A Chemical Strategy for the Degradation of the Main Protease of SARS-CoV-2 in Cells

SARS-CoV-2 is the virus that causes the global pandemic of COVID-19. The main protease (Mpro) of SARS-CoV-2 is essential for viral infection and is one of the major therapeutic targets for COVID-19. Here, we report the design, synthesis, and biological characterization of a novel heterobifunctional small molecule that could effectively induce the degradation of SARS-CoV-2 Mpro and its drug-resistant mutants in HEK 293T cells, thus demonstrating a new alternative strategy for intervening with proteins important for this novel coronavirus.

ABHD2 deficiency aggravates ovalbumin-induced airway remodeling through the PI3K/Akt pathway in an animal model of chronic asthma

Airway remodeling is a major pathological characteristic of chronic obstructive pulmonary disease (COPD). This study aimed to investigate the effect of Abhd2 deficiency on ovalbumin (OVA)-induced airway remodeling and inflammation in vivo. Abhd2-deficient mice were used to establish an OVA-induced asthma model. Lung tissues were analyzed using hematoxylin and eosin (HE) staining, Masson staining, immunohistochemistry, quantitative reverse transcription- polymerase chain reaction (qRT-PCR), and western blotting were used to determine the role of Abhd2 in the regulation of OVA-induced airway remodeling and inflammation. Our findings revealed that the RNA expression of inflammatory factors, including IL-1β, IL-6, IL-4, and IL-13, was significantly increased in OVA-induced Abhd2 Gt/Gt asthmatic mice. The expression of IFN-γ was decreased significantly in OVA-induced Abhd2 Gt/Gt asthmatic mice. The protein expression of airway remodeling factors, including α-SMA, type I collagen, and Ki67, was also increased in OVA-induced Abhd2 Gt/Gt asthmatic mice compared to that in OVA-induced wild-type (WT) mice. Additionally, Abhd2 deficiency promoted the expression of p-Akt in tissues of the asthma model. These results suggest that Abhd2 deficiency exacerbates airway remodeling and inflammation through the PI3K/Akt pathway in chronic asthma.

Increased Ca2 + transport across the mitochondria-associated membranes by Mfn2 inhibiting endoplasmic reticulum stress in ischemia/reperfusion kidney injury

Renal ischemia/reperfusion (I/R) injury, which leads to acute kidney injury (AKI), is a major cause of morbidity and mortality in a variety of clinical situations. This study aimed to investigate the protective role of Mfn2 during renal I/R injury. Overexpression of Mfn2 in NRK-52E rat renal tubular epithelial cells and rats, then we constructed hypoxia reoxygenation (H/R) cells and I/R rat model. Apoptosis, ROS, ATP, Ca2+ levels in cells and rats, as well as renal tissue and functional injury in rats were detected respectively. Endoplasmic reticulum (ER) stress was further examined in cells and rats. The morphological changes of mitochondria-associated ER membranes (MAMs) were also detected. Mfn2 expression is reduced in H/R-treated NRK-52E cells and renal tissue of I/R rats. At the cellular level, overexpression of Mfn2 promoted cell proliferation, inhibited cell apoptosis, attenuated mitochondrial damage and Ca2+ overload, and ER stress. In addition, Mfn2 also restored the MAMs structure. In vivo experiments found that overexpression of Mfn2 could improve renal function and alleviate tissue injury. Concomitant with elevated Mfn2 expression in the kidney, reduced renal cell apoptosis, restored mitochondrial function, and reduced calcium overload. Finally, ER stress in rat kidney tissue was alleviated after overexpression of Mfn2. These results reveal that Mfn2 contributes to ER stress, mitochondrial function, and cell death in I/R injury, which provides a novel therapeutic target for AKI.

Partial cellular reprogramming stably restores the stemness of senescent epidermal stem cells

OBJECTIVE

Adult stem cell senescence and exhaustion are important drivers of organismal age. Restored stem cell self-renewal has revealed novel therapeutic targets for decreasing the incidence of age-associated diseases (AADs) and prolonging the human health span. Transient ectopic expression of the reprogramming factors Oct3/4, Sox2, Klf4 and c-Myc (collectively known as OSKM) in somatic cells can induce partial cellular reprogramming and effectively ameliorate their age-associated hallmarks. However, how this form of rejuvenation is applied to senescent stem cells remains unknown.

MATERIALS AND METHODS

The Integrin-α6highCD71high epidermal stem cells (ESCs) with low self-renewal ability were sorted by flow cytometry and then treated by the interrupted reprogramming induced by transient expression of OSKM. The ability of secondary clones' generation and self-proliferation in vitro, as well as stem cell marker p63, were detected to determine their self-renewal ability. Besides, gene and protein of epidermal cell markers were detected to determine whether their cell identities were retained. Finally, DNA methylation age (eAge) and DNA dehydroxymethylase/methyltransferase were analyzed to explore the alternation of their global DNA methylation pattern during this rejuvenation.

RESULTS

The partial reprogramming restored the youthful self-renewal and proliferation in senescent ESCs, including larger secondary clone generation, higher expression of stem cell marker p63 and proliferation marker Ki67, and faster proliferation speed, in each case without abolishing epithelial cellular identity. Moreover, the rejuvenation of adult stem cells could be maintained for 2 weeks after reprogramming factor withdrawal, which was more stable than that of differentiated somatic cells. Additionally, we found that partial reprogramming counteracted the acceleration of eAge in senescent epidermal stem cells and DNA methyltransferase 1 (DNMT1) may play a crucial role in this process.

CONCLUSIONS

Partial reprogramming has high therapeutic potential for reversing adult stem cell age, providing an advanced way to treat AADs.

CXCR4 Recognition by L- and D-Peptides Containing the Full-Length V3 Loop of HIV-1 gp120

Human immunodeficiency virus-1 (HIV-1) recognizes one of its principal coreceptors, CXC chemokine receptor 4 (CXCR4), on the host cell via the third variable loop (V3 loop) of HIV-1 envelope glycoprotein gp120 during the viral entry process. Here, the mechanism of the molecular recognition of HIV-1 gp120 V3 loop by coreceptor CXCR4 was probed by synthetic peptides containing the full-length V3 loop. The two ends of the V3 loop were covalently linked by a disulfide bond to form a cyclic peptide with better conformational integrity. In addition, to probe the effect of the changed side-chain conformations of the peptide on CXCR4 recognition, an all-D-amino acid analog of the L-V3 loop peptide was generated. Both of these cyclic L- and D-V3 loop peptides displayed comparable binding recognition to the CXCR4 receptor, but not to another chemokine receptor, CCR5, suggesting their selective interactions with CXCR4. Molecular modeling studies revealed the important roles played by many negative-charged Asp and Glu residues on CXCR4 that probably engaged in favorable electrostatic interactions with the positive-charged Arg residues present in these peptides. These results support the notion that the HIV-1 gp120 V3 loop-CXCR4 interface is flexible for ligands of different chiralities, which might be relevant in terms of the ability of the virus to retain coreceptor recognition despite the mutations at the V3 loop.

Discovery of Potential Inhibitors of SARS-CoV-2 Main Protease by a Transfer Learning Method

The COVID-19 pandemic caused by SARS-CoV-2 remains a global public health threat and has prompted the development of antiviral therapies. Artificial intelligence may be one of the strategies to facilitate drug development for emerging and re-emerging diseases. The main protease (Mpro) of SARS-CoV-2 is an attractive drug target due to its essential role in the virus life cycle and high conservation among SARS-CoVs. In this study, we used a data augmentation method to boost transfer learning model performance in screening for potential inhibitors of SARS-CoV-2 Mpro. This method appeared to outperform graph convolution neural network, random forest and Chemprop on an external test set. The fine-tuned model was used to screen for a natural compound library and a de novo generated compound library. By combination with other in silico analysis methods, a total of 27 compounds were selected for experimental validation of anti-Mpro activities. Among all the selected hits, two compounds (gyssypol acetic acid and hyperoside) displayed inhibitory effects against Mpro with IC50 values of 67.6 μM and 235.8 μM, respectively. The results obtained in this study may suggest an effective strategy of discovering potential therapeutic leads for SARS-CoV-2 and other coronaviruses.

A prognostic nomogram based on log odds of positive lymph nodes to predict the overall survival in biliary neuroendocrine neoplasms (NENs) patients after surgery

BACKGROUND

The prognosis of biliary neuroendocrine neoplasms (NENs) patients is affected by the status of metastatic lymph nodes. The purpose of this study was to explore the prognostic value of the log odds of positive lymph nodes (LODDS) and develop a novel nomogram to predict the overall survival (OS) in biliary NENs patients.

METHODS

A total of 125 patients with histologically confirmed biliary NENs were selected from the Surveillance, Epidemiology and End Results (SEER) database and further divided into training and validation cohorts. The discrimination and calibration of the nomogram were evaluated using the concordance index (C-index), the area under the time-dependent receiver operating characteristic curve (time-dependent AUC), and calibration plots. The net benefits and clinical utility of the nomogram were quantified and compared with those of the SEER staging system using decision curve analysis (DCA), net reclassification index (NRI), and integrated discrimination improvement (IDI). The risk stratifications of the nomogram and the SEER staging system were compared.

RESULTS

LODDS showed the highest accuracy in predicting OS for biliary NENs. The C-index (0.789 for the training cohort and 0.890 for the validation cohort) and the time-dependent AUC (> 0.7) indicated the satisfactory discriminative ability of the nomogram. The calibration plots showed a high degree of consistency. The DCA, NRI, and IDI indicated that the nomogram performed significantly better than the SEER staging system.

CONCLUSION

A novel LODDS-incorporated nomogram was developed and validated to assist clinicians in evaluating the prognosis of biliary NENs patients.

The expression of apoptosis related genes in HK-2 cells overexpressing PPM1K was determined by RNA-seq analysis

Chronic kidney disease (CKD) is a serious disease that endangers human health. It is reported that inhibiting renal cell apoptosis can delay the progress of CKD. Our previous study found that the mice with protein phosphatase Mg2+/Mn2+ dependent 1K (PPM1K) gene deletion had obvious symptoms of glomerular vascular and interstitial vascular dilatation, congestion and hemorrhage, glomerular hemorrhage and necrosis, interstitial fibrous tissue proliferation, decreased urinary creatinine clearance, and increased urinary protein level. In addition, studies have found that PPM1K is essential for cell survival, apoptosis and metabolism. However, no study has confirmed that PPM1K can inhibit renal cell apoptosis. In this study, PPM1K was overexpressed in human kidney-2 cells (HK-2), and the biological process of differentially expressed genes and its effect on apoptosis were comprehensively screened by RNA sequencing (RNA-seq). Through sequencing analysis, we found that there were 796 differentially expressed genes in human renal tubular epithelial cells transfected with PPM1K gene, of which 553 were down-regulated and 243 were up-regulated. Enrichment analysis found that differentially expressed genes may play an important role in amino acid metabolism and biosynthesis. In the GO analysis functional pathway list, we also found that multiple genes can be enriched in apoptosis related pathways, such as G0S2, GADD45A, TRIB3, VEGFA, NUPR1 and other up-regulated genes, and IL-6, MAGED1, CCL2, TP53INP1 and other down-regulated genes. Then we verified these differentially expressed genes by RT-PCR, and found that only the RT-PCR results of G0S2, VEGFA and NUPR1 were consistent with the transcriptome sequencing results. We believe that G0S2, VEGFA, NUPR1 and other genes may participate in the apoptosis process of HK-2 cells induced by PPM1K.In conclusion, these findings provide some data support for the study of HK-2 cell apoptosis mechanism, and also provide a scientific theoretical basis for further study of the effect of PPM1K on kidney disease.

Analysis of the Salivary Microbiome in the Periodontal Disease Patients with Hypertension and Non-hypertension

Background:

An improved comprehension of the oral microbiota function in the pathogenesis of disease will contribute to the diagnosis and treatment of both hypertension and periodontal disease. In our study, a comparison of the salivary microbiome between hypertension and Non-hypertension cohorts was designed to reveal microbial signatures.

Methods:

Patients were divided into four sub-groups: Gingivitis, and Periodontitis (stage 2, 3, and 4). Then, hypertension and non-hypertension cohorts were split into periodontal health and periodontitis subgroups. The salivary samples were processed for DNA extraction (n=246). The V3-V4 hypervariable regions of microbiome 16S rRNA genes were amplified. Finally, sequencing libraries were constructed and subjected to bioinformatics and statistical analyses.

Results:

The oral microbial diversity decreased in both hypertension and periodontal disease groups compared to the healthy ones. At the genus level, the diversity showed 100 different operational taxonomic units (OTUs) for differential abundance testing. The first trend showed OTUs decreased in relative abundance with increasing periodontal disease, as well as hypertension and nonhypertensive groups. For this trend, OTUs comprise of a mix of primarily anaerobic commensals and potential acute diarrhea pathogens. The second trend was that the diversity of genera was decreased in the hypertension group relative to the non-hypertension group, including other anaerobic bacteria related to periodontal disease.

Conclusion:

Microbiota diversity decreased in the hypertension group and different stages of periodontal disease groups. However, Neisseria and Solobacterium genera increased in the coexisting hypertension and periodontal disease group. Certainly, these findings indicate that the abundance of genera continues to change due to additional stresses caused by co-existing conditions.

Development of small molecule inhibitors targeting TGF-β ligand and receptor: Structures, mechanism, preclinical studies and clinical usage

Transforming growth factor-β (TGF-β) is a member of a superfamily of pleiotropic proteins that regulate multiple cellular processes such as growth, development and differentiation. Following binding to type I and II TGF-β serine/threonine kinase receptors, TGF-β activates downstream signaling cascades involving both SMAD-dependent and -independent pathways. Aberrant TGF-β signaling is associated with a variety of diseases, such as fibrosis, cardiovascular disease and cancer. Hence, the TGF-β signaling pathway is recognized as a potential drug target. Various organic molecules have been designed and developed as TGF-β signaling pathway inhibitors and they function by either down-regulating the expression of TGF-β or by inhibiting the kinase activities of the TGF-β receptors. In this review, we discuss the current status of research regarding organic molecules as TGF-β inhibitors, focusing on the biological functions and the binding poses of compounds that are in the market or in the clinical or pre-clinical phases of development.

Semi-dominant mutation in the cysteine-rich receptor-like kinase gene, ALS1, conducts constitutive defence response in rice

Plants have evolved a sophisticated two-branch defence system to prevent the growth and spread of pathogen infection. The novel Cys-rich repeat (CRR) containing receptor-like kinases, known as CRKs, were reported to mediate defence resistance in plants. For rice, there are only two reports of CRKs. A semi-dominant lesion mimic mutant als1 (apoptosis leaf and sheath 1) in rice was identified to demonstrate spontaneous lesions on the leaf blade and sheath. A map-based cloning strategy was used for fine mapping and cloning of ALS1, which was confirmed to be a typical CRK in rice. Functional studies of ALS1 were conducted, including phylogenetic analysis, expression analysis, subcellular location and blast resistance identification. Most pathogenesis-related (PR) genes and other defence-related genes were activated and up-regulated to a high degree. ALS1 was expressed mainly in the leaf blade and sheath, in which further study revealed that ALS1 was present in the vascular bundles. ALS1 was located in the cell membrane of rice protoplasts, and its mutation did not change its subcellular location. Jasmonic acid (JA) and salicylic acid (SA) accumulation were observed in als1, and enhanced blast resistance was also observed. The mutation of ALS1 caused a constitutively activated defence response in als1. The results of our study imply that ALS1 participates in a defence response resembling the common SA-, JA- and NH1-mediated defence responses in rice.

Determining the ion temperature and energy distribution in a lithium-plasma interaction test stand with a retarding field energy analyzer

The ThermoElectric-driven Liquid-metal plasma-facing Structures (TELS) experiment at the University of Illinois is a gas-puff driven, theta-pinch plasma source that is used as a test stand for off-normal plasma events incident on materials in the edge and divertor regions of a tokamak. The ion temperatures and resulting energy distributions are crucial for understanding how well a TELS pulse can simulate an extreme event in a larger, magnetic confinement device. A retarding field energy analyzer (RFEA) has been constructed for use with such a transient plasma due to its inexpensive and robust nature. The innovation surrounding the use of a control analyzer in conjunction with an actively sampling analyzer is presented and the conditions of RFEA operation are discussed, with results presented demonstrating successful performance under extreme conditions. Such extreme conditions are defined by heat fluxes on the order of 0.8 GW m^-2 and on time scales of nearly 200 μs. Measurements from the RFEA indicate two primary features for a typical TELS discharge, following closely with the pre-ionizing coaxial gun discharge characteristics. For the case using the pre-ionization pulse (PiP) and the theta pinch, the measured ion signal showed an ion temperature of 23.3 ± 6.6 eV for the first peak and 17.6 ± 1.9 eV for the second peak. For the case using only the PiP, the measured signal showed an ion temperature of 7.9 ± 1.1 eV for the first peak and 6.6 ± 0.8 eV for the second peak. These differences illustrate the effectiveness of the theta pinch for imparting energy on the ions. This information also highlights the importance of TELS as being one of the few linear pulsed plasma sources whereby moderately energetic ions will strike targets without the need for sample biasing.

Modified Numerical Simulation Model of Blood Flow in Bend

The numerical simulation model of blood flow in bend is studied in this paper. The curvature modification is conducted for the blood flow model in bend to obtain the modified blood flow model in bend. The modified model is verified by U tube. By comparing the simulation results with the experimental results obtained by measuring the flow data in U tube, it was found that the modified blood flow model in bend can effectively improve the prediction accuracy of blood flow data affected by the curvature effect.

[The incidence and risk factors of acute renal injury in patients with multiple soft tissue injuries]

OBJECTIVE

To investigate the incidence and risk factors of acute kidney injury (AKI) in patients with multiple soft tissue contusion.

METHODS

A total of 513 patients diagnosed as multiple soft tissue contusion in the First Affiliated Hospital of Xinjiang Medical University from January 1, 2008 to January 1, 2013 were retrospectively analyzed. Demographics, clinical data and laboratory examinations before and after AKI were collected and analyzed.

RESULTS

The age of all subjects was 31.30(12-78) years old with the male to female ratio of 2.1: 1. AKI occurred in 74 cases with an incidence rate of 14.4%. No AKI was observed in patients with assault injuries, while AKI was found in 27 cases (36.5%) with car accident injuries and 4 cases (5.4%) with other injuries. AKI showed in 1 case(1.4%) with damaged area under 1%, in 4 cases (5.4%) with damaged area ranged from 1% to <3%, 10 cases (13.5%) with damaged area ranged from 3% to 5% and 19 cases (25.7%) with damaged area over 5% with significant difference among the groups (P < 0.01). Incidence rate of AKI was significantly higher in patients with chronic kidney disease (CKD) than those without CKD (54.5% vs 20.3%, P < 0.01). Two of the AKI cases died, with a mortality rate of 2.7%. Multivariate logistic regression analysis showed that the followings were the independent risk factors for the occurrence of AKI in patients with multiple soft tissue injuries: age (OR = 1.996), basic serum creatinine (OR = 0.976), basic evaluated GFR (eGFR) (OR = 0.964), serum potassium (OR = 2.117), myoglobin (OR = 0.950) and damaged area (OR = 1.811).

CONCLUSIONS

Incidence rate of AKI is quite high in multiple soft tissue contusion. Age, basic serum creatinine, basic eGFR, serum potassium, myoglobin and damaged area are the independent risk factors for the occurrence of AKI in patients with multiple soft tissue injury.

[Carrier detection and prenatal diagnosis for hemophilia A]

OBJECTIVE

To establish a simple, rapid carrier detection and prenatal diagnosis system for hemophilia A.

METHODS

Intron 22 inversion in FVIII gene was directly examined by long distance polymerase chain reaction. Polymorphism of factor VIII intragenic RFLP of Bcl I, STR within intron 13 and 22, and extragenic DXS 52 (St 14) VNTR loci by hereditary linkage analysis were assayed.

RESULTS

The diagnostic rates of these loci were 47.6% (intron 22 inversion), 27.8% (Bcl I), 28.6% and 29.4% (STR within intron 13 and 22), and 81.3% (DXS52), respectively. The overall diagnostic rate in 21 families was 94.7%.

CONCLUSIONS

The diagnosis in hemophilia A patients or carriers can be made if intron 22 inversion is present. The intragenic and extragenic loci hereditary linkage analysis could be used to establish the diagnosis in intron 22 inversion negative patients.

[Diagnosis and treatment of gastric carcinoid tumors]

OBJECTIVE

To investigate the method for surgical diagnosis and treatment of gastric carcinoid tumors.

METHODS

Clinicopathologic features of 9 patients with gastric carcinoid tumors were analyzed retrospectively. The patients were confirmed by biopsy at endoscopy or surgery.

RESULTS

Eight of the 9 patients underwent elective operation, 6 showed gastric carcinoid tumors before operation found by biopsy at endoscopy. Five tumors were malignant and 4 benign. Two patients showed malignant carcinoid syndrome, but 5-HT and 5-HIAA were normal.

CONCLUSIONS

Benign or malignant gastric carcinoid tumor depends upon tumor size, local lymph node invasion and distant metastases. The prognostic factor is based on benign or malignant tumors. Operation may be the first choice for such patients.