The characteristic of HLA-A, HLA-B, HLA-C, HLA-DRB1, HLA-DRB3/4/5, HLA-DQA1, HLA-DQB1, HLA-DPA1, and HLA-DPB1 alleles in Zhejiang Han population.

The Zhejiang Han population, a subgroup of the Southern Han ethnic group, resides in Zhejiang Province, situated on the southeast coast of China. In this study, we conducted HLA genotyping for 813 voluntary umbilical cord blood donors from the Zhejiang Han population, targeting 11 HLA loci, namely HLA-A, HLA-B, HLA-C, HLA-DRB1, HLA-DRB3/4/5, HLA-DQA1, HLA-DQB1, HLA-DPA1, and HLA-DPB1, using the next-generation sequencing method. Our analysis of the alleles and haplotypes revealed a high degree of polymorphism within these loci. A total of 289 unique HLA alleles were identified, with the HLA-B locus exhibiting the most significant diversity, while HLA-DRB4 displayed the lowest variation. Due to the inherent limitations of the sequencing method, some unresolvable alleles in the specific loci, such as HLA-DRB1, HLA-DPA1, and HLA-DPB1, were assigned as G group designation. In our comprehensive analysis across all 11 HLA loci, a total of 1204 haplotypes were estimated. The distribution of these alleles was similar to those of the Chinese Southern Han population while highly different from the Caucasian population. These findings contribute to a deeper understanding of the genetic characteristics of HLA loci within the Chinese Southern Han population.

Oriented cellulose hydrogel: Directed tissue regeneration for reducing corneal leukoplakia and managing fungal corneal ulcers.

Fungal corneal ulcer is one of the leading causes of corneal blindness in developing countries. Corneal scars such as leukoplakia are formed due to inflammation, oxidative stress and non-directed repair, which seriously affect the patients' subsequent visual and life quality. In this study, drawing inspiration from the oriented structure of collagen fibers within the corneal stroma, we first proposed the directional arrangement of CuTA-CMHT hydrogel system at micro and macro scales based on the 3D printing extrusion method combined with secondary patterning. It played an antifungal role and induced oriented repair in therapy of fungal corneal ulcer. The results showed that it effectively inhibited Candida albicans, Aspergillus Niger, Fusarium sapropelum, which mainly affects TNF, NF-kappa B, and HIF-1 signaling pathways, achieving effective antifungal functions. More importantly, the fibroblasts interacted with extracellular matrix (ECM) of corneal stroma through formation of focal adhesions, promoted the proliferation and directional migration of cells in vitro, induced the directional alignment of collagen fibers and corneal stromal orthogonally oriented repair in vivo. This process is mainly associated with MYLK, MYL9, and ITGA3 molecules. Furthermore, the downregulation the growth factors TGF-ß and PDGF-ß inhibits myofibroblast development and reduces scar-type ECM production, thereby reducing corneal leukoplakia. It also activates the PI3K-AKT signaling pathway, promoting corneal healing. In conclusion, the oriented CuTA-CMHT hydrogel system mimics the orthogonal arrangement of collagen fibers, inhibits inflammation, eliminates reactive oxygen species, and reduces corneal leukoplakia, which is of great significance in the treatment of fungal corneal ulcer and is expected to write a new chapter in corneal tissue engineering.

Identification of the novel HLA-B*51:360 allele in a Chinese individual.

HLA-B*51:360 differs from HLA-B*51:01:01:01 by a single nucleotide substitution at position 955 G > A in exon 5.

Multi-omics analyses reveal aberrant differentiation trajectory with WNT1 loss-of-function in type XV osteogenesis imperfecta.

Osteogenesis imperfecta (OI) is a group of severe genetic bone disorders characterized by congenital low bone mass, deformity and frequent fractures. Type XV OI is a moderate to severe form of skeletal dysplasia caused by WNT1 variants. In this cohort study from southern China, we summarized the clinical phenotypes of patients with WNT1 variants and found that the proportion of type XV patients was around 10.3% (25 out of 243) with a diverse spectrum of phenotypes. Functional assays indicated that variants of WNT1 significantly impaired its secretion and effective activity, leading to moderate to severe clinical manifestations, porous bone structure and enhanced osteoclastic activities. Analysis of proteomic data from human skeleton indicated that the expression of SOST was dramatically reduced in type XV patients when comparing to the patients with COL1A1 quantitative variants. Single-cell transcriptome data generated from the human tibia samples of patients diagnosed with type XV OI and leg-length-discrepancy respectively, revealed aberrant differentiation trajectory of skeletal progenitors and impaired maturation of osteocytes with loss of WNT1, resulting in excessive CXCL12+ progenitors, fewer mature osteocytes and existence of abnormal cell populations with adipogenic characteristics. The integration of multi-omics data from human skeleton delineates how WNT1 regulates the differentiation and maturation of skeletal progenitors, which will provide a new direction for the treatment strategy of type XV osteogenesis imperfecta and relative low bone mass diseases such as early onset osteoporosis.

Osteogenesis imperfecta is a rare disease characterized by low bone mass, frequent fractures and long bone deformity. Type XV osteogenesis imperfect is an autosomal recessive disorder caused by WNT1 variants, while heterozygous variants of WNT1 result in early onset osteoporosis. In this cohort study, we summarized the clinical features of 25 patients diagnosed with type XV osteogenesis imperfect. The WNT1 variants were confirmed by genetic test. Molecular assays were conducted to reveal the impact of variants on WNT1 protein activity and bone structure. We then compared the protein levels in bone tissues isolated from the type XV patients and patients with mild deformity using proteomic method, and found the expression of SOST, mainly produced by mature osteoblasts and osteocytes, was dramatically reduced in type XV patients. We further compared the global mRNA expression levels in the skeletal cells using single-cell RNA sequencing. Analyses of these data indicated that more immature progenitors were identified and maturation of osteocytes was impaired with WNT1 loss-of-function. Our study helps to understand the underlying pathogenesis of type XV osteogenesis imperfecta.

A midgut transcriptional regulatory loop favors an insect host to withstand a bacterial pathogen.

Mounting evidence suggests that insect hormones associated with growth and development also participate in pathogen defense. We have discovered a previously undescribed midgut transcriptional control pathway that modulates the availability of 20-hydroxyecdysone (20E) in a worldwide insect pest (Plutella xylostella), allowing it to defeat the major virulence factor of an insect pathogen Bacillus thuringiensis (Bt). A reduction of the transcriptional inhibitor (PxDfd) increases the expression of a midgut microRNA (miR-8545), which in turn represses the expression of a newly identified ecdysteroid-degrading glucose dehydrogenase (PxGLD). Downregulation of PxGLD reduces 20E degradation to increase 20E titer and concurrently triggers a transcriptional negative feedback loop to mitigate 20E overproduction. The moderately elevated 20E titer in the midgut activates a MAPK signaling pathway to increase Bt tolerance/resistance. These findings deepen our understanding of the functions attributed to these classical insect hormones and help inform potential future strategies that can be employed to control insect pests.

Characterisation of the novel HLA-B*46:96 allele by next-generation sequencing.

HLA-B*46:96 differs from HLA-B*46:01:01:01 by a single nucleotide substitution at position 479 C>T.

Detection of the HLA-C*07:04:29 allele in a Chinese individual.

HLA-C*07:04:29 differs from HLA-C*07:04:01:01 by a single substitution in exon 4.

Identification of two novel HLA-DRB1 alleles, HLA-DRB1*08:03:13 and HLA-DRB1*08:119.

Compared with HLA-DRB1*08:03:02:01, the alleles HLA-DRB1*08:03:13 and HLA-DRB1*08:119 each show one nucleotide substitution, respectively.

Identification of the novel HLA-DPA1*02:02:15 allele by next-generation sequencing.

The novel HLA-DPA1*02:02:15 allele differs from HLA-DPA1*02:02:02:01 by one nucleotide substitution in exon 1.

High-resolution KIR and HLA genotyping in three Chinese ethnic minorities reveals distinct origins.

Polymorphism of killer-cell immunoglobulin-like receptors (KIRs) and their HLA class I ligands impacts the effector activity of cytotoxic NK cell and T cell subsets. Therefore, understanding the extent and implications of KIR and HLA class I genetic polymorphism across various populations is important for immunological and medical research. In this study, we conducted a high-resolution investigation of KIR and HLA class I diversity in three distinct Chinese ethnic minority populations. We studied the She, Yugur, and Tajik, and compared them with the Zhejiang Han population (Zhe), which represents the majority Southern Han ethnicity. Our findings revealed that the Tajik population exhibited the most diverse KIR copy number, allele, and haplotype diversity among the four populations. This diversity aligns with their proposed ancestral origin, closely resembling that of Iranian populations, with a relatively higher presence of KIR-B genes, alleles, and haplotypes compared with the other Chinese populations. The Yugur population displayed KIR distributions similar to those of the Tibetans and Southeast Asians, whereas the She population resembled the Zhe and other East Asians, as confirmed by genetic distance analysis of KIR. Additionally, we identified 12.9% of individuals across the three minority populations as having KIR haplotypes characterized by specific gene block insertions or deletions. Genetic analysis based on HLA alleles yielded consistent results, even though there were extensive variations in HLA alleles. The observed variations in KIR interactions, such as higher numbers of 2DL1-C2 interactions in Tajik and Yugur populations and of 2DL3-C1 interactions in the She population, are likely shaped by demographic and evolutionary mechanisms specific to their local environments. Overall, our findings offer valuable insights into the distribution of KIR and HLA diversity among three distinct Chinese ethnic minority populations, which can inform future clinical and population studies.

Characterisation of the novel HLA-DPB1*1437:01 and HLA-DPB1*1438:01 alleles by next-generation sequencing.

The novel HLA-DPB1*1437:01 and HLA-DPB1*1438:01 alleles first identified in the Chinese individuals.

Enhancing Generalizability in Protein-Ligand Binding Affinity Prediction with Multimodal Contrastive Learning.

Improving the generalization ability of scoring functions remains a major challenge in protein-ligand binding affinity prediction. Many machine learning methods are limited by their reliance on single-modal representations, hindering a comprehensive understanding of protein-ligand interactions. We introduce a graph-neural-network-based scoring function that utilizes a triplet contrastive learning loss to improve protein-ligand representations. In this model, three-dimensional complex representations and the fusion of two-dimensional ligand and coarse-grained pocket representations converge while distancing from decoy representations in latent space. After rigorous validation on multiple external data sets, our model exhibits commendable generalization capabilities compared to those of other deep learning-based scoring functions, marking it as a promising tool in the realm of drug discovery. In the future, our training framework can be extended to other biophysical- and biochemical-related problems such as protein-protein interaction and protein mutation prediction.

Reprogrammable Magnetic Soft Actuators with Microfluidic Functional Modules via Pixel-Assembly.

Magnetic soft actuators and robots have attracted considerable attention in biomedical applications due to their speedy response, programmability, and biocompatibility. Despite recent advancements, the fabrication process of magnetic actuators and the reprogramming approach of their magnetization profiles continue to pose challenges. Here, a facile fabrication strategy is reported based on arrangements and distributions of reusable magnetic pixels on silicone substrates, allowing for various magnetic actuators with customizable architectures, arbitrary magnetization profiles, and integration of microfluidic technology. This approach enables intricate configurations with decent deformability and programmability, as well as biomimetic movements involving grasping, swimming, and wriggling in response to magnetic actuation. Moreover, microfluidic functional modules are integrated for various purposes, such as on/off valve control, curvature adjustment, fluid mixing, dynamic microfluidic architecture, and liquid delivery robot. The proposed method fulfills the requirements of low-cost, rapid, and simplified preparation of magnetic actuators, since it eliminates the need to sustain pre-defined deformations during the magnetization process or to employ laser heating or other stimulation for reprogramming the magnetization profile. Consequently, it is envisioned that magnetic actuators fabricated via pixel-assembly will have broad prospects in microfluidics and biomedical applications.

Fungal community structure shifts in litter degradation along forest succession induced by pine wilt disease.

Fungi play a crucial role in decomposing litter and facilitating the energy flow between aboveground plants and underground soil in forest ecosystems. However, our understanding how the fungal community involved in litter decomposition responds during forest succession, particularly in disease-driven succession, is still limited. This study investigated the activity of degrading enzyme, fungal community, and predicted function in litter after one year of decomposition in different types of forests during a forest succession gradient from coniferous to deciduous forest, induced by pine wilt disease. The results showed that the weight loss of needles/leaves and twigs did not change along the succession process, but twigs degraded faster than needles/leaves in both pure pine forest and mixed forest. In pure pine forest, peak activities of enzymes involved in carbon degradation (ß-cellobiosidase, ß-glucosidase, ß-D-glucuronidase, ß-xylosidase), nitrogen degradation (N-acetyl-glucosamidase), and organic phosphorus degradation (phosphatase) were observed in needles, which subsequently declined. The fungal diversity and evenness (Shannon's diversity and Shannon's evenness) dropped in twig from coniferous forest to mixed forest during the succession. The dominant phyla in needle/leaf and twig litters were Ascomycota (46.9%) and Basidiomycota (38.9%), with Lambertella pruni and Chalara hughesii identified as the most abundant indicator species. Gymnopus and Desmazierella showed positively correlations with most measured enzyme activities. Functionally, saprotrophs constituted the main trophic mode (47.65%), followed by Pathotroph-Saprotroph-Symbiotroph (30.95%) and Saprotroph-Symbiotroph (10.57%). The fungal community and predicted functional structures in both litter types shifted among different forest types along the succession. These findings indicate that the fungal community in litter decomposition responds differently to disease-induced succession, leading to significant shifts in both the fungal community structure and function.

Description of two new HLA alleles: HLA-DRB1*14:234 and HLA-DRB1*14:240 in Chinese individuals.

Compared with HLA-DRB1*14:54:01:01, the alleles HLA-DRB1*14:234 and HLA-DRB1*14:240 each show one nucleotide substitution.

Characterization of the novel HLA-B*40:01:02:48 allele by next-generation sequencing.

HLA-B*40:01:02:48 differs from HLA-B*40:01:02:01 by one nucleotide substitution C to A at position -138 in 5'UTR.

Water Network-Augmented Two-State Model for Protein-Ligand Binding Affinity Prediction.

Water network rearrangement from the ligand-unbound state to the ligand-bound state is known to have significant effects on the protein-ligand binding interactions, but most of the current machine learning-based scoring functions overlook these effects. In this study, we endeavor to construct a comprehensive and realistic deep learning model by incorporating water network information into both ligand-unbound and -bound states. In particular, extended connectivity interaction features were integrated into graph representation, and graph transformer operator was employed to extract features of the ligand-unbound and -bound states. Through these efforts, we developed a water network-augmented two-state model called ECIFGraph::HM-Holo-Apo. Our new model exhibits satisfactory performance in terms of scoring, ranking, docking, screening, and reverse screening power tests on the CASF-2016 benchmark. In addition, it can achieve superior performance in large-scale docking-based virtual screening tests on the DEKOIS2.0 data set. Our study highlights that the use of a water network-augmented two-state model can be an effective strategy to bolster the robustness and applicability of machine learning-based scoring functions, particularly for targets with hydrophilic or solvent-exposed binding pockets.

Knockdown of lncRNA MALAT1 induces pyroptosis by regulating the miR­124/SIRT1 axis in cervical cancer cells.

The aim of the present study was to elucidate the role and downstream mechanism of long non­coding RNA (lncRNA) metastasis­associated lung adenocarcinoma transcript 1 (MALAT1) in the process of cervical cancer cell pyroptosis. The effect of inhibiting lncRNA MALAT1 on cervical cancer cells was determined using primary cells isolated from patients and U14 cervical tumor­bearing nude mice. The level of lncRNA MALAT1 expression and cell viability were determined for relationship analysis. Pyroptosis was then investigated in HeLa cells with lncRNA MALAT1 knockdown or overexpression with or without lipopolysaccharide (LPS) treatment. Bioinformatics tools were used to identify downstream factors of lncRNA MALAT1, which were subsequently verified by gain­ or loss­of­function analyses in the process of cervical cancer cell pyroptosis. It was observed that the level of lncRNA MALAT1 was markedly higher in cervical carcinoma cells compared with expression in paracarcinoma cells, and knockdown of lncRNA MALAT1 induced cervical cancer cell death through pyroptosis. By contrast, overexpression of lncRNA MALAT1 blocked LPS­induced pyroptosis. These results, combined with bioinformatics statistical tools, demonstrated that the microRNA (miR)­124/sirtuin 1 (SIRT1) axis may affect the progression of cervical cancer at least partly by mediating the effect of lncRNA MALAT1 on the pyroptosis of cervical cancer cells. In conclusion, the lncRNA MALAT1/miR­124/SIRT1 regulatory axis in cervical cancer cells may mediate pyroptosis and may provide potential targets against the progression of cervical cancer.

Short-term association of fine particulate matter and its constituents with oxidative stress, symptoms and quality of life in patients with allergic rhinitis: A panel study.

BACKGROUND: Short-term exposure to fine particulate matter (PM2.5) and its specific constituents might exacerbate allergic rhinitis (AR) conditions. However, the evidence is still inconclusive. METHOD: We conducted a panel study of 49 patients diagnosed with AR > 1 year prior to the study in Taiyuan, China, to investigate associations of individual exposure to PM2.5 and its constituents with oxidative parameters, symptoms, and quality of life among AR patients. All participants underwent repeated assessments of health and PM exposure at 4 time points in both the heating and nonheating seasons from June 2017 to January 2018. AR patients' oxidative parameters were assessed using nasal lavage, and their subjective symptoms and quality of life were determined through in-person interviews using a structured questionnaire. Short-term personal exposure to PM2.5 and its constituents was estimated using the time-microenvironment-activity pattern and data from the nearest air sampler, respectively. We applied mixed-effects regression models to estimate the short-term effects of PM2.5 and its constituents. RESULTS: The results showed that exposure to PM2.5 and its constituents, including BaP, PAHs, SO42-, NH4+, V, Cr, Cu, As, Se, Cd, and Pb, was significantly associated with increased oxidative stress, as indicated by an increase in the malondialdehyde (MDA) index. Exposure to PM2.5 and its components (V, Mn, Fe, Zn, As, and Se) was associated with decreased antioxidant activity, as indicated by a decrease in the superoxide dismutase (SOD) index. Additionally, increased visual analog scale (VAS) and rhinoconjunctivitis quality of life questionnaire (RQLQ) scores indicated that exposure to PM2.5 and its constituents exacerbated inflammatory symptoms and affected quality of life in AR patients. CONCLUSION: Exposure to PM2.5 and specific constituents, could exacerbate AR patients' inflammatory symptoms and adversely affect their quality of life in the heavily industrialized city of Taiyuan, China. These findings may have potential biological and policy implications.

Antimycobacterial Activities of Hydroxamic Acids and Their Iron(II/III), Nickel(II), Copper(II) and Zinc(II) Complexes.

Hydroxamic acid (HA) derivatives display antibacterial and antifungal activities. HA with various numbers of carbon atoms (C2, C6, C8, C10, C12 and C17), complexed with different metal ions, including Fe(II/III), Ni(II), Cu(II) and Zn(II), were evaluated for their antimycobacterial activities and their anti-biofilm activities. Some derivatives showed antimycobacterial activities, especially in biofilm growth conditions. For example, 20-100 µM of HA10Fe2, HA10FeCl, HA10Fe3, HA10Ni2 or HA10Cu2 inhibited Mycobacterium tuberculosis, Mycobacterium bovis BCG and Mycobacterium marinum biofilm development. HA10Fe2, HA12Fe2 and HA12FeCl could even attack pre-formed Pseudomonas aeruginosa biofilms at higher concentrations (around 300 µM). The phthiocerol dimycocerosate (PDIM)-deficient Mycobacterium tuberculosis H37Ra was more sensitive to the ion complexes of HA compared to other mycobacterial strains. Furthermore, HA10FeCl could increase the susceptibility of Mycobacterium bovis BCG to vancomycin. Proteomic profiles showed that the potential targets of HA10FeCl were mainly related to mycobacterial stress adaptation, involving cell wall lipid biosynthesis, drug resistance and tolerance and siderophore metabolism. This study provides new insights regarding the antimycobacterial activities of HA and their complexes, especially about their potential anti-biofilm activities.