RT-RPA-Cas12a-based discrimination of SARS-CoV-2 variants of concern

Timely and accurate detection of SARS-CoV-2 variants of concern (VOCs) is urgently needed for pandemic surveillance and control. However, current methods are limited by the low sensitivity, long turn-around time or high cost. Here, we report a nucleic acid testing-based method aiming to detect and discriminate SARS-CoV-2 VOCs by combining RT-RPA and CRISPR-Cas12a detecting assays (RRCd). With a detection limit of 10 copies RNA/reaction, RRCd was validated in 204 clinical samples, showing 99% positive predictive agreement and 100% negative predictive agreement, respectively. Critically, using specific crRNAs, representatives of single nucleotide polymorphisms and small deletions in SARS-CoV-2 VOCs including N501Y, T478K and {Delta}H69-V70 were discriminated by RRCd, demonstrating 100% accuracy in clinical samples with Ct < 33. The method completes within 65 min and could offer visible results without using any electrical devices, which may facilitate point-of-care testing of SARS-CoV-2 and its variants.

Evolutionary insights into a non-coding deletion of SARS-CoV-2 B.1.1.7

Three prevalent SARS-CoV-2 Variants of Concern (VOCs) were emerged and caused epidemic waves. It is essential to uncover the key genetic changes that cause the high transmissibility of VOCs. However, different viral mutations are generally tightly linked so traditional population genetic methods may not reliably detect beneficial mutation. In this study, we proposed a new pandemic-scale phylogenomic approach to detect mutations crucial to transmissibility. We analyzed 3,646,973 high-quality SARS-CoV-2 genomic sequences and the epidemiology metadata. Based on the sequential occurrence order of mutations and the instantaneously accelerated furcation rate, the analysis revealed that two non-coding mutations at the position of 28271 (g.a28271-/t) might be crucial for the high transmissibility of Alpha, Delta and Omicron VOCs. Both two mutations cause an A-to-T change at the core Kozak site of the N gene. The analysis also revealed that the non-coding mutations (g.a28271-/t) alone are unlikely to cause high viral transmissibility, indicating epistasis or multilocus interaction in viral transmissibility. A convergent evolutionary analysis revealed that g.a28271-/t, S:P681H/R and N:R203K/M occur independently in the three-VOC lineages, suggesting a potential interaction among these mutations. Therefore, this study unveils that non-synonymous and non-coding mutations could affect the transmissibility synergistically.

Protective effect of paeoniflorin on H / 中国天然药物

This study was to investigate the protective effect of paeoniflorin (PF) on hydrogen peroxide-induced injury. Firstly, "SMILES" of PF was searched in Pubchem and further was used for reverse molecular docking in Swiss Target Prediction database to obtain potential targets. Injury-related molecules were obtained from GeenCards database, and the predicted targets of PF for injury treatment were selected by Wayne diagram. For mechanism analysis, the protein-protein interactions were constructed by String, and the KEGG analysis was conducted in Webgestalt. Then, cell viability and cytotoxicity assay were established by CCK8 assay. Also, the experimental cells were allocated to control, model (200 μmol·L

Water-related diseases along the eastern route of the South-to-North Water Diversion Project / 中国人兽共患病学报

The aim of this study is to investigate the epidemic condition of water-related diseases in the eastern route of South-to-North Water Diversion Project (SNWDP).All data were extracted from published literatures in Chinese about water-related diseases in the eastern route of SNWDP.Pooled analysis was used to explore geographical distribution and epidemiology of the disease.A total of 325 articles about water-related diseases were retrieved during 1953 to 2013,and 209 articles were included in this study.Pooling analysis showed that Shandong Province had the largest number of cases for water-related diseases,following by Jiangsu,Hebei,Tianjin,and Anhui.The numbers of cases were relative small before 1960s according to epidemic curve,and the curve peaked in the 1970s,and decreased after the 1980s.A total of 1 383 834 cases of bacillary dysentery was reported,accounting for 84％ of all water-related diseases on these regions of SNWDP,and followed by hepatitis A,hepatitis E,Japanese encephalitis,typhoid and paratyphoid fever and hemorrhagic fever with renal syndrome.Other reported diseases displayed scatter condition and a small numbers of cases.The prevalence of water-related diseases is sporadic and a trend of decline along the regions of the eastern route of SNWDP.

Effects of Kaixin Powder on melatonin receptor expression and (125)I-Mel binding affinity in a rat model of depression / 中国结合医学杂志

<p><b>OBJECTIVE</b>To explore the effects of Kaixin Powder (, KXP) on melatonin receptor (MR) expression and (125)I-Mel binding affinity in a depression rat model.</p><p><b>METHODS</b>Seventy-two male Wistar rats were divided into six groups: a blank control group, model group, ramelteon group, KXP high-dosage group (HKXP), medium-dosage group (MKXP) and low-dosage group (LKXP). To establish the depression model, all groups except the blank control group were singly housed and exposed to chronic unpredictable mild stress. Weight gain, sucrose consumption and the open-field test were used to evaluate induction of depression. KXP at 260, 130 and 65 mg/(kg•d) was also respectively administered to the rats in the HKXP, MKXP and LKXP groups for 21 days. Ramelteon [0.83 mg/(kg•d)] was given to the positive drug control group. An equivalent volume of physiological saline was given to the blank and model groups. The liquid chip method was used to measure the concentration of plasma melatonin (MT). Mel1a (MT1) and Mel1b (MT2) expression levels were determined by Western blotting. In addition, a radioactive ligand-binding assay was used to analyze the specific binding properties and dynamic characteristics between MR and (125)I-Mel.</p><p><b>RESULTS</b>The results of weight gain, sucrose consumption and the open-field test showed that our model successfully produced depressive symptoms and depressive-like behavior. The concentration of plasma MT in the model group decreased significantly at night but increased in the MKXP group (P<0.05). The HKXP group showed significantly increased expression of MT1 (P<0.05); however, the expression of MT2 in all groups exhibited no significant differences (P>0.05). The maximum binding capacity (B(max)) for specific binding between MR and 125I-Mel in the MKXP group was significantly higher than that in the model group (P<0.05), but no significant differences were found in the equilibrium dissociation constant (K(d)) of each group (P>0.05).</p><p><b>CONCLUSIONS</b>KXP may have a similar effect as ramelteon. KXP improved depressive-like behavior by increasing the concentration of plasma MT and MT1 expression, thereby increasing three B(max) of MR to achieve the desired antidepressant effect.</p>

Transcriptomics study of the transcriptional response of the spinal dorsal horn to electroacupuncture stimulation with different frequencies / 中国中西医结合杂志

<p><b>OBJECTIVE</b>To explore the effects of low-and high-frequency electroacupuncture (EA) on the gene expression profiles in rat spinal dorsal horn (DH) under the physiological state, thus providing the information to find out the differences of different EA frequencies induced effects.</p><p><b>METHODS</b>Using cDNA microarray, the changes of the gene expressions in the DH were detected and compared between 2 Hz EA and 100 Hz EA at bilateral Zusanli (ST36) and Sanyinjiao (SP6). The differentially expressed genes were identified. The EASE scores were used to comprehensively analyze the gene functions (by Gene Ontology) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways.</p><p><b>RESULTS</b>(1) After EA stimulation 1 150 genes/expressed sequence tags (ESTs) were differentially expressed by 2 Hz EA, while 1 270 genes/ESTs were differentially expressed by 100 Hz EA. (2) Both 2 Hz and 100 Hz EA could induce the modulation of the same 516 genes/ESTs in the same direction, which was correlated with neural signal transmission. (3) The differentially expressed genes regulated specifically by 2 Hz were correlated with neural plasticity. (4) The differentially expressed genes regulated specifically by 100 Hz were correlated with stress and immunoregulation.</p><p><b>CONCLUSIONS</b>Either low-or high-frequency EA could extensively regulate the spinal cord information processing. The low-frequency EA participated more in the regulation of neural plasticity, while high-frequency EA had more significant effects on stress and immunoregulation.</p>

Evaluation of four candidate VNTR Loci for genotyping 225 Chinese clinical Mycobacterium tuberculosis complex strains / 生物医学与环境科学（英文）

<p><b>OBJECTIVE</b>To evaluate four candidate variable number tandem repeat (VNTR) loci for genotyping Mycobacterium tuberculosis complex strains.</p><p><b>METHODS</b>Genomic sequences for two M. tuberculosis strains (CCDC5079 and CCDC5180) were generated, and using published sequence data, four candidate VNTR loci were identified. The VNTRs were used to genotype 225 Chinese clinical M. tuberculosis complex strains. The discriminatory power of the VNTRs was evaluated using BioNumerics 5.0 software.</p><p><b>RESULTS</b>The Hunter-Gaston Index (HGI) for BJ1, BJ2, BJ3, and BJ4 loci was 0.634, 0.917, 0.697, and 0.910, respectively. Combining all four loci gave an HGI value of 0.995, thus confirming that the genotyping had good discriminatory power. The HGI values for BJ1, BJ2, BJ3, and BJ4, obtained from Beijing family strain genotyping, were 0.447, 0.878, 0.315, and 0.850, respectively. Combining all four loci produced an HGI value of 0.988 for genotyping the Beijing family strains. We observed unique patterns for M. bovis and M. africanum strains from the four loci.</p><p><b>CONCLUSION</b>We have shown that the four VNTR loci can be successfully used for genotyping M. tuberculosis complex strains. Notably, these new loci may provide additional information about Chinese M. tuberculosis isolates than that currently afforded by established VNTR loci typing.</p>

Correlation of the expressions of VEGF-C and VEGFR-3 to the pathological grade of prostate cancer / 南方医科大学学报

<p><b>OBJECTIVE</b>To investigate the correlation of the expression of VEGF-C and VEGFR-3 to the pathological grade of human prostate cancer.</p><p><b>METHODS</b>Immunohistochemistry was used to detect the expression of VEGF-C and VEGFR-3 in 25 cases of prostate cancer tissues.</p><p><b>RESULTS</b>The total positivity rates of VEGF-C and VEGFR-3 were 80% and 76% in these cancer tissues, respectively. The positivity rates of VEGF-C was 94.7% in the 19 cases with Gleason scores no less than 6 (group I), significantly higher than the rate (33%) in the 6 cases with Gleason scores between 4 and 6 (group II) (P<0.01). The positivity rates for VEGFR-3 also showed a significant difference between groups I and II (89.5% vs 33.3%, P<0.05). The expression level of VEGF-C was correlated to the Gleason score of prostate cancer (R=0.436, P<0.05), and the correlation between VEGFR-3 and the Gleason score was even more obvious (R=0.608, P<0.01). Their expressions, however, did not show any correlations to the patients age, PSA or the volume of the prostate.</p><p><b>CONCLUSION</b>VEGF-C and VEGFR-3 may serve as new markers for evaluating the malignancy of prostate cancer with Gleason score not less than 4.</p>

Screening and identification of differential expression genes related to stress fracture by cDNA microarray assay / 中华劳动卫生职业病杂志

<p><b>OBJECTIVE</b>To evaluate the differentially expressed genes between the Stress fracture (SF) cases and controls.</p><p><b>METHODS</b>Total RNA was extracted and purified from peripheral blood sample of 3 SF cases and 3 controls who conducted a 1:1 matched case-control study, then used for Human Genome Array analysis. The hybridization data were analyzed using SAM software. Parts of these genes were analyzed and identified by real-time PCR.</p><p><b>RESULTS</b>Upregulated and downregulated genes were 22 and 1, respectively. Thus the highest ratio and most significant cytokine was tumor necrosis factor receptor superfamily, member 10c (TNFRSF10C). The result of real-time PCR shows that TNFRSF10C was over-expressed in 3 cases and low-expressed in 1 case.</p><p><b>CONCLUSION</b>Obvious difference exists in gene expression between SF cases and controls, showing there may be a lot of genes involving in the occurrence and development of SF. Meanwhile, the identification of the specific genes is helpful for biomechanics study, early diagnosis and screening of SF.</p>

Protein array technology applied in high throughput monoclonal antibody generation / 生物工程学报

<p><b>UNLABELLED</b>To reduce the huge labor-cost in the screening in traditional monoclonal antibody generation, We established a new system for monoclonal antibody generation integrating with protein array. BALB/c mice were immunized by eight recombinant proteins respectively, and the positive hybridoma cells were obtained by cell fusion and ELISA screening. All the eight kinds of positive hybridoma cells were mixed, cloned, screened by protein array, and definite dilution cloned.</p><p><b>RESULTS</b>175 single cell clones were obtained by complex cloning, and 119 of those were positive clones. Then 8 positive cell lines were generated by the following 2 rounds definite dilution cloning. By comparing with the traditional method, we got 8 monoclonal antibodies using the combined protein array screening and multiplex cloning method in 1 cycle, and fewer amounts of antigens were used. As a result, the combined protein array and multiplex cloning method could be used as an economical, rapid and simple tool applying in high throughput monoclonal antibody generation.</p>

Expression and significance of PCNA and p27 in benign prostate hypertrophy and prostate carcinoma / 中华肿瘤杂志

<p><b>OBJECTIVE</b>To investigate the expression of PCNA and p27 in human benign prostate hypertrophy (BPH) and prostate carcinoma (PCa) and their effect on the genesis and progression of the tumor.</p><p><b>METHODS</b>The paraffin-embedded sections of 30 cases with BPH and 37 cases with PCa were collected. The expression of p27 and PCNA protein were examined by S-P immunohistochemical method. Comparative analysis for BPH and pathological grade and clinical stage of PCa was performed.</p><p><b>RESULTS</b>The expression of PCNA in BPH (3.3%) was significantly lower than that in Pca (83.8%, P < 0.01). The expression of p27 in BPH (70.0%) was significantly higher than that in Pca (27.0%, P < 0.05). The expression of p27 was not correlated with histological grade and clinical stage in Pca (P > 0.05). An inverse correlation was found between p27 and PCNA expression in BPH (P < 0.01), while no correlation was found in Pca (P > 0.05).</p><p><b>CONCLUSION</b>The loss or decreased expression of p27 protein may be related to the genesis of benign prostate hypertrophy, but not to the development of prostate carcinoma; the overexpression of PCNA may play an important role in the malignant behavior and progression of prostate carcinoma.</p>

Nucleotide sequence and protein sequence analysis of GL-7-ACA acylase from Pseudomonas sp. 130 / 生物工程学报

The nucleotide sequence and N-, C-terminal amino acid sequences of alpha,beta-subunit of glutaryl 7-ACA acylase C130 from Pseudomonas sp. 130 were determined. The alignment of the acylase C130 with the other acylases shows that it has high homology with the acylases from Pseudomonas sp. GK16 and C427, but low homology with the others. There is large difference in the N-terminal of alpha-subunit, while the N-terminal of beta-subunit has significant conservation.

Establishment of gene replacement/disruption system through homologous recombination in Amycolatopsis mediterranei U32 / 生物工程学报

A gene replacement/disruption system of Amycolatopsis mediterranei U32 was developed based on the established electroporation conditions as well as appropriate selective markers. Through two-step selection, ahbas gene in U32 was replaced by a promoterless alpha-amylase gene constructed on the plasmid pDK110 of E. coli. The first single-crossover and the second double-crossover frequencies were approximately 0.5%-0.7% and 2%, respectively. Denaturation of the plasmid pDK110 increased the integration frequency about 7-10 folds, while electric shock treatment of the single-crossover recombinants increased the frequency of second crossover recombination about 5 folds. Employing denatured DNA fragments containing an apramycin-resistance gene flanked with regions of the respective genes, One-step disruption of rifO and amrA genes of U32 was also achieved with an efficiency of 30-50 transformants per microgram of DNA.

Cloning of the replication origin (oriC) of Streptoverticillum caespitosus and transformation of Streptomyces lividans ZX7 / 生物工程学报

Streptoverticillum caespitosus ATCC27422 is a producing strain of mitomycin A for cancer therapy. Taking the advantage of the conserved sequences of genes flanking the oriC of high G + C Gram-positive bacteria, a 1.3 kb DNA fragment containing oriC and its flanking region was cloned by PCR. Nuleotide sequence comparisons revealed that the cloned fragment is more than 80% identical to the same region of S. coelicolor. There are 22 DnaA-boxes in the oriC region, and the conserved sequence of DnaA-box is TTGTCCACA. The plasmid containing the oriC of S. caespitosus was constructed (pMJ9), and it was able to transform the protoplast of Streptomyces lividans ZX7 at the frequency of 3.2 x 10(2) transformants/micrograms plasmid DNA. The colony and mycelia's morphology of the transformants are normal. The constructed plasmid can exist stable in the host as a low copy extra-chromosome replicon. The high rate of the homology and the cross genus replication initiation activity suggests close relationship between Streptomyces and Streptoverticillum in the evolution. While the maximum likelihood phylogenetic tree based upon the oriC of S. caespitosus and several Streptomyces spp. revealed that S. caespitosus differed extensively from the Streptomyces spp. This result supports the separation of Streptoverticillum from Streptomyces.