Integrated analysis of ATAC-seq and transcriptomic reveals the ScDof3-ScproC molecular module regulating the cold acclimation capacity of potato

Low temperature severely affects the geographical distribution and production of potato, which may incur cold damage in early spring or winter. Cultivated potatoes, mainly derived from Solanum tuberosum, are sensitive to freezing stress, but wild species of potato such as S. commersonii exhibit both constitutive freezing tolerance and/or cold acclimation tolerance. Hence, such wild species could assist in cold hardiness breeding. Yet the key transcription factors and their downstream functional genes that confer freezing tolerance are far from clear, hindering the breeding process. Here, we used ATAC-seq (Assay for Transposase-Accessible Chromatin with high-throughput sequencing) alongside RNA-seq to investigate the variation in chromatin accessibility and patterns of gene expression in freezing-tolerant CMM5 (S. commersonii), before and after its cold treatment. Our results suggest that after exposure to cold, transcription factors including Dof3, ABF2, PIF4, and MYB4 were predicted to further control the genes active in the synthetic/metabolic pathways of plant hormones, namely abscisic acid, polyamine, and reductive glutathione (among others). This suggests these transcription factors could regulate freezing tolerance of CMM5 leaves. In particular, ScDof3 was proven to regulate the expression of ScproC (pyrroline-5-carboxylate reductase, P5CR) according to dual-LUC assays. Overexpressing ScDof3 in Nicotiana benthamiana leaves led to an increase in both the proline content and expression level of NbproC (homolog of ScproC). These results demonstrate the ScDof3-ScproC module regulates the proline content and thus promotes freezing tolerance in potato. Our research provides valuable genetic resources to further study the molecular mechanisms underpinning cold tolerance in potato.

Molecular Insights into the Accelerated Sprouting of and Apical Dominance Release in Potato Tubers Subjected to Post-Harvest Heat Stress

Climate change-induced heat stress (HS) increasingly threatens potato (Solanum tuberosum L.) production by impacting tuberization and causing the premature sprouting of tubers grown during the hot season. However, the effects of post-harvest HS on tuber sprouting have yet to be explored. This study aims to investigate the effects of post-harvest HS on tuber sprouting and to explore the underlying transcriptomic changes in apical bud meristems. The results show that post-harvest HS facilitates potato tuber sprouting and negates apical dominance. A meticulous transcriptomic profiling of apical bud meristems unearthed a spectrum of differentially expressed genes (DEGs) activated in response to HS. During the heightened sprouting activity that occurred at 15-18 days of HS, the pathways associated with starch metabolism, photomorphogenesis, and circadian rhythm were predominantly suppressed, while those governing chromosome organization, steroid biosynthesis, and transcription factors were markedly enhanced. The critical DEGs encompassed the enzymes pivotal for starch metabolism, the genes central to gibberellin and brassinosteroid biosynthesis, and influential developmental transcription factors, such as SHORT VEGETATIVE PHASE, ASYMMETRIC LEAVES 1, SHOOT MERISTEMLESS, and MONOPTEROS. These findings suggest that HS orchestrates tuber sprouting through nuanced alterations in gene expression within the meristematic tissues, specifically influencing chromatin organization, hormonal biosynthesis pathways, and the transcription factors presiding over meristem fate determination. The present study provides novel insights into the intricate molecular mechanisms whereby post-harvest HS influences tuber sprouting. The findings have important implications for developing strategies to mitigate HS-induced tuber sprouting in the context of climate change.

Screening for Resistance Resources against Bacterial Wilt in Wild Potato

Potato is an important crop, used not only for food production but also for various industrial applications. With the introduction of the potato as a staple food strategy, the potato industry in China has grown rapidly. However, issues related to bacterial wilt, exacerbated by factors such as seed potato transportation and continuous cropping, have become increasingly severe in the primary potato cultivation regions of China, leading to significant economic losses. The extensive genetic diversity of Ralstonia solanacearum (R. solanacearum), which is the pathogen of bacterial wilt, has led to a lack of highly resistant potato genetic resources. There is a need to identify and cultivate potato varieties with enhanced resistance to reduce the adverse impact of this disease on the industry. We screened 55 accessions of nine different wild potato species against the bacterial wilt pathogen R. solanacearum PO2-1, which was isolated from native potato plants and belongs to phylotype II. Three accessions of two species (ACL24-2, PNT880-3, and PNT204-23) were identified with high resistance phenotypes to the tested strains. We found these accessions also showed high resistance to different phylotype strains. Among them, only PNT880-3 was capable of flowering and possessed viable pollen, and it was diploid. Consistent with the high resistance, decreased growth of R. solanacearum was detected in PNT880-3. All these findings in our study reveal that the wild potato PNT880-3 was a valuable resistance source to bacterial wilt with breeding potential.

The value of MRI in predicting hepatocellular carcinoma with cytokeratin 19 expression: a systematic review and meta-analysis

AIM

To evaluate the overall diagnostic performance of magnetic resonance imaging (MRI), different image features, and different image analysis methods in predicting hepatocellular carcinoma (HCC) with cytokeratin 19 (CK19) expression.

MATERIALS AND METHODS

A systematic literature search was performed to identify studies using MRI to predict HCC with CK19 expression between 2012 and 2023. Data were extracted to calculate the pooled sensitivity and specificity. Overall diagnostic performance was assessed using areas under the summary receiver operating characteristic curve (AUC). Subgroup analyses were conducted for specific image features and according to image analysis methods (traditional image feature, radiomics, and combined methods). Z-test statistics was used to analyse the differences in diagnostic performance between combined and individual methods.

RESULTS

Eleven studies with 14 datasets (1,278 lesions from 1,264 patients) were included. The overall pooled sensitivity, specificity, and AUC with corresponding 95% confidence intervals were estimated to be 0.72 (0.55, 0.85), 0.88 (0.80, 0.93), and 0.89 (0.86, 0.91) for MRI in predicting HCC with CK19 expression. Combined methods had higher sensitivity than image feature methods (0.86 versus 0.54, p=0.001), with no difference in specificity (0.85 versus 0.87, p=0.641). There were no significant differences between radiomics and combined methods regarding sensitivity (p=0.796) and specificity (p=0.535), respectively.

CONCLUSION

MRI shows moderate sensitivity and high specificity in identifying HCC with CK19 expression. The application of radiomics can improve the sensitivity of MRI in identifying HCC with CK19 expression.

StMLP1, as a Kunitz trypsin inhibitor, enhances potato resistance and specifically expresses in vascular bundles during Ralstonia solanacearum infection

Miraculin-like proteins (MLPs), members of the Kunitz trypsin inhibitor (KTI) family that are present in various plants, have been discovered to have a role in defending plants against pathogens. In this study, we identified a gene StMLP1 in potato that belongs to the KTI family. We found that the expression of StMLP1 gradually increases during Ralstonia solanacearum (R. solanacearum) infection. We characterized the promoter of StMLP1 as an inducible promoter that can be triggered by R. solanacearum and as a tissue-specific promoter with specificity for vascular bundle expression. Our findings demonstrate that StMLP1 exhibits trypsin inhibitor activity, and that its signal peptide is essential for proper localization and function. Overexpression of StMLP1 in potato can enhance the resistance to R. solanacearum. Inhibiting the expression of StMLP1 during infection accelerated the infection by R. solanacearum to a certain extent. In addition, the RNA-seq results of the overexpression-StMLP1 lines indicated that StMLP1 was involved in potato immunity. All these findings in our study reveal that StMLP1 functions as a positive regulator that is induced and specifically expressed in vascular bundles in response to R. solanacearum infection.

ScAREB4 promotes potato constitutive and acclimated freezing tolerance associated with enhancing trehalose synthesis and oxidative stress tolerance

Cold is a major environmental factor that restrains potato production. Abscisic acid (ABA) can enhance freezing tolerance in many plant species, but powerful evidence of the ABA-mediated signalling pathway related to freezing tolerance is still in deficiency. In the present study, cold acclimation capacity of the potato genotypes was enhanced alongside with improved endogenous content of ABA. Further exogenous application of ABA and its inhibitor (NDGA) could enhance and reduce potato freezing tolerance, respectively. Moreover, expression pattern of downstream genes in ABA signalling pathway was analysed and only ScAREB4 was identified with specifically upregulate in S. commersonii (CMM5) after cold and ABA treatments. Transgenic assay with overexpression of ScAREB4 showed that ScAREB4 promoted freezing tolerance. Global transcriptome profiling indicated that overexpression of ScAREB4 induced expression of TPS9 (trehalose-6-phosphate synthase) and GSTU8 (glutathione transferase), in accordance with improved TPS activity, trehalose content, higher GST activity and accumulated dramatically less H2 O2 in the ScAREB4 overexpressed transgenic lines. Taken together, the current results indicate that increased endogenous content of ABA is related to freezing tolerance in potato. Moreover, ScAREB4 functions as a downstream transcription factor of ABA signalling to promote cold tolerance, which is associated with increased trehalose content and antioxidant capacity.

StHAB1, a negative regulatory factor in abscisic acid signaling, plays crucial roles in potato drought tolerance and shoot branching

Abscisic acid (ABA) is critical in drought tolerance and plant growth. Group A protein type 2C phosphatases (PP2Cs) are negative regulators of ABA signaling and plant adaptation to stress. Knowledge about the functions of potato group A PP2Cs is limited. Here, we report that the potato group A PP2C StHAB1 is broadly expressed in potato plants and strongly induced by ABA and drought. Suppression of StHAB1 enhanced potato ABA sensitivity and drought tolerance, whereas overexpression of the dominant mutant StHAB1G276D compromised ABA sensitivity and drought tolerance. StHAB1 interacts with almost all ABA receptors and the Snf1-Related Kinase OST1. Suppressing StHAB1 and overexpressing StHAB1G276D alter potato growth morphology; notably, overexpression of StHAB1G276D causes excessive shoot branching. RNA-sequencing analyses identified that the auxin efflux carrier genes StPIN3, StPIN5, and StPIN8 were up-regulated in StHAB1G276D-overexpressing axillary buds. Correspondingly, the auxin concentration was reduced in StHAB1G276D-overexpressing axillary buds, consistent with the role of auxin in repressing lateral branch outgrowth. The expression of BRANCHED1s (StBRC1a and StBRC1b) was unchanged in StHAB1G276D-overexpressing axillary buds, suggesting that StHAB1G276D overexpression does not cause axillary bud outgrowth via regulation of BRC1 expression. Our findings demonstrate that StHAB1 is vital in potato drought tolerance and shoot branching.

Correlation between Lymph Node Regression Grading and Tumor Regression Grading after Neoadjuvant Chemoradiotherapy for Locally Advanced Rectal Cancer

PURPOSE/OBJECTIVE(S)

This study aimed to determine the relationship between tumor regression grading (TRG) and lymph node regression grading (LRG) after neoadjuvant chemoradiotherapy (nCRT) for locally advanced rectal cancer (LARC).

MATERIALS/METHODS

The study was a retrospective analysis of the clinical data of LARC patients who underwent preoperative nCRT at one institution. A total of 101 rectal cancer patients who received nCRT and underwent total rectal mesenteric excision (TME) were included. Pathologists independently assessed the pathological response of the primary tumor and lymph nodes (LN) to nCRT using TRG and LRG, respectively. The highest LRG score for each patient was defined as LRGmax, and LRGsum was the overall tumor burden of all LNs in the specimen.

RESULTS

The study included 101 LARC patients who underwent nCRT and TME. The patient population consisted of 65 males and 36 females with an average age of 54.86 years (range 20-81 years), of which 68 were aged 60 years or younger and 33 were older than 60. The radiotherapy treatment plan consisted of 1.8-2Gy per dose, administered 5 times per week for a total dose of 45-50.4Gy, along with oral capecitabine chemotherapy (825 mg/m2, bid) on the day of radiation therapy. The chemotherapy treatment plan included XELOX, mFOLFOX6, and FOLFOX4. The cTNM stage of the tumor before surgery was cT2 in 2 cases, cT3 in 63 cases, and cT4 in 36 cases. Eight cases were cN0 and 93 were cN+. After surgery, the ypTNM stage was T0 in 19 cases, T1 in 4 cases, T2 in 27 cases, T3 in 45 cases, and T4 in 6 cases. The N stage was N0 in 76 cases, N1 in 20 cases, and N2 in 5 cases. TRG was 0 in 17 cases (16.8%), 1 in 15 cases (14.9%), 2 in 61 cases (60.4%), and 3 in 8 cases (7.9%). LRGmax scores were 0 in 66 cases (65.3%), 1 in 17 cases (16.8%), 2 in 5 cases (5.0%), 3 in 3 cases (3.0%), 4 in 5 cases (5.0%), and 5 in 5 cases (5.0%). LRGsum scores were ≤3 in 85 cases (84.2%), 4-9 in 11 cases (10.9%), and ≥10 in 5 cases (5.0%). Correlation analysis showed that LRGmax was significantly correlated with TRG, ypT, and ypN (P = 0.038, P = 0.015, P < 0.01), with correlation coefficients of 0.184, 0.212, and 0.626, respectively. There was no significant correlation between LRGmax and cT and cN+. Similarly, LRGsum was significantly correlated with TRG, ypT, and ypN (P = 0.022, P = 0.002, P < 0.01) with correlation coefficients of 0.212, 0.276, and 0.707, respectively. There was no significant correlation between LRGsum and cT and cN. The results of our study indicate a significant correlation between LRG and TRG (P = 0.022). Additionally, LRG was found to be positively correlated with the ypT and ypN stages of the primary tumor and lymph nodes post-surgery, with correlation coefficients of 0.276 and 0.707, respectively (P = 0.002 and P<0.01). No significant correlations were observed between LRG and cT and cN+ stages.

CONCLUSION

Our findings demonstrate a significant association between LRG and TRG, as well as a positive correlation between LRG and the ypT and ypN stages of the primary tumor and lymph nodes following surgery.

Evaluating the Effects of Bone Marrow Sparing Radiotherapy on Acute Hematologic Toxicity for Patients with Locoregionally Advanced Cervical Cancer: A Prospective Phase II Randomized Controlled Trial

PURPOSE/OBJECTIVE(S)

Bone marrow sparing intensity modulated radiotherapy (BMS-IMRT) can reduce the incidence of acute hematologic toxicity (HT) for locoregionally advanced cervical cancer (LACC) patients receiving concurrent chemoradiotherapy (CCRT), but the norm has been controversial. The purpose of the study was to evaluate the effects of bone marrow (BM) V40 <25% on decreasing the incidence of acute HT in a prospective clinical trial.

MATERIALS/METHODS

A total of 242 LACC patients were recruited from May 2021 to May 2022, who were evenly randomized into BMS-IMRT group and standard IMRT group according to a computer-generated random number list. All patients received pelvic irradiation with concurrent cisplatin (40 mg/m2 weekly), followed by brachytherapy. For patients in BMS-IMRT group, the outer contour of pelvic bone, lumbar spine and left and right femur heads were additionally delineated as a surrogate for BM, and V40 <25% was prescribed. Blood counts were tested weekly, of which nadirs during external beam radiotherapy (EBRT) were graded to assess acute HT as primary observation index. Second observation index were dosimetric parameters of EBRT plan from the dose volume histograms (DVHs). Binary logistic regression model and receiver operating characteristic (ROC) curve were used for predictive value analysis.

RESULTS

Baseline demographic, disease and treatment characteristics were all balanced between BMS-IMRT group and standard IMRT group. BMS-IMRT was associated with a lower incidence of grade ≥2 and grade ≥3 acute HT, leukopenia and neutropenia (72.70% vs 90.90%, P <0.001*; 16.50% vs 65.30%, P <0.001*; 66.10% vs 85.10%, P = 0.001*; 13.20% vs 54.50%, P <0.001*; 37.20% vs 66.10%, P <0.001*; 10.70% vs 43.80%, P <0.001*). Plan target volume (PTV) for all patients satisfied the clinical requirement of V(100%) ≥95%, and conformity and homogeneity were both comparable between 2 groups. BMS also decreased dose delivered to the organs at risk (OARs) including rectum, bladder and left and right femur head. Univariate and multivariate analyses showed that BM V40 was an independent risk factor for grade ≥3 acute HT (odds ratio [OR] = 2.734, 95% confidence interval [CI] = 1.959-3.815, P <0.001*). Cutoff value was 25.036% and area under the curve (AUC) was 0.786. The nomogram was constructed, which was rigorously evaluated and internally cross-validated, showing good predictive performance.

CONCLUSION

BM V40 <25% can reduce the risks of acute HT for LACC patients receiving CCRT while the dose delivery of target volume and other normal tissues were not compromised. With great practicality and applicability, BM V40 <25% is a promising strategy, making BMS-IMRT widespread especially in the area where application of image guided radiotherapy (IGRT) such as 18F-fluorodeoxyglucose positron emission tomography (18FDG-PET)/CT is not popularized. Chinese clinical trial registry (ChiCTR2200066485).

Astragalus polysaccharides driven stretchable nanofibrous membrane wound dressing for joint wound healing

Joint wound dressings are currently significantly limited in their clinical applications due to their inferior mechanical properties and single therapeutic effect. Therefore, it is imperative to develop a versatile joint wound dressing that integrates adequate stretchability, desirable biocompatibility, and multiple biological effects into one system. We implemented the electrospinning technique in this study to fabricate a novel nanofibrous membrane (NFM) composed of gelatin (GEL) and astragalus polysaccharides (APS), termed GEL/APS NFM. The selection of GEL and APS confers excellent biocompatibility to GEL/APS NFM. Furthermore, the optimally proportioned GEL/APS NFM exhibits satisfactory stretchability and desirable wound healing efficiency. Furthermore, released APS can exert anti-inflammatory, procollagen deposition, and proangiogenic effects to accelerate epithelial tissue, enhancing joint wound healing. In summary, GEL/APS NFM offers a convenient and effective approach to promoting rapid joint wound healing, providing a novel approach to joint wound care.

A novel effector RipBT contributes to Ralstonia solanacearum virulence on potato

Ralstonia solanacearum is one of the most destructive plant-pathogenic bacteria, infecting more than 200 plant species, including potato (Solanum tuberosum) and many other solanaceous crops. R. solanacearum has numerous pathogenicity factors, and type III effectors secreted through type III secretion system (T3SS) are key factors to counteract host immunity. Here, we show that RipBT is a novel T3SS-secreted effector by using a cyaA reporter system. Transient expression of RipBT in Nicotiania benthamiana induced strong cell death in a plasma membrane-localization dependent manner. Notably, mutation of RipBT in R. solanacearum showed attenuated virulence on potato, while RipBT transgenic potato plants exhibited enhanced susceptibility to R. solanacearum. Interestingly, transcriptomic analyses suggest that RipBT may interfere with plant reactive oxygen species (ROS) metabolism during the R. solanacearum infection of potato roots. In addition, the expression of RipBT remarkably suppressed the flg22-induced pathogen-associated molecular pattern-triggered immunity responses, such as the ROS burst. Taken together, RipBT acts as a T3SS effector, promoting R. solanacearum infection on potato and presumably disturbing ROS homeostasis.

Genome sequence analysis provides insights into the mode of 2n egg formation in Solanum malmeanum

KEY MESSAGE

Our genomic investigation confirms the mechanism of 2n eggs formation in S. malmeanum and aid in optimizing the use of wild germplasm. Wild potatoes are a valuable source of agronomic traits. However, substantial reproductive barriers limit gene flow into cultivated species. 2n gametes are instrumental in preventing endosperm abortion caused by genetic imbalances in the endosperm. However, little is known about the molecular mechanisms underlying the formation of 2n gametes. Here, the wild species Solanum malmeanum Bitter (2x, 1EBN, endosperm balance number) was used in inter- and intrapoloid crosses with other Solanum species, with viable seeds being produced only when S. malmeanum was used as the female parent to cross the 2EBN Solanum genus and with the likely involvement of 2n gametes. Subsequently, we substantiated the formation of 2n eggs in S. malmeanum using fluorescence in situ hybridization (FISH) and genomic sequencing technology. Additionally, the transmission rate of maternal heterozygous polymorphism sites was assessed from a genomic perspective to analyze the mode of 2n egg formation in S. malmeanum × S. tuberosum and S. malmeanum × S. chacoense crosses; each cross acquired an average of 31.12% and 22.79% maternal sites, respectively. This confirmed that 2n egg formation in S. malmeanum attributed to second-division restitution (SDR) coupled with the occurrence of exchange events. The high-throughput sequencing technology used in this study has strong advantages over traditional cytological analyses. Furthermore, S. malmeanum, which has a variety of excellent traits not available from present cultivated potato genepool, has received little research attention and has successfully achieved gene flow in cultivated species in the current study. These findings will facilitate the understanding and optimization of wild germplasm utilization in potatoes.

Ralstonia solanacearum type III effector RipAS associates with potato type one protein phosphatase StTOPP6 to promote bacterial wilt

The bacterial pathogen Ralstonia solanacearum (R. solanacearum) delivered type III secretion effectors to inhibit the immune system and cause bacterial wilt on potato. Protein phosphatases are key regulators in plant immunity, which pathogens can manipulate to alter host processes. Here, we show that a type III effector RipAS can reduce the nucleolar accumulation of a type one protein phosphatase (PP1) StTOPP6 to promote bacterial wilt. StTOPP6 was used as bait in the Yeast two-Hybrid (Y2H) assay and acquired an effector RipAS that interacts with it. RipAS was characterized as a virulence effector to contribute to R. solanacearum infection, and stable expression of RipAS in potato impaired plant resistance against R. solanacearum. Overexpression of StTOPP6 showed enhanced disease symptoms when inoculated with wild strain UW551 but not the ripAS deletion mutant, indicating that the expression of StTOPP6 facilitates the virulence of RipAS. RipAS reduced the nucleolar accumulation of StTOPP6, which occurred during R. solanacearum infection. Moreover, the association also widely existed between other PP1s and RipAS. We argue that RipAS is a virulence effector associated with PP1s to promote bacterial wilt.

Long-distance control of potato storage organ formation by SELF PRUNING 3D and FLOWERING LOCUS T-like 1

Plants program their meristem-associated developmental switches for timely adaptation to a changing environment. Potato (Solanum tuberosum L.) tubers differentiate from specialized belowground branches or stolons through radial expansion of their terminal ends. During this process, the stolon apex and closest axillary buds enter a dormancy state that leads to tuber eyes, which are reactivated the following spring and generate a clonally identical plant. The potato FLOWERING LOCUS T homolog SELF-PRUNING 6A (StSP6A) was previously identified as the major tuber-inducing signal that integrates day-length cues to control the storage switch. However, whether some other long-range signals also act as tuber organogenesis stimuli remains unknown. Here, we show that the florigen SELF PRUNING 3D (StSP3D) and FLOWERING LOCUS T-like 1 (StFTL1) genes are activated by short days, analogously to StSP6A. Overexpression of StSP3D or StFTL1 promotes tuber formation under non-inductive long days, and the tuber-inducing activity of these proteins is graft transmissible. Using the non-tuber-bearing wild species Solanum etuberosum, a natural SP6A null mutant, we show that leaf-expressed SP6A is dispensable for StSP3D long-range activity. StSP3D and StFTL1 mediate secondary activation of StSP6A in stolon tips, leading to amplification of this tuberigen signal. StSP3D and StFTL1 were observed to bind the same protein partners as StSP6A, suggesting that they can also form transcriptionally active complexes. Together, our findings show that additional mobile tuber-inducing signals are regulated by the photoperiodic pathway.

[Prevalence and trends of anemia among pregnant women in eight provinces of China from 2016 to 2020]

This study analyzed the anemia status and change trend of 219 835 pregnant women in eight provinces from 2016 to 2020 in the Maternal and Newborn Health Monitoring Program(MNHMP). The results showed that from 2016 to 2020, the anemia rate of pregnant women in eight provinces was 41.27%, and the rates of mild, moderate and severe anemia were 28.56%, 12.59% and 0.12% respectively; the anemia rates in eastern, central and western regions were 41.87%, 36.09% and 44.63% respectively, and the anemia rates in urban and rural areas were 39.87% and 42.23%. From 2016 to 2020, the anemia rate of pregnant women decreased from 44.93% to 38.22%, with an average annual decline of 3.86% (95%CI:-5.84%, -1.85%). The anemia rate among pregnant women of the eastern region (AAPC=-6.16%, 95%CI:-9.79%, -2.38%) fell faster than that among pregnant women of the central region (AAPC=0.71%, 95%CI:-6.59%, 8.57%) and western region (AAPC=-1.53%, 95%CI:-5.19%, 2.28%). From 2016 to 2020, the moderate anemia rate in pregnant women decreased from 14.98% to 10.74%, with an average annual decline of 8.72% (95%CI:-12.90%, -4.34%), with a statistically significant difference (P<0.05); AAPC for mild and severe anemia in pregnant women was 1.56% (95%CI: 3.44%, 0.36%) and 18.86% (95%CI: 39.88%, 9.52%), respectively, without statistically significant difference (P>0.05).

[Expert consensus on late stage of critical care management]

We wished to establish an expert consensus on late stage of critical care (CC) management. The panel comprised 13 experts in CC medicine. Each statement was assessed based on the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) principle. Then, the Delphi method was adopted by 17 experts to reassess the following 28 statements. (1) ESCAPE has evolved from a strategy of delirium management to a strategy of late stage of CC management. (2) The new version of ESCAPE is a strategy for optimizing treatment and comprehensive care of critically ill patients (CIPs) after the rescue period, including early mobilization, early rehabilitation, nutritional support, sleep management, mental assessment, cognitive-function training, emotional support, and optimizing sedation and analgesia. (3) Disease assessment to determine the starting point of early mobilization, early rehabilitation, and early enteral nutrition. (4) Early mobilization has synergistic effects upon the recovery of organ function. (5) Early functional exercise and rehabilitation are important means to promote CIP recovery, and gives them a sense of future prospects. (6) Timely start of enteral nutrition is conducive to early mobilization and early rehabilitation. (7) The spontaneous breathing test should be started as soon as possible, and a weaning plan should be selected step-by-step. (8) The waking process of CIPs should be realized in a planned and purposeful way. (9) Establishment of a sleep-wake rhythm is the key to sleep management in post-CC management. (10) The spontaneous awakening trial, spontaneous breathing trial, and sleep management should be carried out together. (11) The depth of sedation should be adjusted dynamically in the late stage of CC period. (12) Standardized sedation assessment is the premise of rational sedation. (13) Appropriate sedative drugs should be selected according to the objectives of sedation and drug characteristics. (14) A goal-directed minimization strategy for sedation should be implemented. (15) The principle of analgesia must be mastered first. (16) Subjective assessment is preferred for analgesia assessment. (17) Opioid-based analgesic strategies should be selected step-by-step according to the characteristics of different drugs. (18) There must be rational use of non-opioid analgesics and non-drug-based analgesic measures. (19) Pay attention to evaluation of the psychological status of CIPs. (20) Cognitive function in CIPs cannot be ignored. (21) Delirium management should be based on non-drug-based measures and rational use of drugs. (22) Reset treatment can be considered for severe delirium. (23) Psychological assessment should be conducted as early as possible to screen-out high-risk groups with post-traumatic stress disorder. (24) Emotional support, flexible visiting, and environment management are important components of humanistic management in the intensive care unit (ICU). (25) Emotional support from medical teams and families should be promoted through"ICU diaries"and other forms. (26) Environmental management should be carried out by enriching environmental content, limiting environmental interference, and optimizing the environmental atmosphere. (27) Reasonable promotion of flexible visitation should be done on the basis of prevention of nosocomial infection. (28) ESCAPE is an excellent project for late stage of CC management.

Molecular Marker-Assisted Selection for Frost Tolerance in a Diallel Population of Potato

A multi-parental population is an innovative tool for mapping large numbers of loci and genetic modifications, particularly where they have been used for breeding and pre-breeding in crops. Frost injury is an environmental stress factor that greatly affects the growth, development, production efficiency, and geographical distribution of crops. No reported study has focused on genetic mapping and molecular marker development using diallel populations of potatoes. In this study, 23 successful cross combinations, obtained by a half diallel cross among 16 parents, including eight frost-tolerant advanced breeding lines and eight cultivars, were used to map the genetic loci for frost tolerance and to create a molecular marker-assisted selection (MAS) system. Three candidate regions related to frost tolerance on chromosomes II, V, and IX were mapped by bulked segregant analysis (BSA). Furthermore, six SNP markers associated with frost tolerance from candidate regions were developed and validated. Above all, a MAS system for the frost tolerance screening of early breeding offspring was established. This study highlights the practical advantages of applying diallel populations to broaden and improve frost-tolerant germplasm resources.

Protein phosphatase StTOPP6 negatively regulates potato bacterial wilt resistance by modulating MAPK signaling

Potato is the fourth important national staple food in China and plays an important role in the history of world food development. However, its production and quality are severely constrained by bacterial wilt, which is caused by Ralstonia solanacearum (R. solanacearum). In this study, we identified StTOPP6 which belongs to the type one protein phosphatases (TOPPs) family, and silencing StTOPP6 increased resistance against R. solanacearum. RNA-seq analysis shows that silencing of StTOPP6 activated the immune responses, and the defense activation partly depended on the mitogen-activated protein kinase (MAPK) signal pathway. StTOPP6 inhibited the expression of StMAPK3, while the overexpression of StMAPK3 enhanced resistance to R. solanacearum, which supports the negative role of StTOPP6 in plant immunity. Consistent with the silencing of StTOPP6, overexpressing the phosphatase-dead mutant StTOPP6m also attenuated infection and upregulated MAPK3, showing that StTOPP6 activity is required for disease. Furthermore, StTOPP6 affected the StMAPK3-mediated downstream defense pathway, eventually suppressing the accumulation of reactive oxygen species (ROS). Consistent with these findings, plants with silencing of StTOPP6, overexpression of StTOPP6m, and overexpression of StMAPK3 all display ROS accumulation and resistance enhancement to R. solanacearum. All these findings in our study reveal that StTOPP6 negatively regulated resistance to bacterial wilt by affecting the MAPK3-mediated pathway.

A Phytophthora infestans RXLR effector AVR8 suppresses plant immunity by targeting a desumoylating isopeptidase DeSI2

The potato's most devastating disease is late blight, which is caused by Phytophthora infestans. Whereas various resistance (R) genes are known, most are typically defeated by this fast-evolving oomycete pathogen. However, the broad-spectrum and durable R8 is a vital gene resource for potato resistance breeding. To support an educated deployment of R8, we embarked on a study on the corresponding avirulence gene Avr8. We overexpressed Avr8 by transient and stable transformation, and found that Avr8 promotes colonization of P. infestans in Nicotiana benthamiana and potato, respectively. A yeast-two-hybrid (Y2H) screen showed that AVR8 interacts with a desumoylating isopeptidase (StDeSI2) of potato. We overexpressed DeSI2 and found that DeSI2 positively regulates resistance to P. infestans, while silencing StDeSI2 downregulated the expression of a set of defense-related genes. By using a specific proteasome inhibitor, we found that AVR8 destabilized StDeSI2 through the 26S proteasome and attenuated early PTI responses. Altogether, these results indicate that AVR8 manipulates desumoylation, which is a new strategy that adds to the plethora of mechanisms that Phytophthora exploits to modulate host immunity, and StDeSI2 provides a new target for durable resistance breeding against P. infestans in potato.

Potato tonoplast sugar transporter 1 controls tuber sugar accumulation during postharvest cold storage

Cold-induced sweetening (CIS), the undesirable sugar accumulation in cold-stored potato (Solanum tuberosum L.) tubers, is a severe postharvest issue in the potato processing industry. Although the process of sucrose hydrolysis by vacuolar invertase during potato CIS is well understood, there is limited knowledge about the transportation of sucrose from the cytosol to the vacuole during postharvest cold storage. Here, we report that among the three potato tonoplast sugar transporters (TSTs), StTST1 exhibits the highest expression in tubers during postharvest cold storage. Subcellular localization analysis demonstrates that StTST1 is a tonoplast-localized protein. StTST1 knockdown decreases reducing sugar accumulation in tubers during low-temperature storage. Compared to wild-type, potato chips produced from StTST1-silenced tubers displayed significantly lower acrylamide levels and lighter color after cold storage. Transcriptome analysis manifests that suppression of StTST1 promotes starch synthesis and inhibits starch degradation in cold-stored tubers. We further establish that the increased sucrose content in the StTST1-silenced tubers might cause a decrease in the ABA content, thereby inhibiting the ABA-signaling pathway. We demonstrate that the down-regulation of β-amylase StBAM1 in StTST1-silenced tubers might be directly controlled by ABA-responsive element-binding proteins (AREBs). Altogether, we have shown that StTST1 plays a critical role in sugar accumulation and starch metabolism regulation during postharvest cold storage. Thus, our findings provide a new strategy to improve the frying quality of cold-stored tubers and reduce the acrylamide content in potato chips.

Comparative genomic analysis of Ralstonia solanacearum reveals candidate avirulence effectors in HA4-1 triggering wild potato immunity

Ralstonia solanacearum is the causal agent of potato bacterial wilt, a major potato bacterial disease. Among the pathogenicity determinants, the Type III Secretion System Effectors (T3Es) play a vital role in the interaction. Investigating the avirulent T3Es recognized by host resistance proteins is an effective method to uncover the resistance mechanism of potato against R. solanacearum. Two closely related R. solanacearum strains HA4-1 and HZAU091 were found to be avirulent and highly virulent to the wild potato Solanum albicans 28-1, respectively. The complete genome of HZAU091 was sequenced in this study. HZAU091 and HA4-1 shared over 99.9% nucleotide identity with each other. Comparing genomics of closely related strains provides deeper insights into the interaction between hosts and pathogens, especially the mechanism of virulence. The comparison of type III effector repertoires between HA4-1 and HZAU091 uncovered seven distinct effectors. Two predicted effectors RipA5 and the novel effector RipBS in HA4-1 could significantly reduce the virulence of HZAU091 when they were transformed into HZAU091. Furthermore, the pathogenicity assays of mutated strains HA4-1 ΔRipS6, HA4-1 ΔRipO1, HA4-1 ΔRipBS, and HA4-1 ΔHyp6 uncovered that the absence of these T3Es enhanced the HA4-1 virulence to wild potato S. albicans 28-1. This result indicated that these T3Es may be recognized by S. albicans 28-1 as avirulence proteins to trigger the resistance. In summary, this study provides a foundation to unravel the R. solanacearum-potato interaction and facilitates the development of resistance potato against bacterial wilt.

[Evaluation of clinical safety and diagnostic efficacy of domestic liver-specific magnetic resonance contrast agent (gadoxetate disodium)]

Objective: To evaluate the clinical safety and diagnostic efficacy of domestic gadoxetate disodium (GdEOBDTPA). Methods: The imaging data from patients with space-occupying liver lesions who underwent GdEOBDTPA enhanced magnetic resonance examination at West China Hospital of Sichuan University between January 2020 and September 2020 were analyzed retrospectively. Clinical indicators were evaluated by the incidental condition of transient severe respiratory motion artifacts (TSM) in the arterial phase to assess the safety profile.The differences in quantitative and qualitative indicators for the risk factors of TSM in the arterial phase between the TSM group and the non-TSM group were compared by t-test and χ2 test. Observational indicators of the accuracy of diagnostic procedures: The 2018 version of the Liver Imaging Reporting and Data System (LI-RADS) was used to evaluate the main signs, auxiliary signs, and LR grades of lesions. Postoperative pathological findings were used as the gold standard for evaluating and diagnosing hepatocellular carcinoma (HCC). Simultaneously, the relative enhancement degree of the liver, the contrast between the lesion and the liver, and the cholangiography in the hepatobiliary phase were evaluated. The McNemar test was used to compare the differences in the diagnostic efficiency of physician 1 and physician 2 in the diagnosis of hepatocellular carcinoma according to the 2018 version of LI-RADS. Results: A total of 114 cases were included in this study. The incidence rate of TSM was 9.6% (11/114). Age [(53.8 ± 11.3) years vs. (55.4 ± 15.4) years, t = 0.465, P = 0.497], body weight [(65.8 ± 11.1) kg vs. (60.8 ± 7.6) kg, t = 1.468, P = 0.228], body mass index [(23.9 ± 3.1) kg/m(2) vs. (23.4 ± 3.0) kg/m(2), t = 0.171, P = 0.680], liver cirrhosis ratio (39 cases vs. 4 cases, χ (2) =1.776, P = 0.183), proportion of mild to moderate pleural effusion (32 cases vs. 4 cases, χ (2) = 0.000, P = 0.986), and proportion of mild to moderate ascites (47 cases vs. 5 cases χ (2) = 0.000, P = 0.991) had no statistically significant difference between the groups of non-TSM and TSM patients. According to the 2018 version of LI-RADS for the LR5 category, there was no statistically significant difference between the two physicians' HCC diagnoses in terms of sensitivity (91.4% vs.86.4%, χ (2) = 1.500, P = 0.219), specificity (72.7 % vs. 69.7%, χ (2) = 0.000, P = 1.000), positive predictive value (89.2% vs. 87.5%, χ (2) = 2.250, P = 0.125), negative predictive value (77.4% vs. 67.6%, χ (2) = 2.250, P = 0.125), and accuracy (86.0% vs. 81.6%, χ (2) = 0.131, P = 0.125). According to physicians 1 and 2 film review results, 91.2% (104/114) and 89.5% (102/114) of the contrast agent were discharged into the common bile duct or duodenum, respectively. In addition, 86.0% (98/114) of the patients had good liver enhancement, and 91.2% (104/114) of the lesions showed low signals relative to the liver background. Conclusion: Domestic gadoxetate disodium has a good clinical safety profile and diagnostic efficacy.

Transcriptome analysis provides StMYBA1 gene that regulates potato anthocyanin biosynthesis by activating structural genes

Anthocyanin biosynthesis is affected by light, temperature, and other environmental factors. The regulation mode of light on anthocyanin synthesis in apple, pear, tomato and other species has been reported, while not clear in potato. In this study, potato RM-210 tubers whose peel will turn purple gradually after exposure to light were selected. Transcriptome analysis was performed on RM-210 tubers during anthocyanin accumulation. The expression of StMYBA1 gene continued to increase during the anthocyanin accumulation in RM-210 tubers. Moreover, co-expression cluster analysis of differentially expressed genes showed that the expression patterns of StMYBA1 gene were highly correlated with structural genes CHS and CHI. The promoter activity of StMYBA1 was significantly higher in light conditions, and StMYBA1 could activate the promoter activity of structural genes StCHS, StCHI, and StF3H. Further gene function analysis found that overexpression of StMYBA1 gene could promote anthocyanin accumulation and structural gene expression in potato leaves. These results demonstrated that StMYBA1 gene promoted potato anthocyanin biosynthesis by activating the expression of structural genes under light conditions. These findings provide a theoretical basis and genetic resources for the regulatory mechanism of potato anthocyanin synthesis.

Suppression of the tonoplast sugar transporter, StTST3.1, affects transitory starch turnover and plant growth in potato

Transitory starch and vacuolar sugars function as highly dynamic pools of instantly accessible metabolites in plant leaf cells. Their metabolic regulation is critical for plant survival. The tonoplast sugar transporters (TSTs), responsible for sugar uptake into vacuoles, regulate cellular sugar partitioning and vacuolar sugar accumulation. However, whether TSTs are involved in leaf transient starch turnover and plant growth is unclear. Here, we found that suppressing StTST3.1 resulted in growth retardation and pale green leaves in potato plants. StTST3.1-silenced plants displayed abnormal chloroplasts and impaired photosynthetic performance. The subcellular localization assay and the oscillation expression patterns revealed that StTST3.1 encoded a tonoplast-localized protein and responded to photoperiod. Moreover, RNA-seq analyses identified that starch synthase (SS2 and SS6) and glucan water, dikinase (GWD), were downregulated in StTST3.1-silenced lines. Correspondingly, the capacity for starch synthesis and degradation was decreased in StTST3.1-silenced lines. Surprisingly, StTST3.1-silenced leaves accumulated exceptionally high levels of maltose but low levels of sucrose and hexose. Additionally, chlorophyll content was reduced in StTST3.1-silenced leaves. Analysis of chlorophyll metabolic pathways found that Non-Yellow Coloring 1 (NYC1)-like (NOL), encoding a chloroplast-localized key enzyme that catalyzes the initial step of chlorophyll b degradation, was upregulated in StTST3.1-silenced leaves. Transient overexpression of StNOL accelerated chlorophyll b degradation in tobacco leaves. Our results indicated that StTST3.1 is involved in transitory starch turnover and chlorophyll metabolism, thereby playing a critical role in normal potato plant growth.

Circular RNA 0000157 depletion protects human bronchial epithelioid cells from cigarette smoke extract-induced human bronchial epithelioid cell injury through the microRNA-149-5p/bromodomain containing 4 pathway

BACKGROUND

Circular RNA (circRNA) has been reported to regulate respiratory diseases. In the study, we aimed to elucidate the role of circ_0000157 in smoke-related chronic obstructive pulmonary disease (COPD) and the inner mechanism.

METHODS

COPD-like cell injury was induced by treating human bronchial epithelioid cells (16HBE) with cigarette smoke extract (CSE). The expression of circ_0000157, miR-149-5p, bromodomain containing 4 (BRD4), BCL2-associated x protein (Bax) and B-cell lymphoma-2 (Bcl-2) was analyzed by quantitative real-time polymerase chain reaction (qRT-PCR) or Western blotting. Enzyme-linked immunosorbent assay was performed to detect interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α) levels. Malondialdehyde (MDA) production was detected by a lipid peroxidation MDA assay kit. Superoxide dismutase (SOD) activity was analyzed by a SOD activity assay kit.

RESULTS

Circ_0000157 and BRD4 expression were upregulated, while miR-149-5p expression was downregulated in the blood of smokers with COPD and CSE-induced 16HBE cells compared with control groups. CSE treatment inhibited 16HBE cell proliferation and induced cell apoptosis, inflammation, and oxidative stress; however, these effects were remitted when circ_0000157 expression was decreased. In addition, circ_0000157 acted as a miR-149-5p sponge and regulated CSE-caused 16HBE cell damage by targeting miR-149-5p. The overexpression of BRD4, a target gene of miR-149-5p, attenuated the inhibitory effects of miR-149-5p introduction on CSE-induced cell damage. Further, circ_0000157 modulated BRD4 expression by associating with miR-149-5p in CSE-treated 16HBE cells.

CONCLUSION

Circ_0000157 knockdown ameliorated CSE-caused 16HBE cell damage by targeting the miR-149-5p/BRD4 pathway, providing a potential therapeutic strategy for clinic intervention in COPD.

Leaves and stolons transcriptomic analysis provide insight into the role of phytochrome F in potato flowering and tuberization

Photoperiod plays a critical role in controlling the formation of sexual or vegetative reproductive organs in potato. Although StPHYF-silenced plants overcome day-length limitations to tuberize through a systemic effect on tuberigen StSP6A expression in the stolon, the comprehensive regulatory network of StPHYF remains obscure. Therefore, the present study investigated the transcriptomes of StPHYF-silenced plants and observed that, in addition to known components of the photoperiodic tuberization pathway, florigen StSP3D and other flowering-related genes were activated in StPHYF-silenced plants, exhibiting an early flowering response. Additionally, grafting experiments uncovered the long-distance effect of StPHYF silencing on gene expression in the stolon, including the circadian clock components, flowering-associated MADSs, and tuberization-related regulatory genes. Similar to the AtFT-AtAP1 regulatory module in Arabidopsis, the present study established that the AP1-like StMADS1 functions downstream of the tuberigen activation complex (TAC) and that suppressing StMADS1 inhibits tuberization in vitro and delays tuberization in vivo. Moreover, the expression of StSP6A was downregulated in StMADS1-silenced plants, implying the expression of StSP6A may be feedback-regulated by StMADS1. Overall, these results reveal that the regulatory network of StPHYF controls flowering and tuberization and targets the crucial tuberization factor StMADS1 through TAC, thereby providing a better understanding of StPHYF-mediated day-length perception during potato reproduction.

[The prevalence of atrial cardiomyopathy in patients with different types of acute ischemic stroke and its relationship with cryptogenic stroke]

Objective: To investigate the prevalence of atrial cardiomyopathy in patients with different types of acute ischemic stroke and its relationship with cryptogenic stroke. Methods: Patients with acute ischemic stroke within 7 days of onset who were admitted to the Department of Neurology of the First Affiliated Hospital of Zhengzhou University from January to September 2019 were prospectively and consecutively enrolled. All included patients were classified according to TOAST classification of ischemic stroke. Chi-square test was used to compare the prevalence of atrial cardiomyopathy among patients with different TOAST classifications. Multivariate logistic regression model was used to analyze the related factors of cryptogenic stroke. Results: A total of 1 098 patients with acute ischemic stroke were enrolled in the study, including 661 males and 437 females, with a median age [M(Q₁,Q₃)] of 61 (53, 68) years. The prevalence of atrial cardiomyopathy in patients with cryptogenic stroke[53.5% (46/86)] was higher than that in patients with large artery atherosclerosis [38.0%(63/166), P=0.018] and small vessel occlusion [19.4%(37/191), P<0.001], but was lower than that of patients in the cardioembolic group [97.3% (72/74), P<0.001]. Multivariate logistic regression analysis showed that atrial cardiomyopathy was an associated factor for cryptogenic stroke (OR=2.945, 95%CI: 1.766-4.911, P<0.001). Conclusions: Atrial cardiomyopathy is associated with cryptogenic stroke. The prevalence of atrial cardiomyopathy in patients with cryptogenic stroke is higher than that in patients with large artery atherosclerosis and small vessel occlusion, but lower than that in patients with cardiac embolism.

Fabrication of gentamicin loaded Col-I/HA multilayers modified titanium coatings for prevention of implant infection

In this study, gentamicin loaded collagen I/hyaluronic acid multilayers modified titanium coating (TC-AA(C/H)6-G) was fabricated via a layer-by-layer (LBL) covalent immobilization method. The drug releasing properties of collagen I/Hyaluronic acid (Col-I/HA) multilayers and the effect of loaded gentamicin on the antibacterial properties and cytocompatibility of modified TC were investigated. The gentamicin release assay indicated that the Col-I/HA multilayers modified TC exhibited agreeable drug-loading amount (537.22 ± 29.66 µg of gentamicin) and controlled-release performance (240 h of sustained release time). TC-AA(C/H)6-G revealed satisfactory antibacterial activity and inhibited the colonization and biofilm formation of S. aureus. Fortunately, the functions of hMSCs on TC-AA(C/H)6-G did not affected by the loaded gentamicin, and TC-AA(C/H)6-G could improve the adhesion, proliferation and osteogenic differentiation of cells, as well as TC-AA(C/H)6. In vivo animal study indicated that TC-AA(C/H)6-G could effectively control intramedullary cavity infection caused by S. aureus and prevent bone destruction.

SWATH-MS based quantitative proteomics analysis reveals novel proteins involved in PAMP triggered immunity against potato late blight pathogen Phytophthora infestans

Potato is the most important non-grain food in the world, while late blight caused by Phytophthora infestans seriously threatens the production of potato. Since pathogen-associated molecular patterns (PAMPs) are relatively conserved, PAMP-triggered immunity (PTI) can provide durable resistance to late blight for potato. However, knowledge of the regulatory mechanisms of PTI against oomycete pathogens at protein levels remains limited due to the small number of identified proteins. In the present work, changes in the proteome profile of Nicotiana benthamiana leaves upon P. infestans PAMP induction were examined using the SWATH-MS (sequential windowed acquisition of all theoretical mass spectra) approach, which provides quantification of protein abundances and large-scale identification of PTI-related proteins. A total of 4401 proteins have been identified, of which 1429 proteins were differentially expressed at least at one time point of 8, 12, 24 and 48 h after PAMP induction, compared with the expression at 0 h when immediately after PAMP induction. They were further analyzed by expression clustering and gene ontology (GO) enrichment analysis. Through functional verification, six novel DEPs of 19 candidates were proved to be involved in PTI responses, including mitochondrial phosphate carrier protein (MPT) 3, vesicle-associated membrane protein (VAMP) 714, lysophospholipase (LysoPL) 2, ascorbate peroxidase (APX) 1, heat shock 70 kDa protein (HSP) 2 and peptidyl-prolyl cis-trans isomerase FKBP (FKBP) 15-1. Taken together, the time course approach and the resulting large-scale proteomic analyses have enlarged our understanding of PTI mechanisms and provided a valuable resource for the discovery of complex protein networks involved in the resistance response of potato to late blight.

QTL analysis of tuber shape in a diploid potato population

Tuber shape is one of the most important traits for potato breeding. Since poor or irregular shape increases the difficulty of handling and processing, researching the inheritance of potato tuber shape for potato breeding is highly important. To efficiently identify QTL for tuber shape, a diploid potato population (PM7) was generated by self-pollinated M6 (S. chacoense). A QTL TScha6 for tuber shape was identified by the QTL-seq approach at 50.91-59.93 Mb on chromosome 6 in the potato DM reference genome. To confirm TScha6, four SSR and twenty CAPS markers around the QTL were developed and the TScha6 was narrowed down to an interval of ~ 1.85 Mb. The CAPS marker C6-58.27_665 linked to TScha6 was then used to screen 86 potato cultivars and advanced breeding lines. The tuber length/width (LW) ratio was significantly correlated with the presence/absence of C6-58.27_665, and the correlation coefficient was r = 0.55 (p < 0.01). These results showed that C6-58.27_665 could be applied in marker-assisted selection (MAS) for tuber shape breeding in the future. Our research sets the important stage for the future cloning of the tuber shape gene and utilities of the marker in the breeding program.

Comparative transcriptomics analysis reveals a calcineurin B-like gene to positively regulate constitutive and acclimated freezing tolerance in potato

Freezing stress is a major limiting factor in crop production. To increase frost-hardiness of crops via breeding, deciphering the genes conferring freezing-tolerance is vital. Potato cultivars (Solanum tuberosum) are generally freezing-sensitive, but some potato wild species are freezing-tolerant, including Solanum commersonii, Solanum malmeanum and Solanum acaule. However, the underlying molecular mechanisms conferring the freezing-tolerance to the wild species remain to be deciphered. In this study, five representative genotypes of the above-mentioned species with distinct freezing-tolerance were investigated. Comparative transcriptomics analysis showed that SaCBL1-like (calcineurin B-like protein) was upregulated substantially in all of the freezing-tolerant genotypes. Transgenic overexpression and known-down lines of SaCBL1-like were examined. SaCBL1-like was shown to confer freezing-tolerance without significantly impacting main agricultural traits. A functional mechanism analysis showed that SaCBL1-like increases the expression of the C-repeat binding factor-regulon as well as causes a prolonged higher expression of CBF1 after exposure to cold conditions. Furthermore, SaCBL1-like was found to only interact with SaCIPK3-1 (CBL-interacting protein kinase) among all apparent cold-responsive SaCIPKs. Our study identifies SaCBL1-like to play a vital role in conferring freezing tolerance in potato, which may provide a basis for a targeted potato breeding for frost-hardiness.

Methylation level of potato gene OMT30376 regulates tuber anthocyanin transformations

After anthocyanin synthesis, a variety of anthocyanin compounds are produced through further methylation, glycosylation, and acylation. However, the effect of the potato methylase gene on anthocyanin biosynthesis has not been reported. Red and purple mutation types appear in tubers of the potato cultivar 'Purple Viking' with chimeric skin phenotypes. In this study, transcriptome and anthocyanin metabolome analyses were performed on skin of Purple Viking tubers and associated mutants. According to the metabolome analysis, the transformation of delphinidin into malvidin-3-O-glucoside and petunidin 3-O-glucoside and that of cyanidin into rosinidin O-hexoside and peonidin-3-O-glucoside were hindered in red tubers. Expression of methyltransferase gene OMT30376 was significantly lower in red tubers than in purple ones, whereas the methylation level of OMT30376 was significantly higher in red tubers. In addition, red skin appeared in tubers from purple tuber plants treated with S-adenosylmethionine (SAM), indicating the difference between purple and red was caused by the methylation degree of the gene OMT30376. Thus, the results of the study suggest that the OMT30376 gene is involved in the transformation of anthocyanins in potato tubers. The results also provide an important reference to reveal the regulatory mechanisms of anthocyanin biosynthesis and transformation.

How sulfur species can accelerate the biological immobilization of the toxic selenium oxyanions and promote stable hexagonal Se0 formation

Toxic selenium oxyanions and sulfur species are often jointly present in contaminated waters and soils. This study investigated the effect on kinetics and resulting products for bio-reduction of selenium oxyanions in the presence of biologically produced sulfur resulting from bio-oxidation of sulfide in (bio)gas-desulfurization (bio-S⁰) and of sulfate. Selenite and selenate (~2 mmol L^-1) bio-reduction was studied in batch up to 28 days at 30 ^oC and pH 7 using lactic acid and a sulfate-reducing sludge, 'Emmtec'. Bio-S⁰ addition increased the selenite removal rate, but initially slightly decreased selenate reduction rates. Selenite reacted with biologically generated sulfide resulting in selenium-sulfur, which upon further bio-reduction creates a sulfur bio-reduction cycle. Sulfate addition increased the bio-reduction rate for both selenite and sulfate. Bio-S⁰ or sulfate promoted hexagonal selenium formation, whereas without these, mostly amorphous Se⁰ resulted. With another inoculum, 'Eerbeek', bio-S⁰ accelerated the selenite reduction rate less than for 'Emmtec' because of lower sulfur and higher selenite bio-reduction rates. Bio-S⁰ addition increased the selenate reduction rate slightly and accelerated hexagonal selenium formation. Hexagonal selenium formation is advantageous because it facilitates separation and recovery and is less mobile and toxic than amorphous Se⁰. Insights into the interaction between selenium and sulfur bio-reduction are valuable for understanding environmental pathways and considerations regarding remediation and recovery.

Profiling of the Candidate Interacting Proteins of SELF-PRUNING 6A (SP6A) in Solanum tuberosum

SELF-PRUNING 6A (SP6A), a homolog of FLOWERING LOCUS T (FT), has been identified as tuberigen in potato. StSP6A is a mobile signal synthesized in leaves and transmitted to the stolon through phloem, and plays multiple roles in the growth and development of potato. However, the global StSP6A protein interaction network in potato remains poorly understood. In this study, BK-StSP6A was firstly used as the bait to investigate the StSP6A interaction network by screening the yeast two-hybrid (Y2H) library of potato, resulting in the selection of 200 independent positive clones and identification of 77 interacting proteins. Then, the interaction between StSP6A and its interactors was further confirmed by the Y2H and BiFC assays, and three interactors were selected for further expression analysis. Finally, the expression pattern of Flowering Promoting Factor 1.1 (StFPF1.1), No Flowering in Short Days 1 and 2 (StNFL1 and StNFL2) was studied. The three genes were highly expressed in flowers or flower buds. StFPF1.1 exhibited an expression pattern similar to that of StSP6A at the stolon swelling stages. StPHYF-silenced plants showed up-regulated expression of StFPF1.1 and StSP6A, while expression of StNFL1 and StNFL2 was down-regulated in the stolon. The identification of these interacting proteins lays a solid foundation for further functional studies of StSP6A.

The transcription factor StTINY3 enhances cold-induced sweetening resistance by coordinating starch resynthesis and sucrose hydrolysis in potato

The accumulation of reducing sugars in cold-stored tubers, known as cold-induced sweetening (CIS), negatively affects potato processing quality. The starch to sugar interconversion pathways that are altered in cold-stored CIS tubers have been elucidated, but the mechanism that regulates them remains largely unknown. This study identified a CBF/DREB transcription factor (StTINY3) that enhances CIS resistance by both activating starch biosynthesis and repressing the hydrolysis of sucrose to reducing sugars in detached cold-stored tubers. Silencing StTINY3 in a CIS-resistant genotype decreased CIS resistance, while overexpressing StTINY3 in a CIS-sensitive genotype increased CIS resistance, and altering StTINY3 expression was associated with expression changes in starch resynthesis-related genes. We showed first that overexpressing StTINY3 inhibited sucrose hydrolysis by enhancing expression of the invertase inhibitor gene StInvInh2, and second that StTINY3 promoted starch resynthesis by up-regulating a large subunit of the ADP-glucose pyrophosphorylase gene StAGPaseL3, and the glucose-6-phosphate transporter gene StG6PT2. Using electrophoretic mobility shift assays, we revealed that StTINY3 is a nuclear-localized transcriptional activator that directly binds to the dehydration-responsive element/CRT cis-element in the promoters of StInvInh2 and StAGPaseL3. Taken together, these findings established that StTINY3 influences CIS resistance in cold-stored tubers by coordinately modulating the starch to sugar interconversion pathways and is a good target for improving potato processing quality.

Bioinspired aligned wrinkling dressings for monitoring joint motion and promoting joint wound healing

Joint skin wounds are difficult to treat because of the frequent large motion of these active wounds; thus, dressings capable of simultaneous real-time monitoring of joint motion and promoting joint wound healing are highly needed. Herein, inspired by the aligned wrinkling microstructure and sensing functions of normal joint skins, we combine the electrospinning technique with a water-induced self-assembly approach to prepare bioinspired conductive dressings with aligned wrinkles for achieving the above-mentioned bifunctions. The results indicate that both the wavelength and height of the bioinspired aligned wrinkles can be facilely tuned by adjusting the thickness ratio of the two layers and the loading amount of conductive microparticles. Owing to the unique aligned wrinkling structure and good conductivity, the bioinspired dressing can monitor the donor student's diverse joint motions. Interestingly, the dressing can also accurately monitor different types of mouse neck motion, including up/down and left/right movements. The in vivo wound repairing results confirm that the bioinspired dressing can accelerate the healing of active wounds on the mouse neck by promoting collagen deposition, hair follicle regeneration, and epithelialization. The bioinspired dressing with the integration of real-time motion monitoring features and wound repairing functions will open a new avenue to improve the management of joint wounds.

Transcription factor StABI5-like 1 binding to the FLOWERING LOCUS T homologs promotes early maturity in potato

Potato (Solanum tuberosum L.) maturity involves several important traits, including the onset of tuberization, flowering, leaf senescence, and the length of the plant life cycle. The timing of flowering and tuberization in potato is mediated by seasonal fluctuations in photoperiod and is thought to be separately controlled by the FLOWERING LOCUS T-like (FT-like) genes SELF-PRUNING 3D (StSP3D) and SELF-PRUNING 6A (StSP6A). However, the biological relationship between these morphological transitions that occur almost synchronously remains unknown. Here, we show that StABI5-like 1 (StABL1), a transcription factor central to abscisic acid (ABA) signaling, is a binding partner of StSP3D and StSP6A, forming an alternative florigen activation complex and alternative tuberigen activation complex in a 14-3-3-dependent manner. Overexpression of StABL1 results in the early initiation of flowering and tuberization as well as a short life cycle. Using genome-wide chromatin immunoprecipitation sequencing and RNA-sequencing, we demonstrate that AGAMOUS-like and GA 2-oxidase 1 genes are regulated by StABL1. Phytohormone profiling indicates an altered gibberellic acid (GA) metabolism and that StABL1-overexpressing plants are insensitive to the inhibitory effect of GA with respect to tuberization. Collectively, our results suggest that StABL1 functions with FT-like genes to promote flowering and tuberization and consequently life cycle length in potato, providing insight into the pleiotropic functioning of the FT gene.

The Practical Haplotype Graph, a platform for storing and using pangenomes for imputation

MOTIVATION

Pangenomes provide novel insights for population and quantitative genetics, genomics, and breeding not available from studying a single reference genome. Instead, a species is better represented by a pangenome or collection of genomes. Unfortunately, managing and using pangenomes for genomically diverse species is computationally and practically challenging. We developed a trellis graph representation anchored to the reference genome that represents most pangenomes well and can be used to impute complete genomes from low density sequence or variant data.

RESULTS

The Practical Haplotype Graph (PHG) is a pangenome pipeline, database (PostGRES & SQLite), data model (Java, Kotlin, or R), and Breeding API (BrAPI) web service. The PHG has already been able to accurately represent diversity in four major crops including maize, one of the most genomically diverse species, with up to 1000-fold data compression. Using simulated data, we show that, at even 0.1X coverage, with appropriate reads and sequence alignment, imputation results in extremely accurate haplotype reconstruction. The PHG is a platform and environment for the understanding and application of genomic diversity.

AVAILABILITY

All resources listed here are freely available. The PHG Docker used to generate the simulation results is https://hub.docker.com/ as maizegenetics/phg:0.0.27. PHG source code is at https://bitbucket.org/bucklerlab/practicalhaplotypegraph/src/master/. The code used for the analysis of simulated data is at https://bitbucket.org/bucklerlab/phg-manuscript/src/master/. The PHG database of NAM parent haplotypes is in the CyVerse data store (https://de.cyverse.org/de/) and named /iplant/home/shared/panzea/panGenome/PHG_db_maize/phg_v5Assemblies_20200608.db.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Large-Sized GaN Crystal Growth Analysis in an Ammonothermal System Based on a Well-Developed Numerical Model

The ammonothermal method is considered the most promising method of fabricating bulk gallium nitride (GaN) crystals. This paper improves the ammonothermal growth model by replacing the heater-long fixed temperature boundary with two resistance heaters and considering the real thermal boundary outside the shell. The relationship between power values and temperatures of dissolution and crystallization is expressed by the backpropagation (BP) neural network, and the optimal power values for specific systems are found using the non-dominated sorting genetic algorithm (NSGAII). Simulation results show that there are several discrepancies between updated and simplified models. It is necessary to build an ammonothermal system model with resistance heaters as a heat source. Then large-sized GaN crystal growth is analyzed based on the well-developed numerical model. According to the simulation results, both the increasing rate and maximum stable values of the metastable GaN concentration gradient are reduced for a larger-sized system, which is caused by the inhomogeneity of heat transfer in the autoclave.

Surface Kinetic Mechanisms of Epitaxial Chemical Vapour Deposition of 4H Silicon Carbide Growth by Methyltrichlorosilane-H2 Gaseous System

The chemical vapour deposition (CVD) technique could be used to fabricate a silicon carbide (SiC) epitaxial layer. Methyltrichlorosilane (CH₃SiCl₃, MTS) is widely used as a precursor for CVD of SiC with a wide range of allowable deposition temperatures. Typically, an appropriate model for the CVD process involves kinetic mechanisms of both gas-phase reactions and surface reactions. Here, we proposed the surface kinetic mechanisms of epitaxial SiC growth for MTS-H₂ gaseous system where the MTS employed as the single precursor diluted in H₂. The deposition face is assumed to be the Si face with a surface site terminated by an open site or H atom. The kinetic mechanisms for surface reactions proposed in this work for MTS-H₂ gaseous system of epitaxial growth of SiC by CVD technique from mechanisms proposed for H-Si-C-Cl system are discussed in detail. Predicted components of surface species and growth rates at different mechanisms are discussed in detail.

Autophagy-Sirtuin1(SIRT1) Alleviated the Coronary Atherosclerosis (AS)in Mice through Regulating the Proliferation and Migration of Endothelial Progenitor Cells (EPCs) via wnt/β-catenin/GSK3β Signaling Pathway

BACKGROUND AND PURPOSE

SIRT1 was associated with AS risk and EPCs were reported to participate in the endothelial repair in Coronary Atherosclerosis (CAS). In this study, we explored the role of SIRT1 in AS mice and also its modulation in EPCs.

METHODS AND MATERIALS

ApoE-/-mice were fed on high-fat and high-glucose diet to establish the AS animal model with the normally-raised C57BL/6 mice as a control group. SIRT1 activator, SRT 2104 was injected intravenously into 5 ApoE-/-mice and its inhibitor Nicotinamide was injected in tail in another 5 ApoE-/-mice. Weight changes were recorded. Blood samples were taken from posterior orbital venous plexus and were detected by automatic biochemical analyzer. HE staining displayed the pathological conditions while Immunohistochemistry (IHC) evaluated the CD34+/VEGFR2+ relative density in the aorta tissues. EPCs were isolated from bone marrow and verified using immunofluorescence staining (IFS). The modulatory mechanism of SIRT1 in EPCs were studied by using RT-PCR, MTT, Western Blot and colony formation, scratch methods.

RESULTS

SIRT1 activator negatively regulated the weight and TC, TG and LDL levels, alleviated the lesion conditions and decreased the CD34+/VEGFR2+ density compared to the AS control. In vitro, SIRT1 activator promoted the proliferation and migration of EPCs and activated wnt/β-catenin/GSK3β signaling pathway. SIRT1 activator also inhibited the autophagy biomarkers ATG1 and LC3II. Furthermore, inhibitor of autophagy promoted SIRT1 expression and induced EPC proliferation, migration and activated wnt/β-catenin/GSK3β pathway. The suppression of the wnt/β-catenin/GSK3β pathway inhibited SIRT1 expression in EPCs, attenuated the proliferation and migration and promoted autophagy of EPCs.

CONCLUSION

SIRT1 activation might be protective in AS mice through autophagy inhibition in EPCs via wnt/β-catenin/GSK3β signaling pathway.

Global Screening and Functional Identification of Major HSPs Involved in PVY Infection in Potato

HSP40 (also known as DnaJ), HSP70, and HSP90 are major heat shock protein (HSP) families that play critical roles in plant growth and development and stress adaption. Recently, several members of the three HSP families were reported to be widely involved in the plant host-virus interactions. However, their global expression profiles and core members recruited by viruses are largely unknown. In this study, a total of 89 StDnaJs were identified from a genome-wide survey, and their classification, phylogenetic relationships, chromosomal locations, and gene duplication events were further analyzed. Together with 20 StHSP70s and 7 StHSP90s previously identified in the potato genome, the global expression patterns of the members in 3 HSP families were investigated in 2 potato cultivars during Potato virus Y (PVY) infection using RNA-seq data. Of them, 16 genes (including 8 StDnaJs, 6 StHSP70s, and 2 StHSP90s) were significantly up- or downregulated. Further analysis using qRT-PCR demonstrated that 7 of the 16 genes (StDnaJ06, StDnaJ17, StDnaJ21, StDnaJ63, StHSP70-6, StHSP70-19, and StHSP90.5) were remarkably upregulated in the potato cultivar 'Eshu 3' after PVY infection, implying their potential roles in the potato-PVY compatible interaction. Subsequent virus-induced gene silencing (VIGS) assays showed that silencing of the homologous genes of StDnaJ17, StDnaJ21, StHSP70-6, and StHSP90.5 in Nicotiana. benthamiana plants dramatically reduced the accumulation of PVY, which indicated the four genes may function as susceptibility factors in PVY infection. This study provides candidate genes for exploring the mechanism of potato-PVY compatible interaction and benefits breeding work aiming to produce new cultivars with the ability to grow healthily under PVY infection.

Improving the GaN Growth Rate by Optimizing the Nutrient Basket Geometry in an Ammonothermal System Based on Numerical Simulation

The low growth rate of bulk gallium nitride (GaN) when using the ammonothermal method is improved herein by optimizing the nutrient geometry. A numerical model considering the dissolution and crystallization process is developed. Heater powers are employed as thermal boundary conditions to match the real ammonothermal system. The flow field, thermal field, and mass concentration field in the autoclave are calculated with or without a central hole in the nutrient basket. Numerical results show that the mass transfer efficiency and supersaturation on the seed crystal surface can be improved with a hole in the nutrient basket in the center in spite of its diverse effect on the heat transfer, which can be overcome by adjusting the heater powers. As a result, the growth rate of the GaN crystal can be obviously increased.

Susceptibility factor StEXA1 interacts with StnCBP to facilitate potato virus Y accumulation through the stress granule-dependent RNA regulatory pathway in potato

Plant viruses recruit multiple host factors for translation, replication, and movement in the infection process. The loss-of-function mutation of the susceptibility genes will lead to the loss of susceptibility to viruses, which is referred to as 'recessive resistance'. Essential for potexvirus Accumulation 1 (EXA1) has been identified as a susceptibility gene required for potexvirus, lolavirus, and bacterial and oomycete pathogens. In this study, EXA1 knockdown in potato (StEXA1) was found to confer novel resistance to potato virus Y (PVY, potyvirus) in a strain-specific manner. It significantly compromised PVY^O accumulation but not PVY^N:O and PVY^NTN. Further analysis revealed that StEXA1 is associated with the HC-Pro of PVY through a member of eIF4Es (StnCBP). HC-Pro^O and HC-Pro^N, two HC-Pro proteins from PVY^O and PVY^N, exhibited strong and weak interactions with StnCBP, respectively, due to their different spatial conformation. Moreover, the accumulation of PVY^O was mainly dependent on the stress granules (SGs) induced by StEXA1 and StnCBP, whereas PVY^N:O and PVY^NTN could induce SGs by HC-Pro^N independently through an unknown mechanism. These results could explain why StEXA1 or StnCBP knockdown conferred resistance to PVY^O but not to PVY^N:O and PVY^NTN. In summary, our results for the first time demonstrate that EXA1 can act as a susceptibility gene for PVY infection. Finally, a hypothetical model was proposed for understanding the mechanism by which StEXA1 interacts with StnCBP to facilitate PVY accumulation in potato through the SG-dependent RNA regulatory pathway.

Modulation of JA signalling reveals the influence of StJAZ1-like on tuber initiation and tuber bulking in potato

Phytohormones and their interactions play critical roles in Solanum tuberosum (potato) tuberization. The stimulatory role of jasmonic acid (JA) in tuber development is well established because of its significant promotion of tuber initiation and tuber bulking. However, the dynamics and potential function of JA signalling in potato tuberization remain largely unknown. The present study investigated the role of the JAZ1 subtype, a suppressor of JA signalling, in potato tuberization. Using 35S:StJAZ1-like-GUS as a reporter, we showed that JA signalling was attenuated from the bud end to the stem end shortly after tuber initiation. Overexpression of StJAZ1-like suppressed tuber initiation by restricting the competence for tuber formation in stolon tips, as demonstrated by grafting an untransformed potato cultivar to the stock of StJAZ1-like-overexpressing transgenic potato plants (StJAZ1-like ox). In addition, transcriptional profiling analysis revealed that StJAZ1-like modulates the expression of genes associated with transcriptional regulators, cell cycle, cytoskeleton and phytohormones. Furthermore, we showed that StJAZ1-like is destabilised upon treatment with abcisic acid (ABA), and the attenuated tuberization phenotype in StJAZ1-like ox plants can be partially rescued by ABA treatment. Altogether, these results revealed that StJAZ1-like-mediated JA signalling plays an essential role in potato tuberization.