Reaction dynamics for the Cl(2^2P) + XCl →\to XCl + Cl(2^2P) (X = H, D, Mu) reaction on a high-fidelity ground state potential energy surface

Globally accurate full-dimensional ground state potential energy surface (PES) for the Cl($^2$P) + XCl $\to$ HCl + Cl($^2$P) reaction, a prototypical heavy-light-heavy abstract reaction, is developed using permutation invariant polynomial neural network (PIP-NN) method and embedded atom neural network (EANN) method, with the corresponding total root mean square error (RMSE) being only 0.043 and 0.056 kcal/mol, respectively. The saddle point of this reaction system is found to be nonlinear. A full-dimensional approximate quantum mechanical method, ring-polymer molecular dynamics (RPMD) with Cayley propagator, is employed to calculate the thermal rate coefficients and kinetic isotopic effects of title reactions Cl($^2$P) + XCl $\to$ XCl + Cl($^2$P) (X = H, D, Mu) on both new PESs. The results reproduce the experimental results at high temperatures perfectly, but with moderate accuracy at lower temperatures. The similar kinetic behavior is supported by quantum dynamics using wave packet calculations as well.Comment: 23 pages,5 figure

2,2′-(4-{[(E)-4-Meth­oxy­benzyl­idene]amino}­phenyl­imino)­diethanol

In the title compound, C18H22N2O3, the dihedral angle between the aromatic rings is 3.9 (2)°. Both H atoms of the hy­droxy groups are involved in inter­molecular O—H⋯O hydrogen bonding. In the crystal structure, this hydrogen bonding assembles mol­ecules into chains of 21 symmetry extending parallel to the b axis. The almost planar (within 0.09 and 0.06 Å) 4-CH3O–C6H4–CH=N–C6H4– groups are oriented outwards the twofold screw axis

Detection of copy number variations and their effects in Chinese bulls

BACKGROUND: Copy number variations (CNVs) are a main source of genomic structural variations underlying animal evolution and production traits. Here, with one pure-blooded Angus bull as reference, we describe a genome-wide analysis of CNVs based on comparative genomic hybridization arrays in 29 Chinese domesticated bulls and examined their effects on gene expression and cattle growth traits. RESULTS: We identified 486 copy number variable regions (CNVRs), covering 2.45% of the bovine genome, in 24 taurine (Bos taurus), together with 161 ones in 2 yaks (Bos grunniens) and 163 ones in 3 buffaloes (Bubalus bubalis). Totally, we discovered 605 integrated CNVRs, with more “loss” events than both “gain” and “both” ones, and clearly clustered them into three cattle groups. Interestingly, we confirmed their uneven distributions across chromosomes, and the differences of mitochondrion DNA copy number (gain: taurine, loss: yak & buffalo). Furthermore, we confirmed approximately 41.8% (253/605) and 70.6% (427/605) CNVRs span cattle genes and quantitative trait loci (QTLs), respectively. Finally, we confirmed 6 CNVRs in 9 chosen ones by using quantitative PCR, and further demonstrated that CNVR22 had significantly negative effects on expression of PLA2G2D gene, and both CNVR22 and CNVR310 were associated with body measurements in Chinese cattle, suggesting their key effects on gene expression and cattle traits. CONCLUSIONS: The results advanced our understanding of CNV as an important genomic structural variation in taurine, yak and buffalo. This study provides a highly valuable resource for Chinese cattle’s evolution and breeding researches. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-480) contains supplementary material, which is available to authorized users

Optimization of Ganoderma leucocontextum Fermented Tea Medium Formula Based on High-yield Extracellular Crude

To investigate the optimal nutritional conditions and their contributing factors for the secretion of extracellular crude polysaccharides with Ganoderma leucocontextum on a liquid tea substrate, this study optimized the nutritional conditions of its extracellular crude polysaccharides formation by orthogonal experiment and analysis of variance on the basis of the single-factor test, and explored the relevance between its liquid culture characteristics and the secretion of extracellular crude polysaccharides using correlation and path analyses. The results of study revealed that the greatest output of extracellular crude polysaccharide (1.49±0.33 g/L) was achieved on a tea culture medium of 50 g/L potato, 40 g/L glucose, 3 g/L laterite, 20 g/L Pu'er tea and 0.075 mm tea powder particle size, and was affected by each nutritional condition in the descending order of glucose>tea variety>laterite>potato>tea powder particle size. Moreover, the secretion of extracellular crude polysaccharides in G. leucocontextum was significantly impacted by the soluble solids of the fermentation broth and the number of mycelium balls, with the former having the greatest indirect effect while the latter, the greatest direct and combined effect on it. In conclusion, the nutritional conditions (variety, concentration, particle size, etc.) of the tea culture medium and the liquid culture characteristics of G. leucocontextum exerted a significant and interactive effect on the secretion of extracellular crude polysaccharides, and the aforesaid results may provide a theoretical reference for extraction of polysaccharides from this mushroom and development of it as functional foods

Comprehensive molecular expression profiling of SARS-CoV-associated factors in the endometrium across the menstrual cycle and elevated susceptibility in women with recurrent pregnancy loss

Objective: To evaluate the dynamic expression profiling alterations of SARS-CoV-2-associated molecules within the fertile human endometrium throughout the menstrual cycle. Furthermore, to explore the inherent vulnerability of the endometrium to SARS-CoV-2 infection among women experiencing recurrent pregnancy failure, including both recurrent implantation failures (RIF) and recurrent pregnancy losses (RPL).Method: The present study employed multiple datasets to investigate the expression patterns of SARS-CoV-2-associated genes. Firstly, a single-cell RNA-sequencing dataset comprising endometrial samples from 19 healthy women across the menstrual cycle was utilized. Additionally, two microarray datasets encompassing 24 women with RIF, and 24 women with RPL during the peri-implantation phase were included. To complement these analyses, immunohistochemical (IHC) staining was performed on endometrial samples collected from 30 women with RIF, 30 women with RPL, and 20 fertile controls recruited specifically during the implantation period.Results: The investigation revealed a moderate expression percentage of CTSL (22%), TMPRSS4 (15%), FURIN (16%) and MX1 (9%) in endometrium. Conversely, the expression percentages of ACE2 (1%) and TMPRSS2 (4%) were relatively low. Notably, the expression of BSG exhibited an increment towards the window of implantation, reaching its peak during the middle secretary phase. Furthermore, a significant reduction (p < 0.05) in TMPRSS2 expression was observed in the RIF group compared to the control group. While the expression of BSG was significantly increased (p < 0.05) in the RPL group, findings that were corroborated by the IHC staining results.Conclusion: The findings of this study indicate a noteworthy upregulation of BSG expression in the endometrium of women with RPL. These results suggest an augmented susceptibility of endometrium to SARS-CoV-2 infection, potentially contributing to unfavorable pregnancy outcomes

Attenuation of epigenetic regulator SMARCA4 and ERK-ETS signaling suppresses aging-related dopaminergic degeneration

How complex interactions of genetic, environmental factors and aging jointly contribute to dopaminergic degeneration in Parkinson's disease (PD) is largely unclear. Here, we applied frequent gene co‐expression analysis on human patient substantia nigra‐specific microarray datasets to identify potential novel disease‐related genes. In vivo Drosophila studies validated two of 32 candidate genes, a chromatin‐remodeling factor SMARCA4 and a biliverdin reductase BLVRA. Inhibition of SMARCA4 was able to prevent aging‐dependent dopaminergic degeneration not only caused by overexpression of BLVRA but also in four most common Drosophila PD models. Furthermore, down‐regulation of SMARCA4 specifically in the dopaminergic neurons prevented shortening of life span caused by α‐synuclein and LRRK2. Mechanistically, aberrant SMARCA4 and BLVRA converged on elevated ERK‐ETS activity, attenuation of which by either genetic or pharmacological manipulation effectively suppressed dopaminergic degeneration in Drosophila in vivo. Down‐regulation of SMARCA4 or drug inhibition of MEK/ERK also mitigated mitochondrial defects in PINK1 (a PD‐associated gene)‐deficient human cells. Our findings underscore the important role of epigenetic regulators and implicate a common signaling axis for therapeutic intervention in normal aging and a broad range of age‐related disorders including PD

In Silico Identification of Structure Requirement for Novel Thiazole and Oxazole Derivatives as Potent Fructose 1,6-Bisphosphatase Inhibitors

Fructose 1,6-bisphosphatase (FBPase) has been identified as a drug discovery target for lowering glucose in type 2 diabetes mellitus. In this study, a large series of 105 FBPase inhibitors were studied using a combinational method by 3D-QSAR, molecular docking and molecular dynamics simulations for a further improvement in potency. The optimal 3D models exhibit high statistical significance of the results, especially for the CoMFA results with rncv2, q2 values of 0.986, 0.514 for internal validation, and rpred2, rm2 statistics of 0.902, 0.828 statistics for external validation. Graphic representation of the results, as contoured 3D coefficient plots, also provides a clue to the reasonable modification of molecules. (1) Substituents with a proper length and size at the C5 position of the thiazole core are required to enhance the potency; (2) A small and electron-withdrawing group at the C2 position linked to the thiazole core is likely to help increase the FBPase inhibition; (3) Substituent groups as hydrogen bond acceptors at the C2 position of the furan ring are favored. In addition, the agreement between 3D-QSAR, molecular docking and molecular dynamics simulation proves the rationality of the developed models. These results, we hope, may be helpful in designing novel and potential FBPase inhibitors