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Abstract Eukaryotic genomes are extensively transcribed into various types of RNAs, many of which are physically associated with chromatin in cis at their transcription sites or in trans to other genomic loci. Emerging roles have been uncovered for these chromatin-associated RNAs (caRNAs) in gene regulation and genome organization, yet they remain challenging to interrogate. Here, we present TaDRIM-seq, a technique employing Protein G (PG)-Tn5-targeted DNA elements and in situ proximity ligation to concurrently probe caRNAs across diverse genomic regions as well as global RNA-RNA interactions within intact nuclei. Notably, this approach diminishes required cell inputs, minimizes hands-on time compared to established methodologies, and is compatible in both mammalian cells and plants. Using this technique, we identify extensive caRNAs at DNA anchor regions associated with chromatin loops and reveal diurnal variation in RNA-DNA and RNA-RNA connectivity networks within rice.

Abstract Background In response to drought stress (DS), plants undergo complex processes that entail significant transcriptome reprogramming. However, the intricate relationship between the dynamic alterations in the three-dimensional (3D) genome and the modulation of gene co-expression in drought responses remains a relatively unexplored area. Results In this study, we reconstruct high-resolution 3D genome maps based on genomic regions marked by H3K9ac, an active histone modification that dynamically responds to soil water variations in rice. We discover a genome-wide disconnection of 3D genome contact upon DS with over 10,000 chromatin loops lost, which are partially recovered in the subsequent re-watering. Loops integrating promoter–promoter interactions (PPI) contribute to gene expression in addition to basal H3K9ac modifications. Moreover, H3K9ac-marked promoter regions with high affinities in mediating PPIs, termed as super-promoter regions (SPRs), integrate spatially clustered PPIs in a super-enhancer-like manner. Interestingly, the knockout mutation of OsbZIP23, a well-defined DS-responsive transcription factor, leads to the disassociation of over 80% DS-specific PPIs and decreased expression of the corresponding genes under DS. As a case study, we show how OsbZIP23 integrates the PPI cluster formation and the co-expression of four dehydrin genes, RAB16A–D, through targeting the RAB16C SPR in a stress signaling-dependent manner. Conclusions Our high-resolution 3D genome maps unveil the principles and details of dynamic genome folding in response to water supply variations and illustrate OsbZIP23 as an indispensable integrator of the yet unique 3D genome organization that is essential for gene co-expression under DS in rice.

Summary: Histone modification H3K27me3 is an important chromatin mark that plays vital roles in repressing expression of developmental genes. Here, we construct high-resolution 3D genome maps using long-read chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) and characterize H3K27me3-associated chromatin interactions in an elite rice hybrid, Shanyou 63. We find that many H3K27me3-marked regions may function as silencer-like regulatory elements. The silencer-like elements can come into proximity with distal target genes via forming chromatin loops in 3D space of the nuclei, regulating gene silencing and plant traits. Natural and induced deletion of silencers upregulate expression of distal connected genes. Furthermore, we identify extensive allele-specific chromatin loops. We find that genetic variations alter allelic chromatin topology, thus modulating allelic gene imprinting in rice hybrids. In conclusion, the characterization of silencer-like regulatory elements and haplotype-resolved chromatin interaction maps provide insights into the understanding of molecular mechanisms underlying allelic gene silencing and plant trait controlling.

Stomatal closure defense and apoplastic defense are two major immunity mechanisms restricting the entry and propagation of microbe pathogens in plants. Surprisingly, activation of plant intracellular immune receptor NLR genes, while enhancing whole plant disease resistance, was sometimes linked to a defective stomatal defense in autoimmune mutants. Here we report the use of high temperature and genetic chimera to investigate the inter-dependence of stomatal and apoplastic defenses in autoimmunity. High temperature inhibits both stomatal and apoplastic defenses in the wild type, suppresses constitutive apoplastic defense responses and rescues the deficiency of stomatal closure response in autoimmune mutants. Chimeric plants have been generated to activate NLR only in guard cells or the non-guard cells. NLR activation in guard cells inhibits stomatal closure defense response in a cell autonomous manner likely through repressing ABA responses. At the same time, it leads to increased whole plant resistance accompanied by a slight increase in apoplastic defense. In addition, NLR activation in both guard and non-guard cells affects stomatal aperture and water potential. This study thus reveals that NLR activation has a differential effect on immunity in a cell type specific matter, which adds another layer of immune regulation with spatial information.

Cancer immunotherapy has garnered promise in tumor progression, invasion, and metastasis through establishing durable and memorable immunological activity. However, low response rates, adverse side effects, and high costs compromise the additional benefits for patients treated with current chemical and biological agents. Chinese herbal medicines (CHMs) are a potential treasure trove of natural medicines and are gaining momentum in cancer immunomodulation with multi-component, multi-target, and multi-pathway characteristics. The active ingredient extracted from CHMs benefit generalized patients through modulating immune response mechanisms. Additionally, the introduction of nanotechnology has greatly improved the pharmacological qualities of active ingredients through increasing the hydrophilicity, stability, permeability, and targeting characteristics, further enhancing anti-cancer immunity. In this review, we summarize the mechanism of active ingredients for cancer immunomodulation, highlight nano-formulated deliveries of active ingredients for cancer immunotherapy, and provide insights into the future applications in the emerging field of nano-formulated active ingredients of CHMs.

Abstract Chemotherapy treatment outcomes are severely restricted by multidrug resistance (MDR), in which tumors develop a multiple cross‐resistance toward drug involving the pump and nonpump resistance mechanisms, resulting in drug efflux and defending against drug toxicity. Herein, we constructed a pH and near infrared (NIR) light responsive nanomedicine DOX@FG based on gold nanorods (GNRs) that demonstrated the potential to improve chemotherapy outcomes by overcoming MDR. DOX@FG was constructed by conjugating folic acid (FA) and doxorubicin (DOX) derivatives onto GNRs, where the DOX derivatives possessed an acid‐labile hydrazone bond. Stimulated by the acidic media in endocytic organelles, DOX@FG exhibited a responsive dissociation for the controlled release of chemotherapeutic DOX. Surprisingly, we found the mild photothermal effect elicited by GNRs under NIR irradiation simultaneously inhibited the pump and nonpump resistance mechanisms, enhancing the intracellular DOX accumulation and sensitizing the cancer cells to DOX, collectively amplify the chemotherapy efficacy and delay the MCF‐7/ADR breast tumor growth. This intelligent DOX@FG nanomedicine with the potential for two‐pronged reversal of MDR may provide a prospective way to encourage chemotherapy efficacy.

Abstract Background Impairment of cerebral autoregulation (CA) has been observed in patients undergoing cardiopulmonary bypass (CPB), but little is known about its risks and associations with outcomes. The cerebral oximetry index (COx), which is a moving linear correlation coefficient between regional cerebral oxygen saturation (rScO2) and mean blood pressure (MAP), may reflect CA function. When COx approaches 1, it implies that CA is damaged, whereas the CA is functional when the COx value approaches 0. The objective of this study was to analyze the incidence and risks of impaired CA, based on COx assessment, in patients undergoing total aortic arch replacement under systemic moderate hypothermia and circulatory arrest of the lower body (MHCA). We also evaluated the association between impaired CA and patient outcomes. Methods One hundred and fifty-four adult patients who underwent total aortic arch replacement with stented elephant trunk implantation under MHCA at our hospital were retrospectively analyzed. Patients were defined as having new-onset impaired CA if pre-CPB COx 0.3. Pre- and intraoperative factors were tested for independent association with impaired CA. Postoperative outcomes were compared between patients with normal and impaired CA. Results In our 154 patients, 46(29.9%) developed new-onset impaired CA after CPB. Multivariable analysis revealed a prolonged low rScO2 (rScO2

Cisplatin (CDDP) is widely used as one kind of chemotherapy drugs in cancer treatment. It functions by interacting with DNA, leading to the DNA damage and subsequent cellular apoptosis. However, the presence of intracellular PARP1 diminishes the anticancer efficacy of CDDP by repairing DNA strands. Olaparib (OLA), a PARP inhibitor, enhances the accumulation of DNA damage by inhibiting its repair. Therefore, the combination of these two drugs enhances the sensitivity of CDDP chemotherapy, leading to improved therapeutic outcomes. Nevertheless, both drugs suffer from poor water solubility and limited tumor targeting capabilities. To address this challenge, we proposed the self-assembly of two drugs, CDDP and OLA, through hydrogen bonding to form stable and uniform nanoparticles. Self-assembled nanoparticles efficiently target tumor cells and selectively release CDDP and OLA within the acidic tumor microenvironment, capitalizing on their respective mechanisms of action for improved anticancer therapy. In vitro studies demonstrated that the CDDP-OLA NPs are significantly more effective than CDDP/OLA mixture and CDDP at penetrating cancer cells and suppressing their growth. In vivo studies revealed that the nanoparticles specifically accumulated at the tumor site and enhanced the therapeutic efficacy without obvious adverse effects. This approach holds great potential for enhancing the drugs’ water solubility, tumor targeting, bioavailability, and synergistic anticancer effects while minimizing its toxic side effects.

Plant cells have multiple plasma membrane (PM)-localized calcium ATPases (ACAs) pumping calcium ions out of the cytosol. Although the involvement of some of these ACAs in plant growth and immunity has been reported, their individual and combined functions have not been fully examined. Here, we analysed the effects of single and combined mutations of four ACA genes, ACA8, ACA10, ACA12, and ACA13, in a number of processes. We found that these four genes had both overlapping and differential involvements in vegetative growth, inflorescence growth, seeds setting, disease resistance and stomatal movement. Disruption of any of these four genes reduces seed setting, indicating their contribution to the overall fitness of the plants. While ACA10 and ACA8 play major roles in vegetative growth and immunity, ACA13 and ACA12 are also involved in these processes especially when the function of ACA10 and/or ACA8 is compromised. The loss of ACA13 and ACA10 function in combination with a reduction in function of ACA8 leads to seedling death at bolting, revealing the essential role of their collective function in plant growth. Taken together, this study indicates a highly tuned calcium system involving these PM-localized calcium pumps in plant growth and environmental responses. [ABSTRACT FROM AUTHOR]

Abstract Background Rilpivirine (RPV) was approved by the U.S. FDA (Food and Drug Administration) in 2011 to treat individuals infected with human immunodeficiency virus 1 (HIV-1). Significantly, rilpivirine is three fold more potent than etravirine. Once-daily, it is used with a low oral dose (25 mg/tablet), decreasing the drug administration and bringing a better choice to the patients. However, there are many shortcomings in the existing synthesis route of RPV, such as the high cost, prolonged reaction time and low yield (18.5%). Results This article describes our efforts to develop an efficient and practical microwave-promoted method to synthesize rilpivirine using less toxic organic reagents and low boiling solvents. The last step's reaction time decreased from 69 h to 90 min through this optimized synthetic procedure, and the overall yield improved from 18.5 to 21%. In addition, the yield of intermediate 3 increased from 52 to 62% compared to the original patent. Conclusion Overall, through a series of process optimization, we have developed a practical synthesis method of rilpivirine, which is easy to scale with higher yield and shorter reaction time.

Abstract Atherosclerosis with unstable plaques is the dominant pathological basis of lethal cardio‐cerebrovascular diseases, which can cause acute death due to the rupture of plaques. Plaque‐targeted drug delivery to achieve promoted treatment remains the main challenge because of the systemic occurrence of atheroma. Herein, a rapamycin (RAP) spherical nucleic acid (SNA) structure, capable of specifically accumulating in plaques for synergistic atherosclerosis treatment is constructed. By designing consecutive phosphorothioate (PS) at 3’ terminus of the deoxyribonucleic acid (DNA) strand, multiple hydrophobic RAPs are covalently grafted onto the PS segment to form an amphiphilic drug‐grafted DNA (RAP‐DNA), which successively self‐assembles into micellar SNA (RAP‐SNA). Moreover, the phosphodiester‐DNA segment constitutes the outer shell of RAP‐SNA, enabling further hybridization with functional siRNA (targeting lectin‐like oxidized low‐density lipoprotein receptor‐1, LOX‐1) to obtain the drug codelivered SNA (LOX‐1/RAP‐SNA). With two active ingredients inside, LOX‐1/RAP‐SNA can not only induce robust autophagy and decrease the evil apoptosis of the pathological macrophages, but also simultaneously prohibit the LOX‐1‐mediated formation of damageable foam cells, realizing the effect of synergistic therapy. As a result, the LOX‐1/RAP‐SNA significantly reduces the progression of atheroma and stabilizes the plaques, providing a new strategy for synergistically targeted atherosclerosis treatment.

Mitochondria (MITO) play a significant role in various physiological processes and are a key organelle associated with different human diseases including cancer, diabetes mellitus, atherosclerosis, Alzheimer’s disease, etc. Thus, detecting the activity of MITO in real time is becoming more and more important. Herein, a novel class of amphiphilic aggregation-induced emission (AIE) active probe fluorescence (AC-QC nanoparticles) based on a quinoxalinone scaffold was developed for imaging MITO. AC-QC nanoparticles possess an excellent ability to monitor MITO in real-time. This probe demonstrated the following advantages: (1) lower cytotoxicity; (2) superior photostability; and (3) good performance in long-term imaging in vitro. Each result of these indicates that self-assembled AC-QC nanoparticles can be used as effective and promising MITO-targeted fluorescent probes.

Urea is an important source of nitrogen (N) for the growth and development of plants. It occurs naturally in soils, is the major N source in agricultural fertilizers and is an important N metabolite in plants. Therefore, the identification and characterization of urea transporters in higher plants is important for the fundamental understanding of urea-based N nutrition in plants and for designing novel strategies for improving the N-use efficiency of urea based-fertilizers. Progress in this area, however, is hampered due to scarce knowledge of plant urea transporters. From what is known, urea uptake from the soil into plant roots is mediated by two types of transporters: the major intrinsic proteins (MIPs) and the DUR3 orthologs, mediating low- and high-affinity urea transport, respectively. Here we characterized a MIP family member from Cucumis sativus, CsNIP2;1, with regard to its contribution to urea transport. We show that CsNIP2;1 is a plasma membrane transporter that mediates pH-dependent urea uptake when expressed in yeast. We also found that ectopic expression of CsNIP2;1 improves growth of wild-type Arabidopsis thaliana and rescues growth and development of the atdur3-3 mutant on medium with urea as the sole N source. In addition, CsNIP2;1 is transcriptionally up-regulated by N deficiency, urea and NO3-. These data and results from the analyses of the pattern of CsNIP2;1 expression in A. thaliana and cucumber suggest that CsNIP2;1 might be involved in multiple steps of urea-based N nutrition, including urea uptake and internal transport during N remobilization throughout seed germination and N delivery to developing tissues. [ABSTRACT FROM AUTHOR]

Copper (Cu) is an essential micronutrient that performs a remarkable array of functions in plants including photosynthesis, cell wall remodeling, flowering, and seed set. Of the world's major cereal crops, wheat, barley, and oat are the most sensitive to Cu deficiency. Cu deficient soils include alkaline soils, which occupy approximately 30% of the world's arable lands, and organic soils that occupy an estimated 19% of arable land in Europe. We used Brachypodium distachyon (brachypodium) as a proxy for wheat and other grain cereals to initiate analyses of the molecular mechanisms underlying their increased susceptibility to Cu deficiency. In this report, we focus on members of the CTR/COPT family of Cu transporters because their homologs in A. thaliana are transcriptionally upregulated in Cu-limited conditions and are involved either in Cu uptake from soils into epidermal cells in the root, or long-distance transport and distribution of Cu in photosynthetic tissues. We found that of five COPT proteins in brachypodium, BdCOPT3, and BdCOPT4 localize to the plasma membrane and are transcriptionally upregulated in roots and leaves by Cu deficiency. We also found that BdCOPT3, BdCOPT4, and BdCOPT5 confer low affinity Cu transport, in contrast to their counterparts in A. thaliana that confer high affinity Cu transport. These data suggest that increased sensitivity to Cu deficiency in some grass species may arise from lower efficiency and, possibly, other properties of components of Cu uptake and tissue partitioning systems and reinforce the importance of using brachypodium as a model for the comprehensive analyses of Cu homeostasis in cereal crops. [ABSTRACT FROM AUTHOR]

Molecular self-assembly has been regarded as a promising strategy for the construction of chiral sensing devices. Here, (1R,2R)-N,N-didodecylcyclohexane-1,2-dicarboxamide (DDC) was synthesized and then self-assembled in alcohol, and a chiral helical structure could be formed owing to the intermolecular hydrogen bond and the polarity effect of solvent. The chirality of the resultant helical self-assembly was confirmed by circular dichroism (CD) spectra, and then the chiral helical self-assembly was used for electrochemical recognition of tryptophan (Trp) enantiomers. Due to the higher affinity of the self-assembly toward L-Trp than D-Trp, which was revealed by hydrophilicity evaluation, efficient recognition of the Trp enantiomers (IL-Trp/ID-Trp = 8.74) was achieved. Keywords: Chirality, Self-assembly, Chiral helical structure, Electrochemical recognition, Tryptophan enantiomers

Gas water heaters take a major part in the Chinese water heater market, while the existing water heater have either low efficiency because of the single utilization of energy or the high failure rate that is caused by low temperature corrosion. A new structure of heat exchanger in the gas water heater is proposed is this article, the heat transfer method of which is not only forced convection, but also phase change heat transfer, which provides a higher heat transfer coefficient in condition of the same heat exchange area, and consequently promote the efficiency of the heat exchanger. An experimental study is carried out to compare the difference between the new water heater and the existing one on efficiency, and result shows that the new water heater is 6% higher in efficiency. Besides, this kind of water heater has a gentle temperature change when a sudden decrease or increase of gas flow rate occurs. An economic analysis is produced in order to predict the economic efficiency of the new heat exchanger. As a result, the new heat exchanger of the water heater can significantly promote the heat transfer efficiency and decrease the failure rate, and it is more economic efficient than the existing one.