Loading dynamics of one SARS-CoV-2-derived peptide into MHC-II revealed by kinetic models.

Major histocompatibility complex class II (MHC-II) plays an indispensable role in activating CD4 T cell immune responses by presenting antigenic peptides on the cell surface for recognition by T cell receptors. The assembly of MHC-II and antigenic peptide is therefore a prerequisite for the antigen presentation. To date, however, the atomic-level mechanism underlying the peptide-loading dynamics for MHC-II is still elusive.

A systematic survey of LU domain-containing proteins reveals a novel human gene, LY6A, which encodes the candidate ortholog of mouse Ly-6A/Sca-1 and is aberrantly expressed in pituitary tumors.

The Ly-6 and uPAR (LU) domain-containing proteins represent a large family of cell-surface markers. In particular, mouse Ly-6A/Sca-1 is a widely used marker for various stem cells; however, its human ortholog is missing. In this study, based on a systematic survey and comparative genomic study of mouse and human LU domain-containing proteins, we identified a previously unannotated human gene encoding the candidate ortholog of mouse Ly-6A/Sca-1.

Prioritizing sufficient dose to gross tumor volume over normal tissue sparing in intensity-modulated radiotherapy treatment of T4 nasopharyngeal carcinoma.

Background: In intensity-modulated radiation therapy (IMRT) for nasopharyngeal carcinoma (NPC), priority is often given minimize dose to the critical organs at risk (OARs) to avoid potential morbid sequelae. However, in T4 NPC, dosimetric inadequacy enforced by dose constraints on OARs may significantly impact tumor control.

Methods: This was a single-institute cohort that patients diagnosed between July 2005 and December 2010 with T4 NPC treated with IMRT.

Pyruvate dehydrogenase fuels a critical citrate pool that is essential for Th17 cell effector functions.

Pyruvate dehydrogenase (PDH) is the central enzyme connecting glycolysis and the tricarboxylic acid (TCA) cycle. The importance of PDH function in T helper 17 (Th17) cells still remains to be studied. Here, we show that PDH is essential for the generation of a glucose-derived citrate pool needed for Th17 cell proliferation, survival, and effector function.

Rare copy number variation analysis identifies disease-related variants in atrioventricular septal defect patients.

Atrioventricular septal defect (AVSD) is a deleterious subtype of congenital heart diseases (CHD) characterized by atrioventricular canal defect. The pathogenic genetic changes of AVSD remain elusive, particularly for copy number variation (CNV), a large segment variation of the genome, which is one of the major forms of genetic variants resulting in congenital heart diseases. In the present study, we recruited 150 AVSD cases and 100 healthy subjects as controls for whole exome sequencing (WES).

Primary nephrotic syndrome relapse within 1 year after glucocorticoid therapy in children is associated with gut microbiota composition at syndrome onset.

Background: Children with primary nephrotic syndrome (PNS) who relapse after glucocorticoid therapy are shown to have a decreased total proportion of butyrate-producing bacteria in the gut at onset. Glucocorticoid treatment changes the gut microbiota composition. It is unclear whether gut microbiota at remission right after therapy and gut bacteria other than butyrate-producing bacteria are associated with PNS relapse.

HNRNPA2B1 as a potential therapeutic target for thymic epithelial tumor recurrence: An integrative network analysis.

Thymic epithelial tumors (TETs) are rare malignant tumors, and the molecular mechanisms of both primary and recurrent TETs are poorly understood. Here we established comprehensive proteomic signatures of 15 tumors (5 recurrent and 10 non-recurrent) and 15 pair wised tumor adjacent normal tissues. We then proposed an integrative network approach for studying the proteomics data by constructing protein-protein interaction networks based on differentially expressed proteins and a machine learning-based score, followed by network modular analysis, functional enrichment annotation and shortest path inference analysis.

Digital synthetic polymers for information storage.

Digital synthetic polymers with uniform chain lengths and defined monomer sequences have recently become intriguing alternatives to traditional silicon-based information devices or natural biomacromolecules for data storage. The structural diversity of information-containing macromolecules endows the digital synthetic polymers with higher stability and storage density but less occupied space. Through subtly designing each unit of coded structure, the information can be readily encoded into digital synthetic polymers in a more economical scheme and more decodable, opening up new avenues for molecular digital data storage with high-level security.

PPICT: an integrated deep neural network for predicting inter-protein PTM cross-talk.

Post-translational modifications (PTMs) fine-tune various signaling pathways not only by the modification of a single residue, but also by the interplay of different modifications on residue pairs within or between proteins, defined as PTM cross-talk. As a challenging question, less attention has been given to PTM dynamics underlying cross-talk residue pairs and structural information underlying protein-protein interaction (PPI) graph, limiting the progress in this PTM functional research. Here we propose a novel integrated deep neural network PPICT (Predictor for PTM Inter-protein Cross-Talk), which predicts PTM cross-talk by combining protein sequence-structure-dynamics information and structural information for PPI graph.

Characterizing the Specific Recognition of Xanthurenic Acid by GEP1 and GEP1-GCα Interactions in cGMP Signaling Pathway in Gametogenesis of Malaria Parasites.

Gametogenesis is an essential step for malaria parasite transmission and is activated in mosquito by signals including temperature drop, pH change, and mosquito-derived xanthurenic acid (XA). Recently, a membrane protein gametogenesis essential protein 1 (GEP1) was found to be responsible for sensing these signals and interacting with a giant guanylate cyclase α (GCα) to activate the cGMP-PKG-Ca signaling pathway for malaria parasite gametogenesis. However, the molecular mechanisms for this process remain unclear.

Legumain inhibitor prevents breast cancer bone metastasis by attenuating osteoclast differentiation and function.

Breast cancer is the main lethal disease among females, and metastasis to lung and bone poses a serious threat to patients' life. Therefore, identification of novel molecular mediators that can potentially be exploited as therapeutic targets for treating osteolytic bone metastases is needed. A murine model of breast cancer bone metastasis was developed by injection of 4 T1.

Phosphorylation Regulation Mechanism of β2 Integrin for the Binding of Filamin Revealed by Markov State Model.

Leukocyte adhesion deficiency-1 (LAD-1) disorder is a severe immunodeficiency syndrome caused by deficiency or mutation of β2 integrin. The phosphorylation on threonine 758 of β2 integrin acts as a molecular switch inhibiting the binding of filamin. However, the switch mechanism of site-specific phosphorylation at the atom level is still poorly understood.

Characterization and epitope mapping of monoclonal antibodies against PEDV N protein.

Porcine epidemic diarrhea virus (PEDV) causes acute diarrhea, vomiting, dehydration and high mortality in neonatal piglets. The nucleocapsid (N) protein of PEDV is a highly conserved protein with strong immunogenicity and palys an important role in PEDV diagnosis. However, epitopes on the PEDV N protein have not yet been well characterized.

Nucleic acid testing of SARS-CoV-2: A review of current methods, challenges, and prospects.

Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and has brought a huge threat to public health and the global economy. Rapid identification and isolation of SARS-CoV-2-infected individuals are regarded as one of the most effective measures to control the pandemic. Because of its high sensitivity and specificity, nucleic acid testing has become the major method of SARS-CoV-2 detection.

Bacillamide F, Extracted from Marine C89, Preliminary Effects on Leukemia Cell Lines.

Developing new treatments for leukemia is essential since current therapies often suffer from drug resistance and toxicity. Bacillamides are very promising, naturally occurring compounds with various bioactivities. In the present study, we investigated the use of bacillamide analogues, a new thiazole alkaloid bacillamide F that was isolated from marine Bacillus atrophaeus C89 associated with sponge Dysidea avara.

PTMint database of experimentally verified PTM regulation on protein-protein interaction.

Motivation: Post-translational modification (PTM) is an important biochemical process. which includes six most well-studied types: phosphorylation, acetylation, methylation, sumoylation, ubiquitylation and glycosylation. PTM is involved in various cell signaling pathways and biological processes.

ST6GAL1 inhibits metastasis of hepatocellular carcinoma via modulating sialylation of MCAM on cell surface.

The poor prognosis of hepatocellular carcinoma (HCC) is mainly because of its high rate of metastasis. Thus, elucidation of the molecular mechanisms underlying HCC metastasis is of great significance. Glycosylation is an important post-translational modification that is closely associated with tumor progression.

Validity and Test-Retest Reliability of the Vmaxpro Sensor for Evaluation of Movement Velocity in the Deep Squat.

Feuerbacher, JF, Jacobs, MW, Dragutinovic, B, Goldmann, J-P, Cheng, S, and Schumann, M. Validity and test-retest reliability of the Vmaxpro sensor for evaluation of movement velocity in the deep squat. J Strength Cond Res 37(1): 35-40, 2023-We aimed at assessing the validity and test-retest reliability of the inertial measurement unit-based Vmaxpro sensor compared with a Vicon 3D motion capture system and the T-Force sensor during an incremental 1-repetition maximum (1RM) test and at submaximal loads.

Structural and functional insights into CST tethering in Tetrahymena thermophila telomerase.

Telomerase is crucial for telomere maintenance and genome integrity. The most salient feature of Tetrahymena telomerase is that its CST subcomplex (p75-p45-p19) is tethered to the telomerase catalytic core by interacting with the hub p50. Although the cryoelectron microscopy (cryo-EM) structures of Tetrahymena telomerase have recently been reported, the mechanisms of how and why p50 bridges the CST subcomplex to the telomerase catalytic core remain unclear.

Simulation the potential distribution of and its hosts, and , under climate change in China.

Due to climate change, it is significant to explore the impact of rising temperatures on the distribution of Lajonquiere (Lepidoptera) and its host plants, and , and to simulate their suitable future distribution areas in order to provide a theoretical basis for the monitoring of, and early warning about, and the formulation of effective prevention and control policies. Based on the known distribution areas of, and relevant climate data for, , , and , their suitable habitat in China was predicted using the ENMeval data package in order to adjust the maximum entropy (MaxEnt) model parameters. The results showed that the regularization multiplier was 0.

2cChIP-seq and 2cMeDIP-seq: The Carrier-Assisted Methods for Epigenomic Profiling of Small Cell Numbers or Single Cells.

Chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) can profile genome-wide epigenetic marks associated with regulatory genomic elements. However, conventional ChIP-seq is challenging when examining limited numbers of cells. Here, we developed a new technique by supplementing carrier materials of both chemically modified mimics with epigenetic marks and dUTP-containing DNA fragments during conventional ChIP procedures (hereafter referred to as 2cChIP-seq), thus dramatically improving immunoprecipitation efficiency and reducing DNA loss of low-input ChIP-seq samples.

H11-induced immunoprotection is predominantly linked to N-glycan moieties during infection.

Nematodes are one of the largest groups of animals on the planet. Many of them are major pathogens of humans, animals and plants, and cause destructive diseases and socioeconomic losses worldwide. Despite their adverse impacts on human health and agriculture, nematodes can be challenging to control, because anthelmintic treatments do not prevent re-infection, and excessive treatment has led to widespread drug resistance in nematode populations.

Functional metabolomics revealed the dual-activation of cAMP-AMP axis is a novel therapeutic target of pancreatic cancer.

Pancreatic cancer (PC) is one of the most malignant cancers, owing to extremely high aggressiveness and mortality. Yet, this condition currently incurs widely drug resistance and therapeutic deficiency. In this study, we proposed a novel functional metabolomics strategy as Spatial Temporal Operative Real Metabolomics (STORM) to identify the determinant functional metabolites in a dynamic and visualized pattern whose level changes are mechanistically associated with therapeutic efficiency of gemcitabine against PC.