Structure-based prediction of protein-protein interaction network in rice

Comprehensive protein-protein interaction (PPI) maps are critical for understanding the functional organization of the proteome, but challenging to produce experimentally. Here, we developed a computational method for predicting PPIs based on protein docking. Evaluation of performance on benchmark sets demonstrated the ability of the docking-based method to accurately identify PPIs using predicted protein structures. By employing the docking-based method, we constructed a structurally resolved PPI network consisting of 24,653 interactions between 2,131 proteins, which greatly extends the current knowledge on the rice protein-protein interactome. Moreover, we mapped the trait-associated single nucleotide polymorphisms (SNPs) to the structural interactome, and computationally identified 14 SNPs that had significant consequences on PPI network. The protein structural interactome map provided a resource to facilitate functional investigation of PPI-perturbing alleles associated with agronomically important traits in rice.

Streptomyces herbicida sp. nov., a novel actinomycete with antibacterial and herbicidal activity isolated from soil

A novel actinobacterial strain (NEAU-HV9T) showing antibacterial activity against Ralstonia solanacearum and herbicidal activity against Amaranthus retroflexus L. was isolated from soil sampled in Bama yao Autonomous County, Hechi City, Guangxi Zhuang Autonomous Region. The strain is aerobic and Gram-positive. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain NEAU-HV9T belonged to the genus Streptomyces and showed high 16S rRNA sequence similarity to Streptomyces panaciradicis 1MR-8T (98.90 %), Streptomyces sasae JR-39T (98.89 %) and Streptomyces barringtoniae JA03T (98.69 %) and less than 98.5 % similarity to other members of the genus Streptomyces. The cell wall of strain NEAU-HV9T contained ll-diaminopimelic acid and the whole-cell hydrolysates were galactose, mannose and ribose. The predominant menaquinones were composed of MK-9(H2) and MK-9(H8). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylinositol. The major fatty acids were C16 : 0, iso-C16 : 0 and C17 : 1  ω8c. The genomic DNA G+C content of strain NEAU-HV9T was 70.6 mol%. Furthermore, the strain could be clearly distinguished from its closely related type strains by the combination of DNA-DNA hybridization results and some phenotypic characteristics. Meanwhile, strain NEAU-HV9T displayed herbicidal activity. Therefore, strain NEAU-HV9T represents a novel species within the genus Streptomyces, for which the name Streptomyces herbicida sp. nov. is proposed, with strain NEAU-HV9T (=CCTCC AA 2019088T=DSM 113364T) as the type strain.

The transcription factor EMB1444-like affects tomato fruit ripening by regulating YELLOW-FRUITED TOMATO 1, a core component of ethylene signaling transduction

The fleshy fruit of tomato (Solanum lycopersicum) are climacteric and, as such, ethylene plays a pivotal role in their ripening and quality traits. In this study, a basic helix-loop-helix transcription factor, EMB1444-like, was found to induce the expression of YELLOW-FRUITED TOMATO 1 (YFT1), which encodes the SlEIN2 protein, a key element in the ethylene signaling pathway. Yeast one-hybrid and EMSA analyses revealed that EMB1444-like binds to the E-box motif (CACTTG, -1295 bp to -1290 bp upstream of the ATG start codon) of the YFT1 promoter (pYFT1). Suppression of EMB1444-like expression in tomato lines (sledl) using RNAi reduced ethylene production by lowering the expression of 1-AMINOCYCLOPROPANE-1-CARBOXYLATE SYNTHASE 2/4 (ACS2/4) and ACC OXIDASE1 (ACO1) in a positive feedback loop. sledl tomato also showed differences in numerous quality traits related to fruit ripening, compared with the wild type, such as delayed chromoplast differentiation, a decrease in carotenoid accumulation, and delayed fruit ripening in an ethylene-independent manner, or at least upstream of ripening mediated by YFT1/SlEIN2. This study elucidates the regulatory framework of fruit ripening in tomato, providing information that may be used to breed tomato hybrid cultivars with an optimal balance of shelf-life, durability, and high quality.

Analysis of EEG features and study of automatic classification in first-episode and drug-naïve patients with major depressive disorder

BACKGROUND

Major depressive disorder (MDD) has a high incidence and an unknown mechanism. There are no objective and sensitive indicators for clinical diagnosis.

OBJECTIVE

This study explored specific electrophysiological indicators and their role in the clinical diagnosis of MDD using machine learning.

METHODS

Forty first-episode and drug-naïve patients with MDD and forty healthy controls (HCs) were recruited. EEG data were collected from all subjects in the resting state with eyes closed for 10 min. The severity of MDD was assessed by the Hamilton Depression Rating Scale (HAMD-17). Machine learning analysis was used to identify the patients with MDD.

RESULTS

Compared to the HC group, the relative power of the low delta and theta bands was significantly higher in the right occipital region, and the relative power of the alpha band in the entire posterior occipital region was significantly lower in the MDD group. In the MDD group, the alpha band scalp functional connectivity was overall lower, while the scalp functional connectivity in the gamma band was significantly higher than that in the HC group. In the feature set of the relative power of the ROI in each band, the highest accuracy of 88.2% was achieved using the KNN classifier while using PCA feature selection. In the explanatory model using SHAP values, the top-ranking influence feature is the relative power of the alpha band in the left parietal region.

CONCLUSIONS

Our findings reveal that the abnormal EEG neural oscillations may reflect an imbalance of excitation, inhibition and hyperactivity in the cerebral cortex in first-episode and drug-naïve patients with MDD. The relative power of the alpha band in the left parietal region is expected to be an objective electrophysiological indicator of MDD.

[Effect of electroacupuncture pretreatment on ferroptosis in neurons of rats with cerebral ischemia-reperfusion injury]

OBJECTIVE

To observe the effect of electroacupuncture（EA）preconditioning on ferroptosis in rats with cerebral ischemia-reperfusion injury （CIRI）, so as to explore the neuroprotective mechanism of EA preconditioning.

METHODS

Male SD rats were randomly divided into sham operation, model, EA, inhibitor and inducer groups with 20 rats in each group. The CIRI model was established by modified Zea Longa occlusion of the middle cerebral artery. Before modeling, EA treatment （2 Hz/15 Hz, 1-2 mA） was applied to "Baihui"（GV20）, "Fengfu"（GV16） and "Dazhui"（GV14） for rats of the EA group, 20 min a day for 7 consecutive days. Rats of the inhibitor group were intraperitoneally injected with ferristatin-1（25 mg/kg）at a slow and uniform rate. Rats of the inducer group were intraperitoneally injected with Erastin（100 mg/kg） after 7 days of EA preconditioning, once every 2 h for a total of 4 times. The CIRI models were prepared 2 d later after the above interventions finished by thread-occlusion. The degree of neurological impairment was evaluated by modified Zea Longa score. The percentage of infarct size was calculated by TTC staining. The ultrastructure of neurons in hippocampus was observed by transmission electron microscope. The contents of ferrous ion （Fe2+）, malondialdehyde （MDA） and glutathione （GSH） in cerebral tissue and reactive oxygen species （ROS） in serum were determined by biochemical method. The changes of mitochondrial membrane potential in rats brain tissues were detected by flow cytometry. The mRNA and protein expression levels of glutathione peroxidase 4 （GPX4）, acyl-CoA synthetase long-chain family member 4 （ACSL4）, transferrin receptor （TFRC）, 15-lipoxygenase （15-LOX） and cyclooxygenase-2 （COX-2） in the ischemic hippocampal region of CIRI rats were detected by real-time quantitative PCR and Western blot, respectively.

RESULTS

Compared with the sham operation group, the neurological impairment score, the percentage of cerebral infarction area, the contents of MDA and Fe2+ in cerebral tissue as well as ROS in serum, the protein and mRNA expression levels of ACSL4, TFRC, 15-LOX, COX-2 in hippocampal tissue were increased （P<0.01）, while the content of GSH in cerebral tissue, the protein and mRNA expression levels of GPX4 in hippocampal tissue were decreased （P<0.01）, and mitochondria in brain tissue were significantly damaged （P<0.01） in the model group. Compared with the model group, the above indexes were all reversed （P<0.05, P<0.01） in the EA group and inhibitor group. Compared with the EA group, the neurological impairment score, the percentage of cerebral infarction area, the contents of MDA and Fe2+ in cerebral tissue as well as ROS in serum, the protein and mRNA expression le-vels of ACSL4, TFRC, 15-LOX, COX-2 in hippocampal tissue were increased （P<0.05, P<0.01）, while the content of GSH in cerebral tissue, the protein and mRNA expression levels of GPX4 in hippocampal tissue were decreased （P<0.01, P<0.05）, and mitochondria in brain tissue were significantly damaged （P<0.05） in the inducer group.

CONCLUSION

EA preconditioning has neuroprotective effect on CIRI rats, which may be related to inhibiting ACSL4/TFRC/15-LOX/COX-2 expression and increasing GSH/GPX4 expression.

[Effect of Tongdu Tiaoshen electroacupuncture pretreatment on PPARγ-mediated pyroptosis of cerebral cortex in rats with cerebral ischemia reperfusion injury]

OBJECTIVE

To observe the effect of Tongdu Tiaoshen (promoting the circulation of the governor vessel and regulating the spirit) electroacupuncture (EA) pretreatment on pyroptosis mediated by peroxisome proliferators-activated receptor γ (PPARγ) of the cerebral cortex in rats with cerebral ischemia reperfusion injury (CIRI) and explore the potential mechanism of EA for the prevention and treatment of CIRI.

METHODS

A total of 110 clean-grade male SD rats were randomly divided into a sham-operation group, a model group, an EA group, an EA + inhibitor group and an agonist group, 22 rats in each group. In the EA group, before modeling, EA was applied to "Baihui" (GV 20), "Fengfu" (GV 16) and "Dazhui" (GV 14), with disperse-dense wave, 2 Hz/5 Hz in frequency, 1 to 2 mA in intensity, lasting 20 min; once a day, consecutively for 7 days. On the base of the intervention as the EA group, on the day 7, the intraperitoneal injection with the PPARγ inhibitor, GW9662 (10 mg/kg) was delivered in the EA + inhibitor group. In the agonist group, on the day 7, the PPARγ agonist, pioglitazone hydrochloride (10 mg/kg) was injected intraperitoneally. At the end of intervention, except the sham-operation group, the modified thread embolization method was adopted to establish the right CIRI model in the rats of the other groups. Using the score of the modified neurological severity score (mNSS), the neurological defect condition of rats was evaluated. TTC staining was adopted to detect the relative cerebral infarction volume of rat, TUNEL staining was used to detect apoptosis of cerebral cortical nerve cells and the transmission electron microscope was used to observe pyroptosis of cerebral cortical neural cells. The positive expression of PPARγ and nucleotide-binding to oligomerization domain-like receptor protein 3 (NLRP3) in the cerebral cortex was detected with the immunofluorescence staining. The protein expression of PPARγ, NLRP3, cysteinyl aspartate specific protease-1 (caspase-1), gasdermin D (GSDMD) and GSDMD-N terminal (GSDMD-N) in the cerebral cortex was detected with Western blot. Using the quantitative real-time fluorescence-PCR, the mRNA expression of PPARγ, NLRP3, caspase-1 and GSDMD of the cerebral cortex was detected. The contents of interleukin (IL)-1β and IL-18 in the cerebral cortex of rats were determined by ELISA.

RESULTS

Compared with the sham-operation group, the mNSS, the relative cerebral infarction volume and the TUNEL positive cells rate were increased (P<0.01), pyroptosis was severe, the protein and mRNA expression levels of PPARγ, NLRP3, caspase-1 and GSDMD were elevated (P<0.01); and the protein expression of GSDMD-N and contents of IL-1β and IL-18 were increased (P<0.01) in the model group. When compared with the model group, the mNSS, the relative cerebral infarction volume and the TUNEL positive cells rate were decreased (P<0.01), pyroptosis was alleviated, the protein and mRNA expression levels of PPARγ were increased (P<0.01), the protein and mRNA expression levels of NLRP3, caspase-1 and GSDMD were decreased (P<0.01), the protein expression of GSDMD-N was reduced (P<0.01); and the contents of IL-1β and IL-18 were lower (P<0.01) in the EA group and the agonist group; while, in the EA + inhibitor group, the protein expression of PPARγ was increased (P<0.01), the protein and mRNA expression levels of NLRP3 and GSDMD were decreased (P<0.01, P<0.05), the mRNA expression of caspase-1 was reduced (P<0.01); and the contents of IL-1β and IL-18 were lower (P<0.01). When compared with the EA + inhibitor group, the mNSS, the relative cerebral infarction volume and the TUNEL positive cells rate were decreased (P<0.05, P<0.01), pyroptosis was alleviated, the protein and mRNA expression levels of PPARγ were increased (P<0.01), the protein and mRNA expression levels of NLRP3, caspase-1 and GSDMD were decreased (P<0.01), the protein expression of GSDMD-N was reduced (P<0.01); and the contents of IL-1β and IL-18 were declined (P<0.01) in the EA group. Compared with the agonist group, in the EA group, the relative cerebral infarction volume and the TUNEL positive cells rate were increased (P<0.05, P<0.01), the mRNA expression of PPARγ was decreased (P<0.01) and the protein expression of GSDMD-N was elevated (P<0.05); and the contents of IL-1β and IL-18 were higher (P<0.01).

CONCLUSION

Tongdu Tiaoshen EA pretreatment can attenuate the neurological impairment in the rats with CIRI, and the underlying mechanism is related to the up-regulation of PPARγ inducing the inhibition of NLRP3 in the cerebral cortex of rats so that pyroptosis is affected.

Clinical Risk Prediction Models with Meta-Learning Prototypes of Patient Heterogeneity

Hospitalized patients sometimes have complex health conditions, such as multiple diseases, underlying diseases, and complications. The heterogeneous patient conditions may have various representations. A generalized model ignores the differences among heterogeneous patients, and personalized models, even with transfer learning, are still limited to the small amount of training data and the repeated training process. Meta-learning provides a solution for training similar patients based on few-shot learning; however, cannot address common cross-domain patients. Inspired by prototypical networks [1], we proposed a meta-prototype for Electronic Health Records (EHR), a meta-learning-based model with flexible prototypes representing the heterogeneity in patients. We apply this technique to cardiovascular diseases in MIMIC-III and compare it against a set of benchmark models, and demonstrate its ability to address heterogeneous patient health conditions and improve the model performances from 1.2% to 11.9% on different metrics and prediction tasks.Clinical relevance- Developing an adaptive EHR risk prediction model for outcomes-driven phenotyping of heterogeneous patient health conditions.

[Professor HAN Wei's clinical experience of acupuncture and moxibustion with Tongyang Xingshen for adolescent depressive disorder]

Professor HAN Wei 's clinical experience of acupuncture and moxibustion with Tongyang Xingshen (promoting yang and regaining consciousness) for adolescent depressive disorder is introduced. It is believed that the internal causes of adolescent depressive disorder are mostly emotional and physical factors, while the external causes are mainly social factors, and yang-qi stagnation and emotional disorder are the key pathogenesis. The key of acupuncture and moxibustion with Tongyang Xingshen is warming and regulating the governor vessel. The governor vessel acupoints at head, neck and back are selected. At head, Baihui (GV 20) and Yintang (GV 24⁺) are selected; at neck, Fengfu (GV 16) and Dazhui (GV 14) are selected; at back, Taodao (GV 13), Shenzhu (GV 12), Shendao (GV 11), Zhiyang (GV 9) and Jinsuo (GV 8) are selected. The combination of disease differentiation and syndrome differentiation should be highly valued, and the moxibustion with Tongyang and acupuncture with Xingshen should be used simultaneously, and the strong stimulation is suggested.

Designing artificial synthetic promoters for accurate, smart, and versatile gene expression in plants

With the development of high-throughput biology techniques and artificial intelligence, it has become increasingly feasible to design and construct artificial biological parts, modules, circuits, and even whole systems. To overcome the limitations of native promoters in controlling gene expression, artificial promoter design aims to synthesize short, inducible, and conditionally controlled promoters to coordinate the expression of multiple genes in diverse plant metabolic and signaling pathways. Synthetic promoters are versatile and can drive gene expression accurately with smart responses; they show potential for enhancing desirable traits in crops, thereby improving crop yield, nutritional quality, and food security. This review first illustrates the importance of synthetic promoters, then introduces promoter architecture and thoroughly summarizes advances in synthetic promoter construction. Restrictions to the development of synthetic promoters and future applications of such promoters in synthetic plant biology and crop improvement are also discussed.

[Acupuncture combined with Qingfei Qutan decoction for stroke-associated pneumonia with phlegm-heat obstructing lung and its effect on cellular immune function]

OBJECTIVE

To observe the clinical effect of acupuncture combined with Qingfei Qutan decoction for stroke-associated pneumonia (SAP) with phlegm-heat obstructing lung, and explore its possible mechanism.

METHODS

Ninety-nine patients of SAP with phlegm-heat obstructing lung were randomly divided into a combination group (33 cases, 1 case dropped off), a Chinese medication group (33 cases, 1 case dropped off) and an acupuncture group (33 cases, 1 case dropped off). On the basis of routine basic treatment, the patients in the acupuncture group were treated with acupuncture at Tiantu (CV 22), Feishu (BL 13), Taiyuan (LU 9), Sanyinjiao (SP 6), etc., once a day, with an interval of 1 day after continuous 6-day treatment; the patients in the Chinese medication group were treated with Qingfei Qutan decoction, 1 dose per day; the patients in the combination group were treated with acupuncture combined with Qingfei Qutan decoction. Two weeks were taken as a course of treatment, and two courses of treatment were given. Before and after treatment, the clinical pulmonary infection score (CPIS), inflammatory indexes (neutrophil-to-lymphocyte ratio [NLR], procalcitonin [PCT], C-reactive protein [CRP]), cellular immune function (CD⁺₃, CD⁺₄, CD⁺₈ and CD⁺₄/CD⁺₈) were compared in the 3 groups. The clearance of pathogenic bacteria after treatment was observed in the 3 groups. The clinical efficacy of each group was evaluated.

RESULTS

After treatment, the CPIS scores, NLR, PCT, CRP and CD⁺₈ in the each group were lower than those before treatment (P<0.05), while the levels of CD⁺₃, CD⁺₄, CD⁺₄/CD⁺₈ were higher than those before treatment (P<0.05). The above indexes in the combination group were better than those in the acupuncture group and the Chinese medication group (P<0.05), and the above indexes in the Chinese medication group were better than those in the acupuncture group (P<0.05). There was no significant difference in the clearance rate of pathogenic bacteria among three groups (P>0.05). The cured and markedly effective rate was 65.6% (21/32) in the combination group, which was higher than 43.8% (14/32) in the Chinese medication group and 18.8% (6/32) in the acupuncture group (P<0.05). The cured and markedly effective rate in the Chinese medication group was higher than that in the acupuncture group (P<0.05).

CONCLUSION

Acupuncture combined with Qingfei Qutan decoction could effectively improve the clinical symptoms of SAP patients with phlegm-heat obstructing lung, and the mechanism may be related to enhancing the cellular immune function and reducing the level of inflammatory reaction.

[Neuroendoscopy-assisted microneurosurgery for cerebellopontine angle cholesteatoma]

A total of 49 patients with cerebellopontine angle cholesteatoma from the Department of Neurosurgery, Affiliated Hospital of Xuzhou Medical University between January 2013 and January 2021 were recruited. All patients were evaluated by MRI scan before surgery and tumor resection was performed under microscope via retrosigmoid sinus approach. Then residual tumor was searched with 0°and 30°neuroendoscopy, and tumor resection was performed.Residual tumors were foundand resectedin 38 cases under theneuroendoscopy after routine microsurgery.Total and subtotalresections were performed in 44 cases and 5 cases, respectively. Complications included aseptic meningitis (n=8), cerebrospinal fluid leakage (n=1) and intracranial hematoma (n=2). Follow-up[42±3(6-72)months] was available in all patients. During follow-up, 45 cases (91.8%) had a Kar-nofsky Performance Status (KPS)score ≥80.Neuroendoscopy-assisted microsurgery for cerebellopontine angle cholesteatomas helps enhance the total resection rate and decrease the operative risk.

[Bioinformatics screening and analysis of key differentially expressed genes characteristics in nonalcoholic fatty liver disease]

Objective: To screen and analyze the key differentially expressed genes characteristics in nonalcoholic fatty liver disease (NAFLD) with bioinformatics method. Methods: NAFLD-related expression matrix GSE89632 was downloaded from the GEO database. Limma package was used to screen differentially expressed genes (DEGs) in healthy, steatosis (SS), and nonalcoholic steatohepatitis (NASH) samples. WGCNA was used to analyze the output gene module. The intersection of module genes and differential genes was used to determine the differential genes characteristic, and then GO function and KEGG signaling pathway enrichment analysis were performed. The protein-protein interaction network (PPI) was constructed using the online website STRING and Cytoscape software, and the key (Hub) genes were screened. Finally, R software was used to analyze the receiver operating characteristic curve (ROC) of the Hub gene. Results: 92 differentially expressed genes characteristic were obtained through screening, which were mainly enriched in inflammatory response-related functions of "lipopolysaccharide response and molecular response of bacterial origin", as well as cancer signaling pathways of "proteoglycan in cancer" and "T-cell leukemia virus infection-related". 10 hub genes (FOS, CXCL8, SERPINE1, CYR61, THBS1, FOSL1, CCL2, MYC, SOCS3 and ATF3) had good diagnostic value. Conclusion: The differentially expressed hub genes among the 10 NAFLD disease-related characteristics obtained with bioinformatics analysis may become a diagnostic and prognostic marker and potential therapeutic target for NAFLD. However, further basic and clinical studies are needed to validate.

[Tongdu Tiaoshen acupuncture combined with carotid endarterectomy for carotid artery stenosis: a randomized controlled trial]

OBJECTIVE

To observe the clinical therapeutic effect of Tongdu Tiaoshen acupuncture combined with carotid endarterectomy (CEA) and simple CEA on carotid artery stenosis (CAS).

METHODS

A total of 60 patients with CAS were randomized into an observation group (30 cases, 2 cases dropped off) and a control group (30 cases, 3 cases dropped off). Both groups were treated with eversion CEA (eCEA). The conventional treatment of internal medicine and antiplatelet drugs i.e. aspirin enteric-coated tablet and clopidogrel hydrogen sulfate tablet were given in the control group for 4 weeks. On the basis of the treatment in the control group, Tongdu Tiaoshen acupuncture was applied at Baihui (GV 20), Fengfu (GV 16), Yamen (GV 15), cervical Jiaji (EX-B 2), Dazhui (GV 14), etc. in the observation group, once a day, 1-day rest was taken after 6-day treatment, 2 weeks were as one course and totally 2 courses were required. The carotid intima-media thickness (IMT) before and after treatment was detected by ultrasonic diagnostic apparatus, the TCM symptom score was compared before and after treatment and in the follow-up of 6 months after treatment, the clinical efficacy was evaluated in the two groups. The occurrence of endpoints within 1 year was recorded.

RESULTS

After treatment, the carotid IMT and TCM symptom scores were decreased compared before treatment in the both groups (P<0.05), and the changes in the observation group were greater than the control group (P<0.05). In the follow-up, the TCM symptom scores were decreased compared before treatment in the both groups (P<0.05). The total effective rate was 96.4% (27/28) in the observation group, which was superior to 88.9% (24/27) in the control group (P<0.05). There were 1 case of stoke in the observation group and 2 cases of stroke in the control group within 1-year follow-up, and there was no significant difference in the number of endpoints between the two groups within 1 year (P>0.05).

CONCLUSION

Tongdu Tiaoshen acupuncture combined with CEA can effectively reduce the IMT in patients with CAS, improve the TCM symptom score, the efficacy is superior to simple CEA treatment.

Microbacterium stercoris sp. nov., an indole acetic acid-producing actinobacterium isolated from cow dung

A novel growth-promoting and indole acetic acid-producing strain, designated NEAU-LLB^T, was isolated from cow dung collected from Shangzhi, Heilongjiang Province, PR China. Cells of strain NEAU-LLB^T were Gram-stain-positive, non-motile, aerobic and non-spore-forming. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain NEAU-LLB^T belonged to the genus Microbacterium. Strain NEAU-LLB^T had high 16S rRNA sequence similarities of 98.81 and 98.41 % to Microbacterium paludicola DSM 16915^T and Microbacterium marinilacus DSM 18904^T, and less than 98 % to other members of the genus Microbacterium. Chemotaxonomic characteristics showed that MK-11 and MK-12 were detected as the predominant menaquinones. The peptidoglycan contained glutamic acid, aspartic acid, glycine, ornithine and a small amount of alanine, with ornithine as the diagnostic diamino acid. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid. The major fatty acids were identified as anteiso-C_15 : 0, iso-C_16 : 0 and iso-C_17 : 0. The genomic DNA G+C content of strain NEAU-LLB^T was 70.2 mol%. In addition, the average nucleotide identity values between strain NEAU-LLB^T and its reference strains, M. paludicola DSM 16915^T, M. marinilacus DSM 18904^T and M. album SYSU D8007^T, were found to be 81.1, 79.4 and 78.7 %, respectively, and the level of digital DNA-DNA hybridization between them were 23.8, 22.6 and 21.8 %, respectively. Based on the phenotypic, phylogenetic and genotypic data, strain NEAU-LLB^T is considered to represent a novel species of the genus Microbacterium, for which the name Microbacterium stercoris sp. nov is proposed, with NEAU-LLB^T (=CCTCC AA 2018028^T=JCM 32660^T) as the type strain.

[Exploration on the diagnosis and treatment of generalized myasthenia gravis with acupuncture and moxibustion based on the study of ancient medical works]

Through collecting the relevant provisions and medical cases of wei syndrome treated with acupuncture and moxibustion from ancient medical works, the diagnosis and acupoint selection in treatment of generalized myasthenia gravis (gMC) with acupuncture and moxibustion were analyzed systematically from 3 aspects, i.e. meridian differentiation, disease differentiation and syndrome differentiation. In treatment based on meridian differentiation, the acupoints are selected in the light of the running course of meridian and characteristics of meridian disorders. In treatment based on disease differentiation, the acupoints are selected in accordance with etiology, pathogenesis and transmission stages of wei syndrome. Concerning to syndrome differentiation in treatment, the acupoints are selected on the basis of therapeutic principles determined by different syndromes/patterns of wei syndrome. In modern clinical practice, the treatment for gMC should be rooted at ancient literature, thus a standardized regimen can be developed for diagnosis and treatment with acupuncture and moxibustion.

Two homologous Salmonella serogroup C1-specific genes are required for flagellar motility and cell invasion

Background

Salmonella is a major bacterial pathogen associated with a large number of outbreaks of foodborne diseases. Many highly virulent serovars that cause human illness belong to Salmonella serogroup C1, and Salmonella ser. Choleraesuis is a prominent cause of invasive infections in Asia. Comparative genomic analysis in our previous study showed that two homologous genes, SC0368 and SC0595 in Salmonella ser. Choleraesuis were unique to serogroup C1. In this study, two single-deletion mutants (Δ0368 and Δ0595) and one double-deletion mutant (Δ0368Δ0595) were constructed based on the genome. All these mutants and the wild-type strain were subjected to RNA-Seq analysis to reveal functional relationships of the two serogroup C1-specific genes.

Results

Data from RNA-Seq indicated that deletion of SC0368 resulted in defects in motility through repression of σ²⁸ in flagellar regulation Class 3. Consistent with RNA-Seq data, results from transmission electron microcopy (TEM) showed that flagella were not present in △0368 and △0368△0595 mutants resulting in both swimming and swarming defects. Interestingly, the growth rates of two non-motile mutants △0368 and △0368△0595 were significantly greater than the wild-type, which may be associated with up-regulation of genes encoding cytochromes, enhancing bacterial proliferation. Moreover, the △0595 mutant was significantly more invasive in Caco-2 cells as shown by bacterial enumeration assays, and the expression of lipopolysaccharide (LPS) core synthesis-related genes (rfaB, rfaI, rfaQ, rfaY, rfaK, rfaZ) was down-regulated only in the △0368△0595 mutant. In addition, this study also speculated that these two genes might be contributing to serotype conversion for Salmonella C1 serogroup based on their apparent roles in biosynthesis of LPS and the flagella.

Conclusion

A combination of biological and transcriptomic (RNA-Seq) analyses has shown that the SC0368 and SC0595 genes are involved in biosynthesis of flagella and complete LPS, as well as in bacterial growth and virulence. Such information will aid to revealing the role of these specific genes in bacterial physiology and evolution within the serogroup C1.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07759-z.

The transcription factor WRKY32 affects tomato fruit colour by regulating YELLOW FRUITED-TOMATO 1, a core component of ethylene signal transduction

Fruit quality in most fleshy fruit crops is fundamentally linked to ripening-associated traits, including changes in colour. In many climacteric fruits, including tomato (Solanum lycopersicum), the phytohormone ethylene plays a key role in regulating ripening. Previous map-based cloning of YELLOW FRUITED-TOMATO 1 (YFT1) revealed that it encodes the EIN2 protein, a core component in ethylene signal transduction. A YFT1 allele with a genetic lesion was found to be down-regulated in the yft1 tomato mutant that has a yellow fruit phenotype and perturbed ethylene signalling. Based on bioinformatic analysis, yeast one hybrid assays and electrophoretic mobility shift assays, we report that transcription factor WRKY32 regulates tomato fruit colour formation. WRKY32 binds to W-box and W-box-like motifs in the regulatory region of the YFT1 promoter and induces its expression. In tomato fruits of WRKY32-RNAi generated lines, ethylene signalling was reduced, leading to a suppression in ethylene emission, a delay in chromoplast development, decreased carotenoid accumulation, and a yellow fruit phenotype. These results provide new insights into the regulatory networks that govern tomato fruit colour formation via ethylene signal transduction.

MicroRNA-665 regulates the proliferation, apoptosis and adhesion of gastric cancer cells by binding to cadherin 3

Numerous studies have reported that abnormal cadherin 3 (CDH3) and microRNA (miRNA/miR)-665 expression can induce the progression of gastric cancer (GC). However, the mechanism of interaction between miR-665 and CDH3 in GC requires further investigation. The present study aimed to investigate the influence of miR-665 and CDH3 in GC development. The effect of miR-665 and CDH3 on GC tissues and cell lines was examined using reverse transcription-quantitative PCR. Subsequently, CDH3 protein expression in GC cell lines was detected using western blotting. To confirm the association between miR-665 and CDH3, a dual-luciferase reporter assay system was employed. Cell proliferation and adhesion were analyzed using BrdU ELISA, MTT and cell adhesion assays. Finally, caspase-3 activity assay kit and FITC apoptosis detection kit were used for the determination of apoptosis of GC cells. The current findings confirmed the upregulation of CDH3 expression in GC cell lines and tissues. Experimental results indicated that CDH3 overexpression increased cell proliferation and adhesion, but decreased the apoptosis level of the cells. Similarly, the miR-665 inhibitor enhanced cell proliferation and adhesion, but inhibited apoptosis of GC cells. Additionally, it was observed that CDH3 was a direct target of miR-665 in GC cells and that miR-665 inhibited CDH3 expression, thereby repressing the progression of GC. In conclusion, the present study suggested that by targeting CDH3, miR-665 suppressed the progression of GC. These findings may provide a significant theoretical basis for future GC clinical therapy.

Microbacterium helvum sp. nov., a novel actinobacterium isolated from cow dung

A Gram-positive, aerobic, non-motile, non-spore-forming, short rod-shaped strain, NEAU-LLC^T, was isolated from cow dung in Shangzhi City, Heilongjiang Province, Northeast China and identified by a polyphasic taxonomic study. Colonies was light yellow, round, with entire margin. Strain NEAU-LLC^T was grown at 15-45 ℃ and pH 6.0-10.0. NaCl concentration ranged from 0 to 5% (W/V). The 16S rRNA gene sequence of NEAU-LLC^T showed the high similarities with Microbacterium kyungheense JCM 18735^T (98.5%), Microbacterium trichothecenolyticum JCM 1358^T (98.3%) and Microbacterium jejuense JCM 18734^T (98.2%). The whole-cell sugars were glucose, rhamnose and ribose. The menaquinones contained MK-12 and MK-13. Ornithine, glutamic acid, lysine and a small amount of alanine and glycine were the amino acids in the hydrolyzed products of the cell wall. The major fatty acids were iso-C_16:0, iso-C_18:0, anteiso-C_15:0 and anteiso-C_17:0. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid. The genome of NEAU-LLC^T was 4,369,375 bp and G + C content is 70.28 mol%. A combination of DNA-DNA hybridization result and some phenotypic characteristics demonstrated that strain NEAU-LLC^T could be distinguished from its closely related strains. Therefore, the strain NEAU-LLC^T was considered to represent a novel species, which was named Microbacterium helvum sp. (Type strain NEAU-LLC^T = CCTCC AA 2018026^T = JCM 32661^T).

[Effect of moxibustion on expression of GAP-43 in sciatic nerve trunk and ventral horn of spinal cord of rats with primary sciatica and its nerve repair function]

OBJECTIVE

To observe the effect of moxibustion at "Huantiao" (GB 30) on the expression of growth-associated protein-43 (GAP-43) in the sciatic nerve trunk and ventral horn of spinal cord (L₄-L₆) in rats with primary sciatica, and to explore the mechanism of moxibustion in improving primary sciatica.

METHODS

A total of 48 healthy male SD rats were randomly divided into a normal group, a sham operation group, a model group and a moxibustion group, 12 rats in each group. The rat model of primary sciatic pain was established by chronic constriction injury (CCI) of the sciatic nerve in the model group and the moxibustion group. On the 8th day of the experiment, moxibustion was adopted at "Huantiao" (GB 30) in the moxibustion group for 5-10 min, once a day for 14 consecutive days. Sciatic nerve function index (SFI) was measured and compared in each group at day 1, 7, 14 and 21. On the 21st day of the experiment, HE staining was used to observe the morphology of ventral horn of rat spinal cord and sciatic nerve trunk. Immunohistochemical method and real-time PCR were used to detect mRNA and protein expressions of GAP-43 in the spinal cord and sciatic nerve trunk of rats.

RESULTS

On day 7, 14 and 21, there was no statistical difference in SFI between the sham operation group and the normal group (P>0.05); compared with the sham operation group on day 7, 14 and 21, the SFI of the model group was reduced (P<0.01); compared with the model group on day 14 and 21, SFI in the moxibustion group was increased (P<0.01). In the normal group and the sham operation group, neuronal cells were in order in the ventral horn of the spinal cord, nissl bodies were spaced regularly, the myelin sheath structure of sciatic nerve axon was clearly visible. In the model group, neuronal cells were deformed and ruptured in the ventral horn of the spinal cord, the number of nissl bodies was less, and the demyelination of sciatic axons appeared. In the moxibustion group, neuronal cells were found in the ventral horn of spinal cord, and the number of nissl bodies was increased, and less demyelinating changes of axons appeared in sciatic nerve. Compared with the normal group, the expressions of GAP-43 mRNA and GAP-43 protein in the sciatic nerve trunk and GAP-43 protein in the ventral horn of spinal cord were increased in the sham operation group (P<0.01). Compared with the sham operation group, the expression of GAP-43 mRNA and GAP-43 protein in the spinal cord and sciatic nerve trunk of rats in the model group was increased. Compared with the model group, the expression of GAP-43 mRNA and GAP-43 protein in the spinal cord and sciatic nerve trunk of rats in the moxibustion group was increased (P<0.01).

CONCLUSION

Moxibustion at "Huantiao" (GB 30) could improve the sciatic nerve function in rats with primary sciatica and its mechanism may be related to improving the expression of GAP-43 and enhancing the self-repair ability of the sciatic nerve after injury.

Nocardia bovistercoris sp. nov., an actinobacterium isolated from cow dung

A novel actinobacterium, designated strain NEAU-351^T, was isolated from cow dung collected from Shangzhi, Heilongjiang Province, northeast PR China and characterized using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NEAU-351^T belonged to the genus Nocardia, with the highest similarity (98.96 %) to Nocardia takedensis DSM 44801^T and less than 98.0 % identity with other type strains of the genus Nocardia. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. The major menaquinone was observed to contain MK-8(H₄, ω-cycl) (78.2 %). The fatty acid profile mainly consisted of C_16 : 0, C_18 : 1  ω9c and 10-methyl C_18 : 0. Mycolic acids were present. The genomic DNA G+C content of strain NEAU-351^T was 68.1 mol%. In addition, the average nucleotide identity values between strain NEAU-351^T and its reference strains, Nocardia takedensis DSM 44801^T and Nocardia arizonensis NBRC 108935^T, were found to be 81.4 and 82.9 %, respectively, and the level of digital DNA-DNA hybridization between them were 24.8 % (22.5-27.3 %) and 26.3 % (24-28.8 %), respectively. Here we report on the taxonomic characterization and classification of the isolate and propose that strain NEAU-351^T represents a new species of the genus Nocardia, for which the name Nocardia bovistercoris is proposed. The type strain is NEAU-351^T (=CCTCC AA 2019090^T=DSM 110681^T).

Predicting Protein-Protein Interactions Between Rice and Blast Fungus Using Structure-Based Approaches

Rice blast, caused by the fungus Magnaporthe oryzae, is the most devastating disease affecting rice production. Identification of protein-protein interactions (PPIs) is a critical step toward understanding the molecular mechanisms underlying resistance to blast fungus in rice. In this study, we presented a computational framework for predicting plant-pathogen PPIs based on structural information. Compared with the sequence-based methods, the structure-based approach showed to be more powerful in discovering new PPIs between plants and pathogens. Using the structure-based method, we generated a global PPI network consisted of 2,018 interacting protein pairs involving 1,344 rice proteins and 418 blast fungus proteins. The network analysis showed that blast resistance genes were enriched in the PPI network. The network-based prediction enabled systematic discovery of new blast resistance genes in rice. The network provided a global map to help accelerate the identification of blast resistance genes and advance our understanding of plant-pathogen interactions.

Yellow-fruited phenotype is caused by 573 bp insertion at 5' UTR of YFT1 allele in yft1 mutant tomato

The yft1 tomato mutant has a yellow-fruited phenotype controlled by a recessive gene of YFT1 allele, which has been shown by map-based cloning to be a homolog of ETHYLENE INSENSITIVE 2 (EIN2). Genetic lesion of YFT1 allele in yft1 is attributed to a 573 bp DNA fragment (IF₅₇₃) insertion at 1,200 bp downstream of the transcription start site. Transcriptomic analysis revealed that YFT1 lesion resulted in 5,053 differentially expressed genes (DEGs) in yft1 pericarp compared with the M82 wild type cultivar. These were annotated as being involved in ethylene synthesis, chromoplast development, and carotenoid synthesis. The YFT1 lesion caused a reduction in its own transcript levels in yft1 and impaired ethylene emission and signal transduction, delayed chromoplast development and decreased carotenoid accumulation. The molecular mechanism underlying the downregulated YFT1 allele in yft1 was examined at both RNA and DNA levels. The IF₅₇₃ event appeared to introduce two negative regulatory sequences located at -272 to -173 bp and -172 to -73 bp in the YFT1 allele promoter, causing alterative splicing due to introduction of aberrant splicing sites, and breaking upstream open reading frames (uORF) structure in the 5'-UTR. Those results a new provided insight into molecular regulation of color formation in tomato fruit.

Relations between electron yield and temperature rise under low-energy electron irradiation for Au element

Scanning electron microscope (SEM) is a widely used tool for analysing the micro/nanoscale structural information. In the process of the SEM imaging, the temperature rise caused by the electron beam bombardment has already become an issue because the SEM results might thus be modified by it as the specimen downsizes. This work aims to explore the relationship between the total electron yield (TEY) and the temperature rise in order to directly evaluate the heat accumulation inside the solid during the imaging using a Monte Carlo (MC) simulation. The rules of profiles of the TEY and the temperature rise integral with various primary electron (PE) beam energies and incident angles were first investigated focusing on a semi-infinite gold (Au) bulk. Based on this rule, it is concluded that, with the increase of the TEY, the temperature rise integral decreases almost linearly (As the PE energy getting larger, the linear correlation is more obvious). In addition, this result was also applied to evaluate the heat built up for two specific SEM imaging examples: nanoscale Au balls and arbitrary shaped Au particles on a carbon (C) substrate. Their temperature contour maps present an almost inverse contrast compared with their respective SEM images. Furthermore, the influence of external electric field (full extraction and no extraction modes) for thermal effect was discussed. It is concluded that the full extraction mode can effectively avoid the local overheating. The mechanism of these observations was explained in detail. On the one hand, this work gives a better elucidation and understanding for physical mechanism of electron-beam-induced deposition, of which reliability, process control and performance can thus be greatly improved. On the other hand, because some damages caused by nonuniform heat accumulation in various local geometric structures of specimen during imaging process could be effectively analysed and even reduced, this work thus greatly benefits for the analysis of the correlation between thermal effect and the structures of samples.

Developing Personalized Models of Blood Pressure Estimation from Wearable Sensors Data Using Minimally-trained Domain Adversarial Neural Networks

Blood pressure monitoring is an essential component of hypertension management and in the prediction of associated comorbidities. Blood pressure is a dynamic vital sign with frequent changes throughout a given day. Capturing blood pressure remotely and frequently (also known as ambulatory blood pressure monitoring) has traditionally been achieved by measuring blood pressure at discrete intervals using an inflatable cuff. However, there is growing interest in developing a cuffless ambulatory blood pressure monitoring system to measure blood pressure continuously. One such approach is by utilizing bioimpedance sensors to build regression models. A practical problem with this approach is that the amount of data required to confidently train such a regression model can be prohibitive. In this paper, we propose the application of the domain-adversarial training neural network (DANN) method on our multitask learning (MTL) blood pressure estimation model, allowing for knowledge transfer between subjects. Our proposed model obtains average root mean square error (RMSE) of 4.80 ± 0.74 mmHg for diastolic blood pressure and 7.34 ± 1.88 mmHg for systolic blood pressure when using three minutes of training data, 4.64 ± 0.60 mmHg and 7.10 ± 1.79 respectively when using four minutes of training data, and 4.48±0.57 mmHg and 6.79±1.70 respectively when using five minutes of training data. DANN improves training with minimal data in comparison to both directly training and to training with a pretrained model from another subject, decreasing RMSE by 0.19 to 0.26 mmHg (diastolic) and by 0.46 to 0.67 mmHg (systolic) in comparison to the best baseline models. We observe that four minutes of training data is the minimum requirement for our framework to exceed ISO standards within this cohort of patients.

A Streptomyces sp. NEAU-HV9: Isolation, Identification, and Potential as a Biocontrol Agent against Ralstonia Solanacearum of Tomato Plants

Ralstonia solanacearum is an important soil-borne bacterial plant pathogen. In this study, an actinomycete strain named NEAU-HV9 that showed strong antibacterial activity against Ralstonia solanacearum was isolated from soil using an in vitro screening technique. Based on physiological and morphological characteristics and 98.90% of 16S rRNA gene sequence similarity with Streptomyces panaciradicis 1MR-8^T, the strain was identified as a member of the genus Streptomyces. Tomato seedling and pot culture experiments showed that after pre-inoculation with the strain NEAU-HV9, the disease occurrence of tomato seedlings was effectively prevented for R.solanacearum. Then, a bioactivity-guided approach was employed to isolate and determine the chemical identity of bioactive constituents with antibacterial activity from strain NEAU-HV9. The structure of the antibacterial metabolite was determined as actinomycin D on the basis of extensive spectroscopic analysis. To our knowledge, this is the first report that actinomycin D has strong antibacterial activity against R. solanacearum with a MIC (minimum inhibitory concentration) of 0.6 mg L⁻¹ (0.48 μmol L⁻¹). The in vivo antibacterial activity experiment showed that actinomycin D possessed significant preventive efficacy against R. solanacearum in tomato seedlings. Thus, strain NEAU-HV9 could be used as BCA (biological control agent) against R. solanacearum, and actinomycin D might be a promising candidate for a new antibacterial agent against R. solanacearum.

PRAP: Pan Resistome analysis pipeline

Background

Antibiotic resistance genes (ARGs) can spread among pathogens via horizontal gene transfer, resulting in imparities in their distribution even within the same species. Therefore, a pan-genome approach to analyzing resistomes is necessary for thoroughly characterizing patterns of ARGs distribution within particular pathogen populations. Software tools are readily available for either ARGs identification or pan-genome analysis, but few exist to combine the two functions.

Results

We developed Pan Resistome Analysis Pipeline (PRAP) for the rapid identification of antibiotic resistance genes from various formats of whole genome sequences based on the CARD or ResFinder databases. Detailed annotations were used to analyze pan-resistome features and characterize distributions of ARGs. The contribution of different alleles to antibiotic resistance was predicted by a random forest classifier. Results of analysis were presented in browsable files along with a variety of visualization options. We demonstrated the performance of PRAP by analyzing the genomes of 26 Salmonella enterica isolates from Shanghai, China.

Conclusions

PRAP was effective for identifying ARGs and visualizing pan-resistome features, therefore facilitating pan-genomic investigation of ARGs. This tool has the ability to further excavate potential relationships between antibiotic resistance genes and their phenotypic traits.

[Moxibustion at acpoints of governor vessel on regulating PI3K/Akt/mTOR signaling pathway and enhancing autophagy process in APP/PS1 double-transgenic Alzheimer's disease mice]

OBJECTIVE

To observe the eliminating effects of moxibustion at "Baihui" (GV 20), "Fengfu" (GV 16) and "Dazhui" (GV 14) on amyloid β-peptide (Aβ) in brain of the amyloid precursor protein/presenili1 (APP/PS1) double-transgenic mice with Alzheimer's disease (AD) by regulating the phosphoinositide 3-kinases/protein kinase B/mammalian target of rapamycin (PI3K/Akt/mTOR) signaling pathway.

METHODS

A total of 60 APP/PS1 double-transgenic mice with AD were randomly divided into a model group, a moxibustion group, a rapamycin group and a combination group (treated with moxibustion and inhibitor), 15 mice in each group, another 15 male C57BL/6J mice with same age and background were selected as the control group. In the moxibustion group, pressing moxibustion was applied at "Baihui" (GV 20) while the mild moxibustion was applied at "Fengfu" (GV 16) and "Dazhui" (GV 14). The treatment was manipulated for 20 min each time, once a day for 2 weeks. In the rapamycin group, rapamycin (2 mg/kg) was given by intraperitoneal injection once a day for 2 weeks. On the basis of the treatment in the moxibustion group, 3-methyladenine (1.5 mg/kg) was given by intraperitoneal injection once a day for 2 weeks. The mice in the control and the model group received normal diet and no intervention was given for 2 weeks. Immunohistochemica method was used to measure the levels of Aβ_1-42 in the cerebral cortex and hippocampal, transmission electron microscopy was used to observe the formation of autophagosome in hippocampus, and Western blot method was used to observe the levels of PI3K, Akt, p-Akt, mTOR and p-mTOR in hippocampus.

RESULTS

Compared with the control group, the levels of Aβ_1-42 in the cerebral cortex and hippocampal were increased in the model group (P<0.01). Compared with the model group, the levels of Aβ_1-42 in the cerebral cortex and hippocampal were decreased in the moxibustion group, the rapamycin group and the combination group (all P<0.01), compared with the moxibustion group, the levels of Aβ_1-42 in the cerebral cortex and hippocampal were increased in the combination group (P<0.01), while there was no significant difference between the moxibustion group and the rapamycin group in the levels of Aβ_1-42（P>0.05）. Compared with the rapamycin group, the levels of Aβ_1-42 in the cerebral cortex and hippocampal were increased in the combination group (P<0.01). In the model group, the cytoplasmic utophagic vacuoles and organelles of neuron were reduced. In the moxibustion group, the utophagic vacuoles were increased, and the organelles showed deformation and atrophy. In the rapamycin group, the utophagic vacuoles were widely disturbed and few deformed organelles were found. In the combination group, few utophagic vacuoles were found and additional organelles showed deformation and atrophy. Compared with the control group, the levels of PI3K、Akt、p-Akt、mTOR and p-mTOR were increased in the model group (all P<0.01). Compared with the model group, the levels of PI3K、Akt、p-Akt、mTOR and p-mTOR were reduced in the moxibustion group, the rapamycin group and the combination group (all P<0.01). Compared with the moxibustion group, the levels of PI3K、Akt、and p-mTOR were increased in the rapamycin group and the levels of PI3K、Akt、p-Akt、mTOR and p-mTOR were increased in the combination group (all P<0.01). Compared with the rapamycin group, the levels of PI3K、Akt、p-Akt、mTOR and p-mTOR were increased in the combination group (P<0.01).

CONCLUSION

Moxibustion at acupoints of governor vessel can enhance the autophagy process on Aβ_1-42 in brain of the APP/PS1 double-transgenic AD mice, which may be associated with its effects on inhibiting the abnormal activation of PI3K/Akt/mTOR signaling pathway.

micro-Stress EMA: A Passive Sensing Framework for Detecting in-the-wild Stress in Pregnant Mothers

High levels of stress during pregnancy increase the chances of having a premature or low-birthweight baby. Perceived self-reported stress does not often capture or align with the physiological and behavioral response. But what if there was a self-report measure that could better capture the physiological response? Current perceived stress self-report assessments require users to answer multi-item scales at different time points of the day. Reducing it to one question, using microinteraction-based ecological momentary assessment (micro-EMA, collecting a single in situ self-report to assess behaviors) allows us to identify smaller or more subtle changes in physiology. It also allows for more frequent responses to capture perceived stress while at the same time reducing burden on the participant. We propose a framework for selecting the optimal micro-EMA that combines unbiased feature selection and unsupervised Agglomerative clustering. We test our framework in 18 women performing 16 activities in-lab wearing a Biostamp, a NeuLog, and a Polar chest strap. We validated our results in 17 pregnant women in real-world settings. Our framework shows that the question "How worried were you?" results in the highest accuracy when using a physiological model. Our results provide further in-depth exposure to the challenges of evaluating stress models in real-world situations.

Interaction of bZIP transcription factor TGA6 with salicylic acid signaling modulates artemisinin biosynthesis in Artemisia annua

Artemisinin is a sesquiterpene lactone produced by the Chinese traditional herb Artemisia annua and is used for the treatment of malaria. It is known that salicylic acid (SA) can enhance artemisinin content but the mechanism by which it does so is not known. In this study, we systematically investigated a basic leucine zipper family transcription factor, AaTGA6, involved in SA signaling to regulate artemisinin biosynthesis. We found specific in vivo and in vitro binding of the AaTGA6 protein to a 'TGACG' element in the AaERF1 promoter. Moreover, we demonstrated that AaNPR1 can interact with AaTGA6 and enhance its DNA-binding activity to its cognate promoter element 'TGACG' in the promoter of AaERF1, thus enhancing artemisinin biosynthesis. The artemisinin contents in AaTGA6-overexpressing and RNAi transgenic plants were increased by 90-120% and decreased by 20-60%, respectively, indicating that AaTGA6 plays a positive role in artemisinin biosynthesis. Importantly, heterodimerization with AaTGA3 significantly inhibits the DNA-binding activity of AaTGA6 and plays a negative role in target gene activation. In conclusion, we demonstrate that binding of AaTGA6 to the promoter of the artemisinin-regulatory gene AaERF1 is enhanced by AaNPR1 and inhibited by AaTGA3. Based on these findings, AaTGA6 has potential value in the genetic engineering of artemisinin production.

AraPPINet: An Updated Interactome for the Analysis of Hormone Signaling Crosstalk in Arabidopsis thaliana

Protein-protein interactions (PPIs) play fundamental roles in various cellular processes. Here, we present a new version of computational interactome that contains more than 345,000 predicted PPIs involving about 51.2% of the Arabidopsis proteins. Compared to the earlier version, the updated AraPPINet displays a higher accuracy in predicting protein interactions through performance evaluation with independent datasets. In addition to the experimental verifications of the previous version, the new version has been subjected to further validation test that demonstrates its ability to discover novel PPIs involved in hormone signaling pathways. Moreover, network analysis shows that many overlapping proteins are significantly involved in the interactions which mediated the crosstalk among plant hormones. The new version of AraPPINet provides a more reliable interactome which would facilitate the understanding of crosstalk among hormone signaling pathways in plants.

[Moxibustion improves learning-memory ability by promoting cellular autophagy and regulating autophagy-related proteins in hippocampus and cerebral cortex in APP/PS1 transgenic Alzheimer's disease mice]

OBJECTIVE

To observe the effect of moxibustion of acupoints of the Governor Vessel on the levels of cellular autophagy, β amyloid protein (Aβ) immunoactivity, and expression of LC3-Ⅰ， LC3-Ⅱ， p62 and p-P70S6K proteins in the hippocampal tissue of APPswe/PS1de9 (APP/PS1) double-transgenic Alzheimer's disease (AD) mice, so as to reveal its underlying mechanisms in improving AD.

METHODS

APP/PS1 double-transgenic AD mice were randomly divided into AD model, moxibustion, autophagy-inducer (Rapamycin) and autophagy-inhibitor (3-MA)＋moxibustion groups (n＝10 in each group), and other 10 C57BL/6J male mice (the same age) were used as the normal control group. Herbal-cake (made of Chuanwu [Radix Aconiti Praeparata]) partitioned moxibustion was applied to "Baihui"(GV20), moxibustion was applied to "Fengfu"(GV16) and "Dazhui"(GV14), all for 20 min, once daily for 2 weeks, with one day's off between two weeks. For mice of the autophagy-inducer and 3-MA＋moxibustion groups, Rapamycin (2 mg•kg^－1•d^－1) and 3-MA (1.5 mg•kg^－1•d^－1) were separately administered by intraperitoneal injection for 2 weeks. The cognitive ability was examined by Morris water maze tests, and the ultrastructural changes (including autophagic lysosomes, etc.) of hippocampal neurons were observed by using transmission electron microscopy. The immunoactivity of cerebral cortex and hippocampal Amyloid β peptide 1-42 (Aβ_1-42) was detected by immunohistochemistry, and the expression levels of hippocampal LC3-Ⅰ， LC3-Ⅱ， p62 and p-P70S6K proteins were detected by Western blot.

RESULTS

After modeling, the escape latency of Morris water maze tasks was prolonged in the model group than in the normal control group (P<0.05) and obviously shortened in the moxibustion and autophagy-inducer groups (not the autophagy-inhibitor group) than in the model group (P<0.05). Results of transmission electron microscope showed deformed, irregular or atrophic neurons with rough and incomplete and fuzzy nuclear membrane, and decreased intracellular autophagosomes in the hippocampus in the model group, and partial irregular, atrophic neurons with more autophagic vesicles and lysosomes in the moxibustion group. The expression levels of Aβ_1-42 in both cerebral cortex and hippocampus tissues, and LC3-Ⅰ， p62 and p-P70S6K proteins in the hippocampus were consi-derably up-regulated in the model group relevant to the normal control group (P<0.01), and evidently down-regulated in both moxibustion and autophagy-inducer groups (not the autophagy-inhibitor group) than in the model group (P<0.01), while that of hippocampal LC3-Ⅱ protein and LC3-Ⅱ/Ⅰ ratio levels were obviously down-regulated in the model group relevant to the normal control group (P<0.01), and significantly up-regulated in both moxibustion and autophagy-inducer groups (not the autophagy-inhibitor group) than in the model group (P<0.01)．.

CONCLUSION

Moxibustion can improve the cognitive ability of APP/PS1 double-transgenic AD mice, which is associated with its effects in promoting hip-pocampal and cerebral cortex autophagy level, and down-regulating the expression levels of Aβ_1-42, LC3-Ⅰ， p62 and p-P70S6K proteins in the hippocampus.

Beam Focusing and Reduction of Quantum Uncertainty in Width at the Few-Photon Level via Multi-Spatial-Mode Squeezing

We show for the first time that it is possible to realize laser beam focusing at the few-photon level in the four-wave-mixing process, and at the same time reduce the quantum uncertainty in width. The reduction in quantum uncertainty results directly from the strong suppression of local intensity fluctuations. This surprising effect of simultaneous focusing and reduction of width uncertainty is enabled by multi-spatial-mode (MSM) squeezing, and is not possible via any classical optical approach or single-spatial-mode squeezing. Our results open promising possibilities for quantum-enhanced imaging and metrology; as an example, the limit on the measurement of very small beam displacement can be enhanced within feasible experimental parameters because of beam focusing and the noiseless amplification in the MSM squeezing process.

Changes in Fruit Firmness, Cell Wall Composition, and Transcriptional Profile in the yellow fruit tomato 1 ( yft1) Mutant

Fruit firmness is an important trait in tomato ( Solanum lycopersicum), associated with shelf life and economic value; however, the precise mechanism determining fruit softening remains elusive. A yellow fruit tomato 1 ( yft1) mutant harbors a genetic lesion in the YFT1 gene and has significantly firmer fruit than those of the cv. M82 wild type at a red ripe stage, 54 days post-anthesis (dpa). When softening was further dissected, it was found that the yft1 firm fruit phenotype correlated with a difference in cellulose, hemicellulose, and pectin deposition in the primary cell wall (PCW) compared to cv. M82. Alterations in the structure of the pericarp cells, chemical components, hydrolase activities, and expression of genes encoding these hydrolases were all hypothesized to be a result of the loss of YFT1 function. This was further affirmed by RNA-seq analysis, where a total of 183 differentially expressed genes (DEGs, 50/133 down-/upregulated) were identified between yft1 and cv. M82. These DEGs were mainly annotated as participating in ethylene- and auxin-related signal transduction, sugar metabolism, and photosynthesis. This study provides new insights into the mechanism underlying the control of fruit softening.

Comparative Genomic Analysis and Characterization of Two Salmonella enterica Serovar Enteritidis Isolates From Poultry With Notably Different Survival Abilities in Egg Whites

Salmonellaenterica serovar Enteritidis (Salmonella Enteritidis) is a globally important foodborne pathogen, and the contaminated chicken eggs are the major source of salmonellosis in humans. Salmonella Enteritidis strains are differentially susceptible to the hostile environment of egg whites. Strains with superior survival ability in egg whites are more likely to contaminate eggs and consequently infect humans. However, the genetic basis for this phenotype is unclear. We characterized two Salmonella Enteritidis strains isolated from chicken meat that had similar genetic backgrounds but large differences in survival ability in egg whites. Although genome comparisons indicated that the gene content and genomic synteny were highly conserved, variations including six insertions or deletions (INDELs) and 70 single nucleotide polymorphisms (SNPs) were observed between the two genomes. Of these, 38 variations including four INDELs and 34 non-synonymous SNPs (nsSNP) were annotated to result in amino acid substitutions or INDELs in coding proteins. These variations were located in 38 genes involved in lysozyme inhibition, vitamin biosynthesis, cell division and DNA damage response, osmotic and oxidative protection, iron-related functions, cell envelope maintenance, amino acid and carbohydrate metabolism, antimicrobial resistance, and type III secretion system. We carried out allelic replacements for two nsSNPs in bioC (biotin synthesis) and pliC (lysozyme inhibition), and two INDELs in ftsK and yqiJ (DNA damage response) by homologous recombination, and these replacements did not alter the bacterial survival ability in egg whites. However, the bacterial survival ability in egg whites was reduced when deletion mutation of the genes bioC and pliC occurred. This study provides initial correlations between observed genotypes and phenotypes and serves as an important caveat for further functional studies.

Network analysis of ABA-dependent and ABA-independent drought responsive genes in Arabidopsis thaliana

Drought is one of the most severe abiotic factors restricting plant growth and yield. Numerous genes functioning in drought response are regulated by abscisic acid (ABA) dependent and independent pathways, but knowledge of interplay between the two pathways is still limited. Here, we integrated transcriptome sequencing and network analyses to explore interplays between ABA-dependent and ABA-independent pathways responding to drought stress in Arabidopsis thaliana. We identified 211 ABA-dependent differentially expressed genes (DEGs) and 1,118 ABA-independent DEGs under drought stress. Functional analysis showed that ABA-dependent DEGs were significantly enriched in expected biological processes in response to water deprivation and ABA stimulus, while ABA-independent DEGs were preferentially enriched in response to jasmonic acid (JA), salicylic acid (SA) and gibberellin (GA) stimuli. We found significantly enriched interactions between ABA-dependent and ABA-independent pathways with 94 genes acting as core interacting components by combining network analyses. A link between ABA and JA signaling mediated through a direct interaction of the ABA responsive elements-binding factor ABF3 with the basic helix-loop-helix transcription factor MYC2 was validated by yeast two-hybrid and bimolecular fluorescence complementation (BiFC) assays. Our study provides a systematic view of the interplay between ABA-dependent and ABA-independent pathways in response to drought stress.

Network analysis of ABA-dependent and ABA-independent drought responsive genes in Arabidopsis thaliana

Drought is one of the most severe abiotic factors restricting plant growth and yield. Numerous genes functioning in drought response are regulated by abscisic acid (ABA) dependent and independent pathways, but knowledge of interplay between the two pathways is still limited. Here, we integrated transcriptome sequencing and network analyses to explore interplays between ABA-dependent and ABA-independent pathways responding to drought stress in Arabidopsis thaliana. We identified 211 ABA-dependent differentially expressed genes (DEGs) and 1,118 ABA-independent DEGs under drought stress. Functional analysis showed that ABA-dependent DEGs were significantly enriched in expected biological processes in response to water deprivation and ABA stimulus, while ABA-independent DEGs were preferentially enriched in response to jasmonic acid (JA), salicylic acid (SA) and gibberellin (GA) stimuli. We found significantly enriched interactions between ABA-dependent and ABA-independent pathways with 94 genes acting as core interacting components by combining network analyses. A link between ABA and JA signaling mediated through a direct interaction of the ABA responsive elements-binding factor ABF3 with the basic helix-loop-helix transcription factor MYC2 was validated by yeast two-hybrid and bimolecular fluorescence complementation (BiFC) assays. Our study provides a systematic view of the interplay between ABA-dependent and ABA-independent pathways in response to drought stress.

The Genome of Artemisia annua Provides Insight into the Evolution of Asteraceae Family and Artemisinin Biosynthesis

Artemisia annua, commonly known as sweet wormwood or Qinghao, is a shrub native to China and has long been used for medicinal purposes. A. annua is now cultivated globally as the only natural source of a potent anti-malarial compound, artemisinin. Here, we report a high-quality draft assembly of the 1.74-gigabase genome of A. annua, which is highly heterozygous, rich in repetitive sequences, and contains 63 226 protein-coding genes, one of the largest numbers among the sequenced plant species. We found that, as one of a few sequenced genomes in the Asteraceae, the A. annua genome contains a large number of genes specific to this large angiosperm clade. Notably, the expansion and functional diversification of genes encoding enzymes involved in terpene biosynthesis are consistent with the evolution of the artemisinin biosynthetic pathway. We further revealed by transcriptome profiling that A. annua has evolved the sophisticated transcriptional regulatory networks underlying artemisinin biosynthesis. Based on comprehensive genomic and transcriptomic analyses we generated transgenic A. annua lines producing high levels of artemisinin, which are now ready for large-scale production and thereby will help meet the challenge of increasing global demand of artemisinin.

Comprehensive Analysis Reveals Two Distinct Evolution Patterns of Salmonella Flagellin Gene Clusters

Salmonella is one of the primary causes of foodborne disease, especially Salmonella enterica subsp. enterica (I) which has caused ~99% of clinical salmonellosis cases for humans and domestic mammals. The flagella genes, fliC and fljB, which encode the Salmonella phase 1 and phase 2 antigens respectively, are considered as the Salmonella serotype determinant genes, and contribute to the virulence of Salmonella. However, the evolution of the two flagellin genes is still not well-understood. In this study, the fliC and fljB gene clusters were analyzed among 205 S. enterica subspecies I genomes. The dataset covered 87 different serovars of S. enterica subsp. enterica and included 9 genomes (six serovars) of four other Salmonella subspecies. Based on a pan-genome definition and flanked gene linkages, the fliC and fljB gene clusters were identified in 207 (91 serovars) and 138 (61 serovars) genomes, respectively. A phylogenetic tree constructed based on SNPs (Single Nucleotide Polymorphisms) of core genes were used to reflect the essential evolutionary relationships among various serovars. Congruence analysis was performed among the core genome and each gene of fliC and fljB gene clusters, with only fliA and fliS showing congruence to Salmonella core genome. Congruence was also observed among fliB, fliC/fljB, and fliD genes, and their phylogeny revealed a division into two major groups, which strongly corresponded to monophasic and biphasic serovars. Besides, homologous recombination events referring fliB, fliC, and fliD were found to have mainly occurred within each group. These results suggested two distinct evolutionary patterns of Salmonella flagellin gene clusters. Further insight on the evolutionary implication of the two patterns and a framework for phase variation mechanism are needed to be further processed.

Rapid evolutionary divergence of diploid and allotetraploid Gossypium mitochondrial genomes

Background

Cotton (Gossypium spp.) is commonly grouped into eight diploid genomic groups and an allotetraploid genomic group, AD. The mitochondrial genomes supply new information to understand both the evolution process and the mechanism of cytoplasmic male sterility. Based on previously released mitochondrial genomes of G. hirsutum (AD₁), G. barbadense (AD₂), G. raimondii (D₅) and G. arboreum (A₂), together with data of six other mitochondrial genomes, to elucidate the evolution and diversity of mitochondrial genomes within Gossypium.

Results

Six Gossypium mitochondrial genomes, including three diploid species from D and three allotetraploid species from AD genome groups (G. thurberi D₁, G. davidsonii D_3-d and G. trilobum D₈; G. tomentosum AD₃, G. mustelinum AD₄ and G. darwinii AD₅), were assembled as the single circular molecules of lengths about 644 kb in diploid species and 677 kb in allotetraploid species, respectively. The genomic structures of mitochondrial in D group species were identical but differed from the mitogenome of G. arboreum (A₂), as well as from the mitogenomes of five species of the AD group. There mainly existed four or six large repeats in the mitogenomes of the A + AD or D group species, respectively. These variations in repeat sequences caused the major inversions and translocations within the mitochondrial genome. The mitochondrial genome complexity in Gossypium presented eight unique segments in D group species, three specific fragments in A + AD group species and a large segment (more than 11 kb) in diploid species. These insertions or deletions were most probably generated from crossovers between repetitive or homologous regions. Unlike the highly variable genome structure, evolutionary distance of mitochondrial genes was 1/6th the frequency of that in chloroplast genes of Gossypium. RNA editing events were conserved in cotton mitochondrial genes. We confirmed two near full length of the integration of the mitochondrial genome into chromosome 1 of G. raimondii and chromosome A03 of G. hirsutum, respectively, with insertion time less than 1.03 MYA.

Conclusion

Ten Gossypium mitochondrial sequences highlight the insights to the evolution of cotton mitogenomes.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4282-5) contains supplementary material, which is available to authorized users.

Molecular cloning, characterization, and promoter analysis of the isochorismate synthase (AaICS1) gene from Artemisia annua

Isochorismate synthase (ICS) is a crucial enzyme in the salicylic acid (SA) synthesis pathway. The full-length complementary DNA (cDNA) sequence of the ICS gene was isolated from Artemisia annua L. The gene, named AaICS1, contained a 1710-bp open reading frame, which encoded a protein with 570 amino acids. Bioinformatics and comparative study revealed that the polypeptide protein of AaICS1 had high homology with ICSs from other plant species. Southern blot analysis suggested that AaICS1 might be a single-copy gene. Analysis of the 1470-bp promoter of AaICS1 identified distinct cis-acting regulatory elements, including TC-rich repeats, MYB binding site (MBS), and TCA-elements. An analysis of AaICS1 transcript levels in multifarious tissues of A. annua using quantitative real-time polymerase chain reaction (qRT-PCR) showed that old leaves had the highest transcription levels. AaICS1 was up-regulated under wounding, drought, salinity, and SA treatments. This was corroborated by the presence of the predicted cis-acting elements in the promoter region of AaICS1. Overexpressing transgenic plants and RNA interference transgenic lines of AaICS1 were generated and their expression was compared. High-performance liquid chromatography (HPLC) results from leaf tissue of transgenic A. annua showed an increase in artemisinin content in the overexpressing plants. These results confirm that AaICS1 is involved in the isochorismate pathway.

[Application of temporary balloon occlusion of the abdominal aorta in the treatment of complete placenta previa complicated with placenta accreta]

Objective: To investigate the value of temporary balloon occlusion of the abdominal aorta in the treatment of complete placenta previa with placenta accreta. Methods: From January 2015 to February 2016, 24 cases of complete placenta previa with placenta accreta were treated with temporary balloon occlusion of the abdominal aorta(the study group)before cesarean, and 24 cases of complete placenta previa with placenta accreta did not receive balloon occlusion(the control group). The operation time, intraoperative blood loss, intraoperative blood transfusion volume, the perioperative hemoglobin level, the hysterectomy rate and the related complications were compared retrospectively.Also, the hospitalization time, the blood coagulation parameters after operation, including activated partial thromboplastin time(APTT), fibrinogen(FIB), D-Dimer and reperfusion injury parameters including creatine phosphokinase(CK), creatine phosphokinase isoenzyme(CK-MB), lactate dehydrogenase(LDH)and serum creatinine were compared between the 2 groups. Results: The blood loss[750 ml(400- 2 000 ml)vs 2 000 ml(1 500- 2 375 ml); Z=-3.214, P=0.001]and blood transfusion volume[200 ml(0-800 ml)vs 800 ml(0-1 200 ml); Z=- 2.173, P=0.030]in the study group were lower than in the control group. The hemoglobin difference between before and after operation in the study group was lower than the control group[(12.8±13.4)g/L vs(22.9±20.1)g/L; t=-2.041, P=0.047]. In the study group, there were still bleeding in 13 cases after releasing the balloon, 5 of them received uterine artery embolization, 5 cases received uterine artery ligation, and 3 cases received uterine packing. One case had venous thrombosis in the right lower limb. Two cases(8%,2/24)in the control group had hysterectomy, while none in the study group, there was no statistical significance(P= 0.489). Conclusions: Temporary balloon occlusion of the abdominal aorta can effectively reduce blood loss and blood transfusion in the treatment of complete placenta previa with placenta accreta, but there is still the risk of continuing bleeding after releasing the balloon. Other methods of hemostasis might be needed.

Peripherally inserted central catheters for calcium requirements after successful parathyroidectomy: a comparison with centrally inserted catheters

BACKGROUND Intravenous calcium supplements are often required following parathyroidectomy to avoid postoperative hypocalcaemia. The aim of this study was to compare application effect of a femoral central venous catheter (CVC) and peripherally inserted central catheter (PICC) on intravenous calcium supplements after parathyroidectomy. METHODS We retrospectively reviewed the hospital records of 73 patients with secondary hyperparathyroidism who underwent a successful parathyroidectomy at the Huashan Hospital attached to Fudan University between 1 April 2011 and 1 February 2016. RESULTS Of the 73 study participants, 39 (53.4%) had a PICC and 34 (46.6%) had a CVC, respectively. Patients in the CVC group needed 6-7 days of intravenous calcium supplements, while patients in PICC group needed only 2-3 days to achieve normal serum calcium concentration (2.2-2.6 mmol/L). Furthermore, the duration of calcium supplementation was 71.62 ± 4.48 hours in PICC group and 100.4 ± 5.43 hours in CVC group (P < 0.05). Of the patients in PICC group, the incidence of catheter occlusion, operation failure and hypocalcaemia was 0%, which was significantly lower than those in CVC group (2.56%, 7.69% and 7.69%, respectively). CONCLUSIONS PICC is a safe and efficient alternative in contrast to CVC for providing venous access for calcium supplementation in surgical patients after parathyroidectomy.

[Clinical study on the relationship between pancreatic fistula and the degree of pancreatic fibrosis after pancreatic and duodenal resection]

Objective: To explore the risk factors of pancreatic fistula after pancreatoduodenectomy and its relationship with pancreatic fibrosis. Methods: Retrospective analysis was made including 408 patients who underwent pancreaticoduodenectomy from January 2013 to December 2015 in Department of Hepatobiliary Surgery of the First Affiliated Hospital of Third Military Medical University. There were 274 males and females, aging from 14 to 82 years with an average age of 54.6 years. Postoperative pathological diagnosis: 285 cases with pancreatic ductal adenocarcinoma, 81 cases with gastrointestinal tumors, 13 cases with neuroendocrine tumors, 16 cases with inflammatory changes, 8 cases with pancreatic papillary tumors, 4 cases with serous cystadenoma, 1 case with retroperitoneal liposarcoma.Univariate analysis using pearson's χ(2) test, multivariate analysis using binary Logistic regression analysis, correlation analysis using Spearman rank correlation analysis and the predictive value of pancreatic fibrosis in pancreatic fistula after pancreaticoduodenectomy was assessed using the area under the receiver operating characteristic(ROC) curve. Results: There were 123 cases (30.1%) with postoperative pancreatic fistula among 408 patients. Univariate analysis showed that body mass index(BMI)(P=0.005), preoperative gamma-glutamyltranspeptidase content(P=0.046), pancreatic duct diameter(P=0.001), CT value of pancreatic tissue(P=0.049), operation time(P=0.037), pancreatic stiffness (intraoperative judgment)(P=0.001) and percentage of pancreatic fibrosis(P=0.034) were the prognostic factors of pancreatic fistula. Multivariate analysis showed that BMI≥25 kg/m(2), pancreatic duct diameter ≤3 mm, pancreatic tissue CT value <40 Hu, pancreatic hardness (intraoperative judgments) for the soft and pancreatic lobular fibrosis percentage ≤25% of postoperative pancreatic fistula occurrence of high-risk factor(P<0.05). Pancreatic fistula's CT value and percentage of pancreatic fibrosis were significantly lower than non-pancreatic fistula group, the difference was statistically significant(P<0.05). There were significant differences in CT value and pancreatic lobular fibrosis among different grades of pancreatic fistulae(P<0.05). Pancreatic fistula severity was negatively correlated with the CT value of pancreatic body and the percentage of fibrosis of the pancreas(P=0.005, 0.019), and there was a significant correlation between CT value of pancreatic body and the percentage of fibrosis of the pancreas(r=0.699, P=0.028). The areas under the ROC curve of percentage of pancreatic fibrosis and CT value of the pancreatic body were 0.745 and 0.714, respectively. Both of them were moderate predictive value for pancreatic fistula after pancreaticoduodenectomy. Conclusions: The degree of pancreatic fibrosis is a prognostic factor for pancreatic texture and pancreatic fistula after pancreaticoduodenectomy. CT value of pancreatic body can be used as a quantitative index of pancreatic fibrosis, and predict the prognostic of pancreatic fistula after pancreaticoduodenectomy.

A computational interactome for prioritizing genes associated with complex agronomic traits in rice (Oryza sativa)

Rice (Oryza sativa) is one of the most important staple foods for more than half of the global population. Many rice traits are quantitative, complex and controlled by multiple interacting genes. Thus, a full understanding of genetic relationships will be critical to systematically identify genes controlling agronomic traits. We developed a genome-wide rice protein-protein interaction network (RicePPINet, http://netbio.sjtu.edu.cn/riceppinet) using machine learning with structural relationship and functional information. RicePPINet contained 708 819 predicted interactions for 16 895 non-transposable element related proteins. The power of the network for discovering novel protein interactions was demonstrated through comparison with other publicly available protein-protein interaction (PPI) prediction methods, and by experimentally determined PPI data sets. Furthermore, global analysis of domain-mediated interactions revealed RicePPINet accurately reflects PPIs at the domain level. Our studies showed the efficiency of the RicePPINet-based method in prioritizing candidate genes involved in complex agronomic traits, such as disease resistance and drought tolerance, was approximately 2-11 times better than random prediction. RicePPINet provides an expanded landscape of computational interactome for the genetic dissection of agronomically important traits in rice.

GLANDULAR TRICHOME-SPECIFIC WRKY 1 promotes artemisinin biosynthesis in Artemisia annua

Artemisinin is a type of sesquiterpene lactone well known as an antimalarial drug, and is specifically produced in glandular trichomes of Artemisia annua. However, the regulatory network for the artemisinin biosynthetic pathway remains poorly understood. Exploration of trichome-specific transcription factors would facilitate the elucidation of regulatory mechanism of artemisinin biosynthesis. The WRKY transcription factor GLANDULAR TRICHOME-SPECIFIC WRKY 1 (AaGSW1) was cloned and analysed in A. annua. AaGSW1 exhibited similar expression patterns to the trichome-specific genes of the artemisinin biosynthetic pathway and AP2/ERF transcription factor AaORA. A β-glucuronidase (GUS) staining assay further demonstrated that AaGSW1 is a glandular trichome-specific transcription factor. AaGSW1 positively regulates CYP71AV1 and AaORA expression by directly binding to the W-box motifs in their promoters. Overexpression of AaGSW1 in A. annua significantly improves artemisinin and dihydroartemisinic acid contents; moreover, AaGSW1 can be directly regulated by AaMYC2 and AabZIP1, which are positive regulators of jasmonate (JA)- and abscisic acid (ABA)-mediated artemisinin biosynthetic pathways, respectively. These results demonstrate that AaGSW1 is a glandular trichome-specific WRKY transcription factor and a positive regulator in the artemisinin biosynthetic pathway. Moreover, we propose that two trifurcate feed-forward pathways involving AaGSW1, CYP71AV1 and AaMYC2/AabZIP1 function in the JA/ABA response in A. annua.

BnLATE, a Cys2/His2-Type Zinc-Finger Protein, Enhances Silique Shattering Resistance by Negatively Regulating Lignin Accumulation in the Silique Walls of Brassica napus

Silique shattering resistance is one of the most important agricultural traits in oil crop breeding. Seed shedding from siliques prior to and during harvest causes devastating losses in oilseed yield. Lignin biosynthesis in the silique walls is thought to affect silique-shattering resistance in oil crops. Here, we identified and characterized B. napus LATE FLOWERING (BnLATE), which encodes a Cys2/His2-type zinc-finger protein. Heterologous expression of BnLATE under the double enhanced CaMV 35S promoter (D35S) in wild-type Arabidopsis plants resulted in a marked decrease in lignification in the replum, valve layer (carpel) and dehiscence zone. pBnLATE::GUS activity was strong in the yellowing silique walls of transgenic lines. Furthermore, the expression pattern of BnLATE and the lignin content gradient in the silique walls at 48 days after pollination (DAP) of 73290, a B. napus silique shattering-resistant line, are similar to those in transgenic Arabidopsis lines expressing BnLATE. Transcriptome sequencing of the silique walls revealed that genes encoding peroxidases, which polymerize monolignols and lignin in the phenylpropanoid pathway, were down-regulated at least two-fold change in the D35S::BnLATE transgenic lines. pBnLATE::BnLATE transgenic lines were further used to identify the function of BnLATE, and the results showed that lignification in the carpel and dehiscence zone of yellowing silique also remarkably decreased compared with the wild-type control, the silique shattering-resistance and expression pattern of peroxidase genes are very similar to results with D35S::BnLATE. These results suggest that BnLATE is a negative regulator of lignin biosynthesis in the yellowing silique walls, and promotes silique-shattering resistance in B. napus through restraining the polymerization of monolignols and lignin.