Structural variation discovery in wheat using PacBio high-fidelity sequencing.

Structural variations (SVs) pervade plant genomes and contribute substantially to the phenotypic diversity. However, most SVs were ineffectively assayed due to their complex nature and the limitations of early genomic technologies. By applying the PacBio high-fidelity (HiFi) sequencing for wheat genomes, we performed a comprehensive evaluation of mainstream long-read aligners and SV callers in SV detection. The results indicated that the accuracy of deletion discovery is markedly influenced by callers, accounting for 87.73% of the variance, whereas both aligners (38.25%) and callers (49.32%) contributed substantially to the accuracy variance for insertions. Among the aligners, Winnowmap2 and NGMLR excelled in detecting deletions and insertions, respectively. For SV callers, SVIM achieved the best performance. We demonstrated that combining the aligners and callers mentioned above is optimal for SV detection. Furthermore, we evaluated the effect of sequencing depth on the accuracy of SV detection, revealing that low-coverage HiFi sequencing is sufficiently robust for high-quality SV discovery. This study thoroughly evaluated SV discovery approaches and established optimal workflows for investigating structural variations using low-coverage HiFi sequencing in the wheat genome, which will advance SV discovery and decipher the biological functions of SVs in wheat and many other plants.

Asymmetric 1,4-Addition of Diarylphosphine Oxides to α, ß-Unsaturated 2-Acyl Imidazoles.

Here we introduce a metal-free, catalytic and enantioselective strategy from α,ß-unsaturated 2-acyl imidazoles to the chiral phosphorous 2-acyl imidazoles. Interestingly, this methodology was catalyzed by the classical and commercial oxazaborolidine under mild conditions. This strategy features a wide range of substrates scope with good yields and excellent enantioselectivities. The possible mechanism further suggests the key of this reaction through the cleavage of diarylphosphine oxides using Frustrated Lewis Pairs theory.

Long noncoding RNA UCA1 promotes the expression and function of P-glycoprotein by sponging miR-16-5p in human placental BeWo cells.

Investigations on placental P-glycoprotein (P-gp) regulation could provide more therapeutic targets for individualized and safe pharmacotherapy during pregnancy. The role of long noncoding RNA (lncRNA) on placental P-gp regulation is lacking. The present study was carried out to investigate the regulation and underlying mechanisms of lncRNA urothelial carcinoma associated 1 (UCA1) on P-gp in Bewo cells. lncRNA UCA1 inhibition or overexpression could decrease or increase ABCB1 mRNA expression, P-gp expression and its cellular efflux function, respectively. RNA-FISH revealed that lncRNA UCA1 was mainly located in the cytoplasm of Bewo cells. MicroRNA array was applied and 10 significant miRNAs was identified after lncRNA UCA1 inhibition. Databases of LncTarD, LncRNA2Target, and miRcode were further used to search potential target miRNAs of lncRNA UCA1 and miR-16-5p was screened out. Thereafter, we confirmed that miR-16-5p expression was significantly upregulated or reduced after lncRNA UCA1 knockdown or overexpression, respectively. Furthermore, we also proved that ABCB1 mRNA expression, P-gp expression and its cellular efflux function was enhanced or reduced after miR-16-5p inhibition or overexpression, respectively. The rescue experiment further indicated that miR-16-5p was involved in the positive regulation of lncRNA UCA1 on the expression and function of P-gp. Lastly, dual-luciferase reporter system, RNA-binding protein immunoprecipitation and RNA pull-down assays were performed to explore the relationships among lncRNA UCA1, miR-16-5p, and ABCB1. It was found that lncRNA UCA1(1103-1125) could directly interact with miR-16-5p and miR-16-5p could directly target ABCB1 coding DNA sequence region (882-907). In conclusion, LncRNA UCA1 could promote the expression and function of P-gp by sponging miR-16-5p in BeWo cells.

Metal-Free Enantioselective 1,4-Addition of Diarylphosphine Oxides to α,ß-Unsaturated Carboxylic Esters.

The catalytic asymmetric conjugate addition of phosphorus nucleophiles to unsaturated compounds, catalyzed by metallic or nonmetallic catalysts, has been extensively developed. However, the enantioselective transformations involving α,ß-unsaturated carboxylic esters for constructing chiral c-p bonds have been rarely reported, particularly in metal-free processes. In this study, we present a novel metal-free methodology for enantioselective 1,4-addition of diarylphosphine oxides to α,ß-unsaturated carboxylic esters using classical chiral oxazaborolidine catalysts. Remarkably high yields and enantioselectivities were obtained for most of the products. Furthermore, these valuable chiral phosphorus esters serve as crucial intermediates that can be transformed into various derivatives including amides, acids, and alcohols in a single step.

Constructing porous ZnFC-PA/PSF composite spheres for highly efficient Cs+ removal.

Radioisotope leaking from nuclear waste has become an intractable problem due to its gamma radiation and strong water solubility. In this work, a novel porous ZnFC-PA/PSF composite sphere was fabricated by immobilization of ferrocyanides modified zinc phytate into polysulfone (PSF) substrate for the treatment of Cs-contaminated water. The maximum adsorption capacity of ZnFC-PA/PSF was 305.38 mg/g, and the removal efficiency of Cs+ was reached 94.27% within 2 hr. The ZnFC-PA/PSF presented favorable stability with negligible dissolution loss of Zn2+ and Fe2+ (< 2%). The ZnFC-PA/PSF achieved high-selectivity towards Cs+ (Kd = 2.24×104 mL/g) even in actual geothermal water. The adsorption mechanism was inferred to be the ion-exchange between Cs+ and K+. What's more, ZnFC-PA/PSF worked well in the fixed-bed adsorption (E = 91.92%), indicating the application potential for the hazardous Cs+ removal from wastewater.

Dynamic Covalent Bonds Regulate Zinc Plating/Stripping Behaviors for High-Performance Zinc Ion Batteries.

Artificial interfaces provide a comprehensive approach to controlling zinc dendrite and surface corrosion in zinc-based aqueous batteries (ZABs). However, due to consistent volume changes during zinc plating/stripping, traditional interfacial layers cannot consistently adapt to the dendrite surface, resulting in uncontrolled dendrite growth and hydrogen evolution. Herein, dynamic covalent bonds exhibit the Janus effect towards zinc deposition at different current densities, presenting a holistic strategy for stabilizing zinc anode. The PBSC intelligent artificial interface consisting of dynamic B-O covalent bonds is developed on zinc anode to mitigate hydrogen evolution and restrict dendrite expansion. Owing to the reversible dynamic bonds, PBSC exhibits shape self-adaptive characteristics at low current rates, which rearranges the network to accommodate volume changes during zinc plating/stripping, resisting hydrogen evolution. Moreover, the rapid association of B-O dynamic bonds enhances mechanical strength at dendrite tips, presenting a shear-thickening effect and suppressing further dendrite growth at high current rates. Therefore, the assembled symmetrical battery with PBSC maintains a stable cycle of 4500 hours without significant performance degradation and the PBSC@Zn||V2O5 pouch cell demonstrates a specific capacity exceeding 170 mAh g-1. Overall, the intelligent interface with dynamic covalent bonds provides innovative approaches for zinc anode interfacial engineering and enhances cycling performance.

Enantioselective Transformations from Nitriles to NH2 -α-Tertiary Amines.

Organic molecules, containing one or more amine chiral centers, are very common to see in natural products and medicines. Although a large number of methods have been developed to afford enantiopure amines, most of the known approaches are limited with various reasons. For example, many methodologies start from nitrogen protected and activated substrates, which usually need multistep operations and seriously decrease the atom economy. Here we disclose a new catalytic strategy from commercial nitriles to high enantioselective α-tertiary primary amines in up to 90 % yield and 95 % enantiomeric excess. This transformation firstly undergoes an addition process of organolithium reagents to nitriles to generate the imine intermediates in situ. Subsequently, the most challenging step is by employing copper catalytic enantioselective addition of AllylBpin to the imine intermediates to form the final amines in one pot.

Hsp70-Bim interaction facilitates mitophagy by recruiting parkin and TOMM20 into a complex.

BACKGROUND: For cancer therapy, the identification of both selective autophagy targets and small molecules that specifically regulate autophagy is greatly needed. Heat shock protein 70 (Hsp70) is a recently discovered BH3 receptor that forms a protein‒protein interaction (PPI) with Bcl-2-interacting mediator of cell death (Bim). Herein, a specific inhibitor of the Hsp70-Bim PPI, S1g-2, and its analog S1, which is a Bcl-2-Bim disruptor, were used as chemical tools to explore the role of Hsp70-Bim PPI in regulating mitophagy. METHODS: Co-immunoprecipitation and immunofluorescence assays were used to determine protein interactions and colocalization patterns. Organelle purification and immunodetection of LC3-II/LC3-I on mitochondria, endoplasmic reticulum (ER) and Golgi were applied to identify specific types of autophagy. Cell-based and in vitro ubiquitination studies were used to study the role of the Hsp70-Bim PPI in parkin-mediated ubiquitination of outer mitochondrial membrane 20 (TOMM20). RESULTS: We found that after the establishment of their PPI, Hsp70 and Bim form a complex with parkin and TOMM20, which in turn facilitates parkin translocation to mitochondria, TOMM20 ubiquitination and mitophagic flux independent of Bax/Bak. Moreover, S1g-2 selectively inhibits stress-induced mitophagy without interfering with basal autophagy. CONCLUSIONS: The findings highlight the dual protective function of the Hsp70-Bim PPI in regulating both mitophagy and apoptosis. S1g-2 is thus a newly discovered antitumor drug candidate that drives both mitophagy and cell death via apoptosis.

BM3D-based denoising method for color polarization filter array.

Color split-focal plane polarization imaging systems are composed of image sensors with a color polarization filter array (CPFA). The noise generated during image acquisition leads to incorrect estimation of the color polarization information. Therefore, it is necessary to denoise CPFA image data. In this study, we propose a CPFA block-matching and 3D filtering (CPFA-BM3D) algorithm for CPFA image data. The algorithm makes full use of the correlation between different polarization channels and different color channels, restricts the grouping of similar 2D image blocks to form 3D blocks, and attenuates Gaussian noise in the transform domain. We evaluate the denoising performance of the proposed algorithm using simulated and real CPFA images. Experimental results show that the proposed method significantly suppresses noise while preserving the image details and polarization information. Its peak signal-to-noise ratio (PSNR) and structural similarity (SSIM) indicators are superior to those of the other existing methods. The mean values of the PSNR and SSIM of the degree of linear polarization (DoLP) color images calculated through CPFA image interpolation can be increased to 200% and 400%, respectively, by denoising with the proposed method.

Discovery of a Fluorogenic Probe for In Situ Pyruvate Kinase M2 Isoform (PKM2) Labeling through Chemoselective SNAr with a Binding Site Lysine Residue.

The key challenge of developing reaction-based turn-on probes is to establish latent electrophilic fluorophores exhibiting high reactivity only upon binding to a specific protein(s). Herein, we identified such a fluorophore, 6-arylthioether-substituted 3-cyano-1-oxo-1H-phenalene-2-carboxylate, which chemoselectively labels binding site Cys or Lys residues. Based on this fluorophore, we developed the first reaction-based turn-on pyruvate kinase M2 isoform (PKM2) fluorescent probe AT-OPC1, which selectively labels PKM2 with the binding site Lys305. The latent electrophilic reactivity of the fluorophore endows the probe with precise detection of the expression of PKM2 in situ by means of both in-gel fluorescence imaging at the proteome level and real-time no-wash cell imaging approaches, which has the potential to be applied in cancer diagnoses.

Design, synthesis, and biological evaluation of 5-((4-(pyridin-3-yl)pyrimidin-2-yl)amino)-1H-Indole-2-Carbohydrazide derivatives: the methuosis inducer 12A as a Novel and selective anticancer agent.

This study describes the synthesis and vacuole-inducing activity of 5-((4-(pyridin-3-yl)pyrimidin-2-yl)amino)-1H-indole-2-carbohydrazide derivatives, including five potent derivatives 12c, 12 g, 12i, 12n, and 12A that exhibit excellent vacuole-inducing activity. Remarkably, 12A effectively induces methuosis in tested cancer cells but not human normal cells. In addition, 12A exhibits high pan-cytotoxicity against different cancer cell lines but is hardly toxic to normal cells. It is found that the 12A-induced vacuoles are derived from macropinosomes but not autophagosomes. The 12A-induced cytoplasmic vacuoles may originate from the endoplasmic reticulum (ER) and be accompanied by ER stress. The MAPK/JNK signalling pathway is involved in the 12A-induced methuotic cell death. Moreover, 12A exhibits significant inhibition of tumour growth in the MDA-MB-231 xenograft mouse model. The excellent potency and selectivity of 12A prompt us to select it as a good lead compound for further development of methuosis inducers and investigation of the molecular and cellular mechanisms underlying methuosis.

Synthesis and Antiproliferative Activity of New Thiosemicarboxamide Derivatives.

To discover new anticancer agents, two series of thiosemicarboxamide derivatives were synthesized and evaluated for their antiproliferative activity against human cancer cells in vitro. Most target compounds (especially 3f, 3g, and 3h) exhibit potent antiproliferative activity against HeLa cells. Importantly, compound 3h, bearing a 4-methylphenyl substituent at N position of thiourea moiety, has significant and broad-spectrum inhibitory activities against cancer cells (HepG2, HeLa, MDA-MB231, A875, and H460 cells) with low IC50 values (<5.0 µM) and shows low toxicity to normal LO2 and MRC-5 cells. Further studies show that compound 3h exerts high inhibitory activity in cancer cells by inducing the G2/M-phase arrest of cancer cells. Collectively, this study presents compound 3h as a new entity for the development of cell cycle arrest inducers for the treatment of cancer.

CXCR4-SF1 bifunctional adipose-derived stem cells benefit for the treatment of Leydig cell dysfunction-related diseases.

Stem cell transplantation is a candidate method for the treatment of Leydig cell dysfunction-related diseases. However, there are still many problems that limit its clinical application. Here, we report the establishment of CXCR4-SF1 bifunctional adipose-derived stem cells (CXCR4-SF1-ADSCs) and their reparative effect on Leydig cell dysfunction. CD29+ CD44+ CD34- CD45- ADSCs were isolated from adipose tissue and purified by fluorescence-activated cell sorting (FACS). Infection with lentiviruses carrying the CXCR4 and SF1 genes was applied to construct CXCR4-SF1-ADSCs. The CXCR4-SF1-ADSCs exhibited enhanced migration and had the ability to differentiate into Leydig-like cells in vitro. Furthermore, the bifunctional ADSCs were injected into BPA-mediated Leydig cell damage model mice via the tail vein. We found that the CXCR4-SF1-ADSCs were capable of homing to the injured testes, differentiating into Leydig-like cells and repairing the deficiency in reproductive function caused by Leydig cell dysfunction. Moreover, we investigated the mechanism underlying SF1-mediated differentiation and testosterone synthesis in Leydig cells, and the B-box and SPRY Domain Containing Protein (BSPRY) gene was proposed to be involved in this process. This study provides insight into the treatment of Leydig cell dysfunction-related diseases.

Enhanced kinetics and super selectivity toward Cs+ in multicomponent aqueous solutions: A robust Prussian blue analogue/polyvinyl chloride composite membrane.

Developing effective adsorbents for 137Cs removal from complex wastewater systems has been a significant challenge. Although existing spheres adsorbents could improve the post-separation ability and practical operability, the adsorption kinetics are still significantly retarded due to the large intra-particle diffusion resistance. Here, we demonstrate the efficiency of a robust Prussian blue analogue/polyvinyl chloride composite membrane (PPM), which was easily prepared by a simple solvent evaporation method. In virtue of the less dense layer and ion-sieving functionality, it showed enhanced kinetics (5 h) and super selectivity (SF = 248.3-5388.6) towards Cs+. New PPM was robust within a wide pH range (2-10) and exhibited favorable removal capacity (152.8 mg/g), placing it at an outstanding material for Cs+ removal among other adsorbents. Moreover, PPM could be simply eluted and reused using a KCl solution as eluent. A study of the adsorption mechanism confirmed an ion-exchange action during the removal process. Thus, PPM is considered to be a promising candidate for the removal of Cs+ from multicomponent aqueous solutions.

Structure-based design, synthesis, and evaluation of Bcl-2/Mcl-1 dual inhibitors.

Based on our previously reported Bcl-2/Mcl-1 dual inhibitor 4-thiomorpholinyl-2-cyano-3-amidinophenalenone (A1) that simultaneously occupies the p2 and p4 hydrophobic pockets of Bcl-2 and Mcl-1, we optimized molecules with different bond angles of the groups extending to the p4 pocket and bulky hydrophobic groups to explore p2. Research on structure-activity relationship resulted in a new derivative B4 that is capable of occupying both the p2 and p4 more deeply and completely than A1, with Ki values determined by fluorescence polarization assay (FPAs) improving to 0.31 µM for Bcl-2 and 0.16 µM for Mcl-1. Furthermore, B4 exhibited selective lethality on cancer cells over normal cells. It showed stronger apoptosis induction than (-)-gossypol on a Bcl-2/Mcl-1-dependent cancer cell line and killed an Mcl-1-dependent cell line which is resistant to ABT-199 treatment.

Copper-catalysed alkylation of heterocyclic acceptors with organometallic reagents.

Copper-catalysed asymmetric C-C bond-forming reactions using organometallic reagents have developed into a powerful tool for the synthesis of complex molecules with single or multiple stereogenic centres over the past decades. Among the various acceptors employed in such reactions, those with a heterocyclic core are of particular importance because of the frequent occurrence of heterocyclic scaffolds in the structures of chiral natural products and bioactive molecules. Hence, this review focuses on the progress made over the past 20 years for heterocyclic acceptors.

Molecular characterization of grass carp interleukin-6 receptor and the agonistic activity of its soluble form in head kidney leucocytes.

Interleukin (IL)-6 receptor (IL-6R) can specifically bind to IL-6 and the complex subsequently recruits a transmembrane signal transducer, gp130, to trigger the intracellular signal transduction. IL-6R exists in two forms, a transmembrane IL-6R and a soluble IL-6R (sIL-6R), leading to different signal transduction mechanisms as classic signaling and trans-signaling, respectively. There is now a general consensus that these two modes of signal transduction can mediate anti-inflammatory and pro-inflammatory activities of IL-6. The study on Il-6r is limited although Il-6 has been well studied in teleost. In the present study, a cDNA encoding grass carp Il-6r (gcIl-6r) was isolated. An in-silico analysis showed that gcIl-6r shared the same functional domains and conserved gene synteny at its loci with mouse homologue, and its amino acid sequence was conserved in fish species. A tissue distribution assay demonstrated that gcil6r mRNA was expressed with high levels in immune tissues including spleen and head kidney, and its expression was induced by LPS and Poly I:C in grass carp head kidney leucocytes (HKLs). An in vitro binding assay showed that recombinant soluble gcIl-6r (rgcsIl-6r) could specifically bind to recombinant gcIl-6 (rgcIl-6) protein. Moreover, rgcIl-6 stimulated suppressor of cytokine signaling 3 (socs3)'s mRNA expression in grass carp HKLs and it combined with rgcsIl-6r increased socs3 mRNA expression in CIK cells with gp130 but without Il-6r expression. In HKLs, rgcIl-6 stimulated the mRNA levels of both pro-inflammatory (tnfa and il1b) and anti-inflammatory (il10) cytokines, and rgcsIl-6r could augment these stimulatory effects of gcIl-6. Taken these data together, gcsIl-6r can mediate the immuno-regulatory functions of gcIl-6 and has an agonistic property in these actions of Il-6 in grass carp.

Speciation analysis of arsenic in samples containing high concentrations of chloride by LC-HG-AFS.

Chloride widely exists in the environment and will cause serious interference for arsenic speciation analysis. The determination of four arsenic species including arsenite (As(III)), arsenate (As(V)), monomethylarsenate (MMA), and dimethylarsonate (DMA) in samples containing high concentrations of Cl- was carried out in this work by coupling of liquid chromatography (LC) with hydride generation atomic fluorescence spectrometry (HG-AFS). The interference of Cl- was successfully eliminated by coupling two anion-exchange chromatographic columns in series and eluting with 35.0 mmol L-1 (NH4)2HPO4 (pH = 6.00). A novel pre-treatment system was subsequently developed to realize on-line column switch and pre-reduction of As(V). The analysis time was shortened by an isocratic elution but programmed flow rate method, and the sensitivity of As(V) was also enhanced by the introduction of pre-reduction using the developed system. The proposed method can resist at least 10 g L-1 Cl- without any pre-treatment operations. Since LC-HG-AFS is low-cost and can be afforded or self-assembled by most labs, the developed method can be adopted as a routine analysis method for arsenic species in chloride-bearing samples, such as urine and seawater. Graphical abstract.

Presence of White Matter Lesions Associated with Diabetes-Associated Cognitive Decline in Male Rat Models of Pre-Type 2 Diabetes.

BACKGROUND The aim of this study was to determine the association between white matter lesions (WML) and diabetes-associated cognitive decline (DACD) in rat models of type 2 diabetes (T2DM). MATERIAL AND METHODS Sixty Sprague-Dawley male rats were divided into 4 groups: control, control+metformin, T2DM, and T2DM+metformin groups. The T2DM groups were fed a diet high in fat and glucose to induce impaired glucose tolerance (IGT) and then were injected with streptozotocin to induce T2DM. The Morris water maze test was used to evaluate cognitive function. Brain diffusion tensor imaging scans were performed for WML. The expression of myelin basic protein (MBP), oligodendrocyte transcription factor 1 (OLIG1), and OLIG2 (markers of brain damage and repair) was determined using immunofluorescence. After IGT, the fractional anisotropy (FA) values of the right thalamus area were significantly lower in both T2DM groups compared with controls. RESULTS Eight weeks after streptozotocin injection, the FA values of the thalamus were lower in the T2DM (bilateral thalamus) group and T2DM+metformin (left thalamus) group than in controls, while the FA values in the left thalamus area were lower in the T2DM+metformin group than in the control and control+metformin groups. The maze escape latency was longer and the number of rats passing through the platform was smaller in the T2DM and T2DM+metformin groups than in the control group. MBP levels were lower and OLIG1 and OLIG2 levels were higher in both T2DM groups than in controls. CONCLUSIONS WML is associated with DACD and appears before the onset of T2DM and signs of DACD and plays a role in diabetes-associated cognitive decline. Metformin reduces WMLs but does not rescue cognitive dysfunction.

Effects of Active Immunization Against Akirin2 on Muscle Fiber-type Composition in Pigs.

The objective of this study was to investigate effects of active immunization against Akirin2 on muscle fiber-type composition in pigs. Here we showed that the titer of Akirin2 antibody in pigs immunized with porcine Akirin2 (pAkirin2) was significantly increased. Active immunization against pAkirin2 decreased succinic dehydrogenase and malate dehydrogenase activities and increased lactate dehydrogenase activity in the longissimus dorsi muscle of pigs. Active immunization against pAkirin2 significantly decreased MyHC I and MyHC IIa mRNA expressions and MyHC I protein expression and increased mRNA expressions of MyHC IIb as well as protein expressions of MyHC IIb and fast-MyHC. mRNA expressions of nuclear factors of activated T cells c1 (NFATc1), transcriptional coactivator PPARγ coactivator-1α, myocyte enhancer factor 2C, and modulatory calcineurin interacting protein 1 exon 4 isform were also notably decreased by active immunization against pAkirin2. Together, our data imply that active immunization against pAkirin2 may result in a slow to fast fiber-type shift in pigs, and which may be mediated by suppression of the calcineurin/NFATc1 signaling pathway.