Investigating the cis-Regulatory Basis of C3 and C4 Photosynthesis in Grasses at Single-Cell Resolution

While considerable knowledge exists about the enzymes pivotal for C4 photosynthesis, much less is known about cis-regulation important for specifying their expression in distinct cell types. Here, we use single-cell-indexed ATAC-seq to identify cell-type-specific accessible chromatin regions (ACRs) associated with C4 enzymes for five different grass species. This study spans four C4 species, covering three distinct photosynthetic subtypes: Zea mays and Sorghum bicolor (NADP-ME), Panicum miliaceum (NAD-ME), Urochloa fusca (PEPCK), along with the C3 outgroup Oryza sativa. We studied the cis-regulatory landscape of enzymes essential across all C4 species and those unique to C4 subtypes, measuring cell-type-specific biases for C4 enzymes using chromatin accessibility data. Integrating these data with phylogenetic trees revealed diverse co-option of gene family members between species, showcasing the various paths of C4 evolution. We mapped cell-type-specific ACRs surrounding each C4 gene, discovering that, on average, these genes have two to three cell-type-specific ACRs located beyond the core promoter. These results provide a detailed genomic map of potential regulatory sequences operating on key C4 genes. Examining the evolutionary history of these cell-type-specific ACRs revealed a spectrum of conserved and novel ACRs, even among closely related species, indicating ongoing evolution of cis-regulation at these C4 loci. This work illuminates the dynamic and complex nature of CRE evolution in C4 photosynthesis, particularly highlighting the intricate cis-regulatory evolution of key loci. Our findings offer a valuable resource for future investigations, potentially aiding in the optimization of C3 crop performance under changing climatic conditions.

Evolution of plant cell-type-specific cis -regulatory elements

Cis -regulatory elements (CREs) are critical in regulating gene expression, and yet our understanding of CRE evolution remains a challenge. Here, we constructed a comprehensive single-cell atlas of chromatin accessibility in Oryza sativa , integrating data from 104,029 nuclei representing 128 discrete cell states across nine distinct organs. We used comparative genomics to compare cell-type resolved chromatin accessibility between O. sativa and 57,552 nuclei from four additional grass species ( Zea mays, Sorghum bicolor, Panicum miliaceum , and Urochloa fusca ). Accessible chromatin regions (ACRs) had different levels of conservation depending on the degree of cell-type specificity. We found a complex relationship between ACRs with conserved noncoding sequences, cell-type specificity, conservation, and tissue-specific switching. Additionally, we found that epidermal ACRs were less conserved compared to other cell types, potentially indicating that more rapid regulatory evolution has occurred in the L1 epidermal layer of these species. Finally, we identified and characterized a conserved subset of ACRs that overlapped the repressive histone modification H3K27me3, implicating them as potentially critical silencer CREs maintained by evolution. Collectively, this comparative genomics approach highlights the dynamics of cell-type-specific CRE evolution in plants.

[Application of single anterior teeth defect with computer-aided design and computer-aided manufacturing polymethyl methacrylate single-retainer resin-bonded fixed dental prosthesis in children]

Objective: To explore the clinical effect of computer-aided design and computer-aided manufacturing (CAD/CAM) polymethyl methacrylate (PMMA) single-retainer resin-bonded fixed dental prosthesis (RBFDP) for single anterior teeth defect. Methods: A total of 14 children between 10-14 years old (male 8, female 6) who visited the Department of Pediatric Dentistry, School of Stomatology, The Fourth Military Medical University from March to December 2022 with single anterior teeth loss were enrolled in this study. The intraoral scanner was used to obtain their digital impressions, and then the data were imported into CAD software. The single-retainer RBFDP was designed by the CAD software and was manufactured by milling equipment using CAD/CAM PMMA disk. The prosthesis was then tried-in and bonded to the abutment teeth with resin cement and evaluated in a 12 month follow-up observation. The marginal discoloration, marginal adaptation, color match, secondary caries, the occurrence of fractures and loose of abutment tooth were examined on the basis of the modified United States Public Health Services evaluation system. The evaluation was divided into three scores, in which score A indicated ideal restoration effect, score B means that the restoration effect was acceptable (evaluation of restoration integrity, loose of abutment teeth and secondary caries excluded), and score C indicates that the restoration effect is not good. Results: All the 14 CAD/CAM PMMA single-retainer RBFDP had good marginal adaptation and color match with no marginal discoloration, no secondary caries, no fracture of restorations and no abnormal loose of the abutment teeth. All of the six criteria achieved score A evaluation after a three month follow-up observation. One restoration was classified as score B for fracture after a six month follow-up observation, while two restoration were classified as score B for marginal discoloration after 12 month follow-up observation. Conclusions: The CAD/CAM PMMA single-retainer RBFDP was clinically effective in restoration of single anterior teeth defect in children.

Ten-Year Outcomes of Hypofractionated (45 Gy in 9 Fractions) Intensity Modulated Radiotherapy for Localized Prostate Cancer

PURPOSE/OBJECTIVE(S)

We reported 10-year outcomes of localized prostate cancers treated with hypofractionated intensity-modulated radiotherapy of 45 Gy in 9 consecutive fractions.

MATERIALS/METHODS

From October 2011 to April 2017, thirty patients with localized prostate cancer were enrolled in this prospective trial. The median age of the patients was 72.5 years. According to NCCN recurrence risk criteria, eight patients were at low-risk group, 17 at intermediate risk group, 5 at high-risk group. All patients were treated with hypofractionated intensity-modulated radiotherapy (IMRT) of 45 Gy in 9 consecutive fractions to their prostate with or without seminal vesicles. Before radiotherapy, three gold fiducials were implanted into the prostate. In order to reduce the rectal high dose irradiation volume, an inflated rectal balloon was placed in the rectum at simulation and every treatment and patients were treated with comfortable full bladder. Static Intensity-modulated radiotherapy (SIMRT) was applied in 1 patient, Volumetric Modulated Arc Therapy (VMAT) in 27 patients, and tomotherapy in 2 patients. Image guided radiotherapy (IGRT) with gold fiducial registration was adopted. Twenty-six patients also received androgen deprivation therapy (ADT). The median time of ADT was 6 months. Progression⁃free survival (PFS) and overall survival (OS) were analyzed using Kaplan-Meier analysis. All grade ≥1 genitourinary (GU) and gastrointestinal (GI) toxicities were recorded using Common Terminology Criteria for Adverse Event version 5.0 (CTCAE 5.0) and Radiation Therapy Oncology Group (RTOG) late morbidity criteria, and GU and GI toxicities were cumulatively calculated.

RESULTS

After a median follow-up of 102 months (65∼131 months), the 10-year OS was 90.0% (95% confidence interval, 83.3%-96.7%), and the 10-year PFS was 86.5% (95% confidence interval, 79.1%-93.9%). According to CTCAE 5.0, grade 1 acute gastrointestinal (GI) toxicity developed in 12 patients, grade 2 in 2 patients, grade 3 in 2 patients, and grade 1 acute genitourinary (GU) toxicity developed in 12 patients, grade 2 in 2 patients, and no grade 3 or higher toxicity occurred. According to RTOG late morbidity criteria, late (≥3 months after radiotherapy) grade 1 GI toxicity developed in 4 patients (13.3%), grade 2 in 1 (3.3%), grade 3 in 1 (3.3%), and late grade 1 GU toxicity occurred in 1 patient (3.3%), grade 2 in 1 (3.3%), grade 3 in 1 (3.3%). No grade 4 or higher GI and GU toxicities developed. Only one grade 3 GI and one grade 2 GU toxicities were observed for the maximum toxicity at the last follow-up. The potency was not evaluated.

CONCLUSION

The 10-year oncologic outcomes of this shortened hypofractionated IMRT regimen for mainly low/intermediate risk prostate cancer patients is favorable with acceptable acute and late toxicities.

[Value of postoperative radiotherapy and analysis of prognostic factors in early-stage neuroendocrine carcinoma of cervix]

Objective: To evaluate the effect of postoperative radiotherapy and high-risk pathological factors on the prognosis of early-stage neuroendocrine carcinoma of cervix (NECC). Methods: A single-center retrospective cohort study of early-stage NECC in Peking Union Medical College Hospital from January 2011 to April 2022 were enrolled. The patients were treated with radical hysterectomy±adjuvant treatment. They were divided into postoperative non-radiation group and postoperative radiation group. The possible postoperative recurrence risk factors identified by univariate analysis were assessed using multivariate logistic regression. The Kaplan-Meier method was used to analyze the progression free survival (PFS), overall survival (OS), recurrence rate, and mortality rate. Results: (1) Sixty-two cases were included in the study, including 33 cases in postoperative non-radiation group and 29 cases in postoperative radiation group. (2) The median follow-up time was 37 months (ranged 12-116 months), with 23 cases (37%) experienced recurrences. There were 7 cases (11%) pelvic recurrences and 20 cases (32%) distant recurrences, in which including 4 cases (6%) both pelvic and distant recurrences. Compared with postoperative non-radiation group, the postoperative radiation group had a lower pelvic recurrence rate (18% vs 3%; P=0.074) but without statistic difference, a slightly elevated distant recurrence rate (24% vs 41%; P=0.150) and overall recurrence rate (33% vs 41%; P=0.513) without statistically significances. Univariate analysis showed that lymph-vascular space invasion and the depth of cervical stromal invasion≥1/2 were risk factors for postoperative recurrence (all P<0.05). Multivariate analysis showed lymph-vascular space invasion was an independent predictor for postoperative recurrence (OR=23.03, 95%CI: 3.55-149.39, P=0.001). (3) During the follow-up period, 18 cases (29%, 18/62) died with tumor, with 10 cases (30%, 10/33) in postoperative non-radiation group and 8 cases (28%, 8/29) in postoperative radiation group, without significant difference (P=0.814). The postoperative 3-year and 5-year survival rate was 79.2%, 60.8%. The depth of cervical stromal invasion≥1/2 was more common in postoperative radiation group (27% vs 64%; P=0.011), and postoperative radiation in such patients showed an extended trend in PFS (32.3 vs 53.9 months) and OS (39.4 vs 73.4 months) but without statistic differences (P=0.704, P=0.371). Compared with postoperative non-radiation group, the postoperative radiation did not improve PFS (54.5 vs 37.3 months; P=0.860) and OS (56.2 vs 62.4 months; P=0.550) in patients with lymph-vascular space invasion. Conclusions: Postoperative radiation in early-stage NECC patients has a trend to reduce pelvic recurrence but not appear to decrease distant recurrence and overall recurrence, and has not improved mortality. For patients with the depth of cervical stromal invasion≥1/2, postoperative radiation has a trend of prolonging OS and PFS but without statistic difference. Lymph-vascular space invasion is an independent predictor for postoperative recurrence, but postoperative radiation in such patients does not seem to have any survival benefits.

A multi-omic Nicotiana benthamiana resource for fundamental research and biotechnology

Nicotiana benthamiana is an invaluable model plant and biotechnology platform with a ~3 Gb allotetraploid genome. To further improve its usefulness and versatility, we have produced high-quality chromosome-level genome assemblies, coupled with transcriptome, epigenome, microRNA and transposable element datasets, for the ubiquitously used LAB strain and a related wild accession, QLD. In addition, single nucleotide polymorphism maps have been produced for a further two laboratory strains and four wild accessions. Despite the loss of five chromosomes from the ancestral tetraploid, expansion of intergenic regions, widespread segmental allopolyploidy, advanced diploidization and evidence of recent bursts of Copia pseudovirus (Copia) mobility not seen in other Nicotiana genomes, the two subgenomes of N. benthamiana show large regions of synteny across the Solanaceae. LAB and QLD have many genetic, metabolic and phenotypic differences, including disparate RNA interference responses, but are highly interfertile and amenable to genome editing and both transient and stable transformation. The LAB/QLD combination has the potential to be as useful as the Columbia-0/Landsberg errecta partnership, utilized from the early pioneering days of Arabidopsis genomics to today.

Comparative genomic analyses reveal the genetic basis of the yellow-seed trait in Brassica napus

Yellow-seed trait is a desirable breeding characteristic of rapeseed (Brassica napus) that could greatly improve seed oil yield and quality. However, the underlying mechanisms controlling this phenotype in B. napus plants are difficult to discern because of their complexity. Here, we assemble high-quality genomes of yellow-seeded (GH06) and black-seeded (ZY821). Combining in-depth fine mapping of a quantitative trait locus (QTL) for seed color with other omics data reveal BnA09MYB47a, encoding an R2R3-MYB-type transcription factor, as the causal gene of a major QTL controlling the yellow-seed trait. Functional studies show that sequence variation of BnA09MYB47a underlies the functional divergence between the yellow- and black-seeded B. napus. The black-seed allele BnA09MYB47aZY821, but not the yellow-seed allele BnA09MYB47aGH06, promotes flavonoid biosynthesis by directly activating the expression of BnTT18. Our discovery suggests a possible approach to breeding B. napus for improved commercial value and facilitates flavonoid biosynthesis studies in Brassica crops.

Phytohormone ethylene mediates oligogalacturonic acid-induced growth inhibition in tomato etiolated seedlings

Plant growth and immunity are tightly interconnected. Oligogalacturonic acids (OGs) are pectic fragments and have been well investigated in plant immunity as a damage-associated molecular pattern. However, little is known regarding how OGs affect plant growth. Here, we reveal that OGs inhibit the growth of intact etiolated seedling by using the horticultural crop tomato as a model. This inhibitory effect is partially suppressed by the action of ethylene biosynthesis inhibitors, or the gene silencing of SlACS2, an essential rate-limiting enzyme for ethylene biosynthesis, suggesting that SlACS2-mediated ethylene production promotes OG-induced growth inhibition. Furthermore, OGs treatment elevates the SlACS2 protein phosphorylation, and its decrease by the kinase inhibitor K252a partially rescue OG-induced growth inhibition, indicating that SlACS2 phosphorylation involves in OG-induced growth inhibition. Moreover, the mitogen-activated protein kinase SlMPK3 could be activated by OGs treatment and can directly phosphorylate SlACS2 in vitro, and the bimolecular fluorescence complementation combining with the yeast two-hybrid assay shows that SlMPK3 interacts with SlACS2, indicating that SlMPK3 may participate in modulating the OG-induced SlACS2 phosphorylation and growth inhibition. Our results reveal a regulatory mechanism at both the transcriptional and post-transcriptional levels by which OGs inhibit the growth of intact plant seedlings.

[Exploration of making removable partial denture by digital technology]

To explore the digital manufacturing process of distal extension removable partial denture. From November 2021 to December 2022, 12 patients (7 males and 5 females) with free-ending situation were selected from the Department of Prosthodontics, School of Stomatology, The Fourth Military Medical University. Three-dimensional model of the relationship between alveolar ridge and jaw position was obtained by intraoral scanning technique. After routine design, manufacturing and try-in of metal framework for removable partial denture, the metal framework was located in the mouth and scanned again to obtain the composite model of dentition, alveolar ridge and metal framework. The free-end modified model is obtained by merging the digital model of free-end alveolar ridge with the virtual model with the metal framework. The three-dimensional model of artificial dentition, and base plate was designed on the free-end modified model, and the resin model were made by digital milling technology. The removable partial denture was made by accurately positioning the artificial dentition and base plate, bonding metal framework with injection resin, grinding and polishing the artificial dentition and resin base. Compared with the design data after clinical trial, the results showed that there was an error of 0.4-1.0 mm and an error of 0.03-0.10 mm in the connection between the resin base of artificial dentition and the connecting rod of the in-place bolt and the connection between artificial dentition and resin base. After denturen delivery, only 2 patients needed grinding adjustment in follow-up visit due to tenderness, and the rest patients did not find any discomfort. The digital fabrication process of removable partial denture used in this study can basically solve the problems of digital fabrication of free-end modified model and assembly of artificial dentition with resin base and metal framework.

Tomato MED25 regulates fruit ripening by interacting with EIN3-like transcription factors

Fruit ripening relies on the precise spatiotemporal control of RNA polymerase II (Pol II)-dependent gene transcription, and the evolutionarily conserved Mediator (MED) coactivator complex plays an essential role in this process. In tomato (Solanum lycopersicum), a model climacteric fruit, ripening is tightly coordinated by ethylene and several key transcription factors. However, the mechanism underlying the transmission of context-specific regulatory signals from these ripening-related transcription factors to the Pol II transcription machinery remains unknown. Here, we report the mechanistic function of MED25, a subunit of the plant Mediator transcriptional coactivator complex, in controlling the ethylene-mediated transcriptional program during fruit ripening. Multiple lines of evidence indicate that MED25 physically interacts with the master transcription factors of the ETHYLENE-INSENSITIVE 3 (EIN3)/EIN3-LIKE (EIL) family, thereby playing an essential role in pre-initiation complex formation during ethylene-induced gene transcription. We also show that MED25 forms a transcriptional module with EIL1 to regulate the expression of ripening-related regulatory as well as structural genes through promoter binding. Furthermore, the EIL1-MED25 module orchestrates both positive and negative feedback transcriptional circuits, along with its downstream regulators, to fine-tune ethylene homeostasis during fruit ripening.

[Analysis of risk factors for decompensated cirrhosis complicated with sepsis]

Objective: To investigate the related risk factors in patients with decompensated cirrhosis complicated with sepsis. Methods: 1 098 cases with decompensated cirrhosis were collected from January 2018 to December 2020. A total of 492 cases with complete data meeting the inclusion criteria were included. Among them, the sepsis group (240 cases) was complicated with sepsis and the non-sepsis group (252 cases) was not complicated with sepsis. Albumin, cholinesterase, total bilirubin, prothrombin activity, urea, creatinine, international normalized ratio and other indicators of the two groups of patients were collected. Child-Pugh classification and MELD score were performed on two groups of patients. Mann-Whitney U test was used for non-normally distributed measurement data, and rank sum test for grade data. Logistic regression analysis was performed on sepsis-related factors that may affect patients with decompensated cirrhosis complicated with sepsis. Results: 162 cases of gram negative bacteria, 76 cases of gram positive bacteria and 2 cases of Candida were detected. Child-Pugh grade C was mainly in the sepsis group, and Child- Pugh grade A and B was mainly in the non-sepsis group (z=-13.01, P＜0.05). MELD score was significantly higher in patients with sepsis than that of patients without sepsis (z=-12.30, P＜0.05). Neutrophils percentage, C-reactive protein, procalcitonin, and total bilirubin in patients with decompensated cirrhosis complicated with sepsis were 86.90% (79.00%, 91.05%), 48.48 (17.63, 97.55) mg/l,1.34 (0.40, 4.52) ng/l, and 78.50 (32.75149.80) μmol/L, which were significantly higher than that of patients without sepsis [69.55% (58.58%, 75.90%), 5.34 (5.00, 14.94) mg/l, 0.11(0.06,0.24) ng/l, 22.50(15.10,37.55) respectively] μmol/L, P＜0.05], while the albumin level, prothrombin activity level, and the cholinesterase level in sepsis patients were 27.30 (24.45, 30.60) g/L, 46.00% (33.50%, 59.00%), and 1.87 (1.29, 2.66) kU/L, respectively, which was significantly lower than the non-sepsis group [32.65 (28.95, 37.23) g/l, 73.00(59.75～84.85)%, 3.13(2.23～4.59) kU/L, P＜0.05]. Logistic regression analysis showed that serum total bilirubin, albumin, prothrombin activity level and diabetes mellitus were the independent risk factors for complicated sepsis. Conclusion: Patients with decompensated cirrhosis with poor liver function and higher MELD scores are more likely to be complicated with sepsis. Therefore, during the clinical diagnosis and treatment course, patients with decompensated cirrhosis with poor liver reserve function should be actively and dynamically monitored for infection-related indicators such as neutrophil percentage, procalcitonin, C-reactive protein, in an attempt to detect possible potential infections and sepsis, and improve early treatment and prognosis.

P11.75.B Survival benefit of radiotherapy and surgery in patients with lung cancer brain metastases with poor prognosis factors

Background

Radiotherapy and surgery are the standard treatments for lung cancer brain metastases (BMs). However, limitted studies focused on the treatments for patients with lung cancer BMs with poor prognosis factors. The purpose of this study was to investigate the effects of radiotherapy and surgery in patients with lung cancer BMs with poor prognosis factors, providing reference for clinical strategies.

Material and Methods

We analyzed retrospectively 714 patients with lung cancer BMs. A 1:1 propensity score matching (PSM) was performed to balance potential confounders. Analyses of overall survival (OS) and risk factors for OS were assessed by log-rank test and Cox proportional hazard model.

Results

Age ≥65 years, Karnofsky Performance Scale (KPS) score ≤70, anaplastic large-cell lymphoma kinase (ALK)/epidermal growth factor receptor (EGFR) wild type, extracranial metastases, non-surgery and non-radiotherapy led to poor prognosis. Patients were stratified according to these factors. Radiotherapy and surgery showed no survival benefit in patients with aged ≥65 years or pretreatment KPS score ≤70 before and after PSM. Before PSM, whole brain radiotherapy (WBRT) improved the OS and predicted good prognosis in patients with ALK/EGFR wild type or extracranial metastases. WBRT also predicted good prognosis in patients with non-surgery. Stereotactic radiosurgery (SRS) improved the OS and predicted good prognosis in patients with ALK/EGFR wild type or non-surgery. WBRT plus SRS improved the OS and predicted good prognosis in patients with extracranial metastases or non-surgery. WBRT plus SRS also predicted good prognosis in patients with ALK/EGFR wild type. Surgery improved the OS and predicted good prognosis in patients with non-radiotherapy. After PSM, SRS improved the OS and predicted good prognosis in patients with non-surgery. WBRT plus SRS improved the OS and predicted good prognosis in patients with non-surgery or extracranial metastases. WBRT plus SRS also predicted good prognosis in patients with ALK/EGFR wild type. Surgery improved the OS of patients with non-radiotherapy. We defined that the treatment would provide significant survival benefit if it both prolonged the OS and predicted good prognosis. Meanwhile, the results after PSM were more convincing than the results before PSM.

Conclusion

Radiotherapy has significant survival benefit in patients with lung cancer BMs with poor prognosis factors, including patients with ALK/EGFR wild type or extracranial metastases or non-surgery. Surgery only has significant survival benefit in patients with non-radiotherapy.

Characterization of regulatory modules controlling leaf angle in maize

Leaf angle is an important agronomic trait determining maize (Zea mays) planting density and light penetration into the canopy and contributes to the yield gain in modern maize hybrids. However, little is known about the molecular mechanisms underlying leaf angle beyond the ZmLG1 (liguleless1) and ZmLG2 (Liguleless2) genes. In this study, we found that the transcription factor (TF) ZmBEH1 (BZR1/BES1 homolog gene 1) is targeted by ZmLG2 and regulates leaf angle formation by influencing sclerenchyma cell layers on the adaxial side. ZmBEH1 interacted with the TF ZmBZR1 (Brassinazole Resistant 1), whose gene expression was also directly activated by ZmLG2. Both ZmBEH1 and ZmBZR1 are bound to the promoter of ZmSCL28 (SCARECROW-LIKE 28), a third TF that influences leaf angle. Our study demonstrates regulatory modules controlling leaf angle and provides gene editing targets for creating optimal maize architecture suitable for dense planting.

A combinatorial indexing strategy for low-cost epigenomic profiling of plant single cells

Understanding how cis-regulatory elements facilitate gene expression is a key question in biology. Recent advances in single-cell genomics have led to the discovery of cell-specific chromatin landscapes that underlie transcription programs in animal models. However, the high equipment and reagent costs of commercial systems limit their applications for many laboratories. In this study, we developed a combinatorial index and dual PCR barcode strategy to profile the Arabidopsis thaliana root single-cell epigenome without any specialized equipment. We generated chromatin accessibility profiles for 13 576 root nuclei with an average of 12 784 unique Tn5 integrations per cell. Integration of the single-cell assay for transposase-accessible chromatin sequencing and RNA sequencing data sets enabled the identification of 24 cell clusters with unique transcription, chromatin, and cis-regulatory signatures. Comparison with single-cell data generated using the commercial microfluidic platform from 10X Genomics revealed that this low-cost combinatorial index method is capable of unbiased identification of cell-type-specific chromatin accessibility. We anticipate that, by removing cost, instrumentation, and other technical obstacles, this method will be a valuable tool for routine investigation of single-cell epigenomes and provide new insights into plant growth and development and plant interactions with the environment.

[Comparison of efficacy and safety between new oral anticoagulants and traditional anticoagulants in patients with liver cirrhosis requiring anticoagulant therapy]

Objective: To compare the advantages and disadvantages of new oral anticoagulants (NOACs) with traditional anticoagulants, in an attempt to evaluate their efficacy and safety in patients with liver cirrhosis requiring anticoagulant therapy. Methods: Relevant literatures were searched from PubMed, Embase, Cochrane Library, HowNet, Wanfang, VIP and other databases by computer retrieval. The literatures quality was evaluated by NOS. The extracted data were meta-analyzed by RevMan5.3 software. Results: A total of seven studies were included, including one randomized controlled trial and six retrospective cohort studies with a total of 3042 cases. Among them, 1677 and 1365 cases used NOACs and traditional anticoagulants. Meta-analysis results showed that compared with the traditional anticoagulant group, the NOACs group had a lower incidence of massive hemorrhage [OR=0.56, 95%CI (0.37-0.85), P＜0.01] and a higher thrombotic recanalization rate [OR=7.77, 95%CI (3.48~17.34), P＜0.01], and the difference was statistically significant, while there were no statistically significant differences between the two groups in comparison to all-cause bleeding rates [OR=0.72, 95%CI (0.13-3.91), P=0.07], all-cause mortality [OR=0.72, 95%CI (0.25-2.07), P=0.54], recurrent embolism and stroke rates [OR=0.90, 95%CI (0.59-1.39), and P=0.64]. Conclusion: Compared with traditional anticoagulants, NOACs have higher safety and better efficacy in the treatment of patients with liver cirrhosis, but it has not been widely used in China. Therefore, large-scale randomized controlled trials and prospective studies are further needed to confirm it in the future.

SnRK2 subfamily I protein kinases regulate ethylene biosynthesis by phosphorylating HB transcription factors to induce ACO1 expression in apple

Ethylene (ETH) controls climacteric fruit ripening and can be triggered by osmotic stress. However, the mechanism regulating ETH biosynthesis during fruit ripening and under osmotic stress is largely unknown in apple (Malus domestica). Here, we explored the roles of SnRK2 protein kinases in ETH biosynthesis related to fruit ripening and osmoregulation. We identified the substrates of MdSnRK2-I using phosphorylation analysis techniques. Finally, we identified the MdSnRK2-I-mediated signaling pathway for ETH biosynthesis related to fruit ripening and osmoregulation. The activity of two MdSnRK2-I members, MdSnRK2.4 and MdSnRK2.9, was significantly upregulated during ripening or following mannitol treatment. Overexpression of MdSnRK2-I increased ETH biosynthesis under normal and osmotic conditions in apple fruit. MdSnRK2-I phosphorylated the transcription factors MdHB1 and MdHB2 to enhance their protein stability and transcriptional activity on MdACO1. MdSnRK2-I also interacted with MdACS1 and increased its protein stability through two phosphorylation sites. The increased MdACO1 expression and MdACS1 protein stability resulted in higher ETH production in apple fruit. In addition, heterologous expression of MdSnRK2-I or manipulation of SlSnRK2-I expression in tomato (Solanum lycopersicum) fruit altered fruit ripening and ETH biosynthesis. We established that MdSnRK2-I functions in fruit ripening and osmoregulation, and identified the MdSnRK2-I-mediated signaling pathway controlling ETH biosynthesis.

Impact of pre-transplant dialysis modality on kidney transplant outcomes: a systematic review and meta-analysis

OBJECTIVE

For end-stage renal disease (ESRD), patients receiving kidney transplantation, peritoneal dialysis (PD) and hemodialysis (HD) are both appropriate modes of pre-transplant dialysis. The aim of this review is to assess the impact of pre-transplant PD compared to HD on kidney transplant outcomes in ESRD patients.

MATERIALS AND METHODS

A comprehensive search in digital databases, like PubMed, SCOPUS and EMBASE and a manual search were conducted to identify cohort studies comparing the kidney transplant outcomes of both pre-transplant dialysis modalities. The data were subjected to both qualitative and quantitative analysis. A meta-analysis was carried out to calculate the effect estimate for patient survival, graft survival and delayed graft function, death-censored graft survival, acute rejection-free graft survival, graft vessel thrombosis, urological complications, surgical complications, any infections, and onset of diabetes after transplantation. The qualities of the included studies were judged by the New-castle Ottawa scale.

RESULTS

The overall patient survival is shown to be better with patients who underwent pre-transplant PD compared to HD with OR 1.34 95% CI [1.11, 1.61], p = 0.002. Delayed graft function was found to be highly associated with HD compared to PD with OR 0.60 [0.52, 0.70], p<0.0001 with moderate heterogeneity (i2 = 48%). However, no difference was observed in terms of graft survival, complications, infections, and new onset of diabetes mellitus compared to patients undergoing pre-transplant HD.

CONCLUSIONS

Within the limitations of the review, it can be concluded that ESRD patients undergoing pre-transplant PD were found to have better patient survival and lower incidence of delayed graft function.

Identification of Chilling Accumulation-Associated Genes for Litchi Flowering by Transcriptome-Based Genome-Wide Association Studies

Litchi is an important Sapindaceae fruit tree. Flowering in litchi is triggered by low temperatures in autumn and winter. It can be divided into early-, medium-, and late-flowering phenotypes according to the time for floral induction. Early-flowering varieties need low chilling accumulation level for floral induction, whereas the late-flowering varieties require high chilling accumulation level. In the present study, RNA-Seq of 87 accessions was performed and transcriptome-based genome-wide association studies (GWAS) was used to identify candidate genes involved in chilling accumulation underlying the time for floral induction. A total of 98,155 high-quality single-nucleotide polymorphism (SNP) sites were obtained. A total of 1,411 significantly associated SNPs and 1,115 associated genes (AGs) were identified, of which 31 were flowering-related, 23 were hormone synthesis-related, and 27 were hormone signal transduction-related. Association analysis between the gene expression of the AGs and the flowering phenotypic data was carried out, and differentially expressed genes (DEGs) in a temperature-controlled experiment were obtained. As a result, 15 flowering-related candidate AGs (CAGs), 13 hormone synthesis-related CAGs, and 11 hormone signal transduction-related CAGs were further screened. The expression levels of the CAGs in the early-flowering accessions were different from those in the late-flowering ones, and also between the flowering trees and non-flowering trees. In a gradient chilling treatment, flowering rates of the trees and the CAGs expression were affected by the treatment. Our present work for the first time provided candidate genes for genetic regulation of flowering in litchi using transcriptome-based GWAS.

Chromatin and regulatory differentiation between bundle sheath and mesophyll cells in maize

C₄ plants partition photosynthesis enzymes between the bundle sheath (BS) and the mesophyll (M) cells for the better delivery of CO₂ to RuBisCO and to reduce photorespiration. To better understand how C₄ photosynthesis is regulated at the transcriptional level, we performed RNA-seq, ATAC-seq, ChIP-seq and Bisulfite-seq (BS-seq) on BS and M cells isolated from maize leaves. By integrating differentially expressed genes with chromatin features, we found that chromatin accessibility coordinates with epigenetic features, especially H3K27me3 modification and CHH methylation, to regulate cell type-preferentially enriched gene expression. Not only the chromatin-accessible regions (ACRs) proximal to the genes (pACRs) but also the distal ACRs (dACRs) are determinants of cell type-preferentially enriched expression. We further identified cell type-preferentially enriched motifs, e.g. AAAG for BS cells and TGACC/T for M cells, and determined their corresponding transcription factors: DOFs and WRKYs. The complex interaction between cis and trans factors in the preferential expression of C₄ genes was also observed. Interestingly, cell type-preferentially enriched gene expression can be fine-tuned by the coordination of multiple chromatin features. Such coordination may be critical in ensuring the cell type-specific function of key C₄ genes. Based on the observed cell type-preferentially enriched expression pattern and coordinated chromatin features, we predicted a set of functionally unknown genes, e.g. Zm00001d042050 and Zm00001d040659, to be potential key C₄ genes. Our findings provide deep insight into the architectures associated with C₄ gene expression and could serve as a valuable resource to further identify the regulatory mechanisms present in C₄ species.

[Comparison of single incision robot-assisted laparoscopic radical prostatectomy with and without extraperitoneal special channel device]

Objective: To compare the clinical effects of single-incision robot-assisted laparoscopic radical prostatectomy (RARP) with and without extraperitoneal special channel device. Methods: The clinical data of 70 patients who had undergone RARP in the Robotic Minimally Invasive Surgery Center of Sichuan Provincial People's Hospital from September 2020 to February 2021 were analyzed retrospectively, including 29 cases who were operated on without special channel device (group A) and 41 cases with special channel device (group B). All operations were performed by robot-assisted single-incision retrograde bladder neck exfoliation via extraperitoneal approach in patients by the same operator. The operation time, intraoperative blood loss, the bladder neck urethral anastomosis time, postoperative hospital stay, postoperative exhaust time, positive rate of incisal margin, indwelling time of urinary catheter, retention rate of postoperative erectile function, satisfaction rate of immediate postoperative urine control, positive rate of postoperative lymph node pathology, incision length, treatment cost and the rate of prostate specific antigen (PSA)lower than 0.2 μg/L at 6 weeks after operation were compared between the two groups. Results: All 70 cases were operated successfully. The difference of age[ (68.9±3.9) vs (69.4±5.4) years], preoperative PSA level[14.1(6.3, 19.8)vs13.7(5.8, 18.1)μg/L], prostate volume[44.8(30.7,172.6)vs 56.3(40.9,163.4)ml ] of the two groups was not statistically significant(all P>0.05). The difference of operation time [ (59.1±18.5) vs (59.6±18.0) min ], intraoperative blood loss [93(66,198)vs 95(68,203) ml ], bladder neck urethral anastomosis time [ (12.6±1.3) vs (13.7±2.8) min ], postoperative hospital stay [ (8.1±2.3) vs (9.1±1.3) d], postoperative exhaust time [ (1.4±0.6) vs (1.3±0.6) d], positive rate of incisal margin (20.7% vs 19.5%), indwelling time of the urinary catheter after operation [ (6.8±1.5) vs (7.1±2.0) d ], the retention rate of postoperative erectile function (31.0% vs 27.0%), the satisfaction rate of immediate postoperative urine control (79.3% vs 75.6%), the positive rate of postoperative lymph node pathology (17.2% vs 14.6%), the length of incision [ (5.1±0.5) vs (6.1±0.4) cm ], the rate of PSA lower than 0.2 μg/L at 6 weeks after operation (86.2% vs 83.0%) of the two groups was not statistically significant(all P>0.05). The operation cost of group A[(62 000±4 000) yuan]was lower than group B[(68 000±4 000) yuan] (P<0.05). Conclusion: Extraperitoneal non-special channel device single-incision RARP is safe and feasible.

McMYB4 improves temperature adaptation by regulating phenylpropanoid metabolism and hormone signaling in apple

Temperature changes affect apple development and production. Phenylpropanoid metabolism and hormone signaling play a crucial role in regulating apple growth and development in response to temperature changes. Here, we found that McMYB4 is induced by treatment at 28 °C and 18 °C, and McMYB4 overexpression results in flavonol and lignin accumulation in apple leaves. Yeast one-hybrid (Y1H) assays and electrophoretic mobility shift assays (EMSAs) further revealed that McMYB4 targets the promoters of the flavonol biosynthesis genes CHS and FLS and the lignin biosynthesis genes CAD and F5H. McMYB4 expression resulted in higher levels of flavonol and lignin biosynthesis in apple during growth at 28 °C and 18 °C than during growth at 23 °C. At 28 °C and 18 °C, McMYB4 also binds to the AUX/ARF and BRI/BIN promoters to activate gene expression, resulting in acceleration of the auxin and brassinolide signaling pathways. Taken together, our results demonstrate that McMYB4 promotes flavonol biosynthesis and brassinolide signaling, which decreases ROS contents to improve plant resistance and promotes lignin biosynthesis and auxin signaling to regulate plant growth. This study suggests that McMYB4 participates in the abiotic resistance and growth of apple in response to temperature changes by regulating phenylpropanoid metabolism and hormone signaling.

Effects of artificial light at night (ALAN) on gene expression of Aquatica ficta firefly larvae

Artificial light at night (ALAN) is a major driver of firefly population declines, but its physiological effects are not well understood. To investigate the impact of ALAN on firefly development, we exposed larval Aquatica ficta fireflies to ALAN for two weeks. High larval mortality was observed in the periods of 1-68 days and 106-134 days post-treatment, which may represent the short- and long-term impacts of ALAN. We then profiled the transcriptome of larval Aquatica ficta fireflies following two weeks of ALAN exposure. A total of 1262 (1.67% out of 75777 unigenes) were differentially expressed in the treatment group: 1157 were down-regulated, and 105 were up-regulated. Up-regulated unigenes were related to regulation of hormone levels, ecdysteroid metabolic process, and response to stimulus; down-regulated unigenes were related to negative regulation of insulin receptor signaling, germ cell development, oogenesis, spermatid development, and regulation of neuron differentiation. Transcriptome results suggest that the endocrine, reproductive, and neural development of firefly larvae could be impaired by even relatively brief period of ALAN exposure. This report contributes a much-needed molecular perspective to the growing body of research documenting the fitness impacts of ALAN on bioluminescent fireflies.

Missing Nurse Bees-Early Transcriptomic Switch From Nurse Bee to Forager Induced by Sublethal Imidacloprid

The environmental residue/sublethal doses of neonicotinoid insecticides are believed to generate a negative impact on pollinators, including honey bees. Here we report our recent investigation on how imidacloprid, one of the major neonicotinoids, affects worker bees by profiling the transcriptomes of various ages of bees exposed to different doses of imidacloprid during the larval stage. The results show that imidacloprid treatments during the larval stage severely altered the gene expression profiles and may induce precocious foraging. Differential expression of foraging regulators was found in 14-day-old treated adults. A high transcriptome similarity between larvae-treated 14-day-old adults and 20-day-old controls was also observed, and the similarity was positively correlated with the dose of imidacloprid. One parts per billion (ppb) of imidacloprid was sufficient to generate a long-term impact on the bee's gene expression as severe as with 50 ppb imidacloprid. The disappearance of nurse bees may be driven not only by the hive member constitution but also by the neonicotinoid-induced precocious foraging behavior.

[Investigating the causal relationship between human blood metabolites and coronary artery disease using two-sample Mendelian randomization]

OBJECTIVE

To explore the causal relationship between blood metabolites and the risk of coronary artery disease (CAD) using a two-sample Mendelian randomization (MR) approach.

OBJECTIVE

Based on the data from a large-scale metabolome-based genome-wide association study (mGWAS) and the GWAS of CAD, we investigated the causality between blood metabolites and CAD using an inverse variance weighted (IVW) method and another 4 two-sample MR models. Heterogeneity, horizontal pleiotropy, and sensitivity tests were performed to evaluate the stability and reliability of the results.

OBJECTIVE

Among the 486 blood metabolites, 32 metabolites showed nominally causative association with CAD with the IVW method (P < 0.05), including 11 known metabolites and 21 unknown metabolites. Three known metabolites [N-acetylornithine, bradykinin-des-arg(9), and succinylcarnitine] were statistically significant in at least 3 MR models, but their causal effects on CAD were no longer significant after sensitivity analysis using leave-one-out method and elimination of the confounding instrumental variables.

OBJECTIVE

There is no strong evidence to support a robust causal relationship between the 486 blood metabolites and the risk of CAD.

Liquid biopsy by combining 5-hydroxymethylcytosine signatures of plasma cell-free DNA and protein biomarkers for diagnosis and prognosis of hepatocellular carcinoma

BACKGROUND

Liquid biopsy based on 5-hydroxymethylcytosine (5hmC) signatures of plasma cell-free DNA (cfDNA) originating from tumor cells provides a novel approach for early diagnosis in hepatocellular carcinoma (HCC). Here, we sought to develop a reliable model using cfDNA 5hmC signatures and protein biomarkers for diagnosis and prognosis of HCC.

PATIENTS AND METHODS

We carried out genome-wide 5hmC sequencing of cfDNA samples collected from 165 healthy volunteers, 62 liver cirrhosis (LC) patients and 135 HCC patients. A sensitive 5hmC diagnostic model was developed based on 5hmC signatures selected by sparse Partial Least Squares Discriminant Analysis and cross-validation to define the weighted diagnostic score (wd-score). Then, we combined protein biomarkers with the wd-score to build a more robust score (HCC score) by logistic regression.

RESULTS

The distribution pattern of differential 5hmC regions could clearly distinguish HCC patients, LC patients and healthy volunteers. The wd-score based on 64 5hmC signatures in cfDNA achieves 93.24% of area under the curve (AUC) to distinguish HCC patients from non-HCC patients, and the HCC score by combing protein biomarkers achieves 92.75% of AUC to distinguish HCC patients from LC patients. Meanwhile, the HCC score showed high capacity for screening high recurrence risk patients after receiving surgical resection, and appeared to be an independent indicator for both relapse-free survival (P = 0.00865) and overall survival (P = 0.000739). Furthermore, the values of the HCC score in patients' longitudinal plasma samples were positively associated with tumor burden dynamics during follow-up.

CONCLUSION

We have developed and validated a novel non-invasive liquid biopsy strategy for HCC diagnosis, prognosis and surveillance during HCC progression.

[Economic evaluation of plasma exchange combined with dual plasma adsorption therapy for early, mid and late stage liver failure]

Objective: To compare the economic characteristics of the four artificial liver models [plasma exchange, half-dose plasma exchange combined with double plasma adsorption (DPMAS), pre-equal amount of plasma exchange followed by DPMAS, and pre-DPMAS followed by equal amount of plasma exchange] in the treatment of liver failure. Methods: A decision tree model was established with the Treeage pro 2011 software. The cost-effectiveness ratio and incremental cost-effectiveness value of four different treatment modalities were calculated and compared in patients with liver failure at early, mid and late stages, respectively. The sensitivity analysis of the model was performed using data from the preliminary research results of these groups. Results: The cost-effectiveness ratio and incremental cost-effectiveness value of patients treated with artificial liver therapy with half-dose plasma exchange combined with DPAMS plan in early stage liver failure were 89 547.79 and 34 665.34, which was lower than per capita GDP, so the increased cost had cost-effective advantages. In the middle and late stage of liver failure, the cost-effectiveness ratio and incremental cost-effectiveness value of pre-DPMAS followed by equal plasma exchange plan was 122 865.5 and 284 334.97, and 70 744.55 and 75 299.48, respectively, which was less than three times of per capita GDP. The increased cost was acceptable and had economic advantages. The sensitivity analysis results showed that the basic analysis results were reliable. Conclusion: Half-dose plasma exchange combined with DPAMS plan is the most cost-effective treatment for early liver failure, while pre-DPMAS followed by equal plasma exchange plan is the most economical treatment for mid and late stage liver failure.

Manipulation of ZDS in tomato exposes carotenoid- and ABA-specific effects on fruit development and ripening

Spontaneous mutations in fruit-specific carotenoid biosynthetic genes of tomato (Solanum lycopersicum) have led to improved understanding of ripening-associated carotenogenesis. Here, we confirm that ZDS is encoded by a single gene in tomato transcriptionally regulated by ripening transcription factors RIN, NOR and ethylene. Manipulation of ZDS was achieved through transgenic repression and heterologous over-expression in tomato. CaMV 35S-driven RNAi repression inhibited carotenoid biosynthesis in all aerial tissues examined resulting in elevated levels of ζ-carotene isomers and upstream carotenoids, while downstream all trans-lycopene and subsequent photoprotective carotenes and xanthophylls were diminished. Consequently, immature fruit displayed photo-bleaching consistent with reduced levels of the photoprotective carotenes and developmental phenotypes related to a reduction in the carotenoid-derived phytohormone abscisic acid (ABA). ZDS-repressed ripe fruit was devoid of the characteristic red carotenoid, all trans-lycopene and displayed brilliant yellow pigmentation due to elevated 9,9' di-cis-ζ-carotene. Over-expression of the Arabidopsis thaliana ZDS (AtZDS) gene bypassed endogenous co-suppression and revealed ZDS as an additional bottleneck in ripening-associated carotenogenesis of tomato. Quantitation of carotenoids in addition to multiple ripening parameters in ZDS-altered lines and ABA-deficient fruit-specific carotenoid mutants was used to separate phenotypic consequences of ABA from other effects of ZDS manipulation and reveal a unique and dynamic ζ-carotene isomer profile in ripe fruit.

Reconstructing the maize leaf regulatory network using ChIP-seq data of 104 transcription factors

The transcription regulatory network inside a eukaryotic cell is defined by the combinatorial actions of transcription factors (TFs). However, TF binding studies in plants are too few in number to produce a general picture of this complex network. In this study, we use large-scale ChIP-seq to reconstruct it in the maize leaf, and train machine-learning models to predict TF binding and co-localization. The resulting network covers 77% of the expressed genes, and shows a scale-free topology and functional modularity like a real-world network. TF binding sequence preferences are conserved within family, while co-binding could be key for their binding specificity. Cross-species comparison shows that core network nodes at the top of the transmission of information being more conserved than those at the bottom. This study reveals the complex and redundant nature of the plant transcription regulatory network, and sheds light on its architecture, organizing principle and evolutionary trajectory.

Micro-RNA Clusters Integrate Evolutionary Constraints on Expression and Target Affinities: The miR-6/5/4/286/3/309 Cluster in Drosophila

A striking feature of micro-RNAs is that they are often clustered in the genomes of animals. The functional and evolutionary consequences of this clustering remain obscure. Here, we investigated a micro-RNA cluster miR-6/5/4/286/3/309 that is conserved across drosophilid lineages. Small RNA sequencing revealed expression of this micro-RNA cluster in Drosophila melanogaster leg discs, and conditional overexpression of the whole cluster resulted in leg appendage shortening. Transgenic overexpression lines expressing different combinations of micro-RNA cluster members were also constructed. Expression of individual micro-RNAs from the cluster resulted in a normal wild-type phenotype, but either the expression of several ancient micro-RNAs together (miR-5/4/286/3/309) or more recently evolved clustered micro-RNAs (miR-6-1/2/3) can recapitulate the phenotypes generated by the whole-cluster overexpression. Screening of transgenic fly lines revealed downregulation of leg-patterning gene cassettes in generation of the leg-shortening phenotype. Furthermore, cell transfection with different combinations of micro-RNA cluster members revealed a suite of downstream genes targeted by all cluster members, as well as complements of targets that are unique for distinct micro-RNAs. Considered together, the micro-RNA targets and the evolutionary ages of each micro-RNA in the cluster demonstrate the importance of micro-RNA clustering, where new members can reinforce and modify the selection forces on both the cluster regulation and the gene regulatory network of existing micro-RNAs. Key words: micro-RNA, cluster, evolution.

BEL1-LIKE HOMEODOMAIN4 regulates chlorophyll accumulation, chloroplast development, and cell wall metabolism in tomato fruit

Tomato (Solanum lycopersicum) is a model plant for studying fruit development and ripening. In this study, we found that down-regulation of a tomato bell-like homeodomain 4 (SlBL4) resulted in a slightly darker-green fruit phenotype and increased accumulation of starch, fructose, and glucose. Analysis of chlorophyll content and TEM observations was consistent with these phenotypes, indicating that SlBL4 was involved in chlorophyll accumulation and chloroplast formation. Ripened fruit of SlBL4-RNAi plants had noticeably decreased firmness, larger intercellular spaces, and thinner cell walls than the wild-type. RNA-seq identified differentially expressed genes involved in chlorophyll metabolism, chloroplast development, cell wall metabolism, and carotenoid metabolism. ChIP-seq identified (G/A) GCCCA (A/T/C) and (C/A/T) (C/A/T) AAAAA (G/A/T) (G/A) motifs. SlBL4 directly inhibited the expression of protoporphyrinogen oxidase (SlPPO), magnesium chelatase H subunit (SlCHLD), pectinesterase (SlPE), protochlorophyllide reductase (SlPOR), chlorophyll a/b binding protein 3B (SlCAB-3B), and homeobox protein knotted 2 (TKN2). In contrast, it positively regulated the expression of squamosa promoter binding protein-like colorless non-ripening (LeSPL-CNR). Our results indicate that SlBL4 is involved in chlorophyll accumulation, chloroplast development, cell wall metabolism, and the accumulation of carotenoids during tomato fruit ripening, and provide new insights for the transcriptional regulation mechanism of BELL-mediated fruit growth and ripening.

Plant and animal chromatin three-dimensional organization: similar structures but different functions

Chromatin is the main carrier of genetic information and is non-randomly distributed within the nucleus. Next-generation sequence-based chromatin conformation capture technologies have enabled us to directly examine its three-dimensional organization at an unprecedented scale and resolution. In the best-studied mammalian models, chromatin folding can be broken down into three hierarchical levels, compartment, domains, and loops, which play important roles in transcriptional regulation. Although similar structures have now been identified in plants, they might not possess exactly the same functions as the mammalian ones. Here, we review recent Hi-C studies in plants, compare plant chromatin structures with their mammalian counterparts, and discuss the differences between plants with different genome sizes.

Thermal-responsive genetic and epigenetic regulation of DAM cluster controlling dormancy and chilling requirement in peach floral buds

The Dormancy-associated MADS-box (DAM) gene cluster in peach serves as a key regulatory hub on which the seasonal temperatures act and orchestrate dormancy onset and exit, chilling response and floral bud developmental pace. Yet, how different temperature regimes interact with and regulate the six linked DAM genes remains unclear. Here, we demonstrate that chilling downregulates DAM1 and DAM3-6 in dormant floral buds with distinct patterns and identify DAM4 as the most abundantly expressed one. We reveal multiple epigenetic events, with tri-methyl histone H3 lysine 27 (H3K27me3) induced by chilling specifically in DAM1 and DAM5, a 21-nt sRNA in DAM3 and a ncRNA induced in DAM4. Such induction is inversely correlated with downregulation of their cognate DAMs. We also show that the six DAMs were hypermethylated, associating with the production of 24-nt sRNAs. Hence, the chilling-responsive dynamic of the different epigenetic elements and their interactions likely define distinct expression abundance and downregulation pattern of each DAM. We further show that the expression of the five DAMs remains steadily unchanged or continuously downregulated at the ensuing warm temperature after chilling, and this state of regulation correlates with robust increase of sRNA expression, H3K27me3 and CHH methylation, which is particularly pronounced in DAM4. Such robust increase of repressive epigenetic marks may irreversibly reinforce the chilling-imposed repression of DAMs to ensure flower-developmental programming free from any residual DAM inhibition. Taken together, we reveal novel information about genetic and epigenetic regulation of the DAM cluster in peach, which will be of fundamental significance in understanding of the regulatory mechanisms underlying chilling requirement and dormancy release, and of practical application for improvement of plasticity of flower time and bud break in fruit trees to adapt changing climates.

METHYLTRANSFERASE1 and Ripening Modulate Vivipary during Tomato Fruit Development

Vivipary, wherein seeds germinate prior to dispersal while still associated with the maternal plant, is an adaptation to extreme environments. It is normally inhibited by the establishment of dormancy. The genetic framework of vivipary has been well studied; however, the role of epigenetics in vivipary remains unknown. Here, we report that silencing of METHYLTRANSFERASE1 (SlMET1) promoted precocious seed germination and seedling growth within the tomato (Solanum lycopersicum) epimutant Colorless non-ripening (Cnr) fruits. This was associated with decreases in abscisic acid concentration and levels of mRNA encoding 9-cis-epoxycarotenoid-dioxygenase (SlNCED), which is involved in abscisic acid biosynthesis. Differentially methylated regions were identified in promoters of differentially expressed genes, including SlNCED SlNCED knockdown also induced viviparous seedling growth in Cnr fruits. Strikingly, Cnr ripening reversion suppressed vivipary. Moreover, neither SlMET1/SlNCED-virus-induced gene silencing nor transgenic SlMET1-RNA interference produced vivipary in wild-type tomatoes; the latter affected leaf architecture, arrested flowering, and repressed seed development. Thus, a dual pathway in ripening and SlMET1-mediated epigenetics coordinates the blockage of seed vivipary.

Antibiotic-induced role interchange between rare and predominant bacteria retained the function of a bacterial community for denitrifying quinoline degradation

AIM

Quinoline is a recalcitrant pollutant in coking wastewater which has been broadly investigated with many isolates possessing aerobic quinoline-degrading ability. However, studies on anaerobic degradation and the corresponding bacteria are very scarce. This study attempted to investigate the role of diverse functional members and the redundancy of quinoline degradation in a lab-scale quinoline denitrifying bioreactor.

METHODS AND RESULTS

Antibiotics were added to the batch culture under denitrifying conditions to disturb the microbial community of the quinoline-degrading bioreactor. According to the results, the nitrate removal rate remained stable, and the quinoline removal rate increased by 9·7% after treatment with streptomycin. However, PCoA analysis of 16S rRNA gene sequencing data of these samples indicated a significant shift in microbial community structures. Specifically, 12 operational taxonomic units (OTUs), including OTU1 (Pseudomonas) and OTU2 (Achromobacter), were significantly enriched. OTU1 replaced OTU8 (Thauera) as the most predominant denitrifying quinoline-degrading member. However, OTU8 and other predominant OTUs (Comamonas and Pseudoxanthomonas), which were hypothesized to contribute essentially to quinoline degradation in the origin bioreactor, became almost undetectable.

CONCLUSION

Functional redundancy due to high biological diversity allowed the role reversal of predominant quinoline-degrading bacteria and other rare bacteria when disturbed by antibiotic stress. Although the abundance of OTU1 was much lower initially, it replaced the essential role of the predominant member OTU8 in the bioreactor community for quinoline degradation once the environmental condition changed.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study indicated that the high biological diversity in a wastewater treatment bacterial community is crucial for maintaining the degrading function of organic pollutants, especially in a changing environment due to external disturbance or stress.

SlGRAS4 mediates a novel regulatory pathway promoting chilling tolerance in tomato

Tomato (Solanum lycopersicum L.) plants are cold-sensitive, and the fruit are susceptible to postharvest chilling injury when stored at low temperature. However, the mechanisms underlying cold stress responses in tomato are poorly understood. We demonstrate that SlGRAS4, encoding a transcription factor induced by low temperature, promotes chilling tolerance in tomato leaves and fruit. Combined genome-wide ChIP-seq and RNA-seq approaches identified among cold stress-associated genes those being direct targets of SlGRAS4 and protein studies revealed that SlGRAS4 forms a homodimer to self-activate its own promoter. SlGRAS4 can also directly bind tomato SlCBF promoters to activate their transcription without inducing any growth retardation. The study identifies the SlGRAS4-regulon as a new cold response pathway conferring cold stress tolerance in tomato independently of the ICE1-CBF pathway. This provides new track for breeding strategies aiming to improve chilling tolerance of cultivated tomatoes and to preserve sensory qualities of tomato fruit often deteriorated by storage at low temperatures.

Attosecond timing of electron emission from a molecular shape resonance

Shape resonances in physics and chemistry arise from the spatial confinement of a particle by a potential barrier. In molecular photoionization, these barriers prevent the electron from escaping instantaneously, so that nuclei may move and modify the potential, thereby affecting the ionization process. By using an attosecond two-color interferometric approach in combination with high spectral resolution, we have captured the changes induced by the nuclear motion on the centrifugal barrier that sustains the well-known shape resonance in valence-ionized N2. We show that despite the nuclear motion altering the bond length by only 2%, which leads to tiny changes in the potential barrier, the corresponding change in the ionization time can be as large as 200 attoseconds. This result poses limits to the concept of instantaneous electronic transitions in molecules, which is at the basis of the Franck-Condon principle of molecular spectroscopy.

Non-homology-based prediction of gene functions in maize (Zea mays ssp. mays)

Advances in genome sequencing and annotation have eased the difficulty of identifying new gene sequences. Predicting the functions of these newly identified genes remains challenging. Genes descended from a common ancestral sequence are likely to have common functions. As a result, homology is widely used for gene function prediction. This means functional annotation errors also propagate from one species to another. Several approaches based on machine learning classification algorithms were evaluated for their ability to accurately predict gene function from non-homology gene features. Among the eight supervised classification algorithms evaluated, random-forest-based prediction consistently provided the most accurate gene function prediction. Non-homology-based functional annotation provides complementary strengths to homology-based annotation, with higher average performance in Biological Process GO terms, the domain where homology-based functional annotation performs the worst, and weaker performance in Molecular Function GO terms, the domain where the accuracy of homology-based functional annotation is highest. GO prediction models trained with homology-based annotations were able to successfully predict annotations from a manually curated "gold standard" GO annotation set. Non-homology-based functional annotation based on machine learning may ultimately prove useful both as a method to assign predicted functions to orphan genes which lack functionally characterized homologs, and to identify and correct functional annotation errors which were propagated through homology-based functional annotations.

Vertical distribution of microbial communities and their response to metal(loid)s along the vadose zone-aquifer sediments

AIMS

This study attempted to demonstrate the vertical shift in bacterial, archaeal and fungal communities along the vadose zone-aquifer sediments and their respective responses to environmental factors.

METHODS AND RESULTS

We collected samples from the vadose zone and three aquifer sediments along a 42·5 m bore of a typical agricultural land. The results showed that the bacterial community shifted greatly with depth. The classes of Actinobacteria (19·5%) and NC10 (11·0%) were abundant in the vadose zone while Alphaproteobacteria (22·3%) and Gammaproteobacteria (20·1%) were enriched in the aquifer. Archaeal and fungal communities were relatively more homogeneous with no significant trend as a function of depth. Process analyses further indicated that selection dominated in the bacterial community, whereas stochastic processes governed archaeal and fungal communities. Moreover environment-bacteria interaction analysis showed that metal(loid)s, especially alkali metal, had a closer correlation with the bacterial community than physicochemical variables.

CONCLUSIONS

Depth strongly affected bacterial rather than archaeal and fungal communities. Metal(loid)s prevailed over physicochemical variables in shaping the bacterial community in the vadose zone-aquifer continuum.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our study provides a new perspective on the structure of microbial communities from the vadose zone to the deep aquifers.

OP0223 EFFICACY AND SAFETY OF UPADACITINIB IN PATIENTS WITH ACTIVE PSORIATIC ARTHRITIS AND INADEQUATE RESPONSE TO BIOLOGIC DISEASE-MODIFYING ANTI-RHEUMATIC DRUGS (SELECT-PSA-2): A DOUBLE-BLIND, RANDOMIZED CONTROLLED PHASE 3 TRIAL

Background:

Upadacitinib (UPA) is an oral, reversible, JAK inhibitor approved for treatment of moderate to severe rheumatoid arthritis (RA) and currently under evaluation for treatment of psoriatic arthritis (PsA).

Objectives:

To assess the efficacy and safety of UPA versus placebo (PBO) in patients (pts) with PsA and prior inadequate response or intolerance to ≥1 biologic disease-modifying anti-rheumatic drug (bDMARD).

Methods:

In SELECT-PsA-2, pts were randomized 1:1:1 to once daily UPA 15 mg (UPA15), UPA 30 mg (UPA30), or PBO. Pts were stratified by baseline DMARD use, number of prior failed bDMARDs, and extent of psoriasis. The primary endpoint was the proportion of pts achieving ACR20 response at Wk 12. Multiplicity controlled secondary endpoints included change in HAQ-DI, FACIT-Fatigue (FACIT-F), and SF-36 Physical Component Summary (PCS) at Wk 12; static Investigator Global Assessment (sIGA) of Psoriasis of 0 or 1 and at least a 2-point improvement from baseline, PASI75, and change in Self-Assessment of Psoriasis Symptoms (SAPS) at Wk 16; and proportion of pts achieving MDA at Wk 24. Additional key secondary endpoints were ACR50 and ACR70 at Wk 12, and ACR20 at Wk 2. Treatment-emergent adverse events (TEAEs) are reported for pts who received ≥1 dose of study drug.

Results:

641 pts were randomized and received study drug; 54.3% were female with mean age of 53.4 years, and mean duration since PsA diagnosis of 10.1 years. 61% of pts failed 1 bDMARD, 18% failed 2 bDMARDs, and 13% failed ≥3 bDMARDs. 543 (84.6%) pts completed Wk 24 study drug.

At Wk 12, a significantly greater proportion of pts receiving UPA15 and UPA30 vs PBO achieved ACR20 (56.9% and 63.8% vs 24.1%; p < .0001 for both comparisons). Statistically significant improvements were observed in the UPA15 and UPA30 arms vs PBO in all multiplicity controlled secondary endpoints, including ΔHAQ-DI (PBO, -0.10; UPA15, -0.30; UPA30, -0.41), ΔSF-36 PCS (PBO, 1.6; UPA15, 5.2; UPA30, 7.1), ΔFACIT-F (PBO, 1.3; UPA15, 5.0; UPA30, 6.1), and ΔSAPS (PBO, -1.5; UPA15, -24.4; UPA30, -29.7; p < .0001 for all endpoints;Figure 1). In addition, a greater proportion of pts achieved ACR50 and ACR70 at Wk 12 with UPA vs PBO. Generally, TEAEs were reported at similar frequencies in the PBO and UPA15 arms and at a higher frequency in the UPA30 arm (Figure 2). Numerically higher rates of serious AEs were reported in the UPA arms. Herpes zoster was more frequent with UPA30. Three malignancies occurred in each of the UPA arms. One adjudicated non-fatal myocardial infarction and one adjudicated pulmonary embolism were reported with UPA15.

Conclusion:

In this bDMARD-IR PsA population, UPA15 and UPA30 demonstrated significant improvements across PsA domains including improvements in joint and skin signs and symptoms vs PBO through Wk 24 with improvement observed by Wk 2. A greater percentage of pts treated with UPA achieved MDA and ACR50/70, stringent composite measures of disease control. No new safety signals were identified compared to what has been observed with UPA in RA.

Disclosure of Interests:

Mark C. Genovese Grant/research support from: Abbvie, Eli Lilly and Company, EMD Merck Serono, Galapagos, Genentech/Roche, Gilead Sciences, Inc., GSK, Novartis, Pfizer Inc., RPharm, Sanofi Genzyme, Consultant of: Abbvie, Eli Lilly and Company, EMD Merck Serono, Genentech/Roche, Gilead Sciences, Inc., GSK, Novartis, RPharm, Sanofi Genzyme, Apinya Lertratanakul Shareholder of: AbbVie Inc., Employee of: AbbVie Inc., Jaclyn Anderson Shareholder of: AbbVie Inc., Employee of: AbbVie Inc., Kim Papp Grant/research support from: AbbVie, Amgen, Astellas, Baxalta, Boehringer Ingelheim, Bristol-Myers Squibb, Celgene, Centocor, Dermira, Eli Lilly, Galderma, Genentech, GlaxoSmithKline, Janssen, Kyowa-Hakko Kirin, Leo Pharma, MedImmune, Merck-Serono, Merck Sharp & Dohme, Novartis, Pfizer, Regeneron, Roche, Sanofi-Genzyme, Stiefel, Takeda, UCB, and Valeant., Consultant of: AbbVie, Amgen, Astellas, Baxalta, Baxter, Boehringer Ingelheim, Bristol-Myers Squibb, Celgene, Centocor, Dermira, Eli Lilly, Forward Pharma, Galderma, Genentech, GlaxoSmithKline, Janssen, Kyowa-Hakko Kirin, Leo Pharma, MedImmune, Merck-Serono, Merck Sharp & Dohme, Novartis, Pfizer, Regeneron, Roche, Sanofi-Genzyme, Stiefel, Sun Pharma, Takeda, UCB, and Valeant, Speakers bureau: AbbVie, Amgen, Astellas, Baxalta, Baxter, Boehringer Ingelheim, Bristol-Myers Squibb, Celgene, Centocor, Dermira, Eli Lilly, Forward Pharma, Galderma, Genentech, GlaxoSmithKline, Janssen, Kyowa-Hakko Kirin, Leo Pharma, MedImmune, Merck-Serono, Merck Sharp & Dohme, Novartis, Pfizer, Regeneron, Roche, Sanofi-Genzyme, Stiefel, Sun Pharma, Takeda, UCB, and Valeant, William Tillett Grant/research support from: AbbVie, Celgene, Eli Lilly, Janssen, Novartis, Pfizer Inc, UCB, Consultant of: AbbVie, Amgen, Celgene, Lilly, Janssen, Novartis, MSD, Pfizer Inc, UCB, Speakers bureau: AbbVie, Amgen, Celgene, Lilly, Janssen, Novartis, Pfizer Inc, UCB, Filip van den Bosch Consultant of: AbbVie, Celgene Corporation, Eli Lilly, Galapagos, Janssen, Novartis, Pfizer, and UCB, Speakers bureau: AbbVie, Celgene Corporation, Eli Lilly, Galapagos, Janssen, Novartis, Pfizer, and UCB, Shigeyoshi Tsuji Grant/research support from: Eli Lilly, Speakers bureau: AbbVie, Asahi Kasei, Chugai, Daiichi Sankyo, Eli Lilly, Eisai, Mitsubishi Tanabe, Celgene, and Novartis Pharma K.K., Eva Dokoupilova Grant/research support from: Eli Lilly, AbbVie, Novartis, MAURO KEISERMAN Speakers bureau: Pfizer, Abbott, Actelion, AstraZeneca, Amgen, Roche, Bristol Myers Squibb, and Janssen and has received clinical trial honoraria from Pfizer, Amgen, AstraZeneca, Anthera Pharmaceuticals, Bristol-Myers Squibb, Biogen Idec Inc, Celltrion Inc., Eli Lilly, Human Genome Sciences, Novartis, Roche, Sanofi, UCB Inc., xin wang Shareholder of: AbbVie Inc., Employee of: AbbVie Inc., Sheng Zhong Shareholder of: AbbVie Inc., Employee of: AbbVie Inc., Patrick Zueger Shareholder of: AbbVie Inc., Employee of: AbbVie Inc., Aileen Pangan Shareholder of: AbbVie Inc., Employee of: AbbVie Inc., Philip J Mease Grant/research support from: Abbott, Amgen, Biogen Idec, BMS, Celgene Corporation, Eli Lilly, Novartis, Pfizer, Sun Pharmaceutical, UCB – grant/research support, Consultant of: Abbott, Amgen, Biogen Idec, BMS, Celgene Corporation, Eli Lilly, Novartis, Pfizer, Sun Pharmaceutical, UCB – consultant, Speakers bureau: Abbott, Amgen, Biogen Idec, BMS, Eli Lilly, Genentech, Janssen, Pfizer, UCB – speakers bureau

FRI0140 IMPACT OF BASELINE DEMOGRAPHICS AND DISEASE ACTIVITY ON OUTCOMES IN PATIENTS WITH RHEUMATOID ARTHRITIS RECEIVING UPADACITINIB

Background:

Upadacitinib (UPA), an oral selective JAK1 inhibitor, has demonstrated favorable efficacy and acceptable safety in five Phase 3 global studies in patients with moderately to severely active rheumatoid arthritis (RA).1–5

Objectives:

This analysis reports the efficacy and safety of UPA in predefined RA patient subgroups based on differences in baseline demographics and disease activity.

Methods:

Data were pooled from three pivotal, double-blind, PBO-controlled, multicenter, Phase 3 studies in patients with RA who had an inadequate response(IR) to conventional synthetic DMARDs (csDMARD-IR: SELECT-NEXT [N=661]), MTX(MTX-IR; SELECT-COMPARE[N=1629]), or biologic DMARDs(bDMARD-IR: SELECT-BEYOND[N=498]). Two integrated analysis sets were evaluated: one comparing UPA 15 mg QD vs PBO(SELECT-NEXT, SELECT-COMPARE, SELECT-BEYOND) and the other comparing UPA 15 mg QD and UPA 30 mg QD vs PBO(SELECT-NEXT, SELECT-BEYOND). All patients received background treatment with csDMARDs. The proportion of patients achieving ACR20 and DAS28(CRP) ≤3.2 at Week 12 was evaluated by predefined baseline demographics and disease activity measure groups, including age, sex, weight, BMI, race, geographic region, duration of RA, RF, and ACPA status, and level of high sensitivity CRP. Non-responder imputation was used for missing data. Subgroup analyses for safety were performed for age, race, sex, weight, BMI, and Asian region.

Results:

Across the three Phase 3 studies, 1036, 384, and 1041 patients received UPA 15 mg QD, UPA 30 mg QD or PBO, respectively. The demographic and baseline disease characteristics in the two integrated analysis sets were balanced across treatment groups. ACR20 and DAS28 ≤3.2 response rates at Week 12 were consistently higher with UPA 15 mg and UPA 30 mg vs PBO across the evaluated demographic and baseline disease characteristics(Figure 1a,Figure 1b). The efficacy of UPA 15 mg QD was generally similar to that observed with UPA 30 mg QD. At 12 weeks, the proportion of patients with treatment-emergent AEs, serious AEs, severe AEs, and AEs leading to discontinuation were generally comparable across different age, sex, race, weight, and BMI groups. Compared with the global population, patients receiving UPA in the Asian region had a higher rate of CPK elevations(UPA 30 mg only) and herpes zoster; herpes zoster also has been observed to be higher in the Asian region with other JAK inhibitors.6,7

Conclusion:

In this analysis of pooled integrated efficacy data in csDMARD-IR or bDMARD-IR patients with RA, UPA 15 mg or 30 mg QD in combination with csDMARDs improved efficacy outcomes at Week 12 when compared with PBO across all predefined subgroups evaluated.

References:

[1]Burmester GR, et al. Lancet 2018 23;391:2503–2512;

[2]Genovese MC, et al. Lancet 2018; 391:2513–24;

[3]Smolen JS, et al. Lancet 2019 May 23[Epub ahead of print];

[4]van Vollenhoven R, et al. Arthritis Rheumatol 2018;70(Suppl. 10): Abstract 891;

[5]Fleischmann R, et al. Arthritis Rheumatol 2018;70(Suppl. 10): Abstract 890;

[6]Winthrop KL, et al. Arthritis Rheum 2014;66:2675-84;

[7] Winthrop KL, et al. ACR 2016 [Abstract 3027]

Disclosure of Interests:

Michael Weinblatt Grant/research support from: Amgen, Bristol-Myers Squibb, Crescendo, Lily, Sanofi/Regeneron, Consultant of: AbbVie, Amgen, Bristol-Myers Squibb, Crescendo, Gilead, Horizon, Lily, Pfizer, Roche, Eduardo Mysler Grant/research support from: AbbVie, Amgen, Bristol Myers Squibb, Roche, Eli Lilly, Novartis, Janssen, Sanofi, and Pfizer., Speakers bureau: AbbVie, Amgen, Bristol Myers Squibb, Roche, Eli Lilly, Novartis, Janssen, Sanofi, and Pfizer, Andrew Ostor Consultant of: MSD, Pfizer, Lilly, Abbvie, Novartis, Roche, Gilead and BMS, Speakers bureau: MSD, Pfizer, Lilly, Abbvie, Novartis, Roche, Gilead and BMS, Aaron Broadwell Grant/research support from: Janssen Research & Development, LLC, Janssen, Eli Lilly, Consultant of: AbbVie, Amgen, AstraZeneca, Celgene, Eli Lilly, Janssen, Novartis, Pfizer, Sandoz, Speakers bureau: AbbVie, Amgen, Celgene, GSK, Horizon, Janssen, Mallinckrodt, Novartis, Pfizer, Radius, Sanofi-Regeneron, UCB, Sławomir Jeka Grant/research support from: AbbVie, Pfizer, Roche, Novartis, MSD, Sandoz, Eli Lilly, Egis, UCB, Celgene, Speakers bureau: AbbVie, Pfizer, Roche, Novartis, MSD, Sandoz, Eli Lilly, Egis, UCB, Celgene, Kendall Dunlap Shareholder of: AbbVie Inc., Employee of: AbbVie Inc., Jessica Suboticki Shareholder of: AbbVie Inc., Employee of: AbbVie Inc., Jeffrey Enejosa Shareholder of: AbbVie Inc., Employee of: AbbVie Inc., Barbara Hendrickson Shareholder of: AbbVie Inc., Employee of: AbbVie Inc., Sheng Zhong Shareholder of: AbbVie Inc., Employee of: AbbVie Inc., Katya Cherny Shareholder of: AbbVie Inc., Employee of: AbbVie Inc., Grace Wright Consultant of: AbbVie, Amgen, BMS, Exagen, Janssen, Lilly, Medac, Myriad Autoimmune, Novartis, Pfizer, Sanofi Genzyme Regeneron, and UCB, Speakers bureau: AbbVie, Amgen, BMS, Exagen, Lilly, Medical Education Resource, Myriad Autoimmune, Novartis, Sanofi Genzyme Regeneron, UCB, and Vindico

Clipping defoliation and nitrogen addition shift competition between a C3 grass (Leymus chinensis) and a C4 grass (Hemarthria altissima)

Human-induced disturbances, including grazing and clipping, that cause defoliation are common in natural grasslands. Plant functional type differences in the ability to compensate for this tissue loss may influence interspecific competition. To explore the effects of different intensities of clipping and nitrogen (N) addition on compensatory growth and interspecific competition, we measured accumulated aboveground biomass (AGB), belowground biomass (BGB), tiller number, non-structural carbohydrates concentrations and leaf gas exchange parameters in two locally co-occurring species (the C₃ grass Leymus chinensis and the C₄ grass Hemarthria altissima) growing in monoculture and in mixture. For both grasses, the clipping treatment had significant impacts on the accumulated AGB, and the 40% clipping treatment had the largest effect. BGB gradually decreased with increasing defoliation intensity. Severe defoliation caused a significant increase in tiller number. Stored carbohydrates in the belowground biomass were mobilised and transported aboveground for the growth of new leaves to compensate for clipping-induced injury. The net CO₂ assimilation rate (A) of the remaining leaves increased with clipping intensity and peaked under clipping intensities of 20% or 40%. Nitrogen addition, at a rate of 10 g·N·m^-2 ·year^-1 , enhanced A of the remaining leaves and non-structural carbohydrate concentrations, which benefited plant compensatory growth, especially for the C₃ grass. Under the mixed planting conditions, the clipping and N addition treatments lowered the competitive advantage of the C₄ grass. The results suggest that a combination of defoliation and N deposition have the potential to benefit the coexistence of C₃ and C₄ grasses.

Tissue-specific Hi-C analyses of rice, foxtail millet and maize suggest non-canonical function of plant chromatin domains

Chromatins are not randomly packaged in the nucleus and their organization plays important roles in transcription regulation, which is best studied in the mammalian models. Using in situ Hi-C, we have compared the 3D chromatin architectures of rice mesophyll and endosperm, foxtail millet bundle sheath and mesophyll, and maize bundle sheath, mesophyll and endosperm tissues. We found that their global A/B compartment partitions are stable across tissues, while local A/B compartment has tissue-specific dynamic associated with differential gene expression. Plant domains are largely stable across tissues, while new domain border formations are often associated with transcriptional activation in the region. Genes inside plant domains are not conserved across species, and lack significant co-expression behavior unlike those in mammalian TADs. Although we only observed chromatin loops between gene islands in the large genomes, the maize loop gene pairs' syntenic orthologs have shorter physical distances in small genome monocots, suggesting that loops instead of domains might have conserved biological function. Our study showed that plants' chromatin features might not have conserved biological functions as the mammalian ones.

miR-30a-5p modulates traits of cutaneous squamous cell carcinoma (cSCC) via forkhead box protein G1 (FOXG1)

miRNA has shown its potential in the regulation of squamous cell carcinoma (SCC). However, the mechanism of such an effect was not quite clear. Therefore, we aimed to investigate whether miR-30a-5p participated in the regulation of cutaneous SCC (cSCC) and the possible mechanism involved. 5-Ethynyl-2'-deoxyuridine (EdU) and cell cycle were measured using flow cytometry. The formation of cell colony was tested by colony formation assay. The capacities of migration and invasion were tested by wound healing assay and Transwell invasion assay, respectively. The target of miR-30a-5p was predicted by bioinformatics and identified by luciferase assay. Western blot was used for the determination of proteins and qPCR was for mRNA levels. miR-30a-5p expression was lowered in SCL-1 and A431 cells, and its upregulation suppressed EdU positive cells, colony numbers, migration, invasion and Bcl-2 expression, and elevated Bcl-2-associated X protein (Bax) and cleaved Caspase-3 expressions, arresting cell cycle in G1 phase. Moreover, forkhead box protein G1 (FOXG1) was proved to be the target of miR-30a-5p, and FOXG1 overexpression partially offsets the decreased colony numbers, migration and invasion rates due to miR-30a-5p overexpression in SCL-1 and A431 cells. miR-30a-5p showed a regulatory role on the expression of FOXG1 and further modulated the progressing of cSCC cells, which could be a novel pathway intervening the development of cSCC.

A randomised controlled trial of stepwise sputum collection to increase yields of confirmed tuberculosis

<sec> <title>SETTING</title> The proportion of bacteriologically confirmed tuberculosis (TB) in China has decreased far below the worldwide average. </sec> <sec> <title>OBJECTIVE</title> To investigate whether stepwise measures to ensure sputum quality can improve the rate of bacteriologically confirmed TB. </sec> <sec> <title>DESIGN</title> We enrolled 980 adults with suspected TB from three counties in China during 2017 for this multicentre randomised controlled trial. Half the participants (n = 490) were randomly assigned to intervention groups that received instructions by a study nurse, and sputum induction, if necessary. In the remaining 490 patients, sputum samples were collected without observation. The primary outcome was the proportion of patients detected as bacteriologically positive on smear, culture or molecular assays (EasyNAT or Xpert). </sec> <sec> <title>RESULTS</title> Bacteriological confirmation rates were significantly higher in the intervention than in the control group: overall (159/490 [32%] vs. 122/490 [25%]; P = 0.009); confirmation using smear (17% vs. 11%; P = 0.010); confirmation using culture (28% vs. 21%; P = 0.021); and confirmation using molecular assays (27% vs. 18%; P = 0.001). Most of the improvement was in patients who received instruction alone, while improvement was greatest in younger patients (adjusted odds ratio 1.27, 95%CI 1.05-1.53 per 10 years). </sec> <sec> <title>CONCLUSIONS</title> If implemented effectively in resource-limited primary care clinics, our simple stepwise procedure combining instruction and sputum induction could increase the proportion of bacteriologically confirmed TB significantly. </sec>.