Thermogenic adipose tissue, both beige and brown, experiences whitening as animals are exposed to warmth and age, but the potential mechanisms are not fully understood. In this study, we employed single-nucleus RNA-seq to construct a cell atlas during whitening progression and identified the characteristics of thermogenic adipocytes. Our histological studies and bulk transcriptome gene expression analysis confirmed that both perirenal and omental adipose tissues (pAT and oAT) exhibited progressive whitening in goats. Compared to the classic brown adipocytes in mice, goat thermogenic adipocytes were more closely related in gene expression patterns to human beige adipocytes, which was also confirmed by adipocyte type- and lineage-specific marker expression analysis. Furthermore, trajectory analysis revealed beige- and white-like adipocytes deriving from a common origin, coexisting and undergoing the transdifferentiation. In addition, differences in gene expression profiles and cell communication patterns (e.g., FGF and CALCR signaling) between oAT and pAT suggested a lower thermogenic capacity of oAT than that of pAT. We constructed a cell atlas of goat pAT and oAT and descripted the characteristics of thermogenic adipocytes during whitening progression. Altogether, our results make a significant contribution to the molecular and cellular mechanisms behind the whitening of thermogenic adipocytes, and providing new insights into obesity prevention in humans and cold adaptation in animals.
Heterodera avenae and H. filipjevi are major parasites of wheat, reducing production worldwide. Both are sedentary endoparasitic nematodes, and their development and parasitism depend strongly on nutrients obtained from hosts. Secreted fatty acid- and retinol-binding (FAR) proteins are nematode-specific lipid carrier proteins used for nutrient acquisition as well as suppression of plant defenses. In this study, we obtained three novel FAR genes Ha-far-1 (KU877266), Ha-far-2 (KU877267), Hf-far-1 (KU877268). Ha-far-1 and Ha-far-2 were cloned from H. avenae, encoding proteins of 191 and 280 amino acids with molecular masses about 17 and 30 kDa, respectively and sequence identity of 28%. Protein Blast in NCBI revealed that Ha-FAR-1 sequence is 78% similar to the Gp-FAR-1 protein from Globodera pallida, while Ha-FAR-2 is 30% similar to Rs-FAR-1 from Radopholus similis. Only one FAR protein Hf-FAR-1was identified in H. filipjevi; it had 96% sequence identity to Ha-FAR-1. The three proteins are alpha-helix-rich and contain the conserved domain of Gp-FAR-1, but Ha-FAR-2 had a remarkable peptide at the C-terminus which was random-coil-rich. Both Ha-FAR-1 and Hf-FAR-1 had casein kinase II phosphorylation sites, while Ha-FAR-2 had predicted N-glycosylation sites. Phylogenetic analysis showed that the three proteins clustered together, though Ha-FAR-1 and Hf-FAR-1 adjoined each other in a plant-parasitic nematode branch, but Ha-FAR-2 was distinct from the other proteins in the group. Fluorescence-based ligand binding analysis showed the three FAR proteins bound to a fluorescent fatty acid derivative and retinol and with dissociation constants similar to FARs from other species, though Ha-FAR-2 binding ability was weaker than that of the two others. In situ hybridization detected mRNAs of Ha-far-1 and Ha-far-2 in the hypodermis. The qRT-PCR results showed that the Ha-far-1and Ha-far-2 were expressed in all developmental stages; Ha-far-1 expressed 70 times more than Ha-far-2 in all stages. The highest expression level of Ha-far-1 was observed in fourth-stage juvenile (J4), whereas the highest expression level of Ha-far-2 occurred in second-stage juvenile (J2). In conclusion, we have identified two novel far genes from H. avenae and one from H. filipjevi and have provided further indication that nematode far genes are present in a variety of nematode species, where the FAR proteins share similar basic structure, expression pattern and biochemical activities.
The proliferation and differentiation of myoblasts are considered the key biological processes in muscle development and muscle-related diseases, in which the miRNAs involved remain incompletely understood. Previous research reported that miR-424(322)-5p is highly expressed in mouse skeletal muscle. Therefore, C2C12 cells are used as a model to clarify the effect of miR-424(322)-5p on the proliferation and differentiation of myoblasts. The data show that miR-424(322)-5p exhibits a decreasing trend upon myogenic differentiation. Overexpression of miR-424(322)-5p inhibits the proliferation of myoblasts, manifested by downregulation of proliferation marker genes ( CCNB1, CCND2, and CDK4), decreased percentage of EdU + cells, and reduced cell viability. In contrast, these phenotypes are promoted in myoblasts treated with an inhibitor of miR-424(322)-5p. Interestingly, its gain of function inhibits the expression of myogenic regulators, including MyoD, MyoG, MyHC, and Myf5. Additionally, immunofluorescence staining of MyHC and MyoD shows that overexpression of miR-424(322)-5p reduces the number of myotubes and decreases the myotube fusion index. Consistently, inhibition of its function mediated by an inhibitor promotes the expressions of myogenic markers and myotube fusion. Mechanistically, gene prediction and dual-luciferase reporter experiments confirm that enhancer of zeste homolog 1 ( Ezh1) is one of the targets of miR-424(322)-5p. Furthermore, knockdown of Ezh1 inhibits the proliferation and differentiation of myoblasts. Compared with NC and inhibitor treatment, inhibitor+si- EZH1 treatment rescues the phenotypes of proliferation and differentiation mediated by the miR-424(322)-5p inhibitor. Taken together, these data indicate that miR-424(322)-5p targets Ezh1 to negatively regulate the proliferation and differentiation of myoblasts.
The increasing prevalence of antibiotic resistance has become a global health crisis. For the purpose of safety regulation, it is of high importance to identify antibiotic resistance genes (ARGs) in bacteria. Although culture-based methods can identify ARGs relatively more accurately, the identifying process is time-consuming and specialized knowledge is required. With the rapid development of whole genome sequencing technology, researchers attempt to identify ARGs by computing sequence similarity from public databases. However, these computational methods might fail to detect ARGs due to the low sequence identity to known ARGs. Moreover, existing methods cannot effectively address the issue of multidrug resistance prediction for ARGs, which is a great challenge to clinical treatments. To address the challenges, we propose an end-to-end multi-label learning framework for predicting ARGs. More specifically, the task of ARGs prediction is modeled as a problem of multi-label learning, and a deep neural network-based end-to-end framework is proposed, in which a specific loss function is introduced to employ the advantage of multi-label learning for ARGs prediction. In addition, a dual-view modeling mechanism is employed to make full use of the semantic associations among two views of ARGs, i.e. sequence-based information and structure-based information. Extensive experiments are conducted on publicly available data, and experimental results demonstrate the effectiveness of the proposed framework on the task of ARGs prediction.
Fusarium oxysporum f. sp. Lycopersici, a necrotrophic pathogen, is a causal agent of tomato wilt disease. Plants have two major sophisticated innate immune systems, Pathogen-Associated Molecular Pattern (PAMP)-triggered immunity (PTI) and Effector-Triggered Immunity (ETI), to perceive and resist pathogen offences (Jones and Dangl, 2006). MicroRNAs (miRNAs) contribute to PTI and ETI by fine-tuning plant hormones and/or silencing the genes involved in pathogen virulence by regulating the expression of target genes, thereby acting as crucial regulators of the plant immune system (Fei et al., 2016). Many plants produce microRNAs belonging to the miRNA482/2118 superfamily. These miRNAs target R-genes of the class NBS-LRR (nucleotide-binding site-leucine rich repeat) through recognizing the P-loop motif in the NBS-LRR mRNA. Our previous studies showed that SlymiR482e-3p, a members of the miR482/2118 superfamily in tomato, negatively regulated the resistance to Fusarium oxysporum f. sp. lycopersici (race 2) (Fol) by targeting several NBS-LRR genes (Ouyang et al., 2014). However, the exact mechanism underlying the basic function of SlymiR482e-3p during the response to Fol attack needs further exploration. In this study, two near-isogenic tomato cultivars, Moneymaker (susceptible, i-2/i-2) and Motelle (resistant, I-2/I-2) to Fol infection, were recruited (Ouyang et al., 2014). To characterize the functions of SlymiR482e-3p in response to tomato wilt disease, we generated a CRISPR/Cas9-related knock-out mutant lacking the SlymiR482e-3p gene in the susceptible cultivar Moneymaker (Deng et al., 2018). Three regenerated plants, termed as SlymiR482e-3p-KO-Line 3, 7 and 11, carried 2-, 9- and 6-nucleatide deletion in front of the mature miRNA region respectively, were identified (Figure 1a). Compared with the control, the expression levels of SlymiR482e-3p was dramatically reduced by more than 90% in individual transgenic plants (Figure 1b). SlymiR482e-3p has been proved as a negative regulator for several targeted NBS-LRR genes, including Soly08g075630 and Soly08g076000 in tomato (Ouyang et al., 2014). As expected, basal expression levels of both Soly08g075630 and Soly08g076000 were increased in all transgenic Moneymaker plants (Figure 1b). Furthermore, no visible difference in major agronomic traits, including leaves, flowers and fruits, were observed in transgenic plants compared with the control (Figure 1c). To further evaluate the function of SlymiR482e-3p in tomato wilt disease susceptibility, we inoculated the SlymiR482e-3p-KO transgenic plants as well as resistant Motelle and susceptible Moneymaker controls with Fol. As gauged, SlymiR482e-3p-KO plants exhibited enhanced resistance to Fol relative to the Moneymaker control while displayed an appearance similar to the treated Motelle plants (Figure 1d). This result further confirms that SlymiR482e-3p functions as a negative regulator of resistance to tomato wilt disease. We utilized the psRNATarget algorithm (Dai et al., 2018) to predict potential targets of SlymiR482e-3p. Intriguingly, Solyc11g010660, a homolog of SGT1 (suppressor of the G2 allele of skp1), was predicted as a target of SlymiR482e-3p and termed as SlSGT1. SGT1 was first reported as a component of the SCF E3 ubiquitin ligase complex in yeast (Kitagawa et al., 1999) and interacted with RAR1 to trigger disease resistance in plants (Azevedo et al., 2002). It has been documented that SGT1 homologs in plants are triggered by various plant defence response pathways, including ethylene-mediated cross-talk between calcium-dependent protein kinases (CDPK) and mitogen-activated protein kinase (MAPK) signalling (Ludwig et al., 2005; Peart et al., 2002). To determine whether SlymiR482e-3p regulate the SlSGT1 expression, we conducted an Agrobacterium-mediated transient co-expression experiment in N. benthamiana, as previously implemented in our laboratory (Ouyang et al., 2014). qRT-PCR data showed that the SlSGT1 transcripts were greatly decreased in the presence of SlymiR482e-3p (Figure 1e). Consistently, GFP fluorescence and Western blot assays using an anti-GFP antibody further demonstrated that SlSGT1 protein levels were significantly down-regulated in the presence of SlymiR482e-3p (Figure 1f). To identify the cleavage site in the SlSGT1 mRNA targeted by SlymiR482e-3p, we performed a 5′-RNA ligase-mediated rapid amplification of cDNA ends (5′ RLM- RACE) analysis. The result showed the cleavage site occurred at the 999th nt of the SlSGT1 mRNA in 13 out of 14 clones (Figure 1g). AdSGT1 transcripts were strong up-regulated by ethephon resulting in enhanced disease resistance in tobacco and peanut (Kumar and Kirti, 2015). In this study, SlSGT1 was dramatically induced during Fol infection in the susceptible cultivar Moneymaker, meanwhile, the basal level of SlSGT1 was elevated in the SlylmiR482e-3p-KO mutant possibly resulting in the resistance to Fol (Figure 1h). Considering all of the above results, we concluded that SlymiR482e-3p regulates SlSGT1 expression by chopping the intact mRNA. To further understand the role of SlymiR482e-3p in mediating resistance to Fol in tomato, we constructed and sequenced six RNA-seq libraries, including Moneymaker treated with water (MM_H2O) or Fol (MM_Fol), as well as SlymiR482e-3p-KO lines 3 and 7 treated with water or Fol (KO-Line3_H2O, KO-Line3_Fol, KO-Line7_H2O, and KO-Line7_Fol) (The raw sequence data are available in the Genome Sequence Archive in BIG Data Centre, under accession numbers CRA002427). Intriguingly, we determined that genes in several phytohormone signalling pathways, particularly the ethylene (ET) signal transduction pathway, may participate in the response to Fol infection in tomato. To evaluate further a possible role for SlymiR482e-3p in regulating ethylene signalling, we monitored expression of key genes in the pathway in tomato plants after inoculation with Fol spores or water over a 24 h period. The basal expression levels (water control) of SlERF1, SlERF3, SlERF4, SlERF5, SlERF9, and SlERF11 were depressed in all SlymiR482e-3p-KO plants relative to Moneymaker. However, all these genes except SlERF3 were induced after Fol infection in both Moneymaker and SlymiR482e-3p-KO plants (Figure 1i). These results prompted us to speculate that the ethylene signal transduction pathway might be important during the response to Fol infection. We next asked whether application of a precursor of ET biosynthesis, 1-Aminocyclopropane-1-carboxylic acid (ACC), would exacerbate wilt disease symptoms. For these experiments, WT and transgenic plants were treated with Fol followed by spraying 100 μm ACC (optimal concentration was determined through our preliminary experiments). After ACC treatment, all tomato plants displayed aggravated wilt disease symptoms and faster disease progression compared to treatment with Fol alone (Figure 1j). Particularly, ACC overrode the resistance to Fol infection in Motelle against Fol (Figure 1j). In summary, we present evidence that supports a key role of SlylmiR482e-3p-mediated ethylene signalling in promoting resistance to a fungal necrotroph Fol. We propose that during fungal pathogen Fol invasion, endogenous SlylmiR482e-3p promotes SlSGT1 accumulation, thereby triggering CDPK-depending PCD in tomato. Consequently, SlERFs, components of the ethylene signalling pathway are regulated to enhance resistance to tomato wilt disease (Figure 1k). Our research provides a basis to elucidate the complex SlylmiR482e-3p-mediated resistance to Fol in tomato, which will be beneficial for the design of strategies to improve tomato wilt disease resistance. We thank for gracious given of tomato cultivars by Dr. Isgouhi Kaloshian from University of California, Riverside. This work was supported by grant from the National Natural Science Foundation of China (31972351). The authors declare no conflict of interest. SQO designed the experiments. SQO contributed to data analysis and interpretation and wrote the paper. KAB contributed to design this project and revised this manuscript. YG and SJL performed the experiments in cooperation with SWZ, TF, ZYZ, SJL and HYM. All authors read and approved the final manuscript.
In the process of building Theories and Policies on Nationalities into an excellent course at Guangxi University of Nationalities,we made great efforts to train a teaching body with high academic competence,compile an excellent textbook at a high level,reform teaching methods,and improve interactions between teaching and scientific research.By doing so,we built the course into an excellent one of the university with distinctive characteristics of being new,flexible and practical.
The crisis of antibiotic resistance has become a significant global threat to human health. Understanding properties of antibiotic resistance genes (ARGs) is the first step to mitigate this issue. Although many methods have been proposed for predicting properties of ARGs, most of these methods focus only on predicting antibiotic classes, while ignoring other properties of ARGs, such as resistance mechanisms and transferability. However, acquiring all of these properties of ARGs can help researchers gain a more comprehensive understanding of the essence of antibiotic resistance, which will facilitate the development of antibiotics. In this paper, the task of predicting properties of ARGs is modeled as a multi-task learning problem, and an effective subtask-aware representation learning-based framework is proposed accordingly. More specifically, property-specific expert networks and shared expert networks are utilized respectively to learn subtask-specific features for each subtask and shared features among different subtasks. In addition, a gating-controlled mechanism is employed to dynamically allocate weights to subtask-specific semantics and shared semantics obtained respectively from property-specific expert networks and shared expert networks, thus adjusting distinctive contributions of subtask-specific features and shared features to achieve optimal performance for each subtask simultaneously. Extensive experiments are conducted on publicly available data, and experimental results demonstrate the effectiveness of the proposed framework on the task of ARGs properties prediction.
There are some questions in the course name, teaching contents, textbook construction and teachers' quality in teaching current “National Theories and National Policy”. In the context of educational reform, the Central Committee of the CPC and some units concerned should establish the position of the course firmly, revise the teaching program and textbooks, compile the teaching references, hold regular meetings to exchange teaching experiences, make plans for training, strengthen the ties between national units and teaching-research units. In this way, we can improve our teaching greatly.
Apocynum venetum L. belongs to the Apocynaceae family and is a plant that is highly resistant to stress. It is important in the fields of ecology, feeding, industry and medicine. The molecular mechanism underlying salt tolerance has not been elucidated. In this study, RNA-seq based transcriptome sequencing of A . venetum leaves after 0, 2, 6, 12, 24 and 48 h of treatment with 300 mM NaCl was performed. We conducted a comprehensive analysis of the transcriptome expression profiles of A . venetum under salt stress using the WGCNA method and identified red, black, and brown as the core modules regulating the salt tolerance of A . venetum . A co-expression regulatory network was constructed to identify the core genes in the module according to the correlations between genes. The genes TRINITY_DN102_c0_g1 (serine carboxypeptidase), TRINITY_DN3073_c0_g1 (SOS signaling pathway) and TRINITY_DN6732_c0_g1 (heat shock transcription factor) in the red module were determined to be the core genes. Two core genes in the black module, TRINITY_DN9926_c0_g1 and TRINITY_DN7962_c0_g1, are pioneer candidate salt tolerance-associated genes in A . venetum . The genes in the brown module were mainly enriched in two pathways, namely photosynthesis and osmotic balance. Among them, the TRINITY_DN6321_c0_g2 and TRINITY_DN244_c0_g1 genes encode aquaporin, which is helpful for maintaining the cell water balance and plays a protective role in defending A . venetum under abiotic stress. Our findings contribute to the identification of core genes involved in the response of A . venetum to salt stress.
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