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A surprising complexity of ubiquitin signaling has emerged with identification of different ubiquitin chain topologies. However, mechanisms of how the diverse ubiquitin codes control biological processes remain poorly understood. Here, we use quantitative whole-proteome mass spectrometry to identify yeast proteins that are regulated by lysine 11 (K11)-linked ubiquitin chains. The entire Met4 pathway, which links cell proliferation with sulfur amino acid metabolism, was significantly affected by K11 chains and selected for mechanistic studies. Previously, we demonstrated that a K48-linked ubiquitin chain represses the transcription factor Met4. Here, we show that efficient Met4 activation requires a K11-linked topology. Mechanistically, our results propose that the K48 chain binds to a topology-selective tandem ubiquitin binding region in Met4 and competes with binding of the basal transcription machinery to the same region. The change to K11-enriched chain architecture releases this competition and permits binding of the basal transcription complex to activate transcription.

Host immunity is central to the virus's spread dynamics, which is significantly influenced by vaccination and prior infection experiences. In this work, we analyzed the co‐evolution of SARS‐CoV‐2 mutation, angiotensin‐converting enzyme 2 (ACE2) receptor binding, and neutralizing antibody (NAb) responses across various variants in 822 human and mice vaccinated with different non‐Omicron and Omicron vaccines is analyzed. The link between vaccine efficacy and vaccine type, dosing, and post‐vaccination duration is revealed. The classification of immune protection against non‐Omicron and Omicron variants is co‐evolved with genetic mutations and vaccination. Additionally, a model, the Prevalence Score (P‐Score) is introduced, which surpasses previous algorithm‐based models in predicting the potential prevalence of new variants in vaccinated populations. The hybrid vaccination combining the wild‐type (WT) inactivated vaccine with the Omicron BA.4/5 mRNA vaccine may provide broad protection against both non‐Omicron variants and Omicron variants, albeit with EG.5.1 still posing a risk. In conclusion, these findings enhance understanding of population immunity variations and provide valuable insights for future vaccine development and public health strategies. [ABSTRACT FROM AUTHOR]

A new style of tofu coagulated through the fermentation of Lactobacillus plantarum SJ‐L‐1 was produced. L. plantarum SJ‐L‐1 with a high growth rate and excellent acid production ability was isolated and identified from naturally fermented soy yellow whey. The gene annotation indicated the potential outstanding isoflavone conversion capacity of L. plantarum SJ‐L‐1. Furthermore, fermentation tofu was prepared using L. plantarum SJ‐L‐1 and Lactobacillus rhamnosus 1–16 as the starter microbiota. Compared to traditional MgCl2 tofu and fermented soy whey tofu, SJ‐L‐1 tofu exhibited a slight increase in hardness and better structure uniformity. SJ‐L‐1 tofu also possessed the highest levels of total isoflavone content (76.33 µg/g) and volatile compounds (561.54 µg/kg) among the four styles of tofu. This research indicated that this new type of tofu coagulated through a combination of heat and fermentation of L. plantarum SJ‐L‐1 represents a promising candidate for future functional foods. [ABSTRACT FROM AUTHOR]

BioLadder is an online data analysis platform designed for proteomics research. It offers a variety of proteomics analysis modules, as well as modules for other omics data analysis. The platform includes experimental data analysis modules and common data analysis modules. It provides functions for data visualization, preprocessing, quantitative analysis, sequence analysis, abundance mapping, classification analysis, and function analysis. The platform is user-friendly, with simplified input formats, specialized default parameters for proteomics, diverse adjustment methods, powerful color schemes, comprehensive help information, and real-time assistance. The platform is developed using the Vue.js and Laravel frameworks, with data persistence managed by MySQL. The authors of the platform are affiliated with Qinglian Biotech Co., Ltd. The work was supported by the National Key Research Program of China. [Extracted from the article]