PTMoreR-enabled cross-species PTM mapping and comparative phosphoproteomics across mammals.

To support PTM proteomic analysis and annotation in different species, we developed PTMoreR, a user-friendly tool that considers the surrounding amino acid sequences of PTM sites during BLAST, enabling a motif-centric analysis across species. By controlling sequence window similarity, PTMoreR can map phosphoproteomic results between any two species, perform site-level functional enrichment analysis, and generate kinase-substrate networks. We demonstrate that the majority of real P-sites in mice can be inferred from experimentally derived human P-sites with PTMoreR mapping.

A novel web-based risk calculator for predicting surgical site infection in HIV-positive facture patients: a multicenter cohort study in China.

Background: Surgical site infection (SSI) is a common complication in HIV-positive fracture patients undergoing surgery, leading to increased morbidity, mortality, and healthcare costs. Accurate prediction of SSI risk can help guide clinical decision-making and improve patient outcomes. However, there is a lack of user-friendly, Web-based calculator for predicting SSI risk in this patient population.

CRISPLD1 promotes gastric cancer progression by regulating the Ca/PI3K-AKT signaling pathway.

Gastric cancer (GC) is a malignant tumor with poor prognosis. Studies have shown that cysteine-rich secretory protein LCCL domain containing 1 (CRISPLD1) is associated with tumor progression. However, its role in GC is unclear.

A DNA-based and bifunctional nanomedicine for alleviating multi-organ injury in sepsis under diabetic conditions.

Sepsis, defined as a life-threatening organ dysfunction, is associated with increased mortality in individuals with diabetes mellitus. In sepsis under diabetic conditions (SUDC), the superimposed inflammatory response and excessive production of reactive oxygen species (ROS) can cause severe damage to the kidney and liver, making it challenging to effectively repair multi-organ injury. In this study, we report the development of a DNA-based bifunctional nanomedicine, termed IL10-rDON, generated by assembling interleukin 10 (IL10) with rectangular DNA origami nanostructures (rDON) to address multi-organ dysfunction in SUDC.

Antibacterial and DNA-Based Hydrogels In Situ Block TNF-α to Promote Diabetic Alveolar Bone Rebuilding.

Alveolar bone injury under diabetic conditions can severely impede many oral disease treatments. Rebuilding diabetic alveolar bone in clinics is currently challenging due to persistent infection and inflammatory response. Here, an antibacterial DNA-based hydrogel named Agantigel is developed by integrating silver nanoclusters (AgNCs) and tumor necrosis factor-alpha (TNF-α) antibody into DNA hydrogel to promote diabetic alveolar bone regeneration.

Multifunctional DNA-Based Hydrogel Promotes Diabetic Alveolar Bone Defect Reconstruction.

Diabetic alveolar bone defect (DABD) causes persistent bacterial infection, prolonged inflammation, and delayed bone healing, making it a considerable clinical challenge. In this study, by integrating silver nanoclusters (AgNCs) and M2 macrophage-derived extracellular vesicles (M2EVs), a multifunctional DNA-based hydrogel, called Agevgel, is developed with antibacterial, anti-inflammatory, immunomodulatory, and osteogenic properties to promote DABD rebuilding. AgNCs are tightly embedded into the DNA scaffolds and exhibit effective anti-bacterial activity, while immunomodulatory M2EVs are encapsulated within the shape-variable DNA scaffolds and exhibit potent anti-inflammatory and osteogenic properties.

Characterization of site-specific -glycosylation signatures of isolated uromodulin from human urine.

Uromodulin (Umod, Tamm-Horsfall protein) is the most abundant urinary -glycoprotein produced exclusively by the kidney. It can form filaments to antagonize the adhesion of uropathogens. However, the site-specific -glycosylation signatures of Umod in healthy individuals and patients with IgA nephropathy (IgAN) remain poorly understood due to the lack of suitable isolation and analytical methods.

Recent progress of nanomedicine in the treatment of Alzheimer's disease.

Alzheimer's disease (AD) is the most common cause of memory disruption in elderly subjects, with the prevalence continuing to rise mainly because of the aging world population. Unfortunately, no efficient therapy is currently available for the AD treatment, due to low drug potency and several challenges to delivery, including low bioavailability and the impediments of the blood-brain barrier. Recently, nanomedicine has gained considerable attention among researchers all over the world and shown promising developments in AD treatment.

The RNA binding protein MEX3A promotes tumor progression of breast cancer by post-transcriptional regulation of IGFBP4.

Purpose: Breast cancer (BC) is the most frequent malignant tumor in women worldwide with exceptionally high morbidity. The RNA-binding protein MEX3A plays a crucial role in genesis and progression of multiple cancers. We attempted to explore its clinicopathological and functional significance in BC in which MEX3A is expressed.

Annexin A9 promotes cell proliferation by regulating the Wnt signaling pathway in colorectal cancer.

Colorectal cancer (CRC) is one of the leading causes of cancer-related mortality worldwide. Expression of Annexin A9 (ANXA9), a member of the annexin A family, is upregulated in CRC. However, the molecular role of ANXA9 in CRC remains unknown.

Temporal Proteomic and Lipidomic Profiles of Cerulein-Induced Acute Pancreatitis Reveal Novel Insights for Metabolic Alterations in the Disease Pathogenesis.

The pathophysiological mechanisms of acute pancreatitis (AP) are complex and have remained a mystery to date, but metabolism is gradually recognized as an important driver of AP onset and development. We used a cerulein-induced AP mouse model to conduct liquid chromatography-mass spectrometry (LC-MS/MS)-based time-course proteomics and lipidomics in order to better understand the underlying metabolic alterations linked with AP. Results showed that a series of significant changes in proteins over time with a boost in expression were enriched in lipase activity, lipoprotein, and lipids absorption and transport regulation.

Sini Decoction Inhibits Tumor Progression and Enhances the Anti-Tumor Immune Response in a Murine Model of Colon Cancer.

Background: Sini decoction (SND) is a widely used Traditional Chinese Medicine (TCM). The reports of SND application in colorectal cancer (CRC) is limited.

Objective: The objective of this study is to investigate the anti-tumor activity of SND in the treatmeant of CRC.

Function of stem cells in radiation-induced damage.

Purpose: The aim of this review is to discuss previous studies on the function of stem cells in radiation-induced damage, and the factors affecting these processes, in the hope of improving our understanding of the different stem cells and the communication networks surrounding them. This is essential for the development of effective stem cell-based therapies to regenerate or replace normal tissues damaged by radiation.

Conclusion: In salivary glands, senescence-associated cytokines and inflammation-associated cells have a greater effect on stem cells.

Action mechanism of hypoglycemic principle 9-(R)-HODE isolated from cortex lycii based on a metabolomics approach.

The 9-(R)-HODE is an active compound isolated from cortex lycii that showed significant hypoglycemic effects in our previous study. In this study, 9-(R)-HODE's hypoglycemic activity and effect on alleviating diabetic complications, together with its molecular mechanism, was investigated using a metabolomics approach. The monitored regulation on dynamic fasting blood glucose, postprandial glucose, body weight, biochemical parameters and histopathological analysis confirmed the hypoglycemic activity and attenuation effect, i.

Metabolomics-based evidence of the hypoglycemic effect and alleviation of diabetic complications by fruit in diabetic mice.

The hypoglycemic and metabolic effects of fruit were studied in diabetic mice, and its potential mechanisms of hypoglycemic activity and its alleviation of diabetic complications were explored using a metabolomics approach. The histopathological effect of fruit was characterized by hematoxylin and eosin histological staining. Dynamic fasting blood glucose (FBG), postprandial glucose (PPG), body weight, and biochemical parameters, including hepatic-renal function and lipid levels, were monitored to confirm the hypoglycemic activity and attenuation effect.

Temporal metabolic trajectory analyzed by LC-MS/MS based targeted metabolomics in acute pancreatitis pathogenesis and Chaiqin Chengqi decoction therapy.

Background: Acute pancreatitis (AP) is an inflammatory disorder of pancreas that lacks effective specific drugs as well as gold standard laboratory tests for diagnosis and severity assessment. Chaiqin chengqi decoction (CQCQD) has been proven to alleviate the severity and mortality of AP, but its underlying mechanisms remain incompletely understood.

Purpose: To investigate the correlation between metabolic trajectories of the serum and pancreas, the metabolic pathways with respect to the onset and progression of AP, and investigate the effect of CQCQD in modulating the dysregulated pancreatic metabolism of AP.

Stereochemically altered cephalosporins as potent inhibitors of New Delhi metallo-β-lactamases.

Antibiotic resistance caused by β-lactamases, particularly metallo-β-lactamases, has been a major threat to public health globally. New Delhi metallo-β-lactamase-1 (NDM-1) represents one of the most important metallo-β-lactamases; the production of NDM-1 in bacterial pathogen significantly reduces the efficacy of β-lactam antibiotics, including life-saving carbapenems. Herein, we have demonstrated stereochemically altered cephalosporins as potent inhibitors against NDM-1, as well as mutants of NDM.

LncRNA LIMT (LINC01089) contributes to sorafenib chemoresistance via regulation of miR-665 and epithelial to mesenchymal transition in hepatocellular carcinoma cells.

Hepatocellular carcinoma (HCC) is one of the most malignant tumors worldwide and HCC patients often develop drug resisitene. Long non-coding RNAs (LncRNAs) are closely related to cell cycle, growth, development, differentiation, and apoptosis. Abnormally expressed lncRNAs have been proved to mediate drug resistance in tumor cells.

Specific detection of IMP-1 β-lactamase activity using a cephalosporin-based fluorogenic probe.

A fluorogenic probe for the specific detection of IMP-1 β-lactamase activity has been developed. This imaging reagent features a unique -acetylamino cephalosporin as an enzymatic recognition moiety, exhibiting excellent selectivity to IMP-1 β-lactamase over other β-lactamases, including serine- and metallo-β-lactamases. The selective activation of the probe by IMP-1 β-lactamase leads to over 30-fold enhancement in the fluorescence intensity, which allows enzyme activity to be reported with high sensitivity.

Sequential Analysis of the N/O-Glycosylation of Heavily Glycosylated HIV-1 gp120 Using EThcD-sceHCD-MS/MS.

Deciphering the glycosylation of the viral envelope (Env) glycoprotein is critical for evaluating viral escape from the host's immune response and developing vaccines and antiviral drugs. However, it is still challenging to precisely decode the site-specific glycosylation characteristics of the highly glycosylated Env proteins, although glycoproteomics have made significant advances in mass spectrometry techniques and data analysis tools. Here, we present a hybrid dissociation technique, EThcD-sceHCD, by combining electron transfer/higher-energy collisional dissociation (EThcD) and stepped collision energy/higher-energy collisional dissociation (sceHCD) into a sequential glycoproteomic workflow.

O-Glycosylation Landscapes of SARS-CoV-2 Spike Proteins.

The densely glycosylated spike (S) proteins that are highly exposed on the surface of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) facilitate viral attachment, entry, and membrane fusion. We have previously reported all the 22 -glycosites and site-specific -glycans in the S protein protomer. Herein, we report the glycosylation landscapes of SARS-CoV-2 S proteins, which were characterized through high-resolution mass spectrometry.

LncRNA-HOTAIR activates autophagy and promotes the imatinib resistance of gastrointestinal stromal tumor cells through a mechanism involving the miR-130a/ATG2B pathway.

Gastrointestinal stromal tumors (GISTs) are common neoplasms of the gastrointestinal tract that can be treated successfully using C-kit target therapy and surgery; however, imatinib chemoresistance is a major barrier to success in therapy. The present study aimed to discover alternative pathways in imatinib-resistant GISTs. Long noncoding RNAs (lncRNAs) are newly discovered regulators of chemoresistance.

A multi-strategy platform for quality control and Q-markers screen of Chaiqin chengqi decoction.

Background: Acute pancreatitis (AP) is an inflammatory disorder of the pancreas that is associated with substantial morbidity and mortality. Chaiqin chengqi decoction (CQCQD) has been proven clinically to be an effective treatment for AP for decades in West China Hospital. Quality control for CQCQD containing many hundreds of characteristic phytochemicals poses a challenge for developing robust quality assessment metrics.