Polymorphism Discovery Research Articles

QTL mapping provides new insights into emamectin benzoate resistance in salmon lice, Lepeophtheirus salmonis

BackgroundThe salmon louse (Lepeophtheirus salmonis) is a parasite of wild and farmed salmonid fish, causing huge economic damage to the commercial farming of Atlantic salmon (Salmo salar) in the northern hemisphere. The avermectin emamectin benzoate (EMB) is widely used for salmon delousing. While resistance to EMB is widespread in Atlantic populations of L. salmonis, the molecular mechanisms of resistance remain to be elucidated. The aim of the present work was to obtain insights into potential EMB resistance mechanisms by identifying genetic and transcriptomic markers associated with EMB resistance.ResultsCrosses were performed between EMB-susceptible and -resistant L. salmonis, sourced from two parental strains isolated in Scotland, producing fully pedigreed families. The EMB susceptibility of individual parasites was characterised using time-to-response bioassays. Parasites of two families were subjected to double digest restriction site-associated DNA sequencing (ddRAD-seq) for simultaneous discovery of single nucleotide polymorphisms (SNPs) and genotyping. Data analysis revealed that EMB resistance is associated with one quantitative trait locus (QTL) region on L. salmonis chromosome 5. Marker-trait association was confirmed by genotyping assays for 7 SNPs in two additional families. Furthermore, the transcriptome of male parasites of the EMB-susceptible and -resistant L. salmonis parental strains was assessed. Among eighteen sequences showing higher transcript expression in EMB-resistant as compared to drug-susceptible lice, the most strongly up-regulated gene is located in the above QTL region and shows high homology to β spectrin, a cytoskeleton protein that has roles in neuron architecture and function. Further genes differentially regulated in EMB-resistant lice include a glutathione S-transferase (GST), and genes coding for proteins with predicted roles in mitochondrial function, intracellular signalling or transcription.ConclusionsMajor determinants of EMB resistance in L. salmonis are located on Chromosome 5. Resistance can be predicted using a limited number of genetic markers. Genes transcriptionally up-regulated in EMB resistant parasites include a β spectrin, a cytoskeletal protein with still incompletely understood roles in neuron structure and function, as well as glutathione S-transferase, an enzyme with potential roles in the biochemical defence against toxicants.

AI-enabled pipeline for virus detection, validation, and SNP discovery from next-generation sequencing data.

The rapid and accurate detection of viruses and the discovery of single nucleotide polymorphisms (SNPs) are critical for disease management and understanding viral evolution. This study presents a pipeline for virus detection, validation, and SNP discovery from next-generation sequencing (NGS) data. The pipeline processes raw sequencing data to identify viral sequences with high accuracy and sensitivity by integrating state-of-the-art bioinformatics tools with artificial intelligence. Before aligning the reads to the reference genomes, quality control measures, and adapter trimming are performed to ensure the integrity of the data. Unmapped reads are subjected to de novo assembly to reveal novel viral sequences and genetic elements. The effectiveness of the pipeline is demonstrated by the identification of virus sequences, illustrating its potential for detecting known and emerging pathogens. SNP discovery is performed using a custom Python script that compares the entire population of sequenced viral reads to a reference genome. This approach provides a comprehensive overview of viral genetic diversity and identifies dominant variants and a spectrum of genetic variations. The robustness of the pipeline is confirmed by the recovery of complete viral sequences, which improves our understanding of viral genomics. This research aims to develop an auto-bioinformatics pipeline for novel viral sequence discovery, in vitro validation, and SNPs using the Python (AI) language to understand viral evolution. This study highlights the synergy between traditional bioinformatics techniques and modern approaches, providing a robust tool for analyzing viral genomes and contributing to the broader field of viral genomics.

Discovery and Selective Nucleation of Polymorphs of Flexible GABA Molecules: Solvation Effects and Conformational Rearrangement

Discovery and Selective Nucleation of Polymorphs of Flexible GABA Molecules: Solvation Effects and Conformational Rearrangement

Monoclinic LaSb2 Superconducting Thin Films.

Rare-earth diantimondes exhibit coupling between structural and electronic orders, which are tunable under pressure and temperature. Here we present the discovery of a new polymorph of LaSb2 stabilized in thin films synthesized using molecular beam epitaxy. Using diffraction, electron microscopy, and first-principles calculations we identify a YbSb2-type monoclinic lattice as a yet-uncharacterized stacking configuration. The material hosts superconductivity with a Tc = 2 K, which is enhanced relative to the bulk ambient phase, and a long superconducting coherence length of 1730 Å. This result highlights the potential thin film growth has in stabilizing novel stacking configurations in quasi-two-dimensional compounds with competing layered structures.

Discovery of a New Polymorph of 5-Methoxy-1H-Indole-2-Carboxylic Acid: Characterization by X-ray Diffraction, Infrared Spectroscopy, and DFT Calculations.

This study presents a new 5-methoxy-1H-indole-2-carboxylic acid (MI2CA) polymorph investigated by single-crystal X-ray diffraction, infrared spectroscopy, and density functional theory (ωB97X-D) calculations employing two basis sets (6-31++G(d,p) and aug-cc-pVTZ). The compound crystallizes in the monoclinic system, space group P21/c (a = 4.0305(2) Å, b = 13.0346(6) Å, c = 17.2042(9) Å, β = 91.871(5)°, Z = 4). In the crystalline structure, the formation of cyclic dimers via double hydrogen bonds O-H⋯O between MI2CA molecules was observed. Interactions between the NH groups of the indole rings and the adjacent methoxy groups, as well as C-H⋯O contacts, significantly influence the spatial arrangement of molecules. The results from DFT calculations, including dimeric and trimeric structures, agree well with the experimental structural and spectroscopic data. Analysis of the infrared spectra confirms the conclusions drawn from X-ray diffraction studies and reveals differences between the IR spectra of the newly obtained polymorph and that reported earlier in the literature. This comprehensive study sheds some light on the MI2CA polymorphism and is important for a potential pharmacological applications of this compound.

Detection of rare variants among nuclei populating the arbuscular mycorrhizal fungal model species Rhizophagus irregularis DAOM197198.

Identifying genuine polymorphic variants is a significant challenge in sequence data analysis, although detecting low-frequency variants in sequence data is essential for estimating demographic parameters and investigating genetic processes, such as selection, within populations. Arbuscular mycorrhizal (AM) fungi are multinucleate organisms, in which individual nuclei collectively operate as a population, and the extent of genetic variation across nuclei has long been an area of scientific interest. In this study, we investigated the patterns of polymorphism discovery and the alternate allele frequency distribution by comparing polymorphism discovery in 2 distinct genomic sequence datasets of the AM fungus model species, Rhizophagus irregularis strain DAOM197198. The 2 datasets used in this study are publicly available and were generated either from pooled spores and hyphae or amplified single nuclei from a single spore. We also estimated the intraorganismal variation within the DAOM197198 strain. Our results showed that the 2 datasets exhibited different frequency patterns for discovered variants. The whole-organism dataset showed a distribution spanning low-, intermediate-, and high-frequency variants, whereas the single-nucleus dataset predominantly featured low-frequency variants with smaller proportions in intermediate and high frequencies. Furthermore, single nucleotide polymorphism density estimates within both the whole organism and individual nuclei confirmed the low intraorganismal variation of the DAOM197198 strain and that most variants are rare. Our study highlights the methodological challenges associated with detecting low-frequency variants in AM fungal whole-genome sequence data and demonstrates that alternate alleles can be reliably identified in single nuclei of AM fungi.

Crystal size, shape, and conformational changes drive both the disappearance and reappearance of ritonavir polymorphs in the mill

Organic compounds can crystallize in different forms known as polymorphs. Discovery and control of polymorphism is crucial to the pharmaceutical industry since different polymorphs can have significantly different physical properties which impacts their utilization in drug delivery. Certain polymorphs have been reported to 'disappear' from the physical world, irreversibly converting to new ones. These unwanted polymorph conversions, initially prevented by slow nucleation kinetics, are eventually observed driven by significant gains in thermodynamic stabilities. The most infamous of these cases is that of the HIV drug ritonavir (RVR): Once its reluctant form was unwillingly nucleated for the first time, its desired form could no longer be produced with the same manufacturing process. Here we show that RVR's extraordinary disappearing polymorph as well as its reluctant form can be consistently produced by ball-milling under different environmental conditions. We demonstrate that the significant difference in stability between its polymorphs can be changed and reversed in the mill-a process we show is driven by crystal size as well as crystal shape and conformational effects. We also show that those effects can be controlled through careful design of milling conditions since they dictate the kinetics of crystal breakage, dissolution, and growth processes that eventually lead to steady-state crystal sizes and shapes in the mill. This work highlights the huge potential of mechanochemistry in polymorph discovery of forms initially difficult to nucleate, recovery of disappearing polymorphs, and polymorph control of complex flexible drug compounds such as RVR.

Phase Identification and Discovery of an Elusive Polymorph of Drug‐Polymer Inclusion Complex Using Automated 3D Electron Diffraction

Abstract3D electron diffraction (3D ED) has shown great potential in crystal structure determination in materials, small organic molecules, and macromolecules. In this work, an automated, low‐dose and low‐bias 3D ED protocol has been implemented to identify six phases from a multiple‐phase melt‐crystallisation product of an active pharmaceutical ingredient, griseofulvin (GSF). Batch data collection under low‐dose conditions using a widely available commercial software was combined with automated data analysis to collect and process over 230 datasets in three days. Accurate unit cell parameters obtained from 3D ED data allowed direct phase identification of GSF Forms III, I and the known GSF inclusion complex (IC) with polyethylene glycol (PEG) (GSF‐PEG IC‐I), as well as three minor phases, namely GSF Forms II, V and an elusive new phase, GSF‐PEG IC‐II. Their structures were then directly determined by 3D ED. Furthermore, we reveal how the stabilities of the two GSF‐PEG IC polymorphs are closely related to their crystal structures. These results demonstrate the power of automated 3D ED for accurate phase identification and direct structure determination of complex, beam‐sensitive crystallisation products, which is significant for drug development where solid form screening is crucial for the overall efficacy of the drug product.

Phase Identification and Discovery of an Elusive Polymorph of Drug-Polymer Inclusion Complex Using Automated 3D Electron Diffraction.

3D electron diffraction (3D ED) has shown great potential in crystal structure determination in materials, small organic molecules, and macromolecules. In this work, an automated, low-dose and low-bias 3D ED protocol has been implemented to identify six phases from a multiple-phase melt-crystallisation product of an active pharmaceutical ingredient, griseofulvin (GSF). Batch data collection under low-dose conditions using a widely available commercial software was combined with automated data analysis to collect and process over 230 datasets in three days. Accurate unit cell parameters obtained from 3D ED data allowed direct phase identification of GSF Forms III, I and the known GSF inclusion complex (IC) with polyethylene glycol (PEG) (GSF-PEG IC-I), as well as three minor phases, namely GSF Forms II, V and an elusive new phase, GSF-PEG IC-II. Their structures were then directly determined by 3D ED. Furthermore, we reveal how the stabilities of the two GSF-PEG IC polymorphs are closely related to their crystal structures. These results demonstrate the power of automated 3D ED for accurate phase identification and direct structure determination of complex, beam-sensitive crystallisation products, which is significant for drug development where solid form screening is crucial for the overall efficacy of the drug product.

High-pressure minerals and new lunar mineral changesite-(Y) in Chang’e-5 regolith

Forty-five years after the Apollo and Luna missions, China’s Chang’e-5 (CE-5) mission collected ∼1.73 kg of new lunar materials from one of the youngest basalt units on the Moon. The CE-5 lunar samples provide opportunities to address some key scientific questions related to the Moon, including the discovery of high-pressure silica polymorphs (seifertite and stishovite) and a new lunar mineral, changesite-(Y). Seifertite was found to be coexist with stishovite in a silica fragment from CE-5 lunar regolith. This is the first confirmed seifertite in returned lunar samples. Seifertite has two space group symmetries (Pnc2 and Pbcn) and formed from an α-cristobalite-like phase during “cold” compression during a shock event. The aftershock heating process changes some seifertite to stishovite. Thus, this silica fragment records different stages of an impact process, and the peak shock pressure is estimated to be ∼11 to 40 GPa, which is much lower than the pressure condition for coexistence of seifertite and stishovite on the phase diagram. Changesite-(Y), with ideal formula (Ca8Y)□Fe2+(PO4)7 (where □ denotes a vacancy) is the first new lunar mineral to be discovered in CE-5 regolith samples. This newly identified phosphate mineral is in the form of columnar crystals and was found in CE-5 basalt fragments. It contains high concentrations of Y and rare earth elements (REE), reaching up to ∼14 wt. % (Y,REE)2O3. The occurrence of changesite-(Y) marks the late-stage fractional crystallization processes of CE-5 basalts combined with silicate liquid immiscibility. These new findings demonstrate the significance of studies on high-pressure minerals in lunar materials and the special nature of lunar magmatic evolution.

Polymorphism in the Ruddlesden-Popper Nickelate La3Ni2O7: Discovery of a Hidden Phase with Distinctive Layer Stacking.

We report the discovery of a novel form of Ruddlesden-Popper (RP) nickelate that stands as the first example of long-range, coherent polymorphism in this class of inorganic solids. Rather than the well-known, uniform stacking of perovskite blocks ubiquitously found in RP phases, this newly discovered polymorph of the bilayer RP phase La3Ni2O7 adopts a novel stacking sequence in which single-layer and trilayer blocks of NiO6 octahedra alternate in a "1313" sequence. Crystals of this new polymorph are described in space group Cmmm, although we note evidence for a competing Imam variant. Transport measurements at ambient pressure reveal metallic character with evidence of a charge density wave transition with an onset at T ≈ 134 K. The discovery of such polymorphism could reverberate to the expansive range of science and applications that rely on RP materials, particularly the recently reported signatures of superconductivity in bilayer La3Ni2O7 with Tc as high as 80 K above 14 GPa.

Genotyping by sequencing for the construction of oil palm (Elaeis guineensis Jacq.) genetic linkage map and mapping of yield related quantitative trait loci.

Oil palm (Elaeis guineensis Jacq.) is one of the major oil-producing crops. Improving the quality and increasing the production yield of oil palm have been the primary focuses of both conventional and modern breeding approaches. However, the conventional breeding approach for oil palm is very challenging due to its longevity, which results in a long breeding cycle. Thus, the establishment of marker assisted selection (MAS) for oil palm breeding programs would speed up the breeding pipeline by generating new oil palm varieties that possess high commercial traits. With the decreasing cost of sequencing, Genotyping-by-sequencing (GBS) is currently feasible to many researchers and it provides a platform to accelerate the discovery of single nucleotide polymorphism (SNP) as well as insertion and deletion (InDel) markers for the construction of a genetic linkage map. A genetic linkage map facilitates the identification of significant DNA regions associated with the trait of interest via quantitative trait loci (QTL) analysis. A mapping population of 112 F1 individuals from a cross of Deli dura and Serdang pisifera was used in this study. GBS libraries were constructed using the double digestion method with HindIII and TaqI enzymes. Reduced representation libraries (RRL) of 112 F1 progeny and their parents were sequenced and the reads were mapped against the E. guineensis reference genome. To construct the oil palm genetic linkage map, informative SNP and InDel markers were used to discover significant DNA regions associated with the traits of interest. The nine traits of interest in this study were fresh fruit bunch (FFB) yield, oil yield (OY), oil to bunch ratio (O/B), oil to dry mesocarp ratio (O/DM) ratio, oil to wet mesocarp ratio (O/WM), mesocarp to fruit ratio (M/F), kernel to fruit ratio (K/F), shell to fruit ratio (S/F), and fruit to bunch ratio (F/B). A total of 2.5 million SNP and 153,547 InDel markers were identified. However, only a subset of 5,278 markers comprising of 4,838 SNPs and 440 InDels were informative for the construction of a genetic linkage map. Sixteen linkage groups were produced, spanning 2,737.6 cM for the maternal map and 4,571.6 cM for the paternal map, with average marker densities of one marker per 2.9 cM and one per 2.0 cM respectively, were produced. A QTL analysis was performed on nine traits; however, only QTL regions linked to M/F, K/F and S/F were declared to be significant. Of those QTLs were detected: two for M/F, four for K/F and one for S/F. These QTLs explained 18.1-25.6% of the phenotypic variance and were located near putative genes, such as casein kinase II and the zinc finger CCCH domain, which are involved in seed germination and growth. The identified QTL regions for M/F, K/F and S/F from this study could be applied in an oil palm breeding program and used to screen palms with desired traits via marker assisted selection (MAS).

Serendipitous discovery of a novel polymorph of an immunosuppressant drug azathioprine: phase transformation, solubility, dissolution and stability study

A novel polymorph of an immunosuppressant drug azathioprine (AZP) is prepared (F-III) along with two solvates (2-methoxyethanol (MEE) and 1,4-dioxane (DOX)) and a monohydrate of AZP.

Kinship analysis and pedigree reconstruction by RAD sequencing in cattle.

Kinship and pedigree, used for estimating inbreeding, heritability, selection, and gene flow, are useful for breeding and animal conservation. However, as the size of crossbred populations increases, inaccurate generation and parentage assignment in livestock farms increase. Restriction-site-associated DNA sequencing is a cost-effective platform for single nucleotide polymorphism (SNP) discovery and genotyping. Here, we performed a kinship analysis and pedigree reconstruction for Angus and Xiangxi yellow cattle. A total of 975 cattle, including 923 offspring with 24 known sires and 28 known dams, were sampled and subjected to SNP discovery and genotyping. The identified SNP panel included 7,305 SNPs capturing the maximum difference between paternal and maternal genome information, allowing us to distinguish F1 from F2 generations with 90% accuracy. In conclusion, we provided a low-cost and efficient SNP panel for kinship analyses and the improvement of local genetic resources, which are valuable for breed improvement, local resource utilization, and conservation.

Dominant gingers - Discovery and inheritance of a new shell polymorphism in the great pond snail Lymnaea stagnalis.

Color polymorphism is a classic study system for evolutionary genetics. One of the most color-polymorphic animal taxa is mollusks, but the investigation of the genetic basis of color determination is often hindered by their life history and the limited availability of genetic resources. Here, we report on the discovery of shell color polymorphism in a much-used model species, the great pond snail Lymnaea stagnalis. While their shell is usually beige, some individuals from a Greek population show a distinct red shell color, which we nicknamed Ginger. Moreover, we found that the inheritance fits simple, single-locus Mendelian inheritance with dominance of the Ginger allele. We also compared crucial life-history traits between Ginger and wild-type individuals, and found no differences between morphs. We conclude that the relative simplicity of this polymorphism will provide new opportunities for a deeper understanding of the genetic basis of shell color polymorphism and its evolutionary origin.

Electronic Properties of a Novel Boron Polymorph: Ogee-Borophene

In this computational study, a novel borophene polymorph, Ogee-Borophene, characterized by irregular decagon-shaped hollows was reported. The structure involves a deviation from hexagonal configurations found in all other known borophene polymorphs. The decagon-shaped hollow is highly related to the anisotropy of the structure, which results in three types of boron atoms with different electronic properties in the structure. In the study, the electronic structure and density of states of this novel structure were investigated with the help of density functional theory calculations. The electronic structure of Ogee-Borophene shows Dirac cone formations near the Fermi level. The discovery of a novel borophene polymorph, Ogee-Borophene, with irregular-shaped hollows represents a different point of view in the 2D materials field. The unique electronic properties of this material suggest that Ogee-Borophene has the potential to be used in a variety of applications, including transistors, and selective sensor applications without the need for additional doping.

Genotyping-by-sequencing reveals a high number and quality of single nucleotide polymorphisms in guinea pigs (Cavia porcellus) from the Peruvian Andes.

Guinea pigs are a major source of animal protein for Peruvian Andean families. Despite the economic and cultural relevance of guinea pigs, their genomic characterization has been scarcely addressed. Genotyping-by-sequencing (GBS) has emerged as an affordable alternative to genotyping of livestock and native animals. Here, we report the use of GBS for single nucleotide polymorphism (SNP) discovery of traditionally raised guinea pigs from six regions of the Peruvian Andes and one group of breeding animals. The paired-end (2 × 150 bp) sequencing of 40 guinea pig DNA samples generated a mean of 6.4 million high-quality sequencing reads per sample. We obtained an average sequencing depth of 10× with an 88.5% mapping rate to the Cavia porcellus reference genome. A total of 279 965 SNPs (102 SNPs/Mbp) were identified after variant calling and quality filtering. Based on this SNP set, we assessed the genetic diversity and distance within our selected guinea pig populations. An overall average minor allele frequency of 0.13, an observed heterozygosity of 0.31, an expected heterozygosity of 0.35, and an F-value of 0.1 were obtained, while the SNP-based neighbor-joining tree suggests a closer genetic relationship between individuals from geographically close locations. We showed that GBS is a cost-effective tool for SNP discovery and genetic characterization of Peruvian guinea pig populations. Therefore, it may be considered as a suitable and affordable tool for genomic characterization of poorly studied native animal species.

The Human Genetics of Malaria

Human genetic resistance to malaria is the inherited changes in the human DNA that increase resistance to malaria and lead to increased survival of people with these genetic changes. The evolutionary pressure exerted by the malaria parasite is likely what led to the existence of these genotypes. The impact of host genetics on susceptibility to Plasmodium falciparum malaria has been widely studied over the past twenty years. It is now clear that the malaria Plasmodium parasites have imposed strong selective forces on the human genome in endemic regions. Different genes associated with different malaria-related phenotypes have been identified. Recent developments in human genome research technologies, like genome-wide association studies and genotyping tools, have enabled the discovery of several genetic polymorphisms and biomarkers. This review describes and analyses the human gene polymorphisms that have been revealed to be associated with resistance to P. falciparum malaria. Although some polymorphisms play important roles in susceptibility to malaria, several discoveries are inconclusive and conflicting and should be carefully examined. The discovery of genetic polymorphisms associated with resistance to malaria will enable the development of interventions or cures for the malaria disease.

Synthesis and Characterization of Xylazine Hydrochloride Polymorphs, Hydrates, and Cocrystals: A 35Cl Solid-State NMR and DFT Study

Xylazine HCl (X) is a veterinary analgesic with many known solid forms, making it an ideal system for studying the noncovalent interactions, such as hydrogen bonding, that provide stability to polymorphs, solvates/hydrates, and cocrystal of pharmaceuticals. Herein, we report methods for the reliable preparation and interconversion of polymorphs of X (including mechanochemical pathways), the discovery of a novel polymorph, and the synthesis of three cocrystals with coformers containing amide and carboxylic acid moieties. An understanding of ball milling protocols is essential for optimizing these reactions and ensuring clean and reproducible syntheses of the products in high yields. All materials were characterized using thermal analysis, powder and single-crystal X-ray diffraction (PXRD and SCXRD), and multinuclear solid-state NMR (SSNMR) spectroscopy. 35Cl SSNMR is highlighted for its versatility for fingerprinting polymorphs, hydrates, and cocrystals (including the detection of impurity phases that are not always evident from PXRD and offering an avenue for optimizing synthetic protocols) and providing molecular-level structural information. The 35Cl electric field gradient (EFG) tensor is extremely sensitive to the unique hydrogen-bonding network in each solid form of X, resulting in distinct powder patterns. Dispersion-corrected plane-wave density functional theory (DFT) structural refinements yield better models of the hydrogen-bonding environments of the chloride ions than is possible through XRD methods alone. Calculations employing the refined structures yield 35Cl EFG tensors that agree well with experiment. PXRD and 35Cl SSNMR, in tandem with reliable calculations of EFG tensors, are essential for the development of NMR crystallographic and crystal structure prediction protocols and crucial for future studies involving HCl salts and their concomitant solid forms.

Equations of State and Crystal Structures of KCaPO4, KSrPO4, and K2Ce(PO4)2 under High Pressure: Discovery of a New Polymorph of KCaPO4.

We have studied by means of angle-dispersive powder synchrotron X-ray diffraction the structural behavior of KCaPO4, SrKPO4, and K2Ce(PO4)2 under high pressure up to 26, 25, and 22 GPa, respectively. For KCaPO4, we have also accurately determined the crystal structure under ambient conditions, which differs from the structure previously reported. Arguments supporting our structural determination will be discussed. We have found that KCaPO4 undergoes a reversible phase transition. The onset of the transition is at 5.6 GPa. It involves a symmetry decrease. The low-pressure phase is described by space group P3̅m1 and the high-pressure phase by space group Pnma. For KSrPO4 and K2Ce(PO4)2, no evidence of phase transitions has been found up to the highest pressure covered by the experiments. For the three compounds, the linear compressibility for the different crystallographic axes and the pressure-volume equation of states are reported and compared with those of other phosphates. The three studied compounds are among the most compressible phosphates. The results of the study improve the knowledge about the high-pressure behavior of complex phosphates.