Transcriptome analysis of stem development in the tumourous stem mustard Brassica juncea var. tumida Tsen et Lee by RNA sequencing

<p>Abstract</p> <p>Background</p> <p>Tumourous stem mustard (<it>Brassica juncea </it>var. <it>tumida </it>Tsen et Lee) is an economically and nutritionally important vegetable crop of the <it>Cruciferae </it>family that also provides the raw material for <it>Fuling </it>mustard. The genetics breeding, physiology, biochemistry and classification of mustards have been extensively studied, but little information is available on tumourous stem mustard at the molecular level. To gain greater insight into the molecular mechanisms underlying stem swelling in this vegetable and to provide additional information for molecular research and breeding, we sequenced the transcriptome of tumourous stem mustard at various stem developmental stages and compared it with that of a mutant variety lacking swollen stems.</p> <p>Results</p> <p>Using Illumina short-read technology with a tag-based digital gene expression (DGE) system, we performed <it>de novo </it>transcriptome assembly and gene expression analysis. In our analysis, we assembled genetic information for tumourous stem mustard at various stem developmental stages. In addition, we constructed five DGE libraries, which covered the strains <it>Yong'an </it>and <it>Dayejie </it>at various development stages. Illumina sequencing identified 146,265 unigenes, including 11,245 clusters and 135,020 singletons. The unigenes were subjected to a BLAST search and annotated using the GO and KO databases. We also compared the gene expression profiles of three swollen stem samples with those of two non-swollen stem samples. A total of 1,042 genes with significantly different expression levels occurring simultaneously in the six comparison groups were screened out. Finally, the altered expression levels of a number of randomly selected genes were confirmed by quantitative real-time PCR.</p> <p>Conclusions</p> <p>Our data provide comprehensive gene expression information at the transcriptional level and the first insight into the understanding of the molecular mechanisms and regulatory pathways of stem swelling and development in this plant, and will help define new mechanisms of stem development in non-model plant organisms.</p

Modeling Cadmium Contents in a Soil&ndash;Rice System and Identifying Potential Controls

Cadmium (Cd) pollution in a soil&ndash;rice system is closely related to widely concerning issues, such as food security and health risk due to exposure to heavy metals. Therefore, modeling the Cd content in a soil&ndash;rice system and identifying related controls could provide critical information for ensuring food security and reducing related health risks. To archive this goal, in this study, we collected 217 pairs of soil&ndash;rice samples from three subareas in Zhejiang Province in the Yangtze River Delta of China. All soil&ndash;rice samples were air-dried and conducted for chemical analysis. The Pearson&rsquo;s correlation coefficient, ANOVA, co-occurrence network, multiple regression model, and nonlinear principal component analysis were then used to predict the Cd content in rice and identify potential controls for the accumulation of Cd in rice. Our results indicate that although the mean total concentration of Cd in soil samples was higher than that of the background value in Zhejiang Province, the mean concentration of Cd in rice was higher than that of the national regulation value. Furthermore, a significant difference was detected for Cd content in rice planted in different soil groups derived from different parental materials. In addition, soil organic matter and total Cd in the soil are essential factors for predicting Cd concentrations in rice. Additionally, specific dominant factors resulting in Cd accumulation in rice planted at different subareas were identified via nonlinear principal component analysis. Our study provides new insights and essential implications for policymakers to formulate specific prevention and control strategies for Cd pollution and related health risks

The power of humorous audio: exploring emotion regulation in traffic congestion through EEG-based study

Abstract Traffic congestion can lead to negative driving emotions, significantly increasing the likelihood of traffic accidents. Reducing negative driving emotions as a means to mitigate speeding, reckless overtaking, and aggressive driving behaviors is a viable approach. Among the potential methods, affective speech has been considered one of the most promising. However, research on humor-based affective speech interventions in the context of driving negative emotions is scarce, and the utilization of electroencephalogram (EEG) signals for emotion detection in humorous audio studies remains largely unexplored. Therefore, our study first designed a highly realistic experiment scenario to induce negative emotions experienced by drivers in congested traffic conditions. Subsequently, we collected drivers’ EEG signals and subjective questionnaire ratings during the driving process. By employing one-way analysis of variance (ANOVA) and t tests, we analyzed the data to validate the success of our experiment in inducing negative emotions in drivers during congested road conditions and to assess the effectiveness of humorous audio in regulating drivers’ negative emotions. The results indicated that humorous audio effectively alleviated drivers’ negative emotions in congested road conditions, with a 145.84% increase in arousal and a 93.55% increase in valence ratings compared to control conditions. However, it should be noted that humorous audio only restored drivers’ emotions to the level experienced during normal driving. Our findings offer novel insights into regulating drivers’ negative emotions during congested road conditions

San-Huang-Xie-Xin-Tang constituents exert drug-drug interaction of mutual reinforcement at both pharmacodynamics and pharmacokinetic level: a review

Abstract Inflammatory disorders underlie varieties of human diseases. San-huang-xie-xin-tang (SHXXT), composed with Rhizoma Rhei (Rheum palmatum L.), Rhizoma Coptidis (Coptis chinensis Franch), and Radix Scutellaria (Scutellaria baicalensis Georgi), is a famous formula which has been widely used in the fight against inflammatory abnormalities. Mutual reinforcement is one of the basic theories of traditional Chinese medicine. Here this article reviewed and analyzed the recent research on (1) How the main constituents of SHXXT impact on inflammation-associated signaling pathway molecules. (2) The interaction between the main constituents and efflux pumps or intestinal transporters. The goal of this work was to,(1) Provide evidence to support the theory of mutual reinforcement. (2) Clarify the key targets of SHXXT and suggest which targets need further investigation.(3) Give advice for the clinical use of SHXXT to elevated the absorption of main constituents and eventually promote oral bioavailability. We search literatures in scientific databases with key words of ‘each main SHXXT constituent’, in combination with ‘each main inflammatory pathway target molecule’ or each main intestinal transporter, respectively. We report the effect of five main constituents on target molecules which lies in three main inflammatory signaling pathways, we as well investigate the interaction between constituents and intestinal transporter.We conclude,(1)The synergistic effect of constituents at both levels confirm the mutual reinforcement theory of TCM as it is proven in this work. (2) The effect of main constituents on downstream targets in nuclear need more further investigation. (3) Drug elevating the absorption of rhein, berberine and baicalein can be employed to promote oral bioavailability of SHXXT

Engineering a Zirconium MOF through Tandem “Click” Reactions: A General Strategy for Quantitative Loading of Bifunctional Groups on the Pore Surface

Metal–organic frameworks (MOFs) assembled from linkers of identical length but with different functional groups have gained increasing interests recently. However, it is very challenging for precise control of the ratios of different functionalities. Herein, we reported a stable azide- and alkyne-appended Zr-MOF that can undergo quantitative tandem click reactions on the different functional sites, thus providing a unique platform for quantitative loading of bifunctional moieties. As an added advantage, the same MOF product can be obtained via two independent routes. The method is versatile and can tolerate a wide variety of functional groups, and furthermore, a heterogeneous acid–base MOF organocatalyst was synthesized by tandemly introducing both acidic and basic groups onto the predesigned pore surface. The presented strategy provides a general way toward the construction of bifunctional MOFs with a precise control of ratio of different functionalities for desirable applications in future

Identification and characterization of MYH9 locus for high efficient gene knock-in and stable expression in mouse embryonic stem cells

<div><p>Targeted integration of exogenous genes into so-called safe harbors/friend sites, offers the advantages of expressing normal levels of target genes and preventing potentially adverse effects on endogenous genes. However, the ideal genomic loci for this purpose remain limited. Additionally, due to the inherent and unresolved issues with the current genome editing tools, traditional embryonic stem (ES) cell-based targeted transgenesis technology is still preferred in practical applications. Here, we report that a high and repeatable homologous recombination (HR) frequency (>95%) is achieved when an approximate 6kb DNA sequence flanking the MYH9 gene exon 2 site is used to create the homology arms for the knockout/knock-in of diverse nonmuscle myosin II (NM II) isoforms in mouse ES cells. The easily obtained ES clones greatly facilitated the generation of multiple NM II genetic replacement mouse models, as characterized previously. Further investigation demonstrated that though the targeted integration site for exogenous genes is shifted to MYH9 intron 2 (about 500bp downstream exon 2), the high HR efficiency and the endogenous MYH9 gene integrity are not only preserved, but the expected expression of the inserted gene(s) is observed in a pre-designed set of experiments conducted in mouse ES cells. Importantly, we confirmed that the expression and normal function of the endogenous MYH9 gene is not affected by the insertion of the exogenous gene in these cases. Therefore, these findings suggest that like the commonly used ROSA26 site, the MYH9 gene locus may be considered a new safe harbor for high-efficiency targeted transgenesis and for biomedical applications.</p></div