Elucidating the role of highly homologous \u3ci\u3eNicotiana benthamiana\u3c/i\u3e ubiquitin E2 gene family members in plant immunity through an improved virus‑induced gene silencing approach

Background: Virus-induced gene silencing (VIGS) has been used in many plant species as an attractive post transcriptional gene silencing (PTGS) method for studying gene function either individually or at large-scale in a high-throughput manner. However, the specificity and efficiency for knocking down members of a highly homologous gene family have remained to date a significant challenge in VIGS due to silencing of off-targets. Results: Here we present an improved method for the selection and evaluation of gene fragments used for VIGS to specifically and efficiently knock down members of a highly homologous gene family. Using this method, we knocked down twelve and four members, respectively of group III of the gene family encoding ubiquitin-conjugating enzymes (E2) in Nicotiana benthamiana. Assays using these VIGS-treated plants revealed that the group III E2s are essential for plant development, plant immunity-associated reactive oxygen species (ROS) production, expression of the gene NbRbohB that is required for ROS production, and suppression of immunity-associated programmed cell death (PCD) by AvrPtoB, an effector protein of the bacterial pathogen Pseudomons syringae. Moreover, functional redundancy for plant development and ROS production was found to exist among members of group III E2s. Conclusions: We have found that employment of a gene fragment as short as approximately 70 base pairs (bp) that contains at least three mismatched nucleotides to other genes within any 21-bp sequences prevents silencing of off-target(s) in VIGS. This improved approach in the selection and evaluation of gene fragments allows for specific and efficient knocking down of highly homologous members of a gene family. Using this approach, we implicated N. benthamiana group III E2s in plant development, immunity-associated ROS production, and suppression of multiple immunity-associated PCD by AvrPtoB. We also unraveled functional redundancy among group III members in their requirement for plant development and plant immunity-associated ROS production

Novel fungal consortium pretreatment of waste oat straw to enhance economic and efficient biohydrogen production

Bio-pretreatment using a fungal consortium to enhance the efficiency of lignocellulosic biohydrogen production was explored. A fungal consortium comprised of T. viride and P. chrysosporium as microbial inoculum was compared with untreated and single-species-inoculated samples. Fungal bio-pretreatment was carried out at atmospheric conditions with limited external energy input. The effectiveness of the pretreatment is evaluated according to its lignin removal and digestibility. Enhancement of biohydrogen production is observed through scanning electron microscopy (SEM) analysis. Fungal consortium pretreatment effectively degraded oat straw lignin (by >47% in 7 days) leading to decomposition of cell-wall structure as revealed in SEM images, increasing biohydrogen yield. The hydrogen produced from the fungal consortium pretreated straw increased by 165% 6 days later, and was more than produced from either a single fungi species of T. viride or P. chrysosponium pretreated straw (94% and 106%, respectively). No inhibitory effect on hydrogen production was observed

Conventional and unconventional ubiquitination in plant immunity

Ubiquitination is one of the most abundant types of protein post-translational modification (PTM) in plant cells. The importance of ubiquitination in the regulation of many aspects of plant immunity has been increasingly appreciated in recent years. Most of the studies linking ubiquitination to the plant immune system, however, have been focused on the E3 ubiquitin ligases and the conventional ubiquitination that leads to the degradation of the substrate proteins by the 26S proteasome. By contrast, our knowledge about the role of unconventional ubiquitination that often serves as non-degradative, regulatory signal remains a sig- nificant gap. We discuss, in this review, the recent advances in our understanding of ubiquitination in the modulation of plant immunity, with a particular focus on the E3 ubiquitin ligases. We approach the topic from a perspective of two broadly defined types of ubiquitination in an attempt to highlight the importance, yet current scarcity, in our knowledge about the regulation of plant immunity by unconventional ubiquitination

The Tomato U-Box Type E3 Ligase PUB13 Acts With Group III Ubiquitin E2 Enzymes to Modulate FLS2-Mediated Immune Signaling

In Arabidopsis and rice, the ubiquitin ligase PUB13-mediated protein degradation plays a significant role in plant pattern-triggered immunity (PTI) and flowering time control. The Arabidopsis PUB13 has been shown to attenuate the pattern recognition receptor FLS2-mediated immune signaling by ubiquitinating FLS2 and consequently promoting its degradation by the 26S proteasome. Nevertheless, the cognate ubiquitin-conjugating enzymes (E2) with which PUB13 acts to modulate FLS2-mediated PTI are unknown. To address this question, we investigate here the tomato (Solanum lycopersicum) homolog of PUB13, SlPUB13 by utilizing the recently characterized complete set of tomato E2s. Of the 13 groups of tomato E2s, only members in group III are found to interact and act with SlPUB13. Knocking-down of the group III E2 genes enhances callose deposition and induction of the RbohB gene in the immunity-associated, early oxidative burst after flg22 treatment. The group III E2s are also found to work with SlPUB13 to ubiquitinate FLS2 in vitro and are required for PUB13-mediated degradation of FLS2 in vivo upon flg22 treatment, suggesting an essential role for group III E2s in the modulation of FLS2- mediated immune signaling by PUB13. Additionally, another immunity-associated E3, NtCMPG1 is shown to also work specifically with members of group III E2 in the in vitro ubiquitination assay, which implies the group III E2 enzymes may cooperate with many E3 ligases to regulate different aspects of PTI. Taken together, these data corroborate the notion that group III E2 enzymes play an important role in PTI and build a foundation for further functional and mechanistic characterization of tomato PUB13

Enhanced biohydrogen production from oat straw co-digested with cow dung / sewage sludge by combined aerobic digestion and anaerobic fermentation

Hydrogen was produced from oat straw by combined aerobic and anaerobic fermentation with fungi and cow dung. With aerobic pre-digestion, the maximum hydrogen production rate reached 133 ml/g volatile suspended solids per hour. The maximum hydrogen yield was 71.5 ml/g straw in 6 days by biological process. The lignocellulosic conversion of oak-straw waste was 39%, with the complex component converting 68% of the hemi-cellulose and 61% of the cellulose, but only 34% of lignin conversion. Aerobic pre-digestion by Trichoderma viride and Saccharomyces cerevisiae was significantly effective for lignin degradation. Combining aerobic and anaerobic fermentation is a promising low-cost efficient and environmentally friendly method, compared with hydrogen fermentation, not only for hydrogen production, but also for converting straw biomass

Combining hydrogen peroxide addition with sunlight regulation to control algal blooms

The concentration, light conditions during treatment, and the number of hydrogen peroxide (H2O2) additions as well as the H2O2 treatment combined with subsequent shading to control algal blooms were studied in the field (Lake Dianchi, China). The cyanobacterial stress and injury due to H2O2 were dose dependent, and the control effectiveness and degradation of H2O2 were better and faster under full light than under shading. However, H2O2 was only able to control a bloom for a short time, so it may have promoted the recovery of algae and allowed the biomass to rebound due to the growth of eukaryotic algae. A second addition of H2O2 at the same dose had no obvious effect on algal control in the short term, suggesting that a higher concentration or a delayed addition should be considered, but these alternative strategies are not recommended so that the integrity of the aquatic ecosystem is maintained and algal growth is not promoted. Moreover, shading (85%) after H2O2 addition significantly reduced the algal biomass during the enclosure test, no restoration was observed for nearly a month, and the proportion of eukaryotic algae declined. It can be inferred that algal blooms can be controlled by applying a high degree of shading after treatment with H2O2.</p

Application of Bayesian network including Microcystis morphospecies for microcystin risk assessment in three cyanobacterial bloom-plagued lakes, China

Microcystis spp., which occur as colonies of different sizes under natural conditions, have expanded in temperate and tropical freshwater ecosystems and caused seriously environmental and ecological problems. In the current study, a Bayesian network (BN) framework was developed to access the probability of microcystins (MCs) risk in large shallow eutrophic lakes in China, namely, Taihu Lake, Chaohu Lake, and Dianchi Lake. By means of a knowledge-supported way, physicochemical factors, Microcystis morphospecies, and MCs were integrated into different network structures. The sensitive analysis illustrated that Microcystis aeruginosa biomass was overall the best predictor of MCs risk, and its high biomass relied on the combined condition that water temperature exceeded 24 °C and total phosphorus was above 0.2 mg/L. Simulated scenarios suggested that the probability of hazardous MCs (≥1.0 μg/L) was higher under interactive effect of temperature increase and nutrients (nitrogen and phosphorus) imbalance than that of warming alone. Likewise, data-driven model development using a naïve Bayes classifier and equal frequency discretization resulted in a substantial technical performance (CCI = 0.83, K = 0.60), but the performance significantly decreased when model excluded species-specific biomasses from input variables (CCI = 0.76, K = 0.40). The BN framework provided a useful screening tool to evaluate cyanotoxin in three studied lakes in China, and it can also be used in other lakes suffering from cyanobacterial blooms dominated by Microcystis

SpeechUT: Bridging Speech and Text with Hidden-Unit for Encoder-Decoder Based Speech-Text Pre-training

The rapid development of single-modal pre-training has prompted researchers to pay more attention to cross-modal pre-training methods. In this paper, we propose a unified-modal speech-unit-text pre-training model, SpeechUT, to connect the representations of a speech encoder and a text decoder with a shared unit encoder. Leveraging hidden-unit as an interface to align speech and text, we can decompose the speech-to-text model into a speech-to-unit model and a unit-to-text model, which can be jointly pre-trained with unpaired speech and text data respectively. Our proposed SpeechUT is fine-tuned and evaluated on automatic speech recognition (ASR) and speech translation (ST) tasks. Experimental results show that SpeechUT gets substantial improvements over strong baselines, and achieves state-of-the-art performance on both the LibriSpeech ASR and MuST-C ST tasks. To better understand the proposed SpeechUT, detailed analyses are conducted. The code and pre-trained models are available at https://aka.ms/SpeechUT.Comment: 14 pages, accepted by EMNLP 202

Three-dimensional echo-shifted EPI with simultaneous blip-up and blip-down acquisitions for correcting geometric distortion

Purpose: Echo-planar imaging (EPI) with blip-up/down acquisition (BUDA) can provide high-quality images with minimal distortions by using two readout trains with opposing phase-encoding gradients. Because of the need for two separate acquisitions, BUDA doubles the scan time and degrades the temporal resolution when compared to single-shot EPI, presenting a major challenge for many applications, particularly functional MRI (fMRI). This study aims at overcoming this challenge by developing an echo-shifted EPI BUDA (esEPI-BUDA) technique to acquire both blip-up and blip-down datasets in a single shot. Methods: A three-dimensional (3D) esEPI-BUDA pulse sequence was designed by using an echo-shifting strategy to produce two EPI readout trains. These readout trains produced a pair of k-space datasets whose k-space trajectories were interleaved with opposite phase-encoding gradient directions. The two k-space datasets were separately reconstructed using a 3D SENSE algorithm, from which time-resolved B0-field maps were derived using TOPUP in FSL and then input into a forward model of joint parallel imaging reconstruction to correct for geometric distortion. In addition, Hankel structured low-rank constraint was incorporated into the reconstruction framework to improve image quality by mitigating the phase errors between the two interleaved k-space datasets. Results: The 3D esEPI-BUDA technique was demonstrated in a phantom and an fMRI study on healthy human subjects. Geometric distortions were effectively corrected in both phantom and human brain images. In the fMRI study, the visual activation volumes and their BOLD responses were comparable to those from conventional 3D echo-planar images. Conclusion: The improved imaging efficiency and dynamic distortion correction capability afforded by 3D esEPI-BUDA are expected to benefit many EPI applications.Comment: 8 figures, peer-reviewed journal pape