Multitissue Circadian Proteome Atlas of WT and Per1-/-/Per2-/- Mice.

The molecular basis of circadian rhythm, driven by core clock genes such as Per1/2, has been investigated on the transcriptome level, but not comprehensively on the proteome level. Here we quantified over 11,000 proteins expressed in eight types of tissues over 46 h with an interval of 2 h, using WT and Per1/Per2 double knockout mouse models. The multitissue circadian proteome landscape of WT mice shows tissue-specific patterns and reflects circadian anticipatory phenomena, which are less obvious on the transcript level. In most peripheral tissues of double knockout mice, reduced protein cyclers are identified when compared with those in WT mice. In addition, PER1/2 contributes to controlling the anticipation of the circadian rhythm, modulating tissue-specific cyclers as well as key pathways including nucleotide excision repair. Severe intertissue temporal dissonance of circadian proteome has been observed in the absence of Per1 and Per2. The γ-aminobutyric acid might modulate some of these temporally correlated cyclers in WT mice. Our study deepens our understanding of rhythmic proteins across multiple tissues and provides valuable insights into chronochemotherapy. The data are accessible at https://prot-rhythm.prottalks.com/.

Comparative Evaluation of Proteome Discoverer and FragPipe for the TMT-Based Proteome Quantification.

Isobaric labeling-based proteomics is widely applied in deep proteome quantification. Among the platforms for isobaric labeled proteomic data analysis, the commercial software Proteome Discoverer (PD) is widely used, incorporating the search engine CHIMERYS, while FragPipe (FP) is relatively new, free for noncommercial purposes, and integrates the engine MSFragger. Here, we compared PD and FP over three public proteomic data sets labeled using 6plex, 10plex, and 16plex tandem mass tags. Our results showed the protein abundances generated by the two software are highly correlated. PD quantified more proteins (10.02%, 15.44%, 8.19%) than FP with comparable NA ratios (0.00% vs. 0.00%, 0.85% vs. 0.38%, and 11.74% vs. 10.52%) in the three data sets. Using the 16plex data set, PD and FP outputs showed high consistency in quantifying technical replicates, batch effects, and functional enrichment in differentially expressed proteins. However, FP saved 93.93%, 96.65%, and 96.41% of processing time compared to PD for analyzing the three data sets, respectively. In conclusion, while PD is a well-maintained commercial software integrating various additional functions and can quantify more proteins, FP is freely available and achieves similar output with a shorter computational time. Our results will guide users in choosing the most suitable quantification software for their needs.

Optimization of Microflow LC Coupled with Scanning SWATH and Its Application in Hepatocellular Carcinoma Tissues.

Scanning SWATH coupled with normal-flow LC has been recently introduced for high-content, high-throughput proteomics analysis, which requires a relatively large amount of sample injection. Here we established the microflow LC coupled with Scanning SWATH for samples with relatively small quantities. First, we optimized several key parameters of the LC and MS settings, including C18 particle size for the analytical column, LC gradient and flow rate, as well as effective ion accumulation time and isolation window width for MS acquisition. We then compared the optimized Scanning SWATH method with the conventional variable window SWATH (referred to as SWATH) method. Results showed that the total ion chromatogram signals in Scanning SWATH were 10 times higher than that of SWATH, and Scanning SWATH identified 12.2-22.2% more peptides than SWATH. Finally, we employed 120 min Scanning SWATH to acquire the proteomes of 62 formalin-fixed, paraffin-embedded (FFPE) tissue samples from 31 patients with hepatocellular carcinoma (HCC). Altogether, 92 334 peptides and 8516 proteins were quantified. Besides the reported biomarkers, including ANXA2, MCM7, SUOX, and AKR1B10, we identified new potential HCC biomarkers such as CST5, TP53, CEBPB, and E2F4. Taken together, we present an optimal workflow integrating microflow LC and Scanning SWATH that effectively improves the protein identification and quantitation.

[Studies on callus growth and phillyrin accumulation of Forsythia suspensa].

OBJECTIVE: To investigate the effects of physical and chemical factors on callus growth and phillyrin contents of F. suspensa. METHOD: The cell growth index and phyllirin yield in different culture condition such as different plant hormones mixed, mediums, light and dark were compared. HPLC was used to examine phillyrin contents. RESULT AND CONCLUSION: Growth cycle of cells is twenty-eight days. During the course of callus growth, the processes of phillyrin biosynthesis were parallel with the cell growth. The optimum medium is MS. The optimum hormones concentrations are 1 mg.L-1 2,4-D, 0.5 mg.L-1 6-BA and 0.5 mg.L-1KT. The cell culture in light is more suitable than that in dark.

[Production and cytogenetics of hybrids of Ogura CMS Brassica campestris var. purpuraria x Raphanus sativus x Brassica napus].

Crosses of Ogura CMS Brassica campestris var. purpuraria x Raphanus sativus x Brassica napus were made and four hybrids were produced. One plant (PRN-1) was mosaic with yellow and milk white flowers and some flowers had both yellow and white petals. The others (PRN-2, -3, -4) had white flowers. PRN-4 had degenerated anthers, the other three had three to six anthers and could produce some pollens, but the pollens of PRN-2 were unstainable by I2-KI solution. PRN-2 had four normal honey glands, PRN-1 and PRN-3 had two, and PRN-4 had none. PRN-2 had normal leaf color and the other three showed different degrees of chlorophyll deficiency at low temperature. The chromosome number of PRN-1 was 2n = 38 and had the mean chromosome paring configuration of 14.67 I + 10.07 II + 1.06 III, and its chromosome set constitution might be AACR. This chromosome constitution may be due to the fertilization of female gamete of n = 19 (AR) with male gamete of n = 19 (AC) from B. napus. The occurrence of mosaic flower color in this plant may be attributed to the chromosome abnormalities caused by wide hybridization, such as chromosome deficiency and the formation of chromosome fragments and chromosome bridges. The chromosome number of PRN-2 was 2n = 35 and the mean chromosome paring configuration was 13.89 I + 8.33 II + 1.33 III + 0.11 IV. The chromosome number of PRN-3 was 2n = 33 and the mean chromosome paring configuration was 14.00 I + 7.82 II + 1.00 III + 0.09 IV. The chromosome number of PRN-4 was not determined as there was no pollen mother cell formation. Chromosome bridges and laggards were observed in PRN-1-3. Some seeds were harvested from PRN-1-3 but none was harvested from PRN-4 when backcrossed with B. napus. It seems possible for us to overcome the chlorophyll deficiency and honey gland abnormality and restore the male fertility in Ogura CMS by introduction of the nucleus of R. sativus into this cytoplasmic male sterile line.