H3K4me1 recruits DNA repair proteins in plants.

DNA repair proteins can be recruited by their histone reader domains to specific epigenomic features, with consequences on intragenomic mutation rate variation. Here, we investigated H3K4me1-associated hypomutation in plants. We first examined 2 proteins which, in plants, contain Tudor histone reader domains: PRECOCIOUS DISSOCIATION OF SISTERS 5 (PDS5C), involved in homology-directed repair, and MUTS HOMOLOG 6 (MSH6), a mismatch repair protein. The MSH6 Tudor domain of Arabidopsis (Arabidopsis thaliana) binds to H3K4me1 as previously demonstrated for PDS5C, which localizes to H3K4me1-rich gene bodies and essential genes. Mutations revealed by ultradeep sequencing of wild-type and msh6 knockout lines in Arabidopsis show that functional MSH6 is critical for the reduced rate of single-base substitution (SBS) mutations in gene bodies and H3K4me1-rich regions. We explored the breadth of these mechanisms among plants by examining a large rice (Oryza sativa) mutation data set. H3K4me1-associated hypomutation is conserved in rice as are the H3K4me1-binding residues of MSH6 and PDS5C Tudor domains. Recruitment of DNA repair proteins by H3K4me1 in plants reveals convergent, but distinct, epigenome-recruited DNA repair mechanisms from those well described in humans. The emergent model of H3K4me1-recruited repair in plants is consistent with evolutionary theory regarding mutation modifier systems and offers mechanistic insight into intragenomic mutation rate variation in plants.

Preparation of MoS2/MXene/NC Porous Composite Microspheres with Wrinkled Surface and Their Microwave Absorption Performances.

In this paper, a MoS2/MXene/N-doped carbon (NC) porous composite microsphere with a wrinkled surface was designed and constructed. Lithium fluoride exfoliation and lithium-ion etching fabricated two types of 2D assembly elements, MXene (Ti3C2Tx) and MoS2 nanosheets. The two nanosheets were self-assembled by an ultrasonic spray technique with high-temperature reduction, and MoS2/MXene microspheres with 3Dwrinkled shapes were obtained. The coating of the surface NC layer was achieved by the carbonization of a polydopamine (PDA) precursor formed by the self-polymerization of dopamine. The amount of PDA coating and raw material ratio significantly affect the microstructure and electromagnetic wave absorption performance. The optimal MXene to MoS2 mass ratio is 5:1, and the optimal coating time and filler amount are 8 h and 40%. MoS2/MXene/NC composite microspheres exhibit excellent absorption performance with low reflection losses (RLmin) of -52.9 dB at 6.4 GHz and high adequate absorption bandwidths of 5.2 GHz. By adjusting the thickness of the absorber, the full coverage of the C-Ku band (4-18 GHz) can be achieved. As a new composite absorber, it has significant potential applications.

Evolutionary diversification of methanotrophic ANME-1 archaea and their expansive virome.

'Candidatus Methanophagales' (ANME-1) is an order-level clade of archaea responsible for anaerobic methane oxidation in deep-sea sediments. The diversity, ecology and evolution of ANME-1 remain poorly understood. In this study, we use metagenomics on deep-sea hydrothermal samples to expand ANME-1 diversity and uncover the effect of virus-host dynamics. Phylogenetic analyses reveal a deep-branching, thermophilic family, 'Candidatus Methanospirareceae', closely related to short-chain alkane oxidizers. Global phylogeny and near-complete genomes show that hydrogen metabolism within ANME-1 is an ancient trait that was vertically inherited but differentially lost during lineage diversification. Metagenomics also uncovered 16 undescribed virus families so far exclusively targeting ANME-1 archaea, showing unique structural and replicative signatures. The expansive ANME-1 virome contains a metabolic gene repertoire that can influence host ecology and evolution through virus-mediated gene displacement. Our results suggest an evolutionary continuum between anaerobic methane and short-chain alkane oxidizers and underscore the effects of viruses on the dynamics and evolution of methane-driven ecosystems.

Oligodendrocyte lineage cells: Advances in development, disease, and heterogeneity.

Oligodendrocyte progenitor cells (OPCs) originate in the ventricular zone (VZ) of the brain and spinal cord, and their primary function is to differentiate into oligodendrocytes (OLs). Studies have shown that OPCs and OLs are pathologically and physiologically heterogeneous. Previous transcriptome analyses used Bulk RNA-seq, which compares average gene expression in cells and does not allow for heterogeneity. In recent years, the development of single-cell sequencing (scRNA-seq) and single-cell nuclear sequencing (snRNA-seq) has allowed us to study an individual cell. In this review, sc/snRNA-seq was used to study the different subpopulations of OL lineage cells, their developmental trajectories, and their applications in related diseases. These techniques can distinguish different subpopulations of cells, and identify differentially expressed genes in particular cell types under certain conditions, such as treatment or disease. It is of great significance to the study of the occurrence, prevention, and treatment of various diseases.

Combination effects of tebuconazole with Bacillus subtilis to control rice false smut and the related synergistic mechanism.

BACKGROUND: Management of rice false smut is based mainly on chemical control, which poses many safety and environmental challenges. The other option, biological control with biofungicides, does not have such problems but is not as reliable because of low systemic ability, and lower and unstable efficacy. Therefore, it is necessary to combine application of chemical fungicides and biological control agents (BCAs) and elucidate their synergistic mechanism. RESULTS: A combination of tebuconazole and a proven BCA, Bacillus subtilis H158, was evaluated for control of rice false smut. Tebuconazole at low application rates stimulated growth of B. subtilis, prolonged the effective period of B. subtilis by enhancing its persistence on the surface of rice plants, accelerated biofilm formation of the BCA to facilitate colonization, promoted induced systemic resistance in rice by regulating defense-related enzymes and genes, and reduced the natural resistance of the pathogen by suppressing the key gene for fungal resistance to tebuconazole. However, at high application rates, tebuconazole had adverse effects on these factors and showed antagonistic combination effects with B. subtilis. The combination of B. subtilis with tebuconazole at low application rates showed great synergistic effects, but at high application rates showed only antagonistic effects in field experiments over two consecutive years. CONCLUSION: The combination of B. subtilis with tebuconazole had significant synergistic effects at low application rates. The synergistic effects are the result of multiple mechanisms involved in BCA, rice and the fungal pathogen. © 2022 Society of Chemical Industry.

Genome-Wide Identification and Functional Analysis of the bZIP Transcription Factor Family in Rice Bakanae Disease Pathogen, Fusarium fujikuroi.

Fungal basic leucine zipper (bZIP) proteins play a vital role in biological processes such as growth, biotic/abiotic stress responses, nutrient utilization, and invasion. In this study, genome-wide identification of bZIP genes in the fungus Fusarium fujikuroi, the pathogen of bakanae disease, was carried out. Forty-four genes encoding bZIP transcription factors (TFs) from the genome of F. fujikuroi (FfbZIP) were identified and functionally characterized. Structures, domains, and phylogenetic relationships of the sequences were analyzed by bioinformatic approaches. Based on the phylogenetic relationships with the FfbZIP proteins of eight other fungi, the bZIP genes can be divided into six groups (A-F). The additional conserved motifs have been identified and their possible functions were predicted. To analyze functions of the bZIP genes, 11 FfbZIPs were selected according to different motifs they contained and were knocked out by genetic recombination. Results of the characteristic studies revealed that these FfbZIPs were involved in oxygen stress, osmotic stress, cell wall selection pressure, cellulose utilization, cell wall penetration, and pathogenicity. In conclusion, this study enhanced understandings of the evolution and regulatory mechanism of the FfbZIPs in fungal growth, abiotic/biotic stress resistance, and pathogenicity, which could be the reference for other fungal bZIP studies.

Validation of housekeeping genes as internal controls for gene expression studies on biofilm formation in Bacillus velezensis.

Bacillus velezensis is an important bacterium widely applied in agriculture and industry, and biofilms play critical roles in its environmental tolerance. The appropriate choice of reference genes is essential for key gene expression studies. Multiple internal control genes were selected and validated from the 21 housekeeping genes of B. velezensis by expression stability evaluation during biofilm formation and were used to study the expression of key genes involved in the process. The results showed that pyk, gyrA, recA, and gyrB were stably expressed, and the expression of pyk was the most stable during biofilm formation. A pair of two genes, pyk and gyrA, provided high-quality data when used as internal controls, and the combination of three genes, pyk, gyrA, and recA, was even better. The expression levels of pyk, gyrA, and recA approximated those of five key genes, abrB, epsD, kinC, sinR, and tasA, in biofilm formation, meeting the requirements of ideal internal control genes. The expression patterns of 5 key genes were studied with 16S, pyk, the pair of 2 genes, pyk and gyrA, and the combination of 3 genes, pyk, gyrA, and recA, as internal controls during the biofilm formation process. The results proved that pyk was a suitable internal control, as were the pair of 2 genes, pyk and gyrA, and the combination of 3 genes, pyk, gyrA, and recA. This study provided genes and gene combinations which were validated as suitable internal controls for gene expression studies, especially those on the mechanism of biofilm formation in B. velezensis or even other Bacillus spp. KEY POINTS: • Reference genes is necessary for gene expression study in biofilm formation of Bacillus velezensis • Pyk and 2 gene combinations were selected and validated from 21 common used genes • Expression of key genes in biofilm formation was normalized with the selected internal controls.

Bi19S27I3 nanorods: a new candidate for photothermal therapy in the first and second biological near-infrared windows.

Near-infrared (NIR) light-induced photothermal cancer therapy using nanomaterials as photothermal agents has attracted considerable research interest over the past few years. As the key factor in photothermal therapy systems, a variety of photothermal agents have been developed. However, the exploration of novel photothermal therapy nanoplatforms with high NIR absorption remains a significant challenge, especially those working in both NIR-I and NIR-II windows. In this work, Bi19S27I3 nanorods with remarkably high absorption covering the whole visible light to the entire NIR-I and NIR-II regions have been successfully prepared through a facile solvothermal approach. The as-synthesized Bi19S27I3 nanorods have a high photothermal conversion efficiency of 42.7% at 808 nm (NIR-I) and 41.5% at 1064 nm (NIR-II), making them a promising candidate for photothermal therapy. In vitro cell viability assay reveals that the Bi19S27I3 sample has good biocompatibility and exhibits significant cell-killing effect under NIR irradiation. In vivo anti-tumor experiments demonstrate that the tumor growth can be effectively inhibited by fatal hyperthermia ablation mediated by Bi19S27I3 nanorods under the irradiation of an 808 nm or 1064 nm laser. Therefore, this study should be primarily beneficial for the development of new materials for NIR photothermal therapy applications.

Nigrospora oryzae Causing Panicle Branch Rot Disease on Oryza sativa (rice).

The panicle branch, which is the key node for transport of photosynthesis products from source to sink, is vulnerable to many diseases caused by fungal pathogens, such as Magnaporthe oryzae, Cochliobolus miyabeanus. Among these diseases, rice blast is the most important one which causes devastating losses in many regions. In 2019 and 2020, panicle branch rot of rice with a symptom which could be mistaken with rice blast was observed in a paddy field, where is not traditional epidemical region of rice blast, in Fuyang, Zhejiang province. In 2020, similar symptom was also observed in Hubei and Anhui Province. In a paddy field in Fuyang, the symptom appeared on more than 30% investigated panicles. Diseased panicle exhibited brown to black lesions on primary or secondary branches as well as pedicels, however the grain and the neck of spike could not be infected which is the most obvious difference with rice blast. Obviously, the disease can't destroy the entire function of branch and blank grain was rarely observed, so its damage is not comparable with neck blast. Normally, it caused incomplete grain filing commonly leading to 5% - 25% grain weight loss. During the booting stage of rice, local solar irradiation time and temperature were fewer and lower than common years which may be responsible for losses caused by this disease. After surface sterilized, lesion parts cut from infected branches from 25 panicle samples were cultured on 2% water agar at 28℃ for 24-28 h, and fungi were isolated and purified by mycelial tip transferring. Among 31 isolates, 26 showed similar cultural characters. The wool-like mycelia were luxuriant and grew rapidly on PDA spreading the whole 9 cm petri dish in less than a week at 28 ℃. The mycelia were white to ashen at beginning and gradually turned black from center of the plate after 5 days culture at 28 ℃. Hyphae were smooth, branched, septate, hyaline or pale brown. Conidia were single-celled, black, spherical to subspherical, and 10.2 to 14.6 × 12.2 to 15.7 µm (n=50) in dimension and born on tip of hyaline and ampulliform conidiophores. The fungus showed similar morphological characteristics with Nigrospora oryzae (1). ITS sequences of 6 representative strains of the fungus were amplified, sequenced with primer pair, ITS1/ITS4 (2), and submitted into GenBank with an accession number, MW228165. Phylogenetic analysis was conducted with sequences of reference strains (3). The result showed that the fungus obtained in this study was fallen into the same group with N.oryzae. In view of above both morphological and molecular analysis, the strains were finally identified as N. oryzae. Pathogenicity tests were conducted in triplicate with rice panicles in initial heading stage. Fifty panicles were wounded on branches with needles and inoculated by spreading the conidia suspension (10µl, 1 × 106 conidia ml-1) on the wounds. The panicles used as control were treated in same way with 10µl of sterile water. The inoculated and control plants were kept in dark, 25 ℃ and relative humidity of more than 85% for 24 h in culture chamber. Symptoms appeared on 44 of 50 inoculated panicles which were basically similar with those observed in paddy field, while negative controls remained symptomless. The fungi re-isolated from inoculated panicles were also confirmed as N. oryzae by both morphological and molecular analysis. To the best of our knowledge, this is the first report of N. oryzae causing panicle branch rot disease on Oryza sativa (rice). This disease not only cause yield losses and lower milling quality, but could also be mistaken as rice blast incurring unnecessary fungicides spray.

First report of Fusarium incarnatum causing spikelet rot on rice in China.

Rice (Oryza sativa L.) is the most important and widely grown crop, covering about 29.9 million ha of total cultivation area in China. In the last decade, spikelet rot disease on rice became much more frequent in the middle and lower reaches of the Yangtze River, China. Fusarium proliferatum (Matsush.) Nirenberg ex Gerlach & Nirenberg was reported to be a causal agent of spikelet rot on rice in Hangzhou, Zhejiang province (Huang et al. 2012). In September 2019, a survey was conducted to understand the etiology of the disease in the main rice growing regions of Jinshan District of Shanghai. Symptomatic panicles exhibiting reddish or brown discoloration on the glumes were collected from different rice fields, where disease incidence was estimated to be between 20 to 80%. Diseased glumes were cut into small sections (5 × 5 mm) from the boundary of necrotic and healthy tissues, surface-sterilized with 75% ethanol for 30 s and 3% sodium hypochlorite for 90 s, rinsed twice with sterile distilled water, then placed onto 1/5 strength potato dextrose agar (PDA). After 3 to 5 days of incubation at 28°C in the dark, fungal growth with Fusarium-like colonies were transferred to PDA and purified by the single-spore isolation method. A total of 12 isolates were obtained and colonies showed loosely floccose, white mycelium and pale-yellow pigmentation on PDA. Microconidia were ovoid mostly with 0 to 1 septum, and measured 4.2 to 16.6 × 2.5 to 4.1 µm (n = 50). After 5-7 days of inoculation on carnation leaf agar (CLA), macroconidia produced usually had 3 to 5 septa, slightly curved at the apex, ranging from 15.7 to 39.1 × 3.3 to 5.0 µm (n = 50). Chlamydospores were produced in hyphae, most often solitary in short chains or in clumps, ellipsoidal or subglobose with thick and roughened walls. Molecular identification was performed on the representative isolates (JS3, JS9, and JS21). The rDNA internal transcribed spacer (ITS), translation elongation factor (TEF-1α) and ß-tubulin (ß-TUB) genes were amplified and sequenced using the paired primers ITS1/ITS4 (White et al. 1990), EF1/EF2 (O'Donnell et al. 1998) and T1/T22 (O'Donnell and Cigelnik 1997), respectively. The obtained sequences were deposited in GenBank under accession numbers MT889972 to MT889974 (ITS), MT895844 to MT895846 (TEF-1α), and MT895841 to MT895843 (ß-TUB), respectively. BLASTn search of the sequences revealed 99 to 100% identity with ITS (MF356578), TEF-1α (HM770725) and ß-TUB (GQ915444) of Fusarium incarnatum isolates. FUSARIUM-ID (Geiser et al. 2004) analysis showed 99 to 100% similarity with sequences of the F. incarnatum-equiseti species complex (FIESC) (FD_01651 and FD_01628). In addition, a phylogenetic analysis based on the concatenated nucleotide sequences placed the isolates in the F. incarnatum clade at 100% bootstrap support. Thus, both morphological observations and molecular criteria supported identification of the isolates as F. incarnatum (Desm.) Sacc (synonym: Fusarium semitectum) (Leslie and Summerell 2006, Nirenberg 1990). Pathogenicity tests were performed on susceptible rice cultivar 'Xiushui134'. At pollen cell maturity stage, a 2-ml conidial suspension (5 × 105 macroconidia/ml) of each isolate was injected into 10 rice panicles. Control plants were inoculated with sterile distilled water. Then, the pots were kept in a growth chamber at 28°C, 80% relative humidity, and 12 h/12 h light (10,000 lux)/dark. The experiment was repeated two times for each isolate. Two weeks post-inoculation, all inoculated panicles showed similar symptoms with the original samples, whereas no symptoms were observed on the control. The pathogen was re-isolated from inoculated panicles and identified by the method described above to fulfill Koch's postulates. Previous studies reported that F. incarnatum reproduced perithecia to overwinter on rice stubble as the inoculum of Fusarium head blight of wheat in southern China (Yang et al. 2018). To our knowledge, this is the first report of spikelet rot on rice caused by F. incarnatum in China. Further investigation is needed to gain a better understanding its potential geographic distribution of this new pathogen on rice crop. References: (1) Huang, S. W., et al. 2011. Crop Prot. 30: 10. (2) White, T. J., et al. 1990. Page 315 in: PCR Protocols: A Guide to Methods and Applications. Academic Press, San Diego, CA. (3) O'Donnell, K., et al. 1998. Proc. Natl. Acad. Sci. U.S.A. 95: 2044. (4) O'Donnell, K., Cigelnik, E. 1997. Mol. Phylogenet. Evol. 7: 103. (5) Geiser, D. M., et al. 2004. Eur. J. Plant Pathol. 110: 473. (6) Leslie, J. F., and Summerell, B. A. 2006. The Fusarium Laboratory Manual. Blackwell, Ames, IA. (7) Nirenberg, H. I. 1990. Stud. Mycol. 32: 91. (8) Yang, M. X., et al. 2018. Toxins. 10: 115. The author(s) declare no conflict of interest. Funding: Funding was provided by National Natural Science Foundation of China (grant no. 31800133), Zhejiang Provincial Natural Science Foundation of China (grant no. LQ18C140005), Key Research and Development Program of Zhejiang Province (grant no. 2019C02018), Shanghai Science and Technology for Agriculture Promotion Project (2019-02-08-00-08-F01127), and the Agricultural Science and Technology Innovation Program of China Academy of Agricultural Science (CAAS-ASTIP-2013- CNRRI).

A Brain-Inspired Decision-Making Linear Neural Network and Its Application in Automatic Drive.

Brain-like intelligent decision-making is a prevailing trend in today's world. However, inspired by bionics and computer science, the linear neural network has become one of the main means to realize human-like decision-making and control. This paper proposes a method for classifying drivers' driving behaviors based on the fuzzy algorithm and establish a brain-inspired decision-making linear neural network. Firstly, different driver experimental data samples were obtained through the driving simulator. Then, an objective fuzzy classification algorithm was designed to distinguish different driving behaviors in terms of experimental data. In addition, a brain-inspired linear neural network was established to realize human-like decision-making and control. Finally, the accuracy of the proposed method was verified by training and testing. This study extracts the driving characteristics of drivers through driving simulator tests, which provides a driving behavior reference for the human-like decision-making of an intelligent vehicle.

Both insufficient and excessive glucocorticoid receptor-mediated signaling impair neuronal migration.

Glucocorticoids (GCs) are a class of steroid hormones that regulate numerous physiological events in the human body. Clinically, glucocorticoids are used for anti-inflammatory and immunosuppressive actions via binding with glucocorticoid receptors (GRs). Emerging evidence has also indicated that inappropriate GC and GR levels are detrimental for brain development and eventually lead to severe neurological diseases. However, the roles of GC/GR signaling in brain development are not fully understood. Here, we showed that stable GR expression levels were critical for brain development, because both GR knockdown and overexpression severely impaired neuronal migration. Further studies showed that the multipolar-bipolar transition and leading process development were interrupted in GR-knockdown and GR-overexpressing neurons. To elucidate the underlying mechanism, we screened the protein levels of downstream molecules and identified RhoA as a factor negatively regulated by the GR. Restoration of the RhoA protein level partially rescued the neuronal migration defects in the GR-knockdown and GR-overexpressing neurons, indicating that RhoA played a major role in GR-mediated neuronal migration. These data suggest that an appropriate level of GC/GR signaling is essential for precise control of neuronal migration.

Mechanical writing of n-type conductive layers on the SrTiO3 surface in nanoscale.

The fabrication and control of the conductive surface and interface on insulating SrTiO3 bulk provide a pathway for oxide electronics. The controllable manipulation of local doping concentration in semiconductors is an important step for nano-electronics. Here we show that conductive patterns can be written on bare SrTiO3 surface by controllable doping in nanoscale using the mechanical interactions of atomic force microscopy tip without applying external electric field. The conductivity of the layer is n-type, oxygen sensitive, and can be effectively tuned by the gate voltage. Hence, our findings have potential applications in oxide nano-circuits and oxygen sensors.

Polar dependent in-plane electric transport of epitaxial ZnO thin films on SrTiO(3) substrates.

Polar (001) and nonpolar (110) ZnO epitaxial thin films were grown on SrTiO(3) substrates by the pulsed laser deposition method and the in-plane electric transport was investigated. Both films display semiconducting behavior. The polar thin films have linear I-V relations with mobility increasing almost linearly with temperature. In contrast, for nonpolar ZnO thin films, the I-V curves are symmetric and nonlinear with room temperature resistivity 30 times larger than that of polar thin films. We conclude that in nonpolar ZnO thin films the bound polarization charge induced barrier limits the carrier transport. Instead, for polar thin films, the polar effect on the in-plane transport is negligible, and the charged dislocation scattering is dominant. Our observations suggest the polar effect should be considered in the design of ZnO related devices.