[Associations of blood pressure change with change in foods' intake among adults with mild to moderate hypertension]

Objective: To explore the association between the intake and changes in various types of food and the changes in blood pressure in patients with mild to moderate hypertension. Methods: Mild to moderate hypertension participants with complete baseline and outcome data were included from DECIDE-Diet study, a multicenter, randomized controlled trial. Dietary records and blood pressure measurements at both 7-day run-in (baseline) and 28-day intervention phases were collected for enrolled participants. Blood pressure change was defined as the difference between blood pressure at the end of trial and the baseline blood pressure. Baseline intake of food was the average daily intake during the run-in period, and the intake increment was defined as the difference between the average intake during the trial period and the average intake during the run-in period. After adjusting for age, sex, study center, intervention groups, baseline body mass index (kg/m2), antihypertension medication use, and baseline total calorie intake, a linear regression model was used to analyze the associations of the before-after-intervention change in blood pressure with baseline intake and intake increment of foods. Results: A total of 258 patients with mild to moderate hypertension were included, including 133 males, aged (56.5±9.9) years. (1) After adjusting for confounding factors, there was no significant association between baseline intake of food and baseline blood pressure (all P>0.05). The blood pressure change was negatively associated with baseline intakes of tubers, vegetables, and vegetable oils but positively with baseline intake of meats; and was negatively associated with intake increment of whole grains and fish (all P<0.05). (2) The multiple linear regression analysis showed that baseline intake of vegetables (β=-0.021, P=0.004), vegetable oils (β=-0.260, P=0.002), and increment in intake of fish (β=-0.128, P=0.026) were all significantly associated with changes in systolic blood pressure; baseline intake of vegetables (β=-0.017, P=0.002), vegetable oils (β=-0.182, P=0.001), dairy products (β=0.021, P=0.022), and increment in intake of fish (β=-0.092, P=0.010) were all significantly associated with changes in diastolic blood pressure. Conclusion: Increasing the intake of whole grains, vegetables, vegetable oils, and fish and decreasing the intake of meat may be beneficial for blood pressure control in patients with mild to moderate hypertension.

Inhibitor AN3661 reveals biological functions of Arabidopsis CLEAVAGE and POLYADENYLATION SPECIFICITY FACTOR 73

Cleavage and polyadenylation specificity factor (CPSF) is a protein complex that plays an essential biochemical role in mRNA 3'-end formation, including poly(A) signal recognition and cleavage at the poly(A) site. However, its biological functions at the organismal level are mostly unknown in multicellular eukaryotes. The study of plant CPSF73 has been hampered by the lethality of Arabidopsis (Arabidopsis thaliana) homozygous mutants of AtCPSF73-I and AtCPSF73-II. Here, we used poly(A) tag sequencing to investigate the roles of AtCPSF73-I and AtCPSF73-II in Arabidopsis treated with AN3661, an antimalarial drug with specificity for parasite CPSF73 that is homologous to plant CPSF73. Direct seed germination on an AN3661-containing medium was lethal; however, 7-d-old seedlings treated with AN3661 survived. AN3661 targeted AtCPSF73-I and AtCPSF73-II, inhibiting growth through coordinating gene expression and poly(A) site choice. Functional enrichment analysis revealed that the accumulation of ethylene and auxin jointly inhibited primary root growth. AN3661 affected poly(A) signal recognition, resulted in lower U-rich signal usage, caused transcriptional readthrough, and increased the distal poly(A) site usage. Many microRNA targets were found in the 3' untranslated region lengthened transcripts; these miRNAs may indirectly regulate the expression of these targets. Overall, this work demonstrates that AtCPSF73 plays important part in co-transcriptional regulation, affecting growth, and development in Arabidopsis.

Differential alternative polyadenylation of homoeologous genes of allohexaploid wheat ABD subgenomes during drought stress response

Because allohexaploid wheat genome contains ABD subgenomes, how the expression of homoeologous genes is coordinated remains largely unknown, particularly at the co-transcriptional level. Alternative polyadenylation (APA) is an important part of co-transcriptional regulation, which is crucial in developmental processes and stress responses. Drought stress is a major threat to the stable yield of wheat. Focusing on APA, we used poly(A) tag sequencing to track poly(A) site dynamics in wheat under drought stress. The results showed that drought stress led to extensive APA involving 37-47% of differentially expressed genes in wheat. Significant poly(A) site switching was found in stress-responsive genes. Interestingly, homoeologous genes exhibit unequal numbers of poly(A) sites, divergent APA patterns with tissue specificity and time-course dynamics, and distinct 3'-UTR length changes. Moreover, differentially expressed transcripts in leaves and roots used different poly(A) signals, the up- and downregulated isoforms had distinct preferences for non-canonical poly(A) sites. Genes that encode key polyadenylation factors showed differential expression patterns under drought stress. In summary, poly(A) signals and the changes in core poly(A) factors may widely affect the selection of poly(A) sites and gene expression levels during the response to drought stress, and divergent APA patterns among homoeologous genes add extensive plasticity to this responsive network. These results not only reveal the significant role of APA in drought stress response, but also provide a fresh perspective on how homoeologous genes contribute to adaptability through transcriptome diversity. In addition, this work provides information about the ends of transcripts for a better annotation of the wheat genome.

SPR9 encodes a 60 S ribosomal protein that modulates panicle spreading and affects resistance to false smut in rice (Oryza sativa. L)

BACKGROUND

The architecture of inflorescence in crops is a key agronomic feature determining grain yield and thus has been a major target trait of cereal domestication.

RESULTS

In this study, we show that a simple spreading panicle change in rice panicle shape, controlled by the Spreading Panicle 9 (SPR9) locus, also has a significant impact on the resistance to rice false smut (RFS). Meanwhile, we mapped a novel spr9 mutant gene between markers Indel5-18 and Indel5-22 encompassing a genomic region of 43-kb with six candidate genes. Through gene prediction and cDNA sequencing, we confirmed that LOC_Os05g38520 is the target gene in the spr9 mutant, which encodes 60 S ribosomal protein L36-2. Further analysis showed that the spr9 mutant is caused by a 1 bp deletion in the first exon that resulted in premature termination. Knockout experiments showed that the SPR9 gene is responsible for the spreading panicle phenotype of the spr9 mutant. Interestingly, the spr9 mutant was found to improve resistance to RFS without affecting major agronomic traits. Taken together, our results revealed that the spr9 allele has good application prospects in rice breeding for disease resistance and panicle improvement.

CONCLUSIONS

We report the map-based cloning and functional characterization of SPR9, which encodes a 60 S ribosomal protein that regulates spreading panicles and affects the resistance to false smut in rice.

Microglia-containing cerebral organoids derived from induced pluripotent stem cells for the study of neurological diseases

Microglia play an important role in neuroinflammation and neurodegeneration. Here, we report an approach for generating microglia-containing cerebral organoids derived from human pluripotent stem cells involving the supplementation of growth factors (FGF, EGF, heparin) and 10% CO2 culture conditions. Using this platform, Western Pacific Amyotrophic Lateral Sclerosis and Parkinsonism-Dementia Complex (ALS-PDC) cerebral organoids were generated from patient-derived induced pluripotent stem cells (iPSCs). These ALS-PDC-affected organoids had more reactive astrocytes and M1 microglia, and had fewer M2 microglia than their unaffected counterparts, leading to impaired microglia-mediated phagocytosis. RNA-seq analysis of ALS-PDC and control organoids indicated that the most significant changes were microglia- and astrocyte-related genes (IFITM1/2, TGF-β, and GFAP). The most significantly downregulated pathway was type I interferon signaling. Interferon-gamma supplementation increased IFITM expression, enhanced microglia-mediated phagocytosis, and reduced beta-amyloid accumulation in ALS-PDC-affected network. The results demonstrated the feasibility of using microglia-containing organoids for the study of neurodegenerative diseases.

Plastid development of albino viviparous propagules in the woody mangrove species of Kandelia obovata

The process of plastids developing into chloroplasts is critical for plants to survive. However, this process in woody plants is less understood. Kandelia obovata Sheue, Liu & Yong is a viviparous mangrove species; the seeds germinate on the maternal tree, and the hypocotyls continue to develop into mature propagules. We identified rare albino propagules through field observation among normal green and brown ones. Toward unveiling the propagule plastid development mechanism, albino propagule leaves only have etioplasts, low photosynthesis rates, and drastically reduced chlorophyll a/b and carotenoid contents, but with increased superoxide dismutase activities. To identify candidate genes controlling propagule plastid development, a genome-wide association study (GWAS) was performed between the albino and green propagules. Twenty-five significant single nucleotide polymorphisms (SNPs) were associated with albino propagule plastid development, the most significant SNPs being located on chromosomes 1 and 5. Significant differentially expressed genes were identified in porphyrin and chlorophyll metabolisms, carotenoid and flavonoid biosynthesis by combining transcriptome and GWAS data. In particular, KoDELLAs, encoding a transcription factor and KoCHS, encoding chalcone synthase, may be essential to regulate the albino propagules plastid development through weakened chlorophyll and flavonoid biosynthesis pathways while promoting chlorophyll degradation. Our results provide insights into genetic mechanisms regulating propagule plastid development in woody plants.

Analysis of a rice blast resistance gene Pita-Fuhui2663 and development of selection marker

Rice blast is a detrimental rice disease caused by the fungus Magnaporthe oryzae. Here, we identified a resistance gene from the rice cultivar Fuhui 2663 which is resistant to the rice blast isolate KJ201. Through isolated population analyses and sequencing approaches, the candidate gene was traced to chromosome 12. With the use of a map-based cloning strategy, the resistance gene was ultimately mapped to an 80-kb resistance locus region containing the Pita gene. Candidate gene prediction and cDNA sequencing indicated that the target resistance gene in Fuhui 2663 was allelic to Pita, thus being referred to as Pita-Fuhui2663 hereafter. Further analysis showed that the Fuhui 2663 protein had one amino acid change: Ala (A) residue 918 in Pita-Fuhui2663 was replaced by Ser (S) in Pita-S, leading to a significant change in the 3D structure of the Pita-S protein. CRISPR/Cas9 knockout experiments confirmed that Pita-Fuhui2663 is responsible for the resistance phenotype of Fuhui 2663. Importantly, Pita-Fuhui2663 did not affect the main agronomic traits of the variety compared to the Pita gene as verified by knockout experiments, indicative of potential applications of Pita-Fuhui2663 in broader breeding programs. Furthermore, a Pita-Fuhui2663-dCAPS molecular marker with good specificity and high efficiency was developed to facilitate rice breeding for resistance to this devastating disease.

[Application of multiple post labeling delay time arterial spin labeling imaging in the quantitative blood flow analysis of brain subregions in healthy adults]

Objective: To explore the normal ranges of perfusion parameters between cerebral hemisphere, cerebellar hemisphere and brain anatomical subregions (56 pairs) in different gender and age groups with multiple post labeling delay time (Multi-PLD) arterial spin labeling (ASL) imaging. Methods: From November 2020 to December 2020, 42 healthy adult volunteers (Male 25, Female 17) were recruited to perform 7 PLD ASL imaging, including 21 young adults (15 males and 6 females, aged 23-35 years) and 21 seniors (10 males and 11 females, aged 36-74 years). The data was processed offline by Cereflow software to obtain arterial arrival time (ATT) and corrected cerebral blood flow (CBF) and cerebral blood volume (CBV) perfusion parameters. SimpleITK standardization function was used to standardize the calculated perfusion image according to the anatomical automatic labeling (AAL) template. Therefore, CBF, ATT, CBV perfusion values of brain subregions were obtained. Paired samples t test, Wilcoxon rank sum test, independent samples t test and Mann-Whitney U test were used to compare the differences of perfusion parameters in the cerebral hemisphere, the cerebellar hemisphere, brain subregions depending on side, gender and age. Pearson correlation analysis was used to compare the correlations of perfusion parameters with age. Results: CBF in 62.5% (35/56) subregions and CBV in 44.6% (25/56) subregions were higher in right side than those in left side. ATT in most brain anatomical subregions (16/56) were higher in left side. The CBF [(35.30±8.31) vs. (34.34±7.53) ml·100g^-1·min^-1, P=0.021], CBV [(0.47±0.11) vs. (0.45±0.09) ml/100g, P<0.001], ATT [(1.30±0.10) vs. (1.24±0.11) s, P<0.001] in left cerebellar hemisphere were higher than that of right side. The CBF (28/56) of cerebral hemisphere, cerebellar hemisphere and brain subregions was higher in females than that in males, while ATT in 83.9% (47/56) subregions was lower than that in males (all P<0.05). CBV in female subjects was higher only in 5 brain regions (superior occipital gyrus, middle occipital gyrus, inferior occipital gyrus, superior parietal gyrus and cerebelum_7b) (all P<0.05). In young subjects, CBF in 44.6% (25/56) subregions and CBV in 33.9% (19/56) subregions were higher than those in the senior group (all P<0.05). The ATT in most subregions in young group were lower than those in senior group, but the difference was statistically significant only in rectus gyrus (P=0.026) and paracentral lobule (P=0.006). The CBF (r=-0.430, P=0.005) and CBV (r=-0.327, P=0.035) of cerebral hemisphere were negatively correlated with age. The CBF (24/25, r range:-0.497 --0.343, all P<0.05) and CBV (16/19, r range:-0.474 --0.322, all P<0.05) in most subregions were negatively correlated with age, while ATT was positively correlated (gyrus rectus: r=0.311, P=0.045; paracentral lobule: r=0.392, P=0.010). Conclusions: Multi-PLD ASL imaging could be applied for quantitative analysis of brain perfusion. The perfusion parameters of anatomical subregions are different depending on side, gender, and age.

[Applications of the NDR and DIAL models for risk prediction on cardiovascular disease in patients with type 2 diabetes in Ningbo]

Objective: To validate the performance of cardiovascular risk prediction models based on the Sweden National Diabetes Register (NDR) and Diabetes Lifetime-perspective prediction (DIAL) model for assessing risks of 5-year and 10-year cardiovascular disease (CVD) among Chinese patients with type 2 diabetes. Methods: Based on the Chinese Electronic Health Records Research in Yinzhou study, 83 503 patients with type 2 diabetes aged 30-75 years without a history of CVD at baseline were included from January 1, 2010 to December 31, 2020. Recalibrated NDR model was used to estimate 5-year risk, while the recalibrated DIAL model was used to predict 5-year and 10-year risks. The competing events adjusted Kaplan-Meier analysis was used to obtain the observed cardiovascular events. Discrimination C statistics evaluated model accuracy, calibration χ² value, and calibration plots. Results: Through a median follow-up of 7.0 years, 7 326 cardiovascular events, and 2 937 non-vascular deaths were identified among a total of 83 503 subjects. The recalibrated NDR model overestimated 5-year risk by 39.4% in men and 8.6% in women, whereas the overestimation for the recalibrated DIAL model was 14.6% in men and 50.1% in women. The DIAL model had a better discriminative ability (C-statistic=0.681, 95%CI: 0.672-0.690) than NDR model (C-statistic=0.667, 95%CI: 0.657-0.677) in 5-year risk prediction for men, and the models had a similar ability for women (C-statistic=0.699, 95%CI: 0.690-0.708 for NDR and C-statistic=0.698, 95%CI: 0.689-0.706 for DIAL). The prediction accuracy of the DIAL model was improved in the 10-year risk, with the underestimation being 1.6% for men and the overestimation being 12.8% for women. Conclusions: Both recalibrated NDR and DIAL models overestimated 5-year cardiovascular risk in Chinese patients with type 2 diabetes, while the higher overestimation was shown using the DIAL model. However, the improvement was found in predicting 10-year CVD risk using the DIAL model, which suggested the value of lifetime risk prediction and indicated the need for research on the lifetime risk prediction model for cardiovascular risk assessment in Chinese patients with type 2 diabetes.

Signatures of mRNA Alternative Polyadenylation in Arabidopsis Leaf Development

Alternative polyadenylation (APA) of pre-mRNA is an important co-transcriptional mechanism that modulates gene expression, leading to transcriptomic and functional diversities. The role of APA in Arabidopsis leaf development, however, remains elusive. We applied a poly(A)-tag sequencing (PAT-seq) technique to characterize APA-mediated regulation events in cotyledon and in five stages of true leaf development. Over 60% APA was identified in genes expressed in leaves, consistent with the results in previous publications. However, a reduced APA level was detected in younger leaves, reaching 44% in the 18th true leaf. Importantly, we also found that >70% of the poly(A) site usages were altered in the second true leaf relative to the cotyledon. Compared with the cotyledon, more genes in the second true leaf tended to use the distal site of 3′UTR, but this was not found in pairwise comparison among other true leaves. In addition, a significant APA gene was found to be decreased in a pairwise comparison among true leaves, including differentially expressed genes. The APA genes identified herein were associated with specific biological processes, including metabolic and cellular processes and response to stimuli and hormones. These results provide a new insight into the regulation of Arabidopsis leaf development through APA.

[Impact of composite clinical worsening events on outcome of patients with pulmonary arterial hypertension associated with congenital heart disease]

Objective: To explore the impact of composite clinical worsening (cCW) events and its components on the prognosis of patients with pulmonary arterial hypertension associated with congenital heart disease (CHD-PAH). Methods: This is a retrospective study. Patients who were diagnosed with CHD-PAH in Beijing Anzhen Hospital between January 2007 and July 2018, were included, and their baseline clinical data including demographic, clinical manifestations and New York Heart Association (NYHA) classification were collected retrospectively. All-cause deaths and clinical worsening events were recorded, which included syncope, PAH related hospitalization, NYHA classification deterioration and ≥ 2 PAH related clinical symptoms (dyspnea, hemoptysis, edema, chest pain, palpitations, cyanosis) appearance/progress. Three kinds of cCW events were defined: cCW1 (included PAH related hospitalization, NYHA classification deterioration), cCW2 (increased syncope on the basis of cCW1) and cCW3 (increased ≥ 2 PAH related clinical symptoms appearance/progress on the basis of cCW2). The Kaplan-Meier survival curve was used to analyze the long-term survival of the included patients. Univariate and multivariate Cox regression models were used to evaluate the impact of cCW events and their components on the risk of all-cause mortality. Results: A total of 525 patients with CHD-PAH were included in this study. The median age at diagnosis was 20.7 (11.2, 30.3) years. There were 43.8% children (<18 years), and 68.8% female patients. There were 431 patients (82.1%) with NYHA classification II. A total of 180 patients had PAH symptoms at diagnosis. The median follow-up time was 4.5 (2.6, 6.7) years. Forty-seven patients (9.0%) died during the follow-up period. Survival rates at 1, 5 and 10 years after diagnosis of PAH were 98.0%, 89.9% and 84.4%, respectively. Cox multivariate analysis showed that NYHA classification deterioration (HR=3.901, 95%CI 1.863-8.169, P<0.001), ≥2 PAH symptoms appearance/progress (HR=4.458, 95%CI 1.870-10.625, P<0.001), PAH-related hospitalization (HR=4.058, 95%CI 1.851-8.896, P<0.001) and syncope (HR=11.313, 95%CI 4.860-26.332, P<0.001) were independent predictors of increased risk of death. All 3 kinds of cCW events were significantly associated with the significantly increased risk of death, and cCW2 was highly predictive to increased risk of death (HR=15.476, 95%CI 4.346-37.576, P<0.001). Conclusions: The overall long-term prognosis of CHD-PAH patients in this study is relatively good. cCW events and its components (NYHA classification deterioration, ≥2 PAH symptoms occurrence/worsening, PAH-related hospitalization and syncope) have adverse influence on all-cause death in this patient cohort.

Phenotypic and Methylome Responses to Salt Stress in Arabidopsis thaliana Natural Accessions

Salt stress threatens plant growth, development and crop yields, and has become a critical global environmental issue. Increasing evidence has suggested that the epigenetic mechanism such as DNA methylation can mediate plant response to salt stress through transcriptional regulation and transposable element (TE) silencing. However, studies exploring genome-wide methylation dynamics under salt stress remain limited, in particular, for studies on multiple genotypes. Here, we adopted four natural accessions of the model species Arabidopsis thaliana and investigated the phenotypic and genome-wide methylation responses to salt stress through whole-genome bisulfite sequencing (WGBS). We found that salt stress significantly changed plant phenotypes, including plant height, rosette diameter, fruit number, and aboveground biomass, and the change in biomass tended to depend on accessions. Methylation analysis revealed that genome-wide methylation patterns depended primarily on accessions, and salt stress caused significant methylation changes in ∼ 0.1% cytosines over the genomes. About 33.5% of these salt-induced differential methylated cytosines (DMCs) were located to transposable elements (TEs). These salt-induced DMCs were mainly hypermethylated and accession-specific. TEs annotated to have DMCs (DMC-TEs) across accessions were found mostly belonged to the superfamily of Gypsy, a type II transposon, indicating a convergent DMC dynamic on TEs across different genetic backgrounds. Moreover, 8.0% of salt-induced DMCs were located in gene bodies and their proximal regulatory regions. These DMCs were also accession-specific, and genes annotated to have DMCs (DMC-genes) appeared to be more accession-specific than DMC-TEs. Intriguingly, both accession-specific DMC-genes and DMC-genes shared by multiple accessions were enriched in similar functions, including methylation, gene silencing, chemical homeostasis, polysaccharide catabolic process, and pathways relating to shifts between vegetative growth and reproduction. These results indicate that, across different genetic backgrounds, methylation changes may have convergent functions in post-transcriptional, physiological, and phenotypic modulation under salt stress. These convergent methylation dynamics across accession may be autonomous from genetic variation or due to convergent genetic changes, which requires further exploration. Our study provides a more comprehensive picture of genome-wide methylation dynamics under salt stress, and highlights the importance of exploring stress response mechanisms from diverse genetic backgrounds.

Divergence in the Regulation of the Salt Tolerant Response Between Arabidopsis thaliana and Its Halophytic Relative Eutrema salsugineum by mRNA Alternative Polyadenylation

Salt tolerance is an important mechanism by which plants can adapt to a saline environment. To understand the process of salt tolerance, we performed global analyses of mRNA alternative polyadenylation (APA), an important regulatory mechanism during eukaryotic gene expression, in Arabidopsis thaliana and its halophytic relative Eutrema salsugineum with regard to their responses to salt stress. Analyses showed that while APA occurs commonly in both Arabidopsis and Eutrema, Eutrema possesses fewer APA genes than Arabidopsis (47% vs. 54%). However, the proportion of APA genes was significantly increased in Arabidopsis under salt stress but not in Eutrema. This indicated that Arabidopsis is more sensitive to salt stress and that Eutrema exhibits an innate response to such conditions. Both species utilized distal poly(A) sites under salt stress; however, only eight genes were found to overlap when their 3' untranslated region (UTR) lengthen genes were compared, thus revealing their distinct responses to salt stress. In Arabidopsis, genes that use distal poly(A) sites were enriched in response to salt stress. However, in Eutrema, the use of poly(A) sites was less affected and fewer genes were enriched. The transcripts with upregulated poly(A) sites in Arabidopsis showed enriched pathways in plant hormone signal transduction, starch and sucrose metabolism, and fatty acid elongation; in Eutrema, biosynthetic pathways (stilbenoid, diarylheptanoid, and gingerol) and metabolic pathways (arginine and proline) showed enrichment. APA was associated with 42% and 29% of the differentially expressed genes (DE genes) in Arabidopsis and Eutrema experiencing salt stress, respectively. Salt specific poly(A) sites and salt-inducible APA events were identified in both species; notably, some salt tolerance-related genes and transcription factor genes exhibited differential APA patterns, such as CIPK21 and LEA4-5. Our results suggest that adapted species exhibit more orderly response at the RNA maturation step under salt stress, while more salt-specific poly(A) sites were activated in Arabidopsis to cope with salinity conditions. Collectively, our findings not only highlight the importance of APA in the regulation of gene expression in response to salt stress, but also provide a new perspective on how salt-sensitive and salt-tolerant species perform differently under stress conditions through transcriptome diversity.

Alternative polyadenylated mRNAs behave as asynchronous rhythmic transcription in Arabidopsis

Alternative polyadenylation (APA) is a widespread post-transcriptional modification method that changes the 3' ends of transcripts by altering poly(A) site usage. However, the longitudinal transcriptomic 3' end profile and its mechanism of action are poorly understood. We applied diurnal time-course poly(A) tag sequencing (PAT-seq) for Arabidopsis and identified 3284 genes that generated both rhythmic and arrhythmic transcripts. These two classes of transcripts appear to exhibit dramatic differences in expression and translation activisty. The asynchronized transcripts derived by APA are embedded with different poly(A) signals, especially for rhythmic transcripts, which contain higher AAUAAA and UGUA signal proportions. The Pol II occupancy maximum is reached upstream of rhythmic poly(A) sites, while it is present directly at arrhythmic poly(A) sites. Integrating H3K9ac and H3K4me3 time-course data analyses revealed that transcriptional activation of histone markers may be involved in the differentiation of rhythmic and arrhythmic APA transcripts. These results implicate an interplay between histone modification and RNA 3'-end processing, shedding light on the mechanism of transcription rhythm and alternative polyadenylation.

Intragenic heterochromatin-mediated alternative polyadenylation modulates miRNA and pollen development in rice

Despite a much higher proportion of intragenic heterochromatin-containing genes in crop genomes, the importance of intragenic heterochromatin in crop development remains unclear. Intragenic heterochromatin can be recognised by a protein complex, ASI1-AIPP1-EDM2 (AAE) complex, to regulate alternative polyadenylation. Here, we investigated the impact of rice ASI1 on global poly(A) site usage through poly(A) sequencing and ASI1-dependent regulation on rice development. We found that OsASI1 is essential for rice pollen development and flowering. OsASI1 dysfunction has an important impact on global poly(A) site usage, which is closely related to heterochromatin marks. Intriguingly, OsASI1 interacts with the intronic heterochromatin of OsXRNL, a nuclear XRN family exonuclease gene involved in the processing of an miRNA precursor, to promote the processing of full-length OsXRNL and regulate miRNA abundance. We found that OsASI1-mediated regulation of pollen development partially depends on OsXRNL. Finally, we characterised the rice AAE complex and its involvement in alternative polyadenylation and pollen development. Our findings help to elucidate an epigenetic mechanism governing miRNA abundance and rice development, and provide a valuable resource for studying the epigenetic mechanisms of many important processes in crops.

Global gene expression signatures in response to citrate-coated silver nanoparticles exposure

Silver nanoparticles (AgNPs) are widely used in medical and commercial products for their unique antibacterial functions. However, the impact of AgNPs on human neural development is not well understood. To investigate the effect of AgNPs on human neural development, various doses of 20 nm citrate-coated AgNP (AgSC) were administered to human embryonic stem cell derived neural progenitors during the neuronal differentiation. Immunofluorescence staining with neuronal progenitor markers SOX2 (sex determining region Y-box 2) and Nestin (VI intermediate filament protein) showed that AgSC inhibited rosette formation, neuronal progenitor proliferation, and neurite outgrowth. Furthermore, AgSC promoted astrocyte activation and neuronal apoptosis. These adverse effects can be partially recovered with ascorbic acid. A genome-wide transcriptome analysis of both AgSC treated and untreated samples indicated that the most up-graduated genes were a group of Metallothionein (1F, 1E, 2A) proteins, a metal-binding protein that plays an essential role in metal homeostasis, heavy metal detoxification, and cellular anti-oxidative defence. The most significantly down-regulated genes were neuronal differentiation 6 (NEUROD6) and fork head box G1 (FOXG1). GO analyse indicated that the regulation of cholesterol biosynthetic process, neuron differentiation, synapse organization and pattern specification, oliogenesis, and neuronal apoptosis were the most impacted biological processes. KEGG pathway analyse showed that the most significantly impacted pathways were C5 isoprenoid, axon guidance, Notch, WNT, RAS-MAPK signalling pathways, lysosome, and apoptosis. Our data suggests that AgSCs interfered with metal homeostasis and cholesterol biosynthesis which induced oxidative stress, inhibited neurogenesis, axon guidance, and promoted apoptosis. Supplementation with ascorbic acid could act as an antioxidant to prevent AgSC-mediated neurotoxicity.

QuantifyPoly(A): reshaping alternative polyadenylation landscapes of eukaryotes with weighted density peak clustering

The dynamic choice of different polyadenylation sites in a gene is referred to as alternative polyadenylation, which functions in many important biological processes. Large-scale messenger RNA 3' end sequencing has revealed that cleavage sites for polyadenylation are presented with microheterogeneity. To date, the conventional determination of polyadenylation site clusters is subjective and arbitrary, leading to inaccurate annotations. Here, we present a weighted density peak clustering method, QuantifyPoly(A), to accurately quantify genome-wide polyadenylation choices. Applying QuantifyPoly(A) on published 3' end sequencing datasets from both animals and plants, their polyadenylation profiles are reshaped into myriads of novel polyadenylation site clusters. Most of these novel polyadenylation site clusters show significantly dynamic usage across different biological samples or associate with binding sites of trans-acting factors. Upstream sequences of these clusters are enriched with polyadenylation signals UGUA, UAAA and/or AAUAAA in a species-dependent manner. Polyadenylation site clusters also exhibit species specificity, while plants ones generally show higher microheterogeneity than that of animals. QuantifyPoly(A) is broadly applicable to any types of 3' end sequencing data and species for accurate quantification and construction of the complex and dynamic polyadenylation landscape and enables us to decode alternative polyadenylation events invisible to conventional methods at a much higher resolution.

QPAT-seq, a rapid and deduplicatable method for quantification of poly(A) site usages

Alternative polyadenylation (APA) is an essential regulatory mechanism for gene expression. The next generation sequencing provides ample opportunity to precisely delineate APA sites genome-wide. Various methods for profiling transcriptome-wide poly(A) sites were developed. By comparing available methods, the ways for adding sequencing adaptors to fit with the Illumina sequencing platform are different. These methods have identified more than 50% genes that undergo APA in eukaryotes. However, due to the unbalanced PCR during library preparation, accurate quantification of poly(A) sites is still a challenge. Here, we describe an updated poly(A) tag sequencing method that incorporates unique molecular identifier (UMI) into the adaptor for removing quantification bias induced by PCR duplicates. Hence, quantification of poly(A) site usages can be achieved by counting UMIs. This protocol, quantifying poly(A) tag sequencing (QPAT-seq), can be finished in 1 day with reduced cost, and is particularly useful for application with a large number of samples.

Genome-wide distribution and functions of the AAE complex in epigenetic regulation in Arabidopsis

Heterochromatin is widespread in eukaryotic genomes and has diverse impacts depending on its genomic context. Previous studies have shown that a protein complex, the ASI1-AIPP1-EDM2 (AAE) complex, participates in polyadenylation regulation of several intronic heterochromatin-containing genes. However, the genome-wide functions of AAE are still unknown. Here, we show that the ASI1 and EDM2 mostly target the common genomic regions on a genome-wide level and preferentially interacts with genetic heterochromatin. Polyadenylation (poly(A) sequencing reveals that AAE complex has a substantial influence on poly(A) site usage of heterochromatin-containing genes, including not only intronic heterochromatin-containing genes but also the genes showing overlap with heterochromatin. Intriguingly, AAE is also involved in the alternative splicing regulation of a number of heterochromatin-overlapping genes, such as the disease resistance gene RPP4. We provided evidence that genic heterochromatin is indispensable for the recruitment of AAE in polyadenylation and splicing regulation. In addition to conferring RNA processing regulation at genic heterochromatin-containing genes, AAE also targets some transposable elements (TEs) outside of genes (including TEs sandwiched by genes and island TEs) for epigenetic silencing. Our results reveal new functions of AAE in RNA processing and epigenetic silencing, and thus represent important advances in epigenetic regulation.

Adaptive roots of mangrove Avicennia marina: Structure and gene expressions analyses of pneumatophores

The Avicennia marina is a mangrove species widely distributed throughout the tropical and subtropical intertidal wetlands. To adapt to adverse tidal waves and hypoxia environments, A. marina has evolved a sophisticated root system to better secure itself on the muddy soil with downward-grown anchor roots and upward-grown aerial roots, called pneumatophores. However, the process behind the development of a negative-gravitropic pneumatophore is not understood. Paraffin sections reveal anatomical differences among the shoots, anchor roots, and gas exchanging pneumatophores, clearly reflecting their functional diversions. The pneumatophore, in particular, contains abundant aerenchyma tissues and a thin cap structure at the tip. Transcriptomic analyses of both anchor roots and pneumatophores were performed to elucidate gene expression dynamics during the formation of pneumatophores. The results show that the plant hormone auxin regulates multiple different root initiations. The auxin related gene IAA19 plays a key role in pneumatophore development while the interaction of ethylene and abscisic acid is important for aerenchyma formation. Moreover, the molecular mechanisms behind pneumatophore anti-gravitropic growth may be regulated by the reduced strength of the statolith formation signaling pathway. These results shed light on the mechanistic understanding of pneumatophore formation in mangrove plants.

scDAPA: detection and visualization of dynamic alternative polyadenylation from single cell RNA-seq data

MOTIVATION

Alternative polyadenylation (APA) plays a key post-transcriptional regulatory role in mRNA stability and functions in eukaryotes. Single cell RNA-seq (scRNA-seq) is a powerful tool to discover cellular heterogeneity at gene expression level. Given 3' enriched strategy in library construction, the most commonly used scRNA-seq protocol-10× Genomics enables us to improve the study resolution of APA to the single cell level. However, currently there is no computational tool available for investigating APA profiles from scRNA-seq data.

RESULTS

Here, we present a package scDAPA for detecting and visualizing dynamic APA from scRNA-seq data. Taking bam/sam files and cell cluster labels as inputs, scDAPA detects APA dynamics using a histogram-based method and the Wilcoxon rank-sum test, and visualizes candidate genes with dynamic APA. Benchmarking results demonstrated that scDAPA can effectively identify genes with dynamic APA among different cell groups from scRNA-seq data.

AVAILABILITY AND IMPLEMENTATION

The scDAPA package is implemented in Shell and R, and is freely available at https://scdapa.sourceforge.io.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Adaptive transgenerational effects remain significant

The comment by Sánchez-Tójar et al. (2020, Ecol Lett) questioned the methodology, transparency and conclusion of our study (Ecol Lett, 22, 2019, 1976). The comment has overlooked important evolutionary assumptions in their reanalysis, and the issues raised were in fact dealt with through the peer-review process. Far from being biased, the key conclusion of our meta-analysis still stands; transgenerational effects are largely adaptive.

HDA6-dependent histone deacetylation regulates mRNA polyadenylation in Arabidopsis

Eukaryotic histone deacetylation, critical for maintaining nucleosome structure and regulating gene expression, is mediated by histone deacetylases (HDACs). Although nucleosomes have been reported to regulate mRNA polyadenylation in humans, the role of HDACs in regulating polyadenylation has not been uncovered. Taking advantage of phenotypic studies on Arabidopsis, HDA6 (one of HDACs) was found to be a critical part of many biological processes. Here, we report that HDA6 affects mRNA polyadenylation in Arabidopsis. Poly(A) sites of up-regulated transcripts are closer to the histone acetylation peaks in hda6 compared to the wild-type Col-0. HDA6 is required for the deacetylation of histones around DNA on nucleosomes, which solely coincides with up-regulated or uniquely presented poly(A) sites in hda6. Furthermore, defective HDA6 results in an overrepresentation of the canonical poly(A) signal (AAUAAA) usage. Chromatin loci for generating AAUAAA-type transcripts have a comparatively low H3K9K14ac around poly(A) sites when compared to other noncanonical poly(A) signal–containing transcripts. These results indicate that HDA6 regulates polyadenylation in a histone deacetylation–dependent manner in Arabidopsis.

[Risk factors for death and the clinical features of different subtypes of patients with pulmonary arterial hypertension related to congenital heart disease]

Objective: To explore the risk factors for death in patients with pulmonary arterial hypertension related to congenital heart disease (PAH-CHD) and the clinical characteristics of different subtypes in patients with PAH-CHD. Methods: It was a retrospective study. A total of 507 PAH-CHD patients, who were hospitalized in the Department of Pediatric Cardiology of Beijing Anzhen Hospital between September 2005 and May 2019, were included. Patients were divided into 4 subgroups: (1) Eisenmenger syndrome(ES) group. (2) PAH associated with prevalent systemic-to-pulmonary shunts(SP) group. (3) PAH associated with small defects(SD) group. (4) PAH after defect correction(CD) group. According to the complexity of cardiac malformation, patients were divided into simple-medium complex malformation group and complex malformation group. According to the location of shunts, patients were divided into pre-tricuspid group, post-tricuspid group, and mixed group or complex deformity group. Baseline clinical data of patients were collected from the electronic medical record system. Demographic data (age, gender, etc.), percutaneous oxygen saturation(SPO(2)), New York Heart Association(NYHA) cardiac function classification, 6 minutes walking distance(6MWD), and B type natriuretic peptide(BNP), systolic pulmonary arterial pressure(sPAP) estimated by echocardiography and mean pulmonary artery pressure (mPAP), mean right atrial pressure(mRAP), cardiac index(CI), and calculated pulmonary vascular resistance (PVR) estimated by right heart catheterization were compared among various groups. The results of regular follow-up of all enrolled patients were collected, including the status of monotherapy or combination of PAH-targeted drugs during the follow-up period, cardiac-related adverse events(hemopysis, syncope, edema, arrhythmia, etc.) and primary endpoint event(all-cause death) were obtained and analyzed. Risk factors for all-cause death were analyzed using univariate and multivariate Cox regression analysis model. Results: The median age at diagnosis was 23.1(13.9,32.1) years, 345 cases(68.0%) were female. Two hunderds and thirty-five cases(46.4%) were diagnosed with ES; 193 cases(38.1%) were diagnosed with CD, 47 cases (9.3%) were diagnosed with SD. Among them, 32 cases(6.3%) were in the SP group. All 507 patients underwent echocardiography examination, there were significant differences in sPAP among different clinical subgroups(P<0.001). A total of 289 patients(57.0%) received right heart catheterization examination, the results showed that the ES group had the highest mPAP and PVR and the lowest mRAP(all P<0.001), the CD group had the highest mRAP and CI(both P<0.001). The 6MWD in the ES group was significantly shorter than that in the SP, SD, and CD groups(all P<0.001). The proportion of patients with NYHA class Ⅲ/Ⅳ was higher in SD group than in SP group(P<0.001), which was similar between SD, ES and CD groups (P values were 0.077 and 0.072, respectively). At admission, the proportion of patients with NYHA class Ⅰ/Ⅱwas the highest in SP group(96.9% (31/32) ), followed by CD group (85.5%(165/193)) and the ES group(85.1%(200/235)), and the SD group(75.0%(35/47)). The BNP level at admission was also higher in SD group than in SP, ES and CD groups(P<0.001). Of the 507 patients, 379(74.8%) patients received PAH-targeted drug therapy at the last follow-up, and the treatment plan was mainly monotherapy(75.7%(287/379)). The median follow-up time was 3.6(2.0, 5.6) years and 37(7.3%) patients died, including 13 in the CD group, 17 in the ES group, and 7 in the SD group. No deaths occurred in the SP group. Right heart failure was the most common cause of death(11(29.7%)), followed by severe hemoptysis dyspnea(7(18.9%)), sudden cardiac death(6(16.2%)), and pulmonary hypertensive crisis(4(10.8%)). Kaplan-Meier curve showed that survival rates of end-point-free events at 1, 3, 5 and 10 years after diagnosis of PAH were 98.0%, 95.4%, 89.9%, and 84.4%, respectively; there were statistically significant differences in survival among the subgroups(P=0.026); there was no significant difference in the survival rate between the ES group and the CD group(P=0.918), and both were higher than the SD group(P values were 0.011 and 0.013, respectively). Univariate Cox regression analysis showed that NYHA class Ⅲ/Ⅳ and BNP>100 ng/L at admission were the risk factors for all-cause death in patients with PAH-CHD(HR=6.452, 95%CI 3.378-12.346, P<0.001, and HR=2.481, 95%CI 1.225-5.025, P=0.012). Multivariate Cox regression analysis showed that NYHA class Ⅲ/Ⅳ was an independent risk factor for all-cause death in patients with PAH-CHD(HR=4.998, 95%CI 1.246-20.055, P=0.023). Conclusions: PAH-CHD patients with different clinical subtypes have different clinical symptoms, cardiac functional class, hemodynamic characteristics, and mid to long-term survival rates. SP patients have the best prognosis, outcome of ES and CD patients is similar, and SD patients have the worst prognosis. NYHA class Ⅲ/Ⅳ is an independent risk factor for all-cause death in patients with PAH-CHD.

The potential biological functions of circular RNAs during the initiation of atresia in pig follicles

The specific expression profile and function of circular RNAs (circRNAs) in mammalian ovarian follicles, especially during the atresia process, are unclear. In this study, genome-wide deep circRNA sequencing was applied to screen circRNAs in healthy and early atretic antral follicles in pig ovaries. A total of 40,567 distinct circRNAs were identified in follicles, among which 197 circRNAs (108 upregulated and 89 downregulated) were significantly shifted during the early atresia process. Most differentially expressed circRNAs (DECs) lacked protein-coding potential. Annotation analysis of the DECs revealed 162 known host genes, or noncoding RNAs, and 10 intergenic regions. The key pathways in which these host genes are involved include the focal adhesion-PI3K-Akt-mTOR signaling pathway, vascular endothelial growth factor A (VEGFA)-vascular endothelial growth factor receptor 2 signaling pathway and transforming growth factor-beta signaling pathway. Further comparison analysis between host genes of DECs and the differentially expressed linear messenger RNA transcripts revealed the cotranscription of circRNAs and their linear mRNAs in inhibin beta units (INHBA and INHBB), glutathione S-transferase (GSTA1), and VEGFA. In addition, we predicted 196 pairs of potential circRNA-micro RNA (miRNA) interactions among 77 DECs and 101 porcine miRNAs. We have identified 16 functional miRNAs by comparing the 101 miRNAs to the functional miRNAs reported in mammal ovarian follicle atresia and granulosa cell apoptosis studies. Our study adds new knowledge to circRNA distribution profiles in pig ovarian follicles, offers a valuable reference for transcriptomic profiles in the initiation of follicular atresia, highlights warranted circRNAs for further functional investigation, and provides possible biomarkers for ovarian dysfunctions.

[The pH-Sensitive Potassium Channel TASK-1 Is a Chemosensor for Central Respiratory Regulation in Rats]

TWIK-related acid-sensitive potassium channel-1 (TASK-1) is a "leak" potassium channel sensitive to extracellular protons. It contributes to setting the resting potential in mammalian neurons. TASK-1 channels are widely expressed in respiratory-related neurons in the central nervous system. Inhibition of TASK-1 by extracellular acidosis can depolarize and increase the excitability of these cells. Here we describe the distribution of TASK-1 in the rat brainstem and show that TASK-1 mRNAs are present in respiratory-related nuclei in the ventrolateral medulla, which have been proposed as neural substrates for central chemo-reception in rats. After inhalation of 8% CO2 for 30 and 60 min, TASK-1 mRNA levels in positive-expression neurons were remarkably upregulated. Injection of the TASK-1 blocker anandamide (AEA) into the rat lateral cerebral ventricle, showed a significant excitement of respiratory at 10 min posttreatment, with a marked decrease in inspiratory and expiratory durations and an increased frequency of respiration. We suggest that TASK-1 channel may serve as a chemosensor for in central respiration and may contribute to pH-sensitive respiratory effects. TASK-1 channel might be an attractive candidate for sensing H^(+)/CO2 in several respiratory-related nuclei in the brainstem. It is likely that TASK-1 participates in pH-sensitive chemical regulation in the respiratory center under physiological and pathological conditions.

Discovery of alternative polyadenylation dynamics from single cell types

Alternative polyadenylation (APA) occurs in the process of mRNA maturation by adding a poly(A) tail at different locations, resulting increased diversity of mRNA isoforms and contributing to the complexity of gene regulatory network. Benefit from the development of high-throughput sequencing technologies, we could now delineate APA profiles of transcriptomes at an unprecedented pace. Especially the single cell RNA sequencing (scRNA-seq) technologies provide us opportunities to interrogate biological details of diverse and rare cell types. Despite increasing evidence showing that APA is involved in the cell type-specific regulation and function, efficient and specific laboratory methods for capturing poly(A) sites at single cell resolution are underdeveloped to date. In this review, we summarize existing experimental and computational methods for the identification of APA dynamics from diverse single cell types. A future perspective is also provided.

Deletion of the Capn1 Gene Results in Alterations in Signaling Pathways Related to Alzheimer's Disease, Protein Quality Control and Synaptic Plasticity in Mouse Brain

Calpains represent a family of calcium-dependent proteases participating in a multitude of functions under physiological or pathological conditions. Calpain-1 is one of the most studied members of the family, is ubiquitously distributed in organs and tissues, and has been shown to be involved in synaptic plasticity and neuroprotection in mammalian brain. Calpain-1 deletion results in a number of phenotypic alterations. While some of these alterations can be explained by the acute functions of calpain-1, the present study was directed at studying alterations in gene expression that could also account for these phenotypic modifications. RNA-seq analysis identified 354 differentially expressed genes (DEGs) in brain of calpain-1 knock-out mice, as compared to their wild-type strain. Most DEGs were classified in 10 KEGG pathways, with the highest representations in Protein Processing in Endoplasmic Reticulum, MAP kinase and Alzheimer's disease pathways. Most DEGs were down-regulated and validation of a number of these genes indicated a corresponding decreased expression of their encoded proteins. The results indicate that calpain-1 is involved in the regulation of a significant number of genes affecting multiple brain functions. They also indicate that mutations in calpain-1 are likely to be involved in a number of brain disorders.

[The application of intravoxel incoherent motion diffusion imaging and 3D arterial spin labeling perfusion imaging in the evaluation of acute cerebral infarction]

Objective: To investigate the clinical value of magnetic resonance (MR) intravoxel incoherent motion (IVIM) diffusion imaging and 3D pseudo continuous arterial spin labeling (3D-pcASL) perfusion imaging in the evaluation of acute cerebral infarction. Methods: MR images of 49 patients with unilateral acute cerebral infarction diagnosed and treated in Affiliated Yancheng Hospital of Southeast University Medical College from October 2015 to February 2019 were retrospectively analyzed. High signal infarction area (S(D)) on diffusion image slice with the biggest lesion level and abnormal perfusion area (S(CBF)) on the corresponding level were measured. The presence of ischemic penumbra (IP) was represented by S(CBF)> S(D), and patients were divided into group IP and group non-IP. Regions of interest were set on the infarction core, brain tissue near the edge of the lesion (BNL) and their corresponding contralateral regions. The values of apparent diffusion coefficient (ADC), true diffusion coefficient (D), perfusion related diffusion coefficient (D(*)), perfusion fraction (f) and cerebral blood flow (CBF) of each region of interest were recorded and relative values of infarction lesion to its contralateral region (rADC, rD, rD(*), rf, rCBF) were calculated. Differences of each parameter value between infarction core, BNL and their corresponding contralateral regions and of each relative parameter value between infarction core and BNL, and between the two groups were compared.The differential diagnostic efficacy of relative parameter value with differences between groups was analyzed by receiver operating characteristics (ROC) curve. The correlations of each relative parameter value of 3D-pcASL and IVIM sequences were analyzed. Results: The ADC, D, f and CBF values of infarction core were significantly lower than those of contralateral regions in both groups (all P<0.01). Among all parameters of BNL in both groups, only the CBF value of group IP was significantly lower than that of contralateral region ((27.58±3.53) vs (41.20±5.66) ml·100 g(-1)·min(-1), P<0.01). The rADC, rD, rf and rCBF of infarction core were significantly lower than those of BNL in both groups (all P<0.01). The rCBF of BNL in group IP was significantly lower than that in group non-IP (0.68±0.12 vs 0.97±0.15, P<0.01), and the area under the curve was 0.949, the optimal threshold was 0.823, and the youden index was 0.855 for identifying the two groups. Other relative parameters values of infarction core and BNL had no statistical difference between the two groups. There were positive correlations between rCBF and rADC, rD, rf (r=0.428,0.335,0.565) of infarction core, rADC and rD, rf (r=0.853,0.602) of infarction core, also rADC and rD (r=0.336) of BNL (all P<0.05). Conclusions: IVIM can effectively evaluate the difusion and perfusion information of acute cerebral infarction lesions. However, its perfusion related parameters are not as good as 3D-pcASL in IP evaluation, which should be flexibly selected according to the actual needs of patients' condition evaluation.

Genetic admixture accelerates invasion via provisioning rapid adaptive evolution

Genetic admixture, the intraspecific hybridization among divergent introduced sources, can immediately facilitate colonization via hybrid vigor and profoundly enhance invasion via contributing novel genetic variation to adaption. As hybrid vigor is short-lived, provisioning adaptation is anticipated to be the dominant and long-term profit of genetic admixture, but the evidence for this is rare. We employed the 30 years' geographic-scale invasion of the salt marsh grass, Spartina alterniflora, as an evolutionary experiment and evaluated the consequences of genetic admixture by combining the reciprocal transplant experiment with quantitative and population genetic surveys. Consistent with the documentation, we found that the invasive populations in China had multiple origins from the southern Atlantic coast and the Gulf of Mexico in the US. Interbreeding among these multiple sources generated a "hybrid swarm" that spread throughout the coast of China. In the northern and mid-latitude China, natural selection greatly enhanced fecundity, plant height and shoot regeneration compared to the native populations. Furthermore, genetic admixture appeared to have broken the negative correlation between plant height and shoot regeneration, which was genetically-based in the native range, and have facilitated the evolution of super competitive genotypes in the invasive range. In contrast to the evolved northern and mid-latitude populations, the southern invasive populations showed slight increase of plant height and shoot regeneration compared to the native populations, possibly reflecting the heterotic effect of the intraspecific hybridization. Therefore, our study suggests a critical role of genetic admixture in accelerating the geographic invasion via provisioning rapid adaptive evolution.

Transgenerational effects benefit offspring across diverse environments: a meta-analysis in plants and animals

The adaptive value of transgenerational effects (the ancestor environmental effects on offspring) in changing environments has received much attention in recent years, but the related empirical evidence remains equivocal. Here, we conducted a meta-analysis summarising 139 experimental studies in plants and animals with 1170 effect sizes to investigate the generality of transgenerational effects across taxa, traits, and environmental contexts. It was found that transgenerational effects generally enhanced offspring performance in response to both stressful and benign conditions. The strongest effects are in annual plants and invertebrates, whereas vertebrates appear to benefit mostly under benign conditions, and perennial plants show hardly any transgenerational responses at all. These differences among taxonomic/life-history groups possibly reflect that vertebrates can avoid stressful conditions through their mobility, and longer-lived plants have alternative strategies. In addition to environmental contexts and taxonomic/life-history groups, transgenerational effects also varied among traits and developmental stages of ancestors and offspring, but the effects were similarly strong across three generations of offspring. By way of a more comprehensive data set and a different effect size, our results differ from those of a recent meta-analysis, suggesting that transgenerational effects are widespread, strong and persistent and can substantially impact the responses of plants and animals to changing environments.

Root Hair Single Cell Type Specific Profiles of Gene Expression and Alternative Polyadenylation Under Cadmium Stress

Transcriptional networks are tightly controlled in plant development and stress responses. Alternative polyadenylation (APA) has been found to regulate gene expression under abiotic stress by increasing the heterogeneity at mRNA 3'-ends. Heavy metals like cadmium pollute water and soil due to mining and industry applications. Understanding how plants cope with heavy metal stress remains an interesting question. The Arabidopsis root hair was chosen as a single cell model to investigate the functional role of APA in cadmium stress response. Primary root growth inhibition and defective root hair morphotypes were observed. Poly(A) tag (PAT) libraries from single cell types, i.e., root hair cells, non-hair epidermal cells, and whole root tip under cadmium stress were prepared and sequenced. Interestingly, a root hair cell type-specific gene expression under short term cadmium exposure, but not related to the prolonged treatment, was detected. Differentially expressed poly(A) sites were identified, which largely contributed to altered gene expression, and enriched in pentose and glucuronate interconversion pathways as well as phenylpropanoid biosynthesis pathways. Numerous genes with poly(A) site switching were found, particularly for functions in cell wall modification, root epidermal differentiation, and root hair tip growth. Our findings suggest that APA plays a functional role as a potential stress modulator in root hair cells under cadmium treatment.

Liver Tissue-related Metabolic Mechanism of Different Infusion Volumes for Hemorrhagic Shock

OBJECTIVES

To investigate the curative effects of various infusion volumes on liver-related metabolic mechanism in the treatment of hemorrhagic shock.

METHODS

A severe hemorrhagic shock rabbit model was established in 30 rabbits. The rabbits were randomly divided into three groups： non-infusion group （A）, conventional infusion group （B）, and excessive infusion group （C） （n=10 in each group）. Taking group B as the control, groups A and C were observed for the damage of non-infusion and excessive infusion, respectively. The outcomes in the three groups and their relations with liver tissue metabolism changes were analyzed with gas chromatograph-mass spectrometer （GC-MS）.

RESULTS

The mortality in groups A, B, and C group were 80%, 0%, and 70%, respectively. The liver tissue metabolic profile in group B showed statistically significant difference compared with that in groups A and B. In group C, the levels of 21 metabolites were lower than those in group B, and the levels of 8 metabolites were lower than those in group A. The relative contents of various metabolites were correlated with infusion volumes, and the succinic acid content was associated with death events （P<0.05）.

CONCLUSIONS

The conventional infusion has significant curative effect on hemorrhagic shock. The metabolites of liver tissues with excessive infusion are generally decompensated and have longer survival time than those in non-infusion group, which may caused by the excessive infusion-induced blood volume increase after hemorrhagic shock. Tissue fluid dilution is an important cause of death.

Heavy metal rich stone-processing wastewater inhibits the growth and development of plants

Large amounts of wastewater are generated from stone processing, which are toxic and cause serious environmental and health risks. To quantify the content of stone processing wastewater and estimate its effects on plant growth, we collected water samples from sewage outfall of four stone processing factories and nearby water bodies. The concentration of potential toxic metals were much higher in the wastewater than background controls. Wastewater inhibited plant primary root elongation, lateral root formation, and growth of aerial part. Seedlings treated with the effluents were unhealthy with deep purple leaves and usually died before flowering. Chlorophyll a/b contents and chloroplast number were reduced in those abnormal mesophyll cells. Transcriptional levels were decreased for chloroplast formation genes, but increased for those participated in chloroplast degradation and catabolism. Six out of nine tested senescence-associated genes were up-regulated. Furthermore, our results show that endogenous toxic metal levels indeed increased after wastewater treatment. Altogether, these results indicated that the potential toxic metals rich wastewater had significant inhibition on plant growth and led to senescence-associated program cell death, which could be helpful for the government and enterprises to understand the environmental risks and formulate reasonable wastewater emission standards for the stone processing industry.

[Giant cell reparative granuloma originating from the paranasal sinus: a case report]

A 40-year-old man presented with a 10-year history of nasal obstruction of his left nose, a 1-year history of headache and orbital pain. Radiologically, an extensive paranasal sinus mass was seen. Superiorly ,the cribriform plate was demineralized, and the lesion had intracranial extension with mild mass effect over the basal frontal lobes. Histologic examination revealed a central giant cell reparative granuloma. After endoscopic removal, the patient was symptom free at the 2-month follow-up.

Comparison of Single Piece of Dandruff DNA Extraction under Microscope and EZ-tape Method

OBJECTIVES

To collect single piece of dandruff with microscopes to improve the regular EZ-tape method for DNA extraction and genotyping, increase the utilization of samples, reduce the miss rate as well as the proportion of genotyping results of mixed stains.

METHODS

The insides of the hats worn by two volunteers were stuck by EZ-tape and scotch tape respectively. DNA on EZ-tape was directly extracted using traditional method. Single piece of dandruff was collected from the scotch tapes under microscope. The two kinds of methods were both performed under continuous oscillation and standing digestion, respectively. DNA was extracted through Chelex-100 method, and STR genotypes were obtained after amplification and electrophoresis. The results of STR genotypes obtained by EZ-tape method and single piece of dandruff analytical method were compared.

RESULTS

Miss detections happened in 11 samples （45.8%） by EZ-tape method and only single-source typing results were obtained. Ten samples （41.7%） showed the genotype results of mixed stain and six of which showed allele insertions and deletions. The genotype results were obtained successfully using the single piece of dandruff analytical method, and two samples showed mixed stain genotype. The number of exact typing processed by oscillation was higher than that by standing digestion （ P<0.05）.

CONCLUSIONS

The oscillation during the DNA extraction process is in favour of the DNA releasing. Single piece of dandruff analytical method can be used to obtain single-source STR genotype with high successful ratio and low miss rate. This method can be a collection method of special samples such as dandruff in forensic practice.

[Pulmonary hypertensive crisis in children with idiopathic pulmonary arterial hypertension undergoing cardiac catheterization: the risk factors and clinical aspects]

Objective: To investigate the risk factors, clinical features, treatments, and prevention of pulmonary hypertensive crisis (PHC) in children with idiopathic pulmonary arterial hypertension (IPAH) undergoing cardiac catheterization. Methods: This retrospective study included 67 children who were diagnosed with IPAH and underwent cardiac catheterization between April 2009 and June 2017 in Beijing Anzhen Hospital. The medical histories, clinical manifestations, treatments, and outcomes were characterized. Statistical analyses were performed using t test, χ(2) test and a multiple Logistic regression analysis. Results: During cardiac catheterization, five children developed PHC who presented with markedly elevated pulmonary artery pressure and central venous pressure, decline in systemic arterial pressure and oxygen saturation. Heart rate decreased in 4 cases and increased in the remaining one. After the treatments including cardiopulmonary resuscitation, pulmonary vasodilator therapy, improving cardiac output and blood pressure, and correction of acidosis, 4 of the 5 cases recovered, while 1 died of severe right heart failure with irreversible PHC 3 days after operation. Potential PHC was considered in 7 other patients, whose pulmonary artery pressure increased and exceeded systemic arterial pressure, oxygen saturation decreased, and central venous pressure and vital signs were relatively stable. Univariate analysis showed that the risk factors of PHC in children with IPAH undergoing cardiac catheterization were younger age (t=3.160, P=0.004), low weight (t=4.004, P<0.001), general anesthesia (χ(2)=4.970, P=0.026), history of syncope (χ(2)=4.948, P=0.026), and WHO cardiac functional class Ⅲ or Ⅳ (χ(2)=19.013, P<0.001). Multivariate Logistic regression analysis revealed that worse WHO cardiac functional class (Wald=13.128, P<0.001, OR=15.076, 95% CI: 3.475-65.418) was the independent risk factor of PHC. Conclusions: PHC is a severe and extremely dangerous complication in children with IPAH during cardiac catheterization. WHO cardiac functional class may be associated with PHC. Integrated treatment is required for these patients. Reducing risk factors, early identification, and active treatment may help to prevent the occurrence and progression of PHC.

Bioinformatics Analysis of Chicken miRNAs Associated with Monocyte to Macrophage Differentiation and Subsequent IFNγ Stimulated Activation

BACKGROUND

The goal of this project was to characterize the molecular and cellular roles of various gene targets regulated by miRNAs identified in differentiating and stimulating avian macrophages. Once a monocyte arrives to a site of infection, local signals induce a redistribution of resources into a macrophage phenotype. This may involve upregulating pathogen pattern recognizing receptors and increasing the efficiency of lysosomal biogenesis, while simultaneously recycling components involved in circulatory migration and leukocyte extravasation. a monocyte tooled with chemokine surface receptors and an internal cytoskeletal structure geared towards mobility may efficiently sense, react, and migrate toward a site of infection.

METHODS

Peripheral blood derived monocytes were purified and cultured from young chickens. RNA sequencing was performed on both peripheral blood monocytes during differentiation into macrophages and on mature macrophages following stimulation with interferon gamma. A set of microRNAs were identified and investigated using bioinformatics methods to ascertain their potential role in avian macrophage biology.

RESULTS

Among a number of miRNAs that are found to be expressed in avian macrophages, we focused on eight specific miRNAs (miR-1618, miR-1586, miR-1633, miR-1627, miR-1646, miR-1649, miR-1610, miR-1647) associated with macrophage differentiation and activation. Expression profiles of microRNAs were characterized during differentiation and activation. Candidate miRNA targets were implicated in processes including Wnt signaling, ubiquitination, PPAR mediated macrophage function, vesicle mediated cytokine trafficking, and WD40 domain protein functions.

CONCLUSION

A global theme for macrophage function that may be modulated by microRNAs is the comprehensive redistribution of the cell's protein repertoire. This redistribution involves two processes: 1) the degradation and recycling of unneeded cytoplasmic and membrane components and 2) the mobilization of newly synthesized cellular components via vesicular trafficking. Generally, it appears that macrophages need to closely regulate gene expression for differentiation to be able to activate successfully in response to a pathogen. This is a process in which miRNAs participate by affecting several pathways critical for both, differentiation and activation.

Silver nanoparticles induce neurotoxicity in a human embryonic stem cell-derived neuron and astrocyte network

Silver nanoparticles (AgNPs) are among the most extensively used nanoparticles and are found in a variety of products. This ubiquity leads to inevitable exposure to these particles in everyday life. However, the effects of AgNPs on neuron and astrocyte networks are still largely unknown. In this study, we used neurons and astrocytes derived from human embryonic stem cells as a cellular model to study the neurotoxicity that is induced by citrate-coated AgNPs (AgSCs). Immunostaining with the astrocyte and neuron markers, glial fibrillary acidic protein and microtubule-associated protein-2 (MAP2), respectively, showed that exposure to AgSCs at the concentration of 0.1 µg/mL increased the astrocyte/neuron ratio. In contrast, a higher concentration of AgSCs (5.0 µg/ml) significantly changed the morphology of astrocytes. These results suggest that astrocytes are sensitive to AgSC exposure and that low concentrations of AgSCs promote astrogenesis. Furthermore, our results showed that AgSCs reduced neurite outgrowth, decreased the expression of postsynaptic density protein 95 and synaptophysin, and induced neurodegeneration in a concentration-dependent manner. Our findings additionally suggest that the expression and phosphorylation status of MAP2 isoforms, as modulated by the activation of the Akt/glycogen synthase kinase-3/caspase-3 signaling pathway, may play an important role in AgSC-mediated neurotoxicity. We also found that AgNO3 exposure only slightly reduced neurite outgrowth and had little effect on MAP2 expression, suggesting that AgSCs and AgNO3 have different neuronal toxicity mechanisms. In addition, most of these effects were reduced when the cell culture was co-treated with AgSCs and the antioxidant ascorbic acid, which implies that oxidative stress is the major cause of AgSC-mediated astrocytic/neuronal toxicity and that antioxidants may have a neuroprotective effect.

[Analysis of prognosis and associated risk factors in pediatric idiopathic pulmonary arterial hypertension]

Objective: To analyze the prognosis and associated risk factors of pediatric idiopathic pulmonary arterial hypertension. Methods: A total of 119 patients under 18 years of age diagnosed as idiopathic pulmonary arterial hypertension in the Pulmonary Arterial Hypertension Center in Beijing Anzhen Hospital between June 2007 and May 2017 were enrolled in this retrospective study. The clinical informations and follow-up data were collected. The endpoints of follow-up were defined as death or undergoing lung transplantation. Kaplan-Meier survival curve was used to assess the survival,and the COX risk regression model was used to analyze the prognostic risk factors. Results: The mean age at diagnosis was (5.9±4.2) years. For 92 (77.5%) patients, the main reason for visit was decreased activity with shortness of breath after exercise. Seventy patients (58.8%) were in baseline NYHA functional class Ⅲ-Ⅳ and 49 patients (41.2%) were in NYHA functional class Ⅰ-Ⅱ. The mean systolic pulmonary arterial pressure estimated by echocardiography was (90±23) mmHg (1 mmHg=0.133 kPa) . Right heart catheterization was performed in 50 patients. Hemodynamic parameters revealed that the mean pulmonary artery pressure was (66±19) mmHg. Mean right atrium pressure was (8.5±3.4) mmHg. Mean pulmonary vascular resistance index was (17±9) wood·m(2) and the mean cardiac index was (3.4±1.3)L/m(2); 100 patients (84.0%) received targeted therapy in which 55 patients (46.2%) were on monotherapy,40 patients (33.6%) were on dual therapy and 5 patients (4.2%) were on triple therapy. The mean time of follow-up was 22.0 months (0-108 months). During follow-up, 43 patients (36.1%) died and 1 patient received double-lung transplantation. Main causes of death including right heart failure, pulmonary hypertension crisis, asphyxia and massive hemoptysis. The mean survival time from diagnosis was 37.0 months,1-,2-,3-and 5-year survival rates were 86.3%, 72.2%, 51.4%and 37.8% respectively. Survival analysis showed that patients in baseline NYHA functional class Ⅰ-Ⅱ had better prognosis. COX regression analysis showed that NYHA function class, edema, increased total bilirubin and troponin concentration and the pulmonary artery and aorta diameter ratio measured by echocardiogram are risk factors of pediatric IPAH (HR=2.310, 2.723, 1.066, 1.696, 3.719, P=0.028, 0.005, 0.001, 0.024, 0.030) . While the existence of aterial septal defect or patent foramen ovale, using bosentan and phosphodiesterase inhibitors(,) dual or triple therapy were protective factors (HR=0.563, 0.559, 0.603, 0.682, 0.044, P=0.169, 0.076, 0.115, 0.258, 0.220) . In multivariate analysis only edema associated with decreased survival (HR=2.398, P=0.025) . Conclusion: Childhood idiopathic pulmonary arterial hypertension patients are seriously ill at visit. Worse cardiac function classification at visit associate with high mortality. Target therapy including using bosentan, dual or triple therapy can improve survival.

Alternative polyadenylation is involved in auxin-based plant growth and development

Auxin is widely involved in plant growth and development. However, the molecular mechanism on how auxin carries out this work is unclear. In particular, the effect of auxin on pre-mRNA post-transcriptional regulation is mostly unknown. By using a poly(A) tag (PAT) sequencing approach, mRNA alternative polyadenylation (APA) profiles after auxin treatment were revealed. We showed that hundreds of poly(A) site clusters (PACs) are affected by auxin at the transcriptome level, where auxin reduces PAC distribution in 5'-untranslated region (UTR), but increases in the 3'UTR. APA site usage frequencies of 42 genes were switched by auxin, suggesting that auxin affects the choice of poly(A) sites. Furthermore, poly(A) signal selection was altered after auxin treatment. For example, a mutant of poly(A) signal binding protein CPSF30 showed altered sensitivity to auxin treatment, indicating interactions between auxin and the poly(A) signal recognition machinery. We also found that auxin activity on lateral root development is likely mediated by altered expression of ARF7, ARF19 and IAA14 through poly(A) site switches. Our results shed light on the molecular mechanisms of auxin responses relative to its interactions with mRNA polyadenylation.

Role of cleavage and polyadenylation specificity factor 100: anchoring poly(A) sites and modulating transcription termination

CPSF100 is a core component of the cleavage and polyadenylation specificity factor (CPSF) complex for 3'-end formation of mRNA, but it still has no clear functional assignment. CPSF100 was reported to play a role in RNA silencing and promote flowering in Arabidopsis. However, the molecular mechanisms underlying these phenomena are not fully understood. Our genetics analyses indicate that plants with a hypomorphic mutant of CPSF100 (esp5) show defects in embryogenesis, reduced seed production or altered root morphology. To unravel this puzzle, we employed a poly(A) tag sequencing protocol and uncovered a different poly(A) profile in esp5. This transcriptome-wide analysis revealed alternative polyadenylation of thousands of genes, most of which result in transcriptional read-through in protein-coding genes. AtCPSF100 also affects poly(A) signal recognition on the far-upstream elements; in particular it prefers less U-rich sequences. Importantly, AtCPSF100 was found to exert its functions through the change of poly(A) sites on genes encoding binding proteins, such as nucleotide-binding, RNA-binding and poly(U)-binding proteins. In addition, through its interaction with RNA Polymerase II C-terminal domain (CTD) and affecting the expression level of CTD phosphatase-like 3 (CPL3), AtCPSF100 is shown to potentially ensure transcriptional termination by dephosphorylation of Ser2 on the CTD. These data suggest a key role for CPSF100 in locating poly(A) sites and affecting transcription termination.

Genome-Wide Comparative Analysis of Miniature Inverted Repeat Transposable Elements in 19 Arabidopsis thaliana Ecotype Accessions

Miniature inverted repeat transposable elements (MITEs) are prevalent in eukaryotic genomes. They are known to critically influence the process of genome evolution and play a role in gene regulation. As the first study concentrated in the transposition activities of MITEs among different ecotype accessions within a species, we conducted a genome-wide comparative analysis by characterizing and comparing MITEs in 19 Arabidopsis thaliana accessions. A total of 343485 MITE putative sequences, including canonical, diverse and partial ones, were delineated from all 19 accessions. Within the entire population of MITEs sequences, 80.7% of them were previously unclassified MITEs, demonstrating a different genomic distribution and functionality compared to the classified MITEs. The interactions between MITEs and homologous genes across 19 accessions provided a fine source for analyzing MITE transposition activities and their impacts on genome evolution. Moreover, a significant proportion of MITEs were found located in the last exon of genes besides the ordinary intron locality, thus potentially modifying the end of genes. Finally, analysis of the impact of MITEs on gene expression suggests that migrations of MITEs have no detectable effect on the expression level for host genes across accessions.

Genome-wide dynamics of alternative polyadenylation in rice

Alternative polyadenylation (APA), in which a transcript uses one of the poly(A) sites to define its 3'-end, is a common regulatory mechanism in eukaryotic gene expression. However, the potential of APA in determining crop agronomic traits remains elusive. This study systematically tallied poly(A) sites of 14 different rice tissues and developmental stages using the poly(A) tag sequencing (PAT-seq) approach. The results indicate significant involvement of APA in developmental and quantitative trait loci (QTL) gene expression. About 48% of all expressed genes use APA to generate transcriptomic and proteomic diversity. Some genes switch APA sites, allowing differentially expressed genes to use alternate 3' UTRs. Interestingly, APA in mature pollen is distinct where differential expression levels of a set of poly(A) factors and different distributions of APA sites are found, indicating a unique mRNA 3'-end formation regulation during gametophyte development. Equally interesting, statistical analyses showed that QTL tends to use APA for regulation of gene expression of many agronomic traits, suggesting a potential important role of APA in rice production. These results provide thus far the most comprehensive and high-resolution resource for advanced analysis of APA in crops and shed light on how APA is associated with trait formation in eukaryotes.

[Evaluation of therapeutic effect of virtual design for correcting facial asymmetry of skeletal Class Ⅲ deformity]

Objective: To establish a computer-aided surgical simulation procedure based on the natural head position(NHP) for orthognathic surgery and to access the effect for correcting facial asymmetry for skeletal Class Ⅲ deformity. Methods: Thirty-five patients(male: 14 and female: 21, mean age: [21.5±2.3] years) of skeletal Class Ⅲ deformity with facial asymmetry were included and divided into virtual group (16 patients) and control group(19 patients). The computer-aided surgical simulation procedure was used in the virtual group and the intermediate and final splints were fabricated using the rapid protyping technique. The traditional model surgery based on plaster casts was used in control group, and the splints were handmade. To evaluate the symmetry, three-dimensional(3D) photos were taken for all the patients before operation and 6 months after operation using the 3dMD face imaging system. Coordinate system was built based on mirror-original alignment method on the 3D photo. Thirteen soft tissue landmarks were marked on each 3D photo. The asymmetry index(AI) of those soft tissue landmarks was calculated. Results: There was no significant difference in the AI values between the two groups before surgery. Sixth month after operation, the mean AI values in the virtual group were (0.81±0.50) mm for subnasale, (1.01±0.80) mm for labiale superius, (1.94±1.30) mm for crista philtri, (1.60±1.20) mm for pogonion and (5.68±2.25) mm for gonion. The mean AI values in the control group were (1.49±1.10) mm for subnasale, (1.79±1.33) mm for labiale superius, (3.52±2.50) mm for crista philtri, (2.79±2.08) mm for pogonion and (8.43±3.94) mm for gonion and those indexes were significantly different between the two groups(P<0.05). There was no significant difference in the AI values of the pronasale, alare, labiale inferius and cheilion between the two groups sixth month after operation. Conclusions: The introduced procedure of the virtual design based on the estimated NHP could more effectively correct the asymmetry deformity for the skeletal Class Ⅲ patients.

PlantAPA: A Portal for Visualization and Analysis of Alternative Polyadenylation in Plants

Alternative polyadenylation (APA) is an important layer of gene regulation that produces mRNAs that have different 3' ends and/or encode diverse protein isoforms. Up to 70% of annotated genes in plants undergo APA. Increasing numbers of poly(A) sites collected in various plant species demand new methods and tools to access and mine these data. We have created an open-access web service called PlantAPA (http://bmi.xmu.edu.cn/plantapa) to visualize and analyze genome-wide poly(A) sites in plants. PlantAPA provides various interactive and dynamic graphics and seamlessly integrates a genome browser that can profile heterogeneous cleavage sites and quantify expression patterns of poly(A) sites across different conditions. Particularly, through PlantAPA, users can analyze poly(A) sites in extended 3' UTR regions, intergenic regions, and ambiguous regions owing to alternative transcription or RNA processing. In addition, it also provides tools for analyzing poly(A) site selections, 3' UTR lengthening or shortening, non-canonical APA site switching, and differential gene expression between conditions, making it more powerful for the study of APA-mediated gene expression regulation. More importantly, PlantAPA offers a bioinformatics pipeline that allows users to upload their own short reads or ESTs for poly(A) site extraction, enabling users to further explore poly(A) site selection using stored PlantAPA poly(A) sites together with their own poly(A) site datasets. To date, PlantAPA hosts the largest database of APA sites in plants, including Oryza sativa, Arabidopsis thaliana, Medicago truncatula, and Chlamydomonas reinhardtii. As a user-friendly web service, PlantAPA will be a valuable addition to the community of biologists studying APA mechanisms and gene expression regulation in plants.