Bioinformatic identification of ClpI, a distinct class of Clp unfoldases in Actinomycetota

All clades of bacteria possess Hsp100/Clp family unfoldase enzymes that contribute to aspects of protein quality control. In Actinomycetota, these include ClpB, which functions as an independent chaperone and disaggregase, and ClpC, which cooperates with the ClpP1P2 peptidase to carry out regulated proteolysis of client proteins. We initially sought to algorithmically catalog Clp unfoldase orthologs from Actinomycetota into ClpB and ClpC categories. In the process, we uncovered a phylogenetically distinct third group of double-ringed Clp enzymes, which we term ClpI. ClpI enzymes are architecturally similar to ClpB and ClpC, with intact ATPase modules and motifs associated with substrate unfolding and translation. While ClpI possess an M-domain similar in length to that of ClpC, its N-terminal domain is more variable than the strongly conserved N-terminal domain of ClpC. Surprisingly, ClpI sequences are divisible into sub-classes that either possess or lack the LGF-motifs required for stable assembly with ClpP1P2, suggesting distinct cellular roles. The presence of ClpI enzymes likely provides bacteria with expanded complexity and regulatory control over protein quality control programs, supplementing the conserved roles of ClpB and ClpC

Apatheia: A Business Plan for a Fine Art and Design Gallery in New York City

Jialiu and I were both very interested in art when we were young. And we were always fancied by the business side of art. Upon entering Sotheby’s Institute of Art, we learned that the two of us share many things in common especially the ideology towards the art world which is that any career in art has a business aspect to it. We have become friends ever since. Together, we visited gallery shows, went on studio visits, and talked about our plans after graduation. The more we talk, the stronger the idea of the two of us should create something special together becomes. While taking the course of gallery business, a plan of opening up a gallery started to form. The gallery is an emerging fine art and design gallery that represents emerging and midcareer Asian artists especially those with ties to China who create artworks with an emphasis on craftsmanship and also aim to support local artists who share the same artistic value with the gallery. The term “Asian” is not a limitation of our gallery, but rather a fluid concept and aesthetic. Not only by supporting the artists, but also by selling their works of art to young white-collar families to meet their demand for artistically strong crafts, the gallery wants to help and advocate for contemporary craftsmen to get the recognition they deserve in the art world. In general, our business is divided into two major categories. First is providing service and space for exhibitions and educational programs for people who have interests in arts and crafts. Second is providing portable and affordable artworks to young collectors in the city and internationally. The name of our gallery is Apatheia. This is an art gallery with a focus on fine art designs. In English, the word apathy is not quite positive but in Stoicism, apatheia is a state of mind in Stoic philosophy in which one is free from emotional disturbance1. The name was chosen because we feel like this term captures the state of making. When artists are physically focusing on the process of creation, their minds are fixed in the experience

Data_Sheet_1_Bioinformatic identification of ClpI, a distinct class of Clp unfoldases in Actinomycetota.PDF

All clades of bacteria possess Hsp100/Clp family unfoldase enzymes that contribute to aspects of protein quality control. In Actinomycetota, these include ClpB, which functions as an independent chaperone and disaggregase, and ClpC, which cooperates with the ClpP1P2 peptidase to carry out regulated proteolysis of client proteins. We initially sought to algorithmically catalog Clp unfoldase orthologs from Actinomycetota into ClpB and ClpC categories. In the process, we uncovered a phylogenetically distinct third group of double-ringed Clp enzymes, which we term ClpI. ClpI enzymes are architecturally similar to ClpB and ClpC, with intact ATPase modules and motifs associated with substrate unfolding and translation. While ClpI possess an M-domain similar in length to that of ClpC, its N-terminal domain is more variable than the strongly conserved N-terminal domain of ClpC. Surprisingly, ClpI sequences are divisible into sub-classes that either possess or lack the LGF-motifs required for stable assembly with ClpP1P2, suggesting distinct cellular roles. The presence of ClpI enzymes likely provides bacteria with expanded complexity and regulatory control over protein quality control programs, supplementing the conserved roles of ClpB and ClpC.</p

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field