Single-cell transcriptome analysis dissects lncRNA-associated gene networks in Arabidopsis

The plant genome produces an extremely large collection of long noncoding RNAs (lncRNAs) that are generally expressed in a context-specific manner and have pivotal roles in regulation of diverse biological processes. Here, we mapped the transcriptional heterogeneity of lncRNAs and their associated gene regulatory networks at single-cell resolution. We generated a comprehensive cell atlas at the whole-organism level by integrative analysis of 28 published single-cell RNA sequencing (scRNA-seq) datasets from juvenile Arabidopsis seedlings. We then provided an in-depth analysis of cell-type-related lncRNA signatures that show expression patterns consistent with canonical protein-coding gene markers. We further demonstrated that the cell-type-specific expression of lncRNAs largely explains their tissue specificity. In addition, we predicted gene regulatory networks on the basis of motif enrichment and co-expression analysis of lncRNAs and mRNAs, and we identified putative transcription factors orchestrating cell-type-specific expression of lncRNAs. The analysis results are available at the single-cell-based plant lncRNA atlas database (scPLAD; https://biobigdata.nju.edu.cn/scPLAD/). Overall, this work demonstrates the power of integrative single-cell data analysis applied to plant lncRNA biology and provides fundamental insights into lncRNA expression specificity and associated gene regulation.

scPlant: A versatile framework for single-cell transcriptomic data analysis in plants

Single-cell transcriptomics has been fully embraced in plant biological research and is revolutionizing our understanding of plant growth, development, and responses to external stimuli. However, single-cell transcriptomic data analysis in plants is not trivial, given that there is currently no end-to-end solution and that integration of various bioinformatics tools involves a large number of required dependencies. Here, we present scPlant, a versatile framework for exploring plant single-cell atlases with minimum input data provided by users. The scPlant pipeline is implemented with numerous functions for diverse analytical tasks, ranging from basic data processing to advanced demands such as cell-type annotation and deconvolution, trajectory inference, cross-species data integration, and cell-type-specific gene regulatory network construction. In addition, a variety of visualization tools are bundled in a built-in Shiny application, enabling exploration of single-cell transcriptomic data on the fly.

[Analysis of physical growth of preterm infants with different intrauterine growth patterns in Haikou]

Objective: To analyze the physical growth of preterm infants with different intrauterine growth patterns. Methods: A total of 10 856 preterm infants who were born in various districts of Haikou City from October 1st, 2015 to June 1st, 2021 and received regular health care and management were retrospectively enrolled. The preterm infants were divided into appropriate for gestational age (AGA), small for gestational age (SGA) and large for gestational age (LGA) groups according to different intrauterine growth patterns. The general characteristics of preterm infants in different groups were compared by H test (Kruskal and Wallis) or Chi-squared test. And the developmental curves were plotted by local regression (LOESS) with their physical growth indexes. Results: Of the 10 856 preterm infants, 6 317 were boys and 4 539 were girls. The gestational age at birth was 35 (34, 36) weeks, and the birth weight was 2.5 (2.1, 2.8) kg. There were 754 (6.9%) SGA, 9 301 (85.7%) AGA, and 801 (7.4%) LGA preterm infants. All preterm infants were followed up until 18 months of corrected age. The birth weight of the SGA group was lower than that of the AGA and LGA groups (Z=2 274.93, P<0.001). The proportion of exclusive breastfeeding at the first health care interview was higher in the AGA group (68.6% (6 378/9 301)) than in the SGA group (62.9% (474/754)) (χ²=13.82, P=0.003). The LOESS curving fitting showed that the weight and height of the preterm infants in all the 3 groups increased rapidly during 0-6 months of corrected age. The regression prediction values of weight for age Z-score (WAZ), height for age Z-score (HAZ) and weight for height Z-score (WHZ) were around 0 s, while the regression prediction values of these three indicators in SGA were all below 0 s but greater than -1 s. The rates of low birth weight, growth retardation and wasting during 0-17 months of corrected age were 0.3% (16/4 838)-1.9% (47/2 506), 0.4% (18/4 838) -2.4% (51/2 124), and 2.1% (88/4 135) -4.4% (214/4 838) in AGA groups, and 0 (0/296) -1.0% (2/199), 0 (0/341) -1.6% (3/186) and 1.0% (2/199) -2.6% (9/341) in LGA group, whereas 7.6% (25/330) -16.8% (28/167), 5.2% (17/330)-10.6%(32/303) and 3.9% (3/77) -12.6% (21/167) in SGA group. In addition, the monthly growth of weight and height of preterm infants in all the 3 groups decreased with the increasing age, and the monthly weight gain. The length increment was 4.0 cm/month during corrected 0-2 month of age and 2.4 cm/month during corrected 2-5 month of age in the SGA preterm infants. Conclusions: Most of the preterm infants could have an appropriate catch-up growth, but the growth and development in the SGA preterm infants lags behind that of their AGA and LGA peers. The physical growth of SGA premature infants should be paid more attention to, to timely correct the growth deviations.

ChIP-Hub provides an integrative platform for exploring plant regulome

Plant genomes encode a complex and evolutionary diverse regulatory grammar that forms the basis for most life on earth. A wealth of regulome and epigenome data have been generated in various plant species, but no common, standardized resource is available so far for biologists. Here, we present ChIP-Hub, an integrative web-based platform in the ENCODE standards that bundles >10,000 publicly available datasets reanalyzed from >40 plant species, allowing visualization and meta-analysis. We manually curate the datasets through assessing ~540 original publications and comprehensively evaluate their data quality. As a proof of concept, we extensively survey the co-association of different regulators and construct a hierarchical regulatory network under a broad developmental context. Furthermore, we show how our annotation allows to investigate the dynamic activity of tissue-specific regulatory elements (promoters and enhancers) and their underlying sequence grammar. Finally, we analyze the function and conservation of tissue-specific promoters, enhancers and chromatin states using comparative genomics approaches. Taken together, the ChIP-Hub platform and the analysis results provide rich resources for deep exploration of plant ENCODE. ChIP-Hub is available at https://biobigdata.nju.edu.cn/ChIPHub/.

A comprehensive data portal to explore plant regulomes is still unavailable. Here, the authors develop a web-based platform ChIP-Hub in the ENCODE standards and demonstrate its applications in the identification of hierarchical regulatory network, tissue-specific chromatin dynamics, putative enhancers and chromatin states.

[Role and potential value of circular RNAs in the occurrence of primary hepatic cancer]

Circular RNA is a class of non-coding RNAs, which are covalently closed and circular at both ends, showing dissimilar characteristics from linear RNA. Several studies have shown that circular RNAs play an important role in the occurrence and development of primary hepatic cancer. By combining with the latest research progress of this field at home and abroad, we summarized the mechanism regulating the occurrence and development of liver cancer, abnormal expression, and as potential molecular markers for disease diagnosis and treatment.

Architecture of gene regulatory networks controlling flower development in Arabidopsis thaliana

Floral homeotic transcription factors (TFs) act in a combinatorial manner to specify the organ identities in the flower. However, the architecture and the function of the gene regulatory network (GRN) controlling floral organ specification is still poorly understood. In particular, the interconnections of homeotic TFs, microRNAs (miRNAs) and other factors controlling organ initiation and growth have not been studied systematically so far. Here, using a combination of genome-wide TF binding, mRNA and miRNA expression data, we reconstruct the dynamic GRN controlling floral meristem development and organ differentiation. We identify prevalent feed-forward loops (FFLs) mediated by floral homeotic TFs and miRNAs that regulate common targets. Experimental validation of a coherent FFL shows that petal size is controlled by the SEPALLATA3-regulated miR319/TCP4 module. We further show that combinatorial DNA-binding of homeotic factors and selected other TFs is predictive of organ-specific patterns of gene expression. Our results provide a valuable resource for studying molecular regulatory processes underlying floral organ specification in plants.

Homeotic transcription factors and miRNAs promote floral organ specification. Here Chen et al. reconstruct gene regulatory networks in Arabidopsis flowers and find evidence for feed forward loops between transcription factors, miRNAs and their targets that determine organ-specific gene expression.

The HTPmod Shiny application enables modeling and visualization of large-scale biological data

The wave of high-throughput technologies in genomics and phenomics are enabling data to be generated on an unprecedented scale and at a reasonable cost. Exploring the large-scale data sets generated by these technologies to derive biological insights requires efficient bioinformatic tools. Here we introduce an interactive, open-source web application (HTPmod) for high-throughput biological data modeling and visualization. HTPmod is implemented with the Shiny framework by integrating the computational power and professional visualization of R and including various machine-learning approaches. We demonstrate that HTPmod can be used for modeling and visualizing large-scale, high-dimensional data sets (such as multiple omics data) under a broad context. By reinvestigating example data sets from recent studies, we find not only that HTPmod can reproduce results from the original studies in a straightforward fashion and within a reasonable time, but also that novel insights may be gained from fast reinvestigation of existing data by HTPmod.

Dijun Chen et al. present HTPmod, a Shiny web application for modeling and visualization of large-scale genomic and phenomic datasets. The authors show that HTPmod can quickly reproduce analyses of high-throughput biological datasets and produce publication-quality figures.

Treatment of petrochemical secondary effluent by an up-flow biological aerated filter (BAF)

In this study, petrochemical secondary effluent was treated by a 55 cm diameter pilot-scale biological aerated filter (BAF) with a media depth of 220 cm. Volcanic rock grains were filled as the BAF media. Median removal efficiency of chemical oxygen demand (COD) and ammonia nitrogen (NH3-N) was 29.35 and 57.98%, respectively. Moreover, the removal profile of the COD, NH3-N, total nitrogen and total organic carbon demonstrated that the filter height of 140 cm made up to 90% of the total removal efficiency of the final effluent. By gas chromatography-mass spectrometry, removal efficiencies of 2-chloromethyl-1,3-dioxolane, and benzonitrile, indene and naphthalene were obtained, ranging from 30.12 to 63.01%. The biomass and microbial activity of the microorganisms on the filter media were in general reduced with increasing filter height, which is consistent with the removal profile of the contaminants. The detected genera Defluviicoccus, Betaproteobacteria_unclassified and the Blastocatella constituted 1.86-6.75% of the identified gene, enhancing the COD and nitrogen removal in BAF for treating petrochemical secondary effluent.

Spatial features for Escherichia coli genome organization

Background

In bacterial genomes, the compactly encoded genes and operons are well organized, with genes in the same biological pathway or operons in the same regulon close to each other on the genome sequence. In addition, the linearly close genes have a higher probability of co-expression and their protein products tend to form protein–protein interactions. However, the organization features of bacterial genomes in a three-dimensional space remain elusive. The DNA interaction data of Escherichia coli, measured by the genome conformation capture (GCC) technique, have recently become available, which allowed us to investigate the spatial features of bacterial genome organization.

Results

By renormalizing the GCC data, we compared the interaction frequency of operon pairs in the same regulon with that of random operon pairs. The results showed that arrangements of operons in the E. coli genome tend to minimize the spatial distance between operons in the same regulon. A similar global organization feature exists for genes in biological pathways of E. coli. In addition, the genes close to each other spatially (even if they are far from each other on the genome sequence) tend to be co-expressed and form protein–protein interactions. These results provided new insights into the organization principles of bacterial genomes and support the notion of transcription factory.

Conclusions

This study revealed the organization features of Escherichia coli genomic functional units in the 3D space and furthered our understanding of the link between the three-dimensional structure of chromosomes and biological function.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1258-1) contains supplementary material, which is available to authorized users.

Dissecting the chromatin interactome of microRNA genes

Our knowledge of the role of higher-order chromatin structures in transcription of microRNA genes (MIRs) is evolving rapidly. Here we investigate the effect of 3D architecture of chromatin on the transcriptional regulation of MIRs. We demonstrate that MIRs have transcriptional features that are similar to protein-coding genes. RNA polymerase II-associated ChIA-PET data reveal that many groups of MIRs and protein-coding genes are organized into functionally compartmentalized chromatin communities and undergo coordinated expression when their genomic loci are spatially colocated. We observe that MIRs display widespread communication in those transcriptionally active communities. Moreover, miRNA-target interactions are significantly enriched among communities with functional homogeneity while depleted from the same community from which they originated, suggesting MIRs coordinating function-related pathways at posttranscriptional level. Further investigation demonstrates the existence of spatial MIR-MIR chromatin interacting networks. We show that groups of spatially coordinated MIRs are frequently from the same family and involved in the same disease category. The spatial interaction network possesses both common and cell-specific subnetwork modules that result from the spatial organization of chromatin within different cell types. Together, our study unveils an entirely unexplored layer of MIR regulation throughout the human genome that links the spatial coordination of MIRs to their co-expression and function.

The sequencing bias relaxed characteristics of Hi-C derived data and implications for chromatin 3D modeling

The 3D chromatin structure modeling by chromatin interactions derived from Hi-C experiments is significantly challenged by the intrinsic sequencing biases in these experiments. Conventional modeling methods only focus on the bias among different chromatin regions within the same experiment but neglect the bias arising from different experimental sequencing depth. We now show that the regional interaction bias is tightly coupled with the sequencing depth, and we further identify a chromatin structure parameter as the inherent characteristics of Hi-C derived data for chromatin regions. Then we present an approach for chromatin structure prediction capable of relaxing both kinds of sequencing biases by using this identified parameter. This method is validated by intra and inter cell-line comparisons among various chromatin regions for four human cell-lines (K562, GM12878, IMR90 and H1hESC), which shows that the openness of chromatin region is well correlated with chromatin function. This method has been executed by an automatic pipeline (AutoChrom3D) and thus can be conveniently used.

Rank regression for analyzing ordinal qualitative data for treatment comparison

ABSTRACT Ordinal qualitative data are often collected for phenotypical measurements in plant pathology and other biological sciences. Statistical methods, such as t tests or analysis of variance, are usually used to analyze ordinal data when comparing two groups or multiple groups. However, the underlying assumptions such as normality and homogeneous variances are often violated for qualitative data. To this end, we investigated an alternative methodology, rank regression, for analyzing the ordinal data. The rank-based methods are essentially based on pairwise comparisons and, therefore, can deal with qualitative data naturally. They require neither normality assumption nor data transformation. Apart from robustness against outliers and high efficiency, the rank regression can also incorporate covariate effects in the same way as the ordinary regression. By reanalyzing a data set from a wheat Fusarium crown rot study, we illustrated the use of the rank regression methodology and demonstrated that the rank regression models appear to be more appropriate and sensible for analyzing nonnormal data and data with outliers.

Oxidative DNA damage is important to the evolution of antibiotic resistance: evidence of mutation bias and its medicinal implications

Several (1) studies have revealed that the reactive oxygen species (ROS) induced by antibacterial stimulation accelerates the evolution of antibiotic resistance, which uncovered new links between oxygen rise and evolution and inspired new strategies to prevent antibiotic resistance. Considering many other mechanisms cause DNA mutations aside from ROS damage, evaluating the significance of oxidative DNA damage in the development of antibiotic resistance is of great interest. In this study, we examined the ratio of G:C > T:A transversion to G:C > A:T transition in drug-resistant Escherichia coli and Mycobacterium tuberculosis and found that it is significantly higher than the background values. This finding strongly suggests that ROS damage plays a critical role in the development of antibacterial resistance. Considering the long-term co-evolution between host organisms and pathogenic bacteria, we speculate that the hosts may have evolved strategies for combating antibiotic resistance by controlling DNA damage in bacteria. Analysis of the global transcriptional profiles of Staphylococcus aureus treated with berberine (derived from Berberis, a traditional antibacterial medicine) revealed that the transcription of DNA repair enzymes was markedly upregulated, whereas the antioxidant enzymes were significantly downregulated. Thus, we propose that consolidating the DNA repair systems of bacteria may be a viable strategy for preventing antibiotic resistance. (1)These authors contributed equally to this work.

The performance of a two-stage SBR system in treating dye containing wastewater

A two-stage SBR system treating the wastewater containing copper-phthalocyanin dye-Reactive Turquoise Blue KN-G (C. I. Reactive Blue 21, denoted by RTB) was investigated during a 200-cycle operation. The performance of the system, including pollutant removal rates, operating stability and sludge characteristics, may be a concern in the long-term run. The results shows that the system removed RTB efficiently despite the step-up RTB concentration from 13.1 to 107 mg/L in the influent. The average total removal rates of RTB were 81% to 92.5% due to the contribution of both anaerobic and aerobic stages, while stable effluent was produced with the help of the aerobic stage. The sludge in each reactor was in the steady state and of good activity on RTB removal. Moreover, the anaerobic sludge with the SVI value of 109.1 and the aerobic sludge with the SVI value of 103.2 had good settling properties, which was verified by hardly any presence of suspended solids in the effluent and an observation under an electron-scanning microscope. The adsorption and biodegradation were considered as the mechanism for the stability of the SBR system during the long-term run.

Effect of sea anemone toxin anthopleurin-Q on sodium current in guinea pig ventricular myocytes

AIM

To investigate the effects of a sea anemone toxin anthopleurin-Q (AP-Q) isolated from Anthopleura xanthogrammica on sodium current (INa) in isolated guinea pig ventricular myocytes.

METHODS

Single myocytes were dissociated by enzymatic dissociation method. INa was recorded using whole-cell patch-clamp technique.

RESULTS

AP-Q (3 - 300 nmol/L) increased INa in a concentration-dependent manner. The EC50 value for increasing INa was 104 nmol/L (95 % confidence range: 78 - 130 nmol/L). AP-Q 300 nmol/L shifted the I-V curve to the leftward, changed the membrane potential of half maximal activation to more negative potential from (-36.3 +/- 2.3) mV to (-43 +/- 3) mV (n = 6, P < 0.01) and changed the membrane potential of half maximal inactivation to more positive potential from (-75 +/- 6) mV to (-59 +/- 5) mV (n = 6, P < 0.01). AP-Q 300 nmol/L shortened the half-recovery time of INa from (114 +/- 36) ms to (17 +/- 2) ms (n = 6, P < 0.01). The fast inactivation time constant (tauf) of INa was markedly increased by AP-Q 300 nmol/L.

CONCLUSION

AP-Q has a stimulating effect on I(Na) with slowing the inactivation course of INa.

[Effects of 4-aminopyridine on calcium currents and sodium currents in guinea pig ventricular myocytes]

AIM

To investigate the effect of 4-aminopyridine (4-AP) on ion channels of myocytes.

METHODS

L-type calcium channel and sodium channel currents were recorded in guinea pig single ventricular myocyte using whole-cell patch-clamp techniques.

RESULTS

4-AP, 0.1, 0.5 and 1.0 mmol.L-1 were shown to inhibit L-type calcium channel currents (ICa, L) and sodium channel currents (INa) concentration-dependently. The percentage of inhibition were (11.6 +/- 1.7)%, (37.5 +/- 8.3)% and (54.5 +/- 6.9)% (P < 0.01) respectively for ICa, L, and (22.1 +/- 14.3)% (P < 0.05), (39.4 +/- 8.8)% and (62.3 +/- 6.8)% (P < 0.01) respectively for INa. 4-AP 0.5 mmol.L-1 shifted the I-V curves of ICa, L and INa upwardly.

CONCLUSION

4-AP blocked L-type calcium channel and sodium channels in guinea-pig ventricular myocytes concentration-dependently.

Meal-induced oxygen desaturation and dyspnea in chronic obstructive pulmonary disease

OBJECTIVE

To study arterial oxygen saturation (SpO2) obtained by pulse oximetry and dyspnea during active eating (AE) and passive eating (PE) in patients with severe chronic obstructive pulmonary disease (COPD).

DESIGN

Patients were studied on two consecutive days with AE and PE, which occurred in random order. SpO2 was recorded for 20 mins before and during eating, and dyspnea was recorded by the patient using a 10 cm visual analogue scale before and upon completion of eating.

SETTING

Subjects were in-patients at an intermediate care facility who were hospitalized for pulmonary rehabilitation or for convalescence after an exacerbation of COPD.

POPULATION STUDIED

Thirty-five patients with severe COPD (forced expiratory volume in 1 s [FEV1] less than 50% predicted, FEV1 to forced vital capacity ratio less than 65%) were studied. Mean age was 70.5 7.1 years.

MAIN RESULTS

Mean SpO2 decreased significantly (P<0.05) from 91.7 3.4% to 90.1 4.0% during AE, and 91.7 3.2% to 90. 8 3.6% during PE. Mean lowest SpO2 was lower and percentage of time with SpO2 less than 90% was greater during eating compared with corresponding control periods during both AE and PE. Dyspnea increased significantly (P<0.05) from 1.4 1.2 to 3.3 2.3 cm during AE, and from 1.5 1.5 to 2.4 2.2 cm during PE. The increase in dyspnea was significantly greater during AE than PE.

CONCLUSIONS

Eating is an activity that can adversely affect SpO2 and increase dyspnea in patients with severe COPD. Oxygen desaturation and particularly increased dyspnea may at least in part relate to the recruitment of upper extremity muscles during eating.

Treatment of small cell lung carcinoma in the elderly

BACKGROUND

The number of elderly people with small cell lung carcinoma (SCLC) is increasing and currently nearly 25% are older than 70 years. Elderly patients may not tolerate intensive therapy and, therefore, often do not receive such treatment. Additionally, age may be an independent predictor for response and survival. We compared the investigation, staging procedure, and management of patients less than 60 years, 60 to 69, and older than 70 years who were diagnosed with SCLC between 1985 and 1991. We hypothesized that elderly patients were investigated and treated less aggressively, and that their outcome was poorer than that of younger patients with SCLC.

METHODS

Information on weight loss, performance status, coexisting disease, staging investigations, and treatment was recorded. Treatment was categorized as optimal or suboptimal using predetermined criteria, and correlated with patient age. Toxicity grade, response to treatment, and survival were noted.

RESULTS

There were no differences among the 3 age groups with respect to disease stage, and weight loss, although poorer performance status and comorbidity were more common in those patients older than 70 years. Elderly patients were investigated and treated less aggressively than the 2 younger patient groups. The oldest group received smaller chemotherapy dosage, fewer cycles, and had more dose reductions compared to the younger patients. Only 1 of 81 elderly patients was enrolled on an experimental protocol as compared with 19% and 28% of the younger patient groups. Furthermore, elderly patients had the highest frequency of supportive care alone. There was a significant relationship between advanced age and suboptimal treatment, with those older than 70 years having an odds ratio (OR) of 0.30 (95% confidence interval (CI) 0.15-0.61), for having received optimal treatment. Despite this, survival was similar for younger and older groups of patients (OR 0.89, CI 0.6-1.3).

CONCLUSIONS

Elderly patients had poorer pre-treatment performance status, greater comorbidity, were more likely to have suboptimal therapy and were almost never entered into clinical trials. Despite this their survival did not differ from that of younger patients with SCLC. Randomized trials of treatment, with assessment of quality of life, are necessary to determine the effect of modified regimens for elderly patients with SCLC.