Genomic Characterization Provides New Insights Into the Biosynthesis of the Secondary Metabolite Huperzine a in the Endophyte Colletotrichum gloeosporioides Cg01

A reliable source of Huperzine A (HupA) meets an urgent need due to its wide use in Alzheimer's disease treatment. In this study, we sequenced and characterized the whole genomes of two HupA-producing endophytes, Penicillium polonicum hy4 and Colletotrichum gloeosporioides Cg01, to clarify the mechanism of HupA biosynthesis. The whole genomes of hy4 and Cg01 were 33.92 and 55.77 Mb, respectively. We compared the differentially expressed genes (DEGs) between the induced group (with added extracts of Huperzia serrata) and a control group. We focused on DEGs with similar expression patterns in hy4 and Cg01. The DEGs identified in GO (Gene ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways were primarily located in carbon and nitrogen metabolism and nucleolus, ribosome, and rRNA processing. Furthermore, we analyzed the gene expression for HupA biosynthesis genes proposed in plants, which include lysine decarboxylase (LDC), copper amine oxidase (CAO), polyketides synthases (PKS), etc. Two LDCs, one CAO, and three PKSs in Cg01 were selected as prime candidates for further validation. We found that single candidate biosynthesis-gene knock-out did not influence the HupA production, while both LDC gene knock-out led to increased HupA production. These results reveal that HupA biosynthesis in endophytes might differ from that proposed in plants, and imply that the HupA-biosynthesis genes in endophytic fungi might co-evolve with the plant machinery rather than being acquired through horizontal gene transfer (HGT). Moreover, we analyzed the function of the differentially expressed epigenetic modification genes. HupA production of the histone acetyltransferase (HAT) deletion mutant ΔCgSAS-2 was not changed, while that of the histone methyltransferase (HMT) and histone deacetylase (HDAC) deletion mutants ΔCgClr4, ΔCgClr3, and ΔCgSir2-6 was reduced. Recovery of HupA-biosynthetic ability can be achieved by retro-complementation, demonstrating that HMT and HDACs associated with histone modification are involved in the regulation of HupA biosynthesis in endophytic fungi. This is the first report on epigenetic modification in high value secondary metabolite- producing endophytes. These findings shed new light on HupA biosynthesis and regulation in HupA-producing endophytes and are crucial for industrial production of HupA from fungi

GujiBERT and GujiGPT: Construction of Intelligent Information Processing Foundation Language Models for Ancient Texts

In the context of the rapid development of large language models, we have meticulously trained and introduced the GujiBERT and GujiGPT language models, which are foundational models specifically designed for intelligent information processing of ancient texts. These models have been trained on an extensive dataset that encompasses both simplified and traditional Chinese characters, allowing them to effectively handle various natural language processing tasks related to ancient books, including but not limited to automatic sentence segmentation, punctuation, word segmentation, part-of-speech tagging, entity recognition, and automatic translation. Notably, these models have exhibited exceptional performance across a range of validation tasks using publicly available datasets. Our research findings highlight the efficacy of employing self-supervised methods to further train the models using classical text corpora, thus enhancing their capability to tackle downstream tasks. Moreover, it is worth emphasizing that the choice of font, the scale of the corpus, and the initial model selection all exert significant influence over the ultimate experimental outcomes. To cater to the diverse text processing preferences of researchers in digital humanities and linguistics, we have developed three distinct categories comprising a total of nine model variations. We believe that by sharing these foundational language models specialized in the domain of ancient texts, we can facilitate the intelligent processing and scholarly exploration of ancient literary works and, consequently, contribute to the global dissemination of China's rich and esteemed traditional culture in this new era.Comment: 22pages,0 figur

Dechlorination of polyvinyl chloride by hydrothermal treatment with cupric ion

Hydrothermal treatment (HTT) is able to remove chlorine effectively from polyvinyl chloride (PVC), however, the reaction temperature is critical in practical application. Less energy-intensive hydrothermal dechlorination condition with cupric ion (Cu2+) has been proposed in this study. In particular, Cu2+ was applied in HTT of PVC at temperature ranging from 200 °C to 240 °C. It has been found that the introduction of Cu2+ distinctly accelerated PVC decomposition and dechlorination at 220 °C. When Cu2+ concentration was increased from 0.01 mol/L to 0.20 mol/L, the dechlorination efficiency was significantly improved from 15.46 %–67.89 %. Dramatic dechlorination occurred as residence time was longer than 15 min during HTT. Besides, both elimination and substitution dominated the HTT dechlorinaton. The facilitated dechlorination after the addition of Cu2+ was mainly due to the enhanced dispersion and formation of micropores in hydrochar. On the whole, HTT could be a promising pretreatment technology for copper-containing PVC in electronic wastes to prepared chlorine free hydrochar for combustion or pyrolysis applications, the optimal HTT condition would be 220 °C, 60 min with 0.1 mol/L Cu2+.acceptedVersionPeer reviewe

13C-Metabolic Flux Analysis Reveals the Metabolic Flux Redistribution for Enhanced Production of Poly-γ-Glutamic Acid in dlt Over-Expressed Bacillus licheniformis

Poly-γ-glutamic acid (γ-PGA) is an anionic polymer with various applications. Teichoic acid (TA) is a special component of cell wall in gram-positive bacteria, and its D-alanylation modification can change the net negative charge of cell surface, autolysin activity and cationic binding efficiency, and might further affect metabolic production. In this research, four genes (dltA, dltB, dltC, and dltD) of dlt operon were, respectively, deleted and overexpressed in the γ-PGA producing strain Bacillus licheniformis WX-02. Our results implied that overexpression of these genes could all significantly increase γ-PGA synthetic capabilities, among these strains, the dltB overexpression strain WX-02/pHY-dltB owned the highest γ-PGA yield (2.54 g/L), which was 93.42% higher than that of the control strain WX-02/pHY300 (1.31 g/L). While, the gene deletion strains produced lower γ-PGA titers. Furthermore, 13C-Metabolic flux analysis was conducted to investigate the influence of dltB overexpression on metabolic flux redistribution during γ-PGA synthesis. The simulation data demonstrated that fluxes of pentose phosphate pathway and tricarboxylic acid cycle in WX-02/pHY-dltB were 36.41 and 19.18 mmol/g DCW/h, increased by 7.82 and 38.38% compared to WX-02/pHY300 (33.77 and 13.86 mmol/g DCW/h), respectively. The synthetic capabilities of ATP and NADPH were also increased slightly. Meanwhile, the fluxes of glycolytic and by-product synthetic pathways were all reduced in WX-02/pHY-dltB. All these above phenomenons were beneficial for γ-PGA synthesis. Collectively, this study clarified that overexpression of dltB strengthened the fluxes of PPP pathway, TCA cycle and energy metabolism for γ-PGA synthesis, and provided an effective strategy for enhanced production of γ-PGA

Effect of chemical modifications on modulation of gene expression by duplex antigene RNAs that are complementary to non-coding transcripts at gene promoters

Antigene RNAs (agRNAs) are small RNA duplexes that target non-coding transcripts rather than mRNA and specifically suppress or activate gene expression in a sequence-dependent manner. For many applications in vivo, it is likely that agRNAs will require chemical modification. We have synthesized agRNAs that contain different classes of chemical modification and have tested their ability to modulate expression of the human progesterone receptor gene. We find that both silencing and activating agRNAs can retain activity after modification. Both guide and passenger strands can be modified and functional agRNAs can contain 2′F-RNA, 2′OMe-RNA, and locked nucleic acid substitutions, or combinations of multiple modifications. The mechanism of agRNA activity appears to be maintained after chemical modification: both native and modified agRNAs modulate recruitment of RNA polymerase II, have the same effect on promoter-derived antisense transcripts, and must be double-stranded. These data demonstrate that agRNA activity is compatible with a wide range of chemical modifications and may facilitate in vivo applications

The Genomes of Oryza sativa: A History of Duplications

We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped super-scaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000–40,000. Only 2%–3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism (SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family

LICSTER -- A Low-cost ICS Security Testbed for Education and Research

Unnoticed by most people, Industrial Control Systems (ICSs) control entire productions and critical infrastructures such as water distribution, smart grid and automotive manufacturing. Due to the ongoing digitalization, these systems are becoming more and more connected in order to enable remote control and monitoring. However, this shift bears significant risks, namely a larger attack surface, which can be exploited by attackers. In order to make these systems more secure, it takes research, which is, however, difficult to conduct on productive systems, since these often have to operate twenty-four-seven. Testbeds are mostly very expensive or based on simulation with no real-world physical process. In this paper, we introduce LICSTER, an open-source low-cost ICS testbed, which enables researchers and students to get hands-on experience with industrial security for about 500 Euro. We provide all necessary material to quickly start ICS hacking, with the focus on low-cost and open-source for education and research

Impacts of after-action reviews on mathematical learning performance

Reviewing the completed exercises was essential to mathematical learning, but students often jump to the next exercise after finishing the current one without reviewing. It is not clear how to effectively conduct this learning activity. On the other side, after-action reviews (AARs) have proved to be a good learning practice that has been widely used in military and unmilitary training for decades. It helps students learn through reviewing. This study applied AARs in mathematical learning to improve students’ learning effectiveness through reviewing their completed exercises. In addition, the study further investigated how the question types of AARs influence students’ cognitive engagement. Ninth-grade students (N = 125) were randomly assigned to one of three experimental conditions (AARs of general questions, AARs of specific questions, and no AARs). The results revealed that conducting AARs after solving mathematics problems could significantly improve learning performance (p \u3c.05). Compared with AARs of specific questions, AARs of general questions could significantly improve students’ cognitive engagement (p \u3c.001). The findings provide important implications for mathematical education and learning practice

Corrosion Behavior of Ancient White Cast Iron Artifacts from Marine Excavations at Atmospheric Condition

A large number of iron pot artifacts were excavated from the “Nanhai I” shipwreck. The rapid embrittlement and pulverization of these objects (that have a good matrix) in the atmospheric environment is worthy of attention. Metallographic analysis showed that the material of the iron pots was hypereutectic white cast iron. Micro-CT observations revealed that there were numerous microcracks and fissures within the seemingly well-preserved iron. These fissures increased and enlarged with prolonged exposure to air. Scanning electron microscopy exhibited that the microcracks were initially created at the “concave surface” formed by the ferrite corrosion, and the cementite was gradually torn by the local accumulation of large internal stresses. Micro-Raman proved that the structure of rust was varied and complex during the generation and development of fissures. The dimension of corrosion products could expand and contract in mutual transformation, forming local internal stress and promoting the expansion of microcracks. This work proposed a reasonable mechanism for the rapid embrittlement and pulverization in the atmospheric environment of such hypereutectic white cast iron artifacts out of the sea, which provided a scientific reference for future protection

Corrosion Inhibition and Rust Conversion of Catechin on Archaeological Iron of Nanhai I

This work took the iron objects from the Nanhai No. 1 shipwreck in the Southern Song Dynasty of China as the sample to test and analyze the application potential of catechin, an environmentally friendly corrosion inhibitor and rust converter. The article used metallographic microscopy to clarify that the structure of the iron artifact was hypereutectic white iron. By means of micro-Raman, Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), scanning electron microscope (SEM), potentiodynamic polarization and electrochemical impedance spectroscopy, catechin had the ability to react with iron oxyhydroxides such as goethite, akaganeite and lepidocrocite in the rust, forming an amorphous substance with a marked signal about 1380 cm−1 as phenolic-Fe in infrared properties. The new products could make the original rust layer form a laminated dense structure. After the archaeological iron was soaked in 3.0 g/L catechin, the corrosion current density decreased by 37.13% and the corrosion potential shifted positively by 32.67 mV. The anode reaction was more inhibited than the cathode in the polarization curve. The rust resistance in electrochemical impedance increased to 3.75 times and the ion diffusion resistance increased to 6.33 times. The corrosion inhibition efficiency was 21.75% and the rust conversion efficiency was 73.26%. After 36 h of accelerated corrosion, the protection effect of the newly transformed rust layer was still better than that of the original state. Catechin was a mild protection material which showed satisfactory performance for archaeological iron and has a good application prospect