De novo assembly and characterization of the leaf, bud, and fruit transcriptome from the vulnerable tree Juglans mandshurica for the development of 20 new microsatellite markers using Illumina sequencing.

Manchurian walnut (Juglans mandshurica Maxim.) is a vulnerable, temperate deciduous tree valued for its wood and nut, but transcriptomic and genomic data for the species are very limited. Next generation sequencing (NGS) has made it possible to develop molecular markers for this species rapidly and efficiently. Our goal is to use transcriptome information from RNA-Seq to understand development in J. mandshurica and develop polymorphic simple sequence repeats (SSRs, microsatellites) to understand the species' population genetics. In this study, more than 47.7 million clean reads were generated using Illumina sequencing technology. De novo assembly yielded 99,869 unigenes with an average length of 747 bp. Based on sequence similarity search with known proteins, a total of 39,708 (42.32 %) genes were identified. Searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG) identified 15,903 (16.9 %) unigenes. Further, we identified and characterized 63 new transcriptome-derived microsatellite markers. By testing the markers on 4 to 14 individuals from four populations, we found that 20 were polymorphic and easily amplified. The number of alleles per locus ranged from 2 to 8. The observed and expected heterozygosity per locus ranged from 0.209 to 0.813 and 0.335 to 0.842, respectively. These twenty microsatellite markers will be useful for studies of population genetics, diversity, and genetic structure, and they will undoubtedly benefit future breeding studies of this walnut species. Moreover, the information uncovered in this research will also serve as a useful genetic resource for understanding the transcriptome and development of J. mandshurica and other Juglans species.

Metabolism-Based Nontarget-Site Mechanism Is the Main Cause of a Four-Way Resistance in Shortawn Foxtail (Alopecurus aequalis Sobol.).

Alopecurus aequalis Sobol. is a predominant grass weed in Chinese winter wheat fields, posing a substantial threat to crop production owing to its escalating herbicide resistance. This study documented the initial instance of an A. aequalis population (AHFT-3) manifesting resistance to multiple herbicides targeting four distinct sites: acetyl-CoA carboxylase (ACCase), acetolactate synthase, photosystem II, and 1-deoxy-d-xylulose-5-phosphate synthase. AHFT-3 carried an Asp-to-Gly mutation at codon 2078 of ACCase, with no mutations in the remaining three herbicide target genes, and exhibited no overexpression of any target gene. Compared with the susceptible population AHFY-3, AHFT-3 metabolized mesosulfuron-methyl, isoproturon, and bixlozone faster. The inhibition and comparison of herbicide-detoxifying enzyme activities indicated the participation of cytochrome P450s in the resistance to all four herbicides, with glutathione S-transferases specifically linked to mesosulfuron-methyl. Three CYP72As and a Tau class glutathione S-transferase, markedly upregulated in resistant plants, potentially played pivotal roles in the multiple-herbicide-resistance phenotype.

Loop-mediated isothermal amplification for detecting the Ile-2041-Asn mutation in fenoxaprop-P-ethyl-resistant Alopecurus aequalis.

BACKGROUND: Shortawn foxtail (Alopecurus aequalis Sobol.), a competitive grass weed severely infesting overwintering crops worldwide, has evolved resistance to the highly efficient acetyl-CoA carboxylase (ACCase)-inhibiting herbicide fenoxaprop-P-ethyl. The Ile-to-Asn substitution at codon position 2041 of ACCase is a dominant resistance mutation that has been associated with fenoxaprop-P-ethyl resistance in A. aequalis. However, its detection based on conventional methods such as polymerase chain reaction (PCR) and gene sequencing is rather labor- and time-consuming. RESULTS: In order to facilitate its detection in field populations of A. aequalis, a simple and efficient method with high sensitivity to the Ile-2041-Asn mutation was developed based on loop-mediated isothermal amplification (LAMP). A set of four primers was designed to target a 244-bp fragment of ACCase comprising codon position 2041. Using the special primers and genomic DNA of A. aequalis, the concentrations of reaction components, temperature and time each were optimized. The LAMP reaction for the detection of the Ile-2041-Asn mutation was processed at 65 °C for 45 min followed by 80 °C for 10 min to stop the reaction. The LAMP method developed was 1000-fold more sensitive than the conventional PCR method, and the detection was also practicable when using crude DNA of A. aequalis as a template. CONCLUSION: The low cost, simplicity and high sensitivity of the developed LAMP assay make the detection of the Ile-2041-Asn mutation easier and quicker, which may contribute to the monitoring and management of resistance development to fenoxaprop-P-ethyl in A. aequalis. © 2022 Society of Chemical Industry.

Metamifop resistance in Echinochloa glabrescens via glutathione S-transferases-involved enhanced metabolism.

BACKGROUND: Echinochloa glabrescens Munro ex Hook. f. is one of the main Echinochloa spp. seriously invading Chinese rice fields and has evolved resistance to commonly used herbicides. Previously, an E. glabrescens population (LJ-02) with suspected resistance to the acetyl-CoA carboxylase (ACCase)-inhibiting herbicide metamifop was collected. This study aimed to determine its resistance status to metamifop and investigate the internal molecular mechanisms of resistance. RESULTS: Single-dose testing confirmed that the LJ-02 population had evolved resistance to metamifop. Gene sequencing and a relative expression assay of ACCase ruled out target-site based resistance to metamifop in LJ-02. Whole-plant bioassays revealed that, compared with the susceptible population XZ-01, LJ-02 was highly resistant to metamifop and exhibited cross-resistance to fenoxaprop-P-ethyl. Pretreatment with the known glutathione S-transferase (GST) inhibitor, 4-chloro-7-nitrobenzoxadiazole (NBD-Cl), largely reversed the resistance to metamifop by approximately 81%. Liquid chromatography-tandem mass spectrometry analysis indicated that the metabolic rates of one of the major metabolites of metamifop, N-(2-fluorophenyl)-2-hydroxy-N-methylpropionamide (HPFMA), were up to 383-fold faster in LJ-02 plants than in XZ-01 plants. There were higher basal and metamifop-inducible GST activities toward 1-chloro-2,4-dinitrobenzene (CDNB) in LJ-02 than in XZ-01. Six GST genes were metamifop-induced and overexpressed in the resistant LJ-02 population. CONCLUSION: This study reports, for the first time, the occurrence of metabolic metamifop resistance in E. glabrescens worldwide. The high-level metamifop resistance in the LJ-02 population may mainly involve specific isoforms of GSTs that endow high catalytic activity and strong substrate specificity. © 2023 Society of Chemical Industry.

An initial study on the comparison of diagnostic performance of 18F-FDG PET/MR and 18F-FDG PET/CT for thoracic staging of non-small cell lung cancer: Focus on pleural invasion.

OBJECTIVE: To compare the diagnostic performance of 18F-FDG PET/MR and PET/CT preliminarily for the thoracic staging of non-small cell lung cancer (NSCLC) with a special focus on pleural invasion evaluation. METHODS: 52 patients with pathologically confirmed NSCLC were included and followed for another year. Whole-body 18F-FDG PET/CT and subsequent thoracic PET/MR were performed for initial thoracic staging. Thoracic (simultaneous) PET/MR acquired PET images and MRI sequences including T2 weighted imaging, with and without fat saturation, T1 weighted imaging, and diffusion weighted imaging (DWI). Two radiologists independently assessed the thoracic T, N staging and pleural involvement. The McNemar Chi-square test was used to compare the differences between PET/CT and PET/MR in the criteria. The area under the receiver-operating-characteristic curves (AUC) was calculated. RESULTS: Compared to PET/CT, PET/MR exhibited higher sensitivity, specificity in the detection of pleural invasion; 82 % vs. 64% (p = 0.625), 98 % vs. 95% (p = 1.000), PET/MR to PET/CT respectively. The receiver-operating-characteristic analysis results of PET/CT vs PET/MR for the pleural invasion were as follow: AUCPET/CT = 0.79, AUCPET/MR = 0.90, p = 0.21. Both T staging results and N staging results were approximately identical in PET/CT and PET/MR. Differences between PET/CT and PET/MR in T staging, N staging as well as pleural invasion accuracy were not statistically significant (p > 0.05, each). CONCLUSION: PET/MR and PET/CT demonstrated equivalent performance about the evaluation of preoperative thoracic staging of NSCLC patients. PET/MR may have greater potential in pleural invasion evaluation for NSCLC, especially for solid nodules, crucial to clinical decision-making, though our results did not demonstrate statistical significance.

Polymyxin B, Cefoperazone Sodium-Sulbactam Sodium, and Tigecycline against Multidrug-Resistant Acinetobacter baumannii Pneumonia.

Purpose: The purpose of this study is to investigate the significance of polymyxin B in combination with cefoperazone sodium-sulbactam sodium (CSSS) and tigecycline for the treatment of multidrug-resistant Acinetobacter baumannii- (MDRAB-) induced pneumonia on the levels of white blood cell (WBC) count, serum C-reactive protein (CRP), and procalcitonin (PCT). Methods: Fifty-six patients with MDRAB pneumonia admitted to the Fifth People's Hospital of Wuhu from February 2019 to December 2021 were randomized into the observation group (n = 28) and the experimental group (n = 28) by the random table method. The observation group received intravenous infusion of CSSS and tigecycline. The experimental group received intravenous infusion of polymyxin B sulfate plus CSSS and tigecycline. All patients were treated for 14 days. Results: There was no significant difference in the overall response rate between the two groups; the bacterial clearance of the experimental group was significantly higher than that of the observation group; there was no significant difference in the WBC, CRP, and PCT levels between the two groups prior to the treatment; but after treatment, while the WBC, CRP, and PCT levels of the two groups decreased, the WBC count, CRP, and PCT levels of the experimental group were significantly lower than those of the observation group; no significant difference was found in adverse reactions. Conclusion: Polymyxin B-CSSS-tigecycline has good clinical efficacy in the treatment of MDRAB pneumonia. It not only improves the patients' bacterial clearance rate and effectively reduces the levels of WBC count, serum CRP, and PCT, but also raises no risk of adverse reactions. Therefore, it is worthy of clinical promotion.

Characterization of the DNA molecular sequence of complete plastid genome of Paeonia rockii subsp. taibaishanica, an endemic species in China.

Paeonia rockii subsp. taibaishanica (Paeoniaceae), one of the tree peony species, is endemic to the Qinling Mountains in central China. In this study, we characterized its whole plastid genome sequence using the Illumina sequencing platform. The complete plastid genome size of P. rockii subsp. taibaishanica is 153,368 bp in length, including a large single copy (LSC) region of 85,030 bp, a small single copy (SSC) region of 17,042 bp, and a pair of inverted repeats (IRs) of 25,648 bp. The genome contains 131 genes, including 83 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The GC contents in chloroplast genome, LSC region, SSC region, and IR region were 38.3%, 36.6%, 32.6%, and 43.1%, respectively. A total of 16 species are used to construct the phylogenetic tree of Paeoniaceae, the results showed that P. rockii subsp. taibaishanica is more closely related with congeneric Paeonia suffruticosa and Paeonia ostii, these species were clustered into a clade with high bootstrap support.

The complete nucleotide molecular sequence of plastid genome of Zanthoxylum armatum (Rutaceae).

Zanthoxylum armatum DC. (Rutaceae) is a shrub and/or tree species with the important medicinal and economic values. In this study, the plastid genome of Z. armatum was characterized by Illumina Hiseq 2500 sequencing platform. In total, the plastid genome is 158,557 bp in length, and comprises a large single copy region of 85,752 bp, a small single copy region of 17,605 bp, and two inverted repeat regions of 27,600 bp. The complete plastid genome contains 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis suggested that Z. armatum and the congeneric Z. simulans clustered into an evolutionary clade with the high support.

Taxonomic study of Triblemma by using light and scanning electron microscopy.

Triblemma Ching is a genus proposed by Ching Ren-Chang in 1978, and it is composed of two species, Triblemma lancea (Thunb.) Ching and Triblemma zeylanica (Hook.) Ching. There has been much debate on the systematic position of Triblemma, and this genus has always been included in Diplazium. Here, we have described new features of tracheary elements, epidermis, spore, scale, and rachis of Triblemma revealed using light and scanning electron microscopy and proposed that Triblemma is closely related to Athyriopsis, which conflicts with the traditional viewpoint.

Estudio inicial sobre la comparación del rendimiento diagnóstico de la PET/RM con [18F]FDG y la PET/TC con [18F]FDG para la estadificación torácica del cáncer de pulmón de células no pequeñas: enfoque en la invasión pleural / An initial study on the comparison of diagnostic performance of 18F-FDG PET/MR and 18F-FDG PET/CT for thoracic staging of non-small cell lung cancer: Focus on pleural invasion

Objetivo Comparar el rendimiento diagnóstico de la PET/RM con [18F]FDG y la PET/TC de forma preliminar en relación con la estadificación torácica del cáncer de pulmón de células no pequeñas (CPCNP) con un enfoque especial en la evaluación de la invasión pleural. Métodos Se incluyeron 52 pacientes con CPCNP con confirmación histopatológica y sometidos a seguimiento durante un año más. Se realizó una PET/TC con [18F]FDG de cuerpo entero y a continuación una PET/RM torácica para la estadificación torácica inicial. Las imágenes de PET/RM torácica se adquirieron simultáneamente e incluyeron secuencias potenciadas en T2, con y sin saturación grasa, en T1 y de difusión. Dos radiólogos evaluaron de forma independiente la estadificación T, N torácica y la afectación pleural. Se utilizó la prueba de Chi-cuadrado de McNemar para comparar las diferencias entre PET/TC y PET/RM en los criterios de evaluación. Se realizó análisis ROC de eficacia diagnóstica con calculó del área bajo la curva (AUC) para el estudio de la invasión pleural. Resultados La PET/RM mostró una mayor sensibilidad y especificidad en la detección de invasión pleural respecto a la PET/TC; 82 vs. 64% (p=0,625), 98 vs. 95% (p=1.000). Los resultados del análisis ROC de la PET/TC vs. la PET/RM respecto a la invasión pleural fueron los siguientes: AUCPET/TC=0,79, AUCPET/RM=0,90, p=0,21. Los resultados de la estadificación T y N fueron casi idénticos en la PET/TC y la PET/RM. Las diferencias existentes entre la PET/TC y la PET/RM para la estadificación T y N y la precisión de la invasión pleural no fueron estadísticamente significativas (p>0,05 en cada una). Conclusión La PET/RM y la PET/TC demostraron un rendimiento equivalente en la evaluación de la estadificación torácica preoperatoria de los pacientes con CPCNP (AU)

Objective To compare the diagnostic performance of 18F-FDG PET/MR and PET/CT preliminarily for the thoracic staging of non-small cell lung cancer (NSCLC) with a special focus on pleural invasion evaluation. Methods Fifty-two patients with pathologically confirmed NSCLC were included and followed for another year. Whole-body 18F-FDG PET/CT and subsequent thoracic PET/MR were performed for initial thoracic staging. Thoracic (simultaneous) PET/MR acquired PET images and MRI sequences including T2 weighted imaging, with and without fat saturation, T1 weighted imaging, and diffusion weighted imaging. Two radiologists independently assessed the thoracic T, N staging and pleural involvement. The McNemar Chi-square test was used to compare the differences between PET/CT and PET/MR in the criteria. The area under the receiver-operating-characteristic curves (AUC) was calculated. Result Compared to PET/CT, PET/MR exhibited higher sensitivity, specificity in the detection of pleural invasion; 82% vs. 64% (P=.625), 98% vs. 95% (P=1.000), PET/MR to PET/CT, respectively. The receiver-operating-characteristic analysis results of PET/CT vs. PET/MR for the pleural invasion were as follow: AUCPET/CT=0.79, AUCPET/MR=0.90, P=.21. Both T staging results and N staging results were approximately identical in PET/CT and PET/MR. Differences between PET/CT and PET/MR in T staging, N staging as well as pleural invasion accuracy were not statistically significant (P>.05, each). Conclusion PET/MR and PET/CT demonstrated equivalent performance about the evaluation of preoperative thoracic staging of NSCLC patients. PET/MR may have greater potential in pleural invasion evaluation for NSCLC, especially for solid nodules, crucial to clinical decision-making, though our results did not demonstrate statistical significance (AU)