Explore the vast range of titles available.

Pathogenesis-related protein 10 (PR10) family genes play a crucial role in plant defense against various stressors. However, gene member and function identification of PR10 family in sugarcane remain largely unexplored. This study systematically identified and characterized this family genes in Saccharum spontaneum genome as well as their transcriptional expression in two sugarcane cultivars in response to infection by pathogenic bacteria Xanthomonas albilineans ( Xa ) and Acidovorax avenae subsp. avenae ( Aaa ) and foliar application of exogenous salicylic acid (SA). A total of 24 SsPR10 family genes were identified and categorized into two subfamilies, i.e., IPR10 ( SsIPR10-1–14 ) and NCS ( SsNCS-1–10 ). Six and two sets of SsPR10 underwent tandem and fragmental duplication events, respectively. RNA sequencing dataset and quantitative RT-PCR assay uncovered that ShIPR10-1/2/4/7/11/12 and ShNCS-8 genes were dramatically upregulated with increases of 3.2–107.2-fold in LCP85-384 (resistant to leaf scald), while they were slightly upregulated with increases of 1.26–7.1-fold in ROC20 (susceptible to leaf scald) for 24–72 h post inoculation under Xa infection. ShIPR10-1/7/12 and ShNCS-8 were significantly upregulated in both cultivars triggered by Aaa infection with increases of 2.4–21.0-fold. Under exogenous salicylic acid treatment, ShIPR10-1/2/4/7/11/12 were remarkably upregulated by 3.6–6.1-fold in LCP85-384 at 12 h post treatment (hpt) but were downregulated by 81.3% in ROC20 at 24 hpt, as compared to the control 0 hpt. In addition, ShNPR1 and ShPR1 involved in the SA signal transduction pathway displayed positive roles in sugarcane under both bacterial attacks and SA treatment. Collectively, our data provide important genetic resources for improving sugarcane tolerance to pathogenic bacterial stress and disease-resistance breeding in sugarcane for food security.

Currently, many studies on neuropsychiatric disorders have utilized massive trio-based whole-exome sequencing (WES) and whole-genome sequencing (WGS) to identify numerous de novo mutations (DNMs). Here, we retrieved 17 104 DNMs from 3555 trios across four neuropsychiatric disorders: autism spectrum disorder, epileptic encephalopathy, intellectual disability and schizophrenia, in addition to unaffected siblings (control), from 36 studies by WES/WGS. After eliminating non-exonic variants, we focused on 3334 exonic DNMs for evaluation of their association with these diseases. Our results revealed a higher prevalence of DNMs in the probands of all four disorders compared with the one in the controls ( P <1.3 × 10 −7 ). The elevated DNM frequency is dominated by loss-of-function/deleterious single-nucleotide variants and frameshift indels (that is, extreme mutations, P <4.5 × 10 −5 ). With extensive annotation of these ‘extreme’ mutations, we prioritized 764 candidate genes in these four disorders. A combined analysis of Gene Ontology, microRNA targets and transcription factor targets revealed shared biological process and non-coding regulatory elements of candidate genes in the pathology of neuropsychiatric disorders. In addition, weighted gene co-expression network analysis of human laminar-specific neocortical expression data showed that candidate genes are convergent on eight shared modules with specific layer enrichment and biological process features. Furthermore, we identified that 53 candidate genes are associated with more than one disorder ( P <0.000001), suggesting a possibly shared genetic etiology underlying these disorders. Particularly, DNMs of the SCN2A gene are frequently occurred across all four disorders. Finally, we constructed a freely available NPdenovo database, which provides a comprehensive catalog of the DNMs identified in neuropsychiatric disorders.

Circular RNAs (circRNAs), a class of newly discovered endogenous noncoding RNAs, have shown large capabilities in gene regulation. Patients with the grade 3 endometrial cancer (EC) have a generally poor prognosis, and the specific role of circRNAs in the grade 3 EC remains unclear. This study aims to investigate the roles of circRNAs in the grade 3 EC. In the current study, we screened the expression profiles of circRNAs taken from two women with the grade 3 EC and adjacent non-cancerous endometrial tissue using circRNAs sequencing. Bioinformatic analyses were applied to study these differentially expressed circRNAs. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) of six dysregulated circRNAs was performed to validate the sequencing results. Bioinformatic analyses, including the negative correlation network analyses of circRNAs-microRNAs (miRNAs)-messenger RNAs (mRNAs) and the Cytoscape, were used to delineate the interaction of circRNAs/miRNAs of the entire network. Data of circRNA sequencing showed a significant change in 75,928 unique circRNAs ( <0.05). The upregulated hsa_circ_0039569 and hsa_circ_0001610 and downregulated hsa_circ_0000437, hsa_circ_0001776, and hsa_circ_0009043 were validated by qRT-PCR analysis. Using bioinformatical methods, we found that hsa_circ_0039569 has the MRE of hsa-miR-542-3p and hsa-let-7c-5p. Hsa-miR-542-3p and hsa-let-7c-5p were downregulated in the grade 3 EC validated by qRT-PCR analysis. In the clinicopathological parameters, the expression level of hsa_circ_0039569 was significantly correlated with tumor differentiation ( =0.001). This is the first study demonstrated that there were a lot of differences between the tissue of the grade 3 EC and adjacent non-cancerous endometrial in circRNA expression and may offer novel molecular candidates for diagnosis and clinical treatment of the grade 3 EC.

Objectives Recently, several studies documented that de novo mutations (DNMs) play important roles in the aetiology of sporadic diseases. Next-generation sequencing (NGS) enables variant calling at single-base resolution on a genome-wide scale. However, accurate identification of DNMs from NGS data still remains a major challenge. We developed mirTrios, a web server, to accurately detect DNMs and rare inherited mutations from NGS data in sporadic diseases. Methods The expectation-maximisation (EM) model was adopted to accurately identify DNMs from variant call files of a trio generated by GATK (Genome Analysis Toolkit). The GATK results, which contain certain basic properties (such as PL, PRT and PART), are iteratively integrated into the EM model to strike a threshold for DNMs detection. Training sets of true and false positive DNMs in the EM model were built from whole genome sequencing data of 64 trios. Results With our in-house whole exome sequencing datasets from 20 trios, mirTrios totally identified 27 DNMs in the coding region, 25 of which (92.6%) are validated as true positives. In addition, to facilitate the interpretation of diverse mutations, mirTrios can also be employed in the identification of rare inherited mutations. Embedded with abundant annotation of DNMs and rare inherited mutations, mirTrios also supports known diagnostic variants and causative gene identification, as well as the prioritisation of novel and promising candidate genes. Conclusions mirTrios provides an intuitive interface for the general geneticist and clinician, and can be widely used for detection of DNMs and rare inherited mutations, and annotation in sporadic diseases. mirTrios is freely available at http://centre.bioinformatics.zj.cn/mirTrios/.

Correction to: Molecular Psychiatry advance online publication, 7 April 2015; doi:10.1038/mp.2015.40 Following publication of this paper, the authors noticed that the postal address shown for corresponding authors J Wu and ZS Sun was incorrect. The authors also note that the corresponding authors were listed in incorrect order.

Polyunsaturated fatty acid (PUFA) and eicosapentaenoic acid (EPA) are essential for the health of aquatic organisms and human beings. In order to optimize the culture conditions of the diatom Chaetoceros lorenzianus, effects of different iron sources (FeC6H5O7, FeCl3, FeSO4) and different iron concentrations (0.10, 0.25, 0.50, 0.75, 1.00, 1.25 mg L−1) on C. lorenzianus were studied. The results showed that different iron sources and different iron concentrations had significant effects on the growth, chlorophyll a, total lipid and fatty acids of C. lorenzianus. The growth rate (0.47 day−1), chlorophyll a (510.57 μg L−1), total lipids (11.82%), and n-3 PUFA (EPA and DHA) (21.20%) contents were significantly higher in the FeCl3 group when compared to FeSO4 and FeC6H5O7 groups. The optimum concentration of FeCl3 for the growth and synthesis of chlorophyll a was 0.75–1.00 mg L−1 and the optimum concentration for lipid accumulation was 0.25 mg L−1. The secondary culture method can be used in large-scale culture, that is, the initial culture is performed under the optimal iron concentration (0.75 mg L−1 FeCl3) for obtaining higher biomass. Then, the secondary culture would be performed under a low iron concentration (0.25 mg L−1 FeCl3), obtaining high total lipids in algal cells. These findings make tangible contributions to culture C. lorenzianus for potential commercial production of PUFA and EPA.

The applications of single-cell and spatial technologies in recent times have revolutionized the present understanding of cellular states and the cellular heterogeneity inherent in complex biological systems. These advancements offer unprecedented resolution in the examination of the functional genomics of individual cells and their spatial context within tissues. In this review, we have comprehensively discussed the historical development and recent progress in the field of single-cell and spatial genomics. We have reviewed the breakthroughs in single-cell multi-omics technologies, spatial genomics methods, and the computational strategies employed toward the analyses of single-cell atlas data. Furthermore, we have highlighted the advances made in constructing cellular atlases and their clinical applications, particularly in the context of disease. Finally, we have discussed the emerging trends, challenges, and opportunities in this rapidly evolving field.

Macrophage polarization is vital to mounting a host defense or repairing tissue in various liver diseases. Excessive activation of the NLR family pyrin domain containing 3 (NLRP3) inflammasome is related to the orchestration of inflammation and alcohol-associated liver disease (ALD) pathology. Rab GTPases play critical roles in regulating vesicular transport. In this study we investigated the role of Rab11b in ALD, aiming to identify effective therapeutic targets. Here, we first demonstrated a decreased expression of Rab11b in macrophages from ALD mice. Knockdown of Rab11b by macrophage-specific adeno-associated virus can alleviate alcohol induced liver inflammation, injury and steatosis. We found that LPS and alcohol stimulation promoted Rab11b transferring from the nucleus to the cytoplasm in bone marrow-derived macrophages (BMDM) cells. Rab11b specifically activated the NLRP3 inflammasome in BMDMs and RAW264.7 cells to induce M1 macrophage polarization. Rab11b overexpression in BMDMs inhibited autophagic flux, leading to the suppression of LC3B-mediated NLRP3 degradation. We conclude that impaired Rab11b could alleviate alcohol-induced liver injury via autophagy-mediated NLRP3 degradation.

The umbilical cable is a vital component of subsea production systems that provide power, chemical agents, control signals et al., and its requirement for reliability is exceedingly high. However, as the umbilical cable is a composite structure comprising multiple functional units, the reliability analysis of such cables involves numerous parameters that can impact calculation efficiency. In this paper, the reliability analysis of a new kind of umbilical cable with carbon fiber rod under tension is analyzed. The global dynamic analytical model is first established to determine the maximum tension load, then the local analytical model of umbilical cable including each unit are constructed by finite element method (FEM). Based on the mechanical analytical model, the reliability of umbilical cable under tension load is studied using response surface method (RSM) and Monte Carlo method. During the calculation process, a new tangent plane sampling method to calculate the response surface function (RSF) is proposed in this paper, which could make sampling points faster come close to the RSF curve, and it is proved that the calculation efficiency increases about 33% comparing with traditional method.