TransGEM: a molecule generation model based on Transformer with gene expression data

MOTIVATION

It is difficult to generate new molecules with desirable bioactivity through ligand-based de novo drug design, and receptor-based de novo drug design is constrained by disease target information availability. The combination of artificial intelligence and phenotype-based de novo drug design can generate new bioactive molecules, independent from disease target information. Gene expression profiles can be used to characterize biological phenotypes. The Transformer model can be utilized to capture the associations between gene expression profiles and molecular structures due to its remarkable ability in processing contextual information.

RESULTS

We propose TransGEM (Transformer-based model from gene expression to molecules), which is a phenotype-based de novo drug design model. A specialized gene expression encoder is used to embed gene expression difference values between diseased cell lines and their corresponding normal tissue cells into TransGEM model. The results demonstrate that the TransGEM model can generate molecules with desirable evaluation metrics and property distributions. Case studies illustrate that TransGEM model can generate structurally novel molecules with good binding affinity to disease target proteins. The majority of genes with high attention scores obtained from TransGEM model are associated with the onset of the disease, indicating the potential of these genes as disease targets. Therefore, this study provides a new paradigm for de novo drug design, and it will promote phenotype-based drug discovery.

AVAILABILITY AND IMPLEMENTATION

The code is available at https://github.com/hzauzqy/TransGEM.

Metabolites of pathogenic microorganisms database (MPMdb) and its seed metabolite applications

Seed metabolites are the combination of essential compounds required by an organism across various potential environmental conditions. The seed metabolites screening framework based on the network topology approach can capture important biological information of species. This study aims to identify comprehensively the relationship between seed metabolites and pathogenic bacteria. A large-scale data set was compiled, describing the seed metabolite sets and metabolite sets of 124,192 pathogenic strains from 34 genera, by constructing genome-scale metabolic models. The enrichment analysis method was used to screen the specific seed metabolites of each species/genus of pathogenic bacteria. The metabolites of pathogenic microorganisms database (MPMdb) (http://qyzhanglab.hzau.edu.cn/MPMdb/) was established for browsing, searching, predicting, or downloading metabolites and seed metabolites of pathogenic microorganisms. Based on the MPMdb, taxonomic and phylogenetic analyses of pathogenic bacteria were performed according to the function of seed metabolites and metabolites. The results showed that the seed metabolites could be used as a feature for microorganism chemotaxonomy, and they could mirror the phylogeny of pathogenic bacteria. In addition, our screened specific seed metabolites of pathogenic bacteria can be used not only for further tapping the nutritional resources and identifying auxotrophies of pathogenic bacteria but also for designing targeted bactericidal compounds by combining with existing antimicrobial agents.IMPORTANCEMetabolites serve as key communication links between pathogenic microorganisms and hosts, with seed metabolites being crucial for microbial growth, reproduction, external communication, and host infection. However, the large-scale screening of metabolites and the identification of seed metabolites have always been the main technical bottleneck due to the low throughput and costly analysis. Genome-scale metabolic models have become a recognized research paradigm to investigate the metabolic characteristics of species. The developed metabolites of pathogenic microorganisms database in this study is committed to systematically predicting and identifying the metabolites and seed metabolites of pathogenic microorganisms, which could provide a powerful resource platform for pathogenic bacteria research.

[Association between vitamin D level and grip strength in adults aged 50 and older in Shanghai]

Objective: To understand the association between vitamin D level and grip strength in people aged ≥50 years in Shanghai. Methods: Data were obtained from the WHO's Study on Global Ageing and Adult Health in Shanghai during 2018-2019. Logistic regression model was used to analyze the association between vitamin D level and grip strength, and a stratified analysis was conducted for different gender, age and dairy product intake groups. Restricted cubic spline was used to evaluate the dose-response association between vitamin D level and low grip strength. Results: A total of 4 391 participants were included in the study, including 2 054 men (46.8%), with an average age of (67.02±8.81) years. And 1 421 individuals (32.4%) had low grip strength; 1 533 individuals (34.9%) had vitamin D deficiency, and 401 individuals (9.1%) had vitamin D deficiency. After adjusted for confounding factors, the logistic regression results analysis showed that individuals with vitamin D deficiency had a higher risk for low grip strength (OR=1.41, 95%CI: 1.09-1.83). In men, after adjusting for confounding factors, vitamin D deficiency was positively associated with the risk for low grip strength (OR=1.67, 95%CI: 1.12-2.50), but there was no significant association between vitamin D level and grip strength in women (OR=1.30, 95%CI: 0.97-1.74). In age group 60-69 years and ≥80 years, there was significant association between vitamin D deficiency and low grip strength after adjusting for confounding factors (OR=1.57, 95%CI: 1.05-2.35; OR=2.40, 95%CI: 1.08-5.31). In people who had daily intake of dairy product <250 ml, there was positive association between vitamin D deficiency and low grip strength, but there was no significant association in people who had daily dairy product ≥250 ml after adjusting for confounding factors. The restrictive cubic spline demonstrated that risk of low grip strength might decreased with the increase of vitamin D levels, however, the difference was not significant (P>0.05). Conclusions: This study demonstrated that there is association between vitamin D level and grip strength. People with vitamin D deficiency have higher risk for low grip strength.

[Association between dietary pattern and frailty among people aged 50 years and over in Shanghai]

Objective: To investigate dietary patterns of individuals aged ≥50 in Shanghai and analyze their association with frailty. Methods: Using data from the third wave of the Study on Global Ageing and Adult Health in Shanghai conducted between 2018 and 2019. We collected the frequency and average intake of food by the food frequency questionnaire. Factor analysis was used to extract dietary patterns, and a frailty index was constructed using the ratio of the cumulative total score of health deficits to 35 health-related variables considered. We used an ordinal multinomial logistic regression model to analyze the association between dietary patterns and frailty. Results: A total of 3 274 participants aged (67.9±9.2) years were included in the study, including 1 971 (60.2%) men and 1 303 (39.8%) women. We extracted four dietary patterns: high-protein-nuts pattern, potato-bean-vegetable-fruit pattern, poultry-meat pattern, and high-oil-salt pattern. After adjusting for confounding factors, the logistic regression analysis showed that compared with the high-oil-salt pattern, the high-protein-nuts pattern was negatively associated with the risk of higher frailty (OR=0.743, 95%CI: 0.580-0.951). We did not find an association between dietary patterns and frailty between the different gender groups. In the age group 50-64, the high-protein-nuts and potato-bean-vegetable-fruit patterns were negatively correlated with a higher degree of frailty than the high-oil-salt pattern. In the low-level physical activity group, the high-protein-nuts pattern was negatively correlated with a higher degree of frailty than the high-oil-salt pattern (OR=0.509, 95%CI: 0.361-0.720). However, we found no significant effect of the high-protein nuts pattern, potato-bean-vegetable-fruit pattern, and poultry-meat pattern on the risk of higher frailty compared to the high-oil-salt pattern in the moderate to high level of physical activity group. Conclusions: Compared to the high-oil-salt pattern, dietary patterns with a higher intake of high-protein nuts, potatoes, legumes, and fruits and vegetables might be associated with a lower risk of higher frailty in residents aged 50-64 years of age than with a high oil and salt pattern. At the same time, it may have a more significant protective effect in people with lower physical activity levels. It is suggested that a diet rich in high-protein foods, nuts, potatoes, beans, vegetables, and fruits may help reduce and delay the risk of frailty.

Active learning prediction and experimental confirmation of atomic structure and thermophysical properties for liquid Hf_{76}W_{24} refractory alloy

The determination of liquid atomic structure and thermophysical properties is essential for investigating the physical characteristics and phase transitions of refractory alloys. However, due to the stringent experimental requirements and underdeveloped interatomic potentials, acquiring such information through experimentation or simulation remains challenging. Here, an active learning method incorporating a deep neural network was established to generate the interatomic potential of the Hf_{76}W_{24} refractory alloy. Then the achieved potential was applied to investigate the liquid atomic structure and thermophysical properties of this alloy over a wide temperature range. The simulation results revealed the distinctive bonding preferences among atoms, that is, Hf atoms exhibited a strong tendency for conspecific bonding, while W atoms preferred to form an interspecific bonding. The analysis of short-range order (SRO) in the liquid alloy revealed a significant proportion of icosahedral (ICO) and distorted ICO structures, which even exceeded 30% in the undercooled state. As temperature decreased, SRO structures demonstrated an increase in larger coordination number (CN) clusters and a decrease in smaller CNs. The alterations of the atomic structure indicated that the liquid alloy becomes more ordered, densely packed, and energetically favorable with decreasing temperature, consistent with the obtained fact: Both density and surface tension increase linearly. The simulated thermophysical properties were close to experimental values with minor deviations of 2.8% for density and 3.4% for surface tension. The consistency of the thermophysical properties further attested to the accuracy and reliability of active learning simulation.

[Comparison of efficacy and safety of transurethral thulium laser vapoenucleation of prostate and transurethral thulium laser enucleation of prostate in the treatment of benign prostatic hyperplasia]

Objective: To compare early outcomes between transurethral thulium laser vapoenucleation of prostate and transurethral thulium laser enucleation of prostate for the treatment of benign prostatic hyperplasia (BPH). Methods: Retrospective analysis was conducted on the clinical data of 1 638 BPH patients admitted to the Department of Urology of Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine from January 2018 to December 2021. There were 916 patients underwent transurethral thulium laser vapoenucleation of prostate (ThuVEP group) and 722 patients underwent transurethral thulium laser enucleation of prostate (ThuLEP group). The operation time, eliminated tissue weight, surgical complications, duration of post-operative catheter implantation were compared between the two groups. The improvement of International Prostate Symptom Score (IPSS), Quality of Life Index (QoL), maximum uroflow rate (Qmax) and post-void residual urine volume (PVR) at 1 month after operation was compared between the two groups. Results: There were no significant differences in age, preoperative and 1-month postoperative prostate volume, IPSS score, QoL score, Qmax, and PVR between the ThuVEP and ThuLEP group (all P>0.05). There were no significant differences in perioperative indicators such as operation time, cutting or enucleation time, tissue crushing time, tissue weight, hemoglobin change, catheter indwelling time, and postoperative hospital stay between ThuVEP group and ThuLEP group (all P>0.05). The incidence of minor gross hematuria after extubation in the ThuVEP group was 7.8% (56/916), which was lower than 9.4% (65/722) in the ThuLEP group (P=0.026); the incidence of temporary incontinence at 1 month after surgery was 5.2% (38/916) in ThuVEP group, lower than 11.9% (86/722) in ThuLEP group (P<0.001). A total of 3 patients (0.4%) in ThuLEP group required operative intervention for severe post-operation bleeding, but none of ThuVEP group suffered from this kind of surgical complications. Conclusions: ThuVEP has similar efficacy with ThuLEP for the treatment of BPH. ThuVEP can significantly reduce the incidence of post-operation temporary urine incontinence, and has much superiority in stanching bleeding.

Transporter proteins knowledge graph construction and its application in drug development

Transporters are the main determinant for pharmacokinetics characteristics of drugs, such as absorption, distribution, and excretion of drugs in humans. However, it is difficult to perform drug transporter validation and structure analysis of membrane transporter proteins by experimental methods. Many studies have demonstrated that knowledge graphs (KG) could effectively excavate potential association information between different entities. To improve the effectiveness of drug discovery, a transporter-related KG was constructed in this study. Meanwhile, a predictive frame (AutoInt_KG) and a generative frame (MolGPT_KG) were established based on the heterogeneity information obtained from the transporter-related KG by the RESCAL model. Natural product Luteolin with known transporters was selected to verify the reliability of the AutoInt_KG frame, its ROC-AUC (1:1), ROC-AUC (1:10), PR-AUC (1:1), PR-AUC (1:10) are 0.91, 0.94, 0.91 and 0.78, respectively. Subsequently, the MolGPT_KG frame was constructed to implement efficient drug design based on transporter structure. The evaluation results showed that the MolGPT_KG could generate novel and valid molecules and that these molecules were further confirmed by molecular docking analysis. The docking results showed that they could bind to important amino acids at the active site of the target transporter. Our findings will provide rich information resources and guidance for the further development of the transporter-related drugs.

The Holothuria leucospilota genome elucidates sacrificial organ expulsion and bioadhesive trap enriched with amyloid-patterned proteins

Some tropical sea cucumbers of the family Holothuriidae can efficiently repel or even fatally ensnare predators by sacrificially ejecting a bioadhesive matrix termed the Cuvierian organ (CO), so named by the French zoologist Georges Cuvier who first described it in 1831. Still, the precise mechanisms for how adhesiveness genetically arose in CO and how sea cucumbers perceive and transduce danger signals for CO expulsion during defense have remained unclear. Here, we report the first high-quality, chromosome-level genome assembly of Holothuria leucospilota, an ecologically significant sea cucumber with prototypical CO. The H. leucospilota genome reveals characteristic long-repeat signatures in CO-specific outer-layer proteins, analogous to fibrous proteins of disparate species origins, including spider spidroin and silkworm fibroin. Intriguingly, several CO-specific proteins occur with amyloid-like patterns featuring extensive intramolecular cross-β structures readily stainable by amyloid indicator dyes. Distinct proteins within the CO connective tissue and outer surface cooperate to give the expelled matrix its apparent tenacity and adhesiveness, respectively. Genomic evidence offers further hints that H. leucospilota directly transduces predator-induced mechanical pressure onto the CO surface through mediation by transient receptor potential channels, which culminates in acetylcholine-triggered CO expulsion in part or in entirety. Evolutionarily, innovative events in two distinct regions of the H. leucospilota genome have apparently spurred CO's differentiation from the respiratory tree to a lethal defensive organ against predators.

A110 INCIDENCE AND PREDICTORS OF ASYMPTOMATIC ABNORMALITIES IN BIOCHEMICAL AND RADIOLOGIC PANCREATIC MARKERS FOLLOWING UNCOMPLICATED ERCP

Background

Post-endoscopic retrograde cholangiopancreatography (ERCP) pancreatitis (PEP) is common. Its diagnosis relies on characteristic abdominal pain in addition to biochemical and/or radiographic evidence of pancreatic inflammation.

Purpose

Little is known regarding the frequency with which asymptomatic alterations in biochemical and/or imaging parameters occur following uncomplicated ERCP. We sought to assess the incidence and predictors of such alterations following uncomplicated ERCP.

Method

This study was an analysis of a prospectively maintained ERCP registry. All inpatients ³ 18 years old who underwent ERCP between 2018/09/01 and 2022/02/28 were identified. Patients with acute pancreatitis or abdominal pain following ERCP were excluded, as were patients with lipase levels ≥3x the upper limit of normal (ULN) within 7 days preceding ERCP. Primary outcomes were (1) asymptomatic lipase elevation within 48 hours of uncomplicated ERCP or (2) asymptomatic cross-sectional imaging findings of pancreatic inflammation within 14 days of ERCP.Descriptive statistics were presented as means with accompanying standard deviations (SD) and percentages by lipase categories and PEP, or by imaging categories. Multiple logistic regression was used to examine the associations of exposure variables with PEP or imaging findings.

Result(s)

A total of 646 patients were analyzed in the biochemical cohort, and 187 patients were analyzed in the radiologic cohort. In the biochemical cohort, 478 patients (74.0%) had no elevations in pancreatic enzymes, while 81 (12.5%) had elevations up to 2x ULN, 26 (4.0%) had elevations between 2-3x ULN, and 61 (9.4%) had elevations >3x ULN. In the radiologic cohort, 148 (79.1%) had no abnormalities on cross-sectional imaging within 14 days of ERCP, while 39 (20.9%) had one or more imaging finding typically associated with acute pancreatitis. Among these, 22 (11.8%) had peri-pancreatic fluid collections and 2.1-9.6% of patients had pancreatic findings that included edema, enlargement, inflammation, or fat-stranding. On multivariable analysis, predictors of lipasemia >3x ULN included balloon sphincteroplasty (odds ratio, OR, 2.29, 95% confidence intervals, CI, 1.08 to 4.85) and the placement of a common bile duct stent (OR 4.19, 95% CI 1.37 to 12.77), whereas cannulation of the pancreatic duct or performance of a pancreatogram were not significantly associated (OR 0.75, 95% CI 0.24 to 2.35 and OR 1.07, 95% CI 0.18 to 6.26, respectively).

Conclusion(s)

Over 25% of patients will have asymptomatic elevations in pancreatic enzymes following ERCP, while over 20% will have asymptomatic cross-sectional imaging findings suggestive of pancreatic inflammation. Clinical symptoms should guide post-ERCP care rather than biochemical or imaging parameters.

Please acknowledge all funding agencies by checking the applicable boxes below

None

Disclosure of Interest

None Declared

[Bushen Huoxue Fang improves recurrent miscarriage in mice by down-regulating the JAK2/STAT3 pathway]

OBJECTIVE

To investigate the efficacy of Bushen Huoxue Fang (BSHXF, a traditional Chinese medicine formula) for improving recurrent spontaneous abortion (RSA) in mice and the role of tyrosine kinase (JAK2) and transcriptional activator (STAT3) signaling pathway in its therapeutic mechanism.

METHODS

Female CBA/J mice were caged with male DBA/2 mice to establish RSA mouse models, which were randomly divided into model group, dydrogesterone group and BSHXF group, with the female mice caged with male BALB/c mice as the control group (n=6). From the first day of pregnancy, the mice were subjected to daily intragastric administration of BSHXF, dydrogesterone, or distilled water (in control and model groups) for 12 days. After the treatments, serum levels of antithrombin III (AT-III), activated protein C (APC), tissue plasminogen activator (t-PA), progesterone, human chorionic gonadotropin (HCG), and estradiol (E2) were detected in each group using ELISA. HE staining was used to observe the morphological changes of the endometrium of the mice. Western blotting was performed to determine the expressions of p-JAK2, p-Stat3 and Bcl-2 in the placenta of the mice.

RESULTS

Compared with the control mice, the mouse models of RSA showed a significantly increased embryo loss rate with decreased serum levels of AT-III, T-PA, progesterone, APC and HCG, increased placental expressions of p-JAK2, p-STAT3 and Bax, and decreased expression of Bcl-2 (P < 0.05). Treatments with BSHXF and dydrogesterone both increased serum levels of AT-III, t-PA and HCG in the mouse models; Serum APC level was significantly reduced in BSHXF group and serum progesterone level was significantly increased in dydrogesterone group (P < 0.05).

CONCLUSION

BSHXF can improve the prethrombotic state and inhibit cell apoptosis by downregulating the JAK2/STAT3 pathway to increase the pregnancy rate in mouse models of RSA.

[Analysis of genotypes on 850 newborns with SLC26A4 single-allele mutation and the phenotypes of those with second variant]

Objective: To clarify the phenotypes of the newborns with SLC26A4 single-allele mutation in deafness genetic screening and second variant; to analyze the SLC26A4 genotype and hearing phenotype. Methods: 850 newborns born in Beijing from April 2015 to December 2019 were included and there were 468 males and 382 females. They received genetic deafness screening for 9 or 15 variants, with the result of SLC26A4 single-allele mutation. Firstly, three step deafness gene sequencing was adopted in this work, i.e., the first step was "SLC26A4 gene whole exons and splice sites" sequencing; the second step was "SLC26A4 gene promoter, FOXI1 gene and KCNJ10 gene whole exons" sequencing; and the third step was detection for "SLC26A4 gene copy number variation". Secondly, we collected the results of newborn hearing screening for all patients with the second mutation found in the three step test, and conducted audiological examinations, such as acoustic immittance, auditory brainstem response and auditory steady state response. Thirdly, for novel/VUS mutations, we searched the international deafness gene database or software, such as DVD, ClinVar and Mutation Taster, to predict the pathogenicity of mutations according to the ACMG guideline. Lastly, we analyzed the relationship between genotype and phenotype of newborns with SLC26A4 single allele mutation. Results: Among 850 cases, the median age of diagnosis was 4 months. In the first step, 850 cases were sequenced. A total of 32 cases (3.76%, 32/850) of a second variants were detected, including 18 cases (2.12%, 18/850) with identified pathogenic variants; 832 cases were sequenced and 8 cases of KCNJ10 gene missense variants were detected among the second step. No missense mutations in the FOXI1 gene and abnormal SLC26A4 gene promoter were detected; the third step sequencing results were all negative. Genotypes and hearing phenotypes included 18 cases combined with the second clear pathogenic variant, 16 cases (16/18) referred newborn hearing screening and 2 cases (2/18) passed in both ears; degree of hearing loss consisted of 18 profound ears (18/36), 13 severe ears (13/36) and 5 moderate ears (5/36); audiogram patterns comprised 17 high frequency drop ears (17/36), 14 flat ears (14/36), 3 undistinguished ears (3/36), and 2 U shaped ears (2/36); 11 cases underwent imaging examination, all of which were bilateral enlarged vestibular aqueduct. As for 22 cases of other genotypes, all passed neonatal hearing screening and the hearing diagnosis was normal, including 9 cases with VUS or possibly novel benign variants, 8 cases with KCNJ10 double gene heterozygous variants, and 5 cases with double heterozygous variants. Conclusions: The probability of individuals with SLC26A4 single-allele variant who merge with a second pathogenic variant is 2.12%, all of which are SNV, which can provide scientific basis for the genetic diagnosis and genetic counseling of SLC26A4 variants. Those who have merged with second pathogenic variant are all diagnosed with sensorineural hearing loss. Patients with KCNJ10 gene mutations do not manifest hearing loss during the infancy, suggesting the need for further follow-up.

Detecting plasma hsa_circ_0061276 in patients with gastric cancer by reverse transcription-digital polymerase chain reaction

Background

The role of circular RNAs (circRNAs) in the occurrence of gastric cancer is still unclear. Therefore, the diagnostic value and mechanisms underlying hsa_circ_0061276 in the occurrence of gastric cancer were explored.

Methods

Reverse transcription-droplet digital polymerase chain reaction was used to detect the copy number of hsa_circ_0061276 in plasma from healthy individuals, as well as from patients with gastric precancerous lesions or early-stage or advanced gastric cancer. Plasmids overexpressing or knocking down hsa_circ_0061276 expression were transfected into gastric cancer cells. The effects on the growth, migration, and cell cycle distribution of gastric cancer cells were then analyzed. Finally, miRanda and RNAhybrid were used to explore the binding sites between hsa_circ_0061276 and microRNAs (miRNAs). A double luciferase reporter gene assay was used to confirm the miRNA sponge effect.

Results

The results show that plasma hsa_circ_0061276 copy number showed a trend of a gradual decrease when comparing healthy controls to the early cancer group and advanced gastric cancer group. Overexpression of hsa_circ_0061276 inhibited the growth and migration of gastric cancer cells. Through bioinformatic analyses combined with cellular experiments, it was found that hsa_circ_0061276 inhibited the growth of gastric cancer by binding to hsa-miR-7705.

Conclusion

Hsa_circ_0061276 may be a new biomarker for gastric cancer. The tumor suppressor role of hsa_circ_0061276 on gastric cancer likely occurs through a sponge effect on miRNAs such as hsa-miR-7705.

[Frailty trajectories in people aged 50 years and above in China]

Objective: To identify distinct frailty trajectories in a cohort of nationwide community adults aged 50 years and above, and explore the relationship between frailty trajectories and their socioeconomic characteristics and behavioral factors at baseline survey. Methods: Data were from the three waves of "Global Ageing and Adult Health Research" (SAGE) by World Health Organization in China. The frailty index is generated from 32 items. Group-based trajectory modeling using a censored normal model was conducted to identify the patterns in frailty progression over time. Multinomial logistic regression model was used to examine the effect of socioeconomic status and behavioral factors on the frailty trajectories. Results: A total of 4 303 adults aged 50 years and above with complete data from all three rounds of project were included in the final analysis. Three frailty trajectories were identified: low and stable trajectory (LT) (56.8%), moderately increased trajectory (MT) (34.4%) and highly increased trajectory (HT) (8.8%). The results of the multinomial logistic regression analysis showed that the HT group was more likely to be women (OR=1.88, 95%CI:1.22-2.92) and rural residents (OR=1.87, 95%CI:1.29-2.70) compared with the LT group. In terms of household wealth per capita, there was a clear gradient in ORs, the people with lower household wealth were more likely to be classified in the HT group. Conclusion: This study identified three patterns of progression of frailty trajectories in population aged 50 years and above in China and highlighted that interventions should target those vulnerable populations with rapid progression of frailty.

Reconstructed Genome-Scale Metabolic Model Characterizes Adaptive Metabolic Flux Changes in Peripheral Blood Mononuclear Cells in Severe COVID-19 Patients

Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) poses a mortal threat to human health. The elucidation of the relationship between peripheral immune cells and the development of inflammation is essential for revealing the pathogenic mechanism of COVID-19 and developing related antiviral drugs. The immune cell metabolism-targeting therapies exhibit a desirable anti-inflammatory effect in some treatment cases. In this study, based on differentially expressed gene (DEG) analysis, a genome-scale metabolic model (GSMM) was reconstructed by integrating transcriptome data to characterize the adaptive metabolic changes in peripheral blood mononuclear cells (PBMCs) in severe COVID-19 patients. Differential flux analysis revealed that metabolic changes such as enhanced aerobic glycolysis, impaired oxidative phosphorylation, fluctuating biogenesis of lipids, vitamins (folate and retinol), and nucleotides played important roles in the inflammation adaptation of PBMCs. Moreover, the main metabolic enzymes such as the solute carrier (SLC) family 2 member 3 (SLC2A3) and fatty acid synthase (FASN), responsible for the reactions with large differential fluxes, were identified as potential therapeutic targets. Our results revealed the inflammation regulation potentials of partial metabolic reactions with differential fluxes and their metabolites. This study provides a reference for developing potential PBMC metabolism-targeting therapy strategies against COVID-19.

[A prospective cohort study on the association between grip strength and cognitive function in adults aged 50 years and above]

Objective: To evaluate the association between grip strength (GS) and cognitive function in a population-based longitudinal cohort of Chinese adults aged ≥50 years. Methods: The study population of 3 600 adults was from the baseline survey and two rounds of follow up of World Health Organization (WHO) study of global ageing and adult health (SAGE) in five districts of Shanghai (Hongkou, Huangpu, Minhang, Qingpu and Pudong) after excluding individuals with self-report stroke and depression. The effects of baseline GS on cognitive function and its changes were evaluated. Factor analysis was applied to generate an overall cognition score based on verbal recall trials, verbal fluency test, forward digit span test and backward digit span test. Linear mixed effects model was used to examine the predictive capability of baseline GS for changes in cognitive function. Results: A total of 3 600 participants aged (61.2±8.1) years at baseline survey were included in this study, including 1 668 (46.3%) men and 1 932 (53.7%) women. The average of baseline GS and total cognitive function score were (28.19±12.18) kg and (58.93±14.56) respectively. Cognitive function score declined significantly during the follow-up, however, the changes were different among different age groups, education level groups and household income groups. After adjusted for age, education level, marital status, household income, co-morbidity of chronic conditions, drinking status, smoking status, physical activity level, vegetable/fruit intakes and BMI, no relationships between the baseline GS and cognitive score at baseline survey and at 1^st follow-up were observed, however, compared with lower GS quartile group, there was a significant relationship between higher baseline GS level and better cognitive function at 2^nd follow-up. The participants with highest GS quartile had better cognitive performance over time (male: β=1.938,95%CI:0.644-3.231,P=0.003, female: β=2.192,95%CI:0.975-3.409,P<0.001 and those aged 50-64 years: β=1.652,95%CI:0.646-2.659,P=0.001) than those with the lowest quartile. Conclusions: Higher baseline GS was significantly related to better cognitive function with slow decline. Thus, it is an indicator of cognitive function in middle-aged and elderly Chinese.

LncRNA ABHD11-AS1 promotes tumor progression in papillary thyroid carcinoma by regulating EPS15L1/EGFR signaling pathway

OBJECTIVES

lncRNA ABHD11 antisense RNA 1 (ABHD11-AS1) acts as an oncogene involved in papillary thyroid carcinoma (PTC) occurrence and progression. ABHD11-AS1 exerts biologic functions by some miRNAs and proteins to regulate multiple targets. Identification of novel mechanism of ABHD11-AS1 could be helpful in therapeutic targeting for PTC treatment.

METHODS

Differentially expressed lncRNAs were selected from TCGA database. qRT-PCR analysis was applied to examine the expression of ABHD11-AS1 in PTC cell lines and tissues. The relationship of ABHD11-AS1 expression and clinicopathological features was analyzed by Kaplan-Meier analysis. Two PTC cell lines (TPC-1 and KTC-1) were transfected with pcDNA 3.1, pcDNA3.1-ABHD11-AS1, si-NC and si-ABHD11-AS1, respectively, to verify the ABHD11-AS1 oncogene-regulating capacity to promote tumor progression. The cell metastasis and proliferation had been evaluated both in vitro and in vivo.

RESULTS

High expression of ABHD11-AS1 was found in PTC tissues (P < 0.01), which was significantly correlated with lymph node metastasis (P < 0.05). ABHD11-AS1 overexpression noticeably promoted cell proliferation, migration, and invasion capabilities, which were obviously decreased upon ABHD11-AS1 knockdown. ABHD11-AS1 positively regulated EGFR/EPS15L1 pathway, as EGFR, EPS15L1, STAT3, and p-STAT3 were activated.

CONCLUSION

ABHD11-AS1 promotes tumor progression in PTC by regulating EPS15L1/EGFR pathway.

[Cross-sectional study of association between dietary pattern and cognitive performance in people aged 50 and above years in Shanghai]

Objective: To investigate the association between dietary pattern and cognitive performance in local residents aged ≥50 years in Shanghai. Methods: Data were obtained from the second round of Study of Global Ageing and Adult Health (SAGE) survey in Shanghai. Dietary patterns were surveyed by factor analysis. Cognitive tests were conducted to assess subjects' cognitive performance, including verbal recall, verbal fluency and digit test. Multiple linear regression analysis was used to evaluate the relationship between dietary patterns and cognition performance. Results: A total of 4 132 subjects with complete dietary and cognitive performance test data were included. Factor analysis was used to obtain three dietary patterns: including plant-based pattern, high animal-food pattern, high salt-oil pattern. After controlling for gender, age, education level and other factors, it was found that plant-based pattern (β=0.26,95%CI: 0.17-0.36) and high animal-food pattern (β=0.18, 95%CI:0.06-0.29) were positively associated with total cognitive test score while high salt-oil pattern (β=-0.28, 95%CI:-0.85--0.07) was negatively associated with verbal fluency test score. Conclusion: A dietary pattern with high intake of plant food and appropriate intake of animal food might be associated with better cognitive function of residents aged ≥50 years.

Cambridge hybrid closed-loop algorithm in children and adolescents with type 1 diabetes: a multicentre 6-month randomised controlled trial

BACKGROUND

Closed-loop insulin delivery systems have the potential to address suboptimal glucose control in children and adolescents with type 1 diabetes. We compared safety and efficacy of the Cambridge hybrid closed-loop algorithm with usual care over 6 months in this population.

METHODS

In a multicentre, multinational, parallel randomised controlled trial, participants aged 6-18 years using insulin pump therapy were recruited at seven UK and five US paediatric diabetes centres. Key inclusion criteria were diagnosis of type 1 diabetes for at least 12 months, insulin pump therapy for at least 3 months, and screening HbA1c levels between 53 and 86 mmol/mol (7·0-10·0%). Using block randomisation and central randomisation software, we randomly assigned participants to either closed-loop insulin delivery (closed-loop group) or to usual care with insulin pump therapy (control group) for 6 months. Randomisation was stratified at each centre by local baseline HbA1c. The Cambridge closed-loop algorithm running on a smartphone was used with either (1) a modified Medtronic 640G pump, Medtronic Guardian 3 sensor, and Medtronic prototype phone enclosure (FlorenceM configuration), or (2) a Sooil Dana RS pump and Dexcom G6 sensor (CamAPS FX configuration). The primary endpoint was change in HbA1c at 6 months combining data from both configurations. The primary analysis was done in all randomised patients (intention to treat). Trial registration ClinicalTrials.gov, NCT02925299.

FINDINGS

Of 147 people initially screened, 133 participants (mean age 13·0 years [SD 2·8]; 57% female, 43% male) were randomly assigned to either the closed-loop group (n=65) or the control group (n=68). Mean baseline HbA1c was 8·2% (SD 0·7) in the closed-loop group and 8·3% (0·7) in the control group. At 6 months, HbA1c was lower in the closed-loop group than in the control group (between-group difference -3·5 mmol/mol (95% CI -6·5 to -0·5 [-0·32 percentage points, -0·59 to -0·04]; p=0·023). Closed-loop usage was low with FlorenceM due to failing phone enclosures (median 40% [IQR 26-53]), but consistently high with CamAPS FX (93% [88-96]), impacting efficacy. A total of 155 adverse events occurred after randomisation (67 in the closed-loop group, 88 in the control group), including seven severe hypoglycaemia events (four in the closed-loop group, three in the control group), two diabetic ketoacidosis events (both in the closed-loop group), and two non-treatment-related serious adverse events. There were 23 reportable hyperglycaemia events (11 in the closed-loop group, 12 in the control group), which did not meet criteria for diabetic ketoacidosis.

INTERPRETATION

The Cambridge hybrid closed-loop algorithm had an acceptable safety profile, and improved glycaemic control in children and adolescents with type 1 diabetes. To ensure optimal efficacy of the closed-loop system, usage needs to be consistently high, as demonstrated with CamAPS FX.

FUNDING

National Institute of Diabetes and Digestive and Kidney Diseases.

Development of specific and selective bactericide by introducing exogenous metabolite of pathogenic bacteria

The widespread and repeated use of broad-spectrum bactericides has led to an increase in resistance. Developing novel broad-spectrum bactericides cannot solve the resistance problem, and may even aggravate it. The design of specific and selective bactericides has become urgent. A specific bactericidal design strategy was proposed by introducing exogenous metabolites in this study. This strategy was used to optimize two known antibacterial agents, luteolin (M) and Isoprothiolane (D), against Xoo. Based on the prodrug principles, target compound MB and DB were synthesized by combing M or D with exogenous metabolites, respectively. Bactericidal activity test results demonstrated that while the antibacterial ability of target compounds was significantly improved, their selectivity was also well enhanced by the introducing of exogenous metabolites. Comparing with the original compound, the antibacterial activity of target compound was significantly increased 92.0% and 74.5%, respectively. The optimized target compounds were more easily absorbed, and the drug application concentrations were much lower than those of the original agents, which would greatly reduce environmental pollution and relieve resistance risk. Our proposed strategy is of great significance for exploring the specific and selective bactericides against other pathogens.

Formation of Multispecies Biofilms and Their Resistance to Disinfectants in Food Processing Environments: A Review

ABSTRACT

In food processing environments, various microorganisms can adhere and aggregate on the surface of equipment, resulting in the formation of multispecies biofilms. Complex interactions among microorganisms may affect the formation of multispecies biofilms and resistance to disinfectants, which are food safety and quality concerns. This article reviews the various interactions among microorganisms in multispecies biofilms, including competitive, cooperative, and neutral interactions. Then, the preliminary mechanisms underlying the formation of multispecies biofilms are discussed in relation to factors, such as quorum-sensing signal molecules, extracellular polymeric substances, and biofilm-regulated genes. Finally, the resistance mechanisms of common contaminating microorganisms to disinfectants in food processing environments are also summarized. This review is expected to facilitate a better understanding of interspecies interactions and provide some implications for the control of multispecies biofilms in food processing.

HIGHLIGHTS

FN3 Domain Displaying Double Epitopes: A Cost-Effective Strategy for Producing Substitute Antigens

Construction of substitute antigens based on alternative scaffold proteins is a promising strategy in bioassay technology. In this study, we proposed a strategy for constructing substitute antigens derived from 10th human fibronectin type III (FN3) using two peptide epitopes of terminal pro-brain natriuretic peptide (NT-proBNP) as an example. The base sequences encoding the two antigenic epitopes of NT-proBNP were recombined into the FG loop region and the C-terminus of FN3, fused by 4 GS or polyN linker. The fusion proteins (named FN3-epitopes-4GS and FN3-epitopes-polyN, respectively) were expressed and purified cost-effectively using an Escherichia coli expression system. The immunoreactivity of recombinant substitutes was preliminarily confirmed by western blot analysis using epitope-specific antibodies. The sandwich enzyme-linked immunosorbent assay demonstrated that either FN3-epitopes-polyN or FN3-epitopes-4GS was highly sensitive, and FN3-epitopes-polyN exhibited better kinetics to specific antibodies than FN3-epitopes-4GS, showing a linear dose-response relationship in the concentration range of 0.06–12.85 ng/ml, which suggest that the polyN linker was more suitable for constructing the FN3-based substitute antigens compared to the 4 GS linker. Furthermore, the serum stability test and differential scanning calorimetry analysis showed that the recombinant FN3-epitopes-polyN maintained the original stability of FN3. Therefore, it was confirmed that FN3 could be engineered to construct a stable biomacromolecular substitute for displaying double epitopes of antigen proteins, such as NT-proBNP. In summary, a cost-effective strategy to produce NT-proBNP substitute antigens with good immunoreactivity and physicochemical stability was established in this work, which may provide potential uses for the production of other substitute antigens in the future.

Agent Clustering Strategy Based on Metabolic Flux Distribution and Transcriptome Expression for Novel Drug Development

The network module-based method has been used for drug repositioning. The traditional drug repositioning method only uses the gene characteristics of the drug but ignores the drug-triggered metabolic changes. The metabolic network systematically characterizes the connection between genes, proteins, and metabolic reactions. The differential metabolic flux distribution, as drug metabolism characteristics, was employed to cluster the agents with similar MoAs (mechanism of action). In this study, agents with the same pharmacology were clustered into one group, and a total of 1309 agents from the CMap database were clustered into 98 groups based on differential metabolic flux distribution. Transcription factor (TF) enrichment analysis revealed the agents in the same group (such as group 7 and group 26) were confirmed to have similar MoAs. Through this agent clustering strategy, the candidate drugs which can inhibit (Japanese encephalitis virus) JEV infection were identified. This study provides new insights into drug repositioning and their MoAs.

Molecular Identification of Anion Exchange Protein 3 in Pacific White Shrimp (Litopenaeus vannamei): mRNA Profiles for Tissues, Ontogeny, Molting, and Ovarian Development and Its Potential Role in Stress-Induced Gill Damage

Bicarbonate (HCO3 -) transport mechanisms play an essential role in the acid-base homeostasis of aquatic animals, and anion exchange protein 3 (AE3) is a membrane transport protein that exchanges Cl-/HCO3 - across the cell membrane to regulate the intracellular pH. In this study, the full-length cDNA of AE3 (Lv-AE3) was obtained from the Pacific white shrimp (Litopenaeus vannamei). The Lv-AE3 cDNA is 4,943 bp in length, contains an open reading frame of 2,850 bp, coding for a protein of 949 amino acids with 12 transmembrane domains. Lv-AE3 shows high sequence homology with other AE3 at the protein level. Lv-AE3 mRNA was ubiquitously detected in all tissues selected, with the highest expression level in the gill, followed by the ovary, eyestalk and brain. By in situ hybridization, Lv-AE3-positive cells were shown predominant localization in the secondary gill filaments. The expression levels of Lv-AE3 were further investigated during the essential life processes of shrimp, including ontogeny, molting, and ovarian development. In this case, the spatiotemporal expression profiles of Lv-AE3 in L. vannamei were highly correlated with the activities of water and ion absorption; for example, increased mRNA levels were present after hatching, during embryonic development, after ecdysis during the molt cycle, and in the stage IV ovary during gonadal development. After low/high pH and low/high salinity challenges, the transcript levels of Lv-AE3 were reduced in the gill, while the cell apoptosis rate increased. In addition, knockdown of Lv-AE3 mRNA expression induced cell apoptosis in the gill, indicating a potential link between Lv-AE3 and gill damage. Altogether, this study thoroughly investigated the relationship between the mRNA expression profiles of Lv-AE3 and multiple developmental and physiological processes in L. vannamei, and it may benefit the protection of crustaceans from fluctuated aquatic environments.

The tRNA-derived fragment 5026a inhibits the proliferation of gastric cancer cells by regulating the PTEN/PI3K/AKT signaling pathway

Background

Recently, tRNA-derived fragments (tRFs) have been shown to serve important biological functions. However, the role of tRFs in gastric cancer has not been fully elucidated. This study aimed to identify the tumor suppressor role of tRF-5026a (tRF-18-79MP9P04) in gastric cancer.

Methods

Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) was first used to detect tRF-5026a expression levels in gastric cancer tissues and patient plasma. Next, the relationship between tRF-5026a levels and clinicopathological features in gastric cancer patients was assessed. Cell lines with varying tRF-5026a levels were assessed by measuring tRF-5026a using qRT-PCR. After transfecting cell lines with a tRF-5026a mimic or inhibitor, cell proliferation, colony formation, migration, apoptosis, and cell cycle were evaluated. The expression levels of related proteins in the PTEN/PI3K/AKT pathway were also analyzed by Western blotting. Finally, the effect of tRF-5026a on tumor growth was tested using subcutaneous tumor models in nude mice.

Results

tRF-5026a was downregulated in gastric cancer patient tissues and plasma samples. tRF-5026a levels were closely related to tumor size, had a certain diagnostic value, and could be used to predict overall survival. tRF-5026a was also downregulated in gastric cancer cell lines. tRF-5026a inhibited the proliferation, migration, and cell cycle progression of gastric cancer cells by regulating the PTEN/PI3K/AKT signaling pathway. Animal experiments showed that upregulation of tRF-5026a effectively inhibited tumor growth.

Conclusions

tRF-5026a (tRF-18-79MP9P04) is a promising biomarker for gastric cancer diagnostics and has tumor suppressor effects mediated through the PTEN/PI3K/AKT signaling pathway.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13287-021-02497-1.

Interleukin-2 enhancer binding factor 2 (ILF2) in pacific white shrimp (Litopenaeus vannamei): Alternatively spliced isoforms with different responses in the immune defenses against vibrio infection

Alternative splicing is an essential molecular mechanism that increase the protein diversity of a species to regulate important biological processes. As a transcription factor, Interleukin-2 enhancer binding factor 2 (ILF2) regulates the functions of interleukin-2 (IL-2) at the levels of transcription, splicing and translation, and plays other critical roles in the immune system. ILF2 is well-documented in vertebrates, while little is currently known in crustacean species such as the Pacific white shrimp (Litopenaeus vannamei). In the present study, five cDNA for spliced isoforms of Lv-ILF2 were identified, in which four of them are the full-length long isoforms (Lv-ILF2-L1, Lv-ILF2-L2, Lv-ILF2-L3 and Lv-ILF2-L4) and one of them is a truncated short isoform (Lv-ILF2-S). The whole sequence of ILF2 gene from L. vannamei was obtained, which is 11,680 bp in length with 9 exons separated by 8 introns. All five isoforms contain a domain associated with zinc fingers (DZF). Two alternative splicing types (alternative 5' splice site and alternative 3' splice site) were identified in the five isoforms. The Lv-ILF2 mRNA showed a broad distribution in all detected tissues, and the Lv-ILF2-L transcript levels were higher than those of Lv-ILF2-S in corresponding tissues. The mRNA levels of Lv-ILF2-S in the hepatopancreas, heart, muscle and stomach, but not in the eyestalk, were significantly increased after challenges with Vibrio harveyi or lipopolysaccharide (LPS), while no significant changes were observed for the transcript levels of Lv-ILF2-L in these tissues under the same immune stimulants. On the contrary, the transcript levels of neither Lv-ILF2-S nor Lv-ILF2-L were affected by challenges of polyinosinic: polycytidylic acid [Poly (I:C)]. In addition, after knockdown of the Lv-ILF2 mRNA level by siRNA, the mortality of shrimp and the hepatopancreatic bacterial numbers were significantly increased under V. harveyi challenge, indicating that Lv-ILF2 might participate in the immune defenses against V. harveyi invasion. Collectively, our study here supplied the first evidence for a novel splicing mechanism of ILF2 transcripts, and provided a functional link between the Lv-ILF2 isoforms and the capacity against pathogenic Vibrio in penaeid shrimp.

Global profile of tRNA-derived small RNAs in gastric cancer patient plasma and identification of tRF-33-P4R8YP9LON4VDP as a new tumor suppressor

Transfer RNA (tRNA)-derived small RNAs (tsRNAs) have been found to play important roles in the occurrence and development of cancers. However, the tsRNA profile in gastric cancer is unknown. In this study, we aimed to identify the global tsRNA profile in plasma from gastric cancer patients and elucidate the role of tRF-33-P4R8YP9LON4VDP in gastric cancer. Differentially expressed tsRNAs in the plasma of gastric cancer patients and healthy controls were investigated using RNA sequencing. The expression levels of tRF-33-P4R8YP9LON4VDP in the plasma of gastric cancer patients, healthy controls and gastric cancer cell lines were first detected by quantitative reverse transcription-polymerase chain reaction. The effects of tRF-33-P4R8YP9LON4VDP overexpression or downregulation in gastric cancer cells on proliferation, migration, apoptosis, and cell cycle were analyzed using the Cell Counting Kit-8, scratch assay, Transwell assay, and flow cytometry, respectively. There were 21 upregulated and 46 downregulated tsRNAs found in plasma from gastric cancer patients. The significantly upregulated tsRNAs included tRF-18-S3M83004, tRF-31-PNR8YP9LON4VD, tRF-19-3L7L73JD, tRF-33-P4R8YP9LON4VDP, tRF-31-PER8YP9LON4VD, tRF-18-MBQ4NKDJ, and tRF-31-PIR8YP9LON4VD. The significantly downregulated tsRNAs included tRF-41-YDLBRY73W0K5KKOVD, tRF-18-07QSNHD2, tRF-28-86J8WPMN1E0J, tRF-29-86V8WPMN1EJ3, tRF-31-6978WPRLXN4VE, tRF-30-MIF91SS2P46I, tRF-26-MI7O3B1NR8E, tRF-30-RRJ89O9NF5W8, tRF-26-XIP2801MK8E, and tRF-35-V0J8O9YEKPRS93, In vitro studies showed that tRF-33-P4R8YP9LON4VDP inhibited proliferation of gastric cancer cells. In conclusion, tsRNAs such as tRF-33-P4R8YP9LON4VDP could serve as a novel diagnostic biomarker and target for gastric cancer therapeutics.

A novel approach quantifying the periorbital morphology: A comparison of direct, 2-dimensional, and 3-dimensional technologies

BACKGROUND

The measurement of anatomical structures is critical in plastic and reconstructive surgery. However, few detailed and standardized measurements have been widely used in the periorbital region. This study aimed to evaluate the feasibility of a novel detailed and standardized protocol with 2D and 3D technologies, and explore the relationship between them and direct measurements.

METHODS

Fifty healthy Caucasians (100 eyes) between 20 and 68 years old were recruited and captured for 3D photographs by VECTRA M3 3D Imaging System. Subsequently, 24 landmarks were located on each 3D photographs following a standardized protocol, and then 19 linear and 3 angular periorbital variables were measured. Furthermore, two-dimensional (2D) and direct measurements were conducted on each subject and compared with 3D measurements and one another.

RESULTS

The grand r means across all measurements were 0.77, 0.78, and 0.88 for direct vs. 2D values, direct vs. 3D values, and 3D vs. 2D values, respectively. The mean absolute differences were 1 mm (ranging from 0.2 mm to 3.7 mm) between direct and 3D measurements, 1 mm (ranging from 0.04 mm to 2.4 mm) between direct and 2D measurements, and 1 mm and 6.6° (ranging from 0.04 mm or 0.5° to 3 mm or 12.8°) between 2D and 3D measurements.

CONCLUSIONS

This study verified the feasibility of this detailed and standardized landmark localization protocol for assessing the periorbital morphology with 2D and 3D technologies. This protocol may work as a bridge communicating with all studies involving any of the three technologies in the future.

[Association between grip strength, rapid gait speed and cognition in people aged 50 and above in Shanghai during 2009-2010]

Objective: To investigate the association between grip strength, rapid gait speed and cognition in people aged 50 and above in Shanghai. Methods: Cross-sectional data was collected from the World Health Organization (WHO) study on global ageing and adult health (SAGE) wave 1 (2009-2010). A questionnaire survey was conducted among 8 643 participants aged 50 years old and above selected by using multistage random cluster sampling strategies in Shanghai. Factor analysis was applied to evaluate and generate cognitive function overall score.Association between grip strength, rapid gait speed and cognition was examined by a two-level hierarchical linear model. Results: A total of 8 175 participants were included in this study, who were (62.9±9.7) years old, including 3 782 (46.3%) males. The average grip strength and rapid gait speed of participants were (27.46±12.01) kg and (1.44±0.43) m/s respectively. The average scores of verbal recall (VR), verbal fluency (VF), forward digit span (FDS), backward digit span (BDS) and total cognitive scores were (5.72±0.09), (12.67±0.35), (6.84±0.10), (4.32±0.14) and (60.50±0.95) respectively. Grip strength was positively associated with VR, VF, FDS, BDS and overall cognition (standardized β=0.036, 0.079, 0.042, 0.046 and 0.043 respectively, P<0.05), and rapid gait speed was also positively associated with VR, VF and overall cognition (standardized β=0.040, 0.031, 0.039 respectively, P<0.05) after adjusted for age, sex, residence, education level, marital status, household income, co-morbidity of chronic conditions, BMI, drinking, smoking, fruits, vegetables intake and physical activities. Conclusion: Grip strength and rapid gait speed are both positively associated with cognitive function of people aged 50 and above, which would be indicators to evaluate their cognition.

Low expression of hsa_circ_0001811 in gastric cancer and its role in clinical diagnosis

Background

As far as gastric cancer is concerned, there is a lack of specific early diagnostic biomarkers in clinical diagnosis. Circular RNAs (circRNAs) have been found to be stable in gastric cancer tissues and plasma, so they have the potential to become new type of diagnostic biomarkers for gastric cancer.

Materials and Methods

The hsa_circ_0001811 expressions in gastric cancer tissues and paired non‐cancer tissues, preoperative and postoperative plasma of patients with gastric cancer, and plasma of healthy volunteers were detected using quantitative reverse transcription‐polymerase chain reaction. The receiver operating characteristic (ROC) curves were drawn; and the combined ROC curves were used to analyze their diagnostic values. The correlation between the plasma or tissue hsa_circ_0001811 levels and the clinicopathological factors of gastric cancer was further analyzed.

Results

Hsa_circ_0001811 was found to be lowly expressed in gastric cancer tissues and plasma from patients with gastric cancer. The area under the ROC curve (AUC) in the gastric cancer tissues and the plasma of patients with gastric cancer was 0.658 and 0.747, respectively. The AUC increased to 0.824 after combination of both. The expression level of hsa_circ_0001811 in gastric cancer tissue correlated with carcinoembryonic antigen (CEA) (P = .0347), tissue differentiation (P = .0138), and lymph node metastasis (P = .0234), while plasma hsa_circ_0001811 level was related to carbohydrate antigen (CA19‐9) (P = .0278), lymph node metastasis (P = .0469), distant metastasis (P = .0384), and age (P = .0085).

Conclusions

The above results indicate that hsa_circ_0001811 may become a new biomarker for clinical diagnosis of gastric cancer.

Diastereoselective synthesis and conformational analysis of 4,5-difluoropipecolic acids

Stereoselectively-fluorinated analogs of pipecolic acid have been investigated through a combined theoretical and experimental approach. Three of the four possible diastereoisomers of 4,5-difluoropipecolic acid were successfully synthesized via deoxyfluorination chemistry, navigating a complex reaction network that included neighboring group participation, rearrangement, and elimination pathways. A DFT-based conformational study, supported by NMR J-based analysis, revealed that the different diastereoisomers of 4,5-difluoropipecolic acid preferentially adopt different puckers of the six-membered ring. These findings could have future relevance for the conformational control of biologically active peptides.

Stillbirths in China: a nationwide survey

Objective

To estimate a stillbirth rate at 24 or more gestational weeks in 2015–2016 and to explore potentially preventable causes in China.

Design

A multi‐centre cross‐sectional study.

Setting

Ninety‐six hospitals distributed in 24 (of 34) provinces in China.

Population

A total of 75 132 births at 24 completed weeks of gestation or more.

Methods

COX Proportional Hazard Models were performed to examine risk factors for antepartum and intrapartum stillbirths. Population attributable risk percentage was calculated for major risk factors. Correspondence analysis was used to explore region‐specific risk factors for stillbirths.

Main outcome measures

Stillbirth rate and risk factors for stillbirth.

Results

A total of 75 132 births including 949 stillbirths were used for the final analysis, giving a weighted stillbirth rate of 13.2 per 1000 births (95% CI 7.9–18.5). Small for gestational age (SGA) and pre‐eclampsia/eclampsia increased antepartum stillbirths by 26.2% and 11.7%, respectively. Fetal anomalies increased antepartum and intrapartum stillbirths by 17.9% and 7.4%, respectively. Overall, 31.4% of all stillbirths were potentially preventable. Advanced maternal age, pre‐pregnant obesity, chronic hypertension and diabetes mellitus were important risk factors in East China; low education and SGA were major risk factors in Northwest, Southwest, Northeast and South China; and pre‐eclampsia/eclampsia and intrapartum complications were significant risk factors in Central China.

Conclusions

The prevalence of stillbirth was 13.2 per 1000 births in China in 2015–2016. Nearly one‐third of all stillbirths may be preventable. Strategies based on regional characteristics should be considered to reduce further the burden of stillbirths in China.

Tweetable abstract

The stillbirth rate was 13.2 per 1000 births in China in 2015–2016 and nearly one‐third of all stillbirths may be preventable.

The stillbirth rate was 13.2 per 1000 births in China in 2015–2016 and nearly one‐third of all stillbirths may be preventable.

Action mechanisms and research methods of tRNA-derived small RNAs

tRNA-derived small RNAs (tsRNAs), including tRNA-derived fragments (tRFs) and tRNA halves (tiRNAs), are small regulatory RNAs processed from mature tRNAs or precursor tRNAs. tRFs and tiRNAs play biological roles through a variety of mechanisms by interacting with proteins or mRNA, inhibiting translation, and regulating gene expression, the cell cycle, and chromatin and epigenetic modifications. The establishment and application of research technologies are important in understanding the biological roles of tRFs and tiRNAs. To study the molecular mechanisms of tRFs and tiRNAs, researchers have used a variety of bioinformatics and molecular biology methods, such as microarray analysis, real-time quantitative reverse transcription-polymerase chain reaction (qRT-PCR); Northern blotting; RNA sequencing (RNA-seq); cross-linking, ligation and sequencing of hybrids (CLASH); and photoactivatable-ribonucleoside-enhanced cross-linking and immunoprecipitation (PAR-CLIP). This paper summarizes the classification, action mechanisms, and roles of tRFs and tiRNAs in human diseases and the related signal transduction pathways, targeted therapies, databases, and research methods associated with them.

An analysis of the mechanism underlying photocatalytic disinfection based on integrated metabolic networks and transcriptional data

Photocatalytic disinfection has long been used to combat pathogenic bacteria. However, the specific mechanism underlying photocatalytic disinfection and its corresponding targets remain unclear. In this study, an analysis of the potential mechanism underlying photocatalytic disinfection was performed based on integrated metabolic networks and transcriptional data. Two sets of RNA-seq data (wild type and a photocatalysis-resistant mutant mediated by titanium dioxide (TiO₂)) were processed to constrain the genome scale metabolic models (GSMM) of E. coli. By analyzing the metabolic network, the differential metabolic flux of every reaction was computed in constrained GSMM, and several significantly differential metabolic fluxes in reactions were extracted and analyzed. Most of these reactions were involved in the transmembrane transport of substances and occurred on the inner membrane or were an important component of the cell membrane. These results, which are consistent with the reported information, validated our analysis process. In addition, our work also identified other new and valuable metabolic pathways, such as the reaction ALCD2x, which has a great effect on the energy production process under bacterial anaerobic conditions. The DHAK reaction is also related to the metabolic process of ATP. These reactions with large differential metabolic fluxes merit further research. Additionally, to provide a strategy to address photocatalysis-resistant mutant bacteria, a metabolic compensation analysis was also performed. The metabolic compensation analysis results provided suggestions for a combined method that can effectively combat resistant bacteria. This method could also be used to explore the mechanisms of drug resistance in other microorganisms.

Vitellogenin Receptor (VgR) Mediates Oocyte Maturation and Ovarian Development in the Pacific White Shrimp (Litopenaeus vannamei)

Oocyte maturation and ovarian development are sequentially coordinated events critical to reproduction. In the ovaries of adult oviparous animals such as birds, bony fish, insects, and crustaceans, vitellogenin receptor (VgR) is a plasma membrane receptor that specifically mediates vitellogenin (Vg) transport into oocytes. Accumulation of Vg drives sexual maturation of the female crustaceans by acting as a pivotal regulator of nutritional accumulation within oocytes, a process known as vitellogenesis. However, the mechanisms by which VgR mediates vitellogenesis are still not fully understood. In this study, we first identified a unique VgR (Lv-VgR) and characterized its genomic organization and protein structural domains in Litopenaeus vannamei, a predominant cultured shrimp species worldwide. This newly identified Lv-VgR phylogenetically forms a group with VgRs from other crustacean species within the arthropod cluster. Duplicated LBD/EGFD regions are found exclusively among arthropod VgRs but not in paralogs from vertebrates and nematodes. In terms of expression patterns, Lv-VgR transcripts are specifically expressed in ovaries of female shrimps, which increases progressively during ovarian development, and rapidly declines toward embryonic development. The cellular and subcellular locations were For analyzed by in situ hybridization and immunofluorescence, respectively. The Lv-VgR mRNA was found to be expressed in the oocytes of ovaries, and Lv-VgR protein was found to localize in the cell membrane of maturing oocytes while accumulation of the ligand Vg protein assumed an even cytoplasmic distribution. Silencing of VgR transcript expression by RNAi was effective for stunting ovarian development. This present study has thus provided new insights into the regulatory roles of VgR in crustacean ovarian development.

Transcriptome Analysis of Gene Expression in Dermacoccus abyssi HZAU 226 under Lysozyme Stress

Lysozyme acts as a kind of cationic antimicrobial protein and effectively hydrolyzes bacterial peptidoglycan to have a bactericidal effect, which also plays an important role in protecting eggs from microbial contamination. Dermacoccus abyssi HZAU 226, a Gram-positive bacterium isolated from spoiled eggs, has egg white and lysozyme tolerance, but its survival mechanism is unknown, especially from a transcriptomics point of view. In this study, the high lysozyme tolerance of D. abyssi HZAU 226 was characterized by three independent experiments, and then the Illumina RNA-seq was used to compare the transcriptional profiles of this strain in Luria–Bertani (LB) medium with and without 5 mg/mL lysozyme to identify differentially expressed genes (DEGs); 1024 DEGs were identified by expression analysis, including 544 up-regulated genes and 480 down-regulated genes in response to lysozyme treatment. The functional annotation analysis results of DEGs showed that these genes were mainly involved in glutathione biosynthesis and metabolism, ion transport, energy metabolism pathways, and peptidoglycan biosynthesis. This study is the first report of bacterial-related lysozyme RNA-seq, and our results help in understanding the lysozyme-tolerance mechanism of bacteria from a new perspective and provide transcriptome resources for subsequent research in related fields.

Transcriptomic analysis of sea cucumber (Holothuria leucospilota) coelomocytes revealed the echinoderm cytokine response during immune challenge

Background

The sea cucumber Holothuria leucospilota belongs to echinoderm, which is evolutionally the most primitive group of deuterostomes. Sea cucumber has a cavity between its digestive tract and the body wall that is filled with fluid and suspended coelomic cells similar to blood cells. The humoral immune response of the sea cucumber is based on the secretion of various immune factors from coelomocytes into the coelomic cavity. The aim of this study is to lay out a foundation for the immune mechanisms in echinoderms and their origins in chordates by using RNA-seq.

Results

Sea cucumber primary coelomocytes were isolated from healthy H. leucospilota and incubated with lipopolysaccharide (LPS, 10 μg/ml), polyinosinic-polycytidylic acid [Poly (I:C), 10 μg/ml] and heat-inactived Vibrio harveyi (10⁷ cell/ml) for 24 h, respectively. After high-throughput mRNA sequencing on an Illumina HiSeq2500, a de novo transcriptome was assembled and the Unigenes were annotated. Thirteen differentially expressed genes (DEGs) were selected randomly from our data and subsequently verified by using RT-qPCR. The results of RT-qPCR were consistent with those of the RNA-seq (R² = 0.61). The top 10 significantly enriched signaling pathways and immune-related pathways of the common and unique DEGs were screened from the transcriptome data. Twenty-one cytokine candidate DEGs were identified, which belong to 4 cytokine families, namely, BCL/CLL, EPRF1, IL-17 and TSP/TPO. Gene expression in response to LPS dose-increased treatment (0, 10, 20 and 50 μg/ml) showed that IL-17 family cytokines were significantly upregulated after 10 μg/ml LPS challenge for 24 h.

Conclusion

A de novo transcriptome was sequenced and assembled to generate the gene expression profiling across the sea cucumber coelomocytes treated with LPS, Poly (I:C) and V. harveyi. The cytokine genes identified in DEGs could be classified into 4 cytokine families, in which the expression of IL-17 family cytokines was most significantly induced after 10 μg/ml LPS challenge for 24 h. Our findings have laid the foundation not only for the research of molecular mechanisms related to the immune response in echinoderms but also for their origins in chordates, particularly in higher vertebrates.

An Engineered Pathway for Production of Terminally Sialylated N-glycoproteins in the Periplasm of Escherichia coli

Terminally sialylated N-glycoproteins are of great interest in therapeutic applications. Due to the inability of prokaryotes to carry out this post-translational modification, they are currently predominantly produced in eukaryotic host cells. In this study, we report a synthetic pathway to produce a terminally sialylated N-glycoprotein in the periplasm of Escherichia coli, mimicking the sialylated moiety (Neu5Ac-α-2,6-Gal-β-1,4-GlcNAc-) of human glycans. A sialylated pentasaccharide, Neu5Ac-α-2,6-Gal-β-1,4-GlcNAc-β-1,3-Gal-β-1,3-GlcNAc-, was synthesized through the activity of co-expressed glycosyltransferases LsgCDEF from Haemophilus influenzae, Campylobacter jejuni NeuBCA enzymes, and Photobacterium leiognathi α-2,6-sialyltransferase in an engineered E. coli strain which produces CMP-Neu5Ac. C. jejuni oligosaccharyltransferase PglB was used to transfer the terminally sialylated glycan onto a glyco-recognition sequence in the tenth type III cell adhesion module of human fibronectin. Sialylation of the target protein was confirmed by lectin blotting and mass spectrometry. This proof-of-concept study demonstrates the successful production of terminally sialylated, homogeneous N-glycoproteins with α-2,6-linkages in the periplasm of E. coli and will facilitate the construction of E. coli strains capable of producing terminally sialylated N-glycoproteins in high yield.

A141 ENDOSCOPIST PROCEDURAL VOLUME AND COLONOSCOPY OUTCOMES: A SYSTEMATIC REVIEW AND META-ANALYSIS

Background

In addition to monitoring adverse events (AEs) and post-colonoscopy colorectal cancers (PCCRC), several indicators are used to assess the overall quality of colonoscopy performance, including adenoma detection rate (ADR) and cecal intubation rate (CIR). It is unclear whether there is an association between an endoscopist’s annual colonoscopy volumes and ADR, CIR, AEs or PCCRC.

Aims

We performed a systematic review and meta-analysis to determine whether there is an association between annual colonoscopy volume and colonoscopy quality indicators, or between annual volume and colonoscopy outcomes.

Methods

A comprehensive electronic search was performed through March of 2019 for any studies assessing the potential association between annual colonoscopy volume and outcomes, or quality indicators, including ADR, CIR, AEs or PCCRC. Pooled odds ratios (OR) were calculated using DerSimonian and Laird random effects models. Subgroup and sensitivity analyses were also performed to assess for any potential methodological or clinical factors associated with outcomes. These included dividing procedural volume into total procedures or screening procedures performed.

Results

Out of an initial 9,235 studies, 27 were included in our systematic review, representing 11,276,244 colonoscopies performed by over 530 endoscopists. There was no association between procedural volume and ADR (OR 1.00, 95% confidence intervals, CI, 0.98 to 1.02 per additional 100 annual total colonoscopy procedures performed by an endoscopist). CIR was improved with each additional 100 annual colonoscopy procedures (OR 1.17, 95% CI 1.08 to 1.28). There was a trend toward decreased overall adverse events per additional 100 annual procedures that did not meet significance (OR 0.95, 95% CI 0.90 to 1.00), although there was a decreased incidence of colonic perforations with increasing colonoscopy volume. Figure 1 - Forest plots demonstrating the odds of A) detecting an adenoma, B) intubating the cecum, and C) incurring an overall or specific adverse event, per additional 100 annual procedures, for total and screening procedures.

Conclusions

In this meta-analysis, higher annual colonoscopy volumes correlated with higher CIR, but not with ADR or PCCRC. Trends toward lower AE rates were also demonstrated with higher volumes. All studies included in this review examined endoscopists performing above respective recommended minimum volume thresholds for their health region. Thus, data are lacking on endoscopists performing very low numbers or very high numbers of colonoscopies annually. Future studies should focus on measuring colonoscopy quality metrics and outcomes among these extreme performers to more clearly determine associations between annual volume and colonoscopy outcomes.

Funding Agencies

Alberta Health Services Digestive Health Strategic Care Network

Differential Effects of Growth Medium Salinity on Biofilm Formation of Two Salmonella enterica Strains

ABSTRACT

Salmonella enterica is a prominent foodborne pathogen, including diverse serotypes that are prolific biofilm formers. Its ability to form biofilm can be affected by multiple environmental factors. In this study, the effect of salinity on biofilm formation by S. enterica was evaluated by using two recently isolated strains of Salmonella serotypes Enteritidis and Newport. Although supplementing the growth medium with a low concentration (0.5 to 2%) of sodium chloride (NaCl) slightly enhanced biofilm formation for the strain S. enterica serovar Enteritidis 110, it sharply reduced or abolished biofilm formation by the strain S. enterica serovar Newport 193. This differential effect of salinity on S. enterica strains of different serotypes was poorly correlated with inhibition of planktonic growth but strongly correlated with cell motility. Examining genes known to affect biofilm formation showed that the expression of adrA, csgD, and fliC, which encode proteins required for surface adhesion and cell motility, was significantly downregulated with salinity increase in Salmonella Newport 193 but not in Salmonella Enteritidis 110. Therefore, it is plausible that the differential effect of salinity on biofilm formation by Salmonella Enteritidis 110 and Salmonella Newport 193 resulted from the differential regulation to genes required for cell adherence and motility.

HIGHLIGHTS

Functions of circular RNAs and their potential applications in gastric cancer

Introduction: In recent years, circular RNAs (circRNAs) have emerged in the field of RNA research and their biological functions are now being gradually identified. circRNAs are divided into three categories: exonic circular RNAs (ecircRNAs), exon-intron circular RNAs (EIciRNAs), and intronic circular RNAs (ciRNAs). The circular structure of circRNAs confers unique biological characteristics upon them, such as enhanced stability over linear RNAs.Areas covered: circRNAs function to competitively bind with microRNAs (miRNAs) and proteins, participate in protein coding, regulate transcription, and form pseudogenes after reverse transcription. In gastric cancer, the circRNA-miRNA-mRNA axis is the most studied mechanisms underlying gastric cancer occurrence and development. Some specific and sensitive circRNAs, such as hsa_circ_102958, hsa_circ_0000520, and hsa_circ_0001017 may have potential diagnostic potential in early-stage gastric cancer. Abnormal expression of some circRNAs, including circ-LMTK2, circ-PSMC3, and circ-DLST are associated with the development of gastric cancer. Other circRNAs, such as hsa_circ_0001368, circ-ZFR, and circ-ERBB2, may also play important roles in gastric cancer treatment.Expert opinion: Exploring the roles of circRNAs in gastric cancer occurrence and development will help us to elucidate the functions of circRNAs and develop potential tools for early diagnosis and effective treatment of gastric cancer.

A fluorescence immunoassay based on CdTe : Zn/ZnS quantum dots for the rapid detection of bacteria, taking Delftia tsuruhatensis CM’13 as an example

A fluorescence immunoassay has been widely applied in different fields due to its high sensitivity, simple operations, and high accuracy.

Tumor-suppressive circular RNAs: Mechanisms underlying their suppression of tumor occurrence and use as therapeutic targets

Circular RNAs (circRNAs) have a covalently closed circular conformation and are structurally stable. Those circRNAs with tumor-suppressive properties play an important role in tumorigenesis and metastasis and thus may be used as therapeutic targets of cancers. Herein, we review the current understanding of the classification of circRNAs and summarize the functions and mechanisms of circRNAs that have tumor-suppressive roles in various cancers, including liver cancer (circARSP91, circADAMTS13, circADAMTS14, circMTO1, hsa_circ_0079299, and circC3P1), bladder cancer (circFNDC3B, circITCH, circHIPK3, circRNA-3, cdrlas, and circLPAR1), gastric cancer (circLARP4, circYAP1, hsa_cric_0000096, hsa_circ_0000993, and circPSMC3), breast cancer (circ_000911, hsa_circ_0072309, and circASS1), lung cancer (hsa_circ_0000977, circPTK2, circ_0001649, hsa_circ_100395, and circ_0006916), glioma (circ_0001946, circSHPRH, and circFBXW7), and colorectal cancer (circITGA7 and hsa_circ_0014717). Thanks to their structural stability, these tumor-suppressive circRNAs may be used as potential and potent therapeutic targets. Moreover, we propose a new method for the classification of circRNAs. Based on whether they can be translated, circRNAs can be divided into noncoding circRNAs and coding circRNAs.

[Association between edentulism and cognition among people aged 50 and over]

Objective: To investigate the association between edentulism and cognition in people aged 50 and over in China. Methods: Cross-sectional data was collected from the first wave of World Health Organization Study on global AGEing and adult health in China, among people aged 50 and over in China. A comprehensive cognitive test was used to assess cognitive functions, including verbal recall (VR), verbal fluency (VF), forward digit span (FDS) and backward digit span (BDS) among the subjects. Association between edentulism and cognition was examined by a two-level (individual level and community level) linear model. Results: A total of 12 843 individuals aged 50 years and over were included for analysis, with an average age of (63.0±9.3) years. The overall prevalence of edentulism was 11.0%. The edentulous adults had lower mean scores of VR (4.55), VF (10.88), FDS (6.25), BDS (2.96) and overall cognition (49.15) (P<0.001). Edentulism was negatively associated with VR (β=-0.216, 95%CI: -0.370 - -0.062), FDS (β=-0.186, 95%CI: -0.293 - -0.078) and overall cognition (β=-1.703, 95%CI: -3.025 - -0.381) after adjusted for age, sex, residence, education level, marital status, household income, co-morbidity of chronic conditions, BMI, smoking and drinking alcohol. Conclusion: Edentulism was related with lower cognition level in people aged 50 and over in China.

[Association between daily sedentary time and frailty among people aged 50 years and over]

Objective: To investigate the association between daily sedentary time and frailty among people aged 50 years and over. Methods: Cross-sectional data was collected from the first wave of World Health Organization Study on global AGEing and adult health in China. A two-level (individual level and community level) logistic model was performed to identify the association between daily sedentary time and frailty. The dose-response relationship between them was analyzed by restrictive cubic spline curve. Results: A total of 13 175 individuals aged 50 years and over were included for analysis. A positive association between daily sedentary time and frailty was noticed, both in urban (OR=1.22, 95%CI: 1.17-1.27) or rural areas (OR=1.11, 95%CI: 1.05-1.18) under study. The dose-response curve showed that daily sedentary time and frailty might present an approximate linear relationship. Conclusion: Results from this study showed significant association exsited between daily sedentary time and frailty, approximately with a linear dose-response relationship.

[Association between frailty and sleep duration among people aged 50 years and over]

Objective: To investigate the association between sleep duration and frailty among people aged 50 years and over. Methods: Cross-sectional data was collected from the first wave of World Health Organization Study on global AGEing and adult health in China. Frailty index was constructed on the proportion of deficits, out of the 40 variables. A two-level (individual level and community level) linear model was performed to identify the related factors on frailty. All the models were stratified by age, gender, residence (urban/rural). Restricted cubic spline was performed to graphically evaluate the dose-response association between self-reported sleep duration and frailty. Results: A total of 13 175 individuals aged 50 years and over participated in this study. Without adjusting on any confounding factors, shorter or longer sleep duration significantly increased the risk of weakness compared with normal sleep time (OR=2.05, 95%CI: 1.71-2.44; OR=1.35, 95%CI: 1.12-1.63). After adjusting for confounding factors such as gender, age, residence, education, family assets, vegetable, smoking, drinking and physical activity, a positive association between short sleep duration and frailty was noticed compared with normal sleep time (aOR=1.60, 95%CI: 1.27-2.01). The results of stratified analysis on sex, age and urban and rural areas showed that, after adjusting for gender, age, residence, education level, family assets, intake of vegetables and fruits, smoking, drinking and physical activity, only shorter sleep duration was positively correlated with the risk of weakness. In addition, among people aged 65 years and over, adjusted for confounding factors, the risk of weakness increased by 91%, compared with normal sleep time (aOR=1.91, 95%CI: 1.46-2.49). The dose-response curve also showed that the sleep duration and frailty present an approximate "U" shaped relationship. Conclusion: Short sleep duration might be associated with frailty.