The mRNACalc webserver accounts for the N1-methylpseudouridine hypochromicity to enable precise nucleoside-modified mRNA quantification.

Nucleoside-modified messenger RNA (mRNA) technologies necessarily incorporate N1-methylpseudouridine into the mRNA molecules to prevent the over-stimulation of cytoplasmic RNA sensors. Despite this modification, mRNA concentrations remain mostly determined through the measurement of UV absorbance at 260 nm wavelength (A260). Herein, we report that the N1-methylpseudouridine absorbs approximately 40% less UV light at 260 nm than uridine, and its incorporation into mRNAs leads to the under-estimation of nucleoside-modified mRNA concentrations, with 5%-15% error, in an mRNA-sequence-dependent manner. We therefore examined the RNA quantification methods and developed the mRNACalc webserver. It accounts for the molar absorption coefficient of modified nucleotides at 260 nm wavelength, the RNA composition of the mRNA, and the A260 of the mRNA sample to enable accurate quantification of nucleoside-modified mRNAs.

Key genes and regulatory networks for diabetic retinopathy based on hypoxia-related genes: a bioinformatics analysis.

AIM: To prevent neovascularization in diabetic retinopathy (DR) patients and partially control disease progression. METHODS: Hypoxia-related differentially expressed genes (DEGs) were identified from the GSE60436 and GSE102485 datasets, followed by gene ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Potential candidate drugs were screened using the CMap database. Subsequently, a protein-protein interaction (PPI) network was constructed to identify hypoxia-related hub genes. A nomogram was generated using the rms R package, and the correlation of hub genes was analyzed using the Hmisc R package. The clinical significance of hub genes was validated by comparing their expression levels between disease and normal groups and constructing receiver operating characteristic curve (ROC) curves. Finally, a hypoxia-related miRNA-transcription factor (TF)-Hub gene network was constructed using the NetworkAnalyst online tool. RESULTS: Totally 48 hypoxia-related DEGs and screened 10 potential candidate drugs with interaction relationships to upregulated hypoxia-related genes were identified, such as ruxolitinib, meprylcaine, and deferiprone. In addition, 8 hub genes were also identified: glycogen phosphorylase muscle associated (PYGM), glyceraldehyde-3-phosphate dehydrogenase spermatogenic (GAPDHS), enolase 3 (ENO3), aldolase fructose-bisphosphate C (ALDOC), phosphoglucomutase 2 (PGM2), enolase 2 (ENO2), phosphoglycerate mutase 2 (PGAM2), and 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (PFKFB3). Based on hub gene predictions, the miRNA-TF-Hub gene network revealed complex interactions between 163 miRNAs, 77 TFs, and hub genes. The results of ROC showed that the except for GAPDHS, the area under curve (AUC) values of the other 7 hub genes were greater than 0.758, indicating their favorable diagnostic performance. CONCLUSION: PYGM, GAPDHS, ENO3, ALDOC, PGM2, ENO2, PGAM2, and PFKFB3 are hub genes in DR, and hypoxia-related hub genes exhibited favorable diagnostic performance.

DH-Mammo PET: a dual-head positron emission mammography system for breast imaging.

Objective. To develop a simultaneous positron emission tomography-Optical (OPET) breast imaging dual-head PET subsystem, called DH-Mammo PET, for accurate, early diagnosis and efficacy assessment of breast cancer with high resolution and sensitivity.Approach. We developed a breast-dedicated PET based on LYSO crystal, silicon photomultiplier array and multi-voltage threshold sampling technique. It consists of two detector heads, each with a detection area of 216 mm × 145.5 mm. The distance between the detector heads is fixed at 120 mm. In order to extract coincidences and correct data, GPU-based software coincidence processing, random, scatter, normalization, gap-filling and attenuation corrections were applied in turn. The images were reconstructed using maximum likelihood expectation maximization with depth of interaction (DOI) modeling. The performance of DH-Mammo PET was evaluated referring to NEMA NU 4-2008, NU 2-2007 and Chinese industry recommended standard YY/T 1835-2022. Besides, several clinical patient images of DH-Mammo PET were compared with those of a whole-body PET/CT.Main results. The energy resolution was 14.5%, and time resolution was < 1.31 ns. Indicated by the22Na point source imaging, its spatial resolution was 2.60 mm (5.40 mm), 1.00 mm (1.04 mm), and 0.96 mm (0.93 mm) in theX,YandZdirections, respectively, using the system response matrix with (without) DOI modeling. Indicated by the Derenzo phantom imaging, the spatial resolution was ∼3.0 mm, <1.2 mm, and <1.2 mm in theX,YandZdirections. The system sensitivity was 6.87%, 4.89% and 3.37% with an energy window of 100-800, 250-750 and 350-650 keV, respectively. The scatter fraction was 26.43%, and the peak NECR was 162.6 kcps at 24.1 MBq for the modified rat-like phantom. As for the recovery coefficients, they ranged from 0.15 to 1.04 for rods between 1 and 5 mm obtained with a NEMA image quality phantom. The spill-over ratio for the air-filled and water-filled chamber was 0.05 and 0.11, respectively. DH-Mammo PET can provide more image details in clinical experiments and fulfil a fast scan with 60-120 s acquisition time.Significance. Good spatial resolution and high sensitivity of DH-Mammo PET would enable fast and accurate PET imaging of the breast. Besides, combining the DH-Mammo PET with the diffuse optical tomography would make full use of tumor metabolic imaging and tissue endogenous optical imaging, which would improve the accuracy of early clinical diagnosis of small lesions of breast cancers.