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Abstract: RNA editing is a posttranscriptional process that is important in mitochondria and plastids of higher plants. All RNA editing‐specific trans‐factors reported so far belong to PLS‐class of pentatricopeptide repeat (PPR) proteins. Here, we report the map‐based cloning and molecular characterization of a defective kernel mutant dek39 in maize. Loss of Dek39 function leads to delayed embryogenesis and endosperm development, reduced kernel size, and seedling lethality. Dek39 encodes an E sub‐class PPR protein that targets to both mitochondria and chloroplasts, and is involved in RNA editing in mitochondrial NADH dehydrogenase3 (nad3) at nad3‐247 and nad3‐275. C‐to‐U editing of nad3‐275 is not conserved and even lost in Arabidopsis, consistent with the idea that no close DEK39 homologs are present in Arabidopsis. However, the amino acids generated by editing nad3‐247 and nad3‐275 are highly conserved in many other plant species, and the reductions of editing at these two sites decrease the activity of mitochondria NADH dehydrogenase complex I, indicating that the alteration of amino acid sequence is necessary for Nad3 function. Our results indicate that Dek39 encodes an E sub‐class PPR protein that is involved in RNA editing of multiple sites and is necessary for seed development of maize. [ABSTRACT FROM AUTHOR]

We present an approach to fabricate shell objects with thickness parameters, which are computed to maintain the user-specified structural stability. Given a boundary surface and user-specified external forces, we optimize the thickness parameters according to stress constraints to extrude the surface. Our approach mainly consists of two technical components: First, we develop a patch-based shell simulation technique to efficiently support the static simulation of extruded shell objects using finite element methods. Second, we analytically compute the derivative of stress required in the sensitivity analysis technique to turn the optimization into a sequential linear programming problem. Experimental results demonstrate that our approach can optimize the thickness parameters for arbitrary surfaces in a few minutes and well predict the physical properties, such as the deformation and stress of the fabricated object. [ABSTRACT FROM AUTHOR]

Di(2-ethylhexyl) phthalate (DEHP), one of the most important plasticizers, is considered a typical endocrine disruptor. Soil contains high levels of DEHP, and acts as the main medium for its migration into food chain, presenting potential risks to human health. Although soil indigenous microbial communities hold a great potential to degrade DEHP, the kinetics and mechanism of microbial biodegradation for soil DEHP on the long-time scale remain unclear. Here, we analyzed microbial communities from time-series (up to 90 days) samples of laboratory microcosms by sequencing of 16S and ITS rRNA gene amplicons. We found that the kinetics processes of DEHP biodegradation were well fitted by a biphasic model with two independent kinetic phases: phase I as a first-order kinetics process (0–10 days, r2 = 0.975), and phase II as a fractional power kinetics process (11–90 days, r2 = 0.967). Linear discriminant and partial least square regression analyses showed that bacterial genera Clostridium, Sporotomaculum, Mycoplana, and Hyphomicrobium were involved in DEHP biodegradation during phase I, and genera Bacillus and Nannocystis were responsible for DEHP biodegradation during phase II. Moreover, we observed transition in microbial co-occurrence patterns: closer inter-taxa connections between bacterial degrader and fungal genera Aspergillus, Fusarium, and Pleurotus in phase I. Such divergence in the composition of potential DEHP-degrading bacteria and their interactions with fungi may induce the decreased degradation rates from phase I to phase II. This study systematically deciphers the bacterially driven DEHP biodegradation kinetics, and provides fundamental basis for developing strategies for efficient DEHP removal in soil. [ABSTRACT FROM AUTHOR]

Deregulated reactive oxygen species (ROS) production can lead to the disruption of structural and functional integrity of cells as a consequence of reactive interaction between ROS and various biological components. Catalase (CAT) is a common enzyme existing in nearly all organisms exposed to oxygen, which decomposes harmful hydrogen peroxide, into water and oxygen. In this study, the full length sequence that encodes CAT-like protein from Spodoptera litura named siltCAT (GenBank accession number: JQ_663444) was cloned and characterized. Amino acid sequence alignment showed siltCAT shared relatively high conservation with other insect, especially the conserved residues which defined heme and NADPH orientation. Expression pattern analysis showed that siltCAT mRNA was mainly expressed in the fat body, midgut, cuticle and malpighian tube, and as well as over last instar larvae, pupa and adult stages. RNA interference was used to silence CAT gene in SL-1 cells and the fourth-instar stage of S. litura larvae respectively. Our results provided evidence that CAT knockdown induced ROS generation, cell cycle arrest and apoptosis in SL-1 cells. It also confirmed the decrease in survival rate because of increased ROS production in experimental groups injected with double-stranded RNA of CAT (dsCAT). This study implied that ROS scavenging by CAT is important for S. litura survival. [ABSTRACT FROM AUTHOR]

Abstract: We fabricate microfluidic DNA sensors based on the electrochemical method that uses Hoechst 33258 [2′-(4-hydroxyphenyl)-5-(4-methyl-1-piperazinyl)-2,5′-bi(1H-benzimidazole)] as a DNA intercalator. These chips are fabricated without a probe immobilization process, thereby being more simply regenerated than other typical DNA chips. Linear sweep voltammetric measurements show an anodic-current decrease consistent with the DNA duplex formation which occurs when the target is fully complementary to the probe, enabling sequence-specific DNA detection. [Copyright &y& Elsevier]

Interseeding silage corn into an alfalfa stand following its spring harvests to produce mixed silage would feasibly break the restriction of alfalfa production during a hot-rainy summer. In this 2-yr experiment, the alfalfa–silage corn intercropping system (AC) with nitrogen (N) fertilization rates of 0, 60, 120, and 180 kg N ha−1 and corn plant densities of 30,000, 45,000, and 60,000 plants ha−1 was compared with the monocultured corn (CK) managed using the local farmers' practice. Intercropping with alfalfa significantly decreased the dry matter (DM) yield of the corn by 31.5% on average, while increasing the N application rate and corn plant density promoted DM yield and crude protein (CP) accumulation of the intercropped corn, and the intercropping system could achieve the same CP yield as CK—it did in most cases. Although the DM contents, pH values, and NH3-N concentrations were decreased in the mixed silage, its fermentation quality was not reduced and the CP, water soluble carbohydrates, and lactic acid contents were dramatically increased by 16.3%, 17.8%, and 72.9% compared with those of CK, respectively. For the opposite effects of N fertilization and corn density on silage quality, the treatment combination with a medium corn density (45,000 plants ha−1) fertilized at a medium N rate (120 kg N ha−1) was evaluated as the optimum for more balanced system productivity, silage nutritive values and fermentative characteristics during the coexisting period. [ABSTRACT FROM AUTHOR]

• This review assessed the contamination levels of PAE in various ecosystems. • Overviewed the current status of PAE-degrading bacterial isolates and communities. • Discussed the challenges for understanding in situ PAE biodegradation mechanisms. • Proposed a guide of building synthetic community to decipher interaction mechanism. The extensive use of phthalic acid esters (PAEs) has led to their widespread distribution across various environments. As PAEs pose significant threats to human health, it is urgent to develop efficient strategies to eliminate them from environments. Bacteria-driven PAE biodegradation has been considered as an inexpensive yet effective strategy to restore the contaminated environments. Despite great advances in bacterial culturing and sequencing, the inherent complexity of indigenous microbial community hinders us to mechanistically understand in situ PAE biodegradation and efficiently harness the degrading power of bacteria. The synthetic microbial ecology provides us a simple and controllable model system to address this problem. In this review, we focus on the current progress of PAE biodegradation mediated by bacterial isolates and indigenous bacterial communities, and discuss the prospective of synthetic PAE-degrading bacterial communities in PAE biodegradation research. It is anticipated that the theories and approaches of synthetic microbial ecology will revolutionize the study of bacteria-driven PAE biodegradation and provide novel insights for developing effective bioremediation solutions. [ABSTRACT FROM AUTHOR]

Summary: Kernel row number (KRN) is a major yield related trait for maize (Zea mays L.) and is also a major goal of breeders, as it can increase the number of kernels per plant. Thus, identifying new genetic factors involving in KRN formation may accelerate improving yield‐related traits genetically. We herein describe a new kernel number‐related gene (KRN5b) identified from KRN QTL qKRN5b and encoding an inositol polyphosphate 5‐phosphatase (5PTase). KRN5b has phosphatase activity towards PI(4,5)P2, PI(3,4,5)P3, and Ins(1,4,5)P3in vitro. Knocking out KRN5b caused accumulation of PI(4,5)P2 and Ins(1,4,5)P3, resulting in disordered kernel rows and a decrease in the number of kernels and tassel branches. The introgression of the allele with higher expression abundance into different inbred lines could increase the ear weight of the inbred lines and the corresponding hybrids by 10.1%–12.2% via increasing KRN, with no adverse effects on other agronomic traits. Further analyses showed that KRN5b regulates inflorescence development through affecting the synthesis and distribution of hormones. Together, KRN5b contributes to spikelet pair meristem development through inositol phosphate and phosphatidylinositols, making it a selecting target for yield improvement. [ABSTRACT FROM AUTHOR]

Long-range chromatin interactions are important for transcriptional regulation of genes, many of which are related to complex agronomics traits. However, the pattern of three-dimensional chromatin interactions remains unclear in plants. Here we report the generation of chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) data and the construction of extensive H3K4me3- and H3K27ac-centered chromatin interaction maps in maize. Results show that the interacting patterns between proximal and distal regulatory regions of genes are highly complex and dynamic. Genes with chromatin interactions have higher expression levels than those without interactions. Genes with proximal-proximal interactions prefer to be transcriptionally coordinated. Tissue-specific proximal–distal interactions are associated with tissue-specific expression of genes. Interactions between proximal and distal regulatory regions further interweave into organized network communities that are enriched in specific biological functions. The high-resolution chromatin interaction maps will help to understand the transcription regulation of genes associated with complex agronomic traits of maize. Chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) can discover specific protein-centered chromatin interactions in high resolution. Here, the authors use ChIA-PET to reveal the complex and dynamic interactions between proximal and distal regulatory regions of genes in maize. [ABSTRACT FROM AUTHOR]

This article discusses the establishment of a genetic transformation system and gene editing platform for broomcorn millet using CRISPR/Cas12i.3 technology. Broomcorn millet is an ancient crop with desirable traits such as short life cycle, high photosynthetic efficiency, and tolerance to arid and saline-alkali soil. The researchers successfully developed a method for genetic transformation of broomcorn millet using Agrobacterium-mediated techniques. They also used the CRISPR/Cas12i.3 system to edit the BRACHYTIC2 (BR2) gene in broomcorn millet, resulting in dwarf plants with shorter internodes. This research has important implications for improving agronomic traits and developing new varieties of broomcorn millet. [Extracted from the article]

Broomcorn millet (Panicum miliaceum L.) has strong tolerance to abiotic stresses, and is probably one of the oldest crops, with its earliest cultivation that dated back to ca. ~10,000 years. We report here its genome assembly through a combination of PacBio sequencing, BioNano, and Hi-C (in vivo) mapping. The 18 super scaffolds cover ~95.6% of the estimated genome (~887.8 Mb). There are 63,671 protein-coding genes annotated in this tetraploid genome. About ~86.2% of the syntenic genes in foxtail millet have two homologous copies in broomcorn millet, indicating rare gene loss after tetraploidization in broomcorn millet. Phylogenetic analysis reveals that broomcorn millet and foxtail millet diverged around ~13.1 Million years ago (Mya), while the lineage specific tetraploidization of broomcorn millet may be happened within ~5.91 million years. The genome is not only beneficial for the genome assisted breeding of broomcorn millet, but also an important resource for other Panicum species. Broomcorn millet is one of the oldest crops cultivated by human that has strong abiotic stress tolerance. To facilitate genome assisted breeding of this and related species, the authors report its genome assembly and conduct comparative genome structure and evolution analyses with foxtail millet. [ABSTRACT FROM AUTHOR]

Background: Drought is one of the major factors limiting global maize production. Exposure to long-term drought conditions inhibits growth and leads to yield losses. Although several drought-responsive genes have been identified and functionally analyzed, the mechanisms underlying responses to drought and water recovery treatments have not been fully elucidated. To characterize how maize seedling respond to drought stress at the transcriptional level, we analyzed physiological responses and differentially expressed genes (DEGs) in the inbred line B73 under water deficit and recovery conditions. Results: The data for relative leaf water content, leaf size, and photosynthesis-related parameters indicated that drought stress significantly repressed maize seedling growth. Further RNA sequencing analysis revealed that 6107 DEGs were responsive to drought stress and water recovery, with more down-regulated than up-regulated genes. Among the DEGs, the photosynthesis- and hormone-related genes were enriched in responses to drought stress and re-watering. Additionally, transcription factor genes from 37 families were differentially expressed among the three analyzed time-points. Gene ontology enrichment analyses of the DEGs indicated that 50 GO terms, including those related to photosynthesis, carbohydrate metabolism, oxidoreductase activities, nutrient metabolism and other drought-responsive pathways, were over-represented in the drought-treated seedlings. The content of gibberellin in drought treatment seedlings was decreased compared to that of control seedlings, while abscisic acid showed accumulated in the drought treated plants. The deep analysis of DEGs related to cell wall development indicated that these genes were prone to be down-regulated at drought treatment stage. Conclusions: Many genes that are differentially expressed in responses to drought stress and water recovery conditions affect photosynthetic systems and hormone biosynthesis. The identified DEGs, especially those encoding transcription factors, represent potential targets for developing drought-tolerant maize lines. [ABSTRACT FROM AUTHOR]

Summary: The Elongator complex was originally identified as an interactor of hyperphosphorylated RNA polymerase II (RNAPII) in yeast and has histone acetyltransferase (HAT) activity. However, the genome‐wide regulatory roles of Elongator on transcriptional elongation and histone acetylation remain unclear. We characterized a maize miniature seed mutant, mn7 and map‐based cloning revealed that Mn7 encodes one of the subunits of the Elongator complex, ZmELP1. ZmELP1 deficiency causes marked reductions in the kernel size and weight. Molecular analyses showed that ZmELP1 interacts with ZmELP3, which is required for H3K14 acetylation (H3K14ac), and Elongator complex subunits interact with RNA polymerase II (RNAPII) C‐terminal domain (CTD). Genome‐wide analyses indicated that loss of ZmELP1 leads to a significant decrease in the deposition of H3K14ac and the CTD of phosphorylated RNAPII on Ser2 (Ser2P). These chromatin changes positively correlate with global transcriptomic changes. ZmELP1 mutation alters the expression of genes involved in transcriptional regulation and kernel development. We also showed that the decrease of Ser2P depends on the deposition of Elongator complex‐mediated H3K14ac. Taken together, our results reveal an important role of ZmELP1 in the H3K14ac‐dependent transcriptional elongation, which is critical for kernel development. [ABSTRACT FROM AUTHOR]

SUMMARY: Seed number and harvesting ability in maize (Zea mays L.) are primarily determined by the architecture of female inflorescence, namely the ear. Therefore, ear morphogenesis contributes to grain yield and as such is one of the key target traits during maize breeding. However, the molecular networks of this highly dynamic and complex grain‐bearing inflorescence remain largely unclear. As a first step toward characterizing these networks, we performed a high‐spatio‐temporal‐resolution investigation of transcriptomes using 130 ear samples collected from developing ears with length from 0.1 mm to 19.0 cm. Comparisons of these mRNA populations indicated that these spatio‐temporal transcriptomes were clearly separated into four distinct stages stages I, II, III, and IV. A total of 23 793 genes including 1513 transcription factors (TFs) were identified in the investigated developing ears. During the stage I of ear morphogenesis, 425 genes were predicted to be involved in a co‐expression network established by eight hub TFs. Moreover, 9714 ear‐specific genes were identified in the seven kinds of meristems. Additionally, 527 genes including 59 TFs were identified as especially expressed in ear and displayed high temporal specificity. These results provide a high‐resolution atlas of gene activity during ear development and help to unravel the regulatory modules associated with the differentiation of the ear in maize. Significance Statement: This article will provide a full transcriptional landscape of maize ear during its whole development period. [ABSTRACT FROM AUTHOR]

Summary: The CRISPR‐Cas systems have been widely used as genome editing tools, with type II and V systems typically introducing small indels, and type I system mediating long‐range deletions. However, the precision of type I systems for large fragment deletion is still remained to be optimized. Here, we developed a compact Cascade‐Cas3 Dvu I‐C system with Cas11c for plant genome editing. The Dvu I‐C system was efficient to introduce controllable large fragment deletion up to at least 20 kb using paired crRNAs. The paired‐crRNAs design also improved the controllability of deletions for the type I‐E system. Dvu I‐C system was sensitive to spacer length and mismatch, which was benefit for target specificity. In addition, we showed that the Dvu I‐C system was efficient for generating stable transgenic lines in maize and rice with the editing efficiency up to 86.67%. Overall, Dvu I‐C system we developed here is powerful for achieving controllable large fragment deletions. [ABSTRACT FROM AUTHOR]

Rhodojaponin-III is a nonvolatile botanical grayanoid diterpene compound, which has antifeedant and oviposition deterrence effects against many kinds of insects. However, the molecular mechanism of the chemoreception process remains unknown. In this study, the important role of BdorCSP2 in the recognition of Rhodojaponin-III was identified. The full length cDNA encoding BdorCSP2 was cloned from legs of Bactrocera dorsalis. The results of expression pattern revealed that BdorCSP2 was abundantly expressed in the legs of adult B. dorsalis. Moreover, the expression of BdorCSP2 could be up-regulated by Rhodojaponin-III. In order to gain comprehensive understanding of the recognition process, the binding affinity between BdorCSP2 and Rhodojaponin-III was measured by fluorescence binding assay. Silencing the expression of BdorCSP2 through the ingestion of dsRNA could weaken the effect of oviposition deterrence and antifeedant of Rhodojaponin-III. These results suggested that BdorCSP2 of B. dorsalis could be involved in chemoreception of Rhodojaponin-III and played a critical role in antifeedant and oviposition behaviors induced by Rhodojaponin-III. [ABSTRACT FROM AUTHOR]

Rhodojaponin-III is a nonvolatile botanical grayanoid diterpene compound, which has antifeedant and oviposition deterrence effects against many kinds of insects. However, the molecular mechanism of the chemoreception process remains unknown. In this study, the important role of BdorCSP2 in the recognition of Rhodojaponin-III was identified. The full length cDNA encoding BdorCSP2 was cloned from legs of Bactrocera dorsalis. The results of expression pattern revealed that BdorCSP2 was abundantly expressed in the legs of adult B. dorsalis. Moreover, the expression of BdorCSP2 could be up-regulated by Rhodojaponin-III. In order to gain comprehensive understanding of the recognition process, the binding affinity between BdorCSP2 and Rhodojaponin-III was measured by fluorescence binding assay. Silencing the expression of BdorCSP2 through the ingestion of dsRNA could weaken the effect of oviposition deterrence and antifeedant of Rhodojaponin-III. These results suggested that BdorCSP2 of B. dorsalis could be involved in chemoreception of Rhodojaponin-III and played a critical role in antifeedant and oviposition behaviors induced by Rhodojaponin-III. [ABSTRACT FROM AUTHOR]

• The macro and micro performances of the failure cutter rings in TBM are tested. • By comparing the mechanical properties and microstructure of the cutter rings, the influence of these factors on fatigue fracture and the causes of the fracture are analyzed. • The failure causes and fracture mechanisms of fatigue fracture are analyzed by the cutter ring fracture surface. • Some suggestions for optimizing the microstructure and performance of cutter rings are proposed. The service life of cutter rings (CRs) severely limits the development of tunnel boring machines. The fracture of CRs under cyclic rock breaking loads significantly reduce their lifespan. To investigate the mechanisms and causes of fracture in a CR, the chemical composition, tensile strength, hardness, impact toughness and structure morphology of the fractured CR and the normally worn CR were tested and compared. Both CRs were subjected to the same service conditions in an extremely hard rock engineering project. The carbide distribution of the two CRs was statistically analyzed through metallographic imaging of carbides. The fracture morphology of the CR was examined and analyzed. The results indicate that the fractured CR failed due to a fatigue failure mechanism. Compared to the normally worn CR, the fractured CR shows a lower number density of carbides and larger carbide size, resulting in reduced tensile strength, hardness, and fatigue resistance. Cracks or voids appear between the elongated carbides and the matrix, reducing the ability of the CR to resist fracture. The surface defects on the CR edge provide conditions for the initiation of fatigue cracks. The crack propagation path is dominated by the debonding of carbides. The fine carbides have a stronger ability to resist crack initiation and propagation. Recommendations for optimizing the microstructure and performance of CRs were proposed, aiming to reduce the fatigue fracture failure probability of the CRs. [ABSTRACT FROM AUTHOR]