Induced proximity labeling and editing for epigenetic research.

Epigenetic regulation plays a pivotal role in various biological and disease processes. Two key lines of investigation have been pursued that aim to unravel endogenous epigenetic events at particular genes (probing) and artificially manipulate the epigenetic landscape (editing). The concept of induced proximity has inspired the development of powerful tools for epigenetic research. Induced proximity strategies involve bringing molecular effectors into spatial proximity with specific genomic regions to achieve the probing or manipulation of local epigenetic environments with increased proximity. In this review, we detail the development of induced proximity methods and applications in shedding light on the intricacies of epigenetic regulation.

Site-Specific m6 A Erasing via Conditionally Stabilized CRISPR-Cas13b Editor.

N6-methyladenosine (m6 A) on RNAs plays an important role in regulating various biological processes and CRIPSR technology has been employed for programmable m6 A editing. However, the bulky size of CRISPR protein and constitutively expressed CRISPR/RNA editing enzymes can interfere with the native function of target RNAs and cells. Herein, we reported a conditional m6 A editing platform (FKBP*-dCas13b-ALK) based on a ligand stabilized dCas13 editor. The inducible expression of this m6 A editing system was achieved by adding or removing the Shield-1 molecule. We further demonstrated that the targeted recruitment of dCas13b-m6 A eraser fusion protein and site-specific m6 A erasing were achieved under the control of Shield-1. Moreover, the release and degradation of dCas13b fusion protein occurred faster than the restoration of m6 A on the target RNAs after Shield-1 removal, which provides an ideal opportunity to study the m6 A function with minimal steric interference from bulky dCas13b fusion protein.

Star Memristive Neural Network: Dynamics Analysis, Circuit Implementation, and Application in a Color Cryptosystem.

At present, memristive neural networks with various topological structures have been widely studied. However, the memristive neural network with a star structure has not been investigated yet. In order to investigate the dynamic characteristics of neural networks with a star structure, a star memristive neural network (SMNN) model is proposed in this paper. Firstly, an SMNN model is proposed based on a Hopfield neural network and a flux-controlled memristor. Then, its chaotic dynamics are analyzed by using numerical analysis methods including bifurcation diagrams, Lyapunov exponents, phase plots, Poincaré maps, and basins of attraction. The results show that the SMNN can generate complex dynamical behaviors such as chaos, multi-scroll attractors, and initial boosting behavior. The number of multi-scroll attractors can be changed by adjusting the memristor's control parameters. And the position of the coexisting chaotic attractors can be changed by switching the memristor's initial values. Meanwhile, the analog circuit of the SMNN is designed and implemented. The theoretical and numerical results are verified through MULTISIM simulation results. Finally, a color image encryption scheme is designed based on the SMNN. Security performance analysis shows that the designed cryptosystem has good security.

The Progress of Research on Genetic Factors of Recurrent Pregnancy Loss.

Recurrent pregnancy loss (RPL) is both mental and physical health problem affecting about 1-5% of women of childbearing age. The etiology of RPL is complex, involving chromosomal abnormalities, autoimmune diseases, metabolic disorders, and endometrial dysfunction. The causes of abortion are still unknown in more than 50% of these cases. With the development of science and technology, an increasing number of scholars focus on this field and find that genetic factors may play an essential role in unexplained RPL, such as embolism-related genes, immune factor-related genes, and chromosomal numeric, and structural variation. This review summarizes the genetic factors associated with RPL, including genetic mutations and genetic polymorphisms, chromosomal variants, and chromosomal polymorphisms. Many related genetic factors have been found to be demographically and geographically relevant, some of which can be used for risk prediction or screening for the etiology of RPL. However, it is difficult to predict and prevent RPL due to uncertain pathogenesis and highly variable clinical presentation. Therefore, the genetic factors of RPL still need plentiful research to obtain a more accurate understanding of its pathogenesis and to provide more detection means for the screening and prevention of RPL.

A theranostic abscisic acid-based molecular glue.

Molecular glues, capable of selectively controlling the interactions between specific pairs or groups of proteins and the associated downstream effects, have become a promising strategy for manipulating cellular functions and developing novel therapies for human diseases. Theranostics with both diagnostic and therapeutic capabilities acting at disease sites has become a powerful tool to achieve both functions simultaneously with high precision. To selectively activate molecular glues at the desired site and monitor the activation signals at the same time, here we report an unprecedented theranostic modular molecular glue platform integrating signal sensing/reporting and chemically induced proximity (CIP) strategies. We have demonstrated for the first time the integration of imaging and activation capacity with a molecular glue on the same platform to create a theranostic molecular glue. A theranostic molecular glue ABA-Fe(ii)-F1 was rationally designed by conjugating a NIR fluorophore dicyanomethylene-4H-pyran (DCM) with a CIP inducer abscisic acid (ABA) using a unique carbamoyl oxime linker. We have also engineered a new version of ABA-CIP with an enhanced ligand-responding sensitivity. We have validated that the theranostic molecular glue can sense Fe2+ and produce turn-on NIR fluorescence for monitoring as well as releasing the active inducer ligand to control cellular functions including gene expression and protein translocation. This novel molecular glue strategy paves the way to building a new class of molecular glues with theranostic capacity for research and biomedical applications.

[Spatial Distribution Characteristics and Influencing Factors of Soil Organic Carbon Density in Yellow River Basin Based on MGWR Model].

As the largest terrestrial carbon pool, the spatial distribution characteristics and influencing factors of soil organic carbon have important implications for global carbon cycle processes. Soil organic carbon density (SOCD) and influencing factors were predicted in the Yellow River basin using a mixed geographically weighted regression (MGWR) model based on soil organic carbon density data and environmental factors. The results showed that:① the SOCD ranged from 0-14.82 kg·m-2 and 0-32.39 kg·m-2 for the soil depths of 0-20 cm and 0-100 cm, with mean values of 3.48 kg·m-2 and 8.07 kg·m-2 and reserves of 2.76 Pg and 6.48 Pg, respectively. The high SOCD value areas were mainly located in the southern part of the Qinghai-Tibet Plateau and Loess Plateau, and the low value areas were located in the eastern part of the upper Yellow River and the inland flow area. ②Among the ecosystem types, the SOCD of soil depth in 0-20 cm was in the descending order of:forest>water body and wetland>other>grassland>farmland>settlement>desert, with mean values of 4.52, 4.31, 3.84, 3.73, 2.89, 2.78, and 2.22 kg·m-2, respectively, and the SOCD of the 0-100 cm soil depth was in the descending order of:water bodies and wetlands>forest>other>grassland>farmland>settlement>desert, with mean values of 9.58, 9.58, 8.85, 8.66, 7.07, 6.81, and 5.29 kg·m-2, respectively. The SOCR in descending order was:grassland>farmland>forest>desert>water bodies and wetlands>settlement>others, with 1.40, 0.60, 0.47, 0.11, 0.07, 0.06, and 0.05 Pg at a soil depth of 0-20 cm and 3.31, 1.49, 0.99, 0.26, 0.17, 0.14, and 0.12 Pg at a soil depth of 0-100 cm, respectively. ③ The main factors affecting the SOCD distribution were intercept, profile curvature, NDVI, and precipitation; in addition, curvature and silt also had important effects on the deep SOCD distribution in the Yellow River basin. Among the ecosystem types, precipitation and NDVI were the main factors affecting the SOCD distribution. The intercept also had important effects on the SOCD distribution in the all ecosystems except forests, whereas curvature and silt only had important effects on deserts and other ecosystems. These results revealed the spatial distribution of SOCD, influencing factors, and SOCR in the Yellow River basin and can provide a scientific basis for carbon balance, soil quality evaluation, and ecological management restoration and consolidation in the region.

A Split CRISPR/Cas13b System for Conditional RNA Regulation and Editing.

The CRISPR/Cas13b system has been demonstrated as a robust tool for versatile RNA studies and relevant applications. New strategies enabling precise control of Cas13b/dCas13b activities and minimal interference with native RNA activities will further facilitate the understanding and regulation of RNA functions. Here, we engineered a split Cas13b system that can be conditionally activated and deactivated under the induction of abscisic acid (ABA), which achieved the downregulation of endogenous RNAs in dosage- and time-dependent manners. Furthermore, an ABA inducible split dCas13b system was generated to achieve temporally controlled deposition of m6A at specific sites on cellular RNAs through conditional assembly and disassembly of split dCas13b fusion proteins. We also showed that the activities of split Cas13b/dCas13b systems can be modulated by light via using a photoactivatable ABA derivative. Overall, these split Cas13b/dCas13b platforms expand the existing repertoire of the CRISPR and RNA regulation toolkit to achieve targeted manipulation of RNAs in native cellular environments with minimal functional disruption to these endogenous RNAs.

A CRISPR-based Strategy for Temporally Controlled Site-Specific Editing of RNA Modifications.

Chemical modifications on RNA play important roles in regulating its fate and various biological activities. However, the impact of RNA modifications varies depending on their locations on different transcripts and cells/tissues contexts; available tools to dissect context-specific RNA modifications are still limited. Herein, we report the detailed protocol for using a chemically inducible and reversible platform to achieve site-specific editing of the chosen RNA modification in a temporally controlled manner by integrating the clustered regularly interspaced short palindromic repeats (CRISPR) technology and the abscisic acid (ABA)-based chemically induced proximity (CIP) system. The procedures were demonstrated using the example of inducible and reversible N6-methyladenosine (m6A) editing and the evaluation of its impact on RNA properties with ABA addition and reversal with the control of ABA or light.

Effect of Volume Fraction of Reinforcement on Microstructure and Mechanical Properties of In Situ (Ti, Nb)B/Ti2AlNb Composites with Tailored Three-Dimensional Network Architecture.

The mechanical properties of (Ti, Nb)B/Ti2AlNb composites were expected to improve further by utilizing spark plasma sintering (SPS) and inducing the novel three-dimensional network architecture. In this study, (Ti, Nb)B/Ti2AlNb composites with the novel architecture were successfully fabricated by ball milling the LaB6 and Ti2AlNb mixed powders and subsequent SPS consolidation. The influence of the (Ti, Nb)B content on the microstructure and mechanical properties of the composites was revealed by using the scanning electron microscope (SEM), transmission electron microscopy (TEM) and electronic universal testing machine. The microstructural characterization demonstrated that the boride crystallized into a B27 structure and the α2-precipitated amount increased with the (Ti, Nb)B increasing. When the (Ti, Nb)B content reached 4.9 vol%, both the α2 and reinforcement exhibited a continuous distribution along the prior particle boundaries (PPBs). The tensile test displayed that the tensile strength of the composites presented an increasing trend with the increasing (Ti, Nb)B content followed by a decreasing trend. The composite with a 3.2 vol% reinforcement had the optimal mechanical properties; the yield strengths of the composite at 25 and 650 °C were 998.3 and 774.9 MPa, showing an 11.8% and 9.2% improvement when compared with the Ti2AlNb-based alloy. Overall, (Ti, Nb)B possessed an excellent strengthening effect and inhibited the strength weakening of the PPBs area at high temperatures; the reinforcement content mainly affected the mechanical properties of the (Ti, Nb)B/Ti2AlNb composites by altering the α2-precipitated amount and the morphology of (Ti, Nb)B in the PPBs area. Both the continuous precipitation of the brittle α2 phase and the agglomeration of the (Ti, Nb)B reinforcement dramatically deteriorated the mechanical properties.

C-Type Natriuretic Peptide (CNP) Could Improve Sperm Motility and Reproductive Function of Asthenozoospermia.

This study is to analyze the effect of C-type natriuretic peptide (CNP) on sperm motility of asthenozoospermia and explore the influence mechanism of CNP on the reproductive system and sperm motility. Our results showed that the concentration of CNP in asthenospermia patients' semen was lower than in normal people's. The motility of sperm could be improved markedly by CNP and 8-Br-cGMP, while the effect of CNP was inhibited by NPR-B antagonist and KT5823. In the asthenozoospermia mouse model induced by CTX, CNP injection could improve sperm motility in the epididymis, alleviate tissue damage in the testes and epididymis, and increase testosterone levels. The asthenospermia mouse model showed high activity of MDA and proinflammatory factors (TNF-α, IL-6), as well as low expression of antioxidants (SOD, GSH-Px, CAT) in the testis and epididymis, but this situation could be significantly ameliorated after being treated with CNP. Those studies indicated that the concentration of CNP in the semen of asthenospermia patients is lower than in normal people and could significantly promote sperm motility through the NPR-B/cGMP pathway. In the asthenospermia mouse model induced by CTX, CNP can alleviate the damage of cyclophosphamide to the reproductive system and sperm motility. The mechanism may involve increasing testosterone and reducing ROS and proinflammatory factors to damage the tissue and sperm.

Ultra-narrow-linewidth DFB laser array based on dual-cavity feedback.

Herein, we propose a structure to simultaneously compress the distributed feedback (DFB) laser array's linewidth. The proposed structure is meticulously designed to ensure single longitudinal mode operation via the interference phenomenon between the laser's primary cavity and the dual-cavity feedback. Given the weak feedback effect for each wavelength in the laser array, the proposed structure could realize the intense compression of the laser linewidths. The study results show that the side-mode suppression ratios of each DFB laser are over 40 dB, and the linewidths have been compressed from 3 MHz to ∼800 Hz. Thus, we believe the idea of an overall compression linewidth scheme in the present study can be adopted for integrated laser arrays.

Inducible and reversible RNA N6-methyladenosine editing.

RNA modifications, including N6-methyladenosine (m6A), have been reported to regulate fundamental RNA processes and properties, and directly linked to various human diseases. Methods enabling temporal and transcript/locus-specific editing of specific RNA modifications are essential, but still limited, to dissect the dynamic and context-dependent functions of these epigenetic modifications. Here, we develop a chemically inducible and reversible RNA m6A modification editing platform integrating chemically induced proximity (CIP) and CRISPR methods. We show that m6A editing can be temporally controlled at specific sites of individual RNA transcripts by the addition or removal of the CIP inducer, abscisic acid (ABA), in the system. By incorporating a photo-caged ABA, a light-controlled version of m6A editing platform can be developed. We expect that this platform and strategy can be generally applied to edit other RNA modifications in addition to m6A.

Investigating crosstalk between H3K27 acetylation and H3K4 trimethylation in CRISPR/dCas-based epigenome editing and gene activation.

Epigenome editing methods enable the precise manipulation of epigenetic modifications, such as histone posttranscriptional modifications (PTMs), for uncovering their biological functions. While histone PTMs have been correlated with certain gene expression status, the causalities remain elusive. Histone H3 Lysine 27 acetylation (H3K27ac) and histone H3 Lysine 4 trimethylation (H3K4me3) are both associated with active genes, and located at active promoters and enhancers or around transcriptional start sites (TSSs). Although crosstalk between histone lysine acetylation and H3K4me3 has been reported, relationships between specific epigenetic marks during transcriptional activation remain largely unclear. Here, using clustered regularly interspaced short palindromic repeats (CRISPR)/dCas-based epigenome editing methods, we discovered that the ectopic introduction of H3K27ac in the promoter region lead to H3K4me3 enrichment around TSS and transcriptional activation, while H3K4me3 installation at the promoter cannot induce H3K27ac increase and failed to activate gene expression. Blocking the reading of H3K27ac by BRD proteins using inhibitor JQ1 abolished H3K27ac-induced H3K4me3 installation and downstream gene activation. Furthermore, we uncovered that BRD2, not BRD4, mediated H3K4me3 installation and gene activation upon H3K27ac writing. Our studies revealed the relationships between H3K27ac and H3K4me3 in gene activation process and demonstrated the application of CRISPR/dCas-based epigenome editing methods in elucidating the crosstalk between epigenetic mechanisms.

Two New Coordination Polymers: Selective Detection of Cu(II) Ion and Treatment Activity on Inner Ear Damage.

In the current study, on the basis of 1,3,5-tris(2-methylimidazol-1-yl)benzene (timb), a designed tripodal connector, two new transition metal coordination polymers (CPs), {[Cu4(timb)2(Br-IPA)4]·5H2O}n (1) and {[Zn(timb)0.5(NH2-IPA)]·4H2O}n (2) have been generated with the mixed ligand method by the reaction between the timb and corresponding metal salts in the existence of dissimilar functional isophthalic acid (H2IPA) ligands. Furthermore, the Zn(II)-based complex 2 displays high sensitivity in the detection of Cu(II) ion in water. The neural stem cells proliferation after treated via compounds was detected with Cell Counting Kit-8 detection assay. And the real time reverse transcription polymerase chain reaction was carried out for the investigation of the differentiation function of the neural stem cells after the compound 1 treatment and compound 2 treatment. Further, molecular docking simulations confirmed that the biological activity that has been observed from experiments were from the carboxyl group on the Cu complex, in contrast, the imidazole groups were only used for binding with the Cu metal ion to retain the complex structure.

Study on the Evolution of Graphene Defects and the Mechanical and Thermal Properties of GNPs/Cu during CVD Repair Process.

Graphene has extremely high theoretical strength and electrothermal properties, and its application to Cu-based composites is expected to achieve a breakthrough in the performance of existing composites. As a nano-reinforced body, graphene often needs a long time of ball milling to make it uniformly dispersed, but the ball milling process inevitably brings damage to the graphene, causing the performance of the composite to deviate from expectations. Therefore, this paper uses CH4 as a carbon source to repair graphene through a CVD process to prepare low-damage graphene/Cu composites. The process of graphene defect generation was studied through the ball milling process. The effects of defect content and temperature on the graphene repair process were studied separately. The study found that the graphene defect repair process, the decomposition process of oxygen-containing functional groups, and the deposition process of active C atoms existed simultaneously in the CVD process. When the repair temperature was low, the C atom deposition process and the oxygen-containing functional group decomposition process dominated. In addition, when the repair temperature is high, the graphene defect repair process dominated. 3 wt% graphene/Cu composites were prepared by pressure infiltration, and it was found that the bending strength was increased by 48%, the plasticity was also slightly increased, and the thermal conductivity was increased by 10-40%. This research will help reduce graphene defects, improve the intrinsic properties of graphene, and provide theoretical guidance for the regulation of C defects in composites.

Bifunctional small molecule-oligonucleotide hybrid as microRNA inhibitor.

miRNAs are key regulators of various biological processes. Dysregulation of miRNA is linked to many diseases. Development of miRNA inhibitor has implication in disease therapy and study of miRNA function. The biogenesis pathway of miRNA involves the processing of pre-miRNA into mature miRNA by Dicer enzyme. We previously reported a proximity enabled approach that employs bifunctional small molecules to regulate miRNA maturation through inhibiting the enzymatic activity of Dicer. By conjugating to an RNA targeting unit, an RNase inhibitor could be delivered to the cleavage site of specific pre-miRNA to deactivate the complexed Dicer enzyme. Herein, we expanded this bifunctional strategy by showing that antisense oligonucleotides (ASOs), including morpholinos and γPNAs, could be readily used as the RNA recognition unit to generate bifunctional small molecule-oligonucleotide hybrids as miRNA inhibitors. A systematic comparison revealed that the potency of these hybrids is mainly determined by the RNA binding of the targeting ASO molecules. Since the lengths of the ASO molecules used in this approach were much shorter than commonly used anti-miRNA ASOs, this may provide benefits to the specificity and cellular delivery of these hybrids. We expect that this approach could be complementary to traditional ASO and small molecule based miRNA inhibition and contribute to the study of miRNA.

Chemical and Light Inducible Epigenome Editing.

The epigenome defines the unique gene expression patterns and resulting cellular behaviors in different cell types. Epigenome dysregulation has been directly linked to various human diseases. Epigenome editing enabling genome locus-specific targeting of epigenome modifiers to directly alter specific local epigenome modifications offers a revolutionary tool for mechanistic studies in epigenome regulation as well as the development of novel epigenome therapies. Inducible and reversible epigenome editing provides unique temporal control critical for understanding the dynamics and kinetics of epigenome regulation. This review summarizes the progress in the development of spatiotemporal-specific tools using small molecules or light as inducers to achieve the conditional control of epigenome editing and their applications in epigenetic research.

miRNA inhibition by proximity-enabled Dicer inactivation.

microRNAs (miRNAs) are considered as master regulators of biological processes. Dysregulation of miRNA expression has been implicated in many human diseases. Driven by the key biological roles and the therapeutic potential, developing methods for miRNA regulation has become an intense research area. Due to favorable pharmacological properties, small molecule-based miRNA inhibition emerges as a promising strategy and significant progresses have been made. However, it remains challenging to regulate miRNA using small molecules because of the inherent difficulty in RNA targeting and inhibition. Herein we outline the workflow of generating bifunctional small molecule inhibitors blocking miRNA biogenesis through proximity-enabled inactivation of Dicer, an enzyme required for the processing of precursor miRNA (pre-miRNA) into mature miRNA. By conjugating a weak Dicer inhibitor with a pre-miRNA binder, the inhibitor can be delivered to the Dicer processing site associated with the targeted pre-miRNA, and as a result inhibiting Dicer-mediated pre-miRNA processing. This protocol can be applicable in producing bifunctional inhibitors for different miRNAs.