Genome-Wide Identification and Expression Pattern of MYB Family Transcription Factors in Erianthus fulvus.

MYB family genes have many functions and are widely involved in plant abiotic-stress responses. Erianthus fulvus is an important donor material for stress-resistance genes in sugarcane breeding. However, the MYB family genes in E. fulvus have not been systematically investigated. In this study, 133 EfMYB genes, including 48 Ef1R-MYB, 84 EfR2R3-MYB and 1 Ef3R-MYB genes, were identified in the E. fulvus genome. Among them, the EfR2R3-MYB genes were classified into 20 subgroups. In addition, these EfMYB genes were unevenly distributed across 10 chromosomes. A total of 4 pairs of tandemly duplicated EfMYB genes and 21 pairs of segmentally duplicated EfMYB genes were identified in the E. fulvus genome. Protein-interaction analysis predicted that 24 EfMYB proteins had potential interactions with 14 other family proteins. The EfMYB promoter mainly contains cis-acting elements related to the hormone response, stress response, and light response. Expression analysis showed that EfMYB39, EfMYB84, and EfMYB124 could be significantly induced using low-temperature stress. EfMYB30, EfMYB70, EfMYB81, and EfMYB101 responded positively to drought stress. ABA treatment significantly induced EfMYB1, EfMYB30, EfMYB39, EfMYB84, and EfMYB130. All nine genes were induced using MeJA treatment. These results provide comprehensive information on EfMYB genes and can serve as a reference for further studies of gene function.

Corrigendum: Complete genome sequence of biocontrol strain Bacillus velezensis YC89 and its biocontrol potential against sugarcane red rot.

[This corrects the article DOI: 10.3389/fmicb.2023.1180474.].

Complete genome sequence of biocontrol strain Bacillus velezensis YC89 and its biocontrol potential against sugarcane red rot.

Introduction: Sugarcane is one of the most important sugar crops worldwide, however, sugarcane production is seriously limited by sugarcane red rot, a soil-borne disease caused by Colletotrichum falcatum. Bacillus velezensis YC89 was isolated from sugarcane leaves and can significantly inhibited red rot disease caused by C. falcatum. Methods: In this study, the genome of YC89 strain was sequenced, its genome structure and function were analyzed using various bioinformatics software, and its genome was compared with those of other homologous strains. In addition, the effectiveness of YC89 against sugarcane red rot and the evaluation of sugarcane plant growth promotion were also investigated by pot experiments. Results: Here, we present the complete genome sequence of YC89, which consists of a 3.95 Mb circular chromosome with an average GC content of 46.62%. The phylogenetic tree indicated that YC89 is closely related to B. velezensis GS-1. Comparative genome analysis of YC89 with other published strains (B. velezensis FZB42, B. velezensis CC09, B. velezensis SQR9, B. velezensis GS-1, and B. amyloliquefaciens DSM7) revealed that the strains had a part common coding sequences (CDS) in whereas 42 coding were unique of strain YC89. Whole-genome sequencing revealed 547 carbohydrate-active enzymes and identified 12 gene clusters encoding secondary metabolites. Additionally, functional analysis of the genome revealed numerous gene/gene clusters involved in plant growth promotion, antibiotic resistance, and resistance inducer synthesis. In vitro pot tests indicated that YC89 strain controlled sugarcane red rot and promoted the growth of sugarcane plants. Additionally, it increased the activity of enzymes involved in plant defense, such as superoxide dismutase, peroxidase, polyphenol oxidase, chitinase, and ß-1,3-glucanase. Discussion: These findings will be helpful for further studies on the mechanisms of plant growth promotion and biocontrol by B. velezensis and provide an effective strategy for controlling red rot in sugarcane plants.

Genome-Wide Identification, Evolution, and Expression Analyses of AP2/ERF Family Transcription Factors in Erianthus fulvus.

The AP2/ERF transcription factor family is one of the most important gene families in plants and plays a vital role in plant abiotic stress responses. Although Erianthus fulvus is very important in the genetic improvement of sugarcane, there are few studies concerning AP2/ERF genes in E. fulvus. Here, we identified 145 AP2/ERF genes in the E. fulvus genome. Phylogenetic analysis classified them into five subfamilies. Evolutionary analysis showed that tandem and segmental duplication contributed to the expansion of the EfAP2/ERF family. Protein interaction analysis showed that twenty-eight EfAP2/ERF proteins and five other proteins had potential interaction relationships. Multiple cis-acting elements present in the EfAP2/ERF promoter were related to abiotic stress response, suggesting that EfAP2/ERF may contribute to adaptation to environmental changes. Transcriptomic and RT-qPCR analyses revealed that EfDREB10, EfDREB11, EfDREB39, EfDREB42, EfDREB44, EfERF43, and EfAP2-13 responded to cold stress, EfDREB5 and EfDREB42 responded to drought stress, and EfDREB5, EfDREB11, EfDREB39, EfERF43, and EfAP2-13 responded to ABA treatment. These results will be helpful for better understanding the molecular features and biological role of the E. fulvus AP2/ERF genes and lay a foundation for further research on the function of EfAP2/ERF genes and the regulatory mechanism of the abiotic stress response.

The SsWRKY1 transcription factor of Saccharum spontaneum enhances drought tolerance in transgenic Arabidopsis thaliana and interacts with 21 potential proteins to regulate drought tolerance in S. spontaneum.

In this study, we characterized a WRKY family member gene, SsWRKY1, which is located in the nucleus and contains multiple stress-related cis-acting elements. In addition, constructed SsWRKY1-overexpressing Arabidopsis thaliana had higher antioxidant enzyme activity and proline content under drought stress conditions, with lower malondialdehyde content and reactive oxygen species (ROS) accumulation, and the expression levels of six stress-related genes were significantly upregulated. This indicates that the overexpression of SsWRKY1 in Arabidopsis thaliana improves resistance to drought stress. SsWRKY1 does not have transcriptional autoactivation activity in yeast cells. The yeast two-hybrid (Y2H) system and the S. spontaneum cDNA library were used to screen 21 potential proteins that interact with SsWRKY1, and the interaction between SsWRKY1 and ATAF2 was verified by GST pull-down assay. In summary, our results indicate that SsWRKY1 plays an important role in the response to drought stress and provide initial insights into the molecular mechanism of SsWRKY1 in response to drought stress.

Effect of salinity stress on nitrogen and sulfur removal performance of short-cut sulfur autotrophic denitrification and anammox coupling system.

The effects of salinity on anaerobic nitrogen and sulfide removal were investigated in a coupled anammox and short-cut sulfur autotrophic denitrification (SSADN) system. The results revealed that salinity had significant nonlinear effects on the nitrogen and sulfur transformations in the coupled system. When the salinity was <2 %, the anammox and SSADN activities increased with increasing salinity, and the total nitrogen removal rate, S0 production rate, and nitrite production rate were 0.41 kg/(m3·d), 0.37 kg/(m3·d), and 0.28 kg/(m3·d), respectively. With continuous increase of salinity, the performances of the anammox and SSADN gradually decreased, and the three indicators decreased to 0.14 kg/(m3·d), 0.22 kg/(m3·d), and 0.14 kg/(m3·d) at 5 % salinity, respectively. When the salinity reached 5 %, the nitrogen removal contribution of anammox decreased to 68.4 %, while the contribution of the sulfur autotrophic denitrification increased to 31.6 %. The coupled system recovered in a short time after alleviation of the salinity stress, and the SSADN activity recovery was faster than anammox. The microbial community structure and functional microbial abundance in the coupled system changed significantly with increasing salinity, and the functional microbial abundance after recovery was considerably different from the initial state.

A chromosome-level genome assembly for Erianthus fulvus provides insights into its biofuel potential and facilitates breeding for improvement of sugarcane.

Erianthus produces substantial biomass, exhibits a good Brix value, and shows wide environmental adaptability, making it a potential biofuel plant. In contrast to closely related sorghum and sugarcane, Erianthus can grow in degraded soils, thus releasing pressure on agricultural lands used for biofuel production. However, the lack of genomic resources for Erianthus hinders its genetic improvement, thus limiting its potential for biofuel production. In the present study, we generated a chromosome-scale reference genome for Erianthus fulvus Nees. The genome size estimated by flow cytometry was 937 Mb, and the assembled genome size was 902 Mb, covering 96.26% of the estimated genome size. A total of 35 065 protein-coding genes were predicted, and 67.89% of the genome was found to be repetitive. A recent whole-genome duplication occurred approximately 74.10 million years ago in the E. fulvus genome. Phylogenetic analysis showed that E. fulvus is evolutionarily closer to S. spontaneum and diverged after S. bicolor. Three of the 10 chromosomes of E. fulvus formed through rearrangements of ancestral chromosomes. Phylogenetic reconstruction of the Saccharum complex revealed a polyphyletic origin of the complex and a sister relationship of E. fulvus with Saccharum sp., excluding S. arundinaceum. On the basis of the four amino acid residues that provide substrate specificity, the E. fulvus SWEET proteins were classified as mono- and disaccharide sugar transporters. Ortho-QTL genes identified for 10 biofuel-related traits may aid in the rapid screening of E. fulvus populations to enhance breeding programs for improved biofuel production. The results of this study provide valuable insights for breeding programs aimed at improving biofuel production in E. fulvus and enhancing sugarcane introgression programs.

Effects of salinity on nitrite and elemental sulfur accumulation in a double short-cut sulfur autotrophic denitrification process.

Double short-cut sulfur autotrophic denitrification (DSSADN) coupled with Anammox is of great significance in the low-carbon treatment of nitrogen-containing wastewater. In order to achieve high salinity autotrophic nitrogen removal, the effects of different salinities on the accumulation characteristics of NO2--N and S0 and microorganisms in DSSADN process were studied. The results showed that the effect of salinity on the DSSADN process could be categorized into the stimulation, stable, and inhibition. When the salinity gradually increased to 2.5 %, the highest NO2--N production rate (NiPR) and S0 production rate (S0PR) of DSSADN were 0.54 kg/(m3·d) and 1.1 kg/(m3·d) respectively. NiPR and S0PR gradually decreased as the salinity increased to more than 3 %. However, salinity had a relatively low impact on nitrite accumulation efficiency and S0 accumulation efficiency, which were 80 % and 81.5 %, respectively, when the salinity reached 5 %. Salinity has a great influence on the structure and abundance of microbial communities in the system.

EfGD: the Erianthus fulvus genome database.

Erianthus fulvus (TaxID: 154759) is a valuable germplasm resource in sugarcane breeding and research and has excellent agronomic traits, such as drought resistance, cold resistance, barren tolerance and high brix. With a stable chromosome number (2n = 20) and a small genome (0.9 Gb), it is an ideal candidate for research on sugarcane. Next-generation sequencing technology has enabled a growing number of studies to focus on genomics. Due to the large amount of omics data available, a centralized platform is necessary for ensuring the consistency, independence and maintainability of these large-scale datasets through storage, analysis and integration. Here, we present a comprehensive database for the E. fulvus genome, EfGD. By using the new high-quality reference genome and its annotations, the EfGD provides the largest whole-genome sequencing reference dataset for E. fulvus, which archives 27 165 protein-coding genes and 55 564 488 SNPs from 202 newly resequenced genomes. Furthermore, we created a user-friendly graphical interface for visualizing genomic diversity, population structure and evolution and provided other tools on an open platform. Database URL: https://efgenome.ynau.edu.cn.

Preparation of doxorubicin-loaded porous iron Oxide@ polydopamine nanocomposites for MR imaging and synergistic photothermal-chemotherapy of cancer.

Recently, the development of biosafe nanocomposites with integrated diagnosis and therapeutic modality is received great attention in anti-cancer drug delivery. In this sturdy, we developed a multifunctional PION@PDA-PEG nanocomposite that combines the functions of magnetic resonance (MR) imaging, photothermal therapy (PTT) and chemotherapy into one single nanoprobe. The spherical and uniform-sized porous iron oxide nanoparticles (PION) were synthesized via a simple solvothermal method. Subsequently, a near-infrared light (NIR) sensitive polydopamine (PDA) shell was directly coated on the surface of PIONs to form monodisperse and biosafe core-shell nanocomposites, Thereafter, the surface of nanocomposites was further modified with polyethylene glycol (PEG) to prolong their blood circulation lifetime. The prepared PION@PDA-PEG showed excellent biocompatibility and promising MR imaging contrast agent capability. Furthermore, the porous structure of PION and the abundant functional groups of PDA shell permitted the remarkable drug loading capacity of more than 24.1 wt%. In addition, the synergistic photothermal- chemotherapy exhibited obvious enhanced anti-tumor effect in in-vitro cell experiment. These results suggest that the developed PION@PDA-PEG nanocomposite can be utilized as an efficient drug nanocarrier for biomedical applications including MR imaging and photothermal-chemotherapy.

A new method for in-situ treatment of waste gas scrubbing liquid containing both NH3 and H2S based on sulfur autotrophic denitrification and partial nitrification-Anammox coupling system.

In this study, an integrated device with scrubbing and biochemical treatment functions was used, and partial nitrification (PN)-Anammox and sulfur autotrophic denitrification (SADN) processes were coupled in a biochemical treatment pond to explore the feasibility of in-situ autotrophic removal of NH3 and H2S. The results showed that the removal efficiency of NH3 and H2S in waste gas are 95% and 87.5% respectively. The scrubbing liquid was efficiently treated in the biochemical treatment pond. Nitrogenous compounds weren't accumulated in liquid and converted to N2 by SADN and PN-Anammox coupling system. S2- was mainly used by SADN process to reduce NO3-. The scrubbing liquid processed by the biochemical treatment pond was refluxed to the scrubber to achieve continuous absorption of NH3 and H2S. Microbial community and functional microbial analysis showed that the PN-Anammox and SADN processes were the main processes to achieve the conversion of pollutants in the scrubbing liquid.

Voltage-Polarity Dependent Programming Behaviors of Amorphous In-Ga-Zn-O Thin-Film Transistor Memory with an Atomic-Layer-Deposited ZnO Charge Trapping Layer.

Amorphous In-Ga-Zn-O (a-IGZO) thin-film transistor (TFT) memories are attracting many interests for future system-on-panel applications; however, they usually exhibit a poor erasing efficiency. In this article, we investigate voltage-polarity-dependent programming behaviors of an a-IGZO TFT memory with an atomic-layer-deposited ZnO charge trapping layer (CTL). The pristine devices demonstrate electrically programmable characteristics not only under positive gate biases but also under negative gate biases. In particular, the latter can generate a much higher programming efficiency than the former. Upon applying a gate bias pulse of +13 V/1 µs, the device shows a threshold voltage shift (ΔVth) of 2 V; and the ΔVth is as large as -6.5 V for a gate bias pulse of -13 V/1 µs. In the case of 12 V/1 ms programming (P) and -12 V/10 µs erasing (E), a memory window as large as 7.2 V can be achieved at 103 of P/E cycles. By comparing the ZnO CTLs annealed in O2 or N2 with the as-deposited one, it is concluded that the oxygen vacancy (VO)-related defects dominate the bipolar programming characteristics of the TFT memory devices. For programming at positive gate voltage, electrons are injected from the IGZO channel into the ZnO layer and preferentially trapped at deep levels of singly ionized oxygen vacancy (VO +) and doubly ionized oxygen vacancy (VO 2+). Regarding programming at negative gate voltage, electrons are de-trapped easily from neutral oxygen vacancies because of shallow donors and tunnel back to the channel. This thus leads to highly efficient erasing by the formation of additional ionized oxygen vacancies with positive charges.

Automatic Classification of Label-Free Cells from Small Cell Lung Cancer and Poorly Differentiated Lung Adenocarcinoma with 2D Light Scattering Static Cytometry and Machine Learning.

Small cell lung cancer (SCLC) needs to be classified from poorly differentiated lung adenocarcinoma (PDLAC) for appropriate treatment of lung cancer patients. Currently, the classification is achieved by experienced clinicians, radiologists and pathologists based on subjective and qualitative analysis of imaging, cytological and immunohistochemical (IHC) features. Label-free classification of lung cancer cell lines is developed here by using two-dimensional (2D) light scattering static cytometric technique. Measurements of scattered light at forward scattering (FSC) and side scattering (SSC) by using conventional cytometry show that SCLC cells are overlapped with PDLAC cells. However, our 2D light scattering static cytometer reveals remarkable differences between the 2D light scattering patterns of SCLC cell lines (H209 and H69) and PDLAC cell line (SK-LU-1). By adopting support vector machine (SVM) classifier with leave-one-out cross-validation (LOO-CV), SCLC and PDLAC cells are automatically classified with an accuracy of 99.87%. Our label-free 2D light scattering static cytometer may serve as a new, accurate, and easy-to-use method for the automatic classification of SCLC and PDLAC cells. © 2018 International Society for Advancement of Cytometry.

Differentiation of normal and leukemic cells by 2D light scattering label-free static cytometry.

Two-dimensional (2D) light scattering patterns of single microspheres, normal granulocytes and leukemic cells are obtained by label-free static cytometry. Statistical results of experimental 2D light scattering patterns obtained from standard microspheres with a mean diameter of 4.19 µm agree well with theoretical simulations. High accuracy rates (greater than 92%) for label-free differentiation of normal granulocytes and leukemic cells, both the acute and chronic leukemic cells, are achieved by analyzing the 2D light scattering patterns. Our label-free static cytometry is promising for leukemia screening in clinics.

2D light scattering static cytometry for label-free single cell analysis with submicron resolution.

Conventional optical cytometric techniques usually measure fluorescence or scattering signals at fixed angles from flowing cells in a liquid stream. Here we develop a novel cytometer that employs a scanning optical fiber to illuminate single static cells on a glass slide, which requires neither microfluidic fabrication nor flow control. This static cytometric technique measures two dimensional (2D) light scattering patterns via a small numerical aperture (0.25) microscope objective for label-free single cell analysis. Good agreement is obtained between the yeast cell experimental and Mie theory simulated patterns. It is demonstrated that the static cytometer with a microscope objective of a low resolution around 1.30 µm has the potential to perform high resolution analysis on yeast cells with distributed sizes. The capability of the static cytometer for size determination with submicron resolution is validated via measurements on standard microspheres with mean diameters of 3.87 and 4.19 µm. Our 2D light scattering static cytometric technique may provide an easy-to-use, label-free, and flow-free method for single cell diagnostics.