Mapping and functional characterization of structural variation in 1060 pig genomes.

BACKGROUND: Structural variations (SVs) have significant impacts on complex phenotypes by rearranging large amounts of DNA sequence. RESULTS: We present a comprehensive SV catalog based on the whole-genome sequence of 1060 pigs (Sus scrofa) representing 101 breeds, covering 9.6% of the pig genome. This catalog includes 42,487 deletions, 37,913 mobile element insertions, 3308 duplications, 1664 inversions, and 45,184 break ends. Estimates of breed ancestry and hybridization using genotyped SVs align well with those from single nucleotide polymorphisms. Geographically stratified deletions are observed, along with known duplications of the KIT gene, responsible for white coat color in European pigs. Additionally, we identify a recent SINE element insertion in MYO5A transcripts of European pigs, potentially influencing alternative splicing patterns and coat color alterations. Furthermore, a Yorkshire-specific copy number gain within ABCG2 is found, impacting chromatin interactions and gene expression across multiple tissues over a stretch of genomic region of ~200 kb. Preliminary investigations into SV's impact on gene expression and traits using the Pig Genotype-Tissue Expression (PigGTEx) data reveal SV associations with regulatory variants and gene-trait pairs. For instance, a 51-bp deletion is linked to the lead eQTL of the lipid metabolism regulating gene FADS3, whose expression in embryo may affect loin muscle area, as revealed by our transcriptome-wide association studies. CONCLUSIONS: This SV catalog serves as a valuable resource for studying diversity, evolutionary history, and functional shaping of the pig genome by processes like domestication, trait-based breeding, and adaptive evolution.

In silico analysis of embolism in cerebral arteries using fluid-structure interaction method.

Ischemic stroke, particularly embolic stroke, stands as a significant global contributor to mortality and long-term disabilities. This paper presents a comprehensive simulation of emboli motion through the middle cerebral artery (MCA), a prevalent site for embolic stroke. Our patient-specific computational model integrates major branches of the middle cerebral artery reconstructed from magnetic resonance angiography images, pulsatile flow dynamics, and emboli of varying geometries, sizes, and material properties. The fluid-structure interactions method is employed to simulate deformable emboli motion through the middle cerebral artery, allowing observation of hemodynamic changes in artery branches upon embolus entry. We investigated the impact of embolus presence on shear stress magnitude on artery walls, analyzed the effects of embolus material properties and geometries on embolus trajectory and motion dynamics within the middle cerebral artery. Additionally, we evaluated the non-Newtonian behavior of blood, comparing it with Newtonian blood behavior. Our findings highlight that embolus geometry significantly influences trajectory, motion patterns, and hemodynamics within middle cerebral artery branches. Emboli with visco-hyperelastic material properties experienced higher stresses upon collision with artery walls compared to those with hyperelastic properties. Furthermore, considering blood as a non-Newtonian fluid had notable effects on emboli stresses and trajectories within the artery, particularly during collisions. Notably, the maximum von Mises stress experienced in our study was 21.83 kPa, suggesting a very low probability of emboli breaking during movement, impact, and after coming to a stop. However, in certain situations, the magnitude of shear stress on them exceeded 1 kPa, increasing the likelihood of cracking and disintegration. These results serve as an initial step in anticipating critical clinical conditions arising from arterial embolism in the middle cerebral artery. They provide insights into the biomechanical parameters influencing embolism, contributing to improved clinical decision-making for stroke management.

Structural characterization and immunostimulant activities of polysaccharides fractionated by gradient ethanol precipitation method from Panax ginseng C. A. Meyer.

Panax ginseng C. A. Meyer is a dual-purpose plant for medicine and food, its polysaccharide is considered as an immune enhancer. Four polysaccharides, WGP-20-F, WGP-40-F, WGP-60-F and WGP-80-F were obtained from ginseng via water extraction and gradient ethanol precipitation with different molecular weights (Mw) of 1.720 × 106, 1.434 × 106, 4.225 × 104 and 1.520 × 104 Da, respectively. WGP-20-F and WGP-40-F which with higher Mw and a triple-helix structure are glucans composed of 4-ɑ-Glcp, do not show remarkable immunoregulatory effects. WGP-60-F and WGP-80-F are heteropolysaccharides mainly composed of 4-ɑ-Glcp and also contain t-ɑ-Araf, 5-ɑ-Araf and 3,5-ɑ-Araf. They are spherical branched conformations without a triple-helix structure and can effectively increase the index of immune organs, lymphocyte proliferation, activate macrophages to regulate the immune system in mice and further enhance immune functions by improving delayed-type hypersensitivity reaction and antibody response. These results indicated that WGP-60-F and WGP-80-F could be used as potential immune enhancers, and gradient ethanol precipitation can be applied for the preparation of ginseng bioactive polysaccharide.

Identifying specific TLS-associated genes as potential biomarkers for predicting prognosis and evaluating the efficacy of immunotherapy in soft tissue sarcoma.

Background: The tertiary lymphatic structure (TLS) is an important component of the tumor immune microenvironment and has important significance in patient prognosis and response to immune therapy. However, the underlying mechanism of TLS in soft tissue sarcoma remains unclear. Methods: A total of 256 RNAseq and 7 single-cell sequencing samples were collected from TCGA-SARC and GSE212527 cohorts. Based on published TLS-related gene sets, four TLS scores were established by GSVA algorithm. The immune cell infiltration was calculated via TIMER2.0 and "MCPcounter" algorithms. In addition, the univariate, LASSO, and multivariate-Cox analyses were used to select TLS-related and prognosis-significant hub genes. Single-cell sequencing dataset, clinical immunohistochemical, and cell experiments were utilized to validate the hub genes. Results: In this study, four TLS-related scores were identified, and the total-gene TLS score more accurately reflected the infiltration level of TLS in STS. We further established two hub genes (DUSP9 and TNFSF14) prognosis markers and risk scores associated with soft tissue sarcoma prognosis and immune therapy response. Flow cytometry analysis showed that the amount of CD3, CD8, CD19, and CD11c positive immune cell infiltration in the tumor tissue dedifferentiated liposarcoma patients was significantly higher than that of liposarcoma patients. Cytological experiments showed that soft tissue sarcoma cell lines overexpressing TNFSF14 could inhibit the proliferation and migration of sarcoma cells. Conclusion: This study systematically explored the TLS and related genes from the perspectives of bioinformatics, clinical features and cytology experiments. The total-gene TLS score, risk score and TNFSF14 hub gene may be useful biomarkers for predicting the prognosis and immunotherapy efficacy of soft tissue sarcoma.

4-(1H-2,3-Dihydro-naphtho-[1,8-de][1,3,2]di-aza-borinin-2-yl)-1-ethylpyridin-1-ium iodide.

The title compound, C17H17BN3I, is a type of di-aza-borinane featuring substitution at the 1, 2, and 3 positions of the nitro-gen-boron six-membered heterocycle. The organic mol-ecule has a planar structure, the dihedral angle between the pyridyl ring and the fused ring system being 3.46 (4)°. In the crystal, mol-ecules are stacked in a head-to-tail manner. The iodide ion makes close contacts with three organic mol-ecules and supports the alternating stack.

13-Nitro-benzo[a][1,4]benzo-thia-zino[3,2-c]phenoxazine.

In the title compound, C22H11N3O3S, dihedral angle between the phenyl rings on the periphery of the molecule is 8.05 (18)°. In the crystal, aromatic π-π stacking distance and short C-H⋯O contacts are observed. The maximum absorption occurs at 688 nm.

4-(1H-2,3-Dihydronaphtho-[1,8-de][1,3,2]di-aza-borinin-2-yl)-1-ethylpyridin-1-ium iodide monohydrate.

The cation of the title hydrated salt, C17H17BN3 +·I-·H2O, is a di-aza-borinane featuring substitution at the 1, 2, and 3 positions in the nitro-gen-boron six-membered heterocycle. The cation is approximately planar with a dihedral angle between the pyridyl ring and the di-aza-borinane ring system of 5.40 (5)°. In the crystal, the cations stack along [100] in an alternating head-to-tail manner, while the iodide ion and water mol-ecule form one-dimensional hydrogen-bonded chains beside the cation stack. The cation stacks and I--water chains are crosslinked by N-H⋯I and N-H⋯O hydrogen bonds.

Redetermination of germacrone type II based on single-crystal X-ray data.

The extraction and purification procedures, crystallization and crystal structure refinement (single-crystal X-ray data) of germacrone type II, C15H22O, are presented. The structural results are compared with a previous powder X-ray synchrotron study [Kaduk et al. (2022 ▸). Powder Diffr. 37, 98-104], revealing significant improvements in terms of accuracy and precision. Hirshfeld atom refinement (HAR), as well as Hirshfeld surface analysis, give insight into the inter-molecular inter-actions of germacrone type II.

mer-Bis(quinoline-2-carboxaldehyde 4-ethyl-thio-semicarbazonato)nickel(II) methanol 0.33-solvate 0.67-hydrate.

In the title compound, [Ni(C13H13N4S)2]·0.33CH3OH·0.67H2O, the NiII atom is coordinated by two tridentate quinoline-2-carboxaldehyde 4-ethyl-thio-semi-car-ba-zonate ligands in a distorted octa-hedral shape. At 100 K, the crystal symmetry is monoclinic (space group P21/n). A mixture of water and methanol crystallizes with the title complex, and one of the ethyl groups in the coordinating ligands is disordered over two positions, with an occupancy ratio of 58:42. There is inter-molecular hydrogen bonding between the solvent mol-ecules and the amine and thiol-ate groups in the ligands. No other significant inter-actions are present in the crystal packing.

Ethidium benzoate methanol monosolvate.

In the title salt solvate (systematic name: 8-amino-5-ethyl-6-phenyl-phenanthridin-5-ium benzoate methanol monosolvate), C21H20N3 +·C6H5CO2 -·CH3OH, two ethidium cations, C21H20N3 +, dimerize about a twofold axis through π-π inter-actions [inter-centroid separation = 3.6137 (4) Å]. The benzoate anions are connected through hydrogen bonding with the -NH2 groups of the ethidium cations and the -OH group of the MeOH mol-ecule. The MeOH mol-ecule also accepts a hydrogen bond from the -NH2 group of the ethidium cation. The result is a one-dimensional hydrogen-bonded chain along the b-axis direction.

(SC,RS)-Bromido-(N-{4-methyl-1-[(4-methyl-phenyl)sul-fan-yl]-pentan-2-yl}-N'-(pyridin-2-yl)imidazol-2-yl-idene)palladium(II) bromide.

The mol-ecule of the title NCNHCS pincer N-heterocyclic carbene palladium(II) complex, [PdBr(C21H25N3S)]Br, exhibits a slightly distorted square-planar coordination at the palladium(II) atom, with the five-membered chelate ring nearly planar. The six-membered chelate ring adopts an envelope conformation. Upon chelation, the sulfur atom becomes a stereogenic centre with an RS configuration induced by the chiral carbon of the precursor imidazolium salt. There are intra-molecular C-H⋯Br-Pd hydrogen bonds in the structure. The two inter-stitial Br atoms, as the counter-anion of the structure, are both located on crystallographic twofold axes and are connected to the complex cations via C-H⋯·Br hydrogen bonds.

Poly[3-methyl-pyridinium [(µ2-di-hydrogen phosphito)bis(µ3-hydrogen phosphito)dizinc]].

In the title compound, {(C6H8N)[Zn2(HPO3)2(H2PO3)]}n, the constituent ZnO4, HPO3 and H2PO3 polyhedra of the inorganic component are linked into (010) sheets by Zn-O-P bonds (mean angle = 134.4°) and the layers are reinforced by O-H⋯O hydrogen bonds. The protonated templates are anchored to the inorganic sheets via bifurcated N-H⋯(O,O) hydrogen bonds.

Bis[2,3-bis-(thio-phen-2-yl)pyrido[3,4-b]pyrazine]-silver(I) perchlorate methanol disolvate.

The title compound, [Ag(C15H9N3S2)2]ClO4·2CH3OH, is monoclinic. The AgI atom is coordinated by pyrido N atoms and is two-coordinate; however, the AgI atom has nearby O atoms that can be assumed to be weakly bonded - one from the perchlorate anion and one from the methanol solvate molecule. One of the thienyl groups on a 2,3-bis-(thio-phen-2-yl)pyrido[3,4-b]pyrazine is flipped disordered and was refined to occupancies of 68.4 (6) and 31.6 (6)%.

Benzo[a][1,4]benzothia-zino[3,2-c]phenothia-zine.

The title compound, C22H12N2S2, crystallizes in space group P21/c with four mol-ecules in the asymmetric unit. The heterocyclic mol-ecule is quasi-planar with a dihedral angle between the phenyl rings on the periphery of the mol-ecule of 1.73 (19)°. Short H⋯S (2.92 Å) and C-H⋯π [2.836 (3) Å] contacts are observed in the crystal with shorted π-π stacking distances of 3.438 (3) Šalong the b axis. Surprisingly, and unlike a closely related material, this mol-ecule readily forms large crystals by sublimation and by slow evaporation from di-chloro-methane. The maximum absorbance in the UV-Vis spectrum is at 533 nm. Emission was measured upon excitation at 533 nm with a fluorescence λmax of 658 nm and cutoff of 900 nm.

(2E,2'E)-1,1'-([1,1'-Biphen-yl]-4,4'-di-yl)bis-[3-(di-meth-yl-amino)-prop-2-en-1-one].

The title compound, C22H24N2O2, crystallizes in space group P21/n. The mol-ecular structure is almost planar except for a tilt of the phenyl rings. The allyl groups on both ends exhibit the trans-form and the connected N atoms show sp 2 character. The mol-ecules are stacked and assembled along the c-axis direction by C-H⋯π inter-actions.

Differences in Albizia odoratissima genetic diversity between Hainan Island and mainland populations in China.

Background: This study aimed at exploring unique population genetic characteristics of Albizia odoratissima (Linn. f) Benth on Hainan Island to provide a scientific basis for its rational utilization and protection. Methods: It analyzed the genetic diversity and structure of 280 individuals from 10 subpopulations of A. odoratissima from Hainan Island and Baise City using 16 expression sequence markers - simple sequence repeat markers. Results: The genetic diversity of Hainan population (I = 0.7290, He = 0.4483) was lower than that of the Baise population (I = 0.8722, He = 0.5121). Compared with the Baise population (Nm = 2.0709, FST = 0.1077), the Hainan Island population (Nm = 1.7519, FST = 0.1249) exhibited lower gene flow and higher degree of genetic differentiation. Molecular variance and genetic differentiation analyses showed that the main variation originated from individuals within the subpopulation. There were significant differences in the genetic structure between Hainan and Baise populations. It grouped according to geographical distance, consistent with the Mantel test results (R2 = 0.77, p = 0.001). In conclusion, the genetic diversity of the island A. odoratissima population was lower than that distributed on land, the two populations exhibited obvious genetic structure differences. Both the degrees of inbreeding and genetic differentiation were higher in the island population than in the land population.

Synthesis, crystal structure and Hirshfeld analysis of N-ethyl-2-{3-methyl-2-[(2Z)-pent-2-en-1-yl]cyclo-pent-2-en-1-yl-idene}hydrazinecarbo-thio-amide.

The title compound (C14H23N3S, common name: cis-jasmone 4-ethyl-thio-semicarbazone) was synthesized by the equimolar reaction of cis-jasmone and 4-ethyl-thio-semicarbazide in ethanol facilitated by acid catalysis. There is one crystallographically independent mol-ecule in the asymmetric unit, which shows disorder of the terminal ethyl group of the jasmone carbon chain [site-occupancy ratio = 0.911 (5):0.089 (5)]. The thio-semicarbazone entity [N-N-C(=S)-N] is approximately planar, with the maximum deviation of the mean plane through the N/N/C/S/N atoms being 0.0331 (8) Å, while the maximum deviation of the mean plane through the five-membered ring of the jasmone fragment amounts to -0.0337 (8) Å. The dihedral angle between the two planes is 4.98 (7)°. The mol-ecule is not planar due to this structural feature and the sp 3-hybridized atoms of the jasmone carbon chain. Additionally, one H⋯N intra-molecular inter-action is observed, with graph-set motif S(5). In the crystal, the mol-ecules are connected through pairs of H⋯S inter-actions with R 2 2(8) and R 2 1(7) graph-set motifs into centrosymmetric dimers. The dimers are further connected by H⋯N inter-actions with graph-set motif R 2 2(12), which are related by an inversion centre, forming a mono-periodic hydrogen-bonded ribbon parallel to the b-axis. The crystal structure and the supra-molecular assembly of the title compound are compared with four known cis-jasmone thio-semicarbazone derivatives (two crystalline modifications of the non-substituted form, the 4-methyl and the 4-phenyl derivatives). A Hirshfeld surface analysis indicates that the major contributions for the crystal cohesion are from H⋯H (70.7%), H⋯S/S⋯H (13.5%), H⋯C/C⋯H (8.8%), and H⋯N/N⋯H (6.6%) inter-faces (only the disordered atoms with the highest s.o.f. were considered for the evaluation).

Crystal structure and Hirshfeld surface analysis of (Z)-4-({[2-(benzo[b]thio-phen-3-yl)cyclo-pent-1-en-1-yl]meth-yl}(phen-yl)amino)-4-oxobut-2-enoic acid.

In the title compound, C24H21NO3S, the cyclopentene ring adopts an envelope conformation. In the crystal, mol-ecules are linked by C-H⋯π inter-actions, forming ribbons along the a axis. Inter-molecular C-H⋯O hydrogen bonds connect these ribbons to each other, forming layers parallel to the (01) plane. The mol-ecular packing is strengthened by van der Waals inter-actions between the layers. The inter-molecular contacts were qu-anti-fied using Hirshfeld surface analysis and two-dimensional fingerprint plots, revealing the relative contributions of the contacts to the crystal packing to be H⋯H 46.0%, C⋯H/H⋯C 21.1%, O⋯H/H⋯O 20.6% and S⋯H/H⋯S 9.0%.

Crystal structure and Hirshfeld surface analysis of (1H-imidazole-κN3)[4-methyl-2-({[2-oxido-5-(2-phenyl-diazen-1-yl)phen-yl]methyl-idene}amino)penta-noate-κ3O,N,O']copper(II).

The title copper(II) complex, [Cu(C18H19N3O3)(C3H4N2)], consists of a tridentate ligand synthesized from l-leucine and azo-benzene-salicyl-aldehyde. One imidazole mol-ecule is additionally coordinated to the copper(II) ion in the equatorial plane. The crystal structure features N-H⋯O hydrogen bonds. A Hirshfeld surface analysis indicates that the most important contributions to the packing are from H⋯H (52.0%) and C⋯H/H⋯C (17.9%) contacts.

Synthesis, crystal structure and properties of the trigonal-bipyramidal complex tris-(2-methyl-pyridine N-oxide-κO)bis-(thio-cyanato-κN)cobalt(II).

Reaction of Co(NCS)2 with 2-methyl-pyridine N-oxide in a 1:3 ratio in n-butanol leads to the formation of crystals of tris-(2-methyl-pyridine N-oxide-κO)bis-(thio-cyanato-κN)cobalt(II), [Co(NCS)2(C6H7NO)3]. The asymmetric unit of the title compound consists of one CoII cation two thio-cyanate anions and three crystallographically independent 2-methyl-pyridine N-oxide coligands in general positions. The CoII cations are trigonal-bipyramidally coordinated by two terminal N-bonding thio-cyanate anions in the trans-positions and three 2-methyl-pyridine N-oxide coligands into discrete complexes. These complexes are linked by inter-molecular C-H⋯S inter-actions into double chains that elongate in the c-axis direction. Powder X-ray diffraction (PXRD) measurements prove that all batches are always contaminated with an additional and unknown crystalline phase. Thermogravimetry and differential analysis of crystals selected by hand reveal that the title compound decomposes at about 229°C in an exothermic reaction. At about 113°C a small endothermic signal is observed that, according to differential scanning calorimetry (DSC) measurements, is irreversible. PXRD measurements of the residue prove that a poorly crystalline and unknown phase has formed and thermomicroscopy indicates that some phase transition occurs that is accompanied with a color change of the title compound.