Degenerate lower dimensional tori in reversible systems

AbstractIn this paper we prove the persistence of lower dimensional invariant tori with prescribed frequencies and singular normal matrices in reversible systems. The normal variable is two-dimensional and the unperturbed nonlinear terms in the differential equation for this variable have a special structure

Cell identity specification in plants: lessons from flower development

Multicellular organisms display a fascinating complexity of cellular identities and patterns of diversification. The concept of ‘cell type’ aims to describe and categorize this complexity. In this review, we discuss the traditional concept of cell types and highlight the impact of single-cell technologies and spatial omics on the understanding of cellular differentiation in plants. We summarize and compare position-based and lineage-based mechanisms of cell identity specification using flower development as a model system. More than understanding ontogenetic origins of differentiated cells, an important question in plant science is to understand their position- and developmental stage-specific heterogeneity. Combinatorial action and crosstalk of external and internal signals is the key to cellular heterogeneity, often converging on transcription factors that orchestrate gene expression programs.Peer Reviewe

Cold stress induces rapid gene-specific changes in the levels of H3K4me3 and H3K27me3 in Arabidopsis thaliana

When exposed to low temperatures, plants undergo a drastic reprogramming of their transcriptome in order to adapt to their new environmental conditions, which primes them for potential freezing temperatures. While the involvement of transcription factors in this process, termed cold acclimation, has been deeply investigated, the potential contribution of chromatin regulation remains largely unclear. A large proportion of cold-inducible genes carries the repressive mark histone 3 lysine 27 trimethylation (H3K27me3), which has been hypothesized as maintaining them in a silenced state in the absence of stress, but which would need to be removed or counteracted upon stress perception. However, the fate of H3K27me3 during cold exposure has not been studied genome-wide. In this study, we offer an epigenome profiling of H3K27me3 and its antagonistic active mark H3K4me3 during short-term cold exposure. Both chromatin marks undergo rapid redistribution upon cold exposure, however, the gene sets undergoing H3K4me3 or H3K27me3 differential methylation are distinct, refuting the simplistic idea that gene activation relies on a switch from an H3K27me3 repressed chromatin to an active form enriched in H3K4me3. Coupling the ChIP-seq experiments with transcriptome profiling reveals that differential histone methylation only weakly correlates with changes in expression. Interestingly, only a subset of cold-regulated genes lose H3K27me3 during their induction, indicating that H3K27me3 is not an obstacle to transcriptional activation. In the H3K27me3 methyltransferase curly leaf (clf) mutant, many cold regulated genes display reduced H3K27me3 levels but their transcriptional activity is not altered prior or during a cold exposure, suggesting that H3K27me3 may serve a more intricate role in the cold response than simply repressing the cold-inducible genes in naïve conditions.Peer Reviewe

Cold stress induces rapid gene-specific changes in the levels of H3K4me3 and H3K27me3 in Arabidopsis thaliana

When exposed to low temperatures, plants undergo a drastic reprogramming of their transcriptome in order to adapt to their new environmental conditions, which primes them for potential freezing temperatures. While the involvement of transcription factors in this process, termed cold acclimation, has been deeply investigated, the potential contribution of chromatin regulation remains largely unclear. A large proportion of cold-inducible genes carries the repressive mark histone 3 lysine 27 trimethylation (H3K27me3), which has been hypothesized as maintaining them in a silenced state in the absence of stress, but which would need to be removed or counteracted upon stress perception. However, the fate of H3K27me3 during cold exposure has not been studied genome-wide. In this study, we offer an epigenome profiling of H3K27me3 and its antagonistic active mark H3K4me3 during short-term cold exposure. Both chromatin marks undergo rapid redistribution upon cold exposure, however, the gene sets undergoing H3K4me3 or H3K27me3 differential methylation are distinct, refuting the simplistic idea that gene activation relies on a switch from an H3K27me3 repressed chromatin to an active form enriched in H3K4me3. Coupling the ChIP-seq experiments with transcriptome profiling reveals that differential histone methylation only weakly correlates with changes in expression. Interestingly, only a subset of cold-regulated genes lose H3K27me3 during their induction, indicating that H3K27me3 is not an obstacle to transcriptional activation. In the H3K27me3 methyltransferase curly leaf (clf) mutant, many cold regulated genes display reduced H3K27me3 levels but their transcriptional activity is not altered prior or during a cold exposure, suggesting that H3K27me3 may serve a more intricate role in the cold response than simply repressing the cold-inducible genes in naïve conditions

Single-nucleus RNA sequencing of plant tissues using a nanowell‐based system

Single-cell genomics provides unprecedented potential for research on plant development and environmental responses. Here, we introduce a generic procedure for plant nucleus isolation combined with nanowell-based library preparation. Our method enables the transcriptome analysis of thousands of individual plant nuclei. It serves as an alternative to the use of protoplast isolation, which is currently a standard methodology for plant single-cell genomics, although it can be challenging for some plant tissues. We show the applicability of our nucleus isolation method by using different plant materials from different species. The potential of our single-nucleus RNA sequencing method is shown through the characterization of transcriptomes of seedlings and developing flowers from Arabidopsis thaliana. We evaluated the transcriptome dynamics during the early stages of anther development, identified stage-specific activities of transcription factors regulating this process, and predicted potential target genes of these transcription factors. Our nucleus isolation procedure can be applied in different plant species and tissues, thus expanding the toolkit for plant single-cell genomics experiments.Peer Reviewe

A clean and efficient method for purifying crude selenium based on a selective leaching - directed decomposition purification process

The rare element selenium is a key material in supporting the development of high-tech and new products. This research has led to the development of a method of purifying crude selenium based on a selective leaching-directed decomposition purification process. The influence of factors such as the concentration of the leaching solution, leaching temperature, solid-liquid ratio, and leaching time on the leaching rate of Se were investigated in detail. The experimental results show that the optimal conditions for selective leaching of selenium were as follows: the concentration of leaching solution (solute: Na _2 SO _3 ) was 260 g l ^−1 , the stirring speed was 300 rpm, the ratio of liquid to solid was 0.10 g ml ^−1 , the reaction temperature was 90 °C, the reaction time was 180 min, and the leaching rate of selenium on one run was >95%. The products of selenium after two runs meet the requirements of Se99.9 in YS/223–2007, the Chinese nonferrous metal industry standard. The direct yield of Se is greater than 90%, and precious metals such as gold, silver and platinum are enriched in the residue. No waste is produced during the whole purification process, and all products can be recycled. This study provides an efficient and environmentally friendly method for the purification of crude selenium, which has important industrial applications

From Single Cells to Flowers – Biological Complexity Driving Plant Reproductive Development

The rise of data science in biology stimulates interdisciplinary collaborations to address fundamental questions. Here, we report the outcome of the first SINFONIA symposium focused on revealing the mechanisms governing plant reproductive development across biological scales. The intricate and dynamic target networks of known regulators of flower development remain poorly understood. To analyze development from the genome to the final floral organ morphology, high-resolution data that capture spatiotemporal regulatory activities are necessary and require advanced computational methods for analysis and modeling. Moreover, frameworks to share data, practices and approaches that facilitate the combination of varied expertise to advance the field are called for. Training young researchers in interdisciplinary approaches and science communication offers the opportunity to establish a collaborative mindset to shape future research

Prediction of Vessel Arrival Time to Pilotage Area Using Multi-Data Fusion and Deep Learning

This paper investigates the prediction of vessels' arrival time to the pilotage area using multi-data fusion and deep learning approaches. Firstly, the vessel arrival contour is extracted based on Multivariate Kernel Density Estimation (MKDE) and clustering. Secondly, multiple data sources, including Automatic Identification System (AIS), pilotage booking information, and meteorological data, are fused before latent feature extraction. Thirdly, a Temporal Convolutional Network (TCN) framework that incorporates a residual mechanism is constructed to learn the hidden arrival patterns of the vessels. Extensive tests on two real-world data sets from Singapore have been conducted and the following promising results have been obtained: 1) fusion of pilotage booking information and meteorological data improves the prediction accuracy, with pilotage booking information having a more significant impact; 2) using discrete embedding for the meteorological data performs better than using continuous embedding; 3) the TCN outperforms the state-of-the-art baseline methods in regression tasks, exhibiting Mean Absolute Error (MAE) ranging from 4.58 min to 4.86 min; and 4) approximately 89.41% to 90.61% of the absolute prediction residuals fall within a time frame of 10 min.Comment: The 26th IEEE International Conference on Intelligent Transportation Systems (ITSC 2023

Association of sex hormone-binding globulin with nonalcoholic fatty liver disease in Chinese adults

Abstract Background Sex hormone-binding globulin (SHBG), a glycoprotein synthesized by hepatocytes, has been linked to insulin resistance and hepatic lipid metabolism and is suggested to be associated with nonalcoholic fatty liver disease (NAFLD). This study aimed to investigate the association of SHBG with NAFLD in Chinese adults. Methods We conducted a community-based, cross-sectional study in China involving 2912 participants aged 40–75 years old. All participants underwent detection for hepatic fat infiltration by ultrasound in addition to providing complete medical history and undergoing physical and blood biochemical examinations. The association of serum SHBG with the presence of NAFLD was reported by adjusted odds ratio after applying logistic regression models. To further explore the relationship between SHBG and NAFLD, mRNA expression of SHBG and hepatocyte nuclear factor 4-α (HNF4α), as well as intrahepatic triglycerides, were determined from the liver tissues of 32 subjects with different degrees of steatosis. Results Serum SHBG levels in patients with NAFLD (median, 43.8 nmol/L; interquartile range, 33.4–56.8 nmol/L) were significantly lower than those in non-NAFLD subjects (median, 63.4 nmol/L; interquartile range, 47.6–83.1 nmol/L). Serum SHBG levels were inversely correlated with WHR, trunk fat percentage, glucose, HOMA-IR, TG, UA and DHEAS, and were positively correlated with HDL-C levels (all p <  0.001). Logistic regression analysis indicated that serum SHBG levels were negatively associated with the presence of NAFLD in all subjects, as well as the subgroups stratified by sex, BMI and HOMA-IR (all p <  0.05). In human liver tissues, SHBG and HNF4α mRNA expression decreased along with the elevated grade of hepatic steatosis. Both SHBG and HNF4α mRNA expression levels were negatively correlated with intrahepatic triglycerides. Conclusions These results demonstrate that SHBG levels were negatively associated with the presence of NAFLD in middle-aged and elderly Chinese adults