Highly Robust de Novo Full-Length Protein Sequencing.

Accurate full-length sequencing of a purified unknown protein is still challenging nowadays due to the error-prone mass-spectrometry (MS)-based methods. De novo identified peptide sequence largely contain errors, undermining the accuracy of assembly. Bias on the detectability of the peptides also makes low-coverage regions, resulting in gaps. Although recent advances on multi-enzyme hydrolysis and algorithms showed complete assembly of full-length protein sequences in a few examples, the robustness in practical application is still to be improved. Here, inspired by genome assembly strategies, we demonstrate a contig-scaffolding strategy to assemble protein sequences with high robustness and accuracy. This strategy integrates multiple unspecific hydrolysis methods to minimize the bias in the hydrolysis process. After de novo identification of the peptides, our assembly algorithm, named Multiple Contigs & Scaffolding (MuCS), assembles the peptide sequences in a multistep, i.e., contig-scaffold manner, with error correction in each step. MS data from different hydrolysis experiments complement each other for robust contig extension and error correction. We demonstrated that our strategy on three proteins and three replications all reached 100% coverage (except one with 98.85%) and 98.69-100% accuracy. It can also efficiently deal with the membrane protein, although the transmembrane region was missing due to the limitation of the MS. The three replicates reached 88.85-92.57% coverage and 97.57-100% accuracy. In sum, we provided a practical, robust, and accurate solution for full-length protein sequencing. The MuCS software is available at http://chi-biotech.com/mucs/.

Evaluation of the efficiency of peptide receptor radionuclide therapy in patients with metastatic prostate carcinoma: A protocol for systematic review and meta-analysis.

BACKGROUND: Metastatic prostate carcinoma has poor prognoses with a median survival period ranging from 2 to 5 years with existing therapeutic challenges. Currently, peptide receptor radionuclide therapy is permitted as a treatment method for metastatic prostate carcinoma patients. Therefore, it is crucial to comprehend the efficiency and safety of peptide receptor radionuclide therapy among this patient population. This study aims to analyse the efficacy of peptide receptor radionuclide therapy when used to treat metastatic prostate carcinoma patients. METHODS: This research will perform a methodological search in the following electronic databases to find related randomized controlled trials: Cochrane Library, EMBASE, PubMed, Web of Science, Scopus, China National Knowledge Infrastructure (CNKI), WanFang database, and Chinese BioMedical Literature. All the databases are searched from their inauguration till November 2020. Two independent authors will screen and select literature for review. The two authors will independently utilize the Cochrane Risk of Bias tool to assess the bias risk in studies. This study also plans to conduct subgroup and sensitivity analyses to evaluate the robustness in the results. Statistical analyses will be conducted with the RevMan 5.3 software. RESULTS: A high-quality synthesis of existing evidence related to peptide receptor radionuclide therapy in the treatment of metastatic prostate carcinoma will be presented in this study. CONCLUSION: Our findings will provide evidence to judge whether peptide receptor radionuclide treatment is efficient for metastatic prostate carcinoma patients. ETHICS AND DISSEMINATION: An ethics approval is not required because the data of the present study are primarily obtained from published studies.OSF registration number: December 1, 2020.osf.io/3psx7. (https://osf.io/3psx7/).

A multi-center nested case-control study on hospitalization costs and length of stay due to healthcare-associated infection.

Background: In 2018, the Chinese government demanded nationwide implementation of medical insurance payment methods based on Single-Disease Payment (SDP), but during the operation process the medical insurance system did not fully consider the extra economic burden caused by healthcare-associated infection (HAI). HAIs can prolong the length of stay and increase the hospitalization costs, but only a few studies have been conducted in Sichuan province, China. We evaluated the hospitalization costs and length of stay due to HAI in Sichuan province based on the prevalence survey, and provided data reference for China's medical insurance reform. Methods: In the hospitals surveyed on the prevalence of HAI, a multi-center nested case-control study was performed by a paired method. The study period was from 6 September 2016 to 30 November 2016. Binary outcomes were tested using χ2 test, continuous outcomes were tested using Wilcoxon matched-pairs signed rank test, intra-group comparisons were tested using multiple linear regression analysis. Results: A total of 225 pairs/450 patients were selected in 51 hospitals, and 170 pairs/350 patients were successfully matched. The case fatality rate was 5.14% for the HAIs patients and 3.43% for non-HAs patients, there was no significant difference (χ2 = 0.627, P = 0.429); the median length of stay in patients with HAIs was 21 days, longer than that of patients with non-HAI 16 days, the median of the difference between matched-pairs was 5 days, the difference was statistically significant (Z = 4.896, P = 0.000). The median hospitalization costs of patients with HAI were €1732.83, higher than that of patients with non-HAI €1095.29, the median of the difference between matched-pairs were €431.34, the difference was statistically significant (Z = 6.413, P = 0.000). Multiple linear regression results showed that HAIs at different sites have caused different economic burdens, but in different economic regions, the difference was not statistically significant. Conclusions: In Sichuan, the hospitalization costs and length of stay caused by HAI should be given special attention in the current medical insurance reform. The proportion and scope of medical payment for patients with HAI at different sites should be different. Efforts need to be taken to incentivize reduction of HAI rates which will reduce hospitalization costs and length of stay.

Serum level of fetuin B is associated with osteoporosis: a 4-year prospective study in China.

PURPOSE: As a novel hepatokine, fetuin B involves in various functions of energy metabolism. Recent advance reveals a complex interaction between bone and liver via the secretion of hepatokines. The association between serum fetuin B and osteoporosis was evaluated in a 4-year hospital-based prospective study of 1,370 Chinese postmenopausal women. METHODS: Bone mineral densities (BMDs) were obtained on femoral neck and lumbar spines by dual energy X-ray absorptiometry. Serum fetuin B level was tested by enzyme-linked immunosorbent assay. RESULTS: Of the 1,370 participants in the baseline study (2012), 650 subjects were included in the 4-year follow-up study (2016). Serum fetuin B level presented higher in subjects with osteoporosis (106.7 ± 17.6 µg/ml) than it in controls (86.3 ± 17.5 µg/ml) (P < 0.001). Meanwhile, fetuin B positively correlated with triglycerides (r = 0.227, P = 0.001), femoral BMD (r = -0.426, P < 0.001) and lumbar BMD (r = -0.332, P < 0.001). At the 4-year follow-up, 116 subjects had developed osteoporosis. Serum fetuin B concentration was significantly higher in subjects who developed (P < 0.001). The osteoporosis incidence increased from Q1 9.9%, Q2 14.7%, and Q3 17.8% to Q4 30.2% (P for trend < 0.001), among the quartiles of baseline fetuin B. A higher fetuin B baseline level was linked to the incidence of osteoporosis (adjusted OR = 1.179, 95% CI [1.119 - 1.243], P = 0.009). CONCLUSION: Serum fetuin B levels increased with the development of osteoporosis.

Simplified recovery of enzymes and nutrients in sweet potato wastewater and preparing health black tea and theaflavins with scrap tea.

The industry discards generous organic wastewater in sweet potato starch factory and scrap tea in tea production. A simplified procedure to recover all biochemicals from the wastewater of sweet potato starch factory and use them to make health black tea and theaflavins from scrap green tea was developed. The sweet potato wastewater was sequentially treated by isoelectric precipitation, ultrafiltration and nanofiltration to recover polyphenol oxidase (PPO), ß-amylase, and small molecular fractions, respectively. The PPO fraction can effectively transform green tea extracts into black tea with high content of theaflavins through the optimized fed-batch feeding fermentation. The PPO transformed black tea with sporamins can be used to make health black tea, or make theaflavins by fractionation with ethyl acetate. This work provides a resource- and environment-friendly approach for economically utilizing the sweet potato wastewater and the scrap tea, and making biochemical, nutrient and health products.

Proteomic and bioinformatic analysis on endocrine organs of domesticated silkworm, Bombyx mori L. for a comprehensive understanding of their roles and relations.

Three organs of silkworm larva endocrine system, including brain (Br), subesophageal ganglion (SG) and prothoracic glands (PG), were studied employing shotgun LC-MS/MS combined with bioinformatic analysis to comprehensively understand their roles and relations. Totally, 3430, 2683, and 3395 proteins were identified including 1885 common and 652, 253, and 790 organ-specific ones in Br, SG, and PG, respectively. Identified common-expressed proteins indicated the existence of intrinsic complex interactions among these parts of endocrine system. Most of the reputed organs-specific proteins were identified by this approach. KEGG pathway analysis showed 162 same pathways among the 169, 164, and 171 relating Br, SG, and PG. This analysis revealed functional similarities with exceptional resemblance in their metabolism and signaling pathways of the three organs. On the other hand, 70, 57, and 114 organ-specific enzymes related pathways were detected for Br, SG, and PG confirming their functional differences. These results reveal a cooperative mechanism among the three endocrine organs in regulating various physiological and developmental events, and also suggest that the organ-specific proteins might be the fundamental factors responsible for the functional differentiation of these organs.

Comparative proteomic analysis between the domesticated silkworm (Bombyx mori) reared on fresh mulberry leaves and on artificial diet.

To gain an insight into the effects of different diets on growth and development of the domesticated silkworm at protein level, we employed comparative proteomic approach to investigate the proteomic differences of midgut, hemolymph, fat body and posterior silk gland of the silkworms reared on fresh mulberry leaves and on artificial diet. Seventy-six differentially expressed proteins were identified by MALDI TOF/TOF MS, and among them, 41 proteins were up-regulated, and 35 proteins were downregulated. Database searches, combined with GO analysis and KEGG pathway analysis revealed that some hemolymph proteins such as Nuecin, Gloverin-like proteins, PGRP, P50 and beta/-N-acetylglucosamidase were related to innate immunity of the silkworm, and some proteins identified in silkworm midgut including Myosin 1 light chain, Tropomyosin 1, Profilin, Serpin-2 and GSH-Px were involved in digestion and nutrition absorption. Moreover, two up-regulated enzymes in fat body of larvae reared on artificial diet were identified as V-ATPase subunit B and Arginine kinase which participate in energy metabolism. Furthermore, 6 down-regulated proteins identified in posterior silk gland of silkworm larvae reared on artificial diet including Ribosomal protein SA, EF-2, EF-1gamma, AspAT, ERp57 and PHB were related to silk synthesis. Our results suggested that the different diets could alter the expression of proteins related to immune system, digestion and absorption of nutrient, energy metabolism and silk synthesis poor nutrition and absorption of nutrition in silkworm. The results also confirmed that the poor nutrient absorption, weakened innate immunity, decreased energy metabolism and reduced silk synthesis are the main reasons for low cocoons yield, inferior filament quality, low survival rate of young larvae and insufficient resistance against specific pathogens in the silkworms fed on artificial diet.