TopDIA: A Software Tool for Top-Down Data-Independent Acquisition Proteomics.

Top-down mass spectrometry is widely used for proteoform identification, characterization, and quantification owing to its ability to analyze intact proteoforms. In the last decade, top-down proteomics has been dominated by top-down data-dependent acquisition mass spectrometry (TD-DDA-MS), and top-down data-independent acquisition mass spectrometry (TD-DIA-MS) has not been well studied. While TD-DIA-MS produces complex multiplexed tandem mass spectrometry (MS/MS) spectra, which are challenging to confidently identify, it selects more precursor ions for MS/MS analysis and has the potential to increase proteoform identifications compared with TD-DDA-MS. Here we present TopDIA, the first software tool for proteoform identification by TD-DIA-MS. It generates demultiplexed pseudo MS/MS spectra from TD-DIA-MS data and then searches the pseudo MS/MS spectra against a protein sequence database for proteoform identification. We compared the performance of TD-DDA-MS and TD-DIA-MS using Escherichia coli K-12 MG1655 cells and demonstrated that TD-DIA-MS with TopDIA increased proteoform and protein identifications compared with TD-DDA-MS.

Tetrahydrocurcumin Ameliorates Acute Hypobaric Hypoxia-Induced Cognitive Impairment in Mice.

Ma, Xuexinyu, Yang Pan, Yuye Xue, Yao Li, Yan Zhang, Yani Zhao, Xingzhao Xiong, Jianbo Wang, and Zhifu Yang. Tetrahydrocurcumin ameliorates acute hypobaric hypoxia-induced cognitive impairment in mice. High Alt Med Biol. 23:264-272, 2022. Background: Hypobaric hypoxia (HH) impairs spatial learning and increases oxidative stress in rodents. We hypothesized that tetrahydrocurcumin (THC) may attenuate HH-induced neurobehavioral deficits by reducing HH-induced lipid peroxidation and increasing glycolytic activity. Materials and Methods: A C57BL/6 mouse model of acute high altitude brain injury was established using an animal decompression chamber for 24 hours. Cognitive and behavioral assessments were conducted using the Y-maze, open field, and Rotarod tests. We measured superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) activity; malondialdehyde (MDA) and reactive oxygen species levels; anti-neuronal core antigen (NeuN) immunoreactivity; and active occludin, hypoxia-inducible factor-1α, glucose transporter 1 (GLUT1), and GLUT3 expression levels in mice brain tissue. Results: The mice in the THC group showed improved cognitive impairment compared with those in the HH group in cognitive and behavioral tests, but failed to show improvement in the decline in coordination. The mice in the THC group were more effected than those in the HH group in demonstrating alleviation of hyperemia in cortical vessels and cell voids, and cells in the CA1 region were more closely arranged. Compared with those in the mice of the HH group, the concentration of MDA decreased significantly, the expression of occludin, NeuN immunoreactivity, and the activities of SOD and GSH-Px significantly increased in the mice of the THC group. An increase in GLUT1 expression was observed in HH-exposed animals (N group vs. HH group: 0.4 ± 0.08 vs. 0.60 ± 0.07, p < 0.05), and this increase was enhanced in animals treated with THC (HH group vs. THC group: 0.60 ± 0.07 vs. 0.82 ± 0.08, p < 0.05). Conclusions: THC improved cognitive impairment in mice, accompanied by reduced oxidative stress and increased GLUT1 protein levels.

Huangqi-Honghua Combination Prevents Cerebral Infarction with Qi Deficiency and Blood Stasis Syndrome in Rats by the Autophagy Pathway.

BACKGROUND: Cerebral ischemia/reperfusion injury (CI/RI) contributes to the process of autophagy. Huangqi-Honghua combination (HQ-HH) is a traditional Chinese medicine (TCM) combination that has been widely used in the treatment of cerebrovascular diseases in China. The role of autophagy in HQ-HH-mediated treatment of CI/RI is unclear. METHODS: Sprague-Dawley (SD) rats were used to establish the middle cerebral artery occlusion (MCAO) with QDBS syndrome model and evaluate the function of HQ-HH in protecting against CI/RI. RESULTS: HQ-HH significantly improved the neuronal pathology and reduced infarct volume, neurological deficits, and whole blood viscosity in rats with CI/RI. Western blot results showed that the expression of autophagy marker proteins LC3II/LC3I and Beclin1 in the HQ-HH group was significantly lower than that in the model group, while the expression of p62 was significantly higher in the HQ-HH group as compared with the model group. There were no significant differences in PI3K, Akt, and mTOR levels between the HQ-HH group and the model group; however, p-PI3K, p-Akt, and p-mTOR were significantly upregulated. In addition, HQ-HH also changed the composition and function of intestinal flora in MCAO + QDBS model rats. CONCLUSION: HQ-HH protects from CI/RI, and its underlying mechanism may involve the activation of the PI3K-Akt-mTOR signaling pathway, relating to the changes in the composition of intestinal flora.