Unraveling the regulatory mechanisms that govern complex traits is pivotal for advancing crop improvement. Here we present a comprehensive regulome atlas for rice (Oryza sativa), charting the ...chromatin accessibility across 23 distinct tissues from three representative varieties. Our study uncovers 117,176 unique open chromatin regions (OCRs), accounting for ~15% of the rice genome, a notably higher proportion compared to previous reports in plants. Integrating RNA-seq data from matched tissues, we confidently predict 59,075 OCR-to-gene links, with enhancers constituting 69.54% of these associations, including many known enhancer-to-gene links. Leveraging this resource, we re-evaluate genome-wide association study results and discover a previously unknown function of OsbZIP06 in seed germination, which we subsequently confirm through experimental validation. We optimize deep learning models to decode regulatory grammar, achieving robust modeling of tissue-specific chromatin accessibility. This approach allows to predict cross-variety regulatory dynamics from genomic sequences, shedding light on the genetic underpinnings of cis-regulatory divergence and morphological disparities between varieties. Overall, our study establishes a foundational resource for rice functional genomics and precision molecular breeding, providing valuable insights into regulatory mechanisms governing complex traits.The authors present a comprehensive regulome atlas for rice by mapping chromatin accessibility across 23 tissues from three rice varieties. By integrating matched RNA-seq data, they accurately predict numerous associations between non-coding regulatory elements and target genes. This study provides a foundational resource for gene editing and breeding strategies targeting non-coding regions in rice, potentially advancing crop improvement efforts.
Heat sinks are widely used in electronic devices with high heat flux. The design and build of microstructures on heat sinks has shown effectiveness in improving heat dissipation efficiency. In this ...paper, four kinds of treatment methods were used to make different microstructures on heat sink surfaces, and thermal radiation coating also applied onto the heat sink surfaces to improve thermal radiation. The surface roughness, thermal emissivity and heat dissipation performance with and without thermal radiation coating of the heat sinks were studied. The result shows that with an increase of surface roughness, the thermal emissivity can increase up to 2.5 times. With thermal radiation coating on a surface with microstructures, the heat dissipation was further improved because the heat conduction at the coating and heat sink interface was enhanced. Therefore, surface treatment can improve the heat dissipation performance of the heat sink significantly by enhancing the thermal convection, radiation and conduction.
Brain damage is a common tissue damage caused by trauma or diseases, which can be life-threatening. Stem cell implantation is an emerging strategy treating brain damage. The stem cell is commonly ...embedded in a matrix material for implantation, which protects stem cell and induces cell differentiation. Cell differentiation induction by this material is decisive in the effectiveness of this treatment strategy. In this work, we present an injectable fibroin/MXene conductive hydrogel as stem cell carrier, which further enables in-vivo electrical stimulation upon stem cells implanted into damaged brain tissue. Cell differentiation characterization of stem cell showed high effectiveness of electrical stimulation in this system, which is comparable to pure conductive membrane. Axon growth density of the newly differentiated neurons increased by 290% and axon length by 320%. In addition, unfavored astrocyte differentiation is minimized. The therapeutic effect of this system is proved through traumatic brain injury model on rats. Combined with in vivo electrical stimulation, cavities formation is reduced after traumatic brain injury, and rat motor function recovery is significantly promoted.
Chromatin accessibility sequencing has been widely used for uncovering genetic regulatory mechanisms and inferring gene regulatory networks. However, effectively integrating large‐scale chromatin ...accessibility datasets has posed a significant challenge. This is due to the lack of a comprehensive end‐to‐end solution, as many existing tools primarily emphasize data preprocessing and overlook downstream analyses. To bridge this gap, we have introduced cisDynet, a holistic solution that combines streamlined data preprocessing using Snakemake and R functions with advanced downstream analysis capabilities. cisDynet excels in conventional data analyses, encompassing peak statistics, peak annotation, differential analysis, motif enrichment analysis, and more. Additionally, it allows to perform sophisticated data exploration, such as tissue‐specific peak identification, time course data modeling, integration of RNA‐seq data to establish peak‐to‐gene associations, constructing regulatory networks, and conducting enrichment analysis of genome‐wide association study (GWAS) variants. As a proof of concept, we applied cisDynet to reanalyze comprehensive ATAC‐seq datasets across various tissues from the Encyclopedia of DNA Elements (ENCODE) project. The analysis successfully delineated tissue‐specific open chromatin regions (OCRs), established connections between OCRs and target genes, and effectively linked these discoveries with 1861 GWAS variants. Furthermore, cisDynet was instrumental in dissecting the time course open chromatin data of mouse embryonic development, revealing the dynamic behavior of OCRs over developmental stages and identifying key transcription factors governing differentiation trajectories. In summary, cisDynet offers researchers a user‐friendly solution that minimizes the need for extensive coding, ensures the reproducibility of results, and greatly simplifies the exploration of epigenomic data.
cisDynet enables the exploration of the cis‐regulatory chromatin dynamics and networks. It offers a streamlined preprocessing pipeline built on Snakemake, along with an R package for advanced downstream data analysis and visualization. It is free to access on GitHub (https://github.com/tzhu-bio/cisDynet).
Highlights
cisDynet enables comprehensive and efficient processing of chromatin accessibility data, including preprocessing, advanced downstream data analysis, and visualization.
cisDynet provides a range of analytical features, such as processing of time course data, co‐accessibility analysis, linking open chromatin regions (OCRs) to genes, building cis‐regulatory networks, and genome‐wide association study variant enrichment analysis.
cisDynet simplifies the identification of tissue/cell type‐specific OCRs or dynamic OCR changes over time and facilitates the integration of RNA‐seq data to depict temporal trajectories.
, a prevalent saprophytic fungus in the atmosphere, is known to rapidly induce severe invasive aspergillosis (IA) upon inhalation of its conidia by humans or animals. The mortality rate associated ...with IA exceeds 50%. The misuse of antifungal agents has contributed to the emergence of numerous highly pathogenic drug-resistant strains of
. Our study found that the combination of domiphen and itraconazole had sound synergistic antimicrobial effects against wild-type and itraconazole-resistant
and
through MIC, FIC, plate inoculation, growth curve experiments, and
infection model. Drug cytotoxicity and pharmacological tests for acute toxicity assays demonstrated that both itraconazole and domiphen showed minimal cytotoxicity and good biocompatibility. The transcriptome sequencing experiment demonstrated that domiphen exerted a suppressive effect on the expression of various genes, including those involved in drug efflux, redox regulation, and cellular membrane and cell wall remodeling. The present investigation explores the synergistic antimicrobial mechanisms of domiphen and itraconazole, encompassing three key aspects: (i) domiphen inhibited the efflux of itraconazole by reducing the expression of drug efflux-related genes, (ii) the combination has good ability to disrupt the cell membrane and cell wall, (iii) the combination also can remove biofilm more effectively. In summary, the utilization of domiphen as a synergist of itraconazole exhibited disruptive effects on the biofilm, cell wall, and cell membrane of
. This subsequently led to a modified distribution of itraconazole within the fungal organism, ultimately resulting in enhanced antifungal efficacy. The results of this study may provide a new therapeutic strategy for the treatment of IA caused by drug-resistant
.
Morphological properties of surfaces play a key role in natural and man‐made objects. The development of robust methods to fabricate micro/nano surface structures has been a long pursuit. Herein, an ...approach based on molecular self‐assembling of liquid crystal polymers (LCPs) is presented to directly translate 2D molecular director profiles obtained by a photoalignment procedure into 3D topographies, without involving further multi‐step lithographic processes. The principle of surface deformation from a flat morphology into complex topographies is based on the coupling between electrostatic interactions and the anisotropic flow in LCPs. When activated by an electric field, the LCP melts and is driven by electrohydrodynamic instabilities to connect the electrode plates of a capacitor, inducing topographies governed by the director profile of the LCP. Upon switching off the electric field, the formed structures vitrify as the temperature decreases below the glass transition. When heated, the process is reversible as the formed topographies disappear. By pre‐programming the molecular director a variety of structures could be made with increasing complexity. The height, pitch, and the aspect ratio of the textures are further regulated by the conditions of the applied electric field. The proposed approach will open new opportunities for optical and electrical applications.
A technique that stores latent information that can be retrieved repeatedly by subjecting the film to an electrical field is presented. Under the electric field, surfaces morph reversibly from flat to a well‐defined corrugated state, while maintaining its layered molecular organization. Anisotropic polymer flow is generated for this purpose using dielectric energy and directed by an underlying 2D structured monolayer.
Polymyxin-producing bacteria within the
complex have broad-spectrum activities against fungi and bacteria. Their antibacterial activities against soft rot
and
phytopathogens containing multiple ...polymyxin-resistant genes were not clear. Here, we selected nine strains within the
complex having broad-spectrum antagonistic activities against phytopathogenic fungi and a polymyxin-resistant
strain causing stem and root rot disease of sweet potato and did antagonistic assays on nutrient agar and sweet potato tuber slices. These strains within the
complex showed clear antagonistic activities against
in vitro and in vivo. The most effective antagonistic strain
ShX301 showed broad-spectrum antagonistic activities against all the test
and
strains, completely eliminated
from sweet potato seed tubers, and promoted the growth of sweet potato seedlings. Cell-free culture filtrate of
ShX301 inhibited
growth, swimming motility, and biofilm formation and disrupted
plasma membranes, releasing nucleic acids and proteins. Multiple lipopeptides produced by
ShX301 may play a major role in the bactericidal and bacteriostatic actions. This study clarifies that the antimicrobial spectrum of polymyxin-producing bacteria within the
complex includes the polymyxin-resistant
and
phytopathogens and strengthens the fact that bacteria within the
complex have high probability of being effective biocontrol agents and plant growth promoters.
Background
One-pot synthesis of metal nanoparticles under ambient temperature and pressure using reducing and stabilizing materials from microbes is energy-effective and ecofriendly, but upstream ...extraction of biological raw materials and downstream purification of nanoparticles from bioreactors are laborious and expensive. To simplify the productive process for using metal nanoparticles as microbicides to control plant pathogens, we use an endospore-forming
Bacillus
biocontrol agent to produce the nano-microbicide and use the bacterial raw materials as bio-microbicides together with the nano-microbicide.
Results
Bacillus
cells at the stationary phase form endospores and tolerate Ag
+
and Ag nanoparticles (AgNPs), while the cell-free culture supernatant (CFCS) mediates the synthesis of AgNPs. AgNPs produced from the
Bacillus
culture and CFCS show similar physical, chemical, and electrical characteristics, and bactericidal and anti-biofilm activities. Moreover, the diluted products effectively protect the kiwifruit leaves from the infection of the pathogen
Pseudomonas syringae
pv.
actinidiae
.
Conclusions
This coproduction of bio-microbicide and nano-microbicide is a totally green one-pot synthesis process without extraction and purification and without production of waste and can be easily scaled up using the existing fermentation processing of
Bacillus
biocontrol agents. The application of the synergistic bio-microbicide and nano-microbicide can effectively control the bacterial canker disease of kiwifruit plants.
Graphical Abstract
Highlights
Endospore-forming
Bacillus
cells can tolerate metal and metal nanoparticles.
Bacillus
biocontrol agents can be used as bio-microbicides and to produce nano-microbicides.
Coproduction of bio-microbicides and nano-microbicides is a solution of large-scale production of nano-microbicides.
Screening biocontrol
Bacillus
agents producing metal nanoparticle in bacterial culture is a key of this solution.
Cooperation of bio-microbicides and nano-microbicides can effectively control the bacterial canker disease of kiwifruit.
As lab-on-a-chip devices aim to incorporate complex and multi-step microfluidic workflows, active fluid control within these platforms is critical. We use a splay aligned liquid crystal network (LCN) ...photoactuator, capable of deformation upon blue light illumination, as a stimuli responsive material to create integrated fluidic elements. After optimization of the manufacturing parameters, a well-defined actuator material is attained. Illumination with a 455 nm light emitting diode (LED) at 41 mW cm−2 achieves deflection of a 3 × 8 × 0.05 mm LCN film by 380 µm, generating forces of 1.1 mN. The actuator response is stable over time and scalable by light intensity, temperature, and size of the LCN film. By combining with a polydimethylsiloxane (PDMS) membrane, integration into a microfluidic chip is demonstrated and fluid movement of 77 nL in a 2 s stroke is attained. In a pumping setup, the LCN film functions as pumping membrane and two passive PDMS check valves complete the integrated micropump. Constant pumping rates of 0.1 µL min−1 are achieved. An advantage of this micropump setup lies in the non-contact actuation method, which allows for easy integration into microfluidic chips, without the need for chip-to-world connections. Furthermore, with the simple manufacturing procedure and the low operating power, important requirements for application in point-of-care settings are fulfilled.
•A splay aligned liquid crystal network was created as a blue light photoactuator.•Actuation is reversible and continuous deflection at 0.25 Hz was shown for 24 h.•Illumination at 41 mW cm−2 achieved deflection of 380 µm and forces of 1.1 mN.•Temperature dependence of the actuator was characterized from 30 °C to 60 °C.•An integrated microfluidic pump with pumping rates of 0.1 µL min−1 is presented.
In this study, we fabricated a temperature-responsive infrared reflector that adjusts to temperature changes by changing its transmittance of incident IR light. The device utilized a thermally ...induced change in the pitch of a cholesteric liquid crystal (CLC) to achieve near-infrared light reflection in a particular wavelength range. In addition, a polymer-stabilized cholesteric liquid crystal (PSCLC) was used as an alternative to further optimize the device performance. Polyethylene terephthalate (PET) was used as the substrate material to allow the reflector to be flexible. The light transmission performance of the reflector at different bending angles was explored, and no significant effect was found. A simulated solar device was established to study the temperature regulation effects of both CLC and PSCLC devices.
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