Karyotyping of aneuploid and polyploid plants from low coverage whole-genome resequencing.

BACKGROUND: Karyotype, as a basic characteristic of species, provides valuable information for fundamental theoretical research and germplasm resource innovation. However, traditional karyotyping techniques, including fluorescence in situ hybridization (FISH), are challenging and low in efficiency, especially when karyotyping aneuploid and polyploid plants. The use of low coverage whole-genome resequencing (lcWGR) data for karyotyping was explored, but existing methods are complicated and require control samples. RESULTS: In this study, a new protocol for molecular karyotype analysis was provided, which proved to be a simpler, faster, and more accurate method, requiring no control. Notably, our method not only provided the copy number of each chromosome of an individual but also an accurate evaluation of the genomic contribution from its parents. Moreover, we verified the method through FISH and published resequencing data. CONCLUSIONS: This method is of great significance for species evolution analysis, chromosome engineering, crop improvement, and breeding.

Analysis of Phenotypic and Genotypic Susceptibility to Clarithromycin and Amikacin of Mycobacterium abscessus Complex Strains Isolated from Cystic Fibrosis Patients.

Mycobacterium abscessus complex infections are ever on the rise. To curb their increasing evolution, we performed an in-depth study of 43 clinical isolates of cystic fibrosis patients obtained from 2009 to 2020. We identified their subspecies, uncovered their genotypic resistance profiles, characterised their antibiotic-resistant genes, and assessed their phenotypic antibiotic susceptibilities. The phenotypic and genotypic methods showed total agreement in terms of resistance to clarithromycin and amikacin. Of the 43 clinical strains, 28 belonged to M. abscessus subsp. abscessus (65.1%), 13 to M. abscessus subsp. massiliense (30.2%), and 2 to M. abscessus subsp. bolletii (4.6%). The resistant rates for clarithromycin and amikacin, the two main drugs against M. abscessus complex pulmonary infections, were 64.2% and 14.2%, respectively. We found three strains of M. abscessus subsp. abscessus that showed heteroresistance in the rrl and rrs genes, and these strains also presented double-resistance since they were macrolide- and aminoglycoside-resistant. M. abscessus subsp. abscessus showed a high minimum inhibitory concentration (MIC) and a resistant percentage larger than or equal to 88% to cefoxitin, ciprofloxacin, moxifloxacin, doxycycline, imipenem, and trimethoprim-sulfamethoxazole. These results show a panorama of the high resistance of Mycobacterium abscessus complex to current drugs for cystic fibrosis patients. Thus, other treatment methods are urgently needed.

Exploring the Mechanism of White Peony in the Treatment of Lupus Nephritis Based on Network Pharmacology and Molecular Docking.

INTRODUCTION: Lupus nephritis (LN) is still a great burden for patients with systemic lupus erythematosus, and also one of the most severe complications of SLE. Radix Paeoniae Alba (white peony, WP) is proved with potential efficacy in treating LN. This study was to explore the effective ingredients, potential targets, and pathways of WP in treating LN based on network pharmacology and molecular docking. METHODS: The active ingredients and potential protein targets of WP were gathered on Traditional Chinese Medicine Systematic Pharmacology Database and predicted by Swiss Target Prediction. LN-related therapeutic targets were acquired from multiple databases including Genecards, DisGeNET, OMIM, Drugbank, and PharmGKB. The intersection targets of WP and LN were acquired through Veeny 2.1.0. Protein-Protein Interaction (PPI) network was established by STRING. The results were then visualized by Cytoscape version 3.7.1. to study the mechanisms of WP on LN, gene ontology and functional enrichment analysis were carried out. Finally, molecular docking presented with the binding ability of key targets and major active components. RESULTS: We acquired a total of 13 active ingredients and 260 potential targets of WP. Among them, the intersection with targets of LN were 82 proteins. These targets were regarded as potential therapeutic targets. Through PPI network, we found that the top three proteins were RAC-alpha serine/threonine protein kinase (AKT1), vascular endothelial growth factor A (VEGFA), and transcription factor Jun (JUN), and their corresponding components were kaempferol, paeoniflorin, lactiflorin, paeoniflorgenone, etc. The results of enrichment analysis suggested that WP treatment for LN mainly involves in signaling pathways in cancer, lipid and atherosclerosis, advanced glycation end product (AGE)-receptor of AGE (RAGE) pathways, C-type lectin receptor and nuclear factor (NF)-kappa B signaling pathways. Molecular docking predicted that the above components have excellent affinity to AKT1, VEGFA, and JUN. CONCLUSIONS: This study gave an insight into the key target proteins and potential underlying pharmacological mechanism of WP in treating LN, which provided evidence for further researches on the mechanism of WP on LN.

Genome balance and dosage effect drive allopolyploid formation in Brassica.

Polyploidy is a major evolutionary force that has shaped plant diversity. However, the various pathways toward polyploid formation and interploidy gene flow remain poorly understood. Here, we demonstrated that the immediate progeny of allotriploid AAC Brassica (obtained by crossing allotetraploid Brassica napus and diploid Brassica rapa) was predominantly aneuploids with ploidal levels ranging from near-triploidy to near-hexaploidy, and their chromosome numbers deviated from the theoretical distribution toward increasing chromosome numbers, suggesting that they underwent selection. Karyotype and phenotype analyses showed that aneuploid individuals containing fewer imbalanced chromosomes had higher viability and fertility. Within three generations of self-fertilization, allotriploids mainly developed into near or complete allotetraploids similar to B. napus via gradually increasing chromosome numbers and fertility, suggesting that allotriploids could act as a bridge in polyploid formation, with aneuploids as intermediates. Self-fertilized interploidy hybrids ultimately generated new allopolyploids carrying different chromosome combinations, which may create a reproductive barrier preventing allotetraploidy back to diploidy and promote gene flow from diploids to allotetraploids. These results suggest that the maintenance of a proper genome balance and dosage drove the recurrent conversion of allotriploids to allotetraploids, which may contribute to the formation and evolution of polyploids.

The expression of respiratory tract virus in pediatric glomerular disease: a retrospective study of 45 renal biopsy in China.

BACKGROUND: More attention has been put on the relationship between pediatric glomerular disease and respiratory tract virus infection. Children with glomerular illness, however, are uncommonly found to have biopsy-proven pathological evidence of viral infection. The purpose of this study is to determine whether and what kind of respiratory viruses are found in renal biopsy from glomerular disorders. METHODS: We used a multiplex PCR to identify a wide range of respiratory tract viruses in the renal biopsy samples (n = 45) from children with glomerular disorders and a specific PCR to verify their expression. RESULTS: These case series included 45 of 47 renal biopsy specimens, with 37.8% of male and 62.2% of female patients. Indications for a kidney biopsy were present in all of the individuals. In 80% of the samples, respiratory syncytial virus was discovered. Following that, the RSV subtypes in several pediatric renal disorders were found. There were 16 RSVA positives, 5 RSVB positives, and 15 RSVA/B positives, accounting for 44.4%, 13.9%, and 41.7%, respectively. Nephrotic syndrome samples made up 62.5% of RSVA positive specimens. The RSVA/B-positive was detected in all pathological histological types. CONCLUSIONS: Patients with glomerular disease exhibit respiratory tract viral expression in the renal tissues, especially respiratory syncytial virus. This research offers new information on the detection of respiratory tract viruses in renal tissue, which may facilitate the identification and treatment of pediatric glomerular diseases.

Real-world treatment patterns of metastatic non-small cell lung cancer patients receiving epidermal growth factor receptor tyrosine kinase inhibitors.

BACKGROUND: Several epidermal growth factor receptor tyrosine kinase inhibitors (EGFR TKI) have been approved for first-line (1L) treatment of EGFR-mutated metastatic non-small cell lung cancer (mNSCLC) in the United States (US). Real-world analyses of 1L treatment patterns with EGFR TKIs, including the third-generation EGFR TKI osimertinib which was most recently approved in 2018, are still sparse. METHODS: This retrospective observational study used data from IQVIA's prescription claims (LRx) and medical claims (Dx) databases. mNSCLC patients newly treated with any EGFR TKI in the 1L setting were identified from January 1, 2015 to April 30, 2020; the first date of EGFR TKI (third-generation osimertinib, first-generation [erlotinib, gefitinib], or second-generation [afatinib, dacomitinib]) was the index date. Treatment patterns were reported in the cohorts stratified by 1L EGFR TKI. RESULTS: A total of 2505 patients were included in the study (982 osimertinib, 1060 first-generation, and 463 second-generation EGFR TKI). Beginning in 2018, osimertinib became the most common 1L EGFR TKI (66.7%) and in early 2020, it accounted for 90.6% of 1L EGFR TKIs. Nearly all patients (>97%) were treated with 1L EGFR TKI monotherapy. Patients with 1L osimertinib had longer treatment duration compared to patients with 1L first- or second-generation EGFR TKI (median months: 17.8 vs. 8.7 vs. 10.5, respectively; log-rank test for comparisons with osimertinib p < 0.0001) over median follow-up times of 9.8, 20.5, and 19.3 months. 32.5% and 36.3% of the first- and second-generation EGFR TKI cohorts, respectively, had evidence of 2L treatment. Osimertinib monotherapy accounted for the majority of 2L treatments (58.3%/60.7%) and 11.3%/8.9% had 2L chemotherapy or immuno-oncology therapy following 1L first- or second-generation EGFR TKI. CONCLUSION: In this real-world study of a US claims database, 1L treatment duration was longer with osimertinib compared with other EGFR TKIs. Future studies with longer follow-up are recommended to understand treatment patterns after progression on EGFR TKIs.

Chromosome inheritance and meiotic stability in allopolyploid Brassica napus.

Homoeologous recombination, aneuploidy, and other genetic changes are common in resynthesized allopolyploid Brassica napus. In contrast, the chromosomes of cultivars have long been considered to be meiotically stable. To gain a better understanding of the underlying mechanisms leading to stabilization in the allopolyploid, the behavior of chromosomes during meiosis can be compared by unambiguous chromosome identification between resynthesized and natural B. napus. Compared with natural B. napus, resynthesized lines show high rates of nonhomologous centromere association, homoeologous recombination leading to translocation, homoeologous chromosome replacement, and association and breakage of 45S rDNA loci. In both natural and resynthesized B. napus, we observed low rates of univalents, A-C bivalents, and early sister chromatid separations. Reciprocal homoeologous chromosome exchanges and double reductions were photographed for the first time in meiotic telophase I. Meiotic errors were non-uniformly distributed across the genome in resynthesized B. napus, and in particular homoeologs sharing synteny along their entire length exhibited multivalents at diakinesis and polysomic inheritance at telophase I. Natural B. napus appeared to resolve meiotic errors mainly by suppressing homoeologous pairing, resolving nonhomologous centromere associations and 45S rDNA associations before diakinesis, and reducing homoeologous cross-overs.

Comparison of positioning accuracy of different registration methods and dosimetric analysis of adaptive radiotherapy for breast cancer after breast conserving surgery.

BACKGROUND: This study explores the effect of different registration methods on the placement accuracy and dosimetric analysis of adaptive radiation therapy (ART) after breast conserving surgery for breast cancer, based on cone-beam computed tomography (CBCT). METHODS: Thirty breast cancer patients, who underwent breast conserving surgery, were divided into three groups, with 10 patients in each group: automatic grayscale registration (group A), automatic bony marker registration (group B), and automatic grayscale registration combined with manual bony marker registration (group C). Three registration methods were conducted before the first radiotherapy, and once a week under the guidance of CBCT. The dosimetric comparison was made with the original plan. RESULTS: The X direction was significantly different between groups A and B (P=0.036). The X and Y direction were significantly different between groups A and C (P=0.001, P=0.019). The placement errors were significantly different between groups B and C in the X and Y directions (P<0.001, P=0.003). The ART plan was significantly better than the original plan, in terms of the Dmax, Dmean, D90, V90, V100, V95, HI and CI of planning target volume (PTV) (P<0.05). Furthermore, the ART plan was significantly better, in terms of the Dmean, V5, V10, V20 and V30 of the affected lung, the Dmean, V5, V10, V20 and V30 of the double lung, and the Dmean, V5, V10, V20 and V30 of the heart. Moreover, the Dmax, V5 and V10 of the contralateral breast were significantly lower than those in the original CT plan (P<0.05). CONCLUSIONS: For the CBCT placement verification after breast conserving surgery, the accuracy and stability of automatic gray-scale registration combined with manual bone markers are better than those of the automatic gray-scale registration and automatic bone marker registration.

Clinical and Molecular Features of Chronic Granulomatous Disease in Mainland China and a XL-CGD Female Infant Patient After Prenatal Diagnosis.

PURPOSE: Chronic granulomatous disease (CGD) is the most common phagocyte defect disease. Here, we describe 114 CGD patients in our center and report a rare female infant with XL-CGD to provide a better understanding of diagnosis, treatment, and prenatal diagnosis of CGD. METHOD: Patients were diagnosed by DHR-1,2,3 flow cytometry assays and gene analysis. X chromosome inactivation analysis and gp91phox protein test were used for a female infant with XL-CGD. RESULTS: XL-CGD accounts for the majority of cases in China and results in higher susceptibility to some infections than AR-CGD. The DHR assay can help diagnose CGD quickly, and atypical results should be combined with clinical manifestations, genetic analysis, and regular follow-up. For prenatal diagnosis, both gDNA and cDNA genotypes of amniotic fluid cells should be identified, and cord blood DHR assays should be performed to identify female XL-CGD patients.

[Observation on therapeutic effect of surrounded needling therapy on acute gouty arthritis].

OBJECTIVE: To compare clinical therapeutic effect of surrounded needling therapy and medication on acute gouty arthritis. METHODS: Sixty cases of acute gouty arthritis were randomly divided into a surrounded needling therapy group and a western medicine group, 30 cases in each group. The surrounded needling therapy group was treated with shallow needling on local affected area as main and 4-5 distant acupoints as adjuvant, once each day; the western medicine group was treated with oral administration of Indomethacin and Allopurinol, thrice each day. They were treated for 15 days. The clinical therapeutic effects, the changes of serum uric acid content and the adverse reaction were observed in the two groups. RESULTS: The total effective rate was 93.3% in the surrounded needling therapy group and 80.0% in the western medicine group, with a significant difference between the two groups (P < 0.01); the serum uric acid contents before and after treatment were (516.85 +/- 48.63) micromol/L and (293.77 +/- 68.45) micromol/L in the surrounded needling therapy group, and (509.66 +/- 51.11) micromol/L and (333.66 +/- 89.22) mciromol/L in the western medicine group, respectively, with significant differences before and after treatment in the two groups (both P < 0.05), and with a significant difference in the serum uric acid content after treatment between the two groups (P < 0.01). The surrounded needling therapy group had no adverse reaction, and the adverse reaction rate of the western medicine group was 46.7%, with a significant difference between the two groups (P < 0.01). CONCLUSION: Surrounded needling therapy is superior to the western medicine in the therapeutic effect on acute gouty arthritis, and it is a safe and effective method for acute gouty arthritis.