Transcriptome and translatome co-evolution in mammals.

Gene-expression programs define shared and species-specific phenotypes, but their evolution remains largely uncharacterized beyond the transcriptome layer1. Here we report an analysis of the co-evolution of translatomes and transcriptomes using ribosome-profiling and matched RNA-sequencing data for three organs (brain, liver and testis) in five mammals (human, macaque, mouse, opossum and platypus) and a bird (chicken). Our within-species analyses reveal that translational regulation is widespread in the different organs, in particular across the spermatogenic cell types of the testis. The between-species divergence in gene expression is around 20% lower at the translatome layer than at the transcriptome layer owing to extensive buffering between the expression layers, which especially preserved old, essential and housekeeping genes. Translational upregulation specifically counterbalanced global dosage reductions during the evolution of sex chromosomes and the effects of meiotic sex-chromosome inactivation during spermatogenesis. Despite the overall prevalence of buffering, some genes evolved faster at the translatome layer-potentially indicating adaptive changes in expression; testis tissue shows the highest fraction of such genes. Further analyses incorporating mass spectrometry proteomics data establish that the co-evolution of transcriptomes and translatomes is reflected at the proteome layer. Together, our work uncovers co-evolutionary patterns and associated selective forces across the expression layers, and provides a resource for understanding their interplay in mammalian organs.

Engineering Copper-Containing Nanoparticles-Loaded Silicene Nanosheets with Triple Enzyme Mimicry Activities and Photothermal Effect for Promoting Bacteria-Infected Wound Healing.

Skin wounds accompanied by bacterial infections threaten human health, and conventional antibiotic treatments are ineffective for drug-resistant bacterial infections and chronically infected wounds. The development of non-antibiotic-dependent therapeutics is highly desired but remains a challenging issue. Recently, 2D silicene nanosheets with considerable biocompatibility, biodegradability, and photothermal-conversion performance have received increasing attention in biomedical fields. Herein, copper-containing nanoparticles-loaded silicene (Cu2.8O@silicene-BSA) nanosheets with triple enzyme mimicry catalytic (peroxidase, catalase, and oxidase-like) activities and photothermal function are rationally designed and fabricated for efficient bacterial elimination, angiogenesis promotion, and accelerated wound healing. Cu2.8O@silicene-BSA nanosheets display excellent antibacterial activity through synergistic effects of reactive oxygen species generated from multiple catalytic reactions, intrinsic bactericidal activity of released Cu2+ ions, and photothermal effects, achieving high antibacterial efficiencies on methicillin-resistant Staphylococcus aureus (MRSA) of 99.1 ± 0.7% in vitro and 97.2 ± 1.6% in vivo. In addition, Cu2.8O@silicene-BSA nanosheets exhibit high biocompatibility for promoting human umbilical vein endothelial cell (HUVEC) proliferation and angiogenic differentiation. In vivo experiments reveal that Cu2.8O@silicene-BSA nanosheets with synergistic photothermal/chemodynamic therapeutics effectively accelerate MRSA-infected wound healing by eliminating bacteria, alleviating inflammation, boosting collagen deposition, and promoting angiogenesis. This research presents a promising strategy to engineer photothermal-assisted nanozyme catalysis for bacteria-invaded wound healing.

Loss of Hepatic Leucine-Rich Repeat-Containing G-Protein Coupled Receptors 4 and 5 Promotes Nonalcoholic Fatty Liver Disease.

The roof plate-specific spondin-leucine-rich repeat-containing G-protein coupled receptor 4/5 (LGR4/5)-zinc and ring finger 3 (ZNRF3)/ring finger protein 43 (RNF43) module is a master regulator of hepatic Wnt/ß-catenin signaling and metabolic zonation. However, its impact on nonalcoholic fatty liver disease (NAFLD) remains unclear. The current study investigated whether hepatic epithelial cell-specific loss of the Wnt/ß-catenin modulator Lgr4/5 promoted NAFLD. The 3- and 6-month-old mice with hepatic epithelial cell-specific deletion of both receptors Lgr4/5 (Lgr4/5dLKO) were compared with control mice fed with normal diet (ND) or high-fat diet (HFD). Six-month-old HFD-fed Lgr4/5dLKO mice developed hepatic steatosis and fibrosis but the control mice did not. Serum cholesterol-high-density lipoprotein and total cholesterol levels in 3- and 6-month-old HFD-fed Lgr4/5dLKO mice were decreased compared with those in control mice. An ex vivo primary hepatocyte culture assay and a comprehensive bile acid (BA) characterization in liver, plasma, bile, and feces demonstrated that ND-fed Lgr4/5dLKO mice had impaired BA secretion, predisposing them to develop cholestatic characteristics. Lipidome and RNA-sequencing analyses demonstrated severe alterations in several lipid species and pathways controlling lipid metabolism in the livers of Lgr4/5dLKO mice. In conclusion, loss of hepatic Wnt/ß-catenin activity by Lgr4/5 deletion led to loss of BA secretion, cholestatic features, altered lipid homeostasis, and deregulation of lipoprotein pathways. Both BA and intrinsic lipid alterations contributed to the onset of NAFLD.

Bioinspired Aerogel with Vertically Ordered Channels and Low Water Evaporation Enthalpy for High-Efficiency Salt-Rejecting Solar Seawater Desalination and Wastewater Purification.

Solar energy-driven water evaporation is a promising sustainable strategy to purify seawater and contaminated water. However, developing solar evaporators with high water evaporation rates and excellent salt resistance still faces a great challenge. Herein, inspired by the long-range ordered structure and water transportation capability of lotus stem, a biomimetic aerogel with vertically ordered channels and low water evaporation enthalpy for high-efficiency solar energy-driven salt-resistant seawater desalination and wastewater purification is developed. The biomimetic aerogel consists of ultralong hydroxyapatite nanowires as heat-insulating skeletons, polydopamine-modified MXene as a photothermal material with broadband sunlight absorption and high photothermal conversion efficiency, polyacrylamide, and polyvinyl alcohol as reagents to lower the water evaporation enthalpy and as glues to enhance the mechanical performance. The honeycomb porous structure, unidirectionally aligned microchannels, and nanowire/nanosheet/polymer pore wall endow the biomimetic aerogel with excellent mechanical properties, rapid water transportation, and excellent solar water evaporation performance. The biomimetic aerogel exhibits a high water evaporation rate (2.62 kg m-2  h-1 ) and energy efficiency (93.6%) under one sun irradiation. The superior salt-rejecting ability of the designed water evaporator enables stable and continuous seawater desalination, which is promising for application in water purification to mitigate the global water crisis.

All-solid-state potentiometric salicylic acid sensor for in-situ measurement of plant.

Using PEDOT as the conductive polymer, an innovative small-scale sensor for directly measuring salicylate ions in plants was developed, which avoided the complicated sample pretreatment of traditional analytical methods and realized the rapid detection of salicylic acid. The results demonstrate that this all-solid-state potentiometric salicylic acid sensor is easy to miniaturize, has a longer lifetime (≥1 month), is more robust, and can be directly used for the detection of salicylate ions in real samples without any additional pretreatment. The developed sensor has a good Nernst slope (63.6 ± 0.7 mV/decade), the linear range is 10-2 ~ 10-6 M, and the detection limit can reach (2.8 × 10-7 M). The selectivity, reproducibility, and stability of the sensor were evaluated. The sensor can perform stable, sensitive, and accurate in situ measurement of salicylic acid in plants, and it is an excellent tool for determining salicylic acid ions in plants in vivo.

Aerosol and Surface Distribution of Severe Acute Respiratory Syndrome Coronavirus 2 in Hospital Wards, Wuhan, China, 2020.

To determine distribution of severe acute respiratory syndrome coronavirus 2 in hospital wards in Wuhan, China, we tested air and surface samples. Contamination was greater in intensive care units than general wards. Virus was widely distributed on floors, computer mice, trash cans, and sickbed handrails and was detected in air ≈4 m from patients.

Evolutionary and genetic features of drug targets.

In the modern drug discovery pipeline, identification of novel drug targets is a critical step. Despite rapid progress in developing biomedical techniques, it is still a great challenge to find promising new targets from the ample space of human genes. This fact is partially responsible for the situation of "more investments, fewer drugs" in the pharmaceutical industry. A series of recent researches revealed that successfully targeted genes share some common evolutionary and genetic features, which means that the knowledge accumulated in modern evolutionary biology and genetics is very helpful to identify potential drug targets and to find new drugs as well. In this article, we comprehensively summarize the links between human drug targets and genetic diseases and their evolutionary origins, with an attempt to introduce these novel concepts and their medical implications to the biomedical community.

Ternary Acceptor-Donor-Acceptor Asymmetrical Phenanthroimidazole Molecule for Highly Efficient Near-Ultraviolet Electroluminescence with External Quantum Efficiency (EQE) >4 .

A new ternary acceptor (A)-donor (D)-acceptor (A) asymmetrically twisted deep-blue emitting molecule, PPI-2BI, was synthesized by attaching two electrophilic benzimidazole (BI) units to the C2 and N1 positions of a phenanthroimidazole (PI) donor unit. Profiting from the enhanced D-A electronic coupling, the electron injecting and transporting abilities of the new triangle-shaped A-D-A molecule are considerably improved and the molecule shows high photoluminescence (PL) and electroluminescence (EL) efficiencies. By using PPI-2BI as a non-doped emitting layer (EML), the resulting organic light-emitting device exhibits emission with color coordinates of (0.158, 0.124) and a maximum external quantum efficiency (EQE), current efficiency (CE), and power efficiency (PE) of 4.63 %, 4.98 cd A-1 , and 4.82 lm W-1 , respectively. Additionally, a simple bilayer device using PPI-2BI as both the EML and the electron-transporting layer (ETL) also shows an EQE of 3.81 % with little changes to the color purity. Remarkably, a PPI-2BI-based doped device emits efficient near-ultraviolet EL with color coordinates of (0.154, 0.047) and an EQE of 4.12 %, which is comparable to that of the best reported near-UV emitting devices.

Nondestructive In Situ Measurement Method for Kernel Moisture Content in Corn Ear.

Moisture content is an important factor in corn breeding and cultivation. A corn breed with low moisture at harvest is beneficial for mechanical operations, reduces drying and storage costs after harvesting and, thus, reduces energy consumption. Nondestructive measurement of kernel moisture in an intact corn ear allows us to select corn varieties with seeds that have high dehydration speeds in the mature period. We designed a sensor using a ring electrode pair for nondestructive measurement of the kernel moisture in a corn ear based on a high-frequency detection circuit. Through experiments using the effective scope of the electrodes' electric field, we confirmed that the moisture in the corn cob has little effect on corn kernel moisture measurement. Before the sensor was applied in practice, we investigated temperature and conductivity effects on the output impedance. Results showed that the temperature was linearly related to the output impedance (both real and imaginary parts) of the measurement electrodes and the detection circuit's output voltage. However, the conductivity has a non-monotonic dependence on the output impedance (both real and imaginary parts) of the measurement electrodes and the output voltage of the high-frequency detection circuit. Therefore, we reduced the effect of conductivity on the measurement results through measurement frequency selection. Corn moisture measurement results showed a quadric regression between corn ear moisture and the imaginary part of the output impedance, and there is also a quadric regression between corn kernel moisture and the high-frequency detection circuit output voltage at 100 MHz. In this study, two corn breeds were measured using our sensor and gave R² values for the quadric regression equation of 0.7853 and 0.8496.

Electronic instability in pressured black phosphorus under strong magnetic field.

In this paper, we have systematically studied the electronic instability of pressured black phosphorous (BP) under strong magnetic field. We first present an effective model Hamiltonian for pressured BP near theLifshitzpoint. Then we show that when the magnetic field exceeds a critical value, the nodal-line semimetal (NLSM) state of BP with a small band overlap re-enters the semiconductive phase by re-opening a small gap. This results in a narrow-bandgap semiconductor with a partially flat valence band edge. Moreover, we demonstrate that above this critical magnetic field, two possible instabilities, i.e. charge density wave phase and excitonic insulator (EI) phase, are predicted as the ground state for high and low doping concentrations, respectively. By comparing our results with the experiment (Sunet al2018Sci. Bull.631539), we suggest that the field-induced instability observed experimentally corresponds to an EI. Furthermore, we propose that the semimetallic BP under pressure with small band overlaps may provide a good platform to study the magneto-exciton insulators. Our findings bring the first insight into the electronic instability of topological NLSM in the quantum limit.

Salt-rejecting 3D cone flowing evaporator based on bilayer photothermal paper for high-performance solar seawater desalination.

Solar energy-driven water evaporation technology is a promising, low-cost and sustainable approach to alleviate the global clean water shortage, but usually suffers from low water evaporation rate and severe salt deposition on the water evaporation surface. In this work, a hydrophilic bilayer photothermal paper-based three-dimensional (3D) cone flowing evaporator was designed and prepared for stable high-performance seawater desalination with excellent salt-rejecting ability. The as-prepared bilayer photothermal paper consisted of MXene (Ti3C2Tx) and HAA (ultralong hydroxyapatite nanowires, poly(acrylic acid), and poly(acrylic acid-2-hydroxyethyl ester)). The accordion-like multilayered MXene acted as the efficient solar light absorber, and ultralong hydroxyapatite (HAP) nanowires served as the thermally insulating and supporting skeleton with a porous networked structure. A siphon effect-driven unidirectional fluid transportation unit in the 3D cone flowing evaporator could guide the concentrated saline flowing away from the evaporating surface to prevent salt deposition on the evaporation surface, avoiding severe deterioration of the performance in solar water evaporation. Furthermore, combining high solar light absorption and high photothermal conversion efficiencies, low water evaporation enthalpy (1838 ±â€¯11 J g-1), and additional energy taken from the ambient environment, the as-prepared cone flowing evaporator exhibited a high water evaporation rate of 3.22 ±â€¯0.20 kg m-2 h-1 for real seawater under one sun illumination (1 kW m-2), which was significantly higher than many values reported in the literature. This study provides an effective approach for designing high-performance solar energy-driven water evaporators for sustainable seawater desalination and wastewater purification.

A novel framework for three-dimensional electrical impedance tomography reconstruction of maize ear via feature reconfiguration and residual networks.

Electrical impedance tomography (EIT) provides an indirect measure of the physiological state and growth of the maize ear by reconstructing the distribution of electrical impedance. However, the two-dimensional (2D) EIT within the electrode plane finds it challenging to comprehensively represent the spatial distribution of conductivity of the intact maize ear, including the husk, kernels, and cob. Therefore, an effective method for 3D conductivity reconstruction is necessary. In practical applications, fluctuations in the contact impedance of the maize ear occur, particularly with the increase in the number of grids and computational workload during the reconstruction of 3D spatial conductivity. These fluctuations may accentuate the ill-conditioning and nonlinearity of the EIT. To address these challenges, we introduce RFNetEIT, a novel computational framework specifically tailored for the absolute imaging of the three-dimensional electrical impedance of maize ear. This strategy transforms the reconstruction of 3D electrical conductivity into a regression process. Initially, a feature map is extracted from measured boundary voltage via a data reconstruction module, thereby enhancing the correlation among different dimensions. Subsequently, a nonlinear mapping model of the 3D spatial distribution of the boundary voltage and conductivity is established, utilizing the residual network. The performance of the proposed framework is assessed through numerical simulation experiments, acrylic model experiments, and maize ear experiments. Our experimental results indicate that our method yields superior reconstruction performance in terms of root-mean-square error (RMSE), correlation coefficient (CC), structural similarity index (SSIM), and inverse problem-solving time (IPST). Furthermore, the reconstruction experiments on maize ears demonstrate that the method can effectively reconstruct the 3D conductivity distribution.

Structural and energetic analyses of SNPs in drug targets and implications for drug therapy.

Mutations in drug targets can alter the therapeutic effects of drugs. Therefore, evaluating the effects of single-nucleotide polymorphisms (SNPs) on drug-target binding is of significant interest. This study focuses on the analysis of the structural and energy properties of SNPs in successful drug targets by using the data derived from HapMap and the Therapeutic Target Database. The results show the following: (i) Drug targets undergo strong purifying selection, and the majority (92.4%) of the SNPs are located far from the drug-binding sites (>12 Å). (ii) For SNPs near the drug-binding pocket (≤12 Å), nearly half of the drugs are weakly affected by the SNPs, and only a few drugs are significantly affected by the target mutations. These results have direct implications for population-based drug therapy and for chemical treatment of genetic diseases as well.

ELM-KL-LSTM: a robust and general incremental learning method for efficient classification of time series data.

Efficiently analyzing and classifying dynamically changing time series data remains a challenge. The main issue lies in the significant differences in feature distribution that occur between old and new datasets generated constantly due to varying degrees of concept drift, anomalous data, erroneous data, high noise, and other factors. Taking into account the need to balance accuracy and efficiency when the distribution of the dataset changes, we proposed a new robust, generalized incremental learning (IL) model ELM-KL-LSTM. Extreme learning machine (ELM) is used as a lightweight pre-processing model which is updated using the new designed evaluation metrics based on Kullback-Leibler (KL) divergence values to measure the difference in feature distribution within sliding windows. Finally, we implemented efficient processing and classification analysis of dynamically changing time series data based on ELM lightweight pre-processing model, model update strategy and long short-term memory networks (LSTM) classification model. We conducted extensive experiments and comparation analysis based on the proposed method and benchmark methods in several different real application scenarios. Experimental results show that, compared with the benchmark methods, the proposed method exhibits good robustness and generalization in a number of different real-world application scenarios, and can successfully perform model updates and efficient classification analysis of incremental data with varying degrees improvement of classification accuracy. This provides and extends a new means for efficient analysis of dynamically changing time-series data.

Robust electrical impedance tomography for biological application: A mini review.

Electrical impedance tomography (EIT) has been used by researchers across several areas because of its low-cost and no-radiation properties. Researchers use complex conductivity in bioimpedance experiments to evaluate changes in various indicators within the image target. The diverse volumes and edges of biological tissues and the large impedance range impose dedicated demands on hardware design. The EIT hardware with a high signal-to-noise ratio (SNR), fast scanning and suitable for the impedance range of the image target is a fundamental foundation that EIT research needs to be equipped with. Understanding the characteristics of this technique and state-of-the-art design will accelerate the development of the robust system and provide a guidance for the superior performance of next-generation EIT. This review explores the hardware strategies for EIT proposed in the literature.

Plant electrical signals: A multidisciplinary challenge.

Plant electrical signals, an early event in the plant-stimulus interaction, rapidly transmit information generated by the stimulus to other organs, and even the whole plant, to promote the corresponding response and trigger a regulatory cascade. In recent years, many promising state-of-the-art technologies applicable to study plant electrophysiology have emerged. Research focused on expression of genes associated with electrical signals has also proliferated. We propose that it is appropriate for plant electrical signals to be considered in the form of a "plant electrophysiological phenotype". This review synthesizes research on plant electrical signals from a novel, interdisciplinary perspective, which is needed to improve the efficient aggregation and use of plant electrical signal data and to expedite interpretation of plant electrical signals.

Single-cell and bulk transcriptomics of the liver reveals potential targets of NASH with fibrosis.

Fibrosis is characterized by the excessive production of collagen and other extracellular matrix (ECM) components and represents a leading cause of morbidity and mortality worldwide. Previous studies of nonalcoholic steatohepatitis (NASH) with fibrosis were largely restricted to bulk transcriptome profiles. Thus, our understanding of this disease is limited by an incomplete characterization of liver cell types in general and hepatic stellate cells (HSCs) in particular, given that activated HSCs are the major hepatic fibrogenic cell population. To help fill this gap, we profiled 17,810 non-parenchymal cells derived from six healthy human livers. In conjunction with public single-cell data of fibrotic/cirrhotic human livers, these profiles enable the identification of potential intercellular signaling axes (e.g., ITGAV-LAMC1, TNFRSF11B-VWF and NOTCH2-DLL4) and master regulators (e.g., RUNX1 and CREB3L1) responsible for the activation of HSCs during fibrogenesis. Bulk RNA-seq data of NASH patient livers and rodent models for liver fibrosis of diverse etiologies allowed us to evaluate the translatability of candidate therapeutic targets for NASH-related fibrosis. We identified 61 liver fibrosis-associated genes (e.g., AEBP1, PRRX1 and LARP6) that may serve as a repertoire of translatable drug target candidates. Consistent with the above regulon results, gene regulatory network analysis allowed the identification of CREB3L1 as a master regulator of many of the 61 genes. Together, this study highlights potential cell-cell interactions and master regulators that underlie HSC activation and reveals genes that may represent prospective hallmark signatures for liver fibrosis.

Microtensile bond strength of one- and two-step self-etching adhesives on sclerotic dentin: the effects of thermocycling.

This study evaluated the effects of thermocycling on the microtensile bond strength (microTBS) of one- and two-step self-etch adhesives (SEAs) to sclerotic dentin. Two adhesives, Clearfil S3 Bond (S3), a one-step self-etch adhesive (1-SEA), and Clearfil SE Bond (SE), a two-step self-etch adhesive (2-SEA), were applied on cervical lesions in human premolars with sclerotic or normal dentin. After adhesive application, the lesions were restored and built up using a resin composite (Clearfil AP-X). After 24 hours in water storage, the restored teeth were sectioned into 0.7 x 0.7 mm composite-dentin beams. The beams were then aged with 0, 5,000 or 10,000 thermocycles. The use of two adhesives, two substrate types and three thermocycling regimens yielded 12 experimental groups of 14-19 beams each. The beams were subsequently subjected to microTBS testing at a crosshead speed of 1 mm/minute and statistical analyses were computed with three-way ANOVA and Tukey's post hoc test at p < 0.05. Three-way ANOVA showed statistically significant effects on bonding effectiveness by lesion type, adhesive system, thermocycling or combinations of the adhesive system and thermocycling (p < 0.05). With sclerotic dentin, although S3 and SE provided comparable microTBS after 24 hours of water storage, S3 showed significantly lower microTBS than SE after thermocycling (p < 0.05). Regardless of lesion type, the microTBS for S3 decreased significantly after 5,000 or 10,000 thermocycles, while the microTBS for SE showed a significant decrease only after 10,000 thermocycles. Regardless of the extent of thermocycling, the microTBS values for either SE or S3 bonded to sclerotic dentin were significantly lower than to normal dentin (p < 0.05). The results suggested that thermocycling had a significant negative effect on the bond strength of the two SEAs tested. In contrast to 2-SEA, 1-SEA might not be a good choice for sclerotic dentin when seeking durability of the resin-dentin bond.

[Measurement of pork tenderness by using steady spatially-resolved spectroscopy].

Tenderness is one of the main sensory and eating qualities of meat. Conventional measurement of tenderness is a time-consuming and invasive method. Using steady spatially-resolved spectroscopy, a multi-channel visible and near infrared spectroscopy instrument was established to obtain the reduced scattering coefficient mu's. of porcine longissimus muscle samples. After spectra collection, each fresh meat sample was divided into two parts, one was tested by means of C-LM4 tenderness instrument, and the other was measured by conventional method. The results showed that reduced scattering coefficient of the samples was significantly correlated to fresh meat shear force values (R2 = 0.8349) at 700 nm. Also, there was a significant correlation between fresh meat shear force values and shear force values by conventional method (R2 = 0.7716). In conclusion, the potential of the steady spatially-resolved spectroscopy technique as a rapid and non-invasive tool to measure tenderness of pork was found.

[Method for measuring water content in fresh meat using diffusion reflectance near infrared spectroscopy and experiment].

A method was established to determine water content of fresh meat in deep layer based on NIRS diffusion reflectance spectroscopy by using LEDs. The experimental apparatus was established to investigate internal water content with repeated experiments for pork and mince pork; the water concentration and the water content detected by standard method is linear, and the r2 is larger than 0.90. Calculation of coefficient of variability (CV) and intra class correlation (ICC) procedures were applied to assess test-retest reliability of this measuring method. The CV and ICC values were found to be good (CV < or = 5%; ICC = 0.83). The experimental result indicated that the fast non-invasive measurement method for detecting water content in deep layer of fresh meat based on spatially-resolved spectroscopy was feasible.