ProteoFind : A script for finding proteins that are suitable for chemical synthesis

ProteoFind is a computational script for finding proteins that are suitable for fragment ligation-based chemical synthesis. This paper describes the development and case studies of ProteoFind, which searches protein lists obtained from the UniProt website. Its application to visualize areas covered by several one-pot three-fragment ligation methods is also discussed. The results demonstrate that ProteoFind not only saves time when searching for synthetic target proteins, but also proposes many candidate proteins from among which biomedically interesting proteins could be found. It also enables clarification of the features of ligation methods by comparing the areas to which each ligation reaction is accessible

Resin-Bound Crypto-Thioester for Native Chemical Ligation

Resin-bound N–sulfanylethylanilide (SEAlide) peptide was found to function as a crypto-thioester peptide. Exposure of the peptide resin to an aqueous solution under neutral conditions in the presence of thiols affords thioesters without accompanying racemization of C-terminal amino acids. Furthermore, the resin-bound SEAlide peptides react with N-terminal cysteinyl peptides in the absence of phosphate salts to afford ligated products, whereas soluble SEAlide peptides do not. This unexpected difference in reactivity of the SEAlide peptides allows for a one-pot/three-fragment ligation using resin-bound and unbound peptides

Deprotection of S-Acetamidomethyl Cysteine with Copper (II) and 1,2-Aminothiols under Aerobic Conditions

Ring-opening by CuSO4 of a 1,3-thiazolidine carbonyl structure (Thz) as an N-terminal cysteine (Cys) residue revealed that an intramolecular S–acetamidomethyl cysteine (Cys(Acm)) can also be deprotected with concomitant formation of a disulphide bond connecting the two Cys residues. A mechanistic study on the disulphide formation led to a general protocol for deprotection of the S-Acm group by CuSO4 and a 1,2-aminothiol under aerobic conditions. Application of this new deprotection reaction allowed for the synthesis of Apamin, a peptide with two-disulphides in a one-pot/stepwise disulphide-bridging procedure

CAGRA: Highly Parallel Graph Construction and Approximate Nearest Neighbor Search for GPUs

Approximate Nearest Neighbor Search (ANNS) plays a critical role in various disciplines spanning data mining and artificial intelligence, from information retrieval and computer vision to natural language processing and recommender systems. Data volumes have soared in recent years and the computational cost of an exhaustive exact nearest neighbor search is often prohibitive, necessitating the adoption of approximate techniques. The balanced performance and recall of graph-based approaches have more recently garnered significant attention in ANNS algorithms, however, only a few studies have explored harnessing the power of GPUs and multi-core processors despite the widespread use of massively parallel and general-purpose computing. To bridge this gap, we introduce a novel parallel computing hardware-based proximity graph and search algorithm. By leveraging the high-performance capabilities of modern hardware, our approach achieves remarkable efficiency gains. In particular, our method surpasses existing CPU and GPU-based methods in constructing the proximity graph, demonstrating higher throughput in both large- and small-batch searches while maintaining compatible accuracy. In graph construction time, our method, CAGRA, is 2.2~27x faster than HNSW, which is one of the CPU SOTA implementations. In large-batch query throughput in the 90% to 95% recall range, our method is 33~77x faster than HNSW, and is 3.8~8.8x faster than the SOTA implementations for GPU. For a single query, our method is 3.4~53x faster than HNSW at 95% recall

CXCL14 Acts as a Specific Carrier of CpG DNA into Dendritic Cells and Activates Toll-like Receptor 9-mediated Adaptive Immunity

CXCL14 is a primordial chemokine that plays multiple roles in tumor suppression, autoimmune arthritis, and obesity-associated insulin resistance. However, the underlying molecular mechanisms are unclear. Here, we show that CXCL14 transports various types of CpG oligodeoxynucleotide (ODN) into the endosomes and lysosomes of bone marrow-derived dendritic cells (DCs), thereby activating Toll-like receptor 9 (TLR9). A combination of CpG ODN (ODN2395) plus CXCL14 induced robust production of IL-12 p40 by wild-type, but not Tlr9-knockout, DCs. Consistent with this, ODN2395-mediated activation of DCs was significantly attenuated in Cxcl14-knockout mice. CXCL14 bound CpG ODN with high affinity at pH 7.5, but not at pH 6.0, thereby enabling efficient delivery of CpG ODN to TLR9 in the endosome/lysosome. Furthermore, the CXCL14-CpG ODN complex specifically bound to high affinity CXCL14 receptors on DCs. Thus, CXCL14 serves as a specific carrier of CpG DNA to sensitize TLR9-mediated immunosurveillance

Evidence for Activation of Toll-Like Receptor and Receptor for Advanced Glycation End Products in Preterm Birth

Objective. Individuals with inflammation have a myriad of pregnancy aberrations including increasing their preterm birth risk. Toll-like receptors (TLRs) and receptor for advanced glycation end products (RAGE) and their ligands were all found to play a key role in inflammation. In the present study, we reviewed TLR and RAGE expression, their ligands, and signaling in preterm birth. Research Design and Methods. A systematic search was performed in the electronic databases PubMed and ScienceDirect up to July 2010, combining the keywords “preterm birth,” “TLR”, “RAGE”, “danger signal”, “alarmin”, “genomewide,” “microarray,” and “proteomics” with specific expression profiles of genes and proteins. Results. This paper provides data on TLR and RAGE levels and critical downstream signaling events including NF-kappaB-dependent proinflammatory cytokine expression in preterm birth. About half of the genes and proteins specifically present in preterm birth have the properties of endogenous ligands “alarmin” for receptor activation. The interactions between the TLR-mediated acute inflammation and RAGE-mediated chronic inflammation have clear implications for preterm birth via the TLR and RAGE system, which may be acting collectively. Conclusions. TLR and RAGE expression and their ligands, signaling, and functional activation are increased in preterm birth and may contribute to the proinflammatory state

High hydrostatic pressure induces slow contraction in mouse cardiomyocytes

Cardiomyocytes are contractile cells that regulate heart contraction. Ca2+ flux via Ca2+ channels activates actomyosin interactions, leading to cardiomyocyte contraction, which is modulated by physical factors (e.g., stretch, shear stress, and hydrostatic pressure). We evaluated the mechanism triggering slow contractions using a high-pressure microscope to characterize changes in cell morphology and intracellular Ca2+ concentration ([Ca2+]i) in mouse cardiomyocytes exposed to high hydrostatic pressures. We found that cardiomyocytes contracted slowly without an acute transient increase in [Ca2+]i, while a myosin ATPase inhibitor interrupted pressure-induced slow contractions. Furthermore, transmission electron microscopy showed that, although the sarcomere length was shortened upon the application of 20 MPa, this pressure did not collapse cellular structures such as the sarcolemma and sarcomeres. Our results suggest that pressure-induced slow contractions in cardiomyocytes are driven by the activation of actomyosin interactions without an acute transient increase in [Ca2+]i

Facile synthesis of C-terminal peptide thioacids under mild conditions from N-sulfanylethylanilide peptides

A facile procedure has been developed for the synthesis of C-terminal peptide thioacids under mild conditions. A series of N-sulfanylethylanilide peptides prepared using Fmoc-based solid-phase peptide synthesis were successfully converted to the corresponding thioacids via a hydrothiolysis reaction in a phosphate buffer with only trace epimerization of the C-terminal amino acid

Kaplan–Meier survival analysis and Cox regression analyses regarding right ventricular septal pacing: Data from Japanese pacemaker cohort

AbstractThe presented data were obtained from 982 consecutive patients receiving their first pacemaker implantation with right ventricular (RV) lead placement between January 2008 and December 2013 at two centers in Japan. Patients were divided into RV apical and septal pacing groups. Data of Kaplan–Meier survival analysis and Cox regression analysis are presented. Refer to the research article “Implications of right ventricular septal pacing for medium-term prognosis: propensity-matched analysis” (Mizukami et al., in press) [1] for further interpretation and discussion