in the world lead to the continuous emergence of Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) variants of concern. Therefore, it is likely that real-time genomic surveillance will be continuously needed as an unceasing monitoring tool, necessary to follow the spread of the disease and the evolution of the virus. In this context, new genomic variants of SARS-CoV-2, including variants refractory to current vaccines, makes genomic surveillance programs tools of utmost importance. Nevertheless, the lack of appropriate analytical tools to quickly and effectively access the viral composition in meta-transcriptomic sequencing data, including environmental surveillance, represent possible challenges that may impact the fast adoption of this approach to mitigate the spread and transmission of viruses. We propose a statistical model for the estimation of the relative frequencies of SARS-CoV-2 variants in pooled samples. This model is built by considering a previously defined selection of genomic polymorphisms that characterize SARS-CoV-2 variants. The methods described here support both raw sequencing reads for polymorphisms-based markers calling and predefined markers in the variant call format. Results obtained using simulated data show that our method is quite effective in recovering the correct variant proportions. Further, results obtained by considering longitudinal data from wastewater samples of two locations in Switzerland agree well with those describing the epidemiological evolution of COVID-19 variants in clinical samples of these locations. Our results show that the described method can be a valuable tool for tracking the proportions of SARS-CoV-2 variants in complex mixtures such as waste water and environmental samples. http://github.com/rvalieris/LCS. Supplementary data are available at Bioinformatics online.

Mineral Components of Scleractinian Coral Skeletons Cultured Without Symbionts

AbstractSkeletons of contemporary reef‐building scleractinian corals are formed of aragonite, a polymorph of the calcium carbonate (CaCO3), notwithstanding calcite being a more stable phase under the condition of coral habitats. Circumstances developing aragonite in coral calcification have been addressed currently. Considering that the symbiotic relationship between the coral host and dinoflagellate algae (zooxanthellae) is perhaps relevant to coral calcification, we studied the impact of these symbiotic relationships on CaCO3 polymorph selection. Juvenile scleractinian corals (Acropora tenuis and Acropora digitifera) absent symbionts were cultured in seawaters with varied Mg/Ca molar ratios (mMg/Ca), and the mineral phases of the skeletons were detected employing X‐ray diffraction. The findings revealed that diminutive quantities of calcite precipitated as coral skeleton in Acropora digitifera surprisingly in pseudo‐present seawater (mMg/Ca∼5). Additionally, coral developed skeletons from only calcite in seawater with an mMg/Ca < 1. The evidence gathered in this investigation suggests that the symbiotic relationship affects the establishment of aragonite skeletons in the course of coral calcification.

Experimental study of chromium (III) coprecipitation with calcium carbonate

Chromium (Cr) isotope compositions of marine carbonates have widely been used to trace the evolution of oxygen levels in the atmosphere and ocean during geological history. Recent studies have indicated that Cr found in natural carbonates is dominated by trivalent Cr, also known as Cr(III). However, the incorporation behavior of Cr(III) into carbonates remains undefined. Here, we conducted coprecipitation experiments for Cr(III) with calcium carbonate to constrain the behavior of Cr(III) in carbonate deposition environments. Extended X-ray absorption fine structure (EXAFS) results suggest that Cr(III) is incompatible with the calcite crystal lattice. There are likely to be several Cr species in the coprecipitation samples. Most Cr is adsorbed on the crystal surface of calcite or exists as amorphous Cr hydroxide[Cr(OH)3]. A small fraction of Cr can reside in the calcite crystal, but Cr3+ cannot directly substitute for Ca2+. It may exist in interstitial voids in crystals or occupy the position of Ca2+ in the form of divalent Cr hydroxide cation [Cr(OH)2+], leading to a distorted structure. Moreover, we find that Cr(III) can stimulate polymorph selection of vaterite [a metastable polymorph of calcium carbonate (CaCO3)] during CaCO3 precipitation, likely due to the formation of Cr hydroxide on the surface of vaterite crystals, hindering its transformation to calcite. Because Cr(III) is incompatible with the carbonate crystal lattice, we suggest that most Cr in natural carbonates is adsorbed on the crystal surface and may be acquired at water–sediment interfaces after carbonate precipitation. Therefore, Cr isotope compositions of carbonates may easily be affected by post-depositional diagenetic processes, and Cr isotope variations in sedimentary carbonates should not exclusively correspond to changes in oxygen levels in the atmosphere and ocean. Paleoenvironment reconstruction based on Cr isotope compositions of carbonates should take post-depositional processes into consideration.

Polymorph Selection in Zeolite Synthesis Occurs after Nucleation.

Zeolites are porous crystals with extensive polymorphism. The hydrothermal synthesis of zeolites is a multistage process involving amorphous precursors that evolve continuously in solubility and local order toward those of the crystal. These results pose several questions: Why does a first-order transition appear as a continuous transformation? At which stage is the polymorph selected? How large are the barriers and critical sizes for zeolite nucleation? Here we address these questions using nucleation theory with experimental data. We find that the nucleation barriers and critical zeolite nuclei are extremely small at temperatures of hydrothermal synthesis, resulting in spinodal-like crystallization that produces a mosaic of tiny zeolitic crystallites that compete to grow inside each glassy precursor nanoparticle. The subnanometer size of the critical nuclei reveals that the selection between zeolite polymorphs occurs after the nucleation stage, during the growth and coarsening of the crystals around the excluded volume of the structure-directing agents.

Conformational Selectivity and Evolution Affected by the Desolvation Process

The inconsistency between solution chemistry and the crystal structure indicates the potential conformational evolution and rearrangement during the nucleation process. However, the mechanism of how the conformation is selected to form the corresponding polymorph is still not clear due to the complicated crystallization environment. In this work, conformation and polymorph selectivity of three anhydrous forms of gabapentin were investigated. Quantum chemical computation was used to analyze gabapentin conformations in the solution state and explore their transformation pathway. Besides, visual molecular dynamics was adopted to calculate the structural difference of the conformers in solution and crystal states, which was closely related to conformational selectivity. Moreover, the effects of solvent types and the supersaturation on solute–solvent interactions were investigated by Fourier transform infrared spectra and molecular dynamics simulations. Combined with the outcome of rapid cooling experiments, it was found that the solute–solvent interaction may affect the difficulty of desolvation so as to affect the conformational selectivity before nucleation. A special evaporation experiment was designed to obtain the unstable polymorph of gabapentin. Finally, the possible mechanism of selective polymorph crystallization was proposed and analyzed.

Merging genotyping-by-sequencing data from two ex situ collections provides insights on the pea evolutionary history.

Pea (Pisum sativum L. subsp. sativum) is one of the oldest domesticated species and a widely cultivated legume. In this study, we combined next generation sequencing (NGS) data referring to two genotyping-by-sequencing (GBS) libraries, each one prepared from a different Pisum germplasm collection. The selection of single nucleotide polymorphism (SNP) loci called in both germplasm collections caused some loss of information; however, this did not prevent the obtainment of one of the largest datasets ever used to explore pea biodiversity, consisting of 652 accessions and 22 127 markers. The analysis of population structure reflected genetic variation based on geographic patterns and allowed the definition of a model for the expansion of pea cultivation from the domestication centre to other regions of the world. In genetically distinct populations, the average decay of linkage disequilibrium (LD) ranged from a few bases to hundreds of kilobases, thus indicating different evolutionary histories leading to their diversification. Genome-wide scans resulted in the identification of putative selective sweeps associated with domestication and breeding, including genes known to regulate shoot branching, cotyledon colour and resistance to lodging, and the correct mapping of two Mendelian genes. In addition to providing information of major interest for fundamental and applied research on pea, our work describes the first successful example of integration of different GBS datasets generated from ex situ collections – a process of potential interest for a variety of purposes, including conservation genetics, genome-wide association studies, and breeding.

On the mechanism of calcium carbonate polymorph selection via confinement.

Organisms deposit various biominerals in the course of their biomineralisation. The most abundant of these is calcium carbonate, which manifests itself in several polymorphs. While organisms possess the ability to control the specific polymorph deposited, the exact mechanism by which polymorph selection takes place is not yet fully understood. Because biominerals often grow within confined spaces, one of the suggested possibilities was that polymorph selection might be an outcome of confinement. Confining conditions have indeed been extensively shown to have a strong impact on the nucleation and crystal growth of calcium carbonate and, in particular, on its polymorph selection. However, despite numerous studies on the crystal growth of calcium carbonate in confined spaces, the mechanism of polymorph selection under confinement has not been elucidated. Herein, we discuss previously reported results and suggest a mechanistic explanation of the observed selective formation of calcite or aragonite or vaterite. We consider the possible effects of charged confining inner surfaces and of the sizes of the confining pores, and discuss whether the predominantly precipitating phase is amorphous calcium carbonate. We also discuss two possible scenarios of crystallization from amorphous calcium carbonate under conditions of confinement: via solid-state transformation or via a mechanism of dissolution-reprecipitation.

The role of the pre-exponential factor in determining the kinetic selection of polymorphs during solution crystallization of organic compounds

Domain diagram to nucleate metastable or stable form between polymorph pair based on pre-exponential factor values.

Genome-wide Studies of knee Osteoarthritis: Review

Background. Knee osteoarthritis (OA) is a multifactorial disease resulting from the interaction of many environmental, epigenetic and genetic risk factors, and the latter account for 40% to 65%. Genetic bases of the knee OA based on genome-wide association study (GWAS) are being actively studied by many scientific teams around the world. At the same time, the results obtained are often contradictory and ambiguous, as for the conducted replicative studies of knee OA. This dictates the need for additional replicative studies in various populations, including populations of Russia. The aim of the study was to analyze genome-wide studies of knee OA and to establish GWAS-significant polymorphic loci associated with OA. Materials and Methods. The search for publications was carried out in the electronic databases PubMed, PubMedCentral, eLIBRARY, in the GWAS catalog for the period from 2008 to the present by the keywords: knee osteoarthritis, GWAS studies, candidate genes. Results. Firstly, for the period from 2008 to 2021, 15 genome-wide studies of knee OA were performed (8 GWAS, 6 meta-analyzes of GWAS data, 1 study a combination of GWAS and meta-analysis of GWAS data), as a result of which 78 polymorphic loci were found associated with the risk of developing osteoarthritis of the knee joint at p510-08. Second ly, the vast majority of these loci (62 out of 78 SNPs, 79%) showed GWAS-significant associations with OA in meta-analyzes of GWAS data and only 16 loci (21%) in GWAS studies. Third ly, almost 95% of GWAS-significant loci for knee OA (74 SNPs) were found in samples of Caucasian origin. Fourthly, 21 out of 78 GWAS-significant SNPs are associated with isolated knee OA, and 57 SNPs are associated with knee, hip and hand OA (mixed sample). Fifth, all genome-wide studies of knee OA and meta-analyzes of GWAS data were carried out abroad on samples from various foreign populations, and samples from the Russian Federation were not included in these studies. Sixth, only two GWAS-significant polymorphic loci for OA (rs143384 of the GDF5 gene for knee OA isolated localization and rs3771501 of the TGFA gene for OA of any localization) were replicated at the whole genome level of significance (p510-08) in two different studies. Conclusion. The main genome-wide studies of knee OA were reviewed and GWAS-significant polymorphisms associated with OA were identified. The obtained materials on GWAS-significant loci can be used both in the selection of polymorphisms in replicative studies of OA in various populations of Russia, and for expanding the understanding of the molecular genetic mechanisms of the disease development.

Genetic Polymorphism and Natural Selection of Apical Membrane Antigen-1 in Plasmodium falciparum Isolates from Vietnam.

Apical membrane antigen-1 of Plasmodium falciparum (PfAMA-1) is a leading malaria vaccine candidate antigen. However, the genetic diversity of pfama-1 and associated antigenic variation in global P. falciparum field isolates are major hurdles to the design of an efficacious vaccine formulated with this antigen. Here, we analyzed the genetic structure and the natural selection of pfama-1 in the P. falciparum population of Vietnam. A total of 37 distinct haplotypes were found in 131 P. falciparum Vietnamese isolates. Most amino acid changes detected in Vietnamese pfama-1 were localized in the ectodomain, domains I, II, and III. Overall patterns of major amino acid changes in Vietnamese pfama-1 were similar to those of global pfama-1, but the frequencies of the amino acid changes slightly differed by country. Novel amino acid changes were also identified in Vietnamese pfama-1. Vietnamese pfama-1 revealed relatively lower genetic diversity than currently analyzed pfama-1 in other geographical regions, and suggested a distinct genetic differentiation pattern. Evidence for natural selection was detected in Vietnamese pfama-1, but it showed purifying selection unlike the global pfama-1 analyzed so far. Recombination events were also found in Vietnamese pfama-1. Major amino acid changes that were commonly identified in global pfama-1 were mainly localized to predicted B-cell epitopes, RBC-binding sites, and IUR regions. These results provide important information for understanding the genetic nature of the Vietnamese pfama-1 population, and have significant implications for the design of a vaccine based on PfAMA-1.

Polymorph selection of magnesium under different pressures: A simulation study

Molecular dynamics simulations were used to investigate the influence of pressure on the structural properties and dynamics of magnesium (Mg) during rapid solidification. The dynamics analysis revealed that, with an increase in pressure, the dynamics of Mg melt slowed down sharply and the dynamical heterogeneities increased, leading to a denser structure. Atom-level structural analysis using the cluster-type index method suggested that the predominant structure transformed from hexagonal closed-packed to face-centered cubic with increasing pressure from 0 GPa to 5 GPa, and then transformed to the A15 complex crystal structure as the pressure increased above 10 GPa. In addition, the nature of polymorph selection was investigated by analyzing the phonon dispersion of Mg under different pressures. These findings provide a novel insight into polymorphic transitions of Mg under pressure and guide the selection of Mg polymorphs for practical applications.

Population genetic analysis of the Plasmodium falciparum erythrocyte binding antigen-175 (EBA-175) gene in Equatorial Guinea

BackgroundPlasmodium falciparum erythrocyte binding antigen-175 (PfEBA-175) is a candidate antigen for a blood-stage malaria vaccine, while various polymorphisms and dimorphism have prevented to development of effective vaccines based on this gene. This study aimed to investigate the dimorphism of PfEBA-175 on both the Bioko Island and continent of Equatorial Guinea, as well as the genetic polymorphism and natural selection of global PfEBA-175.MethodsThe allelic dimorphism of PfEBA-175 region II of 297 bloods samples from Equatorial Guinea in 2018 and 2019 were investigated by nested polymerase chain reaction and sequencing. Polymorphic characteristics and the effect of natural selection were analyzed using MEGA 7.0, DnaSP 6.0 and PopART programs. Protein function prediction of new amino acid mutation sites was performed using PolyPhen-2 and Foldx program.ResultsBoth Bioko Island and Bata district populations, the frequency of the F-fragment was higher than that of the C-fragment of PfEBA-175 gene. The PfEBA-175 of Bioko Island and Bata district isolates showed a high degree of genetic variability and heterogeneity, with π values of 0.00407 & 0.00411 and Hd values of 0.958 & 0.976 for nucleotide diversity, respectively. The values of Tajima's D of PfEBA-175 on Bata district and Bioko Island were 0.56395 and − 0.27018, respectively. Globally, PfEBA-175 isolates from Asia were more diverse than those from Africa and South America, and genetic differentiation quantified by the fixation index between Asian and South American countries populations was significant (FST > 0.15, P < 0.05). A total of 310 global isolates clustered in 92 haplotypes, and only one cluster contained isolates from three continents. The mutations A34T, K109E, D278Y, K301N, L305V and D329N were predicted as probably damaging.ConclusionsThis study demonstrated that the dimorphism of F-fragment PfEBA-175 was remarkably predominant in the study area. The distribution patterns and genetic diversity of PfEBA-175 in Equatorial Guinea isolates were similar another region isolates. And the levels of recombination events suggested that natural selection and intragenic recombination might be the main drivers of genetic diversity in global PfEBA-175. These results have important reference value for the development of blood-stage malaria vaccine based on this antigen.

Crystallisation and polymorph selection in active Brownian particles

We explore crystallisation and polymorph selection in active Brownian particles with numerical simulation. In agreement with previous work (Wysocki et al. in Europhys Lett 105:48004, 2014), we find that crystallisation is suppressed by activity and occurs at higher densities with increasing Péclet number ({ Pe }). While the nucleation rate decreases with increasing activity, the crystal growth rate increases due to the accelerated dynamics in the melt. As a result of this competition, we observe the transition from a nucleation and growth regime at high { Pe } to “spinodal nucleation” at low { Pe }. Unlike the case of passive hard spheres, where preference for FCC over HCP polymorphs is weak, activity causes the annealing of HCP stacking faults, thus strongly favouring the FCC symmetry at high { Pe }. When freezing occurs more slowly, in the nucleation and growth regime, this tendency is much reduced and we see a trend towards the passive case of little preference for either polymorph.

Effect of Polymer Nano- and Microparticles on Calcium Carbonate Crystallization.

Molecular and macromolecular templates are known to affect the shape, size, and polymorph selectivity on the biomineralization of calcium carbonate (CaCO3). Micro- and nanoparticles of common polymers present in the environment are beginning to show toxicity in living organisms. In this study, the role of plastic nanoparticles in the biomineralization of CaCO3 is explored to understand the ecological impact of plastic pollution. As a model study, luminescent poly(methyl methacrylate) nanoparticles (PMMA-NPs) were prepared using the nanoprecipitation method, fully characterized, and used for the mineralization experiments to understand their influence on nucleation, morphology, and polymorph selectivity of CaCO3 crystals. The PMMA-NPs induced calcite crystal nucleation with spherical morphologies at high concentrations. Microplastic particles collected from a commercial face scrub were also used for CaCO3 nucleation to observe the nucleation of calcite crystals on the particle surface. Microscopic, spectroscopic, and X-ray diffraction data were used to characterize and identify the nucleated crystals. The data presented in this paper add more information on the impact of microplastics on the marine environment.

Positive Selection of Transcription Factors Is a Prominent Feature of the Evolution of a Plant Pathogenic Genus Originating in the Miocene.

Tests based on the dN/dS statistic are used to identify positive selection of nonsynonymous polymorphisms. Using these tests on alignments of all orthologs from related species can provide insights into which gene categories have been most frequently positively selected. However, longer alignments have more power to detect positive selection, creating a detection bias that could create misleading results from functional enrichment tests. Most studies of positive selection in plant pathogens focus on genes with specific virulence functions, with little emphasis on broader molecular processes. Furthermore, no studies in plant pathogens have accounted for detection bias due to alignment length when performing functional enrichment tests. To address these research gaps, we analyze 12 genomes of the phytopathogenic fungal genus Botrytis, including two sequenced in this study. To establish a temporal context, we estimated fossil-calibrated divergence times for the genus. We find that Botrytis likely originated 16–18 Ma in the Miocene and underwent continuous radiation ending in the Pliocene. An untargeted scan of Botrytis single-copy orthologs for positive selection with three different statistical tests uncovered evidence for positive selection among proteases, signaling proteins, CAZymes, and secreted proteins. There was also a strong overrepresentation of transcription factors among positively selected genes. This overrepresentation was still apparent after two complementary controls for detection bias due to sequence length. Positively selected sites were depleted within DNA-binding domains, suggesting changes in transcriptional responses to internal and external cues or protein–protein interactions have undergone positive selection more frequently than changes in promoter fidelity.

A Novel Single Next-Generation Sequencing (NGS) Approach for the Molecular Karyotyping and Genotyping of Patients with Myelodysplastic Syndromes

Myelodysplastic Syndromes (MDS) are a heterogeneous group of diseases, characterized by the clonal acquisition of somatic point mutations and chromosomal alterations. Conventional karyotyping remains one of the most important tools for MDS diagnosis because several cytogenetics abnormalities can be used to stratify patients into subtypes with different prognoses. However, a non-informative cytogenetics due to normal or unsuccessful karyotype could lead to an erroneous estimation of the prognostic risk. To overcome this drawback, we assessed the reliability of a single Next-Generation Sequencing (NGS) assay to simultaneously detect Single Nucleotide Variations (SNVs), including small indels, as well as Copy Number Alterations (CNAs) and copy-neutral Loss of Heterozygosity (cnLOH) for diagnostic application.We combined a custom panel, targeting 40 genes frequently implicated in myeloid neoplasms, with a target enrichment design (OneSeq, Agilent®), having a genome-wide backbone resolution of 1 Mb and 10 Mb for CNAs and cnLOH, respectively. Sequencing libraries were prepared following the “SureSelectQXT Library Prep” protocol and sequenced using the NextSeq 500 platform (Illumina®). Data processing and variant annotation were performed using an integrated in-house bioinformatic pipeline. SNVs and small indels were selected based on allele frequency (VAF ≥ 3%), their absence in the healthy population (UCSC Common SNP; MAF < 1%) and their putative effect on splicing and protein. For CNAs and cnLOH detection, we combined the analysis of the sequencing depth, using the DECoN tool, with the B-allele frequency (BAF) for a selection of high minor allele frequency single nucleotide polymorphisms. The CNA pathogenicity was evaluated taking into account gene content, frequency in the general population (e.g . Database of Genomic Variants) and reports in the literature.We performed a pilot study with a cohort of 30 patients clinically diagnosed with primary MDS at La Fe University Hospital in Valencia. Samples were analysed in parallel by NGS and CytoScanTM HD array (Affymetrix®) in order to establish criteria and thresholds for accurate filtering of sequencing data, especially for CNA identification and calculation of analytical sensitivity. Currently, we are evaluating the reliability of these criteria in a separate cohort of 30 additional patients.Preliminary results in the test cohort showed that we were able to identify at least one point mutation in 29 of 30 patients, with an average of 2 mutations per sample (range 0-7). Mutations were detected in 20 of the 40 genes covered in the panel. The epigenetic modifier TET2 was the most frequently mutated gene in the cohort (9 of 30 cases), followed by two splicing genes, SF3B1 and SRSF2 (each 8 of 30). In addition, we observed some of the described gene correlations, such as the co-occurrence of mutations in IDH2 and SRSF2 genes and the mutually exclusive presence of SF3B1 and SRSF2 .Although cytogenetic studies identified chromosomal abnormalities in 9 of 30 of cases, the number of MDS-related copy number changes detected by sequencing increased to 20 cases, including 9 with normal and 1 with unsuccessful karyotype. We observed the frequent CNAs, such as chromosome 5q and 7q deletions, 4 and 3 cases, respectively, the complete duplication of chr21 in 1 case and 9 cnLOH events. Interestingly, in patients with normal karyotype, although we focused on large chromosomal abnormalities, we have detected at least 3 small events (6-14 Mb) leading to focal deletions of ETV6, BTG1 and RUNX1 genes, as well as 6 cnLOH events, 2 of which involved chr7q22q36.We obtained a high level of concordance between clinical relevant CNAs larger than 1 Mb identified by the CytoScanTM HD array and our sequencing approach. However, the variation in probe distribution in the two backbones was responsible for differences in the detected sizes of deletions and duplications in ~10% of the observed CNAs.This NGS strategy allowed the identification of point mutations and large chromosomal alterations with a resolution of 1 Mb using a single assay, as well as other alterations invisible to conventional cytogenetics, such as cnLOH. Although automating the bioinformatic pipeline is still ongoing, this study demonstrated that a comprehensive NGS-based genomic approach could contribute to improve MDS diagnosis and prognosis. DisclosuresSanz:Gamida Cell: Research Funding.

Lowering Ternary Oxide Synthesis Temperatures by Solid-State Cometathesis Reactions

Low-temperature synthesis routes are necessary for selectively synthesizing many metastable solid-state materials. Here, we identify a cooperative effect that starting materials have in lowering temperatures in solid-state metathesis reactions by studying the formation of yttrium manganese oxide. Previous studies have shown that YMnO3 can be synthesized by ternary metathesis with an alkali halide being produced as a secondary product. In this contribution, we show that by using alkaline earth metals instead of alkali metals, the polymorph selectivity of the reaction is changed, as orthorhombic YMnO3 forms at lower temperatures than the hexagonal polymorph. Reactions were studied using ex post facto synchrotron X-ray diffraction. These experiments reveal that reactions using alkaline earth manganese oxides as a starting material require high temperatures to progress. Reaction temperatures can be lowered from 700 to 550 °C while maintaining phase selectivity by reacting both MgMn2O4 and CaMn2O4 with YOCl in a cooperative “cometathesis” reaction. The nascent halide salts appear to improve the reaction kinetics. Since the onset temperature for YMnO3 formation falls 50 °C below the MgCl2–CaCl2 liquidus, the enhanced reactivity is consistent with the surface melting of a nasscent salt byproduct at the interfaces. Cometathesis routes have similar phase selectivity and temperature reduction in reactions that form TbMnO3, ErMnO3, and DyMnO3. Cometathesis lowers reaction temperatures while preserving the reaction selectivity of the end members, making it a valuable approach for synthesizing metastable targets.

Tuning Polymorphs and Morphology of Microbially Induced Calcium Carbonate: Controlling Factors and Underlying Mechanisms.

Microbially precipitated calcium carbonate (CaCO3) has drawn broad attention due to its potential applications in various areas, for example, biocementation, medicine, and soil reinforcement. Sporosarcina pasteurii (S. pasteurii), formerly known as Bacillus pasteurii, has been investigated for CaCO3 biomineralization due to its high ureolytic activity. A high degree of supersaturation with respect to the presence of bacterial cell wall, extracellular polymeric substances, and organic byproducts of bacterial activity plays an important role in the formation and stabilization of CaCO3 polymorphs. Although microbially induced CaCO3 and its polymorphs have been investigated broadly, the mechanisms of polymorph selection and morphological evolution are not well understood. This study employs ex situ approaches to address the complication of biomineralization in the presence of living organisms and to elucidate how solution chemistry, bacterial activity, and precipitation kinetics alter the polymorphism and morphology of CaCO3 induced by S. pasteurii. The results indicate that in the presence of enough calcium ions and urea (as a carbonate source), the bacterial activity favors the formation and stabilization of vaterite. The morphological observations also provide valuable information on the particles’ microstructure. The morphology of calcite evolves from single crystal to polycrystalline structures, and the morphology of vaterite evolved from spherical to oval-shaped structures on increasing the organic material concentration. Specific functional groups also exert morphological control on CaCO3 polymorphs. However, the sensitivity of the calcite polymorph to the composition and orientation of these functional groups is higher compared to that of the vaterite polymorph. These findings offer important insights that can be used to constrain a set of experimental conditions for synthesizing a certain polymorph ratio for vaterite/calcite or a particular morphology of each polymorph and shed light on the crystallization and phase transformation mechanisms in such complicated bioenvironments.

Assessing single-nucleotide polymorphism selection methods for the development of a low-density panel optimized for imputation in South African Drakensberger beef cattle.

A major obstacle in applying genomic selection (GS) to uniquely adapted local breeds in less-developed countries has been the cost of genotyping at high densities of single-nucleotide polymorphisms (SNP). Cost reduction can be achieved by imputing genotypes from lower to higher densities. Locally adapted breeds tend to be admixed and exhibit a high degree of genomic heterogeneity thus necessitating the optimization of SNP selection for downstream imputation. The aim of this study was to quantify the achievable imputation accuracy for a sample of 1,135 South African (SA) Drakensberger cattle using several custom-derived lower-density panels varying in both SNP density and how the SNP were selected. From a pool of 120,608 genotyped SNP, subsets of SNP were chosen (1) at random, (2) with even genomic dispersion, (3) by maximizing the mean minor allele frequency (MAF), (4) using a combined score of MAF and linkage disequilibrium (LD), (5) using a partitioning-around-medoids (PAM) algorithm, and finally (6) using a hierarchical LD-based clustering algorithm. Imputation accuracy to higher density improved as SNP density increased; animal-wise imputation accuracy defined as the within-animal correlation between the imputed and actual alleles ranged from 0.625 to 0.990 when 2,500 randomly selected SNP were chosen vs. a range of 0.918 to 0.999 when 50,000 randomly selected SNP were used. At a panel density of 10,000 SNP, the mean (standard deviation) animal-wise allele concordance rate was 0.976 (0.018) vs. 0.982 (0.014) when the worst (i.e., random) as opposed to the best (i.e., combination of MAF and LD) SNP selection strategy was employed. A difference of 0.071 units was observed between the mean correlation-based accuracy of imputed SNP categorized as low (0.01 < MAF ≤ 0.1) vs. high MAF (0.4 < MAF ≤ 0.5). Greater mean imputation accuracy was achieved for SNP located on autosomal extremes when these regions were populated with more SNP. The presented results suggested that genotype imputation can be a practical cost-saving strategy for indigenous breeds such as the SA Drakensberger. Based on the results, a genotyping panel consisting of ~10,000 SNP selected based on a combination of MAF and LD would suffice in achieving a <3% imputation error rate for a breed characterized by genomic admixture on the condition that these SNP are selected based on breed-specific selection criteria.

Obesity-related genetic determinants of stroke.

As obesity, circulating lipids and other vascular/metabolic factors influence the risk of stroke, we examined if genetic variants associated with these conditions are related to risk of stroke using a case-control study in Galicia, Spain. A selection of 200 single-nucleotide polymorphisms previously found to be related to obesity, body mass index, circulating lipids, type 2 diabetes, heart failure, obesity-related cancer and cerebral infarction were genotyped in 465 patients diagnosed with stroke and 480 population-based controls. An unsupervised Lasso regression procedure was carried out for single-nucleotide polymorphism selection based on their potential effect on stroke according to obesity. Selected genotypes were further analysed through multivariate logistic regression to study their association with risk of stroke. Using unsupervised selection procedures, nine single-nucleotide polymorphisms were found to be related to risk of stroke overall and after stratification by obesity. From these, rs10761731, rs2479409 and rs6511720 in obese subjects [odds ratio (95% confidence interval) = 0.61 (0.39-0.95) (P = 0.027); 0.54 (0.35-0.84) (P = 0.006) and 0.42 (0.22-0.80) (P = 0.0075), respectively], and rs865686 in non-obese subjects [odds ratio (95% confidence interval) = 0.67 (0.48-0.94) (P = 0.019)], were independently associated with risk of stroke after multivariate logistic regression procedures. The associations between the three single-nucleotide polymorphisms found to be associated with stroke risk in obese subjects were more pronounced among females; for rs10761731, odds ratios among obese males and females were 1.07 (0.58-1.97) (P = 0.84), and 0.31 (0.14-0.69) (P = 0.0018), respectively; for rs2479409, odd ratios were 0.66 (0.34-1.27) (P = 0.21), and 0.49 (0.24-0.99) (P = 0.04), for obese males and females, respectively; the stroke-rs6511720 association was also slightly more pronounced among obese females, odds ratios were 0.33 (0.13-0.87) (P = 0.022), and 0.28 (0.09-0.85) (P = 0.02) for obese males and females, respectively. The rs865686-stroke association was more pronounced among non-obese males [odds ratios = 0.61 (0.39-0.96) (P = 0.029) and 0.72 (0.42-1.22) (P = 0.21), for non-obese males and females, respectively]. A combined genetic score of variants rs10761731, rs2479409 and rs6511720 was highly predictive of stroke risk among obese subjects (P = 2.04 × 10-5), particularly among females (P = 4.28 × 10-6). In summary, single-nucleotide polymorphisms rs1076173, rs2479409 and rs6511720 were found to independently increase the risk of stroke in obese subjects after adjustment for established risk factors. A combined score with the three genomic variants was an independent predictor of risk of stroke among obese subjects in our population.