dbPTM 2025 update: comprehensive integration of PTMs and proteomic data for advanced insights into cancer research.

Post-translational modifications (PTMs) are essential for modulating protein function and influencing stability, activity and signaling processes. The dbPTM 2025 update significantly expands the database to include over 2.79 million PTM sites, of which 2.

Unilateral biportal endoscopic versus microscopic transforaminal lumbar interbody fusion for degenerative lumbar spinal stenosis in China: study protocol for a prospective, randomised, controlled, non-inferiority trial.

Introduction: Degenerative lumbar spinal stenosis is a common cause of low back or leg pain and disability in the elderly population. Patients with spinal stenosis who fail to respond to conservative treatment often require surgical interventions. Minimally invasive transforaminal lumbar interbody fusion (TLIF) with microscopic tubular technique (MT-TLIF) is a well-established procedure for lumbar spinal stenosis.

Multi-Omics Characterization of E3 Regulatory Patterns in Different Cancer Types.

Ubiquitination, a post-translational modification, refers to the covalent attachment of ubiquitin molecules to substrates. This modification plays a critical role in diverse cellular processes such as protein degradation. The specificity of ubiquitination for substrates is regulated by E3 ubiquitin ligases.

KinPred-RNA-kinase activity inference and cancer type classification using machine learning on RNA-seq data.

Kinases as important enzymes can transfer phosphate groups from high-energy and phosphate-donating molecules to specific substrates and play essential roles in various cellular processes. Existing algorithms for kinase activity from phosphorylated proteomics data are often costly, requiring valuable samples. Moreover, methods to extract kinase activities from bulk RNA sequencing data remain undeveloped.

Antidementia medication acetylcholinesterase inhibitors have therapeutic benefits on osteoporotic bone by attenuating osteoclastogenesis and bone resorption.

This study was designed to determine whether the use of acetylcholinesterase inhibitors (AChEIs), a group of drugs that stimulate acetylcholine receptors and are used to treat Alzheimer's disease (AD), is associated with osteoporosis protection and inhibition of osteoclast differentiation and function. Firstly, we examined the effects of AChEIs on RANKL-induced osteoclast differentiation and function with osteoclastogenesis and bone resorption assays. Next, we investigated the impacts of AChEIs on RANKL-induced nuclear factor κB and NFATc1 activation and expression of osteoclast marker proteins CA-2, CTSK and NFATc1, and dissected the MAPK signaling in osteoclasts in vitro by using luciferase assay and Western blot.

Holistic similarity-based prediction of phosphorylation sites for understudied kinases.

Phosphorylation is an essential mechanism for regulating protein activities. Determining kinase-specific phosphorylation sites by experiments involves time-consuming and expensive analyzes. Although several studies proposed computational methods to model kinase-specific phosphorylation sites, they typically required abundant experimentally verified phosphorylation sites to yield reliable predictions.

Extraction of microRNA-target interaction sentences from biomedical literature by deep learning approach.

MicroRNA (miRNA)-target interaction (MTI) plays a substantial role in various cell activities, molecular regulations and physiological processes. Published biomedical literature is the carrier of high-confidence MTI knowledge. However, digging out this knowledge in an efficient manner from large-scale published articles remains challenging.

Identification of chondrocyte subpopulations in osteoarthritis using single-cell sequencing analysis.

Osteoarthritis (OA) is the most common joint disease. Previous studies were focused on general functions of chondrocyte population in OA without elucidating the existence of chondrocyte subpopulations. To investigate the heterogeneity of chondrocyte, here we conducted detailed analysis on the single-cell sequencing data of cartilage cells from OA patients.

MAGE-A3 regulates tumor stemness in gastric cancer through the PI3K/AKT pathway.

Gastric cancer remains a malignant disease of the digestive tract with high mortality and morbidity worldwide. However, due to its complex pathological mechanisms and lack of effective clinical therapies, the survival rate of patients after receiving treatment is not satisfactory. A increasing number of studies have focused on cancer stem cells and their regulatory properties.

Percutaneous Transforaminal Endoscopic Discectomy Versus Microendoscopic Discectomy for Lumbar Disk Herniation: Five-year Results of a Randomized Controlled Trial.

Study Design: A prospective randomized controlled study.

Objective: To compare the efficacy and safety between percutaneous transforaminal endoscopic discectomy (PTED) and microendoscopic discectomy (MED).

Summary Of Background Data: Two kinds of minimally invasive discectomy, PTED and MED, are now widely used for treating lumbar disk herniation (LDH).

KinasePhos 3.0: Redesign and Expansion of the Prediction on Kinase-specific Phosphorylation Sites.

The purpose of this work is to enhance KinasePhos, a machine learning-based kinase-specific phosphorylation site prediction tool. Experimentally verified kinase-specific phosphorylation data were collected from PhosphoSitePlus, UniProtKB, the GPS 5.0, and Phospho.

dbAMP 2.0: updated resource for antimicrobial peptides with an enhanced scanning method for genomic and proteomic data.

The last 18 months, or more, have seen a profound shift in our global experience, with many of us navigating a once-in-100-year pandemic. To date, COVID-19 remains a life-threatening pandemic with little to no targeted therapeutic recourse. The discovery of novel antiviral agents, such as vaccines and drugs, can provide therapeutic solutions to save human beings from severe infections; however, there is no specifically effective antiviral treatment confirmed for now.

dbPTM in 2022: an updated database for exploring regulatory networks and functional associations of protein post-translational modifications.

Protein post-translational modifications (PTMs) play an important role in different cellular processes. In view of the importance of PTMs in cellular functions and the massive data accumulated by the rapid development of mass spectrometry (MS)-based proteomics, this paper presents an update of dbPTM with over 2 777 000 PTM substrate sites obtained from existing databases and manual curation of literature, of which more than 2 235 000 entries are experimentally verified. This update has manually curated over 42 new modification types that were not included in the previous version.

A representation and deep learning model for annotating ubiquitylation sentences stating E3 ligase - substrate interaction.

Background: Ubiquitylation is an important post-translational modification of proteins that not only plays a central role in cellular coding, but is also closely associated with the development of a variety of diseases. The specific selection of substrate by ligase E3 is the key in ubiquitylation. As various high-throughput analytical techniques continue to be applied to the study of ubiquitylation, a large amount of ubiquitylation site data, and records of E3-substrate interactions continue to be generated.

UbiNet 2.0: a verified, classified, annotated and updated database of E3 ubiquitin ligase-substrate interactions.

Ubiquitination is an important post-translational modification, which controls protein turnover by labeling malfunctional and redundant proteins for proteasomal degradation, and also serves intriguing non-proteolytic regulatory functions. E3 ubiquitin ligases, whose substrate specificity determines the recognition of target proteins of ubiquitination, play crucial roles in ubiquitin-proteasome system. UbiNet 2.

PKC-δ deficiency in B cells displays osteopenia accompanied with upregulation of RANKL expression and osteoclast-osteoblast uncoupling.

PKC-δ is an important molecule for B-cell proliferation and tolerance. B cells have long been recognized to play a part in osteoimmunology and pathological bone loss. However, the role of B cells with PKC-δ deficiency in bone homeostasis and the underlying mechanisms are unknown.

Conditional Knockout of PKC-δ in Osteoclasts Favors Bone Mass Accrual in Males Due to Decreased Osteoclast Function.

Protein kinase C delta (PKC-δ) functions as an important regulator in bone metabolism. However, the precise involvement of PKC-δ in the regulation of osteoclasts remains elusive. We generated an osteoclast specific PKC-δ knockout mouse strain to investigate the function of PKC-δ in osteoclast biology.

Casein kinase 1 epsilon facilitates cartilage destruction in osteoarthritis through JNK pathway.

Osteoarthritis (OA) is a high-morbidity skeletal disease worldwide and the exact mechanisms underlying OA pathogenesis are not fully understood. Casein kinase 1 epsilon (CK1ε) is a serine/threonine protein kinase, but its relationship with OA is still unknown. We demonstrated that CK1ε was upregulated in articular cartilage of human patients with OA and mice with experimentally induced OA.

[A liquid chromatography-mass spectrometry-based metabolomic study on the changes of intracellular lipid metabolism regulated by Pokemon].

Pokemon, a transcriptional repressor, inhibits the transcription of tumor suppressor genes and promotes tumor formation by affecting chromatin recombination or binding directly to the tumor suppressor genes. In this study, the mechanism behind the Pokemon regulation of liver cancer cell metabolism was evaluated using liquid chromatography-mass spectrometry (LC-MS)-based metabolomics. Pokemon-overexpressing HL7702 cells were obtained by lipofection.

Amyloid β peptide promotes bone formation by regulating Wnt/β-catenin signaling and the OPG/RANKL/RANK system.

Background: Amyloid β peptide (Aβ) is involved in osteoporosis, but the effects of Aβ on osteoblast and bone formation remain unclear. In this study, we investigated the effect of Aβ on bone formation.

Methods: An animal model of osteoporosis was established by ovariectomy in C57BL/6 mice.

Fangchinoline protects against bone loss in OVX mice via inhibiting osteoclast formation, bone resorption and RANKL-induced signaling.

Osteoporosis is a disease characterized by abnormally increased formation and function of osteoclasts. Anti-RANKL treatment using natural medicine is a potential therapy for osteoporosis. Here, we studied the effect of fangchinoline, which is extracted from the root of Stephania tetrandra S.

Percutaneous Transforaminal Endoscopic Discectomy Versus Microendoscopic Discectomy for Lumbar Disc Herniation: Two-Year Results of a Randomized Controlled Trial.

Study Design: A prospective randomized controlled study.

Objective: To clarify whether percutaneous transforaminal endoscopic discectomy (PTED) has better clinical outcomes and less surgical trauma compared with microendoscopic discectomy (MED).

Summary Of Background Data: Two kinds of minimally invasive spine surgeries, PTED and MED, are now widely used for the treatment of lumbar disc herniation (LDH).